Relative binding free energy calculations of DNA to daunomycin and its 13-dihydro analogue

We present the results of thermodynamic integration/molecular dynamics on the 13-dihydrodaunomycin.d(CGTACG) complex and 13-dihydrodaunomycin in vacuo based on the GROMOS force field. The objective is to calculate the binding free energy differences between two complexes--13-dihydrodaunomycin.d(CGTACG) and daunomycin.d(CGTACG). The results are in agreement with the experimental data, i.e. the theoretical binding free energy difference of 13-dihydrodaunomycin.d(CGTACG) and daunomycin.d(CGTACG) is 2.1 +/- 1.6 kcal/mol which accords well with the experimental value of 0.6 kcal/mol. The free energy contributions of different interactions and different groups have also been analysed.

High levels of Nm23 gene expression in advanced stage of thyroid carcinomas

The product of Nm23 gene has been proposed as a candidate tumour metastasis suppressor protein. A strong association has been observed between reduced expression of Nm23 gene and acquisition of metastatic behaviour in some tumour cells including breast cancer and melanoma, but not in others such as colon cancer, neuroblastoma, and cervical cancer. In the present study, we examined the abundance of Nm23 mRNA in 39 thyroid tissue specimens including five multinodular goitres, one follicular adenoma, 26 papillary and three follicular carcinomas, and four anaplastic carcinomas. Nm23 was found to be expressed in all the tissue specimens. The expression was, however, variable in different stages of thyroid carcinoma. In stages I through III of differentiated thyroid carcinoma, the average level of Nm23 gene expression was comparable to that in multinodular goitres. In advanced stage of thyroid carcinoma (stage IV and anaplastic), 2-fold increase of Nm23 expression was noted. No mutations were found in the coding region of the gene. Nm23 mRNA level cannot, therefore, be used as a marker of low metastatic potential in thyroid carcinomas. The association of high level Nm23 expression with anaplastic thyroid carcinoma suggests its correlation with rapid cell proliferation.

Evidence for physical interaction between the zinc-finger transcription factors YY1 and Sp1

Two promoter elements are important for basal-level transcription, the TATA motif typically located 30 nucleotides upstream of the transcription initiation site and the initiator (Inr) element encompassing the start site. The mechanism of how Inr elements work is poorly understood, partly because very few proteins that bind to Inr elements have been identified and isolated. The recently cloned YY1 is such an Inr-binding protein. YY1 is able to direct transcription upon binding to its recognition sequence in vitro. The ability of YY1 to initiate transcription is augmented by the presence of a TATA motif or binding sites for transcription factor Sp1. To study the mechanism underlying the apparent functional cooperation between YY1 and Sp1, we explored the possibility of protein-protein interactions between these two transcription factors. We found that YY1 and Sp1 can form a physical complex. In addition, we identified domains within YY1 and Sp1 that mediate their interactions with each other. The physical interaction between YY1 and Sp1 may thus form the basis for the functional interplay observed previously.

[High-resolution cytogenetic study of a patient with Prader-Willi syndrome]

We investigated a patient with Prader-Willi syndrome by using the high-resolution banding technique. His clinical findings were also examined in some detail. The patient had interstitial deletion of 15q, with breakpoints at 15q11.2 and 15q13. However, he had a normal karyotype at about 400 bands per haploid-set. During the course of this study, it was realized that a small deletion in the proximal 15q could be easily overlooked when a mitotic spread of about 400-bands or less per haploid-set was used. It is suggested that the high-resolution banding technique is of great importance in identifying microdeletions and other microaberrations of chromosomes.

Temporal masking of human auditory evoked brain stem responses using two simultaneously presented maximum length sequences

Two simultaneously presented maximum length sequences (MLSs) were used to investigate temporal nonlinearities. Not only did the recorded auditory evoked brain stem responses to these stimuli predictably increase in latency and decrease in amplitude as a function of the temporal interactions between MLSs, but thresholds were elevated by more than 20 dB. Simultaneous MLS paradigms make it possible to investigate a number of nonlinearities in the auditory system efficiently. This study also demonstrated that binaural MLS techniques can be used to assess auditory function even in individuals with asymmetric hearing losses without fear of crossover effects.

