Universal attenuators and their interactions with feedback loops in gene regulatory networks.

Using a combination of mathematical modelling, statistical simulation and large-scale data analysis we study the properties of linear regulatory chains (LRCs) within gene regulatory networks (GRNs). Our modelling indicates that downstream genes embedded within LRCs are highly insulated from the variation in expression of upstream genes, and thus LRCs act as attenuators. This observation implies a progressively weaker functionality of LRCs as their length increases. When analyzing the preponderance of LRCs in the GRNs of Escherichia coli K12 and several other organisms, we find that very long LRCs are essentially absent. In both E. coli and M. tuberculosis we find that four-gene LRCs are intimately linked to identical feedback loops that are involved in potentially chaotic stress response, indicating that the dynamics of these potentially destabilising motifs are strongly restrained under homeostatic conditions. The same relationship is observed in a human cancer cell line (K562), and we postulate that four-gene LRCs act as 'universal attenuators'. These findings suggest a role for long LRCs in dampening variation in gene expression, thereby protecting cell identity, and in controlling dramatic shifts in cell-wide gene expression through inhibiting chaos-generating motifs.

Inevitability and containment of replication errors for eukaryotic genome lengths spanning megabase to gigabase.

The replication of DNA is initiated at particular sites on the genome called replication origins (ROs). Understanding the constraints that regulate the distribution of ROs across different organisms is fundamental for quantifying the degree of replication errors and their downstream consequences. Using a simple probabilistic model, we generate a set of predictions on the extreme sensitivity of error rates to the distribution of ROs, and how this distribution must therefore be tuned for genomes of vastly different sizes. As genome size changes from megabases to gigabases, we predict that regularity of RO spacing is lost, that large gaps between ROs dominate error rates but are heavily constrained by the mean stalling distance of replication forks, and that, for genomes spanning ∼100 megabases to ∼10 gigabases, errors become increasingly inevitable but their number remains very small (three or less). Our theory predicts that the number of errors becomes significantly higher for genome sizes greater than ∼10 gigabases. We test these predictions against datasets in yeast, Arabidopsis, Drosophila, and human, and also through direct experimentation on two different human cell lines. Agreement of theoretical predictions with experiment and datasets is found in all cases, resulting in a picture of great simplicity, whereby the density and positioning of ROs explain the replication error rates for the entire range of eukaryotes for which data are available. The theory highlights three domains of error rates: negligible (yeast), tolerable (metazoan), and high (some plants), with the human genome at the extreme end of the middle domain.

Unreplicated DNA remaining from unperturbed S phases passes through mitosis for resolution in daughter cells.

To prevent rereplication of genomic segments, the eukaryotic cell cycle is divided into two nonoverlapping phases. During late mitosis and G1 replication origins are "licensed" by loading MCM2-7 double hexamers and during S phase licensed replication origins activate to initiate bidirectional replication forks. Replication forks can stall irreversibly, and if two converging forks stall with no intervening licensed origin-a "double fork stall" (DFS)-replication cannot be completed by conventional means. We previously showed how the distribution of replication origins in yeasts promotes complete genome replication even in the presence of irreversible fork stalling. This analysis predicts that DFSs are rare in yeasts but highly likely in large mammalian genomes. Here we show that complementary strand synthesis in early mitosis, ultrafine anaphase bridges, and G1-specific p53-binding protein 1 (53BP1) nuclear bodies provide a mechanism for resolving unreplicated DNA at DFSs in human cells. When origin number was experimentally altered, the number of these structures closely agreed with theoretical predictions of DFSs. The 53BP1 is preferentially bound to larger replicons, where the probability of DFSs is higher. Loss of 53BP1 caused hypersensitivity to licensing inhibition when replication origins were removed. These results provide a striking convergence of experimental and theoretical evidence that unreplicated DNA can pass through mitosis for resolution in the following cell cycle.

Replisome stall events have shaped the distribution of replication origins in the genomes of yeasts.

