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Frontiers in Genetics

Corinne Sidler, Olga Kovalchuk, Igor Kovalchuk
Aging is characterized by functional decline of diverse organs and an increased risk for several diseases. Therefore, a high interest exists in understanding the molecular mechanisms that stimulate aging at all levels, from cells and tissues to organs and organisms, in order to develop ways to promote healthy aging. While many molecular and biochemical mechanisms are already understood in some detail, the role of changes in epigenetic regulation has only begun to be considered in recent years. The age-dependent global reduction in heterochromatin, along with site-specific changes in the patterns of DNA methylation and modification of histones, have been observed in several aging model systems...
2017: Frontiers in Genetics
Gustavo Glusman, Denise E Mauldin, Leroy E Hood, Max Robinson
We present an ultrafast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into "genome fingerprints" via locality sensitive hashing. The resulting genome fingerprints can be meaningfully compared even when the input data were obtained using different sequencing technologies, processed using different pipelines, represented in different data formats and relative to different reference versions. Furthermore, genome fingerprints are robust to up to 30% missing data...
2017: Frontiers in Genetics
Ignacio Macpherson, Ignacio Segarra
No abstract text is available yet for this article.
2017: Frontiers in Genetics
Maha Zaki, Michaela Thoenes, Amit Kawalia, Peter Nürnberg, Rolf Kaiser, Raoul Heller, Hanno J Bolz
In an Egyptian girl born to consanguineous parents, whole-exome sequencing (WES) identified a homozygous mutation in PHGDH, c.1273G>A (p.Val425Met), indicating 3-phosphoglycerate dehydrogenase deficiency. This diagnosis was compatible with the patient's microcephaly, severe psychomotor retardation, seizures and cataracts. However, she additionally suffered from recurrent (at least monthly) episodes of prolonged and severe chest infections requiring hospitalization, suggesting a secondary, predisposing and potentially Mendelian, condition...
2017: Frontiers in Genetics
Abdul H Kandhro, Watshara Shoombuatong, Chanin Nantasenamat, Virapong Prachayasittikul, Pornlada Nuchnoi
Background: Dyslipidemia is one of the major forms of lipid disorder, characterized by increased triglycerides (TGs), increased low-density lipoprotein-cholesterol (LDL-C), and decreased high-density lipoprotein-cholesterol (HDL-C) levels in blood. Recently, MicroRNAs (miRNAs) have been reported to involve in various biological processes; their potential usage being a biomarkers and in diagnosis of various diseases. Computational approaches including text mining have been used recently to analyze abstracts from the public databases to observe the relationships/associations between the biological molecules, miRNAs, and disease phenotypes...
2017: Frontiers in Genetics
Pedro L P Xavier, José A Senhorini, Matheus Pereira-Santos, Takafumi Fujimoto, Eduardo Shimoda, Luciano A Silva, Silvio A Dos Santos, George S Yasui
The production of triploid yellowtail tetra Astyanax altiparanae is a key factor to obtain permanently sterile individuals by chromosome set manipulation. Flow cytometric analysis is the main tool for confirmation of the resultant triploids individuals, but very few protocols are specific for A. altiparanae species. The current study has developed a protocol to estimate DNA content in this species. Furthermore, a protocol for long-term storage of dorsal fins used for flow cytometry analysis was established...
2017: Frontiers in Genetics
Ettore Mosca, Matteo Bersanelli, Matteo Gnocchi, Marco Moscatelli, Gastone Castellani, Luciano Milanesi, Alessandra Mezzelani
Autism spectrum disorder (ASD) is marked by a strong genetic heterogeneity, which is underlined by the low overlap between ASD risk gene lists proposed in different studies. In this context, molecular networks can be used to analyze the results of several genome-wide studies in order to underline those network regions harboring genetic variations associated with ASD, the so-called "disease modules." In this work, we used a recent network diffusion-based approach to jointly analyze multiple ASD risk gene lists...