DNA fragmentation induced by cytotoxic T lymphocytes can result in target cell death

Cytotoxic T lymphocyte (CTL)-mediated lysis is accompanied by fragmentation of target cell DNA into an oligonucleosome ladder, a hallmark of apoptosis. Is this a fortuitous coincidence, or could CTL be inducing lysis by activation of the suicide signal? In this report we demonstrate that CTL-mediated target cell death can be blocked with the drug aurintricarboxylic acid (ATA). The abrogation of death correlates with the inhibition of DNA fragmentation. While ATA prevented DNA fragmentation, it failed to significantly alter protein, RNA, or DNA synthesis in the cell lines over the dose range used. In addition, there was no inhibition of cell-cell interaction or granule exocytosis during CTL-mediated killing. ATA also significantly inhibited the cytolysis and DNA fragmentation mediated by isolated cytolytic granules, as well as the granular protein fragmentin. We developed an assay in which target cells could be separated from CTL after binding and programming for lysis. Once they had received the "kiss of death," target cells could be rescued from lysis (as indicated by inhibition of DNA fragmentation and increased target cell viability) by treatment with ATA. These results suggest that ATA blocks target cell death by inhibition of DNA fragmentation, and further, that chromatin degradation is a cause rather than a result of cell death in CTL-mediated lysis.

Binaural maximum length sequence auditory-evoked brain-stem responses in human adults

This study compared monaural and binaural maximum length sequence auditory-evoked brain-stem responses (MLS ABRs) in normal hearing adults. The first experiment demonstrated that reliable binaural MLS ABRs could be recorded which were essentially the same as those recorded monaurally. The second experiment generalized this finding by assessing a range of intensities including threshold stimuli. ABR thresholds, wave V latency x intensity and amplitude x intensity functions, wave V latency and amplitude reproducibility, and waveform reproducibility were comparable for the monaural and binaural MLS ABRs with some minor qualifications. In the third experiment, comparability of monaural and binaural MLS ABRs was generalized to a range of rates from those used conventionally to rates far faster than possible with signal averaging. Again, there was little difference between the binaural and monaural MLS ABRs over the range of rates assessed.

Autoreactive epitopes defined by diabetes-associated human monoclonal antibodies are localized in the middle and C-terminal domains of the smaller form of glutamate decarboxylase

The gamma-aminobutyrate-synthesizing enzyme glutamate decarboxylase (GAD; L-glutamate 1-carboxy-lyase, EC 4.1.1.15) is a major target of autoantibodies associated with both early and late stages of pancreatic beta-cell destruction and development of type 1 diabetes. We have used five monoclonal anti-islet-cell antibodies (MICAs 1,2,3,4, and 6) derived from a newly diagnosed diabetic patient to probe the autoimmune epitopes in the enzyme. All the MICAs specifically recognized the smaller GAD protein, GAD65, and did not recognize the nonallelic GAD67 protein. A series of N-terminal, C-terminal, and internal deletion mutants, as well as protein footprinting, were used to identify the target regions in GAD65. Immunoprecipitation revealed two major native epitope areas in the GAD65 molecule. The first, defined by MICAs 1 and 3, is destroyed by deleting 41 amino acids at the C terminus but is also dependent on intact amino acids 244-295. This epitope (or epitopes) may span both middle and C-terminal domains of the protein. The second conformational epitope region, defined by MICAs 4 and 6, is dependent on intact amino acids 245-295 but is not affected by deletion of 110 amino acids at the C terminus and is therefore confined to domain(s) in the middle of the molecule. MICA 2 recognizes a linear epitope close to the C terminus. Thus, the N-terminal domain of GAD65, which differs most significantly from GAD67, does not harbor the MICA epitopes. Rather subtle amino acid differences in the middle and C-terminal domains define the GAD65-specific autoimmune epitopes. Analysis of sera from 10 type 1 diabetic patients suggests that MICAs 1, 3, 4, and 6 represent a common epitope recognition in this disease, whereas the MICA 2 epitope is rare. Furthermore, autoantibodies in some sera are restricted to the MICA 1/3 epitope, suggesting that this epitope may represent a single dominant epitope in the early phases of beta-cell autoimmunity.

