bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved Luciferase Tagging System for
Listeria monocytogenes
Allows Real-Time Monitoring In Vivo and In Vitro
Authors: Riedel Christian U. , Monk Ian R. , Casey Pat G. , Morrissey David , O'Sullivan Gerald C. , Tangney Mark , Hill Colin , Gahan Cormac G. M. 
Published: March 2007

ABSTRACT

An improved system for luciferase tagging
Listeria monocytogenes
was developed by constructing a highly active, constitutive promoter. This construct gave 100-fold-higher activity in broth than any native promoter tested and allowed for imaging of
lux
-tagged
L. monocytogenes
in food products, during murine infections, and in tumor targeting studies.
Automated Image Analysis for Quantitative Fluorescence In Situ Hybridization with Environmental Samples
Authors: Zhou Zhi , Pons Marie Noëlle , Raskin Lutgarde , Zilles Julie L. 
Published: March 2007

ABSTRACT

When fluorescence in situ hybridization (FISH) analyses are performed with complex environmental samples, difficulties related to the presence of microbial cell aggregates and nonuniform background fluorescence are often encountered. The objective of this study was to develop a robust and automated quantitative FISH method for complex environmental samples, such as manure and soil. The method and duration of sample dispersion were optimized to reduce the interference of cell aggregates. An automated image analysis program that detects cells from 4′,6′-diamidino-2-phenylindole (DAPI) micrographs and extracts the maximum and mean fluorescence intensities for each cell from corresponding FISH images was developed with the software Visilog. Intensity thresholds were not consistent even for duplicate analyses, so alternative ways of classifying signals were investigated. In the resulting method, the intensity data were divided into clusters using fuzzy
c
-means clustering, and the resulting clusters were classified as target (positive) or nontarget (negative). A manual quality control confirmed this classification. With this method, 50.4, 72.1, and 64.9% of the cells in two swine manure samples and one soil sample, respectively, were positive as determined with a 16S rRNA-targeted bacterial probe (S-D-Bact-0338-a-A-18). Manual counting resulted in corresponding values of 52.3, 70.6, and 61.5%, respectively. In two swine manure samples and one soil sample 21.6, 12.3, and 2.5% of the cells were positive with an archaeal probe (S-D-Arch-0915-a-A-20), respectively. Manual counting resulted in corresponding values of 22.4, 14.0, and 2.9%, respectively. This automated method should facilitate quantitative analysis of FISH images for a variety of complex environmental samples.
The WW Domain Protein PRO40 Is Required for Fungal Fertility and Associates with Woronin Bodies
Authors: Engh Ines , Würtz Christian , Witzel-Schlömp Konstanze , Zhang Hai Yu , Hoff Birgit , Nowrousian Minou , Rottensteiner Hanspeter , Kück Ulrich 
Published: March 2007

ABSTRACT

Fruiting body formation in ascomycetes is a highly complex process that is under polygenic control and is a fundamental part of the fungal sexual life cycle. However, the molecular determinants regulating this cellular process are largely unknown. Here we show that the sterile
pro40
mutant is defective in a 120-kDa WW domain protein that plays a pivotal role in fruiting body maturation of the homothallic ascomycete
Sordaria macrospora
. Although WW domains occur in many eukaryotic proteins, homologs of PRO40 are present only in filamentous ascomycetes. Complementation analysis with different
pro40
mutant strains, using full-sized or truncated versions of the wild-type
pro40
gene, revealed that the C terminus of PRO40 is crucial for restoring the fertile phenotype. Using differential centrifugation and protease protection assays, we determined that a PRO40-FLAG fusion protein is located within organelles. Further microscopic investigations of fusion proteins with DsRed or green fluorescent protein polypeptides showed a colocalization of PRO40 with HEX-1, a Woronin body-specific protein. However, the integrity of Woronin bodies is not affected in mutant strains of
S. macrospora
and
Neurospora crassa
, as shown by fluorescence microscopy, sedimentation, and immunoblot analyses. We discuss the function of PRO40 in fruiting body formation.
Multiple Basic Helix-Loop-Helix Proteins Regulate Expression of the
ENO1
Gene of
Saccharomyces cerevisiae
Authors: Chen Meng , Lopes John M. 
Published: March 2007

