Hundreds of conserved non-coding genomic regions are independently lost in mammals

Conserved non-protein-coding DNA elements (CNEs) often encode cis-regulatory elements and are rarely lost during evolution. However, CNE losses that do occur can be associated with phenotypic changes, exemplified by pelvic spine loss in sticklebacks. Using a computational strategy to detect complete loss of CNEs in mammalian genomes while strictly controlling for artifacts, we find >600 CNEs that are independently lost in at least two mammalian lineages, including a spinal cord enhancer near GDF11. We observed several genomic regions where multiple independent CNE loss events happened; the most extreme is the DIAPH2 locus. We show that CNE losses often involve deletions and that CNE loss frequencies are non-uniform. Similar to less pleiotropic enhancers, we find that independently lost CNEs are shorter, slightly less constrained and evolutionarily younger than CNEs without detected losses. This suggests that independently lost CNEs are less pleiotropic and that pleiotropic constraints contribute to non-uniform CNE loss frequencies. We also detected 35 CNEs that are independently lost in the human lineage and in other mammals. Our study uncovers an interesting aspect of the evolution of functional DNA in mammalian genomes. Experiments are necessary to test if these independently lost CNEs are associated with parallel phenotype changes in mammals.     

Exchange mechanism of chromosome loss]

Frequencies of induced losses of autosome 2, free arm of autosome 2 and simultaneous losses of two free arms of autosome 2 were determined as 3.25 x 10(-3), 2.78 x 10(-3), 0.84 x 10(-3), respectively. High frequency of simultaneous losses of two chromosomes may have pointed to the exchange nature of the chromosome losses. The similarity of frequencies of half-translocations in heterochromatin of autosome 2 and frequencies of the losses observed show that the chromosome losses are the consequence of exchanges in chromosomal heterochromatin.     

Increment kinetics of recessive lethal mutations and dominant lethals in offspring of Drosophila melanogaster on storage of methyl-methanesulfonate-treated sperm in females

The frequencies of sex-linked recessive lethal mutations in F1 males after feeding adult male Drosophila melanogaster with 0.25 and 0.5 mM methyl methanesulfonate (MMS) orally for 24 h increased approximately linearly with storage of the treated spermatozoa in females, whereas the number of hits of dominant lethals in the sperm after feeding 0.3 and 0.5 mM MMS increased approximately with the square of the storage time. Chromosome losses and mosaics in F1 males also increased with the dose of MMS to males, but their yields were too low to be analyzed quantitatively, only indicating a slight increase of chromosome loses and a slight decrease of mosaics with the time of storage of sperm. Maternal non-disjunctions (or chromosome losses), detected in F1 males, decreased with the dose of MMS to spermatozoa and their yield decreased with the time of storage of sperm of both MMS-treated and the control groups. A unitary model is proposed to explain the effect of storage on the dominant lethals and recessive lethal mutations.     

Mean airway pressure and mean alveolar pressure during high-frequency jet ventilation in rabbits

Mean airway pressure underestimates mean alveolar pressure during high-frequency oscillatory ventilation. We hypothesized that high inspiratory flows characteristic of high-frequency jet ventilation may generate greater inspiratory than expiratory pressure losses in the airways, thereby causing mean airway pressure to overestimate, rather than underestimate, mean alveolar pressure. To test this hypothesis, we ventilated anesthetized paralyzed rabbits with a jet ventilator at frequencies of 5, 10, and 15 Hz, constant inspiratory-to-expiratory time ratio of 0.5 and mean airway pressures of 5 and 10 cmH2O. We measured mean total airway pressure in the trachea with a modified Pitot probe, and we estimated mean alveolar pressure as the mean pressure corresponding in the static pressure-volume relationship to the mean volume of the respiratory system measured with a jacket plethysmograph. We found that mean airway pressure was similar to mean alveolar pressure at frequencies of 5 and 10 Hz but overestimated it by 1.1 and 1.4 cmH2O at mean airway pressures of 5 and 10 cmH2O, respectively, when frequency was increased to 15 Hz. We attribute this finding primarily to the combined effect of nonlinear pressure frictional losses in the airways and higher inspiratory than expiratory flows. Despite the nonlinearity of the pressure-flow relationship, inspiratory and expiratory net pressure losses decreased with respect to mean inspiratory and expiratory flows at the higher rates, suggesting rate dependence of flow distribution. Redistribution of tidal volume to a shunt airway compliance is thought to occur at high frequencies.(ABSTRACT TRUNCATED AT 250 WORDS)     

