A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons

Although mosquitoes are major transmission vectors for pathogenic arboviruses, viral infection has little impact on mosquito health. This immunity is due in part to mosquito RNA interference (RNAi) pathways that generate antiviral small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). RNAi also maintains genome integrity by potently repressing mosquito transposon activity in the germline and soma. However, viral and transposon small RNA regulatory pathways have not been systematically examined together in mosquitoes. Therefore, we developed an integrated Mosquito Small RNA Genomics (MSRG) resource that analyzes the transposon and virus small RNA profiles in mosquito cell cultures and somatic and gonadal tissues across four medically important mosquito species. Our resource captures both somatic and gonadal small RNA expression profiles within mosquito cell cultures, and we report the evolutionary dynamics of a novel Mosquito-Conserved piRNA Cluster Locus (MCpiRCL) composed of satellite DNA repeats. In the larger culicine mosquito genomes we detected highly regular periodicity in piRNA biogenesis patterns coinciding with the expansion of Piwi pathway genes. Finally, our resource enables detection of crosstalk between piRNA and siRNA populations in mosquito cells during a response to virus infection. The MSRG resource will aid efforts to dissect and combat the capacity of mosquitoes to tolerate and spread arboviruses

Paternal Induction of Hybrid Dysgenesis in Drosophila melanogaster Is Weakly Correlated with Both P-Element and hobo Element Dosage

Transposable elements (TEs) are virtually ubiquitous components of genomes, yet they often impose significant fitness consequences on their hosts. In addition to producing specific deleterious mutations by insertional inactivation, TEs also impose general fitness costs by inducing DNA damage and participating in ectopic recombination. These latter fitness costs are often assumed to be dosage-dependent, with stronger effects occurring in the presence of higher TE copy numbers. We test this assumption in Drosophila melanogaster by considering the relationship between the copy number of two active DNA transposons, P-element and hobo element, and the incidence of hybrid dysgenesis, a sterility syndrome associated with transposon activity in the germline. By harnessing a subset of the Drosophila Genetic Reference Panel (DGRP), a group of fully-sequenced D. melanogaster strains, we describe quantitative and structural variation in P-elements and hobo elements among wild-derived genomes and associate these factors with hybrid dysgenesis. We find that the incidence of hybrid dysgenesis is associated with both P-element and hobo element copy number in a dosage-dependent manner. However, the relationship is weak for both TEs, suggesting that dosage alone explains only a small part of TE-associated fitness costs

Diverse Defenses: A Perspective Comparing Dipteran Piwi-piRNA Pathways.

Animals face the dual threat of virus infections hijacking cellular function and transposons proliferating in germline genomes. For insects, the deeply conserved RNA interference (RNAi) pathways and other chromatin regulators provide an important line of defense against both viruses and transposons. For example, this innate immune system displays adaptiveness to new invasions by generating cognate small RNAs for targeting gene silencing measures against the viral and genomic intruders. However, within the Dipteran clade of insects, Drosophilid fruit flies and Culicids mosquitoes have evolved several unique mechanistic aspects of their RNAi defenses to combat invading transposons and viruses, with the Piwi-piRNA arm of the RNAi pathways showing the greatest degree of novel evolution. Whereas central features of Piwi-piRNA pathways are conserved between Drosophilids and Culicids, multiple lineage-specific innovations have arisen that may reflect distinct genome composition differences and specific ecological and physiological features dividing these two branches of Dipterans. This perspective review focuses on the most recent findings illuminating the Piwi/piRNA pathway distinctions between fruit flies and mosquitoes, and raises open questions that need to be addressed in order to ameliorate human diseases caused by pathogenic viruses that mosquitoes transmit as vectors

Astrochemical model to study the abundances of branched carbon-chain molecules in a hot molecular core with realistic binding energies

Straight-chain (normal-propyl cyanide, n - C3H7CN) and branched-chain (iso-propyl cyanide, i - C3H7CN) alkyl cyanides are recently identified in the massive star-forming regions (Sgr B2(N) and Orion). These branched-chain molecules indicate that the key amino acids (side-chain structures) may also be present in a similar region. The process by which this branching could propagate towards the higher order (butyl cyanide, C4H9CN) is an active field of research. Since the grain catalysis process could have formed a major portion of these species, considering a realistic set of binding energies are indeed essential. We employ quantum chemical calculations to estimate the binding energy of these species considering water as a substrate because water is the principal constituent of this interstellar ice. We find significantly lower binding energy values for these species than were previously used. It is noticed that the use of realistic binding energy values can significantly change the abundance of these species. The branching is more favourable for the higher order alkyl cyanides with the new binding energies. With the inclusion of our new binding energy values and one essential destruction reaction (i - C3H7CN + H -> CH3C(CH3)CN + H-2 , having an activation barrier of 947 K), abundances of t - C4H9CN dramatically increased

Genetic Variation in Host Tolerance of an Invading Transposon in Drosophila melanogaster

Transposable Elements (TEs) are both important drivers of genome evolution and genetic parasites with potentially dramatic consequences for host fitness, including insertional inactivation of functional sequences and genomic instability (Reviewed in Hedges and Deininger 2007). Although host genomes minimize these deleterious eff¬ects by regulating the activity of resident TEs, they are often invaded by new TE families, which they are unable to control (Reviewed in Wallau et al. 2012). We are taking advantage of the historical invasion of the Drosophila melanogaster genome by P-elements (Reviewed in Engels 2003), a family of autonomous DNA transposons, to understand the impact that invading TEs have on their hosts, and the mechanisms through which TE regulation evolves. Using a panel of recombinant inbred lines (RILs), which were generated from naïve genotypes isolated from nature before P-element invasion (King et al. 2012), we have identified genetic variants that allow for tolerance or control of P-element activity. Such variants could have been beneficial after P-elements invaded D. melanogaster genomes ~1950, thereby contributing to the evolution of tolerance of the transposable element by its host.Biology and Biochemistry, Department ofHonors Colleg

Genetic variation in P-element dysgenic sterility is associated with double-strand break repair and alternative splicing of TE transcripts.

