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Background Information: Microvilli are finger-like, straight, and stable cellular protrusions that are filled with F-actin and present a stereotypical length. They are present in a broad range of cell types across the animal tree of life and mediate several fundamental functions, including nutrient absorption, photosensation, and mechanosensation. Therefore, understanding the origin and evolution of microvilli is key to reconstructing the evolution of animal cellular form and function. Here, we review the current state of knowledge on microvilli evolution and perform a bioinformatic survey of the conservation of genes encoding microvillar proteins in animals and their unicellular relatives., Results: We first present a detailed description of mammalian microvilli based on two well-studied examples, the brush border microvilli of enterocytes and the stereocilia of hair cells. We also survey the broader diversity of microvilli and discuss similarities and differences between microvilli and filopodia. Based on our bioinformatic survey coupled with carefully reconstructed molecular phylogenies, we reconstitute the order of evolutionary appearance of microvillar proteins. We document the stepwise evolutionary assembly of the "molecular microvillar toolkit" with notable bursts of innovation at two key nodes: the last common filozoan ancestor (correlated with the evolution of microvilli distinct from filopodia) and the last common choanozoan ancestor (correlated with the emergence of inter-microvillar adhesions)., Conclusion and Significance: We conclude with a scenario for the evolution of microvilli from filopodia-like ancestral structures in unicellular precursors of animals., (© 2024 The Author(s). Biology of the Cell published by Wiley‐VCH GmbH on behalf of Société Française des Microscopies and Société Biologie Cellulaire de France.)

