Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets.

Efficient gene expression requires RNA polymerase II (RNAPII) to find chromatin targets precisely in space and time. How RNAPII manages this complex diffusive search in three-dimensional nuclear space remains largely unknown. The disordered carboxy-terminal domain (CTD) of RNAPII, which is essential for recruiting transcription-associated proteins, forms phase-separated droplets in vitro, hinting at a potential role in modulating RNAPII dynamics. In the present study, we use single-molecule tracking and spatiotemporal mapping in living yeast to show that the CTD is required for confining RNAPII diffusion within a subnuclear region enriched for active genes, but without apparent phase separation into condensates. Both Mediator and global chromatin organization are required for sustaining RNAPII confinement. Remarkably, truncating the CTD disrupts RNAPII spatial confinement, prolongs target search, diminishes chromatin binding, impairs pre-initiation complex formation and reduces transcription bursting. The present study illuminates the pivotal role of the CTD in driving spatiotemporal confinement of RNAPII for efficient gene expression.

DBT is a metabolic switch for maintenance of proteostasis under proteasomal impairment.

Proteotoxic stress impairs cellular homeostasis and underlies the pathogenesis of many neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). The proteasomal and autophagic degradation of proteins are two major pathways for protein quality control in the cell. Here, we report a genome-wide CRISPR screen uncovering a major regulator of cytotoxicity resulting from the inhibition of the proteasome. Dihydrolipoamide branched chain transacylase E2 (DBT) was found to be a robust suppressor, the loss of which protects against proteasome inhibition-associated cell death through promoting clearance of ubiquitinated proteins. Loss of DBT altered the metabolic and energetic status of the cell and resulted in activation of autophagy in an AMP-activated protein kinase (AMPK)-dependent mechanism in the presence of proteasomal inhibition. Loss of DBT protected against proteotoxicity induced by ALS-linked mutant TDP-43 in Drosophila and mammalian neurons. DBT is upregulated in the tissues from ALS patients. These results demonstrate that DBT is a master switch in the metabolic control of protein quality control with implications in neurodegenerative diseases.

CaMeL-Net: Centroid-aware metric learning for efficient multi-class cancer classification in pathology images.

BACKGROUND AND OBJECTIVE: Cancer grading in pathology image analysis is a major task due to its importance in patient care, treatment, and management. The recent developments in artificial neural networks for computational pathology have demonstrated great potential to improve the accuracy and quality of cancer diagnosis. These improvements are generally ascribable to the advance in the architecture of the networks, often leading to increase in the computation and resources. In this work, we propose an efficient convolutional neural network that is designed to conduct multi-class cancer classification in an accurate and robust manner via metric learning. METHODS: We propose a centroid-aware metric learning network for an improved cancer grading in pathology images. The proposed network utilizes centroids of different classes within the feature embedding space to optimize the relative distances between pathology images, which manifest the innate similarities/dissimilarities between them. For improved optimization, we introduce a new loss function and a training strategy that are tailored to the proposed network and metric learning. RESULTS: We evaluated the proposed approach on multiple datasets of colorectal and gastric cancers. For the colorectal cancer, two different datasets were employed that were collected from different acquisition settings. the proposed method achieved an accuracy, F1-score, quadratic weighted kappa of 88.7%, 0.849, and 0.946 for the first dataset and 83.3%, 0.764, and 0.907 for the second dataset, respectively. For the gastric cancer, the proposed method obtained an accuracy of 85.9%, F1-score of 0.793, and quadratic weighted kappa of 0.939. We also found that the proposed method outperforms other competing models and is computationally efficient. CONCLUSIONS: The experimental results demonstrate that the prediction results by the proposed network are both accurate and reliable. The proposed network not only outperformed other related methods in cancer classification but also achieved superior computational efficiency during training and inference. The future study will entail further development of the proposed method and the application of the method to other problems and domains.

Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets.

Efficient gene expression requires RNA Polymerase II (RNAPII) to find chromatin targets precisely in space and time. How RNAPII manages this complex diffusive search in 3D nuclear space remains largely unknown. The disordered carboxy-terminal domain (CTD) of RNAPII, which is essential for recruiting transcription-associated proteins, forms phase-separated droplets in vitro, hinting at a potential role in modulating RNAPII dynamics. Here, we use single-molecule tracking and spatiotemporal mapping in living yeast to show that the CTD is required for confining RNAPII diffusion within a subnuclear region enriched for active genes, but without apparent phase separation into condensates. Both Mediator and global chromatin organization are required for sustaining RNAPII confinement. Remarkably, truncating the CTD disrupts RNAPII spatial confinement, prolongs target search, diminishes chromatin binding, impairs pre-initiation complex formation, and reduces transcription bursting. This study illuminates the pivotal role of the CTD in driving spatiotemporal confinement of RNAPII for efficient gene expression.

