Life Sciences Division Newsletter
In this issue:
Scientific News »
- A New Player Emerges in Mapping Protein Structures, Thanks to Lab Technology »
- Radiotherapy in Girls and the Risk of Breast Cancer Later in Life »
- OpenMSI: A Science Gateway to Sort Through Bio-Imaging’s Big Datasets »
- New Biochip Holds Great Promise for Quickly Triaging People After Radiation Exposure »
- Even Bacteria Use Social Networks »
- Berkeley Lab Confirms Thirdhand Smoke Causes DNA Damage »
- Science at the Theater “New Biology: New World?” Panel Includes Manfred Auer »
- East Bay Consortium of Educational Institutions Visits Berkeley Lab; Ben Bowen Presents »
- In the News »
- Recent Publications »
- Lab Wins Record Eight R&D 100 Awards; Winner Includes Northen Team »
- Jill Fuss Receives Award in Director’s Achievement Awards Ceremony »
- Bahram Parvin Appointed Associate Editor IEEE T-MI Journal »
- Ellie Blakely Re-elected Secretary-Treasurer RRS »
- Earth Scientist Christer Jansson Wins $3.5M ARPA-E Award »
- Life Sciences Division Hosts Sullivan Distinguished Lecture »
- Jonathan Lee Runner up Lab Tennis Tournament »
- Lab Softball Season Concludes with Win for Life Sciences “Animals” »
- New Hires and Departures: Welcomes and Goodbyes »
Cryoelectron microscopy is helping to unlock the secrets of proteins like never before, due in part to technology developed for one of the world’s most powerful electron microscopes, TEAM, located at the National Center for Electron Microscopy. This shift centers around a new generation of direct-conversion electron detectors, in which electrons hit silicon pixels directly. Robert Glaeser, a scientist in the Life Sciences Division, discussed this new technology in a recent Nature Methods’ News and Views article. Go here to read a feature article on how scientists are now using these detectors to image many important proteins with cryo-EM faster and with higher resolution.
Adapted from Today at Berkeley Lab, September 20, 2013
Sylvain Costes (r) and Jonathan Tang (Photo by Roy Kaltschmid, LBNL)
Sylvain Costes and Jonathan Tang of the Life Sciences Division (LSD), working with Mary Helen Barcellos-Hoff, formerly of LSD and now with the New York University School of Medicine, believe they have found out why exposing young women and girls under the age of 20 to ionizing radiation substantially raises the risk of their developing breast cancer later in life. Their study points to increased stem cell self-renewal and subsequent mammary stem cell enrichment as the culprits. Breasts enriched with mammary stem cells as a result of ionizing irradiation during puberty show a later-in-life propensity for developing ER negative tumors – cells that do not have the estrogen receptor, which plays a critical role in the normal development of the female breast. More »
Today at Berkeley Lab, September 11, 2013
Overlay of mass spectrometry images (Image credit: Wolfgang Reindl)
Using cutting-edge mass spectrometry imaging (MSI) technology, scientists can study tissues, cell cultures and bacterial colonies in unprecedented detail at the molecular level. This information is already helping doctors better diagnose diseases, pharmaceutical researchers develop more effective drugs, and leading to the creation of energy efficient and renewable biofuels. Despite the advances, researchers envision these areas of science progressing much faster—if only they had a standard set of computational tools to easily process, analyze and share these massive datasets. Now, they do—it’s called OpenMSI.
The work is part of a larger effort at Berkeley Lab to extend advanced computational techniques to science areas (and scientists) that haven’t benefited from them in the past. OpenMSI was born from the Lab's Integrated Bioimaging Initiative, and is an interdisciplinary collaboration between biologists and computational researchers at Berkeley Lab and the National Energy Research Scientific Computing Center (NERSC). Project leads are Life Sciences Ben Bowen and Oliver Ruebel of the Computational Research Division. More »
Adapted from Today at Berkeley Lab, August 30, 2013; Linda Vu, LBNL Computing Sciences
OpenMSI was recently highlighted in Science Magazine and in the Energy.gov blog “Supercomputing: eye-opening possibilities in imaging”; the OpenMSI Gateway can be found here.
