bluuebunny/crossref_metadata_2025 huggingface dataset:
Gpr125 identifies myoepithelial progenitors at tips of lacrimal ducts and is essential for tear film
Authors: Spina Elena , Handlin Rebecca , Simundza Julia , Incassati Angela , Faiq Muneeb , Sainulabdeen Anoop , Chan Kevin C , Cowin Pamela
Published: September 2020

Gpr125, encoded byAdgra3, is an orphan adhesion G-protein coupled receptor (aGPCR) implicated in modulating Wnt signaling and planar polarity. Here we establish both physiological and pathological roles for Gpr125. We show that mice lacking Gpr125 or its signaling domains display an ocular phenotype with many hallmarks of human dry eye syndrome. These include squinting, abnormal lacrimation, mucus accumulation, swollen eyelids and inflammatory infiltration of lacrimal and meibomian glands. Utilizing a Gpr125-β-gal reporter and scRNAseq, we identify Gpr125 expression in a discrete population of cells located at the tips of migrating embryonic lacrimal ducts. By lineage tracing we show these cells function as progenitors of the adult lacrimal myoepithelium. Beyond defining an essential role for Gpr125 in tear film and identifying its utility as a marker of lacrimal progenitors, this study implicates Gpr125 in the etiology of blepharitis and dry eye syndrome, and defines novel animal models of these common maladies.
Heterogeneity in collective endothelial cell behavior is a driver of arterio-venous remodeling
Authors: Jiang Keyi , Pichol-Thievend Cathy , Neufeld Zoltan , Francois Mathias
Published: September 2020

During vascular development, arteries and veins form in a stepwise process that combines vasculogenesis and sprouting angiogenesis. Despite extensive data on the mechanisms governing blood vessel assembly at the single cell level, little is known about how cell populations migrate in a finely tuned and coordinated manner, and distribute precisely between arteries and veins. Here, we use an endothelial-specific zebrafish reporter,arteriobow, to label small cohorts of arterial cells and trace their progeny from the initial events of vasculogenesis through the process of arterio-venous remodeling. We reveal that the genesis of both arteries and veins relies on the coordination of ten types of collective cell behaviors originating from discrete endothelial cell clusters. Within these behavioral categories, we identify a heterogeneity of collective cell dynamics specific to either arterial or venous remodeling. Using pharmacological blockade, we further show that factors known to control vascular patterning such as cell-intrinsic Notch signaling and cell-extrinsic blood flow, potentially act as regulators by coordinating endothelial cohorts behavior, which in turn instructs the future territory of arterio-venous remodeling.
DWV infection and replication at the early stagein vitrousing honey bee pupal cells
Authors: Wu Yunfei , Li Jing , Kadowaki Tatsuhiko
Published: September 2020

Deformed wing virus (DWV) has been best characterized among honey bee viruses; however, very little is known about the mechanisms of viral infection and replication due to the lack of honey bee cell lines. To resolve this problem, we establishedin vitrosystem to reconstitute DWV binding and entry to the host cell followed by translation of the genome RNA and the polyprotein processing with honey bee pupal cells. Using this system, P-domain of VP1 was found to be essential for DWV infection/replication but not binding/entry to the cell. DWV efficiently infects/replicates in cells derived from early but not late pupa, suggesting that the undifferentiated cells are targeted for the viral infection/replication. Furthermore, we found that inhibitors for mammalian picornavirus 3C-Protease, Rupintrivir and Quercetin suppress DWV infection/replication, indicating that thisin vitrosystem is also useful for screening a compound to modify the viral infection/replication. Ourin vitrosystem should help to understand the mechanisms of DWV infection and replication at the early stage.

Importance

Recent decline of managed honey bee colonies has been driven by the pathogens and parasites. However, studying the mechanisms of pathogen infection and replication in honey bee at molecular and cellular levels has been challenging. DWV is the most prevalent virus in honey bee across the globe and we establishedin vitrosystem to reconstitute the viral infection and replication with the primary pupal cells. Using RNA-dependent RNA polymerase (RdRP) and the negative strand of DWV genome RNA as markers, we show that the pupal cells can support DWV infection and at least replication at the early stage. The results shown in this report indicate that ourin vitrosystem helps to uncover the mechanisms of DWV infection and replication. Furthermore, it is also feasible to conduct a large scale screening for compounds to inhibit or stimulate DWV infection/replication.
Sex dimorphism in European sea bass (Dicentrarchus labraxL.): new insights into sex-related growth patterns during very early life stages
Authors: Faggion Sara , Vandeputte Marc , Vergnet Alain , Clota Frédéric , Blanc Marie-Odile , Sanchez Pierre , Ruelle François , Allal François
Published: September 2020

The European sea bass (Dicentrarchus labrax) exhibits female-biased sexual size dimorphism (SDD) early in development. New tagging techniques provide the opportunity to monitor individual sex-related growth during the post-larval and juvenile stages.

