bluuebunny/crossref_metadata_2025 huggingface dataset:
Conservation of Nematocida microsporidia gene expression and host response in Caenorhabditis nematodes
Authors: Wan Yin Chen , Troemel Emily R. , Reinke Aaron W.
Published: June 2022

Microsporidia are obligate intracellular parasites that are known to infect most types of animals. Many species of microsporidia can infect multiple related hosts, but it is not known if microsporidia express different genes depending upon which host species is infected or if the host response to infection is specific to each microsporidia species. To address these questions, we took advantage of two species of Nematocida microsporidia, N. parisii and N. ausubeli, that infect two species of Caenorhabditis nematodes, C. elegans and C. briggsae. We performed RNA-seq at several time points for each host infected with either microsporidia species. We observed that Nematocida transcription was largely independent of its host. We also observed that the host transcriptional response was similar when infected with either microsporidia species. Finally, we analyzed if the host response to microsporidia infection was conserved across host species. We observed that although many of the genes upregulated in response to infection are not direct orthologs, the same expanded gene families are upregulated in both Caenorhabditis hosts. Together our results describe the transcriptional interactions of Nematocida infection in Caenorhabditis hosts and demonstrate that these responses are evolutionarily conserved.

Significance statement

Microsporidia are a powerful model to study pathogen evolution, but much is still unknown about how these pathogens have evolved to infect multiple host species. We found that microsporidia express most of their genes similarly even when they are infecting different host species and that related host species respond similarly to different microsporidia. Our results suggests that there are conserved transcriptional responses during microsporidia infection.
Differential metabolism between biofilm and suspended Pseudomonas aeruginosa cultures in bovine synovial fluid by 2D NMR-based metabolomics
Authors: Leggett Abigail , Li Da-Wei , Bruschweiler-Li Lei , Sullivan Anne , Stoodley Paul , Brüschweiler Rafael
Published: June 2022

Total joint arthroplasty is a common surgical procedure resulting in improved quality of life; however, a leading cause of surgery failure is periprosthetic joint infection. Periprosthetic infection often involves biofilms, making treatment challenging. Periprosthetic joint infections are difficult to diagnose by traditional culturing methods and there are no clinical biomarkers for the presence of biofilms. Further, the metabolic state of pathogens in the joint space is difficult to diagnose, the mechanism of their tolerance to antibiotics and host defenses is not well understood, and their culturing in the laboratory is challenging. Thus, there is a critical need for improved pathogen- and phenotype-specific diagnosis as well as improved treatment strategies toward better patient outcomes. Here, we present a quantitative, untargeted NMR-based metabolomics strategy for Pseudomonas aeruginosa suspended culture and biofilm phenotypes grown in bovine synovial fluid. We identified 21 unique metabolites as potential markers of P. aeruginosa and one unique marker of the biofilm phenotype in synovial fluid. Significant differences in metabolic pathways were found between the suspended culture and biofilm phenotypes including creatine, glutathione, alanine, and choline metabolism and the tricarboxylic acid cycle. These unique metabolite and pathway differences have the potential to serve as targets for P. aeruginosa and specifically biofilm diagnosis and biofilm control in synovial fluid.

Author Summary

Joint replacement surgery is a common procedure frequently required in later stages of life due to damage in the joint. Over one million joint replacement surgeries are performed annually with rates increasing every year. A devastating complication associated with joint replacement is the development of infection around the implant device in the joint space, known as a periprosthetic joint infection. Bacteria in the joint space can form a biofilm, which is a gel-like matrix encasing the cells that increases resistance to treatment and exacerbates chronic infections. A particular challenge for the diagnosis of biofilm-mediated periprosthetic joint infections is the slowly growing nature of biofilm-mediated phenotypes, resulting in frequent failure to detect these bacteria by clinical microbiological culturing methods. Small molecule metabolites are uniquely produced by strains of bacteria in the biofilm versus planktonic or suspended culture phenotype. Identification of metabolites as specific markers of infection and biofilm could allow a new culture-free diagnostic approach to diagnose infection by biofilm. Furthermore, knowledge of metabolic pathway populations in biofilm in joint fluid could point to specific targets to prevent biofilm formation in the joint space.
Low level of knowledge about COVID-19 among a sample of Deaf persons in Ghana
Authors: Arthur-Mensah Reginald , Quao Jacob Nartey , Yeboah Louisa , Dassah Zanu , Kyei Abigail Agartha
Published: June 2022

Global observations have shown that the success or failure in preventing and controlling the spread of COVID-19 largely relies on human behaviours. Human behaviours in preventing and controlling the spread of the disease principally, is dependent on the level of knowledge of the disease, the attitudes adopted by persons due to the level of knowledge of the disease and the decision to adhere to the preventive practices (KAP) of the disease. Since the beginning of this pandemic, numerous studies have been conducted to investigate the KAP on the novel COVID-19 among diverse demographic groups. However, no reported studies have been found on the KAP of the COVID-19 pandemic among the deaf in various populations around the world. This study sought to assess the KAP of COVID-19 among deaf persons in the Greater Accra region of Ghana.

