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Chloroplasts are organelles found in plant system and other photosynthetic eukaryotes. Since a large number of essential pathways take place in this organelle, proteins in the chloroplast are considered vital. Therefore, knowledge about the subchloroplast localization of the chloroplast proteins will provide precise information in understanding its interaction within the chloroplast. To address this, an AdaBoost-based prediction system to predict the subchloroplast localization of chloroplast proteins (SCLAP) was developed. It integrates three different sequence-based features for prediction, beside the addition of similarity-based module for significant improvement in prediction performance. SCLAP achieved an overall accuracy of 89.3% in jackknife cross-validation test against the benchmark dataset, which was considered highest among existing tools and equals the SubIdent, and 85.9% accuracy in new error-free dataset. Evaluation of SCLAP with the independent dataset, five-fold cross-validation, and their corresponding receiver operator characteristic curve analysis demonstrated the SCLAP's efficient performance. SCLAP is the webserver implementation of our algorithm written in PERL. The server can be used to predict the subchloroplast localization of chloroplast proteins ( http://sclap.bicpu.edu.in/predict.php ).

Plants in nature may face a wide range of favorable or unfavorable biotic and abiotic factors during their life cycle. Any of these factors may cause stress in plants; therefore, they have to be more adaptable to stressful environments and must acquire greater response to different stresses. The objective of this study is to retrieve and arrange data from the literature in a standardized electronic format for the development of information resources on potential stress responsive genes in Arabidopsis thaliana. This provides a powerful mean for manipulation, comparison, search, and retrieval of records describing the nature of various stress responsive genes in Arabidopsis thaliana. The database is based exclusively on published stress tolerance genes associated with plants.

In the title compound, C(17)H(15)NO(4)S, the six-membered ring of the indole unit makes a dihedral angle of 72.40 (5)° with the phenyl ring. The mol-ecular structure features a short C-H⋯O contact.

In the title compound, C(16)H(13)NO(3)S, the sulfonyl-bound phenyl ring forms a dihedral angle of 84.17 (6)° with the indole ring system. An intra-molecular C-H⋯O hydrogen bond generates an S(6) ring motif. The crystal structure exhibits weak inter-molecular C-H⋯O hydrogen bonds and π-π inter-actions between the five- and six-membered rings of the indole group [centroid-centroid distance = 3.6871 (9) Å].

Vibrio abundance generally displays seasonal patterns. In temperate coastal areas, temperature and salinity influence Vibrio growth, whereas in tropical areas this pattern is not obvious. The present study assessed the dynamics of Vibrio in the Arabian Sea, 1-2 km off Mangalore on the south-west coast of India, during temporally separated periods. The two sampling periods were signified by oligotrophic conditions, and stable temperatures and salinity. Vibrio abundance was estimated by culture-independent techniques in relation to phytoplankton community composition and environmental variables. The results showed that the Vibrio density during December 2007 was 10- to 100-fold higher compared with the February-March 2008 period. High Vibrio abundance in December coincided with a diatom-dominated phytoplankton assemblage. A partial least squares (PLS) regression model indicated that diatom biomass was the primary predictor variable. Low nutrient levels suggested high water column turnover rate, which bacteria compensated for by using organic molecules leaking from phytoplankton. The abundance of potential Vibrio predators was low during both sampling periods; therefore it is suggested that resource supply from primary producers is more important than top-down control by predators., (© 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.)

