Biology doi: 10.3390/biology13030195
Authors: Beatriz Ramos-Velasco Rocío Naranjo José M. Izquierdo
T-cell intracellular antigen 1 (TIA1) and TIA1-like/related protein (TIAL1/TIAR) are two members of the classical family of RNA binding proteins. Through their selective interactions with distinct RNAs and proteins, these multifunctional regulators are involved in chromatin remodeling, RNA splicing and processing and translation regulation, linking them to a wide range of diseases including neuronal disorders, cancer and other pathologies. From their discovery to the present day, many studies have focused on the behavior of these proteins in order to understand their impact on molecular and cellular processes and to understand their relationship to human pathologies. The volume of research on these proteins in various fields, including molecular biology, biochemistry, cell biology, immunology and cancer, has steadily increased, indicating a growing interest in these gene expression regulators among researchers. This information can be used to know the most productive institutions working in the field, understand the focus of research, identify key areas of involvement, delve deeper into their relationship and impact on different diseases, and to establish the level of study associated with them.
]]>Biology doi: 10.3390/biology13030194
Authors: Na Zhao Jiahui Zhao Shaoning Li Bin Li Jiankui Lv Xin Gao Xiaotian Xu Shaowei Lu
To uncover the internal mechanisms of various drought stress intensities affecting the soluble sugar content in organs and its regulation by endogenous abscisic acid (ABA), we selected the saplings of Platycladus orientalis, a typical tree species in the Beijing area, as our research subject. We investigated the correlation between tree soluble sugars and endogenous ABA in the organs (comprised of leaf, branch, stem, coarse root, and fine root) under two water treatments. One water treatment was defined as T1, which stopped watering until the potted soil volumetric water content (SWC) reached the wilting coefficient and then rewatered the sapling. The other water treatment, named T2, replenished 95% of the total water loss of one potted sapling every day and irrigated the above-mentioned sapling after its SWC reached the wilt coefficients. The results revealed that (1) the photosynthetic physiological parameters of P. orientalis were significantly reduced (p < 0.05) under fast and slow drought processes. The photosynthetic physiological parameters of P. orientalis in the fast drought–rehydration treatment group recovered faster relative to the slow drought–rehydration treatment group. (2) The fast and slow drought treatments significantly (p < 0.05) increased the ABA and soluble sugar contents in all organs. The roots of the P. orientalis exhibited higher sensitivity in ABA and soluble sugar content to changes in soil moisture dynamics compared to other organs. (3) ABA and soluble sugar content of P. orientalis showed a significant positive correlation (p < 0.05) under fast and slow drought conditions. During the rehydration stage, the two were significantly correlated in the T2 treatment (p < 0.05). In summary, soil drought rhythms significantly affected the photosynthetic parameters, organ ABA, and soluble sugar content of P. orientalis. This study elucidates the adaptive mechanisms of P. orientalis plants to drought and rehydration under the above-mentioned two water drought treatments, offering theoretical insights for selecting and cultivating drought-tolerant tree species.
]]>Biology doi: 10.3390/biology13030193
Authors: Priyanka Mehra Arend Hintze
This study investigates whether reducing epistasis and pleiotropy enhances mutational robustness in evolutionary adaptation, utilizing an indirect encoded model within the “survival of the flattest” (SoF) fitness landscape. By simulating genetic variations and their phenotypic consequences, we explore organisms’ adaptive mechanisms to maintain positions on higher, narrower evolutionary peaks amidst environmental and genetic pressures. Our results reveal that organisms can indeed sustain their advantageous positions by minimizing the complexity of genetic interactions—specifically, by reducing the levels of epistasis and pleiotropy. This finding suggests a counterintuitive strategy for evolutionary stability: simpler genetic architectures, characterized by fewer gene interactions and multifunctional genes, confer a survival advantage by enhancing mutational robustness. This study contributes to our understanding of the genetic underpinnings of adaptability and robustness, challenging traditional views that equate complexity with fitness in dynamic environments.
]]>Biology doi: 10.3390/biology13030192
Authors: Viviane C. L. Gomes Bryce M. Gilbert Carolina Bernal Kassandra R. Crissman Jenny L. Sones
The etiopathogenesis of preeclampsia, a leading hypertensive disorder of pregnancy, has been proposed to involve an abnormal circulating sex hormone profile and misexpression of placental estrogen and progesterone receptors (ER and PR, respectively). However, existing research is vastly confined to third trimester preeclamptic placentas. Consequently, the placental–uterine molecular crosstalk and the dynamic ER and PR expression pattern in the peri-conception period remain overlooked. Herein, our goal was to use the BPH/5 mouse to elucidate pre-pregnancy and early gestation Er and Pr dynamics in a preeclamptic-like uterus. BPH/5 females display low circulating estrogen concentration during proestrus, followed by early gestation hypoestrogenemia, hyperprogesteronemia, and a spontaneous preeclamptic-like phenotype. Preceding pregnancy, the gene encoding Er alpha (Erα, Esr1) is upregulated in the diestrual BPH/5 uterus. At the peak of decidualization, Esr1, Er beta (Erβ, Esr2), and Pr isoform B (Pr-B) were upregulated in the BPH/5 maternal–fetal interface. At the protein level, BPH/5 females display higher percentage of decidual cells with nuclear Erα expression, as well as Pr downregulation in the decidua, luminal and glandular epithelium. In conclusion, we provide evidence of disrupted sex hormone signaling in the peri-conception period of preeclamptic-like pregnancies, potentially shedding some light onto the intricate role of sex hormone signaling at unexplored timepoints of human preeclampsia.
]]>Biology doi: 10.3390/biology13030191
Authors: Marianela Zambrano-Román Jorge R. Padilla-Gutiérrez Yeminia Valle José Francisco Muñoz-Valle Elizabeth Guevara-Gutiérrez Patricia Aidé López-Olmos Laura Cristina Sepúlveda-Loza Luis Alberto Bautista-Herrera Emmanuel Valdés-Alvarado
Background: Skin cancer is one of the most frequent types of cancer, and cutaneous squamous cell carcinoma (cSCC) constitutes 20% of non-melanoma skin cancer (NMSC) cases. PTCH1, a tumor suppressor gene involved in the Sonic hedgehog signaling pathway, plays a crucial role in neoplastic processes. Methods: An analytical cross-sectional study, encompassing 211 cSCC patients and 290 individuals in a control group (CG), was performed. A subgroup of samples was considered for the relative expression analysis, and the results were obtained using quantitative real-time PCR (qPCR) with TaqMan® probes. The functional, splicing, and disease-causing effects of the proposed variants were explored via bioinformatics. Results: cSCC was predominant in men, especially in sun-exposed areas such as the head and neck. No statistically significant differences were found regarding the rs357564, rs2236405, rs2297086, and rs41313327 variants of PTCH1, or in the risk of cSCC, nor in the mRNA expression between the cSCC group and CG. A functional effect of rs357564 and a disease-causing relation to rs41313327 was identified. Conclusion: The proposed variants were not associated with cSCC risk in this Mexican population, but we recognize the need for analyzing larger population groups to elucidate the disease-causing role of rare variants.
]]>Biology doi: 10.3390/biology13030190
Authors: Mahmoud W. Yaish Aya Al-Busaidi Bernard R. Glick Talaat Ahmed Juha M. Alatalo
Salinity severely affects the health and productivity of plants, with root-associated microbes, including fungi, potentially playing a crucial role in mitigating this effect and promoting plant health. This study employed metagenomics to investigate differences in the structures of the epiphyte mycobiomes in the rhizospheres of seedlings of two distinct date palm cultivars with contrasting salinity tolerances, the susceptible cultivar, ‘Zabad’, and the tolerant cultivar, ‘Umsila’. Next-generation sequencing (NGS) of the internal transcribed spacer (ITS) rRNA was utilized as a DNA barcoding tool. The sequencing of 12 mycobiome libraries yielded 905,198 raw sequences of 268,829 high-quality reads that coded for 135 unique and annotatable operational taxonomic units (OTUs). An OTU analysis revealed differences in the rhizofungal community structures between the treatments regardless of genotype, and non-metric dimensional scaling (N-MDS) analyses demonstrated distinct separations between the cultivars under saline stress. However, these differences were not detected under the control environmental conditions, i.e., no salinity. The rhizospheric fungal community included four phyla (Ascomycota, Basidiomycota, Chytridiomycota, and Mucoromycota), with differences in the abundances of Aspergillus, Clonostachys, and Fusarium genera in response to salinity, regardless of the genotype. Differential pairwise comparisons showed that Fusarium falciforme-solani and Aspergillus sydowii-versicolor increased in abundance under saline conditions, providing potential future in vitro isolation guidelines for plant growth-promoting fungi. This study highlights the intricate dynamics of the rhizosphere microbial communities in date palms and their responses to salt stress. Additionally, we found no support for the hypothesis that indigenous epiphytic fungal communities are significantly involved in salinity tolerance in date palms.
]]>Biology doi: 10.3390/biology13030189
Authors: Arjan P. Palstra Wout Abbink Wisdom E. K. Agbeti Leo Kruijt Pauline Jéhannet Martin J. Lankheet
The yellowtail kingfish is a highly active and fast-growing marine fish with promising potential for aquaculture. In this study, essential insights were gained into the energy economy of this species by heart rate and acceleration logging during a swim-fitness test and a subsequent stress challenge test. Oxygen consumption values of the 600–800 g fish, when swimming in the range of 0.2 up to 1 m·s−1, were high—between 550 and 800 mg·kg−1·h−1—and the heart rate values—up to 228 bpm—were even among the highest ever measured for fishes. When swimming at these increasing speeds, their heart rate increased from 126 up to 162 bpm, and acceleration increased from 11 up to 26 milli-g. When exposed to four sequential steps of increasing stress load, the decreasing peaks of acceleration (baseline values of 12 to peaks of 26, 19 and 15 milli-g) indicated anticipatory behavior, but the heart rate increases (110 up to 138–144 bpm) remained similar. During the fourth step, when fish were also chased, peaking values of 186 bpm and 44 milli-g were measured. Oxygen consumption and heart rate increased with swimming speed and was well reflected by increases in tail beat and head width frequencies. Only when swimming steadily near the optimal swimming speed were these parameters strongly correlated.
]]>Biology doi: 10.3390/biology13030188
Authors: Olayinka M. Olajiga Samuel B. Jameson Brendan H. Carter Dawn M. Wesson Dana Mitzel Berlin Londono-Renteria
This review examines the advancements and methodologies of artificial feeding systems for the study of vector-borne diseases, offering a critical assessment of their development, advantages, and limitations relative to traditional live host models. It underscores the ethical considerations and practical benefits of such systems, including minimizing the use of live animals and enhancing experimental consistency. Various artificial feeding techniques are detailed, including membrane feeding, capillary feeding, and the utilization of engineered biocompatible materials, with their respective applications, efficacy, and the challenges encountered with their use also being outlined. This review also forecasts the integration of cutting-edge technologies like biomimicry, microfluidics, nanotechnology, and artificial intelligence to refine and expand the capabilities of artificial feeding systems. These innovations aim to more accurately simulate natural feeding conditions, thereby improving the reliability of studies on the transmission dynamics of vector-borne diseases. This comprehensive review serves as a foundational reference for researchers in the field, proposing a forward-looking perspective on the potential of artificial feeding systems to revolutionize vector-borne disease research.
]]>Biology doi: 10.3390/biology13030187
Authors: Will Casey Thiviya Kumaran Steven E. Massey Bud Mishra
The eukaryotic lineage has enjoyed a long-term “stable” mutualism between nucleus and mitochondrion, since mitochondrial endosymbiosis began about 2 billion years ago. This mostly cooperative interaction has provided the basis for eukaryotic expansion and diversification, which has profoundly altered the forms of life on Earth. While we ignore the exact biochemical details of how the alpha-proteobacterial ancestor of mitochondria entered into endosymbiosis with a proto-eukaryote, in more general terms, we present a signaling games perspective of how the cooperative relationship became established, and has been maintained. While games are used to understand organismal evolution, information-asymmetric games at the molecular level promise novel insights into endosymbiosis. Using a previously devised biomolecular signaling games approach, we model a sender–receiver information asymmetric game, in which the informed mitochondrial sender signals and the uninformed nuclear receiver may take actions (involving for example apoptosis, senescence, regeneration and autophagy/mitophagy). The simulation shows that cellularization is a stabilizing mechanism for Pareto efficient sender/receiver strategic interaction. In stark contrast, the extracellular environment struggles to maintain efficient outcomes, as senders are indifferent to the effects of their signals upon the receiver. Our hypothesis has translational implications, such as in cellular therapy, as mitochondrial medicine matures. It also inspires speculative conjectures about how an analogous human–AI endosymbiosis may be engineered.
]]>Biology doi: 10.3390/biology13030186
Authors: Yuan Li Nan Wang Jianwen Guo Xianjun Zhou Xueyi Bai Muhammad Azeem Liyun Zhu Lin Chen Moli Chu Hui Wang Wei Cheng
Phytophthora blight of pepper is a notorious disease caused by the oomycete pathogen Phytophthora capsici, which poses a great threat to global pepper production. MicroRNA (miRNA) is a class of non-coding small RNAs that regulate gene expressions by altering the translation efficiency or stability of targeted mRNAs, which play important roles in the regulation of a plant’s response to pathogens. Herein, time-series mRNA-seq libraries and small RNA-seq libraries were constructed using pepper roots from the resistant line CM334 and the susceptible line EC01 inoculated with P. capsici at 0, 6, 24, and 48 h post-inoculation, respectively. For mRNA-seq analysis, a total of 2159 and 2971 differentially expressed genes (DEGs) were identified in CM334 and EC01, respectively. For miRNA-seq analysis, 491 pepper miRNAs were identified, including 330 known miRNAs and 161 novel miRNAs. Among them, 69 and 88 differentially expressed miRNAs (DEMs) were identified in CM334 and EC01, respectively. Examination of DEMs and their targets revealed 22 regulatory networks, predominantly featuring up-regulated miRNAs corresponding to down-regulated target genes. Notably, these DEM-DEG regulatory networks exhibited significant overlap between CM334 and EC01, suggesting that they might contribute to pepper’s basal defense against P. capsici. Furthermore, five selected DEMs (miR166, miR1171, miR395, miR530 and miRN2) and their target genes underwent qRT-PCR validation, confirming a consistent negative correlation in the expression patterns of miRNAs and their targets. This comprehensive analysis provides novel insights into the regulatory networks of miRNAs and their targets, offering valuable contributions to our understanding of pepper’s defense mechanisms against P. capsici.
]]>Biology doi: 10.3390/biology13030185
Authors: Atefeh Afsar Li Zhang
Mitochondria are the powerhouse of the cell. Mitochondria serve as the major source of oxidative stress. Impaired mitochondria produce less adenosine triphosphate (ATP) but generate more reactive oxygen species (ROS), which could be a major factor in the oxidative imbalance observed in Alzheimer’s disease (AD). Well-balanced mitochondrial respiration is important for the proper functioning of cells and human health. Indeed, recent research has shown that elevated mitochondrial respiration underlies the development and therapy resistance of many types of cancer, whereas diminished mitochondrial respiration is linked to the pathogenesis of AD. Mitochondria govern several activities that are known to be changed in lung cancer, the largest cause of cancer-related mortality worldwide. Because of the significant dependence of lung cancer cells on mitochondrial respiration, numerous studies demonstrated that blocking mitochondrial activity is a potent strategy to treat lung cancer. Heme is a central factor in mitochondrial respiration/oxidative phosphorylation (OXPHOS), and its association with cancer is the subject of increased research in recent years. In neural cells, heme is a key component in mitochondrial respiration and the production of ATP. Here, we review the role of impaired heme metabolism in the etiology of AD. We discuss the numerous mitochondrial effects that may contribute to AD and cancer. In addition to emphasizing the significance of heme in the development of both AD and cancer, this review also identifies some possible biological connections between the development of the two diseases. This review explores shared biological mechanisms (Pin1, Wnt, and p53 signaling) in cancer and AD. In cancer, these mechanisms drive cell proliferation and tumorigenic functions, while in AD, they lead to cell death. Understanding these mechanisms may help advance treatments for both conditions. This review discusses precise information regarding common risk factors, such as aging, obesity, diabetes, and tobacco usage.
