bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polar lipids are linked to nanoparticles in xylem sap of temperate angiosperm species
Authors: Guan Xinyi , Schenk H. Jochen , Roth Mary R. , Welti Ruth , Werner Julia , Kaack Lucian , Trabi Christophe L. , Jansen Steven 
Published: October 2021

AbstractXylem sap of angiosperm species has been found to include low concentrations of polar lipids and nanoparticles, including surfactant-coated nanobubbles. Although the nanoparticles have been suggested to consist of polar lipids, no attempt has been made to determine if nanoparticle and lipid concentrations are related. Here, we examined concentrations of nanoparticles and lipids in xylem sap and contamination control samples of six temperate angiosperm species with a NanoSight device and based on mass spectrometry. We found (1) that the concentration of nanoparticles and lipids were both diluted when an increasing amount of sap was extracted, (2) that their concentrations were significantly correlated in three species, (3) that their concentrations were affected by vessel anatomy, and (4) that concentrations of nanoparticles and lipids were very low in contamination-control samples. Moreover, there was little seasonal difference, no freezing-thawing effect on nanoparticles, and little seasonal variation in lipid composition. These findings indicate that lipids and nanoparticles are related to each other, and largely do not pass interconduit pit membranes. Further research is needed to examine the formation and stability of nanoparticles in xylem sap in relation to lipid composition, and the complicated interactions among the gas, liquid, and solid phases in xylem conduits.
PermaPhosSer: autonomous synthesis of functional, permanently phosphorylated proteins
Authors: Zhu Phillip , Franklin Rachel , Vogel Amber , Stanisheuski Stanislau , Reardon Patrick , Sluchanko Nikolai N. , Beckman Joseph S. , Karplus P. Andrew , Mehl Ryan A. , Cooley Richard B. 
Published: October 2021

ABSTRACTInstalling stable, functional mimics of phosphorylated amino acids into proteins offers a powerful strategy to study protein regulation. Previously, a genetic code expansion (GCE) system was developed to translationally install non-hydrolyzable phosphoserine (nhpSer), with the γ-oxygen replaced with carbon, but it has seen limited usage. Here, we achieve a 40-fold improvement in this system by engineering into Escherichia coli a biosynthetic pathway that produces nhpSer from the central metabolite phosphoenolpyruvate. Using this “PermaPhosSer” system – an autonomous 21-amino acid E. coli expression system for incorporating nhpSer into target proteins – we show that nhpSer faithfully mimics the effects of phosphoserine in three stringent test cases: promoting 14-3-3/client complexation, disrupting 14-3-3 dimers, and activating GSK3β phosphorylation of the SARS-CoV-2 nucleocapsid protein. This facile access to nhpSer containing proteins should allow nhpSer to replace Asp and Glu as the go-to pSer phosphomimetic for proteins produced in E. coli.
Genomic insights into variation in thermotolerance between hybridizing swordtail fishes
Authors: Payne Cheyenne , Bovio Stephen , Powell Daniel , Gunn Theresa , Banerjee Shreya , Grant Victoria , Rosenthal Gil , Schumer Molly 
Published: October 2021

AbstractUnderstanding how organisms adapt to changing environments is a core focus of research in evolutionary biology. One common mechanism is adaptive introgression, which has received increasing attention as a potential route to rapid adaptation in populations struggling in the face of ecological change, particularly global climate change. However, hybridization can also result in deleterious genetic interactions that may limit the benefits of adaptive introgression. Here, we used a combination of genome-wide quantitative trait locus mapping and differential gene expression analyses between the swordtail fish speciesXiphophorus malincheandX. birchmannito study the consequences of hybridization on thermotolerance. While these two species are adapted to different thermal environments, we document a complicated architecture of thermotolerance in hybrids. We identify a region of the genome that contributes to reduced thermotolerance in individuals heterozygous forX. malincheandX. birchmanniancestry, as well as widespread misexpression in hybrids of genes that respond to thermal stress in the parental species, particularly in the circadian clock pathway. We also show that a previously mapped hybrid incompatibility betweenX. malincheandX. birchmannicontributes to reduced thermotolerance in hybrids. Together, our results highlight the challenges of understanding the impact of hybridization on complex ecological traits and its potential impact on adaptive introgression.
Light-sheet scattering microscopy to visualize long-term interactions between cells and extracellular matrix
Authors: Zhou Xiangda , Zhao Renping , Yanamandra Archana K. , Hoth Markus , Qu Bin 
Published: October 2021

