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Abstract High-altitude environments present formidable challenges for survival and reproduction, with organisms facing limited oxygen availability and scarce nutrient resources. The yak (Bos grunniens), indigenous to the Tibetan Plateau, has notably adapted to these extreme conditions. This study delves into the genomic basis of the yak’s adaptation, focusing on the positive selection acting on genes involved in nutrient assimilation pathways. Employing techniques in comparative genomics and molecular evolutionary analyses, we selected genes in the yak that show signs of positive selection associated with nutrient metabolism, absorption, and transport. Our findings reveal specific genetic adaptations related to nutrient metabolism in harsh climatic conditions. Notably, genes involved in energy metabolism, oxygen transport, and thermoregulation exhibited signs of positive selection, suggesting their crucial role in the yak’s successful colonization of high-altitude regions. The study also sheds light on the yak's immune system adaptations, emphasizing genes involved in response to various stresses prevalent at elevated altitudes. Insights into the yak’s genomic makeup provide valuable information for understanding the broader implications of high-altitude adaptations in mammalian evolution. They may contribute to efforts in enhancing livestock resilience to environmental challenges.

The melon fruit fly, Bactrocera zonata (Coquillett) (Diptera: Tephritidae), is a notorious pest, posing a significant threat to a wide range of fruits and vegetables, leading to substantial agricultural losses worldwide. With growing concerns over chemical pesticide resistance and environmental safety, plant-based insecticides have emerged as eco-friendly and economically sustainable alternatives. In this context, the present study delves into the insecticidal potential of Ricinus communis extracts against B. zonata. The crude extract of R. communis was systematically fractionated using a series of organic solvents with increasing polarities. The fraction demonstrating the highest insecticidal activity was further purified for the isolation of bioactive compounds, employing advanced chromatographic techniques such as Column Chromatography, coupled with state-of-the-art analytical methods including Gas Chromatography-Mass Spectrometry (GC-MS) and Fourier Transform Infrared Spectroscopy (FTIR). Bioassays were conducted on B. zonata using the crude extract and its fractions in n-hexane, methanol, and ethyl acetate. Among the isolated compounds, 11,14,17-Eicosatrienoic acid was identified in both the methanol and ethyl acetate fractions. This compound exhibited remarkable insecticidal efficacy, with an LC50 value of 1.36%, a linearity of R2 = 0.64, and a statistically significant probability (p < 0.01). Particularly, 11,14,17-Eicosatrienoic acid emerged as the most potent bioactive agent against B. zonata highlighting its potential as a natural insecticide. These findings underscore the potential of R. communis as a valuable source of bioactive compounds for the sustainable management of B. cucurbitae. This study not only broadens the scope of plant-based pest control strategies but also opens avenues for further exploration of natural compounds in integrated pest management.

Adipose tissue, both intricate and fundamental to physiological functions, comprises cell types, including adipocytes, pivotal in secreting bioactive peptides known as ‘adipokines.’ Apelin (APLN), Visfatin (VSFTN), and Irisin (IRSN) are novel adipokines involved in regulating energy, carbohydrate, protein, and lipid metabolism. APLN acts as an endogenous ligand for G-protein-coupled receptors, VSFTN is essential in nicotinamide adenine dinucleotide (NAD) biosynthesis, and IRSN is released from skeletal muscle and adipose tissues. Their influence spans various physiological domains, including insulin resistance and sensitivity, cardiovascular functions, angiogenesis, and reproductive systems. This review focuses on the potential roles of APLN, VSFTN, and IRSN in energy regulation mechanisms related to farm animal production. Despite accumulating evidence of their significance, comprehensive understanding is still emerging, with most studies based on model organisms. Thus, there’s a pressing need for targeted research on farm animals. Addressing these knowledge gaps could pave the way for improved health strategies, reproductive efficiency, and productivity in farm animals. Future research should focus on understanding the multifaceted interactions of these adipokines and their implications for promoting sustainable and effective animal production.

