Phylo-geo-network and haplogroup analysis of 611 novel coronavirus (SARS-CoV-2) genomes from India

The novel coronavirus (SARS-CoV-2) from Wuhan China discovered in December 2019 has since developed into a global epidemic. Presently, we constructed and analyzed the phylo-geo-network of SARS-CoV-2 genomes from across India to understand the viral evolution in the country. A total of 611 full-length genomes from different states of India were extracted from the EpiCov repository of GISAID initiative on 6 June, 2020. Their alignment with the reference sequence (Wuhan, NCBI accession number NC_045512.2) uncovered 270 parsimony informative sites. Furthermore, 339 genomes were divided into 51 haplogroups. The network revealed the core haplogroup as that of reference sequence NC_045512.2 (Haplogroup A1) with 157 identical sequences present across 16 states. Remaining haplogroups had <10 identical sequences across a maximum of three states. Some states with fewer samples had more haplogroups. Forty-one haplogroups were localized exclusively to any one state. The two most common lineages are B6 and B1 (Pangolin) whereas clade A2a (Covidex) appears to be the most predominant in India. Because the pandemic is still emerging, the observations need to be monitored.

Whole-Genome Sequence of an Indian Group A Streptococcus emm Type 1-2 Strain Isolated from a Blood Sample in North India

Group A Streptococcus emm type 1-2 is more prevalent than emm type 1 in India. Only partial information is available about the genetic characteristics of this type. Here, genome sequencing of emm type 1-2 strain 1085 (from blood) was conducted. A contig 2,010,300 bp long, with a total of 1,877 annotated proteins, was obtained (NCBI accession number CP047120, assembly accession number ASM983284v1).

Genome Sequence of “Candidatus Rickettsia colombianensi,” a Novel Tick-Associated Bacterium Distributed in Colombia

This is the first report of the genome sequence of “Candidatus Rickettsia colombianensi” strain Adcor 2, deposited in DDBJ/ENA/GenBank under the accession number RAQN00000000. The draft genome showed 36.01% similarity with that of Rickettsia monacensis strain IrR/Munich (NCBI accession number LN794217), 37.81% similarity with that of Rickettsia heilongjiangensis 054 (NCBI accession number CP002912), and 43.88% similarity with that of Rickettsia tamurae AT-1 (NCBI accession number CCMG01000001).

In Silico Analysis of Bioactive Peptides Released from Giant Grouper (Epinephelus lanceolatus) Roe Proteins Identified by Proteomics Approach

Major proteins contained in dried giant grouper roe (GR) such as vitellogenin (from Epinephelus coioides; NCBI accession number: AAW29031.1), apolipoprotein A-1 precursor (from Epinephelus coioides; NCBI accession number: ACI01807.1) and apolipoprotein E (from Epinephelus bruneus; NCBI accession number: AEB31283.1) were characterized through compiled proteomics techniques (SDS-PAGE, in-gel digestion, mass spectrometry and on-line Mascot database analysis). These proteins were subjected to in silico analysis using BLAST and BIOPEP-UWM database. Sequence similarity search by BLAST revealed that the aligned vitellogenin sequences from Epinephelus coioides and Epinephelus lanceolatus share 70% identity, which indicates that the sequence sample has significant similarity with proteins in sequence databases. Moreover, prediction of potential bioactivities through BIOPEP-UWM database resulted in high numbers of peptides predominantly with dipeptidyl peptidase-IV (DPP-IV) and angiotensin-I-converting enzyme (ACE-I) inhibitory activities. Pepsin (pH > 2) was predicted to be the most promising enzyme for the production of bioactive peptides from GR protein, which theoretically released 82 DPP-IV inhibitory peptides and 47 ACE-I inhibitory peptides. Overall, this work highlighted the potentiality of giant grouper roe as raw material for the generation of pharmaceutical products. Furthermore, the application of proteomics and in silico techniques provided rapid identification of proteins and useful prediction of its potential bioactivities.

Identification of Glucoamylase cDNA Sequence of Saccharomycopsis (Syn. Endomycopsis) bubodii 2066

Saccharomycopsis (Syn. Endomycopsis) bubodii 2066 is an isolate from bubod, a starter used in making rice wine in northern Philippines. We have shown that the yeast has amylolytic activity on raw sago starch. In our attempt to identify the putative raw starch-digesting amylase in S. bubodii, we determined the cDNA sequence of a glucoamylase gene. One primer pair that was designed based on a glucoamylase of Saccharomycopsis fibuligera HUT7212 (GLU1, NCBI Accession Number L25641.1) produced a sequence of 1234 base pairs. To obtain a wider coverage, a primer walking strategy was carried out using four primer pairs designed based on GLU1 gene. The generated sequence of 1535 base pairs shows 98.7 to 100% homology when aligned with glucoamylase genes from four strains of S. fibuligera suggesting that this glucoamylase is highly conserved between the Saccharomycopsis species. This work further reports a gene sequence of glucoamylase derived from Philippine-isolated yeast. The sequence is deposited in GenBank and assigned the accession number KP068007.1. The gene may be heterologously expressed in Saccharomyces cerevisiae for possible utilization in the direct conversion of raw sago starch to bioethanol.

