bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure of a bacterial Rhs effector exported by the type VI secretion system
Authors: Günther Patrick , Quentin Dennis , Ahmad Shehryar , Sachar Kartik , Gatsogiannis Christos , Whitney John C. , Raunser Stefan 
Published: September 2021

AbstractThe type VI secretion system (T6SS) is a widespread protein export apparatus found in Gram-negative bacteria. The majority of T6SSs deliver toxic effector proteins into competitor bacteria. Yet, the structure, function, and activation of many of these effectors remains poorly understood. Here, we present the structures of the T6SS effector RhsA from Pseudomonas protegens and its cognate T6SS spike protein, VgrG1, at 3.3 Å resolution. The structures reveal that the rearrangement hotspot (Rhs) repeats of RhsA assemble into a closed anticlockwise β-barrel spiral similar to that found in bacterial insecticidal Tc toxins and in metazoan teneurin proteins. We find that the C-terminal toxin domain of RhsA is autoproteolytically cleaved but remains inside the Rhs ‘cocoon’ where, with the exception of three ordered structural elements, most of the toxin is disordered. The N-terminal ‘plug’ domain is unique to T6SS Rhs proteins and resembles a champagne cork that seals the Rhs cocoon at one end while also mediating interactions with VgrG1. Interestingly, this domain is also autoproteolytically cleaved inside the cocoon but remains associated with it. We propose that mechanical force is required to remove the cleaved part of the plug, resulting in the release of the toxin domain as it is delivered into a susceptible bacterial cell by the T6SS.
Extracellular Matrix Stiffness Alters TRPV4 Regulation in Chondrocytes
Authors: Trompeter Nicholas , Farino Cindy J. , Griffin Mallory , Skinner Ryan , Banda Omar A. , Gleghorn Jason P. , Slater John. H , Duncan Randall L. 
Published: September 2021

AbstractDuring the progression of osteoarthritis (OA), degradation of the extracellular matrix alters the biomechanical properties of cartilage, especially the compressive modulus. The mechanosensitive ion channel transient receptor potential vanilloid 4 (TRPV4) is required for chondrocyte mechanotransduction However, how OA-mediated cartilage degradation influences TRPV4 signaling remains unknown. To determine if ATDC5 cells alter TRPV4-mediated calcium signaling and cell phenotype in response to softer substrates, we created PEGDA-RGDS hydrogels with Young’s moduli that simulated healthy (~350 kPa), OA (~175 kPa) and severe OA (~35 kPa) tissue. We found that softer substrates reduced the influx of calcium through TRPV4 when challenging chondrocytes with hypotonic swelling (HTS). Chondrocyte apoptosis also increased on the OA and severe OA gels due to elevated basal [Ca2+]i, which is attenuated with pharmacological agonism of TRPV4. Pharmacological agonism of TRPV4 rescued the expression of aggrecan and TRPV4 in chondrocytes cultured on OA gels and enhanced the type II collagen (col2) expression in cells on the normal and OA gels. These data suggest that the biomechanical properties of degraded cartilage alter TRPV4-mediated mechanotransduction in chondrocytes. Given that TRPV4 reduced apoptosis and improved the chondrogenic capacity of cells, TRPV4 stimulation could provide a potential therapeutic target in patients with early to moderate OA.
Direct capsid labeling of infectious HIV-1 by genetic code expansion allows detection of largely complete nuclear capsids and suggests nuclear entry of HIV-1 complexes via common routes
Authors: Schifferdecker Sandra , Zila Vojtech , Müller Thorsten G. , Sakin Volkan , Anders-Össwein Maria , Laketa Vibor , Kräusslich Hans-Georg , Müller Barbara 
Published: September 2021

