bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature dependence of Fe(III) and sulfate reduction rates and its effect on growth and composition of bacterial enrichments from an acidic pit lake neutralization experiment
Authors: MEIER J. , COSTA R. , SMALLA K. , BOEHRER B. , WENDT‐POTTHOFF K.
Published: March 2006

Microbial Fe(III) and sulfate reduction are important electron transport processes in acidic pit lakes and stimulation by the addition of organic substrates is a strategy to remove acidity, iron and sulfate. This principle was applied in a pilot‐scale enclosure in pit lake 111 (Brandenburg, Germany). Because seasonal and spatial variation of temperature may affect the performance of in situ experiments considerably, the influence of temperature on Fe(III) and sulfate reduction was investigated in surface sediments from the enclosure in the range of 4–28 °C. Potential Fe(III) reduction and sulfate reduction rates increased exponentially with temperature, and the effect was quantified in terms of the apparent activation energy Ea measuring 42–46 kJ mol−1 and 52 kJ mol−1, respectively. Relatively high respiration rates at 4 °C and relatively low Q10 values (∼2) indicated that microbial communities were well adapted to low temperatures. In order to evaluate the effect of temperature on growth and enrichment of iron and sulfate‐reducing bacterial populations, MPN (Most Probable Number) dilution series were performed in media selecting for the different bacterial groups. While the temperature response of specific growth rates of acidophilic iron reducers showed mesophilic characteristics, the relatively high specific growth rates of sulfate reducers at the lowest incubation temperature indicated the presence of moderate psychrophilic bacteria. In contrast, the low cell numbers and low specific growth rates of neutrophilic iron reducers obtained in dilution cultures suggest that these populations play a less significant role in Fe and S cycling in these sediments. SSCP (Single‐Strand Conformation Polymorphism) or DGGE (Denaturing Gradient Gel Electrophoresis) fingerprinting based on 16S rRNA genes of Bacteria indicated different bacterial populations in the MPN dilution series exhibiting different temperature ranges for growth.
UNRESOLVED ISSUES IN DIALYSIS: Management of Intradialytic Hypertension: The Ongoing Challenge
Authors: Chen Joline , Gul Ambreen , Sarnak Mark J.
Published: March 2006

There is no widely accepted definition of intradialytic hypertension. Arbitrary clinical definitions have included an increase in blood pressure during or immediately after hemodialysis, a rise in blood pressure during the second or third hour of dialysis, and an increase in blood pressure that is resistant to ultrafiltration. To date, no studies have evaluated the prevalence and prognostic importance of intradialytic hypertension. The pathogenesis of intradialytic hypertension is complex and is due in part to extracellular fluid volume expansion, increased cardiac output, activation of the renin‐angiotensin system and the sympathetic nervous system, increased circulating vasoactive substances resulting in peripheral vasoconstriction, erythropoietin use, and fluctuations in electrolytes and removal of antihypertensive medications during the dialysis procedure. Management strategies of intradialytic hypertension are based on expert opinion using the pathophysiologic principles described above. We conclude that additional epidemiologic, basic science, and interventional studies are needed to further elucidate the prevalence, prognostic importance, pathophysiology, and potential treatment of intradialytic hypertension.
Should DSM‐V Include Dimensional Diagnostic Criteria for Alcohol Use Disorders?
Authors: Helzer John E. , Bucholz Kathleen K. , Bierut Laura Jean , Regier Darrel A. , Schuckit Marc A. , Guth Sarah E.
Published: March 2006

This program calls attention to the upcoming timetable for the revision of the Diagnostic and Statistical Manual (DSM)‐IV and the publication of DSM‐V. It is vitally important for Research Society of Alcoholism members to be aware of the current discussions of the important scientific questions related to the next DSM revision and to use the opportunity for input. The title of the symposium highlights 1 key question, i.e., whether the DSM definitions should remain strictly categorical as in the past or whether a dimensional component should be included in this revision. Two substantive and 1 conceptual paper are included in this portion of the symposium. The fourth and final presentation detailing the revision timetable and the opportunities for input is by Dr. Darrel Regier. Dr. Regier is the director of American Psychiatric Institute for Research and Education the research and education branch of the American Psychiatric Association and the organization within the APA that will oversee the DSM revision. The discussion is by Marc Schuckit, who was chair of the Substance Use disorders (SUD) Committee for DSM‐IV and cochair of the international group of experts reviewing the SUD definitions for DSM‐V.
Microstructures and Properties of Plasma‐Sprayed Segmented Thermal Barrier Coatings
Authors: Guo Hongbo , Kuroda Seiji , Murakami Hideyuki
Published: March 2006

Thermal barrier coatings (TBCs) with different levels of segmentation crack density were produced by spraying two types of ZrO2–8Y2O3 powders. The fused and crushed powder has a greater capability of forming segmented coatings than the hollow sphere (HOSP) one. The highly segmented coatings reveal much lower porosity compared with traditionally sprayed coatings, thereby compromising the property of thermal insulation of TBCs. Microstructure and thermal conductivity of the HOSP coatings are more sensitive to the changes in spray conditions. Segmentation cracks had a strong influence in decreasing Young's modulus of coatings. Fifty hours heat treatment at 1250°C had little effect on the mechanical property of the highly segmented coatings.
Results of a Proposed Breath Alcohol Proficiency Test Program
Authors: Gullberg Rod G. , Logan Barry K.
Published: March 2006

