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Long, non-coding (Inc) RNAs emerge as crucial regulators of gene expression. Their ability to interact with DNA and protein mediates the recruitment of regulators to defined chromosomal loci. LncRNAs are particularly abundant in brain tissues where they are involved in cell specification. We described a novel lncRNA, RUS (RNA upstream to Slitrk3), which interacts with epigenetic regulators and contributes to shaping the gene expression program of neural precursor cells towards neurogenesis.

Climate change affects timing of reproduction in many bird species, but few studies have investigated its influence on annual reproductive output. Here, we assess changes in the annual production of young by female breeders in 201 populations of 104 bird species (N = 745,962 clutches) covering all continents between 1970 and 2019. Overall, average offspring production has declined in recent decades, but considerable differences were found among species and populations. A total of 56.7% of populations showed a declining trend in offspring production (significant in 17.4%), whereas 43.3% exhibited an increase (significant in 10.4%). The results show that climatic changes affect offspring production through compounded effects on ecological and life history traits of species. Migratory and larger-bodied species experienced reduced offspring production with increasing temperatures during the chick-rearing period, whereas smaller-bodied, sedentary species tended to produce more offspring. Likewise, multi-brooded species showed increased breeding success with increasing temperatures, whereas rising temperatures were unrelated to reproductive success in single-brooded species. Our study suggests that rapid declines in size of bird populations reported by many studies from different parts of the world are driven only to a small degree by changes in the production of young., This meta-analysis was financed by the grant of the Polish National Science Centre (Narodowe Centrum Nauki) (no. 2017/27/B/NZ8/00465) awarded to Lucyna Hałupka.

MSL2, the DNA-binding subunit of theDrosophiladosage compensation complex, cooperates with the ubiquitous protein CLAMP to bind MSL recognition elements (MREs) on the X chromosome. We explore the nature of the cooperative binding to these GA-rich, composite se-quence elements in reconstituted naïve embryonic chromatin.We found that the cooperativity requires physical interaction between both proteins. Remarkably, disruption of this interaction does not lead to indirect, nucleosome-mediated cooperativity as expected, but to competition. The protein interaction apparently not only increases the affinity for composite binding sites, but also locks both proteins in a defined dimeric state that prevents competition.High Affinity Sites of MSL2 on the X chromosome contain variable numbers of MREs. We find that the cooperation between MSL2/CLAMP is not influenced by MRE clustering or arrangement, but happens largely at the level of individual MREs.The sites where MSL2/CLAMP bind stronglyin vitrolocate to all chromosomes and show little overlap to an expanded set of X-chromosomal MSL2in vivobinding sites generated by CUT&RUN. Apparently, the intrinsic MSL2/CLAMP cooperativity is limited to a small selection of potential sitesin vivo. This restriction must be due to components missing in our reconstitution, such asroX2lncRNA.

Quantum memories capable of storing and retrieving coherent information for extended times at room temperature would enable a host of new technologies. Electron and nuclear spin qubits using shallow neutral donors in semiconductors have been studied extensively but are limited to low temperatures ($\le$10 K); however, the nuclear spins of ionized donors have potential for high temperature operation. We use optical methods and dynamical decoupling to realize this potential for an ensemble of 31P donors in isotopically purified 28Si and observe a room temperature coherence time of over 39 minutes. We further show that a coherent spin superposition can be cycled from 4.2 K to room temperature and back, and report a cryogenic coherence time of 3 hours in the same system., 5 pages, 4 figures

SummaryUnwinding RNA secondary structures by RNA helicases is essential for RNA metabolism. How the basic unwinding reaction of DExH-type helicases is regulated by their accessory domains is unresolved. Here, we combine structural and functional analyses to address this challenge for the prototypic DExH RNA helicase maleless (MLE) fromDrosophila.We captured the helicase cycle of MLE with multiple structural snapshots. We discovered that initially, dsRBD2 flexibly samples substrate dsRNA and aligns it with the open helicase tunnel. Subsequently, dsRBD2 releases RNA and associates with the helicase core, leading to closure of the tunnel around ssRNA. Structure-based MLE mutations confirm the functional relevance of the structural model in cells. We propose a molecular model in which the dsRBD2 domain of MLE orchestrates large structural transitions that depend on substrate RNA but are independent of ATP.Our findings reveal the fundamental mechanics of dsRNA unwinding by DExH helicases with high general relevance for dosage compensation and specific implications for MLE’s human orthologue DHX9/RHA mechanisms in disease.

Metazoan transcription factors distinguish their response elements from a large excess of similar sequences. We explored underlying principles of DNA shape read-out and factor cooperativity in chromatin using a unique experimental system. We reconstituted chromatin on Drosophila genomes in extracts of preblastoderm embryos, mimicking the naïve state of the zygotic genome prior to developmental transcription activation. We then compared the intrinsic binding specificities of three recombinant transcription factors, alone and in combination, with GA-rich recognition sequences genome-wide. For MSL2, all functional elements reside on the X chromosome, allowing to distinguish physiological elements from non-functional ‘decoy’ sites. The physiological binding profile of MSL2 is approximated through interaction with other factors: cooperativity with CLAMP and competition with GAF, which sculpts the profile by occluding non-functional sites. An extended DNA shape signature is differentially read out in chromatin. Our results reveal novel aspects of target selection in a complex chromatin environment.

