The genomic context of retrocopies increases their chance of functional relevancy in mammals

Described as “junk” DNA, pseudogenes are dead structures of previously active genes present in genomes. Pseudogenes are categorized into two main classes: processed pseudogenes, formed through retrotransposition, and non-processed pseudogenes, typically originated from gene decay following duplication events. The term “processed pseudogene” has changed to “retrocopy” since they are likely to evolve new functional roles and became a retrogene. Here, we surveyed 38,080 retrocopies from chimpanzee, dog, human, mouse, and rat genomes to assess their potential adaptive value. The retrocopies inserted in the same chromosome of the parental gene have higher chances of remain potentially “active” (absence of premature stop codons and frameshifts) (~26.1%), while those placed into a different chromosome have a twofold decrease chance of continuing potentially “active” (~7.52%). The genomic context of their placement seems associated with their expression. Retrocopies placed in intragenic regions and the same sense of the “host” gene have higher chances of being expressed relative to other genomic contexts. The proximity of retrocopies to their parental gene is associated with a lower decay rate, and their location likely influence their expression. Thus, despite their unclear role, retrocopies are probably involved in adaptive processes. Our results evidence natural selection acting in retrocopies.     

Transcriptome analysis reveals the difference between “healthy” and “common” aging and their connection with age‐related diseases

A key goal of aging research was to understand mechanisms underlying healthy aging and develop methods to promote the human healthspan. One approach is to identify gene regulations unique to healthy aging compared with aging in the general population (i.e., “common” aging). Here, we leveraged Genotype‐Tissue Expression (GTEx) project data to investigate “healthy” and “common” aging gene expression regulations at a tissue level in humans and their interconnection with diseases. Using GTEx donors' disease annotations, we defined a “healthy” aging cohort for each tissue. We then compared the age‐associated genes derived from this cohort with age‐associated genes from the “common” aging cohort which included all GTEx donors; we also compared the “healthy” and “common” aging gene expressions with various disease‐associated gene expressions to elucidate the relationships among “healthy,” “common” aging and disease. Our analyses showed that 1. GTEx “healthy” and “common” aging shared a large number of gene regulations; 2. Despite the substantial commonality, “healthy” and “common” aging genes also showed distinct function enrichment, and “common” aging genes had a higher enrichment for disease genes; 3. Disease‐associated gene regulations were overall different from aging gene regulations. However, for genes regulated by both, their regulation directions were largely consistent, implying some aging processes could increase the susceptibility to disease development; and 4. Possible protective mechanisms were associated with some “healthy” aging gene regulations. In summary, our work highlights several unique features of GTEx “healthy” aging program. This new knowledge could potentially be used to develop interventions to promote the human healthspan.     

An Analysis of the Formation of Ciliary Primordia in the Hypotrich Ciliate Urostyla weissei*

SYNOPSIS. The protargol technic was used in a study of the development of oral, cirral, and dorsal primordia of Urostyla weissei fixed during division, reorganization, and regeneration following transection at different levels. While the course of development is similar in all situations, differences were observed in the way in which some primordia are initiaily formed. The primordium of the new AZM always appears posterior to the old AZM. It develops into an entire new membranellar band in dividing cells and in opimers (posterior fragments from equatorial transections), while it eventually joins with a portion of the old AZM in reorganizers, promers (anterior fragments from equatorial transections) and “large opimers” (cells whose anterior tip has been cut off). The UM-primordium of proters is derived from disaggregation of the kinetosomes of the 2 old UM's, that of opisthes and opimers is formed “de novo” to the right of the AZM-primordium, while the UM-primordium of reorganizers, promers, and “large opimers” is of composite origin, partly “de novo” and partly from the old UM's. The UM primordium differentiates into the new UM's and the 1st frontal cirrus. The primordia of the remaining frontal, ventral, transversal (F-V-T) and marginal cirri originate as “streaks” of cilia, most of which are derived from re-alignment of the constituent cilia of certain pre-existing cirri. New cirri differendiate from the streaks, and replace the remaining old cirri. The streaks are formed similarly in all developmental situations, except for the 1st 3 F-V-T streaks. In proters, reorganizers, and promers, these originate from the posterior 3 frontal cirri, while in opisthes and opimers they are formed “de novo” to the right of the UM-primordium. In the “large opimers” these streaks are formed “de novo” behind the 1st 3 frontal cirri, in spite of the continued presence of these cirri at the anterior tip of the fragments. The site of formation of these streaks thus appears to be determined by an anteriorposterior gradient, rather than by any preformed cortical structure. The new dorsal bristle rows I to III develop from the proliferation of portions of the old rows, while rows IV and V originate from short kineties formed “de novo” on the right margin. New caudal cirri differentiate at the posterior ends of the new rows I to III. The numbers of ventral cirral rows and transversal cirri are variable; these variations are correlated, and related to variations in numbers of developing streaks. A survey of hypotrich developmental patterns revealed extensive parallels, especially in the sites of appearance of primordia. The primordium site appears to be a more constant feature of cortical development than is the “source” of ciliary units. It is concluded that sites of primordia are determined by cellular gradients, with competent preformed structures being utilized if they are appropriately positioned within these gradients.     

