bluuebunny/crossref_metadata_2025 huggingface dataset:
Splitting hairs: the ‘hamburger sign’ in trichotillomania
Authors: Royer Michael C. , Sperling Leonard C.
Published: September 2006

Background:  A 43‐year‐old male presented with the clinical findings of patchy alopecia that contained persistent hair and re‐growth of hairs of various lengths, consistent with trichotillomania. A biopsy was performed to confirm the diagnosis..

Results:  Histologic evaluation revealed findings consistent with trichotillomania, including trichomalacia. Several hair shafts also showed a vertically oriented split, which contained proteinaceous material and erythrocytes. Morphologically, these were reminiscent of a hamburger within a bun.

Conclusions:  The unusual finding reported in this case has not been previously reported. The “hamburger bun sign” provides an additional clue to traumatic injury in the evaluation of biopsies for trichotillomania.
Fli‐1 expression in mycosis fungoides*
Authors: Quick C. Matthew , Smoller Bruce R. , Hiatt Kim M.
Published: September 2006

Background:  The Fli‐1 transcription factor functions in cellular proliferation and tumorigenesis. Its role in various neoplasms and its presence in lymphocytes suggest a link between Fli‐1 dysregulation and the pathogenesis of mycosis fungoides (MF). In this study, we further elucidate this possible link.

Methods:  Sections from archived specimens were stained using a polyclonal antibody against Fli‐1. The percentage of nuclei showing Fli‐1 expression was recorded. These were compared with reactive dermatoses.

Results:  All of the tumor stage lesions showed high levels of nuclear Fli‐1 expression. Of plaque stage lesions, six of 12 (50%) showed the same intensity, while the remaining six of 12 varied significantly in their Fli‐1 expression. The few patch stage lesions also showed varied expression.

Conclusion:  This study shows diffuse nuclear expression of Fli‐1 in all tumor stage MF, whereas expression of this transcription factor varied widely in the early, epidermotropic stages. Although the numbers are too small to draw statistical significance, this study demonstrates an association between increased expression of Fli‐1 and progression to tumor stage MF that merits further investigation. Additionally, the mixed expression of Fli‐1 in the epidermotropic stages suggests that the role of Fli‐1 in MF is related to neoplasia and not epidermotropism.
KSHV/HHV8‐associated primary cutaneous plasmablastic lymphoma in a patient with Castleman’s disease and Kaposi’s sarcoma
Authors: Liu Wenhua , Lacouture Mario E. , Jiang Jesse , Kraus Madeleine , Dickstein Jerome , Soltani Keyoumars , Shea Christopher R.
Published: September 2006

Abstract:  We report a unique case of Kaposi’s sarcoma (KS)‐associated herpesvirus (KSHV)/human herpesvirus (HHV)8‐associated lymphoma in a 56‐year‐old man with a history of acquired immune deficiency syndrome, Castleman’s disease, KS, and idiopathic thrombocytopenic purpura. Three months following the diagnosis of KS affecting a left cervical lymph node and Castleman’s disease with bone marrow involvement, he presented with a subcutaneous, tender lesion on his left arm. A skin biopsy demonstrated a superficial and deep, interstitial‐nodular infiltrate of severely atypical lymphoid cells showing plasmacytoid features, numerous mitotic figures, and frequent individual apoptotic tumor cells. The morphologic features were those of plasmablastic lymphoma (PBL). Immunohistochemical study showed that the lymphoma cells strongly expressed CD45, CD30, and KSHV/HHV8 latency‐associated nuclear antigen. KSHV/HHV8 was also detected in the biopsy sections of the patient’s KS and Castleman’s disease. Epstein–Barr virus in situ hybridization was diffusely positive. In situ hybridization demonstrated κ‐light chain restriction. Although KSHV/HHV8 has been individually associated with KS, Castleman’s disease, and PBL, this appears to be the first reported case in which all three entities were present simultaneously in one person, suggesting a critical role of KSHV/HHV8 as a common denominator in the pathogenesis of these diseases.
Measuring the Impact of Legal Periodicals
Authors: Maru Olavi
Published: September 2006

In 1972 all but 11 of the 149 law schools approved by the American Bar Association published law reviews. Some schools published more than one. Harvard Law School and the University of Chicago Law School each produced four. Most state bar associations and some local and specialty associations also publish journals, some of which print scholarly articles. A number of legal periodicals are issued by commercial publishers. The Index to Legal Periodicals, the most prominent access tool to periodical legal literature, indexed 285 American legal periodicals and serials in 1972.
The Antibiotics Class Actions
Authors: Wolfram Charles W.
Published: September 2006

Anyone interested in the current doings of the antibiotics antitrust litigation in the spring of 1975l could easily have found seating in the public section of the courtroom of Judge Miles A. Lord in Minneapolis. An instantly striking aspect of the courtroom was that, in contrast to the scattering of young attorneys and an occasional curious onlooker in the public section, there were dozens of people crowded into the area around the central raised bench on which Judge Lord sits. Several attorneys represenr: the defendants-five of the major drug manufacturing companies in the United States. Numerous counsel for the plaintiffs were grouped around a large table to Judge Lord's right. Clerks, court reporters, and marshals sat beneath the bench. The most remarkable feature of the crowd, however, was the presence of two jury boxes containing two separate juries. In fact, two different trials in six different cases were proceeding at once. “Jury One” was hearing evidence in actions brought by the United States, two national classes (one of insurance companies and the other of union health and welfare funds), and a California medical group. “Jury TWQ” was hearing evidence in suits brought in behalf of competitors of the defendant drug companies. For the most part, the juries were hearing evidence common to both sets of cases. When evidence was introduced that was relevant to only one set of cases, the other jvry would be excused.
Introduction: Global Processes, National Institutions, Local Bricolage: Shaping Law in an Era of Globalization
Authors: Fourcade Marion , Savelsberg Joachim J.
Published: September 2006

