The Juan non-LTR retrotransposon in mosquitoes: genomic impact, vertical transmission and indications of recent and widespread activity

<p>Abstract</p> <p>Background</p> <p>In contrast to DNA-mediated transposable elements (TEs), retrotransposons, particularly non-long terminal repeat retrotransposons (non-LTRs), are generally considered to have a much lower propensity towards horizontal transfer. Detailed studies on site-specific non-LTR families have demonstrated strict vertical transmission. More studies are needed with non-site-specific non-LTR families to determine whether strict vertical transmission is a phenomenon related to site specificity or a more general characteristic of all non-LTRs. <it>Juan </it>is a Jockey clade non-LTR retrotransposon first discovered in mosquitoes that is widely distributed in the mosquito family <it>Culicidae</it>. Being a non-site specific non-LTR, <it>Juan </it>offers an opportunity to further investigate the hypothesis that non-LTRs are genomic elements that are primarily vertically transmitted.</p> <p>Results</p> <p>Systematic analysis of the ~1.3 Gbp <it>Aedes aegypti </it>(<it>Ae. aegypti</it>) genome sequence suggests that <it>Juan-A </it>is the only <it>Juan</it>-type non-LTR in <it>Aedes aegypti</it>. <it>Juan-A </it>is highly reiterated and comprises approximately 3% of the genome. Using minimum cutoffs of 90% length and 70% nucleotide (nt) identity, 663 copies were found by BLAST using the published <it>Juan-A </it>sequence as the query. All 663 copies are at least 95% identical to <it>Juan-A</it>, while 378 of these copies are 99% identical to <it>Juan-A</it>, indicating that the <it>Juan-A </it>family has been transposing recently in evolutionary history. Using the 0.34 Kb 5' UTR as the query, over 2000 copies were identified that may contain internal promoters, leading to questions on the genomic impact of <it>Juan-A</it>. <it>Juan </it>sequences were obtained by PCR, library screening, and database searches for 18 mosquito species of six genera including <it>Aedes</it>, <it>Ochlerotatus</it>, <it>Psorophora</it>, <it>Culex</it>, <it>Deinocerites</it>, and <it>Wyeomyia</it>. Comparison of host and <it>Juan </it>phylogenies shows overall congruence with few exceptions.</p> <p>Conclusion</p> <p><it>Juan-A </it>is a major genomic component in <it>Ae. aegypti </it>and it has been retrotransposing recently in evolutionary history. There are also indications that <it>Juan </it>has been recently active in a wide range of mosquito species. Furthermore, our research demonstrates that a Jockey clade non-LTR without target site-specificity has been sustained by vertical transmission in the mosquito family. These results strengthen the argument that non-LTRs tend to be genomic elements capable of persistence by vertical descent over a long evolutionary time.</p

Evolutionary analysis of the kinesin light chain genes in the yellow fever mosquito Aedes aegypti: gene duplication as a source for novel early zygotic genes