Alzheimer's disease (AD) is a brain illness that causes gradual memory loss. AD has no treatment and cannot be cured, so early detection is critical. Various AD diagnosis approaches are used in this regard, but Magnetic Resonance Imaging (MRI) provides the most helpful neuroimaging tool for detecting AD. In this paper, we employ a DenseNet-201 based transfer learning technique for diagnosing different Alzheimer's stages as Non-Demented (ND), Moderate Demented (MOD), Mild Demented (MD), Very Mild Demented (VMD), and Severe Demented (SD). The suggested method for a dataset of MRI scans for Alzheimer's disease is divided into five classes. Data augmentation methods were used to expand the size of the dataset and increase DenseNet-201's accuracy. It was found that the proposed strategy provides a very high classification accuracy. This practical and reliable model delivers a success rate of 98.24%. The findings of the experiments demonstrate that the suggested deep learning approach is more accurate and performs well compared to existing techniques and state-of-the-art methods.

The Leptin-Melanocortin System (LMS) is an important regulatory system involved in appetite and energy balance in many organisms, including sheep. Functional genomics analysis of LMS genes can provide insights into the genetic factors that influence rapid growth and high carcass yield in sheep. However, the genetic potential of sheep growth and reproduction has not been fully exploited. Therefore, identifying genes that regulate growth and reproduction would offer strategies for improving the yield and quality of sheep meat. In this study, to explore the possible molecular mechanisms underlying rapid growth and muscular high-yield carcass in sheep, we screened 14 genes, which were previously claimed to be associated with such traits in humans and rodents. The FST outlier approach implemented in LOSITAN detected the loci under selection. These candidate genes were connected to complicated biological processes, including the regulation of eating behavior, energy balance, and the positive regulation of the cAMP biosynthetic process, according to the gene ontology (GO) study. In addition, the 14 genes' re-sequence data revealed 7,226 SNPs. The MC4R, STAT3, BDNF, and TUB genes were discovered to be an outlier and significantly under positive selection using the fixation index (FST) based technique with the tentative combined allocation of mean heterozygosity and FST. Differentially expressed genes were found, and their functions were assigned using a functional genomics approach. Results showed that these genes are crucial in determining sheep features including size and meat quality. Insights are gained into the molecular mechanisms behind these phenotypic variations, and possible genes for future sheep breeding initiatives are provided. This research proves the value of functional genomics analysis in identifying the heritable components of valuable sheep agriculture traits.

The study aimed to understand the molecular evolution of the pathogen recognition peptidoglycan (PGN) proteins and their role in regulating the immune response against infectious diseases in Drosophila melanogaster. D. melanogasterWe obtained the PGRP proteins from 11 different species of Drosophila and analyzed the different evolutionary trends that might be associated with them. We were able to identify the evidence of strong positive selection taking place for these proteins. We investigated the diversity and function of the PGN proteins in D. melanogaster and related species through a combination of bioinformatics approaches. They found that the PGN proteins have undergone rapid and diverse evolution, with some undergoing positive selection and others experiencing gene duplication and loss. The study also revealed that different PGN proteins play distinct roles in regulating the immune response to bacterial infections, with some responding specifically to certain types of bacteria. The research provides valuable insights into the evolution and function of the PGN proteins in the immune response of D. melanogaster. It highlights their potential relevance to pathogen recognition and immune defence in other organisms.

Context: The SARS-CoV-2 virus is the cause of the COVID-19 pandemic, which is a severe public health crisis worldwide.Aims: To analyze the SARS-CoV-2 isolates of Surabaya and predict ORF1ab polyprotein epitopes through the bioinformatics approach for vaccine candidate development. Methods: Three genomic sequences of Surabaya isolates were obtained from the GISAID, NCBI and PDB Gen-bank databases and MEGA-11 software were used to understand the transformations in the isolates. The IEDB and VaxiJen, AllerTop, and ToxinPred web servers were used to predict B-cell epitopes and analyze their antigenicity, non-allergenicity, non-toxicity, respectively. Moreover, these epitopes were linked by EAAAK for 3D modeling, refinement, and validation through Swiss-Model, Galaxy Refine, and RAMPAGE web tools. Results: The Surabaya isolates, RSDS-RCVTD-UNAIR-49-A, 54-A, and 42-A, had 10, 20, and 16 mutations in nucleotides and depicted a phylogenetically close relationship to isolates of Egypt, Pakistan, and Bangladesh, respectively. A total of 71 sequential Orf1ab B-cell epitopes were predicted, and only three peptides were found to be antigenic, non-allergenic, and non-toxic. These epitopes were linked with the EAAAK linker to develop a 3D refined and validated structure. This construct was docked with TLR-3 receptor by the Cluspro webserver and found a high affinity of ORF1ab+TLR3 due to 15 hydrogen bonds. The construct demonstrated good humoral and cellular immune responses in the C-ImmSim server, and cloning in the expression vector pET28a (+) yielded a colon of 846bp. Conclusions: ORF1ab B-cell epitopes could be useful for developing effective vaccines to combat SARS-CoV-2 infection.

