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Regulation by non-coding RNAs

ISBN: 9783038420057 9783038420101 Year: Volume: 1 Pages: 844 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Added to DOAB on : 2015-01-12 11:03:39
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Regulatory non-protein-coding RNA genes and their transcripts were first found and characterized in bacteria but encompass all biological kingdoms. The complexity of non-coding RNAs (ncRNAs) in terms of number and types increases with degree of biological development, whereby humans and other primates appear to have the largest number. Many regulatory ncRNAs base-pair to a target RNA or DNA and inhibit target function. Bacterial ncRNA genes largely respond to environmental stress conditions and help protect the organism from adverse conditions. The prokaryotic RNAs are for the most part small (<200 bp) and are commonly referred to as small regulatory RNAs (sRNAs). Eukaryotic RNAs consist of small <200 nt RNAs and large >200 nt (termed lncRNAs). The eukaryotic small RNAs include miRNAs, siRNAs, and piRNAs. miRNAs inhibit mRNA functions and may also be associated with cancer. lncRNAs functions are multifaceted and include epigenetic regulation and animal development. The bacterial and archeal immune system CRISPR, and the eukaryotic piwi-interacting RNAs (piRNA) immune system that inhibits mobile elements in germ line cells both function by via RNA transcript/ target DNA heteroduplex base-pairing are a specific class of RNAs that protect cells from invading transposons/and or viruses. siRNAs function in plant and invertebrate immune systems and protect against viral infections. [...]

Regulation by non-coding RNAs

ISBN: 9783038420064 9783038420118 Year: Volume: 2 Pages: 244 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Added to DOAB on : 2015-01-12 11:06:27
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Abstract

Regulatory non-protein-coding RNA genes and their transcripts were first found and characterized in bacteria but encompass all biological kingdoms. The complexity of non-coding RNAs (ncRNAs) in terms of number and types increases with degree of biological development, whereby humans and other primates appear to have the largest number. Many regulatory ncRNAs base-pair to a target RNA or DNA and inhibit target function. Bacterial ncRNA genes largely respond to environmental stress conditions and help protect the organism from adverse conditions. The prokaryotic RNAs are for the most part small (<200 bp) and are commonly referred to as small regulatory RNAs (sRNAs). Eukaryotic RNAs consist of small <200 nt RNAs and large >200 nt (termed lncRNAs). The eukaryotic small RNAs include miRNAs, siRNAs, and piRNAs. miRNAs inhibit mRNA functions and may also be associated with cancer. lncRNAs functions are multifaceted and include epigenetic regulation and animal development. The bacterial and archeal immune system CRISPR, and the eukaryotic piwi-interacting RNAs (piRNA) immune system that inhibits mobile elements in germ line cells both function by via RNA transcript/ target DNA heteroduplex base-pairing are a specific class of RNAs that protect cells from invading transposons/and or viruses. siRNAs function in plant and invertebrate immune systems and protect against viral infections. [...]

Bioinformatics of Non-Coding RNAs with Applications to Biomedicine: Recent Advances and Open Challenges

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450961 Year: Pages: 95 DOI: 10.3389/978-2-88945-096-1 Language: English
Publisher: Frontiers Media SA
Subject: Biotechnology --- General and Civil Engineering
Added to DOAB on : 2017-07-06 13:27:36
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The recent discovery of small and long non-coding RNAs (ncRNAs) has represented a major breakthrough in the life sciences. These molecules add a new layer of complexity to biological processes and pathways by revealing a sophisticated and dynamic interconnected system whose structure is just beginning to be uncovered. Genetic and epigenetic aberrations affecting ncRNA gene sequences and their expression have been linked to a variety of pathological conditions, including cancer, cardiovascular and neurological diseases. Latest advances in the development of high throughput analysis techniques may help to shed light on the complex regulatory mechanisms in which ncRNA molecules are involved. Bioinformatics tools constitute a unique and essential resource for non-coding RNA studies, providing a powerful technology to organize, integrate and analyze the huge amount of data produced daily by wet biology experiments in order to discover patterns, identify relationships among heterogeneous biological elements and formulate functional hypotheses. This Research Topic reviews current knowledge, introduces novel methods, and discusses open challenges of this exciting and innovative field in connection with the most important biomedical applications. It consists of four reviews and six original research and methods articles, spanning the full scope of the Research Topic.

