bluuebunny/crossref_metadata_2025 huggingface dataset:
InDeep : 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions
Authors: Mallet Vincent , Ruano Luis Checa , Franel Alexandra Moine , Nilges Michael , Druart Karen , Bouvier Guillaume , Sperandio Olivier
Published: July 2021

Abstract

Motivation

Protein-protein interactions (PPIs) are key elements in numerous biological pathways and the subject of a growing number of drug discovery projects including against infectious diseases. Designing drugs on PPI targets remains a difficult task and requires extensive efforts to qualify a given interaction as an eligible target. To this end, besides the evident need to determine the role of PPIs in disease-associated pathways and their experimental characterization as therapeutics targets, prediction of their capacity to be bound by other protein partners or modulated by future drugs is of primary importance.

Results

We presentInDeep, a tool for predicting functional binding sites within proteins that could either host protein epitopes or future drugs. Leveraging deep learning on a curated data set of PPIs, this tool can proceed to enhanced functional binding site predictions either on experimental structures or along molecular dynamics trajectories. The benchmark ofInDeepdemonstrates that our tool outperforms state of the art ligandable binding sites predictors when assessing PPI targets but also conventional targets. This offers new opportunities to assist drug design projects on PPIs by identifying pertinent binding pockets at or in the vicinity of PPI interfaces.

Availability

The tool is available on GitHub3along with a PyMol plugin for visualization. Predictions of InDeep can be consulted at iPPI-DB4
Calcium/Calmodulin Dependent Protein Kinase Kinase 2 Regulates the Expansion of Tumor-induced Myeloid-Derived Suppressor Cells
Authors: Huang Wei , Liu Yaping , Luz Anthony , Berrong Mark , Meyer Joel N , Zou Yujing , Swann Excel , Sundaramoorthy Pasupathi , Kang Yubin , Jauhari Shekeab , Lento William , Chao Nelson , Racioppi Luigi
Published: July 2021

Myeloid-derived suppressor cells (MDSCs) are a heterogeneous group of cells, which can suppress the immune response, promote tumor progression and impair the efficacy of immunotherapies. Consequently, the pharmacological targeting of MDSC is emerging as a new immunotherapeutic strategy to stimulate the natural anti-tumor immune response and potentiate the efficacy of immunotherapies. Herein, we leveraged genetically modified models and a small molecule inhibitor to validate Calcium-Calmodulin Kinase Kinase 2 (CaMKK2) as a druggable target to control MDSC accumulation in tumor-bearing mice. The results indicated that deletion of CaMKK2 in the host attenuated the growth of engrafted tumor cells, and this phenomenon was associated with increased antitumor T cell response and decreased accumulation of MDSC. The adoptive transfer of MDSC was sufficient to restore the ability of the tumor to grow in Camkk2-/- mice, confirming the key role of MDSC in the mechanism of tumor rejection. In vitro studies indicated that blocking of CaMKK2 is sufficient to impair the yield of MDSC. Surprisingly, MDSC generated from Camkk2-/- bone marrow cells also showed a higher ability to terminally differentiate toward more immunogenic cell types (e.g inflammatory macrophages and dendritic cells) compared to wild type (WT). Higher intracellular levels of reactive oxygen species (ROS) accumulated in Camkk2-/- MDSC, increasing their susceptibility to apoptosis and promoting their terminal differentiation toward more mature myeloid cells. Mechanistic studies indicated that AMP-activated protein kinase (AMPK), which is a known CaMKK2 proximal target controlling the oxidative stress response, fine-tunes ROS accumulation in MDSC. Accordingly, failure to activate the CaMKK2-AMPK axis can account for the elevated ROS levels in Camkk2-/- MDSC. These results highlight CaMKK2 as an important regulator of the MDSC lifecycle, identifying this kinase as a new druggable target to restrain MDSC expansion and enhance the efficacy of anti-tumor immunotherapy.
Metallothionein 3-zinc axis suppresses caspase-11 inflammasome activation and impairs antibacterial immunity
Authors: Chowdhury Debabrata , Gardner Jason C , Satpati Abhijit , Nookala Suba , Mukundan Santhosh , Porollo Aleksey , Landero Figueroa Julio A. , Vignesh Kavitha Subramanian
Published: July 2021

Non-canonical inflammasome activation by mouse caspase-11 (or human CASPASE- 4/5) is crucial for the clearance of certain gram-negative bacterial infections, but can lead to severe inflammatory damage. Factors that promote non-canonical inflammasome activation are well recognized, but less is known about the mechanisms underlying its negative regulation. Herein, we identify that the caspase-11 inflammasome in mouse and human macrophages (Mϕ) is negatively controlled by the zinc (Zn2+) regulating protein, metallothionein 3 (MT3). Upon challenge with intracellular lipopolysaccharide (iLPS), Mϕ increased MT3 expression that curtailed the activation of caspase-11 and its downstream targets caspase-1 and interleukin (IL)-1β. Mechanistically, MT3 increased intramacrophage Zn2+ to downmodulate the TRIF-IRF3-STAT1 axis that is prerequisite for caspase-11 effector function. MT3 suppressed activation of the caspase-11 inflammasome, while caspase-11 and MT3 synergized in impairing antibacterial immunity. The present study identifies an important yin-yang relationship between the non-canonical inflammasome and MT3 in controlling inflammation and immunity to gram- negative bacteria.

