bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-dimensional structured illumination microscopy with enhanced axial resolution
Authors: Li Xuesong , Wu Yicong , Su Yijun , Rey-Suarez Ivan , Matthaeus Claudia , Updegrove Taylor B. , Wei Zhuang , Zhang Lixia , Sasaki Hideki , Li Yue , Guo Min , Giannini John P. , Vishwasrao Harshad D. , Chen Jiji , Lee Shih-Jong J. , Shao Lin , Liu Huafeng , Ramamurthi Kumaran S. , Taraska Justin W. , Upadhyaya Arpita , La Riviere Patrick , Shroff Hari 
Published: July 2022

AbstractWe present two distinct, complementary methods for improving axial resolution in three-dimensional structured illumination microscopy (3D SIM) with minimal or no modification to the optical system. First, we show that placing a mirror directly opposite the sample enables 4-beam interference with higher spatial frequency content than 3D SIM illumination, offering near-isotropic imaging with ∼120 nm lateral and 160 nm axial resolution. Second, we develop an improved deep learning method that can be directly applied to 3D SIM data, obviating the need for additional hardware. This procedure results in ∼120 nm isotropic resolution and can be combined with denoising to facilitate volumetric imaging spanning dozens of time points. We demonstrate the potential of these advances by imaging a variety of cellular samples, delineating the nanoscale distribution of vimentin and microtubule filaments, observing the relative positions of caveolar coat proteins and lysosomal markers, and visualizing rich cytoskeletal dynamics within T-cells in the early stages of immune synapse formation.
Molecular mechanism of GTP binding- and dimerization-induced enhancement of Sar1-mediated membrane remodeling
Authors: Paul Sanjoy , Audhya Anjon , Cui Qiang 
Published: July 2022

The Sar1 GTPase initiates Coat Protein II (COPII)-mediated protein transport by generating membrane curvature at subdomains on the Endoplasmic Reticulum, where it is activated by the guanine nucleotide exchange factor (GEF) Sec12. Crystal structures of GDP- and GTP-bound forms of Sar1 suggest that it undergoes a conformational switch in which GTP binding enhances the exposure of an amino-terminal amphipathic helix necessary for efficient membrane penetration. However, key residues in the amino-terminus were not resolved in crystal structures, and experimental studies have suggested that the amino-terminus of Sar1 is solvent-exposed in the absence of membrane, even in the GDP-bound state. Therefore, the molecular mechanism by which GTP binding activates the membrane remodeling activity of Sar1 remains unclear. Using atomistic molecular dynamics simulations, we compare the membrane binding and curvature generation activities of Sar1 in its GDP- and GTP-bound states. We show that in the GTP-bound state, Sar1 inserts into the membrane with its complete (residues 1-23) amphipathic amino-terminal helix, while Sar1-GDP binds to the membrane only through its first 12 residues. Such differential membrane binding modes translate into significant differences in the protein volume inserted into the membrane. As a result, Sar1-GTP generates positive membrane curvature 10-20 times higher than Sar1-GDP. Dimerization of the GTP-bound form of Sar1 further amplifies curvature generation. Taken together, our results present a detailed molecular mechanism for how the nucleotide-bound state of Sar1 regulates its membrane binding and remodeling activities in a concentration dependent manner, paving the way toward a better understanding COPII-mediated membrane transport.Significance StatementAmphipathic helices play established roles in penetrating lipid bilayers to produce local membrane curvature. The degree of curvature generated has been suggested to depend on the penetration depth of the amphipathic helix, its amino acid sequence, and the protein volume inserted into the membrane. However, the relative contributions of each of these factors in membrane bending remain unclear. Using the Sar1 protein monomer bound to different nucleotides (GDP vs. GTP) and its GTP-bound dimeric form as examples, we explicitly show that while the precise amino acid sequence and insertion depth of the amphipathic helix are relevant, the generated membrane curvature is most correlated with the volume of protein insertion into the membrane.
Nuanced role for dendritic cell intrinsic IRE1 RNase in the regulation of antitumor adaptive immunity
Authors: Flores-Santibañez Felipe , Rennen Sofie , Fernandez Dominique , De Nolf Clint , Gaete Sandra , Fuentes Camila , Moreno Carolina , Figueroa Diego , Lladser Álvaro , Iwawaki Takao , Bono María Rosa , Janssens Sophie , Osorio Fabiola 
Published: July 2022

