ALBERT

Description: Effects of seawater p CO 2 changes on the calcifying fluid of scleractinian corals Biogeosciences Discussions, 9, 2655-2689, 2012 Author(s): S. Hohn and A. Merico Rising atmospheric CO 2 concentrations due to anthropogenic emissions induce changes in the ocean carbonate chemistry and a drop in ocean pH. This acidification process is expected to harm calcifying organisms like coccolithophores, molluscs, echinoderms, and corals. A severe decline in coral abundance is, for example, expected by the end of this century with associated disastrous effects on reef ecosystems. Despite the growing importance of the topic, little progress has been made with respect to modelling the impact of acidification on coral calcification. Here we present a model for a coral polyp that simulates the carbonate system in four different compartments: the seawater, the polyp tissue, the coelenteron, and the calicoblastic layer. Precipitation of calcium carbonate takes place in the metabolically controlled calicoblastic layer beneath the polyp tissue. The model is adjusted to a state of activity as observed by direct microsensor measurements in the calcifying fluid. Simulated CO 2 perturbation experiments reveal decreasing calcification rates under elevated p CO 2 despite strong metabolic control of the calcifying fluid. Diffusion of CO 2 through the tissue into the calicoblastic layer increases with increasing seawater p CO 2 leading to decreased aragonite saturation in the calcifying fluid of the coral polyp. Our modelling study provides important insights into the complexity of the calcification process at the organism level and helps to quantify the effect of ocean acidification on corals.

Description: The role of the seagrass Posidonia oceanica in the cycling of trace elements Biogeosciences Discussions, 9, 2623-2653, 2012 Author(s): C. Sanz-Lázaro, P. Malea, E. T. Apostolaki, I. Kalantzi, A. Marín, and I. Karakassis The aim of this work was to study the role of the seagrass Posidonia oceanica on the cycling of a wide set of trace elements (Ag, As, Ba, Bi, Cd, Co, Cr, Cs, Cu, Fe, Ga, Li, Mn, Ni, Pb, Rb, Sr, Tl, V and Zn). We measured the concentration of these trace elements in the different compartments of P. oceanica (leaves, rhizomes, roots and epibiota) in a non-polluted seagrass meadow representative of the Mediterranean and calculated the annual budget from a mass balance. We provide novel data on accumulation dynamics of many trace elements in P. oceanica compartments and demonstrate that trace element accumulation patterns are mainly determined by plant compartment rather than by temporal variability. Epibiota was the compartment which showed the greatest concentrations for most trace elements. Thus, they constitute a key compartment when estimating trace element transfer to higher trophic levels by P. oceanica . For most trace elements, translocation seemed to be low and acropetal. Zn, Cd, Sr and Rb were the trace elements that showed the highest release rate through decomposition of plant detritus, while Cs, Tl and Bi the lowest. P. oceanica acts as a sink of potentially toxic trace elements (Ni, Cr, As and Ag), which can be sequestered, decreasing their bioavailability. P. oceanica may have a relevant role in the cycling of trace elements in the Mediterranean.

Description: Direct observations of diel biological CO 2 fixation in the oceans Biogeosciences Discussions, 9, 2153-2168, 2012 Author(s): H. Thomas, S. E. Craig, B. J. W. Greenan, W. Burt, G. J. Herndl, S. Higginson, L. Salt, E. H. Shadwick, and J. Urrego-Blanco Much of the variability in the surface ocean's carbon cycle can be attributed to the availability of sunlight, through processes such as heat fluxes and photosynthesis, which regulate over a wide range of time scales. The critical processes occurring on timescales of a day or less, however, have undergone few investigations, and most of these have been limited to a time span of several days to months, or exceptionally, for longer periods. Optical methods have helped to infer short-term biological variability, however corresponding investigations of the oceanic CO 2 system are lacking. We employ high-frequency CO 2 and optical observations covering the full seasonal cycle on the Scotian Shelf, Northwestern Atlantic Ocean, in order to unravel diel periodicity of the surface ocean carbon cycle and its effects on annual budgets. Significant diel periodicity occurs only if the water column is sufficiently stable as observed during seasonal warming. During that time biological CO 2 drawdown, or net community production (NCP), is delayed for several hours relative to the onset of photosynthetically available radiation (PAR), due to diel cycles in chlorophyll- a concentration and to grazing, both of which, we suggest, inhibit NCP in the early morning hours. In summer, NCP decreases by more than 90 %, coinciding with the seasonal minimum of the mixed layer depth and resulting in the disappearance of the diel CO 2 periodicity in the surface waters.

Description: Contribution of flowering trees to urban atmospheric biogenic volatile organic compound emissions Biogeosciences Discussions, 9, 3145-3172, 2012 Author(s): R. Baghi, D. Helmig, A. Guenther, T. Duhl, and R. Daly Emissions of biogenic volatile organic compounds (BVOC) from urban trees during and after blooming were measured during spring and early summer 2009 in Boulder, Colorado. Air samples were collected onto solid adsorbent cartridges from branch enclosures on the tree species crabapple, horse chestnut, honey locust, and hawthorn. These species constitute ~65 % of the insect-pollinated fraction of the flowering tree canopy (excluding catkin-producing trees) from the street area managed by the City of Boulder. Samples were analyzed for C 10 –C 15 BVOC by thermal desorption and gas chromatography coupled to a flame ionization detector and a mass spectrometer (GC/FID/MS). Identified emissions and emission rates from these four tree species during the flowering phase were found to vary over a wide range. Monoterpene emissions were identified for honey locust, horse chestnut and hawthorn. Sesquiterpene emissions were observed in horse chestnut and hawthorn samples. Crabapple flowers were found to emit significant amounts of benzyl alcohol and benzaldehyde. Floral BVOC emissions increased with temperature, generally exhibiting exponential temperature dependence. Changes in BVOC speciation during and after the flowering period were observed for every tree studied. Emission rates were significantly higher during the blooming compared to the vegetative state for crabapple and honey locust. Total normalized (30 °C) monoterpene emissions from honey locust were higher during flowering (5.26 μg Cg −1 h −1 ) than after flowering (1.23 μg Cg −1 h −1 ). The total normalized BVOC emission rate from crabapple (93 μg Cg −1 h −1 ) during the flowering period is of the same order as isoprene emissions from oak trees, which are among the highest BVOC emissions observed from plants to date. These findings illustrate that during the relatively brief springtime flowering period, floral emissions constitute by far the most significant contribution to the BVOC flux from these tree species, some of which are leafless at this time. Experimental results were integrated into the MEGAN biogenic emission model and simulations were performed to estimate the contribution of floral BVOC emissions to the total urban BVOC flux during the spring flowering period. The floral BVOC emitted during this three-month simulation are equivalent to 11 % of the cumulative monoterpene flux for the Boulder urban area.

Description: Contributions of ectomycorrhizal fungal mats to forest soil respiration Biogeosciences Discussions, 9, 1635-1666, 2012 Author(s): C. L. Phillips, L. A. Kluber, J. P. Martin, B. A. Caldwell, and B. J. Bond Distinct aggregations of fungal hyphae and rhizomorphs, or "mats" formed by some genera of ectomycorrhizal (EcM) fungi are common features of soils in coniferous forests of the Pacific Northwest. We measured in situ respiration rates of Piloderma mats and neighboring non-mat soils in an old-growth Douglas-fir forest in Western Oregon to investigate whether there was an incremental increase in respiration from mat soils, and to estimate mat contributions to total soil respiration. We found that areas where Piloderma mats colonized the organic horizon often had higher soil surface flux than non-mats, with the incremental increase in respiration averaging 16 % across two growing seasons. Both soil physical factors and biochemistry were related to the higher surface flux of mat soils. When air-filled pore space was low (high soil moisture), soil CO 2 production was concentrated into near-surface soil horizons where mats tend to colonize, resulting in greater apparent differences in respiration between mat and non-mat soils. Respiration rates were also correlated with the activity of chitin-degrading soil enzymes. This suggests that the elevated activity of fungal mats may be related to consumption or turnover of chitinous fungal cell-wall materials. We found Piloderma mats present across 57 % of the soil surface in the study area, and use this value to estimate a respiratory contribution from mats at the stand-scale of about 9 % of total soil respiration. The activity of EcM mats, which includes both EcM fungi and microbial associates, was estimated to constitute a substantial portion of total soil respiration in this old-growth Douglas-fir forest.

Description: Remote sensing-based estimation of gross primary production in a subalpine grassland Biogeosciences Discussions, 9, 1711-1758, 2012 Author(s): M. Rossini, S. Cogliati, M. Meroni, M. Migliavacca, M. Galvagno, L. Busetto, E. Cremonese, T. Julitta, C. Siniscalco, U. Morra di Cella, and R. Colombo This study investigates the performances in a terrestrial ecosystem of gross primary production (GPP) estimation of a suite of spectral vegetation indexes (VIs) that can be computed from currently orbiting platforms. Vegetation indexes were computed from near-surface field spectroscopy measurements collected using an automatic system designed for high temporal frequency acquisition of spectral measurements in the visible near-infrared region. Spectral observations were collected for two consecutive years in Italy in a subalpine grassland equipped with an Eddy Covariance (EC) flux tower which provides continuous measurements of net ecosystem carbon dioxide (CO 2 ) exchange (NEE) and the derived GPP. Different VIs were calculated based on ESA-MERIS and NASA-MODIS spectral bands and correlated with biophysical (Leaf Area Index, LAI; fraction of photosynthetically active radiation intercepted by green vegetation, f IPAR g ), biochemical (chlorophyll concentration) and ecophysiological (green light-use efficiency, LUE g ) canopy variables. In this study, the normalized difference vegetation index (NDVI) showed better correlations with LAI and f PAR g ( r = 0.90 and 0.95, respectively), the MERIS terrestrial chlorophyll index (MTCI) with leaf chlorophyll content ( r = 0.91) and the Photochemical Reflectance Index (PRI 551 ), computed as ( R 531 − R 551 )/( R 531 + R 551 ) with LUE g ( r = 0.64). Subsequently, these VIs were used to estimate GPP using different modelling solutions based on the light-use efficiency model describing the GPP as driven by the photosynthetically active radiation absorbed by green vegetation (APAR g ) and by the efficiency (ε) with which plants use the absorbed radiation to fix carbon via photosynthesis. Results show that GPP can be successfully modelled with a combination of VIs and meteorological data or VIs only. Vegetation indexes designed to be more sensitive to chlorophyll content explained most of the variability in GPP in the ecosystem investigated, characterized by a strong seasonal dynamic of GPP. Accuracy in GPP estimation slightly improves when taking into account high frequency modulations of GPP driven by incident PAR or modelling LUE g with the PRI in model formulation. Similar results were obtained for both measured daily VIs and VIs obtained as 16-day composite time series and then downscaled from the compositing period to daily scale (resampled data). However, the use of resampled data rather than measured daily input data decreases the accuracy of the total GPP estimation on an annual basis.

Description: Soil organic carbon storage changes in coastal wetlands of the modern Yellow River Delta from 2000 to 2009 Biogeosciences Discussions, 9, 1759-1779, 2012 Author(s): J. Yu, Y. Wang, Y. Li, H. Dong, D. Zhou, G. Han, H. Wu, G. Wang, P. Mao, and Y. Gao Soil carbon sequestration plays an essential role in mitigating CO 2 increases and the subsequently global greenhouse effect. The storages and dynamics of soil organic carbon (SOC) of 0–30 cm soil depth in different landscape types including beaches, reservoir and pond, reed wetland, forest wetland, bush wetland, farmland, building land, bare land (severe saline land) and salt field in the modern Yellow River Delta (YRD), were studied based on the data of the regional survey and laboratory analysis. The landscape types were classified by the interpretation of remote sensing images of 2000 and 2009, which was calibrated by field survey results. The results revealed an increase of 10.59 km 2 in the modem YRD area from 2000 to 2009. The SOC density varied ranging from 0.73 kg m −2 to 21.60 kg m −2 at depth of 30 cm. There were ~3.97 × 10 6 t and 3.98 × 10 6 t SOC stored in the YRD in 2000 and 2009, respectively. The SOC storages changed greatly in beaches, bush wetland, farm land and salt field which were affected dominantly by anthropogenic activities. The area of the YRD increased greatly within 10 yr, however, the small increase of SOC storage in the region was observed due to landscape changes, indicating that the modern YRD was a potential carbon sink and anthropogenic activity was a key factor for SOC change.

Description: Micro-relief heterogeneity can lead to substantial variability in microclimate and hence niche opportunities on a small scale. We explored the relationship between plant species richness and small-scale heterogeneity of micro-relief on the subtropical island of La Palma, Canary Islands. Overall, we sampled 40 plots in laurel and pine forests at four altitudinal bands. Species richness was recorded separately for various growth forms (i.e., mosses, herbaceous and woody plants). Site conditions such as altitude, slope, aspect, and tree density were measured. Micro-relief heterogeneity was characterized by surface structure and a subsequently derived surface heterogeneity index. The effect of micro-relief heterogeneity on species richness was analysed by means of linear mixed effect models and variance partitioning. Effects of micro-relief heterogeneity on species richness varied considerably between growth forms. While moss richness was affected significantly by micro-relief heterogeneity, herbaceous and woody plants richness responded mainly to larger-scale site conditions such as aspect and tree density. Our results stress the importance of small-scale relief heterogeneity for the explanation of spatial patterns of species richness. This poses new challenges as small-scale heterogeneity is largely underrepresented, e.g. with regard to its application in species distribution models.

Description: Implications of observed inconsistencies in carbonate chemistry measurements for ocean acidification studies Biogeosciences Discussions, 9, 1781-1792, 2012 Author(s): C. J. M. Hoppe, G. Langer, S. D. Rokitta, D. A. Wolf-Gladrow, and B. Rost The growing field of ocean acidification research is concerned with the investigation of organisms' responses to increasing p CO 2 values. One important approach in this context is culture work using seawater with adjusted CO 2 levels. As aqueous p CO 2 is difficult to measure directly in small scale experiments, it is generally calculated from two other measured parameters of the carbonate system (often A T , C T or pH). Unfortunately, the overall uncertainties of measured and subsequently calculated values are often unknown. Especially under high p CO 2 , this can become a severe problem with respect to the interpretation of physiological and ecological data. In the few datasets from ocean acidification research where all three of these parameters were measured, p CO 2 values calculated from A T and C T are typically about 30 % lower (i.e. ~300 μatm at a target p CO 2 of 1000 μatm) than those calculated from A T and pH or C T and pH. This study presents and discusses these discrepancies as well as likely consequences for the ocean acidification community. Until this problem is solved, one has to consider that calculated parameters of the carbonate system (e.g. p CO 2 , calcite saturation state) may not be comparable between studies, and that this may have important implications for the interpretation of CO 2 perturbation experiments.

Description: Riverine influence on the tropical Atlantic Ocean biogeochemistry Biogeosciences Discussions, 9, 1945-1969, 2012 Author(s): L. Cotrim da Cunha and E. T. Buitenhuis We assess the role of riverine inputs of N, Si, Fe, organic and inorganic C in the tropical Atlantic Ocean using a global ocean biogeochemistry model. We use two sensitivity tests to investigate the role of the western (South American Rivers) and eastern (African Rivers) riverine nutrient inputs on the tropical Atlantic Ocean biogeochemistry (between 20° S–20° N and 70° W–20°). Increased nutrient availability from river inputs in this area (compared to an extreme scenario with no river nutrients) leads to an increase in 14 % (0.7 Pg C a −1 ) in open ocean primary production (PP), and 21 % (0.2 Pg C a −1 ) in coastal ocean PP. We estimate very modest increases in open and coastal ocean export production and sea-air CO 2 fluxes. Results suggest that in the tropical Atlantic Ocean, the large riverine nutrient inputs on the western side have a larger impact on primary production and sea-air CO 2 exchanges. On the other hand, African river inputs, although smaller than South American inputs, have larger impact on the coastal and open tropical Atlantic Ocean export production. This is probably due to a combination of nutrient trapping in upwelling areas off the Congo River outflow, and differences in delivered nutrient ratios leading to alleviation in limitation conditions mainly for diatoms.

