Contributors: Tetsuji Okada
... DSA files of human (N to Z, by gene name) : UniProt ID is used for a protein to which no gene name is assigned.
Contributors: Tetsuji Okada
... DSA files of human (A to M, by gene name) : UniProt ID is used for a protein to which no gene name is assigned.
Contributors: Philipp Keller
... Guide's software and data repository- compact version
Top results from Data Repository sources. Show only results like these.
Contributors: Philipp Keller
... Guide's software and data repository- full version
Contributors: Leonardo Diaco, Luca Garofalo, Davide Marchesini
... Dimensionamento e verifica di una rete di acquedotti nel quartiere di Oltrefersina a Trento (IT) tramite il Qgis con il plugin Qepanet
Case Study - Comparing methods used in estimating biodiversity on sandy beaches: Pitfall vs. quadrat sampling
Contributors: Lucia Fanini, James K. Lowry
... We compared the two most commonly used sampling methods, pitfall trapping and quadrat sieving, to study community diversity and talitrid abundance on sandy beaches. They are both widely used methods, however they are related to different behaviors: surface activity (pitfall traps) and burrowing in the substrate (quadrat sieving). To detect bias intrinsically generated by the use of different sampling methods, we applied both methods on a set of five beaches in New South Wales, Australia. The set included non-contiguous beaches, exposed and sheltered, more or less affected by recreational use. The results indicated a high fluctuation in biodiversity features. However, the most human-frequented beaches were grouped together by Multi Dimensional Scaling, and substrate-modifiers talitrid amphipods (sand-hoppers), played a major role in this scaling. The analysis of similarities (ANOSIM) indicated the roles of exposure and human recreational use in shaping the community, while the methods (quadrats vs. traps) resulted in higher fluctuation within samples than between, and informative outliers. Generalized Linear Models developed to estimate the probability of capture of talitrids by sampling method pointed to a higher probability to capture both sand-hoppers and beach-hoppers with the quadrat method. We finally suggest: (1) the comparative use of both sampling methods whenever possible, to capture multiple information and avoid bias in biodiversity estimates; and (2) an ad-hoc strategy when dealing with target populations. In particular, attention should be paid when targeting co-occurring talitrid species characterized by different ecology and behavioral traits: sand-hoppers (substrate modifiers) appeared to be more sensitive than beach-hoppers (non-substrate modifiers) to the impacts considered. In terms of biodiversity assessment the methods were equal, but for talitrid sampling quadrat sieving was more efficient.
Contributors: Andre Acksel, Wulf Amelung, Peter Kühn, Ernst Gehrt, Tom Regier, Peter Leinweber
... The genesis of Chernozems in the Baltic Sea region is still insufficiently understood and the composition of its organic matter may be a key for a better pedogenetic interpretation of the mollic, biogenically mixed (Axh) horizons. Therefore, we investigated the composition of soil organic matter in the Ap/Ah- and Axh-horizons from seven soil profiles at the islands of Poel, Fehmarn (Germany), and Sjalland (Denmark). In a multi-methods approach we carried out synchrotron-based X-ray absorption near edge structure (XANES) spectroscopy at the carbon (C) and nitrogen (N) K-edges, pyrolysis-field ionisation-mass spectrometry (Py-FIMS) and soil color measurements as non-specific, bulk SOM characterization methods, and quantified the benzene polycarboxylic acids (BPCAs) as specific markers for black carbon (BC). The XANES- and Py-FIMS-spectra in good agreement revealed relative enrichments of aromatic C and heterocyclic N compounds in the lower Axh- in comparison to the corresponding upper Ap/Ah-horizons. In almost all horizon pairs, the BC portions in the Axh- (7.6 to 18% of Corg) exceeded those in the Ap/Ah-horizons (6.7 to 12% of Corg) and were similar to the BC portions in typical Phaeozems and Chernozems from European loess areas. The ratios of penta- to hexacarboxylic benzoic acids (B5CA/B6CA) of 0.9 to 2.2, mean 1.2, indicated contributions of combustion residues from domestic and grassland fires. This pyrogenic organic matter and its transformation products governed the soil color, which was closely correlated to the BC portions (L*-value=−0.880 x+52.13; r2=0.539**). In summary, the enrichments of stabilized aromatic and heterocyclic compounds in the Axh-horizons derived from C- and N-XANES, Py-FIMS and the BC-determination are interpreted by an input of pyrogenic matter into the Baltic Chernozems, indicating an anthropo-pedogenesis in the period between Bronze age and the Early Middle Ages.
