bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exosome secretion kinetics are controlled by temperature
Authors: Mahmood Anarkali , Weisgerber Alan W. , Otruba Zdeněk , Palay Max D. , Nguyen Melodie T. , Bills Broderick L. , Knowles Michelle K. 
Published: July 2022

AbstractWhen multivesicular endosomes (MVEs) fuse with the plasma membrane, exosomes are released into the extracellular space where they can affect other cells. Whether exosomes regulate cells nearby or further away depends on whether they remain attached to the secreting cell membrane. The regulation and kinetics of exosome secretion are not well characterized, but probes for directly imaging single MVE fusion events have allowed for visualization of the fusion and release process. In particular, the design of an exosome marker with a pH sensitive dye in the middle of the tetraspanin protein CD63 has facilitated studies of individual MVE fusion events. Using TIRF microscopy, single MVE fusion events were measured in A549 cells held at 23-37°C and events were identified using an automated detection algorithm. Stable docking precedes fusion almost all of the time and a decrease in temperature was accompanied by decrease in the rate of content loss and a decrease in the frequency of fusion events. The loss of CD63-pHluorin fluorescence was measured at fusion sites and fit with a single or double exponential decay, with approximately 50% of the events requiring two components and a plateau because the loss of fluorescence was typically incomplete. To interpret the kinetics, fusion events were simulated as a point source release of tethered/untethered exosomes coupled with the membrane diffusion of CD63. The experimentally observed decay required three components in the simulation: 1) free exosomes, 2) CD63 membrane diffusion from the endosomal membrane into the plasma membrane at a rate of 0.038 µm2/s, as measured by FRAP, and 3) tethered exosomes. The final component of the decay arises from exosomes being secreted but tethered to the surface with one tether that has a lifetime of 8 seconds at 37°C and longer at lower temperatures. Simulating with fixed tethers or the absence of tethers fails to replicate the experimental data. This kinetic analysis increases our understanding of exosome secretion and how it is regulated by temperature. Our model suggests that exosome release from the fusion site is incomplete due to post-fusion, membrane attachment.
Regulation of the cell surface expression of classical and non-classical MHC proteins by the human cytomegalovirus UL40 and rhesus cytomegalovirus rh67 proteins
Authors: Brackenridge Simon , Borrow Persephone , McMichael Andrew 
Published: July 2022

ABSTRACTThe signal sequences of the human cytomegalovirus (CMV) UL40 protein, and its rhesus CMV counterpart, Rh67, contain a peptide (VMAPRT[L/V][F/I/L/V]L, VL9) that can be presented by Major Histocompatibility Complex (MHC) antigen E. The CMV VL9 peptides replace VL9 peptides derived from classical MHC (Ia) signal sequences, which are lost when CMV disrupts MHC Ia expression, as well as antigen processing and presentation. This allows infected cells to maintain surface expression of MHC-E and escape killing by NK cells expressing the inhibitory NKG2A/CD94 receptor. We demonstrate that processing of the Rh67 VL9 peptide mirrors that of UL40, despite the lack of sequence conservation elsewhere in the two proteins. As previously shown for UL40, up-regulation of MHC-E expression by Rh67 only requires its signal sequence, with sequences upstream of VL9 critical for conferring independence from TAP, the Transporter Associated with Antigen Processing. Additionally, we show that processing of both VL9 peptides depends on cleavage of the signal sequences by the host protease Signal Peptide Peptidase. Notably, our results also reveal that the mature UL40 and Rh67 proteins contribute to CMV immune evasion by down-regulating surface expression of MHC Ia. Unexpectedly, while the Rh67 VL9 peptide is resistant to the effects of the Rh67 protein, the UL40 protein is able to counteract up-regulation of MHC-E expression mediated by its own VL9 peptide. This suggests differences in the mechanisms by which the two VL9 peptides up-regulate MHC-E, which may have implications for translating a RhCMV-vectored SIV vaccine to HIV-1 using HCMV as a vector.IMPORTANCECell surface MHC-E expression, which requires a peptide (VMAPRT[L/V][F/I/L/V]L, “VL9”) from the signal sequences of other MHC class I proteins, prevents cells from being killed by CD94/NKG2A-expressing Natural Killer cells. In cells infected with human CMV, the endogenous VL9 peptide is replaced by one from the signal sequence of the HCMV UL40 protein. We show that processing of the VL9 peptide of Rh67, the rhesus CMV equivalent of UL40, mirrors that of UL40, despite a lack of sequence homology between the two proteins. Of note, we also show that the mature UL40 and Rh67 proteins, which have no previously described function, contribute to CMV immune evasion by reducing classical MHC class I surface expression. Importantly, the mature UL40 protein, but not the mature Rh67 protein, can decrease the up-regulation of MHC-E mediated by its signal sequence VL9 peptide, which may have implications for HCMV as a vaccine vector.
Modeling the Cell Cycle Response to Carbon and Nitrogen deprivation in Caulobacter Populations
Authors: Xu Chunrui , Weston Bronson R. , Cao Yang 
Published: July 2022

