bluuebunny/crossref_metadata_2025 huggingface dataset:
Timing of Breakthrough Infection Risk After Vaccination Against SARS-CoV-2
Authors: Fisman David N. , Lee Nelson , Tuite Ashleigh R.
Published: January 2022

Background

Provision of safe and effective vaccines has been a remarkable public health achievement during the SARS-CoV-2 pandemic. The effectiveness and durability of protection of the first two doses of SARS-CoV-2 vaccines is an important area for study, as are questions related to optimal dose combinations and dosing intervals.

Methods

We performed a case-cohort study to generate real-world evidence on efficacy of first and second dose of SARS-CoV-2 vaccines, using a population-based case line list and vaccination database for the province of Ontario, Canada between December 2020 and October 2021. Risk of infection after vaccination was evaluated in all laboratory-confirmed vaccinated SARS-CoV-2 cases, and a 2% sample of vaccinated controls, evaluated using survival analytic methods, including construction of Cox proportional hazards models. Vaccination status was treated as a time-varying covariate.

Results

First and second doses of SARS-CoV-2 vaccine markedly reduced risk of infection (first dose efficacy 68%, 95% CI 67% to 69%; second dose efficacy 88%, 95% CI 87 to 88%). In multivariable models, extended dosing intervals were associated with lowest risk of breakthrough infection (HR for redosing 0.64 (95% CI 0.61 to 0.67) at 6-8 weeks). Heterologous vaccine schedules that mixed viral vector vaccine first doses with mRNA second doses were significantly more effective than mRNA only vaccines. Risk of infection largely vanished during the time period 4-6 months after the second vaccine dose, but rose markedly thereafter.

Interpretation

A case-cohort design provided an efficient means to identify strong protective effects associated with SARS-CoV-2 vaccination, particularly after the second dose of vaccine. However, this effect appeared to wane once more than 6 months had elapsed since vaccination. Heterologous vaccination and extended dosing intervals improved the durability of immune response.
Engineered collagen-targeting therapeutics reverse lung and kidney fibrosis in mice
Authors: White Michael JV , Raczy Michal M , Budina Erica , Yuba Eiji , Solanki Ani , Shim Ha-Na , Zhang Zheng Jenny , Gray Laura T , Cao Shijie , Alpar Aaron T. , Hubbell Jeffrey A
Published: January 2022

Fibrotic diseases are involved in 45% of deaths in the United States. In particular, fibrosis of the kidney and lung are major public health concerns due to their high prevalence and lack of existing treatment options. Here, we harness the pathophysiological features of fibrotic diseases, namely leaky vasculature and aberrant extracellular matrix (ECM) protein deposition (i.e. collagen), to target an anti-fibrotic biologic and a small molecule drug to disease sites of fibrosis, thus improving their therapeutic potential in mouse models of lung and kidney fibrosis. First, we identify and validate collagen-targeting drug delivery systems that preferentially accumulate in the diseased organs: von Willebrand Factor’s A3 domain (VWF-A3) and decorin-derived collagen-binding peptide-conjugated micelles (CBP-micelles). We then engineer and recombinantly express novel candidate biologic therapies based on the anti-inflammatory cytokine IL-10: A3-IL-10 and A3-Serum Albumin-IL-10 (A3-SA-IL-10). Simultaneously, we stably encapsulate the potential anti-fibrotic water-insoluble drug, rapamycin, in CBP-micelles. We show that these novel formulations of therapeutics bind to collagen in vitro and that their efficacy in mouse models of lung and kidney fibrosis is improved, compared to free, untargeted drugs. Our results demonstrate that collagen-targeted anti-fibrotic drugs may be next generation therapies of high clinical potential.
Texture-like representation of objects in human visual cortex
Authors: Jagadeesh Akshay V. , Gardner Justin L.
Published: January 2022

The human visual ability to recognize objects and scenes is widely thought to rely on representations in category-selective regions of visual cortex. These representations could support object vision by specifically representing objects, or, more simply, by representing complex visual features regardless of the particular spatial arrangement needed to constitute real world objects. That is, by representing visual textures. To discriminate between these hypotheses, we leveraged an image synthesis approach that, unlike previous methods, provides independent control over the complexity and spatial arrangement of visual features. We found that human observers could easily detect a natural object among synthetic images with similar complex features that were spatially scrambled. However, observer models built from BOLD responses from category-selective regions, as well as a model of macaque inferotemporal cortex and Imagenet-trained deep convolutional neural networks, were all unable to identify the real object. This inability was not due to a lack of signal-to-noise, as all of these observer models could predict human performance in image categorization tasks. How then might these texture-like representations in category-selective regions support object perception? An image-specific readout from category-selective cortex yielded a representation that was more selective for natural feature arrangement, showing that the information necessary for object discrimination is available. Thus, our results suggest that the role of human category-selective visual cortex is not to explicitly encode objects but rather to provide a basis set of texture-like features that can be infinitely reconfigured to flexibly learn and identify new object categories.

