Molecular ecology studies of marine Synechococcus

Cyanobacteria of the genus Synechococcus is a dominant component of microbial community in the world's oceans, and is a major contributor to marine primary productivity and thus plays an important role in carbon cycling in the oceans. Besides the ecological importance, the cultivability also made Synechococcus a very special group of marine microorganisms, which has attracted great attention from oceanographers and biologists. Great progress in the physiology, biochemistry and phylogeny of Synechococcus has been made since its discovery. We here review the current status of molecular ecology of marine Synechococcus and give a perspective into the future based on our understanding of the literature and our own work

Online Testing of User Profile Resilience Against Inference Attacks in Social Networks

International audienceTo increase awareness about privacy threats, we have designed a tool, SONSAI, for Facebook users to audit their own profiles. SONSAI predicts values of sensitive attributes by machine learning and identifies user public attributes that have guided the learning algorithm towards these sensitive attribute values. Here, we present new aspects of the system such as the automatic combination of link disclosure attacks and attribute prediction. We explain how we defined sensitive subjects from a survey. We also show how the extended tool is fully interfaced with Facebook along different scenarios. In each case a dataset was built from real profiles collected in the user neighbourhood network. The whole analysis process is performed online, mostly automatically and with accuracy of 0.79 in AUC when inferring the political orientation

Application of the rainfall infiltration breakthrough (RIB) model for groundwater recharge estimation in west coastal South Africa

Recharge estimation in arid and semi-arid areas is very challenging. The chloride mass balance method applied in western South Africa fails to provide reliable recharge estimates near coastal areas. A relationship between rainfall events and water level fluctuations (WLF) on a monthly basis was proposed in the rainfall infiltration breakthrough (RIB) model for the purpose of groundwater recharge estimation. In this paper, the physical meaning of parameters in the CRD and previous RIB models is clarified, and the RIB model is reviewed with the algorithm improved to accommodate various time scales, namely, daily, monthly and annual scales. Recharge estimates on a daily and monthly basis using the revised RIB approach in 2 study areas, one in a sandy alluvial aquifer (Riverlands) and the other in the Table Mountain Group (TMG) shallow unconfined aquifer (Oudebosch), are presented, followed by sensitivity analysis. Correlation analysis between rainfall and observed WLF data at daily scale and monthly scale, together with recharge estimates obtained from other methods, demonstrates that the RIB results using monthly data are more realistic than those for daily data, when using long time series. Scenarios using the data from Oudebosch with different rainfall and groundwater abstraction inputs are simulated to explore individual effects on water levels as well as recharge rate estimated on a daily basis. The sensitivity analysis showed that the recharge rate by the RIB model is specifically sensitive to the parameter of specific yield; therefore, the accurate representative specific yield of the aquifer needs to be selected with caution. The RIB model demonstrated in these two cases can be used to estimate groundwater recharge with sufficiently long time series of groundwater level and rainfall available in similar regions. In summary, the RIB model is best suited for shallow unconfined aquifers with relatively lower transmissivity;the utility of the RIB model for application in different climatic areas under different hydrogeological conditions needs to be further explored.Keywords: RIB model, shallow unconfined aquifer, groundwater-level fluctuation, groundwater recharge,Table Mountain Group aquife

Time series observation based InfraRed Epifluorescence Microscopic (TIREM) approach for accurate enumeration of bacteriochlorophyll-containing microbes in marine environments

