<Emphasis Type="Italic">Nonomuraea aegyptia</Emphasis> sp. nov., a novel actinomycete isolated from a sand dune

The taxonomic position of an unknown actinomycete isolated from a sand dune soil sample collected at Borg El-Arab in Egypt was established using a combination of genotypic and phenotypic data. Isolate S136(T) had chemotaxonomic and morphological properties consistent with its classification in the genus Nonomuraea and formed a distinct phyletic line in the Nonomuraea 16S rRNA gene tree. It was most closely related to the type strains of Nonomuraea helvata, Nonomuraea kuesteri and Nonomuraea turkmeniaca, sharing 16S rRNA gene similarities with these species of 97.1, 97.2 and 97.3%, respectively. The organism was distinguished from representatives of validly described Nonomuraea species using a range of phenotypic properties. It is apparent that the isolate belongs to a novel Nonomuraea species. The name proposed for this taxon is Nonomuraea aegyptia sp. nov., the type strain is S136(T) (=CGMCC 4.2054(T) = DSM 45082(T)).     

An efficient in vitro propagation protocol for <Emphasis Type="Italic">Pinguicula lusitanica</Emphasis>, a rare insectivorous plant

In this study, an efficient protocol was developed for in vitro propagation of Pinguicula lusitanica L., a rare insectivorous plant with pharmacological value and limited reproductive capacity. The effects of two concentrations (0.1 and 0.5 mg l⁻¹) of a range of plant growth regulators, including cytokinins (BA, KIN, and ZEA) and auxins (IAA, IBA, and NAA), and three concentrations of MS medium macronutrients (total, 1/2 and 1/4MS) on proliferation and rooting, were investigated. P. lusitanica shoots showed abundant proliferation and rooting capacity, both of which were significantly influenced by MS medium strength. The use of 1/2MS supplemented with 0.5 mg l⁻¹ BA or KIN ensure a 29-fold rate of proliferation. Best rooting frequency and higher root number and length were attained in 1/4MS medium containing 0.2 mg l⁻¹ IAA. Sixty percent of the plantlets were successfully acclimatized to ex vitro conditions, exhibiting normal development. These plantlets can be used to replenish declining populations in the wild and/or for the extraction of bioactive compounds, reducing pressure on wild stocks.     

Genetic map of artichoke × wild cardoon: toward a consensus map for <Emphasis Type="Italic">Cynara cardunculus</Emphasis>

An integrated consensus linkage map is proposed for globe artichoke. Maternal and paternal genetic maps were constructed on the basis of an F₁ progeny derived from crossing an artichoke genotype (Mola) with its progenitor, the wild cardoon (Tolfa), using EST-derived SSRs, genomic SSRs, AFLPs, ten genes, and two morphological traits. For most genes, mainly belonging to the chlorogenic acid pathway, new markers were developed. Five of these were SNP markers analyzed through high-resolution melt technology. From the maternal (Mola) and paternal (Tolfa) maps, an integrated map was obtained, containing 337 molecular and one morphological markers ordered in 17 linkage groups (LGs), linked between Mola and Tolfa. The integrated map covers 1,488.8 cM, with an average distance of 4.4 cM between markers. The map was aligned with already existing maps for artichoke, and 12 LGs were linked via 31 bridge markers. LG numbering has been proposed. A total of 124 EST-SSRs and two genes were mapped here for the first time, providing a framework for the construction of a functional map in artichoke. The establishment of a consensus map represents a necessary condition to plan a complete sequencing of the globe artichoke genome.     

