bluuebunny/crossref_metadata_2025 huggingface dataset:
Immotile cilia of the mouse node sense a fluid flow–induced mechanical force for left-right symmetry breaking
Authors: Katoh Takanobu A. , Omori Toshihiro , Mizuno Katsutoshi , Sai Xiaorei , Minegishi Katsura , Ikawa Yayoi , Nishimura Hiromi , Itabashi Takeshi , Kajikawa Eriko , Hiver Sylvain , Iwane Atsuko H. , Ishikawa Takuji , Okada Yasushi , Nishizaka Takayuki , Hamada Hiroshi
Published: April 2022

Immotile cilia of crown cells at the node of mouse embryos are required for sensing of a leftward fluid flow1 that gives rise to the breaking of left-right (L-R) symmetry2. The flow-sensing mechanism has long remained elusive, however, with both mechanosensing and chemosensing models having been proposed1, 3–5. Here we show that immotile cilia at the mouse node respond to mechanical force. In the presence of a leftward flow, immotile cilia on the left side of the node bend toward the ventral side whereas those on the right side bend toward the dorsal side. Application of mechanical stimuli to immotile cilia along the dorsoventral axis by optical tweezers induced Ca2+ transients and degradation of Dand5 mRNA—the first known L-R asymmetric molecular events—in the targeted cells. The Pkd2 channel protein was found to be preferentially localized to the dorsal side of immotile cilia on both left and right sides of the node, and the observed induction of Ca2+ transients preferentially by mechanical stimuli directed toward the ventral side could explain the differential response of immotile cilia to the directional flow. Our results thus suggest that immotile cilia at the node sense the direction of fluid flow in a manner dependent on a flow-generated mechanical force.
Single sample pathway analysis in metabolomics: performance evaluation and application
Authors: Wieder Cecilia , Lai Rachel PJ , Ebbels Timothy
Published: April 2022

Single sample pathway analysis (ssPA) transforms molecular level omics data to the pathway level, enabling the discovery of patient-specific pathway signatures. Compared to conventional pathway analysis, ssPA overcomes the limitations by enabling multi-group comparisons, alongside facilitating numerous downstream analyses such as pathway-based machine learning. While in transcriptomics ssPA is a widely used technique, there is little literature evaluating its suitability for metabolomics. Here we provide a thorough benchmark of established ssPA methods (ssGSEA, GSVA, SVD (PLAGE), and z-score) using semi-synthetic metabolomics data, alongside the evaluation of two novel methods we propose: ssClustPA and kPCA. While GSEA-based and z-score methods outperformed the others in terms of recall, clustering/dimensionality reduction-based methods provided higher precision at moderate-to-high effect sizes. A case study applying ssPA to inflammatory bowel disease demonstrates how these methods yield a much richer depth of interpretation than conventional approaches, for example by clustering pathway scores to visualise a pathway-based patient subtype-specific correlation network. We also developed the sspa python package (freely available at https://pypi.org/project/sspa/), providing implementations of all the methods benchmarked in this study. This work underscores the value ssPA methods can add to metabolomic studies and provides a useful reference for those wishing to apply ssPA methods to metabolomics data.

Author summary

Pathway analysis is a computational method used to draw insights from omics data by identifying groups of molecules (biological pathways) which are important in a study. Single-sample pathway analysis is based on the same principles as conventional pathway analysis but allows researchers to compute the enrichment of pathways at an individual-sample level. This enables pathway-based patient stratification and facilitates a multitude of downstream analyses based on pathways, such as machine learning, or pathway-based visualization which would not be possible using conventional approaches. In this work we investigated the application of single-sample pathway analysis to metabolomics data, a field in which it has not been widely used to date. We first evaluated the most popular methods for single-sample pathway analysis using simulated metabolomics data, as well as two novel methods we developed. Following these tests, we used metabolomics data from inflammatory bowel disease patients to demonstrate how single-sample pathway analysis methods can be used to infer novel pathway-based insights with the advantage of discriminating between disease subtypes. Overall, our analysis provides readers with information on the performance of single-sample pathway analysis methods, whilst highlighting the potential of such methods in metabolomics research.
Spatial Models of Pattern Formation During Phagocytosis
Authors: Herron J. Cody , Hu Shiqiong , Liu Bei , Watanabe Takashi , Hahn Klaus M. , Elston Timothy C.
Published: April 2022

Phagocytosis, the biological process in which cells ingest large particles such as bacteria, is a key component of the innate immune response. Fcγ receptor (FcγR)-mediated phagocytosis is initiated when these receptors are activated after binding immunoglobulin G (IgG). Receptor activation initiates a signaling cascade that leads to the formation of the phagocytic cup and culminates with ingestion of the foreign particle. In the experimental system termed “frustrated phagocytosis”, cells attempt to internalize micropatterned disks of IgG. Cells that engage in frustrated phagocytosis form “rosettes” of actin-enriched structures called podosomes around the IgG disk. The mechanism that generates the rosette pattern is unknown. We present data that supports the involvement of Cdc42, a member of the Rho family of GTPases, in pattern formation. Cdc42 acts downstream of receptor activation, upstream of actin polymerization, and is known to play a role in polarity establishment. Reaction-diffusion models for GTPase spatiotemporal dynamics exist. We demonstrate how the addition of negative feedback and minor changes to these models can generate the experimentally observed rosette pattern of podosomes. We show that this pattern formation can occur through two general mechanisms. In the first mechanism, an intermediate species forms a ring of high activity around the IgG disk, which then promotes rosette organization. The second mechanism does not require initial ring formation but relies on spatial gradients of intermediate chemical species that are selectively activated over the IgG patch. Finally, we analyze the models to suggest experiments to test their validity.

