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

Although 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 (TFs) and recruit activators directly using a chimeric array of gRNA oligos to target dCas9 fused to the activator VP64-p65-Rta (CARGO-VPR). We show that this approach achieves effective activator recruitment to arbitrary genomic sites, even those inaccessible when targeted with a single guide.

Early prehospital mechanical cardiopulmonary resuscitation use for out-of-hospital cardiac arrest: an observational study.

Background: The use of mechanical cardiopulmonary resuscitation device has been very prevalent in out-of-hospital cardiac arrest rescue. This study aimed to investigate whether the timing of mechanical cardiopulmonary resuscitation device set-up correlated with the the outcome of cardiac arrest patients.

Methods: We retrospectively reviewed adult nontrauma cardiac arrest cases in New Taipei City, Taiwan, from January to December 2022.

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.

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.

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.

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.

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.

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

-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.

Enhancer Histone Acetylation Modulates Transcriptional Bursting Dynamics of Neuronal Activity-Inducible Genes.

Neuronal activity-inducible gene transcription correlates with rapid and transient increases in histone acetylation at promoters and enhancers of activity-regulated genes. Exactly how histone acetylation modulates transcription of these genes has remained unknown. We used single-cell in situ transcriptional analysis to show that Fos and Npas4 are transcribed in stochastic bursts in mouse neurons and that membrane depolarization increases mRNA expression by increasing burst frequency.

Chromatin Regulation of Neuronal Maturation and Plasticity.

Neurons are dynamic cells that respond and adapt to stimuli throughout their long postmitotic lives. The structural and functional plasticity of neurons requires the regulated transcription of new gene products, and dysregulation of transcription in either the developing or adult brain impairs cognition. We discuss how mechanisms of chromatin regulation help to orchestrate the transcriptional programs that underlie the maturation of developing neurons and the plasticity of adult neurons.

BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells.

Single-molecule RNA fluorescence in situ hybridization (smFISH) provides unparalleled resolution in the measurement of the abundance and localization of nascent and mature RNA transcripts in fixed, single cells. We developed a computational pipeline (BayFish) to infer the kinetic parameters of gene expression from smFISH data at multiple time points after gene induction. Given an underlying model of gene expression, BayFish uses a Monte Carlo method to estimate the Bayesian posterior probability of the model parameters and quantify the parameter uncertainty given the observed smFISH data.

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.

Overexpression of human NR2B receptor subunit in LMAN causes stuttering and song sequence changes in adult zebra finches.

Zebra finches (Taeniopygia guttata) learn to produce songs in a manner reminiscent of spoken language development in humans. One candidate gene implicated in influencing learning is the N-methyl-D-aspartate (NMDA) subtype 2B glutamate receptor (NR2B). Consistent with this idea, NR2B levels are high in the song learning nucleus LMAN (lateral magnocellular nucleus of the anterior nidopallium) during juvenile vocal learning, and decreases to low levels in adults after learning is complete and the song becomes more stereotyped.

[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.

[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.

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).

[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.

[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.

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.

[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.