Identification and Characterization of Bmi-1-responding Element within the Human p16 Promoter

Bmi-1, the first functionally identified polycomb gene family member, plays critical roles in cell cycle regulation, cell immortalization, and cell senescence. Bmi-1 is involved in the development and progression of carcinomas and is a potent target for cancer therapy. One important pathway regulated by Bmi-1 is that involving two cyclin-dependent kinase inhibitors, p16^Ink4a and p19^Arf, as Bmi-1 represses the INK4a locus on which they are encoded. A close correlation between the up-regulation of Bmi-1 and down-regulation of p16 has been demonstrated in various tumors; however, how Bmi-1 regulates p16 expression is not clear. In this study, we revealed that Bmi-1 regulates the expression of p16 by binding directly to the Bmi-1-responding element (BRE) within the p16 promoter. The BRE resided at bp −821 to −732 upstream of the p16 ATG codon. BRE alone was sufficient to allow Bmi-1-mediated regulation of the CMV promoter. Bmi-1 typically functions by forming a complex with Ring2; however, regulation of p16 was independent of Ring2. Chromatin immunoprecipitation sequencing of Bmi-1-precipitated chromatin DNA revealed that 1536 genes were targeted by Bmi-1, including genes involved in tissue-specific differentiation, cell cycle, and apoptosis. By analyzing the binding sequences of these genes, we found two highly conserved Bmi-1-binding motifs, which were required for Bmi-1-mediated p16 promoter regulation. Taken together, our results revealed the molecular mechanism of Bmi-1-mediated regulation of the p16 gene, thus providing further insights into the functions of Bmi-1 as well as a sensitive high-throughput platform with which to screen Bmi-1-targeted small molecules for cancer therapy.     

The nuclear cofactor DOR regulates autophagy in mammalian and Drosophila cells

The regulation of autophagy in metazoans is only partly understood, and there is a need to identify the proteins that control this process. The diabetes‐ and obesity‐regulated gene (DOR), a recently reported nuclear cofactor of thyroid hormone receptors, is expressed abundantly in metabolically active tissues such as muscle. Here, we show that DOR shuttles between the nucleus and the cytoplasm, depending on cellular stress conditions, and re‐localizes to autophagosomes on autophagy activation. We demonstrate that DOR interacts physically with autophagic proteins Golgi‐associated ATPase enhancer of 16 kDa (GATE16) and microtubule‐associated protein 1A/1B‐light chain 3. Gain‐of‐function and loss‐of‐function studies indicate that DOR stimulates autophagosome formation and accelerates the degradation of stable proteins. CG11347, the DOR Drosophila homologue, has been predicted to interact with the Drosophila Atg8 homologues, which suggests functional conservation in autophagy. Flies lacking CG11347 show reduced autophagy in the fat body during pupal development. All together, our data indicate that DOR regulates autophagosome formation and protein degradation in mammalian and Drosophila cells.     

Bursaphelenchus anatolius n. sp. (Nematoda: Parasitaphelenchidae), an Associate of Bees in the Genus Halictus

Bursaphelenchus anatolius n. sp., a phoretic associate of Halictus bees from Ankara, Turkey, is described and illustrated. Bursaphelenchus anatolius n. sp. is closest to B. kevini, which is phoretically associated with Halictus bees from the Pacific Northwest. Bursaphelenchus anatolius n. sp. and B. kevini appear to be sister taxa based upon several shared morphological features, similar life histories involving phoresy with soil-dwelling Halictus bees, and molecular analysis of the near-full-length small subunit rDNA, D2D3 expansion segments of the large subunit rDNA, and partial mitochondrial DNA COI. Bursaphelenchus anatolius n. sp. can be differentiated from all other species of Bursaphelenchus based upon spicule morphology. The paired spicules are uniquely shaped and ventrally recurved, and both B. anatolius n. sp. and B. kevini possess extending flaps that open when the spicules are protracted beyond the cloaca. Population growth of B. anatolius n. sp. was measured at 23 °C in the laboratory on cultures of the fungus Monilinia fructicola grown on lactic acid-treated, 5% glycerol-supplemented potato dextrose agar. Nematode population densities rapidly increased from 110 to about 110,000/9-cm-diam. dish within 21 days.     

