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International Journal of Genomics

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https://www.readbyqxmd.com/read/30627531/comparative-transcriptome-analysis-of-temperature-induced-green-discoloration-in-garlic
#1
Ningyang Li, Zhichang Qiu, Xiaoming Lu, Bingchao Shi, Xiudong Sun, Xiaozhen Tang, Xuguang Qiao
Green discoloration is one of the most important problems that cause low quality of product in the processing of garlic, which can be induced by low-temperature stress. But the mechanism of low temperature-induced green discoloration is poorly understood. In the present study, the control garlic and three low temperature-treated garlic samples (stored at 4°C with 10, 15, and 40 days, respectively) were used for genome-wide transcriptome profiling analysis. A total of 49280 garlic unigenes with an average length of 1337 bp were de novo assembled, 20231 of which were achieved for functional annotation...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30622952/transcriptome-analysis-reveals-dynamic-fat-accumulation-in-the-walnut-kernel
#2
Shuang Zhao, Xuemei Zhang, Yanping Su, Yilan Chen, Yang Liu, Meng Sun, Guohui Qi
Walnut ( Juglans regia L.) is an important woody oilseed species cultivated throughout the world. In this study, comparative transcript profiling was performed using high-throughput RNA sequencing technology at the following three stages of walnut fat synthesis in the "Lvling" walnut cultivar: the initial developmental stage (L1), the fast developing stage (L2), and the last developing stage (L3). A total of 68.18 GB of data were obtained on the three developmental stages, and 92% to 94% of clean data were able to be located to the reference genome...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30596084/transcriptome-comparison-reveals-distinct-selection-patterns-in-domesticated-and-wild-agave-species-the-important-cam-plants
#3
Xing Huang, Bo Wang, Jingen Xi, Yajie Zhang, Chunping He, Jinlong Zheng, Jianming Gao, Helong Chen, Shiqing Zhang, Weihuai Wu, Yanqiong Liang, Kexian Yi
Agave species are an important family of crassulacean acid metabolism (CAM) plants with remarkable tolerance to heat and drought stresses ( Agave deserti ) in arid regions and multiple agricultural applications, such as spirit ( Agave tequilana ) and fiber ( Agave sisalana ) production. The agave genomes are commonly too large to sequence, which has significantly restricted our understanding to the molecular basis of stress tolerance and economic traits in agaves. In this study, we collected three transcriptome databases for comparison to reveal the phylogenic relationships and evolution patterns of the three agave species...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30581839/isodb-a-comprehensive-database-of-full-length-isoforms-generated-by-iso-seq
#4
Shang-Qian Xie, Yue Han, Xiao-Zhou Chen, Tai-Yu Cao, Kai-Kai Ji, Jie Zhu, Peng Ling, Chuan-Le Xiao
The accurate landscape of transcript isoforms plays an important role in the understanding of gene function and gene regulation. However, building complete transcripts is very challenging for short reads generated using next-generation sequencing. Fortunately, isoform sequencing (Iso-Seq) using single-molecule sequencing technologies, such as PacBio SMRT, provides long reads spanning entire transcript isoforms which do not require assembly. Therefore, we have developed ISOdb, a comprehensive resource database for hosting and carrying out an in-depth analysis of Iso-Seq datasets and visualising the full-length transcript isoforms...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30581838/prediction-of-blood-lipid-phenotypes-using-obesity-related-genetic-polymorphisms-and-lifestyle-data-in-subjects-with-excessive-body-weight
#5
Omar Ramos-Lopez, Jose I Riezu-Boj, Fermin I Milagro, Marta Cuervo, Leticia Goni, J A Martinez
Background and Aim: Individual lipid phenotypes including circulating total cholesterol (TC), low-density lipoprotein cholesterol (LDL-c), high-density lipoprotein cholesterol (HDL-c), and triglycerides (TG) determinations are influenced by gene-environment interactions. The aim of this study was to predict blood lipid level (TC, LDL-c, HDL-c, and TG) variability using genetic and lifestyle data in subjects with excessive body weight-for-height. Methods: This cross-sectional study enrolled 304 unrelated overweight/obese adults of self-reported European ancestry...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30510960/genome-analysis-of-rhodococcus-sp-dsskp-r-001-a-highly-effective-%C3%AE-estradiol-degrading-bacterium
#6
Hongyan Zhao, Kejian Tian, Qing Qiu, Yu Wang, Hongyan Zhang, Shuang Ma, Shenbao Jin, Hongliang Huo
We screened bacteria that use E2 as its sole source of carbon and energy for growth and identified them as Rhodococcus, and we named them DSSKP-R-001. For a better understanding of the metabolic potential of the strain, whole genome sequencing of Rhodococcus DSSKP-R-001 and annotation of the functional genes were performed. The genomic sketches included a predicted protein-coding gene of approximately 5.4 Mbp with G + C content of 68.72% and 5180. The genome of Rhodococcus strain DSSKP-R-001 consists of three replicons: one chromosome and two plasmids of 5...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30474039/genomic-and-postgenomic-approaches-to-understand-environmental-microorganisms
#7
EDITORIAL
María-Eugenia Guazzaroni, Raul Alberto Platero, Rafael Silva-Rocha
No abstract text is available yet for this article.