The dosage compensation complex (DCC) ofDrosophilaidentifies its X-chromosomal binding sites with exquisite selectivity. The principles that assure this vital targeting are known from theD. melanogastermodel: DCC-intrinsic specificity of DNA binding, cooperativity with the CLAMP protein, and noncoding roX2 RNA transcribed from the X chromosome. We found that inD. virilis, a species separated frommelanogasterby 40 million years of evolution, all principles are active but contribute differently to X specificity. Inmelanogaster, the DCC subunit MSL2 evolved intrinsic DNA-binding selectivity for rare PionX sites, which mark the X chromosome. Invirilis, PionX motifs are abundant and not X-enriched. Accordingly, MSL2 lacks specific recognition. Here, roX2 RNA plays a more instructive role, counteracting a nonproductive interaction of CLAMP and modulating DCC binding selectivity. Remarkably, roX2 triggers a stable chromatin binding mode characteristic of DCC. Evidently, X-specific regulation is achieved by divergent evolution of protein, DNA, and RNA components.

Histone variants are a universal means to alter the biochemical properties of nucleosomes, implementing local changes in chromatin structure. H2A.Z, one of the most conserved histone variants, is incorporated into chromatin by SWR1-type nucleosome remodelers. Here, we summarize recent advances toward understanding the transcription-regulatory roles of H2A.Z and of the remodeling enzymes that govern its dynamic chromatin incorporation. Tight transcriptional control guaranteed by H2A.Z nucleosomes depends on the context provided by other histone variants or chromatin modifications, such as histone acetylation. The functional cooperation of SWR1-type remodelers with NuA4 histone acetyltransferase complexes, a recurring theme during evolution, is structurally implemented by species-specific strategies.

The evolution of brain complexity correlates with an increased expression of long, noncoding (lnc) RNAs in neural tissues. Although prominent examples illustrate the potential of lncRNAs to scaffold and target epigenetic regulators to chromatin loci, only few cases have been described to function during brain development. We present a first functional characterization of the lncRNA

Electron-spin qubits have long coherence times suitable for quantum technologies. Spin–orbit coupling promises to greatly improve spin qubit scalability and functionality, allowing qubit coupling via photons, phonons or mutual capacitances, and enabling the realization of engineered hybrid and topological quantum systems. However, despite much recent interest, results to date have yielded short coherence times (from 0.1 to 1 μs). Here we demonstrate ultra-long coherence times of 10 ms for holes where spin–orbit coupling yields quantized total angular momentum. We focus on holes bound to boron acceptors in bulk silicon 28, whose wavefunction symmetry can be controlled through crystal strain, allowing direct control over the longitudinal electric dipole that causes decoherence. The results rival the best electron-spin qubits and are 104 to 105 longer than previous spin–orbit qubits. These results open a pathway to develop new artificial quantum systems and to improve the functionality and scalability of spin-based quantum technologies. Spin qubits in systems with strong spin–orbit coupling can be electrically controlled, but are usually affected by short coherence times. Here, coherence times up to 10 ms are obtained for strain-engineered hole states bound to boron acceptors in silicon 28.

The MLE DExH helicase and the roX lncRNAs are essential components of the chromatin modifying Dosage Compensation Complex (DCC) in Drosophila. To explore the mechanism of ribonucleoprotein complex assembly, we developed vitRIP, an unbiased, transcriptome-wide in vitro assay that reveals RNA binding specificity. We found that MLE has intrinsic specificity for U-/A-rich sequences and tandem stem-loop structures and binds many RNAs beyond roX in vitro. The selectivity of the helicase for physiological substrates is further enhanced by the core DCC. Unwinding of roX2 by MLE induces a highly selective RNA binding surface in the unstructured C-terminus of the MSL2 subunit and triggers-specific association of MLE and roX2 with the core DCC. The exquisite selectivity of roX2 incorporation into the DCC thus originates from intimate cooperation between the helicase and the core DCC involving two distinct RNA selection principles and their mutual refinement.

Understanding how the genome is structurally organized as chromatin is essential for understanding its function. Here, we review recent developments that allowed the readdressing of old questions regarding the primary level of chromatin structure, the arrangement of nucleosomes along the DNA and the folding of the nucleosome fiber in nuclear space. In contrast to earlier views of nucleosome arrays as uniformly regular and folded, recent findings reveal heterogeneous array organization and diverse modes of folding. Local structure variations reflect a continuum of functional states characterized by differences in post-translational histone modifications, associated chromatin-interacting proteins and nucleosome-remodeling enzymes. Technological advances have led to new insights into genome-wide arrangements of nucleosomes along the DNA and the folding of the chromosome fiber in nuclear space, revealing unexpected diversity.

