Plant species richness–productivity relationships in a low-productive boreal region

Local species richness–productivity (SR–P) relationship is usually reported as unimodal if long productivity gradients are sampled. However, it tends to be monotonically increasing in low-productive environments due to the decreasing part of the SR–P curve being truncated. Previous work indicated that this can hold true for forest herb layers, because of an upper bound on productivity caused mainly by canopy shading. Here, we ask whether the same pattern exists in a region with an upper bound on productivity caused by a harsh climate. We sampled herbaceous vegetation of boreal forests and grasslands in a low-productive region of central Yakutia (NE Siberia) with dry and winter-cool continental climate. We collected data on species composition, herb-layer productivity (aboveground herbaceous biomass), soil chemistry and light availability. We applied regression models to discriminate between monotonically increasing, decreasing and unimodal responses of herb-layer species richness to measured variables and analysed trends in the species-pool size and beta diversity along the productivity gradient. Our expectation of the monotonically increasing SR–P relationship was confirmed for neither forest herb layers nor grasslands. In the forest herb layers, no relationship was detected. In grasslands, the relationship was unimodal with species richness decline starting at much lower productivity levels than in more productive temperate grasslands. Potential causes for this decline are either limitation of local species richness by the species pool, which contains few species adapted to more productive habitats, or competitive exclusion, which can become an important control of species richness under lower levels of productivity than is the case in temperate grasslands.     

Targeting CD44-STAT3 Signaling by Gemini Vitamin D Analog Leads to Inhibition of Invasion in Basal-Like Breast Cancer

Background

CD44, a transmembrane glycoprotein, is a major receptor for extracellular proteins involved in invasion and metastasis of human cancers. We have previously demonstrated that the novel Gemini vitamin D analog BXL0124 [1α,25-dihydroxy-20R-21(3-hydroxy-3-deuteromethyl-4,4,4-trideuterobutyl)-23-yne-26,27-hexafluro-cholecalciferol] repressed CD44 expression in MCF10DCIS.com basal-like human breast cancer cells and inhibited MCF10DCIS xenograft tumor growth. In the present study, we investigated potential factors downstream of CD44 and the biological role of CD44 repression by BXL0124 in MCF10DCIS cells.

Methods and Findings

The treatment with Gemini vitamin D BXL0124 decreased CD44 protein level, suppressed STAT3 signaling, and inhibited invasion and proliferation of MCF10DCIS cells. The interaction between CD44 and STAT3 was determined by co-immunoprecipitation. CD44 forms a complex with STAT3 and Janus kinase 2 (JAK2) to activate STAT3 signaling, which was inhibited by BXL0124 in MCF10DCIS cells. The role of CD44 in STAT3 signaling and invasion of MCF10DCIS cells was further determined by the knockdown of CD44 using small hairpin RNA in vitro and in vivo. MCF10DCIS cell invasion was markedly decreased by the knockdown of CD44 in vitro. The knockdown of CD44 also significantly decreased mRNA expression levels of invasion markers, matrix metalloproteinases (MMPs) and urokinase plasminogen activator (uPA), in MCF10DCIS cells. In MCF10DCIS xenograft tumors, CD44 knockdown decreased tumor size and weight as well as invasion markers.

Conclusions

The present study identifies STAT3 as an important signaling molecule interacting with CD44 and demonstrates the essential role of CD44-STAT3 signaling in breast cancer invasion. It also suggests that repression of CD44-STAT3 signaling is a key molecular mechanism in the inhibition of breast cancer invasion by the Gemini vitamin D analog BXL0124.     

Postgwas: Advanced GWAS Interpretation in R

We present a comprehensive toolkit for post-processing, visualization and advanced analysis of GWAS results. In the spirit of comparable tools for gene-expression analysis, we attempt to unify and simplify several procedures that are essential for the interpretation of GWAS results. This includes the generation of advanced Manhattan and regional association plots including rare variant display as well as novel interaction network analysis tools for the investigation of systems-biology aspects. Our package supports virtually all model organisms and represents the first cohesive implementation of such tools for the popular language R. Previous software of that range is dispersed over a wide range of platforms and mostly not adaptable for custom work pipelines. We demonstrate the utility of this package by providing an example workflow on a publicly available dataset.     

Amyloid aggregation of lysozyme: The synergy study of red wine polyphenols

The amyloidoses are diseases associated with nonnative folding of proteins and characterized by the presence of protein amyloid aggregates. The ability of quercetin, resveratrol, caffeic acid, and their equimolar mixtures to affect amyloid aggregation of hen egg white lysozyme in vitro was detected by Thioflavin T fluorescence assay. The anti‐amyloid activities of tested polyphenols were evaluated by the median depolymerization concentrations DC₅₀ and median inhibition concentrations IC₅₀. Single substances are more efficient (by at least one order) in the depolymerization of amyloid aggregates assay than in the inhibition of the amyloid formation with IC₅₀ in 10^?4 to 10^?5M range. Analyzed mixture samples showed synergic or antagonistic effects in both assays. DC₅₀ values ranged from 10^?5 to 10^?8M and IC₅₀ from 10^?5 to 10^?9M, respectively. We observed that certain mixtures of studied polyphenols can synergistically inhibit production of amyloids aggregates and are also effective in depolymerization of the aggregates. Synergic or antagonistic effects of studied mixtures were correlated with protein–small ligand docking studies and AFM results. Differences in these activities could be explained by binding of each polyphenol to a different amino acid sequence within the protein. Our results indicate that synergic/antagonistic anti‐amyloid effects of studied mixtures depend on the selective binding of polyphenols to the known amyloidogenic sequences in the lysozyme chain. Our findings of the effective reduction of amyloid aggregation of lysozyme by polyphenol mixtures in vitro are of the utter physiological relevance considering the bioavailability and low toxicity of tested phenols. Proteins 2013; © 2012 Wiley Periodicals, Inc.     

Exome Sequencing Identifies Mutations in CCDC114 as a Cause of Primary Ciliary Dyskinesia

Primary ciliary dyskinesia (PCD) is a genetically heterogeneous, autosomal-recessive disorder, characterized by oto-sino-pulmonary disease and situs abnormalities. PCD-causing mutations have been identified in 14 genes, but they collectively account for only ∼60% of all PCD. To identify mutations that cause PCD, we performed exome sequencing on six unrelated probands with ciliary outer dynein arm (ODA) defects. Mutations in CCDC114, an ortholog of the Chlamydomonas reinhardtii motility gene DCC2, were identified in a family with two affected siblings. Sanger sequencing of 67 additional individuals with PCD with ODA defects from 58 families revealed CCDC114 mutations in 4 individuals in 3 families. All 6 individuals with CCDC114 mutations had characteristic oto-sino-pulmonary disease, but none had situs abnormalities. In the remaining 5 individuals with PCD who underwent exome sequencing, we identified mutations in two genes (DNAI2, DNAH5) known to cause PCD, including an Ashkenazi Jewish founder mutation in DNAI2. These results revealed that mutations in CCDC114 are a cause of ciliary dysmotility and PCD and further demonstrate the utility of exome sequencing to identify genetic causes in heterogeneous recessive disorders.     

Two Trichosporon species isolated from Central-European mygalomorph spiders (Araneae: Mygalomorphae)

Trichosporon (Dikarya: Basidiomycota) is a genus of anamorphic yeasts typically associated with soil and water, although many species are causative agents of diseases in animals and man. Here we provide the first compelling evidence that spiders can be occasionally colonized by at least two Trichosporon species. Trichosporon dulcitum (Berkhout) Weijman 1979 was isolated from the exoskeleton of purse-web spider Atypus piceus, while Trichosporon porosum (Stautz) Middelhoven, Scorzetti & Fell 2001 was isolated from the exoskeleton of purse-web spider Atypus affinis. Both of the species were identified based on DNA sequence analysis of the host specimens displaying macroscopic signs of the superficial white mycosis on their exoskeleton. Only two specimens with macroscopic signs of superficial yeast growth were identified among the 125 individuals of A. affinis, A. piceus and Atypus muralis examined that were collected at various sites throughout the Czech Republic. The consistent burrow microclimate, uninterrupted occupancy of the single burrow for several subsequent years, and presence of prey remnants in the burrow below the purse-web may play a role in the course of infection of the mygalomorphs examined. The phylogenetic relationships of Trichosporon species are analyzed, concluding that association with invertebrates clusters predominantly among four groups of closely related species in independent Trichosporon clades.     

HLA-C, DRB1 and DQB1 alleles involved in genetic predisposition to psoriasis vulgaris in the Slovak population

Psoriasis vulgaris is a complex chronic skin disease with immunological and genetic background. The most important predisposing genetic factors in psoriasis are genes of the human leukocyte antigen (HLA) region. Accumulative evidence has shown that several HLA alleles are closely associated with psoriasis; however, they tend to vary in different racial and ethnic backgrounds. One hundred forty-seven unrelated Slovak patients with psoriasis vulgaris (average age at onset 28?±?14 years) were genotyped for the HLA-C, DQB1 and DRB1 alleles by the polymerase chain reaction using sequence-specific primers. Allele frequencies observed in the group of psoriatic patients were compared to those obtained in the ethnically matched control group comprising 194 subjects with no history of psoriasis. Susceptibility to psoriasis vulgaris in our study group is significantly associated with HLA-C*06 (odds ratio (OR)?=?3.85), DRB1*07 (OR?=?2.56) and DQB1*02 (OR?=?1.09), respectively, whereas DRB*01 (OR?=?0.05) is associated negatively. Hereby, we provide the first report on the association of HLA-C, DRB1 and DQB1 alleles with psoriasis in the Slovak population. Our findings confirm HLA-C*06 and DRB1*07 as the most important genetic risk factors for psoriasis. However, the role of HLA genes as causative in the pathogenesis of the disease remains unclear. Identification of genetic factors that increase the risk of psoriasis is a precondition that helps to elucidate the pathogenesis of this troubling disease and identify targets for a more specific and effective therapy.