Using birth-death processes to infer tumor subpopulation structure from live-cell imaging drug screening data

Tumor heterogeneity is a complex and widely recognized trait that poses significant challenges in developing effective cancer therapies. In particular, many tumors harbor a variety of subpopulations with distinct therapeutic response characteristics. Characterizing this heterogeneity by determining the subpopulation structure within a tumor enables more precise and successful treatment strategies. In our prior work, we developed PhenoPop, a computational framework for unravelling the drug-response subpopulation structure within a tumor from bulk high-throughput drug screening data. However, the deterministic nature of the underlying models driving PhenoPop restricts the model fit and the information it can extract from the data. As an advancement, we propose a stochastic model based on the linear birth-death process to address this limitation. Our model can formulate a dynamic variance along the horizon of the experiment so that the model uses more information from the data to provide a more robust estimation. In addition, the newly proposed model can be readily adapted to situations where the experimental data exhibits a positive time correlation. We test our model on simulated data (in silico) and experimental data (in vitro), which supports our argument about its advantages.

Genetic Music System with Synthetic Biology

This article introduces GeMS, a system for music composition informed by synthetic biology. GeMS generates music with simulations of genetic processes, such as transcription, translation, and protein folding, with which biological systems render chains of amino acids from DNA strands. The system comprises the following components: the Miranda machine, the rhythmator, and the pitch processor. The Miranda machine is an abstract Turing-machine-like processor, which manipulates a sequence of DNA symbols according to a set of programming instructions. This process generates a pool of new DNA strands, which are subsequently translated into rhythms. GeMS represents the musical equivalent of amino acids in terms of rhythms, referred to as rhythmic codons. This enables the rhythmator to convert DNA sequences into rhythmic sequences. The pitch processor generates pitches for such rhythmic sequences. It is inspired by the phenomenon of protein folding. The pitch processor considers orientation information of DNA instructions yielded by the Miranda machine in order to activate algorithms for generating pitches. A musical composition, entitled Artibiotics, for percussion ensemble and electronic instruments, is presented to demonstrate the system.

The Ethics of Precision Rationing: Human Genetics and the Need for Debate on Stratifying Access to Medication

Rising prices for new, transformative therapies are challenging health systems around the world, leading many payers and providers to begin rationing access to treatments, even in the countries that have been most resistant to doing so. This is the case for direct-acting antivirals (DAAs) for the treatment of hepatitis C virus (HCV). However, little attention has been paid to the increasing role that human genetics might play in rationing decisions. Researchers have already proposed that genetic markers associated with spontaneous HCV clearance could be used to restrict DAA access for some patients, although treatment would be medically beneficial for those patients. Would such forms of rationing present a form of genetic discrimination? And what of the public health implications of these approaches? Here we present an ethical analysis of such proposals for "precision rationing" and raise 4 key areas of concern. We argue that ethical issues arising in this area are not substantively different from the pressing ethical issues regarding rationing and discrimination more broadly, but provide important impetus for motivating broad public debate to find ethically sound ways of managing genomics and new expensive medications.

[RNAissance: is there a future for RNA therapeutics?]

The central dogma in molecular biology states that genetic information is transmitted from DNA to RNA to proteins, but not the other way round. Thanks to a recent technological revolution - the 'RNAissance' - it has, however, become clear that RNA is not solely a messenger for passing on the genetic information necessary for protein synthesis, but that RNA also plays an important role in sickness and health. In the past 5 years alone more than 100 therapies with (complementary) RNA molecules have been investigated in Phase 1 trials, and a quarter of these have also been investigated in Phase 2 or 3 trials. The dramatic increase in the number of pharmaceutical companies that are developing RNA therapeutics illustrates the enormous potential of these medicines. Once the toxicity and the costs of RNA therapeutics can be limited, these medicines - personalized or not - could soon be prescribed for patients with a wide range of chronic conditions.

Evolved Transistor Array Robot Controllers

For the first time, a field programmable transistor array (FPTA) was used to evolve robot control circuits directly in analog hardware. Controllers were successfully incrementally evolved for a physical robot engaged in a series of visually guided behaviours, including finding a target in a complex environment where the goal was hidden from most locations. Circuits for recognising spoken commands were also evolved and these were used in conjunction with the controllers to enable voice control of the robot, triggering behavioural switching. Poor quality visual sensors were deliberately used to test the ability of evolved analog circuits to deal with noisy uncertain data in realtime. Visual features were coevolved with the controllers to automatically achieve dimensionality reduction and feature extraction and selection in an integrated way. An efficient new method was developed for simulating the robot in its visual environment. This allowed controllers to be evaluated in a simulation connected to the FPTA. The controllers then transferred seamlessly to the real world. The circuit replication issue was also addressed in experiments where circuits were evolved to be able to function correctly in multiple areas of the FPTA. A methodology was developed to analyse the evolved circuits which provided insights into their operation. Comparative experiments demonstrated the superior evolvability of the transistor array medium.

