Reperfusion injury on cardiac myocytes after simulated ischemia

The extent of cardiac injury incurred during reperfusion as opposed to that occurring during ischemia is unclear. This study tested the hypothesis that simulated ischemia followed by simulated reperfusion causes significant "reperfusion injury" in isolated chick cardiomyocytes. Cells were exposed to hypoxia, hypercarbic acidosis, hyperkalemia, and substrate deprivation for 1 h followed by 3 h of reperfusion. Irreversible cell membrane injury, measured by propidium iodide uptake, increased from 4% of cells at the end of ischemia to 73% after reperfusion; death occurred in only 17% of cells kept ischemic for 4 h. Lactate dehydrogenase release was consistent with these changes. Lengthening ischemia from 30 to 90 min increased cell injury as expected, but of the total cell death, > 90% occurred during reperfusion. "Chemical hypoxia" composed of cyanide (2.5 mM) plus 2-deoxyglucose augmented injury before reperfusion compared with simulated ischemia. Inhibition of oxygen radical generation by use of metal chelator 1,10-phenanthroline reduced cell death from 73% to 40% after reperfusion (P = 0.001). We conclude that simulated reperfusion significantly augments the cellular membrane damage elicited by simulated ischemia in isolated cardiomyocytes devoid of other factors and suggest that reactive oxygen species, perhaps from the mitochondria, participate in this injury.

Gramicidin A aggregation in supported gel state phosphatidylcholine bilayers

Using an atomic force microscope, supported bilayers of saturated phosphatidylcholine (in the gel state) containing various amounts of gramicidin A (gA) were imaged in aqueous solutions and at room temperature. gA clusters were directly observed for the first time under these conditions. It was found that, at a lower gA concentration, gA aggregated into domains, composed of small clusters along with a considerable amount of lipids. This basic aggregation unit, most likely a hexamer, remained the same for acyl chain lengths from 14 to 18 carbons. These small clusters were observed to form elongated aggregates (line type) but never into extended pure gA domains. When gA concentrations were increased, for bilayers with 16 carbons or less, gA aggregated into larger domains but the basic unit remained separated by lipid molecules. At about 5 mol % gA, a percolation-like transition occurred at which the line type aggregates were connected to each other. However, for bilayers with more than 16 carbons, multiple lamellar structures were formed at higher gA fractions and the top layer had a ripple-like surface morphology. The molecular mechanism for the formation of these peculiar structures remains to be elucidated.

High resolution surface structure of E. coli GroES oligomer by atomic force microscopy

Using atomic force microscopy (AFM) in aqueous solution, we show that the surface structure of the oligomeric GroES can be obtained up to 10 angstroms resolution. The seven subunits of the heptamer were well resolved without image averaging. The overall dimension of the GroES heptamer was 8.4 +/- 0.4 nm in diameter and 3.0 +/- 0.3 nm high. However, the AFM images further suggest that there is a central protrusion of 0.8 +/- 0.2 nm high and 4.5 +/- 0.4 nm in diameter on one side of GroES which displays a profound seven-fold symmetry. It was found that GroEL could not bind to the adsorbed GroES in the presence of AMP-PNP and Mg2+, suggesting that the side of GroES with the central protrusion faces away from the GroEL lumen, because only one side of GroES was observed under these conditions. Based on the results from both electron and atomic force microscopy, a surface model for the GroES is proposed.

Biological atomic force microscopy: from microns to nanometers and beyond

In recent years, atomic force microscopy (AFM) has become the most rapidly developing imaging method. We summarize its recent applications in structural biology, with emphasis on high-resolution imaging, and illustrate these applications with images of cell membranes, DNA, and soluble and membrane proteins. With present technology, and at room temperature, nanometer resolution of DNA and soluble proteins is achievable, although the resolution attained on cell surfaces is more limited (10-50 nm). We suggest that high-resolution imaging of cell surfaces and very high (sub-nanometer) resolution molecular imaging requires an approach that increases specimen rigidity. Operation at cryogenic temperatures, the most promising approach, is discussed, and a cryo-AFM designed for operating at ambient pressure and liquid nitrogen temperature is described. The results include high-resolution images and evidence of increased molecular rigidity at low temperatures.

