Biology

21 pages, 13044 KiB

Open AccessEditor’s ChoiceArticle

Travelling in Microphis (Teleostei: Syngnathidae) Otoliths with Two-Dimensional X-ray Fluorescence Maps: Twists and Turns on the Road to Strontium Incorporation

by Clara Lord, Vincent Haÿ, Kadda Medjoubi, Sophie Berland and Philippe Keith

Biology 2024, 13(6), 446; https://doi.org/10.3390/biology13060446 - 18 Jun 2024

Cited by 3 | Viewed by 1046

Abstract

Indo-Pacific tropical island streams are home to freshwater pipefish (Microphis spp., Syngnathidae). Otoliths were used to uncover life history traits in four species, including a New Caledonian endemic. All four species present the same methodological challenge: their otoliths are small, fragile and [...] Read more.

Indo-Pacific tropical island streams are home to freshwater pipefish (Microphis spp., Syngnathidae). Otoliths were used to uncover life history traits in four species, including a New Caledonian endemic. All four species present the same methodological challenge: their otoliths are small, fragile and mute for growth marks using basic observation tools. Strontium (Sr) is calcium substituent in the mineral lattice, driven by salinity conditions, and thus useful to study diadromous migrations. Synchrotron-based scanning X-ray fluorescence 2D high-resolution mapping allowed us to tackle the global and hyperfine strontium (Sr) distribution. We developed analytical imaging processes to retrieve biological information from otoliths from the data generated via synchrotron analysis. We uncovered plasticity in the life cycle: all species were amphidromous, apart from some freshwater residents from New Caledonia. Understanding life cycle modalities is crucial to categorize species distribution limits and to implement adapted conservation measures, especially when endemic species are at stake. 2D fine-scale images outlined the heterogeneity of Sr distribution: in addition to the trivial Sr incorporation driven by environmental ionic conditions, there is an unusual mosaic arrangement of Sr distribution and we hypothesize that biological control, especially growth during the early life stages, may sometimes overrule stoichiometry. This shows that it is worth studying otolith formation and element integration at imbricated scales, and our methods and results provide a strong basis for future works and prospects in otolith science. Full article

(This article belongs to the Section Zoology)

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19 pages, 1420 KiB

Open AccessEditor’s ChoiceReview

Mechanobiology of Adipocytes

by Sean P. Blade, Dylan J. Falkowski, Sarah N. Bachand, Steven J. Pagano and LiKang Chin

Biology 2024, 13(6), 434; https://doi.org/10.3390/biology13060434 - 13 Jun 2024

Viewed by 2238

Abstract

The growing obesity epidemic necessitates increased research on adipocyte and adipose tissue function and disease mechanisms that progress obesity. Historically, adipocytes were viewed simply as storage for excess energy. However, recent studies have demonstrated that adipocytes play a critical role in whole-body homeostasis, [...] Read more.

The growing obesity epidemic necessitates increased research on adipocyte and adipose tissue function and disease mechanisms that progress obesity. Historically, adipocytes were viewed simply as storage for excess energy. However, recent studies have demonstrated that adipocytes play a critical role in whole-body homeostasis, are involved in cell communication, experience forces in vivo, and respond to mechanical stimuli. Changes to the adipocyte mechanical microenvironment can affect function and, in some cases, contribute to disease. The aim of this review is to summarize the current literature on the mechanobiology of adipocytes. We reviewed over 100 papers on how mechanical stress is sensed by the adipocyte, the effects on cell behavior, and the use of cell culture scaffolds, particularly those with tunable stiffness, to study adipocyte behavior, adipose cell and tissue mechanical properties, and computational models. From our review, we conclude that adipocytes are responsive to mechanical stimuli, cell function and adipogenesis can be dictated by the mechanical environment, the measurement of mechanical properties is highly dependent on testing methods, and current modeling practices use many different approaches to recapitulate the complex behavior of adipocytes and adipose tissue. This review is intended to aid future studies by summarizing the current literature on adipocyte mechanobiology. Full article

(This article belongs to the Section Biophysics)

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12 pages, 2128 KiB

Open AccessEditor’s ChoiceArticle

Using a Combination of Novel Research Tools to Understand Social Interaction in the Drosophila melanogaster Model for Fragile X Syndrome

by Maja Stojkovic, Milan Petrovic, Maria Capovilla, Sara Milojevic, Vedrana Makevic, Dejan B. Budimirovic, Louise Corscadden, Shuhan He and Dragana Protic

Biology 2024, 13(6), 432; https://doi.org/10.3390/biology13060432 - 12 Jun 2024

Cited by 1 | Viewed by 1308

Abstract

Fragile X syndrome (FXS), the most common monogenic cause of inherited intellectual disability and autism spectrum disorder, is caused by a full mutation (>200 CGG repeats) in the Fragile X Messenger Ribonucleoprotein 1 (FMR1) gene. Individuals with FXS experience various challenges [...] Read more.

Fragile X syndrome (FXS), the most common monogenic cause of inherited intellectual disability and autism spectrum disorder, is caused by a full mutation (>200 CGG repeats) in the Fragile X Messenger Ribonucleoprotein 1 (FMR1) gene. Individuals with FXS experience various challenges related to social interaction (SI). Animal models, such as the Drosophila melanogaster model for FXS where the only ortholog of human FMR1 (dFMR1) is mutated, have played a crucial role in the understanding of FXS. The aim of this study was to investigate SI in the dFMR1^B55 mutants (the groups of flies of both sexes simultaneously) using the novel Drosophila Shallow Chamber and a Python data processing pipeline based on social network analysis (SNA). In comparison with wild-type flies (w¹¹¹⁸), SNA analysis in dFMR1^B55 mutants revealed hypoactivity, fewer connections in their networks, longer interaction duration, a lower ability to transmit information efficiently, fewer alternative pathways for information transmission, a higher variability in the number of interactions they achieved, and flies tended to stay near the boundaries of the testing chamber. These observed alterations indicate the presence of characteristic strain-dependent social networks in dFMR1^B55 flies, commonly referred to as the group phenotype. Finally, combining novel research tools is a valuable method for SI research in fruit flies. Full article

(This article belongs to the Special Issue From Basics to Applications of Gene Regulatory Networks)

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12 pages, 1017 KiB

Open AccessEditor’s ChoiceArticle

Development of a Target Enrichment Probe Set for Conifer (REMcon)

by Raees Khan, Ed Biffin, Kor-jent van Dijk, Robert S. Hill, Jie Liu and Michelle Waycott

Biology 2024, 13(6), 361; https://doi.org/10.3390/biology13060361 - 22 May 2024

Cited by 1 | Viewed by 1116

Abstract

Conifers are an ecologically and economically important seed plant group that can provide significant insights into the evolution of land plants. Molecular phylogenetics has developed as an important approach in evolutionary studies, although there have been relatively few studies of conifers that employ [...] Read more.

Conifers are an ecologically and economically important seed plant group that can provide significant insights into the evolution of land plants. Molecular phylogenetics has developed as an important approach in evolutionary studies, although there have been relatively few studies of conifers that employ large-scale data sourced from multiple nuclear genes. Target enrichment sequencing (target capture, exon capture, or Hyb-Seq) has developed as a key approach in modern phylogenomic studies. However, until now, there has been no bait set that specifically targets the entire conifer clade. REMcon is a target sequence capture probe set intended for family- and species-level phylogenetic studies of conifers that target c. 100 single-copy nuclear loci. We tested the REMcon probe set using 69 species, including 44 conifer genera across six families and four other gymnosperm taxa, to evaluate the efficiency of target capture to efficiently generate comparable DNA sequence data across conifers. The recovery of target loci was high, with, on average, 94% of the targeted regions recovered across samples with high read coverage. A phylogenetic analysis of these data produced a well-supported topology that is consistent with the current understanding of relationships among conifers. The REMcon bait set will be useful in generating relatively large-scale nuclear data sets consistently for any conifer lineage. Full article

(This article belongs to the Section Genetics and Genomics)

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20 pages, 700 KiB

Open AccessEditor’s ChoiceReview

Associations between “Cancer Risk”, “Inflammation” and “Metabolic Syndrome”: A Scoping Review

by Elsa Vitale, Alessandro Rizzo, Kazuki Santa and Emilio Jirillo

Biology 2024, 13(5), 352; https://doi.org/10.3390/biology13050352 - 16 May 2024

Cited by 7 | Viewed by 2355

Abstract

Background: Individuals with metabolic syndrome exhibit simultaneously pro-thrombotic and pro-inflammatory conditions which more probably can lead to cardiovascular diseases progression, type 2 diabetes mellitus, and some types of cancer. The present scoping review is aimed at highlighting the association between cancer risk, inflammation, [...] Read more.

Background: Individuals with metabolic syndrome exhibit simultaneously pro-thrombotic and pro-inflammatory conditions which more probably can lead to cardiovascular diseases progression, type 2 diabetes mellitus, and some types of cancer. The present scoping review is aimed at highlighting the association between cancer risk, inflammation, and metabolic syndrome. Methods: A search strategy was performed, mixing keywords and MeSH terms, such as “Cancer Risk”, “Inflammation”, “Metabolic Syndrome”, “Oncogenesis”, and “Oxidative Stress”, and matching them through Boolean operators. A total of 20 manuscripts were screened for the present study. Among the selected papers, we identified some associations with breast cancer, colorectal cancer, esophageal adenocarcinoma, hepatocellular carcinoma (HCC), and cancer in general. Conclusions: Cancer and its related progression may also depend also on a latent chronic inflammatory condition associated with other concomitant conditions, including type 2 diabetes mellitus, metabolic syndrome, and obesity. Therefore, prevention may potentially help individuals to protect themselves from cancer. Full article

(This article belongs to the Special Issue Effects of Environmental Stress on the Metabolic Dysfunction and Its Mechanism)

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11 pages, 1012 KiB

Open AccessEditor’s ChoiceReview

Symphonies of Growth: Unveiling the Impact of Sound Waves on Plant Physiology and Productivity

by Mario Pagano and Sonia Del Prete

Biology 2024, 13(5), 326; https://doi.org/10.3390/biology13050326 - 7 May 2024

Cited by 1 | Viewed by 6059

Abstract

The application of sound wave technology to different plant species has revealed that variations in the Hz, sound pressure intensity, treatment duration, and type of setup of the sound source significantly impact the plant performance. A study conducted on cotton plants treated with [...] Read more.

