Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus.

Enhancer clusters overlapping disease-associated mutations in Pierre Robin sequence (PRS) patients regulate SOX9 expression at genomic distances over 1.25 Mb. We applied optical reconstruction of chromatin architecture (ORCA) imaging to trace 3D locus topology during PRS-enhancer activation. We observed pronounced changes in locus topology between cell types. Subsequent analysis of single-chromatin fiber traces revealed that these ensemble-average differences arise through changes in the frequency of commonly sampled topologies. We further identified two CTCF-bound elements, internal to the SOX9 topologically associating domain, which promote stripe formation, are positioned near the domain's 3D geometric center, and bridge enhancer-promoter contacts in a series of chromatin loops. Ablation of these elements results in diminished SOX9 expression and altered domain-wide contacts. Polymer models with uniform loading across the domain and frequent cohesin collisions recapitulate this multi-loop, centrally clustered geometry. Together, we provide mechanistic insights into architectural stripe formation and gene regulation over ultra-long genomic ranges.

Co-transcriptional genome surveillance by HUSH is coupled to termination machinery.

The HUSH complex recognizes and silences foreign DNA such as viruses, transposons, and transgenes without prior exposure to its targets. Here, we show that endogenous targets of the HUSH complex fall into two distinct classes based on the presence or absence of H3K9me3. These classes are further distinguished by their transposon content and differential response to the loss of HUSH. A de novo genomic rearrangement at the Sox2 locus induces a switch from H3K9me3-independent to H3K9me3-associated HUSH targeting, resulting in silencing. We further demonstrate that HUSH interacts with the termination factor WDR82 and-via its component MPP8-with nascent RNA. HUSH accumulates at sites of high RNAPII occupancy including long exons and transcription termination sites in a manner dependent on WDR82 and CPSF. Together, our results uncover the functional diversity of HUSH targets and show that this vertebrate-specific complex exploits evolutionarily ancient transcription termination machinery for co-transcriptional chromatin targeting and genome surveillance.

The NMDA receptor subunit GluN3A regulates synaptic activity-induced and myocyte enhancer factor 2C (MEF2C)-dependent transcription.

N-Methyl-d-aspartate type glutamate receptors (NMDARs) are key mediators of synaptic activity-regulated gene transcription in neurons, both during development and in the adult brain. Developmental differences in the glutamate receptor ionotropic NMDA 2 (GluN2) subunit composition of NMDARs determines whether they activate the transcription factor cAMP-responsive element-binding protein 1 (CREB). However, whether the developmentally regulated GluN3A subunit also modulates NMDAR-induced transcription is unknown. Here, using an array of techniques, including quantitative real-time PCR, immunostaining, reporter gene assays, RNA-Seq, and two-photon glutamate uncaging with calcium imaging, we show that knocking down GluN3A in rat hippocampal neurons promotes the inducible transcription of a subset of NMDAR-sensitive genes. We found that this enhancement is mediated by the accumulation of phosphorylated p38 mitogen-activated protein kinase in the nucleus, which drives the activation of the transcription factor myocyte enhancer factor 2C (MEF2C) and promotes the transcription of a subset of synaptic activity-induced genes, including brain-derived neurotrophic factor (Bdnf) and activity-regulated cytoskeleton-associated protein (Arc). Our evidence that GluN3A regulates MEF2C-dependent transcription reveals a novel mechanism by which NMDAR subunit composition confers specificity to the program of synaptic activity-regulated gene transcription in developing neurons.

Efficacy of doxycycline versus azithromycin for the treatment of rectal chlamydia: a systematic review and meta-analysis.

