bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome abnormalities identified in 347 spontaneous abortions collected in Japan
Authors: Nagaishi Masaji , Yamamoto Tatsuo , Iinuma Kazuso , Shimomura Katsunori , Berend Sue Ann , Knops Judith 
Published: May 2004

AbstractObjective: We determined the incidence of specific chromosome abnormalities in this Japanese population so that comparisons could be made to the incidence of chromosome abnormalities reported for other populations.Methods: A total of 423 cases of products of conception aborted spontaneously were collected for cytogenetics analysis from various medical sites located in Japan. The cytogenetic results, along with clinical information including gestational age at the time of the miscarriage and maternal age, were compiled in a database. The incidence of specific chromosome aberrations was determined. The abnormalities were separated by gestational age at the time of the miscarriage and by maternal age.Results: The total number of specimens available for cytogenetic analysis was 407. Cytogenetic results were obtained for 347 cases (85.3%), of which 196 (56.5%) showed chromosome abnormalities. Autosomal trisomy was detected in 120 cases (61.2% of the abnormal cases). Trisomy for each autosome, with the exception of chromosomes 1, 5, 6, 11, 12, and 19, was identified. The most common autosomal trisomy was that of chromosome 16 (30 cases), followed by trisomy 21 (13 cases), and trisomy 22 (13 cases). Eight cases showed double trisomies, and one case showed trisomy for three different chromosomes. Two cases showed monosomy 21, and 24 cases showed 45,X. Triploidy was identified in 27 cases and tetraploidy was detected in five cases. Unbalanced structural rearrangements were found in 11 cases, and balanced translocations were identified in two cases. Six cases showed mosaicism: three cases showed a normal cell line; and three cases had multiple abnormal cell lines. Separating the trisomies by the gestational age at which time the miscarriage occurred revealed that trisomies 7, 8, 14, 15, 16 and 22 occurred exclusively during the first trimester and fetuses with trisomies 4, 13, 18 and 21 survived late into the second trimester.Conclusion: Overall patterns of chromosome abnormalities detected in spontaneous abortions in Japan were similar to those reported in the literature.
Proposal to transfer ‘Aegyptianella ranarum’, an intracellular bacterium of frog red blood cells, to the family Flavobacteriaceae as ‘CandidatusHemobacterium ranarum’ comb. nov.
Authors: Zhang Chunbin , Rikihisa Yasuko 
Published: May 2004

Summary‘Aegyptianella ranarum’ (order Rickettsiales), an ultrastructurally defined small, Gram‐negative rod, is known to replicate in the red blood cells of frogs. Heretofore, this bacterium has not been characterized genetically. We cloned and sequenced the 16S rRNA (1310 bp) andgyrB(718 bp) genes of ‘A. ranarum’ from a Canadian frog blood specimen.In situhybridization (with an ‘A. ranarum’ 16S rRNA gene polymerase chain reaction product as probe) and electron microscopy confirmed that ‘A. ranarum’ forms cytoplasmic inclusions in frog erythrocytes.blastcomparisons with GenBank 16S rRNA andgyrBsequences showed that both ‘A. ranarum’ genes were most similar (91% and 67% identity) to those ofChryseobacterium meningosepticum, a bacterium in the family Flavobacteriaceae.In contrast, ‘A. ranarum’ 16S rRNA shared only 61% identity withAegyptianella pullorum. Phylogenetic analyses of these genes usingphylipsupported ‘A. ranarum’ as a member of Flavobacteriaceae, but suggested that its cladistic sibling may beBergeyella zoohelcumorWeeksella virosa, rather thanC. meningosepticum.We propose to classify ‘Aegyptianella ranarum’ as ‘CandidatusHemobacterium ranarum’ in the family Flavobacteriaceae.Our results provide a starting point for studies of related intraerythrocytic bacterial infections in frogs.
Application and validation of DNA microarrays for the 16S rRNA‐based analysis of marine bacterioplankton
Authors: Peplies Jörg , Lau Stanley Chun Kwan , Pernthaler Jakob , Amann Rudolf , Glöckner Frank Oliver 
Published: May 2004

