bluuebunny/crossref_metadata_2025 huggingface dataset:
University Exams and Psychosocial Stress: Effects on Cortisol Rhythmicity in Students
Authors: Borghi Filipy , da Silva Priscila Cristina , Farias-Silva Elisângela , Canova Fernando , Souza Aglecio Luiz , Arouca Aline Barbedo , Grassi-Kassisse Dora Maria
Published: February 2021

University students often experience heightened stress during exam periods, which can trigger psychosocial stress and increase cortisol production. This study aims to investigate both the short- and long-term effects of exam-related stress on the hypothalamic-pituitary-adrenal (HPA) axis, focusing on cortisol production and rhythmicity. Twenty-seven undergraduate students (18–24 years) from a biological sciences program participated in this study. Hair cortisol was measured for two months (October and November), while salivary cortisol was collected during final exams in November to assess cortisol rhythmicity. Saliva samples were taken five times per day across three consecutive days. Hair cortisol levels were significantly higher in November, reflecting increased chronic stress during exam periods. However, salivary cortisol maintained a normal circadian rhythm and preserved cortisol awakening response (CAR), despite elevated stress levels. The rhythmicity of cortisol production remained stable across the exam period, though an increase in cortisol before bedtime on the second and third days suggests heightened stress or anticipatory anxiety. Although university exams induce psychosocial stress, students demonstrated resilience in maintaining cortisol rhythmicity and CAR. These findings suggest adaptive stress responses in students, mitigating the risk of stress-related mental health issues. Further research using hair cortisol analysis could provide insights into cumulative stress exposure and aid in developing preventive mental health strategies for university students.
Single-cell transcriptomics reveal cell type-specific molecular changes and altered intercellular communications in chronic obstructive pulmonary disease
Authors: Huang Qiqing , Wang Jingshen , Shen Shaoran , Wang Yuanyuan , Chen Yan , Wu Shuangshuang , Xu Wei , Chen Bo , Lin Mingyan , Wu Jianqing
Published: February 2021

Chronic obstructive pulmonary disease (COPD) is a common and heterogeneous respiratory disease, the molecular complexity of which remains poorly understood, as well as the mechanisms by which aging and smoking facilitate COPD development. Here, using single-cell RNA sequencing of more than 65,000 cells from COPD and age-stratified control lung tissues of donors with different smoking histories, we identified monocytes, club cells, and macrophages as the most disease-, aging-, and smoking-relevant cell types, respectively. Notably, we found these highly cell-type specific changes under different conditions converged on cellular dysfunction of the alveolar epithelium. Deeper investigations revealed that the alveolar epithelium damage could be attributed to the abnormally activated monocytes in COPD lungs, which could be amplified via exhaustion of club cell stemness as ages. Moreover, the enhanced intercellular communications in COPD lungs as well as the pro-inflammatory interaction between macrophages and endothelial cells indued by smoking could facilitate signaling between monocyte and the alveolar epithelium. Our findings complement the existing model of COPD pathogenesis by emphasizing the contributions of the previously less appreciated cell types, highlighting their candidacy as potential therapeutic targets for COPD.
TheGossypium stocksiigenome as a novel resource for cotton improvement
Authors: Grover Corrinne E. , Yuan Daojun , Arick Mark A. , Miller Emma R. , Hu Guanjing , Peterson Daniel G. , Wendel Jonathan F. , Udall Joshua A.
Published: February 2021

Cotton is an important textile crop whose gains in production over the last century have been challenged by various diseases. Because many modern cultivars are susceptible to several pests and pathogens, breeding efforts have included attempts to introgress wild, naturally resistant germplasm into elite lines.Gossypium stocksiiis a wild cotton species native to Africa, which is part of a clade of vastly understudied species. Most of what is known about this species comes from pest resistance surveys and/or breeding efforts, which suggests thatG. stocksiicould be a valuable reservoir of natural pest resistance. Here we present a high-qualityde novogenome sequence forG. stocksii. We compare theG. stocksiigenome with resequencing data from a closely related, understudied species (G. somalense) to generate insight into the relatedness of these cotton species. Finally, we discuss the utility of theG. stocksiigenome for understanding pest resistance in cotton, particularly resistance to cotton leaf curl virus.
Cervical Squamous Intraepithelial Lesions are Associated with Changes in the Vaginal Microbiota of Mexican Women
Authors: Nieves-Ramírez ME , Partida-Rodríguez O , Moran P , Serrano-Vázquez A , Pérez-Juárez H , Pérez-Rodríguez ME , Arrieta MC , Ximénez-García C , Finlay BB
Published: February 2021

Cervical cancer is an important health concern worldwide and is one of the leading causes of deaths in Mexican women. Previous studies have shown changes in the female genital tract microbe community related to Human Papillomavirus (HPV) infection and cervical cancer, yet this link remains unexplored in many human populations. This study evaluated the vaginal bacterial community among Mexican women with pre-cancerous Squamous Intraepithelial Lesions (SIL). We sequenced the V3 region of the 16S rRNA gene (Illumina Miseq) in cervical samples from 300 Mexican women, including 157 patients with SIL, most of which were HPV positive, and 143 healthy women without HPV infection or SIL. Beta-diversity analysis showed that 14.6% of the variance in vaginal bacterial community structure is related to the presence of SIL. Presence of SIL was also associated with a higher species richness (Chao 1). MaAsLiN analysis yielded independent associations between SIL/HPV status and an increase in the relative abundanceBrachybacterium conglomeratum, as well as a decrease inSphingobium yanoikuyaeandLactobacillusspp. We also identified independent associations between HPV-16, the most common HPV subtype linked to SIL, andBrachybacterium conglomeratum. Our work indicates that the presence of SIL and HPV infection is associated with important changes in the vaginal microbiome, some of which may be specific to this human population.