The evolution of brain complexity correlates with an increased expression of long, non- coding (lnc) RNAs in neural tissues. Although prominent examples illustrate the potential of lncRNAs to scaffold and target epigenetic regulators to chromatin loci, only few cases have been described to function during brain development. We present a first functional characterization of the lncRNA LINC01322, which we term RUS for ‘RNA upstream of Slitrk3’. The RUS gene is well conserved in mammals by sequence and synteny next to the neurodevelopmental gene Slitrk3. RUS is exclusively expressed in neural cells and its expression increases along with neuronal markers during neuronal differentiation of mouse embryonic cortical neural stem cells. Depletion of RUS locks neuronal precursors in an intermediate state towards neuronal differentiation resulting in arrested cell cycle and increased apoptosis. RUS associates with chromatin in the vicinity of genes involved in neurogenesis, most of which change their expression upon RUS depletion. The identification of a range of epigenetic regulators as specific RUS interactors suggests that the lncRNA may mediate gene activation and repression in a highly context-dependent manner.

The central theme of this study is to identify strength-stiffness correlations for chemically treated subgrade soils in Indiana. This was done by conducting Unconfined Compression (UC) Tests and Resilient Modulus Tests for soils collected at three different sites—US-31, SR-37, and I-65. At each site, soil samples were obtained from 11 locations at 30 ft spacing. The soils were treated in the laboratory with cement, using the same proportions used for construction, and cured for 7 and 28 days before testing. Results from the UC tests were compared with the resilient modulus results that were available. No direct correlation was found between resilient modulus and UCS parameters for the soils investigated in this study. A brief statistical analysis of the results was conducted, and a simple linear regression model involving the soil characteristics (plasticity index, optimum moisture content and maximum dry density) along with UCS and resilient modulus parameters was proposed.

The multi-wavelength spectrum observed from M87 extends from radio wavelengths up to TeV gamma-ray energies. The radio through GeV components have been interpreted successfully using SSC models based on misaligned blazar jets, but the origin of the intense TeV emission detected during flares in 2004, 2005, and 2010 remains puzzling. It has been previously suggested that the TeV flares are produced when a relativistic proton jet originating in the core of M87 collides with a molecular cloud (or stellar atmosphere) located less than one parsec from the central black hole. We explore this scenario in detail here using a self-consistent model for the acceleration of relativistic protons in a shocked, two-fluid ADAF accretion disc. The relativistic protons accelerated in the disc escape to power the observed jet outflows. The distribution function for the jet protons is used to compute the TeV emission produced when the jet collides with a cloud or stellar atmosphere. The simulated broadband radiation spectrum includes radio, X-ray, and GeV components generated via synchrotron, as well as TeV emission generated via the production and decay of muons, positrons, and electrons. The self-consistency of the model is verified by computing the relativistic particle pressure using the distribution function, and comparing it with the relativistic particle pressure obtained from the hydrodynamical model. We demonstrate that the model is able to reproduce the multi-wavelength spectrum from M87 observed by VERITAS and HESS during the high-energy flares in 2004, 2005, and 2010., 27 pages, 9 figures

Kleptoparasitism is an exploitative foraging strategy used across taxa, but factors underlying variation in the foraging performance of individuals using it have not often been addressed. Using longitudinal data on Common Terns stealing food from conspecifics during breeding, we show that variation in the energetic reward of kleptoparasitic behaviour is explained by interactive effects of sex and the attack tactic used by the parasite, as well as by age. Males obtain a higher reward when using an aerial than a terrestrial attack tactic, with decomposition analyses showing that this is due to the energy content of chased after prey items being higher in their aerial attacks. On the other hand, females obtain a higher reward when attacking terrestrially, which is due to their success rate being higher on land than in the air. In addition, the birds show decelerating within-individual improvement with age, which is due to individuals chasing after prey with a higher energy content as they grow older. Our study not only pinpoints factors underlying variation in the foraging performance of kleptoparasites, but also illustrates the importance of modelling individual variation when analyzing foraging performance. Fil: García, Germán Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina Fil: Paterlini, Carla Ángela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina Fil: Favero, Marco. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina Fil: Becker, Peter H.. Institut Fur Vogelforschung "Vogelwarte Helgoland"; Alemania Fil: Bouwhuis, Sandra. Institut Fur Vogelforschung "Vogelwarte Helgoland"; Alemania

Preblastoderm Drosophila embryo development is characterized by fast cycles of nuclear divisions. Extracts from these embryos can be used to reconstitute complex chromatin with high efficiency. We now discovered that this chromatin assembly system contains activities that recognize unprotected DNA ends and signal DNA damage through phosphorylation. DNA ends are initially bound by Ku and MRN complexes. Within minutes, the phosphorylation of H2A.V (homologous to γH2A.X) initiates from DNA breaks and spreads over tens of thousands DNA base pairs. The γH2A.V phosphorylation remains tightly associated with the damaged DNA and does not spread to undamaged DNA in the same reaction. This first observation of long-range γH2A.X spreading along damaged chromatin in an in vitro system provides a unique opportunity for mechanistic dissection. Upon further incubation, DNA ends are rendered single-stranded and bound by the RPA complex. Phosphoproteome analyses reveal damage-dependent phosphorylation of numerous DNA-end-associated proteins including Ku70, RPA2, CHRAC16, the exonuclease Rrp1 and the telomer capping complex. Phosphorylation of spindle assembly checkpoint components and of microtubule-associated proteins required for centrosome integrity suggests this cell-free system recapitulates processes involved in the regulated elimination of fatally damaged syncytial nuclei.

