bluuebunny/crossref_metadata_2025 huggingface dataset:
Inflammation induces pro-NETotic neutrophils via TNFR2 signaling
Authors: Neuenfeldt Friederike , Schumacher Jan Christoph , Grieshaber-Bouyer Ricardo , Habicht Jüri , Schröder-Braunstein Jutta , Gauss Annika , Niesler Beate , Heineken Niko , Dalpke Alexander , Gaida Matthias M. , Giese Thomas , Meuer Stefan , Samstag Yvonne , Wabnitz Guido
Published: June 2021

Cytokines released during chronic inflammatory diseases induce pro-inflammatory properties in polymorphonuclear neutrophils (PMN). Here we show that in vitro cytokine treatment leads to the development of a subgroup of human PMN expressing CCR5, termed CCR5+ cytokine-induced PMN (CCR5+ cPMN). Auto/paracrine TNF signaling increases intracellular neutrophil elastase (ELANE) abundance and induces NETosis in CCR5+ cPMN. Triggering of CCR5 amplifies NETosis. Membranous TNF (mTNF) outside-in signaling induces the formation of reactive oxygen species, a known activator of NETosis. In vivo, we find an increased number of CCR5+ cPMN in the peripheral blood and inflamed lamina propria of patients with ulcerative colitis (UC) but not Crohn’s disease (CD). Notably, failure of anti-TNF therapy is associated with higher frequencies of CCR5+ cPMN. In conclusion, we identify a phenotype of pro-NETotic, CCR5 positive PMN present in inflamed tissue in vivo and inducible in vitro. These cells may reflect an important component of tissue damage during chronic inflammation and could be of diagnostic value.
Antibiotics drive expansion of rare pathogens in a chronic infection microbiome model
Authors: Varga John J. , Zhao Conan , Davis Jacob D. , Hao Yiqi , Farrell Jennifer M. , Gurney James R. , Voit Eberhard , Brown Sam P
Published: June 2021

Chronic (long-lasting) infections are globally a major and rising cause of morbidity and mortality. Unlike typical acute infections, chronic infections are ecologically diverse, characterized by the presence of a polymicrobial mix of opportunistic pathogens and human-associated commensals. To address the challenge of chronic infection microbiomes, we focus on a particularly well-characterized disease, cystic fibrosis (CF), where polymicrobial lung infections persist for decades despite frequent exposure to antibiotics. Epidemiological analyses point to conflicting results on the benefits of antibiotic treatment, and are confounded by the dependency of antibiotic exposures on prior pathogen presence, limiting their ability to draw causal inferences on the relationships between antibiotic exposure and pathogen dynamics. To address this limitation, we develop a synthetic infection microbiome model, and benchmark on clinical data. We show that, in the absence of antibiotics, the microbiome structure in a synthetic sputum medium is highly repeatable and dominated by oral commensals. In contrast, challenge with physiologically relevant antibiotic doses leads to substantial community perturbation characterized by multiple alternate pathogen-dominant states and enrichment of drug-resistant species. These results provide evidence that antibiotics can drive the expansion (via competitive release) of previously rare opportunistic pathogens and offer a path towards microbiome-informed conditional treatment strategies.
Analysis of the H-Ras mobility patternin vivoshows cellular heterogeneity inside epidermal tissue
Authors: Gora Radoslaw J. , de Jong Babette , van Hage Patrick , Rhiemus Mary A. , van Steenis Fjodor , van Noort John , Schmidt Thomas , Schaaf Marcel J.M.
Published: June 2021

Over the last two decades, developments in single-molecule microscopy (SMM) have enabled imaging and tracking of individual, fluorescently labelled proteins in biological systems, and most of these studies have focused on the analysis of protein mobility patterns inside cultured cells. In the present study, SMM was appliedin vivo, using the zebrafish embryo model. We studied the protein dynamics of the membrane protein H-Ras, mutants of this protein, and its membrane-anchoring domain, C10H-Ras, in epidermal cells of living two-day-old embryos, using a total internal reflection fluorescence microscopy (TIRFM) setup. For all proteins studied, our results consistently confirm the presence of a fast- and a slow-diffusing subpopulations of molecules, which both confine to microdomains within the plasma membrane. Although the mobility patterns of H-Ras, mutants of this proteins and its membrane-anchoring domain were remarkably similar, the constitutively active H-Ras mutant, H-RasV12, exhibited significantly higher diffusion rates than the wild-type H-Ras and its inactive mutant, H-RasN17. Ultimately, we characterized variability in our data obtained using the zebrafish embryo model and demonstrated that differences between cells within the same embryo are the largest source of variation in our data. Our findings are in line with a model in which the cellular architecture of individual cells within a tissue determine the mobility of H-Ras proteins anchored in the plasma membrane cytoplasmic leaflet. Thereby, our results underline the growing importance of performing SMM imagingin vivoin order to better understand factors influencing the protein dynamics in an intact living organism.

