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Dogs were the first domesticated species, originating at least 15, 000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185, 805- marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4, 676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations—including those of Vietnam, India, and Egypt—show minimal evidence of European admixture. These populations exhibit a clear gradient of short-range linkage disequilibrium consistent with a Central Asian domestication origin.

We welcome the additional data and analyses of Wang et al. (1), but believe there are some misunderstandings regarding the methods and findings of Shannon et al. (2). First, although we merged Nepal and Mongolia when plotting linkage disequilibrium (LD) decay in figure 5B of ref. 2 for legibility, we did not assume Nepal and Mongolia represented a single, interbreeding population, and indeed computed separate LD scores for each population (figure 5A of ref. 2), matching Wang et al.’s (1) observation of slightly lower LD in Nepal than Mongolia. Although Nepal (along with India) is commonly considered part of South Asia, Nepal borders Central Asia. Dog populations in two Central Asian countries, Mongolia and Afghanistan, both have lower LD than India. Nepal does not border Southeast Asia. Because we cannot, given the resolution of current sampling … [↵][1]1To whom correspondence should be addressed. Email: arb359{at}cornell.edu. [1]: #xref-corresp-1-1

Sulphur mustard is a potent alkylating agent that causes severe vesication as well as systemic and genotoxic effects. Despite its long history as a chemical warfare agent, the mechanism of its toxicity remains unknown and no successful pharmacological intervention has yet been found. In this study we have examined the effects of mustard alkylation of DNA on transcriptional processes. Gel mobility shift analysis shows that mustard alkylation of the lac UV5 promoter increases the stability of the promoter-RNA polymerase binary complex. Following formation of the initiation complex and addition of elongation nucleotides, approximately 45% of the RNA polymerase in the initiated complex remained associated with the alkylated promoter, compared to only 7% remaining associated with the unalkylated promoter. For the RNA polymerase able to escape the initiation complex, mustard alkylation of the DNA template resulted in the production of truncated transcripts. Analysis of these truncated transcripts revealed that sulphur mustard alkylates DNA preferentially at 5'-AA, 5'-GG and 5'-GNC sequences on the DNA template strand and this is significantly different from the alkylation sites observed with nitrogen mustard. This study represents the first report at the molecular level of sulphur mustard-induced effects on transcriptional processes.

Nitrogen mustard and its derivatives such as cyclophosphamide, chlorambucil and melphalan are widely used anti-cancer agents, despite their non-specific reaction mechanism. In this study, the effect of alkylation by nitrogen mustard of DNA and RNA (coding for a single protein) was investigated using both a translation system and a coupled transcription/translation system. When alkylated DNA was used as the template for coupled transcription and translation, a single translation product corresponding to the 62 kDa luciferase protein was synthesised. Production of the translated product encoded by this template was inhibited by mustard concentrations as low as 10 nM, and 50% inhibition occurred with 30 nM mustard. A primer extension assay employed to verify alkylation sites on the DNA revealed that all guanine residues on the DNA template are susceptible to alkylation by nitrogen mustard. Similarly, when alkylated RNA was used as the template for protein synthesis, the amount of the 62 kDa luciferase protein decreased with increasing mustard concentration and a range of truncated polypeptides was synthesised. Under these conditions 50% inhibition of translation occurred with approximately 300 nM mustard (i.e. approximately 10 times that required for similar inhibition using an alkylated DNA template). Furthermore, a gel mobility shift assay revealed that mustard alkylation of the RNA template results in the formation of a more stable retarded RNA complex. The functional activity of the luciferase protein decreased with alkylation of both the DNA and RNA templates, with a half-life of loss of activity of 1.1 h for DNA exposed to 50 nM mustard, and 0.5 h for RNA exposed to 50 microM mustard. The data presented support the notion that DNA is a critical molecule in the mode of action of mustards.

Hepatitis B virus (HBV) genomes are small, semi-double-stranded DNA circular genomes that contain alternating overlapping reading frames and replicate through an RNA intermediary phase. This complex biology has presented a challenge to estimating an evolutionary rate for HBV, leading to difficulties resolving the evolutionary and epidemiological history of the virus. Here, we re-examine rates of HBV evolution using a novel data set of 112 within-host, transmission history (pedigree) and among-host genomes isolated over 20 years from the indigenous peoples of the South Pacific, combined with 313 previously published HBV genomes. We employ Bayesian phylogenetic approaches to examine several potential causes and consequences of evolutionary rate variation in HBV. Our results reveal rate variation both between genotypes and across the genome, as well as strikingly slower rates when genomes are sampled in the Hepatitis B e antigen positive state, compared to the e antigen negative state. This Hepatitis B e antigen rate variation was found to be largely attributable to changes during the course of infection in the preCore and Core genes and their regulatory elements.

