HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing

Nucleic Acids Research, Journal Year: 2016, Volume and Issue: 44(W1), P. W58 - W63

Published: April 15, 2016

Mitochondrial DNA (mtDNA) profiles can be classified into phylogenetic clusters (haplogroups), which is of great relevance for evolutionary, forensic and medical genetics. With the extensive growth underlying tree summarizing published mtDNA sequences, manual process haplogroup classification would too time-consuming. The previously tool HaploGrep provided an automatic way to address this issue. Here, we present completely updated version 2 offering several advanced features, including a generic rule-based system immediate quality control (QC). This allows detecting artificial recombinants missing variants as well annotating rare phantom mutations. Furthermore, handling high-throughput data in form VCF files now directly supported. For output, graphical reports are generated real time, such multiple sequence alignment format, format extended QC reports, all viewable within application. In addition, generates publication-ready input samples encoded relative revised Cambridge Reference Sequence. Finally, new distance measures optimizations algorithm increase accuracy speed-up accessed freely without any registration at http://haplogrep.uibk.ac.at.

Language: Английский

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Big data analytics on Apache Spark

International Journal of Data Science and Analytics, Journal Year: 2016, Volume and Issue: 1(3-4), P. 145 - 164

Published: Oct. 13, 2016

Language: Английский

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EDGAR 2.0: an enhanced software platform for comparative gene content analyses

Nucleic Acids Research, Journal Year: 2016, Volume and Issue: 44(W1), P. W22 - W28

Published: April 20, 2016

The rapidly increasing availability of microbial genome sequences has led to a growing demand for bioinformatics software tools that support the functional analysis based on comparison closely related genomes. By utilizing comparative approaches gene level it is possible gain insights into core genes which represent set shared features organisms under study. Vice versa singleton can be identified elucidate specific properties an individual genome. Since initial publication, EDGAR platform become one most established in field genomics. Over last years, been continuously improved and large number new have added. For version, 2.0, orthology estimation approach was newly designed completely re-implemented. Among other features, 2.0 provides extended phylogenetic like AAI (Average Amino Acid Identity) ANI Nucleotide matrices, size statistics modernized visualizations interactive synteny plots or Venn diagrams. Thereby, supports quick user-friendly survey evolutionary relationships between genomes simplifies process obtaining biological their differential content. All are offered scientific community via web-based therefore platform-independent user interface, allows easy browsing precomputed datasets. web server accessible at http://edgar.computational.bio.

Language: Английский

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Alzheimer’s disease, dementia, and stem cell therapy

Stem Cell Research & Therapy, Journal Year: 2017, Volume and Issue: 8(1)

Published: May 12, 2017

Alzheimer’s disease (AD) represents arguably the most significant social, economic, and medical crisis of our time. Characterized by progressive neurodegenerative pathology, AD is first foremost a condition neuronal synaptic loss. Repopulation regeneration depleted circuitry exogenous stem cells therefore rational therapeutic strategy. This review will focus on recent advances in cell therapies utilizing animal models AD, as well detailing human clinical trials for that are currently undergoing development.

Language: Английский

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Advances in digital polymerase chain reaction (dPCR) and its emerging biomedical applications

Biosensors and Bioelectronics, Journal Year: 2016, Volume and Issue: 90, P. 459 - 474

Published: Sept. 25, 2016

Language: Английский

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Transposable elements are the primary source of novelty in primate gene regulation

Genome Research, Journal Year: 2017, Volume and Issue: 27(10), P. 1623 - 1633

Published: Aug. 30, 2017

Gene regulation shapes the evolution of phenotypic diversity. We investigated liver promoters and enhancers in six primate species using ChIP-seq (H3K27ac H3K4me1) to profile cis-regulatory elements (CREs) RNA-seq characterize gene expression same individuals. To quantify regulatory divergence, we compared CRE activity across by testing differential read depths directly measured for orthologous sequences. show that landscape is largely conserved lineage, with 63% tested human CREs showing similar species. Conserved function associated sequence conservation, proximity coding genes, cell-type specificity, transcription factor binding. Newly evolved are enriched immune response neurodevelopmental functions. further demonstrate bind master regulators, suggesting while contribute adaptation environment, core functions remain intact. young transposable (TEs), including Long-Terminal-Repeats (LTRs) SINE-VNTR-Alus (SVAs), significantly affect expression. Conversely, only 16% overlap TEs. 69 TE subfamilies luciferase reporter assays, spanning all major classes, showed 95.6% TEs can as either transcriptional activators or repressors. In conclusion, demonstrated critical role illustrated potential mechanisms underlying evolutionary divergence among through noncoding genome.