SUMMARY STATEMENT

By application of single-molecule microscopy to living zebrafish embryos, factors altering thein vivodynamics of H-Ras proteins in epidermal cells were analyzed.
Immunological features that determine the strength of antibody responses to BNT162b2 mRNA vaccine against SARS-CoV-2
Authors: Kageyama Takahiro , Tanaka Shigeru , Etori Keishi , Hattori Koto , Miyachi Kazusa , Kasuya Tadamichi , Iwamoto Taro , Ikeda Kei , Igari Hidetoshi , Yokote Koutaro , Nakajima Hiroshi
Published: June 2021

We analyzed peripheral blood mononuclear cells (PBMCs) of each 20 individuals with a high anti-SARS-CoV-2 antibody titer and a low antibody titer out of 1,774 healthcare workers who received BNT162b2 mRNA vaccine. A higher antibody titer was associated with the frequencies of naïve and transitional B cells before vaccination. In addition, fold changes in the frequency of activated CD8+ T cells upon vaccination were correlated with the antibody titers.
A ligated intestinal loop mouse model protocol to study the interactions of Clostridioides difficile spores with the intestinal mucosa during aging
Authors: Castro-Córdova Pablo , Mendoza-Leon María José , Paredes-Sabja Daniel
Published: June 2021

The interaction of the Clostridioides difficile spores with the intestinal mucosa contribute to the persistence and recurrence of the infection. Advanced age is one of the main risk factors to manifest C. difficile infection and recurrence. However, the interaction of C. difficile spores with the intestinal mucosa during aging has not been evaluated. In the present work, we provide a detailed protocol with all the critical information to perform an intestinal ligated loop. Using this technique in a mouse model, we evaluated C. difficile spore adherence and internalization to the ileum and colonic mucosa during aging. Consequently, our data suggest that spore internalization in the ileum and colonic mucosa is higher in elderly than in adults or young mice. Also, our data suggest that spore-adherence to the ileum and colonic mucosa decreases with aging.
One viral sequence for each host? – The neglected within-host diversity as the main stage of SARS-CoV-2 evolution
Authors: Ruan Yongsen , Hou Mei , Li Jiarui , Song Yangzi , Wang Hurng-YI , He Xionglei , Zeng Hui , Lu Jian , Wen Haijun , Chen Chen , Wu Chung-I
Published: June 2021

The standard practice of presenting one viral sequence for each infected individual implicitly assumes low within-host genetic diversity. It places the emphasis on the viral evolution between, rather than within, hosts. To determine this diversity, we collect SARS-CoV-2 samples from the same patient multiple times. Our own data in conjunction with previous reports show that two viral samples collected from the same individual are often very different due to the substantial within-host diversity. Each sample captures only a small part of the total diversity that is transiently and locally released from infected cells. Hence, the global SARS-CoV-2 population is a meta-population consisting of the viruses in all the infected hosts, each of which harboring a genetically diverse sub-population. Advantageous mutations must be present first as the within-host diversity before they are revealed as between-host polymorphism. The early detection of such diversity in multiple hosts could be an alarm for potentially dangerous mutations. In conclusion, the main forces of viral evolution, i.e., mutation, drift, recombination and selection, all operate within hosts and should be studied accordingly. Several significant implications are discussed.
L-form switching confers antibiotic, phage and stress tolerance in pathogenic Escherichia coli
Authors: Fabijan Aleksandra Petrovic , Kamruzzaman Muhammad , Martinez-Martin David , Venturini Carola , Mickiewicz Katarzyna , Flores-Rodriguez Neftali , Errington Jeff , Iredell Jonathan R.
Published: June 2021

The bacterial L-form is induced by exposure to cell wall targeting antibiotics or innate immune effectors such as lysozyme and is likely to be important in many human infections. Here, we demonstrate that the osmotically fragile L-form is a distinct physiological state in Escherichia coli that is highly tolerant of oxidative stress and resistant to powerful antibiotics and common therapeutic bacteriophages. L-forms quickly revert (<20h) to their cell-walled state after antibiotic withdrawal, with apparently normal physiology and with few or no changes in DNA sequence. T4-like phages that are obligately lytic in cell-walled E. coli preferentially pseudolysogenise their L-forms providing them with transient superinfection immunity. Our data indicate that L-form switching is a common response of pathogenic E. coli strains to cell wall-targeting antibiotics and that the most commonly used lytic bacteriophages are ineffective against them in this state.
Introduction of probiotic bacterial consortia promotes plant growth via impacts on the resident rhizosphere microbiome
Authors: Hu Jie , Yang Tianjie , Friman Ville-Petri , Kowalchuk George A. , Hautier Yann , Li Mei , Wei Zhong , Xu Yangchun , Shen Qirong , Jousset Alexandre
Published: June 2021

Plant growth depends on a range of functions provided by their associated rhizosphere microbiome, including nutrient mineralization, hormone co-regulation and pathogen suppression. Improving the ability of plant associated microbiome to deliver these functions is thus important for developing robust and sustainable crop production. However, it is yet unclear how beneficial effects of probiotic microbial inoculants can be optimised and how they are mediated. Here, we sought to enhance the tomato plant growth by targeted introduction of probiotic bacterial consortia consisting of up to eight plant-associated Pseudomonas strains. We found that the effect of probiotic consortium inoculation was richness-dependent: consortia that contained more Pseudomonas strains, reached higher densities in the tomato rhizosphere and had clearer beneficial effects on multiple plant growth characteristics. Crucially, these effects were best explained by changes in the resident community diversity, composition and increase in the relative abundance of initially rare taxa, instead of introduction of plant-beneficial traits into the existing community along with probiotic consortia. Together, our results suggest that beneficial effects of microbial introductions can be driven indirectly through effects on the diversity and composition of resident plant rhizosphere microbiome.
Visualizing sequential compound fusion and kiss-and-run in live excitable cells
Authors: Ge Lihao , Shin Wonchul , Wu Ling-Gang
Published: June 2021

