bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast parametric curve matching (FPCM) for automatic spike detection
Authors: Kleeva Daria , Soghoyan Gurgen , Komoltsev Ilia , Sinkin Mikhail , Ossadtchi Alexei 
Published: January 2022

AbstractEpilepsy is a widely spread neurological disease, whose treatment often requires resection of the pathological cortical tissue. Interictal spike analysis observed in the non-invasively collected EEG or MEG data offers an attractive way to localize epileptogenic cortical structures for surgery planning purposes. Interictal spike detection in lengthy multichannel data is a daunting task that is still often performed manually. This frequently limits such an analysis to a small portion of the data which renders the appropriate risks of missing the potentially epileptogenic region. While a plethora of automatic spike detection techniques have been developed each with its own assumptions and limitations, non of them is ideal and the best results are achieved when the output of several automatic spike detectors are combined. This is especially true in the low signal-to-noise ratio conditions. To this end we propose a novel biomimetic approach for automatic spike detection based on a constrained mixed spline machinery that we dub as fast parametric curve matching (FPCM). Using the peak-wave shape parametrization, the constrained parametric morphological model is constructed and convolved with the observed multichannel data to efficiently determine mixed spline parameters corresponding to each time-point in the dataset. Then the logical predicates that directly map to verbalized text-book like descriptions of the expected interictal event morphology allow us to accomplish the spike detection task. The results of simulations mimicking typical low SNR scenario show the robustness and high ROC AUC values of the FPCM method as compared to the spike detection performed using more conventional approaches such as wavelet decomposition, template matching or simple amplitude thresholding. Applied to the real MEG and EEG data from the human patients and to rat ECoG data, the FPCM technique demonstrates reliable detection of the interictal events and localization of epileptogenic zones concordant with independent conclusions made by the epileptologist. Since the FPCM is computationally light, tolerant to high amplitude artifacts and flexible to accommodate verbalized descriptions of the arbitrary target morphology, it may complement the existing arsenal of means for analysis of noisy interictal datasets.
Thylakoid grana stacking revealed by multiplex genome editing of LHCII encoding genes
Authors: Guardini Zeno , Gomez Rodrigo L. , Caferri Roberto , Stuttmann Johannes , Dall’Osto Luca , Bassi Roberto 
Published: January 2022

SummaryLand plant chloroplasts differ from algal ones for their thylakoid membranes being organized in grana: piles of vesicles paired by their stromal surface, forming domains including Photosystem (PS) II and its antenna while excluding PS I and ATPase to stroma membranes, connecting grana stacks. The molecular basis of grana stacking remain unclear. We obtained genotypes lacking the trimeric antenna complex (Lhcb1-2-3), the monomeric Lhcb4-5-6, or both. Full deletion caused loss of grana, while either monomers or trimers support 50% stacking. The expression of Lhcb5 alone restored stacking at 50%, while Lhcb2 alone produced huge grana which broke down upon light exposure. Cyclic electron transport was maintained in the lack of stacking, while excitation energy balance between photosystems and the repair efficiency of damaged Photosystem II were affected. We conclude that grana evolved for need of regulating energy balance between photosystems under terrestrial canopy involving rapid changes in photon spectral distribution.
The SARS-CoV-2 infection in Thailand: analysis of spike variants complemented by protein structure insights
Authors: Ittisoponpisan Sirawit , Yahangkiakan Shalip , Sternberg Michael J E , David Alessia 
Published: January 2022

AbstractThailand was the first country outside China to officially report COVID-19 cases. Despite the strict regulations for international arrivals, up until February 2021, Thailand had been hit by two major outbreaks. With a large number of SARS-CoV-2 sequences collected from patients, the effects of many genetic variations, especially those unique to Thai strains, are yet to be elucidated. In this study, we analysed 439,197 sequences of the SARS-CoV-2 spike protein collected from NCBI and GISAID databases. 595 sequences were from Thailand and contained 52 variants, of which 6 had not been observed outside Thailand (p.T51N, p.P57T, p.I68R, p.S205T, p.K278T, p.G832C). These variants were not predicted to be of concern. We demonstrate that the p.D614G, although already present during the first Thai outbreak, became the prevalent strain during the second outbreak, similarly to what was described in other countries. Moreover, we show that the most common variants detected in Thailand (p.A829T, p.S459F and p.S939F) do not appear to cause any major structural change to the spike trimer or the spike-ACE2 interaction. Among the variants identified in Thailand was p.N501T. This variant, which involves an asparagine critical for spike-ACE2 binding, was not predicted to increase SARS-CoV-2 binding, thus in contrast to the variant of global concern p.N501Y. In conclusion, novel variants identified in Thailand are unlikely to increase the fitness of SARS-CoV-2. The insights obtained from this study could aid SARS-CoV-2 variants prioritisations and help molecular biologists and virologists working on strain surveillance.
PIP2-Dependent Thermoring Basis for Cold-Sensing of the TRPM8 Biothermometer
Authors: Wang Guangyu 
Published: January 2022

