Analysis Of Diversity Structure Research Articles

Unleashing the potential of cheminformatic analysis for Mycobacterium tuberculosis inhibitors: Insights into chemical space and structural diversity

Mycobacterium tuberculosis (Mtb) remains a major global health concern, causing millions of infections and deaths annually. Drug-resistant tuberculosis poses significant challenges, necessitating the search for new Mtb inhibitors. In this context, a cheminformatic analysis of the currently available antimycobacterial chemical space can be performed to discover structural diversity and new scaffolds. This study conducts a comprehensive cheminformatic analysis of two datasets containing Mtb inhibitors (Mtbs and Phytochemicals), comparing them with Approved drugs and Nutraceuticals datasets. The analysis includes physicochemical properties, molecular scaffolds, structural fingerprints, and structural similarities. The analysis of physicochemical property distributions revealed that Mtb inhibitors are generally less polar or equally polar compared to approved drugs and have similar flexibility. The visual representation of the property space illustrates that the Mtbs dataset is confined to a narrower area, whereas certain compounds within the Phytochemical dataset broaden the scope of the traditional medicinal space. Scaffold analysis identifies several promising candidates in both the Mtbs and Phytochemical datasets. Additionally, employing SkelSpheres descriptors and rubber band scaling for similarity analysis reveals a limited depiction of the chemical space. The analysis of structural diversity indicates that the compounds in the Mtbs dataset exhibit less structural diversity. These findings underscore the necessity to broaden the chemical space of Mtb-targeting molecules by incorporating representative molecules from diverse scaffolds to effectively tackle the issue of drug resistance.

Genome-Wide Identification, Structural Diversity Analysis and Expression Profiling of NBARC Domain-Containing Gene Family in Pisum sativum

Genome-Wide Identification, Structural Diversity Analysis and Expression Profiling of NBARC Domain-Containing Gene Family in Pisum sativum

Characteristics of intestinal flora in patients with primary Sjögren syndrome

To investigate changes in intestinal flora in patients with primary Sj?gren syndrome (pSS) and explore the relationship between pSS disease activity and intestinal flora structure. Fecal samples were collected from 18 female pSS patients, including 9 patients with active disease (group A) and 9 with disease inactivity or low activity (group B), with 10 healthy subjects as the control group. The total bacterial DNA was extracted from the fecal samples for PCR amplification, and Illumina Hiseq 2500 high-throughput sequencing was performed for the v3-v4 region of 16Sr DNA gene to obtain the biological information of the intestinal flora. The intergroup OTU analysis, structural diversity analysis, significant difference analysis and LEFSE analysis were performed with information mining of the literature think tanks. The dilution curves generated based on the OTUshannon index for analysis of sample complexity showed that the measured data were relatively complete and could reflect the diversity of the microorganisms in the subjects. Analysis of the Alpha diversity index showed that the Shannon index differed significantly between group A and group B, and the Simpson index differed significantly between group A and group B and between group A and the control group (P < 0.05). Sequence analysis the 3 groups all consisted mainly of 4 phylum (Firmicutes, Bacteroidetes, Actinobacteria, showed that the intestinal flora in and proteobacteria) and 4 genera (finegoldia, Prevotella, Streptococcus, and Corynebacterium_1), all showing no significant differences among the 3 groups (P > 0.05) with the exception of Streptococcus genus, which differed significantly among the 3 groups (P < 0.05). The 16S v3-v4 region in the genus Alloscardovia, Bacteroides, Barnesiella, Butyricicoccus, Facklamia, Faecalibacterium, Lachnospiraceae_FCS020_group, Lachnospiraceae_ND3007_group, Lachnospiraceae_UCG-001, Lachnospirace, Lachnospirace, Ruminococcaceae_UCG-002, Streptococcus and Coprococcus_1 differed significantly among the 3 groups (P < 0.05). The high-dimensional biometrics and genomic characteristics of the intestinal microorganisms differed significantly among the 3 groups (P < 0.05). According to the size of LDA SCORE (effect size), the core flora in group A included the genera Barnesiellaccae, Aerococcaceae, Family-XIII, Bacteroidaceae, Lachnospiraceae_UCG-001, Barnesiella, Facklamia, Alloscardovia, Faecalibacterium and Bacteroides, as compared with the genera Streptococcaceae, Streptococcus, Coprococcus_1, Ruminococcaceae_ucg-002, Lachnospiraceae_FCS020_group, Lachnospiraceae_ucg-004, Lachnospiraceae_ND3007_group, Lachnospiraceae_ucg-008 and Butyricicoccus in the control group. Patients with pSS have significant changes in the diversity of intestinal flora, especially in some specific bacteria in Streptococcu genus and in 16S v3-v4 region of the bacteria. The differences in the core bacteria in the intestinal flora of pSS patients suggest the role of flora structure changes in the pathogenesis of pSS.

