Structural and kinetic studies on adenylosuccinate lyase from Mycobacterium smegmatis and Mycobacterium tuberculosis provide new insights on the catalytic residues of the enzyme

Adenylosuccinate lyase (ASL), an enzyme involved in purine biosynthesis, has been recognized as a drug target against microbial infections. In the present study, ASL from Mycobacteriumsmegmatis (MsASL) and Mycobacteriumtuberculosis (MtbASL) were cloned, purified and crystallized. The X-ray crystal structure of MsASL was determined at a resolution of 2.16 angstrom. It is the first report of an apo-ASL structure with a partially ordered active site C3 loop. Diffracting crystals of MtbASL could not be obtained and a model for its structure was derived using MsASL as a template. These structures suggest that His149 and either Lys285 or Ser279 of MsASL are the residues most likely to function as the catalytic acid and base, respectively. Most of the active site residues were found to be conserved, with the exception of Ser148 and Gly319 of MsASL. Ser148 is structurally equivalent to a threonine in most other ASLs. Gly319 is replaced by an arginine residue in most ASLs. The two enzymes were catalytically much less active compared to ASLs from other organisms. Arg319Gly substitution and reduced flexibility of the C3 loop might account for the low catalytic activity of mycobacterial ASLs. The low activity is consistent with the slow growth rate of Mycobacteria and their high GC containing genomes, as well as their dependence on other salvage pathways for the supply of purine nucleotides. Structured digital abstract andby()

Successful data recovery from oscillation photographs containing strong polycrystalline diffraction rings from an unknown small-molecule contaminant: preliminary structure solution of Salmonella typhimurium pyridoxal kinase (PdxK)

Pyridoxal kinase (PdxK; EC 2.7.1.35) belongs to the phosphotransferase family of enzymes and catalyzes the conversion of the three active forms of vitamin B-6, pyridoxine, pyridoxal and pyridoxamine, to their phosphorylated forms and thereby plays a key role in pyridoxal 5 `-phosphate salvage. In the present study, pyridoxal kinase from Salmonella typhimurium was cloned and overexpressed in Escherichia coli, purified using Ni-NTA affinity chromatography and crystallized. X-ray diffraction data were collected to 2.6 angstrom resolution at 100 K. The crystal belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with unitcell parameters a = 65.11, b = 72.89, c = 107.52 angstrom. The data quality obtained by routine processing was poor owing to the presence of strong diffraction rings caused by a polycrystalline material of an unknown small molecule in all oscillation images. Excluding the reflections close to powder/polycrystalline rings provided data of sufficient quality for structure determination. A preliminary structure solution has been obtained by molecular replacement with the Phaser program in the CCP4 suite using E. coli pyridoxal kinase (PDB entry 2ddm) as the phasing model. Further refinement and analysis of the structure are likely to provide valuable insights into catalysis by pyridoxal kinases.

Design, Development and Calibration of HTS Wire Based LOX Level Sensor Probe

For space applications, the weight of the liquid level sensors are of major concern as they affect the payload fraction and hence the cost. An attempt is made to design and test a light weight High Temperature Superconductor (HTS) wire based liquid level sensor for Liquid Oxygen (LOX) tank used in the cryostage of the spacecraft. The total resistance value measured of the HTS wire is inversely proportional to the liquid level. A HTS wire (SF12100) of 12mm width and 2.76m length without copper stabilizer has been used in the level sensor. The developed HTS wire based LOX level sensor is calibrated against a discrete diode array type level sensor. Liquid Nitrogen (LN2) and LOX has been used as cryogenic fluid for the calibration purpose. The automatic data logging for the system has been done using LabVIEW11. The net weight of the developed sensor is less than 1 kg.

