Seasonal associations with light pollution trends for nocturnally migrating bird populations

This project was supported by The Leon Levy Foundation, The Wolf Creek Charitable Foundation, Lyda Hill Philanthropies, Amon G. Carter Foundation, National Aeronautics and Space Administration (80NSSC21K1143), and National Science Foundation (ABI sustaining DBI-1939187, GCR-2123405). Computing support was provided by the National Science Foundation (CNS-1059284 and CCF-1522054), and the Extreme Science and Engineering Discovery Environment (XSEDE; National Science Foundation, ACI-1548562) through allocation TG-DEB200010 run on Bridges at the Pittsburgh Supercomputing Center.Artificial light at night (ALAN) is adversely affecting natural systems worldwide, including the disorienting influence of ALAN on nocturnally migrating birds. Understanding how ALAN trends are developing across species' seasonal distributions will inform mitigation efforts, such as Lights Out programs. Here, we intersect ALAN annual trend estimates (1992-2013) with weekly estimates of relative abundance for 42 nocturnally migrating passerine bird species that breed in North America using observations from the eBird community science database for the combined period 2005-2020. We use a cluster analysis to identify species with similar weekly associations with ALAN trends. Our results identified three prominent clusters. Two contained species that occurred in northeastern and western North America during the breeding season. These species were associated with moderate ALAN levels and weak negative ALAN trends during the breeding season, and low ALAN levels and strong positive ALAN trends during the nonbreeding season. The difference between the breeding and nonbreeding seasons was lower for species that occurred in northern South America and greater for species that occurred in Central America during the nonbreeding season. For species that occurred in South America during the nonbreeding season, positive ALAN trends increased in strength as species migrated through Central America, especially in the spring. The third cluster contained species whose associations with positive ALAN trends remained high across the annual cycle, peaking during migration, especially in the spring. These species occurred in southeastern North America during the breeding season where they were associated with high ALAN levels, and in northern South America during the nonbreeding season where they were associated with low ALAN levels. Our findings suggest reversing ALAN trends in Central America during migration, especially in the spring, would benefit the most individuals of the greatest number of species. Reversing ALAN trends in southeastern North America during the breeding season and Central America during the nonbreeding season would generate the greatest benefits outside of migration.Publisher PDFPeer reviewe

Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner.

BackgroundRewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve in a predictable manner using targeted systems.ResultsHere, we report that persistent epigenetic memory required both a DNA methyltransferase (DNMT3A-dCas9) and a histone methyltransferase (Ezh2-dCas9 or KRAB-dCas9). We demonstrate that the histone methyltransferase requirement can be locus specific. Co-targeting Ezh2-dCas9, but not KRAB-dCas9, with DNMT3A-dCas9 and DNMT3L induced long-term HER2 repression over at least 50 days (approximately 57 cell divisions) and triggered an epigenetic switch to a heterochromatic environment. An increase in H3K27 trimethylation and DNA methylation was stably maintained and accompanied by a sustained loss of H3K27 acetylation. Interestingly, substitution of Ezh2-dCas9 with KRAB-dCas9 enabled long-term repression at some target genes (e.g., SNURF) but not at HER2, at which H3K9me3 and DNA methylation were transiently acquired and subsequently lost. Off-target DNA hypermethylation occurred at many individual CpG sites but rarely at multiple CpGs in a single promoter, consistent with no detectable effect on transcription at the off-target loci tested. Conversely, robust hypermethylation was observed at HER2. We further demonstrated that Ezh2-dCas9 required full-length DNMT3L for maximal activity and that co-targeting DNMT3L was sufficient for persistent repression by Ezh2-dCas9 or KRAB-dCas9.ConclusionsThese data demonstrate that targeting different combinations of histone and DNA methyltransferases is required to achieve maximal repression at different loci. Fine-tuning of targeting tools is a necessity to engineer epigenetic memory at any given locus in any given cell type

Artificial escape from XCI by DNA methylation editing of the CDKL5 gene.

