NCBI Accession Number Research Articles

Isolation and optimization of a novel thraustochytrid strain for DHA rich and astaxanthin comprising biomass as aquafeed supplement.

A marine organism, belonging to the Thraustochytrids family was isolated from mangroves of Mumbai, India. The isolated strain was identified asAurantiochytrium limacinum by internal transcribed spacer sequence analysis.Optimization of process parameters yielded 14.47g/L dry cell weight containing 55-58% oil in 3.5days' cultivation on glucose, yeast extract, and peptone in the bioreactor. Docosahexaenoic acid (DHA) was found to be the dominant long-chain polyunsaturated fatty acid, accounting for 32-35% of total fatty acid content. The process parameter was tweaked to simultaneously synthesize astaxanthin along with DHA. The concurrent synthesis of DHA and astaxanthin-containing biomass establishes the isolated strain as a perfect choice for aquafeed. Accession number: NCBI accession number MN046792.

A single dose of a virulent bacteriophage vB PaeP-SaPL, rescues bacteremic mice infected with multi drug resistant Pseudomonas aeruginosa

Multidrug resistant bacterial infections are difficult to treat and contribute to high morbidity and mortality. The phage vB PaeP-SaPL was isolated from a sewage drain (Lahore, Pakistan) against Pseudomonas aeruginosa PA-1 (NCBI Accession number MG763232). SaPL produced circular, transparent plaques, 4−5 mm in diameter and showed broad host range infecting 57 % of tested MDR P. aeruginosa clinical isolates (N = 38), while no infectivity was observed against any tested strains of other genera.SaPL inhibited PA-1 growth until 24 h post infection at MOI of 1. The SaPL showed stability at varying temperature and pH, with optimum stability at pH 7 and 45 °C. The latent period of SaPL was 20 min with burst size of 155 virions. The genome of SaPL was double stranded DNA of 45,796 bps having 63 CDS (13 for known proteins and 50 for hypothetical proteins) with a GC content of 52 %. The termini analysis revealed that SaPL genome ends are redundant and permuted. The packaging strategy used by SaPL was a headful (pac) strategy like P1 phage. Survivability of PA-1 challenged mice, treated with SaPL (100 %) was statistically significant (P < 0.05) than in untreated challenged mice (0%). Based on its efficacy in reducing bacterial growth, selective infectivity against majority of P. aeruginosa strains and its ability to increase survivability in PA-1 challenged mice, SaPL is proposed to be a potential candidate for bacteriophage therapy against difficult to treat MDR P. aeruginosa infections.

Association of polymorphic variant of exons 6 and 11 of lactoferrin gene with mastitis in Murrah buffalo

Lactoferrin is one of the important candidate genes for mastitis resistance in dairy animals. The gene is located on Bos taurus autosome (BTA) 22 and consists of 17 exons spanning over 34.5 kb of genomic DNA. The present study was undertaken to identify allelic variant in exons 6 and 11 of lactoferrin gene and to analyze association with incidence of clinical mastitis in Murrah buffalo. The amplification of exons 6 and 11 of lactoferrin gene yielded 301 and 131 bp amplicon size. Comparison of nucleotide sequence of exonic region of lactoferrin gene with Bos taurus (NCBI accession number AC_000179.1) revealed 6 mutations; among them 3 were in coding DNA sequence and remaining 3 were in flanking intronic region. All these mutations were found in exon 6 and synonymous in nature without affecting the sequence of amino acid. PCR-restriction fragment length polymorphism (RFLP) analysis of 301 bp amplicon using FokI restriction enzyme exhibited polymorphic pattern with two genotypes (AA and AB) with respective frequency of 0.625 and 0.375. The frequencies of two alleles, A and B were estimated as 0.81 and 0.19 respectively. RE Hpy188I and HinfI used for digestion of exon 11 had exhibited monomorphic pattern. The chi-square (χ2) analysis revealed significant association between incidence of clinical mastitis and genetic variant of exon 6 and animals with AA genotype were found to be less susceptible to mastitis. The findings indicate potential scope for incorporation of lactoferrin gene in selection and breeding of Murrah buffaloes for improved genetic resistance to mastitis.

