bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Harpins in
Pseudomonas syringae
pv. tomato DC3000, Which Are Functionally Similar to HrpK1 in Promoting Translocation of Type III Secretion System Effectors
Authors: Kvitko Brian H. , Ramos Adela R. , Morello Joanne E. , Oh Hye-Sook , Collmer Alan 
Published: September 2007

ABSTRACT

Harpins are a subset of type III secretion system (T3SS) substrates found in all phytopathogenic bacteria that utilize a T3SS.
Pseudomonas syringae
pv. tomato DC3000 was previously reported to produce two harpins, HrpZ1 and HrpW1. DC3000 was shown here to deploy two additional proteins, HopAK1 and HopP1, which have the harpin-like properties of lacking cysteine, eliciting the hypersensitive response (HR) when partially purified and infiltrated into tobacco leaves, and possessing a two-domain structure similar to that of the HrpW1 class of harpins. Unlike the single-domain harpin HrpZ1, the two-domain harpins have C-terminal enzyme-like domains: pectate lyase for HopAK1 and lytic transglycosylase for HopP1. Genetic techniques to recycle antibiotic markers were applied to DC3000 to generate a quadruple harpin gene polymutant. The polymutant was moderately reduced in the elicitation of the HR and translocation of the T3SS effector AvrPto1 fused to a Cya translocation reporter, but the mutant was unaffected in the secretion of AvrPto1-Cya. The DC3000
hrpK1
gene encodes a putative translocator in the HrpF/NopX family and was deleted in combination with the four harpin genes. The
hrpK1
quadruple harpin gene polymutant was strongly reduced in HR elicitation, virulence, and translocation of AvrPto1-Cya into plant cells but not in the secretion of representative T3SS substrates in culture. HrpK1, HrpZ1, HrpW1, and HopAK1, but not HopP1, were independently capable of restoring some HR elicitation to the
hrpK1
quadruple harpin gene polymutant, which suggests that a consortium of semiredundant translocators from three protein classes cooperate to form the
P. syringae
T3SS translocon.
Evidence that Bacterial ABC-Type Transporter Imports Free EDTA for Metabolism
Authors: Zhang Hua , Herman Jacob P. , Bolton Harvey , Zhang Zhicheng , Clark Sue , Xun Luying 
Published: September 2007

ABSTRACT

EDTA, a common chelating agent, is becoming a major organic pollutant in the form of metal-EDTA complexes in surface waters, partly due to its recalcitrance to biodegradation. Even an EDTA-degrading bacterium, BNC1, does not degrade stable metal-EDTA complexes. In the present study, an ABC-type transporter was identified for possible uptake of EDTA because the transporter genes and the EDTA monooxygenase gene were expressed from a single operon in BNC1. The ABC-type transporter had a periplasmic-binding protein (EppA) that should confer the substrate specificity for the transporter; therefore, EppA was produced in
Escherichia coli
, purified, and characterized. EppA was shown to bind free EDTA with a dissociation constant as low as 25 nM by using isothermal titration calorimetry. When unstable metal-EDTA complexes, e.g., (Mg-EDTA)
2−
, were added to the EppA solution, binding was also observed. However, experimental data and theoretical analysis supported EppA binding only of free EDTA. When stable metal-EDTA complexes, e.g., (Cu-EDTA)
2−
, were titrated into the EppA solution, no binding was observed. Since EDTA monooxygenase in the cytoplasm uses some of the stable metal-EDTA complexes as substrates, we suggest that the lack of EppA binding and EDTA uptake are responsible for the failure of BNC1 cells to degrade the stable complexes.
The Division Inhibitor EzrA Contains a Seven-Residue Patch Required for Maintaining the Dynamic Nature of the Medial FtsZ Ring
Authors: Haeusser Daniel P. , Garza Anna Cristina , Buscher Amy Z. , Levin Petra Anne 
Published: September 2007

