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https://www.readbyqxmd.com/read/28335577/gc-ms-metabolomic-analysis-to-reveal-the-metabolites-and-biological-pathways-involved-in-the-developmental-stages-and-tissue-response-of-panax-ginseng
#1
Jia Liu, Yang Liu, Yu Wang, Ann Abozeid, Yuan-Gang Zu, Xiao-Ning Zhang, Zhong-Hua Tang
Ginsenosides, the major compounds present in ginseng, are known to have numerous physiological and pharmacological effects. The physiological processes, enzymes and genes involved in ginsenoside synthesis in P. ginseng have been well characterized. However, relatively little information is known about the dynamic metabolic changes that occur during ginsenoside accumulation in ginseng. To explore this topic, we isolated metabolites from different tissues at different growth stages, and identified and characterized them by using gas chromatography coupled with mass spectrometry (GC-MS)...
March 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28335576/genome-wide-identification-and-evolutionary-analysis-of-sarcocystis-neurona-protein-kinases
#2
Edwin K Murungi, Henry M Kariithi
The apicomplexan parasite Sarcocystis neurona causes equine protozoal myeloencephalitis (EPM), a degenerative neurological disease of horses. Due to its host range expansion, S. neurona is an emerging threat that requires close monitoring. In apicomplexans, protein kinases (PKs) have been implicated in a myriad of critical functions, such as host cell invasion, cell cycle progression and host immune response evasion. Here, we used various bioinformatics methods to define the kinome of S. neurona and phylogenetic relatedness of its PKs to other apicomplexans...
March 21, 2017: Pathogens
https://www.readbyqxmd.com/read/28335552/virological-surveillance-of-influenza-a-subtypes-isolated-in-2014-from-clinical-outbreaks-in-canadian-swine
#3
Helena Grgić, Jackie Gallant, Zvonimir Poljak
Influenza A viruses (IAVs) are respiratory pathogens associated with an acute respiratory disease that occurs year-round in swine production. It is currently one of the most important pathogens in swine populations, with the potential to infect other host species including humans. Ongoing research indicates that the three major subtypes of IAV-H1N1, H1N2, and H3N2-continue to expand in their genetic and antigenic diversity. In this study, we conducted a comprehensive genomic analysis of 16 IAVs isolated from different clinical outbreaks in Alberta, Manitoba, Ontario, and Saskatchewan in 2014...
March 21, 2017: Viruses
https://www.readbyqxmd.com/read/28335496/quantitative-analysis-of-the-kshv-transcriptome-following-primary-infection-of-blood-and-lymphatic-endothelial-cells
#4
A Gregory Bruce, Serge Barcy, Terri DiMaio, Emilia Gan, H Jacques Garrigues, Michael Lagunoff, Timothy M Rose
The transcriptome of the Kaposi's sarcoma-associated herpesvirus (KSHV/HHV8) after primary latent infection of human blood (BEC), lymphatic (LEC) and immortalized (TIME) endothelial cells was analyzed using RNAseq, and compared to long-term latency in BCBL-1 lymphoma cells. Naturally expressed transcripts were obtained without artificial induction, and a comprehensive annotation of the KSHV genome was determined. A set of unique coding sequence (UCDS) features and a process to resolve overlapping transcripts were developed to accurately quantitate transcript levels from specific promoters...
March 19, 2017: Pathogens
https://www.readbyqxmd.com/read/28335474/coccolithoviruses-a-review-of-cross-kingdom-genomic-thievery-and-metabolic-thuggery
#5
Jozef I Nissimov, António Pagarete, Fangrui Ma, Sean Cody, David D Dunigan, Susan A Kimmance, Michael J Allen
Coccolithoviruses (Phycodnaviridae) infect and lyse the most ubiquitous and successful coccolithophorid in modern oceans, Emiliania huxleyi. So far, the genomes of 13 of these giant lytic viruses (i.e., Emiliania huxleyi viruses-EhVs) have been sequenced, assembled, and annotated. Here, we performed an in-depth comparison of their genomes to try and contextualize the ecological and evolutionary traits of these viruses. The genomes of these EhVs have from 444 to 548 coding sequences (CDSs). Presence/absence analysis of CDSs identified putative genes with particular ecological significance, namely sialidase, phosphate permease, and sphingolipid biosynthesis...
