bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Novel Biofilm Continuous Culture Method for Simultaneous Assessment of Architecture and Gaseous Metabolite Production
Authors: Yawata Yutaka , Nomura Nobuhiko , Uchiyama Hiroo 
Published: July 2008

ABSTRACT

The way that gaseous metabolite production changes along with biofilm architecture development is poorly understood. To address this question, we developed a novel flow reactor biofilm culture method that allows for simultaneous assessment of gaseous metabolite production and architecture visualization. In this report, we establish the utility of this method using denitrification by
Pseudomonas aeruginosa
biofilms as a model system. Using this method, we were able to collect and analyze gaseous metabolites produced by denitrification and also visualize biofilm architecture in a nondestructive manner. Thus, we propose that this novel method is a powerful tool to investigate potential relationships between biofilm architecture and the gas-producing metabolic activity of biofilms, providing new insights into biofilm ecology.
Global Transcriptional Response of the Alkali-Tolerant CyanobacteriumSynechocystissp. Strain PCC 6803 to a pH 10 Environment
Authors: Summerfield Tina C. , Sherman Louis A. 
Published: July 2008

ABSTRACTMany cyanobacterial strains are able to grow at a pH range from neutral to pH 10 or 11. Such alkaline conditions favor cyanobacterial growth (e.g., bloom formation), and cyanobacteria must have developed strategies to adjust to changes in CO2concentration and ion availability.Synechocystissp. strain PCC 6803 exhibits similar photoautotrophic growth characteristics at pH 10 and pH 7.5, and we examined global gene expression following transfer from pH 7.5 to pH 10 to determine cellular adaptations at an elevated pH. The strategies used to develop homeostasis at alkaline pH had elements similar to those of many bacteria, as well as components unique to phototrophic microbes. Some of the response mechanisms previously identified in other bacteria included upregulation of Na+/H+antiporters, deaminases, and ATP synthase. In addition, upregulated genes encoded transporters with the potential to contribute to osmotic, pH, and ion homeostasis (e.g., a water channel protein, a large-conductance mechanosensitive channel, a putative anion efflux transporter, a hexose/proton symporter, and ABC transporters of unidentified substrates). Transcriptional changes specific to photosynthetic microbes involved NADH dehydrogenases and CO2fixation. The pH transition altered the CO2/HCO3−ratio within the cell, and the upregulation of three inducible bicarbonate transporters (BCT1, SbtA, and NDH-1S) likely reflected a response to this perturbed ratio. Consistent with this was increased transcript abundance of genes encoding carboxysome structural proteins and carbonic anhydrase. Interestingly, the transition to pH 10 resulted in increased abundance of transcripts of photosystem II genes encoding extrinsic and low-molecular-weight polypeptides, although there was little change in photosystem I gene transcripts.
Rapid Identification and Typing of
Listeria
Species by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Authors: Barbuddhe Sukhadeo B. , Maier Thomas , Schwarz Gerold , Kostrzewa Markus , Hof Herbert , Domann Eugen , Chakraborty Trinad , Hain Torsten 
Published: July 2008

ABSTRACT

Listeria monocytogenes
is a food-borne pathogen that is the causative agent of human listeriosis, an opportunistic infection that primarily infects pregnant women and immunologically compromised individuals. Rapid, accurate discrimination between
Listeria
strains is essential for appropriate therapeutic management and timely intervention for infection control. A rapid method involving matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) that shows promise for identification of
Listeria
species and typing and even allows for differentiation at the level of clonal lineages among pathogenic strains of
L. monocytogenes
is presented. A total of 146 strains of different
Listeria
species and serotypes as well as clinical isolates were analyzed. The method was compared with the pulsed-field gel electrophoresis analysis of 48
Listeria
strains comprising
L. monocytogenes
strains isolated from food-borne epidemics and sporadic cases, isolates representing different serotypes, and a number of
Listeria
strains whose genomes have been completely sequenced. Following a short inactivation/extraction procedure, cell material from a bacterial colony was deposited on a sample target, dried, overlaid with a matrix necessary for the MALDI process, and analyzed by MALDI-TOF MS. This technique examines the chemistry of major proteins, yielding profile spectra consisting of a series of peaks, a characteristic “fingerprint” mainly derived from ribosomal proteins. Specimens can be prepared in a few minutes from plate or liquid cultures, and a spectrum can be obtained within 1 minute. Mass spectra derived from
Listeria
isolates showed characteristic peaks, conserved at both the species and lineage levels. MALDI-TOF MS fingerprinting may have potential for
Listeria
identification and subtyping and may improve infection control measures.
Aspergillus fumigatusRasA Regulates Asexual Development and Cell Wall Integrity
Authors: Fortwendel Jarrod R. , Fuller Kevin K. , Stephens Timothy J. , Bacon W. Clark , Askew David S. , Rhodes Judith C. 
Published: July 2008