ABSTRACTThe essential cytoskeletal protein FtsZ assembles into a ring-like structure at the nascent division site and serves as a scaffold for the assembly of the prokaryotic division machinery. We previously characterized EzrA as an inhibitor of FtsZ assembly inBacillus subtilis. EzrA interacts directly with FtsZ to prevent aberrant FtsZ assembly and cytokinesis at cell poles. EzrA also concentrates at the cytokinetic ring in an FtsZ-dependent manner, although its precise role at this position is not known. Here, we identified a conserved patch of amino acids in the EzrA C terminus that is essential for localization to the FtsZ ring. Mutations in this patch (designated the “QNR patch”) abolish EzrA localization to midcell but do not significantly affect EzrA's ability to inhibit FtsZ assembly at cell poles.ezrAQNR patch mutant cells exhibit stabilized FtsZ assembly at midcell and are significantly longer than wild-type cells, despite lacking extra FtsZ rings. These results indicate that EzrA has two distinct activities in vivo: (i) preventing aberrant FtsZ ring formation at cell poles through inhibition of de novo FtsZ assembly and (ii) maintaining proper FtsZ assembly dynamics within the medial FtsZ ring, thereby rendering it sensitive to the factors responsible for coordinating cell growth and cell division.
Regulation of Expression of the Fibronectin-Binding Protein BBK32 in
Borrelia burgdorferi
Authors: He Ming , Boardman Bethany K. , Yan Dalai , Yang X. Frank 
Published: September 2007

ABSTRACT

The BBK32 protein binds to host extracellular ligand fibronectin and contributes to the pathogenesis of
Borrelia burgdorferi
. Here we showed that expression of the BBK32 gene is influenced by multiple environmental factors and that its regulation is governed by the response regulator Rrp2 and RpoN-RpoS (σ
54
-σ
S
) sigma cascade in
B. burgdorferi
.
Phosphate-Controlled Regulator for the Biosynthesis of the Dalbavancin Precursor A40926
Authors: Alduina Rosa , Piccolo Luca Lo , D'Alia Davide , Ferraro Clelia , Gunnarsson Nina , Donadio Stefano , Puglia Anna Maria 
Published: September 2007

ABSTRACT

The actinomycete
Nonomuraea
sp. strain ATCC 39727 produces the glycopeptide A40926, the precursor of the novel antibiotic dalbavancin. Previous studies have shown that phosphate limitation results in enhanced A40926 production. The A40926 biosynthetic gene (
dbv
) cluster, which consists of 37 genes, encodes two putative regulators, Dbv3 and Dbv4, as well as the response regulator (Dbv6) and the sensor-kinase (Dbv22) of a putative two-component system. Reverse transcription-PCR (RT-PCR) and real-time RT-PCR analysis revealed that the
dbv14
-
dbv8
and the
dbv30
-
dbv35
operons, as well as
dbv4
, were negatively influenced by phosphate. Dbv4 shows a putative helix-turn-helix DNA-binding motif and shares sequence similarity with StrR, the transcriptional activator of streptomycin biosynthesis in
Streptomyces griseus
. Dbv4 was expressed in
Escherichia coli
as an N-terminal His
6
-tagged protein. The purified protein bound the
dbv14
and
dbv30
upstream regions but not the region preceding
dbv4
. Bbr, a Dbv4 ortholog from the gene cluster for the synthesis of the glycopeptide balhimycin, also bound to the
dbv14
and
dbv30
upstream regions, while Dbv4 bound appropriate regions from the balhimycin cluster. Our results provide new insights into the regulation of glycopeptide antibiotics, indicating that the phosphate-controlled regulator Dbv4 governs two key steps in A40926 biosynthesis: the biosynthesis of the nonproteinogenic amino acid 3,5-dihydroxyphenylglycine and critical tailoring reactions on the heptapeptide backbone.
The Complete Genome Sequence of
Campylobacter jejuni
Strain 81116 (NCTC11828)
Authors: Pearson Bruce M. , Gaskin Duncan J. H. , Segers Ruud P. A. M. , Wells Jerry M. , Nuijten Piet J. M. , van Vliet Arnoud H. M. 
Published: September 2007

ABSTRACT

Campylobacter jejuni
is a major human enteric pathogen that displays genetic variability via genomic reorganization and phase variation. This variability can adversely affect the outcomes and reproducibility of experiments.
C. jejuni
strain 81116 (NCTC11828) has been suggested to be a genetically stable strain (G. Manning, B. Duim, T. Wassenaar, J. A. Wagenaar, A. Ridley, and D. G. Newell, Appl. Environ. Microbiol. 67:1185-1189, 2001), is amenable to genetic manipulation, and is infective for chickens. Here we report the finished annotated genome sequence of
C. jejuni
strain 81116.
Nestin expression in different tumours and its relevance to malignant grade
Authors: Yang X H , Wu Q L , Yu X B , Xu C X , Ma B F , Zhang X M , Li S N , Lahn B T , Xiang A P 
Published: September 2007

