Intermolecular Protein-Water Coupling Impedes the Coupling Between the Amide A and Amide I Mode in Interfacial Proteins

The coupling between different vibrational modes in proteins is essential for chemical dynamics and biological functions and is linked to the propagation of conformational changes and pathways of allosteric communication. However, little is known about the influence of intermolecular protein-H2O coupling on the vibrational coupling between amide A (NH) and amide I (C═O) bands. Here, we investigate the NH/CO coupling strength in various peptides with different secondary structures at the lipid cell membrane/H2O interface using femtosecond time-resolved sum frequency generation vibrational spectroscopy (SFG-VS) in which a femtosecond infrared pump is used to excite the amide A band, and SFG-VS is used to probe transient spectral evolution in the amide A and amide I bands. Our results reveal that the NH/CO coupling strength strongly depends on the bandwidth of the amide I mode and the coupling of proteins with water molecules. A large extent of protein-water coupling significantly reduces the delocalization of the amide I mode along the peptide chain and impedes the NH/CO coupling strength. A large NH/CO coupling strength is found to show a strong correlation with the high energy transfer rate found in the light-harvesting proteins of green sulfur bacteria, which may understand the mechanism of energy transfer through a molecular system and assist in controlling vibrational energy transfer by engineering the molecular structures to achieve high energy transfer efficiency.

Visualizing Water Monomers and Chiral OH-(H2O) Complexes Infiltrated in a Macroscopic Hydrophobic Teflon Matrix

Insights into the interaction of fluoroalkyl groups with water are crucial to understanding the polar hydrophobicity of fluorinated compounds, such as Teflon. While an ordered hydrophobic-like 2D water layer has been demonstrated to be present on the surface of macroscopically hydrophobic fluorinated polymers, little is known about how the water infiltrates into the Teflon and what is the molecular structure of the water infiltrated into the Teflon. Using highly sensitive femtosecond sum frequency generation vibrational spectroscopy (SFG-VS), we observe for the first time that monomeric H2O and chiral OH-(H2O) complexes are present in macroscopically hydrophobic Teflon. The species are inhomogeneously distributed inside the Teflon matrix and at the Teflon surface. No water clusters or single-file water "wires" are observed in the matrix. SFG free induction decay (SFG-FID) experiments demonstrate that the OH oscillators of physically absorbed molecular water at the surface dephase on the time scale of <230 fs, whereas the water monomers and hydrated hydroxide ions infiltrated in the Teflon matrix dephase much more slowly (680-830 fs), indicating that the embedded monomeric H2O and OH-(H2O) complexes are decoupled from the outer environment. Our findings can well interpret ultrafast water permeation through fluorous nanochannels and the charging mechanism of Teflon, which may tailor the desired applications of organofluorines.

Influence of environmental conditions on accumulated polyhydroxybutyrate in municipal activated sludge

Poly(3-hydroxybutyrate) (PHB) was accumulated in full-scale municipal waste activated sludge at pilot scale. After accumulation, the fate of the PHB-rich biomass was evaluated over two weeks as a function of initial pH (5.5, 7.0 and 10), and incubation temperature (25, 37 and 55°C), with or without aeration. PHB became consumed under aerobic conditions as expected with first order rate constants in the range of 0.19 to 0.55 d^-1. Under anaerobic conditions, up to 63 percent of the PHB became consumed within the first day (initial pH 7, 55°C). Subsequently, with continued anaerobic conditions, the polymer content remained stable in the biomass. Degradation rates were lower for acidic anaerobic incubation conditions at a lower temperature (25°C). Polymer thermal properties were measured in the dried PHB-rich biomass and for the polymer recovered by solvent extraction using dimethyl carbonate. PHB quality changes in dried biomass, indicated by differences in polymer melt enthalpy, correlated to differences in the extent of PHB extractability. Differences in the expressed PHB-in-biomass melt enthalpy that correlated to the polymer extractability suggested that yields of polymer recovery by extraction can be influenced by the state or quality of the polymer generated during downstream processing. Different post-accumulation process biomass management environments were found to influence the polymer quality and can also influence the extraction of non-polymer biomass. An acidic post-accumulation environment resulted in higher melt enthalpies in the biomass and, consequently, higher extraction efficiencies. Overall, acidic environmental conditions were found to be favourable for preserving both quantity and quality after PHB accumulation in activated sludge.

