bluuebunny/crossref_metadata_2025 huggingface dataset:
Conformation-specific RNA aptamers for phenotypic distinction between normal von Willebrand factor and type 2B von Willebrand disease
Authors: Machha Venkata R , Tischer Alexander , Moon-Tasson Laurie , Tange Julie , Santiago-Davis Annyoceli , Pruthi Rajiv K , Chen Dong , Maher L James , Auton Matthew
Published: November 2024

The A1 domain in Von Willebrand Factor (VWF) initiates coagulation through binding to platelet glycoprotein GPIbα receptors. Von Willebrand Disease (VWD)-Mutations in A1 that either impair (type 2M) or enhance (type 2B) platelet adhesion to VWF can locally destabilize and even misfold the domain. We leveraged misfolding in the gain-of-function type 2B VWD phenotype as a target, distinct from the normal conformation. Two nuclease-resistant 2′-fluoropyrimidine RNA aptamers were selected to discriminate normal A1 domains from a type 2B V1314D A1 variant in a glycosylated A1A2A3 tri-domain VWF-fragment. Two aptamers, W9 and V1, were isolated that selectively recognize, bind, and inhibit the A1–GPIbα interaction with WT A1A2A3 and V1314D A1A2A3, respectively. These aptamers were tested against their respective recombinant targets, plasma VWF, VWF concentrates, and patient plasma with the heterozygous type 2B VWD R1306W variant using clinical assays, surface plasmon resonance and inhibition assays of platelet adhesion to recombinant A1 and A1A2A3 domains under shear stress. The specificity of W9 and V1 aptamers confirms that pathological conformations of VWD Type 2B proteins are different from normal VWF. The availability of aptamers that distinguish normal plasma-derived VWF from VWD suggests potential applicability in clinical diagnosis of severe gain-of-function phenotypes.
Unlocking new possibilities in ionic thermoelectric materials: a machine learning perspective
Authors: Wu Yidan , Song Dongxing , An Meng , Chi Cheng , Zhao Chunyu , Yao Bing , Ma Weigang , Zhang Xing
Published: November 2024

The high thermopower of ionic thermoelectric (i-TE) materials holds promise for miniaturized waste-heat recovery devices and thermal sensors. However, progress is hampered by laborious trial-and-error experimentations, which lack theoretical underpinning. Herein, by introducing the simplified molecular-input line-entry system, we have addressed the challenge posed by the inconsistency of i-TE material types, and present a machine learning model that evaluates the Seebeck coefficient with an R2 of 0.98 on the test dataset. Using this tool, we experimentally identify a waterborne polyurethane/potassium iodide ionogel with a Seebeck coefficient of 41.39 mV/K. Furthermore, interpretable analysis reveals that the number of rotatable bonds and the octanol-water partition coefficient of ions negatively affect Seebeck coefficients, which is corroborated by molecular dynamics simulations. This machine learning-assisted framework represents a pioneering effort in the i-TE field, offering significant promise for accelerating the discovery and development of high-performance i-TE materials.
Liquid–solid composites with confined interface behaviors
Authors: Yu Shijie , Jiang Yina , Yu Lejian , Wang Huimeng , Pan Liting , Zhang Jian , Zhang Yunmao , Hou Xu
Published: November 2024

In the evolving landscape of materials science, the journey from traditional composite materials to liquid–solid composites has marked a significant shift. Composite materials, typically solid state, have long been the cornerstone of many applications due to their structural stability and mechanical properties. However, the emergence of liquid–solid composites has introduced a new paradigm, leveraging the dynamic composite interfaces and fluidic nature of liquids. Recent years have witnessed the rapid development of liquid–solid composites, distinguishing themselves by their defect-free, molecularly smooth surfaces and adaptive features. In this review, we introduce liquid-based confined interface materials, which represent a cutting-edge advancement, integrating confined liquids within solid frameworks at mesoscopic scales. Characterized by their confined competitive multiphase interfacial interactions, these materials offer practical functionalities like anti-fouling, multiphase flow control and drag reduction. We summarize the development of the materials, and showcase important applications based on the controllable motions of confined liquids and solid frameworks. We also discuss their design and preparation and address future challenges and outlooks, such as artificial intelligence, in advancing functionalities.
A new model for the extragalactic radio sky at low frequency calibrated using the LOFAR Two-metre Survey
Authors: Lin Jinyang , Zhu Zhenghao , Ma Renyi , Bonaldi Anna , Shan Huanyuan
Published: November 2024