Background:Nestin, an intermediate filament (IF) protein, is expressed in proliferating progenitor cells of developmental and regenerating tissues, and is identified as a neuroepithelial precursor cell marker. Recently, nestin was detected in some neoplasms such as glioma, ependymoma, melanoma, rhabdomyosarcoma, gastrointestinal stromal tumour (GIST), and testicular stromal tumour. Moreover, the expression intensity of nestin exhibited significant correlation with the malignant grade of glioma.Aims:To detect the expression of nestin in different tumours and to analyse the relationship between the expression of nestin and the malignant grade of the tumours.Methods:Formalin-fixed and paraffin-embedded surgical samples of neoplastic tissues were obtained from the Department of Pathology of Sun Yat-sen University. Histological analysis and immunohistochemical staining for nestin were performed. Histoscores were analysed by semi-quantitative evaluation.Results:Nestin was expressed predominantly in the cytoplasm of angiosarcoma, pancreatic adenocarcinoma and GIST samples, and some tumour cells expressed in the nucleus. There was a statistically significant difference between the histoscore of nestin in high malignant GIST (2.2366 (0.6920)) and that in low malignant GIST (1.3783 (0.4268)) (p = 0.003); and also between that in high malignant angiosarcoma (1.9188 (0.2069)) and that in low malignant angiosarcoma (0.6474 (0.3273)) (p = 0.000). Cavernous angioma did not express nestin. The histoscore of nestin in high malignant pancreatic adenocarcinoma (7/14) was 1.1767 (0.4676), and that in low malignant pancreatic adenocarcinoma (3/8) was 0.6577 (0.0056) (no significant difference, p = 0.112).Conclusions:Results suggest that the expression of nestin may play an important role in the development of some neoplasms such as GIST and angiosarcoma.
Comparison of the Split Stacked versus the Split Achilles Allograft for Dual Femoral Tunnel Posterior Cruciate Ligament Reconstruction
Authors: DeBerardino Thomas M. , Lonergan Keith T. , Brooks Daniel E. 
Published: September 2007

Background Cadaveric testing has shown that double-bundle reconstruction better replicates the native anatomy of the posterior cruciate ligament. With the current trend toward allograft Achilles posterior cruciate ligament reconstructions, the need to determine a graft configuration with the highest tensile and pull-out strength has become paramount. Hypothesis The split stacked Achilles allograft construct provides greater graft material to traverse the notch and provides increased load to failure at the tibial point of fixation compared with a standard monoblock Achilles allograft construct. Study Design Controlled laboratory study. Methods Eight matched pairs of Achilles allograft tendons were secured to 8 matched pairs of fresh-frozen human cadaveric tibiae. Group 1 consisted of single-block grafts (n = 8), and group 2 included the split stacked grafts (n = 8). The cross-sectional area of each graft's 2 collagenous bundles was measured with a micrometer. The graft constructs were pulled to ultimate failure at a rate of 50 mm/min on a materials testing machine. Results The mean cross-sectional area of the group 2 split stacked grafts (76.6 ± 3.1 mm2) was significantly greater than that of the group 1 single-block grafts (48.2 ± 3.0 mm2; P = .00006). The maximum load to failure of the group 2 construct was significantly greater (1383 ± 102 N) than that of the group 1 single-block configuration (1020 ± 136 N; P = .01). Conclusion These results indicate that the novel split stacked configuration of an Achilles tendon allograft provides a greater cross-sectional area of graft material across the joint as well as a significant increase in the overall load to failure strength compared with a standard monoblock Achilles allograft construct. Clinical Relevance The split stacked Achilles graft is an efficient method for using the entire allograft. With maintenance and use of all collagen fibers, the split stacked Achilles construct provides essentially 2 grafts in 1 while only using a single tibial tunnel.
The International Knee Documentation Committee Subjective Evaluation Form in a Preadolescent Population
Authors: Slobogean Gerard P. , Mulpuri Kishore , Reilly Christopher W. 
Published: September 2007

