113 research outputs found
Drug Discov Today
RNA interference (RNAi) describes the post-transcriptional silencing of gene expression that occurs in response to the introduction of double-stranded RNA into cells. Application of RNAi in experimental systems has provided a great leap forward in the elucidation of gene function. To facilitate large-scale functional genomics studies using RNAi, several high throughput approaches have been developed based on microarray or microwell assays. Recent establishment of large libraries of RNAi reagents combined with a variety of detection assays further opens the door for genome-wide screens of gene function in mammalian cells. The review provides a comprehensive overview on current RNA interference-based high throughput genomic technologies. The cell array- and microwell plate-based loss-of-function cell assays are presented
LINC00507 Is Specifically Expressed in the Primate Cortex and Has Age-Dependent Expression Patterns
Over the past decade, there has been an increase in the appreciation of the role of non-coding RNA in the development of organism phenotype. It is possible to divide the non-coding elements of the transcriptome into three categories: short non-coding RNAs, circular RNAs and long non-coding RNAs. Long non-coding RNAs are those transcripts that are greater than 200 nts in length and lack any significant open reading frames that produce proteins greater then 100 amino acids. Long intervening non-coding RNAs (lincRNAs) are a subclass of long non-coding RNAs. In contrast to protein coding RNAs, lincRNAs are expressed in a more tissue- and species-specific manner. In particular, many lincRNAs are only conserved amongst higher primates. This coupled with the propensity of many lincRNAs to be expressed in the brain, suggests that they are in fact one of the major drivers of organism complexity. We analysed 39 lincRNAs that are expressed in the frontal cortex and identified LINC00507 as being expressed in a cortex-specific manner in non-human primates and humans. The expression patterns of LINC00507 appear to be age-dependent, suggesting it may be involved in brain development of higher primates. Moreover, the analysis of LINC00507 potential to bind ribosomes revealed that this previously identified non-coding transcript may harbour a micropeptide
Towards Quantum Sensing of Chiral-Induced Spin Selectivity: Probing Donor-Bridge-Acceptor Molecules with NV Centers in Diamond
Photoexcitable donor-bridge-acceptor (D-B-A) molecules that support
intramolecular charge transfer are ideal platforms to probe the influence of
chiral-induced spin selectivity (CISS) in electron transfer and resulting
radical pairs. In particular, the extent to which CISS influences spin
polarization or spin coherence in the initial state of spin-correlated radical
pairs following charge transfer through a chiral bridge remains an open
question. Here, we introduce a quantum sensing scheme to measure directly the
hypothesized spin polarization in radical pairs using shallow nitrogen-vacancy
(NV) centers in diamond at the single- to few-molecule level. Importantly, we
highlight the perturbative nature of the electron spin-spin dipolar coupling
within the radical pair, and demonstrate how Lee-Goldburg decoupling can
preserve spin polarization in D-B-A molecules for enantioselective detection by
a single NV center. The proposed measurements will provide fresh insight into
spin selectivity in electron transfer reactions.Comment: 7 pages and 4 pages appendix including an extensive description of
the initial spin state of photo-generated radical pair
LNA-modified oligodeoxynucleotide hybridization with DNA microarrays printed on nanoporous membrane slides
We report a robust method for the detection of hybridization events using a microarray-based assay on a nanoporous membrane platform. The technique is characterized by a hybridization time of only 1 hour and uses Cy5- labeled, 7-mer oligodeoxynucleotide probes modified with locked nucleic acid (LNA) nucleotides. We show that the volume of the DNA spotted onto a nanomembrane can be reduced to ∼4 nL with detectable signal intensity. Moreover, the amount of the DNA target could be reduced to 4 fmol. The described approach could dramatically increase the throughput of techniques based on sequencing by hybridization, such as oligofingerprinting, by decreasing the total number of probes that are needed for analysis of large clone sets and reduction of the sample/reagent consumption. The method is particularly advantageous when numerous hybridization-based assays must be performed for characterization of sample sets of 100,000 or more
LINC00507 Is Specifically Expressed in the Primate Cortex and Has Age-Dependent Expression Patterns
