bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using the UniFrac metric on Whole Genome Shotgun data
Authors: Wei Wei , Koslicki David 
Published: January 2022

AbstractThe UniFrac metric has proven useful in revealing diversity across metagenomic communities. Due to the phylogeny-based nature of this measurement, UniFrac has historically only been applied to 16S rRNA data. Simultaneously, Whole Genome Shotgun (WGS) metagenomics has been increasingly widely employed and proven to provide more information than 16S data, but a UniFrac-like diversity metric suitable for WGS data has not previously been developed. The main obstacle for UniFrac to be applied directly to WGS data is the absence of phylogenetic distances in the taxonomic relationship derived from WGS data. In this study, we demonstrate a method to overcome this intrinsic difference and compute the UniFrac metric on WGS data by assigning branch lengths to the taxonomic tree obtained from input taxonomic profiles. We conduct a series of experiments to demonstrate that this WGSUniFrac method is comparably robust to traditional 16S UniFrac and is not highly sensitive to branch lengths assignments, be they data-derived or model-prescribed. Code implementing a prototype of WGSUniFrac along with paper reproducible are available at https://github.com/KoslickiLab/WGSUniFrac.
Is mindfulness associated with lower pain reactivity and connectivity of the default mode network? A replication and extension study in healthy and episodic migraine participants
Authors: Hunt Carly , Letzen Janelle E. , Krimmel Samuel R , Burrowes Shana A.B. , Haythornthwaite Jennifer A. , Finan Patrick , Vetter Maria , Seminowicz David A. 
Published: January 2022

AbstractFormal training in mindfulness-based practices promotes reduced experimental and clinical pain, which may be driven by reduced emotional pain reactivity and undergirded by alterations in the default mode network (DMN), implicated in mind-wandering and self-referential processing. Recent results published in this journal suggest that mindfulness, defined here as the day-to-day tendency to maintain a non-reactive mental state in the absence of training, associates with lower pain reactivity, greater heat-pain thresholds, and resting-state DMN functional connectivity (FC) in healthy adults in a similar manner to trained mindfulness. The extent to which these findings extend to chronic pain samples and replicate in healthy samples is unknown. Using data from healthy adults (n = 36) and episodic migraine patients (n = 98) and replicating previously published methods, we observed no significant association between mindfulness and heat-pain threshold (r = -0.05, p = .80), pain intensity (r = -.02, p = .89) or unpleasantness (r = .02, p = .89), or pain catastrophizing (PC; r = .30, p = .08) in healthy controls, or between mindfulness and headache frequency (r = -.11, p = .26), severity (r = .03, p = .77), impact (r = -.17, p = .10) or PC (r = -0.09, p = .36) in patients. There was no association between DMN connectivity and mindfulness in either sample when probed via seed-based FC analyses. In post-hoc whole brain exploratory analyses, a meta-analytically derived DMN node (i.e., posterior cingulate cortex; PCC) showed connectivity with regions unassociated with pain processing as a function of mindfulness, such that healthy adults higher in mindfulness showed greater PCC-cerebellum FC. Collectively, these findings suggest that the relationship between mindfulness and DMN-FC may be nuanced or lacking in robustness, and cast doubt on mindfulness as a clinically meaningful protective factor in migraine.PerspectiveThis study tested relationships between mindfulness and pain, pain reactivity and default mode connectivity in healthy adults and migraine patients. Findings cast doubt on mindfulness as an individual difference marker of the ability to cope with pain in healthy adults, and as a protective factor in episodic migraine.
c-Fos protein shRNA blockade in the central amygdala nucleus interfere with rats emotional reactivity on behavioral and autonomic level
Authors: Robakiewicz Ita 
Published: January 2022

