bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Gene Expression Analysis during Sporulation of the Aquatic Fungus Blastocladiella emersonii
Authors: Vieira André L. G. , Gomes Suely L. 
Published: December 2009

ABSTRACT

The
Blastocladiella emersonii
life cycle presents a number of drastic biochemical and morphological changes, mainly during two cell differentiation stages: germination and sporulation. To investigate the transcriptional changes taking place during the sporulation phase, which culminates with the production of the zoospores, motile cells responsible for the dispersal of the fungus, microarray experiments were performed. Among the 3,773 distinct genes investigated, a total of 1,207 were classified as differentially expressed, relative to time zero of sporulation, at at least one of the time points analyzed. These results indicate that accurate transcriptional control takes place during sporulation, as well as indicating the necessity for distinct molecular functions throughout this differentiation process. The main functional categories overrepresented among upregulated genes were those involving the microtubule, the cytoskeleton, signal transduction involving Ca
2+
, and chromosome organization. On the other hand, protein biosynthesis, central carbon metabolism, and protein degradation were the most represented functional categories among downregulated genes. Gene expression changes were also analyzed in cells sporulating in the presence of subinhibitory concentrations of glucose or tryptophan. Data obtained revealed overexpression of microtubule and cytoskeleton transcripts in the presence of glucose, probably causing the shape and motility problems observed in the zoospores produced under this condition. In contrast, the presence of tryptophan during sporulation led to upregulation of genes involved in oxidative stress, proteolysis, and protein folding. These results indicate that distinct physiological pathways are involved in the inhibition of sporulation due to these two classes of nutrient sources.
Associations between Mucosal Innate and Adaptive Immune Responses and Resolution of Diarrheal Pathogen Infections
Authors: Long Kurt Z. , Rosado Jorge L. , Santos José Ignacio , Haas Meredith , Al Mamun Abdullah , DuPont Herbert L. , Nanthakumar Nanda N. , Estrada-Garcia Teresa 
Published: December 2009

ABSTRACTThe identification of immune response mechanisms that contribute to the control of diarrheal disease in developing countries remains an important priority. We addressed the role of fecal chemokines and cytokines in the resolution of diarrhealEscherichia coliandGiardia lambliainfections. Stools collected from 127 Mexican children 5 to 15 months of age enrolled in a randomized, double-blind, placebo-controlled, vitamin A supplementation trial were screened for enteropathogenicEscherichia coli(EPEC), enterotoxigenicE. coli(ETEC), andGiardia lamblia. Fecal concentrations of tumor necrosis factor alpha (TNF-α), monocyte chemoattractant protein-1 (MCP-1), interleukin-4 (IL-4), IL-5, IL-6, IL-8, IL-10, and interferon-γ (IFN-γ) were determined. Hazard models incorporating cytokine variables were fit to durations of asymptomatic and symptomatic pathogen infections, controlling for treatment group. Increased levels of TNF-α and IL-6 were associated with decreased durations of EPEC infection and increased ETEC durations. Increased IL-4 and IFN-γ levels were associated with decreased and increased durations, respectively, of both EPEC and ETEC infections. Increased IL-10 levels were associated with increased and decreased durations of asymptomatic and symptomatic EPEC infections, respectively, and increased durations of both asymptomatic and symptomatic ETEC infections. Increased levels of MCP-1, IFN-γ, IL-4, and IL-5 were associated with increasedG. lambliainfection duration, while increased IL-8 levels were associated with decreased durations. Differences in proinflammatory and Treg cytokine levels are associated with differences in the resolution of inflammatory and noninflammatory pathogen infections.
Activation of Human and Chicken Toll-Like Receptors by
Campylobacter
spp
Authors: de Zoete Marcel R. , Keestra A. Marijke , Roszczenko Paula , van Putten Jos P. M. 
Published: December 2009

