bluuebunny/crossref_metadata_2025 huggingface dataset:
Monitoring sustainable development goal 5.2: Cross-country cross-time invariance of measures for intimate partner violence
Authors: Yount Kathryn M. , Bergenfeld Irina , Mhamud Nishat , Clark Cari Jo , Kaslow Nadine J. , Cheong Yuk Fai
Published: April 2022

Background

The persistence and impacts of violence against women motivated Sustainable Development Goal (SDG) 5.2 to end such violence. Global psychometric assessment of cross-country, cross-time invariance of items measuring intimate partner violence (IPV) is needed to confirm their utility for comparing and monitoring national trends.

Methods

Analyses of seven physical-IPV items included 377,500 ever-partnered women across 20 countries (44 Demographic and Health Surveys (DHS)). Analyses of five controlling-behaviors items included 371,846 women across 19 countries (42 DHS). We performed multiple-group confirmatory factor analysis (MGCFA) to assess within-country, cross-time invariance of each item set. Pooled analyses tested cross-country, cross-time invariance using DHSs that showed configural invariance in country-level multiple-group confirmatory factor analysis (MGCFAs). Alignment optimization tested approximate invariance of each item set in the pooled sample of all datasets, and in the subset of countries showing metric invariance over at least two repeated cross-sectional surveys in country-level MGCFAs.

Results

In country-level MGCFAs, physical-IPV items and controlling-behaviors items functioned equivalently in repeated survey administrations in 12 and 11 countries, respectively. In MGCFA testing cross-country, cross-time invariance in pooled samples, neither item set was strictly equivalent; however, the physical-IPV items were approximately invariant. Controlling-behaviors items did not show approximate cross-country and cross-time invariance in the full sample or the sub-sample showing country-level metric invariance.

Conclusion

Physical-IPV items approached approximate invariance across 20 countries and were approximately invariant in 11 countries with repeated cross-sectional surveys. Controlling-behaviors items were cross-time invariant within 11 countries but did not show cross-country, cross-time approximate invariance. Currently, the physical-IPV item set is more robust for monitoring progress toward SDG5.2.1, to end IPV against women.
The relation between COVID-19 vaccinations and public governance to improve preparedness of next pandemic impacts and crisis management: a global study
Authors: Coccia Mario , Benati Igor
Published: April 2022

The goal of this study is to analyze the relationship between COVID-19 vaccinations and public governance performing a global analysis of more than 110 countries worldwide. Methodology applies the Independent SamplesT-Test that compares the means of two independent groups (countries with high/low level of vaccinations) to determine whether there is statistical evidence that the associated population means of indicators of public governance are significantly different. Findings suggest that high levels of governance can support a better function of health systems in the rollout of vaccinations to cope with COVID-19 pandemic crisis. This study may assist long-run policy of governments to improve good governance and health systems of countries in order to reinforce the preparedness to face next pandemic threats and in general future crisis management in society.
Interplay between Tumor Mutational Burden and Mutational Profile and its effect on overall survival: A Post Hoc Analysis of Metastatic Patients Treated with Immune Checkpoint Inhibitors
Authors: Xavier Camila B. , Lopes Carlos Diego H. , Awni Beatriz M. , Campos Eduardo F. , Alves João Pedro B. , Camargo Anamaria A. , Guardia Gabriela D. A. , Galante Pedro A. F. , Jardim Denis L.
Published: April 2022

Purpose

Solid tumors harboring tumor mutational burden (TMB) ≥ 10 mutations per megabase (mut/Mb) received agnostic approval for pembrolizumab. However, TMB cut-off alone is not a predictor of overall survival (OS). This work aims to analyze the somatic mutational profile’s influence in the outcomes of patients with TMB-high tumors treated with immune checkpoint inhibitors (ICIs).

Methods

This post-hoc analysis evaluated clinical and molecular features of 1,661 patients with solid tumors treated with ICIs. We performed OS analysis for TMB thresholds of ≥ 10, ≥ 20, and < 10 mut/Mb. For a TMB ≥ 10mut/Mb cutoff, we assessed OS according to mutational profile. For genes exhibiting a correlation with OS (P < 0.05) at the univariate assessment, we conducted a Cox multivariate analysis adjusted by median TMB, sex, age, microsatellite instability (MSI), and histology.

Results

1,661 patients were investigated, and 488 harbored a TMB ≥ 10 mut/Mb (29.4%). The median OS was 42 months for TMB ≥ 10 or 20 mut/Mb, and 15 months for TMB < 10 mut/Mb (P < 0.005). In patients harboring TMB ≥ 10mut/Mb, mutations in E2F3 or STK11 were correlated with worse OS, and mutations inNTRK3, PTPRD, RNF43, TENT5C, TET1orZFHX3with better OS. These associations were confirmed by univariate and multivariate analyses (P < 0.05). Melanoma histology and TMB above the median endowed patients with better OS (P < 0.05). MSI status, age, and gender did not have a consistent statistically significant effect on OS

Conclusion

Combining TMB information and mutation profiles in key cancer genes can be used to better qualify patients for ICI treatment and predict their OS.

