VEGF binding to NRP1 is essential for VEGF stimulation of endothelial cell migration, complex formation between NRP1 and VEGFR2, and signaling via FAK Tyr407 phosphorylation

In endothelial cells, neuropilin-1 (NRP1) binds vascular endothelial growth factor (VEGF)-A and is thought to act as a coreceptor for kinase insert domain-containing receptor (KDR) by associating with KDR and enhancing VEGF signaling. Here we report mutations in the NRP1 b1 domain (Y297A and D320A), which result in complete loss of VEGF binding. Overexpression of Y297A and D320A NRP1 in human umbilical vein endothelial cells reduced high-affinity VEGF binding and migration toward a VEGF gradient, and markedly inhibited VEGF-induced angiogenesis in a coculture cell model. The Y297A NRP1 mutant also disrupted complexation between NRP1 and KDR and decreased VEGF-dependent phosphorylation of focal adhesion kinase at Tyr407, but had little effect on other signaling pathways. Y297A NRP1, however, heterodimerized with wild-type NRP1 and NRP2 indicating that nonbinding NRP1 mutants can act in a dominant-negative manner through formation of NRP1 dimers with reduced binding affinity for VEGF. These findings indicate that VEGF binding to NRP1 has specific effects on endothelial cell signaling and is important for endothelial cell migration and angiogenesis mediated via complex formation between NRP1 and KDR and increased signaling to focal adhesions. Identification of key residues essential for VEGF binding and biological functions provides the basis for a rational design of antagonists of VEGF binding to NRP1.     

Proteomic analysis reveals perturbed energy metabolism and elevated oxidative stress in hearts of rats with inborn low aerobic capacity

Selection on running capacity has created rat phenotypes of high-capacity runners (HCRs) that have enhanced cardiac function and low-capacity runners (LCRs) that exhibit risk factors of metabolic syndrome. We analysed hearts of HCRs and LCRs from generation 22 of selection using DIGE and identified proteins from MS database searches. The running capacity of HCRs was six-fold greater than LCRs. DIGE resolved 957 spots and proteins were unambiguously identified in 369 spots. Protein expression profiling detected 67 statistically significant (p<0.05; false discovery rate <10%, calculated using q-values) differences between HCRs and LCRs. Hearts of HCR rats exhibited robust increases in the abundance of each enzyme of the β-oxidation pathway. In contrast, LCR hearts were characterised by the modulation of enzymes associated with ketone body or amino acid metabolism. LCRs also exhibited enhanced expression of antioxidant enzymes such as catalase and greater phosphorylation of α B-crystallin at serine 59, which is a common point of convergence in cardiac stress signalling. Thus, proteomic analysis revealed selection on low running capacity is associated with perturbations in cardiac energy metabolism and provided the first evidence that the LCR cardiac proteome is exposed to greater oxidative stress.     

Tissue-specific turnover rates of the nitrogen stable isotope as functions of time and growth in a cyprinid fish

Ecological applications of stable isotope data require knowledge on the isotopic turnover rate of tissues, usually described as the isotopic half-life in days (T _0.5) or the change in mass (G _0.5). Ecological studies increasingly analyse tissues collected non-destructively, such as fish fin and scales, but there is limited knowledge on their turnover rates. Determining turnover rates in situ is challenging, with ex situ approaches preferred. Correspondingly, T _0.5 and G _0.5 of the nitrogen stable isotope (δ¹⁵N) were determined for juvenile barbel Barbus barbus (5.5 ± 0.6 g starting weight) using a diet-switch experiment. δ¹⁵N data from muscle, fin and scales were taken during a 125 day post diet-switch period. Whilst isotopic equilibrium was not reached in the 125 days, the δ¹⁵N values did approach those of the new diet. The fastest turnover rates were in more metabolically active tissues, from muscle (highest) to scales (lowest). Turnover rates were relatively slow; T _0.5 was 84 (muscle) to 145 (scale) days; G _0.5 was 1.39 × body mass (muscle) to 2.0 × body mass (scales), with this potentially relating to the slow growth of the experimental fish. These turnover estimates across the different tissues emphasise the importance of estimating half-lives for focal taxa at species and tissue levels for ecological studies.     

