DNA sequencing and genotyping by transcriptional synthesis of chain-terminated RNA ladders and MALDI-TOF mass spectrometry

Sets of RNA ladders can be synthesized by transcription of a bacteriophage-encoded RNA polymerase using 3'-deoxynucleotides as chain terminators. These ladders can be used for sequencing of DNA. Using a nicked form of phage SP6 RNA polymerase in this study substantially enhanced yields of transcriptional sequencing ladders. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of chain-terminated RNA ladders allowed DNA sequence determination of up to 56 nt. It is also demonstrated that A-->G and C-->T variations in heterozygous and homozygous samples can be unambiguously identified by the mass spectrometric analysis. As a step towards single-tube sequencing reactions, alpha-thiotriphosphate nucleotide analogs were used to overcome problems caused by chain terminator-independent, premature termination and by the small mass difference between natural pyrimidine nucleotides.

Insulin-like growth factor-1 protects H9c2 cardiac myoblasts from oxidative stress-induced apoptosis via phosphatidylinositol 3-kinase and extracellular signal-regulated kinase pathways

Oxidative stress plays a critical role in cardiac injuries during ischemia/reperfusion. Insulin-like growth factor-1 (IGF-1) promotes cell survival in a number of cell types, but the effect of IGF-1 on the oxidative stress has not been elucidated in cardiac muscle cells. Therefore, we examined the role of IGF-1 signaling pathway in cell survival against H2O2-induced apoptosis in H9c2 cardiac myoblasts. H2O2 treatment induced apoptosis in H9c2 cells, and pretreatment of cells with IGF-1 suppressed apoptotic cell death. The antiapoptotic effect of IGF-1 was blocked by LY294002 (an inhibitor of phosphatidylinositol 3-kinase) and by PD98059 (an inhibitor of extracellular signal-regulated kinase (ERK)). The protective effect of IGF-1 was also blocked by rapamycin (an inhibitor of p70 S6 kinase). Furthermore, H9c2 cells stably transfected with constitutively active PI 3-kinase (H9c2-p110*) and Akt (H9c2-Gag-Akt) constructs were more resistant to H2O2 cytotoxicity than control cells. Although H2O2 activates both p38 mitogen-activated protein kinase (MAPK) and c-Jun N-terminal kinase (JNK), IGF-1 inhibited only JNK activation. Activated PI 3-kinase (H9c2-p110*) and pretreatment of cells with IGF-1 down-regulated Bax protein levels compared to control cells. Taken together, our results suggest that IGF-1 transmits a survival signal against oxidative stress-induced apoptosis in H9c2 cells via PI 3-kinase and ERK-dependent pathways and the protective effect of IGF-1 is associated with the inhibition of JNK activation and Bax expression.

Development and differentiation of the anuran auditory brainstem during metamorphosis: an acetylcholinesterase histochemical study

The time course of cell differentiation and the presence of histochemically defined areas in brainstem auditory nuclei were examined in developing bullfrogs, Rana catesbeiana, using cresyl violet staining and acetylcholinesterase (AChE) histochemistry. In the medulla, the dorsolateral nucleus (DLN) can be seen as a distinct structure in its adult location only at Gosner stage 40 and beyond. The majority of cells in the DLN are not fully differentiated until late metamorphic climax (stages 45-46) and early postmetamorphosis. The more ventral vestibular nucleus differentiates earlier (stage 37) than the DLN. Adult-like organization of auditory nuclei in the torus semicircularis (TS) of the midbrain cannot be reliably discerned until metamorphic climax stages. Cellular masses in the brainstem reveal AChE from the earliest stage examined (stage 27) but the intensity of staining differs among cell groups. Staining intensity in the DLN is at a peak in recently metamorphosed froglets. The time course of cell differentiation in the DLN precedes slightly or is coincident with the increased, transient presence of AChE. Staining of the superior olive stabilizes at a moderate level in early postmetamorphic stages. Ventral regions of the principal nucleus in the TS stain more intensely than dorsal regions beginning at stage 40. This dorsal-ventral gradient in staining persists in adult stages. There is a transient decline in staining of the laminar nucleus in metamorphic climax stages. Staining intensity in the magnocellular nucleus peaks during stages 40-46 and in early postmetamorphic froglets and then declines in adults, paralleling the pattern seen in the DLN. These data suggest that metamorphic climax and early froglet periods are an important developmental window for major differentiation and maturational events in the auditory brainstem.

Introduction of HIV type 1 subtype E virus into South Korea

Subtype E HIV-1 is the most prevalent strain in Southeast Asia. Although subtype B is prevalent in Korea, geographical distance and increases in travel may lead to the spread of subtype E in Korea. Therefore, we tried to identify and monitor the patterns of HIV subtype E virus introduction into Korea. The divergence of nucleotide sequences within the envelope region (V3 to V5) of Korean subtype E isolates ranged from 4.3 to 14.6% (n = 8; mean, 9.5 +/- 2.8%). In pairwise comparisons of subtype E isolates between Korea and other regions, the divergence of nucleotide sequences between 8 Korean and 16 Asian subtype E variants ranged from 1.3 to 15.2% (mean, 7.8 +/- 2.6%), whereas the divergence of nucleotide sequences between 8 Korean and 2 African variants ranged from 11.7 to 20.7% (mean, 15.4 +/- 2.2%). A phylogenetic tree showed that Korean subtype E isolates cluster with the Asian isolates but far from the African isolates. These epidemiological and molecular epidemiological data suggest that HIV-1 subtype E strains have been transmitted into Korea from endemic areas of Southeast Asia rather from Africa.

Translational suppression by hammerhead ribozymes and inactive variants in S. cerevisiae

The activity of hammerhead ribozymes in S. cerevisiae was assessed using two ribozymes that were designed to intramolecularly attack the hepatitis B viral X mRNA. The ribozymes effectively suppressed the expression of the X-lacZ fusion gene, when they were inserted at the 5' end of the X mRNA. The ribozymes cleaved the target RNA efficiently at the targeted phosphodiester bond, but the inactive mutants carrying G5-to-A substitution in the core did not, as the total RNA preparations of yeast extracts was assayed by primer extension. These G5A mutants, however, exerted the suppression as effectively as the wild-type ribozymes. The results, with several mutations introduced to a ribozyme, suggested that either mere formation of hammerhead-like structures with the three stems, or the formation of any two stems, could inhibit translation. Thus, the hammerhead-like structures, leading to cleavage or not, could effectively suppress translation, especially when formed around the initiation codon. The G5-to-A and U7-to-G mutations and replacement of the stem-II hairpin tetraloop did not appear to affect the formation of the inhibitory structure(s). The inhibition that was observed when stems I and III were directly connected without a loop or with a stem II hairpin was completely relieved when they were connected with only the loop of stem II (not containing the stem portion).

