Quantitative analysis and modeling of katanin function in flagellar length control

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molecular Biology of the Cell 25 (2014): 3686-3698, doi:10.1091/mbc.E14-06-1116.Flagellar length control in Chlamydomonas reinhardtii provides a simple model system in which to investigate the general question of how cells regulate organelle size. Previous work demonstrated that Chlamydomonas cytoplasm contains a pool of flagellar precursor proteins sufficient to assemble a half-length flagellum and that assembly of full-length flagella requires synthesis of additional precursors to augment the preexisting pool. The regulatory systems that control the synthesis and regeneration of this pool are not known, although transcriptional regulation clearly plays a role. We used quantitative analysis of length distributions to identify candidate genes controlling pool regeneration and found that a mutation in the p80 regulatory subunit of katanin, encoded by the PF15 gene in Chlamydomonas, alters flagellar length by changing the kinetics of precursor pool utilization. This finding suggests a model in which flagella compete with cytoplasmic microtubules for a fixed pool of tubulin, with katanin-mediated severing allowing easier access to this pool during flagellar assembly. We tested this model using a stochastic simulation that confirms that cytoplasmic microtubules can compete with flagella for a limited tubulin pool, showing that alteration of cytoplasmic microtubule severing could be sufficient to explain the effect of the pf15 mutations on flagellar length.This work was funded by National Institutes of Health Grant R01 GM097017

Increased rates of large-magnitude explosive eruptions in Japan in the late Neogene and Quaternary

Tephra layers in marine sediment cores from scientific ocean drilling largely record high-magnitude silicic explosive eruptions in the Japan arc for up to the last 20 million years. Analysis of the thickness variation with distance of 180 tephra layers from a global dataset suggests that the majority of the visible tephra layers used in this study are the products of caldera-forming eruptions with magnitude (M) >6, considering their distances at the respective drilling sites to their likely volcanic sources. Frequency of visible tephra layers in cores indicates a marked increase in rates of large magnitude explosive eruptions at ~8 Ma, 6–4 Ma and further increase after ~2 Ma. These changes are attributed to major changes in tectonic plate interactions. Lower rates of large magnitude explosive volcanism in the Miocene are related to a strike-slip dominated boundary (and temporary cessation or deceleration of subduction) between the Philippine Sea Plate and southwest Japan, combined with the possibility that much of the arc in northern Japan was submerged beneath sea level partly due to previous tectonic extension of Northern Honshu related to formation of the Sea of Japan. Changes in plate motions and subduction dynamics during the ~8 Ma to present period led to (1) increased arc-normal subduction in southwest Japan (and resumption of arc volcanism) and (2) shift from extension to compression of the upper plate in northeast Japan, leading to uplift, crustal thickening and favourable conditions for accumulation of the large volumes of silicic magma needed for explosive caldera-forming eruptions

Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6

The protein deacetylase SIRT6 maintains cellular homeostasis through multiple pathways that include the deacetylation of histone H3 and repression of transcription. Prior work suggests that SIRT6 is associated with chromatin and can substantially reduce global levels of H3 acetylation, but how SIRT6 is able to accomplish this feat is unknown. Here, we describe an exquisitely tight interaction between SIRT6 and nucleosome core particles, in which a 2:1 enzyme:nucleosome complex assembles via asymmetric binding with distinct affinities. While both SIRT6 molecules associate with the acidic patch on the nucleosome, we find that the intrinsically disordered SIRT6 C-terminus promotes binding at the higher affinity site through recognition of nucleosomal DNA. Together, multivalent interactions couple productive binding to efficient deacetylation of histones on endogenous chromatin. Unique among histone deacetylases, SIRT6 possesses the intrinsic capacity to tightly interact with nucleosomes for efficient activity

HIV prevalence and undiagnosed infection among a community sample of gay and bisexual men in Scotland, 2005-2011: implications for HIV testing policy and prevention

<b>Objective</b><p></p> To examine HIV prevalence, HIV testing behaviour, undiagnosed infection and risk factors for HIV positivity among a community sample of gay men in Scotland.<p></p> <b>Methods</b><p></p> Cross-sectional survey of gay and bisexual men attending commercial gay venues in Glasgow and Edinburgh, Scotland with voluntary anonymous HIV testing of oral fluid samples in 2011. A response rate of 65.2% was achieved (1515 participants).<p></p> <b>Results</b><p></p> HIV prevalence (4.8%, 95% confidence interval, CI 3.8% to 6.2%) remained stable compared to previous survey years (2005 and 2008) and the proportion of undiagnosed infection among HIV-positive men (25.4%) remained similar to that recorded in 2008. Half of the participants who provided an oral fluid sample stated that they had had an HIV test in the previous 12 months; this proportion is significantly higher when compared to previous study years (50.7% versus 33.8% in 2005, p<0.001). Older age (>25 years) was associated with HIV positivity (1.8% in those <25 versus 6.4% in older ages group) as was a sexually transmitted infection (STI) diagnosis within the previous 12 months (adjusted odds ratio 2.13, 95% CI 1.09–4.14). There was no significant association between age and having an STI or age and any of the sexual behaviours recorded.<p></p> <b>Conclusion</b><p></p> HIV transmission continues to occur among gay and bisexual men in Scotland. Despite evidence of recent testing within the previous six months, suggesting a willingness to test, the current opt-out policy may have reached its limit with regards to maximising HIV test uptake. Novel strategies are required to improve regular testing opportunities and more frequent testing as there are implications for the use of other biomedical HIV interventions.<p></p&gt

