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https://www.readbyqxmd.com/read/28535388/transgenerational-inheritance-perpetuating-rnai
#1
Kristen C Brown, Taiowa A Montgomery
Reversible changes in gene expression independent of the genetic code can be transmitted from one generation to the next via poorly understood mechanisms. In worms, a histone-modifying enzyme is necessary to keep small RNA-guided transgenerational gene silencing in check.
May 22, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28534783/nahal-flex-a-numerical-and-alphabetical-hinge-detection-algorithm-for-flexible-protein-structure-alignment
#2
Samira Fotoohifiroozabadi, Mohd Saberi Mohamad, Safaai Deris
Flexible proteins are proteins that have conformational changes in their structures. Protein flexibility analysis is critical for classifying and understanding protein functionality. For that analysis, the hinge areas where proteins show flexibility must be detected. To detect the location of the hinges, previous methods have utilized the three-dimensional (3D) structure of proteins, which is highly computational. To reduce the computational complexity, this study proposes a novel text-based method using structural alphabets (SAs) for detecting the hinge position, called NAHAL-Flex...
May 17, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28533336/a-coding-variant-in-the-gene-bardet-biedl-syndrome-4-bbs4-is-associated-with-a-novel-form-of-canine-progressive-retinal-atrophy
#3
Tracy Chew, Bianca Haase, Roslyn Bathgate, Cali E Willet, Maria K Kaukonen, Lisa J Mascord, Hannes T Lohi, Claire M Wade
Progressive retinal atrophy is a common cause of blindness in the dog and affects over 100 breeds. It is characterized by gradual vision loss that occurs due to the degeneration of photoreceptor cells in the retina. Similar to the human counterpart retinitis pigmentosa, the canine disorder is clinically and genetically heterogeneous and the underlying cause remains unknown for many cases. We use a positional candidate gene approach to identify putative variants in the Hungarian Puli breed using genotyping data of 14 family-based samples (CanineHD BeadChip array, Illumina) and whole genome sequencing data of two proband and two parental samples (Illumina HiSeq 2000)...
May 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28533181/comparative-genome-analysis-of-lactobacillus-plantarum-gb-lp3-provides-candidates-of-survival-related-genetic-factors
#4
Soomin Jeon, Jaehoon Jung, Kwondo Kim, DongAhn Yoo, Chanho Lee, Jungsun Kang, Kyungjin Cho, Dae-Kyung Kang, Woori Kwak, Sook Hee Yoon, Heebal Kim, Seoae Cho
Lactobacillus plantarum is found in various environmental niches such as in the gastrointestinal tract of an animal host or a fermented food. This species isolated from a certain environment is known to possess a variety of properties according to inhabited environment's adaptation. However, a causal relationship of a genetic factor and phenotype affected by a specific environment has not been systematically comprehended. L. plantarum GB-LP3 strain was isolated from Korean traditional fermented vegetable and the whole genome of GB-LP3 was sequenced...
May 19, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28531368/molecular-phylogeny-of-loliginidae-inferred-from-mitochondrial-dna-sequence-variation
#5
Lisen Kang, Shuyi Zhang, Changwen Wu, Xiaoxu Liu, Mei Ying Xu, Lihua Jiang
Loliginidae includes many economically important species in trophic systems worldwide. Here, we investigated genetic relationships and diversity in this family. Sequence comparisons and phylogenetic analyses revealed considerable variations between mitochondrial 16 S rRNA gene and cytochrome coxidase subunit I gene among nine Loliginid species. We identified three similar non-coding regions in eight Loliginid species, but not in Sepioteuthislessoniana. We detected a single extended termination-associated sequence and three conserved sequence blocks among these eight species...
May 20, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28529692/abnormal-expression-of-atp1a1-and-atp1a2-in-breast-cancer
#6
Alexey Bogdanov, Fedor Moiseenko, Michael Dubina
Breast cancer is the first in incidence and the second in death among all solid tumors occurring in women. The identification of molecular genetic abnormalities in breast cancer is important to improve the results of treatment. In the present study, we analyzed microarray data of breast cancer expression profiling (NCBI GEO database, accession GSE65194), focusing on Na (+)/K (+)-ATPase coding genes. We found overexpression of the ATP1A1 and down-regulation of the ATP1A2. We expect that our research could help to improve the understanding of predictive and prognostic features of breast cancer...
