An improved FIA-system for measuring α-amylase in cultivation media

Summary This paper describes a flow-injection analysis (FIA) system for measuring -amylase in cultivation media. It is based on measuring the decolorization of an iodine-starch complex. The FIA-system is optimized with respect to stability and reproducibility. Monitoring of -amylase during batch cultivations with Aspergillus oryzae indicates that -amylase is constitutively expressed at high glucose concentration.     

Soil carbon dynamics and aquatic metabolism of a wet–dry tropics wetland system

Freshwater wetlands are a key component of the global carbon cycle. Wet–dry tropics wetlands function as wet-season carbon sinks and dry-season carbon sources with low aquatic metabolism controlled by predictably seasonal, yet magnitude-variable flow regimes and inundation patterns. However, these dynamics have not been adequately quantified in Australia’s relatively unmodified wet–dry tropics freshwater wetlands. A baseline understanding is required before analysis of land-use or climate change impacts on these aquatic ecosystems can occur. This study characterises geomorphology and sedimentology within a seasonally connected wet–dry tropics freshwater wetland system at Kings Plains, Queensland, Australia, and quantifies soil carbon stocks and wet- and dry-season aquatic metabolism. Soil carbon stocks derived from loss-on-ignition on samples to 1 m depth were 51.5?±?7.8 kg C m^?2, higher than other wet–dry tropics wetlands globally, with potential for long-term retention at greater depths. Gross primary productivity of phytoplankton (GPP) and planktonic respiration (PR) measured through biological oxygen demand bottle experiments in the water column of sediment inundated under laboratory conditions show overall low GPP and PR in both wet- and dry-season samples (all wetland samples were heterotrophic with GPP/PR?<?1). Despite the short-term dominance of aquatic respiration processes leading to net release of carbon in the water column under these conditions, there is appreciable long-term storage of carbon in sediment in the Kings Plains wetlands. This demonstrates the importance of wet–dry-tropics wetland systems as hotspots of carbon sequestration, locally, regionally and globally, and consideration should be given to their conservation and management in this context.

     

A system dynamics approach in LCA to account for temporal effects—a consequential energy LCI of car body-in-whites

Purpose  

The purpose of this paper is to take steps towards a life cycle assessment that is able to account for changes over time in resource flows and environmental impacts. The majority of life cycle inventory (LCI) studies assume that computation parameters are constants or fixed functions of time. This assumption limits the opportunities to account for temporal effects because it precludes consideration of the dynamics of the product system.     

SSCP-SNP in pearl millet—a new marker system for comparative genetics

A considerable array of genomic resources are in place in pearl millet, and marker-aided selection is already in use in the public breeding programme at ICRISAT. This paper describes experiments to extend these publicly available resources to a single nucleotide polymorphism (SNP)-based marker system. A new marker system, single-strand conformational polymorphism (SSCP)-SNP, was developed using annotated rice genomic sequences to initially predict the intron-exon borders in millet expressed sequence tags (ESTs) and then to design primers that would amplify across the introns. An adequate supply of millet ESTs was available for us to identify 299 homologues of single-copy rice genes in which the intron positions could be precisely predicted. PCR primers were then designed to amplify approximately 500-bp genomic fragments containing introns. Analysis of these fragments on SSCP gels revealed considerable polymorphism. A detailed DNA sequence analysis of variation at four of the SSCP-SNP loci over a panel of eight inbred genotypes showed complex patterns of variation, with about one SNP or indel (insertion-deletion) every 59 bp in the introns, but considerably fewer in the exons. About two-thirds of the variation was derived from SNPs and one-third from indels. Most haplotypes were detected by SSCP. As a marker system, SSCP-SNP has lower development costs than simple sequence repeats (SSRs), because much of the work is in silico, and similar deployment costs and through-put potential. The rates of polymorphism were lower but useable, with a mean PIC of 0.49 relative to 0.72 for SSRs in our eight inbred genotype panel screen. The major advantage of the system is in comparative applications. Syntenic information can be used to target SSCP-SNP markers to specific chromosomal regions or, conversely, SSCP-SNP markers can be used to unravel detailed syntenic relationships in specific parts of the genome. Finally, a preliminary analysis showed that the millet SSCP-SNP primers amplified in other cereals with a success rate of about 50%. There is also considerable potential to promote SSCP-SNP to a COS (conserved orthologous set) marker system for application across species by more specifically designing primers to precisely match the model genome sequence.Electronic Supplementary Material Supplementary material is available for this article at     

