A5081127625- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- Insect and Arachnid Ecology and Behavior
- Bioinformatics and Genomic Networks
- Physics of Superconductivity and Magnetism
- Insect and Pesticide Research
- Molecular Junctions and Nanostructures
- Fish biology, ecology, and behavior
- Gene expression and cancer classification
- Plant and animal studies
- Marine and coastal plant biology
- Quantum and electron transport phenomena
- Iron-based superconductors research
- MicroRNA in disease regulation
- Ichthyology and Marine Biology
- Physiological and biochemical adaptations
- Plant Molecular Biology Research
- Neuroscience of respiration and sleep
- Molecular Biology Techniques and Applications
- Echinoderm biology and ecology
- Health disparities and outcomes
- Surface and Thin Film Phenomena
- Complex Network Analysis Techniques
- Psychological Well-being and Life Satisfaction
Pontificia Universidad Católica de Chile
2012
California Institute of Technology
2006-2008
Ames Research Center
2002-2006
Eloret (United States)
2004-2006
National Aeronautics and Space Administration
2003-2006
Baylor College of Medicine
2006
National Institute of Dental and Craniofacial Research
2006
National Institutes of Health
2006
Stazione Zoologica Anton Dohrn
2006
Brown University
2006
We report the sequence and analysis of 814-megabase genome sea urchin Strongylocentrotus purpuratus , a model for developmental systems biology. The sequencing strategy combined whole-genome shotgun bacterial artificial chromosome (BAC) sequences. This use BAC clones, aided by pooling strategy, overcame difficulties associated with high heterozygosity genome. encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside deuterostomes....
Elucidating the transcribed regions of genome constitutes a fundamental aspect human biology, yet this remains an outstanding problem. To comprehensively identify coding sequences, we constructed series high-density oligonucleotide tiling arrays representing sense and antisense strands entire nonrepetitive sequence genome. Transcribed sequences were located across via hybridization to complementary DNA samples, reverse-transcribed from polyadenylated RNA obtained liver tissue. In addition...
The genome of Ectocarpus, a model organism for brown algae, has been sequenced. Brown algae are complex photosynthetic organisms that have adapted to life in rocky coastal environments. Genome analysis sheds light on this adaptation and reveals an extended set light-harvesting pigment biosynthesis genes novel metabolic processes such as halide metabolism. Comparative genomic analyses highlight the likely importance family receptor kinases related molecules evolution multicellularity plants,...
In this paper, we present a method for computing the resistance of molecular wires and illustrate it with systematic theoretical study particular class organic molecules. These molecules consist one or more benzene rings thiol(-SH) group at ends. This end can attach readily to metallic surfaces, thus allowing molecule function as nanoelectronic interconnect. The conduction through these low bias occurs by tunneling, leading resistances that are typically several tens megaohms. goes up...
Little is known about the genetic basis of convergent traits that originate repeatedly over broad taxonomic scales. The myogenic electric organ has evolved six times in fishes to produce fields used communication, navigation, predation, or defense. We have examined genomic anatomical and physiological origins these organs by assembling genome eel (Electrophorus electricus) sequencing skeletal muscle transcriptomes from three lineages independently organs. Our results indicate that, despite...
Interpreting data from large-scale protein interaction experiments has been a challenging task because of the widespread presence random false positives. Here, we present network-based statistical algorithm that overcomes this difficulty and allows us to derive functions unannotated proteins data. Our uses insight if two share significantly larger number common partners than random, they have close functional associations. Analysis publicly available Saccharomyces cerevisiae reveals...
Formation of complex inorganic structures is widespread in nature. Diatoms create intricately patterned cell walls silicon that are a biomimetic model for design and generation three-dimensional silica nanostructures. To date, only relatively simple can be generated vitro through manipulation known diatom phosphoproteins (silaffins) long-chain polyamines. Here, we report the use genome-wide transcriptome analyses marine Thalassiosira pseudonana to identify additional candidate gene products...
The important role that cilia and flagella play in human disease creates an urgent need to identify genes involved ciliary assembly function. strong specific induction of flagellar-coding during flagellar regeneration Chlamydomonas reinhardtii suggests transcriptional profiling such cells would reveal new flagella-related genes. We have conducted a genome-wide analysis RNA transcript levels by using maskless photolithography method-produced DNA oligonucleotide microarrays with unique probe...
SpBase is a system of databases focused on the genomic information from sea urchins and related echinoderms. It exposed to public through web site served with open source software (http://spbase.org/). The enterprise was undertaken provide an easily used collection directly support experimental work these useful research models in cell developmental biology. emerges draft sequence purple urchin, Strongylocentrotus purpuratus includes data resource descriptions for other members echinoderm...
Using a maskless photolithography method, we produced DNA oligonucleotide microarrays with probe sequences tiled throughout the genome of plant Arabidopsis thaliana. RNA expression was determined for complete nuclear, mitochondrial, and chloroplast genomes by tiling 5 million 36-mer probes. These probes were hybridized to labeled mRNA isolated from liquid grown T87 cells, an undifferentiated cell culture line. Transcripts detected at least 60% nearly 26,330 annotated genes, which included...