GRAPHICAL ABSTRACT
Single voxel autocorrelation uncovers gradients of temporal dynamics in the hippocampus and entorhinal cortex during rest and navigation
Authors: Bouffard Nichole R. , Golestani Ali , Brunec Iva K. , Bellana Buddhika , Park Jun Young , Barense Morgan D. , Moscovitch Morris
Published: July 2021

During navigation, information at multiple scales needs to be integrated. Single- unit recordings in rodents suggest that gradients of temporal dynamics in the hippocampus and entorhinal cortex support this integration. In humans, gradients of representation are observed, such that granularity of information represented increases along the long axis of the hippocampus. The neural underpinnings of this gradient in humans, however, are still unknown. Current research is limited by coarse fMRI analysis techniques that obscure the activity of individual voxels, preventing investigation of how moment-to-moment changes in brain signal are organized and how they are related to behavior. Here, we measured the signal stability of single voxels over time to uncover previously unappreciated gradients of temporal dynamics in the hippocampus and entorhinal cortex. Using our novel, single voxel autocorrelation technique, we show a medial-lateral hippocampal gradient, as well as a continuous autocorrelation gradient along the anterolateral- posteromedial entorhinal extent. Importantly, we show that autocorrelation in the anterior-medial hippocampus was modulated by navigational difficulty, providing the first evidence that changes in signal stability in single voxels are relevant for behavior. This work opens the door for future research on how temporal gradients within these structures support the integration of information for goal- directed behavior.
The universal language network: A cross-linguistic investigation spanning 45 languages and 12 language families
Authors: Malik-Moraleda Saima , Ayyash Dima , Gallée Jeanne , Affourtit Josef , Hoffmann Malte , Mineroff Zachary , Jouravlev Olessia , Fedorenko Evelina
Published: July 2021

To understand the architecture of human language, it is critical to examine diverse languages; yet most cognitive neuroscience research has focused on a handful of primarily Indo-European languages. Here, we report an investigation of the fronto-temporo-parietal language network across 45 languages and establish the robustness to cross-linguistic variation of its topography and key functional properties, including left-lateralization, strong functional integration among its brain regions, and functional selectivity for language processing.
Selective Requirement for Polycomb Repressor Complex 2 in the Generation of Specific Hypothalamic Neuronal Sub-types
Authors: Salmani Behzad Yaghmaeian , Balderson Brad , Bauer Susanne , Ekman Helen , Starkenberg Annika , Perlmann Thomas , Piper Michael , Bodén Mikael , Thor Stefan
Published: July 2021

The hypothalamus displays staggering cellular diversity, chiefly established during embryogenesis by the interplay of several signalling pathways and a battery of transcription factors. However, the contribution of epigenetic cues to hypothalamus development remains unclear. We mutated the Polycomb Repressor Complex 2 gene Eed in the developing mouse hypothalamus, which resulted in the loss of H3K27me3; a fundamental epigenetic repressor mark. This triggered ectopic expression of posteriorly expressed regulators (e.g., Hox homeotic genes), upregulation of cell cycle inhibitors and reduced proliferation. Surprisingly, despite these effects, single cell transcriptomic analysis revealed that the majority of neuronal subtypes were still generated in Eed mutants. However, we observed an increase in Glutamatergic/GABAergic double-positive cells, as well as loss/reduction of dopamine, Hypocretin/Orexin and Tac2 neurons. These findings indicate that many aspects of the hypothalamic gene regulatory flow can proceed without the key H3K27me3 epigenetic repressor mark, and points to a unique sensitivity of particular neuronal sub-types to a disrupted epigenomic landscape.
Reward Enhances Connectivity between the Ventral Striatum and the Default Mode Network
Authors: Dobryakova Ekaterina , Smith David V.
Published: July 2021

The default mode network (DMN) has been theorized to participate in a range of social, cognitive, and affective functions. Yet, previous accounts do not consider how the DMN contributes to other brain regions depending on psychological context, thus rendering our understanding of DMN function incomplete. We addressed this gap by applying a novel network-based psychophysiological interaction (nPPI) analysis to the reward task within the Human Connectome Project. We first focused on the task-evoked responses of the DMN and other networks involving the prefrontal cortex, including the executive control network (salience network) and the left and right frontoparietal networks. Consistent with a host of prior studies, the DMN exhibited a relative decrease in activation during the task, while the other networks exhibited a relative increase during the task. Next, we used nPPI analyses to assess whether these networks exhibit task-dependent changes in connectivity with other brain regions. Strikingly, we found that the experience of reward enhances task-dependent connectivity between the DMN and the ventral striatum, an effect that was specific to the DMN. Surprisingly, the strength of DMN-VS connectivity was correlated with personality characteristics relating to openness. Taken together, these results advance models of DMN by demonstrating how it contributes to other brain systems during task performance and how those contributions relate to individual differences.
The neuropeptide Pth2 modulates social behavior and anxiety in zebrafish
Authors: Anneser Lukas , Gemmer Anja , Eilers Tim , Alcantara Ivan C. , Loos Anett-Yvonn , Ryu Soojin , Schuman Erin M.
Published: July 2021

