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Life Sciences Division E-Newsletter

July, 2009

In this issue:


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DOE scientific focus area notes

 

Low Dose Radiation Research

Range of Metabolites Detectable by ESI-MS Extended
Researchers at Berkeley Lab have extended the range of metabolites detectable by electrospray ionization mass spectrometry (ESI-MS) through the use of a derivatization step.  Mass spectrometry has become an indispensable tool for metabolomics.  However, one of the major challenges facing the rapidly developing field of metabolomics is the comprehensive detection of metabolites. For example, untargeted mass spectrometry based approaches are often used to compare serum from affected with control populations to identify alterations in cellular metabolism. However, one of the most widely used ionization approaches, Electrospray Ionization, does not ionize, and therefore cannot detect, many important classes of metabolites, including many neutral lipids (i.e. steroids, sterols, glycerol lipids, and etc.). In essence this leaves the researcher 'blind' to many important metabolic changes that may be occurring. 

Life Sciences Trent Northen and Gary Siuzdak, also of The Scripps Research Institute, and coworkers present a very simple approach to enhance detection of neutral lipids by chemically modifying them with a cation (phosphonium group) to enhance detection. Northen described the advantages of this technique: “This method is suitable for analysis of serum extracts and can greatly increase the number of features detected, including neutral lipids such as cholesterol, alpha-tocopherol, hexadecanoyl-sn-glycerol, dihydrotachysterol.”  Northen is enthusiastic about the potential of this work, and his group is currently developing methods to extend this approach to other classes of metabolites using LC-ESI-MS/MS analysis.

Woo K-H , Go EP , Hoang L , Trauger SA , Bowen B , Siuzdak G , Northen TR, Phosphonium labeling for increasing metabolomic coverage of neutral lipids using electrospray ionization mass spectrometry. Rapid Communications in Mass Spectrometry, 2009 Jun;23(12):1849-55. PMID: 19449318
Trent Northen, 7/09

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New Technique Developed for Metabolite Imaging
A major challenge in understanding the effects of low dose ionizing radiation is identifying the similarities and differences with endogenous oxidative damage processes. This is complicated by the fact that these are likely cell specific processes that depend critically on the cells tissue microenvironment and genetic background. Given the inherent heterogeneity within tissues, the ‘grind-and-find’ approach averages out locally elevated and clinically relevant metabolite levels and typical tissue culture experiments disregard tissue type variance, immunological, and paracrine effects.

The alternative approach of directly imaging metabolites within tissues has the potential to overcome these limitations by measuring metabolite levels on the cellular level within tissues. Towards this goal Trent Northen and Wolfgang Reindl are applying a new technique for metabolite imaging from frozen tissue sections in collaboration with Steve Yannone. This new technique Nanostructure-Initiator Mass Spectrometry NIMS has a unique combination of high lateral resolution (10-75 µm), sensitivity (highest reported, including single cancer cells), lack of matrix. Reindl has developed a process for producing NIMS surfaces within clean-rooms at the Berkeley MicroLab (UC Berkeley). This provides a state of the art facility with all of the appropriate safety controls and training for the production of the NIMS surfaces. In addition, the new process has been scaled-up the NIMS surfaces to 7cm square (previous surfaces were 3cm sq) which opens up new opportunities for the types of samples which we can study. The group is continuing to develop the novel capabilities to detect small molecule markers associated with responses to ionizing radiation in tissues with cellular and cell-type specific resolution.
Trent Northen, 7/09

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GTL-Genomics

Scientists Track Chemical Changes in Cells as They Endure Extreme Conditions
How do some bacteria survive conditions that should kill them? In groundbreaking research, Berkeley Lab scientists used the Advanced Light Source to track chemical changes in individual cells as they adapt to extreme environments. Until now, scientists had not been able to monitor, at a molecular level, these changes. The ability to watch this Herculean adaptation to stress, from such an up-close and real-time vantage, gives scientists an improved way to study adaptive responses in a range of microbes, such as disease-causing pathogens and microbes that play a role in photosynthesis, energy production, and geochemical phenomena. The work titled “Real-time Molecular Monitoring of Chemical Environment in Obligate Anaerobes during Oxygen Adaptive Response” by Hoi-Ying Holman, Eleanor Wozei, Zhang Lin, Luis Comolli, David Ball, Sharon Borglin, Matthew Fields, Terry Hazen, and Kenneth Downing was published online in an early edition of the Proceedings of the National Academy of Sciences.

"We can now follow chemical changes in living bacteria as they respond to extreme environments. This opens up a new window into how bacteria adapt and carry out some of life’s most important processes," says Hoi-Ying Holman, a staff scientist in the Earth Sciences Division. More> http://newscenter.lbl.gov/feature-stories/2009/07/07/cells-endure-extremes/

Holman HY, Wozei E, Lin Z, Comolli LR, Ball DA, Borglin S, Fields MW, Hazen TC, Downing KH. Real-time molecular monitoring of chemical environment in obligate anaerobes during oxygen adaptive response. Proceedings of the National Academy of Sciences, U S A, 2009 Jun 16. [Epub ahead of print] PMID: 19541631

Berkeley Lab News Center Feature Story, 7/7/09; Today at Berkeley Lab, 7/8/09

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Protein Structures Revealed at Record Pace
Protein Researchers — including Greg Hura and John Tainer — have developed a fast and efficient way to determine the structure of proteins, shortening a process that often takes years into a matter of days. The high-throughput protein pipeline could allow scientists to expedite the development of biofuels, decipher how extremophiles thrive in conditions that kill most organisms, and better understand how proteins carry out life's vital functions.

