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Biology, Volume 12, Issue 11 (November 2023) – 93 articles

Cover Story (view full-size image): Telomeres, the protective endcaps of chromosomes, are repeated nucleotide sequences that progressively shorten across cell divisions; therefore, telomere length is considered an aging marker or an indicator of potential life span. Longevity affects profitability in livestock production systems. Recent studies on livestock report longer telomeres in younger animals, and that inflammatory events shorten telomeres. The identification of factors that affect telomere dynamics (e.g., attrition and repair) will complement genetic strategies to improve animal well-being and the profitability of livestock production systems. View this paper
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32 pages, 2200 KiB  
Review
Polyherbal and Multimodal Treatments: Kaempferol- and Quercetin-Rich Herbs Alleviate Symptoms of Alzheimer’s Disease
Biology 2023, 12(11), 1453; https://doi.org/10.3390/biology12111453 - 20 Nov 2023
Viewed by 2053
Abstract
Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder impairing cognition and memory in the elderly. This disorder has a complex etiology, including senile plaque and neurofibrillary tangle formation, neuroinflammation, oxidative stress, and damaged neuroplasticity. Current treatment options are limited, so alternative treatments such [...] Read more.
Alzheimer’s Disease (AD) is a progressive neurodegenerative disorder impairing cognition and memory in the elderly. This disorder has a complex etiology, including senile plaque and neurofibrillary tangle formation, neuroinflammation, oxidative stress, and damaged neuroplasticity. Current treatment options are limited, so alternative treatments such as herbal medicine could suppress symptoms while slowing cognitive decline. We followed PRISMA guidelines to identify potential herbal treatments, their associated medicinal phytochemicals, and the potential mechanisms of these treatments. Common herbs, including Ginkgo biloba, Camellia sinensis, Glycyrrhiza uralensis, Cyperus rotundus, and Buplerum falcatum, produced promising pre-clinical results. These herbs are rich in kaempferol and quercetin, flavonoids with a polyphenolic structure that facilitate multiple mechanisms of action. These mechanisms include the inhibition of Aβ plaque formation, a reduction in tau hyperphosphorylation, the suppression of oxidative stress, and the modulation of BDNF and PI3K/AKT pathways. Using pre-clinical findings from quercetin research and the comparatively limited data on kaempferol, we proposed that kaempferol ameliorates the neuroinflammatory state, maintains proper cellular function, and restores pro-neuroplastic signaling. In this review, we discuss the anti-AD mechanisms of quercetin and kaempferol and their limitations, and we suggest a potential alternative treatment for AD. Our findings lead us to conclude that a polyherbal kaempferol- and quercetin-rich cocktail could treat AD-related brain damage. Full article
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12 pages, 1945 KiB  
Review
Heteroplasmy and Individual Mitogene Pools: Characteristics and Potential Roles in Ecological Studies
Biology 2023, 12(11), 1452; https://doi.org/10.3390/biology12111452 - 20 Nov 2023
Viewed by 1027
Abstract
The mitochondrial genome (mitogenome or mtDNA), the extrachromosomal genome, is a multicopy circular DNA with high mutation rates due to replication and repair errors. A mitochondrion, cell, tissue, organ, or an individual body may hold multiple variants, both inherited and developed over a [...] Read more.
The mitochondrial genome (mitogenome or mtDNA), the extrachromosomal genome, is a multicopy circular DNA with high mutation rates due to replication and repair errors. A mitochondrion, cell, tissue, organ, or an individual body may hold multiple variants, both inherited and developed over a lifetime, which make up individual mitogene pools. This phenomenon is also called mtDNA heteroplasmy. MtDNA variants influence cellular and tissular functions and are consequently subjected to selection. Although it has long been recognized that only inheritable germline heteroplasmies have evolutionary significance, non-inheritable somatic heteroplasmies have been overlooked since they directly affect individual fitness and thus indirectly affect the fate of heritable germline variants. This review focuses on the characteristics, dynamics, and functions of mtDNA heteroplasmy and proposes the concept of individual mitogene pools to discuss individual genetic diversity from multiple angles. We provide a unique perspective on the relationship between individual genetic diversity and heritable genetic diversity and guide how the individual mitogene pool with novel genetic markers can be applied to ecological research. Full article
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17 pages, 5607 KiB  
Article
The Influence of the Long-Term Outdoor Storage of Rockrose (Cistus laurifolius L.) Shrub Biomass on Biofuel’s Quality, Pre-Treatment and Combustion Processes
Biology 2023, 12(11), 1451; https://doi.org/10.3390/biology12111451 - 19 Nov 2023
Viewed by 842
Abstract
Biomass storage is an essential requirement in the supply chain of bio-refineries and power plants. This research aims to evaluate the influence of long-term outdoor storage (1 year) of baled rockrose (Cistus laurifolius L.) shrub biomass on biofuel’s quality, pre-treatment processes and [...] Read more.
Biomass storage is an essential requirement in the supply chain of bio-refineries and power plants. This research aims to evaluate the influence of long-term outdoor storage (1 year) of baled rockrose (Cistus laurifolius L.) shrub biomass on biofuel’s quality, pre-treatment processes and on combustion emissions in an industrial boiler. The raw material was obtained from different rockrose shrublands in north central Spain. A total of 233 tWM (tones of wet matter) of biomass were used to produce biofuels (30 mm of milled biomass and Ø 8 mm pellets) in the pre-treatment pilot plants at CEDER-CIEMAT. The combustion tests were conducted in an industrial moving grate boiler with a thermal power of 50 MWth, in a 17 MWe power plant. Outdoor storage improved some biofuel quality parameters, mainly the reduction in ash content, which allowed 30 mm of milled material to be classified as class I1 (ISO 17225-9:2022) and pellets as class I3 (ISO 17225-2-2021). No significant differences were observed in the total specific mass flow and energy consumption in the pre-treatment processes. The combustion tests had similar results, with the emissions being below the limits established in the directive (EU) 2015/2193. The results obtained indicated that the 1-year outdoor storage of rockrose-baled biomass, under Mediterranean conditions, was feasible for its subsequent use as biofuel. Full article
(This article belongs to the Section Biotechnology)
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16 pages, 361 KiB  
Review
The Molecular Mechanisms of Fuel Utilization during Exercise
Biology 2023, 12(11), 1450; https://doi.org/10.3390/biology12111450 - 19 Nov 2023
Cited by 1 | Viewed by 1215
Abstract
Exercise is widely recognized for its positive impact on human health and well-being. The process of utilizing substrates in skeletal muscle during exercise is intricate and governed by complex mechanisms. Carbohydrates and lipids serve as the primary fuel sources for skeletal muscle during [...] Read more.
