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Genomics

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https://www.readbyqxmd.com/read/30529640/genome-analysis-provides-insights-into-crude-oil-degradation-and-biosurfactant-production-by-extremely-halotolerant-halomonas-desertis-g11-isolated-from-chott-el-djerid-salt-lake-in-tunisian-desert
#1
Mohamed Neifar, Habib Chouchane, Afef Najjari, Darine El Hidri, Mouna Mahjoubi, Kais Ghedira, Fatma Naili, Leila Soufi, Noura Raddadi, Haïtham Sghaier, Hadda I Ouzari, Ahmed Salaheddine Masmoudi, Ameur Cherif
Here, we report the genomic features and the bioremediation potential of Halomonas desertis G11, a new halophilic species which uses crude oil as a carbon and energy source and displays intrinsic resistance to salt stress conditions (optimum growth at 10% NaCl). G11 genome (3.96 Mb) had a mean GC content of 57.82%, 3622 coding sequences, 480 subsystems and 64 RNA genes. Annotation predicted 38 genes involved in osmotic stress including the biosynthesis of osmoprotectants glycine-betaine, ectoine and osmoregulated periplasmic glucans...
December 7, 2018: Genomics
https://www.readbyqxmd.com/read/30529702/irspot-dts-predict-recombination-spots-by-incorporating-the-dinucleotide-based-spare-cross-covariance-information-into-chou-s-pseudo-components
#2
Shengli Zhang, Kaiwen Yang, Yuqing Lei, Kang Song
Meiotic recombination plays an important role in the process of genetic evolution. Previous researches have shown that the recombination rates provide important information about the mechanism of recombination study. However, at present, most methods ignore the hidden correlation and spatial autocorrelation of the DNA sequence. In this study, we proposed a predictor called iRSpot-DTS to identify hot/cold spots based on the benchmark datasets. We proposed a feature extraction method called dinucleotide-based spatial autocorrelation(DSA) which can incorporate the original DNA properties and spatial information of DNA sequence...
December 6, 2018: Genomics
https://www.readbyqxmd.com/read/30529701/genome-wide-association-mapping-identifies-markers-associated-with-cane-yield-components-and-sucrose-traits-in-the-louisiana-sugarcane-core-collection
#3
Nathanael Fickett, Andres Gutierrez, Mohit Verma, Michael Pontif, Anna Hale, Collins Kimbeng, Niranjan Baisakh
Sugarcane is an economically important crop for both food and biofuel industries. Marker-assisted breeding in sugarcane is becoming a reality with the recent development and deployment of markers linked with disease resistance genes. Large linkage disequilibrium in sugarcane makes genome-wide association studies (GWAS) a better alternative to biparental mapping to identify markers associated with agronomic traits. GWAS was conducted on a Louisiana core collection to identify marker-trait associations (MTA) for 11 cane yield and sucrose traits using single nucleotide polymorphism (SNP) and insertion-deletion (Indel) markers...
December 6, 2018: Genomics
https://www.readbyqxmd.com/read/30529533/convex-hull-principle-for-classification-and-phylogeny-of-eukaryotic-proteins
#4
Xin Zhao, Kun Tian, Rong L He, Stephen Yau
This study quantitatively validates the principle that the biological properties associated with a given genotype are determined by the distribution of amino acids. In order to visualize this central law of molecular biology, each protein was represented by a point in 250-dimensional space based on its amino acid distribution. Proteins from the same family are found to cluster together, leading to the principle that the convex hull surrounding protein points from the same family do not intersect with the convex hulls of other protein families...
December 5, 2018: Genomics
https://www.readbyqxmd.com/read/30529532/ipsw-2l-pseknc-a-two-layer-predictor-for-identifying-promoters-and-their-strength-by-hybrid-features-via-pseudo-k-tuple-nucleotide-composition
#5
Xuan Xiao, Zhao-Chun Xu, Wang-Ren Qiu, Peng Wang, Hui-Ting Ge, Kuo-Chen Chou
The promoter is a regulatory DNA region about 81-1000 base pairs long, usually located near the transcription start site (TSS) along upstream of a given gene. By combining a certain protein called transcription factor, the promoter provides the starting point for regulated gene transcription, and hence plays a vitally important role in gene transcriptional regulation. With explosive growth of DNA sequences in the post-genomic age, it has become an urgent challenge to develop computational method for effectively identifying promoters because the information thus obtained is very useful for both basic research and drug development...
