LATS1 controls CTCF chromatin occupancy and hormonal response of 3D-grown breast cancer cells.

The cancer epigenome has been studied in cells cultured in two-dimensional (2D) monolayers, but recent studies highlight the impact of the extracellular matrix and the three-dimensional (3D) environment on multiple cellular functions. Here, we report the physical, biochemical, and genomic differences between T47D breast cancer cells cultured in 2D and as 3D spheroids. Cells within 3D spheroids exhibit a rounder nucleus with less accessible, more compacted chromatin, as well as altered expression of ~2000 genes, the majority of which become repressed. Hi-C analysis reveals that cells in 3D are enriched for regions belonging to the B compartment, have decreased chromatin-bound CTCF and increased fusion of topologically associating domains (TADs). Upregulation of the Hippo pathway in 3D spheroids results in the activation of the LATS1 kinase, which promotes phosphorylation and displacement of CTCF from DNA, thereby likely causing the observed TAD fusions. 3D cells show higher chromatin binding of progesterone receptor (PR), leading to an increase in the number of hormone-regulated genes. This effect is in part mediated by LATS1 activation, which favors cytoplasmic retention of YAP and CTCF removal.

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence.

To understand the role of the extensive senescence-associated 3D genome reorganization, we generated genome-wide chromatin interaction maps, epigenome, replication-timing, whole-genome bisulfite sequencing, and gene expression profiles from cells entering replicative senescence (RS) or upon oncogene-induced senescence (OIS). We identify senescence-associated heterochromatin domains (SAHDs). Differential intra- versus inter-SAHD interactions lead to the formation of senescence-associated heterochromatin foci (SAHFs) in OIS but not in RS. This OIS-specific configuration brings active genes located in genomic regions adjacent to SAHDs in close spatial proximity and favors their expression. We also identify DNMT1 as a factor that induces SAHFs by promoting HMGA2 expression. Upon DNMT1 depletion, OIS cells transition to a 3D genome conformation akin to that of cells in replicative senescence. These data show how multi-omics and imaging can identify critical features of RS and OIS and discover determinants of acute senescence and SAHF formation.

Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.

Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these methods rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting the amount of extractable biological information. To overcome these limitations, here we develop Deconwolf, an open-source, user-friendly software for high-performance deconvolution of widefield fluorescence microscopy images, which efficiently runs on laptop computers. Deconwolf enables accurate quantification of crowded diffraction limited fluorescence dots in DNA and RNA fluorescence in situ hybridization images and allows robust detection of individual transcripts in tissue sections imaged with ×20 air objectives. Deconvolution of in situ spatial transcriptomics images with Deconwolf increased the number of transcripts identified more than threefold, while the application of Deconwolf to images obtained by fluorescence in situ sequencing of barcoded Oligopaint probes drastically improved chromosome tracing. Deconwolf greatly facilitates the use of deconvolution in many bioimaging applications.

The anti-immune dengue subgenomic flaviviral RNA is present in vesicles in mosquito saliva and is associated with increased infectivity.

Mosquito transmission of dengue viruses to humans starts with infection of skin resident cells at the biting site. There is great interest in identifying transmission-enhancing factors in mosquito saliva in order to counteract them. Here we report the discovery of high levels of the anti-immune subgenomic flaviviral RNA (sfRNA) in dengue virus 2-infected mosquito saliva. We established that sfRNA is present in saliva using three different methods: northern blot, RT-qPCR and RNA sequencing. We next show that salivary sfRNA is protected in detergent-sensitive compartments, likely extracellular vesicles. In support of this hypothesis, we visualized viral RNAs in vesicles in mosquito saliva and noted a marked enrichment of signal from 3'UTR sequences, which is consistent with the presence of sfRNA. Furthermore, we show that incubation with mosquito saliva containing higher sfRNA levels results in higher virus infectivity in a human hepatoma cell line and human primary dermal fibroblasts. Transfection of 3'UTR RNA prior to DENV2 infection inhibited type I and III interferon induction and signaling, and enhanced viral replication. Therefore, we posit that sfRNA present in salivary extracellular vesicles is delivered to cells at the biting site to inhibit innate immunity and enhance dengue virus transmission.

Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery.

