bluuebunny/crossref_metadata_2025 huggingface dataset:
Repeated strand invasion and extensive branch migration are hallmarks of meiotic recombination
Authors: Ahuja Jasvinder S. , Harvey Catherine S. , Wheeler David L. , Lichten Michael
Published: April 2021

Currently favored models for meiotic recombination posit that both noncrossover and crossover recombination are initiated by DNA double strand breaks but form by different mechanisms, noncrossovers by synthesis dependent strand annealing, and crossovers by formation and resolution of double Holliday junctions centered around the break. This dual mechanism hypothesis predicts different hybrid DNA patterns in noncrossover and crossover recombinants. We show that these predictions are not upheld, by mapping with unprecedented resolution, parental strand contributions to recombinants at a model locus. Instead, break repair in both noncrossovers and crossovers involves synthesis-dependent strand annealing, often with multiple rounds of strand invasion. Crossover-specific double Holliday junction formation occurs via processes that involve branch migration as an integral feature and that can be separated from break repair itself. These findings reveal meiotic recombination to be a highly dynamic process and prompt a new view of the relationship between crossover and noncrossover recombination.
Differences between apoplastic and cytosolic reactive oxygen species production inArabidopsisduring pattern-triggered immunity
Authors: Arnaud Dominique , Deeks Michael J. , Smirnoff Nicholas
Published: April 2021

Despite an ever-increasing interest in reactive oxygen species (ROS) signalling during plant-microbe interactions, very little information exists, mainly for technical reasons, on the molecular mechanisms regulating intracellular hydrogen peroxide (H2O2) signalling during PAMP-triggered immunity. Here, we used a sensitive fluorimetry method and the H2O2sensor roGFP2-Orp1, which revealed unsuspected features on the regulation of cytoplasmic H2O2and thiol redox dynamics upon pathogen-associated molecular patterns (PAMPs) perception byArabidopsis thaliana. Extended PAMP-induced cytosolic roGFP2-Orp1 oxidation was distinct from the transient oxidative burst in the apoplast measured by luminol oxidation. Pharmacological and genetic analyses indicate that the prolonged PAMP-induced H2O2increase in the cytoplasm was largely independent on NADPH oxidases and apoplastic peroxidases. By contrast, the NADPH oxidase mutantrbohFwas hyper-sensitive to roGFP2-Orp1 oxidation by H2O2and PAMP indicating a lower antioxidant capacity. Unlike previous reports, therbohFmutant, but notrbohD, was impaired in PAMP-triggered stomatal closure and ROS production measured by a fluorescein-based probe in guard cells resulting in defects in stomatal defences against bacteria. However, stomatal closure was not correlated with an increase in roGFP2-Orp1 oxidation in guard cells. Interestingly, RBOHF also participated in PAMP-induced apoplastic alkalinisation. Altogether, our results provide novel insights on the interplay between apoplastic and cytosolic ROS dynamics and highlight the importance of RBOHF in plant immunity.

Significance statement

Plants mount defence responses to pathogens by detecting pathogen-associated molecular patterns (PAMPs). One response is a rapid and transient burst of reactive oxygen species (ROS, e.g. superoxide and hydrogen peroxide) in the cell wall (apoplast) produced by NADPH oxidases and cell wall peroxidases. Using a genetically-encoded hydrogen peroxide sensor roGFP2-Orp1, we found that, in contrast to the transient apoplastic ROS burst, there is also prolonged hydrogen peroxide production in the cytosol upon PAMP perception which is independent of NADPH oxidase and cell wall peroxidases. Our results suggest that apoplastic ROS rather than intracellular hydrogen peroxide is a signal triggering stomatal closure during PAMP-triggered immunity. Additionally, we re-address the relative contribution of the NADPH oxidases D and F in stomatal immunity.
Highly task-specific and distributed neural connectivity in working memory revealed by single-trial decoding in mice and humans
Authors: Strahnen Daniel , Kapanaiah Sampath K.T. , Bygrave Alexei M. , Liss Birgit , Bannerman David M. , Akam Thomas , Grewe Benjamin F. , Johnson Elizabeth L. , Kätzel Dennis
Published: April 2021

Working memory (WM), the capacity to briefly and intentionally maintain mental items, is key to successful goal-directed behaviour and impaired in a range of psychiatric disorders. To date, several brain regions, connections, and types of neural activity have been correlatively associated with WM performance. However, no unifying framework to integrate these findings exits, as the degree of their species- and task-specificity remains unclear. Here, we investigate WM correlates in three task paradigms each in mice and humans, with simultaneous multi-site electrophysiological recordings. We developed a machine learning-based approach to decode WM-mediated choices in individual trials across subjects from hundreds of electrophysiological measures of neural connectivity with up to 90% prediction accuracy. Relying on predictive power as indicator of correlates of psychological functions, we unveiled a large number of task phase-specific WM-related connectivity from analysis of predictor weights in an unbiased manner. Only a few common connectivity patterns emerged across tasks. In rodents, these were thalamus-prefrontal cortex delta- and beta-frequency connectivity during memory encoding and maintenance, respectively, and hippocampal-prefrontal delta- and theta-range coupling during retrieval, in rodents. In humans, task-independent WM correlates were exclusively in the gamma-band. Mostly, however, the predictive activity patterns were unexpectedly specific to each task and always widely distributed across brain regions. Our results suggest that individual tasks cannot be used to uncover generic physiological correlates of the psychological construct termed WM and call for a new conceptualization of this cognitive domain in translational psychiatry.
Stitching and registering highly multiplexed whole slide images of tissues and tumors using ASHLAR
Authors: Muhlich Jeremy L. , Chen Yu-An , Yapp Clarence , Russell Douglas , Santagata Sandro , Sorger Peter K
Published: April 2021

