bluuebunny/crossref_metadata_2025 huggingface dataset:
A first approach to the usefulness of cytochrome c oxidase I barcodes in the identification of closely related delphinid cetacean species
Authors: Amaral A. R. , Sequeira M. , Coelho M. M.
Published: June 2007

The DNA barcode initiative has gained particular popularity as a promising tool to assist in species identification by using a single mitochondrial gene, cytochrome c oxidase I (COI). In some animal groups, COI barcodes have proved efficient in separating closely related taxa. However, several issues remain for discussion, namely how efficient this tool will be in animal groups with an unresolved taxonomy. Here, we examined COI sequences in delphinid cetaceans, a group where taxonomic uncertainty still exists. We analysed species belonging to the genera Stenella, Tursiops and Delphinus in the North-east Atlantic using cytochrome b gene sequences for comparison. We obtained values of COI interspecific genetic divergence ranging from 1.47% to 2.45%, which suggests a recent separation of the analysed taxa. S. coeruleoalba and D. delphis were the most similar species, with COI phylogenetic trees failing to separate them. On the other hand, the phylogenetic tree obtained with cytochrome b sequences correctly clustered species with high bootstrap support values. We thus consider that the application of COI barcodes in delphinid cetaceans should be done with caution; not only has the cytochrome b gene been shown to be phylogenetically more informative, but relying only on mitochondrial DNA genes alone may be problematic.
Negative regulation of MDA5- but not RIG-I-mediated innate antiviral signaling by the dihydroxyacetone kinase
Authors: Diao Feici , Li Shu , Tian Yang , Zhang Min , Xu Liang-Guo , Zhang Yan , Wang Rui-Peng , Chen Danying , Zhai Zhonghe , Zhong Bo , Tien Po , Shu Hong-Bing
Published: June 2007

Viral infection leads to activation of the transcription factors interferon regulatory factor-3 and NF-κB, which collaborate to induce type I IFNs. The RNA helicase proteins RIG-I and MDA5 were recently identified as two cytoplasmic viral RNA sensors that recognize different species of viral RNAs produced during viral replication. In this study, we identified DAK, a functionally unknown dihydroacetone kinase, as a specific MDA5-interacting protein. DAK was associated with MDA5, but not RIG-I, under physiological conditions. Overexpression of DAK inhibited MDA5- but not RIG-I- or TLR3-mediated IFN-β induction. Overexpression of DAK also inhibited cytoplasmic dsRNA and SeV-induced activation of the IFN-β promoter, whereas knockdown of endogenous DAK by RNAi activated the IFN-β promoter, and increased cytoplasmic dsRNA- or SeV-triggered activation of the IFN-β promoter. In addition, overexpression of DAK inhibited MDA5- but not RIG-I-mediated antiviral activity, whereas DAK RNAi increased cytoplasmic dsRNA-triggered antiviral activity. These findings suggest that DAK is a physiological suppressor of MDA5 and specifically inhibits MDA5- but not RIG-I-mediated innate antiviral signaling.
Integrin α11 regulates IGF2 expression in fibroblasts to enhance tumorigenicity of human non-small-cell lung cancer cells
Authors: Zhu Chang-Qi , Popova Svetlana N. , Brown Ewan R. S. , Barsyte-Lovejoy Dalia , Navab Roya , Shih Warren , Li Ming , Lu Ming , Jurisica Igor , Penn Linda Z. , Gullberg Donald , Tsao Ming-Sound
Published: June 2007

Integrin α11 (ITGA11/α11) is localized to stromal fibroblasts and commonly overexpressed in non-small-cell lung carcinoma (NSCLC). We hypothesized that stromal α11 could be important for the tumorigenicity of NSCLC cells. SV40 immortalized mouse embryonic fibroblasts established from wild-type (WT) andItga11-deficient [knockout (KO)] mice were tested for their tumorigenicity in immune-deficient mice when implanted alone or coimplanted with the A549 human lung adenocarcinoma cells. A549 coimplanted with the fibroblasts showed a markedly enhanced tumor growth rate compared with A549, WT, or KO, which alone formed only small tumors. Importantly, the growth was significantly greater for A549+WT compared with A549+KO tumors. Reexpression of human α11 cDNA in KO cells rescued a tumor growth rate to that comparable with the A549+WT tumors. These findings were validated in two other NSCLC cell lines, NCI-H460 and NCI-H520. Gene expression profiling indicated that IGF2 mRNA expression level was >200 times lower in A549+KO compared with A549+WT tumors. Stable short-hairpin RNA (shRNA) down-regulation of IGF2 in WT (WTshIGF2) fibroblasts resulted in a decreased growth rate of A549+WTshIGF2, compared with A549+WT tumors. The results indicate that α11 is an important stromal factor in NSCLC and propose a paradigm for carcinoma–stromal interaction indirectly through interaction between the matrix collagen and stromal fibroblasts to stimulate cancer cell growth.
Let-7 expression defines two differentiation stages of cancer
Authors: Shell Scott , Park Sun-Mi , Radjabi Amir Reza , Schickel Robert , Kistner Emily O. , Jewell David A. , Feig Christine , Lengyel Ernst , Peter Marcus E.
Published: June 2007

