Kryazhimskiy Lab @ UCSD

Our paper with Elizabeth Jerison and others on genetic variation in adaptability and pleiotropy in yeast now published in eLife.

Sandeep’s preliminary analysis of his sequencing data inspires cautious optimism that his method might be working. Work continues.

ENLACE high-school students interns Lesly Delgado and Kevin Longoria give their final presentation at the ENLACE symposium and leave the lab. Good job!

New postdoc Justin Shaffer (PhD from U. Arizona) and new technician Krypton Carolino join our lab and the Meyer lab to work on gene drive evolution. Welcome!

Internal proposal for the Pew Scholars program rejected, of course. Not surprised – there are several exceptional junior faculty at UCSD very much worthy of the nomination – but was curious about the reason. Well, here it is: lack of creativity and independence. Wow. Respectfully disagree.

Sergey gave a talk at GRC titled “Epistasis and genetic variation in adaptability in yeast”. Although it is hard to gauge people’s true feelings, many people made positive comments after the talk. One useful critical comment from a respected colleague: properly acknowledge prior work, especially when some of those authors are in the audience.

E-mail from Sandeep. Subject: “Data looks good!” Definitely a good day for the lab.

We finally got sequencing data from the Phase I of the TnSeq project. The first run was horrible (overclustering), but the data quality after the re-run is great. Will be analyzing over the next few weeks.

Sergey arrives at the Gordon Research Conference on Microbial Population Biology. Perhaps the best conference for exchanging ideas about evolution in microbes.

We got sequencing data from Sandeep’s genome-wide mutation rate project.

The lab welcomes two high-school students Kevin Longoria (Hilltop High School) and Lesly Delgado (Preparatoria Adolfo Lopez Mateos, Mexico) through the ENLACE program.

High-school student Joshua Chung joins the lab as an intern for the summer.

Sergey submits internal proposal for the Pew Scholars Program. Super-cool project on predicting evolution of antibiotic resistance! So, expecting rejection.

Sergey finishes teaching his first undergraduate course, Population Genetics. What a relief!

Sandeep finishes the sequencing library prep for his pilot experiment and submits it for sequencing. Fingers crossed!

Alena and Shohreh finish Phase I of the TnSeq experiment. Sequencing library submitted. Fingers crossed!

Our paper with Elizabeth Jerison and others on genetic variation in adaptability and pleiotropy in yeast is now on the bioRxiv.

Sean E. Guy joins the lab as a BS/MS student.

Sergey receives the Sloan Research Fellowship in Computational & Evolutionary Molecular Biology.

Sergey gives a talk at the San Diego Microbiology Group on the genetic variation in adaptability and pleiotropy – a work with Elizabeth Jerison and others that will soon appear on bioRxiv. Stay tuned!

Sandeep establishes a pipeline for full-genome sequence data analysis, largely based on previous work by Jeff Barrick and Ben Good.

Sandeep establishes a pipeline for RNAseq data analysis. Sadly, our first data set looks terrible: over 50% of reads map onto ribosomal RNA genes. We do not know why.

Nathan Palmer, a qBio student, starts his 10-week Hacker lab rotation in the SK Lab.

Californian Experimental Evolution Symposium 2017, organized by Sergey and Justin Meyer (with help from many
people), is a success! We had with 21 speakers and a total of 108 participants from all over California.

Got our first full-genome sequencing data from the UCSD IGM Genomics Center. Looks great!

First Microbial Experimental Evolution and Ecology (MEEE) meeting, a joint meeting between Daugherty, Dutton, Kryazhimskiy, and Meyer labs.

First SK Lab meeting! Georg presents his future project.

Dr. Sandeep Venkataram arrives from the Bay Area and joins the lab as a postdoc.

Hang Su finishes her internship. She made progress on RNAseq data analysis and the epistasis theory project.

Dr. Georg Rieckh arrives from Austria and joins the lab as a postdoc.

UCSD Division of Biology retreat.

Application for the Sloan fellowship submitted.

PhD student Alena Martsul arrives from Belarus, and joins the lab as a rotation student.

Eylul Karagoz finishes her internship in the lab. She made progress on growth curve analysis and constructed some strains.

Application for the internal competition for Searle Scholars Program rejected.

Hang Su, a visiting student from Shanghai Jiao Tong University joins the lab as a volunteer for 2 months.

Application for the internal competition for Searle Scholars Program submitted.

Zoe Ge finishes her internship. She calibrated plate-reader OD measurements against the Coulter Counter measurements and CFU measurements.

Medical student from Turkey Eylul Karagoz joins that lab as a volunteer for the summer.

We can count yeast cells with a Coulter Counter.

Marie Adomako finishes her rotation. She will join another lab. Fairwell beer at Rock Bottom Brewery.

Sophomore high-school student from Canyon Crest Academy Zoe Ge joins the lab as a volunteer for the summer.

Application for the Vilcek prize in Creative Promise in Biological Science submitted.

James S. McDonnell Foundation rejects our grant application.

We got a Sorensen 96-well plate semi-automated pipettor.

We got a Coulter Counter installed and working.

We can make electro-competent E.coli cells and transform them.

UCSD Biology PhD student Marie Adomako starts her rotation in the lab.

UCSD undergraduate Jia Huang joins the lab.

We can make RNA-seq libraries.

We can extract RNA.

Sergey gave his first lecture at UCSD as a guest at the BGGN223 course (Graduate Genetics). Topic: Epistasis and evolution. Slides are here.

Another fantastic news! Sandeep Venkataram, currently finishing his PhD at Stanford, also decided to join the lab. He will arrive in late September. With Alena, Georg and Sandeep, the next few years are sure to be very exciting and productive! Will have to start worrying about $$$.

We can transform yeast.

We can do PCR.

Great news! Georg Rieckh, currently finishing his PhD at IST Austria, decided to join the lab in the Fall 2016. We will expect his arrival in September.

Alena Martsul, currently at Belarusian State Technological University, will join the UCSD Biology PhD program through the Ecology,Behavior and Evolution section. Alena expressed interest in the SK Lab. So, we are very much hoping that she will join us in the Fall 2016.

Incubated shaker I26 arrives from Eppendorf. Heratherm incubator arrives from Thermo. We can now culture liquid and solid cultures of yeast.

Benchtop centrifuge 5810R and tabletop centrifuge 5427R arrive from Eppendorf.

Application for the internal competition for Packard fellowship rejected.

Application for the internal competition for Packard fellowship submitted.

Two undercounter freezers (will be kept at –20°C) and one large refrigerator (will be kept at +4°C) arrive from VWR.

Sergey arrives on UCSD campus. SK lab begins. Shohreh Hajizadeh joins the lab.