Reduced Hornbill Abundance Associated with Low Seed Arrival and Altered Recruitment in a Hunted and Logged Tropical Forest

Logging and hunting are two key direct threats to the survival of wildlife in the tropics, and also disrupt important ecosystem processes. We investigated the impacts of these two factors on the different stages of the seed dispersal cycle, including abundance of plants and their dispersers and dispersal of seeds and recruitment, in a tropical forest in north-east India. We focused on hornbills, which are important seed dispersers in these forests, and their food tree species. We compared abundances of hornbill food tree species in a site with high logging and hunting pressures (heavily disturbed) with a site that had no logging and relatively low levels of hunting (less disturbed) to understand logging impacts on hornbill food tree abundance. We compared hornbill abundances across these two sites. We, then, compared the scatter-dispersed seed arrival of five large-seeded tree species and the recruitment of four of those species. Abundances of hornbill food trees that are preferentially targeted by logging were two times higher in the less disturbed site as compared to the heavily disturbed site while that of hornbills was 22 times higher. The arrival of scatter-dispersed seeds was seven times higher in the less disturbed site. Abundances of recruits of two tree species were significantly higher in the less disturbed site. For another species, abundances of younger recruits were significantly lower while that of older recruits were higher in the heavily disturbed site. Our findings suggest that logging reduces food plant abundance for an important frugivore-seed disperser group, while hunting diminishes disperser abundances, with an associated reduction in seed arrival and altered recruitment of animal-dispersed tree species in the disturbed site. Based on our results, we present a conceptual model depicting the relationships and pathways between vertebrate-dispersed trees, their dispersers, and the impacts of hunting and logging on these pathways.

A possible alchemist apparatus from the early islamic period excavated at Ramla, Israel

Abstract: During extensive salvage excavations carried out during the years 2004-2008 in a large Early Islamic industrial area at the vicinities of Ramla, in Central Israel, an unparalleled industrial device was unearthed. The star-shaped, soil embedded installation, whose lower part was preserved, consisted of a central pottery jar surrounded by five minor jars, linked by ceramic pipes. Evidence of heat was observed mainly around the central vessel, and metal hollow cones perforated in the tip were found inside the surrounding jars. Although the manufacturing procedures and operation techniques of the installation are not completely clear, it is proposed that the installation is part of an industrial workshop or an alchemy laboratory. Both industry and alchemy were well-developed during the Early Islamic period and very often closely related, to the point that sometimes it is difficult to distinguish between them. The identification proposed is based on comparisons with tools described in literary sources, and somewhat later drawings and etchings. Circumstantial ceramic evidence was found, as well as the proximity of a bathhouse whose guests could have been the consumers of perfumes and unguents seem to reinforce this possibility. Due to the poor state of preservation of the device and the lack of available comparisons, the identification proposed here is tentative, and future research coupled with eventual new discoveries is needed in order to clarify this matter.

Stock assessment of loggerhead and leatherback sea turtles and An assessment of the impact of the pelagic longline fishery on the loggerhead and leatherback sea turtles of the Western North Atlantic

On September 7, 2000 the National Marine Fisheries Service announced that it was reinitiating consultation under Section 7 of the Endangered Species Act on pelagic fisheries for swordfish, sharks, tunas, and billfish. 1 Bycatch of a protected sea turtle species is considered a take under the Endangered Species Act (PL93-205). On June 30, 2000 NMFS completed a Biological Opinion on an amendment to the Highly Migratory Pelagic Fisheries Management Plan that concluded that the continued operation of the pelagic longline fishery was likely to jeopardize the continued existence of loggerhead and leatherback sea turtles.2 Since that Biological Opinion was issued NMFS concluded that further analyses of observer data and additional population modeling of loggerhead sea turtles was needed to determine more precisely the impact of the pelagic longline fishery on turtles. 3,4 Hence, the reinitiation of consultation. The documents that follow constitute the scientific review and synthesis of information pertaining to the narrowly defined reinitiation of consultation: the impact of the pelagic longline fishery on loggerhead and leatherback sea turtles The document is in 3 parts, plus 5 appendices. Part I is a stock assessment of loggerhead sea turtles of the Western North Atlantic. Part II is a stock assessment of leatherback sea turtles of the Western North Atlantic. Part III is an assessment of the impact of the pelagic longline fishery on loggerhead and leatherback sea turtles of the Western North Atlantic. These documents were prepared by the NMFS Southeast Fisheries Science Center staff and academic colleagues at Duke University and Dalhousie University. Personnel involved from the SEFSC include Joanne Braun-McNeill, Lisa Csuzdi, Craig Brown, Jean Cramer, Sheryan Epperly, Steve Turner, Wendy Teas, Nancy Thompson, Wayne Witzell, Cynthia Yeung, and also Jeff Schmid under contract from the University or Miami. Our academic colleagues, Ransom Myers, Keith Bowen, and Leah Gerber from Dalhousie University and Larry Crowder and Melissa Snover from Duke University, also recipients of a Pew Charitable Trust Grant for a Comprehensive Study of the Ecological Impacts of the Worldwide Pelagic Longline Industry, made significant contributions to the quantitative analyses and we are very grateful for their collaboration. We appreciate the reviews of the stock definition sections on loggerheads and leatherbacks by Brian Bowen, University of Florida, and Peter Dutton, National Marine Fisheries Service Southwest Fisheries Science Center, respectively, and the comments of the NMFS Center of Independent Experts reviewers Robert Mohn, Ian Poiner, and YouGan Wang on the entire document. We also wish to acknowledge all the unpublished data used herein which were contributed by many researchers, especially the coordinators and volunteers of the nesting beach surveys and the sea turtle stranding and salvage network and the contributors to the Cooperative Marine Turtle Tagging Program. (PDF contains 349 pages)