Their work was published in the July 20, 2009 online edition of the journal Nature Methods.  A web version of the Berkeley Lab press release with images and video is available at http://newscenter.lbl.gov/press-releases/2009/07/20/fast-protein-structures/ .
Berkeley Lab Press Release, Dan Krotz, 7/20/09; Today at Berkeley Lab, 7/22/09

 

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Radiotracer Development & Imaging Technology

New ultra-fast, Heavy-atom Scintillator Radiation Detectors
A new class of inorganic scintillators is being developed that can detect gamma rays at rates over ten times faster than currently available scintillators. This will allow the measurement of metabolic processes in living plants and the transport of contaminants in soils to be performed more quickly and with greater statistical accuracy. Other applications include high energy physics and time-of-flight positron emission tomography. This scintillation speed has been demonstrated in recently grown lead iodide crystals doped with impurities that cause the ionization produced by interacting gamma rays to produce a flash of light. This flash lasts only several billionths of a second, close to the theoretical limit. Scintillators in common use produce their light by other processes that are 10 to 100 times slower. The lead iodide crystals were grown in the new Berkeley Lab Crystal Growth Facility.
Stephen Derenzo, 8/09

 

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Scientific & divisional news

 

Discovery in Cause of Down Syndrome and other Genetic Disorders

Scientists have a better understanding of what causes an abnormal number of chromosomes in offspring, a condition called aneuploidy that encompasses the most common genetic disorders in humans, such as Down syndrome, and is a leading cause of pregnancy loss.  To pinpoint what goes awry in these cases, researchers at Berkeley Lab and the University of Tennessee, Knoxville studied mice. They found that if a mother’s egg cell has a mutation in just one copy of a gene, called Bub1, then she is more likely to have fewer offspring that survive to birth.

Francesco Marchetti of the Life Sciences Division is co-author of the article that appeared in the July issue of Proceedings of the National Academy of Sciences.  More> http://newscenter.lbl.gov/feature-stories/2009/07/16/genetic-cause-aneuploidy/
Berkeley Lab News Center, Feature Story, 7/16/09,Today at Berkeley Lab, 7/21/09

 

Early Markers of Alzheimer's Disease Found

A large study of patients with mild cognitive impairment revealed that results from cognitive tests and brain scans can work as an early warning system for the subsequent development of Alzheimer's disease. The research found that among 85 participants in the study with mild cognitive impairment, those with low scores on a memory recall test and low glucose metabolism in particular brain regions, as detected through positron emission tomography (PET), had a 15-fold greater risk of developing Alzheimer's disease within two years, compared with the others in the study. The study was led by Susan Landau, with principal investigation by William Jagust, both with Berkeley Lab’s Life Sciences Division. More > http://www.berkeley.edu/news/media/releases/2009/07/14_alzheimers.shtml
Today at Berkeley Lab, 7/16/09

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Nogales Serves on Search Committee for Lab Director

UC President Mark Yudof has named an 11-member committee of university regents, faculty and researchers to advise him in the search for the next director of Berkeley Lab. Eva Nogales, a biophysicist with the Life Sciences Division, is a member of the search committee. The committee's first meeting will be at the Lab on August 19, 2009 during which committee members will solicit comments from Lab staff.  The goal is to present a candidate for approval to the UC Board of Regents before December 2009. More> http://newscenter.lbl.gov/press-releases/2009/07/01/search-for-new-director/
Today at Berkeley Lab, 7/2/09

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Life Scientist Participates in Symposium on Nanotechnology Safety

Environment, health and safety professionals, scientists, and regulators who make decisions on how to safely handle unbound engineered nanoparticles were invited to attend a daylong symposium on “EH&S Challenges of the Nanotechnology Revolution” on July 29, 2009. The meeting was cosponsored by the Lab’s Materials Sciences Division and Molecular Foundry, as well as UC Berkeley’s Center for Occupational and Environmental Health. Lab speakers included Richard Kelly, facilities manager for the Materials Sciences Division, and life scientist Fanquing Frank Chen.  More > http://www.coehce.org/courses/nano.html

Today at Berkeley Lab, 7/13/09

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UC President’s Associates Visit Berkeley Lab

