Common Ancestor Research Articles

On the Roles of Protein Intrinsic Disorder in the Origin of Life and Evolution

Obviously, the discussion of different factors that could have contributed to the origin of life and evolution is clear speculation, since there is no way of checking the validity of most of the related hypotheses in practice, as the corresponding events not only already happened, but took place in a very distant past. However, there are a few undisputable facts that are present at the moment, such as the existence of a wide variety of living forms and the abundant presence of intrinsically disordered proteins (IDPs) or hybrid proteins containing ordered domains and intrinsically disordered regions (IDRs) in all living forms. Since it seems that the currently existing living forms originated from a common ancestor, their variety is a result of evolution. Therefore, one could ask a logical question of what role(s) the structureless and highly dynamic but vastly abundant and multifunctional IDPs/IDRs might have in evolution. This study represents an attempt to consider various ideas pertaining to the potential roles of protein intrinsic disorder in the origin of life and evolution.

Transcriptomic dynamics of ABA response in Brassica napus guard cells

Drought has a significant, negative impact on crop production; and these effects are poised to increase with climate change. Plants acclimate to drought and water stress through diverse physiological responses, primarily mediated by the hormone abscisic acid (ABA). Because plants lose the majority of their water through stomatal pores on aerial surfaces of plants, stomatal closure is one of the rapid responses mediated by ABA to reduce transpirational water loss. The dynamic changes in the transcriptome of stomatal guard cells in response to ABA have been investigated in the model plant Arabidopsis thaliana. However, guard cell transcriptomes have not been analyzed in agronomically valuable crops such as a major oilseed crop, rapeseed. In this study, we investigated the dynamics of ABA-regulated transcriptomes in stomatal guard cells of Brassica napus and conducted comparison analysis with the transcriptomes of A. thaliana. We discovered changes in gene expression indicating alterations in a host of physiological processes, including stomatal movement, metabolic reprogramming, and light responses. Our results suggest the existence of both immediate and delayed responses to ABA in Brassica guard cells. Furthermore, the transcription factors and regulatory networks mediating these responses are compared to those identified in Arabidopsis. Our results imply the continuing evolution of ABA responses in Brassica since its divergence from a common ancestor, involving both protein-coding and non-coding nucleotide sequences. Together, our results will provide a basis for developing strategies for molecular manipulation of drought tolerance in crop plants.

Cell type and regulatory analysis in amphioxus illuminates evolutionary origin of the vertebrate head

To shed light on the enigmatic origin of the vertebrate head, our study employs an integrated approach that combines single-cell transcriptomics, perturbations in signaling pathways, and cis-regulatory analysis in amphioxus. As a representative of a basal lineage within the chordate phylum, amphioxus retains many characteristics thought to have been present in the common chordate ancestor. Through cell type characterization, we identify the presence of prechordal plate-like, pre-migratory, and migratory neural crest-like cell populations in the developing amphioxus embryo. Functional analysis establishes conserved roles of the Nodal and Hedgehog signaling pathways in prechordal plate-like populations, and of the Wnt signaling pathway in neural crest-like populations’ development. Furthermore, our trans-species transgenic experiments highlight similarities in the regulatory environments that drive neural crest-like and prechordal plate-like developmental programs in both vertebrates and amphioxus. Our findings provide evidence that the key features of vertebrate head development can be traced back to the common ancestor of all chordates.

Intricate Evolution of Multifunctional Lipoxygenase in Red Algae.