ABSTRACT

Campylobacter
infection in humans is accompanied by severe inflammation of the intestinal mucosa, in contrast to colonization of chicken. The basis for the differential host response is unknown. Toll-like receptors (TLRs) sense and respond to microbes in the body and participate in the induction of an inflammatory response. Thus far, the interaction of
Campylobacter
with chicken TLRs has not been studied. Here, we investigated the potential of four
Campylobacter
strains to activate human TLR1/2/6, TLR4, TLR5, and TLR9 and chicken TLR2t2/16, TLR4, TLR5, and TLR21. Live bacteria showed no or very limited potential to activate TLR2, TLR4, and TLR5 of both the human and chicken species, with minor but significant differences between
Campylobacter
strains. In contrast, lysed bacteria induced strong NF-κB activation through human TLR1/2/6 and TLR4 and chicken TLR2t2/16 and TLR4 but not via TLR5 of either species. Interestingly,
C. jejuni
induced TLR4-mediated beta interferon in human but not chicken cells. Furthermore, isolated chromosomal
Campylobacter
DNA was unable to activate human TLR9 in our system, whereas chicken TLR21 was activated by DNA from all of the campylobacters tested. Our data are the first comparison of TLR-induced immune responses in humans and chickens. The results suggest that differences in bacterial cell wall integrity and in TLR responses to
Campylobacter
LOS and/or DNA may contribute to the distinct clinical manifestation between the species.
Cell Sorting-Assisted Microarray Profiling of Host Cell Response to
Cryptosporidium parvum
Infection
Authors: Yang Yi-Lin , Buck Gregory A. , Widmer Giovanni 
Published: December 2009

ABSTRACT

To study the transcriptional response of mammalian cells to infection with the intracellular apicomplexan parasite
Cryptosporidium parvum
, infected and uninfected cells were recovered from
C. parvum
-infected cell monolayers. This approach, which contrasts with a more conventional experimental design that compares infected to uninfected cell monolayers, enabled the identification of functional categories of genes that are differentially transcribed as a direct consequence of the presence of intracellular parasites. Among several categories of upregulated genes, glycoprotein metabolism was significantly overrepresented. To investigate whether these transcriptional changes affected the composition of the surface of infected cells, cells were probed with fluorescently labeled lectins. Among a panel of seven lectins, soybean agglutinin, which recognizes
N
-acetyl-
d
-galactosamine, generated the largest difference in fluorescence between infected and uninfected cells. The origin of the fluorescent signal emitted by infected cells was further investigated and attributed to the overexpression of glycoprotein on the surface of infected cells, as well as the presence of glycoprotein located in the proximity of intracellular parasites.
The
Streptococcus mutans
IrvR Repressor Is a CI-Like Regulator That Functions through Autocleavage and Clp-Dependent Proteolysis
Authors: Niu Guoqing , Okinaga Toshinori , Qi Fengxia , Merritt Justin 
Published: December 2009

ABSTRACT

Previous work has shown that
irvR
is required for the proper regulation of genetic competence and dextran-dependent aggregation due to its ability to repress the transcription regulator
irvA
. In this study, we determined the mechanism used to relieve the repression of
irvA
. We demonstrate that IrvR is a “LexA-like” protein with four conserved amino acid residues likely required for IrvR autocleavage activity. Furthermore, recombinant IrvR protein purified from
Escherichia coli
was competent to undergo autocleavage
in vitro
. Using several truncated IrvR constructs, we show that the amino acids adjacent to the autocleavage site are essential for relieving
irvA
repression and engaging the
irvA-
dependent regulatory pathway primarily through the ClpXP and ClpCP proteases. By extending the IrvR C terminus with an epitope derived from the autocleavage site, we were also able to create a constitutive Clp-dependent degradation of the full-length IrvR protein. This suggests that the derepression of
irvA
occurs through a two-step mechanism involving the initial autocleavage of IrvR and exposure of a proteolytic degradation sequence followed by Clp-dependent degradation of the IrvR DNA binding domain. Thus,
irvA
derepression is highly analogous to the genetic switch mechanism used to regulate lysogeny in bacteriophages.
Roles of RubisCO and the RubisCO-Like Protein in 5-Methylthioadenosine Metabolism in the Nonsulfur Purple Bacterium
Rhodospirillum rubrum
Authors: Singh Jaya , Tabita F. Robert 
Published: December 2009