Gordonia caeni sp. nov., isolated from sludge of a sewage disposal plant.

A Gram-stain-positive, strictly aerobic, short-rod-shaped, non-motile strain (designated MJ32(T)) was isolated from a sludge sample of the Daejeon sewage disposal plant in South Korea. A polyphasic approach was applied to study the taxonomic position of strain MJ32(T). Strain MJ32(T) showed highest 16S rRNA gene sequence similarity to Gordonia hirsuta DSM 44140(T) (98.1%) and Gordonia hydrophobica DSM 44015(T) (97.0%); levels of sequence similarity to the type strains of other recognized Gordonia species were less than 97.0%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ32(T) belonged to the clade formed by members of the genus Gordonia in the family Gordoniaceae. The G+C content of the genomic DNA of strain MJ32(T) was 69.2 mol%. Chemotaxonomically, strain MJ32(T) showed features typical of the genus Gordonia. The predominant respiratory quinone was MK-9(H(2)), the mycolic acids present had C(56)-C(60) carbon atoms, and the major fatty acids were C(16:0) (34.6%), tuberculostearic acid (21.8%), C(16:1)ω7c (19.5%) and C(18:1)ω9c (12.7%). The peptidoglycan type was based on meso-2,6-diaminopimelic acid as the diagnostic diamino acid with glycolated sugars. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ32(T) is considered to represent a novel species of the genus Gordonia, for which the name Gordonia caeni sp. nov. is proposed. The type strain is MJ32(T) (=KCTC 19771(T)=JCM 16923(T)).

ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA.

One-dimensional (1D) target search is a well-characterized phenomenon for many DNA-binding proteins but is poorly understood for chromatin remodelers. Herein, we characterize the 1D scanning properties of SWR1, a conserved yeast chromatin remodeler that performs histone exchange on +1 nucleosomes adjacent to a nucleosome-depleted region (NDR) at gene promoters. We demonstrate that SWR1 has a kinetic binding preference for DNA of NDR length as opposed to gene-body linker length DNA. Using single and dual color single-particle tracking on DNA stretched with optical tweezers, we directly observe SWR1 diffusion on DNA. We found that various factors impact SWR1 scanning, including ATP which promotes diffusion through nucleotide binding rather than ATP hydrolysis. A DNA-binding subunit, Swc2, plays an important role in the overall diffusive behavior of the complex, as the subunit in isolation retains similar, although faster, scanning properties as the whole remodeler. ATP-bound SWR1 slides until it encounters a protein roadblock, of which we tested dCas9 and nucleosomes. The median diffusion coefficient, 0.024 µm2/s, in the regime of helical sliding, would mediate rapid encounter of NDR-flanking nucleosomes at length scales found in cellular chromatin.

Safety and Cost Savings Associated with Reduced Inpatient Hospitalization for Microvascular Decompression.

OBJECTIVES: Microvascular decompression (MVD) has grown as a first-line surgical intervention for severe facial pain from trigeminal neuralgia and/or hemifacial spasm. We sought to examine the safety and cost-benefits of discharging patients with MVD within 1 day of admission. METHODS: We retrospectively reviewed patients undergoing MVD at our institution from 2008 to 2020. Patients were sorted by 1 day, 2 days, or >2 days until discharge and by year from 2008 to 2013, 2014 to 2018, or 2019 to 2020. Patient presenting characteristics, intraoperative measures, and complications were documented. Statistical differences were calculated by one-way analysis of variance and χ2 analyses. RESULTS: Our cohort included 976 patients undergoing MVD, with 231 (23.6%) between 2008 and 2013, 517 (52.9%) between 2014 and 2018, and 228 (23.3%) between 2019 and 2020. Over time, postoperative admission rates to the critical care unit, total inpatient hospital admission times, and Barrow Neurological Institute scores at first follow-up decreased. Postoperative complications, including cerebrospinal fluid leak, decreased significantly. In addition, patients discharged within 1 day of admission incurred a total hospital cost of $26,689, which was $3588 lower than patients discharged within more than 1 day of admission, P < 0.0001. Discharging carefully selected patients who are appropriate for discharge within 1 day of admission could translate to a potential cost-savings of $255,346 per year in our clinical practice. CONCLUSIONS: In our experience, MVDs are a safe, elective intervention. Our findings suggest that postoperative day 1 discharge in patients with an uncomplicated postoperative course may be safe while improving hospital resource use.

Coordinated DNA and histone dynamics drive accurate histone H2A.Z exchange.