Vesicle fusion is assumed to occur at flat membrane of excitable cells. In live neuroendocrine cells, we visualized vesicle fusion at Ω-shape membrane generated by preceding fusion, termed sequential compound fusion, which may be followed by fusion pore closure, termed compound kiss-and-run. These novel fusion modes contribute to vesicle docking, multi-vesicular release, asynchronous release, and endocytosis. We suggest modifying current models of exo-endocytosis to include these new fusion modes.
Structural insights into ligand recognition and activation of the melanocortin-4 receptor
Authors: Zhang Huibing , Chen Li-Nan , Yang Dehua , Mao Chunyou , Shen Qingya , Feng Wenbo , Shen Dan-Dan , Dai Antao , Xie Shanshan , Zhou Yan , Qin Jiao , Sun Jinpeng , Scharf Daniel H. , Hou Tingjun , Zhou Tianhua , Wang Ming-Wei , Zhang Yan
Published: June 2021

Melanocortin-4 receptor (MC4R) plays a central role in the regulation of energy homeostasis. Its high sequence similarity to other MC receptor family members, low agonist selectivity and the lack of structural information concerning receptor activation have hampered the development of MC4R-seletive therapeutics to treat obesity. Here, we report four high-resolution structures of full-length MC4R in complex with the heterotrimeric Gs protein stimulated by the endogenous peptide α-MSH, FDA-approved drugs afamelanotide (Scenesse™) and bremelanotide (Vyleesi™), and selective small-molecule ligand THIQ, respectively. Together with pharmacological studies, our results reveal the conserved binding mode of peptidic agonists, the distinctive molecular details of small-molecule agonist recognition underlying receptor subtype selectivity, and distinct activation mechanism for MC4R, thereby offering new insights into G protein coupling. Our work may facilitate the discovery of selective therapeutic agents targeting MC4R.
High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study
Authors: Nagaraj Geetha , Shamanna Varun , Govindan Vandana , Rose Steffimole , Sravani D. , Akshata K. P. , Shincy M.R. , Venkatesha V.T. , Ravikumar K. L. , Abrudan Monica , Argimón Silvia , Kekre Mihir , Underwood Anthony , Aanensen David M
Published: June 2021

summary

We report insights into genome sequences of Indian K. pneumoniae isolates, highlighting the presence of high-risk international clones and genetic pools different from those predominating in other regions. Identification of multidrug-resistant and hypervirulent K. pneumoniae elicits public health concerns.

Background

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a threat to public health in India due to its high dissemination, mortality, and limited treatment options. Its genomic variability is reflected in the diversity of sequence types, virulence factors, and antimicrobial resistance (AMR) mechanisms. This study aims to characterize the clonal relationships and genetic mechanisms of resistance and virulence in CRKP isolates in India.

Materials and Methods

We characterized 344 retrospective K. pneumoniae clinical isolates collected from 8 centers across India collected in 2013-2019. Susceptibility to antibiotics was tested with VITEK 2. Capsular types, MLST, virulence genes, AMR determinants, plasmid replicon types, and a single-nucleotide polymorphism (SNP) phylogeny were inferred from their whole genome sequences.

Results

Phylogenetic analysis of the 325 Klebsiella isolates that passed QC revealed 3 groups: K. pneumoniae sensu stricto (n=307), K. quasipneumoniae (n=17), and K. varicolla (n=1). Sequencing and capsular diversity analysis of the 307 K. pneumoniae sensu stricto isolates revealed 28 sequence types, 26 K-locus types, and 11 O-locus types, with ST231, KL51, and O1V2 being predominant. blaOXA-48-like and blaNDM-1/5 were present in 73.2% and 24.4% of isolates respectively. The major plasmid replicon types associated with carbapenase genes were IncF (51.0%), and Col group (35.0%).

Conclusion

Our study documents for the first time the genetic diversity of K- and O-antigens circulating in India. The results demonstrate the practical applicability of genomic surveillance and its utility in tracking the population dynamics of CRKP. It alerts us to the urgency for longitudinal surveillance of these virulent and transmissible lineages.

Funding

This work was supported by Official Development Assistance (ODA) funding from the National Institute of Health Research [grant number 16_136_111].

This research was commissioned by the National Institute of Health Research using Official Development Assistance (ODA) funding. The views expressed in this publication are those of the authors and not necessarily those of the NHS, the National Institute for Health Research or the Department of Health.

Conflict of Interest

The authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest.
An Empirical Energy Landscape Reveals Mechanism of Proteasome in Polypeptide Translocation
Authors: Fang Rui , Hon Jason , Zhou Mengying , Lu Ying
Published: June 2021

The ring-like ATPase complexes in the AAA+ family perform diverse cellular functions that require coordination between the conformational transitions of their individual ATPase subunits1,2. How the energy from ATP hydrolysis is captured to perform mechanical work by these coordinated movements is not known. In this study, we developed a novel approach for delineating the nucleotide-dependent free-energy landscape (FEL) of the proteasome’s heterohexameric ATPase complex based on complementary structural and kinetic measurements. We used the FEL to simulate the dynamics of the proteasome and quantitatively evaluated the predicted structural and kinetic properties. The FEL model predictions were widely consistent with experimental observations in this and previous studies and suggested novel features of the mechanism of proteasomal ATPase. We find that the cooperative movements of the ATPase subunits result from the design of the ATPase hexamer entailing a unique free-energy minimum for each nucleotide-binding state. ATP hydrolysis dictates the direction of substrate translocation by triggering an energy-dissipating conformational transition of the ATPase complex.
The functional properties of synapses made by regenerated axons across spinal cord lesion sites
Authors: Parker David
Published: June 2021

While the anatomical properties of regenerated axons across spinal cord lesion sites have been studied extensively, little is known of how the functional properties of regenerated synapses compare to those in unlesioned animals. This comparison has been performed here in the lamprey, a model system for spinal injury research, in which functional locomotor recovery after spinal cord lesions is associated with axonal regeneration across the lesion site.