Significance Statement

Virtually indistinguishable metamers of visual textures, such as wood grain, can be synthesized by matching complex features regardless of their spatial arrangement (1–3). However, humans are not fooled by such synthetic images of scrambled objects. Thus, category-selective regions of human visual cortex might be expected to exhibit representational geometry preferentially sensitive to natural objects. Contrarily, we demonstrate that observer models based on category-selective regions, models of macaque inferotemporal cortex and Imagenet-trained deep convolutional neural networks do not preferentially represent natural images, even while they are able to discriminate image categories. This suggests the need to reconceptualize the role of category-selective cortex as representing a basis set of complex texture-like features, useful for a myriad of visual behaviors.
Theoretical model of efficient phagocytosis driven by curved membrane proteins and active cytoskeleton forces
Authors: Sadhu Raj Kumar , Barger Sarah R , Penič Samo , Iglič Aleš , Krendel Mira , Gauthier Nils C , Gov Nir S
Published: January 2022

Phagocytosis is the process of engulfment and internalization of comparatively large particles by the cell, that plays a central role in the functioning of our immune system. We study the process of phagocytosis by considering a simplified coarse grained model of a three-dimensional vesicle, having uniform adhesion interaction with a rigid particle, in the presence of curved membrane proteins and active cytoskeletal forces. Complete engulfment is achieved when the bending energy cost of the vesicle is balanced by the gain in the adhesion energy. The presence of curved (convex) proteins reduces the bending energy cost by self-organizing with higher density at the highly curved leading edge of the engulfing membrane, which forms the circular rim of the phagocytic cup that wraps around the particle. This allows the engulfment to occur at much smaller adhesion strength. When the curved proteins exert outwards protrusive forces, representing actin polymerization, at the leading edge, we find that engulfment is achieved more quickly and at lower protein density. We consider spherical as well as non-spherical particles, and find that non-spherical particles are more difficult to engulf in comparison to the spherical particles of the same surface area. For non-spherical particles, the engulfment time crucially depends upon the initial orientation of the particles with respect to the vesicle. Our model offers a mechanism for the spontaneous self-organization of the actin cytoskeleton at the phagocytic cup, in good agreement with recent high-resolution experimental observations.

Significance Statement

Phagocytosis is an important process that plays a central role in our immune system, and also during nutrient uptake, drug delivery and pathogen invasion. Despite its biological importance, it is still not understood how the actin cytoskeleton is coordinated spatio-temporally during the phagocytosis process. We present a simple model that explains the dynamics and self-organization of the membrane and the actin cytoskeleton during the engulfment process, based on curved membrane activators of actin polymerization.
Comparative whole plastome and low copy number phylogenetics of the core Saccharinae and Sorghinae
Authors: Evans Dyfed Lloyd , Hughes Ben , Joshi Shailesh Vinay
Published: January 2022

Abstract

Despite over 60 years’ worth of taxonomic efforts, the relationships between sugarcane (Saccharum hybrid cultivars), Sorghum and their closest evolutionary relatives remain largely unresolved. Even relationships between generally accepted genera such as Miscanthus and Saccharum have not been examined in any large-scale molecular detail. Genera such as Erianthus, Miscanthidium and Narenga pose even greater taxonomic contention. Erianthus is not monophyletic and Erianthus sect. Ripidium (Valdés and Scholz 2006, Lloyd Evans et al. 2019a; Welker et al. 2019) represents a distinct and separate genus, Tripidium Scholz. Miscanthidium is placed within Miscanthus by many workers, whilst the New World Erianthus species and Narenga are currently placed within Saccharum. As these species represent a significant portion of the gene pool that sugarcane breeders use for introgression into sugarcane, their taxonomic placement and relationships to Saccharum are of significant economic import. Erianthus species from the Americas have not been significantly employed in sugarcane breeding and may represent an untapped genetic resource. In an attempt to resolve the taxonomic relationships of these genera, we have assembled three novel chloroplasts, from Miscanthidium capense, Miscanthidium junceum and Narenga porphyrocoma (this latter assembled from transcriptomic and long read data). In parallel, five low copy number loci have been assembled from species within Saccharum, Miscanthus, Sarga and Sorghum. Phylogenetic analyses were performed using both low copy number genes and whole chloroplasts. The phylogenetic results were compared with karyotype data to circumscribe the genera most closely related to sugarcane. We reveal that genera Miscanthus and Saccharum are monophyletic and have never undergone polyploidization outside their own genera. Genera Erianthus, Miscanthidium and Narenga are allopolyploids, which excludes them from being members of Saccharum and Miscanthus. Moreover, all three of these genera have divergent evolutionary histories. We therefore support the use of the genera Miscanthus, Miscanthidium, Erianthus (for the New World Species) and Narenga for those species and genera most closely allied to Saccharum. Our data demonstrate that all these genera should be excluded from Saccharum sensu lato.
B1 SINE-binding ZFP266 impedes reprogramming through suppression of chromatin opening mediated by pioneering factors
Authors: Kaemena Daniel F , Yoshihara Masahito , Ashmore James , Beniazza Meryam , Zhao Suling , Bertenstam Mårten , Olariu Victor , Katayama Shintaro , Okita Keisuke , Tomlinson Simon R , Yusa Kosuke , Kaji Keisuke
Published: January 2022

