Early retinal activity and visual circuit development

Does spontaneous retinal activity prior to vision play a role in the establishment of visual maps? In this issue of Neuron, two separate papers by Huberman et al. and Hooks and Chen demonstrate a role for early spontaneous retinal activity in the establishment of ocular dominance columns and synaptic refinement at retinogeniculate synapses.     

The predatory role of white shrimp (<Emphasis Type="Italic">Litopenaeus setiferus</Emphasis>) in seasonal declines of subtidal macrobenthos

The overall purpose of this study was to develop a quantitative model to assess the influence of L. setiferus predation on subtidal macrobenthic abundance cycles in an estuarine creek system. Subtidal macrobenthic populations in temperate marine soft-bottom environments are known to undergo seasonal abundance cycles. Although the factors responsible for driving these seasonal shifts in abundance are difficult to identify, both environmental and biological factors have received credit. Juvenile white shrimp (Litopenaeus setiferus) are seasonally abundant epibenthic predators in the North Inlet estuary that have significant influence upon estuarine macrobenthic densities. Data generated from field and laboratory studies were combined with 20 years of long-term monitoring data to simulate seasonal variations in macrobenthos abundance under different levels of L. setiferus predation. Model simulations generated clear reductions in subtidal macrobenthos densities, confirming the role of L. setiferus as major consumers of macrobenthos. Model uncertainty was small, and model accuracy increased with shrimp density. In years with low or medium shrimp densities, predicted macrobenthos densities tended to be higher than those observed, yet predicted rates of decline still paralleled long-term observations. Model simulations best matched observed data for the representative high shrimp density year tested. Results indicate that variability in multiple factors, including L. setiferus predation, likely control macrobenthos abundance cycles. Predation by earlier-arriving epibenthic feeders may drive initial macrobenthos declines earlier in the year, with L. setiferus predation then intensifying and extending these declines throughout the summer and fall. This modeling approach is an important step toward understanding the role of multiple factors driving seasonal macrobenthos dynamics, and the L. setiferus population was tractable for examining the importance of epibenthic predation on these organisms. Handling editor: Luigi Naselli-Flores     

The C-terminal SH3 domain of CRKL as a dynamic dimerization module transiently exposing a nuclear export signal

CRKL plays essential roles in cell signaling. It consists of an N-terminal SH2 domain followed by two SH3 domains. SH2 and SH3N bind to signaling proteins, but the function of the SH3C domain has remained largely enigmatic. We show here that the SH3C of CRKL forms homodimers in protein crystals and in solution. Evidence for dimer formation of full-length CRKL is also presented. In the SH3C dimer, a nuclear export signal (NES) is mostly buried under the domain surface. The same is true for a monomeric SH3C obtained under different crystallization conditions. Interestingly, partial SH3 unfolding, such as occurs upon dimer/monomer transition, produces a fully-accessible NES through translocation of a single beta strand. Our results document the existence of an SH3 domain dimer formed through exchange of the first SH3 domain beta strand and suggest that partial unfolding of the SH3C is important for the relay of information in vivo.     

MULTBLAST: A web application for multiple BLAST searches

Basic Local Alignment Search Tool, (BLAST) allows the comparison of a query sequence/s to a database of sequences and identifies those sequences that are similar to the query above a user-defined threshold. We have developed a user friendly web application, MULTBLAST that runs a series of BLAST searches on a user-supplied list of proteins against one or more target protein or nucleotide databases. The application pre-processes the data, launches each individual BLAST search on the University of Nevada, Reno''s-TimeLogic DeCypher® system (available from Active Motif, Inc.) and retrieves and combines all the results into a simple, easy to read output file. The output file presents the list of the query proteins, followed by the BLAST results for the matching sequences from each target database in consecutive columns. This format is especially useful for either comparing the results from the different target databases, or analyzing the results while keeping the identification of each target database separate.

Availability

The application is available at the URLhttp://blastpipe.biochem.unr.edu/     

Family Characteristics as Risk Factors for Childhood Acute Lymphoblastic Leukemia: A Population-Based Case-Control Study

Background

To date, few risk factors for childhood acute lymphoblastic leukemia (ALL) have been confirmed and the scientific literature is full of controversial “evidence.” We examined if family characteristics, particularly maternal and paternal age and number of older siblings, were risk factors for childhood acute lymphoblastic leukemia (ALL).

Methodology/Principal Findings

In this population-based nationwide matched case-control study, patients 0–14 years of age with ALL diagnosed 1991–2006 and registered in the Swiss Childhood Cancer Registry were linked with their census records of 1990 and 2000. Eight controls per case were selected from the census. The association between family characteristics and ALL was analyzed by conditional logistic regressions. We found that increasing maternal age was associated with incidence of ALL in the offspring (OR per 5-year increase in maternal age 1.18, 95% CI 1.05–1.31; p = 0.004), remaining stable (trend OR 1.14, 95% CI 0.99–1.31; p = 0.060) after adjustment for other risk factors. The association with paternal age was weaker (OR per 5-year increase 1.14, 95% CI 1.01–1.28, p = 0.032) and disappeared after adjustments. Number of older siblings was not associated with risk of ALL in the overall group of children aged 0–14 years at diagnosis. However, we found a negative trend between number of older siblings and ALL diagnosed at age 0–4 years (OR per sibling 0.85, 95% CI 0.68–1.06; p = 0.141) and a positive trend for ALL diagnosed at age 5–9 (OR 1.34, 95% CI 1.05–1.72; p = 0.019), with some evidence for an effect modification (p-value for interaction  = 0.040).

Conclusions

As in other studies, increasing maternal, but not paternal age was associated with risk of ALL. We found only a weak association with the number of older siblings, suggesting a delay in disease manifestation rather than a decrease in incidence.