CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity.

Hexanucleotide-repeat expansions in the C9ORF72 gene are the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD). The nucleotide-repeat expansions are translated into dipeptide-repeat (DPR) proteins, which are aggregation prone and may contribute to neurodegeneration. We used the CRISPR-Cas9 system to perform genome-wide gene-knockout screens for suppressors and enhancers of C9ORF72 DPR toxicity in human cells. We validated hits by performing secondary CRISPR-Cas9 screens in primary mouse neurons. We uncovered potent modifiers of DPR toxicity whose gene products function in nucleocytoplasmic transport, the endoplasmic reticulum (ER), proteasome, RNA-processing pathways, and chromatin modification. One modifier, TMX2, modulated the ER-stress signature elicited by C9ORF72 DPRs in neurons and improved survival of human induced motor neurons from patients with C9ORF72 ALS. Together, our results demonstrate the promise of CRISPR-Cas9 screens in defining mechanisms of neurodegenerative diseases

Integrating data types to estimate spatial patterns of avian migration across the Western Hemisphere

For many avian species, spatial migration patterns remain largely undescribed, especially across hemispheric extents. Recent advancements in tracking technologies and high-resolution species distribution models (i.e., eBird Status and Trends products) provide new insights into migratory bird movements and offer a promising opportunity for integrating independent data sources to describe avian migration. Here, we present a three-stage modeling framework for estimating spatial patterns of avian migration. First, we integrate tracking and band re-encounter data to quantify migratory connectivity, defined as the relative proportions of individuals migrating between breeding and nonbreeding regions. Next, we use estimated connectivity proportions along with eBird occurrence probabilities to produce probabilistic least-cost path (LCP) indices. In a final step, we use generalized additive mixed models (GAMMs) both to evaluate the ability of LCP indices to accurately predict (i.e., as a covariate) observed locations derived from tracking and band re-encounter data sets versus pseudo-absence locations during migratory periods and to create a fully integrated (i.e., eBird occurrence, LCP, and tracking/band re-encounter data) spatial prediction index for mapping species-specific seasonal migrations. To illustrate this approach, we apply this framework to describe seasonal migrations of 12 bird species across the Western Hemisphere during pre- and postbreeding migratory periods (i.e., spring and fall, respectively). We found that including LCP indices with eBird occurrence in GAMMs generally improved the ability to accurately predict observed migratory locations compared to models with eBird occurrence alone. Using three performance metrics, the eBird + LCP model demonstrated equivalent or superior fit relative to the eBird-only model for 22 of 24 species–season GAMMs. In particular, the integrated index filled in spatial gaps for species with over-water movements and those that migrated over land where there were few eBird sightings and, thus, low predictive ability of eBird occurrence probabilities (e.g., Amazonian rainforest in South America). This methodology of combining individual-based seasonal movement data with temporally dynamic species distribution models provides a comprehensive approach to integrating multiple data types to describe broad-scale spatial patterns of animal movement. Further development and customization of this approach will continue to advance knowledge about the full annual cycle and conservation of migratory birds

Down-regulation of ATM protein sensitizes human prostate cancer cells to radiation-induced apoptosis

Treatment with the protein kinase C activator 12-O-tetradecanoylphorbol 12-acetate (TPA) enables radiation-resistant LNCaP human prostate cancer cells to undergo radiation-induced apoptosis, mediated via activation of the enzyme ceramide synthase ( CS) and de novo synthesis of the sphingolipid ceramide (Garzotto, M., Haimovitz-Friedman, A., Liao, W. C., White-Jones, M., Huryk, R., Heston, D. W. W., Cardon-Cardo, C., Kolesnick, R., and Fuks, Z. ( 1999) Cancer Res. 59, 5194-5201). Here, we show that TPA functions to decrease the cellular level of the ATM ( ataxia telangiectasia mutated) protein, known to repress CS activation ( Liao, W.-C., Haimovitz-Friedman, A., Persaud, R., McLoughlin, M., Ehleiter, D., Zhang, N., Gatei, M., Lavin, M., Kolesnick, R., and Fuks, Z. ( 1999) J. Biol. Chem. 274, 17908 - 17917). Gel shift analysis in LNCaP and CWR22-Rv1 cells demonstrated a significant reduction in DNA binding of the Sp1 transcription factor to the ATM promoter, and quantitative reverse transcription-PCR showed a 50% reduction of ATM mRNA between 8 and 16 h of TPA treatment, indicating that TPA inhibits ATM transcription. Furthermore, treatment of LNCaP, CWR22-Rv1, PC-3, and DU-145 human prostate cells with antisense-ATM oligonucleotides, which markedly reduced cellular ATM levels, significantly enhanced radiation-induced CS activation and apoptosis, leading to apoptosis at doses as a low as 1 gray. These data suggest that the CS pathway initiates a generic mode of radiation- induced apoptosis in human prostate cancer cells, regulated by a suppressive function of ATM, and that ATM might represent a potential target for pharmacologic inactivation with potential clinical applications in human prostate cancer