We produced an experimental population through artificial fertilization and followed a rearing-temperature protocol (∼16 °C from hatching to 112 days post-hatching, dph; ∼20 °C from 117 to 358 dph) targeting a roughly balanced sex ratio. The fish were tagged with microchips between 61 and 96 dph in five tagging trials of 50 fish each; individual standard length (SL) was recorded through repeated biometric measurements performed between 83 to 110 dph via image analyses. Body weight (BW) was modelled using the traits measured on the digital pictures (i.e. SL, area, height, perimeter and volume). At 117 dph, the fish were tagged with microtags and regularly measured for SL and BW until 335 dph. The experiment ended at 358 dph with the sexing of the fish.

The sex-ratio at the end of the experiment was significantly in favor of the females (65.9% vs. 34.1%). The females were significantly longer and heavier than the males from 103 dph (∼30 mm SL, ∼0.44 g BW) to 165 dph. A significant difference in the daily growth coefficient (DGC) was observed only between 96 and 103 dph, suggesting a physiological or biological change occurring during this period.

The female-biased SSD pattern in European sea bass is thus strongly influenced by very early growth differences between sexes, in any case long before gonadal sex differentiation has been started. This leads to the hypothesis that early growth may be a cause rather than a consequence of sex determination in sea bass.
Fractional diffusion theory of balanced heterogeneous neural networks
Authors: Wardak Asem , Gong Pulin
Published: September 2020

Interactions of large numbers of spiking neurons give rise to complex neural dynamics with fluctuations occurring at multiple scales. Understanding the dynamical mechanisms underlying such complex neural dynamics is a long-standing topic of interest in neuroscience, statistical physics and nonlinear dynamics. Conventionally, fluctuating neural dynamics are formulated as balanced, uncorrelated excitatory and inhibitory inputs with Gaussian properties. However, heterogeneous, non-Gaussian properties have been widely observed in both neural connections and neural dynamics. Here, based on balanced neural networks with heterogeneous, non-Gaussian features, our analysis reveals that in the limit of large network size, synaptic inputs possess power-law fluctuations, leading to a remarkable relation of complex neural dynamics to the fractional diffusion formalisms of non-equilibrium physical systems. By uniquely accounting for the leapovers caused by the fluctuations of spiking activity, we further develop a fractional Fokker-Planck equation with absorbing boundary conditions. This body of formalisms represents a novel fractional diffusion theory of heterogeneous neural networks and results in an exact description of the network activity states. This theory is further implemented in a biologically plausible, balanced neural network and identifies a novel type of network state with rich, nonlinear response properties, providing a unified account of a variety of experimental findings on neural dynamics at the individual neuron and the network levels, including fluctuations of membrane potentials and population firing rates. We illustrate that this novel state endows neural networks with a fundamental computational advantage; that is, the neural response is maximised as a function of structural connectivity. Our theory and its network implementations provide a framework for investigating complex neural dynamics emerging from large networks of spiking neurons and their functional roles in neural processing.
Reduced Successor Representation Potentially Interferes with Cessation of Habitual Reward-Seeking
Authors: Shimomura Kanji , Kato Ayaka , Morita Kenji
Published: September 2020

Difficulty in cessation of drinking, smoking, or gambling has been widely recognized. Conventional theories proposed relative dominance of habitual over goal-directed control, but human studies have not convincingly supported them. Referring to the recently suggested “successor representation” of states that enables partially goal-directed control, we propose a dopamine-related mechanism potentially underlying the difficulty in resisting habitual reward-seeking, common to substance and non-substance reward. Consider that a person has long been taking a series of actions leading to a certain reward without resisting temptation. Given the suggestions of the successor representation and the dimension reduction in the brain, we assumed that the person has acquired a dimension-reduced successor representation of states based on the goal state under the established non-resistant policy. Then, we show that if the person changes the policy to resist temptation, a large positive reward prediction error (RPE) becomes generated upon eventually reaching the goal, and it sustains given that the acquired state representation is so rigid that it does not change. Inspired by the anatomically suggested spiral striatum-midbrain circuit and the theoretically proposed spiraling accumulation of RPE bias in addiction, we further simulated the influence of RPEs generated in the goal-based representation system on another system representing individual actions. We then found that such an influence could potentially enhance the propensity of non-resistant choice. These results suggest that the inaccurate value estimation in the reduced successor representation system and its influence through the spiral striatum-midbrain circuit might contribute to the difficulty in cessation of habitual reward-seeking.
Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes inPantoea agglomeransKM1, a potential opportunistic pathogen
Authors: Guevarra Robin B. , Magez Stefan , Peeters Eveline , Chung Mi Sook , Kim Kyung Hyun , Radwanska Magdalena
Published: September 2020