On July 15, 2009, members of the UC President's Associates visited Berkeley Lab for briefings on biosciences work at the Lab. Acting Deputy Director Jay Keasling welcomed the group and gave a brief overview of Berkeley Lab and the long tradition of collaboration with UC campuses. Also making presentations were Paul Adams, Acting Division Director for Physical BioSciences, and Life Sciences Division Director Joe Gray, with UCSF researcher and collaborator Laura Esserman. The President's Associates include the spouses of UC Chancellors, and Mrs. Judy Yudof (front row, third from left), wife of UC President Mark Yudof. Bill Johansen from Life Sciences and Michelle Moskowitz, Government Affairs at UC Berkeley, helped to host the group along with Berkeley Lab Government Affairs Manager Don Medley.
Today at Berkeley Lab, 7/17/09

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Life Sciences Welcomes Korean Delegation

On July 22, 2009, Life Sciences Thomas Budinger, Damir Sudar and Paul Spellman welcomed several delegates of the Korea Research Council, Industrial Science & Technology (Dr. Uk Han); Korea Institute of Geoscience & Mineral Resources (Dr. Byoung-Woo Yum);  Korea Institute of Industrial Technology (Dr. Phil Sung Kim); Korea Institute of Industrial Technology (KITECH) USA (Dr. Jeong Han Kim); and the Energy & Geoscience Institute, University of Utah (Drs. Weon Shik Ha and Brian J. McPherson). The delegation, lead by Dr. Han, Chairman of the Korea Research Council Industrial Science & Technology, was hosted by Earth Sciences Deputy Director Ernest Majer. He arranged for a full agenda including a tour by Budinger of the High Throughput Detector Discovery and Crystal Growing facility as well as a tour of the Biocenter West facility. There, the delegation received an overview by Sudar and Spellman of Life Sciences Division research and efforts in cancer genome sequencing, the latter in collaboration with the University of California, San Francisco.
CG, 7/09

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Life Scientists Contribute to Leading Breast Cancer Reference Book

Paul Spellman, Laura Heiser and Joe Gray of Life Sciences are contributors to the recently published book Diseases of the Breast, 4th edition by editors Jay Harris, Marc Lippman, Monica Morrow and Kent Osborne. In this reference book leading experts summarize the current knowledge of breast diseases, including their clinical features, management, underlying biologies, and epidemiologies. In addition to complete coverage of malignant breast diseases, benign diseases are discussed in relation to subsequent breast cancer development. The book reviews all major clinical trials and summarizes the information they provide on early detection and management of breast cancer. Close attention was also given to the increasing importance of molecular biology and genetics in this field.

Spellman, Heiser and Gray wrote Chapter 27, Breast Cancer Genomics, pgs. 363-373 in Section VI, Pathology and Biological Markers of Invasive Breast Cancer.  According to the authors breast cancer is predominantly a disease of the genome with cancers arising and progressing through accumulation of aberrations that alter the genome - by changing DNA sequence, copy number, and structure in ways that contribute to diverse aspects of cancer pathophysiology. In the chapter they describe current and future directions in genome analysis and summarize studies that provide insights into breast cancer pathophysiology or that suggest strategies to improve breast cancer management. The book is available at http://www.lww.com/product/?978-0-7817-9117-5.
CG, 7/09

 

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Awards

 

Glaeser Selected as Microscopy Society of America Fellow

Life Sciences investigator Robert Glaeser has been selected as a Microscopy Society of America (MSA) Fellow. Glaeser is among a group of 43 inaugural Fellows selected in this first year of the Fellowship program. The designation of MSA Fellow is intended to recognize senior distinguished members of the Society who have made significant contributions to the advancement of the science and practice of microscopy imaging, analysis and diffraction techniques.
Today at Berkeley Lab, 7/7/09

 

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Recent publications (selected)

 

Boutchko R, Canning A, Chaudhry A, Borade R, Bourret-Courchesne E, Derenzo SE. Cerium activated scintillation in yttrium halides: first principles theory and prediction. IEEE Transactions on Nuclear Science, 2009 Jun; 56(3):977-981.

Recently, scintillation has been observed in Ce-doped YI3, YBr3, and YCl3 crystals. In particular, YI3 has been reported to be among the scintillators with the highest luminosity. In this work, we present a systematic study of scintillation in any of the four YHa3:Ce materials where Ha = F, Cl, Br, I, using ab initio calculations. Last year, our group demonstrated successful application of a method of gauging scintillation properties of Ce-doped crystals based on first-principle calculations using density functional theory. This method has been developed as an integral component of a High Throughput Scintillator Discovery facility based at the Lawrence Berkeley National Lab. By analyzing the energies and spatial localization of the highest occupied band in the ground state and in the lowest excited state, we are able to make qualitative predictions about the possibility of scintillation in Ce-doped compounds. In this paper we present the details of our theoretical approach in application to yttrium halides and compare them with the available experiments. Our results yield a prediction of Ce-based scintillation for all four materials: YF3, YCl3, YBr3 and YI3 and are in correspondence with the available experimental data. We believe that our method is the first use of first-principles calculations to predict some of the factors necessary for the activation of Ce3+ ions in crystals.

Canning A, Boutchko R, Chaudhry A, Derenzo SE. First-principles studies and predictions of scintillation in Ce-doped materials. IEEE Transactions on Nuclear Science, 2009 Jun; 56(3): 944-948.

