Yeast genomes: Genetic codes for species of yeasts identified and compared

www.sciencedaily.comIf you think yeast is most useful for beer and pizza crust, here’s something else to chew on: a team of U.S. researchers has identified and compared the genetic codes for all known species of yeasts closely related to bakers’ and brewers’ yeast.

“We hope to learn to read the language of DNA and tell when mutations or differences will cause disease and when they will be advantageous,” said Chris Todd Hittinger, senior author of the work from the Department of Biochemistry and Molecular Genetics at the University of Colorado School of Medicine in Aurora, Colorado. “Providing a complete catalog of diversity among this group of species will allow us to quickly test which changes are responsible for which functions in the laboratory with a level of precision and efficiency not possible in other organisms.”

Using massively parallel next-generation DNA sequencing, the researchers determined the genome sequences, doubling the number of genes available for comparison, and identifying which genes changed in which species. They did this by segmenting each organism’s DNA into small pieces, and then computationally “reassembled” the pieces and compared them to the genome of S. cerevisiae (the species used to make beer, bread, wine, etc.) to identify similarities and differences. The researchers also genetically engineered several of the strains to make them amenable for experimentation. Results from this study will allow researchers to compare the genetics, molecular biology, and ecology of these species. Because yeast genomes and lifestyles are relatively simple, determining how diversity is encoded in their DNA is much easier than with more complex organisms, such as humans.

“The experimental resources described in this paper extend the value of yeasts for understanding biological processes,” said Brenda Andrews, Editor-in-Chief of G3: Genes | Genomes | Genetics, “and if they help us make better pizza crust and beer along the way, all the better.”

Story Source:
The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Genetics Society of America, via EurekAlert!, a service of AAAS.

Journal Reference:
Devin R. Scannell, Oliver A. Zill, Antonis Rokas, Celia Payen, Maitreya J. Dunham, Michael B. Eisen, Jasper Rine, Mark Johnston, Chris Todd Hittinger. The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3: Genes | Genomes | Genetics, 2011; 1 (1): 11-25 DOI: 10.1534/g3.111.000273

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Los pájaros llevan la promiscuidad en los genes

Diamante mandarín El estudio demostró que las hembras también tienen tendencias promicuas.

Científicos en Alemania descubrieron que los genes pueden explicar en buena medida la promiscuidad en una especie de pájaros, los diamantes mandarín (Taeniopygia guttata) y creen que lo mismo puede suceder con otras especies, incluyendo los seres humanos.

El 90% de las especies de aves son clasificadas como monógamas, ya que por lo general crean lazos con una misma pareja con quienes procrean la mayor parte de sus crías.

Se sabe también que para dos terceras partes de éstas, el apareamiento “extramarital” también es común, de manera que los diamantes mandarín no son una excepción.

Pero, por primera vez, los investigadores del Instituto Max Planck de Ornitología de Alemania hallaron que hay un vínculo genético que explica este comportamiento.

En palabras del profesor Wolfgang Forstmeier, quien dirigió el estudio, un porcentaje importante de los individuos de esta especie tienen una “inclinacinación intrínseca a comportarse de forma promiscua”.

Para llegar a esta conclusión, los investigadores estudiaron una población de 1.554 individuos, que cubrían cinco generaciones de diamantes mandarín y que residían en un aviario.

Además, clasificaron los individuos en más promiscuos o menos promiscuos y tomaron muestras de ADN de estos ejemplares para establecer los vínculos genéticos entre cada uno de los integrantes de la población en estudio.

“En el caso de los diamantes mandarín, la conducta de individuos específicos sigue en buena medida la de los padres genéticos y eso es una evidencia de que hay un componente hereditario”

Wolfgang Forstmeier, investigador

“Intercambiamos huevos en diferentes nidos, de manera que las crías no crecieran con sus padres genéticos y aprendieran su conducta de estos, y analizamos si el comportamiento de estas crías seguían la conducta de los padres adoptivos o la de los genéticos”, le explicó Forstmeier a BBC Mundo.