INTRODUCTION Anaemia is common in rheumatoid arthritis (RA). Clinicians may focus on rheumatological issues and assume anaemia of chronic disease (ACD). This study challenged this assumption and investigated the causes of anaemia in a large cohort of RA patients to assess its implications. METHODS The hospital where the study was conducted monitors regular full blood count and erythrocyte sedimentation rate (ESR) monthly in all RA patients on disease modifying drugs to assess efficacy and safety. A computerised system identifies and records abnormal results. The database for 2009 was interrogated to find all patients with two consecutive haemoglobin values <11&emsp14;g/dl. Using a proforma, patients were defined as having iron deficiency anaemia (IDA), ACD, macrocytic anaemia (MCA) or another cause. All results of further tests investigating the anaemia were recorded. RESULTS Among 2000 RA patients on the system, 199 (10%) were identified as having anaemia over a year. Of these, 90 had IDA, 78 had ACD, 25 had MCA, and 6 had postoperative anaemia. Among 90 patients with IDA, investigations were performed in 53, with 23 normal. An explanation for IDA was found in 30: gastrointestinal bleeding in 25, gynaecological blood loss in 3, and urinary bleeding in 2. Among 78 patients with ACD, response to intensification of RA treatment occurred in 45, but erythropoietin therapy was required in 9. Within the 25 patients with MCA, 12 had unrecognised vitamin B(12) deficiency, 4 drug induced changes, 3 myeloid malignancy, 2 hypothyroidism, and 2 alcoholism. CONCLUSIONS Anaemia in RA is common, multifactorial, and potentially both serious and correctable. Established malignancy was present in 10 patients and premalignancy in a further 10 (10% of total). Treatable causes were commonly identified. Clinicians need to investigate the nature and cause of persistent anaemia, and must not assume it to be simply ACD without evidence.

In the title compound, C(22)H(18)N(2)O(4)S, the dihedral angle between the phenyl-sulfonyl ring and the methyl-phenyl ring is 67.78 (7)°. In the crystal, mol-ecules are linked by weak inter-molecular C-H⋯O inter-actions into a zigzag chain along the [101] direction.

In the title compound, C(12)H(14)O(4), the two acet-oxy groups are inclined by 57.92 (5)° and 62.71 (6)° to the benzene ring. An inter-molecular C-H⋯O inter-action involving the two acet-oxy groups generates a centrosymmetric dimer via an R(2) (2)(16) ring motif.

Introduction: Immunisation against pneumococcus has been shown to reduce pneumonia in rheumatoid arthritis (RA). There is concern that methotrexate may reduce its efficacy. There are very few objective data on the effect of methotrexate on the efficacy of pneumococcal vaccination with pneumovax, and no objective evidence on whether revaccination is necessary in RA patients on methotrexate., Methods: The authors collected information from 180 RA patients on methotrexate relating to their vaccination status and assayed their pneumococcal antibody levels. Data on pulmonary infection were retrieved in the same patients over the preceding decade., Results: Full data were available for 152 patients, of whom 28 had never been vaccinated against pneumococcus. Median levels were significantly higher in those who had been vaccinated. Unvaccinated patients and those taking oral prednisone were more likely to have had pneumonia in the previous 10 years. The RR for developing pneumonia among non-vaccinated patients was 9.7 (p=0.005) and among steroid-treated patients was 6.5 (p=0.001), after adjusting for age, gender, disease duration and comorbidity. No significant correlation was found between pneumococcal antibody levels and time since vaccination., Conclusions: This study suggests that a single administration of pneumovax early in RA offers up to 10 years protection against the development of pneumococcal pneumonia in RA patients on methotrexate.

In the title compound, C(15)H(12)INO(2)S, the sulfonyl-bound phenyl ring forms a dihedral angle 82.84 (9)° with the indole ring system. The mol-ecular structure is stabilized by a weak intra-molecular C-H⋯O hydrogen bond. The crystal structure exhibits weak inter-molecular C-H⋯π inter-actions and π-π inter-actions between the indole groups [centroid-centroid distance between the five-membered and six-membered rings of the indole group = 3.7617 (18) Å].

In the title compound, C(26)H(23)NO(4)S, the phenyl, tolyl and ester groups make dihedral angles of 82.28 (5), 77.67 (6) and 8.52 (6)°, respectively, with the indole ring system. The S atom of the sulfonyl group is displaced by 0.1968 (4) Å from the indole mean plane. The mol-ecular structure is stabilized by weak intra-molecular C-H⋯O inter-actions. The crystal structure structure features short intramolecular C-H⋯O contacts and π-π stacking inter-actions between the phenyl and tolyl groups [centroid-centroid distance = 3.9448 (11) Å].

