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Biology, Volume 12, Issue 9 (September 2023) – 118 articles

Cover Story (view full-size image): Cells are exposed to various extrinsic and intrinsic stressors like infections, oxidative stress, endoplasmic reticulum stress, chemotherapeutic agents and stressors in the tumor microenvironment (TME). Cells initiate the Integrated Stress Response (ISR) pathway to maintain cellular homeostasis in the presence of these stressors. The ISR pathway modulates the activation of regulated cell death (RCD) pathways to determine the live-or-die cell fate choice under stress. View this paper
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18 pages, 1175 KiB  
Article
eDNA Metabarcoding- and Microscopic Analysis for Diet Determination in Waterfowl, a Comparative Study in Vejlerne, Denmark
by Anna-Sofie Lützhøft Svendsen, Louise Bach Nielsen, Jakob Braüner Schmidt, Dan Bruhn, Line Holm Andersen and Cino Pertoldi
Biology 2023, 12(9), 1272; https://doi.org/10.3390/biology12091272 - 21 Sep 2023
Cited by 1 | Viewed by 1212
Abstract
Understanding diets and structural food webs are keys to the apprehension of ecological communities, upon which conservation and management biology are based. The understanding of grazing and habitat choice for waterfowl is one of the most important topics for avian ecologists today and [...] Read more.
Understanding diets and structural food webs are keys to the apprehension of ecological communities, upon which conservation and management biology are based. The understanding of grazing and habitat choice for waterfowl is one of the most important topics for avian ecologists today and can, to some degree, be answered by dietary analysis. Droppings collected from four waterfowl, the Eurasian wigeon (Anas penelope), Greylag goose (Anser anser), pink-footed goose (Anser brachyrhynchus) and Barnacle goose (Branta leucopsis) in Vejlerne (Denmark), were analysed microscopically and through eDNA metabarcoding with the use of next generation sequencing (NGS) to accumulate knowledge about the diet of these waterfowl. In total, 120 dropping samples were microscopically analysed, of which the eDNA metabarcoding analysis was done on 79 samples. The prey items were identified according to the taxonomic level of species, and a qualitative method, frequency of occurrence (FO) and FO calculated as a percentage, was used in order to compare the results from the two methods. As neither of the methods was able to encompass all species discovered when combining the two methods, it was concluded in this study that the two methods can support each other in a dietary analysis of waterfowl, but not replace one another. Full article
(This article belongs to the Special Issue Feature Papers in 'Conservation Biology and Biodiversity')
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20 pages, 2422 KiB  
Article
Taxonomic Composition and Salinity Tolerance of Macrozoobenthos in Small Rivers of the Southern Arid Zone of the East European Plain
by Larisa V. Golovatyuk, Larisa B. Nazarova, Irina J. Kalioujnaia and Ivan M. Grekov
Biology 2023, 12(9), 1271; https://doi.org/10.3390/biology12091271 - 21 Sep 2023
Viewed by 1061
Abstract
This study investigated the species composition, distribution, and salinity tolerance of macrozoobenthos in 17 small rivers in the southern arid region of the East European Plain, which are characterized by a small channel gradient, slow-flowing or stagnant water bodies, and a wide range [...] Read more.
This study investigated the species composition, distribution, and salinity tolerance of macrozoobenthos in 17 small rivers in the southern arid region of the East European Plain, which are characterized by a small channel gradient, slow-flowing or stagnant water bodies, and a wide range of water salinity, varying between 0.18 and 30 g L−1. In total, 156 taxa were found, among which 66 were Diptera species. The study revealed that the formation of benthic communities in the rivers is influenced by natural factors of the catchment basins, including the flat landscape with sparsely developed relief differentiation, climate aridity, and the widespread occurrence of saline soils and groundwater, largely related to the sedimentation of the ancient Caspian Sea and modern climate changes. These conditions are favorable for the occurrence of lacustrine macrozoobenthic species in freshwater, euryhaline, and halophilic ecological groups. The investigation revealed a decrease in species richness in response to an increase in water salinity. The five identified halophilic species Tanytarsus kharaensis, Glyptotendipes salinus, Cricotopus salinophilus, Chironomus salinarius, and Palpomyia schmidti can be used as indicators of river ecosystem salinization. Full article
(This article belongs to the Special Issue Palaeolimnology and Hydrobiology)
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22 pages, 6644 KiB  
Article
Isotopic Overlap of Invasive and Native Consumers in the Food Web of Lake Trasimeno (Central Italy)
by Davide Cicala, Maria Teresa Guerra, Roberta Bardelli, Cristina Di Muri, Alessandro Ludovisi, Salvatrice Vizzini and Giorgio Mancinelli
Biology 2023, 12(9), 1270; https://doi.org/10.3390/biology12091270 - 21 Sep 2023
Cited by 1 | Viewed by 1024
Abstract
An advanced characterization of the trophic niche of non-indigenous species (NIS) may provide useful information on their ecological impact on invaded communities. Here, we used carbon and nitrogen stable isotopes to estimate pairwise niche overlaps between non-indigenous and native consumers in the winter [...] Read more.
An advanced characterization of the trophic niche of non-indigenous species (NIS) may provide useful information on their ecological impact on invaded communities. Here, we used carbon and nitrogen stable isotopes to estimate pairwise niche overlaps between non-indigenous and native consumers in the winter food web of Lake Trasimeno (central Italy). Overall, a relatively low pairwise overlap of isotopic niches was observed between NIS and native species. The only exception was the Louisiana crayfish Procambarus clarkii, which showed a relatively high and diffuse overlap with other native invertebrates. Our findings highlighted a high niche divergence between non-indigenous and native species in Lake Trasimeno, suggesting a potentially low degree of interspecific competition that may facilitate coexistence and, in turn, limit the strength of impacts. The divergent results obtained for the Louisiana crayfish indicate that additional control measures for this invasive species are needed to mitigate its impact on the Lake Trasimeno system. Full article
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31 pages, 3113 KiB  
Article
Literature-Based Discovery to Elucidate the Biological Links between Resistant Hypertension and COVID-19
by David Kartchner, Kevin McCoy, Janhvi Dubey, Dongyu Zhang, Kevin Zheng, Rushda Umrani, James J. Kim and Cassie S. Mitchell
Biology 2023, 12(9), 1269; https://doi.org/10.3390/biology12091269 - 21 Sep 2023
Cited by 1 | Viewed by 1883
Abstract
Multiple studies have reported new or exacerbated persistent or resistant hypertension in patients previously infected with COVID-19. We used literature-based discovery to identify and prioritize multi-scalar explanatory biology that relates resistant hypertension to COVID-19. Cross-domain text mining of 33+ million PubMed articles within [...] Read more.