During S phase, the entire genome must be precisely duplicated, with no sections of DNA left unreplicated. Here, we develop a simple mathematical model to describe the probability of replication failing due to the irreversible stalling of replication forks. We show that the probability of complete genome replication is maximized if replication origins are evenly spaced, the largest inter-origin distances are minimized, and the end-most origins are positioned close to chromosome ends. We show that origin positions in the yeast Saccharomyces cerevisiae genome conform to all three predictions thereby maximizing the probability of complete replication if replication forks stall. Origin positions in four other yeasts-Kluyveromyces lactis, Lachancea kluyveri, Lachancea waltii and Schizosaccharomyces pombe-also conform to these predictions. Equating failure rates at chromosome ends with those in chromosome interiors gives a mean per nucleotide fork stall rate of ∼5 × 10(-8), which is consistent with experimental estimates. Using this value in our theoretical predictions gives replication failure rates that are consistent with data from replication origin knockout experiments. Our theory also predicts that significantly larger genomes, such as those of mammals, will experience a much greater probability of replication failure genome-wide, and therefore will likely require additional compensatory mechanisms.

Water is a molecular liquid.

Science and society are failing to grapple with the public health burden of cancer. In this short perspective piece, I contrast reductionism and complexity in cancer research, using water as a simple example, arguing for more 'ecological' approaches to cancer. This is a call to arms to physical scientists, ecologists and others to get involved, to link up with cancer clinicians and cancer biologists, and an appeal to funding agencies to link up across disciplines to make a difference.

Quantifying metastatic inefficiency: rare genotypes versus rare dynamics.

We introduce and solve a 'null model' of stochastic metastatic colonization. The model is described by a single parameter θ: the ratio of the rate of cell division to the rate of cell death for a disseminated tumour cell in a given secondary tissue environment. We are primarily interested in the case in which colonizing cells are poorly adapted for proliferation in the local tissue environment, so that cell death is more likely than cell division, i.e. θ < 1. We quantify the rare event statistics for the successful establishment of a metastatic colony of size N. For N >> 1, we find that the probability of establishment is exponentially rare, as expected, and yet the mean time for such rare events is of the form ~log (N)/(1 - θ) while the standard deviation of colonization times is ~1/(1 - θ). Thus, counter to naive expectation, for θ < 1, the average time for establishment of successful metastatic colonies decreases with decreasing cell fitness, and colonies seeded from lower fitness cells show less stochastic variation in their growth. These results indicate that metastatic growth from poorly adapted cells is rare, exponentially explosive and essentially deterministic. These statements are brought into sharper focus by the finding that the temporal statistics of the early stages of metastatic colonization from low-fitness cells (θ < 1) are statistically indistinguishable from those initiated from high-fitness cells (θ > 1), i.e. the statistics show a duality mapping (1 - θ) --> (θ - 1). We conclude our analysis with a study of heterogeneity in the fitness of colonising cells, and describe a phase diagram delineating parameter regions in which metastatic colonization is dominated either by low or high fitness cells, showing that both are plausible given our current knowledge of physiological conditions in human cancer.

Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol.

In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX-BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX-BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted-from published articles, via printed results of computational chemistry experiments, to 3D models-is now available to BVI scientists too. The possibilities offered by AsteriX-BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).

A pilot study to determine the incidence, type, and severity of non-routine events in neonates undergoing gastrostomy tube placement.