AbstractCaulobacter crescentus inhabits a wide range of aquatic ecosystems, including environments with poor nutrients. It undergoes an asymmetrical cell division cycle, generating a pair of daughter cells with distinct motility and replicative potentials. Caulobacter populations have the flexibility to save energy by halting chromosome replication and reduce intraspecific competition by settling in different places in environments. The control mechanisms underlying Caulobacter cell development have been well studied under nutrient-rich conditions, however, its mechanism of response to stressful changes is not fully understood. Here we present a mathematical model to analyze the starvation responses in Caulobacter. We investigate several known starvation signaling pathways to study how these pathways influence cell cycle development and explain experimental observations of starved Caulobacter populations. We also apply a new parameterization strategy to mathematical modeling of biological systems, whose diverse communities have to be robust with many parameter variations, while still having accurate control to maintain regular cell cycle dynamics. Our model demonstrates that the guanine-based second messenger, c-di-GMP (cdG), plays important roles to immediately arrest the cell cycle of Caulobacter under nutrient deprivation; however, it is not sufficient to cause the robust arrest. Our model suggests there should be unknown pathway(s) reducing the levels of CtrA under starvation condition, which results in a significant delay in cytokinesis of starved stalked Caulobacter cells.
Neural substrates of body ownership and agency during voluntary movement
Authors: Abdulkarim Z , Guterstam A , Hayatou Z , Ehrsson HH 
Published: July 2022

AbstractBody ownership and the sense of agency are two central aspects of bodily self-consciousness. While multiple neuroimaging studies have investigated the neural correlates of body ownership and agency in isolation, few have investigated their relationship during voluntary movement when such experiences naturally combine. By eliciting the moving rubber hand illusion with active or passive finger movements during functional magnetic resonance imaging, we isolated activations reflecting the sense of body ownership and agency, respectively, as well as their interaction, and assessed their overlap and anatomical segregation. We found that perceived hand ownership was associated with activity in premotor, posterior parietal and cerebellar regions whereas the sense of agency over the hand’s movements was related to activity in the dorsal premotor cortex and superior temporal cortex. Moreover, one section of the dorsal premotor cortex showed overlapping activity for ownership and agency, and somatosensory cortical activity reflected the interaction of ownership and agency with higher activity when both agency and ownership was experienced. We further found that activations previously attributed to agency in the left insular cortex and right temporoparietal junction reflected the synchrony or asynchrony of the visuo-proprioceptive stimuli rather than agency. Collectively, these results identify the neural bases of agency and ownership during voluntary movement. Although the neural representations of these two experiences are largely distinct, there are functional neuroanatomical overlap and interactions during their combination, which has bearing on theories on bodily self-consciousness.
Kv2 conductances are not required for C-bouton mediated enhancement of motoneuron output
Authors: Smith Calvin C. , Brownstone Robert M. 
Published: July 2022

