Norovirus Structure and Classification

Norovirus are a major cause of acute gastroenteritis worldwide. Diarrheal disease is now the fourth common cause of mortality children under the age of 5 years but remain the 2nd most cause of morbidity. NoV are associated with 18% diarrheal diseases worldwide where rotavirus vaccinations has been successfully introduced. NoV has become major cause of gastroenteritis in children. NoV belong to family caliciviridae. They are non-enveloped, single stranded positive sense RNA Viruses. The genome consists of 3 Open reading frames, ORF-1 codes for non-structural protein, ORF-2 codes for major capsid protein VP1 and ORF-3 for minor capsid protein VP2. Based on sequence difference of the capsid gene (VP1), NoV have been classified in to seven genogroup GI-GVII with over 30 genotypes. Genogroups I, II, IV are associated with human infection. Despite this extensive diversity a single genotype GII.4 has been alone to be the more prevalent. Basic epidemiological disease burden data are generated from developing countries. NoV are considered fast evolving viruses and present an extensive diversity that is driven by acquisition of point mutations and recombinations. Immunity is strain or genotype specific with little or no protection conferred across genogroups. Majority of outbreaks and sporadic norovirus cases worldwide are associated with a single genotype, GII.4 which was responsible for 62% of reported NoV outbreaks in 5 continents from 2001 to 2007. GII.4 variants have been reported as major cause of global gastroenteritis pandemics starting in 1995 frequent emergence of novel GII.4 variants is known to be due to rapid evolution and antigenic variation in response to herd immunity. Novel GII.4 variants appear almost every 2 years. Recent GII.4 variant reported include Lordsdale 1996, Farmington Hills 2002, Hunter 2004, Yerseke 2006a, Den Haag 2006b, Apeldoon 2007, New Orleans 2009,most recently Sydney 2012. Detailed molecular epidemiologic investigation of NoV is associated for understanding the genetic diversity of NoV strain and emergence of novel NoV variants. However, reports have revealed that not all individuals develop symptoms and a significant proportion remains asymptomatic after NoV infections.

Phylogeny of Graphostromatacea with Three Species Isolated in China

Three species possessing characteristics of Graphostromataceae were observed in China. Morphology of the described species with illustrations and their phylogeny based on regions of internal transcribed spacers (ITS), the second largest subunit of the RNA polymerase II (RPB2), β-tubulin (TUB2) and α-actin (ACT) are provided. Two new species and one new record from China were identified. Morphologically, Biscogniauxia glaucae sp. nov. differs from B. atropunctata var. maritima, B. citriformis var. macrospora, B. fuscella and B. mediterranea by its stromata with raised margins, with clear outlines, with punctate ostioles openings and ascospores which are equilateral with broadly rounded ends, with a straight germ slit on the more concave side, nearly full spore length, lacking appendages and sheathes. ITS sequence difference between Graphostroma guizhouensis sp. nov and type strain of G. platystomum is 7%, which support identifying it as a new species. Camillea broomeana with scanning electron microscope description of ascospores was illustrated as a new record from China. Cryptostroma was proposed in Graphostromataceae based on molecular data. Vivantia was accepted in Graphostromataceae based on its morphological characteristics and Nodulisporiurn anamorphs which is similar with that of Biscogniauxia.

Poorly Expressed Alleles of Several Human Immunoglobulin Heavy Chain Variable Genes are Common in the Human Population

Extensive diversity has been identified in the human heavy chain immunoglobulin locus, including allelic variation, gene duplication, and insertion/deletion events. Several genes have been suggested to be deleted in many haplotypes. Such findings have commonly been based on inference of the germline repertoire from data sets covering antibody heavy chain encoding transcripts. The inference process operates under conditions that may limit identification of genes transcribed at low levels. The presence of rare transcripts that would indicate the existence of poorly expressed alleles in haplotypes that otherwise appear to have deleted these genes has been assessed in the present study. Alleles IGHV1-2*05, IGHV1-3*02, IGHV4-4*01, and IGHV7-4-1*01 were all identified as being expressed from multiple haplotypes, but only at low levels, haplotypes that by inference often appeared not to express these genes at all. These genes are thus not as commonly deleted as previously thought. An assessment of the 5’ untranslated region (up to and including the TATA-box), the signal peptide-encoding part of the gene, and the 3’-heptamer suggests that the alleles have no or minimal sequence difference in these regions in comparison to highly expressed alleles. This suggest that they may be able to participate in immunoglobulin gene rearrangement, transcription and translation. However, all four poorly expressed alleles harbor unusual sequence variants within their coding region that may compromise the functionality of the encoded products, thereby limiting their incorporation into the immunoglobulin repertoire. Transcripts based on IGHV7-4-1*01 that had undergone somatic hypermutation and class switch had mutated the codon that encoded the unusual residue in framework region 3 (cysteine 92; located far from the antigen binding site). This finding further supports the poor compatibility of this unusual residue in a fully functional protein product. Indications of a linkage disequilibrium were identified as IGHV1-2*05 and IGHV4-4*01 co-localized to the same haplotypes. Furthermore, transcripts of two of the poorly expressed alleles (IGHV1-3*02 and IGHV4-4*01) mostly do not encode in-frame, functional products, suggesting that these alleles might be essentially non-functional. It is proposed that the functionality status of immunoglobulin genes should also include assessment of their ability to encode functional protein products.