Background: Hypertrophic Cardiomyopathy (HCM) is characterized by myocardial hypertrophy, fibrosis, and sarcomeric disarray., Objective: To evaluate the expression levels of circulating miR-21 and -29 in patients with HCM and their association with clinical characteristics and myocardial fibrosis., Methods: In this case-control study, 27 subjects with HCM, 13 subjects with hypertensive cardiomyopathy, and 10 control subjects were enrolled. Evaluation of patients' functional capacity was made by the six-minute walk test. Echocardiographic measurements of left ventricle systolic and diastolic function were conducted. Cardiac magnetic resonance late gadolinium enhancement (LGE) -through a semiquantitative evaluation- was used in the assessment of myocardial fibrosis extent in HCM patients. The expression of miR-21 and -29 in peripheral blood samples of all patients was measured via the method of quantitative reverse transcription polymerase chain reaction., Results: Circulating levels of miR-21 were higher in both hypertensive and HCM (p<0.001) compared to controls, while expression of miR-29 did not differ between the three studied groups. In patients with HCM and LGE-detected myocardial fibrosis in more than 4 out of 17 myocardial segments, delta CT miR-21 values were lower than in patients with myocardial LGE in 3 or fewer myocardial segments (2.71 ± 1.06 deltaCT vs. 3.50 ± 0.55 deltaCT, p<0.04), indicating the higher expression of circulating miR-21 in patients with more extensive myocardial fibrosis., Conclusion: MiR-21 was overexpressed in patients with HCM and hypertensive cardiomyopathy. Importantly, in patients with HCM, more extensive myocardial fibrosis was associated with higher levels of miR-21., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Background: The proportion of people with hypertension is increasing, and those affected are relatively younger. Worldwide, it is estimated that people with high blood pressure are more than 1.5 billion people. In Vietnam, from 2002 to 2008, according to a national survey on hypertension and its risk factors within the prevention and control of cardiovascular disease program, the prevalence of hypertension was 25.1%. This is alarming because high blood pressure can cause serious complications, including death., Objective: The study aimed to explore the blood pressure characteristics and hypertension prevalence in adults in a northern delta province of Vietnam, and describe some risk factors in hypertensive subjects screened through the program., Methods: This was a cross-sectional study collecting data from people aged 18 years or older in 10 cantons and the city of Nam Dinh from July 15th to July 31st, 2020. Using semi-automatic OMRON sphygmomanometers, sitting blood pressure was measured three times according to standardized methods specified by the Ministry of Health and two National Vascular Societies., Results: Blood pressure screening of 183,632 adults included 84,438 males, which accounted for 45.98%, with an average age of 60.36 ± 13.18 years. The estimated prevalence of hypertension was 27.20% (95% CI: 27.00% - 27.41%). The older the age, the higher the rate of hypertension in both sexes; the prevalence of hypertension over 65 years was 45.36%. Hypertension grade 1 accounted for 17.14%, followed by hypertension at grade 2 at 6.69%, and grade 3 at 1.15%; notably, the percentage of prehypertension accounted for 49.64%. The percentage of treated hypertension in Nam Dinh province was 56.85%, but the percentage of uncontrolled hypertension was 85.63%., Conclusion: The prevalence of hypertension in Nam Dinh province was relatively high (27.20%), although the number of treated patients was also high (56.85%); moreover, the proportion of uncontrolled hypertension remained extremely high (85.63%). Local campaigns and suitable interventions are required to detect hypertension in the early stages and increase awareness for treatment in the population., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Mediterranean diet is frequently associated with longevity and a lower incidence of adverse cardiovascular events because of the biological activities and health effects of olives - its key component. Olive oil, olive leaf extract, fruits and different by-products contain many bioactive components that exert anti-oxidant, anti-inflammatory and anti-apoptotic activities. In this review, we focus on the recent studies exploring molecular mechanisms underlying the cardioprotective properties of different olive oils, olive leave extracts, and specific micro-constituents (such as oleuropein, tyrosol, hydroxytyrosol and others) in vitro on rodent models and in clinical trials on human subjects. Particularly, hydroxytyrosol and oleuropein were identified as the major bioactive compounds responsible for the antioxidant, anti-inflammatory, anti-platelet aggregation and anti-atherogenic activities of olive oil. In total, the discussed results demonstrated a positive association between the consumption of olive oil and improvement in outcomes in atherosclerosis, diabetes, myocardial infarction, heart failure, hypertension and obesity., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Background: Metabolism of oral anticoagulants (OAC) is affected by P-glycoprotein (P-gp)/ CYP3A4 enzyme. However, the P-gp/CYP3A4 inhibitors are unavoidably used with OACs., Methods: Medline, Cochrane, and Embase were systematically searched for randomized controlled trials and cohort studies from inception till 23rd November, 2022 to assess the safety and effectiveness of OACs when concomitantly used with P-gp/CYP3A4 inhibitors. The primary outcomes were major bleeding and gastrointestinal (GI) bleeding. Secondary outcomes were stroke/systemic embolism (SE), all-cause mortality, any bleeding as well as intracranial hemorrhage (ICH). We estimated summary odds ratios (OR) with 95% credible intervals (CI) using pairwise and network meta-analysis with random effects., Results: A total of 11 studies involving 37,973 patients were included. When concomitantly used with P-pg/ CYP3A4 inhibitors, network meta-analysis indicated that dabigatran, apixaban, and edoxaban were associated with significantly lower risk of major bleeding compared to rivaroxaban, with ORs of 0.56, 0.51 and 0.48, respectively. Rivaroxaban and dabigatran were associated with a significantly increased risk of GI bleeding than warfarin, apixaban and edoxaban. Dabigatran and apixaban were linked with significantly lower risk of any bleeding compared with warfarin (ORs were 0.75 and 0.68, respectively) or rivaroxaban (ORs were 0.67 and 0.60, respectively). Apixaban (OR 0.32) and edoxaban (OR 0.35) were associated with a lower risk of ICH compared with warfarin. There was no difference between any OACs in terms of stroke/SE or all-cause mortality., Conclusion: When concomitantly used with P-gp/CYP3A4 inhibitors, apixaban and edoxaban were associated with a lower risk of bleeding, though no significant difference in effectiveness was observed among all OACs., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Hypertension is one of the primary causes of cardiovascular diseases and death, with a higher prevalence in low- and middle-income countries. The pathophysiology of hypertension remains complex, with 2% to 5% of patients having underlying renal or adrenal disorders. The rest are referred to as essential hypertension, with derangements in various physiological mechanisms potentially contributing to the development of essential hypertension. Hypertension elevates the risk of cardiovascular disease (CVD) events (coronary heart disease, heart failure, and stroke) and mortality. First-line therapy for hypertension is lifestyle change, which includes weight loss, a balanced diet that includes low salt and high potassium intake, physical exercise, and limitation or elimination of alcohol use. Blood pressure-lowering effects of individual lifestyle components are partially additive, enhancing the efficacy of pharmaceutical treatment. The choice to begin antihypertensive medication should be based on the level of blood pressure and the existence of a high atherosclerotic CVD risk. First-line hypertension treatment includes a thiazide or thiazide-like diuretic, an angiotensin-converting enzyme inhibitor or angiotensin receptor blocker, and a calcium channel blocker. Addressing hypertension will require continued efforts to improve access to diagnosis, treatment, and lifestyle interventions., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Cardiovascular disease (CDV) represents the major cause of death globally. Atherosclerosis, as the primary cause of CVD, is a chronic immune-inflammatory disorder with complex multifactorial pathophysiology encompassing oxidative stress, enhanced immune-inflammatory cascade, endothelial dysfunction, and thrombosis. An initiating event in atherosclerosis is the subendothelial accumulation of low-density lipoprotein (LDL), followed by the localization of macrophages to fatty deposits on blood vessel walls, forming lipid-laden macrophages (foam cells) that secrete compounds involved in plaque formation. Given the fact that foam cells are one of the key culprits that underlie the pathophysiology of atherosclerosis, special attention has been paid to the investigation of the efficient therapeutic approach to overcome the dysregulation of metabolism of cholesterol in macrophages, decrease the foam cell formation and/or to force its degradation. Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a secretory serine proteinase that has emerged as a significant regulator of the lipid metabolism pathway. PCSK9 activation leads to the degradation of LDL receptors (LDLRs), increasing LDL cholesterol (LDL-C) levels in the circulation. PCSK9 pathway dysregulation has been identified as one of the mechanisms involved in atherosclerosis. In addition, microRNAs (miRNAs) are investigated as important epigenetic factors in the pathophysiology of atherosclerosis and dysregulation of lipid metabolism. This review article summarizes the recent findings connecting the role of PCSK9 in atherosclerosis and the involvement of various miRNAs in regulating the expression of PCSK9-related genes. We also discuss PCSK9 pathway-targeting therapeutic interventions based on PCSK9 inhibition, and miRNA levels manipulation by therapeutic agents., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Background: Compared to Immediate-Release (IR) metformin, Extended-Release (ER) metformin reduces side effects and pill burden while improving adherence; however, there is little real-life data on patient satisfaction with this innovative formulation to guide physicians toward a more holistic approach., Objective: Our goal is to train general practitioners on holistic patient management, with the aim of increasing patient satisfaction and treatment adherence, reducing side effects, and improving quality of life in patients with poor tolerance to metformin-IR., Materials and Methods: We designed an educational program for physicians called SlowDiab, aimed at establishing a holistic patient approach. In this context, adult patients with T2DM who experienced gastrointestinal discomfort with metformin-IR were enrolled and switched to metformin- ER. Data on glycemic control were collected at baseline and 2 months after switching. A survey was carried out on patients to assess their level of satisfaction., Results: In 69 enrolled patients (mean (min-max) age, 68.2 (41-90)), side effects decreased after switching from 61.8% to 16.2% (p < 0.01), and the mean perceived burden of adverse events on a scale of 1 to 10 also decreased (6.17 vs. 3.82; p < 0.05). Among patients previously intolerant to metformin-IR, 74.3% reported no longer experiencing any side effects after the switch. The mean number of tablets taken daily (2.28 vs. 1.66; p < 0.01) and mean plasma glycated hemoglobin (HbA1c) values (7.0% vs. 6.7%; p < 0.05) decreased, while 93.8% of patients were satisfied with the treatment change. Moreover, 84.2% reported an improvement in glycemic control after the switch., Conclusion: In a real-life setting, an educational program for general practitioners confirmed that metformin ER reduces side effects and improves pill burden, therapeutic adherence, and patient satisfaction compared to metformin IR., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Classical risk factors for atherosclerosis also play a role in the pathogenesis of venous thromboembolism (VTE). Low-density lipoprotein cholesterol has prothrombotic and endothelium- deteriorating effects which are not limited to the arterial system. The association between hypercholesterolemia and VTE has been established, but the benefits of statins in the prevention of VTE assessed by observation studies seemed equivocal. The large, randomized trial Justification for the Use of Statins in Prevention: an Intervention Trial Evaluating Rosuvastatin (JUPITER) recorded the occurrence of VTE as a protocol-specified endpoint and reported a reduced incidence of VTE among subjects taking 20 mg of rosuvastatin daily vs placebo (hazard ratio 0.57; 95% confidence interval 0.37-0.86; p=0.007). Similar results were confirmed by meta-analyses of observation studies and randomized trials. Recently, a Mendelian randomization study that took the presence of gene variants coding for less efficient hydroxymethyl-glutaryl coenzyme A reductase activity as a proxy for statin treatment, confirmed a small, but significant negative association between the score of selected genetic polymorphisms and the incidence of VTE. However, since the protective effects of statins are limited, they should not be substituted for guideline-recommended VTE prophylaxis or anticoagulation treatment., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Background: COVID-19 is characterized by an acute inflammatory response with the formation of endothelial dysfunction and may affect arterial stiffness. Studies of cardio-ankle vascular index in COVID-19 patients with considered cardiovascular risk factors have not been conducted., Objective: The purpose of our study was to assess the association between cardio-ankle vascular index and COVID-19 in hospitalized patients adjusted for known cardiovascular risk factors., Methods: A cross-sectional study included 174 people hospitalized with a diagnosis of moderate COVID-19 and 94 people without COVID-19. Significant differences in the cardio-ankle vascular index values measured by VaSera VS - 1500N between the two groups were analyzed using parametric (Student's t-criterion) and nonparametric (Mann-Whitney) criteria. Independent association between COVID-19 and an increased cardio-ankle vascular index ≥ 9.0 adjusted for known cardiovascular risk factors was assessed by multivariate logistic regression., Results: There were significantly higher values of the right cardio-ankle vascular index 8.10 [7.00;9.40] and the left cardio-ankle vascular index 8.10 [6.95;9.65] in patients undergoing inpatient treatment for COVID-19 than in the control group - 7.55 [6.60;8.60] and 7.60 [6.60;8.70], respectively. A multivariate logistic regression model adjusted for age, hypertension, plasma glucose level, glomerular filtration rate and diabetes mellitus showed a significant association between increased cardio-ankle vascular index and COVID-19 (OR 2.41 [CI 1.09;5.30])., Conclusion: Hospitalized patients with COVID-19 had significantly higher cardio-ankle vascular index values compared to the control group. An association between an increased cardio-ankle vascular index and COVID-19 was revealed, independent of age, hypertension, plasma glucose level, glomerular filtration rate and diabetes mellitus., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Background: Studies have shown the combination treatment effectiveness of using rosuvastatin and ezetimibe in patients with chronic coronary artery disease. Our study aim to evaluate the effectiveness of dyslipidemia treatment with the combination of rosuvastatin and ezetimibe 10mg in patients with chronic coronary artery disease compared with 20 mg rosuvastatin., Objectives: To evaluate the effectiveness of dyslipidemia treatment with the target of LDL-c < 1.4 mmol/L between combination therapy with rosuvastatin 10 mg and ezetimibe 10 mg in patients with chronic coronary artery disease compared with monotherapy increasing the dose of rosuvastatin 20 mg in Vietnam., Methods: A randomized controlled clinical trial, single-blind, parallel-group with a 1:1 randomized ratio in 103 outpatients with chronic coronary syndromes treated with rosuvastatin 10mg daily. Group A received the combination therapy with rosuvastatin 10 mg plus ezetimibe 10 mg daily, and group B received rosuvastatin 20 mg daily. The primary outcome was to assess the efficacy of low-density lipoprotein - cholesterol (LDL-c) control between rosuvastatin 10 mg plus ezetimibe 10 mg versus rosuvastatin 20 mg after 4 weeks and 8 weeks., Results: After 8 weeks of intervention, the proportion of archived treatment target patients with LDL-c < 1.4 mmol/L in groups A and B was 69.2% and 44.2%, respectively (Risk ratio (RR) = 1.57, p < 0.01), 50% LDL reduction was 27.9% and 55.8%, respectively (RR = 2.00, p < 0.01), and archived both targets were 51.9% and 25.6% (RR = 2.03, p < 0.01)., Conclusion: Group A's LDL-c reduction effect and target achievement proportion (Rosuvastatin 10mg + Ezetimibe 10 mg) were significantly higher than Group B's (Rosuvastatin 20 mg). Both medication therapies were safe in patients, and the increased dose of monotherapy showed more side effects than the combination therapy., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Hypothermia and autophagy are critical regulators of cell homeostasis by regulating intra and intercellular cell communication. Myocardiocyte cryotherapy poses multiple cellular and subcellular effects on the injured cell, including upregulation of autophagy. Autophagy plays a crucial role in modifying cell metabolism by regulating downregulation, reducing reactive oxygen species production, and improving the natural cellular antioxidant defense system. Reduction of reactive oxygen species production and improving natural cellular antioxidant defense system. Therapeutic hypothermia ranges from 32-34°C in terms of local myocardiocyte cooling. Hypothermia induces autophagy by phosphorylating the Akt signaling pathway. Hypothermia has a more therapeutic effect when applied at the beginning of reperfusion rather than in the beginning of ischemia. Moderate hypothermia with 33°C poses most therapeutic effect by viability maintaining and reduction of reactive oxygen species release. Application of local hypothermia to myocardiocytes can be applied to infarcted myocardiocytes, anginal and to the cardiomyopathies., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Background: Patients with previous strokes are at a higher risk of stroke recurrence. Current guidelines recommend a range of low-density lipoprotein cholesterol (LDL-C)-lowering treatments to reduce the risk of recurrent stroke. However, the optimal agent for decreasing LDL-C to lower the risk of recurrent stroke remains unclear. This study aimed to assess the relative effects of various LDL-C -lowering agents for secondary stroke prevention., Methods: Several databases were searched from inception up to 2022. Only randomized controlled trials that compared different LDL-C-lowering agents in adult patients with previous strokes were included. The primary endpoint was a recurrent stroke. The surface under the cumulative ranking curve (SUCRA) was also applied to estimate the overall ranking probability of the treatment agents for each outcome., Results: Overall, nine trials comprising 17,226 patients were included. Ezetimibe plus statins (RR: 0.56, 95% CrI: 0.35-0.87) and statins alone (RR: 0.90, 95% CrI: 0.81-1.00) reduced the risk of stroke recurrence. Ezetimibe plus statins was superior to statins alone in decreasing the incidence of recurrent stroke (RR: 0.62, 95% CrI: 0.39-0.95). However, treatment with statins was related to an increased risk of hemorrhagic stroke compared to placebo (RR: 1.57, 95% CrI: 1.13-2.21). All agents were related to a decreased incidence of major adverse cardiovascular events., Conclusion: Treatment with ezetimibe plus statins was suggested as the most efficacious in decreasing the incidence of recurrent stroke. The analysis also revealed that statin monotherapy was related to an increased risk of hemorrhagic stroke., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Hu sheep is a renowned prolific local sheep breed in China, widely distributed across the country due to its excellent reproductive performance. Deciphering the molecular mechanisms underlying the high fecundity of Hu sheep is crucial for improving the litter size of ewes. In this study, we genotyped 830 female Hu sheep using the Illumina OvineSNP50 BeadChip and performed genetic diversity analysis, selection signature detection, and a genome-wide association study (GWAS) for litter size. Our results revealed that the Hu sheep population exhibits relatively high genetic diversity. A total of 4927 runs of homozygosity (ROH) segments were detected, with the majority (74.73%) being short in length. Different genomic inbreeding coefficients (FROH, FHOM, FGRM, and FUNI) ranged from −0.0060 to 0.0126, showing low levels of inbreeding in this population. Additionally, we identified 91 candidate genomic regions through three complementary selection signature methods, including ROH, composite likelihood ratio (CLR), and integrated haplotype score (iHS), and annotated 189 protein-coding genes. Moreover, we observed two significant SNPs related to the litter size of Hu sheep using GWAS analysis based on a repeatability model. Integrating the selection signatures and the GWAS results, we identified 15 candidate genes associated with litter size, among which BMPR1B and UNC5C were particularly noteworthy. These findings provide valuable insights for improving the reproductive performance and breeding of high-fecundity lines of Hu sheep. [ABSTRACT FROM AUTHOR]

