bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional diversity increases the resistance of a tritrophic food web to environmental changes
Authors: Adje George , Wojcik Laurie A. , Gaedke Ursula
Published: July 2022

In the light of global climate change and biodiversity loss, understanding the role of functional diversity in the response of food webs to environmental change is growing ever more important. Using a tritrophic food web model, with a variable degree of functional diversity at each trophic level, we studied the role of functional diversity on the resistance of a system against press perturbations affecting either nutrient availability or the mortality of the species, which can be interpreted as effects of eutrophication and warming respectively. We compared food webs with different levels of functional diversity by investigating the species trait and biomass dynamics, the overall changes in the species’ standing biomass as measured by the warping distance, and the duration of the system transients after the onset of a perturbation (transition time). We found that higher functional diversity increased resistance since it buffered trophic cascading effects and delayed the onset of oscillatory behaviour caused by either bottom-up forcing via perturbations to nutrient concentration or top-down forcing via perturbations to mortality rate. This increased resistance emerged from a higher top-down control of the intermediate species on the basal species. Functional diversity also promoted a higher top biomass, in particular via a higher proportion of top selective species undergoing high mortality rates. Additionally, functional diversity had context-dependent effects on warping distances, and increased transition times. Overall, this study encourages accounting for functional diversity in future investigations about the response of multitrophic systems to global change and in management strategies.
Fasting increases investment in soma upon refeeding at the cost of gamete quality in zebrafish
Authors: Ivimey-Cook Edward R , Murray David S. , de Coriolis Jean-Charles , Edden Nathan , Immler Simone , Maklakov Alexei A.
Published: July 2022

Fasting increases lifespan in invertebrates, improves biomarkers of health in vertebrates, and is increasingly proposed as a promising route to improve human health. Nevertheless, little is known about how fasted animals use resources upon refeeding, and how such decisions affect putative trade-offs between somatic growth and repair, reproduction, and gamete quality. Such fasting-induced trade-offs are based on strong theoretical foundations and have been recently discovered in invertebrates, but the data on vertebrates is lacking. Here we report that fasted female zebrafish, Danio rerio, increase investment in soma upon refeeding but it comes at a cost of egg quality.

Specifically, an increase in fin re-growth was accompanied by a reduction in 24-hours post-fertilization offspring survival. Refed males showed a reduction in sperm velocity and impaired 24-hour post-fertilisation offspring survival. These findings underscore the necessity of considering the impact on eggs and sperm when assessing evolutionary and biomedical implications of lifespan-extending treatments in females and males and call for careful evaluation of the effects of fasting (both during and post) on fertilisation.
Postural sway is not affected by estrogen fluctuations during the menstrual cycle
Authors: Reschechtko Sasha , Nguyen Thuy Ngoc , Tsang Michelle , Giltvedt Kristine , Kern Mark , Hooshmand Shirin
Published: July 2022

When people stand still, they exhibit a phenomenon called postural sway, or spontaneous movement of the body’s center of pressure, which is related to balance control. In general females show less sway than males, but this difference only begins to appear around puberty, pointing to different levels of sex hormones as one potential mechanism for sway sex differences. In this study, we followed one group of young females using oral contraceptives (n = 32) and one group not using oral contraceptives (n = 19), to investigate associations between estrogen availability and postural sway, both over the course of the menstrual cycle (in the group not using oral contraceptives) and long-term (between the two groups). All participants visited the lab four times over the putative 28-day menstrual cycle. At each visit, we performed blood draws to measure plasma estrogen (estradiol) levels, and tests of postural sway using a force plate. Due to the hormone-stabilizing effects of oral contraceptives, estradiol levels were higher in participants not using oral contraceptives (690.45 pmol/L versus 464.50 pmol/L), reflecting higher estradiol concentrations during the late follicular and luteal phase. Postural sway was similar on average for participants not using oral contraceptives (21.47 cm versus 23.56 cm). Overall, we found no significant effects of the estimated menstrual cycle phase – or absolute levels of estradiol – on postural sway.
RatesTools: a Nextflow pipeline for detecting de novo germline mutations in pedigree sequence data
Authors: Armstrong Ellie E. , Campana Michael G.
Published: July 2022

Here, we introduce RatesTools, an automated pipeline to infer de novo mutation rates from parent-offspring trio data of diploid organisms. By providing a reference genome and high-coverage, whole-genome resequencing data of a minimum of three individuals (sire, dam, offspring), RatesTools provides a list of candidate de novo mutations and calculates a putative mutation rate. RatesTools uses several quality filtering steps, such as discarding sites with low mappability and highly repetitive regions, as well as sites with low genotype and mapping qualities to find potential de novo mutations. In addition, RatesTools implements several optional filters based on post hoc assumptions of the heterozygosity and mutation rate of the organism. Filters are highly customizable to user specifications in order to maximize utility across a wide-range of applications.

Availability

RatesTools is freely available at https://github.com/campanam/RatesTools under a Creative Commons Zero (CC0) license. The pipeline is implemented in Nextflow (Di Tommaso et al. 2017), Ruby (http://www.ruby-lang.org), Bash (https://www.gnu.org/software/bash/), and R (R Core Team 2020) with reliance upon several other freely available tools. RatesTools is compatible with macOS and Linux operating systems.

