bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel aminopeptidase in the fat body of the moth Achaea janata as a receptor for Bacillus thuringiensis Cry toxins and its comparison with midgut aminopeptidase
Authors: Budatha Madhusudhan , Meur Gargi , Dutta-Gupta Aparna 
Published: June 2007

Bacillus thuringiensis insecticidal crystal proteins bind to cell-surface receptors which represent a family of aminopeptidases [APN (aminopeptidase N)] present on the brush border membrane of insect midgut cells of susceptible insects leading to pore formation and death of the insect. We report here for the first time the presence of a novel APN in the fat body of the moth Achaea janata. Northern blotting detected at least one APN-specific transcript in the fat body, whereas two transcripts of different sizes were detected in the midgut. We have cloned two full-length APN cDNAs of 3015 bp and 2850 bp from fat body and midgut respectively, which encode proteins of 1004 and 950 amino acids. These two APNs share only 33% amino acid sequence identity, but both display the typical APN features, such as the N-terminal signal peptide, several putative glycosylation sites, C-terminal glycosylphosphatidylinositol anchor signal, the APN-specific zinc-binding/gluzincin motif HEXXHX18E and gluzincin motif GAMENWG. The fat body APN manifested a variation in its expression with respect to tissue and developmental stage. In spite of the abundance of the APN transcript in the fat body, fairly low APN activity was detected in this tissue. The fat-body- and midgut-specific APNs showed differential interaction with various Cry1A toxins. Besides, the level of toxicity of different Cry subtypes varied enormously with mode/site of delivery, such as intrahaemocoelic injections and feeding bioassays. These data indicate that the fat body might be a potential alternative Cry toxin target site in the moth.
Context-sensitive data integration and prediction of biological networks
Authors: Myers Chad L. , Troyanskaya Olga G. 
Published: June 2007

AbstractMotivation: Several recent methods have addressed the problem of heterogeneous data integration and network prediction by modeling the noise inherent in high-throughput genomic datasets, which can dramatically improve specificity and sensitivity and allow the robust integration of datasets with heterogeneous properties.However, experimental technologies capture different biological processes with varying degrees of success, and thus, each source of genomic data can vary in relevance depending on the biological process one is interested in predicting. Accounting for this variation can significantly improve network prediction, but to our knowledge, no previous approaches have explicitly leveraged this critical information about biological context.Results: We confirm the presence of context-dependent variation in functional genomic data and propose a Bayesian approach for context-sensitive integration and query-based recovery of biological process-specific networks. By applying this method to Saccharomyces cerevisiae, we demonstrate that leveraging contextual information can significantly improve the precision of network predictions, including assignment for uncharacterized genes. We expect that this general context-sensitive approach can be applied to other organisms and prediction scenarios.Availability: A software implementation of our approach is available on request from the authors.Contact: ogt@genomics.princeton.eduSupplementary information: Supplementary data are available at http://avis.princeton.edu/contextPIXIE/
Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms
Authors: Glyakina Anna V. , Garbuzynskiy Sergiy O. , Lobanov Michail Yu. , Galzitskaya Oxana V. 
Published: June 2007

AbstractMotivation: Understanding the basis of protein stability in thermophilic organisms raises a general question: what structural properties of proteins are responsible for the higher thermostability of proteins from thermophilic organisms compared to proteins from mesophilic organisms?Results: A unique database of 373 structurally well-aligned protein pairs from thermophilic and mesophilic organisms is constructed. Comparison of proteins from thermophilic and mesophilic organisms has shown that the external, water-accessible residues of the first group are more closely packed than those of the second. Packing of interior parts of proteins (residues inaccessible to water molecules) is the same in both cases. The analysis of amino acid composition of external residues of proteins from thermophilic organisms revealed an increased fraction of such amino acids as Lys, Arg and Glu, and a decreased fraction of Ala, Asp, Asn, Gln, Thr, Ser and His. Our theoretical investigation of folding/unfolding behavior confirms the experimental observations that the interactions that differ in thermophilic and mesophilic proteins form only after the passing of the transition state during folding. Thus, different packing of external residues can explain differences in thermostability of proteins from thermophilic and mesophilic organisms.Availability: The database of 373 structurally well-aligned protein pairs is available at http://phys.protres.ru/resources/termo_meso_base.htmlContact: ogalzit@vega.protres.ruSupplementary information: Supplementary data are available at Bioinformatics online.
Orphan nuclear receptor NGFI‐B forms dimers with nonclassical interface
Authors: Calgaro Marcos R. , Neto Mario de Oliveira , Figueira Ana Carolina M. , Santos Maria A.M. , Portugal Rodrigo V. , Guzzi Carolina A. , Saidemberg Daniel M. , Bleicher Lucas , Vernal Javier , Fernandez Pablo , Terenzi Hernán , Palma Mario Sergio , Polikarpov Igor 
Published: June 2007

