Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression

BACKGROUND: There are many potential sources of variability in a microarray experiment. Variation can arise from many aspects of the collection and processing of samples for gene expression analysis. Oligonucleotide-based arrays are thought to minimize one source of variability as identical oligonucleotides are expected to recognize the same transcripts during hybridization. RESULTS: We demonstrate that although the probes on the U133A GeneChip arrays are identical in sequence to probes designed for the U133 Plus 2.0 arrays the values obtained from an experimental hybridization can be quite different. Nearly half of the probesets in common between the two array types can produce slightly different values from the same sample. Nearly 70% of the individual probes in these probesets produced array specific differences. CONCLUSION: The context of the probe may also contribute some bias to the final measured value of gene expression. At a minimum, this should add an extra level of caution when considering the direct comparison of experiments performed in two microarray formats. More importantly, this suggests that it may not be possible to know which value is the most accurate representation of a biological sample when comparing two formats

Autonomous Light Management in Flexible Photoelectrochromic Films Integrating High Performance Silicon Solar Microcells

Commercial smart window technologies for dynamic light and heat management in building and automotive environments traditionally rely on electrochromic (EC) materials powered by an external source. This design complicates building-scale installation requirements and substantially increases costs for applications in retrofit construction. Self-powered photoelectrochromic (PEC) windows are an intuitive alternative wherein a photovoltaic (PV) material is used to power the electrochromic device, which modulates the transmission of the incident solar flux. The PV component in this application must be sufficiently transparent and produce enough power to efficiently modulate the EC device transmission. Here, we propose Si solar microcells (μ-cells) that are i) small enough to be visually transparent to the eye, and ii) thin enough to enable flexible PEC devices. Visual transparency is achieved when Si μ-cells are arranged in high pitch (i.e. low-integration density) form factors while maintaining the advantages of a single-crystalline PV material (i.e., long lifetime and high performance). Additionally, the thin dimensions of these Si μ-cells enable fabrication on flexible substrates to realize these flexible PEC devices. The current work demonstrates this concept using WO₃ as the EC material and V₂O₅ as the ion storage layer, where each component is fabricated via sol-gel methods that afford improved prospects for scalability and tunability in comparison to thermal evaporation methods. The EC devices display fast switching times, as low as 8 seconds, with a modulation in transmission as high as 33%. Integration with two Si μ-cells in series (affording a 1.12 V output) demonstrates an integrated PEC module design with switching times of less than 3 minutes, and a modulation in transmission of 32% with an unprecedented EC:PV areal ratio

Autonomous Light Management in Flexible Photoelectrochromic Films Integrating High Performance Silicon Solar Microcells

Commercial smart window technologies for dynamic light and heat management in building and automotive environments traditionally rely on electrochromic (EC) materials powered by an external source. This design complicates building-scale installation requirements and substantially increases costs for applications in retrofit construction. Self-powered photoelectrochromic (PEC) windows are an intuitive alternative wherein a photovoltaic (PV) material is used to power the electrochromic device, which modulates the transmission of the incident solar flux. The PV component in this application must be sufficiently transparent and produce enough power to efficiently modulate the EC device transmission. Here, we propose Si solar microcells (μ-cells) that are i) small enough to be visually transparent to the eye, and ii) thin enough to enable flexible PEC devices. Visual transparency is achieved when Si μ-cells are arranged in high pitch (i.e. low-integration density) form factors while maintaining the advantages of a single-crystalline PV material (i.e., long lifetime and high performance). Additionally, the thin dimensions of these Si μ-cells enable fabrication on flexible substrates to realize these flexible PEC devices. The current work demonstrates this concept using WO₃ as the EC material and V₂O₅ as the ion storage layer, where each component is fabricated via sol-gel methods that afford improved prospects for scalability and tunability in comparison to thermal evaporation methods. The EC devices display fast switching times, as low as 8 seconds, with a modulation in transmission as high as 33%. Integration with two Si μ-cells in series (affording a 1.12 V output) demonstrates an integrated PEC module design with switching times of less than 3 minutes, and a modulation in transmission of 32% with an unprecedented EC:PV areal ratio

Tumor exome sequencing and copy number alterations reveal potential predictors of intrinsic resistance to multi-targeted tyrosine kinase inhibitors

Multi-targeted tyrosine kinase inhibitors (TKIs) have broad efficacy and similar FDA-approved indications, suggesting shared molecular drug targets across cancer types. Irrespective of tumor type, 20-30% of patients treated with multi-targeted TKIs demonstrate intrinsic resistance, with progressive disease as a best response. We conducted a retrospective cohort study to identify tumor (somatic) point mutations, insertion/deletions, and copy number alterations (CNA) associated with intrinsic resistance to multi-targeted TKIs. Using a candidate gene approach (n=243), tumor next-generation sequencing and CNA data was associated with resistant and non-resistant outcomes. Resistant individuals (n=11) more commonly harbored somatic point mutations in NTRK1, KDR, TGFBR2, and PTPN11 and CNA in CDK4, CDKN2B, and ERBB2 compared to non-resistant (n=26, p<0.01). Using a random forest classification model for variable reduction and a decision tree classification model, we were able to differentiate intrinsically resistant from non-resistant patients. CNA in CDK4 and CDKN2B were the most important analytical features, implicating the cyclin D pathway as a potentially important factor in resistance to multi-targeted TKIs. Replication of these results in a larger, independent patient cohort has potential to inform personalized prescribing of these widely utilized agents

Reliability of Striatal [11C]Raclopride Binding in Smokers Wearing Transdermal Nicotine Patches