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 Insulin stimulates glucose uptake through the membrane translocation of GLUT4 and GLUT1. Peroxisome proliferator-activated receptor γ (PPARγ) enhances insulin sensitivity. Here, we demonstrate that insulin stimulates GLUT4 and GLUT1 translocation, and glucose uptake, by activating the signaling pathway involving nicotinic acid adenine dinucleotide phosphate (NAADP), a calcium mobilizer, in adipocytes. We also demonstrate that PPARγ mediates insulin sensitization by enhancing NAADP production through upregulation of CD38, the only enzyme identified for NAADP synthesis. Insulin produced NAADP by both CD38-dependent and -independent pathways, whereas PPARγ produced NAADP by CD38-dependent pathway. Blocking the NAADP signaling pathway abrogated both insulin-stimulated and PPARγ-induced GLUT4 and GLUT1 translocation, thereby inhibiting glucose uptake. CD38 knockout partially inhibited insulin-stimulated glucose uptake. However, CD38 knockout completely blocked PPARγ-induced glucose uptake in adipocytes and PPARγ-mediated amelioration of glucose tolerance in diabetic mice. These results demonstrated that the NAADP signaling pathway is a critical molecular target for PPARγ-mediated insulin sensitization. Graphical abstract Highlights ► Insulin induces glucose uptake via NAADP-mediated calcium increase ► PPARγ mediates insulin sensitization by upregulating the NAADP-producing enzyme CD38 ► PPARγ agonists ameliorate glucose tolerance by CD38 upregulation

Description: Available online 27 December 2012 Publication year: 2012 Source: Cell Reports Enveloped viruses have developed various adroit mechanisms to invade their host cells. This process requires one or more viral envelope glycoprotein to achieve cell attachment and membrane fusion. Members of the Flaviviridae such as flaviviruses possess only one envelope glycoprotein, E, whereas pestiviruses and hepacivirus encode two glycoproteins, E1 and E2. Although E2 is involved in cell attachment, it has been unclear which protein is responsible for membrane fusion. We report the crystal structures of the homodimeric glycoprotein E2 from the pestivirus bovine viral diarrhea virus 1 (BVDV1) at both neutral and low pH. Unexpectedly, BVDV1 E2 does not have a class II fusion protein fold, and at low pH the N-terminal domain is disordered, similarly to the intermediate postfusion state of E2 from sindbis virus, an alphavirus. Our results suggest that the pestivirus and possibly the hepacivirus fusion machinery are unlike any previously observed. Graphical abstract Highlights ► Structure of the major antigenically dominant protein of BVDV ► The overall fold of BVDV E2 shows no similarity to the class II fusion proteins ► At low pH, BVDV E2 N-terminal domain is disordered ► Entry mechanism of BVDV is probably applicable to hepatitis C virus

Description: Background: Trypanosoma cruzi, the causal agent of Chagas Disease, affects more than 16 million people in Latin America. The clinical outcome of the disease results from a complex interplay between environmental factors and the genetic background of both the human host and the parasite. However, knowledge of the genetic diversity of the parasite, is currently limited to a number of highly studied loci. The availability of a number of genomes from different evolutionary lineages of T. cruzi provides an unprecedented opportunity to look at the genetic diversity of the parasite at a genomic scale. Results: Using a bioinformatic strategy, we have clustered T. cruzi sequence data available in the public domain and obtained multiple sequence alignments in which one or two alleles from the reference CL-Brener were included. These data covers 4 major evolutionary lineages (DTUs): TcI, TcII, TcIII, and the hybrid TcVI. Using these set of alignments we have identified 288,957 high quality single nucleotide polymorphisms and 1,480 indels. In a reduced re-sequencing study we were able to validate ~ 97% of high-quality SNPs identified in 47 loci. Analysis of how these changes affect encoded protein products showed a 0.77 ratio of synonymous to non-synonymous changes in the T. cruzi genome. We observed 113 changes that introduce or remove a stop codon, some causing significant functional changes, and a number of tri-allelic and tetra-allelic SNPs that could be exploited in strain typing assays. Based on an analysis of the observed nucleotide diversity we show that the T. cruzi genome contains a core set of genes that are under apparent purifying selection. Interestingly, orthologs of known druggable targets show statistically significant lower nucleotide diversity values. Conclusions: This study provides the first look at the genetic diversity of T. cruzi at a genomic scale. The analysis covers an estimated ~ 60% of the genetic diversity present in the population, providing an essential resource for future studies on the development of new drugs and diagnostics, for Chagas Disease. These data is available through the TcSNP database (http://snps.tcruzi.org).

Description: Background: MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate gene expression by targeting mRNAs for translation repression or mRNA degradation. Although many miRNAs have been discovered and studied in human and mouse, few studies focused on porcine miRNAs, especially in genome wide. Results: Here, we adopted computational approaches including support vector machine (SVM) and homology searching to make a global scanning on the pre-miRNAs of pigs. In our study, we built the SVM-based porcine pre-miRNAs classifier with a sensitivity of 100%, a specificity of 91.2% and a total prediction accuracy of 95.6%, respectively. Moreover, 2204 novel porcine pre-miRNA candidates were found by using SVM-based pre-miRNAs classifier. Besides, 116 porcine pre-miRNA candidates were detected by homology searching. Conclusions: We identified the porcine pre-miRNA in genome-wide through computational approaches by utilizing the data sets of pigs and set up the porcine pre-miRNAs library which may provide us a global scanning on the pre-miRNAs of pigs in genome level and would benefit subsequent experimental research on porcine miRNA functional and expression analysis.

Description: Background: Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 are alpha-Proteobacteria that establish nitrogen-fixing symbioses with a range of legume hosts. These strains are broadly used in commercial inoculants for application to common bean (Phaseolus vulgaris) in South America and Africa. Both strains display intrinsic resistance to several abiotic stressful conditions such as low soil pH and high temperatures, which are common in tropical environments, and to several antimicrobials, including pesticides. The genetic determinants of these interesting characteristics remain largely unknown. Results: Genome sequencing revealed that CIAT 899 and PRF 81 share a highly-conserved symbiotic plasmid (pSym) that is present also in Rhizobium leucaenae CFN 299, a rhizobium displaying a similar host range. This pSym seems to have arisen by a co-integration event between two replicons. Remarkably, three distinct nodA genes were found in the pSym, a characteristic that may contribute to the broad host range of these rhizobia. Genes for biosynthesis and modulation of plant-hormone levels were also identified in the pSym. Analysis of genes involved in stress response showed that CIAT 899 and PRF 81 are well equipped to cope with low pH, high temperatures and also with oxidative and osmotic stresses. Interestingly, the genomes of CIAT 899 and PRF 81 had large numbers of genes encoding drug-efflux systems, which may explain their high resistance to antimicrobials. Genome analysis also revealed a wide array of traits that may allow these strains to be successful rhizosphere colonizers, including surface polysaccharides, uptake transporters and catabolic enzymes for nutrients, diverse iron-acquisition systems, cell wall-degrading enzymes, type I and IV pili, and novel T1SS and T5SS secreted adhesins. Conclusions: Availability of the complete genome sequences of CIAT 899 and PRF 81 may be exploited in further efforts to understand the interaction of tropical rhizobia with common bean and other legume hosts.

Description: Background: The objective of the research was to evaluate the current effectiveness of Ciprofloxacin on the uropathogens prevalent in infected urines of a cross-section of patients in Karachi, Pakistan.FindingsAn observational study conducted in a private diagnostic laboratory and its branches in key areas of Karachi City from February 2010 to July 2011. A total of 2963 consecutive urine samples were cultured on chocolate agar, CLED medium and selective EMB agar. Growth of possible uropathogens was noted, and compared retrospectively with earlier lab data of suggestive urine cultures (n = 1997) recorded during January 2009 and December 2009. The isolates were identified using routine procedures and the API 20 system and evaluated for their sensitivity to ciprofloxacin by Kirby-Bauer disk diffusion method. Data was subjected to statistical analysis on SPSS version 16. Out of the present-day culture-positive urines, 2409 (80.4%) yielded gram-negative rods, and 554 (18.5%) gram-positive cocci. E.coli (43.1%) was most frequent, followed by Klebsiella pneumoniae (22.4%) and Staphylococcus aureus (15.5%). 57.2% of the Gram-negative bacteria and 48.7% of the Gram-positive isolates were resistant to ciprofloxacin. In the earlier (2009) screening, 39% of Gram-negative rods and 48% of Gram-positive cocci were indifferent to the drug. Conclusions: A decrease in bacterial susceptibility of uropathogens to ciprofloxacin, a commonly prescribed drug in our population, is underlined, occurring possibly due to overuse pressure. Empirical initial treatment with ciprofloxacin would be inadequate in more than half of UTI cases, thereby counseling increased C/S testing of urines to provide existing sensitivity data for apt drug prescription.

Description: Background: Data accuracy and completeness are crucial for ensuring both the correctness and epidemiological relevance of a given data set. In this study we evaluated a clinical register in the administrative district of Marburg-Biedenkopf, Germany, for these criteria. Methods: The register contained data gathered from a comprehensive integrated breast-cancer network from three hospitals that treated all included incident cases of malignant breast cancer in two distinct time periods from 1996--97 (N=389) and 2003--04 (N=488). To assess the accuracy of this data, we compared distributions of risk, prognostic, and predictive factors with distributions from established secondary databases to detect any deviations from these [prime][prime]true[prime][prime] population parameters. To evaluate data completeness, we calculated epidemiological standard measures as well as incidence-mortality-ratios (IMRs). Results: In total, 12% (13 of 109) of the variables exhibited inaccuracies: 9% (5 out of 56) in 1996--97 and 15% (8 out of 53) in 2003--04. In contrast to raw, unstandardized incidence rates, (in-) directly age-standardized incidence rates showed no systematic deviations. Our final completeness estimates were IMR=36% (1996--97) and IMR=43% (2003--04). Conclusion: Overall, the register contained accurate, complete, and correct data. Regional differences accounted for detected inaccuracies. Demographic shifts occurred. Age-standardized measures indicate an acceptable degree of completeness. The IMR method of measuring completeness was inappropriate for incidence-based data registers. For the rising number of population-based health-care networks, further methodological advancements are necessary. Correct and epidemiologically relevant data are crucial for clinical and health-policy decision-making.

Description: Background: Patients increasingly turn to the Internet for information on medical conditions, including clinical news and treatment options. In recent years, an online patient community has arisen alongside the rapidly expanding world of social media, or "Web 2.0." Twitter provides real-time dissemination of news, information, personal accounts and other details via a highly interactive form of social media, and has become an important online tool for patients. This medium is now considered to play an important role in the modern social community of online, "wired" cancer patients. Results: Fifty-one highly influential "power accounts" belonging to cancer patients were extracted from a dataset of 731 Twitter accounts with cancer terminology in their profiles. In accordance with previously established methodology, "power accounts" were defined as those Twitter accounts with 500 or more followers. We extracted data on the cancer patient (female) with the most followers to study the specific relationships that existed between the user and her followers, and found that the majority of the examined tweets focused on greetings, treatment discussions, and other instances of psychological support. These findings went against our hypothesis that cancer patients' tweets would be centered on the dissemination of medical information and similar "newsy" details. Conclusions: At present, there exists a rapidly evolving network of cancer patients engaged in information exchange via Twitter. This network is valuable in the sharing of psychological support among the cancer community.

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 Controversy has recently arisen over the role of sirtuins in metazoan aging. In this issue of Cell Reports , Banerjee et al. demonstrate that Drosophila Sir2 is necessary for life span extension in response to dietary restriction and that its overexpression in the fat body increases the life span.

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 Inhibition of sirtuin 2 (SIRT2) deacetylase mediates protective effects in cell and invertebrate models of Parkinson’s disease and Huntington’s disease (HD). Here we report the in vivo efficacy of a brain-permeable SIRT2 inhibitor in two genetic mouse models of HD. Compound treatment resulted in improved motor function, extended survival, and reduced brain atrophy and is associated with marked reduction of aggregated mutant huntingtin, a hallmark of HD pathology. Our results provide preclinical validation of SIRT2 inhibition as a potential therapeutic target for HD and support the further development of SIRT2 inhibitors for testing in humans. Graphical abstract Highlights ► Sirtuin 2 (SIRT2) inhibition is neuroprotective in two HD mouse models ► SIRT2 inhibitor treatment markedly reduces huntingtin aggregates in HD mouse brain ► SIRT2 is a promising therapeutic target for neurological protein aggregation disorders

Description: Background: Exposure to early adverse events can result in the development of later psychopathology, and is often associated with cognitive impairment. This may be due to accelerated cell aging, which can be catalogued by attritioned telomeres. Exercise enhances neurogenesis and has been proposed to buffer the effect of psychological stress on telomere length. This study aimed to investigate the impact of early developmental stress and voluntary exercise on telomere length in the ventral hippocampus (VH) and prefrontal cortex (PFC) of the rat. Forty-five male Sprague--Dawley rats were categorised into four groups: maternally separated runners (MSR), maternally separated non-runners (MSnR), non-maternally separated runners (nMSR) and non-maternally separated non-runners (nMSnR). Behavioural analyses were conducted to assess anxiety-like behaviour and memory performance in the rats, after which relative telomere length was measured using qPCR. Results: Maternally separated (MS) rats exhibited no significant differences in either anxiety levels or memory performance on the elevated-plus maze and the open field compared to non-maternally separated rats at 49 days of age. Exercised rats displayed increased levels of anxiety on the day that they were removed from the cages with attached running wheels, as well as improved spatial learning and temporal recognition memory compared to non-exercised rats. Exploratory post-hoc analyses revealed that maternally separated non-exercised rats exhibited significantly longer telomere length in the VH compared to those who were not maternally separated; however, exercise appeared to cancel this effect since there was no difference in VH telomere length between maternally separated and non-maternally separated runners. Conclusions: The increased telomere length in the VH of maternally separated non-exercised rats may be indicative of reduced cellular proliferation, which could, in turn, indicate hippocampal dysfunction. This effect on telomere length was not observed in exercised rats, indicating that voluntary exercise may buffer against the progressive changes in telomere length caused by alterations in maternal care early in life. In future, larger sample sizes will be needed to validate results obtained in the present study and obtain a more accurate representation of the effect that psychological stress and voluntary exercise have on telomere length.

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 Planar cell polarity (PCP) refers to the collective orientation of cells within the epithelial plane. We show that progenitor cells forming the ducts of the embryonic pancreas express PCP proteins and exhibit an active PCP pathway. Planar polarity proteins are acquired at embryonic day 11.5 synchronously to apicobasal polarization of pancreas progenitors. Loss of function of the two PCP core components Celsr2 and Celsr3 shows that they control the differentiation of endocrine cells from polarized progenitors, with a prevalent effect on insulin-producing beta cells. This results in a decreased glucose clearance. Loss of Celsr2 and 3 leads to a reduction of Jun phosphorylation in progenitors, which, in turn, reduces beta cell differentiation from endocrine progenitors. These results highlight the importance of the PCP pathway in cell differentiation in vertebrates. In addition, they reveal that tridimensional organization and collective communication of cells are needed in the pancreatic epithelium in order to generate appropriate numbers of endocrine cells. Graphical abstract Highlights ► PCP proteins are restricted to progenitor cells in the embryonic pancreas ► The PCP core components Celsr2 and Celsr3 control endocrine cell differentiation ► This effect is mediated by the JNK pathway

Description: Background: Graph-based modularity analysis has emerged as an important tool to study the functional organization of biological networks. However, few methods are available to study state-dependent changes in network modularity using biological activity data. We develop a weighting scheme, based on metabolic flux data, to adjust the interaction distances in a reaction-centric graph model of a metabolic network. The weighting scheme was combined with a hierarchical module assignment algorithm featuring the preservation of metabolic cycles to examine the effects of cellular differentiation and enzyme inhibitions on the functional organization of adipocyte metabolism. Results: Our analysis found that the differences between various metabolic states primarily involved the assignment of two specific reactions in fatty acid synthesis and glycerogenesis. Our analysis also identified cyclical interactions between reactions that are robust with respect to metabolic state, suggesting possible co-regulation. Comparisons based on cyclical interaction distances between reaction pairs suggest that the modular organization of adipocyte metabolism is stable with respect to the inhibition of an enzyme, whereas a major physiological change such as cellular differentiation leads to a more substantial reorganization. Conclusion: Taken together, our results support the notion that network modularity is influenced by both the connectivity of the network's components as well as the relative engagements of the connections.

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 MicroRNAs (miRNAs) are small, noncoding RNAs that inhibit translation and promote mRNA decay. The levels of mature miRNAs are the result of different rates of transcription, processing, and turnover. The noncanonical polymerase Gld2 has been implicated in the stabilization of miR-122, possibly through catalyzing 3′ monoadenylation; however, there is little evidence that this relationship is one of cause and effect. Here, we biochemically characterize Gld2’s involvement in miRNA monoadenylation and its effect on miRNA stability. We find that Gld2 directly monoadenylates and stabilizes specific miRNA populations in human fibroblasts and that sensitivity to monoadenylation-induced stability depends on nucleotides in the miRNA 3′ end. These results establish a mechanism of miRNA stability and resulting posttranscriptional gene regulation. Graphical abstract Highlights ► Gld2 monoadenylates specific microRNAs (miRNAs) ► Monoadenylation stabilizes miRNA subpopulations and prolongs their activity ► Sensitivity to monoadenylation and stability depends on nucleotides in the miRNA 3′ end

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 In the cytoplasm, the correct delivery of membrane proteins is an essential and highly regulated process. The posttranslational targeting of the important tail-anchor membrane (TA) proteins has recently been under intense investigation. A specialized pathway, called the guided entry of TA proteins (GET) pathway in yeast and the transmembrane domain recognition complex (TRC) pathway in vertebrates, recognizes endoplasmic-reticulum-targeted TA proteins and delivers them through a complex series of handoffs. An early step is the formation of a complex between Sgt2/SGTA, a cochaperone with a presumed ubiquitin-like-binding domain (UBD), and Get5/UBL4A, a ubiquitin-like domain (UBL)-containing protein. We structurally characterize this UBD/UBL interaction for both yeast and human proteins. This characterization is supported by biophysical studies that demonstrate that complex formation is mediated by electrostatics, generating an interface that has high-affinity with rapid kinetics. In total, this work provides a refined model of the interplay of Sgt2 homologs in TA targeting. Graphical abstract Highlights ► Sgt2 homologs contain dimerization motifs that are novel UBDs ► The UBL of Get5 homologs has features that distinguish it from other UBLs ► Complex formation of Sgt2 and Get5 includes a conserved and dynamic interface ► The system can rapidly discriminate between other UBL pathways

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 Chimera formation after blastocyst injection or morula aggregation is the principal functional assay of the developmental potential of mouse embryonic stem cells (ESCs). This property, which demonstrates functional equivalence between ESCs and the preimplantation epiblast, is not shared by epiblast stem cell (EpiSC) lines. Here, we show that EpiSCs derived either from postimplantation embryos or from ESCs in vitro readily generate chimeras when grafted to postimplantation embryos in whole embryo culture. EpiSC derivatives integrate and differentiate to derivatives of all three embryonic germ layers and primordial germ cells. In contrast, grafted ESCs seldom proliferate in postimplantation embryos, and fail to acquire the identity of their host-derived neighbors. EpiSCs do not incorporate efficiently into embryonic day 8.5 embryos, a stage by which pluripotency has been lost. Thus, chimera formation by EpiSCs requires a permissive environment, the postimplantation epiblast, and demonstrates functional equivalence between this cell type and EpiSCs. Graphical abstract Highlights ► Epiblast stem cells (EpiSCs) form chimeras when injected into postimplantation epiblast ► Embryonic stem cells do not form postimplantation chimeras ► EpiSCs do not integrate if they are injected after gastrulation

Description: 27 December 2012 Publication year: 2012 Source: Cell Reports, Volume 2, Issue 6 An increased understanding of antitumor immunity is necessary for improving cell-based immunotherapies against human cancers. Here, we investigated the roles of two immune system-expressed microRNAs (miRNAs), miR-155 and miR-146a, in the regulation of antitumor immune responses. Our results indicate that miR-155 promotes and miR-146a inhibits interferon γ (IFNγ) responses by T cells and reduces solid tumor growth in vivo. Using a double-knockout (DKO) mouse strain deficient in both miR-155 and miR-146a, we have also identified an epistatic relationship between these two miRNAs. DKO mice had defective T cell responses and tumor growth phenotypes similar to miR-155 −/− mice. Further analysis of the T cell compartment revealed that miR-155 modulates IFNγ expression through a mechanism involving repression of Ship1. Our work reveals critical roles for miRNAs in the reciprocal regulation of CD4 + and CD8 + T cell-mediated antitumor immunity and demonstrates the dominant nature of miR-155 during its promotion of immune responses. Graphical abstract Highlights ► miR-155 promotes and miR-146a inhibits both CD4+ and CD8+ T cell antitumor responses ► DKO mice reveal epistasis between miR-155 and miR-146a during tumor immunity ► miR-155 regulation of IFNγ involves repression of its target Ship1 in T cells

Description: Background: A novel herbal formulation LI10903F, alternatively known as LOWAT was developed based on its ability to inhibit adipogenesis and lipogenesis in 3T3-L1 adipocytes model. The clinical efficacy and tolerability of LI10903F were evaluated in an eight-week, randomized, double-blind, placebo-controlled, clinical trial in 50 human subjects with body mass index (BMI) between 30 and 40 kg/m2 (clinical trial registration number: ISRCTN37381706). Participants were randomly assigned to either a placebo or LI10903F group. Subjects in the LI10903F group received 300 mg of herbal formulation thrice daily, while subjects in the placebo group received 300 mg of placebo capsules thrice daily. All subjects were provided a standard diet (2,000 kcal daily) and participated in a moderate exercise of 30 min walk for five days a week. Additionally, the safety of this herbal formulation was evaluated by a series of acute, sub-acute toxicity and genotoxicity studies in animals and cellular models. Results: After eight weeks of supplementation, statistically significant net reductions in body weight (2.49 kg; p=0.00005) and BMI (0.96 kg/m2; p=0.00004) were observed in the LI10903F group versus placebo group. Additionally, significant increase in serum adiponectin concentration (p=0.0076) and significant decrease in serum ghrelin concentration (p=0.0066) were found in LI10903F group compared to placebo group. Adverse events were mild and were equally distributed between the two groups. Interestingly, LI10903F showed broad spectrum safety in a series of acute, sub-acute toxicity and genotoxicity studies. Conclusions: Results from the current research suggest that LI10903F or LOWAT is well-tolerated, safe and effective for weight management.

