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Biology, Volume 13, Issue 4 (April 2024) – 81 articles

Cover Story (view full-size image): Many proteins are glycosylated, for example, on asparagine residues, which can affect protein function in a variety of ways, but can also shield immunogenic sites in viral proteins from the immune system. This is also the case for highly glycosylated SARS-CoV-2 proteins. In this study, different receptor-binding domains (RBDs) of several SARS-CoV-2 variants of concern (VOCs), a subunit of the highly glycosylated spike protein, and the membrane protein, which has not been extensively studied, were produced in human cells and bacteria for the relevant VOCs. The resulting RBDs were analyzed for their N-glycosylation sites by mass spectrometry and for their ability to bind to IgG antibodies produced in response to SARS-CoV-2 infection by ELISA. View this paper
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23 pages, 2745 KiB  
Article
Genomic Diversity and Recombination Analysis of the Spike Protein Gene from Selected Human Coronaviruses
by Sayed Sartaj Sohrab, Fatima Alsaqaf, Ahmed Mohamed Hassan, Ahmed Majdi Tolah, Leena Hussein Bajrai and Esam Ibraheem Azhar
Biology 2024, 13(4), 282; https://doi.org/10.3390/biology13040282 - 22 Apr 2024
Viewed by 838
Abstract
Human coronaviruses (HCoVs) are seriously associated with respiratory diseases in humans and animals. The first human pathogenic SARS-CoV emerged in 2002–2003. The second was MERS-CoV, reported from Jeddah, the Kingdom of Saudi Arabia, in 2012, and the third one was SARS-CoV-2, identified from [...] Read more.
Human coronaviruses (HCoVs) are seriously associated with respiratory diseases in humans and animals. The first human pathogenic SARS-CoV emerged in 2002–2003. The second was MERS-CoV, reported from Jeddah, the Kingdom of Saudi Arabia, in 2012, and the third one was SARS-CoV-2, identified from Wuhan City, China, in late December 2019. The HCoV-Spike (S) gene has the highest mutation/insertion/deletion rate and has been the most utilized target for vaccine/antiviral development. In this manuscript, we discuss the genetic diversity, phylogenetic relationships, and recombination patterns of selected HCoVs with emphasis on the S protein gene of MERS-CoV and SARS-CoV-2 to elucidate the possible emergence of new variants/strains of coronavirus in the near future. The findings showed that MERS-CoV and SARS-CoV-2 have significant sequence identity with the selected HCoVs. The phylogenetic tree analysis formed a separate cluster for each HCoV. The recombination pattern analysis showed that the HCoV-NL63-Japan was a probable recombinant. The HCoV-NL63-USA was identified as a major parent while the HCoV-NL63-Netherland was identified as a minor parent. The recombination breakpoints start in the viral genome at the 142 nucleotide position and end at the 1082 nucleotide position with a 99% CI and Bonferroni-corrected p-value of 0.05. The findings of this study provide insightful information about HCoV-S gene diversity, recombination, and evolutionary patterns. Based on these data, it can be concluded that the possible emergence of new strains/variants of HCoV is imminent. Full article
(This article belongs to the Special Issue SARS-CoV-2 and Immunology)
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16 pages, 6494 KiB  
Article
Toxicity of Ammonia Stress on the Physiological Homeostasis in the Gills of Litopenaeus vannamei under Seawater and Low-Salinity Conditions
by Yuxiu Nan, Meng Xiao, Yafei Duan and Yukai Yang
Biology 2024, 13(4), 281; https://doi.org/10.3390/biology13040281 - 21 Apr 2024
Viewed by 785
Abstract
Ammonia is a major water quality factor influencing the survival and health of shrimp, among which the gill is the main effector organ for ammonia toxicity. In this study, we chose two types of Litopenaeus vannamei that were cultured in 30‰ seawater and [...] Read more.
Ammonia is a major water quality factor influencing the survival and health of shrimp, among which the gill is the main effector organ for ammonia toxicity. In this study, we chose two types of Litopenaeus vannamei that were cultured in 30‰ seawater and domesticated in 3‰ low salinity, respectively, and then separately subjected to ammonia stress for 14 days under seawater and low-salinity conditions, of which the 3‰ low salinity-cultured shrimp were domesticated from the shrimp cultured in 30‰ seawater after 27 days of gradual salinity desalination. In detail, this study included four groups, namely the SC group (ammonia-N 0 mg/L, salinity 30‰), SAN group (ammonia-N 10 mg/L, salinity 30‰), LC group (ammonia-N 0 mg/L, salinity 3‰), and LAN group (ammonia-N 10 mg/L, salinity 3‰). The ammonia stress lasted for 14 days, and then the changes in the morphological structure and physiological function of the gills were explored. The results show that ammonia stress caused the severe contraction of gill filaments and the deformation or even rupture of gill vessels. Biochemical indicators of oxidative stress, including LPO and MDA contents, as well as T-AOC and GST activities, were increased in the SAN and LAN groups, while the activities of CAT and POD and the mRNA expression levels of antioxidant-related genes (nrf2, cat, gpx, hsp70, and trx) were decreased. In addition, the mRNA expression levels of the genes involved in ER stress (ire1 and xbp1), apoptosis (casp-3, casp-9, and jnk), detoxification (gst, ugt, and sult), glucose metabolism (pdh, hk, pk, and ldh), and the tricarboxylic acid cycle (mdh, cs, idh, and odh) were decreased in the SAN and LAN groups; the levels of electron-transport chain-related genes (ndh, cco, and coi), and the bip and sdh genes were decreased in the SAN group but increased in the LAN group; and the level of the ATPase gene was decreased but the cytc gene was increased in the SAN and LAN groups. The mRNA expression levels of osmotic regulation-related genes (nka-β, ca, aqp and clc) were decreased in the SAN group, while the level of the ca gene was increased in the LAN group; the nka-α gene was decreased in both two groups. The results demonstrate that ammonia stress could influence the physiological homeostasis of the shrimp gills, possibly by damaging the tissue morphology, and affecting the redox, ER function, apoptosis, detoxification, energy metabolism, and osmoregulation. Full article
(This article belongs to the Special Issue Metabolic and Stress Responses in Aquatic Animals)
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18 pages, 31519 KiB  
Article
Genome-Wide Analysis of the HSF Gene Family Reveals Its Role in Astragalus mongholicus under Different Light Conditions
by Zhen Wang, Panpan Wang, Jiajun He, Lingyang Kong, Wenwei Zhang, Weili Liu, Xiubo Liu and Wei Ma
Biology 2024, 13(4), 280; https://doi.org/10.3390/biology13040280 - 19 Apr 2024
Viewed by 680
Abstract
Astragalus mongholicus is a traditional Chinese medicine (TCM) with important medicinal value and is widely used worldwide. Heat shock (HSF) transcription factors are among the most important transcription factors in plants and are involved in the transcriptional regulation of various stress responses, including [...] Read more.