Animal behavior is strongly context-dependent and behavioral performance is often modulated by internal state. In particular, different social contexts can alter anxiety levels and modulate social behavior. The vertebrate-specific neuropeptide parathyroid hormone 2 (pth2) is directly regulated by the presence or absence of conspecifics in zebrafish. As its cognate receptor, the parathyroid hormone 2 receptor (pth2r), is widely expressed across the brain, we tested fish lacking the functional Pth2 peptide in several anxiety-related and social paradigms. Rodents lacking PTH2 display increased anxiety-related behavior. Here we show that the propensity to react to sudden stimuli with an escape response is increased in pth2-/- zebrafish, consistent with elevated anxiety. While overall social preference for conspecifics is maintained in pth2-/- fish until the early juvenile stage, we found that both social preference and shoaling are altered later in development. The data presented suggest that the neuropeptide Pth2 modulates several conserved behavioral features, and may thus enable the animal to react appropriately in different social contexts.
Annexin A1 is a polarity cue that directs planar mitotic spindle orientation during mammalian epithelial morphogenesis
Authors: Fankhaenel Maria , Hashemi Farahnaz Sadat Golestan , Mourao Larissa , Lucas Emily , Hosawi Manal Mosa , Skipp Paul , Morin Xavier , Scheele Colinda L.G.J. , Elias Salah
Published: July 2021

Oriented cell divisions are critical for the formation and maintenance of structured epithelia. Proper mitotic spindle orientation relies on polarised anchoring of force generators to the cell cortex by the evolutionarily conserved Gαi-LGN-NuMA complex. However, the polarity cues that control cortical patterning of this ternary complex remain largely unknown in mammalian epithelia. Here we identify the membrane-associated protein Annexin A1 (ANXA1) as a novel interactor of LGN in mammary epithelial cells. ANXA1 acts independently of Gαito instruct the accumulation of LGN and NuMA at the lateral cortex to ensure cortical anchoring of Dynein-Dynactin and astral microtubules and thereby planar alignment of the mitotic spindle. Loss of ANXA1 randomises mitotic spindle orientation, which in turn disrupts epithelial architecture and luminogenesis in three-dimensional cultures of primary mammary epithelial cells. Our findings establish ANXA1 as an upstream cortical cue that regulates LGN to direct planar cell divisions during mammalian epithelial morphogenesis.
Patient-specific Boolean models of signaling networks guide personalized treatments
Authors: Montagud Arnau , Béal Jonas , Tobalina Luis , Traynard Pauline , Subramanian Vigneshwari , Szalai Bence , Alföldi Róbert , Puskás László , Valencia Alfonso , Barillot Emmanuel , Saez-Rodriguez Julio , Calzone Laurence
Published: July 2021

Prostate cancer is the second most occurring cancer in men worldwide. To better understand the mechanisms of tumorigenesis and possible treatment responses, we developed a mathematical model of prostate cancer which considers the major signalling pathways known to be deregulated.

We personalised this Boolean model to molecular data to reflect the heterogeneity and specific response to perturbations of cancer patients. 488 prostate samples were used to build patient-specific models and compared to available clinical data. Additionally, eight prostate cell-line-specific models were built to validate our approach with dose-response data of several drugs.

The effects of single and combined drugs were tested in these models under different growth conditions. We identified 15 actionable points of interventions in one cell-line-specific model whose inactivation hinders tumorigenesis. To validate these results, we tested nine small molecule inhibitors of five of those putative targets and found a dose-dependent effect on four of them, notably those targeting HSP90 and PI3K. These results highlight the predictive power of our personalized Boolean models and illustrate how they can be used for precision oncology.
A repurposed, non-canonical cytochrome c, chaperones calcium binding by PilY1 for type IVa pili formation
Authors: Herfurth Marco , Treuner-Lange Anke , Glatter Timo , Wittmaack Nadine , Hoiczyk Egbert , Pierik Antonio J. , Søgaard-Andersen Lotte
Published: July 2021

Type IVa pili (T4aP) are versatile bacterial cell surface structures that undergo extension/adhesion/retraction cycles powered by the cell envelope-spanning T4aP machine. In this machine, a complex composed of four minor pilins and PilY1 primes T4aP extension and is also present at the pilus tip mediating adhesion. Similar to many other bacteria, Myxococcus xanthus contains multiple minor pilins/PilY1 sets that are incompletely understood. Here, we report that minor pilins and PilY1 (PilY1.1) of cluster_1 form priming and tip complexes contingent on a non-canonical cytochrome c (TfcP) with an unusual His/Cys heme ligation and calcium. We provide evidence that TfcP is unlikely to participate in electron transport and has been repurposed to promote calcium binding by PilY1.1 at low calcium concentrations, thereby stabilising PilY1.1 and enabling T4aP function in a broader range of calcium concentrations. These results identify a novel function of cytochromes c and illustrate how incorporating an accessory factor expands the environmental range under which the T4aP system functions.
Perception of structurally distinct effectors by the integrated WRKY domain of a plant immune receptor
Authors: Mukhi N , Brown H , Gorenkin D , Ding P , Bentham AR , Jones JDG , Banfield MJ
Published: July 2021

Plants use intracellular immune receptors (NLRs) to detect pathogen-derived effector proteins. The Arabidopsis NLR pair RRS1-R/RPS4 confers disease resistance to different bacterial pathogens by perceiving structurally distinct effectors AvrRps4 from Pseudomonas syringae pv. pisi and PopP2 from Ralstonia solanacearum via an integrated WRKY domain in RRS1-R. How the WRKY domain of RRS1 (RRS1WRKY) perceives distinct classes of effector to initiate an immune response is unknown. We report here the crystal structure of the in planta processed C-terminal domain of AvrRps4 (AvrRps4C) in complex with RRS1WRKY. Perception of AvrRps4C by RRS1WRKY is mediated by the β2-β3 segment of RRS1WRKY that binds an electronegative patch on the surface of AvrRps4C. Structure-based mutations that disrupt AvrRps4C/RRS1WRKY interactions in vitro compromise RRS1/RPS4-dependent immune responses. We also show that AvrRps4C can associate with the WRKY domain of the related but distinct RRS1B/RPS4B NLR pair, and the DNA binding domain of AtWRKY41, with similar binding affinities. This work demonstrates how integrated domains in plant NLRs can directly bind structurally distinct effectors to initiate immunity.