Characterization of Five Microsatellite Markers For Genetic Diversity Structure Analysis of Walnut (Juglans Regia L) in Five Village in Duhok Province

Five microsatellites markers (WGA202, WGA009, WGA332, WGA225 and WGA069) were used to characterize Persian walnuts (Juglans regia L.) populations in five villages (Sharanesh, Bedohe, Kanizarke (Akre), Kashane and Kuzo) of Duhok province. The microsatellites amplified (PCR products) a total of 186 alleles across all populations. The number of alleles per locus ranged from 4 alleles in Sharanesh and Kashane populations to 10 alleles also in Sharanesh and Kashane populations, with an average of 7.4. The molecular sizes of the amplified bands ranged from 158 bp to 289 bp in all populations. The observed heterozygosity (Ho) within populations ranged from 0.59 at WGA225 to 0.65 in the locus WGA202 with an average of 0.61. The PIC value (0.88) indicated that all markers were highly informative and useful for genetic diversity studies in these populations. The proportion of genetic variation presented among populations accounted for 8.4% of the total genetic diversity so it indicated a moderate level of genetic diversity between populations. The Fis average 0.24 indicated that, there was a regular tendency toward heterozygote deficiency and indicated the presence of inbreeding within the populations. The phylogenetic analysis or unrooted neighbor-joining tree highlighted the genetic distance among those five populations and separated them into two main groups placing each population according to its genetic background. The first group consists of populations Bedohe and Sharanesh in one subgroup and Kashane in second subgroup. The second group consists of populations Akre and Kuzo.

Analysis of structural diversity in wolf-like canids reveals post-domestication variants.

BackgroundAlthough a variety of genetic changes have been implicated in causing phenotypic differences among dogs, the role of copy number variants (CNVs) and their impact on phenotypic variation is still poorly understood. Further, very limited knowledge exists on structural variation in the gray wolf, the ancestor of the dog, or other closely related wild canids. Documenting CNVs variation in wild canids is essential to identify ancestral states and variation that may have appeared after domestication.ResultsIn this work, we genotyped 1,611 dog CNVs in 23 wolf-like canids (4 purebred dogs, one dingo, 15 gray wolves, one red wolf, one coyote and one golden jackal) to identify CNVs that may have arisen after domestication. We have found an increase in GC-rich regions close to the breakpoints and around 1 kb away from them suggesting that some common motifs might be associated with the formation of CNVs. Among the CNV regions that showed the largest differentiation between dogs and wild canids we found 12 genes, nine of which are related to two known functions associated with dog domestication; growth (PDE4D, CRTC3 and NEB) and neurological function (PDE4D, EML5, ZNF500, SLC6A11, ELAVL2, RGS7 and CTSB).ConclusionsOur results provide insight into the evolution of structural variation in canines, where recombination is not regulated by PRDM9 due to the inactivation of this gene. We also identified genes within the most differentiated CNV regions between dogs and wolves, which could reflect selection during the domestication process.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-465) contains supplementary material, which is available to authorized users.

Changes in the diversity structure of avian assemblages in North America

AbstractAim To determine the major patterns of change in avian diversity structure over space and time at a local resolution and continental extent in non‐urban areas in North America.Location The contiguous United States and southern Canada.Methods We used 1673 North American Breeding Bird Survey (BBS) routes containing 547 terrestrial and aquatic species to estimate four diversity components: species richness, individual abundance, taxonomic distinctness and species evenness. We implemented three levels of analysis to examine changes in diversity structure on a yearly basis from 1968 to 2003: (1) a canonical analysis of discriminance, (2) a univariate analysis across BBS routes, and (3) a univariate analysis at individual BBS routes. We estimated changes in similarity in species composition over time between 470,730 BBS route pairs. We also estimated the level of human activity at BBS routes using three spatial anthropogenic databases.Results BBS routes were located in non‐urban areas in association with low nighttime light activity and moderately low human population densities. The analysis of diversity structure indicated the presence of two independent patterns: (1) a temporally consistent pattern defined by increasing species richness (12% increase from 1968 to 2003) associated with limited gains in taxonomic distinctness, and (2) an association between species abundance and evenness related to variability in abundance associated with the most abundant species. The similarity analysis indicated that BBS routes located closer to the Atlantic and the Pacific coasts of the United States experienced the strongest patterns of homogenization of species composition.Main conclusions Our results suggest that avian diversity structure has changed at the local scale in non‐urban areas in North America. However, there was no evidence for a consistent continent‐wide pattern. Instead, the evidence pointed to the presence of regional factors influencing diversity patterns. This study provides a foundation for more detailed investigations of the spatiotemporal and taxonomic details of these general patterns.