AbstractThe menthol sensor TRPM8 can be activated by cold and thus serves as a biothermometer in a primary afferent sensory neuron for innocuous-to-noxious cold detection. However, the precise structural origins of specific temperature thresholds and sensitivity have remained elusive. Here, a grid thermodynamic model was employed to examine if the temperature-dependent noncovalent interactions found in the 3D structures of thermo-gated TRPM8 could assemble into a well-organized fluidic grid-like mesh network, featuring the constrained grids as the thermorings for cold-sensing in response to PIP2, Ca2+and chemical agents. The results showed that the different interactions of TRPM8 with PIP2during the thermal incubation induced the formation of the biggest grids with distinct melting temperature threshold ranges. Further, the overlapped threshold ranges between open and pre-open closed states were required for initial cold activation with the matched thermo-sensitivity and the decrease in the systematic thermal instability. Finally, the intact anchor grid near the lower gate was important for channel opening with the active selectivity filter. Thus, PIP2-dependent thermorings in TRPM8 may play a pivotal role in cold sensing. (176 words)
Nested spatial and temporal modeling of environmental conditions associated with genetic markers of Vibrio parahaemolyticus in Washington state Pacific oysters
Authors: Fries Brendan , Davis Benjamin J. K. , Corrigan Anne E. , DePaola Angelo , Curriero Frank C. 
Published: January 2022

AbstractThe Pacific Northwest (PNW) is one of the largest commercial harvesting areas for Pacific oysters (Crassostrea gigas) in the United States. Vibrio parahaemolyticus, a bacterium naturally present in estuarine waters, accumulates in shellfish and is a major cause of seafood-borne illness. Growers, consumers, and public-health officials have raised concerns about rising vibriosis cases in the region. V. parahaemolyticus genetic markers (tlh, tdh, trh) were estimated using an MPN-PCR technique in Washington State Pacific oysters regularly sampled between May and October from 2005 to 2019 (N=2,836); environmental conditions were also measured at each sampling event. Multilevel mixed-effects regression models were used to assess relationships between environmental measures and genetic markers as well as genetic marker ratios (trh:tlh, tdh:tlh, and tdh:trh), accounting for variation across space and time. Spatial and temporal dependence were also accounted for in the model structure. Model fit improved when including environmental measures from previous weeks (1-week lag for air temperature, 3-week lag for salinity). Positive associations were found between tlh and surface water temp, specifically between 15°C and 26°C, and between trh and surface water temperature up to 26°C. tlh and trh were negatively associated with 3-week lagged salinity in the most saline waters (> 27 ppt). There was also a positive relationship between tissue temperature and tdh, but only above 20°C. The tdh:tlh ratio displayed analogous inverted non-linear relationships as tlh. The non-linear associations found between the genetic targets and environmental measures demonstrate the complex habitat suitability of V. parahaemolyticus. Additional associations with both spatial and temporal variables also suggest there are influential unmeasured environmental conditions that could further explain bacterium variability. Overall, these findings confirm previous ecological risk factors for vibriosis in Washington State, while also identifying new associations between lagged temporal effects and pathogenic markers of V. parahaemolyticus.
Microtubules restrict F-actin polymerization to the immune synapse via GEF-H1 to maintain polarity in lymphocytes
Authors: Pineau Judith , Pinon Léa , Mesdjian Olivier , Fattaccioli Jacques , Duménil Ana-Maria Lennon , Pierobon Paolo 
Published: January 2022