Anaerobic biofilm reactors have limitations in treating wastewaters with low organic substrate concentrations (COD value below 1000 mg/L) because the substrate cannot reach the microorganisms present in the interior part of the biogranules. Hence, the performance of these reactors is mainly influenced by the size of the biogranules present within the reactor. An anaerobic hybrid reactor with a tapered configuration has been developed where the self-immobilized biogranules are kept under completely fluidized condition. The tapered configuration can retain smaller sized biogranules more effectively than a cylindrical configuration for the same hydraulic loading rate. A synthetic effluent containing glucose as the sole carbon source was used to study the performance of this reactor. The reactor could handle an organic loading rate up to 19.1 kgCOD/(m3 x d) with a hydraulic retention time (HRT) of 0.63 h, removing around 90% of inlet COD. Even though the strength of the wastewater is low, the resultant organic loading rate is also high because of the high hydraulic loading rate (low HRT). The specific substrate utilization rate study showed that the concentration of methanogenic bacteria within the biogranules increased along the reactor height, whereas the concentration of acidogens decreased. The morphology and hydrodynamic characteristics of the biogranules obtained from the reactor at different heights were also studied. The biogranules obtained from the upper port of the reactor had a lower diameter, lower terminal settling velocity and more cavities than those from the lower port. Biogranules up to the size of 5.2 mm were observed.

Oral methotrexate is the benchmark against which other disease-modifying anti rheumatic drugs are measured. The use of parenteral methotrexate for those failing to tolerate or respond to oral therapy is accepted, but indications for its use and its place in the therapeutic ladder have not been fully investigated. We assessed the use of parenteral methotrexate (MTX) in our rheumatoid arthritis (RA) population and compared the characteristics of these patients to a matched group of those on oral therapy. We compared response rates to each approach using DAS 28 scores, ESR and visual analogue scales. Inferences on costs of parenteral therapy were made and predictors of response defined. We found that 10% of our total RA patient population were on parenteral methotrexate, having failed to tolerate or respond to oral therapy. Seventy-five percent of these met the criteria for the use of anti-tumour necrosis factor (TNF) agents. Overall response rates were equivalent to those obtained by responders to oral MTX. Patients on parenteral therapy were younger and were more likely to have extreme values of body mass index (BMI) than those on oral therapy. The approach was economically viable, although many patients unnecessarily attended hospital to receive their injections. We advocate consideration of parenteral MTX in all RA patients unresponsive to oral therapy prior to treatment with anti-TNF therapy. Response to parenteral therapy can be predicted by low BMI (below 22 kg/m(2)), possibly as a result of malabsorption, or by high BMI (over 30) as a result of gastrointestinal intolerance. A mechanism to deliver this option through self-administration in the community should be encouraged.

Morbidity and mortality from pneumonia is increased in patients with rheumatoid arthritis. Factors contributing to this have been recently identified and a number of recommendations have been implemented in an attempt to reverse this trend. The present paper shows that these measures have combined to produce a fourfold reduction in both admissions and case fatality rates. In the study population, immunisation rates against influenza and pneumococcus have improved to 86% and 65%, oral steroid consumption has halved and disease modifying drugs were usually appropriately suspended during acute infection. These measures may now merit more widespread adoption.

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species., (© 2009 Blackwell Publishing Ltd.)