Induced pluripotent stem cell reprogramming is inherently inefficient and understanding the molecular mechanisms underlying this inefficiency holds the key to successfully control cellular identity. Here, we report 16 novel reprogramming roadblock genes identified by CRISPR/Cas9-mediated genome-wide knockout (KO) screening. Of these, depletion of the predicted KRAB zinc finger protein (KRAB-ZFP) Zfp266 strongly and consistently enhanced iPSC generation in several iPSC reprogramming settings, emerging as the most robust roadblock. Further analyses revealed that ZFP266 binds Short Interspersed Nuclear Elements (SINEs) adjacent to binding sites of pioneering factors, OCT4 (POU5F1), SOX2 and KLF4, and impedes chromatin opening. Replacing the KRAB co-suppressor with a co-activator domain converted ZFP266 from a reprogramming inhibitor to a potent reprogramming facilitator. This work proposes SINE-KRAB-ZFP interaction to be a critical regulator of chromatin accessibility at enhancers for efficient cellular identity changes and also serves as a resource to further illuminate molecular mechanisms hindering reprogramming.
PDBspheres - a method for finding 3D similarities in local regions in proteins
Authors: Zemla Adam T. , Allen Jonathan E. , Kirshner Dan , Lightstone Felice C.
Published: January 2022

We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres comprises an exhaustive library of protein structure regions (“spheres”) adjacent to complexed ligands derived from the Protein Data Bank (PDB), along with methods to find and evaluate structural matches between a protein of interest and spheres in the library. PDBspheres uses the LGA structure alignment algorithm as the main engine for detecting structure similarities between the protein of interest and template spheres from the library, which currently contains more than 2 million spheres. To assess confidence in structural matches an all-atom-based similarity metric takes sidechain placement into account. Here, we describe the PDBspheres method, demonstrate its ability to detect and characterize binding sites in protein structures, show how PDBspheres - a strictly structure-based method - performs on a curated dataset of 2,528 ligand-bound and ligand-free crystal structures, and use PDBspheres to cluster pockets and assess structural similarities among protein binding sites of 4,876 structures in the “refined set” of the PDBbind 2019 dataset.
PACpAInt: a deep learning approach to identify molecular subtypes of pancreatic adenocarcinoma on histology slides
Authors: Saillard C. , Delecourt F. , Schmauch B. , Moindrot O. , Svrcek M. , Bardier-Dupas A. , Emile J-F. , Ayadi M. , Rebours V. , de Mestier L. , Hammel P. , Neuzillet C. , Bachet J-B. , Iovanna J. , Dusetti N. , Blum Y. , Richard M. , Kermezli Y. , Paradis V. , Zaslavskiy M. , Courtiol P. , Kamoun A. , Nicolle R. , Cros J.
Published: January 2022

Pancreatic ductal adenocarcinoma (PAC) is a highly heterogeneous and plastic tumor with different transcriptomic molecular subtypes that hold great prognostic and theranostic values. We developed PACpAInt, a multistep approach using deep learning models to determine tumor cell type and their molecular phenotype on routine histological preparation at a resolution enabling to decipher complete intratumor heterogeneity on a massive scale never achieved before. PACpAInt effectively identified molecular subtypes at the slide level in three validation cohorts and had an independent prognostic value. It identified an interslide heterogeneity within a case in 39% of tumors that impacted survival. Diving at the cell level, PACpAInt identified “pure” classical and basal-like main subtypes as well as an intermediary phenotype and hybrid tumors that co-carried both classical and basal-like phenotypes. These novel artificial intelligence-based subtypes, together with the proportion of basal-like cells within a tumor had a strong prognostic impact.
Deterministic approximation for population dynamics in the presence of advantageous mutants
Authors: Rodriguez-Brenes Ignacio A. , Wodarz Dominik , Komarova Natalia L.
Published: January 2022

Spatial stochastic simulations of evolutionary processes are computationally expensive. Here, based on spatially explicit decoupling approximations (SEDA) introduced in [1], we derive a deterministic approximation to a spatial stochastic birth-death process in the presence of two types: the less advantageous resident type and a more advantageous mutant. At the core of this technique are two essential steps: (1) a system of ODEs that approximate spatial interactions among neighboring individuals must be solved; (2) the time-variable has to be rescaled with a factor (called “α”) that depends on the kinetic parameters of the wild type and mutant individuals. An explicit formula for α is derived, which is a power law of division and death rates of the two types. The method is relatively fast and provides excellent time-series agreement with the stochastic simulation results for the spatial agent-based model. The methodology can be used to describe hard selective sweep events, including the expansion of driver mutations in carcinogenesis, bacterial evolution, and aspects of resistance dynamics.
Automated Landmarking via Multiple Templates
Authors: Zhang Chi , Porto Arthur , Rolfe Sara , Kocatulum Altan , Maga A. Murat
Published: January 2022

Geometric morphometrics based on landmark data has been increasingly used in biomedical and biological research for quantifying complex phenotypes. However, manual landmarking can be laborious and subject to intra and interobserver errors. This has motivated the development of automated landmarking methods. We have recently introduced ALPACA (Automated Landmarking through Point Cloud Alignment and Correspondence), a fast method to automatically annotate landmarks via the use of a landmark template as a part of the SlicerMorph toolkit. Yet, using a single template may not consistently perform well for large study samples, especially when the sample consists of specimens with highly variable morphology, as it is common in evolutionary studies. In this study, we introduce a variation on our ALPACA pipeline that supports multiple specimen templates, which we call MALPACA. We show that MALPACA outperforms ALPACA consistently by testing on two different datasets. We also introduce a method of choosing the templates that can be used in conjunction with MALPACA, when no prior information is available. This K-means method uses an approximation of the total morphological variation in the dataset to suggest samples within the population to be used as landmark templates. While we advise investigators to pay careful attention to the template selection process in any of the template-based automated landmarking approaches, our analyses show that the introduced K-means based method of templates selection is better than randomly choosing the templates. In summary, MALPACA can accommodate larger morphological disparity commonly found in evolutionary studies with performance comparable to human observer.
Apical and basal auxin sources pattern shoot branching in a moss
Authors: Thelander Mattias , Landberg Katarina , Muller Arthur , Cloarec Gladys , Cunniffe Nik , Huguet Stéphanie , Soubigou-Taconnat Ludivine , Brunaud Véronique , Coudert Yoan
Published: January 2022

Shoot branching mechanisms where branches arise in association with leaves – referred to as lateral or axillary branching – evolved by convergence in the sporophyte of vascular plants and the gametophyte of bryophytes, and accompanied independent events of plant architectural diversification1. Previously, we showed that three hormonal cues, including auxin, have been recruited independently to co-ordinate branch patterning in flowering plant leafy shoots and moss gametophores (Coudert, Palubicki et al., 2015)2–4. Moreover, auxin-mediated apical dominance, which relies on local auxin production, has been proposed as a unifying molecular regulatory mechanism of branch development across land plants5. Whilst our previous work in the moss Physcomitrium patens has gathered indirect evidence supporting the notion that auxin synthesized in gametophore apices regulates branch formation at a distance2, direct genetic evidence for a role of auxin biosynthesis in gametophore branching control is still lacking. Here, we show that gametophore apex decapitation promotes branch emergence through massive and rapid transcriptional reprogramming of auxin-responsive genes and altering auxin biosynthesis gene activity. Specifically, we identify a subset of P. patens TRYPTOPHAN AMINO-TRANSFERASE (TAR) and YUCCA FLAVIN MONOOXYGENASE-LIKE (YUC) auxin biosynthesis genes expressed in apical and basal regions of the gametophore, and show that they are essential for branch initiation and outgrowth control. Our results demonstrate that local auxin biosynthesis coordinates branch patterning in moss and thus constitutes a shared and ancient feature of shoot architecture control in land plants.
The formation of a fuzzy complex in the negative arm regulates the robustness of the circadian clock
Authors: Jankowski Meaghan S. , Griffith Daniel , Shastry Divya G. , Pelham Jacqueline F. , Ginell Garrett M. , Thomas Joshua , Karande Pankaj , Holehouse Alex S. , Hurley Jennifer M.
Published: January 2022

The circadian clock times cellular processes to the day/night cycle via a Transcription-Translation negative Feedback Loop (TTFL). However, a mechanistic understanding of the negative arm in both the timing of the TTFL and its control of output is lacking. We posited that the formation of negative-arm protein complexes was fundamental to clock regulation stemming from the negative arm. Using a modified peptide microarray approach termed Linear motif discovery using rational design (LOCATE), we characterized the interaction of the disordered negative-arm clock protein FREQUENCY to its partner protein FREQUENCY-Interacting RNA helicase. LOCATE identified a specific Short Linear Motif (SLiM) and interaction “hotspot” as well as positively charged “islands” that mediate electrostatic interactions, suggesting a model where negative arm proteins form a “fuzzy” complex essential for clock timing and robustness. Further analysis revealed that the positively charged islands were an evolutionarily conserved feature in higher eukaryotes and contributed to proper clock function.
Variable Shh and Fgf8 positioning in regenerating axolotl limb guarantees consistent limb morphogenesis in different limb sizes
Authors: Furukawa Saya , Yamamoto Sakiya , Kashimoto Rena , Morishita Yoshihiro , Satoh Akira
Published: January 2022