Exercise is widely recognized for its positive impact on human health and well-being. The process of utilizing substrates in skeletal muscle during exercise is intricate and governed by complex mechanisms. Carbohydrates and lipids serve as the primary fuel sources for skeletal muscle during exercise. It is now understood that fuel selection during exercise is not solely determined by physical activity itself but is also influenced by the overall metabolic state of the body. The balance between lipid and carbohydrate utilization significantly affects exercise capacity, including endurance, fatigue, and overall performance. Therefore, comprehensively understanding the regulation of substrate utilization during exercise is of utmost importance. The aim of this review is to provide an extensive overview of the current knowledge regarding the pathways involved in the regulation of substrate utilization during exercise. By synthesizing existing research, we can gain a holistic perspective on the intricate relationship between exercise, metabolism, and fuel selection. This advanced understanding has the potential to drive advancements in the field of exercise science and contribute to the development of personalized exercise strategies for individuals looking to optimize their performance and overall health. Full article
22 pages, 6032 KiB  
Article
Assemblage Structure of Ichthyoplankton Communities in the Southern Adriatic Sea (Eastern Mediterranean)
Biology 2023, 12(11), 1449; https://doi.org/10.3390/biology12111449 - 19 Nov 2023
Viewed by 782
Abstract
Studies based on fish early life stages can provide information on spawning grounds and nursery areas, helping to determine the implications for stock biomass fluctuations of recruitment variability. This study describes the composition, abundance, spatial distribution and differences in day/night vertical distribution of [...] Read more.
Studies based on fish early life stages can provide information on spawning grounds and nursery areas, helping to determine the implications for stock biomass fluctuations of recruitment variability. This study describes the composition, abundance, spatial distribution and differences in day/night vertical distribution of ichthyoplankton in the southern Adriatic Sea. Samples were collected within the framework of the COCONET project (Towards COast to COast NETworks of marine protected areas) from 9 to 18 May 2013 by the R/V Urania, using the electronic multinet EZ-NET BIONESS (Bedford Institute of Oceanography Net Environmental Sampling System). A total of 20 species, belonging to 20 genera and 13 families, were identified. Of the collected larvae, 74.3% were meso- or bathypelagic species, 24.7% were epipelagic and 0.9% were demersal. The community was dominated by Gonostomatidae, followed by Engraulidae, Myctophidae and Photychthaidae. The most abundant species was Cyclothone braueri (45.6%), followed by Engraulis encrasicolus, Ceratoscopelus maderensis, Cyclothone pygmaea, Vinciguerria attenuata and Myctophum punctatum. An inshore/offshore increasing gradient in biodiversity and abundance was observed. Different weighted mean depths (WMDs) were observed for larvae and juveniles. No diel vertical migrations were observed. The high abundance of meso- or bathypelagic species in the upper 100 m confirms the epipelagic zone as an important environment for the development of the larval stages of these fish. Full article
(This article belongs to the Section Marine Biology)
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15 pages, 9759 KiB  
Article
Identification of N6-Methyladenosine-Related Factors and the Prediction of the Regulatory Mechanism of Hair Follicle Development in Rex and Hycole Rabbits
Biology 2023, 12(11), 1448; https://doi.org/10.3390/biology12111448 - 17 Nov 2023
Viewed by 1051
Abstract
Hair follicle development directly affects the development of the rabbit fur industry. The growth and development of a hair follicle is modified and regulated by many genes and mechanisms. M6A is an important RNA modification. However, there are few studies on [...] Read more.
Hair follicle development directly affects the development of the rabbit fur industry. The growth and development of a hair follicle is modified and regulated by many genes and mechanisms. M6A is an important RNA modification. However, there are few studies on the effects of the regulation of m6A on hair follicle growth and development. In this study, hematoxylin–eosin (HE) staining was used to explore the difference in hair follicle development between Rex rabbits and Hycole rabbits, and we performed m6A sequencing to identify the key genes with m6A modification in hair follicle growth. The results showed that the hair length, coarse hair percentage, primary hair follicle ratio, and skin thickness of Hycole rabbits were significantly higher than those of Rex rabbits. However, the proportion of secondary hair follicles in Hycole rabbits was significantly lower than that in Rex rabbits. In addition, we found five differential methylases, 20 differential genes, and 24 differential signaling pathways related to hair growth and development. The results of the Sankey diagram showed that 12 genes were related to 13 signal pathways. Finally, we found that five methylases regulated the development of hair follicles through differential genes/signal pathways. These findings laid a molecular foundation for the function of m6A modification in hair development. Full article
(This article belongs to the Section Developmental Biology)
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19 pages, 2590 KiB  
Article
Pilot-Scale Fermentation of Pseudoalteromonas sp. Strain FDHY-MZ2: An Effective Strategy for Increasing Algicidal Activity
Biology 2023, 12(11), 1447; https://doi.org/10.3390/biology12111447 - 17 Nov 2023
Viewed by 968
Abstract
The role of microorganisms in effectively terminating harmful algal blooms (HABs) is crucial for maintaining environmental stability. Recent studies have placed increased emphasis on bio-agents capable of inhibiting HABs. The bacterium Pseudoalteromonas sp. strain FDHY-MZ2 has exhibited impressive algicidal abilities against Karenia mikimotoi [...] Read more.
The role of microorganisms in effectively terminating harmful algal blooms (HABs) is crucial for maintaining environmental stability. Recent studies have placed increased emphasis on bio-agents capable of inhibiting HABs. The bacterium Pseudoalteromonas sp. strain FDHY-MZ2 has exhibited impressive algicidal abilities against Karenia mikimotoi, a notorious global HAB-forming species. To augment this capability, cultures were progressively scaled from shake flask conditions to small-scale (5 L) and pilot-scale (50 L) fermentation. By employing a specifically tailored culture medium (2216E basal medium with 1.5% soluble starch and 0.5% peptone), under precise conditions (66 h, 20 °C, 450 rpm, 30 L/min ventilation, 3% seeding, and constant starch flow), a notable increase in algicidal bacterial biomass was observed; the bacterial dosage required to entirely wipe out K. mikimotoi within a day decreased from 1% to 0.025%. Compared to an unoptimized shake flask group, the optimized fermentation culture caused significant reductions in algal chlorophyll and protein levels (21.85% and 78.3%, respectively). Co-culturing induced increases in algal malondialdehyde and H2O2 by 5.98 and 5.38 times, respectively, leading to further disruption of algal photosynthesis. This study underscores the unexplored potential of systematically utilized microbial agents in mitigating HABs, providing a pathway for their wider application. Full article
(This article belongs to the Special Issue Biology, Ecology and Management of Harmful Algae)
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21 pages, 2051 KiB  
Article
Comparing Seamounts and Coral Reefs with eDNA and BRUVS Reveals Oases and Refuges on Shallow Seamounts
Biology 2023, 12(11), 1446; https://doi.org/10.3390/biology12111446 - 17 Nov 2023
Viewed by 1220
Abstract
Seamounts are the least known ocean biome. Considered biodiversity hotspots, biomass oases, and refuges for megafauna, large gaps exist in their real diversity relative to other ecosystems like coral reefs. Using environmental DNA metabarcoding (eDNA) and baited video (BRUVS), we compared fish assemblages [...] Read more.