Statistical and econometric analysis of the treatment of HIV/AIDS

The epidemic of HIV/AIDS in the United States is constantly changing and evolving, starting from patient zero to now an estimated 650,000 to 900,000 Americans infected. The nature and course of HIV changed dramatically with the introduction of antiretrovirals. This discourse examines many different facets of HIV from the beginning where there wasn't any treatment for HIV until the present era of highly active antiretroviral therapy (HAART). By utilizing statistical analysis of clinical data, this paper examines where we were, where we are and projections as to where treatment of HIV/AIDS is headed.

Chapter Two describes the datasets that were used for the analyses. The primary database utilized was collected by myself from an outpatient HIV clinic. The data included dates from 1984 until the present. The second database was from the Multicenter AIDS Cohort Study (MACS) public dataset. The data from the MACS cover the time between 1984 and October 1992. Comparisons are made between both datasets.

Chapter Three discusses where we were. Before the first anti-HIV drugs (called antiretrovirals) were approved, there was no treatment to slow the progression of HIV. The first generation of antiretrovirals, reverse transcriptase inhibitors such as AZT (zidovudine), DDI (didanosine), DDC (zalcitabine), and D4T (stavudine) provided the first treatment for HIV. The first clinical trials showed that these antiretrovirals had a significant impact on increasing patient survival. The trials also showed that patients on these drugs had increased CD4+ T cell counts. Chapter Three examines the distributions of CD4 T cell counts. The results show that the estimated distributions of CD4 T cell counts are distinctly non-Gaussian. Thus distributional assumptions regarding CD4 T cell counts must be taken, into account when performing analyses with this marker. The results also show the estimated CD4 T cell distributions for each disease stage: asymptomatic, symptomatic and AIDS are non-Gaussian. Interestingly, the distribution of CD4 T cell counts for the asymptomatic period is significantly below that of the CD4 T cell distribution for the uninfected population suggesting that even in patients with no outward symptoms of HIV infection, there exists high levels of immunosuppression.

Chapter Four discusses where we are at present. HIV quickly grew resistant to reverse transcriptase inhibitors which were given sequentially as mono or dual therapy. As resistance grew, the positive effects of the reverse transcriptase inhibitors on CD4 T cell counts and survival dissipated. As the old era faded a new era characterized by a new class of drugs and new technology changed the way that we treat HIV-infected patients. Viral load assays were able to quantify the levels of HIV RNA in the blood. By quantifying the viral load, one now had a faster, more direct way to test antiretroviral regimen efficacy. Protease inhibitors, which attacked a different region of HIV than reverse transcriptase inhibitors, when used in combination with other antiretroviral agents were found to dramatically and significantly reduce the HIV RNA levels in the blood. Patients also experienced significant increases in CD4 T cell counts. For the first time in the epidemic, there was hope. It was hypothesized that with HAART, viral levels could be kept so low that the immune system as measured by CD4 T cell counts would be able to recover. If these viral levels could be kept low enough, it would be possible for the immune system to eradicate the virus. The hypothesis of immune reconstitution, that is bringing CD4 T cell counts up to levels seen in uninfected patients, is tested in Chapter Four. It was found that for these patients, there was not enough of a CD4 T cell increase to be consistent with the hypothesis of immune reconstitution.