Author Summary

Phagocytosis, the process by which cells ingest foreign bodies, plays an important role in innate immunity. Phagocytosis is initiated when antibodies coating the surface of a foreign body are recognized by immune cells, such as macrophages. To study early events in phagocytosis, we used “frustrated phagocytosis”, an experimental system in which antibodies are micropatterned in disks on a cover slip. The cytoskeleton of cells attempting to phagocytose these disks organizes into “rosette” patterns around the disks. To investigate mechanisms that underlie rosette formation we turned to mathematical modeling based on reaction-diffusion equations. Building on existing models for polarity establishment, our analysis revealed two mechanisms for rosette formation. In the first scenario an initial ring of an intermediate signaling molecule forms around the disk, while in the second scenario rosette formation is driven by gradients of positive and negative pathway regulators that are activated over the disk. Finally, we analyze our models to suggest experiments for testing these mechanisms.
Health behaviours the month prior to COVID-19 infection and the development of self-reported long COVID and specific long COVID symptoms: A longitudinal analysis of 1,811 UK adults
Authors: Paul Elise , Fancourt Daisy
Published: April 2022

Background

Demographic and infection-related characteristics have been identified as risk factors for long COVID, but research on the influence of health behaviours (e.g., exercise, smoking) immediately preceding the index infection is lacking.

Methods

1,811 UK adults from the UCL COVID-19 Social Study and who had previously been infected with COVID-19 were analysed. Health behaviours in the month before infection were weekly exercise frequency, days of fresh air per week, sleep quality, smoking, consuming more than the number of recommended alcoholic drinks per week (>14), and the number of mental health care behaviours (e.g., online mental health programme). Logistic regressions controlling for covariates (e.g., COVID-19 infection severity and pre-existing health conditions) examined the impact of health behaviours on long COVID and three long COVID symptoms (difficulty with mobility, cognition, and self-care).

Results

In the month before infection with COVID-19, poor quality sleep increased the odds of long COVID (odds ratio [OR]: 3.53; (95% confidence interval [CI]: 2.01 to 6.21), as did average quality sleep (OR: 2.44; 95% CI: 1.44 to 4.12). Having smoked (OR: 8.39; 95% CI: 1.86 to 37.91) increased and meeting recommended weekly physical activity guidelines (3+ hours) (OR: 0.05; 95% CI: 0.01 to 0.39) reduced the likelihood of difficulty with self-care (e.g., washing all over or dressing) amongst those with long COVID.

Conclusion

Results point to the importance of sleep quality for long COVID, potentially helping to explain previously demonstrated links between stress and long COVID. Results also suggest that exercise and smoking may be modifiable risk factors for preventing the development of difficulty with self-care.

Funding

The Nuffield Foundation [WEL/FR-000022583], the MARCH Mental Health Network funded by the Cross-Disciplinary Mental Health Network Plus initiative supported by UK Research and Innovation [ES/S002588/1], and the Wellcome Trust [221400/Z/20/Z and 205407/Z/16/Z].

What is already known on the topic

Long COVID is rapidly becoming a public health concern. Although existing evidence to date has identified health characteristics such as obesity as risk factors, hardly any research on modifiable risk factors such as health behaviours has been conducted.

What this study adds

This study adds to the dearth of evidence on modifiable risk factors occurring before COVID-19 infection. Findings suggest a role of poor sleep quality for the development of long COVID, and for meeting physical activity guidelines (3+ hours per week) and not smoking as modifiable risk factors for self-care difficulties amongst those with long COVID.
Change in methicillin-resistant Staphylococcus aureus testing in the Intensive Care Unit as an antimicrobial stewardship initiative
Authors: Smith Hayden L. , DuMontier Samuel P. , Bushman Amanda M. , Hurdelbrink Jonathan R. , Yost William J. , Craig Steven R.
Published: April 2022

Background

Methicillin-resistant Staphylococcus aureus (MRSA) associated infections are a cause of morbidity/mortality in the Intensive Care Unit (ICU). Vancomycin is an option for treatment but is not without its own risks.

Purpose

To institute a testing change to decrease time between ordering of MRSA tests and availability of results in patients admitted to the adult ICU.

Procedures

A MRSA testing change was implemented at two adult (i.e., tertiary and community) ICUs located in a U.S. Midwestern health system. The change was implemented in 2018 and included the switch from culture to polymerase chain reaction (PCR) in ICU admitted patients. Study data were collected from 2016-2020 and a Bayesian quantile regression model was fit to examine median level change in time to results and to calculate a counterfactual estimate.

