Investigating soil-water retention characteristics at high suctions using Relative Humidity control

A technique for controlling relative humidity (RH) is presented, which involves supplying a sealed chamber with a continuous flow of air at a computer-regulated RH. The desired value of RH is achieved by mixing dry and wet air at appropriate volumes and is measured for servo-control at three locations in the chamber with capacitive RH sensors and checked with a sensitive VAISALA sensor. The setup is capable of controlling RH steadily and continuously with a deviation of less than 0.2% RH. The technique was adopted to determine wetting soil-water retention curves (SWRC) of statically compacted London Clay, under both free-swelling and constant volume conditions. The RH within the chamber was increased in a step-wise fashion, with each step maintained until vapour equilibrium between the chamber atmosphere and the soil samples was established. Independent filter paper measurements further validate the method, while the obtained retention curves complement those available in the literature for lower ranges of suction

Engineering the indigoidine-synthesising enzyme BpsA for diverse applications in biotechnology

Blue pigment synthase A (BpsA) is a single module non-ribosomal peptide synthetase (NRPS) originally isolated from the bacterium Streptomyces lavendulae. It synthesises an easily detectible blue pigment called indigoidine from two molecules of L-glutamine in an ATP powered reaction. BpsA is readily purified and amenable to in vitro assays that have a variety of useful applications. By spectrophotometrically quantifying indigoidine levels it is possible to accurately measure the amount of L-glutamine in complex biological fluids including urine, blood plasma and cell culture media. This method has several advantages over existing methods for glutamine measurement, including that it directly reports on glutamine levels. Existing commercially available enzymatic kits first convert glutamine into glutamate and then measure the level of glutamate, which requires additional sample processing and introduces complexity if glutamate may also be present in the target sample. Additionally, we have shown that BpsA can also be used to measure ATP concentrations in a similar manner. We have further developed a BpsA based assay to detect inhibitors of 4’-phosphopantetheinyl transferases (PPTases). PPTases are enzymes that attach a phosphopantetheine arm to fatty acid synthases, NRPSs and polyketide synthases, thereby switching them from an inactive apo form to an active holo form. PPTases have been validated as promising drug targets in several pathogenic bacteria including P. aeruginosa and M. tuberculosis. In order to detect PPTase inhibition, we have shown that BpsA can be purified in its inactive apo form and mixed with the target PPTase as well as a candidate inhibitor in vitro. The level of PPTase inhibition can then be calculated by measuring the rate of indigoidine production. The assay has been optimised for high throughput screening and used to identify several compounds from chemical libraries that inhibit essential PPTases of P. aeruginosa and M. tuberculosis

The future of midlatitude cyclones

This is the final version. Available from the publisher via the DOI in this record.Purpose of Review This review brings together recent research on the structure, characteristics, dynamics, and impacts of extratropical cyclones in the future. It draws on research using idealized models and complex climate simulations, to evaluate what is known and unknown about these future changes. Recent Findings There are interacting processes that contribute to the uncertainties in future extratropical cyclone changes, e.g., changes in the horizontal and vertical structure of the atmosphere and increasing moisture content due to rising temperatures. Summary While precipitation intensity will most likely increase, along with associated increased latent heating, it is unclear to what extent and for which particular climate conditions this will feedback to increase the intensity of the cyclones. Future research could focus on bridging the gap between idealized models and complex climate models, as well as better understanding of the regional impacts of future changes in extratropical cyclones.Natural Environment Research Council (NERC

Accessing bacterial dark matter for improved enzyme discovery and engineering

Please click Additional Files below to see the full abstrac

Narrative and Cognitive Modeling: Insights From Beckett Exploring Mind's Complexity

Complex systems exacerbate a common problem for scientific enquiry: the difficulty of creating models able to discriminate fundamental elements or patterns from random behaviours or corollary components in the event or process at issue. This chapter argues that a similar tension between order and randomness has been a chief modelling problem of Samuel Beckett’s narratives, tied to his interest in a specific kind of complex system (the mind) and its emergent properties (consciousness and the narrative sense of self). Bulding on narratology, complex system frameworks, cognitive theories of emergence and of scientific modelling, this chapter introduces the idea of “fictional cognitive modelling”. Through this concept, the chapter analyses Beckett’s treatment of narrative devices as formal tools for the creation of “exploratory models” able to atomise the emerging unity of conscious experience and of a narrative sense of self into its core components (defined as the “narrative dynamic core”). It concludes by suggesting that Beckett’s narrative method shows how literature can occupy a proper position in the investigation and exploration of complex systems