Building the radio sky template are crucial for detecting the 21 cm emission line signal from the epoch of reionization, as well as for other cosmological research endeavours. Utilizing data from the LOFAR Two-meter Sky Survey at 150 MHz, we recalibrated the luminosity function for various types of radio sources, including high excitation radio galaxies, low excitation radio galaxies, radio-quiet active galactic nuclei, and star-forming galaxies. We subsequently updated the Tiered Radio Extragalactic Continuum Simulation (T-RECS) code to generate refined mock radio source catalogues. The simulated source counts from this work align more closely with observed data at redshifts greater than $z\gt 4$. Additionally, the differential source counts in total intensity within the flux density range of $0.1-1~\mathrm{mJy}$ closely mirror actual observations. Due to our model incorporating a lower number of faint sources compared to T-RECS, it predicts a reduced power spectrum for point sources, suggesting a potential advantage in studies in low frequency band.
Adjunctive Use of Gabapentinoids Increases Opioid Consumption Following 1- to 3-Level Anterior Lumbar Interbody Fusion with Posterior Fixation
Authors: Tao Xu , Kaghazchi Aydin , Shukla Geet , Karnati Janesh , Wu Andrew , Shankar Sachin , Ashraf Ahmed , Ranganathan Sruthi , Garcia-Vargas Julia , Barve Parikshit , Childress Kelly , Adogwa Owoicho
Published: November 2024

Study Design.

Retrospective cohort.

Objective.

To evaluate the impact of adjunctive gabapentinoid therapy on postoperative opioid consumption following 1-3 levels anterior lumbar interbody fusion (ALIF) with posterior fixation.

Summary of Background Data.

Gabapentin and pregabalin are analogues of the inhibitory neurotransmitter Gamma-Aminobutyric Acid (GABA) and are frequently employed as adjuncts in multimodal anesthesia strategies for managing acute pain. However, the opioid-sparing effect of gabapentinoids in the context of spine surgery has yet to be consistently demonstrated.

Methods.

The PearlDiver Database was queried from 2010 to 2021 for patients who underwent primary 1-3 levels ALIF with posterior fixation. Patients with opioid or gabapentinoid use within 6 months prior to index surgery were excluded. Patients with both gabapentinoid and opioid treatment were propensity score-matched to patients with opioid-only treatment.

Results.

The propensity score-matching resulted in two equal groups of 2,617 patients with and without adjunctive gabapentinoid treatment for pain management. Adjunctive use of gabapentinoids was associated with a modest 2.9% reduction in average Morphine Milligram Equivalent (MME) per day (Standardized Mean Difference (SMD) −1.33, 95% Confidence Interval (CI) [−2.657, −0.002], P=0.050). However, this was accompanied by a 37.1% increase in the total duration of opioid prescriptions (SMD 94.97, 95% CI [56.976, 132.967], P<0.001) and a 41.7% increase in total MME consumption per patient (SMD 4817.23, 95% CI [1864.410, 7770.044], P=0.001). Additionally, gabapentinoid use was associated with an increased risk of readmission due to pain (Relative Risk (RR) 1.10, 95% CI [1.002, 1.212], P=0.050) and the development of drug abuse (RR 1.37, 95% CI [1.016, 1.833], P=0.046).

Conclusion.

Despite the modest daily opioid-sparing effect observed, adjunctive gabapentinoid treatment appears to increase total opioid consumption due to prolonged opioid use and may compromise pain management in the context of ALIF with posterior fixation.
Remaining Steadfast on Diversity and Inclusion in Plastic Surgery
Authors: Sommer Nicole Z. , Butler Paris D.
Published: November 2024

Organized plastic and reconstructive surgery has recognized the importance of diversity for optimal patient care and advancement of the specialty. Initial goals focused on increasing opportunities for underrepresented members of the society: women and Blacks and Hispanic/Latino members. The diversity lens has expanded to not only include race and sex but also diversity of religion, sexual orientation, gender identity, disability, geography, economic status, membership status, and employment type. In response to diversity antagonists who argue that diversity abandons a system based on “excellence,” we counter that diversity efforts demand excellence but realize that success often requires a more level playing field with the elimination of discriminatory barriers.
Real-world Use of AlloDerm Acellular Dermal Matrix in Head and Neck Procedures in the United States
Authors: Dominguez Annaliza , Liang Yi , Abbed Turkia M. , Mukhatyar Vivek , Shimoga Sandhya
Published: November 2024

Background:

Real-world literature evaluating the use of AlloDerm SELECT Regenerative Tissue Matrix in head- and neck-related procedures is limited. To inform patient care decisions, this study evaluated healthcare resource utilization (HCRU) in US adults undergoing head- and neck-related procedures using AlloDerm.

