David

Short story originally published in Southern Review 7 (Winter 1971): 254-264

Dynamics of Western Juniper Woodland Expansion into Sagebrush Communities in Central Oregon

Western juniper (Juniperus occidentalis) woodlands in Oregon have expanded four-fold from 600,000 ha in 1930 to \u3e 2.6 million ha, often resulting in the reduction and fragmentation of sagebrush (Artemisia spp.) communities. We documented dynamics of western juniper across the John Day Ecological Province in central Oregon by recording size class and growth form at 178 sites. We used stratified random sampling, with strata based on vegetation association (sagebrush, juniper, other) and distance from juniper stands. Only 26 percent of sites contained pre-settlement trees (in other words, \u3e 140 years old), and \u3c 5 percent of the 2,254 junipers tallied were pre-settlement trees. Mean densities of pre-settlement trees by stratum ranged from 0 to 18 trees/ha, suggesting that historically, juniper was widely scattered across the landscape. Current densities of post-settlement trees ranged from 75 to 211 trees/ha in non-woodland strata to 457 trees/ha in the juniper stratum. Juniper in non-woodland strata was most abundant in sites adjacent to juniper stands and in sagebrush communities. Mean densities of post-settlement trees were greatest in the \u3e 2.0-m tall size class (82 trees/ha), followed by the 0.3 to 1-m tall size class (52 trees/ha). These densities pose substantial risk to sagebrush communities in central Oregon. Questions remain about the extent of western juniper woodlands across the species’ range that have replaced or are expanding into sagebrush communities versus sites that historically supported woodlands. However, our findings suggest that within sagebrush communities of the John Day province, intensive management through removal of western juniper may be prudent, while retaining pre-settlement trees

Mutations in KDSR Cause Recessive Progressive Symmetric Erythrokeratoderma

Supplemental Data Supplemental Data include five figures and three tables and can be found with this article online at http://dx.doi.org/10.1016/j.ajhg.2017.05.003. Supplemental Data Document S1. Figures S1–S5 and Tables S1–S3 Download Document S2. Article plus Supplemental Data Download Web Resources 1000 Genomes, http://www.internationalgenome.org/ ANNOVAR, http://annovar.openbioinformatics.org/en/latest/ BWA-MEM, http://bio-bwa.sourceforge.net/index.shtml Database of Genomic Variants, http://dgv.tcag.ca/dgv/app/home dbSNP, https://www.ncbi.nlm.nih.gov/projects/SNP/ Exome Aggregation Consortium (ExAC) Browser, http://exac.broadinstitute.org/ ExonPrimer, https://ihg.helmholtz-muenchen.de/ihg/ExonPrimer.html GenBank, https://www.ncbi.nlm.nih.gov/genbank/ Genome Analysis Toolkit (GATK), https://software.broadinstitute.org/gatk/ Integrative Genomics Viewer (IGV), http://software.broadinstitute.org/software/igv/ OMIM, https://www.omim.org/ SNPmasker, http://bioinfo.ebc.ee/snpmasker/ UCSC Genome Browser, https://genome.ucsc.edu/index.html Variant Effect Predictor, http://useast.ensembl.org/info/docs/tools/vep/index.html The discovery of new genetic determinants of inherited skin disorders has been instrumental to the understanding of epidermal function, differentiation, and renewal. Here, we show that mutations in KDSR (3-ketodihydrosphingosine reductase), encoding an enzyme in the ceramide synthesis pathway, lead to a previously undescribed recessive Mendelian disorder in the progressive symmetric erythrokeratoderma spectrum. This disorder is characterized by severe lesions of thick scaly skin on the face and genitals and thickened, red, and scaly skin on the hands and feet. Although exome sequencing revealed several of the KDSR mutations, we employed genome sequencing to discover a pathogenic 346 kb inversion in multiple probands, and cDNA sequencing and a splicing assay established that two mutations, including a recurrent silent third base change, cause exon skipping. Immunohistochemistry and yeast complementation studies demonstrated that the mutations cause defects in KDSR function. Systemic isotretinoin therapy has achieved nearly complete resolution in the two probands in whom it has been applied, consistent with the effects of retinoic acid on alternative pathways for ceramide generation