December 5, 2018: Genomics
https://www.readbyqxmd.com/read/30529531/exploring-the-effect-of-library-preparation-on-rna-sequencing-experiments
#6
Lei Wang, Sara J Felts, Virginia P Van Keulen, Larry R Pease, Yuji Zhang
RNA sequencing (RNA-seq) has become the widely preferred choice for surveying the genome-wide transcriptome complexity in many organisms. However, the broad adaptation of this methodology into the clinic still needs further evaluation of potential effect of sample preparation factors on its analytical reliability using patient samples. In this study, we examined the impact of three major sample preparation factors (i.e., cDNA library storage time, the quantity of input RNA, and cryopreservation of cell samples) on sequence biases, gene expression profiles, and enriched biological functions using RNAs isolated from primary B cell and CD4+ cell blood samples of healthy subjects...
December 5, 2018: Genomics
https://www.readbyqxmd.com/read/30529539/genetic-variants-and-haplotype-combination-in-the-bovine-crtc3-affected-conformation-traits-in-two-chinese-native-cattle-breeds-bos-taurus
#7
Sen Wu, Yue Ning, Sayed Haidar Abbas Raza, Chengtu Zhang, Le Zhang, Gong Cheng, Hongbao Wang, Nicola Schreurs, Linsen Zan
CREB-regulated transcription coactivator 3 (CRTC3) plays an extensive role in glucose and lipid metabolism. This study investigated the genetic variation and haplotype combination in CRTC3 and verified their contribution to bovine growth traits. Firstly, investigated the mRNA expression of CRTC3 in adult Qinchuan cattle and evaluated the effects that genetic variation of CRTC3 had on conformation and carcass traits in two Chinese cattle breeds (Qinchuan and Jiaxian). Four SNPs (single nucleotide polymorphisms) were identified including two in introns (SNP1: g...
December 4, 2018: Genomics
https://www.readbyqxmd.com/read/30529538/differential-role-of-kruppel-like-factor-1-klf1-gene-in-red-blood-cell-disorders
#8
Priya Hariharan, Roshan Colah, Kanjaksha Ghosh, Anita Nadkarni
The master erythroid regulator KLF1,plays a pivotal role during erythroid lineage development by regulating the expression of many erythroid genes. Variations in the KLF1 gene are found to be associated with varied erythroid phenotypes. With the aim of determining the role of KLF1 gene variations in HbF induction and their genotype phenotype relationship, in this study, we screened 370 individuals with different hemoglobinopathy condition. Hematological analysis was carried out using automated blood cell counter and Variant II HPLC (Biorad)...
December 4, 2018: Genomics
https://www.readbyqxmd.com/read/30529537/a-novel-multiplex-fluorescent-competitive-pcr-for-copy-number-variation-detection
#9
Ke Chen, Shuang-Shuang Dong, Nan Wu, Zhi-Hong Wu, Yu-Xun Zhou, Kai Li, Feng Zhang, Jun-Hua Xiao
The copy number variation (CNV) is an important genetic marker in cancer and other diseases. To detect CNVs of specific genetic loci, the multiplex ligation-dependent probe amplification (MLPA) is an appropriate approach, but the experimental optimization and probe synthesis are still great challenges. The multiplex competitive PCR is an alternative method for CNV detection. However, the construction of internal competitive template and establishment of a stable multiplex PCR system are the main limiting factors for this method...
December 4, 2018: Genomics
https://www.readbyqxmd.com/read/30508561/the-harderian-gland-transcriptomes-of-caraiba-andreae-cubophis-cantherigerus-and-tretanorhinus-variabilis-three-colubroid-snakes-from-cuba
#10
Dany Domínguez-Pérez, Jordi Durban, Guillermin Agüero-Chapin, Javier Torres Lopez, Reinaldo Molina Ruiz, Daniela Almeida, Juan J Calvete, Vítor Vasconcelos, Agostinho Antunes
The Harderian gland is a cephalic structure, widely distributed among vertebrates. In snakes, the Harderian gland is anatomically connected to the vomeronasal organ via the nasolacrimal duct, and in some species can be larger than the eyes. The function of the Harderian gland remains elusive, but it has been proposed to play a role in the production of saliva, pheromones, thermoregulatory lipids and growth factors, among others. Here, we have profiled the transcriptomes of the Harderian glands of three non-front-fanged colubroid snakes from Cuba, the Cuban Lesser Racer, Caraiba andreae; Cubophis cantherigerus (Cuban Racer); and the Caribbean Water Snake, Tretanorhinus variabilis, using Illumina HiSeq2000 100 bp paired-end...