Background Sexually transmissible infections (STI) are common in female sex workers (FSW). Aim: To determine if 3-monthly periodic presumptive treatments (PPT) would reduce the prevalence of STI in FSW. Methods: In a cohort study conducted between November 2003 and September 2004, FSW were enrolled, counselled and interviewed. Informed consent was obtained. Testing by using polymerase chain reaction (PCR) for Chlamydia trachomatis (Ct), Neisseria gonorrhoeae (Ng) and Trichomonas vaginalis (Tv), and serology for HIV were performed at baseline and final follow-up visits. Each FSW received 3-monthly oral amoxicillin, probenecid, a combination of amoxicillin and clavulanic acid, and azithromycin. Tinidazole was administered once. Results: The cohort consisted of 129 FSW at baseline and 71 at final follow-up visit. Of these 71 FSW, there was a significant decline in the proportion with positive PCR results for Ct from 38% to 16% (P = 0.001), Ng from 56% to 23% (P =

Background The use of anti-malarial drug combinations with artemisinin or with one of its derivatives is now widely recommended to overcome drug resistance in falciparum as well as vivax malaria. The fixed oral dose artemisinin-naphthoquine combination (ANQ, ARCO™) is a newer artemisinin-based combination (ACT) therapy undergoing clinical assessment. A study was undertaken to assess the safety, efficacy and tolerability of ANQ combination in areas of multi-drug resistance to generate preliminary baseline data in adult population of Papua New Guinea. Methods The clinical assessment was an open-labeled, two-arm, randomized study comparing ANQ combination as a single dose regimen and three days regimen (10 mg/kg/day) of chloroquine plus single dose sulphadoxine-pyrimethamine (CQ+SP) for the treatment of uncomplicated falciparum malaria with 28 days follow-up in an adult population. The primary outcome measures for efficacy were day 1, 2, 3 7, 14 and 28-day cure rates. Secondary outcomes included parasite clearance time, fever clearance time, and gametocyte carriage. The main outcome measures for safety were incidences of post-treatment clinical and laboratory adverse events. Results Between June 2005 and July 2006, 130 patients with confirmed uncomplicated P. falciparum were randomly assigned to receive ANQ and CQ+SP, only 100 patients (51 in ANQ group and 49 in CQ+SP group) were evaluated for clinical and parasitological outcomes. All the patients treated with ANQ and CQ+SP showed adequate clinical and parasitological response with 28 days follow-up. The cure rate for ANQ on day 1, 2, 3, 7, 14, and 28 was 47%, 86%, 92%, 94%, 94% and 94%, respectively. Recrudescence account for 6%; all were cleared on day 21. For CQ+SP treated group the cure rates were 24%, 67%, 82%, 82%, 84% and 88%, respectively. Recrudescence accounted for 10%; all were cleared on day 28 except for one patient. Both regimens were well tolerated with no serious adverse events. The proportion of gametocyte carriers was higher in CQ+SP treated group than ANQ treatment (41% versus 12%; p < 0.05). Conclusion While these data are not themselves sufficient, it strongly suggests that the ANQ combination as a single dose administration is safe and effective for the treatment of uncomplicated P. falciparum malaria in the adult population of Papua New Guinea and deserves further clinical evaluation.

Urinary Iodine excretion is a useful and important indicator of the iodine status of a population. This study attempts to determine the urinary iodine concentration of non-pregnant, pregnant and lactating women, resident in the National Capital District of Papua New Guinea, so as to evaluate their status of iodine nutrition. The study population was made up of 56 non-pregnant, 40 lactating and 212 pregnant women. Of the 212 pregnant women, 14 were in the first, 64 in the second, and 134 in the third Trimester of pregnancy. Casual urine samples were collected and analysed for urinary iodine by Sandell-Kolthoff reaction. The median urinary iodine concentration for the non-pregnant, lactating and pregnant women was 163.0 micro g/L, 134.0 micro g/L and 180.0 micro g/L, respectively. Median urinary iodine for the first, second and third trimesters were 165.0 micro g/L, 221.5 micro g/L and 178.0 micro g/L, respectively. The 20th percentile urinary iodine values were higher than 50 micro g/L for all the groups. This indicates adequate intake of dietary iodine and optimal status of iodine nutrition amongst women in the various groups. Mild to severe status of iodine nutrition was found in 30.4% of non-pregnant, 35.0% of lactating, 22.2% of pregnant women, 28.5% of women in the first, 18.8% in the second, and 23.1% in the third trimester of pregnancy. To achieve optimal iodine nutrition in pregnant and lactating women, an increase in their intake of dietary iodine is recommended.

