Using Bioconductor Package BiGGR for Metabolic Flux Estimation Based on Gene Expression Changes in Brain

Predicting the distribution of metabolic fluxes in biochemical networks is of major interest in systems biology. Several databases provide metabolic reconstructions for different organisms. Software to analyze flux distributions exists, among others for the proprietary MATLAB environment. Given the large user community for the R computing environment, a simple implementation of flux analysis in R appears desirable and will facilitate easy interaction with computational tools to handle gene expression data. We extended the R software package BiGGR, an implementation of metabolic flux analysis in R. BiGGR makes use of public metabolic reconstruction databases, and contains the BiGG database and the reconstruction of human metabolism Recon2 as Systems Biology Markup Language (SBML) objects. Models can be assembled by querying the databases for pathways, genes or reactions of interest. Fluxes can then be estimated by maximization or minimization of an objective function using linear inverse modeling algorithms. Furthermore, BiGGR provides functionality to quantify the uncertainty in flux estimates by sampling the constrained multidimensional flux space. As a result, ensembles of possible flux configurations are constructed that agree with measured data within precision limits. BiGGR also features automatic visualization of selected parts of metabolic networks using hypergraphs, with hyperedge widths proportional to estimated flux values. BiGGR supports import and export of models encoded in SBML and is therefore interoperable with different modeling and analysis tools. As an application example, we calculated the flux distribution in healthy human brain using a model of central carbon metabolism. We introduce a new algorithm termed Least-squares with equalities and inequalities Flux Balance Analysis (Lsei-FBA) to predict flux changes from gene expression changes, for instance during disease. Our estimates of brain metabolic flux pattern with Lsei-FBA for Alzheimer’s disease agree with independent measurements of cerebral metabolism in patients. This second version of BiGGR is available from Bioconductor.     

Identification of QTL regions and SSR markers associated with resistance to reniform nematode in <Emphasis Type="Italic">Gossypium barbadense</Emphasis> L. accession GB713

The identification of molecular markers that are closely linked to gene(s) in Gossypium barbadense L. accession GB713 that confer a high level of resistance to reniform nematode (RN), Rotylenchulus reniformis Linford & Oliveira, would be very useful in cotton breeding programs. Our objectives were to determine the inheritance of RN resistance in the accession GB713, to identify SSR markers linked with RN resistance QTLs, and to map these linked markers to specific chromosomes. We grew and scored plants for RN reproduction in the P₁, P₂, F₁, F₂, BC₁P₁, and BC₁P₂ generations from the cross of GB713 × Acala Nem-X. The generation means analysis using the six generations indicated that one or more genes were involved in the RN resistance of GB713. The interspecific F₂ population of 300 plants was genotyped with SSR molecular markers that covered most of the chromosomes of Upland cotton (G. hirsutum L.). Results showed two QTLs on chromosome 21 and one QTL on chromosome 18. One QTL on chromosome 21 was at map position 168.6 (LOD 28.0) flanked by SSR markers, BNL 1551_162 and GH 132_199 at positions 154.2 and 177.3, respectively. A second QTL on chromosome 21 was at map position 182.7 (LOD 24.6) flanked by SSR markers BNL 4011_155 and BNL 3279_106 at positions 180.6 and 184.5, respectively. Our chromosome 21 map had 61 SSR markers covering 219 cM. One QTL with smaller genetic effects was localized to chromosome 18 at map position 39.6 (LOD 4.0) and flanked by SSR markers BNL 1721_178 and BNL 569_131 at positions 27.6 and 42.9, respectively. The two QTLs on chromosome 21 had significant additive and dominance effects, which were about equal for each QTL. The QTL on chromosome 18 showed larger additive than dominance effects. Following the precedent set by the naming of the G. longicalyx Hutchinson & Lee and G. aridum [(Rose & Standley) Skovsted] sources of resistance, we suggest the usage of Ren ^barb1 and Ren ^barb2 to designate these QTLs on chromosome 21 and Ren ^barb3 on chromosome 18.     

