bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved peridynamic model and its application to crack propagation in rocks
Authors: Zhou Luming , Zhu Shu , Zhu Zhende , Yu Shuang , Xie Xinghua
Published: October 2022

The conventional bond-based peridynamics (BB-PD) model is suitable for simulating the failure mode of homogeneous elastic-brittle materials. However, the strain hardening and subsequent strain softening characteristics of rocks under loading cannot be reflected. In addition, the fracture mechanisms of rock materials under tension and compression are completely different. To solve these problems, this paper proposes an improved BB-PD model using different fracture criteria in the tensile and compression stages of the bond based on previous improved models, and a critical failure condition obeying the Weibull distribution is introduced to reflect the heterogeneity of the rock. The crack propagation processes of an intact rock specimen, rock specimen with a single pre-existing flaw and rock specimens with two and three pre-existing flaws under compressive loading are simulated using the model, and its feasibility is verified by comparing with the results of previous laboratory tests. Next, the effects of the inclination angle and length on the wing crack propagation length are studied. Finally, the changes in the crack aggregation modes under different rock bridge inclination angles are simulated. Eight types of crack aggregation modes are found, and the conditions under which they may occur are analysed. The improved model proposed can effectively simulate the crack propagation and coalescing processes and has a wide application prospect for rock fracture simulations.
Ranking with multiple types of pairwise comparisons
Authors: Newman Mark E. J.
Published: October 2022

The task of ranking individuals or teams, based on a set of comparisons between pairs, arises in various contexts, including sporting competitions and the analysis of dominance hierarchies among animals and humans. Given data on which competitors beat which others, the challenge is to rank the competitors from best to worst. Here we study the problem of computing rankings when there are multiple, potentially conflicting types of comparison, such as multiple types of dominance behaviours among animals. We assume that we do not knowa prioriwhat information each behaviour conveys about the ranking, or even whether they convey any information at all. Nonetheless, we show that it is possible to compute a ranking in this situation and present a fast method for doing so, based on a combination of an expectation–maximization algorithm and a modified Bradley–Terry model. We give a selection of example applications to both animal and human competition.
Genome-wide selection signatures reveal widespread synergistic effects of two different stressors in
Drosophila melanogaster
Authors: Burny Claire , Nolte Viola , Dolezal Marlies , Schlötterer Christian
Published: October 2022

Experimental evolution combined with whole-genome sequencing (evolve and resequence (E&R)) is a powerful approach to study the adaptive architecture of selected traits. Nevertheless, so far the focus has been on the selective response triggered by a single stressor. Building on the highly parallel selection response of founder populations with reduced variation, we evaluated how the presence of a second stressor affects the genomic selection response. After 20 generations of adaptation to laboratory conditions at either 18°C or 29°C, strong genome-wide selection signatures were observed. Only 38% of the selection signatures can be attributed to laboratory adaptation (no difference between temperature regimes). The remaining selection responses are either caused by temperature-specific effects, or reflect the joint effects of temperature and laboratory adaptation (same direction, but the magnitude differs between temperatures). The allele frequency changes resulting from the combined effects of temperature and laboratory adaptation were more extreme in the hot environment for 83% of the affected genomic regions—indicating widespread synergistic effects of the two stressors. We conclude that E&R with reduced genetic variation is a powerful approach to study genome-wide fitness consequences driven by the combined effects of multiple environmental factors.
Older Women with lower lean mass values have hypermethylated sites in the PI3K-Akt pathway
Authors: Correia Igor Massari , da Silva Rodrigues Guilherme , Noronha Natália Yumi , de Almeida Mariana Luciano , da Silva Sobrinho Andressa Crystine , Nonino Carla Barbosa , Júnior Carlos Roberto Bueno
Published: October 2022

The increase in lean mass is directly related to the loss of independence, muscle strength, and worse quality of life over the years. Studies in epigenetics can provide accurate answers about lean mass, demonstrating changes in DNA methylation patterns and possible changes in gene expression. The objective of this study was to verify whether there is a difference in the methylation profile among Brazilian women aged 50 to 70 years with greater or lesser lean mass. A cross-sectional study comprised 22 women aged 50 to 70 years, with 2 groups of 11 participants (Low Lean Mass and More Lean Mass). Lean mass was measured by dualenergy X-ray emission densitometry (DEXA). Blood DNA was collected for methylation assays using the Illumina 850k EPIC Infinium Methylation BeadChip, analyzing data from the Bioconductor chAMP data package medium in RStudio software. We obtained 1,913 differentially methylated (p ≤ 0.005 of delta β > 5% and delta β < −5 %) with a total of 979 genes with different methylation sites between groups (p ≤ 0.005; −5% > delta β > 5%). In addition, the pathway with the greatest power of significance was PI3K-Akt, presenting an FDR of 4.6 x 10-3. Thus, our results demonstrate a differentiation between specific sites of different genes, which have essential functions in body composition and energy metabolism, supporting future studies that aim to relate lean mass with epigenetics.
Natural Variation inBrachypodium distachyonResponses to Combined Abiotic Stresses
Authors: Ludwig Ella , Polydore Seth , Berry Jeffrey , Sumner Joshua , Ficor Tracy , Agnew Erica , Haines Kristina , Greenham Kathleen , Fahlgren Noah , Mockler Todd C. , Gehan Malia A.
Published: October 2022