ABSTRACT

The basic helix-loop-helix (bHLH) eukaryotic transcription factors have the ability to form multiple dimer combinations. This property, together with limited DNA-binding specificity for the E box (CANNTG), makes them ideally suited for combinatorial control of gene expression. We tested the ability of all nine
Saccharomyces cerevisiae
bHLH proteins to regulate the enolase-encoding gene
ENO1. ENO1
was known to be activated by the bHLH protein Sgc1p. Here we show that expression of an
ENO1-lacZ
reporter was also regulated by the other eight bHLH proteins, namely, Ino2p, Ino4p, Cbf1p, Rtg1p, Rtg3p, Pho4p, Hms1p, and Ygr290wp.
ENO1-lacZ
expression was also repressed by growth in inositol-choline-containing medium. Epistatic analysis and chromatin immunoprecipitation experiments showed that regulation by Sgc1p, Ino2p, Ino4p, and Cbf1p and repression by inositol-choline required three distal E boxes, E1, E2, and E3. The pattern of bHLH binding to the three E boxes and experiments with two dominant-negative mutant alleles of
INO4
and
INO2
support the model that bHLH dimer selection affects
ENO1-lacZ
expression. These results support the general model that bHLH proteins can coordinate different biological pathways via multiple mechanisms.
Differential Bvg Phase-Dependent Regulation and Combinatorial Role in Pathogenesis of Two
Bordetella
Paralogs, BipA and BcfA
Authors: Sukumar Neelima , Mishra Meenu , Sloan Gina Parise , Ogi Tomoo , Deora Rajendar 
Published: March 2007

ABSTRACT

To successfully colonize their mammalian hosts, many bacteria produce multiple virulence factors that play essential roles in disease processes and pathogenesis. Some of these molecules are adhesins that allow efficient attachment to host cells, a prerequisite for successful host colonization.
Bordetella
spp. express a number of proteins which either play a direct role in attachment to the respiratory epithelia or exhibit similarity to known bacterial adhesins. One such recently identified protein is BipA. Despite the similarity of BipA to intimins and invasins, deletion of this protein from
B. bronchiseptica
did not result in any significant defect in respiratory tract colonization. In this study, we identified an open reading frame in
B. bronchiseptica
, designated
bcfA
(encoding BcfA [
b
ordetella
c
olonization
f
actor
A
]), that is similar to
bipA
. In contrast to the maximal expression of
bipA
in the Bvg intermediate (Bvg
i
) phase,
bcfA
is expressed at high levels in both the Bvg
+
and Bvg
i
phases. We show here that BvgA and phosphorylated BvgA bind differentially to the
bcfA
promoter region. Utilizing immunoblot assays, we found that BcfA is localized to the outer membrane and that it is expressed during animal infection. While deletion of either
bipA
or
bcfA
did not significantly affect respiratory tract colonization, concomitant deletion of both genes resulted in a defect in colonization of the rat trachea. Our results indicate that the two paralogous proteins have a combinatorial role in mediating efficient respiratory tract colonization.
Regulation of Hydrogen Peroxide-Dependent Gene Expression in
Rhodobacter sphaeroides
: Regulatory Functions of OxyR
Authors: Zeller Tanja , Mraheil Mobarak A. , Moskvin Oleg V. , Li Kuanyu , Gomelsky Mark , Klug Gabriele 
Published: March 2007

ABSTRACT

Genome-wide transcriptome profiling was used to reveal hydrogen peroxide (H
2
O
2
)-dependent regulatory mechanisms in the facultatively photosynthetic bacterium
Rhodobacter sphaeroides
. In this study we focused on the role of the OxyR protein, a known regulator of the H
2
O
2
response in bacteria. The transcriptome profiles of
R. sphaeroides
wild-type and
oxyR
mutant strains that were exposed to 1 mM H
2
O
2
for 7 min or were not exposed to H
2
O
2
were analyzed. Three classes of OxyR-dependent genes were identified based on their expression patterns in the wild type of
oxyR
mutant strains with differing predicted roles of oxidized and reduced OxyR as activators of transcription. DNA binding studies revealed that OxyR binds upstream of class I genes, which are induced by H
2
O
2
and exhibit similar basal levels of expression in the wild-type and
oxyR
mutant strains. The effect of OxyR on class II genes, which are also induced by H
2
O
2
but exhibit significantly lower basal levels of expression in the wild-type strain than in the mutant, is indirect. Interestingly, reduced OxyR also activates expression of few genes (class III). The role of reduced OxyR as an activator is shown for the first time. Our data reveal that the OxyR-mediated response is fast and transient. In addition, we found that additional regulatory pathways are involved in the H
2
O
2
response.
Molecular Genetics and Genomic Analysis of Scytonemin Biosynthesis in
Nostoc punctiforme
ATCC 29133
Authors: Soule Tanya , Stout V. , Swingley W. D. , Meeks J. C. , Garcia-Pichel F. 
Published: March 2007