Neuroprotective Effects of IVIG against Alzheimer' s Disease via Regulation of Antigen Processing and Presentation by MHC Class I Molecules in 3xTg-AD Mice

BACKGROUND

The results of clinical trials for Alzheimer's disease (AD) patients treated with Intravenous immunoglobulin (IVIG) revealed inconsistency in efficacy.

OBJECTIVE

To explore the neuroprotective effects and possible mechanisms of different IVIG in 3xTg-AD mice.

METHODS

3-month-old 3xTg-AD mice were administered intraperitoneally with different IVIG (A/B/C) for 3 months and then the therapeutic effects were observed and tested at 9 months of age. The bioavailability of IVIG and Aβ40/42 concentrations in parietotemporal cortex was measured by ELISA. Behavioral tests were performed to examine cognitive functions. Immunohistochemistry was utilized to examine the deposition of Aβ, the phosphorylation of tau, the levels of GFAP and Iba-1 in the hippocampus. Proteomics, Luminex assay and parallel reaction monitoring were performed to identify and verify the proteins that showed a marked change in the hippocampus.

RESULTS

IVIG-C was more effective than IVIG-A and IVIG-B in counteracting cognitive deficits, ameliorating Aβ deposits and tau phosphorylation, attenuating the activation of microglia and astrocytes in the hippocampus and inhibiting the secretion of pro-inflammatory factors. IVIG-C affected innate immunity and suppressed the activation of antigen processing and presentation by MHC class I molecule (APP-MHC-I).

CONCLUSION

The efficacy of different IVIG on AD was significantly different, and only IVIG-C has been confirmed to possess significant neuroprotective effects, which are related to the inhibition of APP-MHC-I. IVIG may be a potential therapeutic for AD but further research is needed to evaluate the functional of IVIG before clinical trials of AD treatment.

Ordered Water Layer on the Macroscopically Hydrophobic Fluorinated Polymer Surface and Its Ultrafast Vibrational Dynamics

Hydrophobic-like water monolayers have been predicted at the metal and some polar surfaces by theoretical simulations. However, direct experimental evidence for the presence of this water layer at surfaces, particularly at biomolecule and polymer surfaces, is yet to be validated at room temperature. Here we observe experimentally that an ordered molecular water layer is present at the hydrophobic fluorinated polymer such as polytetrafluoroethylene (PTFE) surface by using sum frequency generation vibrational spectroscopy. The macroscopic hydrophobicity of PTFE surface is actually hydrophilic at the molecular level. The macroscopically hydrophobic character of PTFE is indeed resulting from the hydrophobicity of the ordered two-dimension (2D) water layer, in which cyclic water tetramer structure is found. The water layer at humidity of ≤40% has a vibrational relaxation time of 550 ± 60 fs. The vibrational relaxation time in the frequency range of 3200-3400 cm^-1 shows remarkable difference from the interfacial water at the air/H₂O interface and the lipid/H₂O interface. No discernible frequency dependence of the vibrational relaxation time is observed, indicating the homogeneous dynamics of OH groups in the water layer. These insights into the water layer at the macroscopically hydrophobic surface may contribute to a better understanding of the hydrophobic interaction and interfacial water dynamics.

Identifying a novel 5-gene signature predicting clinical outcomes in acute myeloid leukemia

BACKGROUND

Acute myeloid leukemia (AML) is the most common type of acute leukemia and biologically heterogeneous diseases with poor prognosis. Thus, we aimed to identify prognostic markers to effectively predict the prognosis of AML patients and eventually guide treatment.

