Mitochondrial pseudogenes in the nuclear genome of Aedes aegypti mosquitoes: implications for past and future population genetic studies

<p>Abstract</p> <p>Background</p> <p>Mitochondrial DNA (mtDNA) is widely used in population genetic and phylogenetic studies in animals. However, such studies can generate misleading results if the species concerned contain nuclear copies of mtDNA (Numts) as these may amplify in addition to, or even instead of, the authentic target mtDNA. The aim of this study was to determine if Numts are present in <it>Aedes aegypti </it>mosquitoes, to characterise any Numts detected, and to assess the utility of using mtDNA for population genetics studies in this species.</p> <p>Results</p> <p>BLAST searches revealed large numbers of Numts in the <it>Ae. aegypti </it>nuclear genome on 146 supercontigs. Although the majority are short (80% < 300 bp), some Numts are almost full length mtDNA copies. These long Numts are not due to misassembly of the nuclear genome sequence as the Numt-nuclear genome junctions could be recovered by amplification and sequencing. Numt evolution appears to be a complex process in <it>Ae. aegypti </it>with ongoing genomic integration, fragmentation and mutation and the secondary movement of Numts within the nuclear genome.</p> <p>The PCR amplification of the putative mtDNA nicotinamide adenine dinucleotide dehydrogenase subunit 4 (<it>ND4</it>) gene from 166 Southeast Asian <it>Ae. aegypti </it>mosquitoes generated a network with two highly divergent lineages (clade 1 and clade 2). Approximately 15% of the <it>ND4 </it>sequences were a composite of those from each clade indicating Numt amplification in addition to, or instead of, mtDNA. Clade 1 was shown to be composed at least partially of Numts by the removal of clade 1-specific bases from composite sequences following enrichment of the mtDNA. It is possible that all the clade 1 sequences in the network were Numts since the clade 2 sequences correspond to the known mitochondrial genome sequence and since all the individuals that produced clade 1 sequences were also found to contain clade 2 mtDNA-like sequences using clade 2-specific primers. However, either or both sets of clade sequences could have Numts since the BLAST searches revealed two long Numts that match clade 2 and one long Numt that matches clade 1. The substantial numbers of mutations in cloned <it>ND4 </it>PCR products also suggest there are both recently-derived clade 1 and clade 2 Numt sequences.</p> <p>Conclusion</p> <p>We conclude that Numts are prevalent in <it>Ae. aegypti </it>and that it is difficult to distinguish mtDNA sequences due to the presence of recently formed Numts. Given this, future population genetic or phylogenetic studies in <it>Ae. aegypti </it>should use nuclear, rather than mtDNA, markers.</p

Nowa Konstytucja Państwa Litewskiego

Digitalizacja i deponowanie archiwalnych zeszytów RPEiS sfinansowane przez MNiSW w ramach realizacji umowy nr 541/P-DUN/201

Political transition and emergent forest-conservation issues in Myanmar.

Political and economic transitions have had substantial impacts on forest conservation. Where transitions are underway or anticipated, historical precedent and methods for systematically assessing future trends should be used to anticipate likely threats to forest conservation and design appropriate and prescient policy measures to counteract them. Myanmar is transitioning from an authoritarian, centralized state with a highly regulated economy to a more decentralized and economically liberal democracy and is working to end a long-running civil war. With these transitions in mind, we used a horizon-scanning approach to assess the 40 emerging issues most affecting Myanmar's forests, including internal conflict, land-tenure insecurity, large-scale agricultural development, demise of state timber enterprises, shortfalls in government revenue and capacity, and opening of new deforestation frontiers with new roads, mines, and hydroelectric dams. Averting these threats will require, for example, overhauling governance models, building capacity, improving infrastructure- and energy-project planning, and reforming land-tenure and environmental-protection laws. Although challenges to conservation in Myanmar are daunting, the political transition offers an opportunity for conservationists and researchers to help shape a future that enhances Myanmar's social, economic, and environmental potential while learning and applying lessons from other countries. Our approach and results are relevant to other countries undergoing similar transitions

Political transition and emergent forest-conservation issues in Myanmar.