Chromatin remodeling is essential to allow full development of alternative gene expression programs in response to environmental changes. In fission yeast, oxidative stress triggers massive transcriptional changes including the activation of hundreds of genes, with the participation of histone modifying complexes and chromatin remodelers. DNA transcription is associated to alterations in DNA topology, and DNA topoisomerases facilitate elongation along gene bodies. Here, we test whether the DNA topoisomerase Top1 participates in the RNA polymerase II-dependent activation of the cellular response to oxidative stress. Cells lacking Top1 are resistant to H2O2 stress. The transcriptome of Δtop1 strain was not greatly affected in the absence of stress, but activation of the anti-stress gene expression program was more sustained than in wild-type cells. Top1 associated to stress open reading frames. While the nucleosomes of stress genes are partially and transiently evicted during stress, the chromatin configuration remains open for longer times in cells lacking Top1, facilitating RNA polymerase II progression. We propose that, by removing DNA tension arising from transcription, Top1 facilitates nucleosome reassembly and works in synergy with the chromatin remodeler Hrp1 as opposing forces to transcription and to Snf22 / Hrp3 opening remodelers.

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing.

There is a need for methods that can image chromosomes with genome-wide coverage, as well as greater genomic and optical resolution. We introduce OligoFISSEQ, a suite of three methods that leverage fluorescence in situ sequencing (FISSEQ) of barcoded Oligopaint probes to enable the rapid visualization of many targeted genomic regions. Applying OligoFISSEQ to human diploid fibroblast cells, we show how four rounds of sequencing are sufficient to produce 3D maps of 36 genomic targets across six chromosomes in hundreds to thousands of cells, implying a potential to image thousands of targets in only five to eight rounds of sequencing. We also use OligoFISSEQ to trace chromosomes at finer resolution, following the path of the X chromosome through 46 regions, with separate studies showing compatibility of OligoFISSEQ with immunocytochemistry. Finally, we combined OligoFISSEQ with OligoSTORM, laying the foundation for accelerated single-molecule super-resolution imaging of large swaths of, if not entire, human genomes.

Antagonistic effects of mitochondrial matrix and intermembrane space proteases on yeast aging.

BACKGROUND: In many organisms, aging is characterized by a loss of mitochondrial homeostasis. Multiple factors such as respiratory metabolism, mitochondrial fusion/fission, or mitophagy have been linked to cell longevity, but the exact impact of each one on the aging process is still unclear. RESULTS: Using the deletion mutant collection of the fission yeast Schizosaccharomyces pombe, we have developed a genome-wide screening for mutants with altered chronological lifespan. We have identified four mutants associated with proteolysis at the mitochondria that exhibit opposite effects on longevity. The analysis of the respiratory activity of these mutants revealed a positive correlation between increased respiration rate and prolonged lifespan. We also found that the phenotype of the long-lived protease mutants could not be explained by impaired mitochondrial fusion/fission activities, but it was dependent on mitophagy induction. The anti-aging role of mitophagy was supported by the effect of a mutant defective in degradation of mitochondria, which shortened lifespan of the long-lived mutants. CONCLUSIONS: Our characterization of the mitochondrial protease mutants demonstrates that mitophagy sustains the lifespan extension of long-lived mutants displaying a higher respiration potential.

Multiple Triplet Metal-Centered Jahn-Teller Isomers Determine Temperature-Dependent Luminescence Lifetimes in [Ru(bpy)3 ]2.

Understanding the factors that determine the luminescence lifetime of transition metal compounds is key for applications in photocatalysis and photodynamic therapy. Here we show that for [ Ru ( bpy ) 3 ] 2 + ${[{\rm{Ru}}({\rm{bpy}})_{\rm{3}} ]^{{\rm{2 + }}} }$ (bpy = 2,2'-bipyridine), the generally accepted idea that emission lifetimes can be controlled optimizing the energy barrier from the emissive triplet metal-to-ligand charge-transfer (3 MLCT) state to the thermally-activated triplet metal-centered (3 MC) state or the energy gap between both states is a misconception. Further, we demonstrate that considering a single relaxation pathway determined from the minimum that is lowest in energy leads to wrong temperature-dependent emission lifetimes predictions. Instead, we obtain excellent agreement with experimental temperature-dependent lifetimes when an extended kinetic model that includes all the pathways related to multiple Jahn-Teller isomers and their effective reaction barriers is employed. These concepts are essential to correctly design other luminescent transition metal complexes with tailored emission lifetimes based on theoretical predictions.