Lipoxygenases (LOXs) from lower organisms have substrate flexibility and function versatility in fatty acid oxidation, but it is not clear how these LOXs acquired the ability to execute multiple functions within only one catalytic domain. This work studied a multifunctional LOX from red alga Pyropia haitanensis (PhLOX) which combined hydroperoxidelyase (HPL) and allene oxide synthase (AOS) activity in its active pocket. Molecular docking and site-directed mutagenesis revealed that Phe642 and Phe826 jointly regulated the double peroxidation of fatty acid, Gln777 and Asn575 were essential to the AOS function, and the HPL activity was improved when Asn575, Gln777, or Phe826 was replaced by leucine. Phylogenetic analysis indicated that Asn575 and Phe826 were unique amino acid sites in the separated clades clustered with PhLOX, whereas Phe642 and Gln777 were conserved in plant or animal LOXs. The N-terminal START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) domain of PhLOX was another key variable, as the absence of this domain disrupted the versatility of PhLOX. Moreover, the functions of two homologous LOXs from marine bacterium Shewanella violacea and red alga Chondrus crispus were examined. The HPL activity of PhLOX appeared to be inherited from a common ancestor, and the AOS function was likely acquired through mutations in some key residues in the active pocket. Taken together, our results suggested that some LOXs from red algae attained their versatility by amalgamating functional domains of ancestral origin and unique amino acid mutations.

The Evolution of Extreme Genetic Variability in a Parasite-Resistance Complex.

Genomic regions that play a role in parasite defense are often found to be highly variable, with the MHC serving as an iconic example. Single nucleotide polymorphisms may represent only a small portion of this variability, with Indel polymorphisms and copy number variation further contributing. In extreme cases, haplotypes may no longer be recognized as orthologous. Understanding the evolution of such highly divergent regions is challenging because the most extreme variation is not visible using reference-assisted genomic approaches. Here we analyze the case of the Pasteuria Resistance Complex (PRC) in the crustacean Daphnia magna, a defense complex in the host against the common and virulent bacterium Pasteuria ramosa. Two haplotypes of this region have been previously described, with parts of it being non-homologous, and the region has been shown to be under balancing selection. Using pan-genome analysis and tree reconciliation methods to explore the evolution of the PRC and its characteristics within and between species of Daphnia and other Cladoceran species, our analysis revealed a remarkable diversity in this region even among host species, with many non-homologous hyper-divergent-haplotypes. The PRC is characterized by extensive duplication and losses of Fucosyltransferase (FuT) and Galactosyltransferase (GalT) genes that are believed to play a role in parasite defense. The PRC region can be traced back to common ancestors over 250 million years. The unique combination of an ancient resistance complex and a dynamic, hyper-divergent genomic environment presents a fascinating opportunity to investigate the role of such regions in the evolution and long-term maintenance of resistance polymorphisms. Our findings offer valuable insights into the evolutionary forces shaping disease resistance and adaptation, not only in the genus Daphnia, but potentially across the entire Cladocera class.

Investigating Anthrax-Associated Virulence Genes among Archival and Contemporary Bacillus cereus Group Genomes.

Bacillus anthracis causes anthrax through virulence factors encoded on two plasmids. However, non-B. anthracis organisms within the closely related, environmentally ubiquitous Bacillus cereus group (BCG) may cause an anthrax-like disease in humans through the partial adoption of anthrax-associated virulence genes, challenging the definition of anthrax disease. To elucidate these phenomena and their evolutionary past, we performed whole-genome sequencing on non-anthracis BCG isolates, including 93 archival (1967-2003) and 5 contemporary isolates (2019-2023). We produced annotated genomic assemblies and performed a pan-genome analysis to identify evidence of virulence gene homology and virulence gene acquisition by linear inheritance or horizontal gene transfer. At least one anthrax-associated virulence gene was annotated in ten isolates. Most homologous sequences in archival isolates showed evidence of pseudogenization and subsequent gene loss. The presence or absence of accessory genes, including anthrax-associated virulence genes, aligned with the phylogenetic structure of the BCG core genome. These findings support the hypothesis that anthrax-associated virulence genes were inherited from a common ancestor in the BCG and were retained or lost across different lineages, and contribute to a growing body of work informing public health strategies related to anthrax surveillance and identification.

