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Molecular Survey (molecular + survey)
Selected AbstractsStructural and functional evidence for a singular repertoire of BMP receptor signal transducing proteins in the lophotrochozoan Crassostrea gigas suggests a shared ancestral BMP/activin pathwayFEBS JOURNAL, Issue 13 2005Amaury Herpin The transforming growth factor , (TGF-,) superfamily includes bone morphogenetic proteins, activins and TGF-,sensu stricto (s.s). These ligands, which transduce their signal through a heteromeric complex of type I and type II receptors, have been shown to play a key role in numerous biological processes including early embryonic development in both deuterostomes and ecdyzozoans. Lophochotrozoans, the third major group of bilaterian animals, have remained in the background of the molecular survey of metazoan development. We report the cloning and functional study of the central part of the BMP pathway machinery in the bivalve mollusc Crassostrea gigas (Cg- BMPR1 type I receptor and Cg- TGF,sfR2 type II receptor), showing an unusual functional mode of signal transduction for this superfamily. The use of the zebrafish embryo as a reporter organism revealed that Cg- BMPR1, Cg- TGF,sfR2, Cg- ALR I, an activin Type I receptor or their dominant negative acting truncated forms, when overexpressed during gastrulation, resulted in a range of phenotypes displaying severe disturbance of anterioposterior patterning, due to strong modulations of ventrolateral mesoderm patterning. The results suggest that Cg- BMPR1, and to a certain degree Cg- TGF,sfR2 proteins, function in C. gigas in a similar way to their zebrafish orthologues. Finally, based on phylogenetic analyses, we propose an evolutionary model within the complete TGF-, superfamily. Thus, evidence provided by this study argues for a possible conserved endomesoderm/ectomesoderm inductive mechanism in spiralians through an ancestral BMP/activin pathway in which the singular, promiscuous and probably unique Cg- TGF,sfR2 would be the shared type II receptor interface for both BMP and activin ligands. [source] Nitrification in terrestrial hot springs of Iceland and KamchatkaFEMS MICROBIOLOGY ECOLOGY, Issue 2 2008Laila J. Reigstad Abstract Archaea have been detected recently as a major and often dominant component of the microbial communities performing ammonia oxidation in terrestrial and marine environments. In a molecular survey of archaeal ammonia monooxygenase (AMO) genes in terrestrial hot springs of Iceland and Kamchatka, the amoA gene encoding the ,-subunit of AMO was detected in a total of 14 hot springs out of the 22 investigated. Most of these amoA -positive hot springs had temperatures between 82 and 97 °C and pH range between 2.5 and 7. In phylogenetic analyses, these amoA genes formed three independent lineages within the known sequence clusters of marine or soil origin. Furthermore, in situ gross nitrification rates in Icelandic hot springs were estimated by the pool dilution technique directly on site. At temperatures above 80 °C, between 56 and 159 ,mol NO3, L,1 mud per day was produced. Furthermore, addition of ammonium to the hot spring samples before incubation yielded a more than twofold higher potential nitrification rate, indicating that the process was limited by ammonia supply. Our data provide evidence for an active role of archaea in nitrification of hot springs in a wide range of pH values and at a high temperature. [source] Molecular bacterial community analysis of clean rooms where spacecraft are assembledFEMS MICROBIOLOGY ECOLOGY, Issue 3 2007Christine Moissl Abstract Molecular bacterial community composition was characterized from three geographically distinct spacecraft-associated clean rooms to determine whether such populations are influenced by the surrounding environment or the maintenance of the clean rooms. Samples were collected from facilities at the Jet Propulsion Laboratory (JPL), Kennedy Space Flight Center (KSC), and Johnson Space Center (JSC). Nine clone libraries representing different surfaces within the spacecraft facilities and three libraries from the surrounding air were created. Despite the highly desiccated, nutrient-bare conditions within these clean rooms, a broad diversity of bacteria was detected, covering all the main bacterial phyla. Furthermore, the bacterial communities were significantly different from each other, revealing only a small subset of microorganisms common to all locations (e.g. Sphingomonas, Staphylococcus). Samples from JSC assembly room surfaces showed the greatest diversity of