ABSTRACT: Although proficiency test programs have long been used in both clinical and forensic laboratories, they have not found uniform application in forensic breath alcohol programs. An initial effort to develop a proficiency test program appropriate to forensic breath alcohol analysis is described herein. A total of 11 jurisdictions participated in which 27 modern instruments were evaluated. Five wet bath simulator solutions with ethanol vapor concentrations ranging from 0.0254 to 0.2659 g/210 L were sent to participating programs, instructing them to perform n=10 measurements on each solution using the same instrument. Four of the solutions contained ethanol only and one contained ethanol mixed with acetone. The systematic errors for all instruments ranged from −11.3% to +11.4% while the coefficient of variations ranged from zero to 6.1%. A components‐of‐variance analysis revealed at least 79% of the total variance as being due to the between‐instrument component for all concentrations. Improving proficiency test program development should consider: (1) clear protocol instructions, (2) frequency of proficiency testing, (3) use lower concentrations for determining limits‐of‐detection and ‐quantitation, etc. Despite the lack of a biological component, proficiency test participation should enhance the credibility of forensic breath test programs.
Autoerotic Deaths in the Literature from 1954 to 2004: A Review
Authors: Sauvageau Anny , Racette Stéphanie
Published: March 2006

ABSTRACT:Autoerotic death by hanging or ligature is a method of autoeroticism well known by forensic pathologists. In order to analyze autoerotic deaths of nonclassic hanging or ligature type, this paper reviews all published cases of autoerotic deaths from 1954 to 2004, with the exclusion of homicide cases or cases in which the autoerotic activity was not solitary. These articles were obtained through a systematic Medline database search. A total of 408 cases of such deaths has been reported in 57 articles. For each case, the following characteristics are presented here: sex, age, race, method of autoerotic activity, cause of death, and location where the body was found. Autoerotic death practioners were predominantly Caucasian males. Victims were aged from 9 to 77 years and were mainly found in various indoor locations. Most cases were asphyxia by hanging, ligature, plastic bags, chemical substances, or a mixture of these. Still, atypical methods of autoerotic activity leading to death accounted for about 10.3% of cases in the literature and are classified here into five broad categories: electrocution (3.7%), overdressing/body wrapping (1.5%), foreign body insertion (1.2%), atypical asphyxia method (2.9%), and miscellaneous (1.0%). All these atypical methods are further discussed individually.
Iron chelator‐induced growth arrest and cytochrome c‐dependent apoptosis in immortalized and malignant oral keratinocytes
Authors: Lee Sun‐Kyung , Lee Jae‐Jung , Lee Hwa‐Jeong , Lee Jun , Jeon Byung‐Hun , Jun Chang‐Duk , Lee Suk‐Keun , Kim Eun‐Cheol
Published: March 2006

Background:  Many studies have shown the anti‐proliferative effects of iron deprivation on cancer cells, but the effects of iron‐chelators on oral cancer have not been clearly elucidated.

Methods:  To investigate the effects of an iron chelator, desferrioxamine (DFO), on the growth of immortalized human oral keratinocytes (IHOK), primary oral cancer cells (HN4), metastatic oral cancer cells (HN12) and human skin keratinocytes (HaCaT) in the MTT assay, three‐dimensional (3D) raft cultures, Western blotting, cell cycle analysis, nuclear staining and cytochrome c expression for apoptosis signaling pathway were used.

Results:  Desferrioxamine inhibited the growth of immortalized IHOK and HaCaT and malignant HN4 and HN12 keratinocytes in a time‐ and dose‐dependent manner according to the MTT assay. The 3D organotypic culture also revealed that DFO‐treated cells showed less epithelial maturation, less surface keratinization and decreased epithelial thickness. The major mechanism of growth inhibition with the micromolar DFO treatment was by the induction of apoptosis, which was supported by nuclear DAPI staining, DNA fragmentation analysis and flow cytometric analysis for sub‐G1 phase arrest and Annexin V‐FITC (fluorescein isothiocyanate) staining. Furthermore, Bax expression increased together with p53 and p21WAF1/CIP1, while the Bcl‐2 expression decreased in the immortalized and malignant keratinocytes treated with DFO. Time‐dependent cytochrome c from mitochondria was observed in DFO‐treated IHOK and oral cancer cells and was accompanied by the activation of caspase‐3 in IHOK cells.

Conclusion:  These results demonstrate that DFO has growth inhibitory effects on immortalized and malignant oral keratinocytes through the induction of apoptosis and suggest that further evaluation of DFO as a potential therapeutic agent for human oral precancerous lesions is warranted.
Surgical removal and immediate reattachment of coronal fragment embedded in lip
Authors: Pasini S. , Bardellini E. , Keller E. , Conti G. , Flocchini P. , Majorana A.
Published: March 2006

Abstract –  This case describes a patient with a traumatic crown fracture of an upper incisor, associated with a laceration wound in the lower lip, showing local oedema. While palpating the tissues of the lower lip we felt the presence of a foreign body. This was confirmed by a radiograph of the lip that showed a radiopaque material, being similar to the coronal fragment of the fractured incisor. It was successfully surgically removed and immediately reattached using a composite adhesive technique. At the follow‐up of 1 year later the vitality test on the teeth was positive and neither one of the two traumatized teeth showed any sign of discoloration.
Renewing Kenneth Burke’s “Plea for the Shakespearean Drama”
Authors: Newstok Scott L.
Published: March 2006

