Distribution Of Motifs Research Articles

Loss of Myostatin Affects m6A Modification but Not Semen Characteristics in Bull Spermatozoa

N6-methyladenosine (m6A) modification is a key methylation modification involved in reproductive processes. Myostatin gene editing (MT) in cattle is known to enhance muscle mass and productivity. However, the changes in m6A modification in MT bull sperm remain poorly understood. In the MT and wild-type (WT) groups, we identified 25,542 and 22,253 m6A peaks, respectively, mainly concentrated in the coding sequence (CDS) and 3′ untranslated region (UTR) of genes. The MT group showed an increase in gene transcription, but there was no significant difference in the overall m6A peaks pattern. There was also no significant difference in m6A motif and chromosome distribution between MT and WT groups. Most genes had less m6A modification sites. A total of 1120 m6A peaks were significantly different, corresponding to 1053 differentially m6A-methylated genes (DMMGs). These DMMGs are mainly associated with G protein-coupled receptor signaling pathways and the overall composition of the cell membrane. Furthermore, an MCL clustering analysis of 111 differentially m6A-methylated and expressed genes identified seven key genes (RHOA, DAAM1, EXOC4, GNA12, PRICKLE1, SCN1A, and STXBP5L), with the cytoskeleton and migration-related gene, RHOA, being the most important gene located at the center of the gene network. However, the analysis of sperm morphology and motility indicated no significant changes in semen volume, sperm count, sperm viability, plasma membrane integrity, acrosome membrane integrity, or mitochondrial membrane integrity. This study provides a map of m6A methylation in spermatozoa from MT and WT bulls, identifies key differential m6A genes that are affected by the myostatin gene but do not affect sperm morphology and viability in MT bulls, and provides a theoretical basis for the breeding quality of MT bulls.

Pilbara Fat-Tailed Macropods: Using Multivariate and Morphometric Analyses to Explore Spatial and Stylistic Variability

This paper presents a pioneering analysis of a distinctive engraved motif from the Pilbara region: the fat-tailed macropod (kangaroo). This stylistic analysis has used a combination of conventional qualitative and multivariate techniques with less commonly deployed geometric morphometrics analysis (GMA). Focusing on a distinctive engraved motif in Australia’s northwest, this study has quantified the stylistic characteristics of the fat-tailed macropod depictions by identifying the significant attributes that contribute to this motif’s schema. By using both multivariate analysis and GMA software, we have developed a more nuanced understanding of the synchronic and diachronic dimensions of this deep-time indigenous artistic tradition. Differing levels of stylistic homogeneity across this region are interpreted as distinctive signalling intentionality by the artists. Based on the precepts of information exchange theory, stylistic homogeneity is interpreted as indicating an open social system, while stylistic heterogeneity represents people signalling social difference(s). The geographic distribution of this distinctive motif, and its specific placement within sites demonstrates different inscribing behaviours across the Pilbara. This is interpreted as evidence for intentional identity production by Pilbara artists. GMA identifies that a major contributing factor to the variability in this motif form is in the distinctive depictions of posture and gait. Indigenous knowledge of kangaroo behaviours is demonstrated in these iconic Pilbara motifs.

Comparative study of the 5S rDNA non-transcribed spacers in Lunario and Rosso varieties of Citrus limon (L.) Burm. f.

Lemon (Citrus limon (L.) Burm. f.) is a fruit plant that is widely grown in India and other countries with subtropical climates. The agricultural significance of lemon largely determines the high scientific interest in studying its genome. Such part of a genome as ribosomal DNA (rDNA) is often studied by geneticists with theoretical and applied purposes. In this work, sixteen non-transcribed spacers of the lemon 5S rDNA (8 from Lunario and 8 from Rosso varieties) were amplified with the universal 5S1/5S2 primers, purified, cloned in AT-vector, and sequenced. These sequences were processed, aligned and characterized for length, presence of mutations and distribution of different DNA motifs. Seven NTSs of the Lunario variety were 105 bp in length, and the eighth NTS was 77 bp because a large deletion was found in its start part. Five NTSs of the Rosso variety were 218 bp, two – 216 bp, and one – 185 bp in length. This short NTS has a 31 bp deletion in the middle part of the sequence. The emergence of typical 105 bp lemon NTSs from longer NTSs due to deletion has been suggested. The start-motif analysis and the search for poly-T, poly-C, poly-G and TATA-like motifs were carried out in the sequenced NTSs. Based on the obtained results, conclusions were made about the role of the CTCTTTT, CGCCGG, and GCGGC motifs in the appearance of deletions. Also, the results shed more light on the question of the origin of the Rosso variety. The knowledge obtained can be useful in the selection process involving lemon varieties and an analysis of citrus hybrids.