The early phases of carcinogenesis resemble embryonic development, often involving the reexpression of embryonic mesenchymal genes. The NCI60 panel of human tumor cell lines can genetically be subdivided into two superclusters (SCs) that correspond to CD95 Type I and II cells. SC1 cells are characterized by a mesenchymal and SC2 cells by an epithelial gene signature, suggesting that SC1 cells represent less differentiated, advanced stages of cancer. miRNAs are small 20- to 22-nucleotide-long noncoding RNAs that inhibit gene expression at the posttranscriptional level. By performing miRNA expression analysis on 10 Type I and 10 Type II cells, we have determined that SC1 cells express low and SC2 cells high levels of the miRNA let-7, respectively, suggesting that let-7 is a marker for less advanced cancers. Expression of the let-7 target high-mobility group A2 (HMGA2), an early embryonic gene, but not of classical epithelial or mesenchymal markers such as E-cadherin or vimentin, inversely correlated with let-7 expression in SC1 and SC2 cells. Using ovarian cancer as a model, we demonstrate that expression of let-7 and HMGA2 is a better predictor of prognosis than classical markers such as E-cadherin, vimentin, and Snail. These data identify loss of let-7 expression as a marker for less differentiated cancer.
Open Reading Frame 8a of the Human Severe Acute Respiratory Syndrome Coronavirus Not Only Promotes Viral Replication but Also Induces Apoptosis
Authors: Chen Chia-Yen , Ping Yueh-Hsin , Lee Hsin-Chen , Chen Kuan-Hsuan , Lee Yuan-Ming , Chan Yu-Juin , Lien Te-Cheng , Jap Tjin-Shing , Lin Chi-Hung , Kao Lung-Sen , Chen Yi-Ming Arthur
Published: June 2007

Background

A unique genomic difference between human and civet severe acute respiratory syndrome coronaviruses (SARS-CoVs) is that the former has a deletion of 29 nucleotides from open reading frame (orf) 8d that results in the generation of orf8a and orf8b. The objectives of the present study were to analyze antibody reactivity to ORF8a in patients with SARS and to elucidate the function of ORF8a.

Methods

Western-blot and immunofluorescent antibody assays were used to detect anti-ORF8a antibody. SARS-CoV HKU39849 was used to infect stable clones expressing ORF8a and cells transfected with small interfering RNA (siRNA). The virus loads (VLs) and cytopathic effects (CPEs) were recorded. Confocal microscopy and several mitochondria-related tests were used to study the function of ORF8a.

Results

Two (5.4%) of 37 patients with SARS had anti-ORF8a antibodies. The VLs in the stable clones expressing ORF8a were significantly higher than those in control subjects 5 days after infection. siRNA against orf8a significantly reduced VLs and interrupted the CPE. ORF8a was found to be localized in mitochondria, and overexpression resulted in increases in mitochondrial transmembrane potential, reactive oxygen species production, caspase 3 activity, and cellular apoptosis.

Conclusions

ORF8a not only enhances viral replication but also induces apoptosis through a mitochondria-dependent pathway.
Analysis and identification of β-turn types using multinomial logistic regression and artificial neural network
Authors: Poursheikhali Asgary Mehdi , Jahandideh Samad , Abdolmaleki Parviz , Kazemnejad Anoshirvan
Published: June 2007

Motivation: So far various statistical and machine learning techniques applied for prediction of β-turns. The majority of these techniques have been only focused on the prediction of β-turn location in proteins. We developed a hybrid approach for analysis and prediction of different types of β-turn.

Results: A two-stage hybrid model developed to predict the β-turn Types I, II, IV and VIII. Multinomial logistic regression was initially used for the first time to select significant parameters in prediction of β-turn types using a self-consistency test procedure. The extracted parameters were consisted of 80 amino acid positional occurrences and 20 amino acid percentages in β-turn sequence. The most significant parameters were then selected using multinomial logistic regression model. Among these, the occurrences of glutamine, histidine, glutamic acid and arginine, respectively, in positions i, i + 1, i + 2 and i + 3 of β-turn sequence had an overall relationship with five β-turn types. A neural network model was then constructed and fed by the parameters selected by multinomial logistic regression to build a hybrid predictor. The networks have been trained and tested on a non-homologous dataset of 565 protein chains by 9-fold cross-validation. It has been observed that the hybrid model gives a Matthews correlation coefficient (MCC) of 0.235, 0.473, 0.103 and 0.124, respectively, for β-turn Types I, II, IV and VIII. Our model also distinguished the different types of β-turn in the embedded binary logit comparisons which have not carried out so far.

Availability: Available on request from the authors.

Contact:  parviz@modares.ac.ir
Detection of eQTL modules mediated by activity levels of transcription factors
Authors: Sun Wei , Yu Tianwei , Li Ker-Chau
Published: June 2007

Motivation: Studies of gene expression quantitative trait loci (eQTL) in different organisms have shown the existence of eQTL hot spots: each being a small segment of DNA sequence that harbors the eQTL of a large number of genes. Two questions of great interest about eQTL hot spots arise: (1) which gene within the hot spot is responsible for the linkages, i.e. which gene is the quantitative trait gene (QTG)? (2) How does a QTG affect the expression levels of many genes linked to it? Answers to the first question can be offered by available biological evidence or by statistical methods. The second question is harder to address. One simple situation is that the QTG encodes a transcription factor (TF), which regulates the expression of genes linked to it. However, previous results have shown that TFs are not overrepresented in the eQTL hot spots. In this article, we consider the scenario that the propagation of genetic perturbation from a QTG to other linked genes is mediated by the TF activity. We develop a procedure to detect the eQTL modules (eQTL hot spots together with linked genes) that are compatible with this scenario.

