bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of a genome fragment of a deep‐sea uncultivated Group II euryarchaeote containing 16S rDNA, a spectinomycin‐like operon and several energy metabolism genes
Authors: Moreira David , Rodríguez‐Valera Francisco , López‐García Purificación 
Published: August 2004

SummaryWe have sequenced and analysed a 39.5 kbp genome fragment of a marine Group II euryarchaeote identified in a metagenomic library of 500 m deep plankton at the Antarctic Polar Front. The clone contains a 16S rRNA gene that is separated from the 23S rRNA gene in the genome. This appears to be a trait shared by Thermoplasmatales and Group II euryarchaeota. This genome fragment exhibits a compact organization, including a few overlapping genes in the canonical spectinomycin‐like (spc) operon for ribosomal proteins that is immediately upstream the 16S rDNA. Most open reading frames (ORFs) encoded proteins involved in housekeeping processes and, as expected, exhibited a phylogenetic distribution congruent with that of the 16S rRNA. A considerable number of proteins with predicted transmembrane helices was identified. Among those, two proteins encoded by genes likely forming an operon appear to be part of a membrane terminal electron transport chain. One of these proteins has an unusual domain arrangement including ferredoxin, flavodoxin and one succinate dehydrogenase/fumarate reductase subunit. These proteins probably constitute a new succinate dehydrogenase‐like oxidoreductase involved in what could be a novel pathway for energy metabolism in Group II euryarchaeota.
Characterization of large‐insert DNA libraries from soil for environmental genomic studies of Archaea
Authors: Treusch Alexander H. , Kletzin Arnulf , Raddatz Guenter , Ochsenreiter Torsten , Quaiser Achim , Meurer Guido , Schuster Stephan C. , Schleper Christa 
Published: August 2004

SummaryComplex genomic libraries are increasingly being used to retrieve complete genes, operons or large genomic fragments directly from environmental samples, without the need to cultivate the respective microorganisms. We report on the construction of three large‐insert fosmid libraries in total covering 3 Gbp of community DNA from two different soil samples, a sandy ecosystem and a mixed forest soil. In a fosmid end sequencing approach including 5376 sequence tags of ≈ 700 bp length, we show that mostly bacterial and, to a much lesser extent, archaeal and eukaryotic genome fragments (≈ 1% each) have been captured in our libraries. The diversity of putative protein‐encoding genes, as reflected by their distribution into different COG clusters, was comparable to that encoded in complete genomes of cultivated microorganisms. A huge variety of genomic fragments has been captured in our libraries, as seen by comparison with sequences in the public databases and by the large variation in G+C contents. We dissect differences between the libraries, which relate to the different ecosystems analysed and to biases introduced by different DNA preparations. Furthermore, a range of taxonomic marker genes (other than 16S rRNA) has been identified that allows the assignment of genome fragments to specific lineages. The complete sequences of two genome fragments identified as being affiliated with Archaea, based on a gene encoding a CDC48 homologue and a thermosome subunit, respectively, are presented and discussed. We thereby extend the genomic information of uncultivated crenarchaeota from soil and offer hints to specific metabolic traits present in this group.
Uncultured soil bacteria are a reservoir of new antibiotic resistance genes
Authors: Riesenfeld Christian S. , Goodman Robert M. , Handelsman Jo 
Published: August 2004