Candidate genes involved in biosynthesis and degradation of the main extracellular matrix polysaccharides of brown algae and their probable evolutionary history

BackgroundBrown algae belong to the Stramenopiles phylum and are phylogenetically distant from plants and other multicellular organisms. This independent evolutionary history has shaped brown algae with numerous metabolic characteristics specific to this group, including the synthesis of peculiar polysaccharides contained in their extracellular matrix (ECM). Alginates and fucose-containing sulphated polysaccharides (FCSPs), the latter including fucans, are the main components of ECMs. However, the metabolic pathways of these polysaccharides remain poorly described due to a lack of genomic data.ResultsAn extensive genomic dataset has been recently released for brown algae and their close sister species, for which we previously performed an expert annotation of key genes involved in ECM-carbohydrate metabolisms. Here we provide a deeper analysis of this set of genes using comparative genomics, phylogenetics analyses, and protein modelling. Two key gene families involved in both the synthesis and degradation of alginate were suggested to have been acquired by the common ancestor of brown algae and their closest sister species Schizocladia ischiensis. Our analysis indicates that this assumption can be extended to additional metabolic steps, and thus to the whole alginate metabolic pathway. The pathway for the biosynthesis of fucans still remains biochemically unresolved and we also investigate putative fucosyltransferase genes that may harbour a fucan synthase activity in brown algae.ConclusionsOur analysis is the first extensive survey of carbohydrate-related enzymes in brown algae, and provides a valuable resource for future research into the glycome and ECM of brown algae. The expansion of specific families related to alginate metabolism may have represented an important prerequisite for the evolution of developmental complexity in brown algae. Our analysis questions the possible occurrence of FCSPs outside brown algae, notably within their closest sister taxon and in other Stramenopiles such as diatoms. Filling this knowledge gap in the future will help determine the origin and evolutionary history of fucan synthesis in eukaryotes.

Simultaneous co-circulation of two genotypes of dengue virus serotype 3 causing a large outbreak in Sri Lanka in year 2023.

We observed a discrepancy between dengue NS1 antigen test and molecular diagnostics, with the emergence of (DENV) serotype 3 in Sri Lanka and sought to understand the cause for the rise in cases and high failure rates of molecular diagnostics. Whole genomic sequencing was carried out in 22 DENV-3 samples. Phylogenetic and molecular clock analysis were done for genotype assignment and to understand the rate of evolution. Mutation analysis was done to understand the reasons for PCR non-detection. We identified two DENV-3 genotypes (I and III) co-circulating. DENV-3 genotype III strains shared a common ancestor with a sequence from India collected in 2022, while DENV-3 genotype I, was found to share a common ancestor with DENV-3 sequences from China. DENV-3 genotype III was detected by the modified CDC DENV-3 primers whereas, genotype I evaded detection due to key mutations at forward and reverse primer binding sites. We identified point mutations, C744T and A756G of the forward primer binding sites and in position G795A of the reverse primer binding sites which were not identified in DENV-3 genotype III. Furthermore, our Sri Lankan DENV-3 strains demonstrated a high root to tip ratio, compared to the previous DENV-3 sequences, indicating a high mutation rate during the points of sampling (year 2017 to 2023). The co-circulation of multiple genotypes associated with an increase in cases highlights the importance of continuous surveillance of DENVs to identify mutations resulting in non-detection by diagnostics and differences in virulence.

Genetic aspects of lactase deficiency in indigenous populations of Siberia.

