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International Journal of Genomics

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https://www.readbyqxmd.com/read/30406127/transcriptomic-changes-in-broiler-chicken-hypothalamus-during-growth-and-development
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/30255030/changes-in-mirna-gene-expression-during-wound-repair-in-differentiated-normal-human-bronchial-epithelium
#12
Beata Narożna, Wojciech Langwiński, Claire Jackson, Peter M Lackie, John W Holloway, Zuzanna Stachowiak, Monika Dmitrzak-Węglarz, Aleksandra Szczepankiewicz
Purpose: Airway epithelium acts as a protective barrier against the particles from the inhaled air. Damage to the epithelium may result in loss of the barrier function. Epithelial repair in response to injury requires complex mechanisms, such as microRNA, small noncoding molecules, to regulate the processes involved in wound repair. We aimed to establish if the microRNA gene expression profile is altered during the airway epithelial repair in differentiated cells. Methods: miRNA gene expression profile during the wound closure of differentiated normal human bronchial epithelium (NHBE) from one donor was analysed using quantitative real-time PCR...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30255029/common-dna-variants-accurately-rank-an-individual-of-extreme-height
#13
Corinne E Sexton, Mark T W Ebbert, Ryan H Miller, Meganne Ferrel, Jo Ann T Tschanz, Christopher D Corcoran, Perry G Ridge, John S K Kauwe
Polygenic scores (or genetic risk scores) quantify the aggregate of small effects from many common genetic loci that have been associated with a trait through genome-wide association. Polygenic scores were first used successfully in schizophrenia and have since been applied to multiple phenotypes including multiple sclerosis, rheumatoid arthritis, and height. Because human height is an easily-measured and complex polygenic trait, polygenic height scores provide exciting insights into the predictability of aggregate common variant effect on the phenotype...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30225244/transcriptome-analysis-of-rainbow-trout-oncorhynchus-mykiss-eggs-subjected-to-the-high-hydrostatic-pressure-treatment
#14
Artur Gurgul, Klaudia Pawlina-Tyszko, Monika Bugno-Poniewierska, Tomasz Szmatoła, Igor Jasielczuk, Stefan Dobosz, Konrad Ocalewicz
High hydrostatic pressure (HHP) causes depolymerization of the spindle microtubules. HHP applied to fish eggs prevents extrusion of the second polar body and inhibits the first cell cleavage, and it is used to produce triploids and diploid gynogenetic and androgenetic individuals. HHP has been also found to affect biomolecules including nucleic acids, and it may be presumed that HHP administered to the rainbow trout ( Oncorhynchus mykiss ) eggs disturbs cytoplasmic maternal RNA indispensable for the early embryogenesis...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30211214/whole-exome-sequencing-uncovers-germline-variants-of-cancer-related-genes-in-sporadic-pheochromocytoma
#15
Milena Urbini, Margherita Nannini, Annalisa Astolfi, Valentina Indio, Valentina Vicennati, Matilde De Luca, Giuseppe Tarantino, Federica Corso, Maristella Saponara, Lidia Gatto, Donatella Santini, Guido Di Dalmazi, Uberto Pagotto, Renato Pasquali, Andrea Pession, Guido Biasco, Maria A Pantaleo
Background: Pheochromocytomas (PCCs) show the highest degree of heritability in human neoplasms. However, despite the wide number of alterations until now reported in PCCs, it is likely that other susceptibility genes remain still unknown, especially for those PCCs not clearly syndromic. Methods: Whole exome sequencing of tumor DNA was performed on a set of twelve PCCs clinically defined as sporadic. Results: About 50% of PCCs examined had somatic mutations on the known susceptibility VHL , NF1 , and RET genes...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30211213/metagenomic-approaches-for-understanding-new-concepts-in-microbial-science
#16
REVIEW
Luana de Fátima Alves, Cauã Antunes Westmann, Gabriel Lencioni Lovate, Guilherme Marcelino Viana de Siqueira, Tiago Cabral Borelli, María-Eugenia Guazzaroni
