A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation

Alternative polyadenylation (APA) is a general mechanism of transcript diversification in mammals, which has been recently linked to proliferative states and cancer. Different 3' untranslated region (3' UTR) isoforms interact with different RNA-binding proteins (RBPs), which modify the stability, translation, and subcellular localization of the corresponding transcripts. Although the heterogeneity of pre-mRNA 3' end processing has been established with high-throughput approaches, the mechanisms that underlie systematic changes in 3' UTR lengths remain to be characterized. Through a uniform analysis of a large number of 3' end sequencing data sets, we have uncovered 18 signals, six of which are novel, whose positioning with respect to pre-mRNA cleavage sites indicates a role in pre-mRNA 3' end processing in both mouse and human. With 3' end sequencing we have demonstrated that the heterogeneous ribonucleoprotein C (HNRNPC), which binds the poly(U) motif whose frequency also peaks in the vicinity of polyadenylation (poly(A)) sites, has a genome-wide effect on poly(A) site usage. HNRNPC-regulated 3' UTRs are enriched in ELAV-like RBP 1 (ELAVL1) binding sites and include those of the CD47 gene, which participate in the recently discovered mechanism of 3' UTR-dependent protein localization (UDPL). Our study thus establishes an up-to-date, high-confidence catalog of 3' end processing sites and poly(A) signals, and it uncovers an important role of HNRNPC in regulating 3' end processing. It further suggests that U-rich elements mediate interactions with multiple RBPs that regulate different stages in a transcript's life cycle

Potenzial der Mid-Infrarot-Spektrometrie bei Kuhmilchproben zur Abschätzung der Rationszusammensetzung

Milk composition of dairy animals is influenced by the composition of the ration fed. The objective of this study was to determine if the percentages and absolute amounts of hay, grass silage, pasture, maize silage and concentrate in the feed ration can be estimated using MIR spectrometry of milk. A total of 10200 milk samples from 90 dairy cows were collected, and the intakes of all ration components were measured. Using partial least squares regression (PLS), equations were developed to estimate ration compositions corresponding to each milk sample. To evaluate accuracy, the correlation between observed and estimated values (R) and ratio to performance (RPD) were used. Notable R values (for kg/for %) were observed for the ration proportion of pasture (0.85/0.87), maize silage (0.74/0.75) and concentrate intake (0.75/0.73). Estimation of groups of feedstuffs (all forages, energy-dense feedstuffs) resulted in R values of >0.8. Including the parameters milk yield and/or concentrate intake into PLS improved R values by up to 0.08. The results indicate a potential use of MIR spectra as a promising predictor for ration composition of dairy cows

The use of mid-infrared spectrometry to estimate the ration composition of lactating dairy cows

The composition of cow milk is strongly affected by the feeding regimen. Because milk components are routinely determined using mid-infrared (MIR) spectrometry, MIR spectra could also be used to estimate an animal’s ration composition. The objective of this study was to determine whether and how well amounts of dry matter intake and the proportions of concentrates, hay, grass silage, maize silage, and pasture in the total ration can be estimated using MIR spectra at an individual animal level. A total of 10,200 milk samples and sets of feed intake data were collected from 90 dairy cows at 2 experimental farms of the Agricultural Research and Education Centre in Raumberg-Gumpenstein, Austria. For each run of analysis, the data set was split into a calibration and a validation data set in a 40:60 ratio. Estimated ration compositions were calculated using a partial least squares regression and then compared with the respective observed ration compositions. In separate analyses, the factors milk yield and concentrate intake were included as additional predictors. To evaluate accuracy, the coefficient of determination (R2) and ratio to performance deviation were used. The highest R2 values (for kg of dry matter intake/ for % of ration) for the individual feedstuffs were as follows: pasture, 0.63/0.66; grass silage, 0.32/0.43; concentrate intake, 0.39/0.34; maize silage, 0.32/0.33; and hay, 0.15/0.16. Estimation of groups of feedstuffs (forages, energy-dense feedstuffs) mostly resulted in R2 values >0.50. Including the parameters milk yield or concentrate intake improved R2 values by up to 0.21, with an average improvement of 0.04. The results of this study indicate that not all ration components may be estimated equally accurately. Even if some estimates are good on average, there may be strong deviations between estimated and observed values in individual data sets, and therefore individual estimates should not be overemphasized. Further research including pooled samples (e.g., bulk milk, farm samples) or variations in ration composition is called for