SummaryAn oligonucleotide probe‐based DNA microarray was evaluated for its ability to detect 16S rRNA targets in marine bacterioplankton samples without prior amplification by polymerase chain reaction (PCR). The results obtained were compared with those of quantitative fluorescence in situ hybridization (FISH). For extraction and direct labelling of total RNA, a fast and efficient protocol based on commercially available kits was established. A set of redundant and hierarchically structured probes was applied, and specificity of hybridization was assessed by additional control oligonucleotides comprising single central mismatches. The protocol was initially tested by microarray analysis of bacterial pure cultures. Complete discrimination of all control oligonucleotides was achieved, indicating a high degree of hybridization specificity. In a co‐culture, abundant members were detected by microarray analysis, but signal ratios of positive probes did not correlate well with quantitative data from FISH experiments. A marine picoplankton sample from the German Bight was analysed. Bacterial populations with relative abundances of at least 5% were detected by hybridizing 0.1 µg of total RNA extracted from a sample of 375 ml equivalent to 4.1 × 108 cells. Our results demonstrate that major populations of marine bacterioplankton can be identified by microarray analysis in a fast and reliable way, even in relatively low volumes of sea water.
Repression of Pseudomonas putida phenanthrene‐degrading activity by plant root extracts and exudates
Authors: Rentz Jeremy A. , Alvarez Pedro J. J. , Schnoor Jerald L. 
Published: May 2004

SummaryThe phenanthrene‐degrading activity (PDA) of Pseudomonas putida ATCC 17484 was repressed after incubation with plant root extracts of oat (Avena sativa), osage orange (Maclura pomifera), hybrid willow (Salix alba × matsudana), kou (Cordia subcordata) and milo (Thespesia populnea) and plant root exudates of oat (Avena sativa) and hybrid poplar (Populus deltoides × nigra DN34). Total organic carbon content of root extracts ranged from 103 to 395 mg l−1. Characterization of root extracts identified acetate (not detectable to 8.0 mg l−1), amino acids (1.7–17.3 mg l−1) and glucose (1.6–14.0 mg l−1), indicating a complex mixture of substrates. Repression was also observed after exposure to potential root‐derived substrates, including organic acids, glucose (carbohydrate) and glutamate (amino acid). Carbon source regulation (e.g. catabolite repression) was apparently responsible for the observed repression of P. putida PDA by root extracts. However, we showed that P. putida grows on root extracts and exudates as sole carbon and energy sources. Enhanced growth on root products may compensate for partial repression, because larger microbial populations are conducive to faster degradation rates. This would explain the commonly reported increase in phenanthrene removal in the rhizosphere.
Pathogenic potential of environmental Klebsiella pneumoniae isolates
Authors: Struve Carsten , Krogfelt Karen Angeliki 
Published: May 2004

Summary Klebsiella pneumoniae is an important opportunistic pathogen and a frequent cause of nosocomial infections. K. pneumoniae infections can occur at nearly any body site; however, urinary tract infections and infections of the respiratory tract predominate. Infections are frequently preceded by gastrointestinal colonization, and the gastrointestinal tract is believed to be the most important reservoir for transmission of the bacteria. In contrast to many other bacterial pathogens, K. pneumoniae is ubiquitous in nature. Several studies have described Klebsiella isolates of environmental origin to be nearly identical to clinical isolates with respect to several phenotypic properties. However, the pathogenic potential of environmental K. pneumoniae isolates is essentially unknown. We have evaluated the virulence of K. pneumoniae strains of environmental and clinical origin directly in animal models, i.e. in urinary tract infection and intestinal colonization models. Furthermore, the ability to adhere to and invade human epithelial cell lines was examined. Although strain‐to‐strain differences were observed in the individual infection models, overall, strains of environmental origin were found to be as virulent as strains of clinical origin. The ubiquity of K. pneumoniae in nature and the general ability of K. pneumoniae strains to infect susceptible hosts might explain the high frequency of opportunistic infections caused by this species.
Isolation of haloarchaea that grow at low salinities
Authors: Purdy K. J. , Cresswell‐Maynard T. D. , Nedwell D. B. , McGenity T. J. , Grant W. D. , Timmis K. N. , Embley T. M. 
Published: May 2004

