bluuebunny/crossref_metadata_2025 huggingface dataset:
Sub-clinical triiodothyronine levels predict health, demographic, and socioeconomic outcomes
Authors: Lawton Ralph I. , Sabatini Bernardo L. , Hochbaum Daniel R.
Published: March 2023

The Hypothalamic-Pituitary-Thyroid (HPT) axis is fundamental to human biology, exerting central control over energy expenditure, metabolic rate, and body temperature. However, the consequences of “normal” physiologic HPT-axis variation in non-clinical populations are poorly understood. Using nationally-representative data from the 2007-2012 NHANES, we explore relationships with demographics, mortality, and socio-economic factors. We find much larger variation across age in free T3 than other HPT-axis hormones. T3 and T4 have opposite effects on mortality: free T3 is inversely related and free T4 is positively related with likelihood of death. Free T3 and household income are negatively related, particularly at lower incomes. Finally, free T3 among older adults is associated with labor both on the extensive margin (unemployment) and intensive margin (hours worked). Physiologic TSH/T4 explain only 1% of T3 variation, and neither are appreciably correlated to socio-economic outcomes. Taken together, our data suggest an unappreciated complexity and non-linearity of the HPT-axis signaling cascade broadly such that TSH and T4 may not be accurate surrogates of free T3. Furthermore, we find that sub-clinical variation in the HPT-axis effector hormone T3 is an important and overlooked factor linking socio-economic forces, human biology, and aging.
Circadian clock-gated cell renewal controls time-dependent changes in taste sensitivity
Authors: Matsu-ura Toru , Matsuura Kaoru
Published: March 2023

Circadian regulation of the cell cycle progression produces a diurnal supply of newborn cells to replace the ones that were lost in the organs and tissues. Here we analyzed time-dependent changes in the cell types in the mouse tongue epithelium. We observed circadian regulated alternate oscillations of the stem/progenitor cell maker genes and the differentiated cell marker genes expressions in mouse tongue epithelial organoids. The cell cycle progression was regulated time-dependent manner in the tongue organoids and mice tongue. Single-cell RNA sequencing revealed time-dependent population changes of the stem/progenitor cells and the differentiated cells in mice tongues. Remarkably, we observed time-dependent type II taste cell population changes, resulting in time-dependent taste sensitivity changes. We also found the same population changes in mice intestines and uteruses, suggesting the contributions of the diurnal supply of newborn cells to the time-dependent physiological controls in the broad types of organs and tissues.
Comparative analysis of syngeneic mouse models of high-grade serous ovarian cancer
Authors: Cook David P , Galpin Kristianne JC , Rodriguez Galaxia M , Shakfa Noor , Wilson-Sanchez Juliette , Pereira Madison , Matuszewska Kathy , Haagsma Jacob , Murshed Humaira , Cudmore Alison O , MacDonald Elizabeth , Tone Alicia , Shepherd Trevor G. , Petrik James J , Koti Madhuri , Vanderhyden Barbara C.
Published: March 2023

Ovarian cancers often exhibit high rates of recurrence and poor treatment response. Preclinical models that recapitulate the heterogeneity of human disease are critical to develop new therapeutic approaches. While patient-derived models are a powerful tool for testing various therapeutics, their dependence on immune-compromised mice is severely limiting. Syngeneic mouse models, however, allow for the generation of tumours comprising the full repertoire of non-malignant cell types. Here we have performed a comparative analysis of diverse models of high-grade serous ovarian cancer based on transcriptomic profiling of 22 cell line models, and intrabursal and intraperitoneal tumours from 12 models. Among cell lines, we identify distinct features in signalling activity, such as elevated inflammatory signalling in STOSE and OVE16 models, and MAPK/ERK signalling in ID8 and OVE4 models; metabolic features, such as predicted reduction in glycolysis associated with subsets of engineered ID8 subclones; and relevant functional properties, including differences in EMT activation, PD-L1 and MHC class I expression, and predicted chemosensitivity. Finally, we evaluate variability in properties of the tumour microenvironment among models. We anticipate that this work will serve as a valuable resource, providing new insight to help in the selection of models for specific experimental objectives.
Neuroimmune characterization of optineurin insufficiency mouse model during ageing
Authors: Mohovic Nikolina , Peradinovic Josip , Markovinovic Andrea , Cimbro Raffaello , Minic Zeljka , Dominovic Marin , Jakovac Hrvoje , Nimac Jerneja , Rogelj Boris , Munitic Ivana
Published: March 2023

Optineurin is a multifunctional polyubiquitin-binding protein implicated in inflammatory signalling. Optineurin mutations are associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), neurodegenerative diseases characterised by neuronal loss, neuroinflammation, and peripheral immune disbalance. However, the pathogenic role of optineurin mutations is unclear. We previously observed no phenotype in the unmanipulated young optineurin insufficiency mice (Optn470T), designed to mimic ALS/FTD-linked truncations deficient in polyubiquitin binding. The purpose of this study was to investigate whether ageing would trigger neurodegeneration. We performed a neuroimmune characterization of ageing wild-type (WT) and Optn470Tmice. No motor or cognitive differences were detected between the genotypes. Neuropathological analyses demonstrated signs of ageing including lipofuscin accumulation and microglial activation. However, this was not worsened in Optn470Tmice, and they did not exhibit TAR DNA-binding protein 43 (TDP-43) aggregation or neuronal loss. Spleen immunophenotyping uncovered T cell immunosenescence at two years but without notable differences between the WT and Optn470Tmice. Conventional dendritic cells (cDC) and macrophages exhibited increased expression of activation markers in two-year-old Optn470Tmales but not females, although the numbers of innate immune cells were similar between genotypes. Altogether, a combination of optineurin insufficiency and ageing did not induce ALS/FTD-like neuropathology in mice.
Time-Resolved Chemical Phenotyping of Whole Plant Roots with Printed Electrochemical Sensors and Machine Learning
Authors: Coatsworth Philip , Cotur Yasin , Naik Atharv , Asfour Tarek , Collins Alex Silva-Pinto , Olenik Selin , Gonzalez-Macia Laura , Bozkurt Tolga , Chao Dai-Yin , Güder Firat
Published: March 2023

