bluuebunny/crossref_metadata_2025 huggingface dataset:
The photobiology of the human circadian clock
Authors: Schoonderwoerd Robin A. , de Rover Mischa , Janse Jan A.M. , Hirschler Lydiane , Willemse Channa R. , Scholten Leonie , Klop Ilse , van Berloo Sander , van Osch Matthias J.P. , Swaab Dick F. , Meijer Johanna H.
Published: October 2021

In modern society, the widespread use of artificial light at night disrupts the suprachiasmatic nucleus (SCN), which serves as our central circadian clock. Existing models describe excitatory responses of the SCN to primarily blue light, but direct measures in humans are absent. The combination of state-of-the-art neuroimaging techniques and custom-made MRI compatible LED devices allowed to directly measure the light response of the SCN. In contrast to the general expectation, we found that SCN activity was suppressed by light. The suppressions were observed not only in response to narrowband blue light (λmax: 470nm) but remarkably, also in response to green (λmax: 515nm) and orange (λmax: 590nm), but not to violet light (λmax: 405nm). The broadband sensitivity of the SCN implies that strategies on light exposure should be revised: enhancement of light levels during daytime is possible with wavelengths other than blue, while during nighttime, all colors are potentially disruptive.
Polymer-Assisted Condensation: A Mechanism for Hetero-Chromatin Formation and Epigenetic Memory
Authors: Sommer Jens-Uwe , Merlitz Holger , Schiessel Helmut
Published: October 2021

We consider the formation of droplets from a 2-component liquid mixture induced by a large polymer chain that has preferential solubility with one of the components. We assume that the liquid mixture is in a fully miscible state, but far above the critical interaction limit of the two species. We show that the polymer coil acts as a chemical potential trap, which can shift the mixture inside the polymer volume into the partially miscible state and thus triggers the formation of a polymer-bound droplet of the preferred solvent phase which we denote as polymer-assisted condensation (PAC). We propose a simple mean-field model which can predict the essential feature of PAC and perform molecular-dynamics simulations to show that the predicted phase behavior is robust against fluctuation effects. Our model aims to understand the formation of macromolecular condensates inside the cell nucleus, such as those formed by heterochromatin 1 (HP1). We propose that such droplets organize the spatial structure of chromatin into hetero- and euchromatin and ensure the propagation of epigenetic information through the cell generations.
Increased mTOR signaling, impaired autophagic flux and cell-to-cell viral transmission are hallmarks of SARS-CoV-2 infection
Authors: Maktura Grazielle Celeste , Dias Thomaz Luscher , Zambalde Érika Pereira , Brenha Bianca , Amorim Mariene R. , Santos Luana Nunes , Buscaratti Lucas , de Angeli Elston João Gabriel , Mara Cynthia , Mancini Mariana Camargo Silva , Pavan Isadora Carolina Betim , Toledo-Teixeira Daniel A. , Bispo-dos-Santos Karina , Parise Pierina L. , Muraro Stefanie Primon , de Souza Gabriela Fabiano , Morelli Ana Paula , da Silva Luiz Guilherme Salvino , de Castro Ícaro Maia Santos , Barbosa Guilherme O. , Ludwig Raissa G. , Knittel Thiago L. , Saccon Tatiana D. , Mori Marcelo A. , Granja Fabiana , Carvalho Hernandes F. , da Silva Luis Lamberti Pinto , Nakaya Helder I. , Proenca-Modena Jose Luiz , Simabuco Fernando Moreira , Marques-Souza Henrique
Published: October 2021

The COVID-19 disease caued by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has two characteristics that distinguish it from other viral infections. It affects more severely people with pre-existing comorbidities and viral load peaks prior to the onset of the symptoms. Investigating factors that could contribute to these characteristics, we found increased mTOR signaling and suppressed genes related to autophagy, lysosome, and vesicle fusion in Vero E6 cells infected with SARS-CoV-2. Transcriptomic data mining of bronchoalveolar epithelial cells from severe COVID-19 patients revealed that COVID-19 severity is associated with increased expression of genes related to mTOR signaling and decreased expression of genes related to autophagy, lysosome function, and vesicle fusion. SARS-CoV-2 infection in Vero E6 cells also resulted in virus retention inside the cells and trafficking of virus-bearing vesicles between neighboring cells. Our findings support a scenario where SARS-CoV-2 benefits from compromised autophagic flux and inhibited exocytosis in individuals with chronic hyperactivation of mTOR signaling, which might relate to undetectable proliferation and evasion of the immune system.
Differential and synergistic effects of low birth weight and Western diet on skeletal muscle vasculature, mitochondrial lipid metabolism and insulin signaling in male guinea pigs
Authors: Dunlop Kristyn , Sarr Ousseynou , Stachura Nicole , Zhao Lin , Nygard Karen , Thompson Jennifer A. , Hadway Jennifer , Richardson Bryan S. , Bureau Yves , Borradaile Nica , Lee Ting-Yim , Regnault Timothy R.H.
Published: October 2021

