journal
MENU ▼
Read by QxMD icon Read
search

Briefings in Functional Genomics

journal
https://www.readbyqxmd.com/read/29140409/ebolavirus-interferon-antagonists-protein-interaction-perspectives-to-combat-pathogenesis
#1
Anupam Banerjee, Abantika Pal, Debnath Pal, Pralay Mitra
Zaire ebolavirus, one of the most pathogenic species of Ebolavirus, is a significant threat to the human community being both highly infectious and lethal. The viral proteins (VPs), specifically VP24 and VP35, antagonize the interferon (IFN) proteins accountable for human immune response. Several efforts have been made to design vaccines and therapeutics drugs. However, the success is not encouraging because of limited knowledge about the binding site information of the VPs. Such limitations stem largely from the highly infectious nature of the virus that requires specialized personnel and biosafety laboratories...
November 13, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29136087/the-utility-and-perspectives-of-ngs-based-methods-in-bsl-3-and-bsl-4-laboratory-sequencing-and-analysis-strategies
#2
Tomasz Wolkowicz
Modern diagnostics is in general based on molecular biology methods. Nowadays sequencing-based methods, especially whole genome sequencing, are becoming increasingly important. Implementation of such methods into routine diagnostic of highly dangerous pathogens, like Bacillus anthracis, Francisella tularensis, Yersinia pestis, Ebola virus, MERS, Lassa virus etc. would be very helpful. The best diagnostic strategy would be the metagenomic sequencing directly from the clinical sample. Implementation of majority of currently available WGS platforms inside the BSL-3 or 4 laboratory is impractical because of the size of the equipment and time consuming wet lab part (e...
November 10, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29126257/experimental-design-for-single-cell-rna-sequencing
#3
Jeanette Baran-Gale, Tamir Chandra, Kristina Kirschner
Single-cell RNA sequencing (scRNA-seq) has opened new avenues for the characterization of heterogeneity in a large variety of cellular systems. As this is a relatively new technique, the field is fast evolving. Here, we discuss general considerations in experimental design and the two most popular approaches, plate-based Smart-Seq2 and microdroplet-based scRNA-seq at the example of 10x Chromium. We discuss advantages and disadvantages of both methods and point out major factors to consider in designing successful experiments...
November 8, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29126220/catching-rnas-on-chromatin-using-hybridization-capture-methods
#4
Martin Machyna, Matthew D Simon
The growing appreciation of the importance of long noncoding RNAs (lncRNAs), together with the awareness that some of these RNAs are associated with chromatin, has inspired the development of methods to detect their sites of interaction on a genome-wide scale at high resolution. Hybridization capture methods combine antisense oligonucleotide hybridization with enrichment of RNA from cross-linked chromatin extracts. These techniques have provided insight into lncRNA localization and the interactions of lncRNAs with protein to better understand biological roles of lncRNAs...
November 8, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29106464/application-of-single-cell-sequencing-in-human-cancer
#5
Mattias Rantalainen
Precision medicine is emerging as a cornerstone of future cancer care with the objective of providing targeted therapies based on the molecular phenotype of each individual patient. Traditional bulk-level molecular phenotyping of tumours leads to significant information loss, as the molecular profile represents an average phenotype over large numbers of cells, while cancer is a disease with inherent intra-tumour heterogeneity at the cellular level caused by several factors, including clonal evolution, tissue hierarchies, rare cells and dynamic cell states...
November 2, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29092000/the-human-cell-atlas-technical-approaches-and-challenges
#6
Chung-Chau Hon, Jay W Shin, Piero Carninci, Michael J T Stubbington
The Human Cell Atlas is a large, international consortium that aims to identify and describe every cell type in the human body. The comprehensive cellular maps that arise from this ambitious effort have the potential to transform many aspects of fundamental biology and clinical practice. Here, we discuss the technical approaches that could be used today to generate such a resource and also the technical challenges that will be encountered.
October 28, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29087438/how-low-can-you-go-pushing-the-limits-of-low-input-chip-seq
#7
John Arne Dahl, Gregor D Gilfillan
In the past decade, chromatin immunoprecipitation sequencing (ChIP-seq) has emerged as the dominant technique for those wishing to perform genome-wide protein:DNA profiling. Owing to the tissue- and cell-type-specific nature of epigenetic marks, the field has been driven towards obtaining data from ever-lower cell numbers. In this review, we focus on the methodological developments that have lowered input requirements and the biological findings they have enabled, as we strive towards the ultimate goal of robust single-cell ChIP-seq...
