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Gao S.S.,Rice University | Yuan T.,BCM | Xia A.,Stanford University | Raphael P.,Stanford University | And 3 more authors.
Progress in Biomedical Optics and Imaging - Proceedings of SPIE | Year: 2011

Current medical imaging modalities, such as MRI and CT, do not provide high enough resolution to detect many changes within the cochlea that cause hearing loss. We sought to develop the technique of optical coherence tomography (OCT) to image the cochlea noninvasively and within its native environment. We used spectral domain OCT with 950 nm as the center wavelength and a bandwidth of ~100 nm to image freshly excised normal mouse cochlea at different developmental ages. The OCT system has an axial resolution of ~4 μm (in air) and a lateral resolution of ~10 μm. When we imaged normal adult mouse cochleae through the round window membrane, Reissner's membrane, the basilar membrane, the tectorial membrane, the spiral ligament, the spiral limbus, and the modiolus could be clearly identified. When we imaged intact adult cochleae, we were able to image through ~130 μm of bone and tissue to see up to a depth of ~600 μm, and all of the previously identified structures were still visible. Imaging of early postnatal mice during the timeline of cochlear development permitted visualization of the expected structural differences from adult cochleae. Therefore, we conclude that spectral domain OCT is an effective technique for noninvasive imaging of the murine cochlea. © 2011 Copyright SPIE - The International Society for Optical Engineering. Source

Vanderploeg J.,UTMB | Antunano M.,FAA CAMI | Bagian J.,Hines Veterans Administration Hospital | Bopp E.,Wyle | And 22 more authors.
Aviation Space and Environmental Medicine | Year: 2011

As directed by the Council of the Aerospace Medical Association, the Commercial Spacefl ight Working Group has developed the following position paper concerning medical issues for commercial suborbital spacefl ight crewmembers. This position paper has been approved by the AsMA Council to become a policy of the AsMA. Source

IP6, the natural inhibitor or ligand of Clostridium difficile's toxin, binds weakly to the toxin. This results in the toxin remaining active (center figure). Changing a single atom in IP6 to form IP6(S) results in stronger binding to the toxin and its inactivation (left side figure). Credit: T. Savidge (BCM); K. Prince (TCH) Infections with bacterium Clostridium difficile have rapidly become a significant medical problem in hospitals and long-term care facilities. The bacteria cause diarrhea and life-threatening inflammation of the colon by producing toxins that kill the endothelial cells that form the lining of the gut. Although a natural inhibitor of these toxins, called InsP6, works in the test tube, it is not very efficient when administered orally. Traditional methods to optimize InsP6 have until now not been successful, but researchers at Baylor College of Medicine have discovered that changing one atom in InsP6 can increase its ability to neutralize the toxins by 26-fold. The results appear in Science Advances. "The toxins, called TcdA and TcdB, are very large molecules that kill the cells very efficiently," said Dr. Tor Savidge, associate professor of pathology and immunology and of pediatrics, director of the Savidge Lab at the Texas Children's Microbiome Center and senior author of the paper. "It's like delivering a warhead into the cell. The toxins bind to the cell and the cell internalizes them in a sack of cell membrane called endosome. Not all of the toxin will exit this sack to kill the cell, just the little warhead pokes its head out. Another section of the toxin senses when the warhead is outside the sack and cleaves it. The warhead is released, interferes with basic functions and kills the cell," said Savidge. To neutralize the toxins, the researchers targeted the section that senses when the warhead is inside the cell, called allosteric modulator. "The strategy we have tried is to make the toxin 'think,' before it binds to and enters the cell, that the warhead is ready to be released, so it releases it prematurely," said Savidge. When the warhead is released outside the cell, it is neutralized. InsP6, the toxins' natural inhibitor, works this way, but is not very efficient. Finding molecules that would bind to the allosteric modulator and trigger the premature release of the warhead involved analyzing and testing half a million molecules listed in large databases. Dr. Numan Oezguen, a member of the Savidge Lab, used virtual drug screening to sift through the databases to identify candidate molecules that most likely would bind to the allosteric modulator. One of his screening strategies consists of creating virtual 3-D structures of the molecules, projecting them on a large screen and using 3-D glasses to determine the most likely interactions between molecules. The molecules whose virtual analysis suggested they would bind to the allosteric modulator were then tested in the lab. "We found that allosteric mechanisms are very complicated," said Savidge. "You can find something that binds and you think, well, this is probably a good candidate for this, but it's not right. It binds, but it doesn't trigger the premature release of the warhead." Far from discouraging their efforts, the results motivated the researchers to better understand what makes interactions between molecules stronger or weaker. Their comprehensive analysis of numerous molecules provided insights into how water contributes to molecular interactions, in particular those involving hydrogen bonds, one of the most important bonds between molecules. The roles of water and hydrogen bonding had not been considered in this way before. "When you take water into consideration you need to acknowledge that it can form hydrogen bonds, which may or may not compete or interfere with those formed between other molecules such as C. difficile toxins and their inhibitors, which interact in the gut, surrounded by water," said Savidge. "Before we considered the role of water, the predominant idea was that to strengthen the interaction between molecules the ability to form hydrogen bonds had to be made as strong as possible in the drug. It turns out this is not the case," said Oezguen. Many times drugs designed to be able to make strong hydrogen bonds bind poorly to their targets. The researchers discovered that to enhance the binding of a drug to its target, both sides of the hydrogen bond, the side on the drug and the one on the target, have to have either significantly stronger or significantly weaker hydrogen bonding capabilities. On the other hand, a mixed strong-weak hydrogen bond pairing decreases the overall binding of the drug to its target, in some cases by 3 million fold. The decrease in binding is the result, the researchers propose, of water molecules forming hydrogen bonds with the drug and its target, therefore preventing the drug and the target from forming hydrogen bonds between them. With all this information in hand, the researchers proceeded to make chemical changes in the InsP6 inhibitor to improve its hydrogen bonding capabilities with C. difficile toxins. One of the modifications, changing one single atom in InsP6, strengthened InsP6 binding to the allosteric modulator by 26-fold. This observation builds on a report published by Savidge in Science last year exploring the role of water interactions in the origin of enzymatic catalytic power. Plans are currently underway to exploit these fundamentally new concepts in the precision design of future therapeutic applications. Explore further: Researchers claim to have discovered why warm water freezes faster than cooler water More information: Regulation of protein-ligand binding affinity by hydrogen bond pairing, Science Advances, dx.doi.org/10.1126/sciadv.1501240