La idea, según el experto, fue poner a prueba la tesis de si la promiscuidad era influida por el medio social o por factores genéticos.

“En el caso de los diamantes mandarín, la conducta de individuos específicos sigue en buena medida la de los padres genéticos y eso es una evidencia de que hay un componente hereditario”, afirmó el científico.

En otras palabras, un pájaro con un padre que tiene tendencias promiscuas tenía una alta probabilidad de hacer lo mismo, aunque no hubiera tenido contacto con él.

La investigación determinó, además, que esta conducta no se limitaba sólo a los varones.

La hembra con una madre o padre promiscuos también heredaba estas tendencias.

Los científicos observaron “cómo algunas hembras rechazaban los cortejos de un individuo diferente de su pareja, mientras que otras incluso buscaban activamente aparearse con otros”.

Diamantes mandarín El 90% de las especies de pájaros son clasificadas como monógamas.

Pero asimismo determinaron que las hembras también pasan estos genes a sus crías, aunque en la mayoría de los casos proviene de los machos.

Por muchos tiempo, los investigadores se han preguntado cómo se explica la promiscuidad de las hembras, ya que siguiendo la teoría de la evolución de Charles Darwin no está claro cómo se beneficia la especie.

“Siguiendo la teoría de Darwin se entiende por qué hay machos prosmicuos -ellos se benefician en términos darwinianos porque así tienen más crías y sus características no se pierden-, pero es menos claro por qué las hembras siguen esta conducta”, le dijo Forstmeister a BBC Mundo.

El equipo llegó a la conclusión de que los genes responsables de estas conductas son simplemente pasados a las hembras de sus ancestros por varias generaciones “y no tiene que haber ningún beneficio”.

Según el experto, esto constituye una perspectiva completamente diferente de la que han tenido hasta ahora los científicos.

Los investigadores también sugieren que vínculos genéticos también podrían explicar la promiscuidad en humanos, algo que muchos consideran bastante controvertido.

Forstmeier es consciente de esto: “En la mayoría de los casos se diría que es un poco loco hacer esta extrapolación de los diamantes mandarines a los humanos, porque ambas especies compartían un mismo ancestro hace 300 millones de años y por lo tanto es poco probable que tengan los mismos mecanismos genéticos”.

Sin embargo, afirmó que en este caso se trata de tendencias generales y que, por lo tanto, “es muy probable que ésta sea una explicación posible para la conducta prosmicua en los humanos”.

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Are Birthmarks Genetic?

Are Birthmarks Genetic? The Inheritance of Different Types of Birthmarks

Stork bites, angel’s kisses, and strawberry – these are all names given to birthmarks. So what are birthmarks and are they genetically inherited?

Birthmarks are blemishes or growths formed on the skin before a baby is born. These marks may then be retained as the child grows up or may be lost with time. It is also possible that birthmarks may pop up within a few weeks after birth, though the majority are formed before delivery. Very little is known about the cause of birthmarks and there are no known ways of preventing them either.

Birthmarks can occur anywhere on the body and for the most part are completely harmless. It is generally believed that most are not inherited, although some are. There is plenty of anecdotal information about several generations of family members having similar size, shape and location of birthmarks.

Vascular or Red Birthmarks

Birthmarks can occur anywhere on the skin, and are broadly grouped into pigmented birthmarks and vascular or red birthmarks.

Vascular/Red Birthmark are formed by the overgrowth of blood vessels anywhere on the skin, and they occur with a greater frequency in females than males. In addition Caucasian babies with a body weight of less than 2.2 pounds have a 26% chance of having vascular birthmarks. Vascular birthmarks are further grouped into macular & hemangioma.

Capillary haemangioma - released into public domainMacular birthmarks are caused by capillaries that are visible through the skin. Generally pink in color or shades thereof they mostly occur on the forehead, eyelids and neck regions. These generally fade away as the baby grows up. Hemangiomas are generally caused by a larger number of blood vessels getting closely packed at the surface of the skin. They usually fade with time as well.

