Read by QxMD icon Read

Frontiers in Genetics

Hillary T Graham, Daniel M Rotroff, Skylar W Marvel, John B Buse, Tammy M Havener, Alyson G Wilson, Michael J Wagner, Alison A Motsinger-Reif
Given the high costs of conducting a drug-response trial, researchers are now aiming to use retrospective analyses to conduct genome-wide association studies (GWAS) to identify underlying genetic contributions to drug-response variation. To prevent confounding results from a GWAS to investigate drug response, it is necessary to account for concomitant medications, defined as any medication taken concurrently with the primary medication being investigated. We use data from the Action to Control Cardiovascular Disease (ACCORD) trial in order to implement a novel scoring procedure for incorporating concomitant medication information into a linear regression model in preparation for GWAS...
2016: Frontiers in Genetics
Aharon Nachshon, Hanifa J Abu-Toamih Atamni, Yael Steuerman, Roa'a Sheikh-Hamed, Alexandra Dorman, Richard Mott, Juliane C Dohm, Hans Lehrach, Marc Sultan, Ron Shamir, Sascha Sauer, Heinz Himmelbauer, Fuad A Iraqi, Irit Gat-Viks
A central challenge in pharmaceutical research is to investigate genetic variation in response to drugs. The Collaborative Cross (CC) mouse reference population is a promising model for pharmacogenomic studies because of its large amount of genetic variation, genetic reproducibility, and dense recombination sites. While the CC lines are phenotypically diverse, their genetic diversity in drug disposition processes, such as detoxification reactions, is still largely uncharacterized. Here we systematically measured RNA-sequencing expression profiles from livers of 29 CC lines under baseline conditions...
2016: Frontiers in Genetics
Jinpeng Wang, Jiaxiang Yu, Pengchuan Sun, Yuxian Li, Ruiyan Xia, Yinzhe Liu, Xuelian Ma, Jigao Yu, Nanshan Yang, Tianyu Lei, Zhenyi Wang, Li Wang, Weina Ge, Xiaoming Song, Xiaojian Liu, Sangrong Sun, Tao Liu, Dianchuan Jin, Yuxin Pan, Xiyin Wang
Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ∼100 million years ago. There has been a standing controversy whether there had been five or seven basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses...
2016: Frontiers in Genetics
Nirupama Yalamanchili, Andres Kriete, David Alfego, Kelli M Danowski, Csaba Kari, Ulrich Rodeck
Quiescence is the prevailing state of many cell types under homeostatic conditions. Yet, surprisingly little is known about how quiescent cells respond to energetic and metabolic challenges. To better understand compensatory responses of quiescent cells to metabolic stress, we established, in human primary dermal fibroblasts, an experimental 'energy restriction' model. Quiescence was achieved by short-term culture in serum-deprived media and ATP supply restricted using a combination of glucose transport inhibitors and mitochondrial uncouplers...
2016: Frontiers in Genetics
Zhu Chen, Danmei Chen, Wenyuan Chu, Dongyue Zhu, Hanwei Yan, Yan Xiang
Whole-genome duplication events have occurred more than once in the genomes of some rosids and played a significant role over evolutionary time. Lipoxygenases (LOXs) are involved in many developmental and resistance processes in plants. Our study concerns the subject of the LOX gene family; we tracked the evolutionary process of ancestral LOX genes in four modern rosids. Here we show that some members of the LOX gene family in the Arabidopsis genome are likely to be lost during evolution, leading to a smaller size than that in Populus, Vitis, and Carica...
2016: Frontiers in Genetics
Shivani Sharma, Praveen K Patnaik, Stella Aronov, Ritu Kulshreshtha
Apoptosis, a form of programmed cell death, is a highly regulated process, the deregulation of which has been associated with the tumor initiation, progression, and metastasis in various cancers including breast cancer. Induction of apoptosis is a popular target of various therapies currently being tested or used for breast cancer treatment. Thus, identifying apoptotic mediators and regulators is imperative for molecular biologists and clinicians for benefit of patients. The regulation of apoptosis is complex and involves a tight equilibrium between the pro- and anti-apoptotic factors...