ABSTRACTThe IRE1/XBPls axis of the unfolded protein response (UPR) plays divergent roles in dendritic cell (DC) biology in steady state versus tumor contexts. Whereas tumor associated DCs show dysfunctional IRE1/XBP1s activation that curtails their function, the homeostasis of conventional type 1 DCs (cDC1) in tissues requires intact IRE1 RNase activity. Considering that cDC1s are key orchestrators of antitumor immunity, it is relevant to understand the functional versus dysfunctional roles of IRE1/XBP1s in tumor DC subtypes. Here, we show that cDC1s constitutively activate IRE1 RNase within subcutaneous B16 melanoma and MC38 adenocarcinoma tumor models. Mice lacking XBP1s in DCs display increased melanoma tumor growth, reduced T cell effector responses and accumulation of terminal exhausted CD8+T cells. Transcriptomic studies revealed that XBP1 deficiency in tumor cDCls decreased expression of mRNAs encoding XBPls and regulated IRE1 dependent decay (RIDD) targets. Finally, we find that the dysregulated melanoma growth and impaired T cell immunity noticed in XBP1 deficient mice are attributed to RIDD induction in DCs. This work indicates that IREl RNase activity in melanoma/MC38-associated DCs fine tunes aspects of antitumor immunity independently of XBP1s, revealing a differential role for the UPR axis that depends on the DC subtype and cancer model.
Axonemal regulation by curvature explains sperm flagellar waveform modulation
Authors: Gallagher Meurig T. , Kirkman-Brown Jackson C. , Smith David J. 
Published: July 2022

AbstractFlagellar motility is critical to natural and many forms of assisted reproduction. The rhythmic beating and wave propagation by the flagellum propels sperm through fluid and enables modulation between penetrative progressive motion, activated side-to-side yaw and hyperactivated movement associated with detachment from epithelial binding. These changes occur in response to the properties of the surrounding fluid environment, biochemical activation state, and physiological ligands, however a parsimonious mechanistic explanation of flagellar beat generation that can explain motility modulation is lacking. In this paper we present the Axonemal Regulation of Curvature, Hysteretic model (ARCH), a curvature control-type model based on switching of active moment by local curvature, embedded within a geometrically nonlinear elastic model of the flagellum exhibiting planar flagellar beats, together with nonlocal viscous fluid dynamics. The biophysical system is parameterised completely by four dimensionless parameter groupings. The effect of parameter variation is explored through computational simulation, revealing beat patterns that are qualitatively representative of penetrative (straight progressive), activated (highly yawing) and hyperactivated (non-progressive) modes. Analysis of the flagellar limit cycles and associated swimming velocity reveals a cusp catastrophe between progressive and non-progressive modes, and hysteresis in the response to changes in critical curvature parameter. Quantitative comparison to experimental data on human sperm exhibiting typical penetrative, activated and hyperactivated beats shows a good fit to the time-average absolute curvature profile along the flagellum, providing evidence that the model is capable of providing a framework for quantitative interpretation of imaging data.
Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation
Authors: Gibson William S. , Rodriguez Oscar L. , Shields Kaitlyn , Silver Catherine A. , Dorgham Abdullah , Emery Matthew , Deikus Gintaras , Sebra Robert , Eichler Evan E. , Bashir Ali , Smith Melissa L. , Watson Corey T. 
Published: July 2022

AbstractImmunoglobulins (IGs), crucial components of the adaptive immune system, are encoded by three genomic loci. However, the complexity of the IG loci severely limits the effective use of short read sequencing, limiting our knowledge of population diversity in these loci. We leveraged existing long read whole-genome sequencing (WGS) data, fosmid technology, and IG targeted single-molecule, real-time (SMRT) long-read sequencing (IG-Cap) to create haplotype-resolved assemblies of the IG Lambda (IGL) locus from 6 ethnically diverse individuals. In addition, we generated 10 diploid assemblies of IGL from a diverse cohort of individuals utilizing IG-cap. From these 16 individuals, we identified significant allelic diversity, including 37 novel IGLV alleles. In addition, we observed highly elevated single nucleotide variation (SNV) in IGLV genes relative to IGL intergenic and genomic background SNV density. By comparing SNV calls between our high quality assemblies and existing short read datasets from the same individuals, we show a high propensity for false-positives in the short read datasets. Finally, for the first time, we nucleotide-resolved common 5-10 Kb duplications in the IGLC region that contain functional IGLJ and IGLC genes. Together these data represent a significant advancement in our understanding of genetic variation and population diversity in the IGL locus.
Sequence Dependent Internucleosomal Interactions Dominate Array Assembly
Authors: Wang Yaqing , Stormberg Tommy , Hashemi Mohtadin , Kolomeisky Anatoly B. , Lyubchenko Yuri L. 
Published: July 2022