November 30, 2018: Genomics
https://www.readbyqxmd.com/read/30503747/evolution-patterns-of-peg3-and-h19-icr
#11
Joomyeong Kim
Mammalian imprinted domains are regulated through small genomic regions termed Imprinting Control Regions (ICRs). In the current study, the evolution patterns of the ICRs of Peg3 and H19-imprinted domains were analyzed using the genomic sequences derived from a large number of mammals. The results indicated that multiple YY1 and CTCF binding sites are localized within the Peg3 and H19-ICR in all the mammals tested. The numbers of YY1 and CTCF binding sites are variable among individual species, yet positively correlate with the presence of tandem repeats within the Peg3 and H19-ICRs...
November 29, 2018: Genomics
https://www.readbyqxmd.com/read/30503746/comparative-mitogenome-analysis-of-three-species-and-monophyletic-inference-of-catantopinae-orthoptera-acridoidea
#12
Ran Li, Xiaohan Shu, Xiaodong Li, Ling Meng, Baoping Li
To enrich the genomic database of Catantopinae (Orthoptera: Acrididae), mitogenomes of three species from different genera, Traulia nigritibialis (15,701 bp), Choroedocus capensis (16,293 bp) and Stenocatantops splendens (15,574 bp), were characterized and compared with those of other grasshoppers in the subfamily. All 13 protein-coding genes (PCGs) were initiated by ATN codons except COI with ACC (C. capensis and S.splendens) and ND6 with TTG (S. splendens). All transfer RNA (tRNA) genes had a typical clover-leaf structure, except tRNASer(AGN) in which the base pairs of the dihydrouridine (DHU) arm were reduced...
November 29, 2018: Genomics
https://www.readbyqxmd.com/read/30496782/differential-quantitative-regulation-of-specific-gene-groups-and-pathways-under-drought-stress-in-rice
#13
Eshan Sharma, Mukesh Jain, Jitendra P Khurana
Abiotic stresses like drought are detrimental for growth and development and lead to loss in crop production. To be able to adapt and survive under such adverse conditions, synchronous regulation of a rather large number of genes is required. Here, we have used a bioinformatics approach to identify gene groups and associated pathways from microarray and RNA-seq experiments that are restricted in their gene expression amplitude within fold change intervals (FCIs) under drought stress conditions. We find that the expression of genes as functional groups is coordinated quantitatively, in a fold change specific manner, and differs among three rice cultivars distinct in their drought stress response...
November 26, 2018: Genomics
https://www.readbyqxmd.com/read/30476557/high-throughput-screening-of-small-immune-peptides-and-antimicrobial-peptides-from-the-fish-t1k-database
#14
Yunhai Yi, Yunyun Lv, Xinxin You, Jieming Chen, Chao Bian, Yu Huang, Junmin Xu, Li Deng, Qiong Shi
Analyses of transcriptomic datasets have the potential to reveal genetic markers underlying ecological adaptations. In the present study, we leverage the expanding dataset generated by the Fish-T1K Project (Transcriptomes of 1000 Fishes) to characterize small peptides that may be implicated in the immune system of fishes. We focused our analyses on sequences smaller than 360 bp obtained from gill transcriptomes of 87 ray-finned fishes (Actinopterygii). Functional annotation of short transcripts revealed that the number of small immune peptides varied significantly among the studied species...
November 23, 2018: Genomics
https://www.readbyqxmd.com/read/30476556/genomewide-identification-and-annotation-of-snps-in-bubalus-bubalis
#15
T Surya, M R Vineeth, Jayakumar Sivalingam, M S Tantia, S P Dixit, S K Niranjan, I D Gupta
The present study was carried out to identify and annotate the genome wide SNPs in Murrah buffalo genome. A total of 21.2 million raw reads from 4 pooled female Murrah buffalo samples were obtained using restriction enzyme digestion followed by sequencing with Illumina Hiseq 2000. After quality filtration, the reads were aligned to Murrah buffalo genome (ICAR-NBAGR) and Water buffalo genome (UMD_CASPUR_WB_2.0) which resulted in 99.37% and 99.67% of the reads aligning, respectively. A total of 130,688 high quality SNPs along with 35,110 indels were identified versus the Murrah bufffalo genome...