BACKGROUND: Chlamydia trachomatis infection is the most common sexually transmitted infectious disease and carries a risk of complications. However, the optimal treatment for rectal chlamydial infection remains unclear. OBJECTIVES: To compare the efficacy of doxycycline and azithromycin for the treatment of rectal chlamydia by undertaking a systematic review and meta-analysis of published data. METHODS: We searched PubMed, EMBASE, Cochrane Library, Web of Science and clinicaltrials.gov databases from inception to 7 July 2021 for randomized controlled trials (RCTs) and observational studies that compared the efficacy of doxycycline and single-dose azithromycin on rectal chlamydia cure rates. Data were synthesized using a random-effects model, and subgroup analysis was conducted. RESULTS: All included studies were conducted in developed countries. Two RCTs and nine observational studies, with a total of 2457 patients, were analysed. Doxycycline had a higher microbiological cure rate than azithromycin (risk ratio = 1.21; 95% CI = 1.15-1.28; P < 0.05). Pooled results from two RCTs also revealed a higher microbiological cure rate for doxycycline than azithromycin (risk ratio = 1.27; 95% CI = 1.20-1.35; P < 0.05). The results remained consistent in subgroups of different study designs, countries and sexes. CONCLUSIONS: On the basis of our findings, we recommend doxycycline rather than azithromycin as a first-line treatment for rectal chlamydia in developed countries. More RCTs from developing countries are warranted.

Transcribing the connectome: roles for transcription factors and chromatin regulators in activity-dependent synapse development.

The wiring of synaptic connections in the developing mammalian brain is shaped by both intrinsic and extrinsic signals. One point where these regulatory pathways converge is via the sensory experience-dependent regulation of new gene transcription. Recent studies have elucidated a number of molecular mechanisms that allow nuclear transcription factors and chromatin regulatory proteins to encode aspects of specificity in experience-dependent synapse development. Here we review the evidence for the transcriptional mechanisms that sculpt activity-dependent aspects of synaptic connectivity during postnatal development and discuss how disruption of these processes is associated with aberrant brain development in autism and intellectual disability.

Convergence of Parkin, PINK1, and α-Synuclein on Stress-induced Mitochondrial Morphological Remodeling.

Mutations in PARKIN (PARK2), an ubiquitin ligase, cause early onset Parkinson disease. Parkin was shown to bind, ubiquitinate, and target depolarized mitochondria for destruction by autophagy. This process, mitophagy, is considered crucial for maintaining mitochondrial integrity and suppressing Parkinsonism. Here, we report that under moderate mitochondrial stress, parkin does not translocate to mitochondria to induce mitophagy; rather, it stimulates mitochondrial connectivity. Mitochondrial stress-induced fusion requires PINK1 (PARK6), mitofusins, and parkin ubiquitin ligase activity. Upon exposure to mitochondrial toxins, parkin binds α-synuclein (PARK1), and in conjunction with the ubiquitin-conjugating enzyme Ubc13, stimulates K63-linked ubiquitination. Importantly, α-synuclein inactivation phenocopies parkin overexpression and suppresses stress-induced mitochondria fission, whereas Ubc13 inactivation abrogates parkin-dependent mitochondrial fusion. The convergence of parkin, PINK1, and α-synuclein on mitochondrial dynamics uncovers a common function of these PARK genes in the mitochondrial stress response and provides a potential physiological basis for the prevalence of α-synuclein pathology in Parkinson disease.

The transcription factor calcium-response factor limits NMDA receptor-dependent transcription in the developing brain.