Yamamoto S.,Baylor College of Medicine | Yamamoto S.,Jan and Dan Duncan Neurological Research Institute | Jaiswal M.,BCM | Jaiswal M.,Howard Hughes Medical Institute | And 52 more authors.
Cell | Year: 2014

Invertebrate model systems are powerful tools for studying human disease owing to their genetic tractability and ease of screening. We conducted a mosaic genetic screen of lethal mutations on the Drosophila X chromosome to identify genes required for the development, function, and maintenance of the nervous system. We identified 165 genes, most of whose function has not been studied in vivo. In parallel, we investigated rare variant alleles in 1,929 human exomes from families with unsolved Mendelian disease. Genes that are essential in flies and have multiple human homologs were found to be likely to be associated with human diseases. Merging the human data sets with the fly genes allowed us to identify disease-associated mutations in six families and to provide insights into microcephaly associated with brain dysgenesis. This bidirectional synergism between fly genetics and human genomics facilitates the functional annotation of evolutionarily conserved genes involved in human health. © 2014 Elsevier Inc. Source

News Article
Site: http://www.nature.com/nature/current_issue/

The data on TP53 mutations (including allele frequency) and CNVs in pan-tumours and AML are derived from The Cancer Genome Atlas (TCGA) data in the cBioPortal for Cancer Genomics (http://www.cbioportal.org/; accessed on 29 October 2014). Only sequenced samples with allele frequency information provided were included in our analysis. Considering potential normal tissue contamination, samples with TP53 mutation allele frequency above 0.6 were considered as a homozygous mutation. The SNP data were visualized in IGV and statistics for AML outcome were analysed in Prism 6. Since cBioPortal only has a few non-Hodgkin lymphoma cases available, we used published data to extract TP53 mutation and deletion information18, 30, 31, 32, 33, 34. Clinical outcomes were annotated from follow-up data available within the Gene Expression Omnibus GSE34171 series. CNV analysis was performed using published AML and DLBCL tumour copy number data in Affymetrix SNP Array 6.0 .cel format (http://cancergenome.nih.gov/)18, 35, 36, 37 according to GISTIC2.0 (ref. 14). Specifically, the following GISTIC parameters and values were used following the latest TCGA Copy Number Portal analysis version (3 November 2014 stddata__2014_10_17; http://www.broadinstitute.org/tcga/gistic/browseGisticByTissue): core GISTIC version 2.0.22; reference genome build hg19; amplification threshold 0.1; deletion threshold 0.1; high-level amplification threshold 1.0; high-level deletion threshold 1.0; broad length cut-off 0.50; peak confidence level 0.95; cap 1.5; gene-GISTIC, true; arm-level peel-off, true; significance threshold 0.25; join segment size 8; X chromosome removed, false; maximum segments per sample 2,000; minimum samples per disease 40. To create a conditional 11B3 chromosome deletion, the MICER strategy was used15. Briefly, MICER clones MHPN91j22 (centromeric to Sco1) and MHPP248j19 (telomeric to Alox12) (Sanger Institute) were introduced into AB2.2 ES cells (129S5 strain, Sanger Institute) by sequential electroporation, followed by G418 (neomycin; 180 μg ml−1) and puromycin (1 μg ml−1) selection, respectively. Successful recombination events were confirmed by Southern blotting using the hybridized probes designated in Supplementary Table 2 as described38. The cis- and trans-localizations of two loxP sites in doubly targeted ES cells were further distinguished by PCR with df-F and df-R, or dp-F and dp-R (Supplementary Table 2), respectively, after Adeno-cre infection and HAT (Gibco) selection. Correct cis-ES clones in which two loxP