The growing world population increases demand for agricultural production, which is more challenging as climate change increases global temperature and causes more extreme weather events. High-throughput phenotyping tools can be used to measure plant responses to the environment to identify genomic regions associated with response to stress. This study examines the phenotypic variation of 149 accessions ofBrachypodium distachyonunder drought, heat, and the combination of both stresses. Heat alone causes the largest amounts of tissue damage and the combination of heat and drought causes the largest decrease in plant biomass compared to other treatments. Notably, Bd21-0, the reference line forB. distachyon, was identified as not having very robust growth under stress conditions, especially in the heat-drought combined treatment. Climate data from the collection locations of these accessions (climate of origin) was used to assess whether climate of origin was correlated with responses to stresses and it was found to be significantly associated with height and percent of plant tissue damage. Additionally, genome wide association mapping found a number of genetic loci associated with changes in plant height, biomass, and the amount of damaged tissue under stress. Some SNPs found to be significantly associated with a response to heat or drought are also significantly associated in the combination of stresses, while others are not, and some significantly associated SNPs were only identified in the combined stress treatment. This, combined with the phenotypic data, indicates that the effects of these abiotic stresses are not simply additive, and the responses ofB. distachyonto the combined stresses differ from drought and heat alone. Significant SNPs were closely located to genes known to be involved in plant responses to abiotic stresses.
Targeting the BAG-1 family of co-chaperones in lethal prostate cancer
Authors: Neeb Antje , Figueiredo Ines , Bogdan Denisa , Cato Laura , Stober Jutta , Jimenez-Vacas Juan M. , Gourain Victor , Lee Irene I. , Seeger Rebecca , Muhle-Goll Claudia , Gurel Bora , Welti Jonathan , Rodrigues Daniel Nava , Rekowski Jan , Qiu Xintao , Jiang Yija , Di Micco Patrizio , Mateos Borja , Bielskutė Stasė , Riisnaes Ruth , Ferreira Ana , Miranda Susana , Crespo Mateus , Buroni Lorenzo , Ning Jian , Bräse Stefan , Jung Nicole , Gräßle Simone , Metzger Daniel , Swain Amanda , Salvatella Xavier , Plymate Stephen R. , Al-Lazikani Bissan , Long Henry , Yuan Wei , Brown Myles , Cato Andrew C. B. , de Bono Johann S. , Sharp Adam
Published: October 2022

Therapies that abrogate persistent androgen receptor (AR) signaling in castration resistant prostate cancer (CRPC) remain an unmet clinical need. The N-terminal domain (NTD) of the AR drives transcriptional activity in CRPC but is intrinsically disordered and remains a challenging therapeutic target. Therefore, inhibiting critical co-chaperones, such as BAG-1L, is an attractive alternative strategy. We performed druggability analyses demonstrating the BAG domain to be a challenging drug target. Thio-2, a tool compound, has been reported to bind the BAG domain of BAG-1L and inhibit BAG-1L-mediated AR transactivation. However, despite these data, the mechanism of action of Thio-2 is poorly understood and the BAG domain which is present in all BAG-1 isoforms has not been validated as a therapeutic target. Herein, we demonstrate growth inhibiting activity of Thio-2 in CRPC cell lines and patient derived models with decreased AR genomic binding and AR signaling independent of BAG-1 isoform function. Furthermore, genomic abrogation of BAG-1 isoforms did not recapitulate the described Thio-2 phenotype, and NMR studies suggest that Thio-2 may bind the AR NTD, uncovering a potential alternative mechanism of action, although in the context of low compound solubility. Furthermore, BAG-1 isoform knockout mice are viable and fertile, in contrast to previous studies, and when crossed with prostate cancer mouse models, BAG-1 deletion does not significantly impact prostate cancer development and growth. Overall, these data demonstrate that Thio-2 inhibits AR signaling and growth in CRPC independent of BAG-1 isoforms, and unlike previous studies of the activated AR, therapeutic targeting of the BAG domain requires further validation before being considered a therapeutic strategy for the treatment of CRPC.
PSC niche develops into immune-responsive blood cells capable of transdifferentiating into lamellocytes inDrosophila
Authors: Hirschhäuser Alexander , Molitor Darius , Salinas Gabriela , Großhans Jörg , Rust Katja , Bogdan Sven
Published: October 2022

Drosophilablood cells called hemocytes form an efficient barrier against infections and tissue damage. During metamorphosis, hemocytes undergo tremendous changes in their shape and behavior preparing them for tissue clearance. Yet, the diversity and functional plasticity of pupal blood cells have not been explored. Here, we combine single-cell transcriptomics and high-resolution microscopy to dissect the heterogeneity and plasticity of pupal hemocytes. We identified precursor and effector hemocytes with distinct molecular signatures and cellular functions clearly distinct from other stages of hematopoiesis. Strikingly, we identified that PSC cells, which function as lymph gland niche, are highly migratory and immune responsive cells in the pupa. PSC cells can transdifferentiate to lamellocytes triggered by wasp infection. Altogether, our data highlight a remarkable cell heterogeneity, and identifies a cell population that acts not only as a stem cell niche in larval hematopoiesis, but functions as cell reservoir to pupal and adult blood cells.
AVaccinia-based system for directed evolution of GPCRs in mammalian cells
Authors: Klenk Christoph , Scrivens Maria , Niederer Anina , Shi Shuying , Mueller Loretta , Gersz Elaine , Zauderer Maurice , Smith Ernest , Strohner Ralf , Plückthun Andreas
Published: October 2022