CONTEXT SUMMARY

Key objective

Tumor mutational burden (TMB) of ≥ 10 mutations per megabase (mut/Mb) grant agnostic indication of pembrolizumab for advanced solid tumors’ treatment, however a substantial number of patients do not respond to therapy. This work aims to analyze the somatic mutational profile’s influence in the outcomes of patients with TMB ≥ 10mut/Mb tumors treated with ICIs.

Knowledge generated

Mutation profile can modify survival outcomes to ICIs in patients with TMB ≥ 10 mut/Mb. Mutations inE2F3orSTK11correlate with worse OS, while mutations inNTRK3, PTPRD, RNF43, TENT5C, TET1orZFHX3correlate with better OS in TMB-high patients receiving ICIs.

Relevance

We found that the combination of a high TMB and the somatic mutational profile in key cancer genes can be decisive in better qualify patients for ICI treatment.
Sleep Disruption Selectively Weakens Reactivated Memories
Authors: Whitmore Nathan W. , Paller Ken A.
Published: April 2022

A widely accepted view in memory research is that recently stored information can be reactivated during sleep, leading to memory strengthening. Two recent studies have shown this effect can be reversed in participants with highly disrupted sleep. To test whether weakening of reactivated memories can result directly from sleep disruption, in this experiment we varied the intensity of memory reactivation cues, such that some produced sleep arousals. Prior to sleep, participants (local community members) learned the locations of 75 objects, each accompanied by a sound naturally related to that object. Location recall was tested before and after sleep, and a subset of the sounds were presented during sleep. Reactivation with arousal weakened memories, unlike the improvement typically found. We conclude that reactivated memories can be selectively weakened during sleep, and that memory reactivation may strengthen or weaken memories depending on additional factors such as concurrent sleep disruption.

Statement of Relevance

The results of this study have implications for both human health and basic psychology. Sleep disorders like apnea are associated with memory problems; our results suggest a possible mechanism where frequent arousal may disrupt the naturally occurring reactivation of memory in sleep. These results also highlight the importance of avoiding brief sleep disruption for good sleep hygiene. Finally, we raise the possibility that reactivation with sleep disruption could be used therapeutically to weaken distressing memories.

Our observation that memories can also be either weakened or strengthened by sleep reactivation has implications for understanding the mechanisms of memory consolidation. In particular, we suggest that sleep memory reactivation may be a reconsolidation-like process with memory restabilization required after reactivation. Our findings also suggest avenues for future experiments; such as using sleep disruption to study the time course of memory reactivation.
Fronto-parietal networks shape human conscious report through attention gain and reorienting
Authors: Liu Jianghao , Bayle Dimitri J. , Spagna Alfredo , Sitt Jacobo D. , Bourgeois Alexia , Lehongre Katia , Fernandez-Vidal Sara , Adam Claude , Lambrecq Virginie , Navarro Vincent , Malkinson Tal Seidel , Bartolomeo Paolo
Published: April 2022

How do attention and consciousness interact in the human brain? Rival theories of consciousness disagree on the role of fronto-parietal attentional networks in conscious perception. We recorded neural activity from 727 intracerebral contacts in 13 epileptic patients, while they detected near-threshold targets preceded by attentional cues. Unsupervised clustering revealed three patterns: (1) Attention-enhanced conscious report accompanied sustained right-hemisphere fronto-temporal activity, in networks connected by the superior longitudinal fasciculus (SLF) II-III, and late accumulation in bilateral dorso-prefrontal and right-hemisphere orbitofrontal cortex (SLF I-III). (2) Attentional reorienting affected conscious report through early, sustained activity in a right-hemisphere network (SLF III). (3) Conscious report accompanied left-hemisphere dorsolateral-prefrontal activity. Task modeling with recurrent neural networks identified specific excitatory and inhibitory interactions between attention and consciousness, and their causal contribution to conscious perception of near-threshold targets. Thus, distinct, hemisphere-asymmetric fronto-parietal networks support attentional gain and reorienting in shaping human conscious experience.

One-Sentence Summary

Intracerebral recordings, tractography and modeling reveal the interaction of attention and consciousness in the human brain.
Contrasting effects of reduced phosphatidylcholine synthesis in absence of seipin: embryonic lethality goes down while lipid droplets get even larger
Authors: Zhu Jinglin , Lam Sin Man , Yang Leilei , Liang Jingjing , Ding Mei , Shui Guanghou , Huang Xun
Published: April 2022

Seipin plays a vital role in lipid droplet homeostasis and its deficiency causes congenital generalized lipodystrophy type II in humans. It is not known whether the physiological defects are all caused by cellular lipid droplet defects. Loss-of-function mutation ofseip-1, theC. elegansseipin ortholog, causes embryonic lethality and lipid droplet abnormality. We uncovernhr-114andspin-4as two suppressors ofseip-1embryonic lethality. Mechanistically,nhr-114andspin-4act in the “B12-one-carbon cycle-phosphatidylcholine (PC)” axis and reducing PC synthesis suppresses the embryonic lethality ofseip-1mutants. Conversely, PC deficiency enhances the lipid droplet abnormality ofseip-1mutants. The suppression ofseip-1embryonic lethality by PC reduction requires polyunsaturated fatty acid (PUFA). Therefore, seipin and phosphatidylcholine exhibit opposite actions in embryogenesis, while they function similarly in lipid droplet homeostasis. Our results demonstrate that seipin-mediated embryogenesis is independent of lipid droplet homeostasis.

