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PubMed2006

Efficient estimation of log-normal means with application to pharmacokinetic data.

In this paper, the problem of interest is efficient estimation of log-normal means. Several existing estimators are reviewed first, including the sample mean, the maximum likelihood estimator, the uniformly minimum variance unbiased estimator and a conditional minimal mean squared error estimator. A new estimator is then proposed, and we show that it improves over the existing estimators in terms of squared error risk. The improvement is more significant with small sample sizes and large coefficient of variations, which is common in clinical pharmacokinetic (PK) studies. In addition, the new estimator is very easy to implement, and provides us with a simple alternative to summarize PK data, which are usually modelled by log-normal distributions. We also propose a parametric bootstrap confidence interval for log-normal means around the new estimator and illustrate its nice coverage property with a simulation study. Our estimator is compared with the existing ones via theoretical calculations and applications to real PK studies.

Area Under Curve↗
PubMed1999

The structure of the exo-beta-(1,3)-glucanase from Candida albicans in native and bound forms: relationship between a pocket and groove in family 5 glycosyl hydrolases.

A group of fungal exo-beta-(1,3)-glucanases, including that from the human pathogen Candida albicans (Exg), belong to glycosyl hydrolase family 5 that also includes many bacterial cellulases (endo-beta-1, 4-glucanases). Family members, despite wide sequence variations, share a common mechanism and are characterised by possessing eight invariant residues making up the active site. These include two glutamate residues acting as nucleophile and acid/base, respectively. Exg is an abundant secreted enzyme possessing both hydrolase and transferase activity consistent with a role in cell wall glucan metabolism and possibly morphogenesis. The structures of Exg in both free and inhibited forms have been determined to 1.9 A resolution. A distorted (beta/alpha)8 barrel structure accommodates an active site which is located within a deep pocket, formed when extended loop regions close off a cellulase-like groove. Structural analysis of a covalently bound mechanism-based inhibitor (2-fluoroglucosylpyranoside) and of a transition-state analogue (castanospermine) has identified the binding interactions at the -1 glucose binding site. In particular the carboxylate of Glu27 serves a dominant hydrogen-bonding role. Access by a 1,3-glucan chain to the pocket in Exg can be understood in terms of a change in conformation of the terminal glucose residue from chair to twisted boat. The geometry of the pocket is not, however, well suited for cleavage of 1,4-glycosidic linkages. A second glucose site was identified at the entrance to the pocket, sandwiched between two antiparallel phenylalanine side-chains. This aromatic entrance-way must not only direct substrate into the pocket but also may act as a clamp for an acceptor molecule participating in the transfer reaction.

Amino Acid Sequence↗
PubMed1993

Evidence of natural recombination within the S1 gene of infectious bronchitis virus.

During an outbreak of severe respiratory disease, a field strain of infectious bronchitis virus (IBV), PP14, was isolated from a bird in a Texas flock that had been previously vaccinated with an attenuated Mass serotype virus. After cloning and sequencing the S1 gene from several IBV strains, it was found that the 5' end of the cDNA was 96% identical to the published sequences of Mass41 and 77% identical with Ark99. The following 402 bases which included the hypervariable regions (HVR) of the S1 gene were 94% homologous with Ark99 and only 69% with Mass41. In addition, the HVR in the 3' noncoding region of the genome, which is totally absent in Mass41, was 99% homologous with the Ark99 strain. This abrupt shift in identity of PP14 in the S1 strongly indicated that a recombination event had occurred about 98 bases from the beginning of the S1 gene between an Ark-like and a Mass-like virus. Downstream, 33 bases from the PP14 recombination junction, a second putative "cross-over" site was identified in the S1 of the SE17 strain where the 5'131 bases of the S1 gene of the Ark99 and SE17 were found to be 95% identical and the following 368 base sequence was only 78% homologous. In addition, a second shift in homology in the S1 of SE17 was identified between nucleotide 1112 and 1460 which shared 95% identity with Mass41. The putative recombination junctions which were downstream of the signal sequence and upstream of the S1 HVR may represent a "hot spot," but not an exclusive region, for exchanging genetic material between IBV strains. Genetic shifts are apparently not only common mechanisms for variation in nature, but vaccine strains may actually play a critical role in these events in the evolution of virulent strains of IBV.

