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: Publication year: 2012 Source: Dendrochronologia Kathryn Allen, David M. Drew, Geoffrey M. Downes, Robert Evans, Patrick Baker, Michael Grose The great majority of dendroclimatological work in Australia has thus far relied on ring-width chronologies only. We report novel results from a pilot study that show the potential to develop density-based climatically sensitive chronologies from two long-lived conifers endemic to Tasmania: Pencil Pine and Celery Top Pine. Cross-dating of average ring density profiles within each of the two sites examined was comparable with the better replicated ring-width chronologies from the sites. Cross-dating potential for maximum density was also indicated. Correlations between density and climate for both species were stronger and more persistent across a window of several months than correlations between ring width and climate. These stronger correlations suggest that temperature reconstructions based on average density may be possible. The ability to develop high resolution temperature-sensitive chronologies would allow for spatial comparisons across regions such as Tasmania that are affected by multiple broad-scale climate systems. A particularly novel result was the finding that maximum density was significantly related to stream-flow at the end of the growing season. Further work is required to assess the potential to reconstruct temperature, and to reconstruct stream-flow for important Tasmanian catchments over the past 500–800 years.

Description: Publication year: 2012 Source: Dendrochronologia Hannu Hökkä, Hannu Salminen, Erkki Ahti The climate conditions of the current and previous growing seasons have been shown to influence growth of coniferous trees in mineral soils sites. These dependencies may be different in peatlands where growth is generally more dependent on variations in soil water conditions. In the Nordic and Baltic countries, millions of hectares of peatlands and wetlands have been drained in order to enhance forest production. These drainage networks do not guarantee stable soil water conditions for the whole stand rotation. It is thus likely that precipitation in particular may have a different influence on annual growth in peatland to that in mineral soil sites. We studied the effect of precipitation and temperature on the inter-annual diameter growth of Scots pine ( Pinus sylvestris L.) in Finland in drained peatland forests. The diameter growth data were limited to periods when growth response to drainage had levelled out. For comparison, growth data were also collected from adjacent mineral soil trees. The climate variables were monthly mean temperature and precipitation in a given location estimated from observations at the nearest weather stations by means of spatial smoothing. We used mixed linear models in describing the annual diameter growth of individual trees as a function of tree size and stand properties and expressed the residual variation as a function of climate parameters. The peatland and mineral soil growth variations showed different dependence on climate parameters. Peatland trees within 5 m of a ditch showed different climate responses compared to those located further away. Precipitation in July was negatively correlated with the diameter growth of peatland trees but there was no correlation with temperature. Growth of trees in mineral soils was positively correlated with March and April mean temperatures and May and June mean precipitation. The residual growth indices showed largely similar patterns in peatlands and mineral soil sites.

Description: Publication year: 2012 Source: Dendrochronologia Keyan Fang, Xiaohua Gou, Fahu Chen, Yingjun Li, Fen Zhang, Miklos Kazmer Individual tree-ring series may show changed growth trends and divergent climate–growth associations even within a site, highlighting the need to examine tree growth and its climate association before building a chronology. We provided a case study for the stratification and temporal variability of tree growth and its climate associations of individual cores for three mountain ranges in north central China. Tree growth is mainly limited by moisture conditions in previous July–September and current June–August. Repeated sampling and field investigations of Picea wilsonii at Xinglong Mountain over a growth year of 2004 suggested that the growing season is from about the end of April to the end of September. It appears that the moisture conditions in previous and current growing seasons are crucial for tree growth in this region. However, a decrease in drought limitation was observed for a few tree-ring series. We thereby built the pooled chronology and sub-site chronologies with only drought-sensitive tree rings similar climate–growth relationships from the three mountain slopes. Growth disturbances of tree-ring series are detected by checking the occurrence of successively low values of the biweight series, which are treated by fitting a flexible curve.

Description: Publication year: 2012 Source: Dendrochronologia Esther Jansma, Rowin J. van Lanen, Kit Sturgeon, Steve Mohlke, Peter W. Brewer Dendrochronological data formats in general offer limited space for recording associated metadata. Such information is often recorded separately from the actual time series, and often only on paper. TRiDaBASE has been developed to improve metadata administration. It is a relational Microsoft Access database that allows users to register digital metadata according to TRiDaS, to generate TRiDaS XML for uploading to TRiDaS-based analytical systems and repositories, and to ingest TRiDaS XML created elsewhere for local querying and analyses.

Description: Publication year: 2012 Source: Dendrochronologia Igor Drobyshev, P. Charles Goebel, Yves Bergeron, R. Gregory Corace The study of forests dominated by red pine ( Pinus resinosa Ait.), one of the few fire-resistant tree species of eastern North America, provides an opportunity to reconstruct long-term fire histories and examine the temporal dynamics of climate forcing upon forest fire regimes. We used a 300-year long spatially explicit dendrochronological reconstruction of the fire regime for Seney National Wildlife Refuge (SNWR, 38,531 ha), eastern Upper Michigan to: (1) identify fire size thresholds with strong vs. weak climate controls, (2) evaluate effect of landform type (outwash channel vs. sand ridges) in modifying climate–fire associations, and (3) check for the presence of temporal changes in the climate control of large fire events over the time period 1700–1983. We used a summer drought sensitive red pine chronology (ITRDB code can037 ) as a proxy of past fire-related climate variability. Results indicated that fires 〉60 ha in sand-ridge-dominated portions of SNWR and 〉100 ha in outwash channels were likely climatically driven events. Climate–fire associations varied over time with significant climate–fire linkages observed for the periods 1700–1800 (pre-EuroAmerican), 1800–1900 (EuroAmerican settlement) and 1900–1983 (modern era). Although an increase in fire activity at the turn of 20th century is commonly associated with human sources of ignitions, our results suggest that such an increase was also likely a climatically driven episode.

