Isolation of total ribonucleic acid from fresh and frozen-thawed boar semen and its relevance in transcriptome studies

The main objective of this study was to isolate high-quality total ribonucleic acid (RNA) from raw fresh semen and frozen-thawed boar semen, using a protocol comprising the conventional TRIzol assay and a membrane-based technique, the PureLink RNA mini kit. Bioanalyzer profile revealed that the sperm RNA size distributions comprised mainly intact RNA ranging from 1500 to 1800 bp, without any detectable residual genomic deoxyribonucleic acid (DNA) or 28S ribosomal RNA (rRNA). Spectrophotometric quantifications of the total RNA yielded 1.64 to 2.44 μg/106 spermatozoa, irrespective of the sperm source. The TRIzol/PureLink protocol allowed the isolation of high-quality intact RNA from boar spermatozoa, which is required for transcriptome analysis on high-throughput RNA-sequencing (RNA-Seq) data. Such an approach is relevant to identifying sperm messenger RNA (mRNA transcripts) that are associated with boar semen freezability.Keywords: cryopreservation, RNA-Seq, semen qualit

Temporal trends in mode, site and stage of presentation with the introduction of colorectal cancer screening: a decade of experience from the West of Scotland

background:  Population colorectal cancer screening programmes have been introduced to reduce cancer-specific mortality through the detection of early-stage disease. The present study aimed to examine the impact of screening introduction in the West of Scotland. methods:  Data on all patients with a diagnosis of colorectal cancer between January 2003 and December 2012 were extracted from a prospectively maintained regional audit database. Changes in mode, site and stage of presentation before, during and after screening introduction were examined. results:  In a population of 2.4 million, over a 10-year period, 14 487 incident cases of colorectal cancer were noted. Of these, 7827 (54%) were males and 7727 (53%) were socioeconomically deprived. In the postscreening era, 18% were diagnosed via the screening programme. There was a reduction in both emergency presentation (20% prescreening vs 13% postscreening, P0.001) and the proportion of rectal cancers (34% prescreening vs 31% pos-screening, P0.001) over the timeframe. Within non-metastatic disease, an increase in the proportion of stage I tumours at diagnosis was noted (17% prescreening vs 28% postscreening, P0.001). conclusions:  Within non-metastatic disease, a shift towards earlier stage at diagnosis has accompanied the introduction of a national screening programme. Such a change should lead to improved outcomes in patients with colorectal cancer

Predicting the Next Best View for 3D Mesh Refinement

3D reconstruction is a core task in many applications such as robot navigation or sites inspections. Finding the best poses to capture part of the scene is one of the most challenging topic that goes under the name of Next Best View. Recently, many volumetric methods have been proposed; they choose the Next Best View by reasoning over a 3D voxelized space and by finding which pose minimizes the uncertainty decoded into the voxels. Such methods are effective, but they do not scale well since the underlaying representation requires a huge amount of memory. In this paper we propose a novel mesh-based approach which focuses on the worst reconstructed region of the environment mesh. We define a photo-consistent index to evaluate the 3D mesh accuracy, and an energy function over the worst regions of the mesh which takes into account the mutual parallax with respect to the previous cameras, the angle of incidence of the viewing ray to the surface and the visibility of the region. We test our approach over a well known dataset and achieve state-of-the-art results.Comment: 13 pages, 5 figures, to be published in IAS-1

Field-study science classrooms as positive and enjoyable learning environments

We investigated differences between field-study classrooms and traditional science classrooms in terms of the learning environment and students’ attitudes to science, as well as the differential effectiveness of field-study classrooms for students differing in sex and English proficiency. A modified version of selected scales from the What Is Happening In this Class? questionnaire was used to assess the learning environment, whereas students’ attitudes were assessed with a shortened version of a scale from the Test of Science Related Attitudes. A sample of 765 grade 5 students from 17 schools responded to the learning environment and attitude scales in terms of both their traditional science classrooms and classrooms at a field-study centre in Florida. Large effect sizes supported the effectiveness of the field-studies classroom in terms of both the learning environment and student attitudes. Relative to the home school science class, the field-study class was considerably more effective for students with limited English proficiency than for native English speakers

A dynamical model reveals gene co-localizations in nucleus

Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the observed co-localization of genes within a defined subnuclear region. A simple standard Brownian motion model in two and three dimensions shows that preferential co-localization is possible for co-regulated genes without any direct interaction, and suggests the occurrence may be due to a limitation in the number of available transcription factors. Experimental data of chromatin movements demonstrates that fractional rather than standard Brownian motion is more appropriate to model gene mobilizations, and we tested our dynamical model against recent static experimental data, using a sub-diffusion process by which the genes tend to colocalize more easily. Moreover, in order to compare our model with recently obtained experimental data, we studied the association level between genes and factors, and presented data supporting the validation of this dynamic model. As further applications of our model, we applied it to test against more biological observations. We found that increasing transcription factor number, rather than factory number and nucleus size, might be the reason for decreasing gene co-localization. In the scenario of frequency-or amplitude-modulation of transcription factors, our model predicted that frequency-modulation may increase the co-localization between its targeted genes

Towards Open and Equitable Access to Research and Knowledge for Development

Leslie Chan and colleagues discuss the value of open access not just for access to health information, but also for transforming structural inequity in current academic reward systems and for valuing scholarship from the South

HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation.