Introduction: An increased prevalence of musculoskeletal disease is recognised in diabetes and is a common source of disability. It is known to predominantly affect the upper limbs especially the hand and shoulder. The relationship with other complications of diabetes and glycaemic control is uncertain. We designed this study to clarify these relationships, and to assess differences between types 1 and 2 diabetes., Methods: We identified a group of 96 people with established diabetes and examined them for the presence of locomotor disease focussing on the upper limbs. We recorded the mean HbA1c and the presence of diabetic complications, together with the health assessment questionnaire (HAQ) score. We explored correlations between locomotor disease and these variables using logistic regression. We compared data between type 1 and type 2 diabetics and contrasted the amalgamated data with that of a matched control population of medical out patients using Students t tests., Results: Locomotor disease was present in 75% of diabetics with the upper limb the commonest site for abnormalities. This prevalence was significantly higher than that seen in the controls (53%) [p=0.02]. Shoulder capsulitis (25%), carpal tunnel syndrome (20%), tenosynovitis (29%), limited joint mobility (28%) and Dupuytrens contracture (13%) were the most frequent findings and were much commoner than in controls. Capsulitis usually coexisted with other upper limb abnormalities and best predicted the presence of retinopathy and/or neuropathy. The mean HbA1c was significantly higher in patients with combined shoulder and hand problems (9.1%) than in those with no upper limb problems (8.0%) [p=0.018]. The pattern of results was similar in type 1 and type 2 diabetes, although the prevalence of abnormalities and mean HAQ were significantly greater in type 2 patients, which may be in part a function of their greater mean age., Conclusion: Upper limb locomotor abnormalities are very common in diabetes and are associated with worse glycaemic control and more diabetic complications. Assessment of upper limb locomotor disease in diabetes should include an estimate of glycaemic control and a search for other complications.

In the present work, biofiltration of xylene vapors has been investigated on a laboratory scale biofilter packed with press mud as filter material inoculated with activated sludge from pharmaceutical industry. Four various gas flow rates, i.e. 0.03, 0.06, 0.09 and 0.12 m(3) h(-1), were tested for inlet xylene concentration ranging from 0.2 to 1.2 g m(-3). The biofilter proved to be highly efficient in the removal of xylene at a gas flow rate of 0.2m(3) h(-1) corresponding to a gas residence time of 2.8 min. For all the tested inlet concentrations, the removal efficiency decreased for high gas flow rates. For all the tested gas flow rates, a decrease in the removal efficiency was noticed for high xylene inlet concentration. The follow-up of carbon dioxide concentration profile through the biofilter revealed that the mass ratio of carbon dioxide produced to the xylene removed was approximately 2.52, which confirms complete degradation of xylene if one considers the fraction of the consumed organic carbon used for the microbial growth.

A rapid, sensitive and highly reproducible SYBR green based real-time PCR assay was developed for detection of tdh positive pathogenic Vibrio parahaemolyticus. Minimum detection limit was 0.1 pg of pure V. parahaemolyticus genomic DNA with typical R(2) values >0.99 and coefficient of variation (CV) values ranging from 1.2 to 4.2 on three different days. The method was also used to evaluate the effect of three different enrichment media alkaline peptone water (APW), sodium taurocholate (ST) broth and salt polymyxin broth (SPB) on detection of V. parahaemolyticus. Crude lysates were directly used for real-time PCR. Without enrichment, the detection limit of pure cultures was 10(1) CFU/ml for ST broth and 10(2) CFU/ml in APW and SPB but for shrimp homogenates spiked with pure culture, the minimum detection limit was 10(2) CFU/ml for all three broths with a linear detection range of 10(2)-10(6). Without enrichment, detection in ST broth was more efficient than APW and SPB. After 6 h enrichment, limit of detection was found to be 1 CFU in all three media. However, for iced shrimp, the limit of detection was 10(2) after 6 h enrichment. No significant difference was seen between different enrichment media with respect to tdh gene detection of V. parahaemolyticus. The methodology developed here can be useful for rapid detection of tdh positive V. parahaemolyticus by laboratories involved in monitoring programmes for pathogenic V. parahaemolyticus.

This review article describes our present understanding of interstitial lung disease (ILD) complicating rheumatoid arthritis (RA). It discusses its high prevalence and clinical relevance, our recent improvement in understanding both its pathology and physiology, and our expectations of ongoing research into the immunology and genetics of the disease. An important section relates to the effects of drugs routinely used in the treatment of the articular manifestations of RA on the lung, especially in the presence of ILD. The major focus of the article is on therapeutic intervention, and here we discuss traditional and often unsuccessful approaches to treatment, leading on to discuss newly introduced therapeutic options such as anticoagulation and oral N-acetylcysteine. In the later sections, we focus our attention on several promising new therapeutic agents, including mycophenolate and new monoclonal antibody therapies, reviewing the limited literature available to support the use of these agents, concluding with a number of other aspects of treatment that are worthy of consideration.