Bacteriophage SP6 RNA polymerase mutants with altered termination efficiency and elongation processivity

An Escherichia coli strain containing two plasmids was developed for in vivo isolation of the phage SP6 RNA polymerase mutants. It was developed to isolate mutants with increased proficiency of termination at the SP6 terminator and/or with reduced elongation processivity. Mutations were randomly introduced into an N-terminal third of the polymerase gene that was placed under a lac promoter in one plasmid. In the other plasmid, a promoter-lacking lacZ gene modified for reduced translation efficiency was placed downstream of a tandem pair of the SP6 terminator located downstream of an SP6 promoter-chloramphenicol acetyltransferase gene. Termination-up mutants were selected in vivo as they rendered LacZ activity level lower than the wild-type, without reducing chloramphenicol resistance substantially. Three such mutants (M15L, M15S, and D117G) were purified, and their termination efficiencies were measured in vitro at two different intrinsic termination signals in the E. coli rrnB terminator t1 that are different in requiring RNA hairpin formation. All three mutations enhanced termination efficiencies in vitro at the SP6 terminator and the upstream signal of rrnB t1, but reduced the efficiency at the downstream signal of it. All the mutations reduced elongation processivity, as the mutants produced much less amounts of large transcripts (2.1 kb) than the wild-type but the similar amounts of small transcripts (up to 670 nt). Thus, the mutations, all reducing elongation processivity of the polymerase, exhibited opposite effects on the two types of intrinsic termination signals, suggesting that the two mechanisms involve different interactions with the phage RNA polymerase.

[Studies on separation and identification of Rhizoma coptidis brugs based on microemulsion thin-layer chromatography]

OBJECTIVE

To investigate the use of microemulsion TLC for the separation and identification of Rhizoma Coptidis drugs.

METHOD

Thirteen Rhizoma Coptidis drugs were separated and identified with six kinds of SDS/n-C4H9OH/n-C7H16/H2O microemulsions as mobile phase on polyamide film. Effects of microemulsions on separation were investigated.

RESULTS

The best mobile phase was the O/W microemulsion(containing 75% water). Compared with general mobile phases, the separation and detection could be improved and the test conditions were more tolerant.

CONCLUSION

This new method is simple, accurate and efficient for the separation and identification of Rhizoma Coptidis drugs.

Effects of saturation mutagenesis of the phage SP6 promoter on transcription activity, presented by activity logos

A full set of SP6 promoter variants with all possible single substitutions at positions -17 to +5 was constructed. Transcription activities of these variants were individually measured in vivo and in vitro to determine the contribution of each base pair to the promoter activity. The in vivo activity was measured indirectly by transcriptional interference of the replication of promoter-bearing plasmids. This activity depends most highly on residues -11, -9, -8, -7, and +1 (initiation site). All substitutions at -11, -9, -8, and -7 abolished formation of closed complexes, except for A-8C. These residues are involved in base-specific interactions with the polymerase, and the substitutions exhibit the same strong inhibition in vitro. In contrast, the in vitro activities of some other variants, measured on linearized templates, were different from those in vivo. Some variants at -13, -4, and -2, among others, showed exceptionally higher activities in vivo than in vitro, supporting the possibility that these residues are involved in postbinding steps, including template melting and bending. The A-3T variant showed much lower activity in vivo than in vitro, but it bound to the polymerase 2-fold more than the consensus sequence and is possibly involved in polymerase binding. A quantitative hierarchy of all the base pairs is graphically displayed by activity logos, revealing the energetic contribution of each base pair to the activity.

[Effects of xiaopi yishen oral liquid on hypothalamus-pituitary-adrenal gland-thymus axis in stressed rats]

OBJECTIVE

To investigate the effect of Xiaopi Yishen (XPYS) oral liquid on the rats under repeated forced cold water swimming (RFCWS) stress.

METHODS

The changes of serum monoamine, ascorbic acid levels in adrenal gland, monoamine levels in hypothalamus and hypophysis, and thymus index were determined.

RESULTS

XPYS lowered the increasing of serum DA, 5-HT, improved the reducing of ascorbic acid in adrenal gland and NE, HVA, 5-HT, 5-HITT in hypothalamus and hypophysis of RFCWS-stressed rats.

CONCLUSION

The mechanism of XPYS is in connection with the regulation of hypothalamus-pituitary-adrenal gland-thymus axis.

Modulation of the redox potential of the [Fe(SCys)(4)] site in rubredoxin by the orientation of a peptide dipole

Rubredoxins (Rds) may be separated into two classes based upon the correlation of their reduction potentials with the identity of residue 44; those with Ala44 have reduction potentials that are approximately 50 mV higher than those with Val44. The smaller side chain volume occupied by Ala44 relative to that occupied by Val44 has been proposed to explain the increase in the reduction potential, based upon changes in the Gly43-Ala44 peptide bond orientation and the distance to the [Fe(SCys)(4)] center in the Pyrococcus furiosus (Pf) Rd crystal structure compared to those of Gly43-Val44 in the Clostridium pasteurianum (Cp) Rd crystal structure. As an experimental test of this hypothesis, single-site Val44 <--> Ala44 exchange mutants, [V44A]Cp and [A44V]Pf Rds, have been cloned and expressed. Reduction potentials of these residue 44 variants and pertinent features of the X-ray crystal structure of [V44A]Cp Rd are reported. Relative to those of wild-type Cp and Pf Rds, the V44A mutation in Cp Rd results in an 86 mV increase in midpoint reduction potential and the [A44V] mutation in Pf Rd results in a 95 mV decrease in midpoint reduction potential, respectively. In the crystal structure of [V44A]Cp Rd, the peptide bond between residues 43 and 44 is approximately 0.3 A closer to the Fe center and the hydrogen bond distance between the residue 44 peptide nitrogen and the Cys42 gamma-sulfur decreases by 0.32 A compared to the analogous distances in the wild-type Cp Rd crystal structure. The results described herein support the prediction that the identity of residue 44 alone determines whether a Rd reduction potential of about -50 or 0 mV is observed.

Bipartite modular structure of intrinsic, RNA hairpin-independent termination signal for phage RNA polymerases

The phage SP6 RNA and T7 RNA polymerases, which are closely related to each other, intrinsically stop at two signals in the Escherichia coli rrnB terminator t1 through different mechanisms. The downstream signal functioned without an RNA secondary structure formation, in which the signal was still active when separated from the upstream, hairpin-forming signal, and IMP incorporation enhanced its efficiency. The sequence from -15 to -1 was essential for the downstream, hairpin-independent termination (at -1). The results of SP6 transcription with heteroduplex templates and ribonucleotide analogs suggested that the downstream signal consists of two functionally different modules. The effects of iodo-CMP or IMP incorporation into RNA on termination efficiency were not sensitive to incorporation at -9 and upstream, but they were reactive to incorporation at -6 and -2, as reflected by strong iodo-rC:dG and weak rI:dC base pairing. Thus, the downstream module (from -8 approximately -6 to -1) appears to facilitate the release of RNA. Mismatches in the templates at -6 to +1 allowed for efficient termination, unlike those upstream of the sequence. The upstream module (from -15 to -9 approximately -7) functions as a duplex. Pausing of the SP6 elongation complex at the termination site was detected when RNA release was suppressed by the incorporation of 5-bromo-UMP, and it was dependent on the upstream module. Results of single-round SP6 transcriptions using 3'-deoxynucleotides and immobilized templates indicated that RNA was not released from the elongation complexes halted at the termination site on the template variants carrying mutations in the upstream or downstream module, whereas such complexes on the wild type template were dissociated. Thus, halting or simple pausing was not sufficient for termination even when the downstream module was intact. The upstream module appears to mediate such conformation change necessary for termination.