The application of sound wave technology to different plant species has revealed that variations in the Hz, sound pressure intensity, treatment duration, and type of setup of the sound source significantly impact the plant performance. A study conducted on cotton plants treated with Plant Acoustic Frequency Technology (PAFT) highlighted improvements across various growth metrics. In particular, the treated samples showed increases in the height, size of the fourth expanded leaf from the final one, count of branches carrying bolls, quantity of bolls, and weight of individual bolls. Another study showed how the impact of a 4 kHz sound stimulus positively promoted plant drought tolerance. In other cases, such as in transgenic rice plants, GUS expression was upregulated at 250 Hz but downregulated at 50 Hz. In the same way, sound frequencies have been found to enhance the osmotic potential, with the highest observed in samples treated with frequencies of 0.5 and 0.8 kHz compared to the control. Furthermore, a sound treatment with a frequency of 0.4 kHz and a sound pressure level (SPL) of 106 dB significantly increased the paddy rice germination index, as evidenced by an increase in the stem height and relative fresh weight. This paper presents a complete, rationalized and updated review of the literature on the effects of sound waves on the physiology and growth parameters of sound-treated plants. Full article

(This article belongs to the Special Issue Adaptation of Living Species to Environmental Stress)

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32 pages, 8389 KiB

Open AccessEditor’s ChoiceReview

Connexin Gap Junction Channels and Hemichannels: Insights from High-Resolution Structures

by Maciej Jagielnicki, Iga Kucharska, Brad C. Bennett, Andrew L. Harris and Mark Yeager

Biology 2024, 13(5), 298; https://doi.org/10.3390/biology13050298 - 26 Apr 2024

Cited by 4 | Viewed by 2077

Abstract

Connexins (Cxs) are a family of integral membrane proteins, which function as both hexameric hemichannels (HCs) and dodecameric gap junction channels (GJCs), behaving as conduits for the electrical and molecular communication between cells and between cells and the extracellular environment, respectively. Their proper [...] Read more.

Connexins (Cxs) are a family of integral membrane proteins, which function as both hexameric hemichannels (HCs) and dodecameric gap junction channels (GJCs), behaving as conduits for the electrical and molecular communication between cells and between cells and the extracellular environment, respectively. Their proper functioning is crucial for many processes, including development, physiology, and response to disease and trauma. Abnormal GJC and HC communication can lead to numerous pathological states including inflammation, skin diseases, deafness, nervous system disorders, and cardiac arrhythmias. Over the last 15 years, high-resolution X-ray and electron cryomicroscopy (cryoEM) structures for seven Cx isoforms have revealed conservation in the four-helix transmembrane (TM) bundle of each subunit; an αβ fold in the disulfide-bonded extracellular loops and inter-subunit hydrogen bonding across the extracellular gap that mediates end-to-end docking to form a tight seal between hexamers in the GJC. Tissue injury is associated with cellular Ca²⁺ overload. Surprisingly, the binding of 12 Ca²⁺ ions in the Cx26 GJC results in a novel electrostatic gating mechanism that blocks cation permeation. In contrast, acidic pH during tissue injury elicits association of the N-terminal (NT) domains that sterically blocks the pore in a “ball-and-chain” fashion. The NT domains under physiologic conditions display multiple conformational states, stabilized by protein–protein and protein–lipid interactions, which may relate to gating mechanisms. The cryoEM maps also revealed putative lipid densities within the pore, intercalated among transmembrane α-helices and between protomers, the functions of which are unknown. For the future, time-resolved cryoEM of isolated Cx channels as well as cryotomography of GJCs and HCs in cells and tissues will yield a deeper insight into the mechanisms for channel regulation. The cytoplasmic loop (CL) and C-terminal (CT) domains are divergent in sequence and length, are likely involved in channel regulation, but are not visualized in the high-resolution X-ray and cryoEM maps presumably due to conformational flexibility. We expect that the integrated use of synergistic physicochemical, spectroscopic, biophysical, and computational methods will reveal conformational dynamics relevant to functional states. We anticipate that such a wealth of results under different pathologic conditions will accelerate drug discovery related to Cx channel modulation. Full article

(This article belongs to the Special Issue Hybrid Methods for Structural Biology and Drug Design: A Memorial Issue for Dr. Chris G. Dealwis)

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12 pages, 4016 KiB

Open AccessEditor’s ChoiceArticle

Different Immune Responses of Hemocytes from V. parahaemolyticus-Resistant and -Susceptible Shrimp at Early Infection Stage

by Wenran Du, Shihao Li and Fuhua Li

Biology 2024, 13(5), 300; https://doi.org/10.3390/biology13050300 - 26 Apr 2024

Viewed by 1249

Abstract

Vibrio parahaemolyticus is one of the main causative agents leading to acute hepatopancreatic necrosis disease, the severe bacterial disease that occurs during shrimp aquaculture. Hemocytes play important roles during Vibrio infection. Previously, we found that there were few differentially expressed genes (DEGs) between [...] Read more.

Vibrio parahaemolyticus is one of the main causative agents leading to acute hepatopancreatic necrosis disease, the severe bacterial disease that occurs during shrimp aquaculture. Hemocytes play important roles during Vibrio infection. Previously, we found that there were few differentially expressed genes (DEGs) between hemocytes from V. parahaemolyticus-resistant and -susceptible shrimp before infection. We considered that there should be different immune responses between them after a pathogen infection. Here, the transcriptome data of hemocytes from V. parahaemolyticus-resistant and -susceptible shrimp before and after a pathogen infection were compared. The results showed that there were 157 DEGs responsive to infection in V. parahaemolyticus-resistant shrimp, while 33 DEGs in V. parahaemolyticus-susceptible shrimp. DEGs in V. parahaemolyticus-resistant shrimp were mainly related to immune and glycolytic processes, while those in V. parahaemolyticus-susceptible shrimp were mainly related to metabolism, with only two DEGs in common. A further analysis of genes involved in glucose metabolism revealed that GLUT2, HK, FBP, and PCK1 were lowly expressed while PC were highly expressed in hemocytes of the V. parahaemolyticus-resistant shrimp, indicating that glucose metabolism in shrimp hemocytes was related to a V. parahaemolyticus infection. After the knockdown of PC, the expression of genes in Toll and IMD signaling pathways were down-regulated, indicating that glucose metabolism might function through regulating host immunity during V. parahaemolyticus infection. The results suggest that the immune responses between V. parahaemolyticus-resistant and -susceptible shrimp were apparently different, which probably contribute to their different V. parahaemolyticus resistance abilities. Full article

(This article belongs to the Section Marine Biology)

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19 pages, 3578 KiB

Open AccessEditor’s ChoiceReview

Toward the Exploitation of Sustainable Green Factory: Biotechnology Use of Nannochloropsis spp.

by Davide Canini, Edoardo Ceschi and Federico Perozeni

Biology 2024, 13(5), 292; https://doi.org/10.3390/biology13050292 - 25 Apr 2024

Cited by 1 | Viewed by 1777

Abstract

Securing food, energy, and raw materials for a growing population is one of the most significant challenges of our century. Algae play a central role as an alternative to plants. Wastewater and flue gas can secure nutrients and CO₂ for carbon fixation. [...] Read more.

Securing food, energy, and raw materials for a growing population is one of the most significant challenges of our century. Algae play a central role as an alternative to plants. Wastewater and flue gas can secure nutrients and CO₂ for carbon fixation. Unfortunately, algae domestication is necessary to enhance biomass production and reduce cultivation costs. Nannochloropsis spp. have increased in popularity among microalgae due to their ability to accumulate high amounts of lipids, including PUFAs. Recently, the interest in the use of Nannochloropsis spp. as a green bio-factory for producing high-value products increased proportionally to the advances of synthetic biology and genetic tools in these species. In this review, we summarized the state of the art of current nuclear genetic manipulation techniques and a few examples of their application. The industrial use of Nannochloropsis spp. has not been feasible yet, but genetic tools can finally lead to exploiting this full-of-potential microalga. Full article

(This article belongs to the Special Issue Metabolic Engineering of Microalgae for Sustainable Bioproduction: Successes, Limits, and Future Perspectives)

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21 pages, 10505 KiB

Open AccessEditor’s ChoiceArticle

Cellular Response of Adapted and Non-Adapted Tetrahymena thermophila Strains to Europium Eu(III) Compounds

by Patricia Alonso, Javier Blas, Francisco Amaro, Patricia de Francisco, Ana Martín-González and Juan Carlos Gutiérrez

Biology 2024, 13(5), 285; https://doi.org/10.3390/biology13050285 - 23 Apr 2024

Viewed by 1411

Abstract

Europium is one of the most reactive lanthanides and humans use it in many different applications, but we still know little about its potential toxicity and cellular response to its exposure. Two strains of the eukaryotic microorganism model Tetrahymena thermophila were adapted to [...] Read more.