BitQT: a graph-based approach to the quality threshold clustering of molecular dynamics.

MOTIVATION: Classical Molecular Dynamics (MD) is a standard computational approach to model time-dependent processes at the atomic level. The inherent sparsity of increasingly huge generated trajectories demands clustering algorithms to reduce other post-simulation analysis complexity. The Quality Threshold (QT) variant is an appealing one from the vast number of available clustering methods. It guarantees that all members of a particular cluster will maintain a collective similarity established by a user-defined threshold. Unfortunately, its high computational cost for processing big data limits its application in the molecular simulation field. RESULTS: In this work, we propose a methodological parallel between QT clustering and another well-known algorithm in the field of Graph Theory, the Maximum Clique Problem. Molecular trajectories are represented as graphs whose nodes designate conformations, while unweighted edges indicate mutual similarity between nodes. The use of a binary-encoded RMSD matrix coupled to the exploitation of bitwise operations to extract clusters significantly contributes to reaching a very affordable algorithm compared to the few implementations of QT for MD available in the literature. Our alternative provides results in good agreement with the exact one while strictly preserving the collective similarity of clusters. AVAILABILITY AND IMPLEMENTATION: The source code and documentation of BitQT are free and publicly available on GitHub (https://github.com/LQCT/BitQT.git) and ReadTheDocs (https://bitqt.readthedocs.io/en/latest/), respectively. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Computation of Förster Resonance Energy Transfer in Lipid Bilayer Membranes.

Calculations of Förster Resonance Energy Transfer (FRET) often neglect the influence of different chromophore orientations or changes in the spectral overlap. In this work, we present two computational approaches to estimate the energy transfer rate between chromophores embedded in lipid bilayer membranes. In the first approach, we assess the transition dipole moments and the spectral overlap by means of quantum chemical calculations in implicit solvation, and we investigate the alignment and distance between the chromophores in classical molecular dynamics simulations. In the second, all properties are evaluated integrally with hybrid quantum mechanical/molecular mechanics (QM/MM) calculations. Both approaches come with advantages and drawbacks, and despite the fact that they do not agree quantitatively, they provide complementary insights on the different factors that influence the FRET rate. We hope that these models can be used as a basis to optimize energy transfers in nonisotropic media.

Strong Ligand Stabilization Based on π-Extension in a Series of Ruthenium Terpyridine Water Oxidation Catalysts.

The substitution behavior of the monodentate Cl ligand of a series of ruthenium(II) terpyridine complexes (terpyridine (tpy)=2,2':6',2''-terpyridine) has been investigated. 1 H NMR kinetic experiments of the dissociation of the chloro ligand in D2 O for the complexes [Ru(tpy)(bpy)Cl]Cl (1, bpy=2,2'-bipyridine) and [Ru(tpy)(dppz)Cl]Cl (2, dppz=dipyrido[3,2-a:2',3'-c]phenazine) as well as the binuclear complex [Ru(bpy)2 (tpphz)Ru(tpy)Cl]Cl3 (3 b, tpphz=tetrapyrido[3,2-a:2',3'-c:3'',2''-h:2''',3'''-j]phenazine) were conducted, showing increased stability of the chloride ligand for compounds 2 and 3 due to the extended π-system. Compounds 1-5 (4=[Ru(tbbpy)2 (tpphz)Ru(tpy)Cl](PF6 )3 , 5=[Ru(bpy)2 (tpphz)Ru(tpy)(C3 H8 OS)/(H2 O)](PF6 )3 , tbbpy=4,4'-di-tert-butyl-2,2'-bipyridine) are tested for their ability to run water oxidation catalysis (WOC) using cerium(IV) as sacrificial oxidant. The WOC experiments suggest that the stability of monodentate (chloride) ligand strongly correlates to catalytic performance, which follows the trend 1>2>5≥3>4. This is also substantiated by quantum chemical calculations, which indicate a stronger binding for the chloride ligand based on the extended π-systems in compounds 2 and 3. Additionally, a theoretical model of the mechanism of the oxygen evolution of compounds 1 and 2 is presented; this suggests no differences in the elementary steps of the catalytic cycle within the bpy to the dppz complex, thus suggesting that differences in the catalytic performance are indeed based on ligand stability. Due to the presence of a photosensitizer and a catalytic unit, binuclear complexes 3 and 4 were tested for photocatalytic water oxidation. The bridging ligand architecture, however, inhibits the effective electron-transfer cascade that would allow photocatalysis to run efficiently. The findings of this study can elucidate critical factors in catalyst design.

