Life Sciences Division Newsletter
In this issue:
Scientific News »
- Comparing Proteins at a Glance »
- New Metrics for SAS Analysis of Flexible Macromolecules »
- New Milestone Reached in Mass Spectometry Imaging »
- Hang’s Article on Thirdhand Smoke Recommended by Faculty of 1000 »
- Walking Just as Effective as Running for Bringing Heart Benefits »
- Life Scientists Present April LBNL Integrated Bioimaging Seminar »
- JBEI Researchers Engineer Plant Cell Walls to Boost Sugar Yields for Biofuels »
- Life Scientist Wolfe-Simon Speaks at Chabot Center on Astrobiology »
- Canaria Presents at ACS Women Chemists Committee Meeting »
- In the News »
- Recent Publications »
- Life Sciences Volunteers Reach Out in Upcycle! Richmond Earth Day Event »
- Yoga Classes at Potter Street on Calendar! »
- New Hires and Departures: Welcomes and Goodbyes »
John Tainer and Cynthia McMurray of the Life Sciences Division, working with Greg Hura (Physical Biosciences) and Helen Budworth (Life Sciences), have developed a revolutionary structural comparison map for the study of proteins and other biological macromolecules with small angle X-ray scattering (SAXS). The map enables researchers at a glance to identify structural similarities and differences between multiple proteins under a variety of conditions. It has already been used at the Advanced Light Source to gain valuable new insight into a prime protein target for cancer chemotherapy. Also contributing to this effort were Kevin Dyer, Robert Rambo and Michal Hammel of the Physical Biosciences Division. More »
Adapted from Today at Berkeley Lab, April 29, 2013
John Tainer of the Life Sciences Division and Rob Rambo of the Physical Biosciences Division have developed a new set of metrics for analyzing data from small angle scattering (SAS) experiments that should dramatically improve the ability of scientists to study the structures of macromolecules such as proteins and nanoparticles in solution. Among other advantages, the new SAS metrics will reduce the time required to collect data by up to 20 times and could be a game-changer for accurate high-throughput and objective analyses of flexible macromolecules. More »
Today at Berkeley Lab, April 26, 2013
In a recent publication "Mass spectrometry imaging for in situ kinetic histochemistry" in Nature Scientific Reports, first authors Katherine Louie and Benjamin Bowen (Northen lab) and colleagues present results derived from a new technique they recently developed that maps the spatial distribution of individual, newly synthesized versus pre-existing metabolites in a biological specimen. Louie explains, “Using this new technique, kinetic mass spectrometry imaging (kMSI), applied to a tumor section as part of a low-dose ionizing radiation study, we were able to correlate new synthesis of specific lipids that discriminated high grade versus low grade tumor regions; region grades were confirmed by correlative analysis of traditional histopathology stains. This new technology meets a milestone in requirements for enabling spatial mapping of flux through metabolic pathways in a biological image.”
Co-authors of the study, funded through the DOE Low Dose SFA, are Life Sciences Yurong Huang, Jian-Hua Mao, and Trent Northen; and collaborators John Price (KineMed, Inc.), Stephanie McAlhany (UCSF), and Marc Hellerstein (UCB, UCSF, and KineMed, Inc.).
First and corresponding author Bo Hang’s article on thirdhand smoke (THS)'s genotoxicity entitled “Thirdhand smoke causes DNA damage in human cells,” published in Mutagenesis, 2013 (DOI: 10.3410/f.717987458.793472430), has been recommended as being of special significance in its field by Neil Grunberg from the F1000 Faculty. The findings of this study demonstrate for the first time that exposure to THS is genotoxic in human cell lines. A brief written recommendation of the article can be found here. The recommendation concludes that “The present report is extremely important because it indicates that THS may be a serious carcinogen. This report opens up a new and important set of considerations for tobacco control.”Co-authors of the article were Life Sciences Altaf Sarker and Divya Sharan; Lara Gundel, Hugo Destaillats, and Mohamad Sleiman of the Environmental Energy Technologies Division; as well as Christopher Havel, Saikat Saha, Tapas Hazra, Suzaynn Schick, Peyton Jacob III, Virender Rehan, and Ahmed Chenna of other institutions.
