bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intracellular Symbionts and Other Bacteria Associated with Deer Ticks (Ixodes scapularis) from Nantucket and Wellfleet, Cape Cod, Massachusetts
Authors: Benson Micah J. , Gawronski Jeffrey D. , Eveleigh Douglas E. , Benson David R. 
Published: January 2004

ABSTRACTThe diversity of bacteria associated with the deer tick (Ixodes scapularis) was assessed using PCR amplification, cloning, and sequencing of 16S rRNA genes originating from seven ticks collected from Nantucket Island and Wellfleet, Cape Cod, Mass. The majority of sequences obtained originated from gram-negative proteobacteria. Four intracellular bacteria were detected including strains ofEhrlichia,Rickettsia, andWolbachiaand an organism related to intracellular insect symbionts from theCytophaga-Flavobacterium-Bacteroidesgroup. Several strains of members of theSphingomonadaceaewere also detected in all but one tick. The results provide a view of the diversity of bacteria associated withI. scapularisticks in the field.
Sensitive and Rapid Detection of Edwardsiellosis in Fish by a Loop-Mediated Isothermal Amplification Method
Authors: Savan Ram , Igarashi Arisa , Matsuoka Satoru , Sakai Masahiro 
Published: January 2004

ABSTRACT

Here we report a rapid and sensitive method (using loop-mediated isothermal amplification [LAMP]) for the diagnosis of edwardsiellosis, a fish disease caused by
Edwardsiella tarda
, in Japanese flounder. A set of four primers was designed, and conditions for the detection were optimized for the detection of
E. tarda
in 45 min at 65°C. No amplification of the target hemolysin gene was detected in other related bacteria. When the LAMP primers were used, detection of edwardsiellosis in infected Japanese flounder kidney, and spleen and seawater cultures was possible. We have developed a rapid and sensitive diagnostic protocol for edwardsiellosis detection in fish. This is the first report of the application of LAMP for the diagnosis of a fish pathogen.
Molecular Cloning, Purification, and Biochemical Characterization of Hydantoin Racemase from the Legume Symbiont
Sinorhizobium meliloti
CECT 4114
Authors: Martínez-Rodríguez Sergio , Las Heras-Vázquez Francisco Javier , Mingorance-Cazorla Lydia , Clemente-Jiménez Josefa María , Rodríguez-Vico Felipe 
Published: January 2004

ABSTRACT

Hydantoin racemase from
Sinorhizobium meliloti
was functionally expressed in
Escherichia coli
. The native form of the enzyme was a homotetramer with a molecular mass of 100 kDa. The optimum temperature and pH for the enzyme were 40°C and 8.5, respectively. The enzyme showed a slight preference for hydantoins with short rather than long aliphatic side chains or those with aromatic rings. Substrates, which showed no detectable activity toward the enzyme, were found to exhibit competitive inhibition.
Identification of Bacilysin, Chlorotetaine, and Iturin A Produced by
Bacillus
sp. Strain CS93 Isolated from Pozol, a Mexican Fermented Maize Dough
Authors: Phister Trevor G. , O'Sullivan Daniel J. , McKay Larry L. 
Published: January 2004

ABSTRACT

Three antimicrobial compounds produced by
Bacillus
sp. strain CS93 isolated from pozol were identified by using high-performance liquid chromatography and mass spectrometry. The three compounds were iturin, bacilysin, and chlorotetaine. Production of these compounds by CS93 could account for the medicinal properties attributed to pozol.
Combined Effects of High Hydrostatic Pressure and Temperature for Inactivation of
Bacillus anthracis
Spores
Authors: Cléry-Barraud Cécile , Gaubert Agnès , Masson Patrick , Vidal Dominique 
Published: January 2004