Europium is one of the most reactive lanthanides and humans use it in many different applications, but we still know little about its potential toxicity and cellular response to its exposure. Two strains of the eukaryotic microorganism model Tetrahymena thermophila were adapted to high concentrations of two Eu(III) compounds (EuCl₃ or Eu₂O₃) and compared to a control strain and cultures treated with both compounds. In this ciliate, EuCl₃ is more toxic than Eu₂O₃. LC₅₀ values show that this microorganism is more resistant to these Eu(III) compounds than other microorganisms. Oxidative stress originated mainly by Eu₂O₃ is minimized by overexpression of genes encoding important antioxidant enzymes. The overexpression of metallothionein genes under treatment with Eu(III) compounds supports the possibility that this lanthanide may interact with the -SH groups of the cysteine residues from metallothioneins and/or displace essential cations of these proteins during their homeostatic function. Both lipid metabolism (lipid droplets fusing with europium-containing vacuoles) and autophagy are involved in the cellular response to europium stress. Bioaccumulation, together with a possible biomineralization to europium phosphate, seems to be the main mechanism of Eu(III) detoxification in these cells. Full article

(This article belongs to the Collection Feature Papers in Microbial Biology)

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19 pages, 6346 KiB

Open AccessEditor’s ChoiceReview

Postnatal Growth and Development of the Rumen: Integrating Physiological and Molecular Insights

by Binod Pokhrel and Honglin Jiang

Biology 2024, 13(4), 269; https://doi.org/10.3390/biology13040269 - 18 Apr 2024

Cited by 2 | Viewed by 2719

Abstract

The rumen plays an essential role in the physiology and production of agriculturally important ruminants such as cattle. Functions of the rumen include fermentation, absorption, metabolism, and protection. Cattle are, however, not born with a functional rumen, and the rumen undergoes considerable changes [...] Read more.

The rumen plays an essential role in the physiology and production of agriculturally important ruminants such as cattle. Functions of the rumen include fermentation, absorption, metabolism, and protection. Cattle are, however, not born with a functional rumen, and the rumen undergoes considerable changes in size, histology, physiology, and transcriptome from birth to adulthood. In this review, we discuss these changes in detail, the factors that affect these changes, and the potential molecular and cellular mechanisms that mediate these changes. The introduction of solid feed to the rumen is essential for rumen growth and functional development in post-weaning calves. Increasing evidence suggests that solid feed stimulates rumen growth and functional development through butyric acid and other volatile fatty acids (VFAs) produced by microbial fermentation of feed in the rumen and that VFAs stimulate rumen growth and functional development through hormones such as insulin and insulin-like growth factor I (IGF-I) or through direct actions on energy production, chromatin modification, and gene expression. Given the role of the rumen in ruminant physiology and performance, it is important to further study the cellular, molecular, genomic, and epigenomic mechanisms that control rumen growth and development in postnatal ruminants. A better understanding of these mechanisms could lead to the development of novel strategies to enhance the growth and development of the rumen and thereby the productivity and health of cattle and other agriculturally important ruminants. Full article

(This article belongs to the Section Physiology)

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15 pages, 4176 KiB

Open AccessEditor’s ChoiceArticle

Systemic Effects of a Phage Cocktail on Healthy Weaned Piglets

by Yankun Liu, Yan Lin and Weiyun Zhu

Biology 2024, 13(4), 271; https://doi.org/10.3390/biology13040271 - 18 Apr 2024

Cited by 1 | Viewed by 1697

Abstract

Numerous studies have demonstrated that bacteriophages (phages) can effectively treat intestinal bacterial infections. However, research on the impact of phages on overall body health once they enter the intestine is limited. This study utilized weaned piglets as subjects to evaluate the systemic effects [...] Read more.

Numerous studies have demonstrated that bacteriophages (phages) can effectively treat intestinal bacterial infections. However, research on the impact of phages on overall body health once they enter the intestine is limited. This study utilized weaned piglets as subjects to evaluate the systemic effects of an orally administered phage cocktail on their health. Twelve 21-day-old weaned piglets were divided into control (CON) and phage gavage (Phages) groups. The phage cocktail consisted of five lytic phages, targeting Salmonella enterica serovar Choleraesuis (S. choleraesuis), Enteropathogenic Escherichia coli (EPEC), and Shiga tox-in-producing Escherichia coli (STEC). The phages group received 10 mL of phage cocktail orally for 20 consecutive days. The results show that the phage gavage did not affect the piglets’ growth performance, serum biochemical indices, or most organ indices, except for the pancreas. However, the impact on the intestine was complex. Firstly, although the pancreatic index decreased, it did not affect the secretion of digestive enzymes in the intestine. Secondly, phages increased the pH of jejunum chyme and relative weight of the ileum, and enhanced intestinal barrier function without affecting the morphology of the intestine. Thirdly, phages did not proliferate in the intestine, but altered the intestinal microbiota structure and increased concentrations of microbial metabolites isobutyric acid and isovaleric acid in the colonic chyme. In addition, phages impacted the immune status, significantly increasing serum IgA, IgG, and IgM, as well as serum and intestinal mucosal IFN-γ, IL-1β, IL-17, and TGF-β, and decreasing IL-4 and IL-10. They also activated toll-like receptors TLR-4 and TLR-9. Apart from an increase in basophil numbers, the counts of other immune cells in the blood did not change. This study indicates that the impact of phages on body health is complex, especially regarding immune status, warranting further attention. Short-term phage gavage did not have significant negative effects on health but could enhance intestinal barrier function. Full article

(This article belongs to the Special Issue Potential Applications of Bacteriophages in Livestock and Poultry Production in the Post-antibiotic Era)

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24 pages, 5671 KiB

Open AccessEditor’s ChoiceArticle

Impacts of Invasive Plants on Native Vegetation Communities in Wetland and Stream Mitigation

by Douglas A. DeBerry and Dakota M. Hunter

Biology 2024, 13(4), 275; https://doi.org/10.3390/biology13040275 - 18 Apr 2024

Cited by 1 | Viewed by 2013

Abstract

We sampled vegetation communities across plant invasion gradients at multiple wetland and stream mitigation sites in the Coastal Plain and Piedmont physiographic provinces of Virginia, USA. Impacts of invasion were evaluated by tracking changes in species composition and native vegetation community properties along [...] Read more.

We sampled vegetation communities across plant invasion gradients at multiple wetland and stream mitigation sites in the Coastal Plain and Piedmont physiographic provinces of Virginia, USA. Impacts of invasion were evaluated by tracking changes in species composition and native vegetation community properties along the abundance gradients of multiple plant invaders. We found that native species richness, diversity, and floristic quality were consistently highest at moderate levels of invasion (ca. 5–10% relative abundance of invader), regardless of the identity of the invasive species or the type of mitigation (wetland or stream). Likewise, native species composition was similar between uninvaded and moderately invaded areas, and only diminished when invaders were present at higher abundance values. Currently, low thresholds for invasive species performance standards (e.g., below 5% relative abundance of invader) compel mitigation managers to use non-selective control methods such as herbicides to reduce invasive plant cover. Our results suggest that this could cause indiscriminate mortality of desirable native species at much higher levels of richness, diversity, and floristic quality than previously thought. From our data, we recommend an invasive species performance standard of 10% relative invader(s) abundance on wetland and stream mitigation sites, in combination with vigilant invasive plant mapping strategies. Based on our results, this slightly higher standard would strike a balance between proactive management and unnecessary loss of plant community functions at the hands of compulsory invasive species management. Full article

(This article belongs to the Special Issue Biology, Ecology and Management of Invasive Alien Plants)

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18 pages, 2358 KiB

Open AccessEditor’s ChoiceArticle

Distribution and Genetic Lineages of the Craspedacusta sowerbii Species Complex (Cnidaria, Olindiidae) in Italy

by Massimo Morpurgo, Federico Marrone, Francesca Ciutti, Cristina Cappelletti, Samuel Vorhauser, Renate Alber, Matteo Dossena, Nico Salmaso, Diego Fontaneto, Luciano Caputo and Luca Vecchioni

Biology 2024, 13(4), 202; https://doi.org/10.3390/biology13040202 - 22 Mar 2024

Viewed by 1784

Abstract

Olindiid freshwater jellyfishes of the genus Craspedacusta Lankester, 1880 are native to eastern Asia; however, some species within the genus have been introduced worldwide and are nowadays present in all continents except Antarctica. To date, there is no consensus regarding the taxonomy within [...] Read more.

Olindiid freshwater jellyfishes of the genus Craspedacusta Lankester, 1880 are native to eastern Asia; however, some species within the genus have been introduced worldwide and are nowadays present in all continents except Antarctica. To date, there is no consensus regarding the taxonomy within the genus Craspedacusta due to the morphological plasticity of the medusa stages. The species Craspedacusta sowerbii Lankester, 1880 was first recorded in Italy in 1946, and until 2017, sightings of the jellyfish Craspedacusta were reported for 40 water bodies. Here, we shed new light on the presence of the freshwater jellyfishes belonging to the genus Craspedacusta across the Italian peninsula, Sardinia, and Sicily. First, we report 21 new observations of this non-native taxon, of which eighteen refer to medusae sightings, two to environmental DNA sequencing, and one to the finding of polyps. Then, we investigate the molecular diversity of collected Craspedacusta specimens, using a Bayesian analysis of sequences of the mitochondrial gene encoding for Cytochrome c Oxidase Subunit I (mtDNA COI). Our molecular analysis shows the presence of two distinctive genetic lineages: (i) a group that comprises sequences obtained from populations ranging from central to northern Italy; (ii) a group that comprises three populations from northern Italy—i.e., those from the Lake Levico, the Lake Santo of Monte Terlago, and the Lake Endine—and the single known Sicilian population. We also report for the first time a mtDNA COI sequence obtained from a Craspedacusta medusa collected in Spain. Full article

(This article belongs to the Special Issue Ecological Characteristics and Genetic Population Structure of the Invasive Freshwater Jellyfish Craspedacusta sowerbii Species Complex)

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14 pages, 3767 KiB

Open AccessEditor’s ChoiceReview

Inhibitors against DNA Polymerase I Family of Enzymes: Novel Targets and Opportunities

by Saathvik Kannan, Samuel W. Gillespie, Wendy L. Picking, William D. Picking, Christian L. Lorson and Kamal Singh

Biology 2024, 13(4), 204; https://doi.org/10.3390/biology13040204 - 22 Mar 2024

Cited by 1 | Viewed by 2570

Abstract

DNA polymerases replicate cellular genomes and/or participate in the maintenance of genome integrity. DNA polymerases sharing high sequence homology with E. coli DNA polymerase I (pol I) have been grouped in Family A. Pol I participates in Okazaki fragment maturation and in bacterial [...] Read more.