Zernike Moment Based Classification of Cosmic Ray Candidate Hits from CMOS Sensors.

Reliable tools for artefact rejection and signal classification are a must for cosmic ray detection experiments based on CMOS technology. In this paper, we analyse the fitness of several feature-based statistical classifiers for the classification of particle candidate hits in four categories: spots, tracks, worms and artefacts. We use Zernike moments of the image function as feature carriers and propose a preprocessing and denoising scheme to make the feature extraction more efficient. As opposed to convolution neural network classifiers, the feature-based classifiers allow for establishing a connection between features and geometrical properties of candidate hits. Apart from basic classifiers we also consider their ensemble extensions and find these extensions generally better performing than basic versions, with an average recognition accuracy of 88%.

CNN-Based Classifier as an Offline Trigger for the CREDO Experiment.

Gamification is known to enhance users' participation in education and research projects that follow the citizen science paradigm. The Cosmic Ray Extremely Distributed Observatory (CREDO) experiment is designed for the large-scale study of various radiation forms that continuously reach the Earth from space, collectively known as cosmic rays. The CREDO Detector app relies on a network of involved users and is now working worldwide across phones and other CMOS sensor-equipped devices. To broaden the user base and activate current users, CREDO extensively uses the gamification solutions like the periodical Particle Hunters Competition. However, the adverse effect of gamification is that the number of artefacts, i.e., signals unrelated to cosmic ray detection or openly related to cheating, substantially increases. To tag the artefacts appearing in the CREDO database we propose the method based on machine learning. The approach involves training the Convolutional Neural Network (CNN) to recognise the morphological difference between signals and artefacts. As a result we obtain the CNN-based trigger which is able to mimic the signal vs. artefact assignments of human annotators as closely as possible. To enhance the method, the input image signal is adaptively thresholded and then transformed using Daubechies wavelets. In this exploratory study, we use wavelet transforms to amplify distinctive image features. As a result, we obtain a very good recognition ratio of almost 99% for both signal and artefacts. The proposed solution allows eliminating the manual supervision of the competition process.

Diastereoselective Synthesis of Steroid-[60]Fullerene Hybrids and Theoretical Underpinning.

The reaction of C60 with pregnen-20-carboxaldehyde, a biologically active synthetic steroid, by using a 1,3-dipolar cycloaddition reaction (Prato's protocol) results in the formation of pyrrolidine rings bearing a new stereogenic center on the C2 of the five-membered ring. The formation of the fullerene-steroid hybrids proceeds with preference for the Re face of the 1,3-dipole, with formation of a diastereomeric mixture in 73:15 ratio. The investigation of the chiroptical properties of these conjugates allowed determining the absolute configuration of the new fulleropyrrolidines. In addition, a thorough spectroscopical study permitted to determine the structure of the two mono-cycloadducts. The electrochemical properties of the new hybrids were also evaluated by cyclic voltammetry, both systems exhibit three quasi-reversible reduction waves which are cathodically shifted in regard to the parent C60. Theoretical calculations help supporting the experimental data. A conformational study combining semiempirical methods and density functional theory has predicted the most stable diastereomer. On the basis of this agreement, a possible reaction mechanism is presented. Additionally, a molecular docking simulation has been carried out using the HIV-1 protease as receptor, thus paving the way to study the possible application of these stereoisomers in biomedicine.

Quality Threshold Clustering of Molecular Dynamics: A Word of Caution.

Clustering Molecular Dynamics trajectories is a common analysis that allows grouping together similar conformations. Several algorithms have been designed and optimized to perform this routine task, and among them, Quality Threshold stands as a very attractive option. This algorithm guarantees that in retrieved clusters no pair of frames will have a similarity value greater than a specified threshold, and hence, a set of strongly correlated frames are obtained for each cluster. In this work, it is shown that various commonly used software implementations are flawed by confusing Quality Threshold with another simplistic well-known clustering algorithm published by Daura et al. (Daura, X.; van Gunsteren, W. F.; Jaun, B.; Mark, A. E.; Gademann, K.; Seebach, D. Peptide Folding: When Simulation Meets Experiment. Angew. Chemie Int. Ed. 1999, 38 (1/2), 236-240). Daura's algorithm does not impose any quality threshold for the frames contained in retrieved clusters, bringing unrelated structural configurations altogether. The advantages of using Quality Threshold whenever possible to explore Molecular Dynamic trajectories is exemplified. An in-house implementation of the original Quality Threshold algorithm has been developed in order to illustrate our comments, and its code is freely available for further use by the scientific community.