Results: We first detect 27 eQTL modules from a yeast eQTL data, and estimate TF activity profiles using the method of Yu and Li (2005). Then likelihood ratio tests (LRTs) are conducted to find 760 relationships supporting the scenario of TF activity mediation: (DNA polymorphism → cis-linked gene → TF activity → downstream linked gene). They are organized into 4 eQTL modules: an amino acid synthesis module featuring a cis-linked gene LEU2 and the mediating TF Leu3; a pheromone response module featuring a cis-linked gene GPA1 and the mediating TF Ste12; an energy-source control module featuring two cis-linked genes, GSY2 and HAP1, and the mediating TF Hap1; a mitotic exit module featuring four cis-linked genes, AMN1, CSH1, DEM1 and TOS1, and the mediating TF complex Ace2/Swi5. Gene Ontology is utilized to reveal interesting functional groups of the downstream genes in each module.

Availability: Our methods are implemented in an R package: eqtl.TF, which includes source codes and relevant data. It can be freely downloaded at http://www.stat.ucla.edu/~sunwei/software.htm

Abbreviations: eQTL (expression Quantitative Trait Loci); TF (Transcription Factor); QTG (Quantitative Trait Gene); SNP (Single Nucleotide Polymorphism); FDR (False Discovery Rate); SGD (Saccharomyces Genome Database); LRT (Likelihood Ratio Test).

Contact:  kcli@stat.ucla.edu

Supplementary information:  http://www.stat.ucla.edu/~sunwei/yeast_eQTL_TF/supplementary.pdf
POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix
Authors: Shimizu Kana , Hirose Shuichi , Noguchi Tamotsu
Published: June 2007

Summary: Protein disorder is characterized by a lack of a stable 3D structure, and is considered to be involved in a number of important protein functions such as regulatory and signalling events. We developed a web application, the POODLE-S, which predicts the disordered region from amino acid sequences by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.

Availability: POODLE-S is available from http://mbs.cbrc.jp/poodle/poodle-s.html and can be used by both academic and commercial users.

Contact:  poodle@cbrc.jp
CASVM: web server for SVM-based prediction of caspase substrates cleavage sites
Authors: Wee Lawrence J.K. , Tan Tin Wee , Ranganathan Shoba
Published: June 2007

Summary: Caspases belong to a unique class of cysteine proteases which function as critical effectors of apoptosis, inflammation and other important cellular processes. Caspases cleave substrates at specific tetrapeptide sites after a highly conserved aspartic acid residue. Prediction of such cleavage sites will complement structural and functional studies on substrates cleavage as well as discovery of new substrates. We have recently developed a support vector machines (SVM) method to address this issue. Our algorithm achieved an accuracy ranging from 81.25 to 97.92%, making it one of the best methods currently available. CASVM is the web server implementation of our SVM algorithms, written in Perl and hosted on a Linux platform. The server can be used for predicting non-canonical caspase substrate cleavage sites. We have also included a relational database containing experimentally verified caspase substrates retrievable using accession IDs, keywords or sequence similarity.

Availability:  http://www.casbase.org/casvm/index.html

Contact:  shoba.ranganathan@mq.edu.au

Supplementary information:  http://www.casbase.org/casvm/help/index.html
A statistical approach using network structure in the prediction of protein characteristics
Authors: Chen Pao-Yang , Deane Charlotte M. , Reinert Gesine
Published: June 2007

Motivation: The Majority Vote approach has demonstrated that protein–protein interactions can be used to predict the structure or function of a protein. In this article we propose a novel method for the prediction of such protein characteristics based on frequencies of pairwise interactions. In addition, we study a second new approach using the pattern frequencies of triplets of proteins, thus for the first time taking network structure explicitly into account. Both these methods are extended to jointly consider multiple organisms and multiple characteristics.

Results: Compared to the standard non-network-based method, namely the Majority Vote method, in large networks our predictions tend to be more accurate. For structure prediction, the Frequency-based method reaches up to 71% accuracy, and the Triplet-based method reaches up to 72% accuracy, whereas for function prediction, both the Triplet-based method and the Frequency-based method reach up to 90% accuracy. Function prediction on proteins without homologues showed slightly less but comparable accuracies. Including partially annotated proteins substantially increases the number of proteins for which our methods predict their characteristics with reasonable accuracy. We find that the enhanced Triplet-based method does not currently yield significantly better results than the enhanced Frequency-based method, suggesting that triplets of interactions do not contain substantially more information about protein characteristics than interaction pairs. Our methods offer two main improvements over current approaches—first, multiple protein characteristics are considered simultaneously, and second, data is integrated from multiple species. In addition, the Triplet-based method includes network structure more explicitly than the Majority Vote and the Frequency-based method.

Availability: The program is available upon request.

