MetaTM - a consensus method for transmembrane protein topology prediction

Transmembrane (TM) proteins are proteins that span a biological membrane one or more times. As their 3-D structures are hard to determine, experiments focus on identifying their topology (i. e. which parts of the amino acid sequence are buried in the membrane and which are located on either side of the membrane), but only a few topologies are known. Consequently, various computational TM topology predictors have been developed, but their accuracies are far from perfect. The prediction quality can be improved by applying a consensus approach, which combines results of several predictors to yield a more reliable result. RESULTS: A novel TM consensus method, named MetaTM, is proposed in this work. MetaTM is based on support vector machine models and combines the results of six TM topology predictors and two signal peptide predictors. On a large data set comprising 1460 sequences of TM proteins with known topologies and 2362 globular protein sequences it correctly predicts 86.7% of all topologies. CONCLUSION: Combining several TM predictors in a consensus prediction framework improves overall accuracy compared to any of the individual methods. Our proposed SVM-based system also has higher accuracy than a previous consensus predictor. MetaTM is made available both as downloadable source code and as DAS server at http://MetaTM.sbc.su.se

The readout of the fullerene-based quantum computing by a scanning tunneling microscope

We consider to detect the electron spin of a doped atom, i.e., a nitrogen or a phosphorus, caged in a fullerene by currently available technique of the scanning tunneling microscope (STM), which actually corresponds to the readout of a qubit in the fullerene-based quantum computing. Under the conditions of polarized STM current and Coulomb blockade, we investigate the tunneling matrix elements involving the exchange coupling between the tunneling polarized electrons and the encapsulated polarized electron, and calculate the variation of the tunneling current with respect to different orientations of the encapsulated electron spin. The experimental feasibility of our scheme is discussed under the consideration of some imperfect factors.Comment: RevTex file, 3 figures. To appear in New Journal of Physic

Anaerobic carboxydotrophy in sulfur-respiring haloarchaea from hypersaline lakes

Anaerobic carboxydotrophy is a widespread catabolic trait in bacteria, with two dominant pathways: hydrogenogenic and acetogenic. The marginal mode by direct oxidation to CO2 using an external e-acceptor has only a few examples. Use of sulfidic sediments from two types of hypersaline lakes in anaerobic enrichments with CO as an e-donor and elemental sulfur as an e-acceptor led to isolation of two pure cultures of anaerobic carboxydotrophs belonging to two genera of sulfur-reducing haloarchaea: Halanaeroarchaeum sp. HSR-CO from salt lakes and Halalkaliarchaeum sp. AArc-CO from soda lakes. Anaerobic growth of extremely halophilic archaea with CO was obligatory depended on the presence of elemental sulfur as the electron acceptor and yeast extract as the carbon source. CO served as a direct electron donor and H2 was not generated from CO when cells were incubated with or without sulfur. The genomes of the isolates encode a catalytic Ni,Fe-CODH subunit CooS (distantly related to bacterial homologs) and its Ni-incorporating chaperone CooC (related to methanogenic homologs) within a single genomic locus. Similar loci were also present in a genome of the type species of Halalkaliarchaeum closely related to AArc-CO, and the ability for anaerobic sulfur-dependent carboxydotrophy was confirmed for three different strains of this genus. Moreover, similar proteins are encoded in three of the four genomes of recently described carbohydrate-utilizing sulfur-reducing haloarchaea belonging to the genus Halapricum and in two yet undescribed haloarchaeal species. Overall, this work demonstrated for the first time the potential for anaerobic sulfur-dependent carboxydotrophy in extremely halophilic archaea.Accepted Author ManuscriptBT/Environmental Biotechnolog

