Empowering statistical methods for cellular and molecular biologists.

We provide guidelines for using statistical methods to analyze the types of experiments reported in cellular and molecular biology journals such as Molecular Biology of the Cell. Our aim is to help experimentalists use these methods skillfully, avoid mistakes, and extract the maximum amount of information from their laboratory work. We focus on comparing the average values of control and experimental samples. A Supplemental Tutorial provides examples of how to analyze experimental data using R software

Off-fault tensile cracks: A link between geological fault observations, lab experiments, and dynamic rupture models

We examine the local nature of the dynamic stress field in the vicinity of the tip of a semi-infinite sub-Rayleigh (slower than the Rayleigh wave speed, c_R) mode II crack with a velocity-weakening cohesive zone. We constrain the model using results from dynamic photoelastic experiments, in which shear ruptures were nucleated spontaneously in Homalite-100 plates along a bonded, precut, and inclined interface subject to a far-field uniaxial prestress. During the experiments, tensile cracks grew periodically along one side of the shear rupture interface at a roughly constant angle relative to the shear rupture interface. The occurrence and inclination of the tensile cracks are explained by our analytical model. With slight modifications, the model can be scaled to natural faults, providing diagnostic criteria for interpreting velocity, directivity, and static prestress state associated with past earthquakes on exhumed faults. Indirectly, this method also allows one to constrain the velocity-weakening nature of natural ruptures, providing an important link between field geology, laboratory experiments, and seismology

SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2.

SIRT1 and SIRT3 are NAD+-dependent protein deacetylases that are evolutionarily conserved across mammals. These proteins are located in the cytoplasm/nucleus and mitochondria, respectively. Previous reports demonstrated that human SIRT1 deacetylates Acetyl-CoA Synthase 1 (AceCS1) in the cytoplasm, whereas SIRT3 deacetylates the homologous Acetyl-CoA Synthase 2 (AceCS2) in the mitochondria. We recently showed that 3-hydroxy-3-methylglutaryl CoA synthase 2 (HMGCS2) is deacetylated by SIRT3 in mitochondria, and we demonstrate here that SIRT1 deacetylates the homologous 3-hydroxy-3-methylglutaryl CoA synthase 1 (HMGCS1) in the cytoplasm. This novel pattern of substrate homology between cytoplasmic SIRT1 and mitochondrial SIRT3 suggests that considering evolutionary relationships between the sirtuins and their substrates may help to identify and understand the functions and interactions of this gene family. In this perspective, we take a first step by characterizing the evolutionary history of the sirtuins and these substrate families

Physiological basis for storage life extension in fresh sweet potato: Final technical report

The overall objective of this project was to work towards the identification of the major physiological and environmental factors affecting perishability of the fresh sweet potato root, and thereby to facilitate the identification of strategies for increasing shelf-life through cultivar selection and improved handling practice

MOBILE and the provision of total joint replacement

Modern joint replacements have been available for 45 years, but we still do not have clear indications for these interventions, and we do not know how to optimize the outcome for patients who agree to have them done. The MOBILE programme has been investigating these issues in relation to primary total hip and knee joint replacements, using mixed methods research

Evaluation of the Induction of Immune Memory following Infant Immunisation with Serogroup C Neisseria meningitidis Conjugate Vaccines - Exploratory Analyses within a Randomised Controlled Trial

Aim: We measured meningococcal serogroup C (MenC)-specific memory B-cell responses in infants by Enzyme-Linked Immunospot (ELISpot) following different MenC conjugate vaccine schedules to investigate the impact of priming on immune memory. Methods: Infants aged 2 months were randomised to receive 1 or 2 doses of MenC-CRM197 at 3 or 3 and 4 months, 1 dose of MenC-TT at 3 months, or no primary MenC doses. All children received a Haemophilus influenzae type b (Hib)-MenC booster at 12 months. Blood was drawn at 5, 12, 12 months +6 days and 13 months of age. Results: Results were available for 110, 103, 76 and 44 children from each group respectively. Following primary immunisations, and prior to the 12-month booster, there were no significant differences between 1- or 2-dose primed children in the number of MenC memory B-cells detected. One month following the booster, children primed with 1 dose MenC-TT had more memory B-cells than children primed with either 1-dose (p = 0.001) or 2-dose (p<0.0001) MenC-CRM197. There were no differences in MenC memory B-cells detected in children who received 1 or 2 doses of MenC-CRM197 in infancy and un-primed children. Conclusions: MenC-specific memory B-cell production may be more dependent on the type of primary vaccine used than the number of doses administered. Although the mechanistic differences between MenC-CRM197 and MenC-TT priming are unclear, it is possible that structural differences, including the carrier proteins, may underlie differential interactions with B- and T-cell populations, and thus different effects on various memory B-cell subsets. A MenC-TT/Hib-MenC-TT combination for priming/boosting may offer an advantage in inducing more persistent antibody.peer-reviewe