Plastome Structure and Phylogenetic Relationships of Styracaceae (Ericales)

Background: The Styracaceae are a woody, dicotyledonous family containing 12 genera and an estimated 160 species. Recent studies have shown that Styrax and Sinojackia are monophyletic, Alniphyllum and Bruinsmia cluster into a clade with an approximately 20-kb inversion in the Large Single-Copy (LSC) region. Halesia and Pterostyrax are not supported as monophyletic, while Melliodendron and Changiostyrax always form sister clades . Perkinsiodendron and Changiostyrax were newly established genera of Styracaceae. However, the phylogenetic relationship of Styracaceae at the genera level needs further research.Results: We collected 28 complete plastomes of Styracaceae, including 12 sequences newly reported here and 16 publicly available complete plastome sequences, comprising 11 of the 12 genera of Styracaceae. All species possessed the typical quadripartite structure of angiosperm plastomes, and the sequence difference is small, except for the large 20-kb (14 genes) inversion region found in Alniphyllum and Bruinsmia. Seven coding sequences (rps4, rpl23, accD, rpoC1, psaA, rpoA and ndhH) were identified to possess positively selected sites. Phylogenetic reconstructions based on seven data sets (i.e., LSC, SSC, IR, Coding, Non-coding, combination of LSC+SSC and concatenation of LSC+SSC+one IR) produced similar topologies. In our analyses, all genera were strongly supported as monophyletic. Styrax was sister to the remaining genera. Alniphyllum and Bruinsmia form a clade. Halesia diptera does not cluster with Perkinsiodendron, while Perkinsiodendron and Rehderodendron form a clade. Changiostyrax is sister to a clade of Pterostyrax and Sinojackia,Conclusion: Our results clearly indicate that Pterostyrax is monophyletic, and the establishment of Perkinsiodendron and Changiostyrax are supported. A 20-kb reverse sequence was also found in the newly published sequence of Alniphyllum fortunei, which confirmed the existence of large inversion sequence in Alniphyllum and Bruinsmia.

Investigation of data mining technique and artificial intelligence algorithm in microflora bioinformatics

Bioinformatics has gradually received widespread attention and has shown the characteristics of a large amount of calculation and high complexity. Therefore, it is required to adopt computer algorithms in bioinformatics to improve the efficiency of bioinformatics processing problems. Big data and artificial intelligence technologies have the characteristics of supporting bioinformatics and have achieved certain results in the field of bioinformatics. Introduced the application basis of big data and artificial intelligence in bioinformatics, analyzed data collection, preprocessing, data storage and management, data analysis, and mining technology. Furthermore, typical applications in bioinformatics are discussed in terms of gene expression data analysis, genome sequence information analysis, biological sequence difference and similarity analysis, genetic data analysis, and protein structure and function prediction. Finally, the bottlenecks and challenges in the application of big data and artificial intelligence in bioinformatics are discussed, and the application prospects of related technologies in bioinformatics have prospected.

Plastome Structure and Phylogenetic Relationships of Styracaceae (Ericales)