METHODS

Prognosis-associated genes were determined by Kaplan-Meier and multivariate analyses using the expression and clinical data of 173 AML patients from The Cancer Genome Atlas database and validated in an independent Oregon Health and Science University dataset. A prognostic risk score was computed based on a linear combination of 5-gene expression levels using the regression coefficients derived from the multivariate logistic regression model. The classification of AML was established by unsupervised hierarchical clustering of CALCRL, DOCK1, PLA2G4A, FCHO2 and LRCH4 expression levels.

RESULTS

High FCHO2 and LRCH4 expression was related to decreased mortality. While high CALCRL, DOCK1, PLA2G4A expression was associated with increased mortality. The risk score was predictive of increased mortality rate in AML patients. Hierarchical clustering analysis of the five genes discovered three clusters of AML patients. The cluster1 AML patients were associated with lower cytogenetics risk than cluster2 or 3 patients, and better prognosis than cluster3 patients (P values < 0.05 for all cases, fisher exact test or log-rank test).

CONCLUSION

The gene panel comprising CALCRL, DOCK1, PLA2G4A, FCHO2 and LRCH4 as well as the risk score may offer novel prognostic biomarkers and classification of AML patients to significantly improve outcome prediction.

Acidic Environment Significantly Alters Aggregation Pathway of Human Islet Amyloid Polypeptide at Negative Lipid Membrane

The misfolding and aggregation of human islet amyloid polypeptide (hIAPP) at cell membrane has a close relationship with the development of type 2 diabetes (T2DM). This aggregation process is susceptible to various physiologically related factors, and systematic studies on condition-mediated hIAPP aggregation are therefore essential for a thorough understanding of the pathology of T2DM. In this study, we combined surface-sensitive amide I and amide II spectral signals from the protein backbone, generated simultaneously in a highly sensitive femtosecond broad-band sum frequency generation vibrational spectroscopy system, to examine the effect of environmental pH on the dynamical structural changes of hIAPP at membrane surface in situ and in real time. Such a combination can directly discriminate the formation of β-hairpin-like monomer and oligomer/fibril at the membrane surface. It is evident that, in an acidic milieu, hIAPP slows down its conformational evolution and alters its aggregation pathway, leading to the formation of off-pathway oligomers. When matured hIAPP aggregates are exposed to basic subphase, partial conversion from β-sheet oligomers into ordered β-sheet fibrillar structures is observed. When exposed to acidic environment, however, hIAPP fibrils partially converse into more loosely patterned β-sheet oligomeric structures.

Has_circ_0008274 promotes cell proliferation and invasion involving AMPK/mTOR signaling pathway in papillary thyroid carcinoma

OBJECTIVE

Circular RNAs (circRNAs) have been known as important regulators in tumorigenesis. Whether circRNAs are involved in papillary thyroid carcinoma (PTC) requires to be determined. In the present study, we aimed to investigate the expression and function of has_circ_0008274 in PTC.

PATIENTS AND METHODS

Tissue expression of has_circ_0008274 was evaluated in Gene Expression Omnibus datasets (GSE93522). Real-time PCR assays were used to detect the expression of has_circ_0008274 in human PTC tissues and cell lines. The correlation of has_circ_0008274 expression with clinicopathological factors was statistically analyzed. The MTT assay, colony formation assay, transwell assays were performed to analyze and compare cell viability and invasion. Western blot analysis was used to quantify the expression of AMPK/mTOR signaling pathway proteins.

RESULTS

We found that has_circ_0008274 was significantly upregulated in PTC tissues, and the level of has_circ_0008274 was negatively associated with TNM stage and lymph node metastasis. Loss-of-function assay indicated that knockdown of has_circ_0008274 suppressed PTC cells proliferation and invasion in vitro. Mechanistically, has_circ_0008274 could inhibit the activation of AMPK/mTOR signaling pathway, which was demonstrated by measuring the expression levels of p-AMPK and p-mTOR.

CONCLUSIONS

These results demonstrate that increased has_circ_0008274 expression modulates has_circ_0008274 to enhance PTC cells proliferation and invasion. Has_circ_0008274/ AMPK/mTOR axis may be a novel therapeutic candidate target in PTC treatment.