Motif distribution in genomes gives insights into gene clustering and co-regulation.

We read the genome as proteins in the cell would - by studying the distributions of 5-6 base motifs of DNA in the whole genome or smaller stretches such as parts of, or whole chromosomes. This led us to some interesting findings about motif clustering and chromosome organization. It is quite clear that the motif distribution in genomes is not random at the length scales we examined: 1 kb to entire chromosomes. The observed-to-expected (OE) ratios of motif distributions show strong correlations in pairs of chromosomes that are susceptible to translocations. With the aid of examples, we suggest that similarity in motif distributions in promoter regions of genes could imply co-regulation. A simple extension of this idea empowers us with the ability to construct gene regulatory networks. Further, we could make inferences about the spatial proximity of genomic fragments using these motif distributions. Spatially proximal regions, as deduced by Hi-C or pcHi-C, were ∼3.5 times more likely to have their motif distributions correlated than non-proximal regions. These correlations had strong contributions from the CTCF protein recognizing motifs which are known markers of topologically associated domains. In general, correlating genomic regions by motif distribution comparisons alone is rife with functional information.

Crucial role and conservation of the three [2Fe-2S] clusters in the human mitochondrial ribosome.

Mitochondria synthesize only a small set of their proteins on endogenous mitoribosomes. These particles differ in structure and composition from both their bacterial 70S ancestors and cytosolic 80S ribosomes. Recently published high resolution structures of the human mitoribosome revealed the presence of three [2Fe-2S] clusters in the small and large subunits. Each of these clusters is coordinated in a bridging fashion by cysteine residues from two different mitoribosomal proteins. Here, we investigated the cell biological and biochemical roles of all three Fe/S clusters in mitochondrial function and assembly. First, we found a requirement of both early and late factors of the mitochondrial iron-sulfur cluster assembly machinery for protein translation indicating that not only the mitoribosome [2Fe-2S] clusters but also the [4Fe-4S] cluster of the mitoribosome assembly factor METTL17 are required for mitochondrial translation. Second, siRNA-mediated depletion of the cluster-coordinating ribosomal proteins bS18m, mS25 or mL66 and complementation with either the respective wild-type or cysteine-exchange proteins unveiled the importance of the clusters for assembly, stability, and function of the human mitoribosome. As a consequence, the lack of cluster binding to mitoribosomes impaired the activity of the mitochondrial respiratory chain complexes and led to altered mitochondrial morphology with a loss of cristae membranes. Finally, in silico investigation of the phylogenetic distribution of the cluster-coordinating cysteine motifs indicated their presence in most metazoan mitoribosomes, with exception of ray-finned fish. Collectively, our study highlights the functional need of mitochondrial Fe/S protein biogenesis for both protein translation and respiratory energy supply in most metazoan mitochondria.

Dissecting non-B DNA structural motifs in untranslated regions of eukaryotic genomes