Keywords

bioinformatics --- ncRNA --- microRNA --- RNA Editing --- isomiRs --- networks --- RNAseq --- CLIPseq --- siRNA --- CRISPR

Genome Editing in Neurosciences

Authors: --- ---
Book Series: Research and Perspectives in Neurosciences ISSN: 0945-6082 / 2196-3096 ISBN: 9783319601915 9783319601922 Year: Pages: 123 DOI: https://doi.org/10.1007/978-3-319-60192-2 Language: English
Publisher: Springer Nature
Subject: Neurology --- Genetics
Added to DOAB on : 2017-11-24 13:07:59
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Innovations in molecular biology are allowing neuroscientists to study the brain with unprecedented resolution, from the level of single molecules to integrated gene circuits. Chief among these innovations is the CRISPR-Cas genome editing technology, which has the precision and scalability to tackle the complexity of the brain. This Colloque Médecine et Recherche has brought together experts from around the world that are applying genome editing to address important challenges in neuroscience, including basic biology in model organisms that has the power to reveal systems-level insight into how the nervous system develops and functions as well as research focused on understanding and treating human neurological disorders.

Gene Silencing and Editing Strategies for Neurodegenerative Diseases

Authors: ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889455515 Year: Pages: 115 DOI: 10.3389/978-2-88945-551-5 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Neurology
Added to DOAB on : 2019-01-23 14:53:42
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Neurodegenerative diseases (NDs) are a heterogeneous group of disorders affecting the central nervous system. Despite significant differences in their causes, neuropathological abnormalities, and clinical outcomes, some similarities can be found among them, as for example: 1) frequent aggregation and deposition of misfolded proteins, 2) common molecular mechanisms leading to neurodegeneration, and 3) certain overlap in symptoms and clinical features. To date, there is no cure that could stop or delay the progression of these diseases. The advent of advanced gene therapy techniques such as gene silencing and gene editing opened a new avenue for the development of therapeutic strategies for NDs.The discovery of the RNA interference (RNAi) mechanism, in 1998, by Andrew Fire and Craig Mello allowed an important boost to the gene therapy field, providing a potential therapeutic strategy to treat inherited dominant genetic disorders. The use of small RNA sequences to control the expression of disease-causing genes rapidly implemented in the preclinical studies for different diseases. In the field of NDs, several successful studies using this technology proved its potential as a therapeutic option. However, issues like the type of delivery system (non-viral versus viral) or the potential toxicity of the small RNA molecules, made the translation of gene silencing therapeutics to human application very slow and difficult.Recently, a new hope in the gene therapy field emerged with the development of gene editing techniques like TALENs or CRISPR/Cas9 systems. The opportunity of editing or deleting gene sequences drove the scientific community euphoric, with an enormous increase in the number of published studies using this type of techniques. Recently, the first clinical trial using one of these systems was approved in China. For NDs, gene-editing technology also represents an important therapeutic option, and the first preclinical studies are now being published, showing the potential accomplishment for this technology.

Molecular Genetics, Genomics and Biotechnology of Crop Plants Breeding

Author:
ISBN: 9783039288779 / 9783039288786 Year: Pages: 238 DOI: 10.3390/books978-3-03928-878-6 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology --- Plant Sciences
Added to DOAB on : 2020-06-09 16:38:57
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This Special Issue on molecular genetics, genomics, and biotechnology in crop plant breeding seeks to encourage the use of the tools currently available. It features nine research papers that address quality traits, grain yield, and mutations by exploring cytoplasmic male sterility, the delicate control of flowering in rice, the removal of anti-nutritional factors, the use and development of new technologies for non-model species marker technology, site-directed mutagenesis and GMO regulation, genomics selection and genome-wide association studies, how to cope with abiotic stress, and an exploration of fruit trees adapted to harsh environments for breeding purposes. A further four papers review the genetics of pre-harvest spouting, readiness for climate-smart crop development, genomic selection in the breeding of cereal crops, and the large numbers of mutants in straw lignin biosynthesis and deposition.

