Diagnosing Aging: I. Problem of Reliability of Linear Regression Models of Biological Age

The problem of the reliability of linear regression models of biological age assessment was studied using an experimental population of patients of a geroprophylactic center. The main factors of the model quality (interpopulation difference, method of approximation of biological age, and methods of approximation of statistical significance of parameters of biological age models) were tested. New equations were derived for calculating biological age. All parameters of these equations meet the requirements of significance. It was shown that if the nonlinear character of age dynamics of biological markers of aging and the statistical significance of model parameter estimates are taken into account, the model of biological age is substantially simplified and its reliability increases.     

Immunological markers of ageing

Ageing is a process involving morphological and physiological modifications that gradually appear with time and lead to death. Given the heterogeneous nature of the process among individuals and among the different organs, tissues, and systems in the same individual, the concept of has been developed. The search for parameters that enable us to evaluate biological age--and therefore longevity--and the analysis of the efficacy of strategies to retard the ageing process are the objectives of gerontology. At present, one of the most important theories of ageing is the theory. Given that immune cell function is an excellent marker of health, we review the concepts that enable different functional and oxidative stress parameters in immune cells to be identified as markers of biological age and longevity. None of these parameters is universally accepted as a biomarker of ageing, although they are becoming increasingly important.     

A probabilistic model of biological ageing of the lungs for analysing the effects of smoking,asthma and COPD

Background

Although a large body of literature is available that describes the effects of smoking, asthma and COPD on lung function, most studies are restricted to a small age range and to one factor. As a consequence, available results are incomplete and often difficult to compare, also due to the ways the effects are expressed. Furthermore, current approaches consider one type of measurement only or several types separately.

Methods

We propose a probabilistic model that expresses the effects as number of years added to chronological age or, in other words, that estimates the biological age of the lungs. Using biological age as a measure of the effects has the advantage of facilitating the understanding of their severity and comparison of results. In our model, chronological age and other factors affecting the health status of the lungs generate biological age, which in turn generates lung function measurements. This structure enables the use of multiple types of measurement to obtain a more precise estimate of the effects and parameter sharing for characterization over large age ranges and of co-occurrence of factors with little data. We treat the parameters that model smoking habits and lung diseases as random variables to obtain uncertainty in the estimated effects.

Results

We use the model to investigate the effects of smoking, asthma and COPD on the TwinsUK Registry. Our results suggest that the combination of smoking with lung disease(s) has higher effect than smoking or lung disease(s) alone, and that in smokers, co-occurrence of asthma and COPD is more detrimental than asthma or COPD alone.

Conclusions

The proposed model or other models based on a similar approach could be of help in improving the understanding of factors affecting lung function by enabling characterizations over large age ranges and of co-occurrence of factors with little data and the use of multiple types of measurement. The software implementing the model can be downloaded at the first author’s webpage.     

Markers of cellular senescence in zero hour biopsies predict outcome in renal transplantation

Although chronological donor age is the most potent predictor of long-term outcome after renal transplantation, it does not incorporate individual differences of the aging-process itself. We therefore hypothesized that an estimate of biological organ age as derived from markers of cellular senescence in zero hour biopsies would be of higher predictive value. Telomere length and mRNA expression levels of the cell cycle inhibitors CDKN2A (p16INK4a) and CDKN1A (p21WAF1) were assessed in pre-implantation biopsies of 54 patients and the association of these and various other clinical parameters with serum creatinine after 1 year was determined. In a linear regression analysis, CDKN2A turned out to be the best single predictor followed by donor age and telomere length. A multiple linear regression analysis revealed that the combination of CDKN2A values and donor age yielded even higher predictive values for serum creatinine 1 year after transplantation. We conclude that the molecular aging marker CDKN2A in combination with chronological donor age predict renal allograft function after 1 year significantly better than chronological donor age alone.     