A theoretical approach based on first-principles calculations is used to select candidate Ce activated scintillator materials for synthesis. Our theoretical approach involves the calculation of the ground state band structure of the Ce-doped material as well as the calculation of the (Ce3+)* excited state. From our theoretical studies of known scintillators and non-scintillators we have developed a set of criteria that are necessary characteristics of bright Ce activated scintillators. Applying these criteria to new compounds we were able to successfully predict that Ba2YCl7 : Ce would be a bright scintillator.

Woo H-K , Go  EP, Hoang L , Trauger SA , Bowen   B, Siuzdak   G, Northen TR, Phosphonium labeling for increasing metabolomic coverage of neutral lipids using electrospray ionization mass spectrometry. Rapid Communications in Mass Spectrometry, 2009 Jun;23(12):1849-55. PMID: 19449318

(See Low Dose Highlight.)

Hu P, Janga SC, Babu M, Díaz-Mejía JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, Chandran S, Christopoulos C, Nazarians-Armavil A, Nasseri NK, Musso G, Ali M, Nazemof N, Eroukova V, Golshani A, Paccanaro A, Greenblatt JF, Moreno-Hagelsieb G, Emili A. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biology, 2009 Apr 28;7(4):e96. PMID: 19402753

One-third of the 4,225 protein-coding genes of Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted to E. coli, including pathogenic strains. To elucidate the orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged E. coli strains and generated comprehensive genomic context inferences to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel. Clustering of the respective probabilistic networks revealed putative orphan membership in discrete multiprotein complexes and functional modules together with annotated gene products, whereas a machine-learning strategy based on network integration implicated the orphans in specific biological processes. We provide additional experimental evidence supporting orphan participation in protein synthesis, amino acid metabolism, biofilm formation, motility, and assembly of the bacterial cell envelope. This resource provides a "systems-wide" functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins.

Chen X, Ballin JD, Della-Maria J, Tsai MS, White EJ, Tomkinson AE, Wilson GM. Distinct kinetics of human DNA ligases I, IIIalpha, IIIbeta, and IV reveal direct DNA sensing ability and differential physiological functions in DNA repair. DNA Repair, 2009 Jul 7. [Epub ahead of print] PMID: 19589734

The three human LIG genes encode polypeptides that catalyze phosphodiester bond formation during DNA replication, recombination and repair. While numerous studies have identified protein partners of the human DNA ligases (hLigs), there has been little characterization of the catalytic properties of these enzymes. In this study, we developed and optimized a fluorescence-based DNA ligation assay to characterize the activities of purified hLigs. Although hLigI joins DNA nicks, it has no detectable activity on linear duplex DNA substrates with short, cohesive single-strand ends. By contrast, hLigIIIbeta and the hLigIIIalpha/XRCC1 and hLigIV/XRCC4 complexes are active on both nicked and linear duplex DNA substrates. Surprisingly, hLigIV/XRCC4, which is a key component of the major non-homologous end joining (NHEJ) pathway, is significantly less active than hLigIII on a linear duplex DNA substrate. Notably, hLigIV/XRCC4 molecules only catalyze a single ligation event in the absence or presence of ATP. The failure to catalyze subsequent ligation events reflects a defect in the enzyme-adenylation step of the next ligation reaction and suggests that, unless there is an in vivo mechanism to reactivate DNA ligase IV/XRCC4 following phosphodiester bond formation, the cellular NHEJ capacity will be determined by the number of adenylated DNA ligaseIV/XRCC4 molecules.

Cherepy NJ, Payne SA, Asztalos SJ, Hull G, Kuntz JD, Niedermayr T, Pimputkar S, Roberts JJ, Sanner RD, Tillotson TM, van Loef EV, Wilson CM, Shah KS, Roy UN, Hawrami R, Burger A, Boatner LA, Choong W-S, Moses WW. Scintillators with potential to supersede lanthanum bromide. IEEE Transactions on Nuclear Science, 2009 Jun; 56(3):873-880

New scintillators for high-resolution gamma ray spectroscopy have been identified, grown and characterized. Our development efforts have focused on two classes of high-light-yield materials: europium-doped alkaline earth halides and cerium-doped garnets. Of the halide single crystals we have grown by the Bridgman method-SrI2, CaI2, SrBr2, BaI2 and BaBr2-SrI2 is the most promising. SrI2(Eu) emits into the Eu2+ band, centered at 435 nm, with a decay time of 1,2 µs and a light yield of up to 115,000 photons/MeV. It offers energy resolution better than 3% FWHM at 662 keV, and exhibits excellent light yield proportionality. Transparent ceramic fabrication allows the production of gadolinium- and terbium-based garnets which are not growable by melt techniques due to phase instabilities. The scintillation light yields of cerium-doped ceramic garnets are high, 20,000-100,000 photons/MeV. We are developing an understanding of the mechanisms underlying energy dependent scintillation light yield non-proportionality and how it affects energy resolution. We have also identified aspects of optical design that can be optimized to enhance the energy resolution.

van Loef EV, Wilson CM, Cherepy NJ, Hull G, Payne SA, Choong W-S, Moses WW, Shah KS. Crystal growth and scintillation properties of strontium iodide scintillators. IEEE Transactions on Nuclear Science, 2009 Jun; 56(3):869-872.

