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https://www.readbyqxmd.com/read/28644393/mutations-in-the-genes-for-interphotoreceptor-matrix-proteoglycans-impg1-and-impg2-in-patients-with-vitelliform-macular-lesions
#1
Caroline Brandl, Heidi L Schulz, Peter Charbel Issa, Johannes Birtel, Richard Bergholz, Clemens Lange, Claudia Dahlke, Ditta Zobor, Bernhard H F Weber, Heidi Stöhr
A significant portion of patients diagnosed with vitelliform macular dystrophy (VMD) do not carry causative mutations in the classic VMD genes BEST1 or PRPH2. We therefore performed a mutational screen in a cohort of 106 BEST1/PRPH2-negative VMD patients in two genes encoding secreted interphotoreceptor matrix proteoglycans-1 and -2 (IMPG1 and IMPG2). We identified two novel mutations in IMPG1 in two simplex VMD cases with disease onset in their early childhood, a heterozygous p.(Leu238Pro) missense mutation and a homozygous c...
June 23, 2017: Genes
https://www.readbyqxmd.com/read/28635663/assessing-genetic-diversity-and-population-differentiation-of-colored-calla-lily-zantedeschia-hybrid-for-an-efficient-breeding-program
#2
Zunzheng Wei, Huali Zhang, Yi Wang, Youli Li, Min Xiong, Xian Wang, Di Zhou
Plastome-genome incompatibility (PGI) is prevalent in several plants including the Zantedeschia species, a worldwide commercial flower crop native to South Africa. Generally, hybrids suffering from PGI appear less vigorous and more susceptible than normal plants. Previous reports revealed that the PGI level in interspecific hybrids is correlated with the relatedness of the parental species in the genus Zantedeschia. To provide a basis for utilizing and improving resources in breeding programs, a total of 117 accessions of colored calla lily (Zantedeschia hybrid), collected from New Zealand, the Netherlands and the United States, were genotyped using 31 transferable expressed sequence tags-simple sequence repeats (EST-SSR) markers from the white calla lily (Zantedeschia aethiopica)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28635635/identifying-bird-remains-using-ancient-dna-barcoding
#3
Love Dalén, Vendela K Lagerholm, Johan A A Nylander, Nick Barton, Zbigniew M Bochenski, Teresa Tomek, David Rudling, Per G P Ericson, Martin Irestedt, John R Stewart
Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28635624/effects-of-type-1-diabetes-risk-alleles-on-immune-cell-gene-expression
#4
REVIEW
Ramesh Ram, Grant Morahan
Genetic studies have identified 61 variants associated with the risk of developing Type 1 Diabetes (T1D). The functions of most of the non-HLA (Human Leukocyte Antigen) genetic variants remain unknown. We found that only 16 of these risk variants could potentially be linked to a protein-coding change. Therefore, we investigated whether these variants affected susceptibility by regulating changes in gene expression. To do so, we examined whole transcriptome profiles of 600 samples from the Type 1 Diabetes Genetics Consortium (T1DGC)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28632168/a-comparative-study-of-the-structural-dynamics-of-four-terminal-uridylyl-transferases
#5
Kevin J Cheng, Özlem Demir, Rommie E Amaro
African trypanosomiasis occurs in 36 countries in sub-Saharan Africa with 10,000 reported cases annually. No definitive remedy is currently available and if left untreated, the disease becomes fatal. Structural and biochemical studies of trypanosomal terminal uridylyl transferases (TUTases) demonstrated their functional role in extensive uridylate insertion/deletion of RNA. Trypanosoma brucei RNA Editing TUTase 1 (TbRET1) is involved in guide RNA 3' end uridylation and maturation, while TbRET2 is responsible for U-insertion at RNA editing sites...
