Dynamic contributions to the DNA binding entropy of the EcoRI and EcoRV restriction endonucleases

Molecular Dynamics simulations on DNA-EcoRI and DNA-EcoRV complexes suggest that the DNA within these complexes is significantly more ordered than free DNA. Similarly, both the protein and the DNA are more ordered in the specific (cognate) DNA-EcoRV complex than they are in the non-cognate DNA-protein complex, consistent with recently proposed analogies between protein folding and sequence-specific DNA-protein recognition. Analysis of the trajectories shows that the net entropy gain upon specific binding to be the result of opposing contributions. Solvent release, which increases entropy versus configurational terms (as measured by the magnitude of the atomic fluctuations), and collective terms from tight coupling between the motions of the protein and the DNA.

Tandem genes encode cell-surface polypeptides SspA and SspB which mediate adhesion of the oral bacterium Streptococcus gordonii to human and bacterial receptors

The highly conserved antigen I/II family of polypeptides produced by oral streptococci are believed to be colonization determinants and may mediate adhesion of bacterial cells to salivary glycoproteins absorbed to cells and tissues in the human oral cavity. Streptococcus gordonii is shown to express, on the cell surface, two antigen I/II polypeptides designated SspA and SspB (formerly Ssp-5) that are the products of tandemly arranged chromosomal genes. The structure and arrangement of these genes is similar in two independently isolated strains, DL1 and M5, of S. gordonii. The mature polypeptide sequences of M5 SspA (1539 amino acid (aa) residues) and SspB (1462 aa residues) are almost wholly conserved (98% identical) in the C-terminal regions (from residues 796 in SspA and 719 in SspB, to the respective C-termini), well-conserved (84%) at the N-terminal regions (residues 1-429), and divergent (only 27% identical residues) within the intervening central regions. Insertional inactivation of the sspA gene in S. gordonii DL1 resulted in reduced binding of cells to salivary agglutinin glycoprotein (SAG), human erythrocytes, and to the oral bacterium Actinomyces naeslundii. Further reductions in streptococcal cell adhesion to SAG and to two strains of A. naeslundii were observed when both sspA and sspB genes were inactivated. The results suggest that both SspA and SspB polypeptides are involved in adhesion of S. gordonii cells to human and bacterial receptors.

Spread of murine cytomegalovirus to inner ocular structures following disruption of the blood-retina barrier in immunosuppressed BALB/c mice

PURPOSE

The aims of this study were to determine whether disruption of the blood-retina barrier (BRB) increases spread of murine cytomegalovirus (MCMV) to the eye after intraperitoneal inoculation and whether systemic immunosuppression influences the location of MCMV in the ocular compartment.

METHODS

The BRB of the left eye of normal and immunosuppressed mice was disrupted by supraciliary inoculation of tissue culture medium followed 2 hours later by intraperitoneal injection of MCMV. Plaque assay of homogenized ocular tissue was used to determine the frequency of virus-positive eyes and the titer of virus in the eyes. Beta-galactosidase staining of frozen sections was used to locate virus in the eyes.

RESULTS

In nonimmunosuppressed mice, the frequency of virus isolation, as well as the titer of virus, were significantly higher in eyes in which the BRB had been disrupted. Although the frequency of virus isolation was the same in both eyes of immunosuppressed mice, the titer of virus was significantly higher in the eye in which the BRB had been disrupted. The most striking result was that the location of virus was different in the nondisrupted eyes of immunosuppressed mice than it was in the disrupted eyes of immunosuppressed mice. In the former, virus was seen only in the outer ocular structures (conjunctiva, sclera, lacrimal gland), whereas in the latter, virus was observed in the retina and anterior segment (iris, ciliary body) as well as the outer ocular structures.

CONCLUSIONS

The results of these studies suggest that ocular damage followed by increased spread of virus to and within the eye during systemic infection with CMV may be one mechanism by which development of CMV retinitis is facilitated in patients with acquired immune deficiency syndrome.