The articles by Carruthers and Halliday and by Hagan, Levi, and Ferrales in the present issue of Law and Social Inquiry provide a wonderful opportunity to carry out a brief reflection on the broader field of research on globalization and law. As the discussant and organizer/chair, respectively, of a panel on “Law between Globalization and National Institutions,” from which these two articles emerged, we use the following pages to: (1) show how both articles exemplify, in two different ways, what we call the “process turn” in globalization research, (2) identify four theoretical themes these articles speak to, relating them to the broader literature, and (3) draw some lessons for future law and society scholarship in an age of globalization.

1
Educational Debt and Law Student Failure to Enter Public Service Careers: Bringing Empirical Data to Bear
Authors: McGill Christa
Published: September 2006

It is frequently suggested that law school debt is preventing new law school graduates from entering public service careers. The basis for this contention is largely anecdotal, however. This study puts the presumption to empirical scrutiny. Aggregate data from law schools and individual-level data from law students both point to the same conclusion: law students may indeed be competing in a money chase, but it is not because of their indebtedness. Private firms with prestige and high salaries are appealing to many students regardless of their debt burden. And government and public interest jobs may be in too short supply to meet the demand of non-elite students who are essentially closed out of the high-paying jobs in larger firms. The biggest barrier between these students and public service jobs may be the lack of supply of these jobs, not the lack of demand for them.
Evaluation of the antifungal effects of mineral trioxide aggregate materials
Authors: Mohammadi Zahed , Modaresi Jalil , Yazdizadeh Mohammad
Published: September 2006

The aim of this study was to evaluate and compare the antifungal effect of white‐coloured mineral trioxide aggregate (WMTA) and grey mineral trioxide aggregate (GMTA) using a tube‐dilution test. MTA preparations were freshly mixed and tested after 24 h on Candida albicans. The experiment was carried out in 24‐well culture plates. Fifty wells were used and divided into four experimental groups (freshly mixed WMTA, freshly mixed GMTA, 24 h‐set WMTA and 24 h‐set GMTA) of 10 wells each and control groups of five wells each. Plates of Sabouraud dextrose agar mixed with C. albicans served as positive control, and Sabouraud dextrose agar without C. albicans served as negative control. Fresh inoculate of C. albicans was prepared by growing an overnight culture from a stock culture. Aliquots of C. albicans were then taken from the stock culture and plated on the agar compound of the experimental and control groups. All plates were incubated at 37°C for 1, 24 and 72 h. Growth of fungi was monitored daily by the presence of turbidity. Results showed that in the freshly mixed as well as 24 h‐set MTA cements fungal growth was observed during 1‐h incubation, whereas by increasing the incubation time, no fungal growth was observed in 24 and 72 h. It was concluded that MTA cements (freshly mixed and 24‐h set) were effective against C. albicans.
The Philosophy of Religion: A Programmatic Overview
Authors: Bishop John
Published: September 2006

It is argued that philosophy of religion should focus not only on the epistemic justifiability of holding religious beliefs but also on the moral justifiability of commitment to their truth in practical reasoning. If the truth of classical theism may turn out to be evidentially ambiguous, then pressure is placed on the moral evidentialist assumption that one is morally justified in taking a theistic truth‐claim to be true only if one's total evidence sufficiently supports its truth. After investigating some contemporary attempts to retain evidentialism in the face of ambiguity, a modest fideism is proposed which may serve both to ground an important ‘political turn’ in contemporary philosophy of religion and to prompt re‐examination of dominant assumptions about the content of core theistic beliefs.
Induction of parturition in dairy cattle and its effects on health and subsequent lactation and reproductive performance
Authors: MANSELL PD , CAMERON AR , TAYLOR DP , MALMO J
Published: September 2006

Objective   To determine the effect of induction of parturition on health, milk production and reproductive performance of dairy cows.

Design   A prospective cohort study in 62 dairy herds.

Procedure   Health, milk production and fertility indices were documented for 1449 dairy cows treated with dexamethasone trimethylacetate, with or without prostaglandin to induce calving. Equivalent data was collected for 603 untreated herd mates that calved at approximately the same time.

Results   The median interval from initial treatment to calving was 11 days. Induction was associated with a substantially lower calf survival and commercial value of surviving calves. Calf viability and value was lower when induced cows were at an earlier stage of pregnancy. Retained foetal membranes, photosensitisation and other problems were significantly more frequent in the induced group compared to the untreated group. Milk production of induced cows was approximately 4% lower than untreated ones, but the majority of reproductive indices were not significantly different between the two groups.