Low stability and poor expression levels are inherent in many G protein-coupled receptors, hindering structural and biophysical analyses. Directed evolution in bacterial or yeast display systems has been successfully used to overcome both limitations in some cases. Yet, some receptors cannot be tackled in microbial systems, due to their complex molecular composition or due to unfavorable ligand properties. Here, we report an approach to evolve G protein-coupled receptors in mammalian cells. To achieve clonality of individual mutants, and a rather uniform gene copy number, both prerequisites for strict genotype-phenotype linkage in mammalian cells, we developed a highly efficient viral transduction system based onVacciniavirus. Using rational design of synthetic DNA libraries, we first evolved neurotensin receptor 1 for high stability and expression, reaching levels similar or higher to what has been achieved in bacterial systems. Second, using parathyroid hormone 1 receptor we demonstrate that also receptors with complex molecular architectures and large ligands can be readily evolved in mammalian cells. Furthermore, in our system, the physiological signaling environment in mammalian cells can be employed to evolve functional receptor properties. We obtained fully functional receptor variants exhibiting increased allosteric coupling between the ligand binding site and the G protein interface, resulting in higher signaling efficacy. Thus, our approach provides new means to readily improve the biophysical properties of receptors in a mammalian cellular environment. Moreover, it opens the possibility to modulate receptor signaling and to gain further insights into the intricate molecular interplay required for GPCR activation.
Borrelia burgdorferiDnaA and the nucleoid-associated protein EbfC coordinate expression of thednaX-ebfCoperon
Authors: Krusenstjerna Andrew C. , Arnold William K. , Saylor Timothy C. , Tucker Jamila S. , Stevenson Brian
Published: October 2022

Borrelia burgdorferi, the spirochete agent of Lyme disease, has evolved within a consistent infectious cycle between tick and vertebrate hosts. The transmission of the pathogen from tick to vertebrate is characterized by rapid replication and a change in the outer surface protein profile. EbfC, a highly conserved nucleoid-associated protein, binds throughout the borrelial genome affecting expression of many genes, including the Erp outer surface proteins. InB. burgdorferi, like many other bacterial species,ebfCis co-transcribed withdnaX, an essential component of the DNA polymerase III holoenzyme, which facilitates chromosomal replication. The expression of thednaX-ebfCoperon is tied to the spirochete’s replication rate, but the underlying mechanism for this connection was unknown. In this work, we provide evidence that the expression ofdnaX-ebfCis controlled by direct interactions of DnaA, the chromosomal replication initiator, and EbfC at the unusually longdnaX-ebfC5’ UTR region. Both proteins bind to the 5’ UTR DNA, with EbfC also binding to the RNA. The DNA binding of DnaA to this region was similarly impacted by ATP/ADP.In vitrostudies characterized DnaA as an activator ofdnaX-ebfCand EbfC as an anti-activator. We further found evidence that DnaA may regulate other genes essential for replication.

IMPORTANCE

The dual-life cycle ofBorrelia burgdorferi, the causative agent of Lyme disease, is characterized by periods of rapid and slowed replication. The expression patterns of many of the spirochete’s virulence factors are impacted by these changes in replication rates. The connection between replication and virulence can be understood at thednaX-ebfCoperon. DnaX is a component of the DNA polymerase III holoenzyme that facilitates replication. EbfC is a nucleoid-associated protein that regulates the infection-associated outer surface Erp proteins, as well as other transcripts. The expression ofdnaX-ebfCis tied to replication rate, which we demonstrate is mediated by DnaA, the master chromosomal initiator protein and transcription factor, and EbfC.
Genomic characterization and molecular evolution of human Monkeypox viruses
Authors: Gröhs Ferrareze Patrícia Aline , Alves Pereira e Costa Rute , Thompson Claudia Elizabeth
Published: October 2022

Monkeypox virus is a member of the Poxviridae family, as variola and vaccinia viruses, presenting a linear double-strand DNA genome approximately ≈197 kb long, which encodes ≈190 non overlapping ORFs. Genomic comparison of Central and West African clades shows the presence of unique genes that promote different disease presentations according to the strain. Since the last smallpox vaccination efforts ended in the mid-1980s, nowadays, there is concern about the recent spread of human monkeypox disease around the world. Currently, almost 70,000 human monkeypox cases are diagnosed in the world, of which more than 7,800 are from Brazil. This study aims to evaluate genomic epidemiology and molecular evolution of hMpxV genomes. Using computational biology to analyze 604 hMpxV genomes from 1960 up to 2022, it was possible to observe synteny breaks and gene conservation between Central and West clade genomes, with the presence of strains associated with the 2022 outbreak assigned to West African clade. Evidence of diversifying selective pressure on specific sites from protein coding sequences acting on immunomodulatory processes was identified. The existence of different sites under diversifying - and purifying - selection in paralog genes denotes adaptation mechanisms underlying the host-pathogen interaction of Monkeypox virus in human species.