In Chapter Five, the effectiveness of long-term HAART is analyzed. Survival analysis was conducted on 213 patients on long-term HAART. The primary endpoint was presence of an AIDS defining illness. A high level of clinical failure, or progression to an endpoint, was found.

Chapter Six yields insights into where we are going. New technology such as viral genotypic testing, that looks at the genetic structure of HIV and determines where mutations have occurred, has shown that HIV is capable of producing resistance mutations that confer multiple drug resistance. This section looks at resistance issues and speculates, ceterus parabis, where the state of HIV is going. This section first addresses viral genotype and the correlates of viral load and disease progression. A second analysis looks at patients who have failed their primary attempts at HAART and subsequent salvage therapy. It was found that salvage regimens, efforts to control viral replication through the administration of different combinations of antiretrovirals, were not effective in 90 percent of the population in controlling viral replication. Thus, primary attempts at therapy offer the best change of viral suppression and delay of disease progression. Documentation of transmission of drug-resistant virus suggests that the public health crisis of HIV is far from over. Drug resistant HIV can sustain the epidemic and hamper our efforts to treat HIV infection. The data presented suggest that the decrease in the morbidity and mortality due to HIV/AIDS is transient. Deaths due to HIV will increase and public health officials must prepare for this eventuality unless new treatments become available. These results also underscore the importance of the vaccine effort.

The final chapter looks at the economic issues related to HIV. The direct and indirect costs of treating HIV/AIDS are very high. For the first time in the epidemic, there exists treatment that can actually slow disease progression. The direct costs for HAART are estimated. It is estimated that the direct lifetime costs for treating each HIV infected patient with HAART is between $353,000 to $598,000 depending on how long HAART prolongs life. If one looks at the incremental cost per year of life saved it is only $101,000. This is comparable with the incremental costs per year of life saved from coronary artery bypass surgery.

Policy makers need to be aware that although HAART can delay disease progression, it is not a cure and HIV is not over. The results presented here suggest that the decreases in the morbidity and mortality due to HIV are transient. Policymakers need to be prepared for the eventual increase in AIDS incidence and mortality. Costs associated with HIV/AIDS are also projected to increase. The cost savings seen recently have been from the dramatic decreases in the incidence of AIDS defining opportunistic infections. As patients who have been on HAART the longest start to progress to AIDS, policymakers and insurance companies will find that the cost of treating HIV/AIDS will increase.

Optimal Abandonment of Coal-Fired Stations in the EU

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Uptake and factors that influence the use of 'sit less, move more' occupational intervention strategies in Spanish office employees

