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Briefings in Functional Genomics

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https://www.readbyqxmd.com/read/30010711/rna-dna-structures-recognized-by-rnase-h2
#1
Kenji Kojima, Misato Baba, Motoki Tsukiashi, Takuto Nishimura, Kiyoshi Yasukawa
Ribonuclease H (RNase H) [EC 3.1.26.4] is an enzyme that specifically degrades RNA from RNA/DNA hybrids. Since its discovery in 1969, the enzyme has been extensively studied for its catalytic mechanism and physiological role. RNase H has been classified into two major families, Type 1 and Type 2. Type 1 enzymes are designated RNase HI in prokaryotes and RNase H1 in eukaryotes, while Type 2 enzymes are designated RNase HII in prokaryotes and RNase H2 in eukaryotes. Type 2 enzymes are able to cleave the 5'-phosphodiester bond of one ribonucleotide embedded in a DNA double strand...
July 12, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29992310/recent-advancement-toward-significant-association-between-disordered-transcripts-and-virus-infected-diseases-a-survey
#2
Sagnik Sen, Ujjwal Maulik
In the current era of epigenetics research, we have observed many examples of epigenetic modifications, like histone modification and DNA methylation, in various fatal diseases. These include solid tumors, hematological malignancies and viral infections with DNA or RNA viruses. The purpose of this review is to summarize the role of epigenetic modifications during the abovementioned viral infections, viral-associated and independent malignancies. In this article, the essential biological aspects of DNA methylation are discussed...
July 9, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29992233/cancer-immunotherapy-for-metastasis-past-present-and-future
#3
Xiaobo Wang, Shaoyi Fan, Hehai Pan, Wenli Chen, Hua Wang
Cancer is a complex and refractory disease, which can disseminate from primary site to a different site even at an early stage. Cancer immunotherapy harnesses host immune system to battle against cancer, but only a minority of patients benefit from it. Genetic-based technologies have significantly promoted the development of cancer immunotherapy. Here we describe genetic-based cancer immunotherapies in three aspects: recombinant cancer vaccine, immune checkpoint blockade therapy and adoptive cell transfer. In the future, multi-disciplinary collaboration will greatly increase the scope and effectiveness of cancer immunotherpy...
July 9, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29982427/vaccine-and-antibody-production-in-plants-developments-and-computational-tools
#4
Kashyap Kumar Dubey, Garry A Luke, Caroline Knox, Punit Kumar, Brett I Pletschke, Puneet Kumar Singh, Pratyoosh Shukla
Plants as bioreactors have been widely used to express efficient vaccine antigens against viral, bacterial and protozoan infections. To date, many different plant-based expression systems have been analyzed, with a growing preference for transient expression systems. Antibody expression in diverse plant species for therapeutic applications is well known, and this review provides an overview of various aspects of plant-based biopharmaceutical production. Here, we highlight conventional and gene expression technologies in plants along with some illustrative examples...
July 5, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29982297/functions-of-short-lifetime-biological-structures-at-large-the-case-of-intrinsically-disordered-proteins
#5
Vladimir N Uversky
Although for more than a century a protein function was intimately associated with the presence of unique structure in a protein molecule, recent years witnessed a skyrocket rise of the appreciation of protein intrinsic disorder concept that emphasizes the importance of the biologically active proteins without ordered structures. In different proteins, the depth and breadth of disorder penetrance are different, generating an amusing spatiotemporal heterogeneity of intrinsically disordered proteins (IDPs) and intrinsically disordered protein region regions (IDPRs), which are typically described as highly dynamic ensembles of rapidly interconverting conformations (or a multitude of short lifetime structures)...
July 3, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29982317/next-generation-sequencing-technologies-accelerate-advances-in-t-cell-therapy-for-cancer
#6
Qinan Yin, Jiaxing Tang, Xuekai Zhu
Next-generation sequencing has produced a large quantity of DNA or RNA sequences related to the processes occurring within tumors and their microenvironment in a reasonable time and cost. These data have been used to guide the identification of neoantigens and to determine their specific T-cell receptors. Furthermore, adoptive T-cell therapy targeting neoantigens is under development for cancer treatment. In this review, we first provide an overview of sequencing technologies and the updated findings concerning neoantigens related to adoptive T-cell therapy and then summarize the methods and principles underlying the development of next-generation sequencing-based neoantigen-reactive T-cell therapy for cancer...