Kinetic model of Proteus mirabilis swarm colony development

 Proteus mirabilis colonies display striking symmetry and periodicity. Based on experimental observations of cellular differentiation and group motility, a kinetic model has been developed to describe the swarmer cell differentiation-dedifferentiation cycle and the spatial evolution of swimmer and swarmer cells during Proteus mirabilis swarm colony development. A key element of the model is the age dependence of swarmer cell behaviour, in particular specifying a minimal age for motility and maximum age for septation and dedifferentiation to swimmer cells. Density thresholds for collective motility by mature swarmer cells serve to synchronize the movements of distinct swarmer cell groups and thus help provide temporal coherence to colony expansion cycles. Numerical computations show that the model fits experimental data by generating a complete swarming plus consolidation cycle period that is robust to changes in parameters which affect other aspects of swarmer cell migration and colony development. The kinetic equations underlying this model provide a different mathematical basis for a temporal oscillator from reaction-diffusion partial differential equations. The modelling shows that Proteus colony geometries arise as a consequence of macroscopic rules governing collective motility. Thus, in this case, pattern formation results from the operation of an adaptive bacterial system for spreading on solid substrates, not as an independent biological function. Kinetic models similar to this one may be applicable to periodic phenomena displayed by other biological systems with differentiated components of defined lifetimes. Received 3 July 1996; received in revised form 9 December 1996     

Making the most of survey data: Incorporating age uncertainty when fitting growth parameters

Individual growth is an important parameter and is linked to a number of other biological processes. It is commonly modeled using the von Bertalanffy growth function (VBGF), which is regularly fitted to age data where the ages of the animals are not known exactly but are binned into yearly age groups, such as fish survey data. Current methods of fitting the VBGF to these data treat all the binned ages as the actual ages. We present a new VBGF model that combines data from multiple surveys and allows the actual age of an animal to be inferred. By fitting to survey data for Atlantic herring (Clupea harengus) and Atlantic cod (Gadus morhua), we compare our model with two other ways of combining data from multiple surveys but where the ages are as reported in the survey data. We use the fitted parameters as inputs into a yield‐per‐recruit model to see what would happen to advice given to management. We found that each of the ways of combining the data leads to different parameter estimates for the VBGF and advice for policymakers. Our model fitted to the data better than either of the other models and also reduced the uncertainty in the parameter estimates and models used to inform management. Our model is a robust way of fitting the VBGF and can be used to combine data from multiple sources. The model is general enough to fit other growth curves for any taxon when the age of individuals is binned into groups.     

Parameter Estimation and Model Selection in Computational Biology

A central challenge in computational modeling of biological systems is the determination of the model parameters. Typically, only a fraction of the parameters (such as kinetic rate constants) are experimentally measured, while the rest are often fitted. The fitting process is usually based on experimental time course measurements of observables, which are used to assign parameter values that minimize some measure of the error between these measurements and the corresponding model prediction. The measurements, which can come from immunoblotting assays, fluorescent markers, etc., tend to be very noisy and taken at a limited number of time points. In this work we present a new approach to the problem of parameter selection of biological models. We show how one can use a dynamic recursive estimator, known as extended Kalman filter, to arrive at estimates of the model parameters. The proposed method follows. First, we use a variation of the Kalman filter that is particularly well suited to biological applications to obtain a first guess for the unknown parameters. Secondly, we employ an a posteriori identifiability test to check the reliability of the estimates. Finally, we solve an optimization problem to refine the first guess in case it should not be accurate enough. The final estimates are guaranteed to be statistically consistent with the measurements. Furthermore, we show how the same tools can be used to discriminate among alternate models of the same biological process. We demonstrate these ideas by applying our methods to two examples, namely a model of the heat shock response in E. coli, and a model of a synthetic gene regulation system. The methods presented are quite general and may be applied to a wide class of biological systems where noisy measurements are used for parameter estimation or model selection.     

Combined segregation and linkage analysis of genetic hemochromatosis using affection status, serum iron, and HLA.

Characterizing the distribution of parameters of iron metabolism by hemochromatosis genotype remains an important goal vis-à-vis potential screening strategies to identify individuals at genetic risk, since a specific marker to detect the abnormal gene has not been identified as yet. In the present investigation, we analyze serum iron values in ascertained families using a method which incorporates both segregation of the clinical affection status and the HLA linkage information to identify the underlying genotypes. The analysis is performed using an extension of the model presented by Bonney et al., comprising regressive models for segregation analysis and the multipoint linkage strategy implemented in LINKAGE. The gene was found to be completely recessive with respect to both clinical manifestations and serum iron abnormalities, with significant differences in expression by sex. Clinical manifestations were present for all male homozygotes in this data set, suggesting that the recessive hemochromatosis genotype is fully penetrant at all ages in males. This was not the case for younger females. Significant genotype-specific age and sex effects were found for serum iron values. It is interesting that deletion of the HLA marker information did not affect our ability to resolve the genetic model when we analyzed a bivariate phenotype. This serves as a reminder that a search for relevant biological markers can be equally important in discerning the genetic etiology of a disease trait, as a search for linked genetic markers.     