Astragalus mongholicus is a traditional Chinese medicine (TCM) with important medicinal value and is widely used worldwide. Heat shock (HSF) transcription factors are among the most important transcription factors in plants and are involved in the transcriptional regulation of various stress responses, including drought, salinity, oxidation, osmotic stress, and high light, thereby regulating growth and developmental processes. However, the HFS gene family has not yet been identified in A. mongholicus, and little is known regarding the role of HSF genes in A. mongholicus. This study is based on whole genome analysis of A. mongholicus, identifying a total of 22 AmHSF genes and analyzing their physicochemical properties. Divided into three subgroups based on phylogenetic and gene structural characteristics, including subgroup A (12), subgroup B (9), and subgroup C (1), they are randomly distributed in 8 out of 9 chromosomes of A. mongholicus. In addition, transcriptome data and quantitative real time polymerase chain reaction (qRT-PCR) analyses revealed that AmHSF was differentially transcribed in different tissues, suggesting that AmHSF gene functions may differ. Red and blue light treatment significantly affected the expression of 20 HSF genes in soilless cultivation of A. mongholicus seedlings. AmHSF3, AmHSF3, AmHSF11, AmHSF12, and AmHSF14 were upregulated after red light and blue light treatment, and these genes all had light-corresponding cis-elements, suggesting that AmHSF genes play an important role in the light response of A. mongholicus. Although the responses of soilless-cultivated A. mongholicus seedlings to red and blue light may not represent the mature stage, our results provide fundamental research for future elucidation of the regulatory mechanisms of HSF in the growth and development of A. mongholicus and its response to different light conditions. Full article
(This article belongs to the Section Plant Science)
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26 pages, 4375 KiB  
Article
When Nature Requires a Resource to Be Used—The Case of Callinectes sapidus: Distribution, Aggregation Patterns, and Spatial Structure in Northwest Europe, the Mediterranean Sea, and Adjacent Waters
by Luca Castriota, Manuela Falautano and Patrizia Perzia
Biology 2024, 13(4), 279; https://doi.org/10.3390/biology13040279 - 19 Apr 2024
Viewed by 882
Abstract
The Atlantic blue crab Callinectes sapidus, which is native to the western Atlantic coast and listed among the 100 most invasive alien species in the Mediterranean Sea, is attracting a great deal of interest because of its rapid colonisation of new areas, [...] Read more.
The Atlantic blue crab Callinectes sapidus, which is native to the western Atlantic coast and listed among the 100 most invasive alien species in the Mediterranean Sea, is attracting a great deal of interest because of its rapid colonisation of new areas, the significant increase in its population, and the impacts it may have on ecosystems and ecosystem services. Outside its natural distribution range, the species was first found on European Atlantic coasts in the early 1900s and was introduced into the Mediterranean Sea a few decades later, probably through ballast water. Currently, it is found in almost the entire Mediterranean Basin and is also expanding into the Black Sea and along the north African and Iberian Atlantic coasts. Based on a systematic review of C. sapidus occurrences, this study describes its distribution, aggregation patterns, and spatial structure in Northwest Europe, the Mediterranean Sea, and adjacent waters through a series of ecological indicators elaborated using GIS spatial–temporal statistics. The main results highlight that the species is expanding in the Mediterranean and adjacent waters, while in northern Europe, the population remains confined in some areas. Furthermore, the main species detection methods are analysed, finding that traps and nets are the most frequently used methods, and management suggestions are provided. Full article
(This article belongs to the Special Issue Alien Marine Species in the Mediterranean Sea)
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22 pages, 5732 KiB  
Article
Impaired Spermatogenesis in Infertile Patients with Orchitis and Experimental Autoimmune Orchitis in Rats
by María Sofía Amarilla, Leilane Glienke, Thaisy Munduruca Pires, Cristian Marcelo Sobarzo, Hernán Gustavo Oxilia, María Florencia Fulco, Marcelo Rodríguez Peña, María Belén Maio, Denisse Ferrer Viñals, Livia Lustig, Patricia Verónica Jacobo and María Susana Theas
Biology 2024, 13(4), 278; https://doi.org/10.3390/biology13040278 - 19 Apr 2024
Viewed by 748
Abstract
Experimental autoimmune orchitis (EAO) is a well-established rodent model of organ-specific autoimmunity associated with infertility in which the testis immunohistopathology has been extensively studied. In contrast, analysis of testis biopsies from infertile patients associated with inflammation has been more limited. In this work, [...] Read more.
Experimental autoimmune orchitis (EAO) is a well-established rodent model of organ-specific autoimmunity associated with infertility in which the testis immunohistopathology has been extensively studied. In contrast, analysis of testis biopsies from infertile patients associated with inflammation has been more limited. In this work, testicular biopsies from patients with idiopathic non-obstructive azoospermia diagnosed with hypospermatogenesis (HypoSp) [mild: n = 9, and severe: n = 11], with obstructive azoospermia and complete Sp (spermatogenesis) (control group, C, n = 9), and from Sertoli cell-only syndrome (SCOS, n = 9) were analyzed for the presence of immune cells, spermatogonia and Sertoli cell (SCs) alterations, and reproductive hormones levels. These parameters were compared with those obtained in rats with EAO. The presence of increased CD45+ cells in the seminiferous tubules (STs) wall and lumen in severe HypoSp is associated with increased numbers of apoptotic meiotic germ cells and decreased populations of undifferentiated and differentiated spermatogonia. The SCs showed an immature profile with the highest expression of AMH in patients with SCOS and severe HypoSp. In SCOS patients, the amount of SCs/ST and Ki67+ SCs/ST increased and correlated with high serum FSH levels and CD45+ cells. In the severe phase of EAO, immune cell infiltration and apoptosis of meiotic germ cells increased and the number of undifferentiated and differentiated spermatogonia was lowest, as previously reported. Here, we found that orchitis leads to reduced sperm number, viability, and motility. SCs were mature (AMH-) but increased in number, with Ki67+ observed in severely damaged STs and associated with the highest levels of FSH and inflammatory cells. Our findings demonstrate that in a scenario where a chronic inflammatory process is underway, FSH levels, immune cell infiltration, and immature phenotypes of SCs are associated with severe changes in spermatogenesis, leading to azoospermia. Furthermore, AMH and Ki67 expression in SCs is a distinctive marker of severe alterations of STs in human orchitis. Full article
(This article belongs to the Special Issue Pathophysiology of Testis)
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17 pages, 7028 KiB  
Article
Utilizing 5′ UTR Engineering Enables Fine-Tuning of Multiple Genes within Operons to Balance Metabolic Flux in Bacillus subtilis
by Jiajia You, Yifan Wang, Kang Wang, Yuxuan Du, Xiaoling Zhang, Xian Zhang, Taowei Yang, Xuewei Pan and Zhiming Rao
Biology 2024, 13(4), 277; https://doi.org/10.3390/biology13040277 - 19 Apr 2024
Viewed by 769
Abstract
The application of synthetic biology tools to modulate gene expression to increase yield has been thoroughly demonstrated as an effective and convenient approach in industrial production. In this study, we employed a high-throughput screening strategy to identify a 5′ UTR sequence from the [...] Read more.
The application of synthetic biology tools to modulate gene expression to increase yield has been thoroughly demonstrated as an effective and convenient approach in industrial production. In this study, we employed a high-throughput screening strategy to identify a 5′ UTR sequence from the genome of B. subtilis 168. This sequence resulted in a 5.8-fold increase in the expression level of EGFP. By utilizing the 5′ UTR sequence to overexpress individual genes within the rib operon, it was determined that the genes ribD and ribAB serve as rate-limiting enzymes in the riboflavin synthesis pathway. Constructing a 5′ UTR library to regulate EGFP expression resulted in a variation range in gene expression levels exceeding 100-fold. Employing the same 5′ UTR library to regulate the expression of EGFP and mCherry within the operon led to a change in the expression ratio of these two genes by over 10,000-fold. So, employing a 5′ UTR library to modulate the expression of the rib operon gene and construct a synthetic rib operon resulted in a 2.09-fold increase in riboflavin production. These results indicate that the 5′ UTR sequence identified and characterized in this study can serve as a versatile synthetic biology toolkit for achieving complex metabolic network reconstruction. This toolkit can facilitate the fine-tuning of gene expression to produce target products. Full article
(This article belongs to the Section Biotechnology)
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16 pages, 5161 KiB  
Article
Dissecting Holistic Metabolic Acclimatization of Mucor circinelloides WJ11 Defective in Carotenoid Biosynthesis
by Fanyue Li, Roypim Thananusak, Nachon Raethong, Junhuan Yang, Mingyue Wei, Xingtang Zhao, Kobkul Laoteng, Yuanda Song and Wanwipa Vongsangnak
Biology 2024, 13(4), 276; https://doi.org/10.3390/biology13040276 - 18 Apr 2024
Viewed by 748
Abstract
Mucor circinelloides WJ11 is a lipid-producing strain with industrial potential. A holistic approach using gene manipulation and bioprocessing development has improved lipid production and the strain’s economic viability. However, the systematic regulation of lipid accumulation and carotenoid biosynthesis in M. circinelloides remains unknown. [...] Read more.
