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PubMed1993

A graphical user interface to facilitate patient-specific drug dosing.

This paper describes the development of a graphical user-interface (GUI) designed to facilitate the process of generating patient-specific drug doses using bayesian modelling software. The graphical user interface was developed in Visual Basic (Microsoft, Inc.) and runs under the Windows 3.1 (Microsoft, Inc.) operating system. Patient demographic data are stored in a relational database (Access, Microsoft, Inc.). The GUI and the database communicate via dynamic data exchange links. The largely object-oriented nature of the language allowed us to change the entire look and feel of the system with a few simple changes to the underlying code. Use of the relational database to store patient demographic information allows greater flexibility in searching for and displaying patient specific information. The GUI reduces the time required to enter data. The prototype has allowed us to experiment with different presentation methods, greatly improving the clinical acceptance of the dosing programs.

Computer Simulation↗
PubMed1992

Chemical carcinogenesis of the urinary bladder--a status report.

Cigarette smoking and certain types of occupational exposure to arylamines appear to be the main cause of human urinary bladder cancer. Little is known of the promotion of bladder cancer in humans, although this stage has been demonstrated in rodents. Perhaps as a consequence of initiation, multifactorial alterations of cellular genes occur. These genes include the epidermal growth factor receptor gene, erbB-2, int-2, hst, and H-ras, which exert positive control over cell growth, as well as the suppressor genes Rb-1, and the gene coding for p53. Chromosomal changes such as deletions, translocations and/or amplifications related to these genes may be of significance for prognosis of this disease.

Animals↗
PubMed2001

The bacteriophage lambda attachment site in wild strains of Escherichia coli.

The attachment site (attlambda) of bacteriophage lambda was examined in wild strains of Escherichia coli. Although the att region is non-coding, the DNA sequence was invariant in the 13 strains examined. Two other non-coding regions showed nine changes, all associated with a single strain. In four of 33 strains, sequences were inserted in or near the attlambda site and in two of these the insert was related to lambda. Among strains that can be lysogenized by lambda, integration was via the attlambda site in all cases. Some resistant strains can be lysogenized, and these have been termed "lenient." Most of these fail to give normal phage yield after induction. In some cases rare lysogens have been formed in cells that belong to a mutant subpopulation.

Bacteriophage lambda↗
PubMed2003

Traveling-wave pattern generator controls movement and organization of sensory feedback in a spinal cord model.

A traveling wave in a two-dimensional spinal cord model constitutes a stable pattern generator for quadruped gaits. In the context of the somatotopic organization of the spinal cord, this pattern generator is sufficient to generate stable locomotive limb trajectories. The elastic properties of muscles alone, providing linear negative feedback, are sufficient to stabilize stance and locomotion in the presence of perturbative forces. We further show that such a pattern generator is capable of organizing sensory processing in the spinal cord. A single-layer perceptron was trained to associate the sensory feedback from the limb (coding force, length, and change of length for each muscle) with the two-dimensional activity profile of the traveling wave. This resulted in a well-defined spatial organization of the connections within the spinal network along a rostrocaudal axis. The spinal network driven by peripheral afferents alone supported autonomous locomotion in the positive feedback mode, whereas in the negative feedback mode stance was stabilized in response to perturbations. Systematic variation of a parameter representing the effect of gamma-motor neurons on muscle spindle activity in our model led to a corresponding shift of limb position during stance and locomotion, resulting in a systematic displacement alteration of foot positions.

Feedback, Physiological↗
PubMed1998

Neurotrophic factors and the maldevelopmental hypothesis of schizophrenic psychoses. Review article.

The maldevelopmental model of schizophrenia postulates pathological alterations in embryonal neurogenesis as the etiopathogenetic basis of schizophrenic psychosis; the neurotrophic factor hypothesis explains these changes as the result of disturbances of processes involving the trophic factors. Neurotransmitter deficits are thereby interpreted as epiphenomena of underlying neurotrophic factor deficacy. The functional systems of the various neurotrophic factors are characterized by complex interaction mechanisms. Both primary genetic alterations, and secondary impairments, induced by exogene noxae, of the receptors and signal transducers associated with neurotrophic factors, as well as of the neurotrophic factors themselves are possible. Preliminary clinical studies indicate that schizophrenic psychoses may be associated with changes in the genetic code of certain neurotrophic factors. Various phenomena typical of the schizophrenic psychoses can be interpreted according to the neurotrophic factor hypothesis.

