Estimating Trends of Common Raven Populations in North America, 1966–2018

Over the last half century, common raven (Corvus corax; raven) populations have increased in abundance across much of North America. Ravens are generalist predators known to depredate the eggs and young of several sensitive species. Quantifying raven population increases at multiple spatial scales across North America will help wildlife resource managers identify areas where population increases present the greatest risk to species conservation. We used a hierarchical Bayesian modeling approach to analyze trends of standardized raven counts from 1966 to 2018 using Breeding Bird Survey data within each Level I and II ecoregion of the United States and Canada. We also compared raven abundance within and outside the distributions of 9 sensitive or endangered species. Although we found substantial evidence that raven populations have increased across North America, populations varied in growth rates and relative abundances among regions. We found 73% of Level I (11/15) and II (25/34) ecoregions demonstrated positive annual population growth rates ranging from 0.2–9.4%. We found higher raven abundance inside versus outside the distributions of 7 of the 9 sensitive species included in our analysis. Gunnison sage-grouse (Centrocercus minimus) had the highest discrepancy, with 293% more ravens within compared to outside of their range, followed by greater sandhill crane (Antigone canadensis tabida; 280%), and greater sage-grouse (C. urophasianus; 204%). Only 2 species, least tern (Sternula antillarum) and piping plover (Charadrius melodus), indicated lower raven abundance within relative to outside their distributions. Our findings will help wildlife resource managers identify regional trends in abundance of ravens and anticipate which sensitive species are at greatest risk from elevated raven populations. Future research directed at identifying the underlying regional drivers of these trends could help elucidate the most appropriate and responsive management actions and, thereby, guide the development of raven population management plans to mitigate impacts to sensitive species

DNA Methylation Signatures within the Human Brain

DNA methylation is a heritable modification of genomic DNA central to development, imprinting, transcriptional regulation, chromatin structure, and overall genomic stability. Aberrant DNA methylation of individual genes is a hallmark of cancer and has been shown to play an important role in neurological disorders such as Rett syndrome. Here, we asked whether normal DNA methylation might distinguish individual brain regions. We determined the quantitative DNA methylation levels of 1,505 CpG sites representing 807 genes with diverse functions, including proliferation and differentiation, previously shown to be implicated in human cancer. We initially analyzed 76 brain samples representing cerebral cortex (n=35), cerebellum (n=34), and pons (n=7), along with liver samples (n=3) from 43 individuals. Unsupervised hierarchical analysis showed clustering of 33 of 35 cerebra distinct from the clustering of 33 of 34 cerebella, 7 of 7 pons, and all 3 livers. By use of comparative marker selection and permutation testing, 156 loci representing 118 genes showed statistically significant differences—a ⩾17% absolute change in DNA methylation (P<.004)—among brain regions. These results were validated for all six genes tested in a replicate set of 57 samples. Our data suggest that DNA methylation signatures distinguish brain regions and may help account for region-specific functional specialization

Mitigation Effectiveness for Improving Nesting Success of Greater Sage-Grouse Influenced by Energy Development

Sagebrush Artemisia spp. habitats being developed for oil and gas reserves are inhabited by sagebrush obligate species--including the greater sage-grouse Centrocercus urophasianus (sage-grouse) that is currently being considered for protection under the U.S. Endangered Species Act. Numerous studies suggest increasing oil and gas development may exacerbate species extinction risks. Therefore, there is a great need for effective on-site mitigation to reduce impacts to co-occurring wildlife such as sage-grouse. Nesting success is a primary factor in avian productivity and declines in nesting success are also thought to be an important contributor to population declines in sage-grouse. From 2008 to 2011 we monitored 296 nests of radio-marked female sage-grouse in a natural gas (NG) field in the Powder River Basin, Wyoming, USA, and compared nest survival in mitigated and non-mitigated development areas and relatively unaltered areas to determine if specific mitigation practices were enhancing nest survival. Nest survival was highest in relatively unaltered habitats followed by mitigated, and then non-mitigated NG areas. Reservoirs used for holding NG discharge water had the greatest support as having a direct relationship to nest survival. Within a 5-km2 area surrounding a nest, the probability of nest failure increased by about 15% for every 1.5 km increase in reservoir water edge. Reducing reservoirs was a mitigation focus and sage-grouse nesting in mitigated areas were exposed to almost half of the amount of water edge compared to those in non-mitigated areas. Further, we found that an increase in sagebrush cover was positively related to nest survival. Consequently, mitigation efforts focused on reducing reservoir construction and reducing surface disturbance, especially when the surface disturbance results in sagebrush removal, are important to enhancing sage-grouse nesting success