Seamounts are the least known ocean biome. Considered biodiversity hotspots, biomass oases, and refuges for megafauna, large gaps exist in their real diversity relative to other ecosystems like coral reefs. Using environmental DNA metabarcoding (eDNA) and baited video (BRUVS), we compared fish assemblages across five environments of different depths: coral reefs (15 m), shallow seamounts (50 m), continental slopes (150 m), intermediate seamounts (250 m), and deep seamounts (500 m). We modeled assemblages using 12 environmental variables and found depth to be the main driver of fish diversity and biomass, although other variables like human accessibility were important. Boosted Regression Trees (BRT) revealed a strong negative effect of depth on species richness, segregating coral reefs from deep-sea environments. Surprisingly, BRT showed a hump-shaped effect of depth on fish biomass, with significantly lower biomass on coral reefs than in shallowest deep-sea environments. Biomass of large predators like sharks was three times higher on shallow seamounts (50 m) than on coral reefs. The five studied environments showed quite distinct assemblages. However, species shared between coral reefs and deeper-sea environments were dominated by highly mobile large predators. Our results suggest that seamounts are no diversity hotspots for fish. However, we show that shallower seamounts form biomass oases and refuges for threatened megafauna, suggesting that priority should be given to their protection. Full article
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34 pages, 4361 KiB  
Article
Anatomy of the Female Koala Reproductive Tract
Biology 2023, 12(11), 1445; https://doi.org/10.3390/biology12111445 - 17 Nov 2023
Viewed by 1496
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 Reproductive Biology)
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15 pages, 5749 KiB  
Article
An Evaluation of Suitable Habitats for Amur Tigers (Panthera tigris altaica) in Northeastern China Based on the Random Forest Model
Biology 2023, 12(11), 1444; https://doi.org/10.3390/biology12111444 - 17 Nov 2023
Viewed by 997
Abstract
Amur tigers are at the top of the food chain and play an important role in maintaining the health of forest ecosystems. Scientific and detailed assessment of the habitat quality of Amur tigers in China is the key to maintaining the forest ecosystem [...] Read more.
Amur tigers are at the top of the food chain and play an important role in maintaining the health of forest ecosystems. Scientific and detailed assessment of the habitat quality of Amur tigers in China is the key to maintaining the forest ecosystem and also addressing the urgent need to protect and restore the wild population of Amur tigers in China. This study used the random forest method to predict the potential habitat of Amur tigers in Heilongjiang and Jilin provinces using animal occurrence sites and a variety of environmental variables. Random forests are a combination of tree predictors such that each tree depends on the values of a random vector sampled independently and with the same distribution for all trees in the forest. The generalization error for forests converges to a limit as the number of trees in the forest becomes large. The generalization error of a forest of tree classifiers depends on the strength of the individual trees in the forest and the correlation between them. The results showed that the AUC value of the test set was 0.955. The true skill statistic (TSS) value is 0.5924, indicating that the model had good prediction accuracy. Using the optimal threshold determined by the Youden index as the cutoff value, we found that the suitable habitat for Amur tigers in the field was approximately 107,600 km2, accounting for 16.3% of the total study areas. It was mainly distributed in the Sino-Russian border areas in the south of the Laoyeling Mountains at the junction of Jilin and Heilongjiang provinces, the Sino-Russian border areas of Hulin–Raohe in the eastern part of the Wanda Mountains, and the Lesser Khingan Mountain forest region. The habitat suitability of the Greater Khingan Mountain and the plain areas connecting Harbin and Changchun was relatively low. Prey potential richness was the most critical factor driving the distribution of Amur tigers. Compared with their prey, the potential habitats for Amur tigers in Heilongjiang and Jilin provinces were small in total areas, sporadically distributed, and had low continuity and a lack of connectivity between patches. This indicates that some factors may restrict the diffusion of the Amur tiger, whereas the diffusion of ungulates is less restricted. The Amur tigers in this area face a serious threat of habitat fragmentation, suggesting that habitat protection, restoration, and ecological corridor construction should be strengthened to increase population dispersal and exchange. We provide a reference for future population conservation, habitat restoration, construction of ecological migration corridors, and population exchange of Amur tigers. Full article
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11 pages, 1551 KiB  
Communication
Combination of Host-Associated Rummeliibacillus sp. and Microbacterium sp. Positively Modulated the Growth, Feed Utilization, and Intestinal Microbial Population of Olive Flounder (Paralichthys olivaceus)
Biology 2023, 12(11), 1443; https://doi.org/10.3390/biology12111443 - 17 Nov 2023
Viewed by 842
Abstract
Two novel strains of Rummeliibacillus sp. and Microbacterium sp. were identified from the intestine of olive flounder (Paralichthys olivaceus) and characterized in vitro as potential probiotics. Feeds without probiotic and with a 50:50 mixture of these two strains (1 × 10 [...] Read more.
Two novel strains of Rummeliibacillus sp. and Microbacterium sp. were identified from the intestine of olive flounder (Paralichthys olivaceus) and characterized in vitro as potential probiotics. Feeds without probiotic and with a 50:50 mixture of these two strains (1 × 108 CFU/g feed) were denoted as the control and Pro diets, respectively. Three randomly selected tanks (20 flounders/tank, ~11.4 g each) were used for each diet replication. After 8 weeks of feeding, the growth and feed utilization of the flounder in the Pro group improved (p < 0.05) compared to the control. Among four immune parameters, only myeloperoxidase activity was elevated in the Pro group. Serum biochemistry, intestinal microbial richness (Chao1), and diversity (Shannon index) remained unchanged (p ≥ 0.05), but phylogenetic diversity was enriched in the Pro fish intestine. Significantly lower Firmicutes and higher Proteobacteria were found in the Pro diet; the genus abundance in the control and Pro was as follows: Staphylococcus > Lactobacillus > Corynebacterium and Lactobacillus > Staphylococcus > Corynebacterium, respectively. Microbial linear discriminant scores and a cladogram analysis showed significant modulation. Therefore, the combination of two host-associated probiotics improved the growth and intestinal microbial population of flounder and could be supplemented in the Korean flounder industry. Full article
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14 pages, 2732 KiB  
Article
Novel Covalent Modifier-Induced Local Conformational Changes within the Intrinsically Disordered Region of the Androgen Receptor
Biology 2023, 12(11), 1442; https://doi.org/10.3390/biology12111442 - 17 Nov 2023
Viewed by 1080
Abstract
Intrinsically disordered regions (IDRs) of transcription factors play an important biological role in liquid condensate formation and gene regulation. It is thus desirable to investigate the druggability of IDRs and how small-molecule binders can alter their conformational stability. For the androgen receptor (AR), [...] Read more.
Intrinsically disordered regions (IDRs) of transcription factors play an important biological role in liquid condensate formation and gene regulation. It is thus desirable to investigate the druggability of IDRs and how small-molecule binders can alter their conformational stability. For the androgen receptor (AR), certain covalent ligands induce important changes, such as the neutralization of the condensate. To understand the specificity of ligand–IDR interaction and potential implications for the mechanism of neutralizing liquid–liquid phase separation (LLPS), we modeled and performed computer simulations of ligand-bound peptide segments obtained from the human AR. We analyzed how different covalent ligands affect local secondary structure, protein contact map, and protein–ligand contacts for these protein systems. We find that effective neutralizers make specific interactions (such as those between cyanopyrazole and tryptophan) that alter the helical propensity of the peptide segments. These findings on the mechanism of action can be useful for designing molecules that influence IDR structure and condensate of the AR in the future. Full article
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11 pages, 1463 KiB  
Article
Prostaglandin E2 Boosts the Hyaluronan-Mediated Increase in Inflammatory Response to Lipopolysaccharide by Enhancing Lyve1 Expression
Biology 2023, 12(11), 1441; https://doi.org/10.3390/biology12111441 - 16 Nov 2023
Viewed by 941
Abstract
Macrophages are a highly versatile and heterogenic group of immune cells, known for their involvement in inflammatory reactions. However, our knowledge about distinct subpopulations of macrophages and their specific contribution to the resolution of inflammation remains incomplete. We have previously shown, in an [...] Read more.