AbstractThe cone-shaped mature HIV-1 capsid is the main orchestrator of early viral replication. After cytosolic entry, it transports the viral replication complex along microtubules towards the nucleus. While it was initially believed that the reverse transcribed genome is released from the capsid in the cytosol, recent observations indicate that a high amount of capsid protein (CA) remains associated with subviral complexes during import through the nuclear pore complex (NPC). Observation of post-entry events via microscopic detection of HIV-1 CA is challenging, since epitope shielding limits immunodetection and the genetic fragility of CA hampers direct labeling approaches. Here, we present a minimally invasive strategy based on genetic code expansion and click chemistry that allows for site-directed fluorescent labeling of HIV-1 CA, while retaining virus morphology and infectivity. Thereby, we could directly visualize virions and subviral complexes using advanced microscopy, including nanoscopy and correlative imaging. Quantification of signal intensities of subviral complexes revealed an amount of CA associated with nuclear complexes in HeLa-derived cells and primary T cells consistent with a complete capsid and showed that treatment with the small molecule inhibitor PF74 did not result in capsid dissociation from nuclear complexes. Cone-shaped objects detected in the nucleus by electron tomography were clearly identified as capsid-derived structures by correlative microscopy. High-resolution imaging revealed dose-dependent clustering of nuclear capsids, suggesting that incoming particles may follow common entry routes.
Community diversity determines the evolution of synthetic bacterial communities under artificial selection
Authors: Raynaud Tiffany , Devers Marion , Spor Aymé , Blouin Manuel 
Published: September 2021

AbstractArtificial selection can be conducted at the community level in the laboratory through a differential propagation of the communities according to their level of expression of a targeted function (i.e. community phenotype). Working with communities instead of individuals as selection units brings in additional sources of variation in the considered phenotype that can arise through changes in community structure and influence the outcome of the artificial selection. These sources of variation could even be increased by manipulating species diversity. In this study, we wanted to assess the effect of manipulating initial community richness on artificial selection efficiency, defined as the change in the targeted function over time as compared to a control treatment without artificial selection. We applied artificial selection for a high productivity on synthetic bacterial communities varying for their initial richness level (from one to 16 strains). Our results showed that, overall, the communities that were artificially selected were 16% more productive than the control communities. Community richness positively influenced community productivity and metabolic capacities and was a strong determinant of the dynamics of community evolution. Our results suggested that community richness could influence artificial selection efficiency but a convergence of the community composition might have limited the effect of diversity on artificial selection efficiency. We propose that applying artificial selection on communities varying for their diversity could allow to find communities differing for their level of expression of a function but also for their responsiveness to artificial selection, provided that their initial composition is different enough.
Exocytosis of the silicified cell wall of diatoms involves extensive membrane disintegration
Authors: de Haan Diede , Aram Lior , Peled-Zehavi Hadas , Addadi Yoseph , Ben-Joseph Oz , Rotkopf Ron , Elad Nadav , Rechav Katya , Gal Assaf 
Published: September 2021

AbstractDiatoms are unicellular algae, characterized by silica cell walls. The silica elements are formed intracellularly in a membrane-bound silica deposition vesicle (SDV), and are exocytosed after completion. How diatoms maintain membrane homeostasis during the exocytosis of these large and rigid silica elements is a long-standing enigma. We studied membrane dynamics during cell wall formation and exocytosis in two model diatom species, using live-cell confocal microscopy, transmission electron microscopy and cryo-electron tomography. Our results show that during the formation of the mineral phase it is in tight association with the SDV membranes, which are forming a precise mold of the delicate geometrical patterns. During exocytosis, the distal SDV membrane and the plasma membrane gradually detach from the mineral and disintegrate in the extracellular space, without any noticeable endocytic retrieval or extracellular repurposing. Within the cell, there is no evidence for the formation of a new plasma membrane, thus the proximal SDV membrane becomes the new barrier between the cell and its environment, and assumes the role of a new plasma membrane. These results provide direct structural observations of diatom silica exocytosis, and point to an extraordinary mechanism in which membrane homeostasis is maintained by discarding, rather than recycling, significant membrane patches.Significance StatementExocytosis is a fundamental process for cell metabolism, communication, and growth. During exocytosis, an intracellular vesicle fuses with the plasma membrane to release its contents. In classical exocytosis, where the exocytosed vesicles are much smaller than the cell, membrane homeostasis is maintained by recycling excess membranes back into the cell. However, an extreme case of exocytosis is the extrusion of large and rigid cell wall elements by unicellular marine algae. During this process, the cell needs to deal with a potential doubling of its plasma membrane. This study reports on a unique exocytosis mechanism used by these organisms, in which the cells cope with the geometrical and physical challenges of exocytosis by releasing a significant amount of membranes to the extracellular space.
Multivalent interactions facilitate motor-dependent protein accumulation at growing microtubule plus ends
Authors: Maan Renu , Reese Louis , Volkov Vladimir A. , King Matthew R. , van der Sluis Eli , Andrea Nemo , Evers Wiel , Jakobi Arjen J. , Dogterom Marileen 
Published: September 2021