<p>Abstract</p> <p>Background</p> <p>The maternal zygotic transition marks the time at which transcription from the zygotic genome is initiated and a subset of maternal RNAs are progressively degraded in the developing embryo. A number of early zygotic genes have been identified in <it>Drosophila melanogaster </it>and comparisons to sequenced mosquito genomes suggest that some of these early zygotic genes such as <it>bottleneck </it>are fast-evolving or subject to turnover in dipteran insects. One objective of this study is to identify early zygotic genes from the yellow fever mosquito <it>Aedes aegypti </it>to study their evolution. We are also interested in obtaining early zygotic promoters that will direct transgene expression in the early embryo as part of a <it>Medea </it>gene drive system.</p> <p>Results</p> <p>Two novel early zygotic kinesin light chain genes we call <it>AaKLC2.1 </it>and <it>AaKLC2.2 </it>were identified by transcriptome sequencing of <it>Aedes aegypti </it>embryos at various time points. These two genes have 98% nucleotide and amino acid identity in their coding regions and show transcription confined to the early zygotic stage according to gene-specific RT-PCR analysis. These <it>AaKLC2 </it>genes have a paralogous gene (<it>AaKLC1</it>) in <it>Ae. aegypti</it>. Phylogenetic inference shows that an ortholog to the <it>AaKLC2 </it>genes is only found in the sequenced genome of <it>Culex quinquefasciatus</it>. In contrast, <it>AaKLC1 </it>gene orthologs are found in all three sequenced mosquito species including <it>Anopheles gambiae</it>. There is only one KLC gene in <it>D. melanogaster </it>and other sequenced holometabolous insects that appears to be similar to <it>AaKLC1</it>. Unlike <it>AaKLC2</it>, <it>AaKLC1 </it>is expressed in all life stages and tissues tested, which is consistent with the expression pattern of the <it>An. gambiae </it>and <it>D. melanogaster </it>KLC genes. Phylogenetic inference also suggests that <it>AaKLC2 </it>genes and their likely <it>C. quinquefasciatus </it>ortholog are fast-evolving genes relative to the highly conserved <it>AaKLC1-like </it>paralogs. Embryonic injection of a luciferase reporter under the control of a 1 kb fragment upstream of the <it>AaKLC2.1 </it>start codon shows promoter activity at least as early as 3 hours in the developing <it>Ae. aegypti </it>embryo. The <it>AaKLC2.1 </it>promoter activity reached ~1600 fold over the negative control at 5 hr after egg deposition.</p> <p>Conclusions</p> <p>Transcriptome profiling by use of high throughput sequencing technologies has proven to be a valuable method for the identification and discovery of early and transient zygotic genes. The evolutionary investigation of the KLC gene family reveals that duplication is a source for the evolution of new genes that play a role in the dynamic process of early embryonic development. <it>AaKLC2.1 </it>may provide a promoter for early zygotic-specific transgene expression, which is a key component of the <it>Medea </it>gene drive system.</p

Delineation of buried stream channels using geophysical techniques

This study sets out to evaluate the use of geophysical methods for delineating buried stream channels, which can act as zones of preferential flow within a less hydraulically conductive aquifer. This information is important for gaining an understanding of flow dynamics of alluvial systems. The most reliable method of delineating the dimensions of aquifers is by drilling, which is an expensive proposition and is best preceded by a preliminary geophysical study to help define target zones for a drilling program. The study area is located adjacent to the Coerney River in the Sundays River Valley. Geologically it consists of approximately 5 metres of alluvial fines, covering 3 metres of coarse cobbles and boulders, all underlain by alternating siltstone and sandstone beds of indeterminate thickness. Throughout the area the water is very shallow at approximately 2 metres depth and the groundwater tends to be very saline. An air photo study revealed an old oxbow channel that had been covered over by subsequent agricultural land use. The geophysical methods available for the study were portable seismic refraction, electrical resistivity and electromagnetics. Preliminary field tests clearly showed that seismics did not produce valid results. The methods of electrical resistivity and electromagnetics produced good data and were subjected to further assessment. A grid was surveyed over the study area and both geophysical methods were applied at regularly spaced stations. Soil samples were taken over the same survey grid and analyzed for electrical conductivity in a soils laboratory. The results were compared to the geophysical data in an attempt to quantify the relationship between geophysical response and soil salinity. The data from the electromagnetic survey showed areas of low electrical conductivity which was a possible indication of zones of preferential groundwater flow. A transect of boreholes was drilled over selected electrical conductivity lows and successfully intersected the buried stream channel. A comparison of the borehole logs with the layered earth models from the Vertical Electrical Soundings indicated that the electrical resistivity method was not responding to the features of the buried stream channel and the cobblestone layer. This proved the electromagnetic method to be more valuable for this particular stud

Next-Generation Sequencing Reveals Recent Horizontal Transfer of a DNA Transposon between Divergent Mosquitoes

