You are here: Home / Biochemistry

Using PhADE in single molecule fluorescence imaging

September 9, 2012 By

Anna Loveland, a postdoc in the Grigorieff Lab, has a new paper, “A general approach to break the concentration barrier in single-molecule imaging” that appeared today in Nature Methods online. The paper is based on her PhD work, which was done jointly in the labs of Antoine van Oijen and Johannes Walter at Harvard.

Single-molecule fluorescence imaging is often incompatible with physiological protein concentrations, as fluorescence background overwhelms an individual molecule’s signal. Loveland et al. employ a new imaging approach called PhADE (photoactivation, diffusion and excitation). A protein of interest is fused to a photoactivatable protein (mKikGR) and introduced to its surface-immobilized substrate. After photoactivation of mKikGR near the surface, rapid diffusion of the unbound mKikGR fusion out of the detection volume eliminates background fluorescence, whereupon the bound molecules are imaged. The authors labeled the eukaryotic DNA replication protein flap endonuclease 1 with mKikGR and added it to replication-competent Xenopus laevis egg extracts. PhADE imaging of high concentrations of the fusion construct revealed its dynamics and micrometer-scale movements on individual, replicating DNA molecules. Because PhADE imaging is in principle compatible with any photoactivatable fluorophore, it should have broad applicability in revealing single-molecule dynamics and stoichiometry of macromolecular protein complexes at previously inaccessible fluorophore concentrations.

Anna B Loveland, Satoshi Habuchi, Johannes C Walte & Antoine M van Oijen (2012) A general approach to break the concentration barrier in single-molecule imaging. Nature Methods

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

Riboswitches and fluoride

September 7, 2012 By

Ronald Breaker (Yale and HHMI) gave an inspiring talk today to kick off this year’s Biochemistry-Biophysics Friday Lunchtime Pizza Talks series, discussing his lab’s work on Riboswitches: Biology’s Ancient Regulators. If you missed the talk, here’s a review that might help you catch up.

Breaker ended the talk by discussing the fluoride-sensing riboswitch, and pointing to the new avenues for research to which this called attention. Coincidentally(?), a new paper in PNAS is out today from Chris Miller‘s lab here at Brandeis on exactly that — take a look at Stockbridge et al., Fluoride resistance and transport by riboswitch-controlled CLC antiporters.

 

Filed Under: Biochemistry, labs, seminars Tagged With: , , , , , ,

Tenure track faculty position, Biochemistry

August 31, 2012 By

The Department of Biochemistry at Brandeis University invites applications for a tenure-track faculty position, to begin Fall, 2013. We are searching for a creative scientist who will establish an independent research program and who in addition will maintain a strong interest in teaching Biochemistry at the undergraduate and graduate levels. The research program should address fundamental questions of biological, biochemical, or biophysical mechanism.

Brandeis University offers the rare combination of a vigorous research institution in a liberal-arts college setting. The suburban campus is located 20 minutes from Boston and Cambridge and is part of the vibrant community of academic and biotechnology centers in the Boston area.

The application should include a cover letter, curriculum vitae, statement of research accomplishments and future plans, and three letters of reference. Applications will be accepted only through https://academicjobsonline.org/ajo/jobs/1813. Additional inquiries may be directed to Chris Miller, Professor of Biochemistry (cmiller@brandeis.edu).

First consideration will be given to applications received by December 1, 2012. Brandeis University is an Equal Opportunity Employer, committed to building a culturally diverse intellectual community. We particularly welcome applications from women and minority candidates.

Filed Under: Biochemistry, jobs Tagged With: , , , ,

What a failed drug does (and is there hope for latrepirdine?)

August 17, 2012 By

Latrepirdine (Dimebon) was initially used as an antihistamine drug in Russia. It was later found to be neuroprotective, and entered phase II clinical trials in the US for both Alzheimer’s disease and Huntington’s disease. However, Dimebon failed in a US-based phase II replication trial of a prior successful Russian phase II trial of mild-to-moderate AD. Given the initial promise of the drug and split results,  as well as the lack of treatments for neurodegenerative diseases, there in is significant interest in understanding the underlying molecular mechanism(s) for the drug’s effects.