ABSTRACTImmune synapse formation is a key step for lymphocyte activation. In B lymphocytes, the immune synapse controls the production of high-affinity antibodies, thereby defining the efficiency of humoral immune responses. While the key roles played by both the actin and microtubule cytoskeletons in the formation and function of the immune synapse have become increasingly clear, how the different events involved in synapse formation are coordinated in space and time by actin-microtubule interactions is not understood. Using a microfluidic pairing device, we studied with unprecedented resolution the dynamics of the various events leading to immune synapse formation and maintenance. Our results identify two groups of events, local and global dominated by actin and microtubules dynamics, respectively. They further highlight an unexpected role for microtubules and the GEF-H1-RhoA axis in restricting F-actin polymerization at the immune synapse to define the cell polarity axis, allowing the formation and maintenance of a unique competent immune synapse.
A role for Lin28a in aging-associated decline of adult hippocampal neurogenesis
Authors: Hu Zhechun , Ma Jiao , Yue Huimin , Li Xiaofang , Wang Chao , Wang Liang , Sun Binggui , Chen Zhong , Wang Lang , Gu Yan 
Published: January 2022

AbstractHippocampal neurogenesis declines with aging. Wnt ligands and antagonists within the hippocampal neurogenic niche regulate the proliferation of neural progenitor cells and the development of new neurons, and the changes of their levels in the niche mediate aging-associated decline of neurogenesis. We found that RNA-binding protein Lin28a remained existent in neural progenitor cells and granule neurons in the adult hippocampus, and decreased with aging. Loss of Lin28a inhibited the responsiveness of neural progenitor cells to niche Wnt agonist and reduced neurogenesis, thus impairing pattern separation. Overexpression of Lin28a increased the proliferation of neural progenitor cells, promoted the functional integration of newborn neurons, restored neurogenesis in Wnt-deficient dentate gyrus, and rescued the impaired pattern separation in aging mice. Our data suggest that Lin28a regulates adult hippocampal neurogenesis as an intracellular mechanism by responding to niche Wnt signals, and its decrease is involved in aging-associated decline of hippocampal neurogenesis as well as related cognitive functions.
Essential regulatory functions of CaMKII T286 phosphorylation in LTP and two distinct forms of LTD
Authors: Cook Sarah G. , Rumian Nicole L. , Bayer K. Ulrich 
Published: January 2022

ABSTRACTThe Ca2+/calmodulin-dependent protein kinase II (CaMKII) mediates both long-term potentiation and depression (LTP and LTD) of excitatory synapses, two opposing forms of synaptic plasticity induced by strong versus weak stimulation of NMDA-type glutamate receptors (NMDARs). NMDAR-dependent LTD is prevalent in juvenile hippocampus, but in mature hippocampus, LTD is still readily induced by stimulating metabotropic glutamate receptors (mGluRs). Here we show that mGluR-dependent LTD also requires CaMKII and its T286 autophosphorylation that induces Ca2+-independent autonomous kinase activity. This autophosphorylation (i) accelerated CaMKII movement to excitatory synapses after LTP stimuli and (ii) was required for the movement to inhibitory synapses after NMDAR-LTD stimuli. Similar to NMDAR-LTD, the mGluR-LTD stimuli did not induce any CaMKII movement to excitatory synapses. However, in contrast to NMDAR-LTD, the mGluR-LTD did not involve CaMKII movement to inhibitory synapses and did not require additional T305/306 autophosphorylation. Taken together, even though CaMKII T286 autophosphorylation has a longstanding prominent role in LTP, it is also required for both major forms of LTD in hippocampal neurons, albeit with differential requirements for the heterosynaptic communication of excitatory signals to inhibitory synapses.
A triad of kicknet sampling, eDNA metabarcoding, and predictive modeling to assess aquatic macroinvertebrate biodiversity
Authors: Keck François , Hürlemann Samuel , Locher Nadine , Stamm Christian , Deiner Kristy , Altermatt Florian 
Published: January 2022