Metal binding properties of single amino acid deletion mutants of zinc finger peptides: studies using cobalt(II) as a spectroscopic probe

Peptides corresponding to Cys2His2 zinc finger domains from which one amino acid has been deleted have been synthesized and their metal-binding properties characterized. In contrast to earlier reports (Párraga, G., S. Horvath, L. Hood, E. T. Young, and R. E. Klevit. 1990. Proc. Natl. Acad. Sci. USA. 87:137-141.), such peptides do bind metal ions such as cobalt(II). A peptide with the sequence ProTyrLysCysProGluCysLysSerPheSerGlnLysSerAspLeuValLysHisGlnArgThrHis ThrGly (which corresponds to a previously characterized consensus zinc finger sequence from which a Gly residue immediately following the second Cys residue has been deleted) was found to form a 1:1 peptide to cobalt(II) complex with an absorption spectrum quite similar to those previously observed for zinc finger peptide-cobalt(II) complexes. The dissociation constant for this complex is 6 x 10(-6)M, a factor of 100 times higher than that for the parent peptide. A peptide with the sequence LysProTyrProCysGlyLeuCysArgCysPheThrArgArgAspLeuLeulleArgHisAlaGln - LyslleHisSerGlyAsnLeu corresponding to a similar mutation of the peptide ADR1 was also characterized. Spectroscopic studies with cobalt(II) revealed that this peptide forms both 1:1 and 2:1 peptide to cobalt(II) complexes. The absorption spectra of the two forms and the dissociation constants were determined via deconvolution methods. In contrast, the parent peptide ADR1a was found to form only a 1:1 complex under comparable conditions and this 1:1 complex was found to be more stable than that for the mutant. These results reveal that deletion mutations do adversely affect the stability of zinc finger peptide-metal complexes but that the effects are not as drastic as had been previously described.

[Transformation of recombinant plasmid pRK 41 and amplification of full-length coding region of human brain myelin basic protein cDNA]

Transformation of the recombinant plasmid pRK41 containing 2.15 kd human brain myelin basic protein MBP)-coding sequence and 3' untranslated region (1.2 kb) into the E. coli JM109 was made by using Hanahan's method. Positive colonies were screened with digoxigenin oligo labelled rat brain MBP cDNA fragment (1.2 kb). To remove 3' untranslated region and obtain the full-length coding sequence of MBP cDNA, a pair of specific DNA primers was designed and synthesized. A 600 bp fragment was amplified from the recombinant plasmid, extracted from the positive colony by using polymerase chain reaction (PCR). The PCR fragment was isolated, and then digested with BamH I, Kpn I and BamH I + Kpn I. The results of restriction analysis indicate that the PCR amplified fragment is desirable and can be used directly to constract expression vectors.

[Clinical observation of the effect of pretreatment with nifedipine in preventing oxygen free radicals in the cardiopulmonary release bypass operation]

The effect of pretreatment with nifedipine in preventing oxygen free radicals release was observed in the cardiopulmonary bypass (CPB) operation. Twenty cases were divided into two groups for comparison. Nifedipine (0.6 mg/kg) was given to the test group. MDA, XO, UA and SOD were measured. These examinations were taken at pre-aortic clamping, 15 min after aortic clamping, and 30, 60, 120, 180 min after reperfusion. The results indicated that pretreatment with nifedipine reduced oxygen free radicals release in the CPB operation.

Vaccination of bovines against Schistosomiasis japonica with cryopreserved-irradiated and freeze-thaw schistosomula

Four laboratory tests and one field trial with cryopreserved irradiated (CI) schistosomula vaccine and a freeze-thaw (F/T) vaccine against bovine Schistosomiasis japonica were carried out in 1979 and 1980 with the following results: (1) Single intradermal vaccination in buffalo calves each with 10,000 20 krad CI Schistosomula plus 1 ml BCG gave 62% worm reduction (P < 0.05). Using the same protocol 55% worm reduction (P < 0.01) was obtained in cattle. (2) Buffalo calves immunized twice, at a 1.5 month interval, with 10,000 and 20,000 CI schistosomula, respectively, resulted in a worm reduction 65%. (3) In a preliminary field trial with 10,000 CI schistosomula plus 1 ml BCG resulted in a worm reduction of 53% in buffalo calves. (4) Intradermal vaccination of 30,000 F/T schistosomula with 1 ml BCG was also tried in cattle and revealed a worm reduction of 57% but increasing the number of vaccinations did not improve the protective effect. (5) Evidence regarding the effects of immunization with CI vaccine in buffaloes and F/T vaccine in cattle, on the number of eggs and miracidia and that of female worms themselves was obtained. (6) Immune responses, cellular and humoral, elicited in buffaloes vaccinated with CI schistosomula were detected by means of Lymphocyte Transformation Assay and Enzyme Linked Immunosorbent Assay.