AbstractVisualizing interactions between cells and the extracellular matrix (ECM) mesh is important to understand cell behavior and regulatory mechanisms by the extracellular environment. However, long term visualization of three-dimensional (3D) matrix structures remains challenging mainly due to photobleaching or blind spots perpendicular to the imaging plane. Here, we combine label-free light-sheet scattering microcopy (LSSM) and fluorescence microscopy to solve these problems. We verified that LSSM can reliably visualize structures of collagen matrices from different origin including bovine, human and rat tail. The quality and intensity of collagen structure images acquired by LSSM did not decline with time. LSSM offers abundant wavelength choice to visualize matrix structures, maximizing combination possibilities with fluorescently-labelled cells, allowing visualizing of long-term ECM-cell interactions in 3D. Interestingly, we observed ultrathin thread-like structures between cells and matrix using LSSM, which were not observed by normal fluorescence microscopy. Transient local alignment of matrix by cell-applied forces can be observed. In summary, LSSM provides a powerful and robust approach to investigate the complex interplay between cells and ECM.
The behavioral effects of gestational and lactational benzo[a]pyrene exposure vary by sex and genotype in mice with differences at the Ahr and Cyp1a2 loci
Authors: Honaker Amanda , Kyntchev Angela , Foster Emma , Clough Katelyn , Asiedu Emmanuella , Feltner Mackenzie , Ferguson Victoria , Forrest Philip Tyler , Mullaguru Jayasree , Niang Mame Diarra , Perry Connor , Sene Yvonne , Curran Christine Perdan 
Published: October 2021

AbstractBenzo[a]pyrene (BaP) is a polycyclic aromatic hydrocarbon (PAH) and known carcinogen in the Top 10 on the United States’ list of priority pollutants. Humans are exposed through a variety of sources including tobacco smoke, grilled foods and fossil fuel combustion. Recent studies of children exposed to higher levels of PAHs during pregnancy and early life have identified numerous adverse effects on the brain and behavior that persist into school age and adolescence. Our studies were designed to look for genotype and sex differences in susceptibility to gestational and lactational exposure to BaP using a mouse model with allelic differences in the aryl hydrocarbon receptor and the xenobiotic metabolizing enzyme CYP1A2. Pregnant dams were exposed to 10 mg/kg/day of BaP in corn oil-soaked cereal or the corn oil vehicle alone from gestational day 10 until weaning at postnatal day 25. Neurobehavioral testing began at P60 using one male and one female per litter. We found main effects of sex, genotype and treatment as well as significant gene x treatment and sex x treatment interactions. BaP-treated female mice had shorter latencies to fall in the Rotarod test. High-affinity AhrbCyp1a2(−/−) mice had greater impairments in Morris water maze. Interestingly, poor-affinity AhrdCyp1a2(−/−) mice also had deficits in spatial learning and memory regardless of treatment. We believe our findings provide future directions in identifying human populations at highest risk of early life BaP exposure, because our model mimics known human variation in our genes of interest. Our studies also highlight the value of testing both males and females in all neurobehavioral studies.HighlightsGestational and lactational benzo[a]pyrene (BaP) exposure has sex and genotype-specific neurobehavioral effects in mice.Female mice were more susceptible to motor deficits following developmental BaP exposure. Males were more susceptible to deficits in reversal learning and memory.AhrbCyp1a2(−/−) knockout mice were more susceptible to spatial learning and memory deficits following developmental BaP exposure.Poor-affinity AhrdCyp1a2(−/−) mice had deficits in spatial learning and memory regardless of treatment.
E-Cannula reveals anatomical diversity in sharp-wave ripples as a driver for the recruitment of distinct hippocampal assemblies
Authors: Liu Xin , Terada Satoshi , Kim Jeong-Hoon , Lu Yichen , Ramezani Mehrdad , Grosmark Andres , Losonczy Attila , Kuzum Duygu 
Published: October 2021