IMPORTANCE

HPV plays a critical role in cervical carcinogenesis but is not sufficient for cervical cancer development, indicating involvement of other factors. Vaginal microbiota is an important factor in controlling infections caused by HPV and depending on its composition it can modulate the microenvironment in vaginal mucosa against viral infection. Ethnic and sociodemographic factors influence differences in vaginal microbiome composition, which underlies the dysbiotic patterns linked to HPV infection and cervical cancer across different women populations. Here, we provide evidence for associations between vaginal microbiota patterns and HPV infection, linked to ethnic and sociodemographic factor. To our knowledge, this is the first report ofBrevibacterium aureumandBrachybacterium conglomeratumspecies linked to HPV infection or SIL.
Genetic determinants of intrinsic antibiotic tolerance inMycobacterium avium
Authors: Matern William M. , Parker Harley , Danchik Carina , Hoover Leah , Bader Joel S. , Karakousis Petros C.
Published: February 2021

Mycobacterium aviumcomplex (MAC) is one of the most prevalent causes of nontuberculous mycobacteria pulmonary infection in the United States, yet it remains understudied. Current MAC treatment requires more than a year of intermittent to daily combination antibiotic therapy, depending on disease severity. In order to shorten and simplify curative regimens, it is important to identify the innate bacterial factors contributing to reduced antibiotic susceptibility, namely antibiotic tolerance genes. In this study, we performed a genome-wide transposon screen to elucidateM. aviumgenes that play a role in the bacterium’s tolerance to first- and second-line antibiotics. We identified a total of 193 uniqueM. aviummutants with significantly altered susceptibility to at least one of the four clinically used antibiotics we tested, including two mutants (in DFS55_00905 and DFS55_12730) with panhypersusceptibility. The products of the antibiotic tolerance genes we have identified may represent novel targets for future drug development studies aimed at shortening the duration of therapy for MAC infections.

Importance

The prolonged treatment required to eradicateMycobacterium aviumcomplex (MAC) infection is likely due to the presence of subpopulations of antibiotic-tolerant bacteria with reduced susceptibility to currently available drugs. However, little is known about the genes and pathways responsible for antibiotic tolerance in MAC. In this study, we performed a forward genetic screen to identifyM. aviumantibiotic tolerance genes, whose products may represent attractive targets for the development of novel adjunctive drugs capable of shortening curative treatment for MAC infections.
Synergistic Activity of Minocycline and Rifampin in Combination with Antifungal Drugs againstCandida auris
Authors: Brennan-Krohn Thea , Friar Liam , Ditelberg Sarah , Kirby James E.
Published: February 2021

Candida aurisis an emerging multidrug-resistant fungal pathogen that spreads readily in healthcare settings and has caused numerous hospital outbreaks. Very few treatment options exist forC. aurisinfections. We evaluated the activity of all two-drug combinations of three antifungal agents (amphotericin B, caspofungin, and voriconazole) and two antibacterial agents (minocycline and rifampin) against a collection of 10C. aurisisolates using an automated, inkjet printer-assisted checkerboard array method. Three antibacterial-antifungal combinations (amphotericin B plus rifampin, amphotericin B plus minocycline, and caspofungin plus minocycline) demonstrated synergistic activity by checkerboard array against ≥90% of strains. The two amphotericin B-containing combinations were also synergistic using the time-kill synergy testing method. Our results suggest that combinations of antifungal and antibacterial agents may provide a promising avenue for treatment of this multidrug-resistant pathogen.
Expression patterns ofPlasmodium falciparum clonally variant genes at the onset of a blood infection in non-immune humans
Authors: Pickford Anastasia K. , Michel-Todó Lucas , Dupuy Florian , Mayor Alfredo , Alonso Pedro L. , Lavazec Catherine , Cortés Alfred
Published: February 2021

Clonally variant genes (CVGs) play fundamental roles in the adaptation ofPlasmodium falciparumparasites to the fluctuating conditions of the human host. However, their expression patterns under the natural conditions of the blood circulation have been characterized in detail only for a few specific gene families. Here we provide a detailed characterization of the completeP. falciparumtranscriptome across the full intraerythrocytic development cycle (IDC) at the onset of a blood infection in non-immune human volunteers. We found that the vast majority of transcriptional differences between parasites obtained from the volunteers and the parental parasite line maintained in culture occur in CVGs. Specifically, we observed a major increase in the transcript levels of most members of thepfmc-2tmandgbpfamilies and of specific genes of other families, in addition to previously reported changes invarandclag3genes expression. Large transcriptional differences correlate with changes in the distribution of heterochromatin, confirming their epigenetic nature. The analysis of parasites collected at different time points along the infection indicates that when parasites pass through transmission stages, the epigenetic memory at CVG loci is lost, resulting in a reset of their expression state and reestablishment of new epigenetic patterns.