2017: F1000Research
https://www.readbyqxmd.com/read/28529571/epigenetic-modulation-associated-with-carcinogenesis-and-prognosis-of-human-gastric-cancer
#7
Fuminori Sonohara, Yoshikuni Inokawa, Masamichi Hayashi, Yasuhiro Kodera, Shuji Nomoto
Gastric cancer (GC) is a leading cause of cancer-related death, particularly in Asia. Epidemiological and other clinical studies have identified an association between a number of risk factors, including Helicobacter pylori, and GC. A number of studies have also examined genetic changes associated with the development and progression of GC. When considering the clinical significance of the expression of a specific gene, its epigenetic modulation should be considered. Epigenetic modulation appears to be a primary driver of changes in gastric tissue that promotes carcinogenesis and progression of GC and other neoplasms...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28529542/frequency-and-geographic-distribution-of-tert-promoter-mutations-in-primary-hepatocellular-carcinoma
#8
REVIEW
Francesca Pezzuto, Luigi Buonaguro, Franco M Buonaguro, Maria Lina Tornesello
Primary hepatocellular carcinoma (HCC) mainly develops in subjects chronically infected with hepatitis B (HBV) and C (HCV) viruses through a multistep process characterized by the accumulation of genetic alterations in the human genome. Nucleotide changes in coding regions (i.e. TP53, CTNNB1, ARID1A and ARID2) as well as in non-coding regions (i.e. TERT promoter) are considered cancer drivers for HCC development with variable frequencies in different geographic regions depending on the etiology and environmental factors...
2017: Infectious Agents and Cancer
https://www.readbyqxmd.com/read/28529469/a-comparative-genomics-approach-revealed-evolutionary-dynamics-of-microsatellite-imperfection-and-conservation-in-genus-gossypium
#9
Muhammad Mahmood Ahmed, Chao Shen, Anam Qadir Khan, Muhammad Atif Wahid, Muhammad Shaban, Zhongxu Lin
BACKGROUND: Ongoing molecular processes in a cell could target microsatellites, a kind of repetitive DNA, owing to length variations and motif imperfection. Mutational mechanisms underlying such kind of genetic variations have been extensively investigated in diverse organisms. However, obscure impact of ploidization, an evolutionary process of genome content duplication prevails mostly in plants, on non-coding DNA is poorly understood. RESULTS: Genome sequences of diversely originated plant species were examined for genome-wide motif imperfection pattern, and various analytical tools were employed to canvass characteristic relationships among repeat density, imperfection and length of microsatellites...
2017: Hereditas
https://www.readbyqxmd.com/read/28529064/analysis-of-post-transcriptional-regulation-during-cancer-progression-using-a-donor-derived-isogenic-model-of-tumorigenesis
#10
Laura S Bisogno, Jack D Keene
Post-transcriptional regulation of gene expression by RNA binding proteins (RBPs) and non-coding RNAs plays an important role in global gene expression. Many post-transcriptional regulators are misexpressed and misregulated in cancers, resulting in altered programs of protein biosynthesis that can drive tumor progression. While comparative studies of several RBPs and microRNAs expressed in various cancer types have been reported, a model system that can be used to quantify RBP regulation and functional outcomes during the initiation and early stages of tumorigenesis is lacking...
May 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28528902/x-cells-are-globally-distributed-genetically-divergent-fish-parasites-related-to-perkinsids-and-dinoflagellates
#11
Mark A Freeman, Janina Fuss, Árni Kristmundsson, Marit F M Bjorbækmo, Jean-François Mangot, Javier Del Campo, Patrick J Keeling, Kamran Shalchian-Tabrizi, David Bass
"X-cells" have long been associated with tumor-like formations (xenomas) in marine fish, including many of commercial interest. The name was first used to refer to the large polygonal cells that were found in epidermal xenomas from flatfish from the Pacific Northwest [1]. Similar looking cells from pseudobranchial xenomas had previously been reported from cod in the Atlantic [2] and Pacific Oceans [3]. X-cell pathologies have been reported from five teleost orders: Pleuronectiformes (flatfish), Perciformes (perch-like fish), Gadiformes (cods), Siluriformes (catfish), and Salmoniformes (salmonids)...
May 13, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28527921/drug-induced-fatal-arrhythmias-acquired-long-qt-and-brugada-syndromes
#12
REVIEW
Isik Turker, Tomohiko Ai, Hideki Itoh, Minoru Horie
Since the early 1990s, the concept of primary "inherited" arrhythmia syndromes or ion channelopathies has evolved rapidly as a result of revolutionary progresses made in molecular genetics. Alterations in genes coding for membrane proteins such as ion channels or their associated proteins responsible for the generation of cardiac action potentials (AP) have been shown to cause specific malfunctions which eventually lead to cardiac arrhythmias. These arrhythmic disorders include congenital long QT syndrome, Brugada syndrome, catecholaminergic polymorphic ventricular tachycardia, short QT syndrome, progressive cardiac conduction disease, etc...
May 17, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28527213/sorl1-variants-show-different-association-with-early-onset-and-late-onset-alzheimer-s-disease-risk
#13
Guiyou Liu, Jing-Yi Sun, Meiling Xu, Xiao-Yi Yang, Bao-Liang Sun
A recent study sequenced the full coding region of SORL1 in 1,255 early-onset Alzheimer's disease (EOAD) cases and 1,938 control individuals, and investigated the contribution of genetic variability in SORL1 to EOAD risk in a European cohort. This study identified six common variants and five low frequency variants in the SORL1 coding sequence. However, none of these 11 variants was significantly associated with EOAD risk after adjusting for multiple testing. We consider whether these 11 SORL1 variants identified in European EOAD contribute to late-onset Alzheimer's disease (LOAD) risk in individuals of European ancestry...