Main Findings

During the 58-month period, 71% of 19,975 patients seen at the two ICUs received MRSA testing. In the pre-change period, 91% and 99% of patients at the tertiary and community hospitals received testing via culture, respectively. Culture was used 1% and ∼0% of the time at the hospitals in the post-change period. The counterfactual estimated 36 (95% CrI: 35, 37) and 32 fewer hours (95% CrI: 31, 33) until results were available at the tertiary and community hospital, respectively.

Conclusions

Study revealed MRSA results were available in less time at both facilities after testing change. This information can aid anti-microbial stewardship via possibly delaying initiation and/or quicker de-escalation of therapy when results are known.
Metabolic-imaging of human glioblastoma live tumors: a new precision-medicine approach to predict tumor treatment response early
Authors: Morelli Mariangela , Lessi Francesca , Barachini Serena , Liotti Romano , Montemurro Nicola , Perrini Paolo , Santonocito Orazio Santo , Gambacciani Carlo , Snuderl Matija , Pieri Francesco , Aquila Filippo , Farnesi Azzurra , Naccarato Antonio Giuseppe , Viacava Paolo , Cardarelli Francesco , Ferri Gianmarco , Mulholland Paul , Ottaviani Diego , Paiar Fabiola , Liberti Gaetano , Pasqualetti Francesco , Menicagli Michele , Aretini Paolo , Signore Giovanni , Franceschi Sara , Mazzanti Chiara Maria
Published: April 2022

Background

Glioblastoma (GB) is the most severe form of brain cancer, with a 12-15 month median survival. Surgical resection, temozolomide (TMZ) treatment, and radiotherapy (RT) remain the primary therapeutic options for GB, and no new therapies have been introduced in recent years. This therapeutic standstill is primarily due to preclinical approaches that do not fully respect the complexity of GB cell biology and fail to test efficiently anti-cancer treatments. Therefore, better treatment screening approaches are needed. In this study, we have developed a novel functional precision medicine approach to test the response to anticancer treatments in organoids derived from the resected tumors of glioblastoma patients.

Methods

GB organoids were grown for a short period of time to prevent any genetic and morphological evolution and divergence from the tumor of origin. We chose metabolic imaging by NAD(P)H fluorescence lifetime imaging microscopy (FLIM) to predict early and non-invasively ex-vivo anti-cancer treatment responses of GB organoids. TMZ was used as the benchmark drug to validate the approach. Whole-transcriptome and whole-exome analyses were then performed to characterize tumor cases stratification.

Results

Our functional precision medicine approach was completed within one week after surgery and two groups of TMZ Responder and Non Responder tumors were identified. FLIM-based metabolic tumor stratification was well-reflected at the molecular level, confirming the validity of our approach, highlighting also new target genes associated with TMZ treatment and identifying a new 17 gene molecular signature associated with survival. The number of promoter methylated tumors for the MGMT gene was higher in the responsive group, as expected, however, some non-methylated tumor cases turned out to be nevertheless responsive to TMZ, suggesting that our procedure could be synergistic with the classical MGMT methylation biomarker.

Conclusions

For the first time, FLIM-based metabolic imaging was used on ex-vivo live glioblastoma organoids. Unlike other approaches, ex-vivo patient-tailored drug response is performed at an early stage of tumor culturing with no animal involvement and with minimal tampering with the original tumor cytoarchitecture. This functional precision medicine approach can be exploited in a range of clinical and laboratory settings to improve the clinical management of GB patients and implemented on other cancers as well.
Axonal plasticity in response to active forces generated through magnetic nanopulling
Authors: Falconieri Alessandro , De Vincentiis Sara , Cappello Valentina , Convertino Domenica , Ghignoli Samuele , Figoli Sofia , Luin Stefano , Català-Castro Frederic , Marchetti Laura , Borello Ugo , Krieg Michael , Raffa Vittoria
Published: April 2022

Mechanical force is crucial in guiding axon outgrowth, before and after synapse formation. This process is referred to as “stretch-growth”. However, how neurons transduce mechanical inputs into signaling pathways remains poorly understood. Another open question is how stretch-growth is coupled in time with the intercalated addition of new mass along the entire axon. Here, we demonstrate that active mechanical force generated by magnetic nano-pulling induces a remodeling of the axonal cytoskeleton. Specifically, the increase in the axonal density of microtubules leads to an accumulation of organelles and signaling vesicles which, in turn, promotes local translation by increasing the probability of assembly of the “translation factories”. The modulation of axonal transport and local translation sustains enhanced axon outgrowth and synapse maturation.
Inverse Material Parameter Estimation of Patient Specific Finite Element Models at the Carotid Bifurcation: The Impact of Excluding the Zero Pressure Configuration and Residual Stress
Authors: Johnston R. D , Ghasemi M. , Lally C.
Published: April 2022

Abstract Summary

The carotid bifurcation experiences a complex loading environment due to its anatomical structure. Previousin-vivomaterial parameter estimation methods often use simplified model geometries, isotropic hyperelastic constitutive equations or neglect key aspects of the vessel, such as the zero-pressure configuration or residual stress. These factors have independently been shown to alter the stress environment of the vessel wall. Characterising the location of high stress in the vessel wall has often been proposed as a potential indicator of structural weakness. However, excluding the afore-mentioned zero-pressure configuration, residual stress and patient specific material parameters can lead to an incorrect estimation of the true stress values observed, meaning stress alone as a risk indicator of rupture is insufficient. In this study, we investigate how the estimated material parameters and overall stress distributions in geometries of carotid bifurcations, extracted fromin-vivoMR images, alter with the inclusion of the zero-pressure configuration and residual stress.