Single crystals of SrI2:Eu and SrI2:Ce/Na were grown from anhydrous iodides by the vertical Bridgman technique in evacuated silica ampoules. Growth rates were of the order of 5-30 mm/day. Radioluminescence spectra of SrI2:Eu and SrI2:Ce/Na exhibit a broad band due to Eu2+ and Ce3+ emission, respectively. The maximum in the luminescence spectrum of SrI2:Eu is found at 435 nm. The spectrum of SrI2:Ce/Na exhibits a doublet peaking at 404 and 435 nm attributed to Ce3+ emission, while additional impurity-or defect-related emission is present at approximately 525 nm. The strontium iodide scintillators show very high light yields of up to 120,000 photons/MeV, have energy resolutions down to 3% at 662 keV (Full Width Half Maximum) and exhibit excellent light yield proportionality with a standard deviation of less than 5% between 6 and 460 keV.

Holman HY, Wozei E, Lin Z, Comolli LR, Ball DA, Borglin S, Fields MW, Hazen TC, Downing KH. Real-time molecular monitoring of chemical environment in obligate anaerobes during oxygen adaptive response. Proceedings of the National Academy of Sciences, U S A, 2009 Jun 16. [Epub ahead of print] PMID: 19541631

(See also GTL-Genomics Highlight.)

Determining the transient chemical properties of the intracellular environment can elucidate the paths through which a biological system adapts to changes in its environment, for example, the mechanisms that enable some obligate anaerobic bacteria to survive a sudden exposure to oxygen. Here we used high-resolution Fourier transform infrared (FTIR) spectromicroscopy to continuously follow cellular chemistry within living obligate anaerobes by monitoring hydrogen bond structures in their cellular water. We observed a sequence of well orchestrated molecular events that correspond to changes in cellular processes in those cells that survive, but only accumulation of radicals in those that do not. We thereby can interpret the adaptive response in terms of transient intracellular chemistry and link it to oxygen stress and survival. This ability to monitor chemical changes at the molecular level can yield important insights into a wide range of adaptive responses.

Phillips CM, Meng X, Zhang L, Chretien JH, Urnov FD, Dernburg AF. Identification of chromosome sequence motifs that mediate meiotic pairing and synapsis in C. elegans.  Nature Cell Biology, 2009 Jul 20. [Epub ahead of print] PMID: 19620970

Caenorhabditis elegans chromosomes contain specialized regions called pairing centres, which mediate homologous pairing and synapsis during meiosis. Four related proteins, ZIM-1, 2, 3 and HIM-8, associate with these sites and are required for their essential functions. Here we show that short sequence elements enriched in the corresponding chromosome regions selectively recruit these proteins in vivo. In vitro analysis using SELEX indicates that the binding specificity of each protein arises from a combination of two zinc fingers and an adjacent domain. Insertion of a cluster of recruiting motifs into a chromosome lacking its endogenous pairing centre is sufficient to restore homologous pairing, synapsis, crossover recombination and segregation. These findings help to illuminate how chromosome sites mediate essential aspects of meiotic chromosome dynamics.

Ghajar CM, Meier R, Bissell MJ. Quis custodiet ipsos custodies: who watches the watchmen?  The American Journal of Pathology, 2009 Jun;174(6):1996-9. PMID: 19465642 [Commentary]

This Commentary highlights two articles in this issue of the American Journal of Pathology, discussing the implications of stromal expression of caveolin-1 in breast cancer.  Comment on:  Am J Pathol. 2009 Jun;174(6):2023-34 and Am J Pathol. 2009 Jun;174(6):2035-43.

Liu WL, Coleman RA, Ma E, Grob P, Yang JL, Zhang Y, Dailey G, Nogales E, Tjian R. Structures of three distinct activator-TFIID complexes. Genes and Development, 2009 Jul 1;23(13):1510-21. PMID: 19571180

Sequence-specific DNA-binding activators, key regulators of gene expression, stimulate transcription in part by targeting the core promoter recognition TFIID complex and aiding in its recruitment to promoter DNA. Although it has been established that activators can interact with multiple components of TFIID, it is unknown whether common or distinct surfaces within TFIID are targeted by activators and what changes if any in the structure of TFIID may occur upon binding activators. As a first step toward structurally dissecting activator/TFIID interactions, we determined the three-dimensional structures of TFIID bound to three distinct activators (i.e., the tumor suppressor p53 protein, glutamine-rich Sp1 and the oncoprotein c-Jun) and compared their structures as determined by electron microscopy and single-particle reconstruction. By a combination of EM and biochemical mapping analysis, our results uncover distinct contact regions within TFIID bound by each activator. Unlike the coactivator CRSP/Mediator complex that undergoes drastic and global structural changes upon activator binding, instead, a rather confined set of local conserved structural changes were observed when each activator binds holo-TFIID. These results suggest that activator contact may induce unique structural features of TFIID, thus providing nanoscale information on activator-dependent TFIID assembly and transcription initiation.

