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Low Similarity (low + similarity)
Selected AbstractsActive bacterial community structure along vertical redox gradients in Baltic Sea sedimentENVIRONMENTAL MICROBIOLOGY, Issue 8 2008Anna Edlund Summary Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179, ,64 and ,337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labelled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labelled DNA and DNA from reverse transcription polymerase chain reaction showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences, indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths. [source] Proteome-guided search for influenza A B-cell epitopesFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 1 2009Guglielmo Lucchese Abstract The influenza A linear peptide epitopes recognized by murine antibodies, and currently cataloged at http://www.immuneepitope.org, were examined for the identity score to the host mouse proteome. It was found that almost all of the linear viral determinants are (or contain) regions formed by pentapeptide fragments with no or only very low similarity to the murine proteins. The present study adds to previous reports in suggesting a main role of amino acid sequence similarity in the modulation and definition of the B-cell epitope repertoire, inspiring innovative vaccine approaches able to avoid cross-reactive autoimmune collateral phenomena, and addressing future research in the study of immunity against the influenza A virus and infectious diseases in general. [source] Monoclonal and polyclonal humoral immune response to EC HER-2/NEU peptides with low similarity to the host's proteomeINTERNATIONAL JOURNAL OF CANCER, Issue 5 2002Abraham Mittelman Abstract We are studying peptide immunogenicity as a function of the similarity level to the host's proteome. By using as a model the breast/prostate cancer-associated HER-2/neu antigen, we analyzed the monoclonal and polyclonal humoral immune responses against HER-2/neu peptide motifs not shared with the host proteome. We show here that (i) a mouse monoclonal antibody (MAb) raised against the extracellular domain (EC) of human HER-2/neu oncoprotein recognized a linear peptide motif endowed with low similarity level to the mouse proteome; (ii) likewise, human sera from breast/prostate cancer patients preferentially recognized peptide fragments from the EC of the HER-2/neu oncoprotein having sequences that are not present in the human proteome. Together with previous results obtained in other disease models (cervical cancer-associated HPV16 E7 oncoprotein and Pemphigus vulgaris auto-antigen desmoglein-3), the present data suggest that a low level of sequence similarity to the host's proteome might be an important factor in shaping the pool of B cell epitopes. © 2002 Wiley-Liss, Inc. [source] Phylogenetic analysis of intestinal bacteria in the Chinese mitten crab (Eriocheir sinensis)JOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2007K. Li Abstract Aims:, To identify the dominant intestinal bacteria in the Chinese mitten crab, and to investigate the differences in the intestinal bacteria between pond-raised and wild crabs. Methods and Results:, The diversity of intestinal bacteria in the Chinese mitten crabs was investigated by denaturing gradient gel electrophoresis (DGGE) fingerprinting, 16S rRNA gene clone library analysis and real-time quantitative PCR. The principal component analysis of DGGE profiles indicated that substantial intersubject variations existed in intestinal bacteria in pond-raised crab. The sequencing of 16S rRNA genes revealed that 90,95% of the phylotypes in the clone libraries were affiliated with Proteobacteria and Bacteroidetes. Some genera were identified as unique in wild crabs and in pond-raised crabs, whereas Bacteroidetes was found to be common in all sampled crab groups. Real-time quantitative PCR indicated that the abundance of Bacteroides and the total bacterial load were approximately four-to-10 times higher in pond-raised crabs than in wild crabs. A significant portion of the phylotypes shared low similarity with previously sequenced organisms, indicating that the bacteria in the gut of Chinese mitten crabs are yet to be described. Conclusions:, The intestinal bacteria of pond-raised crabs showed higher intersubject variation, total diversity and abundance than that observed