[CBS News] If you’re a runner, a new study suggests you may be able to slow down and still gain the same health benefits. A study of almost 50,000 Americans finds brisk walking can be just as effective at reducing heart health risks like high blood pressure and cholesterol as going on a full-speed run. “People are always looking for an excuse not to exercise, but now they have a straightforward choice to run or to walk and invest in their future health,” study author Paul Williams of the Life Sciences Division said in a press release. More »
Today at Berkeley Lab, April 10, 2013
The April LBNL Bioimaging Seminar, held “on the Hill” this month, featured the Life Sciences Division’s Erwin Frise (Celniker lab), who spoke on “Fiji: A complete open image processing environment for the biosciences,” and Robert Glaeser, who spoke on “In-focus phase contrast for Cryo-EM.” Frise had stepped in covering for Physical Biosciences colleague Dan Fletcher whose seminar had to be postponed. Seminars are held the first Wednesday of the month and cover diverse topics in the area of bioimaging. Everyone interested in the series can contact email@example.com to be included in the seminar announcements. More »
Adapted from Today at Berkeley Lab, April 2, 2013
Dominique Loque of the Physical Biosciences Division leads a team at the Joint BioEnergy Institute (JBEI) that is using synthetic biology to engineer healthy plants whose lignocellulosic biomass can more easily be broken down into simple sugars for the production of advanced biofuels. Working with Arabidopsis as a demonstration, the team genetically manipulates secondary cell walls to reduce the production of lignin and increase the yield of fuel sugars. The team includes Fan Yang, Prajakta Mitra, Ling Zhang, Lina Prak, Yves Verhertbruggen, Jin-Sun Kim, Lan Sun, Kejian Zheng, Kexuan Tang, Henrik Scheller (left), and Life Sciences staff scientist Manfred Auer. More »
At JBEI, Auer holds the official title of Director of Physical Analysis and as such he “oversees all physical analysis efforts, which includes mechanical characterization/stress testing, polarized Raman Micro spectroscopy, scanning electron microscopy (SEM), and transmission electron microscopy (TEM),” he says.
“For this particular study,” Auer explains, “I oversaw the ultrastructural analysis including precision measurement of secondary plant cell walls using transmission electron microscopy, as well as the compositional analysis of the engineered cell walls using Raman Micro spectroscopy. This allowed us to confirm the effects of the plant metabolic engineering on the plant cell wall organization, including the secondary cell wall’s thickness increase and analysis of its chemical composition (with increased cellulose but not increased lignin). As such we were able to provide an explanation for the overall increased sugar yield upon biomass deconstruction and confirm that secondary cell walls of only certain cells are affected by the cell wall engineering but not others, which are known to require lignin for function.”
Adapted from Today at Berkeley Lab, April 1, 2013
Felisa Wolfe-Simon of the Lab’s Life Sciences Division on April 19 gave a talk at the Chabot Space and Science Center, as part of the center’s “Future Friday” evening speaker series. Wolfe-Simon is a NASA research fellow, in the Tainer lab, who explores the intersection between biology and geology, with a focus in astrobiology. More »
From the event website: “Dr. Felisa Wolfe-Simon is a NASA Astrobiology Research Fellow in residence at Lawrence Berkeley National Laboratory. Her expertise broadly covers the intersection between biology and geology with a focus in astrobiology. Wolfe-Simon uses innovative methods and tools from molecular biology, biochemistry and physiology to address biogeochemistry questions. The focus of her work deliberates on "what chemical elements can support microbial life on Earth?" She earned her B.A. (Biology) and B.M. (Music Performance) from Oberlin College and Conservatory of Music and her Ph.D. in Oceanography from Rutgers University.”
Adapted from Today at Berkeley Lab, April 19, 2013
On Saturday March 30 the Life Sciences Division hosted a meeting of the Women Chemists Committee (WCC), at Potter Street, where Life Sciences Christie Canaria was central to the meeting presenting a talk entitled “Visualizing protein interactions to understand Huntington’s Disease.” Meeting attendees, both female and male, had an opportunity to meet the speaker in a “meet the speaker” session and enjoyed lunch together before Canaria presented.
Canaria earned her B.S. degree in chemistry from the University of California, San Diego and her Ph.D. in chemistry from the California Institute of Technology (Caltech) but has since moved away from chemistry-focused studies, she said. “While my B.S. and Ph.D. were both in chemistry, my current work is most certainly of a biology bend.” Nonetheless, Elaine Yamaguchi, the WCC chair was interested in confirming Canaria as one of the committee’s four 2013 speakers saying her subject area was “relevant to all their members,” and expressing interest in hearing more about her transition to biology.