Flagellar structure and hyperthermophily: analysis of a single flagellin gene and its product in Aquifex pyrophilus

The polytrichously inserted flagella of Aquifex pyrophilus, a marine hyperthermophilic bacterium growing at 85 degrees C, were isolated and purified. Electron micrographs of the 19-nm-diameter flagellar filaments show prominent helical arrays of subunits. The primary structure of these 54-kDa flagellin monomers determining the helical shape and heat stability of filaments was of particular interest. The genomic region encoding the flagellin subunit (flaA gene) and an upstream open reading frame (orf1) were cloned and sequenced. The 1,503-bp flaA and 696-bp orf1 are preceded by separate sigma 28-like promoters and ribosome-binding motifs and succeeded by palindromic transcription terminators. Both genes are actively transcribed, but the nature and function of the orf1-encoded 231-residue polypeptide remain unknown. The deduced primary structure of the 501-amino-acid flagellin encoded by flaA consists of conserved N- and C-terminal regions and a variable 246-residue central domain. In comparison to mesophilic flagellins, the thermostable A. pyrophilus flagellin is characterized by increases in aromatic residues and prolines as well as by a 7.9% +/- 3.2% increase in all hydrophobic residues that is balanced by a respective decrease in hydrophilic residues. This composition is thought to form more compact flagellin monomers and stable interface contacts between neighboring subunits in the polymer.

[Expression of the retinoic acid nuclear receptors and retinoid X receptor gene in human breast cancer]

A number of studies have shown that retinoids can inhibit malignant cell growth including certain breast carcinoma cells. Its inhibitory effect is observed only in ER positive but not in ER negative breast cancer cells. We examined retinoic acid nuclear receptors (RARs) and retinoids X receptors (RXRs) levels in 6 breast carcinoma cell lines and 18 breast cancer biopsy specimens. We found that RAR-alpha mRNA level was significantly higher in ER positive cell lines and samples. RAR-gamma mRNA was expressed at relatively high levels in majority of tumor samples independent of the ER-status while RAR-beta mRNA was expressed at low levels. We also found high RXR-alpha mRNA levels in all of the tumor samples examined while RXR-gamma mRNA could not be detected. Our study suggests a possibility that retinoids inhibit tumor cell growth through RAR-alpha and RAR-alpha levels may serve as a potential marker to determine responsiveness of patients to retinoids therapy.

Ripple phase in asymmetric unilamellar bilayers with saturated and unsaturated phospholipids

In a solution of phosphate-buffered saline (PBS), unilamellar bilayers with saturated phosphatidylcholines in one leaflet and negatively charged, unsaturated phospholipids in the other leaflet were observed in the ripple phase at room temperature using atomic force microscopy (AFM). This is the first observation of the ripple phase in asymmetric bilayers. Sodium and phosphate, components of PBS, were found to be necessary for the formation of the ripple structure in the asymmetric bilayers composed of dipalmitoylphosphatidylcholine (DPPC) and 1-palmitoyl-2-oleoylphosphatidylglycerol (POPG), demonstrating a dependency for specific ions for this phase. These results indicate that the two leaflets of a bilayer are closely coupled to give rise to such a long range and complicated morphology.

An improved Escherichia coli-Rhodococcus shuttle vector and plasmid transformation in Rhodococcus spp. using electroporation

The genetic studies of metabolically diverse Rhodococcus spp. have been hampered by the lack of a system of introducing exogenous DNA. The authors improved an existing Escherichia coli-Rhodococcus shuttle vector (pMVS301) by removing much of the DNA not needed for replication and adding a multicloning site. This improved vector (pBS305) is 7.9 kb in length. Its ability to transform Rhodococcus was tested using electroporation parameters optimized for introduction of pMVS301 into Rhodococcus. Transformation efficiencies as high as 10(5) cfu micrograms-1 DNA were obtained although efficiencies varied depending on the Rhodococcus strain tested. The improved vector pBS305 offers great utility for genetic studies of Rhodococcus because its small size enables movement of large inserts of DNA into Rhodococcus, it has multicloning sites, contains a highly selective thiostrepton marker, and can be replicated in both E. coli and Rhodococcus.

High-resolution atomic-force microscopy of DNA: the pitch of the double helix

Using a cationic lipid bilayer, we show that DNA can be reliably adsorbed to the bilayer surface for atomic force microscopy (AFM) in aqueous buffers at high resolution. The measured width of the dsDNA is close to 2 nm, and a periodic modulation on dsDNA is reproducibly detected by the AFM. The measured period is 3.4 +/- 0.4 nm, in excellent agreement with the known pitch of the double helix. The right-handedness of the double helix is directly discernible in high resolution AFM images. Thus, this approach can be readily applied to the study of DNA-protein interactions, as well as sequence mapping at high resolution.