This article surveys the criticism of the American writer Kenneth Burke (1897–1993), who composed several landmark essays on Shakespeare’s plays and poems throughout his lengthy career. His early writings examined the structures of scenes and the rhetorical appeals of characters, whereas his later pieces ambitiously articulated a ‘recipe’ for Shakespearean drama itself, in the spirit of Aristotle’sPoetics. Burke’s interpretations of Shakespeare anticipated many contemporary academic approaches, as he blended formalist, historical, materialist, psychoanalytic, and sociological critiques of literature. His interpretations continue to be influential, particularly in the United States (although his precedent is typically acknowledged through indirection). As a maverick intellectual, Burke remains difficult to place within the genealogy of literary criticism, as much for his stylistic voice as for ideological reasons.
A proposal for managing wastewater in Harare, Zimbabwe
Authors: Nhapi I. , Siebel M. A. , Gijzen H. J.
Published: March 2006

This paper deals with wastewater management in Harare, in the Lake Chivero catchment area of Zimbabwe. It aims at developing a sustainable system for managing water and nutrients and is based on the literature and a water quality monitoring study conducted from June 2000 to December 2001. This study has shown serious water pollution problems due to urbanisation in the catchment. A ‘three‐step strategic approach’ to urban (waste)water management was used as a basis for formulating solutions. The short‐term solutions include reduction of wastewater volume in industries and households, reducing wastewater flows by 24% and total phosphorus by 5%. The medium‐term solutions involve treating wastewater to high standards, resource recovery and reuse, and controlling upstream sources of pollution, and thus would reduce the lake total nitrogen and total phosphorus levels to about 0.4 and 0.07 mg/L, respectively. A long‐term solution was suggested based on pollution prevention and direct reuse, treatment at onsite and decentralised levels followed by reuse, and minimal disposal of the remaining effluents combined with the stimulation of the self‐purification capacity of the receiving rivers. It was concluded that it is feasible to reduce pollution levels in the catchment by applying these phased developments.
Art, Morality and Ethics: On the (Im)Moral Character of Art Works and Inter‐Relations to Artistic Value
Authors: Kieran Matthew
Published: March 2006

The (im)moral character of art works often affects how we respond to them. But should it affect our evaluation of them as art? The article surveys the contemporary debate whilst outlining further lines of argument and enquiry. The main arguments in favour of aestheticism, the claim that there is no internal relation between artistic value and moral character, are considered. Nonetheless the connection between art's instructional aspirations and artistic value, as well as the ways in which works solicit responses from us, underwrite the claim that a work's moral character can be directly relevant to a work's value as art. Various competing accounts of how the relationship goes, ethicism, moderate moralism and immoralism, are considered. The article goes on to elaborate novel considerations in favour of a suitably qualified cognitive immoralism and suggests avenues of further enquiry with respect to the moral character of art works.
Interstitial cells of Cajal in the deep muscular plexus mediate enteric motor neurotransmission in the mouse small intestine
Authors: Ward Sean M. , McLaren Gerald J. , Sanders Kenton M.
Published: March 2006

Interstitial cells of Cajal (ICC) provide important regulatory functions in the motor activity of the gastrointestinal tract. In the small intestine, ICC in the myenteric region (ICC‐MY), between the circular and longitudinal muscle layers, generate and propagate electrical slow waves. Another population of ICC lies in the plane of the deep muscular plexus (ICC‐DMP), and these cells are closely associated with varicose nerve terminals of enteric motor neurons. Here we tested the hypothesis that ICC‐DMP mediate excitatory and inhibitory neural inputs in the small bowel. ICC‐DMP develop largely after birth. ICC‐DMP, with receptor tyrosine kinase Kit‐like immunoreactivity, appear first in the jejunum and then in the ileum. We performed electrophysiological experiments on mice immediately after birth (P0) or at 10 days post partum (P10) to determine whether neural responses follow development of ICC‐DMP. At P0, slow‐wave activity was present in the jejunum, but neural responses were poorly developed. By P10, after ICC‐DMP developed, both cholinergic excitatory and nitrergic inhibitory neural responses were intact. Muscles of P0 mice were also put into organotypic cultures and treated with a neutralizing Kit antibody. Neural responses developed in culture within 3–6 days in control muscles, but blocking Kit caused loss of ICC and loss of cholinergic and nitrergic neural responses. Non‐cholinergic excitatory responses remained after loss of ICC‐DMP. Our observations are consistent with the idea that cholinergic and nitrergic motor neural inputs are mediated, to a large extent, via ICC‐DMP. Thus, ICC‐DMP appear to serve a function in the small intestine that is similar to the role of the intramuscular ICC in the stomach.
Opposing role of synaptic and extrasynaptic NMDA receptors in regulation of the extracellular signal‐regulated kinases (ERK) activity in cultured rat hippocampal neurons
Authors: Ivanov Anton , Pellegrino Christophe , Rama Sylvain , Dumalska Iryna , Salyha Yuriy , Ben‐Ari Yehezkel , Medina Igor
Published: March 2006

