Two thymosin-repeated molecules with structural and functional diversity coexist in Chinese mitten crab Eriocheir sinensis

Recently, beta-thymosin-like proteins with multiple thymosin domains (defined as thymosin-repeated proteins) have been identified from invertebrate. In the present study, the cDNAs of two thymosin-repeated proteins (designated EsTRP1 and EsTRP2) were cloned from Chinese mitten crab by expressed sequence tags (EST) techniques. BLAST analysis presented three and two thymosin domains in EsTRP1 and EsTRP2, respectively, with the identities amongst the five domains varying from 47% to 100%. Both EsTRP1 and EsTRP2 shared high similarities with previously identified vertebrate beta-thynnosins and invertebrate thymosin-repeated proteins (TRPs) with the identities ranging from 43% to 78%, indicating that EsTRPs were new members of the beta-thymosin family. Real-time RT-PCR assay was adopted to determine the tissue distribution of EsTRPs and their temporal expression profile in hemocytes after pathogen stimulation and injury challenge. The expression of EsTRP1 transcript was predominantly detectable in the tissues of hemocytes, hepatopancreas and gonad with the highest expression in hemocytes, while the highest expression level of EsTRP2 was found in heart. EsTRP1 mRNA expression in hemocytes significantly increased at 3 and 48 h after Listonella anguillarum challenge, but there was no significant variation in EsTRP2 temporal expression profile. The injury challenge reduced the mRNA expression of EsTRPs, with the down-regulation of EsTRP2 expression occurred earlier than that of EsTRP1. The cDNA fragments encoding their mature peptides of EsTRP1 and EsTRP2 were recombined and expressed in Escherichia coli. The activities of recombinant proteins (rEsTRP1 and rEsTRP2) were examined by MTT (3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazoliumbromide) and lysoplate assay. rEsTRP2 could significantly accelerate the growth of human hepatocellular carcinoma cell line, but there was no significant effect of rEsTRP1 on the tumor cell proliferation. Both rEsTRP1 and rEsTRP2 did not possess the ability of killing Micrococcus luteus and L. anguillarum. The differences in the tissue distribution of mRNA transcripts, the response to pathogen stimulation and injury challenge, and the effect of recombinant proteins on human cell proliferation, indicated that there were functional diversity between the two structurally different molecules, EsTRP1 and EsTRP2. (C) 2009 Elsevier Ltd. All rights reserved.

Genetic diversity of the subterranean Gansu zokor in a semi-natural landscape

We studied the relationship between genetic diversity of the subterranean Gansu zokor Myospalax cansus and habitat variability in the Loess Plateau, Qinghai Province, China. We used a combination of geographic information systems and molecular techniques to assess the impact of habitat composition and human activities on the genetic diversity of zokor populations in this semi-natural landscape. Although they occurred relatively infrequently in the landscape, woodland and high-coverage grassland habitats were the main positive contributors to the genetic diversity of zokor populations. Rural residential land, plain agricultural land and low-coverage grassland had a negative effect on genetic diversity. Hilly agricultural land and middle-coverage grassland had little impact on zokor genetic diversity. There were also interactions between some habitat types, that is, habitat types with relatively better quality together promoted conservation of genetic diversity, while the interaction between (among) bad habitat types made situations worse. Finally, habitat diversity, measured as patch richness and Shannon's diversity index, was positively correlated with the genetic diversity. These results demonstrated that: (1) different habitat types had different effects on the genetic diversity of zokor populations and (2) habitat quality and habitat heterogeneity were important in maintaining genetic diversity. Habitat composition was closely related to land use thus emphasizing the importance of human activities on the genetic diversity of subterranean rodent populations in this semi-natural landscape. Although the Gansu zokor was considered to be a pest species in the Loess Plateau, our study provides insights for the management and conservation of other subterranean rodent species.

Combining Associational and Causal Reasoning to Solve Interpretation and Planning Problems

This report describes a paradigm for combining associational and causal reasoning to achieve efficient and robust problem-solving behavior. The Generate, Test and Debug (GTD) paradigm generates initial hypotheses using associational (heuristic) rules. The tester verifies hypotheses, supplying the debugger with causal explanations for bugs found if the test fails. The debugger uses domain-independent causal reasoning techniques to repair hypotheses, analyzing domain models and the causal explanations produced by the tester to determine how to replace faulty assumptions made by the generator. We analyze the strengths and weaknesses of associational and causal reasoning techniques, and present a theory of debugging plans and interpretations. The GTD paradigm has been implemented and tested in the domains of geologic interpretation, the blocks world, and Tower of Hanoi problems.