NemaPath: online exploration of KEGG-based metabolic pathways for nematodes

<p>Abstract</p> <p>Background</p> <p>Nematode.net <url>http://www.nematode.net</url> is a web-accessible resource for investigating gene sequences from parasitic and free-living nematode genomes. Beyond the well-characterized model nematode <it>C. elegans</it>, over 500,000 expressed sequence tags (ESTs) and nearly 600,000 genome survey sequences (GSSs) have been generated from 36 nematode species as part of the Parasitic Nematode Genomics Program undertaken by the Genome Center at Washington University School of Medicine. However, these sequencing data are not present in most publicly available protein databases, which only include sequences in Swiss-Prot. Swiss-Prot, in turn, relies on GenBank/Embl/DDJP for predicted proteins from complete genomes or full-length proteins.</p> <p>Description</p> <p>Here we present the NemaPath pathway server, a web-based pathway-level visualization tool for navigating putative metabolic pathways for over 30 nematode species, including 27 parasites. The NemaPath approach consists of two parts: 1) a backend tool to align and evaluate nematode genomic sequences (curated EST contigs) against the annotated Kyoto Encyclopedia of Genes and Genomes (KEGG) protein database; 2) a web viewing application that displays annotated KEGG pathway maps based on desired confidence levels of primary sequence similarity as defined by a user. NemaPath also provides cross-referenced access to nematode genome information provided by other tools available on Nematode.net, including: detailed NemaGene EST cluster information; putative translations; GBrowse EST cluster views; links from nematode data to external databases for corresponding synonymous <it>C. elegans </it>counterparts, subject matches in KEGG's gene database, and also KEGG Ontology (KO) identification.</p> <p>Conclusion</p> <p>The NemaPath server hosts metabolic pathway mappings for 30 nematode species and is available on the World Wide Web at <url>http://nematode.net/cgi-bin/keggview.cgi</url>. The nematode source sequences used for the metabolic pathway mappings are available via FTP <url>http://www.nematode.net/FTP/index.php</url>, as provided by the Genome Center at Washington University School of Medicine.</p

A Resonant Graphene NEMS Vibrometer

Measuring vibrations is essential to ensuring building structural safety and machine stability. Predictive maintenance is a central internet of things (IoT) application within the new industrial revolution, where sustainability and performance increase over time are going to be paramount. To reduce the footprint and cost of vibration sensors while improving their performance, new sensor concepts are needed. Here, double-layer graphene membranes are utilized with a suspended silicon proof demonstrating their operation as resonant vibration sensors that show outstanding performance for a given footprint and proof mass. The unveiled sensing effect is based on resonant transduction and has important implications for experimental studies involving thin nano and micro mechanical resonators that are excited by an external shaker

Soy food intake behavior by socio-demographic characteristics of Korean housewives

In this study, the soy food intake behaviors including perception and intake frequency of soybean foods by sociodemographic variables were analyzed in housewives. The perception of housewives for soy foods showed that soybean paste, soybean curd, and Dambuk were high in the descending order for nutritional quality and health promotion effect, and soybean paste received the highest score in taste and flavor. Soybean sprouts received the highest evaluation score in the economic aspect. In the aspect of safe food, soybean paste received the highest evaluation score, as mush as a traditional food. The analysis of perception by sociodemographic variables showed that soybean curd, Dambuk, and soybean sprouts had higher perceptions as education level increased, and soy milk had higher perceptions in subjects with younger age and with employment. In the intake frequency, more than 50% of the subjects had soybean curd, soybean sprouts, and soybean paste more than once a week. The analysis for correlation between the intake frequency of soy foods and the degree of perception showed that taste and flavor had high correlation with the intake frequency of soy foods except soybean sprouts. The intake frequency of soybean paste, Dambuk, and soy milk had positive correlations to familiarity and that of soy milk had positive correlations to nutrition and health perception, and those of soybeam paste, soybean sprouts, and soy milk had positive correlations to safe food perception. From the above results, housewives in Korea had very high perceptions to nutritional quality and health promotion effect of soy foods and the degree of perception and accompanied intake frequency had significant differences by age, education level, and economic level among sociodemographic variables

Estimated dietary isoflavone intake among Korean adults

This study estimated the isoflavone intake level in Koreans using Food Frequency Questionnaire and analyzed related variables. The results showed that the average daily intake of isoflavone in adults was shown as 23.1 mg. The isoflavone intake level at 50 percentile was 16.9 mg (0~190 mg), and 10% of adults took almost 50 mg of isoflavone a day and 10% took about 5 mg a day. The major food sources for isoflavone in Koreans were in the order of soybean, soybean paste, soy milk, soybean curd (tofu), and bean sprouts; the intake was different depending on age, educational background, occupation, economic standard, and family type. The result showed higher isoflavone intake levels in the group over 30 years old and the highest isoflavone intake in subjects working in farming/fishery, followed by housemakers. According to the differences by families the families with elderly members showed 50% higher isoflavone intake than young families with friends or siblings. Depending on related ecological variables, therefore, various nutrition education programs should be developed for a variety of intakes of soybean foods, along with easy and simple cooking methods as parts of continuous research