Animals↗
PubMed2006

The norepinephrine transporter in physiology and disease.

The norepinephrine transporter (NET) terminates noradrenergic signalling by rapid re-uptake of neuronally released norepinephrine (NE) into presynaptic terminals. NET exerts a fine regulated control over NE-mediated behavioural and physiological effects including mood, depression, feeding behaviour, cognition, regulation of blood pressure and heart rate. NET is a target of several drugs which are therapeutically used in the treatment or diagnosis of disorders among which depression, attention-deficit hyperactivity disorder and feeding disturbances are the most common. Individual genetic variations in the gene encoding the human NET (hNET), located at chromosome 16q12.2, may contribute to the pathogenesis of those diseases. An increasing number of studies concerning the identification of single nucleotide polymorphisms in the hNET gene and their potential association with disease as well as the functional investigation of naturally occurring or induced amino acid variations in hNET have contributed to a better understanding of NET function, regulation and genetic contribution to disorders. This review will reflect the current knowledge in the field of NET from its initial discovery until now.

Alternative Splicing↗
PubMed1993

Frequency of restriction site polymorphisms in the region surrounding VNTR loci.

Variations in allele size in loci containing tandem repeats result from changes in the number of these repeats. However, digestion of the same DNA samples with two restriction enzymes (i.e. PstI and HaeIII), that have recognition sites predominantly in the DNA region flanking the VNTR, has identified the presence of numerous site polymorphisms. Three loci (D2S44, D4S163, D17S79) were examined for the presence of restriction site polymorphisms in both North American Black and Caucasian populations. At all loci there were alleles with site polymorphisms. This type of variations were more common in the North American Black than in the Caucasian populations.

Alleles↗
PubMed1995

Class IV charge models: a new semiempirical approach in quantum chemistry.

We propose a new criterion for defining partial charges on atoms in molecules, namely that physical observables calculated from those partial charges should be as accurate as possible. We also propose a method to obtain such charges based on a mapping from approximate electronic wave functions. The method is illustrated by parameterizing two new charge models called AM1-CM1A and PM3-CM1P, based on experimental dipole moments and, respectively, on AM1 and PM3 semiempirical electronic wave functions. These charge models yield rms errors of 0.30 and 0.26 D, respectively, in the dipole moments of a set of 195 neutral molecules consisting of 103 molecules containing H, C, N and O, covering variations of multiple common organic functional groups, 68 fluorides, chlorides, bromides and iodides, 15 compounds containing H, C, Si or S, and 9 compounds containing C-S-O or C-N-O linkages. In addition, partial charges computed with this method agree extremely well with high-level ab initio calculations for both neutral compounds and ions. The CM1 charge models provide a more accurate point charge representation of the dipole moment than provided by most previously available partial charges, and they are far less expensive to compute.

Alcohols↗
PubMed1985

[Color change in dental tissue as a sign of thermal damage].

The appearance of hard human tissue after thermal damage permits certain conclusions to be drawn with regard to fire parameters. In addition to morphological destruction, the change in color of dental tissues like enamel, dentine, and cement is also important. We studied teeth extracted from 330 human males and females under well-defined time and temperature conditions. Using the DIN and RAL color indexes, the color phenomenon was evaluated on the basis of the amount of glowing obtained when the teeth were heated. It is easiest to determine the color change in cement, as no calculus or hindering plaques are on the root surface. In addition to this, destruction of the tooth root takes place only during extreme combustion conditions. Determining the dentine color is more difficult and is possible only after the enamel splits. Also, the different dentine thicknesses hinders the observation of color. When the enamel was tested, it was found that the differences in color caused by high temperatures are unimportant. Moreover, the enamel burst into small particles. The effect we observed regarding the anthracite lustre using low temperatures was typical, and the best results were obtained in dental roots with eight color scales. All three dental hard tissues have in common that the variations in color appear regularly and successively according to ascending temperature or duration of time: natural dental color, black, brown, blue, grey, white, and pink. In these processes, the temperature and combustion time are inversely proportional to the velocity of color change. The literature is discussed that deals with temperature- and time-dependent color phenomena of dental hard tissues destroyed as a result of thermal damage.