The design of this study utilized the knowledge, attitude and practice (KAP) survey. Good attitude and adherence to the preventive practices of COVID-19 was observed among the deaf persons. However, knowledge about the science of the disease was lacking. Educational campaigns about COVID-19 should also emphasize the teaching and understanding of the science of the virus and the disease to its audience.
Low back pain care pathways and costs: association with the type of initial contact health care provider. A retrospective cohort study
Authors: Elton David , Kosloff Thomas M. , Zhang Meng , Advani Protima , Guo Yinglong , Shimotsu Scott T. , Sy Sean , Feuer Ari
Published: June 2022

Background

Low back pain (LBP) is prevalent, management benefits from high-quality clinical practice guidelines, and yet LBP is a common source of low value care. The purpose of this retrospective cohort study was to examine the association between the type of initial contact health care provider (HCP), service utilization, and total episode cost for the management of LBP.

Methods

Episode of care was used to analyze a US national sample of LBP episodes completed in 2017-2019. A combined surgical and non-surgical (pooled) sample and a non-surgical sample were separately analyzed. The primary independent variable was the type of the initial contact HCP. Dependent measures included rate and timing of use of 14 types of health care services and total episode cost. The association between initial contact HCP, total episode cost and rate of prescription opioid and NSAID use was tested using a mixed effects model.

Results

The study included 616,766 continuously insured individuals aged 18 years and older with 756,631 episodes of LBP involving 386,795 HCPs and incurring $1,010,495,291 in expenditures. A primary care or specialist HCP was initially contacted in 62.0% of episodes, with these episodes associated with early use of low-value services such as imaging, pharmacologic, and interventional services. A non-prescribing HCP was initially contacted in 32.5% of episodes with these episodes associated with early use of guideline recommended first line services.

Each type of HCP emphasized different initial services with little indication of a stepped approach to managing LBP. Following adjustment for covariates chiropractors were associated with the lowest total episode cost. As an observational study of associations, numerous confounders may have impacted results.

Conclusions

An individual with LBP has different experiences based on the type of HCP initially contacted. Initial contact with primary care or specialist HCPs is associated with second- and third-line services provided before first line services, with little indication of a guideline recommended stepped approach to managing LBP. Increasing the likelihood of guideline- concordant, high-value care for LBP may require systemic changes to the health care delivery system. In the absence of red flags these changes may include increasing the proportion of individuals receiving early non-pharmacological treatment, either through improving direct access to non-prescribing HCPs or increasing timely referrals from primary care and specialist health care providers.
Patterning High to Low Heterogenous Fluid Shear Stress Landscapes with Multiphoton Inner Laser Lithography (MILL) for Live Cell Adhesion and Translocation
Authors: Lim Yean Jin , Zhang Junxiang , Lin Hanqi , Xu Tienan , Li Yongxiao , Zhang Zhiduo , Hicks Sarah M. , Chudinov Ivan , Nechipurenko Dmitry Y , Gardiner Elizabeth E , Lee woei ming
Published: June 2022

Heterogenous fluid shear stress is known to provide mechanical cues for cell adhesion and translocation. To assemble 3D microstructures using current fabrication methods in a single channel and recapitulate in vivo heterogenous fluid flow would require hours of fabrication and specialized equipment. Inspired by the traditional art form of inside painting, we developed a technique for 3D fabrication of micro-patterned flow channels and mixed in vivo fluid flow in a matter of minutes. We termed this technique Multiphoton Inner Laser Lithography (MILL). We further showed that when combined with adaptive optics, MILL is compatible with both flat and curved channel shapes. MILL recapitulated in vivo tissue topology and 3D fluid flow within tissue stroma (low fluid shear, 0 - 3.5 dynes/cm2) and blood vessel (high fluid shear, 0 - 80 dynes/cm2). We demonstrate fibroblast cell and platelets adhere and translocate differently between laminar flow patterns that are homogenous versus heterogeneous in real time. Parallel strips of MILL channels were assembled for simultaneous platelet function test to quantify the efficacy of an antithrombotic GPVI Fab (~2000 microthrombi per test). The MILL technique can be readily reproduced in vivo fluid flow in minutes and benefit preclinical screening of drug pharmacokinetics.
The evolution of an RNA-based memory of self in the face of genomic conflict
Authors: Pliota Pinelopi , Marvanova Hana , Koreshova Alevtina , Kaufman Yotam , Tikanova Polina , Krogull Daniel , Hagmüller Andreas , Widen Sonya A. , Handler Dominik , Gokcezade Joseph , Duchek Peter , Brennecke Julius , Ben-David Eyal , Burga Alejandro
Published: June 2022

Distinguishing endogenous genes from selfish ones is essential for germline integrity. In animals, small regulatory RNAs play a central role in this process; however, the underlying principles are largely unknown. To fill this gap, we studied how selfish toxin-antidote elements (TAs) evade silencing in the nematode Caenorhabditis tropicalis. We found that the slow-1/grow-1 TA is active only when maternally inherited. Surprisingly, this parent-of-origin effect stems from a regulatory role of the toxin’s mRNA: maternal slow-1 mRNA—but not SLOW-1 protein—licenses slow-1 expression in the zygote by counteracting piRNAs. Our results indicate that epigenetic licensing— known to play a role in C. elegans sex-determination—is likely a common mechanism that hinders the spread of selfish genes in wild populations while ensuring a lasting memory of self in the germline.
A multiplex of connectome trajectories enables several connectivity patterns in parallel
Authors: Mostame Parham , Wirsich Jonathan , Alderson Thomas Henry , Ridley Ben , Giraud Anne-Lise , Carmichael David , Vulliemoz Serge , Guye Maxime , Lemieux Louis , Sadaghiani Sepideh
Published: June 2022