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease

Projected avifaunal responses to climate change across the U.S. National Park System

<div><p>Birds in U.S. national parks find strong protection from many longstanding and pervasive threats, but remain highly exposed to effects of ongoing climate change. To understand how climate change is likely to alter bird communities in parks, we used species distribution models relating North American Breeding Bird Survey (summer) and Audubon Christmas Bird Count (winter) observations to climate data from the early 2000s and projected to 2041–2070 (hereafter, mid-century) under high and low greenhouse gas concentration trajectories, RCP8.5 and RCP2.6. We analyzed climate suitability projections over time for 513 species across 274 national parks, classifying them as improving, worsening, stable, potential colonization, and potential extirpation. U.S. national parks are projected to become increasingly important for birds in the coming decades as potential colonizations exceed extirpations in 62–100% of parks, with an average ratio of potential colonizations to extirpations of 4.1 in winter and 1.4 in summer under RCP8.5. Average species turnover is 23% in both summer and winter under RCP8.5. Species turnover (Bray-Curtis) and potential colonization and extirpation rates are positively correlated with latitude in the contiguous 48 states. Parks in the Midwest and Northeast are expected to see particularly high rates of change. All patterns are more extreme under RCP8.5 than under RCP2.6. Based on the ratio of potential colonization and extirpation, parks were classified into overall trend groups associated with specific climate-informed conservation strategies. Substantial change to bird and ecological communities is anticipated in coming decades, and current thinking suggests managing towards a forward-looking concept of ecological integrity that accepts change and novel ecological conditions, rather than focusing management goals exclusively on maintaining or restoring a static set of historical conditions.</p></div

Example of projected bird assemblage changes by mid-century at Golden Gate National Recreation Area.

<p>Under RCP8.5 in summer, climate suitability is projected to improve for the Great Egret (<i>Ardea alba</i>), remain stable for the Nuttall’s Woodpecker (<i>Picoides nuttallii</i>), and worsen for the Wilson’s Warbler (<i>Cardellina pusilla</i>). Climate suitability is at risk of disappearing for the American Robin (<i>Turdus migratorius</i>), potentially resulting in extirpation from the park. Although the Blue Grosbeak (<i>Passerina caerulea</i>) is not currently found in the park, climate is projected to become suitable for this species, potentially resulting in local colonization. Bird illustrations by Kenn Kaufman.</p

Potential changes in bird assemblages by mid-century, by emissions pathway and season, as measured by (1) average ± SE of Bray-Curtis dissimilarity index across parks, average ± SE of (2) the proportion of potential extirpations and (3) potential colonizations across parks, (4) count and percent of parks with more than 25% extirpations, (5) count and percent of parks with more than 25% colonizations, and (6) count and percent of parks where the number of potential colonizations exceeds potential extirpations.

<p>Potential changes in bird assemblages by mid-century, by emissions pathway and season, as measured by (1) average ± SE of Bray-Curtis dissimilarity index across parks, average ± SE of (2) the proportion of potential extirpations and (3) potential colonizations across parks, (4) count and percent of parks with more than 25% extirpations, (5) count and percent of parks with more than 25% colonizations, and (6) count and percent of parks where the number of potential colonizations exceeds potential extirpations.</p

Projected species composition changes from the early 2000s to mid-century across 274 U.S. national parks.

<p>Potential (A) colonizations and (B) extirpations in summer and winter under RCP8.5 are shown as a proportion of the current total number of species. Circle sizes represent proportions in summer, and colors represent proportions in winter. Breaks in classes are based on quartiles. Alaska is shown in the inset on the left and the National Capital region is shown in the inset on the right.</p

Classification of 274 U.S. national parks into trend groups based on the proportion of potential colonizations and extirpations.

<p>Each circle represents a park. The median proportion of colonizations and extirpations across parks under RCP8.5 in summer (represented by solid vertical and horizontal lines in the plot) were used to classify parks into all trend groups except intermediate change. The upper and lower quartiles of each axis (represented by the diamond in the center of the plot) mark the boundaries of the intermediate change group. Alaska is shown in the inset on the left and the National Capital region is shown in the inset on the right.</p