Burns↗
PubMed1992

Quantitation and structures of oligosaccharide chains in human trachea mucin glycoproteins.

Human respiratory mucin glycoproteins from patients with cystic fibrosis were purified and oligosaccharide chains were released by treatment with alkaline borohydride. A neutral oligosaccharide alditol fraction was isolated from mucin obtained from a patient with A blood group determinant by chromatography on DEAE-cellulose and individual oligosaccharide chains were then isolated by gel filtration on BioGel P-6 columns and high performance liquid chromatography with gradient and isocratic solvent systems. The structures of the purified oligosaccharides were determined by methylation analysis, sequential glycosidase digestion and 'H-NMR spectroscopy. The amount of each chain was determined by compositional analysis. A wide array of discrete branched oligosaccharide structures that contain from 3 to 22 sugar residues were found. Many of the oligosaccharides are related and appear to be precursors of larger chains. The predominant branched oligosaccharides which accumulate contain terminal blood group H (Fuc alpha 2Ga1 beta 4) or blood group A (Fuc alpha 2(Ga1NAc alpha 3) (Ga1 beta 4) determinants which stop further branching and chain elongation. The elongation of oligosaccharide chains in respiratory mucins occurs on the beta 3-linked G1cNAc at branch points, whereas the beta 6-linked G1cNAc residue ultimately forms short side chains with a Fuc alpha 2(Ga1NAc alpha 3) Ga1 beta 4 G1cNAc beta 6 structure in individuals with A blood group determinant. The results obtained in the current studies further suggest that even higher molecular weight oligosaccharide chains with analogous branched structures are present in some human respiratory mucin glycoproteins. Increasing numbers of the repeating sequence shown in the oligosaccharide below is present in the higher molecular weight chains. [formula: see text] This data in conjunction with our earlier observations on the extensive branching of these oligosaccharide chains helps to define and explain the enormous range of oligosaccharide structures found in human and swine respiratory mucin glycoproteins. Comparison of the relative concentrations of each oligosaccharide chain suggest that these oligosaccharides represent variations of a common branched core structure which may be terminated by the addition of alpha 2-linked fucose to the beta 3/4 linked galactose residue at each branch point. These chains accumulate and are found in the highest concentrations in these respiratory mucins.

Amino Acids↗
PubMed1986

Radiological analysis of hemifacial spasm with special reference to angiographic manifestations.

Fifty-one patients with hemifacial spasm secondary to facial nerve compression by normal appearing, elongated, tortuous and/or dilated arteries, were treated by microsurgical neurovascular decompression. Post-operatively, 91% of 44 of these patients with one to six year postoperative follow-ups were satisfactory. The angiographic findings showed significant increase in the number of common trunk anomalies. Variations of the anterior and posterior inferior cerebellar and vertebral arteries are discussed in relation to nerve compression.

Adult↗
PubMed1977

[Distribution of aflatoxin M1 in whey and curd during cheese processing (author's transl)].