Fast anaerobic sludge granulation at elevated salinity

It is commonly accepted that high salt concentrations negatively affect microbial activity in biological wastewater treatment reactors such as upflow anaerobic sludge blanket (UASB) reactors. Microbial aggregation in such reactors is equally important. It is well documented that anaerobic granules, when exposed to high salinity become weak and disintegrate, causing wash-out, operational problems and decreasing process performance. In this research, the possibility of microbial granule formation from dispersed biomass was investigated at salinity levels of 5 and 20 g Na⁺/L. High removal efficiencies of soluble influent organics were achieved at both salinity levels and this was accompanied by fast and robust formation of microbial granules. The process was found to be stable for the entire operational period of 217 days. As far as we know this is the first time it has been demonstrated that stable granule formation is possible at a salinity level as high as 20 g Na⁺/L. Methanosaeta was identified as the dominant methanogen at both salinity levels. Streptococcus spp. and bacteria belonging to the family Lachnospiraceae were identified as the dominant microbial population at 5 and 20 and g Na⁺/L, respectively.

L-Tetrahydropalmatine Induces Apoptosis in EU-4 Leukemia Cells by Down-Regulating X-Linked Inhibitor of Apoptosis Protein and Increases the Sensitivity Towards Doxorubicin

BACKGROUND

L-Tetrahydropalmatine (L-THP) is a tetra-hydro protoberberine isoquinoline alkaloid. The phyto-compounds bearing isoquinoline alkaloids have been reported to show a potential effect against a number of human cancers cell lines including leukemia. We hypothesized that L-THP, being an isoquinoline alkaloid, could be a potential molecule against acute lymphoblastic leukemia (ALL), in this study, we evaluate L-THP against p53 deficient leukemia EU-4 cell lines in vitro.

METHODS

For the study, p53 null leukemia EU-4 cells were used and treated with LTHP. The extent of apoptosis and viability of cells were determined. Expression of apoptosis related proteins such as XIAP and MDM2 was done by western blot and PCR studies. The expression of MDM2 and XIAP was knocked down by small interfering RNA (siRNA).

RESULTS

Outcomes of the study suggested that L-THP caused p53-indipendent apoptosis mediated by XIAP in EU-4 cells. The treatment of L-THP caused a decrease in the levels of XIAP protein with increasing dose and time. L-THP caused down-regulation of XIAP protein via inhibiting the expression of MDM2 and involving proteasomedependent pathway. Also, the outcomes of experiments suggested increased sensitivity of leukemia cells towards doxorubicin due to the inhibition of XIAP by L-THP or by siRNA.

CONCLUSION

Findings of the study confirm that L-THP resulted in p53 independent apoptosis via down-regulating XIAP protein by inhibiting MDM2 associated with proteasome-dependent pathway and increased sensitivity of EU-4 cells against doxorubicin. L-THP caused activation of caspase and resulted in apoptosis, L-THP may be a novel molecule for inducing apoptosis specifically in p53 null leukemia EU-4 cells.

Integrated Microfluidic Aptasensor for Mass Spectrometric Detection of Vasopressin in Human Plasma Ultrafiltrate

We present a microfluidic aptamer-based biosensor for detection of low-molecular-weight biomarkers in patient samples. Using a microfluidic device that integrates aptamer-based specific analyte extraction, isocratic elution, and detection by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, we demonstrate rapid, sensitive and label-free detection of arginine vasopressin (AVP) in human plasma ultrafiltrate. AVP molecules in complex matrices are specifically captured by an aptamer that is immobilized on microbeads via affinity binding in a microchamber. After the removal of unbound, contaminating molecules through washing, aptamer-AVP complexes are thermally disrupted via on-chip temperature control. Released AVP molecules are eluted with purified water and transferred to a separate microchamber, and deposited onto a single spot on a MALDI plate via repeated, piezoelectrically actuated ejection, which enriches AVP molecules over the spot area. This integrated on-chip sample processing enables the quantitative detection of low-abundance AVP by MALDI-TOF mass spectrometry in a rapid and label-free manner. Our experimental results show the detection of AVP in human plasma ultrafiltrate as low as physiologically relevant picomolar concentrations via aptamer-based selective preconcentration, demonstrating the potential of our approach as a rapid (~ 1hr), sensitive clinical AVP assay.