ABSTRACT

The indole-alkaloid scytonemin is the most common and widespread sunscreen among cyanobacteria. Previous research has focused on its nature, distribution, ecology, physiology, and biochemistry, but its molecular genetics have not been explored. In this study, a scytonemin-deficient mutant of the cyanobacterium
Nostoc punctiforme
ATCC 29133 was obtained by random transposon insertion into open reading frame NpR1273. The absence of scytonemin under conditions of induction by UV irradiation was the single phenotypic difference detected in a comparative analysis of the wild type and the mutant. A cause-effect relationship between the phenotype and the mutation in NpR1273 was demonstrated by constructing a second scytoneminless mutant through directed mutagenesis of that gene. The genomic region flanking the mutation revealed an 18-gene cluster (NpR1276 to NpR1259). Four putative genes in the cluster, NpR1274 to NpR1271, with no previously known functions, are likely to be involved in the assembly of scytonemin. Also in this cluster, there is a redundant set of genes coding for shikimic acid and aromatic amino acid biosynthesis enzymes, leading to the production of tryptophan and tyrosine, which are likely to be biosynthetic precursors of the sunscreen.
Target Site Selection ofPseudomonas putidaTransposon Tn4652
Authors: Kivistik Paula Ann , Kivisaar Maia , Hõrak Rita 
Published: March 2007

ABSTRACTWe analyzed the target preferences of a Tn3family transposon Tn4652. Alignment of 93 different insertion sites revealed a consensus sequence which resembles that of Tn3, indicating that despite a low similarity between Tn4652and Tn3transposases, their target site recognition is conserved.
Activity Level and Subjective Knee Function 15 Years after Anterior Cruciate Ligament Injury
Authors: Kostogiannis Ioannis , Ageberg Eva , Neuman Paul , Dahlberg Leif , Friden Thomas , Roos Harald 
Published: March 2007

Background The activity level and subjective knee function after an anterior cruciate ligament (ACL) injury treated without reconstruction have not been well elucidated. Hypothesis Patients with ACL injury can achieve good knee function and satisfactory long-term activity level when treated by early activity modification combined with rehabilitation. Study Design Cohort study (prognosis); Level of evidence, 2. Materials and Methods One hundred patients with an acute total ACL injury were observed for 15 years. All patients initially underwent arthroscopic surgery and a rehabilitation program. They were advised to modify their activity level, especially by avoiding contact sports. Patients with recurrent giving-way episodes and/or secondary meniscal injuries that required fixation (n = 6) were subsequently excluded and underwent reconstruction (n = 22). Sixty-seven patients with unilateral nonreconstructed ACL injury remained at the 15-year follow-up. The Lysholm knee score, Tegner activity level, and a visual analog score for global knee function were recorded at regular intervals. At the final follow-up, patients were further evaluated with the Knee injury and Osteoarthritis Outcome Score (KOOS) and International Knee Documentation Committee (IKDC) subjective knee evaluation form. Results Forty patients resumed their preinjury activity level or higher within 3 years. The median activity level 15 years after injury had decreased from 7 to 4 according to Tegner activity scale (P < .001). The mean Lysholm knee score was 96 and 95, 1 and 3 years after injury, respectively, but declined to 86 after 15 years (P < .001). Forty-nine patients had good/excellent results, and 14 had fair (n = 6) or poor function (n = 8) at 15 years. Patients injured in contact sports scored lower in the quality of life sub-scale of KOOS than those injured in noncontact sports (P < .05). Thirteen of the 67 patients (19%) were reoperated with an arthroscopic procedure because of knee symptoms. Conclusion Early activity modification and neuromuscular rehabilitation resulted in a good knee function and an acceptable activity level in the majority of the nonreconstructed patients. The decline in activity level of patients engaged in contact sports at the time of injury affected their subjective quality of life more than patients involved in noncontact sports.
EGO, a novel, noncoding RNA gene, regulates eosinophil granule protein transcript expression
Authors: Wagner Lori A. , Christensen Clarissa J. , Dunn Diane M. , Spangrude Gerald J. , Georgelas Ann , Kelley Linda , Esplin M. Sean , Weiss Robert B. , Gleich Gerald J. 
Published: March 2007