Mucor circinelloides WJ11 is a lipid-producing strain with industrial potential. A holistic approach using gene manipulation and bioprocessing development has improved lipid production and the strain’s economic viability. However, the systematic regulation of lipid accumulation and carotenoid biosynthesis in M. circinelloides remains unknown. To dissect the metabolic mechanism underlying lipid and carotenoid biosynthesis, transcriptome analysis and reporter metabolites identification were implemented between the wild-type (WJ11) and ΔcarRP WJ11 strains of M. circinelloides. As a result, transcriptome analysis revealed 10,287 expressed genes, with 657 differentially expressed genes (DEGs) primarily involved in amino acid, carbohydrate, and energy metabolism. Integration with a genome-scale metabolic model (GSMM) identified reporter metabolites in the ΔcarRP WJ11 strain, highlighting metabolic pathways crucial for amino acid, energy, and nitrogen metabolism. Notably, the downregulation of genes associated with carotenoid biosynthesis and acetyl-CoA generation suggests a coordinated relationship between the carotenoid and fatty acid biosynthesis pathways. Despite disruptions in the carotenoid pathway, lipid production remains stagnant due to reduced acetyl-CoA availability, emphasizing the intricate metabolic interplay. These findings provide insights into the coordinated relationship between carotenoid and fatty acid biosynthesis in M. circinelloides that are valuable in applied research to design optimized strains for producing desired bioproducts through emerging technology. Full article
(This article belongs to the Section Bioinformatics)
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25 pages, 5671 KiB  
Article
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
Viewed by 609
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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14 pages, 2581 KiB  
Article
The Female-Biased General Odorant Binding Protein 2 of Semiothisa cinerearia Displays Binding Affinity for Biologically Active Host Plant Volatiles
by Jingjing Tu, Zehua Wang, Fan Yang, Han Liu, Guanghang Qiao, Aihuan Zhang and Shanning Wang
Biology 2024, 13(4), 274; https://doi.org/10.3390/biology13040274 - 18 Apr 2024
Viewed by 762
Abstract
Herbivorous insects rely on volatile chemical cues from host plants to locate food sources and oviposition sites. General odorant binding proteins (GOBPs) are believed to be involved in the detection of host plant volatiles. In the present study, one GOBP gene, ScinGOBP2, [...] Read more.
Herbivorous insects rely on volatile chemical cues from host plants to locate food sources and oviposition sites. General odorant binding proteins (GOBPs) are believed to be involved in the detection of host plant volatiles. In the present study, one GOBP gene, ScinGOBP2, was cloned from the antennae of adult Semiothisa cinerearia. Reverse-transcription PCR and real-time quantitative PCR analysis revealed that the expression of ScinGOBP2 was strongly biased towards the female antennae. Fluorescence-based competitive binding assays revealed that 8 of the 27 host plant volatiles, including geranyl acetone, decanal, cis-3-hexenyl n-valerate, cis-3-hexenyl butyrate, 1-nonene, dipentene, α-pinene and β-pinene, bound to ScinGOBP2 (KD = 2.21–14.94 μM). The electrical activities of all eight ScinGOBP2 ligands were confirmed using electroantennography. Furthermore, oviposition preference experiments showed that eight host volatiles, such as decanal, cis-3-hexenyl n-valerate, cis-3-hexenyl butyrate, and α-pinene, had an attractive effect on female S. cinerearia, whereas geranyl acetone, 1-nonene, β-pinene, and dipentene inhibited oviposition in females. Consequently, it can be postulated that ScinGOBP2 may be implicated in the perception of host plant volatiles and that ScinGOBP2 ligands represent significant semiochemicals mediating the interactions between plants and S. cinerearia. This insight could facilitate the development of a chemical ecology-based approach for the management of S. cinerearia. Full article
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15 pages, 3029 KiB  
Article
Potential of a Bead-Based Multiplex Assay for SARS-CoV-2 Antibody Detection
by Karla Rottmayer, Mandy Schwarze, Christian Jassoy, Ralf Hoffmann, Henry Loeffler-Wirth and Claudia Lehmann
Biology 2024, 13(4), 273; https://doi.org/10.3390/biology13040273 - 18 Apr 2024
Viewed by 836
Abstract
Serological assays for SARS-CoV-2 play a pivotal role in the definition of whether patients are infected, the understanding of viral epidemiology, the screening of convalescent sera for therapeutic and prophylactic purposes, and in obtaining a better understanding of the immune response towards the [...] Read more.
Serological assays for SARS-CoV-2 play a pivotal role in the definition of whether patients are infected, the understanding of viral epidemiology, the screening of convalescent sera for therapeutic and prophylactic purposes, and in obtaining a better understanding of the immune response towards the virus. The aim of this study was to investigate the performance of a bead-based multiplex assay. This assay allowed for the simultaneous testing of IgG antibodies against SARS-CoV-2 spike, S1, S2, RBD, and nucleocapsid moieties and S1 of seasonal coronaviruses hCoV-22E, hCoV-HKU1, hCoV-NL63, and hCoV-OC43, as well as MERS and SARS-CoV. We compared the bead-based multiplex assay with commercial ELISA tests. We tested the sera of 27 SARS-CoV-2 PCR-positive individuals who were previously tested with different ELISA assays. Additionally, we investigated the reproducibility of the results by means of multiple testing of the same sera. Finally, the results were correlated with neutralising assays. In summary, the concordance of the qualitative results ranged between 78% and 96% depending on the ELISA assay and the specific antigen. Repeated freezing–thawing cycles resulted in reduced mean fluorescence intensity, while the storage period had no influence in this respect. In our test cohort, we detected up to 36% of sera positive for the development of neutralising antibodies, which is in concordance with the bead-based multiplex and IgG ELISA. Full article
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20 pages, 3356 KiB  
Article
Multiomics Picture of Obesity in Young Adults
by Olga I. Kiseleva, Mikhail A. Pyatnitskiy, Viktoriia A. Arzumanian, Ilya Y. Kurbatov, Valery V. Ilinsky, Ekaterina V. Ilgisonis, Oksana A. Plotnikova, Khaider K. Sharafetdinov, Victor A. Tutelyan, Dmitry B. Nikityuk, Elena A. Ponomarenko and Ekaterina V. Poverennaya
Biology 2024, 13(4), 272; https://doi.org/10.3390/biology13040272 - 18 Apr 2024
Viewed by 902
Abstract
Obesity is a socially significant disease that is characterized by a disproportionate accumulation of fat. It is also associated with chronic inflammation, cancer, diabetes, and other comorbidities. Investigating biomarkers and pathological processes linked to obesity is especially vital for young individuals, given their [...] Read more.
