scholarly journals The use of informativity in the development of robust viromics-based examinations

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3281 ◽  
Author(s):  
Siobhan C. Watkins ◽  
Catherine Putonti
Keyword(s):  
Community Structure ◽  
Gene Transfer ◽  
Current Data ◽  
Metagenomic Data ◽  
Specific Gene ◽  
Proof Of Concept ◽  
Robust Method ◽  
Data Repositories ◽  
Sequence Identity ◽  
Insight Into

Metagenomics-based studies have provided insight into many of the complex microbial communities responsible for maintaining life on this planet. Sequencing efforts often uncover novel genetic content; this is most evident for phage communities, in which upwards of 90% of all sequences exhibit no similarity to any sequence in current data repositories. For the small fraction that can be identified, the top BLAST hit is generally posited as being representative of a viral taxon present in the sample of origin. Homology-based classification, however, can be misleading as sequence repositories capture but a small fraction of phage diversity. Furthermore, lateral gene transfer is pervasive within phage communities. As such, the presence of a particular gene may not be indicative of the presence of a particular viral species. Rather, it is just that: an indication of the presence of a specific gene. To circumvent this limitation, we have developed a new method for the analysis of viral metagenomic datasets. BLAST hits are weighted, integrating the sequence identity and length of alignments as well as a taxonomic signal, such that each gene is evaluated with respect to its information content. Through this quantifiable metric, predictions of viral community structure can be made with confidence. As a proof-of-concept, the approach presented here was implemented and applied to seven freshwater viral metagenomes. While providing a robust method for evaluating viral metagenomic data, the tool is versatile and can easily be customized to investigations of any environment or biome.

scholarly journals The Use of Informativity in the Development of Robust Metaviromics-based Examinations

2016 ◽  
Author(s):  
Siobhan C. Watkins ◽  
Thomas Hatzopoulos ◽  
Catherine Putonti
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Information Content ◽  
Sequence Similarity ◽  
Phylogenetic Signal ◽  
Viral Metagenomics ◽  
Proof Of Concept ◽  
Sequence Identity ◽  
Genomic Approach ◽  
Insight Into

AbstractThe field of metagenomics has developed insight into many of the complex microbial communities responsible for maintaining life on this planet. Sequencing efforts often uncover novel genetic content; this is most evident for viral metagenomics, in which upwards of 90% of all sequences demonstrate no sequence similarity with present databases. For the small fraction which can be identified, the top BLAST hit is often posited as being representative of the phage taxon. However, as previous research has shown, the top BLAST hit is sometimes misinterpreted. Furthermore, the appearance of a particular gene homolog is frequently not representative of the presence of the particular taxon in question. To circumvent these limitations, we have developed a new method for the analysis of metaviromic datasets. BLAST hits are weighted, integrating the sequence identity and length of alignments as well as a phylogenetic signal. A genic rather than genomic approach is presented in which each gene is evaluated with respect to its information content. Through this quantifiable metric, predictions of viral community structure can be made with greater confidence. As a proof-of-concept, the approach presented here was implemented and applied to seven metaviromes. While providing a more robust means of evaluating metaviromic data, the tool is versatile and can easily be customized to investigations of any environment or biome.

New Insight into Diabetes Management: From Glycemic Index to Dietary Insulin Index

2020 ◽  
Vol 16 (4) ◽  
pp. 293-300 ◽  
Author(s):  
Zahra Yari ◽  
Vahideh Behrouz ◽  
Hamid Zand ◽  
Katayoun Pourvali
Keyword(s):  
Glycemic Index ◽  
Diabetes Management ◽  
Glycemic Load ◽  
Insulin Response ◽  
Diet Therapy ◽  
Current Data ◽  
Diabetic Patients ◽  
Carbohydrate Counting ◽  
Insulin Requirements ◽  
Insight Into