Berkeley Lab scientists have helped to develop a tiny chip that has big potential for quickly determining whether someone has been exposed to dangerous levels of ionizing radiation. The chip has an array of nanosensors that measure the concentrations of proteins that change after radiation exposure. The technology could lead to a hand-held device that “lights up” if a person needs medical attention in the aftermath of an incident involving radiation. The technology was co-developed by scientists from Berkeley Lab, led by Andy Wyrobek of the Life Sciences Division, and Stanford University. The scientists report their research in the journal Scientific Reports. More »
Today at Berkeley Lab, August 15, 2013
Using several imaging techniques, a team of scientists that includes Life Sciences Manfred Auer, Jonathan Remis, Amita Gorur, and Marcin Zemla found that a common soil bacterium stays connected by a network of chain-like membranes. They believe the bacterium uses its network to coordinate social activities — such as evading bacterial enemies and snaring prey — without revealing its location. The research could shed light on how other bacteria work together to pull off important processes, such as breaking down plant material for biofuel production or cleaning up underground toxins. More »
The work is published online in the journal Environmental Microbiology. It has been highlighted in several news media and made headlines on the September 23 web homepage of The New York Times which featured a video on the research.
Adapted from Today at Berkeley Lab, July 19, 2013
Berkeley Lab scientists (from left) Altaf Sarker, Mohamad Sleiman, Lara Gundel, Bo Hang and Hugo Destaillats. (Photo by Roy Kaltschmid, LBNL)
A study led by researchers from Berkeley Lab has found for the first time that thirdhand smoke—the noxious residue that clings to virtually all surfaces long after the secondhand smoke from a cigarette has cleared out—causes significant genetic damage in human cells.
Their paper, “Thirdhand smoke causes DNA damage in human cells,” was published in the journal Mutagenesis. The lead investigator was Bo Hang, a biochemist in the Life Sciences Division of Berkeley Lab; he worked with an interdisciplinary group, including chemists from Berkeley Lab’s Environmental Energy Technologies Division—Lara Gundel, Hugo Destaillats and Mohamad Sleiman—as well as scientists from UC San Francisco, UCLA Medical Center and the University of Texas. More »
Adapted from Today at Berkeley Lab, June 21, 2013
The Berkeley Repertory Theatre had a full house on September 23 hosting Berkeley Lab’s Science at the Theater. The evening’s theme was “New Biology: New World?” and the panel of speakers included Life Sciences Manfred Auer who spoke on “The future of imaging: A new way to explore biology's uncharted terrain, from breast cancer progression to the social lives of microbes.” Other panel members were Biosciences Area Director Jay Keasling, Physical Biosciences Director Adam Arkin and Carolyn Larabell also of Physical Biosciences. More information - including a recording of the event - can be found on the Friends of Berkeley Lab website.
Ben Bowen presents (Photo by Linda Vu, LBNL)
About 50 students from the East Bay Consortium of Educational Institutions visited Berkeley Lab on July 26 to learn about careers in science, technology, engineering and mathematics. Deb Agarwal of the Computational Research Division (CRD) welcomed the group and gave a brief overview of the Lab. Andy Nonaka (CRD) talked about his research in computational cosmology; Ben Bowen (Life Sciences Division) discussed mass spectrometry and Susan Amrose (EETD) explained engineering for economic and social development. The visit culminated with a tour of the Advanced Light Source led by Christine Beavers, Bruce Rude, Thomas Scarvie and Doug Taube. CRD’s Sarah Poon organized the visit.
Today at Berkeley Lab, August 1, 2013
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.
A Sept. 12 News-Medical.net story covered work by the Lab’s Sylvain Costes and Jonathan Tang on the risks of radiation on young girls.
An August 15 UPI News story covered work by the Lab’s Andy Wyrobek, who developed a biochip that holds promise in identifying radiation exposure. R&D magazine also covered the work.
An August 12 Washington Post story cited work by the Lab’s Paul Williams into the benefits of running. The Examiner also covered his work.
A July 24 Wired magazine story featured work led by the Lab’s Manfred Auer showing a social network for bacteria. The San Francisco Business Times also covered his work.
A July 7 WWJ-AM Detroit radio story featured the Lab’s thirdhand smoke research and interviewed Lara Gundel.
A June 24 China People’s Daily story looked at work led by the Lab’s Bo Hang showing the dangers of thirdhand smoke. Fox News, China News, the Huffington Post, SKN Vibes, Inside Costa Rica, ZipTrials and Men’s Health magazinealso covered the work, with several also quoting the Lab’s Lara Gundel.
A June 24 Men’s Health magazine cited work led by the Lab’s Paul Williams showing how running can reduce osteoarthritis.