Description: Publication year: 2012 Source: Dendrochronologia Maxim Yermokhin This article presents for the first time Scots pine tree-ring chronology created from historical timber (XVII–XIX cc.) from central Belarus. The chronology includes 59 tree-ring series which were collected from the different wood structures in the Nesvizh castle. This samples show different stages of the castle renovations. The chronology presented in this paper embraces 222 years covering the period between 1608 and 1829.

Description: Publication year: 2012 Source: Dendrochronologia Pavel Pavlovich Silkin, Natalia Victorovna Ekimova This study addressed distribution of calcium and strontium in Siberian spruce ( Picea obovata Ledeb.) and Siberian fir ( Abies sibirica Ledeb.) tree-rings and its dependence on these woody species cell structure. Calcium concentration was found to decrease gradually from earlywood to latewood, whereas strontium showed an opposite trend. However, their trends at the scale of several rings are co-directed in the samples analyzed. A strong linear relationship was identified between the distribution of Sr/Ca concentration ratio and tree-ring density profile for both woody species. Radiographic density of Siberian spruce tree-ring cell walls and Ca and Sr concentrations in them were determined to have negative correlation with cell wall thickness. In earlywood of annual rings of a spruce the radiographic density of cell wall reaches 2.0 g/cm 3 and decreases to 1.2 g/cm 3 in latewood. The hypothesis put forward in this study to explain these strontium and calcium distributions in the tree-rings is that the concentrations of the element ions change with development of different cell wall layers. The high value of radiographic density of a cellular wall in earlywood and its relationship with cell wall thickness can be explained by the presence of ions of calcium in a cellular wall. Ions of calcium absorb X-ray radiation more strongly in comparison with light chemical elements. It can become the reason of observable relationship between radiographic density of cell wall and cell wall thickness.

Description: Publication year: 2012 Source: Dendrochronologia Xiaohua Gou, Fen Zhang, Yang Deng, Gregory J. Ettl, Meixue Yang, Linlin Gao, Keyan Fang Tree-line ecotones are strongly climatically limited and serve as potential monitors of climate change. We employed annual growth increment from tree-rings, and tree density and age structure data derived from two Juniperus przewalskii tree-line sites in the eastern part of the Qilian Mountains, northeastern Tibetan Plateau, to detect the responses of tree growth and population dynamics to climate change. High temperature favors tree growth and is associated with increased tree density at tree-line, and an advance in tree-line position. Significantly positive correlations were found between ring-width and mean monthly air temperatures in current and previous June, July and August. Tree recruitment began to increase rapidly at the two sites after the Little Ice Age, but then decreased starting in the 1970s. The number of trees established coincides with temperature changes. The warming trend after the Little Ice Age favors increases of tree density and an advance of tree-line. The majority of trees established during the period of 1931–1970, which coincides well with the rapid radial growth of the trees.

Description: Publication year: 2012 Source: Dendrochronologia, Volume 30, Issue 1 X. Arnan, B.C. López, J. Martínez-Vilalta, M. Estorach, R. Poyatos Trees can reach ages that in some cases amount to thousands of years. In the Mediterranean region, olive trees ( Olea europaea ) have traditionally been considered a particularly long-lived species. The main objective of this study was to assess the age of large olive trees considered to be millenarian and classified as monumental trees in northeastern Spain. We extracted cores of 14 individuals and obtained 8 sections of trees which had already been cut in the area where the largest olive trees in the northeastern Iberian Peninsula are found. The age of the sampled olive trees was assessed by counting the number of annual growth rings. Tree rings did not cross-date well, neither within nor between individuals, but boundaries between likely annual rings were clearly distinct. We found a linear relationship between DBH and tree age (in years) (Age = 2.11 × diameter(cm) + 88.93, R 2 = 0.80), which was used to estimate the age of unsampled olive trees. The maximum estimated age (627 ± 110 years) is among the greatest ages reported for olive trees around the world (700 years) and among the oldest trees in Mediterranean ecosystems.

Description: Publication year: 2012 Source: Dendrochronologia Marc Macias-Fauria, Aslak Grinsted, Samuli Helama, Jari Holopainen Proxy data forms natural time series used to lengthen instrumental climatic records, and may contain a significant portion of autocorrelation. Increased serial correlation limits the number of independent observations, not satisfying the assumptions of conventional statistical methods. We estimate the significance of calibration and verification statistics used in dendroclimatic reconstructions by combining Monte-Carlo iterations with frequency (Ebisuzaki) or time (Burg) domain time series modelling. Significance tests are presented for Coefficient of Determination ( R 2 ), Coefficient of Correlation ( r 2 ), Reduction of Error (RE) and Coefficient of Error (CE) for time series ranging from very low to very high autocorrelation. Increased autocorrelation implies higher occurrences of relatively high but spurious reconstruction statistics. Ebisuzaki time series modelling shows greater robustness and its use is recommended over Burg's method, which penalizes the restriction in the number of autocorrelation coefficients imposed by the Akaike Information Criterion. Positive RE and CE values, traditionally viewed as successful reconstruction statistics, are not necessarily significant and depend on the temporal structure of the time series used. This approach is further implemented successfully to compute confidence intervals based on the temporal structure of the residuals of the transfer function. A Matlab ® package and a Windows executable file for non-Matlab ® users are provided to perform the described analyses.