Background: The Styracaceae are a woody, dicotyledonous family containing 12 genera and an estimated 160 species. Recent studies have shown that Styrax is monophyletic, Alniphyllum and Bruinsmia cluster into a clade with an approximately 20-kb inversion in the LSC. Halesia and Pterostyrax are not supported as monophyletic, while Melliodendron and Changiostyrax always from a clade sister to the rest of the family. However, the phylogenetic relationship of Styracaceae at the level of genera remains ambiguous. Results: We collected 28 complete plastomes of Styracaceae, including 12 sequences newly reported here and 16 publicly available complete plastome sequences, comprising 11 of the 12 genera of Styracaceae. All species possessed the typical quadripartite structure of angiosperm plastomes, and the sequence difference is small, except for the large 20-kb (14 genes) inversion region found in Alniphyllum and Bruinsmia . Seven coding sequences ( rps4 , rpl23 , accD , rpoC1 , psaA , rpoA and ndhH ) were identified to possess positively selected sites. Phylogenetic reconstructions based on seven data sets (i.e., LSC, SSC, IR, Coding, Non-coding, combination of LSC+SSC and concatenation of LSC+SSC+one IR) produced similar topologies and most relationships are consistent with previous findings. In our study, Pterostyrax was strongly supported as monophyletic; Melliodendron and Changiostyrax as successively sister to the rest of the family. Conclusion: Our results clearly indicate that Pterostyrax is monophyletic, and the establishment of Perkinsiodendron and Changiostyrax are supported. A 20-kb reverse sequence was found in the newly published sequence of Alniphyllum fortunei , which confirmed the existence of large inversion sequence in Alniphyllum and Bruinsmia .

Comparative chloroplast genomes of the tea plants and the implications for the different origins of the two Assam teas

Background Tea plants belong to the genus Camellia, whose species are taxonomically complex due to frequent hybridization and polyploidy nature. The genetic genealogy of Camellia has always been a focus of botanical and ecological research, including a debate about whether Assam tea has two different domestication origins (Chinese Assam type and Indian Assam type). The chloroplast genome resources were able to provide useful data for the analysis of the plastome evolutionary relationship and species classification. Here, we determined the first chloroplast genome of the natural triploid tea plant (Camellia sinensis cv. Wuyi Narcissus) and conducted the genome comparison with Chinese type tea (Camellia sinensis var. sinensis), Chinese Assam type tea (Camellia sinensis var. assamica) and Indian Assam type tea (Camellia assamica) to improve our understanding of the evolutionary mechanism and the taxonomic classification of Camellia. Results This study presented detailed sequences and structural variations of chloroplast genomes of four tea plants. The chloroplast genome of the natural triploid tea showed no obvious sequence difference from that of other two types of Chinese teas, while that of Chinese tea and Indian tea was significant sequence difference. The natural selection probably dominated in shaping the codon bias of the chloroplast genome in tea plant, and the codon usage distribution of genome in Indian tea was obviously different from that in Chinese tea. The phylogenetic status of Chinese and Indian Assam teas was in the different branches of the tea plant. Phylogenetic tree clustering was not consistent with the current some taxonomy of Camellia. Conclusions The sequence variation of the chloroplast genome of tea plant was mainly ascribed to the expansion and contraction of the border regions (IR/ SC), which were mainly due to the sequence repeat and indel mutation events of the genome. The codon usage pattern and phylogenetic analysis supported Chinese Assam type and Indian Assam type tea might have different domestication origins and suggested the current some taxonomy of Camellia might need revision.

A terminal α3-galactose modification regulates an E3 ubiquitin ligase subunit in Toxoplasma gondii

Skp1, a subunit of E3 Skp1/Cullin-1/F-box protein ubiquitin ligases, is modified by a prolyl hydroxylase that mediates O2 regulation of the social amoeba Dictyostelium and the parasite Toxoplasma gondii. The full effect of hydroxylation requires modification of the hydroxyproline by a pentasaccharide that, in Dictyostelium, influences Skp1 structure to favor assembly of Skp1/F-box protein subcomplexes. In Toxoplasma, the presence of a contrasting penultimate sugar assembled by a different glycosyltransferase enables testing of the conformational control model. To define the final sugar and its linkage, here we identified the glycosyltransferase that completes the glycan and found that it is closely related to glycogenin, an enzyme that may prime glycogen synthesis in yeast and animals. However, the Toxoplasma enzyme catalyzes formation of a Galα1,3Glcα linkage rather than the Glcα1,4Glcα linkage formed by glycogenin. Kinetic and crystallographic experiments showed that the glycosyltransferase Gat1 is specific for Skp1 in Toxoplasma and also in another protist, the crop pathogen Pythium ultimum. The fifth sugar is important for glycan function as indicated by the slow-growth phenotype of gat1Δ parasites. Computational analyses indicated that, despite the sequence difference, the Toxoplasma glycan still assumes an ordered conformation that controls Skp1 structure and revealed the importance of nonpolar packing interactions of the fifth sugar. The substitution of glycosyltransferases in Toxoplasma and Pythium by an unrelated bifunctional enzyme that assembles a distinct but structurally compatible glycan in Dictyostelium is a remarkable case of convergent evolution, which emphasizes the importance of the terminal α-galactose and establishes the phylogenetic breadth of Skp1 glycoregulation.