64 research outputs found
Evaluation of DNA Extraction Methods of Mule Dung
DNA isolation is a critical step in microbial community analysis of animal dung. DNA isolation from mule dung is challenging due to microbial diversity, composition and chemical nature of mule dung. Therefore, selection of an appropriate DNA isolation method is important to analyse the complete microbial diversity. In the current study, we evaluated the DNA isolation from mule dung samples (n=11) using QiAmp Mini stool kit as per manufacturer’s procedure with modifications. The results suggest that modifications in proprietary column based method improved the DNA quality and quantity suitable for mule dung microbial community analyses
Applications of Personalised Phage Therapy highlighting the importance of Bacteriophage Banks against Emerging Antimicrobial Resistance
Emerging antibiotic resistance is one of the most important microbiological issues of the 21st century. This poses a query regarding the future use of antibiotics and availability of other promising therapeutic alternatives. The awareness about antibiotic misuse has improved insufficiently and is evident by the increased incidences of multidrug resistant infections globally. Amongst different antibacterial therapeutic approaches phage therapy has created a niche of its own due to continuous use for treatment of human infections in Eastern Europe. Synergistic compounds along with phages have also been proposed as a better alternative compared to antibiotics or phage alone for treatment of chronic cases and seriously debilitating diseases. As such, why not allow custom made phage therapy for treatment of chronic infections? However, the success of phage therapy will depend upon instant availability of characterised bacteriophages from bacteriophage banks which may serve as the major catalyst in bringing Phage Therapy to main stream treatment alternatives or in combination therapy at least. In the current article we present a glimpse of comprehensive approach about utility of bacteriophage banks and further present personalised phage therapy in a synergistic role with antibiotics to overcome emerging antimicrobial resistance
Comparative Genome Analysis of 19 <i>Trueperella pyogenes</i> Strains Originating from Different Animal Species Reveal a Genetically Diverse Open Pan-Genome
Trueperella pyogenes is a Gram-positive opportunistic pathogen that causes severe cases of mastitis, metritis, and pneumonia in a wide range of animals, resulting in significant economic losses. Although little is known about the virulence factors involved in the disease pathogenesis, a comprehensive comparative genome analysis of T. pyogenes genomes has not been performed till date. Hence, present investigation was carried out to characterize and compare 19 T. pyogenes genomes originating in different geographical origins including the draftgenome of the first Indian origin strain T. pyogenes Bu5. Additionally, candidate virulence determinants that could be crucial for their pathogenesis were also detected and analyzed by using various bioinformatics tools. The pan-genome calculations revealed an open pan-genome of T. pyogenes. In addition, an inventory of virulence related genes, 190 genomic islands, 31 prophage sequences, and 40 antibiotic resistance genes that could play a significant role in organism’s pathogenicity were detected. The core-genome based phylogeny of T. pyogenes demonstrates a polyphyletic, host-associated group with a high degree of genomic diversity. The identified core-genome can be further used for screening of drug and vaccine targets. The investigation has provided unique insights into pan-genome, virulome, mobiliome, and resistome of T. pyogenes genomes and laid the foundation for future investigations
Not Available
Not AvailableInduced pluripotent stem (iPS) cells
represent a recent innovation in the field of stem cells.
Commonly, iPS cells are generated by viral transduction
of core reprogramming genes, such as Oct4, Sox2, Klf4,
c-Myc, Nanog and Lin28. However, integrating viruses,
like retro- and lentiviral vectors, may cause insertional
mutagenesis and may increase the risk of tumor
formation. Therefore, alternative methods which avoid
these safety concerns are intensively investigated. Here,
we review the current status of transposon-based
methods to induce pluripotency. DNA transposons are
non-viral elements, which can be effectively integrated
into a genome by their corresponding transposase
enzyme. The advantages of transposon-based gene
transfer are their increased safety, their large cargo
capacity, their relatively simple design, and the
availability of hyper-active and mutated transposase
enzymes. For example, integration-deficient, excisioncompetent
transposase variants allow the complete
removal of the reprogramming transposon after
successful reprogramming to obtain transposon-free
reprogrammed cells. Transposon-based reprogramming
broaden the toolbox for iPS cell production and will
advance the establishment of safe, non-viral methods.Not Availabl
Transposon-based reprogramming to induced pluripotency
Induced pluripotent stem (iPS) cells
represent a recent innovation in the field of stem cells.
Commonly, iPS cells are generated by viral transduction
of core reprogramming genes, such as Oct4, Sox2, Klf4,
c-Myc, Nanog and Lin28. However, integrating viruses,
like retro- and lentiviral vectors, may cause insertional
mutagenesis and may increase the risk of tumor
formation. Therefore, alternative methods which avoid
these safety concerns are intensively investigated. Here,
we review the current status of transposon-based
methods to induce pluripotency. DNA transposons are
non-viral elements, which can be effectively integrated
into a genome by their corresponding transposase
enzyme. The advantages of transposon-based gene
transfer are their increased safety, their large cargo
capacity, their relatively simple design, and the
availability of hyper-active and mutated transposase
enzymes. For example, integration-deficient, excisioncompetent transposase variants allow the complete
removal of the reprogramming transposon after
successful reprogramming to obtain transposon-free
reprogrammed cells. Transposon-based reprogramming
broaden the toolbox for iPS cell production and will
advance the establishment of safe, non-viral methods
Not Available
Not AvailableBacteriophages play an important role in bacterial control in natural niche however a little is known about Bacillus sp. phages prevailing in cadaver affected soils. In the current study, the Bacillus sp. phage was isolated from the equine cadaver disposal site and characterised to gain an insight into the issue of role of phages in biological dynamics of manure thus formed over years. Firstly, the host bacterium was isolated and identified as Bacillus cereus group member as assessed by phylogenetic analysis and secondly it’s corresponding phage from same soil sample was also enriched and characterised. The phage (VTCCBPA38) was found to belong to family Myoviridae and was active within the temperature range of 4 °C - 45 °C. As assessed by biological sensitivity by spot test, the phage was active against 6/19 (31.6 %) Bacilli tested including Bacillus cereus from goat mastitis. Thus the phage may find potential use in biocontrol of diseases caused by Bacillus sp. Furthermore, this report is valuable as the first study for investigation of Bacillus sp. phage in carcass burial sites.Not Availabl
Not Available
Not AvailableInduced pluripotent stem (iPS) cells
represent a recent innovation in the field of stem cells.
Commonly, iPS cells are generated by viral transduction
of core reprogramming genes, such as Oct4, Sox2, Klf4,
c-Myc, Nanog and Lin28. However, integrating viruses,
like retro- and lentiviral vectors, may cause insertional
mutagenesis and may increase the risk of tumor
formation. Therefore, alternative methods which avoid
these safety concerns are intensively investigated. Here,
we review the current status of transposon-based
methods to induce pluripotency. DNA transposons are
non-viral elements, which can be effectively integrated
into a genome by their corresponding transposase
enzyme. The advantages of transposon-based gene
transfer are their increased safety, their large cargo
capacity, their relatively simple design, and the
availability of hyper-active and mutated transposase
enzymes. For example, integration-deficient, excisioncompetent
transposase variants allow the complete
removal of the reprogramming transposon after
successful reprogramming to obtain transposon-free
reprogrammed cells. Transposon-based reprogramming
broaden the toolbox for iPS cell production and will
advance the establishment of safe, non-viral methods.ICAR, DBT, NIA
Not Available
Not Availablevirulent Aeromonas veronii biovar sobria and
the corresponding novel, lytic bacteriophage (VTCCBPA5)
were isolated from village pond water. The phage was found
to belong to family Podoviridae. PCR analysis of major
capsid protein gene confirmed its classification to T7-like
genus. The protein profiling by SDS-PAGE indicated the
major structural protein to be ~ 45 kDa. The phage (VTCCBPA5)
is host specific and is stable over a range of pH
(6–10) and temperatures (4–45 °C). On the basis of restriction
endonuclease analysis combined with prediction mapping,
it was observed to vary significantly from previously
reported podophages of Aeromonas sp., viz. phiAS7 and
Ahp1. The phylogenetic analysis on the basis of PCR-amplified
segment of DNA polymerase gene of phage revealed it
being an outgroup from podophages of Klebsiella sp. and
Pseudomonas sp. though a small internal fragment (359 bp)
showed the highest identity (77%) with Vibrio sp. phages.
Thus, this is the first report of a novel Podoviridae phage
against A. veronii. It expands the assemblage of podophages
against Aeromonas sp. and BPA5 could be potentially useful
in biocontrol of environmentally acquired Aeromonas
veronii infections.ICA
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