bluuebunny/crossref_metadata_2025_split huggingface dataset:
A computational method for the analysis and prediction of protein:phosphopeptide‐binding sites
Authors: Joughin Brian A. , Tidor Bruce , Yaffe Michael B. 
Published: December 2004

AbstractPhosphopeptide‐binding domains, including the FHA, SH2, WW, WD40, MH2, and Polo‐box domains, as well as the 14‐3‐3 proteins, exert control functions in important processes such as cell growth, division, differentiation, and apoptosis. Structures and mechanisms of phosphopeptide binding are generally diverse, revealing few general principles. A computational method for analysis of phosphopeptide‐binding domains was therefore developed to elucidate the physical and chemical nature of phosphopeptide binding, given this lack of structural similarity. The surfaces of nine phosphopeptide‐binding proteins, representing seven distinct classes of phosphopeptide‐binding modules, were discretized, and encoded with information about amino acid identity, surface curvature, and electrostatic potential at every point on the surface in order to identify local surface properties enriched in phosphoresidue contact sites. Cross‐validation indicated that propensities corresponding to this enrichment calculated from a subset of the training data could be used to predict the phosphoresidue contact site on proteins not used in training with no false negative results, and with few unconfirmed positive predictions. The locations of phosphoresidue contact sites were then predicted on the surfaces of the checkpoint kinase Chk1 and the BRCA1 BRCT repeat domain, and these predictions are consistent with recent experimental evidence.
Characterization of Splenic Glycosaminoglycans Accumulated In Vivo in Experimentally Induced Amyloid‐Susceptible and Amyloid‐Resistant Mice
Authors: Sugumaran G. , Elliott‐Bryant R. , Phung N. , Vitseva O. , Kuberan B. , Lech M. 
Published: December 2004

AbstractThe pathogenesis of the amyloid deposition diseases is poorly understood. The CE/J mouse, which is naturally protected from amyloid A (AA) protein amyloidosis, has provided a tool to study mechanisms that may be implicated in amyloid deposition diseases by means of comparison of findings with those in an AA‐susceptible mouse strain. We have compared proteoglycan/glycosaminoglycan accumulation in vivo in amyloid‐protected CE/J mouse strain and in AA‐susceptible CBA/J mouse strain in homeostasis and when injected with amyloid‐inducing agents. Results indicate that there is an overall increase in [35S]proteoglycan/glycosaminoglycan accumulation in the spleens of both strains of mice, but with a specific increase in heparan sulfate in only CBA/J mouse spleens that are rich in amyloid. Further, we report the absence of heparan sulfate in the splenic perifollicular areas of amyloid‐free CE/J mouse, whereas in the amyloid‐laden CBA/J mouse there is co‐localization of heparan sulfate with the AA deposits. We have also examined the glycosaminoglycan disaccharide products in both these strains of mice for their sulfation positions and found no differences in the disaccharide composition of chondroitin/dermatan sulfate and heparan sulfate isolated from the control CBA/J and control CE/J mice. There were no differences in chondroitin/dermatan sulfate in both strains after experimental induction. However, analysis of the heparan sulfate disaccharides by means of capillary high‐performance liquid chromatography linked to microelectrospray ionization time‐of‐flight mass spectrometry indicated that the disaccharide composition of the splenic heparan sulfate obtained from the treated CBA/J mice that had developed amyloid was markedly different from that obtained from the control CBA/J mice and the treated amyloid‐resistant CE/J mice. These findings suggest that unique heparan sulfates play a fundamental role in the pathogenesis of amyloid.
B‐Lymphocytes Activated by CD40 Ligand Induce an Antigen‐Specific Anti‐Tumour Immune Response by Direct and Indirect Activation of CD8+ T‐cells
Authors: Ritchie D. S. , Yang J. , Hermans I. F. , Ronchese F. 
Published: December 2004

AbstractIn this report, we describe the ability of CD40‐ligand (CD40L)‐activated, antigen‐loaded B‐cells to initiate antigen‐specific anti‐tumour immune responses in vivo. Mice immunized by means of intravenous administration of CD40L‐activated B‐cells loaded with an MHC class‐I‐binding peptide, and challenged with a tumour cell line expressing the same class‐I epitope, showed a marked delay in tumour growth, compared to non‐immunized controls or to mice receiving either freshly isolated B‐cells or B‐cells activated with lipopolysaccharide or interleukin‐4.The ability of CD40L‐activated B‐cells to induce antigen‐specific T‐cell activation appeared to be through a combination of cross‐presentation of antigen from activated B‐cells to resident antigen‐presenting cells and direct T‐cell activation by the administered B‐cells themselves. Immunization with CD40L‐activated B‐cells may, therefore, represent a means by which to stimulate anti‐tumour CD8+ T‐cell responses in vivo.
Activation of Human Umbilical Vein Endothelial Cells Leads to Relocation and Release of High‐Mobility Group Box Chromosomal Protein 1
Authors: Mullins G. E. , Sunden‐Cullberg J. , Johansson A.‐S. , Rouhiainen A. , Erlandsson‐Harris H. , Yang H. , Tracey K. J. , Rauvala H. , Palmblad J. , Andersson J. , Treutiger C. J. 
Published: December 2004

