SGD Newsletter, Summer 2023

About this newsletter:
This is the Summer 2023 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can view this newsletter as well as previous newsletters, on our Community Wiki.

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Thousands of SGD users run their data against SGD data every day and this can put a heavy load on servers. To improve performance, we have invested in dockerizing our full database so that loads can be better distributed in real time. We are currently at the stage of testing the frontend of our software to look for bugs, which we do for every update. The next phase will entail dockerizing and testing the backend, so we can improve our data uploads.

We hope to see improved performance for you, our users. If you happen to notice faster speeds or fewer hiccups…we’d be quite glad to hear about it! (A message to the SGD Helpdesk reaches us all.)

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SGD triages all the papers that come out each week to find those that add value to our database. In the process, we are continually impressed by the quality of the research done in yeast and we decided it was time to bring back the “Research Spotlight” as a post that appears on the SGD home page in the "New and Noteworthy" section.

The goal is to highlight interesting new work that either continues an ongoing story, makes a twist in the story we all thought we knew (such as an unexpected side gig for a protein), or offers a new technique or perspective for mining the most value from the yeast model. There are numerous intriguing papers in yeast, including those shedding light on human disease by dissecting the cellular biology in yeast, using our remarkable tools, so as to identify new targets or drugs for humans.

As the model organism databases move toward forming the Alliance of Genome Resources, which will streamline and integrate our combined data, we expect this power to make useful connections will only grow.

Upcoming Yeast Genetics Meeting

We may have forgotten how to talk to other people in person, but the Yeast Genetics Meeting is going to give us a chance to practice. The meeting will be held in person for the first time in four years at UCLA, from August 17-21. We hope to see you there!

Of course, it being the COVID era, you can also register to attend virtually, and the cost will not be higher for late registration.

A big congratulations to the award recipients who are the invited speakers for 2022. Tom Petes is receiving the YGM Lifetime Achievement Award, Trisha Davis is giving the Winge-Lindegren Address, Maya Schuldiner is receiving the Ira Herskowitz Award, and Michael Desai is giving the Lee Hartwell Lecture. Learn more about these researchers and their work at the YGM website.

SGD collaborates to add new data links

On the topic of integration, SGD is happy to integrate new data sets that add value to the database. We have the ability to incorporate these datasets directly from research groups, rather than from publications. Most recently we integrated the AlphaFold predicted 3D structures for complexes as links on the SGD Interaction and Protein pages. It is now possible to look for your own proteins or complexes of interest and go straight to the predicted structure.

Another recent example is AnalogYeast, a dataset of analogs to yeast proteins in non-fungal organisms predicted by sequence similarity, which was created by the Schuldiner lab. Links have been added to the Resources sections of SGD Protein and Homology pages.

We are open to more of this collaboration and would be glad to hear from community members who think they have data useful to other researchers. Get in touch!

microPublications - latest yeast papers

​microPublication Biology is part of the emerging genre of rapidly-published research communications. We are seeing a strong set of microPublications come through the database and are glad for this venue to publish brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.

Consider microPubublications when you have a result that doesn't necessarily fit into a larger story, but will be of value to others.

Latest yeast microPublications:

• Daraghmi MM, et al. (2023) Macro-ER-phagy receptors Atg39p and Atg40p confer resistance to aminoglycoside hygromycin B in S. cerevisiae. MicroPubl Biol 2023
• Domeni Zali G and Moriel-Carretero M (2023) Auxin alone provokes retention of ASH1 mRNA in Saccharomyces cerevisiae mother cells. MicroPubl Biol 2023
• Hiestand L, et al. (2023) Chemical Genetics Screen of EVP4593 Sensitivity in Budding Yeast Identifies Effects on Mitochondrial Structure and Function. MicroPubl Biol 2023
• Liu L, et al. (2023) A role for ion homeostasis in yeast ionic liquid tolerance. MicroPubl Biol 2023
• Longan ER, et al. (2023) ADATscan - A flexible tool for scanning exomes for wobble inosine-dependent codons reveals a neurological bias for genes enriched in such codons in humans and mice. MicroPubl Biol 2023
• Miles S, et al. (2023) BY4741 cannot enter quiescence from rich medium. MicroPubl Biol 2023
• Moresi NG, et al. (2023) Caffeine-tolerant mutations selected through an at-home yeast experimental evolution teaching lab. MicroPubl Biol 2023
• Shortt C, et al. (2023) A simple and accessible CRISPR genome editing laboratory exercise using yeast. MicroPubl Biol 2023

List of all yeast microPublications on the SGD website.

Alliance of Genome Resources - Release 5.4

The Alliance of Genome Resources, a collaborative effort from SGD and other model organism databases (MOD), released version 5.4 this past April.

• SimpleMine, which allows you to perform basic batch searches of Alliance data, has a new URL: https://www.alliancegenome.org/agr_simplemine.cgi

• For fans of Facebook, The Alliance of Genome Resources has a new Facebook page:

https://www.facebook.com/AllianceOfGenomeResources

Upcoming Conferences and Courses

• Pacific Northwest Yeast Club
  • Western Washington University, Bellingham, WA
  • July 20, 2023

• Yeast Genetics & Genomics - modern and intensive laboratory course that teaches students the full repertoire of genetic and genomic approaches needed to dissect complex problems using the yeast Saccharomyces cerevisiae
  • Cold Spring Harbor Laboratory, NY
  • July 26 - August 15, 2023

• 2023 Northeast Regional Yeast Meeting (NERY 2023)
  • Cornell University, Ithaca, NY
  • July 27 to July 28, 2023

• ICYGMB31 - 31st International Conference on Yeast Genetics and Molecular Biology
  • Florence, Italy
  • August 20 to August 25, 2023

• 38th Small Meeting on Yeast Transport and Energetics (SMYTE)
  • Blankenberge, Belgium
  • September 13 to September 17, 2023

• CSH Asia: Yeast and Life Sciences
  • Kunibiki Messe (Shimane Prefectural Convention Center), MATSUE, JAPAN
  • October 09 to October 13, 2023

• ISSY2023: Yeast Biotech 2.0
  • National Wine Centre of Australia, Adelaide SA, Australia
  • November 27 to December 01, 2023

• TAGC2024 The Allied Genetics Conference
  • National Harbor | Washington DC Metro Area
  • March 05 to March 10, 2024

• 32nd Fungal Genetics Conference
  • Asilomar Conference Grounds, Pacific Grove, CA
  • March 12 to March 17, 2024

• ICY2024: 16th International Congress on Yeasts
  • Cape Town International Convention Centre, Cape Town, South Africa
  • September 29 to October 03, 2024