Pantoea agglomeransis a Gram-negative aerobic bacillus causing a wide range of opportunistic infections in humans including septicemia, pneumonia, septic arthritis, wound infections and meningitis. To date, the determinants of virulence, antibiotic resistance, metabolic features conferring survival and host-associated pathogenic potential of this bacterium remain largely underexplored. In this study, we sequenced and assembled the whole-genome ofP. agglomeransKM1 isolated from kimchi in South Korea. The genome contained one circular chromosome of 4,039,945 bp, 3 mega plasmids, and 2 prophages. The phage-derived genes encoded integrase, lysozyme and terminase. Six CRISPR loci were identified within the bacterial chromosome. Further in-depth analysis showed that the genome contained 13 antibiotic resistance genes conferring resistance to clinically important antibiotics such as penicillin G, bacitracin, rifampicin, vancomycin, and fosfomycin. Genes involved in adaptations to environmental stress were also identified which included factors providing resistance to osmotic lysis, oxidative stress, as well as heat and cold shock. The genomic analysis of virulence factors led to identification of a type VI secretion system, hemolysin, filamentous hemagglutinin, and genes involved in iron uptake and sequestration. Finally, the data provided here show that, the KM1 isolate exerted strong immunostimulatory properties on RAW 264.7 macrophagesin vitro. Stimulated cells produced Nitric Oxide (NO) and pro-inflammatory cytokines TNF-α, IL-6 and the anti-inflammatory cytokine IL-10. The upstream signaling for production of TNF-α, IL-6, IL-10, and NO depended on TLR4 and TLR1/2. While production of TNF-α, IL-6 and NO involved solely activation of the NF-κB, IL-10 secretion was largely dependent on NF-κB and to a lesser extent on MAPK Kinases. Taken together, the analysis of the whole-genome and immunostimulatory properties provided in-depth characterization of theP. agglomeransKM1 isolate shedding a new light on determinants of virulence that drive its interactions with the environment, other microorganisms and eukaryotic hosts.
Structural Coordinates: A novel approach to predict protein backbone conformation
Authors: Milchevskaya Vladislava , Nikitin Alexei M. , Lukshin Sergey A. , Filatov Ivan V. , Kravatsky Yuri V. , Tumanyan Vladimir G. , Esipova Natalia G. , Milchevskiy Yury V.
Published: September 2020

Motivation

Local protein structure is usually described via classifying each peptide to a unique element from a set of pre-defined structures. These so-called structural alphabets may differ in the number of structures or the length of peptides. Most methods that predict the local structure of a protein from its sequence rely on this kind of classification. However, since all peptides assigned to the same class are indistinguishable, such an approach may not be sufficient to model protein folding with high accuracy.

Results

We developed a method that predicts the structural representation of a peptide from its sequence. For 5-mer peptides, we achieved the Q16 classification accuracy of 67.9%, which is higher than what is currently reported in the literature. Importantly, our prediction method does not utilize information about protein homologues but only physicochemical properties of the amino acids and the statistics of the structures, but relies on a comprehensive feature-generation procedure based only on the protein sequence and the statistics of resolved structures. We also show that the 3D coordinates of a peptide can be uniquely recovered from its structural coordinates, and show the required conditions for that under various geometric constraints.

Availability

The online implementation of the method is provided freely athttp://pbpred.eimb.ru

Contact

milch@eimb.ruorvmilchev@uni-koeln.de

Supplementary information

Supplementary data are available online athttp://pbpred.eimb.ru/S/index.html
MOVICS: an R package for multi-omics integration and visualization in cancer subtyping
Authors: Lu Xiaofan , Meng Jialin , Zhou Yujie , Jiang Liyun , Yan Fangrong
Published: September 2020

Stratification of cancer patients into distinct molecular subgroups based on multi-omics data is an important issue in the context of precision medicine. Here we presentMOVICS, an R package for multi-omics integration and visualization in cancer subtyping.MOVICSprovides a unified interface for 10 state-of-the-art multi-omics integrative clustering algorithms, and incorporates the most commonly used downstream analyses in cancer subtyping researches, including characterization and comparison of identified subtypes from multiple perspectives, and verification of subtypes in external cohort using a model-free approach for multiclass prediction.MOVICSalso creates feature rich customizable visualizations with minimal effort.

Availability and implementation

MOVICSpackage and online tutorial are freely available athttps://github.com/xlucpu/MOVICS.
Individualized cyclic mechanical loading improves callus properties during the remodelling phase of fracture healing in mice as assessed from time-lapsed in vivo imaging
Authors: Wehrle Esther , Paul Graeme R , Tourolle né Betts Duncan C , Kuhn Gisela A , Müller Ralph
Published: September 2020

Fracture healing is regulated by mechanical loading. Understanding the underlying mechanisms during the different healing phases is required for targeted mechanical intervention therapies. Here, the influence of individualized cyclic mechanical loading on the remodelling phase of fracture healing was assessed in a mouse femur defect model. After bridging of the defect, a loading group (n=10) received individualized cyclic mechanical loading (8-16 N, 10 Hz, 5 min, 3x/week) based on computed strain distribution in the callus using animal-specific real-time micro-finite element analysis. Controls (n=10) received 0 N treatment at the same post-operative time-points. By registration of consecutive scans, structural and dynamic callus morphometric parameters were followed in three callus sub-volumes and the adjacent cortex showing that the remodelling phase of fracture healing is highly responsive to cyclic mechanical loading with changes in dynamic parameters leading to significantly larger callus formation and mineralization. Loading-mediated maintenance of callus remodelling was associated with distinct effects on Wnt-signalling-associated molecular targets Sclerostin and RANKL in callus sub-regions and the adjacent cortex. Given these distinct local protein expression patterns induced by cyclic mechanical loading, the femur defect loading model with individualized load application seems suitable to understand the local spatio-temporal mechano-molecular regulation of the different fracture healing phases.
Single-molecule measurements reveal that PARP1 condenses DNA by loop formation
Authors: Bell Nicholas A. W. , Haynes Philip J. , Brunner Katharina , Maia de Oliveira Taiana , Flocco Maria , Hoogenboom Bart W. , Molloy Justin E.
Published: September 2020