Neuronal activity sculpts brain development by inducing the transcription of genes such as brain-derived neurotrophic factor (Bdnf) that modulate the function of synapses. Sensory experience is transduced into changes in gene transcription via the activation of calcium signaling pathways downstream of both L-type voltage-gated calcium channels (L-VGCCs) and NMDA-type glutamate receptors (NMDARs). These signaling pathways converge on the regulation of transcription factors including calcium-response factor (CaRF). Although CaRF is dispensable for the transcriptional induction of Bdnf following the activation of L-VGCCs, here we show that the loss of CaRF leads to enhanced NMDAR-dependent transcription of Bdnf as well as Arc. We identify the NMDAR subunit-encoding gene Grin3a as a regulatory target of CaRF, and we show that expression of both Carf and Grin3a is depressed by the elevation of intracellular calcium, linking the function of this transcriptional regulatory pathway to neuronal activity. We find that light-dependent activation of Bdnf and Arc transcription is enhanced in the visual cortex of young CaRF knockout mice, suggesting a role for CaRF-dependent dampening of NMDAR-dependent transcription in the developing brain. Finally, we demonstrate that enhanced Bdnf expression in CaRF-lacking neurons increases inhibitory synapse formation. Taken together, these data reveal a novel role for CaRF as an upstream regulator of NMDAR-dependent gene transcription and synapse formation in the developing brain. NMDARs promote brain development by inducing the transcription of genes, including brain-derived neurotrophic factor (BDNF). We show that the transcription factor calcium-response factor (CaRF) limits NMDAR-dependent BDNF induction by regulating expression of the NMDAR subunit GluN3A. Loss of CaRF leads to enhanced BDNF-dependent GABAergic synapse formation indicating the importance of this process for brain development. Our observation that both CaRF and GluN3A are down-regulated by intracellular calcium suggests that this may be a mechanism for experience-dependent modulation of synapse formation.

[Haze Spectral Analysis and Detection Algorithm Using Satellite Remote Sensing Data].

Frequent occurring of haze pollution events and high fine particulate matter (PM(2.5)) concentration in China have attracted more and more attention in the world. Satellite remote sensing can be used to characterize the air pollution. However, haze is usually misidentified as fog, thin cloud or bright surface in NASA's Moderate Resolution Imaging Spectrometer (MODIS) cloud and clear days' aerosol products, and the retrieval of its optical properties is not included in MODIS cloud detection and dark target algorithm. This approach first studies the spectral characters of cloud, fog, haze, and land cover pixels. Second, following the previous cloud detection and aerosol retrieval literatures, a threshold algorithm is developed to distinguish haze from other pixels based on MODIS multi-band apparent reflectance and brightness temperature. This algorithm is used to detect the haze distribution over North China Plain in 2008 spring and summer. Our result shows a good agreement with the true-color satellite images, which enhances MODIS's ability to monitor the severe air pollution episodes. In addition, the high AOD data from Beijing and Xiang Aerosol Robotic NETwork (AERONET) sites indicate nearly 80% haze days are detected by our approach. Finally, we analyze the errors and uncertainties in haze detection algorithm, and put forward the potential improvements.

Rem2 is an activity-dependent negative regulator of dendritic complexity in vivo.

A key feature of the CNS is structural plasticity, the ability of neurons to alter their morphology and connectivity in response to sensory experience and other changes in the environment. How this structural plasticity is achieved at the molecular level is not well understood. We provide evidence that changes in sensory experience simultaneously trigger multiple signaling pathways that either promote or restrict growth of the dendritic arbor; structural plasticity is achieved through a balance of these opposing signals. Specifically, we have uncovered a novel, activity-dependent signaling pathway that restricts dendritic arborization. We demonstrate that the GTPase Rem2 is regulated at the transcriptional level by calcium influx through L-VGCCs and inhibits dendritic arborization in cultured rat cortical neurons and in the Xenopus laevis tadpole visual system. Thus, our results demonstrate that changes in neuronal activity initiate competing signaling pathways that positively and negatively regulate the growth of the dendritic arbor. It is the balance of these opposing signals that leads to proper dendritic morphology.

The histone lysine demethylase Kdm6b is required for activity-dependent preconditioning of hippocampal neuronal survival.