Description: Publication year: 2012 Source: Dendrochronologia, Volume 30, Issue 1 Kristof Haneca, Vincent Debonne A detailed dendrochronological survey was performed on the medieval roofs of the Church of Our Lady (CoOL) in Damme, Belgium. Seen its complex architectural history, special attention was paid to the identification of consecutive building phases, based on combined architectural historical research and tree-ring dating. In total 64 increment cores were taken throughout the roof structures of the CoOL. All roof timbers are made of European oak ( Quercus robur / petraea ), of which only few have surviving sapwood or bark. Tree-ring dating confirms the late 13th/early 14th century construction date of the roofs. For all chronologies that were composed, the highest correlation values are found with reference chronologies covering the catchment area of the river Meuse. From the dating results of the timbers of the CoOL it becomes clear that the same timber source was used for nearly a century. On several of the examined roof timbers, rafting joints were observed, demonstrating that the timbers were indeed tied together as a raft and floated down the river. By implementing sapwood estimates in a Bayesian chronological model (OxCal), tree-ring series with surviving sapwood from coeval roof structures were combined in order to narrow down the time range for the felling date. Based on the refined interpretation of the felling dates, several consecutive building phases can now be identified and dated, leading to a new interpretation of the architectural history of the CoOL. Intriguingly, a marked interruption in building activities is observed around 1300. Probably this is related to the instable political situation at that time, caused by the armed conflict that emerged between the Count of Flanders and the king of France. Since Damme served as the outport of the riotous city of Bruges, it was alternately seized by the French and Flemish, both consuming considerable amounts of timber and other building materials for military fortifications. Potentially this led to a shortage in building materials and provoked a stop in building activities. This paper demonstrates the power of Bayesian models to refine the interpretation of dendrochronological dates in architectural analyses of medieval historical buildings.

Description: Publication year: 2012 Source: Dendrochronologia, Volume 30, Issue 1 Kristina Sohar, Adomas Vitas, Alar Läänelaid Pedunculate oak ( Quercus robur L.) is one of the widely used and dendrochronologically investigated species in Europe. Still, it is a problematical dating object if its outermost section is missing partly or totally. Thus, we need sapwood estimation of living trees. As sapwood amount varies geographically, numbers of sapwood rings have been published for different regions in Europe but no such estimation has been done for the Baltic States yet. Therefore, this paper deals with the estimation of pedunculate oak sapwood growing in the eastern Baltic region, i.e. in Finland, Estonia, Latvia, and Lithuania. In total, 668 oak core samples of living trees from 43 stands were investigated. Ring widths were measured and the number of sapwood rings was determined according to two criteria: difference of colour and absence of tyloses in earlywood vessels. The samples were divided into two sets, according to the t H -values between site chronologies and the major geobotanical sub-provinces. Thus, the nine Finnish and western Estonian sites were attributed to the western region and the 34 eastern Estonian, Latvian and Lithuanian sites to the eastern region. As the result of a statistical analysis, we explain that the number of oak sapwood rings ranges from 4.09 to 20.85 and 6.45 to 18.02 within 95% confidence limits in the western and eastern regions, respectively. For the three Baltic countries and southern Finland in general, we recommend to consider a sapwood estimate of 6.18–18.71 rings. Regarding earlier studies, the general European trend of decreasing sapwood ring number towards the east was confirmed. A geographical pattern of eastward decrease of the median sapwood ring number was noticed in the Baltics as well. The chronology based upon 668 samples of living oak trees from all sites covered the period of 1631–2008.

Description: Publication year: 2012 Source: Dendrochronologia, Volume 30, Issue 1 Julia Bartens, Henri D. Grissino-Mayer, Susan D. Day, P. Eric Wiseman Live oak ( Quercus virginiana Mill.) is a long lived, broadleaf, evergreen species native to the lower Coastal Plain of the southern and southeastern United States and is frequently planted in the urban environment. However, live oak has received limited attention for its potential for dendrochronological analyses possibly because its growth-ring boundaries may be less defined due to the absence of a distinct dormancy period. The objective of this explorative study was to determine whether live oak rings in both urban and historic trees could be accurately identified and measured for dendrochronological applications. One hundred urban live oaks were assessed as well as four cross-sectional specimens from historic sites in the southeastern United States. Age of all cored live oak ranged from 7 to 29 (average = 16.8 rings), while cross-sections were taken from trees with an average age of 175 years. A chronology was created from cores that had the highest interseries correlations ( n = 27), resulting in an average interseries correlation of 0.654. The analysis of live oak cross sections revealed that the rings on live oak are very faint and barely discernible, delimited mainly by a faint row of earlywood vessels with no or barely visible terminal parenchyma. Rings on these sections were erratic (i.e., fading out along the circumference) and non-concentric (i.e., a particular ring could be both wide and narrow at certain points along the circumference) so that any attempt to measure the rings on opposing radii would have produced meaningless results. However, based on the results of this study, we conclude that the dendrochronological analysis of live oak is possible with careful sample preparation and analysis and that results would be reliable, even for urban trees. Results of this study suggest that urban tree-ring series with higher interseries correlations were more vigorous than those with lower values, suggesting that urban environmental stresses related to individual sites may decrease the usefulness of crossdating techniques for evaluating annual rings on younger, urban trees.