ABSTRACT

Spores of
Bacillus anthracis
are known to be extremely resistant to heat treatment, irradiation, desiccation, and disinfectants. To determine inactivation kinetics of spores by high pressure,
B. anthracis
spores of a Sterne strain-derived mutant deficient in the production of the toxin components (strain RP42) were exposed to pressures ranging from 280 to 500 MPa for 10 min to 6 h, combined with temperatures ranging from 20 to 75°C. The combination of heat and pressure resulted in complete destruction of
B. anthracis
spores, with a
D
value (exposure time for 90% inactivation of the spore population) of approximately 4 min after pressurization at 500 MPa and 75°C, compared to 160 min at 500 MPa and 20°C and 348 min at atmospheric pressure (0.1 MPa) and 75°C. The use of high pressure for spore inactivation represents a considerable improvement over other available methods of spore inactivation and could be of interest for antigenic spore preparation.
Role of Aminotransferase IlvE in Production of Branched-Chain Fatty Acids by
Lactococcus lactis
subsp.
lactis
Authors: Ganesan Balasubramanian , Weimer Bart C. 
Published: January 2004

ABSTRACT

The objective of this study was to determine the role of a lactococcal branched-chain amino acid aminotransferase gene,
ilvE
, in the production of branched-chain fatty acids.
Lactococcus lactis
subsp.
lactis
LM0230 and an
ilvE
deletion mutant, JLS450, produced branched-chain fatty acids from amino and α-keto acids at levels above α-keto acid spontaneous degradation and the fatty acids' flavor thresholds. The deletion mutant produced the same amounts of branched-chain fatty acids from precursor amino acids as did the parent. This was not the case, however, for the production of branched-chain fatty acids from the corresponding precursor α-keto acids. The deletion mutant produced a set of fatty acids different from that produced by the parent. We concluded from these observations that
ilvE
plays a role in the specific type of fatty acids produced but has little influence on the total amount of fatty acids produced by lactococci.
Neonatal-Mouse Infectivity of IntactCryptosporidium parvumOocysts Isolated after Optimized In Vitro Excystation
Authors: Hou L. , Li X. , Dunbar L. , Moeller R. , Palermo B. , Atwill E. R. 
Published: January 2004

ABSTRACTWe reexamined the finding of Neumann et al. (10) that intactCryptosporidium parvumoocysts obtained after in vitro excystation were infectious for neonatal CD-1 mice. We used both established excystation protocols and our own protocol that maximized excystation (2). Although intact oocysts isolated after any of three protocols were infectious for neonatal CD-1 mice, the infectivity of intact oocysts isolated with our optimized excystation protocol was significantly lower than the infectivity of intact oocysts isolated after established protocols or from fresh oocysts. Excystation should not be considered a valid measure ofC. parvumviability, given that it is biologically implausible for oocysts to be nonviable and yet infectious.
Rapid and Specific Detection ofSalmonellaspp. in Animal Feed Samples by PCR after Culture Enrichment
Authors: Löfström Charlotta , Knutsson Rickard , Axelsson Charlotta Engdahl , Rådström Peter 
Published: January 2004

ABSTRACTA PCR procedure has been developed for routine analysis of viableSalmonellaspp. in feed samples. The objective was to develop a simple PCR-compatible enrichment procedure to enable DNA amplification without any sample pretreatment such as DNA extraction or cell lysis. PCR inhibition by 14 different feed samples and natural background flora was circumvented by the use of the DNA polymeraseTth. This DNA polymerase was found to exhibit a high level of resistance to PCR inhibitors present in these feed samples compared to DyNAzyme II, FastStartTaq, PlatinumTaq,Pwo, rTth,Taq, andTfl. The specificity of theTthassay was confirmed by testing 101Salmonellaand 43 non-Salmonellastrains isolated from feed and food samples. A sample preparation method based on culture enrichment in buffered peptone water and DNA amplification withTthDNA polymerase was developed. The probability of detecting small numbers of salmonellae in feed, in the presence of natural background flora, was accurately determined and found to follow a logistic regression model. From this model, the probability of detecting 1 CFU per 25 g of feed in artificially contaminated soy samples was calculated and found to be 0.81. The PCR protocol was evaluated on 155 naturally contaminated feed samples and compared to an established culture-based method, NMKL-71. Eight percent of the samples were positive by PCR, compared with 3% with the conventional method. The reasons for the differences in sensitivity are discussed. Use of this method in the routine analysis of animal feed samples would improve safety in the food chain.
Utilization of
Escherichia coli
Outer-Membrane Endoprotease OmpT Variants as Processing Enzymes for Production of Peptides from Designer Fusion Proteins
Authors: Okuno Kazuaki , Yabuta Masayuki , Ooi Toshihiko , Kinoshita Shinichi 
Published: January 2004