The untranslated regions (UTRs) of genes significantly impact various biological processes, including transcription, posttranscriptional control, mRNA stability, localization, and translation efficiency. In functional areas of genomes, non-B DNA structures such as cruciform, curved, triplex, G-quadruplex, and Z-DNA structures are common and have an impact on cellular physiology. Although the role of these structures in cis-regulatory regions such as promoters is well established in eukaryotic genomes, their prevalence within UTRs across different eukaryotic classes has not been extensively documented. Our study investigated the prevalence of various non-B DNA motifs within the 5′ and 3′ UTRs across diverse eukaryotic species. Our comparative analysis encompassed the 5′-UTRs and 3′UTRs of 360 species representing diverse eukaryotic domains of life, including Arthropoda (Diptera, Hemiptera, and Hymenoptera), Chordata (Artiodactyla, Carnivora, Galliformes, Passeriformes, Primates, Rodentia, Squamata, Testudines), Magnoliophyta (Brassicales), Fabales (Poales), and Nematoda (Rhabditida), on the basis of datasets derived from the UTRdb. We observed that species belonging to taxonomic orders such as Rhabditida, Diptera, Brassicales, and Hemiptera present a prevalence of curved DNA motifs in their UTRs, whereas orders such as Testudines, Galliformes, and Rodentia present a preponderance of G-quadruplexes in both UTRs. The distribution of motifs is conserved across different taxonomic classes, although species-specific variations in motif preferences were also observed. Our research unequivocally illuminates the prevalence and potential functional implications of non-B DNA motifs, offering invaluable insights into the evolutionary and biological significance of these structures.

Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation.

RNA-binding proteins are essential for gene regulation and the spatial organization of cells. Here, we report that the yeast ribosome biogenesis factor Loc1p is an intrinsically disordered RNA-binding protein with eight repeating positively charged, unstructured nucleic acid binding (PUN) motifs. While a single of these previously undefined motifs stabilizes folded RNAs, multiple copies strongly cooperate to catalyze RNA folding. In the presence of RNA, these multivalent PUN motifs drive phase separation. Proteome-wide searches in pro- and eukaryotes for proteins with similar arrays of PUN motifs reveal a strong enrichment in RNA-mediated processes and DNA remodeling. Thus, PUN motifs are potentially involved in a large variety of RNA- and DNA-related processes by concentrating them in membraneless organelles. The general function and wide distribution of PUN motifs across species suggest that in an ancient 'RNA world' PUN-like motifs may have supported the correct folding of early ribozymes.

Insights and caveats from mining local and global temporal motifs in cryptocurrency transaction networks

Distributed ledger technologies have opened up a wealth of fine-grained transaction data from cryptocurrencies like Bitcoin and Ethereum. This allows research into problems like anomaly detection, anti-money laundering, pattern mining and activity clustering (where data from traditional currencies is rarely available). The formalism of temporal networks offers a natural way of representing this data and offers access to a wealth of metrics and models. However, the large scale of the data presents a challenge using standard graph analysis techniques. We use temporal motifs to analyse two Bitcoin datasets and one NFT dataset, using sequences of three transactions and up to three users. We show that the commonly used technique of simply counting temporal motifs over all users and all time can give misleading conclusions. Here we also study the motifs contributed by each user and discover that the motif distribution is heavy-tailed and that the key players have diverse motif signatures. We study the motifs that occur in different time periods and find events and anomalous activity that cannot be seen just by a count on the whole dataset. Studying motif completion time reveals dynamics driven by human behaviour as well as algorithmic behaviour.

Genome-Wide Characterization of Shi-Related Sequence Gene Family and Its Roles in Response to Zn2+ Stress in Cucumber

Shi-related sequence (SRS) proteins, which consist of the RING-like zinc finger domain and IGGH domain, are plant-specific transcription factors that have been well-studied in several plant species. However, information about SRS genes and their roles in cucumber (Cucumis sativus L.) is limited. Therefore, we performed detailed bioinformatic analysis of the SRS gene family, including gene numbers and positions, genes structures, conserved motif distribution patterns, phylogenetic analysis, and promoter cis-element analysis. Eight SRS genes were identified in cucumber and distributed on all seven cucumber chromosomes. SRS genes are conserved in plants and divided into two groups in cucumber based on their protein sequence. In silico analysis predicted that most genes may function in response to abiotic stresses and phytohormones. Gene ontology analysis predicted the possible involvement of genes in development and reproduction, and DNA and protein binding on a molecular level. Furthermore, the differential expression pattern of SRS genes in leaf, stem and root under the condition of Zn2+ stress suggested their roles in response to Zn2+ stress. Furthermore, our metal tolerance assay suggested that CsSRS2 and CsSRS5 mediated enhanced tolerance to Zn2+ stress in Escherichia coli cells. Our study provides a foundation for the functional study of SRS genes in cucumber.

