bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Characterization of the Nonphotosynthetic Partner Bacterium in the Consortium “
Chlorochromatium aggregatum
”
Authors: Kanzler Birgit E. M. , Pfannes Kristina R. , Vogl Kajetan , Overmann Jörg 
Published: November 2005

ABSTRACT

Phototrophic consortia represent valuable model systems for the study of signal transduction and coevolution between different bacteria. The phototrophic consortium “
Chlorochromatium aggregatum
” consists of a colorless central rod-shaped bacterium surrounded by about 20 green-pigmented epibionts. Although the epibiont was identified as a member of the green sulfur bacteria, and recently isolated and characterized in pure culture, the central colorless bacterium has been identified as a member of the β-
Proteobacteria
but so far could not be characterized further. In the present study, “
C. aggregatum
” was enriched chemotactically, and the 16S rRNA gene sequence of the central bacterium was elucidated. Based on the sequence information, fluorescence in situ hybridization probes targeting four different regions of the 16S rRNA were designed and shown to hybridize exclusively to cells of the central bacterium. Phylogenetic analyses of the 1,437-bp-long sequence revealed that the central bacterium of “
C. aggregatum
” represents a so far isolated phylogenetic lineage related to
Rhodoferax
spp.,
Polaromonas vacuolata
, and
Variovorax paradoxus
within the family
Comamonadaceae
. The majority of relatives of this lineage are not yet cultured and were found in low-temperature aquatic environments or aquatic environments containing xenobiotica or hydrocarbons. In CsCl-bisbenzimidazole equilibrium density gradients, genomic DNA of the central bacterium of “
Chlorochromatium aggregatum
” formed a distinct band which could be detected by quantitative PCR using specific primers. Using this method, the G+C content of the central bacterium was determined to be 55.6 mol%.
Rhodopseudomonas palustris
Regulons Detected by Cross-Species Analysis of Alphaproteobacterial Genomes
Authors: Conlan Sean , Lawrence Charles , McCue Lee Ann 
Published: November 2005

ABSTRACT

Rhodopseudomonas palustris
, an α-proteobacterium, carries out three of the chemical reactions that support life on this planet: the conversion of sunlight to chemical-potential energy; the absorption of carbon dioxide, which it converts to cellular material; and the fixation of atmospheric nitrogen into ammonia. Insight into the transcription-regulatory network that coordinates these processes is fundamental to understanding the biology of this versatile bacterium. With this goal in mind, we predicted regulatory signals genomewide, using a two-step phylogenetic-footprinting and clustering process that we had developed previously. In the first step, 4,963 putative transcription factor binding sites, upstream of 2,044 genes and operons, were identified using cross-species Gibbs sampling. Bayesian motif clustering was then employed to group the cross-species motifs into regulons. We have identified 101 putative regulons in
R. palustris
, including 8 that are of particular interest: a photosynthetic regulon, a flagellar regulon, an organic hydroperoxide resistance regulon, the LexA regulon, and four regulons related to nitrogen metabolism (FixK
2
, NnrR, NtrC, and σ
54
). In some cases, clustering allowed us to assign functions to proteins that previously had been annotated with only putative functions; we have identified RPA0828 as the organic hydroperoxide resistance regulator and RPA1026 as a cell cycle methylase. In addition to predicting regulons, we identified a novel inverted repeat that likely forms a highly conserved stem-loop and that occurs downstream of over 100 genes.
Global Transcriptional Profiling of
Shewanella oneidensis
MR-1 during Cr(VI) and U(VI) Reduction
Authors: Bencheikh-Latmani Rizlan , Williams Sarah Middleton , Haucke Lisa , Criddle Craig S. , Wu Liyou , Zhou Jizhong , Tebo Bradley M. 
Published: November 2005

