Genetic pastures.
PMID: 23482329 [PubMed - in process] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - April 1, 2013 Category: Genetics & Stem Cells Authors: Macrae R Tags: Trends Genet Source Type: research

Molecular advances in QTL discovery and application in pig breeding.
Abstract Thousands of quantitative trait loci (QTL) have been identified for a wide range of economically important phenotypes in pigs. Recently, QTL analyses have begun to use high-density single nucleotide polymorphism (SNP) panels and applications have extended beyond experimental intercrosses to outbred populations by exploiting long-range linkage disequilibrium that results in higher resolution QTL mapping. Relevant phenotypes generally fall under categories of growth and body composition, carcass and meat quality, reproduction, and disease resistance. A few expression QTL (eQTL) studies have been performed t...
Source: Trends in Genetics : TIG - April 1, 2013 Category: Genetics & Stem Cells Authors: Ernst CW, Steibel JP Tags: Trends Genet Source Type: research

WEE1 tyrosine kinase, a novel epigenetic modifier.
Abstract The cell cycle requires cells to duplicate their chromatin, DNA, and histones, while retaining a subset of epigenetic marks, in a highly coordinated manner. The WEE1 kinase was identified as an important regulator during S phase, preventing entry into mitosis until DNA replication has been completed. Interestingly, WEE1 has also emerged as a key player in regulating histone synthesis. It phosphorylates histone H2B at tyrosine 37 in the nucleosomes found upstream of the histone gene cluster, and this suppresses histone transcription in late S phase. These observations highlight a dual role for WEE1 as both...
Source: Trends in Genetics : TIG - March 25, 2013 Category: Genetics & Stem Cells Authors: Mahajan K, Mahajan NP Tags: Trends Genet Source Type: research

Does your gene need a background check? How genetic background impacts the analysis of mutations, genes, and evolution.
Abstract The premise of genetic analysis is that a causal link exists between phenotypic and allelic variation. However, it has long been documented that mutant phenotypes are not a simple result of a single DNA lesion, but are instead due to interactions of the focal allele with other genes and the environment. Although an experimentally rigorous approach focused on individual mutations and isogenic control strains has facilitated amazing progress within genetics and related fields, a glimpse back suggests that a vast complexity has been omitted from our current understanding of allelic effects. Armed with tradit...
Source: Trends in Genetics : TIG - February 28, 2013 Category: Genetics & Stem Cells Authors: Chandler CH, Chari S, Dworkin I Tags: Trends Genet Source Type: research

Evolving approaches to the ethical management of genomic data.
Abstract The ethical landscape in the field of genomics is rapidly shifting. Plummeting sequencing costs, along with ongoing advances in bioinformatics, now make it possible to generate an enormous volume of genomic data about vast numbers of people. The informational richness, complexity, and frequently uncertain meaning of these data, coupled with evolving norms surrounding the sharing of data and samples and persistent privacy concerns, have generated a range of approaches to the ethical management of genomic information. As calls increase for the expanded use of broad or even open consent, and as controversy g...
Source: Trends in Genetics : TIG - February 27, 2013 Category: Genetics & Stem Cells Authors: McEwen JE, Boyer JT, Sun KY Tags: Trends Genet Source Type: research

Genetic basis of cell-cell fusion mechanisms.
Abstract Cell-cell fusion in sexually reproducing organisms is a mechanism to merge gamete genomes and, in multicellular organisms, it is a strategy to sculpt organs, such as muscle, bone, and placenta. Moreover, this mechanism has been implicated in pathological conditions, such as infection and cancer. Studies of genetic model organisms have uncovered a unifying principle: cell fusion is a genetically programmed process. This process can be divided in three stages: competence (cell induction and differentiation); commitment (cell determination, migration, and adhesion); and cell fusion (membrane merging and cyto...
Source: Trends in Genetics : TIG - February 27, 2013 Category: Genetics & Stem Cells Authors: Aguilar PS, Baylies MK, Fleissner A, Helming L, Inoue N, Podbilewicz B, Wang H, Wong M Tags: Trends Genet Source Type: research

The origin of the tetrapod limb: from expeditions to enhancers.
Abstract More than three centuries ago natural philosophers, and later anatomists, recognized a fundamental organization to the skeleton of tetrapod limbs. Composed of three segments, stylopod, zeugopod, and autopod, this pattern has served as the basis for a remarkably broad adaptive radiation from wings and flippers to hands and digging organs. A central area of inquiry has been tracing the origins of the elements of this Bauplan in the fins of diverse fish. Can equivalents of the three segments, and the developmental processes that pattern them, be seen in fish fins? In addition, if so, how do these data inform...
Source: Trends in Genetics : TIG - February 20, 2013 Category: Genetics & Stem Cells Authors: Schneider I, Shubin NH Tags: Trends Genet Source Type: research

