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From PhD to Life

March 15, 2017 By

By Craig W. Stropkay, (PhD ’13, Molecular and Cell Biology, Ren lab)

Reach for the stars, they said. You should definitely go get your PhD, you’d be great for it, they said. Well, I guess they did have a point. Pursuing my doctorate degree in Molecular Biology at Brandeis was definitely one of the most challenging things that I have ever had to do in my life. I could spend hours telling you about the long hours I spent trying to construct my dissertation or the countless nights that I had to wake up and drive into the lab from Medford just to “feed” my cells — but that’s not the point of this article. I want to talk about something that I wish was more openly discussed when I first started my journey towards pursuing a PhD. Something that I believe is important to anyone who is currently working their way towards earning their doctoral degree: a job.

Now I know what you may be thinking: why would I need to worry about a job when I know I will continue onto a postdoc and then a tenure-track academic post? Isn’t that what everyone does? That is precisely my point. Don’t get me wrong: there is absolutely nothing wrong with continuing a career in academia upon completion of your doctorate. It takes a lot of patience, skill, and dedication to remain in the field after you have literally spent years becoming an expert in everything dealing with Life Science. Maybe you’ve considered going that route, feeling that your choices are limited. Many people believe that apart from academia, their only “alternative” option is to go into industry and work in biotech or pharma.

Image from Naturejobs article

[Read more…]

Filed Under: General, grad students, jobs, labs, postdocs Tagged With: , , ,

Introduction to Microfluidics Technology – June 13-17, 2016

March 10, 2016 By

2016 MRSEC Summer Course Announcement

Registration for our annual, one-week summer course, “Introduction to Microfluidics Technology” at Brandeis University, near Boston, MA, is now open. The application deadline is March 31, 2016.

Introduction to Microfluidics Technology is a hands-on laboratory course sponsored by the National Science Foundation’s Bioinspired Soft Materials Research Science and Engineering Center (MRSEC) at Brandeis. It will be offered during the week of June 13 ‐ 17, 2016. The course is intended for graduate students, post docs, faculty, and industrial scientists/engineers interested in utilizing microfluidic technology in their work, both in the physical and life sciences. The course does not assume any specific prerequisites.

“Introduction to Microfluidics Technology” (June 13 – 17, 2016) will be taught by Dr. Nathan Tompkins.

The $750 fee covers course tuition, housing in double-occupancy rooms, and breakfast/lunch/coffee from Monday through Friday. Single rooms are not available. Local students who do not need housing will pay a non-resident fee of $500 (cash and check only please).

More information is available.

Filed Under: grad students, labs, postdocs Tagged With: , , , ,

Taste and smell are intertwined in the rat brain

October 7, 2015 By

A recent paper in Current Biology titled “A Multisensory Network for Olfactory Processing” from the Katz Lab in Psychology tackles the question of where in rat brain the senses of taste and smell are processed, and just how distinct the two senses are. In addition to Katz, authors on the paper include former postdoctoral fellows Joost Maier and Jennifer Li, as well as Neuroscience graduate student Meredith Blankenship.

The paper discusses their finding that the tongue and the nose work together to help you decide what potential foods are actually good to eat. This intimate cooperation leads to an intertwining and interdependence of function; everyone who has had a cold knows that things don’t taste right when the sense of smell is blocked (by snot). They now show that the opposite is true as well–specifically, that the part of the cortex known to be responsible for taste is also required for the sense of smell.

Recordings from taste and olfactory cortex

First, they show that there is a strong neural connection between taste cortex (GC) and olfactory cortex (PC): this connection ensures that information about tastes in the mouth reaches the latter from the former, but also ensures that a constant chatter of action potentials (the language of the brain) flows between the two, even in the total absence of a substance on the tongue. Thus, switching those taste cortex neurons off both removes any evidence of taste information in olfactory cortex AND changes the way olfactory cortex deals with odor information arriving directly from the nose. The result of this impact is striking: a rat utterly fails to recognize a familiar odor when taste cortex is silent; the taste system is a part of the smell system.

The implications of this finding for neuroscience are far-reaching. It suggests a major breakdown of the basic dogma that the different sensory systems, each of which originate in distinct sense organs (the nose for smell, the tongue for taste) process their input independently. In fact, the brain likely doesn’t “see” tastes and smells as separate at all, but as unified parts of holistic objects…FOOD.

Maier JX, Blankenship ML, Li JX, Katz DB. A Multisensory Network for Olfactory Processing. Curr Biol. 2015.