The extracellular signal‐regulated kinases (ERK) signalling cascade is a key pathway that mediates the NMDA receptor (NMDAR)‐dependent neuronal plasticity and survival. However, it is not clear yet how NMDARs regulate ERK activity. Stimulation of the NMDARs induces a complex modification of ERK that includes both ERK activation and inactivation and depends on particular experimental conditions. Here we show that there exists a differential restriction in the regulation of ERK activity that depends on the pool of NMDAR that was activated. The synaptic pool of NMDARs activates ERK whereas the extrasynaptic pool does not; on the contrary, it triggers a signalling pathway that results in the inactivation of ERK. As a result, simultaneous activation of both extrasynaptic and synaptic NMDAR using bath application of NMDA or glutamate (a typical protocol explored in the majority of studies) produced ERK activation that depended on the concentration of agonists and was always significantly weaker than those mediated by synaptic NMDARs. Since the activation of the extrasynaptic NMDA is attributed mainly to global release of glutamate occurring at pathological conditions including hypoxic/ischaemic insults, traumas and epileptic brain damage, the reported differential regulation of ERK cascade by NMDARs provides a unique mechanism for an early identification of the physiological and/or pathophysiological consequences of NMDAR activation. The negative regulation of the ERK activity might be one of the first signalling events determining brain injury and constitutes a putative target of new pharmacological applications.
Quality control for digital mammography in the ACRIN DMIST trial: Part I
Authors: Bloomquist Aili K. , Yaffe Martin J. , Pisano Etta D. , Hendrick R. Edward , Mawdsley Gordon E. , Bright Stewart , Shen Sam Z. , Mahesh Mahadevappa , Nickoloff Edward L. , Fleischman Richard C. , Williams Mark B. , Maidment Andrew D. A. , Beideck Daniel J. , Och Joseph , Seibert J. A.
Published: March 2006

The Digital Mammography Imaging Screening Trial, conducted by the American College of Radiology Imaging Network, is a clinical trial designed to compare the accuracy of full‐field digital mammography (FFDM) versus screen‐film mammography in a screening population. Five FFDM systems from four manufacturers (Fischer, Fuji, General Electric, and Lorad) were employed in the study at 35 clinical sites. A core physics team devised and implemented tests to evaluate these systems. A detailed description of physics and quality control tests is presented, including estimates of: mean glandular dose, modulation transfer function (MTF), 2D noise power spectra, and signal‐to‐noise ratio (SNR). The mean glandular doses for the standard breast ranged from , with being the average across all units and machine types. For the five systems evaluated, the MTF dropped to 50% at markedly different percentages (22% to 87%) of the Nyquist limit, indicating that factors other than detector element (del) size have an important effect on spatial resolution. Noise power spectra and SNR were measured; however, we found that it was difficult to standardize and compare these between units. For each machine type, the performance as measured by the tests was very consistent, and no predictive benefit was seen for many of the tests during the period of the trial. It was found that, after verification of proper operation during acceptance testing, if systems failed they generally did so suddenly rather than through gradual deterioration of performance. Because of the relatively short duration of this study further, investigation of the long‐term failure characteristics of these systems is advisable.
Deformable and rigid registration of MRI and microPET images for photodynamic therapy of cancer in mice
Authors: Fei Baowei , Wang Hesheng , Muzic Raymond F. , Flask Chris , Wilson David L. , Duerk Jeffrey L. , Feyes Denise K. , Oleinick Nancy L.
Published: March 2006

We are investigating imaging techniques to study the tumor response to photodynamic therapy (PDT). Positron emission tomography (PET) can provide physiological and functional information. High‐resolution magnetic resonance imaging (MRI) can provide anatomical and morphological changes. Image registration can combine MRI and PET images for improved tumor monitoring. In this study, we acquired high‐resolution MRI and microPET ‐fluorodeoxyglucose (FDG) images from C3H mice with RIF‐1 tumors that were treated with Pc 4‐based PDT. We developed two registration methods for this application. For registration of the whole mouse body, we used an automatic three‐dimensional, normalized mutual information algorithm. For tumor registration, we developed a finite element model (FEM)‐based deformable registration scheme. To assess the quality of whole body registration, we performed slice‐by‐slice review of both image volumes; manually segmented feature organs, such as the left and right kidneys and the bladder, in each slice; and computed the distance between corresponding centroids. Over 40 volume registration experiments were performed with MRI and microPET images. The distance between corresponding centroids of organs was which is about of microPET images. The mean volume overlap ratios for tumors were 94.7% and 86.3% for the deformable and rigid registration methods, respectively. Registration of high‐resolution MRI and microPET images combines anatomical and functional information of the tumors and provides a useful tool for evaluating photodynamic therapy.
Resonance modes in a one-dimensional medium with two purely resistive boundaries: Calculation methods, orthogonality, and completeness
Authors: Kergomard Jean , Debut Vincent , Matignon Denis
Published: March 2006

Studying the problem of wave propagation in media with resistive boundaries can be made by searching for “resonance modes” or free oscillations regimes. In the present article, a simple case is investigated, which allows one to enlighten the respective interest of different, classical methods, some of them being rather delicate. This case is the one-dimensional propagation in a homogeneous medium having two purely resistive terminations, the calculation of the Green function being done without any approximation using three methods. The first one is the straightforward use of the closed-form solution in the frequency domain and the residue calculus. Then, the method of separation of variables (space and time) leads to a solution depending on the initial conditions. The question of the orthogonality and completeness of the complex-valued resonance modes is investigated, leading to the expression of a particular scalar product. The last method is the expansion in biorthogonal modes in the frequency domain, the modes having eigenfrequencies depending on the frequency. Results of the three methods generalize or∕and correct some results already existing in the literature, and exhibit the particular difficulty of the treatment of the constant mode.
Changes in Surface Water Supply Across Africa with Predicted Climate Change
Authors: de Wit Maarten , Stankiewicz Jacek
Published: March 2006