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30425998/the-effect-of-canertinib-on-sensitivity-of-cytotoxic-drugs-in-tamoxifen-resistant-breast-cancer-cells-in-vitro
#8
Hesham A M Gomaa, Asmaa T Ali, M Abdel Gabbar, M A Kandeil
Aims and Objectives: To investigate and examine the reversal effects of canertinib on the activity of EGFR and tamoxifen resistance in drug-resistant human breast carcinoma cells (MCF-7/TamR). Materials and Methods: The antiproliferative activity of canertinib alone or in combination with a conventional EGFR-targeting chemotherapies cytotoxic drugs differing in the mechanism(s) of action, such as paclitaxel, carboplatin, etoposide, vinorelbine, and daunorubicin as well as resistance mechanisms of EGFR targeting, have been investigated...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30417007/scar-marker-for-gender-identification-in-date-palm-phoenix-dactylifera-l-at-the-seedling-stage
#9
Fahad Al-Qurainy, Abdulhafed A Al-Ameri, Salim Khan, Mohammad Nadeem, Abdel-Rhman Z Gaafar, Mohamed Tarroum
Date palm ( Phoenix dactylifera L.) is cultivated in arid and semiarid regions worldwide. Given the dioecious nature of this plant, gender identification is very important at the seedling stage. Molecular markers are very effective tools that help in gender identification at this stage. A sequence characterized amplified region (SCAR) marker linked to sex-specific regions in the genome of date palm was developed. Of the 300 tested randomly amplified polymorphic DNA (RAPD) primers, only one primer (OPC-06) produced reproducible band (294 bp) in male plants...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30406127/transcriptomic-changes-in-broiler-chicken-hypothalamus-during-growth-and-development
#10
Katarzyna Piórkowska, Kacper Żukowski, Katarzyna Połtowicz, Joanna Nowak, Dorota Wojtysiak, Natalia Derebecka, Joanna Wesoły, Katarzyna Ropka-Molik
The hypothalamus plays an overarching role that is reflected in the physiological processes observed in the entire organism. The hypothalamus regulates selected metabolic processes and activities of the autonomic nervous system. The avian hypothalamus due to the structural complexity is not well described and has a slightly different function than the mammalian hypothalamus that is the subject of numerous studies. The present study evaluated activities of hypothalamic genes in fast-growing chickens during development (at the 1st day and 3rd and 6th weeks after hatching)...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30402456/multiple-regression-analysis-reveals-microrna-regulatory-networks-in-oryza-sativa-under-drought-stress
#11
Jiajia Chen, Liangzhi Li
Drought is a major abiotic stress that reduces rice development and yield. miRNAs (microRNAs) are known to mediate posttranscriptional regulation under drought stress. Although the importance of individual miRNAs has been established, the crosstalks between miRNAs and mRNAs remain unearthed. Here we performed microarray analysis of miRNAs and matched mRNA expression profiles of drought-treated rice cultivar Nipponbare. Drought-responsive miRNA-mRNA regulations were identified by a combination of a partial least square (PLS) regression approach and sequence-based target prediction...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30402455/noncoding-rnas-and-base-modifications-epigenomic-players-implicated-in-neurological-disorders-and-tumorigenesis
#12
EDITORIAL
Yujing Li, Changwon Park, Hong Jiang, Xuekun Li, Luciano Vellón
No abstract text is available yet for this article.