Motivation

Stitching microscope images into a mosaic is an essential step in the analysis and visualization of large biological specimens, particularly human and animal tissues. Recent approaches to highly-multiplexed imaging generate high-plex data from sequential rounds of lower-plex imaging. These multiplexed imaging methods promise to yield precise molecular single-cell data and information on cellular neighborhoods and tissue architecture. However, attaining mosaic images with single-cell accuracy requires robust image stitching and image registration capabilities that are not met by existing methods.

Results

We describe the development and testing of ASHLAR, a Python tool for coordinated stitching and registration of 103or more individual multiplexed images to generate accurate whole-slide mosaics. ASHLAR reads image formats from most commercial microscopes and slide scanners, and we show that it performs better than existing open source and commercial software. ASHLAR outputs standard OME-TIFF images that are ready for analysis by other open-source tools and recently developed image analysis pipelines.

Availability and implementation

ASHLAR is written in Python and available under an MIT license athttps://github.com/labsyspharm/ashlar. An informational website with user guides and test data is available athttps://labsyspharm.github.io/ashlar/.
The Relationship between Stability of Interpersonal Coordination and Inter-Brain EEG Synchronization during Anti-phase Tapping
Authors: Kurihara Yuto , Takahashi Toru , Osu Rieko
Published: April 2021

Inter-brain synchronization is enhanced when individuals perform rhythmic interpersonal coordination tasks, such as playing instruments in music ensembles. Experimentally, synchronization has been shown to correlate with the performance of joint tapping tasks. However, it is unclear whether inter-brain synchronization is related to the stability of interpersonal coordination represented as the standard deviation of relative phase (SDRP). In this study, we simultaneously recorded electroencephalograms of two paired individuals during anti-phase tapping in three speed conditions: slow (reference inter-tap interval [ITI]: 0.5 s), fast (reference ITI: 0.25 s), and free (preferred ITI). We calculated the inter-brain synchronization within six regions of interest: frontal, central, left/right temporal, parietal, and occipital regions. We found that synchronization of the central-temporal regions was positively correlated with SDRP in the theta and alpha bands, while synchronization of the frontal-frontal and frontal-central was positively correlated with SDRP in the beta band. These results demonstrate that inter-brain synchronization occurs only when task requirements are high, and that it increases with the instability of the coordination. This may be explained by the stronger mutual prediction required in unstable coordination than that in stable coordination, which increases inter-brain synchronization.
Alpha-XIC: a deep neural network for scoring the coelution of peak groups improves peptide identification by data-independent acquisition mass spectrometry
Authors: Song Jian , Yu Changbin
Published: April 2021

Motivation

The peptide-centric identification methodologies of data-independent acquisition (DIA) data mainly rely on scores for the mass spectrometric signals of targeted peptides. Among these scores, the coelution scores of peak groups constructed by the chromatograms of peptide fragment ions have a significant influence on the identification. Most of the existing coelution scores are achieved by artificially designing some functions in terms of the shape similarity, retention time shift of peak groups. However, these scores cannot characterize the coelution robustly when the peak group is in the circumstance of interference.

Results

On the basis that the neural network is more powerful to learn the implicit features of data robustly from a large number of samples, and thus minimizing the influence of data noise, in this work, we propose Alpha-XIC, a neural network-based model to score the coelution. By learning the characteristics of the coelution of peak groups derived from identified peptides, Alpha-XIC is capable of reporting robust coelution scores even for peak groups with interference. With this score appending to initial scores generated by the accompanying identification engine, the ensuing statistical validation tool can update the identification result and recover the misidentified peptides. In our evaluation of the HeLa dataset with gradient lengths ranging from 0.5h to 2h, Alpha-XIC delivered 16.7% ~ 49.1% improvements in the number of identified precursors at 1% FDR. Furthermore, Alpha-XIC was tested on LFQbench, a mixed-species dataset with known ratios, and increased the number of peptides and proteins fell within valid ratios by up to 16.6% and 13.8%, respectively, compared to the initial identification.