]]>Biology doi: 10.3390/biology13030184
Authors: Pi-Jing Wei An-Dong Zhu Ruifen Cao Chunhou Zheng
Cancer is a complex and evolutionary disease mainly driven by the accumulation of genetic variations in genes. Identifying cancer driver genes is important. However, most related studies have focused on the population level. Cancer is a disease with high heterogeneity. Thus, the discovery of driver genes at the individual level is becoming more valuable but is a great challenge. Although there have been some computational methods proposed to tackle this challenge, few can cover all patient samples well, and there is still room for performance improvement. In this study, to identify individual-level driver genes more efficiently, we propose the PDGCN method. PDGCN integrates multiple types of data features, including mutation, expression, methylation, copy number data, and system-level gene features, along with network structural features extracted using Node2vec in order to construct a sample–gene interaction network. Prediction is performed using a graphical convolutional neural network model with a conditional random field layer, which is able to better combine the network structural features with biological attribute features. Experiments on the ACC (Adrenocortical Cancer) and KICH (Kidney Chromophobe) datasets from TCGA (The Cancer Genome Atlas) demonstrated that the method performs better compared to other similar methods. It can identify not only frequently mutated driver genes, but also rare candidate driver genes and novel biomarker genes. The results of the survival and enrichment analyses of these detected genes demonstrate that the method can identify important driver genes at the individual level.
]]>Biology doi: 10.3390/biology13030183
Authors: Yangchen Yuan Xinbo Pang Jiushuai Pang Qian Wang Miaomiao Zhou Yan Lu Chenyang Xu Dazhuang Huang
Circular RNAs (circRNAs) are important regulatory molecules involved in various biological processes. However, the potential function of circRNAs in the turning red process of Quercus mongolica leaves is unclear. This study used RNA-seq data to identify 6228 circRNAs in leaf samples from four different developmental stages and showed that 88 circRNAs were differentially expressed. A correlation analysis was performed between anthocyanins and the circRNAs. A total of 16 circRNAs that may be involved in regulating the colour of Mongolian oak leaves were identified. CircRNAs may affect the colour of Q. mongolica leaves by regulating auxin, cytokinin, gibberellin, ethylene, and abscisic acid. This study revealed the potential role of circRNAs in the colour change of Q. mongolica leaves.
]]>Biology doi: 10.3390/biology13030182
Authors: Leticia Silva Miranda Sarah Renee Rudd Oscar Mena Piper Eden Hudspeth José E. Barboza-Corona Hyun-Woo Park Dennis Ken Bideshi
Mosquitoes are the most notorious arthropod vectors of viral and parasitic diseases for which approximately half the world’s population, ~4,000,000,000, is at risk. Integrated pest management programs (IPMPs) have achieved some success in mitigating the regional transmission and persistence of these diseases. However, as many vector-borne diseases remain pervasive, it is obvious that IPMP successes have not been absolute in eradicating the threat imposed by mosquitoes. Moreover, the expanding mosquito geographic ranges caused by factors related to climate change and globalization (travel, trade, and migration), and the evolution of resistance to synthetic pesticides, present ongoing challenges to reducing or eliminating the local and global burden of these diseases, especially in economically and medically disadvantaged societies. Abatement strategies include the control of vector populations with synthetic pesticides and eco-friendly technologies. These “green” technologies include SIT, IIT, RIDL, CRISPR/Cas9 gene drive, and biological control that specifically targets the aquatic larval stages of mosquitoes. Regarding the latter, the most effective continues to be the widespread use of Lysinibacillus sphaericus (Ls) and Bacillus thuringiensis subsp. israelensis (Bti). Here, we present a review of the health issues elicited by vector mosquitoes, control strategies, and lastly, focus on the biology of Ls and Bti, with an emphasis on the latter, to which no resistance has been observed in the field.
]]>Biology doi: 10.3390/biology13030181
Authors: Venkatesan Sundaram Stephanie Mohammed Brian N. Cockburn M. R. Srinivasan Chalapathi R. Adidam Venkata Jenelle Johnson Lester Gilkes Kegan Romelle Jones Nikolay Zyuzikov
In the original publication [...]
]]>Biology doi: 10.3390/biology13030180
Authors: Tetiana Shcholok Eftekhar Eftekharpour
Redox balance is increasingly identified as a major player in cellular signaling. A fundamentally simple reaction of oxidation and reduction of cysteine residues in cellular proteins is the central concept in this complex regulatory mode of protein function. Oxidation of key cysteine residues occurs at the physiological levels of reactive oxygen species (ROS), but they are reduced by a supply of thiol antioxidant molecules including glutathione, glutaredoxin, and thioredoxin. While these molecules show complex compensatory roles in experimental conditions, transgenic animal models provide a comprehensive picture to pinpoint the role of each antioxidant. In this review, we have specifically focused on the available literature on thioredoxin-1 system transgenic models that include thioredoxin and thioredoxin reductase proteins. As the identification of thioredoxin protein targets is technically challenging, the true contribution of this system in maintaining cellular balance remains unidentified, including the role of this system in the brain.
]]>Biology doi: 10.3390/biology13030179
Authors: Franziska C. Sandmeier
This short review focuses on current experimental designs to quantify immune acclimation in animals. Especially in the face of rapidly changing thermal regimes, thermal acclimation of immune function has the potential to impact host–pathogen relationships and the fitness of hosts. While much of the field of ecoimmunology has focused on vertebrates and insects, broad interest in how animals can acclimate to temperatures spans taxa. The literature shows a recent increase in thermal acclimation studies in the past six years. I categorized studies as focusing on (1) natural thermal variation in the environment (e.g., seasonal), (2) in vivo manipulation of animals in captive conditions, and (3) in vitro assays using biological samples taken from wild or captive animals. I detail the strengths and weaknesses of these approaches, with an emphasis on mechanisms of acclimation at different levels of organization (organismal and cellular). These two mechanisms are not mutually exclusive, and a greater combination of the three techniques listed above will increase our knowledge of the diversity of mechanisms used by animals to acclimate to changing thermal regimes. Finally, I suggest that functional assays of immune system cells (such as quantification of phagocytosis) are an accessible and non-taxa-specific way to tease apart the effects of animals upregulating quantities of immune effectors (cells) and changes in the function of immune effectors (cellular performance) due to structural changes in cells such as those of membranes and enzymes.
]]>Biology doi: 10.3390/biology13030178
Authors: Seth Duwor Daniela Brites Pascal Mäser
The present frontrunners in the chemotherapy of infections caused by protozoa are nitro-based prodrugs that are selectively activated by PFOR-mediated redox reactions. This study seeks to analyze the distribution of PFOR in selected protozoa and bacteria by applying comparative genomics to test the hypothesis that PFOR in eukaryotes was acquired through horizontal gene transfer (HGT) from bacteria. Furthermore, to identify other putatively acquired genes, proteome-wide and gene enrichment analyses were used. A plausible explanation for the patchy occurrence of PFOR in protozoa is based on the hypothesis that bacteria are potential sources of genes that enhance the adaptation of protozoa in hostile environments. Comparative genomics of Entamoeba histolytica and the putative gene donor, Desulfovibrio vulgaris, identified eleven candidate genes for HGT involved in intermediary metabolism. If these results can be reproduced in other PFOR-possessing protozoa, it would provide more validated evidence to support the horizontal transfer of pfor from bacteria.
]]>Biology doi: 10.3390/biology13030177
Authors: Jiawei Rao Yu Zhang Haoxiang Zhao Jianyang Guo Fanghao Wan Xiaoqing Xian Nianwan Yang Wanxue Liu
The Mediterranean fruit fly, Ceratitis capitata (Wiedemann), which is native to tropical Africa, has invaded more than 100 countries and constitutes a risk to the citrus sector. Studying its potential geographical distribution (PGD) in the context of global climate change is important for prevention and control efforts worldwide. Therefore, we used the CLIMEX model to project and assess the risk of global invasion by C. capitata under current (1981–2010) and future (2040–2059) climates. In the prevailing climatic conditions, the area of PGD for C. capitata was approximately 664.8 × 105 km2 and was concentrated in South America, southern Africa, southern North America, eastern Asia, and southern Europe. Under future climate conditions, the area of PGD for C. capitata is projected to decrease to approximately 544.1 × 105 km2 and shift to higher latitudes. Cold stress was shown to affect distribution at high latitudes, and heat stress was the main factor affecting distribution under current and future climates. According to the predicted results, countries with highly suitable habitats for C. capitata that have not yet been invaded, such as China, Myanmar, and Vietnam, must strengthen quarantine measures to prevent the introduction of this pest.
]]>Biology doi: 10.3390/biology13030176
Authors: Elena G. Biosca Ricardo Delgado Santander Félix Morán Àngela Figàs-Segura Rosa Vázquez José Francisco Català-Senent Belén Álvarez
Fire blight, caused by the plant-pathogenic bacterium Erwinia amylovora, is a highly contagious and difficult-to-control disease due to its efficient dissemination and survival and the scarcity of effective control methods. Copper and antibiotics are the most used treatments but pose environmental and human health risks. Bacteriophages (phages) constitute an ecological, safe, and sustainable fire blight control alternative. The goal of this study was to search for specific E. amylovora phages from plant material, soil, and water samples in Mediterranean environments. A collection of phages able to specifically infect and lyse E. amylovora strains was generated from former fire blight-affected orchards in Eastern Spain. Following in vitro characterization, assays in immature fruit revealed that preventively applying some of the phages or their combinations delayed the onset of fire blight symptoms and reduced the disease’s severity, suggesting their biocontrol potential in Spain and other countries. The morphological and molecular characterization of the selected E. amylovora phages classified them as members of the class Caudoviricetes (former Myoviridae family) and genus Kolesnikvirus. This study reveals Mediterranean settings as plausible sources of E. amylovora-specific bacteriophages and provides the first effective European phage cocktails in plant material for the development of sustainable fire blight management measures.
]]>Biology doi: 10.3390/biology13030175
Authors: Rachel Rapoport Avraham Greenberg Zohar Yakhini Itamar Simon
Traditional gene set enrichment analysis falters when applied to large genomic domains, where neighboring genes often share functions. This spatial dependency creates misleading enrichments, mistaking mere physical proximity for genuine biological connections. Here we present Spatial Adjusted Gene Ontology (SAGO), a novel cyclic permutation-based approach, to tackle this challenge. SAGO separates enrichments due to spatial proximity from genuine biological links by incorporating the genes’ spatial arrangement into the analysis. We applied SAGO to various datasets in which the identified genomic intervals are large, including replication timing domains, large H3K9me3 and H3K27me3 domains, HiC compartments and lamina-associated domains (LADs). Intriguingly, applying SAGO to prostate cancer samples with large copy number alteration (CNA) domains eliminated most of the enriched GO terms, thus helping to accurately identify biologically relevant gene sets linked to oncogenic processes, free from spatial bias.
]]>Biology doi: 10.3390/biology13030174
Authors: Yuefeng Cai Jie Hu Yepeng Guo Xin Shen
The receptor for activated protein kinase C1 (RACK1) belongs to the typical WD repeat family, which is extremely conservative and important in multiple signal transduction pathways related to growth and development that coordinate the intracellular role of various life activities. As a novel protein with versatile functions, it was found in a variety of organisms. In a previous study, we identified the RACK1 sequence of white shrimp from transcriptome data. In this study, we employed specialized bioinformatics software to conduct an in-depth analysis of EcRACK1 and compare its amino acid sequence homology with other crustaceans. Furthermore, we investigated the expression patterns of RACK1 at different developmental stages and tissues, as well as at various time points after exposure to Aroclor 1245, aiming to elucidate its function and potential response towards Aroclor 1245 exposure. The length of EcRACK1 is 957 nucleotides, which encodes 318 amino acids. Moreover, there were seven typical WD repeats in EcRACK1, which have more than a 96% sequence identity with the RACK1 proteins of Penaeus. The results of tissue expression and spatiotemporal expression showed that it was significantly increased in the II and IV stages, but had a significant tissue specificity in the hepatopancreas, spermary, and muscle tissues of E. carinicauda, adult stage. Compared to the control, EcRACK1 was significantly induced in E. carinicauda zoea larvae exposed to Aroclor 1254 for 6, 10, 20, and 30 d (p < 0.05). These results suggested that EcRACK1 may play an important role in the larval development and environmental defense of E. carinicauda.
]]>Biology doi: 10.3390/biology13030173
Authors: Jaime Toral López Sandra Gómez Martinez María del Refugio Rivera Vega Edgar Hernández-Zamora Sergio Cuevas Covarrubias Belem Arely Ibarra Castrejón Luz María González Huerta
Cleidocranial dysplasia (CCD) is an autosomal dominant skeletal dysplasia characterized by persistent open skull sutures with bulging calvaria, hypoplasia, or aplasia of clavicles permitting abnormal opposition of the shoulders; wide public symphysis; short middle phalanx of the fifth fingers; and vertebral, craniofacial, and dental anomalies. It is a rare disease, with a prevalence of 1–9/1,000,000, high penetrance, and variable expression. The gene responsible for CCD is the Runt-related transcription factor 2 (RUNX2) gene. We characterize the clinical, genetic, and bioinformatic results of four CCD cases: two cases within Mexican families with six affected members, nine asymptomatic individuals, and two sporadic cases with CCD, with one hundred healthy controls. Genomic DNA analyses of the RUNX2 gene were performed for Sanger sequencing. Bioinformatics tools were used to predict the function, stability, and structural changes of the mutated RUNX2 proteins. Three novel heterozygous mutations (c.651_652delTA; c.538_539delinsCA; c.662T>A) and a previously reported mutation (c.674G>A) were detected. In silico analysis showed that all mutations had functional, stability-related, and structural alterations in the RUNX2 protein. Our results show novel mutations that enrich the pool of RUNX2 gene mutations with CCD. Moreover, the proband 1 presented clinical data not previously reported that could represent an expanded phenotype of severe expression.
]]>Biology doi: 10.3390/biology13030172
Authors: Gohar Azhar Koichiro Nagano Pankaj Patyal Xiaomin Zhang Ambika Verma Jeanne Y. Wei
Interleukin-1β converting enzyme (ICE, caspase-1) is a thiol protease that cleaves the pro-inflammatory cytokine precursors of IL-1β and IL-18 into active forms. Given the association between caspase-1 and cardiovascular pathology, we analyzed the hearts of ICE knockout (ICE KO) mice to test the hypothesis that caspase-1 plays a significant role in cardiac morphology and function. We characterized the histological and functional changes in the hearts of ICE KO mice compared to the Wild type. The cardiomyocytes from the neonatal ICE KO mice showed an impaired response to oxidative stress. Subsequently, the hearts from the ICE KO mice were hypertrophied, with a significant increase in the left ventricular and septal wall thickness and a greater LV mass/body weight ratio. The ICE KO mice hearts exhibited irregular myofibril arrangements and disruption of the cristae in the mitochondrial structure. Proapoptotic proteins that were significantly increased in the hearts of ICE KO versus the Wild type included pErk, pJNK, p53, Fas, Bax, and caspase 3. Further, the antiapoptotic proteins Bag-1 and Bcl-2 are activated in ICE KO hearts. Functionally, there was an increase in the left ventricular epicardial diameter and volume in ICE KO. In conclusion, our findings support the important role of caspase-1 in maintaining cardiac health; specifically, a significant decrease in caspase-1 is detrimental to the cardiovascular system.
]]>Biology doi: 10.3390/biology13030171
Authors: Maddalena Sbaffone Marie-Lise Jaffrain-Rea Lucia Cappabianca Francesca Carbonara Francesca Gianno Tiziana Feola Marianna Ruggieri Veronica Zelli Rita Maccarone Stefano Guadagni Marco Clementi Antonietta Arcella Vincenzo Esposito Giulia Carozza Ilaria Martelli Antonietta Rosella Farina Andrew Reay Mackay
Pituitary neuroendocrine tumors (PitNETs) are generally benign but comprise an aggressive, invasive, therapy-resistant, metastatic subset, underpinning a need for novel therapeutic targets. PitNETs exhibit low mutation rates but are associated with conditions linked to alternative splicing, an alternative oncogene pathway activation mechanism. PitNETs express the neurotrophin receptor TrkA, which exhibits oncogenic alternative TrkAIII splicing in other neuroendocrine tumors. We, therefore, assessed whether TrkAIII splicing represents a potential oncogenic participant in PitNETs. TrkAIII splicing was RT-PCR assessed in 53 PitNETs and TrkA isoform(s) expression and activation were assessed by confocal immunofluorescence. TrkAIII splicing was also compared to HIF1α, HIF2α, SF3B1, SRSF2, U2AF1, and JCPyV large T antigen mRNA expression, Xbp1 splicing, and SF3B1 mutation. TrkAIII splicing was detected in all invasive and most non-invasive PitNETs and was significantly elevated in invasive cases. In PitNET lineages, TrkAIII splicing was significantly elevated in invasive PIT1 PitNETs and high in invasive and non-invasive SF1 and TPIT lineages. Immunoreactivity consistent with TrkAIII activation characterized PitNET expressing TrkAIII mRNA, and invasive Pit1 PitNETs exhibited elevated HIF2α expression. TrkAIII splicing did not associate with SF3B1 mutations, altered SF3B1, SRSF2, and U2AF1 or JCPyV large T antigen expression, or Xbp1 splicing. Therefore, TrkAIII splicing is common in PitNETs, is elevated in invasive, especially PIT1 tumors, can result in intracellular TrkAIII activation, and may involve hypoxia. The data support a role for TrkAIII splicing in PitNET pathogenesis and progression and identify TrkAIII as a novel potential target in refractory PitNETs.