Anti-HLA class II antibodies in kidney retransplant patients

The relevance of anti-HLA class II antibodies for kidney graft survival is still controversial. In part, this can be attributed to difficulties to detect and differentiate anti-HLA class II antibodies. Anti-HLA class II IgG antibody screening was performed by enzyme-linked immunosorbent assay. Subsequently, all anti-HLA class II-positive sera were subjected to the determination and specification using color-coded microspheres coated with purified HLA antigens. In a cohort of 934 patients awaiting kidney transplantation, 41 sera (4.4%) were positive for IgG anti-HLA class II antibodies. The presence was confirmed in 90.2% sera by retesting. Subsequently, all anti-HLA class II-positive patients (n = 27) who in the past had undergone a kidney transplantation with an HLA-DR and/or -DQ-mismatched graft were selected. In 25 of 27 sera (92.6%), the alloantibody specificities corresponded to the known previous transplant mismatches on a broad antigen level. In 20 of 27 sera (74.1%), anticlass I antibodies were detected as well. Anti-HLA-DP antibodies were seen in 24 of the 27 sera of this cohort. In the majority of the cases, the reactivities with different DPB1 alleles could be explained by involvement of a single, specific DPB1 epitope. Donor-specific anti-HLA-DR and -DQ antibodies were seen in the majority of cases with graft failure following HLA class II alloantigen exposure in prior kidney transplantations. In addition, HLA-DP may serve as a transplantation antigen in kidney transplantation, leading to a humoral response.

Assembly of alternating polycation and DNA multilayer films by electrostatic layer-by-layer adsorption

The assembly of alternating DNA and positively charged poly(dimethyldiallylammonium chloride) (PDDA) multilayer films by electrostatic layer-by-layer adsorption has been studied. The real-time surface plasmon resonance (BIAcore) technique was used to characterize and monitor the formation of multilayer films in solution in real time continuously. Electrochemical impedance spectroscopy (EIS) and UV-vis absorbance measurements were also used to study the film assembly, and linear film growth was observed. All the results indicate that the uniform multilayer can be obtained on the poly(ethylenimine)- (PEI-) coated substrate surface. The kinetics of the adsorption of DNA on PDDA surface was also studied by the real-time BIAcore technique; the observed rate constant was calculated using a Langmuir model (k(obs) = (1.28 +/- 0.08) x 10(-2) s(-1).

Acute and subacute toxicity and efficacy of S-nitrosylated captopril, an ACE inhibitor possessing nitric oxide activities

The toxicity and efficacy of S-nitrosocaptopril (CapNO), a novel vasodilator possessing the capacities of both a nitric oxide donor and an angiotensin converting enzyme (ACE) inhibitor, were examined in rodents. In single-dose acute toxicity studies in ICR mice, the median lethal dose (LD(50)) for CapNO was 674+/-94 mg/kg (iv) and 2078+/-100 mg/kg (po), whereas for oral captopril was 4286+/-173 mg/kg. S-nitrosoglutathione, containing the same S-nitroso moiety as CapNO, showed an LD(50) equal to CapNO when the values were expressed by the mol/kg. The cause of acute death by the high doses of CapNO was lethal hypotension. In the subacute toxicity studies, oral CapNO was well tolerated in normotensive and hypertensive rats at doses up to 500 mg/kg/day for 3 months, except for considerable reductions in food consumption and growth rate observed in the 500 mg/kg/day group. Serum chemistry and hematology tests performed in the subacute toxicity studies revealed no adverse effects of oral CapNO except for a significant decrease in cholesterol levels in hypertensive SHR rat. At autopsy, no histopathological changes in major organs were observed over the subacute period. Administration of a therapeutic dose of CapNO (iv, 250 microg/kg which produced 25% decreases in blood pressure) revealed no changes in the hematological parameters. Subchronic treatment of SHR and SS/Jr rats with oral CapNO (50 mg/kg/day) significantly reduced mean arterial pressure to the normotensive level. Considering the absence of adverse effects of CapNO in the subchronic toxicity study, CapNO appears to be a safe drug for further clinical trials, but particular caution must be taken because it can cause hypotension when overdosed.

