keyword
MENU ▼
Read by QxMD icon Read
search

de novo assembly

keyword
https://www.readbyqxmd.com/read/28089944/rsm22-mtysxc-and-pnkd-like-proteins-are-required-for-mitochondrial-translation-in-trypanosoma-brucei
#1
Jiří Týč, Lucie Novotná, Priscila Peña-Diaz, Dmitri A Maslov, Julius Lukeš
Mitochondrial ribosomes evolved from prokaryotic ribosomes, with which they therefore share more common features than with their counterparts in the cytosol. Yet, mitochondrial ribosomes are highly diverse in structure and composition, having undergone considerable changes, including reduction of their RNA component and varying degree of acquisition of novel proteins in various phylogenetic lineages. Here, we present functional analysis of three putative mitochondrial ribosome-associated proteins (RSM22, mtYsxC and PNKD-like) in Trypanosoma brucei, originally identified by database mining...
January 12, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28088723/discovery-and-metagenomic-analysis-of-an-anammox-bacterial-enrichment-related-to-candidatus-brocadia-caroliniensis-in-a-full-scale-glycerol-fed-nitritation-denitritation-separate-centrate-treatment-process
#2
Hongkeun Park, Ariane C Brotto, Mark C M van Loosdrecht, Kartik Chandran
A distinctive red biofilm was observed in a glycerol-fed digester liquid effluent treatment process coupling partial nitrification (nitritation) and partial denitrification (denitritation) processes. Based on initial phylogenetic screening using 16S rRNA clone libraries and quantitative polymerase chain reaction, the biofilm was enriched in novel anaerobic ammonium oxidizing bacteria (AMX/anammox) closely related to Candidatus "Brocadia caroliniensis". The metabolic functionality of the C. "Brocadia caroliniensis" enrichment was further explored using high-throughput sequencing and de novo metagenome assembly...
January 6, 2017: Water Research
https://www.readbyqxmd.com/read/28087768/the-rice-paradox-multiple-origins-but-single-domestication-in-asian-rice
#3
Jae Young Choi, Adrian E Platts, Dorian Q Fuller, Yue-Ie Hsing, Rod A Wing, Michael D Purugganan
The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087732/novel-gnb1-mutations-disrupt-assembly-and-function-of-g-protein-heterotrimers-and-cause-global-developmental-delay-in-humans
#4
Katja Lohmann, Ikuo Masuho, Dipak N Patil, Hauke Baumann, Eva Hebert, Sofia Steinrücke, Daniel Trujillano, Nickolas K Skamangas, Valerija Dobricic, Irina Hüning, Gabriele Gillessen-Kaesbach, Ana Westenberger, Dusanka Savic-Pavicevic, Alexander Münchau, Gabriela Oprea, Christine Klein, Arndt Rolfs, Kirill A Martemyanov
Global developmental delay (GDD), often accompanied by intellectual disability, seizures and other features is a severe, clinically and genetically highly heterogeneous childhood-onset disorder. In cases where genetic causes have been identified, de-novo mutations in neuronally expressed genes are a common scenario. These mutations can be best identified by exome sequencing of parent-offspring trios. De novo mutations in the guanine nucleotide-binding protein, beta 1 (GNB1) gene, encoding the Gβ1 subunit of heterotrimeric G proteins, have recently been identified as a novel genetic cause of GDD...
January 13, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28087693/de-novo-genome-and-transcriptome-assembly-of-the-canadian-beaver-castor-canadensis
#5
Si Lok, Tara A Paton, Zhuozhi Wang, Gaganjot Kaur, Susan Walker, Ryan K C Yuen, Wilson W L Sung, Joseph Whitney, Janet A Buchanan, Brett Trost, Naina Singh, Beverly Apresto, Nan Chen, Matthew Coole, Travis J Dawson, Karen Y Ho, Zhizhou Hu, Sanjeev Pullenayegum, Kozue Samler, Arum Shipstone, Fiona Tsoi, Ting Wang, Sergio L Pereira, Pirooz Rostami, Carol Ann Ryan, Amy Hin Yan Tong, Karen Ng, Yogi Sundaravadanam, Jared T Simpson, Burton K Lim, Mark D Engstrom, Christopher J Dutton, Kevin C R Kerr, Maria Franke, William Rapley, Richard F Wintle, Stephen W Scherer
The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long-reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by shortreads (80 ×) and checked for accuracy by congruency against an independent short-read assembly...