May 17, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28526930/micrornas-in-parkinson-s-disease
#14
REVIEW
Abhishek Singh, Dwaipayan Sen
Parkinson's disease is the second most common neurodegenerative disease commonly affecting the older population. Loss of dopaminergic neurons in the substantia nigra of brain leads to impairment of motor activities as well as cognitive defects. There are many underlying causes to this disease, both genetic and epigenetic, which are yet to be fully explored. Non-coding RNAs are significant part of our genome and are involved in various cellular processes. MicroRNAs, which are small non-coding RNAs having 20-22 nucleotides, are involved in many underlying mechanisms of pathogenesis of several neurodegenerative diseases including Parkinson's...
May 19, 2017: Experimental Brain Research. Experimentelle Hirnforschung. Expérimentation Cérébrale
https://www.readbyqxmd.com/read/28526731/validated-bayesian-differentiation-of-causative-and-passenger-mutations
#15
Frederick R Cross, Michal Breker, Kristi Lieberman
In many contexts, the problem arises of determining which of many candidate mutations is the most likely to be causative for some phenotype. It is desirable to have a way to evaluate this probability that relies as little as possible on previous knowledge, to avoid bias against discovering new genes or functions. We are isolating mutants with blocked cell cycle progression in Chlamydomonas, and determining mutant genome sequences. Due to the intensity of UV mutagenesis required for efficient mutant collection, the mutants contain multiple mutations altering coding sequence...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28526340/unfolding-the-pathogenesis-of-scleroderma-through-genomics-and-epigenomics
#16
REVIEW
Pei-Suen Tsou, Amr H Sawalha
With unknown etiology, scleroderma (SSc) is a multifaceted disease characterized by immune activation, vascular complications, and excessive fibrosis in internal organs. Genetic studies, including candidate gene association studies, genome-wide association studies, and whole-exome sequencing have supported the notion that while genetic susceptibility to SSc appears to be modest, SSc patients are genetically predisposed to this disease. The strongest genetic association for SSc lies within the MHC region, with loci in HLA-DRB1, HLA-DQB1, HLA-DPB1, and HLA-DOA1 being the most replicated...
May 16, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28525990/transversions-have-larger-regulatory-effects-than-transitions
#17
Cong Guo, Ian C McDowell, Michael Nodzenski, Denise M Scholtens, Andrew S Allen, William L Lowe, Timothy E Reddy
BACKGROUND: Transversions (Tv's) are more likely to alter the amino acid sequence of proteins than transitions (Ts's), and local deviations in the Ts:Tv ratio are indicative of evolutionary selection on genes. Whether the two different types of mutations have different effects in non-protein-coding sequences remains unknown. Genetic variants primarily impact gene expression by disrupting the binding of transcription factors (TFs) and other DNA-binding proteins. Because Tv's cause larger changes in the shape of a DNA backbone, we hypothesized that Tv's would have larger impacts on TF binding and gene expression...
May 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28525989/determination-of-genetic-effects-of-atf3-and-cdkn1a-genes-on-milk-yield-and-compositions-in-chinese-holstein-population
#18
REVIEW
Bo Han, Weijun Liang, Lin Liu, Yanhua Li, Dongxiao Sun
BACKGROUND: Our previous RNA-sequencing study revealed that the ATF3 and CDKN1A genes were remarkably differentially expressed between the mammary glands of lactating Holstein cows with extremely high and low milk protein and fat percentage so that both of them were considered as candidates for milk composition. Herein, we further verified whether these genes have genetic effects on milk production traits in a Chinese Holstein cow population. RESULTS: By re-sequencing the entire coding and regulatory regions, we identified four SNPs in 5'promoter region, two in exons, seven in 3' un-translated region (UTR), and six in 3'flanking region of ATF3 gene, and one SNP in exon 5, two in 3'UTR, and two in 3'flanking region of CDKN1A gene...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525980/the-distribution-of-mitochondrial-dna-haplogroup-h-in-southern-iberia-indicates-ancient-human-genetic-exchanges-along-the-western-edge-of-the-mediterranean
#19
Candela L Hernández, Jean M Dugoujon, Andrea Novelletto, Juan N Rodríguez, Pedro Cuesta, Rosario Calderón
BACKGROUND: The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These characteristics permit the analysis of ancient migrations between both shores, which may have occurred via primitive sea crafts and early seafaring...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525770/-expand-and-click-a-new-method-for-labeling-hiv-1-envelope-glycoproteins
#20
Melissa V Fernandez, Eric O Freed
In this issue of Cell Chemical Biology, Sakin et al. (2017) investigate the nanoscale behavior of the HIV-1 envelope (Env) glycoprotein complex by using genetic code expansion, bioorthogonal amino acids, synthetic dyes, and click chemistry. This minimally invasive approach allows the measurement of native Env cellular distribution and dynamics.
May 18, 2017: Cell Chemical Biology
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