bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative analysis of morphogenesis and growth dynamics in an obligate intracellular bacterium
Authors: Figueroa-Cuilan Wanda M. , Irazoki Oihane , Feeley Marissa , Smith Erika , Nguyen Trung , Cava Felipe , Goley Erin D.
Published: December 2022

Obligate intracellular bacteria of the order Rickettsiales include numerous arthropod-borne human pathogens. However, our understanding of the basic biology ofRickettsiaspecies is limited by technical challenges imposed by their obligate intracellular lifestyle. To overcome this roadblock, we developed quantitative methods to assess the cell wall composition, intracellular growth, and morphology ofRickettsia parkeri, a human pathogen in the Spotted Fever Group of theRickettsiagenus. Analysis of the cell wall composition ofR. parkerirevealed unique features including a high M3 monomer fraction and absence of LD-crosslinks. Using a novel fluorescence microscopy approach, we quantified the cell morphology ofR. parkeriin live host cells and found that bacterial morphology is maintained stably during exponential growth in two different epithelial cell lines. To assess population growth kinetics in a high-throughput and high-resolution manner, we developed an imaging-based growth assay and applied this to determine the growth rate of up to 24 infected cultures at a time. We also sought to gain insight into the cell cycle regulation ofR. parkeri. To this end, we developed methods to quantify the fraction of the population preparing to divide as well as those undergoing active constriction. These approaches permitted a quantitative analysis of cell cycle status across a population ofR. parkeri.Finally, as a proof of concept, we applied the above tools to quantitatively determine how MreB, a bacterial actin homolog, contributes to the growth and morphogenesis ofR. parkeri. Inhibition of MreB with the small molecule MP265 led to cell rounding and slowed growth, suggesting that MreB is required for the growth and shape maintenance ofR. parkeri. Collectively, we developed a toolkit of high-throughput, quantitative tools to understand intracellular growth and morphogenesis ofR. parkerithat is translatable to other obligate intracellular bacteria.

AUTHOR SUMMARY

The obligate intracellular lifestyle of members of the bacterial order Rickettsiales, which includes important human pathogens, has hindered our progress in understanding their biology. Here we developed and applied high-throughput, quantitative tools to analyze essential features of rickettsial cell biology such as morphology and growth in living host cells. By applying these tools in a proof of concept, we showed that the bacterial actin homolog, MreB is required for the regulation of rod shape and intracytoplasmic growth.
Dysregulation of murine long non-coding single cell transcriptome in non-alcoholic steatohepatitis and liver fibrosis
Authors: Karri Kritika , Waxman David J.
Published: December 2022

LncRNAs are typified by low expression, nuclear enrichment, high tissue-specificity and functional diversity, but the vast majority are uncharacterized. Here, we develop a catalog of 48,000 mouse liver-expressed lncRNAs and use to elucidate lncRNA dysregulation in high fat diet-induced non-alcoholic steatohepatitis and carbon tetrachloride-induced liver fibrosis by single cell RNA-seq. LncRNA zonation patterns across the liver lobule were discovered in five cell populations. Perturbations in lncRNA expression were common in disease-associated cell types, including non-alcoholic steatohepatitis-associated macrophages, a hallmark of fatty liver disease progression, and collagen-producing myofibroblasts, key to liver fibrosis. Gene regulatory network analysis linked individual lncRNAs to biological pathways and network centrality metrics identified network-essential, disease-associated regulatory lncRNAs. Regulatory lncRNAs with network-predicted target gene promoters enriched for triplex-based lncRNA binding were also identified. These findings elucidate hepatic lncRNA cell-type specificities, spatial zonation patterns, linked biological networks and dysregulation in disease progression. A subset of the disease-associated lncRNAs have human orthologs and are promising candidates for biomarkers and therapeutic targets.
The interplay between adsorption and aggregation of von Willebrand factor chains in shear flows
Authors: Amaya-Espinosa Helman , Alexander-Katz Alfredo , Aponte-Santamaría Camilo
Published: December 2022

Abstract

Von Willebrand factor (VWF) is a giant extracellular glycoprotein that carries out a key adhesive function during primary hemostasis. Upon vascular injury and triggered by the shear of flowing blood, VWF establishes specific interactions with several molecular partners in order to anchor platelets to collagen on the exposed sub-endothelial surface. VWF also interacts with itself to form aggregates that, adsorbed on the surface, provide more anchor sites for the platelets. However, the interplay between elongation and subsequent exposure of cryptic binding sites, self-association, and adsorption on the surface, remained unclear for VWF. In particular, the role of shear flow in these three processes is not well understood. In this study, we address these questions by using Brownian dynamics simulations at a coarse-grained level of resolution. We considered a system consisting of multiple VWF-like self-interacting chains that also interact with a surface under a shear flow. By a systematic analysis, we reveal that chain-chain and chain-surface interactions coexist non-trivially to modulate the spontaneous adsorption of VWF and the posterior immobilization of secondary tethered chains. Accordingly, these interactions tune VWF’s extension and its propensity to form shear-assisted functional adsorbed aggregates. Our data highlights the collective behavior VWF self-interacting chains have when bound to the surface, distinct from that of isolated or flowing chains. Furthermore, we show that the extension and the exposure to solvent have a similar dependence on shear flow, at a VWF-monomer level of resolution. Overall, our results highlight the complex interplay that exists between adsorption, cohesion, and shear forces and its relevance for the adhesive hemostatic function of VWF.
Synanthropic flora in the vicinity of the mediaeval Castle Kolno, Stare Kolnie near Brzeg, southwestern Poland
Authors: Kosina Romuald , Marek Lech
Published: December 2022

