Chassalia magnificens sp. nov. and C. chrysoclada comb. nov. (Rubiaceae) from central Africa

Chassalia magnificens, a new species from the Albertine Rift in eastern Democratic Republic of Congo, is described and illustrated. The species is recognised inter alia by its large stipules and montane habitat. Chassalia chrysoclada is a new combination for a widespread, but hitherto overlooked, central African species originally described in the genus Psychotria. Chassalia chrysoclada is related to C. pteropetala (K. Schum.) Cheek but lacks the bicostate twigs and dorsally winged corolla lobes of that species.     

Theoretical and Experimental Investigation of Enhanced Transmission Through Periodic Metal Nanoslits for Sensing in Water Environment

Experimental and theoretical study of sensors based on enhanced transmission through periodic metal nanoslits is presented. Our approach consists of the design of one-dimensional nanoslits array and its application in sensing for water quality control. Rigorous coupled waves analysis was used for the design and fit to the experimental data. Two types of surface plasmon resonance excitations are shown to be possible, one at the upper grating–analyte interface and one at the lower grating–substrate interface. This latter resonance is shown to be affected by the multiple interference or cavity-type effects. Those structures were fabricated by deposition of the metal layer and electron beam lithography of the nanostructure. We found that Ag-based periodic array exhibits the highest sensitivity to refractive index variations. Sensitivity enhancement was measured by ethanol concentrations in water. Stability of the Ag-based sensor was improved by covering the grating with less than 15 nm polymethyl methacrylate capping layer without deterioration of the sensitivity.     

Phylogeography of the cold‐water barnacle Chthamalus challengeri in the north‐western Pacific: effect of past population expansion and contemporary gene flow

Aim Phylogeographical patterns of marine organisms in the north‐western Pacific are shaped by the interaction of past sea‐level fluctuations during glacial maxima and present‐day gene flow. This study examines whether observed population differentiation in the barnacle Chthamalus challengeri, which is endemic to the north‐western Pacific, can be explained by the interactions between historical glacial events and patterns of contemporary gene flow. Location Eleven locations in the north‐western Pacific. Methods Partial sequences of mitochondrial cytochrome c oxidase subunit I (COI), 12S, 16S and nuclear internal transcribed spacer 1 (ITS1) were obtained from 312 individuals. Parsimony haplotype networks and analysis of molecular variance (AMOVA) were used to determine whether the observed genetic structure corresponds to marine provinces (Kuroshio Current and China Sea Coastal Provinces), zoogeographical zones (oriental and Japan warm‐temperate zones) and/or potential refugial areas (Sea of Japan and East China Sea) in the north‐western Pacific. Neutrality tests, mismatch distribution analysis and Bayesian skyline plots were used to infer the demographic history of C. challengeri. Results In total, 312, 117, 182 and 250 sequences were obtained for COI, 12S, 16S and ITS1, respectively. A panmictic population was revealed, which did not conform to the ‘isolation by distance’ model. None of the a priori population groupings based on marine provinces, zoogeographical zones or potential refugial areas was associated with observed genetic patterns. Significant negative values from neutrality tests and the unimodal mismatch distribution and expansion patterns in Bayesian skyline plots for the COI and 16S data sets indicate a population expansion in the mid‐Pleistocene (c. 200 ka). Information from the fossil record suggests that there has been a northward range shift of this species from the East China Sea or the Palaeo‐Pacific coast of Japan to the Sea of Japan since the mid‐Pleistocene. Main conclusions Chthamalus challengeri has experienced a population expansion and range shift since the mid‐Pleistocene. The observed lack of population differentiation can be explained by this past population expansion and present‐day wide‐scale larval dispersal (owing to the long planktonic larval duration) across marine provinces, which have led to the successful establishment of the species in different zoogeographical zones and habitats.     

Genetic variations and treatments that affect the lifespan of the NPC1 mouse

Niemann-Pick type C (NPC) disease is a multisystem disorder caused primarily by a mutation in the npc1 gene. These studies evaluated the effect of genetic background, deletion of additional genes, and administration of several agents on the age at death in a murine model of this disorder. Such factors as differing strain background or genetic drift within a given background in the npc1(-/-) mouse significantly altered the age at death and the degree of organ disease. Genetic deletion of Siat9 (GM3 synthetase) or Nr1h2 [liver X receptor (LXR)beta] shortened the life of the npc1(-/-) animals. Daily treatment of the npc1(-/-) mice with an LXR agonist or administration of a single dose of cyclodextrin, with or without the neurosteroid allopregnanolone, significantly slowed neurodegeneration and increased the lifespan of these animals. These data illustrate that the age at death of the npc1(-/-) mouse can be significantly influenced by many factors, including differences in strain background, other inactivating gene mutations (Siat9 and lxrbeta), and administration of agents such as LXR agonists and, particularly, cyclodextrin. It is currently not clear which of these effects is nonspecific or which might relate directly to the molecular defect present in the NPC1 syndrome.     

Perilipin 2 (PLIN2)-deficiency does not increase cholesterol-induced toxicity in macrophages

Interventions on macrophages/foam cells to redirect intracellular cholesterol towards efflux pathways could become a very valuable addition to our therapeutic arsenal against atherosclerosis. However, certain manipulations of the cholesteryl ester cycle, such as the inhibition of ACAT1, an ER-resident enzyme that re-esterifies cholesterol, are not well tolerated. Previously we showed that targeting perilipin-2 (PLIN2), a major lipid droplet (LD)-associated protein in macrophages, prevents foam cell formation and protects against atherosclerosis. Here we have assessed the tolerance of PLIN2-deficient bone marrow derived macrophages (BMM) to several lipid loading conditions similar to the found during atherosclerosis development, including exposure to modified low-density lipoprotein (mLDL) and 7-ketocholesterol (7-KC), a free cholesterol (FC) metabolite, in media with or without cholesterol acceptors. BMM isolated from mice that do or do not express PLIN2 were tested for apoptosis (TUNEL and cleaved caspase-3), ER stress (CHOP induction and XBP-1 splicing), and inflammation (TNF-α and IL-6 mRNA levels). Like in other cell types, PLIN2 deficiency impairs LD buildup in BMM. However, while most stress parameters were elevated in macrophages under ACAT inhibition and 7-KC loading, PLIN2 inactivation was well tolerated. The data support the safety of targeting PLIN2 to prevent foam cell formation and atherosclerosis.     

A prognostic model for the combined analysis of gene expression profiling in hepatocellular carcinoma

Microarray techniques using cDNA array and comparative genomic hybridization (CGH) have been developed for several discovery applications. They are frequently applied for the prediction and diagnosis of cancer in recent years. Many studies have shown that integrating genomic data from different sources may increase the reliability of gene expression analysis results in understanding cancer progression. Therefore, developing a good prognostic model dealing simultaneously with different types of dataset is important. The challenge with these types of data is high background noise. We describe an analytical two-stage framework with a multi-parallel data analysis method named wavelet-based generalized singular value decomposition and shaving method (WGSVD-shaving). This method is proposed for de-noising and dimension-reduction during early stage prognosis modeling. We also applied a supervised gene clustering technique with penalized logistic regression with Cox-model on an integrated data. We show the accuracy of the method using a simulated dataset with a case study on Hepatocelluar Carcinoma (HCC) cDNA and CGH data. The method shows improved results from GSVD-shaving and has application in the discovery of candidate genes associated with cancer.