Supplementary Information

We document RatesTools’ performance using published datasets in the online Supplementary information.
Predicting the Reprogrammability of Human Cells Based on Transcriptome Data and SGD Classifier with Elastic-Net Regularization
Authors: Saygili Gorkem , Turktas Mine , Gurcan Cansu , Delogu Lucia Gemma , Aktuna Acelya Yilmazer
Published: July 2022

Cell reprogramming has shown considerable importance in recent years; however, the programmability of cells and efficiency of reprogramming varies across different cell types. Considering several weeks of cell programming process and costly programming agents used through the process, every failure in reprogramming comes with a significant burden. Better planning for reprogramming experiments could be possible if there is a way of predicting the outcome of reprogramming before the experiments using transcriptome data. In this study, we have accessed the transcriptome data of successful or unsuccessful programming studies published in literature and constructed a Stochastic Gradient Descent (SGD) classifier with Elastic-Net regularization for predicting whether the cell lines are reprogrammable. We tested our classifier using 10-fold cross validation over cell lines and on each cell separately. Our results showed that it is possible to predict the outcome of cell reprogramming with accuracies up to 98% and Area Under the Curve (AUC) scores up to 0.98%. Considering the success of our experimental outcomes we conclude that an outcome of a cell reprogramming experiment can be predicted with high accuracy using machine learning on transcriptome data.
S100a9 Attenuates Inflammation during Repeated Social Defeat Stress
Authors: Moshfegh Cassandra M. , Elkhatib Safwan K. , Watson Gabrielle F. , Drake John , Taylor Zachary N. , Reed Emily C. , Lauten Tatlock H. , Clopp Amelia J. , Vladimirov Vladimir I. , Case Adam J.
Published: July 2022

Post-traumatic stress disorder (PTSD), a consequence of psychological trauma, is associated with increased inflammation and an elevated risk of developing comorbid inflammatory diseases. However, the mechanistic link between this mental health disorder and inflammation remains elusive. Using a pre-clinical model of PTSD known as repeated social defeat stress (RSDS), we previously identified that S100a8 and S100a9 mRNA, genes that encode the protein calprotectin, were significantly upregulated in T-lymphocytes after psychological trauma. Calprotectin expression positively correlated with inflammatory gene expression and the mitochondrial redox environment in T-lymphocytes, therefore, we hypothesized that genetic deletion of calprotectin would attenuate the inflammatory and redox phenotype displayed after RSDS. Using pharmacological and genetic manipulation of S100a9 (which functionally eliminates calprotectin) in mice, we unexpectedly observed worsening of behavioral pathology, inflammation, and the mitochondrial redox environment in mice after RSDS compared to wild-type (WT) animals. Furthermore, loss of calprotectin significantly enhanced the metabolic demand on T-lymphocytes suggesting this protein may play an undescribed role in mitochondrial regulation. This was further supported by single-cell RNA sequencing analysis demonstrating that RSDS and loss of S100a9 primarily altered genes associated with mitochondrial function and oxidative phosphorylation. Taken together, these data demonstrate the loss of calprotectin potentiates the RSDS-induced phenotype, which suggests its observed upregulation after psychological trauma may provide previously unexplored protective functions.
Pervasive Transcriptome Interactions of Protein-Targeted Drugs
Authors: Fang Linglan , Velema Willem A , Lee Yujeong , Xiao Lu , Mohsen Michael G , Kietrys Anna M , Kool Eric T
Published: July 2022

The off-target toxicity of drugs targeted to proteins imparts substantial health and economic costs. Proteome interaction studies can reveal off-target effects with unintended proteins; however, little attention has been paid to intracellular RNAs as potential off targets that may contribute to toxicity. To begin to assess this, we developed a reactivity-based RNA profiling (RBRP) methodology, and applied it to uncover transcriptome interactions of a set of FDA-approved small-molecule drugs in vivo. We show that these protein-targeted drugs pervasively interact with the human transcriptome and can exert unintended biological effects on RNA function. In addition, we show that many off-target interactions occur at RNA loci associated with protein binding and structural changes, allowing us to generate hypotheses to infer the biological consequences of RNA off-target binding. The results suggest that rigorous characterization of drugs' transcriptome interactions may help assess target specificity and potentially avoid toxicity and clinical failures.
A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use
Authors: Kraemer SA , Barbosa da Costa N , Oliva A , Huot Y , Walsh DA
Published: July 2022

Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome - the diversity of ARGs – under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of ∼350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.
Event integration and temporal differentiation: how hierarchical knowledge emerges in hippocampal subfields through learning
Authors: Bein Oded , Davachi Lila
Published: July 2022

