Pharmacokinetic curve fitting and parameter determination by non-linear,iterative least squares regression analysis using a programmed minicalculator

A pharmacokinetic non-linear, iterative least-squares program for the minicalculator TI-59 with adapted printer is described. The program utilizes the Gauss-Newton gradient method in an iterative, non-linear regression analysis of up to 18 data pairs. Single-dose plasma concentration data of 5-hydroxytryptophan, theophylline and prednisolone were comparatively analysed using both the described program (called NONTI-59) and Metzlers well-established digital computer program NONLIN.     

Chromosome studies on capsicum (Solanaceae) I. Karyotype analysis in C. Chacoënse

The somatic chromosomes and karyotypes of two Argentine populations of Capsicum chacoënse A. T. Hunz. have been studied, both of which have 2n=24. The karyotypes are symmetrical, being composed of 11 m paris + one st pair; two pairs of chromosomes are satellied: pairs 1 and 12 in one population and pairs 11 and 12 in the other one. A heteromorphic pair of satellited chromosomes in one individual suggests a spontaneous reciprocal translocation. Results are compared with previous reports for the species and genus. Data show an intraspecific karyotype variation.     

New softwares for automated microsatellite marker development

Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence ‘experiment file’ format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut.     

GST-PRIME: a genome-wide primer design software for the generation of gene sequence tags

The availability of sequenced genomes has generated a need for experimental approaches that allow the simultaneous analysis of large, or even complete, sets of genes. To facilitate such analyses, we have developed GST-PRIME, a software package for retrieving and assembling gene sequences, even from complex genomes, using the NCBI public database, and then designing sets of primer pairs for use in gene amplification. Primers were designed by the program for the direct amplification of gene sequence tags (GSTs) from either genomic DNA or cDNA. Test runs of GST-PRIME on 2000 randomly selected Arabidopsis and Drosophila genes demonstrate that 93 and 88% of resulting GSTs, respectively, fulfilled imposed length criteria. GST-PRIME primer pairs were tested on a set of 1900 Arabidopsis genes coding for chloroplast-targeted proteins: 95% of the primer pairs used in PCRs with genomic DNA generated the correct amplicons. GST-PRIME can thus be reliably used for large-scale or specific amplification of intron-containing genes of multicellular eukaryotes.     

Effect of the Nematode Contortylenchus brevicomi on Gallery Construction and Fecundity of the Southern Pine Beetle

Field-collected Dendroctonus frontalis were reared in a controlled environment. Male-female beetle pairs retrieved from galleries 1, 2, or 5 wk after introduction into pine bolts were examined for nematode parasites. Data were obtained for each pair on gallery length, egg niche construction, egg viability, and progeny survival. In a separate study, beetle pairs were reared under laboratory conditions for 10 wk. The number of emerged adult progeny of each pair was recorded. Contortylenchus brevicomi, a nematode parasite, was found in 25% of all beetles that established galleries. After 2 and 3 wk, female beetles infected with the nematode had produced fewer eggs and shorter galleries than did uninfected females. Uninfected females mated with nematode-infected males showed similar trends, although the differences in the 2- and 3-wk tests were not significant. Progeny survival or egg viability was not affected by nematode parasitism of either parent beetle. Unikaryon minutum, a microsporidian parasite found in 65% of all colonizing beetles, had no effect on measured variables. The lower fecundity of beetles parasitized by C. brevicomi continued throughout the insect''s reproductive cycle. After 10 wk, nematode-infected beetle pairs produced fewer emerged adult progeny than did uninfected pairs.     

Analysis of the myogenic lineage in chick embryos: I. Studies on the terminal cell division

An antibody prepared against the MM isozyme of creatine phosphokinase (M-CK) stained multinucleated myotubes and post-mitotic mononucleated myoblasts in mass cultures of myogenic cells taken from the breast muscles of 11-day chick embryos. No cycling cells bound the antibody. Single cells isolated either directly from the embryo or from mass cultures were seeded at clonal density and allowed to undergo one division. The resulting pairs of cells were stained with the antibody and were scored as (a) both members of the pair M-CK⁺; (b) both M-CK^?; or (c) mixed (one M-CK⁺ and one M-CK^?). No mixed pairs were observed. Conditioned medium did not induce all myogenic pairs to differentiate and growth medium did not keep myogenic pairs in the cell cycle. About 10% of clonal pairs established from 10 h cultures were M-CK⁺, while about 27% of pairs established from 30 h mass cultures were M-CK⁺. These results indicate that (1) the myogenic lineage ends in a symmetrical division whose products are two post-mitotic M-CK⁺ cells; (2) the expression of the muscle phenotype is not determined exclusively by the environment; (3) the terminal cells are the product of an intrinsic program or cell lineage in which only the last cells can synthesize muscle-specific proteins.     