AbstractThe hippocampus plays a critical role in spatial navigation and episodic memory. However, research on in vivo hippocampal activity dynamics has mostly relied on single modalities such as electrical recordings or optical imaging, with respectively limited spatial and temporal resolution. This technical difficulty greatly impedes multi-level investigations into network state-related changes in cellular activity. To overcome these limitations, we developed the E-Cannula integrating fully transparent graphene microelectrodes with imaging-cannula. The E-Cannula enables the simultaneous electrical recording and two-photon calcium imaging from the exact same population of neurons across an anatomically extended region of the mouse hippocampal CA1 stably across several days. These large-scale simultaneous optical and electrical recordings showed that local hippocampal sharp wave ripples (SWRs) are associated with synchronous calcium events involving large neural populations in CA1. We show that SWRs exhibit spatiotemporal wave patterns along multiple axes in 2D space with different spatial extents (local or global) and temporal propagation modes (stationary or travelling). Notably, distinct SWR wave patterns were associated with, and decoded from, the selective recruitment of orthogonal CA1 cell assemblies. These results suggest that the diversity in the anatomical progression of SWRs may serve as a mechanism for the selective activation of the unique hippocampal cell assemblies extensively implicated in the encoding of distinct memories. Through these results we demonstrate the utility of the E-Cannula as a versatile neurotechnology with the potential for future integration with other optical components such as green lenses, fibers or prisms enabling the multi-modal investigation of cross-time scale population-level neural dynamics across brain regions.
NetGAM: Using generalized additive models to improve the predictive power of ecological network analyses constructed using time-series data
Authors: Gleich Samantha J. , Cram Jacob A. , Weissman Jake L. , Caron David A. 
Published: October 2021

AbstractEcological network analyses are used to identify potential biotic interactions between microorganisms from species abundance data. These analyses are often carried out using time-series data; however, time-series networks have unique statistical challenges. Time-dependent species abundance data can lead to species co-occurrence patterns that are not a result of direct, biotic associations and may therefore result in inaccurate network predictions. Here, we describe a generalize additive model (GAM)-based data transformation that removes time-series signals from species abundance data prior to running network analyses. Validation of the transformation was carried out by generating mock, time-series datasets, with an underlying covariance structure, running network analyses on these datasets with and without our GAM transformation, and comparing the network outputs to the known covariance structure of the simulated data. The results revealed that seasonal abundance patterns substantially decreased the accuracy of the inferred networks. Additionally, the GAM transformation increased the F1 score of inferred ecological networks on average and improved the ability of network inference methods to capture important features of network structure. This study underscores the importance of considering temporal features when carrying out network analyses and describes a simple, effective tool that can be used to improve results.
The Listening Zone of Human Electrocorticographic Field Potential Recordings
Authors: McCarty Meredith J , Woolnough Oscar , Mosher John C. , Seymour John , Tandon Nitin 
Published: October 2021

AbstractIntracranial electroencephalographic (icEEG) recordings provide invaluable insights into neural dynamics in humans due to their unmatched spatiotemporal resolution. Yet, such recordings reflect the combined activity of multiple underlying generators, confounding the ability to resolve spatially distinct neural sources. To empirically quantify the listening zone of icEEG recordings, we computed the correlations between signals as a function of distance (expressed as full width at half maximum; FWHM) between 8,752 recording sites in 71 patients implanted with either subdural electrodes (SDE), stereo-encephalography electrodes (sEEG), or high-density sEEG electrodes. As expected, for both SDE and sEEG electrodes, higher frequency signals exhibited a sharper fall off relative to lower frequency signals. For broadband high gamma (BHG) activity, the mean FWHM of SDEs (6.6 ± 2.5 mm) and sEEGs in gray matter (7.14 ± 1.7 mm) was not significantly different, however the FWHM for low frequencies recorded by sEEGs was 2.45 mm smaller than SDEs. White matter sEEG electrodes showed much lower power for frequencies 17 to 200 Hz (q < 0.01) and a much broader decay (11.3 ± 3.2 mm) than gray matter electrodes (7.14 ± 1.7 mm). The use of a bipolar referencing scheme significantly lowered FWHM for sEEG electrodes, as compared with a white matter reference or a common average reference. These results outline the influence of array design, spectral bands, and referencing schema on local field potential recordings and source localization in icEEG recordings in humans. The metrics we derive have immediate relevance to the analysis and interpretation of both cognitive and epileptic data.
scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data
Authors: Shen Siqi , Zheng Ye , Keleş Sündüz 
Published: October 2021