AbstractThis report is focusing on a function of the c-Fos protein in an associative, stress-induced memory. The shRNA vector injections were utilised to functionally silence the central amygdala nucleus in adult Wistar rats. Subsequently the operated animals and their control counterparts were screened in a selection of an emotionally-dependent tests and in a few standard behavioral neuroscience tools. Rats from the c-Fos silencing (ShFos) group expressed contra-depressive-like behaviors in Porsolt Swimming Test, spending more time actively searching for escape way then the rats from the control group. ShFos rats also had engaged in a more rapid activity in the Open Field Test, showing a decline in the neo-phobia. Micturition was decreased in shFos animals, indicating a change in the emotionality on an autonomic level. Presented results are showcasing a multi-directional regulation of the behaviors from the central amygdala nucleus by the c-Fos activity.
Physiological responses of plants to in vivo XRF radiation damage: insights from anatomical, elemental, histochemical, and ultrastructural analyses
Authors: Montanha Gabriel Sgarbiero , Marques João Paulo Rodrigues , Rodrigues Eduardo Santos , Jones Michael W. M. , de Carvalho Hudson Wallace Pereira 
Published: January 2022

AbstractX-ray fluorescence spectroscopy (XRF) is a powerful technique for the in vivo assessment of plant tissues. However, the potential X-ray exposure damages might affect the structure and elemental composition of living plant tissues leading to artefacts in the recorded data. Herein, we exposed soybean (Glycine max (L.) Merrill) leaves to several X-ray doses through a polychromatic benchtop microprobe X-ray fluorescence spectrometer, modulating the photon flux by adjusting either the beam size, focus, or exposure time. The structure, ultrastructure and physiological responses of the irradiated plant tissues were investigated through light and transmission electron microscopy (TEM). Depending on the dose, the X-ray exposure induced decreased K and X-ray scattering intensities, and increased Ca, P, and Mn signals on soybean leaves. Anatomical analysis indicated necrosis of the epidermal and mesophyll cells on the irradiated spots, where TEM images revealed the collapse of cytoplasm and cell-wall breaking. Furthermore, the histochemical analysis detected the production of reactive oxygen species, as well as inhibition of chlorophyll autofluorescence in these areas. Under certain X-ray exposure conditions, e.g., high photon flux and exposure time, XRF measurements may affect the soybean leaves structures, elemental composition, and cellular ultrastructure, and induce programmed cell death. These results shed light on the characterization of the radiation damage, and thus, help to assess the X-ray radiation limits and strategies for in vivo for XRF analysis.HighlightBy exposing soybean leaves to several X-ray doses, we show that the characteristic X-ray induced elemental changes stem from plants’ physiological signalling or responses rather than only sample dehydration.
Curcumin and NCLX Inhibitors Share Anti-Tumoral Mechanisms in Microsatellite-Instability-Driven Colorectal Cancer
Authors: Guéguinou Maxime , Ibrahim Sajida , Bourgeais Jérôme , Robert Alison , Pathak Trayambak , Zhang Xuexin , Crottès David , Dupuy Jacques , Ternant David , Monbet Valérie , Guibon Roseline , Flores-Romero Hector , Lefèvre Antoine , Lerondel Stéphanie , Le Pape Alain , Dumas Jean-François , Frank Philippe G. , Girault Alban , Chautard Romain , Guéraud Françoise , García-Sáez Ana J. , Ouaissi Mehdi , Emond Patrick , Sire Olivier , Hérault Olivier , Fromont-Hankard Gaëlle , Vandier Christophe , Tougeron David , Trebak Mohamed , Raoul William , Lecomte Thierry 
Published: January 2022