Conclusions   The practice of induction of parturition in seasonal calving dairy herds is a reliable way of shortening the gestation period of cows. Costs associated with morbidity and mortality of induced cows and losses in lactation and calf production are offset by benefits of improved reproductive performance and more efficient management of the herd. The welfare aspects of induction on calf survival must be considered.
Haloalkane Dehalogenase LinB Is Responsible for β- and δ-Hexachlorocyclohexane Transformation inSphingobium indicumB90A
Authors: Sharma Poonam , Raina Vishakha , Kumari Rekha , Malhotra Shweta , Dogra Charu , Kumari Hansi , Kohler Hans-Peter E. , Buser Hans-Rudolf , Holliger Christof , Lal Rup
Published: September 2006

Incubation of resting cells ofSphingobium indicumB90A,Sphingobium japonicumUT26, andSphingobium francenseSp+ showed that they were able to transform β- and δ-hexachlorocyclohexane (β- and δ-HCH, respectively), the most recalcitrant hexachlorocyclohexane isomers, to pentachlorocyclohexanols, but only resting cells of strain B90A could further transform the pentachlorocyclohexanol intermediates to the corresponding tetrachlorocyclohexanediols. Moreover, experiments with resting cells ofEscherichia coliexpressing the LinB proteins of strains B90A, UT26, and Sp+ indicated that LinB was responsible for these transformations. Purified LinB proteins from all three strains also effected the formation of the respective pentachlorocyclohexanols. Although the three LinB enzymes differ only marginally with respect to amino acid sequence, they showed interesting differences with respect to substrate specificity. When LinB from strain B90A was incubated with β- and δ-HCH, the pentachlorocyclohexanol products were further transformed and eventually disappeared from the incubation mixtures. In contrast, the LinB proteins from strains UT26 and Sp+ could not catalyze transformation of the pentachlorocyclohexanols, and these products accumulated in the incubation mixture. A mutant of strain Sp+ lackinglinAandlinBdid not degrade any of the HCH isomers, including β-HCH, and complementation of this mutant bylinBfrom strain B90A restored the ability to degrade β- and δ-HCH.
Identification, Typing, and Insecticidal Activity of
Xenorhabdus
Isolates from Entomopathogenic Nematodes in United Kingdom Soil and Characterization of the
xpt
Toxin Loci
Authors: Sergeant Martin , Baxter Laura , Jarrett Paul , Shaw Eve , Ousley Margaret , Winstanley Craig , Morgan J. Alun W.
Published: September 2006

Xenorhabdus
strains from entomopathogenic nematodes isolated from United Kingdom soils by using the insect bait entrapment method were characterized by partial sequencing of the 16S rRNA gene, four housekeeping genes (
asd
,
ompR
,
recA
, and
serC
) and the flagellin gene (
fliC
). Most strains (191/197) were found to have genes with greatest similarity to those of
Xenorhabdus bovienii
, and the remaining six strains had genes most similar to those of
Xenorhabdus nematophila
. Generally, 16S rRNA sequences and the sequence types based on housekeeping genes were in agreement, with a few notable exceptions. Statistical analysis implied that recombination had occurred at the
serC
locus and that moderate amounts of interallele recombination had also taken place. Surprisingly, the
fliC
locus contained a highly variable central region, even though insects lack an adaptive immune response, which is thought to drive flagellar variation in pathogens of higher organisms. All the
X. nematophila
strains exhibited a consistent pattern of insecticidal activity, and all contained the insecticidal toxin genes
xptA1A2B1C1
, which were present on a pathogenicity island (PAI). The PAIs were similar among the
X. nematophila
strains, except for partial deletions of a peptide synthetase gene and the presence of insertion sequences. Comparison of the PAI locus with that of
X. bovienii
suggested that the PAI integrated into the genome first and then acquired the
xpt
genes. The independent mobility of
xpt
genes was further supported by the presence of
xpt
genes in
X. bovienii
strain I73 on a type 2 transposon structure and by the variable patterns of insecticidal activity in
X. bovienii
isolates, even among closely related strains.
Genetic Distinctions among Clinical and Environmental Strains of
Vibrio vulnificus
Authors: Chatzidaki-Livanis Maria , Hubbard Michael A. , Gordon Katrina , Harwood Valerie J. , Wright Anita C.
Published: September 2006

Vibrio vulnificus
causes rare but frequently fatal septicemia associated with raw oyster consumption by persons with underlying hepatic or immune system dysfunction. The virulence potential of environmental reservoirs appears widely distributed, because most strains are virulent in animal models; however, several investigations recently demonstrated genetic divergence among strains from clinical versus environmental origin at independent genetic loci. The present study used PCR to screen DNA polymorphisms in strains from environmental (
n
= 35) or clinical (
n
= 33) sources, and genomic relationships were determined by repetitive extragenic palindromic DNA PCR (rep-PCR) typing. Significant (
P
< 0.01) association was observed for typical “clinical” or “environmental” polymorphism profiles based on strain origin. Most oyster isolates (88%), including all of those with the “environmental” profile, also formed a single rep-PCR genogroup. Clinical isolates within this group did not have the typical “clinical” profile. On the other hand, clinical isolates with the typical polymorphism profile were distributed among multiple rep-PCR genogroups, demonstrating greater genetic diversity than was evident by profiling genetic polymorphisms. Wound isolates were genetically distinct from typical blood isolates by all assays. Strains from an outbreak of wound infections in Israel (biotype 3) were closely related to several U.S. strains by rep-PCR, indicating potential reservoirs of emerging disease. Strains genetically related to blood isolates appeared to be relatively rare in oysters, as only one had the “clinical” polymorphism profile or clustered by rep-PCR. However, this study was not an extensive survey, and more sampling using rep-PCR for sensitive genetic discrimination is needed to determine the virulence potential of environmental reservoirs.
Optimization of Analytical Parameters for Inferring Relationships among
Escherichia coli
Isolates from Repetitive-Element PCR by Maximizing Correspondence with Multilocus Sequence Typing Data
Authors: Goldberg Tony L. , Gillespie Thomas R. , Singer Randall S.
Published: September 2006