AbstractGrowing microtubule ends provide platforms for the accumulation of plus-end tracking proteins that organize into comets of mixed protein composition. Using a reconstituted fission yeast system consisting of end-binding protein Mal3, kinesin Tea2 and cargo Tip1, we found that these proteins can be driven into liquid phase droplets both in solution and at microtubule ends under crowding conditions. In the absence of crowding agents, cryo-electron tomography revealed that motor-dependent comets consist of disordered networks where multivalent interactions appear to facilitate the non-stoichiometric accumulation of cargo Tip1. We dissected the contribution of two disordered protein regions in Mal3 and found that both are required for the ability to form droplets and Tip1 accumulation, while autonomous Mal3 comet formation only requires one of them. Using theoretical modeling, we explore possible mechanisms by which motor activity and multivalent interactions may lead to the observed enrichment of Tip1 at microtubule ends.
Incidental reinstatement of faces and scenes in medial temporal lobe subregions during word recognition
Authors: Schultz Heidrun , Sommer Tobias , Peters Jan 
Published: September 2021

AbstractDuring associative retrieval, the brain reinstates neural representations that were present during encoding. The human medial temporal lobe (MTL) with its subregions hippocampus (HC), perirhinal cortex (PRC), and parahippocampal cortex (PHC) plays a central role in neural reinstatement. Previous studies have given compelling evidence for reinstatement in the MTL during explicitly instructed associative retrieval. High-confident recognition may be similarly accompanied by recollection of associated information from the encoding context. It is unclear, however, whether high-confident recognition memory elicits reinstatement in the MTL even in the absence of an explicit instruction to retrieve associated information. Here, we addressed this open question using high-resolution fMRI. Twenty-eight male and female human volunteers engaged in a recognition memory task for words that they had previously encoded together with faces and scenes. Using complementary uni- and multivariate approaches, we show that MTL subregions including the PRC, PHC, and HC differentially reinstate category-specific representations during high-confident word recognition, even though no explicit instruction to retrieve the associated category was given. This constitutes novel evidence that high-confident recognition memory is accompanied by incidental reinstatement of associated category information in MTL subregions, and supports a functional model of the MTL that emphasises content-sensitive representations during both encoding and retrieval.
Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display
Authors: Tanaka Shiho , Anders Olson C. , Barnes Christopher O. , Higashide Wendy , Gonzalez Marcos , Taft Justin , Richardson Ashley , Martin-Fernandez Marta , Bogunovic Dusan , Gnanapragasam Priyanthi N.P. , Bjorkman Pamela J. , Spilman Patricia , Niazi Kayvan , Rabizadeh Shahrooz , Soon-Shiong Patrick 
Published: September 2021

AbstractThe increasing prevalence of SARS-CoV-2 variants with the ability to escape existing humoral protection conferred by previous infection and/or immunization necessitates the discovery of broadly-reactive neutralizing antibodies (nAbs). Utilizing mRNA display, we identified a set of antibodies against SARS-CoV-2 spike (S) proteins and characterized the structures of nAbs that recognized epitopes in the S1 subunit of the S glycoprotein. These structural studies revealed distinct binding modes for several antibodies, including targeting of rare cryptic epitopes in the receptor-binding domain (RBD) of S that interacts with angiotensin- converting enzyme 2 (ACE2) to initiate infection, as well as the S1 subdomain 1. A potent ACE2-blocking nAb was further engineered to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants. We demonstrate that mRNA display is a promising approach for the rapid identification of nAbs that can be used in combination to combat emerging SARS-CoV-2 variants.
“Understanding Cortical Arousals during Sleep from Leg Movements: A Pilot Study.”
Authors: Bansal Kanika , Garcia Javier , Feltch Cody , Earley Christopher , Robucci Ryan , Banerjee Nilanjan , Brooks Justin 
Published: September 2021

