bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Vitro Characterization of the Enzyme Properties of the Phospholipid
N
-Methyltransferase PmtA from
Agrobacterium tumefaciens
Authors: Aktas Meriyem , Narberhaus Franz 
Published: January 2009

ABSTRACT

Agrobacterium tumefaciens
requires phosphatidylcholine (PC) in its membranes for plant infection. The phospholipid
N
-methyltransferase PmtA catalyzes all three transmethylation reactions of phosphatidylethanolamine (PE) to PC via the intermediates monomethylphosphatidylethanolamine (MMPE) and dimethylphosphatidylethanolamine (DMPE). The enzyme uses
S
-adenosylmethionine (SAM) as the methyl donor, converting it to
S
-adenosylhomocysteine (SAH). Little is known about the activity of bacterial Pmt enzymes, since PC biosynthesis in prokaryotes is rare. In this article, we present the purification and in vitro characterization of
A. tumefaciens
PmtA, which is a monomeric protein. It binds to PE, the intermediates MMPE and DMPE, the end product PC, and phosphatidylglycerol (PG) and phosphatidylinositol. Binding of the phospholipid substrates precedes binding of SAM. We used a coupled in vitro assay system to demonstrate the enzymatic activity of PmtA and to show that PmtA is inhibited by the end products PC and SAH and the antibiotic sinefungin. The presence of PG stimulates PmtA activity. Our study provides insights into the catalysis and control of a bacterial phospholipid
N
-methyltransferase.
Roles of Germination-Specific Lytic Enzymes CwlJ and SleB in
Bacillus anthracis
Authors: Heffron Jared D. , Orsburn Benjamin , Popham David L. 
Published: January 2009

ABSTRACT

The structural characteristics of a spore enable it to withstand stresses that typically kill a vegetative cell. Spores remain dormant until small molecule signals induce them to germinate into vegetative bacilli. Germination requires degradation of the thick cortical peptidoglycan by germination-specific lytic enzymes (GSLEs).
Bacillus anthracis
has four putative GSLEs, based upon sequence similarities with enzymes in other species: SleB, CwlJ1, CwlJ2, and SleL. In this study, the roles of SleB, CwlJ1, and CwlJ2 were examined. The expression levels of all three genes peak 3.5 h into sporulation. Genetic analysis revealed that, similar to other known GSLEs, none of these gene products are individually required for growth, sporulation, or triggering of germination. However, later germination events are affected in spores lacking CwlJ1 or SleB. Compared to the wild type, germinating spores without CwlJ1 suffer a delay in optical density loss and cortex peptidoglycan release. The absence of SleB also causes a delay in cortex fragment release. A double mutant lacking both SleB and CwlJ1 is completely blocked in cortex hydrolysis and progresses through outgrowth to produce colonies at a frequency 1,000-fold lower than that of the wild-type strain. A null mutation eliminating CwlJ2 has no effect on germination. High-performance liquid chromatography and mass spectroscopy analysis revealed that SleB is required for lytic transglycosylase activity. CwlJ1 also clearly participates in cortex hydrolysis, but its specific mode of action remains unclear. Understanding the lytic germination activities that naturally diminish spore resistance can lead to methods for prematurely inducing them, thus simplifying the process of treating contaminated sites.
Both Thiamine Uptake and Biosynthesis of Thiamine Precursors Are Required for Intracellular Replication ofListeria monocytogenes
Authors: Schauer Kristina , Stolz Jürgen , Scherer Siegfried , Fuchs Thilo M. 
Published: January 2009

