DNA capillary electrophoresis using block copolymer as a new separation medium.
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Automation↗
Biomedical subjects
B Chu
Publications and source records attributed to B Chu.
DNA electrophoresis on a flat surface.
We report a new approach for performing DNA electrophoresis. Using experimental studies and molecular dynamics simulations, we show that a perfectly flat silicon wafer, without any surface features, can be used to fractionate DNA in free solution. We determine that the ability of a flat surface to separate DNA molecules results from the local friction between the surface and the adsorbed DNA segments. We control this friction by coating the Si surface with silane monolayer films and show that it is possible to systematically change the size range of DNA that can be separated.
DNA↗
The single neurofilament subunit of the lamprey forms filaments and regulates axonal caliber and neuronal size in vivo.
Neurofilaments (NFs) are composed of a heteropolymer of three related subunits in mammalian neurons, where they are a major component of the cytoskeleton in large neurons and are thought to regulate axonal diameter. NFs in the lamprey, while ultrastructurally and functionally indistinguishable from mammalian NFs, are polymers of a single subunit protein, NF180. In this study, we use the simplicity of lamprey NFs and the accessibility of the lamprey central nervous system (CNS) to examine the effects of overproducing NFs in an identified giant neuron in vivo, and thus to elucidate the role of NFs in regulating neuronal size and axonal caliber in the vertebrate CNS. We show that overexpression of NF180 tagged with a variant of Green Fluorescent Protein (EYFP) in identified lamprey neurons (ABCs) and in human neuroblastoma (NB2a) cells results in the assembly of exogenous NF180 into ultrastructurally normal NFs that are tightly packed and unphosphorylated. These accumulate in the somata of NB2a cells and produce somatic swelling by 3 days post-transfection. NF180 overexpression in lamprey ABCs in vivo causes exogenous NFs to accumulate in ABC axons, somata, and dendrites, and induces a significant increase in axonal diameter without increasing axonal NF packing density. Overexpression of EYFP alone has none of these effects. We conclude that NF180 normally plays a critical role in determining axonal caliber in ABCs and may influence neuronal size in situations where NFs accumulate in the soma, such as after axonal injury.
Animals↗
Formation of concentration gradient and its application to DNA capillary electrophoresis.
A new method to introduce the concentration gradient into the capillary has been developed and its application to DNA capillary electrophoresis is presented. The concentration gradient produced by mixing 5% w/v polyacrylamide-co-poly(N-dimethylacrylamide) (PAM-co-PDMA) solution and 1 x Tris/N-tris(hydroxymethyl)methyl-3-amino-propanesulfonic acid/EDTA (TT) + 5 M urea buffer was successfully achieved by using two programmable syringe pumps with strict control of dead volume, flow rate, and pressure balance. This method has the advantages of high stability, reproducibility, and versatility. The column with concentration gradient greatly improved the resolution, especially for the large DNA fragments, due to a decrease in band width broadening with time. A column containing 2-4% w/v gradient in four steps had a longer read length, shorter separation time and better resolution (after 380 base) than that of 4% w/v single concentration polymer solution. The number of steps in the gradient had almost no effect on the performance. The change in the average concentration by relocating the position of the same step gradient, i.e., a combination of different low concentration to high concentration polymer solution ratios, resulted in a different migration time, read length and resolution.
Acrylamides↗
Y chromosome analysis of infertile men and their sons conceived through intracytoplasmic sperm injection: vertical transmission of deletions and rarity of de novo deletions.