In model experiments on the distribution of aflatoxin M1 in whey and curd, the influence of the different processing steps was investigated. Taking the same weight ratio between whey and curd, the following results were obtained: a) The aflatoxin M1-distribution in whey and curd was not changed with increasing amounts of rennet, thus decreasing the renneting time at constant renneting temperatures. b) With increasing renneting temperatures, however, the toxin's percentage in the curd decreased at constant amounts of rennet, whereas the whey's content remained stable. For the commonly used temperature variations between 28 and 35 degrees C, the toxin content of the cheese varied in the range of about 12%. c) Processing of curd by acidification with different organic acids at constant temperatures did not show any change in the aflatoxin M1 distribution as compared to rennet coagulation. d) Curd processing by means of starter cultures led to a decrease in the aflatoxin M1 in curd only at higher temperatures; the toxin's percentage in whey remained practically the same. e) Washing of the curd with the 2 1/2 volumes of water decreased the aflatoxin M1 content of cheese by 22%.

Aflatoxins↗
PubMed1981

Mouse liver cell culture. I. Hepatocyte isolation.

A method for isolation of mouse liver cells by a two-step perfusion with calcium and magnesium-free Hanks' salt solution followed by a medium containing collagenase is described. Several variations of the commonly used procedure for rat liver cell isolation were quantitatively compared with respect to cell yield and viability. The optimal isolation technique involved perfusion through the hepatic portal vein and routinely produced an average of 2.3 x 10(6) viable liver cells/g body weight. Optimal perfusate collagenase concentration was found to be 100 U of enzyme activity per milliliter of perfusate. Light and electron microscopic evaluation of liver morphology after several steps of the isolation showed distinct morphologic changes in hepatocytes and other liver cells during perfusion. After perfusion with Hanks' calcium- and magnesium-free solution, many hepatocytes exhibited early reversible cell injury. These changes included vesiculation and slight swelling of the endoplasmic reticulum as well as mitochondrial matrix condensation. Subsequent to perfusion with collagenase, the majority of hepatocytes appeared connected to one another only by tight junctional complexes at the bile canaliculi. Multiple evaginations were seen on the outer membrane resembling microville and probably represented the remains of cell-to-cell interdigitations between hepatocytes and sinusoidal lining cells from the space of Disse. The cytoplasmic injury seen after Hanks' perfusion was reversed after collagenase perfusion. After mechanical dispersion, isolated mouse hepatocytes were spherical in shape and existed as individual cells; many (80 to 85%) were binucleated under hase contrast light microscopy. By electron microscopy, cells appeared morphologically similar in cytoplasmic constitution to that seen in intact nonaltered liver cells.

Animals↗
PubMed2006

Association of the met66 allele of brain-derived neurotrophic factor (BDNF) with smoking.

RATIONALE: It has been suggested that a susceptibility locus near the gene encoding the brain-derived neurotrophic factor (BDNF) contributes to individual differences in human addiction vulnerability. BDNF modulates several behaviors that are associated with addictive drugs, and upregulation of BDNF was found to be associated with several drugs of abuse such as amphetamine, cocaine, and nicotine. In this study, we addressed the question if a common BDNF missense variation (Val66Met) influences the risk for smoking behavior in otherwise healthy human volunteers. MATERIALS AND METHODS: In total, 320 healthy unrelated volunteers (155 male, 165 female, mean age: 38.4 +/- 14.1 years) consisting of 43.3% never smokers, 20.9% former smokers, and 35.6% current smokers were investigated. RESULTS: The frequency of both Met/Met genotype and Met allele was significantly increased in current and in former smokers when compared to never smokers (chi (2) = 10.856, df = 2, p = 0.004 and chi (2) = 4.350, df = 1, p = 0.045, respectively). CONCLUSIONS: Our results suggest that humans who carry the Met allele of the BDNF missense polymorphism might be more vulnerable to initiate and also maintain smoking.

Adult↗
PubMed2004

Peculiarities of the sural nerve complex morphologic types in human fetuses.

The sural nerve is the most frequently used sensory nerve in nerve transplantation. It can be transplanted alone or together with the other elements of the neurovascular stalk within the superficial sural flap. The aim of this study was to define the morphologic types of the sural nerve complex, as well as to describe their specific characteristics. Microdissection was performed on 100 human fetuses (200 calves) after 10% formalin fixation. Five morphologic types of sural nerve complex with different incidence were defined. Two morphologic types dominated: type I (58.5%) in which the sural nerve was formed by merging of a fibular communicating branch and the medial sural cutaneous nerve, and type III (26%) in which the medial sural cutaneous nerve took over the function of the sural nerve. Other morphologic variations were less common.