Nitric oxide — a retrograde messenger for carbon monoxide signaling in ischemic heart

To examine the intracellular signaling mechanism of NO in ischemic myocardium, isolated working rat hearts were made ischemic for 30 min followed by 30 min of reperfusion. A separate group of hearts were pre-perfused with 3 mM L-arginine in the presence or absence of 650 M of protoporphyrin, a heme oxygenase inhibitor for 10 min prior to ischemia. The release of NO was monitored using an on-line amperometric sensor placed into the right atrium. The aortic flow and developed pressure were examined to determine the effects of L-arginine on ischemic/reperfusion injury. Induction for the expression of heme oxygenase was studied by Northern hybridization. For signal transduction experiments, sarcolemmal membranes were radiolabeled by perfusing the isolated hearts with [³H] myoinositol and [¹⁴C] arachidonic acid. Biopsies were processed to determine the isotopic incorporation into various phosphoinositols as well as phosphatidic acid and diacylglycerol. cGMP was assayed by radioimmunoassay and SOD content was determined by enzymatic analysis. The release of NO was diminished following ischemia and reperfusion and was augmented by L-arginine. L-arginine reduced ischemic/reperfusion injury as evidenced by the enhanced myocardial functional recovery. Protoporphyrin modulated the effects of L-arginine. cGMP, which was remained unaffected by ischemia and reperfusion, was stimulated significantly after L-arginine treatment. The NO-mediated augmentation of cGMP was reduced by protoporphyrin suggesting that part of the effects may be mediated by CO generated through the heme oxygenase pathway. Reperfusion of ischemic myocardium resulted in significant accumulation of radiolabeled inositol phosphate, inositol bisphosphate, and inositol triphosphate. Isotopic incorporation of [³H] inositol into phosphatidylinositol, phosphatidylinositol-4-phosphate, and phosphatidylinositol-4,5-bisphosphate was increased significantly during reperfusion. Reperfusion of the ischemic heart prelabeled with [¹⁴C] arachidonic acid resulted in modest increases in [¹⁴C] diacylglycerol and [¹⁴C] phosphatidic acid. Pretreatment of the heart with L-arginine significantly reversed this enhanced phosphodiesteratic breakdown during ischemia and early reperfusion. However, at the end of the reperfision the inhibitory effect of L-arginine on the phosphodiesterases seems to be reduced. In L-arginine treated hearts, SOD activity was progressively decreased with the duration of reperfusion time. The results suggests for the first time that NO plays a significant role in transmembrane signaling in the ischemic myocardium. This signaling appears to be on- and off- nature, and linked with SOD content of the tissue. The signaling is transmitted via cGMP and opposes the effects of phosphodiesterases by inhibiting the ischemia/reperfusion-induced phosphodiesteratic breakdown. Our results also suggest that NO activates heme oxygenase which further stimulates the production of cGMP presumably by CO signaling. Thus, NO not only potentiates cGMP mediated intracellular signaling, it also functions as a retrograde messenger for CO signaling in heart.     

