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Life Sciences Division Newsletter
December 2012
In this issue:
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Scientific News »
- Developing a Quick Way to ID People Exposed to Ionizing Radiation »
- Medical Imaging Goes Underground to Map Soil Changes »
- Lab Scientists Help Develop Promising Therapy for Huntington’s Disease »
- Protein Folding Funnels Apply to Self-Assembly; Should Benefit Biomimicry and Nanosynthesis »
- New Study of Response to Low-Dose Radiation »
- Patent on Semiconductor Material Issued to Stephen Derenzo and Team »
- In the News »
- Recent Publications »
- 2013 Lab Directed Research and Development Awards Announced »
- Celniker Named 2012 AAAS Fellow »
- Researchers Claim Their R&D100 Awards »
- Life Scientists Honored by American Society for Cell Biology »
- Bizarri Wins New Award for Ba-based Scintillators Project »
- Life Sciences Builds Gingerbread House and Support for Ethiopian Project at Holiday Party »
- Early Career Scientists Society Elections Held »
- Final Results of Runaround Race Posted; Winners in Life Sciences »
- Bay Area Congressional and State Legislative Officials' Staff Visit Lab »
- Lab Hosts Thousands at Open House; Life Sciences Dives into Biology with Visitors »
- Chiolo Exchanges Bay View for Los Angeles’ Hollywood Sign »
- Gray Highlighted as All-star Researcher in War on Cancer; Life Scientist Advises on Article »
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Scientific News
Developing a Quick Way to ID People Exposed to Ionizing Radiation
Andy Wryobek (c) with research group
In the aftermath of a dirty bomb or nuclear power plant explosion, emergency personnel will be faced with a deluge of urgent tasks, such as identifying who’s been irradiated, who has an injury-induced infection, and who’s suffering from both. Unfortunately, there isn’t a quick way to screen for exposure to dangerous levels of radiation or distinguish between radiation exposure and infection from injury or chemical exposure. A much faster way could be coming. Research by Lab life scientists could lead to a blood test that detects radiation exposure, measures the dose, and separates people suffering from inflammation injuries — all in a matter of hours.
They report their research in a paper recently published online in the journal PLOS ONE. Life Sciences Andy Wyrobek conducted the research with fellow Life Sciences scientists Helen Budworth and Antoine Snijders, as well as several other scientists from Berkeley Lab and other institutions. More »
Adapted from Today at Berkeley Lab, December 18, 2012
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Medical Imaging Goes Underground to Map Soil Changes
SPECT images of a flow tracer in a sediment column
The same medical imaging technology that doctors use to noninvasively image the heart and brain is now giving scientists a close-up view of the subsurface world. Berkeley Lab scientists are developing a way to use Single Photon Emission Computed Tomography, or SPECT, to map 3-D changes in sediment samples without disturbing them. Their work could help improve the clean up of soil contaminants such as heavy metals. It could also help researchers learn how to best store carbon underground, where it can’t contribute to climate change. The latest results of this research, led by Bill Moses of Berkeley Lab’s Life Sciences Division and Peter Nico of the Earth Sciences Division, were reported December 6 at the 2012 meeting of the American Geophysical Union (AGU) in San Francisco. More »
Adapted from Today at Berkeley Lab, December 14, 2012
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Lab Scientists Help Develop Promising Therapy for Huntington’s Disease
Neuron isolated from a Huntington's disease mouse model (Image by McMurray lab)
There’s new hope in the fight against Huntington’s disease. Researchers in the Life Sciences Division have helped develop a compound that suppresses symptoms of the devastating neurodegenerative disease in mice. The compound is a synthetic antioxidant that targets mitochondria, an organelle within cells that serves as a cell’s power plant. Oxidative damage to mitochondria is implicated in many neurodegenerative diseases including Alzheimer’s, Parkinson’s, and Huntington’s. Cynthia McMurray and Zhiyin Xun helped lead the effort. More »
Today at Berkeley Lab, November 2, 2012
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Protein Folding Funnels Apply to Self-Assembly; Should Benefit Biomimicry and Nanosynthesis