]]>Biology doi: 10.3390/biology13030170
Authors: Jacek Z. Kubiak Małgorzata Kloc
The correct timing of molecular and cellular events is critical for embryo development, cell/tissue homeostasis, and to functions in all organisms throughout their whole lives [...]
]]>Biology doi: 10.3390/biology13030169
Authors: Marcela A. Vidal Nayadet Henríquez Cristian Torres-Díaz Gonzalo Collado Ian S. Acuña-Rodríguez
Resources are limited in global biodiversity conservation efforts, which emphasizes the significance of setting conservation priorities. Using standardized criteria, we evaluated 58 amphibian species in Chile to determine their conservation priority (CP). Species with insufficient historical data had their values marked as missing. With a median value of p = 1.67, the results demonstrated CP values ranging from p = 0.48 to p = 3.0, classifying species into priority and non-priority groups. Four levels were established for the priority categories: no priority, low priority, medium priority, and high priority. Additionally, the Telmatobiidae and Alsodidae families were identified as two more priority families. Notably, the species with the highest priority were found to be T. halli, T. fronteriensis, T. philippii, T. chusmisensis, A. pehuenche, and Alsodes tumultuosus, where T. philippii and T. fronteriensis have equal priority for conservation at the national level according to the conservation priority analysis. Eight priority families—the Alsodidae, Batrachylidae, Bufonidae, Ceratophryidae, Leptodactylidae, Rhinodermatidae, and Telmatobiidae—were determined, and 14 species—or 24% of the species examined—need further study. Based on the conservation priority analysis, the species T. fronteriensis and T. philippii share the highest priority for conservation at the national level (p = 2.50). With 70% of the amphibians under study being threatened mainly by habitat loss, pollution, and emerging diseases, the creation of conservation categories made the threat assessment process easier. Due to a lack of information on geographic distribution and abundance, quantitatively classifying amphibians in Chile remains difficult. The analysis of conservation priorities and potential extinction threats informs appropriate management strategies.
]]>Biology doi: 10.3390/biology13030168
Authors: Yifang Wang Xiaoling Deng Rui Zhang Hao Lyu Shuai Xiao Dong Guo Declan William Ali Marek Michalak Cefan Zhou Xing-Zhen Chen Jingfeng Tang
Transient receptor potential vanilloid-6 (TRPV6) is a cation channel belonging to the TRP superfamily, specifically the vanilloid subfamily, and is the sixth member of this subfamily. Its presence in the body is primarily limited to the skin, ovaries, kidney, testes, and digestive tract epithelium. The body maintains calcium homeostasis using the TRPV6 channel, which has a greater calcium selectivity than the other TRP channels. Several pieces of evidence suggest that it is upregulated in the advanced stages of thyroid, ovarian, breast, colon, and prostate cancers. The function of TRPV6 in regulating calcium signaling in cancer will be covered in this review, along with its potential applications as a cancer treatment target.
]]>Biology doi: 10.3390/biology13030167
Authors: Tal Eliav Rafael Benoliel Olga A. Korczeniewska
Painful traumatic trigeminal neuropathy (PTTN) is a chronic neuropathic pain that may develop following injury to the trigeminal nerve. Etiologies include cranio-orofacial trauma that may result from dental, surgical, or anesthetic procedures or physical trauma, such as a motor vehicle accident. Following nerve injury, there are various mechanisms, including peripheral and central, as well as phenotypic changes and genetic predispositions that may contribute to the development of neuropathic pain. In this article, we review current literature pertaining to the cellular processes that occur following traumatic damage to the trigeminal nerve, also called cranial nerve V, that results in chronic neuropathic pain. We examine the neurobiology and pathophysiology based mostly on pre-clinical animal models of neuropathic/trigeminal pain.
]]>Biology doi: 10.3390/biology13030166
Authors: Serik N. Abdreshov Georgii A. Demchenko Anar N. Yeshmukhanbet Makpal A. Yessenova Sandugash A. Mankibaeva Gulshat K. Atanbaeva Marzhan S. Kulbayeva
This paper provides data regarding the ratios of the functional structures of lymph nodes after inflammation in the abdominal organs. Lymph systems, including lymph nodes, function as filters of tissues and tissue fluids and are places of origin and lymphocyte production for normal physiological functions. They display specific morphological and functional responses in reaction to endogenous and exogenous substances. The morphological pattern of the mesenteric lymph node in experimental rat groups reflects a decrease in its immune function due to the processes of inflammation in the abdominal cavity. These processes work together with the associated organs and their involvement in the abdominal lymph nodes, in which there are discharges of the structure of the paracortical zone under conditions of reduced lymphogenic processes, according to the decrease in the size of the paracortex and the ratios of lymphoid nodes with and without germinal centers. Histological and morphometric analyses show changes in the mesenteric lymph node. These analyses are characterized by changes in the cortical and medullary substances, while the proportion of the cortical structure decreases. We also noted an increase in the number of macrophages in the lymphoid nodes and cerebral sinus, as well as a decrease in the number of mature plasmocytes, the paracortex, and the pulp strands. These changes indicate immunosuppressive effects on the lymph node. Under the conditions of inflammation, the formation of a mixed immune response occurs.
]]>Biology doi: 10.3390/biology13030165
Authors: Stefano Raffaele Giannubilo Daniela Marzioni Giovanni Tossetta Ramona Montironi Maria Liberata Meccariello Andrea Ciavattini
Pregnancy is generally studied as a biological interaction between a mother and a fetus; however, the father, with his characteristics, lifestyle, genetics, and living environment, is by no means unrelated to the outcome of pregnancy. The half of the fetal genetic heritage of paternal derivation can be decisive in cases of inherited chromosomal disorders, and can be the result of de novo genetic alterations. In addition to the strictly pathological aspects, paternal genetics may transmit thrombophilic traits that affect the implantation and vascular construction of the feto-placental unit, lead to placenta-mediated diseases such as pre-eclampsia and fetal growth retardation, and contribute to the multifactorial genesis of preterm delivery. Biological aspects of immunological tolerance to paternal antigens also appear to be crucial for these pathologies. Finally, this review describes the biological findings by which the environment, exposure to pathogens, lifestyle, and nutritional style of the father affect fetal pathophysiological and epigenetic definition.
]]>Biology doi: 10.3390/biology13030164
Authors: Min Xie Pengpeng Wang Qi Deng Si Liu Zhou Zhang Hao Wu Jing Xiang Jie Zhou Xin Yang Rui Song Shaoming Li Zhonggui Xie
To clarify the allometric growth pattern and hunger tolerance of Hemibarbus maculatus Bleeker larvae, the morphological lengths of their functional organs were measured continuously and their primary feeding rates under a state of starvation were studied. A control group and starvation group were set up for this study, and 10 larvae were sampled from each group every day in order to study their allometric growth pattern and starvation tolerance. The results indicated that the Hemibarbus maculatus larvae opened their mouths for feeding at 4 days after hatching, and that the yolk sac disappeared completely at 11 days after hatching. The Hemibarbus maculatus larvae preferentially developed their heads, fins, and eyes, related to the functions of feeding, balancing, and swimming, in order to cope with complex environments. The growth inflection points for the head length, pectoral fin length, dorsal fin length, eye diameter, eye spacing, snout length, and body height were characterized by total lengths of 10.93 mm, 11.67 mm, 11.67 mm, 13.17 mm, 16.53 mm, 15.13 mm, and 15.13 mm, respectively. Prior to and following the inflection point, positive allometric growth was observed in all organs. After the inflection point, the dorsal fin continued to maintain positive allometric growth, while the others changed to isometric allometric growth. A growth inflection point was not observed for trunk length or the lengths of the tail and anal fins. The trunk length always maintained negative allometry, while the tail and anal fin lengths were reversed. The growth inflection point of the tail length was at a total length of 13.68 mm. Before and after the growth inflection point, negative and isometric allometric growths were observed, respectively. According to the relationship between the total length and number of days after hatching, the growth inflection point of the Hemibarbus maculatus larvae was concentrated at TL = 10.93–16.53 mm, which was observed 14–20 days after hatching. The point of no return for the Hemibarbus maculatus larvae was 12–13 days after hatching, and the ratio of days after hatching in the mixed trophic period to the endotrophic period was 1.75, indicating that the larvae had strong hunger tolerance. Therefore, when considering a water temperature of 22.66 ± 1.56 °C, 4–5 days after hatching is the best time to cultivate in the pond, and it should not be carried out later than 12 days after hatching.
]]>Biology doi: 10.3390/biology13030163
Authors: Isabella Bracchi Juliana Morais João Almeida Coelho Ana Filipa Ferreira Inês Alves Cláudia Mendes Beatriz Correia Alexandre Gonçalves João Tiago Guimarães Inês Falcão Pires Elisa Keating Rita Negrão
The consumption of non-sugar sweeteners (NSS) has increased during pregnancy. The European Food Safety Agency suggested that steviol glycosides, such as Rebaudioside A (RebA), the major sweetener component of stevia, are safe for humans up to a dose of 4 mg/kg body weight/day. However, the World Health Organization recommended in 2023 the restraint of using NSS, including stevia, at any life stage, highlighting the need to study NSS safety in early periods of development. We aimed to study the mitochondrial and cardiometabolic effects of long-term RebA consumption during the reproductive stage of the life cycle. Female rats were exposed to RebA (4 mg steviol equivalents/kg body weight/day) in the drinking water from 4 weeks before mating until weaning. Morphometry, food and water consumption, glucose and lipid homeostasis, heart structure, function, and mitochondrial function were assessed. RebA showed an atrophic effect in the heart, decreasing cardiomyocyte cross-sectional area and myocardial fibrosis without repercussions on cardiac function. Mitochondrial and myofilamentary functions were not altered. Glucose tolerance and insulin sensitivity were not affected, but fasting glycemia and total plasma cholesterol decreased. This work suggests that this RebA dose is safe for female consumption during the reproductive stage, from a cardiometabolic perspective. However, studies on the effects of RebA exposure on the offspring are mandatory.
]]>Biology doi: 10.3390/biology13030162
Authors: Daniel Limeira Filho Elidy Rayane de Rezende França Dalton Kaynnan de Prado Costa Renato Correia Lima Maria Histelle Sousa do Nascimento Jacqueline da Silva Batista Maria Claudene Barros Elmary da Costa Fraga
Pimelodus is the most speciose genus of the family Pimelodidae, and is amply distributed in the Neotropical region. The species-level taxonomy and phylogenetic relationships within this genus are still poorly resolved, however. These taxonomic problems and the general lack of data have generated major uncertainties with regard to the identification of specimens from different localities. In the present study, we applied a single-locus species delimitation approach to identify the MOTUs found within the genus Pimelodus and provide sound evidence for the evaluation of the species richness of this genus in the different river basins of the Neotropical region. The study was based on the analysis of sequences of the mitochondrial COI gene of 13 nominal species, which resulted in the identification of 24 consensus MOTUs. Only six nominal species were recovered as well-defined molecular entities by both the traditional barcoding analysis and the molecular delimitation methods, while the other seven presented cryptic diversity or persistent taxonomic uncertainties. The lineages identified from the Parnaíba ecoregions, Amazonas Estuary and Coastal Drainages may represent a much greater diversity of Pimelodus species than that recognized currently, although a more detailed study of this diversity will be necessary to provide a more definitive classification of the genus.
]]>Biology doi: 10.3390/biology13030161
Authors: Isabel Rocha Marta González-García Laura Carrillo-Franco Marc Stefan Dawid-Milner Manuel Victor López-González
Area A5 is a noradrenergic cell group in the brain stem characterised by its important role in triggering sympathetic activity, exerting a profound influence on the sympathetic outflow, which is instrumental in the modulation of cardiovascular functions, stress responses and various other physiological processes that are crucial for adaptation and survival mechanisms. Understanding the role of area A5, therefore, not only provides insights into the basic functioning of the sympathetic nervous system but also sheds light on the neuronal basis of a number of autonomic responses. In this review, we look deeper into the specifics of area A5, exploring its anatomical connections, its neurochemical properties and the mechanisms by which it influences sympathetic nervous system activity and cardiorespiratory regulation and, thus, contributes to the overall dynamics of the autonomic function in regulating body homeostasis.
]]>Biology doi: 10.3390/biology13030160
Authors: Shaw Mlambo Macdonald Mubayiwa Vimbai L. Tarusikirwa Honest Machekano Brighton M. Mvumi Casper Nyamukondiwa
Invasive alien species (IAS) are a major biosecurity threat affecting globalisation and the international trade of agricultural products and natural ecosystems. In recent decades, for example, field crop and postharvest grain insect pests have independently accounted for a significant decline in food quantity and quality. Nevertheless, how their interaction and cumulative effects along the ever-evolving field production to postharvest continuum contribute towards food insecurity remain scant in the literature. To address this within the context of Africa, we focus on the fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), and the larger grain borer, Prostephanus truncatus (Horn) (Coleoptera: Bostrichidae), two of the most important field and postharvest IAS, respectively, that have invaded Africa. Both insect pests have shown high invasion success, managing to establish themselves in >50% of the African continent within a decade post-introduction. The successive and summative nature of field and postharvest damage by invasive insect pests on the same crop along its value chain results in exacerbated food losses. This systematic review assesses the drivers, impacts and management of the fall armyworm and larger grain borer and their effects on food systems in Africa. Interrogating these issues is important in early warning systems, holistic management of IAS, maintenance of integral food systems in Africa and the development of effective management strategies.
]]>Biology doi: 10.3390/biology13030159
Authors: Matthias Wilhelm Voigt Jens Schepers Jacqueline Haas Oliver von Bohlen und Halbach
Neurotrophins, which belong to the family of growth factors, not only play crucial roles during development but are also involved in many processes in the postnatal brain. One representative of neurotrophins is brain-derived neurotrophic factor (BDNF). BDNF plays a role in the regulation of body weight and neuronal plasticity and is, therefore, also involved in processes associated with learning and memory formation. Many of the studies on BDNF have been carried out using BDNF-deficient mice. Unfortunately, homozygous deletion of BDNF is lethal in the early postnatal stage, so heterozygous BDNF-deficient mice are often studied. Another possibility is the use of conditional BDNF-deficient mice in which the expression of BDNF is strongly downregulated in some brain cells, for example, in the neurons of the central nervous system, but the expression of BDNF in other cells in the brain is unchanged. To further reduce BDNF expression, we crossed heterozygous BDNF-deficient mice with mice carrying a deletion of BDNF in neurofilament L-positive neurons. These offspring are viable, and the animals with a strong reduction in BDNF in the brain show a strongly increased body weight, which is accompanied by a reduction in brain weight. In addition, these animals show behavioral abnormalities, particularly with regard to locomotion.
]]>Biology doi: 10.3390/biology13030158
Authors: Efthymios Poulios Eleni Pavlidou Sousana K. Papadopoulou Kalliopi Rempetsioti Athanasios Migdanis Maria Mentzelou Maria Chatzidimitriou Ioannis Migdanis Odysseas Androutsos Constantinos Giaginis
Background: Probiotics, as supplements or food ingredients, are considered to exert promising healthy effects when administered in adequate quantity. Probiotics’ healthy effects are related with the prevention of many diseases, as well as decreasing symptom severity. Currently, the most available data concerning their potential health effects are associated with metabolic disorders, including gestational diabetes mellitus. There is also clinical evidence supporting that they may exert beneficial effects against diverse adverse pregnancy outcomes. The purpose of the current narrative study is to extensively review and analyze the current existing clinical studies concerning the probable positive impacts of probiotics supplementation during pregnancy as a protective agent against adverse pregnancy outcomes beyond gestational diabetes mellitus. Methods: a comprehensive and thorough literature search was conducted in the most precise scientific databases, such as PubMed, Scopus, and Web of Sciences, utilizing efficient, representative, and appropriate keywords. Results: in the last few years, recent research has been conducted concerning the potential beneficial effects against several adverse pregnancy outcomes such as lipid metabolism dysregulation, gestational hypertensive disorders, preterm birth, excessive gestational weight gain, caesarean risk section, vaginal microbiota impairment, mental health disturbances, and others. Conclusion: up to the present day, there is only preliminary clinical data and not conclusive results for probiotics’ healthy effects during pregnancy, and it remains questionable whether they could be used as supplementary treatment against adverse pregnancy outcomes beyond gestational diabetes mellitus.