Low birth weight (LBW) offspring are at increased risk for developing insulin resistance, a key precursor in metabolic syndrome and type 2 diabetes mellitus. Altered skeletal muscle vasculature, extracellular matrix, amino acid and mitochondrial lipid metabolism, and insulin signaling are implicated in this pathogenesis. Using uteroplacental insufficiency (UPI) to induce intrauterine growth restriction (IUGR) and LBW in the guinea pig, we investigated the relationship between UPI-induced IUGR/LBW and later life skeletal muscle arteriole density, fibrosis, amino acid and mitochondrial lipid metabolism, markers of insulin signaling and glucose uptake, and how a postnatal high-fat, high-sugar “Western” diet (WD) modulates these changes. Muscle of 145-day-old male LBW glucose tolerant offspring displayed diminished vessel density and altered acylcarnitine levels. Disrupted muscle insulin signaling despite maintained whole-body glucose homeostasis also occurred in both LBW and WD-fed male ‘lean’ offspring. Additionally, postnatal WD unmasked LBW-induced impairment of mitochondrial lipid metabolism as reflected by increased acylcarnitine accumulation. This study provides evidence that early markers of skeletal muscle metabolic dysfunction appear to be influenced by the in utero environment and interact with a high fat-sugar postnatal environment to exacerbate altered mitochondrial lipid metabolism promoting mitochondrial overload.
Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity
Authors: Kirkwood Kaylie I. , Christopher Michael W. , Burgess Jefferey L. , Littau Sally R. , Pratt Brian S. , Shulman Nicholas , Tamura Kaipo , MacCoss Michael J. , MacLean Brendan X. , Baker Erin S.
Published: October 2021

Lipids play many biological roles including membrane formation, protection, insulation, energy storage, and cell division. These functions have brought great interest to lipidomic studies for understanding their dysregulation in toxic exposure, inflammation, and diseases. However, lipids have shown to be analytically challenging due to their highly isomeric nature and vast concentration ranges in biological matrices. Therefore, powerful multidimensional techniques such as those integrating liquid chromatography, ion mobility spectrometry, collision induced dissociation, and mass spectrometry (LC-IMS-CID-MS) have recently been implemented to separate lipid isomers as well as provide structural information and increased feature identification confidence. These multidimensional datasets are however extremely large and highly complex, resulting in challenges in data processing and annotation. Here, we have overcome these challenges by developing sample-specific multidimensional libraries using the freely available software Skyline. Specifically, the human plasma library developed for this work contains over 500 unique, experimentally validated lipids, which is combined with adapted Skyline functions for highly confident lipid annotations such as indexed retention time (iRT) for retention time prediction and IMS drift time filtering for increased sensitivity and selectivity. For broad comparison with other lipidomic studies, this human plasma database was initially used to annotate LC-IMS-CID-MS data from a NIST SRM 1950 extract, giving comparable results to previous studies. This workflow was then utilized to assess matched plasma and bronchoalveolar lavage fluid (BALF) samples from patients with varying degrees of smoke inhalation injury to identify potential lipid-based patient prognostic and diagnostic markers.

Abstract Figure
Gaussian curvature dilutes the nuclear lamina, favoring nuclear rupture, especially at high strain rate
Authors: Pfeifer Charlotte R. , Tobin Michael P. , Cho Sangkyun , Vashisth Manasvita , Dooling Larry , Vazquez Lizeth Lopez , Ricci-De Lucca Emma G. , Simon Keiann T. , Discher Dennis E.
Published: October 2021

Nuclear rupture has long been associated with deficits or defects in lamins, with recent results also indicating a role for actomyosin stress, but key physical determinants of rupture remain unclear. Here, lamin-B stably interacts with the nuclear membrane at sites of low Gaussian curvature yet dilutes at high-curvature to favor rupture, whereas lamin-A depletes similarly but only at high strain-rates. Live cell imaging of lamin-B1 gene-edited cancer cells is complemented by fixed-cell imaging of ruptured nuclei in: iPS-derived cells from progeria patients, cells within beating chick embryo hearts, and cancer cells that develop multiple ruptures in migrating through small pores. Dilution and curvature-dependent rupture fit a parsimonious model of a stiff filament that detaches from a curved surface, suggesting an elastic-type response of lamin-B, but rupture is also modestly suppressed by inhibiting myosin-II and by hypotonic stress, which slow the strain rates. Lamin-A dilution and nuclear rupture likelihood indeed increase above a threshold rate of pulling into small pipettes, suggesting a viscoplastic coupling to the envelope for protection against nuclear rupture.

Summary statement

High nuclear curvature drives lamina dilution and nuclear envelope rupture even when myosin stress is inhibited. Stiff filaments generally dilute from sites of high Gaussian curvature, providing mathematical fits of experiments.
The secreted neuronal signal Spock1 regulates the blood-brain barrier
Authors: O’Brown Natasha M. , Patel Nikit B. , Hartmann Ursula , Klein Allon M. , Gu Chenghua , Megason Sean G.
Published: October 2021

The blood-brain barrier (BBB) is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick-quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally-expressed Spock1 is cell non-autonomously required for a functional BBB. Leakage inspock1mutants is associated with altered extracellular matrix (ECM), increased endothelial transcytosis, and altered pericyte-endothelial interactions. Furthermore, a single dose of recombinant SPOCK1 partially restores BBB function inspock1mutants by quenching gelatinase activity and restoring vascular expression of BBB genes includingmcamb. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM, thereby regulating pericyte-endothelial interactions and downstream vascular gene expression.