Repetitive-element PCR (rep-PCR) is a method for genotyping bacteria based on the selective amplification of repetitive genetic elements dispersed throughout bacterial chromosomes. The method has great potential for large-scale epidemiological studies because of its speed and simplicity; however, objective guidelines for inferring relationships among bacterial isolates from rep-PCR data are lacking. We used multilocus sequence typing (MLST) as a “gold standard” to optimize the analytical parameters for inferring relationships among
Escherichia coli
isolates from rep-PCR data. We chose 12 isolates from a large database to represent a wide range of pairwise genetic distances, based on the initial evaluation of their rep-PCR fingerprints. We conducted MLST with these same isolates and systematically varied the analytical parameters to maximize the correspondence between the relationships inferred from rep-PCR and those inferred from MLST. Methods that compared the shapes of densitometric profiles (“curve-based” methods) yielded consistently higher correspondence values between data types than did methods that calculated indices of similarity based on shared and different bands (maximum correspondences of 84.5% and 80.3%, respectively). Curve-based methods were also markedly more robust in accommodating variations in user-specified analytical parameter values than were “band-sharing coefficient” methods, and they enhanced the reproducibility of rep-PCR. Phylogenetic analyses of rep-PCR data yielded trees with high topological correspondence to trees based on MLST and high statistical support for major clades. These results indicate that rep-PCR yields accurate information for inferring relationships among
E. coli
isolates and that accuracy can be enhanced with the use of analytical methods that consider the shapes of densitometric profiles.
Two 2[5H]-Furanones as Possible Signaling Molecules inLactobacillus helveticus
Authors: Ndagijimana Maurice , Vallicelli Melania , Cocconcelli P. Sandro , Cappa Fabrizio , Patrignani Francesca , Lanciotti Rosalba , Guerzoni M. Elisabetta
Published: September 2006

Two 2[5H]-furanones, in association with medium-chain fatty acids, were released in whey byLactobacillus helveticusexposed to oxidative and heat stresses. This species plays an important role in cheese technology, particularly for Swiss-type cheeses and Grana cheese. Moreover, it significantly contributes to cheese ripening by means of an early autolysis and the release of enzymes during processing. Experimental evidence of the involvement of the two 2[5H]-furanones, detected by a gas chromatography-mass spectrometry/solid-phase microextraction technique, in the autolysis phenomenon has been obtained. Zymograms performed by using renaturing sodium dodecyl sulfate-polyacrylamide gels were used to detect the bioactivity of the supernatants containing the two furanones on fresh cells of the same strain. In addition to bands corresponding to known autolysins, new autolysins were detected concomitant with the exposure ofLactobacillus helveticusto the supernatants, which can be regarded as conditioned media (CM), and to a commercial furanone, 5-ethyl-3-hydroxy-4-methyl-2[5H]-furanone (HEMFi), having spectral data similar to those of the newly described 2[5H]-furanones. Morphological changes were observed when fresh cells were exposed to CM containing the two 2[5H]-furanones and HEMFi. The two furanones produced byLactobacillus helveticus, which met a number of criteria to be included in cell-cell signaling molecules, have a presumptive molecular mass lower than those of already known 3[2H]-furanones having an autolytic activity and being produced by gram-negative bacteria. Moreover, they present a different chemical structure with respect to the furanones already identified as products ofLactococcus lactissubsp.cremorisor to those identified in some cheeses withLactobacillus helveticusas a starter culture.
Proteomic Profiling and Identification of Immunodominant Spore Antigens of
Bacillus anthracis
,
Bacillus cereus
, and
Bacillus thuringiensis
Authors: DelVecchio Vito G. , Connolly Joseph P. , Alefantis Timothy G. , Walz Alexander , Quan Marian A. , Patra Guy , Ashton John M. , Whittington Jessica T. , Chafin Ryan D. , Liang Xudong , Grewal Paul , Khan Akbar S. , Mujer Cesar V.
Published: September 2006

Differentially expressed and immunogenic spore proteins of the
Bacillus cereus
group of bacteria, which includes
Bacillus anthracis
,
Bacillus cereus
, and
Bacillus thuringiensis
, were identified. Comparative proteomic profiling of their spore proteins distinguished the three species from each other as well as the virulent from the avirulent strains. A total of 458 proteins encoded by 232 open reading frames were identified by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry analysis for all the species. A number of highly expressed proteins, including elongation factor Tu (EF-Tu), elongation factor G, 60-kDa chaperonin, enolase, pyruvate dehydrogenase complex, and others exist as charge variants on two-dimensional gels. These charge variants have similar masses but different isoelectric points. The majority of identified proteins have cellular roles associated with energy production, carbohydrate transport and metabolism, amino acid transport and metabolism, posttranslational modifications, and translation. Novel vaccine candidate proteins were identified using
B. anthracis
polyclonal antisera from humans postinfected with cutaneous anthrax. Fifteen immunoreactive proteins were identified in
B. anthracis
spores, whereas 7, 14, and 7 immunoreactive proteins were identified for
B. cereus
and in the virulent and avirulent strains of
B. thuringiensis
spores, respectively. Some of the immunodominant antigens include charge variants of EF-Tu, glyceraldehyde-3-phosphate dehydrogenase, dihydrolipoamide acetyltransferase, Δ-1-pyrroline-5-carboxylate dehydrogenase, and a dihydrolipoamide dehydrogenase. Alanine racemase and neutral protease were uniquely immunogenic to
B. anthracis
. Comparative analysis of the spore immunome will be of significance for further nucleic acid- and immuno-based detection systems as well as next-generation vaccine development.
Virulence of
Serratia
Strains against
Costelytra zealandica
Authors: Tan Binglin , Jackson Trevor A. , Hurst Mark R. H.
Published: September 2006