ABSTRACTThiamine pyrophosphate is an essential cofactor involved in central metabolism and amino acid biosynthesis and is derived from thiamine (vitamin B1). The extent to which this metabolite is available to bacterial pathogens replicating within host cells is still little understood. Growth studies using modified minimal Welshimer′s broth (mMWB) supplemented with thiamine or the thiamine precursor hydroxymethylpyrimidine (HMP) showed thatListeria monocytogenes, in agreement with bioinformatic prediction, is able to synthesize thiamine only in the presence of HMP. This appears to be due to a lack of ThiC, which is involved in HMP synthesis. The knockout ofthiD(lmo0317), which probably catalyzes the phosphorylation of HMP, inhibited growth in mMWB supplemented with HMP and reduced the replication rate ofL. monocytogenesin epithelial cells. Mutation of a predicted thiamine transporter gene, lmo1429, led to reduced proliferation ofL. monocytogenesin mMWB containing thiamine or thiamine phosphates and also within epithelial cells but had no influence on the expression of the virulence factors Hly and ActA. The toxic thiamine analogue pyrithiamine inhibited growth of wild-type strain EGD but not of the transporter mutant EGDΔthiT. We also demonstrated that ThiT binds thiamine, a finding compatible with ThiT acting as the substrate-binding component of a multimeric thiamine transporter complex. These data provide experimental evidence that Lmo1429 homologs includingBacillusYuaJ are necessary for thiamine transport in gram-positive bacteria and are therefore proposed to be annotated “ThiT.” Taken together, these data indicate that concurrent thiamine uptake and biosynthesis of thiamine precursors is a strategy ofL. monocytogenesand possibly other facultative intracellular pathogens to enable proliferation within the cytoplasm.
Plasmid Capture by the
Bacillus thuringiensis
Conjugative Plasmid pXO16
Authors: Timmery Sophie , Modrie Pauline , Minet Olivier , Mahillon Jacques 
Published: January 2009

ABSTRACT

Conjugation, mobilization, and retromobilization are three related mechanisms of horizontal gene transfer in bacteria. They have been extensively studied in gram-negative species, where retromobilization, the capture of DNA from a recipient by a donor cell, was shown to result from two successive steps: the transfer of the conjugative plasmid from the donor to the recipient followed by the retrotransfer of the mobilizable plasmid to the donor. This successive model was established for gram-negative bacteria but was lacking experimental data from the gram-positive counterparts. In the present work, the mobilization and retromobilization abilities of the conjugative plasmid pXO16 from
Bacillus thuringiensis
subsp.
israelensis
were studied using the mobilizable plasmids pUB110 and pE194 and the “nonmobilizable” element pC194 lacking the
mob
and
oriT
features (all from
Staphylococcus aureus
). Experimental data suggested a successive model, since different retromobilization frequencies were observed between the small plasmids. More importantly, retromobilization was shown to be delayed by 50 and 150 min for pUB110 and pE194, respectively, compared to pXO16 conjugation. Natural liquid foods (cow milk, soy milk, and rice milk) were used to evaluate the putative ecological impact of these transfers. In cow and soy milk, conjugation, mobilization, and retromobilization were shown to occur at frequencies of 8.0 × 10
−1
, 1.0 × 10
−2
, and 1.2 × 10
−4
transconjugants per recipient, respectively. These data are comparable to those obtained with LB medium and about 10-fold lower than in the case of rice milk. Taken together, these results emphasize the potential role of plasmid capture played by
B. thuringiensis
in natural environments.
Pathway of γ-Aminobutyrate Metabolism in
Rhizobium leguminosarum
3841 and Its Role in Symbiosis
Authors: Prell Jurgen , Bourdès Alexandre , Karunakaran Ramakrishnan , Lopez-Gomez Miguel , Poole Philip 
Published: January 2009

ABSTRACT

Pea plants incubated in
15
N
2
rapidly accumulated labeled γ-aminobutyrate (GABA) in the plant cytosol and in bacteroids of
Rhizobium leguminosarum
bv. viciae 3841. Two pathways of GABA metabolism were identified in
R. leguminosarum
3841. In the first, glutamate is formed by GABA aminotransferase (GabT), transferring the amino group from GABA to 2-oxoglutarate. In the second, alanine is formed by two ω-aminotransferases (OpaA and OpaB), transferring the amino group from GABA to pyruvate. While the
gabT
mutant and the
gabT opaA
double mutant grew on GABA as a nitrogen source, the final triple mutant did not. The semialdehyde released from GABA by transamination is oxidized by succinate semialdehyde dehydrogenase (GabD). Five of six potential GabD proteins in
R. leguminosarum
bv. viciae 3841 (GabD1, -D2, -D3, -D4, and -D5) were shown by expression analysis to have this activity. However, only mutations of GabD1, GabD2, and GabD4 were required to prevent utilization of GABA as the sole nitrogen source in culture. The specific enzyme activities of GabT, Opa, and GabD were highly elevated in bacteroids relative to cultured bacteria. This was due to elevated expression of
gabT
,
opaA
,
gabD1
, and
gabD2
in nodules. Strains mutated in aminotransferase and succinate semialdehyde dehydrogenases (
gabT
,
opaA
, or
opaB
and
gabD1
,
gabD2
, or
gabD4
, respectively) that cannot use GABA in culture still fixed nitrogen on plants. While GABA catabolism alone is not essential for N
2
fixation in bacteroids, it may have a role in energy generation and in bypassing the decarboxylating arm of the tricarboxylic acid cycle.
An RNA Hairpin Sequesters the Ribosome Binding Site of the Homing Endonuclease
mobE
Gene
Authors: Gibb Ewan A. , Edgell David R. 
Published: January 2009