SummaryAntibiotic resistance genes are typically isolated by cloning from cultured bacteria or by polymerase chain reaction (PCR) amplification from environmental samples. These methods do not access the potential reservoir of undiscovered antibiotic resistance genes harboured by soil bacteria because most soil bacteria are not cultured readily, and PCR detection of antibiotic resistance genes depends on primers that are based on known genes. To explore this reservoir, we isolated DNA directly from soil samples, cloned the DNA and selected for clones that expressed antibiotic resistance in Escherichia coli. We constructed four libraries that collectively contain 4.1 gigabases of cloned soil DNA. From these and two previously reported libraries, we identified nine clones expressing resistance to aminoglycoside antibiotics and one expressing tetracycline resistance. Based on the predicted amino acid sequences of the resistance genes, the resistance mechanisms include efflux of tetracycline and inactivation of aminoglycoside antibiotics by phosphorylation and acetylation. With one exception, all the sequences are considerably different from previously reported sequences. The results indicate that soil bacteria are a reservoir of antibiotic resistance genes with greater genetic diversity than previously accounted for, and that the diversity can be surveyed by a culture‐independent method.
The genome of Desulfotalea psychrophila, a sulfate‐reducing bacterium from permanently cold Arctic sediments
Authors: Rabus R. , Ruepp A. , Frickey T. , Rattei T. , Fartmann B. , Stark M. , Bauer M. , Zibat A. , Lombardot T. , Becker I. , Amann J. , Gellner K. , Teeling H. , Leuschner W. D. , Glöckner F.‐O. , Lupas A. N. , Amann R. , Klenk H.‐P. 
Published: August 2004

Summary Desulfotalea psychrophila is a marine sulfate‐reducing δ‐proteobacterium that is able to grow at in situ temperatures below 0°C. As abundant members of the microbial community in permanently cold marine sediments, D. psychrophila‐like bacteria contribute  to  the  global  cycles  of  carbon  and sulfur. Here, we describe the genome sequence of D. psychrophila strain LSv54, which consists of a 3 523 383 bp circular chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14 663 bp. Analysis of the genome gave insight into the metabolic properties of the organism, e.g. the presence of TRAP‐T systems as a major route for the uptake of C4‐dicarboxylates, the unexpected presence of genes from the TCA cycle, a TAT secretion system, the lack of a β‐oxidation complex and typical Desulfovibrio cytochromes, such as c553, c3 and ncc. D. psychrophila encodes more than 30 two‐component regulatory  systems,  including  a  new  Ntr  subcluster of hybrid kinases, nine putative cold shock proteins and nine potentially cold shock‐inducible proteins. A comparison of D. psychrophila's genome features with those of the only other published genome from a sulfate reducer, the hyperthermophilic archaeon Archaeoglobus fulgidus, revealed many striking differences, but only a few shared features.
Different SAR86 subgroups harbour divergent proteorhodopsins
Authors: Sabehi Gazalah , Béjà Oded , Suzuki Marcelino T. , Preston Christina M. , DeLong Edward F. 
Published: August 2004

SummaryProteorhodopsins (PRs), bacterial photoactive proton pumps, were originally detected in the uncultured marine γ‐proteobacterial SAR86 group. PRs are now known to occur in both the γ and α marine proteobacterial lineages. Recent environmental shotgun sequence analysis in the Sargasso Sea has added yet more diversity, and a potentially broader taxonomic distribution, to the PR family. Much remains to be learned, however, about within‐taxon PR variability and the broader organismal distribution of different PR types. We report here genomic analyses of large genome fragments from different subgroups of the SAR86 lineage, recovered from naturally occurring bacterioplankton populations in coastal Red Sea and open ocean Pacific waters. Sequence comparisons were performed on large bacterial artificial chromosomes (BACs) bearing both rRNA and PR genes, derived from different SAR86 subgroups. Our analyses indicated the presence of different PR sequence types within the same SAR86 rRNA subgroup. The data suggested that the distribution of particular PR types does not necessarily parallel the phylogenetic relationship inferred from highly conserved genes such as rRNA. Further analyses of the genomic regions flanking PR also revealed a potential pathway for the biosynthesis of retinal, the PR chromophore that is required to generate the functionally active photoprotein. Finally, comparison of our results with recently reported Sargasso Sea environmental shotgun sequence assemblies demonstrated the utility of BAC clones for interpreting environmental shotgun sequence data, much of which is represented in short contigs that have an overall low depth of coverage.
The application of two‐dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms
Authors: Wilmes Paul , Bond Philip L. 
Published: August 2004