Availability and Implementation

Source code are available atwww.github.com/YuAirLab/Alpha-XIC.
Connectomic Assessment of Injury Burden and Longitudinal Structural Network Alterations in Moderate-to-severe Traumatic Brain Injury
Authors: Osmanlıoğlu Yusuf , Parker Drew , Alappatt Jacob A. , Gugger James J. , Diaz-Arrastia Ramon R. , Whyte John , Kim Junghoon J. , Verma Ragini
Published: April 2021

Traumatic brain injury (TBI) is a major public health problem. Caused by external mechanical forces, a major characteristic of TBI is the shearing of axons across the white matter, which causes structural connectivity disruptions between brain regions. This diffuse injury leads to cognitive deficits, frequently requiring rehabilitation. Heterogeneity is another characteristic of TBI as severity and cognitive sequelae of the disease have a wide variation across patients, posing a big challenge for treatment. Thus, measures assessing network-wide structural connectivity disruptions in TBI are necessary to quantify injury burden of individuals, which would help in achieving personalized treatment, patient monitoring, and rehabilitation planning. Despite TBI being a disconnectivity syndrome, connectomic assessment of structural disconnectivity has been very scarce. In this study, we propose a novel connectomic measure that we call network anomaly score (NAS) to capture the integrity of structural connectivity in TBI patients by leveraging two major characteristics of the disease: diffuseness of axonal injury and heterogeneity of the disease. Over a longitudinal cohort of moderate-to-severe TBI patients, we demonstrate that structural network topology of patients are more heterogeneous and are significantly different than that of healthy controls at 3 months post-injury, where dissimilarity further increases up to 12 months. We also show that NAS captures injury burden as quantified by post-traumatic amnesia and that alterations in the structural brain network is not related to cognitive recovery. Finally we compare NAS to major graph theory measures used in TBI literature and demonstrate the superiority of NAS in characterizing the disease.
iRQC, a surveillance pathway for 40S ribosomal quality control during mRNA translation initiation
Authors: Garshott Danielle M. , An Heeseon , Sundaramoorthy Elayanambi , Leonard Marilyn , Vicary Alison , Harper J. Wade , Bennett Eric J.
Published: April 2021

Since multiple ribosomes can engage a single mRNA, nonuniform ribosome progression can result in collisions. Ribosome collisions during translation elongation elicit a multifaceted ribosome-associated quality control (RQC) response. Despite advanced mechanistic understanding of translation initiation, a parallel RQC pathway that acts on collided preinitiation complexes has not been described. Here, we show that blocking progression of scanning or elongating ribosomes past the start codon triggers uS3 and uS5 ribosomal ubiquitylation. We demonstrate that conditions that activate the integrated stress response can also induce preinitiation complex collisions. The ubiquitin ligase, RNF10, and the deubiquitylating enzyme, USP10, are the key regulators of uS3 and uS5 ubiquitylation. Prolonged uS3 and uS5 ubiquitylation results in 40S, but not 60S, ribosomal protein degradation in an autophagy-independent manner. This study identifies a distinct arm in the RQC pathway, initiation RQC (iRQC), that acts on pervasive ribosome collisions during translation initiation to modulate translation activity and capacity.
Patterns of information segregation during working memory and attention revealed by dual-task interference in behavior, pupillometry, and EEG
Authors: Fleming Justin T. , Njoroge J. Michelle , Noyce Abigail L. , Perrahione Tyler K. , Shinn-Cunningham Barbara G.
Published: April 2021

Project Abstract

Making sense of our environment requires us to extract simultaneous temporal and spatial information from multiple sensory modalities, particularly audition and vision. This sensory information can be stored in working memory (WM) to guide future actions, at which point it must be safeguarded against interference from ongoing sensory processing. Recent fMRI research has uncovered regions in human frontal cortex well-suited to coordinate this interplay between attention and WM for multisensory and multidimensional information. Which of these brain regions are engaged depends on both the sensory modality of the input and the information domain of the task, forming the basis of two complementary networks specialized for auditory/temporal and visual/spatial processing. Motivated by the functional specializations of these networks, we examined whether similarity in sensory modality and information domain modulates neural and perceptual interference between two concurrent tasks. Participants stored temporal or spatial information about auditory or visual stimuli in WM, and on some trials, performed an intervening temporal or spatial auditory task during WM retention. WM recall and auditory perceptual judgments were impaired when the two tasks relied on the same sensory modality and/or information domain. Pupil dilations were also larger in these conditions, indicating increased cognitive effort. Event-related potentials (ERPs) revealed a neural signature of domain-based interference that was masked by behavioral ceiling effects. These results demonstrate that modality and information domain jointly affect how task information is represented in WM, and concomitantly, how tasks engage the complementary auditory-temporal and visual/spatial cognitive control networks.
Eicosanoid signaling as a therapeutic target in middle-aged mice with severe COVID-19
Authors: Roy Wong Lok-Yin , Zheng Jian , Wilhelmsen Kevin , Li Kun , Ortiz Miguel E. , Schnicker Nicholas J. , Pezzulo Alejandro A. , Szachowicz Peter J. , Klumpp Klaus , Aswad Fred , Rebo Justin , Narumiya Shuh , Murakami Makoto , Meyerholz David K. , Fortney Kristen , McCray Paul B. , Perlman Stanley
Published: April 2021