C-tactile afferent stimulating touch carries a positive affective value

The rewarding sensation of touch in affiliative interactions is hypothesized to be underpinned by a specialized system of nerve fibers called C-Tactile afferents (CTs), which respond optimally to slowly moving, gentle touch, typical of a caress. However, empirical evidence to support the theory that CTs encode socially relevant, rewarding tactile information in humans is currently limited. While in healthy participants, touch applied at CT optimal velocities (1-10cm/sec) is reliably rated as subjectively pleasant, neuronopathy patients lacking large myelinated afferents, but with intact C-fibres, report that the conscious sensation elicited by stimulation of CTs is rather vague. Given this weak perceptual impact the value of self-report measures for assessing the specific affective value of CT activating touch appears limited. Therefore, we combined subjective ratings of touch pleasantness with implicit measures of affective state (facial electromyography) and autonomic arousal (heart rate) to determine whether CT activation carries a positive affective value. We recorded the activity of two key emotion-relevant facial muscle sites (zygomaticus major—smile muscle, positive affect & corrugator supercilii—frown muscle, negative affect) while participants evaluated the pleasantness of experimenter administered stroking touch, delivered using a soft brush, at two velocities (CT optimal 3cm/sec & CT non-optimal 30cm/sec), on two skin sites (CT innervated forearm & non-CT innervated palm). On both sites, 3cm/sec stroking touch was rated as more pleasant and produced greater heart rate deceleration than 30cm/sec stimulation. However, neither self-report ratings nor heart rate responses discriminated stimulation on the CT innervated arm from stroking of the non-CT innervated palm. In contrast, significantly greater activation of the zygomaticus major (smiling muscle) was seen specifically to CT optimal, 3cm/sec, stroking on the forearm in comparison to all other stimuli. These results offer the first empirical evidence in humans that tactile stimulation that optimally activates CTs carries a positive affective valence that can be measured implicitly

Characterization and genomic analysis of chromate resistant and reducing Bacillus cereus strain SJ1

<p>Abstract</p> <p>Background</p> <p>Chromium is a toxic heavy metal, which primarily exists in two inorganic forms, Cr(VI) and Cr(III). Chromate [Cr(VI)] is carcinogenic, mutational, and teratogenic due to its strong oxidizing nature. Biotransformation of Cr(VI) to less-toxic Cr(III) by chromate-resistant and reducing bacteria has offered an ecological and economical option for chromate detoxification and bioremediation. However, knowledge of the genetic determinants for chromate resistance and reduction has been limited so far. Our main aim was to investigate chromate resistance and reduction by <it>Bacillus cereus </it>SJ1, and to further study the underlying mechanisms at the molecular level using the obtained genome sequence.</p> <p>Results</p> <p><it>Bacillus cereus </it>SJ1 isolated from chromium-contaminated wastewater of a metal electroplating factory displayed high Cr(VI) resistance with a minimal inhibitory concentration (MIC) of 30 mM when induced with Cr(VI). A complete bacterial reduction of 1 mM Cr(VI) was achieved within 57 h. By genome sequence analysis, a putative chromate transport operon, <it>chrIA</it>1, and two additional <it>chrA </it>genes encoding putative chromate transporters that likely confer chromate resistance were identified. Furthermore, we also found an azoreductase gene <it>azoR </it>and four nitroreductase genes <it>nitR </it>possibly involved in chromate reduction. Using reverse transcription PCR (RT-PCR) technology, it was shown that expression of adjacent genes <it>chrA</it>1 and <it>chrI </it>was induced in response to Cr(VI) but expression of the other two chromate transporter genes <it>chrA</it>2 and <it>chrA</it>3 was constitutive. In contrast, chromate reduction was constitutive in both phenotypic and gene expression analyses. The presence of a resolvase gene upstream of <it>chrIA</it>1, an arsenic resistance operon and a gene encoding Tn7-like transposition proteins ABBCCCD downstream of <it>chrIA</it>1 in <it>B. cereus </it>SJ1 implied the possibility of recent horizontal gene transfer.</p> <p>Conclusion</p> <p>Our results indicate that expression of the chromate transporter gene <it>chrA</it>1 was inducible by Cr(VI) and most likely regulated by the putative transcriptional regulator ChrI. The bacterial Cr(VI)-resistant level was also inducible. The presence of an adjacent arsenic resistance gene cluster nearby the <it>chrIA</it>1 suggested that strong selective pressure by chromium and arsenic could cause bacterial horizontal gene transfer. Such events may favor the survival and increase the resistance level of <it>B. cereus </it>SJ1.</p

Amyotrophic lateral sclerosis-associated mutant VAPBP56S perturbs calcium homeostasis to disrupt axonal transport of mitochondria

