Genetics of physiological dysregulation: findings from the long life family study using joint models.

Recently, Mahalanobis distance (DM) was suggested as a statistical measure of physiological dysregulation in aging individuals. We constructed DM variants using sets of biomarkers collected at the two visits of the Long Life Family Study (LLFS) and performed joint analyses of longitudinal observations of DM and follow-up mortality in LLFS using joint models. We found that DM is significantly associated with mortality (hazard ratio per standard deviation: 1.31 [1.16, 1.48] to 2.22 [1.84, 2.67]) after controlling for age and other covariates. GWAS of random intercepts and slopes of DM estimated from joint models found a genome-wide significant SNP (rs12652543, p=7.2×10-9) in the TRIO gene associated with the slope of DM constructed from biomarkers declining in late life. Review of biological effects of genes corresponding to top SNPs from GWAS of DM slopes revealed that these genes are broadly involved in cancer prognosis and axon guidance/synapse function. Although axon growth is mainly observed during early development, the axon guidance genes can function in adults and contribute to maintenance of neural circuits and synaptic plasticity. Our results indicate that decline in axons' ability to maintain complex regulatory networks may potentially play an important role in the increase in physiological dysregulation during aging.

Assessment of MTNR1B Type 2 Diabetes Genetic Risk Modification by Shift Work and Morningness-Eveningness Preference in the UK Biobank.

Night shift work, behavioral rhythms, and the common MTNR1B risk single nucleotide polymorphism (SNP), rs10830963, associate with type 2 diabetes; however, whether they exert joint effects to exacerbate type 2 diabetes risk is unknown. Among employed participants of European ancestry in the UK Biobank (N = 189,488), we aimed to test the cross-sectional independent associations and joint interaction effects of these risk factors on odds of type 2 diabetes (n = 5,042 cases) and HbA1c levels (n = 175,156). Current shift work, definite morning or evening preference, and MTNR1B rs10830963 risk allele associated with type 2 diabetes and HbA1c levels. The effect of rs10830963 was not modified by shift work schedules. While marginal evidence of interaction between self-reported morningness-eveningness preference and rs10830963 on risk of type 2 diabetes was seen, this interaction did not persist when analysis was expanded to include all participants regardless of employment status and when accelerometer-derived sleep midpoint was used as an objective measure of morningness-eveningness preference. Our findings suggest that MTNR1B risk allele carriers who carry out shift work or have more extreme morningness-eveningness preference may not have enhanced risk of type 2 diabetes.

Circadian Rhythm and Sleep Disruption: Causes, Metabolic Consequences, and Countermeasures.

Circadian (∼24-hour) timing systems pervade all kingdoms of life and temporally optimize behavior and physiology in humans. Relatively recent changes to our environments, such as the introduction of artificial lighting, can disorganize the circadian system, from the level of the molecular clocks that regulate the timing of cellular activities to the level of synchronization between our daily cycles of behavior and the solar day. Sleep/wake cycles are intertwined with the circadian system, and global trends indicate that these, too, are increasingly subject to disruption. A large proportion of the world's population is at increased risk of environmentally driven circadian rhythm and sleep disruption, and a minority of individuals are also genetically predisposed to circadian misalignment and sleep disorders. The consequences of disruption to the circadian system and sleep are profound and include myriad metabolic ramifications, some of which may be compounded by adverse effects on dietary choices. If not addressed, the deleterious effects of such disruption will continue to cause widespread health problems; therefore, implementation of the numerous behavioral and pharmaceutical interventions that can help restore circadian system alignment and enhance sleep will be important.

Genes, body clocks and prevention of sleep problems.

Chronobiologists argue that their scientific findings have implications for prevention of sleep problems. They claim that some sleep problems are caused by the fact that people live against their individual body clock rather than adjusted to it. They also claim that by taking the findings of chronobiology seriously in policy-making some sleep problems can be prevented. I investigate applications of chronobiology in two social areas-school schedules and shift work-and show that in order for these applications to be justified certain implicit presumptions have to be justified. The first presumption is explanatory, namely that a chronobiological explanation is an adequate explanation of the sleep problems at hand. In addition I analyse three ethical presumptions. The first ethical presumption is that sleep is of vital value. The second is that sleep is not an exclusively private issue. The third ethical presumption is that the preventive measures to be undertaken are ethically acceptable. My main point is that it is not possible to simply "read off" policy measures from the empirical findings of chronobiology.