DNA polymerases replicate cellular genomes and/or participate in the maintenance of genome integrity. DNA polymerases sharing high sequence homology with E. coli DNA polymerase I (pol I) have been grouped in Family A. Pol I participates in Okazaki fragment maturation and in bacterial genome repair. Since its discovery in 1956, pol I has been extensively studied, primarily to gain deeper insights into the mechanism of DNA replication. As research on DNA polymerases advances, many novel functions of this group of polymerases are being uncovered. For example, human DNA polymerase θ (a Family A DNA pol) has been shown to synthesize DNA using RNA as a template, a function typically attributed to retroviral reverse transcriptase. Increased interest in drug discovery against pol θ has emerged due to its roles in cancer. Likewise, Pol I family enzymes also appear attractive as drug-development targets against microbial infections. Development of antimalarial compounds targeting apicoplast apPOL, an ortholog of Pol I, further extends the targeting of this family of enzymes. Here, we summarize reported drug-development efforts against Family A polymerases and future perspective regarding these enzymes as antibiotic targets. Recently developed techniques, such as artificial intelligence, can be used to facilitate the development of new drugs. Full article

(This article belongs to the Section Medical Biology)

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14 pages, 410 KiB

Open AccessEditor’s ChoiceArticle

Reducing Epistasis and Pleiotropy Can Avoid the Survival of the Flattest Tragedy

by Priyanka Mehra and Arend Hintze

Biology 2024, 13(3), 193; https://doi.org/10.3390/biology13030193 - 17 Mar 2024

Viewed by 1354

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Section Evolutionary Biology)

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16 pages, 2998 KiB

Open AccessEditor’s ChoiceArticle

Personalized Driver Gene Prediction Using Graph Convolutional Networks with Conditional Random Fields

by Pi-Jing Wei, An-Dong Zhu, Ruifen Cao and Chunhou Zheng

Biology 2024, 13(3), 184; https://doi.org/10.3390/biology13030184 - 14 Mar 2024

Viewed by 1875

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue 3rd Edition of Intelligent Computing in Biology and Medicine)

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14 pages, 1951 KiB

Open AccessEditor’s ChoiceArticle

Phylogenetic Analysis of Pyruvate-Ferredoxin Oxidoreductase, a Redox Enzyme Involved in the Pharmacological Activation of Nitro-Based Prodrugs in Bacteria and Protozoa

by Seth Duwor, Daniela Brites and Pascal Mäser

Biology 2024, 13(3), 178; https://doi.org/10.3390/biology13030178 - 9 Mar 2024

Cited by 1 | Viewed by 2111

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Section Infection Biology)

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25 pages, 6188 KiB

Open AccessEditor’s ChoiceArticle

First European Erwinia amylovora Lytic Bacteriophage Cocktails Effective in the Host: Characterization and Prospects for Fire Blight Biocontrol

by Elena G. Biosca, Ricardo Delgado Santander, Félix Morán, Àngela Figàs-Segura, Rosa Vázquez, José Francisco Català-Senent and Belén Álvarez

Biology 2024, 13(3), 176; https://doi.org/10.3390/biology13030176 - 8 Mar 2024

Cited by 2 | Viewed by 2766

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Advances in Research on Diseases of Plants)

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35 pages, 914 KiB

Open AccessEditor’s ChoiceArticle

Probiotics Supplementation during Pregnancy: Can They Exert Potential Beneficial Effects against Adverse Pregnancy Outcomes beyond Gestational Diabetes Mellitus?

by Efthymios Poulios, Eleni Pavlidou, Sousana K. Papadopoulou, Kalliopi Rempetsioti, Athanasios Migdanis, Maria Mentzelou, Maria Chatzidimitriou, Ioannis Migdanis, Odysseas Androutsos and Constantinos Giaginis

Biology 2024, 13(3), 158; https://doi.org/10.3390/biology13030158 - 28 Feb 2024

Cited by 1 | Viewed by 2485

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Pregnancy Health and Complications: Molecular Processes and Mechanisms)

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14 pages, 1722 KiB

Open AccessEditor’s ChoiceReview

Chromatin’s Influence on Pre-Replication Complex Assembly and Function

by Hina Ahmad, Neha Chetlangia and Supriya G. Prasanth

Biology 2024, 13(3), 152; https://doi.org/10.3390/biology13030152 - 27 Feb 2024

Viewed by 2436

Abstract

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. [...] Read more.

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. Full article

(This article belongs to the Special Issue The Replication Licensing System)

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17 pages, 2328 KiB

Open AccessEditor’s ChoiceArticle

Trunk Injection Delivery of Biocontrol Strains of Trichoderma spp. Effectively Suppresses Nut Rot by Gnomoniopsis castaneae in Chestnut (Castanea sativa Mill.)

by Alessandra Benigno, Chiara Aglietti, Santa Olga Cacciola and Salvatore Moricca

Biology 2024, 13(3), 143; https://doi.org/10.3390/biology13030143 - 23 Feb 2024

Cited by 2 | Viewed by 2341

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Plant Mycobiome: Toward the Understanding of Its Role in the Biological Control of Pathogens in Agroforestry Systems)

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16 pages, 488 KiB

Open AccessEditor’s ChoiceReview

Dietary Patterns and Fertility

by Martina Cristodoro, Enrica Zambella, Ilaria Fietta, Annalisa Inversetti and Nicoletta Di Simone

Biology 2024, 13(2), 131; https://doi.org/10.3390/biology13020131 - 19 Feb 2024

Cited by 7 | Viewed by 5628

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Pregnancy Health and Complications: Molecular Processes and Mechanisms)

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12 pages, 2309 KiB

Open AccessEditor’s ChoiceArticle

The Diversity of Wolbachia across the Turtle Ants (Formicidae: Cephalotes spp.)

by Corey Reese, Leland C. Graber, Manuela O. Ramalho and Corrie S. Moreau

Biology 2024, 13(2), 121; https://doi.org/10.3390/biology13020121 - 13 Feb 2024

Viewed by 1883

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Section Conservation Biology and Biodiversity)

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21 pages, 2327 KiB

Open AccessEditor’s ChoiceArticle

Effect of CB1 Receptor Deficiency on Mitochondrial Quality Control Pathways in Gastrocnemius Muscle

by 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 and Antonia Lanni

Biology 2024, 13(2), 116; https://doi.org/10.3390/biology13020116 - 11 Feb 2024

Cited by 2 | Viewed by 2435

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Mitochondrial Metabolism and Function in Health and Disease)

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19 pages, 2436 KiB

Open AccessEditor’s ChoiceReview

Bacterial Biofilm in Chronic Wounds and Possible Therapeutic Approaches

by Ilaria Cavallo, Francesca Sivori, Arianna Mastrofrancesco, Elva Abril, Martina Pontone, Enea Gino Di Domenico and Fulvia Pimpinelli

Biology 2024, 13(2), 109; https://doi.org/10.3390/biology13020109 - 9 Feb 2024

Cited by 15 | Viewed by 5179

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Dermal-Epidermal Cross-Talk and Bioactive Mediators in Physiological and Pathological Skin Conditions)

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14 pages, 5945 KiB

Open AccessEditor’s ChoiceArticle

A New Non-Obese Steatohepatitis Mouse Model with Cardiac Dysfunction Induced by Addition of Ethanol to a High-Fat/High-Cholesterol Diet

by Seiji Shiraishi, Jinyao Liu, Yuki Saito, Yumiko Oba, Yuiko Nishihara and Satomichi Yoshimura

Biology 2024, 13(2), 91; https://doi.org/10.3390/biology13020091 - 1 Feb 2024

Viewed by 1974

Abstract

Non-obese metabolic dysfunction-associated steatotic liver disease (MASLD) has been associated with cardiovascular-related mortality, leading to a higher mortality rate compared to the general population. However, few reports have examined cardiovascular events in non-obese MASLD mouse models. In this study we created a mouse [...] Read more.

Non-obese metabolic dysfunction-associated steatotic liver disease (MASLD) has been associated with cardiovascular-related mortality, leading to a higher mortality rate compared to the general population. However, few reports have examined cardiovascular events in non-obese MASLD mouse models. In this study we created a mouse model to mimic this condition. In this study involving seven-week-old C57BL/6J male mice, two dietary conditions were tested: a standard high-fat/high-cholesterol diet (STHD-01) and a combined diet of STHD-01 and ethanol. Over periods of 6 and 12 weeks, we analyzed the effects on liver and cardiac tissues using various staining techniques and PCR. Echocardiography and blood tests were also performed to assess cardiac function and liver damage. The results showed that mice on the ethanol-supplemented STHD-01 diet developed signs of steatohepatitis and cardiac dysfunction, along with increased sympathetic activity, as early as 6 weeks. At 12 weeks, more pronounced exacerbations accompanied with cardiac dilation, advanced liver fibrosis, and activated myocardial fibrosis with sympathetic activation were observed. This mouse model effectively replicated non-obese MASLD and cardiac dysfunction over a 12-week period using a combined diet of STHD-01 and ethanol. This dietary approach highlighted that both liver inflammation and fibrosis, as well as cardiac dysfunction, could be significantly worsened due to the activation of the sympathetic nervous system. Our results indicate that alcohol, even when completely metabolized on the day of drinking, exacerbates the progression of non-obese MASLD and cardiac dysfunction. Full article

(This article belongs to the Special Issue Biology of Liver Diseases)

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20 pages, 5454 KiB

Open AccessEditor’s ChoiceReview

Friend or Foe: Protein Inhibitors of DNA Gyrase

by Shengfeng Ruan, Chih-Han Tu and Christina R. Bourne

Biology 2024, 13(2), 84; https://doi.org/10.3390/biology13020084 - 29 Jan 2024

Cited by 5 | Viewed by 3502

Abstract

DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as [...] Read more.

DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as exemplified by the highly successful fluoroquinolone class of antibiotics. It is reasonable that the activity of gyrase could be intrinsically regulated within cells, thereby helping to coordinate DNA replication with doubling times. Numerous proteins have been identified to exert inhibitory effects on DNA gyrase, although at lower doses, it can appear readily reversible and therefore may have regulatory value. Some of these, such as the small protein toxins found in plasmid-borne addiction modules, can promote cell death by inducing damage to DNA, resulting in an analogous outcome as quinolone antibiotics. Others, however, appear to transiently impact gyrase in a readily reversible and non-damaging mechanism, such as the plasmid-derived Qnr family of DNA-mimetic proteins. The current review examines the origins and known activities of protein inhibitors of gyrase and highlights opportunities to further exert control over bacterial growth by targeting this validated antibacterial target with novel molecular mechanisms. Furthermore, we are gaining new insights into fundamental regulatory strategies of gyrase that may prove important for understanding diverse growth strategies among different bacteria. Full article

(This article belongs to the Section Biochemistry and Molecular Biology)

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34 pages, 2016 KiB

Open AccessEditor’s ChoiceReview

Mitochondrial Dysfunction in Endothelial Progenitor Cells: Unraveling Insights from Vascular Endothelial Cells

by Azra Kulovic-Sissawo, Carolina Tocantins, Mariana S. Diniz, Elisa Weiss, Andreas Steiner, Silvija Tokic, Corina T. Madreiter-Sokolowski, Susana P. Pereira and Ursula Hiden

Biology 2024, 13(2), 70; https://doi.org/10.3390/biology13020070 - 23 Jan 2024

Cited by 7 | Viewed by 3604

Abstract

Endothelial dysfunction is associated with several lifestyle-related diseases, including cardiovascular and neurodegenerative diseases, and it contributes significantly to the global health burden. Recent research indicates a link between cardiovascular risk factors (CVRFs), excessive production of reactive oxygen species (ROS), mitochondrial impairment, and endothelial [...] Read more.

Endothelial dysfunction is associated with several lifestyle-related diseases, including cardiovascular and neurodegenerative diseases, and it contributes significantly to the global health burden. Recent research indicates a link between cardiovascular risk factors (CVRFs), excessive production of reactive oxygen species (ROS), mitochondrial impairment, and endothelial dysfunction. Circulating endothelial progenitor cells (EPCs) are recruited into the vessel wall to maintain appropriate endothelial function, repair, and angiogenesis. After attachment, EPCs differentiate into mature endothelial cells (ECs). Like ECs, EPCs are also susceptible to CVRFs, including metabolic dysfunction and chronic inflammation. Therefore, mitochondrial dysfunction of EPCs may have long-term effects on the function of the mature ECs into which EPCs differentiate, particularly in the presence of endothelial damage. However, a link between CVRFs and impaired mitochondrial function in EPCs has hardly been investigated. In this review, we aim to consolidate existing knowledge on the development of mitochondrial and endothelial dysfunction in the vascular endothelium, place it in the context of recent studies investigating the consequences of CVRFs on EPCs, and discuss the role of mitochondrial dysfunction. Thus, we aim to gain a comprehensive understanding of mechanisms involved in EPC deterioration in relation to CVRFs and address potential therapeutic interventions targeting mitochondrial health to promote endothelial function. Full article

(This article belongs to the Special Issue Mitochondria: The Diseases' Cause and Cure)

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20 pages, 337 KiB

Open AccessEditor’s ChoiceReview

Assessing Antimicrobial Efficacy on Plastics and Other Non-Porous Surfaces: A Closer Look at Studies Using the ISO 22196:2011 Standard

by Teresa Bento de Carvalho, Joana Bastos Barbosa and Paula Teixeira

Biology 2024, 13(1), 59; https://doi.org/10.3390/biology13010059 - 20 Jan 2024

Cited by 4 | Viewed by 2789

Abstract

The survival and spread of foodborne and nosocomial-associated bacteria through high-touch surfaces or contamination-prone sites, in either healthcare, domestic or food industry settings, are not always prevented by the employment of sanitary hygiene protocols. Antimicrobial surface coatings have emerged as a solution to [...] Read more.

The survival and spread of foodborne and nosocomial-associated bacteria through high-touch surfaces or contamination-prone sites, in either healthcare, domestic or food industry settings, are not always prevented by the employment of sanitary hygiene protocols. Antimicrobial surface coatings have emerged as a solution to eradicate pathogenic bacteria and prevent future infections and even outbreaks. Standardised antimicrobial testing methods play a crucial role in validating the effectiveness of these materials and enabling their application in real-life settings, providing reliable results that allow for comparison between antimicrobial surfaces while assuring end-use product safety. This review provides an insight into the studies using ISO 22196, which is considered the gold standard for antimicrobial surface coatings and examines the current state of the art in antimicrobial testing methods. It primarily focuses on identifying pitfalls and how even small variations in methods can lead to different results, affecting the assessment of the antimicrobial activity of a particular product. Full article

(This article belongs to the Special Issue Microbial Contamination and Food Safety (Volume II))

15 pages, 5701 KiB

Open AccessEditor’s ChoiceReview

Looking Back, Going Forward: Understanding Cardiac Pathophysiology from Pressure–Volume Loops

by Ilaria Protti, Antoon van den Enden, Nicolas M. Van Mieghem, Christiaan L. Meuwese and Paolo Meani

Biology 2024, 13(1), 55; https://doi.org/10.3390/biology13010055 - 19 Jan 2024

Cited by 3 | Viewed by 4465

Abstract

Knowing cardiac physiology is essential for health care professionals working in the cardiovascular field. Pressure–volume loops (PVLs) offer a unique understanding of the myocardial working and have become pivotal in complex pathophysiological scenarios, such as profound cardiogenic shock or when mechanical circulatory supports [...] Read more.

Knowing cardiac physiology is essential for health care professionals working in the cardiovascular field. Pressure–volume loops (PVLs) offer a unique understanding of the myocardial working and have become pivotal in complex pathophysiological scenarios, such as profound cardiogenic shock or when mechanical circulatory supports are implemented. This review provides a comprehensive summary of the left and right ventricle physiology, based on the PVL interpretation. Full article

(This article belongs to the Section Physiology)

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17 pages, 2476 KiB

Open AccessEditor’s ChoiceReview

Schistosome Transgenesis: The Long Road to Success

by Bernd H. Kalinna, Allen G. Ross and Anna K. Walduck

Biology 2024, 13(1), 48; https://doi.org/10.3390/biology13010048 - 16 Jan 2024

Cited by 1 | Viewed by 2376

Abstract

As research on parasitic helminths has entered the post-genomic era, research efforts have turned to deciphering the function of genes in the public databases of genome sequences. It is hoped that, by understanding the role of parasite genes in maintaining their parasitic lifestyle, [...] Read more.

As research on parasitic helminths has entered the post-genomic era, research efforts have turned to deciphering the function of genes in the public databases of genome sequences. It is hoped that, by understanding the role of parasite genes in maintaining their parasitic lifestyle, critical insights can be gained to develop new intervention and control strategies. Methods to manipulate and transform parasitic worms are now developed to a point where it has become possible to gain a comprehensive understanding of the molecular mechanisms underlying host–parasite interplay, and here, we summarise and discuss the advances that have been made in schistosome transgenesis over the past 25 years. The ability to genetically manipulate schistosomes holds promise in finding new ways to control schistosomiasis, which ultimately may lead to the eradication of this debilitating disease. Full article

(This article belongs to the Section Genetics and Genomics)

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19 pages, 3926 KiB

Open AccessEditor’s ChoiceReview

Significance of Histidine Hydrogen–Deuterium Exchange Mass Spectrometry in Protein Structural Biology

by Masaru Miyagi and Takashi Nakazawa

Biology 2024, 13(1), 37; https://doi.org/10.3390/biology13010037 - 9 Jan 2024

Viewed by 3073

Abstract

Histidine residues play crucial roles in shaping the function and structure of proteins due to their unique ability to act as both acids and bases. In other words, they can serve as proton donors and acceptors at physiological pH. This exceptional property is [...] Read more.

Histidine residues play crucial roles in shaping the function and structure of proteins due to their unique ability to act as both acids and bases. In other words, they can serve as proton donors and acceptors at physiological pH. This exceptional property is attributed to the side-chain imidazole ring of histidine residues. Consequently, determining the acid-base dissociation constant (Ka) of histidine imidazole rings in proteins often yields valuable insights into protein functions. Significant efforts have been dedicated to measuring the pKa values of histidine residues in various proteins, with nuclear magnetic resonance (NMR) spectroscopy being the most commonly used technique. However, NMR-based methods encounter challenges in assigning signals to individual imidazole rings and require a substantial amount of proteins. To address these issues associated with NMR-based approaches, a mass-spectrometry-based method known as histidine hydrogen–deuterium exchange mass spectrometry (His-HDX-MS) has been developed. This technique not only determines the pKa values of histidine imidazole groups but also quantifies their solvent accessibility. His-HDX-MS has proven effective across diverse proteins, showcasing its utility. This review aims to clarify the fundamental principles of His-HDX-MS, detail the experimental workflow, explain data analysis procedures and provide guidance for interpreting the obtained results. Full article

(This article belongs to the Special Issue Hybrid Methods for Structural Biology and Drug Design: A Memorial Issue for Dr. Chris G. Dealwis)

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12 pages, 4932 KiB

Open AccessEditor’s ChoiceArticle

Red Ginseng Attenuates the Hepatic Cellular Senescence in Aged Mice

by Da-Yeon Lee, Juliana Arndt, Jennifer F. O’Connell, Josephine M. Egan and Yoo Kim

Biology 2024, 13(1), 36; https://doi.org/10.3390/biology13010036 - 8 Jan 2024

Cited by 4 | Viewed by 2832

Abstract

Cellular senescence is defined as an irreversible cell cycle arrest accompanied by morphological and physiological alterations during aging. Red ginseng (RG), processed from fresh ginseng (Panax ginseng C.A. Meyer) with a one-time steaming and drying process, is a well-known beneficial herbal medicine [...] Read more.

