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Bacterial Endophytes of Spring Wheat Grains and the Potential to Acquire Fe, Cu, and Zn under Their Low Soil Bioavailability -
At the Crossroad of Gene Regulation and Genome Organization: Potential Roles for ATP-Dependent Chromatin Remodelers in the Regulation of CTCF-Mediated 3D Architecture -
MicroRNAs Modulated by Beta Cell Lipid Metabolism: Implications for Type 2 Diabetes
Journal Description
Biology
Biology
is an international, peer-reviewed, open access journal of biological sciences published monthly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
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- Journal Rank: JCR - Q1 (Biology) / CiteScore - Q1 (General Agricultural and Biological Sciences)
- Rapid Publication: manuscripts are peer-reviewed and a first decision provided to authors approximately 15 days after submission; acceptance to publication is undertaken in 3.3 days (median values for papers published in this journal in the first half of 2021).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
- Companion journal: Foundations.
Impact Factor:
5.079 (2020)
Latest Articles
Spatiotemporal Regulation and Functional Analysis of Circular RNAs in Skeletal Muscle and Subcutaneous Fat during Pig Growth
Biology 2021, 10(9), 841; https://doi.org/10.3390/biology10090841 (registering DOI) - 30 Aug 2021
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Recently, thousands of circular RNAs have been reported in different pig breeds. However, researches on the temporal and spatial expression patterns of circRNA over the period of animal growth are limited. Here, we systematically analyzed circRNAs in skeletal muscle and subcutaneous fat in
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Recently, thousands of circular RNAs have been reported in different pig breeds. However, researches on the temporal and spatial expression patterns of circRNA over the period of animal growth are limited. Here, we systematically analyzed circRNAs in skeletal muscle and subcutaneous fat in four growth time points (30 days, 90 days, 150 days and 210 days after birth) of a Chinese native pig breed, Ningxiang pigs. A total of 1171 differentially expressed (DE) circRNAs between muscle and fat were identified, including 562 upregulated and 609 downregulated circRNAs. KEGG pathway enrichment analysis of these DE circRNAs revealed that host genes were mainly involved in glycogen metabolism signaling pathways, muscle development signaling pathways such as ErbB pathway and adipocytokine signaling pathways and AMPK signaling pathways and fatty acid biosynthesis. The circRNAs have striking spatiotemporal specificity in the form of dynamic expression at 90 d. Short Time-Series Expression Miner analysis showed multiple model spectra that are significantly enriched with time changes in muscle and fat. Our findings provide new ideas and perspectives about the role of circular RNAs and their targeting relations with mRNA and miRNA in skeletal muscle and fat tissue during pig growth.
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Open AccessArticle
In Planta Transcriptome and Proteome Profiles of Spongospora subterranea in Resistant and Susceptible Host Environments Illuminates Regulatory Principles Underlying Host–Pathogen Interaction
Biology 2021, 10(9), 840; https://doi.org/10.3390/biology10090840 - 28 Aug 2021
Abstract
Spongospora subterranea is an obligate biotrophic pathogen, causing substantial economic loss to potato industries globally. Currently, there are no fully effective management strategies for the control of potato diseases caused by S. subterranea. To further our understanding of S. subterranea biology during
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Spongospora subterranea is an obligate biotrophic pathogen, causing substantial economic loss to potato industries globally. Currently, there are no fully effective management strategies for the control of potato diseases caused by S. subterranea. To further our understanding of S. subterranea biology during infection, we characterized the transcriptome and proteome of the pathogen during the invasion of roots of a susceptible and a resistant potato cultivar. A total of 7650 transcripts from S. subterranea were identified in the transcriptome analysis in which 1377 transcripts were differentially expressed between two cultivars. In proteome analysis, we identified 117 proteins with 42 proteins significantly changed in comparisons between resistant and susceptible cultivars. The functional annotation of transcriptome data indicated that the gene ontology terms related to the transportation and actin processes were induced in the resistant cultivar. The downregulation of enzyme activity and nucleic acid metabolism in the resistant cultivar suggests a probable influence of these processes in the virulence of S. subterranea. The protein analysis results indicated that the majority of differentially expressed proteins were related to the metabolic processes and transporter activity. The present study provides a comprehensive molecular insight into the multiple layers of gene regulation that contribute to S. subterranea infection and development in planta and illuminates the role of host immunity in affecting pathogen responses.