ABSTRACT

Whole-genome DNA microarrays were used to examine the gene expression profile of
Shewanella oneidensis
MR-1 during U(VI) and Cr(VI) reduction. The same control, cells pregrown with nitrate and incubated with no electron acceptor, was used for the two time points considered and for both metals. U(VI)-reducing conditions resulted in the upregulation (≥3-fold) of 121 genes, while 83 genes were upregulated under Cr(VI)-reducing conditions. A large fraction of the genes upregulated [34% for U(VI) and 29% for Cr(VI)] encode hypothetical proteins of unknown function. Genes encoding proteins known to reduce alternative electron acceptors [fumarate, dimethyl sulfoxide, Mn(IV), or soluble Fe(III)] were upregulated under both U(VI)- and Cr(VI)-reducing conditions. The involvement of these upregulated genes in the reduction of U(VI) and Cr(VI) was tested using mutants lacking one or several of the gene products. Mutant testing confirmed the involvement of several genes in the reduction of both metals:
mtrA
,
mtrB
,
mtrC
, and
menC
, all of which are involved in Fe(III) citrate reduction by MR-1. Genes encoding efflux pumps were upregulated under Cr(VI)- but not under U(VI)-reducing conditions. Genes encoding proteins associated with general (e.g.,
groL
and
dnaJ
) and membrane (e.g.,
pspBC
) stress were also upregulated, particularly under U(VI)-reducing conditions, pointing to membrane damage by the solid-phase reduced U(IV) and Cr(III) and/or the direct effect of the oxidized forms of the metals. This study sheds light on the multifaceted response of MR-1 to U(VI) and Cr(VI) under anaerobic conditions and suggests that the same electron transport pathway can be used for more than one electron acceptor.
Colonization of Mucin by Human Intestinal Bacteria and Establishment of Biofilm Communities in a Two-Stage Continuous Culture System
Authors: Macfarlane Sandra , Woodmansey Emma J. , Macfarlane George T. 
Published: November 2005

ABSTRACT

The human large intestine is covered with a protective mucus coating, which is heavily colonized by complex bacterial populations that are distinct from those in the gut lumen. Little is known of the composition and metabolic activities of these biofilms, although they are likely to play an important role in mucus breakdown. The aims of this study were to determine how intestinal bacteria colonize mucus and to study physiologic and enzymatic factors involved in the destruction of this glycoprotein. Colonization of mucin gels by fecal bacteria was studied in vitro, using a two-stage continuous culture system, simulating conditions of nutrient availability and limitation characteristic of the proximal (vessel 1) and distal (vessel 2) colon. The establishment of bacterial communities in mucin gels was investigated by selective culture methods, scanning electron microscopy, and confocal laser scanning microscopy, in association with fluorescently labeled 16S rRNA oligonucleotide probes. Gel samples were also taken for analysis of mucin-degrading enzymes and measurements of residual mucin sugars. Mucin gels were rapidly colonized by heterogeneous bacterial populations, especially members of the
Bacteroides fragilis
group, enterobacteria, and clostridia. Intestinal bacterial populations growing on mucin surfaces were shown to be phylogenetically and metabolically distinct from their planktonic counterparts.
Distribution, Localization, and Phylogeny of Abundant Populations of
Crenarchaeota
in Anaerobic Granular Sludge
Authors: Collins Gavin , O'Connor Leanne , Mahony Thérèse , Gieseke Armin , de Beer Dirk , O'Flaherty Vincent 
Published: November 2005

ABSTRACT

Eight anaerobic granular sludges were surveyed for
Crenarchaeota
using rRNA gene cloning. Microbial arrangement and substrate uptake patterns were elucidated by fluorescent in situ hybridization and beta imaging. Group 1.3
Crenarchaeota
represented up to 50% of
Archaea
and 25% of the total microbiota in five sludges.
Crenarchaeota
were localized in close association with methanogenic
Archaea.
Application of Measurements of Transepithelial Electrical Resistance of Intestinal Epithelial Cell Monolayers To Evaluate Probiotic Activity
Authors: Klingberg Trine Danø , Pedersen Maja Herold , Cencic Avrelija , Budde Birgitte Bjørn 
Published: November 2005

ABSTRACT

Among five potentially probiotic lactobacilli investigated,
Lactobacillus plantarum
MF1298 and
Lactobacillus salivarius
DC5 showed the highest increase in the transepithelial electrical resistance (TER) of polarized monolayers of Caco-2 cells, and this increase was shown to be dose dependent. Furthermore, preincubation with MF1298 attenuated a decrease in TER induced by
Listeria monocytogenes
.
Strain- and Genotype-Specific Differences in Virulence of
Paenibacillus larvae
subsp.
larvae
, a Bacterial Pathogen Causing American Foulbrood Disease in Honeybees
Authors: Genersch Elke , Ashiralieva Ainura , Fries Ingemar 
Published: November 2005

