bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biochemical and Mutational Analysis of Glutamine Synthetase Type III from the Rumen Anaerobe
Ruminococcus albus
8
Authors: Amaya Kensey R. , Kocherginskaya Svetlana A. , Mackie Roderick I. , Cann Isaac K. O. 
Published: October 2005

ABSTRACT

Two different genes encoding glutamine synthetase type I (GSI) and GSIII were identified in the genome sequence of
R. albus
8. The identity of the GSIII protein was confirmed by the presence of its associated conserved motifs. The
glnN
gene, encoding the GSIII, was cloned and expressed in
Escherichia coli
BL21 cells. The recombinant protein was purified and subjected to biochemical and physical analyses. Subunit organization suggested a protein present in solution as both monomers and oligomers. Kinetic studies using the forward and the γ-glutamyl transferase (γ-GT) assays were carried out. Mutations that changed conserved glutamic acid residues to alanine in the four GSIII motifs resulted in drastic decreases in GS activity using both assays, except for an E380A mutation, which rather resulted in an increase in activity in the forward assay compared to the wild-type protein. Reduced GSIII activity was also exhibited by mutating, individually, two lysines (K308 and K318) located in the putative nucleotide-binding site to alanine. Most importantly, the presence of mRNA transcripts of the
glnN
gene in
R. albus
8 cells grown under ammonia limiting conditions, whereas little or no transcript was detected in cells grown under ammonia sufficient conditions, suggested an important role for the GSIII in the nitrogen metabolism of
R. albus
8. Furthermore, the mutational studies on the conserved GSIII motifs demonstrated, for the first time, their importance in the structure and/or function of a GSIII protein.
Multiple and Interconnected Pathways for
l
-Lysine Catabolism in
Pseudomonas putida
KT2440
Authors: Revelles Olga , Espinosa-Urgel Manuel , Fuhrer Tobias , Sauer Uwe , Ramos Juan L. 
Published: October 2005

ABSTRACT

l
-Lysine catabolism in
Pseudomonas putida
KT2440 was generally thought to occur via the aminovalerate pathway. In this study we demonstrate the operation of the alternative aminoadipate pathway with the intermediates
d
-lysine,
l
-pipecolate, and aminoadipate. The simultaneous operation of both pathways for the use of
l
-lysine as the sole carbon and nitrogen source was confirmed genetically. Mutants with mutations in either pathway failed to use
l
-lysine as the sole carbon and nitrogen source, although they still used
l
-lysine as the nitrogen source, albeit at reduced growth rates. New genes were identified in both pathways, including the
davB
and
davA
genes that encode the enzymes involved in the oxidation of
l
-lysine to δ-aminovaleramide and the hydrolysis of the latter to δ-aminovalerate, respectively. The
amaA
,
dkpA
, and
amaB
genes, in contrast, encode proteins involved in the transformation of Δ
1
-piperidine-2-carboxylate into aminoadipate. Based on
l
-[U-
13
C, U-
15
N]lysine experiments, we quantified the relative use of pathways in the wild type and its isogenic mutants. The fate of
13
C label of
l
-lysine indicates that in addition to the existing connection between the
d
- and
l
-lysine pathways at the early steps of the catabolism of
l
-lysine mediated by a lysine racemase, there is yet another interconnection at the lower end of the pathways in which aminoadipate is channeled to yield glutarate. This study establishes an unequivocal relationship between gene and pathway enzymes in the metabolism of
l
-lysine, which is of crucial importance for the successful colonization of the rhizosphere of plants by this microorganism.
Characterization of Bacterial Drug Antiporters Homologous to Mammalian Neurotransmitter Transporters
Authors: Vardy Eyal , Steiner-Mordoch Sonia , Schuldiner Shimon 
Published: October 2005

ABSTRACT

Multidrug transporters are ubiquitous proteins, and, based on amino acid sequence similarities, they have been classified into several families. Here we characterize a cluster of archaeal and bacterial proteins from the major facilitator superfamily (MFS). One member of this family, the vesicular monoamine transporter (VMAT) was previously shown to remove both neurotransmitters and toxic compounds from the cytoplasm, thereby conferring resistance to their effects. A BLAST search of the available microbial genomes against the VMAT sequence yielded sequences of novel putative multidrug transporters. The new sequences along with VMAT form a distinct cluster within the dendrogram of the MFS, drug-proton antiporters. A comparison with other proteins in the family suggests the existence of a potential ion pair in the membrane domain. Three of these genes, from
Mycobacterium smegmatis
,
Corynebacterium glutamicum
, and
Halobacterium salinarum
, were cloned and functionally expressed in
Escherichia coli
. The proteins conferred resistance to fluoroquinolones and chloramphenicol (at concentrations two to four times greater than that of the control). Measurement of antibiotic accumulation in cells revealed proton motive force-dependent transport of those compounds.
Tol-Dependent Macromolecule Import through theEscherichia coliCell Envelope Requires the Presence of an Exposed TolA Binding Motif
Authors: Pommier Stéphanie , Gavioli Marthe , Cascales Eric , Lloubès Roland 
Published: October 2005