The mediaeval castle Kolno situated near the village Stare Kolnie served as a custom house at the confluence of two rivers, Budkowiczanka and Stobrawa. Numerous diaspores of plants were obtained from the archaeological excavations, from the layers of the 14th-15th centuries A.D. The excavations were located near the former access road, where increased human activity has affected the composition of the fossil macroremains of plants. Two species of cabbage cultivated in small fields near the castle were recognised. Diaspores of weeds and ruderal plants were deposited at the site. The most frequent were:Solanum nigrum, Setaria pumila, Chenopodium album, Rumex acetosella, Polygonum lapathifoliumandUrtica dioica. The botanical set of fossil diaspores was composed of plant species associated with anthropogenic habitats and showing the dispersion dynamics in various micro-niches within them.
Dissociation of direct and peripheral transcranial magnetic stimulation effects in nonhuman primates
Authors: Perera Nipun D , Alekseichuk Ivan , Shirinpour Sina , Wischnewski Miles , Linn Gary , Masiello Kurt , Butler Brent , Russ Brian E , Schroeder Charles E , Falchier Arnaud , Opitz Alexander
Published: December 2022

Transcranial magnetic stimulation (TMS) is a non-invasive brain stimulation method that is rapidly growing in popularity for studying causal brain-behavior relationships. However, its dose-dependent direct neural mechanisms, i.e., due to electric field or connectivity, and peripheral sensory co-stimulation effects remain debated. Understanding how TMS stimulation parameters affect brain responses is vital for the rational design of TMS protocols. Studying these mechanisms in humans is challenging due to the limited spatiotemporal resolution of available non-invasive neuroimaging methods. Here, we leverage invasive recordings of local field potentials in non-human primates to study TMS mesoscale responses. We demonstrate that early TMS-evoked potentials show a sigmoidal dose-response with stimulation intensity. We further show that stimulation responses are spatially specific. We employ several control conditions to dissociate direct neural responses from auditory and somatosensory co-activation. These results provide crucial evidence regarding TMS neural effects at the brain circuit level. Our findings are highly relevant for interpreting human TMS studies and biomarker developments for TMS target engagement in clinical applications.
Development and evaluation of a scalable alternative to chart review for phenotype case adjudication using standardized structured data from electronic health records
Authors: Ostropolets Anna , Hripcsak George , Husain Syed A , Richter Lauren , Spotnitz Matthew , Elhussein Ahmed , Ryan Patrick B
Published: December 2022

Objective

Chart review as the current gold standard for phenotype evaluation cannot support observational research at scale. It is expensive, time-consuming, and variable. We aimed to evaluate the ability of structured data to support efficient patient status ascertainment and develop a standardized and scalable alternative to chart review.

Methods

We developed Knowledge-Enhanced Electronic Patient Profile Review system (KEEPER) that extracts a patient’s structured data elements relevant to a given phenotype and presents them in a standardized fashion that follows clinical reasoning principles. We evaluated its performance compared to manual chart review for four conditions (diabetes type I, acute appendicitis, end stage renal disease and chronic obstructive lung disease) using randomized two-period, two-sequence crossover design. Inter-method agreement, inter-rater agreement, accuracy, and review duration were measured.

Results

Ascertaining patient status with KEEPER was twice as fast compared to manual chart review. 88.1% of the patients were classified concordantly using full chart and KEEPER, but agreement varied depending on the condition. Pairs of clinicians agreed in classification of patient status in 91.2% of the cases when using KEEPER compared to 76.3% when using full chart. Patient classification aligned with the gold standard in 88.1% and 86.9% of the cases respectively.

Conclusion

This proof-of-concept study demonstrated that structured data can be used for efficient patient ascertainment if are limited to only relevant subset and organized according to the clinical reasoning principles. A system that implements these principles can achieve similar accuracy and higher inter-rater reliability compared to chart review at a fraction of time.
Tryptophan metabolism, gut microbiota, and carotid artery plaque in women with and without HIV infection
Authors: Luo Kai , Wang Zheng , Peters Brandilyn A , Hanna David B , Wang Tao , Sollecito Christopher C , Grassi Evan , Wiek Fanua , Peter Lauren St , Usyk Mykhaylo , Post Wendy S , Landay Alan L , Hodis Howard N , Weber Kathleen M , French Audrey , Golub Elizabeth T , Lazar Jason , Gustafson Deborah , Sharma Anjali , Anastos Kathryn , Clish Clary B , Knight Rob , Kaplan Robert C , Burk Robert D , Qi Qibin
Published: December 2022

Background

The perturbation of tryptophan (TRP)-kynurenine (KYN) metabolism has been linked with HIV infection and cardiovascular disease (CVD), but the interrelationship among TRP metabolites, gut microbiota, and atherosclerosis has not yet been fully understood in the context of HIV infection.

Methods

We included 361 women (241 HIV+, 120 HIV-) with carotid artery plaque assessments from the Women’s Interagency HIV Study, measured ten plasma TRP metabolites and profiled fecal gut microbiome. TRP metabolites related gut microbial features were selected through the Analysis of Compositions of Microbiomes with Bias Correction method. The associations of TRP metabolites and related microbial features with plaque were examined using multivariable logistic regression.

