Correlation test to assess low-level processing of high-density oligonucleotide microarray data

Background  

There are currently a number of competing techniques for low-level processing of oligonucleotide array data. The choice of technique has a profound effect on subsequent statistical analyses, but there is no method to assess whether a particular technique is appropriate for a specific data set, without reference to external data.     

High‐Performance Solar Steam Device with Layered Channels: Artificial Tree with a Reversed Design

Solar steam generation, combining the most abundant resources of solar energy and unpurified water, has been regarded as one of the most promising techniques for water purification. Here, an artificial tree with a reverse‐tree design is demonstrated as a cost‐effective, scalable yet highly efficient steam‐generation device. The reverse‐tree design implies that the wood is placed on the water with the tree‐growth direction parallel to the water surface; accordingly, water is transported in a direction perpendicular to what occurs in natural tree. The artificial tree is fabricated by cutting the natural tree along the longitudinal direction followed by surface carbonization (called as C‐L‐Wood). The nature‐made 3D interconnected micro‐/nanochannels enable efficient water transpiration, while the layered channels block the heat effectively. A much lower thermal conductivity (0.11 W m^?1 K^?1) thus can be achieved, only 1/3 of that of the horizontally cut wood. Meanwhile, the carbonized surface can absorb almost all the incident light. The simultaneous optimizations of water transpiration, thermal management, and light absorption results in a high efficiency of 89% at 10 kW m^?2, among the highest values in literature. Such wood‐based high‐performance, cost‐effective, scalable steam‐generation device can provide an attractive solution to the pressing global clean water shortage problem.     

Comparative Polygenic Analysis of Maximal Ethanol Accumulation Capacity and Tolerance to High Ethanol Levels of Cell Proliferation in Yeast

The yeast Saccharomyces cerevisiae is able to accumulate ≥17% ethanol (v/v) by fermentation in the absence of cell proliferation. The genetic basis of this unique capacity is unknown. Up to now, all research has focused on tolerance of yeast cell proliferation to high ethanol levels. Comparison of maximal ethanol accumulation capacity and ethanol tolerance of cell proliferation in 68 yeast strains showed a poor correlation, but higher ethanol tolerance of cell proliferation clearly increased the likelihood of superior maximal ethanol accumulation capacity. We have applied pooled-segregant whole-genome sequence analysis to identify the polygenic basis of these two complex traits using segregants from a cross of a haploid derivative of the sake strain CBS1585 and the lab strain BY. From a total of 301 segregants, 22 superior segregants accumulating ≥17% ethanol in small-scale fermentations and 32 superior segregants growing in the presence of 18% ethanol, were separately pooled and sequenced. Plotting SNP variant frequency against chromosomal position revealed eleven and eight Quantitative Trait Loci (QTLs) for the two traits, respectively, and showed that the genetic basis of the two traits is partially different. Fine-mapping and Reciprocal Hemizygosity Analysis identified ADE1, URA3, and KIN3, encoding a protein kinase involved in DNA damage repair, as specific causative genes for maximal ethanol accumulation capacity. These genes, as well as the previously identified MKT1 gene, were not linked in this genetic background to tolerance of cell proliferation to high ethanol levels. The superior KIN3 allele contained two SNPs, which are absent in all yeast strains sequenced up to now. This work provides the first insight in the genetic basis of maximal ethanol accumulation capacity in yeast and reveals for the first time the importance of DNA damage repair in yeast ethanol tolerance.     

Rapid microsatellite marker isolation for the Pink Stem Borer,Sesamia inferens (Lepidopetera: Noctuidae), through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries and cross amplification in related taxa

Next-generation Roche 454 pyrosequencing was used to rapidly identify polymorphic microsatellites from enriched DNA libraries for the pink stem borer, Sesamia inferens (Walker). A total of 1,459 simple sequence repeats (SSRs) were isolated from the microsatellite-enriched library using 454 sequencing. Thirty-nine microsatellite markers were selected to synthesize for further optimization, and 12 loci exhibited reliable amplification of a single product of expected size. The forward primer of 12 primer pairs was end labeled with a fluorescent dye. All of the 12 microsatellite loci were polymorphic, with 5–13 alleles per locus and observed heterozygosities ranging from 0.097 to 0.957. Here, we also tested these 12 SSRs for cross-species amplification in Chilo suppressalis (Walker), Tryporyza incertulas (Walker) and Cnaphalocrocis medinalis (Guenée). These polymorphic markers will be a valuable tool for analyses of population connectivity and genetic structure in this rice pest.     