ABSTRACTThe Tol-Pal proteins of the cell envelope ofEscherichia coliare required for maintaining outer membrane integrity. This system forms protein complexes in which TolA plays a central role by providing a bridge between the inner and outer membranes via its interaction with the Pal lipoprotein. The Tol proteins are parasitized by filamentous bacteriophages and group A colicins. The N-terminal domain of the Ff phage g3p protein and the translocation domains of colicins interact directly with TolA during the processes of import through the cell envelope. Recently, a four-amino-acid sequence in Pal has been shown to be involved in Pal's interaction with TolA. A similar motif is also present in the sequence of two TolA partners, g3p and colicin A. Here, a mutational study was conducted to define the function of these motifs in the binding activity and import process of TolA. The various domains were produced and exported to the bacterial periplasm, and their cellular effects were analyzed. Cells producing the g3p domain were tolerant to colicins and filamentous phages and had destabilized outer membranes, while g3p deleted of three residues in the motif was affected in TolA binding and had no effect on cell integrity or colicin or phage import. A conserved Tyr residue in the colicin A translocation domain was involved in TolA binding and colicin A import. Furthermore, in vivo and in vitro coprecipitation analyses demonstrated that colicin A and g3p N-terminal domains compete for binding to TolA.
Replacement of Tyrosine 181 by Phenylalanine in Gentisate 1,2-Dioxygenase I from
Pseudomonas alcaligenes
NCIMB 9867 Enhances Catalytic Activities
Authors: Tan Chew Ling , Yeo Chew Chieng , Khoo Hoon Eng , Poh Chit Laa 
Published: October 2005

ABSTRACT

xlnE
, encoding gentisate 1,2-dioxygenase (EC 1.13.11.4), from
Pseudomonas alcaligenes
(P25X) was mutagenized by site-directed mutagenesis. The mutant enzyme, Y181F, demonstrated 4-, 3-, 6-, and 16-fold increases in relative activity towards gentisate and 3-fluoro-, 4-methyl-, and 3-methylgentisate, respectively. The specific mutation conferred a 13-fold higher catalytic efficiency (
k
cat
/

K
m

) on Y181F towards 3-methylgentisate than that of the wild-type enzyme.
2003 Alcan Award Lecture  Roles of the adjacent metals in the coupling of methylene groups promoted by heterobinuclear complexes of Group 8 and 9 metals
Authors: Cowie Martin 
Published: October 2005

The reactivities of the heterobinuclear complexes, [MM′(CO)4(dppm)2][X] (MM′ = RhOs, RhRu, IrRu; dppm =µ-Ph2PCH2PPh2; X = BF4, CF3SO3) with diazomethane are reported. The RhOs species reacts to give three products of methylene-group incorporation, depending on the temperature; at 80 °C the methylene bridged product, [RhOs(CO)4(µ-CH2)(dppm)2][X], is formed exclusively, at ambient temperature only [RhOs(η1-C3H5)(CH3)(CO)3(dppm)2][X], having the allyl group bound to Rh and the methyl group bound to Os, is obtained, while at intermediate temperatures [RhOs(η1:η1-C4H8)(CO)3(dppm)2][X], having the butanediyl fragment chelating on Os, is generated. Based on labeling studies a mechanism is proposed rationalizing formation of the different products. Under the same range of conditions the Rh/Ru and Ir/Ru species yield only the methylene bridged products, [MM′(CO)4(µ-CH2)(dppm)2][X] (MM′ = RhRu, IrRu). A rationalization for the different reactivities observed and a description of the roles of the different metals in coupling of the methylene groups are presented. Attempts to model key intermediates in the methylene coupling sequence promoted by the Rh/Os complexes, through coupling of methylene groups with ethylene or alkynes, are described. Key words: heterobinuclear, rhodium/osmium, rhodium/ruthenium, iridium/ruthenium, methylene coupling, FischerTropsch, alkyne insertions, bimetallic cooperativity.
The ETS factor TEL2 is a hematopoietic oncoprotein
Authors: Carella Cintia , Potter Mark , Bonten Jacqueline , Rehg Jerold E. , Neale Geoffrey , Grosveld Gerard C. 
Published: October 2005

