Leveraging human genomic information to identify nonhuman primate sequences for expression array development

BACKGROUND: Nonhuman primates (NHPs) are essential for biomedical research due to their similarities to humans. The utility of NHPs will be greatly increased by the application of genomics-based approaches such as gene expression profiling. Sequence information from the 3' end of genes is the key resource needed to create oligonucleotide expression arrays. RESULTS: We have developed the algorithms and procedures necessary to quickly acquire sequence information from the 3' end of nonhuman primate orthologs of human genes. To accomplish this, we identified terminal exons of over 15,000 human genes by aligning mRNA sequences with genomic sequence. We found the mean length of complete last exons to be approximately 1,400 bp, significantly longer than previous estimates. We designed primers to amplify genomic DNA, which included at least 300 bp of the terminal exon. We cloned and sequenced the PCR products representing over 5,500 Macaca mulatta (rhesus monkey) orthologs of human genes. This sequence information has been used to select probes for rhesus gene expression profiling. We have also tested 10 sets of primers with genomic DNA from Macaca fascicularis (Cynomolgus monkey), Papio hamadryas (Baboon), and Chlorocebus aethiops (African green monkey, vervet). The results indicate that the primers developed for this study will be useful for acquiring sequence from the 3' end of genes for other nonhuman primate species. CONCLUSION: This study demonstrates that human genomic DNA sequence can be leveraged to obtain sequence from the 3' end of NHP orthologs and that this sequence can then be used to generate NHP oligonucleotide microarrays. Affymetrix and Agilent used sequences obtained with this approach in the design of their rhesus macaque oligonucleotide microarrays

The development and application of bioinformatics core competencies to improve bioinformatics training and education

Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans

Large scale analysis of positional effects of single-base mismatches on microarray gene expression data

<p>Abstract</p> <p>Background</p> <p>Affymetrix GeneChips utilize 25-mer oligonucleotides probes linked to a silica surface to detect targets in solution. Mismatches due to single nucleotide polymorphisms (SNPs) can affect the hybridization between probes and targets. Previous research has indicated that binding between probes and targets strongly depends on the positions of these mismatches. However, there has been substantial variability in the effect of mismatch type across studies.</p> <p>Methods</p> <p>By taking advantage of naturally occurring mismatches between rhesus macaque transcripts and human probes from the Affymetrix U133 Plus 2 GeneChip, we collected the largest 25-mer probes dataset with single-base mismatches at each of the 25 positions on the probe ever used in this type of analysis.</p> <p>Results</p> <p>A mismatch at the center of a probe led to a greater loss in signal intensity than a mismatch at the ends of the probe, regardless of the mismatch type. There was a slight asymmetry between the ends of a probe: effects of mismatches at the 3' end of a probe were greater than those at the 5' end. A cross study comparison of the effect of mismatch types revealed that results were not in good agreement among different reports. However, if the mismatch types were consolidated to purine or pyrimidine mismatches, cross study conclusions could be generated.</p> <p>Conclusion</p> <p>The comprehensive assessment of the effects of single-base mismatches on microarrays provided in this report can be useful for improving future versions of microarray platform design and the corresponding data analysis algorithms.</p

Facial expressions depicting compassionate and critical emotions: the development and validation of a new emotional face stimulus set

Attachment with altruistic others requires the ability to appropriately process affiliative and kind facial cues. Yet there is no stimulus set available to investigate such processes. Here, we developed a stimulus set depicting compassionate and critical facial expressions, and validated its effectiveness using well-established visual-probe methodology. In Study 1, 62 participants rated photographs of actors displaying compassionate/kind and critical faces on strength of emotion type. This produced a new stimulus set based on N = 31 actors, whose facial expressions were reliably distinguished as compassionate, critical and neutral. In Study 2, 70 participants completed a visual-probe task measuring attentional orientation to critical and compassionate/kind faces. This revealed that participants lower in self-criticism demonstrated enhanced attention to compassionate/kind faces whereas those higher in self-criticism showed no bias. To sum, the new stimulus set produced interpretable findings using visual-probe methodology and is the first to include higher order, complex positive affect displays

MICROWAVE SPECTRA AND STRUCTURES OF THE NONLINEAR NNO-HCN, 15NNO−HCN^{15}NNO-HCN, AND NNO-DCN COMPLEXES

$^{1}$ D.C. Dayton and R.E. Miller, 44th Symposium on Molecular Spectroscopy, Paper TF7, The Ohio State University, Columbus, Ohio, June 1989.Author Institution: Department of Chemistry, University of of ArizonaMicrowave spectra were obtained for the bimolecular gas-phase complexes NNO-HCN, $^{15}NNO-HCN$ and NNO-DCN using pulse-beam Fourier transform microwave spectroscopy. These data were fit to determine values for $(A - D_{r}$), B and C, and the quartic distortion parameters, $D_{2}$ and $D_{\pi}$. one quadrupole coupling parameter due to the HCN nitrogen in the complex was obtained by fitting low J transitions. Structural parameters were obtained using moments of inertia, quadrupole coupling, and single isotopic Kraitchman analysis. The first spectra for gas-phase $N_{2}O-HCN$ complexes were measured with an infrared optothermal $technique^{1}$ by Dayton and Miller. In the present work two new sets of isotopic data for $^{15}NNO-HCN$, and NNO-DCN combined with our previous microwave measurements on NNO-HCN have eliminated ambiguities in structure fits. The planar structure can be described with the distance $R_{cm} \simeq 3.25 \pm 0.05 {\AA}$, the angle $\theta \approx 90\deg \pm 6\deg$ between HCN and $R_{cm}$ and the angle $\phi \approx 77^{\circ} \pm 6^{\circ}$ between $N_{2}O$ and $R_{cm}$. Analysis of the data indicate that the oxygen of $N_{2}O$ is tilted slightly towards the hydrogen of HCN [FIGURE

Implicit perceptions of risk and anxiety and pilot involvement in hazardous events

Objective: The aim of the studies was to examine the role of implicit processes in aeronautical risk perception and risk taking. Background: Aeronautical decision making consists of both explicit processes (e.g., comparing options, seeking information) and implicit, or intuitive, processes (e.g., immediate affective reactions). The present studies utilized a novel methodology, adapted from studies in social cognition, to examine the relationship between general aviation pilots' implicit reactions toward risk and their involvement in hazardous events. Method: The Implicit Association Test was used to measure pilots' (Study 1: N = 23; Study 2: N = 32) implicit associations between good and bad weather conditions and perceptions of risk and anxiety. Results: There was a relationship between the pilots' implicit perceptions and previous involvement in hazardous aeronautical events as measured by D. R. Hunter's (1995, 2002) Hazardous Events Scale. The more weather-related hazardous events the pilots had been involved in, the less they associated implicit risk with adverse weather (Study 1) and the less implicitly anxious they were toward adverse weather (Study 2). Conclusion: The results show a relationship between implicit associations and risk-taking behavior. Application: Pilots may be involved in risk-taking behavior because they perceive less risk in, and are implicitly less afraid of, hazardous conditions.11 page(s