Complex brain function comprises a multitude of neural operations in parallel and often at different speeds. Each of these operations is carried out across a network of distributed brain regions. How multiple distributed processes are facilitated in parallel is largely unknown. We postulate that such processing relies on a multiplex of dynamic network patterns emerging in parallel but from different functional connectivity (FC) timescales. Given the dominance of inherently slow fMRI in network science, it is unknown whether the brain leverages such multi-timescale network dynamics. We studied FC dynamics concurrently across a breadth of timescales (from infraslow to γ-range) in rare, simultaneously recorded intracranial EEG and fMRI in humans, and source-localized scalp EEG-fMRI data. We examined spatial and temporal convergence of connectome trajectories across timescales. Spatial convergence refers to spatially similar EEG and fMRI connectome patterns, while temporal convergence signifies the more specific case of spatial convergence at corresponding timepoints in EEG and fMRI. We observed spatial convergence but temporal divergence across FC timescales; connectome states (recurrent FC patterns) with partial spatial similarity were found in fMRI and all EEG frequency bands, but these occurred asynchronously across FC timescales. Our findings suggest that hemodynamic and frequency-specific electrophysiological signals, while involving similar large-scale networks, represent functionally distinct connectome trajectories that operate at different FC speeds and in parallel. This multiplex is poised to enable concurrent connectivity across multiple sets of brain regions independently.
A Method for Selective 19F-Labeling Absent of Probe Sequestration (SLAPS)
Authors: Dixon Austin D. , Trinidad Jonathan C. , Ziarek Joshua J.
Published: June 2022

Fluorine (19F) offers several distinct advantages for biomolecular nuclear magnetic resonance (NMR) spectroscopy such as no background signal, 100% natural abundance, high sensitivity, and a large chemical shift range. Exogenous cysteine-reactive 19F-probes have proven especially indispensable for characterizing large, challenging systems that are less amenable to other isotopic labeling strategies such as G protein-coupled receptors (GPCRs). As fluorine linewidths are inherently broad, limiting reactions with offsite cysteines is critical for spectral simplification and accurate deconvolution of component peaks – especially when analyzing systems with intermediate to slow timescale conformational exchange. Here, we uncovered a second source of offsite labeling: non-covalent probe sequestration by detergent micelles. We present a simple four-step protocol for Selective Labeling Absent of Probe Sequestration (SLAPS): physically-disrupt cell membranes in the absence of detergent, incubate membranes with cysteine-reactive 19F-probes, remove excess unreacted 19F-probe molecules via ultracentrifugation, and finally solubilize in the detergent of choice. SLAPS should be broadly applicable to other lipophilic cysteine-reactive probes and membrane protein classes solubilized in detergent micelles or lipid mimetics.
Effects of hydrological change in fire-prone wetland vegetation: an empirical simulation
Authors: Mason Tanya J. , Popovic Gordana C. , McGillycuddy Maeve , Keith David A.
Published: June 2022

Upland swamps are peat-accumulating, groundwater-dependent and fire-prone wetland ecosystems. Drying caused by anthropogenic processes such as underground mining, ditching and climate change may disrupt surface and groundwater flows effecting a bottom-up control on wetland expression. Fire is an endogenous, recurring disturbance that drives a top-down consumptive force in many of these systems. When compounded with anthropogenic drying, fire may facilitate permanent community transitions. A dearth of ecological data and temporal lags have hampered our ability to predict risks associated with multiple disturbances in wetland plant communities. We collected intact wetland mesocosms from valley floors and lower slopes of four undisturbed swamp sites. We transferred the mesocosms to a glasshouse and established three different soil moisture availability levels to simulate wetland drainage. After 20 months of the hydrological treatment, we simulated a fire event by sequentially applying biomass removal (clipping), heat and smoke to half of the mesocosms. We monitored species biomass, richness and composition over a 3.5-year time frame. We found evidence of a temporal lag in biomass response to low water availability and synergistic hydrological and fire effects on species richness. In unburnt conditions, richness declined with low water availability but was maintained under high and medium water availability. After simulated fire in medium water availability, however, richness also declined and converged with depauperate low water mesocosm richness. Representation by many obligate swamp species declined in low compared with high water availability mesocosms over time, an effect that was amplified by the fire treatment.