Highlights

seip-1suppressors act in the “B12-one-carbon cycle-PC” pathway.

Reducing PC synthesis suppresses the embryonic lethality ofseip-1mutants.

Suppression of the embryonic lethality by PC reduction requires PUFA.

Reduced PC synthesis enhances the large lipid droplet ofseip-1mutants.
Whole-genome duplication in an algal symbiont bolsters coral heat tolerance
Authors: Dougan Katherine E. , Bellantuono Anthony J. , Kahlke Tim , Abbriano Raffaela M. , Chen Yibi , Shah Sarah , Granados-Cifuentes Camila , van Oppen Madeleine J. H. , Bhattacharya Debashish , Suggett David J. , Rodriguez-Lanetty Mauricio , Chan Cheong Xin
Published: April 2022

The algal endosymbiontDurusdinium trenchiienhances the resilience of coral reefs under thermal stress1,2. As an endosymbiont,D. trenchiiis generally expected to have a reduced genome compared to its free-living relatives, due in part to the lack of selective pressure for maintaining redundant gene functions in a stable intracellular environment within the host3. However,D. trenchiican live freely or in endosymbiosis, and the analysis of genetic markers4suggests that this species has undergone whole-genome duplication (WGD). Here we present genome assemblies for twoD. trenchiiisolates, confirm WGD in these taxa, and examine how selection has shaped the duplicated genome regions. We assess how the competing free-living versus endosymbiotic lifestyles ofD. trenchiihave contributed to the retention and divergence of duplicated genes, and how these processes have enhanced thermotolerance of corals hosting these symbionts. We find that lifestyle is the driver of post-WGD evolution inD. trenchii, with the free-living phase being most important, followed by endosymbiosis. Adaptations to both lifestyles collectively result in increased cellular fitness forD. trenchii, which provides enhanced thermal stress protection to the host coral. Beyond corals, this polyploid alga is a valuable model for understanding how genome-wide selective forces act to balance the often, divergent constraints imposed by competing lifestyles.
Omicron neutralizing antibody response following booster vaccination compared with breakthrough infection
Authors: Curlin Marcel E. , Bates Timothy A. , Guzman Gaelen , Schoen Devin , McBride Savannah K. , Carpenter Samuel D. , Tafesse Fikadu G.
Published: April 2022

The rapid spread of the vaccine-resistant Omicron variant of SARS-CoV-2 presents a renewed threat to both unvaccinated and fully vaccinated individuals, and accelerated booster vaccination campaigns are underway to mitigate the ongoing wave of Omicron cases. The degree of immunity provided by standard vaccine regimens, boosted regimens, and immune responses elicited by the combination of vaccination and natural infection remain incompletely understood. The relative magnitude, quality and durability of serological responses, and the likelihood of neutralizing protection against future SARS-CoV-2 variants following these modes of exposure are unknown but are critical to the future trajectory of the COVID-19 pandemic. In this study of 99 vaccinated adults, we find that compared with responses after two doses of an mRNA regimen, the immune responses three months after a third vaccine dose and one month after breakthrough infection due to prior variants show dramatic increases in magnitude, potency, and breadth, including increased antibody dependent cellular phagocytosis and robust neutralization of the recently circulating Omicron variant. These results suggest that as the number of Omicron cases rise and as global vaccination and booster campaigns continue, an increasing proportion of the world’s population will acquire potent immune responses that may be protective against future SARS-CoV-2 variants.
Workplace Infection Prevention Control Measures and Work Engagement During the COVID-19 Pandemic among Japanese Workers: A Prospective Cohort Study
Authors: Ikegami Kazunori , Ando Hajime , Fujino Yoshihisa , Eguchi Hisashi , Muramatsu Keiji , Nagata Tomohisa , Tateishi Seiichiro , Tsuji Mayumi , Ogami Akira ,   the CORoNaWork project
Published: April 2022

Objectives

It has been widely reported that the COVID-19 pandemic may have a psychological influence on people. Thus, it could be important to note how workplace infection prevention and control (IPC) measures for COVID-19 contribute to positive mental health among workers. We hypothesized that if workplace IPC measures are adequately implemented, they would have a positive effect on employees’ work engagement.

Methods

We conducted an internet-based prospective cohort study from December 2020 (baseline) to December 2021 (follow-up after one year) using self-administered questionnaires. At baseline, 27,036 workers completed the questionnaires, while 18,560 (68.7%) participated in the one-year follow-up. After excluding the 6,578 participants who changed jobs or retired during the survey period, or telecommuted more than four days per week, 11,982 participants were analyzed. We asked participants about the implementation of workplace IPC measures at baseline and conducted a nine-item version of the Utrecht Work Engagement Scale (UWES-9) at follow-up.

Results

Four groups were created according to the number of workplace IPC measures implemented. The mean (SD) UWES-9 score of the “0–2” group was the lowest at 18.3 (13.2), while that of the “8” group was the highest at 22.6 (12.6). The scores of the “3– 5,” “6–7,” and “8” groups were significantly higher than that of the “0–2” group (all, p<0.001). The p trend of the four groups was also significant (p<0.001).

