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Frontiers in Genetics

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https://www.readbyqxmd.com/read/28634486/%C3%AE-cell-replacement-strategies-the-increasing-need-for-a-%C3%AE-cell-dogma
#1
REVIEW
Andhira Vieira, Noémie Druelle, Fabio Avolio, Tiziana Napolitano, Sergi Navarro-Sanz, Serena Silvano, Patrick Collombat
Type 1 diabetes is an auto-immune disease resulting in the loss of pancreatic β-cells and, consequently, in chronic hyperglycemia. Insulin supplementation allows diabetic patients to control their glycaemia quite efficiently, but treated patients still display an overall shortened life expectancy and an altered quality of life as compared to their healthy counterparts. In this context and due to the ever increasing number of diabetics, establishing alternative therapies has become a crucial research goal. Most current efforts therefore aim at generating fully functional insulin-secreting β-like cells using multiple approaches...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28620412/single-cell-mrna-sequencing-in-cancer-research-integrating-the-genomic-fingerprint
#2
REVIEW
Sören Müller, Aaron Diaz
Critical cancer mutations are often regional and mosaic, confounding the efficacy of targeted therapeutics. Single cell mRNA sequencing (scRNA-seq) has enabled unprecedented studies of intra-tumor heterogeneity and its role in cancer progression, metastasis, and treatment resistance. When coupled with DNA sequencing, scRNA-seq allows one to infer the in vivo impact of genomic alterations on gene expression. This combination can be used to reliably distinguish neoplastic from non-neoplastic cells, to correlate paracrine-signaling pathways between neoplastic cells and stroma, and to map expression signatures to inferred clones and phylogenies...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28620411/vicar-an-adaptive-and-landmark-free-registration-of-time-lapse-image-data-from-microfluidics-experiments
#3
Georges Hattab, Jan-Philip Schlüter, Anke Becker, Tim W Nattkemper
In order to understand gene function in bacterial life cycles, time lapse bioimaging is applied in combination with different marker protocols in so called microfluidics chambers (i.e., a multi-well plate). In one experiment, a series of T images is recorded for one visual field, with a pixel resolution of 60 nm/px. Any (semi-)automatic analysis of the data is hampered by a strong image noise, low contrast and, last but not least, considerable irregular shifts during the acquisition. Image registration corrects such shifts enabling next steps of the analysis (e...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28611826/the-evolution-of-bacterial-genome-architecture
#4
REVIEW
Louis-Marie Bobay, Howard Ochman
The genome architecture of bacteria and eukaryotes evolves in opposite directions when subject to genetic drift, a difference that can be ascribed to the fact that bacteria exhibit a mutational bias that deletes superfluous sequences, whereas eukaryotes are biased toward large insertions. Expansion of eukaryotic genomes occurs through the addition of non-functional sequences, such as repetitive sequences and transposable elements, whereas variation in bacterial genome size is largely due to the acquisition and loss of functional accessory genes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28611825/epigenetic-combinatorial-patterns-predict-disease-variants
#5
Yu Zhang
Most genetic variants identified in genome-wide association studies are noncoding and are likely tagging nearby causal variants. It is a challenging task to pinpoint the precise locations of disease-causal variants and understand their functions in disease. A promising approach to improve fine mapping is to integrate the functional data currently available on hundreds of human tissues and cell types. Although there are several methods that use functional data to prioritize disease variants, they mainly use linear models, or equivalent naive likelihood-based models for prediction...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28611824/posttranscriptional-regulation-controls-calretinin-expression-in-malignant-pleural-mesothelioma
#6
Jelena Kresoja-Rakic, Merve Sulemani, Michaela B Kirschner, Manuel Ronner, Glen Reid, Steven Kao, Beat Schwaller, Walter Weder, Rolf A Stahel, Emanuela Felley-Bosco
Calretinin (CALB2) is a diagnostic and prognostic marker in malignant pleural mesothelioma (MPM). We previously reported that calretinin expression is regulated at the mRNA level. The presence of a medium-sized (573 nucleotide) 3' untranslated region (3'UTR) predicted to contain binding sites for miR-30a/b/c/d/e and miR-9 as well as an adenine/uridine-rich element (ARE) in all three transcripts arising from the CALB2 gene, suggests that calretinin expression is regulated via posttranscriptional mechanisms. Our aim was to investigate the role of the CALB2-3'UTR in the posttranscriptional regulation of calretinin expression in MPM...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28611823/genetic-variability-as-a-regulator-of-tlr4-and-nod-signaling-in-response-to-bacterial-driven-dna-damage-response-ddr-and-inflammation-focus-on-the-gastrointestinal-gi-tract
#7