PURPOSE: In studies where [(11)C]raclopride (RAC) positron emission tomography (PET) is used to assess changes in striatal dopamine, it is important to control for cognitive states, such as drug craving, that could alter dopamine levels. In cigarette smokers, transdermal nicotine patches (TNP) can control nicotine craving, but the effects of nicotine patches on RAC binding are unknown. Thus, we sought to determine the test-retest reliability of RAC binding in the presence of nicotine patches. METHODS: Eleven male smokers were scanned twice with RAC on separate days while wearing TNP. RESULTS: Across the striatum, test-retest variability was 7.63 ± 5.88; percent change in binding potential was 1.11 ± 9.83; and the intraclass correlation coefficient was 0.91 (p < 0.0001). CONCLUSION: Baseline RAC binding is highly reproducible in smokers wearing nicotine patches. This suggests that TNP are an acceptable method for controlling cigarette craving during studies that utilize RAC to examine changes in dopamine

Microarray comparison of prostate tumor gene expression in African-American and Caucasian American males: a pilot project study

African American Men are 65% more likely to develop prostate cancer and are twice as likely to die of prostate cancer, than are Caucasian American Males. The explanation for this glaring health disparity is still unknown; although a number of different plausible factors have been offered including genetic susceptibility and gene-environment interactions. We favor the hypothesis that altered gene expression plays a major role in the disparity observed in prostate cancer incidence and mortality between African American and Caucasian American Males. To discover genes or gene expression pattern(s) unique to African American or to Caucasian American Males that explain the observed prostate cancer health disparity in African American males, we conducted a micro array pilot project study that used prostate tumors with a Gleason score of 6. We compared gene expression profiling in tumors from African-American Males to prostate tumors in Caucasian American Males. A comparison of case-matched ratios revealed at least 67 statistically significant genes that met filtering criteria of at least +/- 4.0 fold change and p < 0.0001. Gene ontology terms prevalent in African American prostate tumor/normal ratios relative to Caucasian American prostate tumor/normal ratios included interleukins, progesterone signaling, Chromatin-mediated maintenance and myeloid dendritic cell proliferation. Functional in vitro assays are underway to determine roles that selected genes in these onotologies play in contributing to prostate cancer development and health disparity

Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus.

Genome-wide association studies have identified 40 ovarian cancer risk loci. However, the mechanisms underlying these associations remain elusive. In this study, we conducted a two-pronged approach to identify candidate causal SNPs and assess underlying biological mechanisms at chromosome 9p22.2, the first and most statistically significant associated locus for ovarian cancer susceptibility. Three transcriptional regulatory elements with allele-specific effects and a scaffold/matrix attachment region were characterized and, through physical DNA interactions, BNC2 was established as the most likely target gene. We determined the consensus binding sequence for BNC2 in vitro, verified its enrichment in BNC2 ChIP-seq regions, and validated a set of its downstream target genes. Fine-mapping by dense regional genotyping in over 15,000 ovarian cancer cases and 30,000 controls identified SNPs in the scaffold/matrix attachment region as among the most likely causal variants. This study reveals a comprehensive regulatory landscape at 9p22.2 and proposes a likely mechanism of susceptibility to ovarian cancer. SIGNIFICANCE: Mapping the 9p22.2 ovarian cancer risk locus identifies BNC2 as an ovarian cancer risk gene.See related commentary by Choi and Brown, p. 439

Regional to Global Assessments of Phytoplankton Dynamics From The SeaWiFS Mission

Photosynthetic production of organic matter by microscopic oceanic phytoplankton fuels ocean ecosystems and contributes roughly half of the Earth's net primary production. For 13 years, the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) mission provided the first consistent, synoptic observations of global ocean ecosystems. Changes in the surface chlorophyll concentration, the primary biological property retrieved from SeaWiFS, have traditionally been used as a metric for phytoplankton abundance and its distribution largely reflects patterns in vertical nutrient transport. On regional to global scales, chlorophyll concentrations covary with sea surface temperature (SST) because SST changes reflect light and nutrient conditions. However, the oceanmay be too complex to be well characterized using a single index such as the chlorophyll concentration. A semi-analytical bio-optical algorithm is used to help interpret regional to global SeaWiFS chlorophyll observations from using three independent, well-validated ocean color data products; the chlorophyll a concentration, absorption by CDM and particulate backscattering. First, we show that observed long-term, global-scale trends in standard chlorophyll retrievals are likely compromised by coincident changes in CDM. Second, we partition the chlorophyll signal into a component due to phytoplankton biomass changes and a component caused by physiological adjustments in intracellular chlorophyll concentrations to changes in mixed layer light levels. We show that biomass changes dominate chlorophyll signals for the high latitude seas and where persistent vertical upwelling is known to occur, while physiological processes dominate chlorophyll variability over much of the tropical and subtropical oceans. The SeaWiFS data set demonstrates complexity in the interpretation of changes in regional to global phytoplankton distributions and illustrates limitations for the assessment of phytoplankton dynamics using chlorophyll retrievals alone

Individual Preferences and Social Interactions Determine the Aggregation of Woodlice

n°e17389.info:eu-repo/semantics/publishe

Evolutionary Breakpoints in the Gibbon Suggest Association between Cytosine Methylation and Karyotype Evolution

Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15–18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys) and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (<150 bp) have a higher CpG content than other Alus. Bisulphite allelic sequencing reveals that these gibbon Alus have a lower average density of methylated cytosine that their human orthologues. The finding of higher CpG content and lower average CpG methylation suggests that the gibbon Alu elements are epigenetically distinct from their human orthologues. The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution