Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays

BACKGROUND: Long oligonucleotide microarrays are potentially more cost- and management-efficient than cDNA microarrays, but there is little information on the relative performance of these two probe types. The feasibility of using unmodified oligonucleotides to accurately measure changes in gene expression is also unclear. RESULTS: Unmodified sense and antisense 70-mer oligonucleotides representing 75 known rat genes and 10 Arabidopsis control genes were synthesized, printed and UV cross-linked onto glass slides. Printed alongside were PCR-amplified cDNA clones corresponding to the same genes, enabling us to compare the two probe types simultaneously. Our study was designed to evaluate the mRNA profiles of heart and brain, along with Arabidopsis cRNA spiked into the labeling reaction at different relative copy number. Hybridization signal intensity did not correlate with probe type but depended on the extent of UV irradiation. To determine the effect of oligonucleotide concentration on hybridization signal, 70-mers were serially diluted. No significant change in gene-expression ratio or loss in hybridization signal was detected, even at the lowest concentration tested (6.25 μm). In many instances, signal intensity actually increased with decreasing concentration. The correlation coefficient between oligonucleotide and cDNA probes for identifying differentially expressed genes was 0.80, with an average coefficient of variation of 13.4%. Approximately 8% of the genes showed discordant results with the two probe types, and in each case the cDNA results were more accurate, as determined by real-time PCR. CONCLUSIONS: Microarrays of UV cross-linked unmodified oligonucleotides provided sensitive and specific measurements for most of the genes studied

Description of ALARMA: the alarm algorithm developed for the Nuclear Car Wash

The goal of any alarm algorithm should be that it provide the necessary tools to derive confidence limits on whether the existence of fissile materials is present in cargo containers. It should be able to extract these limits from (usually) noisy and/or weak data while maintaining a false alarm rate (FAR) that is economically suitable for port operations. It should also be able to perform its analysis within a reasonably short amount of time (i.e. {approx} seconds). To achieve this, it is essential that the algorithm be able to identify and subtract any interference signature that might otherwise be confused with a fissile signature. Lastly, the algorithm itself should be user-intuitive and user-friendly so that port operators with little or no experience with detection algorithms may use it with relative ease. In support of the Nuclear Car Wash project at Lawrence Livermore Laboratory, we have developed an alarm algorithm that satisfies the above requirements. The description of the this alarm algorithm, dubbed ALARMA, is the purpose of this technical report. The experimental setup of the nuclear car wash has been well documented [1, 2, 3]. The presence of fissile materials is inferred by examining the {beta}-delayed gamma spectrum induced after a brief neutron irradiation of cargo, particularly in the high-energy region above approximately 2.5 MeV. In this region naturally occurring gamma rays are virtually non-existent. Thermal-neutron induced fission of {sup 235}U and {sup 239}P, on the other hand, leaves a unique {beta}-delayed spectrum [4]. This spectrum comes from decays of fission products having half-lives as large as 30 seconds, many of which have high Q-values. Since high-energy photons penetrate matter more freely, it is natural to look for unique fissile signatures in this energy region after neutron irradiation. The goal of this interrogation procedure is a 95% success rate of detection of as little as 5 kilograms of fissile material while retaining at most .1% false alarm rate. Plywood is used to simulate hydrogenous cargo material and steel (pipes) is used to simulate metallic cargo. The wood consists of 120 x 240 cm sheets and has approximately .65 g/cm{sup 3}. The steel pipes have approximately 10 cm diameters x 6.4 mm wall thickness are .6 g/cm{sup 3}. Fissile sources consist of a ''large'' (380 g) and ''small'' (250 g) sample of HEU (U{sub 3}O{sub 8} 94% enriched). Note that the masses of the HEU sources used in our experimental runs are at least an order of magnitude smaller than 5 kilograms. Runs are done with either wood or steel cargoes stacked at various heights and the HEU sources placed at various depths within the cargo

Positional identification of variants of Adamts16 linked to inherited hypertension

A previously reported blood pressure (BP) quantitative trait locus on rat Chromosome 1 was isolated in a short congenic segment spanning 804.6 kb. The 804.6 kb region contained only two genes, LOC306664 and LOC306665. LOC306664 is predicted to translate into A Disintegrin-like and Metalloproteinase with Thrombospondin Motifs-16 (Adamts16). LOC306665 is a novel gene. All predicted exons of both LOC306664 and LOC306665 were sequenced. Non-synonymous variants were identified in only one of these genes, LOC306664. These variants were naturally existing polymorphisms among inbred, outbred and wild rats. The full-length rat transcript of Adamts16 was detected in multiple tissues. Similar to ADAMTS16 in humans, expression of Adamts16 was prominent in the kidney. Renal transcriptome analysis suggested that a network of genes related to BP was differential between congenic and S rats. These genes were also differentially expressed between kidney cell lines with or without knock-down of Adamts16. Adamts16 is conserved between rats and humans. It is a candidate gene within the homologous region on human Chromosome 5, which is linked to systolic and diastolic BP in the Quebec Family Study. Multiple variants, including an Ala to Pro variant in codon 90 (rs2086310) of human ADAMTS16, were associated with human resting systolic BP (SBP). Replication study in GenNet confirmed the association of two variants of ADAMTS16 with SBP, including rs2086310. Overall, our report represents a high resolution positional cloning and translational study for Adamts16 as a candidate gene controlling B

