Agilent Technologies

About: Agilent Technologies is a company organization based out in Santa Clara, California, United States. It is known for research contribution in the topics: Signal & Mass spectrometry. The organization has 7398 authors who have published 11518 publications receiving 262410 citations. The organization is also known as: Agilent Technologies, Inc..

Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data

Abstract: Background: MicroRNAs (miRNAs) are short, non-coding RNA regulators of protein coding genes. miRNAs play a very important role in diverse biological processes and various diseases. Many algorithms are able to predict miRNA genes and their targets, but their transcription regulation is still under investigation. It is generally believed that intragenic miRNAs (located in introns or exons of protein coding genes) are co-transcribed with their host genes and most intergenic miRNAs transcribed from their own RNA polymerase II (Pol II) promoter. However, the length of the primary transcripts and promoter organization is currently unknown. Methodology: We performed Pol II chromatin immunoprecipitation (ChIP)-chip using a custom array surrounding regions of known miRNA genes. To identify the true core transcription start sites of the miRNA genes we developed a new tool (CPPP). We showed that miRNA genes can be transcribed from promoters located several kilobases away and that their promoters share the same general features as those of protein coding genes. Finally, we found evidence that as many as 26% of the intragenic miRNAs may be transcribed from their own unique promoters. Conclusion: miRNA promoters have similar features to those of protein coding genes, but miRNA transcript organization is more complex.

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips

Abstract: Development of cheap, high-throughput and reliable gene synthesis methods will broadly stimulate progress in biology and biotechnology. Currently, the reliance on column-synthesized oligonucleotides as a source of DNA limits further cost reductions in gene synthesis. Oligonucleotides from DNA microchips can reduce costs by at least an order of magnitude, yet efforts to scale their use have been largely unsuccessful owing to the high error rates and complexity of the oligonucleotide mixtures. Here we use high-fidelity DNA microchips, selective oligonucleotide pool amplification, optimized gene assembly protocols and enzymatic error correction to develop a method for highly parallel gene synthesis. We tested our approach by assembling 47 genes, including 42 challenging therapeutic antibody sequences, encoding a total of ∼35 kilobase pairs of DNA. These assemblies were performed from a complex background containing 13,000 oligonucleotides encoding ∼2.5 megabases of DNA, which is at least 50 times larger than in previously published attempts.

Surface Chemistry and Electrical Properties of Germanium Nanowires

Abstract: Germanium nanowires with p- and n-dopants were synthesized by chemical vapor deposition and used to construct complementary field effect transistors . Electrical transport and x-ray photoelectron spectroscopy data are correlated to glean the effects of Ge surface chemistry to the electrical characteristics of GeNWs. Large hysteresis due to water molecules strongly bound to GeO2 on GeNWs is revealed. Different oxidation behavior and hysteresis characteristics and opposite band bending due to Fermi level pinning by interface states between Ge and surface oxides are observed for p- and n-type GeNWs. Vacuum annealing above 400C is used to remove surface oxides and eliminate hysteresis in GeNW FETs. High-k dielectric HfO2 films grown on clean GeNW surfaces by atomic layer deposition (ALD) using an alkylamide precursor is effective serving as the first layer of surface passivation. Lastly, the depletion length along the radial direction of nanowires is evaluated. The result suggests that surface effects could be dominant over the bulk properties of small diameter wires.

Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning.

Abstract: Sonic hedgehog (Shh) acts as a morphogen to mediate the specification of distinct cell identities in the ventral neural tube through a Gli-mediated (Gli1-3) transcriptional network. Identifying Gli targets in a systematic fashion is central to the understanding of the action of Shh. We examined this issue in differentiating neural progenitors in mouse. An epitope-tagged Gli-activator protein was used to directly isolate cis-regulatory sequences by chromatin immunoprecipitation (ChIP). ChIP products were then used to screen custom genomic tiling arrays of putative Hedgehog (Hh) targets predicted from transcriptional profiling studies, surveying 50-150 kb of non-transcribed sequence for each candidate. In addition to identifying expected Gli-target sites, the data predicted a number of unreported direct targets of Shh action. Transgenic analysis of binding regions in Nkx2.2, Nkx2.1 (Titf1) and Rab34 established these as direct Hh targets. These data also facilitated the generation of an algorithm that improved in silico predictions of Hh target genes. Together, these approaches provide significant new insights into both tissue-specific and general transcriptional targets in a crucial Shh-mediated patterning process.

Method of making tunable thin film acoustic resonators

Abstract: An acoustical resonator comprising top and bottom electrodes that sandwich a PZ layer. The resonance frequency of the acoustical resonator may be adjusted after fabrication by utilizing heating elements included in the acoustical resonator and/or by adjusting the thickness of a tuning layer. In the preferred embodiment of the present invention, the electrodes comprise Mo layers. One embodiment of the present invention is constructed on a Si3 N4 membrane. A second embodiment of the present invention is constructed such that it is suspended over a substrate on metallic columns. In the preferred embodiment of the present invention, the electrodes are deposited by a method that minimizes the stress in the electrodes.