Malnutrition is a contributing cause of about half of the 10 million deaths annually worldwide, and contributes to a substantial proportion of the infectious disease morbidity among children in developing countries. Recent epidemiological and clinical evidence has shown that in most developing countries deficiencies of specific micronutrients are partly responsible for the severity of infectious disease morbidity and mortality in malnourished children. Efforts to improve micronutrient status have focused on iron, vitamin A and iodine. Supplementation with iron and vitamin A significantly reduces child mortality, while implementation of the universal salt iodization strategy reduces the incidence of iodine deficiency disorders. These strategies are considered to be among the most cost-effective health interventions in developing countries. A number of recent zinc supplementation studies in developing countries suggest that greater priority should also be given to the correction of mild to moderate zinc deficiency in children, pregnant women and lactating mothers. Some of these studies showed that zinc supplementation reduces the duration of malaria, and the severity of diarrhoea and respiratory infections (including pneumonia), and improves immunocompetence in susceptible children. The results of these studies indicate that zinc may be another specific micronutrient in which there is widespread deficiency in developing countries and that great benefits can be achieved by its supplementation.

The N86Y mutation in pfmdr1 is reported to play an additional role for the chloroquine resistance in Plasmodium falciparum isolates. However, not much has been done to clarify whether this mutation augments the level of chloroquine resistance in the isolates harboring pfcrt K76T mutation. We compared the in vitro chloroquine efficacy between pfcrt K76T mutant parasites with or without N86Y mutation from Papua New Guinea. A total of 57 isolates (4% sensitive, 14% borderline, and 82% resistant) were successfully tested in vitro for chloroquine sensitivity. We found a slightly higher effective concentration of chloroquine needed to inhibit P. falciparum by 50% (mean EC50=107 nM) in isolates with the pfcrt K76T+pfmdr1 N86Y than that in isolates with the pfcrt K76T+pfmdr1 N86 (EC50=88 nM), but this difference was not statistically significant. A significant non-random association was observed between the pfcrt K76T and pfmdr1 N86Y alleles. Our results suggest that the pfmdr1 N86Y mutation plays a compensatory role to chloroquine-resistant isolates under a chloroquine pressure while it may also augment the level of chloroquine resistance in the K76T parasites to a small extent.

The 27-bp deletion in the erythrocyte band 3 gene (B3Delta27) constitutes a genetic basis for Southeast Asian and Melanesian ovalocytosis. The distribution of B3Delta27 has been interpreted to reflect malaria selection or dispersal of the recent expansion of Austronesian-speaking populations. To explore these two hypotheses, we examined eight malarious populations of the East Sepik Province of Papua New Guinea (PNG) that speak both the Austronesian and Papuan languages. The B3Delta27 allele frequencies within populations were not positively correlated with malaria endemicities. In contrast, statistically significant geographical variations in the B3Delta27 allele distribution were observed. B3Delta27 was high (0.06-0.07) in the islands, intermediate (0.02-0.03) in coastal regions, but was absent or rare (0.00-0.01) in inland populations. Furthermore, the prevalence of the mitochondrial DNA region V 9-bp deletion, associated with the Austronesian expansion, was significantly correlated with that of B3Delta27. These results suggest that B3Delta27 was introduced by Austronesian-speaking people within the past 3,500 years and subsequently expanded to populations along the coasts and islands of PNG. This study highlights the contribution of population origins, patterns of gene flow, disease selection and genetic drift in determining the genetic compositions of present populations.

Aims We assessed the disposition of oral amodiaquine (AQ) and CYP2C8 polymorphism in 20 children with falciparum malaria. Methods AQ and DEAQ concentrations were determined with SPE-HPLC method. CYP2C8 genotypes were assessed by PCR-RFLP method. Results AQ was not detectable beyond day 3 postdose. Cmax for DEAQ was reached in 3.0 days. The mean values for t1/2, MRT, and AUCtotal were 10.1 days, 15.5 days and 4512.6 µg l−1 day, respectively. All the children were CYP2C8* homozygous. Conclusion Our data are consistent with those previously reported, and the AQ regimen seems pharmacokinetically adequate in the absence of CYP2C8 polymorphism.