Everyday life is composed of events organized by changes in contexts, with each event containing an unfolding sequence of occurrences. A major challenge facing our memory systems is how to integrate sequential occurrences within events while also maintaining their details and avoiding over-integration across different contexts. Here we asked if and how distinct hippocampal subfields come to hierarchically, and in parallel, represent both event context and subevent occurrences with learning. Participants viewed sequential events defined as sequences of objects superimposed on shared color frames while undergoing high-resolution fMRI. Importantly, these events were repeated to induce learning. Event segmentation, as indexed by increased reaction times at event boundaries, was observed in all repetitions. Temporal memory decisions were quicker for items from the same event compared to across different events, indicating that events shaped memory behavior. With learning, hippocampal CA3 multivoxel activation patterns clustered to reflect the event context, with more clustering correlated with behavioral facilitation during event transitions. In contrast, in the dentate gyrus temporally proximal items that belonged to the same event became associated with more differentiated neural patterns. A computational model explained these results by dynamic inhibition in the dentate gyrus. Additional similarity measures support the notion that CA3 clustered representations reflect shared voxel populations, while dentate gyrus’ distinct item representations reflect different voxel populations. These findings suggest an interplay between temporal differentiation in dentate gyrus and attractor dynamics in CA3. They advance our understanding of how knowledge is structured through integration and separation across time and context.

Significance

A major challenge of our memory system is to integrate experiences occurring in the same context to generalize context-appropriate knowledge, while also maintaining distinct representations of these same occurrences to avoid confusion. Here, we uncover a novel mechanism for hierarchical learning in the human hippocampus that might help to resolve this tension. In the CA3 subregion of the hippocampus, the neural representations of items presented sequentially in the same context, but not in different contexts, became more overlapping with learning. In contrast, adjacent items, appearing close in time and in the same context, became increasingly more differentiated in the dentate gyrus. Thus, multiple representations in different hippocampal subregions encoded in parallel might enable simultaneous generalization and specificity in memory.
Fractionating distraction: how past- and future-relevant distractors influence integrated decisions
Authors: Barnes Lydia , Rangelov Dragan , Mattingley Jason B. , Woolgar Alexandra
Published: July 2022

Many everyday tasks require us to integrate information from multiple steps to make a decision. Dominant accounts of flexible cognition suggest that we are able to navigate such complex tasks by attending to each step in turn, yet few studies measure how we direct our attention to immediate and future task steps. Here, we used a two-step task to test whether participants are sensitive to information that is currently irrelevant, but will be relevant in a future task step. Participants viewed two displays in sequence, each containing two superimposed moving dot clouds of different colours. Participants attended to one cued target colour in each display and reported the average direction of the two target dot clouds. In a subset of trials, we presented a “decoy” distractor: the second target colour appeared as the distractor in the first display. We regressed behavioural responses on the dot clouds’ motion directions to track how this future-relevant “decoy” distractor influenced participants’ reporting of the average target direction. We compared the influence of decoy distractors to never-relevant, recently relevant, and globally relevant distractor baselines. Across four experiments, we found that responses reflected what was immediately relevant, as well as the broader historical relevance of the distractors. However, relevance for a future task step did not reliably influence attention. We propose that attention in multi-step tasks is shaped by what has been relevant in the current setting, and by the immediate demands of each task step.

Public Significance

Our everyday functioning depends on our ability to piece together information to make coherent decisions. Understanding how we efficiently select and integrate goal-relevant information is critical if we wish to anticipate how decision-making can go wrong, whether because of fatigue, mental load, or illness. This study shows that decisions in multi-step tasks reflect two distinct processes: narrow focus on what is relevant in each step, alongside broader awareness of what has been relevant in this setting.
Cross-Modality and Self-Supervised Protein Embedding for Compound–Protein Affinity and Contact Prediction
Authors: You Yuning , Shen Yang
Published: July 2022

Motivation

Computational methods for compound–protein affinity and contact (CPAC) prediction aim at facilitating rational drug discovery by simultaneous prediction of the strength and the pattern of compound–protein interactions. Although the desired outputs are highly structure-dependent, the lack of protein structures often makes structure-free methods rely on protein sequence inputs alone. The scarcity of compound–protein pairs with affinity and contact labels further limits the accuracy and the generalizability of CPAC models.

Results

To overcome the aforementioned challenges of structure naivety and labelled-data scarcity, we introduce cross-modality and self-supervised learning, respectively, for structure-aware and task-relevant protein embedding. Specifically, protein data are available in both modalities of 1D amino-acid sequences and predicted 2D contact maps, that are separately embedded with recurrent and graph neural networks, respectively, as well as jointly embedded with two cross-modality schemes. Furthermore, both protein modalities are pretrained under various self-supervised learning strategies, by leveraging massive amount of unlabelled protein data. Our results indicate that individual protein modalities differ in their strengths of predicting affinities or contacts. Proper cross-modality protein embedding combined with self-supervised learning improves model generalizability when predicting both affinities and contacts for unseen proteins.

Availability

Data and source codes are available at https://github.com/Shen-Lab/CPAC.

Contact

yshen@tamu.edu

Supplementary information

Supplementary data are included.
Cumulative incidence of SARS-CoV-2 infection in the general population of the Valencian Community (Spain) after the surge of the Omicron BA.1 variant
Authors: Camacho Jorge , Giménez Estela , Albert Eliseo , Zulaica Joao , Álvarez-Rodríguez Beatriz , Torres Ignacio , Rusu Luciana , Burgos Javier S. , Peiró Salvador , Vanaclocha Hermelinda , Limón Ramón , Jesús Alcaraz María , Sánchez-Payá José , Díez-Domingo Javier , Comas Iñaki , Gonzáles-Candelas Fernando , Geller Ron , Navarro David
Published: July 2022

Background

Studies investigating the cumulative incidence of and immune status against SARS-CoV-2 infection provide valuable information for shaping public health decision-making.