Plants are non-equilibrium systems consisting of time-dependent biological processes. Phenotyping of chemical responses, however, is typically performed using plant tissues, which behave differently to whole plants, in one-off measurements. Single point measurements cannot capture the information rich time-resolved changes in chemical signals in plants associated with nutrient uptake, immunity or growth. In this work, we report a high-throughput, modular, real-time chemical phenotyping platform for continuous monitoring of chemical signals in the often-neglected root environment of whole plants: TETRIS (Time-resolvedElectrochemicalTechnology for plantRootIn-situchemicalSensing). TETRIS consists of screen-printed electrochemical sensors for monitoring concentrations of salt, pH and H2O2in the root environment of whole plants. TETRIS can detect time-sensitive chemical signals and be operated in parallel through multiplexing to elucidate the overall chemical behavior of living plants. Using TETRIS, we determined the rates of uptake of a range of ions (including nutrients and heavy metals) inBrassica oleracea acephala.We also modulated ion uptake using the ion channel blocker LaCl3, which we could monitor using TETRIS. We developed a machine learning model to predict the rates of uptake of salts, both harmful and beneficial, demonstrating that TETRIS can be used for rapid mapping of ion uptake for new plant varieties. TETRIS has the potential to overcome the urgent “bottleneck” in high-throughput screening in producing high yielding plant varieties with improved resistance against stress.
Dimerization and autophosphorylation of the MST family of kinases are controlled by the same set of residues
Authors: Weingartner Kyler A. , Tran Thao , Tripp Katherine W. , Kavran Jennifer M.
Published: March 2023

The Hippo pathway controls tissue growth and regulates stem cell fate through the activities of core kinase cassette that begins with the Sterile 20-like kinase MST1/2. Activation of MST1/2 relies ontrans-autophosphorylation but the details of the mechanisms regulating that reaction are not fully elucidated. Proposals include dimerization as a first step and include multiple models for potential kinase-domain dimers. Efforts to verify and link these dimers totrans-autophosphorylation were unsuccessful. We explored the link between dimerization andtrans-autophosphorylation for MST2 and the entire family of MST kinases. We analyzed crystal lattice contacts of structures of MST kinases and identified an ensemble of kinase-domain dimers compatible withtrans-autophosphorylation. These dimers share a common dimerization interface comprised of the activation loop and αG-helix while the arrangements of the kinase-domains within the dimer varied depending on their activation state. We then verified the dimerization interface and determined its function using MST2. Variants bearing alanine substitutions of the αG-helix prevented dimerization of the MST2 kinase domain both in solution and in cells. These substitutions also blocked autophosphorylation of full-length MST2 and itsDrosophilahomolog Hippo in cells. These variants retain the same secondary structure as wild-type and capacity to phosphorylate a protein substrate, indicating the loss of MST2 activation can be directly attributed to a loss of dimerization rather than loss of either fold or catalytic function. Together this data functionally links dimerization and autophosphorylation for MST2 and suggests this activation mechanism is conserved across both species and the entire MST family.
Drosophilaoocyte specification is maintained by the dynamic duo of microtubule polymerase Mini spindles/XMAP215 and dynein
Authors: Lu Wen , Lakonishok Margot , Gelfand Vladimir I
Published: March 2023

In many species, only one oocyte is specified among a group of interconnected germline sister cells. InDrosophila melanogaster, 16-cell interconnected cells form a germline cyst, where one cell differentiates into an oocyte, while the rest become nurse cells that supply the oocyte with mRNAs, proteins, and organelles through intercellular cytoplasmic bridges named ring canals via microtubule-based transport. In this study, we find that a microtubule polymerase Mini spindles (Msps), theDrosophilahomolog of XMAP215, is essential for the oocyte fate determination. mRNA encoding Msps is concentrated in the oocyte by dynein-dependent transport along microtubules. Translated Msps stimulates microtubule polymerization in the oocyte, causing more microtubule plus ends to grow from the oocyte through the ring canals into nurse cells, further enhancing nurse cell-to-oocyte transport by dynein. Knockdown ofmspsblocks the oocyte growth and causes gradual loss of oocyte determinants. Thus, the Msps-dynein duo creates a positive feedback loop, enhancing dynein-dependent nurse cell-to-oocyte transport and transforming a small stochastic difference in microtubule polarity among sister cells into a clear oocyte fate determination.