Molecular analyses of the tubby-like protein gene family and their response to salt and high temperature in the foxtail millet (Setaria italica).

Tubby-like proteins (TLPs) are a group of proteins found in both eukaryotes and prokaryotes. They are significant in various physiological and biochemical processes, especially in plants' response to abiotic stress. However, the role of TLP in foxtail millet (Setaria italica) remains unclear. The millet genome has 16 members of the TLP family with typical Tub domains, which can be sorted into five subgroups based on gene structure, motif, and protein domain distribution. SiTLPs were discovered to be predominantly located in the nucleus and also had extracellular distribution. The interspecific evolutionary analysis indicated that SiTLPs had a closer evolutionary relationship with monocots and were consistent with the morphological classification of foxtail millet. When subjected to salt stress, the abundance of SiTLP was affected, and qRT-PCR results showed that the expression levels of certain SiTLP members were induced by salt stress while others remained unresponsive. Except for SiTLP14, all other SiTLP genes were up-regulated in response to high-temperature stress, implying a potentially crucial role for SiTLP in mitigating high-temperature-induced damage. This study provides valuable insights into understanding the functional significance of the TLP gene family in foxtail millet.

Genome-wide identification and characterization of pectin methylesterase inhibitor gene family members related to abiotic stresses in watermelon.

Pectin is a vital component of plant cell walls and its methylation process is regulated by pectin methylesterase inhibitors (PMEIs). PMEIs regulate the structural and functional modifications of cell walls in plants and play an important role in plant processes such as seed germination, fruit ripening, and stress response. Although the PMEI gene family has been well characterized in model plants, the understanding of its molecular evolution and biological functions in watermelon remains limited. In this study, 60 ClPMEI genes were identified and characterized, revealing their dispersion on multiple chromosomes. Based on a systematic developmental analysis, these genes were classified into three subfamilies, which was further supported by the exon, intron, and conserved motif distribution. Analysis of cis-elements and expression patterns indicated that ClPMEIs might be involved in regulating the tolerance of watermelon to various abiotic stresses. Moreover, distinct ClPMEI genes exhibit specific functions under different abiotic stresses. For example, ClPMEI51 and ClPMEI54 showed a significant upregulation in expression levels during the late stage of drought treatments, whereas ClPMEI3 and ClPMEI12 displayed a significant downregulation under low-temperature induction. Subcellular localization prediction and analysis revealed that the ClPMEI family member proteins were localized to the cell membrane. This study provided an important foundation for the further exploration of the functions of ClPMEI genes in watermelon.

Virome-wide analysis of histone modification mimicry motifs carried by viral proteins

Histone mimicry (HM) refers to the presence of short linear motifs in viral proteins that mimic critical regions of host histone proteins. These motifs have the potential to interfere with host cell epigenome and counteract antiviral response. Recent research shows that HM is critical for the pathogenesis and transmissibility of influenza virus and coronavirus. However, the distribution, characteristics, and functions of HM in eukaryotic viruses remain obscure. Herein, we developed a bioinformatic pipeline, Histone Motif Scan (HiScan), to identify HM motifs in viral proteins and predict their functions in silico. By analyzing 592,643 viral proteins using HiScan, we found that putative HM motifs were widely distributed in most viral proteins. Among animal viruses, the ratio of HM motifs between DNA viruses and RNA viruses was approximately 1.9:1, and viruses with smaller genomes had a higher density of HM motifs. Notably, coronaviruses exhibited an uneven distribution of HM motifs, with betacoronaviruses (including most human pathogenic coronaviruses) harboring more HM motifs than other coronaviruses, primarily in the NSP3, S, and N proteins. In summary, our virome-wide screening of HM motifs using HiScan revealed extensive but uneven distribution of HM motifs in most viral proteins, with a preference in DNA viruses. Viral HM may play an important role in modulating viral pathogenicity and virus-host interactions, making it an attractive area of research in virology and antiviral medication.

