Intercenter reliability and validity of the rhesus macaque GeneChip

BACKGROUND: The non-human primate (NHP) research community has been intensely interested in obtaining whole-genome expression arrays for their work. Recently, novel approaches were used to generate the DNA sequence information for a rhesus GeneChip. To test the reliability of the rhesus GeneChip across different centers, RNA was isolated from five sources: cerebral cortex, pancreas, thymus, testis, and an immortalized fibroblast cell line. Aliquots of this RNA were sent to each of three centers: Yerkes National Primate Research Center, Oregon National Primate Research Center and the University of Nebraska Medical Center. Each center labeled the samples and hybridized them with two rhesus macaque GeneChips. In addition, rhesus samples were hybridzed with human GeneChips to compare with samples hybridized with the rhesus GeneChip. RESULTS: The results indicate that center effects were minimal and the rhesus GeneChip appears highly reliable. To test the validity of the rhesus GeneChip, five of the most differentially expressed genes among tissues identified in the reliability experiments were chosen for analysis with Quantitative PCR. For all 5 genes, the qPCR and GeneChip results were in agreement with regard to differential expression between tissues. Significantly more probesets were called present when rhesus samples were hybridized with the rhesus GeneChip than when these same samples were hybridized with a human GeneChip. CONCLUSION: The rhesus GeneChip is both a reliable and a valid tool for examining gene expression and represents a significant improvement over the use of the human GeneChip for rhesus macaque gene expression studies

The comparative evaluation of ERTS-1 imagery for resource inventory in land use planning

The author has identified the following significant results. Multidiscipline team interpretation and mapping of resources for Crook County is complete on 1:250,000 scale enlargements of ERTS imagery and 1:120,000 hi-flight photography. Maps of geology, soils, vegetation-land use and land resources units were interpreted to show limitations, suitabilities, and geologic hazards for land use planning. Mapping of lineaments and structures from ERTS imagery has shown a number of features not previously mapped in Oregon. A multistage timber inventory of Ochoco National Forest was made, using ERTS images as the first stage. Inventory of forest clear-cutting practices was successfully demonstrated with color composites. Soil tonal differences in fallow fields correspond with major soil boundaries in loess-mantled terrain. A digital classification system used for discriminating natural vegetation and geologic material classes was successful in separating most major classes around Newberry Caldera, Mt. Washington, and Big Summit Prairie

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

Electron scale structures and magnetic reconnection signatures in the turbulent magnetosheath

Collisionless space plasma turbulence can generate reconnecting thin current sheets as suggested by recent results of numerical magnetohydrodynamic simulations. The MMS mission provides the first serious opportunity to check if small ion-electron-scale reconnection, generated by turbulence, resembles the reconnection events frequently observed in the magnetotail or at the magnetopause. Here we investigate field and particle observations obtained by the MMS fleet in the turbulent terrestrial magnetosheath behind quasi-parallel bow shock geometry. We observe multiple small-scale current sheets during the event and present a detailed look of one of the detected structures. The emergence of thin current sheets can lead to electron scale structures where ions are demagnetized. Within the selected structure we see signatures of ion demagnetization, electron jets, electron heating and agyrotropy suggesting that MMS spacecraft observe reconnection at these scales

Electron Heating by Debye-Scale Turbulence in Guide-Field Reconnection

We report electrostatic Debye-scale turbulence developing within the diffusion region of asymmetric magnetopause reconnection with amoderate guide field using observations by the Magnetospheric Multiscale mission. We show that Buneman waves and beam modes cause efficient and fast thermalization of the reconnection electron jet by irreversible phase mixing, during which the jet kinetic energy is transferred into thermal energy. Our results show that the reconnection diffusion region in the presence of a moderate guide field is highly turbulent, and that electrostatic turbulence plays an important role in electron heating.Peer reviewe

Solar Wind—Magnetosphere Coupling During Radial Interplanetary Magnetic Field Conditions: Simultaneous Multi-Point Observations