]]>Biology doi: 10.3390/biology13030157
Authors: Alosh Greeny Ayushi Nair Prashant Sadanandan Sairaj Satarker Ademola C. Famurewa Madhavan Nampoothiri
Alzheimer’s disease (AD) is a neurodegenerative condition that predominantly affects the hippocampus and the entorhinal complex, leading to memory lapse and cognitive impairment. This can have a negative impact on an individual’s behavior, speech, and ability to navigate their surroundings. AD is one of the principal causes of dementia. One of the most accepted theories in AD, the amyloid β (Aβ) hypothesis, assumes that the buildup of the peptide Aβ is the root cause of AD. Impaired insulin signaling in the periphery and central nervous system has been considered to have an effect on the pathophysiology of AD. Further, researchers have shifted their focus to epigenetic mechanisms that are responsible for dysregulating major biochemical pathways and intracellular signaling processes responsible for directly or indirectly causing AD. The prime epigenetic mechanisms encompass DNA methylation, histone modifications, and non-coding RNA, and are majorly responsible for impairing insulin signaling both centrally and peripherally, thus leading to AD. In this review, we provide insights into the major epigenetic mechanisms involved in causing AD, such as DNA methylation and histone deacetylation. We decipher how the mechanisms alter peripheral insulin signaling and brain insulin signaling, leading to AD pathophysiology. In addition, this review also discusses the need for newer drug delivery systems for the targeted delivery of epigenetic drugs and explores targeted drug delivery systems such as nanoparticles, vesicular systems, networks, and other nano formulations in AD. Further, this review also sheds light on the future approaches used for epigenetic drug delivery.
]]>Biology doi: 10.3390/biology13030155
Authors: Pedro A. Pereira Marta Tavares Miguel Laires Bárbara Mota Maria Dulce Madeira Manuel M. Paula-Barbosa Armando Cardoso
The basolateral amygdala (BLA) contains interneurons that express neuropeptide Y (NPY) and vasoactive intestinal polypeptide (VIP), both of which are involved in the regulation of functions and behaviors that undergo deterioration with aging. There is considerable evidence that, in some brain areas, the expression of NPY and VIP might be modulated by acetylcholine. Importantly, the BLA is one of the brain regions that has one of the densest cholinergic innervations, which arise mainly from the basal forebrain cholinergic neurons. These cholinergic neurons depend on nerve growth factor (NGF) for their survival, connectivity, and function. Thus, in this study, we sought to determine if aging alters the densities of NPY- and VIP-positive neurons and cholinergic varicosities in the BLA and, in the affirmative, if those changes might rely on insufficient trophic support provided by NGF. The number of NPY-positive neurons was significantly reduced in aged rats, whereas the number of VIP-immunoreactive neurons was unaltered. The decreased NPY expression was fully reversed by the infusion of NGF in the lateral ventricle. The density of cholinergic varicosities was similar in adult and old rats. On the other hand, the density of cholinergic varicosities is significantly higher in old rats treated with NGF than in adult and old rats. Our results indicate a dissimilar resistance of different populations of BLA interneurons to aging. Furthermore, the present data also show that the BLA cholinergic innervation is particularly resistant to aging effects. Finally, our results also show that the reduced NPY expression in the BLA of aged rats can be related to changes in the NGF neurotrophic support.
]]>Biology doi: 10.3390/biology13030156
Authors: Tingting Gao Siqi Gao Yaling Li Ruijing Zhang Honglin Dong
Nanotheranostic agents capable of simultaneously enabling real-time tracking and precise treatment at tumor sites play an increasingly pivotal role in the field of medicine. In this article, we report a novel near-infrared-II window (NIR-II) emitting downconversion rare-earth nanoparticles (RENPs) to improve image-guided therapy for breast cancer. The developed α-NaErF4@NaYF4 nanoparticles (α-Er NPs) have a diameter of approximately 24.1 nm and exhibit superior biocompatibility and negligible toxicity. RENPs exhibit superior imaging quality and photothermal conversion efficiency in the NIR-II range compared to clinically approved indocyanine green (ICG). Under 808 nm laser irradiation, the α-Er NPs achieve significant tumor imaging performance and photothermal effects in vivo in a mouse model of breast cancer. Simultaneously, it combines X-ray computed tomography (CT) and ultrasound (US) tri-modal imaging to guide therapy for cancer. The integration of NIR-II imaging technology and RENPs establishes a promising foundation for future medical applications.
]]>Biology doi: 10.3390/biology13030154
Authors: Valentina Perri Maria Antonella Zingaropoli Patrizia Pasculli Federica Ciccone Matteo Tartaglia Viola Baione Leonardo Malimpensa Gina Ferrazzano Claudio Maria Mastroianni Antonella Conte Maria Rosa Ciardi
Multiple sclerosis (MS) is a debilitating neurological disease that has been classified as an immune-mediated attack on myelin, the protective sheath of nerves. Some aspects of its pathogenesis are still unclear; nevertheless, it is generally established that viral infections influence the course of the disease. Cytomegalovirus (CMV) is a major pathogen involved in alterations of the immune system, including the expansion of highly differentiated cytotoxic CD8+ T cells and the accumulation of adaptive natural killer (NK) cells expressing high levels of the NKG2C receptor. In this study, we evaluated the impact of latent CMV infection on MS patients through the characterization of peripheral NK cells, CD8+ T cells, and NKT-like cells using flow cytometry. We evaluated the associations between immune cell profiles and clinical features such as MS duration and MS progression, evaluated using the Expanded Disability Status Scale (EDSS). We showed that NK cells, CD8+ T cells, and NKT-like cells had an altered phenotype in CMV-infected MS patients and displayed high levels of the NKG2C receptor. Moreover, in MS patients, increased NKG2C expression levels were found to be associated with higher EDSS scores. Overall, these results support the hypothesis that CMV infection imprints the immune system by modifying the phenotype and receptor repertoire of NK and CD8+ T cells, suggesting a detrimental role of CMV on MS progression.
]]>Biology doi: 10.3390/biology13030153
Authors: Yachan Feng Haojie Zhang Jiangtao Shao Chao Du Xiaolei Zhou Xueling Guo Yingze Wang
The prognosis for cancer patients has declined dramatically in recent years due to the challenges in treating malignant tumors. Tumor immunotherapy, which includes immune target inhibition and chimeric antigen receptor cell treatment, is currently evolving quickly. Among them, natural killer (NK) cells are gradually becoming another preferred cell immunotherapy after T cell immunotherapy due to their unique killing effects in innate and adaptive immunity. NK cell therapy has shown encouraging outcomes in clinical studies; however, there are still some problems, including limited efficacy in solid tumors, inadequate NK cell penetration, and expensive treatment expenses. Noteworthy benefits of nanomaterials include their chemical specificity, biocompatibility, and ease of manufacturing; these make them promising instruments for enhancing NK cell anti-tumor immune responses. Nanomaterials can promote NK cell homing and infiltration, participate in NK cell modification and non-invasive cell tracking and imaging modes, and greatly increase the effectiveness of NK cell immunotherapy. The introduction of NK cell-based immunotherapy research and a more detailed discussion of nanomaterial research in NK cell-based immunotherapy and molecular imaging will be the main topics of this review.
]]>Biology doi: 10.3390/biology13030152
Authors: Hina Ahmad Neha Chetlangia Supriya G. Prasanth
In all eukaryotes, the initiation of DNA replication requires a stepwise assembly of factors onto the origins of DNA replication. This is pioneered by the Origin Recognition Complex, which recruits Cdc6. Together, they bring Cdt1, which shepherds MCM2-7 to form the OCCM complex. Sequentially, a second Cdt1-bound hexamer of MCM2-7 is recruited by ORC-Cdc6 to form an MCM double hexamer, which forms a part of the pre-RC. Although the mechanism of ORC binding to DNA varies across eukaryotes, how ORC is recruited to replication origins in human cells remains an area of intense investigation. This review discusses how the chromatin environment influences pre-RC assembly, function, and, eventually, origin activity.
]]>Biology doi: 10.3390/biology13030151
Authors: Moazam Hyder Abdul Mubeen Lodhi Zhaohong Wang Aslam Bukero Jing Gao Runqian Mao
Effective in a variety of insect orders, including dipteran, lepidopteran, and hemipteran, Wolbachia-based control tactics are investigated, noting the importance of sterile and incompatible insect techniques. Encouraging approaches for controlling Aedes mosquitoes are necessary, as demonstrated by the evaluation of a new SIT/IIT combination and the incorporation of SIT into Drosophila suzukii management. For example, Wolbachia may protect plants from rice pests, demonstrating its potential for agricultural biological vector management. Maternal transmission and cytoplasmic incompatibility dynamics are explored, while Wolbachia phenotypic impacts on mosquito and rice pest management are examined. The importance of host evolutionary distance is emphasised in recent scale insect research that addresses host-shifting. Using greater information, a suggested method for comprehending Wolbachia host variations in various contexts emphasises ecological connectivity. Endosymbionts passed on maternally in nematodes and arthropods, Wolbachia are widely distributed around the world and have evolved both mutualistic and parasitic traits. Wolbachia is positioned as a paradigm for microbial symbiosis due to advancements in multiomics, gene functional assays, and its effect on human health. The challenges and opportunities facing Wolbachia research include scale issues, ecological implications, ethical conundrums, and the possibility of customising strains through genetic engineering. It is thought that cooperative efforts are required to include Wolbachia-based therapies into pest management techniques while ensuring responsible and sustainable ways.
]]>Biology doi: 10.3390/biology13030149
Authors: Yan-Shuang Zhao Ding-Xi Liu Fu-Qing Tan Wan-Xi Yang
E. sinensis is an animal model for studying the reproduction and development of crustaceans. In this study, we knocked down the Es-Kif2a gene by injecting dsRNA into E. sinensis and inhibited Es-Plk1 gene expression by injecting PLK1 inhibitor BI6727 into E. sinensis. Then, the cell proliferation level, apoptosis level, and PI3K/AKT signaling expression level were detected. Our results showed that the proliferation level of spermatogenic cells decreased, while the apoptosis level increased after Es-Kif2a knockdown or Es-Plk1 inhibition. In order to verify whether these changes are caused by regulating the PI3K/AKT pathway, we detected the expression of PI3K and AKT proteins after Es-Kif2a knockdown or Es-Plk1 inhibition. Western Blot showed that in both the Es-Kif2a knockdown group and the Es-Plk1 inhibition group, the expression of PI3K and AKT proteins decreased. In addition, immunofluorescence showed that Es-KIF2A and Es-PLK1 proteins were co-localized during E. sinensis spermatogenesis. To further explore the upstream and downstream relationship between Es-KIF2A and Es-PLK1, we detected the expression level of Es-PLK1 after Es-Kif2a knockdown as well as the expression level of Es-KIF2A after Es-Plk1 inhibition. Western Blot showed that the expression of Es-PLK1 decreased after Es-Kif2a knockdown, while there was no significant change of Es-KIF2A after Es-Plk1 inhibition, indicating that Es-PLK1 may be a downstream factor of Es-KIF2A. Taken together, these results suggest that Es-KIF2A upregulates the PI3K/AKT signaling pathway through Es-PLK1 during the spermatogenesis of E. sinensis, thereby affecting the proliferation and apoptosis levels of spermatogenic cells.
]]>Biology doi: 10.3390/biology13030150
Authors: Celia Corral-Vazquez Joan Blanco Zaida Sarrate Ester Anton
Although the microbial communities from seminal fluid were an unexplored field some decades ago, their characteristics and potential roles are gradually coming to light. Therefore, a complex and specific microbiome population with commensal niches and fluctuating species has started to be revealed. In fact, certain clusters of bacteria have been associated with fertility and health, while the outgrowth of several species is potentially correlated with infertility indicators. This constitutes a compelling reason for outlining the external elements that may induce changes in the seminal microbiome composition, like lifestyle factors, gut microbiota, pathologies, prebiotics, and probiotics. In this review, we summarize the main findings about seminal microbiome, its origins and composition, its relationship with fertility, health, and influence factors, while reminding readers of the limitations and advantages introduced from technical variabilities during the experimental procedures.
]]>Biology doi: 10.3390/biology13030148
Authors: Fernanda C. Beveridge Alwyn Williams Robyn Cave Sundaravelpandian Kalaipandian Mirza M. Haque Steve W. Adkins
Understanding how seed functional traits interact with environmental factors to determine seedling recruitment is critical to assess the impact of climate change on ecosystem restoration. This study focused on the effects of environmental factors on the mother plant during early plant life history stages and during seed development. Desmodium brachypodum A. Gray (large tick trefoil, Fabaceae) was used as a model species. Firstly, this study analyzed seed germination traits in response to temperature and moisture stress. Secondly, it investigated how seed burial depth interacts with temperature and soil moisture to influence seedling emergence traits. Finally, it determined if contrasting levels of post-anthesis soil moisture could result in changes in D. brachypodum reproductive biology and seed and seedling functional traits. The results showed that elevated temperature and moisture stress interacted to significantly reduce the seed germination and seedling emergence (each by >50%), while the seed burial improved the seedling emergence. Post-anthesis soil moisture stress negatively impacted the plant traits, reducing the duration of the reproductive phenology stage (by 9 days) and seed production (by almost 50%). Unexpectedly, soil moisture stress did not affect most seed or seedling traits. In conclusion, elevated temperatures combined with low soil moisture caused significant declines in seed germination and seedling emergence. On the other hand, the reproductive output of D. brachypodum had low seed variability under soil moisture stress, which might be useful when sourcing seeds from climates with high variability. Even so, a reduction in seed quantity under maternal moisture stress can impact the long-term survival of restored plant populations.
]]>Biology doi: 10.3390/biology13030147
Authors: Yuichiro Kaibori Saho Tamoto Sayoko Okuda Kazuhiko Matsuo Takashi Nakayama Daisuke Nagakubo
The oral cavity serves as the primary path through which substances from the outside world enter our body. Therefore, it functions as a critical component of host defense. Saliva is essential for maintaining a stable oral environment by catching harmful agents, including pathogens, allergens, and chemicals, in the air or food. CCL28, highly expressed in mucosal tissues, such as the colon and salivary glands, is a chemokine that attracts CCR10/CCR3 expressing cells. However, the role of CCL28 in salivary gland formation remains unclear. In this study, we investigated the salivary gland structure in CCL28-deficient mice. Histological analysis showed decreased staining intensity of Alcian blue, which detects acidic mucous, reduced expression of MUC2, and higher infiltration of gram-positive bacteria in the salivary glands of CCL28-deficient mice. In addition, CCL28-deficient mice contained ectopically MUC2-expressed cells in the ducts and reduced the expression of cytokeratin 18, a marker for ductal cells, within the submandibular glands, resulting in decreased duct numbers. Additionally, the submandibular glands of CCL28-deficient mice showed reduced expression of several stem cell markers. These results suggest that CCL28 regulates saliva production via proper differentiation of salivary gland stem cells and could be a valuable biomarker of salivary gland function.
]]>Biology doi: 10.3390/biology13030146
Authors: Adrien Corne Florine Adolphe Jérôme Estaquier Sébastien Gaumer Jean-Marc Corsi
Cellular integrated stress response (ISR), the mitochondrial unfolded protein response (UPRmt), and IFN signaling are associated with viral infections. Activating transcription factor 4 (ATF4) plays a pivotal role in these pathways and controls the expression of many genes involved in redox processes, amino acid metabolism, protein misfolding, autophagy, and apoptosis. The precise role of ATF4 during viral infection is unclear and depends on cell hosts, viral agents, and models. Furthermore, ATF4 signaling can be hijacked by pathogens to favor viral infection and replication. In this review, we summarize the ATF4-mediated signaling pathways in response to viral infections, focusing on human immunodeficiency virus 1 (HIV-1). We examine the consequences of ATF4 activation for HIV-1 replication and reactivation. The role of ATF4 in autophagy and apoptosis is explored as in the context of HIV-1 infection programmed cell deaths contribute to the depletion of CD4 T cells. Furthermore, ATF4 can also participate in the establishment of innate and adaptive immunity that is essential for the host to control viral infections. We finally discuss the putative role of the ATF4 paralogue, named ATF5, in HIV-1 infection. This review underlines the role of ATF4 at the crossroads of multiple processes reflecting host–pathogen interactions.
]]>Biology doi: 10.3390/biology13030145
Authors: J. Mario Wolosin
The corneal epithelium (CE) is spread between two domains, the outer vascularized limbus and the avascular cornea proper. Epithelial cells undergo constant migration from the limbus to the vision-critical central cornea. Coordinated with this migration, the cells undergo differentiation changes where a pool of unique stem/precursor cells at the limbus yields the mature cells that reach the corneal center. Differentiation is heralded by the expression of the corneal-specific Krt12. Processing data acquired by scRNA-Seq showed that the increase in Krt12 expression occurs in four distinct steps within the limbus, plus a single continuous increase in the cornea. Differential gene analysis demonstrated that these domains reflect discreet stages of CE differentiation and yielded extensive information of the genes undergoing down- or upregulation in the sequential transition from less to more differentiate conditions. The approach allowed the identification of multiple gene cohorts, including (a) the genes which have maximal expression in the most primitive, Krt12-negative cell cohort, which is likely to include the stem/precursor cells; (b) the sets of genes that undergo continuous increase or decrease along the whole differentiation path; and (c) the genes showing maximal positive or negative correlation with the changes in Krt12.