Simple Summary: Positive natural selection increases the frequency of beneficial genetic variations, promoting an organism's adaptability and survival in specific environments. In this study, we conducted whole-genome resequencing and population genetic structure analysis to investigate the genetic diversity of Zaobei cattle, local yellow cattle from China. By comparing Zaobei cattle with Simmental cattle, we identified several genomic regions exhibiting positive selection. Gene annotation of these regions revealed key traits of Zaobei cattle, such as heat tolerance, fertility, and superior meat quality. These findings not only help understand the characteristics of Zaobei cattle but also provide valuable genetic information for future breeding programs, thereby improving their production efficiency and economic value. This investigation provides a comprehensive analysis of genomic diversity and selection signatures in Zaobei beef cattle, an indigenous breed known for its adaptation to hot and humid climates and superior meat quality. Whole-genome resequencing was conducted on 23 Zaobei cattle, compared with 46 Simmental cattle to highlight genetic distinctions. Population structure analysis confirmed the genetic uniqueness of Zaobei cattle. Using methods such as DASDC v1.01, XPEHH, and θπ ratio, we identified 230, 232, and 221 genes through DASDC, including hard sweeps, soft sweeps, and linkage sweeps, respectively. Coincidentally, 109 genes were identified when using XPEHH and θπ ratio methods. Together, these analyses revealed eight positive selection genes (ARHGAP15, ZNF618, USH2A, PDZRN4, SPATA6, ROR2, KCNIP3, and VWA3B), which are linked to critical traits such as heat stress adaptation, fertility, and meat quality. Moreover, functional enrichment analyses showed pathways related to autophagy, immune response, energy metabolism, and muscle development. The comprehensive genomic insights gained from this study provide valuable knowledge for breeding programs aimed at enhancing the beneficial traits in Zaobei cattle. [ABSTRACT FROM AUTHOR]

Many heterotrophic microbial eukaryotes are size-selective feeders. Some microorganisms increase their size by forming multicellular colonies. We used choanoflagellates, Salpingoeca helianthica, which can be unicellular or form multicellular colonies, to study the effects of multicellularity on vulnerability to predation by the raptorial protozoan predator, Amoeba proteus, which captures prey with pseudopodia. Videomicrography used to measure the behavior of interacting S. helianthica and A. proteus revealed that large choanoflagellate colonies were more susceptible to capture than were small colonies or single cells. Swimming colonies produced larger flow fields than did swimming unicellular choanoflagellates, and the distance of S. helianthica from A. proteus when pseudopod formation started was greater for colonies than for single cells. Prey size did not affect the number of pseudopodia formed and the time between their formation, pulsatile kinematics and speed of extension by pseudopodia, or percent of prey lost by the predator. S. helianthica did not change swimming speed or execute escape maneuvers in response to being pursued by pseudopodia, so size-selective feeding by A. proteus was due to predator behavior rather than prey escape. Our results do not support the theory that the selective advantage of becoming multicellular by choanoflagellate-like ancestors of animals was reduced susceptibility to protozoan predation., (© 2022 International Society of Protistologists.)