HIGHLIGHTS

Synteny breaks were identified among West and Central African genomes with sequence identity of 96.5%

Positive selection evidence was found on sites from genes of immunomodulatory functions

Different sites under diversifying and purifying selection were observed in paralog genes

Genomes from the 2022 outbreak are phylogenetically assigned to the West African clade
The faculty-to-faculty mentorship experience: a survey on challenges and recommendations for improvements
Authors: Sarabipour Sarvenaz , Niemi Natalie M , Burgess Steven J , Smith Christopher T , Bisson Filho Alexandre W , Ibrahim Ahmed , Clark Kelly
Published: October 2022

Faculty at research institutions play a central role in advancing knowledge and careers, as well as promoting the well-being of students and colleagues in research environments. Faculty members must balance a host of activities - such as performing research, teaching, sourcing funds, administrative and service duties - with their roles as educators and mentors. Mentorship from experienced peers has been touted as critical for enabling these myriad roles to allow faculty development, career progression, and satisfaction. However, there is little information available on who supports faculty and best ways to structure a faculty mentorship program for early- and mid-career academics. Furthermore, the extent to which mentorship and mentoring programs have been offered to faculty members has not been widely characterized. It is also unclear what challenges faculty receiving mentorship may face and which aspects could be further improved. In the interest of advocating for increased and enhanced faculty mentoring and mentoring programs, we surveyed faculty (i.e., group leaders) around the world to gather data on whether and how they receive mentoring from peers, senior researchers, informal mentoring programs, or formal mentoring programs at their institutions. We received responses from 457 early- and mid-career faculty and found that a substantial portion of respondents either reported having no mentor or a lack of a formal mentoring scheme. Qualitative responses on the quality of mentorship revealed that the most common complaints regarding mentorship included lack of mentor availability, unsatisfactory commitment to mentorship, and non-specific or non-actionable advice. Our findings further identified key mentorship elements desired by faculty mentees. Based on these suggestions, we identify a need for training for faculty mentors as well as strategies for individual mentors, departments, and institutions for funding and design of more intentional and supportive mentorship programs for early- and mid-career faculty.
Transcriptional control ofhgcABby an ArsR-like regulator inPseudodesulfovibrio mercuriiND132
Authors: Gionfriddo Caitlin M. , Soren Ally Bullock , Wymore Ann , Hartnett D. Sean , Podar Mircea , Parks Jerry M. , Elias Dwayne A. , Gilmour Cynthia C.
Published: October 2022

ThehgcABgene pair encodes mercury (Hg) methylation capability in a diverse group of microorganisms, but its evolution and transcriptional regulation remain unknown. Working from the possibility that the evolutionary function of HgcAB may not be Hg methylation, we test a possible link to arsenic resistance. Using model Hg-methylatorPseudodesulfovibrio mercuriiND132, we specifically evaluated transcriptional control ofhgcABby a putative ArsR encoded upstream and co-transcribed withhgcAB. This regulator shares homology with ArsR repressors of arsenic resistance and S-adenosyl-homocysteine (SAH) responsive regulators of methionine biosynthesis but is distinct from other ArsR/SahR inPseudodesulfovibrio mercuriiND132. Using qPCR and RNA-seq analyses we confirmed this ArsR regulateshgcABtranscription, and is responsive to arsenic and SAH. Additionally, RNA-seq indicated a possible link betweenhgcABactivity and arsenic transformations byPseudodesulfovibrio mercuriiND132, with significant up-regulation of other ArsR-regulated arsenic resistance operons alongsidehgcAB. Interestingly, wild-type ND132 was less sensitive to AsV (but not AsIII) than anhgcABknockout strain, supporting the idea thathgcABmay be linked to arsenic resistance. Arsenic significantly impacted Hg-methylation rates by ND132, however, responses varied with culture conditions. Differences in growth and overall metabolic activity did not account for arsenic impacts on methylation. One goal of this research is to better predict MeHg production in nature. However, we found thathgcABgene and transcript abundance was not a good predictor of Hg-methylation rates. Our finding thathgcABactivity is linked to arsenic may hold clues to the possible environmental drivers of horizontal transfer ofhgcAB.

IMPORTANCE

This work reveals a link between microbial mercury methylation and arsenic resistance and may hold clues to the evolution of mercury methylation genes (hgcAB). Microbes withhgcABproduce methylmercury, a strong neurotoxin that readily accumulates in the food web. This study addresses a critical gap in our understanding about the environmental factors that controlhgcABexpression. We show thathgcABexpression is controlled by an ArsR-like regulator responsive to both arsenic and S-adenosyl-homocysteine in our model organism,Pseudodesulfovibrio mercuriiND132. Exposure to arsenic also significantly impactedPseudodesulfovibrio mercuriiND132 mercury methylation rates. However, expression ofhgcABwas not always a good predictor of Hg methylation rates, highlighting the roles of Hg bioavailability and other biochemical mechanisms in methylmercury production. This study improves our understanding of the controls onhgcABexpression which is needed to better predict environmental methylmercury production.
CD8+ tissue-resident memory T cells triggered the erosion of oral lichen planus by the cytokine network
Authors: Qing Maofeng , Shang Qianhui , Yang Dan , Peng Jiakuan , Deng Jiaxin , Jiang Lu , Li Jing , Zhou Yu , Xu Hao , Chen Qianming
Published: October 2022

