A microcomputer method for designing optimal experiments for estimating enzyme kinetic parameters

A computer program, written in BASIC, for designing optimal experiments with the aim of evaluating estimates of the parameters for any enzyme kinetic model is given. This computer program can be run on any microcomputer with less than 32 Kbytes of random access memory. The program uses the termed D-optimization design criterion, which minimizes the determinant of the variance-covariance matrix. The user only supplies the rate equation, the maximum and minimum concentrations of substrates and inhibitors, the weighting pattern, and the best possible values of the parameters. The computer supplies the optimal substrate and inhibitor concentrations (one for each parameters), for estimating the parameter values, and the determinant of the variance-covariance matrix. Likewise, the microcomputer supplies the eigenvalues and eigenvectors of information and redundancy matrices, the sensitivity and the global redundancy.     

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.     

Control of carbon source supply and dissolved oxygen by use of carbon dioxide concentration of exhaust gas in fed-batch culture

Accurate and automatic control strategies for a feedback-control system of volatile carbon source feeding and dissolved oxygen (DO) level were investigated. To maintain the optimal ethanol concentration for microbial growth, carbon dioxide concentration in exhaust gas was used as a stepwise control parameter of ethanol feeding. A proportional-differential (PD) control program was used to correct the errors. The coefficient of stepwise control was calculated stoichiometrically, and parameters of PD were experimentally preset and were not changed during cultivation. DO was also controlled by the PD control and the stepwise program based on carbon dioxide concentration of the exhaust gas. Agitation speed and partial pressure of oxygen of the inlet gas were changed stepwise in accordance with the oxygen consumption rate. The stepwise coefficients were estimated from stoichiometry and material balance of molecular oxygen. The PD control program was only used for the agitation speed control to correct the fluctuations of DO level. The parameters did not need to be changed during cultivation. By use of these sophisticated control programs for fed-batch culture of Candida brassicae, ethanol concentration and DO level were accurately controlled at 3.4–3.7 g/l and 2.2–2.8 ppm, respectively, while cell mass concentration reached about 80 g/l. No manual operation was needed.     

The Calculation of Parameters of the Moffitt Equation for Rotatory Dispersion Data

The least squares calculation of the best values of the parameters of the Moffitt equation and of the Drude equation is examined. It is proved that the least squares evaluation of all three parameters of the Moffitt equation becomes indeterminate as the b_o term approaches zero. Estimates of low helical content based on the Moffitt relationship are therefore also indeterminate and of dubious value. Both the size of b_o and the range of wavelengths chosen affect the standard deviations of the parameters. The magnitude of the effects is illustrated by selected examples. The computer program OPTROT is available for evaluating the extent to which data may be correlated by the equations.     

Exercise reduces circulating biomarkers of cellular senescence in humans

Cellular senescence has emerged as a significant and potentially tractable mechanism of aging and multiple aging‐related conditions. Biomarkers of senescent cell burden, including molecular signals in circulating immune cells and the abundance of circulating senescence‐related proteins, have been associated with chronological age and clinical parameters of biological age in humans. The extent to which senescence biomarkers are affected by interventions that enhance health and function has not yet been examined. Here, we report that a 12‐week structured exercise program drives significant improvements in several performance‐based and self‐reported measures of physical function in older adults. Impressively, the expression of key markers of the senescence program, including p16, p21, cGAS, and TNFα, were significantly lowered in CD3⁺ T cells in response to the intervention, as were the circulating concentrations of multiple senescence‐related proteins. Moreover, partial least squares discriminant analysis showed levels of senescence‐related proteins at baseline were predictive of changes in physical function in response to the exercise intervention. Our study provides first‐in‐human evidence that biomarkers of senescent cell burden are significantly lowered by a structured exercise program and predictive of the adaptive response to exercise.     