Multiple studies have reported new or exacerbated persistent or resistant hypertension in patients previously infected with COVID-19. We used literature-based discovery to identify and prioritize multi-scalar explanatory biology that relates resistant hypertension to COVID-19. Cross-domain text mining of 33+ million PubMed articles within a comprehensive knowledge graph was performed using SemNet 2.0. Unsupervised rank aggregation determined which concepts were most relevant utilizing the normalized HeteSim score. A series of simulations identified concepts directly related to COVID-19 and resistant hypertension or connected via one of three renin–angiotensin–aldosterone system hub nodes (mineralocorticoid receptor, epithelial sodium channel, angiotensin I receptor). The top-ranking concepts relating COVID-19 to resistant hypertension included: cGMP-dependent protein kinase II, MAP3K1, haspin, ral guanine nucleotide exchange factor, N-(3-Oxododecanoyl)-L-homoserine lactone, aspartic endopeptidases, metabotropic glutamate receptors, choline-phosphate cytidylyltransferase, protein tyrosine phosphatase, tat genes, MAP3K10, uridine kinase, dicer enzyme, CMD1B, USP17L2, FLNA, exportin 5, somatotropin releasing hormone, beta-melanocyte stimulating hormone, pegylated leptin, beta-lipoprotein, corticotropin, growth hormone-releasing peptide 2, pro-opiomelanocortin, alpha-melanocyte stimulating hormone, prolactin, thyroid hormone, poly-beta-hydroxybutyrate depolymerase, CR 1392, BCR-ABL fusion gene, high density lipoprotein sphingomyelin, pregnancy-associated murine protein 1, recQ4 helicase, immunoglobulin heavy chain variable domain, aglycotransferrin, host cell factor C1, ATP6V0D1, imipramine demethylase, TRIM40, H3C2 gene, COL1A1+COL1A2 gene, QARS gene, VPS54, TPM2, MPST, EXOSC2, ribosomal protein S10, TAP-144, gonadotropins, human gonadotropin releasing hormone 1, beta-lipotropin, octreotide, salmon calcitonin, des-n-octanoyl ghrelin, liraglutide, gastrins. Concepts were mapped to six physiological themes: altered endocrine function, 23.1%; inflammation or cytokine storm, 21.3%; lipid metabolism and atherosclerosis, 17.6%; sympathetic input to blood pressure regulation, 16.7%; altered entry of COVID-19 virus, 14.8%; and unknown, 6.5%. Full article
(This article belongs to the Special Issue Machine Learning Applications in Biology)
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15 pages, 1409 KiB  
Article
Maternal Cardiovascular Responses to Position Change in Pregnancy
by Alys R. Clark, Hanna Fontinha, John Thompson, Sophie Couper, Devanshi Jani, Ali Mirjalili, Laura Bennet and Peter Stone
Biology 2023, 12(9), 1268; https://doi.org/10.3390/biology12091268 - 21 Sep 2023
Viewed by 1220
Abstract
The maternal cardiovascular-circulatory system undergoes profound changes almost from the conception of a pregnancy until the postpartum period to support the maternal adaptions required for pregnancy and lactation. Maintenance of cardiovascular homeostasis requires changes in the cardiovascular autonomic responses. Here, we present a [...] Read more.
The maternal cardiovascular-circulatory system undergoes profound changes almost from the conception of a pregnancy until the postpartum period to support the maternal adaptions required for pregnancy and lactation. Maintenance of cardiovascular homeostasis requires changes in the cardiovascular autonomic responses. Here, we present a longitudinal study of the maternal cardiovascular autonomic responses to pregnancy and maternal position. Over a normal gestation, in the left lateral position there are significant changes in both time and frequency domain parameters reflecting heart rate variability. We show that cardiovascular autonomic responses to physiological stressors (standing and supine positions in late pregnancy) became significantly different with advancing gestation. In the third trimester, 60% of the subjects had an unstable heart rate response on standing, and these subjects had a significantly reduced sample entropy evident in their heart rate variability data. By 6 weeks, postpartum function returned to near the non-pregnant state, but there were consistent differences in high-frequency power when compared to nulligravid cases. Finally, we review complementary evidence, in particular from magnetic resonance imaging, that provides insights into the maternal and fetal impacts of positioning in pregnancy. This demonstrates a clear relationship between supine position and maternal hemodynamic parameters, which relates to compression of the inferior vena cava (p = 0.05). Together, these studies demonstrate new understanding of the physiology of physiological stressors related to position. Full article
(This article belongs to the Special Issue Maternal Adaptation in Physiological and Pathological Pregnancy)
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22 pages, 2156 KiB  
Review
From Alpha to Omicron: How Different Variants of Concern of the SARS-Coronavirus-2 Impacted the World
by Mickensone Andre, Lee-Seng Lau, Marissa D. Pokharel, Julian Ramelow, Florida Owens, Joseph Souchak, Juliet Akkaoui, Evan Ales, Harry Brown, Rajib Shil, Valeria Nazaire, Marko Manevski, Ngozi P. Paul, Maria Esteban-Lopez, Yasemin Ceyhan and Nazira El-Hage
Biology 2023, 12(9), 1267; https://doi.org/10.3390/biology12091267 - 21 Sep 2023
Cited by 7 | Viewed by 2033
Abstract
SARS-CoV-2, the virus that causes COVID-19, is prone to mutations and the generation of genetic variants. Since its first outbreak in 2019, SARS-CoV-2 has continually evolved, resulting in the emergence of several lineages and variants of concern (VOC) that have gained more efficient [...] Read more.
SARS-CoV-2, the virus that causes COVID-19, is prone to mutations and the generation of genetic variants. Since its first outbreak in 2019, SARS-CoV-2 has continually evolved, resulting in the emergence of several lineages and variants of concern (VOC) that have gained more efficient transmission, severity, and immune evasion properties. The World Health Organization has given these variants names according to the letters of the Greek Alphabet, starting with the Alpha (B.1.1.7) variant, which emerged in 2020, followed by the Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) variants. This review explores the genetic variation among different VOCs of SARS-CoV-2 and how the emergence of variants made a global impact on the pandemic. Full article
(This article belongs to the Special Issue SARS-CoV-2 and Immunology)
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13 pages, 5766 KiB  
Article
Chromosome-Level Genome Assembly of Protosalanx chinensis and Response to Air Exposure Stress
by Yanfeng Zhou, Xizhao Zhang, Xuemei Tang, Yifan Zhou, Yuting Ding and Hong Liu
Biology 2023, 12(9), 1266; https://doi.org/10.3390/biology12091266 - 21 Sep 2023
Viewed by 879
Abstract
Protosalanx chinensis is a suitable particular species for genetic studies on nearly scaleless skin, transparency and high sensitivity to hypoxia stress. Here, we generated a high-quality chromosome-level de novo assembly of P. chinensis. The final de novo assembly yielded 379.47 Mb with [...] Read more.
Protosalanx chinensis is a suitable particular species for genetic studies on nearly scaleless skin, transparency and high sensitivity to hypoxia stress. Here, we generated a high-quality chromosome-level de novo assembly of P. chinensis. The final de novo assembly yielded 379.47 Mb with 28 pseudo-chromosomes and a scaffold N50 length of 14.52 Mb. In total, 21,074 protein-coding genes were predicted. P. chinensis, Esox lucius and Hypomesus transpacificus had formed a clade, which diverged about 115.5 million years ago. In the air exposure stress experiment, we found that some genes play an essential role during P. chinensis hypoxia, such as bhlh, Cry1, Clock, Arntl and Rorb in the circadian rhythm pathway. These genomic data offer a crucial foundation for P. chinensis ecology and adaptation studies, as well as a deeper understanding of the response to air exposure stress. Full article
(This article belongs to the Section Genetics and Genomics)
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25 pages, 6962 KiB  
Article
Expanding the MAPPs Assay to Accommodate MHC-II Pan Receptors for Improved Predictability of Potential T Cell Epitopes
by Katharina Hartman, Guido Steiner, Michel Siegel, Cary M. Looney, Timothy P. Hickling, Katharine Bray-French, Sebastian Springer, Céline Marban-Doran and Axel Ducret
Biology 2023, 12(9), 1265; https://doi.org/10.3390/biology12091265 - 21 Sep 2023
Cited by 1 | Viewed by 1564
Abstract
A critical step in the immunogenicity cascade is attributed to human leukocyte antigen (HLA) II presentation triggering T cell immune responses. The liquid chromatography–tandem mass spectrometry (LC-MS/MS)-based major histocompatibility complex (MHC) II-associated peptide proteomics (MAPPs) assay is implemented during preclinical risk assessments to [...] Read more.