Leucine-rich repeat kinase 2 (LRRK2) c.6055G>A (p.G2019S) is a frequent cause of Parkinson's disease (PD), accounting for >30% of Tunisian Arab-Berber patients. LRRK2 is widely expressed in the immune system and its kinase activity confers a survival advantage against infection in animal models. Here, we assess haplotype variability in cis and in trans of the LRRK2 c.6055G>A mutation, define the age of the pathogenic allele, explore its relationship to the age of disease onset (AOO), and provide evidence for its positive selection. [ABSTRACT FROM AUTHOR]

The majority of the well-known pharmacogenomics research used in the medical sciences contributes to our understanding of medication interactions. It has a significant impact on treatment and drug development. The broad use of pharmacogenomics is required for the progress of therapy. The main focus is on how genes and an intricate gene system affect the body's reaction to medications. Novel biomarkers that help identify a patient group that is more or less likely to respond to a certain medication have been discovered as a result of recent developments in the field of clinical therapeutics. It aims to improve customized therapy by giving the appropriate drug at the right dose at the right time and making sure that the right prescriptions are issued. A combination of genetic, environmental, and patient variables that impact the pharmacokinetics and/or pharmacodynamics of medications results in interindividual variance in drug response. Drug development, illness susceptibility, and treatment efficacy are all impacted by pharmacogenomics. The purpose of this work is to give a review that might serve as a foundation for the creation of new pharmacogenomics applications, techniques, or strategies. [ABSTRACT FROM AUTHOR]

Agriculture involves activities aimed at improving soil quality for food production. In this environment, microorganisms play a vital role, positively and/or negatively affecting plant growth. Given this impact, knowing the microbiota associated with agricultural systems and phytopathogens is crucial. The microbial culture method has proven ineffective in identifying microorganisms in agricultural systems, and more effective methods with greater scope for their identification currently exist. This review compiles updated information on new methods for studying microorganisms in the agricultural system, such as metagenomics, and new proposals for microorganism identification methods, such as Raman spectrometry, nanotechnology, and phytopathogen biosensors. In addition, it discusses the strengths and limitations of the new methods for microorganism identification. [ABSTRACT FROM AUTHOR]

Owing to the rising demand for vegetable soybean products, there is an increasing need for high-yield soybean varieties. However, the complex correlation patterns among quantitative traits with genetic architecture pose a challenge for improving vegetable soybean through breeding. Herein, a genome-wide association study (GWAS) was applied to 6 yield-related traits in 188 vegetable soybean accessions. Using a BLINK model, a total of 116 single nucleotide polymorphisms (SNPs) were identified for plant height, pod length, pod number, pod thickness, pod width, and fresh pod weight. Furthermore, a total of 220 genes were found in the 200 kb upstream and downstream regions of significant SNPs, including 11 genes encoding functional proteins. Among them, four candidate genes, Glyma.13G109100, Glyma.03G183200, Glyma.09G102200, and Glyma.09G102300 were analyzed for significant haplotype variations and to be in LD block, which encode MYB-related transcription factor, auxin-responsive protein, F-box protein, and CYP450, respectively. The relative expression of candidate genes in V030 and V071 vegetable soybean (for the plant height, pod number, and fresh pod weight of V030 were lower than those of the V071 strains) was significantly different, and these genes could be involved in plant growth and development via various pathways. Altogether, we identified four candidate genes for pod yield and plant height from vegetable soybean germplasm. This study provides insights into the genomic basis for improving soybean and crucial genomic resources that can facilitate genome-assisted high-yielding vegetable soybean breeding. [ABSTRACT FROM AUTHOR]

Diatoms are important primary producers in marine and freshwater environments, but little is known about the signalling mechanisms they use to detect changes in their environment. All eukaryotic organisms use Ca2+ signalling to perceive and respond to environmental stimuli, employing a range of Ca2+-permeable ion channels to facilitate the movement of Ca2+ across cellular membranes. We investigated the distribution of different families of Ca2+ channels in diatom genomes, with comparison to other members of the stramenopile lineage. The four-domain voltage-gated Ca2+ channels (Cav) are present in some centric diatoms but almost completely absent in pennate diatoms, whereas single-domain voltage-gated EukCatA channels were found in all diatoms. Glutamate receptors (GLRs) and pentameric ligand-gated ion channels (pLGICs) also appear to have been lost in several pennate species. Transient receptor potential (TRP) channels are present in all diatoms, but have not undergone the significant expansion seen in brown algae. All diatom species analysed lacked the mitochondrial uniporter (MCU), a highly conserved channel type found in many eukaryotes, including several stramenopile lineages. These results highlight the unique Ca2+-signalling toolkit of diatoms and indicate that evolutionary gains or losses of different Ca2+ channels may contribute to differences in cellular-signalling mechanisms between species. [ABSTRACT FROM AUTHOR]

The histological structure of human epithelial tissue is complex, but all epithelia share three major features: cohesion, polarity and attachment. These functions are mainly achieved by the presence of specialized structures such as intercellular junctions, polarity protein complexes and basement membranes. In the present review, we have analyzed the presence of each of these structures in several groups of animals that are considered to be at the base of the animal evolution tree. Interestingly, these characters seem to have evolved independently, and a careful histological and structural analysis of the phylogenetic tree shows different groups of animals in which epithelia are absent and groups in which cells show only some of the specialized structures found in differentiated epithelia. These findings could contribute to understand how epithelial tissues evolved and determine their current protective functions., (©The Author(s) 2023. Open Access. This article is licensed under a Creative Commons CC-BY International License.)

The genus Hartaetosiga Carr, Richter and Nitsche, 2017 comprised up to now only three species, H. gracilis (Kent) Carr, Richter, Nitsche, 2017, H. balthica (Wylezich and Karpov) Carr, Richter and Nitsche, 2017 and H. minima (Wylezich and Karpov) Carr, Richter and Nitsche, 2017. Based on distinct molecular data these species were relocated from the strictly freshwater genus Codosiga (Ehrenberg) Bütschli, 1878 to a new genus comprising brackish and marine species. During the cruise MSM82/2 across the Atlantic Ocean in 2019, surface water samples were taken from 15 stations along a transect ranging from 35°S to 23°N. We were able to isolate and cultivate 14 strains of the genus Hartaetosiga. Morphometric data showed no distinct morphological traits allowing for a species delineation, indicating a cryptic species complex within the genus. Based on cultivation, morphological data, and molecular analyses, we recorded H. gracilis for the first time from off-shelf waters of the Atlantic Ocean and could describe a new species, H. australis n. sp. This new species was recorded from sampling stations in the Southern Hemisphere only, which may indicate a potential biogeographic restriction likely caused by the Equatorial Counter Current (ECC), dividing the northern and southern surface waters., (© 2022 The Authors. Journal of Eukaryotic Microbiology published by Wiley Periodicals LLC on behalf of International Society of Protistologists.)

Atrial fibrillation (AF) is an important medical problem, as it significantly affects patients' quality of life and prognosis. AF often complicates the course of chronic obstructive pulmonary disease (COPD), a widespread disease with heavy economic and social burdens. A growing body of evidence suggests multiple links between COPD and AF. This review considers the common pathogenetic mechanisms (chronic hypoxia, persistent inflammation, endothelial dysfunction, and myocardial remodeling) of these diseases and describes the main risk factors for the development of AF in patients with COPD. The most effective models based on clinical, laboratory, and functional indices are also described, which enable the identification of patients suffering from COPD with a high risk of AF development. Thus, AF in COPD patients is a frequent problem, and the search for new tools to identify patients at a high risk of AF among COPD patients remains an urgent medical problem. [ABSTRACT FROM AUTHOR]

The emergence of the nervous system is one of the most important events in the evolution of life on Earth. The details of this event remain poorly understood; in particular, a great variety of known neurotransmitter substances requires an explanation. We analyze the homologs of neuronal glutamate and gamma-aminobutyric acid (GABA) receptors in Placozoa (animals without a nervous system, but possessing the mobility and behavior). Phylogenetic analysis and comparison of amino acid residues responsible for a ligand specificity demonstrated that these Placozoan receptors are unexpectedly numerous, diverse, and evolutionarily dynamic, and by all these traits, they rather resemble the olfactory receptors of higher animals. Our results indicate that the chemoreceptor system was an important source of diverse receptors for the emerging nervous system, and future neurotransmitter amino acids (glutamate, GABA, glycine) were relevant external signals for the first animals that did not yet have a nervous system. [ABSTRACT FROM AUTHOR]