sites were integrated into the same allele were used to generate chimaera mice by blastocyst injection. The F1 pups were genotyped with 11B3-F and 11B3-R primers (Supplementary Table 2) and those positive backcrossed to C57BL/6 mouse strains for more than 10 generations. All of the mouse experiments were approved by the Institutional Animal Care and Use Committee at the Memorial Sloan Kettering Cancer Center. Eμ-Myc, Vav1-cre, Ella-cre, Trp53LSL-R270H/+, Trp53LSL-R72H/+, Trp53+/−, Trp53fl/+ and Rag1−/− mice were ordered from Jackson Laboratories21, 39, 40, 41, 42, 43, 44 and the Arf+/− mouse strain is a gift from C. Sherr45. Eμ-Myc mice with different Trp53 alterations were monitored weekly with disease state being defined by palpable enlarged solid lymph nodes and/or paralysis. Tumour monitoring was done as blinded experiments. For lymphoma generated by transplantation, 1 million Eμ-Myc HPSCs from embryonic day (E)13.5 fetal liver or autoMACS-purified B220+ B progenitor cells isolated from 6–8-week mouse bone marrow were transduced with retroviruses, followed by tail-vein injection into sublethally irradiated (6 Gy, Cs137) C57BL/6 mice (Taconic; 6–8-week old, female, 5–10 mice per cohort)11, 46. All recipient mice were randomly divided into subgroups before transplantation and monitored as described earlier. The generation of AML proceeded as previously reported29. Briefly, retrovirally infected c-Kit+ haematopoietic stem and progenitor cells were transplanted into sublethally irradiated (6 Gy, Cs137) C57BL/6 mice, followed by routine monitoring of peripheral blood cell counts and Giemsa–Wright blood smear staining. For secondary transplantation experiments, 1 million leukaemia cells were transplanted into sublethally irradiated (4.5 Gy) mice. The immunophenotypes of resulting lymphomas and leukaemias were determined by flow cytometry as previously reported using antibodies purchased from eBioscience11, 29. Statistical analysis of all survival data was carried out using the log-rank test from Prism 6. No statistical methods were used to predetermine sample size. MSCV-Myc-IRES-GFP and MLS-based retroviral constructs harbouring a GFP or mCherry fluorescent reporter and targeting Ren, Trp53, Eif5a, Nf1 or Mll3 have all been reported before11, 29, 47. For the tandem shRNA experiments performed in Fig. 3, mirE-based shRNAs targeting two different genes were cloned into an MLS-based vector in an analogous fashion to what has been previously described48, 49. Retrovirus packaging and infection of HSPCs was done as previously reported11, 29. B220+ cells were isolated from the bone marrow of 6-week-old Eμ-Myc mice by autoMACS positive selection with anti-B220 microbeads (Militeny Biotech). After overnight culture, cells were infected with retroviruses carrying the indicated shRNAs. Two days after infection, 0.5 × 106 cells were washed with PBS followed by annexin V buffer (10 mM HEPES, 140 mM NaCl, 25 mM CaCl , pH 7.4), and incubated at room temperature with Pacific Blue annexin V (BD Biosciences) and propridium iodide (PI; 1 μg ml−1; Sigma-Aldrich) for 15 min and analysed on a LSR II flow cytometer (BD Biosciences). For arachidonic acid treatment, pre-B cells were cultured out from bone marrow cells in pre-B cell medium (RPMI1640, 10% FBS, 1% penicillin/streptomycin, 50 μM β-mercaptoethanol, 3 ng ml−1 IL-7). After 3 days culture, pre-B cells were treated with a series concentration of arachidonic acid (Cayman Chemical) for 20 h, followed by annexin V staining as described earlier. Lymphoma cells isolated from lymph nodes of diseased animals were treated with vehicle (PBS) or 1 μg ml−1 adriamycin for 4 h. Whole cell lysates were extracted in cell lysis buffer (Cell Signaling Technology) supplemented with protease inhibitors (Roche), followed by SDS–PAGE gel electrophoresis and