Conclusions

Promoting workplace IPC measures improves workers’ work engagement, and a dose-response relationship exists between workplace IPC measures and work engagement.
Scalable production of recombinant three-finger proteins: from inclusion bodies to high quality molecular probes
Authors: Xu Jiang , Lei Xiao , Li Ao , Li Jun , Li Shuxing , Chen Lin
Published: April 2022

We introduce a working pipeline for expression, purification and validation of disulfide-bond rich three-finger proteins using E. coli as the expression host. With this pipeline, we have successfully obtained highly purified and bioactive recombinant α-Bungarotoxin, k-Bungarotoxin, Hannalgesin, Mambalgin-1, α-Cobratoxin, MTα, Slurp1, Pate B etc. Milligrams to hundreds of milligrams of recombinant three finger proteins were obtained within weeks in the lab. The recombinant proteins showed specificity in binding assay and six of them were crystallized and structurally validated using X-ray diffraction protein crystallography. As many three finger proteins have attractive therapeutic or research interests and due to the extremely high quality of the recombinant three finger proteins we obtained, our method provides a competitive alternative to either their native counterparts or chemically synthetic ones, and should facilitate related research and applications.
Speech prosody supports speaker selection and auditory stream segregation in a multi-talker situation
Authors: Kovács Petra , Tóth Brigitta , Honbolygó Ferenc , Szalárdy Orsolya , Kohári Anna , Mády Katalin , Magyari Lilla , Winkler István
Published: April 2022

To process speech in a multi-talker environment, listeners need to segregate the mixture of incoming speech streams and focus their attention on one of them. Potentially, speech prosody could aid the segregation of different speakers, the selection of the desired speech stream, and detecting targets within the attended stream. For testing these issues, we recorded behavioral responses and extracted event-related potentials and functional brain networks from electroencephalographic signals recorded while participants listened to two concurrent speech streams, performing a lexical detection and a recognition memory task in parallel. Prosody manipulation was applied to the attended speech stream in one group of participants and to the ignored speech stream in another group. Naturally recorded speech stimuli were either intact, synthetically F0-flattened, or suppressed by the speaker. Results show that prosody – especially the parsing cues mediated by speech rate – facilitates stream selection, while playing a smaller role in auditory stream segmentation and target detection.
Base editor scanning charts the DNMT3A activity landscape
Authors: Lue Nicholas Z. , Garcia Emma M. , Ngan Kevin C. , Lee Ceejay , Doench John G. , Liau Brian B.
Published: April 2022

DNA methylation is critical for regulating gene expression, necessitating its accurate placement by enzymes such as the DNA methyltransferase DNMT3A. Dysregulation of this process is known to cause aberrant development and oncogenesis, yet how DNMT3A is regulated holistically by its three domains remains challenging to study. Here we integrate base editing with a DNA methylation reporter to perform in situ mutational scanning of DNMT3A in cells. We identify mutations throughout the protein that perturb function, including ones at an interdomain interface that block allosteric activation. Unexpectedly, we also find mutations in the PWWP domain, a histone reader, that modulate enzyme activity despite preserving histone recognition and protein stability. These effects arise from altered PWWP domain DNA affinity, which we show is a noncanonical function required for full activity in cells. Our findings highlight mechanisms of interdomain crosstalk and demonstrate a generalizable strategy to probe sequence-activity relationships of nonessential chromatin regulators.
Cell-free, methylated DNA in blood samples reveals tissue-specific, cellular damage from radiation treatment
Authors: Barefoot Megan E. , Loyfer Netanel , Kiliti Amber J. , Schmidt Marcel O. , Shabi-Porat Sapir , Jain Sidharth , Roth Sarah Martinez , McDeed A. Patrick , Shahrour Nesreen , Ballew Elizabeth , Lin Yun-Tien , Li Heng-Hong , Mays Anne Deslattes , Rudra Sonali , Riegel Anna T. , Unger Keith , Kaplan Tommy , Wellstein Anton
Published: April 2022

Radiation therapy is an effective cancer treatment although damage to healthy tissues is common. Here we characterize the methylomes of healthy human and mouse tissues to establish sequencing-based, cell-type specific reference DNA methylation atlases. Identified cell-type specific DNA blocks were mostly hypomethylated and located within genes intrinsic to cellular identity. Cell-free DNA fragments released from dying cells into the circulation were captured from serum samples by hybridization to CpG-rich DNA panels. The origins of the circulating DNA fragments were inferred from mapping to the established DNA methylation atlases. Thoracic radiation-induced tissue damages in a mouse model were reflected by dose-dependent increases in lung endothelial, cardiomyocyte and hepatocyte methylated DNA in serum. The analysis of serum samples from breast cancer patients undergoing radiation treatment revealed distinct tissue-specific epithelial and endothelial responses to radiation across multiple organs. Strikingly, patients treated for right-sided breast cancers also showed increased hepatocyte and liver endothelial DNA in the circulation indicating the impact on liver tissues. Thus, changes in cell-free methylated DNA can uncover cell-type specific effects of radiation and provide a quantitative measure of the biologically effective radiation dose received by healthy tissues.

