Oliver Cromwell : Man of Force

Oliver Cromwell was not born a genius like Napoleon and was well into the latter half of his unimpressive and quiet life by the time he was elected to the Long Parliament. Despite this, in slightly over a decade Cromwell became the strongest person in England. His rise to the top involved many steps and Cromwell never seemed to lose momentum on his way up. Yet he was not a political mastermind. He was not always successful in bringing about his desired results, and he did not show consistently great political abilities that one would think would be necessary to become Lord Protector of England. This raises the question of why Cromwell was able to rise to the top from obscurity in merely thirteen years, and how much of this was because of his abilities, and how much was through luck and position

Heraclius and the Evolution of Byzantine Strategy

The Byzantine military strategy expressed in the 10th century treatise On Skirmishing marked a decisive shift in Byzantine strategy and an entirely new mindset in approaching war. What is unique about this strategy is that it was not created during a war against the Arabs, but before they existed as a military power. The foundation was laid during the Emperor Heraclius\u27s Persian campaigns of 622-628. To demonstrate the key contributions of Heraclius, these Persian campaigns shall be analyzed and compared with the advice prescribed in On Skirmishing. Also, the military events recorded by Theophanes of the 7th and 8th centuries will be compared with Heraclius and On Skirmishing to show the development of the strategy after Heraclius and how it measured up to the final form in On Skirmishing

OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis

Sixteen ovarian tumor (OTU) family deubiquitinases (DUBs) exist in humans, and most members regulate cell-signaling cascades. Several OTU DUBs were reported to be ubiquitin (Ub) chain linkage specific, but comprehensive analyses are missing, and the underlying mechanisms of linkage specificity are unclear. Using Ub chains of all eight linkage types, we reveal that most human OTU enzymes are linkage specific, preferring one, two, or a defined subset of linkage types, including unstudied atypical Ub chains. Biochemical analysis and five crystal structures of OTU DUBs with or without Ub substrates reveal four mechanisms of linkage specificity. Additional Ub-binding domains, the ubiquitinated sequence in the substrate, and defined S1’ and S2 Ub-binding sites on the OTU domain enable OTU DUBs to distinguish linkage types. We introduce Ub chain restriction analysis, in which OTU DUBs are used as restriction enzymes to reveal linkage type and the relative abundance of Ub chains on substrates

Automated DNA Sequencing System

Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow

Screening of DUB activity and specificity by MALDI-TOF mass spectrometry

Deubiquitylases (DUBs) are key regulators of the ubiquitin system which cleave ubiquitin moieties from proteins and polyubiquitin chains. Several DUBs have been implicated in various diseases and are attractive drug targets. We have developed a sensitive and fast assay to quantify in vitro DUB enzyme activity using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Unlike other current assays, this method uses unmodified substrates, such as diubiquitin topoisomers. By analyzing 42 human DUBs against all diubiquitin topoisomers we provide an extensive characterization of DUB activity and specificity. Our results confirm the high specificity of many members of the OTU and JAMM DUB families and highlight that all USPs tested display low linkage selectivity. We also demonstrate that this assay can be deployed to assess the potency and specificity of DUB inhibitors by profiling 11 compounds against a panel of 32 DUBs