Thiol-gelatin-norbornene bioink for laser‐based high‐definition bioprinting

Two-photon polymerization (2PP) is a lithography-based 3D printing method allowing the fabrication of 3D structures with sub-micrometer resolution. This work focuses on the characterization of gelatin-norbornene (Gel-NB) bioinks which enables the embedding of cells via 2PP. The high reactivity of the thiol-ene system allows 2PP processing of cell-containing materials at remarkably high scanning speeds (1000 mm s(-1)) placing this technology in the domain of bioprinting. Atomic force microscopy results demonstrate that the indentation moduli of the produced hydrogel constructs can be adjusted in the 0.2-0.7 kPa range by controlling the 2PP processing parameters. Using this approach gradient 3D constructs are produced and the morphology of the embedded cells is observed in the course of 3 weeks. Furthermore, it is possible to tune the enzymatic degradation of the crosslinked bioink by varying the applied laser power. The 3D printed Gel-NB hydrogel constructs show exceptional biocompatibility, supported cell adhesion, and migration. Furthermore, cells maintain their proliferation capacity demonstrated by Ki-67 immunostaining. Moreover, the results demonstrate that direct embedding of cells provides uniform distribution and high cell loading independently of the pore size of the scaffold. The investigated photosensitive bioink enables high-definition bioprinting of well-defined constructs for long-term cell culture studies

AFM imaging of functionalized double-walled carbon nanotubes

We present a comparative study of several non-covalent approaches to disperse, debundle and noncovalently functionalize double-walled carbon nanotubes (DWNTs). We investigated the ability of bovine serum albumin (BSA), phospholipids grafted onto amine-terminated polyethylene glycol (PLPEG2000-NH2), as well as a combination thereof, to coat purified DWNTs. Topographical imaging with the atomic force microscope (AFM) was used to assess the coating of individual DWNTs and the degree of debundling and dispersion. Topographical images showed that functionalized DWNTs are better separated and less aggregated than pristine DWNTs and that the different coating methods differ in their abilities to successfully debundle and disperse DWNTs. Height profiles indicated an increase in the diameter of DWNTs depending on the functionalization method and revealed adsorption of single molecules onto the nanotubes. Biofunctionalization of the DWNT surface was achieved by coating DWNTs with biotinylated BSA, providing for biospecific binding of streptavidin in a simple incubation step. Finally, biotin-BSA-functionalized DWNTs were immobilized on an avidin layer via the specific avidin–biotin interaction

Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways

The findings that microRNAs (miRNAs) are essential for early development in many species and that embryonic miRNAs can reprogram somatic cells into induced pluripotent stem cells suggest that these miRNAs act directly on transcriptional and chromatin regulators of pluripotency. To elucidate the transcription regulatory networks immediately downstream of embryonic miRNAs, we extended the motif activity response analysis approach that infers the regulatory impact of both transcription factors (TFs) and miRNAs from genome-wide expression states. Applying this approach to multiple experimental data sets generated from mouse embryonic stem cells (ESCs) that did or did not express miRNAs of the ESC-specific miR-290-295 cluster, we identified multiple TFs that are direct miRNA targets, some of which are known to be active during cell differentiation. Our results provide new insights into the transcription regulatory network downstream of ESC-specific miRNAs, indicating that these miRNAs act on cell cycle and chromatin regulators at several levels and downregulate TFs that are involved in the innate immune respons

AFM imaging of functionalized carbon nanotubes on biological membranes

Multifunctional carbon nanotubes are promising for biomedical applications as their nano-size, together with their physical stability, gives access into the cell and various cellular compartments including the nucleus. However, the direct and label-free detection of carbon nanotube uptake into cells is a challenging task. The atomic force microscope (AFM) is capable of resolving details of cellular surfaces at the nanometer scale and thus allows following of the docking of carbon nanotubes to biological membranes. Here we present topographical AFM images of non-covalently functionalized single walled (SWNT) and double walled carbon nanotubes (DWNT) immobilized on different biological membranes, such as plasma membranes and nuclear envelopes, as well as on a monolayer of avidin molecules. We were able to visualize DWNT on the nuclear membrane while at the same time resolving individual nuclear pore complexes. Furthermore, we succeeded in localizing individual SWNT at the border of incubated cells and in identifying bundles of DWNT on cell surfaces by AFM imaging