Abstract The Pacific oyster Crassostrea gigas, a widely cultivated marine bivalve mollusc, is becoming genetically and genomically enabled model for highly fecund metazoans with complex life-histories. A genome sequence available the oyster, as are first-generation, low-density, linkage gene-centromere maps mostly constructed from microsatellite DNA markers. Here, higher density, second-generation, more than 1100 coding (exonic) single-nucleotide polymorphisms (SNPs), well 66 previously...
The sea urchin Strongylocentrotus purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined complete repertoire genes expressed in S. embryo, up to late gastrula stage, by means high-resolution custom tiling arrays covering whole genome. detected spliced structures even known be at low levels only few cells. At least 11,000 12,000 are used embryogenesis. These include most encoding transcription factors and signaling proteins, as...
Abstract Background Non-coding microRNAs (miRNAs) are key regulators of gene expression in eukaryotes. Insect miRNAs help regulate the levels proteins involved with development, metabolism, and other life history traits. The recently sequenced honey bee genome provides an opportunity to detect novel both this species others, begin infer roles development. Results Three independent computational surveys assembled identified a total 65 non-redundant candidate miRNAs, several which appear have...
Fredrickson et al. [Fredrickson BL, (2013) Proc Natl Acad Sci USA 110(33):13684-13689] claimed to have observed significant differences in gene expression related hedonic and eudaimonic dimensions of well-being. Having closely examined both their claims data, we draw substantially different conclusions. After identifying some important conceptual methodological flaws argument, report the results a series reanalyses dataset. We first applied variety exploratory confirmatory factor analysis...
Noncoding RNAs (ncRNAs) perform essential cellular tasks and play key regulatory roles in all organisms. Although several new ncRNAs yeast were recently discovered by individual studies, to our knowledge no comprehensive empirical search has been conducted. We demonstrate a powerful versatile method for global identification of previously undescribed modulating an RNA processing pathway through the depletion ribonucleoprotein enzyme component, monitoring differential transcriptional...
Cis -regulatory modules (CRMs) function by binding sequence specific transcription factors, but the relationship between in vivo physical and regulatory capacity of factor-bound DNA elements remains uncertain. We investigate this for well-studied Twist factor Drosophila melanogaster embryos analyzing genome-wide occupancy testing functional significance occupied regions motifs within regions. ChIP-seq data efficiently identified previously studied Twist-dependent CRMs robustly predicted new...
The self-assembly of well-characterized, nanometer-size Au clusters into ordered monolayer arrays spanning several microns has been achieved. Techniques to insert molecular wires link adjacent in the self-assembled array have also developed. ‘‘Unit cell’’ nanostructures formed from individual supported on a film double-ended thiol molecule p-xylene-α,α′- dithiol show evidence for reproducible single electron effects at room temperature when studied by scanning tunneling microscopy. From...
Antisense transcription is a pervasive phenomenon, but its source and functional significance largely unknown. We took an expression-based approach to explore microRNA (miRNA)-related antisense by computational analyses of published whole-genome tiling microarray transcriptome deep sequencing small RNA (smRNA) data. Statistical support for greater abundance signatures smRNAs was observed miRNA targets than paralogous genes with no cleavage site. were also found associated MIRNA genes. This...
Biologically significant information can be revealed by modeling large-scale protein interaction data using graph theory based network analysis techniques. However, the methods that are currently being used draw conclusions about global features of from local connectivity data. A more systematic approach would to define quantities measure (1) how strongly a ties with other parts and (2) significantly an contributes integrity network, connect them phenotype sources. In this paper, we...
With its unique ability to produce high-voltage electric discharges in excess of 600 volts, the South American strong voltage eel (Electrophorus electricus) has played an important role history science. Remarkably little is understood about molecular nature organs. We present in-depth analysis genome E. electricus, including transcriptomes eight mature tissues: brain, spinal cord, kidney, heart, skeletal muscle, Sachs’ organ, main and Hunter’s organ. A gene set enrichment based on ontology...
We present a general Green's-function-based method that can be used to describe the electrical transport properties of junctions with arbitrary coupling strength involving superconductors unconventional pairing symmetry and band structures. Our correctly takes into account midgap surface states arise in $d$-wave due sign change order parameter. In tunneling limit, we simple expressions effect on dc ac components Josephson current including their temperature dependence. A numerical example is...
The cWINNOWER algorithm detects fuzzy motifs in DNA sequences rich proteinbinding signals. A signal is defined as any short nucleotide pattern having up to d mutations differing from a motif of length l. finds such if clique consisting suffciently large number mutated copies the (i.e., signals) present sequence. substantially improves sensitivity winnower method Pevzner and Sze by imposing consensus constraint, enabling it detect much weaker We studied minimum detectable size q c function...
To determine whether a tricrystal ring [J. R. Kirtley et al., Phys. Rev. Lett. 76, 1336 (1996)] is 0 or \ensuremath{\pi} ring, the following expression has been used for critical current between two d-wave superconductors with misorientation angles ${\mathrm{\ensuremath{\theta}}}_{1}$ and ${\mathrm{\ensuremath{\theta}}}_{2}$: ${\mathrm{I}}_{\mathrm{c}}$=${\mathrm{I}}_{0}$cos 2${\mathrm{\ensuremath{\theta}}}_{1}$cos 2${\mathrm{\ensuremath{\theta}}}_{2}$. We show that recently predicted midgap...