Evolutionary Image Transition and Painting Using Random Walks

We present a study demonstrating how random walk algorithms can be used for evolutionary image transition. We design different mutation operators based on uniform and biased random walks and study how their combination with a baseline mutation operator can lead to interesting image transition processes in terms of visual effects and artistic features. Using feature-based analysis we investigate the evolutionary image transition behaviour with respect to different features and evaluate the images constructed during the image transition process. Afterwards, we investigate how modifications of our biased random walk approaches can be used for evolutionary image painting. We introduce an evolutionary image painting approach whose underlying biased random walk can be controlled by a parameter influencing the bias of the random walk and thereby creating different artistic painting effects.

What determines perceived income justice? Evidence from the German TwinLife study

Whether individuals perceive their income as being fair has far-reaching consequences in the labor market and beyond. Yet we know little about the determinants of variation in perceived income justice across individuals. In this paper, we ask to what extent differences in genes are related to variation in individuals' perceived income justice, and whether there is a gene-environment component. Analyzing data from the German TwinLife study, we find that more than 30% of individuals' perceived income justice can be attributed to genes. The rest is mostly related to an idiosyncratic environment.

Genetic Programming for Evolving Similarity Functions for Clustering: Representations and Analysis

Clustering is a difficult and widely studied data mining task, with many varieties of clustering algorithms proposed in the literature. Nearly all algorithms use a similarity measure such as a distance metric (e.g., Euclidean distance) to decide which instances to assign to the same cluster. These similarity measures are generally predefined and cannot be easily tailored to the properties of a particular dataset, which leads to limitations in the quality and the interpretability of the clusters produced. In this article, we propose a new approach to automatically evolving similarity functions for a given clustering algorithm by using genetic programming. We introduce a new genetic programming-based method which automatically selects a small subset of features (feature selection) and then combines them using a variety of functions (feature construction) to produce dynamic and flexible similarity functions that are specifically designed for a given dataset. We demonstrate how the evolved similarity functions can be used to perform clustering using a graph-based representation. The results of a variety of experiments across a range of large, high-dimensional datasets show that the proposed approach can achieve higher and more consistent performance than the benchmark methods. We further extend the proposed approach to automatically produce multiple complementary similarity functions by using a multi-tree approach, which gives further performance improvements. We also analyse the interpretability and structure of the automatically evolved similarity functions to provide insight into how and why they are superior to standard distance metrics.

Students' Conception of Genetic Phenomena and Its Effect on Their Ability to Understand the Underlying Mechanism

Understanding genetic mechanisms affords the ability to provide causal explanations for genetic phenomena. These mechanisms are difficult to teach and learn. It has been shown that students sometimes conceive of genes as traits or as trait-bearing particles. We termed these "nonmechanistic" conceptions of genetic phenomena because they do not allow the space required for a mechanism to exist in the learner's mind. In this study, we investigated how ninth- and 12th-grade students' conceptions of genetic phenomena affect their ability to learn the underlying mechanisms. We found that ninth- and 12th-grade students with nonmechanistic conceptions are less successful at learning the mechanisms leading from gene to trait than students with mechanistic conceptions. Our results suggest that nonmechanistic conceptions of a phenomenon may create a barrier to learning the underlying mechanism. These findings suggest that an initial description of a phenomenon should hint at a mechanism even if the mechanism would be learned only later.

Mapping of the stochastic Lotka-Volterra model to models of population genetics and game theory

The relationship between the M-species stochastic Lotka-Volterra competition (SLVC) model and the M-allele Moran model of population genetics is explored via timescale separation arguments. When selection for species is weak and the population size is large but finite, precise conditions are determined for the stochastic dynamics of the SLVC model to be mappable to the neutral Moran model, the Moran model with frequency-independent selection, and the Moran model with frequency-dependent selection (equivalently a game-theoretic formulation of the Moran model). We demonstrate how these mappings can be used to calculate extinction probabilities and the times until a species' extinction in the SLVC model.

