Publications by authors named "Sage T Hellerstedt"

8 Publications

  • Page 1 of 1

An Introduction to the Saccharomyces Genome Database (SGD).

Methods Mol Biol 2018 ;1757:21-30

Department of Genetics, Stanford University, Palo Alto, CA, USA.

The Saccharomyces Genome Database (SGD) is a well-established, key resource for researchers studying Saccharomyces cerevisiae. In addition to updating and maintaining the official genomic sequence of this highly studied organism, SGD provides integrated data regarding gene functions and phenotypes, which are extracted from the published literature. The vast amount and variety of data housed in the database can prove challenging to navigate for the first-time user. Therefore, this chapter serves as an introduction describing how to search the database in order to discover new information. We introduce the different types of pages on the website, and describe how to manipulate the tables and diagrams therein to display, download, or analyze the data using various SGD tools.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-7737-6_2DOI Listing
January 2019

Updated regulation curation model at the Saccharomyces Genome Database.

Database (Oxford) 2018 01;2018

Department of Genetics, Stanford University, Stanford, CA 94305, USA.

Database Url: http://www.yeastgenome.org.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/database/bay007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829562PMC
January 2018

Biomarkers' Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1.

Microorganisms 2018 Feb 8;6(1). Epub 2018 Feb 8.

School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA.

Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR) rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent respiring, (DMC) containing, bioaugmentation cultures. In the current study, genome-wide transcriptome and proteome data were first used to confirm the most highly expressed OHR-related enzymes in the bioaugmentation culture, KB-1, including several reductive dehalogenases (RDases) and a Ni-Fe hydrogenase, Hup. Different KB-1™ DMC strains could be resolved at the RNA and protein level through differences in the sequence of a common RDase (DET1545-like homologs) and differences in expression of their vinyl chloride-respiring RDases. The dominant strain expresses VcrA, whereas the minor strain utilizes BvcA. We then used quantitative reverse-transcriptase PCR (qRT-PCR) as a targeted approach for quantifying transcript copies in the KB-1 consortium operated under a range of TCE respiration rates in continuously-fed, pseudo-steady-state reactors. These candidate biomarkers from KB-1 demonstrated a variety of trends in terms of transcript abundance as a function of respiration rate over the range: 7.7 × 10 to 5.9 × 10 microelectron equivalents per cell per hour (μeeq/cell∙h). Power law trends were observed between the respiration rate and transcript abundance for the main DMC RDase (VcrA) and the hydrogenase HupL (R² = 0.83 and 0.88, respectively), but not transcripts for 16S rRNA or three other RDases examined: TceA, BvcA or the RDase DET1545 homologs in KB1. Overall, HupL transcripts appear to be the most robust activity biomarker across multiple DMC strains and in mixed communities including DMC co-cultures such as KB1. The addition of oxygen induced cell stress that caused respiration rates to decline immediately (>95% decline within one hour). Although transcript levels did decline, they did so more slowly than the respiration rate observed (transcript decay rates between 0.02 and 0.03 per hour). Data from strain-specific probes on the pangenome array strains suggest that a minor DMC strain in KB-1™ that harbors a homolog preferentially recovered following oxygen stress relative to the dominant, -containing strain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/microorganisms6010013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5874627PMC
February 2018

Saccharomyces genome database informs human biology.

Nucleic Acids Res 2018 01;46(D1):D736-D742

Department of Genetics, Stanford University, Stanford, CA, 94305-5120 USA.

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and to provide this wealth of information to advance, in many ways, research on other organisms, even those as evolutionarily distant as humans. To build such a bridge between biological kingdoms, SGD is curating data regarding yeast-human complementation, in which a human gene can successfully replace the function of a yeast gene, and/or vice versa. These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkx1112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753351PMC
January 2018

Curated protein information in the Saccharomyces genome database.

Database (Oxford) 2017 01;2017(1)

Department of Genetics, Stanford University, Stanford, CA 94305, USA.

Due to recent advancements in the production of experimental proteomic data, the Saccharomyces genome database (SGD; www.yeastgenome.org ) has been expanding our protein curation activities to make new data types available to our users. Because of broad interest in post-translational modifications (PTM) and their importance to protein function and regulation, we have recently started incorporating expertly curated PTM information on individual protein pages. Here we also present the inclusion of new abundance and protein half-life data obtained from high-throughput proteome studies. These new data types have been included with the aim to facilitate cellular biology research.

Database Url: : www.yeastgenome.org.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/database/bax011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467551PMC
January 2017

Outreach and online training services at the Saccharomyces Genome Database.

Database (Oxford) 2017 01;2017(1)

Department of Genetics, Stanford University, Stanford, CA 94305, USA.

The Saccharomyces Genome Database (SGD; www.yeastgenome.org ), the primary genetics and genomics resource for the budding yeast S. cerevisiae , provides free public access to expertly curated information about the yeast genome and its gene products. As the central hub for the yeast research community, SGD engages in a variety of social outreach efforts to inform our users about new developments, promote collaboration, increase public awareness of the importance of yeast to biomedical research, and facilitate scientific discovery. Here we describe these various outreach methods, from networking at scientific conferences to the use of online media such as blog posts and webinars, and include our perspectives on the benefits provided by outreach activities for model organism databases.

Database Url: http://www.yeastgenome.org.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/database/bax002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467555PMC
January 2017

Integration of new alternative reference strain genome sequences into the Saccharomyces genome database.

Database (Oxford) 2016 1;2016. Epub 2016 Jun 1.

Department of Genetics, Stanford University, Stanford, CA, USA

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. To provide a wider scope of genetic and phenotypic variation in yeast, the genome sequences and their corresponding annotations from 11 alternative S. cerevisiae reference strains have been integrated into SGD. Genomic and protein sequence information for genes from these strains are now available on the Sequence and Protein tab of the corresponding Locus Summary pages. We illustrate how these genome sequences can be utilized to aid our understanding of strain-specific functional and phenotypic differences.Database URL: www.yeastgenome.org.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/database/baw074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4888754PMC
January 2017

The Saccharomyces Genome Database Variant Viewer.

Nucleic Acids Res 2016 Jan 17;44(D1):D698-702. Epub 2015 Nov 17.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkv1250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702884PMC
January 2016