Animals↗
PubMed2003

Pathogenicity, sequence and phylogenetic analysis of Malaysian Chicken anaemia virus obtained after low and high passages in MSB-1 cells.

Specific-pathogen-free (SPF) chickens inoculated with low passage Chicken anaemia virus (CAV), SMSC-1 and 3-1 isolates produced lesions suggestive of CAV infection. Repeated passages of the isolates in cell culture until passage 60 (P60) and passage 123 produced viruses that showed a significantly reduced level of pathogenicity in SPF chickens compared to the low passage isolates. Sequence comparison indicated that nucleotide changes in only the coding region of the P60 passage isolates were thought to contribute to virus attenuation. Phylogenetic analysis indicated that SMSC-1 and 3-1 were highly divergent, but their P60 passage derivatives shared significant homology to a Japanese isolate A2.

Animals↗
PubMed1992

DNA base sequence changes in spontaneous and ethyl methanesulfonate-induced mutations of a chromosomally-integrated gene in Chinese hamster ovary cells.

A series of spontaneous and ethyl methanesulfonate-induced 6-thioguanine-resistant mutants were isolated in the CHO-10T5 cell line. This cell line was constructed by the introduction of a shuttle vector containing the Escherichia coli gpt gene into a hypoxanthine-guanine phosphoribosyltransferase deficient derivative of the Chinese hamster cell line CHO-K1. Shuttle vector sequences were recovered from many of the mutant cell lines by the COS cell fusion technique and the DNA base sequence of the gpt genes was determined whenever possible. The base sequences were determined for gpt genes recovered from 29 spontaneous mutants. Of these 29 mutants, 9 have single base substitutions, 1 has a small duplication, 17 have simple deletions, 1 has a deletion with additional bases inserted at the deletion site, and 1 has no change in the gpt coding sequence. Many of the deletions were less than 20 basepairs in length and several occurred in a region previously observed to be a hotspot for spontaneous deletions. The generation of the deletion/insertion mutation may have involved a quasi-palindromic intermediate. A total of 59 ethyl methansesulfonate-induced mutants were isolated and vector sequences were recovered from 50 mutants. All 50 mutants sequenced had single base substitutions and most (45) were G:C to A:T transitions. While there were no strong hotspots in this collection of mutations, the site distribution was obviously nonrandom. Many of the G:C to A:T transitions either produced a nonsense codon or occurred at glycine codons.

Animals↗
PubMed1992

Genetic drift of hepatitis C virus during an 8.2-year infection in a chimpanzee: variability and stability.

Extensive variability in genomic sequence, especially at "hypervariable regions" within the NS1/E2 region of the long open reading frame, has been reported for RNA cloned from hepatitis C virus (HCV)-infected humans and chimpanzees. However, genetic changes of HCV occurring during the course of chronic infections in humans and animals have been evaluated only for partial sequences of the HCV genome. We compared two full-length cDNA sequences of HCV obtained from a chimpanzee that was experimentally infected with the HC-J4 strain of HCV: one during the early acute phase and another during a chronic phase 8.2 years afterward. Both isolates had 9412 nucleotides plus the 3' poly(U) tail with varying length organized as follows: 5'UTR (1-341); C (342-914); E (915-1490); NS1/E2 (1491-2528); NS2 (2529-3359); NS3 (3360-5186); NS4 (5187-6380); NS5 (6381-9371); and 3'UTR (9372-9412). We found that 111 (1.18%) of the 9412 nucleotides differed between the two isolates and estimated the mutation rate as approximately 1.44 x 10(-3) base substitutions per site per year. Changes in amino acid coding were associated with 42 mutations, 8 of which were clustered at 5' end of NS1/E2 coding region, so-called "HVR-1." We analyzed the HVR-1 and HVR-2 sequences during the course of infection and found that homologous populations were present at the beginning of infection, and sequence heterogeneity within the region had developed 3.5 years later. Two regions of the HCV genome were characterized by a high degree of conservation of nucleotide sequence: 5'UTR and the 3' half of the NS4 region. The possible secondary structure of the 5'UTR suggests a region for internal ribosomal entry. The 3' half of the NS4 region may also have some specific function which depends upon a strict conservation of nucleotide sequence.