EFFECT OF TEMPERATURE AND PH ON PHENOL BIODEGRADATION BY A NEWLY IDENTIFIED SERRATIA SP. AQ5-03

Phenol is mainly used by the industries to produce a variety of chemical products such as resins, textiles, pesticides, plastics and explosive. The wide use of phenol and other phenolic compounds by industries, has resulted in an increased presence of these toxic compounds in the environment as pollutants. Bio-removal of phenol by microorganisms especially bacteria has been demonstrated to be the most effective and economical approach compared to physio-chemical methods. The search for efficient phenol-degraders especially local sources to remediate local phenol pollution is important as indigenous bacteria usually have better survival and resilient to local geographical conditions. In this study, a phenol-degrading microorganism was isolated from local soil and waste water bodies. Identification was carried out using gram staining, 16s rRNA gene sequencing and molecular phylogeny analysis using the Phylip software. The isolates were inoculated in mineral salt media with 0.5 g/L phenol as the sole source of carbon. Phenol degradation was determined using 4-amino antipyrine method. Physical and cultural conditions influencing phenol degradation such as pH and temperature were optimized via one-factor-at-a-time. Through phylogeny analysis, the isolate was identified as Serratia sp. and the sequence was deposited the NCBI Genebank and accession number KT693287 was assigned to the bacteria. The highest degradation was achieved at pH 7.5 (phosphate buffer) and temperature of 30°C. Ammonium sulphate was established to be the best nitrogen source at the concentration of 0.4 g/L and a sodium chloride concentration of 0.15 g/L.&#x0D; Aisami, A. | Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, Selangor, Malaysia

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).

Expression ChiPut-II gene from Serratia plymuthica UBCR_12

Putative chitinase II gene [ChiPut-II] was isolated from rhizosphere bacteria strain UBCR_12 [NCBI accession number KX863673]. The ChiPut-II gene encodes chitinase enzyme which has the ability as a bio fungicide. Expression of the gene could be identified in the extracellular as well as in the intracellular of the host cell. The chitinolytic ability of the ChiPut-II enzyme effectively works on 3% colloidal chitin exhibiting specific activity up to 1.235 U/μg. The inhibition capacity of the ChiPut-II enzyme extracted from intracellular against Colletotrichum gloeosporioides is 15.59%. It’s chitinolytic and inhibition activity indicated the bacteria to be developed as a bio fungicide.

Development of Staphylococcus Enzybiotics: The Ph28 Gene of Staphylococcus epidermidis Phage PH15 Is a Two-Domain Endolysin.

Given the worldwide increase in antibiotic resistant bacteria, bacteriophage derived endolysins represent a very promising new alternative class of antibacterials in the fight against infectious diseases. Endolysins are able to degrade the prokaryotic cell wall, and therefore have potential to be exploited for biotechnological and medical purposes. Staphylococcus epidermidis is a Gram-positive multidrug-resistant (MDR) bacterium of human skin. It is a health concern as it is involved in nosocomial infections. Genome-based screening approach of the complete genome of Staphylococcus virus PH15 allowed the identification of an endolysin gene (Ph28; NCBI accession number: YP_950690). Bioinformatics analysis of the Ph28 protein predicted that it is a two-domain enzyme composed by a CHAP (22-112) and MurNAc-LAA (171-349) domain. Phylogenetic analysis and molecular modelling studies revealed the structural and evolutionary features of both domains. The MurNAc-LAA domain was cloned, and expressed in E. coli BL21 (DE3). In turbidity reduction assays, the recombinant enzyme can lyse more efficiently untreated S. epidermidis cells, compared to other Staphylococcus strains, suggesting enhanced specificity for S. epidermidis. These results suggest that the MurNAc-LAA domain from Ph28 endolysin may represent a promising new enzybiotic.

Bacterial-mediated synthesis of silver nanoparticles and their significant effect against pathogens.

Silver nanoparticles are potent antimicrobials and could be used as a promising alternative of conventional antibiotics. The aim of this study was to isolate bacteria from soil that have ability to produce AgNPs by secondary metabolite activity and their elucidation against human pathogens. These strains Escherichia coli, Exiguobacterium aurantiacumm, and Brevundimonas diminuta with NCBI accession number MF754138, MF754139, and MF754140 respectively were grown for secondary metabolite production. The nanoparticles were confirmed and characterized by UV-Vis spectroscopy and transmission electron microscopy. The optimization study was also carried out to obtain the maximum production of silver nanoparticles. Three parameters, temperature, pH, and AgNO3 concentration, were used to optimize the production of silver nanoparticles. Antimicrobial potential of these nanoparticles was addressed on the Muller-Hinton Agar, and their zones of inhibitions were measured. TEM analysis revealed the size and shape of the silver nanoparticles. All types of AgNPs were spherical in shape; their size range is from 5 to 50nm. The findings of optimization study showed the maximum production of silver nanoparticles at the pH9, temperature 37°C, and 1mM AgNO3 concentration. All the strains exhibited the great potential as antimicrobial agents against MRSA and several other MDR bacteria with minimum 10mm to maximum 28mm zone of inhibition. It was concluded that the present study is an eco-friendly approach for the synthesis of AgNPs that will be beneficial to control the nosocomial infections triggered by MRSA and other human pathogens.

Novel marine Nocardiopsis dassonvillei-DS013 mediated silver nanoparticles characterization and its bactericidal potential against clinical isolates.

The sediment marine samples were obtained from several places along the coastline of the Tuticorin shoreline, Tamil Nadu, India were separated for the presence of bioactive compound producing actinobacteria. The actinobacterial strain was subjected to 16Sr RNA sequence cluster analysis and identified as Nocardiopsis dassonvillei- DS013 NCBI accession number: KM098151. Bacterial mediated synthesis of nanoparticles gaining research attention owing its wide applications in nonmedical biotechnology. In the current study, a single step eco-friendly silver nanoparticles (AgNPs) were synthesized from novel actinobacteria Nocardiopsis dassonvillei- DS013 has been attempted. The actinobacterial mediated silver nanoparticles were characterized by TEM, UV–Visible, XRD, FT-IR spectroscopy. The initial detection of AgNPs was identified using UV–Vis spectrum and confirmed by the appearance of absorbance peak at 408 nm. A Fourier transform infrared spectroscopy (FT-IR) result reveals the presence of protein component in the culture supernatant may act as protecting agents. The XRD pattern indicated that the typical peaks reveal the presence of nanoparticles. The TEM morphology confirms the formation of circular and non uniform distributions of AgNPs with the size range from 30 to 80 nm. The antibacterial activity of both isolated actinobacterial (IA) and silver nanoparticles mediated actinobacterial (SNA) of Nocardiopsis dassonvillei- DS013 were done by well diffusion method against selected clinical isolates of bacteria, namely Escherichia coli, Enterococcus sp., Pseudomonas sp., Klebsiella sp., Proteus sp., Shigella sp., Bacillus subtilis, and Streptococcus sp. When compared to isolated actinobacteria, the SNA shows the better antibacterial activity against clinical isolates.

Antibacterial based on IPBCC.08.610 glucose oxidase against UDP-N-acetyl glucosamine enolpyruvyl transferase and elongation factor G enzymes in silico

The use of a synthetic antibacterial agent as food preservatives could develop several health problems thus the user should be reduced. Enzyme-based antibacterial is a natural antibacterial that could substitute the latter antibacterials. Enzyme-based antibacterials have several ways that can be used to inactivate microbes, one of them utilize enzyme catalysis products. The aim of this research is to study the interaction between IPBCC.08.610 glucose oxidase (NCBI accession number MH593586) catalysis product against MurA and EFG enzymes using computational investigation. We confirmed that the gene sequence from previous research is truly encoding the IPBCC.08.610 glucose oxidase. Gluconolactone and gluconic acid are less effectively absorbed by microbes. Gluconolactone and gluconic acid are capable to interact with Cys115 and Asp305 of MurA, meanwhile, it does not interact with Phe90 and Thr84 of EFG. Gluconolactone and gluconic acid can inhibit MurA effectively but not on EFG.

Incidence of cutaneous habronemosis in Manipuri ponies in India.

Information pertaining to parasitic fauna and parasitic diseases in Manipuri ponies in India is not available. Moreover, no systematic studies have been undertaken on cutaneous habronemosis in Manipuri ponies which is a common skin problem of Manipuri ponies as reported by pony owners. Keeping in the view of the importance of parasitic infections in veterinary health coverage particularly in Manipuri ponies, the present study was planned. A survey of natural cases of cutaneous habronemosis followed by molecular confirmation of species involved and treatments were done. Out of 200 ponies examined, nine cases (4.5%) of cutaneous habronemosis was recorded. Gross examination revealed raised and ulcerated wounds with necrotic tissues covered with yellowish-tan granulation. Histopathological study revealed eosinophilic granuloma and in the center of the granuloma with necrotic debris. Remnants of the Hebronema larvae with infiltrating neutrophils surrounded by proliferating fibrous tissue with numerous eosinophils, macrophages and lymphocytes were also observed. Molecular detection of Habronema sp. was confirmed by semi-nested PCR. Sequence analysis revealed larvae of H. muscae was the common spirurid species responsible for producing cutaneous habronemosis in Manipuri ponies. Subsequently, sequence submitted to NCBI GenBank and accession number obtained (MH038181). Surgical removal of necrotic tissue, ivermectin injection along with antibiotics successfully cured all the lesions in infected ponies.Results confirmed occurrence of cutaneous habronemosis in Manipuri ponies in India.