Methods

The current cross-sectional, population-based study, conducted in April 2022 in the Valencian Community (VC), recruited 935 participants of all ages. Anti-SARS-CoV-2-Receptor Binding Domain-RBD-total antibodies and anti-Nucleocapsid (N)- IgGs were measured by electrochemiluminescence assays. To account for past SARS-CoV-2 infection the VC microbiology registry (RedMiVa) was interrogated. |Quantitation of neutralizing antibodies (NtAb) against the ancestral and Omicron BA.1 and BA.2 (sub)variants by an S-pseudotyped neutralization assay and for enumeration of SARS-CoV-2-S specific-IFNγ-producing CD4+ and CD8+ T cells by Intracellular Cytokine Staining assay was performed in a subset of participants (n=100 and 137, respectively).

Findings

The weighted cumulative incidence was 51□9% (95% CI, 48□7–55□1), and was inversely related to age. Anti-RBD total antibodies were detected in 906/931 (97□3%) participants, those vaccinated and SARS-CoV-2-experienced (VAC-ex;=442) displaying higher levels (P<0.001) than vaccinated/naïve (VAC-n;(n=472) and non-vaccinated/experienced (UNVAC-ex; n(n=63). Antibody levels correlated inversely with the time elapsed since receipt of last vaccine dose in VAC-n (Rho, -0□52; 95% CI, -0□59 to -0□45; P<0.001) but not in VAC-ex. NtAbs against Omicron BA.1 were detected in 94%, 75% and 50% of VAC-ex, VAC-n and UNVAC-ex groups, respectively, while in 97%, 84% and 40%, against Omicron BA.2. SARS-CoV-2-S-reactive IFN-γ T cells were detected in 73%, 75%, and 64% for VAC-ex, VAC-n, UNVAC-ex, respectively.

Interpretation

By April 2022 around half of the VC population had been infected with SARS-CoV-2 and due to extensive vaccination display hybrid immunity. The large percentage of participants with detectable functional antibody and T-cell responses against SARS-CoV-2, which may be cross-reactive to some extent, points towards lower expected severity than in previous waves.

Funding

This research was supported in part by the European Commission NextGenerationEU fund (CSIC’s Global Health Platform).
Menstrual cycle and exogenous attention toward emotional expressions
Authors: Álvarez Fátima , Uxía Fernández-Folgueiras , Méndez-Bértolo Constantino , Kessel Dominique , Carretié Luis
Published: July 2022

Several studies suggest that the menstrual cycle affects emotional processing. However, these results may be biased by including women with premenstrual syndrome (PMS) in the samples. PMS is characterized by negative emotional symptomatology, such as depression and/or anxiety, during the luteal phase. This study aimed to explore the modulation of exogenous attention to emotional facial expressions as a function of the menstrual cycle in women without PMS. For this purpose, 55 women were selected (from an original volunteer sample of 790) according to rigorous exclusion criteria. Happy, angry, and neutral faces were presented as distractors, while both behavioral performance in a perceptual task and event-related potentials (ERPs) were recorded. This task was applied during both phases of the menstrual cycle (luteal and follicular, counterbalanced), and premenstrual symptomatology was monitored daily. Traditional and Bayesian ANOVAs on behavioral data (reaction times and errors in the task) and ERP indices (P1, N170, N2, and LPP amplitudes) confirmed the expected lack of an interaction of phase and emotion. Taken together, these results indicate that women free of PMS present steady exogenous attention levels to emotionally positive and negative stimuli regardless of the menstrual phase.
Group 3 Innate Lymphoid Cells are regulated by WASP in a microbiota-dependent manner
Authors: Biswas Amlan , Redhu Naresh S , Nandy Anubhab , Kang Yu Hui , Field Michael , Kelly Ryan , Konnikova Liza , Goettel Jeremy A. , Tsou Amy M. , Horwitz Bruce , Snapper Scott B.
Published: July 2022

Wiskott-Aldrich syndrome protein (WASP) is a cytoskeletal regulator that is largely restricted to hematopoietic cells. While WASP expression in both lymphocytes and macrophages play a critical role in maintaining intestinal homeostasis, the function of WASP in innate lymphoid cells is unknown. Here we analyzed the role of WASP in the differentiation and function of group 3 innate lymphoid cells (ILC3s). WASP-deficient mice (Was-/-) have a marked reduction in ILC3s. Moreover, antimicrobial peptide expression in response to ILC3-derived IL-22 was also reduced in the absence of WASP. In Was-/- mice, we observed a reduction in CCR6+ ILC3s, cells known to restrict immune responses to commensal bacteria. WASP-deficient mice were more susceptible to Citrobacter rodentium, an enteric infection controlled by ILC3s. Interestingly, there was no reduction in ILC3s in Was-/- germ-free mice when compared to WT germ-free mice. ILC3s lacking WASP expression also demonstrated microbially-dependent alterations in gene expression associated with cell migration. Finally, ILC3-like (Rorgt+CD3-) cells were reduced in the GI tract of WASP-deficient patients. In conclusion, ILC3-specific expression of WASP is critical for the generation and function of ILC3s in the presence of commensal microflora. Aberrant ILC3 function in the setting of WASP-deficiency may contribute to underlying disease pathogenesis.
On the importance of data transformation for data integration in single-cell RNA sequencing analysis
Authors: Park Youngjun , Hauschild Anne-Christin
Published: July 2022

