Yeast Research Research Articles

Efficient linkage mapping using exome capture and extreme QTL in schistosome parasites.

BackgroundIdentification of parasite genes that underlie traits such as drug resistance and host specificity is challenging using classical linkage mapping approaches. Extreme QTL (X-QTL) methods, originally developed by rodent malaria and yeast researchers, promise to increase the power and simplify logistics of linkage mapping in experimental crosses of schistosomes (or other helminth parasites), because many 1000s of progeny can be analysed, phenotyping is not required, and progeny pools rather than individuals are genotyped. We explored the utility of this method for mapping a drug resistance gene in the human parasitic fluke Schistosoma mansoni.ResultsWe staged a genetic cross between oxamniquine sensitive and resistant parasites, then between two F1 progeny, to generate multiple F2 progeny. One group of F2s infecting hamsters was treated with oxamniquine, while a second group was left untreated. We used exome capture to reduce the size of the genome (from 363 Mb to 15 Mb) and exomes from pooled F2 progeny (treated males, untreated males, treated females, untreated females) and the two parent parasites were sequenced to high read depth (mean = 95-366×) and allele frequencies at 14,489 variants compared. We observed dramatic enrichment of alleles from the resistant parent in a small region of chromosome 6 in drug-treated male and female pools (combined analysis: = 11.07, p = 8.74 × 10-29). This region contains Smp_089320 a gene encoding a sulfotransferase recently implicated in oxamniquine resistance using classical linkage mapping methods.ConclusionsThese results (a) demonstrate the utility of exome capture for generating reduced representation libraries in Schistosoma mansoni, and (b) provide proof-of-principle that X-QTL methods can be successfully applied to an important human helminth. The combination of these methods will simplify linkage analysis of biomedically or biologically important traits in this parasite.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-617) contains supplementary material, which is available to authorized users.

Brewing a career.

Protein engineer Jasper Akerboom left his job as a research specialist at the Howard Hughes Medical Institute's (HHMI's) Janelia Farm Research Campus in Virginia to pursue a career as a brewmeister. In this interview (edited for brevity and clarity), Akerboom discusses the Janelia Farm experience, yeast, and what it's like to follow one's microbiological bliss. ![Figure][1] Eventually, every postdoc has to decide, “What are you going to do?” ILLUSTRATION: ROBERT NEUBECKER > Q: What brought you to Janelia Farm? > A:I was doing my Ph.D. in microbiology at Wageningen University in the Netherlands. The focus was on extreme life, organisms living in very hot locations. I was studying the molecular biology and biochemistry of these organisms because their proteins had to be very stable to withstand very high temperatures and salt concentrations. We were collaborating with a postdoc at Stanford, who later moved to HHMI. He asked me if I wanted to postdoc in his lab. > Q: Tell us about Janelia Farm. > A:It's a pretty incredible institution. Principal investigators come in for short-term contracts. They can hire people—but not too many, so the groups are small. After 5 or 6 years, these group leaders are reviewed, and they might not be renewed, so new people come in. There is no teaching. Every year, there is a large amount of funding available, so it is a nice place to be. > Q: How did you get from tracking neurons to brewing beer? > A:I started home brewing in the Netherlands. Lots of us were doing yeast research. When I came to the United States, I began isolating strains from the local area. In 2007, I approached these guys who had just started a local brewery, Lost Rhino Brewing Company, and I said, “I have these local yeast strains. It would be great to collaborate.” I gave them a few tasters of my test batches. They were super excited, and so we did this together. It was a great success. > Q: What made you decide to go from brewing as a hobby to brewmeister as a career? > A:Eventually, every postdoc has to decide, “What are you going to do?” Janelia Farm is a very prestigious institution, so people often get very good jobs afterward. But I wanted to do something else. I saw people around me who were all very stressed. It was just very hard for them to get these papers published, as it was for me. I had been scooped many times, competing with people outside and maybe even inside the institution. And I was like, “This is not something I would like to do forever.” I thought, “Maybe I can just take my success with yeast and get some experience at this brewery, and then take that experience and maybe move somewhere else in the future.” > Q: Would you say the demands at Janelia Farm are too high? > A:This is of course the top. I would compare it to doing a postdoc at Harvard or Stanford. Some people thrive in that environment. The good side is that Janelia pushes people to the limit. You will enrich a whole group of people who are very smart. But the downside is that it can be a very hard environment. > Q: Do you have any regrets about leaving? > A:At first, I felt like I let myself down. When you deviate from the path, you are breaking with what you were always planning on doing. But if I can say one thing that may be of interest to your readers, it is that they shouldn't feel bad about themselves if they make the decision to step off the path, because it might be the right decision, although it might not feel right at the time. > Q: Any other advice for scientists who want to pursue an alternate career path? > A:Take advantage of the freedom that comes with being a postdoc. Use that period to think about what you want. Everyone congratulates the person who gets the professorship at a big-name university or a huge grant. But that is not for everybody, and there is nothing wrong with that. [1]: pending:yes

Improvement of the transformation efficiency of Sacchaaromyces cerevisiae by altering carbon sources in pre-culture.

