Measuring diversity: experimental design of combinatorial libraries for drug discovery

Screening synthetic combinatorial libraries, such as mixtures of oligo(N-substituted)glycines, facilitates rapid drug lead discovery and optimization by vastly increasing the number of candidate molecules made and tested. Discovery efficiency and productivity can be further improved by using experimental design to maximize molecular diversity for a given library size or to bias the library with key features for a specific receptor. We describe new methods to quantify molecular diversity using descriptors that characterize lipophilicity, shape and branching, chemical functionality, and specific binding features. Experimental design methods select sets of side chains that are diverse in these properties, and "flower plots" allow the diversity to be graphically compared. We also quantify the overall diversity accessible to different families of combinatorial chemistry.

v-Abl-mediated apoptotic suppression is associated with SHC phosphorylation without concomitant mitogen-activated protein kinase activation

A temperature-sensitive mutant of the v-Abl protein has previously been shown to exhibit tyrosine protein kinase activity in Interleukin 3 (IL-3)-dependent IC.DP cells grown at the permissive temperature (32 degrees C) but not at the restrictive temperature (39 degrees C). These IC.DP cells are dependent on IL-3 for suppression of apoptosis at 39 degrees C, but at 32 degrees C cells will survive without added growth factor. Both IL-3 and v-Abl stimulated the tyrosine phosphorylation of SHC and GTPase-activating protein. However, while IL-3 stimulated similar levels of tyrosine phosphorylation in p46shc and p52shc, v-Abl preferentially phosphorylated p52shc, an event that occurred within 1 h of temperature switch. v-Abl also differentially associated with p46shc in a temperature-independent manner. In contrast, only IL-3 stimulated detectable increases in both myelin basic protein kinase and mitogen-activated protein (MAP) kinase kinase in in vitro assays, although in more specific MAP kinase activity assays a very slight increase in the activity of this enzyme was observed after 6 h at the permissive temperature. Time course studies suggest that phosphorylation and association of SHC with v-Abl is insufficient to lead to significant activation of MAP kinase and that activation of the MAP kinase kinase/MAP kinase pathway is not required for apoptotic suppression.

Comparison of the anisotropy of apparent integrated ultrasonic backscatter from fixed human tendon and fixed human myocardium

The content and organization of collagen in the cardiac interstitium may represent significant determinants of the ultrasonic scattering properties of myocardium. This study was designed to investigate the anisotropic backscattering properties of a fibrous soft tissue exhibiting an ordered arrangement of fibers similar to myocardium, but possessing a substantially greater content of collagen. Human Achilles tendon was chosen for this study because it possesses a simple unidirectional arrangement of fibers and a high content of collagen compared to normal myocardium. Integrated (frequency-averaged) backscatter was measured from ten formalin fixed samples of tendon as a function of insonifying angle relative to the fiber axis of the tissue. The samples were insonified in a water bath using a 5-MHz center frequency piezoelectric transducer. Maximum backscatter occurred for insonification perpendicular to the fibers, and minimum backscatter occurred for insonification parallel to the fibers. The mean peak to nadir variation, or magnitude of anisotropy, of integrated backscatter for the ten formalin fixed samples of tendon was 36.3 dB. This compares to 14.5 dB for formalin fixed human myocardium measured in an earlier study by our laboratory.

Identification of a cis-acting gene regulatory element from the lemdr1 locus of Leishmania enriettii

The goal of this work is to identify those elements which control gene expression in the parasitic protozoan, Leishmania enriettii. To date there has been no report of a transcriptional controlling element identified in this parasite. In the present study, we have found that a region of the lemdr1 locus of L. enriettii can down-regulate the steady state mRNA level of the reporter neomycin phosphotransferase gene when it is placed in an extrachromosomal expression vector, pALTneo. Through deletion analysis, we have mapped a putative regulatory sequence to the flanking region upstream of the lemdr1 gene. This cis regulatory element is shown to control gene expression in an orientation-dependent and position independent manner. By performing nuclear run-on analysis, we have demonstrated that this element mainly exerts its effect at the transcriptional level by determining the strandedness of transcription on the pALTneo vector. The identification of this novel cis regulatory element should further our understanding of the transcriptional process in Leishmania and other related trypanosomatids.

A homologous recombination strategy to analyze the vinblastine resistance property of the V-circle in Leishmania

The generation of extrachromosomal DNA elements in Leishmania sp. can occur naturally or during in vitro selection with drugs. Previously, we had established a strong association between V-circle amplification and drug resistance in L. enriettii stepwise selected with increasing concentrations of vinblastine. Further, we demonstrated the presence of the lemdr1 gene in the amplified V-circle and subsequent functional analysis by transfection of this gene alone confirmed its role in conferring a drug-resistant phenotype, but the level of resistance was significantly lower than in cell lines obtained from stepwise drug selection. The aim of this work was to determine if other genes either on the V-circle or elsewhere in the genome were necessary for expression of vinblastine resistance. We report here the development of a homologous recombination method to convert the entire V-circle from the LeV160 cell line into a shuttle vector and further the targeted disruption of specific sites within the V-circle. Our results clearly demonstrate that the V-circle alone is sufficient to confer full vinblastine resistance and the disruption of the lemdr1 locus destroys the ability of the V-circle to confer vinblastine resistance.