One-Sentence Summary

Spock1 is a signal secreted by neurons that induces barrier properties in the brain vasculature
CAR modulates plasma membrane nano-organization and immune signaling downstream of RALF1-FERONIA signaling pathway
Authors: Chen Weijun , Zhou Huina , Xu Fan , Yu Meng , Coego Alberto , Rodriguez Lesia , Lu Yuqing , Xie Qijun , Fu Qiong , Chen Jia , Xu Guoyun , Wu Dousheng , Li Xiushan , Li Xiaojuan , Jaillais Yvon , Rodriguez Pedro L. , Zhu Sirui , Yu Feng
Published: October 2021

The receptor-like kinase (RLK) FERONIA (FER) senses peptide ligands in the plasma membrane (PM), modulates plant growth and development, and integrates biotic and abiotic stress signaling for downstream adaptive response. However, the molecular interplay of these diverse processes is largely unknown.

Here, we show that FER, the receptor of Rapid Alkalinization Factor 1 (RALF1), physically interacts with C2 domain ABA–related (CAR) proteins to control the nano-organization of the PM inArabidopsis.

During this process, the RALF1–FER pathway upregulates CAR protein translation, and then more CAR proteins are recruited to PM. This acts as a rapid feedforward loop to stabilize PM liquid-ordered phase. FER interacts with and phosphorylates CARs, and reducing their lipid-binding ability, which breaks the feedback regulation CAR activity at latter time point.

Similar to FER mutant, pentuplecar14569mutants inhibit flg22-induced FLS2-BAK1 immune complex formation, which depends on the integrity of nanodomains.

Together, we propose that the FER-CAR module controls the formation of the PM nano-organization during RALF signaling through a self-contained amplifying loop including both positive and negative feedbacks.
The PRO model accounts for the anterior cingulate cortex role in risky decision-making and monitoring
Authors: Woo Jae Hyung , Azab Habiba , Jahn Andrew , Hayden Benjamin , Brown Joshua W.
Published: October 2021

The anterior cingulate cortex (ACC) has been implicated in a number of functions including performance monitoring and decision making involving effort. The prediction of responses and outcomes (PRO) model has provided a unified account of much human and monkey ACC data involving anatomy, neurophysiology, EEG, fMRI, and behavior. Here we explore the computational nature of ACC with the PRO model, extending it to account specifically for both human and macaque monkey decision-making under risk, including both behavioral and neural data. We show that the PRO model can account for a number of additional effects related to outcome prediction, decision-making under risk, gambling behavior, and we show that the ACC represents the variance of uncertain outcomes, suggesting a link between ACC function and mean-variance theories of decision making. The PRO model provides a unified account of a large set of data regarding the ACC.
Micro-aggregation of a pristine grassland soil selects for bacterial and fungal communities and changes in nitrogen cycling potentials
Authors: Keuschnig Christoph , Martins Jean M.F. , Navel Aline , Simonet Pascal , Larose Catherine
Published: October 2021

Microbial analysis at the micro scale of soil is essential to the overall understanding of microbial organization and interactions, and necessary for a better understanding of soil ecosystem functioning. While bacterial communities have been extensively described, little is known about the organization of fungal communities as well as functional potentials at scales relevant to microbial interactions. Fungal and bacterial communities and changes in nitrogen cycling potentials in the pristine Rothamsted Park Grass soil (bulk soil) as well as in its particle size sub-fractions (PSFs; > 250 μm, 250-63 μm, 63-20 μm, 20-2 μm, < 2 μm and supernatant) were studied. The potential for nitrogen reduction was found elevated in bigger aggregates. The relative abundance of Basidiomycota deceased with decreasing particle size, Ascomycota showed an increase and Mucoromycota became more prominent in particles less than 20 μm.

Bacterial community structures changed below 20 μm at the scale where microbes operate. Strikingly, only members of two bacterial and one fungal phyla (Proteobacteria, Bacteroidota and Ascomycota, respectively) were washed-off the soil during fractionation and accumulated in the supernatant fraction where most of the detected bacterial genera (e.g., Pseudomonas, Massilia, Mucilaginibacter, Edaphobaculum, Duganella, Janthinobacterium and Variovorax) were previously associated with exopolysaccharide production and biofilm formation.

Overall, the applied method shows potential to study soil microbial communities at micro scales which might be useful in studies focusing on the role of specific fungal taxa in soil structure formation as well as research on how and by whom biofilm-like structures are distributed and organized in soil.

Importance

Intensive exploitation of soils has led to increasing environmental concerns such as pollution, erosion, emission of greenhouse gases and, in general, the weakening of its ecosystem services that are mainly regulated by microbial activity. Microbial activity and metabolism drive the formation of soil aggregates, ranging in size from a few micrometres to several millimetres. Understanding biological mechanisms related to aggregate size classes can provide insight into large-scale processes, but most research has focused on macroaggregates. Here, we investigated the microbial community and its functional changes at these smaller scales that are clearly more relevant for assessing microbial activity. We demonstrated that fungal communities are more sensitive to bigger size classes than bacteria, suggesting their dominant role in soil structure formation and turnover. We also identified preferential niches for reductive processes within the nitrogen cycle and a selection of specific taxa by analysing the water used for the wet-fractionation approach.
Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution
Authors: Nunes Danilo Rosa , Braconi Carla Torres , Ludwig-Begall Louisa F. , Arns Clarice Weis , Durães-Carvalho Ricardo
Published: October 2021