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).

Identification of Proteins Released from the Egg Cell Surface During Fertilization

Multiple events occur at the interface between the sperm and egg membrane during fertilization, including sperm‐egg binding, species‐specific discrimination, membrane fusion, and egg activation. Each of these events is believed to rely upon discrete cell surface molecules. To date, only a handful of egg membrane proteins have been identified in any species. The process of fertilization as a whole is not well understood on a molecular level, from the initial sperm and egg binding, to the activation of early development. An excellent model organism to address these problems is the Pacific bat star, Patiria miniata, because they produce a large quantity of synchronized oocytes that are large, nearly transparent, and rigid enough to hold their shape despite removal of extracellular layers. Furthermore, we are learning that their genome is similar to humans with less complexity. Recent work suggests that proteases are necessary for successful fertilization, raising the possibility that fragments of egg membrane proteins could be released from the surface during fertilization. This could provide a mechanism for the identification of fertilization‐relevant membrane proteins. Using biotinylation and western blotting, we show that peptides ranging from 50kD to 250kD are being cleaved from the egg surface and released into the sea water within three minutes of introducing sperm. These peptides have been collected by affinity interaction against streptavidin conjugated mag‐sepharose beads and their identities are being determined by tandem mass spectrometry. Since a proteome has not yet been created for P. miniata, a recently developed transcriptome of the mature unfertilized egg (NCBI accession number: PRJNA398668) will be used to identify the peptides revealed by tandem mass spectrometry. Furthermore, this transcriptome is also being examined computationally with the purpose of identifying and grouping transcripts that may be integral to fertilization, as a whole, and with a specific focus on the egg cell surface. Understanding how fertilization takes place at the molecular level in starfish could eventually lead to understanding infertility issues, as well as offer new possible non‐hormonal prophylactics for use in humans.Support or Funding InformationNIH R15This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Genomic and Functional Characterization of Enterococcus mundtii QAUEM2808, Isolated From Artisanal Fermented Milk Product Dahi.

Microbial strains with a unique combination of technological and bioactive properties are preferred for industrial applications. The present study was conducted to evaluate the potential use of Enterococcus mundtii QAUEM2808 (NCBI Accession Number: LSMC00000000) in milk fermentation. This strain was isolated from Dahi, an indigenous fermented milk product of South-East Asia. The in vitro study confirmed the acidification ability as well as the proteolytic, cellulolytic, and amylolytic enzyme activities of this strain. It also produced a substantial amount of the folate in laboratory media and no physiological dysfunctions in laboratory animals was observed in feeding trials. All these properties were confirmed by in silico genome analysis. The Enterococcus mundtii QAUEM2808 genome consisted of a single, circular chromosome comprising 2,957,300-bp, 2,587 genes with GC content of 38.5%. Moreover, 16t RNAs, 1, 3 (16S, 23S) rRNAs, 4 ncRNAs, and 91 pseudo genes were also predicted. The majority of genome encode genes for protein, amino acids, carbohydrate, cell wall DNA and RNA metabolisms including all genes required for conversion of lactose to lactic acid. It also exhibited antimicrobial activity against E. coli ATCC 10536, S. aureus ATCC 6538, P. aeruginosa ATCC 9027, and L. monocytogenes ATCC 13932 and was found to be sensitive to commonly used antibiotics. The in silico analysis revealed the presence of genes for mundaticin and enterocin production, and CRISPER regions, however, the genes for antibiotic resistance were absent. No genes related to the pathogenicity island and prophages were detected by genome mining. Therefore, it could be inferened that Enterococcus mundtii QAUEM2808 has the potential to be used in milk fermentation as adjunct culture.