Graphical Abstract
Long-term balancing selection and the genetic load linked to the self-incompatibility locus inArabidopsis halleriandA. lyrata
Authors: Le Veve Audrey , Burghgraeve Nicolas , Genete Mathieu , Lepers-Blassiau Christelle , Takou Margarita , De Meaux Juliette , Mable Barbara K. , Durand Eléonore , Vekemans Xavier , Castric Vincent
Published: April 2022

Balancing selection is a form of natural selection maintaining diversity at the sites it targets and at linked nucleotide sites. Due to selection favouring heterozygosity, it has the potential to facilitate the accumulation of a “sheltered” load of tightly linked recessive deleterious mutations. However, precisely evaluating the extent of these effects has remained challenging. Taking advantage of plant self-incompatibility as one of the best-understood examples of long-term balancing selection, we provide a highly resolved picture of the genomic extent of balancing selection on the sheltered genetic load. We used targeted genome resequencing to reveal polymorphism of the genomic region flanking the self-incompatibility locus in three sample sets in each of the two closely related plant speciesArabidopsis halleriandA. lyrata, and used 100 control regions from throughout the genome to factor out differences in demographic histories and/or sample structure. Nucleotide polymorphism increased strongly around theS-locus in all sample sets, but only over a limited genomic region, as it became indistinguishable from the genomic background beyond the first 25-30kb. Genes in this chromosomal interval exhibited no excess of mutations at 0-fold degenerated sites relative to putatively neutral sites, hence revealing no detectable weakening of the efficacy of purifying selection even for these most tightly linked genes. Overall, our results are consistent with the predictions of a narrow genomic influence of linkage to theS-locus, and clarify how natural selection in one genomic region affects the evolution of the adjacent genomic regions.
Binding of different substrate molecules at the docking site and the active site of γ-secretase can trigger toxic events in sporadic and familial Alzheimer’s disease
Authors: Svedružić Željko M. , Jengić Vesna Šendula , Ostojić Lucija
Published: April 2022

Significance

pathogenic changes in γ-secretase activity, and its response to different drugs, can be greatly affected by changes in saturation of γ-secretase with its substrate. The molecular mechanism is unclear.

Results

multiscale molecular dynamics studies show that saturation of γ-secretase with its substrate can result in parallel binding of different substrate molecules at the docking site and the active site. C-terminal domain of the second substrate can bind at cytosolic end of presenilin subunit while γ-secretase is still processing its first substrate. Such interactions can disrupt dynamic presenilin structures that regulate proteolytic steps. Similar disruptions in dynamic presenilin structures can be produced by different drugs and by different disease-causing mutations. Thus, the presented two-substrate mechanism, can explain toxic inhibition of γ-secretase activity and toxic increase in production of the longer, more hydrophobic, Aβ-proteins. Toxic aggregation between N-terminal domains of the two substrates is controlled by nicastrin ectodomain. Such aggregation is more likely to happen with C99-βCTF-APP than with C83-αCTF-APP substrate, which can explain, why β-secretase path is more pathogenic than α-secretase path. The binding of C99-βCTF-APP substrate to γ-secretase can be controlled by substrate-channeling between nicastrin ectodomain and β-secretase.

Conclusions

The presented two-substrate mechanism can explain why different studies consistently show that increase in saturation of γ-secretase with its substrate can support pathogenic changes in different sporadic and familiar cases of the disease. Future drug-development strategies can target different physiological mechanisms that control the balance between cellular levels of γ-secretase activity and the total amyloid metabolism.
Monitoring extracellular ion and metabolite dynamics with recombinant nanobody-fused biosensors
Authors: Burgstaller Sandra , Wagner Teresa R. , Bischof Helmut , Bueckle Sarah , Padamsey Aman , Frecot Desiree I. , Kaiser Philipp D. , Skrabak David , Malli Roland , Lukowski Robert , Rothbauer Ulrich
Published: April 2022

The tumor microenvironment (TME) consists of different cell types that secrete proteins and also control the extracellular concentration of ions and metabolites. Changes in these intra-tumoral analytes and conditions, including K+, glucose, and pH, have been described to alter the metabolic activity of cancer cells, promote tumor cell growth, and impair anti-tumor immunity. However, the mechanisms regulating ion and metabolite levels and their effects on certain characteristics of the TME are still poorly understood. Therefore, accurate determination and visualization of analyte or state changes in real time within the TME is desired.

In this study, we genetically combined FRET-based fluorescent biosensors with nanobodies (Nbs) and used them for targeted visualization and monitoring of extracellular changes in K+, pH, and glucose on cell surfaces. We demonstrated that these recombinant biosensors quantitatively visualize extracellular K+ alterations on multiple cancer and non-cancer cell lines and primary neurons. By implementing a HER2 specific Nb, we generated K+ and pH sensors, which retain their functionality and specifically stained HER2 positive breast cancer cells. Based on the successful technical development of several Nb-biosensor combinations, we anticipate that this approach can be easily extended to design other targeted biosensors. Such versatile probes will open new possibilities for the reliable study of extracellular analytes in advanced 3D cell models or even in vivo systems.
Representation of illusory shapes within the topographic areas of the posterior parietal cortex
Authors: Arsenovic Ana , Ischebeck Anja , Zaretskaya Natalia
Published: April 2022