Bacteriochlorophyll a Containing Microbes (BCM) are a unique group of microorganisms in the marine environment. Accurate determination of their abundance is critical for understanding their role in energy flow and carbon cycle in the ecosystem. The InfraRed Epifluorescence Microscopy (IREM) method, using infrared fluorescence as the diagnostic signal of BCM, is the most convenient means to date for enumeration of BCM in seawater, but IREM methodology suffers from serious errors introduced by cyanobacteria, which also can emit infrared fluorescence and whose abundance is of the same order of magnitude as BCM. In the present study, an advanced "Time-series observation based cyanobacteria-calibrated InfraRed Epifluorescence Microscopy (TIREM)" approach is established for accurate enumeration of BCM in marine environments. The protocol is distinguished by its use of time series observation, auto-imaging and digital analysis. In principle, the correct count of BCM can be obtained by subtracting the cyanobacterial count from the total infrared positive count. The challenge, however, is that Prochlorococcus, the most abundant cyanobacterium in the sea, is readily visible in infrared images but not visible in the initial cyanobacterial images obtained by epifluorescence microscopy because its emission signals are masked by brighter fluorescence from larger cells like Synechococcus coexisting in seawater samples. Prochlorococcus cells become gradually visible when the fluorescence from Synechococcus cells declines after a period of exposure to excitation light. Therefore the plateau (maximum) count of the cyanobacterial cells in time series images rather than in the initial ones, as previously believed, represents the correct count for the total number of cyanobacteria (Synechococcus plus Prochlorococcus cells). Thus, the accurate estimation of BCM abundance can only be calculated from the formula: [BCM cells] = [plateau count of infrared positive cells] - [plateau count of cyanobacterial cells]. The conceptual advance of the TIREM protocol is that in classical epifluorescence microscopy or in IREM protocols, quick observation is recommended to avoid quenching the fluorescence, but in the TIREM protocol, instead, time series observation is the key for obtaining reliable data. The TIREM protocol is validated by studies using BCM and cyanobacterial pure cultures as well as by examination of samples from various marine environments. (c) 2005 Elsevier B.V. All rights reserved

Mirror Descent and Convex Optimization Problems With Non-Smooth Inequality Constraints

We consider the problem of minimization of a convex function on a simple set with convex non-smooth inequality constraint and describe first-order methods to solve such problems in different situations: smooth or non-smooth objective function; convex or strongly convex objective and constraint; deterministic or randomized information about the objective and constraint. We hope that it is convenient for a reader to have all the methods for different settings in one place. Described methods are based on Mirror Descent algorithm and switching subgradient scheme. One of our focus is to propose, for the listed different settings, a Mirror Descent with adaptive stepsizes and adaptive stopping rule. This means that neither stepsize nor stopping rule require to know the Lipschitz constant of the objective or constraint. We also construct Mirror Descent for problems with objective function, which is not Lipschitz continuous, e.g. is a quadratic function. Besides that, we address the problem of recovering the solution of the dual problem

Dusty star forming galaxies at high redshift

The global star formation rate in high redshift galaxies, based on optical surveys, shows a strong peak at a redshift of z=1.5, which implies that we have already seen most of the formation. High redshift galaxies may, however, emit most of their energy at submillimeter wavelengths if they contain substantial amounts of dust. The dust would absorb the starlight and reradiate it as far-infrared light, which would be redshifted to the submillimeter range. Here we report a deep survey of two blank regions of sky performed at submillimeter wavelengths (450 and 850-micron). If the sources we detect in the 850-micron band are powered by star formation, then each must be converting more than 100 solar masses of gas per year into stars, which is larger than the maximum star formation rates inferred for most optically-selected galaxies. The total amount of high redshift star formation is essentially fixed by the level of background light, but where the peak occurs in redshift for the submillimeter is not yet established. However, the background light contribution from only the sources detected at 850-micron is already comparable to that from the optically-selected sources. Establishing the main epoch of star formation will therefore require a combination of optical and submillimeter studies.Comment: 10 pages + 2 Postscript figures, under embargo at Natur

