The dynamic genetic determinants of increased transcriptional divergence in spermatids

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify allele-specific expression during spermatogenic differentiation at single-cell resolution in an F1 hybrid mouse system, allowing for the comprehensive characterisation of cis- and trans-genetic effects, including their dynamics across cellular differentiation. Collectively, almost half of the genes subject to genetic regulation show evidence for dynamic cis-effects that vary during differentiation. Our system also allows us to robustly identify dynamic trans-effects, which are less pervasive than cis-effects. In aggregate, genetic effects were strongest in round spermatids, which parallels their increased transcriptional divergence we identified between species. Our approach provides a comprehensive quantification of the variability of genetic effects in vivo, and demonstrates a widely applicable strategy to dissect the impact of regulatory variants on gene regulation in dynamic systems.

Noncanonical functions of the serine-arginine-rich splicing factor (SR) family of proteins in development and disease

Members of the serine/arginine (SR)-rich protein family of splicing factors play versatile roles in RNA processing steps and are often essential for normal development. Dynamic changes in RNA processing and turnover allow fast cellular adaptions to a changing microenvironment and thereby closely cooperate with transcription factor networks that establish cell identity within tissues. SR proteins play fundamental roles in the processing of pre-mRNAs by regulating constitutive and alternative splicing. More recently, SR proteins have also been implicated in other aspects of RNA metabolism such as mRNA stability, transport and translation. The- emerging noncanonical functions highlight the multifaceted functions of these SR proteins and identify them as important coordinators of gene expression programmes. Accordingly, most SR proteins are essential for normal cell function and their misregulation contributes to human diseases such as cancer.

Loss of 5-methylcytosine alters the biogenesis of vault-derived small RNAs to coordinate epidermal differentiation

The presence and absence of RNA modifications regulates RNA metabolism by modulating the binding of writer, reader, and eraser proteins. For 5-methylcytosine (m5C) however, it is largely unknown how it recruits or repels RNA-binding proteins. Here, we decipher the consequences of m5C deposition into the abundant non-coding vault RNA VTRNA1.1. Methylation of cytosine 69 in VTRNA1.1 occurs frequently in human cells, is exclusively mediated by NSUN2, and determines the processing of VTRNA1.1 into small-vault RNAs (svRNAs). We identify the serine/arginine rich splicing factor 2 (SRSF2) as a novel VTRNA1.1-binding protein that counteracts VTRNA1.1 processing by binding the non-methylated form with higher affinity. Both NSUN2 and SRSF2 orchestrate the production of distinct svRNAs. Finally, we discover a functional role of svRNAs in regulating the epidermal differentiation programme. Thus, our data reveal a direct role for m5C in the processing of VTRNA1.1 that involves SRSF2 and is crucial for efficient cellular differentiation.

Considerations for skin carcinogenesis experiments using inducible transgenic mouse models

OBJECTIVE

This study was designed to estimate the percentage of non-malignant skin tumours (papillomas) progressing to malignant squamous cell carcinomas (SCCs) in a carcinogenesis study using established transgenic mouse models. In our skin cancer model, we conditionally induced oncogenic point mutant alleles of p53 and k-ras in undifferentiated, basal cells of the epidermis.

RESULTS

Upon activation of the transgenes through administration of tamoxifen, the vast majority of mice (> 80%) developed skin papillomas, yet primarily around the mouth. Since these tumours hindered the mice eating, they rapidly lost weight and needed to be culled before the papillomas progressed to SCCs. The mouth papillomas formed regardless of the route of application, including intraperitoneal injections, local application to the back skin, or subcutaneous insertion of a tamoxifen pellet. Implantation of a slow releasing tamoxifen pellet into 18 mice consistently led to papilloma formation, of which only one progressed to a malignant SCC. Thus, the challenges for skin carcinogenesis studies using this particular cancer mouse model are low conversion rates of papillomas to SCCs and high frequencies of mouth papilloma formation.

Application of proteomics to the study of pollination drops

PREMISE OF THE STUDY

Pollination drops are a formative component in gymnosperm pollen-ovule interactions. Proteomics offers a direct method for the discovery of proteins associated with this early stage of sexual reproduction. •

METHODS

Pollination drops were sampled from eight gymnosperm species: Chamaecyparis lawsoniana (Port Orford cedar), Ephedra monosperma, Ginkgo biloba, Juniperus oxycedrus (prickly juniper), Larix ×marschlinsii, Pseudotsuga menziesii (Douglas-fir), Taxus ×media, and Welwitschia mirabilis. Drops were collected by micropipette using techniques focused on preventing sample contamination. Drop proteins were separated using both gel and gel-free methods. Tandem mass spectrometric methods were used including a triple quadrupole and an Orbitrap. •

RESULTS

Proteins are present in all pollination drops. Consistency in the protein complement over time was shown in L. ×marschlinsii. Representative mass spectra from W. mirabilis chitinase peptide and E. monosperma serine carboxypeptidase peptide demonstrated high quality results. We provide a summary of gymnosperm pollination drop proteins that have been discovered to date via proteomics. •

DISCUSSION

Using proteomic methods, a dozen classes of proteins have been identified to date. Proteomics presents a way forward in deepening our understanding of the biological function of pollination drops.

