Faculty Bibliography
Searched for:
school:SOM
Department/Unit:Cell Biology
Total Results:
14019
Purification and properties of recombinant Brassica napus diacylglycerol acyltransferase 1
Diacylglycerol acyltransferase 1 (DGAT1) catalyzes the final step in the acyl-CoA-dependent triacylglycerol biosynthesis. Although the first DGAT1 gene was identified many years ago and the encoded enzyme catalyzes a key step in lipid biosynthesis, no detailed structure-function information is available on the enzyme due to difficulties associated with its purification. This study describes the purification of recombinant Brassica napus DGAT1 (BnaC.DGAT1.a) in active form through solubilization in n-dodecyl-beta-D-maltopyranoside, cobalt affinity chromatography, and size-exclusion chromatography. Different BnaC.DGAT1.a oligomers in detergent micelles were resolved during the size-exclusion process. BnaC.DGAT1.a was purified 126-fold over the solubilized fraction and exhibited a specific activity of 26 nmol TAG/min/mg protein. The purified enzyme exhibited substrate preference for alpha-linolenoyl-CoA>oleoyl-CoA=palmitoyl-CoA>linoleoyl-CoA>stearoyl-CoA.
PMID: 25687632
ISSN: 1873-3468
CID: 2286592
A Method to Quantify FRET Stoichiometry with Phasor Plot Analysis and Acceptor Lifetime Ingrowth
FRET is widely used for the study of protein-protein interactions in biological samples. However, it is difficult to quantify both the FRET efficiency (E) and the affinity (Kd) of the molecular interaction from intermolecular FRET signals in samples of unknown stoichiometry. Here, we present a method for the simultaneous quantification of the complete set of interaction parameters, including fractions of bound donors and acceptors, local protein concentrations, and dissociation constants, in each image pixel. The method makes use of fluorescence lifetime information from both donor and acceptor molecules and takes advantage of the linear properties of the phasor plot approach. We demonstrate the capability of our method in vitro in a microfluidic device and also in cells, via the determination of the binding affinity between tagged versions of glutathione and glutathione S-transferase, and via the determination of competitor concentration. The potential of the method is explored with simulations.
PMCID:4375440
PMID: 25762312
ISSN: 0006-3495
CID: 1495042
Identification of genetic loci that control mammary tumor susceptibility through the host microenvironment
The interplay between host genetics, tumor microenvironment and environmental exposure in cancer susceptibility remains poorly understood. Here we assessed the genetic control of stromal mediation of mammary tumor susceptibility to low dose ionizing radiation (LDIR) using backcrossed F1 into BALB/c (F1Bx) between cancer susceptible (BALB/c) and resistant (SPRET/EiJ) mouse strains. Tumor formation was evaluated after transplantation of non-irradiated Trp53-/- BALB/c mammary gland fragments into cleared fat pads of F1Bx hosts. Genome-wide linkage analysis revealed 2 genetic loci that constitute the baseline susceptibility via host microenvironment. However, once challenged with LDIR, we discovered 13 additional loci that were enriched for genes involved in cytokines, including TGFbeta1 signaling. Surprisingly, LDIR-treated F1Bx cohort significantly reduced incidence of mammary tumors from Trp53-/- fragments as well as prolonged tumor latency, compared to sham-treated controls. We demonstrated further that plasma levels of specific cytokines were significantly correlated with tumor latency. Using an ex vivo 3-D assay, we confirmed TGFbeta1 as a strong candidate for reduced mammary invasion in SPRET/EiJ, which could explain resistance of this strain to mammary cancer risk following LDIR. Our results open possible new avenues to understand mechanisms of genes operating via the stroma that affect cancer risk from external environmental exposures.
PMCID:4352890
PMID: 25747469
ISSN: 2045-2322
CID: 1494442
Partial restoration of protein synthesis rates by the small molecule ISRIB prevents neurodegeneration without pancreatic toxicity
Activation of the PERK branch of the unfolded protein response (UPR) in response to protein misfolding within the endoplasmic reticulum (ER) results in the transient repression of protein synthesis, mediated by the phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2alpha). This is part of a wider integrated physiological response to maintain proteostasis in the face of ER stress, the dysregulation of which is increasingly associated with a wide range of diseases, particularly neurodegenerative disorders. In prion-diseased mice, persistently high levels of eIF2alpha cause sustained translational repression leading to catastrophic reduction of critical proteins, resulting in synaptic failure and neuronal loss. We previously showed that restoration of global protein synthesis using the PERK inhibitor GSK2606414 was profoundly neuroprotective, preventing clinical disease in prion-infected mice. However, this occured at the cost of toxicity to secretory tissue, where UPR activation is essential to healthy functioning. Here we show that pharmacological modulation of eIF2alpha-P-mediated translational inhibition can be achieved to produce neuroprotection without pancreatic toxicity. We found that treatment with the small molecule ISRIB, which restores translation downstream of eIF2alpha, conferred neuroprotection in prion-diseased mice without adverse effects on the pancreas. Critically, ISRIB treatment resulted in only partial restoration of global translation rates, as compared with the complete restoration of protein synthesis seen with GSK2606414. ISRIB likely provides sufficient rates of protein synthesis for neuronal survival, while allowing some residual protective UPR function in secretory tissue. Thus, fine-tuning the extent of UPR inhibition and subsequent translational de-repression uncouples neuroprotective effects from pancreatic toxicity. The data support the pursuit of this approach to develop new treatments for a range of neurodegenerative disorders that are currently incurable.