Amino Acid Sequence↗
PubMed1995

Two consecutive nucleotide substitutions resulting in the T3 receptor beta gene resulting in an 11-amino acid truncation in a patient with generalized resistance to thyroid hormone.

We identified unusual mutations in the T3 receptor (TR) beta gene in a 6-year-old Japanese girl with generalized resistance to thyroid hormone. Two consecutive base substitutions, T to A and C to A at nucleotide positions 1637 and 1638, respectively, changed the 451st codon coding for Phe(TTC) to stop codon (TAA), resulting in an 11-amino acid carboxyl(C)-terminus truncation. The patient was a heterozygote. Western blotting using an anti-TR antibody demonstrated the truncated receptor protein. The patient showed severe mental retardation (IQ41), disturbance in speech development, and attention deficit hyperactivity disorder. Thyroid functional status by clinical evaluation was considered within the normal range in spite of high serum thyroid hormone levels (T4 725.9 nmol/l, T3 12.7 nmol/l, FT4 166.0 pmol/l). TSH increased from 0.6 to 24 mU/L after TRH (150 micrograms) injection. TSH secretion as well as 123I-uptake was suppressed only partially by T3 (75 micrograms/day for a week). Close examination of thyroid functions and TR beta gene analysis were not possible in the family, except for paternal grandmother and one of her two sisters who showed no abnormality. The patient's truncated TR beta showed very low T3 binding activity (Ka = 0.1 x 10-10 M), transcriptional activity, and a very strong dominant negative effect. When co-expressed with wild-type TR beta at the molar ratio 1:1 in CV-1 cells, the mutant receptor inhibited the wild-type TR beta transcriptional activity by 74% at 10 nM T3. Even 1 microM T3 could not normalize these impaired functions.

Amino Acid Sequence↗
PubMed1995

Characterization of the gene encoding carbonic anhydrase I from the pigtail macaque.

The structure of the gene encoding carbonic anhydrase I (CA I) was determined for the pigtail macaque Macaca nemestrina. When the deduced amino-acid sequence was compared with those of five other primates, four non-primate mammals and a turtle, seven residues were found to be unique and invariant to all of the CA I sequences. A scheme is presented for the probable evolutionary order of the six polymorphic nucleotide changes found in the coding regions of the CA I locus of pigtail macaques.

Amino Acid Sequence↗
PubMed2006

Effects of gastrointestinal inflammation on enteroendocrine cells and enteric neural reflex circuits.

Inflammation of the gastrointestinal (GI) tract has pronounced effects on GI function. Many of the functions of the GI tract are subject to neural regulation by the enteric nervous system (ENS) and its extrinsic connections. Therefore, it is possible that inflammatory effects on the ENS contribute to altered function during GI inflammation. The reflex circuitry of the ENS is comprised of sensory transducers in the mucosa (enteroendocrine cells), afferent neurons, interneurons and motor neurons. This review focuses on recent data that describe inflammation-induced changes to the ENS and mucosal enteroendocrine cells. Studies of tissues from patients with inflammatory bowel disease (IBD) and from animal models of IBD have demonstrated marked changes in mucosal enteroendocrine cell signaling. These changes, which have been studied most intensely in 5-HT-containing enterochromaffin cells, involve changes in the number of cells, their signaling molecule content or their means of signal termination. Morphological evidence of enteric neuropathy during inflammation has been obtained from human samples and animal models of IBD. The neuropathy can reduce the number of enteric neurons in the inflamed region and is often accompanied by a change in the neurochemical coding of enteric neurons, both in the inflamed region and at distant sites. Electrophysiological recordings have been made from enteric neurons in inflamed regions of the colon of animal models of IBD. These studies have consistently found that inflammation increases excitability of intrinsic primary afferent neurons and alters synaptic transmission to interneurons and motor neurons. These data set the stage for a comprehensive examination of the role of altered neuronal and enteroendocrine cell signaling in symptom generation during GI inflammation.

Animals↗
PubMed2006

Investigation of the human stem cell factor KIT ligand gene, KITLG, in women with 46,XX spontaneous premature ovarian failure.