UBVRI Light Curves of 44 Type Ia Supernovae

We present UBVRI photometry of 44 type-Ia supernovae (SN Ia) observed from 1997 to 2001 as part of a continuing monitoring campaign at the Fred Lawrence Whipple Observatory of the Harvard-Smithsonian Center for Astrophysics. The data set comprises 2190 observations and is the largest homogeneously observed and reduced sample of SN Ia to date, nearly doubling the number of well-observed, nearby SN Ia with published multicolor CCD light curves. The large sample of U-band photometry is a unique addition, with important connections to SN Ia observed at high redshift. The decline rate of SN Ia U-band light curves correlates well with the decline rate in other bands, as does the U-B color at maximum light. However, the U-band peak magnitudes show an increased dispersion relative to other bands even after accounting for extinction and decline rate, amounting to an additional ~40% intrinsic scatter compared to B-band.Comment: 84 authors, 71 pages, 51 tables, 10 figures. Accepted for publication in the Astronomical Journal. Version with high-res figures and electronic data at http://astron.berkeley.edu/~saurabh/cfa2snIa

Language experience impacts brain activation for spoken and signed language in infancy: Insights from unimodal and bimodal bilinguals

Recent neuroimaging studies suggest that monolingual infants activate a left lateralised fronto-temporal brain network in response to spoken language, which is similar to the network involved in processing spoken and signed language in adulthood. However, it is unclear how brain activation to language is influenced by early experience in infancy. To address this question, we present functional near infrared spectroscopy (fNIRS) data from 60 hearing infants (4-to-8 months): 19 monolingual infants exposed to English, 20 unimodal bilingual infants exposed to two spoken languages, and 21 bimodal bilingual infants exposed to English and British Sign Language (BSL). Across all infants, spoken language elicited activation in a bilateral brain network including the inferior frontal and posterior temporal areas, while sign language elicited activation in the right temporo-parietal area. A significant difference in brain lateralisation was observed between groups. Activation in the posterior temporal region was not lateralised in monolinguals and bimodal bilinguals, but right lateralised in response to both language modalities in unimodal bilinguals. This suggests that experience of two spoken languages influences brain activation for sign language when experienced for the first time. Multivariate pattern analyses (MVPA) could classify distributed patterns of activation within the left hemisphere for spoken and signed language in monolinguals (proportion correct = 0.68; p = 0.039) but not in unimodal or bimodal bilinguals. These results suggest that bilingual experience in infancy influences brain activation for language, and that unimodal bilingual experience has greater impact on early brain lateralisation than bimodal bilingual experience

Positional identification of variants of Adamts16 linked to inherited hypertension

A previously reported blood pressure (BP) quantitative trait locus on rat Chromosome 1 was isolated in a short congenic segment spanning 804.6 kb. The 804.6 kb region contained only two genes, LOC306664 and LOC306665. LOC306664 is predicted to translate into A Disintegrin-like and Metalloproteinase with Thrombospondin Motifs-16 (Adamts16). LOC306665 is a novel gene. All predicted exons of both LOC306664 and LOC306665 were sequenced. Non-synonymous variants were identified in only one of these genes, LOC306664. These variants were naturally existing polymorphisms among inbred, outbred and wild rats. The full-length rat transcript of Adamts16 was detected in multiple tissues. Similar to ADAMTS16 in humans, expression of Adamts16 was prominent in the kidney. Renal transcriptome analysis suggested that a network of genes related to BP was differential between congenic and S rats. These genes were also differentially expressed between kidney cell lines with or without knock-down of Adamts16. Adamts16 is conserved between rats and humans. It is a candidate gene within the homologous region on human Chromosome 5, which is linked to systolic and diastolic BP in the Quebec Family Study. Multiple variants, including an Ala to Pro variant in codon 90 (rs2086310) of human ADAMTS16, were associated with human resting systolic BP (SBP). Replication study in GenNet confirmed the association of two variants of ADAMTS16 with SBP, including rs2086310. Overall, our report represents a high resolution positional cloning and translational study for Adamts16 as a candidate gene controlling BP