Description: Background: The -493G/T polymorphism in the microsomal triglyceride transfer protein (MTP) gene is associated with lower serum low-density lipoprotein cholesterol (LDL-C) and triglyceride (TG) levels and longevity in several populations, but the results are inconsistent in different racial/ethnic groups. The current study was to investigate the plausible association of MTP -493G/T polymorphism with serum lipid levels and longevity in Zhuang long-lived families residing in Bama area, a famous home of longevity in Guangxi, China. Methods: The MTP -493G/T was genotyped by PCR-restriction fragment length polymorphism in 391 Bama Zhuang long-lived families (BLF, n = 1467, age 56.60 +/- 29.43 years) and four control groups recruited from Bama and out-of-Bama area with or without a familial history of exceptional longevity: Bama non-long-lived families (BNLF, n = 586, age 44.81 +/- 26.83 years), Bama non-Zhuang long-lived families (BNZLF, n = 444, age 52.09 +/- 31.91 years), Pingguo long-lived families (PLF, n = 658, age 50.83 +/- 30.30 years), and Pingguo non-long-lived families (PNLF, n = 539, age 38.74 +/- 24.69 years). Correlation analyses between genotypes and serum lipid levels and longevity were then performed. Results: No particularly favorable lipoprotein and clinical phenotypes were seen in BLF as compared to general families in the same area. Instead, the levels of total cholesterol (TC), TG, LDL-C, and the prevalence of dyslipidemia were significantly higher in the three Bama families as compared to the two non-Bama families (P 〈 0.01 for all). There were no differences in the allelic and genotypic frequencies among the tested cohorts (P 〉 0.05 for all), but the TT genotype tended to enrich in the three long-lived cohorts from both areas. In addition, the individuals harboring TT genotype exhibited lower LDL-C and TC levels in the overall populations and Bama populations with a region- and sex-specific pattern. Multiple linear regression analyses unraveled that LDL-C levels were correlated with genotypes in Bama combined population, BNLF, and the total population (P 〈 0.05 for each) but not in Pingguo populations; TC and HDL-C levels were correlated with genotypes in Bama combined population and BLF, respectively (P 〈 0.05 for each). Conclusions: MTP -493G/T polymorphism may play an important role in fashioning the serum lipid profiles of Bama populations, despite no direct association between MTP -493G/T and longevity was detected.

Description: Background: RNA interference (RNAi) becomes an increasingly important and effective genetic tool to study the function of target genes by suppressing specific genes of interest. This system approach helps identify signaling pathways and cellular phase types by tracking intensity and/or morphological changes of cells. The traditional RNAi screening scheme, in which one siRNA is designed to knockdown one specific mRNA target, needs a large library of siRNAs and turns out to be time-consuming and expensive. Results: In this paper, we propose a conceptual model, called compressed sensing RNAi (csRNAi), which employs the unique combination of group of small interfering RNAs (siRNAs) to knockdown a much larger size of genes. This strategy is based on the fact that one gene can be partially bound with several small interfering RNAs (siRNAs) and conversely, one siRNA can bind to a few genes with distinct binding affinity. This model constructs a multi-to-multi correspondence between siRNAs and their targets, with siRNAs much fewer than mRNA targets, compared with the conventional scheme. Mathematically this problem involves an underdetermined system of equations (linear or nonlinear), which is ill-posed in general. However, the recently developed compressed sensing (CS) theory can solve this problem. We present a mathematical model to describe the csRNAi system based on both CS theory and biological concerns. To build this model, we first search nucleotide motifs in a target gene set. Then we propose a machine learning based method to find the effective siRNAs with novel features, such as image features and speech features to describe an siRNA sequence. Numerical simulations show that we can reduce the siRNA library to one third of that in the conventional scheme. In addition, the features to describe siRNAs outperform the existing ones substantially. Conclusions: This csRNAi system is very promising in saving both time and cost for large-scale RNAi screening experiments which may benefit the biological research with respect to cellular processes and pathways.

Description: Background: Copy number variations (CNVs) are genomic structural variants that are found in healthy populations and have been observed to be associated with disease susceptibility. Existing methods for CNV detection are often performed on a sample-by-sample basis, which is not ideal for large datasets where common CNVs must be estimated by comparing the frequency of CNVs in the individual samples. Here we describe a simple and novel approach to locate genome-wide CNVs common to a specific population, using human ancestry as the phenotype. Results: We utilized our previously published Genome Alteration Detection Analysis (GADA) algorithm to identify common ancestry CNVs (caCNVs) and built a caCNV model to predict population structure. We identified a 73 caCNV signature using a training set of 225 healthy individuals from European, Asian, and African ancestry. The signature was validated on an independent test set of 300 individuals with similar ancestral background. The error rate in predicting ancestry in this test set was 2% using the 73 caCNV signature. Among the caCNVs identified, several were previously confirmed experimentally to vary by ancestry. Our signature also contains a caCNV region with a single microRNA (MIR270), which represents the first reported variation of microRNA by ancestry. Conclusions: We developed a new methodology to identify common CNVs and demonstrated its performance by building a caCNV signature to predict human ancestry with high accuracy. The utility of our approach could be extended to large case--control studies to identify CNV signatures for other phenotypes such as disease susceptibility and drug response.

Description: Background: Understanding demographic histories, such as divergence time, patterns of gene flow, and population size changes, in ecologically diverging lineages provide implications for the process and maintenance of population differentiation by ecological adaptation. This study addressed the demographic histories in two independently derived lineages of flood-resistant riparian plants and their non-riparian relatives [Ainsliaea linearis (riparian) and A. apiculata (non-riparian); A. oblonga (riparian) and A. macroclinidioides (non-riparian); Asteraceae] using an isolation-with-migration (IM) model based on variation at 10 nuclear DNA loci. Results: The highest posterior probabilities of the divergence time parameters were estimated to be ca. 25,000 years ago for A. linearis and A. apiculata and ca. 9000 years ago for A. oblonga and A. macroclinidioides, although the confidence intervals of the parameters had broad ranges. The likelihood ratio tests detected evidence of historical gene flow between both riparian/non-riparian species pairs. The riparian populations showed lower levels of genetic diversity and a significant reduction in effective population sizes compared to the non-riparian populations and their ancestral populations. Conclusions: This study showed the recent origins of flood-resistant riparian plants, which are remarkable examples of plant ecological adaptation. The recent divergence and genetic signatures of historical gene flow among riparian/non-riparian species implied that they underwent morphological and ecological differentiation within short evolutionary timescales and have maintained their species boundaries in the face of gene flow. Comparative analyses of adaptive divergence in two sets of riparian/non-riparian lineages suggested that strong natural selection by flooding had frequently reduced the genetic diversity and size of riparian populations through genetic drift, possibly leading to fixation of adaptive traits in riparian populations. The two sets of riparian/non-riparian lineages showed contrasting patterns of gene flow and genetic differentiation, implying that each lineage showed different degrees of reproductive isolation and that they had experienced unique evolutionary and demographic histories in the process of adaptive divergence.

Description: Background: HIV/AIDS has several means of transmission. Exposure to blood and other body fluids is a very important means of transmission. Healthcare workers are exposed to this disease mainly due to the nature of their work. This is an exploration of the perceptions of healthcare workers of the University of Gondar Hospital. Methods: Based on purposive sampling seven healthcare workers were selected from different departments in the hospital so that they could reflect on their perceptions. The selected healthcare workers were asked about the risks related to their work, their experience of HIV related hazards and their general views on the transmission of HIV. The main themes were identified for analysis and the views were summarized under the themes. Results: All the respondents were aware of the risk of acquiring HIV in healthcare settings. Some had experienced accidents that made them take post-exposure prophylaxis, and most witnessed accidents like needle-stick injuries to their colleagues. They also expressed their feelings that their workplace was not the best place to work at. Conclusion: Health professionals are well aware of the possibility of HIV transmission associated with their practice. Accidents like needle stick injuries are apparently common; and at the same time, the practice of healthcare workers towards using universal precautions looks poor.

Description: Background: Members of the family Syngnathidae share a unique reproductive mode termed male pregnancy. Males carry eggs in specialised brooding structures for several weeks and release free-swimming offspring. Here we describe a systematic investigation of pre-release development in syngnathid fishes, reviewing available data for 17 species distributed across the family. This work is complemented by in-depth examinations of the straight-nosed pipefish Nerophis ophidion, the black-striped pipefish Syngnathus abaster, and the potbellied seahorse Hippocampus abdominalis. Results: We propose a standardised classification of early syngnathid development that extends from the activation of the egg to the release of newborn. The classification consists of four developmental periods -- early embryogenesis, eye development, snout formation, and juvenile -- which are further divided into 11 stages. Stages are characterised by morphological traits that are easily visible in live and preserved specimens using incident-light microscopy. Conclusions: Our classification is derived from examinations of species representing the full range of brooding-structure complexity found in the Syngnathidae, including tail-brooding as well as trunk-brooding species, which represent independent evolutionary lineages. We chose conspicuous common traits as diagnostic features of stages to allow for rapid and consistent staging of embryos and larvae across the entire family. In view of the growing interest in the biology of the Syngnathidae, we believe that the classification proposed here will prove useful for a wide range of studies on the unique reproductive biology of these male-brooding fish.

Description: Background: Maize is a major crop plant, grown for human and animal nutrition, as well as a renewable resource forbioenergy. When looking at the problems of limited fossil fuels, the growth of the world's population or theworld's climate change, it is important to find ways to increase the yield and biomass of maize and to studyhow it reacts to specific abiotic and biotic stress situations. Within the OPTIMAS systems biology projectmaize plants were grown under a large set of controlled stress conditions, phenotypically characterised andplant material was harvested to analyse the effect of specific environmental conditions or developmentalstages. Transcriptomic, metabolomic, ionomic and proteomic parameters were measured from the same plantmaterial allowing the comparison of results across different omics domains. A data warehouse wasDescriptionThe OPTIMAS Data Warehouse (OPTIMAS-DW) is a comprehensive data collection for maize and integratesdata from different data domains such as transcriptomics, metabolomics, ionomics, proteomics andphenomics. Within the OPTIMAS project, a 44K oligo chip was designed and annotated to describe thefunctions of the selected unigenes. Several treatment- and plant growth stage experiments were performed andmeasured data were filled into data templates and imported into the data warehouse by a Java based importtool. A web interface allows users to browse through all stored experiment data in OPTIMAS-DW includingall data domains. Furthermore, the user can filter the data to extract information of particular interest. All datacan be exported into different file formats for further data analysis and visualisation. The data analysisintegrates data from different data domains and enables the user to find answers to different systems biologyquestions. Finally, maize specific pathway information is provided. Conclusions: With OPTIMAS-DW a data warehouse for maize was established, which is able to handle different datadomains, comprises several analysis results that will support researchers within their work and supportssystems biological research in particular. The system is available athttp://www.optimas-bioenergy.org/optimas_dw.

Description: Background: Health control beliefs were postulated to be associated with health behaviour. However, the results of studies assessing these associations suggest that they might not be universal. Among young adults associations have been reported, but, the evidence is limited. The objective of this analysis was to re-examine these associations in a sample of university students in Germany.FindingsData from a multicentre cross-sectional study among university students in North Rhine-Westphalia, Germany was used (N=3,306). The Multidimensional Health Locus of Control Scale with three dimensions (one internal and two external) and six aspects of health behaviour (smoking habits, alcohol use, drug consumption, being over-/ or underweight, physical activity, and importance of healthy nutrition) were evaluated. Students with stronger internal locus of control scores paid more attention to healthy nutrition and displayed a higher level of physical activity. Individuals with a stronger belief in health professionals were less likely to use drugs and paid more attention to healthy nutrition. Furthermore, higher scores in the second external locus of control dimension (beliefs in luck or chance) were associated with a higher likelihood of current smoking, lower physical activity and less attention to healthy nutrition. Conclusions: Students engaged more strongly in unhealthy behaviour if they believed that luck determines health. In contrast, believing in having control over one's own health was associated with more healthy behaviour. These findings support the need to consider health control beliefs while designing preventive strategies in this specific population.

Description: Available online 29 December 2012 Publication year: 2012 Source: FEBS Open Bio A water-soluble selenoxide (DHS ox ) having a five-membered ring structure enables rapid and selective conversion of cysteinyl SH groups in a polypeptide chain into SS bonds in a wide pH and temperature range. It was previously demonstrated that the second-order rate constants for the SS formation with DHS ox would be proportional to the number of the free SH groups present in the substrate if there is no steric congestion around the SH groups. In the present study, kinetics of the SS formation with DHS ox was extensively studied at pH 4–10 and 25°C by using reduced ribonuclease A, recombinant hirudin variant (CX-397), insulin A- and B-chains, and relaxin A-chain, which have two to eight cysteine residues, as polythiol substrates. The obtained rate constants showed stochastic SS formation behaviors under most conditions. However, the rate constants for CX-397 at pH 8.0 and 10.0 were not proportional to the number of the free SH groups, suggesting that the SS intermediate ensembles possess densely packed structures under weakly basic conditions. The high two-electron redox potential of DHS ox (375 mV at 25°C) compared to L-cystine supported the high ability of DHS ox for SS formation in a polypeptide chain. Interestingly, the rate constants of the SS formation jumped up at a pH around the p K a value of the cysteinyl SH groups. The SS formation velocity was slightly decreased by addition of a denaturant due probably to the interaction between the denaturant and the peptide. The stochastic behaviors as well as the absolute values of the second-order rate constants in comparison to dithiothreitol (DTT red ) are useful to probe the chemical reactivity and conformation, hence the folding, of polypeptide chains. Graphical abstract Highlights ▸ DHS ox was applied as a SS-forming reagent for five polythiol peptides and DTT red . ▸ The SS formation velocities depend on the kind of substrate and solvent conditions. ▸ The SS-formation rate constants are proportional to the number of free SH groups. ▸ Folded structures and SH p K a modify the stochastic nature and absolute values of the rate constants. ▸ DHS ox is a useful probe of chemical reactivity and intermediate structures in oxidative protein folding.

Description: Background: In higher eukaryotes, gene expression is regulated at different levels. In particular, 3[prime]UTRs play a central role in translation, stability and subcellular localization of transcripts. In recent years, the development of high throughput sequencing techniques has facilitated the acquisition of transcriptional data at a genome wide level. However, annotation of the 3[prime] ends of genes is still incomplete, thus limiting the interpretation of the data generated. For example, we have previously reported two different genes, ADD2 and CPEB3, with conserved 3[prime]UTR alternative isoforms not annotated in the current versions of Ensembl and RefSeq human databases. Results: In order to evaluate the existence of other conserved 3[prime] ends not annotated in these databases we have now used comparative genomics and transcriptomics across several vertebrate species. In general, we have observed that 3[prime]UTR conservation is lost after the end of the mature transcript. Using this change in conservation before and after the 3[prime] end of the mature transcripts we have shown that many conserved ends were still not annotated. In addition, we used orthologous transcripts to predict 3[prime]UTR extensions and validated these predictions using total RNA sequencing data. Finally, we used this method to identify not annotated 3[prime] ends in rats and dogs. As a result, we report several hundred novel 3[prime]UTR extensions in rats and a few thousand in dogs. Conclusions: The methods presented here can efficiently facilitate the identification of not-yet-annotated conserved 3[prime]UTR extensions. The application of these methods will increase the confidence of orthologous gene models across vertebrates.