Context: The current COVID-19 pandemic has significantly impacted health and socio-economic status worldwide. The only way to combat this situation is to develop an effective vaccine and immunize people around the globe. Aims: To construct a multi-epitope spike glycoprotein-based vaccine from the SARS-CoV-2 Surabaya isolate using a bioinformatics approach. Methods: The spike protein was submitted to IEDB, VaxiJen, AllerTOP, and ToxinPred webservers to predict antigenic, non-allergic, non-toxic, B- and T-cell epitopes. To develop a multi-epitope vaccine, an adjuvant cholera toxin B subunit was linked to B-cell and B-cell with T-cell through EAAAK and GPGPG linkers, respectively. The designed vaccine 3D structure development, refinement, and validation were done through PHYRE2, Galaxy Refine, and RAMPAGE webservers. Moreover, the Cluspro-2.0 webserver was used for the molecular docking of the vaccine designed with TLR3. The vaccine+TLR3 complex was docked with Surfactant protein A as a control to validate the docking results. Finally, immune-simulation and in silico cloning of the vaccine were carried out by C-ImmSim webserver and SnapGene software, respectively. Results: A multi-epitopic vaccine containing B and T-cell was developed using 392 amino acids with a molecular weight of 40825.59 Da. The docking and immunogenicity results of the vaccine met all established parameters for constructing a quality vaccine. Furthermore, the optimized sequence of the vaccine was successfully cloned in expression vector pET 28 a (+) that yielded a colon of 2724 bp. Conclusions: The vaccine’s immunogenicity demonstrates its effectiveness against SARS-CoV-2 infection. Further confirmatory testing may therefore be performed as soon as possible in the public interest.

Abstract This study aimed to evaluate the effects of intravenous injection of cysteamine (CS) on body weight (BW), growth hormone (GH), thyroid hormones (TH) secretion, and antioxidant status of growing lambs grazing on mountain pastures. Fifteen lambs (3–4 months of age) were randomly allocated into three experimental groups which received different dosages of CS: 0, 20, and 50 mg/kg BW−1. The CS was injected on the 1st, 10th, and 20th days of the experiment to the lambs through the jugular vein. Assessment of plasma concentration of GH and TH hormones was carried out at days 0 (a day before the start of CS injections), 15, and 30 of the experiment. The antioxidant enzymes were measured at the end of the experiment. Lambs were weighed at days 0, 10, 20, and 30 of the experiment. The results showed that treatment and time affected the BW, GH, triiodothyronine (T3), and tetraiodothyronine (T4) secretion. The intravenous injection of CS increased the BW of growing lambs (p

The Yili goose is the only indigenous goose breed that originates from Anser anser in China, known for its adaptability, strong flying ability, and tender meat with a low body lipid content. The liver plays a crucial role in lipid and glucose metabolism, including the intake, secretion, transportation, and storage of fatty acids (FAs). In this study, RNA-sequencing (RNA-seq) technology was performed to analyze the liver differentially expressed genes of Yili geese and their hybrid geese to investigate differences in liver lipid and glucose metabolism. A total of 452 differentially expressed genes (Q-value < 0.05) were identified. Notably, in KEGG enrichment analysis, four pathways (Q-value < 0.05) were enriched to be associated with lipid and glucose metabolism, including the metabolic pathway, PI3K–Akt signaling pathway, glycolysis/gluconeogenesis, and steroid biosynthesis. This study provides insights into potential candidate genes and metabolic pathways that affect the liver lipid metabolism of Yili goose. These findings provide a better understanding of animal liver lipid deposition and metabolism.