Coronavirus disease 2019 (COVID-19) is especially severe in aged populations1. Resolution of the COVID-19 pandemic has been advanced by the recent development of SARS-CoV-2 vaccines, but vaccine efficacy is partly compromised by the recent emergence of SARS-CoV-2 variants with enhanced transmissibility2. The emergence of these variants emphasizes the need for further development of anti-SARS-CoV-2 therapies, especially in aged populations. Here, we describe the isolation of a new set of highly virulent mouse-adapted viruses and use them to test a novel therapeutic drug useful in infections of aged animals. Initially, we show that many of the mutations observed in SARS-CoV-2 during mouse adaptation (at positions 417, 484, 501 of the spike protein) also arise in humans in variants of concern (VOC)2. Their appearance during mouse adaptation indicates that immune pressure is not required for their selection. Similar to the human infection, aged mice infected with mouse-adapted SARS-CoV-2 develop more severe disease than young mice. In murine SARS, in which severity is also age-dependent, we showed that elevated levels of an eicosanoid, prostaglandin D2 (PGD2) and of a phospholipase, PLA2G2D, contributed to poor outcomes in aged mice3,4. Using our virulent mouse-adapted SARS-CoV-2, we show that infection of middle-aged mice lacking expression of DP1, a PGD2receptor, or PLA2G2D are protected from severe disease. Further, treatment with a DP1 antagonist, asapiprant, protected aged mice from a lethal infection. DP1 antagonism is one of the first interventions in SARS-CoV-2-infected animals that specifically protects aged animals, and demonstrates that the PLA2G2D-PGD2/DP1 pathway is a useful target for therapeutic interventions. (Words: 254)
Characterization of a fiber-coupled EvenField illumination system for fluorescence microscopy
Authors: Berry Kyla , Taormina Mike , Maltzer Zoe , Turner Kristen , Gorham Melissa , Nguyen Thuc , Serafin Robert , Nicovich Philip R
Published: April 2021

Fluorescence microscopy benefits from spatially and temporally homogeneous illumination with illumination area matched to the shape and size of the camera sensor. Fiber-coupled illumination schemes have the added benefit of straightforward and robust alignment and ease of installation compared to free-space coupled illumination. Commercial and open-source fiber-coupled, homogenized illumination schemes have recently become available to the public; however, there have been no published comparisons of speckle reduction schemes to date. We characterize three different multimode fibers in combination with two laser speckle reduction devices and compare spatial and temporal profiles to a commercial unit. This work yields a new design, the EvenField Illuminator, which is freely available along for researchers to integrate into their own imaging systems.
Beech tree masting explains the inter-annual variation in the fall and spring peaks ofIxodes ricinusticks with different time lags
Authors: Bregnard Cindy , Rais Olivier , Herrmann Coralie , Kahl Olaf , Brugger Katharina , Voordouw Maarten J.
Published: April 2021

Background

The tickIxodes ricinusis an important vector of tick-borne diseases including Lyme borreliosis. In continental Europe, the nymphal stage ofI. ricinusoften has a bimodal phenology with a large spring/early summer peak and a smaller fall peak. While there is consensus about the origin of the spring nymphal peak, there are two alternative hypotheses for the fall nymphal peak, direct development versus delayed diapause. These two hypotheses make different predictions about the time lags of the correlations between the spring peak, the fall peak, and seed production (masting) by deciduous trees.

Methods

To determine which hypothesis is most important for explaining the fall peak, we used data from a long-term surveillance study (15 years) on the density ofI. ricinusnymphal ticks at 4 different elevation sites in an area of Switzerland that is endemic for Lyme borreliosis, and long-term data on the mast of the European beech tree from the literature.

Results

I. ricinusnymphs had a bimodal phenology at the three lower elevation sites, but a unimodal phenology at the top elevation site. At the lower elevation sites, the density of nymphs (DON) in the fall was strongly correlated with the DON in the spring of the following year. The inter-annual variation in the densities ofI. ricinusnymphs in the fall and spring were best explained by a 1-year versus a 2-year time lag with the beech tree masting index. Fall nymphs had higher fat content and are younger than spring nymphs. All of these observations are consistent with the direct development hypothesis for the fall peak ofI. ricinusnymphs at our study site. Our study provides new insight into the complex bimodal phenology of this important disease vector.

Conclusions

Public health officials in Europe should be aware that following a strong mast year, the DON will increase 1 year later in the fall and 2 years later in the spring and summer. Population ecology studies ofI. ricinusshould consider that the spring and fall peak in the same calendar year represent different generations of ticks.
Non-structural carbohydrate concentrations in woody organs, but not leaves, of temperate and tropical tree angiosperms are independent of the ‘fast-slow’ plant economic spectrum
Authors: Ramirez J.A. , Craven D. , Posada J.M. , Reu B. , Sierra C.A. , Hoch G. , Handa I.T. , Messier C.
Published: April 2021

Background and Aims

Carbohydrate reserves play a vital role in plant survival during periods of negative carbon balance. Considering active storage of reserves, there is a trade-off between carbon allocation to growth and to reserves and defense. A resulting hypothesis is that allocation to reserves exhibits a coordinated variation with functional traits associated with the ‘fast-slow’ plant economics spectrum.