Background The International Knee Documentation Committee Subjective Knee Evaluation Form is a knee-specific instrument composed of 18 questions. It is commonly used in adult and pediatric studies as a surgical outcome measure. Normative data exist for an adult population, but there have been no published normative results for younger subjects. Purpose To compile and report pilot normative International Knee Documentation Committee Subjective Knee Evaluation Form scores in a preadolescent population. Study Design Cross-sectional study; Level of evidence, 3. Methods The International Knee Documentation Committee Subjective Knee Evaluation Form was administered to 146 seventh-grade students (aged 12–14 years) at 2 local schools. The form was administered in its original format. Demographic and descriptive results were compiled. Results One hundred twenty-five completed responses were eligible for analysis. The mean age was 13.2 years (SD, 0.5; range, 12.2–14.2 years); 15% of participants had a history of knee injury or pain. The mean International Knee Documentation Committee score for all respondents was 89.4 (SD, 10.5; 95% confidence interval, 87.6–91.3; range, 52–100). Conclusion This study provides pilot normative data for mean International Knee Documentation Committee scores in a preadolescent population. The mean score in this younger cohort is consistent with normative data of adults age 35 years or younger. Although the International Knee Documentation Committee Subjective Knee Evaluation Form is often used in adolescent surgical studies, its validity in these populations remains to be established. Further work to establish the psychometric properties of the current form in younger age groups would be of significant benefit to clinicians.
ChIP on SNP-chip for genome-wide analysis of human histone H4 hyperacetylation
Authors: McCann Jennifer A , Muro Enrique M , Palmer Claire , Palidwor Gareth , Porter Christopher J , Andrade-Navarro Miguel A , Rudnicki Michael A 
Published: September 2007

Abstract

Background
SNP microarrays are designed to genotype Single Nucleotide Polymorphisms (SNPs). These microarrays report hybridization of DNA fragments and therefore can be used for the purpose of detecting genomic fragments.

Results
Here, we demonstrate that a SNP microarray can be effectively used in this way to perform chromatin immunoprecipitation (ChIP) on chip as an alternative to tiling microarrays. We illustrate this novel application by mapping whole genome histone H4 hyperacetylation in human myoblasts and myotubes. We detect clusters of hyperacetylated histone H4, often spanning across up to 300 kilobases of genomic sequence. Using complementary genome-wide analyses of gene expression by DNA microarray we demonstrate that these clusters of hyperacetylated histone H4 tend to be associated with expressed genes.

Conclusion
The use of a SNP array for a ChIP-on-chip application (ChIP on SNP-chip) will be of great value to laboratories whose interest is the determination of general rules regarding the relationship of specific chromatin modifications to transcriptional status throughout the genome and to examine the asymmetric modification of chromatin at heterozygous loci.
Adaptive expression responses in the Pol-γ null strain of S. pombe depleted of mitochondrial genome
Authors: Chu Zhaoqing , Li Juntao , Eshaghi Majid , Karuturi R Krishna Murthy , Lin Kui , Liu Jianhua 
Published: September 2007

Abstract

Background
DNA polymerase γ(Pol-γ) has been shown to be essential for maintenance of the mitochondrial genome (mtDNA) in the petite-positive budding yeast Saccharomyces cerevisiae. Budding yeast cells lacking mitochondria exhibit a slow-growing or petite-colony phenotype. Petite strains fail to grow on non-fermentable carbon sources. However, it is not clear whether the Pol-γ is required for mtDNA maintenance in the petite-negative fission yeast Schizosaccharomyces pombe.

Results
We show that disruption of the nuclear gene pog1
+ that encodes Pol-γ is sufficient to deplete mtDNA in S. pombe. Cells bearing pog1Δ allele require substantial growth periods to form petite colonies. Mitotracker assays indicate that pog1Δ cells are defective in mitochondrial function and EM analyses suggest that pog1Δ cells lack normal mitochondrial structures. Depletion of mtDNA in pog1Δ cells is evident from quantitative real-time PCR assays. Genome-wide expression profiles of pog1Δ and other mtDNA-less cells reveal that many genes involved in response to stimulus, energy derivation by oxidation of organic compounds, cellular carbohydrate metabolism, and energy reserve metabolism are induced. Conversely, many genes encoding proteins involved in amino acid metabolism and oxidative phosphorylation are repressed.