Macrophages are a highly versatile and heterogenic group of immune cells, known for their involvement in inflammatory reactions. However, our knowledge about distinct subpopulations of macrophages and their specific contribution to the resolution of inflammation remains incomplete. We have previously shown, in an in vivo peritonitis model, that inhibition of the synthesis of the pro-inflammatory lipid mediator prostaglandin E2 (PGE2) attenuates efficient resolution of inflammation. PGE2 levels during later stages of the inflammatory process further correlate with expression of the hyaluronan (HA) receptor Lyve1 in peritoneal macrophages. In the present study, we therefore aimed to understand if PGE2 might contribute to the regulation of Lyve1 and how this might impact inflammatory responses. In line with our in vivo findings, PGE2 synergized with dexamethasone to enhance Lyve1 expression in bone marrow-derived macrophages, while expression of the predominant hyaluronan receptor CD44 remained unaltered. PGE2-mediated Lyve1 upregulation was strictly dependent on PGE2 receptor EP2 signaling. While PGE2/dexamethasone-treated macrophages, despite their enhanced Lyve1 expression, did not show inflammatory responses upon stimulation with low (LMW) or high-molecular-weight hyaluronan (HMW)-HA, they were sensitized towards LMW-HA-dependent augmentation of lipopolysaccharide (LPS)-induced inflammatory responses. Thus, Lyve1-expressing macrophages emerged as a subpopulation of macrophages integrating inflammatory stimuli with extracellular matrix-derived signals. Full article
(This article belongs to the Special Issue Macrophages and Antimicrobial Immune Response)
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15 pages, 3720 KiB  
Article
Simulation Modeling Unveils the Unalike Effects of Alternative Strategies for Waterbird Conservation in the Coastal Wetlands of Sardinia (Italy)
Biology 2023, 12(11), 1440; https://doi.org/10.3390/biology12111440 - 16 Nov 2023
Viewed by 765
Abstract
The Sardinian wetlands (Italy) act as stopover sites for many migratory birds along the central eastern Mediterranean bird flyway. These wetlands are now severely threatened by human activities and climate change. Accordingly, we built a simulation framework to predict the effects of several [...] Read more.
The Sardinian wetlands (Italy) act as stopover sites for many migratory birds along the central eastern Mediterranean bird flyway. These wetlands are now severely threatened by human activities and climate change. Accordingly, we built a simulation framework to predict the effects of several counterfactual and management scenarios on the level of avian diversity in the coastal wetlands of Sardinia. We found that the alpha avian diversity (i.e., the mean number of avian species per wetland) is destined to (a) decrease due to the most likely increase in water salinity, water discharges, and tourism pressure; and (b) halve (from 14.9 to 7.4, with 9 wetlands out of 22 predicted to host only between two and five waterbird species) in the worst possible scenario. However, the results also showed that proper management strategies could prevent and reverse such outcomes. Restrictions on tourism activities, water desalination, prevention of future saltwater intrusions, and the prohibition of water discharges could markedly favor the avian diversity in these wetlands, with an expected increase in the alpha avian diversity from 14.9 to 24.8 (and 10 wetlands out of 22 predicted to host from 29 to 32 waterbird species) in the best possible scenario. The importance of our results could be emphasized in the management plans of these important wetlands, most of which belong to the Natura 2000 network. Full article
(This article belongs to the Section Conservation Biology and Biodiversity)
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15 pages, 2212 KiB  
Article
Toll-like Receptor 9 Gene in the Development of Type 2 Diabetes Mellitus in the Saudi Arabian Population
Biology 2023, 12(11), 1439; https://doi.org/10.3390/biology12111439 - 16 Nov 2023
Viewed by 870
Abstract
Diabetes mellitus is a complex disease with a wide range of manifestations. Diabetes, notably type 2 diabetes mellitus (T2DM), is becoming more common in Saudi Arabia as a result of obesity and an aging population. T2DM is classified as a noncommunicable disease, and [...] Read more.
Diabetes mellitus is a complex disease with a wide range of manifestations. Diabetes, notably type 2 diabetes mellitus (T2DM), is becoming more common in Saudi Arabia as a result of obesity and an aging population. T2DM is classified as a noncommunicable disease, and its incidence in the Saudi population continues to grow as a consequence of socioeconomic changes. Toll-like receptors (TLRs) are innate immune receptors that mediate the inflammatory response in diabetes mellitus. Previous studies have documented the relationship between different SNPs in the TLR9 gene in different forms of diabetes. As a result, the purpose of this study was to investigate the relationship between rs187084, rs352140, and rs5743836 SNPs in the TLR9 gene among T2DM patients in the Saudi population. This was a case-control study that included 100 T2DM cases and 100 control subjects. The three SNPs were identified in the study population (n = 200) using polymerase chain reaction (PCR), restriction enzymes for rs352140, and Sanger sequencing for rs187084 and rs5783836. Next, statistical analyses were performed using various software to determine the association between the SNPs and T2DM. rs187084 and rs5743836 were associated with an increased risk of T2DM development. rs187084 and rs5743836 allelic frequencies were associated with a 3.2 times increased risk of T2DM development (p < 0.05). DBP was associated with T2DM (p = 0.02). rs187084 was associated with TC and HDLc; rs352140 was associated with DBP, HbA1c, and HDLc; rs5743836 was associated with waist (p < 0.05). The CGT haplotype was strongly associated with T2DM (p < 0.003). Gene–gene interaction, graphical presentation, and dendrogram showed the strong association with T2DM patients (p < 0.05). This study concluded that rs187084 and rs5743836 were strongly associated with T2DM in Saudi Arabian patients. This study provides further evidence that SNPs in the TLR9 gene play a significant role in T2DM development in a Saudi community. Full article
(This article belongs to the Special Issue β-Cells at the Center of Type 1 and Type 2 Diabetes)
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24 pages, 17531 KiB  
Article
CardioRVAR: A New R Package and Shiny Application for the Evaluation of Closed-Loop Cardiovascular Interactions
Biology 2023, 12(11), 1438; https://doi.org/10.3390/biology12111438 - 16 Nov 2023
Viewed by 769
Abstract
CardioRVAR is a new R package designed for the complete evaluation of closed-loop cardiovascular interactions and baroreflex sensitivity estimated from continuous non-invasive heart rate and blood pressure recordings. In this work, we highlight the importance of this software tool in the context of [...] Read more.