Strains of
Serratia
spp. showed a high level of virulence when injected into the hemocoel of larvae
Costelytra zealandica
, with
Serratia entomophila
,
S. plymuthica
, and
S. marcescens
showing significantly higher virulence than
S. proteamaculans
. Toxicity was independent of the amber disease-causing plasmid pADAP, suggesting a generalized
Serratia
toxin.
Global Transcriptional and Physiological Responses of
Saccharomyces cerevisiae
to Ammonium,
l
-Alanine, or
l
-Glutamine Limitation
Authors: Usaite Renata , Patil Kiran R. , Grotkjær Thomas , Nielsen Jens , Regenberg Birgitte
Published: September 2006

The yeast
Saccharomyces cerevisiae
encounters a range of nitrogen sources at various concentrations in its environment. The impact of these two parameters on transcription and metabolism was studied by growing
S. cerevisiae
in chemostat cultures with
l
-glutamine,
l
-alanine, or
l
-ammonium in limitation and by growing cells in an excess of ammonium. Cells grown in
l
-alanine-limited cultures had higher biomass yield per nitrogen mole (19%) than those from ammonium-limited cultures. Whole-genome transcript profiles were analyzed with a genome-scale metabolic model that suggested increased anabolic activity in
l
-alanine-limited cells. The changes in these cells were found to be focused around pyruvate, acetyl coenzyme A, glyoxylate, and α-ketoglutarate via increased levels of
ALT1
,
DAL7
,
PYC1
,
GDH2
, and
ADH5
and decreased levels of
GDH3
,
CIT2
, and
ACS1
transcripts. The transcript profiles were then clustered. Approximately 1,400 transcripts showed altered levels when amino acid-grown cells were compared to those from ammonium. Another 400 genes had low transcript levels when ammonium was in excess. Overrepresentation of the GATAAG element in their promoters suggests that nitrogen catabolite repression (NCR) may be responsible for this regulation. Ninety-one genes had transcript levels on both
l
-glutamine and ammonium that were decreased compared to those on
l
-alanine, independent of the concentration. The GATAAG element in these genes suggests two groups of NCR-responsive genes, those that respond to high levels of nitrogen and those that respond to levels below 30 μM. In conclusion, our results reveal that the nitrogen source has substantial influence on the transcriptome of yeasts and that transcriptional changes may be correlated to physiology via a metabolic model.
New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras
Authors: Ashelford Kevin E. , Chuzhanova Nadia A. , Fry John C. , Jones Antonia J. , Weightman Andrew J.
Published: September 2006

A new computer program, called Mallard, is presented for screening entire 16S rRNA gene libraries of up to 1,000 sequences for chimeras and other artifacts. Written in the Java computer language and capable of running on all major operating systems, the program provides a novel graphical approach for visualizing phylogenetic relationships among 16S rRNA gene sequences. To illustrate its use, we analyzed most of the large libraries of cloned bacterial 16S rRNA gene sequences submitted to the public repository during 2005. Defining a large library as one containing 100 or more sequences of 1,200 bases or greater, we screened 25 of the 28 libraries and found that all but three contained substantial anomalies. Overall, 543 anomalous sequences were found. The average anomaly content per clone library was 9.0%, 4% higher than that previously estimated for the public repository overall. In addition, 90.8% of anomalies had characteristic chimeric patterns, a rise of 25.4% over that found previously. One library alone was found to contain 54 chimeras, representing 45.8% of its content. These figures far exceed previous estimates of artifacts within public repositories and further highlight the urgent need for all researchers to adequately screen their libraries prior to submission. Mallard is freely available from our website athttp://www.cardiff.ac.uk/biosi/research/biosoft/.
Inhibition of Fungal Colonization by
Pseudoalteromonas tunicata
Provides a Competitive Advantage during Surface Colonization
Authors: Franks A. , Egan S. , Holmström C. , James S. , Lappin-Scott H. , Kjelleberg S.
Published: September 2006

The marine epiphytic bacterium
Pseudoalteromonas tunicata
produces a range of extracellular secondary metabolites that inhibit an array of common fouling organisms, including fungi. In this study, we test the hypothesis that the ability to inhibit fungi provides
P. tunicata
with an advantage during colonization of a surface. Studies on a transposon-generated antifungal-deficient mutant of
P. tunicata
, FM3, indicated that a long-chain fatty acid-coenzyme A ligase is involved in the production of a broad-range antifungal compound by
P. tunicata
. Flow cell experiments demonstrated that production of an antifungal compound provided
P. tunicata
with a competitive advantage against a marine yeast isolate during surface colonization. This compound enabled
P. tunicata
to disrupt an already established fungal biofilm by decreasing the number of yeast cells attached to the surface by 66% ± 9%. For in vivo experiments, the wild-type and FM3 strains of
P. tunicata
were used to inoculate the surface of the green alga
Ulva australis
. Double-gradient denaturing gradient gel electrophoresis analysis revealed that after 48 h, the wild-type
P. tunicata
had outcompeted the surface-associated fungal community, whereas the antifungal-deficient mutant had no effect on the fungal community. Our data suggest that
P. tunicata
is an effective competitor against fungal surface communities in the marine environment.
Methane- and Sulfur-Metabolizing Microbial Communities Dominate the Lost City Hydrothermal Field Ecosystem
Authors: Brazelton William J. , Schrenk Matthew O. , Kelley Deborah S. , Baross John A.
Published: September 2006