Significance statement

Oocyte determination inDrosophila melanogasterprovides a valuable model for studying cell fate specification. We describe the crucial role of the duo of microtubule polymerase Mini spindles (Msps) and cytoplasmic dynein in this process. We show that Msps is essential for oocyte fate determination. Msps concentration in the oocyte is achieved through dynein-dependent transport ofmspsmRNA along microtubules. Translated Msps stimulates microtubule polymerization in the oocyte, further enhancing nurse cell-to-oocyte transport by dynein. This creates a positive feedback loop that transforms a small stochastic difference in microtubule polarity among sister cells into a clear oocyte fate determination. Our findings provide important insights into the mechanisms of oocyte specification and have implications for understanding the development of multicellular organisms.
The loss of antioxidant activities impairs intestinal epithelium homeostasis by altering lipid metabolism
Authors: Ramos-León Javier , Valencia Concepción , Gutiérrez-Mariscal Mariana , Rivera-Miranda David-David-Alejandro , García-Meléndrez Celina , Covarrubias Luis
Published: March 2023

The increase in reactive oxygens species (ROS) with aging could be at the origin of many diseases of the elderly. Here we investigated the role of ROS in the renewal of the intestinal epithelium in mice lacking catalase (CAT) and/or nicotinamide nucleotide transhydrogenase (NNT) activities.Cat-/-mice have delayed intestinal epithelium renewal and were prone to develop necrotizing enterocolitis upon starvation. Interestingly, crypts lacking CAT showed fewer intestinal stem cells (ISC) and lower stem cell activity than wild-type, together with less LYS in Paneth cells. In contrast, crypts lacking NNT showed a similar number of ISCs and amount of LYS as wild-type but increased stem cell activity, which was also impaired by the loss of CAT.Catdeficiency caused fat accumulation in crypts, and a fall in the remarkable high amount of adipose triglyceride lipase (ATGL) in PCs. Supporting a role of ATGL in the regulation of ISC activity, its inhibition halt intestinal organoid development. These data suggest that the reduction of the intestine renewal capacity along aging originates from fatty acid metabolic alterations caused by peroxisomal ROS.

Summary statement

Mice with increased peroxisomal or mitochondrial reactive oxygen species develop intestinal phenotypes that are associated with aging and originate from a defective stem cell niche with impaired fatty acid metabolism.
Mediolateral foot placement control can be trained: Older adults learn to walk more stable, when ankle moments are constrained
Authors: Mahaki M. , van Leeuwen A.M. , Bruijn S.M. , Van der Velde N. , van Dieën J.H.
Published: March 2023

Falls are a problem, especially for older adults. Placing our feet accurately relative to the center-of-mass helps us to prevent falling during gait. The degree of foot placement control with respect to the center-of mass kinematic state is decreased in older as compared to young adults. Here, we attempted to train mediolateral foot placement control in healthy older adults. Ten older adults trained by walking on shoes with a narrow ridge underneath (LesSchuh), restricting mediolateral center-of-pressure shifts. As a training effect, we expected improved foot placement control during normal walking. A training session consisted of a normal walking condition, followed by a training condition on LesSchuh and finally an after-effect condition. Participants performed six of such training sessions, spread across three weeks. As a control, before the first training session, we included two similar sessions, but on normal shoes only. We evaluated whether a training effect was observed across sessions and weeks in a repeated-measures design. Whilst walking with LesSchuh, the magnitude of foot placement error reduced half-a-millimeter between sessions within a week (cohen’sd=0.394). As a training effect in normal walking, the magnitude of foot placement errors was significantly lower compared to the control week, by one millimeter in weeks 2 (cohen’sd=0.686) and 3 (cohen’sd=0.780) and by two millimeters in week 4 (cohen’sd=0.875). Local dynamic stability of normal walking also improved significantly. More precise foot placement may thus have led to improved stability. It remains to be determined whether the training effects were the result of walking on LesSchuh or from repeated treadmill walking itself. Moreover, enhancement of mechanisms beyond the scope of our outcome measures may have improved stability. At the retention test, gait stability returned to similar levels as in the control week. Yet, a reduction in foot placement error persisted.
Natural variation in theCaenorhabditis elegansegg-laying circuit modulates an intergenerational fitness trade-off
Authors: Mignerot Laure , Gimond Clotilde , Bolelli Lucie , Bouleau Charlotte , Sandjak Asma , Boulin Thomas , Braendle Christian
Published: March 2023

Evolutionary shifts from egg-laying (oviparity) to live birth (viviparity) are common across diverse taxa, and some species exhibit variability in egg-laying modes or an intermediate mode with eggs containing embryos at various stages of development. How such natural quantitative variation in egg retention arises through differences in genetics, behaviour, and physiology – and how this variation ultimately connects to variation in specific fitness components – remains poorly understood. Here, we investigate intraspecific variation in egg retention in the nematodeCaenorhabditis elegansusing a panel of 316 wild strains. We observe highly variable intra-uterine egg retention, with some strains exhibiting strongly reduced or increased retention with internal hatching. We identify multiple evolutionary origins of these phenotypic extremes and pinpoint candidate loci responsible for the observed variation. Analysis of a subset of strains confirms that natural variation in egg-laying behaviour contributes to differences in egg retention. Using neuromodulatory agents and CRISPR-Cas9-mediated genetic manipulation, we demonstrate that this behavioural variation arises from an evolutionarily divergent neuromodulatory architecture in the egg-laying circuitry. In addressing the question of why natural variation inC. elegansegg retention is maintained, we find that strong egg retention can reduce maternal fertility and survival due to detrimental hatchingin utero. However, genotypes with strong egg retention may benefit from improved offspring protection against environmental insults and gain a competitive advantage with offspring exhibiting a shortened development time to reproductive maturity outside the uterus. The observed natural variation in egg-laying behaviour inC. eleganscould therefore reflect modifications of a trade-off between alternative fitness components across generations. Our study reveals previously underappreciated diversity in theC. elegansegg-laying circuit and provides insights into the fitness consequences of this behavioural variation. We propose that intraspecific variation in nematode egg-laying behaviour offers an ideal system to identify molecular changes underlying evolutionary transitions between oviparity and viviparity in invertebrates.
Real-time in vivo thoracic spinal glutamate sensing reveals spinal hyperactivity during myocardial ischemia
Authors: Salavatian Siamak , Robbins Elaine Marie , Kuwabara Yuki , Castagnola Elisa , Cui Xinyan Tracy , Mahajan Aman
Published: March 2023