The ability to metabolize lactose in adulthood is associated with the persistence of lactase enzyme activity. In European populations, lactase persistence is determined mainly by the presence of the rs4988235-T variant in the MCM6 gene, which increases the expression of the LCT gene, encoding lactase. The highest rates of lactase persistence are characteristic of Europeans, and the lowest rates are found in East Asian populations. Analysis of published data on the distribution of the hypolactasia-associated variant rs4988235-C in the populations of Central Asia and Siberia showed that the frequency of this variant increases in the northeastern direction. The frequency of this allele is 87 % in Central Asia, 90.6 % in Southern Siberia, and 92.9 % in Northeastern Siberia. Consequently, the ability of the population to metabolize lactose decreases in the same geographical direction. The analysis of paleogenomic data has shown that the higher frequency of the rs4988235-T allele in populations of Central Asia and Southern Siberia is associated with the eastward spread of ancient populations of the Eastern European steppes, starting from the Bronze Age. The results of polymorphism analysis of exons and adjacent introns of the MCM6 and LCT genes in indigenous populations of Siberia indicate the possibility that polymorphic variants may potentially be related to lactose metabolism exist in East Asian populations. In East Asian populations, including Siberian ethnic groups, a ~26.5 thousand nucleotide pairs long region of the MCM6 gene, including a combination of the rs4988285-A, rs2070069-G, rs3087353-T, and rs2070068-A alleles, was found. The rs4988285 and rs2070069 loci are located in the enhancer region that regulates the activity of the LCT gene. Analysis of paleogenomic sequences showed that the genomes of Denisovans and Neanderthals are characterized by the above combination of alleles of the MCM6 gene. Thus, the haplotype discovered appears to be archaic. It could have been inherited from a common ancestor of modern humans, Neanderthals, and Denisovans, or it could have been acquired by hybridization with Denisovans or Neanderthals. The data obtained indicate a possible functional significance of archaic variants of the MCM6 gene.

Functional diversification process of opsin genes for teleost visual and pineal photoreceptions

Most vertebrates have a rhodopsin gene with a five-exon structure for visual photoreception. By contrast, teleost fishes have an intron-less rhodopsin gene for visual photoreception and an intron-containing rhodopsin (exo-rhodopsin) gene for pineal photoreception. Here, our analysis of non-teleost and teleost fishes in various lineages of the Actinopterygii reveals that retroduplication after branching of the Polypteriformes produced the intron-less rhodopsin gene for visual photoreception, which converted the parental intron-containing rhodopsin gene into a pineal opsin in the common ancestor of the Teleostei. Additional analysis of a pineal opsin, pinopsin, shows that the pinopsin gene functions as a green-sensitive opsin together with the intron-containing rhodopsin gene for pineal photoreception in tarpon as an evolutionary intermediate state but is missing in other teleost fishes, probably because of the redundancy with the intron-containing rhodopsin gene. We propose an evolutionary scenario where unique retroduplication caused a “domino effect” on the functional diversification of teleost visual and pineal opsin genes.

Intraspecific diversity of Erwinia amylovora strains from northern Algeria

BackgroundFire blight, caused by Erwinia amylovora, is the most destructive bacterial disease affecting plants in the Rosaceae family, leading to significant economic losses. In Algeria, this disease has been reported since 2010. This study aimed to investigate the origin of fire blight in Algeria, in order to increase knowledge of the epidemiology of this serious disease and contribute to its management. A comprehensive characterization of 18 E. amylovora isolates recovered from northern Algeria between 2016 and 2021 to evaluate their phenotypical and genotypical diversity was conducted.ResultsPhenotypic differences, particularly in growth kinetics, virulence, and fatty acid profiles, allowed differentiation of strains into five groups, possibly indicating distinct introduction events. Genetic characterization revealed that only one strain lacked the ubiquitous plasmid pEA29, which is correlated with reduced virulence, while none harbored the pEI70 plasmid. Phylogenetic analysis using concatenated sequences of the recA, groEL, rpoS, ams, and hrpN genes grouped Algerian strains with those from a broadly prevalent clade. CRISPR genotyping identified a novel CR1 pattern and three genotypes, two of them previously unreported.ConclusionsThis study represents the first phenotypic, genetic, and phylogenetic investigation of E. amylovora strains in the region, and provides valuable information on the possible pathways of the introduction of this fire blight pathogen in northern Africa. The findings suggest one or more introduction events from a common ancestor, likely originating in northern Italy, followed by dispersal in various regions of Algeria.

Expression of laccase and ascorbate oxidase affects lignin composition in Arabidopsis thaliana stems.