Computational analysis and expression profiling of NAC transcription factor family involved in biotic stress response in Manihot esculenta.

The Nascent polypeptide-Associated Complex (NAC) family is among the largest plant-specific TF families and plays an important role in plant growth, development, and stress responses. NAC TFs have been extensively studied in plants such as rice and Arabidopsis; however, their characterization, functions, evolution, and expression patterns in Manihot esculenta (cassava) under environmental stress remain largely unexplored. Here, we used bioinformatic analyses and biotic stress responses to investigate the physicochemical properties, chromosome location, phylogeny, gene structure, expression patterns, and cis-elements in promoter regions of the NAC TFs in cassava. We identified 119 M. esculenta NAC (MeNAC) gene families, unevenly distributed on 16 chromosomes. We investigated expression patterns of all identified MeNAC TFs under Xanthomonas axonopodis pv. manihotis (Xam) infection, strain CHN11, at different time points. Only 20 MeNAC TFs showed expression of significant bacterial resistance. Six MeNACs (MeNAC7, 26, 63, 65, 77, and 113) were selected for functional analysis. qRT-PCR assays revealed that MeNAC7, 26, 63, 65, 77, and 113 were induced in response to XamCHN11 infection and may participate in the molecular interaction of cassava and bacterial blight. Interestingly, MeNAC26, MeNAC63, MeNAC65, and MeNAC113 responded to XamCHN11 infection at 3 h post-inoculation. Furthermore, we identified 13 stress-related cis-elements in promoter regions of the MeNAC genes that are involved in diverse environmental stress responses. Phylogenetic analysis revealed that MeNAC genes with similar structures and motif distributions were grouped. This study provides valuable insights into the evolution, diversity, and characterization of MeNAC TFs. It lays the groundwork for a better understanding of their biological roles and molecular mechanisms in cassava.

Genome-Wide Analyses of CCHC Family Genes and Their Expression Profiles under Drought Stress in Rose (Rosa chinensis).

CCHC-type zinc finger proteins (CCHC-ZFPs), ubiquitous across plant species, are integral to their growth, development, hormonal regulation, and stress adaptation. Roses (Rosa sp.), as one of the most significant and extensively cultivated ornamentals, account for more than 30% of the global cut-flower market. Despite its significance, the CCHC gene family in roses (Rosa sp.) remains unexplored. This investigation identified and categorized 41 CCHC gene members located on seven chromosomes of rose into 14 subfamilies through motif distribution and phylogenetic analyses involving ten additional plant species, including Ginkgo biloba, Ostreococcus lucimarinus, Arabidopsis thaliana, and others. This study revealed that dispersed duplication likely plays a crucial role in the diversification of the CCHC genes, with the Ka/Ks ratio suggesting a history of strong purifying selection. Promoter analysis highlighted a rich presence of cis-acting regulatory elements linked to both abiotic and biotic stress responses. Differential expression analysis under drought conditions grouped the 41 CCHC gene members into five distinct clusters, with those in group 4 exhibiting pronounced regulation in roots and leaves under severe drought. Furthermore, virus-induced gene silencing (VIGS) of the RcCCHC25 member from group 4 compromised drought resilience in rose foliage. This comprehensive analysis lays the groundwork for further investigations into the functional dynamics of the CCHC gene family in rose physiology and stress responses.

Genome-wide analysis of MADS-box genes and their expression patterns in unisexual flower development in dioecious spinach

