The Host Cell Sulfonation Pathway Contributes to Retroviral Infection at a Step Coincident with Provirus Establishment

The early steps of retrovirus replication leading up to provirus establishment are highly dependent on cellular processes and represent a time when the virus is particularly vulnerable to antivirals and host defense mechanisms. However, the roles played by cellular factors are only partially understood. To identify cellular processes that participate in these critical steps, we employed a high volume screening of insertionally mutagenized somatic cells using a murine leukemia virus (MLV) vector. This approach identified a role for 3′-phosphoadenosine 5′-phosphosulfate synthase 1 (PAPSS1), one of two enzymes that synthesize PAPS, the high energy sulfate donor used in all sulfonation reactions catalyzed by cellular sulfotransferases. The role of the cellular sulfonation pathway was confirmed using chemical inhibitors of PAPS synthases and cellular sulfotransferases. The requirement for sulfonation was mapped to a stage during or shortly after MLV provirus establishment and influenced subsequent gene expression from the viral long terminal repeat (LTR) promoter. Infection of cells by an HIV vector was also shown to be highly dependent on the cellular sulfonation pathway. These studies have uncovered a heretofore unknown regulatory step of retroviral replication, have defined a new biological function for sulfonation in nuclear gene expression, and provide a potentially valuable new target for HIV/AIDS therapy

Simulation, modelling and development of the metris RCA

In partnership with Metris UK we discuss the utilisation of modelling and simulation methods in the development of a revolutionary 7-axis Robot CMM Arm (RCA). An offline virtual model is described, facilitating pre-emptive collision avoidance and assessment of optimal placement of the RCA relative to scan specimens. Workspace accessibility of the RCA is examined under a range of geometrical assumptions and we discuss the effects of arbitrary offsets resulting from manufacturing tolerances. Degeneracy is identified in the number of ways a given pose may be attained and it is demonstrated how a simplified model may be exploited to solve the inverse kinematics problem of finding the “correct” set of joint angles. We demonstrate how the seventh axis may be utilised to avoid obstacles or otherwise awkward poses, giving the unit greater dexterity than traditional CMMs. The results of finite element analysis and static force modelling on the RCA are presented which provide an estimate of the forces exerted on the internal measurement arm in a range of poses

A Receptor-based Switch that Regulates Anthrax Toxin Pore Formation

Cellular receptors can act as molecular switches, regulating the sensitivity of microbial proteins to conformational changes that promote cellular entry. The activities of these receptor-based switches are only partially understood. In this paper, we sought to understand the mechanism that underlies the activity of the ANTXR2 anthrax toxin receptor-based switch that binds to domains 2 and 4 of the protective antigen (PA) toxin subunit. Receptor-binding restricts structural changes within the heptameric PA prepore that are required for pore conversion to an acidic endosomal compartment. The transfer cross-saturation (TCS) NMR approach was used to monitor changes in the heptameric PA-receptor contacts at different steps during prepore-to-pore conversion. These studies demonstrated that receptor contact with PA domain 2 is weakened prior to pore conversion, defining a novel intermediate in this pathway. Importantly, ANTXR2 remained bound to PA domain 4 following pore conversion, suggesting that the bound receptor might influence the structure and/or function of the newly formed pore. These studies provide new insights into the function of a receptor-based molecular switch that controls anthrax toxin entry into cells