Abstract

Recent advances in single-cell RNA (scRNA) sequencing have opened a multitude of possibilities to study tissues down to the level of cellular populations. Subsequently, this enabled various scRNA studies that reported novel or previously undetected subpopulations and their functions by integrating multiple datasets. However, the heterogeneity in single-cell sequencing data makes it unfeasible to adequately integrate multiple datasets generated from different studies. This heterogeneity originates from various sources of noise due to technological limitations. Thus, particular procedures are required to adjust such effects prior to further integrative analysis. Over the last years, numerous single-cell data analysis workflows have been introduced, implementing various read-count transformation methods for de-noising and batch correction. A detailed review of recent single-cell studies shows while many analysis procedures employ various preprocessing steps, they often neglect the importance of a well-chosen and optimized data transformation. This fact is particularly alarming since these data transformations can alter data distribution and thus have a crucial impact on subsequent downstream cell clustering results. Therefore, this study investigates the effects of the various data transformation methods on three different public data scenarios and evaluates them with the most commonly used dimensionality reduction and clustering analysis. Additionally, we discuss its implications for the subsequent application of different deep neural network approaches, such as auto encoders and transfer learning. In summary, our benchmark analysis shows that a large portion of batch effects and noise can be mitigated by simple but well-chosen data transformation methods. We conclude that such optimized preprocessing is crucial and should be the baseline for all comparative single-cell sequencing studies, particularely for integrative analysis of multiple data sets.
Raltitrexed and Edatrexate drug molecules against human Proton Coupled Folate Transporter to cure cancer
Authors: Raja Yashpal Singh , Mishra Surya , Bhushan Shikha
Published: July 2022

Proton pump inhibitors (PPIs) (e.g.: - rabeprazole, pantoprazole, omeprazole, lansoprazole, and esomeprazole) are widely used to treat gastroesophageal reflux disease and other acid-related disorders. Folic acid transport is important for proper cell proliferation. In human, folic acid is not synthesized in the body, it is obtained externally. Therefore, specific transporters are involved in absorption of folic acid, which is concentrated in intestine. Malignant cancer cells require this folic acid very frequently in large quantities for the rapid reproduction of cancer cell. In the current study, we compared different types of proton pump inhibitor drug molecules that may be potential candidates for preventing the absorption of folate by (hPCFT), its responsible for unusually large and frequent folate production. Each of these anti-drug candidates has 27 finalists based on previous studies. Among these competitors, leukovorin and noletraxid molecules were found to be particularly associated with the hPCFT transporter’s key active site loop(G155XXG158).
WNT stimulation induced conformational dynamics in the Frizzled-Dishevelled interaction
Authors: Bowin Carl-Fredrik , Kozielewicz Pawel , Grätz Lukas , Kowalski-Jahn Maria , Schihada Hannes , Schulte Gunnar
Published: July 2022

Frizzleds (FZD1-10) are G protein-coupled receptors containing an extracellular cysteine-rich-domain (CRD) that presents the orthosteric binding site of the 19 mammalian WNTs, the endogenous agonists of FZDs. FZDs signal via a diverse set of effector proteins, of which Dishevelled (DVL1-3) is the most well studied and which acts as a hub for several FZD-mediated signaling pathways. However, the mechanistic details of how FZD-DVL interaction mediate pathway initiation and provide pathway selectivity remain an enigma. Here, we use bioluminescence resonance energy transfer-based assays employing Venus-tagged DVL2 together with NanoLuciferase-tagged FZD5 to investigate the WNT-3A- and WNT-5A-induced dynamics of the FZD-DVL interaction. Our biophysical assessment suggests that the ligand-induced BRET changes over time originate from conformational dynamics in the FZD5-DVL2 complex rather than recruitment dynamics of DVL2 to FZD5. Thus, we suggest that extracellular agonist and intracellular transducers could cooperate with each other through allosteric interaction with FZDs in a ternary complex reminiscent of that of classical GPCRs.

One Sentence Summary

Analysis of the interaction of FZD5 and DVL2 uncovers WNT-induced conformational dynamics of a WNT-FZD5-DVL2 complex.
Antigenic mapping and functional characterization of human New World hantavirus neutralizing antibodies
Authors: Engdahl Taylor B. , Binshtein Elad , Brocato Rebecca L. , Kuzmina Natalia A. , Principe Lucia M , Kwilas Steven A. , Kim Robert K. , Chapman Nathaniel S. , Porter Monique S. , Guardado-Calvo Pablo , Rey Felix A. , Handal Laura S. , Diaz Summer M. , Zagol-Ikapitte Irene A. , Reidy Joseph X. , Trivette Andrew , Bukreyev Alexander , Hooper Jay W. , Crowe James. E.
Published: July 2022