]]>Biology doi: 10.3390/biology13030144
Authors: Małgorzata Woronkowicz Harry Roberts Piotr Skopiński
The corneal epithelium, comprising three layers of cells, represents the outermost portion of the eye and functions as a vital protective barrier while concurrently serving as a critical refractive structure. Maintaining its homeostasis involves a complex regenerative process facilitated by the functions of the lacrimal gland, tear film, and corneal nerves. Crucially, limbal epithelial stem cells located in the limbus (transitional zone between the cornea and the conjunctiva) are instrumental for the corneal epithelium integrity by replenishing and renewing cells. Re-epithelialization failure results in persistent defects, often associated with various ocular conditions including diabetic keratopathy. The insulin-like growth factor (IGF) system is a sophisticated network of insulin and other proteins essential for numerous physiological processes. This review examines its role in maintaining the corneal epithelium homeostasis, with a special focus on the interplay with corneal limbal stem cells and the potential therapeutic applications of the system components.
]]>Biology doi: 10.3390/biology13030142
Authors: Maria Ines Moreira de Gouveia Annick Bernalier-Donadille Gregory Jubelin
The human gut microbiota plays a crucial role in maintaining host health. Our review explores the prevalence and dynamics of Enterobacteriaceae, a bacterial family within the Proteobacteria phylum, in the human gut which represents a small fraction of the gut microbiota in healthy conditions. Even though their roles are not yet fully understood, Enterobacteriaceae and especially Escherichia coli (E. coli) play a part in creating an anaerobic environment, producing vitamins and protecting against pathogenic infections. The composition and residency of E. coli strains in the gut fluctuate among individuals and is influenced by many factors such as geography, diet and health. Dysbiosis, characterized by alterations in the microbial composition of the gut microbiota, is associated with various diseases, including obesity, inflammatory bowel diseases and metabolic disorders. A consistent pattern in dysbiosis is the expansion of Proteobacteria, particularly Enterobacteriaceae, which has been proposed as a potential marker for intestinal and extra-intestinal inflammatory diseases. Here we develop the potential mechanisms contributing to Enterobacteriaceae proliferation during dysbiosis, including changes in oxygen levels, alterations in mucosal substrates and dietary factors. Better knowledge of these mechanisms is important for developing strategies to restore a balanced gut microbiota and reduce the negative consequences of the Enterobacteriaceae bloom.
]]>Biology doi: 10.3390/biology13030143
Authors: Alessandra Benigno Chiara Aglietti Santa Olga Cacciola Salvatore Moricca
Gnomoniopsis castaneae is responsible for brown or chalky nut rot in sweet chestnut (Castanea sativa), causing heavy reductions in nut production. Controlling it is challenging, due to its inconspicuous infections, erratic colonization of host tissues and endophytic lifestyle. Fungicides are not applicable because they are prohibited in chestnut forests and strongly discouraged in fruit chestnut groves. Trichoderma species are safe and wide-spectrum biocontrol agents (BCAs), with a variety of beneficial effects in plant protection. This study tested selected strains of T. viride, T. harzianum and T. atroviride for their ability to suppress G. castaneae. Field experiments were conducted in four chestnut groves (two test plots plus two controls) at two sites with a different microclimate. As the size of the trees were a major drawback for uniform and effective treatments, the Trichoderma strains were delivered directly by trunk injection, using the BITE® (Blade for Infusion in TrEes) endotherapic tool. The BCA application, repeated twice in two subsequent years, significantly reduced nut rot incidence, with a more marked, presumably cumulative, effect in the second year. Our data showed the tested Trichoderma strains retain great potential for the biological control of G. castaneae in chestnut groves. The exploitation of Trichoderma spp. as biopesticides is a novelty in the forestry sector and proves the benefits of these microbes in plant disease protection.
]]>Biology doi: 10.3390/biology13030141
Authors: Yuqi Sun Xihong Li Jiaqi Mai Wenteng Xu Jiacheng Wang Qi Zhang Na Wang
The sex chromosome, especially specific in one sex, generally determines sexual size dimorphism (SSD), a phenomenon with dimorphic sexual difference in the body size. For Cynoglossus semilaevis, a flatfish in China, although the importance of chromosome W and its specific gene zbed1 in female-biased SSD have been suggested, its family members and regulation information are still unknown. At present, three zbed1 copies gene were identified on chromosome W, with no gametologs. Phylogenetic analysis for the ZBED family revealed an existence of ZBED9 in the fish. Nine members were uncovered from C. semilaevis, clustering into three kinds, ZBED1, ZBED4 and ZBEDX, which is less than the eleven kinds of ZBED members in mammals. The predominant expression of zbed1 in the female brain and pituitary tissues was further verified by qPCR. Transcription factor c/ebpα could significantly enhance the transcriptional activity of zbed1 promoter, which is opposite to its effect on the male determinant factor-dmrt1. When zbed1 was interfered with, piwil1, esr2 and wnt7b were up-regulated, while cell-cycle-related genes, including cdk4 and ccng1, were down-regulated. Thus, zbed1 is involved in cell proliferation by regulating esr2, piwil1, cell cycle and the Wnt pathway. Further research on their interactions would be helpful to understand fish SSD.
]]>Biology doi: 10.3390/biology13030140
Authors: Tomasz Kostka Joanna Kostka
This study aimed to assess the feasibility and reliability of quadriceps maximal short-term power (Pmax) and corresponding optimal movement velocity (υopt—velocity at which the power reaches a maximum value) measurements in different populations of subjects. Five groups of subjects, fifty participants in each group, took part in the study: students; patients of the cardiac rehabilitation program; patients after stroke; older adults; and subjects of different ages who performed repetitive measurements with two different bicycles. The correlations calculated for the pairs of scores ranged from 0.93 to 0.99 for Pmax and from 0.86 to 0.96 for υopt (all with p < 0.001). Intraclass Correlations Coefficients (ICCs) varied from 0.93 to 0.98 for Pmax and from 0.86 to 0.95 for υopt. The standard error of measurement (SEM) varied from 16.9 to 21.4 W for Pmax and from 2.91 to 5.54 rotations(rot)/min for υopt. The coefficients of variation (CVs or SEM%) for Pmax and υopt in the stroke group were 10.6% and 11.4%, respectively; all other CVs were clearly lower than 10%. The minimal detectable change (MDC) varied from 46.6 to 59.3 W for Pmax and from 8.07 to 15.4 rot/min for υopt. MDC% varied from 9.53% to 29.3% for Pmax and from 8.19% to 31.7% for υopt, and was the highest in the stroke group. Therefore, the precision of measurements of Pmax and υopt was confirmed by very good indices of absolute and relative reliability. The proposed methodology is precise, safe, not time-consuming and feasible in older subjects and those with diseases.
]]>Biology doi: 10.3390/biology13030139
Authors: Panyawarin Soommat Nachon Raethong Ratchaprapa Ruengsang Roypim Thananusak Teeraphan Laomettachit Kobkul Laoteng Treenut Saithong Wanwipa Vongsangnak
The genome-scale metabolic model (GSMM) of Cordyceps militaris provides a comprehensive basis of carbon assimilation for cell growth and metabolite production. However, the model with a simple mass balance concept shows limited capability to probe the metabolic responses of C. militaris under light exposure. This study, therefore, employed the transcriptome-integrated GSMM approach to extend the investigation of C. militaris’s metabolism under light conditions. Through the gene inactivity moderated by metabolism and expression (GIMME) framework, the iPS1474-tiGSMM model was furnished with the transcriptome data, thus providing a simulation that described reasonably well the metabolic responses underlying the phenotypic observation of C. militaris under the particular light conditions. The iPS1474-tiGSMM obviously showed an improved prediction of metabolic fluxes in correlation with the expressed genes involved in the cordycepin and carotenoid biosynthetic pathways under the sucrose culturing conditions. Further analysis of reporter metabolites suggested that the central carbon, purine, and fatty acid metabolisms towards carotenoid biosynthesis were the predominant metabolic processes responsible in light conditions. This finding highlights the key responsive processes enabling the acclimatization of C. militaris metabolism in varying light conditions. This study provides a valuable perspective on manipulating metabolic genes and fluxes towards the target metabolite production of C. militaris.
]]>Biology doi: 10.3390/biology13030138
Authors: Sarah Takallou Maryam Hajikarimlou Mustafa Al-gafari Jiashu Wang Thomas David Daniel Kazmirchuk Kamaledin B. Said Bahram Samanfar Ashkan Golshani
Maintaining translation fidelity is a critical step within the process of gene expression. It requires the involvement of numerous regulatory elements to ensure the synthesis of functional proteins. The efficient termination of protein synthesis can play a crucial role in preserving this fidelity. Here, we report on investigating a protein of unknown function, YNR069C (also known as BSC5), for its activity in the process of translation. We observed a significant increase in the bypass of premature stop codons upon the deletion of YNR069C. Interestingly, the genomic arrangement of this ORF suggests a compatible mode of expression reliant on translational readthrough, incorporating the neighboring open reading frame. We also showed that the deletion of YNR069C results in an increase in the rate of translation. Based on our results, we propose that YNR069C may play a role in translation fidelity, impacting the overall quantity and quality of translation. Our genetic interaction analysis supports our hypothesis, associating the role of YNR069C to the regulation of protein synthesis.
]]>Biology doi: 10.3390/biology13030137
Authors: Beltrán Ortolá José-Antonio Daròs
Insect pests rank among the major limiting factors in agricultural production worldwide. In addition to direct effect on crops, some phytophagous insects are efficient vectors for plant disease transmission. Large amounts of conventional insecticides are required to secure food production worldwide, with a high impact on the economy and environment, particularly when beneficial insects are also affected by chemicals that frequently lack the desired specificity. RNA interference (RNAi) is a natural mechanism gene expression regulation and protection against exogenous and endogenous genetic elements present in most eukaryotes, including insects. Molecules of double-stranded RNA (dsRNA) or highly structured RNA are the substrates of cellular enzymes to produce several types of small RNAs (sRNAs), which play a crucial role in targeting sequences for transcriptional or post-transcriptional gene silencing. The relatively simple rules that underlie RNAi regulation, mainly based in Watson–Crick complementarity, have facilitated biotechnological applications based on these cellular mechanisms. This includes the promise of using engineered dsRNA molecules, either endogenously produced in crop plants or exogenously synthesized and applied onto crops, as a new generation of highly specific, sustainable, and environmentally friendly insecticides. Fueled on this expectation, this article reviews current knowledge about the RNAi pathways in insects, and some other applied questions such as production and delivery of recombinant RNA, which are critical to establish RNAi as a reliable technology for insect control in crop plants.
]]>Biology doi: 10.3390/biology13030136
Authors: Pia F. Balàka Pero Ugarković Julia Türtscher Jürgen Kriwet Simone Niedermüller Patrik Krstinić Patrick L. Jambura
Balàka et al [...]
]]>Biology doi: 10.3390/biology13030135
Authors: Alen Soldo Lovrenc Lipej
The authors write that the last checklist for Croatia was carried out in 2009 and that 52 chondrichthyan species were reported in Croatian waters [...]
]]>Biology doi: 10.3390/biology13030134
Authors: Muhammad Asif Ali Gustavo Caetano-Anollés
The slow experimental acquisition of high-quality atomic structures of the rapidly changing proteins of the COVID-19 virus challenges vaccine and therapeutic drug development efforts. Fortunately, deep learning tools such as AlphaFold2 can quickly generate reliable models of atomic structure at experimental resolution. Current modeling studies have focused solely on definitions of mutant constellations of Variants of Concern (VOCs), leaving out the impact of haplotypes on protein structure. Here, we conduct a thorough comparative structural analysis of S-proteins belonging to major VOCs and corresponding latitude-delimited haplotypes that affect viral seasonal behavior. Our approach identified molecular regions of importance as well as patterns of structural recruitment. The S1 subunit hosted the majority of structural changes, especially those involving the N-terminal domain (NTD) and the receptor-binding domain (RBD). In particular, structural changes in the NTD were much greater than just translations in three-dimensional space, altering the sub-structures to greater extents. We also revealed a notable pattern of structural recruitment with the early VOCs Alpha and Delta behaving antagonistically by suppressing regions of structural change introduced by their corresponding haplotypes, and the current VOC Omicron behaving synergistically by amplifying or collecting structural change. Remarkably, haplotypes altering the galectin-like structure of the NTD were major contributors to seasonal behavior, supporting its putative environmental-sensing role. Our results provide an extensive view of the evolutionary landscape of the S-protein across the COVID-19 pandemic. This view will help predict important regions of structural change in future variants and haplotypes for more efficient vaccine and drug development.
]]>Biology doi: 10.3390/biology13030133
Authors: Chun-Yen Wu Da-Fong Song Zhi-Jia Chen Chao-Sheng Hu David Pei-Cheng Lin Han-Hsin Chang
The Klotho loss-of-function mutation is known to cause accelerated senescence in many organs, but its effects on the cornea have not been published. The present study aims to investigate the effects of the Klotho null mutation on cornea degeneration and to characterize the pathological features. Mouse corneas of Klotho homozygous, heterozygous, and wild-type mice at 8 weeks of age for both genders were subject to pathological and immunohistological examinations. The results show an irregular topography on the corneal surface with a Klotho null mutation. Histological examinations revealed a reduced corneal epithelial cell density, endothelial cell-shedding, and decreased cornea stromal layer thickness in the absence of the Klotho function. Furthermore, guttae formation and the desquamation of wing cells were significantly increased, which was comparable to the characteristics of Fuchs endothelial corneal dystrophy and bullous keratopathy. The mechanism analysis showed multi-fold abnormalities, including oxidative stress-induced cornea epithelium apoptosis and inflammation, extracellular matrix remodeling in the stroma, and a disruption of epithelial repair, presumably through the epithelial–mesenchymal transition. In conclusion, cornea degeneration was observed in the Klotho loss-of-function mutant mice. These pathological features support the use of Klotho mutant mice for investigating age-related cornea anomalies, including Fuchs endothelial corneal dystrophy, bullous keratopathy, and dry eye diseases.
]]>Biology doi: 10.3390/biology13020132
Authors: Francesco Vitali Martina De Raffele Michele Malagù Cristina Balla Giorgia Azzolini Federico Gibiino Alberto Boccadoro Marco Micillo Matteo Bertini
Background: At the same conditions of delivered power and contact force, open-irrigated radiofrequency ablation catheters are believed to create deeper lesions, while non-irrigated ones produce shallower lesions. This ex vivo study aims to directly compare the lesion dimensions and characteristics of an irrigated ablation catheter with a flexible tip and a non-irrigated solid-tip catheter. Methods: Radiofrequency lesions were induced on porcine myocardial slabs using both open-tip irrigated and non-irrigated standard 4 mm catheters at three power settings (20 W, 30 W, and 40 W), maintaining a fixed contact force of 10 gr. A lesion assessment was conducted including the lesion depth, depth at the maximum diameter, and lesion surface diameters, with the subsequent calculation of the lesion volume and area being undertaken. Results: Irrigated catheters produced lesions with significantly higher superficial widths at all power levels (3.8 vs. 4.4 mm at 20 W; 3.9 mm vs. 4.4 mm at 30 W; 3.8 mm vs. 4.5 mm at 40 W; p = 0.001, p = 0.019, p = 0.003, respectively). Non-irrigated catheters resulted in significantly higher superficial areas at all power levels (23 mm2 vs. 18 mm2 at 20 W; 25 mm2 vs. 19 mm2 at 30 W; 26 mm2 vs. 19 mm2 at 40 W; p = 0.001, p = 0.005, p = 0.001, respectively). Irrigated catheters showed significantly higher values of lesion maximum depth at 40 W (4.6 mm vs. 5.5 mm; p = 0.007), while non-irrigated catheters had a significantly higher calculated volume at 20 W (202 µL vs. 134 µL; p = 0.002). Conclusions: Radiofrequency ablation using an irrigated catheter with a flexible tip has the potential to generate smaller superficial lesion areas compared with those obtained using a non-irrigated catheter.
]]>Biology doi: 10.3390/biology13020131
Authors: Martina Cristodoro Enrica Zambella Ilaria Fietta Annalisa Inversetti Nicoletta Di Simone
Diet has a key role in the reproductive axis both in males and females. This review aims to analyze the impacts of different dietary patterns on fertility. It appears that the Mediterranean diet has a predominantly protective role against infertility, while the Western diet seems to be a risk factor for infertility. Moreover, we focus attention also on dietary patterns in different countries of the World (Middle Eastern diet, Asian diet). In particular, when analyzing single nutrients, a diet rich in saturated fatty acids, cholesterol, animal proteins, and carbohydrates with high glycemic index is highly associated with male and female infertility. Finally, we evaluate the effects of vegetarian, vegan, and ketogenic diets on fertility, which seem to be still unclear. We believe that comprehension of the molecular mechanisms involved in infertility will lead to more effective and targeted treatments for infertile couples.