Cloning and functional analysis of an extrachromosomally amplified multidrug resistance-like gene in Leishmania enriettii

The goal of this work was to investigate the mechanism of drug resistance in Leishmania enriettii as a model system for drug resistance both in human leishmaniasis and on other parasitic diseases. Parasites were selected in increasing concentrations of vinblastine, an inhibitor of microtubule assembly, and resistant clones were isolated which grew in concentrations 5-30 times the IC50 (30 micrograms ml-1) of parental cells. The vinblastine-resistant parasites were also resistant to puromycin, an unrelated drug which inhibits protein synthesis. This cross-resistance to unrelated drugs had previously been observed in mammalian cells and recently in L. donovani. The proposed mechanism for this cross-resistance is drug efflux mediated by increased expression of a P-glycoprotein molecule encoded by a multidrug resistance (mdr) gene. Here we report the identification, cloning and sequencing of an mdr-like gene from L. enriettii, lemdr1, and demonstrate that this gene is amplified on an extrachromosomal circle of 35-40 kb in vinblastine-resistant L. enriettii. The longest open reading frame in the cloned gene is 1280 amino acids with a predicted protein of 140 kDa. The predicted protein has a structure similar to that for all other reported P-glycoproteins namely 12 transmembrane domains and 2 ATP binding sites, arranged in 2 similar half-molecules. Comparison of the primary amino acid sequence with other known mdr gene products demonstrates a significant homology with 37% amino acid identity with human mdr1 and 83% identity with the L. donovani ldmdr1 gene. The lemdr1 gene was cloned in the expression vector pALTNEO and transfected into wild-type L. enriettii and the resulting transfected cells were resistant to vinblastine but at lower levels than in the selected mutant cells.

A multiple sequence comparison method

This article presents a new method for the comparison of multiple macromolecular sequences. It is based on a hierarchical sequence synthesis procedure that does not require any a priori knowledge of the molecular structure of the sequences or the phylogenetic relations among the sequences. It differs from the existing methods as it has the capability of: (i) generating a statistical-structural model of the sequences through a synthesis process that detects homologous groups of the sequences, and (ii) aligning the sequences while the taxonomic tree of the sequences is being constructed in one single phase. It produces superior results when compared with some existing methods.

Quantification of ventricular remodeling in the tight-skin mouse cardiomyopathy with acoustic microscopy

To determine the role of ultrasonic tissue characterization for the detection of changes in myocardial architecture associated with cardiomyopathy, acoustic microscopy was performed on the hearts of 4- to 6-month-old tight-skin mice [TSK/+, C57-B10.D2 (58B)/SN strain], a model of cardiomyopathy characterized by diffuse interstitial fibrosis. Ultrasonic backscatter was measured from excised segments of left ventricular free walls of five TSK mice and five sex- and age-matched normal controls with a 50 MHz broad band focused piezoelectric transducer operated in a saline-filled water tank at room temperature. Forty-nine radio frequency (RF) lines were digitized from each specimen at 2 ns/sample. Power spectral analysis of RF data was performed and mean integrated backscatter (IB) computed. The TSK group demonstrated greater IB (-53.6 +/- 0.6 dB, n = 5) than did the control group (-56.6 +/- 0.7 dB, n = 5; p < 0.02). Myocardial collagen content determined by hydroxyproline assay increased by 11% in the TSK group (2.54 +/- 0.08 microgram/mg dry wt, n = 5) over that in controls (2.28 +/- 0.07 microgram/mg dry wt, n = 5; p < 0.05). A significant linear relationship was observed between myocardial hydroxyproline concentration and IB (r = 0.74; p < 0.02). Thus, ultrasonic tissue characterization permits sensitive detection of modest changes in the extent of interstitial fibrosis that accompany tissue remodeling in the early stages of cardiomyopathy.

Detection of unique transmural architecture of human idiopathic cardiomyopathy by ultrasonic tissue characterization

BACKGROUND

Noninvasive approaches to the evaluation of idiopathic cardiomyopathy are limited. Recent work from our laboratory has used quantitative ultrasound to define the three-dimensional structure of normal human myocardium and the myocardial remodeling associated with infarction. Our goal was to define the role of ultrasonic tissue characterization for detection of specific alterations in the three-dimensional transmural architecture of idiopathic dilated cardiomyopathy.