Importance

The ability of malaria parasites to adapt to changes in the human blood environment, where they produce long term infection associated with clinical symptoms, is fundamental for their survival. Clonally variant genes, regulated at the epigenetic level, play a major role in this adaptive process, as changes in the expression of these genes result in antigenic and functional alterations that enable immune evasion and provide phenotypic plasticity. However, the way these genes are expressed under the natural conditions of the human circulation or how their expression is affected by passage through transmission stages is not well understood. Here we provide a comprehensive characterization of the expression patterns of these genes at the onset of human blood infections, which reveals major differences within vitrocultured parasites and also distinctive alterations between different families of clonally variant genes. We also show that epigenetic patterns are erased and reestablished during transmission stages.
Operational and biochemical aspects of co-digestion (co-AD) from sugarcane vinasse, filter cake and deacetylation liquor
Authors: Volpi Maria Paula. C. , Ferraz Antonio Djalma N. , Franco Telma T. , Moraes Bruna S.
Published: February 2021

This work performed co-AD from the vinasse and filter cake (from 1G ethanol production) and deacetylation liquor (from the pre-treatment of sugarcane straw for 2G ethanol production) in a semi-Continuous Stirred Tank Reactor (s-CSTR) aiming to provide optimum operational parameters for continuous CH4production. Using filter cake as co-substrate may allow the reactor to operate throughout the year, as it is available in the sugarcane off-season, unlike vinasse. A comparison was made from the microbial community of the seed sludge and the reactor sludge when CH4production stabilized. Lactate, butyrate and propionate fermentation routes were denoted at the start-up of the s-CSTR, characterizing the acidogenic phase: the Oxidation-Reduction Potential (ORP) values ranged from -800 to -100 mV. Once the methanogenesis was initiated, alkalizing addition was no longer needed as its demand by the microrganisms was supplied by the alkali-characteriscs of the deacetylation liquor. The gradual increase of the applied Organic Load Rates (OLR) allowed stabilization of the methanogenesis from 3.20 gVS L-1day-1: the highest CH4yield (230 NmLCH4gSV-1) and average organic matter removal efficiency (83% ± 13) was achieved at ORL of 4.16 gVS L-1day-1. The microbial community changed along the reactor operation, presenting different metabolic routes mainly due to the used lignocellulosic substrates. Bacteria from the syntrophic acetate oxidation (SAO) process coupled to hydrogenotrophic methanogenesis were predominant (∼ 2% Methanoculleus) during the CH4production stability. The overall results are useful as preliminary drivers in terms of visualizing the co-AD process in a sugarcane biorefinery integrated to scale.

Keypoitns

Integration of 1G2G sugarcane ethanol biorefinery from co-digestion of its residues Biogas production from vinasse, filter cake and deacetylation liquor in a semi-CSTR Lignicellulosic substrates affected the biochemical routes and microbial community Biomol confirmed the stablismenht of thermophilic community from mesophilic sludge
Discovery of a AhR flavonoid agonist that counter-regulates ACE2 expression in rodent models of inflammation and attenuates ACE2-SARS-CoV2 interaction in vitro
Authors: Biagioli Michele , Marchianò Silvia , Roselli Rosalinda , Giorgio Cristina Di , Bellini Rachele , Bordoni Martina , Gidari Anna , Sabbatini Samuele , Francisci Daniela , Fiorillo Bianca , Catalanotti Bruno , Distrutti Eleonora , Carino Adriana , Zampella Angela , Costantino Gabriele , Fiorucci Stefano
Published: February 2021

The severe acute respiratory syndrome (SARS)-CoV-2, a newly emerged coronavirus first identified in 2019, is the pathogenetic agent od Corona Virus Induced Disease (COVID)19. The virus enters the human cells after binding to the angiotensin converting enzyme (ACE) 2 receptor in target tissues. ACE2 expression is induced in response to inflammation. The colon expression of ACE2 is upregulated in patients with inflammatory bowel disease (IBD), highlighting a potential risk of intestinal inflammation in promoting viral entry in the human body. Because mechanisms that regulate ACE2 expression in the intestine are poorly understood and there is a need of anti-SARS-CoV2 therapies, we have settled to investigate whether natural flavonoids might regulate the expression of ACE2 in intestinal models of inflammation. The results of these studies demonstrated that pelargonidin, a natural flavonoid bind and activates the Aryl hydrocarbon Receptor (AhR) in vitro and reverses intestinal inflammation caused by chronic exposure to high fat diet or to the intestinal braking-barrier agent DSS in a AhR-dependent manner. In these two models, development of colon inflammation associated with upregulation of ACE2 mRNA expression. Colon levels of ACE2 mRNA were directly correlated with TNFα mRNA levels. In contrast to ACE2 the angiotensin 1-7 receptor MAS was downregulated in the inflamed tissues. Molecular docking studies suggested that pelargonidin binds a fatty acid binding pocket on the receptor binding domain of SARS-CoV2 Spike protein. In vitro studies demonstrated that pelargonidin significantly reduces the binding of SARS-CoV2 Spike protein to ACE2 and reduces the SARS-CoV2 replication in a concentration-dependent manner. In summary, we have provided evidence that a natural flavonoid might hold potential in reducing intestinal inflammation and ACE2 induction in the inflamed colon in a AhR-dependent manner.
Stratification of Chemotherapy-Treated Stage III Colorectal Cancer Patients Using Multiplexed Imaging and Single Cell Analysis of T Cell Populations
Authors: Stachtea Xanthi , Loughrey Maurice B. , Salvucci Manuela , Lindner Andreas U. , Cho Sanghee , McDonough Elizabeth , Sood Anup , Graf John , Santamaria-Pang Alberto , Corwin Alex , Laurent-Puig Pierre , Dasgupta Sonali , Van Schaeybroeck Sandra , Lawler Mark , Prehn Jochen H. M. , Ginty Fiona , Longley Daniel B
Published: February 2021