Steady and oscillatory transnasal pressure-flow relationships in healthy adults.

The influence of flow characteristics and gas physical properties on nasal resistance (NR) is difficult to ascertain with traditional rhinomanometric methods because the respiratory airflows used in these methods are largely uncontrolled. As an alternative, we used a novel method of rhinomanometry in which an externally generated flow is passed through the nasal passage via a mouthpiece. The transnasal pressure-flow relationships for both quasi-steady and oscillating flows and with different gases were obtained in five healthy adults with this method. For quasi-steady nasal flows the dimensionless pressure losses were largely independent of physical properties of the gas and a function of the Reynolds number (Re) of the flow. Values of NR for quasi-steady flows were largely independent of flow direction for Re up to roughly 3,000 in all five subjects and for Re up to roughly 19,000 in two of the five subjects. Airway collapse occurred in two subjects at Re greater than 3,000, suggesting that the nonrigid segments of the nasal passage contribute to the intersubject variations in NR at high flow rates. Pressure losses associated with oscillating flows measured at frequencies between 1 and 16 Hz were similar to steady flow losses provided that Re was less than roughly 3,000. For Re greater than 3,000 the oscillating flow resistances were affected by the phasic redistribution of flow into compliant segments of the nasal passage. These results indicate that, for flow rates and harmonic frequencies associated with breathing at rest, the nasal passage behaves as a rigid rough-walled pipe in which pressure losses are largely determined by forces relating to viscous friction and convective accelerations.     

Rapid dicentric assay of human blood lymphocytes after exposure to low doses of ionizing radiation

The probability of losses of different chromosome aberrations during the dicentric chromosome assay of metaphase cells with incomplete sets of chromosome centromeres was estimated using a mathematical model for low doses of ionizing radiation. A dicentric assay of human blood lymphocytes without determination of the total amount of chromosome centromeres in cells without chromosome aberrations (rapid dicentric assay) has been proposed. The rapid dicentric analysis allows to register chromosome aberrations in full compliance with the conventional classification. The experimental data have shown no statistically significant difference between the frequencies of dicentric chromosomes detected by rapid and classical dicentric chromosome assays of human lymphocytes exposed to 0.5 Gy of 60Co gamma-rays. The rate of the rapid dicentric assay was almost twice as high as that of the classical dicentric assay.     

Refined localization and two additional linked families for the DFNA10 locus for nonsyndromic hearing impairment

DFNA10 originally was mapped to the long arm of chromosome 6 in a large American family segregating for autosomal dominant progressive nonsyndromic hearing impairment. By extending this American family, we have reduced the original DFNA10 candidate region from 13 cM to 3.7 cM. We also report a Belgian family with autosomal dominant nonsyndromic hearing impairment linked to DFNA10 and a Norwegian family with the same condition in which linkage is suggestive, although maximum lod scores are only 2.5. The hearing phenotype in all three DFNA10 families is similar, with losses beginning in the middle frequencies and involving the low and high frequencies later in life.     

Adaptation to lengthening contraction-induced injury in mouse muscle.