A critical step in the immunogenicity cascade is attributed to human leukocyte antigen (HLA) II presentation triggering T cell immune responses. The liquid chromatography–tandem mass spectrometry (LC-MS/MS)-based major histocompatibility complex (MHC) II-associated peptide proteomics (MAPPs) assay is implemented during preclinical risk assessments to identify biotherapeutic-derived T cell epitopes. Although studies indicate that HLA-DP and HLA-DQ alleles are linked to immunogenicity, most MAPPs studies are restricted to using HLA-DR as the dominant HLA II genotype due to the lack of well-characterized immunoprecipitating antibodies. Here, we address this issue by testing various commercially available clones of MHC-II pan (CR3/43, WR18, and Tü39), HLA-DP (B7/21), and HLA-DQ (SPV-L3 and 1a3) antibodies in the MAPPs assay, and characterizing identified peptides according to binding specificity. Our results reveal that HLA II receptor-precipitating reagents with similar reported specificities differ based on clonality and that MHC-II pan antibodies do not entirely exhibit pan-specific tendencies. Since no individual antibody clone is able to recover the complete HLA II peptide repertoire, we recommend a mixed strategy of clones L243, WR18, and SPV-L3 in a single immunoprecipitation step for more robust compound-specific peptide detection. Ultimately, our optimized MAPPs strategy improves the predictability and additional identification of T cell epitopes in immunogenicity risk assessments. Full article
(This article belongs to the Special Issue Proteomics in Immunology and Cell Signaling)
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18 pages, 5423 KiB  
Article
Selective Noradrenaline Depletion in the Neocortex and Hippocampus Induces Working Memory Deficits and Regional Occurrence of Pathological Proteins
by Chiara Prinzi, Anna Kostenko, Gioacchino de Leo, Rosario Gulino, Giampiero Leanza and Antonella Caccamo
Biology 2023, 12(9), 1264; https://doi.org/10.3390/biology12091264 - 21 Sep 2023
Viewed by 1521
Abstract
Noradrenaline (NA) depletion occurs in Alzheimer’s disease (AD); however, its relationship with the pathological expression of Tau and transactive response DNA-binding protein 43 (TDP-43), two major hallmarks of AD, remains elusive. Here, increasing doses of a selective noradrenergic immunotoxin were injected into developing [...] Read more.
Noradrenaline (NA) depletion occurs in Alzheimer’s disease (AD); however, its relationship with the pathological expression of Tau and transactive response DNA-binding protein 43 (TDP-43), two major hallmarks of AD, remains elusive. Here, increasing doses of a selective noradrenergic immunotoxin were injected into developing rats to generate a model of mild or severe NA loss. At about 12 weeks post-lesion, dose-dependent working memory deficits were detected in these animals, associated with a marked increase in cortical and hippocampal levels of TDP-43 phosphorylated at Ser 409/410 and Tau phosphorylated at Thr 217. Notably, the total levels of both proteins were largely unaffected, suggesting a direct relationship between neocortical/hippocampal NA depletion and the phosphorylation of pathological Tau and TDP-43 proteins. As pTD43 is present in 23% of AD cases and pTau Thr217 has been detected in patients with mild cognitive impairment that eventually would develop into AD, improvement of noradrenergic function in AD might represent a viable therapeutic approach with disease-modifying potential. Full article
(This article belongs to the Section Neuroscience)
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17 pages, 1510 KiB  
Review
Matrix Metalloproteinases and the Pathogenesis of Recurrent Corneal Erosions and Epithelial Basement Membrane Dystrophy
by Katarzyna Jadczyk-Sorek, Wojciech Garczorz, Beata Bubała-Stachowicz, Tomasz Francuz and Ewa Mrukwa-Kominek
Biology 2023, 12(9), 1263; https://doi.org/10.3390/biology12091263 - 21 Sep 2023
Cited by 1 | Viewed by 1044
Abstract
Matrix metalloproteinases (MMPs) are a group of proteolytic enzymes which are members of the zinc endopeptidase family. They have the ability to degrade extracellular matrix elements, allowing for the release of binding molecules and cell migration. Although metalloproteinases regulate numerous physiological processes within [...] Read more.
Matrix metalloproteinases (MMPs) are a group of proteolytic enzymes which are members of the zinc endopeptidase family. They have the ability to degrade extracellular matrix elements, allowing for the release of binding molecules and cell migration. Although metalloproteinases regulate numerous physiological processes within the cornea, overexpression of metalloproteinase genes and an imbalance between the levels of metalloproteinases and their inhibitors can contribute to the inhibition of repair processes, the development of inflammation and excessive cellular proliferation. The involvement of MMPs in the pathogenesis of dystrophic corneal diseases needs clarification. Our analyses focus on the involvement of individual metalloproteinases in the pathogenesis of recurrent corneal erosions and highlight their impact on the development of corneal epithelial basement membrane dystrophy (EBMD). We hypothesize that abnormalities observed in patients with EBMD may result from the accumulation and activation of metalloproteinases in the basal layers of the corneal epithelium, leading to basement membrane degradation. A barrier formed from degradation materials inhibits the normal migration of epithelial cells to the superficial layers, which contributes to the development of the aforementioned lesions. This hypothesis seems to be lent support by the elevated concentrations of metalloproteinases in the corneal epithelium of these patients found in our previous studies on the relationships between MMPs and recurrent corneal erosions. Full article
(This article belongs to the Special Issue The Role of Matrix Metalloproteinases in Ocular Pathologies)
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16 pages, 1772 KiB  
Article
Exploring Longitudinal Gut Microbiome towards Metabolic Functional Changes Associated in Atopic Dermatitis in Early Childhood
by Preecha Patumcharoenpol, Amornthep Kingkaw, Massalin Nakphaichit, Pantipa Chatchatee, Narissara Suratannon, Gianni Panagiotou and Wanwipa Vongsangnak
Biology 2023, 12(9), 1262; https://doi.org/10.3390/biology12091262 - 20 Sep 2023
Viewed by 1452
Abstract
Atopic dermatitis (AD) is a prevalent inflammatory skin disease that has been associated with changes in gut microbial composition in early life. However, there are limited longitudinal studies examining the gut microbiome in AD. This study aimed to explore taxonomy and metabolic functions [...] Read more.