Political and economic transitions have had substantial impacts on forest conservation. Where transitions are underway or anticipated, historical precedent and methods for systematically assessing future trends should be used to anticipate likely threats to forest conservation and design appropriate and prescient policy measures to counteract them. Myanmar is transitioning from an authoritarian, centralized state with a highly regulated economy to a more decentralized and economically liberal democracy and is working to end a long-running civil war. With these transitions in mind, we used a horizon-scanning approach to assess the 40 emerging issues most affecting Myanmar's forests, including internal conflict, land-tenure insecurity, large-scale agricultural development, demise of state timber enterprises, shortfalls in government revenue and capacity, and opening of new deforestation frontiers with new roads, mines, and hydroelectric dams. Averting these threats will require, for example, overhauling governance models, building capacity, improving infrastructure- and energy-project planning, and reforming land-tenure and environmental-protection laws. Although challenges to conservation in Myanmar are daunting, the political transition offers an opportunity for conservationists and researchers to help shape a future that enhances Myanmar's social, economic, and environmental potential while learning and applying lessons from other countries. Our approach and results are relevant to other countries undergoing similar transitions

Prevalence and seroprevalence of Plasmodium infection in Myanmar reveals highly heterogeneous transmission and a large hidden reservoir of infection.

Malaria incidence in Myanmar has significantly reduced over recent years, however, completeness and timeliness of incidence data remain a challenge. The first ever nationwide malaria infection and seroprevalence survey was conducted in Myanmar in 2015 to better understand malaria epidemiology and highlight gaps in Annual Parasite Index (API) data. The survey was a cross-sectional two-stage stratified cluster-randomised household survey conducted from July-October 2015. Blood samples were collected from household members for ultra-sensitive PCR and serology testing for P. falciparum and P. vivax. Data was gathered on demography and a priori risk factors of participants. Data was analysed nationally and within each of four domains defined by API data. Prevalence and seroprevalence of malaria were 0.74% and 16.01% nationwide, respectively. Prevalent infection was primarily asymptomatic P. vivax, while P. falciparum was predominant in serology. There was large heterogeneity between villages and by domain. At the township level, API showed moderate correlation with P. falciparum seroprevalence. Risk factors for infection included socioeconomic status, domain, and household ownership of nets. Three K13 P. falciparum mutants were found in highly prevalent villages. There results highlight high heterogeneity of both P. falciparum and P. vivax transmission between villages, accentuated by a large hidden reservoir of asymptomatic P. vivax infection not captured by incidence data, and representing challenges for malaria elimination. Village-level surveillance and stratification to guide interventions to suit local context and targeting of transmission foci with evidence of drug resistance would aid elimination efforts

Co-occurrence of Point Mutations in the Voltage-Gated Sodium Channel of Pyrethroid-Resistant Aedes aegypti Populations in Myanmar

Background:Single amino acid substitutions in the voltage-gated sodium channel associated with pyrethroid resistance constitute one of the main causative factors of knockdown resistance in insects. The kdr gene has been observed in several mosquito species; however, point mutations in the para gene of Aedes aegypti populations in Myanmar have not been fully characterized. The aim of the present study was to determine the types and frequencies of mutations in the para gene of Aedes aegypti collected from used tires in Yangon City, Myanmar.Methodology/Principal Findings:We determined high pyrethroid resistance in Aedes aegypti larvae at all collection sites in Yangon City, by using a simplified knockdown bioassay. We showed that V1016G and S989P mutations were widely distributed, with high frequencies (84.4% and 78.8%, respectively). By contrast, we were unable to detect I1011M (or I1011V) or L1014F mutations. F1534C mutations were also widely distributed, but with a lower frequency than the V1016G mutation (21.2%). High percentage of co-occurrence of the homozygous V1016G/S989P mutations was detected (65.7%). Additionally, co-occurrence of homozygous V1016G/F1534C mutations (2.9%) and homozygous V1016G/F1534C/S989P mutations (0.98%) were detected in the present study.Conclusions/Significance:Pyrethroid insecticides were first used for malaria control in 1992, and have since been constantly used in Myanmar. This intensive use may explain the strong selection pressure toward Aedes aegypti, because this mosquito is generally a domestic and endophagic species with a preference for indoor breeding. Extensive use of DDT for malaria control before the use of this chemical was banned may also explain the development of pyrethroid resistance in Aedes aegypti

