Temporal area approach for distributional data in biogeography

A structural approach to temporality in distributional data for use in palaeobiogeography is described herein. Pre-established areas in the distributional data matrix are split temporally, allowing a single geographical space to have multiple iterations [e.g. Area A (Lower Devonian), Area A (Middle Devonian)]. The resulting temporal matrix will allow the representation and capture of any differing relationships through time. Designed primarily for Parsimony Analysis of Endemicity (PAE) and biotic similarity analyses, this approach simply structures distributional data within a temporal partition, meaning that numerical methods can be used to assess relationships between areas to find a branching diagram. Created through the application of the temporal matrix to a given analysis, Temporal Area Approach (TAAp) is a structural approach that facilitates exploration of the data rather than being a hypothesis-driven model following analysis. Understanding the behaviour of non-phylogenetic palaeobiogeographical data and reducing the prevalence of temporal artefacts will lead to more robust area classifications.     

Exotic flagellates of coastal North Sea waters

Flagellate species have been shown to survive transocean passage by ballast water and the large dinoflagellateGymnodinium catenatum was introduced from Japanese to Tasmanian waters in this way.Gymnodinium mikimotoi—better known asGyrodinium aureolum—andFibrocapsa japonica as well asAlexandrium leeii are good candidates to have been introduced recently. Species which seem to have been introduced recently into the North Sea but apparently are transported from adjacent seas by currents into the region areGymnodinium chlorophorum andAlexandrium minutum. Species reported as introduced due to misidentifications areGymnodinium catenatum andLepidodinium viride. Under other names the speciesProrocentrum minimum, Prorocentrum redfieldii, andHeterosigma akashiwo have been known for a long time in the North Sea. The recent reports of threeChattonella species may be either due to introduction or they have been overlooked. The reasons why the introduction of flagellates into coastal North Sea waters is difficult to prove will be discussed.     

Recent methodological advances in the analysis of nitrite in the human circulation: nitrite as a biochemical parameter of the L-arginine/NO pathway

Nitric oxide (NO) plays a pivotal role in the modulation of multiple physiological processes. It acts as a messenger molecule within the cardiovascular system. NO is a highly unstable free radical in circulating blood and is oxidized rapidly to nitrite and nitrate. Recent studies suggest that nitrite has the potential to function as a surrogate of NO production under physiological and pathophysiological conditions and could therefore be of high relevance as a biochemical parameter in experimental and clinical studies. Under hypoxic conditions nitrite is reduced to bioactive NO by deoxyhemoglobin. This mechanism may represent a dynamic cycle of NO generation to adapt the demand and supply for the vascular system. Because of these potential biological functions the concentration of nitrite in blood is thought to be of particular importance. The determination of nitrite in biological matrices represents a considerable analytical challenge. Methodological problems often arise from pre-analytical sample preparation, sample contamination due to the ubiquity of nitrite, and from lack of selectivity and sensitivity. These analytical difficulties may be a plausible explanation for reported highly diverging concentrations of nitrite in the human circulation. The aim of this article is to review the methods of quantitative analysis of nitrite in the human circulation, notably in plasma and blood, and to discuss pre-analytical and analytical factors potentially affecting accurate quantification of nitrite in these human fluids.     

Inhibition of apoptosis prevents West Nile virus induced cell death

Background  

West Nile virus (WNV) infection can cause severe meningitis and encephalitis in humans. Apoptosis was recently shown to contribute to the pathogenesis of WNV encephalitis. Here, we used WNV-infected glioma cells to study WNV-replication and WNV-induced apoptosis in human brain-derived cells.     

Importance of tRNA interactions with 23S rRNA for peptide bond formation on the ribosome: studies with substrate analogs

The major enzymatic activity of the ribosome is the catalysis of peptide bond formation. The active site -- the peptidyl transferase center -- is composed of ribosomal RNA (rRNA), and interactions between rRNA and the reactants, peptidyl-tRNA and aminoacyl-tRNA, are crucial for the reaction to proceed rapidly and efficiently. Here, we describe the influence of rRNA interactions with cytidine residues in A-site substrate analogs (C-puromycin or CC-puromycin), mimicking C74 and C75 of tRNA on the reaction. Base-pairing of C75 with G2553 of 23S rRNA accelerates peptide bond formation, presumably by stabilizing the peptidyl transferase center in its productive conformation. When C74 is also present in the substrate analog, the reaction is slowed down considerably, indicating a slow step in substrate binding to the active site, which limits the reaction rate. The tRNA-rRNA interactions lead to a robust reaction that is insensitive to pH changes or base substitutions in 23S rRNA at the active site of the ribosome.     