Chrono-proteomics of human saliva: variations of the salivary proteome during human development.

An important contribution to the variability of any proteome is given by the time dimension that should be carefully considered to define physiological modifications. To this purpose, whole saliva proteome was investigated in a wide age range. Whole saliva was collected from 17 preterm newborns with a postconceptional age at birth of 178-217 days. In these subjects sample collection was performed serially starting immediately after birth and within about 1 year follow-up, gathering a total of 111 specimens. Furthermore, whole saliva was collected from 182 subjects aged between 0 and 17 years and from 23 adults aged between 27 and 57 years. The naturally occurring intact salivary proteome of the 316 samples was analyzed by low- and high-resolution HPLC-ESI-MS platforms. Proteins peculiar of the adults appeared in saliva with different time courses during human development. Acidic proline-rich proteins encoded by PRH2 locus and glycosylated basic proline-rich proteins encoded by PRB3 locus appeared following 180 days of postconceptional age, followed at 7 months (±2 weeks) by histatin 1, statherin, and P-B peptide. The other histatins and acidic proline-rich proteins encoded by PRH1 locus appeared in whole saliva of babies from 1 to 3 weeks after the normal term of delivery, S-type cystatins appeared at 1 year (±3 months), and basic proline-rich proteins appeared at 4 years (±1 year) of age. All of the proteinases involved in the maturation of salivary proteins were more active in preterm than in at-term newborns, on the basis of the truncated forms detected. The activity of the Fam20C kinase, involved in the phosphorylation of various proteins, started around 180 days of postconceptional age, slowly increased reaching values comparable to adults at about 2 years (±6 months) of age. Instead, MAPK14 involved in the phosphorylation of S100A9 was fully active since birth also in preterm newborns.

Genetic determinants and dynamics of permanent teeth emergence in Northwest Indian twins: a chronogenetic study.

The understanding of the role of genetic factors in phenotypic variation in the emergence of secondary teeth in humans remains is incomplete. Dental emergence data based on a mixed longitudinal study were collected on 111 twin pairs from an urban population of Chandigarh. The observations over time on a single individual varied from one to nine, thus giving a total of 595 entities. Female twins manifested emergence priority over males. The differences between zygosities in mean emergence ages were significant for only 6 of 16 (37%) instances. Magnitude of variations seen between twins and singletons in their mean emergence timings and duration of the hiatus between two dental phases of emergence were of the order observed among different samples from the same population/ethnic group. Heritability estimates for the specified number of the teeth emerged showed age variations. These estimates were highest in the first two age groups (from 5 to 7 years), when the first molars and incisors emerged. Maxilla-mandible differences were seen for tooth emergence timings and sequence patterns. Heritability for tooth emergence timings was higher in maxilla than in mandible. Multifactorial model of inheritance was the best fit model to explain variations observed in dental emergence timings and dental sequence pattern polymorphisms and there were significant genetic components of variation for both of these. There were sex differences in heritability; females had higher estimates than males. Genetic factors accounted for about 60% of the total phenotypic variation in the length of hiatus interval between two active stages of permanent teeth emergence.

Chronotype: a review of the advances, limits and applicability of the main instruments used in the literature to assess human phenotype / Cronotipo: uma revisão dos avanços, limites e aplicabilidade dos principais instrumentos utilizados na literatura para avaliar o fenótipo humano

