Three-dimensional structure of the complexin/SNARE complex

During neurotransmitter release, the neuronal SNARE proteins synaptobrevin/VAMP, syntaxin, and SNAP-25 form a four-helix bundle, the SNARE complex, that pulls the synaptic vesicle and plasma membranes together possibly causing membrane fusion. Complexin binds tightly to the SNARE complex and is essential for efficient Ca(2+)-evoked neurotransmitter release. A combined X-ray and TROSY-based NMR study now reveals the atomic structure of the complexin/SNARE complex. Complexin binds in an antiparallel alpha-helical conformation to the groove between the synaptobrevin and syntaxin helices. This interaction stabilizes the interface between these two helices, which bears the repulsive forces between the apposed membranes. These results suggest that complexin stabilizes the fully assembled SNARE complex as a key step that enables the exquisitely high speed of Ca(2+)-evoked neurotransmitter release.     

Identifying consensus disease pathways in Parkinson's disease using an integrative systems biology approach

Parkinson's disease (PD) has had six genome-wide association studies (GWAS) conducted as well as several gene expression studies. However, only variants in MAPT and SNCA have been consistently replicated. To improve the utility of these approaches, we applied pathway analyses integrating both GWAS and gene expression. The top 5000 SNPs (p<0.01) from a joint analysis of three existing PD GWAS were identified and each assigned to a gene. For gene expression, rather than the traditional comparison of one anatomical region between sets of patients and controls, we identified differentially expressed genes between adjacent Braak regions in each individual and adjusted using average control expression profiles. Over-represented pathways were calculated using a hyper-geometric statistical comparison. An integrated, systems meta-analysis of the over-represented pathways combined the expression and GWAS results using a Fisher's combined probability test. Four of the top seven pathways from each approach were identical. The top three pathways in the meta-analysis, with their corrected p-values, were axonal guidance (p = 2.8E-07), focal adhesion (p = 7.7E-06) and calcium signaling (p = 2.9E-05). These results support that a systems biology (pathway) approach will provide additional insight into the genetic etiology of PD and that these pathways have both biological and statistical support to be important in PD.     

Systems approaches in global change and biogeochemistry research

Systems approaches have great potential for application in predictive ecology. In this paper, we present a range of examples, where systems approaches are being developed and applied at a range of scales in the field of global change and biogeochemical cycling. Systems approaches range from Bayesian calibration techniques at plot scale, through data assimilation methods at regional to continental scales, to multi-disciplinary numerical model applications at country to global scales. We provide examples from a range of studies and show how these approaches are being used to address current topics in global change and biogeochemical research, such as the interaction between carbon and nitrogen cycles, terrestrial carbon feedbacks to climate change and the attribution of observed global changes to various drivers of change. We examine how transferable the methods and techniques might be to other areas of ecosystem science and ecology.     

Levels of Amyloid Beta-42, Interleukin-6 and Tumor Necrosis Factor-Alpha in Alzheimer’s Disease and Vascular Dementia

Amyloid β42 (Aβ42) and proinflammatory cytokines such as interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α) have been suggested to contribute to the pathogenesis of Alzheimer's disease (AD) and vascular dementia (VaD). Our aim was to examine whether the changes in these parameters would be able to discriminate the patients with AD from those with VaD and from healthy individuals. We have analyzed the levels of Aβ42, IL-6 and TNF-α in the serum of newly diagnosed 28 AD patients, 16 VaD patients and 26 healthy non-demented controls. We also investigated whether there is an association between Aβ42, IL-6 and TNF-α levels and mini-mental state examination (MMSE) scores and body mass indexes (BMI) of patients. Our data showed a significant decrease in serum Aβ-42 levels in AD patients compared to VaD patients and controls. Levels of IL-6 and TNF-α were not different between AD patients, VaD patients and controls. We observed a correlation between Aβ-42 levels and MMSE scores and BMI levels in both AD and VaD patients. However, Aβ-42 levels were not correlated with IL-6 and TNF-α levels. Significantly lower levels of Aβ42 found in the serum of AD patients than that of VaD patients and controls suggests that it can be a specific biochemical marker for AD.     

High‐resolution spatial modelling of greenhouse gas emissions from land‐use change to energy crops in the United Kingdom

We implemented a spatial application of a previously evaluated model of soil GHG emissions, ECOSSE, in the United Kingdom to examine the impacts to 2050 of land‐use transitions from existing land use, rotational cropland, permanent grassland or woodland, to six bioenergy crops; three ‘first‐generation’ energy crops: oilseed rape, wheat and sugar beet, and three ‘second‐generation’ energy crops: Miscanthus, short rotation coppice willow (SRC) and short rotation forestry poplar (SRF). Conversion of rotational crops to Miscanthus, SRC and SRF and conversion of permanent grass to SRF show beneficial changes in soil GHG balance over a significant area. Conversion of permanent grass to Miscanthus, permanent grass to SRF and forest to SRF shows detrimental changes in soil GHG balance over a significant area. Conversion of permanent grass to wheat, oilseed rape, sugar beet and SRC and all conversions from forest show large detrimental changes in soil GHG balance over most of the United Kingdom, largely due to moving from uncultivated soil to regular cultivation. Differences in net GHG emissions between climate scenarios to 2050 were not significant. Overall, SRF offers the greatest beneficial impact on soil GHG balance. These results provide one criterion for selection of bioenergy crops and do not consider GHG emission increases/decreases resulting from displaced food production, bio‐physical factors (e.g. the energy density of the crop) and socio‐economic factors (e.g. expenditure on harvesting equipment). Given that the soil GHG balance is dominated by change in soil organic carbon (SOC) with the difference among Miscanthus, SRC and SRF largely determined by yield, a target for management of perennial energy crops is to achieve the best possible yield using the most appropriate energy crop and cultivar for the local situation.     