Effect of plasminogen activators on human recombinant apolipoprotein(a) having the plasminogen activation cleavage site

The serine-proteinase domain in human apolipoprotein(a) [apo(a)] and plasminogen exhibit 89% sequence identity including the catalytic triad. Cleavage of the Arg(561)-Val(562) activation site in plasminogen by either tissue- or urokinase-type plasminogen activator results in formation of the fibrinolytic enzyme plasmin. Apo(a) does not contain measurable amidolytic activity nor can it be activated by plasminogen activators. It has been suggested that the latter finding might be explained by the substitution of the plasminogen Arg-Val activation site by Ser-Ile in apo(a). To investigate if introduction of the Arg-Val activation site in apo(a) might result in sensitivity towards plasminogen activators, we expressed wild-type and Arg-Val mutant recombinant apo(a) [r-apo(a)] in human embryonic kidney and hepatocyte cell lines. Free r-apo(a) and lipoprotein-like particles [r-Lp(a)] were obtained in the culture supernatants of transfected 293 and HepG2 cells, respectively. Incubation of mutant r-apo(a)/r-Lp(a) with plasminogen activators produced neither plasmin-like activity nor cleavage at the Arg-Val activation site, even in the presence of various stimulators of plasminogen activation. Our data suggest that the high selectivity of activators for plasminogen activation requires interactions with regions in plasminogen distant from the activation disulfide loop which are not present in apo(a).

The effect of region of interest selection on dual energy X-ray absorptiometry measurements of the calcaneus in 55 post-menopausal women

Bone mineral density (BMD) of the calcaneus was assessed by dual energy X-ray absorptiometry (DXA) in four different regions of the calcaneus in 20 pre-menopausal and 55 post-menopausal women, none of whom were on treatment or suffering from conditions affecting bone. The total body option in the small animal software package of a Lunar DPX-L bone densitometer was used. The precision of the technique (%CV) varied from 0.7 to 2.2% depending on the region scanned. For post-menopausal women, BMD results in the mid and posterior parts of the calcaneus varied by < 7% while BMD in the anterior region was about 20% lower. DXA of the calcaneus was compared with measurements at the spine (L2-L4) and hip (femoral neck) and changes with age were estimated from cross-sectional data. BMD of the calcaneus was significantly reduced in 28 post-menopausal women with low lumbar spine BMD (-2SD) compared with women with normal spine BMD. Calcaneal BMD was significantly correlated to axial BMD (r = 0.45-0.77) and to age (r = 0.45 to -0.63). For a subgroup of 33 post-menopausal women measured twice after approximately 1 year, calcaneus BMD decreased by between 1.2% and 2.5% while axial BMD showed no significant change. Unlike spine or femoral neck BMD, the decrease in calcaneus BMD was significantly greater in women with low spine BMD than in normal women, possibly indicating improved detection of skeletal changes. The optimum measurement sites for BMD in the calcaneus were within the mid or posterior part of the calcaneus or enclosing the whole posterior calcaneus. The calcaneus was shown to be a precise, sensitive and simple measurement site suitable for the assessment of osteoporosis, especially in the elderly where degenerative changes in the spine and hip can complicate BMD assessment.

R'2 measured in trabecular bone in vitro: relationship to trabecular separation

Measurement of key parameters of the microstructure of trabecular bone is critical to the study of osteoporosis and bone strength. Density based methods cannot provide this information, and give only the total amount of bone present, and not its arrangement. Magnetic resonance imaging has shown the potential to provide information related to the microarchitecture of the trabecular bone matrix. Twelve samples (8 x 8 x 8 mm3 bone cubes) were cut from sheep vertebrae such that the trabeculae ran either parallel or perpendicular to each face. Detailed measurements of the structure of these bone cubes were made by histomorphometry, and compared to R'2 and R*2 measured with a spin and gradient-echo sequence, Partially Refocused Interleaved Multiple Echo, at 1.5 Tesla. The precision of the R'2 measurement (% coefficient of variation) was 8.7+/-5.1, and 7.7+/-4.3 for R*2. Uncorrected values of R'2 and R*2 were significantly correlated to density measured by quantitative computed tomography (r = 0.87, p = 0.0005, and r = 0.90, p = 0.0002, respectively), and trabecular bone area measured by histomorphometry (r = 0.80, p = 0.002, and r = 0.83, p = 0.0008, respectively). Density correction was effected by imaging the same slice of bone in two orientations (90 degrees and 0 degrees ) to the main magnetic field. For both R'2 and R*2 there was a significant difference between measurements in the 90 degrees and 0 degrees orientations (p < 0.01). The difference between the two values was used, and termed R'2net or R*2net. The net parameters were independent of bone mass. R'2net and R*2net were significantly correlated to trabecular separation (p < 0.05) with r = -0.58 and r = -0.62, respectively. These results demonstrate the ability of magnetic resonance imaging to characterize a key measure of the trabecular microstucture. An increase in trabecular separation has important biomechanical consequences in osteoporosis. This result also strengthens the hypothesis that the sensitivity of R'2 to osteoporosis-related bone changes is due to magnetic susceptibility effects in which rapid transitions between bone and marrow create local magnetic field inhomogeneities that result in an increase in R'2 values.

Z-curve: a computer program calculating DNA helical axis coordinates for three-dimensional graphic presentation of curvature

In order to predict curvature of DNA fragments, we previously developed a computer program for simply calculating a vectorial sum of all individual roll, tilt and twist wedge angles between the nearest base pairs for a given DNA fragment [Lee et al., (1991)]. Now, a new program, called Z-curve, was developed to calculate three-dimensional coordinates of the helical center of each base pair along the DNA, using helical axis deviations from B-form DNA by wedge angles. The output file of the new program was designed to become an input file for a graphics program, Insight II. Thus, we were able to obtain three-dimensional graphic presentations of DNA helical axis curvatures of any length. It visualized spatial details of the DNA curvature, where and how much it curves, and to which direction. It also allowed calculation of the three-dimensional distance between two ends of a DNA fragment, which could provide a measure of its curvature. Here, three DNA fragments, both curved and straight, were subjected to the Z-curve and Insight II programs. The results showed that their curvature details could be visualized to the level of the base pair, whether the DNA fragments contained an oligo(A) track or not. Their estimated curvatures were consistent with the experimental results of permutation gel mobility assay.

