An improved procedure of mapping a quantitative trait locus via the EM algorithm using posterior probabilities

Mapping a locus controlling a quantitative genetic trait (e.g. blood pressure) to a specific genomic region is of considerable contemporary interest. Data on the quantitative trait under consideration and several codominant genetic markers with known genomic locations are collected from members of families and statistically analysed to estimate the recombination fraction, θ, between the putative quantitative trait locus and a genetic marker. One of the major complications in estimating θ for a quantitative trait in humans is the lack of haplotype information on members of families. We have devised a computationally simple two-stage method of estimation of θ in the absence of haplotypic information using the expectation-maximization (EM) algorithm. In the first stage, parameters of the quantitative trait locus (QTL) are estimated on the basis of data of a sample of unrelated individuals and a Bayes’s rule is used to classify each parent into a QTL genotypic class. In the second stage, we have proposed an EM algorithm for obtaining the maximum-likelihood estimate of θ based on data of informative families (which are identified upon inferring parental QTL genotypes performed in the first stage). The purpose of this paper is to investigate whether, instead of using genotypically ‘classified’ data of parents, the use of posterior probabilities of QT genotypes of parents at the second stage yields better estimators. We show, using simulated data, that the proposed procedure using posterior probabilities is statistically more efficient than our earlier classification procedure, although it is computationally heavier.     

An Optimization Algorithm for a Distributed-Loop Model of an Avian Urine Concentrating Mechanism

To better understand how the avian kidney’s morphological and transepithelial transport properties affect the urine concentrating mechanism (UCM), an inverse problem was solved for a mathematical model of the quail UCM. In this model, a continuous, monotonically decreasing population distribution of tubes, as a function of medullary length, was used to represent the loops of Henle, which reach to varying levels along the avian medullary cones. A measure of concentrating mechanism efficiency – the ratio of the free-water absorption rate (FWA) to the total NaCl active transport rate (TAT) – was optimized by varying a set of parameters within bounds suggested by physiological experiments. Those parameters include transepithelial transport properties of renal tubules, length of the prebend enlargement of the descending limb (DL), DL and collecting duct (CD) inflows, plasma Na⁺ concentration, length of the cortical thick ascending limbs, central core solute diffusivity, and population distribution of loops of Henle and of CDs along the medullary cone. By selecting parameter values that increase urine flow rate (while maintaining a sufficiently high urine-to-plasma osmolality ratio (U/P)) and that reduce TAT, the optimization algorithm identified a set of parameter values that increased efficiency by ∼60% above base-case efficiency. Thus, higher efficiency can be achieved by increasing urine flow rather than increasing U/P. The algorithm also identified a set of parameters that reduced efficiency by ∼70% via the production of a urine having near-plasma osmolality at near-base-case TAT.In separate studies, maximum efficiency was evaluated as selected parameters were varied over large ranges. Shorter cones were found to be more efficient than longer ones, and an optimal loop of Henle distribution was found that is consistent with experimental findings.     

Sequence comparison and mutational analysis of elements that may be involved in the regulation of DNA synthesis in HIV-1

The large number of sequenced clones of HIV-1 and related viruses made it possible to indicate conserved elements with potential regulatory or structural functions. Such analysis was combined with directed mutagenesis in order to investigate the importance of elements that may influence the initiation of plus-strand DNA synthesis. The main site for plus-strand initiation is a polypurine tract near the 3′ end of the viral RNA (the 3′ PPT). An exact copy of this PPT is located in the middle of the genome (the internal PPT). Upstream from the internal PPT there is an inverted repeat. Mutants designed to upset the internal PPT (i.e., purine to pyrimidine changes), as well as mutants designed to abolish the potential stem-loop formation (changes around the internal PPT or in the upstream inverted repeat) both resulted in viruses with a reduced ability to replicate. Upsetting the stem-loop formation was, however, less harmful than changing the polypurine nature of the PPT. Changing a conserved T on the 3′ side of the PPT to a C did not affect the phenotype. Presented at the NATO Advanced Research Workshop onGenome Organization and Evolution, Spetsai, Greece, 16–22 September 1992     

<Emphasis Type="Italic">Rpv10</Emphasis>: a new locus from the Asian <Emphasis Type="Italic">Vitis</Emphasis> gene pool for pyramiding downy mildew resistance loci in grapevine

A population derived from a cross between grapevine breeding strain Gf.Ga-52-42 and cultivar ‘Solaris’ consisting of 265 F1-individuals was genetically mapped using SSR markers and screened for downy mildew resistance. Quantitative trait locus (QTL) analysis revealed two strong QTLs on linkage groups (LGs) 18 and 09. The locus on LG 18 was found to be identical with the previously described locus Rpv3 and is transmitted by Gf.Ga-52-42. ‘Solaris’ transmitted the resistance-related locus on LG 09 explaining up to 50% of the phenotypic variation in the population. This downy mildew resistance locus is named Rpv10 for resistance to Plasmopara viticola. Rpv10 was initially introgressed from Vitis amurensis, a wild species of the Asian Vitis gene pool. The one-LOD supported confidence interval of the QTL spans a section of 2.1 centi Morgan (cM) corresponding to 314 kb in the reference genome PN40024 (12x). Eight resistance gene analogues (RGAs) of the NBS–LRR type and additional resistance-linked genes are located in this region of PN40024. The F1 sub-population which contains the Rpv3 as well as the Rpv10 locus showed a significantly higher degree of resistance, indicating additive effects by pyramiding of resistance loci. Possibilities for using the resistance locus Rpv10 in a grapevine breeding programme are discussed. Furthermore, the marker data revealed ‘Severnyi’ × ‘Muscat Ottonel’ as the true parentage for the male parent of ‘Solaris’.     

On the non-existence of an optimal migration rate

 We show that an optimal migration rate may not exist in a population distributed over an infinite number of individual living sites if empty sites occur. This is the case when the mean number of offspring per individual μ is finite. We make the assumption of uniform migration to other sites whose rate is determined by the parent’s genotype or the offspring’s genotype at a single locus in a diploid hermaphrodite population undergoing random mating. In both cases, for μ small enough, any population at fixation would go to extinction. Moreover, in the latter case, for intermediate values of μ, the only fixation state that could resist the invasion of any mutant would lead the population to extinction. These are the two conditions for the non-existence of an optimal migration rate. They become less stringent as the cost for migration expressed by a coefficient of selection 1−β becomes larger, that is, closer to 1. The results are obtained assuming that the allele at fixation is either nondominant or dominant. Although the optimal migration rate is the same in both cases when it exists, the optimality properties may differ. Received 14 December 1995; received in revised form 5 April 1996     

Mapping loci associated with flour colour in wheat (Triticum aestivum L.)

 An RFLP map constructed using 150 single seed descent (SSD) lines from a cross between two hexaploid wheat varieties (‘Schomburgk’בYarralinka’) was used to identify loci controlling flour colour. Flour colour data were obtained from field trials conducted over two seasons at different sites. The estimated heritability of this trait was calculated as 0.67. Two regions identified in the preliminary analysis on chromosomes 3A and 7A, accounted for 13% and 60% of the genetic variation respectively. A detailed analysis of the major locus on 7A was conducted through fine mapping of AFLP markers identified using bulked segregant analysis (BSA). Seven additional markers were identified by the BSA and mapped to the region of the 7A locus. The applicability of these markers to identify wheat lines with enhanced flour colour is discussed. Received: 30 September 1997 / Accepted: 4 February 1998     

Inhibition of CYP3A4 and CYP2C9 by podophyllotoxin: Implication for clinical drug–drug interactions