Poly(ADP-ribose) polymerase 1 (PARP1) is an abundant nuclear enzyme that plays important roles in DNA repair, chromatin organization and transcription regulation. Although binding and activation of PARP1 by DNA damage sites has been extensively studied, little is known about how PARP1 binds to long stretches of undamaged DNA and how it could shape chromatin architecture. Here, using a combination of single-molecule techniques including magnetic tweezers and atomic force microscopy, we show that PARP1 binds and condenses undamaged, kilobase-length DNA subject to sub-picoNewton mechanical forces. Decondensation by high force proceeds through a series of discrete increases in extension, indicating that PARP1 stabilizes loops of DNA. This model is supported by DNA braiding experiments which show that PARP1 can bind at the intersection of two separate DNA molecules. PARP inhibitors do not affect the level of condensation of undamaged DNA, but act to block condensation reversal for damaged DNA in the presence of NAD+. Our findings establish a mechanism for PARP1 in the organization of chromatin structure.
Convergent adaptation in mitochondria of phylogenetically distant birds: does it exist?
Authors: Burskaia Valentina , Artyushin Ilja , Potapova Nadezhda , Konovalov Kirill , Bazykin Georgii A.
Published: September 2020

In a wide range of taxa, proteins encoded by mitochondrial genomes are involved in adaptation to lifestyle that requires oxygen starvation or elevation of metabolism rate. It remains poorly understood to what extent adaptation to similar conditions is associated with parallel changes in these proteins. We search for genetic signal of parallel or convergent evolution in recurrent molecular adaptation to high altitude, migration, diving, wintering, unusual flight abilities, or loss of flight in mitochondrial genomes of birds. Developing on previous work, we design an approach for detection of recurrent coincident changes in genotype and phenotype, indicative of an association between the two. We describe a number of candidate sites involved in recurrent adaptation inNDgenes. However, we find that the majority of convergence events can be explained by random coincidences without invoking adaptation.
Stable transplantation of human mitochondrial DNA by high-throughput, pressurized mitochondrial delivery
Authors: Sercel Alexander J. , Patananan Alexander N. , Man Tianxing , Wu Ting-Hsiang , Yu Amy K. , Guyot Garret W. , Rabizadeh Shahrooz , Niazi Kayvan R. , Chiou Pei-Yu , Teitell Michael A.
Published: September 2020

Generating mammalian cells with specific mtDNA-nDNA combinations is desirable but difficult to achieve and would be enabling for studies of mitochondria-nucleus communication and coordination in controlling cell fates and functions. We developed ‘MitoPunch’, a force-actuated mitochondrial transfer device, to deliver isolated mitochondria into numerous target mammalian cells simultaneously. MitoPunch and MitoCeption, an alternative force-based mitochondrial transfer approach, both yield stable isolated mitochondrial recipient (SIMR) cells that permanently retain exogenous mtDNA, whereas coincubation of mitochondria with cells does not yield SIMR cells. Although a typical MitoPunch or MitoCeption delivery results in dozens of immortalized SIMR clones with restored oxidative phosphorylation, only MitoPunch can produce replication-limited, non-immortal human SIMR clones. The MitoPunch device is versatile, inexpensive to assemble, and easy to use for engineering mtDNA-nDNA combinations to enable fundamental studies and potential translational applications.
Lung lineage transcription factor NKX2-1 epigenetically resolves opposing cell fates in vivo
Authors: Little Danielle R. , Lynch Anne M. , Yan Yun , Akiyama Haruhiko , Kimura Shioko , Chen Jichao
Published: September 2020

Differential use of identical DNA sequences leads to distinct tissue lineages and then multiple cell types within a lineage, an epigenetic process central to progenitor and stem cell biology. The associated genomic changes, especially in native tissues, remain insufficiently understood, and are hereby addressed in the mouse lung, where the same lineage transcription factor NKX2-1 promotes the diametrically opposed alveolar type 1 (AT1) and AT2 cell fates. We show that the cell-type-specific function of NKX2-1 is attributed to its differential chromatin binding that is acquired or retained during development in coordination with partner transcriptional factors. Loss of YAP/TAZ redirects NKX2-1 from its AT1-specific to AT2-specific binding sites, leading to transcriptionally exaggerated AT2 cells when deleted in progenitors or AT1-to-AT2 conversion when deleted after fate commitment.Nkx2-1mutant AT1 and AT2 cells gain distinct accessible sites including those of the opposite fate while adopting the gastrointestinal fate, suggesting an epigenetic plasticity larger than a transcriptional one. Our genomic analysis of single or purified cells, coupled with precision genetics, provides an epigenetic roadmap of alveolar cell fate and potential, and introduces an experimental benchmark for unraveling the in vivo function of lineage transcription factors.
Attention network modulation via tRNS correlates with attention gain
Authors: Contò F. , Edwards G. , Tyler S. , Parrott D. , Grossman E.D. , Battelli L.
Published: September 2020