Lignin is a phenolic polymer that is a major source of biomass. Oxidative enzymes, such as laccase and peroxidase, are required for lignin polymerisation. Laccase is a member of the multicopper oxidase family and has a high amino acid sequence similarity with ascorbate oxidase. However, the process of functional differentiation between the two enzymes remains poorly understood. In this study, the common ancestry sequence of laccase and ascorbate oxidase (AncMCO) was predicted via phylogenetic reconstruction, and its in vivo effect on lignin biosynthesis in Arabidopsis thaliana was assessed. The estimated AncMCO sequence conserved key residues that coordinate with copper ions, implying that the electron transfer system is likely to be conserved in AncMCO. However, multiple insertions/deletions corresponding to protein surface structures have been found between laccase, ascorbate oxidase, and AncMCO. The overexpression of canonical laccase (AtLAC4) and ascorbate oxidase (AtAAO1) in A. thaliana resulted in notable increases of syringyl/guaiacyl lignin unit ratio in stems, whereas, in contrast, the overexpression of AncMCO did not show any detectable change in lignin deposition. Transcriptomic analysis revealed that the AtAAO1-overexpressing line exhibited significant changes in the expression of a wide range of cell wall biosynthesis genes. These results highlight the importance of the molecular evolution of multicopper oxidase, which drives lignin biosynthesis during plant evolution.

From Venom to Vein: Factor VII Activation as a Major Pathophysiological Target for Procoagulant Australian Elapid Snake Venoms.

Australian elapid snake venoms are uniquely procoagulant, utilizing blood clotting enzyme Factor Xa (FXa) as a toxin, which evolved as a basal trait in this clade. The subsequent recruitment of Factor Va (FVa) as a toxin occurred in the last common ancestor of taipans (Oxyuranus species) and brown snakes (Pseudonaja species). Factor II (prothrombin) activation has been stated as the primary mechanism for the lethal coagulopathy, but this hypothesis has never been tested. The additional activation of Factor VII (FVII) by Oxyuranus/Pseudonaja venoms has historically been considered as a minor, unimportant novelty. This study aimed to investigate the significance of toxic FVII activation relative to prothrombin activation by testing a wide taxonomical range of Australian elapid species with procoagulant venoms. The activation of FVII or prothrombin, with and without the Factor Va as a cofactor, was assessed, along with the structural changes involved in these processes. All procoagulant species could activate FVII, establishing this as a basal trait. In contrast, only some lineages could activate prothrombin, indicating that this is a derived trait. For species able to activate both zymogens, Factor VII was consistently more strongly activated than prothrombin. FVa was revealed as an essential cofactor for FVII activation, a mechanism previously undocumented. Species lacking FVa in their venom utilized endogenous plasma FVa to exert this activity. The ability of the human FXa:FVa complex to activate FVII was also revealed as a new feedback loop in the endogenous clotting cascade. Toxin sequence analyses identified structural changes essential for the derived trait of prothrombin activation. This study presents a paradigm shift in understanding how elapid venoms activate coagulation factors, highlighting the critical role of FVII activation in the pathophysiological effects upon the coagulation cascade produced by Australian elapid snake venoms. It also documented the novel use of Factor Va as a cofactor for FVII activation for both venom and endogenous forms of FXa. These findings are crucial for developing better antivenoms and treatments for snakebite victims and have broader implications for drug design and the treatment of coagulation disorders. The research also advances the evolutionary biology knowledge of snake venoms.

7942 Evolution of Insulin, Insulin-like Growth Factor and Their Cognate Receptors in Vertebrates, Invertebrates and Viruses