Synthesis

Our evidence of lagged effects of hydrological change on wetland vegetation and compounding effects of fire should be considered in impact assessments, monitoring programs and ecosystem management to avoid irreversible wetland change in drying environments.
The spatial landscape of Cancer Hallmarks reveals patterns of tumor ecology
Authors: Sibai Mustafa , Cervilla Sergi , Grases Daniela , Musulen Eva , Lazcano Rossana , Mo Chia-Kuei , Davalos Veronica , Fortian Arola , Bernat Adrià , Romeo Margarita , Tokheim Collin , Grande Enrique , Real Francisco , Barretina Jordi , Lazar Alexander J , Ding Li , Esteller Manel , Bailey Matthew H , Porta-Pardo Eduard
Published: June 2022

Tumors are complex ecosystems with dozens of interacting cell types. The concept of Cancer Hallmarks distills this complexity into a set of underlying principles that govern tumor growth. Here, we exploit this abstraction to explore the physical distribution of Cancer Hallmarks across 63 primary untreated tumors from 10 cancer types using spatial transcriptomics. We show that Hallmark activity is spatially organized–with 7 out of 13 Hallmarks consistently more active in cancer cells than within the non-cancerous tumor microenvironment (TME). The opposite is true for the remaining six Hallmarks. Additionally, we discovered that genomic distance between tumor subclones correlates with differences in Cancer Hallmark activity, even leading to clone-Hallmark specialization in some cases. Finally, we demonstrate interdependent relationships between Cancer Hallmarks at the junctions of TME and cancer compartments. In conclusion, including the spatial dimension, particularly through the lens of Cancer Hallmarks, can improve our understanding of tumor ecology.

Significance

We explored Cancer Hallmarks in 63 primary untreated tumors from 10 cancer types using spatial transcriptomics. This study unveiled spatial patterns in Hallmark activity, with some being more active in cancer cells and others in the non-cancerous tumor environment. Genomic distance impacted Hallmark activity, and we identified interdependencies at the TME-cancer junctions, improving our understanding of tumor ecology.
scFLUX: a web server for metabolic flux and variation prediction using transcriptomics data
Authors: Zhang Zixuan , Chang Wennan , Alghamdi Norah , Fei Mengyuan , Wan Changlin , Lu Alex , Zang Yong , Xu Ying , Wu Wenzhuo , Cao Sha , Zhang Yu , Zhang Chi
Published: June 2022

Quantitative assessment of single cell fluxome is critical for understanding the metabolic heterogeneity in diseases. Unfortunately, single cell fluxomics using laboratory approaches is currently infeasible, and none of the current flux estimation tools could achieve single cell resolution. In light of the natural associations between transcriptomic and metabolomic profiles, it remains both a feasible and urgent task to use the available single cell transcriptomics data for prediction of single cell fluxome. We present scFLUX here, which provides an online platform for prediction of metabolic fluxome and variations using transcriptomics data, on individual cell or sample level. This is in contrast to other flux estimation methods that are only able to model the fluxes for cells of pre-defined groups. The scFLUX webserver implements our in-house single cell flux estimation model, namely scFEA, which integrates a novel graph neural network architecture with a factor graph derived from the complex human metabolic network. To the best of our knowledge, scFLUX is the first and only web-based tool dedicated to predicting individual sample-/cell-metabolic fluxome and variations of metabolites using transcriptomics data. scFLUX is available at http://scflux.org/. The stand-alone tools for using scFLUX locally are available at https://github.com/changwn/scFEA.
Lung endothelium instructs dormancy of susceptible metastatic tumour cells
Authors: Jakab Moritz , Lee Ki Hong , Uvarovskii Alexey , Ovchinnikova Svetlana , Kulkarni Shubhada R , Rostalski Till , Anders Simon , Augustin Hellmut G
Published: June 2022

During metastasis, cancer cells hijack blood vessels and travel via the circulation to colonize distant sites1,2. Due to the rarity of these events, the immediate cell fate decisions of arrested circulating tumour cells (aCTC) are poorly understood and the role of the endothelium, as the interface of dissemination, remains elusive3,4. Here, we developed a novel strategy to specifically enrich for aCTC subpopulations capturing all cell states of the extravasation process and, in combination with single cell RNA-sequencing, provide a first blueprint of the transcriptional basis of early aCTC decisions. Upon their arrest at the metastatic site, tumour cells either started proliferating intravascularly or extravasated and preferably reached a state of quiescence. Endothelial-derived angiocrine Wnt factors were found to drive this bifurcation by inducing a mesenchymal-like phenotype in aCTCs instructing them to follow the extravasation-dormancy branch. Surprisingly, homogenous tumour cell pools showed an unexpected baseline heterogeneity in Wnt signalling activity and epithelial-to-mesenchyme-transition (EMT) states. This heterogeneity was established at the epigenetic level and served as the driving force of aCTC behaviour. Hypomethylation enabled high baseline Wnt and EMT activity in tumour cells leading them to preferably follow the extravasation-dormancy route, whereas methylated tumour cells had low activity and proliferated intravascularly. The data identify the pre-determined methylation status of disseminated tumour cells as a key regulator of aCTC behaviour in the metastatic niche. While metastatic niche-derived factors per default instruct the acquisition of quiescence, aCTCs unwind a default proliferation program and only deviate from it if hypomethylation in key gene families renders them responsive towards the microenvironment.
Temperature-Sensitive Contacts in Disordered Loops Tune Enzyme I Activity
Authors: Burns Daniel , Singh Aayushi , Venditti Vincenzo , Potoyan Davit A
Published: June 2022

Homologous enzymes with identical folds often exhibit different thermal and kinetic behaviors. Understanding how enzyme sequence encodes catalytic activity at functionally optimal temperatures is a fundamental problem in biophysics. Recently it was shown that the residues that tune catalytic activities of thermophilic/mesophilic variants of the C-terminal domain of bacterial Enzyme I (EIC) are largely localized within disordered loops, offering a model system with which to investigate this phenomenon. In this work, we employ molecular dynamics simulations and mutagenesis experiments to reveal a mechanism of sequence-dependent activity tuning of EIC homologs.