October 26, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29045542/bacterial-artificial-chromosomes-as-recombinant-reporter-constructs-to-investigate-gene-expression-and-regulation-in-echinoderms
#8
Katherine M Buckley, Ping Dong, R Andrew Cameron, Jonathan P Rast
Genome sequences contain all the necessary information-both coding and regulatory sequences-to construct an organism. The developmental process translates this genomic information into a three-dimensional form. One interpretation of this translation process can be described using gene regulatory network (GRN) models, which are maps of interactions among regulatory gene products in time and space. As high throughput investigations reveal increasing complexity within these GRNs, it becomes apparent that efficient methods are required to test the necessity and sufficiency of regulatory interactions...
October 17, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29040388/rna-structure-interactions-and-ribonucleoprotein-processes-of-the-influenza-a-virus
#9
Wayne K Dawson, Michal Lazniewski, Dariusz Plewczynski
In one more years, we will 'celebrate' an exact centenary of the Spanish flu pandemic. With the rapid evolution of the influenza virus, the possibility of novel pandemic remains ever a concern. This review covers our current knowledge of the influenza A virus: on the role of RNA in translation, replication, what is known of the expressed proteins and the protein products generated from alternative splicing, and on the role of base pairing in RNA structure. We highlight the main events associated with viral entry into the cell, the transcription and replication process, an export of the viral genetic material from the nucleus and the final release of the virus...
October 10, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29028882/enzymatic-methods-for-genome-wide-profiling-of-protein-binding-sites
#10
Robert A Policastro, Gabriel E Zentner
Genome-wide mapping of protein-DNA interactions is a staple approach in many areas of modern molecular biology. Genome-wide profiles of protein-binding sites are most commonly generated by chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq). Although ChIP-seq has played a central role in studying genome-wide protein binding, recent work has highlighted systematic biases in the technique that warrant technical and interpretive caution and underscore the need for orthogonal techniques to both confirm the results of ChIP-seq studies and uncover new insights not accessible to ChIP...
October 6, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29028900/unravelling-the-biological-secrets-of-microchimerism-by-single-cell-analysis
#11
Anders Ståhlberg, Amin El-Heliebi, Peter Sedlmayr, Thomas Kroneis
The presence of microchimeric cells is known for >100 years and well documented since decades. Earlier, microchimeric cells were mainly used for cell-based non-invasive prenatal diagnostics during early pregnancy. Microchimeric cells are also present beyond delivery and are associated to various autoimmune diseases, tissue repair, cancer and immune tolerance. All these findings were based on low complexity studies and occasionally accompanied by artefacts not allowing the biological functions of microchimerism to be determined...
September 28, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29028879/review-of-computational-methods-for-virus-host-protein-interaction-prediction-a-case-study-on-novel-ebola-human-interactions
#12
Anup Kumar Halder, Pritha Dutta, Mahantapas Kundu, Subhadip Basu, Mita Nasipuri
Identification of potential virus-host interactions is useful and vital to control the highly infectious virus-caused diseases. This may contribute toward development of new drugs to treat the viral infections. Recently, database records of clinically and experimentally validated interactions between a small set of human proteins and Ebola virus (EBOV) have been published. Using the information of the known human interaction partners of EBOV, our main objective is to identify a set of proteins that may interact with EBOV proteins...
September 26, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29028866/global-and-targeted-approaches-to-single-cell-transcriptome-characterization
#13
Aleksandra A Kolodziejczyk, Tapio Lönnberg
Analysing transcriptomes of cell populations is a standard molecular biology approach to understand how cells function. Recent methodological development has allowed performing similar experiments on single cells. This has opened up the possibility to examine samples with limited cell number, such as cells of the early embryo, and to obtain an understanding of heterogeneity within populations such as blood cell types or neurons. There are two major approaches for single-cell transcriptome analysis: quantitative reverse transcription PCR (RT-qPCR) on a limited number of genes of interest, or more global approaches targeting entire transcriptomes using RNA sequencing...