in wild crabs. The high proportion of the clones of Proteobacteria and Bacteroidetes in the clone library is an indication that these bacteria may be the dominant population in the gut of the Chinese mitten crab. Significance and Impact of the Study:, This study demonstrated obvious differences in the intestinal bacterial composition of pond-raised crabs and wild crabs. This knowledge will increase our understanding of the effects of aquaculture operations on bacterial community composition in the crab gut and provide necessary data for the development of probiotic products for crab cultivation. [source] REPRODUCTIVE ISOLATION BY SEX PHEROMONES IN THE CLOSTERIUM PERACEROSUM,STRIGOSUM,LITTORALE COMPLEX (ZYGNEMATALES, CHAROPHYCEAE),JOURNAL OF PHYCOLOGY, Issue 5 2008Yuki Tsuchikane The Closterium peracerosum,strigosum,littorale (C. psl.) complex consists of unicellular algae and is known to be composed of several reproductively isolated mating groups of heterothallic strains. Group I-E is completely isolated from mating groups II-A and II-B, groups II-A and II-B are partially isolated from each other, and only mating-type plus (mt+) cells of group II-A and mating-type minus (mt,) cells of group II-B form zygotes. Based on the alignment of 1506 group I introns, significant phylogenetic relationships were observed among mating groups II-A and II-B, while mating group I-E was distant from groups II-A and II-B. Sexual cell division in both mating-type cells of group II-A was stimulated in conditioned media in which cells of group II-B had been cultured. When mt, cells of group II-B were stimulated in conditioned medium derived from group II-A, mt+ cells of group II-B did not respond to the conditioned medium. Conditioned media derived from group I-E did not exhibit sexual cell division (SCD),inducing activity against any strain except those within its own group. From the alignment of deduced amino acid sequences from orthologous protoplast-release-inducing protein (PR-IP) Inducer genes, we detected a significant similarity among groups II-A and II-B, and mating group I-E had low similarity to other mating groups. The existing degree of reproductive isolation can be partially explained by differences in molecular structures and physiological activities of sex pheromones of these heterothallic mating groups. [source] Saccharomyces cerevisiae biodiversity in spontaneous commercial fermentations of grape musts with ,adequate' and ,inadequate' assimilable-nitrogen contentLETTERS IN APPLIED MICROBIOLOGY, Issue 1 2003L. Granchi Abstract Aim: To evaluate whether intraspecific diversity of Saccharomyces cerevisiae in wine fermentations is affected by initial assimilable-nitrogen content. Methods and Results:Saccharomyces cerevisiae isolates from two spontaneous commercial wine fermentations started with adequate and inadequate nitrogen amounts were characterized by mitochondrial DNA restriction analysis. Several strains occurred in each fermentation, two strains, but not the same ones, being predominant at frequencies of about 30%. No significant differences were detected by comparing the biodiversity indices of the two fermentations. Cluster analysis demonstrated that the strain distribution was independent of nitrogen content, the two pairs of closely related dominant strains grouping into clusters at low similarity. Conclusions: The genetic variability of S. cerevisiae in wine fermentations seemed not to depend on the nitrogen availabilty in musts. Significance and Impact of the Study: Nitrogen content did not affect the genetic diversity but may have induced a ,selection effect' on S. cerevisiae strains dominating wine fermentations, with possible consequences on wine properties. [source] Identification and characterization of a novel anthocyanin malonyltransferase from scarlet sage (Salvia splendens) flowers: an enzyme that is phylogenetically separated from other anthocyanin acyltransferasesTHE PLANT JOURNAL, Issue 6 2004Hirokazu Suzuki Summary Anthocyanin acyltransferases (AATs) catalyze a regiospecific acyl transfer from acyl-CoA to the glycosyl moiety of anthocyanins, thus playing an important role in flower coloration. The known AATs are subfamily members of an acyltransferase family, the BAHD family, which play important roles in secondary metabolism in plants. Here, we describe the purification, characterization, and cDNA cloning