The internal ribosome entry site (IRES) of the hepatitis C virus (HCV) drives noncanonical initiation of protein synthesis necessary for viral replication. Functional studies of the HCV IRES have focused on 80S ribosome formation but have not explored its role after the 80S ribosome is poised at the start codon. Here, we report that mutations of an IRES domain that docks in the 40S subunit's decoding groove cause only a local perturbation in IRES structure and result in conformational changes in the IRES-rabbit 40S subunit complex. Functionally, the mutations decrease IRES activity by inhibiting the first ribosomal translocation event, and modeling results suggest that this effect occurs through an interaction with a single ribosomal protein. The ability of the HCV IRES to manipulate the ribosome provides insight into how the ribosome's structure and function can be altered by bound RNAs, including those derived from cellular invaders

Pollen and spores as biological recorders of past ultraviolet irradiance

Solar ultraviolet (UV) irradiance is a key driver of climatic and biotic change. Ultraviolet irradiance modulates stratospheric warming and ozone production, and influences the biosphere from ecosystem-level processes through to the largest scale patterns of diversification and extinction. Yet our understanding of ultraviolet irradiance is limited because no method has been validated to reconstruct its flux over timescales relevant to climatic or biotic processes. Here, we show that a recently developed proxy for ultraviolet irradiance based on spore and pollen chemistry can be used over long (105 years) timescales. Firstly we demonstrate that spatial variations in spore and pollen chemistry correlate with known latitudinal solar irradiance gradients. Using this relationship we provide a reconstruction of past changes in solar irradiance based on the pollen record from Lake Bosumtwi in Ghana. As anticipated, variations in the chemistry of grass pollen from the Lake Bosumtwi record show a link to multiple orbital precessional cycles (19-21 thousand years). By providing a unique, local proxy for broad spectrum solar irradiance, the chemical analysis of spores and pollen offers unprecedented opportunities to decouple solar variability, climate and vegetation change through geologic time and a new proxy with which to probe the Earth system

Mitigating systematic error in topographic models for geomorphic change detection: Accuracy, precision and considerations beyond off‐nadir imagery

Unmanned aerial vehicles (UAVs) and structure-from-motion photogrammetry enable detailed quantification of geomorphic change. However, rigorous precision-based change detection can be compromised by survey accuracy problems producing systematic topographic error (e.g. 'doming'), with error magnitudes greatly exceeding precision estimates. Here, we assess survey sensitivity to systematic error, directly correcting topographic data so that error magnitudes align more closely with precision estimates. By simulating conventional grid-style photogrammetric aerial surveys, we quantify the underlying relationships between survey accuracy, camera model parameters, camera inclination, tie point matching precision and topographic relief, and demonstrate a relative insensitivity to image overlap. We show that a current doming-mitigation strategy of using a gently inclined ( 0 center dot 3 m, representing accuracy issues an order of magnitude greater than precision-based error estimates. For higher-relief topography, and for nadir-imaging surveys of the lower-relief topography, systematic error was <0 center dot 09 m. Modelling and subtracting the systematic error directly from the topographic data successfully reduced error magnitudes to values consistent with twice the estimated precision. Thus, topographic correction can provide a more robust approach to uncertainty-based detection of event-scale geomorphic change than designing surveys with small off-nadir camera inclinations and, furthermore, can substantially reduce ground control requirements. (c) 2020 The Authors. Earth Surface Processes and Landforms published by John Wiley & Sons Lt

Interacting Supernovae: Types IIn and Ibn

Supernovae (SNe) that show evidence of strong shock interaction between their ejecta and pre-existing, slower circumstellar material (CSM) constitute an interesting, diverse, and still poorly understood category of explosive transients. The chief reason that they are extremely interesting is because they tell us that in a subset of stellar deaths, the progenitor star may become wildly unstable in the years, decades, or centuries before explosion. This is something that has not been included in standard stellar evolution models, but may significantly change the end product and yield of that evolution, and complicates our attempts to map SNe to their progenitors. Another reason they are interesting is because CSM interaction is an efficient engine for making bright transients, allowing super-luminous transients to arise from normal SN explosion energies, and allowing transients of normal SN luminosities to arise from sub-energetic explosions or low radioactivity yield. CSM interaction shrouds the fast ejecta in bright shock emission, obscuring our normal view of the underlying explosion, and the radiation hydrodynamics of the interaction is challenging to model. The CSM interaction may also be highly non-spherical, perhaps linked to binary interaction in the progenitor system. In some cases, these complications make it difficult to definitively tell the difference between a core-collapse or thermonuclear explosion, or to discern between a non-terminal eruption, failed SN, or weak SN. Efforts to uncover the physical parameters of individual events and connections to possible progenitor stars make this a rapidly evolving topic that continues to challenge paradigms of stellar evolution.Comment: Final draft of a chapter in the "SN Handbook". Accepted. 25 pages, 3 fig