bluuebunny/crossref_metadata_2025 huggingface dataset:
Primary human colonic mucosal barrier crosstalk with super oxygen-sensitiveFaecalibacterium prausnitziiin continuous culture
Authors: Zhang Jianbo , Huang Yu-Ja , Yoon Jun-Young , Kemmitt John , Wright Charles , Schneider Kirsten , Sphabmixay Pierre , Hernandez-Gordillo Victor , Holcomb Steven J. , Bhushan Brij , Rohatgi Gar , Benton Kyle , Carpenter David , Kester Jemila C. , Eng George , Breault David T. , Yilmaz Omer , Taketani Mao , Voigt Christopher A. , Carrier Rebecca L. , Trumper David L. , Griffith Linda G.
Published: July 2020

The gut microbiome plays an important role in human health and disease. Gnotobiotic animal andin vitrocell-based models provide some informative insights into mechanistic crosstalk. However, there is no existing system for a chronic co-culture of a human colonic mucosal barrier with super oxygen-sensitive commensal microbes, hindering the study of human-microbe interactions in a controlled manner. Here, we investigated the effects of an abundant super oxygen-sensitive commensal anaerobe,Faecalibacterium prausnitzii, on a primary human mucosal barrier using a Gut-MIcrobiome (GuMI) physiome platform that we designed and fabricated. Chronic continuous co-culture ofF. prausnitziifor two days with colon epithelia, enabled by continuous flow of completely anoxic apical media and aerobic basal media, resulted in a strictly anaerobic apical environment fostering growth of and butyrate production byF. prausnitzii, while maintaining a stable colon epithelial barrier. We identified elevated differentiation and hypoxia-responsive genes and pathways in the platform compared with conventional aerobic static culture of the colon epithelia, attributable to a combination of anaerobic environment and continuous medium replenishment. Furthermore, we demonstrated anti-inflammatory effects ofF. prausnitziithrough HDAC and the TLR-NFKB axis. Finally, we identified that butyrate largely contributes to the anti-inflammatory effects by downregulating TLR3 and TLR4. Our results are consistent with some clinical observations regardingF. prausnitzii, thus motivating further studies employing this platform with more complex engineered colon tissues for understanding the interaction between the human colonic mucosal barrier and microbiota, pathogens, or engineered bacteria.
Is structure based drug design ready for selectivity optimization?
Authors: Albanese Steven K. , Chodera John D. , Volkamer Andrea , Keng Simon , Abel Robert , Wang Lingle
Published: July 2020

Alchemical free energy calculations are now widely used to drive or maintain potency in small molecule lead optimization with a roughly 1 kcal/mol accuracy. Despite this, the potential to use free energy calculations to drive optimization of compoundselectivityamong two similar targets has been relatively unexplored in published studies. In the most optimistic scenario, the similarity of binding sites might lead to a fortuitous cancellation of errors and allow selectivity to be predicted more accurately than affinity. Here, we assess the accuracy with which selectivity can be predicted in the context of small molecule kinase inhibitors, considering the very similar binding sites of human kinases CDK2 and CDK9, as well as another series of ligands attempting to achieve selectivity between the more distantly related kinases CDK2 and ERK2. Using a Bayesian analysis approach, we separate systematic from statistical error and quantify the correlation in systematic errors between selectivity targets. We find that, in the CDK2/CDK9 case, a high correlation in systematic errors suggests free energy calculations can have significant impact in aiding chemists in achieving selectivity, while in more distantly related kinases (CDK2/ERK2), the correlation in systematic error suggests fortuitous cancellation may even occur between systems that are not as closely related. In both cases, the correlation in systematic error suggests that longer simulations are beneficial to properly balance statistical error with systematic error to take full advantage of the increase in apparent free energy calculation accuracy in selectivity prediction.
Tolerogenic Nanoparticles Impacting B and T Lymphocyte Responses Delay Autoimmune Arthritis in K/BxN Mice
Authors: Srivastava Amrita , Arlian Britni M. , Pang Lijuan , Kishimoto Takashi K. , Paulson James C.
Published: July 2020

Current treatments for unwanted antibody responses largely rely on immunosuppressive drugs compromising overall immunity. New approaches to achieve antigen-specific tolerance are desirable to avoid unwanted side effects. Several nanoparticle-based approaches designed to tolerize the B or T cell arms of the humoral immune response have shown promise for induction of antigen-specific tolerance, raising the possibility that they could work synergistically if combined. Earlier we showed that Siglec-engaging tolerance-inducing antigenic liposomes (STALs) that display both an antigen (Ag) and glycan ligands of the inhibitory co-receptor CD22 (CD22L) lead to robust antigen-specific B cell tolerance to protein antigens in naïve mice. In another approach, administration of free Ag with poly(lactic co-glycolic acid)-rapamycin nanoparticles (PLGA-R) induced robust antigen-specific tolerance through production of regulatory T cells. Here we illustrate that co-administration of STALs together with PLGA-R to naïve mice induced more robust tolerance to multiple antigen challenges than either nanoparticle alone. Moreover, in K/BxN mice that develop spontaneous autoimmune arthritis to the self-antigen glucose-6-phosphate-isomerase (GPI), co-delivery of GPI-LP-CD22L and PLGA-R delayed onset of disease, and in some mice prevented the disease indefinitely. The results show synergy between B cell-tolerizing STALs and T cell-tolerizing PLGA-R and the potential to induce tolerance in early stage autoimmune disease.
Perturbations in dynamical models of whole-brain activity dissociate between the level and stability of consciousness
Authors: Perl Yonatan Sanz , Pallavicini Carla , Pérez Ipiña Ignacio , Demertzi Athena , Bonhomme Vincent , Martial Charlotte , Panda Rajanikant , Annen Jitka , Ibañez Agustín , Kringelbach Morten , Deco Gustavo , Laufs Helmut , Sitt Jacobo , Laureys Steven , Tagliazucchi Enzo
Published: July 2020

