Search for: All records

Abstract Although an established model organism, Tetrahymena thermophila remains comparatively inaccessible to high throughput screens, and alternative bioinformatic approaches still rely on unconnected datasets and outdated algorithms. Here, we report a new approach to consolidating RNA-seq and microarray data based on a systematic exploration of parameters and computational controls, enabling us to infer functional gene associations from their co-expression patterns. To illustrate the power of this approach, we took advantage of new data regarding a previously studied pathway, the biogenesis of a secretory organelle called the mucocyst. Our untargeted clustering approach recovered over 80% of the genes that were previously verified to play a role in mucocyst biogenesis. Furthermore, we tested four new genes that we predicted to be mucocyst-associated based on their co-expression and found that knocking out each of them results in mucocyst secretion defects. We also found that our approach succeeds in clustering genes associated with several other cellular pathways that we evaluated based on prior literature. We present the Tetrahymena Gene Network Explorer (TGNE) as an interactive tool for genetic hypothesis generation and functional annotation in this organism and as a framework for building similar tools for other systems. 

Stable inheritance of DNA N⁶-methyladenine (6mA) is crucial for its biological functions in eukaryotes. Here, we identify two distinct methyltransferase (MTase) complexes, both sharing the catalytic subunit AMT1, but featuring AMT6 and AMT7 as their unique components, respectively. While the two complexes are jointly responsible for 6mA maintenance methylation, they exhibit distinct enzymology, DNA/chromatin affinity, genomic distribution, and knockout phenotypes. AMT7 complex, featuring high MTase activity and processivity, is connected to transcription-associated epigenetic marks, including H2A.Z and H3K4me3, and is required for the bulk of maintenance methylation. In contrast, AMT6 complex, with reduced activity and processivity, is recruited by PCNA to initiate maintenance methylation immediately after DNA replication. These two complexes coordinate in maintenance methylation. By integrating signals from both replication and transcription, this mechanism ensures the faithful and efficient transmission of 6mA as an epigenetic mark in eukaryotes. 

Although DNAN⁶-adenine methylation (6mA) is best known in prokaryotes, its presence in eukaryotes has recently generated great interest. Biochemical and genetic evidence supports that AMT1, an MT-A70 family methyltransferase (MTase), is crucial for 6mA deposition in unicellular eukaryotes. Nonetheless, the 6mA transmission mechanism remains to be elucidated. Taking advantage of single-molecule real-time circular consensus sequencing (SMRT CCS), here we provide definitive evidence for semiconservative transmission of 6mA inTetrahymena thermophila. In wild-type (WT) cells, 6mA occurs at the self-complementary ApT dinucleotide, mostly in full methylation (full-6mApT); after DNA replication, hemi-methylation (hemi-6mApT) is transiently present on the parental strand, opposite to the daughter strand readily labeled by 5-bromo-2′-deoxyuridine (BrdU). In ΔAMT1cells, 6mA predominantly occurs as hemi-6mApT. Hemi-to-full conversion in WT cells is fast, robust, and processive, whereas de novo methylation in ΔAMT1cells is slow and sporadic. InTetrahymena, regularly spaced 6mA clusters coincide with the linker DNA of nucleosomes arrayed in the gene body. Importantly, in vitro methylation of human chromatin by the reconstituted AMT1 complex recapitulates preferential targeting of hemi-6mApT sites in linker DNA, supporting AMT1's intrinsic and autonomous role in maintenance methylation. We conclude that 6mA is transmitted by a semiconservative mechanism: full-6mApT is split by DNA replication into hemi-6mApT, which is restored to full-6mApT by AMT1-dependent maintenance methylation. Our study dissects AMT1-dependent maintenance methylation and AMT1-independent de novo methylation, reveals a 6mA transmission pathway with a striking similarity to 5-methylcytosine (5mC) transmission at the CpG dinucleotide, and establishes 6mA as a bona fide eukaryotic epigenetic mark. 

