Multiscale simulation of flow-induced texture formation in polymer liquid crystals and carbonaceous mesophases

This paper presents theory and simulation of flow-induced structures in liquid crystalline materials, useful to the creation of synthetic material structures and to the biomimetics of natural fibers. A multiscale theory and simulation of hydrodynamic texture formation is presented; it provides fundamental principles for control and optimization of structures in liquid crystal polymers and carbonaceous mesophases. In thermotropic flow-aligning nematic polymers it is found that as the shear-rate increases, the pathway between an oriented non-planar state and an oriented planar state is through meso-texture formation and coarsening, with temperature and shear rate being efficient fields to control the grain size of the texture. For capillary flow of carbonaceous mesophases, the simulations predict the emergence of macroscopic ring patterns whose thickness and density can be controlled by the applied pressure drops. The results provide insight on microstructure formation and control in liquid crystalline materials.     

A new metriorhynchid crocodylomorph from the Lower Kimmeridge Clay Formation (Late Jurassic) of England,with implications for the evolution of dermatocranium ornamentation in Geosaurini

A new metriorhynchid crocodylomorph from the Lower Kimmeridge Clay Formation (Kimmeridgian, Upper Jurassic) of England is described. This specimen, a three‐dimensionally preserved skull and left mandibular ramus, is referred to a new species: T orvoneustes coryphaeus sp. nov. Within the genus Torvoneustes, T . coryphaeus sp. nov. is unique as it has a long anteromedial process of the frontal, ornamented dermatocranium, and the supraorbital notch forms a strongly acute angle. Our phylogenetic analysis confirms the placement of this specimen in Torvoneustes. The dentition of T . coryphaeus sp. nov. , like that of the type species, has a blunt apex, crown basal–mid regions with numerous tightly packed apicobasally aligned ridges, and apical region with an anastomosed pattern of ridges that interact with the carinae. Within Thalattosuchia these dental characteristics are only found in Torvoneustes and the teleosaurid Machimosaurus. The heavily ornamented dermatocranium of T . coryphaeus sp. nov. is in contrast to the unornamented (nasals and frontal)–lightly ornamented (maxillae and premaxillae) pattern seen in Torvoneustes carpenteri. Curiously, this pattern of reduction and loss of dermatocranium ornamentation is also observed in Metriorhynchus, Dakosaurus, and the subclade Rhacheosaurini. We hypothesize that the ‘smooth’ dermatocranium of Late Jurassic metriorhynchids evolved independently in each subclade (parallel evolution), and would have reduced drag, thereby making locomotion through water more energy efficient. © 2013 The Linnean Society of London     

Pre‐synaptic kainate receptor‐mediated facilitation of glutamate release involves PKA and Ca2+‐calmodulin at thalamocortical synapses

We have investigated the mechanisms underlying the facilitatory modulation mediated by kainate receptor (KAR) activation in the cortex, using isolated nerve terminals (synaptosomes) and slice preparations. In cortical nerve terminals, kainate (KA, 100 μM) produced an increase in 4‐aminopyridine (4‐AP)‐evoked glutamate release. In thalamocortical slices, KA (1 μM) produced an increase in the amplitude of evoked excitatory post‐synaptic currents (eEPSCs) at synapses established between thalamic axon terminals from the ventrobasal nucleus onto stellate neurons of L4 of the somatosensory cortex. In both, synaptosomes and slices, the effect of KA was antagonized by 6‐cyano‐7‐nitroquinoxaline‐2,3‐dione, and persisted after pre‐treatment with a cocktail of antagonists of other receptors whose activation could potentially have produced facilitation of release indirectly. Mechanistically, the observed effects of KA appear to be congruent in synaptosomal and slice preparations. Thus, the facilitation by KA of synaptosomal glutamate release and thalamocortical synaptic transmission were suppressed by the inhibition of protein kinase A and occluded by the stimulation of adenylyl cyclase. Dissecting this G‐protein‐independent regulation further in thalamocortical slices, the KAR‐mediated facilitation of synaptic transmission was found to be sensitive to the block of Ca²⁺ permeant KARs by philanthotoxin. Intriguingly, the synaptic facilitation was abrogated by depletion of intracellular Ca²⁺ stores by thapsigargin, or inhibition of Ca²⁺‐induced Ca²⁺‐release by ryanodine. Thus, the KA‐mediated modulation was contingent on both Ca²⁺ entry through Ca²⁺‐permeable KARs and liberation of intracellular Ca²⁺ stores. Finally, sensitivity to W‐7 indicated that the increased cytosolic [Ca²⁺] underpinning KAR‐mediated regulation of synaptic transmission at thalamocortical synapses, requires downstream activation of calmodulin. We conclude that neocortical pre‐synaptic KARs mediate the facilitation of glutamate release and synaptic transmission by a Ca²⁺‐calmodulin dependent activation of an adenylyl cyclase/cAMP/protein kinase A signalling cascade, independent of G‐protein involvement.