We find that a network of contacts in the catalytic loops is particularly sensitive to changes in temperature, with some contacts exhibiting distinct linear or non-linear temperature-dependent trends. Moreover, these trends define structurally clustered dynamical modes and can distinguish regions that tend toward order or disorder at higher temperatures. Assaying several thermophilic EIC mutants, we show that complementary mesophilic mutations to the most temperature-sensitive positions exhibit the most enhanced activity while mutations to relatively temperature insensitive positions exhibit the least enhanced activities. These results provide a mechanistic explanation of sequence-dependent temperature tuning and offer a computational method for rational enzyme modification.

Significance

Temperature affects the catalytic rates of all enzymes. The impact of temperature on the catalytic activity of an enzyme, however, is convoluted from contributions of protein sequence, structure, and dynamics. As such, understanding and designing the molecular features of enzymes which tune catalytic rates at different temperatures remains a fundamental challenge in biophysics. In this work we have employed molecular simulations and mutagenesis experiments to reveal the temperature tuning mechanism of mesophilic and thermophilic homologues of the C domain of bacterial Enzyme l. We find that enzymes can be tuned to their physiological temperatures through a network of temperature-sensitive residue contacts localized in the disordered loops. Furthermore, we find that among temperature-sensitive contacts some exhibit linear and others non-linear dependence on temperature. These clues offer a promising physics-based approach for tuning enzyme activity.
Magnetothermal control of temperature-sensitive repressors in superparamagnetic iron nanoparticle-coatedBacillus subtilis
Authors: Greeson Emily M. , Madsen Cody S. , Makela Ashley V. , Contag Christopher H.
Published: June 2022

Superparamagnetic iron oxide nanoparticles (SPIONs) are used as contrast agents in magnetic resonance imaging (MRI) and magnetic particle imaging (MPI) and resulting images can be used to guide magnetothermal heating. Alternating magnetic fields (AMF) cause local temperature increases in regions with SPIONs, and we investigated the ability of magnetic hyperthermia to regulate temperature-sensitive repressors (TSRs) of bacterial transcription. The TSR, TlpA39, was derived from a Gram-negative bacterium, and used here for thermal control of reporter gene expression in Gram-positive,Bacillus subtilis. In vitroheating ofB. subtiliswith TlpA39 controlling bacterial luciferase expression, resulted in a 14.6-fold (12-hour; h) and 1.8-fold (1-h) increase in reporter transcripts with a 9.0-fold (12-h) and 11.1-fold (1-h) increase in bioluminescence. To develop magnetothermal control,B. subtiliscells were coated with three SPION variations. Electron microscopy coupled with energy dispersive X-ray spectroscopy revealed an external association with, and retention of, SPIONs onB. subtilis. Furthermore, using long duration AMF we demonstrated magnetothermal induction of the TSRs in SPION-coatedB. subtiliswith a maximum of 4.6-fold increases in bioluminescence. After intramuscular injections of SPION-coatedB. subtilis,histology revealed that SPIONs remained in the same locations as the bacteria. Forin vivostudies, 1-h of AMF is the maximum exposure due to anesthesia constraints. Bothin vitroandin vivo, there was no change in bioluminescence after 1-h of AMF treatment. Pairing TSRs with magnetothermal energy using SPIONs for localized heating with AMF can lead to transcriptional control that expands options for targeted bacteriotherapies.
Systemic silencing and DNA methylation of a host reporter gene induced by a beneficial fungal root endophyte
Authors: Dalakouras Athanasios , Katsaouni Afrodite , Avramidou Marianna , Dadami Elena , Tsiouri Olga , Vasileiadis Sotirios , Makris Athanasios , Georgopoulou Maria Eleni , Papadopoulou Kalliope K.
Published: June 2022

A growing body of evidence suggests that RNA interference (RNAi) plays a pivotal role in the communication between plants and pathogenic fungi, where a bi-directional cross-kingdom RNAi is established to the advantage of either the host or the pathogen. Similar mechanisms acting during plant association with non-pathogenic symbiotic microorganisms have been elusive to this date. Here, we report on an RNAi-based mechanism of communication between a beneficial fungal endophyte,Fusarium solanistrain K (FsK) and its host plants. This soil-borne endophyte that confers resistance and/or tolerance to biotic and abiotic stress in tomato and, as shown in this study, promotes plant growth inNicotiana benthamiana, is restricted to the root system in both host plants. We first showed that the fungus has a functional core RNAi machinery; double stranded RNAs (dsRNAs) are processed into short interfering RNAs (siRNAs) of predominantly 21-nt in size, which lead to the degradation of homologous mRNAs. Importantly, by using an RNAi sensor system, we demonstrated that root colonization ofN. benthamianaby FsK led to the induction of systemic silencing and DNA methylation of a host reporter gene.. These data reflect a more general but so far unrecognized mechanism wherein root endophytes systemically translocate RNAi signals to the aboveground tissues of their hosts to modulate gene expression during symbiosis, which may be translated to the beneficial phenotypes.