ABSTRACT

Virulence variations of
Paenibacillus larvae
subsp.
larvae
, the causative agent of American foulbrood disease of honeybees, were investigated by analysis of 16 field isolates of this pathogen, belonging to three previously characterized genotypes, as well as the type strain (ATCC 9545) of
P. larvae
subsp.
larvae
, with exposure bioassays. We demonstrated that the strain-specific 50% lethal concentrations varied within an order of magnitude and that differences in amount of time for the pathogen to kill 100% of the infected hosts (LT
100
) correlated with genotype. One genotype killed rather quickly, with a mean LT
100
of 7.8 ± 1.7 days postinfection, while the other genotypes acted more slowly, with mean LT
100
s of 11.2 ± 0.8 and 11.6 ± 0.6 days postinfection.
Evidence for Horizontal Transfer of 1-Aminocyclopropane-1-Carboxylate Deaminase Genes
Authors: Hontzeas N. , Richardson A. O. , Belimov A. , Safronova V. , Abu-Omar M. M. , Glick B. R. 
Published: November 2005

ABSTRACT
PCR was used to rapidly identify and isolate 1-aminocyclopropane-1-carboxylate (ACC) deaminase genes from bacteria. The Shimodaira-Hasegawa test was used to assess whether phylogenetically anomalous gene placements suggestive of horizontal gene transfer (HGT) were significantly favored over vertical transmission. The best maximum likelihood (ML) ACC deaminase tree was significantly more likely than four alternative ML trees, suggesting HGT.
Putative Exposed Aromatic and Hydroxyl Residues on the Surface of the N-Terminal Domains of Chi1 from
Aeromonas caviae
CB101 Are Essential for Chitin Binding and Hydrolysis
Authors: Li Qiang , Wang Fengping , Zhou Ying , Xiao Xiang 
Published: November 2005

ABSTRACT

Chitinase Chi1 of
Aeromonas caviae
CB101 possesses chitin binding sites at both its N and C termini. Four putative exposed residues aligned in a line on the surface of the N-terminal domains of Chi1 were found to contribute to the enzyme-chitin binding and hydrolysis via site-directed mutagenesis. Also, it was found that Chi1 requires the cooperation of the N- and C-terminal domains to bind fully with crystalline and colloidal chitin.
Occurrence of
Listeria
spp. in Effluents of French Urban Wastewater Treatment Plants
Authors: Paillard Delphine , Dubois Véronique , Thiebaut Rodolphe , Nathier Fany , Hoogland Emilie , Caumette Pierre , Quentin Claudine 
Published: November 2005

ABSTRACT

Listeria
spp. were found in most treated waters (84.4%) and raw sludge (89.2%) of six French urban wastewater treatment plants and one composting facility, examined monthly over a 1-year period. Most strains belonged to
Listeria monocytogenes
, serotypes 4b/4e being predominant. Sludge composting and liming reduced or prevented
Listeria
contamination.
Rhizobium leguminosarum
Biovar viciae Symbiotic Hydrogenase Activity and Processing Are Limited by the Level of Nickel in Agricultural Soils
Authors: Ureta Ana-Claudia , Imperial Juan , Ruiz-Argüeso Tomás , Palacios Jose M. 
Published: November 2005

ABSTRACT

Analysis of levels of hydrogenase processing and activity in
Rhizobium leguminosarum
biovar viciae bacteroids from pea (
Pisum sativum
) plants showed that the oxidation of nitrogenase-evolved hydrogen is limited by the availability of nickel in agricultural soils. This limitation was overcome by using an inoculant strain engineered for higher hydrogenase expression.
When Coupled to Natural Transformation inAcinetobactersp. Strain ADP1, PCR Mutagenesis Is Made Less Random by Mismatch Repair
Authors: Buchan Alison , Ornston L. Nicholas 
Published: November 2005

ABSTRACTRandom PCR mutagenesis is a powerful tool for structure-function analysis of targeted proteins, especially when coupled with DNA integration through natural transformation followed by selection for loss of function. The technique has been applied successfully to structure-function analysis of transcriptional regulators, enzymes, and transporters inAcinetobactersp. strain ADP1. However, the mismatch repair system prevents the full spectrum of nucleotide substitutions that may be selected at the level of protein function from being recovered. This barrier may be overcome by introducing PCR-mutagenized genes into strains in which the corresponding genes have been deleted.
Identification of Pilus-Like Structures and Genes in
Microcystis aeruginosa
PCC7806
Authors: Nakasugi Kenlee , Neilan Brett A. 
Published: November 2005