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(This article belongs to the Section Microbiology)
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Effect of the MPT Pore Inhibitor Alisporivir on the Development of Mitochondrial Dysfunction in the Heart Tissue of Diabetic Mice
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, , , , , , and
Biology 2021, 10(9), 839; https://doi.org/10.3390/biology10090839 - 28 Aug 2021
Abstract
Diabetes mellitus is a systemic metabolic disorder associated with mitochondrial dysfunction, with the mitochondrial permeability transition (MPT) pore opening being considered as one of its possible mechanisms. The effect of alisporivir, a non-immunosuppressive cyclosporin derivative and a selective inhibitor of the MPT pore
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Diabetes mellitus is a systemic metabolic disorder associated with mitochondrial dysfunction, with the mitochondrial permeability transition (MPT) pore opening being considered as one of its possible mechanisms. The effect of alisporivir, a non-immunosuppressive cyclosporin derivative and a selective inhibitor of the MPT pore opening, on the ultrastructure and functions of the heart mitochondria of mice with diabetes mellitus induced by a high-fat diet combined with streptozotocin injections was studied. The treatment of diabetic animals with alisporivir (2.5 mg/kg ip for 20 days) increased the rate of glucose clearance during the glucose tolerance test. The blood glucose level and the indicator of heart rate in alisporivir-treated diabetic mice tended to restore. An electron microscopy analysis showed that alisporivir prevented mitochondrial swelling and ultrastructural alterations in cardiomyocytes of diabetic mice. Alisporivir canceled the diabetes-induced increases in the susceptibility of heart mitochondria to the MPT pore opening and the level of lipid peroxidation products, but it did not affect the decline in mitochondrial oxidative phosphorylation capacity. The mRNA expression levels of Pink1 and Parkin in the heart tissue of alisporivir-treated diabetic mice were elevated, suggesting the stimulation of mitophagy. In parallel, alisporivir decreased the level of mtDNA in the heart tissue. These findings suggest that targeting the MPT pore opening by alisporivir alleviates the development of mitochondrial dysfunction in the diabetic heart. The cardioprotective effect of the drug in diabetes can be mediated by the induction of mitophagy and the inhibition of lipid peroxidation in the organelles.
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(This article belongs to the Special Issue Mitochondria and Stress Responses)
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Personalized Evaluation of Atrial Complexity of Patients Undergoing Atrial Fibrillation Ablation: A Clinical Computational Study
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, , , , , , , and
Biology 2021, 10(9), 838; https://doi.org/10.3390/biology10090838 - 28 Aug 2021
Abstract
Current clinical guidelines establish Pulmonary Vein (PV) isolation as the indicated treatment for Atrial Fibrillation (AF). However, AF can also be triggered or sustained due to atrial drivers located elsewhere in the atria. We designed a new simulation workflow based on personalized computer
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Current clinical guidelines establish Pulmonary Vein (PV) isolation as the indicated treatment for Atrial Fibrillation (AF). However, AF can also be triggered or sustained due to atrial drivers located elsewhere in the atria. We designed a new simulation workflow based on personalized computer simulations to characterize AF complexity of patients undergoing PV ablation, validated with non-invasive electrocardiographic imaging and evaluated at one year after ablation. We included 30 patients using atrial anatomies segmented from MRI and simulated an automata model for the electrical modelling, consisting of three states (resting, excited and refractory). In total, 100 different scenarios were simulated per anatomy varying rotor number and location. The 3 states were calibrated with Koivumaki action potential, entropy maps were obtained from the electrograms and compared with ECGi for each patient to analyze PV isolation outcome. The completion of the workflow indicated that successful AF ablation occurred in patients with rotors mainly located at the PV antrum, while unsuccessful procedures presented greater number of driving sites outside the PV area. The number of rotors attached to the PV was significantly higher in patients with favorable long-term ablation outcome (1-year freedom from AF: 1.61 ± 0.21 vs. AF recurrence: 1.40 ± 0.20; p-value = 0.018). The presented workflow could improve patient stratification for PV ablation by screening the complexity of the atria.