AbstractThe nuclear protein high‐mobility group box chromosomal protein 1 (HMGB1) was recently described to act as a pro‐inflammatory cytokine and as a late mediator of severe sepsis and septic shock. The protein is released from monocytes in response to endotoxin and activates monocytes and endothelial cells through nuclear factor kappa B. We have previously demonstrated that the B‐box of HMGB1 mediates a pro‐inflammatory effect on endothelial cells including the upregulation of cell‐adhesion molecules and release of interleukin (IL)‐8 and granulocyte colony‐stimulating factor. Here, we report that HMGB1 is released from human umbilical vein endothelial cells (HUVEC) in response to lipopolysaccharide (LPS) and tumour necrosis factor (TNF)‐α. A nuclear relocation of HMGB1 to the cytoplasm was seen at 4 h. Subsequently, high amounts of HMGB1 could be seen in the supernatants from stimulated cells after 16 h. It was also observed that the pro‐inflammatory activity of HMGB1 is sensitive to dexamethasone. Interestingly, the HMGB1‐induced TNF‐α release from monocytes could be inhibited by either the A‐box of the protein or the p38 inhibitor CNI‐1493, but neither had any inhibitory effects on the HMGB1‐dependent upregulation of cell‐adhesion molecules on HUVEC. Altogether, these results suggest that HUVEC may be an important source of HMGB1 secretion in response to systemic infection and that endothelial cells and monocytes may use different signalling pathways.
Gene Expression in Human Macrophages Infected with Dengue Virus Serotype‐2
Authors: Moreno‐Altamirano M. M. B. , Romano M. , Legorreta‐Herrera M. , Sánchez‐García F. J. , Colston M. J. 
Published: December 2004

AbstractInfection by any of the four serotypes of dengue viruses (DEN‐1, ‐2, ‐3 and ‐4) may result in either a relatively benign fever, called dengue fever (DF), a fatal disease, such as dengue haemorrhagic fever (DHF) or dengue shock syndrome (DSS). Several lines of evidence suggest that soluble immune response mediators may be involved in the severity of dengue infections. For instance, elevated seric levels of IL‐8 are a common feature in DHF patients. Because other chemokines, cytokines, adhesion molecules, chemokine and cytokine receptors, as well as cytokine‐related molecules may also be involved in dengue virus pathogenesis, we aimed at analysing the gene expression of such molecules in the course of an in vitro DEN‐2 infection of human peripheral blood monocyte‐derived macrophages, a cell type regarded as a primary target for DEN. Nylon membrane gene arrays containing 375 different human cytokine‐related genes were used as a first step to search for differentially expressed genes upon infection. Transcripts for IL‐8, IL‐1β, osteopontin, GRO‐α, ‐β and ‐γ, I‐309, and some other molecules showed to be upregulated upon infection, whereas others such as MIC‐1, CD27L and CD30L, were downregulated. Four genes were selected for reverse transcriptase‐polymerase chain reaction based gene‐expression analysis as a way to partially confirm microarray results. This approach pointed out 25 macrophage‐expressed cytokine‐related genes that could be relevant in DEN‐2 pathogenesis.
Differential Regulation of MHC Class‐I‐Restricted and Unrestricted Cytotoxicity by the Us3 Protein Kinase of Herpes Simplex Virus‐1
Authors: Cartier A. , Masucci M. G. 
Published: December 2004