AbstractColorectal cancer (CRC) is associated with high mortality worldwide and new targets are needed to overcome treatment resistance. Recent evidences highlight a role of the mitochondria calcium homeostasis in the development of CRC. In this context, we aimed to evaluate the role of the mitochondrial sodium-calcium-lithium exchanger (NCLX) and its targeting in CRC. We also identified curcumin as a new potential inhibitor of NCLX.In vitro, curcumin exerted strong anti-tumoral activity through its action on NCLX with mtCa2+ and reactive oxygen species overload associated with a mitochondrial membrane depolarization, leading to reduced ATP production and apoptosis through mitochondrial permeability transition pore opening concomitant with G2/M cell cycle arrest. NCLX inhibition with either CGP37157 (a benzodiazepine derivative), small interfering RNA-mediated knock-down or knockout approaches reproduced the effects of curcumin. Altered mitochondrial respiration, cellular aerobic glycolysis and endoplasmic reticulum–mitochondria membrane perturbations participated in these mechanisms. In a xenograft mouse model, NCLX inhibitors decreased CRC tumor growth. Both transcriptomic analysis of The Cancer Genome Atlas dataset and immunohistochemical analysis of tissue microarrays from 381 patients with microsatellite instability (MSI)-driven CRC demonstrated that higher NCLX expression was associated with MSI status and for the first time NCLX expression was significantly associated with recurrence-free survival in MSI CRC patients.Our findings provide strong evidence that blocking NCLX inhibits CRC in vitro and in vivo. We highlight a novel anti-tumoral mechanism of curcumin through its action on NCLX and mitochondria calcium overload that could benefit for therapeutic treatment of patients with MSI CRC.
Septins Provide Microenvironment Sensing and Cortical Actomyosin Partitioning in Motile Amoeboid T Lymphocytes
Authors: Zhovmer Alexander S. , Manning Alexis , Smith Chynna , Sáez Pablo J. , Ma Xuefei , Tsygankov Denis , Cartagena-Rivera Alexander X. , Singh Rakesh K. , Tabdanov Erdem D. 
Published: January 2022

ABSTRACTThe all-terrain motility of lymphocytes in tissues and tissue-like gels is best described as amoeboid motility. For amoeboid motility, lymphocytes do not require specific biochemical or structural modifications to the surrounding extracellular matrix. Instead, they rely on changing shape and steric interactions with the microenvironment. However, the exact mechanism of amoeboid motility remains elusive. Here we report that septins shape T cells for amoeboid motility. Specifically, septins form F-actin and alpha-actinin-rich cortical rings at the sites of cortex-indenting collisions of T cells with the extracellular matrix. Cortical rings compartmentalize cells into chains of spherical segments that are spatially conformed to the available lumens, forming transient ‘hourglass’-shaped steric locks onto the surrounding collagen fibers. The steric lock facilitates pressure-driven peristaltic propulsion of cytosolic content by individually contracting cell segments. Our results demonstrate that septins provide microenvironment-guided partitioning of actomyosin contractility and steric pivots for amoeboid motility of T cells in tissue-like microenvironments.GLOSSARYSteric interactions - interactions by the means of their spatial collision dependent on objects’ shapes.Steric guidance - cell navigation within crowded 3D environments, determined by the available passages around and between steric hindrances.Peristaltic treadmilling - locomotion mode by the means of a repeated sequence of polarized cell cortex extension, stabilization, and retraction, accompanied by translocation of nucleus and cytoplasmviacircumferential cortex contractility.Significance StatementT cells can be highly motile, searching for cognate antigens or better yet targets in chimeric antigen receptor therapy settings. However, mechanisms of motility remain elusive for T cells migrating in structurally and biochemically diverse tissues. Here we address one pivotal question of basic and clinical immunology - How T cells achieve the ‘all-terrain’ motility? Here we decipher and report septin-based T cell motility in a 3D tissue-like environment. Specifically, we show that septins facilitate cell morphological responsiveness to the steric obstacles,i.e., collagen fiber-wise partitioning of actomyosin cortex contractility and cell-obstacle steric interactions. These responses coordinate peristaltic propulsion of the lymphocyte’s cytosolic content along its individually contracting cell segments, forming the obstacle-avoiding motility,i.e.,circumnavigation, shared across various tested lymphocytes.
Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device
Authors: Shalon Dari , Culver Rebecca Neal , Grembi Jessica A. , Folz Jacob , Treit Peter , Dethlefsen Les , Meng Xiandong , Yaffe Eitan , Spencer Sean , Shi Handuo , Aranda-Díaz Andrés , Patterson Andrew D. , Triadafilopoulos George , Holmes Susan P. , Mann Matthias , Fiehn Oliver , Relman David A. , Huang Kerwyn Casey 
Published: January 2022