Spatial mosaic and interfacial dynamics in a Müllerian mimicry system

Uncovering why spatial mosaics of mimetic morphs are maintained in a Müllerian mimicry system has been a challenging issue in evolutionary biology. In this article, we analyze the reaction diffusion system that describes two-species Müllerian mimicry in one- and two-dimensional habitats. Due to positive frequency-dependent selection, a local population first approaches the state where one of the comimicking patterns predominates, which is followed by slow movement of boundaries where different patterns meet. We then analyze the interfacial dynamics of the boundaries to find whether a stable cline is maintained and to obtain the wave speed if the cline is unstable. The results are: (1) In a spatially uniform habitat the morph with greater base fitness spreads both in one and two species system. (2) The strength of cross-species interaction determines whether the mimetic morph clines of model and mimic species coalesce into the same geographical region or pass through each other. The joint wave speed of clines decreases by increasing the number of comimicking species in the mimicry ring. (3) In spatial heterogeneous habitats, stable clines can be maintained due to the balance between the base fitness gradient and the biased gene flow by negative curvature of boundary. This allows the persistence of a spatial mosaic even if one of the morphs is in every place advantageous over the other. A balanced cline is also maintained if there is a gradient in the population density. (4) A new advantageous morph occurring at a local region is doomed to go to extinction in a finite time if the "radius" of initial distribution is below a threshold. Possible applications to the heliconiine butterfly mimicry ring, heterozygous disadvantage systems of chromosomal rearrangement and hybrid zone, the third phase of Wright's Shifting Balance theory, and cytoplasmic incompatibility are discussed.     

Who gets the gametes? An argument for a points system for fertility patients

This paper argues that the convention of allocating donated gametes on a ‘first come, first served’ basis should be replaced with an allocation system that takes into account more morally relevant criteria than waiting time. This conclusion was developed using an empirical bioethics methodology, which involved a study of the views of 18 staff members from seven U.K. fertility clinics, and 20 academics, policy‐makers, representatives of patient groups, and other relevant professionals, on the allocation of donated sperm and eggs. Against these views, we consider some nuanced ways of including criteria in a points allocation system. We argue that such a system is more ethically robust than ‘first come, first served’, but we acknowledge that our results suggest that a points system will meet with resistance from those working in the field. We conclude that criteria such as a patient's age, potentially damaging substance use, and parental status should be used to allocate points and determine which patients receive treatment and in what order. These and other factors should be applied according to how they bear on considerations like child welfare, patient welfare, and the effectiveness of the proposed treatment.     

CEUSPEC — a computerized system for fetal home telemetry

We have developed a computerized system whereby the fetal heart rate can be recorded telemetrically from patients' homes, transmitted over conventional public telephone lines, and then computer-processed in real time in the obstetric unit.     

Spatial heterogeneity in whole lake sediments — towards a loading estimate

Studies of nutrient loadings, to shallow culturally eutrophied Alberta lakes, suggest internal inputs are significant. In this regard, estimation of bottom sediment P loads to Lake Wabamun (80 km², 5.5 m depth) were examined. Initially we determined the spatial variability in Total Organic Content (% loss on ignition) and Total Phosphorus, as indicators. Phosphorus fractions and biologically available phosphorus (BAP) were measured at specific stations. These data showed a very uniform distribution in sediment type with a Total Organic Content of 40.6 ± 3.3 (95% C.L.) at the west end, gradually declining to 26.3 ± 0.9 at the east end. Transects performed at routine monitoring stations indicate the representativeness of each station, e.g., station 2, 40.8 ± 1.3 (10 sites). One explanation of this uniformity is provided from²¹⁰Pb analysis of shallow cores which indicate mixing to a depth of 16 cm. This is also thought to explain the mechanics of P loading to the water phase. Finally, Total Organic Content relates well to BAP (r² = 0.80). It is hoped that this simple technique may well permit more precise extrapolation to whole lake BAP estimates at least on this lake.     

An expression system for Gustatory receptors—and why it failed

A recent paper by the Dahankuar laboratory suggested that single Drosophila sugar receptors proteins accurately mediate sugar detection when ectopically expressed in olfactory neurons of the antenna. These findings contra-dict numerous previously published electrophysiological and behavioral investigations, which all point towards heteromultimeric sugar taste receptors. Here, I provide some explanation why this “pseudo-heterologous” expression system may have led to this misleading conclusion.     

