Comparing predictive performance of near infrared spectroscopy at a field, regional, national and continental scales by using spiking and data mining techniques

The development of accurate visible and near infrared (vis-NIR) spectroscopy calibration models for selected soil properties is a crucial step for variable rate application in precision agriculture. The objective of the present study was to compare the prediction performance of vis-NIR spectroscopy at local, regional, national and continental scales using data mining techniques including spiking. Fresh soil samples collected from farms in the UK, Czech Republic, Germany, Denmark and the Netherlands were scanned with a fibre-type vis-NIR spectrophotometer (tec5 Technology for Spectroscopy, Germany), with a spectral range of 305-2200 nm. After dividing spectra into calibration (75%) and validation (25%) sets, spectra in the calibration set were subjected to three multivariate calibration models. The partial least squares regression (PLSR), multivariate adaptive regression splines (MARS) and support vector machines (SVM), with leave-one-out cross-validation were used to establish calibration models of total nitrogen (TN), total carbon (TC) and soil moisture content (MC). The results showed the lowest model performance to be obtained when the single field (local scale) data were used in the calibration models. The effect of spiking was significant and the best model performance was obtained when local samples collected from two fields in the UK were spiked with European soil samples (continental), followed by when the same samples were spiked with UK samples (national). Therefore, these results suggest that continental and national vis-NIR calibration models can be successfully used to predict TN, TC and MC. Therefore, selection of the optimal soil samples with the appropriate data mining technique should be considered when developing vis-NIR calibration models for a non-standard soil to cover a wide variation range

The effects of irradiation on the biological and biomechanical properties of an acellular porcine superflexor tendon graft for cruciate ligament repair

Acellular xenogeneic tissues have the potential to provide ‘off‐the‐shelf’ grafts for anterior cruciate ligament (ACL) repair. To ensure that such grafts are sterile following packaging, it is desirable to use terminal sterilization methods. Here, the effects of gamma and electron beam irradiation on the biological and biomechanical properties of a previously developed acellular porcine superflexor tendon (pSFT) were investigated. Irradiation following treatment with peracetic acid was compared to peracetic acid treatment alone and the stability of grafts following long‐term storage assessed. Irradiation did not affect total collagen content or biocompatibility (determined using a contact cytotoxicity assay) of the grafts, but slightly increased the amount of denatured collagen in and decreased the thermal denaturation temperature of the tissue in a dose dependant fashion. Biomechanical properties of the grafts were altered by irradiation (reduced ultimate tensile strength and Young's modulus, increased failure strain), but remained superior to reported properties of the native human ACL. Long term storage at 4°C had no negative effects on the grafts. Of all the conditions tested, a dose of minimum 25 kGy of gamma irradiation had least effect on the grafts, suggesting that this dose produces a biocompatible pSFT graft with adequate mechanical properties for ACL repair

AtSPX1 affects the AtPHR1 -DNA binding equilibrium by binding monomeric AtPHR1 in solution

Phosphorus is an essential macronutrient for plant growth, and is deficient in about 50% of agricultural soils. The transcription factor Phosphate Starvation Response 1 (PHR1) plays a central role in regulating the expression of a subset of Phosphate Starvation Induced (PSI) genes through binding to a cis acting DNA element termed P1BS. In Arabidopsis and rice, activity of AtPHR1/OsPHR2 is regulated in part by their downstream target SPX proteins through protein-protein interaction. Here we provide kinetic and affinity data for interaction between AtPHR1 and P1BS sites. Using SPR, a tandem P1BS sequence showed ~50-fold higher affinity for MBPAtdPHR1 (a fusion protein comprising the DNA binding domain and coiled-coiled domain of AtPHR1 fused to maltose binding protein) than a single site. The affinity difference was largely reflected in a much slower dissociation rate from the 2x P1BS binding site, suggesting an important role for protein cooperativity. Injection of AtSPX1 in the presence of phosphate or inositol hexakisphosphate (InsP6) failed to alter the MBPAtdPHR1-P1BS dissociation rate, while pre-mixing of these two proteins in the presence of either 5 mM Pi or 500 µM InsP6 resulted in a much lower DNA binding signal from MBPAtdPHR1. These data suggest that in the Pi restored condition, AtSPX1 can bind to monomeric AtPHR1 in solution and therefore regulate PSI gene expression by tuning the AtPHR1-DNA binding equilibrium. This Pi-dependent regulation of AtPHR1-DNA binding equilibrium also generates a negative feedback loop on the expression of AtSPX1 itself, providing a tight control of PSI gene expression

Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection

Streptococcus groups A and B cause serious infections, including early onset sepsis and meningitis in newborns. Rib domain-containing surface proteins are found associated with invasive strains and elicit protective immunity in animal models. Yet, despite their apparent importance in infection, the structure of the Rib domain was previously unknown. Structures of single Rib domains of differing length reveal a rare case of domain atrophy through deletion of 2 core antiparallel strands, resulting in the loss of an entire sheet of the β-sandwich from an immunoglobulin-like fold. Previously, observed variation in the number of Rib domains within these bacterial cell wall-attached proteins has been suggested as a mechanism of immune evasion. Here, the structure of tandem domains, combined with molecular dynamics simulations and small angle X-ray scattering, suggests that variability in Rib domain number would result in differential projection of an N-terminal host-colonization domain from the bacterial surface. The identification of 2 further structures where the typical B-D-E immunoglobulin β-sheet is replaced with an α-helix further confirms the extensive structural malleability of the Rib domain

Tenascin C upregulates interleukin-6 expression in human cardiac myofibroblasts via toll-like receptor 4.