Keywords

phloem metabolites --- electrospray ionisation --- mass spectrometry --- cultivar --- quality groups --- nitrogen --- faba bean --- zt-1 --- linkage map --- SSR --- ISSR --- Brassica napus --- GmDof4 --- GmDof11 --- oleic acid --- fatty acid composition --- differentially expressed genes --- drought --- RNA-seq --- RNA editing --- wheat --- climate change --- mapping populations --- genetic resources --- mutation breeding --- genome editing --- new plant breeding techniques --- “omics” data --- bioinformatics --- rice --- CRISPR/Cas9 --- Wx --- TGW6 --- mutations --- maintainer --- cytoplasmic male sterile --- amylose content --- anther --- protein --- cytoplasmic male sterility --- fertility restoration --- sunflower --- Rf1 gene --- GWAS --- Pentatricopeptide Repeats --- PPR genes --- association mapping --- candidate genes --- gene mapping --- lodicule --- non-open hull 1(noh1) --- rice --- crops --- quantitative genetics --- estimated breeding value --- genomic prediction --- plant breeding --- breeding scheme --- pedigree --- genetic value --- wheat --- pre-harvest sprouting --- seed dormancy --- abscisic acid --- gibberellin --- QTL/genes --- brown midrib --- cell wall --- gold hull and internode --- grass family --- lignin --- monolignol pathway --- mutational breeding --- orange lemma --- transgenic cereals --- SNP --- SSR --- next generation sequencing --- genotyping by sequencing --- Japanese plum --- SSR --- diversity --- genetic structure --- candidate genes --- genomic selection --- mutants --- ddRAD sequencing --- genotyping-by-sequencing --- CRISPR/Cas9 site directed mutagenesis --- genome-wide association scan --- genetic modification --- F1 hybrids --- QTL

Transcriptional Regulation: Molecules, Involved Mechanisms and Misregulation

Authors: ---
ISBN: 9783039212651 9783039212668 Year: Pages: 356 DOI: 10.3390/books978-3-03921-266-8 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-08-28 11:21:27
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Transcriptional regulation is a critical biological process involved in the response of a cell, a tissue or an organism to a variety of intra- and extra-cellular signals. Besides, it controls the establishment and maintenance of cell identity throughout developmental and differentiation programs. This highly complex and dynamic process is orchestrated by a huge number of molecules and protein networks and occurs through multiple temporal and functional steps. Of note, many human disorders are characterized by misregulation of global transcription since most of the signaling pathways ultimately target components of transcription machinery. This book includes a selection of papers that illustrate recent advances in our understanding of transcriptional regulation and focuses on many important topics, from cis-regulatory elements to transcription factors, chromatin regulators and non-coding RNAs, other than several transcriptome studies and computational analyses.