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(This article belongs to the Section Cardiovascular Biology)
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Open AccessCommunication
Absence of Light Exposure Increases Pathogenicity of Pseudomonas aeruginosa Pneumonia-Associated Clinical Isolates
Biology 2021, 10(9), 837; https://doi.org/10.3390/biology10090837 - 27 Aug 2021
Abstract
Pseudomonas aeruginosa can alter its lifestyle in response to changes in environmental conditions. The switch to a pathogenic host-associated lifestyle can be triggered by the luminosity settings, resorting to at least one photoreceptor which senses light and regulates cellular processes. This study aimed
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Pseudomonas aeruginosa can alter its lifestyle in response to changes in environmental conditions. The switch to a pathogenic host-associated lifestyle can be triggered by the luminosity settings, resorting to at least one photoreceptor which senses light and regulates cellular processes. This study aimed to address how light exposure affects the dynamic and adaptability of two P. aeruginosa pneumonia-associated isolates, HB13 and HB15. A phenotypic characterization of two opposing growth conditions, constant illumination and intensity of full-spectrum light and total absence of light, was performed. Given the nature of P. aeruginosa pathogenicity, distinct fractions were characterized, and its inherent pathogenic potential screened by comparing induced morphological alterations and cytotoxicity against human pulmonary epithelial cells (A549 cell line). Growth in the dark promoted some virulence-associated traits (e.g., pigment production, LasA proteolytic activity), which, together with higher cytotoxicity of secreted fractions, supported an increased pathogenic potential in conditions that better mimic the lung microenvironment of P. aeruginosa. These preliminary findings evidenced that light exposure settings may influence the P. aeruginosa pathogenic potential, likely owing to differential production of virulence factors. Thus, this study raised awareness towards the importance in controlling light conditions during bacterial pathogenicity evaluation approaches, to more accurately interpret bacterial responses.
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(This article belongs to the Special Issue New Aspects of Light in Biology and Medicine)
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Open AccessReview
GARP: A Key Target to Evaluate Tumor Immunosuppressive Microenvironment
Biology 2021, 10(9), 836; https://doi.org/10.3390/biology10090836 - 27 Aug 2021
Abstract
Glycoprotein-A repetitions predominant (GARP) is the docking receptor for latent transforming growth factor (LTGF-β) and promotes its activation. In cancer, increased GARP expression has been found in many types of cancer. GARP is expressed by regulatory T cells and platelets in the tumor
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Glycoprotein-A repetitions predominant (GARP) is the docking receptor for latent transforming growth factor (LTGF-β) and promotes its activation. In cancer, increased GARP expression has been found in many types of cancer. GARP is expressed by regulatory T cells and platelets in the tumor microenvironment (TME) and can be also expressed by tumor cells themselves. Thus, GARP can be widely present in tumors in which it plays a major role in the production of active TGF-β, contributing to immune evasion and cancer progression via the GARP-TGF-β pathway. The objective of this review is to highlight GARP expression and function in cancer and to evaluate the potential of membrane GARP as a predictive and therapeutic follow-up biomarker that could be assessed, in real time, by molecular imaging. Moreover, as GARP can be secreted, a focus will also be made on soluble GARP as a circulating biomarker.
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(This article belongs to the Special Issue Role of the Immune System in Cancer)
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Liver Organoids: Updates on Disease Modeling and Biomedical Applications
Biology 2021, 10(9), 835; https://doi.org/10.3390/biology10090835 - 27 Aug 2021
Abstract
Liver organoids are stem cell-derived 3D structures that are generated by liver differentiation signals in the presence of a supporting extracellular matrix. Liver organoids overcome low complexity grade of bidimensional culture and high costs of in vivo models thus representing a turning point
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Liver organoids are stem cell-derived 3D structures that are generated by liver differentiation signals in the presence of a supporting extracellular matrix. Liver organoids overcome low complexity grade of bidimensional culture and high costs of in vivo models thus representing a turning point for studying liver disease modeling. Liver organoids can be established from different sources as induced pluripotent stem cells (iPSCs), embryonic stem cells (ESCs), hepatoblasts and tissue-derived cells. This novel in vitro system represents an innovative tool to deeper understand the physiology and pathological mechanisms affecting the liver. In this review, we discuss the current advances in the field focusing on their application in modeling diseases, regenerative medicine and drug discovery.
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(This article belongs to the Special Issue Pluripotent Stem Cells, Cell Reprogramming and Tissue Modelling)
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Open AccessSystematic Review
Intrinsic Subtypes and Androgen Receptor Gene Expression in Primary Breast Cancer. A Meta-Analysis
Biology 2021, 10(9), 834; https://doi.org/10.3390/biology10090834 - 27 Aug 2021
Abstract
The androgen receptor (AR) is frequently expressed in breast cancer (BC), but its association with clinical and biological parameters of BC patients remains unclear. Here, we investigated the association of AR gene expression according to intrinsic BC subtypes by meta-analysis of large-scale microarray
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The androgen receptor (AR) is frequently expressed in breast cancer (BC), but its association with clinical and biological parameters of BC patients remains unclear. Here, we investigated the association of AR gene expression according to intrinsic BC subtypes by meta-analysis of large-scale microarray transcriptomic datasets. Sixty-two datasets including 10315 BC patients were used in the meta-analyses. Interestingly, AR mRNA level is significantly increased in patients categorized with less aggressive intrinsic molecular subtypes including, Luminal A compared to Basal-like (standardized mean difference, SMD: 2.12; 95% confidence interval, CI: 1.88 to 2.35; p < 0.001) or when comparing Luminal B to Basal-like (SMD: 1.53; CI: 1.33 to 1.72; p < 0.001). The same trend was observed when analyses were performed using immunohistochemistry-based surrogate subtypes. Consistently, the AR mRNA expression was higher in patients with low histological grade (p < 0.001). Furthermore, our data revealed higher levels of AR mRNA in BC patients expressing either estrogen or progesterone receptors (p < 0.001). Together, our findings indicate that high mRNA levels of AR are associated with BC subgroups with the less aggressive clinical features.