Results

While plasma kynurenic acid (KYNA) (odds ratio [OR]=1.93[1.12, 3.32] per one SD increase,P=0.02) and KYNA/TRP (OR=1.83[1.08, 3.09],P=0.02) were positively associated with plaque, indole-3-propionate (IPA) (OR=0.62 [0.40, 0.98],P=0.03) and IPA/KYNA (OR=0.51[0.33, 0.80],P<0.01) were inversely associated with plaque. Five gut bacterial genera and many affiliated species were positively associated with IPA (FDR-q<0.25), includingRoseburia sp.,Eubacterium sp.,Lachnospira sp., andCoprobacter sp.; but no bacterial genera were found to be associated with KYNA. Furthermore, an IPA-associated-bacteria score was inversely associated with plaque (OR=0.47[0.28, 0.79],P<0.01). But no significant effect modification by HIV serostatus was observed in these associations.

Conclusions

In a cohort of women living with and without HIV infection, plasma IPA levels and related gut bacteria were inversely associated with carotid artery plaque, suggesting a potential beneficial role of IPA and its gut bacterial producers in atherosclerosis and CVD.
Discovery of oncogenic ROS1 missense mutations with sensitivity to tyrosine kinase inhibitors
Authors: Iyer Sudarshan R. , Nusser Kevin , Jones Kristen , Shinde Pushkar , Beach Catherine Z. , Keddy Clare , Aguero Erin , Force Jeremy , Shinde Ujwal , Davare Monika A.
Published: December 2022

Chromosomal rearrangements ofROS1generate ROS1 tyrosine kinase fusion proteins that are established oncogenes predicting effectiveness of tyrosine kinase inhibitors (TKI) treatment. The cancer genome reveals nonsynonymous missense mutations inROS1,however, their oncogenic potential remains unknown. We nominated thirty-four tumor-associated missense mutations in ROS1 kinase domain for functional interrogation. Immunoblotting revealed diverse impact of the mutations on the kinase, ranging from loss of function to significant increase in catalytic activity. Notably, Asn and Gly substitutions at the Asp-2113 position in ROS1 kinase domain were TKI- sensitive hyper-activating mutations, and transformative oncogenes in independent cell models. Molecular modeling revealed drastic alterations in the activation loop of ROS1D2113Ncompared to wildtype kinase. Proteomics studies showed that ROS1D2113Nincreases phosphorylation of known effectors akin to ROS1 fusions, and upregulates pathways not previously linked to ROS1, including mTORC2, JNK1/2, AP-1, TGFB1 and CCN1/2.In vivo, ROS1D2113Ndrove tumor formation that was sensitive to inhibition by crizotinib and lorlatinib. Taken together, these data show that select point mutations within ROS1 RTK are oncogenic, and maybe therapeutically targetable with FDA-approved TKI.
Coupling dynamics of 2D Notch-Delta signalling
Authors: Berkemeier Francisco , Page Karen
Published: December 2022

Understanding pattern formation driven by cell-cell interactions has been a significant theme in cellular biology for many years. In particular, due to their implications within many biological contexts, lateral-inhibition mechanisms present in the Notch-Delta signalling pathway led to an extensive discussion between biologists and mathematicians. Deterministic and stochastic models have been developed as a consequence of this discussion, some of which address long-range signalling by considering cell protrusions reaching non-neighbouring cells. The dynamics of such signalling systems reveal intricate properties of the coupling terms involved in these models. In this work, we examine the benefits and limitations of new and existing models of cell signalling and differentiation in a variety of contexts. Using linear and weakly nonlinear stability analyses, we find that pattern selection relies on nonlinear effects that are not covered by such analytical methods.
SCIP: a self-paced, community-based summer coding program creates community and increases coding confidence, lessons learned from the pandemic
Authors: Reyes Rochelle-Jan , Pham Olivia , Fergusson Ryan , Ceberio Niquo , Clark Candace , Cohen C Sarah , Fuse Megumi , Pennings Pleuni
Published: December 2022

In 2020, many students lost summer opportunities due to the COVID-19 pandemic. We wanted to offer students an opportunity to learn computational skills and be part of a community while they were stuck at home. Because the pandemic was very isolating, it was important to support students to learn and build community online. We used lessons learned from literature and our own experience to design, run and test an online program for students called the Science Coding Immersion Program (SCIP). In our program, students worked in small teams for 8 hours a week spread over the week, with one participant as the team leader and Zoom host. Teams worked on an online R or Python class at their own pace with support on Slack from the organizing team. For motivation and career advice, we hosted a weekly webinar with guest speakers. We used pre- and post-program surveys to determine how different aspects of the program impacted students. We were able to recruit a large and diverse group of participants who were happy with the program, found community in their team, and improved their coding confidence. We hope that our work will inspire others to start their own version of SCIP.
In situ genetically targeted chemical assembly of polymers on living neuronal membranes
Authors: Zhang Anqi , Loh Kang Yong , Kadur Chandan S. , Michalek Lukas , Dou Jiayi , Ramakrishnan Charu , Bao Zhenan , Deisseroth Karl
Published: December 2022