AbstractTEL2/ETV7 is highly homologous to the ETS transcription factor TEL/ETV6, a frequent target of chromosome translocation in human leukemia. Although both proteins are transcriptional inhibitors binding similar DNA recognition sequences, they have opposite biologic effects: TEL inhibits proliferation while TEL2 promotes it. In addition, forced expression of TEL2 but not TEL blocks vitamin D3–induced differentiation of U937 and HL60 myeloid cells. TEL2 is expressed in the hematopoietic system, and its expression is up-regulated in bone marrow samples of some patients with leukemia, suggesting a role in oncogenesis. Recently we also showed that TEL2 cooperates with Myc in B lymphomagenesis in mice. Here we show that forced expression of TEL2 alone in mouse bone marrow causes a myeloproliferative disease with a long latency period but with high penetrance. This suggested that secondary mutations are necessary for disease development. Treating mice receiving transplants with TEL2-expressing bone marrow with the chemical carcinogen N-ethyl-N-nitrosourea (ENU) resulted in significantly accelerated disease onset. Although the mice developed a GFP-positive myeloid disease with 30% of the mice showing elevated white blood counts, they all died of T-cell lymphoma, which was GFP negative. Together our data identify TEL2 as a bona fide oncogene, but leukemic transformation is dependent on secondary mutations.
AML engraftment in the NOD/SCID assay reflects the outcome of AML: implications for our understanding of the heterogeneity of AML
Authors: Pearce Daniel J. , Taussig David , Zibara Kazem , Smith Lan-Lan , Ridler Christopher M. , Preudhomme Claude , Young Bryan D. , Rohatiner Ama Z. , Lister T. Andrew , Bonnet Dominique 
Published: October 2005

AbstractThe nonobese diabetic/severe combined immunodeficient (NOD/SCID) assay is the current model for assessment of human normal and leukemic stem cells. We explored why 51% of 59 acute myeloid leukemia (AML) patients were unable to initiate leukemia in NOD/SCID mice. Increasing the cell dose, using more permissive recipients, and alternative tissue sources did not cause AML engraftment in most previously nonengrafting AML samples. Homing of AML cells to the marrow was the same between engrafters and nonengrafters. FLT3 internal tandem duplication (ITD) and nucleophosmin mutations occurred at a similar frequency in engrafters and nonengrafters. The only variable that was related to engraftment ability was the karyotypically defined risk stratification of individual AML cases. Of interest, follow-up of younger patients with intermediate-risk AML revealed a significant difference in overall survival between NOD/SCID engrafting and nonengrafting AMLs. Hence, the ability of AML to engraft in the NOD/SCID assay seems to be an inherent property of AML cells, independent of homing, conditioning, or cell frequency/source, which is directly related to prognosis. Our results suggest an important difference between leukemic initiating cells between engrafting and nonengrafting AML cases that correlates with treatment response.
Epstein-Barr virus: the impact of scientific advances on clinical practice
Authors: Williams Hilary , Crawford Dorothy H. 
Published: October 2005

AbstractEpstein-Barr virus (EBV) is a tumorigenic herpes virus that infects and persists in B lymphocytes in the majority of humans, generally without causing disease. However, in a few individuals the virus is associated with significant pathology, particularly benign and malignant lymphoproliferations. Recently acquired knowledge on the mechanisms of EBV persistence, immune control of primary and persistent infection, and disease pathogenesis is now being translated into the clinic with novel methods of diagnosis, prevention and treatment contributing to improved patient care. This review concentrates on these recent advances in the field of hematology/oncology.
HLA-DPB1 matching status has significant implications for recipients of unrelated donor stem cell transplants
Authors: Shaw Bronwen E. , Marsh Steven G.E. , Mayor Neema P. , Russell Nigel H. , Madrigal J. Alejandro 
Published: October 2005