Biodiversity along riparian corridors

Riparian corridors are integrated ecological units characterized by a diversity of aquatic and terrestrial habitats sustained by fluvial dynamics, Intact riverine corridors provide critical habitat for diverse biotic communities, the species being arrayed along multidimensional environmental gradients. This paper reviews some aspects of biodiversity in this context. Specifically, we address four aspects deemed essential for understanding biodiversity patterns along and within riparian corridors: (1) linking terrestrial and aquatic biodiversity, (2) distinguishing the different components of biodiversity, with an emphasis on the value of beta diversity, (3) establishing a hierarchical framework for examining biodiversity, and (4) identifying the relative importance of regional and local processes in structuring diversity, In addition, we present a major research programme recently initiated to investigate biodiversity along the last morphologically intact riparian corridor in the Alps, the Fiume Tagliamento in NE Italy. Results from an analysis of structural diversity at different scales in the Tagliamento provide insight into the hierarchy of factors that may be responsible for the generation and maintenance of biodiversity.

Biodiversity along riparian corridors

Riparian corridors are integrated ecological units characterized by a diversity of aquatic and terrestrial habitats sustained by fluvial dynamics, Intact riverine corridors provide critical habitat for diverse biotic communities, the species being arrayed along multidimensional environmental gradients. This paper reviews some aspects of biodiversity in this context. Specifically, we address four aspects deemed essential for understanding biodiversity patterns along and within riparian corridors: (1) linking terrestrial and aquatic biodiversity, (2) distinguishing the different components of biodiversity, with an emphasis on the value of beta diversity, (3) establishing a hierarchical framework for examining biodiversity, and (4) identifying the relative importance of regional and local processes in structuring diversity, In addition, we present a major research programme recently initiated to investigate biodiversity along the last morphologically intact riparian corridor in the Alps, the Fiume Tagliamento in NE Italy. Results from an analysis of structural diversity at different scales in the Tagliamento provide insight into the hierarchy of factors that may be responsible for the generation and maintenance of biodiversity.

Alternatively spliced MHC class I mRNAs show specific deletion of sequences encoding the extracellular polymorphic domains.

Analysis of structural diversity at the 5' end of H-2 class I mRNAs showed that a small fraction of Kd mRNA from L1210 lymphoma (approximately 10%) or from various normal tissue (2-3%) of DBA/2 mice carries a precise deletion of the sequences encoding the second extracellular domain. Nucleotide sequence of the coding region of the second domain-lacking Kd mRNA was found to be identical to the known sequence of the Kd gene from DBA/2 liver with the exception of the above deletion and a single nucleotide silent substitution at position 150, suggesting that the novel Kd RNA is a product of the functional Kd gene. In addition, various normal tissues that are known to express varying levels of Kd antigen did not show changes in the expression levels of the second domain-lacking Kd mRNA thus ruling out the possibility that synthesis of this RNA is coupled to control the expression levels of the canonical Kd mRNA, hence the Kd antigen. Analysis by polymerase chain reaction showed that all normal tissues including the testis and sperm express this RNA. Preliminary analysis of the Kb mRNA from the spleen and thymus of C57BL/6 mouse also showed the presence of second domain-lacking Kb mRNA in these mice. Furthermore, preliminary structural analysis of the Dd and Ld mRNAs has revealed additional polymorphic extracellular domain-lacking mRNA species including a first domain-lacking Dd mRNA and two Ld mRNAs that lack sequences encoding either the first extracellular domain or the second extracellular domain respectively. These results together show that H-2 mRNAs lacking sequences that specify individual extracellular polymorphic domains are a frequent feature of the structural diversity at the 5' ends of these mRNAs. Potential significance of these domain-lacking H-2 mRNAs is discussed, particularly with regard to the function of the putative encoded peptides as targets of natural killer cells.

Rarefaction analysis of morphological and taxonomic diversity

Our assessment of morphological diversity is influenced by morphological extremes and therefore depends on sample size (taxonomic richness). Rarefaction predicts the morphological diversity that would probably be observed in a sample of reduced size, thereby allowing both compensation for differences in sample size that may be strictly preservational, and analysis of diversity structure, that is, the relationship between morphological and taxonomic diversity. Middle and Late Cambrian trilobites exhibit a diversity structure characterized by many variations on a few morphological themes. In contrast, Middle and Late Ordovician trilobites occupy a larger range of morphospace per unit of species richness. Diversity structure in the Devonian is similar to that in the Middle and Late Ordovician, but the magnitude of morphological diversity is lower in the Devonian, as many fewer species are observed. For blastoids, different aspects of morphological diversity (range of morphospace occupied, number of character states possessed, and number of different regions in morphospace occupied) exhibit different relationships to taxonomic richness. In all cases Permian blastoids are characterized by a diversity structure in which morphological diversity per unit of taxonomic richness is greater than for Devonian blastoids. Changes in morphological diversity in fissiculate blastoids appear to reflect evolution of continuous variation in thecal morphology more than changes in the number of character states. Saunders and Swan's data on Namurian ammonoids illustrate some significant differences in diversity structure among stratigraphic levels, but many apparent differences in morphological diversity are consistent with the possibility that they reflect the sampling of different numbers of species from the same underlying diversity structure. Rarefaction curves are also presented for idealized increases and decreases in diversity, and these are compared to some of the observed changes in trilobites, blastoids, and ammonoids.