The complete chloroplast genome sequence of Paeonia jishanensis (Paeoniaceae), a rare wild tree peony

Paeonia jishanensis is endemic in China, and has been proven to be one of the most important ancestral species of cultivated tree peonies. Wild P. jishanensis has been over-exploited and becomes quite rare in China. The wild peony of P. jishanensis was used as an experimental material to sequence the chloroplast genome (cpDNA) by high-throughput sequencing (NCBI accession number: MG991935). The cpDNA of P. jishanensis is a typical quadripartite structure with a length of 152,628 bp, including a large single-copy (LSC) region of 84,292 bp and a small single-copy (SSC) region of 17,044 bp separated by a pair of identical inverted repeat regions (IRs) of 25,646 bp each. The cpDNA contains 112 genes, including 78 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. The result of phylogenomic analysis supports the difference of tree peony from the herbaceous peony.

The complete plastome sequence of Microlicia cogniauxiana R. Romero (Melastomataceae): an endemic species from an endangered biome

The complete plastome sequence of Microlicia cogniauxiana R. Romero (Melastomataceae) (NCBI accession number MK726004), a plant endemic to the campos rupestres formations of the Brazilian savannahs, is presented in this study. A genomic unit is 155,883 bp in length, comprising 130 genes, 85 DNA coding sequences, 37 tRNAs, eight rRNAs, and 23 introns, and a GC content of 37%. We recovered a large single-copy (85,691 bp), a small single-copy (16,859 bp), and two inverted repeats (26,667 bp). The M. cogniauxiana plastome resembles the ancestral organization of plastomes of flowering plants, including those of other genera of Melastomataceae.

Proteomic Effects of Magnesium Stress on Biofilm Associated Proteins Isolated from Cellulolytic Bacillus licheniformis YNP5-TSU

Optimization of cellulase activity is vital for synthesizing the end-products of second generation biofuel production. The slightest change in fermentation parameters can reduce the secretion of necessary enzymes to degrade cellulosic biomass. Determining the ecological effects of certain key media components is essential to understand how bacterial species will respond in a fluid environment. For our experiment a cellulosic media was designed to enhance the industrially important thermophile, Bacillus licheniformis YNP5-TSU. After several attempts to simplify the carboxymethylcellulose (CMC) media composition, impaired biofilm maturation and cellulase activity was noticed. This negative artifact occurred only when magnesium sulphate was removed from media. To analyze the shift in gene expression caused by magnesium stress, biofilm associated proteins were extracted from both control (4.0 mM MgSO4) and magnesium depleted (0.0 mM MgSO4) media at 24 hr and 48 hr incubation periods. These proteins were quantified through isobaric labeling and raw data generated from nanoLC-MS/MS identified over 2,000 proteins from the Bacillus licheniformis YNP5-TSU proteome (NCBI accession number ME). After statistical normalization and false discovery rate were calculated, a total of 161 proteins from magnesium depleted media and 238 proteins from control media were deemed statistically relevant. A closer look through STRING interconnected webs, data mining, and NCBI annotations revealed several up/down regulated proteins that had linkage to biofilm formation and cellulase secretion. In this study we are able to provide significant evidence that; (1) biofilm maturation and cellulase production are highly correlated and (2), their optimization is dependent on the expression of several key proteins.

Efficacy of transgenic tobacco carrying synthetic plant-preferred codon-optimized novel VIP3AA44 Gene towards Helicoverpa armigera and Spodoptera litura

Vip3A proteins are synthesized during vegetative growth of Bacillus thuringiensis and are toxic against a wide range of lepidopteran insects. Since the mode of action of vip3A toxins is different from Cry proteins, vip3A proteins are good candidates for gene pyramiding in transgenic crops to combat development of resistance against the currently deployed genes. A synthetic plant-preferred codon-optimized novel vip3Aa44 gene (NCBI accession number HQ650163) was cloned into pBINAR plant transformation vector and tobacco explants were transformed with leaf disc co-cultivation method to evaluate toxicity of this gene against Helicoverpa armigera and Spodoptera litura. The putative transgenics were confirmed by PCR and RT-PCR analysis. The bioassays were performed on detached leaves from putative transgenics using lab-grown population of H. armigera and S. litura. Mortality after 72 hr ranged from 30–56% for H. armigera and 40–60% for S. litura, indicating potential of vip3Aa44 gene against these lepidopteran pests in transgenic development.

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.

Reference gene selection for quantitative RT-PCR normalisation in barley under low-nitrogen stress, based on RNAseq data

The aim of the present study was to identify genes that could be used for the normalisation of qRT-PCR data in barley, using RNAseq data (NCBI accession number PRJNA400519: RNA sequencing of Hordeum vulgare L. under low nitrogen stress). The particular interest was in genes that were stably expressed under different nitrogen conditions, including low-nitrogen stress.