Nucleosomal histone H2A is exchanged for its variant H2A.Z by the SWR1 chromatin remodeler, but the mechanism and timing of histone exchange remain unclear. Here, we quantify DNA and histone dynamics during histone exchange in real time using a three-color single-molecule FRET assay. We show that SWR1 operates with timed precision to unwrap DNA with large displacement from one face of the nucleosome, remove H2A-H2B from the same face, and rewrap DNA, all within 2.3 s. This productive DNA unwrapping requires full SWR1 activation and differs from unproductive, smaller-scale DNA unwrapping caused by SWR1 binding alone. On an asymmetrically positioned nucleosome, SWR1 intrinsically senses long-linker DNA to preferentially exchange H2A.Z on the distal face as observed in vivo. The displaced H2A-H2B dimer remains briefly associated with the SWR1-nucleosome complex and is dissociated by histone chaperones. These findings reveal how SWR1 coordinates DNA unwrapping with histone dynamics to rapidly and accurately place H2A.Z at physiological sites on chromatin.

Paracoccus caeni sp. nov., isolated from sludge.

A Gram-negative, non-motile bacterium, designated MJ17(T), was isolated from sludge at the Daejeon sewage disposal plant in South Korea. Comparative 16S rRNA gene sequence analysis showed that strain MJ17(T) belonged to the genus Paracoccus in the family Rhodobacteraceae of the class Alphaproteobacteria. 16S rRNA gene sequence similarities between strain MJ17(T) and type strains of species of the genus Paracoccus were 94.1-97.4 %. The highest similarities were between strain MJ17(T) and Paracoccus homiensis DD-R11(T), Paracoccus zeaxanthinifaciens ATCC 21588(T) and Paracoccus alcaliphilus JCM 7364(T) (97.4, 97.2 and 96.3 %, respectively). Strain MJ17(T) exhibited <22 % DNA-DNA relatedness with P. homiensis KACC 11518(T) and P. zeaxanthinifaciens JCM 21774(T). The G+C content of the genomic DNA was 58.7 mol%. Strain MJ17(T) contained ubiquinone Q-10. The major fatty acids were C(18 : 0) (11.3 %), C(16 : 0) (10.2 %) and summed feature 7 (containing one or more of C(18 : 1)ω7c, C(18 : 1)ω9c and C(18 : 1)ω12t; 54.3 %). Poly-ß-hydroxybutyrate granules are formed. On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, strain MJ17(T) should be classified in a novel species of the genus Paracoccus, for which the name Paracoccus caeni sp. nov. is proposed. The type strain is MJ17(T) ( = KCTC 22480(T)  = JCM 16385(T)  = KEMB 9004-001(T)).

Her voice lingers on and her memory is strategic: effects of gender on directed forgetting.

The literature on directed forgetting has employed exclusively visual words. Thus, the potentially interesting aspects of a spoken utterance, which include not only vocal cues (e.g., prosody) but also the speaker and the listener, have been neglected. This study demonstrates that prosody alone does not influence directed-forgetting effects, while the sex of the speaker and the listener significantly modulate directed-forgetting effects for spoken utterances. Specifically, forgetting costs were attenuated for female-spoken items compared to male-spoken items, and forgetting benefits were eliminated among female listeners but not among male listeners. These results suggest that information conveyed in a female voice draws attention to its distinct perceptual attributes, thus interfering with retention of the semantic meaning, while female listeners' superior capacity for processing the surface features of spoken utterances may predispose them to spontaneously employ adaptive strategies to retain content information despite distraction by perceptual features. Our findings underscore the importance of sex differences when processing spoken messages in directed forgetting.

A laboratory and pilot study of thermally enhanced soil vapor extraction method for the removal of semi-volatile organic contaminants.

Laboratory and field pilot study was conducted to evaluate the effectiveness of thermally enhanced soil vapor extraction (SVE) system for the removal of semi-volatile organic contaminants (SVOCs) from soils. Several parametric studies were conducted to evaluate the effect of temperature and air flow rate on the removal of SVOCs. Column studies near ambient temperature show very little efficiency for SVOCs removal. The removal rates of SVOCs are highly dependent on temperature. Moving fronts in the effluent concentrations of contaminants are observed, according to the order of volatility of contaminant. This result is attributed to continuous changes in the liquid composition toward less volatile fractions, thus increasing the mole fraction of the less volatile fractions remaining in the liquid mixture. It is also found that increased air flow rate results in high removal rate of contaminants. However, too high air flow rate brings about the mass transfer limitation on the volatilization of the contaminants. Results from steady-state column studies show that mass transfer limitation is reduced at high temperature, possibly due to the increase in the diffusivity of contaminant in the liquid and gas phase. A field pilot study of a hot air injection method for the remediation of diesel-contaminated soil has shown advantages over the conventional SVE. Within 30 days of test operation, TPH concentrations at unsaturated soils were dramatically reduced, corresponding to more than 95% removal. However, temperature profiles and the removal rates of SVOCs near groundwater level indicate that moisture content would be a limiting factor in the real application of hot air injection.