]]>Biology doi: 10.3390/biology13020130
Authors: Jennifer Sosa Akinsola Oyelakin Satrajit Sinha
Follistatin (FST) is a potent neutralizer of the transforming growth factor-β superfamily and is associated with normal cellular programs and various hallmarks of cancer, such as proliferation, migration, angiogenesis, and immune evasion. The aberrant expression of FST by solid tumors is a well-documented observation, yet how FST influences tumor progression and therapy response remains unclear. The recent surge in omics data has revealed new insights into the molecular foundation underpinning tumor heterogeneity and its microenvironment, offering novel precision medicine-based opportunities to combat cancer. In this review, we discuss these recent FST-centric studies, thereby offering an updated perspective on the protean role of FST isoforms in shaping the complex cellular ecosystem of tumors and in mediating drug resistance.
]]>Biology doi: 10.3390/biology13020129
Authors: Lijuan Li Xuwang Yin Qianruo Wan Dilina Rusitanmu Jie Han
Masu salmon, Oncorhynchus masou (Brevoort 1856), a commercially important fish species endemic to the North Pacific Ocean, attained national second-level protected animal status in China in 2021. Despite this recognition, knowledge about the trophic ecology of this fish remains limited. This study investigated the diet diversity of fluviatile Masu salmon in the Mijiang River, China, utilizing the gastrointestinal tract environmental DNA (GITeDNA) metabarcoding and morphological identification. The results revealed a diverse prey composition, ranging from terrestrial and aquatic invertebrates to small fishes. The fluviatile Masu salmon in general consumed noteworthily more aquatic prey than terrestrial prey. There were much more prey taxa and a higher diet diversity detected by GITeDNA metabarcoding than by morphological identification. GITeDNA metabarcoding showed that larger and older Masu salmon consumed significantly more terrestrial insects than aquatic prey species did, with 7366 verses 5012 sequences in the group of ≥20 cm, 9098 verses 4743 sequences in the group of ≥100 g and 11,540 verses 729 sequences in the group of age 3+. GITeDNA metabarcoding also showed size- and age-related diet diversity, indicating that the dietary niche breadth and trophic diversity of larger and older Masu salmon increased with food resources expanding to more terrestrial prey. Terrestrial invertebrates of riparian habitats play a vital role in the diet of fluviatile Masu salmon, especially larger individuals, highlighting their importance in connecting aquatic and terrestrial food webs. Conservation plans should prioritize the protection and restoration of riparian habitats. This study advocates the combined use of GITeDNA metabarcoding and morphological observation for a comprehensive understanding of fish diet diversity.
]]>Biology doi: 10.3390/biology13020128
Authors: Omar Azab Walid Ben Romdhane Salah El-Hendawy Abdelhalim Ghazy Adel M. Zakri Ahmed M. Abd-ElGawad Abdullah Al-Doss
Water scarcity is a critical cause of plant yield loss and decreased quality. Manipulation of root system architecture to minimize the impact of water scarcity stresses may greatly contribute towards an improved distribution of roots in the soil and enhanced water and nutrient uptake abilities. In this study, we explored the potential of TaMYB20 gene, a wheat gene belonging to the R2R3-MYB transcription factor family, to improve root system architecture in transgenic tobacco plants. The full-length TaMYB20 gene was isolated from Triticum aestivum.cv. Sakha94 and used to produce genetically engineered tobacco plants. The transgenic plants exhibited enhanced tolerance to extended osmotic stress and were able to maintain their root system architecture traits, including total root length (TRL), lateral root number (LRN), root surface area (RSa), and root volume (RV), while the wild-type plants failed to maintain the same traits. The transgenic lines presented greater relative water content in their roots associated with decreased ion leakage. The oxidative stress resulted in the loss of mitochondrial membrane integrity in the wild-type (WT) plants due to the overproduction of reactive oxygen species (ROS) in the root cells, while the transgenic lines were able to scavenge the excess ROS under stressful conditions through the activation of the redox system. Finally, we found that the steady-state levels of three PIN gene transcripts were greater in the TaMYB20-transgenic lines compared to the wild-type tobacco. Taken together, these findings confirm that TaMYB20 is a potentially useful gene candidate for engineering drought tolerance in cultivated plants.
]]>Biology doi: 10.3390/biology13020127
Authors: Nat-Anong Mudtham Authen Promariya Chanchanok Duangsri Cherdsak Maneeruttanarungroj Suchanit Ngamkala Nattaphong Akrimajirachoote Sorawit Powtongsook Tiina A. Salminen Wuttinun Raksajit
Glycogen and poly-3-hydroxybutyrate (PHB) are excellent biopolymer products from cyanobacteria. In this study, we demonstrate that nitrogen metabolism is positively influenced by the exogenous application of trehalose (Tre) in Arthrospira platensis under nitrogen-deprived (−N) conditions. Cells were cultivated photoautotrophically for 5 days under −N conditions, with or without the addition of exogenous Tre. The results revealed that biomass and chlorophyll-a content of A. platensis experienced enhancement with the addition of 0.003 M and 0.03 M Tre in the −N medium after one day, indicating relief from growth inhibition caused by nitrogen deprivation. The highest glycogen content (54.09 ± 1.6% (w/w) DW) was observed in cells grown for 2 days under the −N + 0.003 M Tre condition (p < 0.05), while the highest PHB content (15.2 ± 0.2% (w/w) DW) was observed in cells grown for 3 days under the −N + 0.03 M Tre condition (p < 0.05). The RT-PCR analysis showed a significant increase in glgA and phaC transcript levels, representing approximately 1.2- and 1.3-fold increases, respectively, in A. platensis grown under −N + 0.003 M Tre and −N + 0.03 M Tre conditions. This was accompanied by the induction of enzyme activities, including glycogen synthase and PHA synthase with maximal values of 89.15 and 0.68 µmol min−1 mg−1 protein, respectively. The chemical structure identification of glycogen and PHB from A. platensis was confirmed by FTIR and NMR analysis. This research represents the first study examining the performance of trehalose in promoting glycogen and PHB production in cyanobacteria under nitrogen-deprived conditions.
]]>Biology doi: 10.3390/biology13020126
Authors: Franziska Anna Seigfried Stefan Britsch
Neurodevelopmental disorders (NDDs) comprise a diverse group of diseases, including developmental delay, autism spectrum disorder (ASD), intellectual disability (ID), and attention-deficit/hyperactivity disorder (ADHD). NDDs are caused by aberrant brain development due to genetic and environmental factors. To establish specific and curative therapeutic approaches, it is indispensable to gain precise mechanistic insight into the cellular and molecular pathogenesis of NDDs. Mutations of BCL11A and BCL11B, two closely related, ultra-conserved zinc-finger transcription factors, were recently reported to be associated with NDDs, including developmental delay, ASD, and ID, as well as morphogenic defects such as cerebellar hypoplasia. In mice, Bcl11 transcription factors are well known to orchestrate various cellular processes during brain development, for example, neural progenitor cell proliferation, neuronal migration, and the differentiation as well as integration of neurons into functional circuits. Developmental defects observed in both, mice and humans display striking similarities, suggesting Bcl11 knockout mice provide excellent models for analyzing human disease. This review offers a comprehensive overview of the cellular and molecular functions of Bcl11a and b and links experimental research to the corresponding NDDs observed in humans. Moreover, it outlines trajectories for future translational research that may help to better understand the molecular basis of Bcl11-dependent NDDs as well as to conceive disease-specific therapeutic approaches.
]]>Biology doi: 10.3390/biology13020125
Authors: Gustavo Sganzerla Martinez Mansi Dutt David J. Kelvin Anuj Kumar
Poxviridae is a family of large, complex, enveloped, and double-stranded DNA viruses. The members of this family are ubiquitous and well known to cause contagious diseases in humans and other types of animals as well. Taxonomically, the poxviridae family is classified into two subfamilies, namely Chordopoxvirinae (affecting vertebrates) and Entomopoxvirinae (affecting insects). The members of the Chordopoxvirinae subfamily are further divided into 18 genera based on the genome architecture and evolutionary relationship. Of these 18 genera, four genera, namely Molluscipoxvirus, Orthopoxvirus, Parapoxvirus, and Yatapoxvirus, are known for infecting humans. Some of the popular members of poxviridae are variola virus, vaccine virus, Mpox (formerly known as monkeypox), cowpox, etc. There is still a pressing demand for the development of effective vaccines against poxviruses. Integrated immunoinformatics and artificial-intelligence (AI)-based methods have emerged as important approaches to design multi-epitope vaccines against contagious emerging infectious diseases. Despite significant progress in immunoinformatics and AI-based techniques, limited methods are available to predict the epitopes. In this study, we have proposed a unique method to predict the potential antigens and T-cell epitopes for multiple poxviruses. With PoxiPred, we developed an AI-based tool that was trained and tested with the antigens and epitopes of poxviruses. Our tool was able to locate 3191 antigen proteins from 25 distinct poxviruses. From these antigenic proteins, PoxiPred redundantly located up to five epitopes per protein, resulting in 16,817 potential T-cell epitopes which were mostly (i.e., 92%) predicted as being reactive to CD8+ T-cells. PoxiPred is able to, on a single run, identify antigens and T-cell epitopes for poxviruses with one single input, i.e., the proteome file of any poxvirus.
]]>Biology doi: 10.3390/biology13020124
Authors: Lilian Mayagoitia-Novales Ana Lilia Cerda-Molina María Andrea Martín-Guerrero Emmanuel Muñoz-Zamudio Gema R. Estudillo-Mendoza Javier I. Borráz-León
Environmental enrichment improves captive animal welfare by reducing stress-related behaviors. Previous studies in a captive colony of stumptail macaques (Macaca arctoides) reported a reduction of aggression, coprophilia, and stereotypic behaviors after an occupational enrichment program; however, the effect on stress hormones such as glucocorticoids has not been investigated yet. The goal of this study was to compare the effect of sex, age, and social rank on changes in fecal glucocorticoid metabolites (fGCM) after applying two kinds of enrichments (occupational vs. musical) in a captive colony of stumptail macaques. We collected 234 fecal samples from 25 stumptail macaques under the following conditions: (1) basal (no enrichment), (2) three weeks of occupational enrichment, and (3) three weeks of relaxing/classical music. The Generalized Estimated Equation Model showed an increase in fGCM levels after the occupational enrichment only in adult subjects (p = 0.003 compared to basal). The fGCM levels reached by the adults after the occupational enrichment was higher than that of juveniles (p = 0.002) and subadults (p = 0.02). Occupational and musical enrichment decreased fGCM levels only in middle-ranking individuals (p < 0.001 and p = 0.013, respectively). No sex differences were found. In conclusion, there were age and rank differences in individuals’ physiological reactivity to the effects of environmental enrichment which need to be considered when planning enrichment programs.
]]>Biology doi: 10.3390/biology13020123
Authors: Shuting Wang Qiaoli Chen Feng Wang
Under ion imbalance, water deficiency, and salt stress, the osmotic pressure of the tree sap increases, and pine wood nematodes (Bursaphelenchus xylophilus, PWN) parasitizing in the trees may be subjected to high-osmotic-pressure stress. KCl, L-malic acid, sucrose, and glycerol solutions were used as osmolytes to explore the highest osmotic concentration that PWN can tolerate. Survival analysis showed that when the treatment concentration exceeded 90%, only a few nematodes in the glycerol group survived under 6 h treatment, and most of the survivors were third-stage dispersal juveniles (DJ3). Further examination revealed that under different concentrations of glycerol-induced high osmotic pressure, the survival rate and body length change rate were the highest in the DJ3 and the lowest in the second-stage propagative juveniles. In order to explore the molecular mechanism of resistance of DJ3 to high osmotic stress, transcriptome sequencing was performed at each developmental stage of PWN and differentially expressed genes that were up-regulated or down-regulated only in DJ3 were screened. The expression of genes related to CoA in DJ3, a key enzyme in metabolism, was significantly higher than the other developmental stages. In addition, the expression of the anti-reversal signal pathway-related gene AKT-1 in DJ3 was significantly lower than in the other development stages. Therefore, the specific expression of genes in DJ3 under high osmotic pressure may help them rapidly produce and accumulate energy-related compounds and activate the adenosine 5′-monophosphate (AMP)-activated protein kinase (AMPK) pathway to respond to damage caused by high-osmotic-pressure stress in time, thus promoting survival.
]]>Biology doi: 10.3390/biology13020122
Authors: Jinghua Kong Hao Lyu Qian Ouyang Hao Shi Rui Zhang Shuai Xiao Dong Guo Qi Zhang Xing-Zhen Chen Cefan Zhou Jingfeng Tang
Ferroptosis is a non-apoptotic mode of cell death driven by membrane lipid peroxidation and is characterized by elevated intracellular levels of Fe2+, ROS, and lipid peroxidation. Studies have shown that ferroptosis is related to the development of multiple diseases, such as cancer, neurodegenerative diseases, and acute myeloid leukemia. Ferroptosis plays a dual role in the occurrence and development of these diseases. Ferroptosis mainly involves iron metabolism, ROS, and lipid metabolism. Various mechanisms, including epigenetic regulation, have been reported to be deeply involved in ferroptosis. Abnormal epigenetic modifications have been reported to promote tumor onset or other diseases and resistance to chemotherapy drugs. In recent years, diversified studies have shown that epigenetic modification is involved in ferroptosis. In this review, we reviewed the current resistance system of ferroptosis and the research progress of epigenetic modification, such as DNA methylation, RNA methylation, non-coding RNAs, and histone modification in cancer and other diseases by regulating ferroptosis.
]]>Biology doi: 10.3390/biology13020121
Authors: Corey Reese Leland C. Graber Manuela O. Ramalho Corrie S. Moreau
Wolbachia is a widespread and well-known bacterium that can induce a wide range of changes within its host. Ants specifically harbor a great deal of Wolbachia diversity and are useful systems to study endosymbiosis. The turtle ants (Cephalotes) are a widespread group of tropical ants that rely on gut microbes to support their herbivorous diet for their survival, yet little is known of the extent of this diversity. Therefore, studying their endosymbionts and categorizing the diversity of bacteria within Cephalotes hosts could help to delimit species and identify new strains and can help lead to a further understanding of how the microbiome leads to survival and speciation in the wild. In our study, 116 individual samples were initially tested for positive infection with the wsp gene. Of the initial 116 samples, 9 samples were infected with only one strain of Wolbachia, and 7 were able to be used successfully for multilocus sequence typing (MLST). We used the new MLST data to infer a phylogeny with other Formicidae samples from the MLST online database to identify new Wolbachia strains and related genes, of which only one came back as an exact match. The 18 Wolbachia-positive samples ranged across 15 different species and 7 different countries, which we further test for species identity and geographic correlation. This study is the first comprehensive look into the diversity of Wolbachia in the turtle ants, providing insight into how endosymbionts are oriented in widespread species and providing a strong foundation for further research in host-microbe interactions.
]]>Biology doi: 10.3390/biology13020120
Authors: Minos-Timotheos Matsoukas Vasilis Panagiotopoulos Vlasios Karageorgos George P. Chrousos Maria Venihaki George Liapakis
Corticotropin-releasing factor or hormone (CRF or CRH) and the urocortins regulate a plethora of physiological functions and are involved in many pathophysiological processes. CRF and urocortins belong to the family of CRF peptides (CRF family), which includes sauvagine, urotensin, and many synthetic peptide and non-peptide CRF analogs. Several of the CRF analogs have shown considerable therapeutic potential in the treatment of various diseases. The CRF peptide family act by interacting with two types of plasma membrane proteins, type 1 (CRF1R) and type 2 (CRF2R), which belong to subfamily B1 of the family B G-protein-coupled receptors (GPCRs). This work describes the structure of CRF peptides and their receptors and the activation mechanism of the latter, which is compared with that of other GPCRs. It also discusses recent structural information that rationalizes the selective binding of various ligands to the two CRF receptor types and the activation of receptors by different agonists.
]]>Biology doi: 10.3390/biology13020119
Authors: Kenji K. Kojima
Terminal repeat retrotransposons in miniature (TRIMs) are short non-autonomous long terminal repeat (LTR) retrotransposons found from various eukaryotes. Cassandra is a unique TRIM lineage which contains a 5S rRNA-derived sequence in its LTRs. Here, two new groups of TRIMs, designated Helenus and Ajax, are reported based on bioinformatics analysis and the usage of Repbase. Helenus is found from fungi, animals, and plants, and its LTRs contain a tRNA-like sequence. It includes two LTRs and between them, a primer-binding site (PBS) and polypurine tract (PPT) exist. Fungal and plant Helenus generate 5 bp target site duplications (TSDs) upon integration, while animal Helenus generates 4 bp TSDs. Ajax includes a 5S rRNA-derived sequence in its LTR and is found from two nemertean genomes. Ajax generates 5 bp TSDs upon integration. These results suggest that despite their unique promoters, Helenus and Ajax are TRIMs whose transposition is dependent on autonomous LTR retrotransposon. These TRIMs can originate through an insertion of SINE in an LTR of TRIM. The discovery of Helenus and Ajax suggests the presence of TRIMs with a promoter for RNA polymerase III derived from a small RNA gene, which is here collectively termed TRIMp3.
