Modeling of oligomeric-state dependent spectral heterogeneity in the B875 light-harvesting complex of Rhodobacter sphaeroides by numerical simulation

A series of detergent-isolated light-harvesting 1 (LH1, B875) complexes from Rhodobacter sphaeroides, estimated to range in size from (RâBChl2)4 to (RâBChl2)13, was used to study the combined effects of spectral disorder and excitonic interactions on oligomeric-state dependent optical properties. Numerical simulations of absorption and fluorescence emission, excitation, and polarization spectra, based on the structure of the related LH2 complex, were compared to spectra measured experimentally at 77 K (Westerhuis and Niederman, in preparation). The aggregation-state dependence of the polarization spectra was found to be particularly sensitive to the choice of parameters, and vibronic components were included to obtain satisfactory simulations. Good agreement with most experimental features, including the oligomeric-state dependence of the absorption and emission maxima, was obtained only when the inter- and intradimer coupling strengths for adjacent BChls were similar (200-260 cm-1), and the width for the inhomogeneous distribution function (300-400 cm-1) was comparable. The relevance of these findings to existing controversies on the physical origin of spectral heterogeneity observed for the LH1 complex is discussed

The influence of fall and spring herbicide application on winter wheat

Non-Peer ReviewedThe use of 2,4-D for fall control of winter annuals weeds in winter wheat is recommended in the Canadian prairies but not in other winter wheat production areas. Field research was conducted for two years at several locations using 2,4-0, MCPA, dicamba, dicamba plus 2,4-D, bromoxynil, bromoxynil plus MCPA, chlorsulfuron and clopyralid applied fall and spring. Recommended and double recommended rates were tested to establish the existence of a safety margin. Norstar winter wheat was tolerant to fall applications of all herbicides when applied at recommended rates, however, grain yield was reduced at the double rate with 2,4-D, MCPA, bromoxynil, bromoxynil plus MCPA and clopyralid in some station years. Norstar was tolerant to spring applications of all herbicides except MCPA and clopyralid in several station years. Herbicides tested show promise for use in winter wheat production. Caution is warranted for spring application of MCPA and clopyralid

Exploring the transcriptomic data of the Australian paralysis tick, Ixodes holocyclus

Ixodes holocyclus is the paralysis tick commonly found in Australia. I. holocyclus does not cause paralysis in the primary host – bandicoots, but markedly affects secondary hosts such as companion animals, livestock and humans. Holocyclotoxins are the neurotoxin molecules in I. holocyclus responsible for paralysis symptoms. There is a limited understanding of holocyclotoxins due to the difficulties in purifying and expressing these toxins in vitro. Next-generation sequencing technologies were utilised for the first time to generate transcriptome data from two cDNA samples –salivary glands samples collected from female adult ticks engorged on paralysed companion animals and on bandicoots. Contigencoded proteins in each library were annotated according to their best BLAST match against several databases and functionally assigned into six protein categories: housekeeping, transposable elements, pathogen-related, hypothetical, secreted and novel. The “secreted protein” category is comprised of ten protein families: enzymes, protease inhibitors, antigens, mucins, immunity-related, lipocalins, glycinerich, putative secreted, salivary and toxin-like. Comparisons of contig representation between the two libraries reveal the differential expression of tick proteins collected from different hosts. This study provides a preliminary description of the I. holocyclus tick salivary gland transcriptome

Can cartilage loss be detected in knee osteoarthritis (OA) patients with 3–6 months' observation using advanced image analysis of 3T MRI?

SummaryPurposePrior investigations of magnetic resonance imaging (MRI) biomarkers of cartilage loss in knee osteoarthritis (OA) suggest that trials of interventions which affect this biomarker with adequate statistical power would require large clinical studies of 1–2 years duration. We hypothesized that smaller, shorter duration, “Proof of Concept” (PoC) studies might be achievable by: (1) selecting a population at high risk of rapid medial tibio-femoral (TF) progression, in conjunction with; (2) high-field MRI (3T), and; (3) using advanced image analysis. The primary outcome was the cartilage thickness in the central medial femur.MethodsMulti-centre, non-randomized, observational cohort study at four sites in the US. Eligible participants were females with knee pain, a body mass index (BMI)≥25kg/m2, symptomatic radiographic evidence of medial TF OA, and varus mal-alignment. The 29 participants had a mean age of 62 years, mean BMI of 36kg/m2, with eight index knees graded as Kellgren–Lawrence (K&L)=2 and 21 as K&L=3. Eligible participants had four MRI scans of one knee: two MRIs (1 week apart) were acquired as a baseline with follow-up MRI at 3 and 6 months. A trained operator, blind to time-point but not subject, manually segmented the cartilage from the Dual Echo Steady State water excitation MR images. Anatomically corresponding regions of interest were identified on each image by using a three-dimensional statistical shape model of the endosteal bone surface, and the cartilage thickness (with areas denuded of cartilage included as having zero thickness – ThCtAB) within each region was calculated. The percentage change from baseline at 3 and 6 months was assessed using a log-scale analysis of variance (ANOVA) model including baseline as a covariate. The primary outcome was the change in cartilage thickness within the aspect of central medial femoral condyle exposed within the meniscal window (w) during articulation, neglecting cartilage edges [nuclear (n)] (nwcMF·ThCtAB), with changes in other regions considered as secondary endpoints.ResultsAnatomical mal-alignment ranged from −1.9° to 6.3°, with mean 0.9°. With one exception, no changes in ThCtAB were detected at the 5% level for any of the regions of interest on the TF joint at 3 or 6 months of follow-up. The change in the primary variable (nwcMF·ThCtAB) from (mean) baseline at 3 months from the log-scale ANOVA model was −2.1% [95% confidence interval (CI) (−4.4%, +0.2%)]. The change over 6 months was 0.0% [95% CI (−2.7%, +2.8%)]. The 95% CI for the change from baseline did not include zero for the cartilage thickness within the meniscal window of the lateral tibia (wLT·ThCtAB) at 6 month follow-up (−1.5%, 95% CI [−2.9, −0.2]), but was not significant at the 5% level after correction for multiple comparisons.ConclusionsThe small inconsistent compartment changes, and the relatively high variabilities in cartilage thickness changes seen over time in this study, provide no additional confidence for a 3- or 6-month PoC study using a patient population selected on the basis of risk for rapid progression with the MRI acquisition and analyses employed