Worms under stress: C. elegans stress response and its relevance to complex human disease and aging.
Abstract Many organisms have stress response pathways, components of which share homology with players in complex human disease pathways. Research on stress response in the nematode worm Caenorhabditis elegans has provided detailed insights into the genetic and molecular mechanisms underlying complex human diseases. In this review we focus on four different types of environmental stress responses - heat shock, oxidative stress, hypoxia, and osmotic stress - and on how these can be used to study the genetics of complex human diseases. All four types of responses involve the genetic machineries that underlie a numbe...
Source: Trends in Genetics : TIG - February 18, 2013 Category: Genetics & Stem Cells Authors: Rodriguez M, Snoek LB, De Bono M, Kammenga JE Tags: Trends Genet Source Type: research

Improving fruit and wine: what does genomics have to offer?
Abstract Will we still be drinking wines made from Pinot Noir and eating McIntosh apples in the 23rd century? Elite grape and apple cultivars, vegetatively propagated for centuries, are highly susceptible to evolving pathogens. In response, growers continually expand their agrochemical weaponry at enormous environmental costs. By contrast, breeders are seeking disease-resistant, tastier alternatives to the handful of dominant cultivars by exploring genetic diversity in these fruits. However, this is a formidable task because consumers cling to ancient cultivars, and breeding long-lived woody perennials is laboriou...
Source: Trends in Genetics : TIG - February 18, 2013 Category: Genetics & Stem Cells Authors: Myles S Tags: Trends Genet Source Type: research

Amish revisited: next-generation sequencing studies of psychiatric disorders among the Plain people.
Abstract The rapid development of next-generation sequencing (NGS) technology has led to renewed interest in the potential contribution of rarer forms of genetic variation to complex non-mendelian phenotypes such as psychiatric illnesses. Although challenging, family-based studies offer some advantages, especially in communities with large families and a limited number of founders. Here we revisit family-based studies of mental illnesses in traditional Amish and Mennonite communities - known collectively as the Plain people. We discuss the new opportunities for NGS in these populations, with particular emphasis on...
Source: Trends in Genetics : TIG - February 16, 2013 Category: Genetics & Stem Cells Authors: Hou L, Faraci G, Chen DT, Kassem L, Schulze TG, Shugart YY, McMahon FJ Tags: Trends Genet Source Type: research

Rethinking our intellectual origins: response to Kalinka et al.
PMID: 23422050 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - February 16, 2013 Category: Genetics & Stem Cells Authors: Crabtree GR Tags: Trends Genet Source Type: research

Our robust intellect.
PMID: 23419455 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - February 15, 2013 Category: Genetics & Stem Cells Authors: Kalinka AT, Kelava I, Lewitus E Tags: Trends Genet Source Type: research

A population genetics view of animal domestication.
Abstract The fundamental shift associated with the domestication of plants and animals allowed for a dramatic increase in human population sizes and the emergence of modern society. Despite its importance and the decades of research devoted to studying it, questions regarding the origins and processes of domestication remain. Here, we review recent theoretical advances and present a perspective that underscores the crucial role that population admixture has played in influencing the genomes of domestic animals over the past 10000 years. We then discuss novel approaches to generating and analysing genetic data, emp...
Source: Trends in Genetics : TIG - February 14, 2013 Category: Genetics & Stem Cells Authors: Larson G, Burger J Tags: Trends Genet Source Type: research

RNA-binding proteins in Mendelian disease.
Abstract RNA-binding proteins (RBPs) control all aspects of RNA fate, and defects in their function underlie a broad spectrum of human pathologies. We focus here on two recent studies that uncovered the in vivo mRNA interactomes of human cells, jointly implicating over 1100 proteins in RNA binding. Surprisingly, over 350 of these RBPs had no prior RNA binding-related annotation or domain homology. The datasets also contain many proteins that, when mutated, cause Mendelian diseases, prominently neurological, sensory, and muscular disorders and cancers. Disease mutations in these proteins occur throughout their doma...
Source: Trends in Genetics : TIG - February 14, 2013 Category: Genetics & Stem Cells Authors: Castello A, Fischer B, Hentze MW, Preiss T Tags: Trends Genet Source Type: research

Bridging the transgenerational gap with epigenetic memory.
Abstract It is textbook knowledge that inheritance of traits is governed by genetics, and that the epigenetic modifications an organism acquires are largely reset between generations. Recently, however, transgenerational epigenetic inheritance has emerged as a rapidly growing field, providing evidence suggesting that some epigenetic changes result in persistent phenotypes across generations. Here, we survey some of the most recent examples of transgenerational epigenetic inheritance in animals, ranging from Caenorhabditis elegans to humans, and describe approaches and limitations to studying this phenomenon. We al...
Source: Trends in Genetics : TIG - February 11, 2013 Category: Genetics & Stem Cells Authors: Lim JP, Brunet A Tags: Trends Genet Source Type: research