Regenerated synapses below the lesion site did not differ to synapses from unlesioned axons with respect to the amplitude and duration of single excitatory postsynaptic potentials (EPSPs). They also showed the same activity-dependent depression over spike trains. However, regenerated synapses did differ to unlesioned synapses as the estimated number of synaptic vesicles was greater and there was evidence for an increased postsynaptic quantal amplitude. For axons above the lesion site, the amplitude and duration of single synaptic inputs also did not differ significantly to unlesioned animals. However, in this case there was evidence of a reduction in release probability and inputs facilitated rather that depressed over spike trains.

Synaptic inputs from single regenerated axons below the lesion site thus do not increase in amplitude to compensate for the reduced number of descending axons after functional recovery. However, the postsynaptic input is maintained at the unlesioned level using different synaptic properties. Conversely, the facilitation from the same initial amplitude above the lesion site will make the synaptic input over spike trains functionally stronger. This may help to increase propriospinal activity across the lesion site to compensate for the lesion-induced reduction in supraspinal inputs.
Complexity of Genomic Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolates in Colombia Urges the Reinforcement of Whole Genome Sequencing-Based Surveillance Programs
Authors: Saavedra Sandra Yamile , Bernal Johan Fabian , Montilla-Escudero Efraín , Arévalo Stefany Alejandra , Prada Diego Andrés , Valencia María Fernanda , Moreno Jaime Enrique , Hidalgo Andrea Melissa , Abrudan Monica , Argimón Silvia , Kekre Mihir , Underwood Anthony , Aanensen David M , Duarte Carolina , Donado-Godoy Pilar ,   the NIHR Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance
Published: June 2021

Background

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging public health problem. This study explores the specifics of CRKP epidemiology in Colombia based on whole genome sequencing (WGS) of the National Reference Laboratory at Instituto Nacional de Salud (INS)’s 2013-2017 sample collection.

Methods

A total of 425 CRKP isolates from 21 departments were analyzed by HiSeq-X10®Illumina high-throughput sequencing. Bioinformatic analysis was performed, primarily using the pipelines developed collaboratively by the National Institute for Health Research Global Health Research Unit (GHRU) on Genomic Surveillance of AMR, and AGROSAVIA.

Results

Of the 425 CRKP isolates, 91.5% were carbapenemase-producing strains. The data support a recent expansion and the endemicity of CRKP in Colombia with the circulation of 7 high-risk clones, the most frequent being CG258 (48.39% of isolates). We identified genes encoding carbapenemases blaKPC-3, blaKPC-2, blaNDM-1, blaNDM-9, blaVIM-2, blaVIM-4, and blaVIM-24, and various mobile genetic elements (MGE). The virulence of CRKP isolates was low, but colibactin (clb3) was present in 25.2% of isolates, and a hypervirulent CRKP clone (CG380) was reported for the first time in Colombia. ST258, ST512, and ST4851 were characterized by low levels of diversity in the core genome (ANI> 99.9%).

Conclusions

The study outlines complex CRKP epidemiology in Colombia. CG258 expanded clonally and carries specific carbapenemases in specific MGEs, while the other high-risk clones (CG147, CG307, and CG152) present a more diverse complement of carbapenemases. The specifics of the Colombian situation stress the importance of WGS-based surveillance to monitor evolutionary trends of STs, MGE, and resistance and virulence genes.

summary

In Colombia, the dissemination of carbapenemases in carbapenem-resistant Klebsiella pneumoniae is attributed to horizontal gene transfer and successful circulation of CG258, and, to a lesser extent, other clones such as ST307, ST147, and ST152.
EXC-4/CLIC, Gα, and Rho/Rac signaling regulate tubulogenesis in C. elegans
Authors: Arena Anthony F. , Shaye Daniel D.
Published: June 2021

The Rho-family of small GTPases, which play crucial roles in development and disease, are regulated by many signal-transduction cascades, including G-protein-coupled receptor (GPCR)-heterotrimeric G-protein (Gα/β/γ) pathways. Using genetic approaches in C. elegans we identified a new role for Gα and Rho/Rac signaling in cell outgrowth during tubulogenesis and show that the Chloride Intracellular Channel (CLIC) protein EXC-4 is an evolutionarily-conserved player in this pathway. The gene exc-4 was identified by its role in tubulogenesis of the excretory canal (ExCa) cell—a unicellular tube required for osmoregulation and fluid clearance. We identified an exc-4 loss-of-function allele that affects an evolutionarily conserved residue in the C-terminus. Using this mutant we identified genetic interactions between exc-4, Gα, and Rho-family GTPases, defining novel roles for Gα-encoding genes (gpa-12/Gα12/13, gpa-7/Gαi, egl-30/Gαq, gsa-1/Gαs) and the Rho-family members ced-10/Rac and mig-2/RhoG in ExCa outgrowth. EXC-4 and human CLICs have conserved functions in tubulogenesis, and CLICs and Gα-Rho/Rac signaling regulate tubulogenesis during blood vessel development. Therefore, our work defines a primordial role for EXC-4/CLICs in Gα-Rho/Rac-signaling during tubulogenesis.