     

Standardisation of Western blotting to detect HTLV-1 antibodies synthesised in the central nervous system of HAM/TSP patients

Intrathecal synthesis of human T-lymphotropic virus type 1 (HTLV-1) antibodies (Abs) represents conclusive evidence of a specific immune response in the central nervous system of HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP) patients. Western blotting (WB) for HTLV Abs in serum is a confirmatory test for HTLV-1 infection. The aim of this study was to standardise the Western blot to demonstrate the intrathecal pattern of Abs against HTLV-1 proteins in HAM/TSP patients. Paired cerebrospinal fluid (CSF) and serum samples were selected from 20 patients with definite HAM/TSP, 19 HTLV-1 seronegative patients and two HTLV-1 patients without definite HAM/TSP. The presence of reactive bands of greater intensity in the CSF compared to serum (or bands in only the CSF) indicated the intrathecal synthesis of anti-HTLV-1 Abs. All definite HAM/TSP patients presented with an intrathecal synthesis of anti-HTLV-1 Abs; these Abs were not detected in the control patients. The most frequent intrathecal targets of anti-HTLV-1 Abs were GD21, rgp46-I and p24 and, to a lesser extent, p19, p26, p28, p32, p36, p53 gp21 and gp46. The intrathecal immune response against env (GD21 and rgp46-I) and gag (p24) proteins represents the most important humoral pattern in HAM/TSP. This response may be used as a diagnostic marker, considering the frequent association of intrathecal anti-HTLV-1 Ab synthesis with HAM/TSP and the pathogenesis of this neurological disease.     

Activated zeolite—suitable carriers for microorganisms in anaerobic digestion processes?

Plant cell wall structures represent a barrier in the biodegradation process to produce biogas for combustion and energy production. Consequently, approaches concerning a more efficient de-polymerisation of cellulose and hemicellulose to monomeric sugars are required. Here, we show that natural activated zeolites (i.e. trace metal activated zeolites) represent eminently suitable mineral microhabitats and potential carriers for immobilisation of microorganisms responsible for anaerobic hydrolysis of biopolymers stabilising related bacterial and methanogenic communities. A strategy for comprehensive analysis of immobilised anaerobic populations was developed that includes the visualisation of biofilm formation via scanning electron microscopy and confocal laser scanning microscopy, community and fingerprint analysis as well as enzyme activity and identification analyses. Using SDS polyacrylamide gel electrophoresis, hydrolytical active protein bands were traced by congo red staining. Liquid chromatography/mass spectroscopy revealed cellulolytical endo- and exoglucanase (exocellobiohydrolase) as well as hemicellulolytical xylanase/mannase after proteolytic digestion. Relations to hydrolytic/fermentative zeolite colonisers were obtained by using single-strand conformation polymorphism analysis (SSCP) based on amplification of bacterial and archaeal 16S rRNA fragments. Thereby, dominant colonisers were affiliated to the genera Clostridium, Pseudomonas and Methanoculleus. The specific immobilisation on natural zeolites with functional microbes already colonising naturally during the fermentation offers a strategy to systematically supply the biogas formation process responsive to population dynamics and process requirements.     

A cell sorting protocol for selecting high-producing sub-populations of Sf9 and High Five™ cells

Insect cell lines such as Sf9 and High Five™ have been widely used to produce recombinant proteins mostly by the lytic baculovirus vector system. We have recently established an expression platform in Sf9 cells using a fluorescence-based recombinase mediated cassette exchange (RMCE) strategy which has similar development timelines but avoids baculovirus infection. To expedite cell engineering efforts, a robust fluorescence-activated cell sorting (FACS) protocol optimized for insect cells was developed here. The standard sorting conditions used for mammalian cells proved to be unsuitable, resulting in post-sorting viabilities below 10% for both cell lines. We found that the extreme sensitivity to the shear stress displayed by Sf9 and High Five™ cells was the limiting factor, and using Pluronic F-68 in the cell suspension could increase post-sorting viabilities in a dose dependent manner. The newly developed protocol was then used to sort stable populations of both cell lines tagged with a DsRed-expressing cassette. Before sorting, the average fluorescence intensity of the Sf9 cell population was 3-fold higher than that of the High Five™ cell population. By enriching with the 10% strongest DsRed-fluorescent cells, the productivity of both cell populations could be successfully improved. The established sorting protocol potentiates the use of RMCE technology for recombinant protein production in insect cells.     