Selection is a central force underlying evolutionary change and can vary in strength and direction, for example across time and space. The fitness consequences of individual genetic diversity have often been investigated by testing for multilocus heterozygosity-fitness correlations (HFCs), but few studies have been able to assess HFCs across life stages and in both sexes. Here, we test for HFCs using a 26-year longitudinal individual-based data set from a large population of a long-lived seabird (the common tern, Sterna hirundo), where 7,974 chicks and breeders of known age were genotyped at 15 microsatellite loci and sampled for life-history traits over the complete life cycle. Heterozygosity was not correlated with fledging or post-fledging prospecting probabilities, but was positively correlated with recruitment probability. For breeders, annual survival was not correlated with heterozygosity, but annual fledgling production was negatively correlated with heterozygosity in males and highest in intermediately heterozygous females. The contrasting HFCs among life stages and sexes indicate differential selective processes and emphasize the importance of assessing fitness consequences of traits over complete life histories.

Maleless (MLE) is an evolutionary conserved member of the DExH family of helicases in Drosophila. Besides its function in RNA editing and presumably siRNA processing, MLE is best known for its role in remodelling non-coding roX RNA in the context of X chromosome dosage compensation in male flies. MLE and its human orthologue, DHX9 contain two tandem double-stranded RNA binding domains (dsRBDs) located at the N-terminal region. The two dsRBDs are essential for localization of MLE at the X-territory and it is presumed that this involves binding roX secondary structures. However, for dsRBD1 roX RNA binding has so far not been described. Here, we determined the solution NMR structure of dsRBD1 and dsRBD2 of MLE in tandem and investigated its role in double-stranded RNA (dsRNA) binding. Our NMR and SAXS data show that both dsRBDs act as independent structural modules in solution and are canonical, non-sequence-specific dsRBDs featuring non-canonical KKxAXK RNA binding motifs. NMR titrations combined with filter binding experiments and isothermal titration calorimetry (ITC) document the contribution of dsRBD1 to dsRNA binding in vitro. Curiously, dsRBD1 mutants in which dsRNA binding in vitro is strongly compromised do not affect roX2 RNA binding and MLE localization in cells. These data suggest alternative functions for dsRBD1 in vivo.

The variability of the X-ray emission from active galactic nuclei is often characterized using time lags observed between soft and hard energy bands in the detector. The time lags are usually computed using the complex cross-spectrum, which is based on the Fourier transforms of the hard and soft time series data. It has been noted that some active galactic nuclei display soft X-ray time lags, in addition to the more ubiquitous hard lags. Hard time lags are thought to be produced via propagating fluctuations, spatial reverberation, or via the thermal Comptonization of soft seed photons injected into a hot electron cloud. The physical origin of the soft lags has been a subject of debate over the last decade. Currently, the reverberation interpretation is recognized as a leading theory. In this paper, we explore the alternative possibility that the soft X-ray time lags result partially from the thermal and bulk Comptonization of monochromatic seed photons which, in the case of the narrow-line Seyfert 1 galaxy 1H 0707-495, may correlate with fluorescence of iron L-line emission. In our model, the seed photons are injected into a hot, quasi-spherical corona in the inner region of the accretion flow. We develop an exact, time-dependent analytical model for the thermal and bulk Comptonization of the seed photons based on a Fourier-transformed radiation transport equation, and we demonstrate that the model successfully reproduces both the hard and soft time lags observed from 1H 0707-495.

Transcription regulators select their genomic binding sites from a large pool of similar, non-functional sequences. Although general principles that allow such discrimination are known, the complexity of DNA elements often precludes a prediction of functional sites. The process of dosage compensation in Drosophila allows exploring the rules underlying binding site selectivity. The male-specific-lethal (MSL) Dosage Compensation Complex (DCC) selectively binds to some 300 X chromosomal ‘High Affinity Sites’ (HAS) containing GA-rich ‘MSL recognition elements’ (MREs), but disregards thousands of other MRE sequences in the genome. The DNA-binding subunit MSL2 alone identifies a subset of MREs, but fails to recognize most MREs within HAS. The ‘Chromatin-linked adaptor for MSL proteins’ (CLAMP) also interacts with many MREs genome-wide and promotes DCC binding to HAS. Using genome-wide DNA-immunoprecipitation we describe extensive cooperativity between both factors, depending on the nature of the binding sites. These are explained by physical interaction between MSL2 and CLAMP. In vivo, both factors cooperate to compete with nucleosome formation at HAS. The male-specific MSL2 thus synergises with a ubiquitous GA-repeat binding protein for refined X/autosome discrimination.