Consciousness transiently fades away during deep sleep, more stably under anesthesia, and sometimes permanently due to brain injury. The development of an index to quantify the level of consciousness across these different states is regarded as a key problem both in basic and clinical neuroscience. We argue that this problem is ill-defined since such an index would not exhaust all the relevant information about a given state of consciousness. While the level of consciousness can be taken to describe the actual brain state, a complete characterization should also include its potential behavior against external perturbations. We developed and analyzed whole-brain computational models to show that the stability of conscious states provides information complementary to their similarity to conscious wakefulness. Our work leads to a novel methodological framework to sort out different brain states by their stability and reversibility, and illustrates its usefulness to dissociate between physiological (sleep), pathological (brain-injured patients), and pharmacologically-induced (anesthesia) loss of consciousness.
A tyrosine kinase protein interaction map reveals targetable EGFR network oncogenesis in lung cancer
Authors: Kaushik Swati , Haderk Franziska , Zhao Xin , Hu Hsien-Ming , Shah Khyati N. , Jang Gwendolyn M. , Olivas Victor , Nanjo Shigeki , Jascur John , Masto Vincent B. , Ciznadija Daniel , Sloma Ido , Gross Emilie , Weinrich Scott L. , Johnson Jeffery R. , Bivona Trever G. , Krogan Nevan J. , Bandyopadhyay Sourav
Published: July 2020

Signaling networks balance the activities of many physically interacting proteins and perturbations to this network influence downstream signaling, potentially leading to oncogenic states. Using affinity purification-mass spectrometry we defined this network for all 90 human tyrosine kinases revealing 1,463 mostly novel interactions between these key cancer proteins and diverse molecular complexes. Modulation of interactor levels altered growth phenotypes associated with corresponding tyrosine kinase partners suggesting that tumors may alter the stoichiometries of interactors to maximize oncogenic signaling. We show that the levels of EGFR interactors delineates this form of network oncogenesis in 19% of EGFR wild-type lung cancer patients which were mostly otherwise oncogene negative, predicting sensitivity to EGFR inhibitors in vitro and in vivo. EGFR network oncogenesis occurs through mechanistically distinct network alleles often in cooperation with weak oncogenes in the MAPK pathway. Network oncogenesis may be a common and targetable convergent mechanism of oncogenic pathway activation in cancer.

HIGHLIGHTS

A human tyrosine kinome protein interaction map reveals novel physical and functional associations.

Dependence on oncogenic tyrosine kinases is modulated through perturbation of their interactors.

EGFR network oncogenesis in up to 19% of EGFR wild-type lung cancers is targetable.

EGFR network oncogenesis cooperates with weak oncogenes in the MAPK pathway.
Substitutions at Non-Conserved Rheostat Positions Modulate Function by Re-Wiring Long-Range, Dynamic Interactions
Authors: Campitelli Paul , Swint-Kruse Liskin , Ozkan S. Banu
Published: July 2020

Amino acid substitutions at nonconserved protein positions can have non-canonical and “long-distance” outcomes on protein function. Such outcomes might arise from changes in the internal protein communication network, which is often accompanied by changes in structural flexibility. To test this, we calculated flexibilities (“DFI”) and dynamic coupling (“DCI”) for positions in the linker region of the lactose repressor protein (“LacI”). This region contains nonconserved positions for which substitutions alter DNA binding affinity. We first chose to study eleven substitutions at position 52. In computations, substitutions showed long-range effects on flexibilities of DNA binding positions, and the degree of flexibility change correlated with experimentally-measured changes in DNA binding. Substitutions also altered dynamic coupling to DNA binding positions in a manner that captured other experimentally-determined functional changes. Next, we broadened calculations to consider the dynamic coupling between 17 linker positions and the DNA binding domain. Experimentally, these linker positions exhibited a wide range of substitution outcomes: Four conserved positions tolerated almost no substitutions (“toggle”), ten nonconserved positions showed progressive changes from a range of substitutions (“rheostat”), and three nonconserved positions tolerated almost all substitutions (“neutral”). In computations with wild-type LacI, the dynamic couplings between the DNA binding domain and these linker positions showed varied degrees of asymmetry that correlated with the observed toggle/rheostat/neutral substitution outcomes. Thus, we propose that long-range and non-canonical substitutions outcomes at nonconserved positions arise from re-wiring long-range communication among functionally-important positions. Such calculations might enable predictions for substitution outcomes at a range of nonconserved positions.
Optimal evolutionary decision-making to store immune memory
Authors: Schnaack Oskar H , Nourmohammad Armita
Published: July 2020