Nearly two decades after the last epidemic caused by a severe acute respiratory syndrome coronavirus (SARS-CoV), newly emerged SARS-CoV-2 quickly spread in 2020 and precipitated an ongoing global public health crisis. Both the continuous accumulation of point mutations, owed to the naturally imposed genomic plasticity of SARS-CoV-2 evolutionary processes, as well as viral spread over time, allow this RNA virus to gain new genetic identities, spawn novel variants and enhance its potential for immune evasion. Here, through an in-depth phylogenetic clustering analysis of upwards of 200,000 whole-genome sequences, we reveal the presence of not previously reported and hitherto unidentified mutations and recombination breakpoints in Variants of Concern (VOC) and Variants of Interest (VOI) from Brazil, India (Beta, Eta and Kappa) and the USA (Beta, Eta and Lambda). Additionally, we identify sites with shared mutations under directional evolution in the SARS-CoV-2 Spike-encoding protein of VOC and VOI, tracing a heretofore-undescribed correlation with viral spread in South America, India and the USA. Our evidence-based analysis provides well-supported evidence of similar pathways of evolution for such mutations in all SARS-CoV-2 variants and sub-lineages. This raises two pivotal points: the co-circulation of variants and sub-lineages in close evolutionary environments, which sheds light onto their trajectories into convergent and directional evolution (i), and a linear perspective into the prospective vaccine efficacy against different SARS-CoV-2 strains (ii).

Author summary

In this study, through analysis of very robust and comprehensive datasets, we identify a plethora of mutations in the SARS-CoV-2 Spike cell surface protein of several variants of concern and multiple variants of interest. We trace an association of such mutations with viral spread in different countries. We further infer the presence of new SARS-CoV-2 sublineages and show that the vast majority of mutations identified in the SARS-CoV-2 Spike protein are under convergent evolution. If we consider every color of a Rubik’s cube’s face to represent a different mutation of a particular variant, evolutionary convergence can be achieved only when all composite pieces of a single face are of the same color and every face has one unique color. Overall, this raises two important points: we provide insight into the presence of SARS-CoV-2 variants and sub-lineages circulating in very close evolutionary environments and our analyses can serve to facilitate an outlook into the prospective vaccine efficacy against different SARS-CoV-2 strains.
Differential immunogenicity of homologous versus heterologous boost in Ad26.COV2.S vaccine recipients
Authors: Kim Huat Nicholas Khoo , Er Lim Joey Ming , Gill Upkar S. , de Alwis Ruklanthi , Tan Nicole , Nan Toh Justin Zhen , Abbott Jane E. , Usai Carla , Ooi Eng Eong , Hong Low Jenny Guek , Le Bert Nina , Kennedy Patrick T. F. , Bertoletti Antonio
Published: October 2021

Protection offered by COVID-19 vaccines wanes over time, requiring an evaluation of different boosting strategies to revert such a trend and enhance the quantity and quality of Spike-specific humoral and cellular immune responses. These immunological parameters in homologous or heterologous vaccination boosts have thus far been studied for mRNA and ChAdOx1 nCoV-19 vaccines, but knowledge on individuals who received a single dose of Ad26.COV2.S is lacking.

We studied Spike-specific humoral and cellular immunity in Ad26.COV2.S vaccinated individuals (n=55) who were either primed with Ad26.COV2.S only (n=13), or boosted with a homologous (Ad26.COV2.S, n=28) or heterologous (BNT162b2, n=14) second dose. We compared our findings with the results found in individuals vaccinated with a single (n=16) or double (n=44) dose of BNT162b2. We observed that a strategy of heterologous vaccination enhanced the quantity and breadth of both, Spike-specific humoral and cellular immunity in Ad26.COV2.S vaccinated. In contrast, the impact of homologous boost was quantitatively minimal in Ad26.COV2.S vaccinated and Spike-specific antibodies and T cells were narrowly focused to the S1 region. Although a direct association between quantity and quality of immunological parameters and in vivo protection has not been demonstrated, the immunological features of Spike-specific humoral and cellular immune responses support the utilization of a heterologous strategy of vaccine boost in individuals who received Ad26.COV2.S vaccination.
Advancing our understanding of skeletal muscle across the lifecourse: protocol for the MASS_Lifecourse study and characteristics of the first 80 participants
Authors: Dodds R M , Hurst C , Hillman S J , Davies K , Aspray T J , Granic A , Sayer A A
Published: October 2021

Introduction

Sarcopenia, the age-related loss of skeletal muscle strength and mass, carries a significant burden for affected individuals. There has been little investigation of sarcopenia using experimental medicine techniques to study human muscle tissue in detail. The aim of the Muscle Ageing Sarcopenia Studies Lifecourse (MASS_Lifecourse) study is to recruit up to 160 participants, equally divided between females and males between ages 45 and 85 years for detailed phenotyping of skeletal muscle health. Here we describe the protocol for the study and the characteristics of the first 80 participants.

Methods

We are recruiting participants from three sources in the north-east of England. Study fieldwork comprises a home visit (or videocall) for consent and assessment of health, cognition, lifestyle, and wellbeing. This is followed by a visit to a clinical research facility for assessment of sarcopenia status and collection of samples including a vastus lateralis muscle biopsy. We produced descriptive statistics for the first 80 participants, including expressing their grip strength relative to normative data in the form of Z-scores.