Saccharomyces diversity and evolution: a budding model genus.
Abstract Saccharomyces cerevisiae is one of the best-understood and most powerful genetic model systems. Several disciplines are now converging to turn Saccharomyces into an exciting model genus for evolutionary genetics and genomics. Yeast taxonomists and ecologists have dramatically expanded and clarified Saccharomyces diversity, more than doubling the number of bona fide species since 2000. High-quality genome sequences are available (or soon will be) for all seven known species. Haploid laboratory strains are enabling a deep integration of classic genetic approaches with modern genomic tools. Population genomi...
Source: Trends in Genetics : TIG - February 7, 2013 Category: Genetics & Stem Cells Authors: Hittinger CT Tags: Trends Genet Source Type: research

Creating gradients by morphogen shuttling.
Abstract Morphogen gradients are used to pattern a field of cells according to variations in the concentration of a signaling molecule. Typically, the morphogen emanates from a confined group of cells. During early embryogenesis, however, the ability to define a restricted source for morphogen production is limited. Thus, various early patterning systems rely on a broadly expressed morphogen that generates an activation gradient within its expression domain. Computational and experimental work has shed light on how a sharp and robust gradient can be established under those situations, leading to a mechanism termed...
Source: Trends in Genetics : TIG - January 28, 2013 Category: Genetics & Stem Cells Authors: Shilo BZ, Haskel-Ittah M, Ben-Zvi D, Schejter ED, Barkai N Tags: Trends Genet Source Type: research

Genetic determinants of voluntary exercise.
Abstract Variation in voluntary exercise behavior is an important determinant of long-term human health. Increased physical activity is used as a preventative measure or therapeutic intervention for disease, and a sedentary lifestyle has generally been viewed as unhealthy. Predisposition to engage in voluntary activity is heritable and induces protective metabolic changes, but its complex genetic/genomic architecture has only recently begun to emerge. We first present a brief historical perspective and summary of the known benefits of voluntary exercise. Second, we describe human and mouse model studies using geno...
Source: Trends in Genetics : TIG - January 22, 2013 Category: Genetics & Stem Cells Authors: Kelly SA, Pomp D Tags: Trends Genet Source Type: research

Synthetic lethality and cancer: cohesin and PARP at the replication fork.
Abstract Cohesins are mutated in a significant number of tumors of various types making them attractive targets for chemotherapeutic intervention. However, cohesins have a spectrum of cellular roles including sister chromatid cohesion, transcription, replication, and repair. Which of these roles are central to cancer biology and which roles can be exploited for therapeutic intervention? Genetic interaction networks in yeast have identified synthetic lethal interactions between mutations in cohesin and replication fork mediators. These interactions are conserved in worms and in human cells suggesting that inhibitio...
Source: Trends in Genetics : TIG - January 17, 2013 Category: Genetics & Stem Cells Authors: O'Neil NJ, van Pel DM, Hieter P Tags: Trends Genet Source Type: research

Horizontal gene transfer and the evolution of bacterial and archaeal population structure.
Abstract Many bacterial and archaeal lineages have a history of extensive and ongoing horizontal gene transfer and loss, as evidenced by the large differences in genome content even among otherwise closely related isolates. How ecologically cohesive populations might evolve and be maintained under such conditions of rapid gene turnover has remained controversial. Here we synthesize recent literature demonstrating the importance of habitat and niche in structuring horizontal gene transfer. This leads to a model of ecological speciation via gradual genetic isolation triggered by differential habitat-association of n...
Source: Trends in Genetics : TIG - January 15, 2013 Category: Genetics & Stem Cells Authors: Polz MF, Alm EJ, Hanage WP Tags: Trends Genet Source Type: research

Genetic challenges of flavor improvement in tomato.
Abstract In many instances, the intensive breeding of crops over the past half century with a focus on yield has indirectly led to reductions in flavor and nutrient content. Largely, this deterioration of quality relates directly to the genetic and biochemical complexity of such traits. Here, we describe challenges associated with quality improvement, emphasizing tomato fruit flavor. Flavor improvement is particularly problematic because of the difficulty of assessing the phenotype as well as a lack of fundamental knowledge about the chemicals driving consumer preferences, the pathways for their synthesis, and the...
Source: Trends in Genetics : TIG - January 14, 2013 Category: Genetics & Stem Cells Authors: Klee HJ, Tieman DM Tags: Trends Genet Source Type: research