Colorectal cancer (CRC) has one of the highest cancer incidences and mortality rates. In stage III, postoperative chemotherapy benefits <20% of patients, while more than 50% will develop distant metastases. Predictive biomarkers for identification of patients with increased risk for disease recurrence are currently lacking, with progress in biomarker discovery hindered by the disease’s inherent heterogeneity. The immune profile of colorectal tumors has previously been found to have prognostic value. The aims of this study were to evaluate immune signatures in the tumor microenvironment (TME) using anin situmultiplexed immunofluorescence imaging and single cell analysis technology (Cell DIVE™). Tissue microarrays (TMAs) with up to three 1mm diameter cores per patient were prepared from 117 stage III CRC patients treated with adjuvant fluoropyrimidine/oxaliplatin chemotherapy. Single sections underwent multilplexed immunofluorescence with Cy3- and Cy5-conjugated antibodies for immune cell markers (CD45, CD3, CD4, CD8, FOXP3, PD1) and cell segmentation markers (DAPI, pan-cytokeratin, AE1, NaKATPase and S6). We applied a probabilistic multi-class, multi-label classification algorithm based on multi-parametric models to build statistical models of protein expression to classify immune cells. Expert annotations of immune cell markers were made on a range of images, and Support Vector Machines (SVM) were used to derive a statistical model for cell classification. Images were also manually scored independently by a Pathologist as ‘high’, ‘moderate’ or ‘low’, for stromal and total immune cell content. Excellent agreement was found between manual and total automated scores (p<0.0001). Higher levels of multi-marker classified regulatory T cells (CD3+CD4+FOXP3+PD1-) were significantly associated with disease-free survival (DFS) and overall-survival (OS) (p=0.049 and 0.032), compared to FOXP3 alone. Our results also showed that PD1- Tregs rather than PD1+ Tregs were associated with improved survival. Overall, compared to single markers, multi-marker classification provided more accurate quantitation of immune cells with greater potential for predicting patient outcomes.
Mammalian adipogenesis regulators (Aregs) exhibit robust non- and anti-adipogenic properties that arise with age and involve retinoic acid signalling
Authors: Zachara Magda , Rainer Pernille Y. , Russeil Julie M. , Hashimi Horia , Alpern Daniel , Ferrero Radiana , Litovchenko Maria , Deplancke Bart
Published: February 2021

Adipose stem and precursor cells (ASPCs) give rise to adipocytes and determine the composition and plasticity of adipose tissue. Recently, several studies have demonstrated that ASPCs partition into at least three distinct cell subpopulations:Dpp4+ stem-like cells,Aoc3+ pre-adipocyte-like cells, and the enigmatic CD142+ cells. A great challenge now is to functionally characterize these distinct ASPC populations. Here, we focus on CD142+ ASPCs since discrepant properties have been assigned to this subpopulation, from adipogenic to non- and even anti-adipogenic. To address these inconsistencies, we comprehensively characterized mammalian subcutaneous CD142+ ASPCs across various sampling conditions. Our findings demonstrate that CD142+ ASPCs exhibit high molecular and phenotypic robustness, firmly supporting their non- and anti-adipogenic properties. However, these properties emerge in an age-dependent manner, revealing surprising temporal CD142+ ASPC behavioural alterations. Finally, using multi-omic and functional assays, we show that the inhibitory nature of these adipogenesis-regulatory CD142+ ASPCs (Aregs) is driven by specifically expressed secretory factors that cooperate with the retinoic acid signalling pathway to transform the adipogenic state of CD142− ASPCs into a non-adipogenic, Areg-like one.
Alternative developmental and transcriptomic responses to host plant water limitation in a butterfly metapopulation
Authors: Kahilainen Aapo , Oostra Vicencio , Somervuo Panu , Minard Guillaume , Saastamoinen Marjo
Published: February 2021