Hydrothermal venting and the formation of carbonate chimneys in the Lost City hydrothermal field (LCHF) are driven predominantly by serpentinization reactions and cooling of mantle rocks, resulting in a highly reducing, high-pH environment with abundant dissolved hydrogen and methane. Phylogenetic and terminal restriction fragment length polymorphism analyses of 16S rRNA genes in fluids and carbonate material from this site indicate the presence of organisms similar to sulfur-oxidizing, sulfate-reducing, and methane-oxidizing
Bacteria
as well as methanogenic and anaerobic methane-oxidizing
Archaea
. The presence of these metabolic groups indicates that microbial cycling of sulfur and methane may be the dominant biogeochemical processes active within this ultramafic rock-hosted environment. 16S rRNA gene sequences grouping within the
Methylobacter
and
Thiomicrospira
clades were recovered from a chemically diverse suite of carbonate chimney and fluid samples. In contrast, 16S rRNA genes corresponding to the Lost City
Methanosarcinales
phylotype were found exclusively in high-temperature chimneys, while a phylotype of anaerobic methanotrophic
Archaea
(ANME-1) was restricted to lower-temperature, less vigorously venting sites. A hyperthermophilic habitat beneath the LCHF may be reflected by 16S rRNA gene sequences belonging to
Thermococcales
and uncultured
Crenarchaeota
identified in vent fluids. The finding of a diverse microbial ecosystem supported by the interaction of high-temperature, high-pH fluids resulting from serpentinization reactions in the subsurface provides insight into the biogeochemistry of what may be a pervasive process in ultramafic subseafloor environments.
Assessment of Genes Associated with
Streptococcus mutans
Biofilm Morphology
Authors: Motegi Mizuho , Takagi Yuzo , Yonezawa Hideo , Hanada Nobuhiro , Terajima Jun , Watanabe Haruo , Senpuku Hidenobu
Published: September 2006

Streptococcus mutans
, the major pathogen responsible for dental caries in humans, is a biofilm-forming bacterium. In the present study, 17 different pulsed-field gel electrophoresis patterns of genomic DNA were identified in
S. mutans
organisms isolated clinically from whole saliva. The
S. mutans
isolates showed different abilities to form biofilms on polystyrene surfaces in semidefined minimal medium cultures. Following cultivation in a flow cell system in tryptic soy broth with 0.25% sucrose and staining using a BacLight LIVE/DEAD system, two strains, designated FSC-3 and FSC-4, showed the greatest and least, respectively, levels of biofilm formation when examined with confocal laser scanning microscopy. Further, image analyses of spatial distribution and architecture were performed to quantify the merged green (live cells) and red (dead cells) light. The light intensity of the FSC-3 biofilm was greater than that of the FSC-4 biofilm in the bottom area but not in the top area.
S. mutans
whole-genome array results showed that approximately 3.8% of the genes were differentially expressed in the two strains, of which approximately 2.2%, including bacitracin transport ATP-binding protein gene
glrA
and a BLpL-like putative immunity protein gene, were activated in FSC-3. In addition, about 1.6% of the genes, including those associated with phosphotransferase system genes, were repressed. Analyses of the
glrA
-deficient strains and reverse transcription-PCR confirmed the role of the gene in biofilm formation. Differential assessment of biofilm-associated genes in clinical strains may provide useful information for understanding the morphological development of streptococcal biofilm, as well as for colonization of
S. mutans
.
Lysine-Oriented Charges Trigger the Membrane Binding and Activity of Nukacin ISK-1
Authors: Asaduzzaman Sikder M. , Nagao Jun-ichi , Aso Yuji , Nakayama Jiro , Sonomoto Kenji
Published: September 2006

The antibacterial activities and membrane binding of nukacin ISK-1 and its fragments and mutants were evaluated to delineate the determinants governing structure-function relationships. The tail region (nukacin
1-7
) and ring region (nukacin
7-27
) were shown to have no antibacterial activity and also had no synergistic effect on each other or even on nukacin ISK-1. Both a fragment with three lysines in the N terminus deleted (nukacin
4-27
) and a mutant with three lysines in the N terminus replaced with alanine (K1-3A nukacin ISK-1) imparted very low activity (32-fold lower than nukacin ISK-1) and also exhibited a similar antagonistic effect on nukacin ISK-1. Addition of two lysine residues at the N terminus (+2K nukacin ISK-1) provided no further increased antibacterial activity. Surface plasmon resonance sensorgrams and kinetic rate constants determined by a BIAcore biosensor revealed that nukacin ISK-1 has remarkably higher binding affinity to anionic model membrane than to zwitterionic model membrane. Similar trends of strong binding responses and kinetics were indicated by the high affinities of nukacin ISK-1 and +2K nukacin ISK-1, but there was no binding of tail region, ring region, nukacin
4-27
, and K1-3A nukacin ISK-1 to the anionic model membrane. Our findings therefore suggest that the complete structure of nukacin ISK-1 is necessary for its full activity, in which the N-terminus three lysine residues play a crucial role in electrostatic binding to the target membrane and therefore nukacin ISK-1's ability to exert its potent antibacterial activity.
Application of the [
3
H]Leucine Incorporation Technique for Quantification of Bacterial Secondary Production Associated with Decaying Wetland Plant Litter
Authors: Gillies Jane E. , Kuehn Kevin A. , Francoeur Steven N. , Neely Robert K.
Published: September 2006