CardioRVAR is a new R package designed for the complete evaluation of closed-loop cardiovascular interactions and baroreflex sensitivity estimated from continuous non-invasive heart rate and blood pressure recordings. In this work, we highlight the importance of this software tool in the context of human cardiovascular and autonomic neurophysiology. A summary of the main algorithms that CardioRVAR uses are reviewed, and the workflow of this package is also discussed. We present the results obtained from this tool after its application in three clinical settings. These results support the potential clinical and scientific applications of this tool. The open-source tool can be downloaded from a public GitHub repository, as well as its specific Shiny application, CardioRVARapp. The open-source nature of the tool may benefit the future continuation of this work. Full article
(This article belongs to the Special Issue Cardiovascular Autonomic Function: From Bench to Bedside)
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21 pages, 4298 KiB  
Article
Hydroxytyrosol Counteracts Triple Negative Breast Cancer Cell Dissemination via Its Copper Complexing Properties
Biology 2023, 12(11), 1437; https://doi.org/10.3390/biology12111437 - 16 Nov 2023
Viewed by 1051
Abstract
Polyphenols have gained increasing attention for their therapeutic potential, particularly in conditions like cancer, due to their established antioxidant and anti-inflammatory properties. Recent research highlights their ability to bind to transition metals, such as copper. This is particularly noteworthy given the key role [...] Read more.
Polyphenols have gained increasing attention for their therapeutic potential, particularly in conditions like cancer, due to their established antioxidant and anti-inflammatory properties. Recent research highlights their ability to bind to transition metals, such as copper. This is particularly noteworthy given the key role of copper both in the initiation and progression of cancer. Copper can modulate the activity of kinases required for the epithelial–mesenchymal transition (EMT), a process fundamental to tumor cell dissemination. We have previously demonstrated the copper-binding capacity of oleuropein, a secoiridoid found in Olea europaea. In the present study, we investigated the effect of hydroxytyrosol, the primary oleuropein metabolite, on the metastatic potential of three triple-negative breast cancer cell lines (MDA-MB-231, MDA-MB-468, and SUM159). We found that hydroxytyrosol modulated the intracellular copper levels, influencing both the epithelial and mesenchymal markers, by downregulating copper-dependent AKT phosphorylation, a member of the EMT signaling cascade, through Western blot, RT-qPCR, and immunofluorescence. Indeed, by optical spectra, EPR, and in silico approaches, we found that hydroxytyrosol formed a complex with copper, acting as a chelating agent, thus regulating its homeostasis and affecting the copper-dependent signaling cascades. While our results bring to light the copper-chelating properties of hydroxytyrosol capable of countering tumor progression, they also provide further confirmation of the key role of copper in promoting the aggressiveness of triple-negative breast cancer cells. Full article
(This article belongs to the Special Issue Copper Biology in Health and Disease)
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16 pages, 1581 KiB  
Article
Blood Metabolites and Faecal Microbial Communities in Nonpregnant and Early Gestation Ewes in Highly Cold Areas
Biology 2023, 12(11), 1436; https://doi.org/10.3390/biology12111436 - 16 Nov 2023
Viewed by 927
Abstract
Ewes undergo complex metabolic changes during pregnancy. Understanding the specific process of these changes is a necessary prerequisite in ewes for regulating and intervening in order to maintain pregnancies. However, there have been relatively few studies on the specific changes that occur in [...] Read more.
Ewes undergo complex metabolic changes during pregnancy. Understanding the specific process of these changes is a necessary prerequisite in ewes for regulating and intervening in order to maintain pregnancies. However, there have been relatively few studies on the specific changes that occur in nutritional metabolism in pregnant ewes during early gestation, especially for some landrace ewes in highly cold areas. Therefore, this study aimed to (1) elucidate the changes in metabolites and microbial communities in pregnant ewes during early gestation using metabolomics and 16S ribosomal RNA gene (rDNA) amplicon sequencing approaches, and to (2) discover novel early pregnancy-induced biomarkers in the blood and faeces. Rams were placed together with ewes on D0 and removed on D45. During early gestation, blood and faecal samples were collected from ewes in a highly cold area for analysing the metabolites and microbial communities; these were retrospectively classified as the early gestation pregnant (EP) ewe group or the nonpregnant (NP) ewe group based on the lambing status recorded during the expected delivery period. The differences in the plasma biochemical parameters, plasma metabolites, and faecal microbial communities of pregnant and nonpregnant ewes were characterised. The GC, IL-6, O-acetyl-l-serine, L-glutamine, and 6-acetamido-2-oxohexanoic acid were screened out as potential biomarkers for evaluating the occurrence of early pregnancy. These novel early pregnancy-induced metabolites discovered in ewes might allow for the development of technologies to detect early pregnancies in sheep in highly cold areas. Full article
(This article belongs to the Special Issue Metabolic Interactions between the Gut Microbiome and Host)
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14 pages, 2140 KiB  
Opinion
Morphological and Functional Principles Governing the Plasticity Reserve in the Cerebellum: The Cortico-Deep Cerebellar Nuclei Loop Model
Biology 2023, 12(11), 1435; https://doi.org/10.3390/biology12111435 - 16 Nov 2023
Viewed by 1096
Abstract
Cerebellar reserve compensates for and restores functions lost through cerebellar damage. This is a fundamental property of cerebellar circuitry. Clinical studies suggest (1) the involvement of synaptic plasticity in the cerebellar cortex for functional compensation and restoration, and (2) that the integrity of [...] Read more.
Cerebellar reserve compensates for and restores functions lost through cerebellar damage. This is a fundamental property of cerebellar circuitry. Clinical studies suggest (1) the involvement of synaptic plasticity in the cerebellar cortex for functional compensation and restoration, and (2) that the integrity of the cerebellar reserve requires the survival and functioning of cerebellar nuclei. On the other hand, recent physiological studies have shown that the internal forward model, embedded within the cerebellum, controls motor accuracy in a predictive fashion, and that maintaining predictive control to achieve accurate motion ultimately promotes learning and compensatory processes. Furthermore, within the proposed framework of the Kalman filter, the current status is transformed into a predictive state in the cerebellar cortex (prediction step), whereas the predictive state and sensory feedback from the periphery are integrated into a filtered state at the cerebellar nuclei (filtering step). Based on the abovementioned clinical and physiological studies, we propose that the cerebellar reserve consists of two elementary mechanisms which are critical for cerebellar functions: the first is involved in updating predictions in the residual or affected cerebellar cortex, while the second acts by adjusting its updated forecasts with the current status in the cerebellar nuclei. Cerebellar cortical lesions would impair predictive behavior, whereas cerebellar nuclear lesions would impact on adjustments of neuronal commands. We postulate that the multiple forms of distributed plasticity at the cerebellar cortex and cerebellar nuclei are the neuronal events which allow the cerebellar reserve to operate in vivo. This cortico-deep cerebellar nuclei loop model attributes two complementary functions as the underpinnings behind cerebellar reserve. Full article
(This article belongs to the Special Issue Plasticity and Computation in Cerebellar Neurons and Microcircuits)
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16 pages, 4865 KiB  
Article
Liver and Plasma Fatty Acid Characterization in Cultured Brown Trout at Distinct Reproductive Stages
Biology 2023, 12(11), 1434; https://doi.org/10.3390/biology12111434 - 15 Nov 2023
Viewed by 678
Abstract
Fatty acids are energy sources, and their profiles are used as biomarkers of metabolic status and physiological changes in fish. Within this context, the main aim of this study was to identify the fatty acids that best discriminate the reproductive status of male [...] Read more.