AbstractGene expression profiling of early eosinophil development shows increased transcript levels of proinflammatory cytokines, chemokines, transcription factors, and a novel gene, EGO (eosinophil granule ontogeny). EGO is nested within an intron of the inositol triphosphate receptor type 1 (ITPR1) gene and is conserved at the nucleotide level; however, the largest open reading frame (ORF) is 86 amino acids. Sucrose density gradients show that EGO is not associated with ribosomes and therefore is a noncoding RNA (ncRNA). EGO transcript levels rapidly increase following interleukin-5 (IL-5) stimulation of CD34+ hematopoietic progenitors. EGO RNA also is highly expressed in human bone marrow and in mature eosinophils. RNA silencing of EGO results in decreased major basic protein (MBP) and eosinophil derived neurotoxin (EDN) mRNA expression in developing CD34+ hematopoietic progenitors in vitro and in a CD34+ cell line model. Therefore, EGO is a novel ncRNA gene expressed during eosinophil development and is necessary for normal MBP and EDN transcript expression.
Case-control and family-based association studies of candidate genes in autistic disorder and its endophenotypes: TPH2 and GLO1
Authors: Sacco Roberto , Papaleo Veruska , Hager Jorg , Rousseau Francis , Moessner Rainald , Militerni Roberto , Bravaccio Carmela , Trillo Simona , Schneider Cindy , Melmed Raun , Elia Maurizio , Curatolo Paolo , Manzi Barbara , Pascucci Tiziana , Puglisi-Allegra Stefano , Reichelt Karl-Ludvig , Persico Antonio M 
Published: March 2007

Abstract

Background
The TPH2 gene encodes the enzyme responsible for serotonin (5-HT) synthesis in the Central Nervous System (CNS). Stereotypic and repetitive behaviors are influenced by 5-HT, and initial studies report an association of TPH2 alleles with childhood-onset obsessive-compulsive disorder (OCD) and with autism. GLO1 encodes glyoxalase I, the enzyme which detoxifies α-oxoaldehydes such as methylglyoxal in all living cells. The A111E GLO1 protein variant, encoded by SNP C419A, was identifed in autopsied autistic brains and proposed to act as an autism susceptibility factor. Hyperserotoninemia, macrocephaly, and peptiduria represent some of the best-characterized endophenotypes in autism research.

Methods
Family-based and case-control association studies were performed on clinical samples drawn from 312 simplex and 29 multiplex families including 371 non-syndromic autistic patients and 156 unaffected siblings, as well as on 171 controls. TPH2 SNPs rs4570625 and rs4565946 were genotyped using the TaqMan assay; GLO1 SNP C419A was genotyped by PCR and allele-specific restriction digest. Family-based association analyses were performed by TDT and FBAT, case-control by χ2, endophenotypic analyses for 5-HT blood levels, cranial circumference and urinary peptide excretion rates by ANOVA and FBAT.

Results

TPH2 alleles and haplotypes are not significantly associated in our sample with autism (rs4570625: TDT P = 0.27, and FBAT P = 0.35; rs4565946: TDT P = 0.45, and FBAT P = 0.55; haplotype P = 0.84), with any endophenotype, or with the presence/absence of prominent repetitive and stereotyped behaviors (motor stereotypies: P = 0.81 and 0.84, verbal stereotypies: P = 0.38 and 0.73 for rs4570625 and rs4565946, respectively). Also GLO1 alleles display no association with autism (191 patients vs 171 controls, P = 0.36; TDT P = 0.79, and FBAT P = 0.37), but unaffected siblings seemingly carry a protective gene variant marked by the A419 allele (TDT P < 0.05; patients vs unaffected siblings TDT and FBAT P < 0.00001).