Obesity is a socially significant disease that is characterized by a disproportionate accumulation of fat. It is also associated with chronic inflammation, cancer, diabetes, and other comorbidities. Investigating biomarkers and pathological processes linked to obesity is especially vital for young individuals, given their increased potential for lifestyle modifications. By comparing the genetic, proteomic, and metabolomic profiles of individuals categorized as underweight, normal, overweight, and obese, we aimed to determine which omics layer most accurately reflects the phenotypic changes in an organism that result from obesity. We profiled blood plasma samples by employing three omics methodologies. The untargeted GC×GC–MS metabolomics approach identified 313 metabolites. To augment the metabolomic dataset, we integrated a label-free HPLC–MS/MS proteomics method, leading to the identification of 708 proteins. The genomic layer encompassed the genotyping of 647,250 SNPs. Utilizing omics data, we trained sparse Partial Least Squares models to predict body mass index. Molecular features exhibiting frequently non-zero coefficients were selected as potential biomarkers, and we further explored enriched biological pathways. Proteomics was the most effective in single-omics analyses, with a median absolute error (MAE) of 5.44 ± 0.31 kg/m2, incorporating an average of 24 proteins per model. Metabolomics showed slightly lower performance (MAE = 6.06 ± 0.33 kg/m2), followed by genomics (MAE = 6.20 ± 0.34 kg/m2). As expected, multiomic models demonstrated better accuracy, particularly the combination of proteomics and metabolomics (MAE = 4.77 ± 0.33 kg/m2), while including genomics data did not enhance the results. This manuscript is the first multiomics study of obesity in a gender-balanced cohort of young adults profiled by genomic, proteomic, and metabolomic methods. The comprehensive approach provides novel insights into the molecular mechanisms of obesity, opening avenues for more targeted interventions. Full article
(This article belongs to the Special Issue Multi-Omics Co-expression Network Analysis)
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15 pages, 4176 KiB  
Article
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
Viewed by 807
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
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21 pages, 5247 KiB  
Article
Antihypertensive Potential of Japanese Quail (Couturnix Couturnix Japonica) Egg Yolk Oil (QEYO) in Sprague Dawley Rats
by Muhammad Sani Ismaila, Sherifat Olayemi Balogun-Raji, Fahad Hamza, Usman Bello Sadiya, Buhari Salisu, Mohammed Umar, Ishaka Aminu and Kegan Romelle Jones
Biology 2024, 13(4), 270; https://doi.org/10.3390/biology13040270 - 18 Apr 2024
Viewed by 780
Abstract
Oils from animal sources have been used for centuries in the management of diseases. This research was conducted to screen the ex vivo and in vivo toxicity of quail egg yolk oil (QEYO) extracts and assess their effects on the management of hypertension [...] Read more.
Oils from animal sources have been used for centuries in the management of diseases. This research was conducted to screen the ex vivo and in vivo toxicity of quail egg yolk oil (QEYO) extracts and assess their effects on the management of hypertension in rats. QEYO was extracted using gentle heating (GH) and n-hexane (NHN). The extracts were subjected to toxicity testing using the hen’s egg test on chorioallantoic membrane (HET-CAM) and bovine corneal histology test. Acute and sub-chronic toxicity (28 days) were evaluated in rats. Hypertension was induced in rats by administering 80 mg/kg of Nω-L-Arginine Methyl Ester (L-NAME) per day for 28 days. Treatments commenced on the 14th day; Nifedipine at 30 mg/kg and 1 mL of distilled water were administered as positive and negative controls. Blood pressure (BP), lipid profiles, and oxidative stress markers were quantified. No irritation was observed using the HET-CAM test in the egg treated with both extracts. Bovine corneal histology showed no lesions in all treated groups. No signs of toxicity were observed in either acute or sub-chronic toxicity studies. A significant reduction in blood pressure was observed in rats treated with the extracts (p < 0.05). Changes in total cholesterol (TC), triglycerides (TGs), low-density lipoproteins (LDLPs), and high-density lipoproteins (HDLPs) were not significant compared to the control (p > 0.05). Oxidative stress markers (SOD and CAT) increased significantly in the treated groups compared to the control, while the malondialdehyde levels decreased (p < 0.05). QEYO was safe in both ex vivo and in vivo studies and can be said to have the potential to lower blood pressure as well as cardio-protective effects in hypertensive rats. This research provides evidence based on which QEYO could be used safely as an adjuvant therapy in eye drops and cosmetics and can be considered an effective choice for preventing hypertension. Full article
(This article belongs to the Special Issue Pathophysiology of Hypertension and Related Diseases)
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19 pages, 6346 KiB  
Review
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
Viewed by 881
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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14 pages, 1720 KiB  
Article
Analysis of Elimination Effects of Inbreeding on Genotype Frequency in Larval Stages of Chinese Shrimp
by Qiang Fu, Jingxin Zhou, Sheng Luan, Ping Dai, Ding Lyu, Baolong Chen, Kun Luo, Jie Kong and Xianhong Meng
Biology 2024, 13(4), 268; https://doi.org/10.3390/biology13040268 - 17 Apr 2024
Viewed by 769
Abstract
Marine animals possess genomes of considerable complexity and heterozygosity. Their unique reproductive system, characterized by high fecundity and substantial early mortality rates, increases the risk of inbreeding, potentially leading to severe inbreeding depression during various larval developmental stages. In this study, we established [...] Read more.
Marine animals possess genomes of considerable complexity and heterozygosity. Their unique reproductive system, characterized by high fecundity and substantial early mortality rates, increases the risk of inbreeding, potentially leading to severe inbreeding depression during various larval developmental stages. In this study, we established a set of inbred families of Fenneropenaeus chinensis, with an inbreeding coefficient of 0.25, and investigated elimination patterns and the manifestations of inbreeding depression during major larval developmental stages. Reduced-representation genome sequencing was utilized to explore the genotype frequency characteristics across two typical elimination stages. The results revealed notable mortality in hatching and metamorphosis into mysis and post-larvae stages. Inbreeding depression was also evident during these developmental stages, with depression rates of 24.36%, 29.23%, and 45.28%. Segregation analysis of SNPs indicated an important role of gametic selection before hatching, accounting for 45.95% of deviation in the zoea stage. During the zygotic selection phase of larval development, homozygote deficiency and heterozygote excess were the main selection types. Summation of the two types explained 82.31% and 89.91% of zygotic selection in the mysis and post-larvae stage, respectively. The overall distortion ratio decreased from 22.37% to 12.86% in the late developmental stage. A total of 783 loci were identified through selective sweep analysis. We also found the types of distortion at the same locus could change after the post-larvae stage. The predominant shifts included a transition of gametic selection toward normal segregation and other forms of distortion to heterozygous excess. This may be attributed to high-intensity selection on deleterious alleles and genetic hitchhiking effects. Following larval elimination, a greater proportion of heterozygous individuals were preserved. We detected an increase in genetic diversity parameters such as expected heterozygosity, observed heterozygosity, and polymorphic information content in the post-larvae stage. These findings suggest the presence of numerous recessive deleterious alleles and their linkage and suggest a major role of the partial dominance hypothesis. The results provide valuable insights into the mechanisms of inbreeding depression in marine animals and offer guidance for formulating breeding strategies in shrimp populations. Full article
(This article belongs to the Special Issue Advances in Biological Research into Shrimps, Crabs and Lobsters)
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16 pages, 2821 KiB  
Article
Antioxidant Responses and Growth Impairment in Cucurbita moschata Infected by Meloidogyne incognita
by Yuh Tzean, Kuang-Teng Wang, Elena Gamboa Chen, Hung-Wen Wang, Tsung-Meng Wu and Chia-An Liu
Biology 2024, 13(4), 267; https://doi.org/10.3390/biology13040267 - 16 Apr 2024
Viewed by 828
Abstract
Pumpkins (Cucurbita moschata), valued for their nutritional, medicinal, and economic significance, face threats from Meloidogyne incognita, a critical plant-parasitic nematode. This study extensively examines the impact of M. incognita on the growth, physiological, and biochemical responses of C. moschata. [...] Read more.