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30402454/revisiting-key-entry-routes-of-human-epidemic-arboviruses-into-the-mainland-americas-through-large-scale-phylogenomics
#13
Túlio De Lima Campos, Ricardo Durães-Carvalho, Antonio Mauro Rezende, Otávio Valério de Carvalho, Alain Kohl, Gabriel Luz Wallau, Lindomar José Pena
The rapid worldwide spread of chikungunya (CHIKV), dengue (DENV), and Zika (ZIKV) viruses have raised great international concern. Knowledge about the entry routes and geographic expansion of these arboviruses to the mainland Americas remain incomplete and controversial. Epidemics caused by arboviruses continue to cause socioeconomic burden globally, particularly in countries where vector control is difficult due to climatic or infrastructure factors. Understanding how the virus circulates and moves from one country to another is of paramount importance to assist government and health officials in anticipating future epidemics, as well as to take steps to help control or mitigate the spread of the virus...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30363992/the-endophytic-bacterial-microbiota-associated-with-sweet-sorghum-sorghum-bicolor-is-modulated-by-the-application-of-chemical-n-fertilizer-to-the-field
#14
Cintia Mareque, Thais Freitas da Silva, Renata Estebanez Vollú, Martín Beracochea, Lucy Seldin, Federico Battistoni
Sweet sorghum ( Sorghum bicolor ) is a multipurpose crop used as a feedstock to produce bioethanol, sugar, energy, and animal feed. However, it requires high levels of N fertilizer application to achieve the optimal growth, which causes environmental degradation. Bacterial endophytes, which live inside plant tissues, play a key role in the health and productivity of their host. This particular community may be influenced by different agronomical practices. The aim of the work was to evaluate the effects of N fertilization on the structure, diversity, abundance, and composition of endophytic and diazotrophic bacterial community associated with field-grown sweet sorghum...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30363939/comparative-genomics-of-the-first-and-complete-genome-of-actinobacillus-porcitonsillarum-supports-the-novel-species-hypothesis
#15
Valentina Donà, Vincent Perreten
" Actinobacillus porcitonsillarum " is considered a nonpathogenic member of the Pasteurellaceae family, which phenotypically resembles the pathogen Actinobacillus pleuropneumoniae . Previous studies suggested that " A. porcitonsillarum " may represent a new species closely related to Actinobacillus minor , yet no full genome has been sequenced so far. We implemented the Oxford Nanopore and Illumina sequencing technologies to obtain the highly accurate and complete genome sequence of the " A...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30356416/the-maize-corngrass1-mirna-regulated-developmental-alterations-are-restored-by-a-bacterial-adp-glucose-pyrophosphorylase-in-transgenic-tobacco
#16
Ayalew Ligaba-Osena, Kay DiMarco, Tom L Richard, Bertrand Hankoua
Crop-based bioethanol has raised concerns about competition with food and feed supplies, and technologies for second- and third-generation biofuels are still under development. Alternative feedstocks could fill this gap if they can be converted to biofuels using current sugar- or starch-to-ethanol technologies. The aim of this study was to enhance carbohydrate accumulation in transgenic Nicotiana benthamiana by simultaneously expressing the maize Corngrass1 miRNA ( Cg1 ) and E. coli ADP-glucose pyrophosphorylase ( glgC ), both of which have been reported to enhance carbohydrate accumulation in planta ...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30356408/transposable-elements-in-the-organization-and-diversification-of-the-genome-of-aegilops-speltoides-tausch-poaceae-triticeae
#17
Olga Raskina
Repetitive DNA-specifically, transposable elements (TEs)-is a prevailing genomic fraction in cereals that underlies extensive genome reshuffling and intraspecific diversification in the wild. Although large amounts of data have been accumulated, the effect of TEs on the genome architecture and functioning is not fully understood. Here, plant genome organization was addressed by means of cloning and sequencing TE fragments of different types, which compose the largest portion of the Aegilops speltoides genome...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30345292/mutations-in-homocysteine-metabolism-genes-increase-keratin-n-homocysteinylation-and-damage-in-mice
#18
Kamila Borowczyk, Jacek Wróblewski, Joanna Suliburska, Noriyuki Akahoshi, Isao Ishii, Hieronim Jakubowski
Genetic or nutritional deficiencies in homocysteine (Hcy) metabolism increase Hcy-thiolactone, which causes protein damage by forming isopetide bonds with lysine residues, generating N -Hcy-protein. In the present work, we studied the prevalence and genetic determinants of keratin damage caused by homocysteinylation. We found that in mammals and birds, 35 to 98% of Hcy was bound to hair keratin via amide or isopeptide bond (Hcy-keratin), while 2 to 65% was S -Hcy-keratin. A major fraction of hair Hcy-keratin (56% to 93%), significantly higher in birds than in mammals, was sodium dodecyl sulfate-insoluble...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30345291/new-genomic-approaches-to-enhance-biomass-degradation-by-the-industrial-fungus-trichoderma-reesei
#19
REVIEW
Renato Graciano de Paula, Amanda Cristina Campos Antoniêto, Liliane Fraga Costa Ribeiro, Cláudia Batista Carraro, Karoline Maria Vieira Nogueira, Douglas Christian Borges Lopes, Alinne Costa Silva, Mariana Taíse Zerbini, Wellington Ramos Pedersoli, Mariana do Nascimento Costa, Roberto Nascimento Silva
The filamentous fungi Trichoderma reesei is one of the most well-studied cellulolytic microorganisms. It is the most important fungus for the industrial production of enzymes to biomass deconstruction being widely used in the biotechnology industry, mainly in the production of biofuels. Here, we performed an analytic review of the holocellulolytic system presented by T. reesei as well as the transcriptional and signaling mechanisms involved with holocellulase expression in this fungus. We also discuss new perspectives about control of secretion and cellulase expression based on RNA-seq and functional characterization data of T...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30327773/gene-coexpression-network-comparison-via-persistent-homology
#20
Ali Nabi Duman, Harun Pirim
Persistent homology, a topological data analysis (TDA) method, is applied to microarray data sets. Although there are a few papers referring to TDA methods in microarray analysis, the usage of persistent homology in the comparison of several weighted gene coexpression networks (WGCN) was not employed before to the very best of our knowledge. We calculate the persistent homology of weighted networks constructed from 38 Arabidopsis microarray data sets to test the relevance and the success of this approach in distinguishing the stress factors...
2018: International Journal of Genomics
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