Background: Little is known about the types of 'sit less, move more' strategies that appeal to office employees, or what factors influence their use. This study assessed the uptake of strategies in Spanish university office employees engaged in an intervention, and those factors that enabled or limited strategy uptake. Methods: The study used a mixed method design. Semi-structured interviews were conducted with academics and administrators (n = 12; 44 +/- 12 mean SD age; 6 women) at three points across the five-month intervention, and data used to identify factors that influenced the uptake of strategies. Employees who finished the intervention then completed a survey rating (n = 88; 42 +/- 8 mean SD age; 51 women) the extent to which strategies were used [never (1) to usually (4)]; additional survey items (generated from interviewee data) rated the impact of factors that enabled or limited strategy uptake [no influence (1) to very strong influence (4)]. Survey score distributions and averages were calculated and findings triangulated with interview data. Results: Relative to baseline, 67% of the sample increased step counts post intervention (n = 59); 60% decreased occupational sitting (n = 53). 'Active work tasks' and 'increases in walking intensity' were the strategies most frequently used by employees (89% and 94% sometimes or usually utilised these strategies); 'walk-talk meetings' and ` lunchtime walking groups' were the least used (80% and 96% hardly ever or never utilised these strategies). 'Sitting time and step count logging' was the most important enabler of behaviour change (mean survey score of 3.1 +/- 0.8); interviewees highlighted the motivational value of being able to view logged data through visual graphics in a dedicated website, and gain feedback on progress against set goals. 'Screen based work' (mean survey score of 3.2 +/- 0.8) was the most significant barrier limiting the uptake of strategies. Inherent time pressures and cultural norms that dictated sedentary work practices limited the adoption of 'walk-talk meetings' and ` lunch time walking groups'. Conclusions: The findings provide practical insights into which strategies and influences practitioners need to target to maximise the impact of 'sit less, move more' occupational intervention strategies.

Correlação da resposta clínica à vardenafila em dois regimes terapêuticos com parâmetros vasculares e escore de risco cardiovascular em hipertensos com disfunção erétil vasculogênica

A disfunção erétil (DE) tem alta prevalência entre hipertensos e tem sido considerada marcador precoce de risco cardiovascular. A presença e gravidade da DE bem como a resposta clínica aos inibidores da fosfodiesterase tipo 5 (PDE5) parecem depender da biodisponibilidade do óxido nítrico (NO) endotelial e da extensão da doença aterosclerótica. O objetivo deste estudo foi avaliar a resposta clínica da vardenafila usada em dois regimes terapêuticos em hipertensos com DE vasculogênica e sem doença cardiovascular maior, correlacionando a gravidade da DE e a eficácia da vardenafila com dados antropométricos, laboratoriais, escore de risco cardiovascular e parâmetros vasculares funcionais e estruturais. A resposta clínica à vardenafila nos dois regimes foi avaliada conforme o percentual de respostas positivas à questão 3 do Perfil do Encontro Sexual (PES3). Os parâmetros vasculares considerados foram a espessura médio-intimal (EMI) da carótida comum, a dilatação mediada pelo fluxo (DMF) da artéria braquial e a dilatação nitrato-mediada (DNM). Foram incluídos 100 homens hipertensos com idade entre 50 e 70 anos, sendo 74 portadores de DE vasculogênica e 26 com função erétil normal que serviram de grupo controle. Nos pacientes com DE, o índice de massa corporal, relação cintura-quadril, EMI da carótida, níveis séricos de triglicerídeos, colesterol total e LDL foram significativamente maiores que no grupo controle. Após o uso de vardenafila on demand (fase 1), os pacientes com mais de 50% de respostas positivas ao PES3 ou 50% de respostas afirmativas e um incremento de 6 pontos ou mais em relação ao Índice Internacional de Função Erétil (IIEF-FE) basal e/ou resposta positiva a Questão de Avaliação Global (QAG), foram considerados respondedores. O escore do IIEF-FE basal se correlacionou negativamente com a EMI da carótida (r=-0,48, P<0,001) e com o escore de Framingham (r= -0,41, P<0,001) no grupo com DE. Houve forte correlação positiva entre a resposta clínica à vardenafila com a DMF (r= 0,70, P<0,001), que não se observou entre o sub-grupo de diabéticos. Os 35 pacientes considerados não-respondedores na fase 1 foram randomizados e, em desenho duplo-cego, receberam vardenafila ou placebo diariamente durante cinco semanas, podendo usar 10 mg de vardenafila uma hora antes da atividade sexual (fase2). Houve resposta clínica positiva em 38,8% dos que receberam a vardenafila na fase 2 e esta resposta se correlacionou com a frequência sexual (r= 0,68, P<0,01) e com o escore de Framingham (r= -0,65, P<0,01), com a EMI da carótida (r= -0,61, P=0,01) e com o LDL-colesterol (r= -0,64, P<0,01). A vardenafila foi bem tolerada em ambos os regimes terapêuticos. Concluímos que nessa amostra de hipertensos, a gravidade da DE foi relacionada a parâmetros vasculares estruturais (EMI), enquanto a resposta clínica à vardenafila on demand foi mais diretamente dependente da função vascular momentânea (DMF). Houve benefício na utilização de vardenafila diariamente com o objetivo de resgatar a eficácia do inibidor quanto à melhora do desempenho sexual. A falta de eficácia clínica ao inibidor da PDE5 em ambos os regimes terapêuticos pode servir como marcador clínico que identifica homens hipertensos com um risco cardiovascular aumentado.

