HIV-1 Proviral DNA Excision Using an Evolved Recombinase Sarkar, Indrani; Hauber, Ilona; Hauber, Joachim ...
Science (American Association for the Advancement of Science),
06/2007, Letnik:
316, Številka:
5833
Journal Article
Recenzirano
HIV-1 integrates into the host chromosome and persists as a provirus flanked by long terminal repeats (LTRs). To date, treatment regimens primarily target the virus enzymes or virus-cell fusion, but ...not the integrated provirus. We report here the substrate-linked protein evolution of a tailored recombinase that recognizes an asymmetric sequence within an HIV-1 LTR. This evolved recombinase efficiently excised integrated HIV proviral DNA from the genome of infected cells. Although a long way from use in the clinic, we speculate that this type of technology might be adapted in future antiretroviral therapies, among other possible uses.
Unfortunately, in the published paper entitled "Comprehensive profiling of functional attributes, virulence potential and evolutionary dynamics in mycobacterial secretomes" authored by Ayan Roy, ...Arnab Sen, Sourav Chakraborty and Indrani Sarkar, the surname of Sourav Chakraborty was inadvertently wrongly written as Sourav Chakrobarty in the original publication of the article. Name has been corrected in the correction article. We have also included ORCID ID.
Mitochondrial genome provides useful information about species concerning its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to ...sequence the complete mitogenome of Yellow-billed babbler (Turdoides affinis), a species endemic to Peninsular India and Sri Lanka. Both, reference-based and de-novo assemblies of mitogenome were performed and observed that de-novo assembled mitogenome was most appropriate. The complete mitogenome of yellow-billed babbler (assembled de-novo) was 17,672 bp in length with 53.2% AT composition. Thirteen protein-coding genes along with two rRNAs and 22 tRNAs were detected. The arrangement pattern of these genes was found conserved among Leiothrichidae family mitogenomes. Duplicated control regions were found in the newly sequenced mitogenome. Downstream bioinformatics analysis revealed the effect of translational efficiency and purifying selection pressure over thirteen protein-coding genes in yellow-billed babbler mitogenome. Ka/Ks analysis indicated the highest synonymous substitution rate in the nad6 gene. Evolutionary analysis revealed the conserved nature of all the protein-coding genes across Leiothrichidae family mitogenomes. Our limited phylogeny results placed T. affinis in a separate group, a sister group of Garrulax. Overall, our results provide a useful information for future studies on the evolutionary and adaptive mechanisms of birds belong to the Leiothrichidae family.
Psittacula cyanocephala is an endemic parakeet from the Indian sub-continent that is widespread in the illegal bird trade. Previous studies on Psittacula parakeets have highlighted taxonomic ...ambiguities, warranting studies to resolve the issues. Since the mitochondrial genome provides useful information concerning the species evolution and phylogenetics, we sequenced the complete mitogenome of P. cyanocephala using NGS, validated 38.86% of the mitogenome using Sanger Sequencing and compared it with other available whole mitogenomes of Psittacula. The complete mitogenome of the species was 16814 bp in length with 54.08% AT composition. P. cyanocephala mitogenome comprises of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. P. cyanocephala mitogenome organization was consistent with other Psittacula mitogenomes. Comparative codon usage analysis indicated the role of natural selection on Psittacula mitogenomes. Strong purifying selection pressure was observed maximum on nad1 and nad4l genes. The mitochondrial control region of all Psittacula species displayed the ancestral avian CR gene order. Phylogenetic analyses revealed the Psittacula genus as paraphyletic nature, containing at least 4 groups of species within the same genus, suggesting its taxonomic reconsideration. Our results provide useful information for developing forensic tests to control the illegal trade of the species and scientific basis for phylogenetic revision of the genus Psittacula.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Background
Eu is a lesser-known and traditional millet-based fermented brew of the Toto tribe from West Bengal, India. The starter culture used in this brew consists of diverse microflora. ...Identifying those microbes will not only help us gain a deeper understanding of the brew, but also quantify the impacts of this brew on the human system after consumption. Due to the progress in Illumina sequencing technology, the meta-profiling of 16S rRNA has emerged as a valuable resource for exploring the microbiome of any sample. We have utilised this tool (V3–V4 region) to study the microbiome population of Eu.
Results
The microbial diversity present in the brew was mainly constituted of probiotic and fermenting bacteria. The nutrient profiling of Eu estimated the amount of protein, carbohydrate, free amino acid, and free fatty acid. The nutritional substance present in the brew probably supports the growth of the probiotic microflora. Reverse ecology-based network analysis revealed considerable complementary interaction between humans and the microflora present in the Eu. GC–MS outlining enlisted thirteen potent compounds from Eu, and a comprehensive network pharmacological study on those compounds revealed the anti-cancerous properties of Eu, especially against gastrointestinal malignancy, by reducing the proliferation of malignant cells and forming pro-inflammatory cytokines.
Conclusions
The current study focuses on the meta-profiling and nutritional characteristics of Eu, which highlight the beverage’s potential as a probiotic health drink. Reverse ecology analysis demonstrated that the probiotic microflora competes strongly against pathogenic bacteria. Additionally, in silico network pharmacological research identified the drink as a potentially health-promoting and anti-cancer beverage.
