Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism

Background: Alu RNAs are present at elevated levels in stress conditions and, consequently, Alu repeats are increasingly being associated with the physiological stress response. Alu repeats are known to harbor transcription factor binding sites that modulate RNA pol II transcription and Alu RNAs act as transcriptional co-repressors through pol II binding in the promoter regions of heat shock responsive genes. An observation of a putative heat shock factor (HSF) binding site in Alu led us to explore whether, through HSF binding, these elements could further contribute to the heat shock response repertoire. Results: Alu density was significantly enriched in transcripts that are down-regulated following heat shock recovery in HeLa cells. ChIP analysis confirmed HSF binding to a consensus motif exhibiting positional conservation across various Alu subfamilies, and reporter constructs demonstrated a sequence-specific two-fold induction of these sites in response to heat shock. These motifs were over-represented in the genic regions of down-regulated transcripts in antisense oriented Alus. Affymetrix Exon arrays detected antisense signals in a significant fraction of the down-regulated transcripts, 50% of which harbored HSF sites within 5 kb. siRNA knockdown of the selected antisense transcripts led to the over-expression, following heat shock, of their corresponding down-regulated transcripts. The antisense transcripts were significantly enriched in processes related to RNA pol III transcription and the TFIIIC complex. Conclusions: We demonstrate a non-random presence of Alu repeats harboring HSF sites in heat shock responsive transcripts. This presence underlies an antisense-mediated mechanism that represents a novel component of Alu and HSF involvement in the heat shock response

Kloniranje, izražajnost i pročišćavanje bjelančevine 28 iz vanjske membrane Salmonelle enterice serovar Typhimurium za razvoj podjediničnog cjepiva - kratko priopćenje

Salmonella Typhimurium, a major gastrointestinal pathogen, poses a global threat to human health. Public health problems associated with this organism have increased to the extent that it has become a major issue. The bacterium is becoming resistant to the commonly available antibiotics, and vaccines also suffer from limitations such as short lived immunity. Therefore, there is an urgent need for the development of an effective vaccine. The outer membrane proteins (Omps) of Salmonella have proven their capability to be developed as a vaccine candidate for prevention of salmonellosis. With this aim, in the present study the Omp28 gene of Salmonella Typhimurium was amplified, cloned and expressed under an IPTG induction system. The recombinant protein thus produced was purified and tested for its antigenicity. The antigenicity of the purified protein was confirmed by western blotting with antiserum raised in rabbit against Omps of S. Typhimurium. The Omp28 gene was amplified as a 330bp product. The expressed protein was found to be of approximately 28kDa and it produced a strong signal in western blot analysis. This study concluded that Omp28 may be proven to be an effective candidate for the development of r-DNA vaccine against salmonellosis.Salmonella Typhimurium glavni je gastrointestinalni patogen koji je globalna prijetnja ljudskome zdravlju. Javnozdravstveni problemi povezani s ovim organizmom povećali su se do te mjere da je postao glavno pitanje na koje se traže brojni odgovori. Bakterija postaje otporna na najčešće dostupne antibiotike, a ograničavajuća uporaba cjepiva povezana je s kratkotrajnim imunitetom. Zbog toga postoji hitna potreba za razvoj učinkovitog cjepiva. Vanjske bjelančevine membrane (engl. Outer membrane proteins, Omps) salmonele dokazale su svoju sposobnost kandidata za razvoj cjepiva koje bi se koristilo u prevenciji salmoneloze. S tim je ciljem u ovom radu, pod uvjetima IPTG indukcijskog sustava, provedeno umnažanje i kloniranje te provjerena izražajnost gena za Omp28 iz Salmonelle Typhimurium. Tako dobivena rekombinantna bjelančevina pročišćena je i testirana s obzirom na antigenu sposobnost. Antigena sposobnost pročišćene bjelančevine potvrđena je uporabom Western blot metode s antiserumom protiv Omps-a iz S. Typhimurium dobivenim od zeca. Genom Omp28 umnožen je kao 330bp produkt. Bjelančevina je imala približno 28 kDa i Western blot analizom pokazala je izraženost jakog signala. Ovim je istraživanjem zaključeno da Omp28 može poslužiti kao učinkoviti kandidat za razvoj r-DNA cjepiva protiv salmoneloze

Factors Associated with Physician Agreement on Verbal Autopsy of over 27000 Childhood Deaths in India