Podophyllotoxin (PPT) and its derivatives exert significant anti-cancer activities, and one derivative etoposide is often utilized to treat various cancers in the clinic. The aim of the present study is to investigate the inhibitory effects of PPT on major cytochrome P450 (CYP) isoforms in human livers. Inhibition of CYP3A4, CYP2C9, CYP2C8, CYP2D6, CYP2E1 and CYP2A6 by PPT was investigated in the human liver microsomal system. Time-dependent inhibition of CYP3A4 by PPT was also evaluated. The results showed that PPT strongly exhibited inhibitory effects on CYP3A4 and CYP2C9 in a concentration-dependent manner. Half inhibition concentration (IC₅₀) was 1.1 ± 0.3 and 4.6 ± 0.3 μM for CYP3A4 and CYP2C9, respectively. Inhibition kinetic analysis showed that PPT exhibited competitive inhibition towards CYP3A4 and CYP2C9 with K_i of 1.6 and 2.0 μM, respectively. Additionally, PPT exerted time-dependent inhibition towards CYP3A4 and the kinetic parameters were 4.4 ± 2.1 μM and 0.06 ± 0.01 min^–1 for K_I and k_inact, respectively. Our experimental data indicate that potential drug–drug interaction (DDI) might exist when PPT is co-administered with the substrates which mainly undergo CYP3A4- or CYP2C9-mediated metabolism.     

Method for mapping a partial lethal-factor locus on a molecular-marker linkage map of a backcross and doubled-haploid population

 Distorted segregation has been repeatedly observed in various plant species in molecular-marker linkage mapping where distant crosses were made. It may be caused by a partial lethal-factor acting in the filial generations. A method is presented for estimating the recombination values between a partial lethal-factor locus and a linked molecular marker and the relative viability or fertilization ability of zygotes or gametes, respectively affected by the partial lethal factor in backcross (BC) and doubled-haploid (DH) populations using the maximum-likelihood method associated with the expectation maximization (EM) algorithm. The method was applied to segregation data of molecular markers for a population of 150 DH lines developed from the ‘Steptoe’בMorex’ cross in barley. The presence of a partial lethal-factor locus, located on chromosome 4, causing partial selection was suggested. This locus was tightly linked to the ABG500B marker, and the chance of fertilization of female gametes possessing the partial lethal factor was, on average, 59.8% that of a normal one. Two additional partial lethal factors were found on chromosome 5. Received: 3 December 1997 / Accepted: 25 February 1998     

In vitro screening for burrowing nematode, Radopholus citrophilus, tolerance and resistance in commercial Anthurium hybrids

Summary A reliable method to screen Anthurium for burrowing nematode resistance and tolerance in vitro was developed using 17 genetically distinct Anthurium cultivars. Based on nonparametric data analysis, tolerance and resistance were found to be independent traits to be evaluated separately. An effective parameter for tolerance evaluation was ranking of relative leaf retention, whereas an effective parameter for resistance evaluation was the ranking of nematode reproduction, log(Rf+1). A comparison of the ranking of leaf retention with ranking of nematode reproduction clustered the cultivar responses to burrowing nematode infection into four groups: intolerant and resistant, moderately tolerant but susceptible, intolerant and susceptible, and tolerant and susceptible. ‘Ozaki’ was identified as an intolerant reference, ‘Nitta’ as a susceptible reference. ‘Blushing Bride’ was the most tolerant cultivar among those screened, but it may not be an ideal tolerant reference due to its low vigor. Future screening for burrowing nematode-tolerant and-resistant cultivars in Anthurium should include ‘Ozaki’ and ‘Nitta’ as internal controls. Evaluation of resistance should be based on a resistance index obtained by log(Rf of hybrid tested +1) divided by log(Rf of ‘Nitta’ +1); tolerance should be based on ranking of relative leaf retention.     