Comparative Analysis of the Ribosomal Componentsof the Hydrogenosome-Containing Protist, Trichomonas vaginalis

The ribosomes of the amitochondriate but hydrogenosome-containing protist lineage, the trichomonads, have previously been reported to be prokaryotic or primitive eukaryotic, based on evidence that they have a 70S sedimentation coefficient and a small number of proteins, similar to prokaryotic ribosomes. In order to determine whether the components of the trichomonad ribosome indeed differ from those of typical eukaryotic ribosomes, the ribosome of a representative trichomonad, Trichomonas vaginalis, was characterized. The sedimentation coefficient of the T. vaginalis ribosome was smaller than that of Saccharomyces cerevisiae and larger than that of Escherichia coli. Based on two-dimensional PAGE analysis, the number of different ribosomal proteins was estimated to be approximately 80. This number is the same as those obtained for typical eukaryotes (approximately 80) but larger than that of E. coli (approximately 55). N-Terminal amino acid sequencing of 18 protein spots and the complete sequences of 4 ribosomal proteins as deduced from their genes revealed these sequences to display typical eukaryotic features. Phylogenetic analyses of the five ribosomal proteins currently available also clearly confirmed that the T. vaginalis sequences are positioned within a eukaryotic clade. Comparison of deduced secondary structure models of the small and large subunit rRNAs of T. vaginalis with those of other eukaryotes revealed that all helices commonly found in typical eukaryotes are present and conserved in T. vaginalis, while variable regions are shortened or lost. These lines of evidence demonstrate that the T. vaginalis ribosome has no prokaryotic or primitive eukaryotic features but is clearly a typical eukaryotic type.     

Phylogenetic characterization of the purple sulfur bacterium Thiocapsa sp. BBS by analysis of the 16S rRNA, cbbL, and nifH genes and its description as Thiocapsa bogorovii sp. nov., a new species

Strain BBS, the purple sulfur bacterium assigned initially to the species Thiocapsa roseopersicina, is the best studied representative of this species. However, no molecular phylogenetic analysis has been performed to confirm its systematic position. Based on the results of analysis of the sequences of 16S rRNA, cbbL, and nifH genes, DNA-DNA hybridization with the T. roseopersicina type strain, and comparative analysis of the phenotypic characteristics of various species belonging to the genus Thiocapsa, we suggest that strain BBS should be assigned to a new species of the genus Thiocapsa, Thiocapsa bogorovii sp. nov. Original Russian Text ? T.P. Tourova, O.I. Keppen, O.L. Kovaleva, N.V. Slobodova, I.A. Berg, R.N. Ivanovsky, 2009, published in Mikrobiologiya, 2009, Vol. 78, No. 3, pp. 381–392.     

Early succession of bacterial biofilms in paper machines

Formation of biofilms causes severe problems in paper machines, and hence financial costs. It would be preferable to prevent attachment of the primary-colonizing bacteria than to control the growth of secondary communities, which are sheltered by exopolysaccharide slime layers. We have therefore investigated the early succession of paper-machine biofilms by incubating stainless-steel test coupons in the process water-flow lines in two paper machines operating in slightly alkaline conditions in temperatures (45 and 49°C) supporting thermophilic microbes. Microbial succession was profiled using length heterogeneity analysis of PCR-amplified 16S rRNA genes (LH-PCR) and linking the sequence data of the created 16S rRNA gene libraries to the dominant LH-PCR peaks. Although the bacterial fingerprints obtained from the attached surface communities varied slightly in different samples, the biomarker signals of the dominating primary-colonizing bacterial groups remained high over time in each paper machine. Most of the 16S rRNA gene copies in the early biofilms were assigned to the genera Rhodobacter, Tepidimonas, and Cloacibacterium. The dominance of these sequence types decreased in the developing biofilms. Finally, as phylogenetically identical primary-colonizers were detected in the two different paper mills, the machines evidently had similar environmental conditions for bacterial growth and potentially a common source of contamination.     