REVIEW
Evagelia Spanou, Polyxeni Kalisperati, Ioannis S Pateras, Alexandros Papalampros, Alexandra Barbouti, Athanasios G Tzioufas, Athanassios Kotsinas, Stavros Sougioultzis
The fundamental role of human Toll-like receptors (TLRs) and NOD-like receptors (NLRs), the two most studied pathogen recognition receptors (PRRs), is the protection against pathogens and excessive tissue injury. Recent evidence supports the association between TLR/NLR gene mutations and susceptibility to inflammatory, autoimmune, and malignant diseases. PRRs also interfere with several cellular processes, such as cell growth, apoptosis, cell proliferation, differentiation, autophagy, angiogenesis, cell motility and migration, and DNA repair mechanisms...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28596784/indy-a-new-link-to-metabolic-regulation-in-animals-and-humans
#8
REVIEW
Blanka Rogina
The Indy (I'm Not Dead Yet) gene encodes the fly homolog of the mammalian SLC13A5 citrate transporter. Reduced expression of the Indy gene in flies and worms extends their longevity. INDY is expressed in the plasma membrane of metabolically active tissues. Decreased expression of Indy in worms, flies, mice, and rats alters metabolism in a manner similar to calorie restriction. Reducing INDY activity prevents weight gain in flies, worms, and mice, and counteracts the negative effects of age or a high fat diet on metabolism and insulin sensitivity...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28588610/ubiquitination-and-sumoylation-in-telomere-maintenance-and-dysfunction
#9
REVIEW
Zeliha Yalçin, Carolin Selenz, Jacqueline J L Jacobs
Telomeres are essential nucleoprotein structures at linear chromosomes that maintain genome integrity by protecting chromosome ends from being recognized and processed as damaged DNA. In addition, they limit the cell's proliferative capacity, as progressive loss of telomeric DNA during successive rounds of cell division eventually causes a state of telomere dysfunction that prevents further cell division. When telomeres become critically short, the cell elicits a DNA damage response resulting in senescence, apoptosis or genomic instability, thereby impacting on aging and tumorigenesis...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28588609/metabolic-and-genetic-markers-of-biological-age
#10
S Michal Jazwinski, Sangkyu Kim
Biological age is a concept that takes into account the heterogeneity of the aging process in different individuals that results in differences in survival and variations in relative health. Any measure of biological age must be better than chronological age at predicting mortality. Several quantitative measures of biological age have been developed. Among them are frailty indices, one of which called FI34 is discussed here in greater detail. FI34 increases exponentially with age reflecting decline in health and function ability...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28588608/an-enhancer-s-length-and-composition-are-shaped-by-its-regulatory-task
#11
Lily Li, Zeba Wunderlich
Enhancers drive the gene expression patterns required for virtually every process in metazoans. We propose that enhancer length and transcription factor (TF) binding site composition-the number and identity of TF binding sites-reflect the complexity of the enhancer's regulatory task. In development, we define regulatory task complexity as the number of fates specified in a set of cells at once. We hypothesize that enhancers with more complex regulatory tasks will be longer, with more, but less specific, TF binding sites...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28588607/single-cell-rna-sequencing-assessment-of-differential-expression-analysis-methods
#12
Alessandra Dal Molin, Giacomo Baruzzo, Barbara Di Camillo
The sequencing of the transcriptomes of single-cells, or single-cell RNA-sequencing, has now become the dominant technology for the identification of novel cell types and for the study of stochastic gene expression. In recent years, various tools for analyzing single-cell RNA-sequencing data have been proposed, many of them with the purpose of performing differentially expression analysis. In this work, we compare four different tools for single-cell RNA-sequencing differential expression, together with two popular methods originally developed for the analysis of bulk RNA-sequencing data, but largely applied to single-cell data...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28588606/mutations-in-the-not-genes-or-in-the-translation-machinery-similarly-display-increased-resistance-to-histidine-starvation
#13
Martine A Collart, Sari Kassem, Zoltan Villanyi
The NOT genes encode subunits of the conserved Ccr4-Not complex, a global regulator of gene expression, and in particular of mRNA metabolism. They were originally identified in a selection for increased resistance to histidine starvation in the yeast S. cerevisiae. Recent work indicated that the Not5 subunit, ortholog of mammalian CNOT3, determines global translation levels by defining binding of the Ccr4-Not scaffold protein Not1 to ribosomal mRNAs during transcription. This is needed for optimal translation of ribosomal proteins...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28580009/the-emerging-role-of-the-cytoskeleton-in-chromosome-dynamics