METHODS AND RESULTS

We measured frequency-dependent backscatter from 22 cylindrical biopsy specimens from nine explanted fixed hearts of patients who underwent heart transplantation for idiopathic cardiomyopathy, seven specimens from normal portions, and 12 specimens of infarcted tissue from six explanted fixed human hearts. Consecutive transmural levels from each specimen were insonified with a 5-MHz broadband transducer. The dependence of apparent (uncompensated for attenuation) backscatter, B(f), on frequency (f) was computed from radiofrequency (rf) data as: magnitude of B(f)2 = afn, where n is an index that reflects in part the size of the dominant scatterers in myocardial tissue. Myofiber diameter and percentage fibrosis were determined at each transmural level for each specimen. For cardiomyopathic tissue, the frequency dependence of backscatter (n) increased progressively from epicardial to endocardial (0.02 +/- 0.37 to 1.01 +/- 0.12, p less than 0.05) levels in conjunction with a progressive decrease in myofiber diameter (29.5 +/- 0.9 to 21.4 +/- 0.6 microns, p less than 0.0001). In contrast, in tissue from areas of infarction, the frequency dependence decreased progressively from epicardium to endocardium (0.91 +/- 0.20 to 0.23 +/- 0.21, p less than 0.05) in conjunction with a progressive increase in the percentage of fibrosis (23.5 +/- 9.4% to 54.5 +/- 4.9%, p less than 0.005). Normal tissue exhibited no significant transmural trend for frequency dependence, myofiber diameter, or percentage fibrosis.

CONCLUSIONS

These data indicate the presence of a heterogenous transmural distribution of scattering structures associated with human idiopathic cardiomyopathy and myocardial infarction that may be detected by ultrasonic tissue characterization. The divergence of these transmural trends for frequency dependence of backscatter reflects distinct mechanisms of structural heterogeneity for different pathological processes that comprise a transmural gradation of cell size and fibrosis for idiopathic cardiomyopathy and infarction, respectively.

A survey of multiple sequence comparison methods

Multiple sequence comparison refers to the search for similarity in three or more sequences. This article presents a survey of the exhaustive (optimal) and heuristic (possibly sub-optimal) methods developed for the comparison of multiple macromolecular sequences. Emphasis is given to the different approaches of the heuristic methods. Four distance measures derived from information engineering and genetic studies are introduced for the comparison between two alignments of sequences. The use of entropy, which plays a central role in information theory as measures of information, choice and uncertainty, is proposed as a simple measure for the evaluation of the optimality of an alignment in the absence of any a priori knowledge about the structures of the sequences being compared. This article also gives two examples of comparison between alternative alignments of the same set of 5SRNAs as obtained by several different heuristic methods.

Structural remodeling of human myocardial tissue after infarction. Quantification with ultrasonic backscatter

BACKGROUND

Remodeling of myocardial tissue after infarction may culminate in the development of either a well-healed scar or a thin, expanded heart wall segment that predisposes to ventricular aneurysm formation, congestive heart failure, or ventricular tachycardia. The three-dimensional architecture of mature human infarct tissue and the mechanisms that determine it have not been elucidated. We have previously shown that quantitative ultrasonic backscatter can be used to define the transmural organization of human myofibers in the normal ventricular wall by measuring the dependence of backscatter on the angle of insonification, or ultrasonic anisotropy. We propose that measurement of ultrasonic anisotropy of backscatter may permit quantitative characterization of the transmural architecture of tissue from areas of myocardial infarction and facilitate identification of fundamental mechanisms of remodeling of the ventricular wall.

METHODS AND RESULTS

We measured integrated backscatter in 33 transmural sections from 12 cylindrical biopsy specimens (1.4-cm diameter) sampled from central regions of mature infarction in six explanted fixed human hearts. Tissue samples were insonified in two-degree steps around their entire circumference at successive transmural levels with a 5-MHz broad-band piezoelectric transducer. Backscatter radio frequency data were gated from the center of each specimen, and spectral analysis was performed on the gated radio frequency for the computation of integrated backscatter. Histological morphometric analysis was performed on each specimen for determination of the predominant fiber orientation and the percentage of tissue infarcted at consecutive transmural levels. The average percentage of tissue infarcted for all transmural levels was 49 +/- 3% (range, 13-80%). Histological attributes varied from patchy fibrosis to extensive confluent zones of scar tissue. The angle-averaged integrated backscatter for all transmural levels in infarct tissue was approximately 5 dB greater than that previously measured in normal tissue in our laboratory (-48.3 +/- 0.5 versus -53.4 +/- 0.4 dB, infarct versus normal). Marked anisotropy of backscatter was observed in tissue from areas of infarction and was characterized by a sinusoid-like dependence on the angle of insonification at each transmural level. Insonification perpendicular to infarct fibers yielded values for integrated backscatter 14.8 +/- 0.5 dB greater than those for insonification parallel to these fibers. Juxtaposition of the sinusoid-like anisotropy functions from all consecutive transmural levels demonstrated a progressive shift in the orientation of scar tissue elements from epicardial to endocardial levels of 14.6 +/- 1.5 degrees/mm of tissue. The transmural shift in fiber orientation per millimeter of tissue from the area of infarction exceeded that previously measured for normal tissue (9.2 +/- 0.7 degrees/mm) by 59%. This marked augmentation in angular shift per millimeter of tissue results from a generalized structural rearrangement (or reorientation) of fibers across the entire ventricular wall in the infarct zone that we hypothesize is determined in part by dynamic mechanical forces, imposed by the surrounding functional normal tissue, that tether the "infarcted" tissue.