2016: Frontiers in Genetics
Felix L Struebing, Richard K Lee, Robert W Williams, Eldon E Geisert
Retinal ganglion cells (RGCs) are the output neuron of the eye, transmitting visual information from the retina through the optic nerve to the brain. The importance of RGCs for vision is demonstrated in blinding diseases where RGCs are lost, such as in glaucoma or after optic nerve injury. In the present study, we hypothesize that normal RGC function is transcriptionally regulated. To test our hypothesis, we examine large retinal expression microarray datasets from recombinant inbred mouse strains in GeneNetwork and define transcriptional networks of RGCs and their subtypes...
2016: Frontiers in Genetics
Pamela Dakik, Vladimir I Titorenko
Studies employing the budding yeast Saccharomyces cerevisiae as a model organism have provided deep insights into molecular mechanisms of cellular and organismal aging in multicellular eukaryotes and have demonstrated that the main features of biological aging are evolutionarily conserved. Aging in S. cerevisiae is studied by measuring replicative or chronological lifespan. Yeast replicative aging is likely to model aging of mitotically competent human cell types, while yeast chronological aging is believed to mimic aging of post-mitotic human cell types...
2016: Frontiers in Genetics
(no author information available yet)
[This corrects the article on p. 105 in vol. 7, PMID: 27379156.].
2016: Frontiers in Genetics
Edward A Ruiz-Narváez, Lara Sucheston-Campbell, Jeannette T Bensen, Song Yao, Stephen Haddad, Christopher A Haiman, Elisa V Bandera, Esther M John, Leslie Bernstein, Jennifer J Hu, Regina G Ziegler, Sandra L Deming, Andrew F Olshan, Christine B Ambrosone, Julie R Palmer, Kathryn L Lunetta
Recent genetic admixture coupled with striking differences in incidence of estrogen receptor (ER) breast cancer subtypes, as well as severity, between women of African and European ancestry, provides an excellent rationale for performing admixture mapping in African American women with breast cancer risk. We performed the largest breast cancer admixture mapping study with in African American women to identify novel genomic regions associated with the disease. We conducted a genome-wide admixture scan using 2,624 autosomal ancestry informative markers (AIMs) in 3,629 breast cancer cases (including 1,968 ER-positive, 1093 ER-negative, and 601 triple-negative) and 4,658 controls from the African American Breast Cancer Epidemiology and Risk (AMBER) Consortium, a collaborative study of four large geographically different epidemiological studies of breast cancer in African American women...
2016: Frontiers in Genetics
Fengfeng Wang, Fei Meng, Lili Wang
MicroRNAs (miRNAs) are post-transcriptional regulators that regulate gene expression by binding to the 3' untranslated region of target mRNAs. Mature miRNAs transcribed from the miR-17-92 cluster have an oncogenic activity, which are overexpressed in chronic-phase chronic myelogenous leukemia (CML) patients compared with normal individuals. Besides, the tyrosine kinase activity of BCR-ABL oncoprotein from the Philadelphia chromosome in CML can affect this miRNA cluster. Genes with similar mRNA expression profiles are likely to be regulated by the same regulators...
2016: Frontiers in Genetics
Hannes Löwe, Andreas Kremling, Alberto Marin-Sanguino
The time-scale hierarchies of a very general class of models in differential equations is analyzed. Classical methods for model reduction and time-scale analysis have been adapted to this formalism and a complementary method is proposed. A unified theoretical treatment shows how the structure of the system can be much better understood by inspection of two sets of singular values: one related to the stoichiometric structure of the system and another to its kinetics. The methods are exemplified first through a toy model, then a large synthetic network and finally with numeric simulations of three classical benchmark models of real biological systems...
2016: Frontiers in Genetics
Olivier B Poirion, Xun Zhu, Travers Ching, Lana Garmire
The emerging single-cell RNA-Seq (scRNA-Seq) technology holds the promise to revolutionize our understanding of diseases and associated biological processes at an unprecedented resolution. It opens the door to reveal intercellular heterogeneity and has been employed to a variety of applications, ranging from characterizing cancer cells subpopulations to elucidating tumor resistance mechanisms. Parallel to improving experimental protocols to deal with technological issues, deriving new analytical methods to interpret the complexity in scRNA-Seq data is just as challenging...