General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. Abstract Over the past decade, there has been an increase in the appreciation of the role of non-coding RNA in the development of organism phenotype. It is possible to divide the non-coding elements of the transcriptome into three categories: short non-coding RNAs, circular RNAs and long non-coding RNAs. Long non-coding RNAs are those transcripts that are greater than 200 nts in length and lack any significant open reading frames that produce proteins greater then 100 amino acids. Long intervening non-coding RNAs (lincRNAs) are a subclass of long non-coding RNAs. In contrast to protein coding RNAs, lincRNAs are expressed in a more tissue-and species-specific manner. In particular, many lincRNAs are only conserved amongst higher primates. This coupled with the propensity of many lincRNAs to be expressed in the brain, suggests that they are in fact one of the major drivers of organism complexity. We analysed 39 lincRNAs that are expressed in the frontal cortex and identified LINC00507 as being expressed in a cortex-specific manner in non-human primates and humans. The expression patterns of LINC00507 appear to be age-dependent, suggesting it may be involved in brain development of higher primates. Moreover, the analysis of LINC00507 potential to bind ribosomes revealed that this previously identified non-coding transcript may harbour a micropeptide
Single Nitrogen-Vacancy-NMR of Amine-Functionalized Diamond Surfaces
Nuclear magnetic resonance (NMR) imaging with shallow nitrogen-vacancy (NV)
centers in diamond offers an exciting route toward sensitive and localized
chemical characterization at the nanoscale. Remarkable progress has been made
to combat the degradation in coherence time and stability suffered by
near-surface NV centers using suitable chemical surface termination. However,
approaches that also enable robust control over adsorbed molecule density,
orientation, and binding configuration are needed. We demonstrate a diamond
surface preparation for mixed nitrogen- and oxygen-termination that
simultaneously improves NV center coherence times for emitters <10-nm-deep and
enables direct and recyclable chemical functionalization via amine-reactive
crosslinking. Using this approach, we probe single NV centers embedded in
nanopillar waveguides to perform NMR sensing of covalently
bound trifluoromethyl tags in the ca. 50-100 molecule regime. This work
signifies an important step toward nuclear spin localization and structure
interrogation at the single-molecule level.Comment: 21 pages and 16 pages supporting informatio
Diamond surface engineering for molecular sensing with nitrogen-vacancy centers
Quantum sensing using optically addressable atomic-scale defects, such as the
nitrogen--vacancy (NV) center in diamond, provides new opportunities for
sensitive and highly localized characterization of chemical functionality.
Notably, near-surface defects facilitate detection of the minute magnetic
fields generated by nuclear or electron spins outside of the diamond crystal,
such as those in chemisorbed and physisorbed molecules. However, the promise of
NV centers is hindered by a severe degradation of critical sensor properties,
namely charge stability and spin coherence, near surfaces (< ca. 10 nm deep).
Moreover, applications in the chemical sciences require methods for covalent
bonding of target molecules to diamond with robust control over density,
orientation, and binding configuration. This forward-looking Review provides a
survey of the rapidly converging fields of diamond surface science and
NV-center physics, highlighting their combined potential for quantum sensing of
molecules. We outline the diamond surface properties that are advantageous for
NV-sensing applications, and discuss strategies to mitigate deleterious effects
while simultaneously providing avenues for chemical attachment. Finally, we
present an outlook on emerging applications in which the unprecedented
sensitivity and spatial resolution of NV-based sensing could provide unique
insight into chemically functionalized surfaces at the single-molecule level.Comment: Review paper, 36 page
Identification of Specific Circular RNA Expression Patterns and MicroRNA Interaction Networks in Mesial Temporal Lobe Epilepsy
Circular RNAs (circRNAs) regulate mRNA translation by binding to microRNAs (miRNAs), and their expression is altered in diverse disorders, including cancer, cardiovascular disease, and Parkinson’s disease. Here, we compare circRNA expression patterns in the temporal cortex and hippocampus of patients with pharmacoresistant mesial temporal lobe epilepsy (MTLE) and healthy controls. Nine circRNAs showed significant differential expression, including circRNA-HOMER1, which is expressed in synapses. Further, we identified miRNA binding sites within the sequences of differentially expressed (DE) circRNAs; expression levels of mRNAs correlated with changes in complementary miRNAs. Gene set enrichment analysis of mRNA targets revealed functions in heterocyclic compound binding, regulation of transcription, and signal transduction, which maintain the structure and function of hippocampal neurons. The circRNA–miRNA–mRNA interaction networks illuminate the molecular changes in MTLE, which may be pathogenic or an effect of the disease or treatments and suggests that DE circRNAs and associated miRNAs may be novel therapeutic targets
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