When “conservation” leads to land degradation: lessons from Ban Lak Sip, Laos

Land degradation / Soil erosion / Farming systems / Environmental policy / Political ecology / Households / Population growth / Laos / Ban Lak Sip

Comparison of Aviary, Barn and Conventional Cage Raising of Chickens on Laying Performance and Egg Quality

This study intended to compare the productive performance of three different layer raising systems; conventional cage (CC), barn (BR) and aviary (AV). The AV is welfare bestowed housing that allows free locomotion for birds within the BR. The BR allows bird’s free locomotion inside BR but without multilevel structures. Both pullets and cockerels were housed together in both AV and BR, but only pullets in CC. Seventeen weeks old Lohmann Brown Lite (n = 800) pullets were housed in AV during this study. The same age layer pullets were simultaneously assigned to either at CC or BR to compare egg production performance with AV. The duration of experiment was 40 weeks (from 21st to 60th week). There were no remarkable differences in egg production, hen day egg production (HDEP) and average egg weight among three rearing systems. First 20 weeks (phase-1) average HDEP (%) of AV, CC, and BR were 85.9, 88.8, 87.1 and average egg weights (g) were 57.5, 59.9, and 56.9 respectively. Those of the remaining 20 weeks (phase-2) were 87.1, 87.9, 85.5 and 64.2, 63.0 62.1, respectively. Daily feed intakes (122 g, 110 g, 125 g); feed conversion ratio (2.4, 2.1, 2.5) and daily egg mass (53.9 g, 54.4 g, 52.8 g) data from AV, CC, and BR were not influenced significantly by the respective raising systems. Daily feed intake of layers in both AV (124 g) and BR (127 g) tended to be higher than that in CC (113 g) during phase-2. Overall, exterior egg quality (dirty and cracked eggs) in both phases was superior in BR compared with AV and CC, whereas CC generated intermediate results. This study indicated that the HDEP per se in AV and BR were not significantly different from that in CC. The study implied that the facility depreciation cost for AV and cost for increased feed intake in AV compared to CC are believed to be critical to evaluate the cost effectiveness of egg production in AV

Promoter methylation of RASSF1A and DAPK and mutations of K-ras, p53, and EGFR in lung tumors from smokers and never-smokers

<p>Abstract</p> <p>Background</p> <p>Epidemiological studies indicate that some characteristics of lung cancer among never-smokers significantly differ from those of smokers. Aberrant promoter methylation and mutations in some oncogenes and tumor suppressor genes are frequent in lung tumors from smokers but rare in those from never-smokers. In this study, we analyzed promoter methylation in the <it>ras-association domain isoform A (RASSF1A) </it>and the <it>death-associated protein kinase (DAPK) </it>genes in lung tumors from patients with primarily non-small cell lung cancer (NSCLC) from the Western Pennsylvania region. We compare the results with the smoking status of the patients and the mutation status of the K-<it>ras</it>, <it>p53</it>, and <it>EGFR </it>genes determined previously on these same lung tumors.</p> <p>Methods</p> <p>Promoter methylation of the <it>RASSF1A </it>and <it>DAPK </it>genes was analyzed by using a modified two-stage methylation-specific PCR. Data on mutations of K-<it>ras</it>, <it>p53</it>, and <it>EGFR </it>were obtained from our previous studies.</p> <p>Results</p> <p>The <it>RASSF1A </it>gene promoter methylation was found in tumors from 46.7% (57/122) of the patients and was not significantly different between smokers and never-smokers, but was associated significantly in multiple variable analysis with tumor histology (p = 0.031) and marginally with tumor stage (p = 0.063). The <it>DAPK </it>gene promoter methylation frequency in these tumors was 32.8% (40/122) and did not differ according to the patients' smoking status, tumor histology, or tumor stage. Multivariate analysis adjusted for age, gender, smoking status, tumor histology and stage showed that the frequency of promoter methylation of the <it>RASSF1A </it>or <it>DAPK </it>genes did not correlate with the frequency of mutations of the K<it>-ras, p53</it>, and <it>EGFR </it>gene.</p> <p>Conclusion</p> <p>Our results showed that <it>RASSF1A </it>and <it>DAPK </it>genes' promoter methylation occurred frequently in lung tumors, although the prevalence of this alteration in these genes was not associated with the smoking status of the patients or the occurrence of mutations in the K-<it>ras</it>, <it>p53 </it>and <it>EGFR </it>genes, suggesting each of these events may represent independent event in non-small lung tumorigenesis.</p

Investigation into the annotation of protocol sequencing steps in the sequence read archive