The adaptive immune system provides a diverse set of molecules that can mount specific responses against a multitude of pathogens. Memory is a key feature of adaptive immunity, which allows organisms to respond more readily upon re-infections. However, differentiation of memory cells is still one of the least understood cell fate decisions. Here, we introduce a mathematical framework to characterize optimal strategies to store memory to maximize the utility of immune response over an organism’s lifetime. We show that memory production should be actively regulated to balance between affinity and cross-reactivity of immune receptors for an effective protection against evolving pathogens. Moreover, we predict that specificity of memory should depend on the organism’s lifespan, and shorter-lived organisms with fewer pathogenic encounters should store more cross-reactive memory. Our framework provides a baseline to gauge the efficacy of immune memory in light of an organism’s coevolutionary history with pathogens.
Split-wrmScarlet and split-sfGFP: Tools for faster, easier fluorescent labeling of endogenous proteins inCaenorhabditis elegans
Authors: Goudeau Jérôme , Sharp Catherine S. , Paw Jonathan , Savy Laura , Leonetti Manuel D. , York Andrew G. , Updike Dustin L. , Kenyon Cynthia , Ingaramo Maria
Published: July 2020

We create and share a new red fluorophore, along with a set of strains, reagents and protocols, to make it faster and easier to label endogenousC. elegansproteins with fluorescent tags. CRISPR-mediated fluorescent labeling ofC. elegansproteins is an invaluable tool, but it is much more difficult to insert fluorophore-size DNA segments than it is to make small gene edits. In principle, high-affinity asymmetrically split fluorescent proteins solve this problem inC. elegans: the small fragment can quickly and easily be fused to almost any protein of interest, and can be detected wherever the large fragment is expressed and complemented. However, there is currently only one available strain stably expressing the large fragment of a split fluorescent protein, restricting this solution to a single tissue (the germline) in the highly autofluorescent green channel. No availableC. eleganslines express unbound large fragments of split red fluorescent proteins, and even state-of-the-art split red fluorescent proteins are dim compared to the canonical split-sfGFP protein. In this study, we engineer a bright, high-affinity new split red fluorophore, split-wrmScarlet. We generate transgenicC. eleganslines to allow easy single-color labeling in muscle or germline cells and dual-color labeling in somatic cells. We also describe ‘glonads’, a novel expression strategy for the germline, where traditional expression strategies struggle. We validate these strains by targeting split-wrmScarlet to several genes whose products label distinct organelles, and we provide a protocol for easy, cloning-free CRISPR/Cas9 editing. As the collection of split-FP strains for labeling in different tissues or organelles expands, we will post updates at doi.org/10.5281/zenodo.3993663
End-to-end Bayesian analysis of14C dates reveals new insights into lowland Maya demography
Authors: Price Michael Holton , Capriles José M. , Hoggarth Julie A. , Bocinsky Kyle , Ebert Claire E. , Jones James Holland
Published: July 2020

Archaeologists and demographers increasingly employ aggregations of published radiocarbon (14C) dates as demographic proxies summarizing changes in human activity in past societies. Presently, summed probability densities (SPDs) of calibrated radiocarbon dates are the dominant method of using14C dates to reconstruct demographic trends. Unfortunately, SPDs are incapable of converging on their true generating distributions even as the number of observations gets large. To overcome this problem, we propose a more principled alternative that combines finite mixture models and Bayesian inference to identify the generating distribution of a set of radiocarbon dates. Numerical simulations and an assessment of the statistical identifiability of our method demonstrate that it correctly converges on the generating distribution. We apply this novel end-to-end Bayesian approach to reconstruct prehistoric Maya demographic growth using a recently compiled Mesoamerican radiocarbon database. Our results show that the Maya Lowlands experienced a century of rapid growth rates (1%) during the Late Classic, followed by a rapid decrease in population during the Terminal Classic, and a subsequent more-modest resurgence in population during the Postclassic. Additionally, a detailed population reconstruction of the important political center of Tikal verifies that slow population growth between the Preclassic and Early Classic gave pace to rapid growth starting around AD 500 and peaking at the beginning of the eight century. Our proposed method verifies previous reconstructions based on settlement patterns and ceramics, but with far more precise time-resolution and characterization of uncertainty than has been possible.
Microchip based microrheology via Acoustic Force Spectroscopy shows that endothelial cell mechanics follows a fractional viscoelastic model
Authors: Nguyen Alfred , Brandt Matthias , Betz Timo
Published: July 2020

Active microrheology is one of the main methods to determine the mechanical properties of cells and tissue, and the modelling of the viscoelastic properties of cells and tissue is under heavy debate with many competing approaches. Most experimental methods of active microrheology such as optical tweezers or atomic force microscopy based approaches rely on single cell measurements, and thus suffer from a low throughput. Here, we present a novel method for cell based microrheology using acoustic forces which allows multiplexed measurements of several cells in parallel. Acoustic Force Spectroscopy (AFS) is used to generate multi-oscillatory forces in the range of pN-nN on particles attached to primary human umbilical vein endothelial cells (HUVEC) cultivated inside a microfluidic chip. While the AFS was introduced as a single-molecule technique to measure mechanochemical properties of biomolecules, we exploit the AFS to measure the dynamic viscoelastic properties of cells exposed to different conditions, such as flow shear stresses or drug injections. By controlling the force and measuring the position of the particle, the complex shear modulusG*(ω) can be measured continuously over several hours. The resulting power-law shear moduli are consistent with fractional viscoelastic models. In our experiments we confirm a decrease in shear modulus after perturbing the actin cytoskeleton via cytochalasin B. This effect was reversible after washing out the drug. Although these measurements are possible, we provide critical information regarding the AFS as a measurement tool showing its capabilities and limitations. A key result is that for performing viscoelastic measurements with the AFS, a thorough calibration and careful data analysis is crucial, for which we provide protocols and guidelines.
Two- and three-dimensional tracking ofMFA2mRNA molecules in mating yeast
Authors: Geva Polina , Komoshvili Konstantin , Liberman-Aronov Stella
Published: July 2020

