香姜,越南植物一新记录种（英文）

据已有文献记载,香姜(姜科)(Alpinia coriandriodora D. Fang)仅分布于广西,现首次在越南发现其分布。该种在形态上与竹叶山姜(A. bambusifolia D. Fang)相近,但其叶片椭圆状披针形、唇瓣浅黄色及带红褐色条纹和花药附属体三角状而与后者有别。提供该种详细的形态学描述以及图版,亦包括在越南的分布及生态的资料。凭证标本保存于越南国立自然博物馆(VNMN)和中国科学院华南植物园(IBSC)。     

Sex‐biased transmission of a complex life‐cycle parasite: why males matter

Male‐bias in parasite infection exists in a variety of host–parasite systems, but the epidemiological importance of males and, specifically, whether males are responsible for producing a disproportionate amount of onward transmission events (male‐biased transmission) has seldom been tested. The primary goal of our study was to experimentally test for male‐biased transmission in a system with no sex‐biased prevalence. We performed a longitudinal field experiment and continuously removed intestinal nematode parasites from either male or female white‐footed mice and recorded the subsequent transmission among the untreated sex. We predicted males are responsible for the majority of transmission and female mice would have lower infection prevalence under the male‐anthelmintic treatment than controls and that male mice would experience little or no change in infection prevalence under female‐anthelmintic treatment compared to controls. Our second goal was to evaluate physiological hypotheses relating to the mechanisms that could generate the observed transmission pattern. To that end, we examined a cross‐sectional sample of hosts to explicitly test for differences in parasite intensity, parasite egg shedding rate and reproductive output per parasite between male and female hosts. Removing parasites from male mice resulted in lower infection rates among female mice but, in contrast, there was no effect of female‐deworming on infection rates among male mice; providing evidence that males provide disproportionately greater numbers of transmission events than females. We found no difference in prevalence, intensity, or fecundity of parasites between sexes in the cross‐sectional sample of mice and rejected the mechanistic hypotheses. Without male‐biased prevalence, intensity, or parasite fecundity, we concluded that male‐biased transmission is unlikely to be created via physiological differences and the parsimonious explanation is that male behavior spreads infective stages in a more successful manner. We demonstrate that transmission heterogeneities can exist in the absence of individual heterogeneities in infection.     

Applications of functionalized and nanoparticle-modified nanocrystalline cellulose

Nanocrystalline cellulose (NCC), a rod-shaped nanoscale material with exceptional strength and physicochemical properties, can be prepared from inexpensive renewable biomass. Besides its potential use as a reinforcing agent for industrial biocomposites, pristine NCC exhibits low toxicity and poses no serious environmental concerns, providing impetus for its use in bioapplications. Here, we review recent developments in the use of modified NCC for emerging bioapplications, specifically enzyme immobilization, antimicrobial and medical materials, green catalysis, biosensing and controlled drug delivery. We focus on the modification of NCC with chemical functionalities and inorganic nanoparticles, reviewing practical considerations such as reusability, toxicity and scale-up capability.     

Retrocyclins kill bacilli and germinating spores of Bacillus anthracis and inactivate anthrax lethal toxin

Theta-defensins are cyclic octadecapeptides encoded by the modified alpha-defensin genes of certain nonhuman primates. The recent demonstration that human alpha-defensins could prevent deleterious effects of anthrax lethal toxin in vitro and in vivo led us to examine the effects of theta-defensins on Bacillus anthracis (Sterne). We tested rhesus theta-defensins 1-3, retrocyclins 1-3, and several analogues of RC-1. Low concentrations of theta-defensins not only killed vegetative cells of B. anthracis (Sterne) and rendered their germinating spores nonviable, they also inactivated the enzymatic activity of anthrax lethal factor and protected murine RAW-264.7 cells from lethal toxin, a mixture of lethal factor and protective antigen. Structure-function studies indicated that the cyclic backbone, intramolecular tri-disulfide ladder, and arginine residues of theta-defensins contributed substantially to these protective effects. Surface plasmon resonance studies showed that retrocyclins bound the lethal factor rapidly and with high affinity. Retrocyclin-mediated inhibition of the enzymatic activity of lethal factor increased substantially if the enzyme and peptide were preincubated before substrate was added. The temporal discrepancy between the rapidity of binding and the slowly progressive extent of lethal factor inhibition suggest that post-binding events, perhaps in situ oligomerization, contribute to the antitoxic properties of retrocyclins. Overall, these findings suggest that theta-defensins provide molecular templates that could be used to create novel agents effective against B. anthracis and its toxins.     