This approach consists of the following steps: (1) geometry segmentation and hexahedral meshing fromin-vivoMRI images at two known phases; (2) computation of the zero-pressure configuration and the associated residual stresses; (3) minimisation of an objective function built on the difference between the stress states of an “ almost true” stress field at two known phases and a “deformed” stress field by altering the input material parameters to determine patient specific material properties; and (4) comparison of the stress distributions throughout these carotid bifurcations for all cases with estimated material parameters. This numerical approach provides insights into the need for estimation of both the zero-pressure configuration and residual stress for accurate material property estimation and stress analysis for the carotid bifurcation, establishing the reliability of stress as a rupture risk metric.

Graphical Abstract
Stably bound adaptor proteins modulate directionality of RNP transport
Authors: Phea Ly Jane , Ephrussi Anne
Published: April 2022

Kinesin-1 and cytoplasmic dynein are molecular motors that mediate long range transport of cargoes along the microtubule cytoskeleton. oskar RNA has been documented to switch between the motors during its localization in the Drosophila germline syncytium. oskar RNA undergoes dynein-mediated transport from the transcriptionally active nurse cells into the oocyte, following which the RNA translocates via kinesin to the posterior pole. Adaptor proteins link the RNA to its motors: the Egalitarian-Bicaudal-D complex links dynein to oskar RNA for the initial phase of transport, whereas atypical Tropomyosin 1 (aTm1) links kinesin-1 to oskar RNA for the latter phase. Components of the Exon Junction Complex (EJC) as well as the SOLE, a stem loop formed upon splicing of oskar RNA, have also been found to be necessary for kinesin-mediated transport of oskar RNA. In this study, to dissect the minimal elements required for kinesin-based transport, we tethered aTm1 or kinesin-1 to oskar RNA constructs lacking the SOLE. Our results suggest that stably bound aTm1 can indeed bypass the SOLE and EJC to mediate kinesin-1 activity, but the effects of tethered aTm1 are less potent than that of tethered kinesin-1. We also tethered Bicaudal-D to oskar RNA, to test whether this would affect kinesin-directed transport of oskar RNA, and found that tethered Bicaudal-D directs dynein mediated localization. Our results show that activated Bicaudal-D, along with the recruited dynein, is sufficient for dynein activity. We also show that stable binding of kinesin-1 to the RNA cargo is sufficient for strong kinesin-1 activity. Stably bound aTm1, meanwhile, can only mediate mild kinesin activity, suggesting that other factors may be required to stabilize the binding of kinesin-1 to the RNA cargo.
A systematic examination of learning in the invasive antLinepithema humilereveals very rapid development of short and long-term memory
Authors: Wagner Thomas , Galante Henrique , Josens Roxana , Czaczkes Tomer J.
Published: April 2022

The Argentine ant (Linepithema humile) is one of the most damaging and widespread invasive ant species worldwide. However, control attempts often fail due to bait rejection or insufficient bait uptake. Increasing preference for, and consumption of, bait is thus an important requirement for successful control. Learning and within-nest information transfer might be a potential tool for achieving this goal. We conducted a systematic investigation of olfactory learning and route learning in Argentine ants. The ants showed very strong and rapid route learning, choosing the correct arm in a Y-maze 65% of time after just one visit, and 84% correct after two. Odour learning was even more rapid, reaching up to 85% correct choices after just one exposure to flavoured food. Learning is long-lasting, with 73% correct choices after 48h. Food flavour information is transferred efficiently between nestmates in the nest, driving preference: naïve ants housed with ants fed on flavoured food show a strong preference (77%) for that odour after 24h. Overall,Linepithema humileare outstanding learners. This, coupled with efficient intranidal information transfer and strong pheromonal recruitment, may help explain their ability to discover and then dominate resources. However, these strengths could potentially be used against them, by exploiting learning and information transfer to increase toxic bait uptake. Steering ant preference by leveraging learning might be an underappreciated tool in invasive alien species control.
From individual behaviors to collective outcomes: fruiting body formation in Dictyostelium as a group-level phenotype
Authors: Kuzdzal-Fick Jennie F. , Moreno Armando , Broersma Cathleen M.E. , Cooper Tim F. , Ostrowski Elizabeth A.
Published: April 2022