]]>Biology doi: 10.3390/biology13020118
Authors: Marta González-García Laura Carrillo-Franco Carmen Morales-Luque Marc Stefan Dawid-Milner Manuel Víctor López-González
In humans, speech is a complex process that requires the coordinated involvement of various components of the phonatory system, which are monitored by the central nervous system. The larynx in particular plays a crucial role, as it enables the vocal folds to meet and converts the exhaled air from our lungs into audible sounds. Voice production requires precise and sustained exhalation, which generates an air pressure/flow that creates the pressure in the glottis required for voice production. Voluntary vocal production begins in the laryngeal motor cortex (LMC), a structure found in all mammals, although the specific location in the cortex varies in humans. The LMC interfaces with various structures of the central autonomic network associated with cardiorespiratory regulation to allow the perfect coordination between breathing and vocalization. The main subcortical structure involved in this relationship is the mesencephalic periaqueductal grey matter (PAG). The PAG is the perfect link to the autonomic pontomedullary structures such as the parabrachial complex (PBc), the Kölliker–Fuse nucleus (KF), the nucleus tractus solitarius (NTS), and the nucleus retroambiguus (nRA), which modulate cardiovascular autonomic function activity in the vasomotor centers and respiratory activity at the level of the generators of the laryngeal-respiratory motor patterns that are essential for vocalization. These cores of autonomic structures are not only involved in the generation and modulation of cardiorespiratory responses to various stressors but also help to shape the cardiorespiratory motor patterns that are important for vocal production. Clinical studies show increased activity in the central circuits responsible for vocalization in certain speech disorders, such as spasmodic dysphonia because of laryngeal dystonia.
]]>Biology doi: 10.3390/biology13020117
Authors: Zachary S. Lamas Yanping Chen Jay D. Evans
United States commercial beekeepers prepare honey bee colonies for almond pollination in California each year in late January to early February. This represents the largest managed pollination event in the world and involves more than half of all U.S. honey bee colonies. In winter 2023, numerous colonies in Florida, which were graded as suitable for almonds (larger than ten frames of bees), dwindled suddenly or altogether died within several weeks, just prior to movement for almonds. The timing of these losses and the resulting morbidity caused severe economic harm to affected operations. This study reports interviews with affected stakeholders, their economic harm, and analyses of pathogens and parasites found in their colonies.
]]>Biology doi: 10.3390/biology13020114
Authors: Francesco Nobile Alberto Collareta Vittore Perenzin Eliana Fornaciari Luca Giusberti Giovanni Bianucci
Nowadays, the infraorder Delphinida (oceanic dolphins and kin) represents the most diverse extant clade of Cetacea, with delphinids alone accounting for more than 40% of the total number of living cetacean species. As for other cetacean groups, the Early Miocene represents a key interval for the evolutionary history of Delphinida, as it was during this time span that the delphinidans became broadly distributed worldwide, first and foremost with the widespread genus Kentriodon and closely related forms. Here, we report on a new odontocete find from Burdigalian (20.4–19.0 Ma) deposits of the Friulian-Venetian Basin of northeastern Italy, consisting of the partial cranium of a small delphinidan with associated ear bones (right periotic, stapes, malleus and tympanic bulla). Osteoanatomical considerations and comparisons allow us to assign the studied specimen to the genus Kentriodon. This is the first confirmed record of Kentriodon from Europe as well as from the whole proto-Mediterranean region. Stratigraphic and phylogenetic considerations suggest that our new specimen may represent the geologically oldest member of Kentriodon. The evolutionary success of Kentriodon may correlate with the emergence of narrow-band high-frequency echolocation as a possible strategy to escape acoustic detection by large marine predators such as the squalodontids. In addition, the relatively high encephalization quotient of Kentriodon spp. may have provided these early dolphins with some kind of competitive advantage over the coeval non-delphinidan odontocetes.
]]>Biology doi: 10.3390/biology13020116
Authors: Rosalba Senese Giuseppe Petito Elena Silvestri Maria Ventriglia Nicola Mosca Nicoletta Potenza Aniello Russo Francesco Manfrevola Gilda Cobellis Teresa Chioccarelli Veronica Porreca Vincenza Grazia Mele Rosanna Chianese Pieter de Lange Giulia Ricci Federica Cioffi Antonia Lanni
This study aims to explore the complex role of cannabinoid type 1 receptor (CB1) signaling in the gastrocnemius muscle, assessing physiological processes in both CB1+/+ and CB1−/− mice. The primary focus is to enhance our understanding of how CB1 contributes to mitochondrial homeostasis. At the tissue level, CB1−/− mice exhibit a substantial miRNA-related alteration in muscle fiber composition, characterized by an enrichment of oxidative fibers. CB1 absence induces a significant increase in the oxidative capacity of muscle, supported by elevated in-gel activity of Complex I and Complex IV of the mitochondrial respiratory chain. The increased oxidative capacity is associated with elevated oxidative stress and impaired antioxidant defense systems. Analysis of mitochondrial biogenesis markers indicates an enhanced capacity for new mitochondria production in CB1−/− mice, possibly adapting to altered muscle fiber composition. Changes in mitochondrial dynamics, mitophagy response, and unfolded protein response (UPR) pathways reveal a dynamic interplay in response to CB1 absence. The interconnected mitochondrial network, influenced by increased fusion and mitochondrial UPR components, underlines the dual role of CB1 in regulating both protein quality control and the generation of new mitochondria. These findings deepen our comprehension of the CB1 impact on muscle physiology, oxidative stress, and MQC processes, highlighting cellular adaptability to CB1−/−. This study paves the way for further exploration of intricate signaling cascades and cross-talk between cellular compartments in the context of CB1 and mitochondrial homeostasis.
]]>Biology doi: 10.3390/biology13020115
Authors: Yuto Yasuda Lu Wang Pasquale Chitano Chun Y. Seow
Rho-kinase inhibitors have been identified as a class of potential drugs for treating asthma because of their ability to reduce airway inflammation and active force in airway smooth muscle (ASM). Past research has revealed that, besides the effect on the ASM’s force generation, rho-kinase (ROCK) also regulates actin filament formation and filament network architecture and integrity, thus affecting ASM’s cytoskeletal stiffness. The present review is not a comprehensive examination of the roles played by ROCK in regulating ASM function but is specifically focused on passive tension, which is partially determined by the cytoskeletal stiffness of ASM. Understanding the molecular basis for maintaining active force and passive tension in ASM by ROCK will allow us to determine the suitability of ROCK inhibitors and its downstream enzymes as a class of drugs in treating airway hyperresponsiveness seen in asthma. Because clinical trials using ROCK inhibitors in the treatment of asthma have yet to be conducted, the present review focuses on the in vitro effects of ROCK inhibitors on ASM’s mechanical properties which include active force generation, relaxation, and passive stiffness. The review provides justification for future clinical trials in the treatment of asthma using ROCK inhibitors alone and in combination with other pharmacological and mechanical interventions.
]]>Biology doi: 10.3390/biology13020113
Authors: Simona Mariana Popescu Cristian Tigae Aurelian Dobrițescu Dragoș Mihail Ștefănescu
By integrating species distribution modeling techniques, phylogenetic comparative methods, and climatic data, we analyzed how European falcon climatic niches have changed over evolutionary time in order to understand their tempo and mode of evolution and gain phylogenetic insights related to the ecological context of falcon evolution. For this purpose, we tested the relative contributions of niche conservatism, convergent evolution, and divergent evolution in the evolutionary history of this group of species in Europe. The occupation of climatic niche spaces by falcon species in Europe was not similar, considering that their climatic niche evolution was characterized by heterotachy, especially after ca. 4 Mya. Our results indicate that convergent evolution and niche divergence played an important role in the evolutionary history of these species, with no significant evidence of closely related species retaining their fundamental niche over time (phylogenetic niche conservatism). In most analyses, less closely related falcon species occupied similar climatic environments. We found that speciation in the European genus Falco was influenced by climatic niche differentiation, more prevalent in the last 4 million years, with the main climatic niche shifts occurring between closely related falcon species.
]]>Biology doi: 10.3390/biology13020112
Authors: Wen-Wei Feng Hsiu-Chao Chen Gilbert Audira Michael Edbert Suryanto Ferry Saputra Kevin Adi Kurnia Ross D. Vasquez Franelyne P. Casuga Yu-Heng Lai Chung-Der Hsiao Chih-Hsin Hung
Tacrolimus (FK506) is a common immunosuppressant that is used in organ transplantation. However, despite its importance in medical applications, it is prone to adverse side effects. While some studies have demonstrated its toxicities to humans and various animal models, very few studies have addressed this issue in aquatic organisms, especially zebrafish. Here, we assessed the adverse effects of acute and chronic exposure to tacrolimus in relatively low doses in zebrafish in both larval and adult stages, respectively. Based on the results, although tacrolimus did not cause any cardiotoxicity and respiratory toxicity toward zebrafish larvae, it affected their locomotor activity performance in light–dark locomotion tests. Meanwhile, tacrolimus was also found to slightly affect the behavior performance, shoaling formation, circadian rhythm locomotor activity, and color preference of adult zebrafish in a dose-dependent manner. In addition, alterations in the cognitive performance of the fish were also displayed by the treated fish, indicated by a loss of short-term memory. To help elucidate the toxicity mechanism of tacrolimus, molecular docking was conducted to calculate the strength of the binding interaction between tacrolimus to human FKBP12. The results showed a relatively normal binding affinity, indicating that this interaction might only partly contribute to the observed alterations. Nevertheless, the current research could help clinicians and researchers to further understand the toxicology of tacrolimus, especially to zebrafish, thus highlighting the importance of considering the toxicity of tacrolimus prior to its usage.
]]>Biology doi: 10.3390/biology13020111
Authors: Ricardo Villa-Bellosta
The primary cause of worldwide mortality and morbidity stems from complications in the cardiovascular system resulting from accelerated atherosclerosis and arterial stiffening. Frequently, both pathologies are associated with the pathological calcification of cardiovascular structures, present in areas such as cardiac valves or blood vessels (vascular calcification). The accumulation of hydroxyapatite, the predominant form of calcium phosphate crystals, is a distinctive feature of vascular calcification. This phenomenon is commonly observed as a result of aging and is also linked to various diseases such as diabetes, chronic kidney disease, and several genetic disorders. A substantial body of evidence indicates that vascular calcification involves two primary processes: a passive process and an active process. The physicochemical process of hydroxyapatite formation and deposition (a passive process) is influenced significantly by hyperphosphatemia. However, the active synthesis of calcification inhibitors, including proteins and low-molecular-weight inhibitors such as pyrophosphate, is crucial. Excessive calcification occurs when there is a loss of function in enzymes and transporters responsible for extracellular pyrophosphate metabolism. Current in vivo treatments to prevent calcification involve addressing hyperphosphatemia with phosphate binders and implementing strategies to enhance the availability of pyrophosphate.
]]>Biology doi: 10.3390/biology13020110
Authors: Peter N. Ellsworth Jacob A. Herring Aaron H. Leifer Jason D. Ray Weston S. Elison Peter Daniel Poulson Jacqueline E. Crabtree Pam M. Van Ry Jeffery S. Tessem
A commonality between type 1 and type 2 diabetes is the decline in functional β-cell mass. The transcription factor Nkx6.1 regulates β-cell development and is integral for proper β-cell function. We have previously demonstrated that Nkx6.1 depends on c-Fos mediated upregulation and the nuclear hormone receptors Nr4a1 and Nr4a3 to increase β-cell insulin secretion, survival, and replication. Here, we demonstrate that Nkx6.1 overexpression results in upregulation of the bZip transcription factor CEBPA and that CEBPA expression is independent of c-Fos regulation. In turn, CEBPA overexpression is sufficient to enhance INS-1 832/13 β-cell and primary rat islet proliferation. CEBPA overexpression also increases the survival of β-cells treated with thapsigargin. We demonstrate that increased survival in response to ER stress corresponds with changes in expression of various genes involved in the unfolded protein response, including decreased Ire1a expression. These data show that CEBPA is sufficient to enhance functional β-cell mass by increasing β-cell proliferation and modulating the unfolded protein response.
]]>Biology doi: 10.3390/biology13020109
Authors: Ilaria Cavallo Francesca Sivori Arianna Mastrofrancesco Elva Abril Martina Pontone Enea Gino Di Domenico Fulvia Pimpinelli
Wound repair and skin regeneration is a very complex orchestrated process that is generally composed of four phases: hemostasis, inflammation, proliferation, and remodeling. Each phase involves the activation of different cells and the production of various cytokines, chemokines, and other inflammatory mediators affecting the immune response. The microbial skin composition plays an important role in wound healing. Indeed, skin commensals are essential in the maintenance of the epidermal barrier function, regulation of the host immune response, and protection from invading pathogenic microorganisms. Chronic wounds are common and are considered a major public health problem due to their difficult-to-treat features and their frequent association with challenging chronic infections. These infections can be very tough to manage due to the ability of some bacteria to produce multicellular structures encapsulated into a matrix called biofilms. The bacterial species contained in the biofilm are often different, as is their capability to influence the healing of chronic wounds. Biofilms are, in fact, often tolerant and resistant to antibiotics and antiseptics, leading to the failure of treatment. For these reasons, biofilms impede appropriate treatment and, consequently, prolong the wound healing period. Hence, there is an urgent necessity to deepen the knowledge of the pathophysiology of delayed wound healing and to develop more effective therapeutic approaches able to restore tissue damage. This work covers the wound-healing process and the pathogenesis of chronic wounds infected by biofilm-forming pathogens. An overview of the strategies to counteract biofilm formation or to destroy existing biofilms is also provided.
]]>Biology doi: 10.3390/biology13020108
Authors: Weirong Xing Sheila Pourteymoor Anakha Udayakumar Yian Chen Subburaman Mohan
Mice lacking Claudin11 (Cldn11) manifest reduced trabecular bone mass. However, the impact of Cldn11 expression in osteoblasts in vivo remains understudied. Herein, we generated osteoblast-specific transgenic (Tg) mice expressing Cldn11 and characterized their skeletal phenotype. Micro-CT analyses of the distal metaphysis of the femur showed a 50% and a 38% increase in trabecular bone mass in Tg male and female mice, respectively, due to a significant increase in trabecular number and a reduction in trabecular separation. Histomorphometry and serum biomarker studies uncovered that increased trabecular bone mass in Cldn11 Tg mice was the consequence of enhanced bone formation. Accordingly, an abundance of bone formation (Alp, Bsp), but not bone resorption (Ctsk), markers were augmented in the femurs of Cldn11 Tg mice. Since the trabecular bone density is known to inversely correlate with the amount of marrow adipose tissue (MAT), we measured the MAT in osmium-tetroxide-labeled bones by micro-CT scanning. We found 86% less MAT in the proximal tibia of the Tg males. Consistently, the expression levels of the adipogenic markers, adiponectin and leptin, were 50% lower in the femurs of the Tg males. Our data are consistent with the possibility that claudin11 exerts anabolic effects in osteoblastic lineage cells that act via promoting the differentiation of marrow stem cells towards osteoblasts at the expense of adipocytes.
]]>Biology doi: 10.3390/biology13020107
Authors: Rodrigo Zuloaga Luciano Ahumada-Langer Jorge Eduardo Aedo Alfredo Molina Juan Antonio Valdés
In aquaculture, stress can negatively affect fish growth. For years, the cortisol hormone has been thought to play both glucocorticoid and mineralocorticoid functions. Nevertheless, recent research has suggested that 11-deoxycorticosterone (DOC) released during stress could contribute to cortisol actions, though this process is still misunderstood. Here, we evaluated the DOC effects on physiological and early transcriptional responses by RNA-seq. Juvenile rainbow trout were treated with DOC and/or glucocorticoids (mifepristone) or mineralocorticoid (eplerenone) receptor antagonists. Subsequently, plasma was collected, and cDNA libraries were generated from the gills of vehicle (control), DOC, mifepristone, mifepristone with DOC, eplerenone, and eplerenone with DOC groups. Calcium and phosphate levels in plasma were changed. Results revealed 914 differentially expressed transcripts (DETs) induced by DOC compared with control, mainly associated with sodium ion transmembrane transport, gluconeogenesis, negative regulation of transmembrane transport, and activation of innate immune response. DOC versus eplerenone with DOC comparison displayed 444 DETs related to cell-cell junction organization, canonical glycolysis, positive regulation of immune response, and potassium ion transport. Conversely, no DETs were detected in DOC versus mifepristone with DOC comparison. These data suggest that DOC has a relevant role in gill stress response and ion transport, which is differentially regulated by mineralocorticoid receptors.