OBJECTIVE: To investigate mutations in the human KIT ligand gene (KITLG) gene as a mechanism of 46,XX spontaneous premature ovarian failure. The human KIT ligand gene, known also as human stem cell factor, is the ligand of the c-kit transmembrane tyrosine kinase receptor (KIT). This ligand-receptor interaction is known to play important roles in mouse germ cell migration and proliferation. DESIGN: Cross-sectional study. SETTING: Clinical research center. PATIENT(S): Forty women with 46,XX spontaneous premature ovarian failure. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Single-stranded conformational polymorphism analysis and DNA sequencing. RESULT(S): We found one nucleotide change of the KITLG coding region (811G-->T) that led to an alteration of the amino acid composition of the KITLG protein in one Caucasian patient (Asp210Tyr). However, we found the same alteration in two normal control Caucasian samples. Three nucleotide substitutions were found in the noncoding exon of KITLG (exon 10). We also identified two intronic polymorphisms. Thus, we did not identify a single significant mutation in the coding region of the KITLG gene in any of 40 patients (upper 95% confidence limit is 7.2%). CONCLUSION(S): Mutations in the coding regions of the KITLG gene appear not to be a common cause of 46,XX spontaneous premature ovarian failure in North American women.

Adolescent↗
PubMed2005

Bioinformatic analysis of neuropeptide and receptor expression profiles during midgut metamorphosis in Drosophila melanogaster.

Neuropeptides are important messenger molecules in invertebrates, serving as neuromodulators in the nervous system and as regulatory hormones released into the circulation. Understanding the function of neuropeptides will require the integration of genetic, biochemical, physiological and behavioral information. The advent of DNA microarrays and bioinformatic databases provides a wealth of data describing the expression profiles of thousands of genes during biological processes. One such array catalogs the developmental patterns of gene expression during the metamorphic transformation of the Drosophila midgut. We have mined the data from this experiment to explore changes of expression in genes coding for known neuropeptides, peptide hormones, and their receptors during the metamorphosis of the midgut. We found small but significant changes in the expression of the peptides diuretic hormone, FGLa-type allatostatins, myoinhibiting peptide, ecdysis-triggering hormone, drosokinin and the burs subunit of bursicon, as well as the receptors DAR-2, NPFR1, ALCR-2, Lkr and DH-R. Just as advances have been made in understanding the molecular basis of invertebrate neuropeptide action by analysis of genome projects, data mining of gene expression databases can help to integrate molecular, biochemical and physiological knowledge of biological processes.

Animals↗
PubMed1995

A peripherin/retinal degeneration slow mutation (Pro-210-Arg) associated with macular and peripheral retinal degeneration.

BACKGROUND: Mutations in the peripherin/retinal degeneration slow (RDS) gene have been identified in patients with retinitis pigmentosa and pattern macular dystrophy. The authors initially examined a large family affected with both peripheral and macular degeneration, inherited as an autosomal dominant trait. Screening for peripherin/RDS mutations identified a previously unreported nucleotide alteration in all of the affected individuals. Two additional families later were found to have this same mutation. METHODS: DNA samples from the members of three unrelated families were screened for peripherin/RDS mutations by denaturing gradient gel electrophoresis of the polymerase chain reaction-amplified peripherin/RDS coding sequences. The sequence change that was detected was further characterized by DNA sequencing. Family members were examined and evaluated with psychophysical and electrophysiologic methods. RESULTS: A proline to arginine mutation in codon 210 of peripherin/RDS was found in all clinically affected individuals. Macular changes included extensive geographic atrophy, pigment epithelial changes, and/or drusen. The proline to arginine mutation was not found among 100 healthy individuals, making it unlikely to be a nondisease-causing polymorphism. CONCLUSIONS: The authors identified a novel peripherin/RDS gene mutation associated with autosomal dominant retinal degeneration in patients from three different families. The largest family showed a broad variability in the expressivity of the mutation. The overlap of clinical features with those of age-related maculopathy highlights the need to consider photoreceptor-specific genes as potential factors in the etiology of the latter condition.

Adolescent↗
PubMed2002

Cytogenetic aberrations and heterogeneity of mutations in repeat-containing genes in a colon carcinoma from a patient with hereditary nonpolyposis colorectal cancer.