Two real-time PCR assays targeting the small-subunit (SSU) ribosomal DNA (rDNA) were designed to assess the proportional biomass of diatoms and dinoflagellates in marine coastal water. The reverse primer for the diatom assay was designed to be class specific, and the dinoflagellate-specific reverse primer was obtained from the literature. For both targets, we used universal eukaryotic SSU rDNA forward primers. Specificity was confirmed by using a BLAST search and by amplification of cultures of various phytoplankton taxa. Reaction conditions were optimized for each primer set with linearized plasmids from cloned SSU rDNA fragments. The number of SSU rDNA copies per cell was estimated for six species of diatoms and nine species of dinoflagellates; these were significantly correlated to the biovolumes of the cells. Nineteen field samples were collected along the Swedish west coast and subjected to the two real-time PCR assays. The linear regression of the proportion of SSU rDNA copies of dinoflagellate and diatom origin versus the proportion of dinoflagellate and diatom biovolumes or biomass per liter was significant. For diatoms, linear regression of the number of SSU rDNA copies versus biovolume or biomass per liter was significant, but no such significant correlation was detected in the field samples for dinoflagellates. The method described will be useful for estimating the proportion of dinoflagellate versus diatom biovolume or biomass and the absolute diatom biovolume or biomass in various aquatic disciplines.

A mathematical model for a hybrid anaerobic reactor (HAR), which uses self-immobilized anaerobic bacterial granules under completely fluidized condition, has been developed. Stoichiometry of glucose fermentation into methane has been considered in this model. The model includes: (1) a biofilm model which describes substrate conversion kinetics within a single granule; (2) a bed fluidization model which describes the distribution of biogranules within the fluidized bed and (3) a reactor model which links the above two to predict the substrate and products concentration profile along the reactor height. Product and pH inhibition for each group of bacteria has been considered in the kinetic model. The spatial distribution of each group of anaerobic bacteria within granules has been found to play a vital role in bringing about the conversion. Experiments were conducted in the reactor using a synthetic effluent containing glucose as the carbon source to study the treatment efficiency. The model was simulated first assuming a 3-layered distribution [MacLeod, F.A., Guiot, S.R., Costerton, J.W., 1990. Layered structure of bacterial aggregates produced in an upflow anaerobic sludge bed and filter reactor. Applied and Environmental Microbiology 56, 1598-1607.] of anaerobic bacteria within granules and then homogeneous distribution [Grotenhuis, J.T.C., Smit, M., Plugge, C.M., Yuansheng, X., van Lammeren, A.A.M., Stams, A.J.M., Zehnder, A.J.B., 1991. Bacterial composition and structure of granular sludge adapted to different substrates. Applied and Environmental Microbiology 57, 1942-1949.] of anaerobic bacteria. The predictions of model simulation with the assumption of layered structure closely represented the experimental data.

A wide range of web based prediction and annotation tools are frequently used for determining protein function from sequence. However, parallel processing of sequences for annotation through web tools is not possible due to several constraints in functional programming for multiple queries. Here, we propose the development of APAF as an automated protein annotation filter to overcome some of these difficulties through an integrated approach.

A facile, one-pot synthesis of thio and selenourea derivatives from amines using tetrathiomolybdate 1 and tetraselenotungstate 2 as sulfur and selenium transfer reagents, respectively, is reported. The compounds were tested for their activity as urease inhibitors and some of the compounds showed potent activity in the nanomolar range towards jack bean urease.

Shrimp, clam and oysters were obtained at two fish markets and at a fish landing dock, and plankton, water and sediment samples were obtained from four river estuaries, in southern India. The samples were analyzed for Vibrio cholerae by conventional isolation techniques and by polymerase chain reaction (PCR) procedures. V. cholerae was isolated from 2 of 5 shrimp, 2 of 5 clam and 5 of 20 water samples. All biochemically confirmed isolates of V. cholerae were positive for toxR. For direct detection of V. cholerae in enrichment broths, PCR was performed using lysates from 0 and 6 h enrichments. All the V. cholerae isolates and enrichment broth lysates were subjected to PCR analysis for the detection of the genes toxR, ctxA, tcpA, ompU, hly, ace, Nag-ST (stn/sto), and ompU. Enrichment broths of all the samples which yielded V. cholerae were positive for toxR, OmpU and hlyA genes, while one of a fresh fish market sample was positive for the ace gene. Choleragenic V. cholerae were absent from all environmental samples and fresh fish from the markets, but one sample of shrimp was positive for V. cholerae O139.