MMP-2 −1306C > T polymorphism in breast cancer: a case–control study in a South European population

This case control study aims to investigate the role of MMP-2 ?1306C > T polymorphism as a potential risk factor and possible prognostic marker for breast cancer in a South European population. 113 consecutive incident cases of histologically confirmed ductal breast cancer and 124 healthy controls were recruited. MMP-2 ?1306C > T polymorphism was genotyped; multivariate logistic regression as well as Cox regression analysis were performed. MMP-2 ?1306C > T status was not associated with breast cancer risk either at the total sample or at the subanalyses on premenopausal and postmenopausal women. At the survival analysis, a trend towards a favorable association between MMP-2 ?1306C > T allele and disease-free survival as well as overall survival was observed. Regarding subanalyses on ER-negative and ER-positive cases, the favorable association implicating MMP-2 ?1306C > T allele was particularly evident among ER-positive cases; no significant associations emerged among ER-negative cases. MMP-2 ?1306C > T polymorphism does not seem to be a risk factor for breast cancer in South European population; however, a trend towards a favorable association with survival has been observed.     

Transgenic expression of the von Willebrand A domain of the BONZAI 1/COPINE 1 protein triggers a lesion-mimic phenotype in<Emphasis Type="Italic"> Arabidopsis</Emphasis>

The copines are a newly identified, widely distributed class of Ca²⁺-dependent, phospholipid-binding proteins that may be involved in cellular signaling. The copines have a characteristic domain structure: two C2 domains in the N-terminal region and a von Willebrand A (VWA) domain in the C-terminal region. Studies suggest that copines interact with target protein(s) via their VWA domain and recruit the proteins to a membrane location through the activity of the C2 domains. Arabidopsis thaliana (L.) Heynh. plants with loss-of-function mutations in the BONZAI 1/COPINE 1 (BON1/CPN1) gene display aberrant regulation of defense responses, including development of a lesion-mimic phenotype, an accelerated hypersensitive response, and increased resistance to a bacterial and an oomycetous pathogen. The phenotype of mutants in BON1/CPN1 is both humidity- and temperature-sensitive. In this study, we generated transgenic plants expressing either the VWA or the C2 portions of BON1/CPN1 in the wild-type Columbia-0 (Col-0) genetic background. Transgenic plants expressing the BON1/CPN1 C2 domain portion appeared like wild-type plants. However, transgenic plants expressing the BON1/CPN1 VWA domain exhibited a lesion-mimic phenotype that partially phenocopied bon1/cpn1 mutant plants. Our data suggest that BON1/CPN1 VWA domain fragments may interfere with the function of the full-length endogenous BON1/CPN1 protein, possibly by competing with the full-length BON1/CPN1 protein for association with target proteins normally bound to the full-length BON1/CPN1 protein.     

Coherent Infomax as a Computational Goal for Neural Systems

Signal processing in the cerebral cortex is thought to involve a common multi-purpose algorithm embodied in a canonical cortical micro-circuit that is replicated many times over both within and across cortical regions. Operation of this algorithm produces widely distributed but coherent and relevant patterns of activity. The theory of Coherent Infomax provides a formal specification of the objectives of such an algorithm. It also formally derives specifications for both the short-term processing dynamics and for the learning rules whereby the connection strengths between units in the network can be adapted to the environment in which the system finds itself. A central assumption of the theory is that the local processors can combine reliable signal coding with flexible use of those codes because they have two classes of synaptic connection: driving connections which specify the information content of the neural signals, and contextual connections which modulate that signal processing. Here, we make the biological relevance of this theory more explicit by putting more emphasis upon the contextual guidance of ongoing processing, by showing that Coherent Infomax is consistent with a particular Bayesian interpretation for the contextual guidance of learning and processing, by explicitly specifying rules for on-line learning, and by suggesting approximations by which the learning rules can be made computationally feasible within systems composed of very many local processors.     