bacteria, particularly within the Alpha - and Gammaproteobacteria and Actinobacteria. The bacterial community structure of KSC assembly surfaces revealed a high presence of proteobacterial groups, whereas the surface samples collected from the JPL assembly facility showed a predominance of Firmicutes. Our study presents the first extended molecular survey and comparison of NASA spacecraft assembly facilities, and provides new insights into the bacterial diversity of clean room environments . [source] Diversity and abundance of Bacteria and Archaea in the Bor Khlueng Hot Spring in ThailandJOURNAL OF BASIC MICROBIOLOGY, Issue 6 2004Pattanop Kanokratana The prokaryotic diversity in the Bor Khlueng hot spring in Ratchaburi province, Thailand was investigated by a culture-independent molecular approach. This hydrothermal pool is located in the central part of Thailand and contains sulfide-rich mineral water that is believed to relieve muscle ache and pain. The water flow year-round with temperature ranging between 50,57 °C. Community DNA was extracted directly from sediment samples by coring to depth of ,20,30 cm. Small-subunit rRNA genes (16S rDNA) were amplified by PCR using primers specific for the domains Archaea and Bacteria. The PCR products were cloned and sequenced. For the bacterial rDNA clone library, 200 clones were randomly selected for further analyses. After restriction fragment length polymorphism (RFLP) analysis of rDNA clones and exclusion of chimeric sequences 36 phylotypes were obtained. The Bor Khlueng phylotypes spanned a wide range within the domain Bacteria, occupying eleven major lineages (phyla). Almost a quarter (23%) of the clones were classifed as Acidobacteria. The other clones were grouped into the Bacteriodetes (19%), Nitrospirae (13%), Proteobacteria (12%), Deinococcus-Thermus lineage (11%), planctomycetes (6%), and Verrucomicrobia (5%). The four remaining phyla, 5% each, were assigned to Actinobacteria, Chloroflexi, Cyanobacteria, and the candidate division "OP10". For the archaeal 16S rRNA gene sequence library, 25 distinct phylotypes were obtained, 17 clones were found to be associated with Crenarahaeota and 8 clones were associated with Euryarachaeota. The findings of the molecular survey of this so far not investigated site showed that Bor Khlueng hot spring is a potential rich source of unique bacterial and archaeal species. The great majority (,80%) of the prokaryotic sequences detected in Bor Khlueng were unknown. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] A serological and molecular survey of hepatitis B in children 15 years after inception of the national hepatitis B vaccination program in eastern China,JOURNAL OF MEDICAL VIROLOGY, Issue 9 2009Ying Dong Abstract The emergence of mutations in the hepatitis B virus (HBV) S gene has threatened the long-term success of vaccination programs since the worldwide introduction of effective vaccines against hepatitis B. This study was conducted on 5,407 children (0,8 years old) in eastern China in 2007. We analyzed the prevalence of HBsAg, anti-HBs, and "a"-determinant mutations in the HBV S gene by microparticle enzyme immunoassays, PCR, and DNASTAR software. The total HBsAg prevalence was 1.52% (82/5,407) in the children and increased with age. In contrast, the positive rate (65.42%, 2,374/3,629) and the titers of anti-HBs decreased with age. The predominant infection was HBV of genotype C and serotype adr (45/51; 88% of cases). Mutations of I126T, amino acid 137 (nt553T deletion mutation), G145A, G145R, and F158S were found in the children; the mutations of amino acid 137 and F158S have not been reported previously. The total prevalence of mutant strains was 14% (7/51). To investigate whether the infection resulted from maternal transmission, we compared the S gene sequences in 16 mother,child pairs. Fourteen mother,child pairs exhibited the same HBV genotype, with 99.5,100% sequence homology in the S gene, while two pairs exhibited different genotypes. This study suggested that the hepatitis B vaccination strategies in eastern China have been successful. Although the emergence of "a"-determinant mutations in the HBV S gene have resulted in HBV infection in immunized children, this does not pose a threat to the vaccination strategies. The HBV-infected children had contracted the infection via vertical transmission. J. Med. Virol. 