Starting phase of laying chicken life is the building stone for rearing and production stages. Since, fecal microbial transplantation (FMT) regulates the gut microbial diversity and affects the productive performance of the bird. The aim of this study is to evaluate the effect of FMT from feed-efficient broiler chicken could program the diversity of gut microbiota and growth of recipient native slow growing egg-laying chicks. For this, a total of 150 (one-day-old) Jing Hong chicks were randomly assigned into two groups, each group consisted of 5 replicates (n = 15 bird/ replicate). The control group (CON) and FMT recipient birds (FMT) fed on basal diet, the FMT group received an oral daily dose of FMT prepared from Cobb-500 chickens. The FMT performed from the 1d to 28d of age, through the experimental period, feed intake and body weight were recorded weekly. At the end of a 28-day trial, carcass traits were assessed and cecal samples were collected for microbiome assessment via 16S rRNA-based metagenomic analysis to characterize the diversity and functions of microbial communities. The data were statistically analyzed using R software. Body weight and body weight gain increased, and FCR decreased (p = 0.01) in FMT group. The relative abundance of Firmicutes and the Firmicutes/Bacteroidetes (F/B) ratio were increased due to FMT administration (p = 0.01). A higher relative abundance of Lactobacillus, Lactococcus, and Bifidobacterium were presented in the FMT group. Meanwhile, Enterococcus, Helicobacter, and Bacteroides were more abundant in the CON group (p

Abstract Background Sturgeons (Acipenseriformes) are polyploid chondrostean fish that constitute an important model species for studying development and evolution in vertebrates. To better understand the mechanisms of reproduction regulation in sturgeon, this study combined PacBio isoform sequencing (Iso-Seq) with Illumina short-read RNA-seq methods to discover full-length genes involved in early gametogenesis of the Amur sturgeon, Acipenser schrenckii. Results A total of 50.04 G subread bases were generated from two SMRT cells, and herein 164,618 nonredundant full-length transcripts (unigenes) were produced with an average length of 2782 bp from gonad tissues (three testes and four ovaries) from seven 3-year-old A. schrenckii individuals. The number of ovary-specific expressed unigenes was greater than those of testis (19,716 vs. 3028), and completely different KEGG pathways were significantly enriched between the ovary-biased and testis-biased DEUs. Importantly, 60 early gametogenesis-related genes (involving 755 unigenes) were successfully identified, and exactly 50% (30/60) genes of those showed significantly differential expression in testes and ovaries. Among these, the Amh and Gsdf with testis-biased expression, and the Foxl2 and Cyp19a with ovary-biased expression strongly suggested the important regulatory roles in spermatogenesis and oogenesis of A. schrenckii, respectively. We also found the four novel Sox9 transcript variants, which increase the numbers of regulatory genes and imply function complexity in early gametogenesis. Finally, a total of 236,672 AS events (involving 36,522 unigenes) were detected, and 10,556 putative long noncoding RNAs (lncRNAs) and 4339 predicted transcript factors (TFs) were also respectively identified, which were all significantly associated with the early gametogenesis of A. schrenckii. Conclusions Overall, our results provide new genetic resources of full-length transcription data and information as a genomic-level reference for sturgeon. Crucially, we explored the comprehensive genetic characteristics that differ between the testes and ovaries of A. schrenckii in the early gametogenesis stage, which could provide candidate genes and theoretical basis for further the mechanisms of reproduction regulation of sturgeon.

The immune system is most likely developed to reduce the harmful impact of infections on the host homeostasis. This defense approach is based on the coordinated activity of innate and adaptive immune system components, which detect and target infections for containment, killing, or expulsion by the body's defense mechanisms. These immunological processes are responsible for decreasing the pathogen burden of an infected host to maintain homeostasis that is considered to be infection resistance. Immune-driven resistance to infection is connected with a second, and probably more important, defensive mechanism: it helps to minimize the amount of dysfunction imposed on host parenchymal tissues during infection without having a direct adverse effect on pathogens. Disease tolerance is a defensive approach that relies on tissue damage control systems to prevent infections from causing harm to the host. It also uncouples immune-driven resistance mechanisms from immunopathology and disease, allowing the body to fight infection more effectively. This review discussed the cellular and molecular processes that build disease tolerance to infection and the implications of innate immunity on those systems. In addition, we discuss how symbiotic relationships with microbes and their control by particular components of innate and adaptive immunity alter disease tolerance to infection.

Chemokine receptor type 4 (CXCR4) is a G protein-coupled receptor that plays an essential role in immune system function and disease processes. Our study aims to conduct a comparative structural and phylogenetic analysis of the CXCR4 protein to gain insights into its role in emerging and re-emerging diseases that impact the health of mammals. In this study, we analyzed the evolution of CXCR4 genes across a wide range of mammalian species. The phylogenetic study showed species-specific evolutionary patterns. Our analysis revealed novel insights into the evolutionary history of CXCR4, including genetic changes that may have led to functional differences in the protein. This study revealed that the structural homologous human proteins and mammalian CXCR4 shared many characteristics. We also examined the three-dimensional structure of CXCR4 and its interactions with other molecules in the cell. Our findings provide new insights into the genomic landscape of CXCR4 in the context of emerging and re-emerging diseases, which could inform the development of more effective treatments or prevention strategies. Overall, our study sheds light on the vital role of CXCR4 in mammalian health and disease, highlighting its potential as a therapeutic target for various diseases impacting human and animal health. These findings provided insight into the study of human immunological disorders by indicating that Chemokines may have activities identical to or similar to those in humans and several mammalian species.