One Sentence Summary

Gα and Rho/Rac signaling regulates EXC-4/CLIC-mediated cell outgrowth during tubulogenesis in C. elegans, linking elements of G-protein signaling to the enigmatic CLIC family of proteins.
Transcriptomic Analysis of the Innate Immune Response toin vitroTransfection of Plasmid DNA
Authors: Warga Eric , Tucker Matthew , Harris Emily , Elmer Jacob
Published: June 2021

The innate immune response to cytosolic DNA is intended to protect the host from viral infections, but it can also inhibit the delivery and expression of therapeutic transgenes in gene and cell therapies. The goal of this work was to use mRNA-sequencing to reveal correlations between the transfection efficiencies of four cell types (PC-3, Jurkat, HEK-293T, and primary CD3+T cells) and their innate immune responses to nonviral gene delivery. Overall, the highest transfection efficiency was observed in HEK-293T cells (87%), which upregulated only 142 genes with no known anti-viral functions. Lipofection upregulated a much larger number (n = 1,057) of cytokine-stimulated genes (CSGs) in PC-3 cells, which also exhibited a significantly lower transfection efficiency. However, the addition of serum during Lipofection and electroporation significantly increased transfection efficiencies and decreased the number of upregulated genes in PC-3 cells. Finally, while Lipofection of Jurkat and Primary T cells only upregulated a few genes, several anti-viral CSGs that were absent in HEK and upregulated in PC-3 cells were observed to be constitutively expressed in T cells, which may explain their relatively low Lipofection efficiencies (8-21%). Indeed, overexpression of one such CSG (IFI16) significantly decreased transfection efficiency in HEK cells to 33%.
Nucleotide Dynamics During Flossing of Polycation-DNA-Polycation through a Nanopore using Molecular Dynamics
Authors: Mahalik Jyoti P. , Muthukumar Murugappan
Published: June 2021

The full potential of solid state nanopores is yet to be realized for genome sequencing. Due to its robustness it can handle strong voltage amplitude and frequency. The effect of strong alternating voltage on the dynamics of nucleotides during translocation has been explored. We proposed a setup consisting of single stranded DNA covalently linked with symmetric polycations at both ends fashioned after the proposal of Kasianowicz. 1 Such a setup allows for repeated back and forth motion of the DNA along the nanopore (1.45 nm diameter and 1.53 nm thick) by simply switching the voltage polarity if the polycation tail is sufficiently long (≥ 10) and the applied voltage is below 0.72 volts, but the average residence time of the nucleotides are too small to be of any practical use (6-30 ns). When alternating voltage of higher frequency is applied, it enhances the average residence time of the nucleotides by an order of magnitude to ∼ 0.1 µs relative to direct voltage but the individual trajectories are too stochastic. Since, we are able to collect repeated read on the dynamics of individual nucleotides, we obtained the most probable time of appearance of a nucleotide within the nanopore. With such construct we were able to get almost linear dependence of most probable time versus nucleotide index, after gaussian fitting.
Allosteric activation of CwlD amidase activity by the GerS lipoprotein during Clostridioides difficile spore formation
Authors: Feliciano Carolina Alves , Eckenroth Brian E. , Diaz Oscar R. , Doublié Sylvie , Shen Aimee
Published: June 2021

Spore-forming pathogens like Clostridioides difficile depend on germination to initiate infection. Spore germination depends on the degradation of the protective spore peptidoglycan layer known as the spore cortex. Cortex degradation is mediated by enzymes that recognize the spore-specific peptidoglycan modification, muramic-∂-lactam (MAL). In C. difficile, MAL synthesis depends on the activity of the CwlD amidase and the GerS lipoprotein, which directly binds CwlD. To gain insight into how GerS regulates CwlD activity, we solved the crystal structure of the CwlD:GerS complex. In this structure, a GerS homodimer is bound to two CwlD monomers such that the CwlD active sites are exposed. Although CwlD structurally resembles amidase_3 family members, we found that CwlD does not bind zinc stably on its own, unlike previously characterized amidase_3 enzymes. Instead, GerS binding to CwlD promotes CwlD binding to zinc, which is required for its catalytic mechanism. Thus, in determining the first structure of an amidase bound to its regulator, we reveal stabilization of zinc co-factor binding as a novel mechanism for regulating bacterial amidase activity. Our results further suggest that allosteric regulation by binding partners may be a more widespread mode for regulating bacterial amidase activity than previously thought.
TedSim: temporal dynamics simulation of single cell RNA-sequencing data and cell division history
Authors: Pan Xinhai , Li Hechen , Zhang Xiuwei
Published: June 2021

Recently, the combined scRNA-seq and CRISPR/Cas9 genome editing technologies have enabled simultaneous readouts of gene expressions and lineage barcodes, which allows for the reconstruction of the cell division tree, and makes it possible to trace the origin of each cell type. Computational methods are emerging to take advantage of the jointly profiled scRNA-seq and lineage barcode data to better reconstruct the cell division history or to infer the cell state trajectories.