AbstractThe organization of the nucleosome array is a critical component of the chromatin assembly into higher order structure as well as its function. Here we investigated the contribution of the DNA sequence and internucleosomal interactions to the organization of the nucleosomal arrays in compact structures using Atomic Force Microscopy. We assembled nucleosomes on DNA substrates allowing for the formation of tetranucleosomes. We found that nucleosomes are capable of forming constructs with the close positioning of nucleosomes with no discernible space between them, even in the case of assembled dinucleosomes. This morphology of the array is in contrast with that observed for arrays assembled with repeats of the nucleosome positioning motifs separated by uniform spacers. Simulated assembly of tetranucleosomes by random placement along the substrates revealed that nucleosome array compaction is promoted by the interaction of the nucleosomes. We developed a theoretical model to account for the role of DNA sequence and internucleosomal interactions in the formation of the nucleosome structures. These findings suggest that, in the chromatin assembly, the affinity of the nucleosomes to the DNA sequence and the strengths of the internucleosomal interactions are the two major factors defining the compactness of the chromatin.
Adaptive decision making depends on pupil-linked arousal in rats performing tactile discrimination tasks
Authors: Narasimhan Shreya , Schriver Brian J. , Wang Qi 
Published: July 2022

AbstractPerceptual decision making is a dynamic cognitive process and is shaped by many factors, including behavioral state, reward contingency, and sensory environment. To understand the extent to which adaptive behavior in decision making is dependent upon pupil-linked arousal, we trained head-fixed rats to perform perceptual decision making tasks and systematically manipulated the probability of Go and No-go stimuli while simultaneously measuring their pupil size in the tasks. Our data demonstrated that the animals adaptively modified their behavior in response to the changes in the sensory environment. The response probability to both Go and No-go stimuli decreased as the probability of the Go stimulus being presented decreased. Analyses within the signal detection theory framework showed that while the animals’ perceptual sensitivity was invariant, their decision criterion increased as the probability of the Go stimulus decreased. Simulation results indicated that the adaptive increase in the decision criterion will increase possible water rewards during the task. Moreover, the adaptive decision making is dependent upon pupil-linked arousal as the increase in the decision criterion was the largest during low pupil-linked arousal periods. Taken together, our results demonstrated that the rats were able to adjust their decision making to maximize rewards in the tasks, and that adaptive behavior in perceptual decision making is dependent upon pupil-linked arousal.
Single Photon smFRET. II. Application to Continuous Illumination
Authors: Saurabh Ayush , Safar Matthew , Fazel Mohamadreza , Sgouralis Ioannis , Pressé Steve 
Published: July 2022

AbstractHere we adapt the Bayesian nonparametrics (BNP) framework presented in the first companion manuscript to analyze kinetics from single photon, single molecule Förster Resonance Energy Transfer (smFRET) traces generated under continuous illumination. Using our sampler, BNP-FRET, we learn the escape rates and the number of system states given a photon trace. We benchmark our method by analyzing a range of synthetic and experimental data. Particularly, we apply our method to simultaneously learn the number of system states and the corresponding kinetics for intrinsically disordered proteins (IDPs) using two-color FRET under varying chemical conditions. Moreover, using synthetic data, we show that our method can deduce the number of system states even when kinetics occur at timescales of interphoton intervals.Why It MattersIn the first companion manuscript of this series, we developed new methods to analyze noisy smFRET data. These methods eliminate the requirement ofa priorispecifying the dimensionality of the physical model describing a molecular complex’s kinetics. Here, we apply these methods to experimentally obtained datasets with samples illuminated by time-invariant laser intensities. In particular, we study interactions of IDPs.
Prospective investigation of SARS-CoV-2 seroprevalence in relation to natural infection and vaccination between October 2020 and September 2021 in the Czech Republic
Authors: Thon Vojtěch , Piler Pavel , Pavlík Tomáš , Andrýsková Lenka , Doležel Kamil , Kostka David , Pikhart Hynek , Bobák Martin , Klánová Jana 
Published: July 2022