A June 21 Live Science story highlighted work led by the Lab’s Lara Gundel showing the dangers of thirdhand smoke. The Business Standard, Nature World News, the Daily Mail, WWLP TV, Medical News Today, WLS-AM Chicago, and many others also covered the work.
What follows is a review of Life Sciences recent publications.
Alvarado MD, Mohan AJ, Esserman LJ, Park CC, Harrison BL, Howe RJ, Thorsen C, Ozanne EM. Cost-effectiveness analysis of intraoperative radiation therapy for early-stage breast cancer. Annals of Surgical Oncology. 2013 Jun 29. [Epub ahead of print] PMID: 23812769 Abstract »
Bascom JL, Radisky DC, Koh E, Fata JE, Lo A, Mori H, Roosta N, Hirai Y, Bissell MJ. Epimorphin is a novel regulator of the progesterone receptor isoform-A. Cancer Research. 2013 Jul 18. [Epub ahead of print] PMID: 23867473 Abstract »
Budworth H, McMurray CT. A brief history of triplet repeat diseases. Methods Molecular Biology. 2013;1010:3-17. PMID: 23754215 Abstract »
Budworth H, McMurray CT. Bidirectional transcription of trinucleotide repeats: Roles for excision repair. DNA Repair (Amst). 2013 May 10. pii: S1568-7864(13)00100-6. PMID: 23669397 Abstract »
Chao LL, Decarli C, Kriger S, Truran D, Zhang Y, Laxamana J, Villeneuve S, Jagust WJ, Sanossian N, Mack WJ, Chui HC, Weiner MW. Associations between white matter hyperintensities and ß amyloid on integrity of projection, association, and limbic fiber tracts measured with diffusion tensor MRI. Public Library of Science One. 2013 Jun 6;8(6):e65175. PMID: 23762308 Abstract »
Chen X, Chen M, Xu B, Tang R, Han X, Qin Y, Xu B, Hang B, Mao Z, Huo W, Xia Y, Xu Z, Wang X. Parental phenols exposure and spontaneous abortion in Chinese population residing in the middle and lower reaches of the Yangtze River. Chemosphere. 2013 May 25. pii: S0045-6535(13)00665-6. PMID: 23714150 Abstract »
Cheng Q, Kazemian M, Pham H, Blatti C, Celniker SE, Wolfe SA, Brodsky MH, Sinha S. Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. PLoS Genetics. 2013 Aug;9(8):e1003571. Epub 2013 Aug 1. PMID: 23935523 Abstract »
Chiolo I, Tang J, Georgescu W, Costes SV. Nuclear dynamics of radiation-induced foci in euchromatin and heterochromatin. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. 2013 Aug 16. pii: S0027-5107(13)00121-8. [Epub ahead of print] PMID: 23958412 Abstract »
Cianfrocco MA, Nogales E. Regulatory interplay between TFIID's conformational transitions and its modular interaction with core promoter DNA. Transcription. 2013 Jun 21;4(3). [Epub ahead of print] PMID: 23863784 Abstract »
de Val N, McMurray MA, Lam LH, Hsiung CC, Bertin A, Nogales E, Thorner J. Native cysteine residues are dispensable for the structure and function of all five yeast mitotic septins. Proteins. 2013 Jun 15. PMID: 23775754 Abstract »
Dunleavy EM, Zhang W, Karpen GH. Solo or doppio: how many CENP-As make a centromeric nucleosome? Nature Structural Molecular Biology. 2013 Jun;20(6):648-50. PMID: 23739165 Article »
Eichorst SA, Varanasi P, Stavila V, Zemla M, Auer M, Singh S, Simmons BA, Singer SW. Community dynamics of cellulose-adapted thermophilic bacterial consortia. Environmental Microbiology. 2013 May 21. [Epub ahead of print] PMID: 23763762 Abstract »
Fan P, Griffith OL, Agboke FA, Anur P, Zou X, McDaniel RE, Creswell K, Kim SH, Katzenellenbogen JA, Gray JW, Jordan VC. c-Src modulates estrogen-induced stress and apoptosis in estrogen-deprived breast cancer cells. Cancer Research. 2013 Jul 15;73(14):4510-20. Epub 2013 May 23. PMID: 23704208 Abstract »
Fischer CR, Bowen BP, Pan C, Northen TR, Banfield JF. Stable-isotope probing reveals that hydrogen isotope fractionation in proteins and lipids in a microbial community are different and species-specific. American Chemical Society Chemical Biology. 2013 Jun 5. [Epub ahead of print] PMID: 23713674 Abstract »