Sampling seabirdsThe vastness of the worlds' oceans makes them difficult to monitor. Seabirds that forage and breed across oceans globally have been recognized as sentinels of ocean health. Sydemanet al.looked across seabird species of both the Northern and Southern Hemispheres and found varying patterns. Northern Hemisphere species exhibited greater signs of stress and reduced breeding success, indicative of low fish resources. Southern Hemisphere species showed less impact on reproductive output, suggesting that the fish populations there have thus far been less disturbed. The differences across hemispheres indicate different strategies for conservation, with active recovery needed in the north and enhanced protection in the south.Science, abf1772, this issue p.980

The dosage compensation complex (DCC) of Drosophila identifies its X-chromosomal binding sites with exquisite selectivity. The principles that assure this vital targeting are known from the D. melanogaster model: DCC-intrinsic specificity of DNA binding, cooperativity with the CLAMP protein, and noncoding roX2 RNA transcribed from the X chromosome. We found that in D. virilis, a species separated from melanogaster by 40 million years of evolution, all principles are active but contribute differently to X specificity. In melanogaster, the DCC subunit MSL2 evolved intrinsic DNA-binding selectivity for rare PionX sites, which mark the X chromosome. In virilis, PionX motifs are abundant and not X-enriched. Accordingly, MSL2 lacks specific recognition. Here, roX2 RNA plays a more instructive role, counteracting a nonproductive interaction of CLAMP and modulating DCC binding selectivity. Remarkably, roX2 triggers a stable chromatin binding mode characteristic of DCC. Evidently, X-specific regulation is achieved by divergent evolution of protein, DNA, and RNA components.

The fundamentals of rutting behavior for thin full-depth flexible pavements (i.e., asphalt thickness less than 12 inches) are investigated in this study. The scope incorporates an experimental study using full-scale Accelerated Pavement Tests (APTs) to monitor the evolution of each pavement structural layer's transverse profiles. The findings were then employed to verify the local rutting model coefficients used in the current pavement design method, the Mechanistic-Empirical Pavement Design Guide (MEPDG). Four APT sections were constructed using two thin typical pavement structures (seven-and ten-inches thick) and two types of surface course material (dense-graded and SMA). A mid-depth rut monitoring and automated laser profile systems were designed to reconstruct the transverse profiles at each pavement layer interface throughout the process of accelerated pavement deterioration that is produced during the APT. The contributions of each pavement structural layer to rutting and the evolution of layer deformation were derived. This study found that the permanent deformation within full-depth asphalt concrete significantly depends upon the pavement thickness. However, once the pavement reaches sufficient thickness (more than 12.5 inches), increasing the thickness does not significantly affect the permanent deformation. Additionally, for thin full-depth asphalt pavements with a dense-graded Hot Mix Asphalt (HMA) surface course, most pavement rutting is caused by the deformation of the asphalt concrete, with about half the rutting amount observed within the top four inches of the pavement layers. However, for thin full-depth asphalt pavements with an SMA surface course, most pavement rutting comes from the closet sublayer to the surface, i.e., the intermediate layer. The accuracy of the MEPDG’s prediction models for thin full-depth asphalt pavement was evaluated using some statistical parameters, including bias, the sum of squared error, and the standard error of estimates between the predicted and actual measurements. Based on the statistical analysis (at the 95% confidence level), no significant difference was found between the version 2.3-predicted and measured rutting of total asphalt concrete layer and subgrade for thick and thin pavements.

RNA-protein interactions are often mediated by dedicated canonical RNA binding domains. However, interactions through non-canonical domains with unknown specificity are increasingly observed, raising the question how RNA targets are recognized. Knowledge of the intrinsic RNA binding specificity contributes to the understanding of target selectivity and function of an individual protein. The presented in vitro RNA immunoprecipitation assay (vitRIP) uncovers intrinsic RNA binding specificities of isolated proteins using the total cellular RNA pool as a library. Total RNA extracted from cells or tissues is incubated with purified recombinant proteins, RNA-protein complexes are immunoprecipitated and bound transcripts are identified by deep sequencing or quantitative RT-PCR. Enriched RNA classes and the nucleotide frequency in these RNAs inform on the intrinsic specificity of the recombinant protein. The simple and versatile protocol can be adapted to other RNA binding proteins and total RNA libraries from any cell type or tissue. Graphic abstract: Figure 1. Schematic of the in vitro RNA immunoprecipitation (vitRIP) protocol.

This report documents the findings from SPR-4230 (Alternative Quality Assurance Methods for Compacted Subgrade). The main objective of SPR-4230 involved establishing performance-related quality assurance (QA) test methods for pavement subgrade construction. Because INDOT generally prefers specifying subgrade treatment type IBC (i.e., 14-in. cement modified subgrade), this study focused on performance-based QA test methods for constructing cement modified subgrade. Moreover, INDOT prefers using light weight deflectometer (LWD) for chemically modified subgrade construction acceptance, so this study aimed to use LWD deflection measurements as performance-related construction acceptance criteria. A laboratory study was performed to relate LWD deflections with resilient modulus that is the key subgrade performance-related parameter in pavement design. In addition, LWD deflections were related with unconfined compressive strength increase that is the key parameter in chemical soil modification mix design. A rigorous field study consisting of LWD testing and falling weight deflectometer (FWD) testing at INDOT new pavement construction sites was conducted to verify the laboratory developed relationship. Recommendations for implementing results of this study into cement modified subgrade construction acceptance is provided, as are recommendations for future research.