OBJECTIVE: To determine the prevalence and type of Yq microdeletions in 86 consecutive men that fathered 99 sons by intracytoplasmic sperm injection (ICSI) and to determine the incidence of vertical transmission and de novo deletions in these boys. DESIGN: Prospective clinical observational study. SETTING: Genetics laboratory associated with a university IVF unit. PATIENT(S): Eighty-six consecutive infertile men presenting to an IVF clinic and their 99 ICSI-conceived sons. Fifty of the 86 men (58%) had idiopathic seminiferous tubule failure (STF); the remainder had a variety of other clinical indications for ICSI. INTERVENTION(S): Collection of peripheral and cord blood samples. MAIN OUTCOME MEASURE(S): The Yq genetic status of fathers who underwent ICSI and of their sons by the presence or absence of 22 Y-specific markers covering the four azoospermia factor (AZF) subregions. RESULT(S): Yq deletions of the AZFd/c region were detected in two (6.9%) of 29 azoo- or severely oligospermic men with STF. Identical deletions were found in their respective sons. No de novo deletions were detected in the remaining 97 sons conceived by men without deletions. CONCLUSION(S): The detection of Yq deletions only in men with severe STF is consistent with previous studies, with the AZFd/c region being most commonly affected. This study demonstrates the vertical transmission of these Yq deletions through the use of ICSI and supports the notion that, in most cases, Yq deletions will be inherited by male offspring. The absence of de novo Yq deletions in the male offspring indicates that these events are rare following ICSI in men with both STF and other common male factor indications.
Fathers↗
Human tau filaments induce microtubule and synapse loss in an in vivo model of neurofibrillary degenerative disease.
The intracellular accumulation of tau protein and its aggregation into filamentous deposits is the intracellular hallmark of neurofibrillary degenerative diseases such as Alzheimer's Disease and familial tauopathies in which tau is now thought to play a critical pathogenic role. Until very recently, the lack of a cellular model in which human tau filaments can be experimentally generated has prevented direct investigation of the causes and consequences of tau filament formation in vivo. In this study, we show that human tau filaments formed in lamprey central neurons (ABCs) that chronically overexpress human tau resemble the 'straight filaments' seen in Alzheimer's Disease and other neurofibrillary conditions, and are distinguishable from neurofilaments by their ultrastructure, distribution and intracellular behavior. We also show that tau filament formation in ABCs is associated with a distinctive pattern of dendritic degeneration that closely resembles the cytopathology of human neurofibrillary degenerative disease. This pattern includes localized cytoskeletal disruption and aggregation of membranous organelles, distal dendritic beading, and the progressive loss of dendritic microtubules and synapses. These results suggest that tau filament formation may be responsible for many key cytopathological features of neurofibrillary degeneration, possibly via the loss of microtubule based intracellular transport.
Alzheimer Disease↗
Cerebral blood flow on xenon CT: correlation with the blood flow detected at the common carotid artery on ultrasonography.
To correlate cerebral blood flow (CBF) on xenon CT with the flow at common carotid artery (CCA) detected by color doppler ultrasonography, 82 patients (29 men, 53 women; 20-90 yrs) were examined. They included normal volunteers (n = 33), patients with cerebral infarction (n = 8), multiple lacunar infarcts (n = 12), dementia (n = 14), and parkinson disease (n = 15). Flow at the CCA was graded as extremely low (< 0.3 l/min), low (0.3-0.4), and normal (> 0.4). CBF was measured in the following distribution: anterior, middle, posterior cerebral arteries (ACA, MCA, PCA); white matter border zones (BZ); basal ganglia (BA), thalamus in two slices. CBF may be reduced in the BZ, cortical and deep gray matter with extremely low flow at CCA. We suggest that color doppler ultrasonography may aid in triage of patients for further CBF evaluation. As some overlap in CBF exists between normal and diseased groups with respect to low flow at CCA, color doppler ultrasonography must be evaluated in combination with xenon CT to reflect cerebral blood flow.
Adult↗
Novel low molecular weight microtubule-associated protein-2 isoforms contain a functional nuclear localization sequence.