Limb regeneration in Ambystoma mexicanum occurs in various size fields and can recreate consistent limb morphology. The mechanism that supports such stable limb morphogenesis regardless of size is unknown. Sonic hedgehog (SHH) and fibroblasts growth factor 8 (FGF8) play important roles in anteroposterior limb patterning, similar to other tetrapods. Focusing on these two factors, we investigated the detailed expression pattern and function of Shh and Fgf8 in various blastema sizes in axolotl limb regeneration. We measured and functionally analyzed the expression domains of Shh and Fgf8 in regenerating limb blastema of various sizes, and found that, although the position and size of the Shh+ and Fgf8+ domains varied depending on the size of the blastema, the secretion of SHH was maintained at a relatively fixed working distance, regardless of blastema size. This stable secretory distance of SHH resulted in the formation of an active proliferative zone (aPZ) in the vicinity of SHH, regardless of blastema size. The aPZ was under the mitogenic influence of SHH and FGF8, resulting in high cell density in the aPZ. We also examined the impact of the aPZ on digit formation. We found that the first digit formation occurs in the aPZ. Next, the aPZ gradually shifts posteriorly as digits develop, which contributes to new digit formation at the site of the shifted aPZ. We also found that the exogenously formed aPZ caused extra digit formation even after the completion of autopod morphogenesis. Our findings suggest that the variable Shh-Fgf8 positioning in various blastema sizes causes various positioning of the aPZ, and that the aPZ leads to digit formation. The mechanism we propose here accounts for stable digit morphogenesis regardless of blastema sizes and urodele-specific digit formation.

One-Sentence Summary

A unique SHH-FGF8 spatial interaction compensates for robust limb morphogenesis in various limb sizes.
Personal Resilience, Social Support, and Organizational Support Impact Burnout among Nurses During COVID-19
Authors: Daghash Hanan
Published: January 2022

Background

Nurses have been under heavy workloads since the outbreak of COVID-19 and are at a high risk of infection, leading to a high level of psychosocial risk. This can adversely affect nurses both psychologically and physically. Burnout is caused by prolonged stress during work. In the nursing profession, burnout is common, potentially affecting the well-being of nurses and their productivity. The identification of factors that may contribute to maintaining mental health and reducing burnout among frontline nurses during a pandemic is essential.

Purpose

The purpose of this study was to explore how personal resilience, social support, and organizational support impact burnout among frontline staff nurses.

Methods

This study involved 129 registered nurses from a COVID-19 designated hospital using four standardized scales.

Results

The mean age of the respondents was 29.46 years (standard deviation = 4.89). The mean number of years respondents worked in this organization was 5.60 years and the nursing profession was 4.16 years. Most of the respondents were female and held a bachelor’s degree in nursing. Multiple regression analysis was performed to predict burnout. Burnout was statistically significantly predicted by the multiple regression model (R2 = .420, F (3, 125) = 10.941, p < .0001; adjusted R2 = .406). Personal resilience, social support, and organizational support added statistically significantly to the prediction of burnout (p < .05).

Conclusion

Findings from multiple regression analysis showed that nurses with low resilience and those who perceived inadequate social and organizational support had a higher risk of reporting more burnout. As a result of a bivariate analysis, there was no significant correlation between nurse variables and burnout level, except for age, which was negatively correlated with burnout level. Accordingly, young nurses tend to experience burnout, and nurse directors and managers must address this problem.
Spatial scales of competition and a growth-motility tradeoff interact to determine bacterial coexistence
Authors: Kuhn Thierry , Mamin Marine , Bindschedler Saskia , Bshary Redouan , Estoppey Aislinn , Gonzalez Diego , Palmieri Fabio , Junier Pilar , Richter Xiang-Yi Li
Published: January 2022

1.

The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth-motility tradeoff. To test this hypothesis, we let twoPseudomonas putidastrains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth-motility tradeoff promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.
Cryo-EM structure of human somatostatin receptor 2 complex with its agonist somatostatin delineates the ligand binding specificity
Authors: Heo Yunseok , Yoon Eojin , Jeon Ye-Eun , Yun Ji-Hye , Ishimoto Naito , Woo Hyeonuk , Park Sam-Yong , Song Ji-Joon , Lee Weontae
Published: January 2022

Somatostatin is a peptide hormone regulating endocrine systems through binding to G-protein-coupled somatostatin receptors. somatostatin receptor 2 (SSTR2) is one of the human somatostatin receptors and highly implicated in cancers and neurological disorders. Here, we report the high resolution cryo-EM structure of full-length human SSTR2 bound to the agonist somatostatin (SST-14) complex with inhibitory G (Gi) proteins. Our structure shows that seven transmembrane helices form a deep pocket for ligand binding and that the highly conserved Trp-Lys motif of SST-14 positions at the bottom of the pocket. Furthermore, our sequence analysis combined with AlphaFold modeled structures of other SSTR isoforms provide how SSTR family proteins specifically interact with their cognate ligands. This work provides the first glimpse into the molecular recognition of somatostatin receptor and crucial resource to develop therapeutics targeting somatostatin receptors.
Transcriptional and cell type profiles of cortical brain regions showing ultradian cortisol rhythm dependent responses to emotional face stimulation
Authors: Habets Philippe C , Kalafatakis Konstantinos , Dzyubachyk Oleh , van der Werff Steven J.A. , Keo Arlin , Thakrar Jamini , Mahfouz Ahmed , Pereira Alberto M , Russell Georgina M , Lightman Stafford L , Meijer Onno C
Published: January 2022

The characteristic endogenous circadian rhythm of plasma glucocorticoid concentrations is made up from an underlying ultradian pulsatile secretory pattern. Recent evidence has indicated that this ultradian cortisol pulsatility is crucial for normal emotional response in man. In this study, we investigate the anatomical transcriptional and cell type signature of brain regions sensitive to a loss of ultradian rhythmicity in the context of emotional processing. We combine human cell type and transcriptomic atlas data of high spatial resolution with functional magnetic resonance imaging (fMRI) data. We show that the loss of cortisol ultradian rhythm alters emotional processing response in cortical brain areas that are characterized by transcriptional and cellular profiles of GABAergic function. We find that two previously identified key components of rapid non-genomic GC signaling – the ANXA1 gene and retrograde endocannabinoid signaling – show top differential expression and the most significant enrichment. Our results further indicate that specific cell types, including a specific NPY-expressing GABAergic neuronal cell type, and specific G protein signaling cascades underly the cerebral effects of a loss of ultradian cortisol rhythm. Our results provide a biological mechanistic underpinning of our fMRI findings, indicating specific cell types and cascades as a target for manipulation in future experimental studies.
Relaxed risk of predation drives parallel evolution of stickleback behaviour
Authors: Fraimout Antoine , Päiviö Elisa , Merilä Juha
Published: January 2022

The occurrence of similar phenotypes in multiple independent populations (viz. parallel evolution) is a testimony of evolution by natural selection. Parallel evolution implies that populations share a common phenotypic response to a common selection pressure associated with habitat similarity. Examples of parallel evolution at the genetic and phenotypic levels are fairly common, but the driving selective agents often remain elusive. Similarly, the role of phenotypic plasticity in facilitating early stages of parallel evolution is unclear. We investigated whether the relaxation of predation pressure associated with the colonization of freshwater ponds by nine-spined sticklebacks (Pungitius pungitius) likely explains the divergence in complex behaviours between marine and pond populations, and whether this divergence is parallel. Using laboratory-raised individuals exposed to different levels of perceived predation risk, we calculated vectors of phenotypic divergence for four behavioural traits between habitats and predation risk treatments. We found a significant correlation between the directions of evolutionary divergence and phenotypic plasticity, suggesting that habitat divergence in behaviour is aligned with the response to relaxation of predation pressure. Finally, we show that this alignment is found across multiple pairs of populations, and that the relaxation of predation pressure has likely driven parallel evolution of behaviour in this species.
Characterization of alveolar epithelial lineage heterogeneity during the late pseudoglandular stage of mouse lung development
Authors: Jones Matthew R. , Chong Lei , Limgapally Arun Reddy , Wilhem Jochen , Ansari Meshal , Schiller Herbert B. , Carraro Gianni , Bellusci Saverio
Published: January 2022

The specification, characterization, and fate of alveolar type 1 and type 2 (AT1 and 2) progenitors during embryonic lung development remains mostly elusive. In this paper, we build upon our previously published work on the regulation of airway epithelial progenitors by fibroblast growth factor receptor 2b (Fgfr2b) signalling during early (E12.5) and mid (E14.5) pseudoglandular lung development. Here, we looked at the regulation by Fgfr2b signalling on alveolar progenitors during late pseudoglandular/early canalicular (E14.5-E16.5) development. Using a dominant negative mouse model to conditionally inhibit Fgfr2b ligands at E16.5, we used gene array analyses to characterize a set of potential direct targets of Fgfr2b signalling. By mining published single-cell RNA sequence (scRNAseq) datasets, we showed that these Fgfr2b signature genes narrow on a discreet subset of AT2 cells at E17.5 and in adult lungs. Furthermore, we demonstrated that Fgfr2b signalling is lost in AT2 cells in their transition to AT1 cells during repair after injury.

We also used CreERT2-based mouse models to conditionally knock-out the Fgfr2b gene in AT2 and in AT1 progenitors, as well as lineage label these cells. We found, using immunofluorescence, that in wildtype controls AT1 progenitors labeled at E14.5-E15.5 contribute a significant proportion to AT2 cells at E18.5; while AT2 progenitors labeled at the same time contribute significantly to the AT1 lineage. We show, using immunofluorescence and FACS-based analysis, that knocking out of Fgfr2b at E14.5-E15.5 in AT2 progenitors leads to an increase in lineage-labeled AT1 cells at E18.5; while the reverse is true in AT1 progenitors. Furthermore, we demonstrate that increased Fgfr signalling in AT2 progenitors reduces their contribution to the AT1 pool.

Taken together, our results suggest that a significant proportion of AT2 and AT1 progenitors are cross-lineage committed during late pseudoglandular development, and that lineage commitment is regulated in part by Fgfr2b signalling. We have characterized a set of direct Fgfr2b targets at E16.5 which are likely involved in alveolar lineage formation. These signature genes concentrate on a subpopulation of AT2 cells later in development, and are downregulated in AT2 cells transitioning to the AT1 lineage during repair after injury in adults.