We show here that the transformation efficiency of Saccharomyces cerevisiae is improved by altering carbon sources in media for pre-culturing cells prior to the transformation reactions. The transformation efficiency was increased up to sixfold by combination with existing transformation protocols. This method is widely applicable for yeast research since efficient transformation can be performed easily without changing any of the other procedures in the transformation.

Budding Topics: insights from emerging scientists

In this issue, we publish the first of our new review series named ‘Budding Topics’. Alongside the regular research papers, Yeast has published review articles touching on many aspects of yeast biology, some of which have been highly successful. With the ‘Budding Topics’ written by Leopold Parts (pp. 197–205), Yeast starts a series of concise reviews on new and emerging topics, techniques or approaches that are at the forefront of the different fields of yeast research. A major difference with this regular review series is that ‘Budding Topics’ is an invited-only review series specifically targeting young scientists. We feel that young PIs have few opportunities to be asked by mainstream journals to write such reviews; despite the fact that they can be very innovative by proposing new theories and ideas. Finally, we would like to thank all the ‘Budding Topics’ authors for the enthusiastic response to this editorial initiative and for their commitment in timely submission of their high-quality work to Yeast. We wish them good luck for a brilliant career as yeast researchers. We hope you find these reviews articles as exciting as we do. Yeast Yeast 2014; 31: 195. Published online in Wiley Online Library (wileyonlinelibrary.com) DOI: 10.1002/yea.3013

The yeast deletion collection: a decade of functional genomics.

The yeast deletion collections comprise >21,000 mutant strains that carry precise start-to-stop deletions of ∼6000 open reading frames. This collection includes heterozygous and homozygous diploids, and haploids of both MATa and MATα mating types. The yeast deletion collection, or yeast knockout (YKO) set, represents the first and only complete, systematically constructed deletion collection available for any organism. Conceived during the Saccharomyces cerevisiae sequencing project, work on the project began in 1998 and was completed in 2002. The YKO strains have been used in numerous laboratories in >1000 genome-wide screens. This landmark genome project has inspired development of numerous genome-wide technologies in organisms from yeast to man. Notable spinoff technologies include synthetic genetic array and HIPHOP chemogenomics. In this retrospective, we briefly describe the yeast deletion project and some of its most noteworthy biological contributions and the impact that these collections have had on the yeast research community and on genomics in general.

Primers‐4‐Yeast: a comprehensive web tool for planning primers for Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae is a key model organism of functional genomics, due to its ease and speed of genetic manipulations. In fact, in this yeast, the requirement for homologous sequences for recombination purposes is so small that 40 base pairs (bp) are sufficient. Hence, an enormous variety of genetic manipulations can be performed by simply planning primers with the correct homology, using a defined set of transformation plasmids. Although designing primers for yeast transformations and for the verification of their correct insertion is a common task in all yeast laboratories, primer planning is usually done manually and a tool that would enable easy, automated primer planning for the yeast research community is still lacking. Here we introduce Primers-4-Yeast, a web tool that allows primers to be designed in batches for S. cerevisiae gene-targeting transformations, and for the validation of correct insertions. This novel tool enables fast, automated, accurate primer planning for large sets of genes, introduces consistency in primer planning and is therefore suggested to serve as a standard in yeast research. Primers-4-Yeast is available at: http://www.weizmann.ac.il/Primers-4-Yeast

Patents: a tool to bring innovation from the lab bench to the marketplace.

Intellectual property (IP) is creations of the mind. Protecting IP through patents is an important venue for a researcher to reap rewards from his scientific endeavors. It is part of a competitive strategy for bringing one's invention to the marketplace. Using the US and European patent systems as examples, we provide here an overview of how patents protect innovation, with a focus on biotechnology. We explain what a patent is, what a patent owner can do with a patent, and how patents are granted. The article ends with some recent examples of noteworthy patents in the field of yeast research.

Chapter 14 - Assessing Regulated Nuclear Transport in Saccharomyces cerevisiae

Regulated protein transport between the cytoplasm and the nucleoplasm occurs through nuclear pore complexes and is critical to the function of numerous biological pathways. Saccharomyces cerevisiae has been used as a model system to probe the underlying mechanisms of nuclear transport and how they regulate various physiological processes. This has been facilitated, in part, by studies that couple the microscopic observation of a fluorescently tagged transport cargo's in vivo localization with numerous genetic and biochemical tools available to yeast researchers. Here, we describe some of these methods as they pertain to studies on regulated nuclear transport.

Genomic Sequence Diversity and Population Structure ofSaccharomyces cerevisiaeAssessed by RAD-seq

The budding yeast Saccharomyces cerevisiae is important for human food production and as a model organism for biological research. The genetic diversity contained in the global population of yeast strains represents a valuable resource for a number of fields, including genetics, bioengineering, and studies of evolution and population structure. Here, we apply a multiplexed, reduced genome sequencing strategy (restriction site−associated sequencing or RAD-seq) to genotype a large collection of S. cerevisiae strains isolated from a wide range of geographical locations and environmental niches. The method permits the sequencing of the same 1% of all genomes, producing a multiple sequence alignment of 116,880 bases across 262 strains. We find diversity among these strains is principally organized by geography, with European, North American, Asian, and African/S. E. Asian populations defining the major axes of genetic variation. At a finer scale, small groups of strains from cacao, olives, and sake are defined by unique variants not present in other strains. One population, containing strains from a variety of fermentations, exhibits high levels of heterozygosity and a mixture of alleles from European and Asian populations, indicating an admixed origin for this group. We propose a model of geographic differentiation followed by human-associated admixture, primarily between European and Asian populations and more recently between European and North American populations. The large collection of genotyped yeast strains characterized here will provide a useful resource for the broad community of yeast researchers.

