Kulturelna i metagenomska identifikacija mikrobioma kod supkliničkog mastitisa u krava.

Metagenomic and traditional microbial culture based analyses of milk samples from cows harbouring subclinical mastitis pathogens were carried out to identify the microbial community structure of milk. A total of 77 Triple cross (TP), Kankrej and Gir lactating cows and 301 quarters were screened for subclinical mastitis. A total of 106 isolates belonging to five different microbial genera were recovered from 91 quarters of 41 cows, including 15 quarters having mixed bacterial infections by cultural examination. Pyrosequencing readings obtained from the breed wise pooled DNA of subclinical mastitis milk samples were analyzed using the SEED subsystem database of Meta Genome Rapid Annotation with Subsystem Technology (MG-RAST). Among the five genera, Staphylococcus, Streptococcus, Micrococcus, Bacillus and Escherichia, detected in the subclinical mastitis milk samples by culture based methods, four genera, Staphylococcus, Streptococcus, Bacillus and Escherichia, were identified in the corresponding pyrosequencing data, while Micrococcus was not found. In contrast, the pyrosequencing yielded 28 bacterial species, of which only two species, S. aureus and E. coli, were identified by the cultural method. S. agalactiae, the third species identified by cultural method, was not found in the pyrosequencing data. Metagenomic analysis additionally identified 19 genera and 26 species in comparison with the routine cultural methods. Many of the fastidious / anaerobic bacterial organisms, which are difficult to cultivate by routine methods, were identified by metagenomic analyses.Radi identifikacije mikrobne zajednice u mlijeku provedena je metagenomska i uobičajena kulturelna pretraga uzoraka mlijeka krava sa supkliničkim mastitisom. Ukupno je 77 trostruko križanih Kankrej i Gir mliječnih krava i 301 četvrt vimena bilo pretraženo na supklinički mastitis. Izdvojeno je bilo 106 izolata svrstanih u pet različitih rodova iz 91 četvrti od 41 krave uključujući i 15 četvrti kod kojih je kulturelnom pretragom bila ustanovljena mješovita bakterijska infekcija. Sljedovi mješavine DNA izdvojeni iz uzoraka mlijeka kod supkliničkog mastitisa očitani pirosekvenciranjem bili su analizirani po podsustavu SEED baze podataka „Meta Genome Rapid Annotation with Subsystem Technology (MG-RAST)“. Iz pretraženih uzoraka mlijeka bilo je izdvojeno pet rodova: Staphylococcus, Streptococcus, Micrococcus, Bacillus i Escherichia. Četiri su bila dokazana postupkom pirosekvenciranja: Staphylococcus, Streptococcus, Bacillus i Escherichia, dok Micrococcus nije bio dokazan. S druge strane, pirosekvenciranjem je bilo dokazano 28 bakterijskih vrsta, od kojih su samo dvije, S. aureus i E. coli, bile dokazane klasičnom kulturelnom pretragom. S. agalactiae, treća vrsta identificirana kulturelnom pretragom nije bila dokazana postupkom pirosekvenciranja. Metagenomskom analizom dodatno je bilo dokazano 19 rodova i 26 vrsta u usporedbi s rutinskom kulturelnom pretragom. Mnoge anaerobne bakterije, koje je vrlo teško uzgojiti rutinskim metodama, bile su identificirane metagenomskom analizom

Synthesis, characterization, biomolecular interaction, cytotoxicity, and computational studies of quinoxaline-based platinum(II) complexes

The combination of ninhydrin and o-phenylenediamine, followed by their reaction with a phenylhydrazine derivative produces quinoxaline-based ligands (L1 – L6). These ligands react with K2PtCl4 to form Pt(II) complexes (I – VI). The ligands and Pt(II) chelate were characterized through various spectroscopic and analytical techniques, like 1H NMR, 13C NMR, C, H, N-elemental analysis, IR spectroscopy, and mass spectrometry. DFT calculations were used to optimize the structures of metal complexes. To investigate the binding mode of complexes to CT-DNA/BSA, absorption titration, viscosity measurements, and molecular docking analysis were employed. The results indicated that the DNA binding mechanism involved intercalation. The antibacterial efficacy of the compounds was evaluated against five strains of bacteria. The lower minimum inhibitory concentration (MIC) of complexes suggests that they are more potent than quinoxaline-based ligands. The synthesized compounds were evaluated for cytotoxicity using brine shrimp. The LC50 values of ligands and complexes ranged from 7.64 to 11.45 μg/mL and 5.27 to 7.02 μg/mL, respectively. The capacity of the molecule to suppress cell proliferation using the MCF-7 cancer cell was tested, and the IC50 value was discovered to be comparable to that of a standard drug. Thus in this work, complexes demonstrated intercalation as the binding mode with CT-DNA/BSA and exhibited enhanced antibacterial efficacy compared to the ligands. The compounds also showed promising cytotoxicity against brine shrimp and MCF-7 cancer cells, with comparable IC50 values to a standard drug, indicating their potential as therapeutic agents