Space-time resolved approach for interacting quantum field theories

An alternative approach to the usual perturbative S-matrix evaluation of quantum field theories is presented which is nonperturbative and provides full space-time resolution. We study the dynamical development of the force between two fermion wave packets for the Yukawa system. The spatial distribution of the virtual bosons that act as mediators of the force can be analyzed along with the fermionic densities. Using a potential function for the fermion-fermion interaction is a good approximation to the field theoretical calculations when the Fock space is restricted to only one boson, but in the full quantum field theory the fermion-fermion force is enhanced by higher-order multiboson processes. Furthermore, the normally attractive fermion-fermion Yukawa force can, in principle, be manipulated to even be repulsive if the momentum modes available to the virtual bosons are restricted.

Photon-density waves in macroscopic and microscopic plane-parallel scattering samples

We investigate the validity of the Boltzmann equation to predict the reflection and transmission coefficients for an intensity modulated laser beam passing through a microscopic medium consisting of discrete scatterers. For a one-dimensional model system we demonstrate that the Boltzmann equation works remarkably well for small modulation frequencies, even to describe a medium comprised of only 10 scatterers. Discrepancies can be found only if the modulation wavelength of the laser intensity is commensurate with the spacing between the scatterers and if the medium is sufficiently ordered.

Relativistic resonances in combined magnetic and laser fields

We propose a mechanism for experimental investigation of relativistic effects in the laser-atom interaction with moderate (nonrelativistic) laser intensities that involves placing the system in a static magnetic field parallel to the laser's magnetic-field component. The resonantly induced relativistic motion of the atomic electron leads to a variety of novel phenomena: a relativistic dephasing leading to a ringlike spatial probability density, a counterintuitive window of relativistically enhanced motion, and a sequence of sawtooth-shaped resonances that may increase the harmonic generation.

Crying in hospitals: a survey of doctors', nurses' and medical students' experience and attitudes

OBJECTIVE

To investigate doctors', nurses' and medical students' experiences with, and attitudes of health care personnel towards, crying in hospitals.

DESIGN

Descriptive, cross-sectional study, using self-report questionnaires.

SETTING AND PARTICIPANTS

The sample comprised 52 doctors (response rate, 33%) and 103 nurses (response rate, 58%) from three Sydney metropolitan general hospitals, and 101 sixth-year medical students (response rate, 99%).

RESULTS

Crying was frequent in hospitals; 57% of doctors, 76% of nurses and 31% of medical students had cried at work in the hospital at least once, and women cried significantly more often than men. Being a nurse significantly increased, whereas being a medical student significantly decreased, the likelihood of crying. Medical students reported the highest percentage of negative social consequences of their own crying (e.g., being ridiculed or screamed at). The main reason for all respondents' crying was identification and bonding with suffering and dying patients or their families. The respondents generally viewed crying by patients as a healthy response, and they were empathetic towards the crying patient. About one-third of the respondents were interested in (or would consider) using psychological help to explore their own emotional reactions to crying.

CONCLUSION

Despite its limited sample, this study suggests that the topic of "crying" should be included in medical training, and that support be provided for medical staff who are distressed by crying behaviour in hospitals.

Relationship between Cultural Factors and Nematodes on Merion Kentucky Bluegrass

A 2-year study was conducted on Merion Kentucky bluegrass turf (Poa pratensis) to identify potential relationships among seasonal population dynamics of nematodes, chemical applications, thatch, tillering, dollar spot caused by Sclerotinia homoeocarpa, clipping weight, and other factors. Numbers of Tylenchorhynchus maximus determined during June were inversely related to the wet weight of grass from May. One or more monthly counts of Paratylenchus hamatus, Criconemella rusium, and T. maximus negatively correlated with the numbers of spring tillers. Applications of benomyl, used for dollar spot control, decreased numbers of T. maximus and free-living nematodes, and this chemical was associated with acidification of the thatch. Hoplolaimus galeatus levels were associated with an estimated 8% increase in the severity of dollar spot.

Polychlorinated Biphenyl Dechlorination in Aquatic Sediments

The polychlorinated biphenyl (PCB) residues in the aquatic sediments from six PCB spill sites showed changes in PCB isomer and homolog (congener) distribution that indicated the occurrence of reductive dechlorination. The PCB dechlorinations exhibited several distinct congener selection patterns that indicated mediation by several different localized populations of anaerobic microorganisms. The higher (more heavily chlorinated) PCB congeners that were preferentially attacked by the observed dechlorination processes included all those that are either pharmacologically active or persistent in higher animals. All the lower (less heavily chlorinated) PCB congeners formed by the dechlorinations were species that are known to be oxidatively biodegradable by the bacteria of aerobic environments.

