Neurosystems: brain rhythms and cognitive processing

Neuronal rhythms are ubiquitous features of brain dynamics, and are highly correlated with cognitive processing. However, the relationship between the physiological mechanisms producing these rhythms and the functions associated with the rhythms remains mysterious. This article investigates the contributions of rhythms to basic cognitive computations (such as filtering signals by coherence and/or frequency) and to major cognitive functions (such as attention and multi-modal coordination). We offer support to the premise that the physiology underlying brain rhythms plays an essential role in how these rhythms facilitate some cognitive operations.098352 - Wellcome Trust; 5R01NS067199 - NINDS NIH HH

BCFtools/csq: haplotype-aware variant consequences.

MOTIVATION: Prediction of functional variant consequences is an important part of sequencing pipelines, allowing the categorization and prioritization of genetic variants for follow up analysis. However, current predictors analyze variants as isolated events, which can lead to incorrect predictions when adjacent variants alter the same codon, or when a frame-shifting indel is followed by a frame-restoring indel. Exploiting known haplotype information when making consequence predictions can resolve these issues. RESULTS: BCFtools/csq is a fast program for haplotype-aware consequence calling which can take into account known phase. Consequence predictions are changed for 501 of 5019 compound variants found in the 81.7M variants in the 1000 Genomes Project data, with an average of 139 compound variants per haplotype. Predictions match existing tools when run in localized mode, but the program is an order of magnitude faster and requires an order of magnitude less memory. AVAILABILITY AND IMPLEMENTATION: The program is freely available for commercial and non-commercial use in the BCFtools package which is available for download from http://samtools.github.io/bcftools . CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Pilot-scale ceramic membrane filtration of skim milk for the production of a 'humanised' protein base ingredient for infant milk formula

The protein composition of bovine skim milk was modified using pilot scale membrane filtration to produce a whey protein-dominant ingredient with a casein profile closer to human milk. Bovine skim milk was processed at low (8.9 °C) or high (50 °C) temperature using ceramic microfiltration (MF) membranes (0.1 μm mean pore diameter). The resulting permeate stream was concentrated using polyethersulfone ultrafiltration (UF) membranes (10 kDa cut-off). The protein profile of MF and UF retentate streams were determined using reversed phase-high performance liquid chromatography and polyacrylamide gel electrophoresis. Permeate from the cold MF process (8.9 °C) had a casein:whey protein ratio of ∼35:65 with no αS- or κ-casein present, compared with a casein:whey protein ratio of ∼10:90 at 50 °C. This study has demonstrated the application of cold membrane filtration (8.9 °C) at pilot scale to produce a dairy ingredient with a protein profile closer to that of human milk

Short communication: Multi-component interactions causing solidification during industrial-scale manufacture of pre-crystallized acid whey powders

peer-reviewedAcid whey (AW) is the liquid co-product arising from acid-induced precipitation of casein from skim milk. Further processing of AW is often challenging due to its high mineral content, which can promote aggregation of whey proteins, which contributes to high viscosity of the liquid concentrate during subsequent lactose crystallization and drying steps. This study focuses on mineral precipitation, protein aggregation, and lactose crystallization in liquid AW concentrates (∼55% total solids), and on the microstructure of the final powders from 2 independent industrial-scale trials. These AW concentrates were observed to solidify either during processing or during storage (24 h) of pre-crystallized concentrate. The more rapid solidification in the former was associated with a greater extent of lactose crystallization and a higher ash-to-protein ratio in that concentrate. Confocal laser scanning microscopy analysis indicated the presence of a loose network of protein aggregates (≤10 µm) and lactose crystals (100–300 µm) distributed throughout the solidified AW concentrate. Mineral-based precipitate was also evident, using scanning electron microscopy, at the surface of AW powder particles, indicating the formation of insoluble calcium phosphate during processing. These results provide new information on the composition- and process-dependent physicochemical changes that are useful in designing and optimizing processes for AW