Abstract Understanding the brain requires understanding neurons’ functional responses to the circuit architecture shaping them. Here we introduce the MICrONS functional connectomics dataset with dense calcium imaging of around 75,000 neurons in primary visual cortex (VISp) and higher visual areas (VISrl, VISal and VISlm) in an awake mouse that is viewing natural and synthetic stimuli. These data are co-registered with an electron microscopy reconstruction containing more than 200,000 cells and 0.5 billion synapses. Proofreading of a subset of neurons yielded reconstructions that include complete dendritic trees as well the local and inter-areal axonal projections that map up to thousands of cell-to-cell connections per neuron. Released as an open-access resource, this dataset includes the tools for data retrieval and analysis^1,2. Accompanying studies describe its use for comprehensive characterization of cell types^3–6, a synaptic level connectivity diagram of a cortical column⁴, and uncovering cell-type-specific inhibitory connectivity that can be linked to gene expression data^4,7. Functionally, we identify new computational principles of how information is integrated across visual space⁸, characterize novel types of neuronal invariances⁹and bring structure and function together to uncover a general principle for connectivity between excitatory neurons within and across areas^10,11. 

We investigate the origin of the elliptical ring structure observed in the images of the supermassive black hole M87^*, aiming to disentangle contributions from gravitational, astrophysical, and imaging effects. Leveraging the enhanced capabilities of the Event Horizon Telescope (EHT)'s 2018 array, including improved (u,v)-coverage from the Greenland Telescope, we measured the ring's ellipticity using five independent imaging methods, obtaining a consistent average value ofτ = 0.08_−0.02^+0.03with a position angle ofξ = 50.1_−7.6^+6.2 degrees. To interpret this measurement, we compared it to general relativistic magnetohydrodynamic (GRMHD) simulations spanning a wide range of physical parameters including the thermal or nonthermal electron distribution function, spins, and ion-to-electron temperature ratios in both low- and high-density regions. We find no statistically significant correlation between spin and ellipticity in GRMHD images. Instead, we identify a correlation between ellipticity and the fraction of non-ring emission, particularly in nonthermal models and models with higher jet emission. These results indicate that the ellipticity measured from the M87^*emission structure is consistent with that expected from simulations of turbulent accretion flows around black holes, where it is dominated by astrophysical effects rather than gravitational ones. Future high-resolution imaging, including space very long baseline interferometry and long-term monitoring, will be essential to isolate gravitational signatures from astrophysical effects. 

Aims.We investigated the polarization and Faraday properties of Messier 87 (M87) and seven other radio-loud active galactic nuclei (AGNs) atλ0.87 mm (345 GHz) using the Atacama Large Millimeter/submillimeter Array (ALMA). Our goal was to characterize the linear polarization (LP) fractions, measure Faraday rotation measures (RMs), and examine the magnetic field structures in the emission regions of these AGNs. Methods.We conducted full-polarization observations as part of the ALMA Band 7 very long baseline interferometry (VLBI) commissioning during the April 2021 Event Horizon Telescope (EHT) campaign. We analyzed the LP fractions and RMs to assess the nature of Faraday screens and magnetic fields in the submillimeter emission regions. Results.We find LP fractions between 1% and 17% and RMs exceeding 10⁵ rad m⁻², which are 1–2 orders of magnitude higher than typically observed at longer wavelengths (λ>3 mm). This suggests denser Faraday screens or stronger magnetic fields. Additionally, we present the first submillimeter polarized images of the M87 jet and the observed AGNs, revealing RM gradients and sign reversals in the M87 jet indicative of a kiloparsec-scale helical magnetic field structure. Conclusions.Our results provide essential constraints for calibrating, analyzing, and interpreting VLBI data from the EHT at 345 GHz, representing a critical step toward submillimeter VLBI imaging. 