Description: Background: Pineapple (Ananas comosus) is a tropical fruit crop of significant commercial importance. Although the physiological changes that occur during pineapple fruit development have been well characterized, little is known about the molecular events that occur during the fruit ripening process. Understanding the molecular basis of pineapple fruit ripening will aid the development of new varieties via molecular breeding or genetic modification. In this study we developed a 9277 element pineapple microarray and used it to profile gene expression changes that occur during pineapple fruit ripening. Results: Microarray analyses identified 271 unique cDNAs differentially expressed at least 1.5-fold between the mature green and mature yellow stages of pineapple fruit ripening. Among these 271 sequences, 184 share significant homology with genes encoding proteins of known function, 53 share homology with genes encoding proteins of unknown function and 34 share no significant homology with any database accession. Of the 237 pineapple sequences with homologs, 160 were up-regulated and 77 were down-regulated during pineapple fruit ripening. DAVID Functional Annotation Cluster (FAC) analysis of all 237 sequences with homologs revealed confident enrichment scores for redox activity, organic acid metabolism, metalloenzyme activity, glycolysis, vitamin C biosynthesis, antioxidant activity and cysteine peptidase activity, indicating the functional significance and importance of these processes and pathways during pineapple fruit development. Quantitative real-time PCR analysis validated the microarray expression results for nine out of ten genes tested. Conclusions: This is the first report of a microarray based gene expression study undertaken in pineapple. Our bioinformatic analyses of the transcript profiles have identified a number of genes, processes and pathways with putative involvement in the pineapple fruit ripening process. This study extends our knowledge of the molecular basis of pineapple fruit ripening and non-climacteric fruit ripening in general.

Description: Background: Accumulation of extracellular matrix (ECM) and increased matrix metalloproteinase (MMP) activity are hallmarks of liver fibrosis. The aim of the present study was to develop a model of liver fibrosis combining ex vivo tissue culture of livers from CCl4 treated animals with an ELISA detecting a fragment of type III collagen generated in vitro by MMP-9 (C3M), known to be associated with liver fibrosis and to investigate cAMP modulation of MMP activity and liver tissue turnover in this model.FindingsIn vivo: Rats were treated for 8 weeks with CCl4/Intralipid. Liver slices were cultured for 48 hours. Levels of C3M were determined in the supernatants of slices cultured without treatment, treated with GM6001 (positive control) or treated with IBMX (phosphodiesterase inhibitor). Enzymatic activity of MMP-2 and MMP-9 were studied by gelatin zymography.Ex vivo: The levels of serum C3M increased 77% in the CCl4-treated rats at week 8 (p 〈 0.01); Levels of C3M increased significantly by 100% in fibrotic liver slices compared to controls after 48 hrs (p 〈 0.01). By adding GM6001 or IBMX to the media, C3M was restored to control levels. Gelatin zymography demonstrated CCl4-treated animals had highly increased MMP-9, but not MMP-2 activity, compared to slices derived from control animals. Conclusions: We have combined an ex vivo model of liver fibrosis with measurement of a biochemical marker of collagen degradation in the condition medium. This technology may be used to evaluate the molecular process leading to structural fibrotic changes, as collagen species are the predominant structural part of fibrosis. These data suggest that modulation of cAMP may play a role in regulation of collagen degradation associated with liver fibrosis.

Description: Coral Patch seamount (NE Atlantic) – a sedimentological and macrofaunal reconnaissance based on video and hydroacoustic surveys Biogeosciences Discussions, 9, 18707-18753, 2012 Author(s): C. Wienberg, P. Wintersteller, L. Beuck, and D. Hebbeln The present study provides new knowledge about the so far largely unexplored Coral Patch seamount which is located in the NE Atlantic Ocean half-way between the Iberian Peninsula and Madeira. For the first time a detailed hydroacoustic mapping (MBES) in conjunction with video surveys (ROV, camera sled) were performed to describe the sedimentological and biological characteristics of this sub-elliptical ENE-WSW elongated seamount. Video observations were restricted to the south-western summit area of Coral Patch seamount (area: ~ 8 km 2 , water depth: 560–760 m) and revealed that this part of the summit is dominated by exposed hard substrate, whereas soft sediment is just a minor substrate component. Although exposed hardgrounds are dominant for this summit area, and thus, offer suitable habitat for settlement by benthic organisms, the macrofauna shows rather low abundance and diversity. In particular, scleractinian framework-building cold-water corals are apparently rare with very few isolated and small-sized live occurrences of the species Lophelia pertusa and Madrepora oculata . In contrast, dead coral framework and coral rubble are more frequent pointing to a higher abundance of cold-water corals on Coral Patch during the recent past. This is even supported by the observation of fishing lines that got entangled with rather fresh-looking coral frameworks. Overall, long lines and various species of commercially important fish were frequently observed emphasising the potential of Coral Patch as an important target for fisheries that may have impacted the entire benthic community. Hydroacoustic seabed classification covered the entire summit of Coral Patch and its northern and southern flanks (area: 560 km 2 ; water depth: 560–2660 m) and revealed extended areas dominated by mixed and soft sediments at the northern flank and to a minor degree at its easternmost summit and southern flank. Nevertheless, also these data predict most of the summit area to be dominated by exposed bedrock which would offer suitable habitat for benthic organisms. By comparing the locally restricted video observations and the broad-scale monitoring of a much larger and deeper seafloor area as derived by hydroacoustic seabed classification, it becomes obvious that habitat information obtained by in situ sampling may provide a rather scattered pattern about the entire seamount ecosystem. Solely with a combination of both methods, a satisfactory approach to describe the diverse characteristics of a seamount ecosystem can be derived which is in turn indispensable for future scientific monitoring campaigns as well as management and conservation purposes.

Description: High-resolution measurements of atmospheric molecular hydrogen and its isotopic composition at the West African coast of Mauritania Biogeosciences Discussions, 9, 18799-18829, 2012 Author(s): S. Walter, A. Kock, and T. Röckmann Oceans are a net source of molecular hydrogen (N 2 ) to the atmosphere, where nitrogen (N 2 ) fixation is assumed to be the main biological production pathway besides photochemical production from organic material. The sources can be distinguished using isotope measurements because of clearly differing isotopic signatures of the produced hydrogen. Here we present the first ship-borne measurements of atmospheric molecular H 2 mixing ratio and isotopic composition at the West African coast of Mauritania (16–25° W, 17–24° N). This area is one of the biologically most active regions of the world's oceans with seasonal upwelling events and characterized by strongly differing hydrographical/biological properties and phytoplankton community structures. The aim of this study was to identify areas of H 2 production and distinguish H 2 sources by isotopic signatures of atmospheric H 2 . Besides this a diurnal cycle of atmospheric H 2 was investigated. For this more than 100 air samples were taken during two cruises in February 2007 and 2008, respectively. During both cruises a transect from the Cape Verde Island towards the Mauritanian Coast was sampled. In 2007 additionally four days were sampled with a high resolution of one sample per hour. Our results clearly indicate the influence of local sources and suggest the Banc d'Arguin as a pool for precursors for photochemical H 2 production, whereas N 2 fixation could not be identified as a H 2 source during these two cruises. With our experimental setup we could demonstrate that variability in diurnal cycles is probably influenced and biased by released precursors for photochemical H 2 production and the origin of air masses. This means for further investigations that just measuring the mixing ratio of H 2 is insufficient to explain the variability of a diurnal cycle and support is needed, e.g. by isotopic measurements. However, measurements of H 2 mixing ratios, which are easy to conduct online during ship cruises could be a helpful tool to easily identify production areas of biological precursors such as VOC's for further investigations.

Description: Background: Cia5a is a locus on rat chromosome 10 that regulates disease severity and joint damage in two models of rheumatoid arthritis, collagen- and pristane-induced arthritis (PIA). In this study, we aimed to identify cellular and molecular processes regulated by Cia5a using microarray-based gene expression analysis of synovial tissues from MHC identical DA (severe erosive disease) and DA.F344(Cia5a) congenics (mild non-erosive disease) rats. Results: Synovial tissues from six DA and eight DA.F344(Cia5a) rats were analyzed 21 days after the induction of PIA using the Illumina RatRef-12 BeadChip (21,922 genes) and selected data confirmed with qPCR. There was a significantly increased expression of pro-inflammatory mediators such as Il1b (5-fold), Il18 (3.9-fold), Cxcl1 (10-fold), Cxcl13 (7.5-fold) and Ccl7 (7.9-fold), and proteases like Mmp3 (23-fold), Mmp9 (32-fold), Mmp14 (4.4-fold) and cathepsins in synovial tissues from DA, with reciprocally reduced levels in congenics. mRNA levels of 47 members of the Spleen Tyrosine Kinase (Syk) pathway were significantly increased in DA synovial tissues compared with DA.F344(Cia5a), and included Syk (5.4-fold), Syk-activating receptors and interacting proteins, and genes regulated by Syk such as NFkB, and NAPDH oxidase complex genes. Nuclear receptors (NR) such as Rxrg, Pparg and Rev-erba were increased in the protected congenics, and so was the anti-inflammatory NR-target gene Scd1 (54-fold increase). Tnn (72-fold decrease) was the gene most significantly increased in DA. Conclusions: Analyses of gene expression in synovial tissues revealed that the arthritis severity locus Cia5a regulates the expression of key mediators of inflammation and joint damage, as well as the expression of members of the Syk pathway. This expression pattern correlates with disease severity and joint damage and along with the gene accounting for Cia5a could become a useful biomarker to identify patients at increased risk for severe and erosive disease. The identification of the gene accounting for Cia5a has the potential to generate a new and important target for therapy and prognosis.

Description: Background: Traditional candidate gene approach has been widely used for the study of complex diseases including obesity. However, this approach is largely limited by its dependence on existing knowledge of presumed biology of the phenotype under investigation. Our combined strategy of comparative genomics and chromosomal heritability estimate analysis of obesity traits, subscapular skinfold thickness and back-fat thickness in Korean cohorts and pig (Sus scrofa), may overcome the limitations of candidate gene analysis and allow us to better understand genetic predisposition to human obesity. Results: We found common genes including FTO, the fat mass and obesity associated gene, identified from significant SNPs by association studies of each trait. These common genes were related to blood pressure and arterial stiffness (P = 1.65E-05) and type 2 diabetes (P = 0.00578). Through the estimation of variance of genetic component (heritability) for each chromosome by SNPs, we observed a significant positive correlation (r = 0.479) between genetic contributions of human and pig to obesity traits. Furthermore, we noted that the phenotypic variance for obesity can be explained dominantly by chromosome 2, which is syntenic to pig chromosomes 3 and 15. Conclusions: Obesity genetics still awaits further discovery. Navigating syntenic regions suggests obesity candidate genes on chromosome 2 that are previously known to be associated with obesity-related diseases: MRPL33, PARD3B, ERBB4, STK39, and ZNF385B.

Description: Background: Phenotypic evolution in animals is thought to be driven in large part by differences in gene expression patterns, which can result from sequence changes in cis-regulatory elements (cis-changes) or from changes in the expression pattern or function of transcription factors (trans-changes). While isolated examples of trans-changes have been identified, the scale of their overall contribution to regulatory and phenotypic evolution remains unclear. Results: Here, we attempt to examine the prevalence of trans-effects and their potential impact on gene expression patterns in vertebrate evolution by comparing the function of identical human tissue-specific enhancer sequences in two highly divergent vertebrate model systems, mouse and zebrafish. Among 47 human conserved non-coding elements (CNEs) tested in transgenic mouse embryos and in stable zebrafish lines, at least one species-specific expression domain was observed in the majority (83%) of cases, and 36% presented dramatically different expression patterns between the two species. Although some of these discrepancies may be due to the use of different transgenesis systems in mouse and zebrafish, in some instances we found an association between differences in enhancer activity and changes in the endogenous gene expression patterns between mouse and zebrafish, suggesting a potential role for trans-changes in the evolution of gene expression. Conclusions: In total, our results: (i) serve as a cautionary tale for studies investigating the role of human enhancers in different model organisms, and (ii) suggest that changes in the trans environment may play a significant role in the evolution of gene expression in vertebrates.

Description: Physical transport properties of marine microplastic pollution Biogeosciences Discussions, 9, 18755-18798, 2012 Author(s): A. Ballent, A. Purser, P. de Jesus Mendes, S. Pando, and L. Thomsen Given the complexity of quantitative collection, knowledge of the distribution of microplastic pollution in many regions of the world ocean is patchy, both spatially and temporally, especially for the subsurface environment. However, with knowledge of typical hydrodynamic behavior of waste plastic material, models predicting the dispersal of pelagic and benthic plastics from land sources into the ocean are possible. Here we investigate three aspects of plastic distribution and transport in European waters. Firstly, we assess patterns in the distribution of plastics found in fluvial strandlines of the North Sea and how distribution may be related to flow velocities and distance from source. Second, we model transport of non-buoyant preproduction pellets in the Nazaré Canyon of Portugal using the MOHID system after assessing the density, settling velocity, critical and depositional shear stress characteristics of such waste plastics. Thirdly, we investigate the effect of surface turbulences and high pressures on a range of marine plastic debris categories (various densities, degradation states and shapes tested) in an experimental water column simulator tank and pressure laboratory. Plastics deposited on North Sea strandlines varied greatly spatially, as a function of material composition and distance from source. Model outputs indicated that such dense production pellets are likely transported up and down canyon as a function of tidal forces, with only very minor net down canyon movement. Behaviour of plastic fragments under turbulence varied greatly, with the dimensions of the material, as well as density, playing major determining roles. Pressure was shown to affect hydrodynamic behaviours of only low density foam plastics at pressures ≥ 60 bar.

Description: Background: Tourette Syndrome (TS) is a neuropsychiatric disorder in children characterized by motor andverbal tics. Although several genes have been suggested in the etiology of TS, the geneticmechanisms remain poorly understood. Methods: Using cytogenetics and FISH analysis, we identified an apparently balancedt(6,22)(q16.2;p13) in a male patient with TS and obsessive-compulsive disorder (OCD). Inorder to map the breakpoints and to identify additional submicroscopic rearrangements, weperformed whole genome mate-pair sequencing and CGH-array analysis on DNA from theproband. Results: Sequence and CGH array analysis revealed a 400 kb deletion located 1.3 Mb telomeric of thechromosome 6q breakpoint, which has not been reported in controls. The deletion affectsthree genes (GPR63, NDUFA4 and KLHL32) and overlaps a region previously found deletedin a girl with autistic features and speech delay. The proband's mother, also a carrier of thetranslocation, was diagnosed with OCD and shares the deletion. We also describe a furtherpotentially related rearrangement which, while unmapped in Homo sapiens, was consistentwith the chimpanzee genome. Conclusions: We conclude that genome-wide sequencing at relatively low resolution can be used for theidentification of submicroscopic rearrangements.We also show that large rearrangements may escape detection using standard analysis ofwhole genome sequencing data. Our findings further provide a candidate region for TS andOCD on chromosome 6q16.

Description: Background: Secretoglobin 1A1 (SCGB 1A1), also called Clara cell secretory protein, is the most abundantly secreted protein of the airway. The SCGB1A1 gene has been characterized in mammals as a single copy in the genome. However, analysis of the equine genome suggested that horses might have multiple SCGB1A1 gene copies. Non-ciliated lung epithelial cells produce SCGB 1A1 during inhalation of noxious substances to counter airway inflammation. Airway fluid and lung tissue of horses with recurrent airway obstruction (RAO), a chronic inflammatory lung disease affecting mature horses similar to environmentally induced asthma of humans, have reduced total SCGB 1A1 concentration. Herein, we investigated whether horses have distinct expressed SCGB1A1 genes; whether the transcripts are differentially expressed in tissues and in inflammatory lung disease; and whether there is cell specific protein expression in tissues. Results: We identified three SCGB1A1 gene copies on equine chromosome 12, contained within a 512-kilobase region. Bioinformatic analysis showed that SCGB1A1 genes differ from each other by 8 to 10 nucleotides, and that they code for different proteins. Transcripts were detected for SCGB1A1 and SCGB1A1A, but not for SCGB1A1P. The SCGB1A1P gene had most inter-individual variability and contained a non-sense mutation in many animals, suggesting that SCGB1A1P has evolved into a pseudogene. Analysis of SCGB1A1 and SCGB1A1A sequences by endpoint-limiting dilution PCR identified a consistent difference affecting 3 bp within exon 2, which served as a gene-specific "signature". Assessment of gene- and organ-specific expression by semiquantitative RT-PCR of 33 tissues showed strong expression of SCGB1A1 and SCGB1A1A in lung, uterus, Fallopian tube and mammary gland, which correlated with detection of SCGB 1A1 protein by immunohistochemistry. Significantly altered expression of the ratio of SCGB1A1A to SCGB1A1 was detected in RAO-affected animals compared to controls, suggesting different roles for SCGB 1A1 and SCGB 1A1A in this inflammatory condition. Conclusions: This is the first report of three SCGB1A1 genes in a mammal. The two expressed genes code for proteins predicted to differ in function. Alterations in the gene expression ratio in RAO suggest cell and tissue specific regulation and functions. These findings may be important for understanding of lung and reproductive conditions.

Description: Background: To determine the general appearance of normal axillary lymph nodes (LNs) in real-time tissue sonoelastography and to explore the method[prime]s potential value in the prediction of LN metastases. Methods: Axillary LNs in healthy probands (n=165) and metastatic LNs in breast cancer patients (n=15) were examined with palpation, B-mode ultrasound, Doppler and sonoelastography (assessment of the elasticity of the cortex and the medulla). The elasticity distributions were compared and sensitivity (SE) and specificity (SP) were calculated. In an exploratory analysis, positive and negative predictive values (PPV, NPV) were calculated based upon the estimated prevalence of LN metastases in different risk groups. Results: In the elastogram, the LN cortex was significantly harder than the medulla in both healthy (p=0.004) and metastatic LNs (p=0.005). Comparing healthy and metastatic LNs, there was no difference in the elasticity distribution of the medulla (p=0.281), but we found a significantly harder cortex in metastatic LNs (p=0.006). The SE of clinical examination, B-mode ultrasound, Doppler ultrasound and sonoelastography was revealed to be 13.3%, 40.0%, 14.3% and 60.0%, respectively, and SP was 88.4%, 96.8%, 95.6% and 79.6%, respectively. The highest SE was achieved by the disjunctive combination of B-mode and elastographic features (cortex 〉3mm in B-mode or blue cortex in the elastogram, SE=73.3%). The highest SP was achieved by the conjunctive combination of B-mode ultrasound and elastography (cortex 〉3mm in B-mode and blue cortex in the elastogram, SP=99.3%). Conclusions: Sonoelastography is a feasible method to visualize the elasticity distribution of LNs. Moreover, sonoelastography is capable of detecting elasticity differences between the cortex and medulla, and between metastatic and healthy LNs. Therefore, sonoelastography yields additional information about axillary LN status and can improve the PPV, although this method is still experimental.