Immunosuppression induces transcription of murine cytomegalovirus glycoprotein H in the eye and at non-ocular sites

In these studies, DNA PCR was used to identify sites of murine cytomegalovirus (MCMV) latency after inoculation of virus into the supraciliary space of the eye. Reverse transcription (RT) PCR for an immediate early gene and a late gene was used to identify putative sites of virus reactivation after methylprednisolone (steroid)-induced immunosuppression. Ten weeks after inoculation of 5 x 10(2) PFU of MCMV, BALB/c mice were immunosuppressed by intramuscular injection of steroid. Control mice were infected but not immunosuppressed. Two weeks after initiation of immunosuppression, mice were sacrificed. DNA and RNA extracted from homogenized tissues were amplified for immediate early gene 1 (IE1) and late gene, glycoprotein H (gH), DNA and mRNA by PCR and RT-PCR, respectively. Replicating virus was detected in homogenized ocular and non-ocular tissues by plaque assay. In the latently infected PBS-treated control group, viral DNA was detected in the inoculated eye and in several non-ocular tissues; IE1 mRNA was found in most of the DNA-positive tissues, while gH mRNA was amplified only in a few of the MCMV DNA-positive tissues from a single mouse. After immunosuppression, viral DNA and IE1 mRNA were detected at a higher frequency in various tissues of steroid-treated mice. gH mRNA was detected in a significantly higher number of the inoculated eyes, salivary glands and other non-ocular tissues of steroid-treated mice. After immunosuppression, low titers of infectious virus were recovered from the salivary glands of steroid-treated mice, but infectious virus was not recovered from the inoculated eye of either steroid-treated of non-immunosuppressed mice. The DNA PCR results suggest that after inoculation of 5 x 10(2) PFU of MCMV into the supraciliary space of euthymic BALB/c mice, virus becomes latent in the inoculated eye, salivary gland and other extraocular tissues. The RT-PCR results suggest that latent MCMV can be reactivated in multiple tissues by immunosuppression.

Clinical application of modified Anyang type 2 esophageal intubation instrument--a new esophageal intubation method

The preliminary experience in the clinical use of Anyang Type 2 esophageal intubation instrument, designed by ourselves, in 11 patients with severe esophageal obstruction due to advanced carcinoma of the esophageal was reported. The diagnosis of all 11 cases was confirmed by barium-meal roentgenography. After intubation, all the patients could take liquid or soft diet by mouth. There was no operative mortality and the patients survived 2 to 14 months (mean 5.7 months). All of them could take food by mouth before death. The clinical application proved that the intubation has been a safe and suitable management.

[Application of transcranial color Doppler flow imaging in the carotid cavernous sinus fistulae]

Transcranial color Doppler flow imaging (TCCDFI) allows for simultaneous two-dimensional structural imaging and Doppler evaluation of blood flow through intact skull. With this technique, we evaluated 10 patients with carotid cavernous sinus fistulae (CCSF) and 35 normal volunteers. Each of them was confirmed by angiography. TCCDFI showed that patients with CCSF had typical signs in the affected part. The cavernous sinus had mosaic color shade. Pulse-Doppler showed disorderly polydirection vortex blood flow spectra in the mosaic color shade associated with murmur. Two-dimensional sonography and color Doppler imaging demonstrated a dilated superior ophthalmic vein (SOV) with arterialized blood flow. The Vmax of MCA and ACA in the affected side were lower than the healthy and normal side. The RI was lower than that of the healthy side and PCA of both sides was lower than that in normal volunteers. Two patients were examined after tubolization. Mosaic color shade disappeared and SOV returned to normal venous flow in patients completely occluded. Mosaic color shade reduced and SOV still aterialized blood flow in partly occluded patients. This technique helps to confirm the clinical diagnosis and to track the hemodynamics of CCSF patients and evaluate the effect of therapy.

Molecular dynamics simulations suggest that the Eco RI kink is an example of molecular strain

The energy surface in the vicinity of the "Eco RI kink" was investigated by conducting both in vacuo molecular dynamics simulations as well as a simulation with explicit solvent. The in vacuo simulations used the "all atom" AMBER 3.0 force field with a distant dependent dielectric function and "hydrated" counter ions while the simulation with explicit solvent used the AMBER 4.0 force field, fully charged phosphates and counter ions and a dielectric constant of 1.0. The thrust of the simulations was to discriminate between two models of the energy surface of the deformed DNA as found in the recognition complex with Eco RI endonuclease. In the intrinsic model, the kinked DNA is a local minimum of the energy surface intrinsic to the DNA itself while in the strained model there is no significant energy barrier separating kinked and regular B-DNA. The two models have significant implications for theories of indirect recognition of DNA based on sequence-dependent deformability. The simulations suggest that the Eco RI-kinked structure is an example of molecular strain because it is not near a minimum of any of the potential energy functions examined. The simulations leave the question of an energy barrier somewhat open and raise the possibility that the Eco RI kink is at (or near) a point of dynamic instability of the energy surface (either a true maximum or a saddle point).