Abstract Disclosure: M. Chrudinova: None. Y.D. Dogru: None. R. Huang: None. R. Reiners: None. P. De Meyts: None. J. DaCosta: None. E. Altindis: None. The insulin/insulin-like growth factor (IGF) signaling system is an evolutionarily conserved system and controls central processes including metabolism, cellular growth, proliferation, and differentiation in vertebrates. On the other hand, invertebrate insulin-like peptides (ILPs) regulate growth, stress responses, longevity and sex-related functions. In addition, we recently showed that six viruses possess viral insulin-like peptides (VILPs) that can bind to the receptors and stimulate post-receptor signaling. The evolution of these hormones and the origin of VILPs are not completely understood. Here, we collected vertebrate and invertebrate insulin, IGF and their cognate receptor sequences to analyze their evolutionary relations. We analyzed 177 vertebrate insulins, 119 vertebrate IGF-1s, 127 vertebrate IGF-2s, 197 invertebrate ILPs and 6 viral insulin/IGF-1 like peptides. We also analyzed 214 insulin receptor (IR), 160 IGF receptor (IGF1R) and 39 invertebrate receptor sequences to identify conservation and the evolutionary trajectory to reveal conserved motifs. Through phylogenetic analyses, we observed a separate branching of invertebrate ILPs and vertebrate insulins, IGF-1s and IGF-2s with notable exceptions including VILPs. IGF-1 and IGF-2 ligands were evolutionally better conserved compared to insulin ligands. Insulin C-peptide which is processed and cleaved was not well conserved compared to the functional A- and B-chain residues. In contrast, C-peptide of IGF-1 that plays an important role in receptor binding was very well conserved. IGF-1 C-domain showed higher variability in IGF1R binding residues compared to the A and B-domains, while residues important for binding of IGF-2 to IGF1R were well conserved. Insulin residues interacting with IR binding Site 1 were more conserved than those interacting with IR binding Site 2, while residues important for insulin dimerization and hexamerization residues are well conserved across species. We also showed that VILPs contain 14 amino acids that are conserved in insulin and IGFs, indicating their functional importance. Phylogenetic relationships of the receptor sequences suggest vertebrate IRs and IGF1Rs evolved from a common ancestor during early vertebrate evolution. Interestingly, receptor subunits revealed a closer relation of amphibian IR α-subunits to Mammalia IR α-subunits than Aves and Reptilians. The conservation rate of receptor residues essential for ligand-receptor interaction revealed that these residues are best conserved in the L1 domain for IR and IGF1R, with a higher rate of variation in other domains for both receptors. Taken together, our study provides a comprehensive analysis of insulin, IGFs, VILPs and their cognate receptors’ evolution, and opens new avenues to better understand the evolution, function, and structure relations of this complex signaling system. Presentation: 6/3/2024

Genome architecture of the heavy metal tolerant and accumulator Hirschfeldia incana: Insights from genome sequencing, assembly, and comparative analysis

Hirschfeldia incana L., a member of the Brassicaceae family commonly found in Mediterranean regions, is known for its capacity to withstand and accumulate heavy metals, particularly lead (Pb) both in soil environments and hydroponic systems. This plant has been used as a model to study plant responses to heavy metals. Nonetheless, the molecular mechanisms underlying its tolerance and heavy metal accumulation are not fully understood, partly because of the limited knowledge about its genome. In this study, the genome of H. incana was sequenced, assembled, characterized, and annotated. Approximately 8.6 Gpb of data were generated using Oxford Nanopore Technology (ONT), resulting in a genome assembly of 390 Mb, comprising 5196 contigs with an N50 exceeding 131 kb. The genome had a BUSCO score of 97.2 %, with 38,454 genes and a repetition content of 38.25 %. Subsequently, the assembled genome was annotated using several databases including GO, InterPro, MetaCyc, PANTHER, Pfam, Reactome, SUPERFAMILY, and KEGG. This annotation yielded 22,661 GO terms and 143 KEGG maps. A comparative genomic analysis between H. incana and six Brassicaceae species (five hyperaccumulators of heavy metals and one non-hyperaccumulator) was also conducted. This analysis revealed that H. incana shares a substantial proportion of orthologous genes (89.7 % of orthogroups) with six Brassicaceae species. The generated phylogenetic tree suggests that H. incana is closely related to B. juncea, B. napus, and B. oleracea, indicating a common ancestry and potentially shared genetic factors contributing to hyperaccumulation in these species. Moreover, the copy number of twenty-nine genes involved in heavy metal tolerance and accumulation mechanisms in H. incana and six brassicaceae were assayed. This analysis revealed that H. incana and other hyperaccumulator species possess a higher copy number of genes related to heavy metal tolerance than the sensitive plant A. thaliana. Notably, the variation in gene copy numbers highlights their potential role in the adaptation of H. incana to heavy metal stress. This study provides a comprehensive genomic framework that enhance our understanding of H. incana adaptation to heavy metal stress, and offers valuable data for further genomic investigations of the molecular mechanisms of heavy metal tolerance and accumulation in plants.