Anomalies in low-energy Gamma-Ray Burst spectra with the Fermi Gamma-Ray Burst Monitor

A Band function has become the standard spectral function used to describe the prompt emission spectra of gamma-ray bursts (GRBs). However, deviations from this function have previously been observed in GRBs detected by BATSE and in individual GRBs from the \textit{Fermi} era. We present a systematic and rigorous search for spectral deviations from a Band function at low energies in a sample of the first two years of high fluence, long bursts detected by the \textit{Fermi} Gamma-Ray Burst Monitor (GBM). The sample contains 45 bursts with a fluence greater than 2$\times10^{-5}$ erg / cm$^{2}$ (10 - 1000 keV). An extrapolated fit method is used to search for low-energy spectral anomalies, whereby a Band function is fit above a variable low-energy threshold and then the best fit function is extrapolated to lower energy data. Deviations are quantified by examining residuals derived from the extrapolated function and the data and their significance is determined via comprehensive simulations which account for the instrument response. This method was employed for both time-integrated burst spectra and time-resolved bins defined by a signal to noise ratio of 25 $\sigma$ and 50 $\sigma$. Significant deviations are evident in 3 bursts (GRB\,081215A, GRB\,090424 and GRB\,090902B) in the time-integrated sample ($\sim$ 7%) and 5 bursts (GRB\,090323, GRB\,090424, GRB\,090820, GRB\,090902B and GRB\,090926A) in the time-resolved sample ($\sim$ 11%).} The advantage of the systematic, blind search analysis is that it can demonstrate the requirement for an additional spectral component without any prior knowledge of the nature of that extra component. Deviations are found in a large fraction of high fluence GRBs; fainter GRBs may not have sufficient statistics for deviations to be found using this method

Ongoing transients in carbonate compensation

Uptake of anthropogenic CO2 is acidifying the oceans. Over the next 2000 years, this will modify the dissolution and preservation of sedimentary carbonate. By coupling new formulas for the positions of the calcite saturation horizon, zsat, the compensation depth, zcc, and the snowline, zsnow, to a biogeochemical model of the oceanic carbonate system, we evaluate how these horizons will change with ongoing ocean acidification. Our model is an extended Havardton-Bear-type box model, which includes novel kinetic descriptions for carbonate dissolution above, between, and below these critical depths. In the preindustrial ocean, zsat and zcc are at 3939 and 4750 m, respectively. When forced with the IS92a CO2 emission scenario, the model forecasts (1) that zsat will rise rapidly (“runaway” conditions) so that all deep water becomes undersaturated, (2) that zcc will also rise and over 1000 years will pass before it will be stabilized by the dissolution of previously deposited CaCO3, and (3) that zsnow will respond slowly to acidification, rising by ∼1150 m during a 2000 year timeframe. A further simplified model that equates the compensation and saturation depths produces quantitatively different results. Finally, additional feedbacks due to acidification on calcification and increased atmospheric CO2 on organic matter productivity strongly affect the positions of the compensation horizons and their dynamics.

The Fermi GBM Gamma-Ray Burst Spectral Catalog: Four Years Of Data

In this catalog we present the updated set of spectral analyses of GRBs detected by the Fermi Gamma-Ray Burst Monitor (GBM) during its first four years of operation. It contains two types of spectra, time-integrated spectral fits and spectral fits at the brightest time bin, from 943 triggered GRBs. Four different spectral models were fitted to the data, resulting in a compendium of more than 7500 spectra. The analysis was performed similarly, but not identically to Goldstein et al. 2012. All 487 GRBs from the first two years have been re-fitted using the same methodology as that of the 456 GRBs in years three and four. We describe, in detail, our procedure and criteria for the analysis, and present the results in the form of parameter distributions both for the observer-frame and rest-frame quantities. The data files containing the complete results are available from the High-Energy Astrophysics Science Archive Research Center (HEASARC).Comment: Accepted for publication in ApJ