journal
MENU ▼
Read by QxMD icon Read
search

Frontiers in Genetics

journal
https://www.readbyqxmd.com/read/28326099/disease-risk-assessment-using-a-voronoi-based-network-analysis-of-genes-and-variants-scores
#1
Lin Chen, Gouri Mukerjee, Ruslan Dorfman, Seyed M Moghadas
Much effort has been devoted to assess disease risk based on large-scale protein-protein network and genotype-phenotype associations. However, the challenge of risk prediction for complex diseases remains unaddressed. Here, we propose a framework to quantify the risk based on a Voronoi tessellation network analysis, taking into account the disease association scores of both genes and variants. By integrating ClinVar, SNPnexus, and DISEASES databases, we introduce a gene-variant map that is based on the pairwise disease-associated gene-variant scores...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28326098/nuclear-actin-in-development-and-transcriptional-reprogramming
#2
REVIEW
Shinji Misu, Marina Takebayashi, Kei Miyamoto
Actin is a highly abundant protein in eukaryotic cells and dynamically changes its polymerized states with the help of actin-binding proteins. Its critical function as a constituent of cytoskeleton has been well-documented. Growing evidence demonstrates that actin is also present in nuclei, referred to as nuclear actin, and is involved in a number of nuclear processes, including transcriptional regulation and chromatin remodeling. The contribution of nuclear actin to transcriptional regulation can be explained by its direct interaction with transcription machineries and chromatin remodeling factors and by controlling the activities of transcription factors...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28321234/a-review-of-bioinformatics-tools-for-bio-prospecting-from-metagenomic-sequence-data
#3
REVIEW
Despoina D Roumpeka, R John Wallace, Frank Escalettes, Ian Fotheringham, Mick Watson
The microbiome can be defined as the community of microorganisms that live in a particular environment. Metagenomics is the practice of sequencing DNA from the genomes of all organisms present in a particular sample, and has become a common method for the study of microbiome population structure and function. Increasingly, researchers are finding novel genes encoded within metagenomes, many of which may be of interest to the biotechnology and pharmaceutical industries. However, such "bioprospecting" requires a suite of sophisticated bioinformatics tools to make sense of the data...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28321233/heterogeneity-of-the-pancreatic-beta-cell
#4
REVIEW
Giselle Dominguez Gutierrez, Jesper Gromada, Lori Sussel
The pancreatic beta cell functions as a key regulator of blood glucose levels by integrating a variety of signals in response to changing metabolic demands. Variations in beta cell identity that translate into functionally different subpopulations represent an interesting mechanism to allow beta cells to efficiently respond to diverse physiological and pathophysiological conditions. Recently, there is emerging evidence that morphological and functional differences between beta cells exist. Furthermore, the ability of novel single cell technologies to characterize the molecular identity of individual beta cells has created a new era in the beta cell field...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28316610/integrative-approaches-for-studying-mitochondrial-and-nuclear-genome-co-evolution-in-oxidative-phosphorylation
#5
Paul Sunnucks, Hernán E Morales, Annika M Lamb, Alexandra Pavlova, Chris Greening
In animals, interactions among gene products of mitochondrial and nuclear genomes (mitonuclear interactions) are of profound fitness, evolutionary, and ecological significance. Most fundamentally, the oxidative phosphorylation (OXPHOS) complexes responsible for cellular bioenergetics are formed by the direct interactions of 13 mitochondrial-encoded and ∼80 nuclear-encoded protein subunits in most animals. It is expected that organisms will develop genomic architecture that facilitates co-adaptation of these mitonuclear interactions and enhances biochemical efficiency of OXPHOS complexes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28289428/inflammation-dna-damage-helicobacter-pylori-and-gastric-tumorigenesis
#6
REVIEW
Polyxeni Kalisperati, Evangelia Spanou, Ioannis S Pateras, Penelope Korkolopoulou, Anastasia Varvarigou, Ioannis Karavokyros, Vassilis G Gorgoulis, Panayiotis G Vlachoyiannopoulos, Stavros Sougioultzis
Helicobacter pylori (H. pylori) is a Gram negative bacterium that colonizes the stomach of almost half human population. It has evolved to escape immune surveillance, establishes lifelong inflammation, predisposing to genomic instability and DNA damage, notably double strand breaks. The epithelial host cell responds by activation of DNA damage repair (DDR) machinery that seems to be compromised by the infection. It is therefore now accepted that genetic damage is a major mechanism operating in cases of H. pylori induced carcinogenesis...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28270834/metabolic-stress-and-compromised-identity-of-pancreatic-beta-cells
#7
REVIEW
Avital Swisa, Benjamin Glaser, Yuval Dor
Beta cell failure is a central feature of type 2 diabetes (T2D), but the molecular underpinnings of the process remain only partly understood. It has been suggested that beta cell failure in T2D involves massive cell death. Other studies ascribe beta cell failure to cell exhaustion, due to chronic oxidative or endoplasmic reticulum stress leading to cellular dysfunction. More recently it was proposed that beta cells in T2D may lose their differentiated identity, possibly even gaining features of other islet cell types...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28270833/regulatory-features-for-odorant-receptor-genes-in-the-mouse-genome
#8
REVIEW
Andrea Degl'Innocenti, Anna D'Errico
The odorant receptor genes, seven transmembrane receptor genes constituting the vastest mammalian gene multifamily, are expressed monogenically and monoallelicaly in each sensory neuron in the olfactory epithelium. This characteristic, often referred to as the one neuron-one receptor rule, is driven by mostly uncharacterized molecular dynamics, generally named odorant receptor gene choice. Much attention has been paid by the scientific community to the identification of sequences regulating the expression of odorant receptor genes within their loci, where related genes are usually arranged in genomic clusters...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28270832/actin-family-proteins-in-the-human-ino80-chromatin-remodeling-complex-exhibit-functional-roles-in-the-induction-of-heme-oxygenase-1-with-hemin
#9
Yuichiro Takahashi, Hirokazu Murakami, Yusuke Akiyama, Yasutake Katoh, Yukako Oma, Hitoshi Nishijima, Kei-Ichi Shibahara, Kazuhiko Igarashi, Masahiko Harata
Nuclear actin family proteins, comprising of actin and actin-related proteins (Arps), are essential functional components of the multiple chromatin remodeling complexes. The INO80 chromatin remodeling complex, which is evolutionarily conserved and has roles in transcription, DNA replication and repair, consists of actin and actin-related proteins Arp4, Arp5, and Arp8. We generated Arp5 knockout (KO) and Arp8 KO cells from the human Nalm-6 pre-B cell line and used these KO cells to examine the roles of Arp5 and Arp8 in the transcriptional regulation mediated by the INO80 complex...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28270831/genomic-prediction-of-genotypic-effects-with-epistasis-and-environment-interactions-for-yield-related-traits-of-rapeseed-brassica-napus-l
#10
Xiang Luo, Yi Ding, Linzhong Zhang, Yao Yue, John H Snyder, Chaozhi Ma, Jun Zhu
Oilseed rape (Brassica napus) is an economically important oil crop, yet the genetic architecture of its complex traits remain largely unknown. Here, genome-wide association study was conducted for eight yield-related traits to dissect the genetic architecture of additive, dominance, epistasis, and their environment interaction. Additionally, the optimal genotype combination and the breeding value of superior line, superior hybrid and existing best line in mapping population were predicted for each trait in two environments based on the predicted genotypic effects...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28265284/chromosomal-speciation-in-the-genomics-era-disentangling-phylogenetic-evolution-of-rock-wallabies
#11
Sally Potter, Jason G Bragg, Mozes P K Blom, Janine E Deakin, Mark Kirkpatrick, Mark D B Eldridge, Craig Moritz
The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28261264/ferrous-iron-up-regulation-in-fibroblasts-of-patients-with-beta-propeller-protein-associated-neurodegeneration-bpan
#12
Rosaria Ingrassia, Maurizio Memo, Barbara Garavaglia
Mutations in WDR45 gene, coding for a beta-propeller protein, have been found in patients affected by Neurodegeneration with Brain Iron Accumulation, NBIA5 (also known as BPAN). BPAN is a movement disorder with Non Transferrin Bound Iron (NTBI) accumulation in the basal ganglia as common hallmark between NBIA classes (Hayflick et al., 2013). WDR45 has been predicted to have a role in autophagy, while the impairment of iron metabolism in the different NBIA subclasses has not currently been clarified. We found the up-regulation of the ferrous iron transporter (-)IRE/Divalent Metal Transporter1 and down-regulation of Transferrin receptor in the fibroblasts of two BPAN affected patients with splicing mutations 235+1G>A (BPAN1) and 517_519ΔVal 173 (BPAN2)...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28261263/analytical-biases-associated-with-gc-content-in-molecular-evolution
#13
Jonathan Romiguier, Camille Roux
Molecular evolution is being revolutionized by high-throughput sequencing allowing an increased amount of genome-wide data available for multiple species. While base composition summarized by GC-content is one of the first metrics measured in genomes, its genomic distribution is a frequently neglected feature in downstream analyses based on DNA sequence comparisons. Here, we show how base composition heterogeneity among loci and taxa can bias common molecular evolution analyses such as phylogenetic tree reconstruction, detection of natural selection and estimation of codon usage...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28261262/the-evolutionary-relationship-between-alternative-splicing-and-gene-duplication
#14
REVIEW
Luis P Iñiguez, Georgina Hernández
The protein diversity that exists today has resulted from various evolutionary processes. It is well known that gene duplication (GD) along with the accumulation of mutations are responsible, among other factors, for an increase in the number of different proteins. The gene structure in eukaryotes requires the removal of non-coding sequences, introns, to produce mature mRNAs. This process, known as cis-splicing, referred to here as splicing, is regulated by several factors which can lead to numerous splicing arrangements, commonly designated as alternative splicing (AS)...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28261261/the-pancreatic-islet-regulome-browser
#15
Loris Mularoni, Mireia Ramos-Rodríguez, Lorenzo Pasquali
The pancreatic islet is a highly specialized tissue embedded in the exocrine pancreas whose primary function is that of controlling glucose homeostasis. Thus, understanding the transcriptional control of islet-cell may help to puzzle out the pathogenesis of glucose metabolism disorders. Integrative computational analyses of transcriptomic and epigenomic data allows predicting genomic coordinates of putative regulatory elements across the genome and, decipher tissue-specific functions of the non-coding genome...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28239390/using-landscape-genetics-simulations-for-planting-blister-rust-resistant-whitebark-pine-in-the-us-northern-rocky-mountains
#16
Erin L Landguth, Zachary A Holden, Mary F Mahalovich, Samuel A Cushman
Recent population declines to the high elevation western North America foundation species whitebark pine, have been driven by the synergistic effects of the invasive blister rust pathogen, mountain pine beetle (MPB), fire exclusion, and climate change. This has led to consideration for listing whitebark pine (WBP) as a threatened or endangered species under the Endangered Species Act, which has intensified interest in developing management strategies for maintaining and restoring the species. An important, but poorly studied, aspect of WBP restoration is the spatial variation in adaptive genetic variation and the potential of blister rust resistant strains to maintain viable populations in the future...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28224003/darwinism-for-the-genomic-age-connecting-mutation-to-diversification
#17
Xia Hua, Lindell Bromham
A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28210267/mir-30-family-potentially-targeting-pi3k-siah2-predicted-interaction-network-represents-a-novel-putative-theranostic-panel-in-non-small-cell-lung-cancer
#18
Lawrence W C Chan, Fengfeng Wang, Fei Meng, Lili Wang, Sze Chuen Cesar Wong, Joseph S K Au, Sijun Yang, William C S Cho
Non-small cell lung cancer (NSCLC) comprises about 84% of all lung cancers. Many treatment options are available but the survival rate is still very low due to drug resistance. It has been found that phosphoinositide-3-kinase (PI3K) affects sensitivity to tyrosine kinase inhibitors (TKIs), including gefitinib and erlotinib. Expression level of seven in absentia homolog 2 (SIAH2), an E3 ubiquitin-protein ligase, is upregulated in NSCLC and correlated with tumor grade. However, the relationship between PI3K and SIAH2 remains unclear and therefore it is not known whether they can act as treatment co-targets and theranostic dual markers for overcoming TKI resistance...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28197171/genome-wide-microrna-binding-site-variation-between-extinct-wild-aurochs-and-modern-cattle-identifies-candidate-microrna-regulated-domestication-genes
#19
Martin Braud, David A Magee, Stephen D E Park, Tad S Sonstegard, Sinead M Waters, David E MacHugh, Charles Spillane
The domestication of cattle from the now-extinct wild aurochs (Bos primigenius) involved selection for physiological and behavioral traits, with underlying genetic factors that remain largely unknown. Non-coding microRNAs have emerged as key regulators of the spatio-temporal expression of target genes controlling mammalian growth and development, including in livestock species. During the domestication process, selection of mutational changes in miRNAs and/or miRNA binding sites could have provided a mechanism to generate some of the traits that differentiate domesticated cattle from wild aurochs...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28194159/role-of-ucp1-gene-variants-in-interethnic-differences-in-the-development-of-cardio-metabolic-diseases
#20
Andreas D Flouris, Yulii V Shidlovskii, Alexander V Shaposhnikov, Levon Yepiskoposyan, Liliya Nadolnik, Lidia Karabon, Anna Kowalska, Andres E Carrillo, George S Metsios, Paraskevi Sakellariou
Cardio-metabolic diseases (CMDs) comprise a cluster of risk factors that contribute to chronic pathological conditions with adverse consequences for cardiovascular function and metabolic processes. A wide range of CMD prevalence rates among different ethnic groups has been documented. In view of accumulated evidence, there is a trend toward increasing CMD prevalence rates in Eastern Europe and Western Asia. Numerous studies have revealed an association between uncoupling protein 1 (UCP1) gene variants and CMDs...
2017: Frontiers in Genetics
journal
journal
43579
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"