Shoot calcium and magnesium concentrations differ between subtaxa, are highly heritable, and associate with potentially pleiotropic loci in Brassica oleracea

Calcium (Ca) and magnesium (Mg) are the most abundant group II elements in both plants and animals. Genetic variation in shoot Ca and shoot Mg concentration (shoot Ca and Mg) in plants can be exploited to biofortify food crops and thereby increase dietary Ca and Mg intake for humans and livestock. We present a comprehensive analysis of within-species genetic variation for shoot Ca and Mg, demonstrating that shoot mineral concentration differs significantly between subtaxa (varietas). We established a structured diversity foundation set of 376 accessions to capture a high proportion of species-wide allelic diversity within domesticated Brassica oleracea, including representation of wild relatives (C genome, 1n = 9) from natural populations. These accessions and 74 modern F(1) hybrid cultivars were grown in glasshouse and field environments. Shoot Ca and Mg varied 2- and 2.3-fold, respectively, and was typically not inversely correlated with shoot biomass, within most subtaxa. The closely related capitata (cabbage) and sabauda (Savoy cabbage) subtaxa consistently had the highest mean shoot Ca and Mg. Shoot Ca and Mg in glasshouse-grown plants was highly correlated with data from the field. To understand and dissect the genetic basis of variation in shoot Ca and Mg, we studied homozygous lines from a segregating B. oleracea mapping population. Shoot Ca and Mg was highly heritable (up to 40%). Quantitative trait loci (QTL) for shoot Ca and Mg were detected on chromosomes C2, C6, C7, C8, and, in particular, C9, where QTL accounted for 14% to 55% of the total genetic variance. The presence of QTL on C9 was substantiated by scoring recurrent backcross substitution lines, derived from the same parents. This also greatly increased the map resolution, with strong evidence that a 4-cM region on C9 influences shoot Ca. This region corresponds to a 0.41-Mb region on Arabidopsis (Arabidopsis thaliana) chromosome 5 that includes 106 genes. There is also evidence that pleiotropic loci on C8 and C9 affect shoot Ca and Mg. Map-based cloning of these loci will reveal how shoot-level phenotypes relate to Ca(2+) and Mg(2+) uptake and homeostasis at the molecular level.     

Fetal alcohol syndrome: changes in craniofacial form with age, cognition, and timing of ethanol exposure in the macaque

One component of the fetal alcohol syndrome (FAS) facial phenotype is a frontonasal anomaly characterized by a thin upper lip and a smooth philtrum. The expression of this anomaly can diminish with age and occurs infrequently in prenatal alcohol-exposed individuals. This study sought to explain these observations. Standardized craniofacial cephalograms of 18 nonhuman primates exposed weekly to ethanol or sucrose solution in utero were measured at ages 1, 6, 12, and 24 months to assess skeletal changes in craniofacial form with age, cognition, and timing of ethanol exposure. The data suggest that there may be a critical period for induction of alcohol-induced craniofacial alterations that occurs very early in gestation and is very short in duration (gestational days 19 or 20). The alterations were scarcely detectable at age 1 month, were most prominent at 6 months, and diminished progressively at 12 and 24 months in the macaque. The appearance and disappearance of the thin upper lip and smooth philtrum may be explained by underlying changes in skeletal structure with age. The infrequent occurrence of the FAS frontonasal anomaly may be explained, in part, by its short critical period of induction.     

On the role of alphaThr183 in the allosteric regulation and catalytic mechanism of tryptophan synthase

The catalytic activity and substrate channeling of the pyridoxal 5'-phosphate-dependent tryptophan synthase alpha(2)beta(2) complex is regulated by allosteric interactions that modulate the switching of the enzyme between open, low activity and closed, high activity states during the catalytic cycle. The highly conserved alphaThr183 residue is part of loop alphaL6 and is located next to the alpha-active site and forms part of the alpha-beta subunit interface. The role of the interactions of alphaThr183 in alpha-site catalysis and allosteric regulation was investigated by analyzing the kinetics and crystal structures of the isosteric mutant alphaThr183Val. The mutant displays strongly impaired allosteric alpha-beta communication, and the catalytic activity of the alpha-reaction is reduced one hundred fold, whereas the beta-activity is not affected. The structural work establishes that the basis for the missing inter-subunit signaling is the lack of loop alphaL6 closure even in the presence of the alpha-subunit ligands, 3-indolyl-D-glycerol 3'-phosphate, or 3-indolylpropanol 3'-phosphate. The structural basis for the reduced alpha-activity has its origins in the missing hydrogen bond between alphaThr183 and the catalytic residue, alphaAsp60.     

Isolation and characterization of the K5-type yeast killer protein and its homology with an exo-beta-1,3-glucanase

K5-type yeast killer protein in the culture supernatant of Pichia anomala NCYC 434 cells was concentrated by ultrafiltration and purified to homogeneity by ion-exchange chromatography with a POROS HQ/M column followed by gel filtration with a TSK G2000SW column. The protein migrated as a single band on discontinuous gradient SDS-PAGE and had a molecular mass of 49,000 Da. The pI value of the K5-type killer protein was measured at pH 3.7 by high voltage vertical gel electrofocusing. The result of an enzyme immuno assay revealed that it was a glycosylated protein. Its internal amino acid sequencing yielded the sequences LNDFWQQGYHNL, IPIGYWAFQLLDNDPY, and YGGSDYGDVVIGIELL, which are 100% identical to exo-beta-1,3-glucanase (accession no. AJ222862) of Pichia anomala (strain K). The purified protein was highly stable at pH values between 3 and 5.5 and temperatures up to 37 degrees C.