Intracellular mRNA transport contributes to the spatio-temporal regulation of mRNA function and localized translation. In the budding yeast,Saccharomyces cerevisiae, asymmetric mRNA transport localizes ∼30 specific mRNAs including those encoding polarity and secretion factors, to the bud tip. The underlying process involves RNA binding proteins (RBPs), molecular motors, processing bodies (PBs), and the actin cytoskeleton. Recently, pheromone a-factor expression in mating yeast was discovered to depend upon proper localization of its mRNA,MFA2.MFA2mRNAs in conjunction with PBs cluster at the shmoo tip to form “mating bodies”, from which a-factor is locally expressed. The mechanism ensuring the correct targeting of mRNA to the shmoo tip is poorly understood.

Here we analyzed the kinetics and trajectories ofMFA2mRNA transport in living, alpha-factor treated yeast. Two-(2D) and three-dimensional (3D) analyses allowed us to reconstruct the granule tracks and estimate granule velocities. Tracking analysis of singleMFA2mRNA granules, labeled using a fluorescent aptamer system, demonstrated three types movement: vibrational, oscillatory and translocational. The mRNA granule transport was complex; a granule could change its movement behavior and composition during its journey to the shmoo. Processing body assembly and the actin-based motor, Myo4p, were involved in movement ofMFA2mRNA to the shmoo, but neither was required, indicating that multiple mechanisms for translocation were at play. Our visualization studies present a dynamic view of the localization mechanism in shmoo-bearing cells.
Maternal immune activation during pregnancy alters early neurobehavioral development in nonhuman primate offspring
Authors: Vlasova Roza M. , Iosif Ana-Maria , Ryan Amy M. , Murai Takeshi , Lesh Tyler A. , Rowland Douglas J. , Bennett Jeffrey , Hogrefe Casey E. , Maddock Richard J. , Gandal Michael J. , Geschwind Daniel H. , Schumann Cynthia M. , Van de Water Judy , McAllister A. Kimberley , Carter Cameron S. , Styner Martin A. , Amaral David G. , Bauman Melissa D.
Published: July 2020

Background

Human epidemiologic studies have implicated exposure to infectious or inflammatory insults during gestation in the etiology of neurodevelopmental disorders. Rodent models of maternal immune activation (MIA) have identified the maternal immune response as the critical link between maternal infection and aberrant brain and behavior development in offspring. The nonhuman primate MIA model provides an opportunity to maximize the translational utility of this model in a species more closely related to humans.

Methods

Here we evaluate the effects of MIA on brain and behavioral development in the rhesus monkey (Macaca mulatta). A modified form of the viral mimic, Polyinosinic-polycytidylic acid (PolyIC), was delivered to pregnant rhesus monkeys (n=14) in the late first trimester to stimulate a maternal immune response. Control dams received saline injections at the same gestational time points (n=10) or were untreated (n=4).

Results

MIA-treated dams exhibited a strong immune response as indexed by transient increases in sickness behavior, temperature and inflammatory cytokines. MIA-exposed offspring developed species typical milestones and demonstrate subtle changes in early in social development. However, magnetic resonance imaging demonstrated significant gray matter volume reductions in prefrontal and frontal cortices at 6, 12 and 24 months of age.

Conclusions

These findings provide new insights into the emergence of neuropathology in MIA-exposed primates and have implications for the pathophysiology of human psychiatric disorders associated with maternal gestational infection.
Global reinforcement of DNA methylation through enhancement of RNA-directed DNA methylation ensures sexual reproduction in rice
Authors: Wang Lili , Zeng Longjun , Zheng Kezhi , Zhu Tianxin , Yin Yumeng , Xu Dachao , Zhan Huadong , Wu Yufeng , Yang Dong-Lei
Published: July 2020

DNA methylation is an important epigenetic mark that regulates the expression of genes and transposons. RNA-directed DNA methylation (RdDM) is the main molecular pathway responsible forde novoDNA methylation in plants. In Arabidopsis, however, mutations in RdDM genes cause no visible developmental defects, which raising the question of the biological significance of RdDM in plant development. Here, we isolated and clonedFive Elements Mountain 1(FEM1), which encodes an RNA-dependent RNA polymerase. Mutation inFEM1substantially decreased genome-wide CHH methylation levels and abolished the accumulation of 24-nt small interfering RNAs. Moreover, male and female reproductive development was disturbed, which led to the sterility offem1mutants. In wild-type (WT) plants but not infem1mutants, genome-wide CHH DNA methylation levels were greater in panicles, stamens, and pistils than in seedlings. The global increase of methylation in reproductive organs of the WT was attributed to enhancement of RdDM activity including FEM1 activity. More than half of all encoding genes in the rice genome overlapped with hypermethylated regions in the sexual organs of the WT, and many of them appear to be directly regulated by an increase in DNA methylation.