AbstractMonitoring freshwater biodiversity is essential to understand the impacts of human activities and for effective management of ecosystems. Thereby, biodiversity can be assessed through direct collection of targeted organisms, through indirect evidence of their presence (e.g. signs, environmental DNA, camera trap, etc.), or through extrapolations from species distribution models (SDM). Differences in approaches used in biodiversity assessment, however, may come with individual challenges and hinder cross-study comparability. In the context of rapidly developing techniques, we compared a triad of approaches in order to understand assessment of aquatic macroinvertebrate biodiversity. Specifically, we compared the community composition and species richness of three orders of aquatic macroinvertebrates (mayflies, stoneflies, and caddisflies, hereafter EPT) obtained via eDNA metabarcoding and via traditional in situ kicknet sampling to catchment-level based predictions of a species distribution model. We used kicknet data from 24 sites in Switzerland and compared taxonomic lists to those obtained using eDNA amplified with two different primer sets. Richness detected by these methods was compared to the independent predictions made by a statistical species distribution model using landscape-level features to estimate EPT diversity. Despite the ability of eDNA to consistently detect some EPT species found by traditional sampling, we found important discrepancies in community composition between the two approaches, particularly at local scale. Overall, the more specific set of primers, namely fwhF2/EPTDr2n, was most efficient for the detection of target species and for characterizing the diversity of EPT. Moreover, we found that the species richness measured by eDNA was poorly correlated to the richness measured by kicknet sampling and that the richness estimated by eDNA and kicknet were poorly correlated with the prediction of the statistical model. Overall, however, neither eDNA nor the traditional approach had strong links to the predictive models, indicating inherent limitations in upscaling species richness estimates. Future challenges include improving the accuracy and sensitivity of each approach individually yet also acknowledge their respective limitations, in order to best meet stakeholder demands addressing the biodiversity crisis we are facing.
Continuous Daily Head and Trunk Acceleration Recording for the Assessment of Bone Stimulation in Astronauts
Authors: Sugita Yoshino , Clément Gilles 
Published: January 2022

AbstractThe acceleration of the head and hip along the x-, y-, and z-axis of 14 healthy subjects was recorded during two sessions of 12 consecutive hours. The magnitude, frequency content, and root mean square of the acceleration signals were used to determine the type of physical activity (sitting, standing, walking, etc.) during normal daily life on Earth. The acceleration signal slope (jerk) was also calculated to assess whether these activities were sufficient to maintain bone mineral density. These measurements indicated that the changes in vertical acceleration experienced by our subjects during normal daily life were presumably sufficient to maintain bone mineral density. However, these changes might not be sufficient for postmenopausal women and astronauts during long-term exposure to weightlessness during spaceflight.
Directed evolution of angiotensin-converting enzyme 2 (ACE2) peptidase activity profiles for therapeutic applications
Authors: Heinzelman Pete , Romero Philip A. 
Published: January 2022

AbstractAngiotensin Converting-Enzyme 2 (ACE2) is currently being investigated for its ability to beneficially modulate the Angiotensin receptor (ATR) therapeutic axis to treat multiple human diseases, but its broad substrate scope and diverse physiological roles limit its potential as a therapeutic agent. In this work we engineer ACE2 variants with enhanced hydrolytic activity and specificity toward Angiotensin-II (Ang-II) that may lead to new therapeutic candidates with improved efficacy and reduced off-target side effects. We established a yeast display-based liquid chromatography screen that enabled use of directed evolution to discover ACE2 variants with improved Ang-II activity and specificity relative to the off-target peptide substrates Apelin-13 and Angiotensin-I (Ang-I). We screened ACE2 active site libraries to reveal three substitution-tolerant positions (M360, T371 and Y510) that can be mutated to enhance ACE2’s activity profile and followed up on these hits with focused double mutant libraries to further improve the enzyme. Relative to wildtype ACE2, our top variant (T371L/Y510Ile) displayed a sevenfold increase in Ang-II turnover number (kcat), a sixfold diminished catalytic efficiency (kcat/Km) on Apelin-13, and an overall decreased activity on other ACE2 substrates that were not directly assayed in directed evolution screen. At physiologically relevant substrate concentrations, T371L/Y510Ile hydrolyzes more Ang-II than wildtype ACE2 with concomitant Ang-II:Apelin-13 specificity improvements reaching 30-fold. Our efforts have delivered ATR axis-acting therapeutic candidates with relevance to both established and unexplored ACE2 therapeutic applications and provide a foundation for further ACE2 engineering efforts.Significance StatementThe Angiotensin Converting Enzyme 2 (ACE2) carboxypeptidase is being clinically trialed for treatment of acute respiratory distress syndrome (ARDS) related to traumatic injuries and viral infections. We developed an enzyme engineering platform that enabled discovery of ACE2 variants possessing enhanced peptide hydrolysis activity and specificity profiles relevant to ARDS treatment. Beyond their potential utility as ARDS therapeutics, our improved ACE2 variants could be further developed for new unexplored ACE2 therapeutic contexts such as treating Alzheimer’s Disease.
mBeRFP, a versatile fluorescent tool to enhance multichannel live imaging and its applications
Authors: Martin Emmanuel , Suzanne Magali 
Published: January 2022