Recent observations of X-ray pulsars at low luminosities allow, for the first time, to compare theoretical models for the emission from highly magnetized neutron star atmospheres at low mass accretion rates ($\dot{M} \lesssim 10^{15}$ g s$^{-1}$) with the broadband X-ray data. The purpose of this paper is to investigate the spectral formation in the neutron star atmosphere at low $\dot{M}$ and to conduct a parameter study of physical properties of the emitting region. We obtain the structure of the static atmosphere, assuming that Coulomb collisions are the dominant deceleration process. The upper part of the atmosphere is strongly heated by the braking plasma, reaching temperatures of 30-40 keV, while its denser isothermal interior is much cooler (~2 keV). We numerically solve the polarized radiative transfer in the atmosphere with magnetic Compton scattering, free-free processes, and non-thermal cyclotron emission due to possible collisional excitations of electrons. The strongly polarized emitted spectrum has a double-hump shape that is observed in low-luminosity X-ray pulsars. A low-energy "thermal" component is dominated by extraordinary photons that can leave the atmosphere from deeper layers due to their long mean free path at soft energies. We find that a high-energy component is formed due to resonant Comptonization in the heated non-isothermal part of the atmosphere even in the absence of collisional excitations. The latter, however, affect the ratio of the two components. A strong cyclotron line originates from the optically thin, uppermost zone. A fit of the model to NuSTAR and Swift/XRT observations of GX 304-1 provides an accurate description of the data with reasonable parameters. The model can thus reproduce the characteristic double-hump spectrum observed in low-luminosity X-ray pulsars and provides insights into spectral formation., Comment: 18 pages, 10 figures, A&A accepted

RNA-protein interactions are often mediated by dedicated canonical RNA binding domains. However, interactions through non-canonical domains with unknown specificity are increasingly observed, raising the question how RNA targets are recognized. Knowledge of the intrinsic RNA binding specificity contributes to the understanding of target selectivity and function of an individual protein. The presented in vitro RNA immunoprecipitation assay (vitRIP) uncovers intrinsic RNA binding specificities of isolated proteins using the total cellular RNA pool as a library. Total RNA extracted from cells or tissues is incubated with purified recombinant proteins, RNA-protein complexes are immunoprecipitated and bound transcripts are identified by deep sequencing or quantitative RT-PCR. Enriched RNA classes and the nucleotide frequency in these RNAs inform on the intrinsic specificity of the recombinant protein. The simple and versatile protocol can be adapted to other RNA binding proteins and total RNA libraries from any cell type or tissue. Graphic abstract

We present an analysis of X-ray spectra of the high-mass X-ray binary 4U 0115+634 as observed with Suzaku and RXTE in 2011 July, during the fading phase of a giant X-ray outburst. We used a continuum model consisting of an absorbed cutoff power law and an ad hoc Gaussian emission feature centered around 8.5 keV, which we attribute to cyclotron emission. Our results are consistent with a fundamental cyclotron absorption line centered at ∼10.2 keV for all observed flux ranges. At the same time we rule out significant influence of the 8.5 kev Gaussian on the parameters of the cyclotron resonant scattering feature, which are not consistent with the cyclotron line energies or the depths of previously reported flux-dependent descriptions. We also show that some continuum models can lead to artificial line-like residuals in the analyzed spectra, which are then misinterpreted as unphysically strong cyclotron lines. Specifically, our results do not support the existence of a previously claimed additional cyclotron feature at ∼15 keV. Apart from these features, we find for the first time evidence for a He-like Fe XXV emission line at ∼6.7 keV and weak H-like Fe XXVI emission close to ∼7.0 keV. We acknowledge funding by the European Space Agency under contract number C4000115860/15/NL/IB, by the Bundesministerium für Wirtschaft und Technologie under Deutsches Zentrum für Luft- und Raumfahrt grants 50OR0808, 50OR0905, 50OR1113, and 50OR1207, and by the Deutscher Akademischer Austauschdienst. MTW is supported by the NASA Astrophysical Data Analysis Program and the Chief of Naval Research. VG is supported through the Margarethe von Wrangell fellowship by the ESF and the Ministry of Science, Research and the Arts Baden-Württemberg. SMN and JMT acknowledge Spanish Ministerio de Ciencia, Tecnología e Innovación (MICINN) through the grant ESP2016-76683-C3-1-R and ESP2017-85691-P, respectively.