Jim DeYoreo and Carolyn Bertozzi led a team of researchers at the Molecular Foundry that demonstrated the concept that folding funnels applies equally to individual and ensembles of proteins. Their findings provide important guidelines for future efforts in biomimicry — technological innovation inspired by nature — particularly for device fabrication and nanoscale synthesis. Also working on this study were Seong-Ho Shin, Sungwook Chung, Babak Sanii and Life Sciences Luis Comolli. More »
Today at Berkeley Lab, November 1, 2012
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New Study of Response to Low-Dose Radiation
Andy Wyrobek (l) and Antoine Snijders (Photo by Roy Kaltschmid, LBNL)
Berkeley Lab scientists have identified tissue mechanisms that may influence a woman’s susceptibility or resistance to breast cancer after exposure to low-dose ionizing radiation, such as that used in full-body CT scans and radiotherapy. The research could lead to new ways to identify women with higher or lower risks of breast cancer from low-dose radiation, predictive tools that could help guide the treatment of patients who may be better served by nonradiation therapies. The findings also support the idea that a person’s genes play a big role in determining the risk of breast cancer from low-dose radiation. The research was conducted by Andy Wyrobek, Antoine Snijders, Joe Gray, and other Berkeley Lab scientists. More »
Today at Berkeley Lab, October 17, 2012
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Patent on Semiconductor Material Issued to Stephen Derenzo and Team
A team led by Life Sciences Stephen Derenzo has received news of the issuance of their invention, "Semiconductor material BiOI," as United States of America Patent No. 8,304,748. The invention is entitled “Identifying New Semiconductor Detector Materials by D.C. Ionization Conductivity” and was issued on November 6. The team of inventors includes Stephen Derenzo, Edith Bourret-Courchesne (Material Sciences), Yetta Eagleman (formally named Porter-Chapman and formally of Life Sciences), Floyd James, Mattias Klintenberg, Jie Wang, and Jia-Qing Wang.The patent describes a method for identifying semiconductor radiation detector materials based on the mobility of internally generated electrons and holes. It was designed for the early stages of exploration, when samples are not available as single crystals, but as crystalline powders. Samples are confined under pressure in an electric field and the increase in current resulting from exposure to a high-intensity source of ionization current (e.g., 60Co gamma rays) is measured. In the patent a pressure cell device is described to carry out the method. For known semiconductors, the d.c. ionization current depends on voltage according to the Hecht equation, and for known insulators the d.c. ionization current is below detection limits. This shows that the method can identify semiconductors in spite of significant carrier trapping. Using this method and pressure cell, it was determined that new materials BiOI, PbIF, BiPbO2CI, BiPbO2Br, BiPbO2I, Bi2GdO4CI, Pb3O2I2, and Pb5O4I2 are semiconductors.
A copy of the patent is available for viewing or free downloading at http://free.patentfetcher.com/Patent-Fetcher-Form.php (enter the patent number 8304748 in the patent search field).
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In the News
A review of Life Sciences researchers, staff, and students who have appeared in the news media. This is but a sampling of our coverage. Please note that some links may expire after time.
An Oct. 3 Nature story looking at the role of arsenic in bacteria reviewed work by Felisa Wolfe-Simon before she arrived at the Lab. The Christian Science Monitor and LiveScience ran similar stories.
http://www.nature.com/news/arsenic-life-bacterium-prefers-phosphorous-after-all-1.11520
http://www.csmonitor.com/Science/2012/1003/Startling-discovery-debunked-bacteria-can-t-survive-on-arsenic
http://www.livescience.com/23661-arsenic-bacteria-survive-toxic-lake.html
A Dec. 8 Yahoo!Health story on recent advances in breast cancer research included efforts led by the Lab’s Mark LaBarge.
http://health.yahoo.net/experts/breastcancer/we-now-know-why-risk-breast-cancer-increase-woman-ages
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Recent Publications
What follows is a review of Life Sciences recent publications. It is not a complete list, but only a sampling.