Cats, connectivity and conservation: incorporating datasets and integrating scales for wildlife management

Understanding resource selection and quantifying habitat connectivity are fundamental to conservation planning for both land-use and species management plans. However, datasets available to management authorities for resource selection and connectivity analyses are often highly limited and fragmentary. As a result, measuring connectivity is challenging, and often poorly integrated within conservation planning and wildlife management. To exacerbate the challenge, scale-dependent resource use makes inference across scales problematic, resource use is often modelled in areas where the species is not present, and connectivity is typically measured using a source-to-sink approach, erroneously assuming animals possess predefined destinations. Here, we used a large carnivore, the leopard Panthera pardus, to characterise resource use and landscape connectivity across a vast, biodiverse region of southern Africa. Using a range of datasets to counter data deficiencies inherent in carnivore management, we overcame methodological limitations by employing occupancy modelling and resource selection functions across three orders of selection, and estimated landscape-scale habitat connectivity – independent of a priori source and sink locations – using circuit theory. We evaluated whether occupancy modelling on its own was capable of accurately informing habitat connectivity, and identified conservation priorities necessary for applied management. We detected markedly different scale-dependent relationships across all selection orders. Our multi-data, multi-scale approach accurately predicted resource use across multiple scales and demonstrates how management authorities can more suitably utilise fragmentary datasets. We further developed an unbiased landscape-scale depiction of habitat connectivity, and identified key linkages in need of targeted management. We did not find support for the use of occupancy modelling as a proxy for landscape-scale habitat connectivity and further caution its use within a management context. Synthesis and applications. Maintaining habitat connectivity remains a fundamental component of wildlife management and conservation, yet data to inform these biological and ecological processes are often scarce. We present a robust approach that incorporates multi-scale fragmentary datasets (e.g. mortality data, permit data, sightings data), routinely collected by management authorities, to inform wildlife management and land-use planning. We recommend that management authorities employ a multi-data, multi-scale connectivity approach—as we present here—to identify management units at risk of low connectivity

Dynamic Evolution Model of Isothermal Voids and Shocks

We explore self-similar hydrodynamic evolution of central voids embedded in an isothermal gas of spherical symmetry under the self-gravity. More specifically, we study voids expanding at constant radial speeds in an isothermal gas and construct all types of possible void solutions without or with shocks in surrounding envelopes. We examine properties of void boundaries and outer envelopes. Voids without shocks are all bounded by overdense shells and either inflows or outflows in the outer envelope may occur. These solutions, referred to as type $\mathcal{X}$ void solutions, are further divided into subtypes $\mathcal{X}_{\rm I}$ and $\mathcal{X}_{\rm II}$ according to their characteristic behaviours across the sonic critical line (SCL). Void solutions with shocks in envelopes are referred to as type $\mathcal{Z}$ voids and can have both dense and quasi-smooth edges. Asymptotically, outflows, breezes, inflows, accretions and static outer envelopes may all surround such type $\mathcal{Z}$ voids. Both cases of constant and varying temperatures across isothermal shock fronts are analyzed; they are referred to as types $\mathcal{Z}_{\rm I}$ and $\mathcal{Z}_{\rm II}$ void shock solutions. We apply the `phase net matching procedure' to construct various self-similar void solutions. We also present analysis on void generation mechanisms and describe several astrophysical applications. By including self-gravity, gas pressure and shocks, our isothermal self-similar void (ISSV) model is adaptable to various astrophysical systems such as planetary nebulae, hot bubbles and superbubbles in the interstellar medium as well as supernova remnants.Comment: 24 pages, 13 figuers, accepted by ApS

Current practice in Australia and New Zealand for defunctioning ileostomy after rectal cancer surgery with anastomosis: Analysis of the Bi-National Colorectal Cancer Audit (BCCA)