Cellular senescence is defined as an irreversible cell cycle arrest accompanied by morphological and physiological alterations during aging. Red ginseng (RG), processed from fresh ginseng (Panax ginseng C.A. Meyer) with a one-time steaming and drying process, is a well-known beneficial herbal medicine showing antioxidant, anti-inflammatory, and anti-aging properties. The current study aimed to investigate the benefits of RG in alleviating hepatic cellular senescence and its adverse effects in 19-month-old aged mice. We applied two different intervention methods and durations to compare RG’s effects in a time-dependent manner: (1) oral gavage injection for 4 weeks and (2) ad libitum intervention for 14 weeks. We observed that 4-week RG administration was exerted to maintain insulin homeostasis against developing age-associated insulin insensitivity and suppressed cellular senescence pathway in the liver and primary hepatocytes. Moreover, with remarkable improvement of insulin homeostasis, 14-week RG supplementation downregulated the activation of c-Jun N-terminal kinase (JNK) and its downstream transcriptional factor nuclear factor-κB (NF-κB) in aged mice. Lastly, RG treatment significantly reduced the senescence-associated β-galactosidase (SA-β-gal)-positive cells in primary hepatocytes and ionizing radiation (IR)-exposed mouse embryonic fibroblasts (MEFs). Taken together, we suggest that RG can be a promising candidate for a senolytic substance by preventing hepatic cellular senescence. Full article

(This article belongs to the Special Issue Functional Foods: Bioactivity, Bioavailability, and Biological Characteristics)

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34 pages, 4366 KiB

Open AccessEditor’s ChoiceReview

Lysosomal Dysfunction: Connecting the Dots in the Landscape of Human Diseases

by Elisabet Uribe-Carretero, Verónica Rey, Jose Manuel Fuentes and Isaac Tamargo-Gómez

Biology 2024, 13(1), 34; https://doi.org/10.3390/biology13010034 - 7 Jan 2024

Cited by 1 | Viewed by 5209

Abstract

Lysosomes are the main organelles responsible for the degradation of macromolecules in eukaryotic cells. Beyond their fundamental role in degradation, lysosomes are involved in different physiological processes such as autophagy, nutrient sensing, and intracellular signaling. In some circumstances, lysosomal abnormalities underlie several human [...] Read more.

Lysosomes are the main organelles responsible for the degradation of macromolecules in eukaryotic cells. Beyond their fundamental role in degradation, lysosomes are involved in different physiological processes such as autophagy, nutrient sensing, and intracellular signaling. In some circumstances, lysosomal abnormalities underlie several human pathologies with different etiologies known as known as lysosomal storage disorders (LSDs). These disorders can result from deficiencies in primary lysosomal enzymes, dysfunction of lysosomal enzyme activators, alterations in modifiers that impact lysosomal function, or changes in membrane-associated proteins, among other factors. The clinical phenotype observed in affected patients hinges on the type and location of the accumulating substrate, influenced by genetic mutations and residual enzyme activity. In this context, the scientific community is dedicated to exploring potential therapeutic approaches, striving not only to extend lifespan but also to enhance the overall quality of life for individuals afflicted with LSDs. This review provides insights into lysosomal dysfunction from a molecular perspective, particularly in the context of human diseases, and highlights recent advancements and breakthroughs in this field. Full article

(This article belongs to the Special Issue Lysosomes and Diseases Associated with Its Dysfunction)

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19 pages, 985 KiB

Open AccessEditor’s ChoiceReview

Genetics and Genomics of Infectious Diseases in Key Aquaculture Species

by Nguyen Hong Nguyen

Biology 2024, 13(1), 29; https://doi.org/10.3390/biology13010029 - 4 Jan 2024

Cited by 2 | Viewed by 3562

Abstract

Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised [...] Read more.

Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease and species specific and contingent upon a multitude of factors. The fields of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus (WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish, and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease-resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favorable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate-to-high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems and AI algorithms and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development. Full article

(This article belongs to the Special Issue Infectious Diseases in Aquaculture: Mechanisms, Detection, and Control)

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24 pages, 352 KiB

Open AccessEditor’s ChoiceReview

The Use of Non-Apoptotic Sperm Selected by Magnetic Activated Cell Sorting (MACS) to Enhance Reproductive Outcomes: What the Evidence Says

by Nicolás Garrido and María Gil Juliá

Biology 2024, 13(1), 30; https://doi.org/10.3390/biology13010030 - 4 Jan 2024

Cited by 5 | Viewed by 3135

Abstract

Sperm selection of the most competent sperm is a promising way to enhance reproductive outcomes. Apoptosis is the programmed cell death process to maintain tissue homeostasis, and MACS sperm selection of non-apoptotic cells enables the removal of apoptotic sperm from an ejaculate, thus [...] Read more.

Sperm selection of the most competent sperm is a promising way to enhance reproductive outcomes. Apoptosis is the programmed cell death process to maintain tissue homeostasis, and MACS sperm selection of non-apoptotic cells enables the removal of apoptotic sperm from an ejaculate, thus leaving the non-apoptotic available to be microinjected, but given the associated costs of adding these sperm selection steps to the routine practice, there is a need for a careful examination of the literature available to answer questions such as who can benefit from this MACS, how significant this improvement is, and how robust the evidence and data available supporting this choice are. Thus, the aim of this narrative review was to objectively evaluate the available evidence regarding the potential benefits of the use of MACS. From the literature, there are controversial results since its implementation as an in vitro fertilization add-on, and this may be explained in part by the low quality of the evidence available, wrong designs, or even inadequate statistical analyses. We concluded that the benefits of adding MACS are unclear, and further methodologically sound research on specific populations is much needed before offering it clinically. Full article

(This article belongs to the Section Developmental and Reproductive Biology)

15 pages, 871 KiB

Open AccessEditor’s ChoiceReview

Immune Escape in Glioblastoma: Mechanisms of Action and Implications for Immune Checkpoint Inhibitors and CAR T-Cell Therapy

by Catherine Yu, Kristin Hsieh, Daniel R. Cherry, Anthony D. Nehlsen, Lucas Resende Salgado, Stanislav Lazarev and Kunal K. Sindhu

Biology 2023, 12(12), 1528; https://doi.org/10.3390/biology12121528 - 15 Dec 2023

Cited by 4 | Viewed by 2839

Abstract

Glioblastoma, the most common primary brain cancer in adults, is characterized by a poor prognosis and resistance to standard treatments. The advent of immunotherapy has revolutionized the treatment of several cancers in recent years but has failed to demonstrate benefit in patients with [...] Read more.

Glioblastoma, the most common primary brain cancer in adults, is characterized by a poor prognosis and resistance to standard treatments. The advent of immunotherapy has revolutionized the treatment of several cancers in recent years but has failed to demonstrate benefit in patients with glioblastoma. Understanding the mechanisms by which glioblastoma exerts tumor-mediated immune suppression in both the tumor microenvironment and the systemic immune landscape is a critical step towards developing effective immunotherapeutic strategies. In this review, we discuss the current understanding of immune escape mechanisms in glioblastoma that compromise the efficacy of immunotherapies, with an emphasis on immune checkpoint inhibitors and chimeric antigen receptor T-cell therapy. In parallel, we review data from preclinical studies that have identified additional therapeutic targets that may enhance overall treatment efficacy in glioblastoma when administered alongside existing immunotherapies. Full article

(This article belongs to the Special Issue Progression of the Immune Escape Mechanism in Tumors)

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13 pages, 2860 KiB

Open AccessEditor’s ChoiceReview

Vesicular Trafficking, a Mechanism Controlled by Cascade Activation of Rab Proteins: Focus on Rab27

by Camille Menaceur, Océane Dusailly, Fabien Gosselet, Laurence Fenart and Julien Saint-Pol

Biology 2023, 12(12), 1530; https://doi.org/10.3390/biology12121530 - 15 Dec 2023

Cited by 3 | Viewed by 2782

Abstract

Vesicular trafficking is essential for the cell to internalize useful proteins and soluble substances, for cell signaling or for the degradation of pathogenic elements such as bacteria or viruses. This vesicular trafficking also enables the cell to engage in secretory processes for the [...] Read more.

