The adenosine triphosphate (ATP) synthase F0 subunit 8 gene (atp8) had been believed to be absent in mitochondrial genomes of platyhelminths until the late 2010s, since when multiple lines of emergent evidence have suggested that this gene is actually present, albeit in highly derived forms, throughout the entire phylum except for the parasitic Neodermata (tapeworms, flukes, and their kin). Of about 11 non-parasitic (turbellarian) major platyhelminth subtaxa, the existence of atp8 has hitherto been documented in five (Catenulida, Macrostomorpha, Polycladida, Rhabdocoela, and Tricladida), while it remains open in the remaining six (Prorhynchida, Gnosonesmida, Proseriata, Fecampiida, Prolecithophora, and Bothrioplanida). Here we report the mitochondrial genome sequence of an undetermined marine interstitial turbellarian species in the genus NematoplanaMeixner, 1938 as the first representative of Proseriata. This circular genome comprises 16,106 bp (but potentially 18,812–19,277 bp when unresolved, non-coding tandem repeats are considered) and includes 38 genes, viz. 23 transfer RNA genes, 13 protein-coding genes (including the putative atp8), and two ribosomal RNA genes. The putative atp8 in Nematoplana sp. was not annotated by a standard automated procedure but was detected by manual inspection. If it encodes a translated product, it consists of 156 bp, with the potential 52-amino-acid-residue product beginning with MPHV, instead of the metazoan-canonical MPQL, and containing a single putative transmembrane region expanding from the 7th to the 29th amino-acid positions. While our finding seemingly strengthens the hypothesis that atp8 is in the ground pattern of flatworm mitochondrial genomes, whether the putative atp8 in flatworms is actually transcribed and translated to form a functional ATP synthetase F0 subunit should be tested in future studies.

Whole blood has become increasingly utilized in transcriptomic studies because it is easily accessible and can be collected from live animals with minimal invasiveness. However, whole blood represents an extremely complex mixture of cell types, and cell type proportions can confound downstream statistical analyses. Information on cell type proportions may be missing from blood transcriptome studies for a variety of reasons. Experimental approaches for cell counting, such as cell sorting, are arduous and expensive, and therefore may not feasible for studies conducted on a limited budget. Statistical deconvolution can be applied directly to transcriptomic data sets to estimate cell type proportions. In addition to being financially advantageous, computational deconvolution can readily be applied to old datasets, where it may be difficult or impossible to re-analyze for cell type information. In an effort to assist researchers in recovering cell type proportions from porcine whole blood transcriptome samples, we present a manually curated set of porcine blood cell markers that can be utilized in a partial reference-free deconvolution framework to obtain estimates of cell types measured in a standard complete blood count (CBC) panel, which includes neutrophils, lymphocytes, monocytes, eosinophils, basophils, and red blood cells.

Sequencing of mitochondrial genomes is a powerful tool to resolve taxonomic relationships between closely related taxa with high confidence. Syngnathus temminckii is a pipefish species endemic to Southern Africa. The taxonomic status of this species and the phylogenetic relationship with its widely distributed northern hemisphere congener Syngnathus acus has been subject to uncertainty. The current study is the first to assemble, annotate and describe the complete mitochondrial genome of this species, and investigate phylogenetic relationships with its northern hemisphere sister taxa. The mitogenome assembly pipeline reconstructed a circular contig 16,452 bp in length, with an average GC content of 44.8%. A total of 37 mitogenomic features, including 13 protein-coding genes, 22 tRNAs, two rRNAs and a putative control region, were annotated. A Bayesian phylogenetic analysis confirmed that S. temminckii is a distinct southern African species that diverged from a northern hemisphere clade of pipefishes that includes its congener S. acus approximately seven million years ago.

MicroRNAs (miRNAs) are short non-coding RNAs that play an important role in the regulation of gene expression. In addition to being encoded by the host cells, miRNAs are also encoded by certain DNA and RNA viruses, blurring the lines between host and viral genetic regulation. This duality allows miRNAs to assume both antiviral and proviral roles in the viral life cycle. Furthermore, miRNAs exert profound influence over immune responses, viral latency, host susceptibility to infections, cellular differentiations and pathways governing programmed cell death. In this comprehensive discussion, we delve into the current state of knowledge regarding miRNAs, including the diverse types of miRNAs, such as canonical and viral miRNAs, and explore their multifaceted roles in virus replication, pathogenesis, and immune modulation. This exploration enhances our understanding of the intricate interplay between viruses and their host organisms and encompasses various other RNA molecules that contribute to this dynamic landscape.

