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Raman Microspectroscopy for Species Identification andMapping within Bacterial Biofilms
Brooke D Beier, Robert G Quivey, Andrew J Berger
AMB Express , 2012, DOI: 10.1186/2191-0855-2-35
Abstract:
Structure of the yeast histone H3-ASF1 interaction: implications for chaperone mechanism, species-specific interactions, and epigenetics
Andrew J Antczak, Toshiaki Tsubota, Paul D Kaufman, James M Berger
BMC Structural Biology , 2006, DOI: 10.1186/1472-6807-6-26
Abstract: Here we report the structure of a histone/histone chaperone interaction. We have solved the 2.2 ？ crystal structure of the conserved N-terminal immunoglobulin fold domain of yeast Asf1 (residues 2–155) bound to the C-terminal helix of yeast histone H3 (residues 121–134). The structure defines a histone-binding patch on Asf1 consisting of both conserved and yeast-specific residues; mutation of these residues abrogates H3/H4 binding affinity. The geometry of the interaction indicates that Asf1 binds to histones H3/H4 in a manner that likely blocks sterically the H3/H3 interface of the nucleosomal four-helix bundle.These data clarify how Asf1 regulates histone stoichiometry to modulate epigenetic inheritance. The structure further suggests a physical model in which Asf1 contributes to interpretation of a "histone H3 barcode" for sorting H3 isoforms into different deposition pathways.Chromatin structure plays a critical role in all processes involving the genome of eukaryotic organisms. The first step in chromatin establishment de novo is the deposition of an (H3/H4)2 heterotetramer onto DNA by one or more of several histone chaperones including Asf1, CAF-1, and the HIR Complex. The pre-nucleosomal (H3/H4)2 intermediate then binds to two histone H2A/H2B heterodimers, which complete the core histone octamer and allow for proper wrapping of nucleosomal DNA (reviewed in [1]).Histone H3/H4 chaperones participate in two similar, yet functionally distinct pathways. The first involves replication-coupled (RC) histone deposition during S-phase, in which CAF-1-histone complexes are recruited to sites of DNA replication through an interaction with the DNA polymerase processivity factor PCNA [2]. The second pathway is a replication-independent (RI) histone deposition process that occurs during all stages in the cell cycle and involves the HIR Complex [3-5]. RI histone deposition has been linked to chromatin reorginization during both transcription [6] and embryogenesis [7,8].Most
Brain Specificity of Diffuse Optical Imaging: Improvements from Superficial Signal Regression and Tomography
Nicholas M. Gregg,Brian R. White,Benjamin W. Zeff,Andrew J. Berger,Joseph P. Culver
Frontiers in Neuroenergetics , 2010, DOI: 10.3389/fnene.2010.00014
Abstract: Functional near infrared spectroscopy (fNIRS) is a portable monitor of cerebral hemodynamics with wide clinical potential. However, in fNIRS, the vascular signal from the brain is often obscured by vascular signals present in the scalp and skull. In this paper, we evaluate two methods for improving in vivo data from adult human subjects through the use of high-density diffuse optical tomography (DOT). First, we test whether we can extend superficial regression methods (which utilize the multiple source–detector pair separations) from sparse optode arrays to application with DOT imaging arrays. In order to accomplish this goal, we modify the method to remove physiological artifacts from deeper sampling channels using an average of shallow measurements. Second, DOT provides three-dimensional image reconstructions and should explicitly separate different tissue layers. We test whether DOT’s depth-sectioning can completely remove superficial physiological artifacts. Herein, we assess improvements in signal quality and reproducibility due to these methods using a well-characterized visual paradigm and our high-density DOT system. Both approaches remove noise from the data, resulting in cleaner imaging and more consistent hemodynamic responses. Additionally, the two methods act synergistically, with greater improvements when the approaches are used together.
Glycolytic Metabolites Are Critical Modulators of Oocyte Maturation and Viability
Lloyd Berger, Andrew Wilde
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0077612
Abstract: The maturation of an oocyte into an egg is a key step in preparation for fertilization. In Xenopus, oocyte maturation is independent of transcription, being regulated at the level of translation and post-translational modifications of proteins. To identify factors involved in the maturation process we used two-dimensional differential gel electrophoresis to compare the proteome of oocytes and eggs. Protein abundance changes were observed in multiple cellular pathways during oocyte maturation. Most prominent was a general reduction in abundance of enzymes in the glycolytic pathway. Injection into oocytes of the glycolytic intermediates glyceraldehyde-3-phosphate, phosphoenolpyruvate and glucose-6-phosphate prevented oocyte maturation. Instead, these metabolites stimulated ROS production and subsequent apoptosis of the oocyte. In contrast, all other metabolites tested had no effect on oocyte maturation and did not induce apoptosis. These data suggest that a subset of glycolytic metabolites have the capacity to regulate oocyte viability.
Correlating spin transport and electrode magnetization in a graphene spin valve: simultaneous magnetic microscopy and non-local measurements
Andrew J. Berger,Michael R. Page,Hua Wen,Kathleen M. McCreary,Vidya P. Bhallamudi,Roland K. Kawakami,P. Chris Hammel
Physics , 2015, DOI: 10.1063/1.4932673
Abstract: Using simultaneous magnetic force microscopy (MFM) and transport measurements of a graphene spin valve, we correlate the non-local spin signal with the magnetization of the device electrodes. The imaged magnetization states corroborate the influence of each electrode within a one-dimensional spin transport model and provide evidence linking domain wall pinning to additional features in the transport signal.