An expression system for Gustatory receptors—and why it failed

A recent paper by the Dahankuar laboratory suggested that single Drosophila sugar receptors proteins accurately mediate sugar detection when ectopically expressed in olfactory neurons of the antenna. These findings contra-dict numerous previously published electrophysiological and behavioral investigations, which all point towards heteromultimeric sugar taste receptors. Here, I provide some explanation why this “pseudo-heterologous” expression system may have led to this misleading conclusion.     

Possible dynamic anchor points in a benzoxazinone derivative–human oxytocin receptor system — a molecular docking and dynamics calculation

In this study, we performed a molecular docking and dynamics simulation for a benzoxazinone–human oxytocin receptor system to determine the possible hydrophobic and electrostatic interaction points in the dynamic complex. After the homology modeling, the ligand was docked into the putative active using AutoDock 3.05. After the application of energetic and structural filters, the complexes obtained were further refined with a simulated annealing protocol (AMBER8) to remove steric clashes. Three complexes were selected for subjection to the molecular dynamics simulation (5 ns), and the results on the occurrence of average anchor points showed a stable complex between the benzoxazinone derivative and the receptor. The complex could be used as a good starting point for further analysis with site-directed mutagenesis, or further computational research. Figure The location of the ligands (complex B – blue; complex E – red; and complex F – green) in the transmembrane regions (TM1 – red; TM2 – blue; TM3 – yellow; TM4 – purple; TM5 – orange; TM6 – cyan; TM7 – pink) of the hOTR. For clarity, the EC and IC loops are not shown Electronic Supplementary Material Supplementary material is available at     

Asexual reproduction changes predator population dynamics in a life predator–prey system

Many organisms display oscillations in population size. Theory predicts that these fluctuations can be generated by predator–prey interactions, and empirical studies using life model systems, such as a rotifer-algae community consisting of Brachionus calyciflorus as predator and Chlorella vulgaris as prey, have been successfully used for studying such dynamics. B. calyciflorus is a cyclical parthenogen (CP) and clones often differ in their sexual propensity, that is, the degree to which they engage into sexual or asexual (clonal) reproduction. Since sexual propensities can affect growth rates and population sizes, we hypothesized that this might also affect population oscillations. Here, we studied the dynamical behaviour of B. calyciflorus clones representing either CPs (regularly inducing sex) or obligate parthenogens (OPs). We found that the amplitudes of population cycles to be increased in OPs at low nutrient levels. Several other population dynamic parameters seemed unaffected. This suggests that reproductive mode might be an important additional variable to be considered in future studies of population oscillations.     

Morbidity dynamics in proton–photon or photon radiation therapy for locally advanced prostate cancer

Aim

This study evaluated the frequency and long-term dynamics of early and late post irradiation damage after proton–photon or photon therapy for locally advanced prostate cancer.

Is soil carbon disappearing? The dynamics of soil organic carbon in Java

Research in the soil of the tropics mostly has demonstrated the decline of soil organic carbon (SOC) after conversion of primary forest to plantation and cultivated lands. This paper illustrates the dynamics of SOC on the island of Java, Indonesia, from 1930 to 2010. We used 2002 soil profile observations containing organic carbon (C) analysis in the topsoil, which were collected by the Indonesian Center for Agricultural Land Resources Research & Development from 1923 to 2007. Results show the obvious decline of SOC values from around 2% in 1930–1940 to 0.8% in 1960–1970. However, there has been an increase of SOC content since 1970, with a median level of 1.1% in the year 2000. Our analysis suggests that the human influence and agricultural practices on SOC in Java have been a stronger influence than the environmental factors. SOC for the top 10 cm has shown a net accumulation rate of 0.2–0.3 Mg C ha^?1 yr^?1 during the period 1990–2000. These findings give rise to optimism for increased soil C sequestration in the tropics.     