Combining Functional and Structural Reasoning for Safety Analysis of Electrical Designs

C.J.Price, D.R.Pugh, N.A.Snooke, J.E.Hunt, M.S.Wilson, Combining Functional and Structural Reasoning for Safety Analysis of Electrical Designs, Knowledge Engineering Review, vol 12:3, pp.271-287, 1997.

Intrinsic measure of diversity gains in generalised distributed antenna systems with cooperative users

The diversity gains achievable in the generalised distributed antenna system with cooperative users (GDAS-CU) are considered. A GDAS-CU is comprised of M largely separated access points (APs) at one side of the link, and N geographically closed user terminals (UTs) at the other side. The UTs are collaborating together to enhance the system performance, where an idealised message sharing among the UTs is assumed. First, geometry-based network models are proposed to describe the topology of a GDAS-CU. The mean cross-correlation coefficients of signals received from non-collocated APs and UTs are calculated based on the network topology and the correlation models derived from the empirical data. The analysis is also extendable to more general scenarios where the APs are placed in a clustered form due to the constraints of street layout or building structure. Subsequently, a generalised signal attenuation model derived from several stochastic ray-tracing-based pathloss models is applied to describe the power-decaying pattern in urban built-up areas, where the GDAS-CU may be deployed. Armed with the cross-correlation and pathloss model preliminaries, an intrinsic measure of cooperative diversity obtainable from a GDAS-CU is then derived, which is the number of independent fading channels that can be averaged over to detect symbols. The proposed analytical framework would provide critical insight into the degree of possible performance improvement when combining multiple copies of the received signal in such systems.

The emergence of automated high-frequency flow cytometry: revealing temporal and spatial phytoplankton variability

Phytoplankton observation is the product of a number of trade-offs related to sampling processes, required level of diversity and size spectrum analysis capabilities of the techniques involved. Instruments combining the morphological and high-frequency analysis for phytoplankton cells are now available. This paper presents an application of the automated high-resolution flow cytometer Cytosub as a tool for analysing phytoplanktonic cells in their natural environment. High resolution data from a temporal study in the Bay of Marseille (analysis every 30 min over 1 month) and a spatial study in the Southern Indian Ocean (analysis every 5 min at 10 knots over 5 days) are presented to illustrate the capabilities and limitations of the instrument. Automated high-frequency flow cytometry revealed the spatial and temporal variability of phytoplankton in the size range 1−∼50 μm that could not be resolved otherwise. Due to some limitations (instrumental memory, volume analysed per sample), recorded counts could be statistically too low. By combining high-frequency consecutive samples, it is possible to decrease the counting error, following Poisson’s law, and to retain the main features of phytoplankton variability. With this technique, the analysis of phytoplankton variability combines adequate sampling frequency and effective monitoring of community changes.

Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph

A variety of culture-independent techniques have been developed that can be used in conjunction with culture-dependent physiological and metabolic studies of key microbial organisms, in order to better understand how the activity of natural populations influences and regulates all major biogeochemical cycles. In this study, we combined DNA-stable isotope probing with metagenomics and metaproteomics to characterize an as yet uncultivated marine methylotroph that actively incorporated carbon from 13C-labeled methanol into biomass. By metagenomic sequencing of the heavy DNA, we retrieved virtually the whole genome of this bacterium and determined its metabolic potential. Through protein-stable isotope probing, the RuMP cycle was established as the main carbon assimilation pathway, and the classical methanol dehydrogenase-encoding gene mxaF, as well as three out of four identified xoxF homologues were found to be expressed. This proof-of-concept study is the first in which theculture-independent techniques of DNA- and protein-stable isotope probing have been used to characterize the metabolism of a naturally-ocurring Methylophaga-like bacterium in the marine environment (i.e. M. thiooxydans L4) and thus provides a powerful approach to access the genome and proteome of uncultivated microbes involved in key processes in the environment

Identifying predictable foraging habitats for a wide-ranging marine predator using ensemble ecological niche models