The radiolabeled leucine incorporation technique for quantifying rates of bacterial production has increased in popularity since its original description for bacterioplankton communities. Prior studies addressing incorporation conditions (e.g., substrate saturation) for bacterial communities in other habitats, such as decaying plant litter, have reported a wide range of final leucine concentrations (400 nM to 50 μM) required to achieve saturation-level uptake. We assessed the application of the [
3
H]leucine incorporation procedure for measuring bacterial production on decaying wetland plant litter. Substrate saturation experiments (nine concentrations, 10 nM to 50 μM final leucine concentration) were conducted on three dates for microbial communities colonizing the submerged litter of three emergent plant species (
Typha angustifolia
,
Schoenoplectus validus
, and
Phragmites australis
). A modified [
3
H]leucine protocol was developed by coupling previously described incubation and alkaline extraction protocols with microdialysis (500 molecular weight cutoff membrane) of the final radiolabeled protein extract. The incorporation of [
3
H]leucine into protein exhibited a biphasic saturation curve, with lower apparent

K
m

values ranging from 400 nM to 4.2 μM depending on the plant species studied. Upper apparent

K
m

values ranged from 1.3 to 59 μM. These results suggest differential uptake by litter-associated microbial assemblages, with the lower apparent

K
m

values possibly representing bacterial uptake and higher apparent

K
m

values representing a combination of both bacterial and nonbacterial (e.g., eukaryotic) uptake.
Temporal Changes in Microscale Colonization of the Phylloplane by
Aureobasidium pullulans
Authors: McGrath Molly J. , Andrews John H.
Published: September 2006

Colonization of apple leaves by the yeastlike fungus
Aureobasidium pullulans
was followed quantitatively and spatially at a microscale level throughout two growing seasons. Ten field leaves were sampled on 11 dates in 2003 and 15 dates in 2004. Using an
A. pullulans
-specific fluorescence in situ hybridization probe and epifluorescence microscopy, we enumerated total cells, swollen-cells and chlamydospores (SCC), and blastospores/mm
2
on leaf features, including the midvein, other (smaller) veins, and the interveinal regions. By 7 July 2003 and 7 June 2004, the total numbers of
A. pullulans
cells/mm
2
were significantly higher (
P
< 0.05) on the midvein and other veins than in the interveinal regions. This pattern remained consistent thereafter. The primary colonizing morphotype in all regions at all dates was the SCC form, although blastospores always occurred in low numbers. Occupancy was quantified based on the percentage of microscope fields of a particular leaf feature containing ≥1
A. pullulans
cell. In general, as seasons progressed, the percent occupancy of features increased and, for most midvein and veinal features, approximated 100% at the end of both growing seasons. Except for early collections, when
A. pullulans
cell numbers were low, the percent occupancy of interveinal regions was lower than that of the midvein or other veinal regions.
A. pullulans
was distributed primarily as single cells throughout the seasons in interveinal regions. On the midvein and other veins, colonies of ≥4 cells developed over time, and more cells occurred in colonies than as singletons by August. Our results demonstrate that
A. pullulans
primarily colonizes veins, where populations appear to increase by growth in situ. This pattern is established early in the growing season and persists.
Granadaene: Proposed Structure of the Group B Streptococcus Polyenic Pigment
Authors: Rosa-Fraile Manuel , Rodríguez-Granger Javier , Haidour-Benamin Ali , Cuerva Juan Manuel , Sampedro Antonio
Published: September 2006

The goal of this work was to determine the chemical nature of the red pigment produced by
Streptococcus agalactiae
, which has been thought to be a carotene. We extracted the pigment with 0.1 M KOH and purified it by column chromatography on Sephadex LH. Data from elemental analysis and mass and nuclear magnetic resonance spectra lead us to propose the structure to be that of a new ornithine rhamno-polyene with 12 conjugated double bonds, to which we have assigned the trivial name granadaene.
Characterization of (R)-2-Hydroxyisocaproate Dehydrogenase and a Family III Coenzyme A Transferase Involved in Reduction ofl-Leucine to Isocaproate byClostridium difficile
Authors: Kim Jihoe , Darley Daniel , Selmer Thorsten , Buckel Wolfgang
Published: September 2006

The strictly anaerobic pathogenic bacteriumClostridium difficileoccurs in the human gut and is able to thrive from fermentation of leucine. Thereby the amino acid is both oxidized to isovalerate plus CO2and reduced to isocaproate. In the reductive branch of this pathway, the dehydration of (R)-2-hydroxyisocaproyl-coenzyme A (CoA) to (E)-2-isocaprenoyl-CoA is probably catalyzed via radical intermediates. The dehydratase requires activation by an ATP-dependent one-electron transfer (J. Kim, D. Darley, and W. Buckel, FEBS J. 272:550-561, 2005). Prior to the dehydration, a dehydrogenase and a CoA transferase are supposed to be involved in the formation of (R)-2-hydroxyisocaproyl-CoA. Deduced amino acid sequences ofldhAandhadAfrom the genome ofC. difficileshowed high identities tod-lactate dehydrogenase and family III CoA transferase, respectively. Both putative genes encoding the dehydrogenase and CoA transferase were cloned and overexpressed inEscherichia coli; the recombinant Strep tag II fusion proteins were purified to homogeneity and characterized. The substrate specificity of the monomeric LdhA (36.5 kDa) indicated that 2-oxoisocaproate (Km= 68 μM,kcat= 31 s−1) and NADH were the native substrates. For the reverse reaction, the enzyme accepted (R)- but not (S)-2-hydroxyisocaproate and therefore was named (R)-2-hydroxyisocaproate dehydrogenase. HadA showed CoA transferase activity with (R)-2-hydroxyisocaproyl-CoA as a donor and isocaproate or (E)-2-isocaprenoate as an acceptor. By site-directed mutagenesis, the conserved D171 was identified as an essential catalytic residue probably involved in the formation of a mixed anhydride with the acyl group of the thioester substrate. However, neither hydroxylamine nor sodium borohydride, both of which are inactivators of the CoA transferase, modified this residue. The dehydrogenase and the CoA transferase fit well into the proposed pathway of leucine reduction to isocaproate.
Survival of
Salmonella enterica
Serovar Newport in Manure and Manure-Amended Soils
Authors: You Youwen , Rankin Shelley C. , Aceto Helen W. , Benson Charles E. , Toth John D. , Dou Zhengxia
Published: September 2006