Frisoni GB, Bocchetta M, Chételat G, Rabinovici GD, de Leon MJ, Kaye J, Reiman EM, Scheltens P, Barkhof F, Black SE, Brooks DJ, Carrillo MC, Fox NC, Herholz K, Nordberg A, Jack CR Jr, Jagust WJ, Johnson KA, Rowe CC, Sperling RA, Thies W, Wahlund LO, Weiner MW, Pasqualetti P, Decarli C; For ISTAART's NeuroImaging Professional Interest Area. Imaging markers for Alzheimer disease: Which vs how. Neurology. 2013 Jul 30;81(5):487-500. PMID: 23897875 Abstract »
Ghajar CM, Peinado H, Mori H, Matei IR, Evason KJ, Brazier H, Almeida D, Koller A, Hajjar KA, Stainier DY, Chen EI, Lyden D, Bissell MJ. The perivascular niche regulates breast tumour dormancy. Nature Cell Biology. 2013 Jul;15(7):807-17. Epub 2013 Jun 2. PMID: 23728425 Abstract »
Glaeser RM, Sassolini S, Cambie R, Jin J, Cabrini S, Schmid AK, Danev R, Buijsse B, Csencsits R, Downing KH, Larson DM, Typke D, Han BG. Minimizing electrostatic charging of an aperture used to produce in-focus phase contrast in the TEM. Ultramicroscopy. 2013 Jun 8;135C:6-15. [Epub ahead of print] PMID: 23872037 Abstract »
Glaeser RM. Stroboscopic imaging of macromolecular complexes. Nature Methods. 2013 Jun;10(6):475-6. PMID: 23722205 Article »
Grob P, Bean D, Typke D, Li X, Nogales E, Glaeser RM. Ranking TEM cameras by their response to electron shot noise. Ultramicroscopy. 2013 Jan 29;133C:1-7 PMID: 23747527 Abstract »
Haight TJ, Landau SM, Carmichael O, Schwarz C, Decarli C, Jagust WJ; for the Alzheimer's Disease Neuroimaging Initiative. Dissociable effects of Alzheimer Disease and white matter hyperintensities on brain metabolism. Journal of the American Medical Association Neurology. 2013 Jun 17:1-8. PMID: 23779022 Abstract »
Hosseini SA, Horton S, Saldivar JC, Miuma S, Stampfer MR, Heerema NA, Huebner K. Common chromosome fragile sites in human and murine epithelial cells and FHIT/FRA3B loss-induced global genome instability. Genes Chromosomes Cancer. 2013 Aug 9. [Epub ahead of print] PMID: 23929738 Abstract »
Iacovides DC, Johnson AB, Wang N, Boddapati S, Korkola J, Gray JW. Identification and quantification of AKT isoforms and phosphoforms in breast cancer using a novel nanofluidic immunoassay. Molecular Cell Proteomics. 2013 Aug 8. [Epub ahead of print] PMID: 23929892 Abstract »
Jones EF, Sinha SP, Newitt DC, Klifa C, Kornak J, Park CC, Hylton NM. MRI enhancement in stromal tissue surrounding breast tumors: association with recurrence free survival following neoadjuvant chemotherapy. Public Library of Science One. 2013 May 7;8(5):e61969. PMID: 23667451 Abstract »
Kassube SA, Jinek M, Fang J, Tsutakawa S, Nogales E. Structural mimicry in transcription regulation of human RNA polymerase II by the DNA helicase RECQL5. Nature Structural & Molecular Biology. 2013 Jul;20(7):892-9. Epub 2013 Jun 9. PMID: 23748380 Abstract »
Kim D, Marchetti F, Chen Z, Zaric S, Wilson RJ, Hall DA, Gaster RS, Lee JR, Wang J, Osterfeld SJ, Yu H, White RM, Blakely WF, Peterson LE, Bhatnagar S, Mannion B, Tseng S, Roth K, Coleman M, Snijders AM, Wyrobek AJ, Wang SX.. Nanosensor dosimetry of mouse blood proteins after exposure to ionizing radiation. Scientific Reports. 2013 Jul 19;3:2234 PMID: 23868657 Abstract »
Lee do Y, Xun Z, Platt V, Budworth H, Canaria CA, McMurray CT. Distinct pools of non-glycolytic substrates differentiate brain regions and prime region-specific responses of mitochondria. PLoS One. 2013 Jul 17;8(7):e68831. Print 2013. PMID: 23874783 Abstract »