]]>Biology doi: 10.3390/biology13020106
Authors: Zhendong Zhang Qi Liu Zhiwen Deng Jun Liu Shuang Li Mei Hong Yucai Peng
mRNA injection-based protein supplementation has emerged as a feasible treatment for Fabry disease. However, whether the introduction of LNP-encapsulated mRNA results in the alteration of metabolomics in an in vivo system remains largely unknown. In the present study, α-galactosidase A (α-Gal A) mRNA was generated and injected into the Fabry disease mouse model. The α-Gal A protein was successfully expressed. The level of globotriaosylsphingosine (Lyso-Gb3), a biomarker for Fabry disease, as well as pro-inflammatory cytokines such as nuclear factor kappa-B (NF-κB), interleukin 6 (IL-6), and tumor necrosis factor-α (TNF-α), were greatly decreased compared to the untreated control, indicating the therapeutic outcome of the mRNA drug. Metabolomics analysis found that the level of 20 metabolites was significantly altered in the plasma of mRNA-injected mice. These compounds are primarily enriched in the arachidonic acid metabolism, alanine, aspartate and glutamate metabolism, and glycolysis/gluconeogenesis pathways. Arachidonic acid and 5-hydroxyeicosatetraenoic acid (5-HETE), both of which are important components in the eicosanoid pathway and related to inflammation response, were significantly increased in the injected mice, possibly due to the presence of lipid nanoparticles. Moreover, mRNA can effectively alter the level of metabolites in the amino acid and energy metabolic pathways that are commonly found to be suppressed in Fabry disease. Taken together, the present study demonstrated that in addition to supplementing the deficient α-Gal A protein, the mRNA-based therapeutic agent can also affect levels of metabolites that may help in the recovery of metabolic homeostasis in the full body system.
]]>Biology doi: 10.3390/biology13020105
Authors: Giuseppe Giannino Valentina Braia Carola Griffith Brookles Federico Giacobbe Fabrizio D’Ascenzo Filippo Angelini Andrea Saglietto Gaetano Maria De Ferrari Veronica Dusi
The cardiac autonomic nervous system (CANS) plays a pivotal role in cardiac homeostasis as well as in cardiac pathology. The first level of cardiac autonomic control, the intrinsic cardiac nervous system (ICNS), is located within the epicardial fat pads and is physically organized in ganglionated plexi (GPs). The ICNS system does not only contain parasympathetic cardiac efferent neurons, as long believed, but also afferent neurons and local circuit neurons. Thanks to its high degree of connectivity, combined with neuronal plasticity and memory capacity, the ICNS allows for a beat-to-beat control of all cardiac functions and responses as well as integration with extracardiac and higher centers for longer-term cardiovascular reflexes. The present review provides a detailed overview of the current knowledge of the bidirectional connection between the ICNS and the most studied cardiac pathologies/conditions (myocardial infarction, heart failure, arrhythmias and heart transplant) and the potential therapeutic implications. Indeed, GP modulation with efferent activity inhibition, differently achieved, has been studied for atrial fibrillation and functional bradyarrhythmias, while GP modulation with efferent activity stimulation has been evaluated for myocardial infarction, heart failure and ventricular arrhythmias. Electrical therapy has the unique potential to allow for both kinds of ICNS modulation while preserving the anatomical integrity of the system.
]]>Biology doi: 10.3390/biology13020104
Authors: Ema Cetkovská Karolína Brandlová Rob Ogden Barbora Černá Bolfíková
The rapid loss of biodiversity and the associated reduction and fragmentation of habitats means that ex situ populations have become an important part of species conservation. These populations, which are often established from a small number of founders, require careful management to avoid the negative effects of genetic drift and inbreeding. Although the inclusion of molecular data is recommended, their availability for captive breeding management remains limited. The aim of this study was to evaluate the relationship between the levels of genetic diversity in six spiral-horned antelope taxa bred under human care and their respective management strategies, conservation status, demography, and geographic origin, using 10 nuclear DNA microsatellite loci and mitochondrial control region DNA sequences. Our findings include associations between genetic diversity and management intensity but also with the diversity and contribution of wild populations to captive founders, with some populations apparently composed of animals from divergent wild lineages elevating captive genetic diversity. When population sizes are large, the potential advantages of maximizing genetic diversity in widely outcrossed populations may need careful consideration with respect to the potential disruption of adaptive diversity. Genetic data serve as a robust tool for managing captive populations, yet their interpretation necessitates a comprehensive understanding of species biology and history.
]]>Biology doi: 10.3390/biology13020103
Authors: Leonardo de Oliveira Siquara da Rocha Everton Freitas de Morais Lilianny Querino Rocha de Oliveira Andressa Vollono Barbosa Daniel W. Lambert Clarissa A. Gurgel Rocha Ricardo D. Coletta
Oral squamous cell carcinoma (OSCC) is the most common and lethal type of head and neck cancer in the world. Variable response and acquisition of resistance to traditional therapies show that it is essential to develop novel strategies that can provide better outcomes for the patient. Understanding of cellular and molecular mechanisms of cell death control has increased rapidly in recent years. Activation of cell death pathways, such as the emerging forms of non-apoptotic programmed cell death, including ferroptosis, pyroptosis, necroptosis, NETosis, parthanatos, mitoptosis and paraptosis, may represent clinically relevant novel therapeutic opportunities. This systematic review summarizes the recently described forms of cell death in OSCC, highlighting their potential for informing diagnosis, prognosis and treatment. Original studies that explored any of the selected cell deaths in OSCC were included. Electronic search, study selection, data collection and risk of bias assessment tools were realized. The literature search was carried out in four databases, and the extracted data from 79 articles were categorized and grouped by type of cell death. Ferroptosis, pyroptosis, and necroptosis represented the main forms of cell death in the selected studies, with links to cancer immunity and inflammatory responses, progression and prognosis of OSCC. Harnessing the potential of these pathways may be useful in patient-specific prognosis and individualized therapy. We provide perspectives on how these different cell death types can be integrated to develop decision tools for diagnosis, prognosis, and treatment of OSCC.
]]>Biology doi: 10.3390/biology13020102
Authors: Angélica Bautista-Cruz Teodulfo Aquino-Bolaños Jessie Hernández-Canseco Evangelina Esmeralda Quiñones-Aguilar
This review provides insights into cellulolytic bacteria present in global forest and agricultural soils over a period of 11 years. It delves into the study of soil-dwelling cellulolytic bacteria and the enzymes they produce, cellulases, which are crucial in both soil formation and the carbon cycle. Forests and agricultural activities are significant contributors to the production of lignocellulosic biomass. Forest ecosystems, which are key carbon sinks, contain 20–30% cellulose in their leaf litter. Concurrently, the agricultural sector generates approximately 998 million tons of lignocellulosic waste annually. Predominant genera include Bacillus, Pseudomonas, Stenotrophomonas, and Streptomyces in forests and Bacillus, Streptomyces, Pseudomonas, and Arthrobacter in agricultural soils. Selection of cellulolytic bacteria is based on their hydrolysis ability, using artificial cellulose media and dyes like Congo red or iodine for detection. Some studies also measure cellulolytic activity in vitro. Notably, bacterial cellulose hydrolysis capability may not align with their cellulolytic enzyme production. Enzymes such as GH1, GH3, GH5, GH6, GH8, GH9, GH10, GH12, GH26, GH44, GH45, GH48, GH51, GH74, GH124, and GH148 are crucial, particularly GH48 for crystalline cellulose degradation. Conversely, bacteria with GH5 and GH9 often fail to degrade crystalline cellulose. Accurate identification of cellulolytic bacteria necessitates comprehensive genomic analysis, supplemented by additional proteomic and transcriptomic techniques. Cellulases, known for degrading cellulose, are also significant in healthcare, food, textiles, bio-washing, bleaching, paper production, ink removal, and biotechnology, emphasizing the importance of discovering novel cellulolytic strains in soil.
]]>Biology doi: 10.3390/biology13020101
Authors: Xiao Liu Yunxiu Zhang Chengming Tang Huawei Li Haiyong Xia Shoujin Fan Lingan Kong
Ammonium (NH4+) toxicity is ubiquitous in plants. To investigate the underlying mechanisms of this toxicity and bicarbonate (HCO3−)-dependent alleviation, wheat plants were hydroponically cultivated in half-strength Hoagland nutrient solution containing 7.5 mM NO3− (CK), 7.5 mM NH4+ (SA), or 7.5 mM NH4+ + 3 mM HCO3− (AC). Transcriptomic analysis revealed that compared to CK, SA treatment at 48 h significantly upregulated the expression of genes encoding fermentation enzymes (pyruvate decarboxylase (PDC), alcohol dehydrogenase (ADH), and lactate dehydrogenase (LDH)) and oxygen consumption enzymes (respiratory burst oxidase homologs, dioxygenases, and alternative oxidases), downregulated the expression of genes encoding oxygen transporters (PIP-type aquaporins, non-symbiotic hemoglobins), and those involved in energy metabolism, including tricarboxylic acid (TCA) cycle enzymes and ATP synthases, but upregulated the glycolytic enzymes in the roots and downregulated the expression of genes involved in the cell cycle and elongation. The physiological assay showed that SA treatment significantly increased PDC, ADH, and LDH activity by 36.69%, 43.66%, and 61.60%, respectively; root ethanol concentration by 62.95%; and lactate efflux by 23.20%, and significantly decreased the concentrations of pyruvate and most TCA cycle intermediates, the complex V activity, ATP content, and ATP/ADP ratio. As a consequence, SA significantly inhibited root growth. AC treatment reversed the changes caused by SA and alleviated the inhibition of root growth. In conclusion, NH4+ treatment alone may cause hypoxic stress in the roots, inhibit energy generation, suppress cell division and elongation, and ultimately inhibit root growth, and adding HCO3− remarkably alleviates the NH4+-induced inhibitory effects on root growth largely by attenuating the hypoxic stress.
]]>Biology doi: 10.3390/biology13020100
Authors: Lei Xia Mijuan Shi Heng Li Wanting Zhang Yingyin Cheng Xiao-Qin Xia
Parentage assignment is a genetic test that utilizes genetic characteristics, such as molecular markers, to identify the parental relationships within populations, which, in commercial fish farming, are almost always large and where full information on potential parents is known. To accurately find the true parents, the genotypes of all loci in the parentage marker set (PMS) are required for each individual being tested. With the same accuracy, a PMS containing a smaller number of markers will undoubtedly save experimental costs. Thus, this study established a scheme to screen low-redundancy PMSs using the exhaustive algorithm and greedy algorithm. When screening PMSs, the greedy algorithm selects markers based on the parental dispersity index (PDI), a uniquely defined metric that outperforms the probability of exclusion (PE). With the conjunctive use of the two algorithms, non-redundant PMSs were found for more than 99.7% of solvable cases in three groups of random sample experiments in this study. Then, a low-redundancy PMS can be composed using two or more of these non-redundant PMSs. This scheme effectively reduces the number of markers in PMSs, thus conserving human and experimental resources and laying the groundwork for the widespread implementation of parentage assignment technology in economic species breeding.
]]>Biology doi: 10.3390/biology13020099
Authors: Xiao Liu Jie Liu
(1) Background: Diagnosis of glioblastoma (GBM), solitary brain metastases (SBM), and primary central nervous system lymphoma (PCNSL) plays a decisive role in the development of personalized treatment plans. Constructing a deep learning classification network to diagnose GBM, SBM, and PCNSL with multi-modal MRI is important and necessary. (2) Subjects: GBM, SBM, and PCNSL were confirmed by histopathology with the multi-modal MRI examination (study from 1225 subjects, average age 53 years, 671 males), 3.0 T T2 fluid-attenuated inversion recovery (T2-Flair), and Contrast-enhanced T1-weighted imaging (CE-T1WI). (3) Methods: This paper introduces MFFC-Net, a classification model based on the fusion of multi-modal MRIs, for the classification of GBM, SBM, and PCNSL. The network architecture consists of parallel encoders using DenseBlocks to extract features from different modalities of MRI images. Subsequently, an L1−norm feature fusion module is applied to enhance the interrelationships among tumor tissues. Then, a spatial-channel self-attention weighting operation is performed after the feature fusion. Finally, the classification results are obtained using the full convolutional layer (FC) and Soft-max. (4) Results: The ACC of MFFC-Net based on feature fusion was 0.920, better than the radiomics model (ACC of 0.829). There was no significant difference in the ACC compared to the expert radiologist (0.920 vs. 0.924, p = 0.774). (5) Conclusions: Our MFFC-Net model could distinguish GBM, SBM, and PCNSL preoperatively based on multi-modal MRI, with a higher performance than the radiomics model and was comparable to radiologists.
]]>Biology doi: 10.3390/biology13020098
Authors: Nathan A. Ruprecht Sonalika Singhal Kalli Schaefer Om Panda Donald Sens Sandeep K. Singhal
Multi-omics studies have emerged as powerful tools for tailoring individualized responses to various conditions, capitalizing on genome sequencing technologies’ increasing affordability and efficiency. This paper delves into the potential of multi-omics in deepening our understanding of biological age, examining the techniques available in light of evolving technology and computational models. The primary objective is to review the relationship between ionizing radiation and biological age, exploring a wide array of functional, physiological, and psychological parameters. This comprehensive review draws upon an extensive range of sources, including peer-reviewed journal articles, government documents, and reputable websites. The literature review spans from fundamental insights into radiation effects to the latest developments in aging research. Ionizing radiation exerts its influence through direct mechanisms, notably single- and double-strand DNA breaks and cross links, along with other critical cellular events. The cumulative impact of DNA damage forms the foundation for the intricate process of natural aging, intersecting with numerous diseases and pivotal biomarkers. Furthermore, there is a resurgence of interest in ionizing radiation research from various organizations and countries, reinvigorating its importance as a key contributor to the study of biological age. Biological age serves as a vital reference point for the monitoring and mitigation of the effects of various stressors, including ionizing radiation. Ionizing radiation emerges as a potent candidate for modeling the separation of biological age from chronological age, offering a promising avenue for tailoring protocols across diverse fields, including the rigorous demands of space exploration.
]]>Biology doi: 10.3390/biology13020097
Authors: Jan Schlauer Andreas Fleischmann Siegfried R. H. Hartmeyer Irmgard Hartmeyer Heiko Rischer
Chemotaxonomy is the link between the state of the art in analytical chemistry and the systematic classification and phylogenetic analysis of biota. Although the characteristic secondary metabolites from diverse biotic sources have been used in pharmacology and biological systematics since the dawn of mankind, only comparatively recently established reproducible methods have allowed the precise identification and distinction of structurally similar compounds. Reliable, rapid screening methods like TLC (Thin Layer Chromatography) can be used to investigate sufficiently large numbers of samples for chemotaxonomic purposes. Using distribution patterns of mutually exclusive naphthoquinones, it is demonstrated in this review how a simple set of chemical data from a representative sample of closely related species in the sundew family (Droseraceae, Nepenthales) provides taxonomically and phylogenetically informative signal within the investigated group and beyond.
]]>Biology doi: 10.3390/biology13020096
Authors: Roukaya Ben Gaied Imed Sbissi Mohamed Tarhouni Clarisse Brígido
Symbiotic nitrogen fixation is a major contributor of N in agricultural ecosystems, but the establishment of legume–rhizobium symbiosis is highly affected by soil salinity. Our interest is focused on the use of non-rhizobial endophytes to assist the symbiosis between chickpea and its microsymbiont under salinity to avoid loss of production and fertility. Our aims were (1) to investigate the impact of salinity on both symbiotic partners; including on early events of the Mesorhizobium-chickpea symbiosis, and (2) to evaluate the potential of four non-rhizobial endophytes isolated from legumes native to arid regions (Phyllobacterium salinisoli, P. ifriqiyense, Xanthomonas translucens, and Cupriavidus respiraculi) to promote chickpea growth and nodulation under salinity. Our results show a significant reduction in chickpea seed germination rate and in the microsymbiont Mesorhizobium ciceri LMS-1 growth under different levels of salinity. The composition of phenolic compounds in chickpea root exudates significantly changed when the plants were subjected to salinity, which in turn affected the nod genes expression in LMS-1. Furthermore, the LMS-1 response to root exudate stimuli was suppressed by the presence of salinity (250 mM NaCl). On the contrary, a significant upregulation of exoY and otsA genes, which are involved in exopolysaccharide and trehalose biosynthesis, respectively, was registered in salt-stressed LMS-1 cells. In addition, chickpea co-inoculation with LMS-1 along with the consortium containing two non-rhizobial bacterial endophytes, P. salinisoli and X. translucens, resulted in significant improvement of the chickpea growth and the symbiotic performance of LMS-1 under salinity. These results indicate that this non-rhizobial endophytic consortium may be an appropriate ecological and safe tool to improve chickpea growth and its adaptation to salt-degraded soils.
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