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86 results for “HTT”
Allele-specific quantitation of ATXN3 and HTT transcripts in polyQ disease models.
<p>Precise values obtained during the research that led to the publishing of scientific paper entitled 'Allele-specific quantitation of ATXN3 and HTT transcripts in polyQ disease models'.</p>
Full-length HTT purification from HEK293T suspension culture using baculovirus transduction protocol for over-expression 2018/04/02
<p>Structure-function open lab notebook project. Full-length HTT purification from HEK293T suspension culture using baculovirus transduction protocol for over-expression 2018/04/02.</p>
Investigating huntingtin DNA binding – plasmid EMSA with full-length HTT Q23/Q46
<p>Huntingtin structure-function open lab notebook.</p> <p> </p> <p>NB: plasmid concentration should read 0.5 mg/mL not 0.5 mg/uL.</p>
miRNA counts identified by RNA seq in the caudate nucleus of patients neuropathologically diagnosed with late-onset Alzheimer's disease (non-carriers and carriers of intermediate expansions in the HTT gene) and healthy subjects.
<p>These data include the raw miRNA counts identified by RNA-seq in <em>post mortem</em> caudate nucleus samples. Samples with identifier <strong>A</strong> belong to patients with a neuropathological diagnosis of late-onset Alzheimer's disease. Group <strong>B</strong> samples belong to patients with the same neuropathological diagnosis, but carrying CAG expansions in the intermediate range (27-35 CAG) in the <em>HTT</em> gene. Finally, group <strong>C </strong>samples belong to healthy subjects without neuropathological diagnosis. </p> <p> </p>
Large-scale full-length HTT Q19 and Q42 purification from HEK293T – 2018/04/16
<p>Huntingtin structure-function open lab notebook project. Large-scale full-length HTT Q19 and Q42 purification from HEK293T – 2018/04/16.</p>
Large-scale full-length HTT Q23 purification from HEK293T – 2018/04/30
<p>Huntingtin structure-function open lab notebook project. Large-scale full-length HTT Q23 purification from HEK293T – 2018/04/30.</p>
Optimisation of HTT-HAP40 purification using heparin affinity chromatography (2019/01/14)
<p><strong>Project</strong> - Huntingtin structure-function open lab notebook. </p> <p><strong>Experiment</strong> - Optimisation of HTT-HAP40 purification using heparin affinity chromatography.</p> <p><strong>Aims</strong> - The current protocol for HTT and HTT-HAP40 purification I am using requires a long incubation of clarified cell lysate with FLAG resin. To potentially improve yields and sample quality, it would perhaps be beneficial to have a quick heparin resin purification step prior to FLAG binding which may also remove contaminating nucleic acid material. To test this hypothesis, small-scale purification of Q23 HTT-HAP40 samples in different buffer systems will be carried out using heparin and FLAG affinity chromatography. </p>
Optimisation of HTT-HAP40 purification using heparin affinity chromatography - 2019/01/29
<p><strong>Project: </strong>Biophysical investigation of purified HTT protein samples</p> <p><strong>Experiment: </strong>Optimisation of HTT-HAP40 purification using heparin affinity chromatography</p> <p><strong>Date completed:­ </strong>2019/01/29</p> <p><strong>Rationale: </strong>The current protocol for HTT and HTT-HAP40 purification I am using requires a long incubation of clarified cell lysate with FLAG resin. To potentially improve yields and sample quality, it would perhaps be beneficial to have a quick heparin resin purification step prior to FLAG binding which may also remove contaminating nucleic acid material. To test this hypothesis, small-scale purification of Q23 HTT-HAP40 samples in different buffer systems were conducted using heparin and FLAG affinity chromatography which showed the sample bound heparin resin – see <a href="https://zenodo.org/record/2553669">https://zenodo.org/record/2553669</a>. Now this need to be scaled up and tested more stringently. </p>
Coexpression and purification of HTT domains with HAP40 - 2018/12/03
<p><strong>Project: </strong>High resolution structural analysis of purified HTT proteins</p> <p><strong>Experiment: </strong>Coexpression and purification of HTT domains with HAP40</p> <p><strong>Date completed:­ </strong>2018/12/03</p> <p><strong>Rationale: </strong>HTT domain fragments are challenging to express and purify. However, the full-length protein sample was shown to have superior biophysical characteristics when coexpressed and purified with HAP40. As HAP40 has an extensive interaction surface with HTT, it could be possible to copurify domain fragments of HTT with HAP40, stabilizing the individual HEAT domains. </p>