CONCLUSIONS

Myocardial tissue from areas of myocardial infarction manifests substantial anisotropy of ultrasonic scattering that may be useful for quantitative characterization of the alignment and overall three-dimensional anatomic organization of mature infarct scars.

Isolated atrial infarction in a patients with single vessel disease of the sinus node artery

Atrial infarction is found in approximately 17 percent of autopsy-proven cases of myocardial infarction, but is a frequently missed clinical diagnosis. The antemortem diagnosis of atrial infarction occurring in the absence of ventricular infarction has not been previously reported. We present a patient with ischemic chest discomfort associated with paroxysmal atrial fibrillation. Electrocardiographic and enzymatic changes were consistent with atrial infarction. Cardiac catheterization demonstrated single vessel critical stenosis at the origin of the sinus node artery. Combined atrial and ventricular infarction occurs frequently and should be considered in the setting of paroxysmal supraventricular arrhythmias occurring early in the course of ventricular myocardial infarction. Lone atrial infarction is a rare but distinct clinical entity. The tetrad of typical ischemic chest discomfort, paroxysmal supraventricular arrhythmia, P-Ta segment shifts, and elevated cardiac enzyme levels without evidence for ventricular infarction strongly suggests isolated atrial infarction.

Identification of novel single-stranded d(TC)n binding proteins in several mammalian species

A group of single-stranded d(TC)n specific binding proteins has been detected in the nuclear extracts of several mammalian species that included mouse, human, African green monkey, chimpanzee, and Chinese muntjac. Southwestern analysis of 500 mM KCI nuclear extracts has shown that these proteins cluster in a similar size range, 55.5 to 57 kD. An additional 54 kD band was present for the three primate species examined. The single-stranded d(TC)n binding activity was confirmed with bandshift assay. Specific double-stranded binding activity for duplex d(TC)n.d(GA)n or single-stranded d(GA)n was not detected. The conservation of size distribution and d(TC)n-binding activity across the species examined indicates that this class of single-stranded binding proteins may have an important biological function in vivo.

Distribution of CT-rich tracts is conserved in vertebrate chromosomes

The distribution of d(CT)-rich pyrimidine tracts in the karyotypes of a variety of vertebrates was studied by in situ hybridization. The probe for these studies was a 56bp homopyrimidine/homopurine sequence obtained from a mouse genomic library constructed with DNA prepared from a restriction enzyme digestion of metaphase chromosomes. Single-stranded DNA nuclease digestions and two-dimensional gel analysis of topoisomers of this sequence indicated that it is capable of adopting a triplex conformation in vitro. In situ hybridization with this probe to the karyotypes of ten different vertebrate species revealed a highly conserved chromosomal distribution of d(CT)-rich tracts. These tracts are found throughout the chromosomal arms and in some karyotypes they are clustered, producing a banding pattern. However, at the resolution of the light microscope these tracts appeared to be absent from the centromeric regions of all chromosomes examined except those of chicken. The non-random distribution of these tracts to the chromosomal arm regions implies an organizational or functional role for this repeat class. It is unlikely that the 56 bp sequence type contributed to the formation of the triplex DNA structure previously detected in centromeric domains of mouse.

The chromosomal distribution of the major and minor satellite is not conserved in the genus Mus

The cytological distribution of the major and minor satellite first identified in Mus musculus was studied in the karyotypes of three related subspecies and two other species of the genus Mus. Both the major and minor satellite showed species dependent hybridization patterns. The major satellite is confined to the centromere region in M. musculus and related subspecies. However, in M spretus and M. caroli, the chromosomal arm regions contain this sequence class. In contrast the minor satellite is found at the kinetochore region in M. musculus and related subspecies but is distributed throughout the entire centromeric domain in M. spretus and appears to be excluded from the chromosomes of M. caroli. There is an apparent correlation between the chromosomal location of these satellites and their phylogenetic relationship. Determination of the biological roles of the major and minor satellites from M. musculus must take into account their differential chromosomal distribution in other Mus species.

