783 research outputs found

    The lab management practices of “Research Exemplars” that foster research rigor and regulatory compliance: A qualitative study of successful principal investigators

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    IntroductionConducting rigorous scientific inquiry within the bounds of research regulation and acceptable practice requires a principal investigator to lead and manage research processes and personnel. This study explores the practices used by investigators nominated as exemplars of research excellence and integrity to produce rigorous, reproducible research and comply with research regulations.MethodsUsing a qualitative research design, we interviewed 52 principal investigators working in the United States at top research universities and the National Institutes of Health Intramural Research Program. We solicited nominations of researchers meeting two criteria: (1) they are federally-funded researchers doing high-quality, high-impact research, and (2) have reputations for professionalism and integrity. Each investigator received an initial nomination addressing both criteria and at least one additional endorsement corroborating criteria 2. A panel of researchers and our research team reviewed the nominations to select finalists who were invited to participate. The cohort of "Research Exemplars" includes highly accomplished researchers in diverse scientific disciplines. The semi-structured interview questions asked them to describe the routine practices they employ to foster rigor and regulatory compliance. We used inductive thematic analysis to identify common practices.ResultsThe exemplars identified a core set of 8 practices and provided strategies for employing them. The practices included holding regular team meetings, encouraging shared ownership, providing supervision, ensuring adequate training, fostering positive attitudes about compliance, scrutinizing data and findings, and following standard operating procedures. Above all, the use of these practices aim to create a psychologically safe work environment in which lab members openly collaborate to scrutinize their work and share in accountability for rigorous, compliant research.ConclusionsResearchers typically receive limited systematic training in how to lead and manage their research teams. Training and education for principal investigators should include essential leadership and management practices and strategies that support doing high-quality research with integrity

    Genes Encoding Callose Synthase and Phytochrome A Are Adjacent to a MAP3Kα-Like Gene in Beta vulgaris US H20

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    MAP3Kα, a gene that encodes a key conserved protein kinase, is responsible for initiating a rapid cascade of cellular events leading to localized cell death. Hypersensitive response, as it is termed, enables genetically resistant plants to limit microbial invasion under the right environmental conditions. Since knowledge of close physically linked genes is important for genome analysis and possibly for improving disease resistance, systematic DNA sequence analysis, gene annotation, and protein BLASTs were performed to identify and characterize genes in close physical proximity to a MAP3Kα-like gene in Beta vulgaris L. US H20. On the same 125 Kb BAC, callose synthase (BvCS) and phytochrome A (PhyA) genes were within 50 Kb of MAP3Kα. The close physical linkage of these genes may result from selection for coordinated responses to disease pressure. Bert, a new chromodomain-carrying gypsy-like LTR retrotransposon, resides within an intron of the BvCS gene, where it is transcribed from the opposing strand

    Preliminary analysis of the fauna from Buffalo Cave, northern Transvaal, South Africa

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    Main articleSystematic excavations at Buffalo Cave in the Makapan Valley were begun in October 1993. This paper presents our preliminary analysis of the faunal assemblage from this site, including new in situ fossils and the collections which have been housed at the Bernard Price Institute, Palaeontology since the 1940's. Our palaeoecological reconstruction suggests that the local environment at Buffalo Cave at the time of deposition was an open country grassland or savanna, including a high proportion of alcelaphine bovids and other grazing fauna. However, the presence of other taxa, particularly of tragelaphines, hippotragines, and reduncines, may indicate that a more wooded habitat including a local water source, could also have been part of the Buffalo Cave environment during some part of its depositional history. The fauna overall indicates that deposition occurred during the Pleistocene, rather than the Pliocene. Thus, the environmental and temporal information presently available suggests that the Buffalo Cave fauna represents an environment and time period distinct from other sites in the Makapansgat Valley (i.e., the Limeworks and Cave of Hearths).FRD Core Programme grant and a University of the Witwatersrand Research Committee Gran

    ‘Ca. Liberibacter asiaticus’ Proteins Orthologous with pSymA-Encoded Proteins of Sinorhizobium meliloti: Hypothetical Roles in Plant Host Interaction