ABSTRACT

Previous transcript mapping of the bacteriophage Aeh1
nrd
operon revealed a predicted RNA hairpin upstream of the homing endonuclease
mobE
gene. We enzymatically mapped the hairpin, showing that the
mobE
ribosome binding site is sequestered. Cloning of the hairpin upstream of
lacZ
resulted in reduced β-galactosidase activity, consistent with translational regulation.
Late Quaternary paleoproductivity history on the Vancouver Island margin, western Canada: a multiproxy geochemical studyThis article is one of a series of papers published in this Special Issue on the theme Polar Climate Stability Network.
Authors: Chang Alice S. , Pedersen Thomas F. , Hendy Ingrid L. 
Published: January 2009

Multiproxy analysis of a 38 m long sediment core recovered from the Vancouver Island margin (48.97°N, 127.04°W, water depth 1243 m) has yielded a millennial-scale history of upwelling and export production over the last ∼50 ka. Higher concentrations of marine organic carbon, opal, and trace Mo suggest that production was higher, and sedimentary pore waters more anoxic, during the warm Holocene, Bølling–Allerød, and interstadial events between 31 and 44 ka BP. Relatively lower production and higher inputs of terrigenous organic matter occurred during the last glacial (14.7–31 ka BP; Cordilleran ice sheet proximal to coring site at ∼19.5 ka BP) and from 44–50.4 ka BP. Enrichments in sedimentary δ15N during interstadial events are interpreted to reflect episodic delivery and upwelling of isotopically heavy nitrate to the surface waters and subsequent vectoring to the seafloor via settling planktonic detritus. Similar patterns are seen in southern California and other areas along the western margin of North America, implying that heavier nitrate generated by denitrification in the Eastern Tropical North Pacific has in the past been carried northward in the California Undercurrent at least as far as central Vancouver Island. This inference is consistent with modern hydrographic observations in the region. Comparison of the coherent Vancouver Island, Oregon, California, and northwest Mexico margin records with late Pleistocene climate history in Greenland reinforces the conclusion that a tight physical and biogeochemical coupling has existed for at least 50 ka between the North Atlantic and North American margin waters, including those off Vancouver Island.
Functional involvement of RINF, retinoid-inducible nuclear factor (CXXC5), in normal and tumoral human myelopoiesis
Authors: Pendino Frédéric , Nguyen Eric , Jonassen Inge , Dysvik Bjarte , Azouz Abdulkader , Lanotte Michel , Ségal-Bendirdjian Evelyne , Lillehaug Johan R. 
Published: January 2009

AbstractRetinoids triggers differentiation of acute promyelocytic leukemia (APL) blasts by transcriptional regulation of myeloid regulatory genes. Using a microarray approach, we have identified a novel retinoid-responsive gene (CXXC5) encoding a nuclear factor, retinoid-inducible nuclear factor (RINF), that contains a CXXC-type zinc-finger motif. RINF expression correlates with retinoid-induced differentiation of leukemic cells and with cytokine-induced myelopoiesis of normal CD34+ progenitors. Furthermore, short hairpin RNA (shRNA) interference suggests for this gene a regulatory function in both normal and tumoral myelopoiesis. Interestingly, RINF localizes to 5q31.3, a small region often deleted in myeloid leukemia (acute myeloid leukemia [AML]/myelodysplasia [MDS]) and suspected to harbor one or several tumor suppressor gene.
Enolase-1 promotes plasminogen-mediated recruitment of monocytes to the acutely inflamed lung
Authors: Wygrecka Malgorzata , Marsh Leigh M. , Morty Rory E. , Henneke Ingrid , Guenther Andreas , Lohmeyer Juergen , Markart Philipp , Preissner Klaus T. 
Published: January 2009