Christie Canaria (Photo by Alex Madonik)
The project Canaria highlighted in her presentation, one of several projects she has been working on for the last three years in the McMurray lab, focused on studying Huntington's Disease (HD) in a cellular model, Canaria says. “Briefly, I use an optical imaging approach to understand the protein interactions between huntingtin, a genetic mutation of huntingtin leads to onset of HD, and caveolin, a key cholesterol transporter protein. Cholesterol is essential for neuronal and brain health.” She continues, “To put this in context, HD is a devastating and progressive neurodegenerative disease - currently, we don't understand why neurons die, but previous studies in the McMurray lab implicate cholesterol transport/regulation, among other processes, as a key pathway perturbed in HD. In conjunction with MacroLab at UC Berkeley, we created mutagenesis libraries for both huntingtin and caveolin. Each of these mutants was tagged with cyan or yellow fluorescent protein; this lets us visualize mutant huntingtin and caveolin proteins in the cell with fluorescent microscopes. By expressing combinations of proteins from the mutagenesis libraries, we screened interactions by microscopy and FRET, aka fancy photo-physics phenomenon, to identify the domains responsible for protein interaction.”
Since March 1, Canaria has come down from "the Hill," from the McMurray lab, to spend more time at Potter Street contributing her imaging expertise to the Drosophila Protein Localization Atlas LDRD project, she says. The so-called “ATLAS LDRD” is a project of the LBNL Integrated Bioimaging Initiative including Life Sciences Damir Sudar (project lead), Sue Celniker, Erwin Frise, Walter Georgescu, Ann Hammonds, Roger Hoskins, and Gary Karpen; it collaborates closely with the Next-Generation BioImaging project by several colleagues from the Computational Research Division and NERSC, led by David Skinner, group leader at NERSC. About the project Canaria says, “We're creating high-throughput methods to express fluorescently tagged proteins of interest in larval tissues and cell lines; collect high resolution fluorescent images from specimen; and computationally segment and analyze datasets. The resulting database of protein expression localizations will be invaluable to the field.”
Canaria joined Berkeley Lab and the McMurray lab in March 2010 “as a research scientist, microscopist, and imaging expert,” she says. “I just celebrated my 3-year anniversary here!”
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 April 16 San Francisco Chronicle story highlighted research by the Lab’s Paul Williams into the benefits of walking and running.
An April 10 The Scientist story on cancer research quoted the Lab’s Mina Bissell from a recent presentation at the American Association for Cancer Research meeting.
An April 8 Men’s Journal story highlighted work by the Labs’ Paul Williams showing the benefits of walking. His work was also covered this past week by US News and World Report, several TV stations around the country, the New York Daily News and local Berkeley Patch, among others.
An April 4 CBS News story featured research by the Lab’s Paul Williams showing the benefits of walking. His work was extensively covered by NBC Today, WebMD, The Australian, The Daily Mail, The Guardian, Health Day, Times of India, Philadelphia Inquirer, Yahoo News and many others.
What follows is a review of Life Sciences recent publications.
Boutigny S, Saini A, Baidoo EE, Yeung N, Keasling JD, Butland G. Physical and functional interactions of a monothiol glutaredoxin and an iron sulfur cluster carrier protein with the sulfur-nonating radical S-adenosyl-L-methionine enzyme MiaB. Journal of Biological Chemistry. 2013 Mar 29. [Epub ahead of print] PMID: 23543739 Abstract »
Dumont N, Liu B, Defilippis RA, Chang H, Rabban JT, Karnezis AN, Tjoe JA, Marx J, Parvin B, Tlsty TD. Breast fibroblasts modulate early dissemination, tumorigenesis, and metastasis through alteration of extracellular matrix characteristics. Neoplasia. 2013 Mar;15(3):249-62. PMID: 23479504 Abstract »