Collective phenotypes, which arise from the interactions among individuals, can be important for the evolution of higher levels of biological organization. However, how a group’s composition determines its collective phenotype remains poorly understood. When starved, cells of the social amoeba Dictyostelium discoideum cooperate to build a multicellular fruiting body, and the morphology of the fruiting body is likely advantageous to the surviving spores. We assessed how the number of strains, as well as their genetic and geographic relationships to one another, impact the group’s morphology and productivity. We find that some strains consistently enhance or detract from the productivity of their groups, regardless of the identity of the other group members. We also detect extensive pairwise and higher-order genotype interactions, which collectively have a large influence on the group phenotype. Whereas previous work in Dictyostelium has focused almost exclusively on whether spore production is equitable when strains cooperate to form multicellular fruiting bodies, our results suggest a previously unrecognized impact of chimeric co-development on the group phenotype. Our results demonstrate how interactions among members of a group influence collective phenotypes and how group phenotypes might in turn impact selection on the individual.
Proximal Exploration for Model-guided Protein Sequence Design
Authors: Ren Zhizhou , Li Jiahan , Ding Fan , Zhou Yuan , Ma Jianzhu , Peng Jian
Published: April 2022

Designing protein sequences with a particular biological function is a long-lasting challenge for protein engineering. Recent advances in machine-learning-guided approaches focus on building a surrogate sequence-function model to reduce the burden of expensive in-lab experiments. In this paper, we study the exploration mechanism of model-guided sequence design. We leverage a natural property of protein fitness landscape that a concise set of mutations upon the wild-type sequence are usually sufficient to enhance the desired function. By utilizing this property, we propose Proximal Exploration (PEX) algorithm that prioritizes the evolutionary search for high-fitness mutants with low mutation counts. In addition, we develop a specialized model architecture, called Mutation Factorization Network (MuFacNet), to predict low-order mutational effects, which further improves the sample efficiency of model-guided evolution. In experiments, we extensively evaluate our method on a suite of in-silico protein sequence design tasks and demonstrate substantial improvement over baseline algorithms.
Cryo-EM structure of an atypical proton-coupled peptide transporter: Di- and tripeptide permease C
Authors: Killer Maxime , Finocchio Giada , Mertens Haydyn D.T. , Svergun Dmitri I. , Pardon Els , Steyaert Jan , Löw Christian
Published: April 2022

Proton-coupled Oligopeptide Transporters (POTs) of the Major Facilitator Superfamily (MFS) mediate the uptake of short di- and tripeptides in all phyla of life. POTs are thought to constitute the most promiscuous class of MFS transporters, with the potential to transport more than 8400 unique substrates. Over the past two decades, transport assays and biophysical studies have shown that various orthologues and paralogues display differences in substrate selectivity. The E. coli genome codes for four different POTs, known as Di- and Tripeptide permeases A-D (DtpA-D). DtpC was shown previously to favor positively charged peptides as substrates. In this study, we describe, how we determined the structure of the 53 kDa DtpC by cryogenic electron microscopy (cryo-EM), and provide structural insights into the ligand specificity of this atypical POT. We collected and analyzed data on the transporter fused to split superfolder GFP (split sfGFP), in complex with a 52 kDa macrobody and with a 13 kDa nanobody. The latter sample was more stable, rigid and a significant fraction dimeric, allowing us to reconstruct a 3D volume of DtpC at a resolution of 2.7 Å. This work provides a molecular explanation for the selectivity of DtpC, and highlights the value of small and rigid fiducial markers such as nanobodies for structure determination of low molecular weight integral membrane proteins lacking soluble domains.
The SNARE Sec22b regulates phagosome maturation by promoting ORP8-mediated PI(4)P exchange at ER-phagosome contact sites
Authors: Santos Nina Criado , Bouvet Samuel , Bermont Flavien , Castelbou Cyril , Mansour Farah , Azam Maral , Giordano Francesca , Nunes-Hasler Paula
Published: April 2022

The precise control of phagosome maturation is critical for innate and adaptive immunity, determining whether phagocytosed material is destroyed or used to present antigens. We observed previously that non-fusogenic contacts between the endoplasmic reticulum (ER) and phagosomes, called membrane contact sites (MCS), are tethered by the calcium regulator STIM1 and fine-tune phagosomal maturation. The secretory pathway SNARE protein Sec22b has been implicated in controlling phagocytosis, phagosome maturation and antigen presentation, though its effects are controversial, and its mechanism of action poorly understood. Recently, Sec22b was shown to tether MCS at the plasma membrane without mediating membrane fusion. Here, we show that Sec22b localizes to and regulates the frequency of ER-phagosome contacts independently of STIM proteins. Sec22b knockdown and overexpression of a an MCS-disrupting mutant Sec22b-P33 induced only mild or no effect on global and local calcium signalling. However, Sec22b knockdown altered phagosomal phospholipids including PI(3)P, PI(4)P and PS, but not PI(4,5)P2. Increased PI(4)P in shSec22b cells was rescued by re-expression of Sec22b or the artificial MCS tether MAPPER but not the P33 mutant. Moreover, Sec22b co-precipitated and was co-recruited to phagosomes with the PS/PI(4)P lipid exchange protein ORP8. Expression of wild-type, but not mutant ORP8, also rescued phagosomal PI(4)P. Concordantly, Sec22b, MAPPER and ORP8 but not P33 or the ORP8 mutant decreased phagolysosome fusion in shSec22b cells. These results clarify a novel mechanism through which Sec22b controls phagosome maturation and beg a reassessment of the relative contribution of Sec22b-mediated fusion versus tethering to phagosome biology.
Model evolution in SARS-CoV-2 spike protein sequences using a generative neural network
Authors: Kumar Anup
Published: April 2022