AbstractModulation of cytotoxic responses by viral immunoevasins plays an important role in the establishment of latent and persistent viral infections. Together with MHC class‐I‐restricted CD8T‐lymphocytes, non‐MHC‐restricted natural killer (NK) and lymphokine‐activated killer (LAK) cells participate in this anti‐viral control. The Us3 protein kinase of herpes simplex virus‐1 (HSV‐1) inhibits CD8T‐cell cytotoxicity, which correlates with the inhibition of granzyme‐B (GrB)‐induced activation of pro‐apoptotic Bid. We have investigated the effect of Us3 on NK and LAK cytotoxicity, because these effectors are believed to share common mechanisms for inducing cell death. We show that, in contrast to their lower sensitivity to CD8T‐cell lysis, HSV‐1‐infected cells are lysed by NK cells or LAK cells as efficiently as the uninfected controls. Both CD8T and NK/LAK effectors were dependent on the activity of GrB and were efficiently blocked by means of treatment with a GrB inhibitor. However, unlike CD8T cells, LAK cells and NK cells failed to induce Bid cleavage, suggesting that various GrB downstream targets be involved in the induction of cell lysis. This finding explains their various sensitivities to viral modulation, which is likely to be important for the respective role of MHC‐restricted and non‐restricted effectors in the control of HSV‐1 infection.
Cyclorraphan yolk proteins and lepidopteran minor yolk proteins originate from two unrelated lipase families
Authors: Hens K. , Lemey P. , Macours N. , Francis C. , Huybrechts R. 
Published: December 2004

AbstractVitellogenins, cyclorraphan yolk proteins and lepidopteran minor yolk proteins are three classes of female‐specific proteins that serve as an embryonic nutritional store. Similarity to vertebrate lipid‐binding proteins was established for vitellogenins and yolk proteins, vitellogenins being related to apolipoprotein B and yolk proteins to lipases. Recently, similarity between yolk proteins and minor yolk proteins was reported and it was suggested that yolk proteins are more related to minor yolk proteins than to vertebrate lipases. In this study, we cloned five additional yolk proteins from the grey fleshfly Neobellieria bullata, formerly known as Sarcophaga bullata. We used this sequence data, combined with sequence data retrieved from the NCBI protein database to evaluate the yolk protein–lipase and the yolk protein–minor yolk protein relationship. We found no similarity between yolk proteins and minor yolk proteins, but we showed that yolk proteins are related to a family of lipases containing vertebrate hepatic and pancreatic lipases while minor yolk proteins are related to a family of lipases containing vertebrate gastric and lingual lipases. The fact that three different classes of yolk storage proteins show similarity to three different classes of vertebrate lipid‐binding proteins strongly suggests that this lipid‐binding feature is important for insect yolk storage proteins.
Infection patterns of o’nyong nyong virus in the malaria‐transmitting mosquito, Anopheles gambiae
Authors: Brault A. C. , Foy B. D. , Myles K. M. , Kelly C. L. H. , Higgs S. , Weaver S. C. , Olson K. E. , Miller B. R. , Powers A. M. 
Published: December 2004

AbstractArthropod‐borne alphaviruses transmitted by mosquitoes almost exclusively use culicines; however, the alphavirus o’nyong‐nyong (ONNV) has the unusual characteristic of being transmitted primarily by anopheline mosquitoes. This unusual attribute makes ONNV a valuable tool in the characterization of mosquito determinants of infection as well as a useful expression system in Anopheles species. We developed a series of recombinant alphaviruses, based upon the genome of ONNV, designed for the expression of heterologous genes. The backbone genome is a full‐length infectious cDNA clone of ONNV from which wild‐type virus can be rescued. Additional constructs are variants of the primary clone and contain the complete genome plus a duplicated subgenomic promoter element with a multiple cloning site for insertion of heterologous genes. We inserted a green fluorescent protein (GFP) gene downstream of this promoter and used it to characterize infection and dissemination patterns of ONNV within An. gambiae mosquitoes. These experiments allowed us to identify atypical sites of initial infection and dissemination patterns in this mosquito species not frequently observed in comparable culicine infections. The utility of these ONNVs for studies in anopheline mosquitoes includes the potential for identification of vector infection determinants and to serve as tools for antimalaria studies. Viruses that can express a heterologous gene in a vector and rapidly and efficiently infect numerous tissues in An. gambiae mosquitoes will be a valuable asset in parasite–mosquito interaction and interference research.
Survivors of childhood acute lymphoblastic leukaemia, with radiation‐induced GH deficiency, exhibit hyperleptinaemia and impaired insulin sensitivity, unaffected by 12 months of GH treatment
Authors: Bülow Birgitta , Link Katarina , Ahrén Bo , Nilsson Ann‐Sofie , Erfurth Eva Marie 
Published: December 2004