November 23, 2018: Genomics
https://www.readbyqxmd.com/read/30476555/the-role-of-mirna-in-somatic-embryogenesis
#16
Zahid Hameed Siddiqui, Zahid Khorshid Abbas, Mohammad Wahid Ansari, Mohammad Nasir Khan
Somatic embryogenesis (SEG) is one of the best techniques for mass production of economically important plants. It is also used for the study of morphology, anatomy, physiology, genetics and molecular mechanism of embryo development. Somatic Embryos (SE) are bipolar structures that develop from a cell other than a gamete or zygote. SEG reflects the unique developmental potential of plant somatic cells, resulting in the transition of the differentiated somatic cells to embryogenic cells to follow the zygotic embryo stages...
November 23, 2018: Genomics
https://www.readbyqxmd.com/read/30465914/deciphering-mixotrophic-clostridium-formicoaceticum-metabolism-and-energy-conservation-genomic-analysis-and-experimental-studies
#17
Teng Bao, Chi Cheng, Xin Xin, Jufang Wang, Mingqi Wang, Shang-Tian Yang
Clostridium formicoaceticum, a Gram-negative mixotrophic homoacetogen, produces acetic acid as the sole metabolic product from various carbon sources, including fructose, glycerol, formate, and CO2 . Its genome of 4.59-Mbp contains a highly conserved Wood-Ljungdahl pathway gene cluster with the same layout as that in other mixotrophic acetogens, including Clostridium aceticum, Clostridium carboxidivorans, and Clostridium ljungdahlii. For energy conservation, C. formicoaceticum does not have all the genes required for the synthesis of cytochrome or quinone used for generating proton gradient in H+ -dependent acetogens such as Moorella thermoacetica; instead, it has the Rnf system and a Na+ -translocating ATPase similar to the one in Acetobacterium woodii...
November 20, 2018: Genomics
https://www.readbyqxmd.com/read/30465913/early-transcriptome-changes-in-response-to-chemical-long-term-potentiation-induced-via-activation-of-synaptic-nmda-receptors-in-mouse-hippocampal-neurons
#18
Nicola Bliim, Iryna Leshchyns'ka, Ryan Keable, Bei Jun Chen, Ashton Curry-Hyde, Lachlan Gray, Vladimir Sytnyk, Michael Janitz
Long term potentiation (LTP) is a form of synaptic plasticity. In the present study LTP was induced via activation of synaptic NMDA receptors in primary hippocampal neuron cultures from neonate mice and RNA was isolated for RNA sequencing at 20 min following LTP induction. RNA sequencing and differential expression testing was performed to determine the identity and abundance of protein-coding and non-coding RNAs in control and LTP induced neuron cultures. We show that expression levels of a small group of transcripts encoding proteins involved in negative regulation of gene expression (Adcyap1, Id3), protein translation (Rpl22L1), extracellular structure organization (Bgn), intracellular signalling (Ppm1H, Ntsr2, Cldn10) and protein citrullination (PAD2) are downregulated in the stimulated neurons...
November 20, 2018: Genomics
https://www.readbyqxmd.com/read/30465915/transcriptome-sequencing-of-the-gill-and-barbel-of-southern-catfish-silurus-meridionalis-revealed-immune-responses-and-novel-rhamnose-binding-lectins-rbls
#19
Yu Huang, Min Wang, Xiaomeng Zhao, Qiong Shi
Southern catfish (Silurus meridionalis) is an economically important species widely cultured in China. It is well known for its fast growth, strong resistance to diseases and euryphage. However, little is known about the mechanisms for its powerful immune systems. Our Fish-T1K project has finished its first phase of 200 fish transcriptomes, with sequencing of gills in most examined fishes. In this study, we performed transcriptome sequencing of the gill and the maxillary barbel of Southern catfish, with the latter as a control...
November 19, 2018: Genomics
https://www.readbyqxmd.com/read/30458275/complete-genome-sequence-and-in-silico-analysis-of-l-interrogans-canicola-strain-du114-a-virulent-brazilian-isolate-phylogenetically-related-to-serovar-linhai
#20
Sérgio Jorge, Bruno Alonso Miotto, Frederico Schmitt Kremer, Rafael Cagliari, Natasha Rodrigues de Oliveira, Marcos Bryan Heinemann, Luciano da Silva Pinto, Mitika Kuribayashi Hagiwara, Vinicius Farias Campos, Odir Antônio Dellagostin
Canine leptospirosis is often caused by Leptospira interrogans serovar Canicola. Infected dogs may become asymptomatic carriers of the pathogen, which leads to many public health concerns. In this work, we present the complete genome sequencing and in silico analysis from a virulent Brazilian strain of L. interrogans serovar Canicola, previously isolated from a stray dog in Sao Paulo City. Comparative genomic analysis with a reference genome allowed identification of 1031 INDELs and several arrangement variations...
November 17, 2018: Genomics
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