Pigmented Birthmarks

Pigmented birthmarks, as the name suggests are usually colored regions in the skin that differ in shade. The most common form of pigmented birthmark is the port-wine stain, which is caused by dilated blood capillaries. The port-wine stain variety of birthmarks are usually red, blue or purple colored and they are usually permanent. If they are too big and disfiguring, port-wine stain birthmarks can be removed by surgery. Large port-wine birthmarks are sometimes caused by an inherited genetic disorder called neurofibromatosis which produces non-cancerous tumours in nerve cells along the skin.

Characteristic symptoms of neurofibromatosis are multiple port-wine birthmarks and they can be located anywhere on the body, including the tongue.

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A Genome-Wide Enhancer Screen Implicates Sphingolipid Composition in Vacuolar ATPase Function in Saccharomyces cerevisiae [Cellular genetics]

A Genome-Wide Enhancer Screen Implicates Sphingolipid Composition in Vacuolar ATPase Function in Saccharomyces cerevisiae Genetics

Abstract The function of the vacuolar H+-ATPase (V-ATPase) enzyme complex is to acidify organelles; this process is critical for a variety of cellular processes and has implications in human disease. There are five accessory proteins that assist in assembly of the membrane portion of the complex, the V0 domain. To identify additional elements that affect V-ATPase assembly, trafficking, or enzyme activity, we performed a genome-wide enhancer screen in the budding yeast Saccharomyces cerevisiae with two mutant assembly factor alleles, VMA21 with a dysfunctional ER retrieval motif (vma21QQ) and vma21QQ in combination with voa1?, a nonessential assembly factor. These alleles serve as sensitized genetic backgrounds that have reduced V-ATPase enzyme activity. Genes were identified from a variety of cellular pathways including a large number of trafficking-related components; we characterized two redundant gene pairs, HPH1/HPH2 and ORM1/ORM2. Both sets demonstrated synthetic growth defects in combination with the vma21QQ allele. A loss of either the HPH or ORM gene pairs alone did not result in a decrease in vacuolar acidification or defects in V-ATPase assembly. While the Hph proteins are not required for V-ATPase function, Orm1p and Orm2p are required for full V-ATPase enzyme function. Consistent with the documented role of the Orm proteins in sphingolipid regulation, we have found that inhibition of sphingolipid synthesis alleviates Orm-related growth defects.

Footnotes Supporting information is available online at http://www.genetics.org/cgi/content/full/genetics.110.125567/DC1.

Communicating editor: M. D. Rose

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A Genetical Genomics Approach to Genome Scans Increases Power for QTL Mapping [Genetics of complex traits]

A Genetical Genomics Approach to Genome Scans Increases Power for QTL Mapping Genetics

Department of Statistics, University of Georgia, Athens, Georgia 30602 1?Corresponding author: Department of Statistics, 203 Statistics Bldg., University of Georgia, Athens, GA 30602-7952. E-mail: pdschlie{at}stat.uga.edu Abstract We describe a method for integrating gene expression information into genome scans and show that this can substantially increase the statistical power of QTL mapping. The method has three stages. First, standard clustering methods identify small (size 5–20) groups of genes with similar expression patterns. Second, each gene group is tested for a causative genetic locus shared with the clinical trait of interest. This is done using an EM algorithm approach that treats genotype at the putative causative locus as an unobserved variable and combines expression information from all of the genes in the group to infer genotype information at the locus. Finally, expression QTL (eQTL) are mapped for each gene group that shares a causative locus with the clinical trait. Such eQTL are candidates for the causative locus. Simulation results show that this method has far superior power to standard QTL mapping techniques in many circumstances. We applied this method to existing data on mouse obesity. Our method identified 27 putative body weight QTL, whereas standard QTL mapping produced only one. Furthermore, most gene groups with body weight QTL included cis genes, so candidate genes could be immediately identified. Eleven body weight QTL produced 16 candidate genes that have been previously associated with body weight or body weight-related traits, thus validating our method. In addition, 15 of the 16 other loci produced 32 candidate genes that have not been associated with body weight. Thus, this method shows great promise for finding new causative loci for complex traits.

Footnotes Supporting information is available online at http://www.genetics.org/cgi/content/full/genetics.110.123968/DC1.