ABSTRACT

Four putative type IV pilus genes from the toxic, naturally transformable
Microcystis aeruginosa
PCC7806 were identified. Three of these genes were clustered in an arrangement which is identical to that from other cyanobacterial genomes. Type IV pilus-like appendages were also observed by electron microscopy.
Parental consent for newborn screening in southern Taiwan
Authors: Huang M-C , Lee C-K , Lin S-J , Lu I-C 
Published: November 2005

Objects:With the advent of genetic technologies, many genetic/metabolic disorders can be detected asymptomatically but might be untreatable, and the benefits and risks of screening for them are not fully known. The purpose of this study is to explore current practice with regard to the parental consent process in newborn screening (NBS).Design:Staff in 23 obstetric clinics/hospitals that conduct NBS in one city of southern Taiwan were interviewed. Using content analysis, 15 interview transcripts, eight completed questionnaires, and other relevant documents from the 23 clinics/hospitals were analysed to reveal the framework of the parental consent process in NBS in southern Taiwan.Main measures:Three categories—informed consent, informed dissent, and no informed/consent—were developed to analyse the parental consent process in NBS.Results:The parental consent procedures in NBS and the quality of the information provided before obtaining consent vary widely. Because the traditional NBS was incorporated into routine paediatric practices in most clinics/hospitals, the most frequently encountered consent model is “informed dissent” (60.9%) and “no informed/consent” (30.4%); while an “informed consent” model (45.5%) is the frequent model for screening rare metabolic/genetic disorders.Conclusions:Specific guidelines to regulate the parental consent process for NBS are essential. Further studies should investigate parental responses to NBS, taking these as the basis on which to establish an informed consent model in Taiwan.
Death or Declaw: Dealing with Moral Ambiguity in a Veterinary Hospital
Authors: Atwood-Harvey Dana 
Published: November 2005

AbstractThe medical practice of declawing has received much political debate over the past few years. Yet, empirical and theoretical research on how this practice is maintained and the ethical positions of those who actually participate in this work is lacking. Drawing from 9 months of ethnographic fieldwork in a feline-specific veterinary hospital and open-ended interviews with veterinarians and staff, this study examines veterinary staff members' attitudes toward, and strategies for, dealing with the medical practice of declawing. Specifically, findings show that a number of staff felt uncomfortable with their participation in onychectomy (declawing) and relied heavily on organizational support structures to cope both with these feelings and the moral ambiguity about the practice. Relying on these structures, the veterinarians and their staff are able simultaneously to define felines as subjects worthy of respect for their quality of life, protect their own self-identity as people who work toward the best interest of animals, and paradoxically support action toward felines that they find morally objectionable.
Pernicious Portrayals: The Impact of Children's Attachment to Animals of Fiction on Animals of Fact
Authors: Henderson Antonia , Anderson Marla 
Published: November 2005

AbstractThis paper argues that the lack of distinction between human and nonhuman animals in the fantastic world of children's literature and film results in distorted representations of intelligence, capabilities, and morality of nonhuman animals. From the perspective of attachment theory, the paper shows how humans internalize and sustain misrepresentations throughout adulthood and how these misrepresentations influence relationships with real animals. An ongoing search for the ideal "Walt Disney dog" of childhood jeopardizes relationships to companion animals. Trying to recreate the fantasy dog by genetic manipulation of a real animal's characteristics results in needless distress for companion animals. Because the companion does not meet expectations engendered by childhood stories, normal dog behaviour—chewing, digging, and barking—may result in relinquishing the dog for adoption and subsequent euthanasia. Shifting to the scientific realm, the paper discusses the on-going debate on the study of animals' human-like abilities, most salient in ape language programs. In closing, the paper discusses the disservice done to real animals as illusions of childhood and subsequent misunderstandings leave them judged by impossible, anthrocentric standards—which they rarely can fulfill.
The coordination of ky / ' l kn in Cant. i 1-3 and related texts
Authors: Perry T. A. 
Published: November 2005