Predicting how climate change affects biotic interactions and their evolution poses a challenge. Plant-insect herbivore interactions are particularly sensitive to climate change, as climate-induced changes in plant quality cascade into the performance of insect herbivores. Whereas the immediate survival of herbivore individuals depends on plastic responses to climate change induced nutritional stress, long-term population persistence via evolutionary adaptation requires genetic variation for these responses. In order to assess the prospects for population persistence under climate change, it is therefore crucial to characterise response mechanisms to climate change induced stressors, and quantify their variability in natural populations. Here, we test developmental and transcriptomic responses to water limitation induced host plant quality change in a Glanville fritillary butterfly (Melitaea cinxia) metapopulation. We combine nuclear magnetic resonance spectroscopy on the plant metabolome, larval developmental assays and an RNA seq analysis of the larval transcriptome. We observed that responses to feeding on water limited plants, in which amino acids and aromatic compounds are enriched, showed marked intrapopulation variation, with individuals of some families performing better on control and others on water limited plants. The transcriptomic responses were concordant with the developmental responses: Families exhibiting opposite developmental responses also produced opposite transcriptomic responses, e.g. in growth associated intracellular signalling. The opposite developmental and transcriptomic responses are associated with between families differences in organic compound catabolism and storage protein production. The results reveal heritable intrapopulation variability in plasticity, suggesting potential for evolutionary responses to drought-induced changes in host plant quality in the FinnishM. cinxiametapopulation.
Optimized cDICE for efficient reconstitution of biological systems in giant unilamellar vesicles
Authors: Van de Cauter Lori , Fanalista Federico , van Buren Lennard , De Franceschi Nicola , Godino Elisa , Bouw Sharon , Danelon Christophe , Dekker Cees , Koenderink Gijsje H. , Ganzinger Kristina A.
Published: February 2021

Giant unilamellar vesicles (GUVs) are often used to mimic biological membranes in reconstitution experiments. They are also widely used in research on synthetic cells as they provide a mechanically responsive reaction compartment that allows for controlled exchange of reactants with the environment. However, while many methods exist to encapsulate functional biomolecules in GUVs, there is no one-size-fits-all solution and reliable GUV fabrication still remains a major experimental hurdle in the field. Here, we show that defect-free GUVs containing complex biochemical systems can be generated by optimizing a double-emulsion method for GUV formation called continuous droplet interface crossing encapsulation (cDICE). By tightly controlling environmental conditions and tuning the lipid-in-oil dispersion, we show that it is possible to significantly improve the reproducibility of high-quality GUV formation as well as the encapsulation efficiency. We demonstrate efficient encapsulation for a range of minimal systems including a minimal actin cytoskeleton, membrane-anchored DNA nanostructures, and a functional PURE (Protein synthesis Using Recombinant Elements) system. Our optimized cDICE method displays promising potential to become a standard method in biophysics and bottom-up synthetic biology.
Whole-body plethysmography revisited
Authors: Hülsmann Swen , Khan Amara , Hagos Liya , Hindermann Martin , Nägel Torsten , Dullin Christian
Published: February 2021

Whole-body plethysmography (WBP) is an established method to determine physiological parameters and pathophysiological alteration of breathing in animals and animal models of a variety of diseases, reaching from pulmonary diseases to complex neurological syndromes. Although frequently used, there is ongoing debate about what exactly is measured by whole-body-plethysmography and how reliable the data derived from this method are? Here, we designed a simple device that can serve as an artificial lung model that enables a thorough evaluation of different predictions about and around whole-body plethysmography. Using our lung model, we confirmed that during WBP two components contribute to the pressure changes detected in the chamber: 1) the increase of the pressure due to heating and moistening of the air, termed as conditioning, during inspiration; 2) changes of chamber pressure that depend on airway resistance. Both components overlap and contribute to the temporal pressure-profile measured in the chamber or across the wall of the chamber. Our data showed that a precise measurement of the breathing volume appears to be hindered by at least two factors: 1) the unknown relative contribution of each of these components; 2) not only the air in the inspired volume is conditioned during inspiration, but also air within the residual volume and death space that is recruited during inspiration. Moreover, our data suggest that the expiratory negative pressure peak that is used to determine the so called “enhanced pause” (Penh) parameter is not a measure for airway resistance as such but rather a consequence of the animal’s response to the airway resistance, using active expiration to overcome the resistance by a higher thoracic pressure.
Mitochondrial and metabolic remodeling in human skin fibroblasts in response to glucose availability
Authors: Costa Cláudio F. , Pinho Sónia A. , Pinho Sonia L.C. , Miranda-Santos Inês , Bagshaw Olivia , Stuart Jeffrey , Oliveira Paulo J. , Cunha-Oliveira Teresa
Published: February 2021

Cell culture conditions highly influence cell metabolismin vitro. This is relevant for preclinical assays, for which fibroblasts are an interesting cell model, with applications in regenerative medicine, diagnostics and therapeutic development for personalized medicine as well as in the validation of ingredients for cosmetics. Given these cells’ short lifespan in culture, we aimed to identify the best cell culture conditions and promising markers to study mitochondrial health and stress in Normal Human Dermal Fibroblasts (NHDF). We tested the effect of reducing glucose concentration in the cell medium from high glucose (HGm) to a more physiological level (LGm), or its complete removal and replacement by galactose (OXPHOSm), always in the presence of glutamine and pyruvate. We have demonstrated that only with OXPHOSm it was possible to observe the selective inhibition of mitochondrial ATP production. This reliance on mitochondrial ATP was accompanied by changes in oxygen consumption rate (OCR) and extracellular acidification rate (ECAR), oxidation of citric acid cycle substrates, fatty acids, lactate and other substrates, mitochondrial network extension and polarization and changes in several key transcripts related to energy metabolism. We also evaluated the relevance of galactose, glutamine and pyruvate for OXPHOS stimulation, by comparing OCR and ECAR in the presence or absence of these substrates. Galactose and pyruvate seem to be important, but redundant, to promote OXPHOS, whereas glutamine was essential. We concluded that LGm does not promote significant metabolic changes but the short-term adaptation to OXPHOSm is ideal for studying mitochondrial health and stress in NHDF.