Known high and low molecular weight (LMW) MAP2 protein isoforms result from alternative splicing of the MAP2 gene. Contrary to previous reports that MAP2 is neural-specific, we recently identified MAP2 mRNA and protein in somatic and germ cells of rat testis, and showed the predominant testicular isoform is LMW. Although cytoplasmic in neural tissue, MAP2 appeared predominantly nuclear in germ cells using immunohistochemistry. We sought to determine whether this unexpected localization was due to the inclusion of exon 10 within novel LMW MAP2 isoforms. Normally excluded from the LMW MAP2c, exon 10 harbors a putative CcN motif, comprising a nuclear localization sequence (NLS) flanked by regulatory phosphorylation sites for protein kinase CK2 and cdc2 kinase. Characterization of MAP2 mRNA in adult and immature brain and testis, by reverse transcriptase-polymerase chain reaction/Southern analysis and Northern blot, identified novel LMW forms containing exons 10 and 11, previously detected only in high molecular weight MAP2a and 2b. The MAP2 NLS targeted a large heterologous protein to the nucleus, as demonstrated using bacterially expressed MAP2-CcN-beta-galactosidase fusion protein and an in vitro nuclear import assay. Antibodies raised against the fusion protein produced a testicular immunohistochemical staining pattern correlating with MAP2 protein distribution in the nucleus of most germ cells, and precipitated both approximately 70-kDa and >220-kDa proteins recognized by the commercial MAP2-specific HM2 monoclonal antibody, supporting our hypothesis of a novel LMW MAP2 isoform. These results demonstrate the presence of a functional NLS in MAP2 and indicate that novel LMW MAP2 isoforms may be targeted to the nucleus in both neural and non-neuronal tissues.
Alternative Splicing↗
Physical and Chemical Properties of Magnetite and Magnetite-Polymer Nanoparticles and Their Colloidal Dispersions.
The properties of polymer-coated magnetite nanoparticles, which have the potential to be used as effective magnetic resonance contrast agents, have been studied. The magnetite particles were synthesized by using continuous synthesis in an aqueous solution. The polymer-coated magnetite nanoparticles were synthesized by seed precipitation polymerization of methacrylic acid and hydroxyethyl methacrylate in the presence of the magnetite nanoparticles. The particle size was measured by laser light scattering. It was shown that the particle size, variance, magnetic properties, and stability of aqueous magnetite colloidal dispersion strictly depend on the nature of the stabilizing agent. The average hydrodynamic radius of the magnetite particles was found to be 5.7 nm in the stable aqueous colloidal dispersion. An inclusion of the magnetite particle into a hydrophilic polymeric shell increases the stability of the dispersion and decreases the influence of the stabilizing agent on the magnetic and structural properties of the magnetite particles as was shown by X-ray diffraction and Mössbauer and IR spectroscopy, as well as by vibrating sample magnetometry. The variation in the polymeric shell size and the polymer net density can be useful tools for evaluation of the polymer-coated magnetite particles as effective contrast agents. Copyright 1999 Academic Press.
Journal Article↗
Separation of double-stranded DNA fragments in plastic capillary electrophoresis chips by using E99P69E99 as separation medium.
The separation of double-stranded DNA (dsDNA) fragments in polymethylmethacrylate (PMMA) capillary electrophoresis (CE) chips by using E99P69E99 as a separation medium has been demonstrated. The PMMA CE chips were simply manufactured by micromachining and adhesive tape sealing. To make the separation channel compatible with the separation medium, a dynamic nonionic surfactant coating procedure was developed, which made the plastic separation channel sufficiently hydrophilic to allow the separation medium to fill the channel by capillary action. Subsequent separation of DNA fragments was successful with a separation efficiency of the order of 10(4) theoretical plates over an effective separation distance of 1.5 cm. By using an applied electric field strength of 200 V/cm, the separation of low DNA mass ladder was completed within 5 min. The simple coating procedure, together with the self-assembled viscosity-adjustable separation medium, should be useful to meet some of the essential requirements for developing single-use disposable CE chips. Coating the channels with polymer blends of PMMA and the separation medium also showed promise.
Animals↗
Poly(N-isopropylacrylamide)-g-poly(ethyleneoxide) for high resolution and high speed separation of DNA by capillary electrophoresis.
A new separation medium, poly(N-isopropylacrylamide)-g-poly(ethyleneoxide) (PNI-PAM-g-PEO) solution, used for double-stranded (ds) DNA separation by capillary electrophoresis (CE) is presented. This type of grafted copolymer has a good self-coating ability for quartz capillary tubing and a slightly temperature-dependent viscosity-adjustable property, making it easier to use. One bp resolution was achieved within 12.5 min by using 8% w/v PNIPAM-gPEO in 1 x TBE (Tris-borate-ethylenediaminetetraaceticacid) buffer with an effective column length of 10 cm and an applied electric field strength of 200 V/cm. The PNIPAM-g-PEO solutions had a high sieving ability for relatively small sized DNAs with the relative standard derivation for the first 10 runs being less than 0.9% by using the same polymer solution. With 8% w/v PNIPAM-g-PEO solution in a 1.5 cm column and 2400 V as the running voltage, phiX174/HaeIII digest could be clearly separated within 24 s.