SummaryArchaea, the third domain of life, were long thought to be limited to environmental extremes. However, the discovery of archaeal 16S rRNA gene sequences in water, sediment and soil samples has called into question the notion of Archaea as obligate extremophiles. Until now, none of these novel Archaea has been brought into culture, a critical step for discovering their ecological roles. We have cultivated three novel halophilic Archaea (haloarchaea) genotypes from sediments in which the pore‐water salinity was close to that of sea water. All previously reported haloarchaeal isolates are obligate extreme halophiles requiring at least 9% (w/v) NaCl for growth and are typically the dominant heterotrophic organisms in salt and soda lakes, salt deposits and salterns. Two of these three newly isolated genotypes have lower requirements for salt than previously cultured haloarchaea and are capable of slow growth at sea‐water salinity (2.5% w/v NaCl). Our data reveal the existence of Archaea that can grow in non‐extreme conditions and of a diverse community of haloarchaea existing in coastal salt marsh sediments. Our findings suggest that the ecological range of these physiologically versatile prokaryotes is much wider than previously supposed.
Graphite electrodes as electron donors for anaerobic respiration
Authors: Gregory Kelvin B. , Bond Daniel R. , Lovley Derek R. 
Published: May 2004

SummaryIt has been demonstrated previously that Geobacter species can transfer electrons directly to electrodes. In order to determine whether electrodes could serve as electron donors for microbial respiration, enrichment cultures were established from a sediment inoculum with a potentiostat‐poised graphite electrode as the sole electron donor and nitrate as the electron acceptor. Nitrate was reduced to nitrite with the consumption of electrical current. The stoichiometry of electron and nitrate consumption and nitrite accumulation were consistent with the electrode serving as the sole electron donor for nitrate reduction. Analysis of 16 rRNA gene sequences demonstrated that the electrodes supplied with current were specifically enriched in microorganisms with sequences most closely related to the sequences of known Geobacter species. A pure culture of Geobacter metallireducens was shown to reduce nitrate to nitrite with the electrode as the sole electron donor with the expected stoichiometry of electron consumption. Cells attached to the electrode appeared to be responsible for the nitrate reduction. Attached cells of Geobacter sulfurreducens reduced fumarate to succinate with the electrode as an electron donor. These results demonstrate for the first time that electrodes may serve as a direct electron donor for anaerobic respiration. This finding has implications for the harvesting of electricity from anaerobic sediments and the bioremediation of oxidized contaminants.
Pseudomonas putida mutants in the exbBexbDtonB gene cluster are hypersensitive to environmental and chemical stressors
Authors: Godoy Patricia , Ramos‐González María‐Isabel , Ramos Juan L. 
Published: May 2004

SummaryThe genes in the exbBexbDtonB cluster of Pseudomonas putida DOT‐T1E are co‐transcribed. We have generated non‐polar mutants in each of the genes by inserting an aphA3 cassette encoding kanamycin resistance. All three mutants show similar phenotypes: the mutants are unable to grow on minimal medium under iron deficiency conditions. Furthermore, regardless of iron conditions, all mutants are hypersensitive to antibiotics, p‐hydroxybenzoate and toluene, chemicals that are extruded from the cell by efflux pumps. These findings are discussed in terms of the involvement of the TonB system in the energization of outer membrane functions necessary for the import or export of different compounds in P. putida.
Hydrogen threshold concentrations in pure cultures of halorespiring bacteria and at a site polluted with chlorinated ethenes
Authors: Luijten Maurice L. G. C. , Roelofsen Wim , Langenhoff Alette A. M. , Schraa Gosse , Stams Alfons J. M. 
Published: May 2004

SummaryHalorespiring microorganisms are not only able to oxidize organic electron donors such as formate, acetate, pyruvate and lactate, but also H2. Because these microorganisms have a high affinity for H2, this may be the most important electron donor for halorespiration in the environment. We have studied the role of H2‐threshold concentrations in pure halorespiring cultures and compared them with mixed cultures and field data. We have found H2‐threshold values between 0.05 and 0.08 nM for Sulfurospirillum halorespirans, S. multivorans and Dehalobacter restrictus under PCE‐reducing and nitrate‐reducing conditions.The reduction of PCE and TCE can proceed at H2 concentrations of below 1 nM at a polluted site. However, for the reduction of lower chlorinated ethenes a higher H2 concentration is required. This indicates that the measured H2 concentration in situ can be an indicator of the extent of anaerobic reductive dechlorination.
Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae
Authors: Cho Jang‐Cheon , Vergin Kevin L. , Morris Robert M. , Giovannoni Stephen J. 
Published: May 2004