Atopic dermatitis (AD) is a prevalent inflammatory skin disease that has been associated with changes in gut microbial composition in early life. However, there are limited longitudinal studies examining the gut microbiome in AD. This study aimed to explore taxonomy and metabolic functions across longitudinal gut microbiomes associated with AD in early childhood from 9 to 30 months of age using integrative data analysis within the Thai population. Our analysis revealed that gut microbiome diversity was not different between healthy and AD groups; however, significant taxonomic differences were observed. Key gut bacteria with short-chain fatty acids (SCFAs) production potentials, such as Anaerostipes, Butyricicoccus, Ruminococcus, and Lactobacillus species, showed a higher abundance in the AD group. In addition, metabolic alterations between the healthy and AD groups associated with vitamin production and host immune response, such as biosynthesis of menaquinol, succinate, and (Kdo)2-lipid A, were observed. This study serves as the first framework for monitoring longitudinal microbial imbalances and metabolic functions associated with allergic diseases in Thai children during early childhood. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease)
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13 pages, 1311 KiB  
Article
BLTR1 Is Decreased in Steroid Resistant Pro-Inflammatory CD28nullCD8+ T Lymphocytes in Patients with COPD—The Spillover Hypothesis Explained?
by Greg Hodge, Hubertus Jersmann, Mark Holmes, Patrick Asare, Eugene Roscioli, Paul N. Reynolds and Sandra Hodge
Biology 2023, 12(9), 1261; https://doi.org/10.3390/biology12091261 - 20 Sep 2023
Viewed by 838
Abstract
Introduction: Pro-inflammatory CD8+ T cells are increased in the lungs and also in the peripheral circulation of both smokers and chronic obstructive pulmonary disease (COPD) patients. The reason for this is unclear but has been described as a spillover from cells in the [...] Read more.
Introduction: Pro-inflammatory CD8+ T cells are increased in the lungs and also in the peripheral circulation of both smokers and chronic obstructive pulmonary disease (COPD) patients. The reason for this is unclear but has been described as a spillover from cells in the lungs that may cause the systemic inflammation noted in COPD. We have recently shown an increase in steroid-resistant CD28nullCD8+ senescent lymphocytes in the lungs and peripheral blood in COPD. Leukotreine B4 (LB4) receptor 1 (BLTR1) is involved in recruitment of CD8+ T cells to sites of inflammation, and we hypothesized that it may be involved in the migration of these senescent lymphocytes from the lungs in COPD. Methods: Via flow cytometry and Western blot BLTR1, IFNγ, and TNFα expression were measured in peripheral blood, BAL, and large proximal and small distal airway CD28±, CD8± T, and NKT-like cells from COPD patients and healthy control subjects (±prednisolone) following in vitro stimulation. Chemotaxis of leucocyte subsets was determined (±LB4 ± prednisolone). Results: There was an increase in BLTR1-CD28nullCD8+ lymphocytes in the lungs and blood in patients with COPD compared with controls. BLTR1-CD28nullCD8+ T and NKT-like cells produce more IFN/TNF than BLTR+ cells and fail to migrate to LTB4. Treatment with 1 µM prednisolone in vitro resulted in upregulation of BLTR1 expression in pro-inflammatory CD28nullCD8+ cells and migration to LB4. Conclusions: Loss of BLTR1 is associated with an increased inflammatory potential of CD28nullCD8+ T cells and may allow these pro-inflammatory steroid-resistant cells to migrate to peripheral blood. Treatment strategies that upregulate BLTR1 may reduce systemic inflammation and associated co-morbidity in patients with COPD. Full article
(This article belongs to the Special Issue Cellular Senescence in Health and Disease)
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15 pages, 1943 KiB  
Article
Effects of Diet Consistency on Rat Maxillary and Mandibular Growth within Three Generations—A Longitudinal CBCT Study
by Ioannis A. Tsolakis, Christos Verikokos, Despoina Perrea, Paula Perlea, Konstantina-Eleni Alexiou, Zafeiroula Yfanti, Ioannis Lyros, Maria Georgaki, Erofili Papadopoulou and Apostolos I. Tsolakis
Biology 2023, 12(9), 1260; https://doi.org/10.3390/biology12091260 - 20 Sep 2023
Viewed by 913
Abstract
Background: In this study, wistar rats were used to examine the impact of diet consistency on maxillary and mandibular growth over three generations. Methods: In this investigation, a breeding sample of 60 female and 8 male wistar rats was used. Measuring was only [...] Read more.
Background: In this study, wistar rats were used to examine the impact of diet consistency on maxillary and mandibular growth over three generations. Methods: In this investigation, a breeding sample of 60 female and 8 male wistar rats was used. Measuring was only performed on female animals. The first generation’s primary breeding sample consisted of 20 female wistar rats that were 30 days old and 4 male rats that were also 30 days old; two subsequent generations were created from these animals. At the age of 100 days, CBCTs were collected of all male rats. Twenty-eight craniofacial landmarks were selected for the linear measurements on stl format extracted from the DICOM files. A Bonferroni test was performed for the statistical analysis. Results: Means of measurements of all soft diet groups compared to corresponding measurements of the hard diet groups were significantly different. According to linear measurements, there was statistical difference on the maxillary measurements between the soft diet groups of the first and third generation, while the rest did not appear to have any statistical difference. There was significant difference for the mandibular dimensions only when the first generation soft diet group was compared with the third generation soft diet group. Conclusions: Food consistency has a significant impact on the growth and development of the maxilla and mandible. Soft diet habits may result in retrognathic mandible, and narrower maxilla. Full article
(This article belongs to the Section Developmental Biology)
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15 pages, 3834 KiB  
Article
IFNγ-Producing B Cells Play a Regulating Role in Infection-Mediated Inhibition of Allergy
by Sai Qiao, Ying Peng, Chunyan Zhang, Rony Thomas, Shuhe Wang and Xi Yang
Biology 2023, 12(9), 1259; https://doi.org/10.3390/biology12091259 - 20 Sep 2023
Viewed by 839
Abstract
The hygiene hypothesis suggests that some infections may inhibit the development of allergic diseases, but the mechanism remains unclear. Our previous study has shown that Chlamydia muridarum (Cm) lung infection can inhibit local eosinophilic inflammation induced by ovalbumin (OVA) through the modulation of [...] Read more.
The hygiene hypothesis suggests that some infections may inhibit the development of allergic diseases, but the mechanism remains unclear. Our previous study has shown that Chlamydia muridarum (Cm) lung infection can inhibit local eosinophilic inflammation induced by ovalbumin (OVA) through the modulation of dendritic cell (DC) and T cell responses in mice. In this study, we explored the role of B cells in the chlamydial-infection-mediated modulation of allergic responses. The results showed that adoptive transfer of B cells isolated from Cm-infected mice (Cm-B cells), unlike those from naïve mice (naïve B cells), could effectively inhibit allergic airway eosinophilia and mucus overproduction, as well as Th2 cytokine responses. In addition, total IgE/IgG1 and OVA-specific IgE/IgG1 antibodies in the serum were also decreased by the adoptive transfer of Cm-B cells. Intracellular cytokine analysis showed that B cells from Cm-infected mice produced higher levels of IFNγ than those from naïve mice. More interestingly, the inhibiting effect of adoptively transferred Cm-B cells on allergic reactions was virtually abolished by the simultaneous blockade of IFNγ using a monoclonal antibody. The results suggest that B cells modulated by chlamydial lung infection could play a regulatory role in OVA-induced acute allergic responses in the lung via the production of IFNγ. The results provide new insights into the targets related to the prevention and treatment of allergic diseases. Full article
(This article belongs to the Section Immunology)
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17 pages, 2321 KiB  
Review
Macrophages in the Inflammatory Phase following Myocardial Infarction: Role of Exogenous Ubiquitin
by Paige L. Shook, Mahipal Singh and Krishna Singh
Biology 2023, 12(9), 1258; https://doi.org/10.3390/biology12091258 - 20 Sep 2023
Viewed by 1484
Abstract
Cardiovascular disease (CVD) is one of the leading causes of death worldwide. One of the most common implications of CVD is myocardial infarction (MI). Following MI, the repair of the infarcted heart occurs through three distinct, yet overlapping phases of inflammation, proliferation, and [...] Read more.