Each year, more than 10 million children younger than five years of age die. The large majority of these deaths occur in the developing world. The verbal autopsy (VA) is a tool designed to ascertain cause of death in such settings. While VA has been validated against hospital diagnosed cause of death, there has been no research conducted to better understand the factors that may influence individual physicians in determining cause of death from VA.This study uses data from over 27,000 neonatal and childhood deaths from The Million Death Study in which 6.3 million people in India were monitored for vital status between 1998 and 2003. The main outcome variable was physician agreement or disagreement of category of death and the variables were assessed for association using the kappa statistic, univariate and multivariate logistic regression using a conceptual hierarchical model, and a sensitivity and specificity analysis using the final VA category of mortality as the gold standard. The main variables found to be significantly associated with increased physician agreement included older ages and male gender of the deceased. When taking into account confounding factors in the multivariate analysis, we did not find consistent significant differences in physician agreement based on the death being in a rural or urban area, at home or in a health care facility, registered or not, or the respondent's gender, religion, relationship to the deceased, or whether or not the respondent lived with the deceased.Factors influencing physician agreement/disagreement to the greatest degree are the gender and age of the deceased; specifically, physicians tend to be less likely to agree on a common category of death in female children and in younger ages, particularly neonates. Additional training of physician reviewers and continued adaptation of the VA itself, with a focus on gender and age of the deceased, may be useful in increasing rates of physician agreement in these groups

Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection

Primate-specific Alus harbor different regulatory features, including miRNA targets. In this study, we provide evidence for miRNA-mediated modulation of transcript isoform levels during heat-shock response through exaptation of Alu-miRNA sites in mature mRNA. We performed genome-wide expression profiling coupled with functional validation of miRNA target sites within exonized Alus, and analyzed conservation of these targets across primates. We observed that two miRNAs (miR-15a-3p and miR-302d-3p) elevated in stress response, target RAD1, GTSE1, NR2C1, FKBP9 and UBE2I exclusively within Alu. These genes map onto the p53 regulatory network. Ectopic overexpression of miR-15a-3p downregulates GTSE1 and RAD1 at the protein level and enhances cell survival. This Alu-mediated fine-tuning seems to be unique to humans as evident from the absence of orthologous sites in other primate lineages. We further analyzed signatures of selection on Alu-miRNA targets in the genome, using 1000 Genomes Phase-I data. We found that 198 out of 3177 Alu-exonized genes exhibit signatures of selection within Alu-miRNA sites, with 60 of them containing SNPs supported by multiple evidences (global-FST > 0.3, pair-wise-FST > 0.5, Fay-Wu’s H<−20, iHS> 2.0, high ΔDAF) and implicated in p53 network. We propose that by affecting multiple genes, Alu-miRNA interactions have the potential to facilitate population-level adaptations in response to environmental challenges

Medication error in general medicine department of tertiary care Koshi Zonal hospital in Nepal

Background: Medication errors are the leading cause of patient harm, injuries and even death in hospitalized patients. It endangers patient safety and also increases the cost of treatment leading to enhanced financial burden to the individuals and the community as well. The study was aimed to determine the pattern of occurrence of medication errors. Methods: A cross-sectional study was conducted in 188 hospitalized patients in medical ward at a Zonal Hospital. Medication errors were identified and categorized by reviewing the cardex. The data were analyzed to determine the cause of medication errors including rates of harm to patients. The descriptive statistics frequency and percentage were calculated using Microsoft Excel 2007. The findings were presented as tables and graphs. Results: A total of 985 medication errors were found in 650 (38.3%) drugs prescribed in 177 (94.1%) patients. Approximately 72.9% of the errors reached the patients and 32.39% of the errors were harmful. The most common observed errors were administration errors (41.6%) followed by prescribing errors (36.5%), transcription errors (14.3%) and monitoring errors (7.5%). Omission of prescribing information (63.88%) and wrong dosing schedule (34%) were the most common type of prescribing and transcription errors respectively. Omission of dosages administration (57.32%) to patients was the most common types of administration error. All types of medication errors were highest in the alimentary tract and metabolism class of drugs (32.39%). Conclusions: Medication errors were associated with the majority of hospitalized patients signifying the requirement of immediate preventive strategies and policies to ensure patient safety

Scrap computer keyboards a sustainable resource for silver (Ag) and low density oil (L D Oil)

Most neglected part of the scrap computers are the keyboards, which are generally incinerated by the informal recycling sectors creating environmental pollution and leads to the wastage of precious metallic contents present in it. Present paper is focused on a novel chemical processing technique developed to recover silver (Ag) as value added product and low density oil (L D Oil) from the computer keyboards. Initially, scrap keyboards were manually dismantled to separate Mylar sheets and the same were pyrolysed at 300 ◦C for 2 h to recover L D Oil. The obtained pyrolysed Mylar sheets was further crushed, milled and homogenized to reduce particle size (− 100 mesh). The crushed sample was leached using 2 M HNO3 at 60 ◦C in mixing time of 20 min and pulp density of 100 g/L to achieve maximum dissolution of Ag. The leaching kinetics for Ag dissolution well fitted with chemical reaction control dense constant size cylindrical particles, 1-(1-X)1/2 = kct. The obtained leach liquor was put to cementation process using metallic copper (Cu). Almost 99% of Ag gets cemented as Ag powder in 15 min at a constant solution temperature of 60 ◦C and pH 1.1. The developed bench scale process has application orientation to the industry after piloting the process

Factors Associated with Physician Agreement and Coding Choices of Cause of Death Using Verbal Autopsies for 1130 Maternal Deaths in India