LEA gene expression, RNA stability and pigment accumulation in three closely related Linderniaceae species differing in desiccation tolerance

Desiccation-tolerant plants (Craterostigma plantagineum and Lindernia brevidens) evolved a highly efficient strategies to prevent dehydration-induced irreversible damage. The protection system involves synthesis of LEA proteins, decrease of photosynthetic activity and activation of antioxidant systems. The regulation of these processes requires joint action of multiple proteins. Here, we present comparative analyses of accumulation of transcripts encoding components of the protection machinery, such as selected LEA proteins, enzymes of the chlorophyll degradation pathway and anthocyanin biosynthesis enzymes in total and polysomal RNA pools. The analyses revealed that desiccation-tolerant plants recruit mRNAs to ribosomes with higher efficiency than the desiccation-sensitive species L. subracemosa. Desiccation-tolerant species accumulated high amounts of LEA transcripts during dehydration and precisely controlled the amounts of chlorophyll keeping it at a level sufficient to activate photosynthesis after rehydration. In contrast, mRNA of L. subracemosa was prone to dehydration-induced degradation, decomposition of the photosynthetic apparatus and degradation of free chlorophyll. Thus, the results of the studies point to differences in the control of gene expression and degradation of chlorophyll in desiccation-tolerant versus desiccation-sensitive species when the plants were subjected to dehydration.

Structured sparse CCA for brain imaging genetics via graph OSCAR

BACKGROUND

Recently, structured sparse canonical correlation analysis (SCCA) has received increased attention in brain imaging genetics studies. It can identify bi-multivariate imaging genetic associations as well as select relevant features with desired structure information. These SCCA methods either use the fused lasso regularizer to induce the smoothness between ordered features, or use the signed pairwise difference which is dependent on the estimated sign of sample correlation. Besides, several other structured SCCA models use the group lasso or graph fused lasso to encourage group structure, but they require the structure/group information provided in advance which sometimes is not available.

RESULTS

We propose a new structured SCCA model, which employs the graph OSCAR (GOSCAR) regularizer to encourage those highly correlated features to have similar or equal canonical weights. Our GOSCAR based SCCA has two advantages: 1) It does not require to pre-define the sign of the sample correlation, and thus could reduce the estimation bias. 2) It could pull those highly correlated features together no matter whether they are positively or negatively correlated. We evaluate our method using both synthetic data and real data. Using the 191 ROI measurements of amyloid imaging data, and 58 genetic markers within the APOE gene, our method identifies a strong association between APOE SNP rs429358 and the amyloid burden measure in the frontal region. In addition, the estimated canonical weights present a clear pattern which is preferable for further investigation.

CONCLUSIONS

Our proposed method shows better or comparable performance on the synthetic data in terms of the estimated correlations and canonical loadings. It has successfully identified an important association between an Alzheimer's disease risk SNP rs429358 and the amyloid burden measure in the frontal region.

Cerebral cortex expansion and folding: what have we learned?

One of the most prominent features of the human brain is the fabulous size of the cerebral cortex and its intricate folding. Cortical folding takes place during embryonic development and is important to optimize the functional organization and wiring of the brain, as well as to allow fitting a large cortex in a limited cranial volume. Pathological alterations in size or folding of the human cortex lead to severe intellectual disability and intractable epilepsy. Hence, cortical expansion and folding are viewed as key processes in mammalian brain development and evolution, ultimately leading to increased intellectual performance and, eventually, to the emergence of human cognition. Here, we provide an overview and discuss some of the most significant advances in our understanding of cortical expansion and folding over the last decades. These include discoveries in multiple and diverse disciplines, from cellular and molecular mechanisms regulating cortical development and neurogenesis, genetic mechanisms defining the patterns of cortical folds, the biomechanics of cortical growth and buckling, lessons from human disease, and how genetic evolution steered cortical size and folding during mammalian evolution.

To Cooperate or Not to Cooperate: Why Behavioural Mechanisms Matter

Mutualistic cooperation often requires multiple individuals to behave in a coordinated fashion. Hence, while the evolutionary stability of mutualistic cooperation poses no particular theoretical difficulty, its evolutionary emergence faces a chicken and egg problem: an individual cannot benefit from cooperating unless other individuals already do so. Here, we use evolutionary robotic simulations to study the consequences of this problem for the evolution of cooperation. In contrast with standard game-theoretic results, we find that the transition from solitary to cooperative strategies is very unlikely, whether interacting individuals are genetically related (cooperation evolves in 20% of all simulations) or unrelated (only 3% of all simulations). We also observe that successful cooperation between individuals requires the evolution of a specific and rather complex behaviour. This behavioural complexity creates a large fitness valley between solitary and cooperative strategies, making the evolutionary transition difficult. These results reveal the need for research on biological mechanisms which may facilitate this transition.