Veress AI, Raymond GM, Gullberg GT, Bassingthwaighte JB. Coupled modeling of the left ventricle and the systemic circulatory system. SIAM News, 2009 Jun; 42(5):3.

We demonstrate a coupling of a 1-D lumped-parameter system to a 3-D finite element-based model but without the need to have the two systems within the same simulation package. Such a coupled system has to be time varying, and it needs to mimic the responses of a 3-D circulatory system to the contraction of a 3-D ventricle. The work presented and briefly described here can be seen as a first step toward a system of this type; it demonstrates the linking of a circulatory model run under the JSim analysis package (www.physiome.org) to an LV model developed for and analyzed in the nonlinear, large-deformation finite element package NIKE3D.

Huang Q, Xu J, Tsui BM, Gullberg GT. Reconstructing uniformly attenuated rotating slant-hole SPECT projection data using the DBH method. Physics in Medicine and Biology, 2009 Jul 7;54(13):4325-39. PMID: 19531850

This work applies a previously developed analytical algorithm to the reconstruction problem in a rotating multi-segment slant-hole (RMSSH) SPECT system. The RMSSH collimator has greater detection efficiency than the parallel-hole collimator with comparable spatial resolution at the expense of limited common volume-of-view (CVOV) and is therefore suitable for detecting low-contrast lesions in breast, cardiac and brain imaging. The absorption of gamma photons in both the human breast and brain can be assu- med to follow an exponential rule with a constant attenuation coefficient. In this work, the RMSSH SPECT data of a digital NCAT phantom with breast attachment are modeled as the uniformly attenuated Radon transform of the activity distribution. These data are reconstructed using an analytical algorithm called the DBH method, which is an acronym for the procedure of differentiation backprojection followed by a finite weighted inverse Hilbert transform. The projection data are first differentiated along a specific direction in the projection space and then backprojected to the image space. The result from this first step is equal to a one-dimensional finite weighted Hilbert transform of the object; this transform is then numerically inverted to obtain the reconstructed image. With the limited CVOV of the RMSSH collimator, the detector captures gamma photon emissions from the breast and from parts of the torso. The simulation results show that the DBH method is capable of exactly reconstructing the activity within a well-defined region-of-interest (ROI) within the breast if the activity is confined to the breast or if the activity outside the CVOV is uniformly attenuated for each measured projection, while a conventional filtered backprojection algorithm only reconstructs the high frequency components of the activity function in the same geometry.

Reference Genome Group of the Gene Ontology Consortium:  Gaudet P, Chisholm R, Berardini T, Dimmer E, Engel SR, Fey P, Hill DP, Howe D, Hu JC, Huntley R, Khodiyar VK, Kishore R, Li D, Lovering RC, McCarthy F, Ni L, Petri V, Siegele DA, Tweedie S, Van Auken K, Wood V, Basu S, Carbon S, Dolan M, Mungall CJ, Dolinski K, Thomas P, Ashburner M, Blake JA, Cherry JM, Lewis SE, Balakrishnan R, Christie KR, Costanzo MC, Deegan J, Diehl AD, Drabkin H, Fisk DG, Harris M, Hirschman JE, Hong EL, Ireland A, Lomax J, Nash RS, Park J, Sitnikov D, Skrzypek MS, Apweiler R, Bult C, Eppig J, Jacob H, Parkhill J, Rhee S, Ringwald M, Sternberg P, Talmud P, Twigger S, Westerfield M. The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species. PLoS Computational Biology, 2009 Jul;5(7):e1000431. PMID: 19578431

The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in a highly systematic way and in a species-neutral manner with the aim of unifying the representation of gene function across different organisms. Each contributing member of the GO Consortium independently associates GO terms to gene products from the organism(s) they are annotating. Here we introduce the Reference Genome project, which brings together those independent efforts into a unified framework based on the evolutionary relationships between genes in these different organisms. The Reference Genome project has two primary goals: to increase the depth and breadth of annotations for genes in each of the organisms in the project, and to create data sets and tools that enable other genome annotation efforts to infer GO annotations for homologous genes in their organisms. In addition, the project has several important incidental benefits, such as increasing annotation consistency across genome databases, and providing important improvements to the GO's logical structure and biological content.

Leland S, Nagarajan P, Polyzos A, Thomas S, Samaan G, Donnell R, Marchetti F, Venkatachalam S. Heterozygosity for a Bub1 mutation causes female-specific germ cell aneuploidy in mice. Proceedings of the Nationall Academy of Sciences, U S A, 2009 Jul 17. [Epub ahead of print] PMID: 19617567

(See also Scientific and Divisional News.)