Methods

We tested the relationship between non-structural carbohydrates (NSC) of tree organs and functional traits using 61 angiosperm tree species from temperate and tropical forests with phylogenetic hierarchical Bayesian models.

Key Results

Our results provide evidence that NSC concentrations in woody organs and plant functional traits are largely decoupled, meaning that species’ resilience is unrelated to their position on the ‘fast-slow’ plant economics spectrum. In contrast, we found that variation between NSC concentrations in leaves and the fast-slow continuum was coordinated, as species with higher leaf NSC had traits values associated with resource conservative species such as lower SLA, lower Amax, and high wood density. We did not detect an influence of leaf habit on the variation of NSC concentrations in tree organs.

Conclusions

Efforts to predict the response of ecosystems to global change will need to integrate a suite of plant traits, such as NSC concentrations in woody organs, that are independent of the ‘fast-slow’ spectrum and that capture how species respond to a broad range of global change factors.
Inhibition is the hallmark of CA3 intracellular dynamics around awake ripples
Authors: Kajikawa Koichiro , Hulse Brad K. , Siapas Athanassios G. , Lubenov Evgueniy V.
Published: April 2021

Hippocampal ripples are transient population bursts that structure cortico-hippocampal communication and play a central role in memory processing. However, the mechanisms controlling ripple initiation in behaving animals remain poorly understood. Here we combine multisite extracellular and whole cell recordings in awake mice to contrast the brain state and ripple modulation of subthreshold dynamics across hippocampal subfields. We find that entorhinal input to DG exhibits UP and DOWN dynamics with ripples occurring exclusively in UP states. While elevated cortical input in UP states generates depolarization in DG and CA1, it produces persistent hyperpolarization in CA3 neurons. Furthermore, growing inhibition is evident in CA3 throughout the course of the ripple buildup, while DG and CA1 neurons exhibit depolarization transients 100 ms before and during ripples. These observations highlight the importance of CA3 inhibition for ripple generation, while pre-ripple responses indicate a long and orchestrated ripple initiation process in the awake state.
Novel neuroanatomical integration and scaling define avian brain shape evolution and development
Authors: Watanabe Akinobu , Balanoff Amy M. , Gignac Paul M. , Eugenia Gold M. , Norell Mark A.
Published: April 2021

How do large and unique brains evolve? Historically, comparative neuroanatomical studies have attributed the evolutionary genesis of highly encephalized brains to deviations along, as well as from, conserved scaling relationships among brain regions. However, the relative contributions of these concerted (integrated) and mosaic (modular) processes as drivers of brain evolution remain unclear, especially in non-mammalian groups. While proportional brain sizes have been the predominant metric used to characterize brain morphology to date, we perform a high-density geometric morphometric analysis on the encephalized brains of crown birds (Neornithes or Aves) compared to their stem taxa—the non-avialan coelurosaurian dinosaurs. When analyzed together with developmental neuroanatomical data of model archosaurs (Gallus,Alligator), crown birds exhibit a distinct allometric relationship that dictates their brain evolution and development. Furthermore, analyses by neuroanatomical regions reveal that the acquisition of this derived shape-to-size scaling relationship occurred in a mosaic pattern, where the ‘avian’-grade optic lobe and cerebellum evolved first among non-avialan dinosaurs, followed by major changes to the evolutionary and developmental dynamics of cerebrum shape after the origin of Avialae.

Notably, the brain of crown birds is a more integrated structure than non-avialan archosaurs, implying that diversification of brain morphologies within Neornithes proceeded in a more coordinated manner, perhaps due to spatial constraints and abbreviated growth period. Collectively, these patterns demonstrate a plurality in evolutionary processes that generate encephalized brains in archosaurs and across vertebrates.
Object motion influences feedforward motor responses during mechanical stopping of virtual projectiles: A preliminary study
Authors: Gómez-Granados Ana , Kurtzer Isaac , Gordon Sean , Barany Deborah A. , Singh Tarkeshwar
Published: April 2021

An important window into sensorimotor function is how humans interact and stop moving projectiles, such as stopping a door from closing shut or catching a ball. Previous studies have suggested that humans time the initiation and modulate the amplitude of their muscle activity based on the momentum of the approaching object. However, real-world experiments are constrained by laws of mechanics, which cannot be manipulated experimentally to probe the mechanisms of sensorimotor control and learning. An augmented-reality variant of such tasks allows for experimental manipulation of the relationship between motion and force to obtain novel insights into how the nervous system prepares motor responses to interact with moving stimuli. Existing paradigms for studying interactions with moving projectiles use massless object and are primarily focused on quantifying gaze and hand kinematics. Here, we developed a novel collision paradigm using a robotic manipulandum where participants mechanically stopped a virtual object moving in the horizontal plane. On each block of trials, we varied the virtual object’s momentum by increasing either its speed or mass. Participants stopped the object by applying a force impulse that matched the object momentum. We observed that arm force increased as a function of object momentum linked to changes in virtual mass or speed, mirroring results from studies involving catching free-falling objects. In addition, increasing object speed resulted in later onset of hand force relative to the impending time-to-contact. These findings show that the present paradigm can be used to determine how humans process projectile motion for hand motor control.
Transcriptomic Changes During Stage Progression of Mycosis Fungoides
Authors: Xiao M , Hennessey D , Iyer A , O’Keefe S , Zhang F , Sivanand A , Gniadecki R
Published: April 2021

Background

Mycosis fungoides (MF) is the most common cutaneous T cell lymphoma, which in the early patch/plaque stages runs an indolent course. However, ~25% of MF patients develop skin tumors, a hallmark of progression to the advanced stage and associated with high mortality. The mechanisms involved in stage progression are poorly elucidated.