Fatty acids are energy sources, and their profiles are used as biomarkers of metabolic status and physiological changes in fish. Within this context, the main aim of this study was to identify the fatty acids that best discriminate the reproductive status of male and female farmed brown trout. The fatty acid composition in liver and plasma samples from the adults of both sexes was monitored along four distinct reproductive stages, namely the spawning capable (December), regressing (March), regenerating (July), and developing (November) stages. Irrespective of the sex and stage, the most representative fatty acids were palmitic acid (16:0), stearic acid (18:0), oleic acid (18:1 n-9), arachidonic acid (20:4 n-6), eicosapentaenoic acid (EPA, 20:5 n-3), and docosahexaenoic acid (DHA, 22:6 n-3). There were no significant sex differences in fatty acid classes in the liver and plasma. Despite this, there were several changes in individual fatty acid levels between the sexes. In the liver, both males and females showed high monounsaturated fatty acid and low polyunsaturated fatty acid (PUFA) levels during the regressing and regenerating stages. At spawning capable and developing stages, a reverse profile was noted. The plasma profiles were mainly influenced by changes in saturated fatty acids and PUFAs in males and by PUFA in females. Based on the most representative fatty acids, four patterns were established for female plasma samples, one for each reproductive stage. This scenario suggests that female plasma samples are promising for the discrimination of gonadal reproductive status, and this potential can be further explored in aquaculture and environmental monitoring studies. Full article
(This article belongs to the Special Issue Biomarkers in Stress Biology and Ecology)
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17 pages, 3966 KiB  
Article
Effect of Fly Maggot Protein as Dietary on Growth and Intestinal Microbial Community of Pacific White Shrimp Litopenaeus vannamei
Biology 2023, 12(11), 1433; https://doi.org/10.3390/biology12111433 - 15 Nov 2023
Viewed by 1023
Abstract
As the intensive development of aquaculture persists, the demand for fishmeal continues to grow; however, since fishery resources are limited, the price of fishmeal remains high. Therefore, there is an urgent need to develop new sources of protein. They are rich in proteins, [...] Read more.
As the intensive development of aquaculture persists, the demand for fishmeal continues to grow; however, since fishery resources are limited, the price of fishmeal remains high. Therefore, there is an urgent need to develop new sources of protein. They are rich in proteins, fatty acids, amino acids, chitin, vitamins, minerals, and antibacterial substances. Maggot meal-based diet is an ideal source of high-quality animal protein and a new type of protein-based immune enhancer with good application prospects in animal husbandry and aquaculture. In the present study, we investigated the effects of three different diets containing maggot protein on the growth and intestinal microflora of Litopenaeus vannamei. The shrimp were fed either a control feed (no fly maggot protein added), FM feed (compound feed with 30% fresh fly maggot protein added), FF feed (fermented fly maggot protein), or HT feed (high-temperature pelleted fly maggot protein) for eight weeks. The results showed that fresh fly maggot protein in the feed was detrimental to shrimp growth, whereas fermented and high-temperature-pelleted fly maggot protein improved shrimp growth and survival. The effects of different fly maggot protein treatments on the intestinal microbiota of L. vannamei also varied. Fermented fly maggot protein feed and high-temperature-pelleted fly maggot protein feed increased the relative abundance of Ruegeria and Pseudomonas, which increased the abundance of beneficial bacteria and thus inhibited the growth of harmful bacteria. In contrast, fresh fly maggot proteins alter the intestinal microbiome, disrupting symbiotic relationships between bacteria, and causing invasion by Vibrio and antibiotic-resistant bacteria. These results suggest that fresh fly maggot proteins affect the composition of intestinal microorganisms, which is detrimental to the intestinal tract of L. vannamei, whereas fermented fly maggot protein feed affected the growth of L. vannamei positively by improving the composition of intestinal microorganisms. Full article
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15 pages, 5049 KiB  
Article
The Role of the Insulin/Glucose Ratio in the Regulation of Pathogen Biofilm Formation
Biology 2023, 12(11), 1432; https://doi.org/10.3390/biology12111432 - 15 Nov 2023
Viewed by 918
Abstract
During the management of patients in acute trauma the resulting transient hyperglycemia is treated by administration of insulin. Since the effect of insulin, a quorum sensing compound, together with glucose affects biofilm formation in a concentration-specific manner, we hypothesize that the insulin/glucose ratio [...] Read more.
During the management of patients in acute trauma the resulting transient hyperglycemia is treated by administration of insulin. Since the effect of insulin, a quorum sensing compound, together with glucose affects biofilm formation in a concentration-specific manner, we hypothesize that the insulin/glucose ratio over the physiologic range modulates biofilm formation potentially influencing the establishment of infection through biofilm formation. Methods: A variety of Gram-positive and Gram-negative bacteria were grown in peptone (1%) yeast nitrogen base broth overnight in 96-well plates with various concentrations of glucose and insulin. Biofilm formation was determined by the crystal violet staining procedure. Expression of insulin binding was determined by fluorescent microscopy (FITC-insulin). Controls were buffer alone, insulin alone, and glucose alone. Results: Overall, maximal biofilm levels were measured at 220 mg/dL of glucose, regardless of insulin concentration (10, 100, 200 µU/mL) of the organism tested. In general, insulin with glucose over the range of 160–180 mg/dL exhibited a pattern of biofilm suppression. However, either above or below this range, the presence of insulin in combination with glucose significantly modulated (increase or decrease) biofilm formation in a microbe-specific pattern. This modulation appears for some organisms to be reflective of the glucose-regulated intrinsic expression of bacterial insulin receptor expression. Conclusion: Insulin at physiologic levels (normal and hyperinsulinemic) in combination with glucose can affect biofilm formation in a concentration-specific and microbe-specific manner. These findings may provide insight into the importance of co-regulation of the insulin/glucose ratio in patient management. Full article
(This article belongs to the Section Medical Biology)
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15 pages, 3425 KiB  
Article
Vertical Slot Fishways: Incremental Knowledge to Define the Best Solution
Biology 2023, 12(11), 1431; https://doi.org/10.3390/biology12111431 - 15 Nov 2023
Viewed by 773
Abstract
River artificial fragmentation is arguably the most imperilling threat for freshwater-dependent fish species. Fish need to be able to freely move along river networks as not only spawning grounds but also refuge and feeding areas may be spatially and temporally separated. This incapacity [...] Read more.