Myocardial ischemia-reperfusion (IR) can cause ventricular arrhythmias and sudden cardiac death via sympathoexcitation. The spinal cord neural network is crucial in triggering these arrhythmias and evaluating its neurotransmitter activity during IR is critical for understanding ventricular excitability control. To assess the real-timein vivospinal neural activity in a large animal model, we developed a flexible glutamate-sensing multielectrode array. To record the glutamate signaling during IR injury, we inserted the probe into the dorsal horn of the thoracic spinal cord at the T2-T3 where neural signals generated by the cardiac sensory neurons are processed and provide sympathoexcitatory feedback to the heart. Using the glutamate sensing probe, we found that the spinal neural network was excited during IR, especially after 15 mins, and remained elevated during reperfusion. Higher glutamate signaling was correlated with the reduction in the cardiac myocyte activation recovery interval, showing higher sympathoexcitation, as well as dispersion of the repolarization which is a marker for increased risk of arrhythmias. This study illustrates a new technique for measuring the spinal glutamate at different spinal cord levels as a surrogate for the spinal neural network activity during cardiac interventions that engage the cardio-spinal neural pathway.

Graphical abstract
Characterization of adaptation mechanisms in sorghum using a multi-reference back-cross nested association mapping design and envirotyping
Authors: Garin Vincent , Diallo Chiaka , Tekete Mohamed Lamine , Thera Korotimi , Guitton Baptiste , Dagno Karim , Diallo Abdoulaye G. , Kouressy Mamoutou , Leiser Willmar , Rattunde Fred , Sissoko Ibrahima , Toure Aboubacar , Nebie Baloua , Samake Moussa , Kholova Jana , Frouin Julien , Pot David , Vaksmann Michel , Weltzien Eva , Teme Niaba , Rami Jean-Francois
Published: March 2023

The identification of haplotypes influencing traits of agronomic interest, with well-defined effects across environments, is of key importance to develop varieties adapted to their context of use. It requires advanced crossing schemes, multi-environment characterization and relevant statistical tools. Here we present a sorghum multi-reference back-cross nested association mapping (BCNAM) population composed of 3901 lines produced by crossing 24 diverse parents to three elite parents from West and Central Africa (WCA-BCNAM). The population was characterized in environments contrasting for photoperiod, rainfall, temperature, and soil fertility. To analyse this multi-parental and multi-environment design, we developed a new methodology for QTL detection and parental effect estimation. In addition, envirotyping data were mobilized to determine the influence of specific environmental covariables on the genetic effects, which allowed spatial projections of the QTL effects. We mobilized this strategy to analyse the genetic architecture of flowering time and plant height, which represent key adaptation mechanisms in environments like West Africa. Our results allowed a better characterisation of well-known genomic regions influencing flowering time concerning their response to photoperiod with Ma6 and Ma1 being photoperiod sensitive and candidate gene Elf3 being insensitive. We also accessed a better understanding of plant height genetic determinism with the combined effects of phenology dependent (Ma6) and independent (qHT7.1 and Dw3) genomic regions. Therefore, we argue that the WCA-BCNAM constitutes a key genetic resource to feed breeding programs in relevant elite parental lines and develop climate-smart varieties.
In vitrocomparison of SARS-CoV-2 variants
Authors: Phadke Kruttika S. , Higdon Nathaniel B. A. , Bellaire Bryan H.
Published: March 2023

The Coronaviridae family hosts various coronaviruses responsible for many diseases, from the common cold, severe lung infections to pneumonia. SARS-CoV-2 was discovered to be the etiologic agent of the Coronavirus pandemic, and numerous basic and applied laboratory techniques were utilized in virus culture and examination of the disease. Understanding the replication kinetics and characterizing the virus’ effect on different cell lines is crucial for developingin vitrostudies. With the emergence of multiple variants of SARS-CoV-2, a comparison between their infectivity and replication in common cell lines will give us a clear understanding of the characteristic differences in pathogenicity. In this study, we compared the cytopathic effect (CPE) and replication of Wild Type (WT), Omicron (B.1.1.529), and Delta (B.1.617.2) variants on 5 different cell lines; VeroE6, VeroE6 expressing high endogenous ACE2, VeroE6 highly expressing human ACE2 (VeroE6/ACE2) and TMPRSS2 (VeroE6/hACE2/ TMPRSS2), Calu3 cells highly expressing human ACE2 and A549 cells. All 3 VeroE6 cell lines were susceptible to WT strain, where CPE and replication were observed. Along with being susceptible to Wild type, VeroE6/hACE2/TMPRSS2 cells were susceptible to both omicron and delta strains, whereas VeroE6/ACE2 cells were only susceptible to omicron in a dose-dependent manner. No CPE was observed in both human lung cell lines, A549 and Calu3/hACE2, but Wild type and omicron replication was observed. As SAR-CoV-2 continues to evolve, this data will benefit researchers in experimental planning, viral pathogenicity analysis, and providing a baseline for testing future variants.
Self-regulating living material with temperature-dependent light absorption
Authors: Xiong Lealia L. , Garrett Michael A. , Kornfield Julia A. , Shapiro Mikhail G.
Published: March 2023