Communicating editor: H. Zhao

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Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression [Genetics of complex traits]

Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression Genetics

*Natural Resources Canada, Canadian Wood Fibre Centre, Québec City, Québec G1V 4C7, Canada
†Université Laval, Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Québec City, Québec G1V 0A6, Canada
‡Gydle, Québec City, Québec G1T 1Z2, Canada and
§FPInnovations, Vancouver, British Columbia V6S 2L9, Canada 1?Corresponding author: Natural Resources Canada, Canadian Wood Fibre Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec City, Québec G1V 4C7, Canada. E-mail: jean.beaulieu{at}NRCan.gc.ca Abstract Marker-assisted selection holds promise for highly influencing tree breeding, especially for wood traits, by considerably reducing breeding cycles and increasing selection accuracy. In this study, we used a candidate gene approach to test for associations between 944 single-nucleotide polymorphism markers from 549 candidate genes and 25 wood quality traits in white spruce. A mixed-linear model approach, including a weak but nonsignificant population structure, was implemented for each marker–trait combination. Relatedness among individuals was controlled using a kinship matrix estimated either from the known half-sib structure or from the markers. Both additive and dominance effect models were tested. Between 8 and 21 single-nucleotide polymorphisms (SNPs) were found to be significantly associated (P = 0.01) with each of earlywood, latewood, or total wood traits. After controlling for multiple testing (Q = 0.10), 13 SNPs were still significant across as many genes belonging to different families, each accounting for between 3 and 5% of the phenotypic variance in 10 wood characters. Transcript accumulation was determined for genes containing SNPs associated with these traits. Significantly different transcript levels (P = 0.05) were found among the SNP genotypes of a 1-aminocyclopropane-1-carboxylate oxidase, a ß-tonoplast intrinsic protein, and a long-chain acyl-CoA synthetase 9. These results should contribute toward the development of efficient marker-assisted selection in an economically important tree species.

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Detecting Major Genetic Loci Controlling Phenotypic Variability in Experimental Crosses [Genetics of complex traits]

Detecting Major Genetic Loci Controlling Phenotypic Variability in Experimental Crosses Genetics

*Statistics Unit, Dalarna University, SE-781 70 Borlänge, Sweden and †Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7265 Abstract Traditional methods for detecting genes that affect complex diseases in humans or animal models, milk production in livestock, or other traits of interest, have asked whether variation in genotype produces a change in that trait’s average value. But focusing on differences in the mean ignores differences in variability about that mean. The robustness, or uniformity, of an individual’s character is not only of great practical importance in medical genetics and food production but is also of scientific and evolutionary interest (e.g., blood pressure in animal models of heart disease, litter size in pigs, flowering time in plants). We describe a method for detecting major genes controlling the phenotypic variance, referring to these as vQTL. Our method uses a double generalized linear model with linear predictors based on probabilities of line origin. We evaluate our method on simulated F2 and collaborative cross data, and on a real F2 intercross, demonstrating its accuracy and robustness to the presence of ordinary mean-controlling QTL. We also illustrate the connection between vQTL and QTL involved in epistasis, explaining how these concepts overlap. Our method can be applied to a wide range of commonly used experimental crosses and may be extended to genetic association more generally.

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Genetic Architecture of Flowering-Time Variation in Arabidopsis thaliana [Genetics of complex traits]

Genetic Architecture of Flowering-Time Variation in Arabidopsis thaliana Genetics

Abstract The onset of flowering is an important adaptive trait in plants. The small ephemeral species Arabidopsis thaliana grows under a wide range of temperature and day-length conditions across much of the Northern hemisphere, and a number of flowering-time loci that vary between different accessions have been identified before. However, only few studies have addressed the species-wide genetic architecture of flowering-time control. We have taken advantage of a set of 18 distinct accessions that present much of the common genetic diversity of A. thaliana and mapped quantitative trait loci (QTL) for flowering time in 17 F2 populations derived from these parents. We found that the majority of flowering-time QTL cluster in as few as five genomic regions, which include the locations of the entire FLC/MAF clade of transcription factor genes. By comparing effects across shared parents, we conclude that in several cases there might be an allelic series caused by rare alleles. While this finding parallels results obtained for maize, in contrast to maize much of the variation in flowering time in A. thaliana appears to be due to large-effect alleles.