Coexisting stable conformations of gaseous protein ions

For further insight into the role of solvent in protein conformer stabilization, the structural and dynamic properties of protein ions in vacuo have been probed by hydrogen-deuterium exchange in a Fourier-transform mass spectrometer. Multiply charged ions generated by electrospray ionization of five proteins show exchange reactions with 2H2O at 10(-7) torr (1 torr = 133.3 Pa) exhibiting pseudo-first-order kinetics. Gas-phase compactness of the S-S cross-linked RNase A relative to denatured S-derivatized RNase A is indicated by exchange of 35 and 135 hydrogen atoms, respectively. For pure cytochrome c ions, the existence of at least three distinct gaseous conformers is indicated by the substantially different values--52, 113, and 74--of reactive H atoms; the observation of these same values for ions of a number--2, 7, and 5, respectively--of different charge states indicates conformational insensitivity to coulombic forces. For each of these conformers, the compactness in vacuo indicated by these values corresponds directly to that of a known conformer structure in the solution from which the conformer ions are produced by electrospray. S-derivatized RNase A ions also exist as at least two gaseous conformers exchanging 50-140 H atoms. Gaseous conformer ions are isometrically stable for hours; removal of solvent greatly increases conformational rigidity. More specific ion-molecule reactions could provide further details of conformer structures.

High-affinity binding of thyrotropin to the extracellular domain of its receptor transfected in Chinese hamster ovary cells

Thyrotropin (TSH) receptor is a cell surface receptor that shares a high degree of homology with other glycoprotein hormone receptors including lutropin-choriogonadotropin (LH/CG) and follicle-stimulating hormone (FSH) receptors. Although the extracellular domain of TSH receptor is important for ligand binding, no direct information is available on whether extracellular domain alone is sufficient for high-affinity binding. Moreover, mutations made in the second cytoplasmic loop or the cytoplasmic tail of TSH receptor were reported to reduce significantly the affinity of TSH binding. In an attempt to determine whether TSH receptor extracellular domain is sufficient for high-affinity TSH binding or whether it requires transmembrane regions, we made a construct (TSHR-EX/CMV) that encodes for only the extracellular domain plus a foreign hydrophobic tail. The TSHR-EX/CMV was transfected and stably expressed in Chinese hamster ovary (CHO) cells. The truncated receptor was anchored to the cell surface through the hydrophobic tail at the carboxyl terminus. High-affinity TSH binding was observed comparable to that of the cells transfected with full-length TSH receptor. The CHO cells transfected with TSHR-EX/CMV did not respond to TSH stimulation of adenylate cyclase, whereas the cells transfected with the full-length TSH receptor cDNA did. The data presented here show that the extracellular domain of TSH receptor is sufficient to confer high-affinity TSH binding.

Structure-function studies of the C-terminal alpha-helix of human interleukin-2 by site-directed mutagenesis

By using oligonucleotide-mediated site-directed mutagenesis, we obtained three human interleukin-2 analogs with substitution of Pro in the C-terminal amphiphilic alpha-helix, 125Pro-IL-2, 127Pro-IL-2 and 125Pro-127Pro-IL-2. The bioactivities of all these analogs were decreased. The extent of the decrease in bioactivity coincided with the degrees of secondary and tertiary structure destroyed, as evaluated by circular dichroism and intrinsic fluorescence analysis. The results suggested that the integrity of the hydrophobic face in the C terminal alpha-helix is crucial for the structure and function of interleukin-2.

Hypoxia-associated proteins in human cells cultivated in vitro: lack of association with hypoxia-induced cell cycle regulation

The synthesis of proteins expressed in human NHIK 3025 cells following exposure to extremely hypoxic conditions (< 4 ppm O2) has been studied. Populations of cells, either in exponential growth or synchronized by the method of detaching mitotic cells, were exposed to extremely hypoxic conditions for up to 20 h. The rate of total protein synthesis was measured at various time points after reoxygenation, and it appeared to be relatively constant and similar to the control level. The protein expression in cells was studied by pulse labelling for 1 h with [35S]-methionine, and subsequently visualized by SDS-PAGE and autoradiography. Six proteins appeared to have a changed expression after exposure to extreme hypoxia as compared to control cells; four of them (45, 80, 100 and 150 kD) showed increased, while two (46 and 90 kD) showed decreased expression. The response of these proteins to extreme hypoxia seems to be relatively slow, i.e. with half-times of several hours. Since extreme hypoxia influences cell cycle progression by instantaneous blockage at the G1/S border as well as halting DNA synthesis in S cells, these proteins can hardly cause these effects. Neither is the altered expression of these proteins due to the accumulation of G1 cells caused by hypoxia.