Results

The first 80 participants (53.8% female) covered the target ages, ranging from 48 to 84 years. They were regularly physically active, reported good physical function and had a prevalence sarcopenia (including probable sarcopenia) of 11.3% based on the revised European consensus. Their grip strength was similar to that in the general population, with a mean Z-score of 0.09 standard deviations (95% CI: -1.64, 1.83) above that expected.

Conclusions

The MASS_Lifecourse study combines comprehensive health and lifestyle data with a range of biological samples including skeletal muscle. The findings from planned analyses should contribute to improvements in the diagnosis, treatment, and prevention of sarcopenia.
Pneumonia Detection with Semantic Similarity Scores
Authors: Gholamipoor Rahil , Rafiee Nima , Kollmann Markus
Published: October 2021

X-ray images have been widely used for medical diagnoses of cardiothoracic and pulmonary abnormalities due to its noninvasiveness. Advancement in computer-aided diagnostic technologies, such as deep supervised methods, can help radiologists with a reliable early treatment and reduce diagnosis time. Nevertheless, these methods are prone to the small number of labeled samples and are limited to a specific abnormality. In this paper we combined a self-supervised contrastive method with a Mahalanobis distance score to develope an abnormality detection method that uses only healthy images during the training procedure. We were able to outperform previous unsupervised methods for the task of Pneumonia detection. We show that representation learned by the self-supervised method improves the supervised tasks for Pneumonia detection.
ERα-LBD, a novel isoform of estrogen receptor alpha, promotes breast cancer proliferation and endocrine resistance
Authors: Strillacci Antonio , Sansone Pasquale , Rajasekhar Vinagolu K , Turkekul Mesruh , Boyko Vitaly , Meng Fanli , Houck-Loomis Brian , Brown David , Berger Michael F , Hendrickson Ronald C , Chang Qing , de Stanchina Elisa , Pareja Fresia , Reis-Filho Jorge S , Rajappachetty Ramya Segu , Liu Bo , Penson Alex , Mastroleo Chiara , Berishaj Marjan , Borsetti Francesca , Spisni Enzo , Lyden David , Chandarlapaty Sarat , Bromberg Jacqueline
Published: October 2021

Estrogen receptor alpha (ERα) drives mammary gland development and breast cancer (BC) growth through an evolutionarily conserved linkage of DNA binding and hormone activation functions. Therapeutic targeting of the hormone binding pocket is a widely utilized and successful strategy for breast cancer prevention and treatment. However, resistance to this endocrine therapy is frequently encountered and may occur through bypass or reactivation of ER-regulated transcriptional programs. We now identify the induction of a novel ERα isoform, ERα-LBD, that is encoded by an alternative ESR1 transcript and lacks the activation function and DNA binding domains. Despite lacking the transcriptional activity, ERα-LBD is found to promote breast cancer growth and resistance to the ERα antagonist fulvestrant. ERα-LBD is predominantly localized to the cytoplasm and mitochondria of BC cells and leads to enhanced glycolysis, respiration and stem-like features. Intriguingly, ERα-LBD expression and function does not appear to be restricted to cancers that express full length ERα but also promotes growth of triple negative breast cancers and ERα-LBD transcript (ESR1-LBD) is also present in BC samples from both ERα(+) and ERα(−) human tumors. These findings point to ERα-LBD as a potential mediator of breast cancer progression and therapy resistance.

SIGNIFICANCE STATEMENT

Endocrine resistant and metastatic breast cancer (BC) is a clinically significant problem. Our study of fulvestrant resistant cancer cells led to the discovery of a novel ERα isoform which we call ERα-LBD. Encoded by a truncated transcript variant (ESR1-LBD) and lacking the N-terminal domains (activation of transcription and DNA binding), ERα-LBD displays a unique role in BC tumorigenesis and progression by mechanisms that may involve metabolic and cell growth advantages, stemness and therapy resistance. Importantly, ESR1-LBD is preferentially expressed in human breast tumor tissues and may be used as prognostic marker in BC.
Structure-based Design of CDC42 Effector Interaction Inhibitors For the Treatment of Cancer
Authors: Jahid Sohail , Ortega Jose A. , Vuong Linh M. , Acquistapace Isabella Maria , Hachey Stephanie J. , Flesher Jessica L. , La Serra Maria Antonietta , Brindani Nicoletta , La Sala Giuseppina , Manigrasso Jacopo , Arencibia Jose M. , Bertozzi Sine Mandrup , Summa Maria , Bertorelli Rosalia , Armirotti Andrea , Jin Rongsheng , Liu Zheng , Chen Chi-Fen , Edwards Robert , Hughes Christopher C.W. , Vivo Marco De , Ganesan Anand K.
Published: October 2021