ABSTRACT: Hematology and serum biochemistry study may provide antique knowledge about the physical status of individuals, making them a valuable tool to differentiate healthy animals from affected animals. We aimed to investigate Steroid safety levels in birds through ex-situ studies at regular therapeutic doses. A total of 100 birds were used for hematology and serum biochemistry. This study was designed into 2 trials over the summer and winter, each comprised 5, 10, 15, and 20 d. Each study group was based on 5 control group birds and 20 experimental group birds. A sum of 2 groups representing 2 different steroids trial groups was treated with therapeutic doses to the stretch of 5, 10, 15, and 20 d each season. A therapeutic dose of each of the steroids was given at the rate of 3 drops 2 times a day to each bird. Analysis of data reveals that steroids had severe effects on bird's (Coturnix coturnix) hematological parameters. In most trials, the hematological effects of bromocriptine as mesylate showed an increase in red blood cell count and white blood cell count. On the other hand, steroid estradiol valerate showed a decrease in these parameters. Effect of steroids on serum biochemistry profile indicate acute damage to vital organs, especially to liver and kidney, indicating an increase in cholesterol, total protein, albumin, urea, and uric acid. The overall effect of steroids on the bird's serum and biochemistry of quails were nearly similar but different only in their intensity.

The emergence and re-emergence of zoonotic diseases significantly impact human health, particularly those who live in impoverished areas and have close contact with domestic or wild animals. Nearly 75% of zoonotic diseases are transmitted directly from animals to humans or indirectly via vector/agent interactions between animals and humans. Growing populations, globalization, urbanization, and the interaction of the environment with humans and livestock all play roles in the emergence and spread of zoonotic diseases. “One Health” is a multidisciplinary concept aimed at improving human, animal, and environmental health, but this concept is not widely accepted in developing countries. In Pakistan, environmental, human, and animal health are severely affected due to a lack of sufficient resources. This review article provides an overview of the most common zoonotic diseases found in Pakistan and emphasizes the importance of the “One Health” concept in managing these diseases. Given the current situation, interdisciplinary research efforts are required to implement and sustain effective and long-term control measures in animal, human, and environmental health surveillance and accurate diagnostic methods.

The regulated production of filamentous protein complexes is essential in many biological processes and provides a new paradigm in signal transmission. The mitochondrial antiviral signaling protein (MAVS) is a critical signaling hub in innate immunity that is activated when a receptor induces a shift in the globular caspase activation and recruitment domain of MAVS into helical superstructures (filaments). It is of interest whether adaptive evolution affects the proteins involved in innate immunity. Here, we explore and confer the role of selection and diversification on mitochondrial antiviral signaling protein in mammalian species. We obtined the MAVS proteins of mammalian species and examined their differences in evolutionary patterns. We discovered evidence for these proteins being subjected to substantial positive selection. We demonstrate that immune system proteins, particularly those encoding recognition proteins, develop under positive selection using codon-based probability methods. Positively chosen regions within recognition proteins cluster in domains involved in microorganism recognition, implying that molecular interactions between hosts and pathogens may promote adaptive evolution in the mammalian immune systems. These significant variations in MAVS development in mammalian species highlights the involvement of MAVS in innate immunity. Our findings highlight the significance of accounting for how non-synonymous alterations affect structure and function when employing sequence-level studies to determine and quantify positive selection.

