The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling

BACKGROUND: Human immunodeficiency virus (HIV) Nef protein accelerates virulent progression of acquired immunodeficiency syndrome (AIDS) by its interaction with specific cellular proteins involved in signal transduction and host cell activation. Nef has been shown to bind specifically to a subset of the Src family of kinases. The structures of free Nef and Nef bound to Src homology region 3 (SH3) domain are important for the elucidation of how the affinity and specificity for the Src kinase family SH3 domains are achieved, and also for the development of potential drugs and vaccines against AIDS. RESULTS: We have determined the crystal structures of the conserved core of HIV-1 Nef protein alone and in complex with the wild-type SH3 domain of the p59fyn protein tyrosine kinase (Fyn), at 3.0 A resolution. Comparison of the bound and unbound Nef structures revealed that a proline-rich motif (Pro-x-x-Pro), which is implicated in SH3 binding, is partially disordered in the absence of the binding partner; this motif only fully adopts a left-handed polyproline type II helix conformation upon complex formation with the Fyn SH3 domain. In addition, the structures show how an arginine residue (Arg77) of Nef interacts with Asp 100 of the so-called RT loop within the Fyn SH3 domain, and triggers a hydrogen-bond rearrangement which allows the loop to adapt to complement the Nef surface. The Arg96 residue of the Fyn SH3 domain is specifically accommodated in the same hydrophobic pocket of Nef as the isoleucine residue of a previously described Fyn SH3 (Arg96-->lle) mutant that binds to Nef with higher affinity than the wild type. CONCLUSIONS: The three-dimensional structures support evidence that the Nef-Fyn complex forms in vivo and may have a crucial role in the T cell perturbating action of Nef by altering T cell receptor signaling. The structures of bound and unbound Nef reveal that the multivalency of SH3 binding may be achieved by a ligand induced flexibility in the RT loop. The structures suggest possible targets for the design of inhibitors which specifically block Nef-SH3 interactions.     

Slow cellular dynamics in MDCK and R5 cells monitored by time-lapse atomic force microscopy

We have examined dynamic events that occur on a time scale of minutes in an epithelial monolayer of Madine-Darby Canine Kidney (MDCK) cells and in ras-transformed MDCK cells by atomic force microscopy (AFM). Cells were imaged under physiological conditions, and time-lapse movies representing approximately 60 s real time per frame were assembled. In normal MDCK cells, two types of protrusions in the apical plasma membrane exhibit dynamic behavior. First, smooth bulges formed transiently over the time scale of minutes to tens of minutes. Second, spike-like protrusions appear initially as bulges, extend well above the apical surface and, finally, seem to detach. R5, an oncogenic transformant derived from MDCK cells, grows very flat on glass. During AFM imaging, these cells sometimes round up and detach from the substrate. In light microscopic observations of parallel preparations, cells rarely detach, suggesting that this is an active response of these cells to irritation by the AFM tip. R5 cells often extend processes that are supported by actin stress fibers. During imaging with the AFM, these processes withdraw at a rate of 1-5 microns/min, similar to that observed by light microscopy. During the withdrawal, movement of the stress fibers can be clearly seen. In the flat periphery of these cells, the transport of intracellular particles along cytoskeletal elements was seen. In addition, we have observed two types of wave-like movements through the cell, which appear to be an organized rearrangement of cytoplasm. One type of wave moves radially out from center of the cell while the other moves circularly along the cell periphery.     

Effect of wafer thinning methods towards fracture strength and topography of silicon die

This paper characterizes die damage resulting from various wafer thinning processes. Die fracture strength is measured using ball breaker test with respect to die surface finish. Further study on surface roughness and topography of each surface finish is obtained by atomic force microscopy (AFM) and scanning electron microscopy (SEM) techniques. Stress relief process with 25 μm removal is able to strengthen 100 μm wafer by 20.4% using chemical wet etch and 75 μm wafer by 36.4% with plasma etch. Relatively, plasma etching shows higher fracture strength and flexibility compared to chemical wet etch. This is due to topography of the finished surface of plasma etch is smoother and rounded, leading to a reduced stress concentration, hence improved fracture strength.     

The influence of altruism on influenza vaccination decisions

Game theory is based on the assumption that individuals act according to self-interest and make decisions that maximize their personal payoffs. To test this fundamental assumption, we conducted a survey study in the context of influenza vaccination decisions. Contrary to the assumption of self-interest, we found that altruism plays an important role in vaccination decisions. Nevertheless, altruistic motivation has not yet been considered in epidemiological models, in predictions of vaccination decisions or in the design of vaccination policies. To determine the impact of altruism on the adherence to optimal vaccination policies and on resulting disease burden, we incorporated altruism into a game-theoretic epidemiological model of influenza vaccination. We found that altruism significantly shifted vaccination decisions away from individual self-interest and towards the community optimum, greatly reducing the total cost, morbidity and mortality for the community. Therefore, promoting altruism could be a potential strategy to improve public health outcomes.     