Multicellular biological systems, most notably living neural networks, exhibit highly complex physical organization properties that pose challenges for building cell-specific and biocompatible interfaces. We developed a novel approach to genetically program cells to chemically assemble artificial structures that modify the electrical properties of neuronsin situ, opening up the possibility of minimally-invasive cell-specific interfaces with neural circuits in living animals. However, the efficiency and biocompatibility of this approach were challenged by limited membrane targeting of the constructed material. Here, we report a method with significantly improved molecular construct properties, which expresses highly localized enzymes targeted to the plasma membrane of primary neurons with minimal intracellular retention. Polymers synthesizedin situby this approach form dense clusters on the targeted cell membrane, and neurons remain viable after polymerization. This platform can be readily extended to incorporate a broad range of materials onto the surface membranes of specific cells within complex tissues, using chemistry that may further enable the next generation of interfaces with living biological systems.
Genetically-encoded photosensitizers enable light-controlled polymerization on living neuronal membranes
Authors: Zhang Anqi , Kadur Chandan S. , Ramakrishnan Charu , Bao Zhenan , Deisseroth Karl
Published: December 2022

The ability to record, stimulate, and modify brains of living animals would unlock numerous research opportunities and create potential clinical interventions, but it is difficult to interface with a living neural network without damaging it. We previously reported a novel approach to building neural interfaces, namely: genetically programming cells to build artificial structures to modify the electrical properties of neuronsin situ, which opens up the possibility of modifying neural circuits in living animals without surgery. However, the spatiotemporal resolution, efficiency, and biocompatibility of this approach were still limited and lacked selectivity on cell membrane. Here, we demonstrate an approach using genetically-targeted photosensitizers to instruct living cells to synthesize functional materials directly on the plasma membrane under the control of light. Polymers synthesized by this approach were selectively deposited on the membrane of targeted live neurons. This platform can be readily extended to incorporate a broad range of light-controlled reactions onto specific cells, which may enable researchers to grow seamless, dynamic interfaces directly in living animals.
Refinement of AlphaFold-Multimer structures with single sequence input
Authors: Oda Toshiyuki
Published: December 2022

AlphaFold2, introduced by DeepMind in CASP14, demonstrated outstanding performance in predicting protein monomer structures. It could model more than 90% of targets with high accuracy, and so the next step would surely be multimer predictions, since many proteins do not act by themselves but with their binding partners. After the publication of AlphaFold2, DeepMind published AlphaFold-Multimer, which showed excellent performance in predicting multimeric structures. However, its accuracy still has room for improvement compared to that of monomer predictions by AlphaFold2. In this paper, we introduce a fine-tuned version of AlphaFold-Multimer, named AFM-Refine-G, which uses structures predicted by AlphaFold-Multimer as inputs and produces refined structures without the help of multiple sequence alignments or templates. The performance of AFM-Refine-G was assessed using four datasets: Ghani_et_al_Benchmark2 and Yin_et_al_Hard using AlphaFold-Multimer version 2.2 outputs, and CASP15_multimer and Yin_and_Pierce_af23 using AlphaFold-Multimer version 2.3 outputs. Of 1925 predicted structures, 203 had DockQ improvement > 0.05 after refinement, demonstrating that our model is useful for the refinement of multimer structures. However, considering the per target success rate, the overall improvement was modest, suggesting that the original AlphaFold-Multimer network had already learned a biophysical energy function independent of MSAs or templates, as proposed by Roney and Ovchinnikov (Roney and Ovchinnikov, 2022). Furthermore, both the default AlphaFold-Multimer and our refinement model showed lower performance for immune-related targets compared to general targets, indicating that room for improvement remains.

Availability

The inference scripts are available fromhttps://github.com/t-oda-ic/afm_refinerunder the Apache License, Version 2.0. The network parameters are available fromhttps://figshare.com/articles/online_resource/afm_refine_g_20230110_zip/21856407under the license CC BY 4.0.
Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts
Authors: Smug Bogna J. , Szczepaniak Krzysztof , Rocha Eduardo P.C. , Dunin-Horkawicz Stanislaw , Mostowy Rafał J.
Published: December 2022

Biological modularity enhances evolutionary adaptability by allowing rearrangement of functional components. One striking example are bacterial viruses (phages). They exhibit extensive genomic modularity by being built of independent functional modules that evolve separately and combine in various ways, making them astoundingly diverse. While multiple studies have investigated genomic modularity in phages, less attention has been given to protein modularity—proteins having distinct building blocks or domains that can evolve and recombine, enhancing functional and genetic diversity. To better understand the impact of protein modularity on viral evolution, we quantified it by detecting instances of domain mosaicism, defined as a homologous fragment sharing between two otherwise unrelated proteins. We used highly sensitive homology detection to quantify domain mosaicism between pairs of 133,574 representative phage proteins and to understand its relationship with functional diversity in phage genomes. We found that diverse functional classes often shared homologous domains. This phenomenon was often linked to protein modularity, particularly in receptor-binding proteins, endolysins and DNA polymerases. We also identified multiple instances of recent diversification via exchange and gain/loss of domains in receptor-binding proteins, neck passage structures, endolysins and some members of the core replication machinery. Diversification via protein fragment exchange often transcended distant taxonomic and ecological borders. We argue that the ongoing diversification via shuffling of protein domains associated with those functions is reflective of co-evolutionary arms race and the resulting diversifying selection to overcome multiple mechanisms of bacterial resistance against phages.
Metagenomics reveals that Dung Beetles (Coleoptera: Scarabaeinae) broadly feed on Reptile dung and could feed on that of Dinosaurs
Authors: Lopes Fernando , Rossini Michele , Losacco Federica , Montanaro Giulio , Gunter Nicole , Tarasov Sergei
Published: December 2022