Background: Despite efforts to control hyperglycemia, diabetes management is still challenging. This may be due to focusing on reducing hyperglycemia and neglecting the importance of hyperinsulinemia; while insulin resistance and resultant hyperinsulinemia preceded diabetes onset and may contribute to disease pathogenesis. Objective: The present narrative review attempts to provide a new insight into the management of diabetes by exploring different aspects of glycemic index and dietary insulin index. Results: The current data available on this topic is limited and heterogeneous. Conventional diet therapy for diabetes management is based on reducing postprandial glycemia through carbohydrate counting, choosing foods with low-glycemic index and low-glycemic load. Since these indicators are only reliant on the carbohydrate content of foods and do not consider the effects of protein and fat on the stimulation of insulin secretion, they cannot provide a comprehensive approach to determine the insulin requirements. Conclusion: Selecting foods based on carbohydrate counting, glycemic index or glycemic load are common guides to control glycemia in diabetic patients, but neglect the insulin response, thus leading to failure in diabetes management. Therefore, paying attention to insulinemic response along with glycemic response seems to be more effective in managing diabetes.

scholarly journals metaXplor: an interactive viral and microbial metagenomic data manager

GigaScience ◽  
2021 ◽  
Vol 10 (2) ◽  
Author(s):  
Guilhem Sempéré ◽  
Adrien Pétel ◽  
Magsen Abbé ◽  
Pierre Lefeuvre ◽  
Philippe Roumagnac ◽  
...  
Keyword(s):  
Heterogeneous Data ◽  
Metagenomic Data ◽  
Online Data ◽  
Data Repositories ◽  
Ongoing Research ◽  
Efficient Management ◽  
Public Data ◽  
Reference Databases ◽  
Interactive Data ◽  
User Friendly

Abstract Background Efficiently managing large, heterogeneous data in a structured yet flexible way is a challenge to research laboratories working with genomic data. Specifically regarding both shotgun- and metabarcoding-based metagenomics, while online reference databases and user-friendly tools exist for running various types of analyses (e.g., Qiime, Mothur, Megan, IMG/VR, Anvi'o, Qiita, MetaVir), scientists lack comprehensive software for easily building scalable, searchable, online data repositories on which they can rely during their ongoing research. Results metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing, and exploring metagenomic data. Being based on a flexible NoSQL data model, it has few constraints regarding dataset contents and thus proves useful for handling outputs from both shotgun and metabarcoding techniques. By supporting incremental data feeding and providing means to combine filters on all imported fields, it allows for exhaustive content browsing, as well as rapid narrowing to find specific records. The application also features various interactive data visualization tools, ways to query contents by BLASTing external sequences, and an integrated pipeline to enrich assignments with phylogenetic placements. The project home page provides the URL of a live instance allowing users to test the system on public data. Conclusion metaXplor allows efficient management and exploration of metagenomic data. Its availability as a set of Docker containers, making it easy to deploy on academic servers, on the cloud, or even on personal computers, will facilitate its adoption.

scholarly journals Conjugative plasmids: vessels of the communal gene pool

2009 ◽  
Vol 364 (1527) ◽  
pp. 2275-2289 ◽  
Author(s):  
Anders Norman ◽  
Lars H. Hansen ◽  
Søren J. Sørensen
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Significant Contribution ◽  
Prokaryotic Genome ◽  
Whole Genome ◽  
Adaptive Traits ◽  
Conjugative Plasmids ◽  
Environmental Setting ◽  
Genome Analyses ◽  
Insight Into

Comparative whole-genome analyses have demonstrated that horizontal gene transfer (HGT) provides a significant contribution to prokaryotic genome innovation. The evolution of specific prokaryotes is therefore tightly linked to the environment in which they live and the communal pool of genes available within that environment. Here we use the term supergenome to describe the set of all genes that a prokaryotic ‘individual’ can draw on within a particular environmental setting. Conjugative plasmids can be considered particularly successful entities within the communal pool, which have enabled HGT over large taxonomic distances. These plasmids are collections of discrete regions of genes that function as ‘backbone modules’ to undertake different aspects of overall plasmid maintenance and propagation. Conjugative plasmids often carry suites of ‘accessory elements’ that contribute adaptive traits to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized ‘private genes’.

scholarly journals Light-induced adenovirus gene transfer, an efficient and specific gene delivery technology for cancer gene therapy