Growing up abroad: Italian and Romanian migrants’ partial transitions to adulthood

Drawing on in-depth interviews with young Italians and Romanians, representing two of the largest “old” and “new” European populations in Britain, this paper examines migrants’ experiences in the spheres of work, family and “home”, and their narratives of “growing up” abroad, to enhance our understanding of youth transitions to adulthood in the context of intra-EU migration. Contrary to accounts that see migration as a strategy to either delay or advance adulthood, our analysis offers a more complex picture, showing how migration may unevenly affect transitions to adulthood, advancing some, and delaying others. Furthermore, we extend debates around the meaning of adulthood, illustrating the central role migration plays in generating feelings of “growing up”, even when traditional markers of adulthood are absent, and how these are negotiated transnationally in relation to home-based peers, in ways that combine old and new understandings of adulthood.     

DIRECT AND CORRELATED RESPONSES TO SELECTION ON AGE AT REPRODUCTION IN DROSOPHILA MELANOGASTER

Aging may be a consequence of mutation accumulation or of negative pleiotropic correlations between performance late and earlier in the lifespan. This study used artificial selection on flies derived from two different base stocks to produce “young” and “old” lines, propagated by breeding from young and old adults respectively. Virgin and mated adults of both sexes from the “old” lines lived longer than “young” line flies. “Young” and “old” mated females did not differ in fecundity or fertility early in the lifespan, but “old” line females had higher fecundity and fertility late in life. The results therefore suggested either that the response to selection had revealed the effect of mutation accumulation, or that pleiotropy involving characters other than early fecundity must have been involved. Development time from egg to adult was longer in the “old” lines. Competition of selected line larvae from one base stock against mutant marked larvae from the same base stock revealed that, at a wide range of larval densities, “old” line larvae showed lower survival rates than “young” line larvae. Thorax length and wet weight were significantly greater in the “old” line flies from one base stock. The results may imply that the selection regime in the “old” lines favored extended growth during development to produce a more durable adult soma, despite the cost in increased larval mortality and delayed reproduction, because the potential reproductive benefits later in life were increased. However, the differences between larvae from “old” and “young” lines could also be attributable to density differences, and this possibility needs systematic investigation.     

The genetic divergence of three populations

This paper considers the effect of the genetic divergence on the genetic composition of three samples drawn from three populations at some time after the populations had split. It generalizes the two-sample case studied earlier by Watterson (1985a). Under the assumptions that (i) mating is at random, (ii) the genes at a locus can be any of infinitely many alleles and all mutants are assumed to be new alleles, and (iii) no selective differences exist, we find the probability distribution of the sample gene configurations. From this distribution the single-sample allelic distribution after one-step and two-step bottlenecks and the allelic distribution in the two-sample case can be obtained as marginal distributions. Some numerical results on the number of alleles in common in the three samples are compared with those obtained by Watterson's simulation method; the agreement is excellent. Also, the probability that the three samples are monomorphic for the same allele is found, and numerical examples are given.     

Sample size calculations based on ranking and selection in microarray experiments

Summary .   We develop formulae to calculate sample sizes for ranking and selection of differentially expressed genes among different clinical subtypes or prognostic classes of disease in genome-wide screening studies with microarrays. The formulae aim to control the probability that a selected subset of genes with fixed size contains enough truly top-ranking informative genes, which can be assessed on the basis of the distribution of ordered statistics from independent genes. We provide strategies for conservative designs to cope with issues of unknown number of informative genes and unknown correlation structure across genes. Application of the formulae to a clinical study for multiple myeloma is given.     

Structural changes and fluctuations of proteins: I. A statistical thermodynamic model

A general theory of the structural changes and fluctuations of proteins has been proposed based on statistical thermodynanic considerations at the chain level.The “structure” of protein was assumed to be characterized by the state of secondary bonds between unique pairs of specific sites on peptide chains. Every secondary bond changes between the bonded and unboned states by thermal agitation and the “structure” is continuously fluctuating. The free energy of the “structural state” that is defined by the fraction of secondary bonds in the bonded state has been expressed by the bond energy, the cooperative interaction between bonds, the mixing entropy of bonds, and the entropy of polypeptide chains. The most probable “structural state” can be simply determined by graphical analysis and the effect of temperature or solvent composition on it is discussed. The temperature dependence of the free energy, the probability distribution of structural states and the specific heat have been calculated for two examples of structural change.The theory predicts two different types of structural changes from the ordered to disordered state, a “structural transition” and a “gradual structural change” with rising temperature, In the “structural transition”, the probability distribution has two maxima in the temperature range of transition. In the “gradual structural change”, the probability distribution has only one maximum during the change.A considerable fraction of secondary bonds is in the unbonded state and is always fluctuating even in the ordered state at room temperature. Such structural fluctuations in a single protein molecule have been discussed quantitatively.The theory is extended to include small molecules which bind to the protein molecule and affect the structural state. The changes of structural state caused by specific and non-specific binding and allosteric effects are explained in a unified manner.     

On the Divergence of Alleles in Nested Subsamples from Finite Populations

Within-population variation at the DNA level will rarely be studied by sequencing of loci of randomly chosen individuals. Instead, individuals will usually be chosen for sequencing based on some knowledge of their genotype. Data collected in this way require new sampling theory. Motivated by these observations, we have examined the sampling properties of a finite population model with two mutation processes and with no selection or recombination. One mutation process generates new alleles according to an infinite-alleles model, and the other generates polymorphisms at sites according to an infinite-sites model. A sample of n genes is considered. The stationary distribution of the number of segregating sites in a subsample from one of the allelic classes in the sample conditional on the allelic configuration of the sample is studied. A recursive scheme is developed to compute the moments of this distribution, and it is shown that the distribution is functionally independent of the number of additional alleles in the sample and their respective frequencies in the sample. For the case in which the sample contains only two alleles, the distribution of the number of segregating sites in a subsample containing both alleles conditional on the sample frequencies of the alleles is studied. The results are applied to the analysis of DNA sequences of two alleles found at the Adh locus of Drosophila melanogaster. No significant departure from the neutral model is detected.     

Estimating multiple time‐fixed treatment effects using a semi‐Bayes semiparametric marginal structural Cox proportional hazards regression model

Marginal structural models for time‐fixed treatments fit using inverse‐probability weighted estimating equations are increasingly popular. Nonetheless, the resulting effect estimates are subject to finite‐sample bias when data are sparse, as is typical for large‐sample procedures. Here we propose a semi‐Bayes estimation approach which penalizes or shrinks the estimated model parameters to improve finite‐sample performance. This approach uses simple symmetric data‐augmentation priors. Limited simulation experiments indicate that the proposed approach reduces finite‐sample bias and improves confidence‐interval coverage when the true values lie within the central “hill” of the prior distribution. We illustrate the approach with data from a nonexperimental study of HIV treatments.     