Cardiovascular disease (CVD) is one of the leading causes of death worldwide. One of the most common implications of CVD is myocardial infarction (MI). Following MI, the repair of the infarcted heart occurs through three distinct, yet overlapping phases of inflammation, proliferation, and maturation. Macrophages are essential to the resolution of the inflammatory phase due to their role in phagocytosis and efferocytosis. However, excessive and long-term macrophage accumulation at the area of injury and dysregulated function can induce adverse cardiac remodeling post-MI. Ubiquitin (UB) is a highly evolutionarily conserved small protein and is a normal constituent of plasma. Levels of UB are increased in the plasma during a variety of pathological conditions, including ischemic heart disease. Treatment of mice with UB associates with decreased inflammatory response and improved heart function following ischemia/reperfusion injury. This review summarizes the role of macrophages in the infarct healing process of the heart post-MI, and discusses the role of exogenous UB in myocardial remodeling post-MI and in the modulation of macrophage phenotype and function. Full article
(This article belongs to the Section Physiology)
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24 pages, 858 KiB  
Review
Functional Implications of Protein Arginine Methyltransferases (PRMTs) in Neurodegenerative Diseases
by Efthalia Angelopoulou, Efstratios-Stylianos Pyrgelis, Chetana Ahire, Prachi Suman, Awanish Mishra and Christina Piperi
Biology 2023, 12(9), 1257; https://doi.org/10.3390/biology12091257 - 20 Sep 2023
Cited by 2 | Viewed by 1689
Abstract
During the aging of the global population, the prevalence of neurodegenerative diseases will be continuously growing. Although each disorder is characterized by disease-specific protein accumulations, several common pathophysiological mechanisms encompassing both genetic and environmental factors have been detected. Among them, protein arginine methyltransferases [...] Read more.
During the aging of the global population, the prevalence of neurodegenerative diseases will be continuously growing. Although each disorder is characterized by disease-specific protein accumulations, several common pathophysiological mechanisms encompassing both genetic and environmental factors have been detected. Among them, protein arginine methyltransferases (PRMTs), which catalyze the methylation of arginine of various substrates, have been revealed to regulate several cellular mechanisms, including neuronal cell survival and excitability, axonal transport, synaptic maturation, and myelination. Emerging evidence highlights their critical involvement in the pathophysiology of neurodegenerative diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), frontotemporal dementia–amyotrophic lateral sclerosis (FTD-ALS) spectrum, Huntington’s disease (HD), spinal muscular atrophy (SMA) and spinal and bulbar muscular atrophy (SBMA). Underlying mechanisms include the regulation of gene transcription and RNA splicing, as well as their implication in various signaling pathways related to oxidative stress responses, apoptosis, neuroinflammation, vacuole degeneration, abnormal protein accumulation and neurotransmission. The targeting of PRMTs is a therapeutic approach initially developed against various forms of cancer but currently presents a novel potential strategy for neurodegenerative diseases. In this review, we discuss the accumulating evidence on the role of PRMTs in the pathophysiology of neurodegenerative diseases, enlightening their pathogenesis and stimulating future research. Full article
(This article belongs to the Special Issue Epigenetic Modifications and Changes in Neurodegenerative Diseases)
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13 pages, 334 KiB  
Article
Obstetrical and Perinatal Outcomes Are Not Associated with Advanced Paternal Age in IVF or ICSI Pregnancies with Autologous Oocytes
by Ana Navarro-Gomezlechon, María Gil Juliá, Rosa María Pacheco-Rendón, Irene Hervás, Laura Mossetti, Rocío Rivera-Egea and Nicolás Garrido
Biology 2023, 12(9), 1256; https://doi.org/10.3390/biology12091256 - 20 Sep 2023
Viewed by 948
Abstract
Background: In recent years, there has been an evident delay in childbearing and concerns have been raised about whether this increase in age affects reproductive outcomes. This study aimed to evaluate the effect of paternal age on obstetrical and perinatal outcomes in couples [...] Read more.
Background: In recent years, there has been an evident delay in childbearing and concerns have been raised about whether this increase in age affects reproductive outcomes. This study aimed to evaluate the effect of paternal age on obstetrical and perinatal outcomes in couples undergoing in vitro fertilization or intracytoplasmic sperm injection using autologous sperm and oocytes. Methods: This retrospective study evaluated obstetrical and perinatal outcomes from 14,125 couples that were arbitrarily divided into three groups according to paternal age at conception: ≤30 (n = 1164), 31–40 (n = 11,668) and >40 (n = 1293). Statistics consisted of a descriptive analysis followed by univariate and multivariate models, using the youngest age group as a reference. Results: The study showed significantly longer pregnancies for the fathers aged 31–40 compared to ≤30 years. However, there were no significant differences for the type of delivery, gestational diabetes, anaemia, hypertension, delivery threat, premature rupture of membranes, preterm birth, very preterm birth, and the neonate’s sex, weight, low birth weight, very low birth weight, length, cranial perimeter, Apgar score and neonatal intensive care unit admission. Conclusion: Despite our promising results for older fathers, as paternal age was not associated with clinically relevant obstetrical and perinatal outcomes, future well-designed studies are necessary as it has been associated with other important disorders. Full article
15 pages, 2499 KiB  
Article
Genetic Monitoring of Grey Wolves in Latvia Shows Adverse Reproductive and Social Consequences of Hunting
by Agrita Žunna, Dainis Edgars Ruņģis, Jānis Ozoliņš, Alda Stepanova and Gundega Done
Biology 2023, 12(9), 1255; https://doi.org/10.3390/biology12091255 - 19 Sep 2023
Cited by 2 | Viewed by 2862
Abstract
Nowadays, genetic research methods play an important role in animal population studies. Since 2009, genetic material from Latvian wolf specimens obtained through hunting has been systematically gathered. This study, spanning until 2021, scrutinizes the consequences of regulated wolf hunting on population genetic metrics, [...] Read more.
Nowadays, genetic research methods play an important role in animal population studies. Since 2009, genetic material from Latvian wolf specimens obtained through hunting has been systematically gathered. This study, spanning until 2021, scrutinizes the consequences of regulated wolf hunting on population genetic metrics, kinship dynamics, and social organization. We employed 16 autosomal microsatellites to investigate relationships between full siblings and parent–offspring pairs. Our analysis encompassed expected and observed heterozygosity, inbreeding coefficients, allelic diversity, genetic distance and differentiation, mean pairwise relatedness, and the number of migrants per generation. The Latvian wolf population demonstrated robust genetic diversity with minimal inbreeding, maintaining stable allelic diversity and high heterozygosity over time and it is not fragmented. Our findings reveal the persistence of conventional wolf pack structures and enduring kinship groups. However, the study also underscores the adverse effects of intensified hunting pressure, leading to breeder loss, pack disruption, territorial displacement, and the premature dispersal of juvenile wolves. Full article
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13 pages, 2629 KiB  
Article
Effect of Sugar Beet Pulp on the Composition and Predicted Function of Equine Fecal Microbiota
by Tamara Ford, Zachary L. McAdams, Kile S. Townsend, Lynn M. Martin, Philip J. Johnson and Aaron C. Ericsson
Biology 2023, 12(9), 1254; https://doi.org/10.3390/biology12091254 - 19 Sep 2023
Cited by 1 | Viewed by 2634
Abstract
The purpose of this study is to determine the effect of the partial replacement of dietary hay with sugar beet pulp (SBP) on the composition and predicted function of the fecal microbiota of healthy adult horses. Fecal samples were collected daily for 12 [...] Read more.