Enzymes that regulate histone lysine methylation play important roles in neuronal differentiation, but little is known about their contributions to activity-regulated gene transcription in differentiated neurons. We characterized activity-regulated expression of lysine demethylases and lysine methyltransferases in the hippocampus of adult male mice following pilocarpine-induced seizure. Pilocarpine drove a 20-fold increase in mRNA encoding the histone H3 lysine 27-specific demethylase Kdm6b selectively in granule neurons of the dentate gyrus, and this induction was recapitulated in cultured hippocampal neurons by bicuculline and 4-aminopyridine (Bic + 4AP) stimulation of synaptic activity. Because activity-regulated gene expression is highly correlated with neuronal survival, we tested the requirement for Kdm6b expression in Bic + 4AP induced preconditioning of neuronal survival. Prior exposure to Bic + 4AP promoted neuronal survival in control neurons upon growth factor withdrawal; however, this effect was ablated when we knocked down Kdm6b expression. Loss of Kdm6b did not disrupt activity-induced expression of most genes, including that of a gene set previously established to promote neuronal survival in this assay. However, using bioinformatic analysis of RNA sequencing data, we discovered that Kdm6b knockdown neurons showed impaired inducibility of a discrete set of genes annotated for their function in inflammation. These data reveal a novel function for Kdm6b in activity-regulated neuronal survival, and they suggest that activity- and Kdm6b-dependent regulation of inflammatory gene pathways may serve as an adaptive pro-survival response to increased neuronal activity.

[Estimating Biomass Burned Areas from Multispectral Dataset Detected by Multiple-Satellite].

Biomass burning makes up an important part of both trace gases and particulate matter emissions, which can efficiently degrade air quality and reduce visibility, destabilize the global climate system at regional to global scales. Burned area is one of the primary parameters necessary to estimate emissions, and considered to be the largest source of error in the emission inventory. Satellite-based fire observations can offer a reliable source of fire occurrence data on regional and global scales, a variety of sensors have been used to detect and map fires in two general approaches: burn scar mapping and active fire detection. However, both of the two approaches have limitations. In this article, we explore the relationship between hotspot data and burned area for the Southeastern United States, where a significant amount of biomass burnings from both prescribed and wild fire took place. MODIS (Moderate resolution imaging spectrometer) data, which has high temporal-resolution, can be used to monitor ground biomass. burning in time and provided hot spot data in this study. However, pixel size of MODIS hot spot can't stand for the real ground burned area. Through analysis of the variation of vegetation band reflectance between pre- and post-burn, we extracted the burned area from Landsat-5 TM (Thematic Mapper) images by using the differential normalized burn ratio (dNBR) which is based on TM band4 (0.84 µm) and TM band 7(2.22 µm) data. We combined MODIS fire hot spot data and Landsat-5 TM burned scars data to build the burned area estimation model, results showed that the linear correlation coefficient is 0.63 and the relationships vary as a function of vegetation cover. Based on the National Land Cover Database (NLCD), we built burned area estimation model over different vegetation cover, and got effective burned area per fire pixel, values for forest, grassland, shrub, cropland and wetland are 0.69, 1.27, 0.86, 0.72 and 0.94 km2 respectively. We validated the burned area estimates by using the ground survey data from National interagency Fire Center (NIFC), our results are more close to the ground survey data than burned area from Global Fire Emissions Database (GFED) and MODIS burned area product (MCD45), which omitted many small prescribed fires. We concluded that our model can provide more accurate burned area parameters for developing fire emission inventory, and be better for estimating emissions from biomass burning.

[Simulation of Atmospheric Nitrous Oxide Profiles Retrieval from AIRS Observations].

Nitrous Oxide is a very important greenhouse gases and ozone-depleting substances. Due to the limited observations, there are still many uncertainties to quantitatively describe the role of nitrous oxide played in both cases. We can retrieve the methane and carbon dioxide gas using thermal infrared satellite data AIRS, but it is rarely for the nitrous oxide retrieval. Therefore, this paper retrieves nitrous oxide profiles from the AIRS data with an Optimal Estimate Method for the first time in China. The issue of the a priori and channels election is discussed. Comparison of the retrieved AIRS profiles with HIPPO profiles show the retrieved profiles are in good agreement with the smoothed HIPPO profiles, and a notable improvement in this algorithm than the eigen vector regression algorithm. For pressures between 300 and 900 hPa, we got the most accurate profiles and the relative error is only 0.1%, which is consistent with the jacobian peaks of the selected channels.

[Analysis of the Influence of Temperature on the Retrieval of Ozone Vertical Profiles Using the Thermal Infrared CrIS Sounder].