Quantitative structure-retention relationships in doping control

Regression equation modelling was used for the correlation of gas chromatographic relative retention times t_RR of anabolic steroids, stimulants and narcotics with their molecular characteristics in order to create a model for the prediction of t_RR values of unanalysed molecules. Predicting chromatographic retention parameters is one of the main goals of the quantitative structure-retention relationships (QSRR) methodology. To be performed, QSRR studies require two tools; a methodology for the extraction of the structural characteristics and a statistical program for the correlation of these characteristics with the chromatographic data.     

A computer program for the estimation of protein and nucleic acid sequence diversity in random point mutagenesis libraries

A computer program for the generation and analysis of in silico random point mutagenesis libraries is described. The program operates by mutagenizing an input nucleic acid sequence according to mutation parameters specified by the user for each sequence position and type of point mutation. The program can mimic almost any type of random mutagenesis library, including those produced via error-prone PCR (ep-PCR), mutator Escherichia coli strains, chemical mutagenesis, and doped or random oligonucleotide synthesis. The program analyzes the generated nucleic acid sequences and/or the associated protein library to produce several estimates of library diversity (number of unique sequences, point mutations, and single point mutants) and the rate of saturation of these diversities during experimental screening or selection of clones. This information allows one to select the optimal screen size for a given mutagenesis library, necessary to efficiently obtain a certain coverage of the sequence-space. The program also reports the abundance of each specific protein mutation at each sequence position, which is useful as a measure of the level and type of mutation bias in the library. Alternatively, one can use the program to evaluate the relative merits of preexisting libraries, or to examine various hypothetical mutation schemes to determine the optimal method for creating a library that serves the screen/selection of interest. Simulated libraries of at least 10⁹ sequences are accessible by the numerical algorithm with currently available personal computers; an analytical algorithm is also available which can rapidly calculate a subset of the numerical statistics in libraries of arbitrarily large size. A multi-type double-strand stochastic model of ep-PCR is developed in an appendix to demonstrate the applicability of the algorithm to amplifying mutagenesis procedures. Estimators of DNA polymerase mutation-type-specific error rates are derived using the model. Analyses of an alpha-synuclein ep-PCR library and NNS synthetic oligonucleotide libraries are given as examples.     

Can Establishment Success Be Determined through Demographic Parameters? A Case Study on Five Introduced Bird Species

The dominant criterion to determine when an introduced species is established relies on the maintenance of a self-sustaining population in the area of introduction, i.e. on the viability of the population from a demographic perspective. There is however a paucity of demographic studies on introduced species, and establishment success is thus generally determined by expert opinion without undertaking population viability analyses (PVAs). By means of an intensive five year capture-recapture monitoring program (involving >12,000 marked individuals) we studied the demography of five introduced passerine bird species in southern Spain which are established and have undergone a fast expansion over the last decades. We obtained useful estimates of demographic parameters (survival and reproduction) for one colonial species (Ploceus melanocephalus), confirming the long-term viability of its local population through PVAs. However, extremely low recapture rates prevented the estimation of survival parameters and population growth rates for widely distributed species with low local densities (Estrilda troglodytes and Amandava amandava) but also for highly abundant yet non-colonial species (Estrilda astrild and Euplectes afer). Therefore, determining the establishment success of introduced passerine species by demographic criteria alone may often be troublesome even when devoting much effort to field-work. Alternative quantitative methodologies such as the analysis of spatio-temporal species distributions complemented with expert opinion deserve thus their role in the assessment of establishment success of introduced species when estimates of demographic parameters are difficult to obtain, as is generally the case for non-colonial, highly mobile passerines.     

First attempts to crystallize a non-homogeneous sample of thioredoxin from Litopenaeus vannamei: What to do when you have diffraction data of a protein that is not the target?