Adaptations to repeated bouts of injury-inducing lengthening contractions were studied in mouse anterior crural muscles. Five bouts of 150 lengthening contractions were performed in vivo, with each bout separated by 2 wk of rest. Three primary observations were made. First, there was little, if any, attenuation in the immediate isometric torque losses after lengthening contractions at "physiological" stimulation frequencies (i.e., <125 Hz), although there was a pronounced decrease in torque loss at higher frequencies between the first and second bouts. Second, the immediate losses in strength that occurred after all five lengthening contraction bouts could be explained in part by excitation-contraction uncoupling. Third, the most important adaptation was a significant enhancement in the rate of recovery of strength after the lengthening contractions. It is probable that the accelerated rate of strength recovery resulted from the more rapid loss and subsequent recovery of myofibrillar protein observed after the fifth bout.     

Influence of the Local Field and Dipole-Dipole Interactions on the Spectral Characteristics of Simple Metals and Their Nanoparticles

The effect of dipole-dipole interactions of free electrons on the spectral characteristics of simple metals and their nanoparticles is analyzed using Drude theory and the model of the Lorentz local field. It is established that accounting for the dispersion of a local field under conditions of one-dimensional (1D) confinement based on the optical constants of the bulk metal allows the determination of its spectral micro-characteristics in the frequency region of the longitudinal collective motions of the free electrons. This corresponds to the spectra of the dielectric losses of bulk plasma oscillations. A similar procedure for three-dimensional (3D) confinement produces the spectrum of dielectric losses at the frequency of localized plasma oscillations. Using a number of simple metal examples, viz., Li, Na, and K, and also Al, Be, and Mg, it is shown that the frequencies of volume and localized plasma oscillations obtained from a model of dispersion of the local field in the long-wave limit are in good agreement with the actual frequencies of the plasma oscillations of the corresponding metals and the absorption maxima of their nanoparticles with a radius of 2–20 nm. It is shown that the frequencies of the main mode of longitudinal plasma oscillations and the absorption frequency of localized plasmons are well described using the dynamic theory of crystal lattice vibrations.

     

Attention and the detectability of weak taste stimuli

Subjects detected weak solutions of sucrose or citric acid under conditions in which attention was directed toward one of the tastants or the other. Detection thresholds were measured using an adaptive, forced-choice procedure, with a three-down one-up rule, which computer simulations suggest should be more reliable than the popular two-down one-up rule. The thresholds were modestly but systematically lower for attended tastants than for unattended ones. Similar results have been reported in other sense modalities, including vision (greater sensitivity to stimuli presented to attended versus unattended spatial locations) and hearing (greater sensitivity to stimuli presented at attended versus unattended sound frequencies). Taken together, the findings are consistent with a general hypothesis regarding attention in sensory systems: gains or losses in detectability occur when a central attentional mechanism (or, conceivably, a preattentive mechanism) selectively and preferentially monitors signals arising from particular subsets of peripheral neural inputs.      

Comparative study of the clastogenic efficiency of ethyl methanesulfonate and diethyl sulfate in Drosophila melanogaster mature sperm

Chromosome loss and translocation tests were carried out in Drosophila melanogaster sperm, stored in untreated females for up to 24 days, to compare the clastogenicity of ethyl methanesulfonate (EMS) and diethyl sulfate (DES). The sex-linked recessive lethal test was used as a "biological dosimeter" and the following results were obtained: The yield of 2-3 translocations induced by both mutagens increased steadily with storage, being significantly higher after EMS than after DES treatment. The frequencies of partial losses induced by EMS and DES were similar and increased with storage. With up to 11 days' storage, the frequency of complete loss induced by DES was higher than that induced by EMS and remained unchanged when storage was extended to 24 days. Complete loss induced by EMS increased significantly with further storage (12-24 days). With DES, complete (but not partial) loss was detected with a dose at which EMS failed to modify the control values. These data suggest that the lower recovery of II-III translocations after treatment with DES does not result from a low breaking capacity but from a diminished or delayed rejoining of the induced breaks. This could be due to a physiological impairment of the treated cells by the high toxicity of DES or to an actual lower rejoinability of the broken ends. The differential recovery of complete and partial losses after DES treatment further suggests that the mechanisms leading to the fixation of both types of damage are somehow different, and that processes intervening in the recovery of partial losses are less affected, or not at all, by the proposed reduced rejoining of chromosome breaks.     

Apparent trends of amino Acid gain and loss in protein evolution due to nearly neutral variation

It has recently been claimed that certain amino acids have been increasing in frequency in all living organisms for most of the history of life on earth, while other amino acids have been decreasing in frequency. Three lines of evidence have been offered for this assertion, but each has a more plausible alternative interpretation. Here I show that unequal patterns of gains and losses for particular pairs of amino acids (such as more leucine --> phenylalanine than phenylalanine --> leucine substitutions in humans and chimpanzees since they split from a common ancestor) are consistent with a simple neutral model at equilibrium amino acid frequencies. Unequal numbers of gains and losses for particular amino acids (such as more gains than losses of cysteine) are shown by simulations to be consistent with a model of nearly neutral evolution. Unequal numbers of gains and losses for particular amino acids in human polymorphism data are shown by simulations to be explainable by the nearly neutral model as well. In a comparison of protein sequences from four strains of Escherichia coli, polarized by one outgroup strain of Salmonella, the disparity in number of gains and losses for particular amino acids is strong in terminal branches but weaker or nonexistent in internal branches, which is inconsistent with the universal trend model but as expected under the nearly neutral model.     

Allelotyping of human prostatic adenocarcinoma.

Allelotyping (using at least one probe detecting a restriction fragment length polymorphism on each chromosomal arm, with the exception of the short arms of the acrocentric chromosomes), showed loss of genetic information in 11 of 18 prostate adenocarcinoma specimens analyzed (61%). Frequent allelic deletions were detected on the long arm of chromosome 16 (6 of 10 informative cases, 60%), on the short arm of chromosome 8 (3 of 6 informative cases, 50%), and on the short and/or the long arms of chromosome 10 (6 of 11 informative cases (10p), 55% and 4 of 13 informative cases (10q), 30%, respectively). No losses of alleles were detected in any case unless at least one of the chromosomes 8, 10, or 16 also showed deletions. The long arm of chromosome 18 also showed a high frequency of allelic deletions (3 of 7 informative cases, 43%). Allelic deletions on the following chromosomes were detected at lower frequencies: chromosomes 2, 3, 7, 12, 13, 17, 22, and XY. Tumors with allelic deletions on more than one chromosome had a higher histological malignancy grade. Tumors from patients with advanced disease all showed allelic deletions.     

Small tympanic membrane perforations in the inferior quadrants do not impact the manubrium vibration in guinea pigs

Background

It has been believed that location of the perforation has a significant impact on hearing loss. However, recent studies have demonstrated that the perforation sites had no impact on hearing loss. We measured the velocity and pattern of the manubrium vibration in guinea pigs with intact and perforated eardrum using a laser Doppler vibrometer in order to determine the effects of different location perforations on the middle ear transfer functions.

Methods

Two bullas from 2 guinea pigs were used to determine stability of the umbo velocities, and 12 bullas from six guinea pigs to determine the effects of different location perforations on sound transmission. The manubrium velocity was measured at three points on the manubrium in the frequencies of 0.5–8 kHz before and after a perforation was made. The sites of perforations were in anterior-inferior (AI) quadrants of left ears and posterior-inferior (PI) quadrants of right ears.

Results

The manubrium vibration velocity losses were noticed in the perforated ears only below 1.5 kHz. The maximum velocity loss was about 7 dB at 500 Hz with the PI perforation. No significant difference in the velocity loss was found between AI and PI perforations. The average ratio of short process velocity to the umbo velocity was approximately 0.5 at all frequencies. No significant differences were found before and after perforation at all frequencies (p>0.05) except 7 kHz (p = 0.004) for both AI and PI perforations.