Role of Potash Alum in Hepatitis C virus Transmission at Barber's Shop

Hepatitis C virus (HCV) is the main cause of severe liver disease, including hepatocellular carcinoma, cirrhosis and end stage liver disease. In Pakistan most of HCV positive patients have history of facial/armpit shaving from barbers. 79% of barbers are rubbing Potash Alum stone on facial shaving cuts. Dark blood spots are analyzed on Potash Alum stones being used at different barber shops. The aim of the study was to check the viability of hepatitis C virus on potash alum stone being used at barber shops. Blood samples from HCV positive patients were taken and treated with 0.1, 0.2, 0.3, 0.4 and 0.5 molar concentrations of Potash Alum for different periods of time. Blood was centrifuged to isolate the serum; HCV RNA was extracted from serum and subjected to first strand synthesis and PCR. PCR fragments were confirmed by sequencing. PCR amplification was observed in all the samples, treated with different concentrations of Potash Alum, indicated that the virus remains alive on Potash Alum stone for a long period of time. Potash Alum being used by barbers on facial shaving cuts has definite role in HCV transmission in Pakistani population. Therefore use of Potash Alum stone should be banned on facial shaving cuts at barber shops

Effect of Heat Treatment on Fracture Toughness ( K IC ) and Microstructure of a Fluorcanasite-Based Glass-Ceramic

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73358/1/j.1532-849X.2007.00233.x.pd

Sputum ACE2, TMPRSS2 and FURIN gene expression in severe neutrophilic asthma

Background Patients with severe asthma may have a greater risk of dying from COVID-19 disease. Angiotensin converting enzyme-2 (ACE2) and the enzyme proteases, transmembrane protease serine 2 (TMPRSS2) and FURIN, are needed for viral attachment and invasion into host cells. Methods We examined microarray mRNA expression of ACE2, TMPRSS2 and FURIN in sputum, bronchial brushing and bronchial biopsies of the European U-BIOPRED cohort. Clinical parameters and molecular phenotypes, including asthma severity, sputum inflammatory cells, lung functions, oral corticosteroid (OCS) use, and transcriptomic-associated clusters, were examined in relation to gene expression levels. Results ACE2 levels were significantly increased in sputum of severe asthma compared to mild-moderate asthma. In multivariate analyses, sputum ACE2 levels were positively associated with OCS use and male gender. Sputum FURIN levels were significantly related to neutrophils (%) and the presence of severe asthma. In bronchial brushing samples, TMPRSS2 levels were positively associated with male gender and body mass index, whereas FURIN levels with male gender and blood neutrophils. In bronchial biopsies, TMPRSS2 levels were positively related to blood neutrophils. The neutrophilic molecular phenotype characterised by high inflammasome activation expressed significantly higher FURIN levels in sputum than the eosinophilic Type 2-high or the pauci-granulocytic oxidative phosphorylation phenotypes. Conclusion Levels of ACE2 and FURIN may differ by clinical or molecular phenotypes of asthma. Sputum FURIN expression levels were strongly associated with neutrophilic inflammation and with inflammasome activation. This might indicate the potential for a greater morbidity and mortality outcome from SARS-CoV-2 infection in neutrophilic severe asthma

Digital PCR methods improve detection sensitivity and measurement precision of low abundance mtDNA deletions

Mitochondrial DNA (mtDNA) mutations are a common cause of primary mitochondrial disorders, and have also been implicated in a broad collection of conditions, including aging, neurodegeneration, and cancer. Prevalent among these pathogenic variants are mtDNA deletions, which show a strong bias for the loss of sequence in the major arc between, but not including, the heavy and light strand origins of replication. Because individual mtDNA deletions can accumulate focally, occur with multiple mixed breakpoints, and in the presence of normal mtDNA sequences, methods that detect broad-spectrum mutations with enhanced sensitivity and limited costs have both research and clinical applications. In this study, we evaluated semi-quantitative and digital PCR-based methods of mtDNA deletion detection using double-stranded reference templates or biological samples. Our aim was to describe key experimental assay parameters that will enable the analysis of low levels or small differences in mtDNA deletion load during disease progression, with limited false-positive detection. We determined that the digital PCR method significantly improved mtDNA deletion detection sensitivity through absolute quantitation, improved precision and reduced assay standard error