Longitudinal Data Analysis with Event Time as a Covariate

We consider the estimation of a nonparametric smooth function of some event time in a semiparametric mixed effects model from repeatedly measured data when the event time is subject to right censoring. The within-subject correlation is captured by both cross-sectional and time-dependent random effects, where the latter is modeled by a nonhomogeneous Ornstein–Uhlenbeck stochastic process. When the censoring probability depends on other variables in the model, which often happens in practice, the event time data are not missing completely at random. Hence, the complete case analysis by eliminating all the censored observations may yield biased estimates of the regression parameters including the smooth function of the event time, and is less efficient. To remedy, we derive the likelihood function for the observed data by modeling the event time distribution given other covariates. We propose a two-stage pseudo-likelihood approach for the estimation of model parameters by first plugging an estimator of the conditional event time distribution into the likelihood and then maximizing the resulting pseudo-likelihood function. Empirical evaluation shows that the proposed method yields negligible biases while significantly reduces the estimation variability. This research is motivated by the project of hormone profile estimation around age at the final menstrual period for the cohort of women in the Michigan Bone Health and Metabolism Study.     

Conservation genetic assessment of four plant species in a small replica of a steppe ecosystem &gt;30 years after establishment

To counter species loss living ex situ collections in botanic gardens became important elements of robust conservation programs. Several limitations, problems, and risks associated with living ex situ collections have been reported such as appropriate cultivation management to maintain genetic diversity and stochastic effects in small isolated populations in artificial habitats. However, not all small and isolated populations exhibit these predicted genetic changes. In a multi-species in situ/ex situ comparison of sand dune steppe- and grassland vegetation >30 years after the ex situ population establishment, we compared four different species’ population genetic diversities (Alyssum montanum ssp. gmelinii, Gypsophila fastigiata, Helianthemum nummularium ssp. obscurum, Onosma arenaria) by means of ISSR. We observed different species-specific genetic responses to quite similar abiotic selective forces concerning different neutral genetic diversities of wild versus botanic garden populations. The genetic divergence was kept relatively low in two of the four investigated species between the model steppe plant community within the botanic garden where human interference was kept at a minimum and the wild population. However, the moderate genetic divergence of the two other species kept under the same conditions highlights the importance of species-specific intrinsic responses and stochastic effects to ecosystem changes and provides data on population genetic dynamics in small and isolated populations. This contributes to further improve recommendations on how to best conserve endangered plant species in ex situ environments (cultivation in near nature-like replicas of the original site with as little human inference as possible over only certain periods of time, >30 years).     

Conditions for Global Dynamic Stability of a Class of Resource-Bounded Model Ecosystems

This paper studies a class of dynamical systems that model multi-species ecosystems. These systems are ‘resource bounded’ in the sense that species compete to utilize an underlying limiting resource or substrate. This boundedness means that the relevant state space can be reduced to a simplex, with coordinates representing the proportions of substrate utilized by the various species. If the vector field is inward pointing on the boundary of the simplex, the state space is forward invariant under the system flow, a requirement that can be interpreted as the presence of non-zero exogenous recruitment. We consider conditions under which these model systems have a unique interior equilibrium that is globally asymptotically stable. The systems we consider generalize classical multi-species Lotka–Volterra systems, the behaviour of which is characterized by properties of the community (or interaction) matrix. However, the more general systems considered here are not characterized by a single matrix, but rather a family of matrices. We develop a set of ‘explicit conditions’ on the basis of a notion of ‘uniform diagonal dominance’ for such a family of matrices, that allows us to extract a set of sufficient conditions for global asymptotic stability based on properties of a single, derived matrix. Examples of these explicit conditions are discussed.     

Functional inference of the methylenetetrahydrofolate reductase 677 C > T and 1298A > C polymorphisms from a large-scale epidemiological study