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Not AvailableThe study investigated the composition of microorganisms in the camel (Camelus dromedarius) faecal samples, maintained under two groups of intensive (group 1) and extensive (group 2) systems of management at Jaisalmer district of Rajasthan, India by using culture-independent approach. The study included the comparison of camel faecal microbiota to other currently available gut/faecal metagenomes, in order to reveal potential differences in these gut environments. After shotgun sequencing of the camel fecal microbiome, we used the Metagenomics-Rapid Annotation Server Tool (MG-RAST) to identify the microbial diversity and metabolic potential of the camel gut. Of the sequenced data that passed quality control, 1.3% and 2.2% sequences contained ribosomal RNA genes in groups 1 and 2, respectively. The annotated protein features which were assigned to functional categories were 63.6% and 69.5%, in groups 1 and 2, respectively. The domain level breakdown of our samples revealed bacteria was the major domain in both systems of management. At the phylum level, Firmicutes (61.40% and 29.17%), Proteobacteria (11.10% and 47.85%), Bacteroidetes (8.04% and 3.83%) and Verrucomicrobia (7.48% and 10.35%) were predominant in the fecal microbial community of groups 1 and 2, respectively. The fecal metagenomes revealed Euryarchaeota phylum with Methanobrevibacter smithii as the major archaeal species in both these groups. Functional analysis using subsystems of MG-RAST revealed that sequences for protein metabolism were abundant in group 1 and those for metabolism of carbohydrates predominated in group 2. Glycoside hydrolases of carbohydrates functional category were seen in group 2. High taxonomic similarity of group 1 with cow rumen metagenomes, cattle faecal pool, canine gastro-intestine as well as group 2 camels with the termite gut was observed. Functional similarities of camel faecal metagenomes of groups 1 and 2 with cattle faecal pool and camel foregut were noticed. Altogether, these data suggest that agricultural and animal husbandry practices can impose significant selective pressures on the gut microbiota. The present study provided a baseline for understanding the complexity of camel gut microbial ecology while also highlighting striking similarities and differences when compared to other animal gastrointestinal environments and in future could help in developing strategies for improving the existing management conditions.Not Availabl

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Not AvailableRumen microorganisms play an important role in ruminant digestion and absorption of nutrients and have great potential applications in the field of rumen adjusting, food fermentation and biomass utilization etc. In order to investigate the composition of microorganisms in the rumen of camel (Camelus dromedarius), this study delves in the microbial diversity by culture-independent approach. It includes comparison of rumen samples investigated in the present study to other currently available metagenomes to reveal potential differences in rumen microbial systems. Pyrosequencing based metagenomics was applied to analyze phylogenetic and metabolic profiles by MG-RAST, a web based tool. Pyrosequencing of camel rumen sample yielded 8,979,755 nucleotides assembled to 41,905 sequence reads with an average read length of 214 nucleotides. Taxonomic analysis of metagenomic reads indicated Bacteroidetes (55.5 %), Firmicutes (22.7 %) and Proteobacteria (9.2 %) phyla as predominant camel rumen taxa. At a finer phylogenetic resolution, Bacteroides species dominated the camel rumen metagenome. Functional analysis revealed that clusteringbased subsystem and carbohydrate metabolism were the most abundant SEED subsystem representing 17 and 13 % of camel metagenome, respectively. A high taxonomic and functional similarity of camel rumen was found with the cow metagenome which is not surprising given the fact that both are mammalian herbivores with similar digestive tract structures and functions. Combined pyrosequencing approach and subsystems-based annotations available in the SEED database allowed us access to understand the metabolic potential of these microbiomes. Altogether, these data suggest that agricultural and animal husbandry practices can impose significant selective pressures on the rumen microbiota regardless of rumen type. The present study provides a baseline for understanding the complexity of camel rumen microbial ecology while also highlighting striking similarities and differences when compared to other animal gastrointestinal environments.Not Availabl