Load fluctuations drive actin network growth

The growth of actin filament networks is a fundamental biological process that drives a variety of cellular and intracellular motions. During motility, eukaryotic cells and intracellular pathogens are propelled by actin networks organized by nucleation-promoting factors, which trigger the formation of nascent filaments off the side of existing filaments in the network. A Brownian ratchet (BR) mechanism has been proposed to couple actin polymerization to cellular movements, whereby thermal motions are rectified by the addition of actin monomers at the end of growing filaments. Here, by following actin--propelled microspheres using three--dimensional laser tracking, we find that beads adhered to the growing network move via an object--fluctuating BR. Velocity varies with the amplitude of thermal fluctuation and inversely with viscosity as predicted for a BR. In addition, motion is saltatory with a broad distribution of step sizes that is correlated in time. These data point to a model in which thermal fluctuations of the microsphere or entire actin network, and not individual filaments, govern motility. This conclusion is supported by Monte Carlo simulations of an adhesion--based BR and suggests an important role for membrane tension in the control of actin--based cellular protrusions.Comment: To be published in PNA

Neurospora strains incorporating fluffy, and their use as testers.

We have used fluffy (fl) strains extensively as female parents in mating-type tests and for a variety of other applications where high fertility and absence of conidia are advantageous

Evaluation of a present-day climate simulation with a new coupled atmosphere-ocean model GENMOM

We present a new, non-flux corrected AOGCM, GENMOM, that combines the GENESIS version 3 atmospheric GCM (Global Environmental and Ecological Simulation of Interactive Systems) and MOM2 (Modular Ocean Model version 2) nominally at T31 resolution. We evaluate GENMOM by comparison with reanalysis products (e.g., NCEP2) and three models used in the IPCC AR4 assessment. GENMOM produces a global temperature bias of 0.6 °C. Atmospheric features such as the jet stream structure and major semi-permanent sea level pressure centers are well simulated as is the mean planetary-scale wind structure that is needed to produce the correct position of stormtracks. Most ocean surface currents are reproduced except where they are not resolvable at T31 resolution. Overall, GENMOM captures reasonably well the observed gradients and spatial distributions of annual surface temperature and precipitation and the simulations are on par with other AOGCMs. Deficiencies in the GENMOM simulations include a warm bias in the surface temperature over the southern oceans, a split in the ITCZ and weaker-than-observed overturning circulation

Rivaroxaban for Preventing Atherothrombotic Events in People with Acute Coronary Syndrome and Elevated Cardiac Biomarkers: An Evidence Review Group Perspective of a NICE Single Technology Appraisal.

As part of its Single Technology Appraisal process, the National Institute for Health and Care Excellence (NICE) invited the company that manufactures rivaroxaban (Xarelto, Bayer) to submit evidence of the clinical and cost effectiveness of rivaroxaban for the prevention of adverse outcomes in patients after the acute management of acute coronary syndrome (ACS). The School of Health and Related Research Technology Appraisal Group at the University of Sheffield was commissioned to act as the independent Evidence Review Group (ERG). The ERG produced a critical review of the evidence for the clinical and cost effectiveness of the technology, based upon the company's submission to NICE. The evidence was derived mainly from a randomised, double-blind, phase III, placebo-controlled trial of rivaroxaban (either 2.5 or 5 mg twice daily) in patients with recent ACS [unstable angina, non-ST segment elevation myocardial infarction (NSTEMI) or ST segment elevation myocardial infarction (STEMI)]. In addition, all patients received antiplatelet therapy [aspirin alone or aspirin and a thienopyridine either as clopidogrel (approximately 99 %) or ticlopidine (approximately 1 %) according to national or local guidelines]. The higher dose of rivaroxaban (5 mg twice daily) did not form part of the marketing authorisation. A post hoc subgroup analysis of the licensed patients who had ACS with elevated cardiac biomarkers (that is, patients with STEMI and NSTEMI) without prior stroke or transient ischaemic stroke showed that compared with standard care, the addition of rivaroxaban (2.5 mg twice daily) to existing antiplatelet therapy reduced the composite endpoint of cardiovascular mortality, myocardial infarction or stroke, but increased the risk of major bleeding and intracranial haemorrhage. However, there were a number of limitations in the evidence base that warrant caution in its interpretation. In particular, the evidence may be confounded because of the post hoc subgroup analysis, modified intention-to-treat analyses, high dropout rates and missing vital status data. Results from the company's economic evaluation showed that the deterministic incremental cost-effectiveness ratio (ICER) for rivaroxaban in combination with aspirin plus clopidogrel or with aspirin alone compared with aspirin plus clopidogrel or aspirin alone was £6203 per quality-adjusted life-year (QALY) gained. In contrast, the ERG's preferred base case estimate was £5622 per QALY gained. The ICER did not rise above £10,000 per QALY gained in any of the sensitivity analyses undertaken by the ERG, although the inflexibility of the company's economic model precluded the ERG from formally undertaking all desired exploratory analyses. As such, only a crude exploration of the impact of additional bleeding events could be undertaken. The NICE Appraisal Committee concluded that the ICERs presented were all within the range that could be considered cost effective and that the results of the ERG's exploratory sensitivity and scenario analyses suggested that the ICER was unlikely to increase to the extent that it would become unacceptable. The Appraisal Committee therefore concluded that rivaroxaban in combination with aspirin plus clopidogrel, or with aspirin alone, was a cost-effective use of National Health Service (NHS) resources for preventing atherothrombotic events in people with ACS and elevated cardiac biomarkers