Genetic structure of Plasmodium vivax in Nicaragua, a country in the control phase, based on the carboxyl terminal region of the merozoite surface protein-1
Contributors: Sleidher Gutiérrez, Lilia González-Cerón, Alberto Montoya, Marco A. Sandoval, Maritza E. Tórres, Rene Cerritos
... Malaria is still a grave public health problem in tropical areas of the world. The greater genetic diversity of Plasmodium vivax at geographic sites with less control over infection evidences the importance of genetic studies of these parasites. The present genetic study compares P. vivax in Nicaragua, which is still in the control phase, with this species in several other countries. In Nicaragua, P. vivax causes over 80% of malaria cases, most occurring in two remote northern regions. Plasmodium asexual blood-stage antigens, implicated in reticulocyte invasion, are possible molecular markers for analyzing parasite population genetics and for developing vaccines. The aim of this work was to investigate the genetic structure of P. vivax based on the 42kDa merozoite surface protein-1 (PvMSP-142), which may represent a sensitive marker for evaluating malaria transmission control. From blood samples of patients with P. vivax, we amplified PvMSP-142, obtained the nucleotide sequences, and compared them to homologous sequences of parasites from other geographic sites, retrieved from the GenBank. The 92 nucleotide sequences of P. vivax resulted in the resolution of eight haplotypes, six exclusive to Nicaragua. The great nucleotide diversity (π=0.020), the minimal recombination events (Rm=11), and the dN–dS values were similar to other control phase countries. FST values between parasites were low (0.069) for Nicaragua versus Brazil but higher for Nicaragua versus other regions (0.134–0.482). The haplotype network revealed five lineages: two were very frequent in Nicaragua and closely related to American parasites; three have been detected in multiple geographic sites around the world. These results suggest that P. vivax in Nicaragua is a differentiated and genetically diverse population (mainly due to mutation, positive balancing selection and recombination) and that PvMSP-142 may be a sensitive marker for evaluating sustained reduction in malaria transmission and for developing vaccines.
Contributors: James T. Liu, Ray T. Hsu, Jia-Jang Hung, Yuan-Pin Chang, Yu-Huai Wang, Rebecca H. Rendle-Bühring, Chon-Lin Lee, Chih-An Huh, Rick J. Yang
... There are many different source-to-sink dispersal systems around the world, and the Gaoping River (GPR)–Gaoping Submarine Canyon (GPSC) provides an example especially as a canyon-captured system. The GPR, a small mountainous river having an average gradient of 1:150, and the GPSC, which links the river catchment to the deep-sea basin, represent two major topographic features around SW Taiwan. Together, they constitute a terrestrial-to-marine dispersal system that has an overriding impact on the source-to-sink transport of sediment in this region. The GPSC extents from the mouth of the GPR through the shelf and slope and into the northeastern Manila Trench, a distance of about 260km. It is a major conduit for the transport of terrestrial sediment and carbon to the South China Sea and the landward transport of particles of marine and biological origin.
Weed seed bank diversity and community shift in a four-decade-old fertilization experiment in rice–rice system
Contributors: B. Lal, Priyanka Gautam, R. Raja, R. Tripathi, M. Shahid, S. Mohanty, B.B. Panda, P. Bhattacharyya, A.K. Nayak
... The development of management practices that allow the prediction of timing and extent of weed emergence is essential for planning more effective weed control strategies as well as maintenance of biodiversity in agricultural systems. A better understanding of the seed bank could provide useful insights into the long-term effects of organic and chemical fertilization for maintaining diversity. The effects of organic and inorganic fertilization on weed seed bank composition, density and diversity were studied in the soil of a long-term fertilizer experiment established four decades ago in CRRI, Cuttack, India. Weed seed density was lowest for Paspalidium flavidum (22 individuals per m2) and highest for Ammania baccifera (11,616 individuals per m2) irrespective of the treatments. Highest weed seed density was observed in farm yard manure (FYM) treatment whereas, lowest was in NK treatment, which was 232% higher in FYM over NK treatment. Weed seedling emergence was higher in kharif flushes and lowest in rabi. Principal component analysis ordination indicated little similarity in the weed community composition particularly among NP, NPK and NPK+FYM, while application of N alone was quite distant. Weed species diversity was reduced significantly with application of inorganic N either applied with K or alone; therefore, lowest diversity and species richness was observed in NK treatment followed by N alone. The results of the study may contribute to the development of effective weed management strategies as well as maintenance of weed diversity which leads to transition from an herbicide-dependent cropping system to a more environmentally friendly cropping system.