Here, we present TedSim (single cell Temporal dynamics Simulator), a simulator that simulates the cell division events from the root cell to present-day cells, simultaneously generating the lineage barcodes and scRNA-seq data. In particular, TedSim generates cells from multiple cell types through cell division events. TedSim can be used to benchmark and investigate computational methods which use either or both of the two types of data, scRNA-seq and lineage barcodes, to study cell lineages, ancestral cells or cell trajectories. TedSim is available at: https://github.com/Galaxeee/TedSim.
Deamidation of the human eye lens protein γS-crystallin accelerates oxidative aging
Authors: Norton-Baker Brenna , Mehrabi Pedram , Kwok Ashley O. , Roskamp Kyle W. , Sprague-Piercy Marc A. , Stetten David von , Miller R.J. Dwayne , Martin Rachel W.
Published: June 2021

Cataract disease, a clouding of the eye lens due to precipitation of lens proteins, affects millions of people every year worldwide. The proteins that comprise the lens, the crystallins, show extensive post-translational modifications (PTMs) in aged and cataractous lenses, most commonly deamidation and oxidation. Although surface-exposed glutamines and asparagines show the highest rates of deamidation, multiple modifications can accumulate over time in these long-lived proteins, even for buried residues. Both deamidation and oxidation have been shown to promote crystallin aggregation in vitro; however, it is not clear precisely how these modified crystallins contribute to insolubilization. Here, we report six novel crystal structures of a major human lens protein, γS-crystallin (γS): one of the wild-type in a monomeric state, and five of deamidated γS variants, ranging from three to nine deamidation sites, after varying degrees of sample aging. Consistent with previous work that focused on single-to triple-site deamidation, the deamidation mutations do not appear to drastically change the fold of γS; however, increasing deamidation leads to accelerated oxidation and disulfide bond formation. Successive addition of deamidated sites progressively destabilized protein structure as evaluated by differential scanning fluorimetry. Light scattering showed the deamidated variants display an increased propensity for aggregation compared to the wild-type protein. The results suggest the deamidated variants are useful as models for accelerated aging; the structural changes observed over time provide support for redox activity of γS-crystallin in the human lens.

Highlights

Novel structures of cataract-associated variants of human eye lens protein γS-crystallin reported

Increasing deamidation of γS-crystallin decreases stability and affects aggregation propensity

Overall fold of γS-crystallin maintained among deamidated and disulfide-bonded variants

Deamidated γS variants form disulfide bonds more rapidly than wild-type γS

Potential functional advantage of disulfide bonding in the CXCXC motif proposed
Stochastic Resonance Behavior of DNA Translocation with an Oscillatory Electric Field
Authors: Jou Ining A. , Duff Rhys A. , Muthukumar Murugappan
Published: June 2021

Stochastic resonance (SR) describes the synchronization between noise of a system and an applied oscillating field to achieve an optimized response signal. In this work, we use simulations to investigate the phenomenon of SR of a single stranded DNA driven through a nanopore when an oscillating electric field is added. The system is comprised of a MspA protein nanopore embedded in a membrane and different lengths of DNA is driven from one end of the pore to the other via a constant potential difference. We superimposed an oscillating electric field on top of the existing electric field. The source of noise is due to thermal fluctuations, since the system is immersed in solution at room temperature. Here, the signal optimization we seek is the increase in translocation time of DNA through the protein nanopore. Normally, translocation time scales linearly with DNA length and inversely with driving force in a drift dominated regime. We found a non-monotonic dependence of the mean translocation time with the frequency of the oscillating field. This non-monotonic behavior of the translocation time is observed for all lengths of DNA, but SR occurs only for longer DNA. Furthermore, we also see evidence of DNA extension being influenced by the oscillating field while moving through the nanopore.
Role of collagen-like protein BclA3 in the assembly of the exosporium layer of Clostridioides difficile spores
Authors: Pizarro-Guajardo Marjorie , Ortega-Lizárraga César , Cid-Rojas Francisca , Inostroza Ana , Paredes-Sabja Daniel
Published: June 2021

Newly formed spores are essential for persistence of C. difficile in the host, transmission to a new susceptible host (Deakin et al., 2012b) and recurrence of CDI. BclA3 and BclA2 Spore surface proteins are expressed during sporulation under the control of mother-cell specific sigma factors of the RNA polymerase, SigE and SigK. Deletion of bclA3 leads to spores with an electron-dense exosporium layer that lacks bump-like structures in the electron-dense layer and hair-like projections, both structures typically found in the wild type spore. Therefore, in this work, we have addressed the role of the exosporium collagen-like BclA3 glycoprotein in the assembly of the exosporium layer. Immunogold labelling of BclA2CTD and BclA3CTD indicates that both proteins are located in the hairs, with BclA2 located outermost of BclA3. Absence of BclA3 leads to spores with no hair-like projections, and absence of bumps in thick exosporium spores, a phenotype also expressed in by the deletion of the collagen-like region of BclA3. Overall, these results provide insights into the role of BclA3 in the assembly of the exosporium layer of C. difficile spores.
Unfolding of RNA via Translocation Through a Nanopore
Authors: Chalise Sadhana , Muthukumar Murugappan
Published: June 2021