Aim: Ecological niche modelling can provide valuable insight into species' environmental preferences and aid the identification of key habitats for populations of conservation concern. Here, we integrate biologging, satellite remote-sensing and ensemble ecological niche models (EENMs) to identify predictable foraging habitats for a globally important population of the grey-headed albatross (GHA) Thalassarche chrysostoma. Location: Bird Island, South Georgia; Southern Atlantic Ocean. Methods: GPS and geolocation-immersion loggers were used to track at-sea movements and activity patterns of GHA over two breeding seasons (n = 55; brood-guard). Immersion frequency (landings per 10-min interval) was used to define foraging events. EENM combining Generalized Additive Models (GAM), MaxEnt, Random Forest (RF) and Boosted Regression Trees (BRT) identified the biophysical conditions characterizing the locations of foraging events, using time-matched oceanographic predictors (Sea Surface Temperature, SST; chlorophyll a, chl-a; thermal front frequency, TFreq; depth). Model performance was assessed through iterative cross-validation and extrapolative performance through cross-validation among years. Results: Predictable foraging habitats identified by EENM spanned neritic (<500 m), shelf break and oceanic waters, coinciding with a set of persistent biophysical conditions characterized by particular thermal ranges (3–8 °C, 12–13 °C), elevated primary productivity (chl-a > 0.5 mg m−3) and frequent manifestation of mesoscale thermal fronts. Our results confirm previous indications that GHA exploit enhanced foraging opportunities associated with frontal systems and objectively identify the APFZ as a region of high foraging habitat suitability. Moreover, at the spatial and temporal scales investigated here, the performance of multi-model ensembles was superior to that of single-algorithm models, and cross-validation among years indicated reasonable extrapolative performance. Main conclusions: EENM techniques are useful for integrating the predictions of several single-algorithm models, reducing potential bias and increasing confidence in predictions. Our analysis highlights the value of EENM for use with movement data in identifying at-sea habitats of wide-ranging marine predators, with clear implications for conservation and management.

Identifying predictable foraging habitats for a wide-ranging marine predator using ensemble ecological niche models

Aim: Ecological niche modelling can provide valuable insight into species' environmental preferences and aid the identification of key habitats for populations of conservation concern. Here, we integrate biologging, satellite remote-sensing and ensemble ecological niche models (EENMs) to identify predictable foraging habitats for a globally important population of the grey-headed albatross (GHA) Thalassarche chrysostoma. Location: Bird Island, South Georgia; Southern Atlantic Ocean. Methods: GPS and geolocation-immersion loggers were used to track at-sea movements and activity patterns of GHA over two breeding seasons (n = 55; brood-guard). Immersion frequency (landings per 10-min interval) was used to define foraging events. EENM combining Generalized Additive Models (GAM), MaxEnt, Random Forest (RF) and Boosted Regression Trees (BRT) identified the biophysical conditions characterizing the locations of foraging events, using time-matched oceanographic predictors (Sea Surface Temperature, SST; chlorophyll a, chl-a; thermal front frequency, TFreq; depth). Model performance was assessed through iterative cross-validation and extrapolative performance through cross-validation among years. Results: Predictable foraging habitats identified by EENM spanned neritic (<500 m), shelf break and oceanic waters, coinciding with a set of persistent biophysical conditions characterized by particular thermal ranges (3–8 °C, 12–13 °C), elevated primary productivity (chl-a > 0.5 mg m−3) and frequent manifestation of mesoscale thermal fronts. Our results confirm previous indications that GHA exploit enhanced foraging opportunities associated with frontal systems and objectively identify the APFZ as a region of high foraging habitat suitability. Moreover, at the spatial and temporal scales investigated here, the performance of multi-model ensembles was superior to that of single-algorithm models, and cross-validation among years indicated reasonable extrapolative performance. Main conclusions: EENM techniques are useful for integrating the predictions of several single-algorithm models, reducing potential bias and increasing confidence in predictions. Our analysis highlights the value of EENM for use with movement data in identifying at-sea habitats of wide-ranging marine predators, with clear implications for conservation and management.

Tracing nitrate and sulfate in river basins using isotope techniques

The objective of this paper is to outline how stable isotope techniques can contribute to the elucidation of the sources and the fate of riverine nitrate and sulphate in watershed studies. The example used is the Oldman River Basin (OMRB), located in southern Alberta (Canada). Increasing sulphate concentrations and decreasing d34S values along the flowpath of the Oldman River indicate that oxidation of pyrite in tills is a major source of riverine sulphate in the agriculturally used portion of the OMRB. Chemical and isotopic data showed that manure-derived nitrogen contributes significantly to the increase in nitrate concentrations in the Oldman River and its tributaries draining agricultural land. It is suggested that hydrological conditions control agricultural return flows to the surface water bodies in southern Alberta and impart significant seasonal variations on concentrations and isotopic compositions of riverine nitrate. Combining isotopic, chemical, and hydrometric data permitted us to estimate the relative contribution of major sources to the total solute fluxes. Hence, we submit that isotopic measurements can make an important contribution to the identification of nutrient and pollutant sources and to river basin management.