January 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28087610/long-non-coding-rna-exchange-during-the-oocyte-to-embryo-transition-in-mice
#6
Rosa Karlic, Sravya Ganesh, Vedran Franke, Eliska Svobodova, Jana Urbanova, Yutaka Suzuki, Fugaku Aoki, Kristian Vlahovicek, Petr Svoboda
The oocyte-to-embryo transition (OET) transforms a differentiated gamete into pluripotent blastomeres. The accompanying maternal-zygotic RNA exchange involves remodeling of the long non-coding RNA (lncRNA) pool. Here, we used next generation sequencing and de novo transcript assembly to define the core population of 1,600 lncRNAs expressed during the OET (lncRNAs). Relative to mRNAs, OET lncRNAs were less expressed and had shorter transcripts, mainly due to fewer exons and shorter 5' terminal exons. Approximately half of OET lncRNA promoters originated in retrotransposons suggesting their recent emergence...
January 13, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28086783/de-novo-transcriptome-analysis-of-rose-scented-geranium-provides-insights-into-the-metabolic-specificity-of-terpene-and-tartaric-acid-biosynthesis
#7
Lokesh K Narnoliya, Girija Kaushal, Sudhir P Singh, Rajender S Sangwan
BACKGROUND: Rose-scented geranium (Pelargonium sp.) is a perennial herb that produces a high value essential oil of fragrant significance due to the characteristic compositional blend of rose-oxide and acyclic monoterpenoids in foliage. Recently, the plant has also been shown to produce tartaric acid in leaf tissues. Rose-scented geranium represents top-tier cash crop in terms of economic returns and significance of the plant and plant products. However, there has hardly been any study on its metabolism and functional genomics, nor any genomic expression dataset resource is available in public domain...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28077064/an-internet-based-bioinformatics-toolkit-for-plant-biosecurity-diagnosis-and-surveillance-of-viruses-and-viroids
#8
Roberto A Barrero, Kathryn R Napier, James Cunnington, Lia Liefting, Sandi Keenan, Rebekah A Frampton, Tamas Szabo, Simon Bulman, Adam Hunter, Lisa Ward, Mark Whattam, Matthew I Bellgard
BACKGROUND: Detection and preventing entry of exotic viruses and viroids at the border is critical for protecting plant industries trade worldwide. Existing post entry quarantine screening protocols rely on time-consuming biological indicators and/or molecular assays that require knowledge of infecting viral pathogens. Plants have developed the ability to recognise and respond to viral infections through Dicer-like enzymes that cleave viral sequences into specific small RNA products. Many studies reported the use of a broad range of small RNAs encompassing the product sizes of several Dicer enzymes involved in distinct biological pathways...