The purpose of this study is to determine the effect of the partial replacement of dietary hay with sugar beet pulp (SBP) on the composition and predicted function of the fecal microbiota of healthy adult horses. Fecal samples were collected daily for 12 days from six adult horses after removal from pasture, including a five-day acclimation period, and a seven-day period following the introduction of SBP into their diet, and compared to six untreated horses over a comparable period. Fecal DNA was subjected to 16S rRNA amplicon sequencing and a longitudinal analysis was performed comparing the composition and predicted function. While no significant treatment-associated changes in the richness, alpha diversity, or beta diversity were detected, random forest regression identified several high-importance taxonomic features associated with change over time in horses receiving SBP. A similar analysis of the predicted functional pathways identified several high-importance pathways, including those involved in the production of L-methionine and butyrate. These data suggest that feeding SBP to healthy adult horses acutely increases the relative abundance of several Gram-positive taxa, including Cellulosilyticum sp., Moryella sp., and Weissella sp., and mitigates the predicted functional changes associated with removal from pasture. Large-scale studies are needed to assess the protective effect of SBP on the incidence of the gastrointestinal conditions of horses. Full article
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18 pages, 922 KiB  
Perspective
What Determines the Class of Immunity an Antigen Induces? A Foundational Question Whose Rational Consideration Has Been Undermined by the Information Overload
by Peter Bretscher
Biology 2023, 12(9), 1253; https://doi.org/10.3390/biology12091253 - 19 Sep 2023
Cited by 1 | Viewed by 921
Abstract
Activated CD4 T helper cells are required to activate B cells to produce antibody and CD8 T cells to generate cytotoxic T lymphocytes. In the absence of such help, antigens inactivate B cells and CD8 T cells. Thus, the activation or inactivation of [...] Read more.
Activated CD4 T helper cells are required to activate B cells to produce antibody and CD8 T cells to generate cytotoxic T lymphocytes. In the absence of such help, antigens inactivate B cells and CD8 T cells. Thus, the activation or inactivation of CD4 T cells determines whether immune responses are generated, or potentially ablated. Most consider that the activation of CD4 T cells requires an antigen-dependent signal, signal 1, as well as a critical costimulatory signal, initiated when a pattern recognition receptor (PRR) engages with a danger- or pathogen-associated molecular pattern (DAMP or PAMP). Most also envisage that the nature of the DAMP/PAMP signal determines the Th subset predominantly generated and so the class of immunity predominantly induced. I argue that this framework is implausible as it is incompatible with diverse observations of the variables of immunization affecting the class of immunity induced. An alternative framework, the threshold hypothesis, posits that different levels of antigen mediated CD4 T cell interactions lead to the generation of different Th subsets and so different classes of immunity, that it is compatible with these observations. This alternative supports a rational approach to preventing and treating diverse clinical conditions associated with infectious disease and, more speculatively, with cancer. Full article
(This article belongs to the Section Immunology)
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14 pages, 2225 KiB  
Article
Detection of Math6-Expressing Cell Types in Murine Placenta
by Maren Brendel, Marion Scharf, Urs Kindler, Satya Srirama Karthik Divvela and Beate Brand-Saberi
Biology 2023, 12(9), 1252; https://doi.org/10.3390/biology12091252 - 19 Sep 2023
Viewed by 855
Abstract
The transcription factor Math6, mouse atonal homolog 6, belongs to the family of highly conserved basic helix–loop–helix transcription factors. It plays an important role in embryonic development and shows a wide expression pattern in murine tissues. The placenta, as a life-sustaining transient organ [...] Read more.
The transcription factor Math6, mouse atonal homolog 6, belongs to the family of highly conserved basic helix–loop–helix transcription factors. It plays an important role in embryonic development and shows a wide expression pattern in murine tissues. The placenta, as a life-sustaining transient organ for the fetus, also depends on the expression of Math6. The adverse effects of deleting Math6 in mice, leading to deficient placental development and pregnancy loss, have already been demonstrated by us. Until now, detailed investigations regarding the specific mechanisms underlying the improper placental development in these murine mutants have failed, as the Math6 expression could not be confined to a specific cell type due to the lack of a highly specific Math6 antibody. To circumvent this problem, we used transgenic mice, where Math6 is marked with a Flag sequence that functions as a specific epitope. Tissues from these transgenic mice were used to establish immunohistochemical staining and fluorescence-activated cell sorting (FACS). The establishment of these methods yielded initial findings pertaining to the identification of Math6-expressing cell types and their localization. Our results reveal that Math6 shows a wide expression pattern in both maternal and fetal components of the murine placenta. It shows expression in various cell types, but predominantly in trophoblast giant cells, endothelial cells and macrophages. The largest subpopulation that we detected in the group of Math6-positive cells were identified as DBA+ uterine natural killer cells. These findings reveal information and a chance for further investigation on the involvement of Math6 in placental development and the molecular pathomechanisms of spontaneous abortion. Full article
(This article belongs to the Special Issue Development and Pathophysiology of the Placenta)
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14 pages, 4273 KiB  
Article
Seasonal and Daily Xylem Radius Variations in Scots Pine Are Closely Linked to Environmental Factors Affecting Transpiration
by Walter Oberhuber, Andreas Gruber and Gerhard Wieser
Biology 2023, 12(9), 1251; https://doi.org/10.3390/biology12091251 - 18 Sep 2023
Viewed by 858
Abstract
Seasonal and daily radius variations in the xylem (XRV) and inner bark (IBV) of mature Scots pine trees (Pinus sylvestris) were determined during April 2019–October 2021 at a drought-prone inner alpine site (c. 750 m asl; Tyrol, Austria) by [...] Read more.
Seasonal and daily radius variations in the xylem (XRV) and inner bark (IBV) of mature Scots pine trees (Pinus sylvestris) were determined during April 2019–October 2021 at a drought-prone inner alpine site (c. 750 m asl; Tyrol, Austria) by applying point dendrometers. XRVs were also related to environmental factors to evaluate the drivers of XRV during the growing season. XRV records revealed that the xylem width (i) started to shrink around the onset of radial stem growth in April, (ii) consistently decreased by c. 50 µm at the time when air temperature (T) and vapor pressure deficit (VPD) reached their maximum in late June through mid-July, and (iii) recovered until November/December. Although in daily cycles of radius variations XRV preceded IBV by about two hours and the daily amplitude of XRV was about 1/10 that of IBV, XRV and IBV (seasonal trends removed) were closely linked (ρ = 0.755; p < 0.001), indicating tight hydraulic coupling between these tissues. Furthermore, the daily amplitude of XRV was linearly and closely related to daily maximum T (ρ = 0.802; p < 0.001), mean daily solar radiation (ρ = 0.809; p < 0.001), and non-linearly related to daily maximum VPD (R2= 0.837; p < 0.001), indicating that the xylem of Pinus sylvestris reacts like a transpiration-driven passive hydraulic system. Full article
(This article belongs to the Section Plant Science)
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14 pages, 2290 KiB  
Article
Aberrant Water Structure Dynamics in B16 Melanoma-Bearing Mice by Time Domain Refractometry Analysis
by Kahori Furuhata, Haruchika Masuda, Atsuko Sato, Kumiko Miyata, Naoki Shinyashiki, Rio Kita, Kotaro Imagawa, Tadashi Akamatsu and Shin Yagihara
Biology 2023, 12(9), 1250; https://doi.org/10.3390/biology12091250 - 18 Sep 2023
Viewed by 959
Abstract
Living bodies comprise approximately 55–75% water to maintain homeostasis. However, little is known about the comprehensive differences in in vivo water molecule dynamics (water structure dynamics; WSD) between physiological and pathophysiological statuses. Here, we examined the WSD of ex vivo tumor tissues and [...] Read more.