Genetic population structure and gene flow in Aedes aegypti mosquitoes in southeast Asia

Aedes aegypti mosquito is the principle vector for dengue virus transmission. It is the day-biting mosquito which natually breeds in different water containers in and around houses. Dengue/dengue haemorrhagic fever (DF/DHF) is a re-emerging public health problem with > 2.5 billkm people at risk in th world with the greatest disease bilrden in Southeast Asia and the c. An understanding of genetic population structure and dispersal ability in vector populations is important basic Knowledge for effective vector control using both inventional methods and novel strategies such as genetic modification of the vectors.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Sale Forecasting for Hot-Drink Productivity Using Naïve Bayesian Classification

Classification is one of the most popular data mining tasks with a wide ranges of application and lots of algorithms have been proposed to build scalable classifiers. Several data mining techniques and classification methods have been widely applied to extract knowledge from databases. Naïve Bayes is one of the most efficient and effective inductive learning algorithms for machine learning and data mining. Its competitive performance in classification is surprising, because the conditional independence assumption on which it the conditional independence assumption on which it is based, rarely true in real-world applications. This system will present sale forecasting productivity using Naïve Bayesian Classification

Lineage Extinction and Replacement in Dengue Type 1 Virus Populations are due to Stochastic Events Rather Than to Natural Selection

Between 1996 and 1998 two clades (B,C; genotype I) of dengue virus type 1 (DENV-1) appeared in Myanmar (Burma) that were new to that location. Between 1998 and 2000 a third clade (A; genotype III) of DENV-1, which had been circulating at that locality for at least twenty-five years, became extinct. These changes preceded the largest outbreak of dengue recorded in Myanmar, in 2001, in which more than 95% of viruses recovered from patients were DENV-1 but where the incidence of severe disease was much less than in previous years. Phylogenetic analyses of viral genomes indicated that the two new clades of DENV-1 did not arise from the, now extinct, clade A viruses nor was the extinction of this clade due to differences in the fitness of the viral populations. Since the extinction occurred during in an inter-epidemic period, we suggest that it was due to a stochastic event attributable to the low rate of virus transmission in this interval

Forecasting Forest Areas in Myanmar Based on Socioeconomic Factors

National circumstances should be considered in establishing and adjusting forest reference emission levels (FRELs/FRLs) under the United Nations Programme on Reducing Emissions from Deforestation and Forest Degradation (UN-REDD+ Programme). Myanmar, one of the world’s least developed countries may face accelerating deforestation under an open and democratic political system that desires rapid economic development. This research analyzes the impacts of population growth and economic development on forest areas in Myanmar by using panel data analysis, an econometrics approach based on panel data of forest areas, population, and gross domestic product (GDP) by states and regions in 2005, 2010, and 2015. This research revealed that per capita GDP and population density gave statistically significant negative impacts on forest areas. Using the regression model obtained above, medium population growth projections, and three GDP development scenarios, annual forest areas from 2016 to 2020 were forecast. The forecasting results showed possible higher deforestation under higher economic development. Finally, this research showed the necessity of adjusting the current average deforestation for RELs in the REDD+ scheme in Myanmar and the direction in which the adjustment should go