Col-OSSOS: The Distribution of Surface Classes in Neptune's Resonances

The distribution of surface classes of resonant trans-Neptunian objects (TNOs) provides constraints on the protoplanetesimal disk and giant planet migration. To better understand the surfaces of TNOs, the Colours of the Outer Solar System Origins Survey (Col-OSSOS) acquired multi-band photometry of 102 TNOs, and found that the surfaces of TNOs can be well described by two surface classifications, BrightIR and FaintIR. These classifications both include optically red members and are differentiated predominantly based on whether their near-infrared spectral slope is similar to their optical spectral slope. The vast majority of cold classical TNOs, with dynamically quiescent orbits, have the FaintIR surface classification, and we infer that TNOs in other dynamical classifications with FaintIR surfaces share a common origin with the cold classical TNOs. Comparison between the resonant populations and the possible parent populations of cold classical and dynamically excited TNOs reveal that the 3:2 has minimal contributions from the FaintIR class, which could be explained by the $\nu_8$ secular resonance clearing the region near the 3:2 before any sweeping capture occurred. Conversely, the fraction of FaintIR objects in the 4:3 resonance, 2:1 resonance, and the resonances within the cold classical belt, suggest that the FaintIR surface formed in the protoplanetary disk between 34.6 and 47 au, though the outer bound depends on the degree of resonance sweeping during migration. The presence and absence of the FaintIR surfaces in Neptune's resonances provides critical constraints for the history of Neptune's migration, the evolution of the $\nu_8$, and the surface class distribution in the initial planetesimal diskComment: 19 pages, 8 figures. in Press at PS

The State of the Region: Hampton Roads 2007

This is Old Dominion University\u27s eighth annual State of the Region report. While it represents the work of many people connected in various ways to the university, the report does not constitute an official viewpoint of Old Dominion or it\u27s president, Roseann Runte. The report maintains the goal of stimulating thought and discussion that ultimately will make Hampton Roads an even better place to live. We are proud of our region\u27s many successes, but realize that it is possible to improve our performance. In order to do so, we must have accurate information about where we are and a sound understanding of the policy options open to us.https://digitalcommons.odu.edu/economics_books/1011/thumbnail.jp

Variation in inbreeding rates across the range of Northern Spotted Owls (\u3ci\u3eStrix occidentalis caurina\u3c/i\u3e): Insights from over 30 years of monitoring data