June 20, 2017: Genes
https://www.readbyqxmd.com/read/28632161/endogenous-retroviral-insertions-indicate-a-secondary-introduction-of-domestic-sheep-lineages-to-the-caucasus-and-central-asia-between-the-bronze-and-iron-age
#6
Oskar Schroeder, Norbert Benecke, Kai Frölich, Zuogang Peng, Kai Kaniuth, Leonid Sverchkov, Sabine Reinhold, Andrey Belinskiy, Arne Ludwig
Sheep were one of the first livestock species domesticated by humans. After initial domestication in the Middle East they were spread across Eurasia. The modern distribution of endogenous Jaagsiekte sheep retrovirus insertions in domestic sheep breeds suggests that over the course of millennia, successive introductions of improved lineages and selection for wool quality occurred in the Mediterranean region and most of Asia. Here we present a novel ancient DNA approach using data of endogenous retroviral insertions in Bronze and Iron Age domestic sheep from the Caucasus and Pamir mountain areas...
June 20, 2017: Genes
https://www.readbyqxmd.com/read/28621722/comparative-analysis-of-genome-wide-dna-methylation-profiles-for-the-genic-male-sterile-cabbage-line-01-20s-and-its-maintainer-line
#7
Fengqing Han, Xiaoli Zhang, Xing Liu, Henan Su, Congcong Kong, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Yumei Liu, Zhansheng Li, Honghao Lv
Methylation modifications play an important role in multiple biological processes. Several studies have reported altered methylation patterns in male sterile plants such as rice and wheat, but little is known about the global methylation profiles and their possible roles in the cabbage (Brassicaoleracea) male sterile line. In this study, single-base-resolution bisulfite sequencing (BS-Seq) was adopted to identify the pattern and degree of cytosine methylation in the male sterile line 01-20S and its near-isogenic fertile line 01-20F...
June 16, 2017: Genes
https://www.readbyqxmd.com/read/28621718/using-small-rna-seq-data-to-detect-sirna-duplexes-induced-by-plant-viruses
#8
Xiaoran Niu, Yu Sun, Ze Chen, Rugang Li, Chellappan Padmanabhan, Jishou Ruan, Jan F Kreuze, KaiShu Ling, ZhangJun Fei, Shan Gao
Small interfering RNA (siRNA) duplexes are short (usually 21 to 24 bp) double-stranded RNAs (dsRNAs) with several overhanging nucleotides at both 5'- and 3'-ends. It has been found that siRNA duplexes bind the RNA-induced silencing complex (RISC) and cleave the sense strands with endonucleases. In this study, for the first time, we detected siRNA duplexes induced by plant viruses on a large scale using next-generation sequencing (NGS) data. In addition, we used the detected 21 nucleotide (nt) siRNA duplexes with 2 nt overhangs to construct a dataset for future data mining...
June 16, 2017: Genes
https://www.readbyqxmd.com/read/28617333/an-%C3%A2-aukward-tale-a-genetic-approach-to-discover-the-whereabouts-of-the-last-great-auks
#9
Jessica E Thomas, Gary R Carvalho, James Haile, Michael D Martin, Jose A Samaniego Castruita, Jonas Niemann, Mikkel-Holger S Sinding, Marcela Sandoval-Velasco, Nicolas J Rawlence, Errol Fuller, Jon Fjeldså, Michael Hofreiter, John R Stewart, M Thomas P Gilbert, Michael Knapp
One hundred and seventy-three years ago, the last two Great Auks, Pinguinusimpennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which-if any-of Fuller's candidate skins likely belong to either of the two birds...
June 15, 2017: Genes
https://www.readbyqxmd.com/read/28617307/erratum-michael-a-picker-et-al-h-ns-its-family-members-and-their-regulation-of-virulence-genes-in-shigella-species-genes-2016-7-112
#10
https://www.readbyqxmd.com/read/28604635/splice-switching-therapy-for-spinal-muscular-atrophy
#11
REVIEW
Katharina E Meijboom, Matthew J A Wood, Graham McClorey
Spinal muscular atrophy (SMA) is a genetic disorder with severity ranging from premature death in infants to restricted motor function in adult life. Despite the genetic cause of this disease being known for over twenty years, only recently has a therapy been approved to treat the most severe form of this disease. Here we discuss the genetic basis of SMA and the subsequent studies that led to the utilization of splice switching oligonucleotides to enhance production of SMN protein, which is absent in patients, through a mechanism of exon inclusion into the mature mRNA...