AbstractLeg movements during sleep occur in patients with sleep pathology and healthy individuals. Some (but not all) leg movements during sleep are related to cortical arousals which occur without conscious awareness of the patient but have a significant effect of sleep fragmentation. Detecting leg movements during sleep that are associated with cortical arousals can provide unique insight into the nature and quality of sleep in both health and disease. In this study, a novel leg movement monitor is used in conjunction with polysomnography to better understand the relationship between leg movement and electroencephalogram (EEG) defined cortical arousals. In an approach that we call neuro-extremity analysis, graph theoretic, directed connectivity metrics are used to interrogate the causal links between neural activity measured by EEG and leg movements measured by the sensors within the leg movement monitor. The leg movement monitor in this study utilizes novel capacitive displacement sensors, and a 9-axis inertial measurement unit to characterize leg and foot movements. First, the capacitive displacement measures more closely related to EEG-defined cortical arousals than inertial measurements. Second, the neuro-extremity analysis reveals a temporally evolving connectivity pattern that is consistent with a model of cortical arousals in which brainstem dysfunction leads to near-instantaneous leg movements and a delayed, filtered signal to the cortex. Neuro-extremity analysis reveals causal relationships between EEG and leg movement sensor time-series data that may aid researchers to better understand the pathophysiology of cortical arousals associated with leg movements during sleep.
Automated satellite remote sensing of giant kelp at the Falkland Islands (Islas Malvinas)
Authors: Houskeeper Henry F. , Rosenthal Isaac S. , Cavanaugh Katherine C. , Pawlak Camille , Trouille Laura , Byrnes Jarrett E.K. , Bell Tom W. , Cavanaugh Kyle C. 
Published: September 2021

AbstractGiant kelp populations support productive and diverse coastal ecosystems in both hemispheres at temperate and subpolar latitudes but are vulnerable to changing climate conditions as well as direct human impacts. Observations of giant kelp forests are spatially and temporally patchy, with disproportionate coverage in the northern hemisphere, despite the size and comparable density of southern hemisphere kelp forests. Satellite imagery enables the mapping of existing and historical giant kelp populations in understudied regions, but automating the detection of giant kelp in large satellite datasets requires approaches that are robust to the optical complexity of the shallow, nearshore environment. We present and compare two approaches for automating the detection of giant kelp in satellite datasets: one based on crowd sourcing of satellite imagery classifications and another based on a decision tree paired with a spectral unmixing algorithm (automated using Google Earth Engine). Both approaches are applied to satellite imagery (Landsat) of the Falkland Islands or Islas Malvinas (FLK), an archipelago in the southern Atlantic Ocean that supports expansive giant kelp ecosystems. The performance of each method is evaluated by comparing the automated classifications with a subset of expert-annotated imagery cumulatively spanning over 2,700km of coastline. Using the remote sensing approaches evaluated herein, we present the first continuous timeseries of giant kelp observations in the FLK region using Landsat imagery spanning over three decades. We do not detect evidence of long-term change in the FLK region, although we observe a recent decline in total canopy area from 2017-2021. Using a nitrate model based on nearby ocean state measurements obtained from ships and incorporating satellite sea surface temperature products, we find that the area of giant kelp forests in the FLK region is positively correlated with the nitrate content observed during the prior year. Our results indicate that giant kelp classifications using citizen science are approximately consistent with classifications based on a state-of-the-art automated spectral approach. Despite differences in accuracy and sensitivity, both approaches find high interannual variability that impedes the detection of potential long-term changes in giant kelp canopy area, although recent canopy area declines are notable and should continue to be monitored carefully.
Genome-wide identification and gene expression analysis of Clade A protein phosphatase 2C family genes in Brassica juncea var. tumida
Authors: Cheng Chunhong , Cai Zhaoming , Su Rongbin , Zhong Yuanmei , Chen Li , Wang Lixia , Chen Guojian , Yan Lun , Li Changman 
Published: September 2021