Methods

We performed whole-transcriptome and whole-exome sequencing of malignant MF cells from skin biopsies obtained by laser-capture microdissection. We compared three types of MF lesions: early-stage plaques (ESP, n=12), and plaques and tumors from patients in late-stage disease (late-stage plaques, LSP, n=10, and tumors, TMR, n=15). Gene Ontology (GO) and KEGG analysis were used to determine pathway changes specific for different lesions which we linked to the recurrent somatic mutations overrepresented in MF tumors.

Results

The key upregulated pathways during stage progression were those related to cell proliferation and survival (MEK/ERK, Akt-mTOR), Th2/Th9 signaling (IL4, STAT3, STAT5, STAT6), meiomitosis (CT45A1, CT45A3, STAG3, GTSF1, and REC8) and DNA repair (PARP1, MYCN, OGG1). Principal coordinate clustering of the transcriptome revealed extensive gene expression differences between early (ESP) and advanced-stage lesions (LSP and TMR). LSP and TMR showed remarkable similarities at the level of the transcriptome, which we interpreted as evidence of cell percolation between lesions via hematogenous self-seeding.

Conclusion

Stage progression in MF is associated with Th2/Th9 polarization of malignant cells, activation of proliferation, survival, as well as increased genomic instability. Global transcriptomic changes in multiple lesions are probably caused by hematogenous cell percolation between discrete skin lesions.
CMOS electrochemical imaging arrays for the detection and classification of microorganisms
Authors: Arcadia Christopher E. , Hu Kangping , Epstein Slava , Wanunu Meni , Adler Aaron , Rosenstein Jacob K.
Published: April 2021

Microorganisms account for most of the biodiversity on earth. Yet while there are increasingly powerful tools for studying microbial genetic diversity, there are fewer tools for studying microorganisms in their natural environments. In this paper, we present recent advances in CMOS electrochemical imaging arrays for detecting and classifying microorganisms. These microscale sensing platforms can provide non-optical measurements of cell geometries, behaviors, and metabolic markers. We review integrated electronic sensors appropriate for monitoring microbial growth, and present measurements of single-celled algae using a CMOS sensor array with thousands of active pixels. Integrated electrochemical imaging can contribute to improved medical diagnostics and environmental monitoring, as well as discoveries of new microbial populations.
M&Ms: A software for building realistic Microbial Mock communities
Authors: García-García Natalia , Tamames Javier , Puente-Sánchez Fernando
Published: April 2021

Motivation

Advances in sequencing technologies have triggered the development of many bioinformatic tools aimed to analyze these data. As these tools need to be tested, it is important to simulate datasets that resemble realistic conditions. Although there is a large amount of software dedicated to produce reads from ‘in silico’ microbial communities, often the simulated data diverge widely from real situations.

Results

Here, we introduce M&Ms, a user-friendly open-source bioinformatic tool to produce realistic amplicon datasets from reference sequences, based on pragmatic ecological parameters. This tool creates sequence libraries for ‘in silico’ microbial communities with user-controlled richness, evenness, microdiversity, and source environment. M&Ms allows the user to generate simple to complex read datasets based on real parameters that can be used in developing bioinformatic software or in benchmarking current tools. M&Ms also provides additional figures and files with extensive details on how each synthetic community is composed, so that users can make informed choices when designing their benchmarking pipelines.

Availability

The source code of M&Ms is freely available fromhttps://github.com/ggnatalia/MMs

Contact

ngarcia@cnb.csic.es
Developmental Circadian Disruption Alters Placental Signaling in Mice
Authors: Clarkson-Townsend Danielle A. , Bales Katie L. , Hermetz Karen E. , Burt Amber A. , Pardue Machelle T. , Marsit Carmen J.
Published: April 2021

Circadian disruption has been largely overlooked as a developmental exposure. The placenta, a conduit between the maternal and fetal environments, may relay circadian cues to the fetus. We have previously shown that developmental chronodisruption causes visual impairment and increased retinal microglial and macrophage marker expression. Here, we investigated the impacts of environmental circadian disruption on fetal and placental outcomes in a C57BL/6J mouse (Mus musculus) model. Developmental chronodisruption had no effect on embryo count, placental weight, or fetal sex ratio. When measured with RNAseq, mice exposed to developmental circadian disruption (CD) had differential placental expression of several transcripts includingSerpinf1, which encodes pigment-epithelium derived factor (PEDF). Immunofluorescence of microglia/macrophage markers, Iba1 and CD11b, also revealed significant upregulation of immune cell markers in CD-exposed placenta. Our results suggest thatin uterocircadian disruption enhances placental immune cell expression, potentially programming a pro-inflammatory tissue environment that increases the risk of chronic disease in adulthood.
A cancer-associated RNA polymerase III identity drives robust transcription and expression of SNAR-A noncoding RNA
Authors: Van Bortle Kevin , Marciano David P. , Liu Qing , Lipchik Andrew M. , Gollapudi Sanjay , Geller Benjamin S. , Monte Emma , Kamakaka Rohinton T. , Snyder Michael P.
Published: April 2021