In a paper appearing this week in Molecular Psychiatry, Brandeis researchers in the Petsko-Ringe lab, including postdoc Shulin Ju and undergraduate Jessica Liken ’11, used yeast models of neurodegenerative disease associated proteins to show that Dimebon specifically protects yeast from the cytotoxiciy of α-synuclein, a protein involved in Parkinson’s disease. They further showed that protection is mediated through its up-regulation of autophagy pathway. In collaboration with Sam Gandy‘s group at Mount Sinai School of Medicine, these findings were further confirmed and validated in neuronal cell and animal models.

Given these observations, disparities in the contribution of α-synuclein to the neuropathology between the Russian and US Dimebon studies might also explain, at least in part, the inconsistency of the cognitive benefit in the two trials. If this speculation is correct, then it may be interesting to test for benefits of Dimebon in treating synucleinopathies such as Parkinson’s disease, Lewy body dementia, REM sleep disorder and/or multiple system atrophy.

see also: press release from Mt. Sinai Alzheimer’s Diesease Research Center

Steele JW (*), Ju S(*), Lachenmayer ML(*), Liken J, Stock A, Kim SH, Delgado LM, Alfaro IE, Bernales S, Verdile G, Bharadwaj P, Gupta V, Barr R, Friss A, Dolios G, Wang R, Ringe D, Protter AA, Martins RN, Ehrlich ME, Yue Z, Petsko GA, Gandy S. Latrepirdine stimulates autophagy and reduces accumulation of alpha-synuclein in cells and in mouse brain. Molecular psychiatry. 2012.

Steele JW(*), Lachenmayer ML(*), Ju S, Stock A, Liken J, Kim SH, Delgado LM, Alfaro IE, Bernales S, Verdile G, Bharadwaj P, Gupta V, Barr R, Friss A, Dolios G, Wang R, Ringe D, Fraser P, Westaway D, St George-Hyslop PH, Szabo P, Relkin NR, Buxbaum JD, Glabe CG, Protter AA, Martins RN, Ehrlich ME, Petsko GA, Yue Z, Gandy S. Latrepirdine improves cognition and arrests progression of neuropathology in an Alzheimer’s mouse model. Molecular psychiatry. 2012.

Filed Under: Biochemistry, labs Tagged With: , , , , , , , ,

Unraveling mutations in pediatric brain cancer

July 26, 2012 By

Medulloblastoma is the most common malignant brain tumor of childhood, with an overall mortality of 40 to 50 percent. Surviving children often have significant long-term cognitive and physical sequelae resulting from existing treatments. Therefore, identifying and understanding the genetic events that drive these tumors is critical for the development of more effective therapies.

In the 2 August issue of the journal Nature, Brandeis Biochemistry faculty member Daniel Pomeranz Krummel contributed his structural biological expertise in collaboration with colleagues at Children’s Hospital Boston, Dana-Farber Cancer Institute, Harvard University, the Broad Institute (MIT), Stanford and the Hospital for Sick Children in Toronto. The paper titled, “Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations,” unravels a landscape of mutations that are peculiar to medulloblastomas. This paper represents a landmark study of medulloblastomas. More specifically, Pomeranz Krummel’s collaborators noticed that a protein called DDX3X had numerous mutations in medulloblastoma. Pomeranz Krummel was able to create a structural model of DDX3X that provided insight into the functional significance of the critical mutations in children with medulloblastoma (below, image).

DDX3X is an ATP-dependent RNA helicase. RNA helicases are fascinating proteins that function to drive the restructuring of RNA and/or RNA-protein assemblies, and have proven to be of great importance in cancer biology and HIV research. Pomeranz Krummel’s long-standing interest is in RNA-protein interactions and application of methods to visualize the enzymes critical to processing of RNA in the human cell. Thus, thinking about the structure-function relationship of this RNA helicase DDX3X was a problem of much interest to Pomeranz Krummel. This collaboration involved forging links between basic and translational scientists, thus giving rise to promising new horizons of treatment options for children with medulloblastoma.