Small and midsize deletions and insertions (InDels) are major events that play a crucial role in the evolution of genome size and contribute to the genetic and phenotypic diversity of species. In recent years, considerable attention has been given to studying small indels associated with various developmental, growth, and production traits in domestic chicken breeds. Additionally, small and midsize indels have been studied between chicken and phylogenetically more distant species such as duck, turkey, rock pigeon, and other passerine birds. However, the investigation of small and midsize deletions in the wild relatives of chickens has been relatively overlooked until now. To address this gap, our study aimed to identify the presence and distribution of midsize deletions (> 1 Kb) in the wild relatives of chickens. We conducted a comparative genomic analysis using high-quality genomic data from four species belonging to the Gallus genus. Our analysis revealed the existence of >125 midsize deletions in the three other species compared to Gallus gallus (red junglefowl). These midsize deletions were found to be distributed in intergenic regions and within introns of various protein-coding genes but not in the exonic regions of protein-coding genes. Furthermore, we observed a trend between the number of midsize deletions and the phylogenetic distance in the phylogeny of the Gallus genus. The most ancestral species, Gallus varius (green junglefowl), exhibited the highest deletions, followed by Gallus lafayettii (Ceylon junglefowl) and Gallus sonneratii (grey junglefowl). Some protein-coding genes harboring deletions in their introns and upstream regions were associated with body development, production, growth traits, abdominal fat deposition, behavioral patterns such as stress, fear, anxiety, plumage color, and adaptation to extreme climatic conditions. Our study finds that the midsize deletions identified in wild relatives of red junglefowl contribute <1% of DNA loss with a rate of 8–44 Kb/My during the evolution of the Gallus genus.

The Kirsten rat sarcoma (KRAS) gene is one of the most critical proto-oncogene to target in combating various cancers as its mutation is one of the major cancer-causing causes in most cancers. In this study, we investigated all 32 primate KRAS nucleotide and protein sequences found within the public GenBank database. The Tibetan macaque KRAS protein supersedes the others in terms of amino acid length, molecular weight and isoelectric point. The motif distribution of the Tibetan macaque was also found to vary significantly from the other KRAS proteins examined. Nevertheless, the predicted protein three-dimensional structure of Tibetan macaque did not differ much from that of human and Ugandan red colobus. Fascinatingly, the Coquerel’s sifaka KRAS protein structure and conformation is distinctive from all other 31 primate KRAS proteins. The maximum likelihood phylogenetic tree revealed several potential candidates that are closely related to that of the human KRAS protein to aid future human personalised therapy studies.

The ‘Bharal’ or ‘Himalayan Blue Sheep’ (Pseudois nayaur) is endemic to the Himalayan and Tibetan Regions. There are gaps in the available database for the blue sheep mitogenome sequencing from the Indian region. We sequenced and characterized the whole mitogenome of one blue sheep individual using the Illumina Nova-seq 6000 platform, which was 16,718 bp in length. It included 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one non-coding control region (D loop). It was compared with other complete mitochondrial DNA sequences of blue sheep from the NCBI database. The whole mitogenome of blue sheep was found to be highly AT-biased (60%) and had a positive AT skew (0.121) and a negative GC skew (−0.341). In 13 PCGs of blue sheep, Leucine (15.58%) and tryptophan (2.72%) occurred most frequently. A typical secondary cloverleaf structure was observed for all tRNA genes except for tRNA-Ser, where a stable structure of dihydrouridine did not develop. The phylogenetic analysis showed Indian blue sheep population formed a separate clade with a genetic distance of 3.7 to 4.1% from the Chinese blue sheep population, suggesting it to be of a different lineage and genetically qualifies the status of distinct subspecies. The results of this study will help in further phylogenetic analysis of Indian blue sheep populations in the Western and Eastern Himalayan regions and in understanding lineage identification and evolution for further research.