AbstractNeural motor systems have evolved complex circuits that afford animals a range of behaviours essential for survival. C-bouton synapses arising from cholinergic V0C interneurons amplify motoneuron activity via muscarine type 2 receptors, thus increasing muscle contraction force. Recent work in neonatal mouse motoneurons suggests that delayed rectifier currents carried by post-synaptically clustered KV2.1 channels are crucial to C-bouton amplification. Here we use a motoneuron conditional KV2.1 knockout to show that while KV2.1 modulates maximal firing in neonatal mice, its removal minimally affects either mature motoneuron firing or the enhanced firing rates in response to exogenously applied muscarine. In keeping with this, pharmacological blockade of KV2 currents has minimal electrophysiological effects on mature motoneurons. Furthermore, amplification of electromyography activity during high force tasks was unchanged following KV2.1 deletion. We next show that KV2.2 is also expressed by spinal motoneurons and colocalises with KV2.1 opposite C-boutons. We suggest that the primary function of KV2 proteins – KV2.1 and KV2.2 – is non-conducting in motoneurons, and that KV2.2 can function in the absence of KV2.1, perhaps to ensure the integrity of the synapse.
Wireless Measurements Using Electrical Impedance Spectroscopy to Monitor Fracture Healing
Authors: Fukase Naomasa , Duke Victoria , Lin Monica C. , Stake Ingrid K. , Huard Matt , Huard Johnny , Marmor Meir T. , Maharbiz Michel M. , Ehrhart Nicole P. , Bahney Chelsea S. , Herfat Safa T. 
Published: July 2022

AbstractThere is an unmet need for improved, clinically relevant methods to longitudinally quantify bone healing during fracture care. Here we develop a smart bone plate to wirelessly monitor healing utilizing electrical impedance spectroscopy (EIS) to provide real-time data on tissue com-position within the fracture callus. To validate our technology, we created a 1-mm rabbit tibial defect and fixed the bone with a standard veterinary plate modified with a custom-designed housing that included two impedance sensors capable of wireless transmission. Impedance magnitude and phase measurements were transmitted every 48-hours for up to 10-weeks. Bone healing was assessed by X-ray, μCT, and histomorphometry. Our results indicated the sensors successfully incorporated into the fracture callus and did not impede repair. Electrical impedance, resistance, and reactance increased steadily from weeks 3 to 7—corresponding to the transition from hematoma to cartilage to bone within the fracture gap—then plateaued as the bone began to consolidate. These three electrical readings significantly correlated with traditional measurements of bone healing and successfully distinguished between union and not healed fractures, with the strongest relationship found with impedance magnitude. These results suggest that our EIS smart bone plate can provide continuous and highly sensitive quantitative tissue measurements throughout the course of fracture healing to better guide personalized clinical care.
Effects of wearing FFP2 masks on SARS-CoV-2 infection rates in classrooms
Authors: Jarnig Gerald , Kerbl Reinhold , van Poppel Mireille N.M. 
Published: July 2022

ABSTRACTImportanceDifferent mitigation measures are mandated in schools worldwide to control the spread of SARS-CoV-2. The efficacy of most measures, however, has not been investigated thus far.ObjectiveTo investigate the usefulness of FFP-2 masks in classrooms to prevent the spread of SARS-CoV-2.DesignA retrospective comparative cohort study of infection rates (evaluated by PCR screening in school) in students wearing FFP-2 masks continuously and students in sports classes with limited face mask use.SettingA single-center evaluation comparing classes (middle school: age 10-16 years, 4-year high school: age 14-20 years) with a high sports focus (SF), with regular classes during the Delta and Omicron waves (September 2021–April 2022).ParticipantsIn total, 616 children/families were invited to participate in the comparative evaluation, and 614 (99.7%) followed this invitation by providing relevant information concerning their SARS-CoV-2 infection status. A total of 213 legal guardians (for children < 14 years) and 401 adolescents (≥14 years) reported SARS-CoV-2 infections during the 2021/22 school year.Main Outcomes and MeasuresA comparative analysis of cumulative SARS-CoV-2 infection rates in sports and non-sports classes (the 7-day classroom incidence of SARS-CoV-2 infections, and potential secondary infections among school classmates).ResultsCumulative SARS-CoV-2 infection rates were clearly higher in sports classes (with limited mask use) than in non-sports classes (continuous mask use). After the relaxation of the mitigation measures, students in non-sports classes, however, showed a clear “catch-up” of infections, leading to a higher incidence of infections during this phase. By the end of the observation period (April 30, 2022), only a small difference in cumulative SARS-CoV-2 infection rates (p=0.037, φ=0.09) was detected between classes with a sports focus and those without a sports focus.Conclusions and RelevanceWearing FFP2 face masks reduces the risk of SARS-CoV-2 infection if strict mitigation measures are applied. Following the relaxation of strict measures, previously “protected” students show a significant “catch-up” infection rate. Thus, continuous face mask use postpones rather than avoids SARS-CoV-2 infection in many cases. Therefore, the advantage of reduced transmission must be carefully balanced against the disadvantages associated with mask wearing throughout schools.
The Role Of Serum Electrolyte Level In Stroke Prognosis
Authors: Taywade Onjal , Chourasiya Neeta , Hiwarkar Monali , Nillawar Anup 
Published: July 2022