Modelling evolutionary elements inherent in protein sequences, emerging from one clade into another of the SARS-CoV-2 virus, would provide insights to augment our understanding of its impact on public health and may help in formulating better strategies to contain its spread. Deep learning methods have been used to model protein sequences for SARS-CoV-2 viruses. A few significant drawbacks in these studies include being deficient in modelling end-to-end protein sequences, modelling only those genomic positions that show high activity and upsampling the number of sequences at each genomic position for balancing the frequency of mutations. To mitigate such drawbacks, the current approach uses a generative model, an encoder-decoder neural network, to learn the natural progression of spike protein sequences through adjacent clades of the phylogenetic tree of Nextstrain clades. Encoder transforms a set of spike protein sequences from the source clade (20A) into its latent representation. Decoder uses the latent representation, along with Gaussian distributed noise, to generate a different set of protein sequences that are closer to the target clade (20B). The source and target clades are adjacent nodes in the phylogenetic tree of different evolving clades of the SARS-CoV-2 virus. Sequences of amino acids are generated, for the entire length, at each genomic position using the latent representation of the amino acid generated at a previous step. Using trained models, protein sequences from the source clade are used to generate sequences that form a collection of evolved sequences belonging to all children clades of the source clade. A comparison of this predicted evolution (between source and generated sequences) of proteins with the true evolution (between source and target sequences) shows a high pearson correlation (> 0.7). Moreover, the distribution of the frequencies of substitutions per genomic position, including high- and low-frequency positions, in source-target sequences and source-generated sequences exhibit a high resemblance (pearson correlation > 0.7). In addition, the model partially predicts a few substitutions at specific genomic positions for the sequences of unseen clades (20J (Gamma)) where they show little activity during training. These outcomes show the potential of this approach in learning the latent mechanism of evolution of SARS-CoV-2 viral sequences.

Codebase

https://github.com/anuprulez/clade_prediction
Individual transcription factors modulate both the micromovement of chromatin and its long-range structure
Authors: Shaban Haitham A. , Friman Elias , Deluz Cédric , Tollenaere Armelle , Katanayeva Natalya , Suter David M.
Published: April 2022

The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear how nucleus-wide chromatin organization responds dynamically to the activity of specific TFs. Here we examined how two TFs with opposite effects on local chromatin accessibility modulate chromatin dynamics nucleus-wide. We combine High-resolution Diffusion mapping (Hi-D) and Dense Flow reConstruction and Correlation (DFCC) in living cells to obtain an imaging-based, nanometer-scale analysis of local diffusion processes and long-range coordinated movements of both chromatin and TFs. We show that the expression of either an individual transcriptional activator (CDX2) or repressor (SIX6) increases local chromatin mobility nucleus-wide, yet induces opposite coherent chromatin motions at the micron scale. Hi-C analysis of higher-order chromatin structures shows that induction of CDX2 leads to changes in local chromatin interactions and compartmentalization. These results thus document a close relation between chromatin dynamics on the microscale and changes in compartmental structures. Given that inhibition of transcription initiation and elongation by RNA Pol II have almost no impact on the global chromatin dynamics induced by CDX2, we suggest that CDX2 alters chromatin structures independently from transcription. Our biophysical analysis shows that sequence-specific TFs mobilize long-range chromatin structure on multiple levels, providing evidence that local chromatin changes brought about by TFs can alter both the dynamics and the long-range organization of chromatin in living cells.

Significance statement

In eukaryotes, DNA is embedded into a higher-order structure called chromatin that varies between a closed state that is inaccessible to DNA-binding proteins, and an open state that allows the assembly of the transcriptional machinery on DNA. The state of chromatin is dynamic and locally controlled by sequence-specific transcription factors (TFs). How local chromatin opening and closing initiated by TFs alter long-range dynamics of chromatin structures is unknown. Here we combine two nucleus-wide live-imaging techniques, Hi-D and DFCC, along with Hi-C (genomic analysis technique) to quantify both local and global chromatin dynamics, then to correlate these dynamics to structural changes. Our quantitative analysis reveals a differential impact of TFs in shaping and mobilizing long-range chromatin structures in living cells.
Modulation of Arabidopsis growth by volatile organic compounds from a root-derived bacterial community
Authors: Türksoy Gözde Merve , Carron Réjane , Koprivova Anna , Kopriva Stanislav , Wippel Kathrin , Andersen Tonni Grube
Published: April 2022