The sucrose synthase (SS) is an important enzyme family which play a vital role in sugar metabolism to improve the fruit quality of the plants. In many plant species, the members of SS family have been investigated but the detailed information is not available in legumes particularly and Glycine max specifically. In the present study, we found thirteen SS members (GmSS1-GmSS13) in G. max genome. High conserved regions were present in the GmSS sequences that may due to the selection pressure during evolutionary events. The segmental duplication was the major factor to increase the number of GmSS family members. The identified thirteen GmSS genes were divided into Class I, Class II and Class III with variable numbers of genes in each class. The protein interaction of GmSS gave the co-expression of sucrose synthase with glucose-1-phosphate adenylyltransferase while SLAC and REL test found number of positive sites in the coding sequences of SS family members. All the GmSS family members except GmSS7 and few of class III members, were highly expressed in all the soybean tissues. The expression of the class I members decreased during seed development, whireas, the class II members expression increased during the seed developing, may involve in sugar metabolism during seed development. Solexa sequencing libraries of acidic condition (pH 4.2) stress samples showed that the expression of class I GmSS genes increased 1- to 2-folds in treated samples than control. The differential expression pattern was observed between the members of a paralogous. This study provides detailed genome-wide analysis of GmSS family in soybean that will provide new insights for future evolutionary and soybean breeding to improve the plant growth and development.

Background. Antibiotic supplementation in feed has been continued for the previous 60 years as therapeutic use. They can improve the growth performance and feed efficiency in the chicken flock. A favorable production scenario could favor intestinal microbiota interacting with antibiotic growth promoters and alter the gut bacterial composition. Antibiotic growth promoters did not show any beneficial effect on intestinal microbes. Scope and Approach. Suitable and direct influence of growth promoters are owed to antimicrobial activities that reduce the conflict between host and intestinal microbes. Unnecessary use of antibiotics leads to resistance in microbes, and moreover, the genes can relocate to microbes including Campylobacter and Salmonella, resulting in a great risk of food poisoning. Key Findings and Conclusions. This is a reason to find alternative dietary supplements that can facilitate production, growth performance, favorable pH, and modulate gut microbial function. Therefore, this review focus on different nutritional components and immune genes used in the poultry industry to replace antibiotics, their influence on the intestinal microbiota, and how to facilitate intestinal immunity to overcome antibiotic resistance in chicken.

Transition nuclear proteins (TNPs), the principal proteins identified in the condensing spermatids chromatin, have been found to play a key role in histone displacement and chromatin condensation during mammalian spermatogenesis. One such gene belonging to the TNP family called TNP1 gene is abundantly expressed in the regulation of spermatogenesis, and its sequence is remarkably well conserved among mammals. Genomic analysis, by sequencing and computational approach, was used to identify the novel polymorphisms and to evaluate the molecular regulation of TNP1 gene expression in Sahiwal cattle breeding bulls. DNA samples were sequenced to identify novel single nucleotide polymorphisms (SNPs) in the TNP1 gene. Modern computational tools were used to predict putative transcription factor binding in the TNP1 promoter and CpG islands in the TNP1 promoter region. In the TNP1 gene, four SNPs, three TATA boxes, and one CAAT box were identified. One CAAT box was discovered at 89 bp upstream of start site ATG. The computational analyses indicated that the polymorphisms inside the promoter sequence results in an added HNF-1 transcription factor binding site. In contrast, the other variations may remove the naturally occurring SRF transcription factor binding site. The CpG islands in the TNP1 promoter region were predicted to be absent by the MethPrimer program before and after SNP site mutations. These findings pave the way for more research into the TNP1 gene’s promoter activity and the links between these SNPs and reproductive attributes in the Sahiwal breeding bulls.

Abstract The bacterial microbiota in the gut varies among species, as well as with habitat, diet, age, and other factors. Intestinal microbiota homeostasis allows a host to adjust metabolic and immune performances in response to environmental changes. Therefore, potential implications of the gut microbiota in sustaining the health of the host have gained increasing attention in the field of endangered animal conservation. However, the effect of host intraspecies genetic variation on the gut microbiota is unknown. Moreover, little is known about the complexity of the gut mycobiota. Tigers are listed as endangered species, raising worldwide concern. Potential influences of subspecies, diet, and age on the gut microbiota in tigers were investigated in this study to provide a better understanding of the response of the tiger gut microbiota to external changes. The results revealed that the impacts of the factors listed above on gut bacterial and fungal communities are versatile. Host intraspecies genetic variation significantly impacted only fungal alpha diversity of the gut microbiota. Differences in diet, on the other hand, had a significant impact on alpha diversity of the gut microbiota, but exerted different effects on beta diversity of gut bacterial and fungal communities. Host age had no significant impact on the diversity of the gut fungal communities, but significantly impacted beta diversity of gut bacterial communities. This comprehensive study of tiger gut microbiota is an essential reference for tiger conservation when considering feeding and management strategies, and will contribute to a better understanding of the mycobiota in wildlife.