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(This article belongs to the Section Cancer Biology)
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Neurotherapeutic Potential of Cervus elaphus Sibericus on Axon Regeneration and Growth Cone Reformation after H2O2-Induced Injury in Rat Primary Cortical Neurons
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Biology 2021, 10(9), 833; https://doi.org/10.3390/biology10090833 - 26 Aug 2021
Abstract
Cervus elaphus sibericus (CES), commonly known as deer antler, has been used as a medicinal herb because of its various pharmacological activities, including its anti-infective, anti-arthritic, anti-allergic, and anti-oxidative properties. However, the precise mechanisms by which CES functions as a potent anti-oxidative agent
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Cervus elaphus sibericus (CES), commonly known as deer antler, has been used as a medicinal herb because of its various pharmacological activities, including its anti-infective, anti-arthritic, anti-allergic, and anti-oxidative properties. However, the precise mechanisms by which CES functions as a potent anti-oxidative agent remain unknown; particularly, the effects of CES on cortical neurons and its neurobiological mechanism have not been examined. We used primary cortical neurons from the embryonic rat cerebral cortex and hydrogen peroxide to induce oxidative stress and damage in neurons. After post-treatment of CES at three concentrations (10, 50, and 200 µg/mL), the influence of CES on the neurobiological mechanism was assessed by immunocytochemistry, flow cytometry, and real-time PCR. CES effectively prevented neuronal death caused by hydrogen peroxide-induced damage by regulating oxidative signaling. In addition, CES significantly induced the expression of brain-derived neurotrophic factor and neurotrophin nerve growth factor, as well as regeneration-associated genes. We also observed newly processing elongated axons after CES treatment under oxidative conditions. In addition, filopodia tips generally do not form a retraction bulb, called swollen endings. Thus, CES shows therapeutic potential for treating neurological diseases by stimulating neuron repair and regeneration.
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(This article belongs to the Special Issue Mechanisms in Neuronal Injury and Regeneration)
Open AccessArticle
The Regulatory Mechanism of Feeding a Diet High in Rice Grain on the Growth and microRNA Expression Profiles of the Spleen, Taking Goats as an Artiodactyl Model
Biology 2021, 10(9), 832; https://doi.org/10.3390/biology10090832 - 26 Aug 2021
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Several researchers have testified that feeding with diets high in rice grain induces subacute ruminal acidosis and increases the risk of gastrointestinal inflammation. However, whether diets high in rice grain affect spleen growth and related molecular events remains unknown. Therefore, the present study
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Several researchers have testified that feeding with diets high in rice grain induces subacute ruminal acidosis and increases the risk of gastrointestinal inflammation. However, whether diets high in rice grain affect spleen growth and related molecular events remains unknown. Therefore, the present study was conducted to investigate the effects of feeding a high-concentrate (HC) diet based on rice on the growth and microRNA expression profiles in goat spleen. Sixteen Liuyang black goats were used as an artiodactyl model and fed an HC diet for five weeks. Visceral organ weight, LPS (lipopolysaccharide) concentration in the liver and spleen, and microRNA expression were analyzed. The results showed that feeding an HC diet increased the heart and spleen indexes and decreased the liver LPS concentration (p < 0.05). In total, 596 microRNAs were identified, and twenty-one of them were differentially expressed in the spleens of goats fed with the HC diet. Specifically, several microRNAs (miR-107, miR-512, miR-51b, miR-191, miR-296, miR-326, miR-6123 and miR-433) were upregulated. Meanwhile, miR-30b, miR-30d, miR-1468, miR-502a, miR-145, miR-139, miR-2284f, miR-101 and miR-92a were downregulated. Additionally, their target gene CPPED1, CDK6, CCNT1 and CASP7 expressions were inhibited (p < 0.05). These results indicated that the HC diet promoted the growth of the heart and spleen. The HC diet also regulated the expression of miR-326, miR-512-3p, miR-30b, miR-30d, miR-502a and their target genes (CPPED1, CDK6 and CCNT1) related to the enhancement of splenocyte proliferation. The HC diet also modulated the expression of miR-15b-5p, miR-1468 and miR-92a, related to the suppression of splenocyte apoptosis.