Description: Background: The use of food-grade Lactic Acid Bacteria (LAB) as DNA delivery vehicles represents an attractive strategy to deliver DNA vaccines at the mucosal surfaces as they are generally regarded as safe (GRAS). We previously showed that either native Lactococcus lactis (LL) or recombinant invasive LL expressing Fibronectin Binding Protein A of Staphylococcus aureus (LL-FnBPA+) or Internalin A of Listeria monocytogenes (LL-InlA+), were able to deliver and trigger DNA expression by epithelial cells, either in vitro or in vivo. InlA does not bind to its receptor, the murine E-cadherin, thus limiting the use of LL-InlA+in in vivo murine models. Moreover, FnBPA binds to its receptors, integrins, via fibronectin introducing another limiting factor. In order to avoid the limitations of LL-InlA+and LL-FnBPA+, a new L. lactis strain was engineered to produce a previously described mutated form of InlA (LL-mInlA+) allowing the binding of mInlA on murine E-cadherin. Results: After showing the expression of mInLA at the surface of LL-mInlA+strain, in vitro gentamycin survival assay in Caco-2 cells showed that LL-mInlA+is 1000 times more invasive than LL. LL-mInlA+invasivity was also validated by fluorescence microscopy. LL and LL-mInlA+were transformed with pValacBLG, a plasmid containing the cDNA of bovine beta-Lactoglobulin (BLG), resulting in strains LL-BLG and LL-mInlA+BLG. The plasmid transfer in vitro using LL-mInlA+BLG was increased 10 times compared to LL-BLG. Moreover, the number of mice producing BLG in isolated enterocytes after oral administration of LL-mInlA+BLG in vivo was slightly higher than after oral administration of LL-BLG. Conclusions: We confirmed in this study that the production of mInlA at the surface of L. lactis is a promising strategy for plasmid transfer in vitro and in vivo.

Description: Background: The 22q11.2 deletion syndrome (22q11.2DS) is caused by hemizygous microdeletions on chromosome 22q11.2 with highly variable physical and neuropsychiatric manifestations. We explored the genotype-phenotype relationship in a relatively large 22q11.2DS cohort treated and monitored in our clinic using comprehensive clinical evaluation and detailed molecular characterization of the deletion. Methods: Molecular analyses in 142 subjects with 22q11.2DS features were performed by FISH and MLPA methods. Participants underwent clinical assessment of physical symptoms and structured psychiatric and cognitive evaluation. Results: Deletions were found in 110 individuals including one with an atypical nested distal deletion which was missed by the FISH test. Most subjects (88.2%) carried the 3Mb typically deleted region and 11.8% carried 4 types of deletions differing in size and location. No statistically significant genotype-phenotype correlations were found between deletion type and clinical data although some differences in hypocalcemia and cardiovascular anomalies were noted.Analysis of the patient with the distal nested deletion suggested a redundancy of genes causing the physical and neuropsychiatric phenotype in 22q11.2DS and indicating that the psychiatric and cognitive trajectories may be governed by different genes. Conclusions: MLPA is a useful and affordable molecular method combining accurate diagnosis and detailed deletion characterization. Variations in deletion type and clinical manifestations impede the detection of significant differences in samples of moderate size, but analysis of individuals with unique deletions may provide insight into the underlying biological mechanisms.Future genotype-phenotype studies should involve large multicenter collaborations employing uniform clinical standards and high-resolution molecular methods.

Description: Background: In eukaryotic cells, dynamin and flotillin are involved in processes such as endocytosis and lipid raft formation, respectively. Dynamin is a GTPase that exerts motor-like activity during the pinching off of vesicles, while flotillins are coiled coil rich membrane proteins with no known enzymatic activity. Bacteria also possess orthologs of both classes of proteins, but their function has been unclear. Results: We show that deletion of the single dynA or floT genes lead to no phenotype or a mild defect in septum formation in the case of the dynA gene, while dynA floT double mutant cells were highly elongated and irregularly shaped, although the MreB cytoskeleton appeared to be normal. DynA colocalizes with FtsZ, and the dynA deletion strain shows aberrant FtsZ rings in a subpopulation of cells. The mild division defect of the dynA deletion is exacerbated by an additional deletion in ezrA, which affects FtsZ ring formation, and also by the deletion of a late division gene (divIB), indicating that DynA affects several steps in cell division. DynA and mreB deletions generated a synthetic defect in cell shape maintenance, showing that MreB and DynA play non-epistatic functions in cell shape maintenance. TIRF microscopy revealed that FloT forms many dynamic membrane assemblies that frequently colocalize with the division septum. The deletion of dynA did not change the pattern of localization of FloT, and vice versa, showing that the two proteins play non redundant roles in a variety of cellular processes. Expression of dynamin or flotillin T in eukaryotic S2 cells revealed that both proteins assemble at the cell membrane. While FloT formed patch structures, DynA built up tubulated structures extending away from the cells. Conclusions: Bacillus subtilis dynamin ortholog DynA plays a role during cell division and in cell shape maintenance. It shows a genetic link with flotillin T, with both proteins playing non-redundant functions at the cell membrane, where they assemble even in the absence of any bacterial cofactor.

Description: Background: To derive post-genomic, neutral insight into the peptidoglycan (PG) distribution among organisms, we mined 1,644 genomes listed in the Carbohydrate-Active Enzymes database for the presence of a minimal 3-gene set that is necessary for PG metabolism. This gene set consists of one gene from the glycosyltransferase family GT28, one from family GT51 and at least one gene belonging to one of five glycoside hydrolase families (GH23, GH73, GH102, GH103 and GH104). Results: None of the 103 Viruses or 101 Archaea examined possessed the minimal 3-gene set, but this set was detected in 1/42 of the Eukarya members (Micromonas sp., coding for GT28, GT51 and GH103) and in 1,260/1,398 (90.1%) of Bacteria, with a 100% positive predictive value for the presence of PG. Pearson correlation test showed that GT51 family genes were significantly associated with PG with a value of 0.963 and a p value less than 10-3. This result was confirmed by a phylogenetic comparative analysis showing that the GT51-encoding gene was significantly associated with PG with a Pagel's score of 60 and 51 (percentage of error close to 0%). Phylogenetic analysis indicated that the GT51 gene history comprised eight loss and one gain events, and suggested a dynamic on-going process. Conclusions: Genome analysis is a neutral approach to explore prospectively the presence of PG in uncultured, sequenced organisms with high predictive values.

Description: Background: Toxin complex (Tc) family proteins were first identified as insecticidal toxins in Photorhabdus luminescens and have since been found in a wide range of bacteria. The genome of Yersinia pestis, the causative agent of bubonic plague, contains a locus that encodes the Tc protein homologues YitA, YitB, YitC, and YipA and YipB. Previous microarray data indicate that the Tc genes are highly upregulated by Y. pestis while in the flea vector; however, their role in the infection of fleas and pathogenesis in the mammalian host is unclear. Results: We show that the Tc proteins YitA and YipA are highly produced by Y. pestis while in the flea but not during growth in brain heart infusion (BHI) broth at the same temperature. Over-production of the LysR-type regulator YitR from an exogenous plasmid increased YitA and YipA synthesis in broth culture. The increase in production of YitA and YipA correlated with the yitR copy number and was temperature-dependent. Although highly synthesized in fleas, deletion of the Tc proteins did not alter survival of Y. pestis in the flea or prevent blockage of the proventriculus. Furthermore, YipA was found to undergo post-translational processing and YipA and YitA are localized to the outer membrane of Y. pestis. YitA was also detected by immunofluorescence microscopy on the surface of Y. pestis. Both YitA and YipA are produced maximally at low temperature but persist for several hours after transfer to 37[degree sign]C. Conclusions: Y. pestis Tc proteins are highly expressed in the flea but are not essential for Y. pestis to stably infect or produce a transmissible infection in the flea. However, YitA and YipA localize to the outer membrane and YitA is exposed on the surface, indicating that at least YitA is present on the surface when Y. pestis is transmitted into the mammalian host from the flea.

Description: Background: Fermentative bacteria offer the potential to convert lignocellulosic waste-streams into biofuels such as hydrogen (H2) and ethanol. Current fermentative H2 and ethanol yields, however, are below theoretical maxima, vary greatly among organisms, and depend on the extent of metabolic pathways utilized. For fermentative H2 and/or ethanol production to become practical, biofuel yields must be increased. We performed a comparative meta-analysis of (i) reported end-product yields, and (ii) genes encoding pyruvate metabolism and end-product synthesis pathways to identify suitable biomarkers for screening a microorganism's potential of H2 and/or ethanol production, and to identify targets for metabolic engineering to improve biofuel yields. Our interest in H2 and/or ethanol optimization restricted our meta-analysis to organisms with sequenced genomes and limited branched end-product pathways. These included members of the Firmicutes, Euryarchaeota, and Thermotogae. Results: Bioinformatic analysis revealed that the absence of genes encoding acetaldehyde dehydrogenase and bifunctional acetaldehyde/alcohol dehydrogenase (AdhE) in Caldicellulosiruptor, Thermococcus, Pyrococcus, and Thermotoga species coincide with high H2 yields and low ethanol production. Organisms containing genes (or activities) for both ethanol and H2 synthesis pathways (i.e. Caldanaerobacter subterraneus subsp. tengcongensis, Ethanoligenens harbinense, and Clostridium species) had relatively uniform mixed product patterns. The absence of hydrogenases in Geobacillus and Bacillus species did not confer high ethanol production, but rather high lactate production. Only Thermoanaerobacter pseudethanolicus produced relatively high ethanol and low H2 yields. This may be attributed to presence of genes encoding proteins that promote NADH production. Lactate dehydrogenase and pyruvate:formate lyase are not conducive for ethanol and/or H2 production. While the type(s) of encoded hydrogenases appear to have little impact on H2 production in organisms that do not encode ethanol producing pathways, they do influence reduced end-product yields in those that do. Conclusions: Here we show that composition of genes encoding pathways involved in pyruvate catabolism and end-product synthesis pathways can be used to approximate potential end-product distribution patterns. We have identified a number of genetic biomarkers for streamlining ethanol and H2 producing capabilities. By linking genome content, reaction thermodynamics, and end-product yields, we offer potential targets for optimization of either ethanol or H2 yields through metabolic engineering.

Description: Background: Endolysins produced by bacteriophages lyse bacteria, and are thus considered a novel type of antimicrobial agent. Several endolysins from Bacillus phages or prophages have previously been characterized and used to target Bacillus strains that cause disease in animals and humans. B. thuringiensis phage BtCS33 is a Siphoviridae family phage and its genome has been sequenced and analyzed. In the BtCS33 genome, orf18 was found to encode an endolysin protein (PlyBt33). Results: Bioinformatic analyses showed that endolysin PlyBt33 was composed of two functional domains, the N-terminal catalytic domain and the C-terminal cell wall binding domain. In this study, the entire endolysin PlyBt33, and both the N- and C-termini,were expressed in Escherichia coli and then purified. The lytic activities of PlyBt33 and its N-terminus were tested on bacteria. Both regions exhibited lytic activity, although PlyBt33 showed a higher lytic activity than the N-terminus. PlyBt33 exhibited activity against all Bacillus strains tested from five different species, but was not active against Gram-negative bacteria. Optimal conditions for PlyBt33 reactivity were pH 9.0 and 50[degree sign]C. PlyBt33 showed high thermostability, with 40% of initial activity remaining following 1 h of treatment at 60[degree sign]C. The C-terminus of PlyBt33 bound to B. thuringiensis strain HD-73 and Bacillus subtilis strain 168. This cell wall binding domain might be novel, as its amino acid sequence showed little similarity to previously reported endolysins. Conclusions: PlyBt33 showed potential as a novel antimicrobial agent at a relatively high temperature and had a broad lytic spectrum within the Bacillus genus. The C-terminus of PlyBt33 might be a novel kind of cell wall binding domain.

Description: Background: In plants, the multistep phosphorelay signaling pathway mediates responses to environmental factors and plant hormones. This system is composed of three successive partners: hybrid Histidine-aspartate Kinases (HKs), Histidine-containing Phosphotransfer proteins (HPts), and Response Regulators (RRs). Among the third partners, B-type RR family members are the final output elements of the pathway; they act as transcription factors and clearly play a pivotal role in the early response to cytokinin in Arabidopsis. While interactions studies between partners belonging to the multistep phosphorelay system are mainly focused on protagonists involved in cytokinin or ethylene pathways, very few reports are available concerning partners of osmotic stress signaling pathway. Results: In Populus, we identified eight B-type RR proteins, RR12-16, 19, 21 and 22 in the Dorskamp genotype. To assess HPt/B-type RR interactions and consequently determine potential third partners in the osmosensing multistep phosphorelay system, we performed global yeast two-hybrid (Y2H) assays in combination with Bimolecular Fluorescence Complementation (BiFC) assays in plant cells. We found that all B-type RRs are able to interact with HPt predominant partners (HPt2, 7 and 9) of HK1, which is putatively involved in the osmosensing pathway. However, different profiles of interaction are observed depending on the studied HPt. HPt/RR interactions displayed a nuclear localization, while the nuclear and cytosolic localization of HPt and nuclear localization of RR proteins were validated. Although the nuclear localization of HPt/RR interaction was expected, this work constitutes the first evidence of such an interaction in plants. Furthermore, the pertinence of this partnership is reinforced by highlighting a co-expression of B-type RR transcripts and the other partners (HK1 and HPts) belonging to a potential osmosensing pathway. Conclusion: Based on the interaction studies between identified B-type RR and HPt proteins, and the co-expression analysis of transcripts of these potential partners in poplar organs, our results favor the model that RR12, 13, 14, 16 and 19 are able to interact with the main partners of HK1, HPt2, 7 and 9, and this HPt/RR interaction occurs within the nucleus. On the whole, the five B-type RRs of interest could be third protagonists putatively involved in the osmosensing signaling pathway in Populus.

Description: Background: A measles outbreak was detected at Ndanga Hospital in Zaka district Masvingo Province on the 5th of May 2010 and there were five deaths. Source of infection was not known and an investigation was carried out to determine factors associated with contracting measles in Zaka district.Materials and methodsA 1:1 unmatched case control study was conducted. A case was a person residing in Zaka district who developed signs and symptoms of measles or tested IgM positive from 06 May 2010 to 30 August 2010. A control was a person residing in the same community who did not have history of signs and symptoms of measles during the same period. A structured interviewer administered questionnaire (translated into shona) was used to solicit information from cases and controls. Ethical consideration like written consent from all participants, respect and confidentiality were observed. Permission to carry out the study was obtained from the medical research Council of Zimbabwe and the provincial Medical Directors Masvingo. Epi info was used to calculate frequencies, odds ratios and perform logistic regression to control for confounding variables.FindingsA total of 110 cases and 110 controls were recruited. Most cases (63.03%) were from the apostolic sect while 44.7% of controls were from orthodox churches. Contact with a measles case [AOR= 41.14, 95% CI (7.47-226.5)],being unvaccinated against measles [AOR= 3.96, 95%CI (2.58-6.08)] and not receiving additional doses of measles vaccine [AOR 5.48, 95% CI (2.16-11.08)] were independent risk factor for contracting measles . Measles vaccination coverage for Zaka district was 75%. The median duration for seeking treatment after onset of illness was three days (Q1=2; Q3=7). There were no emergency preparedness plans in place. Conclusion: This outbreak occurred due to a large number of unvaccinated children and a boarding school that facilitated person to person transmission. We recommend mandatory vaccination for all children before enrolling into schools. As a result of the study one day training on outbreak management and surveillance was done with all District Nursing Officers and Environmental Health Officers in personnel in the province.

Description: Available online 19 December 2012 Publication year: 2012 Source: FEBS Open Bio The green fluorescent protein (GFP) is the most commonly used reporter protein for monitoring gene expression and protein localization in a variety of living and fixed cells, including not only prokaryotes, but also eukaryotes, e.g., yeasts, mammals, plants and fish. In general, it is thought that GFP is nontoxic to cells, although there are some reports on the side effect of GFP. However, details of the molecular mechanism concerning the side effect of GFP remain unclear. Here we show that Ku80, but not XRCC4, plays an important role in the mechanism of the resistance to cytotoxicity induced by enhanced GFP (EGFP). EGFP inhibited both cell proliferation and colony formation, and induced cell death in Ku80-deficient hamster cells, i.e., xrs-6 cells. In addition, Ku80 attenuated EGFP-induced cytotoxicity in the xrs-6 cells. No EGFP-induced cytotoxicity was observed in the NHEJ core protein XRCC4-deficient hamster cells, i.e., XR-1 cells. Furthermore, EGFP markedly enhanced X-ray-induced cytotoxicity in the xrs-6 cells. These results suggest that Ku80 plays a key role in the novel NHEJ-independent defense mechanism against EGFP-induced cytotoxicity. Caution should be taken in considering of the potential influence by the stress response mechanism, namely, the Ku80-dependent elimination mechanism of EGFP-induced cytotoxicity, being activated, even when using EGFP-expressing cells in which Ku80 functions normally.

Description: Background: The localized scleroderma (LS) known as morphea, presents a variety of clinical manifestations that can include systemic involvement. Current classification schemes divide morphea into categories based solely on cutaneous morphology, without reference to systemic disease or autoimmune phenomena. This classification is likely incomplete. Autoimmune phenomena such as vitiligo and Hashimoto thyroiditis associated with LS have been reported in some cases suggesting an autoimmune basis. To our knowledge this is the first case of a morphea forming part of a multiple autoimmune syndrome (MAS) and presenting simultaneously with autoimmune thrombocytopenic purpura and central nervous system vasculitis.Case presentationWe report an uncommon case of a white 53 year old female patient with LS as part of a multiple autoimmune syndrome associated with pneumonitis, autoimmune thrombocytopenic purpura and central nervous system vasculitis presenting a favorable response with thrombopoietin receptor agonists, pulses of methylprednisolone and cyclophosphamide. Conclusion: Is likely that LS have an autoimmune origin and in this case becomes part of MAS, which consist on the presence of three or more well-defined autoimmune diseases in a single patient.