2002 ◽  
Vol 9 (4) ◽  
pp. 365-371 ◽  
Author(s):  
Anders Høgset ◽  
Birgit Øvstebø Engesæter ◽  
Lina Prasmickaite ◽  
Kristian Berg ◽  
Øystein Fodstad ◽  
...  
Keyword(s):  
Gene Therapy ◽  
Gene Transfer ◽  
Gene Delivery ◽  
Cancer Gene Therapy ◽  
Specific Gene ◽  
Cancer Gene ◽  
Delivery Technology

scholarly journals Draft Genome of Shewanella frigidimarina Ag06-30, a Marine Bacterium Isolated from Potter Peninsula, King George Island, Antarctica

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Gisela Parmeciano Di Noto ◽  
Susana C. Vázquez ◽  
Walter P. MacCormack ◽  
Andrés Iriarte ◽  
Cecilia Quiroga
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Marine Bacterium ◽  
Draft Genome ◽  
Mobile Genetic Elements ◽  
King George Island ◽  
Genetic Elements ◽  
Shewanella Frigidimarina ◽  
Insight Into ◽  
Potter Peninsula

We present the draft genome of Shewanella frigidimarina Ag06-30, a marine bacterium from King George Island, Antarctica, which encodes the carbapenemase SFP-1. The assembly contains 4,799,218 bp (G+C content 41.24%). This strain harbors several mobile genetic elements that provide insight into lateral gene transfer and bacterial plasticity and evolution.

scholarly journals Tumor-specific gene transfer via an adenoviral vector targeted to the pan-carcinoma antigen EpCAM

Gene Therapy ◽  
1999 ◽  
Vol 6 (8) ◽  
pp. 1469-1474 ◽  
Author(s):  
H J Haisma ◽  
H M Pinedo ◽  
A van Rijswijk ◽  
I van der Meulen-Muileman ◽  
B A Sosnowski ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Adenoviral Vector ◽  
Specific Gene

scholarly journals Avian sarcoma leukosis virus receptor-envelope system for simultaneous dissection of multiple neural circuits in mammalian brain

2015 ◽  
Vol 112 (22) ◽  
pp. E2947-E2956 ◽  
Author(s):  
Makoto Matsuyama ◽  
Yohei Ohashi ◽  
Tadashi Tsubota ◽  
Masae Yaguchi ◽  
Shigeki Kato ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Gene Delivery ◽  
Cross Reactivity ◽  
Vector System ◽  
Target Cells ◽  
Specific Gene ◽  
Multiple Target ◽  
Neuronal Systems ◽  
Avian Sarcoma

Pathway-specific gene delivery is requisite for understanding complex neuronal systems in which neurons that project to different target regions are locally intermingled. However, conventional genetic tools cannot achieve simultaneous, independent gene delivery into multiple target cells with high efficiency and low cross-reactivity. In this study, we systematically screened all receptor–envelope pairs resulting from the combination of four avian sarcoma leukosis virus (ASLV) envelopes (EnvA, EnvB, EnvC, and EnvE) and five engineered avian-derived receptors (TVA950, TVBS3, TVC, TVBT, and DR-46TVB) in vitro. Four of the 20 pairs exhibited both high infection rates (TVA–EnvA, 99.6%; TVBS3–EnvB, 97.7%; TVC–EnvC, 98.2%; and DR-46TVB–EnvE, 98.8%) and low cross-reactivity (<2.5%). Next, we tested these four receptor–envelope pairs in vivo in a pathway-specific gene-transfer method. Neurons projecting into a limited somatosensory area were labeled with each receptor by retrograde gene transfer. Three of the four pairs exhibited selective transduction into thalamocortical neurons expressing the paired receptor (>98%), with no observed cross-reaction. Finally, by expressing three receptor types in a single animal, we achieved pathway-specific, differential fluorescent labeling of three thalamic neuronal populations, each projecting into different somatosensory areas. Thus, we identified three orthogonal pairs from the list of ASLV subgroups and established a new vector system that provides a simultaneous, independent, and highly specific genetic tool for transferring genes into multiple target cells in vivo. Our approach is broadly applicable to pathway-specific labeling and functional analysis of diverse neuronal systems.

Sign in / Sign up

Export Citation Format

Share Document