Vesicular trafficking is essential for the cell to internalize useful proteins and soluble substances, for cell signaling or for the degradation of pathogenic elements such as bacteria or viruses. This vesicular trafficking also enables the cell to engage in secretory processes for the elimination of waste products or for the emission of intercellular communication vectors such as cytokines, chemokines and extracellular vesicles. Ras-related proteins (Rab) and their effector(s) are of crucial importance in all of these processes, and mutations/alterations to them have serious pathophysiological consequences. This review presents a non-exhaustive overview of the role of the major Rab involved in vesicular trafficking, with particular emphasis on their involvement in the biogenesis and secretion of extracellular vesicles, and on the role of Rab27 in various pathophysiological processes. Therefore, Rab and their effector(s) are central therapeutic targets, given their involvement in vesicular trafficking and their importance for cell physiology. Full article

(This article belongs to the Special Issue Cell Transport in Health and Disease)

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16 pages, 1539 KiB

Open AccessEditor’s ChoiceArticle

Octopus vulgaris Exhibits Interindividual Differences in Behavioural and Problem-Solving Performance

by Andrea Dissegna, Luciana Borrelli, Giovanna Ponte, Cinzia Chiandetti and Graziano Fiorito

Biology 2023, 12(12), 1487; https://doi.org/10.3390/biology12121487 - 4 Dec 2023

Cited by 2 | Viewed by 3418

Abstract

By presenting individual Octopus vulgaris with an extractive foraging problem with a puzzle box, we examined the possible correlation between behavioural performances (e.g., ease of adaptation to captive conditions, prevalence of neophobic and neophilic behaviours, and propensity to learn individually or by observing [...] Read more.

By presenting individual Octopus vulgaris with an extractive foraging problem with a puzzle box, we examined the possible correlation between behavioural performances (e.g., ease of adaptation to captive conditions, prevalence of neophobic and neophilic behaviours, and propensity to learn individually or by observing conspecifics), biotic (body and brain size, age, sex) and abiotic (seasonality and place of origin) factors. We found more neophilic animals showing shorter latencies to approach the puzzle box and higher probability of solving the task; also, shorter times to solve the task were correlated with better performance on the individual learning task. However, the most neophilic octopuses that approached the puzzle box more quickly did not reach the solution earlier than other individuals, suggesting that strong neophilic tendency may lead to suboptimal performance at some stages of the problem-solving process. In addition, seasonal and environmental characteristics of location of origin appear to influence the rate of expression of individual traits central to problem solving. Overall, our analysis provides new insights into the traits associated with problem solving in invertebrates and highlights the presence of adaptive mechanisms that promote population-level changes in octopuses’ behavioural traits. Full article

(This article belongs to the Section Behavioural Biology)

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12 pages, 1824 KiB

Open AccessEditor’s ChoiceArticle

SLC16a6, mTORC1, and Autophagy Regulate Ketone Body Excretion in the Intestinal Cells

by Takashi Uebanso, Moeka Fukui, Chisato Naito, Takaaki Shimohata, Kazuaki Mawatari and Akira Takahashi

Biology 2023, 12(12), 1467; https://doi.org/10.3390/biology12121467 - 26 Nov 2023

Cited by 1 | Viewed by 2418

Abstract

Ketone bodies serve several functions in the intestinal epithelium, such as stem cell maintenance, cell proliferation and differentiation, and cancer growth. Nevertheless, there is limited understanding of the mechanisms governing the regulation of intestinal ketone body concentration. In this study, we elucidated the [...] Read more.

Ketone bodies serve several functions in the intestinal epithelium, such as stem cell maintenance, cell proliferation and differentiation, and cancer growth. Nevertheless, there is limited understanding of the mechanisms governing the regulation of intestinal ketone body concentration. In this study, we elucidated the factors responsible for ketone body production and excretion using shRNA-mediated or pharmacological inhibition of specific genes or functions in the intestinal cells. We revealed that a fasting-mimicked culture medium, which excluded glucose, pyruvate, and glutamine, augmented ketone body production and excretion in the Caco2 and HT29 colorectal cells. This effect was attenuated by glucose or glutamine supplementation. On the other hand, the inhibition of the mammalian target of rapamycin complex1 (mTORC1) recovered a fraction of the excreted ketone bodies. In addition, the pharmacological or shbeclin1-mediated inhibition of autophagy suppressed ketone body excretion. The knockdown of basigin, a transmembrane protein responsible for targeting monocarboxylate transporters (MCTs), such as MCT1 and MCT4, suppressed lactic acid and pyruvic acid excretion but increased ketone body excretion. Finally, we found that MCT7 (SLC16a6) knockdown suppressed ketone body excretion. Our findings indicate that the mTORC1–autophagy axis and MCT7 are potential targets to regulate ketone body excretion from the intestinal epithelium. Full article

(This article belongs to the Special Issue The Effect of Food- and Nutrient-Derived Molecules on Cells and Tissue)

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34 pages, 4361 KiB

Open AccessEditor’s ChoiceArticle

Anatomy of the Female Koala Reproductive Tract

by Sara Pagliarani, Chiara Palmieri, Michael McGowan, Frank Carrick, Jackson Boyd and Stephen D. Johnston

Biology 2023, 12(11), 1445; https://doi.org/10.3390/biology12111445 - 17 Nov 2023

Cited by 1 | Viewed by 4729

Abstract

The koala (Phascolarctos cinereus), while being an iconic Australian marsupial, has recently been listed as endangered. To establish an improved understanding of normal reproductive anatomy, this paper brings together unpublished research which has approached the topic from two perspectives: (1) the [...] Read more.

The koala (Phascolarctos cinereus), while being an iconic Australian marsupial, has recently been listed as endangered. To establish an improved understanding of normal reproductive anatomy, this paper brings together unpublished research which has approached the topic from two perspectives: (1) the establishment of an artificial insemination program, and (2) the definition of Chlamydia spp.-derived histopathological changes of the female koala urogenital system. Based on the presentation and histological processing of over 70 opportunistic specimens, recovered from wildlife hospitals in Southeast Queensland (Australia), we describe the gross and microanatomy of the koala ovary, oviduct, uteri, vaginal complex, and urogenital sinus during the interestrous, proliferative, and luteal phases of the reproductive cycle. Full article

(This article belongs to the Section Developmental and Reproductive Biology)

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15 pages, 3055 KiB

Open AccessEditor’s ChoiceReview

Iron Homeostasis in Azotobacter vinelandii

by Elena Rosa-Núñez, Carlos Echavarri-Erasun, Alejandro M. Armas, Viviana Escudero, César Poza-Carrión, Luis M. Rubio and Manuel González-Guerrero

Biology 2023, 12(11), 1423; https://doi.org/10.3390/biology12111423 - 12 Nov 2023

Viewed by 2046

Abstract

Iron is an essential nutrient for all life forms. Specialized mechanisms exist in bacteria to ensure iron uptake and its delivery to key enzymes within the cell, while preventing toxicity. Iron uptake and exchange networks must adapt to the different environmental conditions, particularly [...] Read more.

Iron is an essential nutrient for all life forms. Specialized mechanisms exist in bacteria to ensure iron uptake and its delivery to key enzymes within the cell, while preventing toxicity. Iron uptake and exchange networks must adapt to the different environmental conditions, particularly those that require the biosynthesis of multiple iron proteins, such as nitrogen fixation. In this review, we outline the mechanisms that the model diazotrophic bacterium Azotobacter vinelandii uses to ensure iron nutrition and how it adapts Fe metabolism to diazotrophic growth. Full article

(This article belongs to the Special Issue 18th SEFIN Meeting and 1st Spanish-Portuguese Congress on Beneficial Plant-Microorganism Interactions)

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20 pages, 3870 KiB

Open AccessEditor’s ChoiceReview

The Skin and Inflamm-Aging

by Rashi Agrawal, Anne Hu and Wendy B. Bollag

Biology 2023, 12(11), 1396; https://doi.org/10.3390/biology12111396 - 2 Nov 2023

Cited by 20 | Viewed by 6971

Abstract

With its unique anatomical location facing both the external and internal environment, the skin has crucial functions, including shielding the body from damage caused by ultraviolet radiation and chemicals, preventing water loss, acting as a primary barrier against pathogens, participating in metabolic processes [...] Read more.

With its unique anatomical location facing both the external and internal environment, the skin has crucial functions, including shielding the body from damage caused by ultraviolet radiation and chemicals, preventing water loss, acting as a primary barrier against pathogens, participating in metabolic processes like vitamin D production and temperature control and relaying information to the body through sensory and proprioceptor nerves. Like all organ systems, skin is known to undergo multiple changes with aging. A better understanding of the mechanisms that mediate aging-related skin dysfunction may allow the creation of targeted therapeutics that have beneficial effects not only on aged skin but also on other organs and tissues that experience a loss of or decline in function with aging. The skin is the largest organ of the body and can contribute to serum inflammatory mediator levels. One alteration known to occur with age is an impairment of skin barrier function; since disruption of the barrier is known to induce inflammation, skin may be a major contributor to the sustained, sub-clinical systemic inflammation associated with aging. Such “inflamm-aging” may underlie many of the deleterious changes observed in aged individuals. This review explores the role of age-related skin changes, skin inflammation and inflamm-aging. Full article

(This article belongs to the Collection Molecular Mechanisms of Aging)

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18 pages, 385 KiB

Open AccessEditor’s ChoiceReview

Telomere Dynamics in Livestock

by Nan Zhang, Emilie C. Baker, Thomas H. Welsh, Jr. and David G. Riley

Biology 2023, 12(11), 1389; https://doi.org/10.3390/biology12111389 - 31 Oct 2023

Cited by 2 | Viewed by 2544

Abstract

Telomeres are repeated sequences of nucleotides at the end of chromosomes. They deteriorate across mitotic divisions of a cell. In Homo sapiens this process of lifetime reduction has been shown to correspond with aspects of organismal aging and exposure to stress or other [...] Read more.