Heritability, family, school and academic achievement in adolescence

We demonstrate how genetically informed designs can be applied to administrative exam data to study academic achievement. ACE mixture latent class models have been used with Year 6 and 9 exam data for seven cohorts of Polish students which include 24,285 pairs of twins. Depending on a learning domain and classroom environment history, from 58% to 88% of variance in exam results is attributable to heritability, up to 34% to shared environment and from 8% to 15% depends on unique events in students' lives. Moreover, between 54% and 66% of variance in students' learning gains made between Years 6 and 9 is explained by heritability. The unique environment accounts for between 34% and 46% of that variance. However, we find no classroom effects on student progress made between Years 6 and 9. We situate this finding against the view that classroom peer groups and teachers matter for adolescent learning.

Research on laser marking speed optimization by using genetic algorithm

Laser Marking Machine is the most common coding equipment on product packaging lines. However, the speed of laser marking has become a bottleneck of production. In order to remove this bottleneck, a new method based on a genetic algorithm is designed. On the basis of this algorithm, a controller was designed and simulations and experiments were performed. The results show that using this algorithm could effectively improve laser marking efficiency by 25%.

[Association and interaction between 10 SNP of peroxisome proliferator-activated receptor and non-HDL-C]

OBJECTIVE

To examine the main effect of 10 Peroxisome proliferators-activated receptor (PPAR) SNP in contribution to non-HDL-C and study whether there is an interaction in the 10 SNPs.

METHODS

Participants were recruited within the framework of the PMMJS (Prevention of Multiple Metabolic Disorders and Metabolic Syndrome in Jiangsu province) cohort-population-survey, which was initiated from April 1999 to June 2004, and 5-year follow-up data from total 4 582 subjects were obtained between March 2006 and October 2007. A total of 4 083 participants received follow-up examination. After excluding subjects who had experienced stroke or exhibited cardiovascular disease, type 2 diabetes or a BMI <18.5 kg/m(2), a total of 820 unrelated individual subjects were selected from 3 731 subjects on October of 2009. Blood samples which were collected at the baseline were subjected to PPARα, PPARδ and PPARγ 10 SNPs genotype analysis. Logistic regression model was used to examine the association between 10 SNPs in the PPARs and non-HDL-C. Interactions within the 10 SNP were explored by using the Generalized Multifactor Dimensionality Reduction (GMDR).

RESULTS

A total of 820 participants (mean age was 50.05±9.41) were included in the study and 270 were males and 550 were females. Single-locus analysis showed that after adjusting gender, age, smoking, alcohol consumption, physical activity, high-fat diet and low-fiber diet factors, rs1800206-V and rs3856806-T were significantly associated with higher non-HDL-C levels. V allele (LV + VV genotype) carriers of rs1800206 have a average non-HDL-C levels on (3.15 ± 0.89)mg/L (F = 15.01, P = 0.002); T allele (CT+TT genotype) carriers of rs3856806 have a average non-HDL-C levels on (3.03±1.01) mg/L (F = 9.87, P = 0.005). GMDR model analysis showed that after adjusting the same factors, two-locus model, five-locus model, six-locus model and seven-order interaction models were all statistically significant (P<0.05), and the seven-locus model (rs1800206, rs3856806, rs135539, rs4253778, rs2016520, rs1805192, rs709158) was the best model (P = 0.001), the cross-validation consistency was 10/10 and testing accuracy was 0.656.

CONCLUSION

Rs1800206 and rs3856806 were significantly associated with non-HDL-C. And there was an gene-gene interaction among rs1800206, rs3856806, rs1800206, rs135539, rs4253778, rs2016520, rs1805192, rs3856806 and rs709158 which could influence the non-HDL-C levels.

IN SEARCH OF A FATHER: LEGAL CHALLENGES SURROUNDING POSTHUMOUS PATERNITY TESTING

This article interrogates the workings of the Human Tissue Act 2004, as it applies to paternity testing by DNA analysis after the death of the putative father. We use a case series methodology more usually seen in medical research, through which we present three real case studies involving posthumous paternity testing of retained tissue. We argue that the criminal offence in section 45 of the Human Tissue Act 2004, which is being used to regulate this activity, is inappropriate and inadequate to do so. The threat of the shadow of the criminal law is too blunt an instrument to address the subtleties of the issues that arise in the context of posthumous paternity testing. We call for reform of the Human Tissue Act 2004 and the creation of a specific exception to properly deal with requests of this nature.

[Genetic discrimination and the difficulties of its regulatory prohibition]

This article analyses the difficulties faced by the legal prohibition of genetic discrimination. It highlights the rationality and exceptionality of this kind of discrimination, its "private" nature, the doubtful status as suspect classification, its better fit with the neutrality approach than the non-subordination approach, and the need to replace the "perfection-imperfection" duality by the respect for genetic diversity.