Filed Under: labs, Neuroscience, Psychology Tagged With: , , , ,

TIDAL-Fly: a new database resource of Transposon Landscapes for understanding animal genome dynamics.

August 17, 2015 By

We tend to think of our genomes as nicely-ordered encyclopedias,  curated with only useful information that makes up our genes.  In actuality, nature and evolution is extremely sloppy.  All animal genomes, from us humans to the simple fruit fly, are littered with genetic baggage.  This baggage is sizeable, making up at least 11% of the fly genome and more than 45% of our genome.  The scientific term for this baggage is transposable elements (TEs) or transposons, which are mobile entities that must copy themselves to other places of the genome to ensure their survival during animal evolution.

Because there are so many copies of transposons, they can be difficult to analyze by most standard genetic methods. Brandeis postdoctoral fellow Reazur Rahman and a team in Nelson Lau’s lab have formulated a new tool called the Transposon Insertion and Depletion AnaLyzer (TIDAL). TIDAL aims to provide an accurate and user-friendly program to reveal how frequently transposons can move around in animal genomes.  Currently, the TIDAL tool has been applied to over 360 fruit fly genomes that have been sequenced and deposited in the NIH NCBI Sequencing Read Archive.  The outputs from this program are available to the whole genetics community through the TIDAL-FLY database.

tidal fly banner

The TIDAL-Fly database will allow geneticists to pick their favorite fly strain and see if a transposon has landed near to their gene and perhaps affect gene expression. Fruit flies are key model organisms utilized by many researchers, including here at Brandeis, to study human diseases, from infertility to insulin signaling to aging to sleep disorders.  Since these new transposon insertions are not available in the standard genome databases, this tool and website may provide answers to previously puzzling genetic effects not revealed by typical DNA sequencing studies.  It is Reazur’s and the Lau lab’s goal to continue updating the TIDAL-Fly database with more genomes as fly genome re-sequencing becomes easier and easier to perform.

see also: Rahman R, Chirn GW, Kanodia A, Sytnikova YA, Brembs B, Bergman CM, Lau NC. Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. Nucleic Acids Res. 2015.

Filed Under: Biology, postdocs Tagged With: , , , , , , ,

Putting “umpolung” to work in synthesis of nitrogen-bearing stereocenters

July 25, 2015 By

Professor Li Deng‘s lab in the Brandeis Chemistry Department has recently published a high-profile paper in Nature, disclosing an important advance in the chemical synthesis of organic molecules containing nitrogen. Li Deng writeup 1

A great number of important drugs contain at least one nitrogen atom connected to a “stereogenic” carbon atom. Stereogenic carbons are connected to four different groups, making possible two different configurations called “R-” or “S-”. In synthesizing a drug, it can be disastrous if the product does not have the correct R/S configuration.  For instance, the morning-sickness drug Thalidomide caused birth defects in ~10,000 children because it was a mixture of R and S molecules.Li Deng writeup 2

Selective preparation of only R or only S molecules containing nitrogen is a major challenge in organic chemistry. Many recent approaches have formed such stereocenters by use of an electron rich “nucleophile” to attack an electron poor “imine”. Deng is now the first to report an unconventional strategy in which the polarity of the reaction partners is reversed. In the presence of base and a creatively designed catalyst, the imine is converted into an electron rich nucleophile, and can attack a variety of electrophiles. Deng’s catalysts are effective in minute quantities (as low as 0.01 % of the reaction mixture), and yield products with R- or S- purities of 95-98 %.

In addition to Professor Deng, authors on the paper included former graduate student Yongwei Wu PhD ’14, current Chemistry PhD student Zhe Li, and Chemistry postdoctoral associate Lin Hu.

Wu Y, Hu L, Li Z, Deng L. Catalytic asymmetric umpolung reactions of imines. Nature. 2015;523(7561):445-50. (commentary)

Filed Under: chemistry Tagged With: , , , , , , , ,

Summer 2015: “Introduction to Microfluidics Technology”

February 27, 2015 By
Students are in the cleanroom during training.

Students in the clean room during training

The annual one-week course offered during the summer of 2015 is “Introduction to Microfluidics Technology” (June 22 – 26). It will be held at Brandeis University and sponsored by the National Science Foundation’s Bioinspired Soft Materials Research Science and Engineering Center (MRSEC) at Brandeis. It is intended for graduate students, post docs, faculty and industrial scientists and engineers interested in utilizing microfluidic technology in their work, in both physical sciences and life sciences, and does not assume any specific prerequisites.

SUMMER COURSE ANNOUNCEMENT 2015

Microfluidic Xmas Tree

Filed Under: labs, postdocs Tagged With: , , ,

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