In recent years, virtual learning is growing rapidly. Universities, colleges, and secondary schools are now delivering training and education over the internet. Beside this, resources available over the WWW are huge and understanding the various techniques employed in the field of Bioinformatics is increasingly complex for students during implementation. Here, we discuss its importance in developing and delivering an educational system in Bioinformatics based on e-learning environment.

Objective: To determine whether drugs used in the treatment of rheumatoid arthritis (RA) contribute to the increased risk of respiratory infection or influence its outcome., Methods: We identified all episodes of lower respiratory tract infection (LRTI) in our RA population over a 12 month period. A detailed drug history was recorded in each case, together with the clinical outcome. Premorbid illnesses and admission data were collected and analyzed to assess the influence of oral steroids and disease modifying antirheumatic drugs (DMARD) on outcome., Results: The overall annual incidence of LRTI in patients with RA was 2.3% with a mortality rate of 22.5%. Demographic factors predicting LRTI included older age and male sex. Oral steroids and not taking DMARD were also associated with an increased risk of hospital admission with LRTI. Being male and having RA for over 10 years trended to the prediction of death as a result of infection. Taking DMARD was not associated with any adverse outcome., Conclusion: Respiratory infection is common in patients with RA and carries a high mortality. Oral steroids predispose to infection, while DMARD do not. Increasing age and male sex also predispose to respiratory tract infection.

Development of aerobic granules in the aeration tank of an activated sludge system has been studied. The introduction of activated carbon particles into the aeration tank resulted in the formation of biogranules containing activated carbon as core nuclei. The presence of activated carbon also induced the formation of self-immobilized granules, which did not have any carrier particle at their core. The presence of aerobic granules enhanced the treatment efficiency of the reactor. At an organic loading rate of 32.8 kg COD m(-3)d(-1) and 0.78 h hydraulic retention time (HRT), the reactor showed 96% COD removal efficiency. At an HRT of 0.272 h and organic loading rate of 46.7 kg COD m(-3)d(-1), the reactor outlet COD remained below 100 mg l(-1). Settling velocity studies carried out on the biogranules showed that the drag coefficient of biogranules is greater than that of the rigid particle at the same Reynolds number.

Anaerobic treatment has become a technically as well as economically feasible option for treatment of liquid effluents after the development of reactors such as the upflow anaerobic sludge blanket (UASB) reactor, expanded granular sludge bed (EGSB) reactor, anaerobic biofilter and anaerobic fluidized bed reactor (AFBR). Considerable effort has gone into developing mathematical models for these reactors in order to optimize their design, design the process control systems used in their operation and enhance their operational efficiency. This article presents a critical review of the different mathematical models available for these reactors. The unified anaerobic digestion model (ADM1) and its application to anaerobic biofilm reactors are also outlined.

Objective: There is little information on the natural history of patients with rheumatoid arthritis (RA) and associated interstitial lung disease (ILD). Cryptogenic fibrosing alveolitis (CFA) is known to have a poor longterm prognosis, and we compared the 2 conditions through a longitudinal prospective study., Methods: We previously compared baseline clinical, physiological, and radiological characteristics in 18 RA-ILD patients with 18 case controls with CFA. Clinical, physiological, and radiological assessment was repeated in all survivors at 5 years, and data on treatment and mortality were collected., Results: The median age in each group was 77 years and 10 patients in each group were male. More patients with RA-ILD survived to 5 years (8 RA-ILD vs 2 CFA; p = 0.03), and median survival was significantly longer for patients with RA-ILD (60 mo) compared to CFA (27 mo; p