blotting onto PVDF membranes (Millipore). Eμ-Myc;Arf−/− lymphoma cell lines were used as a positive control for p53 induction. The p53 antibody used was obtained from Novocastra (NCL-p53-505) and horseradish peroxidase (HRP)-conjugated β-actin antibody from Sigma (AC-15). Alox15b expressions were examined in NIH3T3 cells, which were infected by shRNAs targeting Ren or Alox15b and then selected by G418. Anti-Alox15b antibody is from Sigma (SAB2100110), and HRP-conjugated GAPDH antibody is from ThermoFisher Scientific (MA5-15738-HRP). RNA-seq and data analysis were performed by the Integrated Genomic and Bioinformatics core at the Memorial Sloan Kettering Cancer Center. Briefly, total RNA from 11B3fl/Trp53fl;shNf1;shMll3;Vav1-cre or Trp53fl/fl;shNf1;shMll3;Vav1-cre leukaemia cells (four lines per cohort), isolated from the bone marrow of moribund mice, was isolated by Trizol extraction (Life Technologies). After ribogreen quantification (Life Technologies) and quality control on an Agilent BioAnalyzer, 500 ng of total RNA (RNA integrity number > 8) underwent polyA selection and Truseq library preparation according to instructions provided by Illumina (TruSeq RNA Sample Prep Kit v.2) with 6 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 in a 50 bp/50 bp paired-end run, using the TruSeq SBS Kit v.3 (Illumina). An average of 45 million paired reads were generated per sample. At the most the ribosomal reads represented 0.1% and the percentage of mRNA bases was close to 65% on average. The output from the sequencers (FASTQ files) was mapped to the mouse genome (mm9) using the rnaStar (https://code.google.com/p/rna-star/) aligner, with the two-pass mapping methods. After mapping, the expression counts of each individual gene were computed using HTSeq (http://www-huber.embl.de/users/anders/HTSeq), followed by normalization and differential expression analysis among samples using the R/Bioconductor package DESeq (http://www-huber.embl.de/users/anders/DESeq). Gene set enrichment analysis (GSEA) was performed with Broad’s GSEA algorithm. A list of all primers used for PCR analysis is given in Supplementary Table 2. For detection and quantification of 11B3 recombination/deletion two methods were employed. In both cases genomic DNA (gDNA) was extracted from lymphoma or leukaemia cells using Puregene DNA purification kit (Qiagen). Initially, semi-quantitative PCR was used to detect the recombined 11B3 allele using primers df-F and df-R, generating a 2.2 kb product (Fig. 2d). The estimated frequency of recombination was determined by dropping gDNA from 11B3+/− into 11B3fl/+ at various ratios. For qPCR of the 11B3 deletion (Fig. 2e), SYBR Green PCR Master Mix (Applied Biosystems) was used and cycling and analysis was carried out on a ViiA 7 (Applied Biosystems). Primers 11B3-Q-F and 11B3-Q-R were used to detect the floxed allele, and to estimate the frequency of 11B3 deletion. Allelic frequency in UPD analysis (Extended Data Fig. 5a) was determined similarly, in this case with serial dilution of wild-type gDNA into DNase-free water to construct a standard curve. Two-tailed t-test is used for statistics analysis by Prism 6. For p21 gene expression examination by RT–qPCR, RNA was isolated with Trizol, cDNA was synthesized with SuperScript III First-Strand Synthesis System (Life Technologies) and qPCR was performed as described earlier with primers p21-Q-F and p21-Q-R. Trp53 exons (2–10) were amplified from genomic DNAs of 11B3-deleted lymphomas by PCR (see Supplementary Table 2 for primer sequences) and subjected to Sanger sequencing. Mutations were called only if detected in sequencing reads carried out in the forward and reverse direction. SNP analysis of isolated lymphoma (tumour) or tail (normal) genomic DNAs from the same tumour-bearing mouse were carried out by Charles River