Mechanism research of cryoanalgesia

The sciatic nerves of rabbits were frozen at different temperatures (-20 degrees C, -60 degrees C, -100 degrees C, -140 degrees C, and -180 degrees C). The morphology and function of the frozen nerves were examined with light microscopy (hematoxylin and eosinophilin stain and a histochemical thiocholine method) and electron microscopy. The function of the nerve after freezing was assessed using short latency somatosensory evoked potentials, sensory conduction velocity, and electromyogram at various intervals after freezing. There were no changes in morphology or function of nerves cryolesioned at -20 degrees C. The nerve fibers cryolesioned at -60 degrees C showed signs of freezing degeneration and lost their conductive function although, these nerves all recovered. Approximately half of nerve fibers cryolesioned at -100 degrees C showed Wallerian degeneration, and although the time to remyelination was delayed, nerve regeneration was still complete. At -140 degrees C and -180 degrees C the nerve fibers showed immediate necrosis, with destruction of basal membranes and proliferation of collagen fibers. The results explained the mechanism of cryoanalgesia. Our study demonstrates that cryo-temperatures lower than -140 degrees C will cause permanent alterations in nerve morphology and function, whereas warmer temperatures do not result in permanent nerve damage and are therefore not likely to provide long-term analgesia to patients.

Cryo atomic force microscopy: a new approach for biological imaging at high resolution

A low-temperature atomic force microscope (cryo-AFM), operated in liquid nitrogen vapor, has been constructed for biological applications. The system provides an adjustable imaging temperature from 77 to 220 K with atomic resolution achieved on crystalline specimens. Imaging with NaCl microcrystals demonstrates that the system is free from surface contamination. Below 100 K, several biological specimens, including immunoglobulins and DNA as well as red blood cell ghosts, were imaged at high spatial resolution. Measurements on individual macromolecules showed that the mechanical strength is significantly greater at cryogenic temperatures with an estimated Young's modulus 1000-10,000 times that of a hydrated protein at room temperature, providing a solid basis for future improvements and applications of cryo-AFM in structural biology.

Conjugation fidelity and bistability in a high-efficiency mutually pumped phase conjugator with ring channels

We describe a high-efficiency mutually pumped phase conjugator with ring channels in a bird-wing incident geometry in copper-doped potassium sodium strontium barium niobate. A transmissivity as great as 35% is measured. Optical switching is obtained. The dependence of phase-conjugation fidelity on the geometric parameters and the input-beam ratio is discussed. Some suggestions are proposed to improve the fidelity further. The response times as a function of the input-beam ratio with the input beam kept constant are measured, and the least-squares minimum is used to simulate the fitting curve equations and to explain the formation of optical switching and the reduction or improvement of image fidelity.

Atomic force microscopy of cholera toxin B-oligomers bound to bilayers of biologically relevant lipids

Cholera toxin B-oligomer was imaged by atomic force microscopy (AFM) on biologically relevant model membranes, such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine and egg yolk phosphatidylcholine at room temperature in solution at a resolution in the range of 1 to 2 nm. In addition, two-dimensional arrays were grown directly on these model membranes without any special treatment, and were also imaged by AFM. These results demonstrate the ability of AFM for imaging membrane proteins at high resolution without the need of chemical cross-linking, either within the membrane or to the substratum.

Progress in high resolution atomic force microscopy in biology

The atomic force microscope (AFM) was invented by Binnig, Quate and Gerber less than 10 years ago (Binniget al. 1986). In their first prototype, a piece of goldfoil was used as the cantilever, with a crushed diamond tip mounted at the end. On the back of the cantilever, a tunnelling junction was used to monitor the deflection of the cantilever (the gold-foil) when the specimen was scanned with the tip in contact with the surface. Thus, the surface topography of the specimen was obtained with a resolution critically dependent on the sharpness of the tip provided the deformation of the specimen was not serious. Even with such a crude set-up, they managed to obtain a lateral resolution of ˜ 30 Å and a vertical resolution of better than 1 Å on an amorphous A12O3surface. The operating principle of such an instrument is deceptively simple. However, such an arrangement was inconvenient for routine operations and unsuitable for imaging hydrated specimens, because the tunnelling junction is easily contaminated in air and works poorly in aqueous solutions (Alexanderet al. 1989). As a result, the application of this type of AFM to biological samples was rare (Engel, 1991).

The retinoblastoma susceptibility gene product represses transcription when directly bound to the promoter

Rb represses E2F-mediated transcription in part by blocking the trans-activation domain of E2F. In addition, Rb can convert an E2F binding site from a positive to a negative element. To examine the effect of a Rb-DNA-bound complex on transcription, full-length Rb was fused to the DNA binding domain of GAL4. Here, we report that GAL4-Rb can repress transcription mediated by either Sp1, AP-1, or p53, dependent upon the presence of both the GAL4 DNA binding domain and GAL4 binding sites. Moreover, GAL4-Rb inhibited the activity of the herpes simplex virus tk promoter from GAL4 binding sites located at a distance from the promoter. In contrast, GAL4-Rb was unable to repress basal transcription. Cotransfection of specific cyclins and cyclin-dependent kinases or SV40 T-antigen abolished the repressive activity of GAL4-Rb. The domains of Rb involved in mediating the repression of transcription were mapped to regions that are overlapping, but not identical, to those required for the interaction with E2F. We propose that Rb can function as a general repressor of transcription when bound to the promoter region.