According to traditional views, the evolution of dung beetles (Coleoptera: Scarabaeinae) and their feeding habits are largely attributed to mammal dung. In this paper, we challenge this view and provide evidence that many dung beetle communities are actually associated with the dung of reptiles and birds (= Sauropsida). In turn, this indicates that sauropsid dung may have played a crucial evolutionary role that was previously underestimated. We argue that it is physiologically realistic to consider that coprophagy in dung beetles could have evolved during the Cretaceous in response to the massive amount of dung produced by dinosaurs. Furthermore, we demonstrate that sauropsid dung may be one of the major factors driving the emergence of insular dung beetle communities across the globe. We support our findings with amplicon-metagenomic analyses, trapping experiments, and meta-analysis of the published literature.
Precise Traits From Sloppy Components: Perception and the Origin of Phenotypic Response
Authors: Frank Steven A.
Published: December 2022

Organisms perceive their environment and respond. The origin of perception-response traits presents a puzzle. Perception provides no value without response. Response requires perception. Recent advances in machine learning may provide a solution. A randomly connected network creates a reservoir of perceptive information about the recent history of environmental states. In each time step, a relatively small number of inputs drives the dynamics of the relatively large network. Over time, the internal network states retain memory of past inputs. To achieve a functional response to past states or to predict future states, a system must learn only how to match states of the reservoir to the target response. In the same way, a random biochemical or neural network of an organism can provide an initial perceptive basis. With a solution for one side of the two-step perception-response challenge, evolving an adaptive response may not be so difficult. Two broader themes emerge. First, organisms may often achieve precise traits from sloppy components. Second, evolutionary puzzles often follow the same outlines as the challenges of machine learning. In each case, the basic problem is how to learn, either by artificial computational methods or by natural selection.
Effect ofAscosphaera apisinfestation on the activities of four antioxidant enzymes in Asian honey bee larval guts
Authors: Zhang Kaiyao , Fu Zhongmin , Fan Xiaoxue , Wang Zixin , Wang Siyi , Guo Sijia , Gao Xuze , Zhao Haodong , Jing Xin , Zou Peiyuan , Li Qiming , Chen Mengjun , Chen Dafu , Guo Rui
Published: December 2022

Ascosphaera apisexclusively infects bee larvae and causes chalkbrood, a lethal fungal disease that results in the sharp reduction in adult bees and colony productivity. However, little is known about the effect ofA. apisinfestation on the activities of antioxidant enzymes in bee larvae. Here,A. apisspores were purified and used to inoculate Asian honey bee (Apis cerana) larvae, followed by detection of the host survival rate and evaluation of the activities of four major antioxidant enzymes. At 6 days post inoculation (dpi) withA. apisspores, white mycelia penetrated the posterior end of the larva, extended to the anterior end, and eventually covered the entire larval body surface, presenting an obvious symptom of chalkbrood disease similar to that occurs inApis melliferalarvae. Additionally, PCR identification showed that the expected fragment was amplified from theA. apis-inoculated larval guts and theA. apisspores, verifying theA. apisinfection ofA. ceranalarvae. The survival rate of larvae inoculated withA. apiswas high at 1–2 dpi, sharply decreased to 4.16% at 4 dpi, and reached 0% at 5 dpi; whereas that of un-inoculated larvae was always high at 1~8 dpi, with an average survival rate of 95.37%, indicating the negative impact ofA. apisinfection on larval survival. Furthermore, in comparison with those in the corresponding un-inoculated groups, the superoxide dismutase (SOD) and catalase (CAT) activities in the 4-day-old larval gut in theA. apis-inoculated groups were reduced (p> 0.05), while those in the 5- and 6-day-old larval guts were significantly decreased (p< 0.05); the glutathione S-transferase (GST) activity in the 4- and 5-day-old larval guts was significantly increased (p< 0.05), while that in the 6-day-old larval gut was reduced (p> 0.05); the polyphenol oxidase (PPO) activity in 4-day-old larval gut was increased (p> 0.05) and that in the 5-day-old larval gut was significantly increased (p< 0.05), whereas that in the 6-day-old larval gut was significantly reduced (p< 0.01). These results together suggested that the activities of SOD and CAT in the larval guts were suppressed during the process ofA. apisinfestation, while the GST activity was induced to activation, and the PPO activity was first enhanced and then inhibited. Our findings not only unravel the response ofA. ceranalarvae toA. apisinfestation from a biochemical perspective, but also offer a valuable insight into the interaction between Asian honey bee larvae andA. apis.
Structural damping renders the insect exoskeleton mechanically insensitive to non-sinusoidal deformations
Authors: Wold Ethan S. , Lynch James , Gravish Nick , Sponberg Simon
Published: December 2022