Keywords

major depressive disorder --- glioblastoma --- differentially expressed genes --- transcriptomics --- common pathway --- mouse --- miR-25-3p --- Akt1 --- AP-2? --- promoter --- cell metabolism --- p57Kip2 --- CDKN1C --- epigenetics --- disease --- cell differentiation --- placenta --- long non-coding RNA (lncRNA) --- human --- pregnancy --- high-throughput RNA sequencing (RNA-Seq) --- transcriptome --- Rsh regulon --- Novosphingobium pentaromativorans US6-1 --- sphingomonads --- RNA-seq --- N-acyl-l-homoserine lactone --- ppGpp --- selenium --- selenocysteine --- selenoproteins --- selenocysteine insertion sequence --- nonsense-mediated decay --- G-quadruplex --- transcriptional regulation --- promoter --- CRISPR/Cas9 --- PRDM gene family --- TCGA data analysis --- somatic mutations --- transcriptome profiling --- human malignancies --- tristetraprolin (TTP) --- tumorigenesis --- posttranscriptional regulation --- adenosine and uridine-rich elements (AREs) --- circRNA-disease associations --- pathway --- heterogeneous network --- Patau Syndrome --- cytogenetics --- FOXO1 --- transcription factor --- molecular pathways --- bioinformatics --- molecular docking --- and drug design --- transcription regulation --- gene expression --- causal inference --- enhancer activity --- insect --- transcription factors --- structures and functions --- research methods --- progress and prospects --- Pax3 --- Pteria penguin (Röding, 1798) --- tyrosinase --- melanin --- RNA interference --- liquid chromatograph-tandem mass spectrometer (LC-MS/MS) --- epigenetics --- gene expression --- nutrition --- transcription --- disorders --- mechanisms --- Crassostrea gigas --- Pacific oyster --- pediveliger larvae --- bioadhesive --- transcriptome --- gene expression --- interactome --- microscopy --- fertilization --- self-incompatibility --- transcriptome --- tea --- long non-coding RNAs --- cancer --- acute leukemia --- therapeutic targets --- Adiponectin --- cancer --- Adiponectin receptors --- obesity --- inflammatory response --- inflammation --- nutritional status --- n/a

Molecular Advances in Wheat and Barley

Author:
ISBN: 9783039213719 9783039213726 Year: Pages: 290 DOI: 10.3390/books978-3-03921-372-6 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-12-09 11:49:15
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Allohexaploid bread wheat and diploid barley are two of the most cultivated crops in the world. This book reports novel research and reviews concerning the use of modern technologies to understand the molecular bases for wheat and barley improvement. The contributions published in this book illustrate research advances in wheat and barley knowledge using modern molecular techniques. These molecular approaches cover genomic, transcriptomic, proteomic, and phenomic levels, together with new tools for gene identification and the development of novel molecular markers. Overall, the contributions for this book lead to a further understanding of regulatory systems in order to improve wheat and barley performance.

Keywords

Triticum durum --- Aegilops tauschii --- Triticum aestivum --- marker-trait associations --- genes --- bread wheat --- genetic biofortification --- favorable alleles --- allohexaploid --- homoeolog --- hybrid necrosis --- molecular marker --- wheat --- wheat --- rye --- 6R --- small segment translocation --- powdery mildew --- transgenic wheat --- 12-oxophytodienoate reductase --- jasmonates --- freezing tolerance --- HIGS --- transgene --- wheat --- barley --- cereal cyst nematodes --- wheat --- barely --- breeding --- biotechnology --- resistance --- Triticum aestivum --- Landrace --- Powdery mildew --- Bulked segregant analysis-RNA-Seq (BSR-Seq) --- Single nucleotide polymorphism (SNP) --- Kompetitive Allele Specific PCR (KASP) --- Blumeria graminis f. sp. tritici --- protein two-dimensional electrophoresis --- mass spectrometry --- Pm40 --- Barley --- Grain development --- Transcriptional dynamics --- RNA editing --- RNA-seq --- durum wheat --- Tunisian landraces --- center of diversity --- genetic diversity --- population structure --- DArTseq technology --- chromatin --- 3D-FISH --- nucleus --- introgression --- rye --- hybrid --- wheat --- genome stability --- wheat --- Thinopyrum --- chromosome --- ND-FISH --- oligo probe --- barley --- wheat --- protease --- germination --- grain --- abiotic stress --- antioxidant enzymes --- aquaporin --- TdPIP2 --- 1 --- histochemical analysis --- transgenic wheat --- transpiration --- wheat --- Aegilops tauschii --- Lr42 --- disease resistance --- molecular mapping --- KASP markers --- marker-assisted selection --- phytase --- wheat --- barley --- purple acid phosphatase phytase --- PAPhy --- mature grain phytase activity (MGPA) --- genome assembly --- bread wheat --- barley --- optical mapping --- BAC --- ribosomal DNA --- cereals --- CRISPR --- crops --- genetic engineering --- genome editing --- plant --- Triticeae --- n/a