Lehmann M, Ghosh PM, Madison C, Karydas A, Coppola G, O'Neil JP, Huang Y, Miller BL, Jagust WJ, Rabinovici GD. Greater medial temporal hypometabolism and lower cortical amyloid burden in ApoE4-positive AD patients. Journal of Neurology, Neurosurgery & Psychiatry. 2013 Aug 21. [Epub ahead of print] PMID: 23965289 Abstract »
Lehmann M, Madison CM, Ghosh PM, Seeley WW, Mormino E, Greicius MD, Gorno-Tempini ML, Kramer JH, Miller BL, Jagust WJ, Rabinovici GD. Intrinsic connectivity networks in healthy subjects explain clinical variability in Alzheimer's disease. Proceedings of the National Academy of Sciences U S A. 2013 Jul 9;110(28):11606-11. Epub 2013 Jun 24. PMID: 23798398 Abstract »
Louie SM, Roberts LS, Mulvihill MM, Luo K, Nomura DK. Cancer cells incorporate and remodel exogenous palmitate into structural and oncogenic signaling lipids. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids. 2013 Jul 19. pii: S1388-1981(13)00146-7. [Epub ahead of print] PMID: 23872477 Abstract »
Lu J, Wen M, Huang Y, He X, Wang Y, Wu Q, Li Z, Castellanos-Martin A, Abad M, Cruz-Hernandez JJ, Rodriguez CA, Pérez-Losada J, Mao JH, Wei G. C2ORF40 suppresses breast cancer cell proliferation and invasion through modulating expression of M phase cell cycle genes. Epigenetics. 2013 Apr 26;8(6). [Epub ahead of print] PMID: 23770814 Abstract »
Mander BA, Rao V, Lu B, Saletin JM, Ancoli-Israel S, Jagust WJ, Walker MP. Impaired prefrontal sleep spindle regulation of hippocampal-dependent learning in older adults. Cerebral Cortex. 2013 Jul 30. [Epub ahead of print] PMID: 23901074 Abstract »
Musinipally V, Howes S, Alushin GM, Nogales E. The microtubule binding properties of CENP-E's C-Terminus and CENP-F. Journal of Molecular Biology. 2013 Jul 25. pii: S0022-2836(13)00474-9. [Epub ahead of print] PMID: 23892111 Abstract »
Nam JM, Ahmed KM, Costes S, Zhang H, Onodera Y, Olshen AB, Hatanaka KC, Kinoshita R, Ishikawa M, Sabe H, Shirato H, Park CC. Beta1-integrin via NF-kappaB signaling is essential for acquisition of invasiveness in a model of radiation treated in situ breast cancer. Breast Cancer Research. 2013 Jul 25;15(4):R60. [Epub ahead of print] PMID: 23883667 Abstract »
Orellana R, Leavitt JJ, Comolli LR, Csencsits R, Janot N, Flanagan KA, Gray AS, Leang C, Izallalen M, Mester T, Lovley DR. U(VI) Reduction by a diversity of outer surface C-type cytochromes of Geobacter sulfurreducens. Applied and Environmental Microbiology 2013 Aug 9. [Epub ahead of print] PMID: 23934497 Abstract »
Ozkan E, Carrillo RA, Eastman CL, Weiszmann R, Waghray D, Johnson KG, Zinn K, Celniker SE, Garcia KC. An extracellular interactome of immunoglobulin and LRR proteins reveals receptor-ligand networks. Cell. 2013 Jul 3;154(1):228-39. PMID: 23827685 Abstract »
Platt V, Lee do Y, Canaria CA, Frankel K, Bernstein S, McMurray CT. Towards understanding region-specificity of triplet repeat diseases: coupled immunohistology and mass spectrometry imaging. Methods in Molecular Biology. 2013;1010:213-30. PMID: 23754228 Abstract »
Rajeev L, da Rocha UN, Klitgord N, Luning EG, Fortney J, Axen SD, Shih PM, Bouskill NJ, Bowen BP, Kerfeld CA, Garcia-Pichel F, Brodie EL, Northen TR, Mukhopadhyay A. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. International Society for Microbial Ecology Journal. 2013 Jun 6. [Epub ahead of print] PMID: 23739051 Abstract »
Remis JP, Wei D, Gorur A, Zemla M, Haraga J, Allen S, Witkowska HE, Costerton JW, Berleman JE, Auer M. Bacterial social networks: structure and composition of Myxococcus xanthus outer membrane vesicle chains. Environmental Microbiology. 2013 Jun 18. PMID: 23848955 Abstract »
Rosu S, Zawadzki KA, Stamper EL, Libuda DE, Reese AL, Dernburg AF, Villeneuve AM. The C. elegans DSB-2 protein reveals a regulatory network that controls competence for meiotic DSB formation and promotes crossover assurance. PLoS Genetics. 2013 Aug;9(8):e1003674. Epub 2013 Aug 8. PMID: 23950729 Abstract »