Engineered living materials (ELMs) exhibit desirable characteristics of the living component, including growth and repair, and responsiveness to external stimuli.Escherichia coliare a promising constituent of ELMs because they are very tractable to genetic engineering, produce heterologous proteins readily, and grow exponentially. However, seasonal variation in ambient temperature presents a challenge in deploying ELMs outside of a laboratory environment, becauseE. coligrowth rate is impaired both below and above 37°C. Here, we develop a genetically-encoded mechanism for autonomous temperature homeostasis in ELMs containingE. coliby engineering circuits that control the expression of a light-absorptive chromophore in response to changes in temperature. We demonstrate that below 36°C, our engineeredE. coliincrease in pigmentation, causing an increase in sample temperature and growth rate above non-pigmented counterparts in a model planar ELM. On the other hand, above 36°C, they decrease in pigmentation, protecting their growth compared to bacteria with temperature-independent high pigmentation. Integrating our temperature homeostasis circuit into an ELM has the potential to improve living material performance by optimizing growth and protein production in the face of seasonal temperature changes.
A molecular glue approach to control the half-life of CRISPR-based technologies
Authors: Sreekanth Vedagopuram , Jan Max , Zhao Kevin T. , Lim Donghyun , Davis Jessie R. , McConkey Marie , Kovalcik Veronica , Barkal Sam , Law Benjamin K. , Fife James , Tian Ruilin , Vinyard Michael E. , Becerra Basheer , Kampmann Martin , Sherwood Richard I. , Pinello Luca , Liu David R. , Ebert Benjamin L. , Choudhary Amit
Published: March 2023

Cas9 is a programmable nuclease that has furnished transformative technologies, including base editors and transcription modulators (e.g., CRISPRi/a), but several applications of these technologies, including therapeutics, mandatorily require precision control of their half-life. For example, such control can help avert any potential immunological and adverse events in clinical trials. Current genome editing technologies to control the half-life of Cas9 are slow, have lower activity, involve fusion of large response elements (> 230 amino acids), utilize expensive controllers with poor pharmacological attributes, and cannot be implementedin vivoon several CRISPR-based technologies. We report a general platform for half-life control using the molecular glue, pomalidomide, that binds to a ubiquitin ligase complex and a response-element bearing CRISPR-based technology, thereby causing the latter’s rapid ubiquitination and degradation. Using pomalidomide, we were able to control the half-life of large CRISPR-based technologies (e.g., base editors, CRISPRi) and small anti-CRISPRs that inhibit such technologies, allowing us to build the first examples of on-switch for base editors. The ability to switch on, fine-tune and switch-off CRISPR-based technologies with pomalidomide allowed complete control over their activity, specificity, and genome editing outcome. Importantly, the miniature size of the response element and favorable pharmacological attributes of the drug pomalidomide allowed control of activity of base editorin vivousing AAV as the delivery vehicle. These studies provide methods and reagents to precisely control the dosage and half-life of CRISPR-based technologies, propelling their therapeutic development.
NRF2 deficiency promotes ferroptosis of astrocytes mediated by oxidative stress in Alzheimer’s disease
Authors: Tang Zhi , Chen Zhuyi , Min Guo , Peng Yaqian , Xiao Yan , Guan ZhiZhong , Ni Ruiqing , Qi Xiaolan
Published: March 2023

Oxidative stress is involved in the pathogenesis of Alzheimer’s disease (AD), which is linked to reactive oxygen species (ROS), lipid peroxidation, and neurotoxicity. Emerging evidence suggests a role of nuclear factor (erythroid-derived 2)-like 2 (Nrf2), a major source of antioxidant response elements in AD. The molecular mechanism of oxidative stress and ferroptosis in astrocytes in AD is not yet fully understood. Here, we aim to investigate the mechanism by which Nrf2 regulates the ferroptosis of astrocytes in AD. Postmortem frontal cortex tissues from patients with AD and nondemented controls and brain tissue from the 3×Tg AD mouse model and wild-type mice (10 months old) were used. Immunofluorescence staining for Nrf2, the ROS marker NADPH oxidase 4 (NOX4), and GFAP was performed. We further induced Nrf2 deficiency in mouse astrocytes by using RNAi and assessed the changes in ROS, ferroptosis, lipid peroxidation, and mitochondrial dysfunction by using western blotting and immunofluorescence staining. We found decreased expression of Nrf2 and upregulated expression of NOX4 in the frontal cortex from patients with AD and in the cortex of 3×Tg mice compared to control mice. We demonstrated that Nrf2 deficiency led to ferroptosis-dependent oxidative stress-induced ROS with downregulated heme oxygenase-1 and glutathione peroxidase 4 and upregulated cystine glutamate expression. Moreover, Nrf2 deficiency increased lipid peroxidation, DNA oxidation, and mitochondrial fragmentation in mouse astrocytes. In conclusion, these results suggest that Nrf2 promotes ferroptosis of astrocytes involving oxidative stress in AD.
Phase separation and molecular ordering of the prion-like domain of the thermosensory protein EARLY FLOWERING 3
Authors: Hutin Stephanie , Kumita Janet R. , Strotmann Vivien I. , Dolata Anika , Ling Wai Li , Louafi Nessim , Popov Anton , Milhiet Pierre-Emmanuel , Blackledge Martin , Nanao Max H. , Wigge Philip A. , Stahl Yvonne , Costa Luca , Tully Mark D. , Zubieta Chloe
Published: March 2023