River artificial fragmentation is arguably the most imperilling threat for freshwater-dependent fish species. Fish need to be able to freely move along river networks as not only spawning grounds but also refuge and feeding areas may be spatially and temporally separated. This incapacity of free displacement may result in genetic depletion of some populations, density reduction and even community changes, which may in turn affect how meta-community balances are regulated, potentially resulting in functional resilience reduction and ecosystem processes’ malfunction. Fishways are the most common and widely used method to improve connectivity for fish species. These structures allow fish to negotiate full barriers, thus reducing their connectivity impairment. Among all technical fishway types, vertical slot fishways (VSF) are considered to be the best solution, as they remain operational even with fluctuating water discharges and allow fish to negotiate each cross-wall at their desired depth. In the present study, we collected both published and original data on fish experiments within VSF, to address two questions, (1) What variables affect fish passage during experimental fishway studies? and (2) What is the best VSF configuration? We used Bayesian Generalized Mixed Models accounting for random effects of non-controlled factors, limiting inherent data dependencies, that may influence the model outcome. Results highlight that fish size, regardless of the species, is a good predictor of fishway negotiation success. Generally, multiple slot fishways with one orifice proved to be the best solution. Future work should be focused on small-sized fish to further improve the design of holistic fishways. Full article
(This article belongs to the Section Conservation Biology and Biodiversity)
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10 pages, 291 KiB  
Article
Effect of Polystyrene Microplastics on the Antioxidant System and Immune Response in GIFT (Oreochromis niloticus)
Biology 2023, 12(11), 1430; https://doi.org/10.3390/biology12111430 - 14 Nov 2023
Viewed by 1071
Abstract
Recent studies have revealed a significant presence of microplastics (MPs) in freshwater ecosystems, raising concerns about their potential negative impacts on the growth and development of freshwater organisms. The present study was conducted to examine the effects of chronic sub-lethal doses of polystyrene [...] Read more.
Recent studies have revealed a significant presence of microplastics (MPs) in freshwater ecosystems, raising concerns about their potential negative impacts on the growth and development of freshwater organisms. The present study was conducted to examine the effects of chronic sub-lethal doses of polystyrene microsphere MPs on the oxidative status (ROS, SOD) and the immune response (IL-1ß, TNF-α) of genetically improved farmed tilapia (a kind of tilapia hereafter referred to as GIFT). GIFT juveniles (5.1 ± 0.2 g) were exposed to different concentrations of substances. The experimental groups were as follows: group A (control, no exposure), group B (exposed to a concentration of 75 nm), group C (exposed to a concentration of 7.5 μm), group D (exposed to a concentration of 750 μm), group E (exposed to a combination of 75 nm, 7.5 μm, and 750 μm), and group F (exposed to a combination of 75 nm and Chlorella). The ROS contents in the brain and gills were significantly decreased in group F, while a significant increase was observed in group D following a 14-day exposure. SOD activities in the intestine showed an elevation in group F, as did those in the brain and gills in group D, while the SOD levels in the gills generally decreased over time in groups B and F. Notably, the highest ROS and SOD were observed in the brain of group D, whereas the lowest were in the intestines at the same concentration. The activity of IL-1β in the liver was significantly up-regulated in all of the exposure groups. IL-1β was significantly up-regulated in the brain of group B and in the gills of group D. Similarly, TNF-α was significantly up-regulated in the brain of groups B/D/E, in the liver of groups B/C/D, in the intestine of group B, and in the gills of group D. Notably, the highest levels of IL-1β and TNF-α activities were recorded in the brain, while the lowest were recorded in the intestine of group D. Overall, this study revealed that GIFT’s immune response and antioxidant system can be affected by MPs. Full article
14 pages, 3442 KiB  
Article
Prediction of Ross River Virus Incidence Using Mosquito Data in Three Cities of Queensland, Australia
Biology 2023, 12(11), 1429; https://doi.org/10.3390/biology12111429 - 13 Nov 2023
Viewed by 937
Abstract
Ross River virus (RRV) is the most common mosquito-borne disease in Australia, with Queensland recording high incidence rates (with an annual average incidence rate of 0.05% over the last 20 years). Accurate prediction of RRV incidence is critical for disease management and control. [...] Read more.
Ross River virus (RRV) is the most common mosquito-borne disease in Australia, with Queensland recording high incidence rates (with an annual average incidence rate of 0.05% over the last 20 years). Accurate prediction of RRV incidence is critical for disease management and control. Many factors, including mosquito abundance, climate, weather, geographical factors, and socio-economic indices, can influence the RRV transmission cycle and thus have potential utility as predictors of RRV incidence. We collected mosquito data from the city councils of Brisbane, Redlands, and Mackay in Queensland, together with other meteorological and geographical data. Predictors were selected to build negative binomial generalised linear models for prediction. The models demonstrated excellent performance in Brisbane and Redlands but were less satisfactory in Mackay. Mosquito abundance was selected in the Brisbane model and can improve the predictive performance. Sufficient sample sizes of continuous mosquito data and RRV cases were essential for accurate and effective prediction, highlighting the importance of routine vector surveillance for disease management and control. Our results are consistent with variation in transmission cycles across different cities, and our study demonstrates the usefulness of mosquito surveillance data for predicting RRV incidence within small geographical areas. Full article
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20 pages, 3743 KiB  
Article
Preserving Pure Siamese Crocodile Populations: A Comprehensive Approach Using Multi-Genetic Tools
Biology 2023, 12(11), 1428; https://doi.org/10.3390/biology12111428 - 13 Nov 2023
Viewed by 1145
Abstract
Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to the impact of anthropogenic activities. A previous study used microsatellite [...] Read more.
Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to the impact of anthropogenic activities. A previous study used microsatellite and mitochondrial DNA data to establish the criteria for identifying species and their hybrids; however, the results may have been influenced by biased allelic frequencies and genetic drift within the examined population. To overcome these limitations and identify the true signals of selection, alternative DNA markers and a diverse set of populations should be employed. Therefore, this study used DArT sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in both species and confirm the genetic scenario of the parental species and their hybrids. A population of saltwater crocodiles from Australia was used to compare the distribution of species-diagnostic SNPs. Different analytical approaches were compared to diagnose the level of hybridization when an admixture was present, wherein three individuals had potential backcrossing. Approximately 17.00–26.00% of loci were conserved between the Siamese and saltwater crocodile genomes. Species-diagnostic SNP loci for Siamese and saltwater crocodiles were identified as 8051 loci and 1288 loci, respectively. To validate the species-diagnostic SNP loci, a PCR-based approach was used by selecting 20 SNP loci for PCR primer design, among which 3 loci were successfully able to differentiate the actual species and different hybridization levels. Mitochondrial and nuclear genetic information, including microsatellite genotyping and species-diagnostic DNA markers, were combined as a novel method that can compensate for the limitations of each method. This method enables conservation prioritization before release into the wild, thereby ensuring sustainable genetic integrity for long-term species survival through reintroduction and management programs. Full article
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16 pages, 4037 KiB  
Article
Genetic Diversity and Signatures of Selection in the Roughskin Sculpin (Trachidermus fasciatus) Revealed by Whole Genome Sequencing
Biology 2023, 12(11), 1427; https://doi.org/10.3390/biology12111427 - 13 Nov 2023
Viewed by 813
Abstract
The roughskin sculpin (Trachidermus fasciatus) is an endangered fish species in China. In recent years, artificial breeding technology has made significant progress, and the population of roughskin sculpin has recovered in the natural environment through enhancement programs and the release of [...] Read more.