Response of soil organic matter pools to elevated CO2 and warming in a semi-arid grassland

Warming and elevated atmospheric CO₂ (eCO₂) can elicit contrasting responses on different SOM pools, thus to understand the effects of combined factors it is necessary to evaluate individual pools. Over two years, we assessed responses to eCO₂ and warming of SOM pools, their susceptibility to decomposition, and whether these responses were mediated by plant inputs in a semi-arid grassland at the PHACE (Prairie Heating and CO₂ Enrichment) experiment. We used long-term soil incubations and assessed relationships between plant inputs and the responses of the labile and resistant pools. We found strong and contrasting effects of eCO₂ and warming on the labile C pool. In 2008 labile C was increased by eCO₂ and was positively related to plant biomass. In contrast, in 2007 eCO₂ and warming had interactive effects on the labile C, and the pool size was not related to plant biomass. Effects of warming and eCO₂ in this year were consistent withtreatment effects on soil moisture and temperature and their effects on labile C decomposition. The decomposition rate of the resistant C was positively related to indicators of plant C inputs. Our approach demonstrated that SOM pools in this grassland can have early and contrasting responses to climate change factors. The labile C pool in the mixed-grass prairie was highly responsive to eCO₂ and warming but the factors behind such responses were highly dynamic across years. Results suggest that in this grassland the resistant C pool could be negatively affected by increases in plant-production driven available soil C.     

THE FINE STRUCTURE OF TWO UNUSUAL STALKED BACTERIA

Two strains of bacteria that produce slender appendages (pseudostalks) from their lateral surfaces were studied using the electron microscope. The pseudostalks were shown to be extensions of the cytoplasm and peripheral membranes of the cell proper. Both strains of bacteria produce holdfasts at the poles of the cells by the means of which attachment can take place. The pseudostalks are not involved in the attachment of cells. No specialized intracytoplasmic structures are present at the point of juncture of pseudostalk and cell. A discussion of the possible functions of the pseudostalks, based on the electron microscope findings, is presented.     

Telemetered electromyography of peroneus longus in Varecia variegata and Eulemur rubriventer: implications for the functional significance of a large peroneal process

A foot specialized for grasping small branches with a divergent opposable hallux (hallucal grasping) represents a key adaptive complex characterizing almost all arboreal non-human euprimates. Evolution of such grasping extremities probably allowed members of a lineage leading to the common ancestor of modern primates to access resources available in a small-branch niche, including angiosperm products and insects. A better understanding of the mechanisms by which euprimates use their feet to grasp will help clarify the functional significance of morphological differences between the euprimate grasp complex and features representing specialized grasping in other distantly related groups (e.g., marsupials and carnivorans) and in closely related fossil taxa (e.g., plesiadapiforms). In particular, among specialized graspers euprimates are uniquely characterized by a large peroneal process on the base of the first metatarsal, but the functional significance of this trait is poorly understood. We tested the hypothesis that the large size of the peroneal process corresponds to the pull of the attaching peroneus longus muscle recruited to adduct the hallux during grasping. Using telemetered electromyography on three individuals of Varecia variegata and two of Eulemur rubriventer, we found that peroneus longus does not generally exhibit activity consistent with an important function in hallucal grasping. Instead, extrinsic digital flexor muscles and, sometimes, the intrinsic adductor hallucis are active in ways that indicate a function in grasping with the hallux. Peroneus longus helps evert the foot and resists its inversion. We conclude that the large peroneal tuberosity that characterizes the hallucal metatarsal of prosimian euprimates does not correlate to "powerful" grasping with a divergent hallux in general, and cannot specifically be strongly linked to vertical clinging and climbing on small-diameter supports. Thus, the functional significance of this hallmark, euprimate feature remains to be determined.     

Myelin protein zero/P0 phosphorylation and function require an adaptor protein linking it to RACK1 and PKC alpha

Point mutations in the cytoplasmic domain of myelin protein zero (P0; the major myelin protein in the peripheral nervous system) that alter a protein kinase Calpha (PKCalpha) substrate motif (198HRSTK201) or alter serines 199 and/or 204 eliminate P0-mediated adhesion. Mutation in the PKCalpha substrate motif (R198S) also causes a form of inherited peripheral neuropathy (Charcot Marie Tooth disease [CMT] 1B), indicating that PKCalpha-mediated phosphorylation of P0 is important for myelination. We have now identified a 65-kD adaptor protein that links P0 with the receptor for activated C kinase 1 (RACK1). The interaction of p65 with P0 maps to residues 179-197 within the cytoplasmic tail of P0. Mutations or deletions that abolish p65 binding reduce P0 phosphorylation and adhesion, which can be rescued by the substitution of serines 199 and 204 with glutamic acid. A mutation in the p65-binding sequence G184R occurs in two families with CMT, and mutation of this residue results in the loss of both p65 binding and adhesion function.     