Across Africa, perennial drainage density as a function of mean annual rainfall defines three regimes separated by threshold values of precipitation. This nonlinear response of drainage to rainfall will most seriously affect regions in the intermediate, unstable regime. A 10% decrease in precipitation in regions on the upper regime boundary (1000 millimeters per year) would reduce drainage by 17%, whereas in regions receiving 500 millimeters per year, such a drop would cut 50% of surface drainage. By using predicted precipitation changes, we calculate that a decrease in perennial drainage will significantly affect present surface water access across 25% of Africa by the end of this century.
Evidence for a Functional Second Thymus in Mice
Authors: Terszowski Grzegorz , Müller Susanna M. , Bleul Conrad C. , Blum Carmen , Schirmbeck Reinhold , Reimann Jörg , Pasquier Louis Du , Amagai Takashi , Boehm Thomas , Rodewald Hans-Reimer
Published: March 2006

The thymus organ supports the development of T cells and is located in the thorax. Here, we report the existence of a second thymus in the mouse neck, which develops after birth and grows to the size of a small lymph node. The cervical thymus had a typical medulla-cortex structure, was found to support T cell development, and could correct T cell deficiency in athymic nude mice upon transplantation. The identification of a regular second thymus in the mouse may provide evolutionary links to thymus organogenesis in other vertebrates and suggests a need to reconsider the effect of thoracic thymectomy on de novo T cell production.
Deposition of
Cryptosporidium
Oocysts in Streambeds
Authors: Searcy Kristin E. , Packman Aaron I. , Atwill Edward R. , Harter Thomas
Published: March 2006

The transfer of
Cryptosporidium
oocysts from the surface water to the sediment beds of streams and rivers influences their migration in surface waters. We used controlled laboratory flume experiments to investigate the deposition of suspended
Cryptosporidium parvum
oocysts in streambeds. The experimental results demonstrate that hydrodynamic interactions between an overlying flow and a sediment bed cause oocysts to accumulate in the sediments and reduce their concentrations in the surface water. The association of
C. parvum
with other suspended sediments increased both the oocysts' effective settling velocity and the rate at which oocysts were transferred to the sediment bed. A model for the stream-subsurface exchange of colloidal particles, including physical transport and physicochemical interactions with sediment grains, accurately represented the deposition of both free
C. parvum
oocysts and oocysts that were attached to suspended sediments. We believe that these pathogen-sediment interactions play an important role in regulating the concentrations of
Cryptosporidium
in streams and rivers and should be taken into consideration when predicting the fate of pathogens in the environment.
Selective Removal of DNA from Dead Cells of Mixed Bacterial Communities by Use of Ethidium Monoazide
Authors: Nocker Andreas , Camper Anne K.
Published: March 2006

The distinction between viable and dead bacterial cells poses a major challenge in microbial diagnostics. Due to the persistence of DNA in the environment after cells have lost viability, DNA-based quantification methods overestimate the number of viable cells in mixed populations or even lead to false-positive results in the absence of viable cells. On the other hand, RNA-based diagnostic methods, which circumvent this problem, are technically demanding and suffer from some drawbacks. A promising and easy-to-use alternative utilizing the DNA-intercalating dye ethidium monoazide bromide (EMA) was published recently. This chemical is known to penetrate only into “dead” cells with compromised cell membrane integrity. Subsequent photoinduced cross-linking was reported to inhibit PCR amplification of DNA from dead cells. We provide evidence here that in addition to inhibition of amplification, most of the DNA from dead cells is actually lost during the DNA extraction procedure, probably together with cell debris which goes into the pellet fraction. Exposure of bacteria to increasing stress and higher proportions of dead cells in defined populations led to increasing loss of genomic DNA. Experiments were performed using
Escherichia coli
O157:H7 and
Salmonella enterica
serovar Typhimurium as model pathogens and using real-time PCR for their quantification. Results showed that EMA treatment of mixed populations of these two species provides a valuable tool for selective removal of DNA of nonviable cells by using conventional extraction protocols. Furthermore, we provide evidence that prior to denaturing gradient gel electrophoresis, EMA treatment of a mature mixed-population drinking-water biofilm containing a substantial proportion of dead cells can result in community fingerprints dramatically different from those for an untreated biofilm. The interpretation of such fingerprints can have important implications in the field of microbial ecology.
A Three-Dimensional Computer Model of Four Hypothetical Mechanisms Protecting Biofilms from Antimicrobials
Authors: Chambless Jason D. , Hunt Stephen M. , Stewart Philip S.
Published: March 2006

Four hypothetical mechanisms for protection of biofilms against antimicrobials were incorporated into a three-dimensional model of biofilm growth and development. The model integrated processes of substrate utilization, diffusion, growth, cell migration, death, and detachment in a cellular automaton framework. Compared to simulations of unprotected biofilms, each of the protective mechanisms provided some tolerance to antimicrobial action. When the mechanisms were compared to each other, the behaviors of the four protective mechanisms produced distinct shapes of killing curves, nonuniform spatial patterns of survival and cell type distribution, and anticipated susceptibility patterns for dispersed biofilm cells. The differences between the protective mechanisms predicted in these simulations could guide the design of experiments to discriminate antimicrobial tolerance mechanisms in biofilms. Each of the mechanisms could be a plausible avenue of biofilm protection.
Non-Sulfate-Reducing, Syntrophic Bacteria Affiliated withDesulfotomaculumCluster I Are Widely Distributed in Methanogenic Environments
Authors: Imachi Hiroyuki , Sekiguchi Yuji , Kamagata Yoichi , Loy Alexander , Qiu Yan-Ling , Hugenholtz Philip , Kimura Nobutada , Wagner Michael , Ohashi Akiyoshi , Harada Hideki
Published: March 2006