Description: Publication year: 2012 Source: Dendrochronologia, Volume 30, Issue 1 Rob Wilson, C. Richard Bates Following the successful utilisation of lake preserved sub-fossil woody material to extend living Scots pine chronologies in Scandinavia, ongoing research in the Scottish Highlands aims to build a similar multi-millennial long climatically sensitive pine chronology. This paper details explorative research testing the use of sonar methods to facilitate the search for sub-fossil material in lake environments. Although the method clearly identifies elongate anomalies that are consistent with submerged tree stems in water depths 〉1.5 m, it does not allow the identification of sub-fossil wood remnants in shallow water (〈1.0 m) or heavily vegetated bays. Therefore, for the successful survey of lakes, a combination of traditional and sonar methods must be applied. Ongoing research will now explore the utilisation of these methods to more remote locations where boat access is not possible.

Description: Publication year: 2011 Source: Dendrochronologia, Volume 29, Issue 4 Yongxiang Zhang, Xuemei Shao, Martin Wilmking Knowledge of the spatial pattern and temporal relationships between tree-growth and climatic factors are important not only for the projection of forest growth under varying climate but for dendroclimatology in general. Here, we systematically investigated tree-growth climate relationships of Picea crassifolia at upper treeline in the Qilian Mts., northwestern China. 297 trees from eleven sites, covering a large part of the natural range of this species, show increasing and partly divergent correlations with temperature in the most recent decades. The dominant signal at all sites was a strengthening of negative correlations of annual radial growth with summer temperature. In a subset of trees at six sites, a strengthening positive correlation with summer temperatures existed as well. Wetter and high altitude sites tended to show a higher percentage of trees that are positively correlated with warming temperatures, indicating that some individuals there may take advantage of warmer conditions. Divergent responses between the two sub-populations clustered by their response to climate factor were significantly stronger in the last 30 years compared to earlier time slices. In the same time frame, hydrothermal conditions of the investigation area changed to a drier and warmer combination. Drought conditions, most likely affecting the radial growth of most P. crassifolia , have been intensifying over time and expanding spatially from the middle Qilian Mts. to most of our study area during the last half century. While explanations such as methodological effects due to trend removal or human disturbance at the sampling sites might be able to explain the result at single sites, the spatial and temporal co-occurrence of large scale changes in climate and tree growth suggests a causal link between them.

Description: Publication year: 2011 Source: Dendrochronologia, Volume 29, Issue 3 Martin de Luis, Klemen Novak, José Raventós, Jožica Gričar, Peter Prislan, Katarina Čufar Research was carried out on the wood formation process and the intra-annual density fluctuations (IADFs) in Mediterranean Aleppo pine ( Pinus halepensis Mill.) trees from the coastal site of Guardamar, and inland Maigmo in south-eastern Spain. Samples taken at breast height of the trees were inspected to define the frequency of tree rings with latewood-like cells in earlywood (E-ring) and with earlywood-like cells in latewood (L-ring). L-rings were generally more frequent, especially on the warmer, dryer, coastal site of Guardamar. Dendrochronological techniques using tree-ring features vs. climate showed that L-rings were formed in Guardamar when August and/or September precipitation was higher than normal and in Maigmo when August precipitation was higher than normal. The formation of E-rings was promoted when winter and early spring were warmer than long term average. By studying intra-annual tree-ring formation at a cellular level, we found that at Maigmo in 2004 (MAI2004) all monitored trees presented a normal ring with normal earlywood and latewood and gradual transition between both. At Guardamar in 2005 (GUA2005) a typical L-ring was formed in the majority of monitored trees. In GUA2005 the wood formation started before February and the transition from early- to latewood occurred in late spring. In summer, the cambial cell production occurred at a very low rate, but an increased production of xylem cells took place in September when the amount of precipitation was twice as high as the long term average. During this period, a band of earlywood-like cells was formed, followed by the production of latewood-like cells that continued until the end of December. The normal ring in MAI2004 was formed because climatic factors triggering IADF did not occur (no precipitation in August 2004). After a modest cell production of cambium in September, only few latewood-like cells were produced. According to the strong agreement of results obtained from studying long-term dendrochronological series and intra-annual information on wood formation, such combined study indicates a high potential for use in explaining the environmental signals registered by a tree during different phases of wood formation.

Description: Publication year: 2011 Source: Dendrochronologia, Volume 29, Issue 1 Peter H. Nishimura, Colin P. Laroque Despite their suitability for dendroclimatological research, the boreal regions of central and western Labrador remain under-researched. In an attempt to evaluate the growth trends and climatic response of this region's trees, master chronologies have been developed for its four dominant conifer species. Balsam fir ( Abies balsamea (L.) Mill.), white spruce ( Picea glauca (Moench) Voss), black spruce ( Picea mariana (Mill.) Britton, Sterns, Poggenb.) and eastern larch ( Larix laricina (DuRoi) K. Koch) were sampled systematically within a 3 × 4 grid of twelve sites at the intersection of 62°W, 64°W and 66°W longitude, and latitudes 52°N, 53°N, 54°N and 55°N. The two most dominant species at each site were sampled, yielding a total of twenty-four master chronologies, all of which reflected a highly significant common signal at each site. The chronologies were subjected to a response function analysis to determine the nature of the growth–climate relationships in the region. Summer temperature proved to be the predominant limiting factor with regard to radial growth at most sites. The onset of the optimum temperature regime, however, varies across the network of sites, revealing evidence of a gradient of continentality in the data. Growth–temperature correlations indicated a significant relationship with July temperature at most eastern sites, while western sites tended to correlate with May, June and August temperatures. Central sites tended to correlate with June–July temperatures. We interpret these results as demonstrating the bioclimatic gradient of change between coastally proximal, maritime-influenced sites and inland, continentally influenced locales. This transition occurs approximately 330 km inland from the open Labrador Sea.

Description: Publication year: 2011 Source: Dendrochronologia, Volume 29, Issue 4 S. Szymczak, M.M. Joachimski, A. Bräuning, T. Hetzer, J. Kuhlemann Stable isotopes in tree rings have widely been used for palaeoclimate reconstructions since tree rings record climatic information at annual resolution. However, various wood components or different parts of an annual tree-ring may differ in their isotopic compositions. Thus, sample preparation and subsequent laboratory analysis are crucial for the isotopic signal retained in the final tree-ring isotope series used for climate reconstruction and must therefore be considered for the interpretation of isotope–climate relationships. This study focuses on wood of Corsican Pine trees ( Pinus nigra ssp. laricio ) as this tree species allows to reconstruct the long-term climate evolution in the western Mediterranean. In a pilot study, we concentrated on methodological issues of sample preparation techniques in order to evaluate isotope records measured on pooled whole tree-ring cellulose and whole tree-ring bulk wood samples. We analysed 80-year long carbon and oxygen chronologies of Corsican Pine trees growing near the upper tree line on Corsica. Carbon and oxygen isotope records of whole tree-ring bulk wood and whole tree-ring cellulose from a pooled sample of 5 trees were correlated with the climate parameters monthly precipitation, temperature and the self-calibrating Palmer Drought Severity Index (sc-PDSI). Results show that the offsets in carbon and oxygen isotopes of bulk wood and cellulose are not constant over time. Both isotopes correlate with climate parameters from late winter and summer. The carbon and oxygen isotope ratios of cellulose are more sensitive to climatic variables than those of bulk wood. The results of this study imply that extraction of cellulose is a pre-requisite for the reconstruction of high-resolution climate records from stable isotope series of P. nigra ssp. laricio .

Description: Publication year: 2011 Source: Dendrochronologia, Volume 29, Issue 3 Annie Deslauriers, Sergio Rossi, Audrey Turcotte, Hubert Morin, Cornélia Krause Continuous measurements of stem radius variation in trees are obtained with automatic dendrometers that provide time series composed of seasonal tree growth and circadian rhythms of water storage and depletion. Several variables can be extracted from the raw data, such as amplitude and duration of radius increase and contraction, which are useful for understanding intra-annual tree growth, tree physiology and for performing growth–climate relationships. These measurements constitute a large dataset whose manipulation needs numerous algorithms and automatic procedures to efficiently and rapidly extract the information. This paper presents a three-step procedure using two SAS routines to extract the time series describing radius variation and associate them with environmental parameters. The first routine organizes and corrects data and generates outputs in the form of files and plots to visualize the results and improve data correction (first step). The second step consists of a reclassification of the hours of contraction or expansion that have been misclassified by the automatic process. The second routine classifies the daily patterns of stem variation into the three phases of contraction, expansion and radius increment and associates the environmental parameters (third step). An example of the procedure is given, with an explanation of the outputs generated. The advantages and shortcomings of the procedure and its importance for the intra-annual analyses of tree growth are discussed.

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: Schizophrenia is a very common psychiatric disorder. However, its etiology and pathogenesis is still unknown. Current theory saying that neurotransmitter imbalance such as serotonin or dopamine only provides limited effectiveness in schizophrenia treatment by drugs changing serotonin and dopamine concentration. Despite of such treatment, majority of schizophrenia patients still have very poor prognosis. Thus, the neurotransmitter imbalance theory is not correct. Here, I propose that schizophrenia is actually a TH2 dominant autoimmune disorder. The candidate of autoantigen could be acetylcholine receptors of CNS. My theory can explain the positive as well as negative symptoms of schizophrenia. By microarray analysis of PBMCS, one-tenth of the total 519 significantly expressed genes are immune-related genes. Among them, TH2 related genes are significantly up-regulated including IL-4, histidine decarboxylase, aldehyde dehydrogenase, CCR9, IgE Fc receptor, GATA2, serotonin receptor, phospholipase A2, and prostaglandin D2 synthase. Besides, TH1 and TH17 related genes are down-regulated including CXCL5, cathepsin C, and neutrophil related S100 binding proteins. The new theory sheds a light to better control this detrimental illness. Anti-inflammatory agents could be used to manage schizophrenia in the near future.

Description: Animal models are often used to obtain a better understanding of psychiatric, neurodegenerative, and neurodevelopmental disorders. Despite many years of research, these models have not led to many novel therapies or treatments. Translating results between species will always be difficult, and it is argued that inappropriate statistical analyses, failure to identify the experimental unit, lack of random assignment to treatment conditions, and unblinded assessment of outcomes contribute to the low rate of translating preclinical in vivo studies into successful therapies. It is known that these shortcomings can generate biased estimates, too many false positives and false negatives, and unreproducible results. These issues have been raised repeatedly, but have largely gone unheeded by scientists. Two recommendations are made to improve the situation.

Description: Mobile Platform Informatics (MPI) and Smartphone Informatics (SPI) methods like Mobile Image Ratiometry (MIR) are potentially transformative point-of-use instantaneous analysis tools that are useful across a variety of industries. In agriculture, MIR-compatible immuno test strips allow early detection of a number of biotic stressors before devastating crop losses occur. Here we describe a low-cost and easy-to-use Smartphone and/or tablet-based protocol (Mobile Assay Inc., www.mobileassay.com) for the detection and on-sight instantaneous analysis of B. cinerea, a fungus that causes significant damage to a variety of plants and flowers. Early detection and tracking of the B. cinerea fungus before the visible gray mold appears has the potential to increase agricultural productivity especially in the developing world.

Description: Here we show a new interaction mechanism of colliding population waves. It provides a stable coexistence of two similar but different species competing for the same limiting resource during their asexual propagation in a limited homogeneous environment under constant conditions. The revealed mechanism opens new opportunities in conservation biology.

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: Two erectoid hominids from Sarstedt prompted a detailed examination of the course of the impressions of the Arteria meningea media and their characteristics within the line of hominidae.

Description: Genomic Replikin CountsTM of Infectious Salmon Anemia Virus (ISAV) in Canada Exceed the Counts in Lethal Outbreaks in Norway, Chile, and Scotland. Real-Time Tracking of the Evolution of the ISAV Genome and the Resultant Replikins Solid Phase ISAV Vaccine Make ISAV Pandemic Prevention Possible.

Description: Background: The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).Description: The HTRIdb is an open-access database of experimentally validated interactions among human TFs and their TGs. HTRIdb can be searched via a user-friendly web interface and the retrieved TF-TG interactions data and the associated protein-protein interactions can be downloaded or interactively visualized as a network using the Cytoscape Web software. Moreover, users can improve the database quality by uploading their own interactions and indicating inconsistencies in the data. So far, HTRIdb has been populated with 283 TFs that regulate 11886 genes, totaling 18160 TF-TG interactions. HTRIdb is freely available at http://www.lbbc.ibb.unesp.br/htri.Conclusions: HTRIdb is a powerful user-friendly tool from which human experimentally validated TF-TG interactions can be easily extracted and used to construct transcriptional regulation interaction networks enabling researchers to decipher the regulation of biological processes.

Description: Genome-wide association studies (GWAS) have become a standard method for finding genetic variations that contribute to common, complex diseases. Recently, it is suggested that these diseases may be caused by epistatic interactions of multiple genetic variations. Although tens of software tools have been developed for epistasis detection, few are able to infer pathway importance from the identified epistatic interactions. AntEpiSeeker is originally an algorithm for detecting epistatic interactions in case-control studies, using a two-stage ant colony optimization (ACO) algorithm. We have developed AntEpiSeeker2.0, which extends the AntEpiSeeker algorithm to inference of epistasis-associated pathways, based on a natural use of the ACO pheromones. By looking at pheromone distribution across pathways, epistasis-associated pathways can be easily identified. The effectiveness of AntEpiSeeker2.0 in inferring epistasis-associated pathways is demonstrated through a simulation study and a real data application. AntEpiSeeker 2.0 was designed to provide efficient inference of epistasis-associated pathways based on ant colony optimization and is freely available at http://lambchop.ads.uga.edu/antepiseeker2/.

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: The next generation Nature Reviews Microbiology 10, 157 (2012). doi:10.1038/nrmicro2759 A better understanding of the factors that affect children's desire to follow a career in science is vital if we are to inspire the next generation of scientists.

Description: Bacterial pathogenesis: Controlling Fic proteins Nature Reviews Microbiology 10, 160 (2012). doi:10.1038/nrmicro2757 Author: Sheilagh Molloy A general mechanism for controlling the adenylylation activity of Fic proteins has been identified.

Description: Cellular microbiology: An unconventional exit for Brucella Nature Reviews Microbiology 10, 160 (2012). doi:10.1038/nrmicro2749 Author: Rachel David Brucella abortus hijacks autophagy components to complete its life cycle.