The importance of sample homogeneity and purity in protein crystallization is essential to obtain high-quality diffracting crystals. Here, in an attempt to determine the crystal structure of thioredoxin 1 from whiteleg shrimp Litopenaeus vannamei (LvTrx), we inadvertently crystallized the hexameric inorganic pyrophosphatase of Escherichia coli (E-PPase) from a non-homogeneous sample product during the initial over-expression steps and partial purification of LvTrx. The structure determination and identification of the crystallized protein were derived from several clues: the failures in the Molecular Replacement (MR) trials using LvTrx coordinates as a search model, the unit cell parameters and space group determination, and essentially by the use of the program BALBES. After using the previously deposited E-PPase structure (PDB entry 1mjw) as a search model and the correct space group assignation, the MR showed an E-PPase complexed with SO₄^?2 with small changes in the sulfate ion binding region when it compares to previously deposited E-PPases in the PDB. This work stresses the importance of protein purity to avoid the risk of crystallizing a contaminant protein or how pure need to be a protein sample in order to increase the possibility to obtain crystals, but also serves as a reminder that crystallization is by itself a purification process and how the program BALBES can be useful in the crystal structure determination of previously deposited structures in the PDB.     

Monte Carlo simulation of malignant growth. Examples of the behavior of chloroleukemia after specific perturbations

This paper describes a stochastic model of cell population growth constructed to simulate biological reality in different experimental conditions. Using the computer program developed, the behavior of the cell population and of several experimentally measurable kinetic parameters was studied after specific perturbations, especially those involving sudden changes in the duration of the G₁ phase of the cell cycle (chalone action). It was demonstrated that mere prolongation of the G₁ phase can lead to tumor regression. The results also showed that it is sometimes difficult, if not impossible, intuitively to reach a correct interpretation of seemingly unequivocal biological data and, hence, that conclusions regarding cell population kinetics are hazardous without the aid of a rigorous model.     

A Gene Regulatory Program for Meiotic Prophase in the Fetal Ovary

The chromosomal program of meiotic prophase, comprising events such as laying down of meiotic cohesins, synapsis between homologs, and homologous recombination, must be preceded and enabled by the regulated induction of meiotic prophase genes. This gene regulatory program is poorly understood, particularly in organisms with a segregated germline. We characterized the gene regulatory program of meiotic prophase as it occurs in the mouse fetal ovary. By profiling gene expression in the mouse fetal ovary in mutants with whole tissue and single-cell techniques, we identified 104 genes expressed specifically in pre-meiotic to pachytene germ cells. We characterized the regulation of these genes by 1) retinoic acid (RA), which induces meiosis, 2) Dazl, which is required for germ cell competence to respond to RA, and 3) Stra8, a downstream target of RA required for the chromosomal program of meiotic prophase. Initial induction of practically all identified meiotic prophase genes requires Dazl. In the presence of Dazl, RA induces at least two pathways: one Stra8-independent, and one Stra8-dependent. Genes vary in their induction by Stra8, spanning fully Stra8-independent, partially Stra8-independent, and fully Stra8-dependent. Thus, Stra8 regulates the entirety of the chromosomal program but plays a more nuanced role in governing the gene expression program. We propose that Stra8-independent gene expression enables the stockpiling of selected meiotic structural proteins prior to the commencement of the chromosomal program. Unexpectedly, we discovered that Stra8 is required for prompt down-regulation of itself and Rec8. Germ cells that have expressed and down-regulated Stra8 are refractory to further Stra8 expression. Negative feedback of Stra8, and subsequent resistance to further Stra8 expression, may ensure a single, restricted pulse of Stra8 expression. Collectively, our findings reveal a gene regulatory logic by which germ cells prepare for the chromosomal program of meiotic prophase, and ensure that it is induced only once.     