 

 

Filed Under: Biochemistry, labs Tagged With: , , , ,

Methylgloxal and anxiety disorder

May 19, 2012 By

methylglyoxal, aka pryuvaldehyde

A recent paper in The Journal of Clinical Investigation by researchers from the University of Chicago, working together with Assistant Research Professor of Biochemistry Leigh Plant from Brandeis, reveals a new mechanism for anxiety disorders involving the metabolite methylglyoxal (MG) (right).  The researchers investigated the effect of Glyoxalase 1 (Glo1) expression in mice. Increasing Glo1 copy number, and hence expression, in mice increased anxiety-like behavior. Since Glo1 metabolizes MG, they looked for a direct effect by administering MG, and found it had an anxiolytic effect in the mouse model (n.b.. MG is toxic, so don’t take it to treat anxiety). Inhibitors of Glo1 might therefore have anxiolytic effects, which they showed for the inhibitor S-bromobenzylglutathione cyclopentyl diester

Electrophysiology experiments were conducted to elucidate the mechanism of action of MG, suggesting that it had a GABAergic effect in vivo, and specifically that it is an agonist of the GABAA receptor in multiple neuron types.

So why is a relatively reactive small molecule, normally considered a by-product of glycolysis in animals, acting at neuronal receptors? Can this be exploited with pharmacological methods? What other functions does methylglyoxal have in the nervous system?  It may have many — another very recent paper in Nature Medicine suggests a role for MG in pain sensitivity and diabetic neuropathy, so there may be many interesting parts to this story.

Pre-med undergraduates should take note — keeping track of all those metabolites in glycolysis that you learn about in introductory biochemistry is far from irrelevant to modern medicine!

 

 

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

2012 Brandeis Achievement Awards

April 27, 2012 By

Four out of five 2012 recipients of Brandeis Achievement Awards are science majors.

  • Fiona Aguilar  (biology, Haber lab)
  • Daniel Boyle (biochemistry and neuroscience, Lovett lab)
  • Ariana Boltax (biology and chemistry)
  • Sara Shahanaghi (economics and mathematics)

For the full story, see Brandeis NOW.

Filed Under: awards, Biochemistry, Biology, chemistry, Undergrads Tagged With: ,

Surgeon-scientist Friedlander ’87 to speak on Wednesday, Feb 29

February 24, 2012 By

Robert Friedlander, MD, Chairman and Professor of Neurological Surgery at Univ. Pittsburgh Medical Center, will visit campus on Wednesday, Feb 29. Dr. Friedlander is a graduate of the Biochemistry Department at Brandeis (BA/MA, 1987). He graduated from Harvard Medical School in 1991 followed by a residency in neurosurgery (also at Harvard).

Dr. Friedlander is a leading scientist investigating the mechanisms of neuronal cell death in a broad spectrum of neurological diseases. His work has developed new approaches for the treatment of stroke, brain and spinal cord injury as well as Huntington’s disease and ALS (Lou Gehrig’s disease). He is one of a very select group of authors to have been invited by the New England Journal of Medicine to write both a basic science review (mechanisms of neuronal cell death), as well as a clinical review (management of AVMs).

Friedlander will lecture on the Role of CASPASES in Neurologic Issues in the Joint Biology/Biochemistry Seminar Series at 4:00 pm in Gerstenzang 121.

Friedlander has also kindly agreed to be available to talk to pre-medical students who might want to hear about medical school, the ins-and-outs of an academic career as a surgeon scientist, and strategies for getting into med school. The meeting will be held at 5:15 pm on Wednesday, also in Gerstenzang 121.

 

Filed Under: Biochemistry, Biology, seminars Tagged With: , , ,

Protected by Akismet
Blog with WordPress

Welcome Guest | Login (Brandeis Members Only)