CDC42 family GTPases (RHOJ, RHOQ, CDC42) are upregulated but rarely mutated in cancer and control both the ability of tumor cells to invade surrounding tissues and the ability of endothelial cells to vascularize tumors. Here we use computer-aided drug design to discover a new chemical entity (ARN22089) that targets CDC42 GTPases and blocks CDC42 effector interactions without affecting the binding between closely related GTPases (RAC1, RAS, RAL) and their downstream effectors. Our lead compound has broad activity against a panel of cancer cell lines, inhibits S6 phosphorylation and MAPK activation, activates pro-inflammatory and apoptotic signaling, and blocks tumor growth and angiogenesis in three-dimensional vascularized microtumor models (VMT)in vitro. In addition, ARN22089 has a favorable pharmacokinetic profile and can inhibit the growth of BRAF mutant mouse melanomas and patient-derived xenograftsin vivo. Taken together, this work identifies a promising new class of therapeutic agents that influence tumor growth by modulating CDC42 signaling in both the tumor cell and its microenvironment.
The CRP-like transcriptional regulator MrpC curbs c-di-GMP and 3’, 3’ cGAMP nucleotide levels during development in Myxococcus xanthus
Authors: Kuzmich Sofya , Blumenkamp Patrick , Meier Doreen , Goesmann Alexander , Becker Anke , Søgaard-Andersen Lotte
Published: October 2021

Myxococcus xanthus has a nutrient-regulated biphasic lifecycle forming predatory swarms in the presence of nutrients and spore-filled fruiting bodies in the absence of nutrients. The second messenger c-di-GMP is essential during both stages of the lifecycle; however, different enzymes involved in c-di-GMP synthesis and degradation as well as several c-di-GMP receptors are important during distinct lifecycle stages. To address this stage specificity, we determined transcript levels using RNA-seq and transcription start sites using Cappable-seq during growth and development at a genome-wide scale. All 70 genes encoding c-di-GMP associated proteins were expressed, with 28 up-regulated and 10 down-regulated during development. In particular, the three genes encoding enzymatically active proteins with a stage-specific function were expressed stage-specifically. By combining operon mapping with published ChIP-seq data for MrpC (Robinson et al., 2014), the CRP-like master regulator of development, we identified nine developmentally regulated genes as regulated by MrpC. In particular, MrpC directly represses expression of dmxB, which encodes the diguanylate cyclase DmxB that is essential for development and responsible for the c-di-GMP increase during development. Moreover, MrpC directly activates transcription of pmxA, which encodes a bifunctional phosphodiesterase that degrades c-di-GMP and 3’, 3’ cGAMP in vitro and is essential for development. Thereby, MrpC regulates and curbs the cellular pools of c-di-GMP and 3’, 3’ cGAMP during development. We conclude that temporal regulation of the synthesis of proteins involved in c-di-GMP metabolism contributes to c-di-GMP signaling specificity. MrpC is important for this regulation, thereby being a key regulator of developmental cyclic di-nucleotide metabolism in M. xanthus.

Importance

The second messenger c-di-GMP is important during both stages of the nutrient-regulated biphasic lifecycle of Myxococcus xanthus with the formation of predatory swarms in the presence of nutrients and spore-filled fruiting bodies in the absence of nutrients. However, different enzymes involved in c-di-GMP synthesis and degradation are important during distinct lifecycle stages. Here, we show that the three genes encoding enzymatically active proteins with a stage-specific function are expressed stage-specifically. Moreover, we find that the master transcriptional regulator of development MrpC directly regulates expression of dmxB, which encodes the diguanylate cyclase DmxB that is essential for development, and of pmxA, which encodes a bifunctional phosphodiesterase that degrades c-di-GMP and 3’, 3’ cGAMP in vitro and is essential for development. We conclude that temporal regulation of the synthesis of proteins involved in c-di-GMP metabolism contributes to c-di-GMP signaling specificity, and that MrpC plays an important role in this regulation.
Nucleocapsid mutations in SARS-CoV-2 augment replication and pathogenesis
Authors: Johnson Bryan A. , Zhou Yiyang , Lokugamage Kumari G. , Vu Michelle N. , Bopp Nathen , Crocquet-Valdes Patricia A. , Kalveram Birte , Schindewolf Craig , Liu Yang , Scharton Dionna , Plante Jessica A. , Xie Xuping , Aguilar Patricia , Weaver Scott C. , Shi Pei-Yong , Walker David H. , Routh Andrew L. , Plante Kenneth S. , Menachery Vineet D.
Published: October 2021

While SARS-CoV-2 continues to adapt for human infection and transmission, genetic variation outside of the spike gene remains largely unexplored. This study investigates a highly variable region at residues 203-205 in the SARS-CoV-2 nucleocapsid protein. Recreating a mutation found in the alpha and omicron variants in an early pandemic (WA-1) background, we find that the R203K+G204R mutation is sufficient to enhance replication, fitness, and pathogenesis of SARS-CoV-2. The R203K+G204R mutant corresponds with increased viral RNA and protein both in vitro and in vivo. Importantly, the R203K+G204R mutation increases nucleocapsid phosphorylation and confers resistance to inhibition of the GSK-3 kinase, providing a molecular basis for increased virus replication. Notably, analogous alanine substitutions at positions 203+204 also increase SARS-CoV-2 replication and augment phosphorylation, suggesting that infection is enhanced through ablation of the ancestral ‘RG’ motif. Overall, these results demonstrate that variant mutations outside spike are key components in SARS-CoV-2’s continued adaptation to human infection.