Highlight

A root-restricted, beneficial fungal endophyte can induce systemic silencing and epigenetic modifications to its host plant.
Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide is dependent on the resident microbiota
Authors: Hoces Daniel , Greter Giorgia , Arnoldini Markus , Moresi Claudia , Berent Sara , Kolinko Isabel , Bansept Florence , Woller Aurore , Häfliger Janine , Martens Eric , Hardt Wolf-Dietrich , Loverdo Claude , Slack Emma
Published: June 2022

Many microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. However, we remain largely blind to the quantitative effects of processes determining colonization success. In this study, we used genetically-barcoded Bacteroides thetaiotaomicron (B.theta) strains in combination with mathematical modeling to quantify population bottlenecks experienced by B.theta during gut colonization. Integrating population bottlenecks sizes with careful quantification of net growth rates in vivo and in vitro allows us to build models describing the events during intestinal colonization in the context of gnotobiotic and complex microbiotas. Using these models, we estimated the decrease in niche size for B.theta colonization with increasing microbiota complexity. In addition, our system can be applied to mechanistically dissect colonization defects of mutant strains. As a proof of concept, we demonstrated that the competitive disadvantage of a B.theta mutant lacking capsular polysaccharide is due to a combination of an increased lag-phase before growth initiation in the gut, combined with an increased clearance rate. Crucially, the requirement for the B.theta capsule depended strongly on microbiota composition, suggesting that the dominant role may be protection from bacterial or phage aggression rather than from host-induced bactericidal mechanisms.
Extensive substrate recognition by the streptococcal antibody-degrading enzymes IdeS and EndoS
Authors: Sudol Abigail S. L. , Butler John , Ivory Dylan P. , Tews Ivo , Crispin Max
Published: June 2022

Enzymatic cleavage of IgG antibodies is a common strategy used by pathogenic bacteria to ablate immune effector function. The Streptococcus pyogenes bacterium secretes the protease IdeS and the glycosidase EndoS, which specifically catalyse cleavage and deglycosylation of human IgG, respectively. IdeS has received clinical approval for kidney transplantation in hypersensitised individuals, while EndoS has found application in engineering antibody glycosylation. Here, we present crystal structures of both enzymes in complex with their IgG1 Fc substrate, which was achieved using Fc engineering to disfavour preferential Fc crystallisation. The IdeS protease displays extensive Fc recognition and encases the antibody hinge. Conversely, the glycan hydrolase domain in EndoS traps the Fc glycan in a flipped-out conformation, while additional recognition of the Fc peptide is driven by the so-called carbohydrate binding module. Understanding the molecular basis of antibody recognition by bacterial enzymes will facilitate the development of next-generation enzymes for clinical and biotechnological use.
Inhibited KdpFABC resides in an E1 off-cycle state
Authors: Silberberg Jakob M. , Stock Charlott , Hielkema Lisa , Corey Robin A. , Rheinberger Jan , Wunnicke Dorith , Dubach Victor R. A. , Stansfeld Phillip J. , Hänelt Inga , Paulino Cristina
Published: June 2022

KdpFABC is a high-affinity prokaryotic K+ uptake system that forms a functional chimera between a channel-like subunit (KdpA) and a P-type ATPase (KdpB). At high K+ levels, KdpFABC needs to be inhibited to prevent excessive K+ accumulation to the point of toxicity. This is achieved by a phosphorylation of the serine residue in the TGES162 motif in the A domain of the pump subunit KdpB (KdpBS162-P). Here, we explore the structural basis of inhibition by KdpBS162 phosphorylation by determining the conformational landscape of KdpFABC under inhibiting and non-inhibiting conditions. Under turnover conditions, we identified a new inhibited KdpFABC conformation that we termed E1-P tight, which is not part of the canonical Post-Albers transport cycle of P-type ATPases. It likely represents the biochemically described stalled E1-P state adopted by KdpFABC upon KdpBS162 phosphorylation. The E1-P tight state exhibits a compact fold of the three cytoplasmic domains and is likely adopted when the transition from high-energy E1-P states to E2-P states is unsuccessful. This study represents a structural characterization of a biologically relevant off-cycle state in the P-type ATPase family and supports the emerging discussion of P-type ATPase regulation by such conformations.
Cortical dynamics following real-time MEG neurofeedback training of the speed of shifting spatial attention: a pilot study
Authors: Rana Kunjan D. , Khan Sheraz , Hämäläinen Matti S. , Vaina Lucia M.
Published: June 2022

Neurofeedback is a technique that directs self-regulated modulation of neural activity. This is achieved by delivering real-time feedback derived from brain signals. In our previous work, we introduced a novel method, state-based neurofeedback (sb-NFB) that targets patterns of MEG signals related to shifts in spatial attention. In this pilot study, we used sb-NFB to train participants to decrease the time required to covertly shift spatial attention from one visual hemifield to the other. We characterized the changes to cortical connectivity during each training session. In addition, we run a separate, Posner-like validation task before the training sessions and after the training was complete. We found a significant main effect of training on the reaction time linked to switching spatial attention in both the training task and the validation task. This indicates the achieved improvement in shifting spatial attention generalized to another situation requiring this capability.
Dispersal-behavioral plasticity within an insect-host system undergoing human-induced rapid environmental change (HIREC)
Authors: Bernat Anastasia , Cenzer Meredith
Published: June 2022