Conclusion

TPH2 gene variants are unlikely to contribute to autism or to the presence/absence of prominent repetitive behaviors in our sample, although an influence on the intensity of these behaviors in autism cannot be excluded. GLO1 gene variants do not confer autism vulnerability in this sample, but allele A419 apparently carries a protective effect, spurring interest into functional correlates of the C419A SNP.
Evaluation of the structural quality of modeled proteins by using globularity criteria
Authors: Costantini Susan , Facchiano Angelo M , Colonna Giovanni 
Published: March 2007

Abstract

Background
The knowledge of the three-dimensional structure of globular proteins is fundamental for a detailed investigation of their functional properties. Experimental methods are too slow for structure investigation on a large scale, while computational prediction methods offer alternatives that are continuously being improved. The international Comparative Assessment of Structure Prediction (CASP), an "a posteriori" evaluation of the quality of theoretical models when the experimental structure becomes available, demonstrates that predictions can be successful as well as unsuccessful, and this suggests the necessity for evaluations able to discard "a priori" the wrong models.

Results
We analyzed different structural properties of globular proteins for experimentally solved proteins belonging to the four different structural classes: "mainly alpha", "mainly beta", "alpha/beta" and "alpha+beta". The properties were found to be linearly correlated to protein molecular weight, but with some differences among the four classes. These results were applied to develop an evaluation test of theoretical models based on the expected globular properties of proteins. To verify the success of our test, we applied it to several protein models submitted to the sixth edition of CASP. The best theoretical models, as judged by CASP assessors, were in agreement with the expected properties, while most of the low-quality models had not passed our evaluations.

Conclusion
This study supports the need for careful checks to avoid the diffusion of incorrect structural models. Our test allows the evaluation of models in the absence of experimental reference structures, thereby preventing the diffusion of incorrect structural models and the formulation of incorrect functional hypotheses. It can be used to check the globularity of predicted models, and to supplement other methods already used to evaluate their quality.
Can cancer patients assess the influence of pain on functions? A randomised, controlled study of the pain interference items in the Brief Pain Inventory
Authors: Stenseth Guri , Bjørnnes Marit , Kaasa Stein , Klepstad Pål 
Published: March 2007

Abstract

Background
The Brief Pain Inventory (BPI) is recommended as a pain measurement tool by the Expert Working Group of the European Association of Palliative Care. The BPI is designed to assess both pain severity and interference with functions caused by pain. The purpose of this study was to investigate if pain interference items are influenced by other factors than pain.

Methods
We asked adult cancer patients to complete the original and a revised BPI on two study days. In the original version of the BPI the patients were asked how, during the last 24 hours, pain has interfered with functions. In the revised BPI this question was changed to how, during the last 24 hours, these functions are affected in general. Heath related quality of life was assessed at both study days applying the European Organization for Research and Treatment of Cancer quality of life questionnaire.

Results
Forty-eight of the 55 included patients completed both assessments. The BPI pain intensities scores and the health related quality of life scores were similar at the two study days. Except for mood this study observed no significant distinctions between the patients' BPI interference items scores in the original (pain influence on function) and the revised BPI (function in general). Seventeen patients reported higher influence from pain on functions than the total influence on function from all causes.

Conclusion
We observed similar scores in the original BPI interference scores (pain influence on function) compared with the revised BPI interference scores (decreased function in general). This finding might imply that the BPI interference scale measures are partly responded to as more of a global interference measure.
Sex Differences in Heritability of Neck Pain
Authors: Fejer René , Hartvigsen Jan , Kyvik Kirsten Ohm 
Published: March 2007

AbstractExperimental studies have suggested biological factors as a possible explanation for gender disparities in perception of pain. Recently, heritability of liability to neck pain (NP) has been found to be statistically significantly larger in women compared to men. However, no studies have been conducted to determine whether the sex differences in heritability of NP are due to sex-specific genetic factors. Data on lifetime prevalence of NP from a populationbased cross-sectional survey of 33,794 Danish twins were collected and age-stratified univariate biometrical modeling using sex-limitation models was performed based on 10,605 dizygotic (DZ) twins of opposite sex to estimate the qualitative sex differences. In a full sex-limitation model the genetic component in females were higher than in males, but the genetic and the shared environmental correlations were equal to what is normally assumed between same-sex DZ twins. A ‘no-sex-effects’ model showed the overall best model fit which confirms absence of sex-related gene interaction. The age-stratified sex-limitation models showed similar results. Thus, there is no evidence for a sex-specific genetic influence in the liability of heritability of NP.