ABSTRACTThe Ras family of proteins is a large group of monomeric GTPases. Members of the fungal Ras family act as molecular switches that transduce signals from the outside of the cell to signaling cascades inside the cell.A. fumigatusRasA is 94% identical to the essential RasA gene ofAspergillus nidulansand is the Ras family member sharing the highest identity to Ras homologs studied in many other fungi. In this study, we report thatrasAis not essential inA. fumigatus, but its absence is associated with slowed germination and a severe defect in radial growth. The ΔrasAhyphae were more than two times the diameter of wild-type hyphae, and they displayed repeated changes in the axis of polarity during hyphal growth. The deformed hyphae accumulated numerous nuclei within each hyphal compartment. The ΔrasAmutant conidiated poorly, but this phenotype could be ameliorated by growth on osmotically stabilized media. The ΔrasAmutant also showed increased susceptibility to cell wall stressors, stained more intensely with calcofluor white, and was refractory to lysing enzymes used to make protoplasts, suggesting an alteration of the cell wall. All phenotypes associated with deletion ofrasAcould be corrected by reinsertion of the wild-type gene. These data demonstrate a crucial role for RasA in both hyphal growth and asexual development inA. fumigatusand provide evidence that RasA function is linked to cell wall integrity.
Genetic Analysis of Trimethylamine
N
-Oxide Reductases in the Light Organ Symbiont
Vibrio fischeri
ES114
Authors: Dunn Anne K. , Stabb Eric V. 
Published: July 2008

ABSTRACT

Trimethylamine
N
-oxide (TMAO) reductases are widespread in bacteria and often function in anaerobic respiration. The regulation and expression of TMAO reductase operons have been well studied in model genera such as
Escherichia
,
Shewanella
, and
Rhodobacter
, although TMAO reductases are present in many other bacteria, including the marine
Vibrio
species. The genome sequence of
Vibrio fischeri
revealed three putative TMAO reductase operons, and a previous report identified TMAO reductase activity in symbiotic
V. fischeri
isolates associated with the light organs of adult Hawaiian bobtail squid,
Euprymna scolopes
. We examined the roles and regulation of these three operons using mutational analyses and promoter-reporter fusions. We found that the
torECA
promoter, and to a lesser extent the
torYZ
and
dmsABC
promoters, were active during symbiotic colonization of juvenile
E. scolopes
; however, a
V. fischeri
strain lacking TMAO reductase activity displays no discernible colonization defect over the first 48 h. Our studies also revealed that
torECA
has the most active promoter of the putative TMAO reductase operons, and TorECA is the major contributor to TMAO-dependent growth in
V. fischeri
under the conditions tested. Interestingly, the transcriptional regulation of TMAO reductase operons in
V. fischeri
appears to differ from that in previously studied organisms, such as
Escherichia coli
, which may reflect differences in gene arrangement and bacterial habitat. This study lays the foundation for using
V. fischeri
as a model system for studying TMAO reductases in the
Vibrionaceae
.
Lawsonia intracellularisContains a Gene Encoding a Functional Rickettsia-Like ATP/ADP Translocase for Host Exploitation
Authors: Schmitz-Esser Stephan , Haferkamp Ilka , Knab Silvia , Penz Thomas , Ast Michelle , Kohl Christian , Wagner Michael , Horn Matthias 
Published: July 2008