Kinetic analysis of phenylalanine dehydrogenase mutants designed for aliphatic amino acid dehydrogenase activity with guidance from homology-based modelling.

Through comparison with the high-resolution structure of Clostridium symbiosum glutamate dehydrogenase, the different substrate specificities of the homologous enzymes phenylalanine dehydrogenase and leucine dehydrogenase were attributed to two residues, glycine 124 and leucine 307, in Bacillus sphaericus phenylalanine dehydrogenase, which are replaced with alanine and valine in leucine dehydrogenases. As predicted, making these substitutions in phenylalanine dehydrogenase decreased the specific activity towards aromatic substrates and enhanced the activity towards some aliphatic amino acids in standard assays with fixed concentrations of both substrates. This study did not, however, distinguish effects on affinity from those on maximum catalytic rate. A fuller kinetic characterization of the single- and double-mutant enzymes now reveals that the extent of the shift in specificity was underestimated in the earlier study. The maximum catalytic rates for aromatic substrates are reduced for all the mutants, but, in addition, the apparent Km values are higher for the single-mutant G124A and double-mutant G124A/L307V compared with the wild-type enzyme. Conversely, specificity constants (kcat/Km) for the nonpolar aliphatic amino acids and the corresponding 2-oxoacids for the mutants are all markedly higher than for the wild type, with up to a 40-fold increase for l-norvaline and a 100-fold increase for its 2-oxoacid in the double mutant. In some cases a favourable change in Km was found to outweigh a smaller negative change in kcat. These results emphasize the risk of misjudging the outcome of protein engineering experiments through too superficial an analysis. Overall, however, the success of the predictions from molecular modelling indicates the usefulness of this strategy for engineering new specificities, even in advance of more detailed 3D structural information.     

Is increased chromosomal diversity in house mice from Lombardy (Italy) congruent with genic divergence?

Recent studies in metacentric (MC) populations of the house mouse, Mus musculus domesticus, singled out underdominance more so than recombination suppression as the foremost barrier to gene flow. Here, MC populations from Lombardy (Italy) were sampled to identify the nature and strength of the barriers to gene flow. The chromosomal analysis recovered the three major MC populations (abbreviated to IBIN, IGAL, both with 2n = 24 and ICRE, 2n = 22), but revealed the existence of a new one (IONE, 2n = 24) which likely derived from IGAL through a single WART (Whole‐Arm Reciprocal Translocation). This, once again, highlights the paramount role of WARTs in the chromosomal diversification of this subspecies. Contacts between MC and standard populations coincided with rivers confirming these hybrid zones as tension zones. Divergence between populations was estimated using available allozyme data. Although the overall low genetic structure globally agreed with the chromosome structure, a large variation in divergence levels was retrieved that only partially matched the underdominance degree. This disparity from expectations highlighted the additional contribution of physical barriers and geographic isolation to the differential rate of evolution of the MC populations of the house mouse.     

Functional Interplay between Type I and II Interferons Is Essential to Limit Influenza A Virus-Induced Tissue Inflammation