ABSTRACT

Escherichia coli
outer-membrane endoprotease OmpT has suitable properties for processing fusion proteins to produce peptides and proteins. However, utilization of this protease for such production has been restricted due to its generally low cleavage efficiency at Arg (or Lys)-Xaa, where Xaa is a nonbasic N-terminal amino acid of a target polypeptide. The objective of this study was to generate a specific and efficient OmpT protease and to utilize it as a processing enzyme for producing various peptides and proteins by converting its substrate specificity. Since OmpT Asp
97
is proposed to interact with the P1′ amino acid of its substrates, OmpT variants with variations at Asp
97
were constructed by replacing this amino acid with 19 natural amino acids to alter the cleavage specificity at Arg (P1)-Xaa (P1′). The variant OmpT that had a methionine at this position, but not the wild-type OmpT, efficiently cleaved a fusion protein containing the amino acid sequence -Arg-Arg-Arg-Ala-Arg↓motilin, in which motilin is a model peptide with a phenylalanine at the N terminus. The OmpT variants with leucine and histidine at position 97 were useful in releasing human adrenocorticotropic hormone (1-24) (serine at the N terminus) and human calcitonin precursor (cysteine at the N terminus), respectively, from fusion proteins. Motilin was produced by this method and was purified up to 99.0% by two chromatographic steps; the yield was 160 mg/liter of culture. Our novel method in which the OmpT variants are used could be employed for production of various peptides and proteins.
Saccharomyces cerevisiae JEN1Promoter Activity Is Inversely Related to Concentration of Repressing Sugar
Authors: Chambers Prima , Issaka Aminatu , Palecek Sean P. 
Published: January 2004

ABSTRACTWhen carbon sources are changed,Saccharomyces cerevisiaetranscriptional patterns drastically change. To identify genes whose transcription can be used to quantitatively measure sugar concentrations, we searched genomic expression databases for a set of genes that are highly induced during the diauxic shift, and we used the promoters from these genes to drive expression of green fluorescent protein (GFP). Certain sugars, including glucose, fructose, and mannose, repress the promoter ofJEN1, which encodes a lactate-pyruvate transporter, in a dose-dependent manner. Nonrepressing carbon sources include galactose, raffinose, ethanol, lactate, and glycerol.JEN1promoter activity is a linear function of glucose concentration when organisms are grown at a steady-state glucose concentration below 1 g/liter.JEN1promoter repression is specific to carbon source; heat or cold shock, osmotic stress, DNA damage, and nitrogen starvation do not significantly affect promoter activity. Activation of theJEN1promoter requires the Snf1 protein kinase, but multiple regulatory elements most likely combine to provide the linear relationship betweenJEN1promoter activity and sugar concentration. Thus, aJEN1promoter-reporter system appears to provide a good living cell biosensor for the concentration of certain sugars. TheJEN1promoter also permits quantitative regulation of cellular functions not normally controlled by sugar concentrations. For example, a strain expressingFLO1under control of theJEN1promoter flocculates at a low glucose concentration.
Campylobacter
spp.
, Giardia
spp.
, Cryptosporidium
spp., Noroviruses, and Indicator Organisms in Surface Water in Southwestern Finland, 2000-2001
Authors: Hörman Ari , Rimhanen-Finne Ruska , Maunula Leena , von Bonsdorff Carl-Henrik , Torvela Niina , Heikinheimo Annamari , Hänninen Marja-Liisa 
Published: January 2004