Histone acetylation and deposition of H2A.Z variant are integral aspects of active transcription. In Drosophila, the single DOMINO chromatin regulator complex is thought to combine both activities via an unknown mechanism. Here we show that alternative isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly specify two distinct multi-subunit complexes. Both complexes are necessary for transcriptional regulation but through different mechanisms. The DOM-B complex incorporates H2A.V (the fly ortholog of H2A.Z) genome-wide in an ATP-dependent manner, like the yeast SWR1 complex. The DOM-A complex, instead, functions as an ATP-independent histone acetyltransferase complex similar to the yeast NuA4, targeting lysine 12 of histone H4. Our work provides an instructive example of how different evolutionary strategies lead to similar functional separation. In yeast and humans, nucleosome remodeling and histone acetyltransferase complexes originate from gene duplication and paralog specification. Drosophila generates the same diversity by alternative splicing of a single gene., eLife digest Cells contain a large number of proteins that control the activity of genes in response to various signals and changes in their environment. Often these proteins work together in groups called complexes. In the fruit fly Drosophila melanogaster, one of these complexes is called DOMINO. The DOMINO complex alters gene activity by interacting with other proteins called histones which influence how the genes are packaged and accessed within the cell. DOMINO works in two separate ways. First, it can replace certain histones with other variants that regulate genes differently. Second, it can modify histones by adding a chemical marker to them, which alters how they interact with genes. It was not clear how DOMINO can do both of these things and how that is controlled; but it was known that cells can make two different forms of the central component of the complex, called DOM-A and DOM-B, which are both encoded by the same gene. Scacchetti et al. have now studied fruit flies to understand the activities of these forms. This revealed that they do have different roles and that gene activity in cells changes if either one is lost. The two forms operate as part complexes with different compositions and only DOM-A includes the TIP60 enzyme that is needed to modify histones. As such, it seems that DOM-B primarily replaces histones with variant forms, while DOM-A modifies existing histones. This means that each form has a unique role associated with each of the two known behaviors of this complex. The presence of two different DOMINO complexes is common to flies and, probably, other insects. Yet, in other living things, such as mammals and yeast, their two roles are carried out by protein complexes originating from two distinct genes. This illustrates a concept called convergent evolution, where different organisms find different solutions for the same problem. As such, these findings provide an insight into the challenges encountered through evolution and the diverse solutions that have developed. They will also help us to understand the ways in which protein activities can adapt to different needs over evolutionary time.

Vibration compaction is the most effective way of compacting coarse-grained materials. The effects of vibration frequency and amplitude on the compaction density of different backfill materials commonly used by INDOT (No. 4 natural sand, No. 24 stone sand, and No. 5, No. 8, No. 43 aggregates) were studied in this research. The test materials were characterized based on the particle sizes and morphology parameters using digital image analysis technique. Small-scale laboratory compaction tests were carried out with variable frequency and amplitude of vibrations using vibratory hammer and vibratory table. The results show an increase in density with the increase in amplitude and frequency of vibration. However, the increase in density with the increase in amplitude of vibration is more pronounced for the coarse aggregates than for the sands. A comparison of the maximum dry densities of different test materials shows that the dry densities obtained after compaction using the vibratory hammer are greater than those obtained after compaction using the vibratory table when both tools were used at the highest amplitude and frequency of vibration available. Large-scale vibratory roller compaction tests were performed in the field for No. 30 backfill soil to observe the effect of vibration frequency and number of passes on the compaction density. Accelerometer sensors were attached to the roller drum (Caterpillar, model CS56B) to measure the frequency of vibration for the two different vibration settings available to the roller. For this roller and soil tested, the results show that the higher vibration setting is more effective. Direct shear tests and direct interface shear tests were performed to study the impact of particle characteristics of the coarse-grained backfill materials on interface shear resistance. The more angular the particles, the greater the shear resistance measured in the direct shear tests. A unique relationship was found between the normalized surface roughness and the ratio of critical-state interface friction angle between sand-gravel mixture with steel to the internal critical-state friction angle of the sand-gravel mixture.

Telomeres are protective caps at the end of chromosomes, and their length is positively correlated with individual health and lifespan across taxa. Longitudinal studies have provided mixed results regarding the within-individual repeatability of telomere length. While some studies suggest telomere length to be highly dynamic and sensitive to resource-demanding or stressful conditions, others suggest that between-individual differences are mostly present from birth and relatively little affected by the later environment. This dichotomy could arise from differences between species, but also from methodological issues. In our study, we used the highly reliable Terminal Restriction Fragment analysis method to measure telomeres over a 10-year period in adults of a long-lived seabird, the common tern (Sterna hirundo). Telomeres shortened with age within individuals. The individual repeatability of age-dependent telomere length was high (>0.53), and independent of the measurement interval (i.e., one vs. six years). A small (R-2 = .01), but significant part of the between-individual variation in telomere length was, however, explained by the number of fledglings produced in the previous year, while reproduction in years prior to the previous year had no effect. We confirmed that age-dependent telomere length predicted an individual's remaining lifespan. Overall, our study suggests that the majority of between-individual variation in adult telomere length is consistent across adult life, and that a smaller part of the variation can be explained by dynamic factors, such as reproduction.