The human visual system consists of multiple topographic maps that extend from the early visual cortex along the dorsal and ventral processing streams. Responses to illusory shapes within these maps have been demonstrated in the ventral stream areas, in particular the lateral occipital complex. Recently, the intraparietal sulcus of the dorsal stream has been linked to the processing of illusory shapes defined by motion. It therefore remains unclear whether the topographically organized parietal areas also respond to static illusory shapes, which would suggest their generic role in representing illusory content. Here we measured brain responses using fMRI while human participants observed flickering inducers around the fixation task. The inducers either formed an illusory diamond in the center, a triangle in the left or in the right hemifield, or were inverted such that no illusory figure was formed. We compared responses of parietal regions IPS0-IPS5 and SPL1 to each illusory figure with the non-illusory condition. To determine the role of attention in illusory shape responses we manipulated the difficulty of the fixation task. Our results show that all IPS areas responded to illusory shapes. The more posterior areas IPS0-IPS3 additionally displayed a preference towards the contralateral shapes, while the more anterior areas IPS4 and IPS5 showed response attenuation with increased task difficulty. We suggest that the IPS can represent illusory content irrespective of the perceptual mechanism that generated it. These responses may serve as a potential feedback signal that drives illusory shape responses in early and ventral visual areas.

Significance statement

The traditional view of the ventral visual pathway being solely responsible for representation of objects has recently been challenged by demonstrating illusory shape representation within the dorsal visual pathway with moving bistable stimuli. Our results provide evidence for the dorsal stream contribution to representing not only moving, but also static illusory shapes. Our results also show a functional subdivision along the topographic maps, with spatially specific shape responses in the more posterior, and attention-dependent responses in the more anterior areas. IPS areas of the dorsal stream should thus be considered in the theoretical accounts and neural models of how subjective content is generated in the brain.
Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5
Authors: Clasen Sara J. , Bell Michael E. W. , Lee Du-Hwa , Henseler Zachariah M. , Borbón Andrea , de la Cuesta-Zuluaga Jacobo , Parys Katarzyna , Zou Jun , Youngblut Nicholas D. , Gewirtz Andrew T. , Belkhadir Youssef , Ley Ruth E.
Published: April 2022

Flagellin, the protein unit of the bacterial flagellum, stimulates the innate immune receptor Toll-like receptor (TLR)5 following pattern recognition, or evades TLR5 through lack of recognition. This binary response fails to explain the weak agonism of flagellins from commensal bacteria, raising the question of how TLR5 response is tuned. Here, we describe a novel class of flagellin-TLR5 interaction, termed silent recognition. Silent flagellins are weak agonists despite high affinity binding to TLR5. This dynamic response is tuned by TLR5-flagellin interaction distal to the site of pattern recognition. Silent flagellins are produced primarily by the abundant gut bacteria Lachnospiraceae and are enriched in non-Western populations. These findings provide a mechanism for the innate immune system to tolerate commensal-derived flagellins.

One-Sentence Summary

TLR5 sensitively recognizes, but responds weakly to, flagellins from gut commensal bacteria.
Melatonin suppression does not automatically alter sleepiness, vigilance, sensory processing, or sleep
Authors: Blume Christine , Niedernhuber Maria , Spitschan Manuel , Slawik Helen C. , Meyer Martin P. , Bekinschtein Tristan A. , Cajochen Christian
Published: April 2022

Pre-sleep exposure to short-wavelength light suppresses melatonin and decreases sleepiness with activating effects extending to sleep. This has mainly been attributed to melanopic effects, but mechanistic insights are missing. Thus, we investigated whether two light conditions only differing in the melanopic effects (123 vs. 59 lux melanopic EDI) differentially affect sleep besides melatonin. Additionally, we studied whether the light differentially modulates sensory processing during wakefulness and sleep.

Twenty-nine healthy volunteers (18-30 years, 15 women) were exposed to two metameric light conditions (high-vs. low-melanopic, ≈60 photopic lux) for 1 hour ending 50 min prior to habitual bed time. This was followed by an 8-h sleep opportunity with polysomnography. Objective sleep measurements were complemented by self-report. Salivary melatonin, subjective sleepiness, and behavioural vigilance were sampled at regular intervals. Sensory processing was evaluated during light exposure and sleep on the basis of neural responses related to violations of expectations in an oddball paradigm.

We observed suppression of melatonin by ≈14 % in the high-compared to the low-melanopic condition. However, conditions did not differentially affect sleep, sleep quality, sleepiness, or vigilance. A neural mismatch response was evident during all sleep stages, but not differentially modulated by light.

Suppression of melatonin by light targeting the melanopic system does not automatically translate to acutely altered levels of vigilance or sleepiness or to changes in sleep, sleep quality, or basic sensory processing. Given contradicting earlier findings and the retinal anatomy, this may suggest that an interaction between melanopsin and cone-rod signals needs to be considered.