Hantaviruses are high-priority emerging pathogens carried by rodents and transmitted to humans by aerosolized excreta or, in rare cases, person-to-person contact. While sporadic in North and South America, many infections occur in Europe and Asia, with mortality ranging from 1 to 40% depending on the hantavirus species. There are currently no FDA-approved vaccines or therapeutics for hantaviruses, and the only treatment for infection is supportive care for respiratory or kidney failure. Additionally, the humoral immune response to hantavirus infection is incompletely understood, especially the location of major antigenic sites on the viral glycoproteins and conserved neutralizing epitopes. Here, we report antigenic mapping and functional characterization for four neutralizing hantavirus antibodies. The broadly neutralizing antibody SNV-53 targets an interface between Gn/Gc, neutralizes through fusion inhibition and cross-protects against the Old World hantavirus species Hantaan virus when administered pre- or post-exposure. Another broad antibody, SNV-24, also neutralizes through fusion inhibition but targets domain I of Gc and demonstrates weak neutralizing activity across hantavirus species. ANDV-specific, neutralizing antibodies (ANDV-5 and ANDV-34) neutralize through attachment blocking and protect against hantavirus cardiopulmonary syndrome (HCPS) in animals but target two different antigenic faces on the head domain of Gn. Determining the antigenic sites for neutralizing antibodies will contribute to further therapeutic development for hantavirus-related diseases and inform the design of new broadly protective hantavirus vaccines.
The catalase contributes to microaerophilic H2O2 priming and the peroxiredoxins AhpC, Tpx and Bcp confer resistance to organic hydroperoxides in Staphylococcus aureus
Authors: Linzner Nico , Van Loi Vu , Antelmann Haike
Published: July 2022

Staphylococcus aureus is a major human pathogen, which has to cope with oxidative stress as part of the host innate immune defense under macrophage and neutrophil infections. In this study, we have investigated the role of the catalase KatA and the peroxiredoxins AhpC, Tpx, and Bcp for priming and resistance under oxidative stress in S. aureus during aerobic and microaerophilic growth. The results revealed that S. aureus is resistant to high doses of up-to 100 mM H2O2 during the aerobic growth. While KatA is essential for this high aerobic H2O2 resistance, the peroxiredoxin AhpC contributes to detoxification of 0.4 mM H2O2 in the absence of KatA. In addition, AhpC, Tpx and Bcp were shown to be required for detoxification of cumene hydroperoxide (CHP) and regeneration of the reduced state of the bacillithiol (BSH) redox potential during recovery from CHP stress in S. aureus. The high H2O2 tolerance of aerobic S. aureus cells was associated with priming by endogenous H2O2 levels, which was supported by an oxidative shift of the basal level of EBSH (−291 mV) compared to that in microaerophilic cells (−310 mV). In contrast, S. aureus can be primed by sub-lethal doses of 100 µM H2O2 during the microaerophilic growth to acquire an improved resistance towards the otherwise lethal triggering stimulus of 10 mM H2O2. This microaerophilic priming was dependent on increased katA transcription and elevated KatA activity, whereas aerobic control cells showed already constitutive high KatA activity. Thus, KatA is the major player contributing to the high H2O2 resistance of aerobic cells and to microaerophilic H2O2 priming to survive the subsequent lethal triggering doses of H2O2, allowing the adaptation of S. aureus to oxidative stress under infections in different oxygen environments.
Epinephrine inhibits PI3K alpha via the Hippo kinases
Authors: Lin Ting-Yu , Ramsamooj Shakti , Liberatore Katarina , Lantier Louise , Vasan Neil , Karukurichi Kannan , Hwang Seo-Kyoung , Kesicki Edward A. , Kastenhuber Edward R. , Wiederhold Thorsten , Yaron Tomer M. , Zhu Mengmeng , Ma Yilun , Paddock Marcia N. , Zhang Guoan , Hopkins Benjamin D. , McGuinness Owen , Schwartz Robert E. , Cantley Lewis C. , Johnson Jared L. , Goncalves Marcus D.
Published: July 2022

The phosphoinositide 3-kinase, p110α, is an essential mediator of insulin signaling and glucose homeostasis. We systematically interrogated the human serine, threonine, and tyrosine kinome to search for novel regulators of p110α and found that the Hippo kinases phosphorylate and completely inhibit its activity. This inhibitory state corresponds to a conformational change of a membrane binding domain on p110α, which impairs its ability to engage membranes. In human primary hepatocytes, cancer cell lines, and rodent tissues, activation of the Hippo kinases, MST1/2, using forskolin or epinephrine is associated with phosphorylation and inhibition of p110α, impairment of downstream insulin signaling, and suppression of glycolysis and glycogen synthesis. These changes are abrogated when MST1/2 are genetically deleted or inhibited with small molecules. Our study reveals a novel inhibitory pathway of PI3K signaling and a previously unappreciated link between epinephrine and insulin signaling.
Bivalent mRNA vaccine booster induces robust antibody immunity against Omicron subvariants BA.2, BA.2.12.1 and BA.5
Authors: Fang Zhenhao , Chen Sidi
Published: July 2022

