The DaVinci Center For Community Progress: Making The Community More Liveable

There are many innovations, projects, and programs which can make a community more liveable. The elements that they have in common are 1) the vision of the founder (or co-founders), 2) a dedicated connection to the community and populations in which the innovation or project is located, 3) the necessary social skills and contacts of the founder(s) and other key people involved in the innovation, 4) hard work, and 5) funding sources that continue over time to keep the services (or project) going, as well as to add services as needs change. The DaVinci Center for Community Progress, in Providence, RI, is an excellent example of how to make a community more liveable for diverse populations for whom it has provided services since it opened its doors in 1972. The DaVinci Center is a multi-purpose facility based on the settlement house model in regard to many of the services it offers. It differs from the settlement house model in that the DaVinci Center staff does not live at the Center. The Center was co-founded by John DeLuca who has also served as its longtime Executive Director. The content for this article was gathered, in part, through a lengthy, structured interview both authors conducted with John at the Center, a review of written materials produced by the Center, and information provided on the Center’s website

Transposable element control disrupted by meiotic drive in a stalk-eyed fly genome

Some stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio (SR) meiotic drive and impact the fitness of male and female carriers. Here, we produce a chromosome-level genome assembly of the stalk-eyed fly, T. dalmanni, to elucidate the pattern of genomic divergence associated with the presence of drive elements. We find evidence for multiple nested inversions along the sex ratio haplotype and widespread differentiation and divergence between the inversion types along the entire X chromosome. In addition, the genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally active TE families that have produced new insertions. Moreover, we find that many TE families are expressed at a significantly higher level in SR male testis, suggesting a molecular connection between these two types of selfish genetic elements in this species. We identify T. dalmanni orthologs of genes involved in genome defense via the piRNA pathway, including core members maelstrom, piwi and Argonaute3, that are diverging in sequence, expression or copy number between the SR and standard (ST) chromosomes, and likely influence TE regulation in flies carrying a sex ratio X chromosome

The origins, evolution, and functions of lineage-specific genes in Drosophila

To understand how species evolve and adapt to their environments, we must understand the nature of the genetic variation causing differences between and within species. Recent studies have identified entire genes that are unique to a single species (lineage-specific genes), but little is yet known about how these genes originate or function. Here I present the results of a number of studies of lineage-specific genes in a model organism, the fruit fly, Drosophila melanogaster. First (Chapter two), I show that even within species, genes can greatly expand or contract in size demonstrating that novel protein domains are segregating even within a species. Secondly (Chapter three), I show that two genes that appeared to be newly evolved and lineage specific are actually rapidly evolving, and surprisingly are essential. Finally, I find that a number of genes that arose recently from non-coding sequence (de novo genes) are diverse in their apparent mechanism of origin, but are surprisingly similar in their gene expression pattern and functions (Chapters four and five). Like the two rapid evolving genes, the de novo genes I studied appear to contribute to an essential function, as their loss causes lethality. This work represents the widest molecular screen for the function of lineage-specific genes yet attempted, and reveals surprising functional similarities between these novel genes despite their diverse evolutionary origins

Fluorinated halon replacement agents in explosion inerting

The US Federal Aviation Administration (FAA) observed during explosion tests that at a low concentration of agent, some candidate halon replacement agents increased the explosion severity instead of mitigating the event. At UTC Aerospace Systems a test program was developed to assess the behaviour of alternative agents at values below inerting concentration. Two agents were selected, C2HF5 (Penta- fluoroethane, HFC-125) and C6F12O (FK-5-1-12, Novec™1230). Baseline tests were performed with unsuppressed C3H8 (propane)/air mixtures and C3H8/air mixtures with CF3Br (Halon 1301) and N2 (nitrogen). Using CF3Br or N2 at below inerting concentrations mitigated the explosion. C2HF5 was tested against C3H8 at stoichiometric (4 vol%) and lower explosion limit (LEL) (2 vol%). Against 4 vol% C3H8 the combustion was mitigated, proportional to agent concentration; however, low concentrations of C2HF5 with 2 vol% C3H8 enhanced the explosion. Tests with N2 against a volatile mixture of C3H8 with C2HF5 showed that N2 mitigated the events. Final tests were performed with low concentrations of C6F12O against C3H8/air mixtures. This showed similar behaviour to that observed with the C2HF5 tests. Normally during qualification tests for new agents the stoichiometric concentration of a fuel is deemed to be the worst case scenario and the baseline against which agents are tested. The above described test results show that this assumption may need to be reconsidered. This work shows that contrary to common assumption the agents investigated are unlikely to have acted chemically at the flame front, but most likely, mainly cooled the flame and changed the stoichiometry, i.e. the ratio of components of the flammable mixture