Rapid in vivo measurement of B-amyloid reveals biphasic clearance kinetics in an Alzheimer\u27s mouse model

Accumulation of ?-amyloid peptide is a key step in Alzheimer?s disease pathogenesis. Yuede et al. propose a novel method to track ?-amyloid levels in vivo

Anti-CfaE nanobodies provide broad cross-protection against major pathogenic enterotoxigenic Escherichia coli strains, with implications for vaccine design

Enterotoxigenic Escherichia coli (ETEC) is estimated to cause approximately 380,000 deaths annually during sporadic or epidemic outbreaks worldwide. Development of vaccines against ETEC is very challenging due to the vast heterogeneity of the ETEC strains. An effective vaccines would have to be multicomponent to provide coverage of over ten ETEC strains with genetic variabilities. There is currently no vaccine licensed to prevent ETEC. Nanobodies are successful new biologics in treating mucosal infectious disease as they recognize conserved epitopes on hypervariable pathogens. Cocktails consisting of multiple nanobodies could provide even broader epitope coverage at a lower cost compared to monoclonal antibodies. Identification of conserved epitopes by nanobodies can also assist reverse engineering of an effective vaccine against ETEC. By screening nanobodies from immunized llamas and a naive yeast display library against adhesins of colonization factors, we identified single nanobodies that show cross-protective potency against eleven major pathogenic ETEC strains in vitro. Oral administration of nanobodies led to a significant reduction of bacterial colonization in animals. Moreover, nanobody-IgA fusion showed extended inhibitory activity in mouse colonization compared to commercial hyperimmune bovine colostrum product used for prevention of ETEC-induced diarrhea. Structural analysis revealed that nanobodies recognized a highly-conserved epitope within the putative receptor binding region of ETEC adhesins. Our findings support further rational design of a pan-ETEC vaccine to elicit robust immune responses targeting this conserved epitope

Examining racial and ethnic disparities in adult emergency department patient visits for concussion in the United States

Background Racial and ethnic differences in emergency department (ED) visits have been reported among adolescent patients but are unsubstantiated among adults. Therefore, our purpose in this study was to examine the relationship between race/ethnicity and adult ED visits for concussions, their injury mechanisms, and computed tomography (CT) scan use among a nationally representative sample. Methods We used the National Hospital Ambulatory Medical Care Survey database from 2010–2015 to examine 63,725 adult (20–45 years old) patient visits, representing an estimated 310.6 million visits presented to EDs. Of these visits, 884 (4.5 million national estimate) were diagnosed with a concussion. Visit records detailed patient information (age, sex, race/ethnicity, geographic region, primary payment type), ED visit diagnoses, injury mechanism (sport, motor vehicle, fall, struck by or against, “other”), and head CT scan use. The primary independent variable was race/ethnicity (non-Hispanic Asian, non-Hispanic Black or African American, Hispanic/Latinx, non-Hispanic multiracial or another, and non-Hispanic White). We used multivariable logistic and multinomial regression models with complex survey sampling design weighting to examine the relationship between concussion ED visits, injury mechanisms, and CT scan use separately by race/ethnicity while accounting for covariates. Results There were no associations between race/ethnicity and concussion diagnosis among adult ED visits after accounting for covariates. Relative to sports-related injuries, non-Hispanic Black or African American patient visits were associated with a motor vehicle (OR = 2.69, 95% CI: 1.06–6.86) and “other” injury mechanism (OR = 4.58, 95% CI: 1.34–15.69) compared to non-Hispanic White patients. Relative to sports-related injuries, non-Hispanic Asian, multiracial, or patients of another race had decreased odds of falls (OR = 0.20, 95% CI: 0.04–0.91) and “other” injuries (OR = 0.09, 95% CI: 0.01–0.55) compared to non-Hispanic White patients. The odds of a CT scan being performed were significantly lower among Hispanic/Latinx patient visits relative to non-Hispanic White patients (OR = 0.52, 95% CI: 0.30–0.91), while no other race/ethnicity comparisons differed. Conclusion Our findings indicate that the overarching concussion ED visit likelihood may not differ by race/ethnicity in adults, but the underlying mechanism causing the concussion and receiving a CT scan demonstrates considerable differences. Prospective future research is warranted to comprehensively understand and intervene in the complex, multi-level race/ethnicity relationships related to concussion health care to ensure equitable patient treatment

Individual common variants exert weak effects on the risk for autism spectrum disorders.

While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest P-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest