In Drosophila melanogaster the single male chromosome X undergoes an average twofold transcriptional upregulation for balancing the transcriptional output between sexes. Previous literature ...hypothesised that a global change in chromosome structure may accompany this process. However, recent studies based on Hi-C failed to detect these differences. Here we show that global conformational differences are specifically present in the male chromosome X and detectable using Hi-C data on sex-sorted embryos, as well as male and female cell lines, by leveraging custom data analysis solutions. We find the male chromosome X has more mid-/long-range interactions. We also identify differences at structural domain boundaries containing BEAF-32 in conjunction with CP190 or Chromator. Weakening of these domain boundaries in male chromosome X co-localizes with the binding of the dosage compensation complex and its co-factor CLAMP, reported to enhance chromatin accessibility. Together, our data strongly indicate that chromosome X dosage compensation affects global chromosome structure.
The aim of this study was to evaluate the efficacy of oral transmucosal (OTM) cannabidiol (CBD), in addition to a multimodal pharmacological treatment for chronic osteoarthritis-related pain in dogs. ...Twenty-one dogs were randomly divided into two groups: in group CBD (n = 9), OTM CBD (2 mg kg−1 every 12 h) was included in the therapeutic protocol (anti-inflammatory drug, gabapentin, amitriptyline), while in group C (n = 12), CBD was not administered. Dogs were evaluated by owners based on the Canine Brief Pain Inventory scoring system before treatment initiation (T0), and one (T1), two (T2), four (T3) and twelve (T4) weeks thereafter. Pain Severity Score was significantly lower in CBD than in C group at T1 (p = 0.0002), T2 (p = 0.0043) and T3 (p = 0.016). Pain Interference Score was significantly lower in CBD than in C group at T1 (p = 0.0002), T2 (p = 0.0007) and T4 (p = 0.004). Quality of Life Index was significantly higher in CBD group at T1 (p = 0.003). The addition of OTM CBD showed promising results. Further pharmacokinetics and long-term studies in larger populations are needed to encourage its inclusion into a multimodal pharmacological approach for canine osteoarthritis-related pain.
Water stress during grain filling has a marked effect on grain yield, leading to a reduced endosperm cell number and thus sink capacity to accumulate dry matter. The bread wheat cultivar Chinese ...Spring (CS), a Chinese Spring terminal deletion line (CS_5AL-10) and the durum wheat cultivar Creso were subjected to transcriptional profiling after exposure to mild and severe drought stress at the grain filling stage to find evidences of differential stress responses associated to different wheat genome regions.
The transcriptome analysis of Creso, CS and its deletion line revealed 8,552 non redundant probe sets with different expression levels, mainly due to the comparisons between the two species. The drought treatments modified the expression of 3,056 probe sets. Besides a set of genes showing a similar drought response in Creso and CS, cluster analysis revealed several drought response features that can be associated to the different genomic structure of Creso, CS and CS_5AL-10. Some drought-related genes were expressed at lower level (or not expressed) in Creso (which lacks the D genome) or in the CS_5AL-10 deletion line compared to CS. The chromosome location of a set of these genes was confirmed by PCR-based mapping on the D genome (or the 5AL-10 region). Many clusters were characterized by different level of expression in Creso, CS and CS_AL-10, suggesting that the different genome organization of the three genotypes may affect plant adaptation to stress. Clusters with similar expression trend were grouped and functional classified to mine the biological mean of their activation or repression. Genes involved in ABA, proline, glycine-betaine and sorbitol pathways were found up-regulated by drought stress. Furthermore, the enhanced expression of a set of transposons and retrotransposons was detected in CS_5AL-10.
Bread and durum wheat genotypes were characterized by a different physiological reaction to water stress and by a substantially different molecular response. The genome organization accounted for differences in the expression level of hundreds of genes located on the D genome or controlled by regulators located on the D genome. When a genomic stress (deletion of a chromosomal region) was combined with low water availability, a molecular response based on the activation of transposons and retrotransposons was observed.
By two-three months, infants show active social expressions during face-to-face interactions. These interactions are important, as they provide the foundation for later emotional regulation and ...cognition, but little is known about how infant social expressiveness develops. We considered two different accounts. One emphasizes the contingency of parental responsiveness, regardless of its form; the other, the functional architecture account, emphasizes the preparedness of both infants and parents to respond in specific ways to particular forms of behaviour in their partner. We videotaped mother-infant interactions from one to nine weeks, and analysed them with a micro-analytic coding scheme. Infant social expressiveness increased through the nine-week period, particularly after 3 weeks. This development was unrelated to the extent of maternal contingent responsiveness, even to infant social expressions. By contrast, specific forms of response that mothers used preferentially for infant social expressions-mirroring, marking with a smile- predicted the increase in these infant behaviours over time. These results support a functional architecture account of the perceptual and behavioural predispositions of infants and parents that allow young infants to capitalize on relatively limited exposure to specific parental behaviours, in order to develop important social capacities.
Improvements in genome sequence annotation revealed discrepancies in the original probeset/gene assignment in Affymetrix microarray and the existence of differences between annotations and effective ...alignments of probes and transcription products. In the current generation of Affymetrix human GeneChips, most probesets include probes matching transcripts from more than one gene and probes which do not match any transcribed sequence.
We developed a novel set of custom Chip Definition Files (CDF) and the corresponding Bioconductor libraries for Affymetrix human GeneChips, based on the information contained in the GeneAnnot database. GeneAnnot-based CDFs are composed of unique custom-probesets, including only probes matching a single gene.