SummaryOBJECTIVE  Adult survivors of childhood acute lymphoblastic leukaemia (ALL) often exhibit GH deficiency (GHD), due to prophylactic cranial radiotherapy (CRT). It is not known whether the observed risk for adiposity in these patients is associated with impaired insulin sensitivity and whether the insulin sensitivity is affected by GH replacement therapy.SUBJECTS AND DESIGN  Eleven patients with GHD (median age 29 years), previously given prophylactic CRT for ALL, and 11 sex‐, age‐ and body mass index (BMI)‐matched controls were investigated with bioimpedance analysis (BIA) and analysis of serum leptin, serum free fatty acids (FFA) and serum insulin. Insulin sensitivity was measured by a euglycaemic–hyperinsulinaemic clamp technique (IS‐clamp). Moreover, the effects of 12 months of individually titrated GH treatment (median dose 0·5 mg/day) on these parameters were investigated.RESULTS  At baseline, the patients had lower fat free mass (FFM) (P = 0·003), higher percentage fat mass (FM) (P = 0·05), serum insulin (P = 0·02) and serum leptin/kg FM (P = 0·01) than controls. The patients had a tendency towards impaired IS‐clamp (P = 0·06), which disappeared after correction for body composition (IS‐clamp/kg FFM; P > 0·5). In the patients, time since CRT was positively correlated with percentage FM (r = 0·70, P = 0·02), and there was an independent negative association between serum FFA and IS‐clamp (P = 0·05). Twelve months of GH treatment increased serum IGF‐I (P = 0·003) and FFM (P = 0·02) and decreased percentage FM (P = 0·03), but no significant changes were seen in serum leptin/kg FM, serum FFA, FFA‐clamp, serum insulin or IS‐clamp (all, P ≥ 0·2).CONCLUSIONS  Young adult survivors of childhood ALL with GHD had increased fat mass, hyperleptinaemia and impaired insulin sensitivity, which could be a consequence of radiation‐induced impairment of GH secretion or mediated by other hypothalamic dysfunctions, such as leptin resistance or other unknown factors, affected by CRT. Twelve months of individualized GH replacement therapy led to positive effects on body composition, but the hyperleptinaemia, hyperinsulinaemia and the impaired insulin sensitivity remained unchanged.
Seminal elastase‐inhibitor complex, a marker of genital tract inflammation, and negative IVF outcome measures: role for a silent inflammation?
Authors: Zorn Branko , Virant‐klun Irma , Vidmar Gaj , Sešek‐Briški Alenka , Kolbezen Mojca , Meden‐vrtovec Helena 
Published: December 2004

SummaryThere is no consensus on whether and how male genital tract inflammation affects sperm fertilizing potential. The aims of this prospective study were to evaluate the elastase‐inhibitor complex in seminal plasma (s‐EI) level, a marker of male genital tract inflammation, in men undergoing in vitro fertilization (IVF) having no clinical signs of inflammation, and its association with semen characteristics, and the predictive role of s‐EI for the outcome of IVF in terms of fertilization, embryo development to the blastocyst stage and pregnancy. The study involved 104 male partners of infertile couples with normal spermiogram undergoing IVF. On the day of oocyte retrieval, spermiogram and s‐EI assessment using homogeneous immunoassay were performed. The outcome of IVF according to the s‐EI level was assessed in 85 cycles with two or more oocytes. In 67 cycles embryos were cultured to the blastocyst stage. Spearman's and Pearson's correlation tests, chi‐square test, and multiple linear and logistic regression analyses were used for statistical evaluation. Increased s‐EI level (≥250 μg/L) was detected in semen of 32% of men, and in 24% of men without leucocytospermia. We found an association between the s‐EI level and semen leucocytes (r = 0.49, p = 0.004) but not with classical sperm characteristics. No correlation between the s‐EI level and fertilization was observed. Increased s‐EI levels were associated with a poorer blastocyst development rate (p = 0.03) and a higher number of arrested embryos (p = 0.04). Extended embryo culture to the blastocyst stage shows a negative effect of clinically silent male genital tract inflammation on embryo developmental potential.
Hormonal regulation of spermatogenesis
Authors: Holdcraft Robert W. , Braun Robert E. 
Published: December 2004

SummaryProper functioning of the mammalian testis is dependent upon an array of hormonal messengers acting through endocrine, paracrine, and autocrine pathways. Within the testis, the primary messengers are the gonadotrophins, follicle stimulating hormone and luteinizing hormone, and the androgens. Abundant evidence indicates that the role of the gonadotrophins is to maintain proper functioning of testicular somatic cells. It is the androgens, primarily testosterone, which act through the somatic cells to regulate germ cell differentiation. Despite extensive research in this area, little is known about the cell‐specific requirements for androgens and even less is understood about the downstream effectors of androgen signalling. However, recent work using cell‐specific ablation of androgen receptor function has demonstrated a clear requirement for androgen signalling at multiple, discrete time points during spermatogenesis. These models also provide useful tools for identifying the targets of androgen receptor activity. The purpose of this review is to provide a brief overview of recent advances in our understanding of hormonal regulation of spermatogenesis, with an emphasis on the role of testosterone within the testis, and to pose important questions for future research in this field.
The links between allergen skin test sensitivity, airway responsiveness and airway response to allergen
Authors: Cockcroft D. W. , Davis B. E. , Boulet L.‐P. , Deschesnes F. , Gauvreau G. M. , O'Byrne P. M. , Watson R. M. 
Published: December 2004