Relationship between myocardial metabolites and contractile abnormalities during graded regional ischemia. Phosphorus-31 nuclear magnetic resonance studies of porcine myocardium in vivo

The mechanisms responsible for changes in myocardial contractility during regional ischemia are unknown. Since changes in high-energy phosphates during ischemia are sensitive to reductions in myocardial blood flow, it was hypothesized that myocardial function under steady-state conditions of graded regional ischemia is closely related to changes in myocardial high-energy phosphates. Therefore, phosphorus-31 nuclear magnetic resonance spectroscopy was employed in an in vivo porcine model of graded coronary stenosis. Simultaneous measurements of regional subendocardial blood flow, high-energy phosphates, pH, and myocardial segment shortening were made during various degrees of regional ischemia in which subendocardial blood flow was reduced by 16-94%. During mild reductions in myocardial blood flow (subendocardial blood flow = 83% of nonischemic myocardium), only the ratio of phosphocreatine to inorganic phosphate (PCr/Pi), Pi, and [H+] were significantly changed from control. PCr, ATP, and PCr/ATP were not significantly reduced from control with mild reductions in blood flow. Changes in myocardial segment shortening were most closely associated with changes in PCr/Pi (r = 0.94). Pi and [H+] were negatively correlated with segment shortening (r = -0.64 and -0.58, respectively) and increased over twofold when blood flow was reduced by 62%. Thus, these data demonstrate that PCr/Pi is sensitive to reductions in myocardial blood flow and closely correlates with changes in myocardial function. These data are also consistent with a role for Pi or H+ as inhibitors of myocardial contractility during ischemia.

Evidence that precursor cells of monocytes and B-lymphocytes are closely related

Various data in the literature suggest that progenitor cells of monocytes and B cells are closely related. In this study we have investigated this notion by using two-dimensional gel electrophoresis patterns of total cellular phosphoproteins to assess the similarity and thus the close relationships between erythroid, granulocyte, monocyte, and B-lymphocyte cell lines that typify immature cells of these lineages. In previous studies, six proteins had been identified whose constitutive phosphorylation correlated with the capacity of HL60 variant cell lines to differentiate towards either neutrophils (four proteins) or monocytes (two proteins). The presence or absence of five of these phosphoproteins in autoradiographs obtained for the pre-B-cell lines Nalm6 and SMSB showed that the pre-B-cell lines most closely resembled lines able to differentiate towards monocytes (HL6015-12, HL60M2, U937, and ML-1) as opposed to lines restricted to neutrophil (HL60Ast3) or erythroid differentiation (K562). The K562 phosphoprotein pattern resembled that obtained for HL60Ast3. Progressive changes in the constitutive phosphorylation of the five proteins were observed suggesting that cells that have acquired the potential for either neutrophil, monocyte, or B-cell differentiation have initially diversified in a linear progressive manner. This observation supports a model for hemopoiesis that suggests that, during progenitor cell development, differentiation potentials are expressed individually in the above order. Two additional phosphoprotein spots were found to be restricted to the pre-B-cell lines. These phosphoproteins, together with those that change their intensity in autoradiographs of erythroid, myeloid, and B-cell lines, suggest that protein phosphorylation plays an important role during cell diversification.

Sequence organization and cytological localization of the minor satellite of mouse

A complete 120 bp genomic consensus sequence for the mouse minor satellite has been determined from enriched L929 centromeric sequences. The extensive sequence homology existing between the major and minor satellite suggests an evolutionary relationship. Some sequences flanking the minor satellite has also been identified and they provide insight into centromeric DNA organization. Isotopic in situ hybridization analysis of the minor satellite to mouse L929 and Mus musculus metaphase spreads showed that this repetitive DNA class is localized specifically to centromeres of all chromosomes of the karyotype. With the use of high resolution non-isotopic fluorescence in situ hybridization the minor satellite is further localized to the outer surface of the centromere in a discrete region at or immediately adjacent to the kinetochore. Our cytological data suggests that the minor satellite might play a role in the organization of the kinetochore region rather than, as previously suggested, sites for general anchoring of the genome to the nuclear matrix.

Changes in phosphoproteins during commitment of HL60 cells to monocyte differentiation: evidence for multiple protein kinase involvement

The human promyeloid cell line HL60 differentiates toward monocytes when treated with TPA. We have analyzed, by two-dimensional gel electrophoresis, the phosphoprotein patterns within HL60 cells, labeled to equilibrium with [32P]orthophosphate when cells were treated with suboptimal (1 nM), optimal (5 and 10 nM), and supraoptimal (40 and 100 nM) concentrations of 12-O-tetradecanylphorbol-13-acetate (TPA) as regards the induction of differentiation. No change was detected in the phosphoprotein pattern at 1 nM TPA, whereas four phosphoproteins showed increased levels of phosphorylation at 5 and 10 nM TPA. When cells were treated with 40 and 100 nM TPA, in total eight and ten proteins, respectively, were phosphorylated, including the above four proteins. Two proteins were dephosphorylated when cells were treated with 40 and 100 nM TPA. A 15-kd protein, phosphorylated when HL60 cells were treated with 5 nM TPA, was observed as an intense spot in autoradiographs of total cellular phosphoproteins of two variant HL60 cell lines that are unable to differentiate toward monocytes and prior to treatment with TPA. In the case of three variant cell lines, which like HL60 differentiate toward monocytes, the phosphoprotein spot was almost absent. Thus, paradoxically, the 15-kd phosphoprotein is affected by TPA although its constitutive level of expression or increased phosphorylation state is inversely related to the potential for monocyte differentiation. This observation, together with the TPA dose-response effects on protein phosphorylation, is discussed in relation to multiple protein kinase involvement.