AIM: To investigate the effect of Tenascin C (TNC) on the expression of pro-inflammatory cytokines and matrix metalloproteinases in human cardiac myofibroblasts (CMF). METHODS: CMF were isolated and cultured from patients undergoing coronary artery bypass grafting. Cultured cells were treated with either TNC (0.1 μmol/L, 24 h) or a recombinant protein corresponding to different domains of the TNC protein; fibrinogen-like globe (FBG) and fibronectin type III-like repeats (TNIII 5-7) (both 1 μmol/L, 24 h). The expression of the pro-inflammatory cytokines; interleukin (IL)-6, IL-1β, TNFα and the matrix metalloproteinases; MMPs (MMP1, 2, 3, 9, 10, MT1-MMP) was assessed using real time RT-PCR and western blot analysis. RESULTS: TNC increased both IL-6 and MMP3 (P < 0.01) mRNA levels in cultured human CMF but had no significant effect on the other markers studied. The increase in IL-6 mRNA expression was mirrored by an increase in protein secretion as assessed by enzyme-linked immunosorbant assay (P < 0.01). Treating CMF with the recombinant protein FBG increased IL-6 mRNA and protein (P < 0.01) whereas the recombinant protein TNIII 5-7 had no effect. Neither FBG nor TNIII 5-7 had any significant effect on MMP3 expression. The expression of toll-like receptor 4 (TLR4) in human CMF was confirmed by real time RT-PCR, western blot and immunohistochemistry. Pre-incubation of cells with TLR4 neutralising antisera attenuated the effect of both TNC and FBG on IL-6 mRNA and protein expression. CONCLUSION: TNC up-regulates IL-6 expression in human CMF, an effect mediated through the FBG domain of TNC and via the TLR4 receptor

Bariatric surgery or non-surgical weight loss for idiopathic intracranial hypertension? A systematic review and comparison of meta-analyses

Background: Idiopathic intracranial hypertension (IIH) is associated with obesity and weight loss by any means is considered beneficial in this condition. Objectives: This study aims to appraise bariatric surgery vs. non-surgical weight-loss (medical, behavioural and lifestyle) interventions in IIH management. Methods: A systematic review and meta-analyses of surgical and non-surgical studies. Results: Bariatric surgery achieved 100% papilloedema resolution and a reduction in headache symptoms in 90.2%. Non-surgical methods offered improvement in papilloedema in 66.7%, visual field defects in 75.4% and headache symptoms in 23.2%. Surgical BMI decrease was 17.5 vs. 4.2 for non-surgical methods. Conclusions: Whilst both bariatric surgery and non-surgical weight loss offer significant beneficial effects on IIH symptomatology, future studies should address the lack of prospective and randomised trials to establish the optimal role for these interventions

GPVI (Glycoprotein VI) Interaction With Fibrinogen Is Mediated by Avidity and the Fibrinogen αC-Region

Objective: GPVI (glycoprotein VI) is a key molecular player in collagen-induced platelet signaling and aggregation. Recent evidence indicates that it also plays important role in platelet aggregation and thrombus growth through interaction with fibrin(ogen). However, there are discrepancies in the literature regarding whether the monomeric or dimeric form of GPVI binds to fibrinogen at high affinity. The mechanisms of interaction are also not clear, including which region of fibrinogen is responsible for GPVI binding. We aimed to gain further understanding of the mechanisms of interaction at molecular level and to identify the regions on fibrinogen important for GPVI binding. Approach and Results: Using multiple surface- and solution-based protein-protein interaction methods, we observe that dimeric GPVI binds to fibrinogen with much higher affinity and has a slower dissociation rate constant than the monomer due to avidity effects. Moreover, our data show that the highest affinity interaction of GPVI is with the αC-region of fibrinogen. We further show that GPVI interacts with immobilized fibrinogen and fibrin variants at a similar level, including a nonpolymerizing fibrin variant, suggesting that GPVI binding is independent of fibrin polymerization. Conclusions: Based on the above findings, we conclude that the higher affinity of dimeric GPVI over the monomer for fibrinogen interaction is achieved by avidity. The αC-region of fibrinogen appears essential for GPVI binding. We propose that fibrin polymerization into fibers during coagulation will cluster GPVI through its αC-region, leading to downstream signaling, further activation of platelets, and potentially stimulating clot growth

Trivalent Gd-DOTA reagents for modification of proteins

The development of novel protein-targeted MRI contrast agents crucially depends on the ability to derivatise suitable targeting moieties with a high payload of relaxation enhancer (e.g., gadolinium(III) complexes such as Gd-DOTA), without losing affinity for the target proteins. Here, we report robust synthetic procedures for the preparation of trivalent Gd-DOTA reagents with various chemical handles for site-specific modification of biomolecules. The reagents were shown to successfully label proteins through isothiocyanate ligation or through site-specific thiol–maleimide ligation and strain-promoted azide–alkyne cycloaddition

Bacteriophage MS2 genomic RNA encodes an assembly instruction manual for its capsid

Using RNA-coat protein crosslinking we have shown that the principal RNA recognition surface on the interior of infectious MS2 virions overlaps with the known peptides that bind the high affinity translational operator, TR, within the phage genome. The data also reveal the sequences of genomic fragments in contact with the coat protein shell. These show remarkable overlap with previous predictions based on the hypothesis that virion assembly is mediated by multiple sequences-specific contacts at RNA sites termed Packaging Signals (PSs). These PSs are variations on the TR stem-loop sequence and secondary structure. They act co-operatively to regulate the dominant assembly pathway and ensure cognate RNA encapsidation. In MS2, they also trigger conformational change in the dimeric capsomere creating the A/B quasi-conformer, 60 of which are needed to complete the T=3 capsid. This is the most compelling demonstration to date that this ssRNA virus, and by implications potentially very many of them, assemble via a PS-mediated assembly mechanism