AbstractPurposeMonitoring the seroprevalence of COVID-19 antibodies is an important tool to design and adjust preventive strategies. We used prospective data on a large population sample with repeated IgG antibody measurement to examine changes in seropositivity before and during the national vaccination campaign in the Czech Republic.Methods22,130 persons provided blood samples for COVID-19 IgG antibody measurement at two time points approximately 5-7 months apart, between October 2020 and March 2021 (Phase 1, before vaccination), and between April and September 2021 (during vaccination campaign).ResultsBefore vaccination (Phase 1), seroprevalence increased from 15% in October 2020 to 56% in March 2021. By the end of Phase 2, in September 2021, prevalence increased to 91%; the highest seroprevalence was seen among vaccinated persons with and without previous SARS-CoV-2 infection (99.7% and 97.2%, respectively), while the lowest seroprevalence was found among unvaccinated persons with no signs of disease (26%). Vaccination rates were lower in persons who were seropositive in phase 1 but increased with age and body mass index. Only 9% of unvaccinated subjects who were seropositive in phase 1 became seronegative by phase 2.ConclusionThe rapid increase in seropositivity during the 2nd wave of the COVID-19 epidemic (covered by phase 1 of this study) was followed by a similarly steep rise in seroprevalence during the national vaccination campaign, reaching seropositivity rates of over 97% among vaccinated persons.
The Effect of SARS-COV-2 Variant on Respiratory Features and Mortality Among Vaccinated and Non-Fully Vaccinated Patients
Authors: Hughes Thomas D. , Subramanian Ajan , Chakraborty Rana , Cotton Shannon A. , Giraldo Herrera Maria Del Pilar , Huang Yong , Lambert Natalie , Pinto Melissa D. , Rahmani Amir M. , Sierra Carmen Josefa , Downs Charles A. 
Published: July 2022

AbstractBackgroundSARS-CoV-2 (COVID-19) has caused over 80 million infections and 973,000 deaths in the United States, and mutations are linked to increased transmissibility. This study aimed to determine the effect of SARS-CoV-2 variants on respiratory features and mortality and to determine the effect of vaccination status.MethodA retrospective review of medical records (n=63,454 unique patients) using The University of California Health COvid Research Data Set (UC CORDS) was performed to identify respiratory features, vaccination status, and mortality. Variants were identified using the CDC data tracker.ResultsIncreased odds of death were observed among those not fully vaccinated (Delta OR: 1.64, p = 0.052; Omicron OR: 1.96, p < 0.01). Later variants (i.e., Delta and Omicron) demonstrated a reduction in the frequency of lower respiratory tract features with a concomitant increase in upper respiratory tract features. Vaccination status was associated with survival and a decrease in the frequency of many upper and lower respiratory tract features.DiscussionSARS-CoV-2 variants show a reduction in lower respiratory tract features with an increase in upper respiratory tract features. Being fully vaccinated results in fewer respiratory features and higher odds of survival, supporting vaccination in preventing morbidity and mortality from COVID-19.
Expansion microscopy of nuclear structure and dynamics in neutrophils
Authors: Holsapple Jason Scott , Schnitzler Lena , Rusch Louisa , Baldeweg Tobias Horst , Neubert Elsa , Kruss Sebastian , Erpenbeck Luise 
Published: July 2022

