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https://www.readbyqxmd.com/read/28346895/wheat-genomics-comes-of-age
#1
REVIEW
Cristobal Uauy
Advances in wheat genomics have lagged behind other major cereals (e.g., rice and maize) due to its highly repetitive and large polyploid genome. Recent technological developments in sequencing and assembly methods, however, have largely overcome these barriers. The community now moves to an era centred on functional characterisation of the genome. This includes understanding sequence and structural variation as well as how information is integrated across multiple homoeologous genomes. This understanding promises to uncover variation previously hidden from natural and human selection due to the often observed functional redundancy between homoeologs...
March 24, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28346815/improvement-of-identification-methods-for-honeybee-specific-lactic-acid-bacteria-future-approaches
#2
Sepideh Lamei, Yue O O Hu, Tobias C Olofsson, Anders F Andersson, Eva Forsgren, Alejandra Vásquez
Honeybees face many parasites and pathogens and consequently rely on a diverse set of individual and group-level defenses to prevent disease. The crop microbiota of Apis mellifera, composed of 13 Lactic Acid Bacterial (LAB) species within the genera Lactobacillus and Bifidobacterium, form a beneficial symbiotic relationship with each other and the honeybee to protect their niche and their host. Possibly playing a vital role in honeybee health, it is important that these honeybee specific Lactic Acid Bacterial (hbs-LAB) symbionts can be correctly identified, isolated and cultured, to further investigate their health promoting properties...
2017: PloS One
https://www.readbyqxmd.com/read/28346136/environment-determines-evolutionary-trajectory-in-a-constrained-phenotypic-space
#3
David T Fraebel, Harry Mickalide, Diane Schnitkey, Jason Merritt, Thomas E Kuhlman, Seppe Kuehn
Constraints on phenotypic variation limit the capacity of organisms to adapt to the multiple selection pressures encountered in natural environments. To better understand evolutionary dynamics in this context, we select Escherichia coli for faster migration through a porous environment, a process which depends on both motility and growth. We find that a trade-off between swimming speed and growth rate constrains the evolution of faster migration. Evolving faster migration in rich medium results in slow growth and fast swimming, while evolution in minimal medium results in fast growth and slow swimming...
March 27, 2017: ELife
https://www.readbyqxmd.com/read/28345627/heterologous-protein-dna-interactions-lead-to-biased-allelic-expression-of-circadian-clock-genes-in-interspecific-hybrids
#4
Danny W-K Ng, Helen H Y Chen, Z Jeffrey Chen
Genomic interactions in allopolyploids create expression variation of homoeologous alleles through protein-protein and protein-DNA interactions. However, the molecular basis for this is largely unknown. Here we investigated the protein-protein and protein-DNA interactions among homoeologous transcription factors in the circadian-clock feedback loop, consisting of CCA1 HIKING EXPEDITION (CHE), CIRCADIAN CLOCK ASSOCIATED1 (CCA1), and TIMING OF CAB EXPRESSION1 (TOC1), plus the interaction with a chromatin factor, HISTONE DEACETYLASE1 (HD1)...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345611/copy-number-variation-profile-in-the-placental-and-parental-genomes-of-recurrent-pregnancy-loss-families
#5
Laura Kasak, Kristiina Rull, Siim Sõber, Maris Laan
We have previously shown an extensive load of somatic copy number variations (CNVs) in the human placental genome with the highest fraction detected in normal term pregnancies. Hereby, we hypothesized that insufficient promotion of CNVs may impair placental development and lead to recurrent pregnancy loss (RPL). RPL affects ~3% of couples aiming at childbirth and idiopathic RPL represents ~50% of cases. We analysed placental and parental CNV profiles of idiopathic RPL trios (mother-father-placenta) and duos (mother-placenta)...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345042/human-genetic-and-metabolite-variation-reveals-that-methylthioadenosine-is-a-prognostic-biomarker-and-an-inflammatory-regulator-in-sepsis
#6
Liuyang Wang, Emily R Ko, James J Gilchrist, Kelly J Pittman, Anna Rautanen, Matti Pirinen, J Will Thompson, Laura G Dubois, Raymond J Langley, Sarah L Jaslow, Raul E Salinas, D Clayburn Rouse, M Arthur Moseley, Salim Mwarumba, Patricia Njuguna, Neema Mturi, Thomas N Williams, J Anthony G Scott, Adrian V S Hill, Christopher W Woods, Geoffrey S Ginsburg, Ephraim L Tsalik, Dennis C Ko
Sepsis is a deleterious inflammatory response to infection with high mortality. Reliable sepsis biomarkers could improve diagnosis, prognosis, and treatment. Integration of human genetics, patient metabolite and cytokine measurements, and testing in a mouse model demonstrate that the methionine salvage pathway is a regulator of sepsis that can accurately predict prognosis in patients. Pathway-based genome-wide association analysis of nontyphoidal Salmonella bacteremia showed a strong enrichment for single-nucleotide polymorphisms near the components of the methionine salvage pathway...