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    Sinorhizobium meliloti strain 1021, a nitrogen-fixing, root-nodulating bacterial microsymbiont of alfalfa, has a 3.5 Mbp circular chromosome and two megaplasmids including 1.3 Mbp pSymA carrying nonessential ‘accessory’ genes for nitrogen fixation (nif), nodulation and host specificity (nod). A related bacterium, psyllid-vectored ‘Ca. Liberibacter asiaticus,’ is an obligate phytopathogen with a reduced genome that was previously analyzed for genes orthologous to genes on the S. meliloti circular chromosome. In general, proteins encoded by pSymA genes are more similar in sequence alignment to those encoded by S. meliloti chromosomal orthologs than to orthologous proteins encoded by genes carried on the ‘Ca. Liberibacter asiaticus’ genome. Only two ‘Ca. Liberibacter asiaticus’ proteins were identified as having orthologous proteins encoded on pSymA but not also encoded on the chromosome of S. meliloti. These two orthologous gene pairs encode a Na+/K+ antiporter (shared with intracellular pathogens of the family Bartonellacea) and a Co++, Zn++ and Cd++ cation efflux protein that is shared with the phytopathogen Agrobacterium. Another shared protein, a redox-regulated K+ efflux pump may regulate cytoplasmic pH and homeostasis. The pSymA and ‘Ca. Liberibacter asiaticus’ orthologs of the latter protein are more highly similar in amino acid alignment compared with the alignment of the pSymA-encoded protein with its S. meliloti chromosomal homolog. About 182 pSymA encoded proteins have sequence similarity (≤E-10) with ‘Ca. Liberibacter asiaticus’ proteins, often present as multiple orthologs of single ‘Ca. Liberibacter asiaticus’ proteins. These proteins are involved with amino acid uptake, cell surface structure, chaperonins, electron transport, export of bioactive molecules, cellular homeostasis, regulation of gene expression, signal transduction and synthesis of amino acids and metabolic cofactors. The presence of multiple orthologs defies mutational analysis and is consistent with the hypothesis that these proteins may be of particular importance in host/microbe interaction and their duplication likely facilitates their ongoing evolution

    The Exposed Surface Area To Volume Ratio: Is Shell More Efficient Than Limestone In Promoting Oyster Recruitment?

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    Planting oyster cultch is a common management approach used to enhance recruitment. The two most popular cultch materials are shell and limestone. Both are sold by volume or weight; however, once deposited on oyster grounds, only a small portion of the total surface area of each particle is available for recruitment. Shell and limestone have different surface area to volume properties, and thus provide differential settlement opportunities. Exposed surface area to volume (expSA/V) ratios of oyster shell and limestone fragments were compared, as an indicator of their recruitment potential and cost-effectiveness for cultch planting. Samples were collected from the Primary Public Oyster Seed Grounds in Louisiana by vibracore, and from the Pass Christian Tonging Grounds in Mississippi by dredge. Shell (including whole shell and fragments) and limestone particles greater than or equal to 8 mm by geometric shape were classified and their expSA/V was calculated. Mean expSA/V ratios of shell were approximately three to nine times higher than limestone. For limestone of similar particle size to provide an equivalent recruitment benefit for the same cost would require that the cost of purchase, transport, and planting be three to nine times lower than shell. Thus, shell is likely to be a more efficient material than limestone for recruitment enhancement. Nevertheless, the higher variability in expSA/V of shell and other factors such as the expected lifetime and the relative performance of small and large particles of materials should also be considered. Analysis of a Louisiana limestone plant and associated oyster cultch showed that the proportion of small and large limestone particles and the relative proportion of whole shells and fragments can greatly alter expSA/V. In this case, the a priori expectation that oyster shell would outperform limestone did not materialize because of the quantity of small limestone particles of favorable shapes in the deployed material. Even so, as yet unknown is the possible reduction in performance in situ of smaller particles that might occur if they increase the one-dimensionality of the plant

    ZnO-Al2O3 and ZnO-TiO2 core-shell nanowire dye-sensitized solar cells

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    We describe the construction and performance of dye-sensitized solar cells (DSCs) based on arrays of ZnO nanowires coated with thin shells of amorphous Al2O3 or anatase TiO2 by atomic layer deposition. We find that alumina shells of all thicknesses act as insulating barriers that improve cell open-circuit voltage (VOC) only at the expense of a larger decrease in short-circuit current density (JSC). However, titania shells 10-25 nm in thickness cause a dramatic increase in VOC and fill factor with little current falloff, resulting in a substantial improvement in overall conversion efficiency, up to 2.25% under 100 mW cm(-2) AM 1.5 simulated sunlight. The superior performance of the ZnO-TiO2 core-shell nanowire cells is a result of a radial surface field within each nanowire that decreases the rate of recombination in these devices. In a related set of experiments, we have found that TiO2 blocking layers deposited underneath the nanowire films yield cells with reduced efficiency, in contrast to the beneficial use of blocking layers in some TiO2 nanoparticle cells. Raising the efficiency of our nanowire DSCs above 2.5% depends on achieving higher dye loadings through an increase in nanowire array surface area

    Conservation of Gene Order and Content in the Circular Chromosomes of ‘Candidatus Liberibacter asiaticus’ and Other Rhizobiales