Satoh Y, Yokota T, Sudo T, Kondo M, Lai A, Kincade PW, Kouro T, Iida R, Kokame K, Miyata T, Habuchi Y, Matsui K, Tanaka H, Matsumura I, Oritani K, Kohwi-Shigematsu T, Kanakura Y. The Satb1 protein directs hematopoietic stem cell differentiation toward lymphoid lineages. Immunity. 2013 Jun 27;38(6):1105-15. Epub 2013 Jun 20. PMID: 23791645 Abstract »
Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophysical Society Journal. 2013 Aug 20;105(4):962-74. PMID: 23972848 Abstract »
Shin SH, Comolli LR, Tscheliessnig R, Wang C, Nam KT, Hexemer A, Siegerist CE, De Yoreo JJ, Bertozzi CR. Self-assembly of "s-bilayers", a step toward expanding the dimensionality of s-layer assemblies. American Chemical Society Nano. 2013 Jun 25;7(6):4946-53 PMID: 23705800 Abstract »
Spring FA, Griffiths RE, Mankelow TJ, Agnew C, Parsons SF, Chasis JA, Anstee DJ. Tetraspanins CD81 and CD82 facilitate a4ß1-mediated adhesion of human erythroblasts to vascular cell adhesion molecule-1. Public Library of Science One. 2013 May 21;8(5):e62654. PMID: 23704882 Abstract »
Sun C, Querol-Audí J, Mortimer SA, Arias-Palomo E, Doudna JA, Nogales E, Cate JH. Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation. Nucleic Acids Research. 2013 Jun 13. [Epub ahead of print] PMID: 23766293 Abstract »
Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM. Report of the wwPDB Small-Angle Scattering Task Force: Data requirements for biomolecular modeling and the PDB. Structure. 2013 Jun 4;21(6):875-81. PMID: 23747111 Abstract »
Weier JF, Hartshorne C, Nguyen HN, Baumgartner A, Polyzos AA, Lemke KH, Zeng H, Weier HU. Analysis of human invasive cytotrophoblasts using multicolor fluorescence in situ hybridization. Methods. 2013 Jun 6. pii: S1046-2023(13)00185-0 PMID: 23748112 Abstract »
Wu W, Qin Y, Li Z, Dong J, Dai J, Lu C, Guo X, Zhao Y, Zhu Y, Zhang W, Hang B, Sha J, Shen H, Xia Y, Hu Z, Wang X. Genome-wide microRNA expression profiling in idiopathic non-obstructive azoospermia: significant up-regulation of miR-141, miR-429 and miR-7-1-3p. Human Reproduction. 2013 Jul;28(7):1827-36. PMID: 23559187 Abstract »
Xia Y, Chen M, Zhu P, Lu C, Fu G, Zhou X, Chen D, Wang H, Hang B, Wang S, Zhou Z, Sha J, Wang X. Urinary phytoestrogen levels related to idiopathic male infertility in Chinese men. Environment International. 2013 Jun 29;59C:161-167. PMID: 23820060 Abstract »
Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF.Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea. BMC Genomics. 2013 Jul 17;14:485. PMID: 23865623 Abstract »
Zan Y, Boutchko R, Huang Q, Li B, Chen K, Gullberg GT. Fast direct estimation of the blood input function and myocardial time activity curve from dynamic SPECT projections via reduction in spatial and temporal dimensions. Medical Physics. 40(9), 092503 (10 pages), September 2013. Abstract »
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A generator that uses a virus to convert mechanical energy to electricity and a new material that will boost power storage in rechargeable batteries by 30 percent are among seven inventions by Berkeley Lab scientists that were honored with a 2013 R&D 100 Award, often dubbed the “Oscars of Innovation.” In addition to the generator, winners included these technologies: better batteries with a conducting polymer binder; the On-demand Secure Circuits and Reservation System (OSCARS); universal smart window coating; the Campanile nano-optical imaging probe; optically-detected oil well logging by MRI; cheap, rugged fuel cells that provide electricity where none exists; and high-throughput NIMS screening for low-cost, large-scale molecular samples.