Host control of influenza A virus (IAV) is associated with exuberant pulmonary inflammation characterized by the influx of myeloid cells and production of proinflammatory cytokines including interferons (IFNs). It is unclear, however, how the immune system clears the virus without causing lethal immunopathology. Here, we demonstrate that in addition to its known anti-viral activity, STAT1 signaling coordinates host inflammation during IAV infection in mice. This regulatory mechanism is dependent on both type I IFN and IFN-γ receptor signaling and, importantly, requires the functional interplay between the two pathways. The protective function of type I IFNs is associated with not only the recruitment of classical inflammatory Ly6C^hi monocytes into IAV-infected lungs, but also the prevention of excessive monocyte activation by IFN-γ. Unexpectedly, type I IFNs preferentially regulate IFN-γ signaling in Ly6C^lo rather than inflammatory Ly6C^hi mononuclear cell populations. In the absence of type I IFN signaling, Ly6C^lo monocytes/macrophages, become phenotypically and functionally more proinflammatory than Ly6C^hi cells, revealing an unanticipated function of the Ly6C^lo mononuclear cell subset in tissue inflammation. In addition, we show that type I IFNs employ distinct mechanisms to regulate monocyte and neutrophil trafficking. Type I IFN signaling is necessary, but not sufficient, for preventing neutrophil recruitment into the lungs of IAV-infected mice. Instead, the cooperation of type I IFNs and lymphocyte-produced IFN-γ is required to regulate the tissue neutrophilic response to IAV. Our study demonstrates that IFN interplay links innate and adaptive anti-viral immunity to orchestrate tissue inflammation and reveals an additional level of complexity for IFN-dependent regulatory mechanisms that function to prevent excessive immunopathology while preserving anti-microbial functions.     

Characterizing the trophic niches of stocked and resident cyprinid fishes: consistency in partitioning over time,space and body sizes

Hatchery‐reared fish are commonly stocked into freshwaters to enhance recreational angling. As these fishes are often of high trophic position and attain relatively large sizes, they potentially interact with functionally similar resident fishes and modify food‐web structure. Hatchery‐reared barbel Barbus barbus are frequently stocked to enhance riverine cyprinid fish communities in Europe; these fish can survive for over 20 years and exceed 8 kg. Here, their trophic consequences for resident fish communities were tested using cohabitation studies, mainly involving chub Squalius cephalus, a similarly large‐bodied, omnivorous and long‐lived species. These studies were completed over three spatial scales: pond mesocosms, two streams and three lowland rivers, and used stable isotope analysis. Experiments in mesocosms over 100 days revealed rapid formation of dietary specializations and discrete trophic niches in juvenile B. barbus and S. cephalus. This niche partitioning between the species was also apparent in the streams over 2 years. In the lowland rivers, where fish were mature individuals within established populations, this pattern was also generally apparent in fishes of much larger body sizes. Thus, the stocking of these hatchery‐reared fish only incurred minor consequences for the trophic ecology of resident fish, with strong patterns of trophic niche partitioning and diet specialization. Application of these results to decision‐making frameworks should enable managers to make objective decisions on whether cyprinid fish should be stocked into lowland rivers according to ecological risk.     

Otolith microstructure reveals consequences for juvenile growth of fractional spawning in an invasive goldfish Carassius auratus (Linnaeus, 1758) population

The consequences of fractional spawning on the early‐life growth rates of invasive goldfish (Carassius auratus) from the Qinghai‐Tibet Plateau were studied using the otolith microstructure of samples collected in June 2011. The effect of the estimated hatching date on the subsequent growth of individual fish was determined by back‐calculating their number of growth days, daily growth rates and the onset of their second growth season. The number of growth days in the first growth season ranged from 93 to 186 days. Following hatching, daily growth rates increased rapidly to a maximum of 0.55 mm days^?1 before declining to 0.09 mm days^?1. The effect of the duration of the first growth season on individuals was significant (P < 0.01), with later spawned fish having faster growth rates. These later spawned fish were, however, still significantly smaller in body length at the end of the first growth season (37 ± 4 mm in late hatched fish vs 55 ± 9 mm in early hatched fish). However, the smaller, later hatched fish started growing earlier in their second growth season than all other fish (P < 0.01) and subsequently achieved larger growth increments (P < 0.01), suggesting that the larger, early‐hatched fish were investing more resources in gonadal growth than somatic growth in their second growth year. Thus, this invasive population revealed considerable plasticity in their early‐life growth rates that were associated with the hatching date, potentially having substantial effects on their development in their second year of life.