Significance

This study reveals a mechanism of effector recognition by a plant NLR immune receptor that carries an integrated domain (ID) which mimics an authentic pathogen effector target. An Arabidopsis immune receptor carrying RRS1 and RPS4 NLR proteins detects the Pseudomonas syringae pv. pisi secreted effector AvrRps4 via a WRKY ID in RRS1. We used structural biology to reveal the mechanisms of AvrRps4/WRKY interaction and demonstrated that this binding is essential for effector recognition in planta. Our analysis revealed distinctive features of the WRKY ID that mediate the recognition of structurally distinct effectors from different bacterial pathogens. These insights could enable engineering NLRs with novel recognition specificities, and enhances our understanding of how effectors interact with host proteins.
Chromatin Patterns Distinguish Breast Tumor Subtypes and Disease Progression in Association withANP32Elevels
Authors: Ruff Garrett L. , Murphy Kristin E. , Vertino Paula M. , Murphy Patrick J.
Published: July 2021

Despite highly advanced diagnosis and treatment strategies, breast cancer patient outcomes vary extensively, even among individuals with the same diagnosis. Thus, a better understanding of the unique molecular characteristics that underlie tumor trajectories and responses to therapy remains a central goal. We report that chromatin patterns represent an important characteristic, capable of stratifying tumor identity and progression. We find that patterns of chromatin accessibility can be classified into 3 major groups, representing Basal-like tumors, hormone receptor (HR)-expressing tumors, and invasive lobular Luminal-A tumors. Major chromatin differences occur throughout the genome at motifs for the transcription factor FOXA1 in HR-positive tumors, and motifs for SOX9 in Basal-like tumors. A large portion of lobular Luminal-A tumors display a chromatin signature defined by accessibility at FOXA1 binding motifs, distinguishing them from others within this subtype. Expression of the histone chaperoneANP32Eis inversely correlated with tumor progression and chromatin accessibility at FOXA1 binding sites. Tumors with high levels of ANP32E exhibit an immune response and proliferative gene expression signature, whereas tumors with low ANP32E levels appear programmed for differentiation. Our results indicate that ANP32E may function through chromatin state regulation to control breast cancer differentiation and tumor plasticity.
In situ cryo-electron tomography reveals local cellular machineries for axon branch development
Authors: Nedozralova Hana , Basnet Nirakar , Ibiricu Iosune , Bodakuntla Satish , Biertümpfel Christian , Mizuno Naoko
Published: July 2021

Neurons are highly polarized cells forming an intricate network of dendrites and axons. They are shaped by the dynamic reorganization of cytoskeleton components and cellular organelles. Axon branching allows to form new paths and increases circuit complexity. However, our understanding of branch formation is sparse due to technical limitations. Using in situ cellular cryo-electron tomography on primary mouse neurons, we directly visualized the remodeling of organelles and cytoskeleton structures at axon branches. Strikingly, branched areas functioned as hotspots concentrating organelles to support dynamic activities. Unaligned actin filaments assembled at the base of premature branches and remained while filopodia diminished. Microtubules and ER co-migrated into preformed branches to support outgrowth together with accumulating compact ~500 nm mitochondria and locally clustered ribosomes. We obtained a roadmap of events and present the first direct evidence of local protein synthesis selectively taking place at axon branches, allowing to serve as unique control hubs for axon development and downstream neural network formation.
Developmental coupling of cerebral blood flow and fMRI fluctuations in youth
Authors: Baller Erica B. , Valcarcel Alessandra M. , Adebimpe Azeez , Alexander-Bloch Aaron , Cui Zaixu , Gur Ruben C. , Gur Raquel E. , Larsen Bart L. , Linn Kristin A. , O’Donnell Carly M. , Pines Adam R. , Raznahan Armin , Roalf David. R. , Sydnor Valerie J. , Tapera Tinashe M. , Dylan Tisdall M. , Vandekar Simon , Xia Cedric H. , Detre John A. , Shinohara Russell T. , Satterthwaite Theodore D.
Published: July 2021

To support brain development during youth, the brain must balance energy delivery and consumption. Previous studies in adults have demonstrated high coupling between cerebral blood flow and brain function as measured using functional neuroimaging, but how this relationship evolves over adolescence is unknown. To address this gap, we studied a sample of 831 children and adolescents (478 females, ages 8-22) from the Philadelphia Neurodevelopmental Cohort who were scanned at 3T with both arterial spin labeled (ASL) MRI and resting-state functional MRI (fMRI). Local coupling between cerebral blood flow (CBF, from ASL) and the amplitude of low frequency fluctuations (ALFF, from fMRI) was first quantified using locally weighted regressions on the cortical surface. We then used generalized additive models to evaluate how CBF-ALFF coupling was associated with age, sex, and executive function. Enrichment of effects within canonical functional networks was evaluated using spin-based permutation tests. Our analyses revealed tight CBF-ALFF coupling across the brain. Whole-brain CBF-ALFF coupling decreased with age, largely driven by coupling decreases in the inferior frontal cortex, precuneus, visual cortex, and temporoparietal cortex (pfdr <0.05). Females had stronger coupling in the frontoparietal network than males (pfdr <0.05). Better executive function was associated with decreased coupling in the somatomotor network (pfdr <0.05). Overall, we found that CBF-ALFF coupling evolves in development, differs by sex, and is associated with individual differences in executive function. Future studies will investigate relationships between maturational changes in CBF-ALFF coupling and the presence of psychiatric symptoms in youth.