Plant roots are surrounded by fluctuating biotic and abiotic factors. The living component – the microbiota – is actively shaped by the plant and plays an important role in overall plant health. While it has been shown that specialized metabolites exuded from the plant are involved in shaping host interactions with the microbiota, it is unclear how underground volatile organic compounds (VOCs) influence this communication. This is especially true for root-associated bacteria which are known to release VOCs that can influence plant growth. Using a simplified synthetic bacterial community (SynCom) representing the phylogenetic diversity of bacteria in the root microbiome, we set out to characterize plant growth and defense metabolites when subjected to bacterial VOCs (bVOCs). Moreover, by profiling the SynCom community composition after co-cultivation with the plant, we explored how members of the community influenced each other in our growth setup. Our findings reveal that plant growth promotion can occur via VOCs from a bacterial SynCom, but that the plant response differs for individual community members. In addition, we find that bVOCs are able to repress chemical defense responses in the plant, possibly to facilitate colonization. By removing key species from the SynCom, we find that complex bacteria-bacteria interactions are likely to underlie this phenomenon, and that bVOC-induced modulation of plant responses in the rhizosphere may be an emergent property of bacterial communities rather than depending on individual species.
Machine learning-assisted fluoroscopy of bladder function in awake mice
Authors: De Bruyn Helene , Corthout Nikky , Munck Sebastian , Everaerts Wouter , Voets Thomas
Published: April 2022

Understanding the lower urinary tract (LUT) and development of highly needed novel therapies to treat LUT disorders depends on accurate techniques to monitor LUT (dys)function in preclinical models. We recently developed videocystometry in rodents, which combines intravesical pressure measurements with X-ray-based fluoroscopy of the LUT, allowing the in vivo analysis of the process of urine storage and voiding with unprecedented detail. Videocystometry relies on the precise contrast-based determination of the bladder volume at high temporal resolution, which can readily be achieved in anesthetized or otherwise motion-restricted mice but not in awake and freely moving animals. To overcome this limitation, we developed a machine-learning method, in which we trained a neural network to automatically detect the bladder in fluoroscopic images, allowing the automatic analysis of bladder filling and voiding cycles based on large sets of time-lapse fluoroscopic images (>3 hours at 30 images/second) from behaving mice and in a non-invasive manner. With this approach, we found that urethane, an injectable anesthetic that is commonly used in preclinical urological research, has a profound, dose-dependent effect on urethral relaxation and voiding duration and that implantation of a suprapubic catheter, as is standardly performed for cystometric analyses, leads to a ∼4-fold reduction in bladder capacity. Our findings provide a paradigm for the non-invasive, in vivo monitoring of a hollow organ in behaving animals and pinpoint important limitations of the current gold standard techniques to study the LUT in mice.
An Inhibitory Function of TRPA1 Channels in TGF-β1-driven Fibroblast to Myofibroblast Differentiation
Authors: Geiger Fabienne , Zeitlmayr Sarah , Staab-Weijnitz Claudia A. , Rajan Suhasini , Breit Andreas , Gudermann Thomas , Dietrich Alexander
Published: April 2022

Transient receptor potential ankyrin 1 (TRPA1) is a non-selective Ca2+ permeable cation channel, which was originally cloned from human lung fibroblasts (HLFs). TRPA1-mediated Ca2+ entry is evoked by exposure to several chemicals, including allyl isothiocyanate (AITC), and a protective effect of TRPA1 activation in the development of cardiac fibrosis has been proposed. Yet, the function of TRPA1 in transforming growth factor β1 (TGF-β1)-driven fibroblast to myofibroblast differentiation and the development of pulmonary fibrosis remains elusive. TRPA1 expression and function was analyzed in cultured primary HLFs, and mRNA levels were significantly reduced after adding TGF-β1. Expression of genes encoding fibrosis markers, e.g. alpha smooth muscle actin (ACTA2), plasminogen activator inhibitor 1 (SERPINE1), fibronectin (FN1) and type I collagen (COL1A1) was increased after siRNA-mediated down-regulation of TRPA1-mRNA in HLFs. Moreover, AITC-induced Ca2+ entry in HLFs was decreased after TGF-β1 treatment and by application of TRPA1 siRNAs, while AITC treatment alone did not reduce cell viability or enhanced apoptosis. Cell barrier function increased after addition of TRPA1 siRNAs or TGF-β1 treatment. Most interestingly, AITC-induced TRPA1 activation augmented ERK1/2 phosphorylation, which might inhibit TGF-β-receptor signaling. Our results suggest an inhibitory function of TRPA1 channels in TGF-β1-driven fibroblast to myofibroblast differentiation. Therefore, activation of TRPA1 channels might be protective during the development of pulmonary fibrosis in patients.
Differential gene expression underlying the biosynthesis of Dufour’s gland signals in Bombus impatiens
Authors: Derstine Nathan , Galbraith David , Villar Gabriel , Amsalem Etya
Published: April 2022