SummaryIn the post‐genomic era, the focus of numerous researchers has moved to studying the functional products of gene expression. In microbiology, these ‘omic’ approaches have largely been limited to pure cultures of microorganisms. Consequently, they do not provide information on gene expression in a complex mixture of microorganisms as found in the environment. Our method enabled the successful extraction and purification of the entire proteome from a laboratory‐scale activated sludge system optimized for enhanced biological phosphorus removal, its separation by two‐dimensional polyacrylamide gel electrophoresis and the mapping of this metaproteome. Highly expressed protein spots were excised and identified using quadrupole time‐of‐flight mass spectrometry with de novo peptide sequencing. The proteins isolated were putatively identified as an outer membrane protein (porin), an acetyl coenzyme A acetyltransferase and a protein component of an ABC‐type branched‐chain amino acid transport system. These proteins possibly stem from the dominant and uncultured Rhodocyclus‐type polyphosphate‐accumulating organism in the activated sludge. We propose the term ‘metaproteomics’ for the large‐scale characterization of the entire protein complement of environmental microbiota at a given point in time.
A comparison of 3 alloy surface treatments for resin‐bonded prostheses
Authors: Petrie Cynthia S. , Eick J. David , Williams Karen , Spencer Paulette 
Published: August 2004

Purpose The most frequent cause of clinical failure of resin‐bonded fixed partial dentures is a debonding at the metal‐cement interface. The purpose of this in vitro study was to compare the tensile bond strengths of 3 different alloy‐surface treatments when cemented to human enamel with a resin cement.Materials and Methods Cylinders of a nickel‐chromium‐beryllium (Ni‐Cr‐Be) and a gold‐palladium (Au‐Pd) alloy were fabricated and assigned to different surface treatment groups as follows: Group 1: Ni‐Cr‐Be, chemically etched; Group 2: Au‐Pd, airborne particle–abraded and tin‐plated; and Group 3: Au‐Pd, airborne particle–abraded and treated with the Alloy Primer (Kuraray Co, LTD, Osaka, Japan). The cylinders were bonded to the enamel surfaces of extracted, human third molars and stored in normal saline at 37°C for 48 hours. The tensile bond strength of 21 specimens from each group was measured on a Universal Testing Machine (Instron, Canton, MA). Three failed specimens of each group were evaluated using scanning electron microscopy and energy dispersive spectroscopy.Results Statistically significant differences (p < .05) were found between all 3 treatment groups. The mean tensile bond strengths (± the standard error of mean) recorded as follows: Group 1: 10.6 MPa (±1.3), Group 2: 0.9 MPa (±0.2), and Group 3: 13.4 MPa (±1.0). Specimens from groups 1 and 3 revealed a trend towards mixture of cohesive, within the resin cement, and adhesive failures at the metal‐cement interface. Group 2 specimens exhibited primarily adhesive failures at the metal‐cement interface.Conclusion The tensile bond strength of Au‐Pd alloy specimens was significantly increased with the Alloy Primer.
In vitro examination of the fracture strength of 3 different fiber‐reinforced composite and 1 all‐ceramic posterior inlay fixed partial denture systems
Authors: Kolbeck Carola , Rosentritt Martin , Behr Michael , Lang Reinhold , Handel Gerhard 
Published: August 2004