ABSTRACT

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) catalyzes the assimilation of atmospheric CO
2
into organic matter and is thus central to the existence of life on earth. The beginning of the 2000s was marked by the discovery of a new family of proteins, the RubisCO-like proteins (RLPs), which are structural homologs of RubisCO. RLPs are unable to catalyze CO
2
fixation. The RLPs from
Chlorobaculum tepidum
,
Bacillus subtilis
,
Geobacillus kaustophilus
, and
Microcystis aeruginosa
have been shown to participate in sulfur metabolism. Whereas the precise function of
C. tepidum
RLP is unknown, the
B. subtilis
,
G. kaustophilus
, and
M. aeruginosa
RLPs function as tautomerases/enolases in a methionine salvage pathway (MSP). Here, we show that the form II RubisCO enzyme from the nonsulfur purple bacterium
Rhodospirillum rubrum
is also able to function as an enolase
in vivo
as part of an MSP, but only under anaerobic conditions. However, unlike
B. subtilis
RLP,
R
.
rubrum
RLP does not catalyze the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate. Instead, under aerobic growth conditions,
R. rubrum
RLP employs another intermediate of the MSP, 5-methylthioribulose-1-phosphate, as a substrate, resulting in the formation of different products. To further determine the interrelationship between RubisCOs and RLPs (and the potential integration of cellular carbon and sulfur metabolism), the functional roles of both RubisCO and RLP have been examined
in vivo
via the use of specific knockout strains and complementation studies of
R. rubrum
. The presence of functional, yet separate, MSPs in
R. rubrum
under both aerobic (chemoheterotrophic) and anaerobic (photoheterotrophic) growth conditions has not been observed previously in any organism. Moreover, the aerobic and anaerobic sulfur salvage pathways appear to be differentially controlled, with novel and previously undescribed steps apparent for sulfur salvage in this organism.
Multidrug Efflux Pump MdtBC of
Escherichia coli
Is Active Only as a B
2
C Heterotrimer
Authors: Kim Hong-Suk , Nagore Daniel , Nikaido Hiroshi 
Published: December 2009

ABSTRACT

RND (resistance-nodulation-division) family transporters in Gram-negative bacteria frequently pump out a wide range of inhibitors and often contribute to multidrug resistance to antibiotics and biocides. An archetypal RND pump of
Escherichia coli
, AcrB, is known to exist as a homotrimer, and this construction is essential for drug pumping through the functionally rotating mechanism. MdtBC, however, appears different because two pump genes coexist within a single operon, and genetic deletion data suggest that both pumps must be expressed in order for the drug efflux to occur. We have expressed the corresponding genes, with one of them in a His-tagged form. Copurification of MdtB and MdtC under these conditions showed that they form a complex, with an average stoichiometry of 2:1. Unequivocal evidence that only the trimer containing two B protomers and one C protomer is active was obtained by expressing all possible combinations of B and C in covalently linked forms. Finally, conversion into alanine of the residues, known to form a proton translocation pathway in AcrB, inactivated transport only when made in MdtB, not when made in MdtC, a result suggesting that MdtC plays a different role not directly involved in drug binding and extrusion.
Flavobacterium johnsoniae gldN
and
gldO
Are Partially Redundant Genes Required for Gliding Motility and Surface Localization of SprB
Authors: Rhodes Ryan G. , Samarasam Mudiarasan Napoleon , Shrivastava Abhishek , van Baaren Jessica M. , Pochiraju Soumya , Bollampalli Sreelekha , McBride Mark J. 
Published: December 2009

ABSTRACT

Cells of the gliding bacterium
Flavobacterium johnsoniae
move rapidly over surfaces. Mutations in
gldN
cause a partial defect in gliding. A novel bacteriophage selection strategy was used to aid construction of a strain with a deletion spanning
gldN
and the closely related gene
gldO
in an otherwise wild-type
F. johnsoniae
UW101 background. Bacteriophage transduction was used to move a
gldN
mutation into
F. johnsoniae
UW101 to allow phenotypic comparison with the
gldNO
deletion mutant. Cells of the
gldN
mutant formed nonspreading colonies on agar but retained some ability to glide in wet mounts. In contrast, cells of the
gldNO
deletion mutant were completely nonmotile, indicating that cells require GldN, or the GldN-like protein GldO, to glide. Recent results suggest that
Porphyromonas gingivalis
PorN, which is similar in sequence to GldN, has a role in protein secretion across the outer membrane. Cells of the
F. johnsoniae gldNO
deletion mutant were defective in localization of the motility protein SprB to the cell surface, suggesting that GldN may be involved in secretion of components of the motility machinery. Cells of the
gldNO
deletion mutant were also deficient in chitin utilization and were resistant to infection by bacteriophages, phenotypes that may also be related to defects in protein secretion.
The Maturation of Synthetic Scaffolds for Osteochondral Donor Sites of the Knee
Authors: Bedi Asheesh , Foo Li Foong , Williams Riley J. , Potter Hollis G. ,   the Cartilage Study Group
Published: December 2009