AbstractThe orphan receptor nerve growth factor‐induced B (NGFI‐B) is a member of the nuclear receptor's subfamily 4A (Nr4a). NGFI‐B was shown to be capable of binding both as a monomer to an extended half‐site containing a single AAAGGTCA motif and also as a homodimer to a widely separated everted repeat, as opposed to a large number of nuclear receptors that recognize and bind specific DNA sequences predominantly as homo‐ and/or heterodimers. To unveil the structural organization of NGFI‐B in solution, we determined the quaternary structure of the NGFI‐B LBD by a combination of ab initio procedures from small‐angle X‐ray scattering (SAXS) data and hydrogen–deuterium exchange followed by mass spectrometry. Here we report that the protein forms dimers in solution with a radius of gyration of 2.9 nm and maximum dimension of 9.0 nm. We also show that the NGFI‐B LBD dimer is V‐shaped, with the opening angle significantly larger than that of classical dimer's exemplified by estrogen receptor (ER) or retinoid X receptor (RXR). Surprisingly, NGFI‐B dimers formation does not occur via the classical nuclear receptor dimerization interface exemplified by ER and RXR, but instead, involves an extended surface area composed of the loop between helices 3 and 4 and C‐terminal fraction of the helix 3. Remarkably, the NGFI‐B dimer interface is similar to the dimerization interface earlier revealed for glucocorticoid nuclear receptor (GR), which might be relevant to the recognition of cognate DNA response elements by NGFI‐B and to antagonism of NGFI‐B–dependent transcription exercised by GR in cells.
Probing mechanisms of resistance to the tuberculosis drug isoniazid: Conformational changes caused by inhibition of InhA, the enoyl reductase from Mycobacterium tuberculosis
Authors: Kruh Nicole A. , Rawat Richa , Ruzsicska Béla P. , Tonge Peter J. 
Published: June 2007

AbstractThe frontline tuberculosis drug isoniazid (INH) inhibits InhA, the NADH‐dependent fatty acid biosynthesis (FAS‐II) enoyl reductase from Mycobacterium tuberculosis (MTB), via formation of a covalent adduct with NAD+ (the INH‐NAD adduct). Resistance to INH can be correlated with many mutations in MTB, some of which are localized in the InhA cofactor binding site. While the InhA mutations cause a substantial decrease in the affinity of InhA for NADH, surprisingly the same mutations result in only a small impact on binding of the INH‐NAD adduct. Based on the knowledge that InhA interacts in vivo with other components of the FAS‐II pathway, we have initiated experiments to determine whether enzyme inhibition results in structural changes that could affect protein–protein interactions involving InhA and how these ligand‐induced conformational changes are modulated in the InhA mutants. Significantly, while NADH binding to wild‐type InhA is hyperbolic, the InhA mutants bind the cofactor with positive cooperativity, suggesting that the mutations permit access to a second conformational state of the protein. While cross‐linking studies indicate that enzyme inhibition causes dissociation of the InhA tetramer into dimers, analytical ultracentrifugation and size exclusion chromatography reveal that ligand binding causes a conformational change in the protein that prevents cross‐linking across one of the dimer–dimer interfaces in the InhA tetramer. Interestingly, a similar ligand‐induced conformational change is also observed for the InhA mutants, indicating that the mutations modulate communication between the subunits without affecting the two conformational states of the protein that are present.
The role of protein homochirality in shaping the energy landscape of folding
Authors: Nanda Vikas , Andrianarijaona Aina , Narayanan Chitra 
Published: June 2007