Animal domestication is considered a complex and multistage process that altered behaviorally, morphologically, and physiologically the domesticates relative to their wild ancestors. Ever since Darwin, scientists have been concerned about the history of domestication. To determine the domestication origins of the species, it is crucial to discover their ancestors and identify the approximate local domestication. Domestication has been the focus of several studies from different specialties. Studying when, where, and how domestication happened is essential to understand the origins of civilizations and the evolution of domesticated species. The development of both humans and domestic animals is hard to justify, and the genetic variations that occurred during the early animal domestication process remain vague. The recent and potential applications of evolutionary biology may deliver answers for main social challenges. It is important to examine the relationship among the environment and the traits of organisms that have been influenced through the adaptation to modern environments and the patterns of selection triggered by their environments during domestication period. Once domestication occurred, several events such as gene flow and selective pressures occurred, leading to genomic and phenotypic alterations. In this review, we discuss the current knowledge about the spatiotemporal outlines of domestication and debates surrounding the intent, speed, and evolutionary landscapes of this event. We also focus on the core challenges for future research. In conclusion, we argue that although the current growth in domestication information has been remarkable, the next era will produce even more significant insights into not only how domestication occurred but also where and when it did so.

Abstract Background Chikungunya virus (CHIKV), causes massive outbreaks of chikungunya infection in several regions of Asia, Africa and Central/South America. Being positive sense RNA virus, CHIKV replication within the host resulting in its genome mutation and led to difficulties in creation of vaccine, drugs and treatment strategies. Vector control strategy has been a gold standard to combat spreading of CHIKV infection, but to eradicate a species from the face of earth is not an easy task. Therefore, alongside vector control, there is a dire need to prevent the infection through vaccine as well as through antiviral strategies. Methods This study was designed to find out conserved B cell and T cell epitopes of CHIKV structural proteins through immuno-informatics and computational approaches, which may play an important role in evoking the immune responses against CHIKV. Results Several conserved cytotoxic T-lymphocyte epitopes, linear and conformational B cell epitopes were predicted for CHIKV structural polyprotein and their antigenicity was calculated. Among B-cell epitopes “PPFGAGRPGQFGDI” showed a high antigenicity score and it may be highly immunogenic. In case of T cell epitopes, MHC class I peptides ‘TAECKDKNL’ and MHC class II peptides ‘VRYKCNCGG’ were found extremely antigenic. Conclusion The study led to the discovery of various epitopes, conserved among various strains belonging to different countries. The potential antigenic epitopes can be successfully utilized in designing novel vaccines for combating and eradication of CHIKV disease.

Makorin ring finger proteins (MKRNs) are part the of ubiquitin-proteasome system; a complex system important for cell functions. Ubiquitin fate through proteolytic, non-proteolytic pathways varies, depending on covalent linkage between ubiquitin and protein substrates. Makorin ring finger protein 3 is an integral part of covalent linkage of ubiquitin to protein substrates. Similar to others imprinted genes, MKRN3 also evolve under positive selection; however, which codons are specifically selected in MKRN3 during evolution are needed to be explored. Different maximum-likelihood (ML) codon-based methodologies were used to ascertain positive selection signatures in 22 mammalian sequences of MKRN3 to probe an individual codon for positive selection signatures. By applying the HyPhy software package implemented in the Data Monkey Web Server and CODEML implemented in PAML, evolutionary analysis based on two Ml frameworks were conducted. The analysis was executed by comparing M1a against M2a, M7 against M8, and PAML models and 2∆Lnl ( LRT ) was resulted by likelihood logs. M1a contributed ω1 ( dN/dS ) with LRT value ( ∆Lnl ) 12.01, and positive selection was found in M2a with ω3 = 2.23603. To further improve selection test, M8 was compared to M7 with 2∆ Lnl ( LRT ) 30.17, and M8 showed positive selection with ω = 1.55759. The data were fit to M8 than M7, which suggests that M8 was the most significant model of selection. M8 was judged encouraging for this analysis and used to establish a positive selection of MKRN3 proteins. We found Gly312 as a positively selected amino acid in a zinc finger motif/Really Interesting New Gene (RING) finger motif; the former ones’ region is involved in RNA binding and the later ones in ubiquitin ligase activity of the protein, vital for protein function. Selection analyses of MKRNs might advance the developments in unique approaches that could lead to genetic progress over the selection of superior individuals with the breeding values higher for certain traits as ancestries to get the next generation.