Peak High-Frequency HRV and Peak Alpha Frequency Higher in PTSD

Posttraumatic stress disorder (PTSD) is difficult to treat and current PTSD treatments are not effective for all people. Despite limited evidence for its efficacy, some clinicians have implemented biofeedback for PTSD treatment. As a first step in constructing an effective biofeedback treatment program, we assessed respiration, electroencephalography (EEG) and heart rate variability (HRV) as potential biofeedback parameters for a future clinical trial. This cross-sectional study included 86 veterans; 59 with and 27 without PTSD. Data were collected on EEG measures, HRV, and respiration rate during an attentive resting state. Measures were analyzed to assess sensitivity to PTSD status and the relationship to PTSD symptoms. Peak alpha frequency was higher in the PTSD group (F(1,84) = 6.14, p = 0.01). Peak high-frequency HRV was lower in the PTSD group (F(2,78) = 26.5, p < 0.00005) when adjusting for respiration rate. All other EEG and HRV measures and respiration were not different between groups. Peak high-frequency HRV and peak alpha frequency are sensitive to PTSD status and may be potential biofeedback parameters for future PTSD clinical trials.     

AutoDecon, a deconvolution algorithm for identification and characterization of luteinizing hormone secretory bursts: description and validation using synthetic data

Hormone signaling is often pulsatile, and multiparameter deconvolution procedures have long been used to identify and characterize secretory events. However, the existing programs have serious limitations, including the subjective nature of initial peak selection, lack of statistical verification of presumed bursts, and user-unfriendliness of the application. Here we describe a novel deconvolution program, AutoDecon, which addresses these concerns. We validate AutoDecon for application to serum luteinizing hormone (LH) concentration time series using synthetic data mimicking real data from normal women and then comparing the performance of AutoDecon with the performance of the widely employed hormone pulsatility analysis program Cluster. The sensitivity of AutoDecon is higher than that of Cluster (∼ 96% vs. 80%, P = 0.001). However, Cluster had a lower false-positive detection rate than did AutoDecon (6% vs. 1%, P = 0.001). Further analysis demonstrated that the pulsatility parameters recovered by AutoDecon were indistinguishable from those characterizing the synthetic data and that sampling at 5- or 10-min intervals was optimal for maximizing the sensitivity rates for LH. Accordingly, AutoDecon presents a viable nonsubjective alternative to previous pulse detection algorithms for the analysis of LH data. It is applicable to other pulsatile hormone concentration time series and many other pulsatile phenomena. The software is free and downloadable at http://mljohnson.pharm.virginia.edu/home.html.     

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.     

Exercise training in childhood-onset systemic lupus erythematosus: a controlled randomized trial

Introduction

Exercise training has emerged as a promising therapeutic strategy to counteract physical dysfunction in adult systemic lupus erythematosus. However, no longitudinal studies have evaluated the effects of an exercise training program in childhood-onset systemic lupus erythematosus (C-SLE) patients. The objective was to evaluate the safety and the efficacy of a supervised aerobic training program in improving the cardiorespiratory capacity in C-SLE patients.

Methods

Nineteen physically inactive C-SLE patients were randomly assigned into two groups: trained (TR, n = 10, supervised moderate-intensity aerobic exercise program) and non-trained (NT, n = 9). Gender-, body mass index (BMI)- and age-matched healthy children were recruited as controls (C, n = 10) for baseline (PRE) measurements only. C-SLE patients were assessed at PRE and after 12 weeks of training (POST). Main measurements included exercise tolerance and cardiorespiratory measurements in response to a maximal exercise (that is, peak VO₂, chronotropic reserve (CR), and the heart rate recovery (ΔHRR) (that is, the difference between HR at peak exercise and at both the first (ΔHRR1) and second (ΔHRR2) minutes of recovery after exercise).

Results

The C-SLE NT patients did not present changes in any of the cardiorespiratory parameters at POST (P > 0.05). In contrast, the exercise training program was effective in promoting significant increases in time-to-exhaustion (P = 0.01; ES = 1.07), peak speed (P = 0.01; ES = 1.08), peak VO₂ (P = 0.04; ES = 0.86), CR (P = 0.06; ES = 0.83), and in ΔHRR1 and ΔHRR2 (P = 0.003; ES = 1.29 and P = 0.0008; ES = 1.36, respectively) in the C-SLE TR when compared with the NT group. Moreover, cardiorespiratory parameters were comparable between C-SLE TR patients and C subjects after the exercise training intervention, as evidenced by the ANOVA analysis (P > 0.05, TR vs. C). SLEDAI-2K scores remained stable throughout the study.