Enuameh MS, Asriyan Y, Richards A, Christensen RG, Hall VL, Kazemian M, Zhu C, Pham H, Cheng Q, Blatti C, Brasefield JA, Basciotta MD, Ou J, McNulty JC, Zhu LJ, Celniker SE, Sinha S, Stormo GD, Brodsky MH, Wolfe SA. Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Research. 2013 Mar 7. [Epub ahead of print] PMID: 23471540 Abstract »
El Bitar Z, Huesman RH, Boutchko R, Bekaert V, Brasse D, Gullberg GT. A detector response function design in pinhole SPECT including geometrical calibration. Physics in Medicine and Biology. 58(7):2395–2411, April 7, 2013. Abstract »
Galbraith CG, Keller PJ, Nogales E. New technologies in imaging. Molecular Biology of the Cell. 2013 Mar;24(6):669 PMID: 23486393 Article »
Grim JQ, Ucer KB, Burger A, Bhattacharya P, Tupitsyn E, Rowe E, Buliga VM, Trefilova L, Gektin A, Bizarri GA, Moses WW, Williams RT. Nonlinear quenching of densely excited states in wide-gap solids. Physical Review B. 87(12):125117, March 15, 2013. Abstract »
Hang B, Sarker AH, Havel C, Saha S, Hazra TK, Schick S, Jacob P 3rd, Rehan VK, Chenna A, Sharan D, Sleiman M, Destaillats H, Gundel LA. Thirdhand smoke causes DNA damage in human cells. Mutagenesis. 2013 Mar 5. [Epub ahead of print] PMID: 23462851 Abstract »
Hegde ML, Tsutakawa SE, Hegde PM, Holthauzen LM, Li J, Oezguen N, Hilser VJ, Tainer JA, Mitra S. The disordered C-terminal domain of human DNA glycosylase NEIL1 contributes to its stability via intramolecular interactions. Journal of Molecular Biology. 2013 Mar 26. pii: S0022-2836(13)00193-9. [Epub ahead of print] PMID: 23542007 Abstract »
Junk DJ, Cipriano R, Stampfer M, Jackson MW. Constitutive CCND1/CDK2 activity substitutes for p53 loss, or MYC or oncogenic RAS expression in the transformation of human mammary epithelial cells. PLoS One. 2013;8(2):e53776. Epub 2013 Feb 4. PMID: 23390492 Abstract »
Landau SM, Lu M, Joshi AD, Pontecorvo M, Mintun MA, Trojanowski JQ, Shaw LM, Jagust WJ; Alzheimer's Disease Neuroimaging Initiative. Comparing PET imaging and CSF measurements of Aß. Annals of Neurology. 2013 Mar 28. [Epub ahead of print] PMID: 23536396 Abstract »
Lander GC, Martin A, Nogales E. The proteasome under the microscope: the regulatory particle in focus. Current Opinion in Structural Biology. 2013 Mar 13. pii: S0959-440X(13)00033-X. [Epub ahead of print] PMID: 23498601 Abstract »
Mosier AC, Justice NB, Bowen BP, Baran R, Thomas BC, Northen TR, Banfield JF. Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics. MBio. 2013 Mar 12;4(2). pii: e00484-12. PMID: 23481603 Abstract »
Muñoz DP, Kawahara M, Yannone SM. An autonomous chromatin/DNA-PK mechanism for localized DNA damage signaling in mammalian cells. Nucleic Acids Research. 2013 Mar 1;41(5):2894-906. Epub 2013 Jan 15. PMID: 23325849 Abstract »
Neng L, Zhang W, Hassan A, Zemla M, Kachelmeier A, Fridberger A, Auer M, Shi X. Isolation and culture of endothelial cells, pericytes and perivascular resident macrophage-like melanocytes from the young mouse ear. Nature Protocols. 2013 Mar 14;8(4):709-20. Epub 2013 Mar 14. PMID: 23493068 Abstract »
Ossenkoppele R, Madison C, Oh H, Wirth M, van Berckel BN, Jagust WJ. Is verbal episodic memory in elderly with amyloid deposits preserved through altered neuronal function? Cerebral Cortex. 2013 Mar 28. [Epub ahead of print] PMID: 23537530 Abstract »
Rambo RP, Tainer JA. Super-resolution in solution x-ray scattering and its applications to structural systems biology. Annual Review of Biophysics. 2013 Mar 11. [Epub ahead of print] PMID: 23495971 Abstract »
Swaminathan S, Risacher SL, Yoder KK, West JD, Shen L, Kim S, Inlow M, Foroud T, Jagust WJ, Koeppe RA, Mathis CA, Shaw LM, Trojanowski JQ, Soares H, Aisen PS, Petersen RC, Weiner MW, Saykin AJ; Alzheimer's Disease Neuroimaging Initiative. Association of plasma and cortical amyloid beta is modulated by APOE e4 status. Alzheimers Dementia. 2013 Mar 26. pii: S1552-5260(13)00039-3. [Epub ahead of print] PMID: 23541187 Abstract »
Wirth M, Madison CM, Rabinovici GD, Oh H, Landau SM, Jagust WJ. Alzheimer's disease neurodegenerative biomarkers are associated with decreased cognitive function but not ß-Amyloid in cognitively normal older individuals. Journal of Neuroscience. 2013 Mar 27;33(13):5553-63. PMID: 23536070 Abstract »