Statement of Significance

Metameric light allows to mechanistically investigate the contribution of one specific retinal receptor. Using this approach, we here investigated the effects of high-vs. low-melanopic light for 1 hour in the evening at ecologically valid screen illuminance (≈60 photopic lux). Going beyond earlier research, we also investigated effects on sleep. We found that despite significant suppression of melatonin, other endpoints including sleep and sleep quality were not differentially affected. This underlines that melatonin suppression does not automatically translate to alterations of sleep, sleepiness, or vigilance. Further, it suggests that melanopsin effects may need to be studied in the context of cone-rod signals. Future research should thus investigate the relevance of such an interaction, which may vary between endpoints.
Control and coding of pupil size by hypothalamic orexin neurons
Authors: Grujic Nikola , Tesmer Alexander , Bracey Ed F. , Peleg-Raibstein Daria , Burdakov Denis
Published: April 2022

Brain orexin (hypocretin) neurons are implicated in sleep-wake switching and reward-seeking, but their roles in rapid arousal dynamics and reward perception remain unclear. Here, cellspecific stimulation, deletion, and in vivo recordings revealed strong correlative and causal links between pupil dilation - a quantitative arousal marker - and orexin cell activity. Coding of arousal and reward was distributed across orexin cells, indicating that they specialize in rapid, multiplexed communication of momentary arousal and reward states.
Expanding adult tubular microvessels on stiff substrates with endothelial cells and pericytes from the same tissue
Authors: Song Xiuyue , Yu Yali , Mu Jie , Wang Zihan , Leng Yu , Xu Yalan , Zhu Hai , Qiu Xuefeng , Li Peifeng , Li Jing , Wang Dong
Published: April 2022

Microvessels are essential for tissue engineering and regeneration. In current methods, endothelial cells are usually cultured in commercially available media and form a monolayer of cell sheets on stiff substrates and a tubular structure when cultured with soft hydrogels. To mimic the microvessels in vivo, researchers usually coculture the endothelial cells and pericytes from different adult tissues or derived from pluripotent stem cells in a three-dimensional hydrogel. However, there is a challenge for these models to reflect tissue-specific characteristics due to the vascular heterogeneity throughout the body. Here, we established a culture model for expanding adult tubular microvessels on stiff substrates with endothelial cells and pericytes derived from the same tissue. We isolated microvessels from adult rat subcutaneous soft connective tissue and cultured them on regular plastic dishes. We performed a series of screenings and formulated a custom-made medium (Medium-X), containing mainly antioxidants and three small molecules, Chir99021, A83-01, and Y27632. Medium-X significantly promoted adult microvessel growth while maintaining their characteristic tubular morphology up to 8 weeks in vitro, contrary to the monolayer of endothelial cell sheets in the commercially available medium EGM2MV. Transcriptomic analysis showed that Medium-X maintained the tubular morphology of microvessels by promoting angiogenesis and vascular remodeling while suppressing oxidation and lipid metabolic pathways. The model presented in this study can be applied to other organs for expanding organ-specific microvessels for tissue engineering and vascular regeneration.
BirdFlow: Learning Seasonal Bird Movements from eBird Data
Authors: Fuentes Miguel , Van Doren Benjamin M. , Fink Daniel , Sheldon Daniel
Published: April 2022

Large-scale monitoring of seasonal animal movement is integral to science, conservation, and outreach. However, gathering representative movement data across entire species ranges is frequently intractable. Citizen science databases collect millions of animal observations throughout the year, but it is challenging to infer individual movement behavior solely from observational data. We present BirdFlow, a probabilistic modeling framework that draws on citizen science data from the eBird database to model the population flows of migratory birds. We apply the model to 11 species of North American birds, using GPS and satellite tracking data to tune and evaluate model performance. We show that BirdFlowmodels can accurately infer individual seasonal movement behavior directly from eBird relative abundance estimates. Supplementing the model with a sample of tracking data from wild birds improves performance. Researchers can extract a number of behavioral inferences from model results, including migration routes, timing, connectivity, and forecasts. The BirdFlowframework has the potential to advance migration ecology research, boost insights gained from direct tracking studies, and serve a number of applied functions in conservation, disease surveillance, aviation, and public outreach.
Climatic niche conservatism and ecological diversification in the Holarctic cold-dwelling butterfly genusErebia
Authors: Klečková Irena , Klečka Jan , Fric Zdeněk Faltýnek , Česánek Martin , Dutoit Ludovic , Pellissier Loïc , Matos-Maraví Pável
Published: April 2022

The diversification of alpine species has been modulated by their climatic niches interacting with changing climatic conditions. The relative roles of climatic niche conservatism promoting geographical speciation and of climatic niche diversification are poorly understood in diverse temperate groups. Here, we investigate the climatic niche evolution in a species rich butterfly genus,Erebia. This Holarctic cold-dwelling genus reaches the highest diversity in European mountains. We generated a nearly complete molecular phylogeny and modelled the climatic niche evolution using geo-referenced occurrence records. We reconstructed the evolution of the climatic niche and tested how the species’ climatic niche width changes across the occupied climate gradient and compared two mainErebiaclades, the European and the Asian clade. We further explored climatic niche overlaps among species. Our analyses revealed that the evolution ofErebiahas been shaped by climatic niche conservatism, supported by a strong phylogenetic signal and niche overlap in sister species, likely promoting allopatric speciation. The European and the Asian clades evolved their climatic niches toward different local optima. In addition, species in the European clade have narrower niches compared to the Asian clade. Contrasts among the clades may be related to regional climate differences, with lower climate seasonality in Europe compared to Central Asia favouring the evolution of narrower niches. Further, adaptive divergence could appear in other traits, such as habitat use, which can be reflected by narrower climatic niches detected in the European clade. In conclusion, our study extends knowledge about the complexity of evolutionary drivers in temperate insects.
Purification and Characterization of Inorganic Pyrophosphatase for in vitro RNA Transcription
Authors: Tersteeg Scott , Mrozowich Tyler , Henrickson Amy , Demeler Borries , Patel Trushar R
Published: April 2022