September 25, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29028886/analysis-of-protein-targets-in-pathogen-host-interaction-in-infectious-diseases-a-case-study-on-plasmodium-falciparum-and-homo-sapiens-interaction-network
#14
Sovan Saha, Kaustav Sengupta, Piyali Chatterjee, Subhadip Basu, Mita Nasipuri
Infection and disease progression is the outcome of protein interactions between pathogen and host. Pathogen, the role player of Infection, is becoming a severe threat to life as because of its adaptability toward drugs and evolutionary dynamism in nature. Identifying protein targets by analyzing protein interactions between host and pathogen is the key point. Proteins with higher degree and possessing some topologically significant graph theoretical measures are found to be drug targets. On the other hand, exceptional nodes may be involved in infection mechanism because of some pathway process and biologically unknown factors...
September 23, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29028873/mirna-in-tumour-metabolism-and-why-could-it-be-the-preferred-pathway-for-energy-reprograming
#15
Aliaa A Alamoudi, Amina Alnoury, Hoda Gad
The current literature on the role of microRNA (miRNA) in tumour metabolism is growing, and a number of studies regularly confirm the impact miRNA can have in energy reprograming in tumours. However, there remains to be a lack of understanding of the larger perspective of the role of miRNA in the metabolism story. In the first part of this review, we provide a comprehensive and up-to-date description of the extensive role of miRNAs in tumour metabolism including glucose, lipid and amino acid metabolism. However, in the second part, we aim to provide a description of the multidimensional role miRNA can be playing in tumour metabolism...
September 23, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28968725/a-brief-review-of-single-cell-transcriptomic-technologies
#16
Tomer Kalisky, Sarit Oriel, Tali Hana Bar-Lev, Nissim Ben-Haim, Ariel Trink, Yishay Wineberg, Itamar Kanter, Shlomit Gilad, Saumyadipta Pyne
In recent years, there has been an effort to develop new technologies for measuring gene expression and sequence information from thousands of individual cells. Large data sets that were obtained using these 'single cell' technologies have allowed scientists to address fundamental questions in biomedicine ranging from stems cells and development to cancer and immunology. Here, we provide a brief review of recent developments in single-cell technology. Our intention is to provide a quick background for newcomers to the field as well as a deeper description of some of the leading technologies to date...
September 1, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28968729/a-survey-on-ebola-genome-and-current-trends-in-computational-research-on-the-ebola-virus
#17
Pritha Dutta, Anup Kumar Halder, Subhadip Basu, Mahantapas Kundu
A detailed understanding of the Ebola virus (EBOV) pathogenesis has not been possible because of safety concerns, which arise while handling the live EBOV. Understanding the mechanisms involved in EBOV entry, replication and inhibition of the antiviral response in the host cell are crucial for the development of effective therapeutic measures. In this article, we provide a description of the EBOV genome and the role of each EBOV protein in spreading infection in the host cell. We also discuss some of the major computational works done on EBOV for the purpose of developing effective vaccines and drugs...
August 29, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28968632/integration-of-amplification-efficiency-in-qpcr-analysis-allows-precise-and-relative-quantification-of-transcript-abundance-of-genes-from-large-gene-families-using-rna-isolated-from-difficult-tissues
#18
Rex Arunraj, Marcus A Samuel
The performance of the quantitative polymerase chain reaction (qPCR) assay in the analysis of gene expression belonging to multigene families in tissues rich in secondary metabolites is technically complicated. Here, we present the qPCR analysis of PMT2 gene, a predominant member of a multigene family from tobacco, expressed in the root tissues and is involved in the biosynthesis of nicotine. Consequently, we provide insight into the effect of polymerase chain reaction (PCR) amplification efficiency (AE) of reference and target genes of calibrator and test samples on the qPCR assay performance...
August 25, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29140479/editorial
#19
Greg Elgar
No abstract text is available yet for this article.
November 1, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28957458/omics-approaches-to-study-gene-regulatory-networks-for-development-in-echinoderms
#20
Elijah K Lowe, Claudia Cuomo, Maria I Arnone
Gene regulatory networks (GRNs) describe the interactions for a developmental process at a given time and space. Historically, perturbation experiments represent one of the key methods for analyzing and reconstructing a GRN, and the GRN governing early development in the sea urchin embryo stands as one of the more deeply dissected so far. As technology progresses, so do the methods used to address different biological questions. Next-generation sequencing (NGS) has become a standard experimental technique for genome and transcriptome sequencing and studies of protein-DNA interactions and DNA accessibility...
September 1, 2017: Briefings in Functional Genomics
journal
journal
42954
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"