Genetic control theory of developmental events

An earlier theory of cell differentiation and morphogenesis (Wassermann, 1972, 1973, 1978) is combined with the genetic control model of Davidson and Britten (e.g. 1979). The resulting new theory suggests how, bysystematic process algorithms, specifically enumerated combinations of batteries of structural genes can become switched on in particularly enumerated cells, via battery-specific enumerable regulator genes. The systematization is idealized. Up to a certain stage of development in each mitotically arising cell a unique cell-specific combination of structural genes called ‘marker genes’ is active. Marker genes are assumed to code for cell-specifying marker proteins (CSMPs) which permit cells carrying related markers to recognize each other, thus permitting specific cell sorting.Batteries of marker genes could ensure great developmental precision and can safeguard—via redundancies of CSMP types—against accidental loss or detrimental mutational modification of CSMPs or marker genes, respectively. This paper is much concerned with cell lineage in relation to ‘microdifferentiation’, where ‘microdifferentiation’ of a cell refers to a cell's active marker genes and its syntheses of CSMPs. A drastic distinction is made between ‘microdifferentiation’ and ‘gross’ differentiation of a cell, where the same ‘gross’ differentiation may be shared by a large number of cells that could each be uniquely ‘microdifferentiated’. Typical ‘gross’ differentiation could manifest itself in tissue specificity, whereas, up to certain stages of development, all cells of the same gross differentiation type (say tissue specificity) could each be uniquely ‘microdifferentiated’. The theory also assumes that at certain stages of the developmental process some (or in some organisms all) of the previously uniquely specified cells could give rise to small (or occasionally large) clones of equispecified cells, some of which might form clusters that represent complete ‘morphogenetic fields’ Tentative implementation mechanisms are proposed which suggest how the theory could operate in molecular biological terms. In particular, CSMPs could endow cell surface membranes with a highly specific protein network, and an associated equally specific cell surface coat. It is suggested how these highly specified cell surface coats and other systems could provide an ‘extracellular guidance network’ which could help to direct cells to attain energetically optimal locations relative to each other based on the matching of their surface specificities. In numerous experimental situations, where normally present optimal matching of cells is excluded, ‘alternative matching’ based on experiment-specific suboptimal matching could explain many data, notably in experimental development neurobiology (Wassermann, 1978).     

Process and measurement errors of population size: their mutual effects on precision and bias of estimates for demographic parameters

Knowing the parameters of population growth and regulation is fundamental for answering many ecological questions and the successful implementation of conservation strategies. Moreover, detecting a population trend is often a legal obligation. Yet, inherent process and measurement errors aggravate the ability to estimate these parameters from population time-series. We use numerical simulations to explore how the lengths of the time-series, process and measurement error influence estimates of demographic parameters. We first generate time-series of population sizes with given demographic parameters for density-dependent stochastic population growth, but assume that these population sizes are estimated with measurement errors. We then fit parameters for population growth, habitat capacity, total error and long-term trends to the ‘measured’ time-series data using non-linear regression. The length of the time-series and measurement error introduce a substantial bias in the estimates for population growth rate and to a lesser degree on estimates for habitat capacity, while process error has little effect on parameter bias. The total error term of the statistical model is dominated by process error as long as the latter is larger than the measurement error. A decline in population size is difficult to document as soon as either error becomes moderate, trends are not very pronounced, and time-series are short (<10–15 seasons). Detecting an annual decline of 1% within 6-year reporting periods, as required for the European Union for the species of Community Interest, appears unachievable.     

Uncertainty in Calculations of Net Primary Production for Grasslands

Net primary production (NPP) is a fundamental characteristic of all ecosystems and foundational to understanding the fluxes of energy and nutrients. Because NPP cannot be measured directly, researchers use field-measured surrogates as input variables in various equations designed to estimate ‘true NPP’. This has led to considerable debate concerning which equations most accurately estimate ‘true NPP’. This debate has influenced efforts to assess NPP in grasslands, with researchers often advocating more complex equations to avoid underestimation. However, this approach ignores the increase in statistical error associated with NPP estimates as a greater number of parameters and more complex mathematical functions are introduced into the equation. Using published grassland data and Monte Carlo simulation techniques, we assessed the relative variability in NPP estimates obtained using six different NPP estimation equations that varied in both the number of parameters and intricacy of mathematical operations. Our results indicated that more complex equations may result in greater uncertainty without reducing the probability of underestimation. The amount of uncertainty associated with estimates of NPP was influenced by the number of parameters as well as the variability in the data and the nature of the mathematical operations. For example, due to greater variability in the field-measured belowground data than aboveground data, estimates of belowground NPP tended to have more uncertainty than estimates of aboveground NPP. An analysis in which the input data were standardized allowed us to isolate the details of the calculations from the variability in the data in assessing the propagation of uncertainty. This analysis made clear that equations with product terms have the potential to magnify the uncertainty of the inputs in the estimates of NPP although this relationship was complicated by interactions with data variability and number of parameters. Our results suggest that more complex NPP estimation equations can increase uncertainty without necessarily reducing risk of underestimation. Because estimates can never be tested by comparison to “true NPP”, we recommend that researchers include an assessment of propagation of statistical error when evaluating the ‘best’ estimation method.     