Author Summary

Since its emergence, SARS-CoV-2 has continued to adapt for human infection resulting in the emergence of variants with unique genetic profiles. Most studies of genetic variation have focused on spike, the target of currently available vaccines, leaving the importance of variation elsewhere understudied. Here, we characterize a highly variable motif at residues 203-205 in nucleocapsid. Recreating the prominent nucleocapsid R203K+G204R mutation in an early pandemic background, we show that this mutation is alone sufficient to enhance SARS-CoV-2 replication and pathogenesis. We also link augmentation of SARS-CoV-2 infection by the R203K+G204R mutation to its modulation of nucleocapsid phosphorylation. Finally, we characterize an analogous alanine double substitution at positions 203-204. This mutant was found to mimic R203K+G204R, suggesting augmentation of infection occurs by disrupting the ancestral sequence. Together, our findings illustrate that mutations outside of spike are key components of SARS-CoV-2’s adaptation to human infection.
Deep learning based on stacked sparse autoencoder applied to viral genome classification of SARS-CoV-2 virus
Authors: Coutinho Maria G. F. , Câmara Gabriel B. M. , Barbosa Raquel de M. , Fernandes Marcelo A. C.
Published: October 2021

Since December 2019, the world has been intensely affected by the COVID-19 pandemic, caused by the SARS-CoV-2 virus, first identified in Wuhan, China. In the case of a novel virus identification, the early elucidation of taxonomic classification and origin of the virus genomic sequence is essential for strategic planning, containment, and treatments. Deep learning techniques have been successfully used in many viral classification problems associated with viral infections diagnosis, metagenomics, phylogenetic, and analysis. This work proposes to generate an efficient viral genome classifier for the SARS-CoV-2 virus using the deep neural network (DNN) based on stacked sparse autoencoder (SSAE) technique. We performed four different experiments to provide different levels of taxonomic classification of the SARS-CoV-2 virus. The confusion matrix presented the validation and test sets and the ROC curve for the validation set. In all experiments, the SSAE technique provided great performance results. In this work, we explored the utilization of image representations of the complete genome sequences as the SSAE input to provide a viral classification of the SARS-CoV-2. For that, a dataset based onk-mers image representation, withk= 6, was applied. The results indicated the applicability of using this deep learning technique in genome classification problems.
An archaeal histone-like protein regulates gene expression in response to salt stress
Authors: Sakrikar Saaz , Schmid Amy
Published: October 2021

Histones, ubiquitous in eukaryotes as DNA-packing proteins, find their evolutionary origins in archaea. Unlike the characterized histone proteins of a number of methanogenic and themophilic archaea, previous research indicated that HpyA, the sole histone encoded in the model halophile Halobacterium salinarum, is not involved in DNA packaging. Instead, it was found to have widespread but subtle effects on gene expression and to maintain wild type cell morphology; however, its precise function remains unclear. Here we use quantitative phenotyping, genetics, and functional genomic to investigate HpyA function. These experiments revealed that HpyA is important for growth and rod-shaped morphology in reduced salinity. HpyA preferentially binds DNA at discrete genomic sites under low salt to regulate expression of ion uptake, particularly iron. HpyA also globally but indirectly activates other ion uptake and nucleotide biosynthesis pathways in a salt-dependent manner. Taken together, these results demonstrate an alternative function for an archaeal histone-like protein as a transcriptional regulator, with its function tuned to the physiological stressors of the hypersaline environment.
Cross-seeding Controls Aβ Fibril Populations and Resulting Function
Authors: Lucas Michael J. , Pan Henry S. , Verbeke Eric J. , Partipilo Gina M. , Helfman Ethan C. , Kann Leah , Keitz Benjamin K. , Taylor David W. , Webb Lauren J.
Published: October 2021

Amyloid peptides nucleate from monomers to aggregate into fibrils through primary nucleation; pre-existing fibrils can then act as seeds for additional monomers to fibrillize through secondary nucleation. Both nucleation processes can occur simultaneously, yielding a distribution of fibril polymorphs that can generate a spectrum of neurodegenerative effects. Understanding the mechanisms driving polymorph structural distribution during both nucleation processes is important for uncovering fibril structure-function relationships, as well creating polymorph distributions in vitro that better match distributions found in vivo. Here, we explore how cross-seeding WT Aβ1-40 with Aβ1-40 mutants E22G (Arctic) and E22Δ (Osaka), as well as with WT Aβ1-42 affects the distribution of fibril structural polymorphs, and how changes in structural distribution impact toxicity. Transmission electron microscopy analysis reveals that fibril seeds derived from mutants of Aβ1-40 impart their structure to WT Aβ1-40 monomer during secondary nucleation, but WT Aβ1-40 fibril seeds do not affect the structure of fibrils assembled from mutant Aβ1-40 monomers, despite kinetics data indicating accelerated aggregation when cross-seeding of any combination of mutants. Additionally, WT Aβ1-40 fibrils seeded with mutant fibrils to produce similar structural distributions to the mutant seeds also produced similar cytotoxicity on neuroblastoma cell lines. This indicates that mutant fibril seeds not only impart their structure to growing WT Aβ1-40 aggregates, but they also impart cytotoxic properties. Our findings provide clear evidence that there is a relationship between fibril structure and phenotype on a polymorph population level, and that these properties can be passed on through secondary nucleation of succeeding generations of fibrils.
In situ Alphavirus Assembly and Budding Mechanism Revealed by Cellular CryoET
Authors: Chmielewski David , Schmid Michael F. , Simmons Graham , Jin Jing , Chiu Wah
Published: October 2021

