Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans

Transcriptional regulation, a primary mechanism for controlling the development of multicellular organisms, is carried out by transcription factors (TFs) that recognize and bind to their cognate binding sites. In Caenorhabditis elegans, our knowledge of which genes are regulated by which TFs, through binding to specific sites, is still very limited. To expand our knowledge about the C. elegans regulatory network, we performed a comprehensive analysis of the C. elegans, Caenorhabditis briggsae, and Caenorhabditis remanei genomes to identify regulatory elements that are conserved in all genomes. Our analysis identified 4959 elements that are significantly conserved across the genomes and that each occur multiple times within each genome, both hallmarks of functional regulatory sites. Our motifs show significant matches to known core promoter elements, TF binding sites, splice sites, and poly-A signals as well as many putative regulatory sites. Many of the motifs are significantly correlated with various types of experimental data, including gene expression patterns, tissue-specific expression patterns, and binding site location analysis as well as enrichment in specific functional classes of genes. Many can also be significantly associated with specific TFs. Combinations of motif occurrences allow us to predict the location of cis-regulatory modules and we show that many of them significantly overlap experimentally determined enhancers. We provide access to the predicted binding sites, their associated motifs, and the predicted cis-regulatory modules across the whole genome through a web-accessible database and as tracks for genome browsers

Neuropathic Nav1.3-mediated sensitization to P2X activation is regulated by protein kinase C

<p>Abstract</p> <p>Background</p> <p>Increased neuronal excitability and spontaneous firing are hallmark characteristics of injured sensory neurons. Changes in expression of various voltage-gated Na⁺channels (VGSCs) have been observed under neuropathic conditions and there is evidence for the involvement of protein kinase C (PKC) in sensory hyperexcitability. Here we demonstrate the contribution of PKC to P2X-evoked VGSC activation in dorsal root ganglion (DRG) neurons in neuropathic conditions.</p> <p>Results</p> <p>Using the spinal nerve ligation (SNL) model of neuropathic pain and whole-cell patch clamp recordings of dissociated DRG neurons, we examined changes in excitability of sensory neurons after nerve injury and observed that P2X3 purinoceptor-mediated currents induced by α,β-meATP triggered activation of TTX-sensitive VGSCs in neuropathic nociceptors only. Treatment of neuropathic DRGs with the PKC blocker staurosporine or calphostin C decreased the α,β-meATP-induced Na⁺channels activity and reversed neuronal hypersensitivity. In current clamp mode, α,β-meATP was able to evoke action-potentials more frequently in neuropathic neurons than in controls. Pretreatment with calphostin C significantly decreased the proportion of sensitized neurons that generated action potentials in response to α,β-meATP. Recordings measuring VGSC activity in neuropathic neurons show significant change in amplitude and voltage dependence of sodium currents. In situ hybridization data indicate a dramatic increase in expression of embryonic Na_v1.3 channels in neuropathic DRG neurons. In a CHO cell line stably expressing the Na_v1.3 subunit, PKC inhibition caused both a significant shift in voltage-dependence of the channel in the depolarizing direction and a decrease in current amplitude.</p> <p>Conclusion</p> <p>Neuropathic injury causes primary sensory neurons to become hyperexcitable to ATP-evoked P2X receptor-mediated depolarization, a phenotypic switch sensitive to PKC modulation and mediated by increased activity of TTX-sensitive VGSCs. Upregulation in VGSC activity after injury is likely mediated by increased expression of the Na_v1.3 subunit, and the function of the Na_v1.3 channel is regulated by PKC.</p

A model for assessing water quality risk in catchments prone to wildfire

Post-fire debris flows can have erosion rates up to three orders of magnitude higher than background rates. They are major sources of fine suspended sediment, which is critical to the safety of water supply from forested catchments. Fire can cover parts or all of these large catchments and burn severity is often heterogeneous. The probability of spatial and temporal overlap of fire disturbance and rainfall events, and the susceptibility of hillslopes to severe erosion determine the risk to water quality. Here we present a model to calculate recurrence intervals of high magnitude sediment delivery from runoff-generated debris flows to a reservoir in a large catchment (>100 km2) accounting for heterogeneous burn conditions. Debris flow initiation was modelled with indicators of surface runoff and soil surface erodibility. Debris flow volume was calculated with an empirical model, and fine sediment delivery was calculated using simple, expert-based assumptions. In a Monte-Carlo simulation, wildfire was modelled with a fire spread model using historic data on weather and ignition probabilities for a forested catchment in central Victoria, Australia. Multiple high intensity storms covering the study catchment were simulated using Intensity–Frequency–Duration relationships, and the runoff indicator calculated with a runoff model for hillslopes. A sensitivity analysis showed that fine sediment is most sensitive to variables related to the texture of the source material, debris flow volume estimation, and the proportion of fine sediment transported to the reservoir. As a measure of indirect validation, denudation rates of 4.6–28.5 mm ka−1 were estimated and compared well to other studies in the region. From the results it was extrapolated that in the absence of fire management intervention the critical sediment concentrations in the studied reservoir could be exceeded in intervals of 18–124 years

Effect of angiotensin receptor neprilysin inhibitors on left atrial remodeling and prognosis in heart failure

Aims The angiotensin receptor–neprilysin inhibitor (ARNI), sacubitril/valsartan, confers additional protective effects compared with angiotensin-converting enzyme inhibitors/angiotensin II receptor blockers (ACEIs/ARBs) in terms of reversed left ventricular (LV) remodelling and improves the prognosis of patients with heart failure (HF). However, few studies have examined the effects of ARNI on the left atrium. Accordingly, this study compared the effects of ARNI and ACEI/ARB on left atrial (LA) remodelling in heart failure with reduced ejection fraction (HFrEF). Methods and results This was a single-centre retrospective study of patients with HFrEF hospitalized at the First Affiliated Hospital of Dalian Medical University between 26 February 2016 and 8 July 2020. Patients were classified into ARNI and ACEI/ARB groups and further subgroups based on the left atrial volume index (LAVI): mildly abnormal (29 mL/m2 ≤ LAVI < 34 mL/m2), moderately abnormal (34 mL/m2 ≤ LAVI < 40 mL/m2), and severely abnormal (LAVI ≥ 40 mL/m2). The primary endpoint was changes in LA parameters by echocardiography. The secondary endpoint was all-cause mortality. A total of 336 patients (mean age: 64.11 ± 12.86, 30.06% female) were included. Except those lost to follow-up, 274 HFrEF patients remained, with 144 cases in the ARNI group and 130 cases in the ACEI/ARB group. Greater reductions from baseline were seen with ARNI in LA diameter (LAD) (P = 0.013, t-test), superior and LA superior–inferior diameter (LASID) (P < 0.0001), LA transverse diameter (LATD) (P < 0.0001), LA volume (LAV) (P < 0.0001), LAVI (P < 0.0001), and LA sphericity index (LASI) (P < 0.0001). Over a mean follow-up of 19.40 months, 97 patients (67.3%) in the ARNI group and 29 patients (22.3%) in the ACEI/ARB group showed LA reverse remodelling (LARR). Kaplan–Meier analysis showed significantly lower overall mortality in the ARNI group compared with the ACEI/ARB group (P = 0.048, log-rank test). The mildly abnormal LAVI group of ARNI patients showed a reduction in mortality compared with ACEI/ARB patients (P = 0.044). However, no significant difference was observed for the moderately abnormal (P = 0.571) or severely abnormal LAVI groups (P = 0.609), suggesting that early initiation of ARNI was associated with a better prognosis. Conclusions In this proof-of-concept study, ARNI use showed greater effects on LARR and was associated with a better prognosis compared with ACEI/ARB use in HFrEF. Early initiation of ARNI in the HF disease process may produce greater benefit, but this needs to be confirmed in future studies

The Common Core Writing Standards: A Descriptive Study of Content and Alignment with A Sample of Former State Standards