A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations

Complex phenotypes such as the transformation of a normal population of cells into cancerous tissue result from a series of molecular triggers gone awry. We describe a method that searches for a genetic network consistent with expression changes observed under the knock-down of a set of genes that share a common role in the cell, such as a disease phenotype. The method extends the Nested Effects Model of Markowetz et al. (2005) by using a probabilistic factor graph to search for a network representing interactions among these silenced genes. The method also expands the network by attaching new genes at specific downstream points, providing candidates for subsequent perturbations to further characterize the pathway. We investigated an extension provided by the factor graph approach in which the model distinguishes between inhibitory and stimulatory interactions. We found that the extension yielded significant improvements in recovering the structure of simulated and Saccharomyces cerevisae networks. We applied the approach to discover a signaling network among genes involved in a human colon cancer cell invasiveness pathway. The method predicts several genes with new roles in the invasiveness process. We knocked down two genes identified by our approach and found that both knock-downs produce loss of invasive potential in a colon cancer cell line. Nested effects models may be a powerful tool for inferring regulatory connections and genes that operate in normal and disease-related processes

G-quadruplex organic frameworks

Two-dimensional covalent organic frameworks often π stack into crystalline solids that allow precise spatial positioning of molecular building blocks. Inspired by the hydrogen-bonded G-quadruplexes found frequently in guanine-rich DNA, here we show that this structural motif can be exploited to guide the self-assembly of naphthalene diimide and perylene diimide electron acceptors end-capped with two guanine electron donors into crystalline G-quadruplex-based organic frameworks, wherein the electron donors and acceptors form ordered, segregated π-stacked arrays. Time-resolved optical and electron paramagnetic resonance spectroscopies show that photogenerated holes and electrons in the frameworks have long lifetimes and display recombination kinetics typical of dissociated charge carriers. Moreover, the reduced acceptors form polarons in which the electron is shared over several molecules. The G-quadruplex frameworks also demonstrate potential as cathode materials in Li-ion batteries because of the favourable electron- and Li-ion-transporting capacity provided by the ordered rylene diimide arrays and G-quadruplex structures, respectively

Characterizing and Mitigating Chemomechanical Degradation in High-Energy Lithium-Ion Battery Cathode Materials

Conspectus Lithium-ion batteries (LIBs) are nearly ubiquitous energy storage solutions, powering devices ranging from consumer electronics to electric vehicles. To advance these applications, current LIB research efforts are directed toward improving energy and power densities, cyclic lifetimes, charging speeds, and safety. These parameters are intrinsically tied to properties of the active electrode materials, such as the redox mechanism, chemical composition, and crystal structure. One particularly challenging issue is that the active electrode materials that possess higher theoretical energy densities are generally more susceptible to degradation during cycling. A notable example is the family of layered multicomponent transition metal oxides, which is the incumbent class of active LIB cathode materials for electric vehicles. To increase their theoretical capacities, the transition metal fraction in these materials is trending toward higher Ni content. However, Ni-rich chemistries suffer from electrochemical, crystallographic, and mechanical degradation that increase in severity with increasing Ni content. Furthermore, alternative high-energy cathode materials, including overlithiated layered oxides and disordered rock salt materials, present additional stability challenges that must be overcome before they can be realistically incorporated into LIB technology. The chemomechanical degradation in high-energy LIB cathode materials occurs at multiple length scales. Point defects, such as antisite defects or vacancies, are commonly generated during electrochemical cycling and can contribute to the loss of cyclable active material. At both the primary and secondary particle level, electrochemical cycling also induces significant volumetric changes and state-of-charge heterogeneity, generating regions of high stress and strain that are precursors to mechanical fracture. Finally, at the electrode level, nonuniform charge transfer reactions throughout the electrode can lead to locally overcharged regions that become sites of enhanced degradation. To address these issues, active cathode material design and electrode engineering are being heavily pursued to accelerate improvements in LIB energy density. To consolidate the current understanding of chemomechanical degradation and provide guidance on mitigation strategies, a comprehensive overview of degradation mechanisms across multiple length scales is critically needed. In this Account, we first outline the origins of chemomechanical degradation for high-energy LIB cathodes, including layered oxides, overlithiated layered oxides, and disordered rock salt structures. Specifically, we delineate the thermodynamic and kinetic origins of defect generation at the atomic level and then progress to the kinetic origins of broader degradation mechanisms at the particle level and electrode level. Next, we discuss strategies for minimizing chemomechanical degradation in high-energy LIB cathodes at multiple length scales. Finally, we provide a forward-looking perspective on how to accelerate progress toward practical high-energy LIB cathodes, including emerging methods to map state-of-charge heterogeneity, efficient data processing techniques, and improved strategies for spatially identifying chemomechanical degradation. We also propose engineering solutions for mitigating chemomechanical degradation, such as grain boundary engineering, modifying the active material particle morphology, and electrode architecture design. Since many of these suggestions can be applied irrespective of cathode chemistry, this Account is likely to be broadly applicable to the diverse set of ongoing efforts to realize high-energy LIBs.11Nscopu