The study of circadian typology differences has increased in the last few years. As a result, new instruments have been developed to estimate the individual circadian phase of temporal human behavior, also referred as chronotype. The current review was conducted to evaluate the differences among the questionnaires most frequently used to assess chronotype: the Morningness-Eveningness Questionnaire (MEQ), the Composite Scale of Morningness (CSM), and the Munich Chronotype Questionnaire (MCTQ). Each instrument evaluates a different aspect of chronotype. MEQ is considered to evaluate the phase preferences of individual behavior over a 24-hour day, while MCTQ measures the phase of sleep positions for both free and work days. CSM is similar to MEQ, but is more sensitive to measure shift work. The concept of chronotype has been used to refer to phase positions or phase preferences in the literature reviewed. Most of the time this is a consequence of different interpretations: it is not clear whether phase preferences are a direct manifestation of the individual’s internal clock or a result of external cues, e.g., social interaction (including the alarm clock). Also, phase preferences are not uniform throughout life. Therefore, a single assessment, not taking age into consideration, will not accurately describe the sample. We suggest that MCTQ is the best instrument for investigators dealing with desynchronization and as an instrument for sleep phase. Conversely, if the goal is to assess characteristics that change under specific situations - chronotype -, the MEQ should be used

O estudo das diferenças de tipologia circadiana tem aumentado nos últimos anos. Como resultado, novos instrumentos têm sido desenvolvidos para estimar as preferências interindividuais de fase circadiana, denominada de cronotipo, responsável pela organização temporal do processo de regulação do organismo. O objetivo desta revisão foi avaliar as diferenças dos principais questionários utilizados para avaliar cronotipos: o Questionário de Matutinidade e Vespertinidade (Morningness-Eveningness Questionnaire, MEQ), o Composite Scale of Morningness (CSM) e o Questionário de Cronotipo de Munique (Munich Chronotype Questionnaire, MCTQ). Cada instrumento avalia um aspecto diferente dos cronotipos. Considera-se que o MEQ avalia as preferências de fase do comportamento individual ao longo de um dia de 24 horas, ao passo que o MCTQ mede a posição da fase de sono tanto em dias livres como em dias de trabalho. O CSM é semelhante ao MEQ, mas é mais sensível para ser utilizado em indivíduos que realizam trabalho em turnos. O conceito de cronotipo tem sido utilizado para se referir a posições de fase ou preferências de fase na literatura revisada. Na maioria das vezes, isso é consequência de diferentes interpretações: não está claro se as preferências de fase são uma manifestação direta do relógio interno do indivíduo ou um resultado de sinais externos, como por exemplo, interação social (incluindo o uso de despertador). Além disso, as preferências de fase não são uniformes ao longo da vida. Sendo assim, uma única avaliação, sem levar em consideração a idade do indivíduo nos escores utilizados nessas escalas, não descreverá a amostra com precisão. Sugerimos, através desta revisão, que o MCTQ deve ser considerado como instrumento para investigações que lidam com dessincronização e como instrumento de medida de fase de sono. Por outro lado, se o objetivo é avaliar características que mudam em determinadas situações - cronotipo -, o MEQ deve ser utilizado

The exact distribution of divergence times.

The recent work of Haubold and Wiehe (Mol. Biol. Evol. 18:1157-1160, 2001) considered statistical inference of the divergence time. However, there appears to be a fundamental flaw in the paper since it treated the divergence time as a random variable and not as a parameter. In this note, we derive a valid statistical inference for the divergence time. We derive an estimator for the divergence time as well as explicit expressions for its the probability density function, cumulative distribution function and the means. We also provide a 5-line computer program for computing the associated confidence intervals. We expect that the results presented could be useful for statistical modeling of divergence times.

Evolutionary history of mammalian transposons determined by genome-wide defragmentation.

The constant bombardment of mammalian genomes by transposable elements (TEs) has resulted in TEs comprising at least 45% of the human genome. Because of their great age and abundance, TEs are important in comparative phylogenomics. However, estimates of TE age were previously based on divergence from derived consensus sequences or phylogenetic analysis, which can be unreliable, especially for older more diverged elements. Therefore, a novel genome-wide analysis of TE organization and fragmentation was performed to estimate TE age independently of sequence composition and divergence or the assumption of a constant molecular clock. Analysis of TEs in the human genome revealed approximately 600,000 examples where TEs have transposed into and fragmented other TEs, covering >40% of all TEs or approximately 542 Mbp of genomic sequence. The relative age of these TEs over evolutionary time is implicit in their organization, because newer TEs have necessarily transposed into older TEs that were already present. A matrix of the number of times that each TE has transposed into every other TE was constructed, and a novel objective function was developed that derived the chronological order and relative ages of human TEs spanning >100 million years. This method has been used to infer the relative ages across all four major TE classes, including the oldest, most diverged elements. Analysis of DNA transposons over the history of the human genome has revealed the early activity of some MER2 transposons, and the relatively recent activity of MER1 transposons during primate lineages. The TEs from six additional mammalian genomes were defragmented and analyzed. Pairwise comparison of the independent chronological orders of TEs in these mammalian genomes revealed species phylogeny, the fact that transposons shared between genomes are older than species-specific transposons, and a subset of TEs that were potentially active during periods of speciation.