Larval development of nemerteans of the genus Quasitetrastemma (Nemertea: Monostilifera)

Data on the larval development of Quasitetrastemma stimpsoni and Q. nigrifrons are presented. In both species, fertilization is external; the development passes through a free-swimming larval stage, the “hidden larva.” The larva has three pairs of eyes. After settling, the eyes of the second pair fuse with eyes of the first pair or are completely reduced. The basis and stylets are formed in 7–8 days after fertilization. Larvae of Q. stimpsoni settle on day 9–10 after fertilization; and Q. nigrifrons, on day 7–8.     

Timing of arrival at breeding grounds determines spatial patterns of productivity within the population of white stork (Ciconia ciconia)

Early arrival at breeding grounds have important fitness consequences for migratory birds, both at individual and population level. The aim of this study was to investigate how the timing of arrival at the breeding territories affects the spatial patterns of reproductive success within a population of white storks (Ciconia ciconia). Data were gathered annually for ca. 200 pairs of storks breeding in central Poland between 1994 and 2011. Geostatistical analysis of data indicated that in years of delayed arrival of the population (measured by the first quartile arrival date), the reproductive output of storks was negatively autocorrelated, which indicated that there was a tendency for pairs of high breeding success to neighbour with pairs of low success. By contrast, in years when first storks returned in early dates to the breeding grounds, their reproductive success did not show any kind of spatial autocorrelation. These results suggest that delayed return of the first-arriving storks of the population may increase intensity of intra-specific competition to the level at which high-quality breeding pairs monopolize most of available resources at the expense of neighbouring low-quality pairs, which have lower reproductive success as a consequence. Such hypothesis was further supported with the analysis of nesting densities, showing that the late-arriving breeding pairs incurred greater fitness costs (or derived lower fitness benefits) while breeding in high densities comparatively to the early-arriving conspecifics.     

detectIR: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation

Inverted repeats are present in abundance in both prokaryotic and eukaryotic genomes and can form DNA secondary structures – hairpins and cruciforms that are involved in many important biological processes. Bioinformatics tools for efficient and accurate detection of inverted repeats are desirable, because existing tools are often less accurate and time consuming, sometimes incapable of dealing with genome-scale input data. Here, we present a MATLAB-based program called detectIR for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. A novel algorithm is adopted in detectIR to convert the conventional sequence string comparison in inverted repeat detection into vector calculation of complex numbers, allowing non-complementary pairs (mismatches) in the pairing stem and a non-palindromic spacer (loop or gaps) in the middle of inverted repeats. Compared with existing popular tools, our program performs with significantly higher accuracy and efficiency. Using genome sequence data from HIV-1, Arabidopsis thaliana, Homo sapiens and Zea mays for comparison, detectIR can find lots of inverted repeats missed by existing tools whose outputs often contain many invalid cases. detectIR is open source and its source code is freely available at: https://sourceforge.net/projects/detectir.     

Computer programming for nucleic acid studies II. Total chemical shifts calculation of all protons of double-stranded helices

A FORTRAN computer program called SHIFTS is described. Through SHIFTS, one can calculate the NMR chemical shifts of the proton resonances of single and double-stranded nucleic acids of known sequences and of predetermined conformations. The program can handle RNA and DNA for an arbitrary sequence of a set of 4 out of the 6 base types A, U, G, C, I and T. Data files for the geometrical parameters are available for A-, A′-, B-, D- and S-conformations.The positions of all the atoms are calculated using a modified version of the SEQ program [1]. Then, based on this defined geometry three chemical shift effects exerted by the atoms of the neighboring nucleotides on the protons of each monomeric unit are calculated separately: the ring current shielding effect; the local atomic magnetic susceptibility effect (including both diamagnetic and paramagnetic terms); and the polarization or electric field effect. Results of the program are compared with experimental results for a γ(ApApGpCpUpU)₂ helical duplex and with calculated results on this same helix based on model building of A′-form and B-form and on graphical procedure for evaluating the ring current effects.     

RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire

The problem of systematic and objective identification of canonical and non-canonical base pairs in RNA three-dimensional (3D) structures was studied. A probabilistic approach was applied, and an algorithm and its implementation in a computer program that detects and analyzes all the base pairs contained in RNA 3D structures were developed. The algorithm objectively distinguishes among canonical and non-canonical base pairing types formed by three, two and one hydrogen bonds (H-bonds), as well as those containing bifurcated and C-H...X H-bonds. The nodes of a bipartite graph are used to encode the donor and acceptor atoms of a 3D structure. The capacities of the edges correspond to probabilities computed from the geometry of the donor and acceptor groups to form H-bonds. The maximum flow from donors to acceptors irectly identifies base pairs and their types. A complete repertoire of base pairing types was built from the detected H-bonds of all X-ray crystal structures of a resolution of 3.0 Å or better, including the large and small ribosomal subunits. The base pairing types are labeled using an extension of the nomenclature recently introduced by Leontis and Westhof. The probabilistic method was implemented in MC-Annotate, an RNA structure analysis computer program used to determine the base pairing parameters of the 3D modeling system MC-Sym.     

A novel stable isotope labelling assisted workflow for improved untargeted LC–HRMS based metabolomics research

Many untargeted LC–ESI–HRMS based metabolomics studies are still hampered by the large proportion of non-biological sample derived signals included in the generated raw data. Here, a novel, powerful stable isotope labelling (SIL)-based metabolomics workflow is presented, which facilitates global metabolome extraction, improved metabolite annotation and metabolome wide internal standardisation (IS). The general concept is exemplified with two different cultivation variants, (1) co-cultivation of the plant pathogenic fungi Fusarium graminearum on non-labelled and highly ¹³C enriched culture medium and (2) experimental cultivation under native conditions and use of globally U-¹³C labelled biological reference samples as exemplified with maize and wheat. Subsequent to LC–HRMS analysis of mixtures of labelled and non-labelled samples, two-dimensional data filtering of SIL specific isotopic patterns is performed to better extract truly biological derived signals together with the corresponding number of carbon atoms of each metabolite ion. Finally, feature pairs are convoluted to feature groups each representing a single metabolite. Moreover, the correction of unequal matrix effects in different sample types and the improvement of relative metabolite quantification with metabolome wide IS are demonstrated for the F. graminearum experiment. Data processing employing the presented workflow revealed about 300 SIL derived feature pairs corresponding to 87–135 metabolites in F. graminearum samples and around 800 feature pairs corresponding to roughly 350 metabolites in wheat samples. SIL assisted IS, by the use of globally U-¹³C labelled biological samples, reduced the median CV value from 7.1 to 3.6 % for technical replicates and from 15.1 to 10.8 % for biological replicates in the respective F. graminearum samples.     

Biology and behaviour of reintroduced gibbons

We observed and recorded the behaviours of gibbons undergoing rehabilitation, before and after release, to document the behavioural and social changes of gibbons in the rehabilitation program and develop criteria for determining the suitability of a pair of gibbons for release. Hylobates albibarbis were observed at the Kalaweit Gibbon Rehabilitation Project in Kalimantan, Indonesia. Data were collected on animals both pre- and post-release and on wild gibbons for comparison. Data presented here show that reintroduced gibbons are capable of surviving without human intervention. In addition, their behaviour is similar to that of wild gibbons in terms of activity budgets, position in the canopy, body posture, pair association (PA) and diet. Prior to this study, no attempt has been made to quantify the rehabilitation process for gibbons, and rehabilitation project personnel require data reporting all aspects of a release so that improvements can be made. It is important to report these data for the benefit of future releases. Criteria, based on the behaviour of wild gibbons, are proposed to assist rehabilitation centers in assessing the suitability of gibbon pairs for release.     