GeneAnnot-based custom CDFs solve the problem of a reliable reconstruction of expression levels and eliminate the existence of more than one probeset per gene, which often leads to discordant expression signals for the same transcript when gene differential expression is the focus of the analysis. GeneAnnot CDFs are freely distributed and fully compliant with Affymetrix standards and all available software for gene expression analysis. The CDF libraries are available from http://www.xlab.unimo.it/GA_CDF, along with supplementary information (CDF libraries, installation guidelines and R code, CDF statistics, and analysis results).
Unrepaired DNA damage during embryonic development can be potentially inherited by a large population of cells. However, the quality control mechanisms that minimize the contribution of damaged cells ...to developing embryos remain poorly understood. Here, we uncovered an ATR- and CHK1-mediated transcriptional response to replication stress (RS) in mouse embryonic stem cells (ESCs) that induces genes expressed in totipotent two-cell (2C) stage embryos and 2C-like cells. This response is mediated by
, a multicopy retrogene defining the cleavage-specific transcriptional program in placental mammals. In response to RS, DUX triggers the transcription of 2C-like markers such as murine endogenous retrovirus-like elements (MERVL) and
. This response can also be elicited by ETAA1-mediated ATR activation in the absence of RS. ATR-mediated activation of DUX requires GRSF1-dependent post-transcriptional regulation of
mRNA. Strikingly, activation of ATR expands ESCs fate potential by extending their contribution to both embryonic and extra-embryonic tissues. These findings define a novel ATR dependent pathway involved in maintaining genome stability in developing embryos by controlling ESCs fate in response to RS.
Inferior parietal lobule (IPL) neurons were studied when monkeys performed motor acts embedded in different actions and when they observed similar acts done by an experimenter. Most motor IPL neurons ...coding a specific act (e.g., grasping) showed markedly different activations when this act was part of different actions (e.g., for eating or for placing). Many motor IPL neurons also discharged during the observation of acts done by others. Most responded differentially when the same observed act was embedded in a specific action. These neurons fired during the observation of an act, before the beginning of the subsequent acts specifying the action. Thus, these neurons not only code the observed motor act but also allow the observer to understand the agent's intentions.
Despite an increasing research conducted on ocean plastic pollution over the last decade, there are still large knowledge gaps in our current understanding of how floating plastic debris accumulating ...in subtropical oceanic gyres may harm the surface-associated pelagic community known as neuston. Removing floating plastic debris from the surface ocean can minimize potentially adverse effects of plastic pollution on the neuston, as well as prevent the formation of large quantities of secondary micro- and nanoplastics. However, due to the scarcity of observational data from remote and difficult to access offshore waters, neuston dynamics in subtropical oceanic gyres and thus the potential impacts of plastic pollution as well as of cleanup activities on the neuston remain uncertain. Here, we provide rare observational data of the relative distribution of floating plastic debris (0.05–5 cm in size) and members of the neuston in the eastern North Pacific Ocean. Our results reveal that the dominant neustonic species co-occurring with high concentrations of floating plastic debris in the North Pacific Garbage Patch (NPGP) such as
Porpita porpita
,
Halobates
spp., pteropods, isopods, heteropods, and crabs depict either a low atmospheric drag due to physical attributes or a potential plastic-associated fitness benefit such as increased surface area for oviposition and structure for habitat. We further observe relatively higher plastic to organism ratios inside the NPGP for most target species compared to waters outside the NPGP. The findings presented here provide a first observational baseline to develop ecological models that can help evaluate the long-term risks of plastic pollution and of offshore cleanup activities for neuston in the eastern North Pacific Ocean. We further suggest that offshore mitigation strategies aiming at removing floating plastic debris from the ocean surface need to evaluate both, the direct impact of neuston bycatch during plastic removal on neuston population dynamics, as well as the potential benefits of reducing the negative effects of plastic pollution on the neuston.
Abstract The aim of this work is to argue for the idea that processes and process-based entities are to be modelled as relational structures. Relational structures are genuine structures, namely ...entities not committed to the existence of basic objects. My argument moves from the analysis of Whitehead’s original insight about process-based entities that, despite some residual of substance metaphysics, has the merit of grounding the intrinsic dynamism of reality on the holistic and relational characters of process-based entities. The current model of process ontology requires genuine emergence and this, in turn, requires organizations, i.e., emergence in organizations. Another view about processes rely on a structural specification of processes. I suggest that the two views can be made compatible by the help of a specific sort of structures, namely relational structures. The appeal to the mathematical theory of genuine structures, category theory, reveals the formal plausibility of this convergence. According to this formal approach, genuine structures are essentially dynamic entities for they are relational, namely, as well as organizations, they are not existentially committed to particulars.
Pinch point singularities, associated with flat band magnetic excitations, are tell-tale signatures of Coulomb spin liquids. While their properties in the presence of quantum fluctuations have been ...widely studied, the fate of the complementary nonanalytic features—shaped as half moons and stars—arising from adjacent shallow dispersive bands has remained unexplored. Here, we address this question for the spin S=1/2 Heisenberg antiferromagnet on the kagome lattice with second and third neighbor couplings, which allows one to tune the classical ground state characterized by flat bands to one that is governed by shallow dispersive bands for intermediate coupling strengths. Employing the complementary strengths of variational Monte Carlo, pseudofermion functional renormalization group, and density-matrix renormalization group, we establish the quantum phase diagram of the model. The U(1) Dirac spin liquid ground state of the nearest-neighbor antiferromagnet remains remarkably robust till intermediate coupling strengths when it transitions into a pinwheel valence bond crystal displaying signatures of half moons in its structure factor. Our Letter thus identifies a microscopic setting that realizes one of the proximate orders of the Dirac spin liquid identified in a recent work Song, Wang, Vishwanath, and He, Nat. Commun. 10, 4254 (2019)2041-172310.1038/s41467-019-11727-3. For larger couplings, we obtain a collinear magnetically ordered ground state characterized by starlike patterns.
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