A multi-stage model of adenoma development

The overwhelming proportion of colorectal carcinomas are believed to originate as adenomatous polyps (adenomas), and the identification and removal of adenomas is an important component of colorectal cancer prevention efforts. Mathematical modeling of adenomas can increase our understanding of the natural history and biology of adenomas and colorectal cancer and can help in the effort to devise optimal prevention and screening strategies. Here we adapt the multi-stage model of carcinogenesis to the problem of the development and growth of adenomas. We show that, using plausible values for the biological parameters, the model can fit various aspects of adenoma data including adenoma prevalence by age, the size distribution of adenomas, clustering of adenomas within individuals and the correlation between distal and proximal adenomas. Explaining the clustering of adenomas within individuals, as well as other findings, requires heterogeneity in risk in the population; we show how such heterogeneity can be related to the distribution of biological parameters in the population. The model can also be adapted to account for adenoma development in two major syndromes related to colorectal cancer, familial adenomatous polyposis and hereditary non-polyposis colorectal cancer.     

A Conceptual Framework for the Interpretation of Biological Markers for Environmental Exposure Assessment

Human exposure to environmental contaminants occurs via air, water, soil, dust, food, and other environmental media. Given this multitude of sources, environmental exposure assessment is moving away from single route exposure assessment to more integrated measures of exposure. Biological markers are frequently advocated as appropriate exposure assessment tools since they provide a measure of internal dose integrated over all routes of exposure. However, contributing sources may be difficult to identify through use of biological markers, and thus, have had limited utility in the regulatory community. To explore the different perspectives on the use and application of biological markers for exposure assessors, epidemiologists, and regulatory personnel, we have developed a biological marker conceptual framework. This framework is developed as a paradigm for the interpretation of biological markers for environmental exposure assessment linking the exposure assessment and the health effects assessment perspectives regarding biological markers. Further, it incorporates issues of source-specific exposures, aggregate exposure assessment, route-specific contributions, and biological variation in response to exposure. This structure provides an approach to explore the current constraints in using biological markers to evaluate source-specific exposures. This framework is discussed in the context of currently available biological markers for lead, carbon monoxide, and toluene. Biological markers represent a complex tool to assess human exposures to environmental contaminants; the biological marker framework presents a structure for their interpretation recognizing that many of the determinants of exposure, bioavailablity, and toxicokinetics are still being evaluated. The conceptual framework presented here provides another tool for the researcher in assessing the utility of biological markers in exposure assessment and epidemiology.     

The metabolome as a biomarker of aging in Drosophila melanogaster

Many biomarkers have been shown to be associated not only with chronological age but also with functional measures of biological age. In human populations, it is difficult to show whether variation in biological age is truly predictive of life expectancy, as such research would require longitudinal studies over many years, or even decades. We followed adult cohorts of 20 Drosophila Genetic Reference Panel (DGRP) strains chosen to represent the breadth of lifespan variation, obtain estimates of lifespan, baseline mortality, and rate of aging, and associate these parameters with age‐specific functional traits including fecundity and climbing activity and with age‐specific targeted metabolomic profiles. We show that activity levels and metabolome‐wide profiles are strongly associated with age, that numerous individual metabolites show a strong association with lifespan, and that the metabolome provides a biological clock that predicts not only sample age but also future mortality rates and lifespan. This study with 20 genotypes and 87 metabolites, while relatively small in scope, establishes strong proof of principle for the fly as a powerful experimental model to test hypotheses about biomarkers and aging and provides further evidence for the potential value of metabolomic profiles as biomarkers of aging.     

Diagnosis of Aging. Report II. Age Dynamics of Correlation between the Biological Markers of Aging

The correlation analysis of the relationship between the biological age markers in three age groups revealed alterations in the number and rate of correlations up to the inversion of these relations in some cases. As a whole, the observed changes can be characterized as a rearrangement at the regulatory interactions with an increase at the strain of the functioning of the body organs and systems at the middle age and an alteration in the coordination of the body system functioning at the elderly age. The ways of the optimization of the standard methods for the biological age measurement are discussed with regard to these changes.     