Simple Summary: Pigs are important in agriculture as they produce animal-based protein for human consumption. The analysis of selection signatures has implications for the maintenance and utilization of genetic diversity and can reveal genes associated with phenotypic traits, either as a result of natural or of artificial selection. Pig populations are poorly characterised in South Africa. Hence, studies aimed at evaluating genetic distinctiveness and pig breed diversity will contribute to developing a rational plan for population conservation programs among other applications. South Africa boasts a diverse range of pig populations, encompassing intensively raised commercial breeds, as well as indigenous and village pigs reared under low-input production systems. The aim of this study was to investigate how natural and artificial selection have shaped the genomic landscape of South African pig populations sampled from different genetic backgrounds and production systems. For this purpose, the integrated haplotype score (iHS), as well as cross population extended haplotype homozygosity (XP-EHH) and Lewontin and Krakauer's extension of the Fst statistic based on haplotype information (HapFLK) were utilised. Our results revealed several population-specific signatures of selection associated with the different production systems. The importance of natural selection in village populations was highlighted, as the majority of genomic regions under selection were identified in these populations. Regions under natural and artificial selection causing the distinct genetic footprints of these populations also allow for the identification of genes and pathways that may influence production and adaptation. In the context of intensively raised commercial pig breeds (Large White, Kolbroek, and Windsnyer), the identified regions included quantitative loci (QTLs) associated with economically important traits. For example, meat and carcass QTLs were prevalent in all the populations, showing the potential of village and indigenous populations' ability to be managed and improved for such traits. Results of this study therefore increase our understanding of the intricate interplay between selection pressures, genomic adaptations, and desirable traits within South African pig populations. [ABSTRACT FROM AUTHOR]

Purpose: Medical diagnosis and treatment processes exhibit a high degree of variability, as during the process execution, healthcare professionals can decide on additional steps, change the execution order or skip a task. Process models can help to document and to discuss such processes. However, depicting variability in graphical process models using standardized languages, such as Business Process Model and Notation (BPMN), can lead to large and complicated diagrams that medical staff who do not have formal training in modeling languages have difficulty understanding. This study proposes a pattern-based process visualization that medical doctors can understand without extensive training. The process descriptions using this pattern-based visualization can later be transformed into formal business process models in languages such as BPMN. Design/methodology/approach: The authors derived patterns for expressing variability in healthcare processes from the literature and medical guidelines. Then, the authors evaluated and revised these patterns based on interviews with physicians in a Danish hospital. Findings: A set of business process variability patterns was proposed to express situations with variability in hospital treatment and diagnosis processes. The interviewed medical doctors could translate the patterns into their daily work practice, and the patterns were used to model a hospital process. Practical implications: When communicating with medical personnel, the patterns can be used as building blocks for documenting and discussing variable processes. Originality/value: The patterns can reduce complexity in process visualization. This study provides the first validation of these patterns in a hospital. [ABSTRACT FROM AUTHOR]

Kashmir cattle, which were kept by local pastoralists for centuries, are exceptionally resilient and adaptive to harsh environments. Despite its significance, the genomic characteristics of this cattle breed remain elusive. This study utilized whole genome sequences of Kashmir cattle (n = 20; newly sequenced) alongside published whole genomes of 32 distinct breeds and seven core cattle populations (n = 135). The analysis identified ~25.87 million biallelic single nucleotide polymorphisms in Kashmir cattle, predominantly in intergenic and intron regions. Population structure analyses revealed distinct clustering patterns of Kashmir cattle with proximity to the South Asian, African and Chinese indicine cattle populations. Genetic diversity analysis of Kashmir cattle demonstrated lower inbreeding and greater nucleotide diversity than analyzed global breeds. Homozygosity runs indicated less consanguineous mating in Kashmir cattle compared with European taurine breeds. Furthermore, six selection sweep detection methods were used within Kashmir cattle and other cattle populations to identify genes associated with vital traits, including immunity (BOLA-DQA5, BOLA-DQB, TNFAIP8L, FCRL4, AOAH, HIF1AN, FBXL3, MPEG1, CDC40, etc.), reproduction (GOLGA4, BRWD1, OSBP2, LEO1 ADCY5, etc.), growth (ADPRHL1, NRG2, TCF12, TMOD4, GBP4, IGF2, RSPO3, SCD, etc.), milk composition (MRPS30 and CSF1) and high-altitude adaptation (EDNRA, ITPR2, AGBL4 and SCG3). These findings provide essential genetic insights into the characteristics and establish the foundation for the scientific conservation and utilization of Kashmir cattle breed., (© 2024 Stichting International Foundation for Animal Genetics.)

Animal genetic resources are crucial for ensuring global food security. However, in recent years, a noticeable decline in the genetic diversity of livestock has occurred worldwide. This decline is pronounced in developing countries, where the management of these resources is insufficient. In the current study, we performed whole genome sequencing for 20 Wuxue (WX) and five Guizhou White (GW) goats. Additionally, we utilized the published genomes of 131 samples representing five different goat breeds from various regions in China. We investigated and compared the genetic diversity and selection signatures of WX goats. Whole genome sequencing analysis of the WX and GW populations yielded 120 425 063 SNPs, which resided primarily in intergenic and intron regions. Population genetic structure revealed that WX exhibited genetic resemblance to GW, Chengdu Brown, and Jintang Black and significant differentiation from the other goat breeds. In addition, three methods (nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity) showed moderate genetic diversity in WX goats. We used nucleotide diversity and composite likelihood ratio methods to identify within-breed signatures of positive selection in WX goats. A total of 369 genes were identified using both detection methods, including genes related to reproduction (GRID2, ZNF276, TCF25, and SPIRE2), growth (HMGA2 and GJA3), and immunity (IRF3 and SRSF3). Overall, this study explored the adaptability of WX goats, shedding light on their genetic richness and potential to thrive in challenges posed by climatic changes and diseases. Further investigations are warranted to harness these insights to enhance more efficient and sustainable goat breeding initiatives., (© 2024 Stichting International Foundation for Animal Genetics.)

The review considers modern ideas about the evolution and phylogeny of the obligate intracellular eukaryotic parasites (microsporidia). In the process of adaptation to intracellular parasitism, the genome and functional apparatus of these organisms underwent a significant reduction and modification. The systematic position of this group remained unclear for a long time, and it was unknown for certain how the evolution of microsporidia occurred, when and how their unique adaptations to a parasitic lifestyle occurred. A true breakthrough in the study of the evolution of microsporidia was made only in the last few years. The groups occupying a position on the tree of life closest to microsporidia were discovered and described: Cryptomycota (Rozellida) and Aphelida. Sequencing of the genomes of representatives of these groups (that also belong to intracellular parasites) and the first genomic data on representatives of basal branches of microsporidia (obtained in 2013–2020) allowed to take a fresh look at the evolution of microsporidia and their closest relatives, to detect intermediate forms along the pathway of adaptation to intracellular parasitism. [ABSTRACT FROM AUTHOR]

Simple Summary: Genomic association analyses for milk yield and milk quality traits including mastitis were accomplished in a dairy cattle population from the harsh and challenging tropical savanna climate of Bengaluru, India. A further effect of selection was due to social–ecological drivers, i.e., specific constraints that are prevalent in small-sized family farms. As a time report, this study identified footprints of selection among the dairy cattle breeds in this region. The genome-wide association study (GWAS) identified two SNPs, rs109340659 and rs41571523, significantly associated with test-day milk yield. Fibrosin-like 1 (FBRSL) and calcium voltage-gated channel auxiliary subunit gamma 3 (CACN) were the respective annotated potential candidate genes. Furthermore, the genomic regions under selection were associated with pathways and mechanisms involving ubiquitination, cell signaling and immune response. Hence, contrasting dairy breeds genomically contributed to the detection of genomic regions under selection, with strong effects on adaptation and overall disease resistance. A study was designed to identify the genomic regions associated with milk production traits in a dairy cattle population reared by smallholder farmers in the harsh and challenging tropical savanna climate of Bengaluru, India. This study is a first-of-its-kind attempt to identify the selection sweeps for the dairy cattle breeds reared in such an environment. Two hundred forty lactating dairy cows reared by 68 farmers across the rural–urban transiting regions of Bengaluru were selected for this study. A genome-wide association study (GWAS) was performed to identify candidate genes for test-day milk yield, solids-not-fat (SNF), milk lactose, milk density and clinical mastitis. Furthermore, the cross-population extended haplotype homozygosity (XP-EHH) methodology was adopted to scan the dairy cattle breeds (Holstein Friesian, Jersey and Crossbred) in Bengaluru. Two SNPs, rs109340659 and rs41571523, were observed to be significantly associated with test-day milk yield. No significant SNPs were observed for the remaining production traits. The GWAS for milk lactose revealed one SNP (rs41634101) that was very close to the threshold limit, though not significant. The potential candidate genes fibrosin-like 1 (FBRSL) and calcium voltage-gated channel auxiliary subunit gamma 3 (CACN) were identified to be in close proximity to the SNP identified for test-day milk yield. These genes were observed to be associated with milk production traits based on previous reports. Furthermore, the selection signature analysis revealed a number of regions under selection for the breed-group comparisons (Crossbred-HF, Crossbred-J and HF-J). Functional analysis of these annotated genes under selection indicated pathways and mechanisms involving ubiquitination, cell signaling and immune response. These findings point towards the probable selection of dairy cows in Bengaluru for thermotolerance. [ABSTRACT FROM AUTHOR]