Author Contributions

CC, SAP, SLCP and IMS performed experiments. TCO and PJO designed research and acquired funding. JS, and OB analyzed data. CC and TCO analyzed data and wrote the paper. All authors contributed to the final version of the manuscript.
Activation of Cytochrome C Peroxidase Function Through Coordinated Foldon Loop Dynamics upon Interaction with Anionic Lipids
Authors: Li Mingyue , Sun Wanyang , Tyurin Vladimir A. , DeLucia Maria , Ahn Jinwoo , Kagan Valerian E. , van der Wel Patrick C.A.
Published: February 2021

Cardiolipin (CL) is a mitochondrial anionic lipid that plays important roles in the regulation and signaling of mitochondrial apoptosis. CL peroxidation catalyzed by the assembly of CL-cytochrome c (cyt c) complexes at the inner mitochondrial membrane is a critical checkpoint. The structural changes in the protein, associated with peroxidase activation by CL and different anionic lipids, are not known at a molecular level. To better understand these peripheral protein-lipid interactions, we compare how phosphatidylglycerol (PG) and CL lipids trigger cyt c peroxidase activation, and correlate functional differences to structural and motional changes in membrane-associated cyt c. Structural and motional studies of the bound protein are enabled by magic angle spinning solid state NMR spectroscopy, while lipid peroxidase activity is assayed by mass spectrometry. PG binding results in a surface-bound state that preserves a nativelike fold, which nonetheless allows for significant peroxidase activity, though at a lower level than binding its native substrate CL. Lipid-specific differences in peroxidase activation are found to correlate to corresponding differences in lipid-induced protein mobility, affecting specific protein segments. The dynamics of omega loops C and D are upregulated by CL binding, in a way that is remarkably controlled by the protein:lipid stoichiometry. In contrast to complete chemical denaturation, membrane-induced protein destabilization reflects a destabilization of select cyt c foldons, while the energetically most stable helices are preserved. Our studies illuminate the interplay of protein and lipid dynamics in the creation of lipid peroxidase-active proteolipid complexes implicated in early stages of mitochondrial apoptosis.
Nuclear Hormone Receptor NHR-49 controls a HIF-1-independent hypoxia adaptation pathway inCaenorhabditis elegans
Authors: Doering Kelsie R. S. , Cheng Xuanjin , Milburn Luke , Ratnappan Ramesh , Ghazi Arjumand , Miller Dana L. , Taubert Stefan
Published: February 2021

The response to insufficient oxygen (hypoxia) is orchestrated by the conserved Hypoxia-Inducible Factor (HIF). However, HIF-independent hypoxia response pathways exist that act in parallel to HIF to mediate the physiological hypoxia response. Here, we describe a HIF-independent hypoxia response pathway controlled byCaenorhabditis elegansNuclear Hormone Receptor NHR-49, an orthologue of mammalian Peroxisome Proliferator-Activated Receptor alpha (PPARα). We show thatnhr-49is required for worm survival in hypoxia and is synthetic lethal withhif-1in this context, demonstrating that these factors act independently. RNA-seq analysis shows that in hypoxianhr-49regulates a set of genes that arehif-1-independent, including autophagy genes that promote hypoxia survival. We further show that Nuclear Hormone Receptornhr-67is a negative regulator and Homeodomain-interacting Protein Kinasehpk-1is a positive regulator of the NHR-49 pathway. Together, our experiments define a new, essential hypoxia response pathway that acts in parallel to the well-known HIF-mediated hypoxia response.
qc3C: reference-free quality control for Hi-C sequencing data
Authors: DeMaere Matthew Z. , Darling Aaron E.
Published: February 2021

Hi-C is a sample preparation method that enables high-throughput sequencing to capture genome-wide spatial interactions between DNA molecules. The technique has been successfully applied to solve challenging problems such as 3D structural analysis of chromatin, scaffolding of large genome assemblies and more recently the accurate resolution of metagenome-assembled genomes (MAGs). Despite continued refinements, however, Hi-C library preparation remains a complex laboratory protocol and diligent quality management is recommended to avoid costly failure. Current wet-lab protocols for Hi-C library QC provide only a crude assay, while commonly used sequence-based QC methods demand a reference genome; the quality of which can skew results. We propose a new, reference-free approach for Hi-C library quality assessment that requires only a modest amount of sequencing data. The algorithm builds upon the observation that proximity ligation events are likely to createk-mers that would not naturally occur in the sample. Our software tool (qc3C) is to our knowledge the first to implement a reference-free Hi-C QC tool, and also provides reference-based QC, enabling Hi-C to be more easily applied to non-model organisms and environmental samples. We characterise the accuracy of the new algorithm on simulated and real datasets and compare it to reference-based methods.
A synaptic novelty signal to switch hippocampal attractor networks from generalization to discrimination
Authors: Gómez-Ocádiz Ruy , Trippa Massimiliano , Posani Lorenzo , Cocco Simona , Monasson Rémi , Schmidt-Hieber Christoph
Published: February 2021