Muscles act through elastic and dissipative elements to mediate movement, but these elements can introduce dissipation and filtering which are important for energetics and control. The high power requirements of flapping flight can be reduced by the insect’s exoskeleton, which acts as a structurally damped spring under purely sinusoidal deformation. However, this purely sinusoidal dynamic regime does not encompass the asymmetric wing strokes of many insects or non-periodic deformations induced by external perturbations. As such, it remains unknown whether a structural damping model applies broadly and what implications it has for control. We used a vibration testing system to measure the mechanical properties of isolatedManduca sextathoraces under symmetric, asymmetric, and band-limited white noise deformations. We measured a thoracic stiffness of 2980Nm−1at 25 Hz and physiological peak-to-peak amplitude of 0.92 mm. Power savings and dissipation were indistinguishable between symmetric and asymmetric conditions, demonstrating that no additional energy is required to deform the thorax non-sinusoidally. Under white noise conditions, stiffness and damping were invariant with frequency, which is consistent with a structural damping model and suggests the thorax has no frequency-dependent filtering properties. A simple flat frequency response function fits our measured frequency response. This work demonstrates the potential of structurally damped materials to simplify motor control by eliminating any velocity-dependent filtering that viscoelastic elements usually impose between muscle and appendage.
Improved genetically encoded fluorescent biosensors for monitoring of intra- and extracellular L-lactate
Authors: Nasu Yusuke , Aggarwal Abhi , Le Giang N. T. , Kamijo Yuki , Boisvert Marc , Paquet Marie-Eve , Drobizhev Mikhail , Podgorski Kaspar , Campbell Robert E.
Published: December 2022

l-Lactate is increasingly appreciated as a key metabolite and signaling molecule in mammals. To enable investigations of both the inter- and intra-cellular dynamics ofl-Lactate, we develop a second-generation green fluorescent extracellularl-Lactate biosensor, designated eLACCO2.1, and a red fluorescent intracellularl-Lactate biosensor, designated R-iLACCO1. Compared to the first-generation eLACCO1.1 (ΔF/F= 1.5 in cultured neurons), eLACCO2.1 exhibits better membrane localization and fluorescence response (ΔF/F= 8.1 in cultured neurons) with faster response kinetics to extracellularl-Lactate on the surface of live mammalian cells. R-iLACCO1 and its affinity variants exhibit large fluorescence responses to changes inl-Lactate concentrationin vitro(ΔF/F= 15 to 22) and in live mammalian cells (ΔF/F= 5.5 to 11). We demonstrate that these biosensors enable cellular-resolution imaging of extracellular and intracellularl-Lactate in cultured mammalian cells.
Effects of canagliflozin and irbesartan on renal fibrosis in Dahl salt-sensitive rats
Authors: Zhai Jianlong , Wang Zhongli , Zhang Tingting , He Lili , Ma Sai , Zuo Qingjuan , Zhang Guorui , Wang Xinyu , Guo Yifang
Published: December 2022

Hypertension is one of the major contributors to cardiovascular and chronic kidney disease (CKD). Sodium-glucose cotransporter 2 (SGLT2) inhibitors and angiotensin receptor blockers (ARBs) have become the preferred treatment for patients with CKD. However, the renoprotective effects of the combined therapy of the two drugs on hypertensive renal fibrosis are still largely understood. The aim of this study was to compare the antifibrotic effects of canagliflozin, with or without irbesartan, in the kidneys of Dahl salt-sensitive (Dahl SS) rats on a high salt (HS) diet. After the preconditioning stage, Dahl SS rats (n = 47) were divided into 5 experimental groups as follows: low salt control (n=7), HS control (n=10), high salt with canagliflozin (n=10), high salt with irbesartan (n=10), and high salt with canagliflozin plus irbesartan (n=10). Mean food and water intake, body weight (BW), and systolic blood pressure (SBP) were measured during the whole experimental period. After 12 weeks, the rats were euthanized, and the kidneys were excised for histomorphometric evaluation and immunohistochemical evaluation. An HS diet increased SBP, renal fibrosis, expression of fibrotic protein factors, and TGF-β/Smad2/3 pathway compared to the LS group. We found that irbesartan reduced SBP and slowed the loss of renal function. Canagliflozin significantly reduced BW and renal fibrosis and downregulated the TGF-β/Smad2/3 pathway. The combined therapy showed better renoprotection in all outcome parameters. In conclusion, these results indicate that canagliflozin and irbesartan exert different benefits on nephroprotection in salt-sensitive hypertensive rats.
Muscle function during locomotion on skis at varying speed and incline conditions
Authors: Werkhausen Amelie , Lundervold Anders , Gløersen Øyvind
Published: December 2022

The human musculoskeletal system is well adapted to use energy efficient muscle-tendon mechanics during walking and running but muscle behaviour during on-snow locomotion is unknown. Therefore, we examined muscle and muscle-tendon unit behaviour during diagonal style roller skiing at three speed and incline conditions.

We assessed lower leg muscle and muscle-tendon unit mechanics and muscle activity in thirteen high-level skiers during treadmill roller skiing using synchronised ultrasound, motion capture, electromyography and ski-binding force measurements. Participants skied using diagonal style at 2.5 and 3.5 m·s−1at 5°, and at 2.5 m·s−1at 10°.

We found an uncoupling of muscle and joint behaviour during most parts of the propulsive kick phase in all conditions (P<0.01). Gastrocnemius muscle fascicles actively shortened ~9 mm during the kick phase, while the muscle-tendon unit went through a stretch-shortening cycle. Peak muscle-tendon unit shortening velocity was five times higher than fascicle velocity (375 vs 74 mm·s−1,P<0.01). Increased incline was met by greater muscle activity (24%,P=0.04) and slower fascicle shortening velocities (34 vs. 45 mm·s−1,P<0.01). Increased speed was met by greater peak muscle activity (23%,P<0.01) and no change in fascicle shortening velocity.