Dysregulation of the RNA polymerase III (Pol III) transcription program, which synthesizes tRNA and other classes of small noncoding RNA critical for cell growth and proliferation, is associated with cancer and human disease. Previous studies have identified two distinct Pol III isoforms defined by the incorporation of either subunit POLR3G (RPC7α) during early development, or POLR3GL (RPC7β) in specialized tissues. Though POLR3G is re-established in cancer and immortalized cell lines, the contributions of these isoforms to transcription potential and transcription dysregulation in cancer remain poorly defined. Using an integrated Pol III genomic profiling approach in combination within vitrodifferentiation and subunit disruption experiments, we discover that loss of subunit POLR3G is accompanied by a restricted repertoire of genes transcribed by Pol III. In particular, we observe that a specific class of small noncoding RNA,SNAR-A, is exquisitely sensitive to the availability of subunit POLR3G in proliferating cells. Taken further, large-scale analysis of Pol III subunit expression and downstream chromatin features identifies concomitant loss of POLR3G andSNAR-Aactivity across a multitude of differentiated primary immune cell lineages, and conversely, coordinate re-establishment of POLR3G expression andSNAR-Afeatures in a variety of human cancers. These results altogether argue against strict redundancy models for subunits POLR3G and POLR3GL, and instead support a model in which Pol III identity itself functions as an important transcriptional regulatory mechanism. Upregulation of POLR3G, which is driven by MYC, identifies a subgroup of patients with unfavorable survival outcomes in specific cancers, further implicating the POLR3G-enhanced transcription repertoire as a potential disease factor.
Counting of Enzymatically Amplified Affinity Reactions in Hydrogel Particle-Templated Drops
Authors: Wang Yilian , Shah Vishwesh , Lu Angela , Pachler Ella , Cheng Brian , Di Carlo Dino
Published: April 2021

Counting of numerous compartmentalized enzymatic reactions underlies quantitative and high sensitivity immunodiagnostic assays. However, digital enzyme-linked immunosorbent assays (ELISA) require specialized instruments which have slowed adoption in research and clinical labs. We present a lab-on-a-particle solution to digital counting of thousands of single enzymatic reactions. Hydrogel particles are used to bind enzymes and template the formation of droplets that compartmentalize reactions with simple pipetting steps. These hydrogel particles can be made at a high throughput, stored, and used during the assay to create ~500,000 compartments within 2 minutes. These particles can also be dried and rehydrated with sample, amplifying the sensitivity of the assay by driving affinity interactions on the hydrogel surface. We demonstrate digital counting of β-galactosidase enzyme at a femtomolar detection limit with a dynamic range of 3 orders of magnitude using standard benchtop equipment and experiment techniques. This approach can faciliate the development of digital ELISAs with reduced need for specialized microfluidic devices, instruments, or imaging systems.
Tempo and mode of gene expression evolution in the brain across Primates
Authors: Bauernfeind Amy L. , Zintel Trisha M. , Pizzollo Jason , Ely John J. , Raghanti Mary Ann , Hopkins William D. , Hof Patrick R. , Sherwood Chet C. , Babbitt Courtney C.
Published: April 2021

Primate evolution has led to a remarkable diversity of behavioral specializations and pronounced brain size variation among species1,2. Gene expression provides a promising opportunity for studying the molecular basis of brain evolution, but it has been explored in very few primate species to date e.g.3,4. To understand the landscape of gene expression evolution across the primate lineage, we generated and analyzed RNA-Seq data from four brain regions in an unprecedented eighteen species. Here we show a remarkable level of variation in gene expression among hominid species, including humans and chimpanzees, despite their relatively recent divergence time from other primates. We found that individual genes display a wide range of expression dynamics across evolutionary time reflective of the diverse selection pressures acting on genes within primate brain tissue. Using our sample that represents an unprecedented 190-fold difference in primate brain size, we identified genes with variation in expression most correlated with brain size and found several with signals of positive selection in their regulatory regions. Our study extensively broadens the context of what is known about the molecular evolution of the brain across primates and identifies novel candidate genes for study of genetic regulation of brain development and evolution.
Integrin-dependent migratory switches regulate the translocation ofToxoplasma-infected dendritic cells across brain endothelial monolayers
Authors: Ross Emily C. , ten Hoeve Arne L. , Barragan Antonio
Published: April 2021