SummaryTwo phylogenetically distinct marine strains producing transparent exopolymers (TEP), designated HTCC2155T and HTCC2160, were cultivated from Oregon coast seawater by dilution to extinction in a high throughput culturing format. When cultured in low‐nutrient seawater media, these strains copiously produced Alcian Blue‐stainable viscous TEP. Growing cells were attached to each other by the TEP in a three dimensional network. Polymerase chain reaction employing 16S rDNA primers specific for the novel isolates indicated that they are indigenous to the water column of the Atlantic and Pacific oceans. The abundance of the isolates as determined by 16S rRNA dot blots, however, indicated that they are less than 1% of the total bacterial community. In phylogenetic analyses, the strains consistently formed a new phylum‐level lineage within the domain Bacteria, together with members of the candidate phylum VadinBE97, which consists of Victivallis, the first cultured genus in the candidate phylum, and 16S rRNA gene clones from DNA extracted from marine or anaerobic terrestrial habitats. Five putative subgroups were delineated within this phylum‐level lineage, including a marine group and an anaerobic group. The isolates are Gram negative, strictly aerobic, chemoheterotrophic, and facultatively oligotrophic sphere‐shaped bacteria. The DNA G+C content of strain HTCC2155T was 48.3 mol% and the genome size was 2.9 mb. It is proposed from these observations that the strains be placed into a new genus and a new species named Lentisphaera araneosa (type strain HTCC2155T = ATCC BAA‐859T = KCTC 12141T) gen. nov., sp. nov., the cultured marine representative of the Lentisphaerae phyl. nov., and the phylum be divided into two novel orders named the Lentisphaerales ord. nov. and the Victivallales ord. nov.
Biofilm formation by the small colony variant phenotype of Pseudomonas aeruginosa
Authors: Häußler Susanne 
Published: May 2004

Summary Pseudomonas aeruginosa is an ubiquitous environmental bacterium and an opportunistic human pathogen. Not only in most natural habitats but also within the human host, e.g. within the chronically infected cystic fibrosis lung, P. aeruginosa is associated with surfaces in structures known as biofilms. These functional communities represent a unique mode of bacterial growth where bacteria display particular phenotypes that are fundamentally different from planktonic cells. In this review the issue of the molecular mechanisms underlying the emergence of small colony variant (SCV) P. aeruginosa morphotypes that are especially capable of forming biofilms is addressed. It is assumed that the expression of the chaperone usher pathway (cup) genes encoding putative fimbrial adhesins is responsible for the phenotypic switch to an autoaggregative SCV phenotype. The elucidation of phenotypic switching in response to environmental stimuli will significantly increase our understanding of regulatory processes during bacterial adaptation and might be the basis for the initiation of the development of new antimicrobial treatment strategies.
Vertical and temporal shifts in microbial communities in the water column and sediment of saline meromictic Lake Kaiike (Japan), as determined by a 16S rDNA‐based analysis, and related to physicochemical gradients
Authors: Koizumi Yoshikazu , Kojima Hisaya , Oguri Kazumasa , Kitazato Hiroshi , Fukui Manabu 
Published: May 2004

SummaryThe vertical and temporal changes in microbial communities were investigated throughout the water column and sediment of the saline meromictic Lake Kaiike by PCR‐denaturing gradient gel electrophoresis (DGGE) of 16S rDNA. Marked depth‐related changes in microbial communities were observed at the chemocline and the sediment–water interface. However, no major temporal changes in the microbial community below the chemocline were observed during the sampling period, suggesting that the ecosystem in the anoxic zone of Lake Kaiike was nearly stable. Although the sequence of the most conspicuous DGGE band throughout the anoxic water and in the top of the microbial mat was most similar to that of an anoxic, photosynthetic, green sulphur bacterium, Pelodyction luteolum DSM273 (97% similarity), it represented a new phylotype. A comparison of DGGE banding patterns of the water column and sediment samples demonstrated that specific bacteria accumulated on the bottom from the anoxic water layers, and that indigenous microbial populations were present in the sediment. The measurements of bicarbonate assimilation rates showed significant phototrophic assimilation in the chemocline and lithoautotrophic assimilation throughout the anoxic water, but were not clearly linked with net sulphide turnover rates, indicating that sulphur and carbon metabolisms were not directly correlated.
Bacterial signal transduction network in a genomic perspective†
Authors: Galperin Michael Y. 
Published: May 2004