Pumpkins (Cucurbita moschata), valued for their nutritional, medicinal, and economic significance, face threats from Meloidogyne incognita, a critical plant-parasitic nematode. This study extensively examines the impact of M. incognita on the growth, physiological, and biochemical responses of C. moschata. We demonstrate that M. incognita infection leads to significant growth impairment in C. moschata, evidenced by reduced plant height and biomass, along with the significant development of nematode-induced galls. Concurrently, a pronounced oxidative stress response was observed, characterized by elevated levels of hydrogen peroxide and a significant increase in antioxidant defense mechanisms, including the upregulation of key antioxidative enzymes (superoxide dismutase, glutathione reductase, catalase, and peroxidase) and the accumulation of glutathione. These responses highlight a dynamic interaction between the plant and the nematode, wherein C. moschata activates a robust antioxidant defense to mitigate the oxidative stress induced by nematode infection. Despite these defenses, the persistence of growth impairment underscores the challenge posed by M. incognita to the agricultural production of C. moschata. Our findings contribute to the understanding of plant–nematode interactions, paving the way for the development of strategies aimed at enhancing resistance in Cucurbitaceae crops against nematode pests, thus supporting sustainable agricultural practices. Full article
(This article belongs to the Section Plant Science)
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41 pages, 20319 KiB  
Review
From Psychostasis to the Discovery of Cardiac Nerves: The Origins of the Modern Cardiac Neuromodulation Concept
by Beatrice Paradiso, Dainius H. Pauza, Clara Limback, Giulia Ottaviani and Gaetano Thiene
Biology 2024, 13(4), 266; https://doi.org/10.3390/biology13040266 - 16 Apr 2024
Viewed by 802
Abstract
This review explores the historical development of cardiology knowledge, from ancient Egyptian psychostasis to the modern comprehension of cardiac neuromodulation. In ancient Egyptian religion, psychostasis was the ceremony in which the deceased was judged before gaining access to the afterlife. This ritual was [...] Read more.
This review explores the historical development of cardiology knowledge, from ancient Egyptian psychostasis to the modern comprehension of cardiac neuromodulation. In ancient Egyptian religion, psychostasis was the ceremony in which the deceased was judged before gaining access to the afterlife. This ritual was also known as the “weighing of the heart” or “weighing of the soul”. The Egyptians believed that the heart, not the brain, was the seat of human wisdom, emotions, and memory. They were the first to recognize the cardiocentric nature of the body, identifying the heart as the center of the circulatory system. Aristotle (fourth century BC) considered the importance of the heart in human physiology in his philosophical analyses. For Galen (third century AD), the heart muscle was the site of the vital spirit, which regulated body temperature. Cardiology knowledge advanced significantly in the 15th century, coinciding with Leonardo da Vinci and Vesalius’s pioneering anatomical and physiological studies. It was William Harvey, in the 17th century, who introduced the concept of cardiac circulation. Servet’s research and Marcello Malpighi’s discovery of arterioles and capillaries provided a more detailed understanding of circulation. Richard Lower emerged as the foremost pioneer of experimental cardiology in the late 17th century. He demonstrated the heart’s neural control by tying off the vagus nerve. In 1753, Albrecht von Haller, a professor at Göttingen, was the first to discover the heart’s automaticity and the excitation of muscle fibers. Towards the end of the 18th century, Antonio Scarpa challenged the theories of Albrecht von Haller and Johann Bernhard Jacob Behrends, who maintained that the myocardium possessed its own “irritability”, on which the heartbeat depended, and was independent of neuronal sensitivity. Instead, Scarpa argued that the heart required innervation to maintain life, refuting Galenic notions. In contemporary times, the study of cardiac innervation has regained prominence, particularly in understanding the post-acute sequelae of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) infection (PASC), which frequently involves cardiorespiratory symptoms and dysregulation of the intrinsic cardiac innervation. Recently, it has been recognized that post-acute sequelae of acute respiratory infections (ARIs) due to other pathogens can also be a cause of long-term vegetative and somatic symptoms. Understanding cardiac innervation and modulation can help to recognize and treat long COVID and long non-COVID-19 (coronavirus disease 2019) ARIs. This analysis explores the historical foundations of cardiac neuromodulation and its contemporary relevance. By focusing on this concept, we aim to bridge the gap between historical understanding and modern applications. This will illuminate the complex interplay between cardiac function, neural modulation, cardiovascular health, and disease management in the context of long-term cardiorespiratory symptoms and dysregulation of intrinsic cardiac innervations. Full article
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11 pages, 1684 KiB  
Systematic Review
Prognostic Electrocardiographic Signs in Arrhythmogenic Cardiomyopathy
by Elisabetta Tonet, Francesco Vitali, Veronica Amantea, Giorgia Azzolini, Cristina Balla, Marco Micillo, Davide Lapolla, Luca Canovi and Matteo Bertini
Biology 2024, 13(4), 265; https://doi.org/10.3390/biology13040265 - 16 Apr 2024
Viewed by 693
Abstract
Arrhythmogenic cardiomyopathy (ACM) is a rare cardiac disease, characterized by the progressive replacement of myocardial tissue with fibrous and fatty deposits. It can involve both the right and left ventricles. It is associated with the development of life-threatening arrhythmias and culminates in sudden [...] Read more.
Arrhythmogenic cardiomyopathy (ACM) is a rare cardiac disease, characterized by the progressive replacement of myocardial tissue with fibrous and fatty deposits. It can involve both the right and left ventricles. It is associated with the development of life-threatening arrhythmias and culminates in sudden cardiac death. Electrocardiography (ECG) has emerged as a pivotal tool, offering diagnostic insights and prognostic information. The specific ECG abnormalities observed in ACM not only contribute to early detection but also hold the key to the prediction of the likelihood of severe complications. The recognition of these nuanced ECG manifestations has become imperative for clinicians as it guides them in the formulation of tailored therapeutic strategies that address both the present symptoms and the potential future risks. Full article
(This article belongs to the Section Medical Biology)
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16 pages, 1776 KiB  
Article
First Observations of Buzzards (Buteo) as Definitive Hosts of Sarcocystis Parasites Forming Cysts in the Brain Tissues of Rodents in Lithuania
by Petras Prakas, Marius Jasiulionis, Tautvilė Šukytė, Evelina Juozaitytė-Ngugu, Vitalijus Stirkė, Linas Balčiauskas and Dalius Butkauskas
Biology 2024, 13(4), 264; https://doi.org/10.3390/biology13040264 - 16 Apr 2024
Viewed by 858
Abstract
Representatives of the genus Sarcocystis are worldwide distributed apicomplexan parasites characterised by two-host prey-predator relationships. Sarcocystis spp. produce sarcocysts in the muscles and brains of intermediate hosts and develop sporocysts in the intestines of definitive hosts. Two species, Sarcocystis glareoli and Sarcocystis microti [...] Read more.