Pheromones regulating social behavior are one of the most explored phenomena in social insects. However, compound identity, biosynthesis and their genetic regulation are known in only a handful of species. Here we conducted chemical and RNA-seq analyses of the Dufour’s gland in the bumble bee Bombus impatiens and examined the signals and the pathways regulating signal production in queens and workers. Across Hymenopterans, the Dufour’s gland contains mostly long-chained hydrocarbons and esters that signal reproductive and social status in several bee species. In bumble bees, the Dufour’s gland contains queen- and worker-specific esters, in addition to terpenes and terpene-esters only found in gynes and queens. These compounds are assumed to be synthesized de novo in the gland, however, their genetic regulation is unknown. A whole transcriptome gene expression analysis of the gland in queens, gynes, queenless and queenright workers showed distinct transcriptomic profiles, with thousands of differentially expressed genes between the groups. Workers and queens express genes associated with key enzymes in the biosynthesis of wax esters, while queens and gynes preferentially express key genes in terpene biosynthesis. In contrast, no genes were differentially expressed in queenless and queenright workers, despite differences in their Dufour’s gland chemistry and reproductive state, suggesting the quantitative differences in worker secretion are not regulated at the level of production. Overall, our data demonstrate gland-specific regulation of chemical signals associated with social behavior and identifies genes and pathways regulating caste-specific chemical signals in social insects.
Calibration allows accurate estimation of the axonal volume fraction with diffusion MRI
Authors: Papazoglou Sebastian , Ashtarayeh Mohammad , Oeschger Jan Malte , Callaghan Martina F. , Does Mark D. , Mohammadi Siawoosh
Published: April 2022

Biophysical models enable the non-invasive estimation of microstructural tissue features of the central nervous system such as the axonal volume fraction using diffusion weighted imaging (DWI)-data. However, these models trade accuracy with complexity and demands for time-efficient data acquisition. In this study, we hypothesise that their accuracy can be improved substantially through biophysically motivated, linear calibration. We test this hypothesis in the context of axonal volume fraction estimation in four different DWI-models of different complexity using multi-modal data including ex-vivo diffusion MRI- and electron microscopy (EM)-data in mice with broad dynamic range, whereby the latter served as gold standard. We found that two calibration parameters, an offset accounting for the fraction of unmyelinated axons in severely hypomyelinated mice and a scaling accounting for the compartment-specific relaxation, substantially improved the accuracy of axonal volume fraction. Furthermore, we theoretically predict the scaling parameter, and demonstrate that similar accuracy improvement can be achieved for a subset of DWI-models, if the scaling parameter is fixed to the predicted value instead of estimating it on basis of data. This is of practical relevance because it allows to estimate the remaining offset calibration parameter from a limited amount of multi-modal data and thus makes the proposed method usable in human brain data.
Viral origin of eukaryotic type IIA DNA topoisomerases
Authors: Guglielmini Julien , Gaia Morgan , Da Cunha Violette , Criscuolo Alexis , Krupovic Mart , Forterre Patrick
Published: April 2022

Type II DNA topoisomerases of the family A (Topo IIA) are present in all bacteria (DNA gyrase) and eukaryotes. In eukaryotes, they play a major role in transcription, DNA replication, chromosome segregation and modulation of chromosome architecture. The origin of eukaryotic Topo IIA remains mysterious since they are very divergent from their bacterial homologues and have no orthologues in Archaea. Interestingly, eukaryotic Topo IIA have close homologues in viruses of the phylum Nucleocytoviricota, an expansive assemblage of large and giant viruses formerly known as the nucleocytoplasmic large DNA viruses (NCLDV). Topo IIA are also encoded by some bacterioviruses of the class Caudoviricetes (tailed bacteriophages). To elucidate the origin of the eukaryotic Topo IIA, we performed in-depth phylogenetic analyses combining viral and cellular Topo IIA homologs. Topo IIA encoded by bacteria and eukaryotes form two monophyletic groups nested within Topo IIA encoded by Caudoviricetes and Nucleocytoviricota, respectively. Importantly, Nucleocytoviricota remained well separated from eukaryotes after removing both bacteria and Caudoviricetes from the dataset, indicating that the separation of Nucleocytoviricota and eukaryotes is probably not due to long branch attraction artefact. The topology of our tree suggests that the eukaryotic Topo IIA was probably acquired from an ancestral member of the Nucleocytoviricota of the class Megaviricetes, before the emergence of the last eukaryotic common ancestor (LECA). This result further highlights a key role of these viruses in eukaryogenesis and suggests that early proto-eukaryotes used a Topo IIB instead of a Topo IIA for solving their DNA topological problems.
The cellular poly(rC)-binding protein 2 prevents the early steps of hepatitis C virus virion assembly
Authors: Cousineau Sophie E. , Sagan Selena M.
Published: April 2022

Poly(rC)-binding protein 2 (PCBP2) was previously shown to bind to the hepatitis C virus (HCV) genome; however, its precise role in the viral life cycle remained unclear. Herein, we found that PCBP2 does not directly affect viral entry, translation, genome stability, replication, or virion egress. Rather, our data suggests that endogenous PCBP2 normally limits virion assembly, thereby indirectly promoting translation and replication by increasing the translating/replicating pool of viral RNAs. Additionally, we found that an alternative RNA conformation (SLIIalt) was important for efficient virion assembly, but functions in a PCBP2-independent manner. The latter may explain why the Japanese fulminant hepatitis 1 isolate is able to produce infectious particles in cell culture, while other HCV isolates are lost in translation. Taken together, our results suggest that PCBP2 and SLIIaltindependently modulate HCV genome packaging and alter the balance of viral RNAs in the translating/replicating pool and those engaged in virion assembly.

Graphical Abstract