BACKGROUND: Non-routine events (NRE) are defined as any suboptimal occurrences in a process being measured in the opinion of the reporter and comes from the field of human factors engineering. These typically occur well up-stream of an adverse event and NRE measurement has not been applied to the complex context of neonatal surgery. We sought to apply this novel safety event measurement methodology to neonates in the NICU undergoing gastrostomy tube placement. METHODS: A prospective pilot study was conducted between November 2016 and August 2020 in the Level IV NICU and the pediatric operating rooms of an urban academic children's hospital to determine the incidence, severity, impact, and contributory factors of clinician-reported non-routine events (NREs, i.e., deviations from optimal care) and 30-day NSQIP occurrences in neonates receiving a G-tube. RESULTS: Clinicians reported at least one NRE in 32 of 36 (89%) G-tube cases, averaging 3.0 (Standard deviation: 2.5) NRE reports per case. NSQIP-P review identified 7 cases (19%) with NSQIP-P occurrences and each of these cases had multiple reported NREs. One case in which NREs were not reported was without NSQIP-P occurrences. The odds ratio of having a NSQIP-P occurrence with the presence of an NRE was 0.695 (95% CI 0.06-17.04). CONCLUSION: Despite being considered a "simple" operation, >80% of neonatal G-tube placement operations had at least one reported NRE by an operative team member. In this pilot study, NRE occurrence was not significantly associated with the subsequent reporting of an NSQIP-P occurrence. Understanding contributory factors of NREs that occur in neonatal surgery may promote surgical safety efforts and should be evaluated in larger and more diverse populations. LEVEL OF EVIDENCE: IV.

Defining the Epidemiology of Safety Risks in Neonatal Intensive Care Unit Patients Requiring Surgery.

OBJECTIVE: The aim of the study was to determine the incidence, type, severity, preventability, and contributing factors of nonroutine events (NREs)-events perceived by care providers or skilled observers as a deviations from optimal care based on the clinical situation-in the perioperative (i.e., preoperative, operative, and postoperative) care of surgical neonates in the neonatal intensive care unit and operating room. METHODS: A prospective observational study of noncardiac surgical neonates, who received preoperative and postoperative neonatal intensive care unit care, was conducted at an urban academic children's hospital between November 1, 2016, and March 31, 2018. One hundred twenty-nine surgical cases in 109 neonates were observed. The incidence and description of NREs were collected via structured researcher-administered survey tool of involved clinicians. Primary measurements included clinicians' ratings of NRE severity and contributory factors and trained research assistants' ratings of preventability. RESULTS: One or more NREs were reported in 101 (78%) of 129 observed cases for 247 total NREs. Clinicians reported 2 (2) (median, interquartile range) NREs per NRE case with a maximum severity of 3 (1) (possible range = 1-5). Trained research assistants rated 47% of NREs as preventable and 11% as severe and preventable. The relative risks for National Surgical Quality Improvement Program - pediatric major morbidity and 30-day mortality were 1.17 (95% confidence interval = 0.92-1.48) and 1.04 (95% confidence interval = 1.00-1.08) in NRE cases versus non-NRE cases. CONCLUSIONS: The incidence of NREs in neonatal perioperative care at an academic children's hospital was high and of variable severity with a myriad of contributory factors.

Catechol-o-methyltransferase genotype and childhood trauma may interact to impact schizotypal personality traits.

We attempt to identify gene by childhood abuse interactions which predispose to the development of schizotypal traits in a familial bipolar disorder (BD) sample. Self-report measures of schizotypal personality traits (Schizotypal Personality Scale) and childhood maltreatment (Childhood Trauma Questionnaire) were administered to 222 participants from 44 families with BD. Variants of catechol-o-methyltransferase (COMT) and four other dopamine pathway-related genes: DRD4, DRD2,MAOA, and SLC6A3, were typed. BD type I (BD I) subjects scored significantly higher than their unaffected relatives on the Schizotypal Personality Scale. The val allele of the Val158 Met polymorphism of the COMT gene was associated with increased schizotypal personality trait scores in individuals exposed to higher levels of self-reported childhood trauma (p < 0.05). There was no direct effect of the val158met polymorphism on schizotypal personality traits. Further, no passive correlation between COMT genotype and childhood trauma was found. We raise the possibility that genetically-driven variation in COMT may interact with childhood trauma to contribute to the risk of developing schizotypal personality traits.