Description: Background: Extensive research effort has advanced our understanding of Caenorhabditis as a model system, but its natural association with bacteria remains to be explored in an ecological context. Explored associations vary vastly from mutualistic to parasitic. Serratia marcescens has been shown to be pathogenic to Caenorhabditis with a fitness cost. The recent isolation of an entomopathogenic Caenorhabditis briggsae KT0001/S. marcescens SCBI association from the wild has allowed us to examine under laboratory conditions whether such an association poses a serious cost to Caenorhabditis as previously surmised for other Serratia. Results: A fecundity table of Caenorhabditis briggsae KT0001 fed on S. marcescens SCBI and the control fed on E. coli OP50 is presented. We found no significant difference in survivorship or total fecundity between the S. marcescens SCBI fed and E. coli OP50 fed Caenorhabditis briggsae KT0001. Only the mean onset of reproduction was significantly different between the two groups with E. coli fed C. briggsae maturing earlier (2.12 days) than those fed on Serratia (2.42 days). Conclusion: S. marcescens SCBI is not highly pathogenic to C. briggsae KT0001 indicating that the entomopathogenicity reported for this association may be beneficial for both the nematode and bacteria. In light of the fact that hitherto conducted experimental tests conform to widely held view that Serratia are highly pathogenic to Caenorhabditis, the absence of a high fitness cost for C. briggsae we report here may indicate that this entomopathogenic association is non-transient suggesting nematode/bacterial associations in the wild may vary greatly. Consequently, broad generalizations about nematode/bacterial associations should be interpreted with care.

Description: Available online 20 December 2012 Publication year: 2012 Source: Cell Reports In the fission yeast Schizosaccharomyces pombe , a chromosomal imprinting event controls the asymmetric pattern of mating-type switching. The orientation of DNA replication at the mating-type locus is instrumental in this process. However, the factors leading to imprinting are not fully identified and the mechanism is poorly understood. Here, we show that the replication fork pause at the mat1 locus ( MPS1 ), essential for imprint formation, depends on the lysine-specific demethylase Lsd1. We demonstrate that either Lsd1 or Lsd2 amine oxidase activity is required for these processes, working upstream of the imprinting factors Swi1 and Swi3 (homologs of mammalian Timeless and Tipin, respectively). We also show that the Lsd1/2 complex controls the replication fork terminators, within the rDNA repeats. These findings reveal a role for the Lsd1/2 demethylases in controlling polar replication fork progression, imprint formation, and subsequent asymmetric cell divisions. Graphical abstract Highlights ► The lysine-specific demethylase, Lsd1, is a mating-type switching mutant ► Lsd1 is essential for replication fork pausing at the mat1 locus ► Lsd1 is essential for replication fork arrest at the replication fork block at rDNA loci ► Lsd1 and Lsd2 act in a redundant manner for replication fork pausing

Description: Available online 21 December 2012 Publication year: 2012 Source: Cell Reports Chromatin dynamics play a central role in maintaining genome integrity, but how this is achieved remains largely unknown. Here, we report that microrchidia CW-type zinc finger 2 (MORC2), an uncharacterized protein with a derived PHD finger domain and a conserved GHKL-type ATPase module, is a physiological substrate of p21-activated kinase 1 (PAK1), an important integrator of extracellular signals and nuclear processes. Following DNA damage, MORC2 is phosphorylated on serine 739 in a PAK1-dependent manner, and phosphorylated MORC2 regulates its DNA-dependent ATPase activity to facilitate chromatin remodeling. Moreover, MORC2 associates with chromatin and promotes gamma-H2AX induction in a PAK1 phosphorylation-dependent manner. Consequently, cells expressing MORC2-S739A mutation displayed a reduction in DNA repair efficiency and were hypersensitive to DNA-damaging agent. These findings suggest that the PAK1-MORC2 axis is critical for orchestrating the interplay between chromatin dynamics and the maintenance of genomic integrity through sequentially integrating multiple essential enzymatic processes. Graphical abstract Highlights ► MORC2 is a DNA damage-responsive phosphoprotein activated by PAK1 kinase ► MORC2 regulates phosphorylation-coupled, ATPase-dependent chromatin remodeling ► MORC2 facilitates gamma-H2AX induction independently of PIKK kinases ► MORC2 promotes DSB repair in a PAK1 phosphorylation-dependent manner

Description: Effects of precipitation on soil respiration and its temperature/moisture sensitivity in three subtropical forests in Southern China Biogeosciences Discussions, 9, 15667-15698, 2012 Author(s): H. Jiang, Q. Deng, G. Zhou, D. Hui, D. Zhang, S. Liu, G. Chu, and J. Li Both long-term observation data and model simulations suggest an increasing chance of serious drought in the dry season and extreme flood in the wet season in Southern China, yet little is known about how changes in precipitation pattern will affect soil respiration in the region. We conducted a field experiment to study the responses of soil respiration to precipitation manipulations – precipitation exclusion to mimic drought, double precipitation to simulate flood, and ambient precipitation (Abbr. EP, DP and AP, respectively) – in three subtropical forests in Southern China. The three forests include Masson pine forest (PF), coniferous and broadleaved mixed forest (MF) and monsoon evergreen broadleaved forest (BF). Our observations showed that altered precipitation can strongly influence soil respiration, not only through the well-known direct effects of soil moisture, but also by modification on both moisture and temperature sensitivity of soil respiration. In the dry season, soil respiration and its temperature sensitivity in the three forests showed rising trends with precipitation increase, and its moisture sensitivity showed an opposite trend. In the wet season, the EP treatment also decreased soil respiration and its temperature sensitivity, and enhanced moisture sensitivity in all three forests. Soil respiration under the DP treatment increased significantly in the PF only, and no significant change was found for either moisture or temperature sensitivity. However, the DP treatment in the MF and BF reduced temperature sensitivity significantly. Our results indicated that soil respiration would decrease in the three subtropical forests if soil moisture continues to decrease in the future. More rainfall in the wet season could have limited effect on the response of soil respiration to the rising of temperature in the BF and MF.

Description: First paragraph (this article has no abstract)What is regeneration? {1st level heading}Historically, philosophers, naturalists and biologists alike have referred to the restoration of missing body parts after traumatic injury as regeneration. While still valid today, the concept of regeneration has expanded through the years to include a diverse set of phenomena. For instance, August Weisman considered physiological cell renewal to be regeneration and wrote so in a chapter dedicated to regeneration in his seminal 1893 book The Germ Plasm: 'the functions of certain organs depend on the fact that their parts continually undergo destruction, and are then correspondingly renewed. In this case it is the process of life itself, and not an external enemy, that destroys the life of a cell' [1].

Description: Background The robust identification of isotope patterns originating from peptides being analyzed through mass spectrometry (MS) is often significantly hampered by noise artifacts and the interference of overlappingpatterns arising e.g. from post-translational modifications. As the classification of the recorded data points into either 'noise' or 'signal' lies at the very root of essentially every proteomic application, the quality of the automated processing of mass spectra can significantly influence the way the data might be interpreted within a given biological context.Results We propose non-negative least squares/non-negative least absolute deviation regression to fit a raw spectrum by templates imitating isotope patterns. In a carefully designed validation scheme, we show that the method exhibits excellent performance in pattern picking. It is demonstrated that the method is able to disentangle complicated overlaps of patterns. Conclusions: We find that regularization is not necessary to prevent overfitting and that thresholding is an effective and user-friendly way to perform feature selection. The proposed method avoids problems inherent in regularization-based approaches, comes with a set of well-interpretable parameters whose default configuration is shown to generalize well without the need for fine-tuning, and is applicable to spectra of different platforms. The R package IPPD implements the method and is available from the Bioconductor platform (http://bioconductor.fhcrc.org/help/bioc-views/devel/bioc/html/IPPD.html).

Description: Background: Monosporascus cannonballus is the main causal agent of melon vine decline disease. Several studies have been carried out mainly focused on the study of the penetration of this pathogen into melon roots, the evaluation of symptoms severity on infected roots, and screening assays for breeding programs. However, a detailed molecular view on the early interaction between M. cannonballus and melon roots in either susceptible or resistant genotypes is lacking. In the present study, we used a melon oligo-based microarray to investigate the gene expression responses of two melon genotypes, Cucumis melo 'Piel de sapo' ('PS') and C. melo 'Pat 81', with contrasting resistance to the disease. This study was carried out at 1 and 3 days after infection (DPI) by M. cannonballus. Results: Our results indicate a dissimilar behavior of the susceptible vs. the resistant genotypes from 1 to 3 DPI. 'PS' responded with a more rapid infection response than 'Pat 81' at 1 DPI. At 3 DPI the total number of differentially expressed genes identified in 'PS' declined from 451 to 359, while the total number of differentially expressed transcripts in 'Pat 81' increased from 187 to 849. Several deregulated transcripts coded for components of Ca2+ and jasmonic acid (JA) signalling pathways, as well as for other proteins related to defence mechanisms. Transcriptional differences in the activation of the JA-mediated response in 'Pat 81' compared to 'PS' suggested that JA response might be partially responsible for their observed differences in resistance. Conclusions: As a result of this study we have identified for the first time a set of candidate genes involved in the root response to the infection of the pathogen causing melon vine decline. This information is useful for understanding the disease progression and resistance mechanisms few days after inoculation.

Description: Background: [NiFe] hydrogenases are enzymes that catalyze the oxidation of hydrogen into protons and electrons, to use H2 as energy source, or the production of hydrogen through proton reduction, as an escape valve for the excess of reduction equivalents in anaerobic metabolism. Biosynthesis of [NiFe] hydrogenases is a complex process that occurs in the cytoplasm, where a number of auxiliary proteins are required to synthesize and insert the metal cofactors into the enzyme structural units. The endosymbiotic bacterium Rhizobium leguminosarum requires the products of eighteen genes (hupSLCDEFGHIJKhypABFCDEX) to synthesize an active hydrogenase. hupF and hupK genes are found only in hydrogenase clusters from bacteria expressing hydrogenase in the presence of oxygen. Results: HupF is a HypC paralogue with a similar predicted structure, except for the C-terminal domain present only in HupF. Deletion of hupF results in the inability to process the hydrogenase large subunit HupL, and also in reduced stability of this subunit when cells are exposed to high oxygen tensions. A DeltahupF mutant was fully complemented for hydrogenase activity by a C-terminal deletion derivative under symbiotic, ultra low-oxygen tensions, but only partial complementation was observed in free living cells under higher oxygen tensions (1% or 3%). Co-purification experiments using StrepTag-labelled HupF derivatives and mass spectrometry analysis indicate the existence of a major complex involving HupL and HupF, and a less abundant HupF-HupK complex. Conclusions: The results indicate that HupF has a dual role during hydrogenase biosynthesis: it is required for hydrogenase large subunit processing and it also acts as a chaperone to stabilize HupL when hydrogenase is synthesized in the presence of oxygen.

Description: Background: Blood coagulation is an essential determinant of coronary artery disease (CAD). Soluble Endothelial Protein C Receptor (sEPCR) may be a biomarker of a hypercoagulable state. We prospectively investigated the relationship between plasma sEPCR levels and the risk of cardiovascular events (CVE). Methods: We measured baseline sEPCR levels in 1673 individuals with CAD (521 with acute coronary syndrome [ACS] and 1152 with stable angina pectoris [SAP]) from the AtheroGene cohort. During a median follow up of 3.7 years, 136 individuals had a CVE. In addition, 891 of these CAD patients were genotyped for the PROCR rs867186 (Ser219Gly) variant. Results: At baseline, sEPCR levels were similar in individuals with ACS and SAP (median: 111 vs. 115 ng/mL respectively; p=0.20). Increased sEPCR levels were found to be associated with several cardiovascular risk factors including gender (p=0.006), soluble Tissue Factor levels (p=0.0001), diabetes (p=0.0005), and factors reflecting impaired renal function such as creatinine and cystatin C (p

Description: Background: Fungal load quantification is a critical component of fungal community analyses. Limitation of current approaches for quantifying the fungal component in the human microbiome suggests the need for new broad-coverage techniques. Methods: We analyzed 2,085 18S rRNA gene sequences from the SILVA database for assay design. We generated and quantified plasmid standards using a qPCR-based approach. We evaluated assay coverage against 4,968 sequences and performed assay validation following the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines. Results: We designed FungiQuant, a TaqMan(R) qPCR assay targeting a 351 bp region in the fungal 18S rRNA gene. Our in silico analysis showed that FungiQuant is a perfect sequence match to 90.0% of the 2,617 fungal species analyzed. We showed that FungiQuant's is 100% sensitive and its amplification efficiencies ranged from 76.3% to 114.5%, with r2-values of 〉0.99 against the 69 fungal species tested. Additionally, FungiQuant inter- and intra-run coefficients of variance ranged from

Description: Background: Hyperelastosis cutis is an inherited autosomal recessive connective tissue disorder. Affected horses are characterized by hyperextensible skin, scarring, and severe lesions along the back. The disorder is caused by a mutation in cyclophilin B. Results: The crystal structures of both wild-type and mutated (Gly6-〉Arg) horse cyclophilin B are presented. The mutation neither affects the overall fold of the enzyme nor impairs the catalytic site structure. Instead, it locally rearranges the flexible N-terminal end of the polypeptide chain and also makes it more rigid. Conclusions: Interactions of the mutated cyclophilin B with a set of endoplasmic reticulum-resident proteins must be affected.

Description: Background: In plants, a large family of calmodulin (CaM) and CaM-like (CML) proteins transduce the increase in cytosolic Ca2+ concentrations by binding to and altering the activities of target proteins, and thereby affecting the physiological responses to a vast array of stimuli. Here, transcript expression analysis of Cam and CML gene family members in rice (Oryza sativa L.) was extensively examined. Results: Cam and CML genes in rice exhibited differential expression patterns in tissues/organs. Under osmotic stress and salt stress, expression of OsCam1-1, OsCML4, 5, 8, and 11 was induced with different kinetics and magnitude. OsCML4 and 8 mRNA levels significantly increased by 3 h after treatment and remained elevated for at least 24 h while expression of OsCam1-1, OsCML5 and 11 was up-regulated as early as 1--3 h before rapidly returning to normal levels. Several cis-acting elements in response to abiotic stresses, including DREs (important promoter elements responsive to drought, high salt, and cold stress), were detected in the 5[prime] upstream regions of these genes. The observed induction of the GUS activity of transgenic rice plants via the OsCam1-1 promoter appeared to be biphasic and dependent on the severity of salt stress. Conclusions: Large OsCam and OsCML gene family members likely play differential roles as signal transducers in regulating various developmental processes and represent important nodes in the signal transduction and transcriptional regulation networks in abiotic stresss responses mediated by the complex Ca2+ signals in plants, which are rich in both spatial and temporal information.

Description: Background: Plant microRNAs (miRNAs) play key roles in the transcriptional responses to environmental stresses. However, the role of miRNAs in responses to insect herbivory has not been thoroughly explored. To identify herbivory-responsive miRNAs, we first identified conserved miRNAs in the ecological model plant Nicotiana attenuata whose interactions with herbivores have been well-characterized in both laboratory and field studies. Results: We identified 59 miRNAs from 36 families, and two endogenous trans-acting small interfering RNAs (tasiRNA) targeted by miRNAs. We characterized the response of the precursor and mature miRNAs to simulated attack from the specialist herbivore Manduca sexta by quantitative PCR analysis and used ir-aoc RNAi transformants, deficient in jasmonate biosynthesis, to identify jasmonate-dependent and -independent miRNA regulation. Expression analysis revealed that groups of miRNAs and tasiRNAs were specifically regulated by either mechanical wounding or wounding plus oral secretions from M. sexta larvae, and these small RNAs were accumulated in jasmonate-dependent or -independent manners. Moreover, cDNA microarray analysis indicated that the expression patterns of the corresponding target genes were correlated with the accumulation of miRNAs and tasiRNAs. Conclusions: We show that a group of miRNAs and tasiRNAs orchestrates the expression of target genes involved in N. attenuata's responses to herbivore attack.

Description: Background: Estrogen receptors alpha (ER) are implicated in many types of female cancers, and are the common target for anti-cancer therapy using selective estrogen receptor modulators (SERMs, such as tamoxifen). However, cell-type specific and patient-to-patient variability in response to SERMs (from suppression to stimulation of cancer growth), as well as frequent emergence of drug resistance, represents a serious problem. The molecular processes behind mixed effects of SERMs remain poorly understood, and this strongly motivates application of systems approaches. In this work, we aimed to establish a mathematical model of ER-dependent gene expression to explore potential mechanisms underlying the variable actions of SERMs. Results: We developed an equilibrium model of ER binding with 17beta-estradiol, tamoxifen and DNA, and linked it to a simple ODE model of ER-induced gene expression. The model was parameterised on the broad range of literature available experimental data, and provided a plausible mechanistic explanation for the dual agonism/antagonism action of tamoxifen in the reference cell line used for model calibration. To extend our conclusions to other cell types we ran global sensitivity analysis and explored model behaviour in the wide range of biologically plausible parameter values, including those found in cancer cells. Our findings suggest that transcriptional response to tamoxifen is controlled in a complex non-linear way by several key parameters, including ER expression level, hormone concentration, amount of ER-responsive genes and the capacity of ER-tamoxifen complexes to stimulate transcription (e.g. by recruiting co-regulators of transcription). The model revealed non-monotonic dependence of ER-induced transcriptional response on the expression level of ER, that was confirmed experimentally in four variants of the MCF-7 breast cancer cell line. Conclusions: We established a minimal mechanistic model of ER-dependent gene expression, that predicts complex non-linear effects in transcriptional response to tamoxifen in the broad range of biologically plausible parameter values. Our findings suggest that the outcome of a SERM's action is defined by several key components of cellular micro-environment, that may contribute to cell-type-specific effects of SERMs and justify the need for the development of combinatorial biomarkers for more accurate prediction of the efficacy of SERMs in specific cell types.