AbstractAlthough the locution ky ' l kn introducing adverbial clauses of cause is well known, the coordination of its separate parts is virtually unstudied. My interest here is in how causality is expressed by groups of clauses in which ky is coordinated with ' l kn, creating a total structure of "since" / "therefore." A clearer understanding of this structure has important implications for the interpretation of well-known passages of Hebrew Scripture, notably the opening strophes of The Song of Songs and Psalms.
Free-Sorting of Colors Across Cultures: Are there Universal Grounds for Grouping?
Authors: Roberson Debi , Davies Ian , Corbett Greville , Vandervyver Marieta 
Published: November 2005

Abstract
These studies examined naming and free-sorting behavior by informants speaking a wide range of languages, from both industrialized and traditional cultures. Groups of informants, whose color vocabularies varied from 5 to 12 basic terms, were given an unconstrained color grouping task to investigate whether there are systematic differences between cultures in grouping behavior that mirror linguistic differences and, if there are not, what underlying principles might explain any universal tendencies. Despite large differences in color vocabulary, there were substantial similarities in grouping behavior across language groups, and substantial within-language variation across informants. It seems that all informants group stimuli based on some criterion of perceptual similarity, but those with large color vocabularies are more likely to group stimuli in line with their basic color terms. The data are best accounted for by a hybrid system that combines a universal principle of grouping by similarity with culture-specific category salience.
Reflections on Therapeutic Practice Guided by a Husserlian Perspective
Authors: Giorgi Barbro 
Published: November 2005

AbstractIn this article, there is a suggestion that the application of certain key concepts or procedures of Husserlian phenomenology can be helpful in the practice of therapy. It is well known that how a therapist is present to a client and his or her story is critical for the success of therapy. What is less clear, however, is how to address this "way of being" in therapy and what kinds of interventions are helpful to clients. In addressing some of these difficult issues, the Husserlian concepts found to be helpful are (1) Husserl's chief directive to go "back to the matters themselves," (2) the distinction among real and irreal objects, (3) presence to the order of phenomena, the phenomenal realm, (4) the intentional-fulfilling-identifying nature of conscious acts, (5) the phenomenological-psychological reduction, and (6) the discovery and description of eidetic structures of experience. These fundamental philosophical distinctions are taken up within a psychological perspective and elaborated and used within a phenomenological psychological perspective.
Living Through Some Positive Experiences of Psychotherapy
Authors: Giorgi Amedeo , Gallegos Nico 
Published: November 2005

AbstractIn this article three clients were asked to describe some alleviation of symptoms that they may have experienced in psychotherapy. The descriptions were broad enough so that they were able to be characterized as positive experiences. Positive experiences were easy to come by but they took place within a context of ongoing therapy that included as well negative experiences and lack of progress. Instrumental for the existence of the positive experiences was a high quality relationship with the therapist that was safe, trusting, caring and non-judgmental. Phenomenological reflections on the empirical findings indicated 1) that focused symptom relief was not necessarily the best strategy for outcome evaluation of therapy, 2) threw doubt on termination of therapy as a good criterion for the experience of therapy and 3) concluded that the relationship between therapist and client is complex but unified in a way that needs further clarification.
D-space and Deform Closure Grasps of Deformable Parts
Authors: Gopalakrishnan K. “Gopal” , Goldberg Ken 
Published: November 2005

Building on the well-established form closure framework for holding rigid parts, in this paper we propose a new framework for holding deformable parts. We consider the class of deformable parts that can be modeled as linearly elastic polygons with a triangular finite element mesh and given stiffness matrix. We define the D-space (deformation-space) of a part as the C-space of all its mesh nodes. Free space is the intersection of the set of topology-preserving mesh configurations with the complement of the union of all D-obstacles that represent collisions of the part with finger bodies. Consider a given set of finger bodies in frictionless contact with a part. When positive work is needed to release the part, we say that it is in deform closure. We present numerical examples and prove two results: (1) if a contact set holds a rigid part in form closure, it will hold the equivalent deformable part in deform closure and (2) deform closure is frame invariant.We then consider frictionless deform closure grasps with two contact points. We define a measure of grasp quality based on balancing the potential energy needed to release the part against the potential energy that would result in plastic deformation. Given two jaw contacts at the perimeter nodes, we develop numerical algorithms to determine the optimal jaw separation based on this metric. For a part with n mesh nodes and p perimeter nodes, we give an algorithm that computes the optimal separation in time O(n3 p2 +p6 log p) and an approximation algorithm that runs in time O(n3 p2 +(p2 /ε)log p) .