M6 Membrane Protein Plays an Essential Role in Drosophila Oogenesis

We had previously shown that the transmembrane glycoprotein M6a, a member of the proteolipid protein (PLP) family, regulates neurite/filopodium outgrowth, hence, M6a might be involved in neuronal remodeling and differentiation. In this work we focused on M6, the only PLP family member present in Drosophila, and ortholog to M6a. Unexpectedly, we found that decreased expression of M6 leads to female sterility. M6 is expressed in the membrane of the follicular epithelium in ovarioles throughout oogenesis. Phenotypes triggered by M6 downregulation in hypomorphic mutants included egg collapse and egg permeability, thus suggesting M6 involvement in eggshell biosynthesis. In addition, RNAi-mediated M6 knockdown targeted specifically to follicle cells induced an arrest of egg chamber development, revealing that M6 is essential in oogenesis. Interestingly, M6-associated phenotypes evidenced abnormal changes of the follicle cell shape and disrupted follicular epithelium in mid- and late-stage egg chambers. Therefore, we propose that M6 plays a role in follicular epithelium maintenance involving membrane cell remodeling during oogenesis in Drosophila

Neuronal lysosomal dysfunction releases exosomes harboring APP C-terminal fragments and unique lipid signatures

Defects in endolysosomal and autophagic functions are increasingly viewed as key pathological features of neurodegenerative disorders. A master regulator of these functions is phosphatidylinositol-3-phosphate (PI3P), a phospholipid synthesized primarily by class III PI 3-kinase Vps34. Here we report that disruption of neuronal Vps34 function in vitro and in vivo impairs autophagy, lysosomal degradation as well as lipid metabolism, causing endolysosomal membrane damage. PI3P deficiency also promotes secretion of unique exosomes enriched for undigested lysosomal substrates, including amyloid precursor protein C-terminal fragments (APP-CTFs), specific sphingolipids, and the phospholipid bis(monoacylglycero)phosphate (BMP), which normally resides in the internal vesicles of endolysosomes. Secretion of these exosomes requires neutral sphingomyelinase 2 and sphingolipid synthesis. Our results reveal a homeostatic response counteracting lysosomal dysfunction via secretion of atypical exosomes eliminating lysosomal waste and define exosomal APP-CTFs and BMP as candidate biomarkers for endolysosomal dysfunction associated with neurodegenerative disorders.Fan Wang for the kind gift of the Pi3kc3flox/flox mice. We thank Basant Abdulrahman and Hermann Schaetzl for providing the gene-edited Atg5 KO N2a cells. We are also grateful to Zhenyu Yue, Ralph Nixon, and Jean Gruenberg for the kind gift of anti-Atg14L, Cathepsin D, and BMP antibodies, respectively. We thank Thomas Südhof for sharing Cre recombinase lentiviruses. We thank the OCS Microscopy Core of New York University Langone Medical Center for the support of the EM work and Rocio Perez-Gonzalez and Efrat Levy of New York University for their support during optimization of the brain exosome isolation technique. We thank Elizabeta Micevska for the maintenance and genotyping of the animal colony and Bowen Zhou for the preliminary lipidomic analysis of conditional Pi3kc3 cKO mice. We also thank Rebecca Williams and Catherine Marquer for critically reading the manuscript. This work was supported by grants from the Fundação para a Ciência e Tecnologia (PD/BD/105915/2014 to A.M.M.); the National Institute of Health (R01 NS056049 to G.D.P., transferred to Ron Liem, Columbia University; T32-MH015174 to Rene Hen (Z.M.L.)). Z.M.L. and R.B.C. received pilot grants from ADRC grant P50 AG008702 to S.A.S.info:eu-repo/semantics/publishedVersio

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid Loci

The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses

Waste-Surface Mapping of the Fernald K-65 Silos Using a Structured Light Measurement System

During FY 1991, a remotely operated surface-mapping measurement system was developed by the Robotics & Process Systems Division at Oak Ridge National Laboratory for use in the K-65 waste-storage silos at Fernald, Ohio. The mapping system used three infrared line-generating laser diodes as illumination sources and three high-resolution, low-lux, calibrated, black-and-white, chargecoupled- device video cameras as receivers. These components were combined to form structured light source range and direction sensors with six different possible emitter-receiver pairs. A technology demonstration and predeployment tests were performed at Fernald during July and August 1991, using the empty Silo 4 into which was placed rectangular objects of known dimensions. These objects were scanned by the structured light sources to demonstrate functionality and verify that the system was giving sufficiently accurate range data in three dimensions. The tests provided a checkout of installation and operational logistics, prior to field deployment, as well as verification of accuracy and repeatability. In September and October 1991, the structured light sources were then deployed in Silos 1 and 2 to scan the waste surfaces. The resulting data were merged to create three-dimensional maps of those surfaces. A bentonite clay cap was placed over the waste surfaces in November 1991. Surface maps were obtained in December 1991 of the bentonite clay caps. The change in surface height before and after bentonite addition was utilized as a measure of clay cap thickness. Verification of clay cap thickness was required to support a Department of Energy (DOE) Removal Action Milestone defined in the Amended Consent Agreement with the Environmental Protection Agency under Comprehensive Environmental Response, Compensation, and Liability Act Section 106 and 120. This report includes final results of the surface mapping campaign as well as a description of system components. Mapping system sensors and control hardware are described. Calibration and data acquisition methodology are described as well as the operator interface that facilitated these operations. The sensor system development was sponsored by the DOE Office of Technology Development, Robotics Technology Development Program. Field deployment in the K-65 silos was funded by the DOE Office of Environmental Restoration