Silicon-29 solid-state nuclear magnetic resonance spectroscopy of composite interfaces

The types of structures and bonds that are formed with silicons in the composite interface were studied using ²⁹Si cross-polarization/magic angle sample spinning (CP/MAS) nuclear magnetic resonance spectroscopy (NMR). The change in mobility of silane coupling agent bonded to silica, as compared with bulk hydrolyzed silane coupling agent, can be monitored by the change in line width and the shift of resonances to higher fields, as well as by the change in the silicon-proton cross-polarization time T_SiH. In the silane coupling agent-matrix resin interface, the T_SiH values reflect the change in mobility as a function of the concentration and degree of hydrolysis of the silane coupling agent. It has been demonstrated that quantitative measurements of T_SiH can be used to investigate relative mobilities.     

Contact resistance in liquid nitrogen

The resistances of Cu, stainless steel, brass, Al, Fe, Ag and Au contacts in liquid nitrogen were measured. The contact resistance in liquid nitrogen was higher than that in air varying from several times to one thousand times greater. The resistance was seen to decrease inversely with an increase of current, but, only the Au contact was very little influenced by cooling.     

Using WinWin Quality Requirements Management Tools: A Case Study

Negotiating stakeholder WinWin relationships among software quality requirements is a technique that emerged during the 1990's in order to overcome the difficulties arising from contract-oriented specification compliance (popular in the 1970's) and service-oriented customer satisfaction (popular in the 1980's). Obstacles to adoption of negotiated win-win relationships include coordination of multiple stakeholder interests and priorities, reasoning of complicated dependencies, and scalability of an exponentially increasing resolution option space. Conflict identification and resolution techniques are key success factors to overcome the obstacles. This paper describes two exploratory knowledge-based tools (called QARCC and S-COST)^* for conflict identification and resolution and how they were used in the digital library projects of a USC Software Engineering class during the 1996/97 school year. A comparative analysis with the artifacts surfaced by stakeholders and the artifacts generated and analyzed by QARCC and S-COST focused on the conflict resolution process, stakeholders' roles and their relationships to quality artifacts, and tool effectiveness. We conclude that the tools helped stakeholders: (1) surface and negotiate conflicts; (2) identify conflicts among functional and quality requirements; and (3) generate, visualize, and negotiate potential resolution options for the conflicts.     

Fractionating the nonspatial pretraining effect in the water maze task.

Nonspatial pretraining (NSP) enables rats to learn the general strategies of the water maze task (WMIs; e.g., learning to swim away from the wall and to climb onto the hidden platform), reduces sensorimotor disturbances, and eliminates acquisition impairments caused by scopolamine hydrobromide, a muscarinic antagonist. To evaluate the contributions of the components of NSP to these effects, NSP was fractionated so that different groups of male rats swam, were placed onto the hidden platform, climbed onto the hidden platform, or were placed into an empty maze before spatial training under scopolamine. No single component of the NSP procedure was sufficient to produce its full effects on sensorimotor disturbances and WMT acquisition. Experience with most or perhaps all of the specific behaviors required in the WMT appears to be important for NSP to produce its full effects. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Efficacy and safety of 0.3% carbomer gel compared to placebo in patients with moderate-to-severe dry eye syndrome

PURPOSE: Carbomer gel is a water-soluble polymeric resin that has been reported to maintain the tear film in contact with the eye for an extended period. The efficacy and safety of this new artificial tear were assessed. METHODS: A multicenter, single-masked, randomized, placebo-controlled study was carried out on 123 patients with moderate-to-severe dry eyes. The placebo was a mannitol solution with benzalkonium chloride 0.008% as preservative. Patients were observed over an 8-week period, and subjective and objective changes analyzed, compared to a baseline of no therapy, after 1 to 7 days washout period from previous medication. RESULTS: All primary subjective symptoms decreased significantly in the carbomer gel-treated group compared to the placebo group (i.e., dryness, discomfort, and foreign body sensation). The carbomer gel also significantly improved the rose bengal staining score relative to placebo. When data for the primary subjective efficacy variables were stratified for disease severity, there was a statistically significant improvement from baseline by day 10 for severely affected patients and from day 42 for patients with moderate disease. Secondary subjective symptoms that improved significantly in the tear gel group compared to placebo were photophobia, erythema, tear breakup time, blurry-filmy, dry-sandy sensation, and physician impression. However, no significant improvements in the secondary subjective symptoms of tearing, itching, scaling, conjuctival discharge, palpebral conjunctival redness, bulbar conjuctival redness, conjunctival luster, relief of discomfort, ease of use, and overall acceptability were found in either group over the baseline score. In addition, neither carbomer gel nor placebo improved the baseline fluorescein staining score or the Schirmer test score. Two patients suffered local allergic reactions to the carbomer gel or its preservative, which settled on withdrawal of the medication. CONCLUSIONS: Carbomer gel was more efficacious than was placebo in improving a number of subjective and objective symptoms of moderate-to-severe dry eye syndrome. The results of this study indicate that carbomer gel was a safe as was the placebo.