The majority of tumors from patients affected by hereditary nonpolyposis colorectal cancer (HNPCC) exhibit a mutator phenotype characterized by widespread microsatellite instability (MSI) and somatic mutations in repeated sequences in several cancer-associated genes. An inverse relationship between MSI and chromosomal instability (CIN) has been demonstrated and HNPCC-associated tumors are generally characterized by diploid or near-diploid cells with few or no chromosomal rearrangements. We have studied MSI, somatic mutations in repeat-containing genes, DNA-ploidy, and cytogenetic aberrations in a colon carcinoma from a patient with a germline MLH1 mutation. Mutations in coding repeats were assessed in 10 macroscopically separate areas of the primary tumor and in two lymph nodes. Some of the genes studied (E2F4, MSH3, MSH6, TCF4, and TGFBRII) showed a consistent lack of mutations, whereas others (BAX, Caspase-5 and IGFIIR) displayed alterations in some tumor regions but not in others. The tumor had DNA-index 1.1-1.2 and a stable, aberrant karyotype with extra copies of chromosomes 7 and 12 and the structural aberrations i(1q), der(20)t(8;20), and der(22)t(1;22). The finding of CIN, MSI, and somatic mutations in coding repeats in this tumor suggests that these phenomena may act together in HNPCC tumorigenesis. Furthermore, the observed intratumoral heterogeneity of mutations in coding repeats implies these changes occur late in tumorigenesis and, thus, probably play a role in tumor progression rather than initiation.

Adaptor Proteins, Signal Transducing↗
PubMed2002

Polymorphisms in the DNA repair gene XRCC1 and susceptibility to alcoholic liver cirrhosis in older Southeastern Brazilians.

The population of Southeastern Brazil has a very high mortality rate from liver cirrhosis, a disease that is considered an irreversible pre-malignant condition. This is largely due to the high prevalence of alcohol abuse in the region. Chronic alcohol consumption is associated with the production of free radical intermediates that can cause several DNA lesions. Reduced repair of these DNA lesions would, therefore, constitute a significant risk factor for liver cirrhosis and subsequent cancer. Recently, a number of polymorphisms in several DNA repair genes have been discovered, and it is possible that these polymorphisms may affect DNA repair capacity and thus modulate susceptibility to the disease. In this study, we tested the hypothesis that polymorphisms in the DNA repair gene XRCC1 are associated with increased risk of liver cirrhosis in Southeastern Brazilians. We conducted a pilot case-control study of 97 liver cirrhosis cases and 96 controls (matched for age, sex, and ethnicity) to investigate the role of two allelic variants coding for amino acid changes in the XRCC1 gene (the Arg194Trp and the Arg399Gln polymorphisms). Overall, we observed a 1.8-fold increase in the relative risk of liver cirrhosis associated with the 399Gln allele (either the heterozygous Arg/Gln or the homozygous Gln/Gln genotypes). The adjusted odds ratio (OR) was 1.82 (95% confidence limit (CL) 1.10-3.30). The relative risk appears to be highest among the Mestiso ethnic group (OR 2.60, 95% CL 0.92-7.34). There was a significant association between the 399Gln polymorphism and the risk of liver cirrhosis in older individuals over the age of 45 years (OR 2.70 (95% CL 1.14-6.48) compared to an OR of 1.24 (95% CL 0.55-2.78) for those under 45 years of age. No association was observed between the XRCC1 194Trp polymorphism and risk of liver cirrhosis. These preliminary results suggest that the XRCC1 399Gln polymorphism may be a significant risk modifier for alcoholic liver cirrhosis and justifies additional studies in that direction.

Adult↗
PubMed2001

Plantar stimulation can affect subjective straight-ahead in neglect patients.

The rightward orientation bias of neglect patients has been shown to be decreased by postural changes, suggesting that afferences coding the posture relative to gravity might influence the body-centred spatial reference frame. In order to test this hypothesis, we evaluated the effects of plantar stimulations on the subjective straight-ahead (SSA) of two neglect patients presenting with a strong rightward shift, as well as two non-neglect patients and three normal subjects. Vibratory or electrical stimulations were applied to the left or right plantar sole. Data showed that these manipulations influenced the SSA position in neglect patients only. The observed improvement could be explained by a direction-specific effect of vibration, in addition to a non-specific activation induced by both stimulations.

Adult↗