AbstractThe spatiotemporal structure of the human microbiome and metabolome reflects and determines regional intestinal physiology and may have implications for disease. Yet, we know little about the distribution of microbes and their products in the gut because of reliance on stool samples and limited access only to some regions of the gut using endoscopy in fasting or sedated individuals. To address these deficiencies, we developed and evaluated a safe, ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion. The collection of 240 intestinal samples from 15 healthy individuals using the device revealed significant differences between microbes and metabolites present in the intestines versus stool. Certain microbial taxa were differentially enriched, and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundance predicted species that altered the bile acid pool through deconjugation. Overall, we identified heterogeneous intestinal profiles of bacterial taxa and metabolites indicating that non-invasive multi-regional sampling of the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in human physiology and disease.
Membrane-mediated interactions between hinge-like particles
Authors: Li Bing , Abel Steven M. 
Published: January 2022

AbstractAdsorption of nanoparticles on a membrane can give rise to interactions between particles, mediated by membrane deformations, that play an important role in self-assembly and membrane remodeling. Previous theoretical and experimental research has focused on nanoparticles with fixed shapes, such as spherical, rod-like, and curved nanoparticles. Recently, hinge-like DNA origami nanostructures have been designed with tunable mechanical properties. Inspired by this, we investigate the equilibrium properties of hinge-like particles adsorbed on an elastic membrane using Monte Carlo and umbrella sampling simulations. The configurations of an isolated particle are influenced by competition between bending energies of the membrane and the particle, which can be controlled by changing adsorption strength and hinge stiffness. When two adsorbed particles interact, they effectively repel one another when the strength of adhesion to the membrane is weak. However, a strong adhesive interaction induces an effective attraction between the particles, which drives their aggregation. The configurations of the aggregate can be tuned by adjusting the hinge stiffness: Tip-to-tip aggregation occurs for flexible hinges, whereas tip-to-middle aggregation also occurs for stiffer hinges. Our results highlight the potential for using the mechanical features of deformable nanoparticles to influence their self-assembly when the particles and membrane mutually influence one another.
FoodMicrobionet v4: a large, integrated, open and transparent database for food bacterial communities
Authors: Parente Eugenio , Zotta Teresa , Ricciardi Annamaria 
Published: January 2022

AbstractWith the availability of high-throughput sequencing techniques our knowledge of the structure and dynamics of food microbial communities has made a quantum leap. However, this knowledge is dispersed in a large number of papers and hard data are only partly available through powerful on-line databases and tools such as QIITA, MGnify and the Integrated Microbial Next Generation Sequencing platform, whose annotation is not optimized for foods.Here, we present the 4th iteration of FoodMicrobionet, a database of the composition of bacterial microbial communities of foods and food environments. With 180 studies and 10,151 samples belonging to 8 major food groups FoodMicrobionet 4.1.2 is arguably the largest and best annotated database on food bacterial communities. This version includes 1,684 environmental samples and 8,467 food samples, belonging to 16 L1 categories and 196 L6 categories of the EFSA FoodEx2 classification and is approximately 4 times larger than previous version (3.1, https://doi.org/10.1016/j.ijfoodmicro.2019.108249).Using data in FoodMicrobionet we confirm that taxonomic assignment at the genus level can be performed confidently for the majority of amplicon sequence variants using the most commonly used 16S RNA gene target regions (V1-V3, V3-V4, V4), with best results with higher quality sequences and longer fragment lengths, but that care should be exercised in confirming the assignment at species level.Both FoodMicrobionet and related data and software conform to FAIR (findable, accessible, interoperable, reusable/reproducible) criteria for scientific data and software and are freely available on public repositories (GitHub, Mendeley data).Even if FoodMicrobionet does not have the sophistication of QIITA, IMNGS and MGnify, we feel that this iteration, due to its size and diversity, provides a valuable asset for both the scientific community and industrial and regulatory stakeholders.
High abundance of transcription regulators compacts the nucleoid in Escherichia coli
Authors: Yilmaz Cihan , Schnetz Karin 
Published: January 2022