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Open AccessArticle
Mechanical Behavior of Blood Vessels: Elastic and Viscoelastic Contributions
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Biology 2021, 10(9), 831; https://doi.org/10.3390/biology10090831 - 26 Aug 2021
Abstract
The mechanical properties of the cerebral bridging veins (CBVs) were studied using advanced microtensile equipment. Detailed high-quality curves were obtained at different strain rates, showing a clearly nonlinear stress–strain response. In addition, the tissue of the CBVs exhibits stress relaxation and a preconditioning
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The mechanical properties of the cerebral bridging veins (CBVs) were studied using advanced microtensile equipment. Detailed high-quality curves were obtained at different strain rates, showing a clearly nonlinear stress–strain response. In addition, the tissue of the CBVs exhibits stress relaxation and a preconditioning effect under cyclic loading, unequivocal indications of viscoelastic behavior. Interestingly, most previous literature that conducts uniaxial tensile tests had not found significant viscoelastic effects in CBVs, but the use of more sensitive tests allowed to observe the viscoelastic effects. For that reason, a careful mathematical analysis is presented, clarifying why in uniaxial tests with moderate strain rates, it is difficult to observe any viscoelastic effect. The analysis provides a theoretical explanation as to why many recent studies that investigated mechanical properties did not find a significant viscoelastic effect, even though in other circumstances, the CBV tissue would clearly exhibit viscoelastic behavior. Finally, this study provides reference values for the usual mechanical properties, as well as calculations of constitutive parameters for nonlinear elastic and viscoelastic models that would allow more accurate numerical simulation of CBVs in Finite Element-based computational models in future works.
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(This article belongs to the Special Issue Mechanobiology)
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Comprehensive CircRNA Profiling and Selection of Key CircRNAs Reveal the Potential Regulatory Roles of CircRNAs throughout Ovarian Development and Maturation in Cynoglossus semilaevis
Biology 2021, 10(9), 830; https://doi.org/10.3390/biology10090830 - 26 Aug 2021
Abstract
CircRNAs are novel endogenous non-coding small RNAs involved in the regulation of multiple biological processes. However, little is known regarding circRNAs in ovarian development and maturation of fish. Our study, for the first time, provides the genome-wide overview of the types and relative
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CircRNAs are novel endogenous non-coding small RNAs involved in the regulation of multiple biological processes. However, little is known regarding circRNAs in ovarian development and maturation of fish. Our study, for the first time, provides the genome-wide overview of the types and relative abundances of circRNAs in tongue sole tissues during three ovarian developmental stages. We detected 6790 circRNAs in the brain, 5712 in the pituitary gland, 4937 in the ovary and 4160 in the liver. Some circRNAs exhibit tissue-specific expression, and qRT-PCR largely confirmed 6 differentially expressed (DE) circRNAs. Gene Ontology and KEGG pathway analyses of DE mRNAs were performed. Some DE circRNA parental genes were closely associated with biological processes in key signalling pathways and may play essential roles in ovarian development and maturation. We found that the selected circRNAs were involved in 10 pathways. RNase R digestion experiment and Sanger sequencing verified that the circRNA had a ring structure and was RNase R resistant. qRT-PCR results largely confirmed differential circRNA expression patterns from the RNA-seq data. These findings indicate that circRNAs are widespread in terms of present in production-related tissues of tongue sole with potentially important regulatory roles in ovarian development and maturation.
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(This article belongs to the Special Issue The Application of Genetic and Genomic Biotechnology in Aquaculture)
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Open AccessReview
Type I Interferons in COVID-19 Pathogenesis
Biology 2021, 10(9), 829; https://doi.org/10.3390/biology10090829 - 26 Aug 2021
Abstract
Among the many activities attributed to the type I interferon (IFN) multigene family, their roles as mediators of the antiviral immune response have emerged as important components of the host response to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. Viruses likewise have
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Among the many activities attributed to the type I interferon (IFN) multigene family, their roles as mediators of the antiviral immune response have emerged as important components of the host response to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. Viruses likewise have evolved multiple immune evasion strategies to circumvent the host immune response and promote virus propagation and dissemination. Therefore, a thorough characterization of host–virus interactions is essential to understand SARS-CoV-2 pathogenesis. Here, we summarize the virus-mediated evasion of the IFN responses and the viral functions involved, the genetic basis of IFN production in SARS-CoV-2 infection and the progress of clinical trials designed to utilize type I IFN as a potential therapeutic tool.