Comparative analyses reveal conserved and modified steps in the testis descent and scrotum development in mouse and opossum.

In many mammals, the testes descend from its abdominal position on the mesonephric kidney, and are housed in the scrotum. It has been speculated that metatherians and eutherians might have acquired the scrotal testis independently, because metatherians have the scrotum cranially to the phallus, while eutherians, such as humans and mice, possess it caudally. Rather, recent studies, based on sequence comparisons of testis-descent-related genes indicate that the metatherian-eutherian common ancestor might already possess the descent mechanisms. To further elucidate the path of scrotal testis evolution, it is informative to compare the processes of the descent and scrotum development between metatherian and eutherian model animals. In this study, we histologically and molecularly compare these processes in gray short-tailed opossum (Monodelphis domestica), the most commonly used metatherian experimental model, and compare them with those in mouse. Our observations indicate that, while trans-abdominal phase of the descent appears to be largely similar, scrotal phase differs, due to their distinct scrotum positions. Our cell-labeling analyses and dynamic expression of Gsc1 reveal extensive cell/tissue rearrangements in murine scrotal development. In contrast, Gsc1 is not expressed in the developing genitalia and scrotal primordium of the opossum. Our results suggest recruitment of new regulatory pathways for the scrotum development and the scrotal phase of the testis descent during the evolution of eutherian mammals.

Socio-monetary and Demographic Profile of Gujjar and Bakkarwals of Poonch District

The present study is an attempt to understand the educational backwardness of scheduled tribes of district Poonch of Jammu and Kashmir. The Scheduled Tribes (ST’s) are the socially and educationally deprived people in India. Scheduled Tribes have specific histories of social and monetary deprivation and the underlying reasons in their educational marginalization are also strikingly awesome. Schooling forms a crucial factor inside the average improvement of people, enabling them to get extra awareness, higher comprehension in their social, political and cultural surroundings and additionally facilitating inside the development of their socio-monetary conditions. The time period “tribe” was earlier used for a network which constituted a homogenous institution that lived in overall isolation having a particularly self-sustaining economic system independent political setup and which maintained wonderful customs, religions practices inherited from one common place ancestor. The scheduled tribes are the oldest settlers, if no longer the primary in India and India has the second one biggest concentration of the tribes inside internationally. Scheduled tribe population constitutes 8.6% of the entire population in India. Jammu and Kashmir has many tribal communities having their own traditions, cultures and customs. Scheduled Tribe groups have traditionally lived in remote and some difficult terrains in the direction of forests and natural assets. Most of the tribes live in inaccessible areas.

Integrative Analysis of Vibrio Cholerae Genomic Data for Understanding its Pathogenicity and Evolution

Cholera remains a significant global health threat, with substantial mortality rates, yet limited information exists on the pathogenicity, genomic data, and evolutionary relationships of Vibrio cholerae. This study presents a comprehensive genomic analysis of ten V. cholerae strains, examining nucleotide sequence length, virulence factors, pathogenicity islands, and mobile genetic elements. Using tools like NCBI, VFDV, ISLANDviewer, VRprofile, and CLUSTAL OMEGA, the analysis revealed notable variation in nucleotide sequence lengths, with the Amazonia strain and P16 strain showing the highest numbers. Virulence factor analysis identified that some strains, such as Amazonia and C1, possess significantly more virulence factors than others, contributing to cholera pathogenesis. Pathogenicity island analysis showed variability, with some strains like P16 and Amazonia containing more islands, while others, such as strain 0395-B, have fewer, underscoring their role in disease causation. Mobile genetic elements were identified in nine of the ten strains, facilitating the spread of crucial traits across bacterial populations. Evolutionary analysis indicated that all strains share a common ancestor, with Amazonia and strain 1 showing the greatest evolutionary distance from other strains. Additionally, sequence similarity analysis revealed that regions with 80-100% similarity are conserved, while those with less than 80% similarity are non-conserved. These findings offer valuable insights into the genetic diversity, virulence, and evolutionary relationships among V. cholerae strains, contributing to a deeper understanding of cholera pathogenesis and potential avenues for intervention.