Ozone is a particularly critical trace gas in the Earth's atmosphere, since this molecule plays a key role in the photochemical reactions and climate change. The TIR measurements can capture the variability of ozone and are weakly sensitive to the lowermost tropospheric ozone content but can provide accurate measurements of tropospheric ozone and higher vertical resolution ozone profiles, with the additional advantage that measurements are also possible during the night. Because of the influence of atmospheric temperature, the ozone profile retrieval accuracy is severely limited. This paper analyze and discuss the ozone absorption spectra and weighting function sensitivity of temperature and its influence on ozone profile retrieval in detail. First, we simulate the change of atmospheric transmittance and radiance by importing 1 K temperature uncertainty, using line-by-line radiative transfer mode under 6 different atmosphere modes. The results show that the transmittance change ratio for 1 K temperature variation was consistent with the transmittance change ratio for 5%-6% change of ozone density variation in all layers of the profile. Then, we calculate the change of weighting function by a temperature error of 1 K, using the Community Radiative Transfer Model (CRTM) for the Cross-track Infrared Sounder (CrIS) on the Suomi National Polar-orbiting Partnership (Suomi NPP) satellite and calculate the corresponding change of retrieval result. The results demonstrate that CrIS is sensitive to Ozone in the middle to upper stratosphere, with the peak vertical sensitivity between 10-100 hPa and the change of weighting function for 1 K temperature variation was consistent with 6% change in the ozone profile. Finally, the paper retrieves ozone profiles from the CrIS radiances with a nonlinear Newton iteration method and use the eigenvector regression algorithm to construct the a priori state. In order to resolve the problem of temperature uncertainty and get high accuracy ozone profile, atmospheric temperature profile and ozone profile are simultaneously retrieved. Comparison of the CrIS retrieved ozone profile with high-vertical-resolution ozonesonde profiles provided by the World Ozone and Ultraviolet Radiation Data Centre (WOUDC) and ERA-Interim ozone profiles indicated that the retrieved ozone profiles are in good agreement with the ozonesonde profiles, and a notable improvement in this algorithm than the retrieval without atmospheric temperature profile, are also better than the ECMWF model profiles. The relative differences are less than 20% for the stratosphere and 50% for the lower troposphere.

[A quickly atmospheric correction method for HJ-1 CCD with deep blue algorithm].

In the present, for the characteristic of HJ-1 CCD camera, after receiving aerosol optical depth (AOD) from deep blue algorithm which was developed by Hsu et al. assisted by MODerate-resolution imaging spectroradiometer (MODIS) surface reflectance database, bidirectional reflectance distribution function (BRDF) correction with Kernel-Driven Model, and the calculation of viewing geometry with auxiliary data, a new atmospheric correction method of HJ-1 CCD was developed which can be used over vegetation, soil and so on. And, when the CCD data is processed to correct atmospheric influence, with look up table (LUT) and bilinear interpolation, atmospheric correction of HJ-1 CCD is completed quickly by grid calculation of atmospheric parameters and matrix operations of interface define language (IDL). The experiment over China North Plain on July 3rd, 2012 shows that by our method, the atmospheric influence was corrected well and quickly (one CCD image of 1 GB can be corrected in eight minutes), and the reflectance after correction over vegetation and soil was close to the spectrum of vegetation and soil. The comparison with MODIS reflectance product shows that for the advantage of high resolution, the corrected reflectance image of HJ-1 is finer than that of MODIS, and the correlation coefficient of the reflectance over typical surface is greater than 0.9. Error analysis shows that the recognition error of aerosol type leads to 0. 05 absolute error of surface reflectance in near infrared band, which is larger than that in visual bands, and the 0. 02 error of reflectance database leads to 0.01 absolute error of surface reflectance of atmospheric correction in green and red bands.

[Simulation of atmospheric temperature and moisture profiles retrieval from CrIS observations].