Activation-induced apoptosis in lymphoid systems

Lymphocytes become activated when antigen receptors on the cell surface are cross-linked, or when they are exposed to agents that mimic this signal. Although such activation is usually associated with the production of immune mediators (e.g. antibodies, cytokines) and entry into the cell cycle, it can alternatively lead to death via apoptosis. This activation-induced apoptosis was first observed in developing lymphocytes and has been proposed as a mechanism for negative selection, by which immature cells with potential for autoreactivity are eliminated from the maturation pathway. Activation-induced apoptosis has also been observed in normal, mature lymphocytes under some conditions, and this may account for the phenomena of peripheral deletion, in which mature T cells are eliminated upon exposure to high doses of antigen. It may also be an important mechanism whereby CD4+ T cells are depleted in HIV+ individuals. Although the phenomenon of activation-induced apoptosis is not understood, recent studies have begun to implicate specific signal transduction pathways and gene products in the process. Among the latter is the c-myc proto-oncogene, which paradoxically can play an essential role in several forms of apoptosis, including that induced by activation of lymphocytes.

The modulation transfer function in impedance imaging

The concepts of the point spread function (PSF) and its Fourier transform, the modulation transfer function (MTF) are introduced to evaluate an impedance imaging system. The effects of some practical factors which should be taken into account in calculating the MTF are analysed. Experimental results from the groups in Sheffield, Barcelona and Toulouse are presented.

Antisense oligodeoxynucleotides as probes of T-lymphocyte gene function

Conventional and thiophosphonate-derivatized oligonucleotides were employed to specifically regulate functional gene expression in murine T-cell hybridomas. For example, induction of apoptotic cell death following activation of T-cell hybridomas was examined using antisense oligonucleotides corresponding to several protooncogenes. We found that antisense oligodeoxynucleotides corresponding to c-myc inhibited both the characteristic DNA fragmentation and the loss of cell viability following activation without affecting production of lymphokines. Functional antisense oligonucleotides corresponding to c-fos had no effect in this system. These results demonstrate the use of antisense oligonucleotides to regulate function in T-cell hybridomas and provide valuable insights into the molecular bases of this biological phenomenon. Antisense oligonucleotides were also used to study another problem, the relation of T-cell-derived antigen-specific immunoregulatory factors to the T-cell receptor (TCR). Because the translation start of each TCR gene usually varies from one T cell to another, antisense oligonucleotides corresponding to the TCR V alpha or V beta of different cells were shown to act in a cell-specific manner. Furthermore, this method was used to demonstrate that a soluble antigen-specific regulatory activity produced by one of the T-cell lines depends on expression of the specific TCRa, an observation that has since been confirmed by gene transfer experiments. Expression of the CD3-TCR complex on the cell surface was also blocked by antisense oligonucleotides corresponding to CD3 gamma and CD3 zeta; however, neither these nor TCR V beta antisense oligonucleotides had any effect on production of the soluble regulatory activity.

Displacement of BrdUrd-induced YY1 by serum response factor activates skeletal alpha-actin transcription in embryonic myoblasts

Muscle-restricted transcription of the skeletal alpha-actin gene is controlled in part by a positive regulator, serum response factor (SRF), and a negative regulator, F-ACT1, which bind competitively to the most proximal serum response element (SRE1). We show here that F-ACT1 is identical to a transcription factor recently cloned and described as YY1, NF-E1, delta, or UCRBP. We found that although the DNA-binding activity of SRF accumulates during myogenesis, that of YY1 diminishes simultaneously. Myoblasts rendered incapable of differentiation by BrdUrd treatment exhibited the highest level of YY1 and the lowest level of SRF activities. Transfected SRF could directly transactivate the skeletal alpha-actin promoter by overcoming the inhibitory effect of BrdUrd-induced YY1. The transactivation depends on intact SRE DNA elements and requires the DNA-binding/dimerization domain of SRF as well as its C-terminal half rich in serines and threonines. Since the functions of YY1 and SRF appear to be developmentally regulated, the convergence of their binding sites upon the SRE constitutes an integrated mechanism whereby temporal and spatial muscle gene expression may be accomplished.