Evolution of unisexual flowers involves extreme changes in floral development. Spinach is one of the species to discern the formation and evolution of dioecy. MADS-box gene family is involved in regulation of floral organ identity and development and in many other plant developmental processes. However, there is no systematic analysis of MADS-box family genes in spinach. A comprehensive genome-wide analysis and transcriptome profiling of MADS-box genes were undertaken to understand their involvement in unisexual flower development at different stages in spinach. In total, 54 MADS-box genes found to be unevenly located across 6 chromosomes and can be divided into type I and type II genes. Twenty type I MADS-box genes are subdivided into Mα, Mβ and Mγ subgroups. While thirty-four type II SoMADSs consist of 3 MIKC*, and 31 MIKCC -type genes including sixteen floral homeotic MADS-box genes that are orthologous to the proposed Arabidopsis ABCDE model of floral organ identity determination, were identified in spinach. Gene structure, motif distribution, physiochemical properties, gene duplication and collinearity analyses for these genes are performed in detail. Promoters of both types of SoMADS genes contain mainly MeJA and ABA response elements. Expression profiling indicated that MIKCc genes exhibited more dynamic and intricate expression patterns compared to M-type genes and the majority of type-II genes AP1, SVP, and SOC1 sub-groups showed female flower-biased expression profiles, suggesting their role in carpel development, while PI showed male-biased expression throughout flower developmental stages, suggesting their role in stamen development. These results provide genomic resources and insights into spinach dioecious flower development and expedite spinach improvement.

Mining GATA Transcription Factor Encoding Genes in The Cocoa Tree (<i>Theobroma cacao</i> L.) Suggests Their Potential Roles in Embryo Development and Biotic Stress Response

GATA transcription factors (TFs) are widely recognized as significant regulators, characterized by a DNA-binding domain that consists of a type IV zinc finger motif. This TF family has been widely investigated in numerous higher plant species. The purpose of the present work was to comprehensively analyze the GATA TF in cocoa plant (Theobroma cacao L.) by using various bioinformatics tools. As a result, a total of 24 members of the GATA TFs have been identified and annotated in the assembly of the cocoa plant. According to phylogenetic analysis, these TcGATA proteins were classified into four distinct groups, including groups I (10 members), II (seven members), III (five members), and IV (two members). Next, our investigation indicated that the TcGATA proteins in different groups exhibited a high variation in their physic-chemical features due to their different protein lengths, gene structures, and conserved motif distributions, whereas the TcGATA proteins in the same clade might share the common conserved motifs. Additionally, the gene duplication of the TcGATA genes in the cocoa plant was also investigated. Of our interest, the relative expression levels of the TcGATA genes were investigated according to available transcriptome databases. The results exhibited differential expression patterns of all TcGATA genes in various developmental stages of zygotic and somatic embryogenesis, indicating that these TcGATA genes divergently function during various developmental stages of the zygotic and somatic embryos. Moreover, TcGATA genes were differently expressed under Phytophthora megakarya treatment across different points of treatment and cocoa varieties. To sum up, our findings could provide a basis for a further deep understanding of the GATAs in the cocoa plant.

Comprehensive genomic screening and expression profiling of trihelix family in pearl millet under abiotic stresses with emphasis on functional insights of PgTHX24

The trihelix transcription factors (THX TFs) play a crucial role in light responses and are involved in plant growth, development, and stress responses. In this study, we have identified 35 trihelix TFs in pearl millet (Pennisetum glaucum), which is one of the most widely grown C4 cereal crops in tropical semi-arid regions. Identified PgTHXs (Trihelix members of P. glaucum) were classified into 5 subgroups (GT1, GT2, GTγ, SH4, and SIP1) based on phylogenetic analysis, and these subgroup members shared similar gene structure and motif distribution pattern. Collinearity analysis exhibited gene duplication events of trihelix family members in pearl millet across the genome. Gene ontology (GO) annotation and cis-regulatory elements (CREs) analysis of PgTHXs suggested their involvement in diverse biological and molecular functions associated with plant growth, development, and stress responses. RNA sequencing data and expression profile displayed differential expression patterns of PgTHXs under abiotic stress and phytohormone treatments. The induced expression pattern of the PgTHX4, PgTHX5, PgTHX24, and PgTHX30 suggested their potential involvement in abiotic stress responses through phytohormonal signalling pathways. Among these, PgTHX24, a GT-3b member, was localized in the nucleus with self-transactivation ability. Overexpression of PgTHX24 positively regulated expression of stress-related markers in transformed pearl millet calli under drought stress conditions. Promoter activity analysis also highlighted the stress-inducible nature of PgTHX24’s promoter. Overall, our findings provide a comprehensive understanding of PgTHXs with a framework for further functional characterization to understand their regulatory role in pearl millet’s growth, development, and stress responses. Key messageThirty-five trihelix TFs were identified in pearl millet, and a comprehensive expression profile highlighted their functional diversity. Overexpression of PgTHX24 exhibited its potential involvement in abiotic stress responses.