June 12, 2017: Genes
https://www.readbyqxmd.com/read/28604630/haplotypes-of-the-ovine-adiponectin-gene-and-their-association-with-growth-and-carcass-traits-in-new-zealand-romney-lambs
#12
Qingming An, Huitong Zhou, Jiang Hu, Yuzhu Luo, Jon G H Hickford
Adiponectin plays an important role in energy homeostasis and metabolism in mammalian adipose tissue. In this study, the relationship between adiponectin gene (ADIPOQ) haplotypes and variation in growth and carcass traits in New Zealand (NZ) Romney lambs was investigated using General Linear Models (GLMs). Eight haplotypes were found in these lambs and they were composed of the four previously reported promoter fragment sequences (A₁-D₁) and three previously reported intron 2-exon 3 sequences (A₃-C₃)...
June 12, 2017: Genes
https://www.readbyqxmd.com/read/28590415/the-dual-roles-of-myc-in-genomic-instability-and-cancer-chemoresistance
#13
REVIEW
Alpana Kumari, Watson P Folk, Daitoku Sakamuro
Cancer is associated with genomic instability and aging. Genomic instability stimulates tumorigenesis, whereas deregulation of oncogenes accelerates DNA replication and increases genomic instability. It is therefore reasonable to assume a positive feedback loop between genomic instability and oncogenic stress. Consistent with this premise, overexpression of the MYC transcription factor increases the phosphorylation of serine 139 in histone H2AX (member X of the core histone H2A family), which forms so-called γH2AX, the most widely recognized surrogate biomarker of double-stranded DNA breaks (DSBs)...
June 7, 2017: Genes
https://www.readbyqxmd.com/read/28587281/genome-wide-identification-and-characterization-of-salinity-stress-responsive-mirnas-in-wild-emmer-wheat-triticum-turgidum-ssp-dicoccoides
#14
Kewei Feng, Xiaojun Nie, Licao Cui, Pingchuan Deng, Mengxing Wang, Weining Song
MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs which regulate diverse molecular and biochemical processes at a post-transcriptional level in plants. As the ancestor of domesticated wheat, wild emmer wheat (Triticum turgidum ssp. dicoccoides) has great genetic potential for wheat improvement. However, little is known about miRNAs and their functions on salinity stress in wild emmer. To obtain more information on miRNAs in wild emmer, we systematically investigated and characterized the salinity-responsive miRNAs using deep sequencing technology...
June 6, 2017: Genes
https://www.readbyqxmd.com/read/28587229/ataxin-2-from-rna-control-to-human-health-and-disease
#15
REVIEW
Lauren A Ostrowski, Amanda C Hall, Karim Mekhail
RNA-binding proteins play fundamental roles in the regulation of molecular processes critical to cellular and organismal homeostasis. Recent studies have identified the RNA-binding protein Ataxin-2 as a genetic determinant or risk factor for various diseases including spinocerebellar ataxia type II (SCA2) and amyotrophic lateral sclerosis (ALS), amongst others. Here, we first discuss the increasingly wide-ranging molecular functions of Ataxin-2, from the regulation of RNA stability and translation to the repression of deleterious accumulation of the RNA-DNA hybrid-harbouring R-loop structures...