Our fragile intellect: response to Dr Mitchell.
PMID: 23312928 [PubMed - as supplied by publisher] (Source: Trends in Genetics : TIG)
Source: Trends in Genetics : TIG - January 10, 2013 Category: Genetics & Stem Cells Authors: Crabtree G Tags: Trends Genet Source Type: research

Mobile element biology: new possibilities with high-throughput sequencing.
Abstract Mobile elements comprise more than half of the human genome, but until recently their large-scale detection was time consuming and challenging. With the development of new high-throughput sequencing (HTS) technologies, the complete spectrum of mobile element variation in humans can now be identified and analyzed. Thousands of new mobile element insertions (MEIs) have been discovered, yielding new insights into mobile element biology, evolution, and genomic variation. Here, we review several high-throughput methods, with an emphasis on techniques that specifically target MEIs in humans. We highlight recent...
Source: Trends in Genetics : TIG - January 9, 2013 Category: Genetics & Stem Cells Authors: Xing J, Witherspoon DJ, Jorde LB Tags: Trends Genet Source Type: research

Resequencing rice genomes: an emerging new era of rice genomics.
Abstract Rice is a model system for crop genomics studies. Much of the early work on rice genomics focused on analyzing genome-wide genetic variation to further understand rice gene functions in agronomic traits and to generate data and resources for rice research. The advent of next-generation high-throughput DNA sequencing technologies and the completion of high-quality reference genome sequences have enabled the development of sequencing-based genotyping and genome-wide association studies (GWAS) that have significantly advanced rice genetics research. This has led to the emergence of a new era of rice genomics...
Source: Trends in Genetics : TIG - January 4, 2013 Category: Genetics & Stem Cells Authors: Huang X, Lu T, Han B Tags: Trends Genet Source Type: research

Genetic tracking of mice and other bioproxies to infer human history.
, Searle JB Abstract The long-distance movements made by humans through history are quickly erased by time but can be reconstructed by studying the genetic make-up of organisms that travelled with them. The phylogeography of the western house mouse (Mus musculus domesticus), whose current widespread distribution around the world has been caused directly by the movements of (primarily) European people, has proved particularly informative in a series of recent studies. The geographic distributions of genetic lineages in this commensal have been linked to the Iron Age movements within the Mediterranean region and Wes...
Source: Trends in Genetics : TIG - January 2, 2013 Category: Genetics & Stem Cells Authors: Jones EP, Eager HM, Gabriel SI, Jóhannesdóttir F, Searle JB Tags: Trends Genet Source Type: research

Robustness in angiogenesis: Notch and BMP shaping waves.
Abstract Vascular patterning involves sprouting of blood vessels, which is governed by orchestrated communication between cells in the surrounding tissue and endothelial cells (ECs) lining the blood vessels. Single ECs are selected for sprouting by hypoxia-induced stimuli and become the 'tip' or leader cell that guides new sprouts. The 'stalk' or trailing ECs proliferate for tube extension and lumenize the nascent vessel. Stalk and tip cells can dynamically switch their identities during this process in a Notch-dependent manner. Here, we review recent studies showing that bone morphogenetic protein (BMP) signaling...
Source: Trends in Genetics : TIG - December 29, 2012 Category: Genetics & Stem Cells Authors: Beets K, Huylebroeck D, Moya IM, Umans L, Zwijsen A Tags: Trends Genet Source Type: research

Bridging the gap between genome analysis and precision breeding in potato.
Abstract Efficiency and precision in plant breeding can be enhanced by using diagnostic DNA-based markers for the selection of superior cultivars. This technique has been applied to many crops, including potatoes. The first generation of diagnostic DNA-based markers useful in potato breeding were enabled by several developments: genetic linkage maps based on DNA polymorphisms, linkage mapping of qualitative and quantitative agronomic traits, cloning and functional analysis of genes for pathogen resistance and genes controlling plant metabolism, and association genetics in collections of tetraploid varieties and ad...
Source: Trends in Genetics : TIG - December 19, 2012 Category: Genetics & Stem Cells Authors: Gebhardt C Tags: Trends Genet Source Type: research

The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation.
Abstract As the global population and global wealth both continue to increase, so will the demand for livestock products, especially those that are highly nutritious. However, competition with other uses for land and water resources will also intensify, necessitating more efficient livestock production. In addition, as climate change escalates, reduced methane emissions from cattle and sheep will be a critical goal. Application of new technologies, including genomic selection and advanced reproductive technologies, will play an important role in meeting these challenges. Genomic selection, which enables prediction...
Source: Trends in Genetics : TIG - December 19, 2012 Category: Genetics & Stem Cells Authors: Hayes BJ, Lewin HA, Goddard ME Tags: Trends Genet Source Type: research