Transcriptomic analyses in the gametophytes of the apomictic fern Dryopteris affinis

Main conclusionA novel genomic map of the apogamous gametophyte of the fern Dryopteris affinis unlocks oldest hindrance with this complex plant group, to gain insight into evo-devo approaches.The gametophyte of the fern Dryopteris affinis ssp. affinis represents a good model to explore the molecular basis of vegetative and reproductive development, as well as stress responses. Specifically, this fern reproduces asexually by apogamy, a peculiar case of apomixis whereby a sporophyte forms directly from a gametophytic cell without fertilization. Using RNA-sequencing approach, we have previously annotated more than 6000 transcripts. Here, we selected 100 of the inferred proteins homolog to those of Arabidopsis thaliana, which were particularly interesting for a detailed study of their potential functions, protein–protein interactions, and distance trees. As expected, a plethora of proteins associated with gametogenesis and embryogenesis in angiosperms, such as FERONIA (FER) and CHROMATING REMODELING 11 (CHR11) were identified, and more than a dozen candidates potentially involved in apomixis, such as ARGONAUTE family (AGO4, AGO9, and AGO 10), BABY BOOM (BBM), FASCIATED STEM4 (FAS4), FERTILIZATION-INDEPENDENT ENDOSPERM (FIE), and MATERNAL EFFECT EMBRYO ARREST29 (MEE29). In addition, proteins involved in the response to biotic and abiotic stresses were widely represented, as shown by the enrichment of heat-shock proteins. Using the String platform, the interactome revealed that most of the protein–protein interactions were predicted based on experimental, database, and text mining datasets, with MULTICOPY SUPPRESSOR OF IRA4 (MSI4) showing the highest number of interactions: 16. Lastly, some proteins were studied through distance trees by comparing alignments with respect to more distantly or closely related plant groups. This analysis identified DCL4 as the most distant protein to the predicted common ancestor. New genomic information in relation to gametophyte development, including apomictic reproduction, could expand our current vision of evo-devo approaches.

Self-Organizing a Latent Hierarchy of Sketch Patterns for Controllable Sketch Synthesis.

Encoding sketches as Gaussian mixture model (GMM)-distributed latent codes is an effective way to control sketch synthesis. Each Gaussian component represents a specific sketch pattern, and a code randomly sampled from the Gaussian can be decoded to synthesize a sketch with the target pattern. However, existing methods treat the Gaussians as individual clusters, which neglects the relationships between them. For example, the giraffe and horse sketches heading left are related to each other by their face orientation. The relationships between sketch patterns are important messages to reveal cognitive knowledge in sketch data. Thus, it is promising to learn accurate sketch representations by modeling the pattern relationships into a latent structure. In this article, we construct a tree-structured taxonomic hierarchy over the clusters of sketch codes. The clusters with the more specific descriptions of sketch patterns are placed at the lower levels, while the ones with the more general patterns are ranked at the higher levels. The clusters at the same rank relate to each other through the inheritance of features from common ancestors. We propose a hierarchical expectation-maximization (EM)-like algorithm to explicitly learn the hierarchy, jointly with the training of encoder-decoder network. Moreover, the learned latent hierarchy is utilized to regularize sketch codes with structural constraints. Experimental results show that our method significantly improves controllable synthesis performance and obtains effective sketch analogy results.