Description: Publication year: 2012 Source: Cell Reports Hong Zan, Clayton A. White, Lisa M. Thomas, Thach Mai, Guideng Li, Zhenming Xu, Jinsong Zhang, Paolo Casali By diversifying the biological effector functions of antibodies, class switch DNA recombination (CSR) plays a critical role in the maturation of the immune response. It is initiated by activation-induced cytidine deaminase (AID)-mediated deoxycytosine deamination, yielding deoxyuridine (dU), and dU glycosylation by uracil DNA glycosylase (Ung) in antibody switch (S) region DNA. Here we showed that the translesion DNA synthesis polymerase Rev1 directly interacted with Ung and targeted in an AID-dependent and Ung-independent fashion the S regions undergoing CSR. Rev1 −/− Ung +/+ B cells reduced Ung recruitment to S regions, DNA-dU glycosylation, and CSR. Together with an S region spectrum of mutations similar to that of Rev1 +/+ Ung −/− B cells, this suggests that Rev1 operates in the same pathway as Ung, as emphasized by further decreased CSR in Rev1 −/− Msh2 −/− B cells. Rescue of CSR in Rev1 −/− B cells by a catalytically inactive Rev1 mutant shows that the important role of Rev1 in CSR is mediated by Rev1’s scaffolding function, not its enzymatic function. Graphical abstract Graphical Abstract Highlights ► Rev1 DNA polymerase plays an important role in class switch DNA recombination ► This role is mediated by Rev1’s scaffolding function, not its enzymatic function ► Rev1 interacts with Ung and recruits it to switch region DNA ► Rev1 enhances Ung-mediated dU glycosylation in DNA

Description: Publication year: 2012 Source: Cell Reports Michihiko Sugimoto, Masayo Kondo, Michiko Hirose, Misao Suzuki, Kazuyuki Mekada, Takaya Abe, Hiroshi Kiyonari, Atsuo Ogura, Nobuo Takagi, Karen Artzt, Kuniya Abe After implantation, pluripotent epiblasts are converted to embryonic ectoderm through cell–cell interactions that significantly change the transcriptional and epigenetic networks. An entrée to understanding this vital developmental transition is the t w5 mutation of the mouse t complex. This mutation produces highly specific defects in the embryonic ectoderm before gastrulation, leading to death of the embryonic ectoderm. Using a positional cloning approach, we have now identified the mutated gene, completing a decades-long search. The gene, vacuolar protein sorting 52 ( Vps52 ), is a mouse homolog of yeast VPS52 that is involved in the retrograde trafficking of endosomes. Our data suggest that Vps52 acts in extraembryonic tissues to support the growth and differentiation of embryonic ectoderm via cell–cell interactions. It is also required in the formation of embryonic structures at a later stage of development, revealing hitherto unknown functions of Vps52 in the development of a multicellular organism. Graphical abstract Graphical Abstract Highlights ► Vps52 , part of retrograde transport to the Golgi, causes the t w5 lethal phenotype ► Vps52 acts in extraembryonic tissues to dictate embryonic ectoderm differentiation ► VPS52’s essential function in the embryo involves cell–cell interactions ► VPS52 also has an indispensable function later in development

Description: Publication year: 2012 Source: Cell Reports Myrto Denaxa, Melanie Kalaitzidou, Anna Garefalaki, Angeliki Achimastou, Reena Lasrado, Tamara Maes, Vassilis Pachnis The generation of cortical interneuron subtypes is controlled by genetic programs that are activated in the ventral forebrain and unfold during the prolonged period of inhibitory neuron development. The LIM-homeodomain protein LHX6 is critical for the development of all cortical interneurons originating in the medial ganglionic eminence, but the molecular mechanisms that operate downstream of LHX6 to control the terminal differentiation of somatostatin- and parvalbumin-expressing interneurons within the cortex remain unknown. Here, we provide evidence that the nuclear matrix and genome organizer protein SATB1 is induced by neuronal activity and functions downstream of Lhx6 to control the transition of tangentially migrating immature interneurons into the terminally differentiated Somatostatin (SST)-expressing subtype. Our experiments provide a molecular framework for understanding the genetic and epigenetic mechanisms by which specified but immature cortical interneurons acquire the subtype-defining molecular and morphophysiological characteristics that allow them to integrate and function within cortical circuits. Graphical abstract Graphical Abstract Highlights ► Satb1 is specifically expressed in MGE-derived cortical interneurons ► Satb1 is required for the maturation of MGE-derived cortical interneurons in vivo ► Satb1 promotes the maturation of SST+ cortical interneurons downstream of Lhx6 ► Neuronal activity induces expression of Satb1 in immature cortical interneurons

Description: After publication of this manuscript [Lipids in Health and Disease 2012, 11:95], we noted that one of the monounsaturated fatty acid isomers had been mislabelled in the results, and in figure 2A and table 2.In the Results and discussion, the sentence, "Concerning plasma MUFA levels, long-chain MUFA C20:1 (n-9 and n-7) and C22:1 (n-11 and n-9) peaked at 2 hr post-ingestion (Figure 2a and b)" should read, "Concerning plasma MUFA levels, long-chain MUFA C20:1 (n-11, n-9 and n-7) and C22:1 (n-11 and n-9) peaked at 2 hr post-ingestion (Figure 2a and b)".The figure and table have also been corrected (figure 1, table 1).We apologize for this error, which was due to a misreading of the gas chromatography reading.

Description: Background: The inference of homologies among DNA sequences, that is, positions in multiple genomes that share a common evolutionary origin, is a crucial, yet difficult task facing biologists. Its computational counterpart is known as the multiple sequence alignment problem. There are various criteria and methods available to perform multiple sequence alignments, and among these, the minimization of the overall cost of the alignment on a phylogenetic tree is known in combinatorial optimization as the Tree Alignment Problem. This problem typically occurs as a subproblem of the Generalized Tree Alignment Problem, which looks for the tree with the lowest alignment cost among all possible trees. This is equivalent to the Maximum Parsimony problem when the input sequences are not aligned, that is, when phylogeny and alignments are simultaneously inferred. Results: For large data sets, a popular heuristic is Direct Optimization (DO). DO provides a good tradeoff between speed, scalability, and competitive scores, and is implemented in the computer program POY. All other (competitive) algorithms have greater time complexities compared to DO. Here, weintroduce and present experiments a new algorithm Affine-DO to accommodate the indel (alignment gap) models commonly used in phylogenetic analysis of molecular sequence data. Affine-DO has the same time complexity as DO, but is correctly suited for the affine gap edit distance. We demonstrateits performance with more than 330,000 experimental tests. These experiments show that the solutions of Affine-DO are close to the lower bound inferred from a linear programming solution. Moreover, iterating over a solution produced using Affine-DO shows little improvement. Conclusions: Our results show that Affine-DO is likely producing near-optimal solutions, with approximations within 10% for sequences with small divergence, and within 30% for random sequences, for which Affine-DO produced the worst solutions. The Affine-DO algorithm has the necessary scalability andoptimality to be a significant improvement in the real-world phylogenetic analysis of sequence data.

Description: Background: Previous work has shown that leaf-cutting ants prefer to cut leaf material with relatively low fungal endophyte content. This preference suggests that fungal endophytes exact a cost on the ants or on the development of their colonies. We hypothesized that endophytes may play a role in their host plants' defense against leaf-cutting ants. To measure the long-term cost to the ant colony of fungal endophytes in their forage material, we conducted a 20-week laboratory experiment to measure fungal garden development for colonies that foraged on leaves with low or high endophyte content. Results: Colony mass and the fungal garden dry mass did not differ significantly between the low and high endophyte feeding treatments. There was, however, a marginally significant trend toward greater mass of fungal garden per ant worker in the low relative to the high endophyte treatment. This trend was driven by differences in the fungal garden mass per worker from the earliest samples, when leaf-cutting ants had been foraging on low or high endophyte leaf material for only 2 weeks. At two weeks of foraging, the mean fungal garden mass per worker was 77% greater for colonies foraging on leaves with low relative to high endophyte loads. Conclusions: Our data suggest that the cost of endophyte presence in ant forage material may be greatest to fungal colony development in its earliest stages, when there are few workers available to forage and to clean leaf material. This coincides with a period of high mortality for incipient colonies in the field. We discuss how the endophyte-leaf-cutter ant interaction may parallel constitutive defenses in plants, whereby endophytes reduce the rate of colony development when its risk of mortality is greatest.

Description: Background: Extant sauropsids (reptiles and birds) are divided into two major lineages, the lineage of Testudines (turtles) and Archosauria (crocodilians and birds) and the lineage of Lepidosauria (tuatara, lizards, worm lizards and snakes). Karyotypes of these sauropsidan groups generally consist of macrochromosomes and microchromosomes. In chicken, microchromosomes exhibit a higher GC-content than macrochromosomes. To examine the pattern of intra-genomic GC heterogeneity in lepidosaurian genomes, we constructed a cytogenetic map of the Japanese four-striped rat snake (Elaphe quadrivirgata) with 183 cDNA clones by fluorescence in situ hybridization, and examined the correlation between the GC-content of exonic third codon positions (GC3) of the genes and the size of chromosomes on which the genes were localized. Results: Although GC3 distribution of snake genes was relatively homogeneous compared with those of the other amniotes, microchromosomal genes showed significantly higher GC3 than macrochromosomal genes as in chicken. Our snake cytogenetic map also identified several conserved segments between the snake macrochromosomes and the chicken microchromosomes. Cross-species comparisons revealed that GC3 of most snake orthologs in such macrochromosomal segments were GC-poor (GC3 〈 50%) whereas those of chicken orthologs in microchromosomes were relatively GC-rich (GC3 〉= 50%). Conclusion: Our results suggest that the chromosome size-dependent GC heterogeneity had already occurred before the lepidosaur-archosaur split, 275 million years ago. This character was probably present in the common ancestor of lepidosaurs and but lost in the lineage leading to Anolis during the diversification of lepidosaurs. We also identified several genes whose GC-content might have been influenced by the size of the chromosomes on which they were harbored over the course of sauropsid evolution.

Description: Background: Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on complex traits. We examine the effects of multi-trait selection on the genome of a population of US registered Angus beef cattle born over a 50-year period representing approximately 10 generations of selection. We present results from the application of a quantitative genetic model, called Birth Date Selection Mapping, to identify signatures of recent ongoing selection. Results: We show that US Angus cattle have been systematically selected to alter their mean additive genetic merit for most of the 16 production traits routinely recorded by breeders. Using Birth Date Selection Mapping, we estimate the time-dependency of allele frequency for 44,817 SNP loci using genomic best linear unbiased prediction, generalized least squares, and BayesCpi analyses. Finally, we reconstruct the primary phenotypes that have historically been exposed to selection from a genome-wide analysis of the 16 production traits and gene ontology enrichment analysis. Conclusions: We demonstrate that Birth Date Selection Mapping utilizing mixed models corrects for time-dependent pedigree sampling effects that lead to spurious SNP associations and reveals genomic signatures of ongoing selection on complex traits. Because multiple traits have historically been selected in concert and most quantitative trait loci have small effects, selection has incrementally altered allele frequencies throughout the genome. Two quantitative trait loci of large effect were not the most strongly selected of the loci due to their antagonistic pleiotropic effects on strongly selected phenotypes. Birth Date Selection Mapping may readily be extended to temporally-stratified human or model organism populations.

Description: Background: The rise of high mountain chains is widely seen as one of the factors driving rapid diversification of land plants and the formation of biodiversity hotspots. Supporting evidence was reported for the impact of the rapid rise of the Andean mountains but this hypothesis has so far been less explored for the impact of the "roof of the world". The formation of the Himalaya, and especially the rise of the Qinghai--Tibetan Plateau in the recent 20 million years, altered the monsoon regimes that dominate the current climates of South East Asia. Here, we infer the hypothesis that the rise of Himalaya had a strong impact on the plant diversity in the biodiversity hotspot of the Southwest Chinese Mountains. Results: Our analyses of the diversification pattern of the derived fern genus Lepisorus recovered evidence for changes in plant diversity that correlated with the strengthening of South East Asian monsoon. Southwest China or Southwest China and Japan was recovered as the putative area of origin of Lepisorus and enhancing monsoon regime were found to shape the early diversification of the genus as well as subsequent radiations during the late Miocene and Pliocene. Conclusions: We report new evidence for a coincidence of plant diversification and changes of the climate caused by the uplift of the Himalaya. These results are discussed in the context of the impact of incomplete taxon sampling, uncertainty of divergence time estimates, and limitations of current methods used to assess diversification rates.

Description: Background: Breast cancer is one of the leading causes of cancer morbidity and mortality worldwide. In Cameroon, breast cancer causes as many as 10.7 deaths per 100,000 women making it the second cause of cancer mortality. Better documenting women's knowledge and practices on breast cancer and breast self-exam (BSE) would be useful in the design of interventions aimed at preventing breast cancer. This study sought to 1. describe Cameroonian women's knowledge of breast self-examination (BSE); 2. assess their impression on the practice of BSE and 3. describe their perceptions on the causes, risk factors and prevention of breast cancer. Methods: A cross-sectional survey was conducted in a volunteer sample of 120 consenting women in Buea, Cameroon. Data were collected using a structured questionnaire self-administered by study participants. Results: The sample was fairly educated with close to three quarters (70.83%) having completed high school. Nearly three quarters (74.17%) of participants had previously heard about BSE, however as many as 40% had never done a BSE. Although 95% of participants believed that breast cancer could be prevented, only 36.67% recognized breast examination as a prevention method. A substantial 13.33% thought that breast cancer could be prevented with a vaccine while 45% thought that dieting or exercising would prevent breast cancer. Similarly, 70% of participants thought that breast cancer could be treated, with 35.83% thinking that it could be treated medically while 34.17% thought it could be treated traditionally or spiritually. Conclusions: The practice of BSE while perceived as being important is not frequent in these women in Buea, Cameroon. Health education campaigns are imperative to elucidate the public on the causes, risk factors and prevention of breast cancer. Further studies need to explore what interventions could be best used to improve the uptake and practice of BSE.

Description: Background: Cultivated peanut or groundnut (Arachis hypogaea L.) is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20), which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut. Results: A total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat) markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons) derived from 70,771 long-read (Sanger) and 270,957 short-read (454) sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639) and GKBSPSc 30081 (PI 468327) in the B - genome species A. batizocoi. A high degree of macrosynteny was observed when comparing the homoeologous linkage groups between A (A. duranensis) and B (A. batizocoi) genomes. Comparison of the A - and B - genome genetic linkage maps also showed a total of five inversions and one major reciprocal translocation between two pairs of chromosomes under our current mapping resolution. Conclusions: Our findings will contribute to understanding tetraploid peanut genome origin and evolution and eventually promote its genetic improvement. The newly developed EST-SSR markers will enrich current molecular marker resources in peanut.

Description: Background: Hypertrophic Cardiomyopathy (HCM) is a genetically heterogeneous disease. One specific mutation in the MYBPC3 gene is highly prevalent in center east of France giving an opportunity to define the clinical profile of this specific mutation. Methods: HCM probands were screened for mutation in the MYH7, MYBPC3, TNNT2 and TNNI3 genes. Carriers of the MYBPC3 IVS20-2A〉G mutation were genotyped with 8 microsatellites flanking this gene. The age of this MYBPC3 mutation was inferred with the software ESTIAGE. The age at first symptom, diagnosis, first complication, first severe complication and the rate of sudden death were compared between carriers of the IVS20-2 mutation (group A) and carriers of all other mutations (group B) using time to event curves and log rank test. Results: Out of 107 HCM probands, 45 had a single heterozygous mutation in one of the 4 tested sarcomeric genes including 9 patients with the MYBPC3 IVS20-2A〉G mutation. The IVS20-2 mutation in these 9 patients and their 25 mutation carrier relatives was embedded in a common haplotype defined after genotyping 4 polymorphic markers on each side of the MYBPC3 gene. This result supports the hypothesis of a common ancestor. Furthermore, we evaluated that the mutation occurred about 47 generations ago, approximately at the 10th century.We then compared the clinical profile of the IVS20-2 mutation carriers (group A) and the carriers of all other mutations (group B). Age at onset of symptoms was similar in the 34 group A cases and the 73 group B cases but group A cases were diagnosed on average 15 years later (log rank test p = 0.022). Age of first complication and first severe complication was delayed in group A vs group B cases but the prevalence of sudden death and age at death was similar in both groups. Conclusion: A founder mutation arising at about the 10th century in the MYBPC3 gene accounts for 8.4% of all HCM in center east France and results in a cardiomyopathy starting late and evolving slowly but with an apparent risk of sudden death similar to other sarcomeric mutations.

Description: Background: Extensive studies have demonstrated that the COBRA gene is critical for biosynthesis of cell wall constituents comprising structural tissues of roots, stalks, leaves and other vegetative organs, however, its role in fruit development and ripening remains largely unknown. Results: We identified a tomato gene (SlCOBRA-like) homologous to Arabidopsis COBRA, and determined its role in fleshy fruit biology. The SlCOBRA-like gene is highly expressed in vegetative organs and in early fruit development, but its expression in fruit declines dramatically during ripening stages, implying a primary role in early fruit development. Fruit-specific suppression of SlCOBRA-like resulted in impaired cell wall integrity and up-regulation of genes encoding proteins involved in cell wall degradation during early fruit development. In contrast, fruit-specific overexpression of SlCOBRA-like resulted in increased wall thickness of fruit epidermal cells, more collenchymatous cells beneath the epidermis, elevated levels of cellulose and reduced pectin solubilization in the pericarp cells of red ripe fruits. Moreover, transgenic tomato fruits overexpressing SlCOBRA-like exhibited desirable early development phenotypes including enhanced firmness and a prolonged shelf life. Conclusions: Our results suggest that SlCOBRA-like plays an important role in fruit cell wall architecture and provides a potential genetic tool for extending the shelf life of tomato and potentially additional fruits.

Description: Background: Experimental datasets are becoming larger and increasingly complex, spanning different data domains, thereby expanding the requirements for respective tool support for their analysis. Networks provide a basis for the integration, analysis and visualization of multi-omics experimental datasets. Results: Here we present VANTED (version 2), a framework for systems biology applications, which comprises a comprehensive set of seven main tasks. These range from network reconstruction, data visualization, integration of various data types, network simulation to data exploration combined with a manifold support of systems biology standards for visualization and data exchange. The offered set of functionalities is instantiated by combining several tasks in order to enable users to view and explore a comprehensive dataset from different perspectives. We describe the system as well as an exemplary workflow. Conclusions: VANTED is a stand-alone framework which supports scientists during the data analysis and interpretation phase. It is available as a Java open source tool from http://www.vanted.org.