AbstractCell and developmental biology increasingly require live imaging of protein dynamics in cells, tissues or living organisms. Thanks to the discovery and the development of a panel of fluorescent proteins over the last decades, live imaging has become a powerful and commonly used approach. However, multicolor live imaging remains challenging. The generation of long Stokes shift red fluorescent proteins, such as mBeRFP, offers interesting new perspectives to bypass this limitation. Here, we constructed a set of mBeRFP-expressing vectors and provided a detailed characterization of this fluorescent protein for in vivo live imaging and its applications in Drosophila. Briefly, we showed that a single illumination source is sufficient to simultaneously stimulate mBeRFP and GFP. We demonstrated that mBeRFP can be easily combined with classical green and red fluorescent protein without any crosstalk. We also showed that the low photobleaching of mBeRFP is suitable for live imaging, and that this protein can be used for quantitative applications such as FRAP or laser ablation. Finally, we believe that this fluorescent protein, with the set of new possibilities it offers, constitutes an important tool for cell, developmental and mechano biologists in their current research.
The RNA binding protein Swm is critical for Drosophila melanogaster intestinal progenitor cell maintenance
Authors: Ariyapala Ishara S. , Buddika Kasun , Hundley Heather A. , Calvi Brian R. , Sokol Nicholas S. 
Published: January 2022

ABSTRACTThe regulation of stem cell survival, self-renewal, and differentiation is critical for the maintenance of tissue homeostasis. Although the involvement of signaling pathways and transcriptional control mechanisms in stem cell regulation have been extensively investigated, the role of post-transcriptional control is still poorly understood. Here we show that the nuclear activity of the RNA-binding protein Second Mitotic Wave Missing (Swm) is critical for Drosophila intestinal stem cells (ISCs) and their daughter cells, enteroblasts (EBs), to maintain their identity and function. Loss of swm in these intestinal progenitor cells leads ISCs and EBs to lose defined cell identities, fail to proliferate, and detach from the basement membrane, resulting in severe progenitor cell loss. swm loss further causes nuclear accumulation of poly(A)+ RNA in progenitor cells. Swm associates with transcripts involved in epithelial cell maintenance and adhesion, and the loss of swm, while not generally affecting the levels of these Swm-bound mRNAs, leads to elevated expression of proteins encoded by some of them, including the fly orthologs of Filamin and Talin. Taken together, this study indicates a role for Swm in adult stem cell maintenance, and raises the possibility that nuclear post-transcriptional gene regulation plays vital roles in controlling adult stem cell maintenance and function.
E3 ubiquitin ligase MARCHF5 controls BAK apoptotic activity independently of BH3-only proteins
Authors: Huang Shuai A. , Chin Hui San , Reljic Boris , Djajawi Tirta M. , Tan Iris K.L. , Stroud David A. , Huang David C.S. , van Delft Mark F. , Dewson Grant 
Published: January 2022

SUMMARYIntrinsic apoptosis is principally governed by the BCL-2 family of proteins, but some non-BCL-2 proteins are also critical to control this process. To identify novel apoptosis regulators, we performed a genome-wide CRISPR-Cas9 library screen, and it identified the mitochondrial E3 ubiquitin ligase MARCHF5/MITOL/RNF153 as an important regulator of BAK apoptotic function. Deleting MARCHF5 in diverse cell lines dependent on BAK conferred profound resistance to BH3-mimetic drugs. The loss of MARCHF5 or its E3 ubiquitin ligase activity surprisingly drove BAK to adopt an activated conformation, with resistance to BH3-mimetics afforded by the formation of inhibitory complexes with pro-survival proteins MCL-1 and BCL-XL. Importantly, these changes to BAK conformation and pro-survival association occurred independently of BH3-only proteins and influence on pro-survival proteins. This study identifies a new mechanism by which MARCHF5 regulates apoptotic cell death and provides new insight into how cancer cells respond to BH3-mimetic drugs. These data also highlight the emerging role of ubiquitin signalling in apoptosis that may be exploited therapeutically.