Near neighbour analysis of variant cell lines derived from the promyeloid cell line HL60

The human promyeloid cell line H60 can be induced to differentiate towards either neutrophils or monocytes. Variant cell lines, derived from HL60, which show reduced capacities for neutrophil and monocyte differentiation can be arranged in a developmental sequence which suggests that the potentials for neutrophil and monocyte differentiation are expressed sequentially by HL60 cells in this order. Analysis of the patterns of total cellular phosphoproteins within HL60 and 5 variant cell lines, by two-dimensional gel electrophoresis, has identified 6 distinct phosphoproteins which show progressive differences in the intensity of spots between the variant lines. The changes in these phosphoproteins relate to the position of the lines within the proposed development sequence. Similarly, lines placed close together in the sequence are more similar, as regards phosphoprotein profiles, than lines placed far apart. These studies provide direct evidence in favour of the hypothesis that the potentials for neutrophil and monocyte differentiation are expressed sequentially during myelopoiesis. Furthermore, two phosphoprotein spots were found to be restricted to lines able to differentiate towards monocytes. These proteins may play important roles during commitment to monocyte differentiation.

An apparent deletion of an oligonucleotide detected by RNA fingerprint in the nondiabetogenic B variant of encephalomyocarditis virus is caused by a point mutation

The diabetogenic D variant of encephalomyocarditis virus (EMC-D) was previously shown to be different from the nondiabetogenic B variant of encephalomyocarditis virus (EMC-B) by a single spot in an oligonucleotide fingerprint after RNase T1 digestion of their genomic RNAs. An oligoribonucleotide was missing from EMC-B but was present in EMC-D. The oligoribonucleotide specific to EMC-D was isolated from a two-dimensional polyacrylamide gel and sequenced as 5'-ACAAUCUCACUUUUCCAACAACAG-3'. Molecular hybridizations of EMC-D and EMC-B genomic RNAs with a DNA primer complementary to the EMC-D-specific oligoribonucleotide revealed that the absence of a corresponding spot in EMC-B was due to a point mutation rather than a deletion. By sequencing a cloned cDNA of EMC-B corresponding to the EMC-D-specific oligoribonucleotide, the point mutation was identified as a G for EMC-B and an A for EMC-D transversion at base 9 of the oligonucleotide. Comparative sequence analysis of eight randomly picked RNA segments around the EMC-D-specific oligoribonucleotide revealed that there were no base changes between EMC-D and EMC-B. It is concluded that the diabetogenic EMC-D viral genome differs from the nondiabetogenic EMC-B viral genome by at least a point mutation.

Synthesizing statistical knowledge from incomplete mixed-mode data

The difficulties in analyzing and clustering (synthesizing) multivariate data of the mixed type (discrete and continuous) are largely due to: 1) nonuniform scaling in different coordinates, 2) the lack of order in nominal data, and 3) the lack of a suitable similarity measure. This paper presents a new approach which bypasses these difficulties and can acquire statistical knowledge from incomplete mixed-mode data. The proposed method adopts an event-covering approach which covers a subset of statistically relevant outcomes in the outcome space of variable-pairs. And once the covered event patterns are acquired, subsequent analysis tasks such as probabilistic inference, cluster analysis, and detection of event patterns for each cluster based on the incomplete probability scheme can be performed. There are four phases in our method: 1) the discretization of the continuous components based on a maximum entropy criterion so that the data can be treated as n-tuples of discrete-valued features; 2) the estimation of the missing values using our newly developed inference procedure; 3) the initial formation of clusters by analyzing the nearest-neighbor distance on subsets of selected samples; and 4) the reclassification of the n-tuples into more reliable clusters based on the detected interdependence relationships. For performance evaluation, experiments have been conducted using both simulated and real life data.

Structuring free space as a hypergraph for roving robot path planning and navigation

This paper presents a method of structuring the free space of a roving robot's environment into a set of overlapping convex regions ideally suited to path planning and navigation tasks. The structure of the free space environment is maintained as a hypergraph with each convex region represented by a hyperedge identifying the boundary walls of the region. A new methodology reveals the structure of free space and constructs the hypergraph representation through a directed search for a set of fundamental circits in an abstract graphical representation of the environment geometry.