SIGNIFICANCE

The functions of the human brain are metabolically expensive and reliant on coupling between cerebral blood flow and neural activity. Previous neuroimaging studies in adults demonstrate tight physiology-function coupling, but how this coupling evolves over development is unknown. Here, we examine the relationship between blood flow as measured by arterial spin labeling and the amplitude of low frequency fluctuations from resting-state magnetic resonance imaging across a large sample of youth. We demonstrate regionally specific changes in coupling over age and show that variations in coupling are related to biological sex and executive function. Our results highlight the importance of CBF-ALFF coupling throughout development; we discuss its potential as a future target for the study of neuropsychiatric diseases.
Transgenic expression of Nix converts genetic females into males and allows automated sex sorting in Aedes albopictus
Authors: Lutrat Célia , Olmo Roenick P. , Baldet Thierry , Bouyer Jérémy , Marois Eric
Published: July 2021

Aedes albopictus is a major vector of arboviruses. Better understanding of its sex determination is crucial for developing mosquito control tools, especially genetic sexing strains. In Aedes aegypti, Nix is the primary gene responsible for masculinization and Nix-expressing genetic females develop into fertile, albeit flightless, males. In Ae. albopictus, Nix has also been implicated in masculinization but its role remains to be further characterized.

In this work, we established Ae. albopictus transgenic lines ectopically expressing Nix. Several were composed exclusively of genetic females, with transgenic individuals being phenotypic and functional males due to the expression of the Nix transgene. Their reproductive fitness was marginally impaired, while their flight performance was similar to controls. Overall, our results show that Nix is sufficient for full masculinization in Ae. albopictus. Moreover, the transgene construct contains a fluorescence marker allowing efficient automated sex sorting. Consequently, such strains constitute valuable sexing strains for genetic control.
Pharmacokinetics and biodistribution of extracellular vesicles administered intravenously and intranasally to Macaca nemestrina
Authors: Driedonks Tom , Jiang Linglei , Carlson Bess , Han Zheng , Liu Guanshu , Queen Suzanne E. , Shirk Erin N. , Gololobova Olesia , Nyberg Lyle H. , Lima Gabriela , Paniushkina Liliia , Garcia-Contreras Marta , Schonvisky Kayla , Castell Natalie , Stover Mitchel , Guerrero-Martin Selena , Richardson Riley , Smith Barbara , Mahairaki Vasiliki , Lai Charles P. , Izzi Jessica M. , Hutchinson Eric K. , Pate Kelly A.M. , Witwer Kenneth W.
Published: July 2021

Extracellular vesicles (EVs) have great potential as novel drug carriers for the treatment of various diseases. These lipid bilayer vesicles are naturally abundant in mammalian tissues and circulation, can be loaded with therapeutic small molecule drugs, (si)RNA, proteins and CRISPR/Cas9, and may be engineered for retention by specific tissues. However, many questions remain on the optimal dosing, administration route, and pharmacokinetics of EVs. Previous studies have addressed biodistribution and pharmacokinetics in rodents, but little evidence is available from larger animals. Here, we investigated the pharmacokinetics and biodistribution of Expi293F-derived EVs labelled with a highly sensitive nanoluciferase reporter (palmGRET) in a non-human primate model (Macaca nemestrina), comparing intravenous (IV) and intranasal (IN) administration over a 125-fold dose range. We report that EVs administered IV had markedly longer circulation times in plasma than previously reported in mice, and were detectable in cerebrospinal fluid (CSF) after 30-60 minutes. Already after one minute following IV administration, we observed EV uptake by PBMCs, most notably B-cells. EVs were detected in liver and spleen within one hour of IV administration. None of the IN doses resulted in readily detectable EV levels in plasma, CSF, or organs, suggesting that IN delivery of EVs in large animals including humans may require reconsideration or pretreatment approaches. Furthermore, EV circulation times strongly decreased after repeated IV administration, possibly due to immune responses and with clear implications for xenogeneic EV-based therapeutics. We hope that our findings from this baseline study in macaques will help to inform future research and therapeutic development of EVs.
Keratin 19 interacts with GSK3β to regulate its nuclear accumulation and degradation of cyclin D3
Authors: Sharma Pooja , Tiufekchiev Sarah , Lising Victoria , Chung Seung Woo , Suk Jung Soo , Chung Byung Min
Published: July 2021

Cyclin D3 regulates the G1/S transition and is frequently overexpressed in several cancer types including breast cancer, where it promotes tumor progression. Here, we show that a cytoskeletal protein keratin 19 (K19) physically interacts with a serine/threonine kinase GSK3β and prevents GSK3β-dependent degradation of cyclin D3. The absence of K19 allowed active GSK3β to accumulate in the nucleus and degrade cyclin D3. Specifically, the head domain of K19 was required to sustain inhibitory phosphorylation of GSK3β Ser9, prevent nuclear accumulation of GSK3β, and maintain cyclin D3 levels and cell proliferation. K19 was found to interact with GSK3β and K19-GSK3β interaction was mapped out to require Ser10 and Ser35 residues on the head domain of K19. Unlike wildtype K19, S10A and S35A mutants failed to maintain total and nuclear cyclin D3 levels and induce cell proliferation. Finally, we show that the K19-GSK3β-cyclin D3 pathway affected sensitivity of cells towards inhibitors to cyclin dependent kinase 4 and 6 (CDK4/6). Overall, these findings establish a role for K19 in the regulation of GSK3β-cyclin D3 pathway and demonstrate a potential strategy for overcoming resistance to CDK4/6 inhibitors.
Prediction of DNA from context using neural networks
Authors: Grønbæk Christian , Liang Yuhu , Elliott Desmond , Krogh Anders
Published: July 2021

One way to better understand the structure in DNA is by learning to predict the sequence. Here, we train a model to predict the missing base at any given position, given its left and right flanking contexts.