As environments change, often drastically, due to human activities, dispersal-behavioral plasticity can become a key mediator of metapopulation connectivity and the interactions between an individual and its altered environment. Our goal was to investigate the traits and ecological processes that affect plastic dispersal responses within an insect-host system undergoing human-induced rapid evolutionary change (HIREC). Since the 1960s, populations of the red-shouldered soapberry bug from Florida, USA, originally feeding on the seeds of Cardiospermum corindum on the islands, quickly adapted to feeding on an invasive, ornamental tree, Koelreuteria elegans, on the mainland, which led to host-specific wing polyphenism. Here, we measured the morphology of >3,500 soapberry bugs field collected from 2013 to 2020 and the flight performance of 378 total soapberry bugs tested in a flight mill during Fall 2019 and Winter 2020. Flight tests showed females and mainland natives exhibited variable flight responses mediated by mass, while males were consistent, wing-dependent flyers. However, historical specimens showed annual rises in flightless morphs for males and dwindling wing-to-body sizes for island natives since 2013. Despite uncertain future fitness consequences, plasticity could help predict mobility character and agent dispersal behavior and ultimately help identify whether recent trends signal adjustment or maladaptation to HIREC.
The domain-separation low-dimensional language network dynamics in the resting-state support the flexible functional segregation and integration during language and speech processing
Authors: Yuan Binke , Xie Hui , Wang Zhihao , Xu Yangwen , Zhang Hanqing , Liu Jiaxuan , Chen Lifeng , Li Chaoqun , Tan Shiyao , Lin Zonghui , Hu Xin , Gu Tianyi , Lu Junfeng , Liu Dongqiang , Wu Jinsong
Published: June 2022

Modern linguistic theories and network science propose that the language and speech processing is organized into hierarchical, segregated large-scale subnetworks, with a core of dorsal (phonological) stream and ventral (semantic) stream. The two streams are asymmetrically recruited in receptive and expressive language or speech tasks, which showed flexible functional segregation and integration. We hypothesized that the functional segregation of the two streams was supported by the underlying network segregation. A dynamic conditional correlation approach was employed to construct frame-wise time-varying language networks and investigate the temporal reoccurring patterns. We found that the time-varying language networks in the resting-state robustly clustered into four low-dimensional states, which dynamically reconfigured following a domain-separation manner. Spatially, the hub distributions of the first three states highly resembled the neurobiology of primary auditory processing and lexical-phonological processing, motor and speech production processing, and semantic processing, respectively. The fourth state was characterized by the weakest functional connectivity and subserved as a baseline state. Temporally, the first three states appeared exclusively in limited time bins (∼15%), and most of the time (> 55%), the language network kept inactive in state 4. Machine learning-based dFC-linguistics prediction analyses showed that dFCs of the four states significantly predicted individual linguistic performance. These findings suggest a domain-separation manner of language network dynamics in the resting-state, which forms a dynamic “meta-networking” (network of networks) framework.

Highlights

The time-varying language network in the resting-state is robustly clustered into four low-dimensional states.

Spatially, the first three dFC states are cognitively meaningful, which highly resemble the neurobiology of primary auditory processing and lexical-phonological representation, speech production processing, and semantic processing, respectively.

Temporally, the first three states appeared exclusively in limited time bins (∼15%), and most of the time (> 55%), the language network kept inactive in state 4.

A dynamic “meta-networking” framework of language network in the resting-state is proposed.
Normalization of MRI T1w between-scan effects for improved longitudinal volumetric estimates
Authors: Sederevičius Donatas , Bjørnerud Atle , Walhovd Kristine B. , Fjell Anders M.
Published: June 2022

Variations in image intensities and contrasts between magnetic resonance imaging (MRI) acquisitions affect the subsequent image processing and its derived outcomes. Therefore, comparability between acquisitions is improved if we reduce these variations. This is especially relevant for longitudinal studies where a change of scanner or acquisition protocol often happens between subsequent examinations. In this study, we use a robust intensity distribution alignment (RIDA) method to reduce between-scan effects and improve longitudinal volume change estimates between two MRI scanners – Siemens 1.5T Avanto and 3T Skyra. The method is based on MRI T1w images acquired in close succession and robustly aligns two cumulative distribution functions of voxel intensities to harmonize image intensities and improve image-derived outcomes of a range of subcortical brain. We compare RIDA with volume-based correction - a simple linear regression model. In both cases, we derive intensity and volume transformations from a training dataset of 20 participants scanned on both scanners on the same day and apply to an independent longitudinal test dataset of 243 participants. All participants in the test set were scanned at the Avanto scanner at the baseline and then at the Avanto and Skyra scanners on the same day at the follow-up, on average 4.4 years (sd = 0.5 years) later. This allowed us to directly assess the effect of scanner and protocol change on the longitudinal change estimates. Eight subcortical brain regions were segmented using SAMSEG, and annualized symmetrized percent change in volume between time points was calculated. We find that RIDA significantly reduces between-scan effects and improves longitudinal volume estimates for the amygdala and lateral ventricles. It also reduces between-scan effects for caudate, putamen, and thalamus, but not as much as linear regression models. Whether the method will be useful for a particular study will depend on the image intensity profiles of the scans. Therefore, a pilot study of double-scanned participants is recommended to assess the advantages of the method for the analysis in question.
Investigating the eukaryotic host-like SLiMs in microbial mimitopes and their potential as novel drug targets for treating autoimmune diseases
Authors: Garg Anjali , Singhal Neelja , Kumar Manish
Published: June 2022