The retinoblastoma-susceptibility gene product binds directly to the human TATA-binding protein-associated factor TAFII250

RB, the protein product of the retinoblastoma tumor-suppressor gene, regulates the activity of specific transcription factors. This regulation appears to be mediated either directly through interactions with specific transcription factors or through an alternative mechanism. Here we report that stimulation of Sp1-mediated transcription by RB is partially abrogated at the nonpermissive temperature in ts13 cells. These cells contain a temperature-sensitive mutation in the TATA-binding protein-associated factor TAFII250, first identified as the cell cycle regulatory protein CCG1. The stimulation of Sp1-mediated transcription by RB in ts13 cells at the nonpermissive temperature could be restored by the introduction of wild-type human TAFII250. Furthermore, we demonstrate that RB binds directly to hTAFII250 in vitro and in vivo. These results suggest that RB can confer transcriptional regulation and possibly cell cycle control and tumor suppression through an interaction with TFIID, in particular with TAFII250.

Asymmetric transmission device using Fe-doped KTa(x)Nb(1-x)O(3) crystal

A new type of asymmetric optical transmission device based on contradirectional two-wave mixing between an incident beam and its backward-scattering beams in Fe-doped KTa(x)Nb(1-x)O(3) crystal is demonstrated. The transmittance ratio of the beams propagating in opposite directions can be adjusted by a change in the angle between the incident beam and the c axis; the maximum ratio is nearly 50:1 at only one incident beam. Approximate solutions of two opposite transmittances are derived and discussed. It is possible to use this device as an optical isolator or an optical diode.

Differential regulation of E2F and Sp1-mediated transcription by G1 cyclins

Cyclins have been demonstrated to mediate phosphorylation of the retinoblastoma tumor suppressor gene product (Rb) and/or to bind directly to Rb. Since Rb is a regulator of E2F and Sp1-mediated transcription, we have examined the effect of overexpression of cyclins on transcription mediated by E2F-dependent adenovirus E2 promoter and by Sp1 in a cotransfection assay in 3T3 cells. All the G1 cyclins tested, C, D1, D2, D3 and E, as well as cyclin A were able to stimulate E2 promoter activity to various levels with D3 showing the strongest stimulation. For stimulation of the E2 promoter by cyclins A, E and D-type cyclins was dependent upon the presence of functional E2F and ATF binding sites. Cyclin C, however, was able to stimulate both E2F and ATF-dependent transcription to the same level as the wild type E2 promoter. In addition, cyclin C was able to stimulate transcription mediated by Sp1, GAL4-Sp1 and GAL4-VP16, suggesting that cyclin C affects a general pathway of transcriptional activation. In contrast, cyclin D1 was able to repress specifically Sp1-mediated transcription through an Rb-independent pathway. These results suggest that cyclins can regulate transcription mediated by specific transcription factors in both positive and negative manners. Furthermore, the results demonstrate clear functional differences between the G1 cyclins, in particular, functional differences between the related D-type cyclins.

Recent advances in biological atomic force microscopy

Recent developments in biological atomic force microscopy are reviewed. In addition to the advances in methodology, new structural information of different biological systems revealed by the atomic force microscopy is also presented. A discussion regarding the contrast, resolution and specimen deformation is provided based on a theoretical model.

A physical map of the hyperthermophilic bacterium Aquifex pyrophilus chromosome

A genomic map of the hyperthermophilic hydrogen-oxidizing bacterium Aquifex pyrophilus was established with NotI (GC/GGCCGC), SpeI (A/CTAGT), and XbaI (T/CTAGA). Linking clones and cross-hybridization of restriction fragments revealed a single circular chromosome of 1.6 Mbp. A single flagellin gene and six rRNA gene units were located on this map by Southern hybridization.

Regulation of pml messenger-RNA expression in human breast-carcinoma cells

We examined the mRNA expression profile of PML, a novel nuclear protein recently characterized from acute promyelocytic leukemia (APL) blast cells, in a number of breast carcinoma cell lines. PML mRNA was found to be differentially expressed among the cell lines examined. A correlation of borderline significance between PML mRNA expression and the proliferative capacity of the cell Lines was noted. Serum stimulation significantly elevated the PML mRNA levels in the T47D and MDA-MB-231 cells. These results would suggest that PML may function as a positive regulator of cellular proliferation in breast carcinoma cells.