RNA unfolding and refolding are important biological phenomena, which occur during the transfer of genetic information from DNA to RNA to proteins. During these processes, RNA is found in single stranded, secondary and tertiary structures, including secondary conformations like hairpins and pseudoknots. Understanding the diverse conformations of RNA and how these influence the dynamics of unfolding and refolding is crucial to gain insight to fundamental biological processes. In this work, we employ coarse-grained Langevin dynamics simulations of a simple model of different RNA hairpins passing through a geometric nanopore to find the influence of structural changes on the translocation dynamics. The threshold voltage of unfolding depends on the length of the hairpin attached to the tail. The lag time to unfold is longer for smaller applied voltages and for the architectures containing a longer hairpin attached to the tail. Chain translocation dynamics for different architectures are largely collapsed by the threshold. A distinct signature for the base unfolding time was observed for the bases around the unpaired bases in all the RNA hairpin models. These results can motivate future technologies or experiments that use translocation to predict secondary structures of polynucleotides.
Online Reference Trajectory Adaptation: A Personalized Control Strategy for Lower Limb Exoskeletons
Authors: Shushtari Mohammad , Nasiri Rezvan , Arami Arash
Published: June 2021

This paper presents a novel method for reference trajectory adaptation in lower limb rehabilitation exoskeletons during walking. Our adaptation rule is extracted from a cost function that penalizes both interaction force and trajectory modification. By adding trajectory modification term into the cost function, we restrict the boundaries of the reference trajectory adaptation according to the patient’s motor capacity. The performance of the proposed adaptation method is studied analytically in terms of convergence and optimality. We also developed a realistic dynamic walking simulator and utilized it in performance analysis of the presented method. The proposed trajectory adaptation technique guarantees convergence to a stable, reliable, and rhythmic reference trajectory with no prior knowledge about the human intended motion. Our simulations demonstrate the convergence of exoskeleton trajectories to those of simulated healthy subjects while the exoskeleton trajectories adapt less to the trajectories of patients with reduced motor capacity (less reliable trajectories). Furthermore, the gait stability and spatiotemporal parameters such as step time symmetry and minimum toe off clearance enhanced by the adaptation in all subjects. The presented mathematical analysis and simulation results show the applicability and effectiveness of the proposed method and its potential to be applied for trajectory adaptation in lower limb rehabilitation exoskeletons.
Power spectrum slope confounds estimation of instantaneous oscillatory frequency
Authors: Samaha Jason , Cohen Michael X
Published: June 2021

Oscillatory neural dynamics are highly non-stationary and require methods capable of quantifying time-resolved changes in rhythmic activity in order to understand neural function. Recently, a method termed ‘frequency sliding’ was introduced to estimate the instantaneous frequency of oscillatory activity, providing a means of tracking temporal changes in the dominant frequency within a sub-band of field potential recordings. Here, the ability of frequency sliding to recover ground-truth oscillatory frequency in simulated data is tested while the exponent (slope) of the 1/fxcomponent of the signal power spectrum is systematically varied, mimicking real electrophysiological data. The results show that 1) in the presence of 1/factivity, frequency sliding systematically underestimates the true frequency of the signal, 2) the magnitude of underestimation is correlated with the steepness of the slope, suggesting that, if unaccounted for, slope changes could be misinterpreted as frequency changes, 3) the impact of slope on frequency estimates interacts with oscillation amplitude, indicating that changes in oscillation amplitude alone may also influence instantaneous frequency estimates in the presence of strong 1/factivity; and 4) analysis parameters such as filter bandwidth and location also mediate the influence of slope on estimated frequency, indicating that these settings should be considered when interpreting estimates obtained via frequency sliding. The origin of these biases resides in the output of the filtering step of frequency sliding, whose energy is biased towards lower frequencies precisely because of the 1/fstructure of the data. We discuss several strategies to mitigate these biases and provide a proof-of-principle for a 1/f normalization strategy.
Targeting riboswitches with synthetic small RNAs for metabolic engineering
Authors: da Costa Ribeiro Lins Milca Rachel , da Silva Amorim Laura Araujo , Correa Graciely Gomes , Picão Bruno Willian , Mack Matthias , Cerri Marcel Otávio , Pedrolli Danielle Biscaro
Published: June 2021

Our growing knowledge of the diversity of non-coding RNAs in natural systems and our deepening knowledge of RNA folding and function have fomented the rational design of RNA regulators. Based on that knowledge, we designed and implemented a small RNA (sRNA) tool to target bacterial riboswitches and activate gene expression. The synthetic sRNA is suitable for regulation of gene expression both in cell-free and in cellular systems. It targets riboswitches to promote the antitermination folding regardless the cognate metabolite concentration. Therefore, it prevents transcription termination increasing gene expression up to 103-fold. We successfully used sRNA arrays for multiplex targeting of riboswitches. Finally, we used the synthetic sRNA to engineer an improved riboflavin producer strain. The easiness to design and construct, and the fact that the riboswitch-targeting sRNA works as a single genome copy, make it an attractive tool for engineering industrial metabolite-producing strains.