Female↗
PubMed2003

The glutamate/neutral amino acid transporter family SLC1: molecular, physiological and pharmacological aspects.

The solute carrier family 1 (SLC1) includes five high-affinity glutamate transporters, EAAC1, GLT-1, GLAST, EAAT4 and EAAT5 (SLC1A1, SLC1A2, SLC1A3, SLC1A6, and SLC1A7, respectively) as well as the two neutral amino acid transporters, ASCT1 and ASCT2 (SLC1A4 and ALC1A5, respectively). Although each of these transporters have similar predicted structures, they exhibit distinct functional properties which are variations of a common transport mechanism. The high-affinity glutamate transporters mediate transport of l-Glu, l-Asp and d-Asp, accompanied by the cotransport of 3 Na(+) and 1 H(+), and the countertransport of 1 K(+), whereas ASC transporters mediate Na(+)-dependent exchange of small neutral amino acids such as Ala, Ser, Cys and Thr. The unique coupling of the glutamate transporters allows uphill transport of glutamate into cells against a concentration gradient. This feature plays a crucial role in protecting neurons against glutamate excitotoxicity in the central nervous system. During pathological conditions, such as brain ischemia (e.g. after a stroke), however, glutamate exit can occur due to "reversed glutamate transport", which is caused by a reversal of the electrochemical gradients of the coupling ions. Selective inhibition of the neuronal glutamate transporter EAAC1 (SLC1A1) may be of therapeutic interest to block glutamate release from neurons during ischemia. On the other hand, upregulation of the glial glutamate transporter GLT1 (SLC1A2) may help protect motor neurons in patients with amyotrophic lateral sclerosis (ALS), since loss of function of GLT1 has been associated with the pathogenesis of certain forms of ALS.

Amino Acid Transport System X-AG↗
PubMed2002

Intronic mutations outside of Alu-repeat-rich domains of the LDL receptor gene are a cause of familial hypercholesterolemia.

Familial hypercholesterolemia (FH), a frequent monogenic condition complicated by premature cardiovascular disease, is characterized by high allelic heterogeneity at the low-density lipoprotein receptor ( LDLR) locus. Despite more than a decade of genetic testing, knowledge about intronic disease-causing mutations has remained limited because of lack of available genomic sequences. Based on the finding from bioinformatic analysis that Alu repeats represent 85% of LDLR intronic sequences outside exon-intron junctions, we designed a strategy to improve the exploration of genomic regions in the vicinity of exons in 110 FH subjects from an admixed population. In the first group of 42 patients of negative mutation carriers, as previously established by former screening strategies (denaturing gradient gel electrophoresis, DNA sequencing with former primers overlapping splice-sites, Southern Blotting), about half ( n=22) were found to be carriers of at least one heterozygous mutation. Among a second group of 68 newly recruited patients, 27% of mutation carriers ( n=37) had a splicing regulatory mutation. Overall, out of the 54 mutations identified, 13 were intronic, and 18 were novel, out of which nearly half were intronic. Two novel intronic mutations (IVS8-10G-->A within the polypyrimidine tract and IVS7+10G-->A downstream of donor site) might create potential aberrant splice sites according to neural-network computed estimation, contrary to 31 common single nucleotide variations also identified at exon-intron junctions. This new strategy of detecting the most likely disease-causing LDLR mutations outside of Alu-rich genomic regions reveals that intronic mutations may have a greater impact than previously reported on the molecular basis of FH.

Base Sequence↗
PubMed2005

Expression of constitutive and inducible chemical defenses in native and invasive populations of Alliaria petiolata.