As the immune protection conferred by first booster shot wanes over time and new Omicron subvariant emerges with stronger immune evasion, the need for variant-adapted COVID vaccine booster is increasingly imminent. However, the rapid replacement of dominant Omicron subvariants (from BA.1 to BA.2, then BA.2.12.1 and now BA.4/5) poses a great challenge to update COVID vaccine targeting the fast-evolving variants while maintaining potency against existing variants. It is a crucial question to ask which variant-based antigen(s) to use in the next generation COVID vaccine to elicit potent and broad response to past, present, and potential rising variants. Bivalent vaccine candidates have been under active clinical testing such as Modern mRNA-1273.214. In this study, we generate a Delta + BA.2 bivalent mRNA vaccine candidate and tested in animals. We compare the antibody response elicited by ancestral (wild type, WT), Delta, BA.2 spike based monovalent or Delta & BA.2 bivalent mRNA boosters against Omicron BA.2, BA.2.12.1 and BA.4/5 subvariants. In mice pre-immunized with two doses of WT lipid nanoparticle mRNA (LNP-mRNA), all three monovalent and one bivalent boosters elevated Omicron neutralizing antibody titers to various degree. The boosting effect of Delta and BA.2 specific monovalent or bivalent LNP-mRNAs is universally higher than that of WT LNP-mRNA, which modestly increased antibody titer in neutralization assays of Omicron BA.5, BA.2.12.1 and BA.2. The Delta & BA.2 bivalent LNP-mRNA showed better performance of titer boosting than either monovalent counterparts, which is especially evident in neutralization of Omicron BA.4 or BA.5. Interestingly compared to the neutralizing titers of BA.2 and BA.2.12.1 pseudovirus, BA.2 monovalent but not Delta & BA.2 bivalent booster suffered a significant loss of BA.4/5 neutralizing titer, indicative of broader activity of bivalent booster and strong neutralization evasion of Omicron BA.4 or BA.5 even in the BA.2 mRNA vaccinated individuals. These data provide evaluation of WT, Delta, BA.2 monovalent and bivalent boosters antibody potency against Omicron BA.2, BA.2.12.1 and BA.4/5 subvariants.
Coordinated control of the ADP-heptose/ALPK1 signalling network by the E3 ligases TRAF6, TRAF2/c-IAP1 and LUBAC
Authors: Snelling Tom , Shpiro Natalia , Gourlay Robert , Lamoliatte Frederic , Cohen Philip
Published: July 2022

ADP-heptose activates the protein kinase ALPK1 triggering TIFA phosphorylation at Thr9, the recruitment of TRAF6 and the subsequent production of inflammatory mediators. Here, we demonstrate that ADP-heptose also stimulates the formation of Lys63- and Met1-linked ubiquitin chains to activate the TAK1 and canonical IKK complexes, respectively. We further show that the E3 ligases TRAF6 and c-IAP1 operate redundantly to generate the Lys63-linked ubiquitin chains required for pathway activation, which we demonstrate are attached to TRAF6, TRAF2 and c-IAP1, and that c-IAP1 is recruited to TIFA by TRAF2. ADP-heptose also induces activation of the kinase TBK1 by a TAK1-independent mechanism, which require TRAF2 and TRAF6. We establish that ALPK1 phosphorylates TIFA directly at Thr177 as well as Thr9 in vitro. Thr177 is located within the TRAF6-binding motif and its mutation to Asp prevents TRAF6 but not TRAF2 binding, indicating a role in restricting ADP-heptose signalling. We conclude that ADP-heptose signalling is controlled by the combined actions of TRAF2/c-IAP1 and TRAF6.
mTORC2 couples fasting to mitochondrial fission
Authors: Martinez-Lopez Nuria , Mattar Pamela , Toledo Miriam , Bains Henrietta , Kalyani Manu , Aoun Marie Louise , Sharma Mridul , McIntyre Laura Beth J. , Gunther-Cummins Leslie , Macaluso Frank P. , Aguilan Jennifer T. , Sidoli Simone , Bourdenx Mathieu , Singh Rajat
Published: July 2022

Fasting triggers diverse cellular and metabolic adaptations to facilitate organismal survival1,2. During nutrient deprivation, increases in circulating fatty acids support mitochondrial respiration2. The mechanisms driving mitochondrial adaptations and respiratory sufficiency during nutrient deprivation remain incompletely understood. Here we show that extended periods of fasting, or lipid availability stimulates mTORC2 activity. Activation of mTORC2 and phosphorylation of its target NDRG13 at S336 sustains mitochondrial fission and respiratory sufficiency. Timelapse imaging reveals that wildtype NDRG1, but not phosphorylation-deficient NDRG1S336A mutant, engages with mitochondria to facilitate its scission. Using proteomics, and an siRNA screen, we show that mTORC2-phosphorylated NDRG1 cooperates with the small GTPase Cdc424 and Cdc42-specific effectors and regulators to orchestrate fission. Accordingly, RictorKO, NDRG1S336A mutants, and Cdc42-deficient cells each display mitochondrial phenotypes reminiscent of fission failure. During nutrient surplus, mTOR complexes perform anabolic functions5; however, paradoxical reactivation of mTORC2 during fasting plays an unexpected role in driving mitochondrial fission and respiration.
Mitotic clustering of pulverized chromosomes from micronuclei
Authors: Lin Yu-Fen , Valle-Inclan Jose Espejo , Mazzagatti Alice , Hu Qing , Maurais Elizabeth G. , Guyer Alison , Sanders Jacob T. , Engel Justin , Nguyen Giaochau , Bronder Daniel , Bakhoum Samuel F. , Cortés-Ciriano Isidro , Ly Peter
Published: July 2022