BACKGROUND: The workflow for the production of high-throughput sequencing data from nucleic acid samples is complex. There are a series of protocol steps to be followed in the preparation of samples for next-generation sequencing. The quantification of bias in a number of protocol steps, namely DNA fractionation, blunting, phosphorylation, adapter ligation and library enrichment, remains to be determined. RESULTS: We examined the experimental metadata of the public repository Sequence Read Archive (SRA) in order to ascertain the level of annotation of important sequencing steps in submissions to the database. Using SQL relational database queries (using the SRAdb SQLite database generated by the Bioconductor consortium) to search for keywords commonly occurring in key preparatory protocol steps partitioned over studies, we found that 7.10%, 5.84% and 7.57% of all records (fragmentation, ligation and enrichment, respectively), had at least one keyword corresponding to one of the three protocol steps. Only 4.06% of all records, partitioned over studies, had keywords for all three steps in the protocol (5.58% of all SRA records). CONCLUSIONS: The current level of annotation in the SRA inhibits systematic studies of bias due to these protocol steps. Downstream from this, meta-analyses and comparative studies based on these data will have a source of bias that cannot be quantified at present

Containment of Antibiotic REsistance-measures to improve antibiotic use in pregnancy, childbirth and young children (CAREChild): a protocol of a prospective, quasiexperimental interventional study in Lao PDR.

INTRODUCTION: Antibiotics are essential to treat infections during pregnancy and to reduce both maternal and infant mortality. Overall use, but especially non-indicated use, and misuse of antibiotics are drivers of antibiotic resistance (ABR). High non-indicated use of antibiotics for uncomplicated vaginal deliveries is widespread in many parts of the world. Similarly, irrational use of antibiotics is reported for children. There is scarcity of evidence regarding antibiotic use and ABR in Lao PDR (Laos). The overarching aim of this project is to fill those knowledge gaps and to evaluate a quality improvement intervention. The primary objective is to estimate the proportion of uncomplicated vaginal deliveries where antibiotics are used and to compare its trend before and after the intervention. METHODS AND ANALYSIS: This 3-year, prospective, quasiexperimental study without comparison group includes a formative and interventional phase. Data on antibiotic use during delivery will be collected from medical records. Knowledge, attitudes and reported practices on antibiotic use in pregnancy, during delivery and for children, will be collected from women through questionnaires. Healthcare providers' knowledge, attitudes and practices of antibiotics administration for pregnant women, during delivery and for children, will be collected via adapted questionnaires. Perceptions regarding antibiotics will be explored through focus group discussions with women and individual interviews with key stakeholders. Faecal samples for culturing of Escherichia coli and Klebsiella spp. and antibiotic susceptibility testing will be taken before, during and 6 months after delivery to determine colonisation of resistant strains. The planned intervention will comprise training workshops, educational materials and social media campaign and will be evaluated using interrupted time series analysis. ETHICS AND DISSEMINATION: The project received ethical approval from the National Ethics Committee for Health Research, Ministry of Health, Laos. The results will be disseminated via scientific publications, conference presentations and communication with stakeholders. TRAIL REGISTRATION NUMBER: ISRCTN16217522; Pre-results

Antibiotic Prescribing in Connection to Childbirth: An Observational Study in Two Districts in Lao PDR

Overuse and misuse of antibiotics has frequently been reported for obstetric conditions and procedures, which may impact both the mother and the unborn baby and increase antibiotic resistance. This study aimed to investigate the antibiotic prescribing pattern in connection to childbirth in two districts in Lao PDR. It is a cross-sectional observational study. Antibiotic prescription data related to childbirth was collected via reviews of medical records in two district hospitals and five health centers in Lao PDR from September 2019 to November 2020. In total, antibiotic prescription data for 1777 women were extracted from their medical records. It was found that all women received antibiotics during in-patient care irrespective of delivery mode. When in hospital, 85.5% of the women who underwent a caesarean section got antibiotic treatment for 5 days and women who had a vaginal delivery usually had antibiotic treatment for one day or less. All the women got oral antibiotics for an additional 4–5 days upon discharge. Antibiotic prescription rate in connection to childbirth was very high in comparison with the WHO guidelines, and antibiotics were used extensively in the participating health facilities. Interventions to guide appropriate prescribing behavior in relation to childbirth are urgently needed in Lao PDR

Estimating Genetic Variability in Non-Model Taxa: A General Procedure for Discriminating Sequence Errors from Actual Variation

Genetic variation is the driving force of evolution and as such is of central interest for biologists. However, inadequate discrimination of errors from true genetic variation could lead to incorrect estimates of gene copy number, population genetic parameters, phylogenetic relationships and the deposition of gene and protein sequences in databases that are not actually present in any organism. Misincorporation errors in multi-template PCR cloning methods, still commonly used for obtaining novel gene sequences in non-model species, are difficult to detect, as no previous information may be available about the number of expected copies of genes belonging to multi-gene families. However, studies employing these techniques rarely describe in any great detail how errors arising in the amplification process were detected and accounted for. Here, we estimated the rate of base misincorporation of a widely-used PCR-cloning method, using a single copy mitochondrial gene from a single individual to minimise variation in the template DNA, as 1.62×10−3 errors per site, or 9.26×10−5 per site per duplication. The distribution of errors among sequences closely matched that predicted by a binomial distribution function. The empirically estimated error rate was applied to data, obtained using the same methods, from the Phospholipase A2 toxin family from the pitviper Ovophis monticola. The distribution of differences detected closely matched the expected distribution of errors and we conclude that, when undertaking gene discovery or assessment of genetic diversity using this error-prone method, it will be informative to empirically determine the rate of base misincorporation