AbstractSummaryQuantitative tools are needed to leverage the unprecedented resolution of single-cell high-throughput chromatin conformation (scHi-C) data and to integrate it with other single-cell data modalities. We present single-cell gene associating domain (scGAD) scores as a dimension reduction and exploratory analysis tool for scHi-C data. scGAD enables summarization at the gene level while accounting for inherent gene-level genomic biases. Low-dimensional projections with scGAD capture clustering of cells based on their 3D structures. scGAD enables identifying genes with significant chromatin interactions within and between cell types. We further show that scGAD facilitates the integration of scHi-C data with other single-cell data modalities by enabling its projection onto reference low-dimensional embeddings.AvailabilityscGAD is part of the BandNorm R package at https://sshen82.github.io/BandNorm/articles/scGAD-tutorial.html.Contactkeles@stat.wisc.edu, yzheng23@fredhutch.orgSupplementary informationSupplementary data are available at Bioinformatics online.
Coding of latent variables in sensory, parietal, and frontal cortices during closed-loop virtual navigation
Authors: Noel Jean-Paul , Balzani Edoardo , Avila Eric , Lakshminarasimhan Kaushik , Bruni Stefania , Alefantis Panos , Savin Cristina , Angelaki Dora E. 
Published: October 2021

AbstractWe do not understand how neural nodes operate and coordinate within the recurrent action-perception loops that characterize naturalistic self-environment interactions. Here, we record single-unit spiking activity and local field potentials (LFPs) simultaneously from the dorsomedial superior temporal area (MSTd), parietal area 7a, and dorsolateral prefrontal cortex (dlPFC) as monkeys navigate in virtual reality to “catch fireflies.” This task requires animals to actively sample from a closed-loop virtual environment while concurrently computing continuous latent variables: (i) the distance and angle travelled (i.e., path integration) and (ii) the distance and angle to a memorized firefly location (i.e., a hidden spatial goal). We observed a patterned mixed selectivity, with the prefrontal cortex most prominently coding for latent variables, parietal cortex coding for sensorimotor variables, and MSTd most often coding for eye-movements. However, even the traditionally considered sensory area (i.e., MSTd) tracked latent variables, demonstrating path integration and vector-coding of hidden spatial goals. Further, global encoding profiles and unit-to-unit coupling (i.e., noise correlations) suggested a functional subnetwork composed by MSTd and dlPFC, and not between these and 7a, as anatomy would suggest. We show that the greater the unit-to-unit coupling between MSTd and dlPFC, the more the animals’ gaze position was indicative of the ongoing location of the hidden spatial goal. We suggest this MSTd-dlPFC subnetwork reflects the monkeys’ natural and adaptive task strategy wherein they continuously gaze toward the location of the (invisible) target. Together, these results highlight the distributed nature of neural coding during closed action-perception loops and suggest that fine-grain functional subnetworks may be dynamically established to subserve (embodied) task strategies.
Accurate estimation of intrinsic biases for improved analysis of bulk and single-cell chromatin accessibility sequencing data using SELMA
Authors: Hu Shengen Shawn , Liu Lin , Li Qi , Ma Wenjing , Guertin Michael J. , Meyer Clifford A. , Deng Ke , Zhang Tingting , Zang Chongzhi 
Published: October 2021