Horizontal transfer of genetic material between complex organisms often involves transposable elements (TEs). For example, a DNA transposon mariner has been shown to undergo horizontal transfer between different orders of insects and between different phyla of animals. Here we report the discovery and characterization of an ITmD37D transposon, MJ1, in Anopheles sinensis. We show that some MJ1 elements in Aedes aegypti and An. sinensis contain intact open reading frames and share nearly 99% nucleotide identity over the entire transposon, which is unexpectedly high given that these two genera had diverged 145–200 million years ago. Chromosomal hybridization and TE-display showed that MJ1 copy number is low in An. sinensis. Among 24 mosquito species surveyed, MJ1 is only found in Ae. aegypti and the hyrcanus group of anopheline mosquitoes to which An. sinensis belongs. Phylogenetic analysis is consistent with horizontal transfer and provides the basis for inference of its timing and direction. Although report of horizontal transfer of DNA transposons between higher eukaryotes is accumulating, our analysis is one of a small number of cases in which horizontal transfer of nearly identical TEs among highly divergent species has been thoroughly investigated and strongly supported. Horizontal transfer involving mosquitoes is of particular interest because there are ongoing investigations of the possibility of spreading pathogen-resistant genes into mosquito populations to control malaria and other infectious diseases. The initial indication of horizontal transfer of MJ1 came from comparisons between a 0.4x coverage An. sinensis 454 sequence database and available TEs in mosquito genomes. Therefore we have shown that it is feasible to use low coverage sequencing to systematically uncover horizontal transfer events. Expanding such efforts across a wide range of species will generate novel insights into the relative frequency of horizontal transfer of different TEs and provide the evolutionary context of these lateral transfer events

Improved reference genome of the arboviral vector Aedes albopictus

Background: The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes. Results: We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes. Conclusion: The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures

RNA polymerase III drives alternative splicing of the potassium channel–interacting protein contributing to brain complexity and neurodegeneration

An RNA polymerase III–transcribed noncoding RNA promotes alternative splicing of KCNIP4, altering amyloid precursor protein processing and contributing to neurodegeneration

Water Project ToolKit - Water Resources Management for Sustainable Development

The Water Project Toolkit addresses the sustainable development of the water sector and contributes to translating the international development policies on freshwater resources management into actual development cooperation activities. The Water Project Toolkit is intended to be used by sector stakeholders such as governments, private sector, civil society, development partners, Universities and other training institutions, international organisations and all other practitioners involved in the water sector. The Toolkit provides a comprehensive framework for all activities relating to water resources development; its application involves a radical change from previous attitudes towards water management, and the introduction of good practices for fostering a sustainable and inclusive approach. The first part of the Toolkit introduces the rationale, the challenges and the key concepts behind international development policies and practices of the water sector. It identifies policy principles and translates them into practical actions to support the sustainable management and implementation of water resources development. It clusters programme activity into six Focus Areas, within which the policy principles are to be applied. The second part of the Water Project Toolkit is the core practical material of the book. It consists of step-by-step suggestions for the planning, identification, formulation, implementation and evaluation of water development activities. The third and final part of the Toolkit provides a brief summary of the latest policies and tools for development cooperation in the water sector.JRC.H.5-Land Resources Managemen

PKA and PDE4D3 anchoring to AKAP9 provides distinct regulation of cAMP signals at the centrosome

Previous work has shown that the protein kinase A (PKA)–regulated phosphodiesterase (PDE) 4D3 binds to A kinase–anchoring proteins (AKAPs). One such protein, AKAP9, localizes to the centrosome. In this paper, we investigate whether a PKA–PDE4D3–AKAP9 complex can generate spatial compartmentalization of cyclic adenosine monophosphate (cAMP) signaling at the centrosome. Real-time imaging of fluorescence resonance energy transfer reporters shows that centrosomal PDE4D3 modulated a dynamic microdomain within which cAMP concentration selectively changed over the cell cycle. AKAP9-anchored, centrosomal PKA showed a reduced activation threshold as a consequence of increased autophosphorylation of its regulatory subunit at S114. Finally, disruption of the centrosomal cAMP microdomain by local displacement of PDE4D3 impaired cell cycle progression as a result of accumulation of cells in prophase. Our findings describe a novel mechanism of PKA activity regulation that relies on binding to AKAPs and consequent modulation of the enzyme activation threshold rather than on overall changes in cAMP levels. Further, we provide for the first time direct evidence that control of cell cycle progression relies on unique regulation of centrosomal cAMP/PKA signals