The classical perception of members of the gram-positiveDesulfotomaculumcluster I as sulfate-reducing bacteria was recently challenged by the isolation of new representatives lacking the ability for anaerobic sulfate respiration. For example, the two described syntrophic propionate-oxidizing species of the genusPelotomaculumform the novelDesulfotomaculumsubcluster Ih. In the present study, we applied a polyphasic approach by using cultivation-independent and culturing techniques in order to further characterize the occurrence, abundance, and physiological properties of subcluster Ih bacteria in low-sulfate, methanogenic environments. 16S rRNA (gene)-based cloning, quantitative fluorescence in situ hybridization, and real-time PCR analyses showed that the subcluster Ih population composed a considerable part of theDesulfotomaculumcluster I community in almost all samples examined. Additionally, five propionate-degrading syntrophic enrichments of subcluster Ih bacteria were successfully established, from one of which the new strain MGP was isolated in coculture with a hydrogenotrophic methanogen. None of the cultures analyzed, including previously describedPelotomaculumspecies and strain MGP, consumed sulfite, sulfate, or organosulfonates. In accordance with these phenotypic observations, a PCR-based screening fordsrAB(key genes of the sulfate respiration pathway encoding the alpha and beta subunits of the dissimilatory sulfite reductase) of all enrichments/(co)cultures was negative with one exception. Surprisingly, strain MGP containeddsrAB, which were transcribed in the presence and absence of sulfate. Based on these and previous findings, we hypothesize that members ofDesulfotomaculumsubcluster Ih have recently adopted a syntrophic lifestyle to thrive in low-sulfate, methanogenic environments and thus have lost their ancestral ability for dissimilatory sulfate/sulfite reduction.
Phylogenetic Analysis and In Situ Identification of
Bacteria
Community Composition in an Acidic
Sphagnum
Peat Bog
Authors: Dedysh Svetlana N. , Pankratov Timofei A. , Belova Svetlana E. , Kulichevskaya Irina S. , Liesack Werner
Published: March 2006

The
Bacteria
community composition in an acidic
Sphagnum
peat bog (pH 3.9 to 4.5) was characterized by a combination of 16S rRNA gene clone library analysis, rRNA-targeted fluorescence in situ hybridization (FISH), and cultivation. Among 84 environmental 16S rRNA gene clones, a set of only 16 cloned sequences was closely related (≥95% similarity) to taxonomically described organisms. Main groups of clones were affiliated with the
Acidobacteria
(24 clones),
Alphaproteobacteria
(20),
Verrucomicrobia
(13),
Actinobacteria
(8),
Deltaproteobacteria
(4),
Chloroflexi
(3), and
Planctomycetes
(3). The proportion of cells that hybridized with oligonucleotide probes specific for members of the domains
Bacteria
(EUB338-mix) and
Archaea
(ARCH915 and ARC344) accounted for only 12 to 22% of the total cell counts. Up to 24% of the EUB338-positive cells could be assigned by FISH to specific bacterial phyla.
Alphaproteobacteria
and
Planctomycetes
were the most numerous bacterial groups (up to 1.3 × 10
7
and 1.1 × 10
7
cells g
−1
peat, respectively). In contrast to conventional plating techniques, a novel biofilm-mediated enrichment approach allowed us to isolate some representatives of predominant
Bacteria
groups, such as
Acidobacteria
and
Planctomycetes
. This novel strategy has great potential to enable the isolation of a significant proportion of the peat bog bacterial diversity.
Kinetics of Single Cells: Observation and Modeling of a Stochastic Process
Authors: Pin Carmen , Baranyi József
Published: March 2006

The successive generation times for single cells of
Escherichia coli
K-12 were measured as described by A. Elfwing, Y. LeMarc, J. Baranyi, and A. Ballagi (Appl. Environ. Microbiol. 70:675-678, 2004), and the histograms they generated were used as empirical distributions to simulate growth of the population as the result of the multiplication of its single cells. This way, a stochastic birth model in which the underlying distributions were measured experimentally was simulated. To validate the model, analogous bacterial growth curves were generated by the use of different inoculum levels. The agreement with the simulation was very good, proving that the growth of the population can be predicted accurately if the distribution of the first few division times for the single cells within that population is known. Two questions were investigated by the simulation. (i) To what extent can we say that the distribution of the detection time, i.e., the time by which a single-cell-generated subpopulation reaches a detectable level, can be identified with that of the lag time of the original single cell? (ii) For low inocula, how does the inoculum size affect the lag time of the population?
Assessing the Impact of Denitrifier-Produced Nitric Oxide on Other Bacteria
Authors: Choi Peter S. , Naal Zeki , Moore Charles , Casado-Rivera Emerilis , Abruña Hector D. , Helmann John D. , Shapleigh James P.
Published: March 2006