Complex genome rearrangements can be generated by the catastrophic shattering of mis-segregated chromosomes trapped within micronuclei through a process known as chromothripsis. Since each chromosome harbors a single centromere, how acentric fragments derived from shattered chromosomes are inherited between daughter cells during mitosis remains unknown. Here we tracked micronucleated chromosomes by live-cell imaging and show that acentric fragments cluster in close spatial proximity throughout mitosis for biased partitioning to a single daughter cell. Mechanistically, the CIP2A-TOPB1 complex prematurely associates with DNA lesions within ruptured micronuclei during interphase, which poises chromosome fragments for clustering upon mitotic entry. Inactivation of CIP2A or TOPBP1 caused pulverized chromosomes to untether and disperse throughout the mitotic cell, consequently resulting in the mis-accumulation of DNA fragments in the cytoplasm. The inheritance of shattered chromosomes by a single daughter cell suggests that micronucleation can drive complex rearrangements that lack the DNA copy number oscillations characteristic of canonical chromothripsis. Comprehensive analysis of pan-cancer whole-genome sequencing data revealed clusters of DNA copy number-neutral rearrangements – termed balanced chromothripsis – across diverse cancer types resulting in the acquisition of known driver events. Thus, distinct patterns of chromothripsis can be explained by the spatial mitotic clustering of pulverized chromosomes from micronuclei.
Compartment-specific and ELAVL1-coordinated regulation of intronic polyadenylation isoforms by doxorubicin
Authors: Chakraborty Alina , Cadix Mandy , Relier Sébastien , Taricco Nicolò , Alaeitabar Tina , Devaux Alexandre , Labbé Céline M. , Martineau Sylvain , Heneman-Masurel Amélie , Gestraud Pierre , Inga Alberto , Servant Nicolas , Vagner Stéphan , Dutertre Martin
Published: July 2022

Intronic polyadenylation (IPA) isoforms, which contain alternative last exons, are widely regulated in various biological processes and by many factors. However, little is known about their cytoplasmic regulation and translational status. In this study, we provide the first evidence that the genome-wide patterns of IPA isoform regulation during a biological process can be very distinct between the transcriptome and translatome, and between the nucleus and cytosol. Indeed, by 3′-seq analyses on breast cancer cells, we show that the genotoxic anticancer drug, doxorubicin, preferentially down-regulates the IPA to the last-exon (IPA:LE) isoform ratio in whole cells (as previously reported) but preferentially up-regulates it in polysomes. We further show that in nuclei, doxorubicin almost exclusively down-regulates the IPA:LE ratio, whereas in the cytosol, it preferentially up-regulates the isoform ratio, as in polysomes. Then, focusing on IPA isoforms that are up-regulated by doxorubicin in the cytosol and highly translated (up-regulated and/or abundant in polysomes), we identify several IPA isoforms that promote cell survival to doxorubicin. Mechanistically, by using an original approach of condition- and compartment-specific CLIP-seq (CCS-iCLIP) to analyze ELAVL1-RNA interactions in the nucleus and cytosol in the presence and absence of doxorubicin, as well as 3′-seq analyses upon ELAVL1 depletion, we show that the RNA-binding protein ELAVL1 mediates both nuclear down-regulation and cytosolic up-regulation of the IPA:LE isoform ratio in distinct sets of genes in response to doxorubicin. Altogether, these findings reveal differential regulation of the IPA:LE isoform ratio across subcellular compartments during drug response and its coordination by an RNA-binding protein.
Analytic description of nanowires II: morphing of regular cross sections for zincblende- and diamond-structures to match arbitrary shapes
Authors: König Dirk , Smith Sean C.
Published: July 2022

Setting out from our recent publication [König & Smith (2021). Acta Cryst. B77, 861], we extend our analytic description of the regular cross sections of zincblende- and diamond-structure nanowires (NWires) by introducing cross section morphing to arbitrary convex shapes featuring linear interfaces as encountered in experiment. To this end, we provide add-on terms to the existing number series with their respective running indices for zinc-blende- (zb-) and diamond-structure NWire cross sections. Such add-on terms to all variables yield the required flexibility for cross section morphing, with main variables presented by the number of NWire atoms N
Wire(d
Wire[i]), bonds between NWire atoms N
bnd(d
Wire[i]) and interface bonds N
IF(d
Wire[i]). Other basic geometric variables, such as the specific length of interface facets, as well as widths, heights and total area of the cross section, are given as well. The cross sections refer to the six high-symmetry zb NWires with low-index faceting frequently occurring in the bottom-up and top-down approaches of NWire processing. The fundamental insights into NWire structures revealed here offer a universal gauge and thus enable major advancements in data interpretation and the understanding of all zb- and diamond-structure-based NWires with arbitrary convex cross sections. We corroborate this statement with an exact description of irregular Si NWire cross sections and irregular InGaAs/GaAs core-shell NWire cross sections, where a radially changing unit-cell parameter can be included.