Our results demonstrate that a global increase of DNA methylation through enhancement of RdDM activity in reproductive organs ensures sexual reproduction of rice.
Persistence: Using Protein Turnover to Expand the Applications of Transcriptomics
Authors: Smail Marissa A. , Reigle James K. , McCullumsmith Robert E.
Published: July 2020

One of the major issues with RNA sequencing is the lack of reproducibility between RNA and protein expression. Transcriptomics offers a holistic view of the molecular landscape of a tissue at an RNA level. However, RNA and protein expression are often at odds when measured in the same sample, raising the question whether or not changes in RNA expression translate to functional differences. This problem creates a need to devise a way to approximate protein abundance from transcriptomics data, in order to create a more complete picture of the functional landscape of a tissue. One additional measure that could be useful here is protein turnover or half-life. Once RNA is transcribed into protein, that protein can either be quickly degraded or remain in the cell for an extended period of time. The longer a protein’s half-life, the more influence it can have on its surroundings. Recently, a study used stable isotope labeling in mammals (SILAM) in combination with mass spectrometry to determine the turnover ratio of ∼2200 protein in mouse synaptosomes. This data offers a valuable opportunity to integrate protein turnover with RNA expression to gain deeper insight into the functional meaning of RNA expression changes. Here, we present the concept of this combination of protein turnover and RNA expression, which we coined as persistence. We then demonstrate the application of persistence using schizophrenia (SCZ) transcriptomics datasets. Calculating persistence for these datasets greatly improved our ability to predict protein expression from RNA expression. Furthermore, this approach successfully identified persistent genes and pathways known to have impactful changes in SCZ. These results suggest that persistence is a valuable metric for improving the functional insight that can be gained from transcriptomics data.
The attachment of Sso7d-like protein improves processivity and resistance to inhibitors of M-MuLV reverse transcriptase
Authors: Oscorbin Igor P. , Wong Pei Fong , Boyarskikh Ulyana A. , Khrapov Evgeny A. , Filipenko Maksim L.
Published: July 2020

Reverse transcriptases, RTs, are a standard tool in both fundamental studies and diagnostics used for transcriptome profiling, virus RNA testing and other tasks. RTs should possess elevated temperature optimum, high thermal stability, processivity, and tolerance to contaminants originating from the biological substances under analysis or the purification reagents. Here, we have constructed a set of chimeric RTs, based on the combination of MuLV-RT and DNA-binding domains: the DNA-binding domain of DNA ligasePyrococcus abyssiand Sto7d protein, Sso7d counterpart, fromSulfolobus tokodaii. Chimeric RTs showed the same optimal temperature and the efficacy of terminal transferase reaction as the original M-MuLV RT. Processivity and the efficiency in cDNA synthesis of the chimeric RT with Sto7d at C-end were increased several-fold. The attachment of Sto7d enhanced the M-MuLV RT tolerance to the most common amplification inhibitors: NaCl, urea, guanidinium chloride, formamide, components of human whole blood, and human blood plasma. Thus, fusing M-MuLV RT with an additional domain resulted in more robust and efficient RTs.
Arrhythmogenesis as the failure of repolarization
Authors: Heitmann Stewart , Vandenberg Jamie I , Hill Adam P
Published: July 2020

Contemporary theories of cardiac fibrillation typically rely on the emergence of rotors to explain the transition from regular sinus rhythm to disordered electrophysiological activity. How those rotors spontaneously arise in the absence of re-entrant anatomical circuits is not fully understood. Here we propose a novel mechanism where arrhythmias are initiated by cardiac cells that fail to repolarize following a normal heartbeat. Those cells subsequently act as a focal ectopic source that drive the ensuing fibrillation. We used a simple computational model to investigate the impact of such cells in both homogeneous and heterogeneous excitable media. We found that heterogeneous media can tolerate a surprisingly large number of abnormal cells and still support normal rhythmic activity. At a critical limit the medium becomes chronically arrhythmogenic. Numerical analysis revealed that the critical threshold for arrhythmogenesis depends on both the strength of the coupling between cells and the extent to which the abnormal cells resist repolarization. Arrhythmogenesis was also found to emerge first at tissue boundaries where cells naturally have fewer neighbors to influence their behavior. These findings may explain why atrial fibrillation typically originates from the cuff of the pulmonary vein.