AbstractAbscisic acid (ABA) plays crucial roles in plant response to environmental stresses and development. The clade A phosphatases (PP2Cs) play a crucial role in ABA signaling. However, little is known about the details regarding PP2Cs family genes in Brassica juncea var. tumida. Here, 20 clade A PP2Cs family genes were identified in tuber mustard genome, including BjuABI1s, BjuABI2s, BjuAHG1s, BjuAHG3s, BjuHAB1, BjuHAB2s, BjuHAI1s, BjuHAI2s and BjuHAI3. The promoters of BjuPP2Cs family genes contained various of cis-acting elements, such as ABRE, GT1GMSCAM4, ARFAT and MYB1AT. We also analyzed the expression pattern of clade A BjuPP2Cs under abiotic stresses (low temperature, NaCl and ABA) treatment, pathogen Plasmodiophora brassicae treatment and different stages of stem swollen. The results suggested that clade A BjuPP2Cs regulated tuber mustard response to P. brassicae to mediate the formation of clubroot and might play roles in stem swelling and response to abiotic stresses. This study provides valuable information for further functional investigations of clade A PP2Cs family genes in B. juncea var. tumida.
Structural Basis of Substrate Recognition by the Mitochondrial ADP/ATP Transporter
Authors: Yao Shihao , Yi Qiuzi , Ma Boyuan , Mao Xiaoting , Chen Ye , Guan Min-Xin , Cang Xiaohui 
Published: September 2021

AbstractSpecific import of ADP and export of ATP by ADP/ATP carrier (AAC) across the inner mitochondrial membrane are crucial for sustainable energy supply in all eukaryotes. However, mechanism for highly specific substrate recognition in the dynamic transport process remains largely elusive. Here, unguided MD simulations of 22 microseconds in total reveal that AAC in ground c-state uses the second basic patch (K91K95R187), tyrosine ladder (Y186Y190Y194), F191 and N115 in the upper region of the cavity to specifically recognize ADP and confer selectivity for ADP over ATP. Mutations of these residues in yeast AAC2 reduce ADP transport across the L. lactis membrane and induce defects in OXPHOS and ATP production in yeast. Sequence analyses also suggest that AAC and other adenine nucleotide transporters use the upper region of the cavity, rather than the central binding site to discriminate their substrates. Identification of the new site unveils the unusually high substrate specificity of AAC, and together with central binding site support early biochemical findings about existence of two substrate binding sites. Our results imply that using different sites for substrate recognition and conformational transition could be a smart strategy for transporters to cope with substrate recognition problem in the highly dynamic transport process.
A review of data mining ontologies
Authors: Sinha Prashant Kumar , Gajbe Sagar Bhimrao , Debnath Sourav , Sahoo Subhranshubhusan , Chakraborty Kanu , Mahato Shiva Shankar 
Published: September 2021

PurposeThis work provides a generic review of the existing data mining ontologies (DMOs) and also provides a base platform for ontology developers and researchers for gauging the ontologies for satisfactory coverage and usage.Design/methodology/approachThe study uses a systematic literature review approach to identify 35 DMOs in the domain between the years 2003 and 2021. Various parameters, like purpose, design methodology, operations used, language representation, etc. are available in the literature to review ontologies. Accompanying the existing parameters, a few parameters, like semantic reasoner used, knowledge representation formalism was added and a list of 20 parameters was prepared. It was then segregated into two groups as generic parameters and core parameters to review DMOs.FindingsIt was observed that among the 35 papers under the study, 26 papers were published between the years 2006 and 2016. Larisa Soldatova, Saso Dzeroski and Pance Panov were the most productive authors of these DMO-related publications. The ontological review indicated that most of the DMOs were domain and task ontologies. Majority of ontologies were formal, modular and represented using web ontology language (OWL). The data revealed that Ontology development 101, METHONTOLOGY was the preferred design methodology, and application-based approaches were preferred for evaluation. It was also observed that around eight ontologies were accessible, and among them, three were available in ontology libraries as well. The most reused ontologies were OntoDM, BFO, OBO-RO, OBI, IAO, OntoDT, SWO and DMOP. The most preferred ontology editor was Protégé, whereas the most used semantic reasoner was Pellet. Even ontology metrics for 16 DMOs were also available.Originality/valueThis paper carries out a basic level review of DMOs employing a parametric approach, which makes this study the first of a kind for the review of DMOs.