The cytochrome P450 (CYP) isozyme CYP2C19 metabolizes clinically important drugs, including the anti-malarial proguanil currently used for multi-drug resistant Plasmodium falciparum malaria. CYP2C19 activity varies among geographical regions due to high frequencies of two null alleles (CYP2C19*2/*3) in Asian and especially Pacific populations. Previously, we reported an unprecedentedly high frequency of CYP2C19 poor metabolizers (PM) within populations of Vanuatu, which suggested even higher PM frequencies in Papua New Guinea. We examined CYP2C19 allele frequencies of three malarious populations from inland East Sepik Province, Papua New Guinea to evaluate this prediction and the use of proguanil in malaria treatment programs. These Papua New Guinean populations have PM frequencies intermediate between island South-east Asia and Vanuatu, most likely resulting from genetic drift during the settlement of the Pacific. This study highlights the medical consequences of population origins and the need for a better understanding of the genetic diversity of our global species.

The distribution of microorganisms in the subsurfaces of hydrothermal vents was investigated by using subvent rock core samples. Microbial cells and ATP were detected from cores taken at depths of less than 99.4 and 44.8 m below the seafloor (mbsf), respectively. Cores from various depths were incubated anaerobically with a heterotrophic medium. Growth at 60 and 90°C was ascribed to a Geobacillus sp. in the 448.6- to 99.4-mbsf cores and a Deinococcus sp. in the 64.8- to 128.9-mbsf cores, respectively, based on the 16S ribosomal DNA analysis.

Compounds containing the chloroethyl group are potent inhibitors of DNA synthesis and cell growth. Tacrine, a choline carrier inhibitor, was found to protect both HeLa cells and rat thymocytes against the effects of nitrogen mustard. DNA synthesis was restored from 13 to 71% of the control value and cell viability restored from 27 to 57% of the control value by exposure of the cells to an equimolar concentration of tacrine immediately prior to nitrogen mustard. In contrast, tacrine was unable to significantly protect rat thymocytes against the toxic effects of sulphur mustard. These results have implications for the clinical use of nitrogen mustard.

DNA was alkylated with nitrogen mustard (HN2) and the rate of release of the alkylpurines was quantitated by HPLC. The half life of depurination of the major product (7-alkylguanine) was 9.1 h at 37 degrees C. End-labelled DNA was used to show that depurination occurred dominantly at 5'-GA, 5'-GG and 5'-GT sequences. Although extensive alkylation was observed at all 5'-GNC and 5'GNT sequences, no depurination was observed at these sites during a depurination time of 20 h at 37 degrees C. Since these sites are potential interstrand crosslinking sequences (G-adduct-G and G-adduct-A, both spanning an intervening base pair), this suggests that these regions have a greatly enhanced stability or that simultaneous depurination of both ends of the crosslink is necessary before these lesions are removed (with a predicted half-life of approximately 80 h at 37 degrees C). Depurination at the lac UV5 promoter impaired the association of Escherichia coli RNA polymerase with that promoter, while in the elongation phase two distinctly different sequence-specific processes were apparent. At 5'-GNC and 5'-GNT sequences transcriptional blockages were maintained with increasing elongation time, whereas at monoadduct sites, the blockage decreased with elongation time (predominantly at 5'-GG and 5'-GC sequences), with an average half-life of approximately 10.7 h. Collectively, these results suggest that the observed read-through past monoadduct sites is due to depurination of the DNA at those sites. E. coli RNA polymerase is therefore able to transcribe efficiently past apurinic sites and presumably does so by incorporating an incorrect base into the nascent RNA.

Background: Sexually transmissible infections (STIs) are common in female sex workers (FSWs), most of which are asymptomatic and therefore under-reported. Our aim was to determine the sensitivity and specificity of reported symptoms obtained via questionnaire augmented with leukocyte esterase (LE) urine dipstick test for the detection of Chlamydia trachomatis (Ct), Neisseria gonorrhea (Ng) and Trichomonas vaginalis (Tv) detected using polymerase chain reaction (PCR). Methods: In November 2003, a cohort of FSWs was screened for STIs and completed a questionnaire. Results: We enrolled 129 FSWs (90% participation rate) of whom 48 (37%), 30 (23%) and 53 (41%) were diagnosed with Ng, Ct and Tv, respectively, by PCR. Of those diagnosed with any of these infections, 78% reported anogenital symptoms and of those without infections, 28% reported symptoms. Anogenital symptoms were present in over 50% FSWs. Genital odour (present in 26%), lower abdominal pain (present in 29%), dysuria (present in 19%) had a sensitivity around (50%), specificity (>80%) and all were significantly associated with positive PCR results for individual organisms; however, the sensitivity of these symptoms to detect the presence of any positive PCR result was low (1 was combined with the presence of three reported symptoms the sensitivity was 86%, specificity of 73% and a positive predictive value of 72%; a better predictor of infections. Conclusions: Our finding suggest an approach that incorporates LE urine dipstick test >1 and multiple symptoms may be a feasible option for screening infections among FSWs in resource constraint settings.