Our data show that muscle behaviour was uncoupled from the joint movement, which enables beneficial contractile conditions and energy utilisation during diagonal style at different slopes and speeds. Active preloading in the end of the glide phase may benefit the mechanisms.

Summary statement

We examined muscle function during diagonal style cross country skiing in competitive cross-country skiers. Our data show an uncoupling of muscle and joint behaviour in the lower leg during skiing.
ISG15-modification of the Arp2/3 complex restricts pathogen spread
Authors: Zhang Yifeng , Ripley Brittany , Ouyang Wei , Sturtz Miranda , Upton Ellen , Luhmann Emma , Vessely Madeleine , Coloma Rocio , Schwery Nathan , Anthony Scott M. , Goeken Adam , Moninger Thomas O. , Harty John T. , Klingelhutz Aloysius , Lundberg Emma , Meyerholz David K. , Manicassamy Balaji , Stipp Christopher , Guerra Susana , Radoshevich Lilliana
Published: December 2022

The ubiquitin-like protein, ISG15, can act as a cytokine or can covalently modify host and pathogen-derived proteins. The consequences of ISG15 modification on substrate fate remain unknown. Here we reveal that ISGylation of the Arp2/3 complex slows actin filament formation and stabilizes Arp2/3 dependent structures including cortical actin and lamella. When properly controlled, this serves as an antibacterial and antiviral host defense strategy to directly restrict actin-mediated pathogen spread. However,Listeria monocytogenestakes advantage in models of dysregulated ISGylation, leading to increased mortality due to augmented spread. The underlying molecular mechanism responsible for the ISG15-dependent impact on actin-based motility is due to failed bacterial separation after division. This promotes spread by enabling the formation of multi-headed bacterial “bazookas” with stabilized comet tails that can disseminate deeper into tissues. A bacterial mutant that cannot recruit Arp2/3 or a non-ISGylatable mutant of Arp3 is sufficient to rescue slowed comet tail speed and restrict spread. Importantly, ISG15-deficient neonatal mice have aberrant epidermal epithelia characterized by keratinocytes with diffuse cortical actin, which could underlie observed defects in wound healing in human patients who lack ISG15. Ultimately, our discovery links host innate immune responses to cytoskeletal dynamics with therapeutic implications for viral infection and metastasis.
Viral and host small RNA transcriptome analysis of SARS-CoV-1 and SARS-CoV-2-infected human cells reveals novel viral short RNAs
Authors: Driedonks Tom , Nyberg Lyle H. , Conte Abigail , Ma Zexu , Pekosz Andrew , Duban Eduard , Sültmann Holger , Turchinovich Andrey , Witwer Kenneth
Published: December 2022

RNA viruses have been shown to express various short RNAs, some of which have regulatory roles during replication, transcription, and translation of viral genomes. However, short viral RNAs (svRNAs) generated by SARS-CoV-1 and SARS-CoV-2 remained largely unexplored, mainly due limitations of the widely used library preparation methods for small RNA deep sequencing and corresponding data processing. By analyzing publicly available small RNA-seq datasets, we observed that human cells infected by SARS-CoV-1 or SARS-CoV-2 produce multiple short viral RNAs (svRNAs), ranging in size from 15 to 26 nt and deriving predominantly from (+) RNA strands. In addition, we verified the presence of the five most abundant SARS-CoV-2 svRNAs in SARS-CoV-2-infected human lung adenocarcinoma cells by qPCR. Interestingly, the copy number of the observed SARS-CoV-2 svRNAs dramatically exceeded the expression of previously reported viral miRNAs in the same cells. We hypothesize that the reported SARS-CoV-2 svRNAs could serve as biomarkers for early infection stages due to their high abundance. Finally, we found that both SARS-CoV-1 and SARS-CoV-2 infection induced up- and down-regulation of multiple endogenous human short RNAs that align predominantly to protein-coding and lncRNA transcripts. Interestingly, a significant proportion of short RNAs derived from full-length viral genomes also aligned to various hg38 sequences, suggesting opportunities to investigate regulatory roles of svRNAs during infection. Further characterization of the small RNA landscape of both viral and host genomes is clearly warranted to improve our understanding of molecular events related to infection and to design more efficient strategies for therapeutic interventions as well as early diagnosis.
Biocontainment strategies forin vivoapplications ofSaccharomyces boulardii
Authors: Hedin Karl Alex , Kruse Vibeke , Vazquez-Uribe Ruben , Sommer Morten Otto Alexander
Published: December 2022

The human gastrointestinal tract is a complex and dynamic environment, playing a crucial role in human health. Microorganisms engineered to express a therapeutic activity have emerged as a novel modality to manage numerous diseases. Such advanced microbiome therapeutics (AMTs) must be contained within the treated individual. Hence safe and robust biocontainment strategies are required to prevent the proliferation of microbes outside the treated individual. Here we present the first biocontainment strategy for a probiotic yeast, demonstrating a multilayered strategy combining an auxotrophic and environmental-sensitive strategy. We knocked out the genesTHI6andBTS1, causing thiamine auxotrophy and increased sensitivity to cold, respectively. The biocontainedSaccharomyces boulardiiwas unable to grow in the absence of thiamine above 1 ng/mL and exhibited a severe growth defect at temperatures below 20°C. The biocontained strain was well tolerated and viable in mice and demonstrated equal efficiency in peptide production as the ancestral non-biocontained strain. In combination, the data support thatthi6Δ andbts1Δ enable biocontainment ofS. boulardii, which could be a relevant chassis for future yeast-based AMTs.
Validation of the EEG signal of the URGOnight neurofeedback device, associated with a new SMR detection method
Authors: Saulnier Rudy , Spiluttini Béatrice , Touré-Cuq Emma , Benchenane Karim
Published: December 2022