Acrylamides↗
Non-steroidal anti-inflammatory drugs inhibit the expression of cytokines and induce HSP70 in human monocytes.
Recent studies have shown that the non-steroidal anti-inflammatory drugs (NSAIDs) activate heat shock transcription factor (HSF1) from a latent cytoplasmic form to a nuclear, DNA binding state. As HSF1 can function as both an activator of heat shock genes and a repressor of non-heat shock genes such as IL1B and c- fos, we have examined the potential role of HSF1 in the effects of NSAIDs on gene expression in a human monocytic cell line THP-1. We found that two members of the NSAIDs, sodium salicylate and sulindac repress the IL1B promoter to similar degree to heat shock or HSF1 overexpression. In addition, sodium salicylate and additional NSAIDs used at concentrations that activate HSF1 also inhibited the expression of other monocytic genes (TNF-alpha, IL-1beta, IL-6, IL-8, IL-10, ICAM-1) activated by exposure to a pro-inflammatory stimulus (lipopolysaccharide, LPS). At least in the case of the IL1B promoter, repression did not seem to involve another factor whose activity is affected by the NSAIDs, NFkappaB as the IL1B promoter fragment used in our studies is not NFkappaB responsive and binds specifically to HSF1. Exposure to NSAIDs had a complex effect on HSP gene expression and while sulindac activated the stress responsive HSP70B promoter, sodium salicylate did not. In addition, only a subset of the NSAIDs induced HSP70 mRNA species. These findings reflect the properties of HSF1 which can be activated to at least two DNA binding forms only one of which activates heat shock promoters and suggest that individual NSAID family members may differentially induce one or other of these forms. Overall therefore, exposure to NSAIDs leads to a profound switch in gene expression in monocytic cells, with suppression of genes involved in macrophage activation and induction of stress genes and HSF1 appears to play a regulatory role in these effects.
Anti-Inflammatory Agents, Non-Steroidal↗
Downregulation and abnormal expression of E-cadherin and beta-catenin in nasopharyngeal carcinoma: close association with advanced disease stage and lymph node metastasis.
Nasopharyngeal carcinoma (NPC) is predominantly of the undifferentiated histological subtype. Histological differentiation is of limited prognostic significance in NPC. Recent studies have suggested that downregulation of the cadherin-catenin cell adhesion complex may play a crucial role in the initial stage of cancer invasion and metastasis and is associated with poor prognosis in human cancers. Expression of E-cadherin has not been reported previously in NPC, and its prognostic value in NPC is unknown. The purpose of this study was to examine the expression pattern of E-cadherin and its associated partner, beta-catenin, in NPC and their possible applications as prognostic markers to predict the clinical outcome of NPC. Expression of the E-cadherin and beta-catenin was examined by immunohistochemical methods in 74 cases of primary NPC and 17 of their corresponding lymph node metastases. Normal nasopharyngeal epithelium showed strong and homogeneous immunocytochemical staining of E-cadherin and beta-catenin at the cell membranes and intercellular junctions. In contrast, primary NPC showed variable and heterogeneous staining patterns of E-cadherin and beta-catenin. Loss of membranous E-cadherin expression was significantly associated with advanced stages of diseases (P<.001). Eighty percent to ninety percent of NPC in stages IV and V (Ho's staging), respectively, showed a reduced (<35%) membranous staining of E-cadherin compared with normal nasopharyngeal epithelium. Expression of beta-catenin also was downregulated in advanced NPC. Ninety percent to one hundred percent of NPC in stages IV and V (Ho's staging) expressed a reduction (<35%) of imnmunocytochemical staining of beta-catenin. The expression pattern of beta-catenin staining was strongly associated with the expression of E-cadherin (P<.001). Unlike E-cadherin, nuclear staining of beta-catenin expression was observed in some of the primary NPC and lymph node metastasis. Reduced expression of E-cadherin and beta-catenin expression was associated with a shorter survival of NPC patients (P<.001). In advanced NPC patients (stages IV and V), a significant difference in survival was observed in tumors with higher or lower levels of E-cadherin expression (P=.0224, log-rank test). These observations suggests that expression of E-cadherin and beta-catenin may have prognostic values in NPC patients.