Preparation of dephosphorylated HTT samples for cryoEM analysis 2019/03/20
<p><strong>Project: </strong>High resolution structural analysis of purified HTT samples</p> <p><strong>Experiment: </strong>Preparation of dephosphorylated HTT samples for cryoEM analysis</p> <p><strong>Date completed:­ </strong>2019/03/20</p> <p><strong>Rationale: </strong>We now have a good understanding of the global structure of HTT when in complex with HAP40 and our MALS and SAXS data suggest that apo HTT is likely self-associating and heterogenous in nature, despite high levels of purity. Dephosphorylating HTT from Sf9 cell production could alter its global structure sufficiently to allow high resolution structure determination by cryoEM. </p>
Optimisation of HTT-HAP40 purification using heparin affinity chromatography - 2019/04/02
<p><strong>Project: </strong>Biophysical investigation of purified HTT protein samples</p> <p><strong>Experiment: </strong>Optimisation of HTT-HAP40 purification using heparin affinity chromatography</p> <p><strong>Date completed:­ </strong>2019/04/02</p> <p><strong>Rationale: </strong>Previous attempts to generate a much purer and homogenous HTT-HAP40 sample showed that the complex can bind heparin resin. In addition, I will incorporate helpful suggestions from scientists at the CHDI Palm Springs meeting full-length HTT research breakout group i.e. ATP wash to remove HSP proteins. The experiment will include 3 affinity chromatography steps with FLAG, heparin and NiNTA resin and finally a gel filtration step. </p>
Cloning and test expression of HTT fragment clones - 2019/02/28
<p><strong>Project: </strong>High resolution structural analysis of purified HTT proteins</p> <p><strong>Experiment: </strong>Cloning and test expression of HTT fragment clones</p> <p><strong>Date completed:­ </strong>2019/02/28</p> <p><strong>Rationale: </strong>I aim to complement our previous work on purifying stable regions of huntingtin by cloning further regions of huntingtin corresponding to discrete HEAT repeats for eukaryotic expression. Constructs will initially be screened by BVES in insect sf9 cells. High quality constructs will undergo extensive crystallization experiments and structure determination by X-ray crystallography using well established high-throughput and systematic protocols in place at the SGC. Any solved structures may allow generation of a pseudoatomic resolution (<4 Å) model of the HTT protein using the cryoEM model as a guide. </p>
Large-scale purification of HTT domain constructs 2019/04/01
<p><strong>Project: </strong>High resolution structural analysis of purified HTT samples</p> <p><strong>Experiment: </strong>Large-scale purification of HTT domain constructs</p> <p><strong>Date completed:­ </strong>2019/04/01</p> <p><strong>Rationale: </strong>Domain fragments of the huntingtin protein are useful reagents for examining protein-protein interaction characteristics of huntingtin and to map interaction interfaces. Stable, monodisperse and pure samples may also be amenable to high resolution structure solution by X-ray crystallography. Previously huntingtin fragments were cloned and screened for expression in small-scale (3 mL) culture experiments. Positive hits were scaled for production as detailed in the table on the next page. All previous work is described in this post:<a href="https://zenodo.org/record/2600051#.XKU89aeZPOQ">https://zenodo.org/record/2600051#.XKU89aeZPOQ</a>.</p>
Analysis of dephosphorylated HTT samples for cryoEM analysis and further sample preparation 2019/04/15
<p><strong>Project: </strong>High resolution structural analysis of purified HTT samples</p> <p><strong>Experiment: </strong>Analysis of dephosphorylated HTT samples for cryoEM analysis and further sample preparation</p> <p><strong>Date completed:­ </strong>2019/04/15</p> <p><strong>Rationale: </strong>We now have a good understanding of the global structure of HTT when in complex with HAP40 and our MALS and SAXS data suggest that apo HTT is likely self-associating and heterogenous in nature, despite high levels of purity. Dephosphorylating HTT from Sf9 cell production could alter its global structure sufficiently to allow high resolution structure determination by cryoEM. </p>
Coexpression and purification of HTT and HTT-HAP40 with NEDD4L and HAP1 2019/05/02