June 5, 2017: Genes
https://www.readbyqxmd.com/read/28587228/fine-mapping-and-transcriptome-analysis-reveal-candidate-genes-associated-with-hybrid-lethality-in-cabbage-brassica-oleracea
#16
Zhiliang Xiao, Yang Hu, Xiaoli Zhang, Yuqian Xue, Zhiyuan Fang, Limei Yang, Yangyong Zhang, Yumei Liu, Zhansheng Li, Xing Liu, Zezhou Liu, Honghao Lv, Mu Zhuang
Hybrid lethality is a deleterious phenotype that is vital to species evolution. We previously reported hybrid lethality in cabbage (Brassica oleracea) and performed preliminary mapping of related genes. In the present study, the fine mapping of hybrid lethal genes revealed that BoHL1 was located on chromosome C1 between BoHLTO124 and BoHLTO130, with an interval of 101 kb. BoHL2 was confirmed to be between insertion-deletion (InDels) markers HL234 and HL235 on C4, with a marker interval of 70 kb. Twenty-eight and nine annotated genes were found within the two intervals of BoHL1 and BoHL2, respectively...
June 5, 2017: Genes
https://www.readbyqxmd.com/read/28587191/new-insights-in-the-cytogenetic-practice-karyotypic-chaos-non-clonal-chromosomal-alterations-and-chromosomal-instability-in-human-cancer-and-therapy-response
#17
REVIEW
Nelson Rangel, Maribel Forero-Castro, Milena Rondón-Lagos
Recently, non-clonal chromosomal alterations previously unappreciated are being proposed to be included in cytogenetic practice. The aim of this inclusion is to obtain a greater understanding of chromosomal instability (CIN) and tumor heterogeneity and their role in cancer evolution and therapy response. Although several genetic assays have allowed the evaluation of the variation in a population of cancer cells, these assays do not provide information at the level of individual cells, therefore limiting the information of the genomic diversity within tumors (heterogeneity)...
June 3, 2017: Genes
https://www.readbyqxmd.com/read/28574479/r-loops-in-the-regulation-of-antibody-gene-diversification
#18
REVIEW
Rushad Pavri
For nearly three decades, R loops have been closely linked with class switch recombination (CSR), the process that generates antibody isotypes and that occurs via a complex cascade initiated by transcription-coupled mutagenesis in switch recombination sequences. R loops form during transcription of switch recombination sequences in vitro and in vivo, and there is solid evidence that R loops are required for efficient class switching. The classical model of R loops posits that they boost mutation rates by generating stable and long tracts of single-stranded DNA that serve as the substrate for activation induced deaminase (AID), the enzyme that initiates the CSR reaction cascade by co-transcriptionally mutating ssDNA in switch recombination sequences...
June 2, 2017: Genes
https://www.readbyqxmd.com/read/28561745/hiseeker-detecting-high-order-snp-interactions-based-on-pairwise-snp-combinations
#19
Jie Liu, Guoxian Yu, Yuan Jiang, Jun Wang
Detecting single nucleotide polymorphisms' (SNPs) interaction is one of the most popular approaches for explaining the missing heritability of common complex diseases in genome-wide association studies. Many methods have been proposed for SNP interaction detection, but most of them only focus on pairwise interactions and ignore high-order ones, which may also contribute to complex traits. Existing methods for high-order interaction detection can hardly handle genome-wide data and suffer from low detection power, due to the exponential growth of search space...
May 31, 2017: Genes
https://www.readbyqxmd.com/read/28556790/dna-methylation-profiling-of-human-prefrontal-cortex-neurons-in-heroin-users-shows-significant-difference-between-genomic-contexts-of-hyper-and-hypomethylation-and-a-younger-epigenetic-age
#20
Alexey Kozlenkov, Andrew E Jaffe, Alisa Timashpolsky, Pasha Apontes, Sergei Rudchenko, Mihaela Barbu, William Byne, Yasmin L Hurd, Steve Horvath, Stella Dracheva
We employed Illumina 450 K Infinium microarrays to profile DNA methylation (DNAm) in neuronal nuclei separated by fluorescence-activated sorting from the postmortem orbitofrontal cortex (OFC) of heroin users who died from heroin overdose (N = 37), suicide completers (N = 22) with no evidence of heroin use and from control subjects who did not abuse illicit drugs and died of non-suicide causes (N = 28). We identified 1298 differentially methylated CpG sites (DMSs) between heroin users and controls, and 454 DMSs between suicide completers and controls (p < 0...
May 30, 2017: Genes
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