Coming of age: orphan genes in plants

Sizable minorities of protein-coding genes from every sequenced eukaryotic and prokaryotic genome are unique to the species. These so-called ‘orphan genes’ may evolve de novo from non-coding sequence or be derived from older coding material. They are often associated with environmental stress responses and species-specific traits or regulatory patterns. However, difficulties in studying genes where comparative analysis is impossible, and a bias towards broadly conserved genes, have resulted in underappreciation of their importance. We review here the identification, possible origins, evolutionary trends, and functions of orphans with an emphasis on their role in plant biology. We exemplify several evolutionary trends with an analysis of Arabidopsis thaliana and present QQS as a model orphan gene.

Mater semper incertus est: who's your mummy?

In English law, the legal term for father has been given a broad definition but the definition of mother remains rooted in biology with the Roman law principle mater semper certa est (the mother is always certain) remaining the norm. However, motherhood may be acquired through giving birth to a child, by donation of gametes or by caring and nurturing a child so that the identity of the mother is no longer certain particularly in the case of surrogacy arrangements. While the law in the UK may automatically recognise the parental status of a commissioning father in a traditional surrogacy arrangement, the parental status of the commissioning mother is not automatically recognised in either a traditional or a gestational surrogacy arrangement. Thus the maxim mater est quam gestation demonstrat (meaning the mother is demonstrated by gestation) is also not approached consistently in the legal interpretation of parentage or motherhood in surrogacy as against other assisted reproduction methods. This raises questions about the extent to which motherhood should be affected by the method of reproduction and whether the sociological and philosophical concept of motherhood should, in the case of surrogacy, give rise to a new principle of 'mater semper incertus est' (the mother is uncertain). This article will argue that the time has come to move away from a legal definition of 'mother' that is based on biology to one that recognises the different forms of motherhood.

Genetic and environmental influences on negative life events from late childhood to adolescence

This multiwave longitudinal study tested two quantitative genetic developmental models to examine genetic and environmental influences on exposure to negative dependent and independent life events. Participants (N = 457 twin pairs) completed measures of life events annually from ages 9 to 16. The same genetic factors influenced exposure to dependent events across time and increased in magnitude during the transition to adolescence. Independent events were less genetically influenced than dependent events in boys, but not girls. Shared environmental influences decreased in magnitude as youth transitioned into adolescence. Nonshared environmental influences were mostly age specific and contributed significantly to both types of events at all ages. Results provide theoretical implications for developmental risk pathways to stress exposure and stress-related psychopathology.

Fetal and maternal genes' influence on gestational age in a quantitative genetic analysis of 244,000 Swedish births

Although there is increasing evidence that genetic factors influence gestational age, it is unclear to what extent this is due to fetal and/or maternal genes. In this study, we apply a novel analytical model to estimate genetic and environmental contributions to pregnancy history records obtained from 165,952 Swedish families consisting of offspring of twins, full siblings, and half-siblings (1987-2008). Results indicated that fetal genetic factors explained 13.1% (95% confidence interval (CI): 6.8, 19.4) of the variation in gestational age at delivery, while maternal genetic factors accounted for 20.6% (95% CI: 18.1, 23.2). The largest contribution to differences in the timing of birth were environmental factors, of which 10.1% (95% CI: 7.0, 13.2) was due to factors shared by births of the same mother, and 56.2% (95% CI: 53.0, 59.4) was pregnancy specific. Similar models fit to the same data dichotomized at clinically meaningful thresholds (e.g., preterm birth) resulted in less stable parameter estimates, but the collective results supported a model of homogeneous genetic and environmental effects across the range of gestational age. Since environmental factors explained most differences in the timing of birth, genetic studies may benefit from understanding the specific effect of fetal and maternal genes in the context of these yet-unidentified factors.

[Role of oxidative RNA damage in aging and neurodegenerative disorders]

It is now clear that RNA species not only encode proteins but also fulfill critical roles in regulating gene expression. Compared to other species, humans probably contain more non-coding RNAs, especially in the brain, where the non-coding RNAs may play a significant role in cognition. In neurons of human and rodent brains, oxidative damage to nucleic acids, predominantly to RNA, increases as a function of age; this may play a crucial role in the development of age-associated neurodegeneration. Indeed, compared to age-matched controls, patients with neurodegenerative disorders, including Alzheimer disease, Parkinson disease, dementia with Lewy bodies, and amyotrophic lateral sclerosis, show higher levels of neuronal RNA oxidation. Furthermore, oxidative damage to RNA has been found in cellular and animal models of neurodegeneration. RNA oxidation has been hypothesized to cause aberrant expression of microRNAs and proteins and subsequently initiate inappropriate cell fate pathways. Interestingly, accumulating evidence obtained from studies on either human samples or experimental models coincidentally suggests that RNA oxidation is a feature of neurons in the aging brain and more prominently observed in vulnerable neurons at an early-stage of age-associated neurodegenerative disorders, indicating that RNA oxidation actively contributes to the prodromal stage, onset, and development of these disorders. Further investigations aimed at understanding the processing mechanisms related to oxidative RNA damage and its consequences may provide significant insights into the pathogenesis of neurodegenerative disorders and pave the way for novel therapeutic strategies.