A first-principles model of early evolution: emergence of gene families, species, and preferred protein folds.

In this work we develop a microscopic physical model of early evolution where phenotype--organism life expectancy--is directly related to genotype--the stability of its proteins in their native conformations-which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the "Big Bang" scenario whereby exponential population growth ensues as soon as favorable sequence-structure combinations (precursors of stable proteins) are discovered. Upon that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. We observe that protein folds remain stable and abundant in the population at timescales much greater than mutation or organism lifetime, and the distribution of the lifetimes of dominant folds in a population approximately follows a power law. The separation of evolutionary timescales between discovery of new folds and generation of new sequences gives rise to emergence of protein families and superfamilies whose sizes are power-law distributed, closely matching the same distributions for real proteins. On the population level we observe emergence of species--subpopulations that carry similar genomes. Further, we present a simple theory that relates stability of evolving proteins to the sizes of emerging genomes. Together, these results provide a microscopic first-principles picture of how first-gene families developed in the course of early evolution.

RNA in situ hybridizations on Drosophila whole mounts.

RNA in situ hybridization is a commonly used technique to achieve spatiotemporal detection of transcripts in tissues. This chapter gives an overview of novel techniques using fluorescent dyes, signal amplification methods, and confocal microscopy in regard to chronobiological applications on Drosophila adult brains.

William J. Cunliffe Scientific Awards. Characteristics and pathomechanisms of endogenously aged skin.

The skin, being in direct contact with several environmental factors (e.g. UV irradiation), does not only undergo endogenous aging, which has to do with the 'biological clock' of the skin cells per se, but also exogenous aging. While exogenous skin aging has been extensively studied, the pathomechanisms of endogenous skin aging remain far less clear. Endogenous skin aging reflects reduction processes, which are common in internal organs. These processes include cellular senescence and decreased proliferative capacity, decrease in cellular DNA repair capacity and chromosomal abnormalities, loss of telomeres, point mutations of extranuclear mtDNA, oxidative stress and gene mutations. As a consequence, aged skin in nonexposed areas shows typical characteristics including fine wrinkles, dryness, sallowness and loss of elasticity. Recent data have illustrated that lack of hormones occurring with age may also contribute to the aging phenotype. Improvement of epidermal skin moisture, elasticity and skin thickness, enhanced production of surface lipids, reduction of wrinkle depth, restoration of collagen fibers and increase of the collagen III/I ratio have been reported after hormone replacement therapy or local estrogen treatment in postmenopausal women. Furthermore, an in vitro model of endogenous skin aging consisting of human SZ95 sebocytes which were incubated under a hormone-substituted environment illustrated that hormones at age- and sex-specific levels were able to alter the development of cells by regulating their transcriptome. In conclusion, among other factors the hormone environment plays a distinct role in the generation of aged skin.

[Desynchronization: mechanisms of development from molecular to systemic levels]. / Desinkhronoz: mekhanizmy razvitiia ot molekuliarno-geneticheskogo do organizmennogo urovnia.