Synopsis of a new collection of sea spiders (Arthropoda: Pycnogonida) from the Ross Sea,Antarctica

The biodiversity research expedition TAN0204 with RS Tangaroa to the Ross Sea in 2004 yielded a new collection of 2,687 specimens of pycnogonids. As much as 25 different species encompassing 14 genera and eight families were identified and their records are discussed herein. The collection is archived in the Marine Invertebrate Collection of the New Zealand National Institute of Water and Atmospheric Research (NIWA). The majority (69%) of specimens are from the Nymphon australe group (Nymphonidae), although species richness and abundance varied among the stations sampled. The collection includes several specimens from polymerous taxa; Pentanymphon antarcticum (Nymphonidae), Decolopoda australis (Colossendeidae) and Pentapycnon bouvieri (Pycnogonidae). All species were classified based on morphological characters, and DNA sequences (from the 18S, 12S, 16S and COI regions) for 21 of the representative morphotypes are given. The DNA sequences confirmed the species-level distinctiveness of these morphotypes. No species new to science were identified, although further detailed morphometric and/or molecular analyses may reveal cryptic or sibling species, especially in species such as the highly abundant Nymphon australe group. An erratum to this article can be found at     

Molecular analysis of <Emphasis Type="Italic">Ixodes granulatus</Emphasis>, a possible vector tick for <Emphasis Type="Italic">Borrelia burgdorferi</Emphasis> sensu lato in Taiwan

The genetic identity of Ixodes granulatus ticks was determined for the first time in Taiwan. The phylogenetic relationships were analyzed by comparing the sequences of mitochondrial 16S ribosomal DNA gene obtained from 19 strains of ticks representing seven species of Ixodes and two outgroup species (Rhipicephalus sanguineus and Haemaphysalis inermis). Four major clades could be easily distinguished by neighbour-joining analysis and were congruent by maximum-parsimony method. All these I. granulatus ticks of Taiwan were genetically affiliated to a monophyletic group with highly homogeneous sequences (92.2–99.3% similarity), and can be discriminated from other Ixodes species and other genera of ticks with a sequence divergence ranging from 11.7 to 30.8%. Moreover, intraspecific analysis revealed that two distinct lineages are evident between the same species of I. granulatus ticks collected from Taiwan and Malaysia. Our results demonstrate that all these I. granulatus ticks of Taiwan represent a unique lineage distinct from the common vector ticks (I. ricinus complex) for Borrelia burgdorferi spirochetes.     

牛蛙无乳链球菌病病原的分离鉴定

{{@ convertAbstractHtml(article.abstractinfoCn, "cn")}}       

Widespread desert affiliation of trebouxiophycean algae (Trebouxiophyceae,Chlorophyta) including discovery of three new desert genera

Unlike most other green algae, trebouxiophyceans are predominantly aerophytic and contain many symbiotic representatives. In recent years, a number of new terrestrial trebouxiophycean taxa were described from soils, tree bark, and lichens. The present phylogenetic study reveals three new lineages of free‐living trebouxiophyceans found in North American desert soil crusts and proposes new generic names to accommodate them: Desertella, Eremochloris, and Xerochlorella. This survey of desert isolates also led to discovery of representatives of seven existing genera of trebouxiophyceans. Two of these genera have never been reported to contain desert representatives and one was known previously only from aquatic habitats. Furthermore, we expand the known geographic range of the recently described genus Chloropyrula, heretofore only known from the Ural Mountains. We demonstrate that the diversity of trebouxiophyceans is still underestimated and poorly understood, and that most major trebouxiophycean lineages contain desert‐dwelling taxa.