Soluble expression of cloned phage K11 RNA polymerase gene in Escherichia coli at a low temperature

The gene 1 of the Klebsiella phage K11 encoding the phage RNA polymerase was amplified using the polymerase chain reaction of the Pfu DNA polymerase, cloned and expressed under the control of tac promoter in Escherichia coli. Although the gene was efficiently expressed in E. coli BL21 cells at 37 degrees C, most of the K11 RNA polymerase produced was insoluble, in contrast to soluble expression of the cloned T7 RNA polymerase gene. Coexpression of the bacterial chaperone GroES and GroEL genes together did not help solubilize the K11 RNA polymerase. When the temperature of cell growth was lowered, however, solubility of the K11 RNA polymerase was increased substantially. It was found much more soluble when expressed at 25 degrees C than at 30 and 37 degrees C. Thus, the cloned K11 RNA polymerase gene was expressed in E. coli mostly to the soluble form at 25 degrees C. The protein was purified to homogeneity by chromatography using DEAE-Sephacel and Affigel-blue columns and was found to be active in vitro with the K11 genome or a K11 promoter. The purified K11 RNA polymerase showed highly stringent specificity for the K11 promoter. Low-level cross-reactivity was shown with the SP6 and T7 consensus promoters, while no activity shown with the T3 consensus promoter at all.

Repression of hepatitis B virus X gene expression by hammerhead ribozymes

The X protein (HBx) of human hepatitis B virus (HBV) is a transcriptional activator protein. The HBx protein plays an important role in viral replication in HBV infected cells and the liver diseases including hepatitis, cirrhosis, and hepatocellular carcinoma (HCC). Therefore, the repression of HBx gene expression by hammerhead ribozymes may be a good way to inhibit HBV replication and cure HBV-related liver diseases. We designed two hammerhead ribozymes, RzA and RzB, to cleave target sites at nucleotides 114 and 309 in the HBx open reading frame (ORF), respectively. In vitro, RzA and RzB cleaved HBx RNAs at their target sites up to 52 and 75%, respectively; however, the disabled ribozymes (dRzs) which have mutations in the catalytic site did not cleave the target RNAs at all. When each of the ribozymes were cotransfected into HepG2 cells with HBx expression plasmid, RzA and RzB reduced the level of HBx mRNA to 40 and 57%, respectively. The transactivation activity of HBx protein was also reduced dramatically by the ribozymes. These results suggest that the hammerhead ribozymes, RzA and RzB, can be used for the gene therapy of liver diseases caused by HBV.

Stabilization of the i-motif by intramolecular adenine-adenine-thymine base triple in the structure of d(ACCCT)

The crystal structure of d(ACCCT), solved by molecular replacement, shows a four-stranded i-motif conformation, where two parallel duplexes intercalate with one another in opposite orientations. Each duplex is stabilized by hemi-protonated C-C+ base pairing between parallel strands, and a string of water molecules bridge the cytosine N4 atoms to phosphate O atoms. This structure of d(ACCCT) shows examples of reversed Hoogsteen and Watson-Crick base pairing in both intermolecular and intramolecular manners to stabilize the tetraplex. Noticeably, the four-stranded complex is further stabilized at one end by a three-base hydrogen-bonding network, in which two adenines and a thymine form four hydrogen bonds via a reverse Hoogsteen and an asymmetric adenine-adenine base pairing. The structure of d(ACCCT) shows a similar local structure to that found in the d(TAA) part of the crystal structure of d(TAACCC) and provides further structural evidence that these base arrangements are essential for stabilizing these novel DNA super-secondary structures.

In vivo MRI measurements of bone quality in the calcaneus: a comparison with DXA and ultrasound

Magnetic resonance imaging (MRI) has shown promise in the assessment of bone architecture. The precision and feasibility of MRI measurements in osteoporosis in vivo have been assessed in this study. T2' was calculated from measurements of T2 and T2* in the calcaneus of 32 postmenopausal women using a gradient-echo sequence PRIME (Partially Refocused Interleaved Multiple Echo). This sequence allows the measurement of T2 and T2* in one acquisition. In vivo measurements of bone mineral density (BMD) by dual-energy X-ray absorptiometry (DXA) were made in the calcaneus, spine and femoral neck. The ultrasound parameters broadband ultrasound attenuation (BUA) and speed of sound (SOS) were also measured in the calcaneus. These three techniques have not previously been compared in the same study population. The precision of the MRI technique was poor relative to the DXA and ultrasound techniques, with a CV of 6.9% +/- 4.4% for T2' and 5.5% +/- 3.6% for T2*. Approximately 4% of this is due to system error as determined by phantom measurements. The postmenopausal women were classified as having low BMD if they had a lumbar spine (L2-4) BMD of less than 0.96 g/cm2 (more than 2 standard deviations below normal peak bone mass). Calcaneal T2' was significantly correlated with calcaneal BMD (r = -0.79, p < 0.0001), BUA (r = -0.59, p = 0.0004) and SOS (r = -0.58, p = 0.0006). T2' was significantly different in postmenopausal women with normal BMD and those with low BMD (p < 0.01). However, the difference was of only borderline significance (p < 0.06) after adjustment for age and years since menopause.

Effects of reflection-induced retardance on the immunity of bulk optic-material current sensors

Reflection-induced phase retardance inside bulk optic-material current sensors makes the state of polarization of the light change, which reduces the immunity of the sensors against electromagnetic interference. These effects are analyzed theoretically for the first time, to our knowledge. A comparison between the theoretical analysis and the experimental results are given.

Requirement of heavy neurofilament subunit in the development of axons with large calibers

Neurofilaments (NFs) are prominent components of large myelinated axons. Previous studies have suggested that NF number as well as the phosphorylation state of the COOH-terminal tail of the heavy neurofilament (NF-H) subunit are major determinants of axonal caliber. We created NF-H knockout mice to assess the contribution of NF-H to the development of axon size as well as its effect on the amounts of low and mid-sized NF subunits (NF-L and NF-M respectively). Surprisingly, we found that NF-L levels were reduced only slightly whereas NF-M and tubulin proteins were unchanged in NF-H-null mice. However, the calibers of both large and small diameter myelinated axons were diminished in NF-H-null mice despite the fact that these mice showed only a slight decrease in NF density and that filaments in the mutant were most frequently spaced at the same interfilament distance found in control. Significantly, large diameter axons failed to develop in both the central and peripheral nervous systems. These results demonstrate directly that unlike losing the NF-L or NF-M subunits, loss of NF-H has only a slight effect on NF number in axons. Yet NF-H plays a major role in the development of large diameter axons.

Viability of E. coli cells containing phage RNA polymerase and promoter: interference of plasmid replication by transcription

Strong transcription of phage promoters often renders the host E. coli cells containing the phage RNA polymerase inviable. When expression of the phage SP6 RNA polymerase gene in one plasmid was induced in the E. coli JM109 cells, cells that bear an active SP6 promoter were inviable. When it was not induced (the polymerase was still produced in low levels), viability of the host cells and stability of the promoter-bearing plasmids depended on the orientation of the promoter with respect to that of the replication origin and on the sequence of the origin. A group of SP6 promoter-bearing plasmids (group I plasmids) that had the promoter directed towards the ColE1 replication origin, rendered the polymerase-containing host cells inviable in selective media. When the sequence of the origin was different (group II plasmids), this adverse effect was not observed. When the promoter direction was same as the replication origin and the ampicillin-resistant gene (group III plasmids), many satellites formed around the colonies on ampicillin-containing agar plates. These effects were caused by strong transcription of the phage SP6 promoter by its RNA polymerase, since they were reduced or eliminated by inserting an active terminator just downstream of the promoter. The viability of host cells and copy number of the promoter/terminator-bearing plasmids appear to be quantitatively related with efficiency of initiation and termination of the phage transcription. These systems may be useful for in vivo screening for mutant variants of the phage promoter, polymerase and terminator that are affected in their efficiency.