Identifying the influence of geology, land use, and anthropogenic activities on riverine sulfate on a watershed scale by combining hydrometric, chemical and isotopic approaches

Throughout the last few decades, sulfate concentrations in streamwater have received considerable attention due to their dominant role in anthropogenic acidification of surface waters. The objectives of this study conducted in the Oldman River Basin in Alberta (Canada) were to determine the influence of geology, land use and anthropogenic activities on sources, concentrations and fluxes of riverine sulfate on a watershed scale. This was achieved by combining hydrological, chemical and isotopic techniques. Surface water samples were collected from the main stem and tributaries of the Oldman River on a monthly basis between December 2000 and March 2003 and analyzed for chemical and isotopic compositions. At a given sampling site, sulfate sources were primarily dependent on geology and did not vary with time or flow condition. With increasing flow distance a gradual shift from ?34S values > 10 ‰ and ?18O values > 0 ‰ of riverine sulfate indicating evaporite dissolution and soil-derived sulfate in the predominantly forested headwaters, to negative ?34S and ?18O values suggested that sulfide oxidation was the predominant sulfate source in the agriculturally used downstream part of the watershed. Significant increases in sulfate concentrations and fluxes with downstream distance were observed, and were attributed to anthropogenically enhanced sulfide oxidation due to the presence of an extensive irrigation drainage network with seasonally varying water levels. Sulfate-S exports in an artificially drained subbasin (64 kg S/ha/yr) were found to exceed those in a naturally drained subbasin (4 kg S/ha/yr) by an order of magnitude. Our dataset suggests that the naturally occurring process of sulfide oxidation has been enhanced in the Oldman River Basin by the presence of an extensive network of drainage and irrigation canals.

Combining biomarker screening and mass-spectrometric analysis to detect hormone abuse in cattle

Since the introduction of the European ban on hormones in 1989, its implementation has proved to be an enormous challenge to regulatory authorities, because the great economic benefits that result from illegal misuse of growth promoters in animal production encourage their continued use. In efforts to challenge black-market trade in hormones, there have been many analytical advances. Recently, both effect-based bioanalysis for screening to target illegal misuse and improved mass-spectrometry-based confirmatory analysis have greatly increased the likelihood of detecting hormone abuse. This review outlines analytical methods currently used for detecting hormone abuse and presents advances in new approaches based on biological determinants that may complement these techniques in the future. (C) 2009 Elsevier Ltd. All rights reserved.

A 76-84 GHz SiGe power amplifier array employing low-loss four-way differential combining transformer

This paper presents holistic design of a novel four-way differential power-combining transformer for use in millimeter-wave power-amplifier (PA). The combiner with an inner radius of 25 µm exhibits a record low insertion loss of 1.25 dB at 83.5 GHz. It is designed to simultaneously act as a balanced-to-unbalanced converter, removing the need for additional BALUNs typically required in differential circuits. A complete circuit comprised of a power splitter, two-stage differential cascode PA array, a power combiner as well as input and output matching elements was designed and realized in SiGe technology with f/f 170/250 GHz. Measured small-signal gain of at least 16.8 dB was obtained from 76.4 to 85.3 GHz with a peak 19.5 dB at 83 GHz. The prototype delivered 12.5 dBm output referred 1 dB compression point and 14 dBm saturated output power when operated from a 3.2 V dc supply voltage at 78 GHz.

Combining missing-feature theory, speech enhancement, and speaker-dependent/-independent modeling for speech separation

This paper considers the separation and recognition of overlapped speech sentences assuming single-channel observation. A system based on a combination of several different techniques is proposed. The system uses a missing-feature approach for improving crosstalk/noise robustness, a Wiener filter for speech enhancement, hidden Markov models for speech reconstruction, and speaker-dependent/-independent modeling for speaker and speech recognition. We develop the system on the Speech Separation Challenge database, involving a task of separating and recognizing two mixing sentences without assuming advanced knowledge about the identity of the speakers nor about the signal-to-noise ratio. The paper is an extended version of a previous conference paper submitted for the challenge.

Generalized Selection Combining in Cognitive MIMO Relay Networks

We propose transmit antenna selection with receive generalized selection combining (TAS/GSC) in dual-hop cognitive decode-and-forward (DF) relay networks for reliability enhancement and interference relaxation. In this paradigm, a single antenna which maximizes the receive signal-to-noise ratio (SNR) is selected at the secondary transmitter and a subset of receive antennas with the highest SNRs are combined at the secondary receiver. To demonstrate the impact of multiple primary users on the cognitive relay network, we derive new closed-form expressions for the exact and asymptotic outage probability with TAS/GSC in the secondary network. Several important design insights are reached. We corroborate that the full diversity gain is achieved, which is entirely determined by the total number of antennas in the secondary network. The negative impact of the primary network on the secondary network is reflected in the SNR gain.