CD8+tissue-resident memory T (CD8+Trm) cells play key roles in many immune-inflammation-related diseases. However, their characteristics in the pathological process of oral lichen planus (OLP) are unclear. Therefore, we investigated the function of CD8+Trm cells in the process of OLP. Single-cell RNA sequencing profiling and spatial transcriptomics revealed that compared with non-erosive OLP, CD8+Trm cells, which were mainly distributed in the lamina propria close to the basement membrane, were increased and functionally more active by secreting multiple cytokines in patients with erosive oral lichen planus (EOLP), including IFN-γ, TNF-α, and IL17. And our clinical cohort of 1-year follow-up was also supported the above results in RNA level and protein level. In summary, this study provided a novel molecular mechanism for triggering OLP erosion by CD8+Trm cells to secrete multiple cytokines, and new insight into the pathological development of OLP.
Prioritizing Annotated miRNAs: Only a Small Percentage are Candidates for Biological Regulation
Authors: Johnson Krystal C. , Johnson Samantha T. , Liu Jing , Chu Yongjun , Corey David R.
Published: October 2022

The potential for miRNAs to regulate gene expression remains controversial. DROSHA initiates the biogenesis of miRNAs while Argonaute (AGO) and TNRC6 proteins form complexes with miRNAs that recognize RNA. Here we investigate the fate of miRNAs in the absence of critical RNAi protein factors. Knockout ofDROSHAexpression reduced levels of some miRNAs, but not others. Knocking out AGO proteins, which directly contact the mature miRNA, decreased expression of miRNAs. Quantitative analysis indicates compensation to maintain the overall pool of AGO after knockout of AGO variants. Evaluation of miRNA binding to AGO proteins revealed that association between AGO and miRNAs was similar for AGO1 - 4. Contrary to the assumptions underlying many peer-reviewed reports, not all annotated miRNAs have equal potential as biological regulators. Cellular abundance, DROSHA dependence, and physical association with AGO must be considered when forming hypotheses related to their function. Our data prioritize sixty miRNAs – under two percent of the overall annotated miRNA repertoire – as being most likely to function as robust gene regulators. Our approach will facilitate identifying biologically active miRNAs.
Asymmetric dimethylation of Ribosomal S6 Kinase 2 regulates its cellular localisation and pro-survival function
Authors: Khalil Mahmoud I. , Ismail Heba M. , Panasyuk Ganna , Gout Ivan , Pardo Olivier E.
Published: October 2022

Ribosomal S6 Kinases (S6Ks) are critical regulators of cell growth, homeostasis, and survival, with dysregulation of these kinases being associated with various malignancies. While S6K1 has been extensively studied, S6K2 has been neglected despite its reported involvement in cancer progression. Protein arginine methylation is a widespread post-translational modification regulating a plethora of biological responses in mammalian cells. Here we report that p54-S6K2 is asymmetrically dimethylated at Arg-475 and Arg-477, two conserved residues within the AT-hook motif of the S6K2 family and some AT-hook-containing proteins. We demonstrate that PRMT1, PRMT3, and PRMT6 bind to and methylate S6K2in vitroandin vivo. This methylation localises S6K2 to the nucleus where it rescues cells from starvation-induced cell death. Taken together, our findings highlight a novel mechanism regulating the biological function of p54-S6K2 that may be relevant to cancer where Arg-methylation is often found elevated.
Distinct contact guidance mechanisms in single endothelial cells and in monolayers
Authors: Leclech Claire , Krishnamurthy Apoorvaa , Muller Laurent , Barakat Abdul I.
Published: October 2022

In many tissues, cell shape and orientation are controlled by a combination of internal and external biophysical cues. Anisotropic substrate topography is a ubiquitous cue that leads to cellular elongation and alignment, a process termed contact guidance, whose underlying mechanisms remain incompletely understood. Additionally, whether contact guidance responses are similar in single cells and in cellular monolayers is unknown. Here, we address these questions in vascular endothelial cells (ECs) thatin vivoform a monolayer that lines blood vessels. Culturing single ECs on microgrooved substrates that constitute an idealized mimic of anisotropic basement membrane topography elicits a strong, groove depth-dependent contact guidance response. Interestingly, this response is greatly attenuated in confluent monolayers. While contact guidance in single cells is principally driven by persistence bias of cell protrusions in the direction of the grooves and is surprisingly insensitive to actin stress fiber disruption, cell shape and alignment in dense EC monolayers are driven by the organization of the basement membrane secreted by the cells, which leads to a loss of interaction with the microgrooves. The findings of distinct contact guidance mechanisms in single ECs and in EC monolayers promise to inform strategies aimed at designing topographically patterned endovascular devices.
A Novel Biosensor Reveals Dynamic Changes of C-di-GMP in Differentiating Cells with Ultra-High Temporal Resolution
Authors: Kaczmarczyk Andreas , van Vliet Simon , Jakob Roman Peter , Reinders Alberto , Klotz Alexander , Maier Timm , Jenal Urs
Published: October 2022