Models of race and cline

Computer models have been constructed to depict in the form of two-dimensional maps the effect of local selection on gene frequencies, particularly where partial barriers to gene flow are present at some points in an area. It was found that small amounts of uniform gene flow between foci of contrasting selection tend to produce evenly spaced isogenes, giving a “clinal” pattern. The interposition of partial barriers causes isogenes to become closer together in the region of the barriers and to become parallel to the barriers. A corollary result is that in the region of the barriers the isogene systems for different genes tend to become parallel to one another even though the exact foci of active selection for the genes do not coincide. This resembles a “racial” rather than “clinal” trait distribution. It was further observed that if a focus of active selection was peripheral in position (i.e., far from a genetic barrier) a clinal pattern extended across the area it affected between it and the barrier. If such a focus lies close to the barrier, the area it affects becomes rather uniform in gene frequency, with the “hinterland” approximating the gene frequency of the focus of active selection. On the basis of these models interpretation of the distribution of cold-adapted Mongoloid traits, and of the distribution of skin color across Europe and Africa, are suggested.     

Triosephosphate isomerase from young and old Turbatrix aceti.

Triosephosphate isomerase (EC 5.3.1.1) has been purified from young and old Tubatrix aceti. The enzyme shows a sharply lower specific activity in homogenates from old nematodes compared to similar preparations from young animals. However, when the enzyme activity of the respective homogenates was adjusted to the same level, equal amounts of antiserum (prepared to pure “young” triosephosphate isomerase) were required to remove the activity. Therefore, the lower specific activity observed in “old” homogenates was due to the presence of less enzyme and not to “altered” enzyme. The same results were obtained by immunotitrations of pure preparations of “young” and “old” enzyme. Moreover, in contrast to results reported for other enzymes, the specific activity of “old” triosephosphate isomerase, during purification, rose to the same value as that of pure “young” enzyme. The evidence indicates that altered triosephosphate isomerase does not exist in old T. aceti. The above results contradict the idea of an “error theory” in which all proteins would develop altered sequences. Pure triosephosphate isomerase (old or young) from T. aceti consists of two subunits, each of molecular weight 26,500. No isozymes could be detected.     

Estimating summary statistics in the spike-train space

Estimating sample averages and sample variability is important in analyzing neural spike trains data in computational neuroscience. Current approaches have focused on advancing the use of parametric or semiparametric probability models of the underlying stochastic process, where the probabilistic distribution is characterized at each time point with basic statistics such as mean and variance. To directly capture and analyze the average and variability in the observation space of the spike trains, we focus on a data-driven approach where statistics are defined and computed in a function space in which the spike trains are viewed as individual points. Based on the definition of a “Euclidean” metric, a recent paper introduced the notion of the mean of a set of spike trains and developed an efficient algorithm to compute it under some restrictive conditions. Here we extend this study by: (1) developing a novel algorithm for mean computation that is quite general, and (2) introducing a notion of covariance of a set of spike trains. Specifically, we estimate the covariance matrix using the geometry of the warping functions that map the mean spike train to each of the spike trains in the dataset. Results from simulations as well as a neural recording in primate motor cortex indicate that the proposed mean and covariance successfully capture the observed variability in spike trains. In addition, a “Gaussian-type” probability model (defined using the estimated mean and covariance) reasonably characterizes the distribution of the spike trains and achieves a desirable performance in the classification of the spike trains.     

Sample size planning for developing classifiers using high-dimensional DNA microarray data

Many gene expression studies attempt to develop a predictor of pre-defined diagnostic or prognostic classes. If the classes are similar biologically, then the number of genes that are differentially expressed between the classes is likely to be small compared to the total number of genes measured. This motivates a two-step process for predictor development, a subset of differentially expressed genes is selected for use in the predictor and then the predictor constructed from these. Both these steps will introduce variability into the resulting classifier, so both must be incorporated in sample size estimation. We introduce a methodology for sample size determination for prediction in the context of high-dimensional data that captures variability in both steps of predictor development. The methodology is based on a parametric probability model, but permits sample size computations to be carried out in a practical manner without extensive requirements for preliminary data. We find that many prediction problems do not require a large training set of arrays for classifier development.     