Mycobacterium is an interesting genus which not only includes intimidating pathogens, associated with severe devastations globally, but also comprises of non-pathogenic eco-friendly members that ...detoxify environmental pollutants. Secretory proteins of the mycobacterial communities are essential components which are firmly believed to facilitate proper cross-talk and apt communication with host cellular surroundings and environmental niche. Secretory elements also play vital roles in mycobacterial pathogenesis. In the present endeavor, an extensive profiling of mycobacterial secretomes, considering both pathogenic and non-pathogenic members, has been executed. Thorough analysis on amino acid composition and functional behavior of the mycobacterial secretory proteins has also been performed. In-depth scrutiny of biosynthetic cost of the secretory proteins with respect to the non-secretory ones indicated that the genus
Mycobacterium
strictly follows the policy of cost-minimization among the sets of imperative secretory proteins. Comprehensive assessment of potential virulence among the key secretory components signified that the pathogenic mycobacterial members possess a larger share of potentially virulent secretory elements in comparison to their non-pathogenic counterparts. Present analysis also revealed contrasted evolutionary features of the secretomes wherein secretory proteins were found to evolve faster than non-secretory proteins in mycobacterial pathogens but not in the concerned non-pathogens. Outcomes of present investigation promise to provide novel insights into the enigma of mycobacterial pathogenesis, bioremediation and adaptation in diverse niche and aid further scientific investigations associated with concerned research area.
Endemic fermented vegetables play a crucial role in local cuisine and culture, with traditionally fermented raw green vegetables such as gundruk being a popular practice in North Bengal and Sikkim, ...India. However, there is a gap in the microbial profiling of these vegetables. This study aimed to explore the diversity of dominant bacterial populations in fermented leafy vegetables using both culture-dependent and culture-independent methods. In addition to isolating bacteria using conventional methods, we conducted phenotypic and biochemical characterization, community DNA isolation, and amplicon sequencing. We also introduced a new approach in bioinformatics analysis: reverse ecology, which analyzes complementation and competition among participant microbes. In conventional culture-dependent techniques, LAB genera such as Lactobacillus, Enterococcus, Leuconostoc, and Pediococcus have been identified as predominant consortia, whereas metagenomic analysis revealed that the microbiome of fermented dried leafy vegetables was mainly composed of Firmicutes, Proteobacteria, Actinobacteria, Bacteroides, and Planctomycetes at the phylum level. Within the Lactobacillaceae family, predominant types included Lactobacillus, Lactococcus, Pediococcus, Leuconostoc, Enterococcus, Vagococcus, Weissella, and Carnobacterium. The microbial metabolism revealed key pathways, such as carbon metabolism, glycolysis, gluconeogenesis, and glyoxylate. Aromatic amino acid degradation, fatty acid metabolism, amino sugar metabolism, nucleotide sugar metabolism, and biosynthesis of nucleotide sugar pathways were also active. The competition index among microbes and human metabolic data was low (0.32–0.44), indicating minimal competition for nutrition. Complementation indices between bacteria and humans were high (0.76–0.88), suggesting a beneficial impact of gundruk microbial populations on human health.
The actinorhizal symbiosis is a mutualistic relationship between an actinobacterium from the genus
Frankia
and a wide variety of dicotyledonous plants representing 8 different families of ...angiosperms. Molecular phylogenetic approaches have identified four major
Frankia
lineages that have distinctive plant host ranges. Since the first published three
Frankia
genomes, an effort was undertaken to provide full genomic databases covering all four well established
Frankia
lineages and to provide depth of the number of strains covered. Here, we report on the updated status of these sequencing efforts. At present, there are 25 complete or draft
Frankia
genomes that have been sequenced and annotated, and several others are now in the pipeline being sequenced. An overview of the
Frankia
genomes will be presented focusing on their general genomic properties including size of the pan- and core-gene pool, size relationship and genome plasticity. Furthermore, a description of biosynthetic potential and a discussion about genes (nitrogenase, hopanoid biosynthesis, truncated hemoglobin, hydrogenase uptake gene clusters) involved in the symbiosis will be discussed. The absence of common
nod
genes within these
Frankia
genomes provides clues about the host-microbe recognition process for the actinorhizal symbiosis
Monkeypox Virus (MPV) is the cause of zoonotic disease characterized by skin-eruption with pus cell formation and lymphadenopathy. This virus belongs to the Orthopoxvirus genus with DNA as its ...genetic material. Previously, this infection was reported from Africa and occasionally from USA and UK. However, recently there is a sudden surge of infection in non-epidemic countries and a new strain of MPVhas been discovered. Therefore it is important to revisit the phylogeny of MPV with the addition of new strains. Recently WHO also stressed the need of developing vaccines for new strains. In this scenario we have two objectives for this study -first, to reveal the exact phylogenetic position of the 2022 strain and second, to identify specific peptides which may be used for vaccine development in the future.
The phylogenetic analysis was done with the help of Bayesian phylogeny. The dN/dS calculation was performed based on DNA polymerase genes of selected MPV strains. The peptidyl-epitope was searched in MPV2022/2 SLO strain with the help of several algorithms implemented in Allergen FP v.1.0, NetMHCII 2.3, MHCpred and Toxin Pred. The structure prediction of the proteins and peptides was performed through Hpepdock. The quality of the structures was validated through the Ramachandran plot. The molecular dynamics and simulation were performed through Gromacs software. The interaction between peptide and protein was assessed through Ligplot software.
The phylogenetic analysis revealed that the considered 2022 MPVstrains were close to the USA strains. The evolutionary analysis showed the volatile nature of the genome. Moreover, 9-mer peptide sequence was identified as an epitope for vaccine development.
The emergence of more virulent strains in near future may not be ruled out. Immunocompromised patients are more susceptible to this virus hence sub-unit vaccine is a better choice than a recombinant or attenuated vaccine against monkeypox. We have identified a small stretch of specific peptide which may be used for developing a subunit vaccine against this virus.
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