2017: Frontiers in Genetics
Jason P Chan, Jaylene Brown, Brandon Hark, Abby Nolan, Dustin Servello, Hannah Hrobuchak, Trisha A Staab
Sphingolipid metabolism is important to balance the abundance of bioactive lipid molecules involved in cell signaling, neuronal function, and survival. Specifically, the sphingolipid sphingosine mediates cell death signaling, whereas its phosphorylated form, sphingosine-1-phosphate (S1P), mediates cell survival signaling. The enzyme sphingosine kinase produces S1P, and the activity of sphingosine kinase impacts the ability of cells to survive under stress and challenges. To examine the influence of sphingolipid metabolism, particularly enzymes regulating sphingosine and S1P, in mediating aging, neuronal function and stress response, we examined life history traits, locomotor capacities and heat stress responses of young and old animals using the model organism Caenorhabditis elegans...
2017: Frontiers in Genetics
Gratien Dalpé, Ida Ngueng Feze, Shahad Salman, Yann Joly, Julie Hagan, Emmanuelle Lévesque, Véronique Dorval, Jolyane Blouin-Bougie, Nabil Amara, Michel Dorval, Jacques Simard
Genetic stratification approaches in personalized medicine may considerably improve our ability to predict breast cancer risk for women at higher risk of developing breast cancer. Notwithstanding these advantages, concerns have been raised about the use of the genetic information derived in these processes, outside of the research and medical health care settings, by third parties such as insurers. Indeed, insurance applicants are asked to consent to insurers accessing their medical information (implicitly including genetic) to verify or determine their insurability level, or eligibility to certain insurance products...
2017: Frontiers in Genetics
Khyobeni Mozhui, Beverly M Snively, Stephen R Rapp, Robert B Wallace, Robert W Williams, Karen C Johnson
Genes encoding mitochondrial ribosomal proteins (MRPs) have been linked to aging and longevity in model organisms (i.e., mice, Caenorhabditis elegans). Here we evaluated if the MRPs have conserved effects on aging traits in humans. We utilized data from 4,504 participants of the Women's Health Initiative Memory Study (WHIMS) who had both longitudinal cognitive data and genetic data. Two aging phenotypes were considered: (1) gross lifespan (time to all-cause mortality), and (2) cognitive aging (longitudinal rate of change in modified mini-mental state scores)...
2017: Frontiers in Genetics
Milena Ferreira, Caroline Garcia, Daniele A Matoso, Isac S de Jesus, Marcelo de B Cioffi, Luiz A C Bertollo, Jansen Zuanon, Eliana Feldberg
Bunocephalus is the most species-rich Aspredinidae genus, corresponding to a monophyletic clade with 13 valid species. However, many species have their classification put in question. Here, we analyzed individuals from four Amazonian populations of Bunocephalus coracoideus by cytogenetic and molecular procedures. The geographic distribution, genetic distances and karyotype data indicate that each population represents an Evolutionary Significant Unit (ESU). Cytogenetic markers showed distinct 2n and karyotype formulas, as well as different numbers and locations of the rDNA sites among ESUs...
2017: Frontiers in Genetics
Glenn J Bryan, Karen McLean, Robbie Waugh, David M Spooner
DNA-based marker analysis of plant genebank material has become a useful tool in the evaluation of levels of genetic diversity and for the informed use and maintenance of germplasm. In this study, we quantify levels of amplified fragment length polymorphism (AFLP) in representative accessions of wild and cultivated potato species of differing geographic origin, ploidy, and breeding system. We generated 449 polymorphic AFLP fragments in 619 plants, representing multiple plants (16-23) from 17 accessions of 14 potato taxa as well as single plants sampled from available accessions (from 3 to 56) of the same 14 taxa...
2017: Frontiers in Genetics
Omolara-Chinue Glenn, Lidia Tagliafierro, Thomas G Beach, Randy L Woltjer, Ornit Chiba-Falek
The SNCA intronic single nucleotide polymorphism (SNP), rs356168, has been associated with Parkinson's disease (PD) in large genome wide association studies (GWAS). Recently, the PD-risk allele, rs356168-G was shown to increase SNCA-mRNA expression using genome edited human induced pluripotent stem cells (iPSC)-derived neurons. In this study, as means of validation, we tested the effect of rs356168 on total SNCA-mRNA levels using brain tissues, temporal and frontal cortex, from healthy control donors. Carriers of the rs356168-G allele demonstrated a borderline significant decrease of SNCA-mRNA levels in temporal brain tissues (p = 0...