[The template principle: paradigm of modern genetics]

The idea of continuity in living systems, which was initially developed in mid-19th century, reached its peak in 1928 thanks to N.K. Koltsov, who proposed the template principle in chromosome reproduction. The determination of genetic functions of nucleic acids and the advent of molecular genetics led to F. Crick's statement of the central dogma of molecular biology in 1958. This dogma became a contemporary version of the template principle (templates of the first order). The discovery of "protein inheritance" underlay the notion of steric or conformational templates (second order) for reproducing conformation in a number of proteins. The template principle supplemented by this notion claims to be the main paradigm of modern genetics.

Retrogenes moved out of the z chromosome in the silkworm

Previous studies on organisms with well-differentiated X and Y chromosomes, such as Drosophila and mammals, consistently detected an excess of genes moving out of the X chromosome and gaining testis-biased expression. Several selective evolutionary mechanisms were shown to be associated with this nonrandom gene traffic, which contributed to the evolution of the X chromosome and autosomes. If selection drives gene traffic, such traffic should also exist in species with Z and W chromosomes, where the females are the heterogametic sex. However, no previous studies on gene traffic in species with female heterogamety have found any nonrandom chromosomal gene movement. Here, we report an excess of retrogenes moving out of the Z chromosome in an organism with the ZW sex determination system, Bombyx mori. In addition, we showed that those "out of Z" retrogenes tended to have ovary-biased expression, which is consistent with the pattern of non-retrogene traffic recently reported in birds and symmetrical to the retrogene movement in mammals and fruit flies out of the X chromosome evolving testis functions. These properties of gene traffic in the ZW system suggest a general role for the heterogamety of sex chromosomes in determining the chromosomal locations and the evolution of sex-biased genes.

Photoacoustic tomography: in vivo imaging from organelles to organs

Photoacoustic tomography (PAT) can create multiscale multicontrast images of living biological structures ranging from organelles to organs. This emerging technology overcomes the high degree of scattering of optical photons in biological tissue by making use of the photoacoustic effect. Light absorption by molecules creates a thermally induced pressure jump that launches ultrasonic waves, which are received by acoustic detectors to form images. Different implementations of PAT allow the spatial resolution to be scaled with the desired imaging depth in tissue while a high depth-to-resolution ratio is maintained. As a rule of thumb, the achievable spatial resolution is on the order of 1/200 of the desired imaging depth, which can reach up to 7 centimeters. PAT provides anatomical, functional, metabolic, molecular, and genetic contrasts of vasculature, hemodynamics, oxygen metabolism, biomarkers, and gene expression. We review the state of the art of PAT for both biological and clinical studies and discuss future prospects.

Probing the input-output behavior of biochemical and genetic systems system identification methods from control theory

A key aspect of the behavior of any system is the timescale on which it operates: when inputs change, do responses take milliseconds, seconds, minutes, hours, days, months? Does the system respond preferentially to inputs at certain timescales? These questions are well addressed by the methods of frequency response analysis. In this review, we introduce these methods and outline a procedure for applying this analysis directly to experimental data. This procedure, known as system identification, is a well-established tool in engineering systems and control theory and allows the construction of a predictive dynamic model of a biological system in the absence of any mechanistic details. When studying biochemical and genetic systems, the required experiments are not standard laboratory practice, but with advances in both our ability to measure system outputs (e.g., using fluorescent reporters) and our ability to generate precise inputs (with microfluidic chambers capable of changing cells' environments rapidly and under fine control), these frequency response methods are now experimentally practical for a wide range of biological systems, as evidenced by a number of successful recent applications of these techniques. We use a yeast G-protein signaling cascade as a running example, illustrating both theoretical concepts and practical considerations while keeping mathematical details to a minimum. The review aims to provide the reader with the tools required to design frequency response experiments for their own biological system and the background required to analyze and interpret the resulting data.