Adult↗
Alcohol modulation of calcium-activated potassium channels.
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Animals↗
Transcriptional activity of heat shock factor 1 at 37 degrees C is repressed through phosphorylation on two distinct serine residues by glycogen synthase kinase 3 and protein kinases Calpha and Czeta.
Heat shock factor 1 (HSF1) is the key transcriptional regulator of the heat shock genes that protect cells from environmental stress. However, because heat shock gene expression is deleterious to growth and development, we have examined mechanisms for HSF1 repression at growth temperatures, focusing on the role of phosphorylation. Mitogen-activated protein kinases (MAPKs) of the ERK family phosphorylate HSF1 and represses transcriptional function. The mechanism of repression involves initial phosphorylation by MAP kinase on serine 307, which primes HSF1 for secondary phosphorylation by glycogen synthase kinase 3 on a key residue in repression (serine 303). In vivo expression of glycogen synthase kinase 3 alpha or beta thus represses HSF1 through phosphorylation of serine 303. HSF1 is also phosphorylated by MAPK in vitro on a second residue (serine 363) adjacent to activation domain 1, and this residue is additionally phosphorylated by protein kinase C. In vivo, HSF1 is repressed through phosphorylation of this residue by protein kinase Calpha or -zeta but not MAPK. Regulation at 37 degrees C, therefore, involves the action of three protein kinase cascades that repress HSF1 through phosphorylation of serine residues 303, 307, and 363 and may promote growth by suppressing the heat shock response.
3T3 Cells↗
Viscosity-adjustable block copolymer for DNA separation by capillary electrophoresis.
The viscosity-adjustable property of F127 block copolymer PEO99PPO69PEO99, PEO and PPO being poly(ethylene oxide) and poly(propylene oxide), respectively, was found to be useful for the development of automated capillary electrophoresis (CE). The polymer solution can form a gel-like structure with sieving ability and can also serve as a dynamic coating material, thereby effectively suppressing the electroosmotic flow induced by the ionization of the silanol group on the quartz capillary inner wall. When applied to CE as a separation medium, F127 block copolymer can provide the advantages of high separation resolution, easy injection and replacement of the triblock copolymer solution and convenient capillary column treatment. High reproducibility of DNA electrophoretic migration time in CE by replenishing F127 solution in acid-washed capillary tubings can be achieved. The relative standard deviation of the DNA migration time is less than 2%. In the investigation of F127 concentration and temperature effects on the performance of DNA separation in CE, we have found that the DNA electrophoretic migration behavior in the F127 gel-like solution cannot be described by any one of the existing models.
DNA↗
High speed separation of DNA fragments by capillary electrophoresis in poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) triblock polymer.
The high speed separation of DNA fragments by using a triblock copolymer, 25% w/v F127 (PEO99PPO69PEO99 with PEO and PPO denoting polyethylene oxide and polypropylene oxide, respectively) which is easy to handle and does not need coating of the quartz capillary, has been investigated. Two ways to decrease the run time are presented: one is to shorten the effective capillary length and the other to increase the electric field strength. In a short capillary, the sieving ability of the separation medium versus the initial band width, and the band width spreading as a function of distance traveled dominate the resolution; at high electric field strength, Joule heating could deteriorate the separation. By taking both effects into account, the phi X174/HaeIII digest could be separated within 100 s by using an 8 mm effective length, 50 microns diameter capillary operating at 300 V/cm.
Bacteriophage phi X 174↗
Two beta-tubulin genes, TUB1 and TUB8, of Arabidopsis exhibit largely nonoverlapping patterns of expression.
Chimeric reporter genes were used to investigate the patterns of expression of two beta-tubulin genes, TUB1 and TUB8, in Arabidopsis thaliana. The TUB1 chimeric gene was preferentially expressed in epidermal and cortical cells of primary roots, whereas the TUB8 chimeric gene was preferentially expressed in the endodermal and phloem cells of primary roots and in the vascular tissues of leaves, stems, and flowers of transgenic plants.
Arabidopsis↗