The Evolution of Increased Competitive Ability (EICA) hypothesis posits that invasive plants in introduced habitats with reduced herbivore pressure will evolve reduced levels of costly resistance traits. In light of this hypothesis, we examined the constitutive and inducible expression of five chemical defense traits in Alliaria petiolata from four invasive North American and seven native European populations. When grown under common conditions, significant variation among populations within continents was found for trypsin inhibitors and peroxidase activity, and glucosinolates and trypsin inhibitors were significantly jasmonate-inducible across populations. Across populations, constitutive levels of glucosinolates and trypsin inhibitors were negatively correlated with their degree of induction, with three North American populations tending to have lower constitutive levels and higher inducibility of glucosinolates than the seven European populations. Alliarinoside and isovitexin 6"-O-beta-glucopyranoside levels were both higher in North American plants than in European plants, but levels of these compounds were generally increased by jasmonate in European plants and decreased by the same treatment in North American plants. Aside from the tendency for invasive populations to have reduced constitutive glucosinolate levels coupled with increased inducibility, little support for the predictions of EICA was evident in the chemical defenses that we studied.

Adaptation, Physiological↗
PubMed1992

Incorporation of dietary oleate, linoleate, alpha-linolenate and eicosapentaenoate into the plasma lipid fractions of four strains of rat.

Four strains of rat (Dark Agouti, DA; Ginger Hooded, GH; Portion, P; Hooded Wistar, HW) were fed elemental diets containing different sources of fat at the 10% (w/w) level. The dietary fats used included the following oils; olive (rich in oleate), sunflower (rich in linoleate), linseed (rich in alpha-linolenate) and fish (rich in eicosapentaenoate and docosahexaenoate). Differences between strains in response to individual diets were modest compared with the much greater differences achieved by the dietary treatments. In general, the changes in polyunsaturated fatty acid (PUFA) levels in the plasma lipids of all rat strains followed the major PUFA in the diet. There were, however, strong interactions between dietary n-6 and n-3 PUFA which affected not only the level of particular PUFA in lipid fractions but also the lipid fraction in which a particular PUFA appeared. Our findings indicate that a response to dietary fats in the plasma lipids of one strain of rat can be expected to occur with relatively minor variations in other commonly used rat strains.

Animals↗
PubMed1991

Drug metabolizing enzyme activities in rat liver epithelial cell lines, hepatocytes and bile duct cells.

P450-dependent mono-oxygenase and conjugating enzyme activities were studied in rat liver epithelial cells (RLEs) and compared to those in hepatocytes and bile duct cells. Various RLE cell lines were investigated since (a) they are suspected to be derived from cells in the lineage from putative pluripotent stem cells to either hepatocytes or bile duct cells, and (b) they may represent targets of chemical carcinogens. Despite considerable variation between lines, common features were recognized. P450-dependent monooxygenase activities (7-ethoxyresorufin O-deethylase and 7-ethoxycoumarin O-deethylase) were undetectable in all RLEs and bile duct cells, and were uninducible by benz(a)anthracene. In contrast, glucuronosyltransferase (GT), sulfotransferase and GSH transferase activities were clearly detectable. Conjugating enzyme activities increased until confluency of the cell cultures was reached. Under the latter conditions, GT activities towards 4-methylumbelliferone or benzo(a)pyrene-3,6-quinol (substrates of a 3-methylcholanthrene-inducible phenol GT) were similar to those found in hepatocytes or bile duct cells. Using a selective cDNA probe, phenol GT mRNA was clearly detectable in RLE1. In contrast, GT activity towards 4-hydroxybiphenyl was much lower than in hepatocytes or bile duct cells (0.04- and 0.03-fold). Sulfotransferase and GSH transferase activities were also roughly comparable to those found in hepatocytes and in bile duct cells. The results suggest that RLEs and bile duct cells exhibit both high conjugating enzyme activities and a lack of P450-dependent mono-oxygenase activities, a pattern resembling the 'toxin-resistance phenotype' found in putative preneoplastic hepatocyte foci and nodules.

Aging↗