The germline mobilization of transposable elements (TEs) by small RNA mediated silencing pathways is conserved across eukaryotes and critical for ensuring the integrity of gamete genomes. However, genomes are recurrently invaded by novel TEs through horizontal transfer. These invading TEs are not targeted by host small RNAs, and their unregulated activity can cause DNA damage in germline cells and ultimately lead to sterility. Here we use hybrid dysgenesis-a sterility syndrome of Drosophila caused by transposition of invading P-element DNA transposons-to uncover host genetic variants that modulate dysgenic sterility. Using a panel of highly recombinant inbred lines of Drosophila melanogaster, we identified two linked quantitative trait loci (QTL) that determine the severity of dysgenic sterility in young and old females, respectively. We show that ovaries of fertile genotypes exhibit increased expression of splicing factors that suppress the production of transposase encoding transcripts, which likely reduces the transposition rate and associated DNA damage. We also show that fertile alleles are associated with decreased sensitivity to double-stranded breaks and enhanced DNA repair, explaining their ability to withstand high germline transposition rates. Together, our work reveals a diversity of mechanisms whereby host genotype modulates the cost of an invading TE, and points to genetic variants that were likely beneficial during the P-element invasion

Effect of Phenotype Selection on Genome Size Variation in Two Species of Diptera

Genome size varies widely across organisms yet has not been found to be related to organismal complexity in eukaryotes. While there is no evidence for a relationship with complexity, there is evidence to suggest that other phenotypic characteristics, such as nucleus size and cell-cycle time, are associated with genome size, body size, and development rate. However, what is unknown is how the selection for divergent phenotypic traits may indirectly affect genome size. Drosophila melanogaster were selected for small and large body size for up to 220 generations, while Cochliomyia macellaria were selected for 32 generations for fast and slow development. Size in D. melanogaster significantly changed in terms of both cell-count and genome size in isolines, but only the cell-count changed in lines which were maintained at larger effective population sizes. Larger genome sizes only occurred in a subset of D. melanogaster isolines originated from flies selected for their large body size. Selection for development time did not change average genome size yet decreased the within-population variation in genome size with increasing generations of selection. This decrease in variation and convergence on a similar mean genome size was not in correspondence with phenotypic variation and suggests stabilizing selection on genome size in laboratory conditions

Identification and Characterization of Small RNA Markers of Age in the Blow Fly Cochliomyia macellaria (Fabricius) (Diptera: Calliphoridae)

Blow fly development is important in decomposition ecology, agriculture, and forensics. Much of the impact of these species is from immature samples, thus knowledge of their development is important to enhance or ameliorate their effects. One application of this information is the estimation of immature insect age to provide temporal information for death investigations. While traditional markers of age such as stage and size are generally accurate, they lack precision in later developmental stages. We used miRNA sequencing to measure miRNA expression, throughout development, of the secondary screwworm, Cochliomyia macellaria (Fabricius) (Diptera: Calliphoridae) and identified 217 miRNAs present across the samples. Ten were identified to be significantly differentially expressed in larval samples and seventeen were found to be significantly differentially expressed in intrapuparial samples. Twenty-eight miRNAs were identified to be differentially expressed between sexes. Expression patterns of two miRNAs, miR-92b and bantam, were qPCR-validated in intrapuparial samples; these and likely food-derived miRNAs appear to be stable markers of age in C. macellaria. Our results support the use of miRNAs for developmental markers of age and suggest further investigations across species and under a range of abiotic and biotic conditions

Chemical Complexity of Phosphorous-bearing Species in Various Regions of the Interstellar Medium

Phosphorus-related species are not known to be as omnipresent in space as hydrogen, carbon, nitrogen, oxygen, and sulfur-bearing species. Astronomers spotted very few P-bearing molecules in the interstellar medium and circumstellar envelopes. Limited discovery of the P-bearing species imposes severe constraints in modeling the P-chemistry. In this paper, we carry out extensive chemical models to follow the fate of P-bearing species in diffuse clouds, photon-dominated or photodissociation regions (PDRs), and hot cores/corinos. We notice a curious correlation between the abundances of PO and PN and atomic nitrogen. Since N atoms are more abundant in diffuse clouds and PDRs than in the hot core/corino region, PO/PN reflects <1 in diffuse clouds, MUCH LESS-THAN1 in PDRs, and >1 in the late warm-up evolutionary stage of the hot core/corino regions. During the end of the post-warm-up stage, we obtain PO/PN > 1 for hot core and <1 for its low-mass analog. We employ a radiative transfer model to investigate the transitions of some of the P-bearing species in diffuse cloud and hot core regions and estimate the line profiles. Our study estimates the required integration time to observe these transitions with ground-based and space-based telescopes. We also carry out quantum chemical computation of the infrared features of PH3, along with various impurities. We notice that SO2 overlaps with the PH3 bending-scissoring modes around similar to 1000-1100 cm(-1). We also find that the presence of CO2 can strongly influence the intensity of the stretching modes around similar to 2400 cm(-1) of PH3