ABSTRACTATP/ADP translocases are a hallmark of obligate intracellular pathogens related to chlamydiae and rickettsiae. These proteins catalyze the highly specific exchange of bacterial ADP against host ATP and thus allow bacteria to exploit their hosts' energy pool, a process also referred to as energy parasitism. The genome sequence of the obligate intracellular pathogenLawsonia intracellularis(Deltaproteobacteria), responsible for one of the most economically important diseases in the swine industry worldwide, revealed the presence of a putative ATP/ADP translocase most similar to known ATP/ADP translocases of chlamydiae and rickettsiae (around 47% amino acid sequence identity). The gene coding for the putative ATP/ADP translocase ofL. intracellularis(L. intracellularisnucleotide transporter 1 [NTT1Li]) was cloned and expressed in the heterologous hostEscherichia coli. The transport properties of NTT1Liwere determined by measuring the uptake of radioactively labeled substrates byE. coli. NTT1Litransported ATP in a counterexchange mode with ADP in a highly specific manner; the substrate affinities determined were 236.3 (± 36.5) μM for ATP and 275.2 (± 28.1) μM for ADP, identifying this protein as a functional ATP/ADP translocase. NTT1Liis the first ATP/ADP translocase from a bacterium not related toChlamydiaeorRickettsiales, showing that energy parasitism by ATP/ADP translocases is more widespread than previously recognized. The occurrence of an ATP/ADP translocase inL. intracellularisis explained by a relatively recent horizontal gene transfer event with rickettsiae as donors.
RNase Activity of Polynucleotide Phosphorylase Is Critical at Low Temperature inEscherichia coliand Is Complemented by RNase II
Authors: Awano Naoki , Inouye Masayori , Phadtare Sangita 
Published: July 2008

ABSTRACTInEscherichia coli, the cold shock response is exerted upon a temperature change from 37°C to 15°C and is characterized by induction of several cold shock proteins, including polynucleotide phosphorylase (PNPase), during acclimation phase. InE. coli, PNPase is essential for growth at low temperatures; however, its exact role in this essential function has not been fully elucidated. PNPase is a 3′-to-5′ exoribonuclease and promotes the processive degradation of RNA. Our screening of anE. coligenomic library for an in vivo counterpart of PNPase that can compensate for its absence at low temperature revealed only one protein, another 3′-to-5′ exonuclease, RNase II. Here we show that the RNase PH domains 1 and 2 of PNPase are important for its cold shock function, suggesting that the RNase activity of PNPase is critical for its essential function at low temperature. We also show that its polymerization activity is dispensable in its cold shock function. Interestingly, the third 3′-to-5′ processing exoribonuclease, RNase R ofE. coli, which is cold inducible, cannot complement the cold shock function of PNPase. We further show that this difference is due to the different targets of these enzymes and stabilization of some of the PNPase-sensitive mRNAs, likefis, in the Δpnpcells has consequences, such as accumulation of ribosomal subunits in the Δpnpcells, which may play a role in the cold sensitivity of this strain.
Toxic Introns and Parasitic Intein in
Coxiella burnetii
: Legacies of a Promiscuous Past
Authors: Raghavan Rahul , Hicks Linda D. , Minnick Michael F. 
Published: July 2008

ABSTRACT

The genome of the obligate intracellular pathogen
Coxiella burnetii
contains a large number of selfish genetic elements, including two group I introns (Cbu.L1917 and Cbu.L1951) and an intervening sequence that interrupts the 23S rRNA gene, an intein (Cbu.DnaB) within
dnaB
and 29 insertion sequences. Here, we describe the ability of the intron-encoded RNAs (ribozymes) to retard bacterial growth rate (toxicity) and examine the functionality and phylogenetic history of Cbu.DnaB. When expressed in
Escherichia coli
, both introns repressed growth, with Cbu.L1917 being more inhibitory. Both ribozymes were found to associate with ribosomes of
Coxiella
and
E. coli
. In addition, ribozymes significantly reduced in vitro luciferase translation, again with Cbu.L1917 being more inhibitory. We analyzed the relative quantities of ribozymes and genomes throughout a 14-day growth cycle of
C. burnetii
and found that they were inversely correlated, suggesting that the ribozymes have a negative effect on
Coxiella
's growth. We determined possible sites for ribozyme associations with 23S rRNA that could explain the observed toxicities. Further research is needed to determine whether the introns are being positively selected because they promote bacterial persistence or whether they were fixed in the population due to genetic drift. The intein, Cbu.DnaB, is able to self-splice, leaving the host protein intact and presumably functional. Similar inteins have been found in two extremophilic bacteria (
Alkalilimnicola ehrlichei
and
Halorhodospira halophila
) that are distantly related to
Coxiella
, making it difficult to determine whether the intein was acquired by horizontal gene transfer or was vertically inherited from a common ancestor.
A novel combination: ranpirnase and rosiglitazone induce a synergistic apoptotic effect by down-regulating Fra-1 and Survivin in cancer cells
Authors: Ramos-Nino Maria E. , Littenberg Benjamin 
Published: July 2008