A genomic study was conducted to identify the effects of urbanization and environmental contaminants with heavy metals on selection footprints in dairy cattle populations reared in the megacity of Bengaluru, South India. Dairy cattle reared along the rural–urban interface of Bengaluru with/without access to roughage from public lakeshores were selected. The genotyped animals were subjected to the cross-population–extended haplotype homozygosity (XP-EHH) methodology to infer selection sweeps caused by urbanization (rural, mixed, and urban) and environmental contamination with cadmium and lead. We postulated that social-ecological challenges contribute to mechanisms of natural selection. A number of selection sweeps were identified when comparing the genomes of cattle located in rural, mixed, or urban regions. The largest effects were identified on BTA21, displaying pronounced peaks for selection sweeps for all three urbanization levels (urban_vs_rural, urban_vs_mixed and rural_vs_mixed). Selection sweeps are located in chromosomal segments in close proximity to the genes lrand rab interactor 3 (RIN3), solute carrier family 24 member 4 (SLC24A4), tetraspanin 3 (TSPAN3), and proline-serine-threonine phosphatase interacting protein 1 (PSTPIP1). Functional enrichment analyses of the selection sweeps for all three comparisons revealed a number of gene ontology (GO) and KEGG terms, which were associated with reproduction, metabolism, and cell signaling-related functional mechanisms. Likewise, a number of the chromosomal segments under selection were observed when creating cattle groups according to cadmium and lead contaminations. Stronger and more intense positive selection sweeps were observed for the cadmium contaminated group, i.e., signals of selection on BTA 16 and BTA19 in close proximity to genes regulating the somatotropic axis (growth factor receptor bound protein 2 (GRB2) and cell ion exchange (chloride voltage-gated channel 6 (CLCN6)). A few novel, so far uncharacterized genes, mostly with effects on immune physiology, were identified. The lead contaminated group revealed sweeps which were annotated with genes involved in carcass traits (TNNC2, SLC12A5, and GABRA4), milk yield (HTR1D, SLCO3A1, TEK, and OPCML), reproduction (GABRA4), hypoxia/stress response (OPRD1 and KDR), cell adhesion (PCDHGC3), inflammatory response (ADORA2A), and immune defense mechanism (ALCAM). Thus, the findings from this study provide a deeper insight into the genomic regions under selection under the effects of urbanization and environmental contamination. [ABSTRACT FROM AUTHOR]

Atherosclerosis and one of its most serious consequences, coronary artery disease, are important sources of morbidity and mortality globally, necessitating early detection and treatment. Considering their complex pathophysiology, including several harmful processes, a comprehensive approach to diagnosis, prognosis, and therapy is very desirable. Extracellular matrix remodeling is a major component of this dangerous cascade, including the cleavage of constituents (collagen, elastin, proteoglycans) and the propagation or exacerbation of the inflammatory response. Several extracellular matrix degradation indicators have been hypothesized to correlate with the existence, severity, and prognosis of coronary artery disease. The potency of matrix metalloproteinases, notably collagenases and gelatinases, has been the most thoroughly investigated in clinical studies. Stromelysins, matrilysins, transmembrane matrix metalloproteinases, collagen and laminin turnover indicators, as well as fibronectin, have also been studied to a lesser level. Among the most well-studied markers, MMP-1, MMP-2, MMP-8, and MMP-9 have been found increased in patients with cardiovascular risk factors such as metabolic syndrome, its components (obesity, dyslipidemia, diabetes mellitus), and smoking. Increasing concentrations are detected in acute coronary syndromes compared to stable angina pectoris and healthy control groups. It should also be stressed that those extracellular matrix biomarkers may also be detected in high concentrations in other vascular pathologies such as peripheral artery disease, carotid artery disease, aortic aneurysms, and dissections. Despite the advances gained, future research should focus on their importance and, more crucially, their added utility as biomarkers in identifying persons at risk of developing overt coronary artery disease. At the same time, determining the prognosis of coronary artery disease patients using such biomarkers may be important for their adequate care., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Background: It has been established that an increase in triglyceride-rich lipoprotein levels is associated with the development of systemic low-grade inflammation. Data on the prognostic role of hypertriglyceridemia (HTG) dependent on the state of low-grade inflammation are limited., Objective: The study's objective was to evaluate the predictive value of mild-to-moderate HTG (2.3- 11.2 mmol/L) regarding the development of cardiovascular events in patients at high and very high cardiovascular risk (CVR), depending on the high-sensitivity C-reactive protein (hsCRP) values., Methods: The study included 185 patients with high and very high CVR. The concentration of hsCRP in blood serum was measured using an enzyme-linked immunosorbent assay kit. The combined endpoint was cardiovascular death, nonfatal myocardial infarction or unstable angina (which required hospitalization), nonfatal stroke, and coronary revascularization., Results: HTG was revealed in 17.3% of the patients. An increase in hsCRP ≥2.0 mg/L was observed in 51.9% of the patients. The event-free survival of patients with HTG was not statistically different from that in patients with TG <2.3 mmol/L (RR 1.61; 95% CI 0.86-3.00; p=0.133). In the subgroup of patients with hsCRP <2.0 mg/L, patients with HTG were not significantly different from patients without HTG. In the subgroup of patients with hsCRP≥2.0 mg/L, the presence of HTG was associated with a 4.63 times increase in the RR of adverse cardiovascular events (95% CI 1.35-15.8; p=0.015) after adjusting for potential confounders., Conclusion: In patients with high and very high CVR, an increase in TG ≥2.3 mmol/L was associated with the development of adverse cardiovascular events only in the subgroup of patients with an increase in hsCRP ≥2.0 mg/L. The presence of HTG was associated with a 4.63 times increase in RR of adverse cardiovascular events (95% CI 1.35-15.8; p=0.015)., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

The long-distance spreading and transport of airborne particulate matter (PM) of biogenic or chemical compounds, which are thought to be possible carriers of SARS-CoV-2 virions, can have a negative impact on the incidence and severity of COVID-19 viral disease. Considering the total Aerosol Optical Depth at 550 nm (AOD) as an atmospheric aerosol loading variable, inhalable fine PM with a diameter ≤2.5 µm (PM2.5) or coarse PM with a diameter ≤10 µm (PM10) during 26 February 2020–31 March 2022, and COVID-19's five waves in Romania, the current study investigates the impact of outdoor PM on the COVID-19 pandemic in Bucharest city. Through descriptive statistics analysis applied to average daily time series in situ and satellite data of PM2.5, PM10, and climate parameters, this study found decreased trends of PM2.5 and PM10 concentrations of 24.58% and 18.9%, respectively compared to the pre-pandemic period (2015–2019). Exposure to high levels of PM2.5 and PM10 particles was positively correlated with COVID-19 incidence and mortality. The derived average PM2.5/PM10 ratios during the entire pandemic period are relatively low (<0.44), indicating a dominance of coarse traffic-related particles' fraction. Significant reductions of the averaged AOD levels over Bucharest were recorded during the first and third waves of COVID-19 pandemic and their associated lockdowns (~28.2% and ~16.4%, respectively) compared to pre-pandemic period (2015–2019) average AOD levels. The findings of this research are important for decision-makers implementing COVID-19 safety controls and health measures during viral infections. [ABSTRACT FROM AUTHOR]