Improved inference of relationship for pairs of individuals

Linkage analyses of genetic diseases and quantitative traits generally are performed using family data. These studies assume the relationships between individuals within families are known correctly. Misclassification of relationships can lead to reduced or inappropriately increased evidence for linkage. Boehnke and Cox (1997) presented a likelihood-based method to infer the most likely relationship of a pair of putative sibs. Here, we modify this method to consider all possible pairs of individuals in the sample, to test for additional relationships, to allow explicitly for genotyping error, and to include X-linked data. Using autosomal genome scan data, our method has excellent power to differentiate monozygotic twins, full sibs, parent-offspring pairs, second-degree (2 degrees ) relatives, first cousins, and unrelated pairs but is unable to distinguish accurately among the 2 degrees relationships of half sibs, avuncular pairs, and grandparent-grandchild pairs. Inclusion of X-linked data improves our ability to distinguish certain types of 2 degrees relationships. Our method also models genotyping error successfully, to judge by the recovery of MZ twins and parent-offspring pairs that are otherwise misclassified when error exists. We have included these extensions in the latest version of our computer program RELPAIR and have applied the program to data from the Finland-United States Investigation of Non-Insulin-Dependent Diabetes Mellitus (FUSION) study.     

A computerized system for rapid interpretation of acid/base disorders

Rapid and correct interpretation of arterial blood gas results is necessary in the operating room or intensive care unit. However, manual calculation and interpretation is tedious and prone to error. A computer system consisting of two programs written in BASIC has been created to address these problems. The program uses a series of decisions to arrive at a conclusion. Data generated by the Interpreter may be used by a subsequent program, the Manager, in determining ventilation parameters.     

DANCER: a program for digital anatomical reconstruction of gene expression data

A digital anatomy construction (DANCER) program was developed for gene expression data. DANCER can be used to reconstruct anatomical images from in situ hybridization images, microarray or other gene expression data. The program fills regions of a drawn figure with the corresponding values from a gene expression data set. The output of the program presents the expression levels of a particular gene in a particular region relative to other regions. The program was tested with values from experimental in situ hybridization autoradiographs and from a microarray experiment. Reconstruction of in situ hybridization data from adult rat brain made by DANCER corresponded well with the original autoradiograph. Reconstruction of microarray data from adult mouse brains provided images that reflect actual expression levels. This program should help to provide visualization and interpretation of data derived from gene expression experiments. DANCER may be freely downloaded.     

Genetic dissection of developmental behavior of grain weight in wheat under diverse temperature and water regimes

As a quantitatively inherited trait related to high yield potential, grain weight (GW) development in wheat is constrained by abiotic stresses such as limited water supply and high temperature. Data from a doubled haploid population, derived from a cross of (Hanxuan 10?×?Lumai 14), grown in four environments were used to explore the genetic basis of GW developmental behavior in unconditional and conditional quantitative trait locus (QTL) analyses using a mixed linear model. Thirty additive QTLs and 41 pairs of epistatic QTLs were detected, and were more frequently observed on chromosomes 1B, 2A, 2D, 4A, 4B and 7B. No single QTL was continually active during all stages or periods of grain growth. The QTLs with additive effects (A-QTLs) expressed in the period S1|S0 (the period from the flowering to the seventh day after) formed a foundation for GW development. GW development at these stages can be used as an index for screening superior genotypes under diverse abiotic stresses in a wheat breeding program. One QTL, i.e. Qgw.cgb-6A.2, showed high adaptability for water-limited and heat-stress environments. Many A-QTLs interacted with more than one other QTL in the two genetic models, such as Qgw.cgb-4B.2 interacted with five QTLs, showing that the genetic architecture underlying GW development involves a collective expression of genes with additive and epistatic effects.     

The DynDom database of protein domain motions

A relational database has been developed based on the results from the application of the DynDom program to a number of proteins for which multiple X-ray conformers are available. The database is populated via a web-based tool that allows visitors to the website to run the DynDom program server-side by selecting pairs of X-ray conformers by Protein Data Bank code and chain identifier. AVAILABILITY: The website can be found at: http://www.sys.uea.ac.uk/dyndom.