Abstract
Accumulating evidence supports the idea that two known phosphatidylinositol 3′-kinase (PI3K) downstream proteins, Fra-1 and Survivin, are potential targets for cancer therapy. Increased expression of Fra-1, a Fos family member of the transcription factor activator protein-1, has been implicated in both the maintenance and the progression of the transformed state of several cancer cells. In addition, high Survivin expression in tumors correlates with more aggressive behavior, lower response to chemotherapeutic drugs, and shortened survival time. Previously, we reported that, in malignant mesothelioma cells with increased PI3K activity, small-molecule inhibitors of the PI3K/AKT pathway acted cooperatively with the amphibian RNase chemotherapeutic drug ranpirnase to inhibit cell growth. Because the thiazolidinedione antidiabetic drug rosiglitazone targets the PI3K/AKT pathway, we investigated the effect of the combination of these two drugs in cell survival in several cancer cell lines. We show here that the combination of ranpirnase and rosiglitazone synergistically decreases cell viability and increases cell apoptosis in several cancer cell lines. Cell killing is associated with decreased Fra-1 and Survivin expression and knockdown of Fra-1 increases cell killing by ranpirnase in a dose-dependent manner but not by rosiglitazone. The drug combination does not have a synergistic effect on killing in Fra-1 knockdown cells, showing that Fra-1 modulation accounts in part for the synergism. The novel drug combination of ranpirnase and rosiglitazone is a promising combination to treat cancers with increased PI3K-dependent Fra-1 expression or Survivin. [Mol Cancer Ther 2008;7(7):1871–9]
Exploring Contextual Theology in Australia in Dialogue with Indigenous People
Authors: Budden Chris 
Published: July 2008

AbstractThis article considers the difference made to contextual theology (in belief and practice) in Australia, if it takes seriously the claim that the primary relationship shaping such a theology is with the First People of the continent. Hence, it considers how theology takes shape in the context of invasion, dispossession and ongoing oppression. Drawing on the insights gained during a gathering of Indigenous people, which began to explore the outlines of a Christian theology that would provide a foundation for more than simple survival, this article seeks to identify the primary issues shaping contextual theology in Australia. It is an invitation for others to join the conversation, and to take seriously the reality that theology in Australia is done on what has always been and still is Aboriginal land.
The War on Terror in Ruatoki
Authors: Rae Murray 
Published: July 2008

AbstractThis article offers some theological reflections on a recent episode in Aotearoa (New Zealand) in which a Maori community housing an alleged terrorist network was subjected to a police raid. Many innocent people, including children, were caught up in the raid thus bringing to mind other episodes in New Zealand's history in which Maori have been subjected to police and state aggression. These episodes provide a starting point for reflection upon public theology and the limits of state power, upon the nature of forgiveness, and upon the offering of public apologies for past offences.
Yes, No, Cancel: Clicking Our Way to a Public Theology of Cyberdemocracy
Authors: Stoddart Eric 
Published: July 2008

AbstractThis article defines cyberdemocracy within the framework of a digital and social space. It places this emerging practice in the context of the displacement of political power and action, and a range of visions for digital technologies in general. A number of dimensions of the 'digital divide' are explored. Representative theological perspectives on technology are used to develop a theological digital technology that identifies it as a dimension of giftedness instantiated in human co-creativity with God. In this article the bifurcation of 'spiritual' and 'technology' is rejected in favour of a model that encourages the celebratory and ethical aspects of digital technology. It finds contemporary predilections for multiple 'data-images' in our online presence promiscuous and inhibiting to relationality when viewed from a Christian perichoretic perspective. Finally, the article draws conclusions that encourage political responses to the ideology of interactivity and that contend for both state and civil society to be in partnership in addressing the multiple factors of the 'digital divide'.
The Construction of Public Theology: An Ethnographic Study of the Relationship between the Theological Academy and Local Clergy in South Africa
Authors: Day Katie 
Published: July 2008