Episodic memory formation and recall are complementary processes that put conflicting requirements on neuronal computations in the hippocampus. How this challenge is resolved in hippocampal circuits is unclear. To address this question, we obtainedin vivowhole-cell patch-clamp recordings from dentate gyrus granule cells in head-fixed mice trained to explore and distinguish between familiar and novel virtual environments. We find that granule cells consistently show a small transient depolarization of their membrane potential upon transition to a novel environment. This synaptic novelty signal is sensitive to local application of atropine, indicating that it depends on metabotropic acetylcholine receptors. A computational model suggests that the observed transient synaptic response to novel environments may lead to a bias in the granule cell population activity, which can in turn drive the downstream attractor networks to a new state, thereby favoring the switch from generalization to discrimination when faced with novelty. Such a novelty-driven cholinergic switch may enable flexible encoding of new memories while preserving stable retrieval of familiar ones.
Characterization of late structural maturation with a neuroanatomical marker that considers both cortical thickness and intracortical myelination
Authors: Maingault Sophie , Pepe Antonietta , Mazoyer Bernard , Tzourio-Mazoyer Nathalie , Crivello Fabrice
Published: February 2021

The cortical ribbon changes throughout a person’s lifespan, with the most significant changes occurring during crucial development and aging periods. Changes during adulthood are rarely investigated due to the scarcity of neuroimaging data during this period. After childhood, the brain loses gray matter, which is evidenced by an apparent reduction in cortical thickness (CT); one factor of this thinning process is intense ongoing intracortical myelination (MYEL). Here, we report age-related changes in CT, MYEL, and their ratio in 447 participants aged 18 to 57 years (BIL&GIN cohort). We propose the CT/MYEL ratio to be a multimodal cortical maturation index (MATUR) capable of reflecting 1) stages during which CT and MYEL patterns diverge and 2) the regional differences in cortical maturation that occur in adulthood. Age mainly decreased CT in all cortical regions, with larger reductions occurring in the bilateral insular lobes, temporal and frontal poles, and cingulate cortices. Age led to a linear increase in MYEL in the entire cortex and larger increases in the primary motor, auditory, and visual cortices. The effects of age on the MATUR index were characterized by both linear and quadratic components. The linear component mimicked the pattern found in CT, with 1) a robust amplification of the global and regional effects of age on CT and 2) evidence of new bilateral linear decreases in the frontal and cortical cortices. Most importantly, age exhibited additional large quadratic effects on the MATUR index in the bilateral frontal (more prominent in the right hemisphere), parietal, temporal, and cingulate regions that were not highlighted by the CT metric. Thus, the MATUR index was more sensitive to age-related cortical structural changes during adulthood than was either CT or MYEL alone. As evidenced by the large quadratic component of the effect of age, the newly proposed maturation index dramatically improved the characterization of the regional cortical territories, uncovering the latest brain maturation steps that occur before stabilization and deterioration occur in mid- and late adulthood.
Catching a liar through facial expression of fear
Authors: Shen Xunbing , Fan Gaojie , Niu Caoyuan , Chen Zhencai
Published: February 2021

The leakage theory in the field of deception detection predicted that liars could not repress the leaked felt emotions (e.g., the fear or delight); and people who were lying would feel fear (to be discovered), especially under the high-stake situations. Therefore, we assumed that the aim of revealing deceits could be reached via analyzing the facial expression of fear. Detecting and analyzing the subtle leaked fear facial expressions is a challenging task for laypeople. It is, however, a relatively easy job for computer vision and machine learning. To test the hypothesis, we analyzed video clips from a game show “The moment of truth” by using OpenFace (for outputting the Action Units of fear and face landmarks) and WEKA (for classifying the video clips in which the players was lying or telling the truth). The results showed that some algorithms could achieve an accuracy of greater than 80% merely using AUs of fear. Besides, the total durations of AU 20 of fear were found to be shorter under the lying condition than under the truth-telling condition. Further analysis found the cause why durations of fear were shorter was that the duration from peak to offset of AU20 under the lying condition was less than that under the truth-telling condition. The results also showed that the facial movements around the eyes were more asymmetrical while people telling lies. All the results suggested that there do exist facial clues to deception, and fear could be a cue for distinguishing liars from truth-tellers.
Influenza virus ribonucleoprotein complex formation occurs in the nucleolus
Authors: Miyamoto Sho , Nakano Masahiro , Morikawa Takeshi , Hirabayashi Ai , Tamura Ryoma , Fujita Yoko , Hirose Nanami , Muramoto Yukiko , Noda Takeshi
Published: February 2021

Influenza A virus double-helical ribonucleoprotein complex (vRNP) performs transcription and replication of viral genomic RNA (vRNA). Unlike most RNA viruses, vRNP formation accompanied by vRNA replication is carried out in the nucleus of virus-infected cell. However, the precise subnuclear site remains unknown. Here, we report the subnuclear site of vRNP formation in influenza virus. We found that all vRNP components were colocalized in the nucleolus of virus-infected cells at early stage of infection. Mutational analysis showed that nucleolar localization of viral nucleoprotein, a major vRNP component, is critical for functional double-helical vRNP formation. Furthermore, nucleolar disruption of virus-infected cells inhibited vRNP component assembly into double-helical vRNPs, resulting in decreased vRNA transcription and replication. Collectively, our findings demonstrate that the vRNA replication-coupled vRNP formation occurs in the nucleolus, demonstrating the importance of the nucleolus for influenza virus life cycle.
Could Italy host the new coronavirus before China?
Authors: Tichopád Aleš , Pecen Ladislav
Published: February 2021