Hot, tenuous advection-dominated accretion flows around black holes are ideal sites for the Fermi acceleration of relativistic particles at standing shock waves in the accretion disc. Previous work has demonstrated that the shock-acceleration process can be efficient enough to power the observed, strong outflows in radio-loud active galaxies such as M87. However, the dynamical effect (back-reaction) on the flow, exerted by the pressure of the relativistic particles, has not been previously considered, and this effect can have a significant influence on the disc structure. We reexamine the problem by developing a new, two-fluid model for the structure of the accretion disc that includes the dynamical effect of the relativistic particle pressure, combined with the pressure of the background (thermal) gas. The new model is analogous to the two-fluid model of cosmic ray acceleration in supernova-driven shock waves. As part of the model, we also develop a new set of shock jump conditions, which are solved along with the hydrodynamic conservation equations to determine the structure of the accretion disc. The solutions include the formation of a mildly relativistic outflow (jet) at the shock radius, driven by the relativistic particles accelerated in the disc. One of our main conclusions is that in the context of the new two-fluid accretion model, global smooth (shock-free) solutions do not exist, and the disc must always contain a standing shock wave, at least in the inviscid case considered here., Comment: 34 pages, 9 figures

Multiwavelength monitoring of the blazar 3C 279 observed a very bright, 12-hour, orphan gamma-ray flare on 20 Dec 2013 with a uniquely hard Fermi-LAT spectrum and high Compton dominance. We work with a one-zone, leptonic model with both first- and second-order Fermi acceleration, which now reproduces the unique flaring behavior. We present a simplified analytic electron energy distribution to provide intuition about how particle acceleration shapes multi-wavelength blazar jet emission spectra. The contributions of individual processes in relativistic jets is fundamental to understanding the particle energy budget in the formation and propagation of astrophysical jets. We show that first- and second-order Fermi acceleration are sufficient to explain the flare, and that magnetic reconnection is not needed. Our analysis suggests that the flare is initiated by an increase in the particle energies due to shock acceleration, which also increases the stochastic acceleration. The higher energy particle preferentially occupy the outer jet, along the sheath, which decreases the apparent magnetic field and synchrotron radiation, while increasing electron exposure to the broad line region photon fields, driving up the external Compton emission., 7 pages, 4 figures, High Energy Phenomena in Relativistic Outflows VII (HEPRO VII) Meeting

In flies, the chromosomal kinase JIL-1 is responsible for most interphase histone H3S10 phosphorylation and has been proposed to protect active chromatin from acquiring heterochromatic marks, such as dimethylated histone H3K9 (H3K9me2) and HP1. Here, we show that JIL-1’s targeting to chromatin depends on a PWWP domain-containing protein JASPer (JIL-1 Anchoring and Stabilizing Protein). JASPer-JIL-1 (JJ)-complex is the major form of kinase in vivo and is targeted to active genes and telomeric transposons via binding of the PWWP domain of JASPer to H3K36me3 nucleosomes, to modulate transcriptional output. JIL-1 and JJ-complex depletion in cycling cells lead to small changes in H3K9me2 distribution at active genes and telomeric transposons. Finally, we identify interactors of the endogenous JJ-complex and propose that JIL-1 not only prevents heterochromatin formation but also coordinates chromatin-based regulation in the transcribed part of the genome., The chromosomal kinase JIL-1 is responsible for interphase histone H3S10 phosphorylation and has been proposed to protect active chromatin from heterochromatinisation. Here, the authors show that JIL-1 is stabilized and anchored to active genes and telomeric transposons by JASPer, which binds to H3K36me3 nucleosomes via its PWWP domain.

Due to the complexity of modeling the radiative transfer inside the accretion columns of neutron star binaries, their X-ray spectra are still commonly described with phenomenological models, for example, a cutoff power law. While the behavior of these models is well understood and they allow for a comparison of different sources and studying source behavior, the extent to which the underlying physics can be derived from the model parameters is very limited. During recent years, several physically motivated spectral models have been developed to overcome these limitations. Their application, however, is generally computationally much more expensive and they require a high number of parameters which are difficult to constrain. Previous works have presented an analytical solution to the radiative transfer equation inside the accretion column assuming a velocity profile that is linear in the optical depth. An implementation of this solution that is both fast and accurate enough to be fitted to observed spectra is available as a model in XSPEC. The main difficulty of this implementation is that some solutions violate energy conservation and therefore have to be rejected by the user. We propose a novel fitting strategy that ensures energy conservation during the $\chi^2$-minimization which simplifies the application of the model considerably. We demonstrate this approach as well a study of possible parameter degeneracies with a comprehensive Markov-chain Monte Carlo analysis of the complete parameter space for a combined NuSTAR and Swift/XRT dataset of Cen X-3. The derived accretion-flow structure features a small column radius of $\sim$63 m and a spectrum dominated by bulk-Comptonization of bremsstrahlung seed photons, in agreement with previous studies., Comment: 14 pages, 7 figures, A&A accepted