PMCID:4385927
PMID: 25741597
ISSN: 2041-4889
CID: 2354072
Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution
The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25-50%) than euchromatic reference regions (3-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4-3.6 vs. 8.4-8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.
PMCID:4426361
PMID: 25740935
ISSN: 2160-1836
CID: 3159302
Improved gate effect enantioselectivity of phenylalanine-imprinted polymers in water by blending crosslinkers
In this work, the anodic current at an electrode grafted with a molecularly imprinted polymer (MIP) crosslinked via a combination of hydrophobic ethyleneglycol dimethacrylate (EDMA) and hydrophilic methylene bisacrylamide (MBAA) was found to exhibit enantioselective sensitivity to the phenylalanine template in aqueous solution. An MIP-grafted electrode crosslinked with a 2:1 mixture of EDMA and MBAA was observed to respond to the template with the highest enantioselectivity, such that the change in current induced by the imprinted template was more than four times that induced by the enantiomer of the template. The contact angle of a water droplet on an MIP-coated electrode prepared using the optimal crosslinker blending ratio was also sensitive to the template and again exhibited chiral selectivity. The change in the contact angle induced by the template was more than twice as large as that obtained from the template's enantiomer. Atomic force microscopy showed that the surface of the MIP layer fabricated using a mixture of crosslinkers was rougher than that made with a single crosslinking agent, although there was no apparent correlation between the roughness and the enantioselectivity of the layer. These results indicate that the appropriate combination of crosslinkers enables the chiral-selective gate effect by modulating the flexibility and hydrophilicity of the MIP layer. The approach described herein therefore represents a new means of improving the selectivity of MIPs by blending crosslinkers having different chemical properties.
PMID: 25682431
ISSN: 1873-4324
CID: 3115712
TRP channels localize to subdomains of the apical plasma membrane in human fetal retinal pigment epithelium
Purpose: Calcium regulates many functions of retinal pigment epithelium (RPE). Its concentration in the subretinal space and RPE cytoplasm is closely regulated. Transient receptor potential (TRP) channels are a superfamily of ion channels that are moderately calcium-selective. This study investigates the subcellular localization and potential functions of TRP channels in a first-passage culture model of human fetal RPE (hfRPE). Methods: RPE isolated from 15-16 week-gestation fetuses were maintained in serum-free media. Cultures were treated with BaCl2 in the absence and presence of TRP channel inhibitors and monitored by the transepithelial electrical resistance (TER). The expression of TRP channels was determined using quantitative RT-PCR, immunoblotting, and immunofluorescence confocal microscopy. Results: BaCl2 substantially decreased TER and disrupted cell-cell contacts when added to the apical surface of RPE, but not when added to the basolateral surface. The effect could be partially blocked by the general TRP inhibitor, LaCl3, (~75%) or an inhibitor of calpain (~25%). Family member-specific inhibitors, ML204 (TRPC4) and HC-067047 (TRPV4), had no effect on basal channel activity. Expression of TRPC4, TRPM1, TRPM3, TRPM7, and TRPV4 were detected by RT-PCR and immunoblotting. TRPM3 localized to the base of the primary cilium, and TRPC4 and TRPM3 localized to apical tight junctions. TRPV4 localized to apical microvilli in a small subset of cells. Conclusions: TRP channels localized to subdomains apical membrane, and BaCl2 was only able to dissociate tight junctions when presented to the apical membrane. The data suggest a potential role for TRP channels as sensors of [Ca2+] in the subretinal space.
PMCID:4364639
PMID: 25736794
ISSN: 0146-0404
CID: 1480602
Purification of polysomes
Isolated polysomes (also known as translating ribosomes or polyribosomes) are mRNA-ribosome complexes that are frequently used for the in vitro study of the regulation of protein synthesis. Here we describe a protocol for the isolation of prokaryotic and plant polysomes by sucrose gradient sedimentation. The protocol allows for the separation of multiple ribosomes attached to mRNA from run-off ribosome monomers. In addition to collecting the polysome pellet, if the sucrose gradients used in this protocol are fractionated, it is possible to isolate and quantify the polysomes, the ribosome monomers, and the ribosomal subunits.
PMID: 25734067
ISSN: 1940-3402
CID: 1480502
Purification of 70S Ribosomes
Here we describe the further purification of prokaryotic ribosomal particles obtained after the centrifugation of a crude cell lysate through a sucrose cushion. In this final purification step, a fraction containing ribosomes, ribosomal subunits, and polysomes is centrifuged through a 7%-30% (w/w) linear sucrose gradient to isolate tight couple 70S ribosomes, as well as dissociated 30S and 50S subunits. The tight couples fraction, or translationally active ribosome fraction, is composed of intact vacant ribosomes that can be used in cell-free translation systems.
PMID: 25734066
ISSN: 1940-3402
CID: 1480492
Isolation of ribosomes and polysomes
Here we describe a preparative differential centrifugation protocol for the isolation of ribosomes from a crude cell homogenate. The subcellular fraction obtained is enriched in ribosome monomers and polysomes. The protocol has been optimized for the homogenization and collection of the ribosomal fraction from prokaryotic cells, mammalian and plant tissues, reticulocytes, and chloroplasts. The quality of the ribosomal preparation is enhanced by the removal of the remaining cellular components and adsorbed proteins by pelleting through a sucrose cushion with a high concentration of monovalent salts, NH4Cl or KCl. The different components of the ribosomal fraction isolated using this protocol can be further purified by sucrose gradient centrifugation.
PMID: 25734065
ISSN: 1940-3402
CID: 1480482