81:1517,1524, 2009. © 2009 Wiley-Liss, Inc. [source] Momordica mossambica sp. nov. (Cucurbitaceae) from miombo woodland in northern MozambiqueNORDIC JOURNAL OF BOTANY, Issue 5 2009Hanno Schaefer Momordica mossambica, a new species of the Cucurbitaceae from miombo woodland in northern Mozambique is described. In spite of being known only from the type collected in 1964, a morphological and molecular survey of all known species of Momordica indicates that M. mossambica is a distinct species. The closest relatives are M. calantha and M. cabrae from Tanzania and central Africa, respectively, from which it is distinguished easily by its 7-lobed, maple-like leaves. [source] Vector transmission of Bartonella species with emphasis on the potential for tick transmissionMEDICAL AND VETERINARY ENTOMOLOGY, Issue 1 2008S. A. BILLETER AbstractBartonella species are gram-negative bacteria that infect erythrocytes, endothelial cells and macrophages, often leading to persistent blood-borne infections. Because of the ability of various Bartonella species to reside within erythrocytes of a diverse number of animal hosts, there is substantial opportunity for the potential uptake of these blood-borne bacteria by a variety of arthropod vectors that feed on animals and people. Five Bartonella species are transmitted by lice, fleas or sandflies. However, Bartonella DNA has been detected or Bartonella spp. have been cultured from numerous other arthropods. This review discusses Bartonella transmission by sandflies, lice and fleas, the potential for transmission by other vectors, and data supporting transmission by ticks. Polymerase chain reaction (PCR) or culture methods have been used to detect Bartonella in ticks, either questing or host-attached, throughout the world. Case studies and serological or molecular surveys involving humans, cats and canines provide indirect evidence supporting transmission of Bartonella species by ticks. Of potential clinical relevance, many studies have proposed co-transmission of Bartonella with other known tick-borne pathogens. Currently, critically important experimental transmission studies have not been performed for Bartonella transmission by many potential arthropod vectors, including ticks. [source] Gene trees: A powerful tool for exploring the evolutionary biology of species and speciationPLANT SPECIES BIOLOGY, Issue 3 2000Alan R. Templeton Abstract Evolutionary trees can be constructed from the haplotypes observed with molecular surveys of sequence or restriction site variation. Such gene trees can be constructed regardless of whether or not all of the individual specimens came from one or many species. Hence, these gene trees can straddle the species/population interface, thereby providing a powerful tool for studying the meaning of species and the process of speciation. We illustrate how historical approaches using gene trees can be used to separate the effects of population structure from population history, in order to rigorously test the species status of a group, and to test hypotheses about the process of speciation. A worked example of species status in the Piriqueta caroliniana complex is presented. Species status is evaluated under the cohesion species concept that defines a species as an evolutionary lineage with boundaries arising from the forces that create reproductive communities. Such forces are collectively called cohesion mechanisms and consist of two main subtypes: (i) genetic exchangeability, and (ii) ecological interchangeability. To make this definition operational, populations that behave as separate evolutionary lineages are first identified. A method is reviewed for inferring lineages using explicit statistical criteria from geographic overlays upon gene trees. Once lineages have been identified, the next step is to use the cohesion mechanisms to identify candidate traits that should contribute to genetic exchangeability and/or ecological interchangeability. The cohesion species are then identified by performing overlays upon gene trees in order to identify significant transitions in the candidate traits. Cohesion species are recognized only when statistically significant reproductive/ecological transitions occur that are concordant with the lineages defined earlier. This data-rich method of recognizing species automatically generates much information about the biogeography, population structure, historical events, and ecology and/or reproductive biology of the group under study. In turn, this information provides much insight into the process of speciation. It also makes the criteria, data, methods of analysis and degree of support for the species inference completely explicit, thereby avoiding confusion, inconsistency and artificial controversies that plague much of the literature on species concepts. [source] | ||||||||||