July 2, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29762641/functional-genomics-paving-the-way-for-more-successful-cancer-immunotherapy
#7
Reham Ajina, Danielle Zamalin, Louis M Weiner
Immunotherapies have revolutionized cancer treatment. Immunotherapy is effective for the treatment of a wide range of cancer types and can mediate complete and durable tumor regression. Nonetheless, the field still faces many significant challenges, such as the need for personalized therapeutic strategies and better biomarkers, the difficulty of selecting the right combination therapy, and resistance to currently available immunotherapies. Both cancer and host immunity comprise significantly diverse and complex ecosystems, making immunogenomics an ideal field for functional genomics analysis...
May 11, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29741584/translating-gwas-in-rheumatic-disease-approaches-to-establishing-mechanism-and-function-for-genetic-associations-with-ankylosing-spondylitis
#8
Julie A Osgood, Julian C Knight
Ankylosing spondylitis (AS) is a highly heritable chronic inflammatory arthritis characterized by osteoproliferation, fusion of affected joints and systemic manifestations. Many disease associations for AS have been reported through genome-wide association studies; however, identifying modulated genes and functional mechanism remains challenging. This review summarizes current genetic associations involving AS and describes strategic approaches for functional follow-up of disease-associated variants. Fine mapping using methods leveraging Bayesian approaches are outlined...
May 5, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29697785/host-parasite-interactions-and-ecology-of-the-malaria-parasite-a-bioinformatics-approach
#9
Dariusz Izak, Joanna Klim, Szymon Kaczanowski
Malaria remains one of the highest mortality infectious diseases. Malaria is caused by parasites from the genus Plasmodium. Most deaths are caused by infections involving Plasmodium falciparum, which has a complex life cycle. Malaria parasites are extremely well adapted for interactions with their host and their host's immune system and are able to suppress the human immune system, erase immunological memory and rapidly alter exposed antigens. Owing to this rapid evolution, parasites develop drug resistance and express novel forms of antigenic proteins that are not recognized by the host immune system...
April 25, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29688255/role-of-genomics-in-promoting-the-utilization-of-plant-genetic-resources-in-genebanks
#10
Peterson W Wambugu, Marie-Noelle Ndjiondjop, Robert J Henry
Global efforts have seen the world's plant genetic resources (PGRs) conserved in about 1625 germ plasm repositories. Utility of these resources is important in increasing the resilience and productivity of agricultural production systems. However, despite their importance, utility of these resources has been poor. This article reviews the real and potential application of the current advances in genomic technologies in improving the utilization of these resources. The actual and potential application of these genomic approaches in plant identification, phylogenetic analysis, analysing the genetic value of germ plasm, facilitating germ plasm selection in genebanks as well as instilling confidence in international germ plasm exchange system is discussed...
May 1, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29240875/the-expanding-roles-of-argonautes-rna-interference-splicing-and-beyond
#11
Xiaoxia Ma, Ziwei Zuo, Weishan Shao, Yongfeng Jin, Yijun Meng
Argonaute (AGO) protein family is highly conserved in eukaryotes and prokaryotes, reflecting its evolutionarily indispensible role in maintaining normal life cycle of the organisms. Small RNA-guided, AGO-dependent RNA interference (RNAi) is a well-studied pathway for gene expression regulation, which can be performed at transcriptional, posttranscriptional or translational level. In addition to RNAi, growing pieces of evidence point to a novel role of AGOs in pre-mRNA (messenger RNA precursor) splicing in animals...
May 1, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29228117/aneuploidy-an-important-model-system-to-understand-salient-aspects-of-functional-genomics
#12
Shriram N Rajpathak, Deepti D Deobagkar
Maintaining a balance in gene dosage and protein activity is essential to sustain normal cellular functions. Males and females have a wide range of genetic as well as epigenetic differences, where X-linked gene dosage is an essential regulatory factor. Basic understanding of gene dosage maintenance has emerged from the studies carried out using mouse models with FCG (four core genotype) and chromosomal aneuploidy as well as from mono-chromosomal hybrid cells. In mammals, aneuploidy often leads to embryonic lethality particularly in early development with major developmental and structural abnormalities...
