Genome Wide Identification, Characterization and Evolutionary Analysis of T6SS in Burkholderia cenocepacia Strains

Pathogens of the Burkholderia genus are causing diseases in a diverse variety of hosts. After the discovery of T6SS, it was found to play a pivotal role in virulence and other pathogenicity factors in different pathogenic Burkholderia species. For this study, three strains of Burkholderia cenocepacia were selected from different ecological niches; J2315 from humans, MC0-3 from the rhizosphere of maize, and YG-3 from the Populus tree. The sequenced genomes were retrieved from PATRIC. It was found that B. cenocepacia J2315 and MC0-3 strains had only 1 cluster of T6SS in their genomes while the YG-3 strain had 3 clusters. The circular genomic map and phylogenetic tree suggested major differences in T6SS clusters 2 and 3 of the YG-3 strain from other clusters. From the results obtained in the study and reviewing the literature, it was concluded that all 3 strains harbor T6SS-1 type cluster that is involved in causing virulence in eukaryotic organisms and several bacterial species. This factor of causing virulence in the bacteria species might be helpful for B. cenocepacia strains J2315, MC0-3 and YG-3 in survival and niche adaptation

Somatic Cell Cycle Regulation By Histone H3 Modifications: Action of OGT and Kinases

Abstract.-Histone H3 is amongst the most evolutionarily conserved proteins, and is located along with histone 2A, 2B and 4 in the core of the nucleosome. The N-terminal tails of the histone protrude the chromatin structure and become accessible to various enzymes for post translational modifications (PTMs). Phosphorylation of H3 has been found to have an impact on progression of the cell cycle, especially during mitosis. Another equally abundant PTM is the glycosylation at serine/threonine by O-GlcNAc (O-linked glycosylation) that occurs on the same or neighboring Ser or Thr residues, which also are accessible to kinases (Yin Yang sites). O-GlcNAc is added by O-GlcNAc transferase (OGT), and is found exclusively in the nucleus or cytoplasm of the cell. By using computational methods like Netphos 2.0 and Yinoyang 1.2 we found that OGT, Aurora B kinase and OGT, Death-associated protein (DAP)-like kinase, work together in a Yin Yang way, and thereby control specific checkpoints during mitosis. Bioinformatics tool, thus, are very helpful to elucidate the function of the protein by predicting the PTMs in proteins

Fungal systematics and evolution : FUSE 6

Fungal Systematics and Evolution (FUSE) is one of the journal series to address the “fusion” between morphological data and molecular phylogenetic data and to describe new fungal taxa and interesting observations. This paper is the 6th contribution in the FUSE series—presenting one new genus, twelve new species, twelve new country records, and three new combinations. The new genus is: Pseudozeugandromyces (Laboulbeniomycetes, Laboulbeniales). The new species are: Albatrellopsis flettioides from Pakistan, Aureoboletus garciae from Mexico, Entomophila canadense from Canada, E. frigidum from Sweden, E. porphyroleucum from Vietnam, Erythrophylloporus flammans from Vietnam, Marasmiellus boreoorientalis from Kamchatka Peninsula in the Russian Far East, Marasmiellus longistipes from Pakistan, Pseudozeugandromyces tachypori on Tachyporus pusillus (Coleoptera, Staphylinidae) from Belgium, Robillarda sohagensis from Egypt, Trechispora hondurensis from Honduras, and Tricholoma kenanii from Turkey. The new records are: Arthrorhynchus eucampsipodae on Eucampsipoda africanum (Diptera, Nycteribiidae) from Rwanda and South Africa, and on Nycteribia vexata (Diptera, Nycteribiidae) from Bulgaria; A. nycteribiae on Eucampsipoda africanum from South Africa, on Penicillidia conspicua (Diptera, Nycteribiidae) from Bulgaria (the first undoubtful country record), and on Penicillidia pachymela from Tanzania; Calvatia lilacina from Pakistan; Entoloma shangdongense from Pakistan; Erysiphe quercicola on Ziziphus jujuba (Rosales, Rhamnaceae) and E. urticae on Urtica dioica (Rosales, Urticaceae) from Pakistan; Fanniomyces ceratophorus on Fannia canicularis (Diptera, Faniidae) from the Netherlands; Marasmiellus biformis and M. subnuda from Pakistan; Morchella anatolica from Turkey; Ophiocordyceps ditmarii on Vespula vulgaris (Hymenoptera, Vespidae) from Austria; and Parvacoccum pini on Pinus cembra (Pinales, Pinaceae) from Austria. The new combinations are: Appendiculina gregaria, A. scaptomyzae, and Marasmiellus rodhallii. Analysis of an LSU dataset of Arthrorhynchus including isolates of A. eucampsipodae from Eucampsipoda africanum and Nycteribia spp. hosts, revealed that this taxon is a complex of multiple species segregated by host genus. Analysis of an SSU–LSU dataset of Laboulbeniomycetes sequences revealed support for the recognition of four monophyletic genera within Stigmatomyces sensu lato: Appendiculina, Fanniomyces, Gloeandromyces, and Stigmatomyces sensu stricto. Finally, phylogenetic analyses of Rhytismataceae based on ITS–LSU ribosomal DNA resulted in a close relationship of Parvacoccum pini with Coccomyces strobi.http://www.sydowia.at/index.htmpm2021Medical Virolog

Mutational analysis and clinical investigations of medically diagnosed GSD 1a patients from Pakistan.