The Modest Beginnings of One Genome Project

One of the top things on a geneticist's wish list has to be a set of mutants for every gene in their particular organism. Such a set was produced for the yeast, Saccharomyces cerevisiae near the end of the 20th century by a consortium of yeast geneticists. However, the functional genomic analysis of one chromosome, its smallest, had already begun more than 25 years earlier as a project that was designed to define most or all of that chromosome's essential genes by temperature-sensitive lethal mutations. When far fewer than expected genes were uncovered, the relatively new field of molecular cloning enabled us and indeed, the entire community of yeast researchers to approach this problem more definitively. These studies ultimately led to cloning, genomic sequencing, and the production and phenotypic analysis of the entire set of knockout mutations for this model organism as well as a better concept of what defines an essential function, a wish fulfilled that enables this model eukaryote to continue at the forefront of research in modern biology.

BiotecVisions 2013, March

BiotecVisions 2013, March

BiotecVisions 2013, February

BiotecVisions 2013, February

BioFab: Applying Moore's Law to DNA Synthesis

Industrial BiotechnologyVol. 9, No. 1 Catalyzing InnovationBioFab: Applying Moore's Law to DNA SynthesisMartin GoldbergMartin GoldbergSearch for more papers by this authorPublished Online:15 Feb 2013https://doi.org/10.1089/ind.2012.1552AboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View articleFiguresReferencesRelatedDetailsCited byMoore’s Law revisited through Intel chip density18 August 2021 | PLOS ONE, Vol. 16, No. 8Competition and the Future of Reading and Writing DNA30 March 2018Recent advances in DNA assembly technologies23 June 2014 | FEMS Yeast Research, Vol. 35Integration of microfluidics into the synthetic biology design flow1 January 2014 | Lab Chip, Vol. 14, No. 18Self-assembly of one dimensional DNA-templated structures1 January 2014 | J. Mater. Chem. C, Vol. 2, No. 34Designing living matter. Can we do better than evolution?30 July 2013 | Complexity, Vol. 18, No. 6 Volume 9Issue 1Feb 2013 InformationCopyright 2013, Mary Ann Liebert, Inc.To cite this article:Martin Goldberg.BioFab: Applying Moore's Law to DNA Synthesis.Industrial Biotechnology.Feb 2013.10-12.http://doi.org/10.1089/ind.2012.1552Published in Volume: 9 Issue 1: February 15, 2013Online Ahead of Print:January 29, 2013PDF download

Genomic stability disorders from budding yeast to humans

Fundamental aspects of eukaryotic molecular and cellular biology are extensively studied in the budding yeast Saccharomyces cerevisiae. Genome maintenance pathways are highly conserved and research into a number of human genetic disorders with increased genome instability and cancer predisposition have benefited greatly from studies in budding yeast. Here, we present some of the examples where yeast research into DNA damage responses and telomere maintenance pathways paved the way to understanding these processes, and their involvement in selected human diseases.

Yeast Stress, Aging, and Death

Yeast Stress, Aging, and Death

BiotecVisions 2013, January

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BiotecVisions 2012, November

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BiotecVisions 2012, October

A Mass Spectrometry Proteomics Data Management Platform

Mass spectrometry-based proteomics is increasingly being used in biomedical research. These experiments typically generate a large volume of highly complex data, and the volume and complexity are only increasing with time. There exist many software pipelines for analyzing these data (each typically with its own file formats), and as technology improves, these file formats change and new formats are developed. Files produced from these myriad software programs may accumulate on hard disks or tape drives over time, with older files being rendered progressively more obsolete and unusable with each successive technical advancement and data format change. Although initiatives exist to standardize the file formats used in proteomics, they do not address the core failings of a file-based data management system: (1) files are typically poorly annotated experimentally, (2) files are "organically" distributed across laboratory file systems in an ad hoc manner, (3) files formats become obsolete, and (4) searching the data and comparing and contrasting results across separate experiments is very inefficient (if possible at all). Here we present a relational database architecture and accompanying web application dubbed Mass Spectrometry Data Platform that is designed to address the failings of the file-based mass spectrometry data management approach. The database is designed such that the output of disparate software pipelines may be imported into a core set of unified tables, with these core tables being extended to support data generated by specific pipelines. Because the data are unified, they may be queried, viewed, and compared across multiple experiments using a common web interface. Mass Spectrometry Data Platform is open source and freely available at http://code.google.com/p/msdapl/.

BiotecVisions 2012, April

BiotecVisions 2012, April