Graphical Abstract
Genomics analysis ofDrosophila sechelliaresponse toMorinda citrifoliafruit diet
Authors: Drum Z.A. , Lanno S.M. , Gregory S.M. , Shimshak  , Barr W. , Gatesman A. , Schadt M. , Sanford J. , Arkin A. , Assignon B. , Colorado S. , Dalgarno C. , Devanny T. , Ghandour T. , Griffin R. , Hogan M. , Horowitz E. , McGhie E. , Multer J. , O’Halloran H. , Ofori-Darko K. , Pokushalov D. , Richards N. , Sagarin K. , Taylor N. , Thielking A. , Towle P. , Coolon J. D.
Published: June 2021

Drosophila sechelliais an island endemic host specialist that has evolved to consume the toxic fruit ofMorinda citrifolia, also known as noni fruit. Recent studies by our group and others have examined genome-wide gene expression responses of fruit flies to individual highly abundant compounds found in noni responsible for the fruit’s unique chemistry and toxicity. In order to relate these reductionist experiments to the gene expression responses to feeding on noni fruit itself, we fed rotten noni fruit to adult femaleD. sechelliaand performed RNA-sequencing. Combining the reductionist and more wholistic approaches, we have identified candidate genes that may contribute to each individual compound and those that play a more general role in response to the fruit as a whole. Using the compound specific and general responses, we used transcription factor prediction analyses to identify the regulatory networks and specific regulators involved in the responses to each compound and the fruit itself. The identified genes and regulators represent the possible genetic mechanisms and biochemical pathways that contribute to toxin resistance and noni specialization inD. sechellia.
Essential role for Ggct in erythrocyte antioxidant defense
Authors: He Zaoke , Sun Xiaoqin , Wang Shixiang , Bai Dongsheng , Zhao Xiangyu , Han Ying , Hao Piliang , Liu Xue-Song
Published: June 2021

GGCT encodes γ-glutamyl cyclotransferase enzyme activity, and its expression is up-regulated in various human cancers. γ-glutamyl cyclotransferase enzyme activity was originally purified from human red blood cells (RBCs), however physiological function of GGCT in RBCs is still not clear. Here we reported that Ggct deletion in mouse leads to splenomegaly and progressive anemia phenotypes, due to elevated oxidative damage and shortened life span of Ggct−/− RBCs. Ggct−/− RBCs have increased reactive oxygen species (ROS), and are more sensitive to H2O2 induced damage compared to control RBCs. Glutathione (GSH) and GSH synthesis precursor L-cysteine are decreased in Ggct−/− RBCs. Our study suggests a critical function of Ggct in RBC redox balance and life span maintenance through regulating GSH metabolism.
GABAA and NMDA receptor density alterations and their behavioral correlates in the gestational methylazoxymethanol acetate model for schizophrenia
Authors: Kiemes Amanda , Gomes Felipe V. , Cash Diana , Uliana Daniela L. , Simmons Camilla , Singh Nisha , Vernon Anthony C. , Turkheimer Federico , Davies Cathy , Stone James M. , Grace Anthony A. , Modinos Gemma
Published: June 2021

Hippocampal hyperactivity driven by GABAergic interneuron deficits and NMDA receptor hypofunction is associated with the hyperdopaminergic state often observed in schizophrenia. Furthermore, previous research in the methylazoxymethanol acetate (MAM) rat model has demonstrated that repeated peripubertal diazepam administration can prevent the emergence of adult hippocampal hyperactivity, dopamine system hyperactivity, and associated psychosis-relevant behaviors. Here, we sought to characterize hippocampal GABAA and NMDA receptors in MAM-treated rats and to elucidate the receptor mechanisms underlying the promising effects of peripubertal diazepam exposure. Quantitative receptor autoradiography was used to measure receptor density in dorsal hippocampus CA1, ventral hippocampus CA1, and in ventral subiculum. Specifically, [3H]-Ro15-4513 was used to quantify the density of α5 GABAA receptors (α5GABAAR), [3H]-flumazenil to quantify α1-3;5GABAAR, and [3H]-MK801 to quantify NMDA receptors. MAM rats exhibited anxiety and schizophrenia-relevant behaviors as measured by elevated plus maze and amphetamine-induced hyperlocomotion (AIH), although diazepam only partially rescued these behaviors. α5GABAAR density was reduced in MAM-treated rats in all hippocampal sub-regions, and negatively correlated with AIH. Ventral hippocampus CA1 α5GABAAR density was positively correlated with anxiety-like behavior. Dorsal hippocampus CA1 NMDA receptor density was increased in MAM-treated rats, and positively correlated with AIH. [3H]-Flumazenil revealed no significant effects. Finally, we found no significant effect of diazepam treatment on receptor densities, potentially related to the only partial rescue of schizophrenia-relevant phenotypes. Overall, our findings provide first evidence of α5GABAAR and NMDA receptor abnormalities in the MAM model, suggesting that more selective pharmacological agents may become a novel therapeutic mechanism in schizophrenia.
Kinetic pathways of water exchange in the first hydration shell of magnesium: Influence of water model and ionic force field
Authors: Falkner Sebastian , Schwierz Nadine
Published: June 2021

Water exchange between the first and second hydration shell is essential for the role of Mg2+ in biochemical processes. In order to provide microscopic insights into the exchange mechanism, we resolve the exchange pathways by all-atom molecular dynamics simulations and transition path sampling. Since the exchange kinetics relies on the choice of the water model and the ionic force field, we systematically investigate the influence of seven different polarizable and non-polarizable water and three different Mg2+ models. In all cases, water exchange can occur either via an indirect or direct mechanism (exchanging molecules occupy different/same position on water octahedron). In addition, the results reveal a crossover from an interchange dissociative (Id) to an associative (Ia) reaction mechanism dependent on the range of the Mg2+-water interaction potential of the respective force field. Standard non-polarizable force fields follow the Id mechanism in agreement with experimental results. By contrast, polarizable and long-ranged non-polarizable force fields follow the Ia mechanism. Our results provide a comprehensive view on the influence of the water model and ionic force field on the exchange dynamics and the foundation to assess the choice of the force field in biomolecular simulations.