Contact:  pchen@stats.ox.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance
Authors: Wang Chunlin , Mitsuya Yumi , Gharizadeh Baback , Ronaghi Mostafa , Shafer Robert W.
Published: June 2007

The detection of mutant spectra within a population of microorganisms is critical for the management of drug-resistant infections. We performed ultra-deep pyrosequencing to detect minor sequence variants in HIV-1 protease and reverse transcriptase (RT) genes from clinical plasma samples. We estimated empirical error rates from four HIV-1 plasmid clones and used them to develop a statistical approach to distinguish authentic minor variants from sequencing errors in eight clinical samples. Ultra-deep pyrosequencing detected an average of 58 variants per sample compared with an average of eight variants per sample detected by conventional direct-PCR dideoxynucleotide sequencing. In the clinical sample with the largest number of minor sequence variants, all 60 variants present in ≥3% of genomes and 20 of 35 variants present in <3% of genomes were confirmed by limiting dilution sequencing. With appropriate analysis, ultra-deep pyrosequencing is a promising method for characterizing genetic diversity and detecting minor yet clinically relevant variants in biological samples with complex genetic populations.
Specific reactions ofS‐nitrosothiols with cysteine hydrolases: A comparative study between dimethylargininase‐1 and CTP synthetase
Authors: Braun Oliver , Knipp Markus , Chesnov Serge , Vašák Milan
Published: June 2007

S‐Transnitrosation is an important bioregulatory process whereby NO+equivalents are transferred betweenS‐nitrosothiols and Cys of target proteins. This reaction proceeds through a common intermediate R–S–N(O−)–S–R′ and it has been proposed that products different fromS‐nitrosothiols may be formed in protein cavities. Recently, we have reported on the formation of such a product, anN‐thiosulfoximide, at the active site of the Cys hydrolase dimethylargininase‐1 (DDAH‐1) upon reaction withS‐nitroso‐l‐homocysteine (HcyNO). Here we have addressed the question of whether this novel product can also be formed with the endogenously occurringS‐nitrosothiolsS‐nitroso‐l‐cysteine (CysNO) andS‐nitrosoglutathione (GSNO). Further, to explore the reason responsible for the unique formation of anN‐thiosulfoximide in DDAH‐1 we have expanded these studies to cytidine triphosphate synthetase (CTPS), which shows a similar active site architecture. ESI‐MS and activity measurements showed that the bulky GSNO does not react with both enzymes. In contrast, S‐nitrosylation of the active site Cys occurred in DDAH‐1 with CysNO and in CTPS with CysNO and HcyNO. Although kinetic analysis indicated that these compounds act as specific irreversible inhibitors, noN‐thiosulfoximide was formed. The reasons likely responsible for the absence of theN‐thiosulfoximide formation are discussed using molecular models of DDAH‐1 and CTPS. In tissue extracts DDAH was inhibited only by HcyNO, with an IC50value similar to that of the isolated protein. Biological implications of these studies for the function of both enzymes are discussed.
Cleavage of recombinant proteins at poly‐His sequences by Co(II) and Cu(II)
Authors: Andberg Martina , Jäntti Jussi , Heilimo Sara , Pihkala Päivi , Paananen Arja , Koskinen Ari M.P. , Söderlund Hans , Linder Markus B.
Published: June 2007

Improved ways to cleave peptide chains at engineered sites easily and specifically would form useful tools for biochemical research. Uses of such methods include the activation or inactivation of enzymes or the removal of tags for enhancement of recombinant protein expression or tags used for purification of recombinant proteins. In this work we show by gel electrophoresis and mass spectroscopy that salts of Co(II) and Cu(II) can be used to cleave fusion proteins specifically at sites where sequences of His residues have been introduced by protein engineering. The His residues could be either consecutive or spaced with other amino acids in between. The cleavage reaction required the presence of low concentrations of ascorbate and in the case of Cu(II) also hydrogen peroxide. The amount of metal ions required for cleavage was very low; in the case of Cu(II) only one to two molar equivalents of Cu(II) to protein was required. In the case of Co(II), 10 molar equivalents gave optimal cleavage. The reaction occurred within minutes, at a wide pH range, and efficiently at temperatures ranging from 0°C to 70°C. The work described here can also have implications for understanding protein stability in vitro and in vivo.
Local quality assessment in homology models using statistical potentials and support vector machines
Authors: Fasnacht Marc , Zhu Jiang , Honig Barry
Published: June 2007

In this study, we address the problem of local quality assessment in homology models. As a prerequisite for the evaluation of methods for predicting local model quality, we first examine the problem of measuring local structural similarities between a model and the corresponding native structure. Several local geometric similarity measures are evaluated. Two methods based on structural superposition are found to best reproduce local model quality assessments by human experts. We then examine the performance of state‐of‐the‐art statistical potentials in predicting local model quality on three qualitatively distinct data sets. The best statistical potential, DFIRE, is shown to perform on par with the best current structure‐based method in the literature, ProQres. A combination of different statistical potentials and structural features using support vector machines is shown to provide somewhat improved performance over published methods.
DosT and DevS are oxygen‐switched kinases in Mycobacterium tuberculosis
Authors: Sousa Eduardo Henrique Silva , Tuckerman Jason Robert , Gonzalez Gonzalo , Gilles‐Gonzalez Marie‐Alda
Published: June 2007