March 18, 2017: Viruses
https://www.readbyqxmd.com/read/28335224/structural-changes-induced-in-grapevine-vitis-vinifera-l-dna-by-femtosecond-ir-laser-pulses-a-surface-enhanced-raman-spectroscopic-study
#6
Nicoleta E Dina, Cristina M Muntean, Nicolae Leopold, Alexandra Fălămaș, Adela Halmagyi, Ana Coste
In this work, surface-enhanced Raman spectra of ten genomic DNAs extracted from leaf tissues of different grapevine (Vitis vinifera L.) varieties, respectively, are analyzed in the wavenumber range 300-1800 cm(-1). Furthermore, structural changes induced in grapevine genomic nucleic acids upon femtosecond (170 fs) infrared (IR) laser pulse irradiation (λ = 1100 nm) are discussed in detail for seven genomic DNAs, respectively. Surface-enhanced Raman spectroscopy (SERS) signatures, vibrational band assignments and structural characterization of genomic DNAs are reported for each case...
May 25, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335076/fine-mapping-of-chromosome-5p15-33-identifies-novel-lung-cancer-susceptibility-loci-in-han-chinese
#7
Jing Dong, Yang Cheng, Meng Zhu, Yang Wen, Cheng Wang, Yuzhuo Wang, Liguo Geng, Wei Shen, Jia Liu, Zhihua Li, Jiahui Zhang, Hongxia Ma, Juncheng Dai, Guangfu Jin, Zhibin Hu, Hongbing Shen
Genome-wide association studies in European and Asian populations have consistently identified chromosome 5p15.33 as a lung cancer susceptibility region. To investigate further the genetic architecture of common variants in this region, we conducted a two-stage fine-mapping analysis discovered by targeted resequencing of 200 cases and 300 controls individually, and validated in multiethnic lung cancer GWASs with 12,843 cases and 12,639 controls. Two independent variants were identified in approximate conditional analysis with GCTA and consistently validated in lung cancer GWASs in both Asian and European populations...
March 23, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28335028/defining-the-5%C3%AE-and-3%C3%AE-landscape-of-the-drosophila-transcriptome-with-exo-seq-and-rnaseh-seq
#8
Shaked Afik, Osnat Bartok, Maxim N Artyomov, Alexander A Shishkin, Sabah Kadri, Mor Hanan, Xiaopeng Zhu, Manuel Garber, Sebastian Kadener
Cells regulate biological responses in part through changes in transcription start sites (TSS) or cleavage and polyadenylation sites (PAS). To fully understand gene regulatory networks, it is therefore critical to accurately annotate cell type-specific TSS and PAS. Here we present a simple and straightforward approach for genome-wide annotation of 5΄- and 3΄-RNA ends. Our approach reliably discerns bona fide PAS from false PAS that arise due to internal poly(A) tracts, a common problem with current PAS annotation methods...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28335020/znhit3-is-defective-in-peho-syndrome-a-severe-encephalopathy-with-cerebellar-granule-neuron-loss
#9
Anna-Kaisa Anttonen, Anni Laari, Maria Kousi, Yawei J Yang, Tiina Jääskeläinen, Mirja Somer, Eija Siintola, Eveliina Jakkula, Mikko Muona, Saara Tegelberg, Tuula Lönnqvist, Helena Pihko, Leena Valanne, Anders Paetau, Melody P Lun, Johanna Hästbacka, Outi Kopra, Tarja Joensuu, Nicholas Katsanis, Maria K Lehtinen, Jorma J Palvimo, Anna-Elina Lehesjoki
Progressive encephalopathy with oedema, hypsarrhythmia, and optic atrophy (PEHO) syndrome is an early childhood onset, severe autosomal recessive encephalopathy characterized by extreme cerebellar atrophy due to almost total granule neuron loss. By combining homozygosity mapping in Finnish families with Sanger sequencing of positional candidate genes and with exome sequencing a homozygous missense substitution of leucine for serine at codon 31 in ZNHIT3 was identified as the primary cause of PEHO syndrome. ZNHIT3 encodes a nuclear zinc finger protein previously implicated in transcriptional regulation and in small nucleolar ribonucleoprotein particle assembly and thus possibly to pre-ribosomal RNA processing...