De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences

Funding for Open Access provided by the UMD Libraries Open Access Publishing Fund.How non-coding DNA gives rise to new protein-coding genes (de novo genes) is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs), while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important.This work was supported by NSF Grant #mcb0920196 and a Royster Society Fellowship from the University of North Carolina. Open Access publication fees were provided by the University of Maryland Libraries Open Access Publishing Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

DNA methylation predicts age and provides insight into exceptional longevity of bats

This work was supported by a Paul G. Allen Frontiers Group grant to S.H., the University of Maryland, College of Computer, Mathematical and Natural Sciences to G.S.W., an Irish Research Council Consolidator Laureate Award to E.C.T., a UKRI Future Leaders Fellowship (MR/T021985/1) to S.C.V. and a Discovery Grant from the Natural Sciences and Engineering Research Council (NSERC) of Canada to P.A.F. S.C.V. and P.D. were supported by a Max Planck Research Group awarded to S.C.V. by the Max Planck Gesellschaft, and S.C.V. and E.Z.L. were supported by a Human Frontiers Science Program Grant (RGP0058/2016) awarded to S.C.V. L.J.G. was supported by an NSERC PGS-D scholarship.Exceptionally long-lived species, including many bats, rarely show overt signs of aging, making it difficult to determine why species differ in lifespan. Here, we use DNA methylation (DNAm) profiles from 712 known-age bats, representing 26 species, to identify epigenetic changes associated with age and longevity. We demonstrate that DNAm accurately predicts chronological age. Across species, longevity is negatively associated with the rate of DNAm change at age-associated sites. Furthermore, analysis of several bat genomes reveals that hypermethylated age- and longevity-associated sites are disproportionately located in promoter regions of key transcription factors (TF) and enriched for histone and chromatin features associated with transcriptional regulation. Predicted TF binding site motifs and enrichment analyses indicate that age-related methylation change is influenced by developmental processes, while longevity-related DNAm change is associated with innate immunity or tumorigenesis genes, suggesting that bat longevity results from augmented immune response and cancer suppression.Publisher PDFPeer reviewe

Widespread Polymorphism in the Positions of Stop Codons in Drosophila melanogaster

The mechanisms underlying evolutionary changes in protein length are poorly understood. Protein domains are lost and gained between species and must have arisen first as within-species polymorphisms. Here, we use Drosophila melanogaster population genomic data combined with between species divergence information to understand the evolutionary forces that generate and maintain polymorphisms causing changes in protein length in D. melanogaster. Specifically, we looked for protein length variations resulting from premature termination codons (PTCs) and stop codon losses (SCLs). We discovered that 438 genes contained polymorphisms resulting in truncation of the translated region (PTCs) and 119 genes contained polymorphisms predicted to lengthen the translated region (SCLs). Stop codon polymorphisms (SCPs) (especially PTCs) appear to be more deleterious than other polymorphisms, including protein amino acid changes. Genes harboring SCPs are in general less selectively constrained, more narrowly expressed, and enriched for dispensable biological functions. However, we also observed exceptional cases such as genes that have multiple independent SCPs, alleles that are shared between D. melanogaster and Drosophila simulans, and high-frequency alleles that cause extreme changes in gene length. SCPs likely have an important role in the evolution of these genes