Our best-performing model is a neural network that obtains an accuracy close to 54% on the human genome, which is 2% points better than modelling the data using a Markov model. In likelihood-ratio tests, we show that the neural network is significantly better than any of the alternative models by a large margin. We report on where the accuracy is obtained, observing first that the performance appears to be uniform over the chromosomes. The models perform best in repetitive sequences, as expected, although they are far from random performance in the more difficult coding sections, the proportions being ~ 70:40%. Exploring further the sources of the accuracy, Fourier transforming the predictions reveals weak but clear periodic signals. In the human genome the characteristic periods hint at connections to nucleosome positioning. To understand this we find similar periodic signals in GC/AT content in the human genome, which to the best of our knowledge have not been reported before.

On other large genomes similarly high accuracy is found, while lower predictive accuracy is observed on smaller genomes. Only in mouse did we see periodic signals in the same range as in human, though weaker and of different type. Interestingly, applying a model trained on the mouse genome to the human genome results in a performance far below that of the human model, except in the difficult coding regions.

Despite the clear outcomes of the likelihood ratio tests, there is currently a limited superiority of the neural network methods over the Markov model. We expect, however, that there is great potential for better modelling DNA using different neural network architectures.
Mitochondria dysfunction in Charcot Marie Tooth 2B Peripheral Sensory Neuropathy
Authors: Gu Yingli , Guerra Flora , Hu Mingzheng , Pope Alexander , Sung Kijung , Yang Wanlin , Jetha Simone , Shoff Thomas A. , Gunatilake Tessanya , Dahlkamp Owen , Shi Linda Zhixia , Manganelli Fiore , Nolano Maria , Zhou Yue , Ding Jianqing , Bucci Cecilia , Wu Chengbiao
Published: July 2021

Recent evidence has uncovered an important role of Rab7 in regulating mitochondrial morphology and function. Missense mutation(s) of Rab7 underlies the pathogenesis of Charcot Marie Tooth 2B (CMT2B) peripheral neuropathy. Herein, we investigated how mitochondrial morphology and function were impacted by the CMT2B associated Rab7V162M mutation in fibroblasts from human CMT2B patients as well as in a knockin mouse model. In contrast to recently published results from studies of using heterologous overexpression systems, our results have demonstrated significant mitochondrial fragmentation in fibroblasts of both human CMT2B patients and CMT2B mouse embryonic fibroblasts (MEFs). Furthermore, we have shown that mitochondria were fragmented and axonal mitochondrial movement was dysregulated in primary cultured E18 dorsal root ganglion (DRG) sensory neurons, but not in E18 hippocampal and cortical primary neurons. We also show that inhibitors to either the mitochondrial fission protein Drp1 or to the nucleotide binding to Rab7 normalized the mitochondrial deficits in both MEFs and E18 cultured DRG neurons. Our study has revealed, for the first time, that expression of CMT2B Rab7 mutation at physiological level enhances Drp1 activity to promote mitochondrial fission, that may potentially underlie selective vulnerability of peripheral sensory neurons in CMT2B pathogenesis.
Full-length, single-cell RNA-sequencing of human bone marrow subpopulations reveals hidden complexity
Authors: Schmidt Marcel O. , Mays Anne Deslattes , Barefoot Megan E. , Riegel Anna T. , Wellstein Anton
Published: July 2021

Bone marrow progenitor cell differentiation has frequently been used as a model for studying cellular plasticity and cell-fate decisions. Recent analysis at the level of single-cells has expanded knowledge of the transcriptional landscape of human hematopoietic cell lineages. Using single-molecule real-time (SMRT) full-length RNA sequencing, we have previously shown that human bone marrow lineage-negative (Lin-neg) cell populations contain a surprisingly diverse set of mRNA isoforms. Here, we report from single cell, full-length RNA sequencing that this diversity is also reflected at the single-cell level. From fresh human bone marrow unselected and lineage-negative progenitor cells were isolated by droplet-based single-cell selection (10xGenomics). The single cell-derived mRNAs were analyzed by full-length SMRT and short-read sequencing. In both samples we detected an average of 8000 different genes using short-read sequencing. Differential expression analysis arranged the single-cells of the total bone marrow into only four clusters whereas the Lin-neg population was much more diverse with nine clusters. mRNA isoform analysis of the single-cell populations using full-length sequencing revealed that Lin-neg cells contain on average 24% more novel splice variants than the total bone marrow cells. Interestingly, among the most frequent genes expressing novel isoforms were members of the spliceosome, e.g. HNRNPs, DEAD box helicases and SRSFs. Mapping the isoforms from all genes to the cell type clusters revealed that total bone marrow cells express novel isoforms only in a small subset of clusters. On the other hand, lineage-negative progenitor cells expressing novel isoforms were present in nearly all subpopulations. In conclusion, on a single-cell level lineage-negative cells express a higher diversity of genes and more alternatively spliced novel isoforms suggesting that cells in this subpopulation are poised for different fates.