Multiple cellular processes, such as immune responses and cancer cell metastasis, crucially depend on interconvertible migration modes. However, knowledge is scarce on how infectious agents impact the processes of cell adhesion and migration at restrictive biological barriers. In extracellular matrix, dendritic cells (DCs) infected by the obligate intracellular protozoanToxoplasma gondiiundergo mesenchymal-to-amoeboid transition (MAT) for rapid integrin-independent migration. Here, in a cellular model of the blood-brain barrier, we report that parasitised DCs adhere to polarised endothelium and shift to integrin-dependent motility, accompanied by elevated transendothelial migration (TEM). Upon contact with endothelium, parasitised DCs dramatically reduced velocities and adhered under both static and shear stress conditions, thereby obliterating the infection-induced amoeboid motility displayed in collagen matrix. The motility of adherent parasitised DCs on endothelial monolayers was restored by blockade of β1 and β2 integrins or ICAM-1, which conversely reduced motility on collagen-coated surfaces. Moreover, parasitised DCs exhibited enhanced translocation across highly polarised primary murine brain endothelial cell monolayers. Blockade of β1, β2 integrins, ICAM-1 and PECAM-1 reduced TEM frequencies. Finally, gene silencing of the pan-integrin-cytoskeleton linker talin (Tln1) or of β1 integrin (Itgb1) in primary DCs resulted in increased motility on endothelium and decreased TEM. Adding to the paradigms of leukocyte diapedesis, the findings provide novel insights in how an intracellular pathogen impacts the migratory plasticity of leukocytes in response to the cellular environment, to promote infection-related dissemination.
OXSR1 inhibits inflammasome activation by limiting potassium efflux during mycobacterial infection
Authors: Hortle Elinor , Tran Lam Vi , Fontaine Angela RM , Pinello Natalia , Wong Justin J-L , Britton Warwick J , Oehlers Stefan H
Published: April 2021

Pathogenic mycobacteria inhibit inflammasome activation as part of their pathogenesis. While it is known that potassium efflux is a trigger for inflammasome activation, the interaction between mycobacterial infection, potassium efflux and inflammasome activation has not been investigated. Here we useMycobacterium marinuminfection of zebrafish embryos andMycobacterium tuberculosisof human THP-1 cells to demonstrate that pathogenic mycobacteria upregulate the host WNK signalling pathway kinases SPAK and OXSR1 which control intracellular potassium balance. We show that genetic depletion or inhibition of OXSR1 decreases bacterial burden and intracellular potassium levels. The protective effects of OXSR1 depletion are mediated by NLRP3 inflammasome activation and are dependent on caspase-mediated release of IL-1β and the downstream activation of protective TNF-α. The elucidation of this druggable pathway to potentiate inflammasome activation provides a new avenue for the development of host-directed therapies against intracellular infections.
The fall and rise of group BStreptococcusin dairy cattle: reintroduction due to human-to-cattle host jumps?
Authors: Crestani Chiara , Forde Taya L , Lycett Samantha J , Holmes Mark A , Fasth Charlotta , Persson-Waller Karin , Zadoks Ruth N
Published: April 2021

Group BStreptococcus(GBS;Streptococcus agalactiae) is a major neonatal and opportunistic bacterial pathogen of humans and an important cause of mastitis in dairy cattle with significant impacts on food security. Following the introduction of mastitis control programs in the 1950s, GBS was nearly eradicated from the dairy industry in northern Europe, followed by re-emergence in the 21st century. Here, we sought to explain this re-emergence based on short and long read sequencing of historical (1953-1978; n = 44) and contemporary (1997-2012; n = 76) bovine GBS isolates. Our data show that a globally distributed bovine-associated lineage of GBS was commonly detected among historical isolates but never among contemporary isolates. By contrast, tetracycline resistance, which is present in all major GBS clones adapted to humans, was commonly and uniquely detected in contemporary bovine isolates. These observations provide evidence for strain replacement and suggest a human origin of newly emerged strains. Three novel GBS plasmids were identified, including two showing >98% homology with plasmids fromStreptococcus pyogenesandStreptococcus dysgalactiaesubsp.equisimilis, which co-exist with GBS in the human oropharynx. Our findings support introduction of GBS into the dairy population due to human to-cattle jumps on multiple occasions and demonstrate that reverse zoonotic transmission can erase successes of animal disease control campaigns.

IMPACT STATEMENT

Pathogens can jump between humans and animals. Animal domestication and intensification of livestock production systems have caused multiple human to animal spill-over events, sometimes with significant impact on animal health and food production. The most common production-limiting disease of dairy cattle is mastitis, inflammation of the mammary gland, which can be caused by group BStreptococcus,a common commensal and pathogen of humans. Using genomic data from historical and recent isolates, we show that re-emergence of this pathogen in the dairy industry in northern Europe is due to strains with genomic signatures of human host-adaptation, including antimicrobial resistance genes and plasmids. This shows how elimination of animal diseases may be hampered by humans serving as a reservoir of multi-host pathogens, and reverse zoonotic transmission.

REPOSITORIES

Reads for all isolates sequenced in this study have been submitted to the ENA Sequence Read Archive (SRA). SRA accession numbers are included in Table S1, supplementary material, available in the online version of this article.