SummaryBacterial signalling network includes an array of numerous interacting components that monitor environmental and intracellular parameters and effect cellular response to changes in these parameters. The complexity of bacterial signalling systems makes comparative genome analysis a particularly valuable tool for their studies. Comparative studies revealed certain general trends in the organization of diverse signalling systems. These include (i) modular structure of signalling proteins; (ii) common organization of signalling components with the flow of information from N‐terminal sensory domains to the C‐terminal transmitter or signal output domains (N‐to‐C flow); (iii) use of common conserved sensory domains by different membrane receptors; (iv) ability of some organisms to respond to one environmental signal by activating several regulatory circuits; (v) abundance of intracellular signalling proteins, typically consisting of a PAS or GAF sensor domains and various  output  domains;  (vi)  importance  of secondary messengers, cAMP and cyclic diguanylate; and (vii) crosstalk between components of different signalling pathways. Experimental characterization of the novel domains and domain combinations would be needed for achieving a better understanding of the mechanisms of signalling response and the intracellular hierarchy of different signalling pathways.
Core and periphery of the ‘collective’: labour segmentation in the Russian industrial enterprise
Authors: Schwartz Gregory 
Published: May 2004

ABSTRACTThe present paper tries to fill an important gap in our understanding of the specific nature of wage and employment differentiation in Russia during the period of transition. By presenting evidence from case studies at Russian industrial enterprises the account examines the role played by hierarchies in production, specifically the dynamics of core/periphery workforce segmentation, in helping to explain how the present economic conditions have acted to re‐entrench specific forms of inequality. Exploring the processes of decision‐making regarding employment, work and pay allocation, and promotion the paper will conclude with some central inferences as to why workforce segmentation is seen as an important means of obtaining control over labour.
Single‐copy gene markers isolated from the Caribbean coral, Montastraea annularis
Authors: Severance E. G. , Szmant A. M. , Karl S. A. 
Published: May 2004

AbstractWe report the isolation of seven single‐copy nuclear DNA loci from the Caribbean reef‐building coral, Montastraea annularis. All loci are polymorphic at the nucleotide level, and three loci have readily screened restriction enzyme site polymorphisms that can help to rapidly assess population genetic structure. Use of these markers can provide baseline genetic information concerning the population dynamics of dominant stony corals and fuel the implementation and management of appropriate conservation strategies.
Isolation and characterization of microsatellite markers in the new world screw‐worm Cochliomyia hominivorax (Diptera: Calliphoridae)
Authors: Torres T. T. , Brondani R. P. V. , Garcia J. E. , Azeredo‐Espin A. M. L. 
Published: May 2004

AbstractThe new world screw‐worm, Cochliomyia hominivorax, is one of the most important parasitic insect pests. This species causes myiasis and, consequently, significant losses to livestock industries in neotropical regions. As part of an investigation into the genetic variability and population structure of the new world screw‐worm, a set of 10 polymorphic microsatellite markers was isolated from an AC‐enriched genomic library. Amplification of the reported loci in 30 screw‐worms revealed an average of 6.9 alleles per locus with expected heterozygosities ranging from 0.3831 to 0.8022. Cross‐species amplifications suggested that these loci may be useful in other Calliphoridae species.
Optimization of novel polymorphic microsatellites in the endangered Sumatran rhinoceros (Dicerorhinus sumatrensis)
Authors: Scott C. , Foose T. , Morales J. C. , Fernando P. , Melnick D. J. , Boag P. T. , Davila J. A. , Van Coeverden De Groot P.J. 
Published: May 2004

AbstractLoss of habitat and poaching have led to a drastic reduction in numbers of the Sumatran rhinoceros (Dicerorhinus sumatrensis). To aid in the conservation management of this species, we isolated and optimized 10 polymorphic Sumatran rhinoceros microsatellite loci. A survey of six individuals yielded a mean number of alleles of 3.7, mean expected heterozygosity of 0.551 and probability of identity of 3.46 × 10−8. Although this estimate is similar to estimates of microsatellite variability in the Black, Indian and White rhinoceroses, such a conclusion is premature as locus purity, sample size and number of loci surveyed vary significantly among studies.