Calcium-binding properties of SSP-5, the Streptococcus gordonii M5 receptor for salivary agglutinin

Streptococcus gordonii M5 expresses a lectin on its surface (SSP-5) which binds to human salivary agglutinin (SAG). This interaction requires sialic acid residues of SAG and divalent cations and may mediate the colonization of oral tissues by this organism. In this report, we show that the binding of SAG to SSP-5 requires calcium and that SSP-5 is a high-affinity calcium-binding protein. SAG-mediated aggregation of S. gordonii M5 was inhibited by 1 mM EDTA, and the restoration of aggregation occurred only upon the readdition of calcium. To ascertain the level at which calcium exerts its effects, the calcium-binding properties of SSP-5 were evaluated by using a 45Ca binding assay. In addition, a kinetic analysis of calcium binding was carried out by using fura2, a fluorescent calcium-binding dye. These analyses showed that SSP-5 is a high-affinity calcium-binding protein that binds 1 mol of calcium per mol of protein and has a dissociation constant of 0.45 +/- 0.2 microM. The calcium-binding capacity of SSP-5 was also calculated independently to be 1.0 +/- 0.2 mol of Ca per mol of SSP-5 by column chromatography on Sephadex G-25 equilibrated with 10 microM 45Ca. To localize the calcium binding site of SSP-5, a series of C-terminal deletion mutants were expressed in Escherichia coli and evaluated for calcium-binding activity. Deletion of the 250 C-terminal residues of SSP-5 had little effect on calcium binding. However, deletion of residues 1168 to 1250 resulted in the loss of calcium-binding activity, suggesting that this region is important for calcium binding by SSP-5.

[Immunological cross-reaction of serotype I Marek's disease virus 38kD phosphorylated protein with serotype II and III viruses]

Marek's disease virus (MDV) 38kD phosphorylated protein (pp38), which was identified by monoclonal antibody (mAb) H19 specific to pathogenic serotype I of MDV, has been recognized as a transformation-associated antigen specific to serotype I of MDV. The recombinant pp38 was prepared and purified from pp38-expressing recombinant baculovirus infected Sf9 cell lysates through a mAb H19-affinity column. In indirect fluorescence antibody test, the mouse sera against the purified recombinant pp38 not only gave a high titer to serotype I strain GA-infected CEF but also gave a reasonable titers to serotype II strain Z4- and serotype III HVT strain Fc126-infected CEF. In another way, the pp38- expressing recombinant baculovirus infected Sf9 cells reacted with anti-serotype I MDV chicken sera as well as with anti-serotype II and serotype III MDV chicken sera respectively. The results imply that both serotypes II and III of MDV probably contain a homologue to pp38 of serotype I.

Purification and characterization of multiple forms of the pineapple-stem-derived cysteine proteinases ananain and comosain

A mixture of ananain (EC 3.4.22.31) and comosain purified from crude pineapple stem extract was found to contain numerous closely related enzyme forms. Chromatographic separation of the major enzyme forms was achieved after treatment of the mixture with thiol-modifying reagents: reversible modification with 2-hydroxyethyl disulphide provided enzyme for kinetic studies, and irreversible alkylation with bromotrifluoroacetone or iodoacetamide gave enzyme for structural analyses by 19F-n.m.r. and electrospray mass spectrometry respectively. Structural and kinetic analyses revealed comosain to be closely related to stem bromelain (EC 3.4.22.32), whereas ananain differed markedly from both comosain and stem bromelain. Nevertheless, differences were seen between comosain and stem bromelain in amino acid composition and kinetic specificity towards the epoxide inhibitor E-64. Differences between five isolatable alternative forms of ananain were characterized by amidolytic activity, thiol stoichiometry and accurate mass determinations. Three of the enzyme forms displayed ananain-like amidolytic activity, whereas the other two forms were inactive. Thiol-stoichiometry determinations revealed that the active enzyme forms contained one free thiol, whereas the inactive forms lacked the reactive thiol required for enzyme activity. M.s. provided direct evidence for oxidation of the active-site thiol to the corresponding sulphinic acid.

Dissemination and replication of MCMV after supraciliary inoculation in immunosuppressed BALB/c mice

PURPOSE

To study replication and dissemination of murine cytomegalovirus (MCMV) in immunosuppressed (IS) and non-IS BALB/c mice after ocular inoculation via the supraciliary route.

