Control of gene conversion and somatic hypermutation by immunoglobulin promoter and enhancer sequences

It is thought that gene conversion (GCV) and somatic hypermutation (SHM) of immunoglobulin (Ig) genes occur in two steps: the generation of uracils in DNA by activation-induced cytidine deaminase, followed by their subsequent repair by various DNA repair pathways to generate sequence-diversified products. It is not known how either of the two steps is targeted specifically to Ig loci. Because of the tight link between transcription and SHM, we have investigated the role of endogenous Ig light chain (IgL) transcriptional control elements in GCV/SHM in the chicken B cell line DT40. Promoter substitution experiments led to identification of a strong RNA polymerase II promoter incapable of supporting efficient GCV/SHM. This surprising finding indicates that high levels of transcription are not sufficient for robust GCV/SHM in Ig loci. Deletion of the IgL enhancer in a context in which high-level transcription was not compromised showed that the enhancer is not necessary for GCV/SHM. Our results indicate that cis-acting elements are important for Ig gene diversification, and we propose that targeting specificity is achieved through the combined action of several Ig locus elements that include the promoter

AXES at TRECVid 2011

The AXES project participated in the interactive known-item search task (KIS) and the interactive instance search task (INS) for TRECVid 2011. We used the same system architecture and a nearly identical user interface for both the KIS and INS tasks. Both systems made use of text search on ASR, visual concept detectors, and visual similarity search. The user experiments were carried out with media professionals and media students at the Netherlands Institute for Sound and Vision, with media professionals performing the KIS task and media students participating in the INS task. This paper describes the results and findings of our experiments

Ultra-fast, programmable, and electronics-free soft robots enabled by snapping metacaps

Soft robots have a myriad of potentials because of their intrinsically compliant bodies, enabling safe interactions with humans and adaptability to unpredictable environments. However, most of them have limited actuation speeds, require complex control systems, and lack sensing capabilities. To address these challenges, here we geometrically design a class of metacaps whose rich nonlinear mechanical behaviors can be harnessed to create soft robots with unprecedented functionalities. Specifically, we demonstrate a sensor-less metacap gripper that can grasp objects in 3.75 ms upon physical contact and a pneumatically actuated gripper with tunable actuation behaviors that have little dependence on the rate of input. Both grippers can be readily integrated into a robotic platform for practical applications. Furthermore, we demonstrate that the metacap enables propelling of a swimming robot, exhibiting amplified swimming speed as well as untethered, electronics-free swimming with tunable speeds. Our metacaps provide new strategies to design the next-generation soft robots that require high transient output energy and are capable of autonomous and electronics-free maneuvering.Comment: 19 pages, 5 figure

ATP-independent reversal of a membrane protein aggregate by a chloroplast SRP subunit

Membrane proteins impose enormous challenges to cellular protein homeostasis during their post-translational targeting, and they require chaperones to keep them soluble and translocation competent. Here we show that a novel targeting factor in the chloroplast signal recognition particle (cpSRP), cpSRP43, is a highly specific molecular chaperone that efficiently reverses the aggregation of its substrate proteins. In contrast to 'ATPases associated with various cellular activities' (AAA+) chaperones, cpSRP43 uses specific binding interactions with its substrate to mediate its 'disaggregase' activity. This disaggregase capability can allow targeting machineries to more effectively capture their protein substrates and emphasizes a close connection between protein folding and trafficking processes. Moreover, cpSRP43 provides the first example to our knowledge of an ATP-independent disaggregase and shows that efficient reversal of protein aggregation can be attained by specific binding interactions between a chaperone and its substrate

Chaperone Spy Protects Outer Membrane Proteins from Folding Stress via Dynamic Complex Formation

Gram-negative bacteria have a multicomponent and constitutively active periplasmic chaperone system to ensure the quality control of their outer membrane proteins (OMPs). Recently, OMPs have been identified as a new class of vulnerable targets for antibiotic development, and therefore a comprehensive understanding of OMP quality control network components will be critical for discovering antimicrobials. Here, we demonstrate that the periplasmic chaperone Spy protects certain OMPs against protein-unfolding stress and can functionally compensate for other periplasmic chaperones, namely Skp and FkpA, in the Escherichia coli K-12 MG1655 strain. After extensive; in vivo; genetic experiments for functional characterization of Spy, we use nuclear magnetic resonance and circular dichroism spectroscopy to elucidate the mechanism by which Spy binds and folds two different OMPs. Along with holding OMP substrates in a dynamic conformational ensemble, Spy binding enables OmpX to form a partially folded β-strand secondary structure. The bound OMP experiences temperature-dependent conformational exchange within the chaperone, pointing to a multitude of local dynamics. Our findings thus deepen the understanding of functional compensation among periplasmic chaperones during OMP biogenesis and will promote the development of innovative antimicrobials against pathogenic Gram-negative bacteria.; IMPORTANCE; Outer membrane proteins (OMPs) play critical roles in bacterial pathogenicity and provide a new niche for antibiotic development. A comprehensive understanding of the OMP quality control network will strongly impact antimicrobial discovery. Here, we systematically demonstrate that the periplasmic chaperone Spy has a role in maintaining the homeostasis of certain OMPs. Remarkably, Spy utilizes a unique chaperone mechanism to bind OmpX and allows it to form a partially folded β-strand secondary structure in a dynamic exchange of conformations. This mechanism differs from that of other E. coli periplasmic chaperones such as Skp and SurA, both of which maintain OMPs in disordered conformations. Our study thus deepens the understanding of the complex OMP quality control system and highlights the differences in the mechanisms of ATP-independent chaperones