Living bodies comprise approximately 55–75% water to maintain homeostasis. However, little is known about the comprehensive differences in in vivo water molecule dynamics (water structure dynamics; WSD) between physiological and pathophysiological statuses. Here, we examined the WSD of ex vivo tumor tissues and organs from tumor-bearing mice with engrafted mouse malignant melanoma cells (B16-F10) in the right flanks to compare with those in healthy mice, using time domain reflectometry of dielectric spectroscopy at days 9, 11, and 14 after engrafting. The relaxation parameters of relaxation time (τ), relaxation time distribution parameter (β), and relaxation strength (∆ε) were measured on tumor tissues and lung, liver, kidney, and skin tissues. Immediately afterward, the water contents (%) in the tumor and the other organs were calculated by measuring their weights before and after freeze-drying. Each parameter of the tumor was compared to that of pooled values of other organs in tumor-bearing (TO) and healthy mice (HO). The tumor water content temporarily increased compared to that of HO at day 11; the tumor volume was also prone to increase. In contrast, tumor tissues exhibited significantly higher values of β close to 1 of ultrapure water and ∆ε compared to TO and HO at all times. Moreover, β in the viscera of TO was prone to increase compared to that of HO with significantly higher levels at day 11. Conclusively, tumor-bearing mice exhibited systemically aberrant WSD, unlike healthy mice. Thus, dielectric spectroscopy in terms of WSD may provide novel pathophysiological perspectives in tumor-bearing living bodies. Full article
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15 pages, 6628 KiB  
Article
Ocean Acidification Affects the Response of the Coastal Coccolithophore Pleurochrysis carterae to Irradiance
by Fengxia Wu, Jia Guo, Haozhen Duan, Tongtong Li, Yanan Wang, Yuntao Wang, Shiqiang Wang and Yuanyuan Feng
Biology 2023, 12(9), 1249; https://doi.org/10.3390/biology12091249 - 18 Sep 2023
Viewed by 1045
Abstract
The ecologically important marine phytoplankton group coccolithophores have a global distribution. The impacts of ocean acidification on the cosmopolitan species Emiliania huxleyi have received much attention and have been intensively studied. However, the species-specific responses of coccolithophores and how these responses will be [...] Read more.
The ecologically important marine phytoplankton group coccolithophores have a global distribution. The impacts of ocean acidification on the cosmopolitan species Emiliania huxleyi have received much attention and have been intensively studied. However, the species-specific responses of coccolithophores and how these responses will be regulated by other environmental drivers are still largely unknown. To examine the interactive effects of irradiance and ocean acidification on the physiology of the coastal coccolithophore species Pleurochrysis carterae, we carried out a semi-continuous incubation experiment under a range of irradiances (50, 200, 500, 800 μmol photons m−2 s−1) at two CO2 concentration conditions of 400 and 800 ppm. The results suggest that the saturation irradiance for the growth rate was higher at an elevated CO2 concentration. Ocean acidification weakened the particulate organic carbon (POC) production of Pleurochrysis carterae and the inhibition rate was decreased with increasing irradiance, indicating that ocean acidification may affect the tolerating capacity of photosynthesis to higher irradiance. Our results further provide new insight into the species-specific responses of coccolithophores to the projected ocean acidification under different irradiance scenarios in the changing marine environment. Full article
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20 pages, 382 KiB  
Review
Lichens and Mosses as Biomonitors of Indoor Pollution
by Luca Paoli, Elena Bandoni and Luigi Sanità di Toppi
Biology 2023, 12(9), 1248; https://doi.org/10.3390/biology12091248 - 18 Sep 2023
Cited by 1 | Viewed by 1143
Abstract
Biomonitoring in indoor environments is a recent application, and so far, indoor air quality (IAQ) has been investigated only in a few cases using photosynthesising biomonitors. On the whole, 22 studies have been selected and reviewed, being specifically focused on the assessment of [...] Read more.
Biomonitoring in indoor environments is a recent application, and so far, indoor air quality (IAQ) has been investigated only in a few cases using photosynthesising biomonitors. On the whole, 22 studies have been selected and reviewed, being specifically focused on the assessment of IAQ using biomonitors, such as lichens (9 papers), mosses (10), or their combination (3). In general, indoor samples face an altered light regime, ventilation, and a reduced hydration, which should be taken into consideration during the design and implementation of indoor monitoring. This review highlights critical issues (and some solutions) related to sample devitalisation (moss), hydration during exposure, preparation of the exposure device (mostly lichen and moss bags), duration of the exposure, post-exposure treatments, assessment of the vitality of the samples, as well as data elaboration and interpretation. This review evidences the feasibility and usefulness of lichen/moss monitoring in indoor environments and the need to develop standardised protocols. Full article
(This article belongs to the Special Issue Biological Response of Plants to Environmental Changes)
12 pages, 3145 KiB  
Article
Macroinvertebrate Response to Internal Nutrient Loading Increases in Shallow Eutrophic Lakes
by Kai Peng, Rui Dong, Boqiang Qin, Yongjiu Cai, Jianming Deng and Zhijun Gong
Biology 2023, 12(9), 1247; https://doi.org/10.3390/biology12091247 - 18 Sep 2023
Viewed by 1072
Abstract
In eutrophic lakes, even if external loading is controlled, internal nutrient loading delays the recovery of lake eutrophication. When the input of external pollutants is reduced, the dissolved oxygen environment at the sediment interface improves in a season without algal blooms. As an [...] Read more.