The Indian Sample Registration System (SRS) with verbal autopsy methods provides estimations of cause specific mortality for maternal deaths, where the majority of deaths occur at home, unregistered. We aim to examine factors that influence physician agreement and coding choices in assigning causes of death from verbal autopsies.Among adult deaths identified in the SRS, pregnancy-related deaths recorded in 2001-2003 were assigned ICD-10 codes by two independent physicians. Inter-rater reliability was estimated using Landis Koch Kappa classification ≤0.4--poor to fair agreement; >0.4 ≤0.6--moderate agreement; >0.6 ≤0.8--substantial agreement; >8--high agreement. We identified factors associated with physician agreement using multivariate logistic regression. A central consensus panel reviewed cases for errors and reclassified as needed based on 2011 ICD-10 coding guidelines. Of 1130 pregnancy-related deaths, 1040 were assigned ICD-10 codes by two physicians. We found substantial agreement regardless of the woman's residence, whether the death was registered, religion, respondent's or deceased's education, age, hospital admission or gestational age. Physician agreement was not influenced by the above variables, with the exception of greater agreement in cases where the respondent did not live with the deceased, or early gestational age at the time of death. A central consensus panel reviewed all cases and recoded 10% of cases due to insufficient use of information in the verbal autopsy by the coding physicians and rationale for this reclassification are discussed.In the absence of complete vital registration and universal healthcare services, physician coded verbal autopsies continues to be heavily relied upon to ascertain pregnancy-related death. From this study, two independent physicians had good inter-rater reliability for assigning pregnancy-related causes of death in a nationally-represented sample, and physician coding does not appear to be heavily influenced by case characteristics or demographics

Leaching of Korean monazite for the recovery of rare earth metals

The technological innovations resulted in various applications using rare earth metals (REM), which lead to a steep increase in their demand. Monazite is the second most essential naturally occurring phosphate mineral containing REM. The present work reports the recovery of REM from Korean monazite which contained mainly 50.12% rare earth oxide and 29.4% phosphate. For the recovery of REM from monazite, the hydrometallurgical process consisting of alkaline leaching of phosphate followed by acid dissolution of REM has been reported. As the presence of phosphate decreases the leaching efficiency of REM from monazite, the studies were carried out initially for hot digestion of phosphate present in the monazite in an autoclave using sodium hydroxide, which resulted in the formation of RE oxide and soluble sodium phosphate. To get the optimum condition for phosphate decomposition by alkaline leaching, the various process parameters such as concentration of sodium hydroxide, temperature, mixing time and pulp density were studied. The obtained slurry was washed with hot water and filtered to get sodium phosphate in the solution. A maximum of 99% phosphate was removed from monazite concentrate using 50% sodium hydroxide solutions (wt./vol.) at 170oC in 4 h mixing time maintaining the pulp density of 100 g/L. From the phosphate free monazite sample, REM was leached out using hydrochloric acid. More than 95% of REM was found to be leached out using 6M HCl at constant pulp density 100 g/L, temperature 90oC and mixing time 2 h. Further studies are in progress to obtain pure solution and salts of REM from chloride leach liquor using recipitation/ solvent extraction/ ion-exchange techniques

Capturing the Context of Maternal Deaths from Verbal Autopsies: A Reliability Study of the Maternal Data Extraction Tool (M-DET)

BACKGROUND: The availability of quality data to inform policy is essential to reduce maternal deaths. To characterize maternal deaths in settings without complete vital registration systems, we designed and assessed the inter-rater reliability of a tool to systematically extract data and characterize the events that precede a nationally representative sample of maternal deaths in India. METHOD/PRINCIPAL FINDINGS: Of 1017 nationally representative pregnancy-related deaths, which occurred between 2001 and 2003, we randomly selected 105 reports. Two independent coders used the maternal data extraction tool (questions with coding guidelines) to collect information on antenatal care access, final pregnancy outcome; planned place of birth and care provider; community consultation, transport, admission, hospital referral; and verification of cause of death assignment. Kappa estimated inter-rater agreement was calculated and classified as poor (K≤0.4), moderate (K = 0.4≤0.6), substantial (K = 0.6≤ 0.8) and high (K>0.8) using the criteria from Landis & Koch. The data extraction tool had high agreement for gestational age, pregnancy outcome, transport, death en route and admission to hospital; substantial agreement for receipt of antenatal care, planned place of birth, readmission and referral to higher level hospital, and whether or not death occurred in the intrapartum period; moderate to substantial agreement for classification of deaths as direct or indirect obstetric deaths or incidental deaths; moderate agreement for classification of community healthcare consultation and total number of healthcare contacts; and poor agreement for the classification of deaths as sudden deaths and other/unknown cause of death. The ability of the tool to identify the most-responsible-person in labour varied from moderate agreement to high agreement. CONCLUSIONS: This data extraction tool achieved good inter-rater reliability and can be used to collect data on events surrounding maternal deaths and for verification/improvement of underlying cause of death