G-spots cause incorrect expression measurement in Affymetrix microarrays

Abstract Background High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in that gene's probe set will provide a consistent message signifying the gene's presence. However, probes that contain a G-spot (a sequence of four or more guanines) behave abnormally and it has been suggested that these probes are responding to some biochemical effect such as the formation of G-quadruplexes. Results We have tested this expectation by examining the correlation coefficients between pairs of probes using the data on thousands of arrays that are available in the NCBI Gene Expression Omnibus (GEO) repository. We confirm the finding that G-spot probes are poorly correlated with others in their probesets and reveal that, by contrast, they are highly correlated with one another. We demonstrate that the correlation is most marked when the G-spot is at the 5' end of the probe. Conclusion Since these G-spot probes generally show little correlation with the other members of their probesets they are not fit for purpose and their values should be excluded when calculating gene expression values. This has serious implications, since more than 40% of the probesets in the HG-U133A GeneChip contain at least one such probe. Future array designs should avoid these untrustworthy probes. </jats:sec

Heat Transfer to Liquid Metals in a Thermal Entrance Region

The purpose of the present work is to explore analytically and experimentally the heat transfer to liquid metals in turbulent flow within the thermal entrance region of circular tubes having uniform wall temperature. Since liquid metals are characterized by high thermal conductivity, emphasis has been placed on analytical conduction solutions which neglect the contribution to heat transfer that is made by the eddy motion of a fluid in turbulent flow. Three solutions, which differ only in the postulated velocity distribution of the fluid, have been selected for comparison. The postulated velocity distributions are: (l) uniform, (2) parabolic and, (3) velocity proportional to distance from the channel wall raised to the one-seventh power. The third distribution is usually referred to as the one-seventh power law distribution. Other related entrance region solutions are briefly surveyed

Affymetrix probes containing runs of contiguous guanines are not gene-specific

High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in the designated probe set will provide a consistent message signifying the gene&#x27;s presence. However, we demonstrate by data mining thousands of CEL files from NCBI&#x27;s GEO database that 4G-probes (defined as probes containing sequences of four or more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes, most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It follows that 4G-probes should be ignored when calculating gene expression levels. Furthermore, future microarray designs should make no use of 4G-probes

Geology of Michigan

The research staff at Western Michigan University\u27s Michigan Geological Repository for Research and Education regularly participates in industry workshops across the state of Michigan. Here is a an educational PowerPoint on Michigan geology

Establishing MICHCARB, a geological carbon sequestration research and education center for Michigan, implemented through the Michigan Geological Repository for Research and Education, part of the Department of Geosciences at Western Michigan University

The Michigan Geological Repository for Research and Education (MGRRE), part of the Department of Geosciences at Western Michigan University (WMU) at Kalamazoo, Michigan, established MichCarb—a geological carbon sequestration resource center by: • Archiving and maintaining a current reference collection of carbon sequestration published literature • Developing statewide and site-specific digital research databases for Michigan’s deep geological formations relevant to CO2 storage, containment and potential for enhanced oil recovery • Producing maps and tables of physical properties as components of these databases • Compiling all information into a digital atlas • Conducting geologic and fluid flow modeling to address specific predictive uses of CO2 storage and enhanced oil recovery, including compiling data for geological and fluid flow models, formulating models, integrating data, and running the models; applying models to specific predictive uses of CO2 storage and enhanced oil recovery • Conducting technical research on CO2 sequestration and enhanced oil recovery through basic and applied research of characterizing Michigan oil and gas and saline reservoirs for CO2 storage potential volume, injectivity and containment. Based on our research, we have concluded that the Michigan Basin has excellent saline aquifer (residual entrapment) and CO2/Enhanced oil recovery related (CO2/EOR; buoyant entrapment) geological carbon sequestration potential with substantial, associated incremental oil production potential. These storage reservoirs possess at least satisfactory injectivity and reliable, permanent containment resulting from associated, thick, low permeability confining layers. Saline aquifer storage resource estimates in the two major residual entrapment, reservoir target zones (Lower Paleozoic Sandstone and Middle Paleozoic carbonate and sandstone reservoirs) are in excess of 70-80 Gmt (at an overall 10% storage efficiency factor; an approximately P50 probability range for all formations using DOE-NETL, 2010, storage resource estimation methodology). Incremental oil production resulting from successful implementation of CO2/EOR for the highest potential Middle Paleozoic reef reservoirs (Silurian, Northern Niagaran Reef trend) in Michigan is estimated at 130 to over 200 MMBO (22-33 Mm3). In addition, between 200 and 400 Mmt of CO2 could be sequestered in the course of successful deployment of CO2/EOR in the northern reef trend’s largest depleted (primary production) oil fields (those that have produced in excess of 500,000 BO; 80,000 m3of oil). • Effecting technology transfer to members of industry and governmental agencies by establishing an Internet Website at which all data, reports and results are accessible; publishing results in relevant journals; conducting technology transfer workshops as part of our role as the Michigan Center of the Petroleum Technology Transfer Council or any successor organization