ABSTRACT

A total of 139 surface water samples from seven lakes and 15 rivers in southwestern Finland were analyzed during five consecutive seasons from autumn 2000 to autumn 2001 for the presence of various enteropathogens (
Campylobacter
spp.,
Giardia
spp
., Cryptosporidium
spp., and noroviruses) and fecal indicators (thermotolerant coliforms,
Escherichia coli
,
Clostridium perfringens
, and F-RNA bacteriophages) and for physicochemical parameters (turbidity and temperature); this was the first such systematic study. Altogether, 41.0% (57 of 139) of the samples were positive for at least one of the pathogens; 17.3% were positive for
Campylobacter
spp. (45.8% of the positive samples contained
Campylobacter jejuni
, 25.0% contained
Campylobacter lari
, 4.2% contained
Campylobacter coli
, and 25.0% contained
Campylobacter
isolates that were not identified), 13.7% were positive for
Giardia
spp., 10.1% were positive for
Cryptosporidium
spp., and 9.4% were positive for noroviruses (23.0% of the positive samples contained genogroup I and 77.0% contained genogroup II). The samples were positive for enteropathogens significantly (
P
< 0.05) less frequently during the winter season than during the other sampling seasons. No significant differences in the prevalence of enteropathogens were found when rivers and lakes were compared. The presence of thermotolerant coliforms,
E. coli
, and
C. perfringens
had significant bivariate nonparametric Spearman's rank order correlation coefficients (
P
< 0.001) with samples that were positive for one or more of the pathogens analyzed. The absence of these indicators in a logistic regression model was found to have significant predictive value (odds ratios, 1.15 × 10
8
, 7.57, and 2.74, respectively;
P
< 0.05) for a sample that was negative for the pathogens analyzed. There were no significant correlations between counts or count levels for thermotolerant coliforms or
E. coli
or the presence of F-RNA phages and pathogens in the samples analyzed.
Mur-LH, the Broad-Spectrum Endolysin of
Lactobacillus helveticus
Temperate Bacteriophage φ-0303
Authors: Deutsch Stéphanie-Marie , Guezenec Stéphane , Piot Michel , Foster Simon , Lortal Sylvie 
Published: January 2004

ABSTRACT

φ-0303 is a temperate bacteriophage isolated from
Lactobacillus helveticus
CNRZ 303 strain after mitomycin C induction. In this work, the gene coding for a lytic protein of this bacteriophage was cloned using a library of φ-0303 in
Escherichia coli
DH5α. The lytic activity was detected by its expression, using whole cells of the sensitive strain
L. helveticus
CNRZ 892 as the substrate. The lysin gene was within a 4.1-kb DNA fragment of φ-0303 containing six open reading frames (ORFs) and two truncated ORFs. No sequence homology with holin genes was found within the cloned fragment. An integrase-encoding gene was also present in the fragment, but it was transcribed in a direction opposite that of the lysin gene. The lysin-encoding
lys
gene was verified by PCR amplification from the total phage DNA and subcloned. The
lys
gene is a 1,122-bp sequence encoding a protein of 373 amino acids (Mur-LH), whose product had a deduced molecular mass of 40,207 Da. Comparisons with sequences in sequence databases showed homology with numerous endolysins of other bacteriophages. Mur-LH was expressed in
E. coli
BL21, and by renaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis with
L. helveticus
CNRZ 892 as the substrate, the recombinant protein showed an apparent molecular mass of 40 kDa. The N-terminal sequence of the protein confirmed the start codon. Hydrolysis of cell walls of
L. helveticus
CNRZ 303 by the endolysin and biochemical analysis of the residues produced demonstrated that Mur-LH has
N
-acetylmuramidase activity. Last, the endolysin exhibited a broad spectrum of lytic activity, as it was active on different species, mainly thermophilic lactobacilli but also lactococci, pediococci,
Bacillus subtilis
,
Brevibacterium linens
, and
Enterococcus faecium
.
INTELLIGENT DATA ANALYSIS OF BREAST CANCER BASED ON ROUGH SET THEORY
Authors: HASSANIEN ABOUL ELLA 
Published: January 2004