Paleolithic cave art at Simanya Gran (Northeast of Spain): New graphic and symbolic expressions in novel territories

Recent years have witnessed significant advancement in the understanding of prehistoric behavior, leading to the discovery of new assemblages that challenge established knowledge within the discipline. This study presents a newly discovered Paleolithic art site in the northeast region of the Iberian Peninsula, specifically within the Simanya Gran cave complex. Excavations conducted since 2019 have revealed Neanderthal human remains and a complex litho-stratigraphic sequence dating back to the Middle Paleolithic, indicating human occupation spanning multiple periods. The documented graphic device (engravings and painting) exhibits thematic and formal characteristics comparable to Paleolithic art found in Spain and France. Through stylistic and contextual analysis, the paper proposes a tentative chronology for the graphic evidence, situating it within the mid-late Magdalenian period. Furthermore, the study explores the concept of graphic territories, suggesting that the distribution of similar graphic motifs across distant regions reflects intense socio-cultural interactions among prehistoric human groups. The significance of this discovery extends beyond its immediate geographic location, contributing to a broader understanding of Paleolithic art in the Mediterranean region and highlighting the importance of continued research in this field.

Comprehensive molecular evolutionary analysis of small heat shock proteins in five diploid Gossypium species.

The small heat shock proteins (sHSPs) are important components in plant growth and development, and stress response. However, a systematical understanding of the sHSP family is yet to be reported in five diploid Gossypium species. In this study, 34 GlsHSPs, 36 GrsHSPs, 37 GtsHSPs, 37 GasHSPs, and 38 GhesHSPs were identified in Gossypium longicalyx, Gossypium raimondii, Gossypium turneri, Gossypium arboreum, and Gossypium herbaceum, respectively. These sHSP members can be clustered into 10 subfamilies. Different subfamilies had different member numbers, motif distributions, gene structures, gene duplication events, gene loss numbers, and cis-regulatory elements. Besides, the paleohexaploidization event in cotton ancestor led to expanding the sHSP members and it was also inherited by five diploid Gossypium species. After the cotton ancestor divergence, the sHSP members had the relatively conserved evolution in five diploid Gossypium species. The comprehensive evolutionary history of the sHSP family was revealed in five diploid Gossypium species. Furthermore, several GasHSPs and GhesHSPs were important candidates in plant growth and development, and stress response. These current findings can provide valuable information for the molecular evolution and further functional research of the sHSP family in cotton.

In silico analysis on frequency and distribution of microsatellites in genes associated with spinal cord astrocytoma

Microsatellites, also called short tandem repeats (STRs) or simple sequence repeats (SSRs) are short DNA sequence segments consisting of tandemly repeated motifs. SSRs are regarded as one of the most effective tools for genetic research. In this study, we conducted an in silico analysis to investigate the presence, distribution, and characteristics of SSRs within the genes associated with spinal cord astrocytoma. The aim of this study was to identify SSRs in coding and non-coding regions, analyze their correlation with gene parameters, and determine the GC content in the gene sequences. The results revealed that the widespread presence of SSRs within the genes is associated with spinal cord astrocytoma (SCA). The distribution of SSR motifs varied among the analyzed genes, and certain motifs were common across multiple genes. Additionally, we observed a strong positive correlation between the total number of SSRs and gene size, indicating that larger genes tend to have a higher number of microsatellites. Furthermore, we identified SSRs in both coding and non-coding regions of the genes. The incidence of SSRs and cSSRs differed among genes, suggesting potential functional implications for gene expression and regulation. Our study provides valuable insights into the genetic diversity within the astrocytoma genes and highlights the potential significance of SSRs in gene regulation. In conclusion, this study contributes to a better understanding of the role of microsatellites within the genes associated with spinal cord astrocytoma. The observed patterns of SSR distribution and characteristics suggest their potential functional relevance in the development and progression of astrocytoma.