January 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28071753/de-novo-assembly-annotation-and-characterization-of-the-whole-brain-transcriptome-of-male-and-female-syrian-hamsters
#9
Katharine E McCann, David M Sinkiewicz, Alisa Norvelle, Kim L Huhman
Hamsters are an ideal animal model for a variety of biomedical research areas such as cancer, virology, circadian rhythms, and behavioural neuroscience. The use of hamsters has declined, however, most likely due to the dearth of genetic tools available for these animals. Our laboratory uses hamsters to study acute social stress, and we are beginning to investigate the genetic mechanisms subserving defeat-induced behavioural change. We have been limited, however, by the lack of genetic resources available for hamsters...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28070488/transcriptome-profiling-of-elettaria-cardamomum-l-maton-small-cardamom
#10
F Nadiya, N Anjali, Jinu Thomas, A Gangaprasad, K K Sabu
Elettaria cardamomum (L.) Maton, known as 'queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base) and 24,889,197 (75 base) raw reads accounting for approximately 8...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28069632/a-few-sequence-polymorphisms-among-isolates-of-maize-bushy-stunt-phytoplasma-associate-with-organ-proliferation-symptoms-of-infected-maize-plants
#11
Zigmunds Orlovskis, Maria Cristina Canale, Mindia Haryono, João Roberto Spotti Lopes, Chih-Horng Kuo, Saskia A Hogenhout
BACKGROUND AND AIMS: Maize bushy stunt phytoplasma (MBSP) is a bacterial pathogen of maize (Zea mays L.) across Latin America. MBSP belongs to the 16SrI-B sub-group within the genus 'Candidatus Phytoplasma'. MBSP and its insect vector Dalbulus maidis (Hemiptera: Cicadellidae) are restricted to maize; both are thought to have coevolved with maize during its domestication from a teosinte-like ancestor. MBSP-infected maize plants show a diversity of symptoms. and it is likely that MBSP is under strong selection for increased virulence and insect transmission on maize hybrids that are widely grown in Brazil...
January 9, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28069422/identification-of-ecdysteroid-receptor-mediated-signaling-pathways-in-the-hepatopancreas-of-the-red-swamp-crayfish-procambarus-clarkii
#12
Baojian Zhu, Lin Tang, Yingying Yu, Huimin Yu, Lei Wang, Cen Qian, Guoqing Wei, Chaoliang Liu
The hepatopancreas of crustaceans plays an important role in lipid and carbohydrate metabolism, digestion of food, and biogenesis. In this study, the hepatopancreas transcriptome from the red crayfish Procambarus clarkii was characterized for the first time using high-throughput sequencing, producing approximately 41.4 million reads were obtained. After de novo assembly, 57,363 unigenes with an average length of 725bp were identified, Gene Ontology analysis categorized 22,580 as being involved in biological processes, among which metabolic process and cellular process groups were the most highly enriched...
January 6, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28068919/construction-of-high-resolution-recombination-maps-in-asian-seabass
#13
Le Wang, Bin Bai, Peng Liu, Shu Qing Huang, Zi Yi Wan, Elaine Chua, Baoqing Ye, Gen Hua Yue
BACKGROUND: A high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a number of genomic resources are available in Asian seabass (Lates calcarifer), a high-density linkage map is still lacking. To facilitate QTL mapping for marker-assisted selection and genome assembly, and to understand the genome-wide recombination rates, we constructed high density linkage maps using three families and genotyping by sequencing...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28068432/transcriptome-analysis-of-leaves-flowers-and-fruits-perisperm-of-coffea-arabica-l-reveals-the-differential-expression-of-genes-involved-in-raffinose-biosynthesis
#14
Suzana Tiemi Ivamoto, Osvaldo Reis, Douglas Silva Domingues, Tiago Benedito Dos Santos, Fernanda Freitas de Oliveira, David Pot, Thierry Leroy, Luiz Gonzaga Esteves Vieira, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, Luiz Filipe Protasio Pereira
Coffea arabica L. is an important crop in several developing countries. Despite its economic importance, minimal transcriptome data are available for fruit tissues, especially during fruit development where several compounds related to coffee quality are produced. To understand the molecular aspects related to coffee fruit and grain development, we report a large-scale transcriptome analysis of leaf, flower and perisperm fruit tissue development. Illumina sequencing yielded 41,881,572 high-quality filtered reads...