BitClust: Fast Geometrical Clustering of Long Molecular Dynamics Simulations.

The growing computational capacity allows the investigation of large biomolecular systems by increasingly extensive molecular dynamics simulations. The resulting huge trajectories demand efficient partition methods to discern relevant structural dissimilarity. Clustering algorithms are available to address this task, but their implementations still need to be improved to gain in computational speed and to reduce the consumption of random access memory. We propose the BitClust code which, based on a combination of Python and C programming languages, performs fast structural clustering of long molecular trajectories. BitClust takes advantage of bitwise operations applied to a bit-encoded pairwise similarity matrix. Our approach allowed us to process a half-million frame trajectory in 6 h using less than 35 GB, a task that is not affordable with any of the similar alternatives.

An amygdala-cingulate network underpins changes in effort-based decision making after a fitness program.

When humans make decisions, objective rewards are mainly discounted by delay, risk and effort. Whereas recent research has demonstrated that several brain areas process costs and code subjective value in effort-based decision making, it remains obscure how neural activity patterns change when effort costs are reduced due to the acquisition of healthy habits, such as moving from sedentary to active lifestyles. Here, a sample of sedentary volunteers was behaviorally assessed and fMRI-scanned before and after completing a 3-month fitness plan. The impact of effort cost on decisions, measured as the constant defining a hyperbolic decaying function, was reduced after the plan. A logistic mixed model demonstrated that the explanatory power of effort decreased with time. At a neural level, there was a marginally significant disruption of effort-cost related functional activity in the anterior cingulate after the plan. Functional connectivity between the amygdala and anterior cingulate cortex was strengthened after habit acquisition. In turn, this interaction was stronger in those participants with lower effort discounting. Thus, we show for the first time changes in value-based decision making after moving from a sedentary to an active lifestyle, which points to the relevance of the amygdala-cingulate interplay when the impact of effort on decisions fades away.

Skin changes in the obese patient.

Obesity is a worldwide major public health problem with an alarmingly increasing prevalence over the past 2 decades. The consequences of obesity in the skin are underestimated. In this paper, we review the effect of obesity on the skin, including how increased body mass index affects skin physiology, skin barrier, collagen structure, and wound healing. Obesity also affects sebaceous and sweat glands and causes circulatory and lymphatic changes. Common skin manifestations related to obesity include acanthosis nigricans, acrochordons, keratosis pilaris, striae distensae, cellulite, and plantar hyperkeratosis. Obesity has metabolic effects, such as causing hyperandrogenism and gout, which in turn are associated with cutaneous manifestations. Furthermore, obesity is associated with an increased incidence of bacterial and Candida skin infections, as well as onychomycosis, inflammatory skin diseases, and chronic dermatoses like hidradenitis suppurativa, psoriasis, and rosacea. The association between atopic dermatitis and obesity and the increased risk of skin cancer among obese patients is debatable. Obesity is also related to rare skin conditions and to premature hair graying. As physicians, understanding these clinical signs and the underlying systemic disorders will facilitate earlier diagnoses for better treatment and avoidance of sequelae.

Trichotillomania (hair pulling disorder): Clinical characteristics, psychosocial aspects, treatment approaches, and ethical considerations.

Trichotillomania (hair pulling disorder) is a fairly common but underreported disorder characterized by recurrent episodes of pulling hair from different parts of the body. Currently classified in Diagnostic and Statistical Manual of Psychiatric Disorders (DSM-5) under the heading of the "Obsessive-compulsive spectrum and related disorders." The estimated prevalence data suggest that 0.5-2% of the general population suffers from this disorder. Stress and anxiety are directly correlated to the production of trichotillomania symptoms. The psychosocial aspects of trichotillomania are greatly underestimated, but recent literature suggests an increased interest in this neglected area. Although no FDA approved medications are available for the treatment of trichotillomania, a variety of medications including N-acetylcysteine have shown benefit in case reports. Combined liaison clinics, with an interdisciplinary approach, are highly advisable in the treatment of these cases.