Sensorimotor (SMR) neurofeedback is a promising therapy for several health disorders but is still not widely used due to the high cost of the equipment. URGOnight offers a low-cost solution to democratize these therapies by providing an at-home EEG headband with dry electrodes connected to a mobile application. The first aim of this study is both to validate the URGOnight EEG signal and to compare it to Enobio-20, a medical grade EEG device. The second aim of the study is to propose a new method to detect SMR rhythm based on its oscillatory properties and discriminate it from alpha oscillations.

In our study, we compared the URGOnight headband EEG signal (C3/C4) to Enobio-20 (CP3/CP4), placed on subjects simultaneously equipped with the two headbands. All subjects (n=33) performed a dual blocking task inspired by Kulhman (1978) based on the blocking effect of movement and eyes opening on SMR and alpha respectively. This task was followed by SSVEP stimulations to evaluate the frequency response of the two EEG devices. The performance of the EEG headbands was statistically identical for most of the characteristics of the EEG signal, including the frequency response to SSVEP (from 4Hz to 20Hz). The main difference was a larger amplitude in the 8-15Hz due to the location of the reference in URGOnight that did not impair the detection of both alpha and SMR.

In addition, we show that our new method allows to discriminate alpha and SMR rhythms based on their oscillatory properties with a single recording site (C3/C4). The method is fast enough to be used in real time. We show that the detected SMR rhythm is modulated by movement as opposed to the 12-15Hz frequency band often used as indicator of SMR in most neurofeedback studies.

Altogether, our results validate the quality of the EEG recordings obtained with URGOnight since it gives similar results as the one obtained with Enobio-20, a validated EEG medical grade system. In addition, we provide a new method allowing the identification and the separation of the alpha and SMR with a single recording site C3/C4. This method opens up a new research lead to improve SMR neurofeedback efficiency and thus of its clinical possibilities by focusing on the reinforcement of the SMR oscillation strictly speaking.

Highlights

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Validation of the URGOnight EEG device suitable for neurofeedback at home

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New method for the detection and the discrimination of alpha rhythm and SMR rhythm with a small number of recording sites

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The oscillatory activity related to the SMR displays different properties compared to the 12-15Hz frequency band.

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Description of a full validation procedure for wireless EEG devices usable at home for neurofeedback

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Comparison of the signal of URGOnight (dry electrodes) with a wet electrode EEG device
Social defeat induces REM sleep fragmentation through the PFC-VLPO pathway
Authors: Chouvaeff M. , Bagur S. , Mace L. , Gallopin T. , Benchenane K.
Published: December 2022

The brainstem and hypothalamic structures implementing the daily cycles of wake, REM and NREM sleep have now been identified in remarkable detail. However, sleep structure dynamically adapts to environmental stressors, likely requiring top-down cortical feedback that is as yet unidentified. Here, we investigate the role of projections from prefrontal cortex (PFC), a key hub in stress regulation, to the ventro-lateral preoptic areas (VLPO), a master regulator of sleep states. Usingex vivooptogenetics, we demonstrate that activation of PFC terminals induces monosynaptic excitatory glutamatergic currents in VLPO NREM-promoting neurons.In vivo, activation of PFC-VLPO projections interrupts ongoing REM in favour of NREM, leading to fragmented REM bouts. Remarkably, chemogenetic inhibition of PFC-VLPO projections has no effect in baseline conditions but it blocks the REM fragmentation induced by Social Defeat Stress. Therefore, the PFC-VLPO pathway provides a top-down regulation specifically recruited in stressful conditions to induce short, fragmented REM bouts and favor NREM sleep.
A microscopic investigation of the effect of random envelope fluctuations on phoneme-in-noise perception
Authors: Osses Alejandro , Varnet Léo
Published: December 2022

In this study, we investigated the effect of specific noise realizations on the discrimination of two consonants, /b/ and /d/. For this purpose, we collected data from twelve participants, who listened to the words /aba/ or /ada/ embedded in one of three background noises. All noises had the same long-term spectrum but differed in the amount of random envelope fluctuations. The data were analyzed on a trial-by-trial basis using the reverse-correlation method. The results revealed that it is possible to predict the categorical responses with better-than-chance accuracy purely based on the spectro-temporal distribution of the random envelope fluctuations of the corresponding noises, without taking into account the actual targets or the signal-to-noise ratios used in the trials. The effect of the noise fluctuations explained on average 8.1% of the participants’ responses in white noise, a proportion that increased up to 13.3% for noises with a larger amount of fluctuations. The estimated time-frequency weights revealed that the measured effect originated from confusions between noise fluctuations and relevant acoustic cues from the target words. Substantially similar conclusions were obtained from simulations using an artificial listener. We argue that this token-specific effect of noise is a form of informational masking.