AbstractStudies in unrelated donor (UD) hematopoietic stem cell transplantations (HSCT) show an effect of the matching status of HLA-DPB1 on complications. We analyzed 423 UD-HSCT pairs. Most protocols included T-cell depletion (TCD). All pairs had high-resolution tissue typing performed for 6 HLA loci. Two hundred eighty-two pairs were matched at 10 of 10 alleles (29% were DPB1 matched). In 141 HLA-mismatched pairs, 28% were matched for DPB1. In the 10 of 10 matched pairs (n = 282), the 3-year probability of relapse was 61%. This was significantly higher in DPB1-matched pairs (74%) as compared with DPB1-mismatched pairs (56%) (log rank, P = .001). This finding persisted in multivariate analysis. In the group overall (n = 423), relapse was also significantly increased if DPB1 was matched (log rank; P < .001). These results were similar in chronic myeloid leukemia (CML; P < .001) and acute lymphoblastic leukemia (ALL; P = .013). In ALL, DPB1-matched pairs had a significantly worse overall survival (log rank; P = .025). Thus, in recipients of TCD UD-HSCT, a match for DPB1 is associated with a significantly increased risk of disease relapse, irrespective of the matching status for the other HLA molecules. It is possible that this effect is especially apparent following TCD transplantations and invites speculation about the function of DPB1 within the immune system.
Differential roles for β2 integrins in experimental autoimmune bullous pemphigoid
Authors: Liu Zhi , Zhao Minglang , Li Ning , Diaz Luis A. , Mayadas Tanya N. 
Published: October 2005

AbstractBullous pemphigoid (BP) is an autoimmune disease associated with autoantibodies directed against the hemidesmosomal antigens anti-BP230 and anti-B180. Neonatal mice injected with rabbit anti-mouse BP180 (mBP10) IgG develop a BP-like disease. Complement, immune complexes, mast cells, and neutrophils play a key role in subepidermal blistering in this animal model. In this study we investigated the role of β2 integrins in experimental BP. Wild-type (WT) mice pretreated with neutralizing antibody against CD11a (LFA-1), CD11b (Mac-1), CD11a plus CD11b, or CD18 alone failed to develop BP when injected with pathogenic anti-mBP180 IgG. This was associated with a significant reduction in neutrophil accumulation in neutralizing antibody-treated mice. Mac-1-deficient (Mac-1 knockout [KO]) mice were resistant to experimental BP despite normal complement deposition and mast cell and neutrophil degranulation. Neutrophil infiltration in Mac-1 KO mice was severely impaired at 24 hours. However, more neutrophils accumulated in the skin of Mac-1 KO mice compared with WT mice at early time points (2-4 hours), which was associated with an increase in their survival as determined by apoptosis markers. These data suggest that β2 integrins play differential roles in experimental BP: LFA-1 is required for neutrophil recruitment, while Mac-1 mediates late neutrophil accumulation and apoptosis of infiltrating neutrophils.
Psoriasin, one of several new proteins identified in nasal lavage fluid from allergic and non-allergic individuals using 2-dimensional gel electrophoresis and mass spectrometry
Authors: Bryborn Malin , Adner Mikael , Cardell Lars-Olaf 
Published: October 2005

AbstractBackgroundExtravasation and luminal entry of plasma occurs continuously in the nose. This process is markedly facilitated in patients with symptomatic allergic rhinitis, resulting in an increased secretion of proteins. Identification of these proteins is an important step in the understanding of the pathological mechanisms in allergic diseases. DNA microarrays have recently made it possible to compare mRNA profiles of lavage fluids from healthy and diseased patients, whereas information on the protein level is still lacking.MethodsNasal lavage fluid was collected from 11 patients with symptomatic allergic rhinitis and 11 healthy volunteers. 2-dimensional gel electrophoresis was used to separate proteins in the lavage fluids. Protein spots were picked from the gels and identified using mass spectrometry and database search. Selected proteins were confirmed with western blot.Results61 spots were identified, of which 21 were separate proteins. 6 of these proteins (psoriasin, galectin-3, alpha enolase, intersectin-2, Wnt-2B and hypothetical protein MGC33648) had not previously been described in nasal lavage fluids. The levels of psoriasin were markedly down-regulated in allergic individuals. Prolactin-inducible protein was also found to be down-regulated, whereas different fragments of albumin together with Ig gamma 2 chain c region, transthyretin and splice isoform 1 of Wnt-2B were up-regulated among the allergic patients.ConclusionThe identification of proteins in nasal lavage fluid with 2-dimensional gelelectrophoresis in combination with mass spectrometry is a novel tool to profile protein expression in allergic rhinitis and it might prove useful in the hunt for new therapeutic targets or diagnostic markers for allergic diseases. Psoriasin is a potent chemotactic factor and its down-regulation during inflammation might be of importance for the outcome of the disease.
Liquid chromatography/mass spectrometry analysis of exhaled leukotriene B4 in asthmatic children
Authors: Montuschi Paolo , Martello Simona , Felli Marialinda , Mondino Chiara , Barnes Peter J , Chiarotti Marcello 
Published: October 2005