Transcranial Random Noise Stimulation (tRNS) can enhance vision in the healthy and diseased brain. Yet, the impact of tRNS on large-scale cortical networks is still unknown. We investigated the impact of tRNS coupled with behavioral training on resting-state functional connectivity and attention. We trained human subjects for four consecutive days on two attention tasks, while receiving tRNS over the intraparietal sulci, the middle temporal areas, or sham stimulation. We measured resting state functional connectivity of nodes of the dorsal and ventral attention network (DVAN) before and after training. We found a strong behavioral improvement and increased connectivity within the DVAN after parietal stimulation only. Crucially, behavioral improvement positively correlated with connectivity measures. We conclude changes in connectivity is a marker for the enduring effect of tRNS upon behavior. Our results suggest that tRNS has strong potential to augment cognitive capacity in healthy individuals and promote recovery in the neurological population.
Predicting MEG brain functional connectivity using microstructural information
Authors: Messaritaki Eirini , Foley Sonya , Schiavi Simona , Magazzini Lorenzo , Routley Bethany , Jones Derek K. , Singh Krish D.
Published: September 2020

Understanding how human brain microstructure influences functional connectivity is an important endeavor. In this work, magnetic resonance imaging data from ninety healthy participants were used to calculate structural connectivity matrices using the streamline count, fractional anisotropy, radial diffusivity and a myelin measure (derived from multicomponent relaxometry) to assign connection strength. Unweighted binarized structural connectivity matrices were also constructed. Magnetoencephalography resting-state data from those participants were used to calculate functional connectivity matrices, via correlations of the Hilbert envelopes of beamformer timeseries at the delta, theta, alpha and beta frequency bands. Non-negative matrix factorization was performed to identify the components of the functional connectivity. Shortest-path-length and search-information analyses of the structural connectomes were used to predict functional connectivity patterns for each participant.

The microstructure-informed algorithms predicted the components of the functional connectivity more accurately than they predicted the total functional connectivity. This provides a methodology for better understanding of functional mechanisms. The shortest-path-length algorithm exhibited the highest prediction accuracy. Of the weights of the structural connectivity matrices, the streamline count and the myelin measure gave the most accurate predictions, while the fractional anisotropy performed poorly. Overall, different structural metrics paint very different pictures of the structural connectome and its relationship to functional connectivity.
Neural selectivity for visual motion in macaque area V3A
Authors: Nakhla Nardin , Korkian Yavar , Krause Matthew R. , Pack Christopher C.
Published: September 2020

The processing of visual motion is carried out by dedicated pathways in the primate brain. These pathways originate with populations of direction-selective neurons in the primary visual cortex, which project to dorsal structures like the middle temporal (MT) and medial superior temporal (MST) areas. Anatomical and imaging studies have suggested that area V3A might also be specialized for motion processing, but there have been very few studies of single-neuron direction selectivity in this area. We have therefore performed electrophysiological recordings from V3A neurons in two macaque monkeys (one male and one female) and measured responses to a large battery of motion stimuli that includes translation motion, as well as more complex optic flow patterns. For comparison, we simultaneously recorded the responses of MT neurons to the same stimuli. Surprisingly, we find that overall levels of direction selectivity are similar in V3A and MT and moreover that the population of V3A neurons exhibits somewhat greater selectivity for optic flow patterns. These results suggest that V3A should be considered as part of the motion processing machinery of the visual cortex, in both human and non-human primates.

Significance statement

Although area V3A is frequently the target of anatomy and imaging studies, little is known about its functional role in processing visual stimuli. Its contribution to motion processing has been particularly unclear, with different studies yielding different conclusions. We report a detailed study of direction selectivity in V3A. Our results show that single V3A neurons are, on average, as capable of representing motion direction as are neurons in well-known structures like MT. Moreover, we identify a possible specialization for V3A neurons in representing complex optic flow, which has previously been thought to emerge in higher-order brain regions. Thus it appears that V3A is well-suited to a functional role in motion processing.
Early Emergence and Long-Term Persistence of HIV-Infected T Cell Clones in Children
Authors: Bale Michael J. , Katusiime Mary Grace , Wells Daria , Wu Xiaolin , Spindler Jonathan , Halvas Elias K. , Cyktor Joshua C. , Wiegand Ann , Shao Wei , Cotton Mark F. , Hughes Stephen H. , Mellors John W. , Coffin John M. , Van Zyl Gert U. , Kearney Mary F.
Published: September 2020

Little is known about the emergence and persistence of HIV-infected T cell clones in perinatally-infected children. We analyzed peripheral blood mononuclear cells for clonal expansion in 11 children who initiated antiretroviral therapy (ART) between 1.8-17.4 months of age and with viremia suppressed for 6-9 years. We obtained 8,662 HIV-1 integration sites from pre-ART and 1,861 sites on ART. Expanded clones of infected cells were detected pre-ART in 10/11 children. In 8 children, infected cell clones detected pre-ART persisted for 6-9 years on ART. A comparison of integration sites in the samples obtained on ART with healthy donor PBMC infectedex-vivoshowed selection for cells with proviruses integrated inBACH2andSTAT5B. Our analyses indicate that, despite marked differences in T cell composition and dynamics between children and adults, HIV-infected cell clones are established early in children, persist for up to 9 years on ART, and can be driven by proviral integration in proto-oncogenes.
TDP-43 stabilizes transcripts encoding stress granule protein G3BP1: potential relevance to ALS/FTD
Authors: Sidibé Hadjara , Khalfallah Yousra , Xiao Shangxi , Gómez Nicolás B. , Tank Elizabeth M.H. , Di Tomasso Geneviève , Bareke Eric , Aulas Anaïs , McKeever Paul M. , Melamed Ze’ev , Destroimaisons Laurie , Deshaies Jade-Emmanuelle , Zinman Lorne , Parker J. Alex , Legault Pascale , Tétreault Martine , Barmada Sami J. , Robertson Janice , Vande Velde Christine
Published: September 2020