AbstractGenome-wide profiling of chromatin accessibility by DNase-seq or ATAC-seq has been widely used to identify regulatory DNA elements and transcription factor binding sites. However, enzymatic DNA cleavage exhibits intrinsic sequence biases that confound chromatin accessibility profiling data analysis. Existing computational tools are limited in their ability to account for such intrinsic biases and not designed for analyzing single-cell data. Here, we present Simplex Encoded Linear Model for Accessible Chromatin (SELMA), a computational method for systematic estimation of intrinsic cleavage biases from genomic chromatin accessibility profiling data. We demonstrate that SELMA yields accurate and robust bias estimation from both bulk and single-cell DNase-seq and ATAC-seq data. SELMA can utilize internal mitochondrial DNA data to improve bias estimation. We show that transcription factor binding inference from DNase footprints can be improved by incorporating estimated biases using SELMA. Furthermore, we show strong effects of intrinsic biases in single-cell ATAC-seq data, and develop the first single-cell ATAC-seq intrinsic bias correction model to improve cell clustering. SELMA can enhance the performance of existing bioinformatics tools and improve the analysis of both bulk and single-cell chromatin accessibility sequencing data.
Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution
Authors: Akıl Caner , Ali Samson , Tran Linh T. , Gaillard Jeremie , Li Wenfei , Hayashida Kenichi , Hirose Mika , Kato Takayuki , Oshima Atsunori , Fujishima Kosuke , Blanchoin Laurent , Narita Akihiro , Robinson Robert C. 
Published: October 2021

AbstractTubulins are critical for the internal organization of eukaryotic cells, and understanding their emergence is an important question in eukaryogenesis. Asgard archaea are the closest known prokaryotic relatives to eukaryotes. Here, we elucidated the apo and nucleotide-bound X-ray structures of an Asgard tubulin from hydrothermal-living Odinarchaeota (OdinTubulin). The GTP-bound structure resembles a microtubule protofilament, with GTP bound between subunits, coordinating the “+” end subunit through a network of water molecules and unexpectedly by two cations. A water molecule is located suitable for GTP hydrolysis. Time course crystallography and electron microscopy revealed conformational changes on GTP hydrolysis. OdinTubulin forms tubules at high temperatures, with short curved protofilaments coiling around the tubule circumference, more similar to FtsZ, rather than running parallel to its length, as in microtubules. Thus, OdinTubulin represents an evolution intermediate between prokaryotic FtsZ and eukaryotic microtubule-forming tubulins.
EnterotoxigenicEscherichia colidegrades the host MUC2 mucin barrier to facilitate critical pathogen-enterocyte interactions in human small intestine
Authors: Sheikh Alaullah , Wangdi Tamding , Vickers Tim J , Aaron Bailey , Palmer Margot , Miller Mark J. , Kim Seonyoung , Herring Cassandra , Simoes Rita , Crainic Jennifer A. , Gildersleeve Jeffrey C. , van der Post Sjoerd , Hansson Gunnar C. , Fleckenstein James M. 
Published: October 2021

AbstractEnterotoxigenicEscherichia coli(ETEC) are a genetically diverse pathologic variant ofE. colidefined by the production of heat-labile (LT) and/or heat-stable (ST) toxins. ETEC are estimated to cause hundreds of millions of cases of diarrheal illness annually. However, it is not clear that all strains are equally equipped to cause disease and asymptomatic colonization with ETEC is common in low-middle income regions lacking basic sanitation and clean water where ETEC are ubiquitous. Recent molecular epidemiology studies have revealed a significant association between strains which produce EatA, a secreted autotransporter protein, and the development of symptomatic infection. Here, we demonstrate that LT stimulates production of MUC2 mucin by goblet cells in human small intestine, enhancing the protective barrier between pathogens and enterocytes. In contrast, using explants of human small intestine as well as small intestinal enteroids, we show that EatA counters this host defense by engaging and degrading the MUC2 mucin barrier to promote bacterial access to target enterocytes and ultimately toxin delivery suggesting that EatA plays a crucial role in the molecular pathogenesis of ETEC. These findings may inform novel approaches to prevention of the acute diarrheal illness as well as the sequelae associated with ETEC and other pathogens that rely on EatA and similar proteases for efficient interaction with their human hosts.