#14
REVIEW
Maya Spichal, Emmanuelle Fabre
Chromosomes underlie a dynamic organization that fulfills functional roles in processes like transcription, DNA repair, nuclear envelope stability, and cell division. Chromosome dynamics depend on chromosome structure and cannot freely diffuse. Furthermore, chromosomes interact closely with their surrounding nuclear environment, which further constrains chromosome dynamics. Recently, several studies enlighten that cytoskeletal proteins regulate dynamic chromosome organization. Cytoskeletal polymers that include actin filaments, microtubules and intermediate filaments can connect to the nuclear envelope via Linker of the Nucleoskeleton and Cytoskeleton (LINC) complexes and transfer forces onto chromosomes inside the nucleus...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28559915/combining-results-from-distinct-microrna-target-prediction-tools-enhances-the-performance-of-analyses
#15
Arthur C Oliveira, Luiz A Bovolenta, Pedro G Nachtigall, Marcos E Herkenhoff, Ney Lemke, Danillo Pinhal
Target prediction is generally the first step toward recognition of bona fide microRNA (miRNA)-target interactions in living cells. Several target prediction tools are now available, which use distinct criteria and stringency to provide the best set of candidate targets for a single miRNA or a subset of miRNAs. However, there are many false-negative predictions, and consensus about the optimum strategy to select and use the output information provided by the target prediction tools is lacking. We compared the performance of four tools cited in literature-TargetScan (TS), miRanda-mirSVR (MR), Pita, and RNA22 (R22), and we determined the most effective approach for analyzing target prediction data (individual, union, or intersection)...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28555154/amyloid-%C3%AE-modification-a-key-to-the-sporadic-alzheimer-s-disease
#16
Evgeny P Barykin, Vladimir A Mitkevich, Sergey A Kozin, Alexander A Makarov
No abstract text is available yet for this article.
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28553318/non-coding-rnas-in-the-ovarian-follicle
#17
Rosalia Battaglia, Maria E Vento, Placido Borzì, Marco Ragusa, Davide Barbagallo, Desirée Arena, Michele Purrello, Cinzia Di Pietro
The mammalian ovarian follicle is the complex reproductive unit comprising germ cell, somatic cells (Cumulus and Granulosa cells), and follicular fluid (FF): paracrine communication among the different cell types through FF ensures the development of a mature oocyte ready for fertilization. This paper is focused on non-coding RNAs in ovarian follicles and their predicted role in the pathways involved in oocyte growth and maturation. We determined the expression profiles of microRNAs in human oocytes and FF by high-throughput analysis and identified 267 microRNAs in FF and 176 in oocytes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28553317/meta-analysis-of-human-alzgene-database-benefits-and-limitations-of-using-c-elegans-for-the-study-of-alzheimer-s-disease-and-co-morbid-conditions
#18
Behrad Vahdati Nia, Christine Kang, Michelle G Tran, Deborah Lee, Shin Murakami
Human genome-wide association studies (GWAS) and linkage studies have identified 695 genes associated with Alzheimer's disease (AD), the vast majority of which are associated with late-onset AD. Although orthologs of these AD genes have been studied in several model species, orthologs in the nematode, Caenorhabditis elegans, remain incompletely identified, with orthologs to only 17 AD-related genes identified in the C. elegans database, WormBase. Therefore, we performed a comprehensive search for additional C...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28536601/geneticizing-ethnicity-and-diet-anti-doping-science-and-its-social-impact-in-the-age-of-post-genomics
#19
Jaehwan Hyun
While gene doping and other technological means of sport enhancement have become a topic of ethical debate, a major outcome from genomic research in sports is often linked to the regulation of doping. In particular, researchers within the field of anti-doping science, a regulatory science that aims to develop scientific solutions for regulating doped athletes, have conducted genomic research on anabolic-androgenic steroids. Genomic knowledge on anabolic-androgenic steroids, a knowledge base that has been produced to improve doping regulation, has caused the 'geneticization' of cultural objects such as ethnic identities and dietary habits...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28536600/evolinc-a-tool-for-the-identification-and-evolutionary-comparison-of-long-intergenic-non-coding-rnas
#20
Andrew D L Nelson, Upendra K Devisetty, Kyle Palos, Asher K Haug-Baltzell, Eric Lyons, Mark A Beilstein
Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering ~90% of the genome. In addition to elucidating function, there is particular interest in understanding the origin and evolution of lincRNAs. Aside from mammals, lincRNA populations have been sparsely sampled, precluding evolutionary analyses focused on their emergence and persistence...
2017: Frontiers in Genetics
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