Representatives of the genus Sarcocystis are worldwide distributed apicomplexan parasites characterised by two-host prey-predator relationships. Sarcocystis spp. produce sarcocysts in the muscles and brains of intermediate hosts and develop sporocysts in the intestines of definitive hosts. Two species, Sarcocystis glareoli and Sarcocystis microti, previously assigned to the genus Frenkelia, form cysts in the brains of rodents and are transmitted through the common buzzard (Buteo buteo). In our study, brain samples of 694 small mammals caught in different regions of Lithuania were examined for Sarcocystis spp. Additionally, 10 B. buteo and two rough-legged buzzards (Buteo lagopus) were tested for sporocysts of the analysed parasites. Sarcocystis species were identified based on 28S rRNA sequence comparison. Of the eleven species of small mammals tested, Sarcocystis parasites were observed only in the bank vole (Clethrionomys glareolus). Cysts of S. glareoli were detected in 34 out of 374 C. glareolus (9.1%, 95% CI = 6.4–12.5%). Molecular investigation showed the presence of only S. glareoli in the intestines of 50% of B. buteo. Furthermore, two species, Sarcocystis sp. Rod3 and Sarcocystis sp. Rod4, were confirmed in B. lagopus. Our results demonstrate the need for further studies on Sarcocystis cycling between rodents and birds. Full article
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14 pages, 3496 KiB  
Article
Effects of Chronic Stress from High Stocking Density in Mariculture: Evaluations of Growth Performance and Lipid Metabolism of Rainbow Trout (Oncorhychus mykiss)
by Zhao Li, Qinfeng Gao, Shuanglin Dong, Kang Dong, Yuling Xu, Yaoping Mei and Zhishuai Hou
Biology 2024, 13(4), 263; https://doi.org/10.3390/biology13040263 - 16 Apr 2024
Viewed by 887
Abstract
(1) Background: In aquaculture, chronic stress due to high stocking density impairs animals’ welfare and results in declined fishery production with low protein quality. However, most previous studies evaluated the effects of high stocking density on trout in freshwater rather than seawater. (2) [...] Read more.
(1) Background: In aquaculture, chronic stress due to high stocking density impairs animals’ welfare and results in declined fishery production with low protein quality. However, most previous studies evaluated the effects of high stocking density on trout in freshwater rather than seawater. (2) Methods: Juvenile trout were reared for 84 days in circular tanks under three stocking densities, including low density (“LD”, 9.15 kg/m3), moderate density (“MD”, 13.65 kg/m3), and high density (“HD”, 27.31 kg/m3) in seawater. The final densities of LD, MD, and HD were 22.00, 32.05 and 52.24 kg/m3, respectively. Growth performance and lipid metabolism were evaluated. (3) Results: Growth performance and feeding efficiency were significantly reduced due to chronic stress under high density in mariculture. The digestive activity of lipids was promoted in the gut of HD fish, while the concentration of triglycerides was decreased in the blood. Furthermore, decreased acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS), increased hormone-sensitive lipase (HSL) concentrations, and activated hepatic β-oxidation processes were observed in trout under HD. Redundancy analysis showed that glycerol and HSL can be used as potential markers to evaluate the growth performance of trout in mariculture. (4) Conclusions: We showed that chronic high stocking density led to negative effects on growth performance, reduced de novo synthesis of fatty acids, and enhanced lipolysis. Full article
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12 pages, 6719 KiB  
Article
Activation of Cryptochrome 4 from Atlantic Herring
by Anders Frederiksen, Mandus Aldag, Ilia A. Solov’yov and Luca Gerhards
Biology 2024, 13(4), 262; https://doi.org/10.3390/biology13040262 - 15 Apr 2024
Viewed by 844
Abstract
Marine fish migrate long distances up to hundreds or even thousands of kilometers for various reasons that include seasonal dependencies, feeding, or reproduction. The ability to perceive the geomagnetic field, called magnetoreception, is one of the many mechanisms allowing some fish to navigate [...] Read more.
Marine fish migrate long distances up to hundreds or even thousands of kilometers for various reasons that include seasonal dependencies, feeding, or reproduction. The ability to perceive the geomagnetic field, called magnetoreception, is one of the many mechanisms allowing some fish to navigate reliably in the aquatic realm. While it is believed that the photoreceptor protein cryptochrome 4 (Cry4) is the key component for the radical pair-based magnetoreception mechanism in night migratory songbirds, the Cry4 mechanism in fish is still largely unexplored. The present study aims to investigate properties of the fish Cry4 protein in order to understand the potential involvement in a radical pair-based magnetoreception. Specifically, a computationally reconstructed atomistic model of Cry4 from the Atlantic herring (Clupea harengus) was studied employing classical molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) methods to investigate internal electron transfers and the radical pair formation. The QM/MM simulations reveal that electron transfers occur similarly to those found experimentally and computationally in Cry4 from European robin (Erithacus rubecula). It is therefore plausible that the investigated Atlantic herring Cry4 has the physical and chemical properties to form radical pairs that in turn could provide fish with a radical pair-based magnetic field compass sensor. Full article
(This article belongs to the Special Issue The Rules of Life Rethought: Latest Progress in Quantum Biology)
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20 pages, 3266 KiB  
Article
Genome-Wide Association Study of Early Vigour-Related Traits for a Rice (Oryza sativa L.) japonica Diversity Set Grown in Aerobic Conditions
by Wenliu Gong, Christopher Proud, Ricky Vinarao, Shu Fukai and Jaquie Mitchell
Biology 2024, 13(4), 261; https://doi.org/10.3390/biology13040261 - 15 Apr 2024
Viewed by 879
Abstract
Aerobic rice production is a relatively new system in which rice is direct-seeded and grown in non-flooded but well-watered conditions to improve water productivity. Early vigour-related traits are likely to be important in aerobic conditions. This study aimed to identify quantitative trait loci [...] Read more.
Aerobic rice production is a relatively new system in which rice is direct-seeded and grown in non-flooded but well-watered conditions to improve water productivity. Early vigour-related traits are likely to be important in aerobic conditions. This study aimed to identify quantitative trait loci (QTL) and candidate genes associated with early vigour-related traits in aerobic conditions using a japonica rice diversity set. Field experiments and glasshouse experiments conducted under aerobic conditions revealed significant genotypic variation in early vigour-related traits. Genome-wide association analysis identified 32 QTL associated with early vigour-related traits. Notably, two QTL, qAEV1.5 and qAEV8, associated with both early vigour score and mesocotyl length, explained up to 22.1% of the phenotypic variance. In total, 23 candidate genes related to plant growth development and abiotic stress response were identified in the two regions. This study provides novel insights into the genetic basis of early vigour under aerobic conditions. Validation of identified QTL and candidate genes in different genetic backgrounds is crucial for future studies. Moreover, testing the effect of QTL on yield under different environments would be valuable. After validation, these QTL and genes can be considered for developing markers in marker-assisted selection for aerobic rice production. Full article
(This article belongs to the Section Plant Science)
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15 pages, 940 KiB  
Article
Risk Assessment and Sources Apportionment of Toxic Metals in Two Commonly Consumed Fishes from a Subtropical Estuarine Wetland System
by Md. Moudud Ahmed, As-Ad Ujjaman Nur, Salma Sultana, Yeasmin N. Jolly, Bilal Ahamad Paray, Takaomi Arai, Jimmy Yu and Mohammad Belal Hossain
Biology 2024, 13(4), 260; https://doi.org/10.3390/biology13040260 - 14 Apr 2024
Cited by 1 | Viewed by 958
Abstract
The widespread occurrence of heavy metals in aquatic environments, resulting in their bioaccumulation within aquatic organisms like fish, presents potential hazards to human health. This study investigates the concentrations of five toxic heavy metals (Pb, Hg, Zn, Cu, and Cr) and their potential [...] Read more.