May 1, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29165573/an-emerging-role-for-epigenetic-factors-in-relation-to-executive-function
#13
Omar Ibrahim, Heidi G Sutherland, Larisa M Haupt, Lyn R Griffiths
Background: Executive function (EF) includes a range of decision-making and higher-order thinking processes. Although the genetic basis of EF has been studied and reviewed, epigenetic factors that influence EF are an emerging field of interest; here, we summarize the current research. Methods: Work relating to different word combinations of 'Executive Function' and 'Epigenetic' was identified through three academic search directories. Inclusion criteria were human populations, EF testing, epigenetic testing or genotyping related to epigenetic regulation...
May 1, 2018: 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
#14
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...
May 1, 2018: 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
#15
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...
May 1, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28968626/the-differential-expression-of-chironomus-spp-genes-as-useful-tools-in-the-search-for-pollution-biomarkers-in-freshwater-ecosystems
#16
Javier G Mantilla, Lucimar Gomes, Marco A Cristancho
Insects of the Chironomidae family are characterized by a wide ecological diversity in freshwater ecosystems. The larvae have the physiological potential to tolerate environmental stress even when there is a low concentration of oxygen, the presence of toxic substances or when there are changes in temperature and salinity. On the other hand, it is important to consider that at a cellular level, when individual insects are exposed to environmental changes, it induces responses of groups of genes that govern the molecular mechanisms related to such tolerance...
May 1, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29912293/crispr-cas9-in-plants-at-play-in-the-genome-and-at-work-for-crop-improvement
#17
Babar Hussain, Stuart James Lucas, Hikmet Budak
The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system uses single-guide RNAs for genome editing, making it a simple, robust, powerful tool for targeted gene mutagenesis, knockout and knock-in/replacement, as well as transcriptional regulation. Here, we review the working principles, components and potential modifications of CRISPR/Cas9 for efficient single and multiplex gene editing in plants. We also describe recent work that has used CRISPR/Cas9 to improve economically important traits in crop plants...
April 17, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29579147/cas9-sgrna-based-genome-editing-and-other-reverse-genetic-approaches-for-functional-genomic-studies-in-rice
#18
Mazahar Moin, Achala Bakshi, M S Madhav, P B Kirti
One of the important and direct ways of investigating the function of a gene is to characterize the phenotypic consequences associated with loss or gain-of-function of the corresponding gene. These mutagenesis strategies have been successfully deployed in Arabidopsis, and subsequently extended to crop species including rice. Researchers have made vast advancements in the area of rice genomics and functional genomics, as it is a diploid plant with a relatively smaller genome size unlike other cereals. The advent of rice genome research and the annotation of high-quality genome sequencing along with the developments in databases and computer searches have enabled the functional characterization of unknown genes in rice...
March 22, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29579146/the-application-of-crispr-cas9-genome-editing-tool-in-cancer-immunotherapy
#19
Hong-Yan Wu, Chun-Yu Cao
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) system was originally discovered in prokaryotes functioned as a part of the adaptive immune system. Because of its high efficiency and easy operability, CRISPR-Cas9 system has been developed to be a powerful and versatile gene editing tool shortly after its discovery. Given that multiple genetic alterations are the main factors that drive genesis and development of tumor, CRISPR-Cas9 system has been applied to correct cancer-causing gene mutations and deletions and to engineer immune cells, such as chimeric antigen receptor T (CAR T) cells, for cancer immunotherapeutic applications...
March 22, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29579145/quantitative-single-cell-transcriptomics
#20
Christoph Ziegenhain, Beate Vieth, Swati Parekh, Ines Hellmann, Wolfgang Enard
Single-cell RNA sequencing (scRNA-seq) is currently transforming our understanding of biology, as it is a powerful tool to resolve cellular heterogeneity and molecular networks. Over 50 protocols have been developed in recent years and also data processing and analyzes tools are evolving fast. Here, we review the basic principles underlying the different experimental protocols and how to benchmark them. We also review and compare the essential methods to process scRNA-seq data from mapping, filtering, normalization and batch corrections to basic differential expression analysis...
March 22, 2018: Briefings in Functional Genomics
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