Author summary

Cardiac fibrillation is a medical condition where normal heart function is compromised as electrical activity becomes disordered. How fibrillation arises spontaneously is not fully understood. It is generally thought to be triggered by premature depolarization of the cardiac action potential in one or more cells. Those premature beats, known as early-afterdepolarizations, subsequently initiate a self-sustaining rotor in the otherwise normal heart tissue. In this study, we propose an alternative mechanism whereby arrhythmias are initiated by cardiac cells that fail to repolarize of their own accord but still operate normally when embedded in functional heart tissue. We find that such cells can act as focal ectopic sources under appropriate conditions of inter-cellular coupling. Moreover, cells on natural tissue boundaries are more susceptible to arrhythmia because they are coupled to fewer cells. This may explain why the pulmonary vein is often implicated as a source of atrial fibrillation.
Macrophage-specific responses to human- and animal-adapted tubercle bacilli reveal pathogen and host factors driving multinucleated cell formation
Authors: Queval Christophe J. , Fearns Antony , Botella Laure , Smyth Alicia , Schnettger Laura , Mitermite Morgane , Wooff Esen , Villarreal-Ramos Bernardo , Garcia-Jimenez Waldo , Heunis Tiaan , Trost Matthias , Werling Dirk , Salguero Francisco J. , Gordon Stephen V. , Gutierrez Maximiliano G.
Published: July 2020

TheMycobacterium tuberculosiscomplex (MTBC) is a group of related pathogens that cause tuberculosis (TB) in mammals. MTBC species are distinguished by their ability to sustain in distinct host populations. WhileMycobacterium bovis(Mbv) sustains transmission cycles in cattle and wild animals and causes zoonotic TB,M. tuberculosis(Mtb) affects human populations and seldom causes disease in cattle. However, the host and pathogen determinants driving host tropism between MTBC species are still unknown. Macrophages are the main host cell that encounters mycobacteria upon initial infection and we hypothesised that early interactions between the macrophage and mycobacteria influence species-specific disease outcome. To identify factors that contribute to host tropism, we analysed both blood-derived primary human and bovine macrophages (hMϕ or bMϕ, respectively) infected with Mbv and Mtb. We show that Mbv and Mtb reside in different cellular compartments and differentially replicate in hMϕ whereas both Mbv and Mtb efficiently replicate in bMϕ. Specifically, we show that out of the four infection combinations, only the infection of bMϕ with Mbv promoted the formation of multinucleated cells (MNCs), a hallmark of tuberculous granulomas. Mechanistically, we demonstrate that both MPB70 from Mbv and extracellular vesicles released by Mbv-infected bMϕ promote macrophage multi-nucleation. Importantly, we extend ourin vitrostudies to show that granulomas from Mbv-infected but not Mtb-infected cattle contained higher numbers of MNCs. Our findings implicate MNC formation in the contrasting pathology between Mtb and Mbv for the bovine host, and identify MPB70 from Mbv and extracellular vesicles from bMϕ as mediators of this process.
Fine-scale Population Structure and Demographic History of Han Chinese Inferred from Haplotype Network of 111,000 Genomes
Authors: Lan Ao , Kang Kang , Tang Senwei , Wu Xiaoli , Wang Lizhong , Li Teng , Weng Haoyi , Deng Junjie ,   WeGene Research Team, Zheng Qiang , Yao Xiaotian , Chen Gang
Published: July 2020

Han Chinese is the most populated ethnic group across the globe with a comprehensive substructure that resembles its cultural diversification. Studies have constructed the genetic polymorphism spectrum of Han Chinese, whereas high-resolution investigations are still missing to unveil its fine-scale substructure and trace the genetic imprints for its demographic history. Here we construct a haplotype network consisted of 111,000 genome-wide genotyped Han Chinese individuals from direct-to-consumer genetic testing and over 1.3 billion identity-by-descent (IBD) links. We observed a clear separation of the northern and southern Han Chinese and captured 5 subclusters and 17 sub-subclusters in haplotype network hierarchical clustering, corresponding to geography (especially mountain ranges), immigration waves, and clans with cultural-linguistic segregation. We inferred differentiated split histories and founder effects for population clans Cantonese, Hakka, and Minnan-Chaoshanese in southern China, and also unveiled more recent demographic events within the past few centuries, such asZou XikouandChuang Guandong. The composition shifts of the native and current residents of four major metropolitans (Beijing, Shanghai, Guangzhou, and Shenzhen) imply a rapidly vanished genetic barrier between subpopulations. Our study yields a fine-scale population structure of Han Chinese and provides profound insights into the nation’s genetic and cultural-linguistic multiformity.
Amino acid substitutions associated with treatment failure of hepatitis C virus infection
Authors: Soria María Eugenia , García-Crespo Carlos , Martínez-Gónzalez Brenda , Vázquez-Sirvent Lucía , Lobo-Vega Rebeca , de Ávila Ana Isabel , Gallego Isabel , Chen Qian , García-Cehic Damir , Llorens-Revull Meritxell , Briones Carlos , Gómez Jordi , Ferrer-Orta Cristina , Verdaguer Nuria , Gregori Josep , Rodríguez-Frías Francisco , Buti María , Esteban Juan Ignacio , Domingo Esteban , Quer Josep , Perales Celia
Published: July 2020

Despite the high virological response rates achieved with current directly-acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 2% to 5% of treated patients do not achieve a sustained viral response. Identification of amino acid substitutions associated with treatment failure requires analytical designs, such as subtype-specific ultra-deep sequencing (UDS) methods for HCV characterization and patient management. Using this procedure, we have identified six highly represented amino acid substitutions (HRSs) in NS5A and NS5B of HCV from 220 patients who failed therapy, which are notbona fideresistance-associated substitutions (RAS). They were present frequently in basal and post-treatment virus of patients who failed therapy to different DAA-based therapies. Contrary to several RAS, HRSs belong to the acceptable subset of substitutions according to the PAM250 replacement matrix. Coherently, their mutant frequency, measured by the number of deep sequencing reads within the HCV quasispecies that encode the relevant substitutions, ranged between 90% and 100% in most cases. Also, they have limited predicted disruptive effects on the three-dimensional structures of the proteins harboring them. Possible mechanisms of HRS origin and dominance, as well as their potential predictive value of treatment response are discussed.
Accelerated tissue repair through cell proliferative effect by a size controlled aqueous based Fullerene C60nanoformulation
Authors: Sinha Nabodita , Gahane Avinash Y. , Thakur Ashwani Kumar
Published: July 2020