Ion-induced rectification of nanoparticle quantized capacitance charging in aqueous solutions

Ion-induced rectification of nanoparticle quantized capacitance charging was studied using nanoparticle self-assembled monolayers in aqueous solutions in the presence of some unique electrolyte ions. The rectified charging features were interpreted on the basis of a Randles equivalent circuit where the binding of hydrophobic electrolyte ions to surface-confined particle molecules led to the manipulation of the electrode interfacial capacitance. It was found that the rectification effects were directly related to the ion hydrophobicity, manifested by the cathodic (anodic) shift of the onset potential with anions (cations) of increasing hydrophobicity Additionally, the voltammetric responses evolved from those similar to conventional molecular diodes to those of quantized charging rectifiers with increasing anion hydrophobicity. Electron-transfer kinetics evaluated by using various electrochemical methods yielded a rate constant within the range of 10-100 s(-1) which decreased with increasing length of the alkyl spacers with a coupling coefficient (beta) within the range of 0.8-0.9. Comparisons with conventional electroactive functional moieties were also discussed.

Amplification of antigen-antibody interactions based on biotin labeled protein-streptavidin network complex using impedance spectroscopy

Antibody was covalently immobilized by amine coupling method to gold surfaces modified with a self-assembled monolayer of thioctic acid. The electrochemical measurements of cyclic voltammetry and impedance spectroscopy showed that the hexacyanoferrate redox reactions on the gold surface were blocked due to the procedures of self-assembly of thioctic acid and antibody immobilization. The binding of a specific antigen to antibody recognition layer could be detected by measurements of the impedance change. A new amplification strategy was introduced for improving the sensitivity of impedance measurements using biotin labeled protein-streptavidin network complex. This amplification strategy is based on the construction of a molecular complex between streptavidin and biotin labeled protein. This complex can be formed in a cross-linking network of molecules so that the amplification of response signal will be realized due to the big molecular size of complex. The results show that this amplification strategy causes dramatic improvement of the detection sensitivity of hIgG and has good correlation for detection of hIgG in the range of 2-10 microg/ml.

The stability of cytokeratin 18 in human liver cells during colchicine-induced microtubule disruption

The cytoskeleton plays important roles in cell function and is therefore implicated in the pathogenesis of many human liver diseases, including malignant tumors. The stability of cytokeratin proteins during tumor transformation in human hepatocellular carcinoma has been studied with a molecular approach previously. The results demonstrate that the cytokeratin is modulated in human hepatocellular carcinoma. Besides this, three low molecular weight cytokeratin molecules (named HCC CK) are found. This indicates that these HCC CKs have undergone modulation from the human hepatocyte cytokeratin 18. We also checked the cytokeratin profile of the human hepatoma cell line PLC/PRF/5 with the same methods to ensure the HCC CK molecules are produced by modulation but not protein degradation. The stability of cytokeratin molecules was studied by a different approach. The cytokeratin compositions of human liver cells (Chang cell line) were analysed under the effects of microtubule-disrupting drug (colchicine) by SDS-PAGE, Western blot, immunoprecipitation using a commercially available monoclonal anti-cytokeratin 18 antibody and immunofluorescent staining. Within 1 h of treatment, the microtubule began to collapse and the filamentous structure was shortening. The microtubule had almost collapsed and became fragmented to form a lattice-like network after 24 h of treatment. The cytokeratin was modulated after long-term (24 h) treatment of colchicine, and the molecular weight became 14 kD and the antigenicity was lost. The stability of cytokeratin molecules was related to the intact microtubule network, after disruption of the microtubule the cytokeratin would be modulated. The intact microtubule network was a stabilizing factor of cytokeratin 18 in human liver cells.