Purpose This in vitro study was carried out to examine the fracture strength of metal‐ free posterior inlay fixed partial dentures (IFPDs). The 3‐unit IFPDs were made of either a polyethylene fiber–reinforced composite, 3 glass fiber–reinforced composites, or an all‐ceramic material.Materials and Methods Eight IFPDs were fabricated of each material in accordance with the manufacturer's instructions and luted to extracted human molars with a dual‐cure adhesive system. The molars were positioned in PMMA resin 10 mm apart mesiodistally. Inlay cavity preparations with enamel finishing lines were used. After thermal cycling and mechanical loading in an artificial oral environment, the cemented IFPDs were mechanically loaded until failure. Visual and radiologic examinations were done out to discern the different forms of fracture. Median and 25%/75% percentile values were calculated. Statistical analysis was performed using the Mann‐Whitney U test and the Kruskal‐Wallis test (p≤0.05).Results With a median (and 25%/75% percentile) fracture strength of 368 N (234 N/424 N), the FibreKor/Conquest Sculpture showed significantly lower values than the Connect/BelleGlass [898 N (736 N/1033 N)], Vectris/Targis [723 N (692 N/806 N)], Everstick/Sinfony [634 N (532 N/673 N)], and Empress2 [520 N (385 N/706 N)].Conclusions Assuming maximum chewing forces of ≥500N in posterior areas, all systems showed sufficient fracture strength in most cases and warrant further investigation for potential clinical use.
Behavior Therapy in a Family Context: Treating Elective Mutism
Authors: ROSENBERG JOHN B. , LINDBLAD MARION B. 
Published: August 2004

This paper discusses the necessity of using both behavioral and family approaches in combination, while working with electively mute children. The symptom and its significance within the family system is presented along with a rationale for avoiding the pitfalls of individual approaches with such children. A case history outlining specific behavioral techniques is described in detail with an exploration of the use of reinforcement theory, counter‐conditioning, and successive approximations in bringing about change in electively mute children. The need for bringing about changes within the family system so as to maintain the changes that have occurred through use of the behavior techniques is discussed and presented as crucial to the treatment process.The paper takes the position that either approach, by itself, will not be effective in helping electively mute children but that the treatment of choice is a combination of therapeutic techniques.
Learning Multiple Family Therapy Through Simulated Workshops
Authors: RAASOCH JOHN , LAQUEUR H. PETER 
Published: August 2004

Multiple Family Therapy (MFT) can be learned more rapidly through simulated workshops. A chronological approach to a simulated workshop is outlined describing mechanics and techniques.The hardest parts of simulated and real MFT are taking off and landing. Specific exercises are detailed to facilitate the early phases when professionals tend to simulate excessive psychopathology. However, recovery is usually rapid and dramatic in simulations; thus, the workshop leaders appear impressive.How to end “healthily” is the final challenge. Group input for assessment of simulated and real MFT is essential. From this feedback, subassertives and schizophrenics may be at the highest risk for deleterious effects from real MFT.
A Family Myth: Sex Therapy Gone Awry
Authors: SEDERER LLOYD I. , SEDERER NOOY 
Published: August 2004

The treatment of sexual disorders has achieved considerable popularity and respectability within the mental health profession and the lay community. As a consequence, it has become increasingly difficult to elude requests for this type of treatment and even more difficult to balance sexual concerns with the numerous other modes of relating that exist within a dyadic relationship.This paper will report two versions of a case study in which sexual dysfunction served as a myth that was carefully constructed to veil certain more fundamental problems.
A Study of the Relationship Between Family Interaction and Individual Symptomology Over Time
Authors: STRAKER G. , JACOBSON R. 
Published: August 2004

The study was designed to answer two questions: (a) Can a relationship over time between family interaction and individual symptomatology be demonstrated? (b) Can it be shown that changes in interaction have more influence on changes in the symptom than vice versa.Five interaction dimensions were taped in weekly, three‐quarter hour sessions over 20 weeks in five families, each consisting of a mother‐father‐child triad who met certain criteria and had an encopretic child. The interaction dimension scores were abstracted weekly from these sessions by content analyses relying on various scales. The derived ratio scores were then related to the number of days the child soiled himself in the week preceding and following the interaction measurement. The relationship was assessed by Pearson correlation coefficients and step‐wise multiple regression analyses adjusted to account for the possible inflationary effects of taking measures from the same subjects more than once. The results of the analyses answered both questions posed by the study in the affirmative, thus supporting the rationale underlying family therapy.
The Effects of Sibling Death on the Surviving Child: A Family Perspective
Authors: KRELL ROBERT , RABKIN LESLIE 
Published: August 2004