Two functional single nucleotide polymorphisms, 677C > T and 1298A > C have been described for the methylenetetrahydrofolate (MTHFR) gene. Both are associated with reduced enzyme activity in vitro. For the 677T, but not the 1298C allele, significantly lower serum folate and higher plasma total homocysteine (tHcy) have been reported. We genotyped 10,034 middle-aged (50–64 years old) subjects and measured serum folate and tHcy. Within strata of 677 genotypes, 1,298 genotypes had significantly different serum folate and tHcy (P ≤ 0.03 for all comparisons). Each additional 1298C allele reduced mean serum folate and increased mean tHcy, by (on average) 4.5 and 3.0%, respectively. In comparison, within strata of 1,298 genotypes, the increase from no, to one 677T-allele reduced serum folate and increased tHcy by, 7.1 and 6.3%, respectively. Lowest serum folate and highest tHcy level was found for the 677TT/1298AA genotype. The difference in tHcy was significantly larger at low folate than at high folate when genotypes 677TT/1298AA and 677CT/1298AA, 677CT/1298AC and 677CC/1298AC, and genotypes 677CT/1298AC and 677CT/1298AA were compared. We interpreted these data in the context of a model of the MTHFR enzyme that describes the enzyme as a dimer that mainly exist in six different configurations. The model reconciled the observed phenotypic effects of the 677/1,298 combination genotypes with previous in vitro measurements, and identified enzyme configurations that are sensitive to low folate levels. In conclusion, this report demonstrates functional inference of the MTHFR 677 C > T and 1,298 A > C polymorphisms from a large-scale epidemiological study.     

Workload characterization in a high-energy data grid and impact on resource management

The analysis of data usage in a large set of real traces from a high-energy physics collaboration revealed the existence of an emergent grouping of files that we coined “filecules”. This paper presents the benefits of using this file grouping for prestaging data and compares it with previously proposed file grouping techniques along a range of performance metrics. Our experiments with real workloads demonstrate that filecule grouping is a reliable and useful abstraction for data management in science Grids; that preserving time locality for data prestaging is highly recommended; that job reordering with respect to data availability has significant impact on throughput; and finally, that a relatively short history of traces is a good predictor for filecule grouping. Our experimental results provide lessons for workload modeling and suggest design guidelines for data management in data-intensive resource-sharing environments.

Quantitative trait loci for porcine baseline erythroid traits at three growth ages in a White Duroc × Erhualian F<Subscript>2</Subscript> resource population

Baseline erythroid indices are increasingly involved as risk factors for common complex diseases in humans. However, little is known about the genetic architecture of baseline erythroid traits in pigs. In this study, hematocrit (Hct), hemoglobin (Hgb), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), mean corpuscular volume (MCV), red blood cell (RBC), and red cell distribution width (RDW) were measured in 1420 (day 18), 1410 (day 46), and 1033 (day 240) F(2) pigs from a White Duroc x Erhualian intercross resource population. The entire resource population was genotyped for 183 microsatellite loci across the pig genome, and the quantitative trait loci (QTL) analysis was performed for all erythroid-related traits measured with QTL Express based on a least-squares method. A total of 101 QTL, including 46 genome-wide significant QTL and 55 chromosome-wide significant QTL, regulating erythroid traits were found on all pig chromosomes (SSC) except for SSC15 and SSC18. The genome-wide significant QTL were mainly localized on SSC1, 7, 8, 10, and X. These results confirmed most of QTL previously identified in the swine. More importantly, this study detected age-specific QTL for baseline erythroid traits in pigs for the first time. Notably, the QTL for MCV and MCH on day 18 on SSC8 with small intervals of 3 and 4 cM, respectively, provided a good starting point for identifying causal genes underlying MCV and MCH in the future.     