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(This article belongs to the Special Issue Type I Interferons: A Double-Edged Sword of Immune Regulation and Cancer Progression)
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Open AccessArticle
Key Roles of De-Domestication and Novel Mutation in Origin and Diversification of Global Weedy Rice
Biology 2021, 10(9), 828; https://doi.org/10.3390/biology10090828 - 26 Aug 2021
Abstract
Agricultural weeds pose great challenges to sustainable crop production, owing to their complex origins and abundant genetic diversity. Weedy rice (WD) infests rice fields worldwide causing tremendous losses of rice yield/quality. To explore WD origins and evolution, we analyzed DNA sequence polymorphisms of
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Agricultural weeds pose great challenges to sustainable crop production, owing to their complex origins and abundant genetic diversity. Weedy rice (WD) infests rice fields worldwide causing tremendous losses of rice yield/quality. To explore WD origins and evolution, we analyzed DNA sequence polymorphisms of the seed shattering genes (sh4 and qsh1) in weedy, wild, and cultivated rice from a worldwide distribution. We also used microsatellite and insertion/deletion molecular fingerprinting to determine their genetic relationship and structure. Results indicate multiple origins of WD with most samples having evolved from their cultivated progenitors and a few samples from wild rice. WD that evolved from de-domestication showed distinct genetic structures associated with indica and japonica rice differentiation. In addition, the weed-unique haplotypes that were only identified in the WD samples suggest their novel mutations. Findings in this study demonstrate the key role of de-domestication in WD origins, in which indica and japonica cultivars stimulated further evolution and divergence of WD in various agroecosystems. Furthermore, novel mutations promote continued evolution and genetic diversity of WD adapting to different environments. Knowledge generated from this study provides deep insights into the origin and evolution of conspecific weeds, in addition to the design of effective measures to control these weeds.
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(This article belongs to the Section Plant Science)
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Open AccessArticle
Plant Resources Utilization among Different Ethnic Groups of Ladakh in Trans-Himalayan Region
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Biology 2021, 10(9), 827; https://doi.org/10.3390/biology10090827 - 26 Aug 2021
Abstract
The nomadic pastoral indigenous communities of the Ladakhi people share roots with Tibetan culture in terms of food, clothing, religion, festivals, and habits, and rely widely on plant resources for survival and livelihood. This survey was conducted during 2019–2021 to document the indigenous
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The nomadic pastoral indigenous communities of the Ladakhi people share roots with Tibetan culture in terms of food, clothing, religion, festivals, and habits, and rely widely on plant resources for survival and livelihood. This survey was conducted during 2019–2021 to document the indigenous knowledge about plant resources of the Balti, Beda, and Brokpa communities of the Ladakh region, trans-Himalayas. Open- and close-ended semi-structured interviews (N = 184) and group discussions (N = 17) were used to collect the data. Quantitative data was further analyzed using various statistical tools. A total of 105 plant species belonging to 82 genera and 39 families were used as medicine, fuel wood, fragrance, oil, food, flavor, fodder, decoration, and dye. Among these, medicinal use was most prevalent, with 70% of use reports, followed by fodder and fuel wood. Leaves (27%) were the most preferred plant part used, followed by roots and flowers. The principal component analysis revealed five clusters of ethnobotanical usage, i.e., food, medicine, fuel wood, fodder, and fragrance, oil, dye, and flavor. The maximum number of plant species used was reported by the Brokpa, while the Beda reported the minimum number of plant species uses. Delphinium brunonianum, Waldheimia tomentosa, and Juniperus indica played a significant role in the cultural and religious ritual aspects, whereas Allium przewalskianum, Waldheimia tomentosa, Juniperus indica, and Hippophae rhamnoides were commonly used as a livelihood source among Ladakhi communities. The local people collected most plants (65%) for self-consumption, while the rest (35%) were sold in markets as a source of income. The sustainable utilization and management of plant resources by local people is a strategy to boost livelihoods and food security and alleviate poverty.