AbstractThe homochirality, or isotacticity, of the natural amino acids facilitates the formation of regular secondary structures such as α‐helices and β‐sheets. However, many examples exist in nature where novel polypeptide topologies use both l‐ and d‐amino acids. In this study, we explore how stereochemistry of the polypeptide backbone influences basic properties such as compactness and the size of fold space by simulating both lattice and all‐atom polypeptide chains. We formulate a rectangular lattice chain model in both two and three dimensions, where monomers are chiral, having the effect of restricting local conformation. Syndiotactic chains with alternating chirality of adjacent monomers have a very large ensemble of accessible conformations characterized predominantly by extended structures. Isotactic chains on the other hand, have far fewer possible conformations and a significant fraction of these are compact. Syndiotactic chains are often unable to access maximally compact states available to their isotactic counterparts of the same length. Similar features are observed in all‐atom models of isotactic versus syndiotactic polyalanine. Our results suggest that protein isotacticity has evolved to increase the enthalpy of chain collapse by facilitating compact helical states and to reduce the entropic cost of folding by restricting the size of the unfolded ensemble of competing states.
Effect of Asp69 and Arg310 on the pK of His68, a key catalytic residue of adenylosuccinate lyase
Authors: Sivendran Sharmila , Segall Mark L. , Rancy Pumtiwitt C. , Colman Roberta F. 
Published: June 2007

AbstractAdenylosuccinate lyase (ASL) of Bacillus subtilis contains three conserved histidines, His68, His89, and His141, identified by affinity labeling and site‐directed mutagenesis as critical to the intersubunit catalytic site. The pH‐Vmax profile for wild‐type ASL is bell‐shaped (pK1 = 6.74 and pK2 = 8.28). Only the alkaline side changes with temperature, characteristic of histidine pKs. To identify determinants of pK2 in the enzyme‐substrate complex, we replaced residues at two positions close to His68 (but not to His89 or His141) in the structure. Compared with the specific activity of 1.75 μmol adenylosuccinate reacting/min/mg of wild‐type enzyme at pH 7.0, mutant enzymes D69E, D69N, R310Q, and R310K exhibit specific activities of 0.40, 0.04, 0.00083, and 0.10, respectively. While D69E has a Km for adenylosuccinate similar to that of wild‐type ASL, D69N and R310K exhibit modest increases in Km, and R310Q has an 11‐fold increase in Km. The mutant enzymes show no significant change in molecular weight or secondary structure. The major change is in the pH‐Vmax profile: pK2 is 8.48 for the D69E mutant and is decreased to 7.83 in D69N, suggesting a proximal negative charge is needed to maintain the high pK of 8.28 observed for wild‐type enzyme and attributed to His68. Similarly, R310Q exhibits a decrease in its pK2 (7.33), whereas R310K shows little change in pK2 (8.24). These results suggest that Asp69 interacts with His68, that Arg310 interacts with and orients the β‐carboxylate of Asp69, and that His68 must be protonated for ASL to be active.
Clinical experience with a highly purified factor IX concentrate in patients undergoing surgical operations
Authors: Thomas D. P. , Lee C. A. , Colvin B. T. , Dasani H. , Dolan G. , Giangrande P. L. F. , Jones P. , Lucas G. , Cantwell O. , Harman C. T. 
Published: June 2007

SummaryThe haemostatic efficacy of a new highly purified factor IX concentrate, prepared by metal chelate affinity chromatography, was assessed in 13 patients with haemophilia B undergoing a variety of surgical operations. Four of the patients had developed post‐operative thromboembolic complications following previous operations, when treated with a prothrombin complex concentrate. None of the patients in the present series developed any evidence of post‐operative thrombotic complications. Effective haemostasis was achieved in all patients, with the exception of a surgical bleed in one case, and late post‐operative bleeding in a second patient when the factor IX activity fell below 20iu/dl. The product is treated with a solvent‐detergent process that destroys lipid‐enveloped viruses, while the affinity chromatography process during manufacture removes in excess of 4 log10 of a non‐lipid‐enveloped virus. In follow‐up studies, none of the patients has shown evidence of fresh infection from the concentrate, when assessed by virological markers. It is concluded that this high‐purity concentrate (tradenane ‘Replenine’) is effective for the treatment of patients with haemophilia B who undergo surgical operations.
Prophylaxis for Pneumocystis carinii pneumonia: its impact on the natural history of HIV infection in men with haemophilia
Authors: Sabin Caroline A. , Elford Jonathan , Phillips Andrew N. , Janossy George , Lee Christine A. 
Published: June 2007