Exposure of Mycobacterium tuberculosis to hypoxia is known to alter the expression of many genes, including ones thought to be involved in latency, via the transcription factor DevR (also called DosR). Two sensory kinases, DosT and DevS (also called DosS), control the activity of DevR. We show that, like DevS, DosT contains a heme cofactor within an N‐terminal GAF domain. For full‐length DosT and DevS, we determined the ligand‐binding parameters and the rates of ATP reaction with the liganded and unliganded states. In both proteins, the heme state was coupled to the kinase such that the unliganded, CO‐bound, and NO‐bound forms were active, but the O2‐bound form was inactive. Oxygen‐bound DosT was unusually inert to oxidation to the ferric state (half life in air >60 h). Though the kinase activity of DosT was unaffected by NO, this ligand bound 5000 times more avidly than O2 to DosT (Kd [NO] ∼5 nM versus Kd [O2] = 26 μM). These results demonstrate direct and specific O2 sensing by proteins in M. tuberculosis and identify for the first time a signal ligand for a sensory kinase from this organism. They also explain why exposure of M. tuberculosis to NO donors under aerobic conditions can give results identical to hypoxia, i.e., NO saturates DosT, preventing O2 binding and yielding an active kinase.
A single mutation in the active site swaps the substrate specificity of N‐acetyl‐L‐ornithine transcarbamylase and N‐succinyl‐L‐ornithine transcarbamylase
Authors: Shi Dashuang , Yu Xiaolin , Cabrera‐Luque Juan , Chen Tony Y. , Roth Lauren , Morizono Hiroki , Allewell Norma M. , Tuchman Mendel
Published: June 2007

Transcarbamylases catalyze the transfer of the carbamyl group from carbamyl phosphate (CP) to an amino group of a second substrate such as aspartate, ornithine, or putrescine. Previously, structural determination of a transcarbamylase from Xanthomonas campestris led to the discovery of a novel N‐acetylornithine transcarbamylase (AOTCase) that catalyzes the carbamylation of N‐acetylornithine. Recently, a novel N‐succinylornithine transcarbamylase (SOTCase) from Bacteroides fragilis was identified. Structural comparisons of AOTCase from X. campestris and SOTCase from B. fragilis revealed that residue Glu92 (X. campestris numbering) plays a critical role in distinguishing AOTCase from SOTCase. Enzymatic assays of E92P, E92S, E92V, and E92A mutants of AOTCase demonstrate that each of these mutations converts the AOTCase to an SOTCase. Similarly, the P90E mutation in B. fragilis SOTCase (equivalent to E92 in X. campestris AOTCase) converts the SOTCase to AOTCase. Hence, a single amino acid substitution is sufficient to swap the substrate specificities of AOTCase and SOTCase. X‐ray crystal structures of these mutants in complexes with CP and N‐acetyl‐L‐norvaline (an analog of N‐acetyl‐L‐ornithine) or N‐succinyl‐L‐norvaline (an analog of N‐succinyl‐L‐ornithine) substantiate this conversion. In addition to Glu92 (X. campestris numbering), other residues such as Asn185 and Lys30 in AOTCase, which are involved in binding substrates through bridging water molecules, help to define the substrate specificity of AOTCase. These results provide the correct annotation (AOTCase or SOTCase) for a set of the transcarbamylase‐like proteins that have been erroneously annotated as ornithine transcarbamylase (OTCase, EC 2.1.3.3).
FR258900, a potential anti‐hyperglycemic drug, binds at the allosteric site of glycogen phosphorylase
Authors: Tiraidis Costas , Alexacou Kyra‐Melinda , Zographos Spyros E. , Leonidas Demetres D. , Gimisis Thanasis , Oikonomakos Nikos G.
Published: June 2007

FR258900 has been discovered as a novel inhibitor of human liver glycogen phosphorylase a and proved to suppress hepatic glycogen breakdown and reduce plasma glucose concentrations in diabetic mice models. To elucidate the mechanism of inhibition, we have determined the crystal structure of the cocrystallized rabbit muscle glycogen phosphorylase b–FR258900 complex and refined it to 2.2 Å resolution. The structure demonstrates that the inhibitor binds at the allosteric activator site, where the physiological activator AMP binds. The contacts from FR258900 to glycogen phosphorylase are dominated by nonpolar van der Waals interactions with Gln71, Gln72, Phe196, and Val45′ (from the symmetry‐related subunit), and also by ionic interactions from the carboxylate groups to the three arginine residues (Arg242, Arg309, and Arg310) that form the allosteric phosphate‐recognition subsite. The binding of FR258900 to the protein promotes conformational changes that stabilize an inactive T‐state quaternary conformation of the enzyme. The ligand‐binding mode is different from those of the potent phenoxy‐phthalate and acyl urea inhibitors, previously described, illustrating the broad specificity of the allosteric site.
Impact of 21st century climate change on the Baltic Sea fish community and fisheries
Authors: MACKENZIE BRIAN R. , GISLASON HENRIK , MÖLLMANN CHRISTIAN , KÖSTER FRIEDRICH W.
Published: June 2007