The death of a child invariably affects the family, who in effect become survivors. Adaptations are made in order to secure a new family equilibrium attendant upon such a loss. Surviving siblings not infrequently become the focus of maneuvers unconsciously designed to alleviate guilt and control fate through silence and efforts to maintain silence, through substitution for the lost child, and through endowing the survivor‐child with qualities of the deceased. Three types of clinically identifiable types of survivor‐children are described. Families that emphasize silence and focus on guilt, families in which the child becomes incomparably precious, and families in which substitution and replacement provide the major theme lead respectively to the “haunted,”“bound,” and “resurrected” child.These children share many features, as do their families, but there appears to be a connection between the family defensive maneuver and the specific consequences for a child of the bereaved family.
‘To each according to his needs’: public libraries and socially excluded people
Authors: Hicken Mandy 
Published: August 2004

AbstractTo deliver a comprehensive and efficient service to all the community, public libraries must first identify needs and allocate an appropriate level of resources. This article focuses on public libraries in England. It outlines: the Government's policy on social inclusion; the needs of the various socially excluded groups; partnerships and funding; staff training and motivation; and examples of good practice.
Social inclusion and the City of Swan public libraries in Western Australia
Authors: Lockyer‐Benzie Maureena 
Published: August 2004

AbstractThe focus of this paper is on an understanding of social exclusion/inclusion: the concept and how a specific public library service, namely the City of Swan Public Library service, has responded to this social issue. The terms social inclusion/exclusion are explored and clarified from an international, Western Australian State Government, and public library perspective. This is followed by a brief overview of Western Australia as an Australian state, and how public libraries operate based on a partnership with the State Library of Western Australia and Local Government. The City of Swan Public Libraries are described in some depth and also portrayed in their local setting namely the City of Swan, a city of extensive growth that offers a unique environment of both rural and urban areas. The concept of social inclusion is then applied to the City of Swan Public Library service and how the library service addresses social inclusion within its physical environment, policies, operations, future planning, programmes and services. This includes the results of a Library Non‐user Survey that was conducted in 2001. The aims of this survey were to: ascertain why non‐users within the City of Swan do not make use of the library facilities; explore why past members were not using the library services; examine the effectiveness of library promotions; and investigate the access to and usage of the Internet. The paper concludes with a list of the potential social conditions of which public libraries need to be aware in their strategic planning activities so that community members are not excluded from participating and accessing the public library service.
Developing health website quality assessment guidelines for the voluntary sector: outcomes from the Judge Project
Authors: Childs Sue 
Published: August 2004

AbstractBackground:  This paper describes the Judge project, the aim of which was to explore the need for health website quality assessment guidelines for the voluntary sector. Such guidelines would enable health consumers to assess the quality of health sites and assist support groups to produce their own good quality sites. The project was a partnership between the Information Management Research Institute, School of Informatics, Northumbria University and Contact a Family. It was supported by the Health Foundation.Methods:  The views of health consumers and support group members and workers were obtained by focus groups (35 attendees) and questionnaires (55 responses). They were asked questions about quality issues and concerns about Internet health information and any help they needed with judging the quality of health websites.Results:  The results supported the need for guidelines. The guidelines were written to reflect the requirements of health consumers and support groups articulated from the focus group and questionnaire data. They were then disseminated via a website.Conclusions:  There is a need to improve communication and information exchange between health consumers and professionals and official organizations; publicise support groups to patients and carers; set up local Webs of Trust, linking together voluntary and statutory organizations within a locality. Professionals and official organizations in the public sector should make information provision to patients and health consumers a priority. Information provision should be embedded in the clinical setting via guidelines, protocols and administrative structures. Professionals should be trained in the role of information and how to provide it in appropriate ways. Support groups should use the Judge guidelines to assist them in producing good quality websites. Support groups should promote the Judge guidelines to health consumers, to help them make their own quality judgement about health‐information websites.