Detecting instability in animal social networks: genetic fragmentation is associated with social instability in rhesus macaques

The persistence of biological systems requires evolved mechanisms which promote stability. Cohesive primate social groups are one example of stable biological systems, which persist in spite of regular conflict. We suggest that genetic relatedness and its associated kinship structure are a potential source of stability in primate social groups as kinship structure is an important organizing principle in many animal societies. We investigated the effect of average genetic relatedness per matrilineal family on the stability of matrilineal grooming and agonistic interactions in 48 matrilines from seven captive groups of rhesus macaques. Matrilines with low average genetic relatedness show increased family-level instability such as: more sub-grouping in their matrilineal groom network, more frequent fighting with kin, and higher rates of wounding. Family-level instability in multiple matrilines within a group is further associated with group-level instability such as increased wounding. Stability appears to arise from the presence of clear matrilineal structure in the rhesus macaque group hierarchy, which is derived from cohesion among kin in their affiliative and agonistic interactions with each other. We conclude that genetic relatedness and kinship structure are an important source of group stability in animal societies, particularly when dominance and/or affilative interactions are typically governed by kinship.

Simulating linkage disequilibrium structures in a human population for SNP association studies

Existing simulation methods usually simulate linkage disequilibrium (LD) structures starting with an initial population that is randomly generated according to specified allele frequencies. These at random based methods might be unstable because the LD level of the initial population is generally extremely low. This study presents a new algorithm, SIMLD, to simulate genome populations with real LD structures. SIMLD begins from an initial population with possibly the highest LD level, and then the LD decays to fit the desired level through processes of mating and recombination over generations. SIMLD can produce case-control samples according to various disease models. Using empirical SNP marker information from three populations of HapMap data, we implement the proposed algorithm and demonstrate a set of experimental results.

[Phenome-genome relations and pathogenetics of multifactorial diseases]

This study of phenome-genome relations in multifactorial diseases is focused on the principal notions and concepts, such as "arthritism", syntropies and syntropic gene, diseasome, orthologic phenotypes (phenologs). The results of original investigations into synthropic genes responsible for predisposition to multifactorial diseases are presented along with analysis of DNA methylation in atherosclerotic plaques and whole-genome analysis of asthma. A hypothesis is proposed that ischaemic preconditioning may be a mechanism underlying the stable cardiovascular disease continuum as a special form of synthropy. Two principal lines of research on genetics of multifactorial disease are distinguished, viz. ontogenesis of multifactorial diseases and epigenetic inheritance.

DNA nanomedicine: Engineering DNA as a polymer for therapeutic and diagnostic applications

Nanomedicine, the application of nanotechnology to medicine, encompasses a broad spectrum of fields including molecular detection, diagnostics, drug delivery, gene regulation and protein production. In recent decades, DNA has received considerable attention for its functionality and versatility, allowing it to help bridge the gap between materials science and biological systems. The use of DNA as a structural nanoscale material has opened a new avenue towards the rational design of DNA nanostructures with different polymeric topologies. These topologies, in turn, possess unique characteristics that translate to specific therapeutic and diagnostic strategies within nanomedicine.

Pleiotropy of the branching locus (B) masks linked and unlinked quantitative trait loci affecting seed traits in sunflower

The discovery of unbranched, monocephalic natural variants was pivotal for the domestication of sunflower (Helianthus annuus L.). The branching locus (B), one of several loci apparently targeted by aboriginal selection for monocephaly, pleiotropically affects plant, seed and capitula morphology and, when segregating, confounds the discovery of favorable alleles for seed yield and other traits. The present study was undertaken to gain deeper insights into the genetics of branching and seed traits affected by branching. We produced an unbranched hybrid testcross recombinant inbred line (TC-RIL) population by crossing branched (bb) and unbranched (BB) RILs to an unbranched (BB) tester. The elimination of branching concomitantly eliminated a cluster of B-linked seed trait quantitative trait loci (QTL) identified by RIL per se testing. We identified a seed oil content QTL linked in repulsion and a 100-seed weight QTL linked in coupling to the B locus and additional unlinked QTL, previously masked by B-locus pleiotropy. Genomic segments flanking the B locus harbor multiple loci for domestication and post-domestication traits, the effects of which are masked by B-locus pleiotropy in populations segregating for branching and can only be disentangled by genetic analyses in unbranched populations. QTL analyses of NILs carrying wild B alleles substantiated the pleiotropic effects of the B locus. The effect of the B locus on branching was masked by the effects of wild alleles at independent branching loci in hybrids between monocephalic domesticated lines and polycephalic wild ecotypes; hence, the B locus appears to be necessary, but not sufficient, for monocephaly in domesticated sunflower.