Language: Английский

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Tolerance of citrus plants to the combination of high temperatures and drought is associated to the increase in transpiration modulated by a reduction in abscisic acid levels

BMC Plant Biology, Journal Year: 2016, Volume and Issue: 16(1)

Published: April 27, 2016

In natural environments, several adverse environmental conditions occur simultaneously constituting a unique stress factor. this work, physiological parameters and the hormonal regulation of Carrizo citrange Cleopatra mandarin, two citrus genotypes, in response to combined action high temperatures water deprivation were studied. The objective was characterize particular responses combination. Experiments indicated that is more tolerant combination than mandarin. Furthermore, an experimental design spanning 24 h duration, heat applied alone induced higher stomatal conductance transpiration both genotypes whereas partially counteracted response. Comparing showed phostosystem-II efficiency lower oxidative damage Hormonal profiling leaves revealed salicylic acid (SA) accumulated individual stresses but extent samples subjected drought (showing additive response). SA accumulation correlated with up-regulation pathogenesis-related gene 2 (CsPR2), as downstream On contrary, abscisic (ABA) water-stressed plants followed by observed under ABA signaling these confirmed expression responsive ABA-related 18 (CsRAB18). Modulation levels likely carried out induction 9-neoxanthin cis-epoxicarotenoid dioxygenase (CsNCED) 8'-hydroxylase (CsCYP707A) while conversion ABA-glycosyl ester (ABAGE) less prominent process despite strong O-glycosyl transferase (CsAOG). mandarin susceptible citrange. This result rate could allow efficient cooling leaf surface ensuring optimal CO2 intake. Hence, not sufficient protect PSII from photoinhibition, resulting malondialdehyde (MDA) build-up. Inhibition during achieved primarily through CsCYP707A leading phaseic (PA) dehydrophaseic (DPA) production. To sum up, data indicate specific exist citrus. addition, are differently modulated depending on tolerance genotypes.

Language: Английский

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Profiling of 2′-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity

Nucleic Acids Research, Journal Year: 2016, Volume and Issue: 44(16), P. 7884 - 7895

Published: June 1, 2016

Ribose methylation is one of the two most abundant modifications in human ribosomal RNA and believed to be important for ribosome biogenesis, mRNA selectivity translational fidelity. We have applied RiboMeth-seq rRNA from HeLa cells ribosome-wide, quantitative mapping 2′-O-Me sites obtained a comprehensive set 106 sites, including novel with plausible box C/D guide RNAs assigned all but three sites. find approximately two-thirds fully methylated remainder fractionally modified support heterogeneity at level modifications. A comparison HCT116 reveals similar profiles distinct differences several This study constitutes first using high throughput sequencing approach. It establishes existence core constitutively positions subset variable, potentially regulatory positions, paves way experimental analyses role variations under different physiological or pathological settings.

Language: Английский

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Genotype by environment interactions in forest tree breeding: review of methodology and perspectives on research and application

Tree Genetics & Genomes, Journal Year: 2017, Volume and Issue: 13(3)

Published: May 9, 2017

Genotype by environment interaction (G×E) refers to the comparative performances of genotypes differing among environments, representing differences in genotype rankings or level expression genetic environments. G×E can reduce heritability and overall gain, unless breeding programmes are structured address different categories Understanding impact G×E, role environments generating problems opportunities is vital efficient programme design deployment material. We review current main analytical methods for identifying G×E: factor analytic models, biplot analysis reaction norm. also biological statistical evidence growth, form wood properties forest species global economic importance, including some pines, eucalypts, Douglas-fir, spruces poplars. Among these species, high levels tend be reported growth traits, with low traits properties. Finally, we discuss possible ways exploiting maximise gain tree breeding. Characterising interactions seen as basic platform, allowing testing candidate genotypes. importance level-of-expression interaction, relative rank-change being greater than many past reports, especially decisions. examine impacts on breeding, environmental factors that cause strategies dealing future genomics.

Language: Английский

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A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing

BMC Genomics, Journal Year: 2017, Volume and Issue: 18(1)

Published: May 22, 2017

Despite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most transcriptomic studies have been based on Saccharum officinarum gene indices (SoGI), expressed sequence tags (ESTs) de novo assembled transcript contigs from short-reads; hence knowledge transcriptome limited relation to length number isoforms.The was sequenced using PacBio isoform sequencing (Iso-Seq) pooled RNA sample derived leaf, internode root tissues, different developmental stages, 22 varieties, explore potential for capturing full-length isoforms. A total 107,598 unique isoforms were obtained, representing about 71% predicted genes. The majority this dataset (92%) matched plant protein database, while just over 2% novel transcripts, putative long non-coding RNAs. About 56% 23% sequences annotated against ontology KEGG pathway databases, respectively. Comparison with Illumina RNA-Sequencing (RNA-Seq) samples same experiment public databases showed that Iso-Seq method recovered more isoforms, had higher N50 average largest 1,000 proteins; whereas greater representation content diversity captured RNA-Seq. Only 62% 67% contigs, non-matched proportions attributed inclusion leaf/root tissues normalization PacBio, classes assembly, 69% 41% aligned sorghum genome, indicating high conservation orthologs genic regions two genomes.The should contribute improved models predictions; will serve as database analysis expression sugarcane.

Language: Английский

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