Deforestation and Reforestation of Latin America and the Caribbean (2001–2010)

Forest cover change directly affects biodiversity, the global carbon budget, and ecosystem function. Within Latin American and the Caribbean region (LAC), many studies have documented extensive deforestation, but there are also many local studies reporting forest recovery. These contrasting dynamics have been largely attributed to demographic and socio‐economic change. For example, local population change due to migration can stimulate forest recovery, while the increasing global demand for food can drive agriculture expansion. However, as no analysis has simultaneously evaluated deforestation and reforestation from the municipal to continental scale, we lack a comprehensive assessment of the spatial distribution of these processes. We overcame this limitation by producing wall‐to‐wall, annual maps of change in woody vegetation and other land‐cover classes between 2001 and 2010 for each of the 16,050 municipalities in LAC, and we used nonparametric Random Forest regression analyses to determine which environmental or population variables best explained the variation in woody vegetation change. Woody vegetation change was dominated by deforestation (?541,835 km²), particularly in the moist forest, dry forest, and savannas/shrublands biomes in South America. Extensive areas also recovered woody vegetation (+362,430 km²), particularly in regions too dry or too steep for modern agriculture. Deforestation in moist forests tended to occur in lowland areas with low population density, but woody cover change was not related to municipality‐scale population change. These results emphasize the importance of quantitating deforestation and reforestation at multiple spatial scales and linking these changes with global drivers such as the global demand for food.     

Importance of the interaction protein–protein of the CaM–PDE1A and CaM–MLCK complexes in the development of new anti‐CaM drugs

Protein–protein interactions play central roles in physiological and pathological processes. The bases of the mechanisms of drug action are relevant to the discovery of new therapeutic targets. This work focuses on understanding the interactions in protein–protein–ligands complexes, using proteins calmodulin (CaM), human calcium/calmodulin‐dependent 3′,5′‐cyclic nucleotide phosphodiesterase 1A active human (PDE1A), and myosin light chain kinase (MLCK) and ligands αII–spectrin peptide (αII–spec), and two inhibitors of CaM (chlorpromazine (CPZ) and malbrancheamide (MBC)). The interaction was monitored with a fluorescent biosensor of CaM (hCaM M124C–mBBr). The results showed changes in the affinity of CPZ and MBC depending on the CaM–protein complex under analysis. For the Ca²⁺–CaM, Ca²⁺–CaM–PDE1A, and Ca²⁺–CaM–MLCK complexes, CPZ apparent dissociation constants (K_ds) were 1.11, 0.28, and 0.55 μM, respectively; and for MBC K_ds were 1.43, 1.10, and 0.61 μM, respectively. In competition experiments the addition of calmodulin binding peptide 1 (αII–spec) to Ca²⁺–hCaM M124C–mBBr quenched the fluorescence (K_d = 2.55 ± 1.75 pM) and the later addition of MBC (up to 16 μM) did not affect the fluorescent signal. Instead, the additions of αII–spec to a preformed Ca²⁺–hCaM M124C–mBBr–MBC complex modified the fluorescent signal. However, MBC was able to displace the PDE1A and MLCK from its complex with Ca²⁺–CaM. In addition, docking studies were performed for all complexes with both ligands showing an excellent correlation with experimental data. These experiments may help to explain why in vivo many CaM drugs target prefer only a subset of the Ca²⁺–CaM regulated proteins and adds to the understanding of molecular interactions between protein complexes and small ligands. Copyright © 2013 John Wiley & Sons, Ltd.     

Richness and composition of Calliphoridae in an Atlantic Forest fragment: implication for the use of dipteran species as bioindicators

Studies measuring the damage in degraded environments have increased, and it is necessary to obtain reliable biological and ecological indicators for the recovery of such degraded environments and subsequent preservation. This study aimed to conduct a survey of local insects and evaluate their utility in monitoring forest restoration in a degraded area in the Atlantic Forest biome in Ribeirao Grande, State of São Paulo, Brazil. Collections with Shuey traps were conducted from 2006 to 2011 in four distinct forest fragments characterized by environmental impacts, human actions, and phytophysiognomic profiles: Forest (FO), a preserved area with native plant species; “Capoeira” (CA), an area in the natural regeneration process; Planting (PL), an area reforested with native plants; and Pasture (PA), an area with only shrubs. A total of 2,456 specimens of Calliphoridae (Diptera) were collected. Mesembrinella bellardiana was the most abundant (n = 1,884) and dominant species in all environments sampled. The relative abundance of M. bellardiana in the most preserved environment (60.2 % FO, 24.4 % CA, 8.6 % PL, and 6.7 % PA) and other ecological parameters showed that it could be a bioindicator species, i.e., data on its presence or absence directly reflected the status of local preservation. Information on Neotropical dipterans associated with the forested environment is very scarce in the literature. To our knowledge, this is the first study describing the occurrence of Calliphora lopesi (Calliphoridae) in the State of São Paulo.