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    ‘Ca. Liberibacter asiaticus,’ an insect-vectored, obligate intracellular bacterium associated with citrus-greening disease, also called “HLB," is a member of the Rhizobiales along with nitrogen-fixing microsymbionts Sinorhizobium meliloti and Bradyrhizobium japonicum, plant pathogen Agrobacterium tumefaciens and facultative intracellular mammalian pathogen Bartonella henselae. Comparative analyses of their circular chromosomes identified 514 orthologous genes shared among all five species. Shared among all five species are 50 identical blocks of microsyntenous orthologous genes (MOGs), containing a total of 283 genes. While retaining highly conserved genomic blocks of microsynteny, divergent evolution, horizontal gene transfer and niche specialization have disrupted macrosynteny among the five circular chromosomes compared. Highly conserved microsyntenous gene clusters help define the Rhizobiales, an order previously defined by 16S RNA gene similarity and herein represented by the three families: Bartonellaceae, Bradyrhizobiaceae and Rhizobiaceae. Genes without orthologs in the other four species help define individual species. The circular chromosomes of each of the five Rhizobiales species examined had genes lacking orthologs in the other four species. For example, 63 proteins are encoded by genes of ‘Ca. Liberibacter asiaticus’ not shared with other members of the Rhizobiales. Of these 63 proteins, 17 have predicted functions related to DNA replication or RNA transcription, and some of these may have roles related to low genomic GC content. An additional 17 proteins have predicted functions relevant to cellular processes, particularly modifications of the cell surface. Seventeen unshared proteins have specific metabolic functions including a pathway to synthesize cholesterol encoded by a seven-gene operon. The remaining 12 proteins encoded by ‘Ca. Liberibacter asiaticus’ genes not shared with other Rhizobiales are of bacteriophage origin. ‘Ca. Liberibacter asiaticus’ shares 11 genes with only Sinorhizobium meliloti and 12 genes are shared with only Bartonella henselae

    The Layer 0 Inner Silicon Detector of the D0 Experiment

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    This paper describes the design, fabrication, installation and performance of the new inner layer called Layer 0 (L0) that was inserted in the existing Run IIa Silicon Micro-Strip Tracker (SMT) of the D0 experiment at the Fermilab Tevatron collider. L0 provides tracking information from two layers of sensors, which are mounted with center lines at a radial distance of 16.1 mm and 17.6 mm respectively from the beam axis. The sensors and readout electronics are mounted on a specially designed and fabricated carbon fiber structure that includes cooling for sensor and readout electronics. The structure has a thin polyimide circuit bonded to it so that the circuit couples electrically to the carbon fiber allowing the support structure to be used both for detector grounding and a low impedance connection between the remotely mounted hybrids and the sensors.Comment: 28 pages, 9 figure

    Comparison of the ‘Ca. Liberibacter asiaticus’ Genome Adapted for an Intracellular Lifestyle with Other Members of the Rhizobiales

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    An intracellular plant pathogen ‘Candidatus Liberibacter asiaticus,’ a member of the Rhizobiales, is related to Sinorhizobium meliloti, Bradyrhizobium japonicum, nitrogen fixing endosymbionts, Agrobacterium tumefaciens, a plant pathogen, and Bartonella henselae, an intracellular mammalian pathogen. Whole chromosome comparisons identified at least 50 clusters of conserved orthologous genes found on the chromosomes of all five metabolically diverse species. The intracellular pathogens ‘Ca. Liberibacter asiaticus’ and Bartonella henselae have genomes drastically reduced in gene content and size as well as a relatively low content of guanine and cytosine. Codon and amino acid preferences that emphasize low guanosine and cytosine usage are globally employed in these genomes, including within regions of microsynteny and within signature sequences of orthologous proteins. The length of orthologous proteins is generally conserved, but not their isoelectric points, consistent with extensive amino acid substitutions to accommodate selection for low GC content. The ‘Ca. Liberibacter asiaticus’ genome apparently has all of the genes required for DNA replication present in Sinorhizobium meliloti except it has only two, rather than three RNaseH genes. The gene set required for DNA repair has only one rather than ten DNA ligases found in Sinorhizobium meliloti, and the DNA PolI of ‘Ca. Liberibacter asiaticus’ lacks domains needed for excision repair. Thus the ability of ‘Ca. Liberibacter asiaticus’ to repair mutations in its genome may be impaired. Both ‘Ca. Liberibacter asiaticus and Bartonella henselae lack enzymes needed for the metabolism of purines and pyrimidines, which must therefore be obtained from the host. The ‘Ca. Liberibacter asiaticus’ genome also has a greatly reduced set of sigma factors used to control transcription, and lacks sigma factors 24, 28 and 38. The ‘Ca. Liberibacter asiaticus’ genome has all of the hallmarks of a reduced genome of a pathogen adapted to an intracellular lifestyle
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