S. Toledo-Redondo and J. Fornieles acknowledge support of the Ministry of Economy and Competitiveness (MINECO) of Spain (grant FIS2017-90102-R) and of Ministry of Science and Innovation (grant PID2020-112805GA-I00). Research at IRAP was supported by CNRS, CNES, and the University of Toulouse. We acknowledge support of the ISSI teams MMS and Cluster observations of magnetic reconnection and Cold plasma of ionospheric in the Earth's magnetosphere, and of the ESAC Science faculty.In-situ spacecraft missions are powerful assets to study processes that occur in space plasmas. One of their main limitations, however, is extrapolating such local measurements to the global scales of the system. To overcome this problem at least partially, multi-point measurements can be used. There are several multi-spacecraft missions currently operating in the Earth's magnetosphere, and the simultaneous use of the data collected by them provides new insights into the large-scale properties and evolution of magnetospheric plasma processes. In this work, we focus on studying the Earth's magnetopause (MP) using a conjunction between the Magnetospheric Multiscale and Cluster fleets, when both missions skimmed the MP for several hours at distant locations during radial interplanetary magnetic field (IMF) conditions. The observed MP positions as a function of the evolving solar wind conditions are compared to model predictions of the MP. We observe an inflation of the magnetosphere (similar to 0.7 R-E), consistent with magnetosheath pressure decrease during radial IMF conditions, which is less pronounced on the flank (<0.2 R-E). There is observational evidence of magnetic reconnection in the subsolar region for the whole encounter, and in the dusk flank for the last portion of the encounter, suggesting that reconnection was extending more than 15 R-E. However, reconnection jets were not always observed, suggesting that reconnection was patchy, intermittent or both. Shear flows reduce the reconnection rate up to similar to 30% in the dusk flank according to predictions, and the plasma beta enhancement in the magnetosheath during radial IMF favors reconnection suppression by the diamagnetic drift.Ministry of Economy and Competitiveness (MINECO) of Spain FIS2017-90102-RSpanish Government PID2020-112805GA-I00Centre National de la Recherche Scientifique (CNRS)European CommissionCentre National D'etudes SpatialesUniversity of ToulouseESAC Science facult

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

Does vascular endothelial growth factor (VEGF) predict local relapse and survival in radiotherapy-treated node-negative breast cancer?

The aim of this study was to determine the association of vascular endothelial growth factor (VEGF) content in 302 consecutive node-negative breast cancer (NNBC) patients treated with only locoregional radiotherapy to relapse free- (RFS) and overall survival (OS). VEGF content in tumour cytosols was measured by an enzymatic immunoassay for the major isoform VEGF165. The median age was 56 years, the median follow-up time 56 months. A wide range (0.01–144.79 pg μg−1 DNA) of VEGF content was found (median 1.92). Significant associations were found between VEGF and oestrogen receptor (ER) content, progesterone receptor (PR) and tumour size (P = 0.005). Univariate analysis displayed significant reduced RFS and OS for patients with higher VEGF content (P = 0.0113 and P = 0.0075 respectively). A total of 43 recurrences have been found (ten local relapses within the breast, five in the axillary or supraclavicular lymph nodes and 28 distant metastasis). There was no significant correlation between the localization of the relapse and the VEGF content. Multivariate analysis suggested VEGF as the only predictor of OS (relative risk (RR) = 3.6, 95% confidence interval (CI) = 0.97–13.37), and in patients with T1 tumours (n = 236) the multivariate analysis clearly displayed VEGF as the only independent predictor of both RFS and OS (RR = 5.1, CI = 1.07–24.59). In the sub-group with ER-positive tumours (n = 229), multivariate analysis showed VEGF as the only significant predictor of RFS and OS (RR = 10.44, CI = 1.26–86.38). The results suggest VEGF165 as a predictor of RFS and OS in NNBC patients treated with locoregional radiotherapy, comprising especially patients with favourable prognosis of T1 tumours, or ER-positive tumours. The high VEGF expression might define a radioresistant phenotype, or indicate an early distant spread which might require adjuvant systemic treatment. © 1999 Cancer Research Campaig

Gene targeting in adult rhesus macaque fibroblasts

<p>Abstract</p> <p>Background</p> <p>Gene targeting in nonhuman primates has the potential to produce critical animal models for translational studies related to human diseases. Successful gene targeting in fibroblasts followed by somatic cell nuclear transfer (SCNT) has been achieved in several species of large mammals but not yet in primates. Our goal was to establish the protocols necessary to achieve gene targeting in primary culture of adult rhesus macaque fibroblasts as a first step in creating nonhuman primate models of genetic disease using nuclear transfer technology.</p> <p>Results</p> <p>A primary culture of adult male fibroblasts was transfected with hTERT to overcome senescence and allow long term <it>in vitro </it>manipulations. Successful gene targeting of the HPRT locus in rhesus macaques was achieved by electroporating S-phase synchronized cells with a construct containing a SV40 enhancer.</p> <p>Conclusion</p> <p>The cell lines reported here could be used for the production of null mutant rhesus macaque models of human genetic disease using SCNT technology. In addition, given the close evolutionary relationship and biological similarity between rhesus macaques and humans, the protocols described here may prove useful in the genetic engineering of human somatic cells.</p