The roughskin sculpin (Trachidermus fasciatus) is an endangered fish species in China. In recent years, artificial breeding technology has made significant progress, and the population of roughskin sculpin has recovered in the natural environment through enhancement programs and the release of juveniles. However, the effects of released roughskin sculpin on the genetic structure and diversity of wild populations remain unclear. Studies on genetic diversity analysis based on different types and numbers of molecular markers have yielded inconsistent results. In this study, we obtained 2,610,157 high-quality SNPs and 494,698 InDels through whole-genome resequencing of two farmed populations and one wild population. Both farmed populations showed consistent levels of genomic polymorphism and a slight increase in linkage compared with wild populations. The population structure of the two farmed populations was distinct from that of the wild population, but the degree of genetic differentiation was low (overall average Fst = 0.015). Selective sweep analysis showed that 523,529 genes were selected in the two farmed populations, and KEGG enrichment analysis showed that the selected genes were related to amino acid metabolism, which might be caused by artificial feeding. The findings of this study provide valuable additions to the existing genomic resources to help conserve roughskin sculpin populations. Full article
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29 pages, 1744 KiB  
Review
Types of Cell Death from a Molecular Perspective
Biology 2023, 12(11), 1426; https://doi.org/10.3390/biology12111426 - 13 Nov 2023
Cited by 1 | Viewed by 1520
Abstract
The former conventional belief was that cell death resulted from either apoptosis or necrosis; however, in recent years, different pathways through which a cell can undergo cell death have been discovered. Various types of cell death are distinguished by specific morphological alterations in [...] Read more.
The former conventional belief was that cell death resulted from either apoptosis or necrosis; however, in recent years, different pathways through which a cell can undergo cell death have been discovered. Various types of cell death are distinguished by specific morphological alterations in the cell’s structure, coupled with numerous biological activation processes. Various diseases, such as cancers, can occur due to the accumulation of damaged cells in the body caused by the dysregulation and failure of cell death. Thus, comprehending these cell death pathways is crucial for formulating effective therapeutic strategies. We focused on providing a comprehensive overview of the existing literature pertaining to various forms of cell death, encompassing apoptosis, anoikis, pyroptosis, NETosis, ferroptosis, autophagy, entosis, methuosis, paraptosis, mitoptosis, parthanatos, necroptosis, and necrosis. Full article
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11 pages, 2121 KiB  
Article
Detection and Quantification of Acrylamide in Second Trimester Amniotic Fluid Using a Novel LC-MS/MS Technique to Determine Whether High Acrylamide Content during Pregnancy Is Associated with Fetal Growth
Biology 2023, 12(11), 1425; https://doi.org/10.3390/biology12111425 - 13 Nov 2023
Viewed by 1001
Abstract
Introduction: Acrylamide, an organic compound, is, chemically speaking, a vinyl-substituted primary amide. It is produced industrially, principally as a precursor to polyacrylamides, for use in such products as plastics and cosmetics. This same compound, however, forms naturally in certain foods, both home-cooked and [...] Read more.
Introduction: Acrylamide, an organic compound, is, chemically speaking, a vinyl-substituted primary amide. It is produced industrially, principally as a precursor to polyacrylamides, for use in such products as plastics and cosmetics. This same compound, however, forms naturally in certain foods, both home-cooked and packaged, especially when prepared at high temperatures. We developed and validated a novel reliable technique for the determination of acrylamide in amniotic fluid. Multiple reaction monitoring (MRM) is a targeted mass spectrometry (MS) technique which enables the detection and quantification of particular molecules in a complex mixture. Thanks to its throughput, selectivity, and sensitivity, MRM-MS has been identified as offering an alternative to antibody-based studies for the purpose of biomarker verification. Our aim was to investigate the presence of acrylamide in amniotic fluid and, via the MRM-MS technique, to determine whether there is any correlation between maternal exposure to acrylamide, through a woman’s diet, and fetal growth. Methods: Our amniotic fluid bank included 40 samples from various fetal growth rates, as objectively denoted by the neonatal weight centile at delivery, while our analytical detection method was based on liquid chromatography-tandem mass spectrometry (LC-MS/MS). Acrylamide was determined with reversed phase chromatography and monitoring of two multiple reaction monitoring (MRM) transitions. Quantification was performed using the matrix-matched calibration curve. Results: Acrylamide was detected at concentrations between 7.1 and 1468 ng/mL in six out of the total of 40 amniotic fluid samples that were used. Our method limit of detection and quantification was 1.4 ng/mL and 4.6 ng/mL, respectively. The repeatability of our method ranged between 11 and 14%, expressed as relative standard deviation levels between 5 and 100 ng/mL. Conclusions: Detection of acrylamide in early second trimester amniotic fluid, for the first time in the literature to our knowledge, raises concerns about fetal health, given that published data on animal studies have attributed a number of birth defects to acrylamide. Our novel LC-MS/MS method for the determination of acrylamide in amniotic fluid proved to be effective and its performance in practice was very accurate, simple, and fast. Validation of the method revealed that the use of a matrix-matched curve is necessary for the quantification. Full article
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20 pages, 7627 KiB  
Article
Seasonal Patterns of Picocyanobacterial Community Structure in the Kuroshio Current
Biology 2023, 12(11), 1424; https://doi.org/10.3390/biology12111424 - 13 Nov 2023
Viewed by 825
Abstract
The nutrient-scarce, warm, and high-salinity Kuroshio current has a profound impact on both the marine ecology of the northwestern Pacific Ocean and the global climate. This study aims to reveal the seasonal dynamics of picoplankton in the subtropical Kuroshio current. Our results showed [...] Read more.
The nutrient-scarce, warm, and high-salinity Kuroshio current has a profound impact on both the marine ecology of the northwestern Pacific Ocean and the global climate. This study aims to reveal the seasonal dynamics of picoplankton in the subtropical Kuroshio current. Our results showed that one of the picocyanobacteria, Synechococcus, mainly distributed in the surface water layer regardless of seasonal changes, and the cell abundance ranged from 104 to 105 cells mL−1. In contrast, the maximum concentration of the other picocyanobacteria, Prochlorococcus, was maintained at more than 105 cells mL−1 throughout the year. In the summer and the autumn, Prochlorococcus were mainly concentrated at the water layer near the bottom of the euphotic zone. They were evenly distributed in the euphotic zone in the spring and winter. The stirring effect caused by the monsoon determined their distribution in the water column. In addition, the results of 16S rRNA gene diversity analysis showed that the seasonal changes in the relative abundance of Synechococcus and Prochlorococcus in the surface water of each station accounted for 20 to 40% of the total reads. The clade II of Synechococcus and the High-light II of Prochlorococcus were the dominant strains in the waters all year round. Regarding other picoplankton, Proteobacteria and Actinobacteria occupied 45% and 10% of the total picoplankton in the four seasons. These data should be helpful for elucidating the impacts of global climate changes on marine ecology and biogeochemical cycles in the Western Boundary Currents in the future. Full article
(This article belongs to the Special Issue Climate Change and Marine Plankton)
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