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Cancer Research UK to launch genetic testing programme

Cancer Research UK’s chief executive Harpal Kumar today spoke of a ‘golden era’ for cancer research as the UK is poised to lead the world in individualising the practice of medicine by understanding which treatments are best suited to an individual patient’s particular genetic type of cancer.

New discoveries are already producing personalised treatments that promise to be more targeted than conventional medicine, he told the annual National Cancer Intelligence Network (NCIN) conference in London.

Cancer Research UK is launching a programme in the UK to show how cancer gene tests can be carried out systematically within the NHS to help clinicians choose the best treatment for their patients and, in turn, influence research.

Harpal Kumar, Cancer Research UK’s chief executive, said: “This is an immensely exciting time for cancer research. New genetic tests will improve treatment decisions and will transform the way we treat this disease, ultimately improving survival and sparing thousands of patients from suffering side effects from treatments that will not work for their individual cancer.

“It will mean that rather than just treating cancer patients based on which organ their cancer is in, their treatment will be tailored to the genetic profile of their tumour.

Cancer Research UK will shortly be starting a two year programme in seven hospitals and three labs. It will collect and test 9,000 tumour samples for breast, bowel, lung, prostate and melanoma and ovarian cancers. This information will not only help us design better tests but will also provide us with information to help us find out/research which tumour type responds best to which treatment.”

This investment is part of a unique national partnership including Cancer Research UK, the government and industry. The Department of Health’s latest cancer strategy has committed to improve genetic testing, while the Technology Strategy Board has just invested £6m in partnerships between universities and private companies to develop new tests and databases.

“Because we have mapped so many cancer genomes across the world, we now know much more about what causes cancer and what causes cells to grow out of control. This has led to exciting discoveries which are benefitting patients now. These include the drugs imatinib and erlotinib which target precise mutations. By combining routine hospital treatment and research in our Stratified Medicine Programme, we can accelerate this progress, and develop more targeted treatments for patients.”

Chris Carrigan, head of the NCIN, said: “Over the next two years we will see a huge growth in the data available about cancer patients and their treatments, especially in the area of genetics. The NCIN has a key role to play to safely link traditional and new data to facilitate whole new areas of analysis, research and understanding.”

Source: Cancer Research UK

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Un estudio probará la eficacia de una terapia con células madre para tratar la pérdida de visión

La Universidad de California en Los Ángeles (UCLA) ha comenzado a reclutar pacientes para los primeros ensayos clínicos con una novedosa terapia con células madre embrionarias de Advanced Cell Technology, con la que pretenden tratar la degeneración macular, la causa más común de pérdida de visión.

Según informa la compañía, los primeros pacientes ya han sido inscritos en el Instituto del Ojo Jules Stein de la UCLA, después de que la Agencia Americana del Medicamentos (FDA, en sus siglas en inglés) diese su visto bueno a estos ensayos en enero de este año.

De hecho, meses antes, en noviembre de 2010, ya habían aprobado un ensayo con el mismo método para tratar a personas con una forma progresiva de ceguera llamada distrofia macular de Stargardt.

Ambos ensayos probarán la seguridad y tolerabilidad del epitelio pigmentario retinal o células EPR, que Advanced Cell Technology fabrica a partir de células madre de embriones humanos.

Cada estudio incluirá a 12 pacientes, divididos en grupos de tres en los que se probarán diferentes dosis de esta terapia.

Según explica el director científico de la compañía, el doctor Robert Lanza, el objetivo es comenzar los trasplantes de células madre en las próximas semanas “después de una década de amplias investigaciones y estudios preclínicos”.

“Esperamos que estas células permitan en el futuro un tratamiento no sólo para estas dos enfermedades intratables, sino también para pacientes que sufren otras patologías oculares degenerativas”, agregó.

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