Enhanced surface plasmon resonance immunosensing using a streptavidin-biotinylated protein complex

In this paper, we present a novel strategy for improving the sensitivity of surface plasmon resonance immunosensing using a streptavidin-biotinylated protein complex. This amplification strategy is based on the construction of a molecular complex between streptavidin and biotin labeled protein. The complex can be formed in a cross-linking network of molecules so that the amplification of the response signal will be realized due to the big molecular size of the complex. The results show that the amplification strategy causes a dramatic improvement of the detection sensitivity. hIgG protein could be detected in the range of 0.005-10 micrograms ml-1.

Flow cytometric detection of HLA antibodies using a spectrum of microbeads

We describe here the use of HLA antigen coated beads for specificity and class determination of HLA antibodies by flow cytometry. The HLA specificity of antibodies was determined by use of beads containing eight levels of fluorescence. HLA antigens isolated from eight cultured cells were coated onto these beads so that each bead was the equivalent of one cell. By using four sets of eight beads, an equivalent of 32 cells could be examined in four test tubes. A total of 76 class I and 25 class II specificities could be determined by the 32 class I bead-panel and 32 class II bead-panel used, respectively. We noted no cross-reactivity of reactions between class I and II. The sensitivity of the test was shown to be higher than that of the standard cytotoxicity by dilution experiments and detection of additional cross-reacting antigens. By use of these coated beads, we achieved improved standardized detection of HLA antibodies. Antigen-coated beads have several advantages over the use of spleens or lymphocytes. (a) A highly selected panel of antigens can be routinely used. (b) Class I and class II antibodies can be readily distinguished from each other, even when they are present as mixtures in one serum. (c) Non-HLA antibodies are not detected because the beads do not have any other antigens than HLA on them. (d) The quantity of antigens coated on beads is more uniform than that found in cells from different individuals. (e) Beads are more convenient for storage and daily use.

Simultaneous HLA Class I and Class II antibodies screening with flow cytometry

A flow cytometric method of simultaneously screening both HLA Class I and Class II panel reactive antibodies (PRA) was developed using a pool of 30 different Class I and 30 different Class II microbeads coated with purified HLA antigens. The antibodies in the serum that react specifically to the coated HLA antigens are detected by using a FITC-conjugated antibody against human IgG. Percent PRA can be determined by the percentage of microbeads that react positively to the serum. There is no cross-reactivity between the Class I and Class II microbeads. A mixture of Class I and Class II microbeads can be distinguished by their different fluorescent properties on the flow cytometry analysis. Thus, both Class I and Class II PRA can be detected from a single tube reaction.

A simultaneous negative and positive selection method that can detect chimerism at a frequency of 1 per 10,000 by flow cytometry

A three-color flow cytometric method with a simultaneous negative and positive selection (SNAPS) approach has been developed to detect blood chimerism using a FITC-conjugated recipient-specific HLA monoclonal antibody, a biotinylated donor-specific HLA monoclonal antibody and Cy5-PE-conjugated streptavidin and a PE-conjugated CD3 monoclonal antibody. Detection of simulated blood chimerism at a frequency of 0.01% was achieved by SNAPS. In contrast, by one-color flow cytometry methods, chimerism can be detected at only about 3-4% with the same donor-specific HLA monoclonal antibody. The percentages of donor CD3 cells detected by SNAPS are proportional to the percentages of donor CD3 cells counted. SNAPS method provides a fast, sensitive and reliable way to analyze trace amounts of donor cells in a recipient's blood.