AbstractBackground and introductionAcute stroke is one of the common medical emergencies in India that contribute to mortality as well as morbidity. NIHSS scale is still the best clinical conglomerate for initial evaluation of stroke, while Modified Rankin scale performed at 3 months is a simple scale to gauge long-term neurological deficit. Hyponatremia is a common accompanying electrolyte disturbance with short as well as long-term implications in stroke.Aim and objectivesWith this background, a study with the following objectives was planned: 1. To estimate the incidence of electrolyte disturbance in acute ischemic stroke, 2. To determine the association of electrolyte disturbances with clinical assessment scales like NIHSS scale, ASPECT score, and MRS-3-month score.Material and MethodsA prospective observational study was conducted on forty-five patients presenting with acute ischemic stroke diagnosed on imaging studies and evaluated for electrolytes (Na+, K+, Cl-).Results55% patients had some or other electrolyte disturbance, hyponatremia(33%) being the most common, while hyperchloremia(15%) was the second. The NIHSS score showed better correlation with MRS score than ASPECT score or electrolyte disturbances.ConclusionHyponatremia was found to be the most common electrolyte disturbance in acute ischemic stroke. This study attempted to underscore the role of electrolyte disturbance in the prognostication of acute stroke. As electrolyte measurement is feasible in low resource settings; its relevance and utility are even more pronounced.
A benchmarking of deep neural network models for cancer subtyping using single point mutations
Authors: Parhami Pouria , Fateh Mansoor , Rezvani Mohsen , Rokny Hamid Alinejad 
Published: July 2022

AbstractIt is now well-known that genetic mutations contribute to development of tumors, in which at least 15% of cancer patients experience a causative genetic abnormality includingDe Novosomatic point mutations. This highlights the importance of identifying responsible mutations and the associated biomarkers (e.g., genes) for early detection in high-risk cancer patients. The next-generation sequencing technologies have provided an excellent opportunity for researchers to study associations betweenDe Novosomatic mutations and cancer progression by identifying cancer subtypes and subtype-specific biomarkers. Simple linear classification models have been used for somatic point mutation-based cancer classification (SMCC); however, because of cancer genetic heterogeneity (ranging from 50% to 80%), high data sparsity, and the small number of cancer samples, the simple linear classifiers resulted in poor cancer subtypes classification. In this study, we have evaluated three advanced deep neural network-based classifiers to find and optimized the best model for cancer subtyping. To address the above-mentioned complexity, we have used pre-processing clustered gene filtering (CGF) and indexed sparsity reduction (ISR), regularization methods, a Global-Max-Pooling layer, and an embedding layer. We have evaluated and optimized the three deep learning models CNN, LSTM, and a hybrid model of CNN+LSTM on publicly available TCGA-DeepGene dataset, a re-formulated subset of The Cancer Genome Atlas (TCGA) dataset and tested the performance measurement of these models is 10-fold-cross-validation accuracy. Evaluating all the three models using a same criterion on the test dataset revealed that the CNN, LSTM, and CNN+LSTM have 66.45% accuracy, 40.89% accuracy, and 41.20% accuracy in somatic point mutation-based cancer classification. Based on our results, we propose the CNN model for further experiments on cancer subtyping based on DNA mutations.
Myostatin gene deletion alters gut microbiota stimulating fast-twitch glycolytic muscle growth
Authors: Luo Zhao-Bo , Han Shengzhong , Yin Xi-Jun , Liu Hongye , Wang Junxia , Xuan Meifu , Hao Chunyun , Wang Danqi , Liu Yize , Chang Shuangyan , Li Dongxu , Gao Kai , Li Huiling , Quan Biaohu , Quan Lin-Hu , Kang Jin-Dan 
Published: July 2022