The pandemic of the COVID-19 disease caused by the SARS-CoV-2 virus has been believed to originate in China and spread later to other parts of the world. It is well acknowledged that the first diseased individuals appeared in China as early as in December 2019, and possibly even earlier in November. It has also been well established that the virus stroke Italy later in January or in February 2020, distinctly after the outbreak in China. Paper by Apolone et al. published in a local Italian medical journal in November 2020 however exposed this chronology to doubt.

By fitting early part of the epidemic curve with the exponential model and extrapolating it backwards in time, we could estimate the day-zero of the epidemic and calculated its confidence intervals in Italy and China. We also calculated how probable it is that Italy encountered the virus prior 1 January 2020.

We determined an early portion of the epidemic curve representing unhindered exponential growth which fit the exponential model with high determination >0.97 in both countries. We suggest that the day-zero in China and Italy was 8 December (95% CI: 3 Dec., 20 Dec.) and 22 January (95% CI: 16 Jan., 29 Jan.), respectively. We could with high confidence reject that Italy encountered the virus earlier than China (p <0.01).

Based on our analysis we oppose the findings published by Apolone at al. and view the proposed pre-pandemic presence of the virus in Italy as very unlikely.
Characterization of growth and development of sorghum genotypes with differential susceptibility toStriga hermonthica
Authors: Kawa Dorota , Taylor Tamera , Thiombiano Benjamin , Musa Zayan , Vahldick Hannah E. , Walmsley Aimee , Bucksch Alexander , Bouwmeester Harro , Brady Siobhan M.
Published: February 2021

Variation in strigolactone composition in sorghum root exudates underlies its resistance to the parasitic weed,Striga hermonthica. Root exudates of the Striga susceptible variety Shanqui Red (SQR) contain primarily 5-deoxystrigol, which has a high efficiency of inducing Striga germination. SRN39 roots primarily exude orobanchol, leading to reduced Striga germination and making this variety resistant to Striga. This structural diversity in exuded strigolactones is determined by the polymorphism in theLGS1(LOW GERMINATION STIMULANT 1) locus. Yet, the effects of thelgs1mutation as well as the consequences of the vast genetic diversity between SQR and SRN39 have not been addressed in terms of growth and development. Here, we demonstrate additional consequences ofLGS1loss-of-function by phenotypic and molecular characterization. A suite of genes related to metabolism was differentially expressed between SQR and SRN39. Increased levels of gibberellin precursors in SRN39 were accompanied with its slower growth rate and developmental delay and we observed an overall increased SRN39 biomass. The slow-down in growth and differences in transcriptome profiles of SRN39 were strongly associated with plant age. Additionally, analyses of multipleLGS1loss-of-function genotypes indicated that strigolactone stereochemistry influences root system architecture. In summary, we demonstrate that the consequences of thelgs1mutation reach further than the changes in strigolactone profile in the root exudate and translate into alterations in growth and development.

Highlight

SRN39 and Shanqui Red are models for sorghum genotypes that are resistant and susceptible, respectively, toStriga hermonthica. Additional differences in plant growth, development, and hormone abundance should be considered when assessing Striga tolerance.
Differences in gait stability and acceleration characteristics between healthy young and older females
Authors: Zhang Yuge , Zhou Xinglong , Pijnappels Mirjam , Bruijn Sjoerd M.
Published: February 2021

Our aim was to evaluate differences in gait acceleration intensity, variability and stability of feet and trunk between older females and young females using inertial sensors. Twenty older females (OF; mean age 68.4, SD 4.1 years) and eighteen young females (YF; mean age 22.3, SD 1.7 years) were asked to walk straight for 100 meters at their preferred speed, while wearing inertial sensors on heels and lower back. We calculated spatiotemporal measures, foot and trunk acceleration characteristics and their variability, as well as trunk stability using the local divergence exponent (LDE). Two-way analysis of variance (including the factors foot and age), Student’s t-test, and Mann–Whitney U test were used to compare statistical differences of measures between groups. Cohen’s d effects were calculated for each variable. Foot maximum vertical acceleration and amplitude, trunk-foot vertical acceleration attenuation, as well as their variability were significantly smaller in OF than in YF. In contrast, trunk mediolateral acceleration amplitude, maximum vertical acceleration, and amplitude, as well as their variability were significantly larger in OF than in YF. Moreover, OF showed lower stability (i.e., higher LDE values) in mediolateral acceleration, mediolateral and vertical angular velocity of the trunk. Even though we measured healthy older females, these participants showed lower vertical foot accelerations with higher vertical trunk acceleration, lower trunk-foot vertical acceleration attenuation, less gait stability, and more variability of the trunk, and hence, were more likely to fall. These findings suggest that instrumented gait measurements may help for early detection of changes or impairments in gait performance, even before this can be observed by clinical eye or gait speed.