In order to get higher vertical resolution atmosphere profile information, the present paper retrieves atmospheric temperature and moisture profiles from the Cross-track Infrared Sounder (CrIS) on the newly-launched Suomi National Polar-orbiting Partnership (Suomi NPP) and future Joint Polar Satellite System (JPSS) with a nonlinear Newton iteration method by using the profiles retrieved via statical regression method as the first guess, and the issue of channel selection is discussed. The retrieved profiles are compared with radiosonde observations, and National Centers for Environmental Prediction (NCEP) Global Data Assimilation System (GDAS) analyses show that the physical retrievals of temperature and moisture are in good agreement with the distributions from GDAS analysis fields and radiosonde observations, and have a notable improvements of the atmospheric profile retrieval accuracy as compared with the eigenvector regression algorithm. For pressures between 200 and 700 hPa the accuracy is of the order of 1 K for the temperature profile, and 20% for the relative humidity profile is consistent with the jacobian peaks of the selected channels.

Long range regulation of transcription scales with genomic distance in a gene specific manner.

While critical for tuning the timing and level of transcription, enhancer communication with distal promoters is not well understood. Here we bypass the need for sequence-specific transcription factors and recruit activators directly using CARGO-VPR, an approach for targeting dCas9-VPR using a multiplexed array of RNA guides. We show that this approach achieves effective activator recruitment to arbitrary genomic sites, even those inaccessible by single dCas9. We utilize CARGO-VPR across the Prdm8-Fgf5 locus in mESCs, where neither gene is expressed. We demonstrate that while activator recruitment to any tested region results in transcriptional induction of at least one gene, the expression level strongly depends on the genomic distance between the promoter and activator recruitment site. However, the expression-distance relationship for each gene scales distinctly in a manner not attributable to differences in 3D contact frequency, promoter DNA sequence or presence of the repressive chromatin marks at the locus.

Topology regulatory elements: From shaping genome architecture to gene regulation.

The importance of 3D genome topology in the control of gene expression is becoming increasingly apparent, while regulatory mechanisms remain incompletely understood. Several recent studies have identified architectural elements that influence developmental gene expression by shaping locus topology. We refer to these elements as topological regulatory elements (TopoREs) to reflect their dual roles in genome organisation and gene expression. Importantly, these elements do not harbour autonomous transcriptional activation capacity, and instead appear to facilitate enhancer-promoter interactions, contributing to robust and precise timing of transcription. We discuss examples of TopoREs from two classes that are either dependent or independent of CTCF binding. Importantly, identification and interpretation of TopoRE function may shed light on multiple aspects of gene regulation, including the relationship between enhancer-promoter proximity and transcription, and enhancer-promoter specificity. Ultimately, understanding TopoRE diversity and function will aid in the interpretation of how human sequence variation can impact transcription and contribute to disease phenotypes.

Recent progress and challenges in single-cell imaging of enhancer-promoter interaction.

In the past two years, approaches relying on high-resolution microscopy and live-cell imaging have increasingly contributed to our understanding of the 3D genome organization and its importance for transcriptional control. Here, we describe recent progress that has highlighted how flexible and heterogeneous 3D chromatin structure is, on the length scales relevant to transcriptional control. We describe work that has investigated how robust transcriptional outcomes may be derived from such flexible organization without the need for clearly distinct structures in active and silent cells. We survey the latest state of the art in directly observing the dynamics of chromatin interactions, and suggest how some recent, apparently contradictory conclusions may be reconciled.

Methodological flaws in"diagnostic accuracy of blood biomarkers for Alzheimer's disease and amnestic mild cognitive impairment: A meta-analysis".

We read with interest the review by Chen et al. They intended to examine the diagnostic accuracy of blood-based biomarkers for detecting Alzheimer's disease and amnestic mild cognitive impairment. We believe that there were substantial methodological flaws in their meta-analysis. These methodological flaws included no comprehensive literature search details, neglect of the negative result research, no prespecified cut-off values, erroneous data input in their meta-analysis, and the issue of prevalence determined by the included studies. These factors potentially contributed to overestimation of the discriminative accuracy of blood-based biomarkers. Subsequently, the conclusion that blood-based biomarkers are effective tools for detecting Alzheimer's disease is debatable without correction of these methodological flaws and providing robust and trustworthy estimates.