Graphical abstract
Machine learning uncovers a data-driven transcriptional regulatory network for the Crenarchaeal thermoacidophile Sulfolobus acidocaldarius
Authors: Chauhan Siddharth M. , Poudel Saugat , Rychel Kevin , Lamoureux Cameron , Yoo Reo , Bulushi Tahani Al , Yuan Yuan , Palsson Bernhard O. , Sastry Anand V.
Published: July 2021

Dynamic cellular responses to environmental constraints are coordinated by the transcriptional regulatory network (TRN), which modulates gene expression. This network controls most fundamental cellular responses, including metabolism, motility, and stress responses. Here, we apply independent component analysis, an unsupervised machine learning approach, to 95 high-quality Sulfolobus acidocaldarius RNA-seq datasets and extract 45 independently modulated gene sets, or iModulons. Together, these iModulons contain 755 genes (32% of the genes identified on the genome) and explain over 70% of the variance in the expression compendium. We show that 5 modules represent the effects of known transcriptional regulators, and hypothesize that most of the remaining modules represent the effects of uncharacterized regulators. Further analysis of these gene sets results in: (1) the prediction of a DNA export system composed of 5 uncharacterized genes, (2) expansion of the LysM regulon, and (3) evidence for an as-yet-undiscovered global regulon. Our approach allows for a mechanistic, systems-level elucidation of an extremophile’s responses to biological perturbations, which could inform research on gene-regulator interactions and facilitate regulator discovery in S. acidocaldarius. We also provide the first global TRN for S. acidocaldarius. Collectively, these results provide a roadmap towards regulatory network discovery in archaea.
Using Bayesian Inference to Estimate Plausible Muscle Forces in Musculoskeletal Models
Authors: Johnson Russell T. , Lakeland Daniel , Finley James M.
Published: July 2021

Background

Musculoskeletal modeling is currently a preferred method for estimating the muscle forces that underlie observed movements. However, these estimates are sensitive to a variety of assumptions and uncertainties, which creates difficulty when trying to interpret the muscle forces from musculoskeletal simulations. Here, we describe an approach that uses Bayesian inference to identify plausible ranges of muscle forces for a simple motion while representing uncertainty in the measurement of the motion and the objective function used to solve the muscle redundancy problem.

Methods

We generated a reference elbow flexion-extension motion by simulating a set of muscle excitation signals derived from the computed muscle control tool built into OpenSim. We then used a Markov Chain Monte Carlo (MCMC) algorithm to sample from a posterior probability distribution of muscle excitations that would result in the reference elbow motion trajectory. We constructed a prior over the excitation parameters which down-weighted regions of the parameter space with greater muscle excitations. We used muscle excitations to find the corresponding kinematics using OpenSim, where the error in position and velocity trajectories (likelihood function) was combined with the sum of the cubed muscle excitations integrated over time (prior function) to compute the posterior probability density.

Results

We evaluated the muscle forces that resulted from the set of excitations that were visited in the MCMC chain (five parallel chains, 450,000 iterations per chain, runtime = 71 hours). The estimated muscle forces compared favorably with the reference motion from computed muscle control, while the elbow angle and velocity from MCMC matched closely with the reference with an average RMSE for angle and velocity equal to 0.008° and 0.18°/s, respectively. However, our rank plot analysis and potential scale reduction statistics, which we used to evaluate convergence of the algorithm, indicated that the parallel chains did not fully mix.

Conclusions

While the results from this process are a promising step towards characterizing uncertainty in muscle force estimation, the computational time required to search the solution space with, and the lack of MCMC convergence indicates that further developments in MCMC algorithms are necessary for this process to become feasible for larger-scale models.
High-resolution protein fragment interactions using AVA-Seq on a human reference set
Authors: Schaefer-Ramadan Stephanie , Aleksic Jovana , Al-Thani Nayra M. , Mohamoud Yasmin A. , Hill David E. , Malek Joel A.
Published: July 2021

Protein-protein interactions (PPIs) are important in understanding numerous aspects of protein function. Here, the recently developed all-vs-all sequencing (AVA-Seq) approach to determine protein-protein interactions was tested on a gold-standard human protein interaction set (hsPRS-v2). Initially, these data were interpreted strictly from a binary PPI perspective to compare AVA-Seq to other binary PPI methods tested on the same hsPRS-v2. AVA-Seq recovered 20 of 47 (43%) binary PPIs from this reference set comparing favorably with other methods. The same experimental data allowed for the determination of >500 known and novel PPIs including interactions between wildtype fragments of tumor protein p53 and minichromosomal maintenance complex proteins 2, and 5 (MCM2 and MCM5) that could be of interest in human disease. Additional results gave a better understanding of why interactions might be missed using AVA-Seq and aide future PPI experimental design for maximum recovery of information.
SUITOR: selecting the number of mutational signatures through cross-validation
Authors: Lee Donghyuk , Wang Difei , Yang Xiaohong R. , Shi Jianxin , Landi Maria Teresa , Zhu Bin
Published: July 2021