The widespread occurrence of heavy metals in aquatic environments, resulting in their bioaccumulation within aquatic organisms like fish, presents potential hazards to human health. This study investigates the concentrations of five toxic heavy metals (Pb, Hg, Zn, Cu, and Cr) and their potential health implications in two economically important fish species (Otolithoides pama and Labeo bata) from a subtropical estuarine wetland system (Feni estuary, Bangladesh). Muscle and gill samples from 36 individual fish were analyzed using energy dispersive X-ray fluorescence (EDXRF). The results revealed that the average quantities of heavy metals in both fishes’ muscle followed the declining order of Zn (109.41–119.93 mg/kg) > Cu (45.52–65.43 mg/kg) > Hg (1.25–1.39 mg/kg) > Pb (0.68–1.12 mg/kg) > Cr (0.31–5.82 mg/kg). Furthermore, Zn was found to be present in the highest concentration within the gills of both species. While the levels of Cu, Zn, and Cr in the fish muscle were deemed acceptable for human consumption, the concentrations of Pb and Hg exceeded the permissible limits (>0.5 mg/kg) for human consumption. Different risk indices, including estimated daily intake (EDI), target hazard quotient (THQ), hazard index (HI), and carcinogenic or target risk (TR), revealed mixed and varying degrees of potential threat to human health. According to the EDI values, individuals consuming these fish may face health risks as the levels of Zn, Cu, and Cr in the muscle are either very close to or exceed the maximum tolerable daily intake (MTDI) threshold. Nevertheless, the THQ and HI values suggested that both species remained suitable for human consumption, as indicated by THQ (<1) and HI (<1) values. Carcinogenic risk values for Pb, Cr, and Zn all remained within permissible limits, with TR values falling below the range of (10−6 to 10−4), except for Zn, which exceeded it (>10−4). The correlation matrix and multivariate principal component analysis (PCA) findings revealed that Pb and Cr primarily stemmed from natural geological backgrounds, whereas Zn, Cu, and Hg were attributed to human-induced sources such as agricultural chemicals, silver nanoparticles, antimicrobial substances, and metallic plating. Given the significance of fish as a crucial and nutritious element of a balanced diet, it is essential to maintain consistent monitoring and regulation of the levels and origins of heavy metals found within it. Full article
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11 pages, 1089 KiB  
Article
Population Genetic Assessment Model Reveals Conservation Priorities for Gymnocypris Species Resources on the Qinghai-Tibetan Plateau
by Jinqiang Quan, Yuling Qu, Yongqing Li, Yue Ren, Guiyan Zhao, Lanlan Li and Junhao Lu
Biology 2024, 13(4), 259; https://doi.org/10.3390/biology13040259 - 14 Apr 2024
Viewed by 633
Abstract
The Qinghai-Tibetan Plateau (QTP) has nurtured a rich diversity of species because of its unique geographical and environmental conditions. Gymnocypris species (subfamily Schizopygopsinae) are primitive fishes that live in the special environment of the plateau, and their evolution and distribution are inseparable from [...] Read more.
The Qinghai-Tibetan Plateau (QTP) has nurtured a rich diversity of species because of its unique geographical and environmental conditions. Gymnocypris species (subfamily Schizopygopsinae) are primitive fishes that live in the special environment of the plateau, and their evolution and distribution are inseparable from the historical changes of the QTP. Recently, the resources of Gymnocypris species have been decreasing due to habit deterioration and the intensification of human activities. Therefore, the scientific conservation of the genetic resources of Gymnocypris species is urgently required. In this study, we established two models for the priority conservation assessment of germplasm resources of Gymnocypris species on the basis of the genetic diversity and phylogenetic relationships of 674 individuals from eight Gymnocypris species populations. The results show that the Gymnocypris potanini (GPO), Gymnocypris eckloni (GE), and Gymnocypris przewalskii (GPR) populations are the most genetically diverse in terms of combined genetic diversity values and should be prioritized for conservation. In terms of genetic contribution, the GPO, GE, and GPR populations have a positive impact on maintaining the distinctiveness and diversity of the entire Gymnocypris species population and should be prioritized for conservation. However, in terms of different evolutionary clades, the Gymnocypris namensis, Gymnocypris waddellii, Gymnocypris dobula, and GE populations in clade A should be given priority for protection, the GE population in clade B should be given priority, and the GPR population in clade C should be given priority. In conclusion, the two models and assessment of conservation priorities will provide a scientific basis for the conservation of Gymnocypris species. Full article
(This article belongs to the Section Conservation Biology and Biodiversity)
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14 pages, 1849 KiB  
Review
The MCM2-7 Complex: Roles beyond DNA Unwinding
by Brooke D. Rankin and Susannah Rankin
Biology 2024, 13(4), 258; https://doi.org/10.3390/biology13040258 - 13 Apr 2024
Viewed by 1037
Abstract
The MCM2-7 complex is a hexameric protein complex that serves as a DNA helicase. It unwinds the DNA double helix during DNA replication, thereby providing the single-stranded replication template. In recent years, it has become clear that the MCM2-7 complex has additional functions [...] Read more.
The MCM2-7 complex is a hexameric protein complex that serves as a DNA helicase. It unwinds the DNA double helix during DNA replication, thereby providing the single-stranded replication template. In recent years, it has become clear that the MCM2-7 complex has additional functions that extend well beyond its role in DNA replication. Through physical and functional interactions with different pathways, it impacts other nuclear events and activities, including folding of the genome, histone inheritance, chromosome segregation, DNA damage sensing and repair, and gene transcription. Collectively, the diverse roles of the MCM2-7 complex suggest it plays a critical role in maintaining genome integrity by integrating the regulation of DNA replication with other pathways in the nucleus. Full article
(This article belongs to the Special Issue The Replication Licensing System)
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13 pages, 677 KiB  
Article
Comparison of Polymerase Chain Reaction and Urine Culture in the Evaluation of Patients with Complex Urinary Tract Infections
by Deepak A. Kapoor, Mara R. Holton, Jason Hafron, Rima Aljundi, Bernadette Zwaans and Mitchell Hollander
Biology 2024, 13(4), 257; https://doi.org/10.3390/biology13040257 - 13 Apr 2024
Viewed by 775
Abstract
To compare organism identification using polymerase chain reaction (PCR) and urine culture (UC) in patients with complex urinary tract infections (cUTIs), we reviewed the results of 3395 patients seen during 2022 with cUTI who underwent concomitant PCR and UC testing. We compared the [...] Read more.
To compare organism identification using polymerase chain reaction (PCR) and urine culture (UC) in patients with complex urinary tract infections (cUTIs), we reviewed the results of 3395 patients seen during 2022 with cUTI who underwent concomitant PCR and UC testing. We compared the overall positivity rates as well as the ability of each test to identify fastidious organisms (FOs) and the presence of polymicrobial infections (PMOs) and conducted concordance analysis between the tests. PCR detected 36.4% more organisms than UC and was 20 and nearly 36 times more likely to detect PMOs and FOs, respectively. PCR identified 90.6% of organisms found in UC, whereas UC identified 40.7% of organisms found in PCR testing. We found that 62.4% of organisms found in PCR were not found in urine culture, while UC found 9.4% of organisms not identified in polymerase chain reaction. All these differences were statistically significant (p < 0.05). Although we found that PCR was superior to UC in overall pathogen detection, and detection of both PMOs and FOs, both identified potentially pathogenic organisms not found in the corresponding test. Our data strongly suggest that the evaluation of patients with cUTI is best accomplished using PCR in conjunction with UC. Full article
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17 pages, 5810 KiB  
Article
Development and Application of a High-Throughput Method for the Purification and Analysis of Surface Carbohydrates from Klebsiella pneumoniae
by Francesca Nonne, Mariagrazia Molfetta, Rebecca Nappini, Chiara La Guidara, Roberta Di Benedetto, Siwaphiwe Mfana, Barbara Bellich, Maria Michelina Raso, Gianmarco Gasperini, Renzo Alfini, Paola Cescutti, Francesco Berlanda Scorza, Neil Ravenscroft, Francesca Micoli and Carlo Giannelli
Biology 2024, 13(4), 256; https://doi.org/10.3390/biology13040256 - 12 Apr 2024
Viewed by 992
Abstract
Klebsiella pneumoniae (Kp) is a Gram-negative bacterium, and a leading cause of neonatal sepsis in low- and middle-income countries, often associated with anti-microbial resistance. Two types of polysaccharides are expressed on the Kp cell surface and have been proposed as key antigens for [...] Read more.