March 2017: Science Advances
https://www.readbyqxmd.com/read/28344646/comparative-insights-into-the-saccharification-potentials-of-a-relatively-unexplored-but-robust-penicillium-funiculosum-glycoside-hydrolase-7-cellobiohydrolase
#7
Funso Emmanuel Ogunmolu, Navya Bhatt Kammachi Jagadeesha, Rakesh Kumar, Pawan Kumar, Dinesh Gupta, Syed Shams Yazdani
BACKGROUND: GH7 cellobiohydrolases (CBH1) are vital for the breakdown of cellulose. We had previously observed the enzyme as the most dominant protein in the active cellulose-hydrolyzing secretome of the hypercellulolytic ascomycete-Penicillium funiculosum (NCIM1228). To understand its contributions to cellulosic biomass saccharification in comparison with GH7 cellobiohydrolase from the industrial workhorse-Trichoderma reesei, we natively purified and functionally characterized the only GH7 cellobiohydrolase identified and present in the genome of the fungus...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28343122/genetic-and-epigenetic-variation-of-transposable-elements-in-arabidopsis
#8
REVIEW
Charles J Underwood, Ian R Henderson, Robert A Martienssen
Transposable elements are mobile genetic elements that are prevalent in plant genomes and are silenced by epigenetic modification. Different epigenetic modification pathways play distinct roles in the control of transposable element transcription, replication and recombination. The Arabidopsis genome contains families of all of the major transposable element classes, which are differentially enriched in particular genomic regions. Whole genome sequencing and DNA methylation profiling of hundreds of natural Arabidopsis accessions has revealed that transposable elements exhibit significant intraspecific genetic and epigenetic variation, and that genetic variation often underlies epigenetic variation...
March 23, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28341884/mitochondrial-genome-of-the-nematode-endoparasitic-fungus-hirsutella-vermicola-reveals-a-high-level-of-synteny-in-the-family-ophiocordycipitaceae
#9
Yong-Jie Zhang, Hong-Yue Zhang, Xing-Zhong Liu, Shu Zhang
Ophiocordycipitaceae is a diverse fungal family comprising multiple ecologically, economically, medicinally, and culturally important fungal species; however, only four species of the family have available mitochondrial genomes (mitogenomes). In this study, the complete mitogenome of the nematode endoparasitic fungus Hirsutella vermicola in Ophiocordycipitaceae was sequenced, and a comparative mitogenomic analysis of Ophiocordycipitaceae was performed. We found that the 53,793-bp circular mitogenome of H. vermicola, except for standard fungal mitochondrial genes, harbors seven introns acquired possibly through lateral transfer from other fungi and three free-standing open reading frames (ORFs) coding for hypothetical proteins...
March 24, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28341840/comparison-of-two-massively-parallel-sequencing-platforms-using-83-single-nucleotide-polymorphisms-for-human-identification
#10
Dame Loveliness T Apaga, Sheila E Dennis, Jazelyn M Salvador, Gayvelline C Calacal, Maria Corazon A De Ungria
The potential of Massively Parallel Sequencing (MPS) technology to vastly expand the capabilities of human identification led to the emergence of different MPS platforms that use forensically relevant genetic markers. Two of the MPS platforms that are currently available are the MiSeq(®) FGx™ Forensic Genomics System (Illumina) and the HID-Ion Personal Genome Machine (PGM)™ (Thermo Fisher Scientific). These are coupled with the ForenSeq™ DNA Signature Prep kit (Illumina) and the HID-Ion AmpliSeq™ Identity Panel (Thermo Fisher Scientific), respectively...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28341679/industrial-relevance-of-chromosomal-copy-number-variation-in-saccharomyces-yeasts
#11
Arthur R Gorter de Vries, Jack T Pronk, Jean-Marc G Daran
Chromosomal copy number variation (CCNV) plays a key role in evolution and health of eukaryotes. The unicellular yeast Saccharomyces cerevisiae is an important model for studying the generation, physiological impact and evolutionary significance of CCNV. Fundamental studies on this yeast have contributed to an extensive set of methods for analyzing and introducing CCNV. Moreover, these studies provided insight into the balance between negative and positive impacts of CCNV in evolutionary contexts. A growing body of evidence indicates that CCNV not only frequently occurs in industrial strains of Saccharomyces yeasts but is also a key contributor to the diversity of industrially relevant traits...