Towards Mechanism-based Treatments for Fragile X Syndrome

Authors: ---
ISBN: 9783039215058 9783039215065 Year: Pages: 250 DOI: 10.3390/books978-3-03921-506-5 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-12-09 11:49:15
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It has been more than 25 years since the identification of the FMR1 gene and the demonstration of the causative role of CGG-repeat expansion in the disease pathology of fragile X syndrome (FXS), but the underlying mechanisms involved in the expansion mutation and the resulting gene silencing still remain elusive. Our understanding of the pathways impacted by the loss of FMRP function has grown tremendously, and has opened new avenues for targeted treatments for FXS. However, the failure of recent clinical trials that were based on successful preclinical studies using the Fmr1 knockout mouse model has forced the scientific community to revisit clinical trial design and identify objective outcome measures. There has also been a renewed interest in restoring FMR1 gene expression as a possible treatment approach for FXS. This special issue of Brain Sciences highlights the progress that has been made towards understanding the disease mechanisms and how this has informed the development of treatment strategies that are being explored for FXS.

Keywords

fragile X syndrome --- clinical trials --- targeted treatments --- drug development --- fragile X syndrome --- clinical trials --- treatment development --- best practices --- fragile X syndrome --- newborn screening --- early identification --- fragile X syndrome --- X chromosome --- females --- FMR1 --- anxiety --- avoidance --- cognition --- behavior --- brain --- Fragile X --- FMRP --- Fxr2 --- Fmr1 --- fragile X syndrome --- executive function --- working memory --- set-shifting --- cognitive flexibility --- inhibitory control --- attention --- planning --- processing speed --- Fragile X syndrome 1 --- Fragile X-associated Tremor/Ataxia Syndrome 2 --- CRISPR 3 --- Trinucleotide Repeat 4 --- Gene editing --- fragile X syndrome --- FMR1 gene --- voice of the person --- voice of the patient --- characteristics that have the greatest impact --- developmental disorders --- fragile X syndrome --- language development --- automated vocal analysis --- adeno-associated virus --- autism spectrum disorders --- cerebral spinal fluid --- fragile X mental retardation protein --- neurodevelopmental disorders --- viral vector --- fragile X syndrome --- gene reactivation --- RNA:DNA hybrid --- FMRP --- histone methylation --- DNA methylation --- FMR1 --- PRC2 --- fragile X syndrome --- unstable repeat diseases --- epigenetic gene silencing --- DNA methylation --- repeat instability --- pluripotent stem cells --- CGG Repeat Expansion Disease --- DNA instability --- expansion --- contraction --- mismatch repair (MMR) --- base excision repair (BER) --- transcription coupled repair (TCR) --- double-strand break repair (DSBR) --- Non-homologous end-joining (NHEJ) --- mosaicism --- protein synthesis --- Fragile X Syndrome --- biomarker --- iPSC --- fibroblast --- lymphoblast --- fragile X syndrome --- molecular biomarkers --- FMR1 --- FMRP --- intellectual disability --- Fmr1 KO mouse --- ASD --- n/a