Testing the Generality of a Trophic-cascade Model for Plague

Climate may affect the dynamics of infectious diseases by shifting pathogen, vector, or host species abundance, population dynamics, or community interactions. Black-tailed prairie dogs (Cynomys ludovicianus) are highly susceptible to plague, yet little is known about factors that influence the dynamics of plague epizootics in prairie dogs. We investigated temporal patterns of plague occurrence in black-tailed prairie dogs to assess the generality of links between climate and plague occurrence found in previous analyses of human plague cases. We examined long-term data on climate and plague occurrence in prairie dog colonies within two study areas. Multiple regression analyses revealed that plague occurrence in prairie dogs was not associated with climatic variables in our Colorado study area. In contrast, plague occurrence was strongly associated with climatic variables in our Montana study area. The models with most support included a positive association with precipitation in April–July of the previous year, in addition to a positive association with the number of “warm” days and a negative association with the number of “hot” days in the same year as reported plague events. We conclude that the timing and magnitude of precipitation and temperature may affect plague occurrence in some geographic areas. The best climatic predictors of plague occurrence in prairie dogs within our Montana study area are quite similar to the best climatic predictors of human plague cases in the southwestern United States. This correspondence across regions and species suggests support for a (temperature-modulated) trophic-cascade model for plague, including climatic effects on rodent abundance, flea abundance, and pathogen transmission, at least in regions that experience strong climatic signals.     

GuiTope: an application for mapping random-sequence peptides to protein sequences

Background  

Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task.     

Human non-secretory ribonucleases. II. Structural characterization of theN-glycans of the kidney, liver and spleen enzymes by NMR spectroscopy and electrospray mass spectrometry

The N-glylycans have been removed by peptide-N-glycosidase F(PNGase F) from purified human non-secretory RNases derivedfrom kidney, liver and spleen. The spleen RNase was purifiedby two procedures, one of which did not include the usual acidtreatment step (0.25 M H₂SO₄, 45 min, 4C), to determine ifacid treatment alters the carbohydrate moieties. TheN-glycansof the RNases were fractionated by Bio-Gel P-4 chromatographyand analysed by 600 MHz ¹H-NMR spectroscopy and electrospraymass spectrometry. All four non-secretory RNase preparationscontained the following structures: The relative amounts of the trisaccharide, pentasaccharide andhexasaccharide appeared to vary slightly in the different tissueRNases. The overall results indicate: (i) that acid treatmentduring purification does not alter the N-glycans of non-secretoryRNases; (ii) that the N-glycans from kidney, liver and spleennon-secretory RNases are very similar, if not identical, toone another, but different from the N-glycan structures reportedfor secretory RNase. N-glycans non-secretory RNases     

The concept of threshold and its potential application to landscape planning

The concept of threshold can potentially be applied to conservation planning of species, habitats, and ecosystems. It also has significance in managing social–ecological systems for resilience. However, our understanding and use of threshold has been scattered among various disciplines, and the link to conservation planning and social–ecological system management has not been strongly established. The review of the use of threshold in various disciplines reveals that the term is used in a similar manner in both natural and social sciences: a threshold is a point or a zone on an independent variable, and if it is crossed, a sudden, large change in the state of a dependent variable occurs. Even a small change in the independent variable brings this drastic change; nonlinear relationship characterizes the threshold response. Thresholds also separate alternative regimes in a social–ecological system. The discussion of the application of threshold concept to watershed planning concludes that although using one threshold value of impervious surfaces in a watershed to regulate new developments and retrofit old ones is a cost-effective method, a more integrated approach is needed. The use of habitat amount threshold to conserve species promotes proactive planning that would prioritize areas for protection before the threshold is reached and would restore habitat based on the threshold target. However, species-specific data to decide on the threshold is often lacking, and the identification of thresholds is not straightforward. Nonetheless, the concept of threshold is appealing for proactive planning and significant in managing social–ecological systems for resilience.