March 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28341418/a-novel-y-chromosome-microdeletion-potentially-associated-with-defective-spermatogenesis-identified-by-custom-array-comparative-genome-hybridization
#12
Tianwen He, Xiangzhong Zhang, Hua Deng, Weiping Zhou, Xin Zhao, Hui Zhao, Jian Lu, Yichun Zheng, Changbin Zhang, Liang Zhang, Aihua Yin
Male infertility is a major health problem worldwide. Oligospermia and azoospermia are the most common symptoms of this disorder. Despite recent advances, the aetiopathogenesis of defective spermatogenesis remains largely uncertain. The aim of this study is to discover unknown or novel chromosome aberrations associated with male reproductive failure. We developed a high-resolution custom array comparative genomic hybridization for initial screening of copy number variations in 10 patients with idiopathic oligozoospermia and azoospermia and eight normal fertile men...
January 2017: Reproductive Biomedicine Online
https://www.readbyqxmd.com/read/28340771/a-dnazyme-sensor-based-on-target-catalyzed-hairpin-assembly-for-enzyme-free-and-non-label-single-nucleotide-polymorphism-genotyping
#13
Huiyan Xu, Qiwang Wu, Hong Shen
Single nucleotide polymorphisms (SNPs) are widely existed in human genome and associated with many diseases. Traditional PCR-based methods for SNP genotyping require protein enzyme, precise control of temperature and removal of resultant products, making the whole process labor intensive and time consuming. Although G-quadruplex DNAzyme-based assays provide many advantages over traditional approaches, the relatively low catalytic activity of DNAzyme becomes an unfavorable factor in its application process. Therefore, amplification of DNAzyme for further determination is of great desire in bioanalysis...
May 15, 2017: Talanta
https://www.readbyqxmd.com/read/28340469/characterization-and-expression-patterns-of-key-c4-photosynthetic-pathway-genes-in-bread-wheat-triticum-aestivum-l-under-field-conditions
#14
Daoura Goudia Bachir, Iqbal Saeed, Quanhao Song, Tay Zar Linn, Liang Chen, Yin-Gang Hu
Wheat is a C3 plant with relatively low photosynthetic efficiency and is a potential target for C4 photosynthetic pathway engineering. Here we reported the characterization of four key C4 pathway genes and assessed their expression patterns and enzymatic activities at three growth stages in flag leaves of 59 bread wheat genotypes. The C4-like genes homologous to PEPC, NADP-ME, MDH, and PPDK in maize were identified in the A, B, and D sub-genomes of bread wheat, located on the long arms of chromosomes 3 and 5 (TaPEPC), short arms of chromosomes 1 and 3 (TaNADP-ME), long arms of chromosomes 1 and 7 (TaMDH), and long arms of chromosome 1 (TaPPDK), respectively...
March 9, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28340408/ongoing-evolution-of-pseudomonas-aeruginosa-pao1-sublines-complicates-studies-of-dna-damage-repair-and-tolerance
#15
Julia Sidorenko, Tatjana Jatsenko, Maia Kivisaar
Sublines of the major P. aeruginosa reference strain PAO1 are derivatives of the original PAO1 isolate, which are maintained in laboratories worldwide. These sublines display substantial genomic and phenotypic variation due to ongoing microevolution. Here, we examined four sublines, MPAO1, PAO1-L, PAO1-DSM and PAO1-UT, originated from different laboratories, and six DNA polymerase-deficient mutants from the P. aeruginosa MPAO1 transposon library for their employment in elucidation of DNA damage repair and tolerance mechanisms in P...