of a novel anthocyanin malonyltransferase from scarlet sage (Salvia splendens) flowers. The purified enzyme (hereafter referred to as Ss5MaT2) is a monomeric 46-kDa protein that catalyzes the transfer of the malonyl group from malonyl-CoA to the 4,,,-hydroxyl group of the 5-glucosyl moiety of anthocyanins. Thus, it is a malonyl-CoA:anthocyanin 5-glucoside 4,,,- O -malonyltransferase. On the basis of the partial amino acid sequences of the purified enzyme, we isolated a cDNA that encodes an acyltransferase protein. The steady-state transcript level of the gene was the highest in recently opened, fully pigmented flowers and was also correlated with the trend observed for an AAT gene responsible for the first malonylation step during salvianin biosynthesis. Immunoprecipitation studies using antibodies against the recombinant acyltransferase protein corroborated the identity of this cDNA as that encoding Ss5MaT2. The deduced amino acid sequence of Ss5MaT2 showed a low similarity (22,24% identity) to those of AATs and lacked the AAT-specific signature sequence. A phylogenetic analysis suggested that Ss5MaT2 is more related to acetyl-CoA:benzylalcohol acetyltransferase (BEAT) rather than to AAT. This is another example in which enzymes with similar, although not identical, substrate evolved from different branches of the BAHD family. [source] Phyllostomid Bat Community Structure and Abundance in Two Contrasting Tropical Dry Forests,BIOTROPICA, Issue 4 2005Kathryn E. Stoner ABSTRACT Although tropical wet forests are generally more diverse than dry forests for many faunal groups, few studies have compared bat diversity among dry forests. I compared ground level phyllostomid bat community structure between two tropical dry forests with different precipitation regimes. Parque National Palo Verde in northwestern Costa Rica represents one of the wettest tropical dry forests (rainfall 1.5 m/yr), whereas the Chamela-Cuixmala Biosphere Reserve on the Pacific coast of central Mexico represents one of the driest (750 mm/yr). Mist net sampling was conducted at the two study sites to compare changes in ground level phyllostomid bat community structure between regions and seasons. Palo Verde was more diverse than Chamela and phyllostomid species showed low similarity between sites (Classic Jaccard = 0.263). The distinct phyllostomid communities observed at these two dry forest sites demonstrates that variants of tropical dry forest can be sufficiently different in structure and composition to affect phyllostomid communities. At both dry forest sites, abundance of the two most common foraging guilds (frugivores and nectarivores) differed between seasons, with greatest numbers of individuals captured coinciding with highest chiropterophilic resource abundance. RESUMEN A pesar de que los bosques tropicales húmedos, en general, son más diversos que los bosques tropicales secos para muchos grupos de fauna, pocos estudios han comparado la diversidad de murciélogos en los bosques tropicales secos. El presente estudio compara la estructura de la comunidad de los murciélagos filostómidos a nivel del suelo entre dos tipos de bosque tropical seco con diferentes regimenes de precipitación. El parque Nacional Palo Verde esta localizado en el Noroeste de Costa Rica y representa uno de los bosques tropicales secos mas húmedos (con una precipitación de 1.5 m/año), mientras que la Reserva de la Biosfera Chamela-Cuixmala esta localizada en la costa oeste del pacífico de México y representa uno de los bosques más secos (750 mm/año). Se realizó un muestreo con redes de niebla en los dos sitios para comparar los cambios en la estructura de la comunidad de murciélagos filostómidos a nivel de suelo. Palo Verde fue más diverso que Chamela y se encontró la simultud de las especies filostomidos entre los dos sitio fue bajo (Classic Jaccard = 0.263). Las comunidades distintas de filostomidos observado en estos dos sitios de bosque seco demuestra que las variantes en el bosque tropical seco pueden ser suficientemente diferentes en estructura y composición para poder afectar la comunidad de filostomidos. En ambos bosques secos la abundancia de lo dos gremios tróficos más comunes (frugívoros y nectarívoros) fue diferente en las estaciones, con un mayor número de individuos capturados coincidiendo con una mayor abundancia de recursos quiropterofílicos. [source] | |||||||||||||