Chikungunya virus (CHIKV) is an alphavirus and the etiological agent for debilitating arthritogenic disease in humans. Previous studies with purified virions or budding mutants have not resolved the structural mechanism of alphavirus assembly in situ. Here we used cryogenic electron tomography (cryoET) imaging of CHIKV-infected human cells and subvolume classification to resolve distinct assembly intermediate conformations. These structures revealed that particle formation is driven by the spike envelope layer. Additionally, we showed that asymmetric immature nucleocapsids (NCs) provide scaffolds to trigger assembly of the icosahedral spike lattice, which progressively transforms immature NCs into icosahedral cores during virus budding. Further, cryoET of the infected cells treated with neutralizing antibodies (NAbs) showed that NAb-induced blockage of CHIKV assembly was achieved by preventing spike-spike lateral interactions that are required to bend the plasma membrane around NC cores. These findings provide molecular mechanisms for designing antivirals targeting spike-driven assembly/budding of viruses.
Maximizing completeness in single-crystal high-pressure diffraction experiments: phase transitions in 2°AP
Authors: Tchoń D. , Makal A.
Published: October 2021

Sufficiently high completeness of diffraction data is necessary to correctly determine the space group, observe solid-state structural transformations or investigate charge density distribution under pressure. Regrettably, experiments performed at high pressure in a diamond anvil cell (DAC) yield inherently incomplete datasets. The present work systematizes the combined influence of radiation wavelength, DAC opening angle and sample orientation in a DAC on the completeness of diffraction data collected in a single-crystal high-pressure (HP) experiment with the help of dedicated software. In particular, the impact of the sample orientation on the achievable data completeness is quantified and proved to be substantial. Graphical guides for estimating the most beneficial sample orientation depending on the sample Laue class and assuming a few commonly used experimental setups are proposed. The usefulness of these guides has been tested in the case of luminescent 1,3-diacetylpyrene, suspected to undergo transitions from the α phase (Pnma) to the γ phase (Pn21
a) and δ phase (P1121/a) under pressure. Effective sample orientation has ensured over 90% coverage even for the monoclinic system and enabled unrestrained structure refinements and access to complete systematic extinction patterns.
Regulating Chinese education in colonial Macao: political struggle and the role of “the Chinese Educators' Association of Macau” (c. 1914–1949)
Authors: Cheong Hang
Published: October 2021

Purpose

The study aims to trace the history of Chinese education in Macao in the first half of the 20th century, emphasizing macro- and meso-level political influences.

Design/methodology/approach

The paper reviews published works including official documents, rare books, newspapers, etc. and provides a three-part analysis: first, discussion of the colonial Government's education policy during the early 20th century and the establishment of the Chinese Educators' Association of Macau (CEAM); second, contextualization of the major upset and change in educational policy during the Sino-Japanese War (World War II in Asia); and third, considering the reinstatement of laissez-faire education policies regarding Macao's Chinese community and the CEAM's shifting political loyalties in the post-war period.

Findings

The colonial Government created a vacuum into which both the Kuomintang (KMT) and the Chinese Communist Party (CCP) muscled, seeking to manipulate education from across the border via control of the CEAM. Mainland China's shifting political landscapes thus significantly altered the political orientation of the CEAM, especially around 1949. Soon afterward, various Catholic and other schools withdrew from the CEAM, primarily separating Chinese schools in Macao into blue (Catholic et al.) and red (pro-CCP) camps.

Originality/value

The paper reviews Macao Chinese education history from 1914 to 1949 while providing better comprehension of an analogous situation in neighboring Hong Kong.
Investigating the prevalence and predictors of food insecurity: a comparison of HFSSM and EU-SILC indicators
Authors: Beacom Emma , McLaughlin Christopher , Furey Sinéad , Hollywood Lynsey Elizabeth , Humphreys Paul
Published: October 2021

Purpose

Data from the Northern Ireland (NI) Health Survey 2014/15 (n = 2,231) were statistically analysed to examine the prevalence of food insecurity according to both indicators. Pearson'sX2test for association and logistic regressions were used to examine associations between food security status and predictor variables.

Design/methodology/approach

Household food insecurity has been identified as a significant societal issue in both developed and developing nations, but there exists no universal indicator to approximate its prevalence. In NI, two indicators (United States Household Food Security Survey Module [HFSSM] and the European Union Statistics on Income and Living Conditions [EU-SILC] food deprivation questions) have been used. This study examines how both indicators differ in their classification of food insecurity prevalence in a population sample and also examines the relationship between various demographic and household factors and food security status.

Findings

According to the EU-SILC food deprivation questions, 8.3% (n = 185) were indicated to be food insecure, while according to the HFSSM, 6.5% (n = 146) were indicated to be food insecure. The HFSSM and EU-SILC regression models differed in the underlying variables they identified as significant predictors of food insecurity. Significant variables common to both modules were tenure, employment status, health status, anxiety/depression and receipt of benefits.

Originality/value

Findings can inform policy action with regards to targeting the key contributors and can inform policy decisions in NI and elsewhere with regards to choosing the most appropriate food insecurity indicator.