Over the past thirty years, since the dawn of metagenomic studies, a completely new (micro) universe was revealed, with the potential to have profound impacts on many aspects of the society. Remarkably, the study of human microbiome provided a new perspective on a myriad of human traits previously regarded as solely (epi-) genetically encoded, such as disease susceptibility, immunological response, and social and nutritional behaviors. In this context, metagenomics has established a powerful framework for understanding the intricate connections between human societies and microbial communities, ultimately allowing for the optimization of both human health and productivity...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30159320/meta-analysis-of-genome-wide-association-studies-identifies-novel-functional-cpg-snps-associated-with-bone-mineral-density-at-lumbar-spine
#17
Chuan Qiu, Hui Shen, Xiaoying Fu, Chao Xu, Hongwen Deng
Osteoporosis is a serious public health issue, which is mostly characterized by low bone mineral density (BMD). To search for additional genetic susceptibility loci underlying BMD variation, an effective strategy is to focus on testing of specific variants with high potential of functional effects. Single nucleotide polymorphisms (SNPs) that introduce or disrupt CpG dinucleotides (CpG-SNPs) may alter DNA methylation levels and thus represent strong candidate functional variants. Here, we performed a targeted GWAS for 63,627 potential functional CpG-SNPs that may affect DNA methylation in bone-related cells, in five independent cohorts ( n = 5905)...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30155473/protein-engineering-strategies-to-expand-crispr-cas9-applications
#18
REVIEW
Lucas F Ribeiro, Liliane F C Ribeiro, Matheus Q Barreto, Richard J Ward
The development of precise and modulated methods for customized manipulation of DNA is an important objective for the study and engineering of biological processes and is essential for the optimization of gene therapy, metabolic flux, and synthetic gene networks. The clustered regularly interspaced short palindromic repeat- (CRISPR-) associated protein 9 is an RNA-guided site-specific DNA-binding complex that can be reprogrammed to specifically interact with a desired DNA sequence target. CRISPR-Cas9 has been used in a wide variety of applications ranging from basic science to the clinic, such as gene therapy, gene regulation, modifying epigenomes, and imaging chromosomes...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30148158/the-effect-of-citalopram-on-genome-wide-dna-methylation-of-human-cells
#19
Riya R Kanherkar, Bruk Getachew, Joseph Ben-Sheetrit, Sudhir Varma, Thomas Heinbockel, Yousef Tizabi, Antonei B Csoka
Commonly used pharmaceutical drugs might alter the epigenetic state of cells, leading to varying degrees of long-term repercussions to human health. To test this hypothesis, we cultured HEK-293 cells in the presence of 50  μ M citalopram, a common antidepressant, for 30 days and performed whole-genome DNA methylation analysis using the NimbleGen Human DNA Methylation 3x720K Promoter Plus CpG Island Array. A total of 626 gene promoters, out of a total of 25,437 queried genes on the array (2.46%), showed significant differential methylation ( p < 0...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/30116731/discovery-of-novel-caeridins-from-the-skin-secretion-of-the-australian-white-s-tree-frog-litoria-caerulea
#20
Lei Li, Qing Wu, Xi Wang, Huimin Lu, Xinping Xi, Mei Zhou, Chris J Watson, Tianbao Chen, Lei Wang
Abundant biologically active peptides have been discovered from frog skin secretions, a rich natural source of bioactive compounds with great potential in drug discovery. In this study, three Caeridin peptides, namely, Caeridin-1, S5-Caeridin-1, and Caeridin-a1, were discovered from the skin secretion of the Australian White's tree frog, Litoria caerulea , for the first time, by means of combining transcriptomic and peptidomic analyses. It also represents the first report on bioactive Caeridins since this family of peptides was initially studied 20 years ago...
2018: International Journal of Genomics
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