Regioselectivity in rat microsomal metabolism of benzo[a]pyrene: evidence for involvement of two distinct binding sites

The metabolic profile of benzo[a]pyrene (BP) in cumene hydroperoxide-(CHP)-dependent reaction by male rat liver microsomes was dependent on CHP concentration. At 0.05 mM CHP, 3-hydroxy-BP was the major metabolite. Increase in CHP reduced 3-hydroxy-BP formation but increased BP quinone formation simultaneously. This change in metabolic profile was reversed by preincubation with pyrene. Pyrene (PY) selectively inhibited quinone formation but enhanced 3-hydroxy-BP formation. Naphthalene (NP) had no effect on BP quinone formation but inhibited BP 3-hydroxylation. Phenanthrene (PA) and benz[a]anthracene (BA) inhibited effectively 3-hydroxy-BP formation but only slightly quinone formation. BP binding to microsomal protein correlated to quinone formation and not BP 3-hydroxylation. BP metabolism by female rat liver microsomes also depended on CHP concentration but was much less efficient than the male. Quinones were consistently predominant metabolites and their formation was also inhibited by pyrene. Our data provide evidence that regioselectivity in BP metabolism involves at least two distinct binding sites. One site recognizes the benzo region of BP in BP 3-hydroxylation and the other recognizes the pyrene region in quinone formation. The different ratios of 3-hydroxy-BP to quinone formation by male and female rat liver microsomes suggest that the two binding sites are probably located at separate cytochrome P-450 isozymes.

Dependence of benzo[a]pyrene metabolic profile on the concentration of cumene hydroperoxide with uninduced and induced rat liver microsomes

The effect of cumene hydroperoxide (CHP) in microsomal metabolism of benzo [a]pyrene (BP) was studied using liver microsomes from mature male Wistar rats induced with phenobarbital (PB), 3-methylcholanthrene (MC), Aroclor 1254 or olive oil (uninduced). In contrast to NADPH-supported metabolism, these inducers did not increase the CHP-dependent metabolism. Total BP metabolism was dependent on CHP concentration and was maximal at 0.15 mM, except for PB-induced microsomes, which had a maximum at 0.5 mM CHP. At 0.05 mM CHP, the major metabolites were phenols. However, increasing CHP concentration enhanced the formation of dihydrodiols, quinones and protein-bound BP but reduced phenol production. At and above 0.15 mM CHP, the profile of BP metabolites was essentially constant, with at least 66% quinones but no more than 10% phenols. The effect of CHP on inhibition of phenol formation and enhancement of quinone formation was reversed by preincubation of microsomes with BP or by increasing BP concentration. These results suggest that CHP-dependent metabolism of BP is selectively mediated by constitutive cytochrome P-450 isozyme(s) and that two forms of BP binding sites exist in cytochrome P-450 isozymes and are responsible for the hydroxylation of BP at C-3 and C-6.

Entropy and distance of random graphs with application to structural pattern recognition

The notion of a random graph is formally defined. It deals with both the probabilistic and the structural aspects of relational data. By interpreting an ensemble of attributed graphs as the outcomes of a random graph, we can use its lower order distribution to characterize the ensemble. To reflect the variability of a random graph, Shannon's entropy measure is used. To synthesize an ensemble of attributed graphs into the distribution of a random graph (or a set of distributions), we propose a distance measure between random graphs based on the minimum change of entropy before and after their merging. When the ensemble contains more than one class of pattern graphs, the synthesis process yields distributions corresponding to various classes. This process corresponds to unsupervised learning in pattern classification. Using the maximum likelihood rule and the probability computed for the pattern graph, based on its matching with the random graph distributions of different classes, we can classify the pattern graph to a class.

Hypersensitivity to rat saliva

A patient who rapidly developed impressive local edema around a rat bite site is described. An interesting differential diagnosis was presented since the offending rat was experiencing an opiate withdrawal syndrome. A discussion of the possibilities of animal product allergy, local infection, and edema produced by opiate histamine releasers was considered.

Bullous lichen sclerosus et atrophicus on the palms and wrists

A 54-year-old woman with bullous lichen sclerosus et atrophicus of the palms and wrists is presented. The location of the disease and the appearance of hemorrhagic bullae within the lesions are unusual.

In vitro binding of propranolol and progesterone to native and desialylated human orosomucoid

A comparison of propranolol and progesterone binding to native and desialylated human orosomucoid was studied by means of equilibrium dialysis. The association constants of propranolol and progesterone binding to native human orosomucoid under physiological conditions were 8.4 X 10(5) and 3.2 X 10(5) M-1, respectively. Enzymatic desialylation of human orosomucoid removed 95% of the sialic acid content and reduced the binding affinity of propranolol from 8.4 X 10(5) to 6.0 X 10(5) M-1, but the affinity of progesterone was not affected. In addition, desialylation reduced the percent binding for propranolol, indicating that electrostatic attraction of the positive charge on propranolol by sialic acid residues on human orosomucoid had some effect on the binding ability of purified orosomucoid for propranolol. The present data suggest that the electrostatic attraction between sialic acid and propranolol is partially responsible for the preferential binding of basic drugs to orosomucoid in plasma.