The award winning high-throughput screening tool to support the development of lignocellulosic biofuels was developed by researchers at the Joint BioEnergy Institute (JBEI), led by Trent Northen, a staff scientist at JBEI and Berkeley Lab’s Life Sciences Division. High-Throughput Nanostructure-Initiator Mass Spectrometry (HT-NIMS) is a high-speed chemical screening system that can precisely determine the molecular composition of thousands of samples arrayed on a small slide of silicon at speeds 100 times faster than conventional methods.
HT-NIMS makes novel use of miniaturization, lasers, specialized chemistries, and robotics. In addition to the biofuels applications, the technology can also be used for a host of biological, bio-industrial, and medical uses, including discovering new drug prospects, cancer diagnostics, and clinical testing. Co-inventors with Northen were Berkeley Lab scientist Xiaoliang Cheng and San Diego, California-based Nextval Inc. More »
Adapted from Today at Berkeley Lab, July 8, 2013
Jill Fuss and Paul Alivisatos
In a ceremony recognizing recipients of the 2013 Director’s Award for Exceptional Achievement and the Berkeley Lab Prize – Life Time Achievement Awards (as announced in May), Jill Fuss received her Exceptional Achievement Award in the area of diversity on August 8, in the Building 50 Auditorium. Go here view the full list of award recipients.
Fuss is the chair of the Work-Life Balance subgroup of the Women Scientists & Engineers Council (WSEC). The group, initiated, spearheaded and led by Fuss, is engaged in the discovery of new ways to balance employees’ professional and personal quality of life.
“I feel truly honored to receive a Director's Achievement Award,” says Fuss, “especially since I was nominated by two of my Life Sciences colleagues. I am also grateful for the amazing women of the WSEC and for Laboratory senior management that has been very supportive of our efforts. Together we've been able to bring a fantastic and flexible back-up care program to the Lab that employees can use to provide care to children of any age, elders, and even themselves. And we've just recently launched the myfamily.lbl.gov web portal that employees can use to find diverse work-life resources from lactation rooms to where to take a shower after biking to work. The website has been a major focus for the Work-Life Balance subgroup so I was thrilled to see that it has had an incredible number of page views since its launch in July.”
The website, created by the WSEC and the Diversity and Inclusion Office, is called “MyFamily at LBNL” and was launched in July and highlighted in Today at Berkeley Lab that month.
Adapted from Today at Berkeley Lab, August 5, 2013
Bahram Parvin has been appointed Associate Editor of IEEE Transactions on Medical Imaging (IEEE T-MI). The journal encourages the submission of manuscripts on imaging of body structure, morphology and function, and imaging of microscopic biological entities. It publishes original contributions on medical imaging achieved by various modalities and focuses on a unified common ground where instrumentation, systems, components, hardware and software, mathematics and physics contribute to the studies.
Ellie Blakely has been re-elected Secretary-Treasurer of the Radiation Research Society (RRS) by the society’s members for an additional term of three years starting with the annual RRS meeting in September. The society's objectives are threefold: To encourage in the broadest manner the advancement of radiation research in all areas of the natural sciences; to facilitate cooperative research between the disciplines of physics, chemistry, biology and medicine in the study of the properties and effects of radiation; and to promote dissemination of knowledge in these and related fields through publications, meetings and educational symposia.
Christer Jansson of the Earth Sciences Division has won a $3.5 million ARPA-E Award aimed at enabling low-cost, energy-efficient fuel production from natural gas. Jansson’s goal is to design a novel and unique enzyme, a PEP methylase, by engineering an existing enzyme to accept methane instead of carbon dioxide. This methylation process will be employed with metabolic pathway engineering to convert methane to liquid transportation fuel. The research team also includes John Tainer and Steve Yannone of the Life Sciences Division, Romy Chakraborty of the Earth Sciences Division, and industrial partners. Jansson is one of 15 awardees in a category called REMOTE, recently announced by the DOE’s ARPA-E initiative. More »
Today at Berkeley Lab, September 23, 2013
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The Life Sciences Division hosted Catherine Park, associate professor, Department of Radiation Oncology, University of California, San Francisco, in its first Sullivan Distinguished Lecture on August 22. Park’s lecture on “Imaging and targeting tumor stroma for breast cancer therapy” was extremely well received. The Sullivan endowment was established many years ago to sponsor collaboration between practicing medical doctors of nuclear science with researchers at Berkeley Lab.