laboratory. Briefly, a SNP Taqman assay with competing FAM- or VIC-labelled probes was used to detect the relevant C57BL/6 and 129S SNPs (D11Mit4 and D11NDS16) as described previously50. Genomic DNA was extracted from freshly isolated lymphoma cells from one Eμ-Myc;11B3fl/+;Vav-cre mice. One microgram of DNA was sonicated (17 W, 75 s) on an E220 sonicator (Covaris). Samples were subsequently prepared using standard Illumina library preparation (end repair, poly A addition, and adaptor ligation). Libraries were purified using AMPure XP magnetic beads (Beckman Coulter), PCR enriched, and sequenced on an Illumina HiSeq instrument in a multiplexed format. Sequencing reads per sample were mapped using Bowtie with PCR duplicates removed. Approximately 2.5 million uniquely mappable reads were further processed for copy number determination using the ‘varbin’ algorithm51, 52 with 5,000 bins, allowing for a median resolution of ~600 kb. GC content normalization, segmentation and copy number estimation was calculated as described53. A custom shRNA library was designed to target mouse homologues (six shRNAs for one gene) to all human protein-coding genes on chromosome 17p13.1 from ALOX12 to SCO1, except TP53 and EIF5A. shRNAs were cloned into a retrovirus-based vector MLS by pool-specific PCR as previously described11. Eμ-Myc HSPCs infected with pooled shRNAs were transplanted into sublethally irradiated recipient mice. Resulting tumours were harvested, and used to extract contained shRNAs, followed by HiSeq in HiSeq 2500 (Illumina). Twenty-two oligonucleotides of shRNAs used in this study are listed in Supplementary Table 3. Total lipids were extracted using Folch’s method54 and analysed by LC-MS as previously described55. Briefly, freshly harvested cells were homogenized by chloroform/methanol (2:1, v-v). After being washed by water, the lipid-containing chloroform phase is evaporated. Dried lipids were dissolved in 100 μl 95% acetonitrile (in H O), sonicated for 3–5 min, and spiked with 10 μl of 500 ng ml−1 deuterated internal standard solution (IS; arachidonic acid-d8; Cayman Chemical, 390010). Then, 5 μl samples were injected into Acquity ultra performance liquid chromatography (UPLC) system (Waters), equipped with Acquity UPLC BEH C18 column (100 mm × 2.1 mm I.D., 1.7 μm; Waters). Samples were washed through the column with a gradient 0.1% formic acid: acetonitrile mobile elution from 35:65 (v:v) to 5:95 for 10 min. Flow rate was 0.25 ml min−1. Right after HPLC, samples were analysed in a Quattro Premier EX triple quadrupole mass spectrometer (Waters), which has electrospray negative mode and MasslynxV4.1 software. For each run, a standard curve was generated with different concentration of arachidonic acid lipid maps MS standard (Cayman Chemical, 10007268) mixed with IS (50 ng ml−1 final concentration). Arachidonic acid standard m/z is 303.2, and IS is 311.3. Three Eμ-Myc lymphoma cell lines generated from Trp53fl/+;Vav1-cre or 11B3fl/+;Vav1-cre tumour-bearing mice were cultured in BCM medium (45% DMEM, 45% IMDM, 10% FBS, 2 mM glutamine, 50 μM β- mercaptoethanol, 1× penicillin/streptomycin) in 96-well plates. Cells were treated with the indicated concentrations of 4-hydroxycyclophosphamide (Toronto Research Chemicals) or vincristine (Bedford Laboratories) for 3 days. The number of living cells was determined by PI staining and cell counting on a Guava EasyCyte (EMD Millipore). Leukaemia cell lines from Trp53∆/∆ or 11B3∆/Trp53∆;shNf1;shMll3 mice were treated with cytarabine (araC; Bedford Laboratories) or JQ1 (a gift from J. Bradner) in stem cell medium (BCM medium supplemented with 1 ng ml−1 IL-3, 4 ng ml−1 IL-6 and 10 ng ml−1 SCF) and cell viability after 3 days was determined similarly. All cytokines are from Invitrogen.

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