Production of phosphinothricin-tolerant rice (Oryza sativa L.) through the application of phosphinothricin as growth regulator

 A novel procedure has been developed to produce rice (Oryza sativa L.) tolerant to the herbicide phosphinothricin (PPT) by means of in vitro selection. First, sublethal and lethal concentrations of PPT on 7-day-old seedlings were determined and morphogenetic events in response to the PPT treatment evaluated. Differentiation of 6–30 microshoots on 5–40% of the treated plant material was observed on a hormone-free culture medium supplemented with a sublethal concentration of PPT. We proved that PPT is morphogenetically active, similar to the action of many other herbicides, showing cytokinin-like effects in rice tissue culture. Fertile plants were grown from those microshoots having PPT tolerance under greenhouse conditions. To the best of our knowledge, this is the first report on the production of rice plants tolerant to this herbicide without genetic transformation. Since PPT is a competitive inhibitor of glutamine synthetase (GS), total GS activity in PPT-tolerant and PPT-sensitive plants was examined comprehensively in order to decide whether this enzyme has any role in PPT tolerance. An elevated GS activity was detected in PPT-tolerant plant material which could result in an elevated PPT tolerance at unchanged concentrations of the herbicide. Received: 20 February 2000 / Accepted: 19 June 2000     

Data-based identifiability analysis of non-linear dynamical models

MOTIVATION: Mathematical modelling of biological systems is becoming a standard approach to investigate complex dynamic, non-linear interaction mechanisms in cellular processes. However, models may comprise non-identifiable parameters which cannot be unambiguously determined. Non-identifiability manifests itself in functionally related parameters, which are difficult to detect. RESULTS: We present the method of mean optimal transformations, a non-parametric bootstrap-based algorithm for identifiability testing, capable of identifying linear and non-linear relations of arbitrarily many parameters, regardless of model size or complexity. This is performed with use of optimal transformations, estimated using the alternating conditional expectation algorithm (ACE). An initial guess or prior knowledge concerning the underlying relation of the parameters is not required. Independent, and hence identifiable parameters are determined as well. The quality of data at disposal is included in our approach, i.e. the non-linear model is fitted to data and estimated parameter values are investigated with respect to functional relations. We exemplify our approach on a realistic dynamical model and demonstrate that the variability of estimated parameter values decreases from 81 to 1% after detection and fixation of structural non-identifiabilities.     

Oud-leerling versus ancien élève: A Comparative Study of Adjectives Grammaticalizing into Prefixes in Dutch and French

This article analyzes the grammaticalization of adjectives into prefixes in Dutch and French. In the first part, the notion of ‘affixoids’, hybrid elements that combine properties of free lexemes and bound morphemes, will be defined and illustrated. It will be claimed that affixoids can be seen as a result of a grammaticalization process for which we will advance phonological, morphological, semantic and distributional parameters applying to the evolution of adjectives into prefixes. The second part will be devoted to a specific case study in which these grammaticalization parameters will be applied to the Dutch adjectives oud ‘old’ and nieuw ‘new’ and their French counterparts ancien ‘old’ and nouveau ‘new’ when used in word-formation. More particularly, we will examine whether these adjectives may develop prefix-like properties when embedded in a compound structure and determine their degree of grammaticalization. Kristel Van Goethem is a Postdoctoral fellow of the Research Foundation-Flanders (FWO)     