The Berkeley Lab Tennis Club’s annual tournament was held during the evenings of August 21 and 22 at the Davie Tennis Stadium in Oakland. The winner was Mikal Bajdich (center), with runners up Jin-Young Jung (left) and Life Sciences Jonathan Lee (right) of the LaBarge lab. Anyone interested to participate in daily noontime tennis can call Joe Harkins (x7486).
Adapted from Today at Berkeley Lab, August 28, 2013
With the start of Fall the 2013 Life Sciences Team “Animals” celebrated their very first Summer Softball League Championship. The Berkeley Lab league was composed of eight teams, including current and retired staff and their partners. The competing teams were: Rated X, Animals, Small Ball, SUDZ, NERSC, Ballpark Estimates, Clone Warriors, and EETD; Steve Blair was league commissioner. Games were played every Wednesday evening on UC Berkeley’s Maxwell Field next to Memorial Stadium. Here some questions for Life Sciences team co-captain Ken Wan of the Celniker lab:
- Why the name “Animals”?
It turns out that the team was originally formed by employees working with former Animal Care Facility Manager Randy Deguzman. “The team pre-dates my employment at the Lab, and may have been started by Randy Deguzman and Bob Springsteen,” explains Wan. “Randy has been captain for the past 30+ years, until his retirement in June 2013. He handed the reins to myself and Noah Schwartz, but managed to come out to some games this year, particularly the playoffs, where he resumed his manager duties. Winning the championship was a perfect way to cap off Randy’s retirement.”
- Who are the animals?
“There are too many to list,” says Wan, “We fielded the most players of any team, every game; it wasn’t even close.” The team roster reveals a total of 26 players, including (ex) Life Sciences co-captains Ken Wan and Noah Schwartz, David Acevedo, Christie Canaria, William Cox, Gabriela Fuentes-Creollo, Julio Gonzales, Justin Ishida, Brandon Mannion, Charlotte Mermier, Ann Parplys, Molly Robertsen, and Tony Smith.
- I heard Rated X were your main competition?
Wan: “Actually, many of the teams gave us a hard time. Rated X and the Sudz beat us in the regular season, and we had to fight hard to beat both teams in the playoffs (Sudz took us to extra-innings in the first playoff game, and we had to come from 3 runs down to beat Rated X in the championship game). Ball Park Estimates is another long-time competitor, but they had personnel issues this year. And it was sad to see some other old teams drop out of the league this year, namely Over-Fifty and Silver and Black. Small Ball always plays us tough, on the field and at La Val’s.”
- Did you find a particular strategy most effective?
Wan: “Yes, have the most fun and have even more fun after the game at La Val’s!”
- How did your team celebrate their win?
Wan: “La Val’s, of course.”
Rebecca Lau, research assistant, Northen lab, per September 18
Stefan Jenkins, biochemist project scientist, Northen lab, per September 16
Maria Rojec, research assistant, Costes lab, per September 16
Valentine Viviane Trotter, biochemist postdoc fellow, Butland lab, per September 16
(James) Ben Brown, computational biologist staff scientist, per September 3
Tami L Swenson, chemist postdoc fellow, Northen lab, per August 12
Devin Clunn, research assistant, Pluth lab, per August 2
Shiena Trinidad Enerio, research assistant, Pluth lab, per August 2
Ivan Rodic, systems administrator 1, Tainer lab, per September 21
Yin Zhou, student assistant, Parvin lab, per September 7
Wen-Ting Katie Tsai, student assistant, Auer lab, per September 6
Daojing Wang, biophysicist research scientist, per September 1
Karen Chong, student assistant, Tsai lab, per August 26
Samaneh Bolourchi, student assistant, Conboy lab, per August 10
Jeffrey Hao Yang Shi, student assistant, LaBarge lab, per August 10
Chloe S Courchesne, research assistant, Moses lab, per August 6
Danielle M Jorgens, UC graduate student research associate, Auer lab, per August 1
Yueyong Liu, biologist postdoc fellow, Mao lab, per August 1
Hidetoshi Mori, biologist project scientist, Bissell lab, August 1
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