Insulin-like growth factor I controls a mutually exclusive association of RACK1 with protein phosphatase 2A and beta1 integrin to promote cell migration

The WD repeat scaffolding protein RACK1 can mediate integration of the insulin-like growth factor I receptor (IGF-IR) and integrin signaling in transformed cells. To address the mechanism of RACK1 function, we searched for regulatory proteins that associate with RACK1 in an IGF-I-dependent manner. The serine threonine phosphatase protein phosphatase 2A (PP2A) was found associated with RACK1 in serum-starved cells, and it dissociated immediately upon stimulation with IGF-I. This dissociation of PP2A from RACK1 and an IGF-I-mediated decrease in cellular PP2A activity did not occur in cells expressing either the serine 1248 or tyrosine 1250/1251 mutants of the IGF-IR that do not interact with RACK1. Recombinant RACK1 could bind to PP2A in vitro and restore phosphatase activity to PP2A from IGF-I-stimulated cells. Ligation of integrins with fibronectin or Matrigel was sufficient to facilitate IGF-I-mediated dissociation of PP2A from RACK1 and also to recruit beta1 integrin as PP2A dissociated. By using TAT-fused N-terminal and C-terminal deletion mutants of RACK1, we determined that both PP2A and beta1 integrin interact in the C terminus of RACK1 within WD repeats 4 to 7. This suggests that integrin ligation displaces PP2A from RACK1. MCF-7 cells overexpressing RACK1 exhibited enhanced motility, which could be reversed by the PP2A inhibitor okadaic acid. Small interfering RNA-mediated suppression of RACK1 also decreased the migratory capacity of DU145 cells. Taken together, our findings indicate that RACK1 enhances IGF-I-mediated cell migration through its ability to exclusively associate with either beta1 integrin or PP2A in a complex at the IGF-IR.     

Association Studies Identify Natural Variation at PHYC Linked to Flowering Time and Morphological Variation in Pearl Millet

The identification of genes selected during and after plant domestication is an important research topic to enhance knowledge on adaptative evolution. Adaptation to different climates was a key factor in the spread of domesticated crops. We conducted a study to identify genes responsible for these adaptations in pearl millet and developed an association framework to identify genetic variations associated with the phenotype in this species. A set of 90 inbred lines genotyped using microsatellite loci and AFLP markers was used. The population structure was assessed using two different Bayesian approaches that allow inbreeding or not. Association studies were performed using a linear mixed model considering both the population structure and familial relationships between inbred lines. We assessed the ability of the method to limit the number of false positive associations on the basis of the two different Bayesian methods, the number of populations considered and different morphological traits while also assessing the power of the methodology to detect given additive effects. Finally, we applied this methodology to a set of eight pearl millet genes homologous to cereal flowering pathway genes. We found significant associations between several polymorphisms of the pearl millet PHYC gene and flowering time, spike length, and stem diameter in the inbred line panel. To validate this association, we performed a second association analysis in a different set of pearl millet individuals from Niger. We confirmed a significant association between genetic variation in this gene and these characters.DOMESTICATION and dispersion of cultivated plants were associated with their adaptation to the agricultural environment. These adaptations led to genetic changes shared by all individuals of a cultivated species (domestication genes) or to variations between varieties within a cultivated species (genes controlling varietal differences). Domestication genes like tb1 (Doebley et al. 1997; Wang et al. 1999) in maize (Zea mays) were selected very early by human populations (Jaenicke-Després et al. 2003). After the first early selection, adaptation of the flowering phenotype to different climatic conditions was certainly a key innovation that enabled colonization of new environments. One of the most well-known examples was the adaptation of maize—a tropical plant—to northern climates. Maize cultivation spread late to northeastern America. By 1000 YBP, only maize was an established staple crop (Fritz 1995). A genetic variant of the Dwarf8 gene led to an earlier flowering phenotype (Thornsberry et al. 2001). This early allele was present at a high frequency in North America and was certainly selected after the domestication of maize under northern climatic conditions (Camus-Kulandaivelu et al. 2006).Pearl millet (Pennisetum glaucum [(L.) R. Br.]), one of the most important West African cereals, was most likely domesticated once in the Sahelian zone of West Africa (Oumar et al. 2008). By 3500 YBP, it was already being cultivated throughout Sahelian and tropical West African countries (D''Andrea et al. 2001; D''Andrea and Casey 2002). The adaptation of pearl millet in West Africa was also associated with an environmental gradient (Haussmann et al. 2006). Pearl millet varieties from tropical coastal West Africa flower very late (up to 160 days from planting to female flowering) as compared to varieties from Sahelian West Africa, which may have a flowering time as short as 45 days (Haussmann et al. 2006). The genetic factors underlying the differences between these varieties are still unknown.Association studies offer new opportunities for assessing the role of a particular gene on a phenotype. Contrary to QTL analysis, association studies have the challenging task of taking an unknown evolutionary history of studied individuals into account. For example, population structure is a common confounding effect in association studies (Pritchard et al. 2000a). Allele frequencies evolve between divergent structured populations via drift, mutation, and selection. Differences in allele frequencies may be correlated with any morphological traits that differentiate two populations. Then a statistical correlation between a gene and a trait is not necessarily associated with a “causative” relationship between the gene and the morphology, which can lead to a high number of false positives. The use of population structure to correct the number of false positives was a significant breakthrough in plant studies (Thornsberry et al. 2001). This approach was recently further refined by also using a matrix of kinship coefficients, which proves efficient when there is a complex structure and familial relationship between individuals (Yu et al. 2006; Kang et al. 2008; Stich et al. 2008). Complex structures and familial relationships are common in inbred cultivated crop material. In the current association study framework (Thornsberry et al. 2001; Yu et al. 2006; Casa et al. 2008; Kang et al. 2008; Stich et al. 2008), population structure was assessed using STRUCTURE software (Pritchard et al. 2000b). This tool is not implemented to deal with selfed inbred materials or inbred species (Pritchard et al. 2000b). Through new methodological developments, population structure analysis can now be performed using Bayesian methods in these particular cases (Gao et al. 2007). The extent to which the power of association studies will differ when dealing with inbred material or selfing species using either Bayesian method has yet to be evaluated.In this study, we developed an association framework for pearl millet to assess the role of flowering pathway genes. We assessed the ability of the method to control the number of false positives, while taking different methodological inferences of population structure that allow inbreeding or not into account. We also assessed the power of the association framework to detect given additive genetic effects. Finally, we applied this method to a set of eight flowering time gene homologs sequenced in pearl millet. We assessed sequence variation in light perception genes (PHYA, PHYB, PHYC, and CRY2) and downstream regulators of flowering (GI, Hd6, Hd1, and FLORICAULA). Variation was detected in the PHYC gene associated with variations in flowering time and morphological traits. This association was noted in two different data sets.     