The gut microbiota is an essential part of metabolism, assists in the breakdown of complex carbohydrates, proteins and lipids that enter into the digestive tract. Numerous microbial metabolites thus produced can have local and systemic effects which may influence health positively or negatively. The microbial population's dominance in the gut depends on the number of compounds present in the organ. Hence we have focused on analyzing the role of Moringa oleifera as phytobiotic supplementation in enhancing the beneficial gut microbiota in chicken models. Probiotics improve gut health in chickens through several mechanisms, including tight junction enhancement, nutrient uptake, niche colonization and co-aggregation with enteropathogens. The bacteria from the gut samples obtained from M.oleifera treated chickens were analyzed for various standard morphological and biochemical tests, genotypic classification using 16S rRNA gene sequencing and evaluation of evolutionary marks among the gut bacteria to determine whether they fit the criteria for probiotic traits. A variety of the consequences of beneficial gut microorganisms for hosts could attribute to bacterial communities' processes and the host's capacity for influencing the same processes. According to our study, phylogenetic analysis and taxonomy of the host significantly shape the intestinal flora across a range of host taxonomic levels. However, host ecology (i.e., diet) can further alter these gut flora, particularly in the case of many closely related host species.

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by aberrant lipid metabolism and mitochondrial dysfunction, features related to mitochondria-associated ER membranes (MAM). ApoE is recognized as the major AD risk factor. Human ApoE has three isoforms including Apoε2, Apoε3 and Apoε4. It has revealed that ε4 allele carriers are at higher risk of developing AD than ε3 allele carriers. Given that Apoε4 is a major AD risk factor and that MAM dysfunction in lipid metabolism may affect mitochondrial function, we assessed the expression pattern of cardiolipin synthetase (CLS) and glycerol-3-phosphate acyltransferase 2 (MINO) genes in Drosophila model of AD. To the best of our knowledge, this is the first study to investigate the effect of ApoE isoforms on mitochondrial function in Drosophila model of AD. RNA extraction was performed using glazt2a.gal4.UAS.hapoe transgenic flies harboring Apoε isoforms. Following cDNA synthesis, mRNA expression levels of target (CLS and MINO) and housekeeping (eEF1α) genes were measured by qRT-PCR. Our results did not show a significant decrease in CLS and MINO expression level in Apoɛ3 and Apoɛ4 groups as compared to the control. Although this reduction was not statistically significant, the decreasing trend indicates a kind of disruption in lipid biosynthesis and may directly affect mitochondrial function. Though the impact of Apoɛ4 on AD pathogenesis has been elucidated, the exact mechanism through which Apoɛ4 mediates AD progression is still unknown. Investigating the biology of ApoE isoforms using both human and AD animal models is recommended.

The genome of Mycobacterium orygis encodes 3767 proteins that includes 442 functionally uncharacterized proteins, known as hypothetical proteins (HPs). These functionally unknown proteins may play significant biological role in bacterium's survivability, virulence etc., hence functional annotation of these HPs with bioinformatics techniques might shed light on these aspects. So, the present study aimed to assign functions to those HPs in M. orygis genome. With the help of an extensive in silico workflow involving several bioinformatic tools, physicochemical characteristics, protein-protein interaction, sub-cellular localization, functional classification, and antigenicity of the HPs were analyzed. Out of 4039 genes and 3767 encoded proteins, 422 were annotated as “hypothetical protein, unknown function” in NCBI database. Out of 422 HPs, the FASTA sequences of 400 proteins, available in the NCBI database, were extracted. Preliminarily 400 proteins were screened for presence of conserved domain by different bioinformatic tools and 32 shortlisted proteins were further analyzed. The analysis revealed that these proteins may be involved in enzymatic, toxin-antitoxin system, cellular and other processes. Virulence and antigenicity of the complete set of HPs were also predicted. Based on antigenicity scores and sub-cellular localization, four proteins were selected for secondary and tertiary structure modelling. Molecular docking and MD-simulation of four proteins with TLR1 showed stable binding. B-cell and T-cell epitopes were identified for two proteins (QOY47331.1 and QOY49361.1) with highest antigenicity scores. The result of the present study may facilitate better understanding of virulence, pathogenesis and therapeutic target. The information about the structures of the HPs with highest antigenicity score could aid in structure-based inhibitor design and devising novel diagnostic assays.