Thermal resistance parameters of the air environment at various altitudes

 The thermal properties of atmospheric air surrounding the human body at various altitudes are characterized with a system of parameters. This system comprises resistance of the air to convective heat transfer h _c ^–1, °C (W/m²)⁻¹ and to water vapour transfer h _D ^–1, s/m. The concept of ’evaporative resistance’h _e ^–1, hPa (W/m²)⁻¹) following the similarity of the processes is introduced. In obtaining the altitude dependencies of investigated paramters, a respective heat transfer equation expressing the rate of heat exchange at the boundary body surface – ambient air is applied. The use of the body thermal state of the established altitude dependencies is discussed. The concept of ’thermal stability’ related to the evaporative resistance parameter h _e ^–1 is introduced. This parameter is assumed as: (1) an indicator of the human body thermal stability and (2) distributor and predictor of environmental influence on the body thermal state. Received: 5 January 1996 / Accepted 5 November 1996     

A derivation of a rote learning curve from the total uncertainty of a task

The derivation of H. D. Landahl’s learning curve (1941,Bull. Math. Biophysics,3, 71–77) from a single information-theoretical assumption obtained previously (Rapoport, 1956,Bull. Math. Biophysics,18, 317–21) is extended to obtain the entire family of such curves with the number of stimuliM (to each of which one ofN responses is to be associated) as a parameter. No additional assumptions are required. The entire family thus appears as a function of a single free parameter,k, all other parameters being experimentally determined. The theory is compared with a set of experiments involving the learning of artificial languages. An alternative quasi-neurological model leading to the same equation is offered.     

Science through the internet: Researching, evaluating and citing websites

This article attempts to convey the joys and frustrations of skimming the Internet trying to find relevant information concerning an academic’s work as a scientist, a student or an instructor. A brief overview of the Internet and the “do’s and don’ts” for the neophyte as well for the more seasoned “navigator” are given. Some guidelines of “what works and what does not” and “what is out there” are provided for the scientist with specific emphasis for biologists, as well as for all others having an interest in science but with little interest in spending countless hours “surfing the net”. An extensive but not exhaustive list of related websites is provided.     

Genetic analysis of durable leaf rust resistance in winter wheat

Quantitative resistance that delays the epidemic development of leaf rust in wheat is an important source for durable resistance breeding. The Swiss winter wheat variety ’Forno’ shows a high level of quantitative resistance against leaf rust. This resistance has been effective for more than 10 years and can therefore be considered to be durable. In order to map quantitative trait loci (QTL) for durable leaf rust resistance we analysed 204 F₅ recombinant inbred lines (RILs) of the cross between the winter wheat ’Forno’ and the winter spelt ’Oberkulmer’ for their level of leaf rust resistance (LR) and leaf tip necrosis (LTN) in four different environments. Both traits showed a continuous distribution and were significantly correlated (r=−0.5). Across environments we detected 8 QTL for leaf rust resistance (6 inherited from ’Forno’) and 10 QTL for the quantitative expression of LTN (6 inherited from ’Forno’). Of the 6 QTL responsible for the durable leaf rust resistance of ’Forno’, 1 major QTL coincided with a thaumatin locus on 7BL explaining 35% of the phenotypic variance. Four QTL for LR coincided with QTL for LTN. At these loci the alleles of ’Forno’ increased the level of resistance as well as the extent of LTN, indicating pleiotropy. Received: 1 July 1999 / Accepted: 30 July 1999     

Application of microsatellites in wheat (Triticum aestivum L.) for studying genetic differentiation caused by selection for adaptation and use

For studying genetic differentiation caused by selection for adaptation and end-use, the allele frequencies of 42 microsatellites (MS), representative of the three wheat genomes, were analysed in a total of 60 wheat cultivars. The cultivars originate from three agroecological areas (AEAs) – Germany, Austria and Hungary – and represent equal numbers of ’quality wheats’ and ’feed wheats’ for each country. For the 42 loci, 202 alleles were detected using PAGE and silver staining. The average number of alleles per locus was 4.8, including four monomorphic loci. For 16 loci, null alleles were detected. Cluster analysis clearly differentiated the varieties according to the three AEAs and, within each AEA, into quality wheats from feed wheats. Analysis of variance revealed highly significant differences of distance data between AEAs as well as between quality groups. The correlation between genetic distance (GD) and pedigree data (coefficient of diversity, COD) was r _s=0.45. The results have proven the excellent resolving power of MS in varietal differentiation, which arises through breeding under specific environmental conditions, and for different end-use. Received: 15 March 1999 / 17 June 1999