Effects of cigarette smoking and 12-h abstention on working memory during a serial-probe recognition task

Nicotine has been shown to affect attentional and mnemonic processes. However, whether these effects are due to changes in perceptual and/or motor aspects of the tasks is not at all clear. This study tested the hypothesis that nicotine from cigarette smoking has differential effects on perceptual and motor processes, as reflected by event-related potentials (ERPs) and reaction times (RTs), respectively, and that perceptual effects may be specific to changes in working memory. ERPs. RTs and performance accuracy were recorded from smokers and nonsmokers during a serial-probe recognition memory task in which lists of words or "memory sets" were followed by a probe word that was either in-set or out-of-set. Smokers were tested in a "smoking" and a 12-h "deprived" condition. Smoking-smokers and deprived-smokers exhibited fast RTs to in-set and out-of-set probes relative to a group of nonsmokers. They exhibited even faster RTs when the inset probe word matched the first or last item in the memory set. Thus, smokers as a group showed enhanced primacy and recency effects suggesting that smoking specifically facilitates processes related to the motor output aspects of working memory. Different effects characterized the electrophysiology. Larger P300s were recorded to in-set compared to out-of-set probes by both subject groups. Smoking smokers exhibited enhanced P300s to both types of probes. When smokers abstained for 12 h (deprived smokers), the differences in P300 amplitude were reduced but not eliminated. Smoking smokers exhibited faster P300 latencies to in-set probes, while deprived smokers showed delayed latencies relative to nonsmokers. Primacy and recency P300 effects characterized nonsmokers and deprived smokers. However, this relationship was reversed in the Smoking condition. These results support the hypotheses that nicotine has distinct effects on memory-related perceptual and motor aspects of working memory. The increase in efficiency of the memory search with nicotine is consistent with the functional role of the cholinergic system in maintaining a state "appropriate for efficient information processing."

Probing RegA/RNA interactions using electrospray ionization-fourier transform ion cyclotron resonance-mass spectrometry

The interactions of bacteriophage T4 regA protein, a unique translational regulator, with RNAs of various size and sequence were studied using electrospray ionization-Fourier transform ion cyclotron resonance-mass spectrometry. Using very gentle interface conditions, regA/RNA complexes with a 1:1 binding stoichiometry were observed for all four target RNAs studied, consistent with solution binding studies. Competitive binding of target RNAs and their degradation products with regA demonstrated that the loss of a single nucleotide resulted in a dramatic change in binding affinity in some cases. Competitive binding of regA with four target RNAs revealed similar relative binding affinity order to that suggested by previous in vitro repression experiments. The use of sustained off-resonance irradiation for collisionally induced dissociation of a regA/RNA complex suggested the potential for directly obtaining information regarding the regA binding domain.

Comparison of ultrasound and dual energy X-ray absorptiometry measurements in the calcaneus

Ultrasound measurements have been proposed as a means of providing structural information on bone but have also been shown to correlate with density. High correlation coefficients have been obtained in vitro, but are lower for in vivo work. The aim of this study was to investigate the relationship of broadband ultrasound attenuation (BUA), speed of sound (SOS) and stiffness, to bone mineral density (BMD) measured in the calcaneus at a closely matched region of interest (ROI). Measurements were made in 55 post-menopausal and 20 young, normal women. Calcaneus BMD measurements were made using an ROI (fixed by reference to external axes) to represent the area and location of the ultrasound transducers and an ROI based on anatomical markers, positioned in the posterior part of the calcaneus. BUA was significantly correlated with calcaneus BMD in the fixed ROI (r = 0.77, p < 0.0001) and the anatomical ROI (r = 0.78, p < 0.0001). Correlation of BUA with axial BMD was lower at r = 0.63, p < 0.0001 for the spine (L2-L4) and r = 0.59, p < 0.0001 for the femoral neck. Results for SOS and stiffness were very similar. From the calcaneus dual energy X-ray absorptiometry (DXA) scan images the region representing the ultrasound measurement area was found to contain cortical bone edges in 60% of cases. In 16% of scans a small part (4.5 +/- 4.0%) of the ROI measurement area fell partially outside the heel. However, there was no obvious discrepancy in the ultrasound results in the individual cases where this occurred. The correlation between calcaneus BMD and BUA was improved from r = 0.72 to r = 0.86 when scans with a cortical edge in the measurement ROI were excluded. The values for SOS were similar. In summary, BMD of the calcaneus, when closely matched to the site of ultrasound measurement shows significant correlation with ultrasound measurements. By excluding scans in which the ultrasound measurement appeared to include bone edges, correlations of approximately r = 0.86 were obtained. However, the BMD result still does not explain all of the variance in the ultrasound results.

Absence of the mid-sized neurofilament subunit decreases axonal calibers, levels of light neurofilament (NF-L), and neurofilament content

Neurofilaments (NFs) are prominent components of large myelinated axons and probably the most abundant of neuronal intermediate filament proteins. Here we show that mice with a null mutation in the mid-sized NF (NF-M) subunit have dramatically decreased levels of light NF (NF-L) and increased levels of heavy NF (NF-H). The calibers of both large and small diameter axons in the central and peripheral nervous systems are diminished. Axons of mutant animals contain fewer neurofilaments and increased numbers of microtubules. Yet the mice lack any overt behavioral phenotype or gross structural defects in the nervous system. These studies suggest that the NF-M subunit is a major regulator of the level of NF-L and that its presence is required to achieve maximal axonal diameter in all size classes of myelinated axons.

[Surgical treatment of epispadias]

OBJECTIVE

To analyse the surgical treatment of 124 cases of epispadias (incomplete 27 cases, complete 21 and complex 76).

METHOD

Leadbetter's operation was used for anti-incontinence. Urethral tightening was used in 4 cases of complete female epispadias. Penile straightening was adopted for incomplete epispadias and penile lengthening for complete and complex male epispadias.

RESULT

In 97 cases of urinary incontinence, complete continence was achieved in 73.

CONCLUSION

The orthopedic effects of external genitals were satisfactory.

[Study on the power of O/E method]

This paper addresses the methodology of calculating the power of O/E method and introduces the relevant algorithm for estimating the sample size. Based on the principles of hyporthesis testing and Poisson distribution, the power can be worked out for given sample size, baseline rate(pi 0) and the factor of increasing (gamma). The power increases with the increase in sample size, pi 0 and gamma. In shape the power is not a continuous smooth line but a zigzag line. The method illustrated in this paper can be also used for estimaging the sample size of studies on the intervention of diseases.