Conclusion

A 3-month aerobic exercise training was safe and capable of ameliorating the cardiorespiratory capacity and the autonomic function in C-SLE patients.

Trial registration

NCT01515163.     

Safety and possible effects of low-intensity resistance training associated with partial blood flow restriction in polymyositis and dermatomyositis

Introduction

Our aim was to evaluate the safety and efficacy of a low-intensity resistance training program combined with partial blow flow restriction (BFR training) in a cohort of patients with polymyositis (PM) and dermatomyositis (DM).

Methods

In total, 13 patients with PM and DM completed a 12-week twice a week low-intensity (that is, 30% one-repetition-maximum (1RM)) resistance exercise training program combined with partial blood flow restriction (BFR). Assessments of muscle strength, physical function, quadriceps cross sectional (CSA) area, health-related quality of life, and clinical and laboratory parameters were assessed at baseline and after the intervention.

Results

The BFR training program was effective in increasing the maximal dynamic strength in both the leg-press (19.6%, P <0.001) and knee-extension exercises (25.2% P <0.001), as well as in the timed-stands (15.1%, P <0.001) and timed-up-and-go test (−4.5%, P =0.002). Quadriceps CSA was also significantly increased after the intervention (4.57%, P =0.01). Similarly, all of the components of the Short Form-36 Health Survey, the Health Assessment Questionnaire scores, and the patient- and physician reported Visual Analogue Scale were significantly improved after training (P <0.05). Importantly, no clinical evidence or any other self-reported adverse event were found. Laboratory parameters (creatine kinase and aldolase) were also unchanged (P >0.05) after the intervention.

Conclusions

We demonstrated that a 12-week supervised low-intensity resistance training program associated with partial blood flow restriction may be safe and effective in improving muscle strength and function as well as muscle mass and health-related quality of life in patients with PM and DM.

Trial registration

Clinicaltrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01501019","term_id":"NCT01501019"}}NCT01501019. Registered November 29, 2011.     

A comparison of approaches to estimate the inbreeding coefficient and pairwise relatedness using genomic and pedigree data in a sheep population

Genome-wide SNP data provide a powerful tool to estimate pairwise relatedness among individuals and individual inbreeding coefficient. The aim of this study was to compare methods for estimating the two parameters in a Finnsheep population based on genome-wide SNPs and genealogies, separately. This study included ninety-nine Finnsheep in Finland that differed in coat colours (white, black, brown, grey, and black/white spotted) and were from a large pedigree comprising 319 119 animals. All the individuals were genotyped with the Illumina Ovine SNP50K BeadChip by the International Sheep Genomics Consortium. We identified three genetic subpopulations that corresponded approximately with the coat colours (grey, white, and black and brown) of the sheep. We detected a significant subdivision among the colour types (F _ST = 5.4%, P<0.05). We applied robust algorithms for the genomic estimation of individual inbreeding (F _SNP) and pairwise relatedness (Φ _SNP) as implemented in the programs KING and PLINK, respectively. Estimates of the two parameters from pedigrees (F _PED and Φ _PED) were computed using the RelaX2 program. Values of the two parameters estimated from genomic and genealogical data were mostly consistent, in particular for the highly inbred animals (e.g. inbreeding coefficient F>0.0625) and pairs of closely related animals (e.g. the full- or half-sibs). Nevertheless, we also detected differences in the two parameters between the approaches, particularly with respect to the grey Finnsheep. This could be due to the smaller sample size and relative incompleteness of the pedigree for them.We conclude that the genome-wide genomic data will provide useful information on a per sample or pairwise-samples basis in cases of complex genealogies or in the absence of genealogical data.