Extensive amounts of knowledge and data stored in medical databases require the development of specialized tools for storing, accessing, analysis, and effectiveness usage of stored knowledge and data. Intelligent methods such as neural networks, fuzzy sets, decision trees, and expert systems are, slowly but steadily, applied in the medical fields. Recently, rough set theory is a new intelligent technique was used for the discovery of data dependencies, data reduction, approximate set classification, and rule induction from databases.In this paper, we present a rough set method for generating classification rules from a set of observed 360 samples of the breast cancer data. The attributes are selected, normalized and then the rough set dependency rules are generated directly from the real value attribute vector. Then the rough set reduction technique is applied to find all reducts of the data which contains the minimal subset of attributes that are associated with a class label for classification. Experimental results from applying the rough set analysis to the set of data samples are given and evaluated. In addition, the generated rules are also compared to the well-known ID3 classifier algorithm. The study showed that the theory of rough sets seems to be a useful tool for inductive learning and a valuable aid for building expert systems.
'SWAHILI ENLIGHTENMENT'? EAST AFRICAN REFORMIST DISCOURSE AT THE TURNING POINT: THE EXAMPLE OF SHEIKH MUHAMMAD KASIM MAZRUI
Authors: Kresse Kai 
Published: January 2004

AbstractThis article discusses Sheikh Muhammad Kasim Mazrui, an influential yet largely ignored figure within East African Islamic reformism, which shifted from internal to external domination in the second half of the 20th century. His educational booklet 'Hukumu za sharia', written in Kiswahili, is analysed and contextualised. Advising local Muslims, by way of clear argument and reference to authoritative texts, on how to deal with controversial local practices from an Islamic point of view, it pushed for the development of self-reliance, and criticised dependence on Islamic clerics and dignitaries. The text itself displays the rational principles that the reformist movement relied on and propagated, while it also contains hints of a more dogmatic tone that was yet to dominate reformist discourse. Overall, the article establishes a wider comparison in discussing this African Islamic reformism as an 'enlightenment' movement. The focus hereby is on structure rather than substance, as Islamic reform is incompatible with secularism. Common features, however, can be seen in the emphasis on rationality and self-reliance of individual actors, as well as the internal dialectic of the movements, oscillating between liberation and dogmatism.
Interleukin-10 and tumor necrosis factor alpha region haplotypes predict transplant-related mortality after unrelated donor stem cell transplantation
Authors: Keen Leigh J. , DeFor Todd E. , Bidwell Jeffrey L. , Davies Stella M. , Bradley Benjamin A. , Hows Jill M. 
Published: January 2004