Objective: The purpose of this study was to analyze the morphological imaging characteristics and incorporation of TruFit bone graft substitute (BGS) plugs using cartilage-sensitive magnetic resonance imaging (MRI) and quantitative T2 mapping. Design: Twenty-six patients (mean age, 28.72 years; range, 11-56 years) underwent osteochondral autologous transplantation (OATS) for chondral defects with filling of the knee joint donor sites using Trufit BGS plugs. The mean follow-up interval between implantation and MRI analysis was 21.3 months (range, 6-39 months). During this period, 43 cartilage-sensitive and 25 quantitative T2-mapping MRI studies were performed. The donor sites were assessed for plug and interface morphology, displacement, hypertrophy, subchondral edema, presence of bony overgrowth, percentage fill, and degree of incorporation. T2 relaxation times were measured for the superficial and deep layers of the repair tissue. A linear regression and correlational analysis was performed with Bonferroni correction, and P < 0.05 was defined as significant. Results: Longitudinal analysis revealed favorable plug appearance at early follow-up (≤6 months), with 75% of plugs demonstrating flush morphology and 78% demonstrating near complete to complete fill. Plug appearance deteriorated at intermediate follow-up (~12 months), with only 26% of plugs demonstrating flush morphology and 52% with near complete or complete fill. Plug appearance substantially improved with longer follow-up (≥16 months), with 70% of plugs demonstrating flush morphology and 90% demonstrating near complete or complete fill. Interface resorption was common at ~12 months ( P < 0.0001) and was associated with older age ( P = 0.01) or a single-plug configuration ( P = 0.04). T2 values for the repair cartilage approached that of normal cartilage with increasing duration after surgery ( P < 0.004), more so for single- compared with multiple-plug configurations ( P = 0.03). Conclusions: The Trufit BGS plug demonstrates a predictable pattern of postoperative maturation on MRI images that parallels its biological incorporation. An intermediate postoperative interval can be associated with unfavorable MRI findings. However, the plug appearance significantly improves with greater postoperative duration and has mean T2 relaxation times that approach those of normal articular cartilage.
Idiopathic CD4+ T-cell lymphocytopenia is associated with impaired membrane expression of the chemokine receptor CXCR4
Authors: Scott-Algara Daniel , Balabanian Karl , Chakrabarti Lisa A. , Mouthon Luc , Dromer Françoise , Didier Céline , Arenzana-Seisdedos Fernando , Lortholary Olivier 
Published: December 2009

AbstractIdiopathic CD4+ T-cell lymphocytopenia (ICL) is a rare acquired T-cell immunodeficiency of unknown pathogenic basis. Six adults with ICL who developed opportunistic infections were investigated using extensive immunophenotyping analysis and functional evaluation of the chemokine receptor CXCR4. For all 6 patients studied, a profound defect in CXCR4 expression was detected at the surface of CD4+ T lymphocytes, in association with an abnormal intracellular accumulation of CXCR4 and of its natural ligand, the chemokine CXCL12. For all patients studied, CD4+ T-cell chemotactic response toward CXCL12 was decreased, whereas sensitivity to CXCL8 was preserved. CXCR4 recovery after ligand-induced endocytosis was impaired in ICL CD4+ T cells. Upon in vitro addition of interleukin-2 (IL-2), membrane expression of CXCR4 returned to normal levels in 5 of 6 patients, whereas intracellular accumulation of CXCR4 and CXCL12 disappeared. Upon therapeutic administration of IL-2, CD4+ T-cell count and membrane CXCR4 expression and function improved over time in 3 of 4 patients treated. Therefore, our data indicate that ICL is associated with defective surface expression of CXCR4, which may be reversed by IL-2.
Placenta growth factor in sickle cell disease: association with hemolysis and inflammation
Authors: Brittain Julia E. , Hulkower Ben , Jones Susan K. , Strayhorn Dell , De Castro Laura , Telen Marilyn J. , Orringer Eugene P. , Hinderliter Alan , Ataga Kenneth I. 
Published: December 2009

Abstract
Placenta growth factor (PlGF) is released by immature erythrocytes and is elevated in sickle cell disease (SCD). Previous data generated in vitro suggest that PlGF may play a role in the pathophysiology of SCD-associated pulmonary hypertension (PHT) by inducing the release of the vasoconstrictor, endothelin-1. In this cross-sectional study of 74 patients with SCD, we confirm that PlGF is significantly elevated in SCD compared with healthy control subjects. We found significantly higher levels of PlGF in SCD patients with PHT but observed no association of PlGF with the frequency of acute pain episodes or history of acute chest syndrome. The observed correlation between PlGF and various measures of red cell destruction suggests that hemolysis, and the resultant erythropoietic response, results in the up-regulation of PlGF. Although relatively specific, PlGF, as well as N-terminal pro-brain natriuretic peptide and soluble vascular cell adhesion molecule, has low predictive accuracy for the presence of PHT. Prospective studies are required to conclusively define the contribution of PlGF to the pathogenesis of PHT and other hemolytic complications in SCD.
CC chemokine receptor 7 and 9 double-deficient hematopoietic progenitors are severely impaired in seeding the adult thymus
Authors: Krueger Andreas , Willenzon Stefanie , Łyszkiewicz Marcin , Kremmer Elisabeth , Förster Reinhold 
Published: December 2009