Inbreeding has been difficult to quantify in wild populations because of incomplete parentage information. We applied and extended a recently developed framework for addressing this problem to infer inbreeding rates in Northern Spotted Owls (Strix occidentalis caurina) across the Pacific Northwest, USA. Using pedigrees from 14,187 Northern Spotted Owls, we inferred inbreeding rates for 14 types of matings among relatives that produce pedigree inbreeding coefficients of F=0.25 or F=0.125. Inbreeding was most common in the Washington Cascades, where an estimated 15% of individuals are inbred. Inbreeding was lowest in western Oregon (3.5%) and northern California (2.7%), and intermediate for the Olympic Peninsula of Washington (6.1%). Estimates from the Olympic Peninsula were likely underestimates because of small sample sizes and the presence of few pedigrees capable of resolving inbreeding events. Most inbreeding resulted from matings between full siblings or half siblings, although a high rate of inbreeding from mother–son pairs was identified in the Olympic Peninsula. Geographic variation in inbreeding rates may reflect population declines and bottlenecks that have been detected in prior investigations. We show that there is strong selection against inbred birds. Only 3 of 44 inbred birds were later identified as parents (6.8%), whereas 2,823 of 10,380 birds that represented a comparable cross section of the data were later seen as reproducing parents (27.2%). Habitat loss and competition with Barred Owls (S. varia) remain primary threats to Northern Spotted Owls. However, given the negative consequences of inbreeding, Spotted Owl populations in Washington with suitable habitat and manageable numbers of Barred Owls may benefit from translocations of individuals from Oregon and California to introduce new genetic variation and reduce future inbreeding events. La endogamia ha sido dif´ıcil de cuantificar en las poblaciones silvestres debido a la falta de informaci ´on sobre los parentescos. Aplicamos y extendimos un marco conceptual recientemente desarrollado para encarar el problema de inferir las tasas de endogamia en Strix occidentalis caurina a trav´es del noroeste del Pac´ıfico, EEUU. Usando los pedigr´ıes provenientes de 14187 individuos, inferimos las tasas de endogamia para 14 tipos de apareamiento entre parientes que producen coeficientes de endogamia de pedigr´ı de F=0.25 o F=0.125. La endogamia fue ma´s com´un en las Cascadas de Washington, donde se estima que 15% de los individuos son endoga´micos. La endogamia fue menor en el oeste de Oreg´on (3.5%) y el norte de California (2.7%), e intermedia en la Pen´ınsula Ol´ımpica de Washington (6.1%). Las estimaciones de la Pen´ınsula Ol´ımpica fueron probablemente subestimadas debido a los peque ˜nos tama ˜nos de muestreo y a la presencia de pocos pedigr´ıes capaces de resolver los eventos de endogamia. La mayor´ıa de la endogamia result ´o de los apareamientos entre hermanos completos o medios hermanos, aunque se identific ´o una alta tasa de endogamia en parejas madre/hijo en la Pen´ınsula Ol´ımpica. La variaci ´on geogra´ fica en las tasas de endogamia puede reflejar disminuciones poblacionales y cuellos de botella que han sido detectados en investigaciones previas. Mostramos que hay una fuerte selecci ´on contra las aves endoga´micas. Solo tres de 44 aves endoga´micas fueron ma´s tarde identificadas como progenitores (6.8%), mientras que 2823 de 10380 aves que representaron una secci ´on transversal comparable de datos fueron vistas ma´s tarde como progenitores reproductivos (27.2%). La p´erdida de ha´bitat y la competencia con Strix varia sigue siendo la principal amenaza para S. o. caurina. Sin embargo, dadas las consecuencias negativas de la endogamia, las poblaciones de S. occidentalis en Washington con ha´bitat adecuado y n´umeros manejables de Strix varia pueden beneficiarse de traslocaciones de individuos de Oreg´on y California para introducir nueva variaci ´on gen´etica y reducir futuros eventos de endogamia

Src-family kinases mediate an outside-in signal necessary for β2 integrins to achieve full activation and sustain firm adhesion of polymorphonuclear leucocytes tethered on E-selectin

In cell suspensions subjected to high-shear rotatory motion, human PMN (polymorphonuclear cells) adhered to E-selectin-expressing CHO (Chinese-hamster ovary) cells (CHO-E), and formed homotypic aggregates when challenged by E-selectin–IgG fusion protein, by a mechanism that involved β2 integrins. Both heterotypic and homotypic PMN adhesion was accompanied by tyrosine phosphorylation of a 110 kDa protein (P110). This event was prevented by blocking anti-(β2 integrin) antibodies and by inhibitors of Src-family kinases, suggesting that it was part of an ‘outside-in’ signalling that was initiated by integrin engagement. Interestingly, Src-family kinase inhibitors prevented β2-integrin-mediated (i) homotypic PMN adhesion triggered by E-selectin–IgG, (ii) heterotypic CHO-E/PMN adhesion in mixed-cell suspensions, and (iii) firm adhesion of PMN to CHO-E monolayers under physiological flow. Similarly to PMN treated with Src-family kinase inhibitors, PMN from hck−/−fgr−/− and hck−/−fgr−/−lyn−/− mice showed significant impairment of β2-integrin-mediated adhesion to CHO-E. Moreover, the expression of β2 integrin activation epitopes at the sites of cell–cell contact in CHO-E/PMN conjugates was abolished by Src-family kinase inhibitors. One component of P110 was identified as the FAK (focal adhesion kinase) Pyk2 (proline-rich tyrosine kinase 2), which was phosphorylated in a β2 integrin- and Src-family-kinase-dependent manner. Thus, Src-family kinases, and perhaps Pyk2, mediate a signal necessary for β2 integrin function in PMN tethered by E-selectin