In eutrophic lakes, even if external loading is controlled, internal nutrient loading delays the recovery of lake eutrophication. When the input of external pollutants is reduced, the dissolved oxygen environment at the sediment interface improves in a season without algal blooms. As an important part of lake ecosystems, macroinvertebrates are sensitive to hypoxia caused by eutrophication; however, how this change affects macroinvertebrates is still unknown. In this study, we analysed the monitoring data of northern Lake Taihu from 2007 to 2019. After 2007, the external loading of Lake Taihu was relatively stable, but eutrophication began to intensify after 2013, and the nutrients in the sediments also began to decline, which was related to the efficient use of nutrients by algal blooms. The community structure and population density of macroinvertebrates showed different responses in different stages. In particular, the density of oligochaetes and the Shannon–Wiener index showed significant differences in their response to different stages, and their sensitivity to eutrophication was significantly reduced. Under eutrophication conditions dominated by internal loading, frequent hypoxia occurs at the sediment interface only when an algal bloom erupts. When there is no bloom, the probability of sediment hypoxia is significantly reduced under the disturbance of wind. Our results indicate that the current method for evaluating lake eutrophication based on oligochaetes and the Shannon–Wiener diversity index may lose its sensitivity. Full article
(This article belongs to the Section Ecology)
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20 pages, 2815 KiB  
Article
Contrasting Marine Microbial Communities of the Fram Strait with the First Confirmed Record of Cyanobacteria Prochlorococcus marinus in the Arctic Region
by Monika Mioduchowska, Joanna Pawłowska, Karol Mazanowski and Agata Weydmann-Zwolicka
Biology 2023, 12(9), 1246; https://doi.org/10.3390/biology12091246 - 17 Sep 2023
Cited by 1 | Viewed by 1339
Abstract
The seawater microbiome is crucial in marine ecosystems because of its role in food chains and biogeochemical cycles; thus, we studied the composition of the pelagic marine microbiome collected in the upper 50 m on the opposite sides of Fram Strait: Spitsbergen and [...] Read more.
The seawater microbiome is crucial in marine ecosystems because of its role in food chains and biogeochemical cycles; thus, we studied the composition of the pelagic marine microbiome collected in the upper 50 m on the opposite sides of Fram Strait: Spitsbergen and Greenland shelves. We found out that it differed significantly, with salinity being the main environmental variable responsible for these differences. The Spitsbergen shelf was dominated by Atlantic Waters, with a rather homogenous water column in terms of salinity and temperature down to 300 m; hence, the marine microbial community was also homogenous at all sampled depths (0, 25, 50 m). On the contrary, stations on the Greenland shelf were exposed to different water masses of both Arctic and Atlantic origin, which resulted in a more diverse microbial community there. Unexpectedly, for the very first time, we identified cyanobacterium Prochlorococcus marinus in Arctic waters (Spitsbergen shelf, 75–77° N). Till now, the distribution of this cyanobacteria in oceans has been described only between 40° N and 40° S. Considering the accelerated rate of climate warming in the Arctic, our results indicated that the seawater microbiome can be viewed as an amplifier of global change and that the Atlantification is in progress. Full article
(This article belongs to the Special Issue Climate Change and Marine Plankton)
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15 pages, 3069 KiB  
Article
Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary
by Kanghui Kim, Gea-Jae Joo, Kwang-Seuk Jeong, Jeong-Soo Gim, Yerim Lee, Donghyun Hong and Hyunbin Jo
Biology 2023, 12(9), 1245; https://doi.org/10.3390/biology12091245 - 16 Sep 2023
Viewed by 879
Abstract
Environmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam Corbicula fluminea to examine biodiversity within estuarine ecosystem. Field [...] Read more.
Environmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam Corbicula fluminea to examine biodiversity within estuarine ecosystem. Field sampling was conducted at three points in the Nakdong River Estuary, which is characterised by closed estuarine features resulting from the presence of an estuarine barrage. The collected C. fluminea samples were dissected to separate the gut contents, and the extracted eDNA was amplified using 18S V9 primer targeting all eukaryote-derived DNA. The amplified DNA was sequenced using a next-generation sequencing (NGS) technique, and a BLASTn search was performed based on the National Centre for Biotechnology Information (NCBI) database for taxa identification. We obtained 23 unique operational taxonomic units (OTUs), including fish (approximately 8.70%), copepods (approximately 17.39%), and green algae (approximately 21.74%), representing a wide range of habitats. Furthermore, 8 out of the 20 families were identified through comparisons with reference data from conventional field surveys, and the OTUs of elusive migratory fish were detected. The results support the application of C. fluminea as an eDNA sampler for supplementary biodiversity monitoring. Full article
(This article belongs to the Section Ecology)
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26 pages, 6238 KiB  
Article
Comparative Analysis of Tylosema esculentum Mitochondrial DNA Revealed Two Distinct Genome Structures
by Jin Li and Christopher Cullis
Biology 2023, 12(9), 1244; https://doi.org/10.3390/biology12091244 - 16 Sep 2023
Cited by 1 | Viewed by 1433
Abstract
Tylosema esculentum, commonly known as the marama bean, is an underutilized legume with nutritious seeds, holding potential to enhance food security in southern Africa due to its resilience to prolonged drought and heat. To promote the selection of this agronomically valuable germplasm, [...] Read more.
Tylosema esculentum, commonly known as the marama bean, is an underutilized legume with nutritious seeds, holding potential to enhance food security in southern Africa due to its resilience to prolonged drought and heat. To promote the selection of this agronomically valuable germplasm, this study assembled and compared the mitogenomes of 84 marama individuals, identifying variations in genome structure, single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), heteroplasmy, and horizontal transfer. Two distinct germplasms were identified, and a novel mitogenome structure consisting of three circular molecules and one long linear chromosome was discovered. The structural variation led to an increased copy number of specific genes, nad5, nad9, rrnS, rrn5, trnC, and trnfM. The two mitogenomes also exhibited differences at 230 loci, with only one notable nonsynonymous substitution in the matR gene. Heteroplasmy was concentrated at certain loci on chromosome LS1 (OK638188). Moreover, the marama mitogenome contained an over 9 kb insertion of cpDNA, originating from chloroplast genomes, but had accumulated mutations and lost gene functionality. The evolutionary and comparative genomics analysis indicated that mitogenome divergence in marama might not be solely constrained by geographical factors. Additionally, marama, as a member from the Cercidoideae subfamily, tends to possess a more complete set of mitochondrial genes than Faboideae legumes. Full article
(This article belongs to the Section Plant Science)
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19 pages, 1762 KiB  
Systematic Review
A549 as an In Vitro Model to Evaluate the Impact of Microplastics in the Air
by Chman Shahzadi, Alessandra Di Serafino, Eleonora Aruffo, Alessandra Mascitelli and Piero Di Carlo
Biology 2023, 12(9), 1243; https://doi.org/10.3390/biology12091243 - 15 Sep 2023
Viewed by 1559
Abstract
Airborne microplastics raise significant concerns due to their potential health impacts. Having a small size, larger surface area, and penetrative ability into the biological system, makes them hazardous to health. This review article compiles various studies investigating the mechanism of action of polystyrene [...] Read more.
Airborne microplastics raise significant concerns due to their potential health impacts. Having a small size, larger surface area, and penetrative ability into the biological system, makes them hazardous to health. This review article compiles various studies investigating the mechanism of action of polystyrene micro- and nanoplastics affecting lung epithelial cells A549. These inhalable microplastics damage the respiratory system, by triggering a proinflammatory environment, genotoxicity, oxidative stress, morphological changes, and cytotoxic accumulation in A549 cells. PS-NP lung toxicity depends on various factors such as size, surface modifications, concentration, charge, and zeta potential. However, cellular uptake and cytotoxicity mechanisms depend on the cell type. For A549 cells, PS-NPs are responsible for energy imbalance by mitochondrial dysfunction, oxidative stress-mediated cytotoxicity, immunomodulation, and apoptosis. Additionally, PS-NPs have the ability to traverse the placental barrier, posing a risk to offspring. Despite the advancements, the precise mechanisms underlying how prolonged exposure to PS-NPs leads to the development and progression of lung diseases have unclear points, necessitating further investigations to unravel the root cause. This review also sheds light on data gaps, inconsistencies in PS-Nos research, and provides recommendations for further research in this field. Full article
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