The Baltic Sea is a large brackish semienclosed sea whose species‐poor fish community supports important commercial and recreational fisheries. Both the fish species and the fisheries are strongly affected by climate variations. These climatic effects and the underlying mechanisms are briefly reviewed. We then use recent regional – scale climate – ocean modelling results to consider how climate change during this century will affect the fish community of the Baltic and fisheries management. Expected climate changes in northern Europe will likely affect both the temperature and salinity of the Baltic, causing it to become warmer and fresher. As an estuarine ecosystem with large horizontal and vertical salinity gradients, biodiversity will be particularly sensitive to changes in salinity which can be expected as a consequence of altered precipitation patterns. Marine‐tolerant species will be disadvantaged and their distributions will partially contract from the Baltic Sea; habitats of freshwater species will likely expand. Although some new species can be expected to immigrate because of an expected increase in sea temperature, only a few of these species will be able to successfully colonize the Baltic because of its low salinity. Fishing fleets which presently target marine species (e.g. cod, herring, sprat, plaice, sole) in the Baltic will likely have to relocate to more marine areas or switch to other species which tolerate decreasing salinities. Fishery management thresholds that trigger reductions in fishing quotas or fishery closures to conserve local populations (e.g. cod, salmon) will have to be reassessed as the ecological basis on which existing thresholds have been established changes, and new thresholds will have to be developed for immigrant species. The Baltic situation illustrates some of the uncertainties and complexities associated with forecasting how fish populations, communities and industries dependent on an estuarine ecosystem might respond to future climate change.
Electron transfer of dissolved organic matter and its potential significance for anaerobic respiration in a northern bog
Authors: HEITMANN TOBIAS , GOLDHAMMER TOBIAS , BEER JULIA , BLODAU CHRISTIAN
Published: June 2007

We investigated electron transfer processes of dissolved organic matter (DOM) and their potential importance for anaerobic heterotrophic respiration in a northern peatland. Electron accepting and donating capacities (EAC, EDC) of DOM were quantified using dissolved H2S and ferric iron as reactants. Carbon turnover rates were obtained from porewater profiles (CO2, CH4) and inverse modeling. Carbon dioxide was released at rates of 0.2–5.9 mmol m−2 day−1 below the water table. Methane (CH4) formation contributed <10%, and oxygen consumption 2% to 40%, leaving a major fraction of CO2 production unexplained. DOM oxidized H2S to thiosulfate and was reduced by dissolved ferric iron. Reduction with H2S increased the subsequently determined EDC compared to untreated controls, indicating a reversibility of the electron transfer. In situ redox capacities of DOM ranged from 0.2 to 6.1 mEq g−1 C (EAC) and from 0.0 to 1.4 mEq g−1 C (EDC), respectively. EAC generally decreased with depth and changed after a water table drawdown and rebound by 20 and −45 mEq m−2, respectively. The change in EAC during the water table fluctuation was similar to CH4 formation rates. In peatlands, electron transfer of DOM may thus significantly contribute to the oxidation of reduced organic substrates by anaerobic heterotrophic respiration, or by maintaining the respiratory activity of sulfate reducers via provision of thiosulfate. Part of the anaerobic electron flow in peat soils is thus potentially diverted from methanogenesis, decreasing its contribution to the total carbon emitted to the atmosphere.
Bird densities are associated with household densities
Authors: TRATALOS JAMIE , FULLER RICHARD A. , EVANS KARL L. , DAVIES RICHARD G. , NEWSON STUART E. , GREENWOOD JEREMY J. D. , GASTON KEVIN J.
Published: June 2007

Increasing housing density is an important component of global land transformation, with major impacts on patterns of biodiversity. However, while there have been many studies of the changes in biodiversity across rural–urban gradients, which are influenced in large part by housing densities, how biodiversity changes across the full range of regional variation in housing density remains poorly understood. Here, we explore these relationships for the richness and abundance of breeding birds across Britain. Total richness, and that of 27 urban indicator species, increased from low to moderate household densities and then declined at greater household densities. The richness of all species increased initially faster with household density than did that of the urban indicator species, but nonurban indicator species richness declined consistently after peaking at a very low housing density. Avian abundance showed a rather different pattern. Total abundance and that summed across all urban indicator species increased over a wide range of household densities, and declined only at the highest household densities. The abundance of individual urban indicator species generally exhibited a hump‐shaped relationship with housing density. While there was marked intraspecific variation in the form of such relationships, almost invariably avian abundance declined at housing densities below that at which the UK government requires new developments to be built. Our data highlight the difficulties of maintaining biodiversity while minimising land take for new development. High‐density housing developments are associated with declines in many of those species otherwise best able to exploit urban environments, and those components of native biodiversity with which human populations are often most familiar.
Long‐term survival of HIV‐infected patients with haemophilia
Authors: Stieltjes N. , Sultan Y. , Rothschild C. , Torchet M. F. , Laurian Y. , Navarro R. , Fressinaud E. , Gernez A. Parquet , Fonlupt J. , Berthier A. M.
Published: June 2007

In France, patients with haemophilia were infected by HIV up until October 1985, with a maximum of seroconversion between 1983 and 1985. There was a progressive development of AIDS in the 1158 infected patients as reported by Health Authorities. By the end of 1992, 32% of the haemophilia population had developed AIDS and 38 had developed clinical or biological symptoms of immunodeficiency. However, 27% had no clinical symptoms and no severe disorder of the immune system. The present study was established to determine factors common to patients with prolonged survival.
Results in three Australian haemophilia B patients with high‐responding inhibitors treated with the Malmö model
Authors: NILSSON INGA MARIE , BERNTORP ERIK , RICKARD KEVIN A.
Published: June 2007

Development of inhibitors to factor IX (F IX) is a serious complication of the treatment of patients with severe haemophilia B. Three Australian haemophilia B patients, a 22‐year‐old man and two 5‐year‐old identical twins, with high‐responding inhibitors and resistant to treatment, were admitted to the centre in Malmö, Sweden, for tolerance induction according to the Malmö treatment model. This tratment consists of a combination of cyclophosphamide, F VIII of F IX, and high‐dose intravenous IgG.