AIM: This study aimed to investigate the use of defunctioning stomas after rectal cancer surgery in Australia and New Zealand (ANZ), as current practice is unknown. METHODS: From the Bi-National Colorectal Cancer Audit (BCCA) database, rectal cancer patients who underwent a resection between 2007 and 2019 with the formation of an anastomosis were extracted and analysed. Primary outcome was the rate of defunctioning stoma formation. Secondary outcomes were: anastomotic leakage (AL) rates and other postoperative complications, length of hospital stay (LOS), readmissions and 30-day mortality rates between stoma and no stoma groups. Propensity score-matching was performed to correct for differences in baseline characteristics between stoma and no-stoma groups. RESULTS: In total, 2,581 (89%) received a defunctioning stoma and 319 (11%) did not. There were more male patients in the stoma group (65.5 vs. 57.7% for the no-stoma group; p=0.006). The median age was 64 years in both groups. The stoma group underwent more ultra-low anterior resections (79.9 vs. 30.1%; p<0.0001), included more AJCC stage III patients (53.7 vs. 29.2%; p<0.0001) and received more neoadjuvant therapy (66.9 vs. 16.3%; p<0.0001). The AL rate was similar in both groups (5.1 vs. 6.0%; p=0.52). LOS was longer in the stoma group (8 vs. 6 days; p<0.0001) with higher 30-day readmission rates (14.9 vs. 8.3%; p=0.003). After propensity score-matching (n=208 in both groups), AL rates remained similar (2.9% for stoma vs. 5.8% for no stoma group; p=0.15), but stoma patients required less reoperations (0% vs. 8%; p=0.016). The stoma group had higher postoperative ileus rates and an increased LOS. CONCLUSION: In ANZ, most patients who underwent rectal cancer resections with the formation of an anastomosis received a defunctioning stoma. A defunctioning stoma does not prevent anastomotic leakage from occurring but is mostly associated with a lower reoperation rate. Patients with a defunctioning stoma experienced a higher postoperative ileus rate and had an increased length of hospital stay.Vera E. M. Grupa, Hidde M. Kroon, Izel Ozmen, Sergei Bedrikovetski, Nagendra N. Dudi-Venkata, Ronald A. Hunter, Tarik Sammou

Vertical distribution and migration of fish larvae in the NW Iberian upwelling system during the winter mixing period: implications for cross-shelf distribution

The vertical distribution and vertical migrations of fish larvae and implications for their cross-shelf distribution were investigated in the northern limit of the NE Atlantic upwelling region during the late winter mixing period of 2012. The average positive values of the upwelling index for February and March of this year were far from normal, although the average hydrographic conditions during the period of study were of downwelling and the water column was completely mixed. Fish larvae, most in the preflexion stage, were concentrated in the upper layers of the water column and their distribution was depth stratified, both day and night. However, the larval fish community was not structured in the vertical plane and fish larvae did not show significant diel vertical migration (DVM), although five species showed ontogenetic vertical migration. In regions of coastal upwelling and in the absence of DVM, the location of fish larvae in the water column is crucial for their cross-shelf distribution. Thus, the cross-shelf distribution of the six most abundant species collected in this study can be explained by the surface onshore flow associated with coastal downwelling, retaining larvae of the coastal spawning species with a relatively shallow distribution in the shelf region and transporting larvae of slope spawning species onto the shelf. The wide vertical distribution shown by larvae of the offshore spawning species could be an adaptation of these species to ensure that some larvae reach the inshore nursery areasPlan Nacional de I+D+i (CRAMERCTM2010- 21856-CO3-02), Junta de Galicia (ECOPREGA-10MMA602021PR), Principado de Asturias (GRUPIN14-144)Postprint2,044

Structure and reactivity of Trypanosoma brucei pteridine reductase: inhibition by the archetypal antifolate methotrexate

The protozoan Trypanosoma brucei has a functional pteridine reductase (TbPTR1), an NADPH-dependent short-chain reductase that participates in the salvage of pterins, which are essential for parasite growth. PTR1 displays broad-spectrum activity with pterins and folates, provides a metabolic bypass for inhibition of the trypanosomatid dihydrofolate reductase and therefore compromises the use of antifolates for treatment of trypanosomiasis. Catalytic properties of recombinant TbPTR1 and inhibition by the archetypal antifolate methotrexate have been characterized and the crystal structure of the ternary complex with cofactor NADP(+) and the inhibitor determined at 2.2 Å resolution. This enzyme shares 50% amino acid sequence identity with Leishmania major PTR1 (LmPTR1) and comparisons show that the architecture of the cofactor binding site, and the catalytic centre are highly conserved, as are most interactions with the inhibitor. However, specific amino acid differences, in particular the placement of Trp221 at the side of the active site, and adjustment of the β6-α6 loop and α6 helix at one side of the substrate-binding cleft significantly reduce the size of the substrate binding site of TbPTR1 and alter the chemical properties compared with LmPTR1. A reactive Cys168, within the active site cleft, in conjunction with the C-terminus carboxyl group and His267 of a partner subunit forms a triad similar to the catalytic component of cysteine proteases. TbPTR1 therefore offers novel structural features to exploit in the search for inhibitors of therapeutic value against African trypanosomiasis