SummaryIt has been suggested that the range of AIDS‐defining conditions witnessed in patients with HIV infection has changed since the early years of the HIV epidemic. In this paper we consider the range of AIDS‐defining conditions in a cohort of 111 HIV‐positive men with haemophilia registered at the Royal Free Hospital Haemophilia Centre. In particular we assess whether the incidence of Pneumocystis carinii pneumonia (PCP) has changed over time. The men were all infected between 1979 and 1985 after treatment with infected blood products and have now been followed prospectively for up to 13 years from HIV seroconversion. By the end of 1992, 44/111 patients had developed AIDS. Of the 44 men, 18 (41%) presented with PCP as their first AIDS‐defining condition (ADC), mainly before the initiation of primary prophylaxis in 1989. The remaining 26 patients presented with a range of conditions as their first ADC, but there were no more than four cases in any one disease category. It is estimated that patients suffer from 0.7 further ADCs per year after being diagnosed with AIDS. After taking account of the increased levels of immuno‐suppression in the cohort with time, it appears that the incidence of PCP, both as the first ADC or as any ADC, has declined since the introduction of primary prophylaxis for the disease in 1989. However, non‐compliance with prophylaxis for PCP appears to have played a major role in the continuing occurrence of PCP since 1988. Improvements in compliance with therapy should result in a further reduction in the incidence of PCP both as a first ADC and as any ADC.
Long‐term surveillance for human anti‐murine antibodies of a group of haemophiliacs treated only with immunoaffinity‐purified FVIII concentrates
Authors: BRACKMANN H. H. , GOMPERTS E. D. , COURTER S. C. , VIDOR A. , O'BRIEN S. , OLDENBURG J. 
Published: June 2007

SummaryAn immunoaffinity purified, solvent/detergent virally inactivated factor VIII (FVIII) concentrate (Hemofil® M) has been in clinical use in persons with haemophilia A since March 1987 and under clinical trial prior to licencing in the USA, Europe and Japan.The specification set and consistently met for the monoclonal antibody (mAb) content of the final product is 0.1 ng/IU FVIII. This level was considered non‐immunogenic, based upon animal studies, recommendations of the European PHarmacopoeia with ovalbumin contamination of influenza vaccine and also the experience during clinical research studies using aAb for diagnostic or other clinical purpose as reported in the medical literature.This research communication documents the surveillance for human anti‐murine antibodies (HAMA) in 13 patients with serve haemophilia A. These patients have been treated with a large amount of product (mean 14,026 IU), numerous different lots of Hemofil M (total 45; mean 17) over a substantial period of time (mean 28 months).The data generated from this group of 13 patients before and during therapeutic Hemofil M administration failed to show the development of any HAMA response at any timepoint. Therefore Hemofil M prepared by mAb resin immunoaffinity column chromatography under the currently set specifications for mAb contaminant of 0.1 ng/IU FVIII or less is a safe therapeutic agent in the management and prevention of bleeding episodes in persons with haemophilia A.
Spontaneous infection of soft tissue haematomas in two HIV seropositive haemophilia patients
Authors: MERCHAN E. C. RODRIGUEZ , VILLAR ANA , MAGALLON MANUEL , DE ORBE ARANZAZU 
Published: June 2007

SummaryTwo HIV seropostiive haemophilic patients with spontaneous infected soft tissue haematomas are described. In one patient the prepatellar bursa was infected, and in the other the posterior aspect of the shoulder. Treatmetn included evacuation of the suppurative focus, antibiotic therapy and prompt rehabilitation. The results were good in both cases and therefore operative management is recommended.
Clinical experience of factor XI deficiency: the role of fresh frozen plasma and factor XI concentrate
Authors: COLLINS P.W. , GOLDMAN E. , LILLEY P. , PASI K. J. , LEE C. A. 
Published: June 2007