Polyamine Metabolism in Disease and Polyamine-Targeted Therapies

Author:
ISBN: 9783039211524 9783039211531 Year: Pages: 240 DOI: 10.3390/books978-3-03921-153-1 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-12-09 11:49:15
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Polyamines are ubiquitous polycations essential for all cellular life. The most common polyamines in eukaryotes, spermine, spermidine, and putrescine, exist in millimolar intracellular concentrations that are tightly regulated through biosynthesis, catabolism, and transport. Polyamines interact with, and regulate, negatively charged macromolecules, including nucleic acids, proteins, and ion channels. Accordingly, alterations in polyamine metabolism affect cellular proliferation and survival through changes in gene expression and transcription, translation, autophagy, oxidative stress, and apoptosis. Dysregulation of these multifaceted polyamine functions contribute to multiple disease processes, thus their metabolism and function have been targeted for preventive or therapeutic intervention. The correlation between elevated polyamine levels and cancer is well established, and ornithine decarboxylase, the rate-limiting biosynthetic enzyme in the production of putrescine, is a bona fide transcriptional target of the Myc oncogene. Furthermore, induced polyamine catabolism contributes to carcinogenesis that is associated with certain forms of chronic infection and/or inflammation through the production of reactive oxygen species. These and other characteristics specific to cancer cells have led to the development of polyamine-based agents and inhibitors aimed at exploiting the polyamine metabolic pathway for chemotherapeutic and chemopreventive benefit. In addition to cancer, polyamines are involved in the pathologies of neurodegenerative diseases including Alzheimer’s and Parkinson’s, parasitic and infectious diseases, wound healing, ischemia/reperfusion injuries, and certain age-related conditions, as polyamines are known to decrease with age. As in cancer, polyamine-based therapies for these conditions are an area of active investigation. With recent advances in immunotherapy, interest has increased regarding polyamine-associated modulation of immune responses, as well as potential immunoregulation of polyamine metabolism, the results of which could have relevance to multiple disease processes. The goal of this Special Issue of Medical Sciences is to present the most recent advances in polyamine research as it relates to health, disease, and/or therapy.

Keywords

polyamine transport inhibitor --- Drosophila imaginal discs --- difluoromethylorthinine --- DFMO --- polyamine --- cancer --- metabolism --- difluoromethylornithine --- polyamine transport inhibitor --- pancreatic ductal adenocarcinoma --- curcumin --- diferuloylmethane --- ornithine decarboxylase --- polyamine --- NF-?B --- chemoprevention --- carcinogenesis --- polyphenol --- ornithine decarboxylase --- polyamines --- untranslated region --- polyamines --- ?-difluoromethylornithine --- polyamine transport system --- melanoma --- mutant BRAF --- spermine --- spermidine --- putrescine --- polyamine metabolism --- mast cells --- eosinophils --- neutrophils --- M2 macrophages --- airway smooth muscle cells --- Streptococcus pneumoniae --- polyamines --- pneumococcal pneumonia --- proteomics --- capsule --- complementation --- metabolism --- cadaverine --- polyamines --- ornithine decarboxylase --- difluoromethylornithine --- eflornithine --- DFMO --- African sleeping sickness --- hirsutism --- colorectal cancer --- neuroblastoma --- aging --- atrophy --- autophagy --- oxidative stress --- polyamines --- skeletal muscle --- spermidine --- spermine oxidase --- transgenic mouse --- immunity --- T-lymphocytes --- B-lymphocytes --- tumor immunity --- metabolism --- epigenetics --- autoimmunity --- polyamines --- ornithine decarboxylase --- polyamine analogs --- spermidine/spermine N1-acetyl transferase --- spermine oxidase --- bis(ethyl)polyamine analogs --- breast cancer --- MCF-7 cells --- transgenic mice --- polyamines --- MYC --- protein synthesis in cancer --- neuroblastoma --- protein expression --- antizyme 1 --- ornithine decarboxylase --- CRISPR --- human embryonic kidney 293 (HEK293) --- cell differentiation --- DFMO --- ornithine decarboxylase --- osteosarcoma --- polyamines --- polyamines --- polyamine metabolism --- antizyme --- antizyme inhibitors --- ornithine decarboxylase --- Snyder-Robinson Syndrome --- spermine synthase --- X-linked intellectual disability --- polyamine transport --- spermidine --- spermine --- transglutaminase

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