Methods:

A retrospective claims analysis was conducted using MarketScan Commercial and Medicare Supplemental Databases (study period: October 1, 2015, to March 31, 2022; index period: November 1, 2015, to March 1, 2022). Adults aged 18 years or older with (1) medical claims for AlloDerm and a skin substitute on the same day during the index period, (2) a head/neck procedure diagnostic code, and (3) 30 or more days of continuous enrollment before and after first AlloDerm use index date. Descriptive statistics were used to describe surgery types and 30-day follow-up reoperations, graft complications, and all-cause HCRU.

Results:

Among 431 patients (51.7% women), mean (SD) age was 52.2 (15.8) years. AlloDerm was most used with oral cavity reconstruction (35.3%), septal perforation repair/rhinoplasty (16.5%), and parotidectomy (13.0%). Most procedures were performed in outpatient settings (hospital, 90.0%; ambulatory surgical center, 8.6%). Over 30 days, less than 1% of patients (4 of 431) required reoperation with AlloDerm; 0.5% (2 of 431) had graft-related complications. Most (75.6%) patients had an outpatient visit; few had an emergency room visit (7.9%) or inpatient claim (3.0%).

Conclusions:

Real-world evidence indicates that AlloDerm is used in head- and neck-related procedures in US adults, particularly oral reconstruction. Postprocedure complications and reoperations are uncommon during the follow-up period.
Arginyltransferase1 drives a mitochondria-dependent program to induce cell death
Authors: Kumar Akhilesh , O’Shea Corin R. , Yadav Vikas K. , Kandasamy Ganapathi , Moorthy Balaji T. , Ambrose Evan A. , Mulati Aliya , Fontanesi Flavia , Zhang Fangliang
Published: November 2024

Cell death regulation is essential for stress adaptation and/or signal response. Past studies have shown that eukaryotic cell death is mediated by an evolutionarily conserved enzyme, arginyltransferase1 (Ate1). The downregulation of Ate1, as seen in many types of cancer, prominently increases cellular tolerance to a variety of stressing conditions. Conversely, in yeast and mammalian cells, Ate1 is elevated under acute oxidative stress conditions and this change appears to be essential for triggering cell death. However, studies of Ate1 were conventionally focused on its function in inducing protein degradation via the N-end rule pathway in the cytosol, leading to an incomplete understanding of the role of Ate1 in cell death. Our recent investigation shows that Ate1 dually exists in the cytosol and mitochondria, the latter of which has an established role in cell death initiation. Here, by using budding yeast as a model organism, we found that mitochondrial translocation of Ate1 is promoted by the presence of oxidative stressors and is essential for inducing cell death with characteristics of apoptosis. Also, we found that Ate1-induced cell death is dependent on the formation of the mitochondrial permeability pore and at least partly dependent on the action of mitochondria-contained factors including the apoptosis-inducing factor, but is not directly dependent on mitochondrial electron transport chain activity or its derived reactive oxygen species (ROS). Furthermore, our evidence suggests that, contrary to widespread assumptions, the cytosolic protein degradation pathways including ubiquitin-proteasome, autophagy, or endoplasmic reticulum (ER) stress response has little or negligible impacts on Ate1-induced cell death. We conclude that Ate1 controls the mitochondria-dependent cell death pathway.
Heat shock factor 2 positively regulates oncogenic herpesvirus gene expression by remodeling the chromatin landscape
Authors: Cutrone Lorenza , Djupenström Hedvig , Peltonen Jasmin , Klimova Elena Martinez , Corso Simona , Giordano Silvia , Sistonen Lea , Gramolelli Silvia
Published: November 2024

Human gamma-herpesviruses, Kaposi’s sarcoma herpesvirus (KSHV) and Epstein-Barr virus (EBV) are causally associated to a wide range of cancers. While the default infection program for these viruses is latent, sporadic lytic reactivation supports virus dissemination and oncogenesis. Despite its relevance, the repertoire of host factors governing the transition from latent to lytic phase is not yet complete, leaving much of this complex process unresolved. Here, we show that heat shock factor 2 (HSF2), a transcription factor involved in regulation of acute stress responses and specific cell differentiation processes, promotes gamma-herpesvirus lytic gene expression. In lymphatic endothelial cells infected with KSHV and gastric cancer cells positive for EBV, ectopic HSF2 enhances the expression of lytic genes, while knocking down HSF2 significantly decreases their expression. Mechanistically, HSF2 overexpression results in decreased levels of repressive chromatin histone marks, at the promoters of the master regulators of the oncogenic lytic cascade, KSHV ORF50 and EBV BZLF1. Our results demonstrate that endogenous HSF2 binds to the ORF50 promoter in latent cells and sustains a transcriptionally permissive state. In contrast, in lytic cells, HSF2 occupancy at the ORF50 promoter is lost in conjunction with its proteasomal degradation. These findings establish HSF2 as a conserved regulator of gamma-herpesvirus lytic gene expression in latency and offer new functional insights on the cellular role of HSF2 at target promoters.
How to Predict Effective Drug Combinations - Moving beyond Synergy Scores
Authors: Eckhart Lea , Lenhof Kerstin , Herrmann Lutz , Rolli Lisa-Marie , Lenhof Hans-Peter
Published: November 2024