Genetic perspectives on marine biological invasions

The extent to which the geographic distributions of marine organisms have been reshaped by human activities remains underappreciated, and so does, consequently, the impact of invasive species on marine ecosystems. The application of molecular genetic data in fields such as population genetics, phylogeography, and evolutionary biology have improved our ability to make inferences regarding invasion histories. Genetic methods have helped to resolve longstanding questions regarding the cryptogenic status of marine species, facilitated recognition of cryptic marine biodiversity, and provided means to determine the sources of introduced marine populations and to begin to recover the patterns of anthropogenic reshuffling of the ocean's biota. These approaches stand to aid materially in the development of effective management strategies and sustainable science-based policies. Continued advancements in the statistical analysis of genetic data promise to overcome some existing limitations of current approaches. Still other limitations will be best addressed by concerted collaborative and multidisciplinary efforts that recognize the important synergy between understanding the extent of biological invasions and coming to a more complete picture of both modern-day and historical marine biogeography.

Two neo-Darwinisms

There are two extant theories of evolution, each of which deserves the honourific "neo-Darwinism": Modern Synthesis Replicator theory and a theory I shall call Developmental Darwinism. The principal difference concerns the canonical unit of biological organization. Modern Synthesis replicator theory explains the process of evolution by appeal to the activities of genes or replicators. Developmental Darwinism explains the process of evolution by appeal to the capacities of organisms. In particular, it is the plasticity of organisms, manifested most distinctly during development, that causes adaptive evolution. Despite the fact that each, in its own way, traces its origin to the theory outlined by Darwin, they are radically different. The objectives of this essay are twofold: to underscore the differences between these theories, and to argue that Developmental Darwinism, though nascent, is a viable alternative to Modern Synthesis replicator theory.

One-carbon metabolism-genome interactions in folate-associated pathologies

Impairments in folate-mediated 1-carbon metabolism are associated with several common diseases and developmental anomalies including intestinal cancers, vascular disease, cognitive decline, and neural tube defects. The etiology of folate-associated pathologies involves interactions among multiple genetic risk alleles and environmental factors, although the causal mechanisms that define the role of folate and other B-vitamins in these complex disorders remain to be established. Folate and other B-vitamins fundamentally differ from other nutrients that interact with the genome in determining health and disease outcomes in that their interaction is reciprocal. Common gene variants influence the activity of folate-dependent enzymes and anabolic pathways; folate-mediated 1-carbon metabolism is essential for the high-fidelity synthesis of DNA and activated methyl groups that are required for DNA methylation and regulation of chromatin structure. This review focuses on the regulation of folate-mediated 1-carbon metabolism and its role in maintaining genome integrity and on strategies for establishing the metabolic pathways and mechanisms that underlie folate-associated pathologies.

Nature versus nurture in determining athletic ability

This chapter provides an overview of the truism that both nature and nurture determine human athletic ability. The major thesis developed is that environmental effects work through the process of growth and development and interact with an individual's genetic background to produce a specific adult phenotype, i.e. an athletic or nonathletic phenotype. On the nature side (genetics), a brief historical review is provided with emphasis on several areas that are likely to command future attention including the rise of genome-wide association as a mapping strategy, the problem of false positives using association approaches, as well as the relatively unknown effects of gene-gene interaction(epistasis), gene-environment interaction, and genome structure on complex trait variance. On the nurture side (environment), common environmental effects such as training-level and sports nutrition are largely ignored in favor of developmental environmental effects that are channeled through growth and development processes. Developmental effects are difficult to distinguish from genetic effects as phenotypic plasticity in response to early life environmental perturbation can produce lasting effects into adulthood. In this regard, the fetal programming (FP) hypothesis is reviewed in some detail as FP provides an excellent example of how developmental effects work and also interact with genetics. In general, FP has well-documented effects on adult body composition and the risk for adult chronic disease, but there is emerging evidence that FP affects human athletic performance as well.

From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later

Comparative genomics is the cornerstone of identification of gene functions. The immense number of living organisms precludes experimental identification of functions except in a handful of model organisms. The bacterial domain is split into large branches, among which the Firmicutes occupy a considerable space. Bacillus subtilis has been the model of Firmicutes for decades and its genome has been a reference for more than 10 years. Sequencing the genome involved more than 30 laboratories, with different expertises, in a attempt to make the most of the experimental information that could be associated with the sequence. This had the expected drawback that the sequencing expertise was quite varied among the groups involved, especially at a time when sequencing genomes was extremely hard work. The recent development of very efficient, fast and accurate sequencing techniques, in parallel with the development of high-level annotation platforms, motivated the present resequencing work. The updated sequence has been reannotated in agreement with the UniProt protein knowledge base, keeping in perspective the split between the paleome (genes necessary for sustaining and perpetuating life) and the cenome (genes required for occupation of a niche, suggesting here that B. subtilis is an epiphyte). This should permit investigators to make reliable inferences to prepare validation experiments in a variety of domains of bacterial growth and development as well as build up accurate phylogenies.