A significant number of X-linked genes escape from X chromosome inactivation and are associated with a distinct epigenetic signature. One epigenetic modification that strongly correlates with X-escape is reduced DNA methylation in promoter regions. Here, we created an artificial escape by editing DNA methylation on the promoter of CDKL5, a gene causative for an infantile epilepsy, from the silenced X-chromosomal allele in human neuronal-like cells. We identify that a fusion of the catalytic domain of TET1 to dCas9 targeted to the CDKL5 promoter using three guide RNAs causes significant reactivation of the inactive allele in combination with removal of methyl groups from CpG dinucleotides. Strikingly, we demonstrate that co-expression of TET1 and a VP64 transactivator have a synergistic effect on the reactivation of the inactive allele to levels >60% of the active allele. We further used a multi-omics assessment to determine potential off-targets on the transcriptome and methylome. We find that synergistic delivery of dCas9 effectors is highly selective for the target site. Our findings further elucidate a causal role for reduced DNA methylation associated with escape from X chromosome inactivation. Understanding the epigenetics associated with escape from X chromosome inactivation has potential for those suffering from X-linked disorders

An optimized method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7

Analysis of microbial gene expression during host colonization provides valuable information on the nature of interaction, beneficial or pathogenic, and the adaptive processes involved. Isolation of bacterial mRNA for in planta analysis can be challenging where host nucleic acid may dominate the preparation, or inhibitory compounds affect downstream analysis, e.g., quantitative reverse transcriptase PCR (qPCR), microarray, or RNA-seq. The goal of this work was to optimize the isolation of bacterial mRNA of food-borne pathogens from living plants. Reported methods for recovery of phytopathogen-infected plant material, using hot phenol extraction and high concentration of bacterial inoculation or large amounts of infected tissues, were found to be inappropriate for plant roots inoculated with Escherichia coli O157:H7. The bacterial RNA yields were too low and increased plant material resulted in a dominance of plant RNA in the sample. To improve the yield of bacterial RNA and reduce the number of plants required, an optimized method was developed which combines bead beating with directed bacterial lysis using SDS and lysozyme. Inhibitory plant compounds, such as phenolics and polysaccharides, were counteracted with the addition of high-molecular-weight polyethylene glycol and hexadecyltrimethyl ammonium bromide. The new method increased the total yield of bacterial mRNA substantially and allowed assessment of gene expression by qPCR. This method can be applied to other bacterial species associated with plant roots, and also in the wider context of food safety

Pharmaceutical innovation and parallel trade

This paper was accepted for publication in the journal International Journal of Industrial Organization and the definitive published version is available at https://doi.org/10.1016/j.ijindorg.2014.02.009This paper proposes a North–South model to study the interaction between price regulation policies and parallel trade, with a particular focus on the pharmaceutical sector. We show that, under parallel trade, R&D investment can rise only when the South government takes into full account its impact both on investment and on the firm's decision to supply the regulated country. This arises because of a complete withdrawal from price regulation. When policy choices are endogenized, indeed the South wants to achieve this level of full commitment when it is large in size. When instead it is smaller in size, the South chooses an intermediate form of commitment whereby it anticipates its effect only on local distribution and delivery, but not on global R&D investment. As a response to these credible levels of price control commitments, the North reacts by allowing parallel imports from the South

2018 Advent Devotional

2018 Advent Devotions written by the students of Concordia Seminary, St. Louishttps://scholar.csl.edu/osp/1014/thumbnail.jp

Gene Expression Patterns of Dengue Virus-Infected Children from Nicaragua Reveal a Distinct Signature of Increased Metabolism

Dengue is a widespread viral disease for which over 3 billion people are at risk. There are no drug treatments or vaccines available for this disease. It is also difficult for physicians to predict which patients are at highest risk for the severe manifestations known as dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). We used genome-wide transcriptional profiling analysis to study peripheral blood responses to dengue among patients from Nicaragua. We found that patients with severe manifestations involving shock had very different transcriptional profiles from dengue patients with mild and moderate illness. We then compared our results with other microarray experiments on dengue patients available from public databases and confirmed that dengue is often associated with large changes to the metabolic processes within cells. This approach could identify prognostic markers for severe dengue as well as provide a better understanding of the pathophysiology associated with different grades of disease severity