Klebsiella pneumoniae (Kp) is a Gram-negative bacterium, and a leading cause of neonatal sepsis in low- and middle-income countries, often associated with anti-microbial resistance. Two types of polysaccharides are expressed on the Kp cell surface and have been proposed as key antigens for vaccine design: capsular polysaccharides (known as K-antigens, K-Ags) and O-antigens (O-Ags). Historically, Kp has been classified using capsule serotyping and although 186 distinct genotypes have been predicted so far based on sequence analysis, many structures are still unknown. In contrast, only 11 distinct OAg serotypes have been described. The characterization of emerging strains requires the development of a high-throughput purification method to obtain sufficient K- and O-Ag material to characterize the large collection of serotypes and gain insight on structural features and potential cross-reactivity that could allow vaccine simplification. Here, this was achieved by adapting our established method for the simple purification of O-Ags, using mild acetic acid hydrolysis performed directly on bacterial cells, followed by filtration and precipitation steps. The method was successfully applied to purify the surface carbohydrates from different Kp strains, thereby demonstrating the robustness and general applicability of the purification method developed. Further, antigen characterization showed that the purification method had no impact on the structural integrity of the polysaccharides and preserved labile substituents such as O-acetyl and pyruvyl groups. This method can be further optimized for scaling up and manufacturing to support the development of high-valency saccharide-based vaccines against Kp. Full article
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19 pages, 3481 KiB  
Article
Screening of Microalgae for Bioactivity with Antiviral, Antibacterial, Anti-Inflammatory and Anti-Cancer Assays
by Jorge Hernández-Urcera, Alejandro Romero, Pedro Cruz, Vitor Vasconcelos, Antonio Figueras, Beatriz Novoa and Francisco Rodríguez
Biology 2024, 13(4), 255; https://doi.org/10.3390/biology13040255 - 12 Apr 2024
Viewed by 1342
Abstract
Marine microalgae are a rich reservoir of natural compounds, including bioactives. Nonetheless, these organisms remain fairly unexplored despite their potential biotechnological applications. Culture collections with diverse taxonomic groups and lifestyles are a good source to unlock this potential and discover new molecules for [...] Read more.
Marine microalgae are a rich reservoir of natural compounds, including bioactives. Nonetheless, these organisms remain fairly unexplored despite their potential biotechnological applications. Culture collections with diverse taxonomic groups and lifestyles are a good source to unlock this potential and discover new molecules for multiple applications such as the treatment of human pathologies or the production of aquaculture species. In the present work extracts from thirty-three strains (including twenty dinoflagellates, four diatoms and nine strains from seven other algal classes), cultivated under identical conditions, were examined for their antiviral, antibacterial, anti-inflammatory and anti-cancer activities. Among these, antiviral and anti-inflammatory activities were detected in a few strains while the antibacterial tests showed positive results in most assays. In turn, most trials did not show any anti-cancer activity. Significant differences were observed between species within the same class, in particular dinoflagellates, which were better represented in this study. These preliminary findings pave the way for an in-depth characterization of the extracts with highest signals in each test, the identification of the compounds responsible for the biological activities found and a further screening of the CCVIEO culture collection. Full article
(This article belongs to the Section Marine Biology)
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12 pages, 1366 KiB  
Article
Bacterial Community Structure Responds to Soil Management in the Rhizosphere of Vine Grape Vineyards
by Barnabás Kovács, Marco Andreolli, Silvia Lampis, Borbála Biró and Zsolt Kotroczó
Biology 2024, 13(4), 254; https://doi.org/10.3390/biology13040254 - 12 Apr 2024
Viewed by 774
Abstract
The microbial communities of the rhizospheres of vineyards have been subject to a considerable body of research, but it is still unclear how the applied soil cultivation methods are able to change the structure, composition, and level of diversity of their communities. Rhizosphere [...] Read more.
The microbial communities of the rhizospheres of vineyards have been subject to a considerable body of research, but it is still unclear how the applied soil cultivation methods are able to change the structure, composition, and level of diversity of their communities. Rhizosphere samples were collected from three neighbouring vineyards with the same time of planting and planting material (rootstock: Teleki 5C; Vitis vinifera: Müller Thurgau). Our objective was to examine the diversity occurring in bacterial community structures in vineyards that differ only in the methods of tillage procedure applied, namely intensive (INT), extensive (EXT), and abandoned (AB). For that we took samples from two depths (10–30 cm (shallow = S) and 30–50 cm (deep = D) of the grape rhizosphere in each vineyard and the laboratory and immediately prepared the slices of the roots for DNA-based analysis of the bacterial communities. Bacterial community structure was assessed by means of PCR-DGGE analysis carried out on the v3 region of 16S rRNA gene. Based on the band composition of the DGGE profiles thus obtained, the diversity of the microbial communities was evaluated and determined by the Shannon–Weaver index (H′). Between the AB and EXT vineyards at the S depth, the similarity of the community structure was 55%; however, the similarity of the D samples was more than 80%, while the difference between the INT samples and the other two was also higher than 80%. Based on our results, we can conclude that intensive cultivation strongly affects the structure and diversity of the bacterial community. Full article
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Article
Mesenchymal Stem Cell-Derived Exosomes Loaded with Selenium or Nano Selenium as a Novel Therapeutic Paradigm for Streptozotocin-Induced Type 1 Diabetes in Rats
by Dlovan Y. Khalil, Ridah H. Hussein and Wafaa M. El-Kholy
Biology 2024, 13(4), 253; https://doi.org/10.3390/biology13040253 - 11 Apr 2024
Viewed by 925
Abstract
Type 1 diabetes mellitus (T1DM) is a metabolic disorder characterized by hyperglycemia due to insulin insufficiency as a consequence of the pancreatic β-cells’ auto-immune attack. Nowadays, the application of mesenchymal stem cell-derived exosomes (MSCs-Exs) as the main cell-free therapy for diabetes treatment is [...] Read more.
Type 1 diabetes mellitus (T1DM) is a metabolic disorder characterized by hyperglycemia due to insulin insufficiency as a consequence of the pancreatic β-cells’ auto-immune attack. Nowadays, the application of mesenchymal stem cell-derived exosomes (MSCs-Exs) as the main cell-free therapy for diabetes treatment is becoming more and more extensive. In non-autologous therapy, researchers are moving towards a new strategy based on loading MSC-Exs with certain drugs, aimed at maintaining and maximizing the function of exosomes at the function site and enhancing their efficiency and safety. This study aims to explore and compare the therapeutic potentialities of mesenchymal stem cell-derived exosomes (MSCs-Exs) loaded with either selenium (Se) or nano selenium (NSe), a natural antioxidant micronutrient, in the management of T1DM in rats. In our 4-week experiment, six rat groups were included, namely, control, Ex+Se, Ex+NSe, STZ-diabetic (D), D+ Ex+Se, and D+Ex+NSe groups. Both diabetic-treated groups showed marked pancreatic regenerative antioxidant, immunomodulatory, anti-inflammatory, and anti-apoptotic capacities, with the D+Ex+NSe injection showing superiority in managing diabetes hazards, as evidenced by various biochemical and histological assessments. Full article
(This article belongs to the Special Issue Animal Models of Pancreatic Diseases)
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