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(This article belongs to the Special Issue Linking Biodiversity and Cultural Diversity: New Approaches for Fostering the Sustainable Use of Natural Resources)
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Open AccessArticle
Insights into Alexandrium minutum Nutrient Acquisition, Metabolism and Saxitoxin Biosynthesis through Comprehensive Transcriptome Survey
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Biology 2021, 10(9), 826; https://doi.org/10.3390/biology10090826 - 25 Aug 2021
Abstract
The toxin-producing dinoflagellate Alexandrium minutum is responsible for the outbreaks of harmful algae bloom (HABs). It is a widely distributed species and is responsible for producing paralytic shellfish poisoning toxins. However, the information associated with the environmental adaptation pathway and toxin biosynthesis in
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The toxin-producing dinoflagellate Alexandrium minutum is responsible for the outbreaks of harmful algae bloom (HABs). It is a widely distributed species and is responsible for producing paralytic shellfish poisoning toxins. However, the information associated with the environmental adaptation pathway and toxin biosynthesis in this species is still lacking. Therefore, this study focuses on the functional characterization of A. minutum unigenes obtained from transcriptome sequencing using the Illumina Hiseq 4000 sequencing platform. A total of 58,802 (47.05%) unigenes were successfully annotated using public databases such as NCBI-Nr, UniprotKB, EggNOG, KEGG, InterPRO and Gene Ontology (GO). This study has successfully identified key features that enable A. minutum to adapt to the marine environment, including several carbon metabolic pathways, assimilation of various sources of nitrogen and phosphorus. A. minutum was found to encode homologues for several proteins involved in saxitoxin biosynthesis, including the first three proteins in the pathway of saxitoxin biosynthesis, namely sxtA, sxtG and sxtB. The comprehensive transcriptome analysis presented in this study represents a valuable resource for understanding the dinoflagellates molecular metabolic model regarding nutrient acquisition and biosynthesis of saxitoxin.
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(This article belongs to the Section Marine Biology)
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The Evolution of Trait Disparity during the Radiation of the Plant Genus Macrocarpaea (Gentianaceae) in the Tropical Andes
Biology 2021, 10(9), 825; https://doi.org/10.3390/biology10090825 - 25 Aug 2021
Abstract
The evolutionary processes responsible for the extraordinary diversity in the middle elevation montane forests of the Tropical Andes (MMF; 1000–3500 m) remain poorly understood. It is not clear whether adaptive divergence, niche conservatism or geographical processes were the main contributors to the radiation
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The evolutionary processes responsible for the extraordinary diversity in the middle elevation montane forests of the Tropical Andes (MMF; 1000–3500 m) remain poorly understood. It is not clear whether adaptive divergence, niche conservatism or geographical processes were the main contributors to the radiation of the respective lineages occurring there. We investigated the evolutionary history of plant lineages in the MMF. We used the vascular plant genus Macrocarpaea (Gentianaceae) as a model, as it consists of 118 morphologically diverse species, a majority of which are endemic to the MMF. We used a time-calibrated molecular phylogeny and morphological and climatic data to compare a set of evolutionary scenarios of various levels of complexity in a phylogenetic comparative framework. In this paper, we show that the hypothesis of adaptive radiation for Macrocarpaea in the MMF is unlikely. The genus remained confined to the upper montane forests (UMF > 1800 m) during more than a half of its evolutionary history, possibly due to evolutionary constraints. Later, coinciding with the beginning of the Pleistocene (around 2.58 Ma), a phylogenetically derived (recently branching) clade, here referred to as the M. micrantha clade (25 species), successfully colonized and radiated in the lower montane forests (LMF < 1800 m). This colonization was accompanied by the evolution of a new leaf phenotype that is unique to the species of the M. micrantha clade that likely represents an adaptation to life in this new environment (adaptive zone). Therefore, our results suggest that niche conservatism and geographical processes have dominated most of the diversification history of Macrocarpaea, but that a rare adaptive divergence event allowed a transition into a new adaptive zone and enabled progressive radiation in this zone through geographical processes.