Negotiating the new medicines regulatory framework: Some basic facts and observations
J Berger
Southern African Journal of HIV Medicine , 2004,
Abstract:
Nucleolar size in lymphocytes and haemocytes of different species
J Berger
European Journal of Histochemistry , 2008, DOI: 10.4081/1205
Abstract: The number of nucleoli in a cell and nucleolar area vary according to the cell. We compared nucleoli in mammalian circulating lymphocytes and insect circulating haemocytes. An increased nucleolar coefficient correlated with a lowered nucleoli size. The smaller nucleolar size in mammalian lymphocytes indicates a lower proteosynthetic cellular activity in both mammalian lymphocytes and insect haemocytes. Moreover, in insect haemocytes, the smaller size of the nucleoli may reflect a lowered potential to transform into another cell type.
The Optical Afterglow and z=0.92 Early-type Host Galaxy of the Short GRB 100117A
Wen-fai Fong,Edo Berger,Ryan Chornock,Nial R. Tanvir,Andrew J. Levan,John F. Graham,Andrew S. Fruchter,Antonino Cucchiara,Derek B. Fox
Physics , 2010, DOI: 10.1088/0004-637X/730/1/26
Abstract: We present the discovery of the optical afterglow and early-type host galaxy of the short-duration GRB 100117A. The faint afterglow is detected 8.3 hr after the burst with r_AB = 25.46 +/- 0.20 mag. Follow-up optical and near-IR observations uncover a coincident compact red galaxy, identified as an early-type galaxy at a photometric redshift of z~0.6-0.9 (2-sigma) with a mass of 3x10^10 M_Sun, an age of ~1 Gyr, and a luminosity of L_B~0.5L_star. Spectroscopic observations of the host reveal a notable break corresponding to the Balmer 4000-Angstrom break at z~0.9, and stellar population spectral evolution template fits indicate z~0.915, which we adopt as the redshift of the host, with stellar population ages of ~1-3 Gyr. From a possible weak detection of [OII]-3727 emission at z=0.915 we infer an upper bound on the star formation rate of ~0.1 M_Sun per yr, leading to a specific star formation rate of <0.004 per Gyr. Thus, GRB 100117A is only the second short burst to date with a secure early-type host (the other being GRB 050724 at z=0.257) and it has one of the highest short GRB redshifts. The offset between the host center and the burst position, 470 +/- 310 pc, is the smallest to date. Combined with the old stellar population age, this indicates that the burst likely originated from a progenitor with no significant kick velocity. However, from the brightness of the optical afterglow we infer a relatively low density of n~3x10^-4 cm^-3 when epsilon_e and epsilon_B = 0.1. The combination of an optically faint afterglow and host suggest that previous such events may have been missed, thereby potentially biasing the known short GRB host population against z>1 early-type hosts.
Donor/recipient enhancement of memory in rat hippocampus
Sam A. Deadwyler,Theodore W. Berger,Andrew J. Sweatt,Dong Song,Rosa H. M. Chan,Ioan Opris,Vasilis Z. Marmarelis,Robert E. Hampson
Frontiers in Systems Neuroscience , 2013, DOI: 10.3389/fnsys.2013.00120
Abstract: The critical role of the mammalian hippocampus in the formation, translation and retrieval of memory has been documented over many decades. There are many theories of how the hippocampus operates to encode events and a precise mechanism was recently identified in rats performing a short-term memory task which demonstrated that successful information encoding was promoted via specific patterns of activity generated within ensembles of hippocampal neurons. In the study presented here, these “representations” were extracted via a customized non-linear multi-input multi-output (MIMO) mathematical model which allowed prediction of successful performance on specific trials within the testing session. A unique feature of this characterization was demonstrated when successful information encoding patterns were derived online from well-trained “donor” animals during difficult long-delay trials and delivered via online electrical stimulation to synchronously tested na？ve “recipient” animals never before exposed to the delay feature of the task. By transferring such model-derived trained (donor) animal hippocampal firing patterns via stimulation to coupled na？ve recipient animals, their task performance was facilitated in a direct “donor-recipient” manner. This provides the basis for utilizing extracted appropriate neural information from one brain to induce, recover, or enhance memory related processing in the brain of another subject.
A versatile LabVIEW and FPGA-based scanned probe microscope for in-operando electronic device characterization
Andrew J. Berger,Michael R. Page,Jan Jacob,Justin R. Young,Jim Lewis,Lothar Wenzel,Vidya P. Bhallamudi,Ezekiel Johnston-Halperin,Denis V. Pelekhov,P. Chris Hammel
Physics , 2014, DOI: 10.1063/1.4902934
Abstract: Understanding the complex properties of electronic and spintronic devices at the micro- and nano-scale is a topic of intense current interest as it becomes increasingly important for scientific progress and technological applications. In-operando characterization of such devices by scanned probe techniques is particularly well-suited for the microscopic study of these properties. We have developed a scanned probe microscope (SPM) which is capable of both standard force imaging (atomic, magnetic, electrostatic) and simultaneous electrical transport measurements. We utilize flexible and inexpensive FPGA (field programmable gate array) hardware and a custom software framework developed in National Instrument's LabVIEW environment to perform the various aspects of microscope operation and device measurement. The FPGA-based approach enables sensitive, real-time cantilever frequency-shift detection. Using this system, we demonstrate electrostatic force microscopy of an electrically-biased graphene FET device. The combination of SPM and electrical transport also enables imaging of the transport response to a localized perturbation provided by the scanned cantilever tip. Facilitated by the broad presence of LabVIEW in the experimental sciences and the openness of our software solution, our system permits a wide variety of combined scanning and transport measurements by providing standardized interfaces and flexible access to all aspects of a measurement (input and output signals, and processed data). Our system also enables precise control of timing (synchronization of scanning and transport operations) and implementation of sophisticated feedback protocols, and thus should be broadly interesting and useful to practitioners in the field.
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