C-Terminal 23 kDa polypeptide of soybean Gly m Bd 28 K is a potential allergen

Gly m Bd 28 K is a major soybean (Glycine max Merr.) glycoprotein allergen. It was originally identified as a 28 kDa polypeptide in soybean seed flour. However, the full-length protein is encoded by an open reading frame (ORF) of 473 amino acids, and contains a 23 kDa C-terminal polypeptide of as yet unknown allergenic and structural characteristics. IgE-binding (allergenic potential) of the Gly m Bd 28 K protein including the 23 kDa C-terminal portion as well as shorter fragments derived from the full-length ORF were evaluated using sera from soy-sensitive adults. All of these sera contained IgE that efficiently recognized the C-terminal region. Epitope mapping demonstrated that a dominant linear C-terminal IgE binding epitope resides between residues S256 and A270. Alanine scanning of this dominant epitope indicated that five amino acids, Y260, D261, D262, K264 and D266, contribute most towards IgE-binding. A model based on the structure of the subunit of soybean -conglycinin revealed that Gly m Bd 28 K contains two cupin domains. The dominant epitope is on the edge of the first -sheet of the C-terminal cupin domain and is present on a potentially solvent-accessible loop connecting the two cupin domains. Thus, the C-terminal 23 kDa polypeptide of Gly m Bd 28 K present in soy products is allergenic and apparently contains at least one immunodominant epitope near the edge of a cupin domain. This knowledge could be helpful in the future breeding of hypoallergenic soybeans.Abbreviations Ara h 1 Arachis hypogaea allergen 1 - Ara h 3 Arachis hypogaea allergen 3 - BCA Bicinchoninic acid - Gly m Bd 28 K Glycine max band 28 kDa allergen - Gly m Bd 30 K Glycine max band 30 kDa allergen - Gly m Bd 68 K Glycine max band 68 kDa allergen - IgE Immunoglobulin E     

Allelopathy as a mechanism for the invasion of <Emphasis Type="Italic">Typha angustifolia</Emphasis>

The direct competitive effects of exotic plants on natives are among the leading causes of plant extinctions worldwide. Allelopathy, one type of direct plant competition, has received relatively little research, particularly in aquatic and wetland systems, even though allelopathy can be a potent mechanism through which plant communities are structured. Typha angustifolia (narrow-leaved cattail) is an invasive exotic plant in North America that often forms monocultures in disturbed wetlands and is more invasive than native members of its genus. We tested whether T. angustifolia was allelopathic and whether it produced different biochemicals than a native congener by growing it with the native bulrush Bolboschoenus fluviatilis (river bulrush) in soil with and without activated carbon and by qualitatively and quantitatively comparing soluble phenolics produced in the roots of T. angustifolia and the native Typha latifolia (broad-leaved cattail). T. angustifolia had a strong allelopathic effect on B. fluviatilis, reducing the longest leaf length and root, shoot, and total biomass of B. fluviatilis. When the allelopathy of T. angustifolia was ameliorated by activated carbon, however, longest leaf length, ramet number, root biomass, shoot biomass, and total biomass of T. angustifolia were greatly reduced due to resource competition with B. fluviatilis. Furthermore, T. angustifolia produced different, but not more, soluble phenolics than T. latifolia suggesting that the identity of the phenolics is different between the two species rather than the concentrations. The allelopathic effects of T. angustifolia on a North American native wetland plant and its production of root biochemicals that appear to differ from those produced by a native congener are consistent with the possibility that T. angustifolia may use a novel allelochemical in its invasion of North American wetlands.     

Invasion ecology of quagga mussels (<Emphasis Type="Italic">Dreissena rostriformis bugensis</Emphasis>): a review of evolutionary and phylogenetic impacts

Two invasive freshwater mussels, Dreissena rostriformis bugensis (quagga mussel) and D. polymorpha (zebra mussel), reveal differences in patterns and timing of their invasions in Europe. They belong to different clades in Dreissena phylogenetics: D. rostriformis bugensis genetically is coupled with the brackish water, lacustrine D. r. distincta and the two are believed to represent a single species. As such, the guaqqa mussel has environmental requirements that differ from the congeneric D. polymorpha. D. rostriformis bugensis invasions were confined to reservoirs of the Dnieper, Don and Dniester Rivers of the Black Sea basin. We recorded D. r. bugensis outside the Black Sea basin for the first time between 1992 and 2001, along the Volga River reservoir cascade including the Northern Caspian Sea shallows. This represents a 40-year invasion time lag since an invasion corridor through the Volgo-Don Waterway was established in 1952 (a corridor used extensively by many invertebrate species from the Black Sea region). We attribute the postponed invasion of Europe by D. r. bugensis, including peculiarities in establishment and its absence in fossil records, to its phylogenetically close relationship with D. r. distincta and its recent evolutionary origin. The relatively rapid range expansion of D. r. bugensis in eastern Europe during the past several decades was facilitated by human-mediated ecosystem transformation, notably impoundment of large eastern European rivers, that have allowed this species to utilize newly transformed ecosystems.     

