NeuroSeq and cell diversity in the nervous system

The central nervous system has the most cellular diversity of any organ in the body, but how does this diversity arise?

While the presumption is that genetic programs specify each neuron type, our understanding of these programs is in its infancy. To begin uncovering the underlying design principles of neuronal architecture in the brain, scientists from the Nelson Lab at Brandeis University and the HHMI Janelia Research Campus jointly formed the NeuroSeq project to profile genetic programs in a monumental number of neurons throughout the nervous system. Selected neurons were from transgenic animals to facilitate access among the scientific community for future functional studies. While single cell sequencing is the most popular method for transcriptome profiling, its technical limitations only provide a shallow view of molecular profiles. To go deeper, the NeuroSeq program assessed transcription in pools of nearly 200 genetically identified mouse cell types. NeuroSeq captured 80% of single gene copies and could even assess splice isoforms.

What did the NeuroSeq effort find?

Interestingly, two unique classes of genes lie at the heart of adult neuronal identity. Homeobox transcription factors and long genes explain a great deal of the neuronal diversity in the central nervous system. This extends the role of homeobox genes well beyond development and into neuronal identity maintenance. It also highlights long genes as an important class of neuronal identity effectors. Long genes are long due to insertion of foreign elements, and they come with costs, namely increased energy consumption and risk of mutations. These costs seem to be overcome by the benefits of neuronal diversification. We are excited to spotlight the NeuroSeq project in providing a unique resource for future discoveries concerning neuronal diversity and function.

The data resource is available at neuroseq.janelia.org, and the findings are described in a recent paper in eLife. Brandeis-affiliated authors on the paper include Professor Sacha Nelson, former postdoc Ken Sugino PhD ’05 (now at HHMI Janelia), current postdoc Erin Clark, and former research scientist Yasuyuki Shima.

Genome illustration

Undergrad summer research funding, 2019

The Division of Science announces the opening of the Division of Science Summer Undergraduate Research Fellowship competition for Brandeis students who will be doing undergraduate research in Summer 2019.  These fellowships are funded by generous alumni donations and by grants. Winners will get $5000 stipends for the summer.

Some funding programs have changed since last year; please see the Div Sci website for details of the programs which fund students across all the sciences. We expect to fund about 30 students this summer.

The due date for applications  is February 27, 2019  at 6:00 PM EST.

Students who will be rising Brandeis sophomores, juniors, or seniors in Summer 2019 (classes of ’20, ’21 and ’22), who in addition are working in a lab in the Division of Science at the time of application, are eligible to apply. A commitment from a Brandeis faculty member to serve as your mentor in Summer 2019 is required.

The Division of Science Summer Program will run from June 3 – Aug 9, 2019. Recipients are expected to be available to do full time laboratory research during that period, and must commit to presenting a poster at the final poster session (SciFest IX) on Aug 8, 2019.

Interested students should apply online (Brandeis login required). Questions that are not answered in the online FAQs may be addressed to Steven Karel <divsci at brandeis.edu>.

Rodal lab find surprising new link between inflammation and Lowe Syndrome

Could a disease with symptoms in the brain, eyes, and kidneys actually be caused by problems with immune cells? A team of scientists from the Rodal Lab, co-first authored by Steven Del Signore and Sarah Biber and including three Brandeis undergraduates (Katy Lehmann ‘16, Stephanie Heimler ‘17, and Ben Rosenfeld ’18), think this just might be the case with Lowe Syndrome, in a new paper published Oct 13th in PLOS Genetics.

Patients with Lowe Syndrome suffer from kidney failure, congenital cataracts, and several neurological problems including intellectual disability and seizures. Scientists have known for some time that the disease is caused by mutations in a gene called OCRL, but remain unsure how its loss causes such a diverse array of symptoms. A big problem has been that OCRL appears to do many different jobs inside cells, including controlling how they divide, how they sense their surroundings, and how they store and transport materials inside small packages called endosomes.

Fly immune cells showing the tracks of moving endosomes. Single tracks represent the path of individual endosomes over time.

To try to solve this mystery, a team of researchers from the Rodal lab used the fruit fly, which has its own version of the OCRL gene and allowed the investigators to perform powerful genetic experiments to figure out precisely what OCRL is doing, and where. To do this, the group created a fly missing its OCRL gene. They were surprised to find that, rather than eye or neurological defects, loss of OCRL hyper-activated cells of the innate immune system. The innate immune system is the first line of defense against infection in humans (and the only defense in fruit flies), when cells release inflammatory signals that mobilize specialized cells to attack invading pathogens.

