New & Noteworthy
Deadline extended to April 22 for the 2024 Yeast Genetics and Genomics Course
April 09, 2024
The application deadline for the 2024 Yeast Genetics and Genomics Course has been extended to April 22 – don’t miss your chance! Significant financial aid may be available for trainees applying, covering up to 50% of the cost of the course!
Find all the details and application form at the CSHL Meetings & Courses site.
For over 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory, though the name didn’t include “Genomics” in the beginning. The list of people who have taken the course reads like a Who’s Who of yeast research, including Nobel laureates and many of today’s leading scientists.
This year’s instructors – Grant Brown, Soni Lacefield, and Greg Lang – have designed a course (July 23 – August 13) that provides a comprehensive education in all things yeast, from classical genetics through up-to-the-minute genomics. Students will perform and interpret experiments, learning about things like:
- Transformation & Genome Engineering
- Microscopy
- Manipulating Yeast
- Dissecting Tetrads
- Isolating Mutants
- Working with Essential Genes
- Synthetic Genetic Arrays
- Fluctuation Assays
- Whole Genome Sequencing & Analysis
- QTLMapping
Techniques have been summarized in the accompanying course manual, published by CSHL Press.
Who should attend? Scientists who aren’t part of large, well-known yeast labs are especially encouraged to apply – for example, professors and instructors who want to incorporate yeast into their undergraduate genetics classrooms; scientists who want to transition from mathematical, computational, or engineering disciplines into bench science; and researchers from small labs or institutions where it would otherwise be difficult to learn the fundamentals of yeast genetics and genomics.
What else goes on there? Besides its scientific content, the fun and camaraderie at the course is also legendary. In between all the hard work there are late-night chats at the bar and swimming at the beach. There’s a fierce competition between students at the various CSHL courses in the Plate Race, which is a relay in which teams have to carry stacks of 40 Petri dishes (used, of course). There’s also typically a sailboat trip, a microscopy contest, and a mysterious “Dr. Evil” lab!
The Yeast Genetics & Genomics Course is loads of fun – don’t miss out!
Categories: Conferences
Tags: dna, genetics, genomics, science
Changes to Saccharomyces cerevisiae GFF3 file
March 01, 2024
The saccharomyces_cerevisiae.gff contains sequence features of Saccharomyces cerevisiae and related information such as Locus descriptions and GO annotations. It is fully compatible with Generic Feature Format Version 3. It is updated weekly.
After November 2020, SGD updated the transcripts in the GFF file to reflect the experimentally determined transcripts (Pelechano et al. 2013, Ng et al. 2020), when possible. The longest transcripts were determined for two different growth media – galactose and dextrose. When available, experimentally determined transcripts for one or both conditions were added for a gene. When this data was absent, transcripts matching the start and stop coordinates of an open reading frame (ORF) were used.
Beginning in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition. This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023).
This is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource.
Categories: Announcements, Data updates
Tags: biology, blog, genetics, news, Saccharomyces cerevisiae
Educational Resources on the SGD Community Wiki
February 21, 2014
Did you know you can find and contribute teaching and other educational resources to SGD? We have updated our Educational Resources page, found on the SGD Community Wiki. There are links to teaching resources such as classroom materials, courses, and fun sites, as well as pointers to books, dedicated learning sites, and tutorials that can help you learn more about basic genetics. Many thanks to Dr. Erin Strome and Dr. Bethany Bowling of Northern Kentucky University for being the first to contribute to this updated site by providing a series of Bioinformatics Project Modules designed to introduce undergraduates to using SGD and other bioinformatics resources.
We would like to encourage others to contribute additional teaching or general educational resources to this page. To do so, just request a wiki account by contacting us at the SGD Help desk – you will then be able to edit the SGD Community Wiki. If you prefer, we would also be happy to assist you directly with these edits.
Note that there are many other types of information you can add to the SGD Community Wiki, including information about your favorite genes, protocols, upcoming meetings, and job postings. The Community Wiki can be accessed from most SGD pages by clicking on “Community” on the main menu bar and selecting “Wiki.” The Educational Resources page is linked from the left menu bar under “Resources” from all the SGD Community Wiki pages. For more information on this newly updated page, please view the video below, “Educational Resources on the SGD Community Wiki.”
Categories: New Data, Website changes
Tags: educational, genetics, Saccharomyces cerevisiae, teaching
Cancer’s Chromosomal Chaos Explained (Partly)
June 01, 2012
Because they have the wrong number of chromosomes, cancers can sample many different genetic combinations.
One reason cancer is so tricky to treat has to do with its adaptability. It can quickly try out new genetic combinations until it hits upon one that can survive whatever treatment a doctor is currently throwing at it. The result is return of the cancer after remission.
One way cancer is able to change its genetics so rapidly has to do with chromosome instability. The number of chromosomes in a cancer cell is much less stable than in a normal cell. This allows the cancer cell to constantly explore a wide range of chromosomal combinations.
It is still an open question how this dynamic instability happens. The gene-centric theory suggests that mutations in key genes are the main driving force. The chromosome-centric model says that having the wrong number of chromosomes is the critical component.
Distinguishing between these two models using cancer cells has proven difficult because these cells always have mutated genes. There is simply no way to look at just chromosome numbers in this system. This is where yeast can help.
In a recent paper published in PLoS Genetics, Zhu and coworkers used yeast to explore whether altered chromosome number was sufficient to explain chromosome instability. They found that chromosome numbers alone can explain some but not all of chromosomal instability.
The authors created various chromosomal combinations in yeast by sporulating isogenic triploid yeast cells. These cells had different numbers of genetically identical chromosomes. They then explored the stability of each chromosome number combination using both FACS and qPCR.
What they found was that chromosome number certainly impacted chromosomal stability. Chromosome number became less and less stable as the chromosome number veered further and further from the haploid state. Of course, once the cells became diploid, stability returned.
The authors explain this with the idea that there is only so much cellular machinery to move chromosomes to the proper place during mitosis. As more and more chromosomes are added to the cell, the machinery becomes increasingly taxed, resulting in more and more errors.
But once the diploid state is reached, all the genes are present to make twice as much mitotic machinery. Now stable chromosome segregation can happen.
This was the broad pattern Zhu and coworkers observed but it certainly wasn’t the whole story. The authors found islands of stability in the chromosomal chaos.
For example, very often when there were equal numbers of chromosome VII (ChrVII) and chromosome X (ChrX), the chromosome number was more stable than predicted. They explored this further and found evidence that suggested that at least part of this was due to the MAD1 gene on ChrVII and the MAD2 gene on ChrX.
Stable chromosome numbers required that these genes be present in a 1:1 ratio. Once the ratio strayed from one, chromosomal instability increased. But these genes don’t explain everything. There were unstable combinations where the MAD1/MAD2 ratio was correct. As might be expected, there are other gene combinations that can lead to instability as well.
So incorrect chromosome number alone can explain the chromosomal instability seen in cancer cells. But genes clearly play a role too, as evidenced by the islands of stability and the MAD1 gene and MAD2 genes. As usual, reality is probably a combination of the two models.
So it looks like chromosome number does play an important role in chromosomal instability. Too many chromosomes may overtax the mitotic machinery so that chromosomes end up mis-segregated.
by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics
Categories: Research Spotlight, Yeast and Human Disease
Tags: cancer, chromosomal instability, chromosome, genetics, Saccharomyces cerevisiae, yeast