A non-additive interaction of a functional MAO-A VNTR and testosterone predicts antisocial behavior.

A functional VNTR polymorphism in the promoter of the monoamine oxidase A gene (MAOA-LPR) has previously been shown to be an important predictor of antisocial behavior in men. Testosterone analogues are known to interact with the MAOA promoter in vitro to influence gene transcription as well as in vivo to influence CSF levels of the MAO metabolite 3-methoxy-4-hydroxyphenylglycol (MHPG) in human males. We examined the possible joint effects of testosterone (measured in CSF) and MAOA-LPR genotype on antisocial personality disorder and scores on the Brown-Goodwin Aggression scale in 95 unrelated male criminal alcoholics and 45 controls. The results confirm that MAOA genotype and CSF testosterone interact to predict antisocial behaviors. The MAOA/testosterone interaction also predicted low levels of CSF MHPG, which tentatively suggests the possibility that the interaction may be mediated by a direct effect on gene transcription. If replicated these findings offer plausible explanations for previous inconsistencies in studies of the relationship between testosterone and male human aggression, as well as for how MAOA genotype may influence aggressive behavior in human males.

Modeling cell rheology with the Subcellular Element Model.

Recently, the Subcellular Element Model (SEM) has been introduced, primarily to compute the dynamics of large numbers of three-dimensional deformable cells in multicellular systems. Within this model framework, each cell is represented by a collection of elastically coupled elements, interacting with one another via short-range potentials, and dynamically updated using over-damped Langevin dynamics. The SEM can also be used to represent a single cell in more detail, by using a larger number of subcellular elements exclusively identified with that cell. We have tested whether, in this context, the SEM yields viscoelastic properties consistent with those measured on single living cells. Employing virtual methods of bulk rheology and microrheology we find that the SEM successfully captures many cellular rheological properties at intermediate time scales and moderate strains, including weak power law rheology. In its simplest guise, the SEM cannot describe long-time/large-strain cell responses. Capturing these cellular properties requires extensions of the SEM which incorporate active cytoskeletal rearrangement. Such extensions will be the subject of a future publication.

Early maternal rejection affects the development of monoaminergic systems and adult abusive parenting in rhesus macaques (Macaca mulatta).

This study investigated the effects of early exposure to variable parenting style and infant abuse on cerebrospinal fluid (CSF) concentrations of monoamine metabolites and examined the role of monoaminergic function in the intergenerational transmission of infant abuse in rhesus monkeys (Macaca mulatta). Forty-three infants reared by their biological mothers and 15 infants that were cross-fostered at birth and reared by unrelated mothers were followed longitudinally through their first 3 years of life or longer. Approximately half of the infants were reared by abusive mothers and half by nonabusive controls. Abused infants did not differ from controls in CSF concentrations of 5-hydroxyindoleacetic acid (5-HIAA), homovanillic acid (HVA), or 3-methoxy-4-hydroxyphenylgycol (MHPG). Abused infants, however, were exposed to higher rates of maternal rejection, and highly rejected infants had lower CSF 5-HIAA and HVA than low-rejection infants. The abused females who became abusive mothers in adulthood had lower CSF 5-HIAA than the abused females who did not. A similar trend was also observed among the cross-fostered females, suggesting that low serotonergic function resulting from early exposure to high rates of maternal rejection plays a role in the intergenerational transmission of infant abuse.

Warriors versus worriers: the role of COMT gene variants.

Behavioral phenotypes are generally complex, reflecting the action of multiple different genes. Nevertheless, there is growing evidence that key gene variants can alter activity within specific neuronal circuits and, therefore, influence particular cognitive-affective phenomena. One example is the catechol-O-methyltransferase (COMT) gene, which has a common variant at codon 158. Those with valine (Val158) alleles have increased greater COMT activity and lower prefrontal extracellular dopamine compared with those with the methionine (Met158) substitution. Val158 alleles may be associated with an advantage in the processing of aversive stimuli (warrior strategy), while Met158 alleles may be associated with an advantage in memory and attention tasks (worrier strategy). Under conditions of increased dopamine release (eg, stress), individuals with Val158 alleles may have improved dopaminergic transmission and better performance, while individuals with Met158 alleles may have less efficient neurotransmission and worse performance. Some evidence suggests that Val158 alleles are associated with schizophrenia, while Met158 alleles are associated with anxiety.