Construction of a Coix BAC library and isolation of the 22 kDa &alpha;-coixin gene cluster

Coix lacryma-jobi L. (Coix) is a close relative of maize and is considered a valuable genetic resource for crop improvement. Here we report the construction of the first Coix bacterial artificial chromosome (BAC) library using accession PI 324059. This BAC library contains about 230?400 clones with an average insert size of 113?kb, has low organellar DNA contamination, and provides 16.3-fold coverage of the genome. The library was stored in 12?× 96 pools that could be screened with a PCR protocol. Library screening was performed for the 22?kDa α-coixin gene family. A total of 57 positive pools were identified, and single clones were isolated from 19 of these pools. Based on DNA fingerprinting and Southern blot analysis, these 19 BAC clones form a single contig of about 340?kb in length, indicating that the 22 kDa α-coixin genes occur in a cluster. These results demonstrated the suitability of this BAC library for gene isolation and comparative genomics studies of the Coix genome.     

Diffusion as a Ruler: Modeling Kinesin Diffusion as a Length Sensor for Intraflagellar Transport

An important question in cell biology is whether cells are able to measure size, either whole cell size or organelle size. Perhaps cells have an internal chemical representation of size that can be used to precisely regulate growth, or perhaps size is just an accident that emerges due to constraint of nutrients. The eukaryotic flagellum is an ideal model for studying size sensing and control because its linear geometry makes it essentially one-dimensional, greatly simplifying mathematical modeling. The assembly of flagella is regulated by intraflagellar transport (IFT), in which kinesin motors carry cargo adaptors for flagellar proteins along the flagellum and then deposit them at the tip, lengthening the flagellum. The rate at which IFT motors are recruited to begin transport into the flagellum is anticorrelated with the flagellar length, implying some kind of communication between the base and the tip and possibly indicating that cells contain some mechanism for measuring flagellar length. Although it is possible to imagine many complex scenarios in which additional signaling molecules sense length and carry feedback signals to the cell body to control IFT, might the already-known components of the IFT system be sufficient to allow length dependence of IFT? Here we investigate a model in which the anterograde kinesin motors unbind after cargo delivery, diffuse back to the base, and are subsequently reused to power entry of new IFT trains into the flagellum. By mathematically modeling and simulating such a system, we are able to show that the diffusion time of the motors can in principle be sufficient to serve as a proxy for length measurement. We found that the diffusion model can not only achieve a stable steady-state length without the addition of any other signaling molecules or pathways, but also is able to produce the anticorrelation between length and IFT recruitment rate that has been observed in quantitative imaging studies.     

Spatiotemporal Dynamics of the Epidemic Transmission in a Predator-Prey System

Epidemic transmission is one of the critical density-dependent mechanisms that affect species viability and dynamics. In a predator-prey system, epidemic transmission can strongly affect the success probability of hunting, especially for social animals. Predators, therefore, will suffer from the positive density-dependence, i.e., Allee effect, due to epidemic transmission in the population. The rate of species contacting the epidemic, especially for those endangered or invasive, has largely increased due to the habitat destruction caused by anthropogenic disturbance. Using ordinary differential equations and cellular automata, we here explored the epidemic transmission in a predator-prey system. Results show that a moderate Allee effect will destabilize the dynamics, but it is not true for the extreme Allee effect (weak or strong). The predator-prey dynamics amazingly stabilize by the extreme Allee effect. Predators suffer the most from the epidemic disease at moderate transmission probability. Counter-intuitively, habitat destruction will benefit the control of the epidemic disease. The demographic stochasticity dramatically influences the spatial distribution of the system. The spatial distribution changes from oil-bubble-like (due to local interaction) to aggregated spatially scattered points (due to local interaction and demographic stochasticity). It indicates the possibility of using human disturbance in habitat as a potential epidemic-control method in conservation.