Abstract
T-cell development depends on recruitment of bone marrow–derived precursor cells to the thymus via a multistep adhesion cascade involving the chemokine receptor CCR9. However, CCR9 deficiency does not result in complete abrogation of progenitor entry into the adult thymus. Therefore, we tested the hypothesis that additional chemokine/chemokine receptor systems might play a role in this process. To this end, we generated mice deficient in both CCR9 and CCR7. Deficiency in both chemokine receptors resulted in severely reduced numbers of early T-cell progenitors and in near-complete abrogation of thymus reconstitution. Progenitors in bone marrow and peripheral blood remained largely unaffected in CCR7−/−CCR9−/− mice, and direct intrathymic transfer of precursors from CCR7−/−CCR9−/− mice as well as single-mutant mice showed that intrathymic differentiation of these precursors remained functional. Thus, our data reveal a previously unrecognized role of CCR7 in progenitor seeding of the adult thymus, which is largely masked by compensatory effects of CCR9 signals. In turn, CCR7 signals can partially compensate for CCR9 signals, thus explaining the rather mild phenotype of CCR9−/− mice with respect to progenitor seeding.
Membrane remodeling during reticulocyte maturation
Authors: Liu Jing , Guo Xinhua , Mohandas Narla , Chasis Joel A. , An Xiuli 
Published: December 2009

AbstractThe transition of reticulocytes into erythrocytes is accompanied by extensive changes in the structure and properties of the plasma membrane. These changes include an increase in shear resistance, loss of surface area, and acquisition of a biconcave shape. The processes by which these changes are effected have remained largely undefined. Here we examine how the expression of 30 distinct membrane proteins and their interactions change during murine reticulocyte maturation. We show that tubulin and cytosolic actin are lost, whereas the membrane content of myosin, tropomyosin, intercellular adhesion molecule-4, glucose transporter-4, Na-K-ATPase, sodium/hydrogen exchanger 1, glycophorin A, CD47, Duffy, and Kell is reduced. The degradation of tubulin and actin is, at least in part, through the ubiquitin-proteasome degradation pathway. In regard to the protein-protein interactions, the formation of membrane-associated spectrin tetramers from dimers is unperturbed, whereas the interactions responsible for the formation of the membrane-skeletal junctions are weaker in reticulocytes, as is the attachment of transmembrane proteins to these structures. This weakness, in part, results from the elevated phosphorylation of 4.1R in reticulocytes, which leads to a decrease in shear resistance by reducing its interaction with spectrin and actin. These observations begin to unravel the mechanistic basis of crucial changes accompanying reticulocyte maturation.
Acute erythroid leukemia: a reassessment using criteria refined in the 2008 WHO classification
Authors: Hasserjian Robert P. , Zuo Zhuang , Garcia Christine , Tang Guilin , Kasyan Armen , Luthra Rajyalakshmi , Abruzzo Lynne V. , Kantarjian Hagop M. , Medeiros L. Jeffrey , Wang Sa A. 
Published: December 2009

Abstract
Acute erythroid leukemia (AEL) is a rare type of acute myeloid leukemia (AML) for which diagnostic criteria have been refined in the 2008 World Health Organization (WHO) classification of AML. The relationship of AEL to myelodysplastic syndromes (MDSs) and to AML with myelodysplasia-related changes (AML-MRC) is not clearly defined. We conducted a retrospective, multi-institutional study of patients with AEL and compared them with patients with MDS or AML-MRC with erythroid hyperplasia (≥ 50% erythroid cells). Among a total of 124 patients with AEL, 32% had a history of MDS or chronic cytopenia, 32% had therapy-related disease, and 35% had de novo disease. Sixty-four percent of patients had unfavorable AML risk-group karyotypes. FLT3 and RAS mutations were infrequent, occurring in 6% and 2%, respectively. The median overall survival (OS) of all AEL patients was 8 months, comparable with that of patients with MDS or AML-MRC with erythroid hyperplasia. The OS was related to cytogenetic risk group, but not blast count or morphologic dysplasia. Our findings suggest that AEL is in the continuum of MDS and AML with erythroid hyperplasia, where karyotype rather than an arbitrary blast cutoff represents the most important prognostic factor.