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(This article belongs to the Special Issue Biological Novelty as Source of Biodiversity in Mountains)
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The Measurement of the Neutron Yield of the 7Li(p,n)7Be Reaction in Lithium Targets
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Biology 2021, 10(9), 824; https://doi.org/10.3390/biology10090824 - 24 Aug 2021
Abstract
A compact accelerator-based neutron source has been proposed and created at the Budker Institute of Nuclear Physics in Novosibirsk, Russia. An original design tandem accelerator is used to provide a proton beam. The neutron flux is generated as a result of the 7
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A compact accelerator-based neutron source has been proposed and created at the Budker Institute of Nuclear Physics in Novosibirsk, Russia. An original design tandem accelerator is used to provide a proton beam. The neutron flux is generated as a result of the 7Li(p,n)7Be threshold reaction using the solid lithium target. A beam shaping assembly is applied to convert this flux into a beam of epithermal neutrons with characteristics suitable for BNCT. The BNCT technique is being tested in in vitro and in vivo studies, and dosimetry methods are being developed. Currently, the BNCT technique has entered into clinical practice in the world: after successful clinical trials, two clinics in Japan began treating patients, and four more BNCT clinics are ready to start operating. The neutron source proposed at the Budker Institute of Nuclear Physics served as a prototype for a facility created for a clinic in Xiamen (China). It is planned to equip the National Medical Research Center of Oncology (Moscow, Russia) and National Oncological Hadron Therapy Center (Pavia, Italy) with the same neutron sources. Due to the impending use of an accelerator neutron source for treating patients, the validation of the neutron yield of the 7Li(p,n)7Be reaction in lithium metal targets is required. The theoretical neutron yield has not been evaluated experimentally so far.
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(This article belongs to the Special Issue Boron Neutron Capture Therapy: From Nuclear Physics to Biomedicine)
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Open AccessArticle
Assessment and Prognosis in CSA-AKI Using Novel Kidney Injury Biomarkers: A Prospective Observational Study
by
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Biology 2021, 10(9), 823; https://doi.org/10.3390/biology10090823 - 24 Aug 2021
Abstract
Background: There is a need for early diagnostic solutions for cardiac surgery associated acute kidney injury (CSA-AKI) as serum creatinine changes do not occur dynamically enough. Moreover, new approaches are needed for kidney protective strategy in patients undergoing cardiac surgery procedures; Methods: Samples
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Background: There is a need for early diagnostic solutions for cardiac surgery associated acute kidney injury (CSA-AKI) as serum creatinine changes do not occur dynamically enough. Moreover, new approaches are needed for kidney protective strategy in patients undergoing cardiac surgery procedures; Methods: Samples of serum and urine were taken from the selected group of patients undergoing elective cardiac surgery procedures. The aim of this study was to assess the utility of specific inflammation and kidney injury biomarkers in the early diagnostic of CSA-AKI and in the prognosis of long-term postoperative kidney function; Results: At 6 h after weaning from cardiopulmonary bypass, there were significant differences in IL-6, IL-8, TNF-α, MMP-9 and NGAL concentrations in patients with CSA-AKI, compared to the control group. Serum IL-8 and urine NGAL 6 h after weaning from CPB proved to be independent acute kidney injury predictors. The TNF-α, MMP-9, IL-18, TIMP-1 and MMP-9/TIMP-1 ratio in the early postoperative period correlated with long-term kidney function impairment; Conclusions: Novel kidney injury biomarkers are an eligible tool for early diagnosis of CSA-AKI. They are also reliable indicators of long-term postoperative kidney function impairment risk after cardiac surgery procedures.
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(This article belongs to the Section Cardiovascular Biology)
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Open AccessArticle
Profile of Bacterial Infections in COVID-19 Patients: Antimicrobial Resistance in the Time of SARS-CoV-2
Biology 2021, 10(9), 822; https://doi.org/10.3390/biology10090822 - 24 Aug 2021
Abstract
The global onset of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infections happened suddenly, hence imposing a rapid definition of effective therapeutic approaches. Antibiotics were included among the prophylactic agents because of both the similarity between SARS-CoV-2 and atypical pneumonia symptoms, and
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The global onset of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infections happened suddenly, hence imposing a rapid definition of effective therapeutic approaches. Antibiotics were included among the prophylactic agents because of both the similarity between SARS-CoV-2 and atypical pneumonia symptoms, and the immune-modulating and anti-inflammatory properties of such drugs. Although, this approach could exacerbate the emergence of antimicrobial resistance. To evaluate the impact of the COVID-19 pandemic on the spread and characteristics of bacterial infections, as well as on the frequency of antimicrobial resistance, we investigated and compared clinical bacterial strains isolated in an Italian hospital from COVID-19 patients and non-COVID-19 patients during and before the COVID-19 outbreak. Data clearly indicate the impact of the COVID-19 pandemic on bacterial infections: not only some bacterial species were found in either COVID-19 positive or in COVID-19 negative patients, but isolates from COVID-19 patients also showed higher levels of antimicrobial resistance. Nevertheless, despite some bacterial species were isolated only before or over the pandemic, no differences were observed among the antimicrobial resistance levels. Overall, these results recapitulate the current situation of microbial infections and could also provide an overview of the impact of COVID-19 on bacterial pathogens spread and resistance.
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(This article belongs to the Special Issue Microbial Diversity and Microbial Resistance)
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