AbstractCell surface–associated proteolysis plays a crucial role in the migration of mononuclear phagocytes to sites of inflammation. The glycolytic enzyme enolase-1 (ENO-1) binds plasminogen at the cell surface, enhancing local plasmin production. This study addressed the role played by ENO-1 in lipopolysaccharide (LPS)–driven chemokine-directed monocyte migration and matrix invasion in vitro, as well as recruitment of monocytes to the alveolar compartment in vivo. LPS rapidly up-regulated ENO-1 cell-surface expression on human blood monocytes and U937 cells due to protein translocation from cytosolic pools, which increased plasmin generation, enhanced monocyte migration through epithelial monolayers, and promoted matrix degradation. These effects were abrogated by antibodies directed against the plasminogen binding site of ENO-1. Overexpression of ENO-1 in U937 cells increased their migratory and matrix-penetrating capacity, which was suppressed by overexpression of a truncated ENO-1 variant lacking the plasminogen binding site (ENO-1ΔPLG). In vivo, intratracheal LPS application in mice promoted alveolar recruitment of monocytic cells that overexpressed ENO-1, but not of cells overexpressing ENO-1ΔPLG. Consistent with these data, pneumonia-patients exhibited increased ENO-1 cell-surface expression on blood monocytes and intense ENO-1 staining of mononuclear cells in the alveolar space. These data suggest an important mechanism of inflammatory cell invasion mediated by increased cell-surface expression of ENO-1.
Lenalidomide, adriamycin, and dexamethasone (RAD) in patients with relapsed and refractory multiple myeloma: a report from the German Myeloma Study Group DSMM (Deutsche Studiengruppe Multiples Myelom)
Authors: Knop Stefan , Gerecke Christian , Liebisch Peter , Topp Max S. , Platzbecker Uwe , Sezer Orhan , Vollmuth Christina , Falk Karina , Glasmacher Axel , Maeder Uwe , Einsele Hermann , Bargou Ralf C. 
Published: January 2009

AbstractWe conducted a phase 1/2 trial combining lenalidomide (R) with adriamycin (A) and dexamethasone (D) for relapsed and relapsed-refractory myeloma to determine tolerability and efficacy of this novel regimen, RAD, delivered for six 28-day cycles. A total of 69 intensively pretreated patients with a median age of 65 years (range, 46-77 years) were enrolled. Using pegfilgrastim (G), the maximum tolerated dose (MTD) was formally not reached at the highest dose level (R, 25 mg on days 1-21; A, 9 mg/m2 intravenously on days 1-4; and D, 40 mg on days 1-4 and 17-20; dose level 5+G), which was then used to determine efficacy. Grades 3/4 neutropenia and thrombocytopenia were seen in 48% and 38% of patients, respectively. Thromboembolic events occurred in 4.5% and severe infections in 10.5% of patients. On an intent-to treat analysis, overall response rate (ORR) was 73% for the whole study and 77% including 74% complete response (CR) plus very good partial response (VGPR) for dose level 5+G. Response rates and progression-free survival did not differ between relapsed and relapsed-refractory patients. Deletion of chromosome 17p and elevated β2-microglobulin were associated with significantly inferior response and shortened time to progression. In conclusion, RAD induces substantial and durable remission with an acceptable toxicity profile in patients with relapsed and relapsed-refractory myeloma. This trial was registered at www.ClinicalTrials.gov as no. NCT00306813.
Depletion of CD4 T cells enhances immunotherapy for neuroblastoma after syngeneic HSCT but compromises development of antitumor immune memory
Authors: Jing Weiqing , Gershan Jill A. , Johnson Bryon D. 
Published: January 2009

AbstractHigh-risk neuroblastoma remains a clinically challenging disease. Here, we report that a multifaceted immunotherapeutic approach including syngeneic hematopoietic stem cell transplantation (HSCT), adoptive transfer of sensitized T cells (from syngeneic donors vaccinated to tumor antigens), and early posttransplantation tumor vaccination can effectively treat mice with established neuroblastoma. Vaccination was an important component of this immunotherapy, as it resulted in enhanced and prolonged tumor-specific CD8 T-cell activity and improved antitumor efficacy. Surprisingly, CD4 cell depletion of mice given sensitized T cells resulted in better tumor-free survival, which was associated with an early increased expansion of CD8 T cells with an effector phenotype, increased numbers of tumor-reactive CD8 T cells, and increased tumor infiltration by CD8 T cells. However, in the absence of CD4 T cells, development of long-term tumor immunity (memory) was severely compromised as reflected by diminished CD8 T-cell recall responses and an inability to resist tumor rechallenge in vivo. Based on these results, a major challenge with this immunotherapeutic approach is how to obtain the ideal initial antitumor response but still preserve antitumor immune memory. These data suggest that identification and selective depletion of immune inhibitory CD4 T cells may be a strategy to enhance early antitumor immunity and induce a long-lasting tumor response after HSCT.
Finding optimal threshold for correction error reads in DNA assembling
Authors: Chin Francis YL , Leung Henry CM , Li Wei-Lin , Yiu Siu-Ming 
Published: January 2009