Abstract

Background
The role of leukotriene (LT) B4, a potent inflammatory mediator, in atopic asthmatic and atopic nonasthmatic children is largely unknown. The lack of a gold standard technique for measuring LTB4 in exhaled breath condensate (EBC) has hampered its quantitative assessment in this biological fluid. We sought to measure LTB4 in EBC in atopic asthmatic children and atopic nonasthmatic children. Exhaled nitric oxide (NO) was measured as an independent marker of airway inflammation.

Methods
Fifteen healthy children, 20 atopic nonasthmatic children, 25 steroid-naïve atopic asthmatic children, and 22 atopic asthmatic children receiving inhaled corticosteroids were studied. The study design was of cross-sectional type. Exhaled LTB4 concentrations were measured using liquid chromatography/mass spectrometry-mass spectrometry (LC/MS/MS) with a triple quadrupole mass spectrometer. Exhaled NO was measured by chemiluminescence with a single breath on-line method. LTB4 values were expressed as the total amount (in pg) of eicosanoid expired in the 15-minute breath test. Kruskal-Wallis test was used to compare groups.

Results
Compared with healthy children [87.5 (82.5–102.5) pg, median and interquartile range], exhaled LTB4 was increased in steroid-naïve atopic asthmatic [255.1 (175.0–314.7) pg, p < 0.001], but not in atopic nonasthmatic children [96.5 (87.3–102.5) pg, p = 0.59)]. Asthmatic children who were receiving inhaled corticosteroids had lower concentrations of exhaled LTB4 than steroid-naïve asthmatics [125.0 (25.0–245.0) pg vs 255.1 (175.0–314.7) pg, p < 0.01, respectively]. Exhaled NO was higher in atopic nonasthmatic children [16.2 (13.5–22.4) ppb, p < 0.05] and, to a greater extent, in atopic steroid-naïve asthmatic children [37.0 (31.7–57.6) ppb, p < 0.001] than in healthy children [8.3 (6.1–9.9) ppb]. Compared with steroid-naïve asthmatic children, exhaled NO levels were reduced in asthmatic children who were receiving inhaled corticosteroids [15.9 (11.5–31.7) ppb, p < 0.01].

Conclusion
In contrast to exhaled NO concentrations, exhaled LTB4 values are selectively elevated in steroid-naïve atopic asthmatic children, but not in atopic nonasthmatic children. Although placebo control studies are warranted, inhaled corticosteroids seem to reduce exhaled LTB4 in asthmatic children. LC/MS/MS analysis of exhaled LTB4 might provide a non-invasive, sensitive, and quantitative method for airway inflammation assessment in asthmatic children.
SpectralNET – an application for spectral graph analysis and visualization
Authors: Forman Joshua J , Clemons Paul A , Schreiber Stuart L , Haggarty Stephen J 
Published: October 2005

Abstract
Background
Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices) and interactions (edges) that can carry different weights. SpectralNET is a flexible application for analyzing and visualizing these biological and chemical networks.

Results
Available both as a standalone .NET executable and as an ASP.NET web application, SpectralNET was designed specifically with the analysis of graph-theoretic metrics in mind, a computational task not easily accessible using currently available applications. Users can choose either to upload a network for analysis using a variety of input formats, or to have SpectralNET generate an idealized random network for comparison to a real-world dataset. Whichever graph-generation method is used, SpectralNET displays detailed information about each connected component of the graph, including graphs of degree distribution, clustering coefficient by degree, and average distance by degree. In addition, extensive information about the selected vertex is shown, including degree, clustering coefficient, various distance metrics, and the corresponding components of the adjacency, Laplacian, and normalized Laplacian eigenvectors. SpectralNET also displays several graph visualizations, including a linear dimensionality reduction for uploaded datasets (Principal Components Analysis) and a non-linear dimensionality reduction that provides an elegant view of global graph structure (Laplacian eigenvectors).

Conclusion
SpectralNET provides an easily accessible means of analyzing graph-theoretic metrics for data modeling and dimensionality reduction. SpectralNET is publicly available as both a .NET application and an ASP.NET web application from http://chembank.broad.harvard.edu/resources/. Source code is available upon request.