March 1, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28335007/a-class-of-circadian-long-non-coding-rnas-mark-enhancers-modulating-long-range-circadian-gene-regulation
#10
Zenghua Fan, Meng Zhao, Parth D Joshi, Ping Li, Yan Zhang, Weimin Guo, Yichi Xu, Haifang Wang, Zhihu Zhao, Jun Yan
Circadian rhythm exerts its influence on animal physiology and behavior by regulating gene expression at various levels. Here we systematically explored circadian long non-coding RNAs (lncRNAs) in mouse liver and examined their circadian regulation. We found that a significant proportion of circadian lncRNAs are expressed at enhancer regions, mostly bound by two key circadian transcription factors, BMAL1 and REV-ERBα. These circadian lncRNAs showed similar circadian phases with their nearby genes. The extent of their nuclear localization is higher than protein coding genes but less than enhancer RNAs...
March 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28335003/identification-of-genetic-variants-affecting-vitamin-d-receptor-binding-and-associations-with-autoimmune-disease
#11
Giuseppe Gallone, Wilfried Haerty, Giulio Disanto, Sreeram V Ramagopalan, Chris P Ponting, Antonio J Berlanga-Taylor
Large numbers of statistically significant associations between sentinel SNPs and case-control status have been replicated by genome-wide association studies. Nevertheless, few underlying molecular mechanisms of complex disease are currently known. We investigated whether variation in binding of a transcription factor, the vitamin D receptor (VDR) whose activating ligand vitamin D has been proposed as a modifiable factor in multiple disorders, could explain any of these associations. VDR modifies gene expression by binding DNA as a heterodimer with the Retinoid X receptor (RXR)...
March 9, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334950/downstream-targets-of-gwas-detected-genes-for-breast-lung-and-prostate-and-colon-cancer-converge-to-g1-s-transition-pathway
#12
Olga Y Gorlova, Eugene I Demidenko, Christopher I Amos, Ivan P Gorlov
Genome-wide association studies (GWASs) identified over 500 single nucleotide polymorphisms (SNPs) influencing cancer risk. It is logical to expect the cancer-associated genes to cluster in pathways directly involved in carcinogenesis, e.g. cell cycle. Nevertheless, analyses of the GWAS-detected cancer risk genes usually show no or weak enrichment by known cancer genes.We hypothesized that GWAS-detected cancer risk-associated genes function as upstream regulators of the genes directly involved in carcinogenesis...
March 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334937/dynamically-and-epigenetically-coordinated-gata-ets-sox-transcription-factor-expression-is-indispensable-for-endothelial-cell-differentiation
#13
Yasuharu Kanki, Ryo Nakaki, Teppei Shimamura, Taichi Matsunaga, Kohei Yamamizu, Shiori Katayama, Jun-Ichi Suehiro, Tsuyoshi Osawa, Hiroyuki Aburatani, Tatsuhiko Kodama, Youichiro Wada, Jun K Yamashita, Takashi Minami
Although studies of the differentiation from mouse embryonic stem (ES) cells to vascular endothelial cells (ECs) provide an excellent model for investigating the molecular mechanisms underlying vascular development, temporal dynamics of gene expression and chromatin modifications have not been well studied. Herein, using transcriptomic and epigenomic analyses based on H3K4me3 and H3K27me3 modifications at a genome-wide scale, we analysed the EC differentiation steps from ES cells and crucial epigenetic modifications unique to ECs...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334930/rcas-an-rna-centric-annotation-system-for-transcriptome-wide-regions-of-interest
#14
