Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1

Methanoculleus marisnigri Romesser et al. 1981 is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain, JR1, was isolated from anoxic sediments of the Black Sea. M. marisnigri is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. marisnigri type strain JR1 and its annotation. This is part of a Joint Genome Institute 2006 Community Sequencing Program to sequence genomes of diverse Archaea.     

Gene selection via the BAHSIC family of algorithms

MOTIVATION: Identifying significant genes among thousands of sequences on a microarray is a central challenge for cancer research in bioinformatics. The ultimate goal is to detect the genes that are involved in disease outbreak and progression. A multitude of methods have been proposed for this task of feature selection, yet the selected gene lists differ greatly between different methods. To accomplish biologically meaningful gene selection from microarray data, we have to understand the theoretical connections and the differences between these methods. In this article, we define a kernel-based framework for feature selection based on the Hilbert-Schmidt independence criterion and backward elimination, called BAHSIC. We show that several well-known feature selectors are instances of BAHSIC, thereby clarifying their relationship. Furthermore, by choosing a different kernel, BAHSIC allows us to easily define novel feature selection algorithms. As a further advantage, feature selection via BAHSIC works directly on multiclass problems. RESULTS: In a broad experimental evaluation, the members of the BAHSIC family reach high levels of accuracy and robustness when compared to other feature selection techniques. Experiments show that features selected with a linear kernel provide the best classification performance in general, but if strong non-linearities are present in the data then non-linear kernels can be more suitable. AVAILABILITY: Accompanying homepage is http://www.dbs.ifi.lmu.de/~borgward/BAHSIC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Rabies in vaccinated raccoons from Ontario, Canada

From 1999 to 2006, 132 cases of raccoon rabies, caused by the raccoon variant of rabies virus, were confirmed in eastern Ontario, Canada. Trap-vaccinate-release (TVR) and point infection control (PIC) programs were implemented to control the disease; 43,014 raccoons (Procyon lotor) were vaccinated against rabies by injection (Imrab3) during that period. Two vaccinated raccoons were diagnosed with rabies at 6 mo and at 2 wk postvaccination. One may have been due to a vaccination failure. The other was likely due to the animal being in the late stages of incubation for rabies at the time of vaccination. This information will be useful to wildlife rehabilitators and agencies that hold raccoons in captivity in that a vaccinated raccoon is not necessarily immune to rabies.     

Structure and secretion of CofJ,a putative colonization factor of enterotoxigenic Escherichia coli

Enterotoxigenic Escherichia coli (ETEC) colonize the human gut, causing severe cholera‐like diarrhoea. ETEC utilize a diverse array of pili and fimbriae for host colonization, including the Type IVb pilus CFA/III. The CFA/III pilus machinery is encoded on the cof operon, which is similar in gene sequence and synteny to the tcp operon that encodes another Type IVb pilus, the Vibrio cholerae toxin co‐regulated pilus (TCP). Both pilus operons possess a syntenic gene encoding a protein of unknown function. In V. cholerae, this protein, TcpF, is a critical colonization factor secreted by the TCP apparatus. Here we show that the corresponding ETEC protein, CofJ, is a soluble protein secreted via the CFA/III apparatus. We present a 2.6 Å resolution crystal structure of CofJ, revealing a large β‐sandwich protein that bears no sequence or structural homology to TcpF. CofJ has a cluster of exposed hydrophobic side‐chains at one end and structural homology to the pore‐forming proteins perfringolysin O and α‐haemolysin. CofJ binds to lipid vesicles and epithelial cells, suggesting a role in membrane attachment during ETEC colonization.     

Simulated warming does not impair seedling survival and growth of Nothofagus pumilio in the southern Andes

It has been predicted that subalpine forests will be negatively affected by global warming; however, direct responses to experimental warming have been scarcely examined in these systems. In this study we evaluated the effects of higher temperatures with and without water addition on the survival and growth of recently emerged (small) and large seedlings of the widely distributed species Nothofagus pumilio in subalpine forests of the southern Chilean Andes. We also examined the variations in seedling traits related to carbon balance in order to infer the causal mechanisms of survival and growth responses. Treatments of open top chambers (OTCs) were combined with watering in two locations with differing climates: Antillanca (40°S, humid) and Cerro Castillo (46°S, drier). OTCs increased mean and maximum air temperatures by 0.6 °C and 2–3 °C, respectively, and decreased soil humidity by 56% in Antillanca and 30% in Cerro Castillo, fulfilling methodological expectations and climate model predictions. After two complete growing seasons, the survival, relative growth rate (RGR), biomass, and a suite of seedling traits were measured and analyzed using mixed-effects models. Warming and warming in combination with watering significantly increased large seedling survival in Cerro Castillo. In Antillanca, warmer conditions increased the height, biomass, and leaf area of small seedlings, and the RGR of large seedlings. In this location, warming also caused lower leaf carbon isotopic composition in both age classes and higher specific leaf area in small seedlings, suggesting whole-plant carbon gain improvements; warming did not produce any drought effects. Our results indicate that warming produces positive effects on the seedling establishment of N. pumilio in the southern Andes, highlighting the importance of site-specific effects in response to climate change in widespread species. Site-specific effects can most likely explain the discrepancies between the results of this study and the predictions outlined by previous studies for these forests.     

The Cytochrome b5 Tail Anchors and Stabilizes Subdomains of Human DNA Topoisomerase IIα in the Cytoplasm of Retrovirally Infected Mammalian Cells

DNA topoisomerase II (topo II) is the target of many anticancer drugs and is often altered in drug-resistant cell lines. In some tumor cell lines truncated isoforms of topo IIα are localized to the cytoplasm. To study the localization and function of individual enzyme domains, we have epitope-tagged several fragments of human topo IIα and expressed them by retroviral infection of rodent and human cells. We find that fusion of the topo II fragments to the hydrophobic tail of human liver cytochrome b₅ anchors the fusion protein to the outer face of cytoplasmic membranes, as determined by colocalization with calnexin and selective detergent permeabilization. Moreover, whereas the minimal ATPase domain (aa 1–266) is weakly and diffusely expressed, addition of the cytb₅ anchor (1–266-b₅) increases its steady-state level 16-fold with no apparent toxicity. Similar results are obtained with the complete ATPase domain (aa 1–426). A C-terminal domain (aa 1030–1504) of human topo IIα containing an intact dimerization motif is stably expressed and accumulates in the nucleus. Fusion to the cytb₅ anchor counteracts the nuclear localization signal and relocalizes the protein to cytoplasmic membranes. In conclusion, we describe a technique that stabilizes and targets retrovirally expressed proteins such that they are exposed on the cytoplasmic surface of cellular membranes. This approach may be of general use for regulating the nuclear accumulation of drugs or proteins in living cells.