2017: PloS One
https://www.readbyqxmd.com/read/28066917/balancing-exploration-and-exploitation-in-population-based-sampling-improves-fragment-based-de-novo-protein-structure-prediction
#15
David Simoncini, Thomas Schiex, Kam Y J Zhang
Conformational search space exploration remains a major bottleneck for protein structure prediction methods. Population-based meta-heuristics typically enable the possibility to control the search dynamics and to tune the balance between local energy minimization and search space exploration. EdaFold is a fragment-based approach that can guide search by periodically updating the probability distribution over the fragment libraries used during model assembly. We implement the EdaFold algorithm as a Rosetta protocol and provide two different probability update policies: a cluster-based variation (EdaRosec ) and an energy-based one (EdaRoseen ) We analyze the search dynamics of our new Rosetta protocols and show that EdaRosec EdaRosec is able to provide predictions with lower Cα RMSD to the native structure than EdaRoseen and Rosetta AbInitio Relax protocol...
January 9, 2017: Proteins
https://www.readbyqxmd.com/read/28066713/sequencing-and-de-novo-transcriptome-assembly-of-anthopleura-dowii-verrill-1869-from-mexico
#16
Jorge-Tonatiuh Ayala-Sumuano, Alexei Licea-Navarro, Enrique Rudiño-Piñera, Estefanía Rodríguez, Claudia Rodríguez-Almazán
Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Moreover, the development of tools for big data set analysis has allowed the identification of molecules and networks involved in metabolism, evolution or behavior. By natural habitats aquatic organisms have implemented molecular strategies for survival, including the production and secretion of toxic compounds for their predators; therefore these organisms are possible sources of proteins or peptides with potential biotechnological application...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28066712/de-novo-transcriptome-assembly-of-shrimp-palaemon-serratus
#17
Alejandra Perina, Ana M González-Tizón, Iago F Meilán, Andrés Martínez-Lage
: The shrimp Palaemon serratus is a coastal decapod crustacean with a high commercial value. It is harvested for human consumption. In this study, we used Illumina sequencing technology (HiSeq 2000) to sequence, assemble and annotate the transcriptome of P. serratus. RNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The raw data in this study was deposited in NCBI SRA database with study accession number of SRP090769...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28064006/versatile-rna-tetra-u-helix-linking-motif-as-a-toolkit-for-nucleic-acid-nanotechnology
#18
My N Bui, M Brittany Johnson, Mathias Viard, Emily Satterwhite, Angelica N Martins, Zhihai Li, Ian Marriott, Kirill A Afonin, Emil F Khisamutdinov
RNA nanotechnology employs synthetically modified ribonucleic acid (RNA) to engineer highly stable nanostructures in one, two, and three dimensions for medical applications. Despite the tremendous advantages in RNA nanotechnology, unmodified RNA itself is fragile and prone to enzymatic degradation. In contrast to use traditionally modified RNA strands e.g. 2'-fluorine, 2'-amine, 2'-methyl, we studied the effect of RNA/DNA hybrid approach utilizing a computer-assisted de novo RNA tetra-uracil (tetra-U) motif as a toolkit to address questions related to assembly efficiency, versatility, stability, and the production costs of hybrid RNA/DNA nanoparticles...
January 4, 2017: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/28062442/sine_scan-an-efficient-tool-to-discover-short-interspersed-nuclear-elements-sines-in-large-scale-genomic-datasets
#19
Hongliang Mao, Hao Wang
MOTIVATION: Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences. RESULTS: Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element...
January 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28061749/organelle_pba-a-pipeline-for-assembling-chloroplast-and-mitochondrial-genomes-from-pacbio-dna-sequencing-data
#20
Aboozar Soorni, David Haak, David Zaitlin, Aureliano Bombarely
BACKGROUND: The development of long-read sequencing technologies, such as single-molecule real-time (SMRT) sequencing by PacBio, has produced a revolution in the sequencing of small genomes. Sequencing organelle genomes using PacBio long-read data is a cost effective, straightforward approach. Nevertheless, the availability of simple-to-use software to perform the assembly from raw reads is limited at present. RESULTS: We present Organelle-PBA, a Perl program designed specifically for the assembly of chloroplast and mitochondrial genomes...
January 7, 2017: BMC Genomics
keyword
keyword
114082
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"