A proline-to-serine substitution at position 56 in the gene encoding vesicle-associated membrane protein-associated protein B (VAPB; VAPBP56S) causes some dominantly inherited familial forms of motor neuron disease, including amyotrophic lateral sclerosis (ALS) type-8. Here, we show that expression of ALS mutant VAPBP56S but not wild-type VAPB in neurons selectively disrupts anterograde axonal transport of mitochondria. VAPBP56S-induced disruption of mitochondrial transport involved reductions in the frequency, velocity and persistence of anterograde mitochondrial movement. Anterograde axonal transport of mitochondria is mediated by the microtubule-based molecular motor kinesin-1. Attachment of kinesin-1 to mitochondria involves the outer mitochondrial membrane protein mitochondrial Rho GTPase-1 (Miro1) which acts as a sensor for cytosolic calcium levels ([Ca2+]c); elevated [Ca2+]c disrupts mitochondrial transport via an effect on Miro1. To gain insight into the mechanisms underlying the VAPBP56S effect on mitochondrial transport, we monitored [Ca2+]c levels in VAPBP56S-expressing neurons. Expression of VAPBP56S but not VAPB increased resting [Ca2+]c and this was associated with a reduction in the amounts of tubulin but not kinesin-1 that were associated with Miro1. Moreover, expression of a Ca2+ insensitive mutant of Miro1 rescued defective mitochondrial axonal transport and restored the amounts of tubulin associated with the Miro1/kinesin-1 complex to normal in VAPBP56S-expressing cells. Our results suggest that ALS mutant VAPBP56S perturbs anterograde mitochondrial axonal transport by disrupting Ca2+ homeostasis and effecting the Miro1/kinesin-1 interaction with tubulin

Congenital Heart Block Maternal Sera Autoantibodies Target an Extracellular Epitope on the α1G T-Type Calcium Channel in Human Fetal Hearts

Background:Congenital heart block (CHB) is a transplacentally acquired autoimmune disease associated with anti-Ro/SSA and anti-La/SSB maternal autoantibodies and is characterized primarily by atrioventricular (AV) block of the fetal heart. This study aims to investigate whether the T-type calcium channel subunit α1G may be a fetal target of maternal sera autoantibodies in CHB.Methodology/Principal Findings:We demonstrate differential mRNA expression of the T-type calcium channel CACNA1G (α1G gene) in the AV junction of human fetal hearts compared to the apex (18-22.6 weeks gestation). Using human fetal hearts (20-22 wks gestation), our immunoprecipitation (IP), Western blot analysis and immunofluorescence (IF) staining results, taken together, demonstrate accessibility of the α1G epitope on the surfaces of cardiomyocytes as well as reactivity of maternal serum from CHB affected pregnancies to the α1G protein. By ELISA we demonstrated maternal sera reactivity to α1G was significantly higher in CHB maternal sera compared to controls, and reactivity was epitope mapped to a peptide designated as p305 (corresponding to aa305-319 of the extracellular loop linking transmembrane segments S5-S6 in α1G repeat I). Maternal sera from CHB affected pregnancies also reacted more weakly to the homologous region (7/15 amino acids conserved) of the α1H channel. Electrophysiology experiments with single-cell patch-clamp also demonstrated effects of CHB maternal sera on T-type current in mouse sinoatrial node (SAN) cells.Conclusions/Significance:Taken together, these results indicate that CHB maternal sera antibodies readily target an extracellular epitope of α1G T-type calcium channels in human fetal cardiomyocytes. CHB maternal sera also show reactivity for α1H suggesting that autoantibodies can target multiple fetal targets. © 2013 Strandberg et al

Evaluation of PMIP2 and PMIP3 simulations of mid-Holocene climate in the Indo-Pacific, Australasian and Southern Ocean regions

This study uses the simplified patterns of temperature and effective precipitation approach from the Australian component of the international palaeoclimate synthesis effort (INTegration of Ice core, MArine and TErrestrial records - OZ-INTIMATE) to compare atmosphere–ocean general circulation model (AOGCM) simulations and proxy reconstructions. The approach is used in order to identify important properties (e.g. circulation and precipitation) of past climatic states from the models and proxies, which is a primary objective of the Southern Hemisphere Assessment of PalaeoEnvironment (SHAPE) initiative. The AOGCM data are taken from the Paleoclimate Modelling Intercomparison Project (PMIP) mid-Holocene (ca. 6000 years before present, 6 ka) and pre-industrial control (ca. 1750 CE, 0 ka) experiments. The synthesis presented here shows that the models and proxies agree on the differences in climate state for 6 ka relative to 0 ka, when they are insolation driven. The largest uncertainty between the models and the proxies occurs over the Indo-Pacific Warm Pool (IPWP). The analysis shows that the lower temperatures in the Pacific at around 6 ka in the models may be the result of an enhancement of an existing systematic error. It is therefore difficult to decipher which one of the proxies and/or the models is correct. This study also shows that a reduction in the Equator-to-pole temperature difference in the Southern Hemisphere causes the mid-latitude westerly wind strength to reduce in the models; however, the simulated rainfall actually increases over the southern temperate zone of Australia as a result of higher convective precipitation. Such a mechanism (increased convection) may be useful for resolving disparities between different regional proxy records and model simulations. Finally, after assessing the available datasets (model and proxy), opportunities for better model–proxy integrated research are discussed.Duncan Ackerley, Jessica Reeves, Cameron Barr, Helen Bostock, Kathryn Fitzsimmons, Michael-Shawn Fletcher, Chris Gouramanis, Helen McGregor, Scott Mooney, Steven J. Phipps, John Tibby and Jonathan Tyle