Wirth M, Oh H, Mormino EC, Markley C, Landau SM, Jagust WJ. The effect of amyloid ß on cognitive decline is modulated by neural integrity in cognitively normal elderly. Alzheimers Dementia. 2013 Mar 7. pii: S1552-5260(12)02575-7. [Epub ahead of print] PMID: 23474040 Abstract »
Zeng GL, Gullberg GT. (Featured Article) On the bias of finite-view interior tomography using piecewise-constant and non-negativity constraints. Physics in Medicine and Biology. 58(5):L13–L16, March 2013. Article »
Zhu ZJ, Schultz AW, Wang J, Johnson CH, Yannone SM, Patti GJ, Siuzdak G. Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nature Protocols. 2013 Mar;8(3):451-60. Epub 2013 Feb 7. PMID: 23391889 Abstract »
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(Photo by Mary Connolly)
The Lab’s Center for Science and Engineering Education Berkeley Lab (CSEE) in School Settings (BLISS) program participated at Richmond Art Center’s “Upcycle!,” Richmond’s Earth Day event for families, on Saturday, April 20. Lab volunteers monitored tabletop stations for the Bubble Festival, which featured hands-on science activities that explore surface tension, shape, and patterns with bubbles. The afternoon’s set-up included Bubble Walls, Bubble Windows, Bubble Shapes, Bubble Technology, and Bubble Colors. Life Sciences Ciccina Guagliardo, Daniele Jorgens (Auer lab), Ross (Zhijian) Wang (O’Neil group), and Charles Yu (Celniker lab), together with Deborah Ash (EETD) and Jun Donna Hamamoto (ALS); and Mary Connolly and Ken Roberts of CSEE enjoyed a fun and sunny afternoon of education outreach in Richmond.
Getting ready to shake hands through a bubble wall
Jorgens, who guided both kids and parents at the Technology and Colors stations, “found the experience of interacting with the parents just as interesting as the kids,” she said. “A few parents asked what bubbles have to do with science or LBL. It was fun to get to explain to them the purpose of using bubbles to reach out and make science fun for their kids, as well as how the science of bubbles is relevant to research. Other than that, just the sheer joy and pride of accomplishment on the kids' faces when they would master making bubbles within bubbles -- that was fantastic!”
Adapted from Today at Berkeley Lab, April 11, 2013
Every Wednesday, starting April 10, Potter Street conference room 141 is being transformed into a yoga studio. Co-organizers Helen Cademartori and Shraddha Ravani identified Michael Glassoff, a yoga teacher in the Bay Area since 2005, to lead a yoga class that day from 5:30 to 6:45 p.m.
Life scientist Miaw-Sheue Tsai, who has taken this opportunity to practice yoga on site, calls the yoga class “a godsend.” She explains: “It's so convenient to have the class on site. It takes fewer than 5 minutes to get ready for yoga practice. I feel great after the class. The collective positive energy from the class certainly helps me to stay on track.” She hopes more colleagues will enjoy the benefits she is experiencing.
Classes will continue weekly should there be enough interest. The classes are open to all interested in yoga, beginners are welcome; a few yoga mats are available at each session. Cost: $15/class (for drop in), $12 each for 5 classes (if paid in advance); student discount available. For more information, or to express interest, contact Cademartori or Ravani.
Ivan Khodyuk, physicist postdoctoral fellow, Bizarri lab, per March 22
Zhijian (Ross) Wang, radiochemist postdoctoral fellow, O’Neil lab, per March 11
Daniel Hartono, student assistant, Northen lab, per March 7
Manpreet Kaur, student assistant, Northen lab, per March 7
Aniek Janssen, biologist postdoctoral fellow, Karpen lab, per March 1
Pan Mao, biophysicist postdoctoral fellow, Weier lab, per March 30
Chi-Chih Kang, biologist postdoctoral fellow, Yaswen lab, March 21
Wade Carlton Wilson, research assistant, Pluth lab, per March 9
Aki Minoda, biologist project scientist, Karpen lab, per March 9
Hannah Hopp, research assistant, Karpen lab, per March 1
Do Yup Lee, biochemist research scientist, McMurray lab, per March 1
Vivek Anand Menon, student assistant, Parvin lab, per March 1
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