Abstract

We have developed Fullerene-C60nanoformulations containing discrete sized nanoparticles by dispersing concentration range of Fullerene. Small sized particles are cytotoxic while larger ones are cell proliferative. The cell proliferative property is used for tissue repair in cellular and animal wound models.
In-vitroevaluation ofPseudomonas fluorescensantibacterial activity againstListeriaspp. isolated from New Zealand horticultural environments
Authors: Mohan Vathsala , Fletcher Graham , Leroi Françoise
Published: July 2020

Beneficial bacteria with antibacterial properties are an attractive alternative to chemical-based antibacterial or bactericidal agents. The aim of our study was to source such bacteria from horticultural produce and environments and to explore the mechanisms of their antimicrobial properties. Four strains ofPseudomonas fluorescenswere isolated that possessed antibacterial activity against the pathogenListeria monocytogenes.These strains (PFR46H06, PFR46H07, PFR46H08 and PFR46H09) were tested againstL. monocytogenes(n=31),L. seeligeri(n=1) andL. innocua(n=1) isolated from seafood and horticultural sources, and twoL. monocytogenesfrom clinical cases (Scott A and ATCC 49594, n=2). AllListeriastrains were inhibited by the three strains PFR46H07, PFR46H08 and PFR46H09 with average zones of inhibition of 14.8, 15.1 and 18.2 mm, respectively, with PFR46H09 having significantly more inhibition than the other two (p<0.05). PFR46H06 showed minimal inhibition towards theL. seeligeriandL. innocuaisolates and no inhibition towards most of theL. monocytogenesisolates. In order to investigate the functional protein differences between these strains, all four strains were subjected to whole cell lysate proteomics; data are available via ProteomeXchange with identifier PXD019965. We found significant differences in the peptide profiles and protein summaries between these isolates. The total number of proteins identified was 1781 in PFR46H06, 2030 in PFR46H07, 2228 in PFR46H08 and 1994 in PFR46H09. We paid special attention to secretion system proteins as these play a main role in the defense mechanisms of bacteria, particularly those of the type VI secretion system (T6SS) and found that they varied significantly (p<0.001) among the four isolates. PFR46H06 and PFR46H07 possessed the fewest secretion system structural proteins (12 and 11 respectively) while PFR46H08 and PFR46H09 each had 18. PFR46H09, which showed the greatest antimicrobial effect, had nine T6SS proteins compared to just four in the other three strains.
Passage of transmissible cancers in the Tasmanian devil is due to a dominant, shared peptide motif and a limited repertoire of MHC-I allotypes
Authors: Gastaldello A , Ramarathinam SH , Bailey A , Owen R , Turner S , Kontouli A , Elliott T , Skipp P , Purcell AW , Siddle HV
Published: July 2020

Transmissible cancers are spread via the passage of malignant cells. The survival of the Tasmanian devil, the largest marsupial carnivore, is threatened by two independent transmissible cancers, devil facial tumour (DFT) 1 and devil facial tumour 2 (DFT2). To aid the development of a peptide vaccine and to interrogate how histocompatibility barriers can be overcome, we analysed the peptides bound to Major Histocompatibility Complex class I molecules from the Tasmanian devil and its transmissible tumours. Comparison of the peptidomes from DFT1+IFNγ, DFT2 and host fibroblast cells demonstrates a shared motif, despite differences in MHC-I allotypes between the cell lines. Importantly, DFT1+IFNγ and DFT2 share the presentation of peptides derived from neural proteins, reflecting a common cellular origin that should be exploited for vaccine design. These results suggest that some polymorphisms between tumours and host are ‘hidden’ by a common peptide motif, providing the potential for permissive passage of infectious cells.
Mechanics and Differential Healing Outcomes of Small and Large Defect Injuries of the Tendon-Bone Attachment in the Rat Rotator Cuff
Authors: Sullivan Anna Lia , Locke Ryan C. , Klink Rachel K. , Leek Connor C. , Killian Megan L.
Published: July 2020

The size of rotator cuff tears affects clinical outcomes following rotator cuff repair and is correlated with risk of re-injury. This study aimed to understand how defect size influences the structural and mechanical outcomes of the injured rotator cuff attachmentin vivo. We used our previously established model of full-thickness injury of the rotator cuff tendon-bone attachment in Long Evans rats to compare differences in healing outcomes between small and large defects. Biomechanical properties, gross morphology, bone remodeling, and cell and tissue morphology were assessed at 3- or 8-weeks of healing. At the time of injury (no healing), large defects had decreased mechanical properties compared to small defects, and both defect sizes had decreased mechanical properties compared to intact attachments. The mechanical properties of the defect groups were comparable after 8-weeks of healing and significantly improved compared to no healing but failed to return to intact levels. Local bone volume at the defect site was higher in large compared to small defects on average and increased from 3- to 8-weeks. Contrastingly, bone quality, measured as bone volume percentage and trabecular morphometry, of the total epiphysis and greater tubercle decreased from 3- to 8-weeks of healing and these changes were not dependent on defect size. Qualitatively, we observed that large defects had increased disorganized collagen and neovascularization compared to small defects. In this study, we demonstrated that not only small but also large defects do not regenerate the mechanical and structural integrity of the intact rat rotator cuff attachment following healingin vivo.