Extracorporeal adsorption to protein A in columns, which is included in the protocol when the inhibitor titre is high at the start of treatment, had to be perforemed in the case of the twin brothers. High‐purity F IX concentrates were used. The tolerance inductin was successful in the 22‐year‐old man and in one of the twins; they been toleant for 4 and 2 years, respectively, and are now on a home‐treatment programme taking 30–40 IU F IX/kg twice weekly. These patients have no demonstrable coagulation inhibitory antibodies and in vivo reovery and half‐life of infused F IX are normal. In the other twin it has not been possible to induce tolerance, though after removal of the antibodies by protein A adsorpation it is possible to achieve significant circulalting levels of F IX for 8–10 days.
Recombinant coagulation factor products
Authors: BRETTLER DOREEN B.
Published: June 2007

Summary There are numerous new coagulation factor concentrates that are being manufactured using recombinant technology. Some are available for use currently for the treatment of bleeding disorders and others are in clinical trials. Recombinant factor VIII concentrates are licenced in most countries and one FVIII concentrate with the B domain deleted should be available in the near future. Recombinant VIIa concentrate is in advanced phase III testing for the treatment of patients with inhibitor antibodies. Recombinant factor IX has been used successfully in animals and will be tested in humans shortly. This paper reviews these products and discusses their uses and possible side‐effects.
Hepatitis A immunization in HIV‐infected haemophilic patients
Authors: Wilde Jonathan T. , RYMES NICOLA , SKIDMOE SUSAN , SWANN MARGARET , LININ JANE
Published: June 2007

Summary Forty‐seven HIV‐infected haemophilic patients were entered into a hepatitis A vaccination programme. 10 patients (21%) were lgG seropositive for hepatitis A consistent with past exposure. Of the 37 patients offered vaccination, one refused and 31 completed the vaccination course, 17/13 (55%) seroconverted, nine after the second and eight after the third injection, and 14 patients failed to seroconvert. The CD4 lymphocyte counts immediately prior to vaccination were significantly higher in the patients who developed immunity compared to the nonresponders (median CD4 count in the immune group 380 × 106/1 (range 170–1290), median CD4 count in nonimmune group 110 × 106/1 (range 10–590), P== 0.003). No patient with a CD4 count < 170 × 106/1 seroconverted and five patients with well‐preserved CD4 counts also failed to seroconvert. We conclude that HIV‐infected haemophilic patients, especially those with more advanced disease, have an impaired response to hepatitis A vaccination. Due to the likely failure of response in patients with CD4 counts < 150 × 106/1, it is reasonable not to include these patients in a hepatitis A vaccination programme.
The knowledge and perception of factor concentrate in persons with haemophilia A
Authors: BOLIVAR EDNA P. , SHOPNICK RINAH I. , MANNUCCI PIER M. , GRINGERI ALESSANDRO , BRETTLER DOREEN B.
Published: June 2007

Summary.
Objectiues. To evaluate haemophilia patients' knowledge and understanding of factor concentrate products and to assess their feelings regarding purity and viral safety of these products.

Methods. Sixty questionnaires were distributed and completed by patients or parents of patients with severe/ moderate haemophilia A at two large comprehensive haemophilia centres in the USA and Italy.

Results. Most patients knew what brand of factor concentrate they used, but less than half were aware of how their concentrate was virally inactivated. The majority of responders perceived recombinant factor VlII as being the concentrate with the highest degree of purity. The majority felt the decision of which concentrate to use should be the care‐givers not the patients.

Conclusions. It appears that patients need more education concerning the concentrate they are using, and its method of viral inactivation and purity.
A longitudinal study of immunological status in Chinese haemophiliacs: importance of the heat viral inactivation of factor concentrates. I. Immunological associations with the consumption of factor concentrates
Authors: MING‐CHING SHEN , FUEI‐YUEN LIU , YEN‐PING KUO , RON‐FON HSIE
Published: June 2007

Summary. Twenty‐four of 117 cases of haemophilia A (20.5%) and none of 18 cases of haemophilia B reported in this study had an antibody to the human immuno‐deficiency virus (HIV). Both groups of patients showed similar immunological alterations. HIV‐seropositive haemophilia A patients had an increased CD8 cell count and a similarly decreased CD4/CD8 ratio as compared to HIV‐seronegative haemophilia A patients. Multiple regression analysis for the association of CD4/CD8 ratio with HIV infection status and dosage of plasma products in haemophilia A and B patients, respectively, revealed that there was a significant negative association of ln(CD4/CD8) with dosage of factor VlII concentrates (P = 0.0435) and factor IX concentrates (P = O.O028), respectively. N o association occurred between CD4/CD8 ratio and HIV infection as well as dosage of other plasma products. These data indicate that the immunological abnormalities of our haemophilia A and B patients in their early years were primarily caused by various viral infections and/or a suppressive effect of allogeneic protein through infusion of factor concentrates and not caused simply by HIV infection.
Ipsilateral total shoulder and elbow prosthetic replacement in a patient with severe haemophilia B
Authors: PHILLIPS A. M. , RIBBANS W. J. , GODDARD N. J.
Published: June 2007

Since factor replacement concentrates became widely available in the 1970s, total prosthetic replacement of joints in haemophilic patients has become increasingly common, with success particularly in the knee and hip. However, there has been no published series of elbow or shoulder replacements large enough to draw conclusions about the advisability of these procedures in this group of patients.