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Not AvailableRumen microorganisms play an important role in ruminant digestion and absorption of nutrients and have great potential applications in the field of rumen adjusting, food fermentation and biomass utilization etc. In order to investigate the composition of microorganisms in the rumen of camel (Camelus dromedarius), this study delves in the microbial diversity by culture-independent approach. It includes comparison of rumen samples investigated in the present study to other currently available metagenomes to reveal potential differences in rumen microbial systems. Pyrosequencing based metagenomics was applied to analyze phylogenetic and metabolic profiles by MG-RAST, a web based tool.Pyrosequencing of camel rumen sample yielded 8,979,755 nucleotides assembled to 41,905 sequence reads with an average read length of 214 nucleotides. Taxonomic analysis of metagenomic reads indicated Bacteroidetes (55.5 %), Firmicutes (22.7 %) and Proteobacteria (9.2 %) phyla as predominant camel rumen taxa. At a finer phylogenetic resolution, Bacteroides species dominated the camel rumen metagenome. Functional analysis revealed that clustering-based subsystem and carbohydrate metabolism were the most abundant SEED subsystem representing 17 and 13 % of camel metagenome, respectively. A high taxonomic and functional similarity of camel rumen was found with the cow metagenome which is not surprising given the fact that both are mammalian herbivores with similar digestive tract structures and functions. Combined pyrosequencing approach and subsystems-based annotations available in the SEED database allowed us access to understand the metabolic potential of these microbiomes. Altogether, these data suggest that agricultural and animal husbandry practices can impose significant selective pressures on the rumen microbiota regardless of rumen type. The present study provides a baseline for understanding the complexity of camel rumen microbial ecology while also highlighting striking similarities and differences when compared to other animal gastrointestinal environments.Not Availabl

Genomic analysis of a novel strain of Bacillus nealsonii, isolated from Surti buffalo rumen

Exercise can be prescribed as closed-loop bouts with a set task or time as the endpoint. Healthcare professionals may be able to create more individualized programs for clients by understanding their preference for, or performance in a specific endpoint oriented bout. Additionally, mental toughness has been reviewed as an important factor in determining success in high stress environments. The aim of this study was to examine differences in performance between task and time-oriented exercise bouts and to examine relationships between performance and levels mental toughness. A total of 14 participants (Males, N=10; Females, N=4) attended 3 sessions of data collection. Anthropometric measurements and mental toughness (via the Mental Toughness Scale) were assessed in session one. All subjects performed task and time-oriented running bouts during sessions 2 and 3 respectively. Heart rate, Ratings of Perceived Exertion, and treadmill speed were measured in each bout. Between-sessions differences reported significantly lower average RPE (p= 0.003), peak RPE (p= 0.022), and peak heart rate reserve (p= 0.017) for time-oriented sessions. Pearson correlation analyses reported no significant relationship between mental toughness and performance (p= 0.937). In conclusion, this study indicates significantly lower differences in performance variables in time-oriented bouts compared to task-oriented bouts

Metagenomic data of DNA viruses of poultry affected with respiratory tract infection

The incidence and severity of respiratory diseases in commercial broiler chicken flocks have increased recently in India because of intensification of the broiler industry. Viral population are predominant in respiratory tract infections and they pose continuous economic burden to poultry industry by causing severe economic losses through decreased productivity [1, 2]. To understand viral metagenome of poultry associated with respiratory infections, we performed DNA virome sequencing and data analysis of broilers from 8 districts of Gujarat State in India. We report high quality sequencing reads and highly abundant DNA viral population present in the infected broiler birds. The raw sequencing data used to perform metagenomic analysis is available in the Sequence Read Archive (SRA) under the BioProject No. PRJNA322592 and Accession No. MAUZ00000000, MAVA00000000, MAVB00000000, MAVC00000000, MAVD00000000, MAVE00000000, MAVF00000000, MAVG00000000 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA322592). Keywords: DNA Virome, Metagenomics, Next generation sequencin

Characterization of Canine Retina Using High-Throughput Sequencing

We performed transcriptome sequencing of canine retinal tissue by 454 GS-FLX and Ion Torrent PGM platforms. RNA-Seq analysis by CLC Genomics Workbench mapped expression of 10,360 genes. Gene ontology analysis of retinal transcriptome revealed abundance of transcripts known to be involved in vision associated processes. The de novo assembly of the sequences using CAP3 generated 29,683 contigs with mean length of 560.9 and N50 of 619 bases. Further analysis of contigs predicted 3,827 fulllength cDNAs and 29,481 (99%) open reading frames (ORFs). In addition, 3,782 contigs were assigned to 316 KEGG pathways which included melanogenesis, phototransduction, and retinol metabolism with 33, 15, and 11 contigs, respectively. Among the identified microsatellites, dinucleotide repeats were 68.84%, followed by trinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides in proportions of 25.76, 9.40, 2.52, and 0.96%, respectively. This study will serve as a valuable resource for understanding the biology and function of canine retina