Phylogenetic analysis of the nef gene reveals a distinctive monophyletic clade in Korean HIV-1 cases

To study the genetic variation of the HIV-1 strains prevalent in South Korea, we analyzed the nef sequences derived from 46 HIV-1-positive individuals living in various geographic regions in Korea. Phylogenetic analysis revealed four subtypes of HIV-1: A (3 patients), B (41 patients), D (1 patient), and a type that could not be clearly classified to any known subtype (1 patient). Thirty-five of the 41 Korean subtype B isolates formed a distinct monophyletic clade that is not related to any of the international sequences from the Los Alamos Database or GenBank as of June 1997. Indeed, the presence of unique conserved sequences was identified among the Korean isolates in this Korean subtype B group. The variations in the nucleotide sequences of a majority (32 of 35) subtype B samples within the Korean clade were 1.9% to 8.8%, and amino acid sequences varied from 3.9% to 15.5%. These results suggest that HIV-1 strains currently present in South Korea might have originated from a few sources or might be developing through a certain selective pressure. This is the first report on the molecular nature of the HIV-1 infection present in South Korea.

Lipoprotein(a) isoforms display differences in affinity for plasminogen-like binding to human mononuclear cells

Binding of lipoprotein(a) (Lp(a)) to membrane proteins of the monocyte-macrophage cell lineage may be an important event in atheroma formation. Since Lp(a) with distinct apolipoprotein(a) (apo(a)) isoforms may show differences in their affinity with regard to fibrin binding, the existence of such a functional behavior in the interaction of apo(a) in Lp(a) with these cells was explored using the monocytic cell line THP-1. Lp(a) preparations containing small size apo(a) isoforms (M(r) = 450,000 to 550,000) and high molecular mass isoforms (M(r) > or = 700,000) were purified from plasmas containing > 0.35 g/L of Lp(a) obtained from subjects (n = 14) with cardiovascular atherosclerotic disease. Binding of plasminogen to THP-1 cells was performed using the method of radioisotopic dilution. For binding of Lp(a) to cells, the THP-1 monocytic cells were incubated with varying concentrations of the different Lp(a) preparations; cells were then washed and the amount of Lp(a) bound was detected with a radiolabeled polyclonal antibody directed against apo(a). Binding due to kringle interactions with lysine residues was calculated by subtracting from the total bound the amount of Lp(a) bound (approximately 10%) in the presence of 6-aminohexanoic acid. Analysis of data with the Langmuir equation indicated identical and independent (non-interacting) sites and allowed evaluation of the Kd. Binding isotherms of small size isoforms showed saturation and a high affinity (Kd = 25.8 +/- 19 nmol/L) relative to that of plasminogen (Kd = 1750 +/- 760 nmol/L). A similar difference (Kd = 17.5 +/- 7.9 nmol/L versus Kd = 600 +/- 220 nmol/L) was found when binding experiments were performed with a fibrin surface. In contrast, binding isotherms of the high molecular mass isoforms did not show saturation at the highest Lp(a) concentrations used, thus indicating a lower affinity. In conclusion, these results show that apo(a) isoforms may display polymorphism-linked functional heterogeneity with regard to cell binding, which may explain the higher association with cardiovascular risk of small size isoforms. These qualitative differences in the binding of apo(a) isoforms to fibrin or cells may modulate the cardiovascular risk associated with high levels of Lp(a).

A common core for binding single-stranded DNA: structural comparison of the single-stranded DNA-binding proteins (SSB) from E. coli and human mitochondria

The crystal structure of the DNA-binding domain of E. coli SSB (EcoSSB) has been determined to a resolution of 2.5 A. This is the first reported structure of a prokaryotic SSB. The structure of the DNA-binding domain of the E. coli protein is compared to that of the human mitochondrial SSB (HsmtSSB). In spite of the relatively low sequence identity between them, the two proteins display a high degree of structural similarity. EcoSSB crystallises with two dimers in the asymmetric unit, unlike HsmtSSB which contains only a dimer. This is probably a consequence of the different polypeptide chain lengths in the EcoSSB heterotetramer. Crucial differences in the dimer-dimer interface of EcoSSB may account for the inability of EcoSSB and HsmtSSB to form cross-species heterotetramers, in contrast to many bacterial SSBs.

Single-stranded RNA recognition by the bacteriophage T4 translational repressor, regA

The T4 protein, RegA, is a translational repressor that blocks ribosome binding to multiple T4 messages by interacting with the mRNAs near their respective AUG start codons. Other than the AUG, there are no obvious similarities between the affected mRNAs. High affinity RNA ligands to RegA were isolated using SELEX (systematic evolution of ligands by exponential enrichment). The selected RNAs exhibited the consensus sequence 5'-AAAAUUGUUAUGUAA-3'. The AUG was invariant, suggesting that it is the primary effector of binding specificity. The UU immediately 5' to the AUG and the upstream poly(A) tract were highly conserved among the selected RNAs. Boundary and footprinting experiments are consistent with the consensus sequence defining the RegA-binding site. Interestingly, chemical modification and nuclease digestion data indicate that the RNA-binding site is single-stranded, as if RegA discriminates between targets based on their primary sequence, not their secondary structure. Minor variations from the consensus at positions other than the universally conserved AUG have little effect on RegA binding, but accumulation of mutations has a profound effect on the interaction. Comparison of the in vivo targets for RegA to the SELEX-generated consensus suggests a repression pattern whereby the translation of individual messages is sequentially halted until the least similarly affected message, the regA gene itself, is repressed.

Residues essential for catalysis and stability of the active site of Escherichia coli adenylosuccinate synthetase as revealed by directed mutation and kinetics

Examined here by directed mutation, circular dichroism spectroscopy, and kinetics are the relationships of five residues, Asp13, Glu14, Lys16, His41, and Arg131, to the catalytic function and structural organization of adenylosuccinate synthetase from Escherichia coli. The D13A mutant has no measurable activity. Mutants E14A and H41N exhibit 1% of the activity of the wild-type enzyme and 2-7-fold increases in the Km of substrates. The mutant K16Q has 34% of the activity of wild-type enzyme and Km values for substrates virtually unchanged from those of the wild-type system. Mutation of Arg131 to leucine caused only a 4-fold increase in the Km for aspartate relative to the wild-type enzyme. The dramatic effects of the D13A, E14A, and H41N mutations on kcat are consistent with the putative roles assigned to Asp13 (catalytic base), His41 (catalytic acid), and Glu14 (structural organization of the active site). The modest effect of the R131L mutation on the binding of aspartate is also in harmony with recent crystallographic investigations, which suggests that Arg131 stabilizes the conformation of the loop that binds the beta-carboxylate of aspartate. The modest effect of the K16Q mutation, however, contrasts with significant changes brought about by the mutation of the corresponding lysines in the P-loop of other GTP- and ATP-binding proteins. Crystallographic structures place Lys16 in a position of direct interaction with the gamma-phosphate of GTP. Furthermore, lysine is present at corresponding positions in all known sequences of adenylosuccinate synthetase. We suggest that along with a modest role in stabilizing the transition state of the phosphotransfer reaction, Lys16 may stabilize the enzyme structurally. In addition, the modest loss of catalytic activity of the K16Q mutant may confer such a selective disadvantage to E. coli that this seemingly innocuous mutation is not tolerated in nature.