TDP-43 nuclear depletion and concurrent cytoplasmic accumulation in vulnerable neurons is a hallmark feature of progressive neurodegenerative proteinopathies such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Cellular stress signalling and stress granule dynamics are now recognized to play a role in ALS/FTD pathogenesis. Defective stress granule assembly is associated with increased cellular vulnerability and death. G3BP1 (Ras-GAP SH3-domain-binding protein 1) is a critical stress granule assembly factor. Here, we define that TDP-43 stabilizesG3BP1transcripts via direct binding of a highly conservedcisregulatory element within the 3’UTR. Moreover, we showin vitroandin vivothat nuclear TDP-43 depletion is sufficient to reduce G3BP1 protein levels. Finally, we establish thatG3BP1transcripts are reduced in ALS/FTD patient neurons bearing TDP-43 cytoplasmic inclusions/nuclear depletion. Thus, our data suggest that, in ALS/FTD, there is a compromised stress granule response in disease-affected neurons due to impairedG3BP1mRNA stability caused by TDP-43 nuclear depletion. These data implicate TDP-43 and G3BP1 loss of function as contributors to disease.
Generation of glucocorticoid resistant SARS-CoV-2 T-cells for adoptive cell therapy
Authors: Basar Rafet , Uprety Nadima , Ensley Emily , Daher May , Klein Kimberly , Martinez Fernando , Aung Fleur , Shanley Mayra , Hu Bingqian , Gokdemir Elif , Mendt Mayela , Silva Francia Reyes , Acharya Sunil , Laskowski Tamara , Muniz-Feliciano Luis , Banerjee Pinaki , Li Ye , Li Sufang , Garcia Luciana Melo , Lin Paul , Shaim Hila , Yates Sean G. , Marin David , Kaur Indreshpal , Rao Sheetal , Mak Duncan , Lin Angelique , Miao Qi , Dou Jinzhuang , Chen Ken , Champlin Richard , Shpall Elizabeth J. , Rezvani Katayoun
Published: September 2020

Adoptive cell therapy with viral-specific T cells has been successfully used to treat life-threatening viral infections, supporting the application of this approach against COVID-19. We expanded SARS-CoV-2 T-cells from the peripheral blood of COVID-19-recovered donors and non-exposed controls using different culture conditions. We observed that the choice of cytokines modulates the expansion, phenotype and hierarchy of antigenic recognition by SARS-CoV-2 T-cells. Culture with IL-2/4/7 but not other cytokine-driven conditions resulted in >1000 fold expansion in SARS-CoV-2 T-cells with a retained phenotype, function and hierarchy of antigenic recognition when compared to baseline (pre-expansion) samples. Expanded CTLs were directed against structural SARS-CoV-2 proteins, including the receptor-binding domain of Spike. SARS-CoV-2 T-cells could not be efficiently expanded from the peripheral blood of non-exposed controls. Since corticosteroids are used for the management of severe COVID-19, we developed an efficient strategy to inactivate the glucocorticoid receptor gene (NR3C1) in SARS-CoV-2 CTLs using CRISPR-Cas9 gene editing.
SUMOylation regulates protein cargo in Astrocyte-derived small extracellular vesicles
Authors: Fernández Anllely , Méndez Maxs , Santis Octavia , Corvalan Katherine , Gomez Maria-Teresa , Landgraf Peter , Kahne Thilo , Rojas-Fernandez Alejandro , Wyneken Ursula
Published: September 2020