AbstractThis article presents findings of research conducted in the summer of 2006, and it focuses on how public theology is understood in the academy in relation to the realities encountered by clergy and lay leaders in a challenging ministry context. Through ethnographic research based in South Africa, I examined the relationship between congregations confronting the AIDS epidemic and widespread poverty, and the construction of public theology in the theological academy at Stellenbosch University, South Africa. The research asked: what is the nature of the correspondence between 'formal' public theology and the local, 'lived' theologies of those doing ministry in South Africa; how does local experience influence the ways that the academy prepares leaders for public ministry. The findings from this study, as discussed in this article, have implications for theological education, in terms of enhancing the public orientation of institutions and understanding the link between context and curriculum.
Developing narrative research in supportive and palliative care: the focus on illness narratives
Authors: Bingley AF , Thomas C , Brown J , Reeve J , Payne S 
Published: July 2008

The phenomenon of the ‘illness narrative’ is well-documented, in the last 25 years, of increasing interest to researchers in health and social sciences. Personal stories about the experience of facing the end of life also have an established history of particular relevance for palliative care clinicians. In this article, we review and describe a range of narrative analysis approaches that may be of use in palliative care. In particular, we distinguish between qualitative analysis applied to narratives and narrative analysis as a method. We discuss the potential benefits and challenges in the use of narrative research methods as a means to deepen our understanding of patient, carer and health professionals’ experience, and to support improvements in end of life care policy and practice.
The nature and use of bereavement support services in a hospice setting
Authors: Roberts A , McGilloway S 
Published: July 2008

This study formed part of a larger project designed to evaluate a hospice-based bereavement support service in Ireland. It involved a detailed assessment of the views of service attenders and non-attenders. A postal survey was administered to all bereaved clients who were invited to one or more bereavement support services ( n = 517). Respondents ( n = 243; 47%) completed: 1) a Bereavement Services Questionnaire; 2) a measure of grief reaction (TRIG) and 3) a measure of religiosity (SCSORF). A total of 243 people (47%) returned completed questionnaires, most of whom were satisfied with the service, (although not all had attended all elements of the bereavement service). However, a number of improvements were emphasised. Several statistically significant differences ( P < 0.05) also emerged between service attenders and non-attenders with respect to grief reaction and other key factors (e.g., the age and relationship to the deceased). The findings emphasise the needs and views of both attenders and non-attenders and provide important lessons for the implementation and development of hospice-based bereavement support services.
Persistent T1 hypointensity as an MRI marker for treatment efficacy in multiple sclerosis
Authors: van den Elskamp IJ , Lembcke J , Dattola V , Beckmann K , Pohl C , Hong W , Sandbrink R , Wagner K , Knol DL , Uitdehaag B , Barkhof F 
Published: July 2008

Background MRI is often used as primary outcome measure in phase II clinical trials in multiple sclerosis (MS). Since persistent T1 hypointense lesions are a surrogate parameter for axonal damage and demyelination, they may serve as a marker for monitoring the efficacy of neuroprotective drugs. At present, a power analysis using black hole (BH) evolution as primary outcome measure has not been performed. Objective To assess the feasibility of using BH evolution on serial brain MR images as primary outcome measure in proof of concept studies in MS. Methods MRI-data obtained from 169 active RRMS patients were analysed for BH evolution by determining the cumulative number of contrast enhancing lesions (CEL) evolving into a persistent black hole (PBH) after 3 months. With a parametric simulation procedure, based on a statistical distribution fitting the data, sample sizes were calculated. Results 21.2% of the total number of CELs observed during the study period evolved into a PBH. Ring enhancing lesions evolved most frequently into a PBH (59.4%), followed by lesions larger than 10 mm (57.4%) and periventricular CELs (30.6%). The simulation procedure, based on the statistical negative binomial (NB) model resulted in a sample sizes between 200 subjects and 30 subjects per arm, for treatment effects ranging from 50% to 90% reduction of the number of CELs evolving into a PBH, respectively. Conclusion To perform a MRI monitored phase II clinical trial with a feasible sample size, using the evolution of CELs into PBHs as primary outcome parameter, a potent drug is required to obtain sufficient power.