Conclusion
By showing that Pol-γ is essential for mtDNA maintenance and disruption of pog1
+ alters the genome-wide expression profiles, we demonstrated that cells lacking mtDNA exhibit adaptive nuclear gene expression responses in the petite-negative S. pombe.
The nicotinic acetylcholine receptor gene family of the silkworm, Bombyx mori
Authors: Shao Ya-Ming , Dong Ke , Zhang Chuan-Xi 
Published: September 2007

Abstract

Background
Nicotinic acetylcholine receptors (nAChRs) mediate fast synaptic cholinergic transmission in the insect central nervous system. The insect nAChR is the molecular target of a class of insecticides, neonicotinoids. Like mammalian nAChRs, insect nAChRs are considered to be made up of five subunits, coded by homologous genes belonging to the same family. The nAChR subunit genes of Drosophila melanogaster, Apis mellifera and Anopheles gambiae have been cloned previously based on their genome sequences. The silkworm Bombyx mori is a model insect of Lepidoptera, among which are many agricultural pests. Identification and characterization of B. mori nAChR genes could provide valuable basic information for this important family of receptor genes and for the study of the molecular mechanisms of neonicotinoid action and resistance.

Results
We searched the genome sequence database of B. mori with the fruit fly and honeybee nAChRs by tBlastn and cloned all putative silkworm nAChR cDNAs by reverse transcriptase-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) methods. B. mori appears to have the largest known insect nAChR gene family to date, including nine α-type subunits and three β-type subunits. The silkworm possesses three genes having low identity with others, including one α and two β subunits, α9, β2 and β3. Like the fruit fly and honeybee counterparts, silkworm nAChR gene α6 has RNA-editing sites, and α4, α6 and α8 undergo alternative splicing. In particular, alternative exon 7 of Bmα8 may have arisen from a recent duplication event. Truncated transcripts were found for Bmα4 and Bmα5.

Conclusion

B. mori possesses a largest known insect nAChR gene family characterized to date, including nine α-type subunits and three β-type subunits. RNA-editing, alternative splicing and truncated transcripts were found in several subunit genes, which might enhance the diversity of the gene family.
Measurement error adjustment in essential fatty acid intake from a food frequency questionnaire: alternative approaches and methods
Authors: Beydoun May A , Kaufman Jay S , Ibrahim Joseph , Satia Jessie A , Heiss Gerardo 
Published: September 2007

Abstract

Background
We aimed at assessing the degree of measurement error in essential fatty acid intakes from a food frequency questionnaire and the impact of correcting for such an error on precision and bias of odds ratios in logistic models. To assess these impacts, and for illustrative purposes, alternative approaches and methods were used with the binary outcome of cognitive decline in verbal fluency.

Methods
Using the Atherosclerosis Risk in Communities (ARIC) study, we conducted a sensitivity analysis. The error-prone exposure – visit 1 fatty acid intake (1987–89) – was available for 7,814 subjects 50 years or older at baseline with complete data on cognitive decline between visits 2 (1990–92) and 4 (1996–98). Our binary outcome of interest was clinically significant decline in verbal fluency. Point estimates and 95% confidence intervals were compared between naïve and measurement-error adjusted odds ratios of decline with every SD increase in fatty acid intake as % of energy. Two approaches were explored for adjustment: (A) External validation against biomarkers (plasma fatty acids in cholesteryl esters and phospholipids) and (B) Internal repeat measurements at visits 2 and 3. The main difference between the two is that Approach B makes a stronger assumption regarding lack of error correlations in the structural model. Additionally, we compared results from regression calibration (RCAL) to those from simulation extrapolation (SIMEX). Finally, using structural equations modeling, we estimated attenuation factors associated with each dietary exposure to assess degree of measurement error in a bivariate scenario for regression calibration of logistic regression model.

Results and conclusion
Attenuation factors for Approach A were smaller than B, suggesting a larger amount of measurement error in the dietary exposure. Replicate measures (Approach B) unlike concentration biomarkers (Approach A) may lead to imprecise odds ratios due to larger standard errors. Using SIMEX rather than RCAL models tends to preserve precision of odds ratios. We found in many cases that bias in naïve odds ratios was towards the null. RCAL tended to correct for a larger amount of effect bias than SIMEX, particularly for Approach A.