<p><strong>Project: </strong>Biophysical investigation of purified HTT protein and protein complex samples</p> <p><strong>Experiment: </strong>Coexpression and purification of HTT and HTT-HAP40 with NEDD4L and HAP1</p> <p><strong>Date completed:­ </strong>2019/05/02</p> <p><strong>Rationale: </strong>HAP1 and NEDD4L have been suggested as high probability interaction partners of HTT although it is unclear if they interact with HTT or HTT-HAP40. Coexpression of the constructs was conducted in baculoviral expression system (Sf9 cells) to determine if they copurify with HTT or HTT-HAP40. </p>
Analysis of dephosphorylated HTT samples by cryoEM analysis 2019/05/01
<p><strong>Project: </strong>High resolution structural analysis of purified HTT samples</p> <p><strong>Experiment: </strong>Analysis of dephosphorylated HTT samples by cryoEM analysis </p> <p><strong>Date completed:­ </strong>2019/05/01</p> <p><strong>Rationale: </strong>We now have a good understanding of the global structure of HTT when in complex with HAP40 and our MALS and SAXS data suggest that apo HTT is likely self-associating and heterogenous in nature, despite high levels of purity. Dephosphorylating HTT from Sf9 cell production could alter its global structure sufficiently to allow high resolution structure determination by cryoEM. </p> <p> </p>
Purification of HTT mutant samples 2019/05/17
<p><strong>Project: </strong>Investigation of purified HTT protein samples</p> <p><strong>Experiment: </strong>Purification of HTT mutant samples</p> <p><strong>Date completed:­ </strong>2019/05/27</p> <p><strong>Rationale: </strong>To assess HTT function <em>in vitro</em></p>
Large-scale stringent purification of HTT-HAP40 using heparin affinity chromatography 2019/05/12
<p><strong>Project: </strong>Biophysical investigation of purified HTT protein samples</p> <p><strong>Experiment: </strong>Large-scale stringent purification of HTT-HAP40 using heparin affinity chromatography</p> <p><strong>Date completed:­ </strong>2019/05/12</p> <p><strong>Rationale: </strong>Previous attempts to generate a much purer and homogenous HTT-HAP40 sample showed that the complex can bind heparin resin. In small-scale experiment, I also incorporated helpful suggestions from scientists at the CHDI Palm Springs meeting full-length HTT research breakout group i.e. ATP wash to remove HSP proteins. The experiment included 3 affinity chromatography steps with FLAG, heparin and NiNTA resin and finally a gel filtration step and yielded a highly pure HTT-HAP40 sample: <a href="https://zenodo.org/record/2628064">https://zenodo.org/record/2628064</a>. </p>
Large-scale stringent purification of Q23 HTT and HTT-HAP40 using heparin affinity chromatography 2019/05/22
<p><strong>Project: </strong>Biophysical investigation of purified HTT protein samples</p> <p><strong>Experiment: </strong>Large-scale stringent purification of Q23 HTT and HTT-HAP40 using heparin affinity chromatography</p> <p><strong>Date completed:­ </strong>2019/05/22</p> <p><strong>Rationale: </strong>Previous attempts to generate a much purer and homogenous HTT-HAP40 sample showed that the complex can bind heparin resin. In small-scale experiment, I also incorporated helpful suggestions from scientists at the CHDI Palm Springs meeting full-length HTT research breakout group i.e. ATP wash to remove HSP proteins. The experiment included 3 affinity chromatography steps with FLAG, heparin and NiNTA resin and finally a gel filtration step and yielded a highly pure HTT-HAP40 sample: https://zenodo.org/record/3234174.I now want to try this purification with apo HTT. </p>
Purification of the HTT C-HEAT domain (2088-3144)
<p>The purification of HTT fragments is a useful approach to learn more about the function of huntingtin in the cell. By obtaining soluble and monomeric samples of HTT domains namely the HTT C-HEAT, N-HEAT and bridge domains, specific protein-protein interactions can be studied. Furthermore, domains of HTT in soluble monomeric form could enable crystallization studies. </p> <p>Expression and purification of these fragments can be found on these posts <a href="https://zenodo.org/record/2600051#.XKU89aeZPOQ">https://zenodo.org/record/2600051#.XKU89aeZPOQ</a> and <a href="https://zenodo.org/record/2628060#.XULMtnspDb0">https://zenodo.org/record/2628060#.XULMtnspDb0</a> (performed by Dr. Rachel Harding). The latest post shows the successful purification of a monomeric and mono disperse sample of the HTT C-HEAT domain. The results here presented are a follow up of those experiments and aim to further characterize the HTT C-HEAT domain as well as explore strategies to improve buffer conditions for crystallization purposes.</p>
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