Liquid-liquid phase separation (LLPS) is an important mechanism enabling the dynamic compartmentalisation of macromolecules, including complex polymers such as proteins and nucleic acids, and occurs as a function of the physicochemical environment. In the model plant,Arabidopsis thaliana, LLPS by the protein EARLY FLOWERING3 (ELF3) occurs in a temperature sensitive manner and controls thermoresponsive growth. ELF3 contains a largely unstructured prion-like domain (PrLD) that acts as a driver of LLPS in vivo and in vitro. The PrLD contains a poly-glutamine (polyQ) tract, whose length varies across natural Arabidopsis accessions. Here, we use a combination of biochemical, biophysical and structural techniques to investigate the dilute and condensed phases of the ELF3 PrLD with varying polyQ lengths. We demonstrate that the dilute phase of the ELF3 PrLD forms a monodisperse higher order oligomer that does not depend on the presence of the polyQ sequence. This species undergoes LLPS in a pH and temperature-sensitive manner and the polyQ region of the protein tunes the initial stages of phase separation. The liquid phase rapidly undergoes aging and forms a hydrogel as shown by fluorescence and atomic force microscopies. Furthermore, we demonstrate that the hydrogel assumes a semi-ordered structure as determined by small angle X-ray scattering, electron microscopy and X-ray diffraction. These experiments demonstrate a rich structural landscape for a PrLD protein and provide a framework to describe the structural and biophysical properties of biomolecular condensates.
Dual role of CASP8AP2/FLASH in regulating epithelial-to-mesenchymal (EMT) plasticity
Authors: Catalanotto Madison , Vaz Joel Markus , Abshire Camille , Youngblood Reneau , Chu Min , Levine Herbert , Jolly Mohit Kumar , Dragoi Ana-Maria
Published: March 2023

Metastasis consists of sequential steps initiated by cancer cells invading from the primary tumor site into neighboring tissues, followed by entry into the circulatory system and completed by extravasation and growth in distal organs where secondary tumors are formed. Circulating tumor cells, thus, encounter and adapt to multiple environmental changes during their transition from the primary to the secondary tumor sites. Epithelial-to-mesenchymal transition (EMT) is a developmental program that consists of loss of epithelial features concomitant with acquisition of mesenchymal features. Activation of EMT in cancer facilitates acquisition of aggressive traits and cancer invasion. EMT plasticity (EMP), the dynamic transition between multiple hybrid states in which cancer cells display both epithelial and mesenchymal phenotypes, confers survival advantages for cancer cells in the constantly changing environment. Therefore, understanding the molecular mechanisms regulating intermediate phenotypic states along the E–M spectrum is critical. Core EMT transcription factors (EMT-TFs), ZEB, SNAI and TWIST families, play an important role in EMT and its plasticity. In the present study we characterize FLASH as a regulator of EMP and multiple EMT-TFs. We demonstrate that loss of FLASH gives rise to a hybrid E/M phenotype with high epithelial scores even in the presence of TGFβ, as determined by computational methods using expression of predetermined sets of epithelial and mesenchymal genes. We demonstrate that FLASH is regulating expression of multiple cell junction proteins with an established role in cancer progression and that its role in EMT is independent of its histone biogenesis role. Further, we show that FLASH expression in cancer lines is inversely correlated with the epithelial score, consistent with its function as a repressor of the epithelial phenotype. Nonetheless, activation of a distinct set of mesenchymal markers concomitant with epithelial markers reveals the complex role of FLASH in EMT and indicates that intermediate E/M states could arise from opposing control by FLASH on different families of EMT-TFs.
Pump-free and high-throughput generation of monodisperse hydrogel beads by microfluidic step emulsification for dLAMP-on-a-chip
Authors: George Jijo Easo , Manna Riddha , Roy Shomdutta , Kumari Savita , Paul Debjani
Published: March 2023

Step emulsification (SE), which generates droplets by a sharp change in confinement, has emerged as a potential alternative to flow-focusing technology. Water/dispersed phase is continuously pumped through a shallow inlet channel into a deep chamber pre-filled with the oil/continuous phase. The need for one or more pumps to maintain a continuous flow for droplet generation, and the consequent use of high sample volumes, limit this technique to research labs. Here, we report a pumpfree SE technique for rapid and high-throughput generation of monodisperse hydrogel (agarose) beads using <40µl sample volume. Instead of using syringe pumps, we sequentially pipetted oil and liquid agarose into a microfluidic SE device to generate between 20000 and 80000 agarose beads in ∼ 2 min. We also demonstrated the encapsulation of loop-mediated isothermal amplification mixture inside these beads at the time of their formation. Finally, using these beads as reaction chambers, we amplified nucleic acids fromP. falciparumand SARS-CoV-2 inside them. The pump-free operation, tiny sample volume, and high-throughput generation of droplets by SE make our technique suitable for point-of-care diagnostics.
An open-source photogrammetry workflow for reconstructing 3D models
Authors: Zhang Chi , Maga A. Murat
Published: March 2023