METHODS

BALB/c mice were immunosuppressed by injections of methylprednisolone, and MCMV was injected via the supraciliary route. Ocular and nonocular tissues from both IS and non-IS mice were studied by plaque assay of tissue homogenates. The frequency of virus-positive leukocytes was determined by PCR.

RESULTS

In the inoculated eye, virus replication was significantly higher in both the anterior segment and the posterior segment of IS mice. Virus spread to extraocular sites in both IS and non-IS mice; however, significantly higher titers of virus were recovered from the salivary glands and lungs of IS mice than from non-IS mice, and clearance of virus from these sites was delayed in IS mice. Virus spread from the injected eye via leukocytes, and PCR amplification revealed that the frequency of virus-infected leukocytes was approximately 200-fold higher in IS mice.

CONCLUSIONS

The results of these studies suggest that immunosuppression significantly enhances virus replication in the inoculated eye, salivary glands, and lungs, leads to a higher frequency of virus-positive leukocytes, and delays clearance of virus from ocular and nonocular tissues. These results also suggest that retinitis in the injected eye of IS mice correlates with significantly higher titers of virus in the posterior segment.

Protease substrate specificity mapping using membrane-bound peptides

A method is described for assessing the substrate specificity of proteases by screening for proteolytic activity against large numbers of peptides. All 400 possible peptides derived from the 20 common amino acids were synthesized on small membrane disks in the arrangement FTC-spacer-amino acid P1-amino acid P'1-spacer-membrane, where FTC is a chromophoric group. The disks are incubated simultaneously with the protease, resulting in cleavage of the peptide between the P1 and P'1 amino acids, and the absorbance of the released chromophore is measured as a function of time. As demonstrated for chymotrypsin and papain, plots of the resulting data present a perspective view of the amino acid preferences on both sides of the scissile bond. This technique is fast, requires relatively little enzyme, and can be extended to the systematic screening of longer peptides, including analogs with unnatural amino acids. It has potential use for characterizing the specificity of proteases, assessing the results of site-specific mutagenesis, and searching for optimal substrates and inhibitors.

Changes in bone formation during experimental tooth movement after denervation of the rabbit inferior alveolar nerve

The effects of nerve fibers on bone formation during tooth movement were examined using eight rabbits with denervation of inferior alveolar nerve (IAN). IAN on one side for all the animals was denervated and and sham operation was performed on the other side of denervation. The distance of tooth movement on the denervated and sham operated sides was very similar and 1.20 +/- 0.17 and 1.24 +/- 0.12 (mean +/- S.D. mm), respectively. From the fluorescent observations, the denervated and sham operated sides in the animals without tooth movement i.e. control group showed similar morphology. The animals with tooth movement i.e. experimental group showed significant new bone formation than the control group. However, the amount of new bone formation on the denervated side was less than the sham operated side. It was suggested that the nerve fibers might play some roles on bone formation during the tooth movement.

Effect of centrifugal force on growth of mouse osteoblastic MC3T3-E1 cells in vitro

The effect of biomechanical force on growth of skeletal tissue was studied in monolayer cultures of mouse osteoblastic MC3T3-E1 cells which were centrifuged at 320 g for 15 min to 72 h in a CO2 incubator. Centrifugation of the cells for 30 min in low concentrations (0.3 or 1%) of fetal bovine serum (FBS) caused a two-fold increase of [3H]thymidine incorporation at 20 h from the start of centrifugation. However, centrifugation under 10% FBS caused no increase in [3H]thymidine incorporation into DNA. Under 0.3% FBS, [3H]thymidine incorporation increased in a manner dependent on the period of centrifugation and reached a maximum when the cells were centrifuged for 3 h. Stimulation of DNA synthesis by centrifugation was abolished in the presence of H-7, an inhibitor of protein kinase C. Moreover, conditioned medium collected from the centrifuged cultures increased [3H]thymidine incorporation by two-fold over the basal when added to a quiescent culture of MC3T3-E1 cells. These results suggest that centrifugal force stimulates growth of osteoblastic cells through autocrine secretion of some diffusible growth-promoting activity. On the other hand, centrifugation of the cells inhibited induction by FBS of alkaline phosphatase activity and calcium-uptake, two indices of the differentiated phenotype of osteoblasts.

Haptoglobin types in Chinese ethnic groups

The distribution of haptoglobin (HP) types was examined in six different Chinese ethnic groups. The gene frequencies were compared among these groups and to those reported in other Chinese Han populations. The effects of sex and age on the distribution of HP types are also discussed.