Aneuploidy, the most common chromosomal abnormality at birth and the main ascertained cause of pregnancy loss in humans, originates primarily from chromosome segregation errors during oogenesis. Here, we report that heterozygosity for a mutation in the mitotic checkpoint kinase gene, Bub1, induces aneuploidy in female germ cells of mice and that the effect increases with advancing maternal age. Analysis of Bub1 heterozygous oocytes showed that aneuploidy occurred primarily during the first meiotic division and involved premature sister chromatid separation. Furthermore, aneuploidy was inherited in zygotes and resulted in the loss of embryos after implantation. The incidence of aneuploidy in zygotes was sufficient to explain the reduced litter size in matings with Bub1 heterozygous females. No effects were seen in germ cells from heterozygous males. These findings show that Bub1 dysfunction is linked to inherited aneuploidy in female germ cells and may contribute to the maternal age-related increase in aneuploidy and pregnancy loss.

Trushina E, Rana S, McMurray CT, Hua DH. Tricyclic pyrone compounds prevent aggregation and reverse cellular phenotypes caused by expression of mutant huntingtin protein in striatal neurons. BMC Neuroscience, 2009 Jul 8;10(1):73. [Epub ahead of print]PMID: 19586540

BACKGROUND: Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG repeat expansion mutation in the coding region of a novel gene. The mechanism of HD is unknown. Most data suggest that polyglutamine-mediated aggregation associated with expression of mutant huntingtin protein (mhtt) contributes to the pathology. However, recent studies have identified early cellular dysfunctions that preclude aggregate formation. Suppression of aggregation is accepted as one of the markers of successful therapeutic approaches. Previously, we demonstrated that tricyclic pyrone (TP) compounds efficiently inhibited formation of amyloid-beta (Abeta) aggregates in cell and mouse models representing Alzheimer's Disease (AD). In the present study, we aimed to determine whether TP compounds could prevent aggregation and restore early cellular defects in primary embryonic striatal neurons from animal model representing HD. RESULTS: TP compounds effectively inhibit aggregation caused by mhtt in neurons and glial cells. Treatment with TP compounds also alleviated cholesterol accumulation and restored clathrin-independent endocytosis in HD neurons. CONCLUSIONS: We have found that TP compounds not only blocked mhtt-induced aggregation, but also alleviated early cellular dysfunctions that preclude aggregate formation. Our data suggest TP molecules may be used as lead compounds for prevention or treatment of multiple neurodegenerative diseases including HD and AD.

Rodier F, Coppé JP, Patil CK, Hoeijmakers WA, Muñoz DP, Raza SR, Freund A, Campeau E, Davalos AR, Campisi J. Persistent DNA damage signalling triggers senescence-associated inflammatory cytokine secretion. Nature Cell Biology, 2009 Jul 13. [Epub ahead of print] PMID: 19597488

Cellular senescence suppresses cancer by stably arresting the proliferation of damaged cells. Paradoxically, senescent cells also secrete factors that alter tissue microenvironments. The pathways regulating this secretion are unknown. We show that damaged human cells develop persistent chromatin lesions bearing hallmarks of DNA double-strand breaks (DSBs), which initiate increased secretion of inflammatory cytokines such as interleukin-6 (IL-6). Cytokine secretion occurred only after establishment of persistent DNA damage signalling, usually associated with senescence, not after transient DNA damage responses (DDRs). Initiation and maintenance of this cytokine response required the DDR proteins ATM, NBS1 and CHK2, but not the cell-cycle arrest enforcers p53 and pRb. ATM was also essential for IL-6 secretion during oncogene-induced senescence and by damaged cells that bypass senescence. Furthermore, DDR activity and IL-6 were elevated in human cancers, and ATM-depletion suppressed the ability of senescent cells to stimulate IL-6-dependent cancer cell invasiveness. Thus, in addition to orchestrating cell-cycle checkpoints and DNA repair, a new and important role of the DDR is to allow damaged cells to communicate their compromised state to the surrounding tissue.

George KA, Hada M, Jackson LJ, Elliott T, Kawata T, Pluth JM, Cucinotta FA. Dose response of gamma rays and iron nuclei for induction of chromosomal aberrations in normal and repair-deficient cell lines. Radiation Research, 2009 Jun;171(6):752-63. PMID: 19580482

We studied the effects of DNA double-strand break (DSB) repair deficiencies on chromosomal aberration frequency using low doses (<1 Gy) of gamma rays and high-energy iron ions (LET = 151 keV/microm). Chromosomal aberrations were measured using the fluorescence whole-chromosome painting technique. The cell lines included fibroblasts deficient in ATM (product of the gene that is mutated in ataxia telangiectasia patients) or NBS (product of the gene mutated in the Nijmegen breakage syndrome) and gliomablastoma cells proficient in or lacking DNA-dependent protein kinase (DNA-PK) activity. The yields of both simple and complex chromosomal aberrations were increased in DSB repair-defective cells compared to normal cells; the increase was more than twofold higher for gamma rays compared to iron nuclei. For gamma-ray-induced aberrations, the ATM- and NBS-defective lines were found to have significantly larger quadratic components compared to normal fibroblasts for both simple and complex aberrations, while the linear dose-response term was significantly higher only for the NBS cells. For simple and complex aberrations induced by iron nuclei, regression models preferred purely linear and quadratic dose responses, respectively, for each cell line studied. RBEs were reduced relative to normal cells for all of the DSB repair-defective lines, with the DNA-PK-deficient cells found to have RBEs near unity. The large increase in the quadratic dose-response terms in the DSB repair-deficient cell lines points to the importance of the functions of ATM and NBS in chromatin modifications to facilitate correct DSB repair and to minimize aberration formation. The differences found between AT and NBS cells at lower doses suggest important questions about the applicability of observations of radiation sensitivity at high doses to low-dose exposures.