Many students do not meet expected standards of writing performance, despite the need for writing competence in and out of school. As policy instruments, writing content standards have an impact on what is taught and how students perform. This study reports findings from an evaluation of the content of a sample of seven diverse states’ current writing standards compared to content of the Common Core State Standards for writing and language (CCSS-WL). Standards were evaluated for breadth of content coverage (range), how often content was referenced (frequency), the degree of emphasis placed on varied content elements (balance), and the degree of overlap between one set of standards and another (alignment). The study addressed two research questions: (1) What is the nature of the CCSS-WL and the sample states’ standards for writing with respect to content breadth, frequency, and balance? (2) To what degree do the states\u27 writing standards align with the CCSS-WL? Results indicated that CCSS-WL are succinct and balanced, with breadth of coverage in some aspects of writing but not others. The seven states’ standards represented varying degrees of breadth, frequency, and balance with few patterns across states. None of the states’ standards had strong alignment with CCSS-WL, indicating a potential mismatch between prior curricular materials and instructional methods developed with former standards as guides to help students meet grade-level writing expectations in the new CCSS

Optimal linear reconstruction of dark matter from halo catalogs

We derive the weight function w(M) to apply to dark-matter halos that minimizes the stochasticity between the weighted halo distribution and its underlying mass density field. The optimal w(M) depends on the range of masses being used in the estimator. In N-body simulations, the Poisson estimator is up to 15 times noisier than the optimal. Implementation of the optimal weight yields significantly lower stochasticity than weighting halos by their mass, bias or equal. Optimal weighting could make cosmological tests based on the matter power spectrum or cross-correlations much more powerful and/or cost-effective. A volume-limited measurement of the mass power spectrum at k=0.2h/Mpc over the entire z<1 universe could ideally be done using only 6 million redshifts of halos with mass M>6\times10^{13}h^{-1}M_\odot (1\times10^{13}) at z=0 (z=1); this is 5 times fewer than the Poisson model predicts. Using halo occupancy distributions (HOD) we find that uniformly-weighted catalogs of luminous red galaxies require >3 times more redshifts than an optimally-weighted halo catalog to reconstruct the mass to the same accuracy. While the mean HODs of galaxies above a threshold luminosity are similar to the optimal w(M), the stochasticity of the halo occupation degrades the mass estimator. Blue or emission-line galaxies are about 100 times less efficient at reconstructing mass than an optimal weighting scheme. This suggests an efficient observational approach of identifying and weighting halos with a deep photo-z survey before conducting a spectroscopic survey. The optimal w(M) and mass-estimator stochasticity predicted by the standard halo model for M>10^{12}h^{-1}M_\odot are in reasonable agreement with our measurements, with the important exceptions that the halos must be assumed to be linearly biased samples of a "halo field" that is distinct from the mass field. (Abridged)Comment: Added Figure 3 to show the scatter between the weighted halo field vs the mass field, Accepted for publication in MNRA

Rapid exchange of mammalian topoisomerase IIα at kinetochores and chromosome arms in mitosis

Astable cell line (GT2-LPk) derived from LLC-Pk was created in which endogenous DNA topoisomerase IIα (topoIIα) protein was downregulated and replaced by the expression of topoIIα fused with enhanced green fluorescent protein (EGFP–topoIIα). The EGFP–topoIIα faithfully mimicked the distribution of the endogenous protein in both interphase and mitosis. In early stages of mitosis, EGFP–topoIIα accumulated at kinetochores and in axial lines extending along the chromosome arms. During anaphase, EGFP–topoIIα diminished at kinetochores and increased in the cytoplasm with a portion accumulating into large circular foci that were mobile and appeared to fuse with the reforming nuclei. These cytoplasmic foci appearing at anaphase were coincident with precursor organelles of the reforming nucleolus called nucleolus-derived foci (NDF). Photobleaching of EGFP–topoIIα associated with kinetochores and chromosome arms showed that the majority of the protein rapidly exchanges (t1/2 of 16 s). Catalytic activity of topoIIα was essential for rapid dynamics, as ICRF-187, an inhibitor of topoIIα, blocked recovery after photobleaching. Although some topoIIα may be stably associated with chromosomes, these studies indicate that the majority undergoes rapid dynamic exchange. Rapid mobility of topoIIα in chromosomes may be essential to resolve strain imparted during chromosome condensation and segregation

Low lopinavir plasma or hair concentrations explain second-line protease inhibitor failures in a resource-limited setting.

In resource-limited settings, many patients, with no prior protease inhibitor (PI) treatment on a second-line, high genetic barrier, ritonavir-boosted PI-containing regimen have virologic failure