Cyclic diguanylate (c-di-GMP) is a ubiquitous second messenger that regulates a wide range of biological processes in bacteria, including motility, surface attachment, virulence and persistence. The regulatory networks controlling c-di-GMP are generally complex and understudied. This is largely due to a lack of appropriate tools to monitor dynamic changes of c-di-GMP concentrationsin vivoin a non-invasive manner. Here, we develop a genetically-encoded ratiometric c-di-GMP biosensor, called cdGreen2, by applying a powerful directed evolution approach based on iterative fluorescence-activated cell sorting (FACS) under alternating c-di-GMP regimes. We demonstrate that cdGreen2 can robustly track c-di-GMP dynamics in live cells with ultra-high temporal resolution over multiple generations. To validate its exquisite diagnostic power, we utilize cdGreen2 to dissect the regulatory networks driving bimodal developmental programs in the environmental model organismCaulobacter crescentusand the human pathogenPseudomonas aeruginosa. These studies disclose the molecular determinants governing cell cycle-dependent c-di-GMP oscillations inC. crescentusand surface-induced c-di-GMP asymmetry inP. aeruginosa. The sensitivity and versatility of cdGreen2 will help unveil c-di-GMP dynamics in a wide range of organisms with unprecedented temporal resolution. The simple, yet powerful design principles underlying cdGreen2 will serve as a blueprint for the development of similar, orthogonal biosensors for other signaling molecules, metabolites or antibiotics, paving the way to uncover the complex interplay of small molecule-based networks with unprecedented spatiotemporal resolution.
Abundant Aβ fibrils in ultracentrifugal supernatants of aqueous extracts from Alzheimer’s disease brains
Authors: Stern Andrew M. , Yang Yang , Meunier Angela L. , Liu Wen , Cai Yuqi , Ericsson Maria , Liu Lei , Goedert Michel , Scheres Sjors H. W. , Selkoe Dennis J.
Published: October 2022

Soluble aggregates of amyloid-β (Aβ), often called oligomers, are believed to be principal drivers of neurotoxicity, spreading of pathology, and symptoms in Alzheimer’s disease (AD), but little is known about their structures in human brain. Aβ oligomers have been defined as aggregates found in supernatants following ultracentrifugation of aqueous extracts. We now report the unexpected presence of abundant Aβ fibrils in high-speed supernatants from AD brains that were extracted by soaking in aqueous buffer. The fibrils did not appear to form during extract preparation, and their numbers by EM correlated with ELISA quantification of aggregated Aβ42. Cryo-EM structures of Aβ fibrils from aqueous extracts were identical to those from sarkosyl-insoluble AD brain homogenates. The fibrils in aqueous extracts were immunolabeled by lecanemab, an Aβ aggregate-directed antibody reported to improve cognitive outcomes in AD. We conclude that Aβ fibrils are abundant in aqueous extracts from AD brains and have the same structures as those from amyloid plaques. These findings have implications for understanding the nature of Aβ oligomers and for designing oligomer-preferring therapeutic antibodies.
The Calpain-7 protease functions together with the ESCRT-III protein IST1 within the midbody to regulate the timing and completion of abscission
Authors: Paine Elliott L. , Skalicky Jack J. , Whitby Frank G. , Mackay Douglas R. , Ullman Katharine S. , Hill Christopher P. , Sundquist Wesley I.
Published: October 2022

The Endosomal Sorting Complexes Required for Transport (ESCRT) machinery mediates the membrane fission step that completes cytokinetic abscission and separates dividing cells. Filaments composed of ESCRT-III subunits constrict membranes of the intercellular bridge midbody to the abscission point. These filaments also bind and recruit cofactors whose activities help execute abscission and/or delay abscission timing in response to mitotic errors via the NoCut/Abscission checkpoint. We previously showed that the ESCRT-III subunit IST1 binds the cysteine protease CAPN7 (Calpain-7) and that CAPN7 is required for both efficient abscission and NoCut checkpoint maintenance (Wenzelet al., 2022). Here, we report biochemical and crystallographic studies showing that the tandem MIT domains of CAPN7 bind simultaneously to two distinct IST1 MIT interaction motifs. Structure-guided point mutations in either CAPN7 MIT domain disrupted IST1 binding in vitro and in cells, and depletion/rescue experiments showed that the CAPN7-IST1 interaction is required for: 1) CAPN7 recruitment to midbodies, 2) efficient abscission, and 3) NoCut checkpoint arrest. CAPN7 proteolytic activity is also required for abscission and checkpoint maintenance. Hence, IST1 recruits CAPN7 to midbodies, where its proteolytic activity is required to regulate and complete abscission.
The MTIST platform: a microbiome time series inference standardized test simulation, dataset, and scoring systems
Authors: Hussey Grant A. , Zhang Chenzhen , Sullivan Alexis P. , Fenyö David , Schluter Jonas
Published: October 2022

The human gut microbiome is promising therapeutic target, but development of interventions is hampered by limited understanding of the microbial ecosystem. Therefore, recent years have seen a surge in the engineering of inference algorithms seeking to unravel rules of ecological interactions from metagenomic data. Research groups score algorithmic performance in a variety of different ways, however, there exists no unified framework to score and rank each inference approach. The machine learning field presents a useful solution to this issue: a unified set of validation data and accompanying scoring metric. Here, we present MTIST: a platform for benchmarking microbial ecosystem inference tools. We use a generalized Lotka-Volterra framework to simulate microbial abundances over time, akin to what would be obtained by quantitative metagenomic sequencing studies or lab experiments, to generate a massivein silicotraining dataset (MTIST) for algorithmic validation, as well as an “ecological sign” score (ES score) to rate them. MTIST comprises 24,570 time series of microbial abundance data packaged into 648 datasets. Together, the MTIST dataset and the ES score serve as a platform to develop and compare microbiome ecosystem inference approaches.
MagPEG: a complete extracellular vesicle isolation/analysis solution
Authors: Sun Li , York Sara , Pate Brandon , Zhang Yanping , Meckes David G.
Published: October 2022