Inorganic pyrophosphatase (iPPase) is an enzyme that cleaves pyrophosphate into two phosphate molecules. This enzyme is an essential component of in vitro transcription (IVT) reactions for RNA preparation as it prevents pyrophosphate from precipitating with magnesium, ultimately increasing the rate of the IVT reaction. Large-scale RNA production is often required for biochemical and biophysical characterization studies of RNA, therefore requiring large amounts of IVT reagents. Commercially purchased iPPase is often the most expensive component of any IVT reaction. In this paper, we demonstrate that iPPase can be produced in large quantities and of high quality using a reasonably generic laboratory facility and that laboratory-purified iPPase is as effective as commercially available iPPase. Furthermore, using size-exclusion chromatography coupled with multi-angle light scattering and dynamic light scattering (SEC-MALS-DLS), analytical ultracentrifugation (AUC), and small-angle X-ray scattering (SAXS), we demonstrate that yeast iPPase can form tetramers and hexamers in solution as well as the enzymatically active dimer. Our work provides a robust protocol for labs involved with RNA in vitro transcription to efficiently produce active iPPase, significantly reducing the financial strain of large-scale RNA production.

Statement of Significance

We show an easy two-step purification procedure to efficiently produce large quantities of iPPase, an expensive component of IVT reactions. Laboratory-produced iPPase can significantly reduce the financial strain on research labs that rely on large-scale RNA production for experiments. Furthermore, we show for the first time, using a combination of orthogonal biophysical techniques, that yeast iPPase assembles into higher-order oligomers similar to bacterial iPPase.
The effect of trans-cinnamic acid isolated from the root cultures of the Baikal skullcap (Scutellaria baicalensis) on the life expectancy and survival of Caenorhabditis elegans
Authors: Dyshlyuk Lyubov Sergeevna , Drozdova Margarita Yuryevna , Dolganyuk Vyacheslav Fedorovich
Published: April 2022

Oxidative stress is an increase in reactive oxygen species, which are signaling molecules of various pathologies in the body of living beings. Baikal skullcap (Scutellaria baicalensis) is a valuable source of biologically active substances with various pharmacological activity. The aim of the study is to study the effect of trans-cinnamic acid isolated from root cultures of Scutellaria baicalensis on the lifespan of a model organism of C. elegans, as well as its survival under conditions of oxidative and thermal stress. It was shown that trans-cinnamic acid increased the lifespan of nematodes, while the best concentration of phytomaterials was 50 microns. In addition, all tested concentrations (10-200) had a positive effect on nematodes under oxidative stress caused by paraquat. No positive effect of trans-cinnamic acid was detected during thermal exposure. In general, the results show the antioxidant potential of trans-cinnamic acid from plant material under oxidative stress, as well as the positive effect of the substance on the lifespan of C. elegans.
Polar growth protein Wag31 undergoes changes in homo-oligomeric network topology, and has distinct functions at both cell poles and the septum
Authors: Arejan Neda Habibi , Patel Parthvi Bharatkumar , Quintanilla Samantha Y. , Saleh Arash Emami , Boutte Cara C.
Published: April 2022

Mycobacterial cell elongation occurs at the cell poles; however, it is not clear how cell wall insertion is restricted to the pole and organized. Wag31 is a pole-localized cytoplasmic protein that is essential for polar growth, but its molecular function has not been described. Wag31 homo-oligomerizes in a network at the poles, but it is not known how the structure of this network affects Wag31 function. In this study we used a protein fragment complementation assay to identify Wag31 residues involved in homo-oligomeric interactions, and found that amino acids all along the length of the protein mediate these interactions. We then used both N-terminal and C-terminal splitGFP fusions to probe Wag31 network topology at different sites in the cell, and found that Wag31 C-terminal-C-terminal interactions predominate at the septa, while C-terminal-C-terminal and C-terminal-N-terminal interactions are found equally at the poles. This suggests the Wag31 network is formed through an ordered series of associations. We then dissected Wag31’s functional roles by phenotyping a series of wag31 alanine mutants; these data show that Wag31 has separate functions in not only new and old pole elongation, but also inhibition of both septation and new pole elongation. This work establishes new functions for Wag31, and indicates that changes in Wag31 homo-oligomeric network topology may contribute to cell wall regulation in mycobacteria.

Importance

Many bacteria restrict cell wall elongation to their cell poles, but it is not known how polar growth is affected on the molecular level. Wag31 is a protein that is required for this polar elongation. In this work, we show that Wag31 actually has at least four distinct functions in regulating the cell wall: it promotes elongation at both poles in different ways, and it can also inhibit cell wall metabolism at the new pole and the septum. In addition, we propose a new model for how Wag31 self-associates into a protein network. This work is important because it shows that a DivIVA homolog can have distinct functions depending on cell context. And, this work clarifies that Wag31 is doing several different things in the cell, and gives us genetic tools to disentangle its functions.