Simple Summary: Of all the Arctic seas, the prokaryotic communities of the Barents Sea are the most affected by climate change and are strongly influenced by microbiota from the Atlantic Ocean. Using 16S metabarcoding, we analyzed samples of prokaryotic plankton communities in the Barents Sea and found two types of communities. The origin of these communities is discussed in terms of biogeography. The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied the diversity of prokaryotic communities using 16S metabarcoding in the western and northeastern parts of the Barents Sea along the Kola Section and the section from Novaya Zemlya to Franz Joseph Land. The hypothesis-independent clustering method revealed the existence of two distinct types of communities. The most common prokaryotic taxa were shared between two types of communities, but their relative abundance was different. It was found that the geographic location of the sampling sites explained more than 30% of the difference between communities, while no statistically significant correlation between environmental parameters and community composition was found. The representatives of the Psychrobacter, Sulfitobacter and Polaribacter genera were dominant in samples from both types of communities. The first type of community was also dominated by members of Halomonas, Pseudoalteromonas, Planococcaceae and an unclassified representative of the Alteromonadaceae family. The second type of community also had a significant proportion of Nitrincolaceae, SAR92, SAR11 Clade I, NS9, Cryomorphaceae and SUP05 representatives. The origin of these communities can be explained by the influence of environmental factors or by the different origins of water masses. This research highlights the importance of studying biogeographic patterns in the Barents Sea in comparison with those in the North Atlantic and Arctic Ocean prokaryote communities. [ABSTRACT FROM AUTHOR]

Inference of deep phylogenies has almost exclusively used protein rather than DNA sequences based on the perception that protein sequences are less prone to homoplasy and saturation or to issues of compositional heterogeneity than DNA sequences. Here, we analyze a model of codon evolution under an idealized genetic code and demonstrate that those perceptions may be misconceptions. We conduct a simulation study to assess the utility of protein versus DNA sequences for inferring deep phylogenies, with protein-coding data generated under models of heterogeneous substitution processes across sites in the sequence and among lineages on the tree, and then analyzed using nucleotide, amino acid, and codon models. Analysis of DNA sequences under nucleotide-substitution models (possibly with the third codon positions excluded) recovered the correct tree at least as often as analysis of the corresponding protein sequences under modern amino acid models. We also applied the different data-analysis strategies to an empirical dataset to infer the metazoan phylogeny. Our results from both simulated and real data suggest that DNA sequences may be as useful as proteins for inferring deep phylogenies and should not be excluded from such analyses. Analysis of DNA data under nucleotide models has a major computational advantage over protein-data analysis, potentially making it feasible to use advanced models that account for among-site and among-lineage heterogeneity in the nucleotide-substitution process in inference of deep phylogenies. [ABSTRACT FROM AUTHOR]

The first data on the composition and diversity of the summer community of planktonic protists in Usinsky Bay and the adjacent water area of the Kuybyshev Reservoir, obtained using high-throughput sequencing of the 18S ribosomal RNA gene, are presented. In the composition of the protist community, 1150 operational taxonomic units (OTU) were found; among them, representatives of the Stramenopiles–Alveolata–Rhizaria (SAR) supergroup predominate. In the complete library, Stramenopiles predominate by the number of OTU, represented (in descending order) by Chrysophyceae (8.5%), Opalozoa (8.3%), Diatomea (4.7%), and Oomycetes (Peronosporomycetes) (3.7%); by the number of nucleotide sequences, Alveolata (62.0%) and, first of all, Ciliata (56.9%). There are four interconnected communities of protists: of the river area, the bay itself, the mouth zone, and the reservoir outside the influence of the bay (above the mouth). The communities of the river area and the reservoir area above the mouth have the greatest contrast in composition. In general, the estuarine system studied has features of both ecocline and ecotone. The competitive relationships with cyanobacteria have the main effect on the development of the phototrophic component of eukaryotic plankton. Cyanobacterial "bloom" also affects the structure of the heterotrophic part of the community, although this effect is less pronounced. The development of Archaeplastida, Rhizaria, and minor groups of protists positively correlates with the portion of Metazoa sequences in the samples, which reflects the intensity of the metazooplankton press. Sequences belonging to Bolidophyceae and Rhodelphida, the taxa rare for freshwater, were found. These findings expand the biogeography of these groups that were found so far in very few freshwater reservoirs. [ABSTRACT FROM AUTHOR]

A panel of 106 insertion/deletion (InDel) polymorphisms and a method of their genotyping on biochips were proposed as a new approach to genetic personal identification. Short lengths and low mutation rates are basic properties of InDel markers, which thus have significant advantages over short tandem repeats (STRs) widely used in forensics. The allele frequency distributions of all known InDel polymorphisms were studied in the five largest world populations (European, East Asian, South Asian, African, and American). Markers were selected to meet the following criteria: the minor allele frequency (MAF) is higher than 0.30; the physical distance between markers is greater than 3 Mb; there are no polymorphisms, tandem repeats, and palindromes in the flanking sequences; the AT/GC ratio is close to 1. A panel of 106 polymorphisms was thus formed; the average MAF was estimated at 0.396 in the five populations. The method developed for panel genotyping included one-step multiplex PCR and subsequent hybridization on a biological microarray. The average amplicon length was 72 bp. A sample of 201 residents of Moscow and St. Petersburg was tested to determine the main characteristics of the panel: the random matching probability (MP) was 1.89× 10–43 and the combined probability of paternity exclusion (CPE) was 0.99999999063. The method provides an alternative to molecular genetic personal identification based on the STR length variations. [ABSTRACT FROM AUTHOR]

An astonishing range of morphologies and life strategies has arisen across the vast diversity of protists, allowing them to thrive in most environments. In model protists, like Tetrahymena, Dictyostelium, or Trypanosoma, life cycles involving multiple life stages with different morphologies have been well characterized. In contrast, knowledge of the life cycles of free-living protists, which primarily consist of uncultivated environmental lineages, remains largely fragmentary. Various life stages and lineage-specific cellular innovations have been observed in the field for uncultivated protists, but such innovations generally lack functional characterization and have unknown physiological and ecological roles. In the actual state of knowledge, evidence of sexual processes is confirmed for 20% of free-living protist lineages. Nevertheless, at the onset of eukaryotic diversification, common molecular trends emerged to promote genetic recombination, establishing sex as an inherent feature of protists. Here, we review protist life cycles from the viewpoint of life cycle transitions and genetics across major eukaryotic lineages. We focus on the scarcely observed sexual cycle of free-living protists, summarizing evidence for its existence and describing key genes governing its progression, as well as, current methods for studying the genetics of sexual cycles in both cultivable and uncultivated protist groups., (© 2024 The Author(s). Journal of Eukaryotic Microbiology published by Wiley Periodicals LLC on behalf of International Society of Protistologists.)

Peptidases of the papain family play a key role in protein degradation, regulated proteolysis, and the host–pathogen arms race. Although the papain family has been the subject of many studies, knowledge about its diversity, origin, and evolution in Eukaryota, Bacteria, and Archaea is limited; thus, we aimed to address these long-standing knowledge gaps. We traced the origin and expansion of the papain family with a phylogenomic analysis, using sequence data from numerous prokaryotic and eukaryotic proteomes, transcriptomes, and genomes. We identified the full complement of the papain family in all prokaryotic and eukaryotic lineages. Analysis of the papain family provided strong evidence for its early diversification in the ancestor of eukaryotes. We found that the papain family has undergone complex and dynamic evolution through numerous gene duplications, which produced eight eukaryotic ancestral paralogous C1A lineages during eukaryogenesis. Different evolutionary forces operated on C1A peptidases, including gene duplication, horizontal gene transfer, and gene loss. This study challenges the current understanding of the origin and evolution of the papain family and provides valuable insights into their early diversification. The findings of this comprehensive study provide guidelines for future structural and functional studies of the papain family. [ABSTRACT FROM AUTHOR]

