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The Aedes Fauna: Different Aedes Species Inhabiting the Earth
Published in Jagriti Narang, Manika Khanuja, Small Bite, Big Threat, 2020
Annette Angel, Bennet Angel, Neelam Yadav, Jagriti Narang, Surender Singh Yadav, Vinod Joshi
Another whole genome sequencing (AaegL4) was attempted using the Hi-C sequencing technology that generated chromosome length scaffolds (Dudchenko et al., 2017). Mathews and coworkers attempted for a more refined genome sequencing (AaegL5) as was done by Nene et al. but could not provide the wholesome data. They used the Pacific Biosciences sequencing and Hi-C sequencing method, which presented the genome with a decrease in the percentage of contigs (more contigs were found in Dudchenko et al.’s work). Their current data speaks that the genome is actually 1.25 Bp in size.
Molecular Genetic Approaches to Obesity
Published in Claude Bouchard, The Genetics of Obesity, 2020
Streamson C. Chua, Rudolph L. Leibel
These vector systems, combined with contigs of the genome, can be used to access large segments of genomic DNA which span a region demonstrated by classical genetic studies (linkage or deletion analysis) to contain a gene of interest. The next step is usually the most difficult: the identification of expressed genes from the large stretch of genomic DNA obtained with the chromosome walk. There is no method currently available which will reliably identify all of the genes in a given stretch of genomic DNA. Each mutation must be identified by a mutation-specific strategy. If no prior information exists about the nature of the mutant gene, the identification of the gene may be extremely difficult. The gene may be located in a gene-rich region, with a density of one gene in every 10,000 bp. Positional information, which is derived from translocations or meiotic recombinations, generally has a resolution of 100,000 to 1 million bp. Thus, up to 100 genes may be candidates for the mutation, and each gene must be tested. However, if it is known that the mutation is expressed in a given tissue (e.g., pancreas), the search can be limited to those genes which are expressed in that organ. All other genes which are not expressed in the pancreas can be ignored. An additional consideration is the stage of development at which the mutated gene is expressed in a specific tissue. One might miss an expressed gene if the mRNA used is isolated from the right organ at an inappropriate stage of organogenesis.
A Survey of Newer Gene Probing Techniques
Published in Victor A. Bernstam, Pocket Guide to GENE LEVEL DIAGNOSTICS in Clinical Practice, 2019
The top-down approach identifies and makes assignments of progressively smaller fragments of DNA from a given chromosome. The bottom-up strategy identifies and aligns, in a continuum of sequences, overlapping sets of DNA clones (contigs). Techniques known as chromosome walking, chromosome jumping, and probe walking are used in these strategies.
Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome
Published in Gut Microbes, 2020
Tanya M. Monaghan, Tim J. Sloan, Stephen R. Stockdale, Adam M. Blanchard, Richard D. Emes, Mark Wilcox, Rima Biswas, Rupam Nashine, Sonali Manke, Jinal Gandhi, Pratishtha Jain, Shrejal Bhotmange, Shrikant Ambalkar, Ashish Satav, Lorraine A. Draper, Colin Hill, Rajpal Singh Kashyap
For the reference-independent approach, proteins for all contigs were predicted using Prodigal (version 2.6.3)61 with the ‘meta’ option enabled for small contigs and Shine-Dalgarno training bypassed. Proteins were subsequently queried against the prokaryote Viral Orthologous Groups database (pVOGs)62 using HMMER (version 3.1b2),63 with a minimum score requirement of 15. Putative reference-independent discovered viruses needed to fulfill three basic requirements: (i) ≥1.5kb, (ii) encode two distinct proteins with similarity to two unique pVOGs, and (iii) encode ≥2 pVOGs per 10kb-equivalent genome length. Additional stringent dynamic filtering was applied to contigs based on their actual genome length. For contigs <5kb, it was required that there were at least ≥5 distinct pVOG hits; contigs ≥5kb and <10kb, ≥6 pVOG hits; contigs ≥10kb and <20kb, ≥7 pVOG hits; contigs ≥20kb and <40kb, ≥8 pVOG hits; contigs ≥40kb and <60kb, 9 pVOG hits; and contigs ≥60kb, 10 pVOG hits.
The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency
Published in Gut Microbes, 2019
Chloe Matthews, Fiona Crispie, Eva Lewis, Michael Reid, Paul W. O’Toole, Paul D. Cotter
The rumen microbiota is a topic that has been covered in great detail since the emergence of NGS technologies.38,94–96 Most studies use reference databases such as Kraken (shotgun sequencing)9 and Greengenes (16S rRNA),10 among many others, to characterise the microbiota. The use of contigs or longer contiguous sequences97 for metagenomic analysis, may provide a deeper insight into the workings of the microbiome. Shorter reads, although having its advantages, do not represent complete genomes and may contain contamination. Studies have shown that the use of contigs may be an invaluable technique for the recovery of microbial genomes. Hess et al. (2011)98 were the first to use metagenomic binning techniques for the analysis of the rumen microbiota. Fifteen uncultured microbial genomes were assembled to > 60% completeness. The technique was also used in a study of the moose rumen microbiome, which recovered 99 metagenome-assembled genomes.99 The most recent study by Stewart et al. (2018),100 assembled 913 microbial genomes from metagenomic data of the rumen of cattle. This resulted in over 69,000 proteins thought to be involved in carbohydrate metabolism, in addition to the expansion of the Erysipelotrichales order. The study has, therefore, contributed immensely to improved metagenomic classification.
Extensive drug resistant Salmonella enterica serovar Senftenberg carrying blaNDM encoding plasmid p5558 (IncA/C) from India
Published in Pathogens and Global Health, 2019
Balaji Veeraraghavan, Jobin John Jacob, John Antony Jude Prakash, Agila Kumari Pragasam, Ayyanraj Neeravi, Vignesh Narasimman, Shalini Anandan
WGS was performed using Ion Torrent PGM platform (Life Technologies, Carlsbad, CA) using 400 bp read chemistry. Sequencing was performed as per the protocol recommended by Life Technologies. Raw reads were assembled de novo using AssemblerSPAdes software v4.4.0.1 in Torrent suite server version 4.4.3. Sequencing generated 5,234,212 bp sequences with 188 contigs (≥500 bp) of 36 X coverage. The genome was annotated using the RAST server (Rapid Annotation using Subsystem Technology- http://rast.nmpdr.org) available from the PATRIC database (Pathosystems Resource Integration Centre -https://www.patricbrc.org) [15,16]. Multilocus sequence typing (MLST) of strain P5558 was determined using Enterobase database (https://enterobase.warwick.ac.uk) available in pubMLST (https://pubmlst.org/mlst/) based on concentrated sequences of seven loci (aroC, dnaN, hemD, hisD, purE, sucA, and thrA) [17]. Serotype of the isolate was further confirmed using the web based tool SeqSero (www.denglab.info/SeqSero) [18]. Molecular characterisation of the isolate was further established using CRISPR sequence type analysis (http://crispr.i2bc.paris-saclay.fr/Server/) based on Pasteur CRISPR database for Salmonella.