Partitioning of genomic variance reveals biological pathways associated with udder health and milk production traits in dairy cattle

Background

We have used a linear mixed model (LMM) approach to examine the joint contribution of genetic markers associated with a biological pathway. However, with these markers being scattered throughout the genome, we are faced with the challenge of modelling the contribution from several, sometimes even all, chromosomes at once. Due to linkage disequilibrium (LD), all markers may be assumed to account for some genomic variance; but the question is whether random sets of markers account for the same genomic variance as markers associated with a biological pathway?

Results

We applied the LMM approach to identify biological pathways associated with udder health and milk production traits in dairy cattle. A random gene sampling procedure was applied to assess the biological pathways in a dataset that has an inherently complex genetic correlation pattern due to the population structure of dairy cattle, and to linkage disequilibrium within the bovine genome and within the genes associated to the biological pathway.

Conclusions

Several biological pathways that were significantly associated with health and production traits were identified in dairy cattle; i.e. the markers linked to these pathways explained more of the genomic variance and provided a better model fit than 95 % of the randomly sampled gene groups. Our results show that immune related pathways are associated with production traits, and that pathways that include a causal marker for production traits are identified with our procedure.We are confident that the LMM approach provides a general framework to exploit and integrate prior biological information and could potentially lead to improved understanding of the genetic architecture of complex traits and diseases.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0132-6) contains supplementary material, which is available to authorized users.     

Leukocyte telomere length in the Thoroughbred racehorse

Thoroughbred racehorses possess superior cardiorespiratory fitness levels and are at the pinnacle of athletic performance compared to other breeds of horses. Although equine athletes have undergone years of artificial selection for racing performance, musculoskeletal injuries and illnesses are common and concerns relating to animal welfare have been proposed. Leukocyte telomere length is indicative of biological age, and accelerated telomere shortening occurs with excess physical and psychological stress. This study was designed to explore the association between leukocyte telomere length, biological factors (age, sex and coat colour), training status, winnings and race history parameters. Blood was collected from 146 Thoroughbred racehorses from around Geelong, Victoria, Australia. DNA was extracted from leukocytes; telomere length was measured using qPCR and analysed in context with traits obtained from the Racing Australia website. Age was inversely correlated with telomere length (r = ?0.194, P = 0.019). The oldest horses (≥11 years) in the highest age quartile possessed shorter telomeres compared to younger horses in the first, second and third quartiles (≤2, 3–5 and 6–10 years respectively; P < 0.05). No statistically significant associations were observed between telomere length and biological factors, training status, winnings or race history parameters in age‐adjusted analyses. The study findings suggest that Thoroughbred horses may undergo age‐related telomere shortening similar to other mixed breeds and humans. Despite concerns from some quarters regarding the welfare of racehorses, there was a lack of accelerated biological ageing observed in the present study, as indicated by leukocyte telomere length.     

Genome-wide association studies for the number of teats and teat asymmetry patterns in Large White pigs

The number of teats is a morphological trait that influences the mothering ability of the sows and thus their reproduction performances. In this study, we carried out GWASs for the total number of teats and other 12 related parameters in 821 Italian Large White heavy pigs. All pigs were genotyped with the Illumina PorcineSNP60 BeadChip array. For four investigated parameters (total number of teats, the number of teats of the left line, the number of teats of the right line and the maximum number of teats comparing the two sides), significant markers were identified on SSC7, in the region of the vertnin (VRTN) gene. Significant markers for the numbers of posterior teats and the absolute difference between anterior and posterior teat numbers were consistently identified on SSC6. The most significant SNP for these parameters was an intron variant in the TOX high mobility group box family member 3 (TOX3) gene. For the other four parameters (absolute difference between the two sides; anterior teats; the ratio between the posterior and the anterior number of teats; and the absence or the presence of extra teats) only suggestively significant markers were identified on several other chromosomes. This study further supported the role of the VRTN gene region in affecting the recorded variability of the number of teats in the Italian Large White pig population and identified a genomic region potentially affecting the biological mechanisms controlling the developmental programme of morphological features in pigs.     

Study on the toxic effects of pharmaceutical drugs – Norfloxacin using Pangasius Sp. fish model and its mitigation using Artemisia pallens

In the present times, international environmental regulations are earnest on the risk caused by the release of toxins into the aquatic biome; predominantly the water bodies. The discharge of active pharmaceutical compounds in the environment is found to have fatal effects on the biota of the oceanic ecosystem. The key objective of the study is to scrutinize the toxicological reprecussion of norfloxacin, an antibiotic used to treat bacterial infections which being prescribed as human medicine was found to have the possibility to pollute the water resource and sediments via input from sewage treatment plants. To explicate this study, Pangasius sp. The fish model was tested with the drug and its effects were studied thereby. This study focuses on the oxidative stress parameters which can be probed by virtue of biological markers, hormonal changes after acclimatizing the fish at suitable LC₅₀ concentration of norfloxacin and the tissue damage assessed using histopathological analysis. The oxidative stress parameters were procured by analysis of biological markers such as Lipid peroxides, Conjugated diene, Protein sulfhydryl, Protein Carbonyl, Inorganic phosphorus, Superoxide dismutase and Catalase. The hormonal changes were studied concerning the changes in cortisol levels, which are influenced by oxidative stress. The mitigation effect and hepato-protective activity of Artemisia pallens were also studied with Norfloxacin treated fish, to imbibe the bioremediation as a strategic upfront for remediation.     

Genetic and family structure in a group of 165 common bottlenose dolphins caught off the Japanese coast

The biological and genetic structure of common bottlenose dolphins (Tursiops truncatus) that migrate seasonally near Japan remains largely unknown. We investigated the genetic and family structure in a group of 165 common bottlenose dolphins caught off the coast of Japan using mitochondrial DNA (mtDNA) and 20 microsatellite DNA markers. Phylogenetic analysis of the mtDNA control region sequences suggested that the dolphins were related more closely to oceanic types from Chinese waters than other geographic regions. The information on sex, sexual maturation and age together with the genetic markers revealed a strong likelihood for 37 familial relationships related mostly to maternity and an under‐representation of juvenile female offspring. The maternal dolphins had a similar offspring‐birth interval as the coastal types from North Atlantic Ocean, but a slightly younger first‐progeny age. The sex bias in the captured group was particularly marked towards an over‐representation of males among the young and immature dolphins, whereas the mature adults had an equal number of males and females. These results should be useful for future comparative biological, genetic and evolutionary investigations of bottlenose dolphins from the North Pacific Ocean with those from other regions.     

RADseq as a valuable tool for plants with large genomes—A case study in cycads

Full genome sequencing of organisms with large and complex genomes is intractable and cost ineffective under most research budgets. Cycads (Cycadales) represent one of the oldest lineages of the extant seed plants and, partly due to their age, have incredibly large genomes up to ~60 Gbp. Restriction site‐associated DNA sequencing (RADseq) offers an approach to find genome‐wide informative markers and has proven to be effective with both model and nonmodel organisms. We tested the application of RADseq using ezRAD across all 10 genera of the Cycadales including an example data set of Cycas calcicola representing 72 samples from natural populations. Using previously available plastid and mitochondrial genomes as references, reads were mapped recovering plastid and mitochondrial genome regions and nuclear markers for all of the genera. De novo assembly generated up to 138,407 high‐depth clusters and up to 1,705 phylogenetically informative loci for the genera, and 4,421 loci for the example assembly of C. calcicola. The number of loci recovered by de novo assembly was lower than previous RADseq studies, yet still sufficient for downstream analysis. However, the number of markers could be increased by relaxing our assembly parameters, especially for the C. calcicola data set. Our results demonstrate the successful application of RADseq across the Cycadales to generate a large number of markers for all genomic compartments, despite the large number of plastids present in a typical plant cell. Our modified protocol was adapted to be applied to cycads and other organisms with large genomes to yield many informative genome‐wide markers.     

Inverse analysis of constitutive models: biological soft tissues

The paper describes a procedure for estimating the material parameters of biological soft tissue by fitting model prediction to experimental load-deformation data. This procedure minimizes the error between data and theoretical model prediction through systematically adjusting the parameters in the latter. The procedure uses commercially available software and is not specific to any particular model; nevertheless, for illustration purposes, we employ a six parameter fibril-reinforced poroelastic cartilage model. We are able to estimate any and all of these parameters by the procedure. Convergence of the parameters and convergence of the arbitrary initial stress relaxation to the data was demonstrated in all cases. Though we illustrate the optimization procedure here for unconfined compression only, it can be adapted easily to other experimental configurations such as confined compression, indentation and tensile test. Furthermore, the procedure can be applied in other areas of biomechanics where material parameters need to be extracted from experimental data.