BUILDING A NETWORK FOR NEUTRON SCATTERING EDUCATION

In a concerted effort supported by the National Science Foundation, the Department of Commerce, and the Department of Energy, the United States is rebuilding its leadership in neutron scattering capability through a significant investment in U.S. neutron scattering user facilities and related instrumentation. These unique facilities provide opportunities in neutron scattering to a broad community of researchers from academic institutions, federal laboratories, and industry. However, neutron scattering is often considered to be a tool for 'experts only' and in order for the U.S. research community to take full advantage of these new and powerful tools, a comprehensive education and outreach program must be developed. The workshop described below is the first step in developing a national program that takes full advantage of modern education methods and leverages the existing educational capacity at universities and national facilities. During March 27-28, 2008, a workshop entitled 'Building a Network for Neutron Scattering Education' was held in Washington, D.C. The goal of the workshop was to define and design a roadmap for a comprehensive neutron scattering education program in the United States. Successful implementation of the roadmap will maximize the national intellectual capital in neutron sciences and will increase the sophistication of research questions addressed by neutron scattering at the nation's forefront facilities. (See Appendix A for the list of attendees, Appendix B for the workshop agenda, Appendix C for a list of references. Appendix D contains the results of a survey given at the workshop; Appendix E contains summaries of the contributed talks.) The workshop brought together U.S. academicians, representatives from neutron sources, scientists who have developed nontraditional educational programs, educational specialists, and managers from government agencies to create a national structure for providing ongoing neutron scattering education. A concerted effort was made to involve representatives from historically black colleges and universities (HBCUs) and minority educational institutions (MEIs). The roadmap contained herein provides the path to a national infrastructure for education of students, faculty, and professional researchers who wish to make use of national neutron scattering facilities but do not have (or do not believe they have) the educational background to do so. Education of other stakeholders, including the public, students in kindergarten through twelfth grade (K-12), and policy makers is also included. The opening sessions of the workshop provided the current status of neutron scattering education in North America, Europe, and Australia. National neutron sources have individually developed outreach and advertising programs aimed at increasing awareness among researchers of the potential applications of neutron scattering. However, because their principal mission is to carry out scientific research, their outreach efforts are necessarily self-limiting. The opening session was designed to build awareness that the individual programs need to be coupled with, and integrated into, a broader education program that addresses the complete range of experience, from the student to the experienced researcher, and the wide range of scientific disciplines covered by neutron scattering. Such a program must also take full advantage of existing educational programs and expertise at universities and expand them using modern distance learning capabilities, recognizing that the landscape of education is changing

MINDY-1 is a member of an evolutionarily conserved and structurally distinct new family of Deubiquitinating enzymes

Deubiquitinating enzymes (DUBs) remove ubiquitin (Ub) from Ub-conjugated substrates to regulate the functional outcome of ubiquitylation. Here we report the discovery of a new family of DUBs, which we have named MINDY (motif interacting with Ub-containing novel DUB family). Found in all eukaryotes, MINDY-family DUBs are highly selective at cleaving K48-linked polyUb, a signal that targets proteins for degradation. We identify the catalytic activity to be encoded within a previously unannotated domain, the crystal structure of which reveals a distinct protein fold with no homology to any of the known DUBs. The crystal structure of MINDY-1 (also known as FAM63A) in complex with propargylated Ub reveals conformational changes that realign the active site for catalysis. MINDY-1 prefers cleaving long polyUb chains and works by trimming chains from the distal end. Collectively, our results reveal a new family of DUBs that may have specialized roles in regulating proteostasis

Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability

Deubiquitinating enzymes (DUBs) are important regulators of ubiquitin signaling. Here, we report the discovery of deubiquitinating activity in ZUFSP/C6orf113. High-resolution crystal structures of ZUFSP in complex with ubiquitin reveal several distinctive features of ubiquitin recognition and catalysis. Our analyses reveal that ZUFSP is a novel DUB with no homology to any known DUBs, leading us to classify ZUFSP as the seventh DUB family. Intriguingly, the minimal catalytic domain does not cleave polyubiquitin. We identify two ubiquitin binding domains in ZUFSP: a ZHA (ZUFSP helical arm) that binds to the distal ubiquitin and an atypical UBZ domain in ZUFSP that binds to polyubiquitin. Importantly, both domains are essential for ZUFSP to selectively cleave K63-linked polyubiquitin. We show that ZUFSP localizes to DNA lesions, where it plays an important role in genome stability pathways, functioning to prevent spontaneous DNA damage and also promote cellular survival in response to exogenous DNA damage. </p

Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne

The post-translational modification of proteins with polyubiquitin regulates virtually all aspects of cell biology. Eight distinct chain linkage types in polyubiquitin co-exist and are independently regulated in cells. This ‘ubiquitin code’ determines the fate of the modified protein1. Deubiquitinating enzymes of the Ovarian Tumour (OTU) family regulate cellular signalling by targeting distinct linkage types within polyubiquitin2, and understanding their mechanisms of linkage specificity gives fundamental insights into the ubiquitin system. We here reveal how the deubiquitinase Cezanne/OTUD7B specifically targets Lys11-linked polyubiquitin. Crystal structures of Cezanne alone and in complex with mono- and Lys11-linked diubiquitin, in combination with hydrogen-deuterium exchange mass spectrometry, enable reconstruction of the enzymatic cycle in exquisite detail. An intricate mechanism of ubiquitin-assisted conformational changes activate the enzyme, and while all chain types interact with the enzymatic S1 site, only Lys11-linked chains can bind productively across the active site and stimulate catalytic turnover. Our work highlights the fascinating plasticity of deubiquitinases, and indicates that new conformational states can occur when a true substrate, such as diubiquitin, is bound at the active site