AbstractNeutrophils are key players of the immune system and possess an arsenal of effector functions, including the ability to form and expel neutrophil extracellular traps (NETs) in a process termed NETosis. During NETosis, the nuclear DNA/chromatin expands until it fills the whole cell and is released into the extracellular space. NETs are composed of DNA decorated with histones, proteins or peptides and NETosis is implicated in many diseases. Resolving the structure and dynamics of the nucleus in great detail is essential to understand the underlying processes but so far super-resolution methods have not been applied. Here, we developed an expansion microscopy-based method and determined the spatial distribution of chromatin/DNA, histone H1, and nucleophosmin (NPM1) with a 4.9-fold improved resolution (< 40 nm) and increased information content. It allowed us to identify the punctate localization of NPM1 in the nucleus and histone-rich domains in NETotic cells with a size of 54 nm. The technique could also be applied to components of the nuclear envelope (lamins B1 and B2) and myeloperoxidase (MPO) providing a complete picture of nuclear dynamics and structure. In conclusion, expansion microscopy enables super-resolved imaging of the highly dynamic structure of nuclei in immune cells.Why it mattersAccessibility to high-resolution imaging is critical to advancing research across various disciplines. However, conventionally this requires demanding optical hardware, special fluorophores or data analysis. Expansion microscopy is a technique adaptable to different cell and tissue types and is comparatively inexpensive and easy to perform. Applying this technique to cells and compartments such as the nucleus of immune cells that are difficult to image due to their size and morphology, yields valuable structural insights that would otherwise require more difficult super-resolution methods.
Listeria motility increases the efficiency of goblet cell invasion during intestinal infection
Authors: Wortel Inge M. N. , Kim Seonyoung , Liu Annie Y. , Ibarra Enid C. , Miller Mark J. 
Published: July 2022

AbstractListeria monocytogenes (Lm) is a food-borne pathogen that causes severe bacterial gastroenteritis, with high rates of hospitalization and mortality. Lm is ubiquitous in soil, water and livestock, and can survive and proliferate at low temperatures. Following oral ingestion of contaminated food, Lm crosses the epithelial through intestinal goblet cells in a mechanism depending on Lm InlA and host E-cadherin. Importantly, human infections typically occur with Lm growing at or below room temperature, which are flagellated and motile. Even though many important human bacterial pathogens are flagellated, little is known regarding the effect of bacterial motility on invasion and immune evasion.Here, we used complementary imaging and computer modeling approaches to test the hypothesis that bacterial motility helps Lm locate and engage target cells permissive for invasion. Imaging explanted mouse and human intestine, we confirmed that Lm grown at room temperature uses motility to scan the epithelial surface and preferentially attach to target cells. Furthermore, we integrated quantitative parameters from our imaging experiments to construct a versatile “layered” cellular Potts model (L-CPM) that simulates host-pathogen dynamics. Simulated data are consistent with the hypothesis that bacterial motility enhances invasion by allowing bacteria to search the epithelial surface for their preferred invasion targets. Indeed, our model consistently predicts that motile bacteria have invaded ∼2-fold more at the 1-hour mark. This invasion advantage persists even in the presence of host phagocytes, with the balance between invasion and phagocytosis governed almost entirely by bacterial motility.In conclusion, our simulations provide insight into host pathogen interactions and challenge fundamental assumptions regarding how phagocytes might limit bacterial invasion early during infection.
Divergence of olfactory receptors associated with the evolution of assortative mating and reproductive isolation in mice
Authors: Smadja Carole M. , Loire Etienne , Caminade Pierre , Severac Dany , Gautier Mathieu , Ganem Guila 
Published: July 2022

AbstractDeciphering the genetic bases of behavioural traits is essential to understanding how they evolve and contribute to adaptation and biological diversification, but it remains a substantial challenge, especially for behavioural traits with polygenic architectures. In this study, we developed a population genomics approach coupled with functional predictions to address the evolution and genetic basis of olfactory-based assortative mate preferences in the house mouse, suspected to have evolved as a response to selection against hybridisation. We used whole genome resequencing data and theC2statistic of the program BayPass, which contrasts allele frequencies corrected for population structure, to characterize genetic differentiation between sets of populations with strong contrast in behaviour (expressing or not assortative mate preferences) and we identified some regions of the genome showing the expected significant and consistent association with behavioural divergence. A series of Olfactory and Vomeronasal Receptor genes, among the most differentiated genomic regions and in line with functional predictions, stand out as the prime candidates underlying this olfactory-based behavioural divergence. These genes form large gene clusters in the genome, with two main candidate clusters extending up to 1.8 Mb. Variant analyses indicate a potential dual role of regulatory and protein-coding changes in the evolution of choosiness. This study shows that combining expectations on the genomic patterns of divergence with functional expectations represents a promising route to unravelling the genetic architecture of complex trait variation and provides novel insights into the role of olfactory and vomeronasal receptors in mammal adaptation and speciation.