Fish tracking technology development. Phases 1 and 2, project definition desk study and equipment

The document reports on the major findings from a definition study to appraise the options to develop fish tracking equipment, in particular tags and data logging systems, in order to improve the effeciency of the Agency tracking studies and to obtain a greater understanding of fish biology. The definition study was in two parts. The first, Phase 1, collated and evaluated all the known tracking systems that may be suitable for studies of fish which are either produced commercially or have been constructed for specific in-house studies. Phase 2 was an evaluation of all the tracking equipment considered to merit further investigation in Phase 1. The deficiencies between existing and required technologies to improve the efficiency of Agency's tracking studies and to obtain a greater understanding of fish biology are also identified.

Fish tracking technology development. Phase 1 project definition desk study

The document reports on Phase 1 of a definition study to appraise the options to develop fish tracking equipment, in particular tags and data logging systems in order to improve the efficiency of the Environment Agency's tracking studies and to obtain a greater understanding of fish biology. Covered in this report are radio telemetry, audio telemetry, High Resolution Position Fixing, data storage and archival tags and other fish tracking systems such as biosonics.

Lune, Wyre & Furness Fisheries Advisory Committee 9th September, 1974

This is the report from the Lune, Wyre and Furness Fisheries Advisory Committee meeting, which was held on the 9th September 1974. The report looks at comments of the Regional Fisheries Officer on the report 'Taking Stock', and information including the aims of a report entitled 'Coarse Fisheries'. The report also includes sections on the improvement of fisheries in the River Leven, coarse fish salvage and stocking, fishery prosecutions, and biological work on the River Kent. Fish mortalities are also given as well as fish monitoring figures for areas on the Rivers Lune and Leven for 1974. The Fisheries Advisory Committee was part of the Regional Water Authorities, in this case the North West Water Authority. This preceded the Environment Agency which came into existence in 1996.

South Lancashire Fisheries Advisory Committee 11th September, 1974

This is the report from the South Lancashire Fisheries Advisory Committee meeting, which was held on the 11th September 1974. The report looks at comments of the Regional Fisheries Officer on the report 'Taking Stock', and information including the aims of a report entitled 'Coarse Fisheries'. The report also covers sections on the working of Langcliffe Rearing Station, coarse fish salvage and stocking, fishery prosecutions, and biological work on Hoddlesdon Reservoir. Fish mortalities are also given as well as fish monitoring figures for areas on the Rivers Ribble and Hodder for 1974. The Fisheries Advisory Committee was part of the Regional Water Authorities, in this case the North West Water Authority. This preceded the Environment Agency which came into existence in 1996.

Lune, Wyre & Furness Fisheries Advisory Committee 9th December, 1974

This is the report from the Lune, Wyre and Furness Fisheries Advisory Committee meeting, which was held on the 9th December 1974. The report looks at information on the Water Bailiffs establishment, including the organisation and the duties of both the Fisheries Inspector and the Senior Bailiff. It also covers the comments from the Regional Fisheries Officer on the report on 'Coarse Fisheries', and the report by the Unit Fisheries Officer on fisheries activities. This looks at coarse fish salvage and stocking, fisheries management, biological work carried out, which include initial studies of the utilisation of sonic tagging methods in the monitoring of salmon in estuaries, fish mortalities, and the fish monitoring figures for areas on the Rivers Lune and Leven. The last section looks at bank erosion on the River Lune. The Fisheries Advisory Committee was part of the Regional Water Authorities, in this case the North West Water Authority. This preceded the Environment Agency which came into existence in 1996.