Current extracellular vesicle (EV) isolation methods depend on large expensive equipment like ultracentrifuges and are laborious and time consuming. There is also currently no method available for high throughput isolation to meet clinical demands. Here, we present a method that combines our previous published ExtraPEG method and magnetic beads. Western blot and nanoparticle tracking analysis (NTA) of the purified EVs revealed higher or equivalent recovery and purity with this method compared to ExtraPEG or size exclusion chromatography (SEC) methods. With this newly developed workflow and automated liquid handling instrument, we have successfully isolated up to 96 EV samples from 5 µL pre-cleared serum in 45 minutes. Moreover, DNA / small RNA / protein purification and profiling steps could be seamlessly integrated into the isolation workflow. To profile EV protein markers, EVs were lysed from the binding step and covalently bound to the surface of the beads. TotalSeq or ELISA antibody can be applied with under a standard protocol. With this extended protocol, researchers can easily complete EV isolation and protein profiling experiment within 8 hours. Taken together, we provide a high throughput method for EV isolation and molecular analyses that may be used for sensitive biomarker detection from biological fluids.
The Opto-inflammasome in zebrafish: a tool to study cell and tissue responses to speck formation and cell death
Authors: de Carvalho Eva Hasel , Dharmadhikari Shivani , Shkarina Kateryna , Xiong Jingwei Rachel , Reversade Bruno , Broz Petr , Leptin Maria
Published: October 2022

The inflammasome is a conserved system for the intracellular detection of danger or pathogen signals. By forming a large intracellular multiprotein signaling platform, it activates downstream effectors that initiate a rapid necrotic programmed cell death (PCD) termed pyroptosis and activation and secretion of pro-inflammatory cytokines to warn and activate surrounding cells. However, inflammasome activation is difficult to control on a single-cell level using canonical triggers. We constructed Opto-Asc, a light-responsive form of the inflammasome adaptor protein ASC (Apoptosis-Associated Speck-Like Protein Containing a CARD) which allows tight control of inflammasome formationin vivo.

We introduced a cassette of this construct under the control of a heat shock element into zebrafish in which we can now induce Asc inflammasome (speck) formation in single cells of the skin.

We find that cell death resulting from Asc speck formation is morphological distinct from apoptosis in periderm but not in basal cells. Asc induced PCD in can lead to apical or basal extrusion from the periderm. The apical extrusion in periderm cells depends on Caspb but and triggers a strong Ca2+signaling response in nearby cells.
Understanding social media users' engagement intention toward emergency information: the role of experience and information usefulness in a reciprocity framework
Authors: Li Yixiao , Hu Yaoqi , Yang Shuiqing
Published: October 2022

Purpose

The aim of this study is to investigate how social media users' experience of seeking emergency information affects their engagement intention toward emergency information with a reciprocity framework integrated with information adoption model.

Design/methodology/approach

Drawing on reciprocity theory, indebtedness theory, and information adoption model, an integrative research model is developed. This study employs a questionnaire survey to collect data of 325 social media users in China. Structural equation modeling analyses are conducted to test the proposed theoretical model.

Findings

Social media users' experience of seeking emergency information has a strong effect on their perceived information usefulness and indebtedness, while perceived information usefulness further influences community norm, indebtedness, and engagement intention. The authors also found that perceived information usefulness mediates the relationships between experience of seeking emergency information and community norm/indebtedness.

Originality/value

This study offers a new perspective to explain social media users' engagement intention in the diffusion of emergency information. This study contributes to the literature by extending the theoretical framework of reciprocity and applying it to the context of emergency information diffusion. The findings of this study could benefit the practitioners who wish to leverage social media tools for emergency response purposes.
Searching while sick: How does disease affect foraging decisions and contact rates?
Authors: Tillman Francis E. , Adelman James S.
Published: October 2022

Infection often changes an animal's motivation or ability to forage, which should alter rates of contact with uninfected hosts. However, links are likely complex and remain poorly understood. Here, we explore relationships among infection, foraging decisions and contact rates and how these could interact with ecological factors to drive pathogen transmission.

Under optimal foraging theory, animals should gather the highest quality resources from a patch, leaving only once the cost of continued foraging outweighs the amount of energy gained. However, the ability to locate and evaluate resources will vary with many factors, including disease, temperature and habitat fragmentation. Although modelling suggests that such variation in foraging decisions can alter contact rates among infected and uninfected hosts, and thus transmission and evolution of infectious agents, empirical studies have only begun to test the direction and strength of such relationships.

We propose that foraging behaviour will often change with infection, thereby affecting contact rates, because of sickness behaviours, self‐medication, parasite manipulation of the host and nonadaptive behavioural responses to infection. We recommend that future studies empirically test how such associations vary with ambient temperature and habitat fragmentation, as human activity continues to alter these environmental pressures. Furthermore, we suggest that such relationships among infection, foraging and environmental factors could help shape not only population‐level disease dynamics, but also surrounding ecological communities.

By revealing how environmental factors impact such links, we can improve our understanding and prediction of animal disease dynamics in the face of changing ecosystems.

Read the freePlain Language Summaryfor this article on the Journal blog.
Illness wellness scale: novel grading system for performance status of patients under surgical care
Authors: Kumar Arun , Puri Gopal , Rathore Yashwant Singh , Chumber Sunil , Trikha Anjan , Ranjan Piyush , Kataria Kamal , Bhattacharjee Hemanga K.
Published: October 2022

Background

Grading the illness using clinical parameters is essential for the daily progress of inpatients. Existing systems do not incorporate these parameters holistically. The study was designed to internally validate the illness wellness scale, based upon clinical assessment of the patients requiring surgical care, for their risk stratification and uniformity of communication between health care providers.