Template or ligand? : Different structural behaviours of aromatic amines in combination with zincophosphite networks

We thank the EPSRC National Crystallography Service (University of Southampton) for the X-ray data collection for (I)Peer reviewedPublisher PD

Genome wide signatures of positive selection: The comparison of independent samples and the identification of regions associated to traits

<p>Abstract</p> <p>Background</p> <p>The goal of genome wide analyses of polymorphisms is to achieve a better understanding of the link between genotype and phenotype. Part of that goal is to understand the selective forces that have operated on a population.</p> <p>Results</p> <p>In this study we compared the signals of selection, identified through population divergence in the Bovine HapMap project, to those found in an independent sample of cattle from Australia. Evidence for population differentiation across the genome, as measured by F_ST, was highly correlated in the two data sets. Nevertheless, 40% of the variance in F_STbetween the two studies was attributed to the differences in breed composition. Seventy six percent of the variance in F_STwas attributed to differences in SNP composition and density when the same breeds were compared. The difference between F_STof adjacent loci increased rapidly with the increase in distance between SNP, reaching an asymptote after 20 kb. Using 129 SNP that have highly divergent F_STvalues in both data sets, we identified 12 regions that had additive effects on the traits residual feed intake, beef yield or intramuscular fatness measured in the Australian sample. Four of these regions had effects on more than one trait. One of these regions includes the <it>R3HDM1 </it>gene, which is under selection in European humans.</p> <p>Conclusion</p> <p>Firstly, many different populations will be necessary for a full description of selective signatures across the genome, not just a small set of highly divergent populations. Secondly, it is necessary to use the same SNP when comparing the signatures of selection from one study to another. Thirdly, useful signatures of selection can be obtained where many of the groups have only minor genetic differences and may not be clearly separated in a principal component analysis. Fourthly, combining analyses of genome wide selection signatures and genome wide associations to traits helps to define the trait under selection or the population group in which the QTL is likely to be segregating. Finally, the F_STdifference between adjacent loci suggests that 150,000 evenly spaced SNP will be required to study selective signatures in all parts of the bovine genome.</p

A Preliminary Annotated Checklist of Mississippi Mecoptera (Insecta)

We summarize distribution records for 22 Mecoptera species known to occur in Mississippi. These include the fi rst specimens of Bittacus occidentis Walker, B. strigosus Hagen, Hylobittacus apicalis (Hagen) and Panorpa insolens Carpenter to be recorded from the state

A Preliminary Annotated Checklist of Mississippi Mecoptera (Insecta)

We summarize distribution records for 22 Mecoptera species known to occur in Mississippi. These include the fi rst specimens of Bittacus occidentis Walker, B. strigosus Hagen, Hylobittacus apicalis (Hagen) and Panorpa insolens Carpenter to be recorded from the state