Polarization-preserving totally reflecting prisms with a single medium layer

When reflectors with layers are used at non-normal incidence, the two planes of polarization generally have different phase shifts. The difference in the shifts is known as phase retardance. For prisms with a single layer, this retardance depends on four factors: prism index, layer index, the ratio of the optical thickness of the layer to the wavelength, and angle of incidence. When the retardance is kept at zero and the reflectance for both p and s components of a polarized light are controlled at almost 100% after reflection, a polarization-preserving total reflection is realized. Polarization-preserving totally reflecting prisms (PPTRP's) have many applications in scientific research and optical engineering. Designers of the PPTRP's need references concerning the phase properties of the PPTRP's. However, few papers can be found in which the effects of the four factors on the retardance of the PPTRP's were investigated and compared thoroughly, although the theory concerned has been known and the influences from some (not all) factors have been reported. Therefore it is still necessary to study the behavior of the PPTRP's from all aspects. The effects of all four factors on the retardance are analyzed and compared from all aspects. A general method of designing PPTRP's is proposed. As an example, a special PPTRP is designed and both theoretical and experiment results are given.

Detection of resistance to isoniazid, rifampin, and streptomycin in clinical isolates of Mycobacterium tuberculosis by molecular methods

Molecular techniques can detect drug resistance in Mycobacterium tuberculosis, but whether these methods are practical for clinical laboratory use and the management of tuberculosis is unclear. We evaluated several available molecular methods (restriction fragment length polymorphism [RFLP], heteroduplex, and direct DNA sequence analyses) for detecting resistance to isoniazid, rifampin, and streptomycin and compared these methods with conventional methods for susceptibility testing. RFLP analysis detected the mutation at position S315T in katG in 12 (44.4%) of 27 isoniazid-resistant strains. Heteroduplex analysis of rpoB, detected 16 (76.2%) of 21 rifampin-resistant strains, whereas direct DNA sequencing detected all rifampin-resistant strains. RFLP analysis of the rpsL gene detected only nine (28.1%) of 32 streptomycin-resistant strains, while direct DNA sequencing detected nearly 68% of streptomycin-resistant strains. The specificity of all of the above-mentioned methods was excellent. RFLP analysis for katG and direct DNA sequencing of rpoB and rpsL may be practical methods for routine use in clinical microbiology laboratories or molecular pathology laboratories with good molecular capabilities and autosequencers. Despite the less than optimal sensitivity for some assays, resistance can be detected rapidly. However, molecular methods are not yet capable of replacing more traditional methods of susceptibility testing for M. tuberculosis.

Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 A resolution

We solved the crystal structure of the homotetrameric single-stranded DNA binding (SSB) protein from human mitochondria at a resolution of 2.4 A. The tetramer is formed by two dimers interacting head-to-head and shows D2 symmetry. Sequence-related tetrameric SSB proteins occur in prokaryotes and eukaryotic mitochondria; this is the first report of an atomic resolution structure of this type of protein. Using biochemical data and analysis of sequence homologies, we were able to correlate the functional properties with structure. We propose that ssDNA wraps around the tetrameric HsmtSSB protein through electropositive channels guided by flexible loops.

The number of identical kringle IV repeats in apolipoprotein(a) affects its processing and secretion by HepG2 cells

A variable number of 5.6-kilobase kringle IV repeats in the human apolipoprotein(a) (apo(a)) gene results in a size polymorphism of the protein and correlates inversely with the plasma levels of the atherogenic lipoprotein(a) (Lp(a)). In order to analyze whether this association reflects a direct effect of kringle IV repeat number on Lp(a) plasma concentration, we have studied the expression of recombinant apo(a) (r-apo(a)) isoforms in the human hepatocarcinoma cell line HepG2. Following transient transfection of apo(a) cDNA expression plasmids that differed only in the number of kringle IV repeats, we observed a gradual decrease of Lp(a) in the medium of the cells with an increasing number of kringle IV repeats, mimicking the relationship present in humans in vivo. The analysis of apo(a) protein in the lysate and in the medium of cells that were transfected with a plasmid encoding an apo(a) isoform with 22 kringles revealed a predominant intracellular precursor with little secretion of the mature apo(a) protein. In contrast, transfection of a plasmid encoding an isoform with 11 kringles led to effective secretion of the mature peptide into the medium, indicating differential processing rates of apo(a) isoforms in the secretory path way. The intracellular accumulation of an apo(a) precursor in the endoplasmic reticulum was demonstrated by cell fractionation and [35S]Met metabolic labeling/temperature block experiments using HepG2 cells stably transfected with recombinant apo(a). The direct and causal effect of kringle IV repeat number on the expression of recombinant apo(a) in HepG2 cells, and presumably liver cells, provides a novel mechanism for the genetic regulation of the concentration of a protein.

Subunit complementation of Escherichia coli adenylosuccinate synthetase

Data are presented, based upon subunit complementation experiments, that suggest that Escherichia coli adenylosuccinate synthetase contains two shared active sites between its dimeric interface. This conclusion was alluded to by use of mutant forms of adenylosuccinate synthetase previously prepared by site-directed mutagenesis. The experiments indicate that, although the R143L and D13A mutants have low or no activity independently, when they are mixed, a significant amount of activity was obtained. These results indicate that the subunits exchange with each other to form heterodimers with a single viable wild-type active site. The kcat value for the active hybrid active site in the R143L-D13A heterodimer is virtually identical to that observed with the wild-type enzyme, and the other kinetic parameters are very similar to those found for the wild-type enzyme. An analysis of the restoration of the activity in the presence of substrates suggests that GTP and IMP stabilize the dimeric structure of the protein. A comparison of the restoration of the activity using different combinations of mutants provides evidence indicating that some of the GTP binding elements, including the P-loop, in the protein are important for subunit integrity. Also, for the first time, a comprehensive analysis of subunit complementation is performed for the two inactive mutants (R143L and D13A) where the dissociation constants for the R143L-D13A heterodimer and the D13A homodimer were determined to be 21 and 2.9 microM, respectively. A concentration dependence of the specific activity of the wild-type protein in this study shows that the Kd for dimer dissociation is approximately 1 microM.

[Anti-reflux ureterocysto-reimplantation in treatment of ectopic ureters: report of 51 cases]

From 1974 to 1994, anti-reflux ureterocysto-reimplantation was performed on 51 children (1 boy, 50 Girls) aged from 10 months to 13 years. The follow-up duration of 45 cases was 3 months to 14 years. The clinical symptoms of frequency of urination, lumbago and repeatedly fever, etc, were not observed except urinary incontinence in 2 cases. The results showed that ureterocysto-reimplantation is simple and traumatic. Some important aspects such as preoperative location and intraoperative identification of the unilateral or bilateral ectopic ureters were analyzed.