Context.The 2017 observing campaign of the Event Horizon Telescope (EHT) delivered the first very long baseline interferometry (VLBI) images at the observing frequency of 230 GHz, leading to a number of unique studies on black holes and relativistic jets from active galactic nuclei (AGN). In total, eighteen sources were observed, including the main science targets, Sgr A* and M 87, and various calibrators. Sixteen sources were AGN. Aims.We investigated the morphology of the sixteen AGN in the EHT 2017 data set, focusing on the properties of the VLBI cores: size, flux density, and brightness temperature. We studied their dependence on the observing frequency in order to compare it with the Blandford-Königl (BK) jet model. In particular, we aimed to study the signatures of jet acceleration and magnetic energy conversion. Methods.We modeled the source structure of seven AGN in the EHT 2017 data set using linearly polarized circular Gaussian components (1749+096, 1055+018, BL Lac, J0132–1654, J0006–0623, CTA 102, and 3C 454.3) and collected results for the other nine AGN from dedicated EHT publications, complemented by lower frequency data in the 2–86 GHz range. Combining these data into a multifrequency EHT+ data set, we studied the dependences of the VLBI core component flux density, size, and brightness temperature on the frequency measured in the AGN host frame (and hence on the distance from the central black hole), characterizing them with power law fits. We compared the observations with the BK jet model and estimated the magnetic field strength dependence on the distance from the central black hole. Results.Our observations spanning event horizon to parsec scales indicate a deviation from the standard BK model, particularly in the decrease of the brightness temperature with the observing frequency. Only some of the discrepancies may be alleviated by tweaking the model parameters or the jet collimation profile. Either bulk acceleration of the jet material, energy transfer from the magnetic field to the particles, or both are required to explain the observations. For our sample, we estimate a general radial dependence of the Doppler factorδ ∝ r^≤0.5. This interpretation is consistent with a magnetically accelerated sub-parsec jet. We also estimate a steep decrease of the magnetic field strength with radiusB ∝ r⁻³, hinting at jet acceleration or efficient magnetic energy dissipation. 

The Event Horizon Telescope (EHT) observation of M87^∗in 2018 has revealed a ring with a diameter that is consistent with the 2017 observation. The brightest part of the ring is shifted to the southwest from the southeast. In this paper, we provide theoretical interpretations for the multi-epoch EHT observations for M87^∗by comparing a new general relativistic magnetohydrodynamics model image library with the EHT observations for M87^∗in both 2017 and 2018. The model images include aligned and tilted accretion with parameterized thermal and nonthermal synchrotron emission properties. The 2018 observation again shows that the spin vector of the M87^∗supermassive black hole is pointed away from Earth. A shift of the brightest part of the ring during the multi-epoch observations can naturally be explained by the turbulent nature of black hole accretion, which is supported by the fact that the more turbulent retrograde models can explain the multi-epoch observations better than the prograde models. The EHT data are inconsistent with the tilted models in our model image library. Assuming that the black hole spin axis and its large-scale jet direction are roughly aligned, we expect the brightest part of the ring to be most commonly observed 90 deg clockwise from the forward jet. This prediction can be statistically tested through future observations. 

Context.Many active galaxies harbor powerful relativistic jets, however, the detailed mechanisms of their formation and acceleration remain poorly understood. Aims.To investigate the area of jet acceleration and collimation with the highest available angular resolution, we study the innermost region of the bipolar jet in the nearby low-ionization nuclear emission-line region (LINER) galaxy NGC 1052. Methods.We combined observations of NGC 1052 taken with VLBA, GMVA, and EHT over one week in the spring of 2017. Our study is focused on the size and continuum spectrum of the innermost region containing the central engine and the footpoints of both jets. We employed a synchrotron-self absorption model to fit the continuum radio spectrum and we combined the size measurements from close to the central engine out to ∼1 pc to study the jet collimation. Results.For the first time, NGC 1052 was detected with the EHT, providing a size of the central region in-between both jet bases of 43 μas perpendicular to the jet axes, corresponding to just around 250 R_S(Schwarzschild radii). This size estimate supports previous studies of the jets expansion profile which suggest two breaks of the profile at around 3 × 10³ R_Sand 1 × 10⁴ R_Sdistances to the core. Furthermore, we estimated the magnetic field to be 1.25 Gauss at a distance of 22 μas from the central engine by fitting a synchrotron-self absorption spectrum to the innermost emission feature, which shows a spectral turn-over at ∼130 GHz. Assuming a purely poloidal magnetic field, this implies an upper limit on the magnetic field strength at the event horizon of 2.6 × 10⁴ Gauss, which is consistent with previous measurements. Conclusions.The complex, low-brightness, double-sided jet structure in NGC 1052 makes it a challenge to detect the source at millimeter (mm) wavelengths. However, our first EHT observations have demonstrated that detection is possible up to at least 230 GHz. This study offers a glimpse through the dense surrounding torus and into the innermost central region, where the jets are formed. This has enabled us to finally resolve this region and provide improved constraints on its expansion and magnetic field strength.