Extensive degradation of Aroclors and environmentally transformed polychlorinated biphenyls by Alcaligenes eutrophus H850

We have isolated and characterized a strain of Alcaligenes eurtrophus, designated H850, that rapidly degrades a broad and unusual spectrum of polychlorinated biphenyls (PCBs) including many tetra- and pentachlorobiphenyls and several hexachlorobiphenyls. This strain, which was isolated from PCB-containing dredge spoils by enrichment on biphenyl, grows well on biphenyl and 2-chlorobiphenyl but poorly on 3- and 4-chlorobiphenyl. Capillary gas-chromatographic analysis showed that biphenyl-grown resting cells of H850 degraded the components of 38 of the 41 largest peaks of Aroclor 1242 and 15 of the 44 largest peaks of Aroclor 1254, resulting in an overall reduction of PCBs by 81% for Aroclor 1242 (10 ppm) and 35% for Aroclor 1254 (10 ppm) in 2 days. Furthermore, H850 metabolized the predominantly ortho-substituted PCB congeners that resulted from the environmental transformation of the more highly chlorinated congeners of Aroclor 1242 by the upper Hudson River anaerobic meta-, para-dechlorination agent system C (J. F. Brown, R. E. Wagner, Jr., D. L. Bedard, M. J. Brennan, J. C. Carnahan, R. J. May, and J. J. Tofflemire, Northeast Environ. Sci. 3:167-179, 1984). The congener selectivity patterns indicate that a two-step process consisting of anaerobic dechlorination followed by oxidation by H850 can effectively degrade all of the congeners in Aroclor 1242 and possibly all those in Aroclor 1254.

Coupling efficiency of optics in single-mode fiber components

Many single-mode fiber components include some form of optics, such as lenses or mirrors, for collecting light from a source fiber or laser and concentrating it on a receiving fiber. For such components there is a direct and simple relationship between coupling efficiency and optical aberrations. This paper combines fiber-coupling fundamentals, classical optics, and diffraction theory to provide a compact description of coupling efficiency that includes the effects of aberrations, fiber misalignments, and fiber-mode mismatch.

Interference effects in optical fiber connections

Optical interference may occur in fiber connections, and this can have an important effect on transmission loss. A theoretical analysis shows that the effect occurs in both single-mode and multimode fibers and depends on fiber end face separation, the source spectrum, and the modal power distribution in the fiber. Experimental observations of interference in dry multimode fiber connections confirm the analysis for both laser diode and LED sources.

Electrically controlled optical switch for multimode fiber applications

An electrically controlled optical switch based on polarization principles is described. It uses a liquid crystal twist cell that rotates polarization by 90 degrees , and it operates on an ac voltage that switches between 0.8 and 2.5 V rms. The switch has a loss of ~0.4 dB, neglecting reflections, in an unpolarized incoherent beam and a cross-talk ratio of ~-20 dB. It operates in collimated light, but it can be applied to multimode fibers using collimating lenses, which are expected to add <0.8 dB to the loss.

Postprocessing of imagery from active optics: some pitfalls

There may be pitfalls to watch for when recording imagery from active phase compensation devices located in the exit pupil of the system. At least three of these pitfalls are identified, and each is manifested as a degradation in the imagery. Both nearby and high altitude atmospheric disturbances contribute to the degradation. The first pitfall is identified as residual phase errors caused by measurement and hardware limitations. The second pitfall is identified as nonisoplanatism, and it occurs because wavefronts from different source points experience different high altitude disturbances. The third pitfall is identified as amplitude fluctuations in the exit pupil of the system, and it is also caused by the high altitude atmospheric disturbances. The two pitfalls caused by the high altitude disturbances are reduced by applying additional phase compensation in a plane that is the image of the high altitude disturbances. But even this may not be sufficient to eliminate the need for postprocessing of the image ry of extended sources.

A mechanism for initiation of genetic recombination

A mechanism for the initiation of genetic recombination is proposed. Its key features are the pairing, nicking, and cross-annealing of palindromic loops, i.e., structures formed by DNA with sequences of inverted complementary repeats. This mechanism may provide a simple, yet specific means of producing crossed strand connections between homologous DNA duplexes to form structures which can be intermediates in the process of genetic recombination.

Physical model for predicting grinding rates

When grinding an optical surface, the material removal rate depends linearly upon pressure and velocity and upon a proportionality constant which accounts for differences in material properties. A physical description of the grinding process has been postulated which results in the linear pressure and velocity relationships and which also allows the value of the proportionality constant to be determined from a knowledge of material properties alone. Previous attempts at predicting material removal rely strictly upon experimental data to determine the proportionality constant. The postulated description incorporates the combined effects of many individual abrasive particles to statistically determine the proportionality constant in terms of abrasive size and the breaking stress of the glass. A simple example indicates that the result is consistent with experiment.

Fabrication of aspherics using a mathematical model for material removal

A mathematica model has been developed that predicts the aspheric surface that a typical optical surfacing machine will produce. The model, which combines two basic assumptions concerning material wear with the kinematics of the machine, has been verified experimentally for the grinding process. In regions of the surface where the tool extends beyond the edge of the workpiece, pressure becomes nonuniform, and the model must be altered. The established model has been used to synthesize those machine strokes required to produce a desired aspheric surface.