Bora Uyar, Dilmurat Yusuf, Ricardo Wurmus, Nikolaus Rajewsky, Uwe Ohler, Altuna Akalin
In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334900/cdk12-regulates-alternative-last-exon-mrna-splicing-and-promotes-breast-cancer-cell-invasion
#15
Jerry F Tien, Alborz Mazloomian, S-W Grace Cheng, Christopher S Hughes, Christalle C T Chow, Leanna T Canapi, Arusha Oloumi, Genny Trigo-Gonzalez, Ali Bashashati, James Xu, Vicky C-D Chang, Sohrab P Shah, Samuel Aparicio, Gregg B Morin
CDK12 (cyclin-dependent kinase 12) is a regulatory kinase with evolutionarily conserved roles in modulating transcription elongation. Recent tumor genome studies of breast and ovarian cancers highlighted recurrent CDK12 mutations, which have been shown to disrupt DNA repair in cell-based assays. In breast cancers, CDK12 is also frequently co-amplified with the HER2 (ERBB2) oncogene. The mechanisms underlying functions of CDK12 in general and in cancer remain poorly defined. Based on global analysis of mRNA transcripts in normal and breast cancer cell lines with and without CDK12 amplification, we demonstrate that CDK12 primarily regulates alternative last exon (ALE) splicing, a specialized subtype of alternative mRNA splicing, that is both gene- and cell type-specific...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334899/association-analyses-of-east-asian-individuals-and-trans-ancestry-analyses-with-european-individuals-reveal-new-loci-associated-with-cholesterol-and-triglyceride-levels
#16
Cassandra N Spracklen, Peng Chen, Young Jin Kim, Xu Wang, Hui Cai, Shengxu Li, Jirong Long, Ying Wu, Ya Xing Wang, Fumihiko Takeuchi, Jer-Yuarn Wu, Keum-Ji Jung, Cheng Hu, Koichi Akiyama, Yonghong Zhang, Sanghoon Moon, Todd A Johnson, Huaixing Li, Rajkumar Dorajoo, Meian He, Maren E Cannon, Tamara S Roman, Elias Salfati, Keng-Hung Lin, Xiuqing Guo, Wayne H H Sheu, Devin Absher, Linda S Adair, Themistocles L Assimes, Tin Aung, Qiuyin Cai, Li-Ching Chang, Chien-Hsiun Chen, Li-Hsin Chien, Lee-Ming Chuang, Shu-Chun Chuang, Shufa Du, Qiao Fan, Cathy S J Fann, Alan B Feranil, Yechiel Friedlander, Penny Gordon-Larsen, Dongfeng Gu, Lixuan Gui, Zhirong Guo, Chew-Kiat Heng, James Hixson, Xuhong Hou, Chao Agnes Hsiung, Yao Hu, Mi Yeong Hwang, Chii-Min Hwu, Masato Isono, Jyh-Ming Jimmy Juang, Chiea-Chuen Khor, Yun Kyoung Kim, Woon-Puay Koh, Michiaki Kubo, I-Te Lee, Sun-Ju Lee, Wen-Jane Lee, Kae-Woei Liang, Blanche Lim, Sing-Hui Lim, Jianjun Liu, Toru Nabika, Wen-Harn Pan, Hao Peng, Thomas Quertermous, Charumathi Sabanayagam, Kevin Sandow, Jinxiu Shi, Liang Sun, Pok Chien Tan, Shu-Pei Tan, Kent D Taylor, Yik-Ying Teo, Sue-Anne Toh, Tatsuhiko Tsunoda, Rob M van Dam, Aili Wang, Feijie Wang, Jie Wang, Wen Bin Wei, Yong-Bing Xiang, Jie Yao, Jian-Min Yuan, Rong Zhang, Wanting Zhao, Yii-Der Ida Chen, Stephen S Rich, Jerome I Rotter, Tzung-Dau Wang, Tangchun Wu, Xu Lin, Bok-Ghee Han, Toshihiro Tanaka, Yoon Shin Cho, Tomohiro Katsuya, Weiping Jia, Sun-Ha Jee, Yuan-Tsong Chen, Norihiro Kato, Jost B Jonas, Ching-Yu Cheng, Xiao-Ou Shu, Jiang He, Wei Zheng, Tien-Yin Wong, Wei Huang, Bong-Jo Kim, E-Shyong Tai, Karen L Mohlke, Xueling Sim
Large-scale meta-analyses of genome-wide association studies (GWAS) have identified >175 loci associated with fasting cholesterol levels, including total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). With differences in linkage disequilibrium (LD) structure and allele frequencies between ancestry groups, studies in additional large samples may detect new associations. We conducted staged GWAS meta-analyses in up to 69,414 East Asian individuals from 24 studies with participants from Japan, the Philippines, Korea, China, Singapore, and Taiwan...