Porter-Chapman YD, Bourret-Courchesne ED, Bizarri GA, Weber MJ, Derenzo SE. Scintillation and luminescence properties of undoped and cerium-doped LiGdCl4 and NaGdCl4. IEEE Transactions on Nuclear Science, 2009 Jun; 56(3):881-886.

We report the scintillation properties of the undoped and cerium-doped variations of LiGdCl4 and NaGdCl4. Powder samples of these materials exhibit significant scintillation under X-rays. The samples were synthesized by solid-state methods from a 1:1 molar ratio of lithium or sodium chloride and gadolinium trichloride. Cerium trichloride was used as the dopant. The physical, optical, and scintillation properties of these materials were analyzed by powder X-ray diffraction, photoluminescence, X-ray excited luminescence, and pulsed X-ray luminosity measurements. Increases in light yields are observed as the concentration of cerium increases. The highest light yields occurred at 20% cerium doping for both compounds. At larger concentrations neither compound formed, indicating a breakdown of the lattice with the addition of large amounts of cerium cations. At 20% cerium, LiGdCl4 and NaGdCl4 display scintillation light 3.6 times and 2.2 times the light yield of the reference material, YAlO3 : Ce3+, respectively. Both emit in the ranges of 340-350 nm and 365-370 nm and display multiexponential decays with cerium-like decay components at 33 ns (LiGdCl4 : Ce) and 26 ns (NaGdCl4 : Ce).

Hura GL, Menon AL, Hammel M, Rambo RP, Poole Ii FL, Tsutakawa SE, Jenney Jr FE, Classen S, Frankel KA, Hopkins RC, Yang SJ, Scott JW, Dillard BD, Adams MW, Tainer JA. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS).  Nature Methods, 2009 Jul 20. [Epub ahead of print] PMID: 19620974

We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.

Durinck S, Spellman PT, Birney E, Huber W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.  Nature Protocols, 2009;4(8):1184-91. [Epub 2009 Jul 23] PMID: 19617889

Genomic experiments produce multiple views of biological systems, among them are DNA sequence and copy number variation, and mRNA and protein abundance. Understanding these systems needs integrated bioinformatic analysis. Public databases such as Ensembl provide relationships and mappings between the relevant sets of probe and target molecules. However, the relationships can be biologically complex and the content of the databases is dynamic. We demonstrate how to use the computational environment R to integrate and jointly analyze experimental datasets, employing BioMart web services to provide the molecule mappings. We also discuss typical problems that are encountered in making gene-to-transcript-to-protein mappings. The approach provides a flexible, programmable and reproducible basis for state-of-the-art bioinformatic data integration.

Williams PT, Hoffman KM. Optimal Body Weight for the Prevention of Coronary Heart Disease in Normal-weight Physically Active Men.  Obesity (Silver Spring),  2009 Jul;17(7):1428-34. PMID: 19553927

Although 36% of US men are normal weight (BMI <25 kg/m(2)), the health benefits of greater leanness in normal-weight individuals are seldom acknowledged. To assess the optimal body weight with respect to minimizing coronary heart disease (CHD) risk, we applied Cox proportional hazard analyses of 20,525 nonsmoking, nondiabetic, normal-weight men followed prospectively for 7.7 years, including 20,301 who provided follow-up questionnaires. Two-hundred and forty two men reported coronary artery bypass graph (CABG) or percutaneous transluminal coronary angioplasty (PTCA) and 82 reported physician-diagnosed incident myocardial infarction (267 total). The National Death Index identified 40 additional ischemic heart disease deaths. In these normal-weight men, each kg/m(2) decrement in baseline BMI was associated with 11.2% lower risk for total CHD (P = 0.005), 13.2% lower risk for nonfatal CHD (P = 0.002), 19.0% lower risk for nonfatal myocardial infarction (P = 0.01), and 12.2% lower risk for PTCA or CABG (P = 0.007). Compared to men with BMI between 22.5 and 25 kg/m(2), those <22.5 kg/m(2) had 24.1% lower total CHD risk (P = 0.01), 27.9% lower nonfatal CHD risk (P = 0.01), 37.8% lower nonfatal myocardial infarction risk (P = 0.05), and 27.8% lower PTCA or CABG risk (P = 0.02). In nonabdominally obese men (waist circumference <102 cm), CHD risk declined linearly with declining waist circumference. CHD risk was unrelated to change in waist circumference between 18 years old and baseline except as it contributed to baseline circumference. These results suggest that the optimal BMI for minimizing CHD risk lies somewhere <22.5 kg/m(2), as suggested from our previous analyses of incident diabetes, hypertension, and hypercholesterolemia in these men.