When expressed in Escherichia coli, the recombinant coat protein (rCP) of Sesbania mosaic virus (SeMV) was shown to self-assemble into T = 3 capsids encapsidating CP mRNA and 23S rRNA derived from the host. Expression of CP-P53A, in which a conserved proline at position 53 in the beta-annulus was substituted by alanine (CP-P53A), also produced similar capsids. Purified rCP and CP-P53A particles were crystallized and X-ray crystal structures of their mutant capsids were determined to resolutions of 3.6 and 4.1 A, respectively. As in the native viral CP, the CPs in these recombinant capsids adopt the jelly-roll beta-sandwich fold. The amino-terminal residues of the C subunits alone are ordered and form the beta-annulus structure at the quasi-sixfold axes. A characteristic bend in the beta-annulus remains unaffected in CP-P53A. The quasi-threefold interfaces of the capsids harbour calcium ions coordinated by ligands from the adjacent threefold-related subunits in a geometry that is analogous to that observed in the native capsid. Taken together with studies on deletion and substitution mutants of SeMV CP, these results suggest the possibility that the beta-annulus and nucleic acid-mediated interactions may be less important for the assembly of sobemoviruses than previously envisaged.

The bed expansion characteristics of a fluidized bed containing bacterial granules have been studied. These biogranules were obtained from an anaerobic hybrid reactor, which uses biogranules (without carrier particle) in fluidized condition. The settling velocity study of biogranules has shown that the drag coefficient of biogranule is greater than that of the rigid particle at the same Reynolds number. A new correlation based on this finding has been developed. The bed expansion study has demonstrated that a linear relationship exists between the natural logarithm of bed porosity and the natural logarithm of upflow superficial liquid velocity for the bed containing either a particular fraction of biogranule size or biogranules with wide size distribution. For a fluidized bed having a particular granule size, the bed porosity, and liquid superficial velocity could be related by the classic equation suggested by Richardson and Zaki (1954). The characteristic parameter of this correlation, the slope of the line n, has been related with Reynolds number. The intercept of the line gave a smaller value than the unhindered settling velocity of the particle. For fluidized bed having wide size distribution, the characteristic parameter n could not be related to Reynolds number. But the correlation suggested for single biogranule size has been found to predict n value with an average error of 2.3%., ((c) 2005 Wiley Periodicals, Inc.)

Sesbania mosaic virus (SeMV) capsids are stabilized by RNA-protein, protein-protein and calcium-mediated protein-protein interactions. The removal of calcium has been proposed to be a prerequisite for the disassembly of the virus. The crystal structure of native T=3 SeMV capsid revealed that residues D146 and D149 from one subunit and Y205, N267 and N268 of the neighboring subunit form the calcium-binding site (CBS). The CBS environment is found to be identical even in the recombinant CP-NDelta65 T=1 capsids. Here, we have addressed the role of calcium and the residues involved in calcium co-ordination in the assembly and stability of T=3 and T=1 capsids by mutational analysis. Deletion of N267 and N268 did not affect T=3 or T=1 assembly, although the capsids were devoid of calcium, suggesting that assembly does not require calcium ions. However, the stability of the capsids was reduced drastically. Site-directed mutagenesis revealed that either a single mutation (D149N) or a double mutation (D146N-D149N) of SeMV coat protein affected drastically both the assembly and stability of T=3 capsids. On the other hand, the D146N-D149N mutation in CP-NDelta65 did not affect the assembly of T=1 capsid, although their stability was reduced considerably. Since the major difference between the T=3 and T=1 capsids is the absence of the N-terminal arginine-rich motif (N-ARM) and the beta-annulus from the subunits forming the T=1 capsids, it is possible that D149 initiates the N-ARM-RNA interactions that lead to the formation of the beta-annulus, which is essential for T=3 capsid assembly.

