Genome sequences of three hpAfrica2 strains of Helicobacter pylori

We present the genome sequences of three hpAfrica2 strains of Helicobacter pylori, which are postulated to have evolved in isolation for many millennia in people of San ethnicity. Although previously considered to be ancestral to Helicobacter acinonychis, the hpAfrica2 strains differ markedly from H. acinonychis in their gene arrangement. These data provide new insights into Helicobacter evolution

Wide-field Imaging Interferometry Testbed II: Implementation, Performance, and Plans

The Wide-Field Imaging Interferometry Testbed (WIIT) will provide valuable information for the development of space-based interferometers. This laboratory instrument operates at optical wavelengths and provides the ability to test operational algorithms and techniques for data reduction of interferometric data. Here we present some details of the system design and implementation, discuss the overall performance of the system to date, and present our plans for future development of WIIT. In order to make best use of the interferometric data obtained with this system, it is critical to limit uncertainties within the system and to accurately understand possible sources of error. The WIIT design addresses these criteria through a number of ancillary systems. The use of redundant metrology systems is one of the most important features of WIIT, and provides knowledge of the delay line position to better than 10 nm. A light power detector is used to monitor the brightness of our light sources to ensure that small fluctuations in brightness do not affect overall performance. We have placed temperature sensors on critical components of the instrument, and on the optical table, in order to assess environmental effects on the system. The use of these systems provides us with estimates of the overall system uncertainty, and allows an overall characterization of the results to date. These estimates allow us to proceed forward with WIIT, adding rotation stages for 2-D interferometry. In addition, they suggest possible avenues for system improvement. Funding for WIIT is provided by NASA Headquarters through the ROSS/SARA Program and by the Goddard Space Flight Center through the IR&D Program.Comment: 11 pages, 9 figure

Helping the Working Poor: Employer- vs. Employee-Based Subsidies

In the United States and Europe there has been renewed interest in subsidizing firms that employ disadvantaged workers as a means of addressing poverty and other social problems. In contrast, the prevailing practice is largely to provide social welfare benefits directly to individuals. Which approach is better? We re-examine the relative merits of employee- versus employer-based labor market subsidies and conclude there are good reasons to continue to rely on the direct, employee-based approach. In practice, low-wage workers are seldom either low-skill or low-income workers. Furthermore, workers who might quality for a firm-based subsidy are reluctant to so identify themselves for fear of being stigmatized or labeled as needy. Thus, employer-based subsidy programs have lower participation rates and correspondingly higher per capita expenditures than employee-based subsidy programs

Chickasaw plum for wildlife in Oklahoma

The Oklahoma Cooperative Extension Service periodically issues revisions to its publications. The most current edition is made available. For access to an earlier edition, if available for this title, please contact the Oklahoma State University Library Archives by email at [email protected] or by phone at 405-744-6311

Extreme Ultraviolet Reflective Grating Characterization and Simulationsfor the Aspera SmallSat Mission

The Aspera SmallSat mission is designed to detect and map the warm-hot gaseous component of the halos of nearby galaxies through long-slit spectroscopy of the ionized O VI emission line (103.2 nm) for the first time. The Aspera Rowland circle type spectrograph uses a toroidal grating coated with a multilayer film consisting of aluminum, lithium fluoride, and magnesium fluoride capping to optimize reflectivity in the extreme ultraviolet (EUV) waveband from 103 to 104nm. We discuss the grating characterization test setup at the University of Arizona (UA), which will validate the multilayer coating and grating efficiency in a UV vacuum chamber. We also simulate the reflectivity of the multilayer thin film coating using IMD IDL software to compare simulated results with measured reflectivity. Additionally, non-sequential ray trace simulations and 3D CAD modeling are used for verification of the test setup. Finally, the implications of the differences between the measured and simulated reflectivity and grating efficiencies are considered, including impact to the mission

Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine

Translating whole exome sequencing (WES) for prospective clinical use may impact the care of cancer patients; however, multiple innovations are necessary for clinical implementation. These include: (1) rapid and robust WES from formalin-fixed paraffin embedded (FFPE) tumor tissue, (2) analytical output similar to data from frozen samples, and (3) clinical interpretation of WES data for prospective use. Here, we describe a prospective clinical WES platform for archival FFPE tumor samples. The platform employs computational methods for effective clinical analysis and interpretation of WES data. When applied retrospectively to 511 exomes, the interpretative framework revealed a “long tail” of somatic alterations in clinically important genes. Prospective application of this approach identified clinically relevant alterations in 15/16 patients. In one patient, previously undetected findings guided clinical trial enrollment leading to an objective clinical response. Overall, this methodology may inform the widespread implementation of precision cancer medicine

Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis

Multiple sclerosis (MS), a chronic disorder of the central nervous system and common cause of neurological disability in young adults, is characterized by moderate but complex risk heritability. Here we report the results of a genome-wide association study performed in a 1000 prospective case series of well-characterized individuals with MS and group-matched controls using the Sentrix® HumanHap550 BeadChip platform from Illumina. After stringent quality control data filtering, we compared allele frequencies for 551 642 SNPs in 978 cases and 883 controls and assessed genotypic influences on susceptibility, age of onset, disease severity, as well as brain lesion load and normalized brain volume from magnetic resonance imaging exams. A multi-analytical strategy identified 242 susceptibility SNPs exceeding established thresholds of significance, including 65 within the MHC locus in chromosome 6p21.3. Independent replication confirms a role for GPC5, a heparan sulfate proteoglycan, in disease risk. Gene ontology-based analysis shows a functional dichotomy between genes involved in the susceptibility pathway and those affecting the clinical phenotyp

Problems of multi-species organisms: endosymbionts to holobionts

The organism is one of the fundamental concepts of biology and has been at the center of many discussions about biological individuality, yet what exactly it is can be confusing. The definition that we find generally useful is that an organism is a unit in which all the subunits have evolved to be highly cooperative, with very little conflict. We focus on how often organisms evolve from two or more formerly independent organisms. Two canonical transitions of this type—replicators clustered in cells and endosymbiotic organelles within host cells—demonstrate the reality of this kind of evolutionary transition and suggest conditions that can favor it. These conditions include co-transmission of the partners across generations and rules that strongly regulate and limit conflict, such as a fair meiosis. Recently, much attention has been given to associations of animals with microbes involved in their nutrition. These range from tight endosymbiotic associations like those between aphids and Buchnera bacteria, to the complex communities in animal intestines. Here, starting with a reflection about identity through time (which we call “Theseus’s fish”), we consider the distinctions between these kinds of animal–bacteria interactions and describe the criteria by which a few can be considered jointly organismal but most cannot

Genome-wide Association Analysis Identifies 14 New Risk Loci for Schizophrenia

Schizophrenia is a heritable disorder with substantial public health impact. We conducted a multi-stage genome-wide association study (GWAS) for schizophrenia beginning with a Swedish national sample (5,001 cases, 6,243 controls) followed by meta-analysis with prior schizophrenia GWAS (8,832 cases, 12,067 controls) and finally by replication of SNPs in 168 genomic regions in independent samples (7,413 cases, 19,762 controls, and 581 trios). In total, 22 regions met genome-wide significance (14 novel and one previously implicated in bipolar disorder). The results strongly implicate calcium signaling in the etiology of schizophrenia, and include genome-wide significant results for CACNA1C and CACNB2 whose protein products interact. We estimate that ∼8,300 independent and predominantly common SNPs contribute to risk for schizophrenia and that these collectively account for most of its heritability. Common genetic variation plays an important role in the etiology of schizophrenia, and larger studies will allow more detailed understanding of this devastating disorder