Salmonella enterica
serovar Newport has undergone a rapid epidemic spread in dairy cattle. This provides an efficient mechanism for pathogen amplification and dissemination into the environment through manure spreading on agricultural land. The objective of this study was to determine the survival characteristics of
Salmonella
serovar Newport in manure and manure-amended soils where the pathogen may be amplified. A multidrug-resistant (MDR)
Salmonella
serovar Newport strain and a drug-susceptible (DS) strain, both bovine isolates, were inoculated into dairy manure that was incubated under constant temperature and moisture conditions alone or after being mixed with sterilized or nonsterilized soil.
Salmonella
serovar Newport concentrations increased by up to 400% in the first 1 to 3 days following inoculation, and a trend of steady decline followed. With manure treatment, a sharp decline in cell concentration occurred after day 35, possibly due to microbial antagonism. For all treatments, decreases in
Salmonella
serovar Newport concentrations over time fit a first-order kinetic model. Log reduction time was 14 to 32 days for 1 log
10
, 28 to 64 days for 2 log
10
, and 42 to 96 days for 3 log
10
declines in the organisms' populations from initially inoculated concentrations. Most-probable-number monitoring data indicated that the organisms persisted for 184, 332, and 405 days in manure, manure-amended nonsterilized soil, and manure-amended sterilized soil, respectively. The MDR strain and the DS strain had similar survival patterns.
Characterization of Phototrophic Purple Nonsulfur Bacteria Forming Colored Microbial Mats in a Swine Wastewater Ditch
Authors: Okubo Yoko , Futamata Hiroyuki , Hiraishi Akira
Published: September 2006

The community structure of pink-colored microbial mats naturally occurring in a swine wastewater ditch was studied by culture-independent biomarker and molecular methods as well as by conventional cultivation methods. The wastewater in the ditch contained acetate and propionate as the major carbon nutrients. Thin-section electron microscopy revealed that the microbial mats were dominated by rod-shaped cells containing intracytoplasmic membranes of the lamellar type. Smaller numbers of oval cells with vesicular internal membranes were also found. Spectroscopic analyses of the cell extract from the biomats showed the presence of bacteriochlorophyllaand carotenoids of the spirilloxanthin series. Ubiquinone-10 was detected as the major quinone. A clone library of the photosynthetic gene,pufM, constructed from the bulk DNA of the biomats showed that all of the clones were derived from members of the generaRhodobacterandRhodopseudomonas. The dominant phototrophic bacteria from the microbial mats were isolated by cultivation methods and identified as being of the generaRhodobacterandRhodopseudomonasby studying 16S rRNA andpufMgene sequence information. Experiments of oxygen uptake with lower fatty acids revealed that the freshly collected microbial mats and theRhodopseudomonasisolates had a wider spectrum of carbon utilization and a higher affinity for acetate than did theRhodobacterisolates. These results demonstrate that the microbial mats were dominated by the purple nonsulfur bacteria of the generaRhodobacterandRhodopseudomonas, and the bioavailability of lower fatty acids in wastewater is a key factor allowing the formation of visible microbial mats with these phototrophs.
Occurrence of 1-Glyceryl-1-myo-Inosityl Phosphate in Hyperthermophiles
Authors: Lamosa Pedro , Gonçalves Luís G. , Rodrigues Marta V. , Martins Lígia O. , Raven Neil D. H. , Santos Helena
Published: September 2006

The accumulation of compatible solutes was studied in the hyperthermophilic bacteriumAquifex pyrophilusas a function of the temperature and the NaCl concentration of the growth medium. Nuclear magnetic resonance analysis of cell extracts revealed the presence of α- and β-glutamate, di-mannosyl-di-myo-inositol phosphate, di-myo-inositol phosphate, and an additional compound here identified as 1-glyceryl-1-myo-inosityl phosphate. All solutes accumulated byA. pyrophilusare negatively charged at physiological pH. The intracellular levels of di-myo-inositol phosphate increased in response to supraoptimal growth temperature, while α- and β-glutamate accumulated in response to osmotic stress, especially at growth temperatures below the optimum. The newly discovered compound, 1-glyceryl-1-myo-inosityl phosphate, appears to play a double role in osmo- and thermoprotection, since its intracellular pool increased primarily in response to a combination of osmotic and heat stresses. This work also uncovered the nature of the unknown compound, previously detected inArchaeoglobus fulgidus(L. O. Martins et al., Appl. Environ. Microbiol. 63:896-902, 1997). The curious structural relationship between diglycerol phosphate (found only inArchaeoglobusspecies), di-myo-inositol phosphate (a canonical solute of hyperthermophiles), and the newly identified solute is highlighted. This is the first report on the occurrence of 1-glyceryl-1-myo-inosityl phosphate in living systems.