Conclusions

The manubrium vibration velocity losses from eardrum perforation were frequency-dependent and the largest losses occur at low frequencies. Manubrium velocity losses caused by small acute inferior perforations in guinea pigs have no significant impact on middle ear sound transmission at any frequency tested. The manubrium vibration axis may be perpendicular to the manubrium below 8 kHz in guinea pigs.     

Selection at the ABO locus in the Japanese population

Hiraizumi et al. (1973b) concluded that maternal-fetal ABO incompatibility effect upon the frequency of prenatal deaths was totally absent in two modern Japanese cities, Ohdate and Akita. However, they found a significant heterogeneity in the frequency of prenatal deaths among 16 mating types and suggested that the viability of A-bearing fetuses was higher than that of others, hence the frequency of prenatal deaths decreased with the increasing probability of producing A-bearing fetuses. Further analyses were performed in the present study and the above suggestion was confirmed. Then, the average numbers of prenatal deaths and pregnancies per couple were analyzed separately for their relationships with the probability of producing an A-bearing fetus. The results were found to be consistent with the model that the average numbers of prenatal losses per couple are approximately the same between two groups of matings, one producing and the other not producing A-bearing fetuses, but such losses occur more frequently for the A-bearing fetuses than others at the very early stage of pregnancy such that wives may not recognize such losses. Although the stages of losses are different between A-bearing and other fetuses, the net losses are nearly the same between them, so that such losses will not be reflected in the segregation frequencies among children, as shown by Hiraizumi et al. (1973a).     

Nitrogen retention efficiency and nitrogen losses of a managed and phytodiverse temperate grassland

Maintaining nitrogen retention efficiency (NRE) is crucial in minimizing N losses when intensifying management of temperate grasslands. Our aim was to evaluate how grassland management practices and sward compositions affect NRE (1 − N losses/soil available N), defined as the efficiency with which soil available N is retained in an ecosystem. A three-factorial grassland management experiment was established with two fertilization treatments (without and combined N, phosphorus and potassium fertilization), two mowing frequencies (cut once and thrice per year) and three sward compositions (control, monocot- and dicot-enhanced swards). We measured N losses as leaching and nitrous oxide emissions, and soil available N as gross N mineralization rates. Fertilization increased N losses due to increased nitrification and decreased microbial N immobilization, and consequently decreased NRE. Intensive mowing partly dampened high N losses following fertilization. Sward compositions influenced NRE but not N losses: control swards that developed for decades under extensive management had the highest NRE, whereas monocot-enhanced sward had the lowest NRE. NRE was highly correlated with microbial NH₄⁺ immobilization and microbial biomass and only marginally correlated with plant N uptake, underlining the importance of microbial N retention in the soil-plant system. Microbial N retention is reflected in NRE but not in indices commonly used to reflect plant response. NRE was able to capture the effects of sward composition and fertilization whereas N losses were only sensitive to fertilization; thus, NRE is a better index when evaluating environmental sustainability of sward compositions and management practices of grasslands.     

Colour and luminance interactions in the visual perception of motion

We sought to determine the extent to which red-green, colour-opponent mechanisms in the human visual system play a role in the perception of drifting luminance-modulated targets. Contrast sensitivity for the directional discrimination of drifting luminance-modulated (yellow-black) test sinusoids was measured following adaptation to isoluminant red-green sinusoids drifting in either the same or opposite direction. When the test and adapt stimuli drifted in the same direction, large sensitivity losses were evident at all test temporal frequencies employed (1-16 Hz). The magnitude of the loss was independent of temporal frequency. When adapt and test stimuli drifted in opposing directions, large sensitivity losses were evident at lower temporal frequencies (1-4 Hz) and declined with increasing temporal frequency. Control studies showed that this temporal-frequency-dependent effect could not reflect the activity of achromatic units. Our results provide evidence that chromatic mechanisms contribute to the perception of luminance-modulated motion targets drifting at speeds of up to at least 32 degrees s(-1). We argue that such mechanisms most probably lie within a parvocellular-dominated cortical visual pathway, sensitive to both chromatic and luminance modulation, but only weakly selective for the direction of stimulus motion.     

Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis

Aneura mirabilis is a parasitic liverwort that exploits an existing mycorrhizal association between a basidiomycete and a host tree. This unusual liverwort is the only known parasitic seedless land plant with a completely nonphotosynthetic life history. The complete plastid genome of A. mirabilis was sequenced to examine the effect of its nonphotosynthetic life history on plastid genome content. Using a partial genomic fosmid library approach, the genome was sequenced and shown to be 108,007 bp with a structure typical of green plant plastids. Comparisons were made with the plastid genome of Marchantia polymorpha, the only other liverwort plastid sequence available. All ndh genes are either absent or pseudogenes. Five of 15 psb genes are pseudogenes, as are 2 of 6 psa genes and 2 of 6 pet genes. Pseudogenes of cysA, cysT, ccsA, and ycf3 were also detected. The remaining complement of genes present in M. polymorpha is present in the plastid of A. mirabilis with intact open reading frames. All pseudogenes and gene losses co-occur with losses detected in the plastid of the parasitic angiosperm Epifagus virginiana, though the latter has functional gene losses not found in A. mirabilis. The plastid genome sequence of A. mirabilis represents only the second liverwort, and first mycoheterotroph, to have its plastid genome sequenced. We observed a pattern of genome evolution congruent with functional gene losses in parasitic angiosperms but suggest that its plastid genome represents a genome in the early stages of decay following the relaxation of selection pressures.     

The Ncl-1 Gene and Genetic Mosaics of Caenorhabditis Elegans

A ncl-1 mutation results in enlarged nucleoli, which can be detected in nearly all cells of living animals by Nomarski microscopy. Spontaneous mitotic loss of a ncl-1(+)-containing free duplication in an otherwise homozygous ncl-1 mutant animal results in mosaicism for ncl-1 expression, and the patterns of mosaicism lead us to conclude that ncl-1 acts cell autonomously. The probability of mitotic loss of the duplication sDp3 is approximately constant over many cell divisions. About 60% of the losses of sDp3 at the first embryonic cell division involve nondisjunction. Frequencies of mitotic loss of different ncl-1(+)-bearing free duplications varied over a 200-fold range. The frequencies of mitotic loss were enhanced by a chromosomal him-10 mutation. We have used ncl-1 as a cell autonomous marker in the mosaic analysis of dpy-1 and lin-37. The focus of action of dpy-1 is in hypodermis. A mutation in lin-37 combined with a mutation in another gene results in a synthetic multivulva phenotype. We show that lin-37 acts cell nonautonomously and propose that it plays a role, along with the previously studied gene lin-15, in the generation of an intercellular signal by hyp7 that represses vulval development.     

Cuckoldry and the stability of biparental care

In socially monogamous species, females may engage in extra-pair fertilizations to gain direct or indirect benefits not provided by the social mate, with the potential risk of a reduction in the social mate’s paternal effort. I present an ESS model of cuckoldry frequencies, which considers both facultative and nonfacultative male responses to losses in paternity. Two possible equilibria exist: stable social monogamy with varying degrees of extra-pair paternity, and polygamy with little or no male care. Monogamy with limited cuckoldry can be stable only if the initial cuckoldry frequency is low, intrinsic cuckoldry benefits are not high, males can reasonably accurately detect cuckoldry, and female compensation for losses in male care is incomplete. Deviations from these assumptions lead to stronger mate acquisition in males at the expense of paternal care, and eventually to runaway evolution towards polygamy. Average female fitness is reduced in the runaway, although it is initiated by females maximizing the survival of offspring – a potential “tragedy of the commons” in breeding systems.