Effects of Aroclor 1254-induced rat liver S-9 fraction on benzo[a]pyrene-mediated DNA damage and benzo[a]pyrene metabolism in cultured human skin fibroblasts

Incubation of cultured normal human skin fibroblasts with benzo[a]pyrene (B[a]P) resulted in covalent binding of B[a]P to protein, RNA and DNA. B[a]P adduct formation was increased when the cultured cells were also treated with the 9,000 g hepatic microsomal supernatant (S-9) fraction from rats pretreated with Aroclor 1254, a commercial preparation of polychlorinated biphenyls (PCBs). Comparison with control experiments which included the incubation with corn oil-induced S-9 fraction indicated that the enhanced B[a]P-adduct formation in the host cells was related to the induction of hepatic NADPH-dependent microsomal monooxygenase activity by Aroclor 1254 in the S-9 fraction. Parallel experiments showed that this Aroclor-induced enzymic activity was responsible for B[a]P-mediated DNA damage as measured by unscheduled DNA synthesis (UDS) in the cells. Similarly, administration of rat hepatic S-9 induced by 3-methylcholanthrene (MC) and phenobarbitone (PB) caused B[a]P-mediated DNA damage in cultured human skin fibroblasts.

Random graphs: structural-contextual dichotomy

A formal definition of random graphs is introduced which is applicable to graphical pattern recognition problems. The definition is used to formulate rigorously the structural-contextual dichotomy of random graphs. The probability of outcome graphs is expressed as the product of two terms, one due to the statistical variability of structure among the outcome graphs and the other due to their contextual variability. Expressions are obtained to estimate the various probability, typicality, and entropy measures. The members in an ensemble of signed digraphs are interpreted as outcome graphs of a random graph. The synthesized random graph is used to quantify the structural, contextual, and overall typicality of the outcome graphs with respect to the random graph.

DECA: A Discrete-Valued Data Clustering Algorithm

This paper presents a new clustering algorithm for analyzing unordered discrete-valued data. This algorithm consists of a cluster initiation phase and a sample regrouping phase. The first phase is based on a data-directed valley detection process utilizing the optimal second-order product approximation of high-order discrete probability distribution, together with a distance measure for discrete-valued data. As for the second phase, it involves the iterative application of the Bayes' decision rule based on subgroup discrete distributions. Since probability is used as its major decision criterion, the proposed method minimizes the disadvantages of yielding solutions sensitive to the arbitrary distance measure adopted. The performance of the proposed algorithm is evaluated by applying it to four different sets of simulated data and a set of clinical data. For performance comparison, the decision-directed algorithm [11] is also applied to the same set of data. These evaluation experiments fully demonstrate the validity and the operational feasibility of the proposed algorithm and its superiority as compared to the decision-directed algorithm.

PFS Clustering Method

This paper presents a method of cluster analysis based on a pseudo F-statistic (PFS) criterion function. It is designed to subdivide an ensemble into an optimal set of groups, where the number of groups is not specified and no ad hoc parameters are employed. Univariate and multivariate F-statistic and pseudo F-statistic consistency is displayed. Algorithms for feasible application of PFS are given. Results from simulations are utilized to demonstrate the capabilities of the PFS clustering method and to provide a comparative guide for other users.

Orthodontic elastic materials

Latex elastics and synthetic elastomers have certain similarities and differences. In the fracture tests the latex elastics showed a greater amount of loss in strength than plastic elastomers when stretched over a 21 day period. There is a great variability, as much as 50%, in the tensile strength of the plastic materials taken from the same batch and stretched under the same conditions. The Ormco Power Chain was more resilient than the Unitek AlastiK chain. The Unitek AlastiKs had more force and stretched less. The force decay of synthetic elastomers, stretched over a specific length and time, exhibited a great loss in force. This loss could be as great as 73% during the first day. The decay of force continued at a slower rate during the rest of the 21 day period. Unitek AlastiK C2 double links, when stretched 17 millimeters, had a higher initial force averaging 641 grams (22.5 ounces) than the Ormco Power Chain which averages 342 grams (12.0 ounces). In one day the force was reduced to 171 grams (6.0 ounces) for both materials. The elastic materials within the same batch showed a great variation in the modulus of elasticity under different test conditions. The approximate force generated when stretched dry, within the elastic limit, was 22 grams per millimeter for 3/16 inches heavy latex elastics. The Unitek AlastiK C2 gave a force of 89 grams per millimeter, while the Ormco Power Chain had a value of 46 grams per millimeter. The modulus of elasticity of all of the materials was much lower after immersion in the water bath. The force decay under constant force application to latex, elastic, polymer chains, and tied loops showed that the greatest amount of force decay occurred during the first three hours in the water bath. The forces remained relatively the same throughout the rest of the test period. The elastic materials undergo permanent deformation in shape. The synthetic elastomers exhibited plastic deformation when the elastomers were stretched 17 millimeters for 21 days. In the dry condition the force decay was 63% for the Unitek chains and 42% for the Ormco Power Chain. The synthetic elastomers should be prestretched before being placed in the mouth. The elastomers should be used within their resilient ranges. Clinical treatment procedures should take into consideration the rapid initial force decay of elastic materials that occurs during the first day and the residual forces remaining.