A series of experiments was undertaken to learn more about the impact on other bacteria of nitric oxide (NO) produced during denitrification. The denitrifier
Rhodobacter sphaeroides
2.4.3 was chosen as a denitrifier for these experiments. To learn more about NO production by this bacterium, NO levels during denitrification were measured by using differential mass spectrometry. This revealed that NO levels produced during nitrate respiration by this bacterium were in the low μM range. This concentration of NO is higher than that previously measured in denitrifiers, including
Achromobacter cycloclastes
and
Paracoccus denitrificans
. Therefore, both 2.4.3 and
A. cycloclastes
were used in this work to compare the effects of various NO levels on nondenitrifying bacteria. By use of bacterial overlays, it was found that the NO generated by
A. cycloclastes
and 2.4.3 cells during denitrification inhibited the growth of both
Bacillus subtilis
and
R. sphaeroide
s 2.4.1 but that
R. sphaeroides
2.4.3 caused larger zones of inhibition in the overlays than
A. cycloclastes
. Both
R. sphaeroides
2.4.3 and
A. cycloclastes
induced the expression of the NO stress response gene
hmp
in
B. subtilis
. Taken together, these results indicate that there is variability in the NO concentrations produced by denitrifiers, but, irrespective of the NO levels produced, microbes in the surrounding environment were responsive to the NO produced during denitrification.
Preferential Utilization of Aromatic Compounds over Glucose by
Pseudomonas putida
CSV86
Authors: Basu Aditya , Apte Shree K. , Phale Prashant S.
Published: March 2006

Pseudomonas putida
CSV86, a naphthalene-degrading organism, exhibited diauxic growth on aromatic compounds plus glucose, with utilization of aromatics in the first log phase and of glucose in the second log phase. Glucose supplementation did not suppress the activity of degrading enzymes, which were induced upon addition of aromatic compounds. The induction was inhibited by chloramphenicol, suggesting that de novo protein synthesis was essential. Cells showed cometabolism of aromatic compounds and organic acids; however, organic acids suppressed glucose utilization.
Tolerance of
Listeria monocytogenes
to Cell Envelope-Acting Antimicrobial Agents Is Dependent on SigB
Authors: Begley Máire , Hill Colin , Ross R. Paul
Published: March 2006

Mutation of
sigB
impairs the ability of
Listeria monocytogenes
to grow in sublethal levels, and to survive in lethal concentrations, of the bacteriocins nisin and lacticin 3147 and the antibiotics ampicillin and penicillin G. SigB may therefore represent an attractive target for the development of new control and treatment strategies for this important pathogen.
Synbiotic Microcapsules That Enhance Microbial Viability during Nonrefrigerated Storage and Gastrointestinal Transit
Authors: Crittenden Ross , Weerakkody Rangika , Sanguansri Luz , Augustin MaryAnn
Published: March 2006

A
Bifidobacterium infantis
strain was microencapsulated within a film-forming protein-carbohydrate-oil emulsion. This novel encapsulant incorporated prebiotics and substantially protected the bacterium during nonrefrigerated storage and gastrointestinal transit. The dried microcapsules were small (15 to 20 μm), had low water activity (0.2 to 0.3), and rapidly released the bacteria in simulated intestinal fluid.
Analysis of 525 Samples To Determine the Usefulness of PCR Amplification and Sequencing of the 16S rRNA Gene for Diagnosis of Bone and Joint Infections
Authors: Fenollar Florence , Roux Véronique , Stein Andréas , Drancourt Michel , Raoult Didier
Published: March 2006

The 16S rRNA gene PCR in the diagnosis of bone and joint infections has not been systematically tested. Five hundred twenty-five bone and joint samples collected from 525 patients were cultured and submitted to 16S rRNA gene PCR detection of bacteria in parallel. The amplicons with mixed sequences were also cloned. When discordant results were observed, culture and PCR were performed once again. Bacteria were detected in 139 of 525 samples. Culture and 16S rRNA gene PCR yielded identical documentation in 475 samples. Discrepancies were linked to 13 false-positive culture results, 5 false-positive PCR results, 9 false-negative PCR results, 16 false-negative culture results, and 7 mixed infections. Cloning and sequencing of 16S rRNA gene amplicons in 6 of 8 patients with mixed infections identified 2 to 8 bacteria per sample. Rarely described human pathogens such as
Alcaligenes faecalis
,
Comamonas terrigena
, and 21 anaerobes were characterized. We also detected, by 16S rRNA gene PCR, four previously identified bacteria never reported in human infection,
Alkanindiges illinoisensis
, dehydroabietic acid-degrading bacterium DhA-73, unidentified Hailaer soda lake bacterium, and uncultured bacterium clone HuCa4. Seven organisms representing new potential species were also detected. PCR followed by cloning and sequencing may help to identify new pathogens involved in mixed bone infection.
First Report of
Leishmania infantum
in French Guiana: Canine Visceral Leishmaniasis Imported from the Old World
Authors: Rotureau Brice , Ravel Christophe , Aznar Christine , Carme Bernard , Dedet Jean-Pierre
Published: March 2006

The first two cases of canine visceral leishmaniasis in French Guiana are described. One infected dog was most probably imported from France. A second dog was then infected with
Leishmania infantum
in French Guiana. These observations exemplify the intercontinental transportation theory for
L. infantum
.
Isolation of a Strictly Anaerobic Strain of
Staphylococcus epidermidis
Authors: Rowlinson Marie-Claire , LeBourgeois Phyllis , Ward Kevin , Song Yuli , Finegold Sydney M. , Bruckner David A.
Published: March 2006