The von Hippel-Lindau tumor suppressor protein controls ciliogenesis by orienting microtubule growth

Cilia are specialized organelles that play an important role in several biological processes, including mechanosensation, photoperception, and osmosignaling. Mutations in proteins localized to cilia have been implicated in a growing number of human diseases. In this study, we demonstrate that the von Hippel-Lindau (VHL) protein (pVHL) is a ciliary protein that controls ciliogenesis in kidney cells. Knockdown of pVHL impeded the formation of cilia in mouse inner medullary collecting duct 3 kidney cells, whereas the expression of pVHL in VHL-negative renal cancer cells rescued the ciliogenesis defect. Using green fluorescent protein-tagged end-binding protein 1 to label microtubule plus ends, we found that pVHL does not affect the microtubule growth rate but is needed to orient the growth of microtubules toward the cell periphery, a prerequisite for the formation of cilia. Furthermore, pVHL interacts with the Par3-Par6-atypical PKC complex, suggesting a mechanism for linking polarity pathways to microtubule capture and ciliogenesis.     

Trinucleosome compaction studied by fluorescence energy transfer and scanning force microscopy

The effect of the salt concentration, linker histone H1, and histone acetylation on the structure of trinucleosomes reconstituted on a 608 bp DNA containing one centered nucleosome positioning signal was studied. Fluorescence resonance energy transfer (FRET) in solution and scanning force microscopy (SFM) measurements in liquid were done on the same samples. The distance between the DNA ends decreases under the effect of an increasing salt concentration and also by the incorporation of the H1 linker histone. A decrease of internucleosomal center-to-center (cc) distances by H1 was observed that was limited to a minimal value of about 20 nm. The distribution of the angle formed between consecutive nucleosomes was narrowed by H1. The effect of acetylation of all histones leads to decompaction, measured as an increased distance between the DNA ends, and also increased the internucleosomal distances. Selective acetylation of histone H4, however, compacts the structure as measured by FRET.     

The Hepatitis C Virus Non-structural NS5A Protein Impairs Both the Innate and Adaptive Hepatic Immune Response in Vivo

The role of hepatitis C virus (HCV) protein non-structural (NS) 5A in HCV-associated pathogenesis is still enigmatic. To investigate the in vivo role of NS5A for viral persistence and virus-associated pathogenesis a transgenic (Tg) mouse model was established. Mice with liver-targeted NS5A transgene expression were generated using the albumin promoter. Alterations in the hepatic immune response were determined by Western blot, infection by lymphocytic choriomeningitis virus (LCMV), and using transient NS3/4A Tg mice generated by hydrodynamic injection. Cytotoxic T lymphocyte (CTL) activity was investigated by the Cr-release assay. The stable NS5A Tg mice did not reveal signs of spontaneous liver disease. The intrahepatic immunity was disrupted in the NS5A Tg mice as determined by clearance of LCMV infection or transiently NS3/4A Tg hepatocytes in vivo. This impaired immunity was explained by a reduced induction of interferon β, 2′,5′-OAS, and PKR after LCMV infection and an impairment of the CTL-mediated elimination of NS3-expressing hepatocytes. In conclusion, these data indicate that in the present transgenic mouse model, NS5A does not cause spontaneous liver disease. However, we discovered that NS5A could impair both the innate and the adaptive immune response to promote chronic HCV infection.Chronic hepatitis C virus (HCV)⁴ infection is associated with an increased risk of liver cirrhosis and hepatocellular carcinoma (HCC). The HCV genome is a single-stranded positive-sense RNA molecule of ∼9600 bp (1). The viral RNA codes for one large polyprotein of ∼3100 amino acids that is post-translationally processed by cellular and viral proteases, leading to the structural proteins core, E1 and E2, the p7 protein, and the non-structural proteins NS2, NS3, NS4A, NS4B, NS5A, and NS5B (2). The mature NS5A protein is generated by the action of the NS3/NS4A serine protease. NS5A is a phosphoprotein that exists in a basal or in a hyperphosphorylated state (p56 and p58) (3). Through an amphipathic α-helix, NS5A is associated with the cytoplasmic face of the ER (4) and is an integral part of the replication complex (5). Mutations in NS5A affect the rate of HCV replication suggesting a role of NS5A in modulating viral expression and replication (6). Moreover, NS5A is able to interfere with a variety of cellular proteins. Some of these interaction partners, such as Grb2, PI3K, p53, or Raf-1 are important key players in host cell signal transduction, enabling NS5A to deregulate important cellular check points (7–10). Recent reports even suggest that NS5A may deregulate cell cycle progression by modulating the expression of cell cycle regulatory genes (11). In light of these observations and that it has been suggested to transform murine fibroblasts (12), it is speculated that NS5A could represent an important factor for the development of HCV-associated HCC (13).Infection of transgenic mice expressing the complete HCV polyprotein with lymphocytic choriomeningitis virus (LCMV) showed a reduced IFN response and a delayed viral elimination (14). Cell culture-based experiments have shown that NS5A interacts directly with the interferon-dependent induced protein kinase R (PKR), a key player in the cellular antiviral response and that this interaction results in an inhibition of PKR function (15). Therefore, a role of NS5A for the establishment of a chronic HCV infection by inhibiting the innate immunity is conceivable.To enable in vivo studies of NS5A-specific effects transgenic mice were generated with a liver-specific expression of NS5A. We used these mice to show that NS5A affects both the innate and the adaptive hepatic immunity.