ZEB1 Regulates the Latent-Lytic Switch in Infection by Epstein-Barr Virus

The immediate-early (IE) BZLF1 gene of Epstein-Barr virus (EBV) regulates the switch between latent and lytic infection by EBV. We previously showed that the cellular transcription factor ZEB1 binds to a sequence element, ZV, located at nt −17 to −12 relative to the transcription initiation site of the BZLF1 promoter, Zp, repressing transcription from Zp in a transient transfection assay. Here, we report the phenotype in the context of a whole EBV genome of a variant of EBV strain B95.8 containing a 2-bp substitution mutation in the ZV element of Zp that reduced, but did not eliminate, ZEB1 binding to Zp. Strikingly, epithelial 293 cells latently infected with the EBV ZV mutant spontaneously produced IE-, early-, and late-gene products and infectious virus, while wild-type (WT)-infected 293 cells did not and have never been reported to do so. Furthermore, treatment with the chemical inducers sodium butyrate and 12-O-tetradecanoyl-phorbol-13-acetate (TPA) led to an additional order-of-magnitude production of infectious virus in the ZV mutant–infected 293 cells, but still no virus in the WT-infected 293 cells. Similarly, ZV mutant–infected Burkitt's lymphoma BJAB cells accumulated at least 10-fold more EBV IE mRNAs than did WT-infected BJAB cells, with TPA or sodium butyrate treatment leading to an additional 5- to 10-fold accumulation of EBV IE mRNAs in the ZV mutant–infected cells. Thus, we conclude that ZEB1 binding to Zp plays a central role in regulating the latent-lytic switch in EBV-infected epithelial and B cells, suggesting ZEB1 as a target for lytic-induction therapies in EBV-associated malignancies

Robust and Listening-Efficient Contention Resolution

This paper shows how to achieve contention resolution on a shared communication channel using only a small number of channel accesses -- both for listening and sending -- and the resulting algorithm is resistant to adversarial noise. The shared channel operates over a sequence of synchronized time slots, and in any slot agents may attempt to broadcast a packet. An agent's broadcast succeeds if no other agent broadcasts during that slot. If two or more agents broadcast in the same slot, then the broadcasts collide and both broadcasts fail. An agent listening on the channel during a slot receives ternary feedback, learning whether that slot had silence, a successful broadcast, or a collision. Agents are (adversarially) injected into the system over time. The goal is to coordinate the agents so that each is able to successfully broadcast its packet. A contention-resolution protocol is measured both in terms of its throughput and the number of slots during which an agent broadcasts or listens. Most prior work assumes that listening is free and only tries to minimize the number of broadcasts. This paper answers two foundational questions. First, is constant throughput achievable when using polylogarithmic channel accesses per agent, both for listening and broadcasting? Second, is constant throughput still achievable when an adversary jams some slots by broadcasting noise in them? Specifically, for $N$ packets arriving over time and $J$ jammed slots, we give an algorithm that with high probability in $N+J$ guarantees $\Theta(1)$ throughput and achieves on average $O(\texttt{polylog}(N+J))$ channel accesses against an adaptive adversary. We also have per-agent high-probability guarantees on the number of channel accesses -- either $O(\texttt{polylog}(N+J))$ or $O((J+1) \texttt{polylog}(N))$, depending on how quickly the adversary can react to what is being broadcast

The distribution of H13CN in the circumstellar envelope around IRC+10216

H13CN J=8-7 sub-millimetre line emission produced in the circumstellar envelope around the extreme carbon star IRC+10216 has been imaged at sub-arcsecond angular resolution using the SMA. Supplemented by a detailed excitation analysis the average fractional abundance of H13CN in the inner wind (< 5E15 cm) is estimated to be about 4E-7, translating into a total HCN fractional abundance of 2E-5 using the isotopic ratio 12C/13C=50. Multi-transitional single-dish observations further requires the H13CN fractional abundance to remain more or less constant in the envelope out to a radius of about 4E16 cm, where the HCN molecules are effectively destroyed, most probably, by photodissociation. The large amount of HCN present in the inner wind provides effective line cooling that can dominate over that generated from CO line emission. It is also shown that great care needs to be taken in the radiative transfer modelling where non-local, and non-LTE, effects are important and where the radiation field from thermal dust grains plays a major role in exciting the HCN molecules. The amount of HCN present in the circumstellar envelope around IRC+10216 is consistent with predicted photospheric values based on equilibrium chemical models and indicates that any non-equilibrium chemistry occurring in the extended pulsating atmosphere has no drastic net effect on the fractional abundance of HCN molecules that enters the outer envelope. It further suggests that few HCN molecules are incorporated into dust grains.Comment: Accepted for publication in ApJ. 20 pages, 7 figure

Economic benefits from instream flow in a Colorado mountain stream

Submitted to Office of Water Research and Technology, U.S. Department of Interior.Bibliography: pages [131]-135.OWRT project no. A-035-COLO and OWRT project no. A-040-COLO