March 16, 2017: Mutation Research
https://www.readbyqxmd.com/read/28340313/linkage-between-mitochondrial-genome-alterations-telomere-length-and-aging-population
#16
Egija Zole, Krista Zadinane, Liana Pliss, Renate Ranka
We studied telomere length (TL) and mitochondrial DNA (mtDNA) copy number variations in individuals from Latvian Caucasian population in different age groups. We showed a positive correlation between TL and mtDNA copy number in individuals of up to 90 years of age; however, this correlation was not observed in the 90-100 years age group. While TL shortened with age and mtDNA content decreased with increasing age, in this study it was observed that mtDNA copy number in nonagenarians was slightly higher than in the 60-89 years age group...
March 24, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28339981/transcriptome-analysis-of-comb-and-testis-from-rose-comb-silky-chicken-r1-r1-and-beijing-fatty-wild-type-chicken-r-r
#17
Y Wang, J Li, C Feng, Y Zhao, X Hu, N Li
Rose-comb was one of the chicken comb-variants first used by Bateson and Punnet in 1902 to demonstrate Mendelian inheritance in animals. Rose-comb is a monogenic trait that has been widely described in chickens. It is caused by a large structural rearrangement that leads to mis-expression of transcription factor MNR2 on chromosome 7. Rose-comb has pleiotropic effects in homozygous roosters, which is associated with poor sperm mobility. It was postulated that this is caused by the disruption of the CCDC108 gene located at the distal inversion breakpoint...
March 2, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339723/leveraging-molecular-datasets-for-biomarker-based-clinical-trial-design-in-glioblastoma
#18
Shyam K Tanguturi, Lorenzo Trippa, Shakti H Ramkissoon, Kristine Pelton, David Knoff, David Sandak, Neal I Lindeman, Azra H Ligon, Rameen Beroukhim, Giovanni Parmigiani, Patrick Y Wen, Keith L Ligon, Brian M Alexander
Background.: Biomarkers can improve clinical trial efficiency, but designing and interpreting biomarker-driven trials require knowledge of relationships among biomarkers, clinical covariates, and endpoints. We investigated these relationships across genomic subgroups of glioblastoma (GBM) within our institution (DF/BWCC), validated results in The Cancer Genome Atlas (TCGA), and demonstrated potential impacts on clinical trial design and interpretation. Methods.: We identified genotyped patients at DF/BWCC, and clinical associations across 4 common GBM genomic biomarker groups were compared along with overall survival (OS), progression-free survival (PFS), and survival post-progression (SPP)...
February 20, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28339094/f221y-mutation-in-hepatitis-b-virus-reverse-transcriptase-is-associated-with-hepatocellular-carcinoma-prognosis-following-liver-resection
#19
Huiming Li, Jian'an Jia, Mengmeng Wang, Hui Wang, Xing Gu, Meng Fang, Chunfang Gao
Hepatitis B virus (HBV) reverse transcriptase (RT) is encoded by the polymerase gene in the reverse transcriptase region, which overlaps with the S gene. The association between mutations of HBV RT and the pathobiological features of hepatocellular carcinoma (HCC) remain to be elucidated. The present study aimed to examine mutations in this region of the HBV genome and its clinical significance. Briefly, HBV total DNA was extracted from 84 pairs of HCC tumor tissue and corresponding adjacent non‑tumor tissue samples...
March 23, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28339057/gpr143-mutations-in-chinese-patients-with-ocular-albinism-type-1
#20
Xiuhua Jia, Jin Yuan, Xiaoyun Jia, Shiqi Ling, Shiqiang Li, Xiangming Guo
The aim of the present study was to evaluate mutations of the G protein-coupled receptor 143 (GPR143) gene for ocular albinism type 1 (OA1) in Chinese patients. For the current study, 8 patients with OA1 were selected from the database of ocular genetic diseases. Genomic DNA of OA1 was prepared from venous leukocytes collected from the patients. Cycle sequencing was used to analyze the exons and adjacent introns of GPR143. The variation detected was analyzed by bidirectional DNA sequencing and further evaluated in 96 controls using heteroduplex‑single strand conformational polymorphism analysis...
March 23, 2017: Molecular Medicine Reports
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