Several pathogens sustain themselves inside the host by mimicking short linear motifs (SLiMs) of the host proteins. SLiMs are short stretches of 3-10 amino acids which are functionally diverse and mediate various signaling and protein-protein interactions (PPIs). Hence, mimicry of the host- SLiMs helps the microbes in modulating/disrupting the host defense mechanisms. This is the first report investigating the evolutionary characteristics and presence of eukaryotic host-like SLiMs in microbial peptides (mimitopes). Evaluation of the selection pressure revealed that 60% of the bacterial and 25% of the viral mimitopes which overlapped with the host-like SLiMs were evolutionarily conserved (ω < 1). Interestingly, host-like SLiMs were abundant in mimicry proteins but were less frequent in microbial mimitopes. This reflects that the majority of the pathogens cannot potentially rewire the host PPI networks for their advantage, but some can. Of the 152 bacterial and 43 viral mimitopes investigated only 10 bacterial and 4 viral mimitopes showed SLiMs. This indicates that mimitopes of some pathogens can be explored as novel drug targets for eliminating the etiopathological agent and treating the autoimmune disease, thereof. The repertoire of mimitopes identified here might provide important clues for the discovery of new drugs/protein-based immune-modulatory molecules against the pathogens.

Key points

Mimicry of the host- SLiMs helps the microbes in modulating/disrupting the host defense mechanisms.

Host-like SLiMs were abundant in mimicry proteins but were less frequent in microbial mimitopes.

Evaluation of the selection pressure revealed that 60% of the bacterial and 25% of the viral mimitopes which overlapped with the host-like SLiMs were evolutionarily conserved.
Exchangeable HaloTag Ligands (xHTLs) for multi-modal super-resolution fluorescence microscopy
Authors: Kompa Julian , Bruins Jorick , Glogger Marius , Wilhelm Jonas , Frei Michelle S. , Tarnawski Miroslaw , D’Este Elisa , Heilemann Mike , Hiblot Julien , Johnsson Kai
Published: June 2022

We introduce exchangeable ligands for fluorescence labeling of HaloTag7 as an alternative to covalently bound probes. The exchangeable ligands open up new possibilities in imaging for a widely used labeling approach, including applications in points accumulation for imaging in nanoscale topography (PAINT), MINFLUX and live-cell, multi-frame stimulated emission depletion (STED) microscopy. We furthermore introduce orthogonal pairs of exchangeable ligands and HaloTags for dual-color PAINT and STED microscopy.

Graphical Abstract
Epigenetic alterations in gut and brain of adult rats after oral administration of miR-320-3p and miR-375-3p at mid-lactation, and preventive potential of miR-320-3p on early weaning stress
Authors: Tavares Gabriel A , Torres Amada , Le Drean Gwenola , Queignec Maïwenn , Castellano Blandine , Tesson Laurent , Remy Séverine , Annegone Ignacio , de Souza Sandra L , Pitard Bruno , Kaeffer Bertrand
Published: June 2022

Aim

To investigate if the artificial delivery of microRNAs naturally present in the breastmilk can impact the gut and brain of young rats according to weaning.

Methods

Animals from a new transgenic rat line expressing green-fluorescent protein in the endocrine lineage (cholecystokinin expressing cells) received at Day-12, near neural diversification, a single oral bolus of mir-320-3p or miR-375-3p, embedded in DiOleyl-Succinyl-Paromomycin (DOSP), and were further early (Day-15) or regularly (Day-30) weaned. Relevant miRNA (miR-320-3p, miR-375-3p, miR-375-5p, miR-16-5p, miR-132-3p, miR-504), polr3d, hspb6, inflammation, enteroendocrine, and circadian clock-related mRNAs, chromatin complexes, and duodenal cell density were assayed at 8h post-inoculation and at Day-45.

Results

The miR-320-3p/DOSP induced immediate effects on H3K4me3 chromatin complexes with polr3d promoter (p<0.05) but no long-term effects. On regular weaning, at Day-45, both miR-320-3p and 375-3p were down-regulated in the stomach, up-regulated in the hypothalamus (p<0.001) but only miR-320-3p was up-regulated in the duodenum. After early weaning, the miR-320-3p and miR-375-3p levels were down-regulated in the stomach and the duodenum, but up-regulated in the hypothalamus and the hippocampus. Combining miR-320-3p/DOSP with early weaning enhanced miR-320-3p and chromogranin A expression in the duodenum. In the hippocampus, the miR-504 was down-regulated for both sexes, but in the brain stem, up regulated only for females, along with miR-320-3p and miR-16-5p levels. In the hypothalamus, clock levels were up regulated for both sexes. In the miR-375-3p/DOSP group, the density of enteroendocrine duodenal cells increased. The long-term effect of miR-375-3p/DOSP was more limited, according to the fourfold lower number of predicted targets than with miR-320-3p.

Conclusion

Addressing oral miRNA-320-3p loads to duodenal cell lineage is paving the way for the design of new therapeutics, manipulating long term consequences of early life stress.