The Sacred Calf Pipe Bundle: It’s Effect on the Present Teton Dakota*

Abstract

In the legends of the Teton Dakota the White Buffalo Calf Maiden, as a messenger from Wakan Tanka, gave the people the Sacred Calf Pipe Bundle. This bundle became the center of the Teton’s religious beliefs, for with the bundle the Calf Maiden also gave the people certain religious ceremonies. Chief among these were the Sun Dance, the Hunkalowanpi and the Spirit-keeping ritual. From the old days to the present this bundle has been held in great reverence. To date there have been 11 keepers of the bundle, the present keeper being a 15 year old boy. To some extent the attitudes and views toward the old religion have been modified by the present generation. However, through the efforts of certain individuals a reawakening of the people towards things “Indian” is taking place. One example is a new course of studies in some Indian schools on “How to be a Modern Indian.” A second is the proposed building of a new Catholic church at Pine Ridge, South Dakota, in the image of a tipi decorated with the symbols and meanings of the old Teton religion, and a third is the use of the “peace pipe” in Catholic services.     

Biosynthesis of the photosynthetic membranes of rhodopseudomonas sphaeroides

The steady-state biosynthesis of the photosynthetic membrane (ICM) of Rhodopseudomonas sphaeroides has been reviewed. At moderate light intensities, 500 ft-c, preexisting ICM serves as the insertion matrix for newly synthesized membrane components. Whereas the bulk of the membrane protein, protein-pigment complexes, and pigments are inserted into preexisting ICM throughout the cell cycle, phospholipid is transferred from outside the ICM to the ICM only at the time of cell division. Because the site of cellular phospholipid synthesis is the cytoplasmic membrane, these results infer that despite the physical continuity of cytoplasmic membrane and ICM, there must exist between these membranous domains a “barrier” to the free diffusion of cellular phospholipid. The cyclical alternation in protein to phospholipid ratio of the ICM infers major structural and functional alternations, such as changes in the protein to lipid ratio of the membrane, specific density of the membrane, lipid structure within the membrane, and the rate of cyclic electron flow. When biochemical studies are correlated with detailed electron microscopic investigations we can further conclude that the number of photosynthetic units within the plane of the membrane can vary by nearly a factor of two over the course of the cell cycle. The average physical size of the photosynthetic units is constant for a given light intensity but inversely proportional to light intensity. The distribution of photosynthetic unit size classes within the membrane can be interpreted as suggesting that the “core” of the photosynthetic unit (reaction center plus fixed antenna complex) is inserted into the membrane coordinately as a structural entity. The variable antenna complex is, on the other hand, inserted independent of the “core” and randomly associates with both old and new core complexes. Finally, we conclude that there is substantial substructure to the distribution of photosynthetic units within the ICM, ie, they are highly ordered and exist in a defined spatial orientation to one another.     

Blessed are the meek for they shall inherit the earth: quietness component of introversion is associated with single nucleotide polymorphisms in two circadian clock genes

Individual differences studied by chronobiologists and personality psychologists are usually shaped by polygenic selection occurring by small allele frequency shifts spreading across many loci. Therefore, the candidate gene association studies suffer from increased likelihood of false positive findings. We previously associated a PER3 single nucleotide polymorphism (SNP, rs228697) with self-ratings on personality-relevant nouns exemplifying personality dimension of Extraversion/Introversion in a sample of 88 female students. To replicate and extend this finding, we genotyped three more SNPs in three circadian clock genes. The results indicated that the minor alleles of PER3 rs228697 and PER2 rs934945 were rather similar in terms of their association with a personality type nicknamed “demure persona” (i.e. described by such nouns as “quietness”, “restraint”, “taciturnity”, “bashfulness”, “timidity”, “constraint”, and “reticence”). Analysis of data from populations of the 1000 Genomes Project suggested that, like frequencies of the minor alleles of many SNPs in circadian clock genes, the frequencies of these two SNPs were higher in populations of out-of-African ancestry compared to populations of African ancestry. We suggested that genetic candidates for Extraversion/Introversion can be prioritized in future association studies by means of identification of genetic signatures of polygenic selection imposed by out-of-Africa expansion of ancestral populations.