The early detection of damaged (partially broken) outdoor insulators in primary distribution systems is of paramount importance for continuous electricity supply and public safety. Unmanned aerial vehicles (UAVs) present a safer, autonomous, and efficient way to examine the power system components without closing the power distribution system. In this work, a novel dataset is designed by capturing real images using UAVs and manually generated images collected to overcome the data insufficiency problem. A deep Laplacian pyramid-based super-resolution network is implemented to reconstruct high-resolution training images. To improve the visibility of low-light images, a low-light image enhancement technique is used for the robust exposure correction of the training images. A different fine-tuning strategy is implemented for fine-tuning the object detection model to increase detection accuracy for the specific faulty insulators. Several flight path strategies are proposed to overcome the shuttering effect of insulators, along with providing a less complex and time- and energy-efficient approach for capturing a video stream of the power system components. The performance of different object detection models is presented for selecting the most suitable one for fine-tuning on the specific faulty insulator dataset. For the detection of damaged insulators, our proposed method achieved an F1-score of 0.81 and 0.77 on two different datasets and presents a simple and more efficient flight strategy. Our approach is based on real aerial inspection of in-service porcelain insulators by extensive evaluation of several video sequences showing robust fault recognition and diagnostic capabilities. Our approach is demonstrated on data acquired by a drone in Swat, Pakistan.

Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses. In addition, an understanding of the genetic processes underlying horse domestication, especially the origin of Chinese native populations, is still lacking. In our study, we generated whole genome sequences from 4 Chinese native horses and combined them with 48 publicly available full genome sequences, from which 15 341 213 high-quality unique single-nucleotide polymorphism variants were identified. Kazakh and Lichuan horses are 2 typical Asian native breeds that were formed in Kazakh or Northwest China and South China, respectively. We detected 1390 loss-of-function (LoF) variants in protein-coding genes, and gene ontology (GO) enrichment analysis revealed that some LoF-affected genes were overrepresented in GO terms related to the immune response. Bayesian clustering, distance analysis, and principal component analysis demonstrated that the population structure of these breeds largely reflected weak geographic patterns. Kazakh and Lichuan horses were assigned to the same lineage with other Asian native breeds, in agreement with previous studies on the genetic origin of Chinese domestic horses. We applied the composite likelihood ratio method to scan for genomic regions showing signals of recent selection in the horse genome. A total of 1052 genomic windows of 10 kB, corresponding to 933 distinct core regions, significantly exceeded neutral simulations. The GO enrichment analysis revealed that the genes under selective sweeps were overrepresented with GO terms, including “negative regulation of canonical Wnt signaling pathway,” “muscle contraction,” and “axon guidance.” Frequent exercise training in domestic horses may have resulted in changes in the expression of genes related to metabolism, muscle structure, and the nervous system.

The genus Jasminum L., of the family Oleaceae, includes many species occurring in the wild, or cultivated worldwide. A preliminary investigation based on inter-simple sequence repeats (ISSR) was performed to assess the genetic diversity among 28 accessions, representing nine species of Jasminum from various regions, representing a range of altitudes in Pakistan. A total of 21 ISSR primers were used, which produced 570 amplified bands of different sizes, with a mean polymorphic band percentage of 98.26%. The maximum resolving power, polymorphism information content, and index values of the ISSR markers recorded for primers 6, 16, and 19 were 0.40, 12.32, and 24.21, respectively. Based on the data of the ISSR markers, the resulting UPGMA dendrogram with the Jaccard coefficient divided the 28 accessions into two main clades. At the species level, the highest values for Shannon's information index, polymorphism percentage, effective allele number, Nei's genetic variations, and genetic unbiased diversity were found in Jasminum sambac L. and J. humile L., while the lowest were observed in J. mesnyi Hance and J. nitidum Skan. Based on Nei's unbiased genetic identity pairwise population matrix, the maximum identity (0.804) was observed between J. elongatum Willd and J. multiflorum (Burm. f.) Andrews, and the lowest (0.566) between J. nitidum Skan. and J. azoricum L. Molecular variance analysis displayed a genetic variation of 79% among the nine populations. The study was aimed to established genetic diversity in Jasminum species using ISSR markers. With the help of this technique, we were able to establish immense intra- and interspecific diversity across the Jasminum species.