Statement of Clinical Significance

Our rat model of full-thickness rotator cuff tears may be beneficial to understand and prevent tear enlargementin vivo.
Natural combinatorial genetics and prolific polyamine production enable siderophore diversification in Serratia plymuthica
Authors: Cleto Sara , Haslinger Kristina , Prather Kristala L.J. , Lu Timothy K.
Published: July 2020

Siderophores are small molecules with unmatched capacity to scavenge iron from proteins and the extracellular milieu, where it mostly occurs as insoluble Fe3+. Siderophores chelate Fe3+for uptake into the cell, where it is reduced to soluble Fe2+. As iron is essential for bacterial survival, siderophores are key molecules in low soluble iron conditions. Bacteria have devised many strategies to synthesize proprietary siderophores to avoid siderophore piracy by competing organisms, e.g., by incorporating different polyamine backbones into siderophores, while maintaining the catechol moieties. We report thatSerratia plymuthicaV4 produces a variety of siderophores, which we term thesiderome, and which are assembled by the concerted action of enzymes encoded in two independent gene clusters. Besides assembling serratiochelin with diaminopropane,S. plymuthicautilizes putrescine and the same set of enzymes to assemble photobactin, a siderophore described forPhotorhabdus luminescens. The enzymes encoded by one of the gene clusters can independently assemble enterobactin. A third, independent operon is responsible for biosynthesis of the hydroxamate siderophore aerobactin, initially described inEnterobacter aerogenes. Mutant strains not synthesizing polyamine-siderophores significantly increased enterobactin production levels, though lack of enterobactin did not impact serratiochelin production. Knocking out SchF0, an enzyme involved in the assembly of enterobactin alone, significantly reduced bacterial fitness. This study illuminates the interplay between siderophore biosynthetic pathways and polyamine production superpathways, indicating routes of molecular diversification. Given its natural yields of diaminopropane (97.75 μmol/g DW) and putrescine (30.83 μmol/g DW),S. plymuthicacan be exploited for the industrial production of these compounds.

Significance Statement

Siderophores are molecules crucial for bacterial survival in low iron environments. Bacteria have evolved the capacity to pirate siderophores made by other bacterial strains and to diversify the structure of their own siderophores, to prevent piracy. We found thatSerratia plymuthicaV4 produces five different siderophores using three gene clusters and a polyamine production superpathway. The most well studied siderophore, enterobactin, rather than the strain’s proprietary and by far most abundant siderophore, serratiochelin, displayed a crucial role in the fitness ofS. plymuthica. Our results also indicate that this strain is a good candidate for engineering the large-scale production of diaminopropane (DAP), as without any optimization it produced the highest amounts of DAP reported for wild-type strains.
Prior hypotheses or regularization allow inference of diversification histories from extant timetrees
Authors: Morlon Hélène , Hartig Florian , Robin Stéphane
Published: July 2020

Phylogenies of extant species are widely used to study past diversification dynamics1. The most common approach is to formulate a set of candidate models representing evolutionary hypotheses for how and why speciation and extinction rates in a clade changed over time, and compare those models through their probability to have generated the corresponding empirical tree. Recently, Louca & Pennell2reported the existence of an infinite number of ‘congruent’ models with potentially markedly different diversification dynamics, but equal likelihood, for any empirical tree (see also Lambert & Stadler3). Here we explore the implications of these results, and conclude that they neither undermine the hypothesis-driven model selection procedure widely used in the field nor show that speciation and extinction dynamics cannot be investigated from extant timetrees using a data-driven procedure.
Aminoglycoside antibiotics inhibit mycobacteriophage infection
Authors: Jiang Zheng , Wei Junwei , Peng Nan , Li Yingjun
Published: July 2020

Antibiotic resistance is becoming the biggest current threat to global health. At the same time, phage therapy is witnessing a return of interest. The therapeutic use of bacteriophages, that infect and kill bacteria, is well suited to be a good strategy to combat antibiotic resistance. Furthermore, bacteriophages are increasingly used in combination with standard antibiotics against the drug-resistant pathogens. Interestingly, we found that the engineered mycobacteriophage phAE159 and natural phage D29 can not infect theMycobacterium tuberculosisin the presence of kanamycin, hygromycin or streptomycin, but there is no effect on the phage infection in the presence of spectinomycin. Based on a series of studies and structural analysis of the above four aminoglycoside antibiotics, we can speculate as to the mechanism by which amino sugar group of aminoglycoside was able to selectively inhibit mycobacteriophage DNA replication. This is a rare discovery that broad-spectrum antibiotics inhibit phage infection. We envisioned that this study will provide guidance for people to combine phage and antibiotics to treatM. tuberculosis.