Monoamine oxidase A gene promoter variation and rearing experience influences aggressive behavior in rhesus monkeys.

BACKGROUND: Allelic variation of the monoamine oxidase A (MAOA) gene has been implicated in conduct disorder and antisocial, aggressive behavior in humans when associated with early adverse experiences. We tested the hypothesis that a repeat polymorphism in the rhesus macaque MAOA gene promoter region influences aggressive behavior in male subjects. METHODS: Forty-five unrelated male monkeys raised with or without their mothers were tested for competitive and social group aggression. Functional activity of the MAOA gene promoter polymorphism was determined and genotypes scored for assessing genetic and environmental influences on aggression. RESULTS: Transcription of the MAOA gene in rhesus monkeys is modulated by an orthologous polymorphism (rhMAOA-LPR) in its upstream regulatory region. High- and low-activity alleles of the rhMAOA-LPR show a genotype x environment interaction effect on aggressive behavior, such that mother-reared male monkeys with the low-activity-associated allele had higher aggression scores. CONCLUSIONS: These results suggest that the behavioral expression of allelic variation in MAOA activity is sensitive to social experiences early in development and that its functional outcome might depend on social context.

Interaction between serotonin transporter gene variation and rearing condition in alcohol preference and consumption in female primates.

BACKGROUND: Serotonin neurotransmission and limbic-hypothalamic-pituitary-adrenal (LHPA) axis hormones are thought to be involved in the reinforcement of alcohol intake and contribute to the risk for alcoholism. In humans and macaques, a promoter polymorphism that decreases transcription of the serotonin transporter gene is associated with anxiety and altered LHPA-axis responses to stress, and in female macaques, exposure to early-life stress alters LHPA-axis activation in response to alcohol. We wanted to determine whether serotonin transporter gene promoter variation (rh-5HTTLPR) and rearing condition would interact to influence alcohol preference in female rhesus macaques. Because of the involvement of stress and LHPA-axis activity in symptoms of withdrawal and relapse, we also wanted to determine whether serotonin transporter gene variation and rearing condition would influence changes in the patterns of alcohol consumption across a 6-week alcohol consumption paradigm. METHODS: Female macaques were reared with their mothers in social groups (n = 18) or in peer-only groups (n = 14). As young adults, they were given access to an aspartame-sweetened 8.4% alcohol solution and vehicle for 1 hour per day, and volumes of consumption of alcoholic and nonalcoholic solutions were recorded. Serotonin transporter genotype (l/l and l/s) was determined using polymerase chain reaction followed by gel electrophoresis. RESULTS: We found interactions between rearing condition and serotonin transporter genotype, such that l/s peer-reared females demonstrated higher levels of ethanol preference. We also found an effect of rearing condition on the percentage change in alcohol consumed during the 6 weeks as well as a phase by rearing interaction, such that peer-reared animals progressively increased their levels of consumption across the course of the study. This was especially evident for peer-reared females with the l/s rh5-HTTLPR genotype. CONCLUSION: These data suggest a potential interaction between serotonin transporter gene variation and early experience in vulnerability to alcoholism.

Genetic contributions to social impulsivity and aggressiveness in vervet monkeys.