Structural and functional-annotation of an equine whole genome oligoarray

<p>Abstract</p> <p>Background</p> <p>The horse genome is sequenced, allowing equine researchers to use high-throughput functional genomics platforms such as microarrays; next-generation sequencing for gene expression and proteomics. However, for researchers to derive value from these functional genomics datasets, they must be able to model this data in biologically relevant ways; to do so requires that the equine genome be more fully annotated. There are two interrelated types of genomic annotation: structural and functional. Structural annotation is delineating and demarcating the genomic elements (such as genes, promoters, and regulatory elements). Functional annotation is assigning function to structural elements. The Gene Ontology (GO) is the <it>de facto </it>standard for functional annotation, and is routinely used as a basis for modelling and hypothesis testing, large functional genomics datasets.</p> <p>Results</p> <p>An Equine Whole Genome Oligonucleotide (EWGO) array with 21,351 elements was developed at Texas A&M University. This 70-mer oligoarray was designed using the approximately 7× assembled and annotated sequence of the equine genome to be one of the most comprehensive arrays available for expressed equine sequences. To assist researchers in determining the biological meaning of data derived from this array, we have structurally annotated it by mapping the elements to multiple database accessions, including UniProtKB, Entrez Gene, NRPD (Non-Redundant Protein Database) and UniGene. We next provided GO functional annotations for the gene transcripts represented on this array. Overall, we GO annotated 14,531 gene products (68.1% of the gene products represented on the EWGO array) with 57,912 annotations. GAQ (GO Annotation Quality) scores were calculated for this array both before and after we added GO annotation. The additional annotations improved the <it>meanGAQ </it>score 16-fold. This data is publicly available at <it>AgBase </it><url>http://www.agbase.msstate.edu/</url>.</p> <p>Conclusion</p> <p>Providing additional information about the public databases which link to the gene products represented on the array allows users more flexibility when using gene expression modelling and hypothesis-testing computational tools. Moreover, since different databases provide different types of information, users have access to multiple data sources. In addition, our GO annotation underpins functional modelling for most gene expression analysis tools and enables equine researchers to model large lists of differentially expressed transcripts in biologically relevant ways.</p

Crumble: reference free lossy compression of sequence quality values

Motivation: The bulk of space taken up by NGS sequencing CRAM files consists of per-base quality values. Most of these are unnecessary for variant calling, offering an opportunity for space saving. Results: On the Syndip test set, a 17 fold reduction in the quality storage portion of a CRAM file can be achieved while maintaining variant calling accuracy. The size reduction of an entire CRAM file varied from 2.2 to 7.4 fold, depending on the non-quality content of the original file (see Supplementary Material S6 for details). Availability and implementation: Crumble is OpenSource and can be obtained from https://github.com/jkbonfield/crumble. Supplementary information: Supplementary data are available at Bioinformatics online.This work was funded by the Wellcome Trust [WT098051]

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.

We are rapidly approaching the point where we have sequenced millions of human genomes. There is a pressing need for new data structures to store raw sequencing data and efficient algorithms for population scale analysis. Current reference-based data formats do not fully exploit the redundancy in population sequencing nor take advantage of shared genetic variation. In recent years, the Burrows-Wheeler transform (BWT) and FM-index have been widely employed as a full-text searchable index for read alignment and de novo assembly. We introduce the concept of a population BWT and use it to store and index the sequencing reads of 2705 samples from the 1000 Genomes Project. A key feature is that, as more genomes are added, identical read sequences are increasingly observed, and compression becomes more efficient. We assess the support in the 1000 Genomes read data for every base position of two human reference assembly versions, identifying that 3.2 Mbp with population support was lost in the transition from GRCh37 with 13.7 Mbp added to GRCh38. We show that the vast majority of variant alleles can be uniquely described by overlapping 31-mers and show how rapid and accurate SNP and indel genotyping can be carried out across the genomes in the population BWT. We use the population BWT to carry out nonreference queries to search for the presence of all known viral genomes and discover human T-lymphotropic virus 1 integrations in six samples in a recognized epidemiological distribution