Cloning of a transcriptionally active human TATA binding factor

Transcription factor IID (TFIID) binds to the TATA box promoter element and regulates the expression of most eukaryotic genes transcribed by RNA polymerase II. Complementary DNA (cDNA) encoding a human TFIID protein has been cloned. The human TFIID polypeptide has 339 amino acids and a molecular size of 37,745 daltons. The carboxyl-terminal 181 amino acids of the human TFIID protein shares 80% identity with the TFIID protein from Saccharomyces cerevisiae. The amino terminus contains an unusual repeat of 38 consecutive glutamine residues and an X-Thr-Pro repeat. Expression of DNA in reticulocyte lysates or in Escherichia coli yielded a protein that was competent for both DNA binding and transcription activation.

Yeast TATA-box transcription factor gene

The first step in the transcription of most protein-encoding genes in eukaryotes is the binding of a transcription factor to the TATA-box promoter element. This TATA-box transcription factor was purified from extracts of the yeast Saccharomyces cerevisiae by using reconstitution of in vitro transcription reactions as an assay. The activity copurified with a protein whose sodium dodecyl sulfate/polyacrylamide gel mobility is 25 kDa. The sequence of the amino-terminal 21 residues of this protein was determined by sequential Edman degradation. A yeast genomic library was screened with mixed oligonucleotides encoding six residues of the protein sequence. The yeast TATA-box factor gene was cloned, and DNA sequencing revealed a 720-base-pair open reading frame encoding a 27,016-Da protein. The identity of the clone was confirmed by expressing the gene in Escherichia coli and detecting TATA-box factor DNA binding and transcriptional activities in extracts of the recombinant E. coli. The TATA-box factor gene was mapped to chromosome five of S. cerevisiae. RNA blot hybridization and nuclease S1 analysis indicated that the major TATA-box factor mRNA is 1.3 kilobases, including an unusually long 5' untranslated region of 188 +/- 5 nucleotides. Homology searches showed a region of distant similarity to the calcium-binding structures of calpains, a structure that has a conformation similar to the helix-turn-helix motif of DNA binding proteins.

Multiple transcription factor binding sites mediate adenovirus E1A transactivation

We studied the response of simple synthetic promoter regions to transactivation by the adenovirus early region 1A (E1A) protein. Binding sites for one or two host cell transcription factors were substituted for the E1B promoter region in reconstructed virus mutants, and the response to E1A transactivation was assayed during the early phase of infection. We found that a single CREB/ATF binding site resulted in a surprisingly strong promoter which responded to E1A. A CREB/ATF binding site placed upstream of the E1B TATA box behaved much like the wild-type E1B promoter, which is composed of a single Sp1 binding site plus a TATA box. A single E2F binding site resulted in an extremely weak promoter which did not respond to E1A, much like a single Sp1 site. Two E2F sites in an inverted orientation with the same spacing as in the adenovirus type 2 E2 early promoter produced a strong, E1A-responsive promoter. Substitution of the E4 TATA box region for the E1B TATA box region produced a promoter about five times stronger than the wild-type E1B promoter in the absence of E1A. However, the E4 TATA box substitution did not respond significantly to E1A transactivation. These results directly demonstrate that many different transcription factor binding sites, including the E1B TATA box, a CREB/ATF binding site, and two E2F sites, can mediate E1A transactivation. Other transcription factor binding sites cannot mediate an E1A response; these other sites include the E4 TATA box, a single Sp1 binding site, and a single E2F binding site. Implications of these findings for the mechanism of E1A transactivation are discussed.

Differential stability of c-myc mRNAS in a cell-free system

We have developed a simple cell-free system for studying the stability of different mRNAs in vitro. We demonstrate that the threefold greater stability in vivo of truncated c-myc mRNA (lacking exon 1) compared with that of full-length c-myc mRNA is maintained in our in vitro system. Chimeric mRNAs in which the first exon of c-myc was fused to immunoglobulin C alpha heavy chain or glyceraldehyde-3-phosphate dehydrogenase mRNAs were not rapidly degraded, demonstrating that c-myc exon 1 alone is not sufficient to tag mRNAs for rapid degradation. Competition experiments show that full-length c-myc mRNA is specifically recognized by a factor(s) responsible for its rapid degradation. This system will allow further characterization and purification of these factors.