Telomeres are repeated sequences of nucleotides at the end of chromosomes. They deteriorate across mitotic divisions of a cell. In Homo sapiens this process of lifetime reduction has been shown to correspond with aspects of organismal aging and exposure to stress or other insults. The early impetus to characterize telomere dynamics in livestock related to the concern that aged donor DNA would result in earlier cell senescence and overall aging in cloned animals. Telomere length investigations in dairy cows included breed effects, estimates of additive genetic control (heritability 0.12 to 0.46), and effects of external stressors on telomere degradation across animal life. Evaluation of telomeres with respect to aging has also been conducted in pigs and horses, and there are fewer reports of telomere biology in beef cattle, sheep, and goats. There were minimal associations of telomere length with animal productivity measures. Most, but not all, work in livestock has documented an inverse relationship between peripheral blood cell telomere length and age; that is, a longer telomere length was associated with younger age. Because livestock longevity affects productivity and profitability, the role of tissue-specific telomere attrition in aging may present alternative improvement strategies for genetic improvement while also providing translational biomedical knowledge. Full article

(This article belongs to the Section Biotechnology)

21 pages, 957 KiB

Open AccessEditor’s ChoiceReview

Prevalence of Cobalt in the Environment and Its Role in Biological Processes

by Giuseppe Genchi, Graziantonio Lauria, Alessia Catalano, Alessia Carocci and Maria Stefania Sinicropi

Biology 2023, 12(10), 1335; https://doi.org/10.3390/biology12101335 - 16 Oct 2023

Cited by 16 | Viewed by 5630

Abstract

Cobalt (Co) is an essential trace element for humans and other animals, but high doses can be harmful to human health. It is present in some foods such as green vegetables, various spices, meat, milk products, seafood, and eggs, and in drinking water. [...] Read more.

Cobalt (Co) is an essential trace element for humans and other animals, but high doses can be harmful to human health. It is present in some foods such as green vegetables, various spices, meat, milk products, seafood, and eggs, and in drinking water. Co is necessary for the metabolism of human beings and animals due to its key role in the formation of vitamin B₁₂, also known as cobalamin, the biological reservoir of Co. In high concentrations, Co may cause some health issues such as vomiting, nausea, diarrhea, bleeding, low blood pressure, heart diseases, thyroid damage, hair loss, bone defects, and the inhibition of some enzyme activities. Conversely, Co deficiency can lead to anorexia, chronic swelling, and detrimental anemia. Co nanoparticles have different and various biomedical applications thanks to their antioxidant, antimicrobial, anticancer, and antidiabetic properties. In addition, Co and cobalt oxide nanoparticles can be used in lithium-ion batteries, as a catalyst, a carrier for targeted drug delivery, a gas sensor, an electronic thin film, and in energy storage. Accumulation of Co in agriculture and humans, due to natural and anthropogenic factors, represents a global problem affecting water quality and human and animal health. Besides the common chelating agents used for Co intoxication, phytoremediation is an interesting environmental technology for cleaning up soil contaminated with Co. The occurrence of Co in the environment is discussed and its involvement in biological processes is underlined. Toxicological aspects related to Co are also examined in this review. Full article

(This article belongs to the Special Issue Essential Trace Elements in the Human Metabolism)

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23 pages, 2259 KiB

Open AccessEditor’s ChoiceReview

Bioactive Components in Fruit Interact with Gut Microbes

by Yuanyuan Jin, Ling Chen, Yufen Yu, Muhammad Hussain and Hao Zhong

Biology 2023, 12(10), 1333; https://doi.org/10.3390/biology12101333 - 13 Oct 2023

Cited by 4 | Viewed by 2771

Abstract

Fruits contain many bioactive compounds, including polysaccharides, oligosaccharides, polyphenols, anthocyanins, and flavonoids. All of these bioactives in fruit have potentially beneficial effects on gut microbiota and host health. On the one hand, fruit rich in active ingredients can act as substrates to interact [...] Read more.

Fruits contain many bioactive compounds, including polysaccharides, oligosaccharides, polyphenols, anthocyanins, and flavonoids. All of these bioactives in fruit have potentially beneficial effects on gut microbiota and host health. On the one hand, fruit rich in active ingredients can act as substrates to interact with microorganisms and produce metabolites to regulate the gut microbiota. On the other hand, gut microbes could promote health effects in the host by balancing dysbiosis of gut microbiota. We have extensively analyzed significant information on bioactive components in fruits based on Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA). Although the deep mechanism of action of bioactive components in fruits on gut microbiota needs further study, these results also provide supportive information on fruits as a source of dietary active ingredients to provide support for the adjunctive role of fruits in disease prevention and treatment. Full article

(This article belongs to the Special Issue Gut Microbiome in Health and Disease)

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23 pages, 2416 KiB

Open AccessEditor’s ChoiceReview

An Overview of D7 Protein Structure and Physiological Roles in Blood-Feeding Nematocera

by Patricia H. Alvarenga and John F. Andersen

Biology 2023, 12(1), 39; https://doi.org/10.3390/biology12010039 - 26 Dec 2022

Cited by 3 | Viewed by 2724

Abstract

Each time an insect bites a vertebrate host, skin and vascular injury caused by piercing triggers a series of responses including hemostasis, inflammation and immunity. In place, this set of redundant and interconnected responses would ultimately cause blood coagulation, itching and pain leading [...] Read more.

Each time an insect bites a vertebrate host, skin and vascular injury caused by piercing triggers a series of responses including hemostasis, inflammation and immunity. In place, this set of redundant and interconnected responses would ultimately cause blood coagulation, itching and pain leading to host awareness, resulting in feeding interruption in the best-case scenario. Nevertheless, hematophagous arthropod saliva contains a complex cocktail of molecules that are crucial to the success of blood-feeding. Among important protein families described so far in the saliva of blood sucking arthropods, is the D7, abundantly expressed in blood feeding Nematocera. D7 proteins are distantly related to insect Odorant-Binding Proteins (OBP), and despite low sequence identity, observation of structural similarity led to the suggestion that like OBPs, they should bind/sequester small hydrophobic compounds. Members belonging to this family are divided in short forms and long forms, containing one or two OBP-like domains, respectively. Here, we provide a review of D7 proteins structure and function, discussing how gene duplication and some modifications in their OBP-like domains during the course of evolution lead to gain and loss of function among different hematophagous Diptera species. Full article

(This article belongs to the Special Issue New Sights in Odorant-Binding Proteins)

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14 pages, 2621 KiB

Open AccessEditor’s ChoiceArticle

Linoleate-Enrichment of Mitochondrial Cardiolipin Molecular Species Is Developmentally Regulated and a Determinant of Metabolic Phenotype

by Genevieve C. Sparagna, Raleigh L. Jonscher, Sydney R. Shuff, Elisabeth K. Phillips, Cortney E. Wilson, Kathleen C. Woulfe, Anastacia M. Garcia, Brian L. Stauffer and Kathryn C. Chatfield

Biology 2023, 12(1), 32; https://doi.org/10.3390/biology12010032 - 24 Dec 2022

Cited by 2 | Viewed by 2391

Abstract

Cardiolipin (CL), the major mitochondrial phospholipid, regulates the activity of many mitochondrial membrane proteins. CL composition is shifted in heart failure with decreases in linoleate and increases in oleate side chains, but whether cardiolipin composition directly regulates metabolism is unknown. This study defines [...] Read more.

Cardiolipin (CL), the major mitochondrial phospholipid, regulates the activity of many mitochondrial membrane proteins. CL composition is shifted in heart failure with decreases in linoleate and increases in oleate side chains, but whether cardiolipin composition directly regulates metabolism is unknown. This study defines cardiolipin composition in rat heart and liver at three distinct ages to determine the influence of CL composition on beta-oxidation (ß-OX). CL species, expression of ß-OX and glycolytic genes, and carnitine palmitoyltransferase (CPT) activity were characterized in heart and liver from neonatal, juvenile, and adult rats. Ventricular myocytes were cultured from neonatal, juvenile, and adult rats and cardiolipin composition and CPT activity were measured. Cardiolipin composition in neonatal rat ventricular cardiomyocytes (NRVMs) was experimentally altered and mitochondrial respiration was assessed. Linoleate-enrichment of CL was observed in rat heart, but not liver, with increasing age. ß-OX genes and CPT activity were generally higher in adult heart and glycolytic genes lower, as a function of age, in contrast to liver. Palmitate oxidation increased in NRVMs when CL was enriched with linoleate. Our results indicate (1) CL is developmentally regulated, (2) linoleate-enrichment is associated with increased ß-OX and a more oxidative mitochondrial phenotype, and (3) experimentally induced linoleate-enriched CL in ventricular myocytes promotes a shift from pyruvate metabolism to fatty acid ß-OX. Full article

(This article belongs to the Special Issue The Role of Cardiolipin in Mitochondrial Health and Disease)

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15 pages, 2965 KiB

Open AccessEditor’s ChoiceArticle

Methionine Metabolism Is Down-Regulated in Heart of Long-Lived Mammals

by Natalia Mota-Martorell, Mariona Jové, Rebeca Berdún, Èlia Òbis, Gustavo Barja and Reinald Pamplona

Biology 2022, 11(12), 1821; https://doi.org/10.3390/biology11121821 - 14 Dec 2022

Cited by 3 | Viewed by 2773

Abstract

Methionine constitutes a central hub of intracellular metabolic adaptations leading to an extended longevity (maximum lifespan). The present study follows a comparative approach analyzing methionine and related metabolite and amino acid profiles using an LC-MS/MS platform in the hearts of seven mammalian species [...] Read more.

Methionine constitutes a central hub of intracellular metabolic adaptations leading to an extended longevity (maximum lifespan). The present study follows a comparative approach analyzing methionine and related metabolite and amino acid profiles using an LC-MS/MS platform in the hearts of seven mammalian species with a longevity ranging from 3.8 to 57 years. Our findings demonstrate the existence of species-specific heart phenotypes associated with high longevity characterized by: (i) low concentration of methionine and its related sulphur-containing metabolites; (ii) low amino acid pool; and (iii) low choline concentration. Our results support the existence of heart metabotypes characterized by a down-regulation in long-lived species, supporting the idea that in longevity, less is more. Full article

(This article belongs to the Special Issue Genetic and Epigenetic Mechanisms of Longevity and Aging)

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