February 21, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334889/the-primary-transcriptome-of-neisseria-meningitidis-and-its-interaction-with-the-rna-chaperone-hfq
#17
Nadja Heidrich, Saskia Bauriedl, Lars Barquist, Lei Li, Christoph Schoen, Jörg Vogel
Neisseria meningitidis is a human commensal that can also cause life-threatening meningitis and septicemia. Despite growing evidence for RNA-based regulation in meningococci, their transcriptome structure and output of regulatory small RNAs (sRNAs) are incompletely understood. Using dRNA-seq, we have mapped at single-nucleotide resolution the primary transcriptome of N. meningitidis strain 8013. Annotation of 1625 transcriptional start sites defines transcription units for most protein-coding genes but also reveals a paucity of classical σ70-type promoters, suggesting the existence of activators that compensate for the lack of -35 consensus sequences in N...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334874/efficient-cnv-breakpoint-analysis-reveals-unexpected-structural-complexity-and-correlation-of-dosage-sensitive-genes-with-clinical-severity-in-genomic-disorders
#18
Ling Zhang, Jingmin Wang, Cheng Zhang, Dongxiao Li, Claudia M B Carvalho, Haoran Ji, Jianqiu Xiao, Ye Wu, Weichen Zhou, Hongyan Wang, Li Jin, Yang Luo, Xiru Wu, James R Lupski, Feng Zhang, Yuwu Jiang
Genomic disorders are the clinical conditions manifested by submicroscopic genomic rearrangements including copy number variants (CNVs). The CNVs can be identified by array-based comparative genomic hybridization (aCGH), the most commonly used technology for molecular diagnostics of genomic disorders. However, clinical aCGH only informs CNVs in the probe interrogated regions. Neither orientational information nor the resulting genomic rearrangement structure is provided, which is a key to uncovering mutational and pathogenic mechanisms underlying genomic disorders...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334860/genetic-regulation-of-gene-expression-in-the-epileptic-human-hippocampus
#19
Nasir Mirza, Richard Appleton, Sasha Burn, Daniel du Plessis, Roderick Duncan, Jibril Osman Farah, Bjarke Feenstra, Anders Hviid, Vivek Josan, Rajiv Mohanraj, Arif Shukralla, Graeme J Sills, Anthony G Marson, Munir Pirmohamed
Epilepsy is a serious and common neurological disorder. Expression quantitative loci (eQTL) analysis is a vital aid for the identification and interpretation of disease-risk loci. Many eQTLs operate in a tissue- and condition-specific manner. We have performed the first genome-wide cis-eQTL analysis of human hippocampal tissue to include not only normal (n = 22) but also epileptic (n = 22) samples. We demonstrate that disease-associated variants from an epilepsy GWAS meta-analysis and a febrile seizures (FS) GWAS are significantly more enriched with epilepsy-eQTLs than with normal hippocampal eQTLs from two larger independent published studies...
March 3, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334855/slc30a9-mutation-affecting-intracellular-zinc-homeostasis-causes-a-novel-cerebro-renal-syndrome
#20
Yonatan Perez, Zamir Shorer, Keren Liani-Leibson, Pauline Chabosseau, Rotem Kadir, Michael Volodarsky, Daniel Halperin, Shiran Barber-Zucker, Hanna Shalev, Ruth Schreiber, Libe Gradstein, Evgenia Gurevich, Raz Zarivach, Guy A Rutter, Daniel Landau, Ohad S Birk
A novel autosomal recessive cerebro-renal syndrome was identified in consanguineous Bedouin kindred: neurological deterioration was evident as of early age, progressing into severe intellectual disability, profound ataxia, camptocormia and oculomotor apraxia. Brain MRI was normal. Four of the six affected individuals also had early-onset nephropathy with features of tubulo-interstitial nephritis, hypertension and tendency for hyperkalemia, though none had rapid deterioration of renal function. Genome wide linkage analysis identified an ∼18 Mb disease-associated locus on chromosome 4 (maximal logarithm of odds score 4...
February 9, 2017: Brain: a Journal of Neurology
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