Super-sparse principal component analyses for high-throughput genomic data

Background  

Principal component analysis (PCA) has gained popularity as a method for the analysis of high-dimensional genomic data. However, it is often difficult to interpret the results because the principal components are linear combinations of all variables, and the coefficients (loadings) are typically nonzero. These nonzero values also reflect poor estimation of the true vector loadings; for example, for gene expression data, biologically we expect only a portion of the genes to be expressed in any tissue, and an even smaller fraction to be involved in a particular process. Sparse PCA methods have recently been introduced for reducing the number of nonzero coefficients, but these existing methods are not satisfactory for high-dimensional data applications because they still give too many nonzero coefficients.     

Identification of recurrent regions of copy-number variants across multiple individuals

Background  

Algorithms and software for CNV detection have been developed, but they detect the CNV regions sample-by-sample with individual-specific breakpoints, while common CNV regions are likely to occur at the same genomic locations across different individuals in a homogenous population. Current algorithms to detect common CNV regions do not account for the varying reliability of the individual CNVs, typically reported as confidence scores by SNP-based CNV detection algorithms. General methodologies for identifying these recurrent regions, especially those directed at SNP arrays, are still needed.     

Annotated regions of significance of SELDI-TOF-MS spectra for detecting protein biomarkers

Peak detection is a key step in the analysis of SELDI-TOF-MS spectra, but the current default method has low specificity and poor peak annotation. To improve data quality, scientists still have to validate the identified peaks visually, a tedious and time-consuming process, especially for large data sets. Hence, there is a genuine need for methods that minimize manual validation. We have previously reported a multi-spectral signal detection method, called RS for 'region of significance', with improved specificity. Here we extend it to include a peak quantification algorithm based on annotated regions of significance (ARS). For each spectral region flagged as significant by RS, we first identify a dominant spectrum for determining the number of peaks and the m/z region of these peaks. From each m/z region of peaks, a peak template is extracted from all spectra via the principal component analysis. Finally, with the template, we estimate the amplitude and location of the peak in each spectrum with the least-squares method and refine the estimation of the amplitude via the mixture model.We have evaluated the ARS algorithm on patient samples from a clinical study. Comparison with the standard method shows that ARS (i) inherits the superior specificity of RS, and (ii) gives more accurate peak annotations than the standard method. In conclusion, we find that ARS alleviates the main problems in the preprocessing of SELDI-TOF spectra. The R-package ProSpect that implements ARS is freely available for academic use at http://www.meb.ki.se/ yudpaw.     

Highly Conductive,Lightweight, Low‐Tortuosity Carbon Frameworks as Ultrathick 3D Current Collectors

The growing demand for advanced energy storage techniques and devices has driven the energy storage market to strive for higher performance, longer cycling life, and better safety. Thick electrode design enabling more electroactive materials has the potential to significantly improve the energy density on device level yet faces major challenges of slow ion transport and high deformability. Here, inspired by natural wood materials with aligned channels along the tree growth direction, a highly conductive, lightweight, and low‐tortuosity carbon framework (CF) directly carbonized from natural wood as an ultrathick 3D current collector is demonstrated. Benefiting from the uniqueness of the multichanneled CF, an ultrathick 3D electrode of lithium iron phosphate filled carbon framework with a large thickness of 800 µm and active material mass loading of 60 mg cm^?2 delivers a rational capacity of 7.6 mAh cm^?2 (95 Ah L^?1 based on volume), long cycling life, and lower deformability with enhanced mechanical properties. This work presents a design concept for thick electrode toward high performance energy storage devices that are not limited to lithium‐ion batteries.     

Valuable ingredients and feed toxicity evaluation of Microcystis aeruginosa acidolysis product in mice

This research studied the extraction from Microcystis aeruginosa using hydrochloric acid method as a potentially valuable protein resource from eutrophic lakes. Amino acid composition, residual algal toxins, and heavy metals of the acidolysis product were studied. After 18 h of hydrochloric acid treatment, the product of M. aeruginosa contained 17 amino acids, 51.34% of total amino acid requirements, and 30.25% of the livestock and poultry essential amino acid (Eaa). The residual microcystin-LR (MC-LR) was 0.94 µg kg⁻¹, which was less than WHO drinking water limit of microcystins. The removal ratio of microcystins was higher than 99.99% during the process of hydrolysis. The concentration of heavy metals of the product was in compliance with feed standards. Furthermore, using Horn’s method, Mouse Micronucleus Test and Sperm Shape Abnormality Test were conducted to study the forage safety of the product. Half lethal dose (LD₅₀) of acidolysis product in mice was >9.09 g kg⁻¹ body weight, actually belonging to non-toxic grade. Every dose treatment did not significantly increase activities of alkaline phosphatase (ALP), lactate dehydrogenase (LDH), and γ-glutamyltransferase (γ-GT). The results of both micronucleus test and sperm shape abnormality test were negative, which suggested the product with no mutagenicity and sperm malformation effects. This study indicated that the acidolysis product of M. aeruginosa was safe to be used as a feed ingredient.