scholarly journals Applications of Metagenomics for Unrevealing the Extended Horizons of Microbiota Prevalence from Soil to Human Health

2021 ◽  
Vol 15 (1) ◽  
pp. 177-187
Author(s):  
Vrishty Sharma ◽  
Muneer Ahmad Malla ◽  
Rajesh Kumar Kori ◽  
Rajesh Singh Yadav ◽  
Zaffar Azam

Phylogenetic analysis of different ecosystems has shown that the number of microbial communities in a single sample exceeds their cultured counterparts. Microbes have been found throughout nature and can thrive in adverse conditions. Besides inhabiting diverse environments, they also play a key role in the maintenance of the ecosystem. Most of these microbes are either unculturable or difficult to culture with conventional culturing methods. Metagenomics is an emerging field of science that has been in the light for a decade and offers a potential way to assess microbial diversity. The development of metagenomics opens new ways to study genetic material directly from the environmental samples. DNA sequencing and synthesis technologies are making it possible to read and write entire genomes. The huge amount of data obtained from genome sequencing inevitably requires bioinformatics tools to handle and further process them for analysis. Advances in DNA sequencing and high-performance computing have brought about exemplar improvement in metagenomics, allowing in-depth study of the largely unexplored frontier of microbial life. This culture-independent method provides extensive information regarding the structure, composition, and function of the diverse assemblages of the environmental microbes. The current review presents an overview of the technical aspects of metagenomics along with its diverse applications.

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
László Kaján ◽  
Guy Yachdav ◽  
Esmeralda Vicedo ◽  
Martin Steinegger ◽  
Milot Mirdita ◽  
...  

We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome.


Author(s):  
Tahsin Kurc ◽  
Shannon Hastings ◽  
Vijay Kumar ◽  
Stephen Langella ◽  
Ashish Sharma ◽  
...  

Integrative biomedical research projects query, analyze, and integrate many different data types and make use of datasets obtained from measurements or simulations of structure and function at multiple biological scales. With the increasing availability of high-throughput and high-resolution instruments, the integrative biomedical research imposes many challenging requirements on software middleware systems. In this paper, we look at some of these requirements using example research pattern templates. We then discuss how middleware systems, which incorporate Grid and high-performance computing, could be employed to address the requirements.


Author(s):  
Mark H. Ellisman

The increased availability of High Performance Computing and Communications (HPCC) offers scientists and students the potential for effective remote interactive use of centralized, specialized, and expensive instrumentation and computers. Examples of instruments capable of remote operation that may be usefully controlled from a distance are increasing. Some in current use include telescopes, networks of remote geophysical sensing devices and more recently, the intermediate high voltage electron microscope developed at the San Diego Microscopy and Imaging Resource (SDMIR) in La Jolla. In this presentation the imaging capabilities of a specially designed JEOL 4000EX IVEM will be described. This instrument was developed mainly to facilitate the extraction of 3-dimensional information from thick sections. In addition, progress will be described on a project now underway to develop a more advanced version of the Telemicroscopy software we previously demonstrated as a tool to for providing remote access to this IVEM (Mercurio et al., 1992; Fan et al., 1992).


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