Sesbania mosaic virus particles consist of 180 coat protein subunits of 29kDa organized on a T=3 icosahedral lattice. N-terminal deletion mutants of coat protein that lack 36 (CP-NDelta36) and 65 (CP-NDelta65) residues from the N terminus, when expressed in Escherichia coli, produced similar T=1 capsids of approximate diameter 20nm. In contrast to the wild-type particles, these contain only 60 copies of the truncated protein subunits (T=1). CP-NDelta65 lacks the "beta-annulus" believed to be responsible for the error-free assembly of T=3 particles. Though the CP-NDelta36 mutant has the beta-annulus segment, it does not form a T=3 capsid, presumably because it lacks an arginine-rich motif found close to the amino terminus. Both CP-NDelta36 and CP-NDelta65 T=1 capsids retain many key features of the T=3 quaternary structure. Calcium binding geometries at the coat protein interfaces in these two particles are also nearly identical. When the conserved aspartate residues that coordinate the calcium, D146 and D149 in the CP-NDelta65, were mutated to asparagine (CP-NDelta65-D146N-D149N), the subunits assembled into T=1 particles but failed to bind calcium ions. The structure of this mutant revealed particles that were slightly expanded. The analysis of the structures of these mutant capsids suggests that although calcium binding contributes substantially to the stability of T=1 particles, it is not mandatory for their assembly. In contrast, the presence of a large fraction of the amino-terminal arm including sequences that precede the beta-annulus and the conserved D149 appear to be indispensable for the error-free assembly of T=3 particles.

Rheumatoid arthritis (RA) is a common cause of disability in the western population, with an annual incidence of 0.05% and a prevalence of 1%. Although a small percentage of patients go into natural remission, the untreated disease progresses to cause disability, morbidity and early mortality. Unravelling of the cytokine network in the pathogenesis of RA has led to the development of drugs that target these cytokines and prevent joint damage. Three biological anticytokine agents, etanercept, infliximab and anakinra, are now available for use in RA. More experience will quantify their safety and benefits. The potency of the older disease-modifying antirheumatic drugs (DMARDs), such as methotrexate and sulfasalazine, is also being realised, especially when used early in the disease process and in combination. Leflunomide is a new DMARD with efficacy similar to methotrexate and sulfasalazine. Symptomatic treatment of RA with nonsteroidal anti-inflammatory drugs has also undergone a revolution with the availability of a new class of COX-2-specific inhibitors. These drugs control inflammation and provide pain relief with less GI toxicity. Management of comorbid conditions associated with RA and its treatment (i.e., osteoporosis, cardiovascular and lung disease) has also become a priority for the rheumatologist. It is hoped that more aggressive use of conventional DMARDs and biological agents will result in less disability and a higher proportion of patients achieving remission.

BACKGROUND: Patients with rheumatoid arthritis (RA) frequently develop dyspepsia which may be due to peptic ulceration. There have been conflicting published data on the possible interactive roles of nonsteroidal anti-inflammatory drugs (NSAIDs) and colonisation of the gastric antrum with Helicobacter pylori in the development of peptic ulceration. METHODS: We have prospectively assessed the prevalence of peptic ulcers in dyspeptic RA patients and investigated the factors responsible. We endoscoped 100 RA patients comparing the endoscopic findings to those in 100 age- and sex-matched dyspeptic control subjects. Data on NSAID consumption and Helicobacter colonisation were collected for each patient. RESULTS: Endoscopic evidence of peptic ulceration was found in 29 RA patients and in 16 of the control subjects (P=0.03). Multiple ulcers (>2) were found in significantly more RA patients than in controls (10 vs. 2). NSAIDs were being used by 60 RA patients and 22 controls (P<0.001). Helicobacter was found in 41 RA patients and in 33 controls (P=NS). The consumption of NSAIDs conferred a relative risk (RR) of ulceration of 8.67 (1.19-62.87), while the presence of Helicobacter gave a RR for ulcers of 3.71 (0.37-37.35) in RA patients. The RR for the combination of NSAID consumption and Helicobacter colonisation was 14.44 (2.05-101). The corresponding RRs for the dyspeptic controls were 2.13, 1.57 and 1.42 (all P=NS). CONCLUSIONS: Rheumatoid patients have more major and more multiple pathology than age-, sex- and symptom-matched controls. This is due mainly to their increased consumption of NSAIDs. The prevalence of Helicobacter was no greater in RA patients than in controls, but Helicobacter infection increased the risk of NSAID-induced ulceration.