Description: Bacterial genomics: Universal bacterial barcode Nature Reviews Microbiology 10, 161 (2012). doi:10.1038/nrmicro2754 Author: Andrew Jermy Although analysis of 16S ribosomal RNA has revolutionized the ability to classify bacteria and understand their phylogenetic relationships, it is less useful for classifying related strains of bacteria that share similar or identical 16S rRNA gene sequences but exhibit distinct properties. To address this, Jolley

Description: Viral infection: Promiscuous packaging Nature Reviews Microbiology 10, 161 (2012). doi:10.1038/nrmicro2755 Author: Andrew Jermy The high error rate of viral polymerases allows viruses to rapidly adapt to a new host, and each replication cycle results in a heterogeneous population of viruses with distinct genetic content. Routh et al. used an unbiased next-generation sequencing approach to look at the

Description: Biofilms: Biofilms take shape Nature Reviews Microbiology 10, 162 (2012). doi:10.1038/nrmicro2756 Author: Sheilagh Molloy Phenol-soluble modulins have a key role in the structuring and detachment of Staphylococcus aureus biofilms.

Description: Adapting to domesticity Nature Reviews Microbiology 10, 163 (2012). doi:10.1038/nrmicro2752 Author: Adam J. Reid This month's Genome Watch highlights new insights into the impact of food production on the evolution of microorganisms.

Description: In the news Nature Reviews Microbiology 10, 164 (2012). doi:10.1038/nrmicro2760 Our monthly round up of infectious diseases news, which this month includes the spread of a new virus affecting livestock in Europe, the H5N1 controversy and a report that mortality from malaria may be much higher than was previously suspected.

Description: Bacterial pathogenesis: UPEC helps host to exfoliate Nature Reviews Microbiology 10, 159 (2012). doi:10.1038/nrmicro2758 Author: Andrew Jermy UPEC pore-forming toxin α-haemolysin (HlyA) stimulates the proteolysis of host proteins involved in cell adhesion, resulting in uroepithelial cell exfoliation.

Description: A bacterial siren song: intimate interactions between Neisseria and neutrophils Nature Reviews Microbiology 10, 178 (2012). doi:10.1038/nrmicro2713 Authors: Alison K. Criss & H. Steven Seifert Neisseria gonorrhoeae and Neisseria meningitidis are Gram-negative bacterial pathogens that are exquisitely adapted for growth at human mucosal surfaces and for efficient transmission between hosts. One factor that is essential to neisserial pathogenesis is the interaction between the bacteria and neutrophils, which are

Description: Phage biology: T4 to TA, checkmate Nature Reviews Microbiology 10, 160 (2012). doi:10.1038/nrmicro2748 Author: Andrew Jermy Phage T4 encodes an antitoxin that is active against multiple Escherichia coli toxins.

Description: ppGpp: magic beyond RNA polymerase Nature Reviews Microbiology 10, 203 (2012). doi:10.1038/nrmicro2720 Authors: Zachary D. Dalebroux & Michele S. Swanson During stress, bacteria undergo extensive physiological transformations, many of which are coordinated by ppGpp. Although ppGpp is best known for enhancing cellular resilience by redirecting the RNA polymerase (RNAP) to certain genes, it also acts as a signal in many other cellular processes in bacteria.

Description: Structural insights into the coupling of virion assembly and rotavirus replication Nature Reviews Microbiology 10, 165 (2012). doi:10.1038/nrmicro2673 Authors: Shane D. Trask, Sarah M. McDonald & John T. Patton Viral replication is rapid and robust, but it is far from a chaotic process. Instead, successful production of infectious progeny requires that events occur in the correct place and at the correct time. Rotaviruses (segmented double-stranded RNA viruses of the Reoviridae family) seem to

Description: Genome analyses highlight the different biological roles of cellulases Nature Reviews Microbiology 10, 227 (2012). doi:10.1038/nrmicro2729 Authors: Felix Mba Medie, Gideon J. Davies, Michel Drancourt & Bernard Henrissat Cellulolytic enzymes have been the subject of renewed interest owing to their potential role in the conversion of plant lignocellulose to sustainable biofuels. An analysis of ∼1,500 complete bacterial genomes, presented here, reveals that ∼40% of the genomes of sequenced bacteria encode at least one

Description: Host response: Phagocytosis runs like clockwork Nature Reviews Microbiology 10, 162 (2012). doi:10.1038/nrmicro2751 Author: Christina Tobin Kåhrström In Drosophila melanogaster, phagocytosis of specific bacteria is regulated by a circadian protein.

Description: From self sufficiency to dependence: mechanisms and factors important for autotransporter biogenesis Nature Reviews Microbiology 10, 213 (2012). doi:10.1038/nrmicro2733 Authors: Denisse L. Leyton, Amanda E. Rossiter & Ian R. Henderson Autotransporters are a superfamily of proteins that use the type V secretion pathway for their delivery to the surface of Gram-negative bacteria. At first glance, autotransporters look to contain all the functional elements required to promote their own secretion: an amino-terminal signal peptide to mediate

Description: Virophages question the existence of satellites Nature Reviews Microbiology 10, 234 (2012). doi:10.1038/nrmicro2676-c3 Authors: Christelle Desnues & Didier Raoult In a recent Comment (Virophages or satellite viruses? Nature Rev. Microbiol.9 762–763(2011)), Mart Krupovic and Virginija Cvirkaite-Krupovic argued that the recently described virophages, Sputnik and Mavirus, should be classified as satellite viruses. In a response, to which Krupovic and

Description: Evolution: Co-evolution promotes innovation Nature Reviews Microbiology 10, 161 (2012). doi:10.1038/nrmicro2753 Author: Christina Tobin Kåhrström The interaction between a viral ligand and its cellular receptor is highly specific and limits host range. A recent paper describes a mutant form of bacteriophage λ that targets an alternative receptor after co-evolution with Escherichia coli. When phage cI26 was cultured with E.