The team determined that OCRL is required in one of these specialized immune cells in the fly, and that the immune-cell activation was caused by problems in a particular step of intracellular transport. Every cell of the body has its own postal service, which is used to pack and ship signals that tell the cell or its neighbors to grow, divide, or jump into action (see movie here to watch endosomes moving inside living fly immune cells). The OCRL mutant immune cells had a problem in a key step that controls whether signals get thrown in the trash or shipped outside the cell, and this caused the immune activation.

How do these findings relate to Lowe Syndrome? The authors think these results suggest a possible cause for the seizures that patients experience. When similar immune-like cells in the brain release excessive inflammatory signals, it can cause several forms of epilepsy. Further, OCRL has been linked to at least one mouse model of epilepsy. Going forward, the researchers will try to identify which immune signals are responsible, and how these findings translate to human cells.

Del Signore SJ (*), Biber SA (*), Lehmann KS, Heimler SR, Rosenfeld BH, Eskin TL, Sweeney ST, Rodal AA. dOCRL maintains immune cell quiescence by regulating endosomal traffic. Plos Genet. 2017;13(10):e1007052.

 

 

Rosbash, Hall & Young Awarded Nobel Prize

Michael Rosbash, Nobel Laureate

Brandeis researchers Michael Rosbash, the Peter Gruber Endowed Chair in Neuroscience, and Professor Emeritus of Biology Jeffrey C. Hall have received this year’s Nobel Prize in Physiology or Medicine, together with Michael Young from The Rockefeller University,  for their pioneering work on the molecular mechanisms controlling circadian rhythm.

More about Michael

More about Jeff

More about Drosophila

 

Research Funding For Undergrads: MRSEC Summer Materials Undergraduate Research Fellowships

The Division of Science wishes to announce that, in 2017, we will offer seven MRSEC Summer  Materials Undergraduate Research Fellowships (SMURF) for Brandeis students doing undergraduate research, sponsored by the Brandeis Materials Research Science and Engineering Center.

The fellowship winners will receive $5,000 stipends (housing support is not included) to engage in an intensive and rewarding research and development program that consists of full-time research in a MRSEC lab, weekly activities (~1-2 hours/week) organized by the MRSEC Director of Education, and participation in SciFest VII on Aug 3, 2017.

The due date for applications is February 27, 2017, at 6:00 PM EST.

To apply, the application form is online and part of the Unified Application: https://goo.gl/9LcSpG (Brandeis login required).


Eligibility

Students are eligible if they will be rising Brandeis sophomores, juniors, or seniors in Summer 2017 (classes of ’18, ’19, and ’20). No prior lab experience is required. A commitment from a Brandeis MRSEC member to serve as your mentor in Summer 2017 is required though. The MRSEC faculty list is: http://www.brandeis.edu/mrsec/people/index.html

Conflicting Commitments
SMURF recipients are expected to be available to do full time laboratory research between May 30 – August 4, 2017. During that period, SMURF students are not allowed to take summer courses, work another job or participate in extensive volunteer/shadowing experiences in which they commit to being out of the lab for a significant amount of time during the summer. Additionally, students should not be paid for doing lab research during this period from other funding sources.

Application Resources
Interested students should apply online (Brandeis login required). Questions that are not answered in the online FAQ may be addressed to Steven Karel <divsci at brandeis.edu>.

Brandeis University and NCBI to host Genomics Hackathon in April

Brandeis University is partnering with NCBI to host a Boston-area genomics hackathon April 25-27, 2016. Two previous hackathons held at NCBI successfully integrated scientists from across the country with different skill sets to tackle challenges in RNA-seq and genomics.

The August 2015 NCBI hackathon identified gaps in usability of current RNA-seq analysis tools and in just three days created software that greatly improved ease-of-use.

The August 2015 NCBI hackathon identified gaps in usability of current RNA-seq analysis tools and in just three days created software that greatly improved ease-of-use.

NCBI hackathons identify gaps in the current state-of-the-art analysis pipelines and outline feasible solutions to bring users, especially novices, closer to understanding genomic data and analysis. This hackathon will be highly cooperative: teams of 5-6 individuals will work on non-overlapping projects and share their expertise in a collaborative way. Projects planned for this session include:

  • Network Analysis of Variants
  • Structural Variation
  • RNA-Seq
  • Streaming Data and Metadata
  • Neuroscience/Immunity
  • Command-line user-interface design

The hackathon is an exciting opportunity to meet researchers in similar fields at different institutions, learn new ways of applying your work, and work with a team to contribute original work to the genomics field. Participants are also provided with the opportunity to publish their work in a newly-created F1000 hackathon channel.

Brandeis University and NCBI invite all genomics researchers to apply and visit the NCBI announcement for more information. Participants will need to bring their own laptops to the event and have some knowledge of a scripting language (Python, PERL, Shell, etc).

Please apply by 5:00 PM March 22, 2016.

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