Our findings highlight the extensive heterogeneity of alveolar cells by elucidating the role of Fgfr2b signalling in these cells during early alveolar lineage formation, as well as during repair after injury.
Full Spectrum Flow Cytometry for High-Dimensional Immunophenotyping of Mouse Innate Lymphoid Cells
Authors: Mincham Kyle T. , Snelgrove Robert J.
Published: January 2022

Purpose and appropriate sample types

This 25-parameter, 22-colour full spectrum flow cytometry panel was designed and optimised for the comprehensive enumeration and functional characterisation of innate lymphoid cell (ILC) subsets in mouse tissues (Table 1). The panel presented here allows the discrimination of ILC progenitors (ILCP), ILC1, ILC2, NCR+ILC3, NCR−ILC3, CCR6+lymphoid tissue-inducer (LTi)-like ILC3 and mature natural killer (NK) cell populations. Further characterisation of ILC and NK cell functional profiles in response to stimulation is provided by the inclusion of subset-specific cytokine markers, and proliferation markers. Development and optimisation of this panel was performed on freshly isolated cells from adult BALB/c lungs and small intestine lamina propria, andex vivostimulation with phorbol 12-myrisate 13-acetate, ionomycin and pro-ILC activating cytokines.

Ethical compliance statement

All mouse experiments were performed in accordance with the recommendations in the Guide for the Use of Laboratory Animals of Imperial College London, with the ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines. All animal procedures and care conformed strictly to the UK Home Office Guidelines under the Animals (Scientific Procedures) Act 1986, and the protocols were approved by the Home Office of Great Britain.
Investigating the NRAS 5’ UTR as a Target for Small Molecules
Authors: Balaratnam Sumirtha , Torrey Zachary R. , Calabrese David R. , Banco Michael T. , Yazdani Kamyar , Liang Xiao , Ferré-D’Amaré Adrian R. , Incarnato Danny , Schneekloth John S.
Published: January 2022

Neuroblastoma RAS (NRAS) is an oncogene that is deregulated and highly mutated in cancers including melanomas and acute myeloid leukemias. Constitutively activated NRAS induces the MAPK and AKT signaling pathways and leads to uncontrolled proliferation and cell growth, making it an attractive target for small molecule inhibition. Like all RAS-family proteins, it has proven difficult to identify small molecules that directly inhibit the protein. An alternative approach would involve targeting the NRAS mRNA. The 5′ untranslated region (5′ UTR) of the NRAS mRNA is reported to contain a G-quadruplex (G4) that regulates translation ofNRASmRNA. Stabilizing the G4 structure with small molecules could reduce NRAS protein expression in cancer cells by impacting translation. Here we report a novel class of small molecule that binds to the G4 structure located in the 5′ UTR of the NRAS mRNA. We used a small molecule microarray (SMM) screen to identify molecules that selectively bind to the NRAS-G4. Biophysical studies demonstrated that compound18binds reversibly to the NRAS-G4 structure with submicromolar affinity. A Luciferase based reporter assay indicated that18inhibits the translation of NRAS via stabilizing the NRAS-G4in vitrobut showed only moderate effects on the NRAS levelsin cellulo. Rapid Amplification of cDNA Ends (RACE), RT-PCR analysis on 14 differentNRAS-expressing cell lines, coupled with analysis of publicly available CAGE seq experiments, revealed that predominant NRAS transcript does not possess the G4 structure. Further analysis of published rG4 and G4 sequencing data indicated the presence of G4 structure in the promoter region ofNRASgene (DNA) but not in the mRNA. Thus, although manyNRAStranscripts lack a G4 in many cell lines the broader concept of targeting folded regions within 5’ UTRs to control translation remains a highly attractive strategy and this work represents an intriguing example of transcript heterogeneity impacting targetability.
Injury suppresses Ras cell competitive advantage through enhanced wild-type cell proliferation
Authors: Gallini Sara , Rahman Nur-Taz , Annusver Karl , Gonzalez David G. , Yun Sangwon , Matte-Martone Catherine , Xin Tianchi , Lathrop Elizabeth , Suozzi Kathleen C. , Kasper Maria , Greco Valentina
Published: January 2022

Healthy skin is a tapestry of wild-type and mutant clones. Although injury can cooperate with Ras mutations to promote tumorigenesis, the consequences in genetically mosaic skin are unknown. Here, we show that wild-type cells prevent oncogenic Ras-induced aberrant growth after injury. Although HrasG12V/+and KrasG12D/+cells outcompete wild-type cells in uninjured, mosaic tissue, their competitive advantage is suppressed after injury due to a selective increase in wild-type cell proliferation. EGFR inhibition abolishes the competitive advantage of wild-type cells after injury of HrasG12V/+-mosaic skin. Global loss of the cell cycle inhibitor p21 increases wild-type cell proliferation even without injury, suppressing the competitive advantage of HrasG12V/+cells. Thus, injury plays an unanticipated role in switching the competitive balance between oncogenic and wild-type cells in genetically mosaic skin.