Description: Towards a more comprehensive classification of satellite viruses Nature Reviews Microbiology 10, 234 (2012). doi:10.1038/nrmicro2676-c4 Authors: Mart Krupovic & Virginija Cvirkaite-Krupovic Our recent Comment on the nature and place of the so-called virophages in the viral world (Virophages or satellite viruses? Nature Rev. Microbiol.9 762–763 (2011)) has caught the attention of researchers favouring the virophage concept and initiated a debate on this

Description: Computational tools for the synthetic design of biochemical pathways Nature Reviews Microbiology 10, 191 (2012). doi:10.1038/nrmicro2717 Authors: Marnix H. Medema, Renske van Raaphorst, Eriko Takano & Rainer Breitling As the field of synthetic biology is developing, the prospects for de novo design of biosynthetic pathways are becoming more and more realistic. Hence, there is an increasing need for computational tools that can support these efforts. A range of algorithms has been developed

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: Natural agricultural production functions in open system, where energy and matter are exchanged freely between geosphere (especially pedosphere), biosphere, and atmosphere. The self regulation of biophysical processes in these spheres is crucial for global sustainability. However, modern farming practices have stressed the system to the extent that damaged C, N, and P cycles are threatening catastrophic consequences. High food-wastage coupled with high food price, high soil fertility zones but low crop productivity, and highly productive irrigated farming marred with ecological disasters are examples of global paradoxes associated with modern farming. High incidence of pesticide residues in soil and water bodies, low use efficiency of agricultural inputs, vulnerability to climate, and low conversion of energy by crops leaving high amount of residues and their subsequent burden on environment, and hunger and malnutrition in many parts of the world are threatening civilizations to crumble. Nanotechnology promises to break these vicious cycles, because technology is based on applying exact amounts of inputs for use by the crops, and only when they are required. Some of the examples are: nanofabricating nutrient ions to improve nutrient use efficiency, targeted use of nano-pesticides, holding of water and then releasing it at the time of crop need by nps, forecasting and elimination of diseases, packaging of food to improve shelf-life, protecting food during storage, DNA nanotechnology, smart treatment delivery systems, bioanalytical nanosensors, bioselective surfaces, nanobioprocessing, protection of the environment by the reduction and conversion of agricultural materials into valuable products, design and development of new nanocatalysts to convert vegetable oils into biobased fuels and biodegradable industrial solvents, and controlled ecological life support system.

Description: Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties The ISME Journal 7, 37 (January 2013). doi:10.1038/ismej.2012.77 Authors: Anja B Dohrmann, Meike Küting, Sebastian Jünemann, Sebastian Jaenicke, Andreas Schlüter & Christoph C Tebbe

Description: Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years The ISME Journal 7, 72 (January 2013). doi:10.1038/ismej.2012.83 Authors: Júlia Rosa de Rezende, Kasper Urup Kjeldsen, Casey R J Hubert, Kai Finster, Alexander Loy & Bo Barker Jørgensen

Description: Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat The ISME Journal 7, 50 (January 2013). doi:10.1038/ismej.2012.79 Authors: J Kirk Harris, J Gregory Caporaso, Jeffrey J Walker, John R Spear, Nicholas J Gold, Charles E Robertson, Philip Hugenholtz, Julia Goodrich, Daniel McDonald, Dan Knights, Paul Marshall, Henry Tufo, Rob Knight & Norman R Pace

Description: Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation The ISME Journal 7, 122 (January 2013). doi:10.1038/ismej.2012.82 Authors: María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V Del Pozo, José María Vieites, Martin von Bergen, José Luis R Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert & Manuel Ferrer

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: Extracellular Ca2+ is a danger signal activating the NLRP3 inflammasome through G protein-coupled calcium sensing receptors Nature Communications 3, 1329 (2012). doi:10.1038/ncomms2339 Authors: Manuela Rossol, Matthias Pierer, Nora Raulien, Dagmar Quandt, Undine Meusch, Kathrin Rothe, Kristin Schubert, Torsten Schöneberg, Michael Schaefer, Ute Krügel, Sanela Smajilovic, Hans Bräuner-Osborne, Christoph Baerwald & Ulf Wagner

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: Phospho-dependent ubiquitination and degradation of PAR-1 regulates synaptic morphology and tau-mediated Aβ toxicity in Drosophila Nature Communications 3, 1312 (2012). doi:10.1038/ncomms2278 Authors: Seongsoo Lee, Ji-Wu Wang, Wendou Yu & Bingwei Lu

Description: Atomic-scale engineering of magnetic anisotropy of nanostructures through interfaces and interlines Nature Communications 3, 1313 (2012). doi:10.1038/ncomms2316 Authors: S. Ouazi, S. Vlaic, S. Rusponi, G. Moulas, P. Buluschek, K. Halleux, S. Bornemann, S. Mankovsky, J. Minár, J.B. Staunton, H. Ebert & H. Brune

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.