Recent studies have described a new mechanism of intercellular communication mediated by various types of extracellular vesicles (EVs). In particular, exosomes are small EVs (sEVs) released to the extracellular environment by the fusion of the endosomal pathway-related multivesicular bodies (containing intraluminal vesicles) with the plasma membrane. sEVs contain a molecular cargo consisting of lipids, proteins, and nucleic acids. However, the loading mechanisms for this complex molecular cargo have not yet been completely elucidated. In that line, the post translational modification SUMO (Small Ubiquitin-like Modifier) has been shown to impact the incorporation of select proteins into sEVs. We therefore decided to investigate whether SUMOylation is a mechanism that defines protein loading to sEVs. In order to investigate the role of SUMOylation in cargo loading into sEVs, we utilized astrocytes, an essential cell type of the central nervous system with homeostatic functions, to study the impact of SUMOylation on the protein cargo of sEVs. Following SUMO overexpression, achieved by transfection of SUMO plasmids or experimental conditions that modulate SUMOylation in primary astrocyte cultures, we detected proteins related to cell division, translation, and transcription by mass-spectrometry. In astrocyte cultures treated with the general SUMOylation inhibitor 2-D08 (2′,3′,4′-trihydroxy-flavone, 2-(2,3,4-Trihydroxyphenyl)-4H-1-Benzopyran-4-one) we observed an increase in the number of sEVs and a decreased amount of protein cargo within them. In turn, in astrocytes treated with the stress hormone corticosterone, we found an increase of SUMO-2 conjugated proteins and sEVs from these cells contained an augmented protein cargo. In this case, the proteins detected with mass-spectrometry were mostly proteins related to protein translation. To test whether astrocyte-derived sEVs obtained in these experimental conditions could modulate protein synthesis in target cells, we incubated primary neurons with astrocyte-derived sEVs. sEVs from corticosterone-treated astrocytes stimulated protein synthesis while no difference was found with sEVs derived from 2-D08-treated astrocytes. Our results show that SUMO conjugation plays a fundamental role in defining the protein cargo of sEVs impacting the physiological function of target cells.
The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification
Authors: Aono Alexandre Hild , Pimenta Ricardo José Gonzaga , Garcia Ana Letycia Basso , Correr Fernando Henrique , Hosaka Guilherme Kenichi , Carrasco Marishani Marin , Cardoso-Silva Cláudio Benício , Mancini Melina Cristina , Sforça Danilo Augusto , dos Santos Lucas Borges , Nagai James Shiniti , Pinto Luciana Rossini , Landell Marcos Guimarães de Andrade , Carneiro Monalisa Sampaio , Balsalobre Thiago Willian , Quiles Marcos Gonçalves , Pereira Welison Andrade , Margarido Gabriel Rodrigues Alves , de Souza Anete Pereira
Published: September 2020

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here we identified and profiled the complete kinomes of the polyploidSaccharum spontaneum(Ssp) andSorghum bicolor(Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, which were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between these species, this study offers insights about Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq, identifying significant similarities between Sbi and Ssp. Moreover, through coexpression networks, we inferred a core structure of kinase interactions with specific key elements. This study is the first to categorize the allele specificity of a kinome and provides a wide reservoir of molecular and genetic information, enhancing the understanding of the evolutionary history of Sbi and Ssp PKs.

Highlight

This study describes the catalog of kinase gene family inSaccharum spontaneumandSorghum bicolor, providing a reservoir of molecular features and expression patterns based on RNA-Seq and co-expression networks.
When conflicts get heated, so does the planet: social-climate dynamics under inequality
Authors: Menard Jyler , Bury Thomas M. , Bauch Chris T. , Anand Madhur
Published: September 2020

Climate dynamics are inextricably linked to processes in social systems that are highly unequal. This suggests a need for coupled social-climate models that capture pervasive real-world asymmetries in the population distribution of the consequences of anthropogenic climate change and climate (in)action. Here we develop a simple social-climate model with group structure to investigate how anthropogenic climate change and population heterogeneity co-evolve. We find that greater homophily and resource inequality cause an increase in the global peak temperature anomaly by as much as 0.7°C. Also, climate change can structure human populations by driving opinion polarization. Finally, climate mitigation achieved by reducing the cost of mitigation measures paid by individuals tends to be contingent upon socio-economic conditions, whereas policies that achieve communication between different strata of society show climate mitigation benefits across a broad socio-economic regime. We conclude that advancing climate change mitigation efforts can benefit from a social-climate systems perspective.
Description, measurement, and automatic classification of thePlasmodium bergheioocyst morphology during early differentiation
Authors: Recio-Tótoro Benito , Guerrero Adán , Lanz-Mendoza Humberto
Published: September 2020

After colonization of the mosquito midgut by the malaria parasite,Plasmodiumdifferentiates from an invasive, motile ookinete to a multiplicative, sessile oocyst. Despite their importance in establishing the infection and increasing its population, the morphological transformation associated with these changes in function has been scarcely explored. Oocyst differentiation begins with the formation of a spherical protrusion near the center of the crescent-shaped ookinete. As this protuberance grows, it engulfs the content of the two distal ends, thus rounding the cell. In this work, scrutinized observations of the overall changes in shape, coupled with the migration of the malaria pigment granules and the nucleus into the protuberance, revealed that the movement of the cell content happens in an anteroposterior manner. The resulting data, formalized as morphometric measurements, led to the identification of 5 transitional stages and to the development of a computer training algorithm that automatically classifies them. Since cell differentiation has been associated with redox fluctuations, the classification algorithm was tested with parasites stained with a glutathione-specific fluorescent probe, revealing a redox modulation during differentiation.
Engineering sensitivity and specificity of AraC-based biosensors responsive to triacetic acid lactone and orsellinic acid
Authors: Wang Zhiqing , Doshi Aarti , Chowdhury Ratul , Wang Yixi , Maranas Costas D. , Cirino Patrick C.
Published: September 2020