We report a case of prosthetic replacement of the shoulder in a 58‐year‐old man with haemophilia B, and replacement of the elbow joint of the same limb 21 months later. The results are initially very encouraging, with no pain in either joint since the early post‐operative period. There have been no bleeds into either joint since surgery. Ranges of movement are satisfactory. Follow‐up is now 37 months for the shoulder and 16 months for the elbow.
Association of severe haemophilia A and factor V Leiden: report of three cases
Authors: ARRUDA VALDER R. , ANNICHINO‐BIZZACCHI JOYCE M. , ANTUNES SANDRA V. , COSTA FERNANDO F.
Published: June 2007

Summary. The clinical severity of haemophilia is usually related to residual clotting factor activity. Reports of factor V deficiency or protein C have been described in haemophilic patients and both are involved in the activated protein C pathway. Recently, the poor response to activated protein C due to factor V Leiden (FQ506) has been associated with an increased risk of thrombosis and its incidence in the normal population is given as 2–7%. We describe three cases of severe haemophilia A heterozygous for factor V Leiden and its influence on phenotype.
Desmopressin and type II B von Willebrand disease
Authors: CASTAMAN G. , RODEGHIERO F.
Published: June 2007

Summary. Type II B von Willebrand disease (vWD) is a rare subtype of vWD characterized by the presence of an abnormal von Willebrand factor (vWF) with enhanced affinity for the platelet membrane receptor glycoprotein Ib. The phenotypic hallmarks of the disease are represented by heightened ristocetin‐induced platelet aggregation, occurring at very low ristocetin concentration, and the lack of high‐molecular‐weight vWF multimers in plasma. When infused with desmopressin, a variable degree of thrombocytopenia usually occurs in these patients, resulting from in vivo platelet aggregation caused by the release of abnormal vWF multimers from endogenous stores. We have reviewed the available literature data concerning the biological and clinical effects of desmopressin in the few cases so far reported. Despite the fear of thrombotic or haemorrhagic events, no significant side‐effects have been reported also in the cases (70%) with severe thrombocytopenia. Moreover, the few clinical reports with the use of desmopressin in type II B patients showed a favourable effect in the prevention of bleeding during surgery or dental extraction. Thus, it appears that desmopressin could be safely used in selected clinical situations in patients with type II B vWD.
Socioeconomic impact of haemophilia care: results of a pilot study
Authors: SZUCS T. D. , ÖFFNER A. , SCHRAMM W.
Published: June 2007

Summary. Fifty consecutive haemophiliacs were entered into a pilot study of socioeconomic impact of haemophilia treatment. The Short Form 36 was used as an instrument for the assessment of quality of life. Direct and indirect costs were analysed. Incremental cost‐effectiveness was expressed as additional costs per joint bleed avoided by prophylactic treatment over on‐demand treatment. Thirtynine patients (mean age 35.14 years) were substituting factor VIII according to an on‐demand and 11 patients according to a modified prophylactic regimen. There were an average of 9.84 joint bleeds per patient across all patients during the 6‐month observation period: on‐demand group 10.74 bleeds, prophylactic group 6.64 bleeds. This difference was not statistically different. Significant differences between haemophiliac patients and healthy men were seen in the assessment of their limitations of physical activities, limiting pain and general health. The total cost per patient during the 6 months was DM 24 601 in all patients, DM 17 253 in those on an on‐demand base and DM 28 245 in the modified prophylactic group. Patients experienced an average 4.71 days off work: on demand 5.81 days, prophylactic regimen 0 days. The total indirect cost per patient was DM 683; therapy cost per patient was DM 25 284; cost per avoided bleed DM 1680 for on‐demand therapy and DM 4228 on prophylaxis. The incremental cost‐effectiveness, i.e. the additional costs to avoid one additional joint bleed by prophylactic treatment, was DM 2536. In conclusion, patients receiving prophylactic clotting factor therapy require less additional health care resources, mainly due to the reduction in the number of joint bleeds.
Immune tolerance induction in haemophiliacs with inhibitor to FVIII: high‐ or low‐dose programme
Authors: KUCHARSKI W. , SCHARF R. , NOWAK T.
Published: June 2007

Summary. In 1993–94, 15 high responders were treated in our centre according to the Malmo protocol which was modified as follows: serial plasmapheresis was performed instead of extracorporeal adsorbtion to protein A for reducing inhibitor levels and, after the bolus dose to neutralize the inhibitor, factor VIII concentrate was administered by a continuous infusion. Thus, this regimen included continuous infusion of factor VIII(FVIII) for 1–4 weeks, iv cyclophosphamide for 2 days and orally for 8–10 days, and intravenous immunoglobulin (IVIG) from the fourth day for 5 days. All patients had been qualified for the treatment when the antibody level was < 15 BU mL−1. Tolerance was induced in 10 patients (66.6% very good and good results). The treatment failed in five cases in which, due to a high inhibitor level, it was not possible to maintain a measurable factor VIII:C concentration throughout the whole period of infusion. We compared these results with results of our low‐dose regimen: 25 IU FVIII kg−1 b.w. twice a week (1985–89, 11 high responders). The modified Malmo Protocol is much shorter than the low‐dose programme and this is a method of first choice in patients undergoing surgery in the near future.