Abstract
Certain cytokine gene polymorphisms have been shown to correlate with outcome of human leukocyte antigen (HLA) identical sibling donor stem cell transplantation (SCT), but in unrelated donor SCT such information is scarce. We have studied the association between cytokine gene polymorphism and transplant-related mortality (TRM) in 182 unrelated SCTs performed at a single center. We found association of polymorphism in the tumor necrosis factor alpha (TNFα) and interleukin-10 (IL-10) gene and TRM. Both the TNFd4 allele and the TNFα -1031C alleles are associated with high risk for TRM. Statistical analysis showed that both polymorphisms were present on a single haplotype. This haplotype was associated with high risk of TRM when present in recipient or donor, 55% (43%-67%) compared with 21% (12%-30%) when absent from both (P &lt; .01). A further allele associated with this haplotype, TNFa5, is also associated with increased risk of TRM. For IL-10, presence of the donor R2-G-C-C haplotype was associated with decreased risk of TRM, 61% (43%-79%) versus 34% (25%-43%), P = .01. In contrast, possession of the R3-G-C-C haplotype by the donor predicted reduced risk of TRM, 30% (19%-41%, 95% CI) versus 53% (40%-66%, 95% CI), P = .01. No independent associations of cytokine polymorphisms with acute graft-versus-host disease were shown. (Blood. 2004;103:3599-3602)
5′-Flanking region polymorphisms of CYP2C9 and their relationship to S-warfarin metabolism in white and Japanese patients
Authors: Takahashi Harumi , Ieiri Ichiro , Wilkinson Grant R. , Mayo Gail , Kashima Toshitaka , Kimura Sosuke , Otsubo Kenji , Echizen Hirotoshi 
Published: January 2004

Abstract
White and Japanese patients require different warfarin dosages to achieve therapeutic anticoagulation, but this can be only partly explained by genetic variability in the coding region of CYP2C9—a critical enzyme in the drug's metabolism. Accordingly, analysis of the -2.1-kb 5′-flanking region of CYP2C9 was undertaken in 22 white and 38 Japanese patients whose unbound oral clearance of S-warfarin had been previously determined. Thirteen single nucleotide polymorphisms (SNPs) were identified, some of which were in linkage disequilibrium with functionally defective coding region variants. Those 5′-flanking patterns linked with at least one CYP2C9*3 allele or CYP2C9*2/*3 were associated with reduced CYP2C9 activity and warfarin dose. Japanese patients possessing the wild-type promoter and coding sequences had significantly (P &lt; .01) greater CYP2C9 activity than white patients with the corresponding genotype. In conclusion, either unidentified polymorphisms further upstream in the promoter region or environmental factor(s) account for the differences in the warfarin doses between whites and Japanese. (Blood. 2004;103: 3055-3057)
Hematopoietic-repopulating defects from STAT5-deficient bone marrow are not fully accounted for by loss of thrombopoietin responsiveness
Authors: Bradley Heath L. , Couldrey Christine , Bunting Kevin D. 
Published: January 2004

Abstract
Signal transducer and activator of transcription-5 (STAT5) plays an important role in repopulating activity of hematopoietic stem cells (HSCs). However, the relationship of STAT5 activation with early acting cytokine receptors is not well established. We have directly compared bone marrow (BM) from mice mutant for STAT5a and STAT5b (STAT5ab-/-) with that from mice lacking c-Mpl (c-Mpl-/-), the thrombopoietin receptor. Both STAT5 and c-Mpl deficiency only mildly affected committed myeloid progenitors assayed in vitro, but STAT5ab-/- BM showed lower Gr-1+ (4.4-fold), B220+ (23-fold), CD4+ (20-fold), and Ter119+ (17-fold) peripheral blood repopulating activity than c-Mpl-/- BM against wild-type competitor in long-term repopulating assays in vivo. Direct head-to-head competitions of STAT5ab-/- BM and c-Mpl-/- BM showed up to a 25-fold reduction in STAT5ab-/- contribution. Differences affecting reconstitution of primitive c-Kit+Lin-Sca-1+ multipotent progenitor (MPP)/HSC (1.8-fold) and c-Kit+Lin-Sca-1- oligopotent progenitor BM fractions (3.3-fold) were more modest. In serial transplantation experiments, STAT5ab-/- and c-Mpl-/- BM both failed to provide consistent engraftment in tertiary hosts and could not radioprotect lethally irradiated quaternary recipients. These results indicate substantial overlap in c-Mpl-STAT5 signaling defects at the MPP/HSC level but indicate that STAT5 is activated independent of c-Mpl to promote multilineage hematopoietic differentiation. (Blood. 2004;103:2965-2972)