Glycogen storage disease type I (GSD I) is a rare autosomal recessive inborn error of carbohydrate metabolism caused by the defects of glucose-6-phosphatase complex (G6PC). Disease causing variants in the G6PC gene, located on chromosome 17q21 result in glycogen storage disease type Ia (GSD Ia). Age of onset of GSD Ia ranges from 0.5 to 25 years with presenting features including hemorrhage, hepatic, physical and blood related abnormalities. The overall goal of proposed study was clinical and genetic characterization of GSD Ia cases from Pakistani population. This study included forty GSD Ia cases presenting with heterogeneous clinical profile including hypoglycemia, hepatomegaly, lactic acidosis i.e., pH less than 7.2, hyperuricemia, seizures, epistaxis, hypertriglyceridemia (more than180 mg/dl) and sometimes short stature. All coding exons and intron-exon boundaries of G6PC gene were screened to identify pathogenic variant in 20 patients based on availability of DNA samples and willingness to participate in molecular analysis. Pathogenic variant analysis was done using PCR-Sanger sequencing method and pathogenic effect predictions for identified variants were carried out using PROVEAN, MutationTaster, Polyphen 2, HOPE, Varsome, CADD, DANN, SIFT and HSF software. Overall, 21 variants were detected including 8 novel disease causing variants i.e., G6PC (NM_000151.4):c.71A>C (p.Gln24Pro), c.109G>C(p.Ala37Pro), c.133G>C(p.Val45Leu), c.49_50insT c.205G>A(p.Asp69Asn), c.244C>A(p.Gln82Lys) c.322A>C(p.Thr108Pro) and c.322A>C(p.Cys284Tyr) in the screened regions of G6PC gene. Out of 13 identified polymorphisms, 3 were identified in heterozygous condition while 10 were found in homozygous condition. This study revealed clinical presentation of GSD Ia cases from Pakistan and identification of novel disease-causing sequence variants in coding region and intron-exon boundaries of G6PC gene

Band structure tuning of ZnO/CuO composites for enhanced photocatalytic activity

The toxic dye pigments, even in small quantities, can damage ecosystems. Removing organic, inorganic, and microbiological contaminants from wastewater via heterogeneous photocatalysis is a promising method. Herein, we report the band structure tuning of ZnO/CuO nanocomposites to enhance photocatalytic activity. The nanocomposites were synthesized by a chemical approach using step-wise implantation of p-type semiconductor CuO to n-type semiconductor ZnO. Various characterization techniques such as X-ray diffraction analysis (XRD), field emission scanning electron microscopy (FESEM), energy dispersive X-ray analysis (EDX) and UV spectroscopy were used to investigate the crystal structure, surface morphology, elemental composition and optical properties of the synthesized samples. As the CuO content increased from 10% to 50% in ZnO/CuO nanocomposites, the optical bandgap decreased from 3.36 to 2.14 eV. The photocatalytic activity of the samples was evaluated against the degradation of methylene blue (MB) under visible irradiation. Our study demonstrates a novel p–n junction oxide photocatalyst based on wt. 10% CuO/ZnO with superior photocatalytic activity. Effectively 66.6% increase in degradation rate was achieved for wt. 10% CuO/ZnO nanocomposite compared to pure ZnO nanoparticles

Consensus Sequences as Targets for Phosphorylation of Amino Acids in Phosphoproteins: Statistical Computing Analysis

Abstract.-Phosphorylation is a post-translational modification (PTM) of a protein on hydroxyl function of Ser/Thr/Tyr (O-linked phosphorylation) or on amino function of His (N-linked phosphorylation) by a phosphate group utilising a specific kinase. Post translational modification has effect on protein conformation and as a consequence results in alteration of protein's function. Present study analyzes the putative target sequence of O-phosphorylation of Ser, Thr and Tyr. The objective is to evaluate the preferential pattern of amino acids on both (right and left) sides of O-phosphorylated amino acid. Calculation of frequency of occurrence of each amino acid around O-linked phosphorylated amino acid residue followed by deviation parameter will serve as the source to define preferential behaviour of each amino acid to develop possible consensus prerequisite pattern for O-linked phosphorylation. These patterns will provide with means to predict phosphorylation potential of proteins and its multifunctional nature based on dynamic and reversible phosphorylation at specific sites

Fungal Systematics and Evolution: FUSE 6

With only 138,000 formally described fungal species (Kirk 2019) out of an estimated 2.2–3.8 million (Hawksworth & Lücking 2017) to 6 million (Taylor et al. 2014), between 97.7 and 93.7% of fungal species are left to be characterized. These may be discovered in poorly studied habitats and geographic areas (e.g., tropical rainforests), as molecular novelties, within cryptic taxa, in fungal collections (e.g., new species hidden under current names and in unidentified material), and during studies of plant and insect collections (Hawksworth & Lücking 2017, Wijayawardene et al. 2020). This large discrepancy between described and undescribed species needs to be addressed and recent work has shown that mycologists are nowhere near levelling off the curve in describing new species (Hyde et al. 2020b). Together with other series—Fungal Biodiversity Profiles (Rossi et al. 2020), Fungal Diversity Notes (Hyde et al. 2020a), Fungal Planet (Crous et al. 2020a), Mycosphere Notes (Pem et al. 2019), New and Interesting Fungi (Crous et al. 2020b)—the Fungal Systematics and Evolution series published by Sydowia contributes to a much-needed acceleration of discovery and description of fungal diversity. The present paper is the sixth contribution in the FUSE series published by Sydowia, after Crous et al. (2015), Hernández-Restrepo et al. (2016), KrisaiGreilhuber et al. (2017), Liu et al. (2018), and Song et al. (2019). Altogether, one family, six genera, 67 species, and 22 combinations have been introduced in the FUSE series.publishedVersio