AbstractThe host genome may influence the composition of the intestinal microbiota, and intestinal microbiota performs an important role in muscle growth and development. Here, we showed that Myostatin (MSTN), a key factor for muscle growth, deletion alters muscularis, plica, and intestinal barrier in pigs. Mice transplanted with MSTN−/− pig intestinal flora showed increase in the cross-sectional area of myofibers and fast-twitch glycolytic muscle mass. The microbes responsible for the production of short chain fatty acids (SCFAs) were enriched in both MSTN−/− pigs and recipient mice, and SCFAs levels were elevated in the colon contents. We demonstrated that valeric acid can stimulate type IIb myofiber growth by activation of the Akt/mTOR pathway via GPR43 and improve muscle atrophy induced by dexamethasone. This is the first study to identify the MSTN gene-gut microbiota-SCFA axis and its regulatory role in fast-twitch glycolytic muscle growth.
Enhanced epithelial to mesenchymal transition and chemoresistance in advanced Retinoblastoma tumors is driven by miR-181a
Authors: Babu Vishnu Suresh , Bisht Anadi , Mallipatna Ashwin , SA Deepak , Dudeja Gagan , Kannan Ramaraj , Shetty Rohit , Heymans Stephane , Guha Nilanjan , Ghosh Arkasubhra 
Published: July 2022

AbstractAdvanced retinoblastoma (Rb) tumors can infiltrate distant tissues and cause a potent threat to vision and life. Through transcriptomic profiling, we discovered key epithelial to mesenchymal transition (EMT) and chemotherapy resistance genes at higher expression levels in advanced Rb tumors. Rb-/- tumor cells acquire metastasis-like phenotype through the EMT program that critically contributes to chemoresistance. We demonstrate that prolonged chemo-drug exposure in Rb cells elicits an EMT program through ZEB1 and SNAI2 that further acquires therapeutic resistance through cathepsin L and MDR1 mediated drug efflux mechanisms. Further, 16 significantly differentially expressed miRNAs were identified in patient tumors, of which miR-181a-5p was significantly reduced in advanced Rb tumors and associated with altered EMT and drug resistance genes. Enhancing miR-181a-5p levels in Rb-/- cells and Rb-/- chemo-resistant sublines controls EMT transcription factors ZEB1 and SNAI2 and halts the transition switch, thereby reversing drug resistance. We thus identify miR-181a-5p as a potential therapeutic target for EMT triggered drug-resistant cancers that can halt their invasion and sensitize them to low dose chemotherapy drugs.Graphical Abstract
Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate
Authors: Dougan Katherine E. , Deng Zhi-Luo , Wöhlbrand Lars , Reuse Carsten , Bunk Boyke , Chen Yibi , Hartlich Juliane , Hiller Karsten , John Uwe , Kalvelage Jana , Mansky Johannes , Neumann-Schaal Meina , Overmann Jörg , Petersen Jörn , Sanchez-Garcia Selene , Schmidt-Hohagen Kerstin , Shah Sarah , Spröer Cathrin , Sztajer Helena , Wang Hui , Bhattacharya Debashish , Rabus Ralf , Jahn Dieter , Chan Cheong Xin , Wagner-Döbler Irene 
Published: July 2022

Abstract“Red tides” are harmful algal blooms (HABs) caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humansviaconsumption of contaminated seafood. Increasingly frequent, HABs are driven by a combination of environmental factors including nutrient enrichment, particularly in warm waters. Here, we present thede novoassembled genome (~4.75 Gbp), transcriptome, proteome, and metabolome fromProrocentrum cordatum, a globally abundant, bloom-forming dinoflagellate. Using axenic algal cultures, we studied the molecular mechanisms that underpin response to temperature stress, which is relevant to current ocean warming trends. We discovered a complementary interplay between RNA editing and exon usage that regulates the expression and functional diversity of biomolecules, reflected by reduction in photosynthesis, central metabolism, and protein synthesis. Our multi-omics analyses uncover the molecular response to heat stress in an important HAB species, which is driven by complex gene structures in a large, high-G+C genome, combined with multi-level transcriptional regulation.