For de novo mutational signature analysis, the critical first step is to decide how many signatures should be expected in a cancer genomics study. An incorrect number could mislead downstream analyses. Here we present SUITOR (Selecting the nUmber of mutatIonal signaTures thrOugh cRoss-validation), an unsupervised cross-validation method that requires little assumptions and no numerical approximations to select the optimal number of signatures without overfitting the data. In vitro studies and in silico simulations demonstrated that SUITOR can correctly identify signatures, some of which were missed by other widely used methods. Applied to 2,540 whole-genome sequenced tumors across 22 cancer types, SUITOR selected signatures with the smallest prediction errors and almost all signatures of breast cancer selected by SUITOR were validated in an independent breast cancer study. SUITOR is a powerful tool to select the optimal number of mutational signatures, facilitating downstream analyses with etiological or therapeutic importance.
SARS-CoV-2 exposure in wild white-tailed deer (Odocoileus virginianus)
Authors: Chandler Jeffrey C. , Bevins Sarah N. , Ellis Jeremy W. , Linder Timothy J. , Tell Rachel M. , Jenkins-Moore Melinda , Root J. Jeffrey , Lenoch Julianna B. , Robbe-Austerman Suelee , DeLiberto Thomas J. , Gidlewski Thomas , Torchetti Mia K. , Shriner Susan A.
Published: July 2021

Widespread human SARS-CoV-2 infections combined with human-wildlife interactions create the potential for reverse zoonosis from humans to wildlife. We targeted white-tailed deer (Odocoileus virginianus) for serosurveillance based on evidence these deer have ACE2 receptors with high affinity for SARS-CoV-2, are permissive to infection, exhibit sustained viral shedding, can transmit to conspecifics, and can be abundant near urban centers. We evaluated 624 pre- and post-pandemic serum samples from wild deer from four U.S. states for SARS-CoV-2 exposure. Antibodies were detected in 152 samples (40%) from 2021 using a surrogate virus neutralization test. A subset of samples was tested using a SARS-CoV-2 virus neutralization test with high concordance between tests. These data suggest white-tailed deer in the populations assessed have been exposed to SARS-CoV-2.

One-Sentence Summary

Antibodies to SARS-CoV-2 were detected in 40% of wild white-tailed deer sampled from four U.S. states in 2021.
In-plane crystalline anisotropy of bulk β-Ga2O3
Authors: Ma Xiaocui , Xu Rui , Xu Jianfang , Ying Leiying , Mei Yang , Long Hao , Zhang Baoping
Published: July 2021

The anisotropy of X-ray diffraction scanning of (201) β-Ga2O3 bulk material has been investigated. Symmetric rocking curves (RCs) exhibit distinctly different broadening along different azimuths, with a maximum along [102] and a minimum along a direction rotated by 30° from [010]. Williamson–Hall analysis was applied to study possible factors causing the broadening in these RCs, including instrumental factors, mosaic tilt and coherent scattering. It was found that the RC broadening is determined by both isotropic mosaic tilt and anisotropy in the length over which the crystal structure is not disrupted by limiting factors such as grain boundaries or stacking faults, which we term the `lateral limited size'. In this case, the lateral limited size is governed by {200} stacking faults along the [102] direction and grain boundaries along the [010] direction. The result presents a new anisotropy characteristic of (201) β-Ga2O3.
The three-dimensional structure of Drosophila melanogaster (6–4) photolyase at room temperature
Authors: Cellini Andrea , Yuan Wahlgren Weixiao , Henry Léocadie , Pandey Suraj , Ghosh Swagatha , Castillon Leticia , Claesson Elin , Takala Heikki , Kübel Joachim , Nimmrich Amke , Kuznetsova Valentyna , Nango Eriko , Iwata So , Owada Shigeki , Stojković Emina A. , Schmidt Marius , Ihalainen Janne A. , Westenhoff Sebastian
Published: July 2021

(6–4) photolyases are flavoproteins that belong to the photolyase/cryptochrome family. Their function is to repair DNA lesions using visible light. Here, crystal structures of Drosophila melanogaster (6–4) photolyase [Dm(6–4)photolyase] at room and cryogenic temperatures are reported. The room-temperature structure was solved to 2.27 Å resolution and was obtained by serial femtosecond crystallography (SFX) using an X-ray free-electron laser. The crystallization and preparation conditions are also reported. The cryogenic structure was solved to 1.79 Å resolution using conventional X-ray crystallography. The structures agree with each other, indicating that the structural information obtained from crystallography at cryogenic temperature also applies at room temperature. Furthermore, UV–Vis absorption spectroscopy confirms that Dm(6–4)photolyase is photoactive in the crystals, giving a green light to time-resolved SFX studies on the protein, which can reveal the structural mechanism of the photoactivated protein in DNA repair.
Protein structure prediction by AlphaFold2: are attention and symmetries all you need?
Authors: Bouatta Nazim , Sorger Peter , AlQuraishi Mohammed
Published: July 2021

The functions of most proteins result from their 3D structures, but determining their structures experimentally remains a challenge, despite steady advances in crystallography, NMR and single-particle cryoEM. Computationally predicting the structure of a protein from its primary sequence has long been a grand challenge in bioinformatics, intimately connected with understanding protein chemistry and dynamics. Recent advances in deep learning, combined with the availability of genomic data for inferring co-evolutionary patterns, provide a new approach to protein structure prediction that is complementary to longstanding physics-based approaches. The outstanding performance of AlphaFold2 in the recent Critical Assessment of protein Structure Prediction (CASP14) experiment demonstrates the remarkable power of deep learning in structure prediction. In this perspective, we focus on the key features of AlphaFold2, including its use of (i) attention mechanisms and Transformers to capture long-range dependencies, (ii) symmetry principles to facilitate reasoning over protein structures in three dimensions and (iii) end-to-end differentiability as a unifying framework for learning from protein data. The rules of protein folding are ultimately encoded in the physical principles that underpin it; to conclude, the implications of having a powerful computational model for structure prediction that does not explicitly rely on those principles are discussed.