2016: Frontiers in Genetics
Otto K-W Cheung, Alfred S-L Cheng
Liver cancer is the third most common cancer type and the second leading cause of deaths in men. Large population studies have demonstrated remarkable gender disparities in the incidence and the cumulative risk of liver cancer. A number of emerging risk factors regarding metabolic alterations associated with obesity, diabetes and dyslipidemia have been ascribed to the progression of non-alcoholic fatty liver diseases (NAFLD) and ultimately liver cancer. The deregulation of fat metabolism derived from excessive insulin, glucose, and lipid promotes cancer-causing inflammatory signaling and oxidative stress, which eventually triggers the uncontrolled hepatocellular proliferation...
2016: Frontiers in Genetics
Elie Maza
In the past 5 years, RNA-Seq has become a powerful tool in transcriptome analysis even though computational methods dedicated to the analysis of high-throughput sequencing data are yet to be standardized. It is, however, now commonly accepted that the choice of a normalization procedure is an important step in such a process, for example in differential gene expression analysis. The present article highlights the similarities between three normalization methods: TMM from edgeR R package, RLE from DESeq2 R package, and MRN...
2016: Frontiers in Genetics
Eirini Lionaki, Ilias Gkikas, Nektarios Tavernarakis
The coordination of nuclear and mitochondrial genomes plays a pivotal role in maintenance of mitochondrial biogenesis and functionality during stress and aging. Environmental and cellular inputs signal to nucleus and/or mitochondria to trigger interorganellar compensatory responses. Loss of this tightly orchestrated coordination results in loss of cellular homeostasis and underlies various pathologies and age-related diseases. Several signaling cascades that govern interorganellar communication have been revealed up to now, and have been classified as part of the anterograde (nucleus to mitochondria) or retrograde (mitochondrial to nucleus) response...
2016: Frontiers in Genetics
Hoang T Nguyen, James Boocock, Tony R Merriman, Michael A Black
Copy-number variation (CNV) has been associated with increased risk of complex diseases. High-throughput sequencing (HTS) technologies facilitate the detection of copy-number variable regions (CNVRs) and their breakpoints. This helps in understanding genome structure as well as their evolution process. Various approaches have been proposed for detecting CNV breakpoints, but currently it is still challenging for tools based on a single analysis method to identify breakpoints of CNVs. It has been shown, however, that pipelines which integrate multiple approaches are able to report more reliable breakpoints...
2016: Frontiers in Genetics
Piet Kramer, Alexander T Jung, Andrea Hamann, Heinz D Osiewacz
The mitochondrial permeability transition pore plays a key role in programmed cell death and the induction of autophagy. Opening of the pore is regulated by the mitochondrial peptidyl prolyl-cis, trans-isomerase cyclophilin D (CYPD). Previously it was shown in the aging model organism Podospora anserina that PaCYPD abundance increases during aging and that PaCypD overexpressors are characterized by accelerated aging. Here, we describe a role of PaCYPD in the regulation of autophagy. We found that the accelerated aging phenotype observed in a strain overexpressing PaCypD is not metacaspase-dependent but is accompanied by an increase of general autophagy and mitophagy, the selective autophagic degradation of mitochondria...
2016: Frontiers in Genetics
Siegfried Hekimi, Ying Wang, Alycia Noë
It has become clear that mitochondrial reactive oxygen species (mtROS) are not simply villains and mitochondria the hapless targets of their attacks. Rather, it appears that mitochondrial dysfunction itself and the signaling function of mtROS can have positive effects on lifespan, helping to extend longevity. If events in the mitochondria can lead to better cellular homeostasis and better survival of the organism in ways beyond providing ATP and biosynthetic products, we can conjecture that they act on other cellular components through appropriate signaling pathways...
2016: Frontiers in Genetics
Muhammad S Iqbal, Muhammad N Hafeez, Javed I Wattoo, Arfan Ali, Muhammad N Sharif, Bushra Rashid, Bushra Tabassum, Idrees A Nasir
Potato virus Y has emerged as a threatening problem in all potato growing areas around the globe. PVY reduces the yield and quality of potato cultivars. During the last 30 years, significant genetic changes in PVY strains have been observed with an increased incidence associated with crop damage. In the current study, computational approaches were applied to predict Potato derived miRNA targets in the PVY genome. The PVY genome is approximately 9 thousand nucleotides, which transcribes the following 6 genes:CI, NIa, NIb-Pro, HC-Pro, CP, and VPg...
2016: Frontiers in Genetics
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"