Background:  The allergen‐induced early asthmatic response [provocation concentration (PC)20, the concentration causing a 20% forced expiratory volume in 1 s (FEV)1 fall] depends on the level of IgE sensitivity and the degree of nonallergic airway hyperresponsiveness (AHR) and can be predicted from histamine PC20 and allergen skin test endpoint.Objectives:  We examined the relationships between allergen PC20, methacholine PC20, and allergen skin test endpoint and assessed the accuracy of both the histamine PC20‐based prediction of allergen PC20 (using methacholine) and a new methacholine PC20‐based prediction equation.Methods:  From 158 allergen challenges, the allergen PC20, the methacholine PC20, and the skin test endpoint were recorded and relationships between these three were sought. We compared the measured allergen PC20 to that predicted from the previous histamine PC20‐based and the new methacholine‐based formulae.Results:  In single regressions, allergen PC20 correlated with both methacholine PC20 (r = 0.25, P = 0.0015) and skin test endpoint (r = 0.52, P < 0.00005). The relationship was improved by multiple regression of log‐allergen PC20vs. log‐methacholine PC20 and log‐endpoint (r = 0.61, P < 0.00005). The histamine‐based formula predicted allergen PC20 to within 2 doubling concentrations in 80% and within 3 in 92%. The new methacholine‐based formula to within 2 and 3 concentrations in 81% and 94%, respectively; only nine of 158 subjects were outside the 3 concentrations.Conclusions:  We have confirmed the dependence of the allergen‐induced early asthmatic response upon the level of allergic sensitivity and the degree of AHR, the latter as assessed by methacholine challenge. The allergen PC20 can be predicted to within 3 doubling concentrations in 94% of cases.
Association of hepatitis A virus infection with allergic sensitization in a population with high prevalence of hepatitis A virus exposure
Authors: Gonzalez‐Quintela A. , Gude F. , Boquete O. , Aguilera A. , Rey J. , Meijide L. M. , Fernandez‐Merino M. C. , Vidal C. 
Published: December 2004

Background:  An inverse association between allergic sensitization and markers of exposure to food‐borne and orofecal infections (particularly hepatitis A virus, HAV) has been reported. The prevalence of HAV exposure and allergic sensitization vary widely in different areas, and vary along with age within a given area.Aim:  To investigate the association between HAV exposure and allergic sensitization in adults from a mostly rural area of Spain.Methods:  An age‐stratified random sample of 720 subjects was drawn from the population older than 18 years of A‐Estrada, Spain. From 697 eligible subjects, 469 (67.2%, median age 54 years, range: 18–92) participated in the study. Positive skin prick tests to a panel of aeroallergens defined allergic sensitization. Positive serum HAV antibodies (assayed in 465 subjects) defined HAV exposure.Results:  The prevalence of HAV exposure was 83.6% (95% CI: 80.7–86.5). The prevalence of allergic sensitization was lower in subjects with HAV exposure than in patients without it (25.0%vs 40.0%, OR 0.44, 95% CI: 0.25–0.77, P = 0.004), but this association became substantially altered after adjusting for age, which was closely linked to both allergic sensitization and HAV exposure (adjusted OR 1.15, 95% CI: 0.60–2.19, P = 0.66).Conclusions:  In a population with high prevalence of HAV exposure, no significant association between HAV exposure and allergic sensitization is observed after controlling for the confounding effect of age.
Biscogniauxia nummularia: pathogenic agent of a beech decline
Authors: Granata G. , Sidoti A. 
Published: December 2004

SummaryDecline of European beech (Fagus sylvatica) in Sicily and Calabria (Italy) was observed to be associated with the ascomycete Biscogniauxia nummularia. This fungus is naturally present in beech stands and to date has not been considered a primary pathogenic agent. Artificial inoculations were performed to assess its pathogenicity on beech and to determine if Sicilian and Calabrian isolates differ in virulence. Biscogniauxia nummularia played an evident primary pathogenic role under the environmental conditions studied. Virulence of the isolates was variable and did not depend neither on the geographic origin nor the environmental conditions at the sites where pathogenicity testing was performed.