Accurate phylogenies are fundamental to our understanding of the pattern and process of evolution. Yet, phylogenies at deep evolutionary timescales, with correspondingly long branches, have been fraught with controversy resulting from conflicting estimates from models with varying complexity and goodness of fit. Analyses of historical as well as current empirical datasets, such as alignments including Microsporidia, Nematoda, or Platyhelminthes, have demonstrated that inadequate modeling of across-site compositional heterogeneity, which is the result of biochemical constraints that lead to varying patterns of accepted amino acids along sequences, can lead to erroneous topologies that are strongly supported. Unfortunately, models that adequately account for across-site compositional heterogeneity remain computationally challenging or intractable for an increasing fraction of contemporary datasets. Here, we introduce "compositional constraint analysis," a method to investigate the effect of site-specific constraints on amino acid composition on phylogenetic inference. We show that more constrained sites with lower diversity and less constrained sites with higher diversity exhibit ostensibly conflicting signals under models ignoring across-site compositional heterogeneity that lead to long-branch attraction artifacts and demonstrate that more complex models accounting for across-site compositional heterogeneity can ameliorate this bias. We present CAT-posterior mean site frequencies (PMSF), a pipeline for diagnosing and resolving phylogenetic bias resulting from inadequate modeling of across-site compositional heterogeneity based on the CAT model. CAT-PMSF is robust against long-branch attraction in all alignments we have examined. We suggest using CAT-PMSF when convergence of the CAT model cannot be assured. We find evidence that compositionally constrained sites are driving long-branch attraction in two metazoan datasets and recover evidence for Porifera as the sister group to all other animals. [Animal phylogeny; cross-site heterogeneity; long-branch attraction; phylogenomics.] [ABSTRACT FROM AUTHOR]

SUMMARY: In plants, variations in seed size and number are outcomes of different reproductive strategies. Both traits are often environmentally influenced, suggesting that a mechanism exists to coordinate these phenotypes in response to available maternal resources. Yet, how maternal resources are sensed and influence seed size and number is largely unknown. Here, we report a mechanism that senses maternal resources and coordinates grain size and number in the wild rice Oryza rufipogon, a wild progenitor of Asian cultivated rice. We showed that FT‐like 9 (FTL9) regulates both grain size and number and that maternal photosynthetic assimilates induce FTL9 expression in leaves to act as a long‐range signal that increases grain number and reduces size. Our findings highlight a strategy that benefits wild plants to survive in a fluctuating environment. In this strategy, when maternal resources are sufficient, wild plants increase their offspring number while preventing an increase in offspring size by the action of FTL9, which helps expand their habitats. In addition, we found that a loss‐of‐function allele (ftl9) is prevalent among wild and cultivated populations, offering a new scenario in the history of rice domestication. Significance Statement: Offspring number and size are the cornerstones of the life history of wild plants and are essential in crop yield. By using the phenotypic variation of grain traits among Oryza rufipogon, a wild progenitor of Asian cultivated rice, we found that FT‐like 9 (FTL9) mediates maternal‐offspring signaling that senses maternal resource availability and coordinates grain size and number. [ABSTRACT FROM AUTHOR]

The dynamic equilibrium between death and regeneration is well established at the cell level. Conversely, no study has investigated the homeostatic control of shape at the whole organism level through processes involving apoptosis. To address this fundamental biological question, we took advantage of the morphological and functional properties of the carnivorous sponge Lycopodina hypogea. During its feeding cycle, this sponge undergoes spectacular shape changes. Starved animals display many elongated filaments to capture prey. After capture, prey are digested in the absence of any centralized digestive structure. Strikingly, the elongated filaments actively regress and reform to maintain a constant, homeostatically controlled number and size of filaments in resting sponges. This unusual mode of nutrition provides a unique opportunity to better understand the processes involved in cell renewal and regeneration in adult tissues. Throughout these processes, cell proliferation and apoptosis are interconnected key actors. Therefore, L. hypogea is an ideal organism to study how molecular and cellular processes are mechanistically coupled to ensure global shape homeostasis. [ABSTRACT FROM AUTHOR]

This review describes the role of silicon (Si) in plants. Methods of silicon determination and speciation are also reported. The mechanisms of Si uptake by plants, silicon fractions in the soil, and the participation of flora and fauna in the Si cycle in terrestrial ecosystems have been overviewed. Plants of Fabaceae (especially Pisum sativum L. and Medicago sativa L.) and Poaceae (particularly Triticum aestivum L.) families with different Si accumulation capabilities were taken into consideration to describe the role of Si in the alleviation of the negative effects of biotic and abiotic stresses. The article focuses on sample preparation, which includes extraction methods and analytical techniques. The methods of isolation and the characterization of the Si-based biologically active compounds from plants have been overviewed. The antimicrobial properties and cytotoxic effects of known bioactive compounds obtained from pea, alfalfa, and wheat were also described. [ABSTRACT FROM AUTHOR]

There is still no consensus as to how to select models in Bayesian phylogenetics, and more generally in applied Bayesian statistics. Bayes factors are often presented as the method of choice, yet other approaches have been proposed, such as cross-validation or information criteria. Each of these paradigms raises specific computational challenges, but they also differ in their statistical meaning, being motivated by different objectives: either testing hypotheses or finding the best-approximating model. These alternative goals entail different compromises, and as a result, Bayes factors, cross-validation, and information criteria may be valid for addressing different questions. Here, the question of Bayesian model selection is revisited, with a focus on the problem of finding the best-approximating model. Several model selection approaches were re-implemented, numerically assessed and compared: Bayes factors, cross-validation (CV), in its different forms (k -fold or leave-one-out), and the widely applicable information criterion (wAIC), which is asymptotically equivalent to leave-one-out cross-validation (LOO-CV). Using a combination of analytical results and empirical and simulation analyses, it is shown that Bayes factors are unduly conservative. In contrast, CV represents a more adequate formalism for selecting the model returning the best approximation of the data-generating process and the most accurate estimates of the parameters of interest. Among alternative CV schemes, LOO-CV and its asymptotic equivalent represented by the wAIC, stand out as the best choices, conceptually and computationally, given that both can be simultaneously computed based on standard Markov chain Monte Carlo runs under the posterior distribution. [Bayes factor; cross-validation; marginal likelihood; model comparison; wAIC.] [ABSTRACT FROM AUTHOR]

Phylogenomic analysis of large genome-wide sequence data sets can resolve phylogenetic tree topologies for large species groups, help test the accuracy of and improve resolution for earlier multi-locus studies and reveal the level of agreement or concordance within partitions of the genome for various tree topologies. Here we used a target-capture approach to sequence 1088 single-copy exons for more than 200 labrid fishes together with more than 100 outgroup taxa to generate a new data-rich phylogeny for the family Labridae. Our time-calibrated phylogenetic analysis of exon-capture data pushes the root node age of the family Labridae back into the Cretaceous to about 79 Ma years ago. The monotypic Centrogenys vaigiensis , and the order Uranoscopiformes (stargazers) are identified as the sister lineages of Labridae. The phylogenetic relationships among major labrid subfamilies and within these clades were largely congruent with prior analyses of select mitochondrial and nuclear datasets. However, the position of the tribe Cirrhilabrini (fairy and flame wrasses) showed discordance, resolving either as the sister to a crown julidine clade or alternatively sister to a group formed by the labrines, cheilines and scarines. Exploration of this pattern using multiple approaches leads to slightly higher support for this latter hypothesis, highlighting the importance of genome-level data sets for resolving short internodes at key phylogenetic positions in a large, economically important groups of coral reef fishes. More broadly, we demonstrate how accounting for sources of biological variability from incomplete lineage sorting and exploring systematic error at conflicting nodes can aid in evaluating alternative phylogenetic hypotheses. [coral reefs; divergence time estimation; exon-capture; fossil calibration; incomplete lineage sorting.] [ABSTRACT FROM AUTHOR]

The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the "Opisthosporidia hypothesis"). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium , suggested that the aphelids are sister to fungi (the "Aphelida |$+$| Fungi hypothesis"). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (Aphelidium insulamus and Aphelidium tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida |$+$| Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid–fungal split and the remaining 12 likely evolved de novo , constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favor of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia. [Aphelida, fungi, Holomycota, horizontal gene transfer, phylogenomics, synapomorphy.] [ABSTRACT FROM AUTHOR]