We previously described the design of triacetic acid lactone (TAL) biosensor “AraC-TAL1”, based on the AraC regulatory protein. While useful as a tool to screen for enhanced TAL biosynthesis, this variant shows elevated background (leaky) expression, poor sensitivity, and relaxed inducer specificity, including responsiveness to orsellinic acid (OA). More sensitive biosensors specific to either TAL or OA can aid in the study and engineering of polyketide synthases that produce these and similar compounds. In this work, we employed a TetA-based dual-selection to isolate new TAL-responsive AraC variants showing reduced background expression and improved TAL sensitivity. To improve TAL specificity, OA was included as a “decoy” ligand during negative selection, resulting in isolation of a TAL biosensor that is inhibited by OA. Finally, to engineer OA-specific AraC variants, the IPRO computational framework was employed, followed by two rounds of directed evolution, resulting in a biosensor with 24-fold improved OA/TAL specificity, relative to AraC-TAL1.
Alpha fluctuations regulate the accrual of visual information to awareness
Authors: Torralba Mireia , Drew Alice , Sabaté San José Alba , Morís Fernández Luis , Soto-Faraco Salvador
Published: September 2020

Endogenous brain processes play a paramount role in shaping up perceptual phenomenology. This is illustrated by the alternations experienced by humans (and other animals) when watching perceptually ambiguous, static images. We hypothesised that endogenous alpha fluctuations in the visual cortex pace the accumulation of sensory information leading to perceptual outcomes. Here, we addressed this hypothesis using binocular rivalry combined with visual entrainment and electroencephalography in humans (64 female, 53 male). The results revealed a correlation between the individual frequency of alpha oscillations in the occipital cortex and perceptual alternation rates experienced during binocular rivalry. In subsequent experiments we show that regulating endogenous brain activity via rhythmic entrainment produced corresponding changes in perceptual alternation rate. These changes were observed only in the alpha range but not at lower entrainment frequencies, and were much reduced when using arrhythmic stimulation. Additionally, entraining at frequencies above the alpha range did not result in speeding up perceptual alternation rates. Overall, these findings support the notion that visual information is accumulated via alpha cycles to promote the emergence of conscious perceptual representations. We suggest that models of binocular rivalry incorporating posterior alpha as a pacemaker can provide an important advance in the comprehension of the dynamics of visual awareness.
Discovery of a Novel Polymer for Xeno-free, Long-term Culture of Human Pluripotent Stem Cell Expansion
Authors: Thorpe Jordan , Nasir Aishah , Burroughs Laurence , Meurs Joris , Pijuan-Galito Sara , Irvine Derek J. , Alexander Morgan R. , Denning Chris
Published: September 2020

Human pluripotent stem cells (hPSCs) can be expanded and differentiatedin vitrointo almost any adult tissue cell type, and thus have great potential as a source for cell therapies with biomedical application. In this study, a fully-defined polymer synthetic substrate is identified for hPSC culture in completely defined, xeno-free conditions. This system can overcome the cost, scalability and reproducibility limitations of current hPSC culture strategies, and facilitate large-scale production. A high-throughput, multi-generational polymer microarray platform approach was used to test over 600 unique polymers and rapidly assess hPSC-polymer interactions in combination with the fully defined xeno-free medium, Essential 8TM(E8). This study identifies as novel nanoscale phase separated blend of poly(tricyclodecane-dimethanol diacrylate) and poly(butyl acrylate) (2:1 v/v), which supports long-term expansion of hPSCs and can be readily coated onto standard cultureware. Analysis of cell-polymer interface interactions through mass spectrometry and integrin blocking studies provides novel mechanistic insight into the role of the E8 proteins in promoting integrin-mediated hPSC attachment and maintaining hPSC signaling, including ability to undergo multi-lineage differentiation. This study therefore identifies a novel substrate for long-term serial passaging of hPSCs in serum-free, commercial chemically-defined E8, which provides a promising and economic hPSC expansion platform for clinical-scale application.
Genome-scale phylogenetic analyses confirmOlpidiumas the closest living zoosporic fungus to the non-flagellated, terrestrial fungi
Authors: Chang Ying , Rochon D’Ann , Sekimoto Satoshi , Wang Yan , Chovatia Mansi , Sandor Laura , Salamov Asaf , Grigoriev Igor V. , Stajich Jason E. , Spatafora Joseph W.
Published: September 2020

The zoosporic obligate endoparasites,Olpidium, hold a pivotal position to the reconstruction of the flagellum loss in fungi, one of the key morphological transitions associated with the colonization of land by the early fungi. We generated genome and transcriptome data from non-axenic zoospores ofOlpidium bornovanusand used a metagenome approach to extract phylogenetically informative fungal markers. Our phylogenetic reconstruction strongly supportedOlpidiumas the closest zoosporic relative of the non-flagellated terrestrial fungi. Super-alignment analyses resolvedOlpidiumas sister to the non-flagellated terrestrial fungi, whereas a super-tree approach recovered different placements ofOlpidium, but without strong support. Further investigations detected little conflicting signal among the sampled markers but revealed a potential polytomy in early fungal evolution associated with the branching order amongOlpidium, Zoopagomycota and Mucoromycota. The branches defining the evolutionary relationships of these lineages were characterized by short branch lengths and low phylogenetic content and received equivocal support for alternative phylogenetic hypotheses from individual markers. These nodes were marked by important morphological innovations, including the transition to hyphal growth and the loss of flagellum, which enabled early fungi to explore new niches and resulted in rapid and temporally concurrent Precambrian diversifications of the ancestors of several phyla of fungi.