Acquiring accurate 3D biological models efficiently and economically is important for morphological data collection and analysis in organismal biology. In recent years, structure-from-motion (SFM) photogrammetry has become increasingly popular in biological research due to its flexibility and being relatively low cost. SFM photogrammetry registers 2D images for reconstructing camera positions as the basis for 3D modeling and texturing. However, most studies of organismal biology still rely on commercial software to reconstruct the 3D model from photographs, which impedes the adoption of this workflow in our field due the blocking issues such as cost and affordability. Also, prior investigations in photogrammetry did not sufficiently assess the geometric accuracy of the models reconstructed. Consequently, this study has two goals. First, we present an affordable and highly flexible structure-from-motion photogrammetry pipeline based on the open-source package OpenDroneMap (ODM) and its user interface WebODM. Second, we assess the geometric accuracy of the photogrammetric models acquired from the ODM pipeline by comparing them to the models acquired via microCT scanning, the de facto method to image skeleton. Our sample comprises fifteenAplodontia rufa(mountain beaver) skulls. Using models derived from microCT scans of the samples as reference, our results show that the geometry of the models derived from ODM is sufficiently accurate for gross metric and morphometric analysis as the measurement errors are usually around or below 2%, and morphometric analysis captures consistent patterns of shape variations in both modalities. However, subtle but distinct differences between the photogrammetric and microCT-derived 3D models can affect the landmark placement, which in return affect the downstream shape analysis, especially when the variance within a sample is relatively small. At the minimum, we strongly advise not combining 3D models derived from these two modalities for geometric morphometric analysis. Our findings can be indictive of similar issues in other SFM photogrammetry tools since the underlying pipelines are similar. We recommend that users run a pilot test of geometric accuracy before using photogrammetric models for morphometric analysis. For the research community, we provide detailed guidance on using our pipeline for building 3D models from photographs.
Transcription repression of Cry2 via Per2 interaction promotes adipogenesis
Authors: Li Weini , Xiong Xuekai , Kiperman Tali , Ma Ke
Published: March 2023

The circadian clock is driven by a transcriptional-translational feedback loop, and Cryptochrome 2 (Cry2) represses CLOCK/Bmal1-induced transcription activation. Despite the established role of clock in adipogenic regulation, whether the Cry2 repressor activity functions in adipocyte biology remains unclear. Here we identify a critical cysteine residue of Cry2 that mediates interaction with Per2, and demonstrate that this mechanism is required for clock transcriptional repression that inhibits Wnt signaling to promote adipogenesis. Cry2 protein is enriched in white adipose depots and was robustly induced by adipocyte differentiation. Via site-directed mutagenesis, we identified that a conserved Cry2 Cysteine at 432 within the loop interfacing with Per2 mediates heterodimer complex formation that confers transcription repression. C432 mutation disrupted Per2 association without affecting Bmal1 binding, leading to loss of repression of clock transcription activation. In preadipocytes, whereas Cry2 enhanced adipogenic differentiation, the repression-defective C432 mutant suppressed this process. Furthermore, silencing of Cry2 attenuated, while stabilization of Cry2 by KL001 markedly augmented adipocyte maturation. Mechanistically, we show that transcriptional repression of Wnt pathway components underlies Cry2 modulation of adipogenesis. Collectively, our findings elucidate a Cry2-mediated repression mechanism that promotes adipocyte development, and implicate its potential as a clock intervention target for obesity.
Differential translation of mRNA isoforms underlies oncogenic activation of cell cycle kinase Aurora A
Authors: Cacioppo Roberta , Akman H. Begum , Tuncer Taner , Erson-Bensan A. Elif , Lindon Catherine
Published: March 2023

Aurora Kinase A (AURKA) is an oncogenic kinase with major roles in mitosis, but also exerts cell cycle- and kinase-independent functions linked to cancer. Therefore control of its expression, as well as its activity, is crucial. A short and a long 3’UTR isoform exist for AURKA mRNA, resulting from alternative polyadenylation (APA). We initially observed that in Triple Negative Breast Cancer, where AURKA is typically overexpressed, the short isoform is predominant and this correlates with faster relapse times of patients. The short isoform is characterized by higher translational efficiency since translation and decay rate of the long isoform are targeted byhsa-let-7atumor-suppressor miRNA. Additionally,hsa-let-7aregulates the cell cycle periodicity of translation of the long isoform, whereas the short isoform is translated highly and constantly throughout interphase. Finally, disrupted production of the long isoform led to an increase in proliferation and migration rates of cells. In sum, we uncovered a new mechanism dependent on the cooperation between APA and miRNA targeting likely to be a route of oncogenic activation of human AURKA.
Crystal structure and Hirshfeld surface analysis of (22
RS,23
SR,25
RS,26
SR)-23,25,5-trimethyl-21-(2,2,2-trifluoroacetyl)-5-aza-2(2,6)-piperidina-1,3(2,5)-difuranacyclohexaphan-24-one
Authors: Yıldırım Sema Öztürk , Akkurt Mehmet , Ershova Anastasia A. , Grigoriev Mikhail S. , Rocha Bruno G.M. , Bhattarai Ajaya
Published: March 2023