Riddle NC, Jung YL, Gu T, Alekseyenko AA, Asker D, Gui H, Kharchenko PV, Minoda A, Plachetka A, Schwartz YB, Tolstorukov MY, Kuroda MI, Pirrotta V, Karpen GH, Park PJ, Elgin SC. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. PLoS Genetics, 2012 Sep;8(9):e1002954. Epub 2012 Sep 20. PMID:23028361 Abstract »
Brosey CA, Tsutakawa SE, Chazin WJ. Sample preparation methods to analyze DNA-induced structural changes in replication protein A. Methods Molecular Biology, 2012;922:101-22. PMID: 22976179 Abstract »
Finger LD, Atack JM, Tsutakawa S, Classen S, Tainer J, Grasby J, Shen B. The wonders of flap endonucleases: structure, function, mechanism and regulation. Subcellular Biochemistry, 2012;62:301-26. PMID: 22918592 Abstract »
Liu JS, Farlow JT, Paulson AK, Labarge MA, Gartner ZJ. Programmed cell-to-cell variability in Ras activity triggers emergent behaviors during mammary epithelial morphogenesis. Cell Reports, 2012 Oct 3. pii: S2211-1247(12)00278-1. [Epub ahead of print] PMID: 23041312 Abstract »
Mroue R, Bissell MJ. Three-dimensional cultures of mouse mammary epithelial cells. Methods Molecular Biology, 2013;945:221-50. PMID: 23097110 Abstract »
Vidi PA, Bissell MJ, Lelièvre SA. Three-dimensional culture of human breast epithelial cells: the how and the why. Methods Molecular Biology, 2013;945:193-219. PMID: 23097109 Abstract »
Luef B, Fakra SC, Csencsits R, Wrighton KC, Williams KH, Wilkins MJ, Downing KH, Long PE, Comolli LR, Banfield JF. Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth. ISME Journal, 2012 Oct 4. [Epub ahead of print] PMID: 23038172 Abstract »
Schmid TE, Grant PG, Marchetti F, Weldon RH, Eskenazi B, Wyrobek AJ. Elemental composition of human semen is associated with motility and genomic sperm defects among older men. Human Reproduction, 2012 Oct 5. [Epub ahead of print] PMID: 23042799 Abstract »
Lee DY, Bowen BP, Nguyen DH, Parsa S, Huang Y, Mao JH, Northen TR. Low-dose ionizing radiation-induced blood plasma metabolic response in a diverse genetic mouse population. Radiation Research, 2012 Oct 10. [Epub ahead of print] PMID: 23051006 Abstract »
Lin CH, Lee JK, Labarge MA. Fabrication and use of microenvironment microArrays (MEArrays). Journal of Visualized Experiments, 2012 Oct 11;(68). pii: 4152. PMID: 23093325 Abstract »
Snijders AM, Marchetti F, Bhatnagar S, Duru N, Han J, Hu Z, Mao JH, Gray JW, Wyrobek AJ. Genetic differences in transcript responses to low-dose ionizing radiation identify tissue functions associated with breast cancer susceptibility. PLoS One, 2012;7(10):e45394. Epub 2012 Oct 15. PMID: 23077491 Abstract »
Limbo O, Moiani D, Kertokalio A, Wyman C, Tainer JA, Russell P. Mre11 ATLD17/18 mutation retains Tel1/ATM activity but blocks DNA double-strand break repair. Nucleic Acids Research, 2012 Oct 17. [Epub ahead of print] PMID: 23080121 Abstract »
Blakely EA. Lauriston S. Taylor Lecture on radiation protection and measurements: What makes particle radiation so effective? Health Physics, 2012 Nov;103(5):508-28. PMID: 23032880 Abstract »
Baran R, Bowen BP, Price MN, Arkin AP, Deutschbauer AM, Northen TR. Metabolic footprinting of mutant libraries to map metabolite utilization to genotype. ACS Chemical Biology, 2012 Oct 19. [Epub ahead of print] PMID: 23082955 Abstract »
Alushin GM, Musinipally V, Matson D, Tooley J, Stukenberg PT, Nogales E. Multimodal microtubule binding by the Ndc80 kinetochore complex. Nature Structural Molecular Biology, 2012 Oct 21. [Epub ahead of print] PMID: 23085714 Abstract
Haight TJ, Jagust WJ. Alzheimer’s Disease Neuroimaging Initiative. Relative contributions of biomarkers in Alzheimer's disease. Annals of Epidemiology, 2012 Oct 23. pii: S1047-2797(12)00364-X. [Epub ahead of print] PMID: 23102709 Abstract »
Walian PJ, Allen S, Shatsky M, Zeng L, Szakal ED, Liu H, Hall SC, Fisher SJ, Lam BR, Singer ME, Geller JT, Brenner SE, Chandonia JM, Hazen TC, Witkowska HE, Biggin MD, Jap BK. High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. Journal of Proteome Research, 2012 Oct 25. [Epub ahead of print] PMID: 23098413 Abstract »
Sadanandam A, Lal A, Benz SC, Eppenberger-Castori S, Scott G, Gray JW, Spellman P, Waldman F, Benz CC. Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells? Breast Cancer Research and Treatment, 2012 Oct 27. [Epub ahead of print] PMID: 23104223 Abstract »
Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer JA, Pommier Y, Aihara H. Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2. Nature Structural Molecular Biology, 2012 Oct 28. [Epub ahead of print] PMID: 23104058 Abstract »
Wilkinson OJ, Latypov V, Tubbs JL, Millington CL, Morita R, Blackburn H, Marriott A, McGown G, Thorncroft M, Watson AJ, Connolly BA, Grasby JA, Masui R, Hunter CA, Tainer JA, Margison GP, Williams, DM. Alkyltransferase-like protein (Atl1) distinguishes alkylated guanines for DNA repair using cation-p interactions. Proc Natl Acad Sci U S A, 2012 Nov 13;109(46):18755-18760. Epub 2012 Oct 29. PMID: 23112169 Abstract »
Ciferri C, Lander GC, Maiolica A, Herzog F, Aebersold R, Nogales E. Molecular architecture of human polycomb repressive complex 2. eLife, 2012;1:e00005. Epub 2012 Oct 30. PMID: 23110252 Abstract »
Xun Z, Rivera-Sánchez S, Ayala-Peña S, Lim J, Budworth H, Skoda EM, Robbins PD, Niedernhofer LJ, Wipf P, McMurray CT. Targeting of XJB-5-131 to mitochondria suppresses oxidative DNA damage and motor decline in a mouse model of Huntington's disease. Cell Reports, 2012 Oct 30. pii: S2211-1247(12)00335-X. [Epub ahead of print] PMID: 23122961 Abstract »
McElwee JL, Mohanan S, Griffith OL, Breuer HC, Anguish LJ, Cherrington BD, Palmer AM, Howe LR, Subramanian V, Causey CP, Thompson PR, Gray JW, Coonrod SA. Identification of PADI2 as a potential breast cancer biomarker and therapeutic target. BMC Cancer, 2012 Oct 30;12(1):500. [Epub ahead of print] PMID: 23110523 Abstract »
Landau SM, Mintun MA, Joshi AD, Koeppe RA, Petersen RC, Aisen PS, Weiner MW, Jagust WJ; for the Alzheimer's Disease Neuroimaging Initiative. Amyloid deposition, hypometabolism, and longitudinal cognitive decline. Annals of Neurology, 2012 Oct;72(4):578-586. PMID: 23109153 Abstract »
Toledo JB, Toledo E, Weiner MW, Jack CR Jr, Jagust W, Lee VM, Shaw LM, Trojanowski JQ; Alzheimer's Disease Neuroimaging Initiative. Cardiovascular risk factors, cortisol, and amyloid-ß deposition in Alzheimer's Disease Neuroimaging Initiative. Alzheimer’s and Dementia: the Journal of the Alzheimer’s Association, 2012 Nov;8(6):483-9. PMID: 23102118 Abstract »
Kronenberg A, Cucinotta FA. Space radiation protection issues. Health Physics, 2012 Nov;103(5):556-67. PMID: 23032885 Abstract »
Budworth H, Snijders AM, Marchetti F, Mannion B, Bhatnagar S, Kwoh E, Tan Y, Wang SX, Blakely WF, Coleman M, Peterson L, Wyrobek AJ. DNA repair and cell cycle biomarkers of radiation exposure and inflammation stress in human blood. PLoS One, 2012;7(11):e48619. doi: 10.1371/journal.pone.0048619. Epub 2012 Nov 7. PMID:23144912 Abstract »
Vandehey NT, O’Neil JP, Slowey AJ, Boutchko R, Druhan JL, Moses WW, Nico PS. Monitoring Tc dynamics in a bioreduced sediment: an investigation with gamma camera imaging of 99mTc-pertechnetate and 99mTc-DTPA. Environmental Science & Technology, 46(22):12583–12590, November 20, 2012 Abstract »
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Awards & Grants Highlights
2013 Lab Directed Research and Development Awards Announced
Director Alivisatos has announced the awards for the FY2013 Laboratory Directed Research and Development (LDRD) program. A total of about $22.3 million was allocated for 85 projects. A significant portion of the projects address the reduction of the impact of energy use at each stage of the carbon cycle, or advance the boundaries of ultrafast photon science in support of laboratory initiatives. Funded projects can be viewed here. Evaluations for the traditional Track 1 proposals used input from area and divisional review committees. A much smaller number of proposals of Lab-Wide significance went through a parallel scientific review process led by the Associate Lab Directors. Out of 31 Lab-Wide proposals submitted, 19 projects were funded (noted with asterisk in list).
Today at Berkeley Lab, December 18, 2012
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Celniker Named 2012 AAAS Fellow
Susan Celniker (Photo by Roy Kaltschmid, LBNL)
Susan Celniker of the Life Sciences Division and Wim Leemans of the Accelerator and Fusion Research Division have been n