Is Bagging Effective in the Classification of Small-Sample Genomic and Proteomic Data?

There has been considerable interest recently in the application of bagging in the classification of both gene-expression data and protein-abundance mass spectrometry data. The approach is often justified by the improvement it produces on the performance of unstable, overfitting classification rules under small-sample situations. However, the question of real practical interest is whether the ensemble scheme will improve performance of those classifiers sufficiently to beat the performance of single stable, nonoverfitting classifiers, in the case of small-sample genomic and proteomic data sets. To investigate that question, we conducted a detailed empirical study, using publicly-available data sets from published genomic and proteomic studies. We observed that, under t-test and RELIEF filter-based feature selection, bagging generally does a good job of improving the performance of unstable, overfitting classifiers, such as CART decision trees and neural networks, but that improvement was not sufficient to beat the performance of single stable, nonoverfitting classifiers, such as diagonal and plain linear discriminant analysis, or 3-nearest neighbors. Furthermore, as expected, the ensemble method did not improve the performance of these classifiers significantly. Representative experimental results are presented and discussed in this work.     

Cellular and body scale morphology of Heterocapsa huensis sp. nov. (Peridiniales, Dinophyceae) found in Hue, Vietnam

Cellular and body scale structure of a new armored dinoflagellate Heterocapsa huensis , collected from Hue, Vietnam were investigated. Morphology of motile cell was observed by light, fluorescent and scanning electron microscopy, and body scale structure was examined by whole mounts of transmission electron microscopy. Cells of H. huensis were ellipsoid with a spherical nucleus located in the posterior and multiple pyrenoids located above the nucleus; this arrangement was similar to that of Heterocapsa pygmaea . Transmission electron microscopy revealed ultrastructure of the body scales consisted of a rounded triangular basal plate and three-dimensional ornaments. Structure of the basal plate resembles that of Heterocapsa illdefina ; however, the number of the peripheral spine is different from that of H. illdefina and this structure has never been reported from Heterocapsa species. A new Heterocapsa species, H. huensis Iwataki et Matsuoka sp. nov., is described based on positions of organelles and body scale ultrastructure.     

Homology model of RSK2 N-terminal kinase domain, structure-based identification of novel RSK2 inhibitors, and preliminary common pharmacophore

Ribosomal S6 kinase 2 (RSK2) is a serine/threonine kinase that plays a role in human cancer and Coffin-Lowry syndrome and is comprised of two nonidentical kinase domains, each domain with its own ATP-binding site. RSK2 can be inactivated by different types of small organic molecules. Potent RSK2 inhibitors include the two classic bisindole maleimide PKC inhibitors, Ro31-8220 and GF109203X, and the natural product SL0101 that was shown to bind specifically to the ATP pocket of the N-terminal domain (NTD). In this paper, we present an atomic model of the RSK2 NTD (residues 68-323), which was built to simultaneously bind the distinctive molecular scaffolds of SL0101, Ro31-8220, and GF109203X. The RSK2 NTD model was used to identify two novel RSK2 inhibitors from the National Cancer Institute open chemical repository and to develop a preliminary structure-based pharmacophore model.