Staphylococcus epidermidis
is a well-characterized, nonfastidious, aerobic gram-positive coccus commonly isolated in the clinical microbiology laboratory. Although coagulase-negative staphylococci, including
Staphylococcus epidermidis
, are often considered a contaminant in the clinical laboratory, an increasing number of reports describe their pathogenesis, in particular in infections of prosthetic devices. This article describes the isolation of a strictly anaerobic strain of
Staphylococcus epidermidis
in pure culture from the site of an infected prosthetic hip. This isolate was unique in that it grew only under strictly anaerobic conditions. Initially, the isolate was thought to be a known anaerobic gram-positive coccus. However, certain key biochemical and antimicrobial tests performed as part of the standard laboratory identification procedure were not consistent with results expected for any known anaerobic gram-positive coccus; the isolate was catalase positive and metronidazole and penicillin resistant. This isolate was characterized by further biochemical analysis, antimicrobial testing, and nucleic acid sequencing. This paper presents the first documented isolation of a strictly anaerobic
Staphylococcus epidermidis
strain, confirmed by
rpoB
gene sequencing.
Characterization of
Neisseria meningitidis
Isolates from Recent Outbreaks in Ethiopia and Comparison with Those Recovered during the Epidemic of 1988 to 1989
Authors: Norheim Gunnstein , Rosenqvist Einar , Aseffa Abraham , Yassin Mohammed Ahmed , Mengistu Getahun , Kassu Afework , Fikremariam Dereje , Tamire Wegene , Høiby E. Arne , Alebel Tsegaye , Berhanu Degu , Merid Yarid , Harboe Morten , Caugant Dominique A.
Published: March 2006

The objectives of this study were to collect and characterize epidemic meningococcal isolates from Ethiopia from 2002 to 2003 and to compare them to 21 strains recovered during the previous large epidemic of 1988 to 1989. Ninety-five patients in all age groups with clinical signs of meningitis and a turbid cerebrospinal fluid (CSF) sample were included in the study of isolates from 2002 to 2003. Seventy-one patients (74.7%) were confirmed as having
Neisseria meningitidis
either by culture (
n
= 40) or by
porA
PCR (
n
= 31) of their CSF. The overall case fatality rate (CFR) was 11.6%; the
N. meningitidis
-specific CFR was 4.2%. All 40 strains were fully susceptible to all antibiotics tested except sulfonamide, were serotyped as A:4/21:P1.20,9, and belonged to sequence type 7 (ST-7). The strains from 1988 to 1989 were also equally susceptible and were characterized as A:4/21:P1.20,9, but they belonged to ST-5. Antigenic characterization of the strains revealed differences in the repertoire of lipooligosaccharides and Opa proteins between the old and the recent strains. PCR analysis of the nine
lgt
genes revealed the presence of the
lgtAHFG
genes in both old and recent strains;
lgtB
was present in only some of the strains, but no correlation with sequence type was observed. Further analysis showed that in addition to their
pgm
alleles, the Ethiopian ST-5 and ST-7 strains also differed in their
tbpB
,
opa
,
fetA
, and
lgtA
genes. The occurrence of new antigenic structures in strains sharing the same serogroup, PorA, and PorB may help explain the replacement of ST-5 by ST-7 in the African meningitis belt.
Differentiating Host-Associated Variants ofMycobacterium aviumby PCR for Detection of Large Sequence Polymorphisms
Authors: Semret Makeda , Turenne Christine Y. , de Haas Petra , Collins Desmond M. , Behr Marcel A.
Published: March 2006

TheMycobacterium aviumspecies consists of a group of organisms that are genetically related but phenotypically diverse, with certain variants presenting clear differences in terms of their host association and disease manifestations. The ability to distinguish between these subtypes is of relevance for accurate diagnosis and for control programs. Using a comparative genomics approach, we have uncovered large sequence polymorphisms that are, respectively, absent from bird-typeM. aviumisolates and from cattle types and sheep types ofM. aviumsubsp.paratuberculosis. By evaluating the distribution of these genomic polymorphisms across a panel of strains, we were able to assign unique genomic signatures to these host-associated variants. We propose a simple PCR-based strategy based on these polymorphisms that can rapidly typeM. aviumisolates into these subgroups.
Detection and Genotyping of SHV β-Lactamase Variants by Mass Spectrometry after Base-Specific Cleavage of In Vitro-Generated RNA Transcripts
Authors: Stürenburg Enno , Storm Niels , Sobottka Ingo , Horstkotte Matthias A. , Scherpe Stefanie , Aepfelbacher Martin , Müller Susanne
Published: March 2006

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) after base-specific cleavage of PCR-amplified and in vitro-transcribed
bla
SHV
genes was used for the identification and genotyping of SHV β-lactamases. For evaluation,
bla
SHV
stretches of 21 clinical
Enterobacteriaceae
isolates were PCR amplified using T7 promoter-tagged forward and reverse primers, respectively. In vitro transcripts were generated with T7 RNA and DNA polymerase in the presence of modified analogues replacing either CTP or UTP. Using RNase A, the in vitro transcripts were base-specifically cleaved at every “T” or “C” position. Resulting cleavage products were analyzed by MALDI-TOF MS, generating a characteristic signal pattern based on the fragment masses. All 21 individual SHV genes were identified unambiguously using reference sequences, and the results were in perfect concordance with those obtained by fluorescent dideoxy sequencing, which represents the current standard method. As multiple point mutations can be detected in a single assay and newly emerged mutations which are not yet described in public databases can be identified too, MALDI-TOF MS appears to be an ideal tool for analysis of sequence polymorphisms in resistance-associated gene loci.