Anomalous Effects of "Guest" Charges Immersed in Electrolyte: Exact 2D Results

We study physical situations when one or two "guest" arbitrarily-charged particles are immersed in the bulk of a classical electrolyte modelled by a Coulomb gas of positive/negative unit point-like charges, the whole system being in thermal equilibrium. The models are treated as two-dimensional with logarithmic pairwise interactions among charged constituents; the (dimensionless) inverse temperature $\beta$ is considered to be smaller than 2 in order to ensure the stability of the electrolyte against the collapse of positive-negative pairs of charges. Based on recent progress in the integrable (1+1)-dimensional sine-Gordon theory, exact formulas are derived for the chemical potential of one guest charge and for the asymptotic large-distance behavior of the effective interaction between two guest charges. The exact results imply, under certain circumstances, anomalous effects such as an effective attraction (repulsion) between like-charged (oppositely-charged) guest particles and the charge inversion in the electrolyte vicinity of a highly-charged guest particle. The adequacy of the concept of renormalized charge is confirmed in the whole stability region of inverse temperatures and the related saturation phenomenon is revised.Comment: 21 pages, 1 figur

Myocarditis and pericarditis associated with SARS-CoV-2 vaccines: A population-based descriptive cohort and a nested self-controlled risk interval study using electronic health care data from four European countries

COVID-19 vaccine; Adverse drug reaction; MyocarditisVacuna contra el COVID-19; Reacció adversa a fàrmacs; MiocarditisVacuna contra el COVID-19; Reacción adversa a medicamentos; MiocarditisBackground: Estimates of the association between COVID-19 vaccines and myo-/pericarditis risk vary widely across studies due to scarcity of events, especially in age- and sex-stratified analyses. Methods: Population-based cohort study with nested self-controlled risk interval (SCRI) using healthcare data from five European databases. Individuals were followed from 01/01/2020 until end of data availability (31/12/2021 latest). Outcome was first myo-/pericarditis diagnosis. Exposures were first and second dose of Pfizer, AstraZeneca, Moderna, and Janssen COVID-19 vaccines. Baseline incidence rates (IRs), and vaccine- and dose-specific IRs and rate differences were calculated from the cohort The SCRI calculated calendar time-adjusted IR ratios (IRR), using a 60-day pre-vaccination control period and dose-specific 28-day risk windows. IRRs were pooled using random effects meta-analysis. Findings: Over 35 million individuals (49·2% women, median age 39–49 years) were included, of which 57·4% received at least one COVID-19 vaccine dose. Baseline incidence of myocarditis was low. Myocarditis IRRs were elevated after vaccination in those aged < 30 years, after both Pfizer vaccine doses (IRR = 3·3, 95%CI 1·2-9.4; 7·8, 95%CI 2·6-23·5, respectively) and Moderna vaccine dose 2 (IRR = 6·1, 95%CI 1·1-33·5). An effect of AstraZeneca vaccine dose 2 could not be excluded (IRR = 2·42, 95%CI 0·96-6·07). Pericarditis was not associated with vaccination. Interpretation: mRNA-based COVID-19 vaccines and potentially AstraZeneca are associated with increased myocarditis risk in younger individuals, although absolute incidence remains low. More data on children (≤ 11 years) are needed.The project received support from the European Medicines Agency (EMA/2018/23/PE)

Non-mean-field screening by multivalent counterions

Screening of a strongly charged macroion by its multivalent counterions can not be described in the framework of mean field Poisson-Boltzmann (PB) theory because multivalent counterions form a strongly correlated liquid (SCL) on the surface of the macroion. It was predicted that a distant counterion polarizes the SCL as if it were a metallic surface and creates an electrostatic image. The attractive potential energy of the image is the reason why the charge density of counterions decreases faster with distance from the charged surface than in PB theory. Using the Monte Carlo method to find the equilibrium distribution of counterions around the macroion, we confirm the existence of the image potential energy. It is also shown that due to the negative screening length of the SCL, $-2\xi$, the effective metallic surface is actually above the SCL by $|\xi|$.Comment: 9 pages, 6 figures; v5: new section added to address bulk screening by monovalent sal