BACKGROUND: Impulsivity contributes to multiple psychiatric disorders and sociobehavioral problems, and the more serious consequences of impulsivity are typically manifest in social situations. This study assessed the genetic contribution to impulsivity and aggressiveness in a social context using a nonhuman primate model. METHODS: Subjects were 352 adolescent and adult vervet monkeys from an extended multigenerational pedigree. Behavior was assessed in the Intruder Challenge Test, a standardized test that measures impulsivity and aggressiveness toward a stranger. Genetic and maternal contributions to variation in the Social Impulsivity Index and its two subscales, impulsive approach and aggression, were estimated using variance components analyses. RESULTS: The results found significant genetic contributions to social impulsivity (h2 =.35 +/-.11) and to each of the subscales, with no significant influence of maternal environment. There was a high genetic correlation between the impulsive approach and aggression subscales (rho =.78 +/-.12). CONCLUSIONS: This is the first study to demonstrate heritability of social impulsivity in adolescents and adults for any nonhuman primate species. The high genetic correlation suggests the same genes may influence variation in both impulsive approach and aggression. These results provide a promising basis for identification of susceptibility loci for impulsivity and aggressiveness.

Rearing condition and rh5-HTTLPR interact to influence limbic-hypothalamic-pituitary-adrenal axis response to stress in infant macaques.

BACKGROUND: In humans and macaques, a promoter polymorphism that decreases transcription of the serotonin transporter gene is associated with anxiety. Serotonin transporter gene disruption in rodents produces anxious animals with exaggerated limbic-hypothalamic-pituitary-adrenal (LHPA) responses to stress. We wanted to determine whether serotonin transporter gene promoter variation (rh-5HTTLPR) and rearing condition would interact to influence endocrine responses to stress in infant rhesus macaques. METHODS: Animals were reared with their mothers (MR, n = 141) or in peer-only groups (PR, n = 67). At 6 months of age, adrenocorticotropic hormone (ACTH) and cortisol levels were determined at baseline and during separation stress. Serotonin transporter genotype (l/l and l/s) was determined with polymerase chain reaction followed by gel electrophoresis. RESULTS: Cortisol levels increased during separation, and there was a main effect of rearing condition, with decreased cortisol levels among PR macaques. Animals with l/s rh5-HTTLPR genotypes had higher ACTH levels than did l/l animals. Adrenocorticotropic hormone levels increased during separation, and there was a separation x rearing x rh5-HTTLPR interaction, such that PR-l/s animals had higher ACTH levels during separation than did other animals studied. CONCLUSIONS: These data demonstrate that serotonin transporter gene variation affects LHPA axis activity and that the influence of rh5-HTTLPR on hormonal responses during stress is modulated by early experience.

The use of adolescent nonhuman primates to model human alcohol intake: neurobiological, genetic, and psychological variables.

Traits characteristic of type I and type II alcoholism are thought to relate to dysregulated central nervous system serotonin functioning. In this review, we discuss variables associated with high adolescent alcohol consumption and other risk-taking behaviors in a nonhuman primate model. Adolescent primates with low CSF concentrations of the serotonin metabolite 5-HIAA are more impulsive and exhibit increased levels of alcohol consumption. Both genetic and environmental factors contribute to alcohol-seeking behavior in adolescent macaques. Sequence variation within serotonin system genes, for example, a repeat polymorphism in the transcriptional control region of the monoamine oxidase gene (MAOA-LPR), increases the propensity for adolescent males to consume alcohol. Environmental factors, such as early life stress in the form of peer-rearing or early age of exposure to alcohol, are also associated with increased alcohol consumption. Peer-reared females, especially those exposed to alcohol during early adolescence, exhibit increased rates of alcohol consumption compared to those exposed to alcohol later in development. When genetic variables are also considered, there is an interaction between the low activity serotonin transporter gene promoter s allele (rh5-HTTLPR) and rearing condition on alcohol preference in females but not males, suggesting that the interactions between genes and the environment may be sexually dichotomous. By learning more about the interactions between genes, early experience, and alcohol intake in the adolescent nonhuman primate, we may be able to identify factors that contribute to the susceptibility, pathogenesis, and progression of impulse control disorders, such as alcoholism.