Summary. Factor XI deficiency is a rare autosomally transmitted coagulopathy that is associated with a variable bleeding tendency. Recently there have been reports of thrombotic events following the administration of a virally inactivated factor XI concentrate (BPL) to factor XI deficient patients. We have therefore reviewed a single centre's experience of the use of factor XI concentrate over a 6‐year period and compared this to our previous experience of either no treatment or treatment with fresh frozen plasma (FFP) in 103 patients.There were 156 procedures performed without haemo‐ static cover. The incidence of bleeding was greatest following tonsillectomy (71%) and dental extraction (Sl'h). There was a trend for bleeding complications to be associated with lower levels of factor XI but patients with all levels of factor XI suffered bleeding complica‐ tions. There were 38 procedures carried out under FFP cover, with only one patient suffering excessive bleeding and no serious complications.Factor XI concentrate was given to 25 patients to cover 45 episodes. There were no bleeding complications. Three patients suffered serious complications. One patient, with a previous history of cardiovascular disease, died of a myocardial infarction and a second had an ischaemic episode resulting in a %day hospital admission. These episodes both occurred on the same day as the factor XI infusion. A third patient suffered bilateral pulmonary emboli 7 weeks after a prolonged course of factor XI concentrate.These finding suggest that factor XI concentrate should be contraindicated in patients with a history of cardiovascular disease, when FFP should be used. Guide‐ lines for the use of factor XI concentrates should be revised, and work performed to establish the mechanism of these thrombotic events.
Resection of the radial head and partial open synovectomy of the elbow in the young adult with haemophilia: long‐term results
Authors: MERCHAN E. C. RODRIGUEZ , GALINDO E. , MAGALLON M. , GAGO J. , VILLAR A. , SANJURJO M. J. 
Published: June 2007

SummaryResection of the radial head and partial open synovectomy of the elbow have been used in the treatment of repeated haemarthroses of the elbows in 15 patients with haemophilia. The indications for the index operation were: severe pain and bleeding in the elbow that occurred in spite of appropriate, episodic, replacement therapy over a period of more than 6 months, associated with hypertrophy of the radial head and a significant loss of pronation‐supination.The long‐term results were assessed retrospectively according to the classification recommended by the Orthopaedic Advisory Committee of the World Federation of Hemophilia. In the operated group, three patients had a good result, seven were fair, and five poor. It is concluded that this procedure appears to reduce the incidence of haemarthrosis but did not slow the rate of evolution of radiographic changes.
Counselling challenges in haemophilia and HIV infection/AIDS
Authors: PITTADAKI JANE 
Published: June 2007

Summary. The advent of AIDS has had such a deep‐reaching effect on the international haemophilia community that one can make a reasonable distinction between a pre‐AIDS and a post‐AIDS era in haemophilia management. In the context of counselling, however, talking about a ‘before’ and an ‘after’ in haemophilia does not (and, in our opinion, should not) necessarily imply a separation of the past from the present. Dealing with the psycho‐social implications of haemophilia and HIV infection does not mean focusing exclusively on HIV‐generated problems at the expense of haemophilia‐related issues.Since the HIV crisis, counselling has posed the multiple challenge of: (a) assessing and alleviating the more immediate emotional effects of HIV infection; (b) paying due attention to the underlying influence of haemophilia on reaction, defence and coping; (c) formulating a flexible approach that is based on close cooperation with the medical staff and effective interpersonal communication with the counsellees.*In practice, the flexibility and effectiveness of the counselling model are promoted by means of: (a) ongoing counselling, (b) multiple counselling sites (i.e. the Haemophilia Centre and other appropriate locations), (c) interdisciplinary team‐work, (d) respect for individual/ ethnic values, (e) maintenance of exo‐empathy (i.e. neutrality), and (f) transfer of coping skills.The above framework can help maximize the effectiveness of counselling sessions through a personalized rapport of mutual trust and confidence between the counselling team and the counsellees.