Rehydration behaviour of spray-dried micellar casein concentrates produced using microfiltration of skim milk at cold or warm temperatures

peer-reviewedMicrofiltration (MF) of skim milk, when combined with diafiltration (DF), facilitates the manufacture of liquid micellar casein concentrate (MCC), which can be spray-dried into high-protein (≥80% protein, dry-basis) powders. MCC powders rehydrate slowly, which is typically considered a defect by end-users. This study compared the impact of cold (<10 °C) or warm (50 °C) MF/DF on the rehydration characteristics of MCC powders (MCCcold and MCCwarm, respectively). The wetting properties of the MCC powders, measured using optical tensiometry, were found to be equivalent. However, pronounced differences in dispersion characteristics were measured, and, after 90 min rehydration at 50 °C, liberated casein micelles accounted for only 7.5% of total particle volume in MCCwarm compared with 48% in MCCcold. Due to its superior dispersion characteristics, MCCcold yielded 50–60% less sediment during analytical centrifugation experiments. Cold MF/DF may improve the solubility of MCC powders by accelerating the release of casein micelles from powder particles during rehydration

Efficient iterative Hi-C scaffolder based on N-best neighbors.

BACKGROUND: Efficient and effective genome scaffolding tools are still in high demand for generating reference-quality assemblies. While long read data itself is unlikely to create a chromosome-scale assembly for most eukaryotic species, the inexpensive Hi-C sequencing technology, capable of capturing the chromosomal profile of a genome, is now widely used to complete the task. However, the existing Hi-C based scaffolding tools either require a priori chromosome number as input, or lack the ability to build highly continuous scaffolds. RESULTS: We design and develop a novel Hi-C based scaffolding tool, pin_hic, which takes advantage of contact information from Hi-C reads to construct a scaffolding graph iteratively based on N-best neighbors of contigs. Subsequent to scaffolding, it identifies potential misjoins and breaks them to keep the scaffolding accuracy. Through our tests on three long read based de novo assemblies from three different species, we demonstrate that pin_hic is more efficient than current standard state-of-art tools, and it can generate much more continuous scaffolds, while achieving a higher or comparable accuracy. CONCLUSIONS: Pin_hic is an efficient Hi-C based scaffolding tool, which can be useful for building chromosome-scale assemblies. As many sequencing projects have been launched in the recent years, we believe pin_hic has potential to be applied in these projects and makes a meaningful contribution

Three-Point Correlation Functions of SDSS Galaxies: Luminosity and Color Dependence in Redshift and Projected Space

The three-point correlation function (3PCF) provides an important view into the clustering of galaxies that is not available to its lower order cousin, the two-point correlation function (2PCF). Higher order statistics, such as the 3PCF, are necessary to probe the non-Gaussian structure and shape information expected in these distributions. We measure the clustering of spectroscopic galaxies in the Main Galaxy Sample of the Sloan Digital Sky Survey (SDSS), focusing on the shape or configuration dependence of the reduced 3PCF in both redshift and projected space. This work constitutes the largest number of galaxies ever used to investigate the reduced 3PCF, using over 220,000 galaxies in three volume-limited samples. We find significant configuration dependence of the reduced 3PCF at 3-27 Mpc/h, in agreement with LCDM predictions and in disagreement with the hierarchical ansatz. Below 6 Mpc/h, the redshift space reduced 3PCF shows a smaller amplitude and weak configuration dependence in comparison with projected measurements suggesting that redshift distortions, and not galaxy bias, can make the reduced 3PCF appear consistent with the hierarchical ansatz. The reduced 3PCF shows a weaker dependence on luminosity than the 2PCF, with no significant dependence on scales above 9 Mpc/h. On scales less than 9 Mpc/h, the reduced 3PCF appears more affected by galaxy color than luminosty. We demonstrate the extreme sensitivity of the 3PCF to systematic effects such as sky completeness and binning scheme, along with the difficulty of resolving the errors. Some comparable analyses make assumptions that do not consistently account for these effects.Comment: 27 pages, 21 figures. Updated to match accepted version. Published in Ap