2017: Frontiers in Genetics
Savio T de Farias, Ariosvaldo P Dos Santos Junior, Thais G Rêgo, Marco V José
RNA-dependent RNA polymerases (RdRp) are very ancient enzymes and are essential for all viruses with RNA genomes. We reconstruct the origin and evolution of this polymerase since the initial stages of the origin of life. The origin of the RdRp was traced back from tRNA ancestors. At the origin of the RdRp the most ancient part of the protein is the cofactor-binding site that had the capacity of binding to simple molecules as magnesium, calcium, and ribonucleotides. Our results suggest that RdRp originated from junctions of proto-tRNAs that worked as the first genes at the emergence of the primitive translation system, where the RNA was the informational molecule...
2017: Frontiers in Genetics
Elena V Savvateeva-Popova, Aleksandr V Zhuravlev, Václav Brázda, Gennady A Zakharov, Alena N Kaminskaya, Anna V Medvedeva, Ekaterina A Nikitina, Elena V Tokmatcheva, Julia F Dolgaya, Dina A Kulikova, Olga G Zatsepina, Sergei Y Funikov, Sergei S Ryazansky, Michail B Evgen'ev
Genomic disorders, the syndromes with multiple manifestations, may occur sporadically due to unequal recombination in chromosomal regions with specific architecture. Therefore, each patient may carry an individual structural variant of DNA sequence (SV) with small insertions and deletions (INDELs) sometimes less than 10 bp. The transposable elements of the Tc1/mariner superfamily are often associated with hotspots for homologous recombination involved in human genetic disorders, such as Williams Beuren Syndromes (WBS) with LIM-kinase 1-dependent cognitive defects...
2017: Frontiers in Genetics
Christian Ineichen, Nikola Biller-Andorno, Anna Deplazes-Zemp
This study explores the image of synthetic biology and nanotechnology in comparison to agricultural biotechnology and communication technology by examining spontaneous associations with, and deliberate evaluations of, these technologies by university students. Data were collected through a self-completion online questionnaire by students from two universities in Switzerland. The survey aimed to capture implicit associations, explicit harm-benefit evaluations and views on regulation. The data suggest overall positive associations with emerging technologies...
2017: Frontiers in Genetics
David G Mahal, Ianis G Matsoukas
The Jats represent a large ethnic community that has inhabited the northwest region of India and Pakistan for several thousand years. It is estimated the community has a population of over 123 million people. Many historians and academics have asserted that the Jats are descendants of Aryans, Scythians, or other ancient people that arrived and lived in northern India at one time. Essentially, the specific origin of these people has remained a matter of contention for a long time. This study demonstrated that the origins of Jats can be clarified by identifying their Y-chromosome haplogroups and tracing their genetic markers on the Y-DNA haplogroup tree...
2017: Frontiers in Genetics
Kelsey E Grinde, Jaron Arbet, Alden Green, Michael O'Connell, Alessandra Valcarcel, Jason Westra, Nathan Tintle
To date, gene-based rare variant testing approaches have focused on aggregating information across sets of variants to maximize statistical power in identifying genes showing significant association with diseases. Beyond identifying genes that are associated with diseases, the identification of causal variant(s) in those genes and estimation of their effect is crucial for planning replication studies and characterizing the genetic architecture of the locus. However, we illustrate that straightforward single-marker association statistics can suffer from substantial bias introduced by conditioning on gene-based test significance, due to the phenomenon often referred to as "winner's curse...
2017: Frontiers in Genetics
Changming Lu, Mary MacDougall
Singleton-Merten syndrome (SMS) is an autosomal dominant, multi-system innate immune disorder characterized by early and severe aortic and valvular calcification, dental and skeletal abnormalities, psoriasis, glaucoma, and other varying clinical findings. Recently we identified a specific gain-of-function mutation in IFIH1, interferon induced with helicase C domain 1, segregated with this disease. SMS disease without hallmark dental anomalies, termed atypical SMS, has recently been reported caused by variants in DDX58, DEXD/H-box helicase 58...
2017: Frontiers in Genetics
Lee F Greer
No abstract text is available yet for this article.
2017: Frontiers in Genetics
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