Description: Background: Empirical evaluations of sexually dimorphic expression of genes on the mammalian X-chromosome are needed to understand the evolutionary forces and the gene-regulatory mechanisms controlling this chromosome. We performed a large-scale sex-bias expression analysis of genes on the X-chromosome in six different somatic tissues from mouse. Results: Our results show that the mouse X-chromosome is enriched with female-biased genes and depleted of male-biased genes. This suggests that feminisation as well as de-masculinisation of the X-chromosome has occurred in terms of gene expression in non-reproductive tissues. Several mechanisms may be responsible for the control of female-biased expression on chromosome X, and escape from X-inactivation is a main candidate. We confirmed escape in case of Tmem29 using RNA-FISH analysis. In addition, we identified novel female-biased non-coding transcripts located in the same female-biased cluster as the well-known coding X-inactivation escapee Kdm5c, likely transcribed from the transition-region between active and silenced domains. We also found that previously known escapees only partially explained the overrepresentation of female-biased X-genes, particularly for tissue-specific female-biased genes. Therefore, the gene set we have identified contains tissue-specific escapees and/or genes controlled by other sexually skewed regulatory mechanisms. Analysis of gene age showed that evolutionarily old X-genes (〉0100 myr, preceding the radiation of placental mammals) are more frequently female-biased than younger genes. Conclusion: Altogether, our results have implications for understanding both gene regulation and gene evolution of mammalian X-chromosomes, and suggests that the final result in terms of the X-gene composition (masculinisation versus feminisation) is a compromise between different evolutionary forces acting on reproductive and somatic tissues.

Description: Background: The genomes of three major mosquito vectors of human diseases, Anopheles gambiae, Aedes aegypti, and Culex pipiens quinquefasciatus, have been previously sequenced. C. p. quinquefasciatus has the largest number of predicted protein-coding genes, which partially results from the expansion of three detoxification gene families: cytochrome P450 monooxygenases (P450), glutathione S-transferases (GST), and carboxyl/cholinesterases (CCE). However, unlike An. gambiae and Ae. aegypti, which have large amounts of gene expression data, C. p. quinquefasciatus has limited transcriptomic resources. Knowledge of complete gene expression information is very important for the exploration of the functions of genes involved in specific biological processes. In the present study, the three detoxification gene families of C. p. quinquefasciatus were analyzed for phylogenetic classification and compared with those of three other dipteran insects. Gene expression during various developmental stages and the differential expression responsible for parathion resistance were profiled using the digital gene expression (DGE) technique. Results: A total of 302 detoxification genes were found in C. p. quinquefasciatus, including 71 CCE, 196 P450, and 35 cytosolic GST genes. Compared with three other dipteran species, gene expansion in Culex mainly occurred in the CCE and P450 families, where the genes of alpha-esterases, juvenile hormone esterases, and CYP325 of the CYP4 subfamily showed the most pronounced expansion on the genome. For the five DGE libraries, 3.5-3.8 million raw tags were generated and mapped to 13314 reference genes. Among 302 detoxification genes, 225 (75%) were detected for expression in at least one DGE library. One fourth of the CCE and P450 genes were detected uniquely in one stage, indicating potential developmentally regulated expression. A total of 1511 genes showed different expression levels between a parathion-resistant and a susceptible strain. Fifteen detoxification genes, including 2 CCEs, 6 GSTs, and 7 P450s, were expressed at higher levels in the resistant strain. Conclusions: The results of the present study provide new insights into the functions and evolution of three detoxification gene families in mosquitoes and comprehensive transcriptomic resources for C. p. quinquefasciatus, which will facilitate the elucidation of molecular mechanisms underlying the different biological characteristics of the three major mosquito vectors.

Description: Background: There are several methods for quantitating bacterial cells, each with advantages and disadvantages. The most common method is bacterial plating, which has the advantage of allowing live cell assessment through colony forming unit (CFU) counts but is not well suited for high throughput screening (HTS). On the other hand, spectrophotometry is adaptable to HTS applications but does not differentiate between dead and living bacteria and has low sensitivity. Results: Here, we report a bacterial cell counting method termed Start Growth Time (SGT) that allows rapid and serial quantification of the absolute or relative number of live cells in a bacterial culture in a high throughput manner. We combined the methodology of quantitative polymerase chain reaction (qPCR) calculations with a previously described qualitative method of bacterial growth determination to develop an improved quantitative method. We show that SGT detects only live bacteria and is sensitive enough to differentiate between 40 and 400 cells/mL. SGT is based on the re-growth time required by a growing cell culture to reach a threshold, and the notion that this time is proportional to the number of cells in the initial inoculum. We show several applications of SGT, including assessment of antibiotic effects on cell viability and determination of an antibiotic tolerant subpopulation fraction within a cell population. SGT results do not differ significantly from results obtained by CFU counts. Conclusion: SGT is a relatively quick, highly sensitive, reproducible and non-laborious method that can be used in HTS settings to longitudinally assess live cells in bacterial cell cultures.

Description: Background: The INNER NO OUTER (INO) gene, which encodes a YABBY-type transcription factor, specifies and promotes the growth of the outer integument of the ovule in Arabidopsis. INO expression is limited to the abaxial cell layer of the developing outer integument of the ovule and is regulated by multiple regions of the INO promoter, including POS9, a positive element that when present in quadruplicate can produce low-level expression in the normal INO pattern. Results: Significant redundancy in activity between different regions of the INO promoter is demonstrated. For specific regulatory elements, multimerization or the addition of the cauliflower mosaic virus 35S general enhancer was able to activate expression of reporter gene constructs that were otherwise incapable of expression on their own. A new promoter element, POS6, is defined and is shown to include sufficient positive regulatory information to reproduce the endogenous pattern of expression in ovules, but other promoter regions are necessary to fully suppress expression outside of ovules. The full-length INO promoter, but not any of the INO promoter deletions tested, is able to act as an enhancer-blocking insulator to prevent the ectopic activation of expression by the 35S enhancer. Sequence conservation between the promoter regions of Arabidopsis thaliana, Brassica oleracea and Brassica rapa aligns closely with the functional definition of the POS6 and POS9 regions, and with a defined INO minimal promoter. The B. oleracea INO promoter is sufficient to promote a similar pattern and level of reporter gene expression in Arabidopsis to that observed for the Arabidopsis promoter. Conclusions: At least two independent regions of the INO promoter contain sufficient regulatory information to direct the specific pattern but not the level of INO gene expression. These regulatory regions act in a partially redundant manner to promote the expression in a specific pattern in the ovule and suppress expression outside of ovules. Establishment of this pattern requires cooperation and competition between multiple positive and negative regulatory elements.

Description: Background: Induced defense responses to herbivores are generally believed to have evolved as cost-saving strategies that defer the fitness costs of defense metabolism until these defenses are needed. The fitness costs of jasmonate (JA)-mediated defenses have been well documented. Those of the early signaling units mediating induced resistance to herbivores have yet to be examined. Early signaling components that mediate herbivore-induced defense responses in Nicotiana attenuata, have been well characterized and here we examine their growth and fitness costs. Two mitogen-activated protein kinases (MAPKs), salicylic acid (SA)-induced protein kinase (SIPK) and wound-induced protein kinase (WIPK) are rapidly activated after perception of herbivory and both kinases regulate herbivory-induced JA levels and JA-mediated defense metabolite accumulations. Since JA-induced defenses result in resource-based trade-offs that compromise plant productivity, we evaluated if silencing SIPK (irSIPK) and WIPK (irWIPK) benefits the growth and fitness of plants competiting with wild type (WT) plants, as has been shown for plants silenced in JA-signaling by the reduction of Lipoxygenase 3 (LOX3) levels. Results: As expected, irWIPK and irLOX3 out-performed their competing WT plants. Surprisingly, irSIPK plants, which have the largest reductions in JA signaling, did not out-perform their competing WT plants. Phytohormone profiling of leaves revealed that irSIPK plants accumulated higher levels of SA compared to WT. To test the hypothesis that these higher levels of SA, and their presumed associated fitness costs of pathogen associated defenses in irSIPK plants had nullified the JA-deficiency-mediated growth benefits in these plants, we genetically reduced SA levels in irSIPK plants. Reducing SA levels partially recovered the biomass and fitness deficits of irSIPK plants. We also evaluated whether the increased fitness of plants with reduced SA or JA levels resulted from increased nitrogen or CO2 aquisition rates, and found no evidence that greater intake of these fitness-limiting resources were responsible. Conclusions: Defense signaling mediated by herbivory-induced WIPK, but not SIPK, is associated with large fitness costs in N. attenuata, demonstrating the contrasting roles the two MAPKs play in regulating the plants' growth-defense balance. We discuss the role of SIPK as an important regulator of plant fitness, possibly by modulating SA-JA crosstalk through ethylene signaling.

Description: Background: Homeodomain transcription factors play critical roles in metazoan development. BELLRINGER (BLR), one such transcription factor, is involved in diverse developmental processes in Arabidopsis, acting in vascular differentiation, phyllotaxy, flower and fruit development. BLR also has a redundant role in meristem maintenance. Cell wall remodelling underpins many of these processes, and BLR has recently been shown to regulate expression of PECTIN METHYL-ESTERASE 5 (PME5), a cell wall modifying enzyme in control of phyllotaxy.We have further explored the role of BLR in plant development by analysing phenotypes and gene expression in a series of plants over-expressing BLR, and generating combinatorial mutants with blr, brevipedicellus (bp), a member of the KNOX1 family of transcription factors that has previously been shown to interact with blr), and the homeodomain transcription factor revoluta (rev), required for radial patterning of the stem. Results: Plants over-expressing BLR exhibited a wide range of phenotypes. Some were defective in cell size and showed misregulation of genes predominantly affecting cell wall development. Other lines with more extreme phenotypes failed to generate lateral organs, consistent with BLR repressing transcription in the shoot apex.Cell wall dynamics are also affected in blr mutant plants, and BLR has previously been shown to regulate vascular development in conjunction with BP. We found that when bp and blr were combined with rev, a set of defects were observed that were distinct from those of bp blr lines. In these triple mutants xylem development was most strikingly affected, resulting in an almost complete lack of vessels and xylem parenchyma with secondary thickening. Conclusions: Our data support a role for BLR in ordering the shoot apex and, in conjunction with BP and REV, playing a part in determining the composition and organisation of the vascular system. Microarray analysis strongly indicates that the striking vascular phenotypes of blr bp rev triple mutants and plants over-expressing BLR result from the misregulation of a suite of genes, targets of BLR in wild type plants, that determine cell size and structure in the developing vasculature.

Description: Background: Interaction of non-structural protein 5A (NS5A) of Hepatitis C virus (HCV) with human kinases namely, casein kinase 1alpha (ck1alpha) and protein kinase R (PKR) have different functional implications such as regulation of viral replication and evasion of interferon induced immune response respectively. Understanding the structural and molecular basis of interactions of the viral protein with two different human kinases can be useful in developing strategies for treatment against HCV. Results: Serine 232 of NS5A is known to be phosphorylated by human ck1alpha. A structural model of NS5A peptide containing phosphoacceptor residue Serine 232 bound to ck1alpha has been generated using the known 3-D structures of kinase-peptide complexes. The substrate interacting residues in ck1alpha has been identified from the model and these are found to be conserved well in the ck1 family. ck1alpha -- substrate peptide complex has also been used to understand the structural basis of association between ck1alpha and its other viral stress induced substrate, tumour suppressor p53 transactivation domain which has a crystal structure available.Interaction of NS5A with another human kinase PKR is primarily genotype specific. NS5A from genotype 1b has been shown to interact and inhibit PKR whereas NS5A from genotype 2a/3a are unable to bind and inhibit PKR efficiently. This is one of the main reasons for the varied response to interferon therapy in HCV patients across different genotypes. Using PKR crystal structure, sequence alignment and evolutionary trace analysis some of the critical residues responsible for the interaction of NS5A 1b with PKR have been identified. Conclusions: The substrate interacting residues in ck1alpha have been identified using the structural model of kinase - substrate peptide. The PKR interacting NS5A 1b residues have also been predicted using PKR crystal structure, NS5A sequence analysis along with known experimental results. Functional significance and nature of interaction of interferon sensitivity determining region and variable region 3 of NS5A in different genotypes with PKR which was experimentally shown are also supported by the findings of evolutionary trace analysis. Designing inhibitors to prevent this interaction could enable the HCV genotype 1 infected patients respond well to interferon therapy.

Description: BMC Research Notes recently published a research article regarding the use of ligated DNA extracted from formalin-fixed paraffin embedded (FFPE) tissue on the Illumina Infinium methylation platform - "Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed, paraffin-embedded paired tumor and normal tissue" Jasmine et al. BMC Research Notes 2012, 5:117. This article repeatedly refers to our previous work and concludes that methylation data obtained from ligated FFPE extracted DNA should be used with great caution. In this Discussion we review the data analysis performed in Jasmine et al's paper and suggest limitations which subsequently lead the authors to draw what we believe are incorrect conclusions. Moreover, we continue to analyse genome-wide methylation data from DNA extracted from FFPE tissue successfully on both the HumMeth27 and 450K arrays.

Description: Background: The sequencing of the genome of the pea aphid Acyrthosiphon pisum revealed an unusual expansion of the miRNA machinery, with two argonaute-1, two dicer-1 and four pasha gene copies. In this report, we have undertaken a deeper evolutionary analysis of the phylogenetic timing of these gene duplications and of the associated selective pressures by sequencing the two copies of ago-1 and dcr-1 in different aphid species of the subfamily Aphidinae. We have also carried out an analysis of the expression of both copies of ago-1 and dcr-1 by semi-quantitative PCR in different morphs of the pea aphid life cycle. Results: The analysis has shown that the duplication of ago-1 occurred in an ancestor of the subfamily Aphidinae while the duplication of dcr-1 appears to be more recent. Besides, it has confirmed a pattern of one conserved copy and one accelerated copy for both genes, and has revealed the action of positive selection on several regions of the fast-evolving ago-1b. On the other hand, the semi-quantitative PCR experiments have revealed a differential expression of these genes between the morphs of the parthenogenetic and the sexual phases of Acyrthosiphon pisum. Conclusions: The discovery of these gene duplications in the miRNA machinery of aphids opens new perspectives of research about the regulation of gene expression in these insects. Accelerated evolution, positive selection and differential expression affecting some of the copies of these genes suggests the possibility of a neofunctionalization of these duplicates, which might play a role in the display of the striking phenotypic plasticity of aphids.

Description: Background: The evolution of mycoplasmas from a common ancestor with Firmicutes has been characterized not only by genome down-sizing but also by horizontal gene transfer between mycoplasma species sharing a common host. The mechanisms of these gene transfers remain unclear because our knowledge of the mycoplasma mobile genetic elements is limited. In particular, only a few plasmids have been described within the Mycoplasma genus. Results: We have shown that several species of ruminant mycoplasmas carry plasmids that are members of a large family of elements and replicate via a rolling-circle mechanism. All plasmids were isolated from species that either belonged or were closely related to the Mycoplasma mycoides cluster; none was from the Mycoplasma bovis-Mycoplasma agalactiae group. Twenty one plasmids were completely sequenced, named and compared with each other and with the five mycoplasma plasmids previously reported. All plasmids share similar size and genetic organization, and present a mosaic structure. A peculiar case is that of the plasmid pMyBK1 from M. yeatsii; it is larger in size and is predicted to be mobilizable. Its origin of replication and replication protein were identified. In addition, pMyBK1 derivatives were shown to replicate in various species of the M. mycoides cluster, and therefore hold considerable promise for developing gene vectors. The phylogenetic analysis of these plasmids confirms the uniqueness of pMyBK1 and indicates that the other mycoplasma plasmids cluster together, apart from the related replicons found in phytoplasmas and in species of the clade Firmicutes. Conclusions: Our results unraveled a totally new picture of mycoplasma plasmids. Although they probably play a limited role in the gene exchanges that participate in mycoplasma evolution, they are abundant in some species. Evidence for the occurrence of frequent genetic recombination strongly suggests they are transmitted between species sharing a common host or niche.

Description: Publication year: 2012 Source: FEBS Open Bio Yusuke Ito, Suguru Shigemori, Takashi Sato, Tomoyuki Shimazu, Konomi Hatano, Hajime Otani, Haruki Kitazawa, Takeshi Shimosato We designed class I/II hybrid inhibitory oligodeoxynucleotides (iODNs), called iSG, and found that the sequence 5′-TTAGGG-3′, which has a six-base loop head structure, and a 3′-oligo (dG) 3–5 tail sequence are important for potent immunosuppressive activity. Interestingly, splenocytes isolated from ovalbumin (OVA)-immunized mice and treated with iSG3 showed suppression of not only interleukin (IL)-6, IL-12p35, IL-12p40, and interferon (IFN) γ mRNA expression, but also IL-4 and IL-13 mRNA expression. Thus, both Th2 and Th1 immune responses can be strongly suppressed by iODNs in splenocytes from allergen-immunized mice, suggesting usefulness in the treatment of diseases induced by over-active immune activation.

Description: Publication year: 2012 Source: FEBS Open Bio Katsuhiro Tanaka, Maiko Soeda, Yoichiro Hashimoto, Shigeo Takenaka, Masayuki Komori Pex14p is a peroxisomal membrane protein that is involved in both peroxisome biogenesis and selective peroxisome degradation. Previously, we showed that Hansenula polymorpha Pex14p was phosphorylated in vivo . In this study, we identified its phosphorylation site by mass spectrometry. Recombinant His-tagged Pex14p (H6-Pex14p) was overexpressed and purified from the yeast. The protein band corresponding to H6-Pex14p was in-gel digested with trypsin and subjected to LC/MS. As a result of LC/MS, Thr 248 and Ser 258 were identified as the phosphorylated sites. To confirm the phosphorylation sites and explore its functions, we made Ala mutants of the candidate amino acids. In the western blot analysis with anti-Pex14p, S258A mutant gave doublet bands while wild type (WT) and T248A mutants gave triplet bands. Moreover, the double mutant (T248A/S258A) gave a single band. WT and all mutant Pex14p labeled with [ 32 P] orthophosphate were immunoprecipitated and analyzed by autoradiography. The phosphorylation of Pex14p was suppressed in S258A mutant, but enhanced in T248A mutant compared to WT. Moreover, the phosphorylated Pex14p was not detected in the T248A/S258A double mutant. All mutants were able to grow on methanol and their matrix proteins (alcohol oxidase and amine oxidase) were mostly localized in peroxisomes. Furthermore all mutants showed selective degradation of peroxisome like WT during the glucose-induced macropexophagy.