Striking progress in the field of molecular chronobiology has been made during the last years. It renders us to reconsider some traditional viewpoints concerning circadian system functioning. Not only we are able now to explain basic concept of how clock genes pass through transcriptional and post-transcriptional pathways and how circadian system eventually "comes to life" at the cellular level, but we are also in position to speculate on how the whole organism constitutes its space-temporal order and how certain ultradians and infradians could be generated. Herein we propose a concept of multifuctorial genesis of chronomes and suggest terms such as "input rhythm" (or influencing rhythm) and "output rhythm" (or modulated rhythm). We stress on a viewpoint that the majority of investigated variables are multifuctorial by its nature because of vast net of regulatory mechanisms lied down in between the molecular basis of the clock and the output rhythms which are actually measurable by investigators. An attempt to follow down mechanisms of loss in the circadian temporal order (desynchronization) from the molecular level to that of a whole organism has been provided.

A transcriptional timetable of autumn senescence.

BACKGROUND: We have developed genomic tools to allow the genus Populus (aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag (EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. RESULTS: On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree (Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. CONCLUSIONS: We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.

Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks.

Drosophila melanogaster has been a canonical model organism to study genetics, development, behavior, physiology, evolution, and population genetics for nearly a century. Despite this emphasis and the completion of its nuclear genome sequence, the timing of major speciation events leading to the origin of this fruit fly remain elusive because of the paucity of extensive fossil records and biogeographic data. Use of molecular clocks as an alternative has been fraught with non-clock-like accumulation of nucleotide and amino-acid substitutions. Here we present a novel methodology in which genomic mutation distances are used to overcome these limitations and to make use of all available gene sequence data for constructing a fruit fly molecular time scale. Our analysis of 2977 pairwise sequence comparisons from 176 nuclear genes reveals a long-term fruit fly mutation clock ticking at a rate of 11.1 mutations per kilobase pair per Myr. Genomic mutation clock-based timings of the landmark speciation events leading to the evolution of D. melanogaster show that it shared most recent common ancestry 5.4 MYA with D. simulans, 12.6 MYA with D. erecta+D. orena, 12.8 MYA with D. yakuba+D. teisseri, 35.6 MYA with the takahashii subgroup, 41.3 MYA with the montium subgroup, 44.2 MYA with the ananassae subgroup, 54.9 MYA with the obscura group, 62.2 MYA with the willistoni group, and 62.9 MYA with the subgenus Drosophila. These and other estimates are compatible with those known from limited biogeographic and fossil records. The inferred temporal pattern of fruit fly evolution shows correspondence with the cooling patterns of paleoclimate changes and habitat fragmentation in the Cenozoic.

Clock genes in calendar cells as the basis of annual timekeeping in mammals--a unifying hypothesis.

Melatonin-based photoperiod time-measurement and circannual rhythm generation are long-term time-keeping systems used to regulate seasonal cycles in physiology and behaviour in a wide range of mammals including man. We summarise recent evidence that temporal, melatonin-controlled expression of clock genes in specific calendar cells may provide a molecular mechanism for long-term timing. The agranular secretory cells of the pars tuberalis (PT) of the pituitary gland provide a model cell-type because they express a high density of melatonin (mt1) receptors and are implicated in photoperiod/circannual regulation of prolactin secretion and the associated seasonal biological responses. Studies of seasonal breeding hamsters and sheep indicate that circadian clock gene expression in the PT is modulated by photoperiod via the melatonin signal. In the Syrian and Siberian hamster PT, the high amplitude Per1 rhythm associated with dawn is suppressed under short photoperiods, an effect that is mimicked by melatonin treatment. More extensive studies in sheep show that many clock genes (e.g. Bmal1, Clock, Per1, Per2, Cry1 and Cry2) are expressed in the PT, and their expression oscillates through the 24-h light/darkness cycle in a temporal sequence distinct from that in the hypothalamic suprachiasmatic nucleus (central circadian pacemaker). Activation of Per1 occurs in the early light phase (dawn), while activation of Cry1 occurs in the dark phase (dusk), thus photoperiod-induced changes in the relative phase of Per and Cry gene expression acting through PER/CRY protein/protein interaction provide a potential mechanism for decoding the melatonin signal and generating a long-term photoperiodic response. The current challenge is to identify other calendar cells in the central nervous system regulating long-term cycles in reproduction, body weight and other seasonal characteristics and to establish whether clock genes provide a conserved molecular mechanism for long-term timekeeping.