Abstract

Background
DNA assembling is the problem of determining the nucleotide sequence of a genome from its substrings, called reads. In the experiments, there may be some errors on the reads which affect the performance of the DNA assembly algorithms. Existing algorithms, e.g. ECINDEL and SRCorr, correct the error reads by considering the number of times each length-k substring of the reads appear in the input. They treat those length-k substrings appear at least M times as correct substring and correct the error reads based on these substrings. However, since the threshold M is chosen without any solid theoretical analysis, these algorithms cannot guarantee their performances on error correction.

Results
In this paper, we propose a method to calculate the probabilities of false positive and false negative when determining whether a length-k substring is correct using threshold M. Based on this optimal threshold M that minimizes the total errors (false positives and false negatives). Experimental results on both real data and simulated data showed that our calculation is correct and we can reduce the total error substrings by 77.6% and 65.1% when compared to ECINDEL and SRCorr respectively.

Conclusion
We introduced a method to calculate the probability of false positives and false negatives of the length-k substring using different thresholds. Based on this calculation, we found the optimal threshold to minimize the total error of false positive plus false negative.
Using random forest for reliable classification and cost-sensitive learning for medical diagnosis
Authors: Yang Fan , Wang Hua-zhen , Mi Hong , Lin Cheng-de , Cai Wei-wen 
Published: January 2009

Abstract

Background
Most machine-learning classifiers output label predictions for new instances without indicating how reliable the predictions are. The applicability of these classifiers is limited in critical domains where incorrect predictions have serious consequences, like medical diagnosis. Further, the default assumption of equal misclassification costs is most likely violated in medical diagnosis.

Results
In this paper, we present a modified random forest classifier which is incorporated into the conformal predictor scheme. A conformal predictor is a transductive learning scheme, using Kolmogorov complexity to test the randomness of a particular sample with respect to the training sets. Our method show well-calibrated property that the performance can be set prior to classification and the accurate rate is exactly equal to the predefined confidence level. Further, to address the cost sensitive problem, we extend our method to a label-conditional predictor which takes into account different costs for misclassifications in different class and allows different confidence level to be specified for each class. Intensive experiments on benchmark datasets and real world applications show the resultant classifier is well-calibrated and able to control the specific risk of different class.

Conclusion
The method of using RF outlier measure to design a nonconformity measure benefits the resultant predictor. Further, a label-conditional classifier is developed and turn to be an alternative approach to the cost sensitive learning problem that relies on label-wise predefined confidence level. The target of minimizing the risk of misclassification is achieved by specifying the different confidence level for different class.
Integrative disease classification based on cross-platform microarray data
Authors: Liu Chun-Chi , Hu Jianjun , Kalakrishnan Mrinal , Huang Haiyan , Zhou Xianghong Jasmine 
Published: January 2009

Abstract

Background
Disease classification has been an important application of microarray technology. However, most microarray-based classifiers can only handle data generated within the same study, since microarray data generated by different laboratories or with different platforms can not be compared directly due to systematic variations. This issue has severely limited the practical use of microarray-based disease classification.

Results
In this study, we tested the feasibility of disease classification by integrating the large amount of heterogeneous microarray datasets from the public microarray repositories. Cross-platform data compatibility is created by deriving expression log-rank ratios within datasets. One may then compare vectors of log-rank ratios across datasets. In addition, we systematically map textual annotations of datasets to concepts in Unified Medical Language System (UMLS), permitting quantitative analysis of the phenotype "distance" between datasets and automated construction of disease classes. We design a new classification approach named ManiSVM, which integrates Manifold data transformation with SVM learning to exploit the data properties. Using the leave one dataset out cross validation, ManiSVM achieved the overall accuracy of 70.7% (68.6% precision and 76.9% recall) with many disease classes achieving the accuracy higher than 80%.

Conclusion
Our results not only demonstrated the feasibility of the integrated disease classification approach, but also showed that the classification accuracy increases with the number of homogenous training datasets. Thus, the power of the integrative approach will increase with the continuous accumulation of microarray data in public repositories. Our study shows that automated disease diagnosis can be an important and promising application of the enormous amount of costly to generate, yet freely available, public microarray data.