An Optimization to Protein Coding Regions Identification in Eukaryotes

Significant improvement in coding regions identification was observed over many real datasets, which were obtained from the national center for bioinformatics. Quantitatively, the authors monitored a gain of 80.5% in coding identification with the Complex method, 42.5% with the Binary method, and 15% with the EIIP indicator sequence method over Mus Musculus Domesticus (House rat), NCBI Accession number: NC_006914, Length of gene: 7700 bp with number of coding regions: 4. Continuous improvement in significance with dyadic wavelet transforms will be observed as a future expectation.

Identification and Diagnostic Utility of Leishmania infantum Proteins Found in Urine Samples from Patients with Visceral Leishmaniasis

ABSTRACTDespite the clear need to control visceral leishmaniasis (VL), the existing diagnostic tests have serious shortcomings. Here, we introduce an innovative approach to directly identifyLeishmania infantumantigens producedin vivoin humans with VL. We combined reverse-phase high-performance liquid chromatography (RP-HPLC) with mass spectrometry and categorized three distinctL. infantumproteins presumably produced in bone marrow/spleen/liver and excreted in the urine of patients with VL. The genes coding for these proteins (L. infantumiron superoxide dismutase, NCBI accession numberXP_001467866.1;L. infantumtryparedoxin, NCBI accession numberXP_001466642.1; andL. infantumnuclear transport factor 2, NCBI accession numberXP_001463738.1) were cloned, and the recombinant molecules were produced inEscherichia coli. Antibodies to these proteins were produced in rabbits and chickens and were used to develop a capture enzyme-linked immunosorbent assay (ELISA) designed to detect theseL. infantumantigens in the urine of VL patients. Specificity of the antibodies was confirmed by a Western blot analysis using both recombinant proteins and whole parasite extract. Importantly, a urinary antigen detection assay assembled with pairs of antibodies specific for each of these antigens identified 17 of 19 patients with VL. These results indicate that an improved antigen detection assay based onL. infantumproteins present in the urine of patients with VL may represent an important new strategy for the development of a specific and accurate diagnostic test that has the potential to both distinguish active VL from asymptomatic infection and serve as an important tool to monitor therapy efficacy.

An Optimization to Protein Coding Regions Identification in Eukaryotes

Significant improvement in coding regions identification was observed over many real datasets, which were obtained from the national center for bioinformatics. Quantitatively, the authors monitored a gain of 80.5% in coding identification with the Complex method, 42.5% with the Binary method, and 15% with the EIIP indicator sequence method over Mus Musculus Domesticus (House rat), NCBI Accession number: NC_006914, Length of gene: 7700 bp with number of coding regions: 4. Continuous improvement in significance with dyadic wavelet transforms will be observed as a future expectation.

USE OF 16S rRNA GENE FOR CHARACTERIZATION OF PHOSPHATE-SOLUBILIZING BACTERIA ASSOCIATED WITH CORN

Thirty-six strains of phosphate-solubilizing bacteria (PSB) isolated from the rhizosphere and rhizoplane of corn (Zea mays L.) crops in different states of México were subjected to phenotypic and genotypic characterization. The phosphate-solubilizing activity of each strain was first evaluated using tricalcium phosphate as the phosphorus source in the NBRIP-BPB culture medium. Phosphatesolubilizing capacity was also evaluated by adding the pH buffering agent MES (2-[Morpholine] ethanosulfonic acid) to the growth medium. Amplified ribosomal RNA restriction pattern analysis (ARDRA) was used to evaluate the genetic diversity. From the data matrix obtained, a dendrogram was built using the UPGMA method. The 16S rRNA gene of the BUAP29, BUAP36 and CP08 strains was amplified, cloned and sequenced for taxonomic identification. The 36 bacterial strains exhibited different levels of tricalcium phosphate solubilizing activity. Only BUAP33, BUAP17 and BUAP21 strains did not show the typical solubilization halo when the MES buffering agent was added to the growth medium. The analysis of ARDRA patterns as well as the dendrogram exhibited a large genetic diversity among the 36 PSB analyzed, with BUAP36 and BUAP15 strains showing 100 % similarity. The 16S rRNA gene sequence alignment of CP08, BUAP29 and BUAP36 strains showed 99 % identity with the sequences of Advenella incenata strain R-16599 (NCBI accession number AY569458.1), Burkholderia sp (NCBI accession number AY353696) and Burkholderia gladioli strain 223-1 (NCBI accession number DQ355168.1), respectively. In this study the A. incenata strain is reported as a PSB for the first time.