The title compound, C20H21F3N2O4, features a main twelve-membered difuryl ring with which the furan rings make dihedral angles of 76.14 (5) and 33.81 (5)°. The dihedral angle between the furan rings is 42.55 (7)°. The six-membered nitrogen heterocycle has a twist-boat conformation. In the crystal, pairs of molecules are connected by intermolecular C—H...O interactions, generating an R
2
2(14) ring motif. These pairs of molecules form zigzag chains along the a-axis direction by means of C—H...F interactions. Furthermore, C—H...π and C–F...π interactions link the molecules into chains along the b-axis direction, forming sheets parallel to the (001) plane. These sheets are also connected by van der Waals interactions.
Two polymorphs of N,N′-diphenyl-2-[1-(propylamino)ethylidene]propanediamide
Authors: Herbig Marcus , Böhme Uwe
Published: March 2023

Two polymorphs of the title compound, C20H23N3O2, have been isolated. Polymorph (I) crystallizes in the monoclinic space group P2
1/n and polymorph (II) in the tetragonal space group I4
1/a. The main difference between the two polymorphs on the molecular level is the orientation of the n-propyl group. This group is antiperiplanar in (I) and synclinal in (II). The core of the molecule consists of two carbamoyl units bound to an enamine unit. The most prominent features are intramolecular N—H...O hydrogen bonds in both polymorphs. Both polymorphs form dimers with graph set R
2
2(12) via intermolecular N—H...O hydrogen bonds. Adjacent dimers of (I) are connected via a weak C—H...O interaction, resulting in a chain parallel to the crystallographic a-axis. The dimers of (II) are connected by weak C—H...π interactions, forming intermolecular chains along the c-axis direction.
Co-crystal of nadifloxacin with oxalic acid
Authors: Karthammaiah Geethanjali N. , Rao Amaraneni Sreenivasa , Solomon Anand K.
Published: March 2023

The 2:1 co-crystal of nadifloxacin [systematic name: 9-fluoro-8-(4-hydroxypiperidin-1-yl)-5-methyl-1-oxo-6,7-dihydro-1H,5H-pyrido[3,2,1-ij]quinoline-2-carboxylic acid] with oxalic acid, C19H21FN2O4·0.5C2H2O4, was prepared by slow evaporation from a chloroform:acetone solvent system. Nadifloxacin belongs to the group of antibacterial drugs. The co-crystal is stabilized through an intramolecular O—H...O bond and intermolecular hydrogen bonds. It was studied by FT–IR spectroscopy, differential scanning calorimetry and X-ray diffraction. Hirshfeld surface analysis indicated that the major contribution to the packing is from O...H/H...O interactions.
Methods that bridge business models and business processes: a synthesis of the literature
Authors: Lara Machado Paola , van de Ven Montijn , Aysolmaz Banu , Athanasopoulou Alexia , Ozkan Baris , Turetken Oktay
Published: March 2023

Purpose

Business models are increasingly recognized as a concept to support innovation in organizations. The implementation and operation of a new or altered business model involves the (re-)design of an organization's business processes and their successful execution. This study reviews and synthesizes the existing body of literature to guide organizations in systematically moving from a business model design to the implementation and operation of the business model through their underlying business processes.

Design/methodology/approach

A systematic literature review of the methods that bridge business models and business processes is performed. The selected 34 studies are classified according to the method's characteristics and the support in the design, implementation and operation of business models.

Findings

The results of the systematic review provide an overview of existing methods that organizations can adopt when moving from business model design into the implementation and operation of their business model using processes.

Originality/value

This work provides a comprehensive overview and detailed insight into the existing methods that align business models and business processes. It increases the understanding on how these two concepts can be synthesized to support more effective digital innovation in organizations. Based on the review results, knowledge gaps are identified and an agenda for future research bridging the fields of business models and business processes is proposed.
Connecting and reconnecting: a phenomenological study of the meanings extra care tenants attribute to using the internet for social contact
Authors: Wales Jill , Cook Glenda , Bailey Cathy
Published: March 2023

Purpose

This paper aims to explore the perceptions and experiences of a group of extra care tenants, who, as novice internet users, began to maintain their social relationships online. Housing transitions in later life may jeopardise existing social relationships, leading to loneliness and social isolation. More recently, Covid-19 restrictions have limited familial face-to-face contact and wider social interactions. Thus, extra care tenants, who are not already online, may benefit from acquiring internet skills. This paper aims to enhance understanding of the participants’ transition from novices to experienced internet users and the impact on their social relationships and sense of self.

Design/methodology/approach

A longitudinal, hermeneutic phenomenological study was conducted over eight months in two extra care housing schemes in north east England. Ten participants (56–98 years) with age-related physical, sensory and cognitive losses were recruited to the study. A series of semi-structured interviews and participant diaries captured the participants’ experience as they developed internet skills and communicated online.

Findings

All participants, including a blind individual, learnt to communicate online. Personalised adaptive strategies, peer support, training and management involvement facilitated internet uptake. Participants felt their social relationships were supported, and they regained biographical continuity, through being and feeling they belonged in the modern digital world.

Originality/value

The online experiences of extra care tenants are rarely voiced. Their perceptions may assist others to engage online, maintaining social connections, which could otherwise be lost.