AbstractIn enteric bacteria organization of the circular chromosomal DNA into a highly dynamic and toroidal shaped nucleoid involves various factors such as DNA supercoiling, nucleoid-associated proteins (NAPs), the structural maintenance of chromatin (SMC) complex, and macro-domain organizing proteins. Here we show that ectopic expression of transcription regulators at high levels leads to nucleoid compaction. This serendipitous result was obtained by fluorescence microscopy upon ectopic expression of the transcription regulator and phosphodiesterase PdeL of Escherichia coli of a strain expressing the mCherry-tagged HU-α subunit (HupA) for nucleoid staining. Nucleoid compaction by PdeL depends on DNA-binding, but not on its enzymatic phosphodiesterase activity. Nucleoid compaction was also observed upon high-level ectopic expression of the transcription regulators LacI, RutR, RcsB, LeuO and Cra, which range from single target gene regulators to global regulators. In case of LacI its high-level expression in presence of the gratuitous inducer IPTG also led to nucleoid compaction indicating that compaction is caused by unspecific DNA-binding. In all cases nucleoid compaction correlated with misplacement of the FtsZ ring and loss of MukB foci, a subunit of the SMC complex. Thus, high levels of several transcription regulators cause nucleoid compaction with consequences on transcription, replication, and cell division.ImportanceThe bacterial nucleoid is a highly organized and dynamic structure for simultaneous, transcription, replication and segregation of the bacterial genome. Compaction of the nucleoid and disturbance of DNA segregation and cell division by artificially high levels of transcription regulators, as described here, reveals that an excess of DNA-binding protein disturbs nucleoid structuring. The results suggest that ectopic expression levels of DNA-binding proteins for genetic studies of their function but also for their purification should be carefully controlled and adjusted.
Hurricane Harvey Impacts on Water Quality and Microbial Communities in Houston, TX Waterbodies
Authors: LaMontagne Michael G. , Zhang Yan , Guillen George J. , Gentry Terry J. , Allen Michael S. 
Published: January 2022

AbstractHurricanes, and other extreme weather events, can temporarily alter the structure of coastal systems and generate floodwaters that are contaminated with fecal-associated microbes; however, every coastal system and extreme weather event is unique, so identification of trends and commonalities in these episodic events is challenging. To improve our understanding of the resilience of coastal systems to the disturbance of extreme weather events and the risk exposure to floodwaters poses to the public, we monitored water quality, fecal indicator bacteria (FIB) at three stations within Clear Lake, an estuary between Houston and Galveston, and three stations in bayous that feed into the estuary. Water samples were collected immediately before Hurricane Harvey (pre-HH, August 25th, 2017), immediately after (HH, August 30th) and then throughout the fall of 2017 (post-HH). FIB levels were monitored by culturing E. coli and Enterococci. Microbial community structure was profiled by high throughput sequencing of PCR-amplified 16S rRNA gene fragments. Water quality and FIB data was also compared to historical data for these water body segments. Before Harvey, salinity within Clear Lake ranged from 9 to 11 practical salinity units (PSU). Immediately after the storm, salinity dropped to < 1 PSU and then gradually increased to pre-storm and historical levels over two months. Dissolved inorganic nutrient levels were also relatively low immediately after Harvey and returned, within a couple of months, to pre-HH and historical levels. FIB levels were elevated immediately after the storm; however, after one week, E. coli levels had decreased to acceptable levels for freshwater. Enterococci levels collected several weeks after the storm were within the range of historical levels for these water bodies. Microbial community structure shifted from a system dominated by Cyanobacteria sp. before HH to a system dominated by Proteobacteria and Bacteroidetes immediately after. Further, several sequences observed only in floodwater showed similarity to sequences previously reported for samples collected following Hurricane Irene. These changes in beta diversity corresponded to salinity and nitrate/nitrite concentrations. Differential abundance analysis of metabolic pathways, predicted from 16S sequences, suggested that pathways associated with virulence and antibiotic resistance were elevated in floodwater. Overall, these results suggest that recovery of the Clear Lake system following Hurricane Harvey took at least a month and floodwater generated from these extreme events may have high levels of fecal contamination, antibiotic resistant bacteria and bacteria rarely observed in other systems.