Methods

Prospective observational study conducted at a tertiary care hospital. An expert panel devised the scale, and it was modified after feedback from 100 health care providers. A total of 210 patients (150 for internal validation and 60 for inter‐observer variability) who required care under the department of surgical disciplines were enrolled. This included patients presenting to surgery OPD, admitted to COVID/non‐COVID surgical wards and ICUs, aged ≥16 years.

Results

The response rate of the final illness wellness scale was 95% with 86% positive feedback and a mean of 1.7 on the Likert scale for ease of use (one being very easy and five being difficult). It showed excellent consistency and minimal inter‐observer variability with the intra‐class correlation coefficient (ICC) above 0.9. In the internal validation cohort (n = 150), univariate and multivariable analysis of factors affecting mortality revealed that categorical risk stratification, age ≥ 60 years, presence or absence of co‐morbidities especially hypertension and chronic kidney disease significantly affect mortality.

Conclusions

The Illness wellness scale is an effective tool for uniformly communicating between health care professionals and is also a strong predictor of risk stratification and mortality in patients requiring surgical care.
Scale morphological variation across the flank in four Tonguefishes species collected from the Gulf of Oman (Pleuronectiforms; Cynoglossidae)
Authors: Kishipour Sanaz , Teimori Azad , Askari Hesni Majid , Motamedi Mina
Published: October 2022

The scale morphology of pleuronectiforms in the Gulf of Oman remains insufficiently known. This study used light microscopy and morphological analysis to examine scale variation across the flank of four Tonguefishes species; Cynoglossus arel, C. bilineatus, C. lingua, and C. puncticeps. Scales were extracted from six flank regions, three on the eyed and blind sides, respectively. The most differentiated species was C. arel, which showed significant differences in four size variables in five regions. In Cynoglossus arel and C. lingua, the scales of the eyed side were ctenoid, and those scales from the blind side were cycloid; C. puncticeps have ctenoid scales on both flank sides and C. bilineatus has cycloid scales on both sides. All species' scales on the blind side have fewer ctenial spines (except in C. bilineatus). This study indicated that scale morphology demonstrated considerable variation among the flank regions of the examined species. As a result, the scales from the head and the trunk regions of the eyed side and the scales from the head region of the blind side have a good power of species separation in this family.
The Distributional Effect of Trade on the CEO Market
Authors: Correa Juan A. , Parro Francisco , Sánchez Rafael
Published: October 2022

We study the relationship between trade openness and CEO pay dispersion across firms. Using US firm‐level data, we show that trade has an unequal effect on CEO equilibrium pay at firms of different sizes (sales). An increase of 10% in the industry openness degree raises CEO compensation by about 14% in firms at the 99th percentile of the size distribution. However, CEO compensation falls by 5% in firms at the 1st percentile. Analogous results are derived for other points of the distribution. Our results show that trade openness impacts inequality within the very top of the income distribution, where skill differentials are less evident.
Effect of mitral valve transcatheter edge‐to‐edge repair on indices of left atrial performance in chronic mitral regurgitation
Authors: Biersmith Michael , Orsinelli David A. , Harfi Thura T. , Lilly Scott , Boudoulas Konstantinos Dean
Published: October 2022

Introduction

Effect of transcatheter edge‐to‐edge repair (TEER) using MitraClip in patients with mitral regurgitation (MR) on left atrial (LA) kinetic energy (LAKE), an index of LA work, and LA strain, a measure of LA performance, have not been well defined.

Methods

Patients with chronic primary or secondary 3+ or 4+ MR were analyzed pre‐ and post‐TEER using MitraClip. LAKE was determined by echocardiography using LA stroke volume and A‐wave velocity. Peak atrial longitudinal strain (PALS), peak atrial strain in early diastole, and peak atrial contraction strain (PACS) were obtained by speckle tracking echocardiography.

Results

Thirty‐nine patients undergoing TEER with MitraClip were screened, 12 met criteria for analysis (9 primary and 3 secondary MR). Compared to pre‐TEER, there was a significant increase post‐TEER in LAKE (71.0 ± 64.1 vs. 177.5 ± 167.9 dyne·cm·103, respectively; p = .008) and Doppler transmitral A‐wave velocity (87.8 ± 41.4 vs. 138.5 ± 43.7 cm/s, respectively; p < .001); LA stroke volume did not change significantly. Mitral valve mean gradient significantly increased post‐TEER compared to pre‐TEER (5.7 ± 2.1 vs. 3.3 ± 2.1 mmHg, respectively; p = .01). There was a trend toward decrease in PALS post‐TEER compared to pre‐TEER (16.2 ± 4.8 vs. 20.7 ± 9.9%, respectively; p = .05). Peak atrial strain in early diastole significantly decreased post‐TEER compared to pre‐TEER (7.2 ± 3.0 vs. 14.1 ± 7.2%; respectively, p < .001), while PACS did not significantly change (9.1 ± 3.5 vs. 6.7 ± 5.2%, respectively; p = .07).

Conclusion

In patients with chronic MR, LAKE increases after TEER with MitraClip driven by an increase in LA emptying velocities. Changes were also seen in LA strain with MitraClip. These procedurally induced changes due to mild mitral stenosis may have clinical implications.