Involvement of arginine 143 in nucleotide substrate binding at the active site of adenylosuccinate synthetase from Escherichia coli

Adenylosuccinate synthetase from Escherichia coli is inactivated in a biphasic reaction by guanosine 5'-O-[S-(4-bromo-2,3-dioxobutyl)thio]phosphate (GMPSBDB) at pH 7.1 and 25 degrees C. Reaction of the enzyme with [8-3H]GMPSBDB results in the incorporation of 2 mol of the reagent/mol of subunit; in the presence of active site ligands the incorporation is reduced to 1 mol of reagent/mol of subunit. GMPSBDB reacts with Cys-291 in the initial rapid reaction which is accompanied by loss of 50% of the enzymatic activity; this reaction is not affected by the presence of active site ligands. In the slower reaction, GMPSBDB inactivates the enzyme by reacting with Arg-143. The inactivation kinetics of the slower phase are consistent with the formation of an enzyme--GMPSBDB complex having a Kd of 42 microM. Active site nucleotides, either adenylosuccinate or IMP + GTP, prevent both slower phase inactivation and labeling of Arg-143. Replacement of Arg-143 with a Leu by site-directed mutagenesis does not change the catalytic constant or the K(m) for aspartate but does significantly impair nucleotide binding: the Michaelis constants for IMP and GTP increase by 60-fold and 10-fold, respectively, in the R143L mutant. The crystal structure of the E. coli enzyme [Poland, B.W., Silva, M.M., Serra, M.A., Cho, Y., Kim, K. H., Harris, E.M.S., & Honzatko, R.B. (1993) J. Biol. Chem. 268, 25334--25342] shows that Arg-143 from one subunit projects into the putative active site of the other subunit. These results indicate that both subunits of dimeric adenylosuccinate synthetase contribute to each active site and that Arg-143 plays an important role in nucleotide binding.

Raman signature of the four-stranded intercalated cytosine motif in crystal and solution structures of DNA deoxycytidylates d(CCCT) and d(C8)

The Raman spectral signature of the four-stranded cytosine structure formed by intercalation of two hemiprotonated and parallel-stranded oligodeoxycytidylate duplexes (so-called i motif) has been obtained from the crystal structure of d(CCCT) [Kang, C.H., Berger, I., Lockshin, C., Ratliff, R., Moyzis, R., & Rich, A. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 11636-11640]. Identification of Raman markers diagnostic of the cytosine quadruplex is complemented by results obtained in a pH titration of 2'-deoxycytosine-5'-monophosphate (5'-dCMP) to show that the spectral fingerprint associated with N3 protonation of cytosine is distinct from that of quadruplex formation. The Raman spectrum thus provides a definitive basis for evaluating quantitatively both the extent of cytosine quadruplex formation and the degree of cytosine N3 protonation in DNA. Application to aqueous d(CCCT) and d(C8) demonstrates that the four-stranded intercalated structure is formed by both of these oligodeoxycytidylates in aqueous solution. Whereas both 5'-dCMP and the d(CCCT) quadruplex exhibit a midpoint of titration (apparent pKc) of 4.5 +/- 0.2 at 10 degrees C, cytosine protonation in d(C8) is shifted significantly toward the physiological range, with pKc = 5.8 +/- 0.2. The difference in pKc between the two quadruplexes is equivalent to a free energy difference of 1.7 kcal/mol at 10 degrees C. The present findings extend the library of Raman conformation markers to deoxycytidylate residues in the novel i quadruplex. The significance of these results for probing solution conformations of telomeric DNA sequences is also considered.

Detection of hammerhead ribozyme-mediated cleavage and reduced expression of LacZ' mRNA in E. coli

Hammerhead ribozymes have been shown to specifically suppress the expression of target genes in various cells, but their in vivo cleavage products have seldom been directly detected. A hammerhead ribozyme sequence was designed to cleave the phosphodiester bond just 3' to the GUC of SalI site of M13mp 18. The ribozyme was inserted some base pairs upstream of the target region without disrupting the reading frame of the lacZ' gene and without introducing any translational stop codons. More than 90% RNAs synthesized in vitro were cleaved at the expected site after 1-h incubation in the presence of 10 mM magnesium ion at 37 and 50 degrees C. Inclusion of the designed ribozyme sequence was also shown to suppress the expression of the fused lacZ' gene in E. coli cells. When the cells were infected by the ribozyme-containing phage, they remained colourless in the presence of X-gal, and the cellular beta-galactosidase activity was reduced by more than 90%. Insertion of the same ribozyme sequence in reverse orientation showed little effect on beta-galactosidase activity. Furthermore, a primer extension by reverse transcriptase revealed a cleavage product that resulted from cleavage of LacZ' mRNA at the targeted site as designed. Thus, our data demonstrated that the designed hammerhead ribozyme cleaves and reduces the expression of a fused LacZ' mRNA in E. coli cells.

In situ hybridization studies of cytomegalovirus and Epstein-Barr virus in reactive histiocytic hyperplasia with hemophagocytosis

We studied 14 adult patients presenting with fever and cytopenia of the peripheral blood and histiocytic hyperplasia with hemophagocytosis (HHH) in the bone marrow regarding an association of cytomegalovirus (CMV) and Epstein-Barr virus (EBV) by using in situ hybridization (ISH) and also evaluated the clinical and laboratory findings according to the encountered organisms. ISH using a CMV RNA probe demonstrated infected cells in 6 out of 14 cases (43%), and ISH using an EBV EBER RNA probe demonstrated infected nuclei in 5 out of the same 14 cases (36%) of HHH. No cases showed a positive reaction with both probes. Three cases showed a negative reaction with both probes. The mean age of all patients was 29 years; and that of the CMV-positive patients was 27 years and that of the EBV-positive patients was 36 years. Organomegaly was found in 3 out of 6 CMV-positive patients (1 hepatomegaly, 1 splenomegaly, 1 hepatosplenomegaly), and 4 out of 5 EBV-positive patients (lymphadenopathy in all 4 cases, hepatosplenomegaly in 2 cases). One of the CMV-positive case had acute myeloblastic leukemia, and 2 EBV-positive cases had underlying malignancy (1 Hodgkin's disease, 1 non-Hodgkin's lymphoma). Seven out of the 14 HHH cases (50%) died within several months after diagnosis. Nucleic acid hybridization methods can be used for the routine examination of the association of CMV or EBV.

Molecular structure of the halogenated anti-cancer drug iododoxorubicin complexed with d(TGTACA) and d(CGATCG)

4'-Deoxy-4'-iododoxorubicin, a halogenated anthracycline derivative, is an anticancer agent currently under Phase II clinical trials. In preclinical studies, it has demonstrated significantly reduced levels of cardiotoxicity compared to currently employed anthracyclines. It also has modified pharmacological properties resulting in an altered spectrum of experimental antitumor activity. The iodine atom at the 4' position of the sugar ring reduces the basicity and enhances the lipophilicity of this compound as compared to related anthracycline drugs. We report here single crystal X-ray diffraction studies of the complexes of 4'-deoxy-4'-iododoxorubicin with the hexanucleotide duplex sequences d(TGTACA) and d(CGATCG) at 1.6 and 1.5 A, respectively. The iodine substituent does not alter the geometry of intercalation as compared to previously solved anthracycline complexes, but appears to markedly affect the solvent environment of the structures. This could have consequences for the interaction of this drug with DNA and DNA binding proteins in cells.