One sentence Summary

Injury-repair selectively induces wild-type cell proliferation to suppress oncogenic growth in Ras-mosaic skin epithelium.
Phosphate transporter PHT1;1 as a key determinant of phosphorus acquisition in Arabidopsis natural accessions
Authors: Chien Pei-Shan , Chao Ya-Ting , Chou Chia-Hui , Hsu Yu-Ying , Chiang Su-Fen , Tung Chih-Wei , Chiou Tzyy-Jen
Published: January 2022

To understand the genetic basis in governing phosphorus (P) acquisition, we performed genome-wide association studies (GWAS) on a diversity panel of Arabidopsis thaliana by two primary determinants of P acquisition, phosphate (Pi)-uptake activity and PHOSPHATE TRANSPORTER 1 (PHT1) protein abundance. Association mapping revealed a shared significant peak on chromosome 5 (Chr5) where the PHT1;1/2/3 genes reside, suggesting a strong correlation between the regulation of Pi-uptake activity and PHT1 protein abundance. Genes encoding transcription factors, kinases, and a metalloprotease associated with both traits were also identified. Conditional GWAS followed by statistical analysis of genotype-dependent expression of PHT1;1 and transcription activity assays revealed an epistatic interaction between PHT1;1 and MYB DOMAIN PROTEIN 52 (MYB52) on Chr1. Analyses of F1 hybrids generated by crossing two subgroups of natural accessions carrying specific SNPs associated with PHT1;1 and MYB52 further revealed the strong effects of potential variants on PHT1;1 expression and Pi uptake activity. Notably, the soil P contents in A. thaliana habitats were found to coincide with PHT1;1 haplotype, underscoring how fine-tuning of the activity of P acquisition by natural variants allows plants to adapt to their environments. This study sheds light on the complex regulation of P acquisition and offers a framework to systematically assess the effectiveness of GWAS approaches in the study of quantitative traits.

One sentence summary

Stepwise GWAS analyses reveal insights into the genetic basis in regulating phosphorus acquisition and associations between the phosphate transporter PHT1;1 haplotype and Arabidopsis habitats.
Synaptic plasticity of inhibitory synapses onto medial olivocochlear efferent neurons
Authors: Cadenas Lester Torres , Cheng Hui , Weisz Catherine J.C.
Published: January 2022

The descending auditory system modulates the ascending system at every level. The final descending, or efferent stage, is comprised of lateral olivocochlear (LOC) and medial olivocochlear (MOC) neurons. MOC somata in the ventral brainstem project axons to the cochlea to synapse onto outer hair cells (OHC), inhibiting OHC-mediated cochlear amplification. MOC suppression of OHC function is implicated in cochlear gain control with changing sound intensity, detection of salient stimuli, attention, and protection against acoustic trauma. Thus, sound excites MOC neurons to provide negative feedback of the cochlea. Sound also inhibits MOC neurons via medial nucleus of the trapezoid body (MNTB) neurons. However, MNTB-MOC synapses exhibit short-term depression, suggesting reduced MNTB-MOC inhibition during sustained stimuli. Further, due to high rates of both baseline and sound-evoked activity in MNTB neurons in vivo, MNTB-MOC synapses may be tonically depressed. To probe this, we characterized short-term plasticity of MNTB-MOC synapses in mouse brain slices. We mimicked in vivo-like temperature and extracellular calcium conditions, and in vivo-like activity patterns of fast synaptic activation rates, sustained activation, and prior tonic activity. Synaptic depression was sensitive to extracellular calcium concentration and temperature. During rapid MNTB axon stimulation, post-synaptic currents (PSCs) in MOC neurons summated but with concurrent depression, resulting in smaller, sustained currents, suggesting tonic inhibition of MOC neurons during rapid circuit activity. Low levels of baseline MNTB activity did not significantly reduce responses to subsequent rapid activity that mimics sound stimulation, indicating that, in vivo, MNTB inhibition of MOC neurons persists despite tonic synaptic depression.

Key points summary

Inhibitory synapses from MNTB onto MOC neurons exhibit short-term plasticity that is sensitive to calcium and temperature, with enhanced synaptic depression occurring at higher calcium concentrations and at room temperature

High rates of background synaptic activity that mimic the upper limits of spontaneous MNTB activity cause tonic synaptic depression of MNTB-MOC synapses that limits further synaptic inhibition

High rates of activity at MNTB-MOC synapses cause synaptic summation concurrent depression to yield a response with an initial large amplitude that decays to a tonic inhibition
The neural dynamics associated with computational complexity
Authors: Franco Juan Pablo , Bossaerts Peter , Murawski Carsten
Published: January 2022

Many everyday tasks require people to solve computationally complex problems. However, little is known about the effects of computational hardness on the neural processes associated with solving such problems. Here, we draw on computational complexity theory to address this issue. We performed an experiment in which participants solved several instances of the 0-1 knapsack problem, a combinatorial optimization problem, while undergoing ultra-high field (7T) functional magnetic resonance imaging (fMRI). Instances varied in two task-independent measures of intrinsic computational hardness: complexity and proof hardness. We characterise a network of brain regions whose activation was correlated with both measures but in distinct ways, including the anterior insula, dorsal anterior cingulate cortex and the intra-parietal sulcus/angular gyrus. Activation and connectivity changed dynamically as a function of complexity and proof hardness, in line with theoretical computational requirements. Overall, our results suggest that computational complexity theory provides a suitable framework to study the effects of computational hardness on the neural processes associated with solving complex cognitive tasks.