Plankton time — space dynamics in German Bight — a systems approach

Summary Long term continuous plankton measurements at Helgoland (North Sea) have provided a set of data which could be used for ecological functional analysis with respect to prey predator theory. Local dynamics display trophic feedback between selected populations. Phytoplankton, small copepods, Noctiluca miliaris, Pleurobrachia pileus and Beroe gracilis conform with theoretical assumptions. The functional relationships are less significant in averaged population dynamics compared with single ear processes. The local prey-predator cycles are to be understood as population waves travelling through German Bight. Such population waves over an area of 18 000 km² have been investigated and are displayed for the above given zooplankton populations as computer graphics and analysed in their progression for the population of P. pileus.     

How organic carbon derived from multiple sources contributes to carbon sequestration processes in a shallow coastal system?

Carbon captured by marine organisms helps sequester atmospheric CO₂, especially in shallow coastal ecosystems, where rates of primary production and burial of organic carbon (OC) from multiple sources are high. However, linkages between the dynamics of OC derived from multiple sources and carbon sequestration are poorly understood. We investigated the origin (terrestrial, phytobenthos derived, and phytoplankton derived) of particulate OC (POC) and dissolved OC (DOC) in the water column and sedimentary OC using elemental, isotopic, and optical signatures in Furen Lagoon, Japan. Based on these data analysis, we explored how OC from multiple sources contributes to sequestration via storage in sediments, water column sequestration, and air–sea CO₂ exchanges, and analyzed how the contributions vary with salinity in a shallow seagrass meadow as well. The relative contribution of terrestrial POC in the water column decreased with increasing salinity, whereas autochthonous POC increased in the salinity range 10–30. Phytoplankton‐derived POC dominated the water column POC (65–95%) within this salinity range; however, it was minor in the sediments (3–29%). In contrast, terrestrial and phytobenthos‐derived POC were relatively minor contributors in the water column but were major contributors in the sediments (49–78% and 19–36%, respectively), indicating that terrestrial and phytobenthos‐derived POC were selectively stored in the sediments. Autochthonous DOC, part of which can contribute to long‐term carbon sequestration in the water column, accounted for >25% of the total water column DOC pool in the salinity range 15–30. Autochthonous OC production decreased the concentration of dissolved inorganic carbon in the water column and thereby contributed to atmospheric CO₂ uptake, except in the low‐salinity zone. Our results indicate that shallow coastal ecosystems function not only as transition zones between land and ocean but also as carbon sequestration filters. They function at different timescales, depending on the salinity, and OC sources.     

MicroTom—a high-throughput model transformation system for functional genomics

We have developed a high-throughput Agrobacterium-mediated transformation model system using both nptII and the 5-enolpyruvylshikimate-3-phosphate synthase gene from Agrobacterium tumefaciens strain CP4 (cp4) based selections in MicroTom, a miniature rapid-cycling cherry tomato variety. With the NPTII selection system, transformation frequency calculated as independent transgenic events per inoculated explant ranged from 24 to 80% with an average of 56%, in industrial production scale transformation experiments. For CP4, with glyphosate selection, the average transformation frequency was 57%. Stable transformation frequency was positively correlated with transient expression (R=0.85), and variable with the genes of interest. DNA integration and germline transformation were confirmed by biological assay, Southern Blot analysis, and R₁ phenotype segregation. Transgene expression was observed in leaf, root, stem, flower, and fruit tissues of the transgenic plants. Ninety-five percent of transgenic events coexpressed two introduced genes based on β-glucuronidase (GUS) and neonmycin phosphotransferase II (NPTII) expression. Seventy-five percent of transgenic events contained one to two copies of the introduced uidA (GUS) gene based on Southern analysis. Transgenic plants from the cotyledon explants to the transgenic plants transferred to soil were produced within about 2–3 months depending on the genes of interest. The utility of this MicroTom model transformation system for functional genomic studies, such as identification of genes related to important agricultural traits and gene function, is discussed.