To improve our understanding of multi-drug therapies, cancer cell line panels screened with drug combinations are frequently studied using machine learning (ML). ML models trained on such data typically focus on predicting synergy scores, which support drug development and repurposing efforts but have limitations when deriving personalized treatment recommendations. To simulate a more realistic personalized treatment scenario, we pioneer ML models that predict the relative growth inhibition (instead of synergy scores), and that can be applied to previously unseen cell lines. Our approach is highly flexible: it enables the reconstruction of dose-response curves and matrices, as well as various measures of drug sensitivity (and synergy) from model predictions, which can finally even be used to derive cell line-specific prioritizations of both mono- and combination therapies.
Local High-Protein, Plant-Based Ready-to-Use Therapeutic Food Enhances Recovery from Malnutrition in Rats
Authors: Bechoff Aurélie , Akomo Peter , Muleya Molly , Tsaousis Anastasios D. , Nikolaou Charoula Konstantia , Utume Laura , Schneider Aviv , Khalaf Mona , Reifen Ram , Monsonego-Ornan Efrat
Published: November 2024

Infant child malnutrition is a major public health issue. We conducted a preclinical study with young rats to mimic the conditions of child malnutrition (combined wasting and stunting) and evaluate recovery using a novel plant-based ready-to-use-therapeutic food (RUTF) formulation.

Three-week old female Sprague Dawley rats were assigned to six treatments groups in a 6-week experiment. The treatments included: 1) control balanced diet (CT), 2) A protein-deficient diet to induce malnutrition (MN), 3) and 4) A control balanced diet followed by either commercial RUTF (CT-PM) or a locally produced plant-based RUTF (CT-ChSMS), and 5) and 6) a protein deficient diet followed by either commercial RUTF (MN-PM) or locally produced plant based RUTF (MN-ChSMS), respectively. In treatments 3-6, rats were initially fed either a control-balanced or protein-deficient diet for 3 weeks, followed by 3 weeks of either the commercial or the locally plant-based RUTF.

Results showed that rats in the CT-ChSMS group exhibited growth and weight comparable to CT group, while those in the MN-PM group showed no significant improvement compared to the MN group. Notably, rats in the MN-ChSMS group demonstrated significant catch-up growth, whereas those in the MN-PM group did not.

Additionally, consumption of ChSMS and PM RUTFs differed significantly. ChSMS RUTF which contained 14% protein over total energy with better amino-acid composition and a higher Protein Digestibility-Corrected Amino Acid Score (PDCAAS), resulted in significantly greater weight gain and length compared to PM RUTF, which contained 10% protein over total energy. These findings indicate that a locally produced, culturally acceptable and affordable plant-based RUTF formulated with high protein quality and quantity may be effective in treating acute and chronic malnutrition in children.
Mechanical stresses govern myoblast fusion and myotube growth
Authors: Le Toquin Yoann , Dubey Sushil , Ardaševa Aleksandra , Balasubramaniam Lakshmi , Delaune Emilie , Morin Valérie , Doostmohammadi Amin , Marcelle Christophe , Ladoux Benoît
Published: November 2024

Myoblast fusion into myotubes is critical for muscle formation, growth and repair. While the cellular and molecular mechanisms regulating myoblast fusion are increasingly understood, the role of biomechanics in this process remains largely unexplored. Here, we reveal that a dynamic feedback loop between evolving cell mechanics and cell-generated stresses shape the fusion of primary myoblastsin vitro. Applying principles from active nematics, we show that myoblast and myotube patterning follows physical rules similar to liquid crystal organization. Remarkably, fusion predominantly occurs at comet-shaped topological defects in cellular alignment, which we identified as regions of high compressive stress. We further find that this stress-driven organization depends on extracellular matrix (ECM) deposition, which mirrors the nematic order of the cell population. Our integrated data, supported by active nematics-based mathematical modeling, accurately predict self-organization patterns and mechanical stresses that regulate myoblast fusion. By revealing the essential role of biomechanics and ECM interplay in myogenesis, this work establishes a foundational framework for understanding biomechanical principles in morphogenesis.
Introducing SPROUT (Semi-automated Parcellation of Region Outputs Using Thresholding): an adaptable computer vision tool to generate 3D segmentations
Authors: He Yichen , Camaiti Marco , Roberts Lucy E. , Mulqueeney James M. , Didziokas Marius , Goswami Anjali
Published: November 2024

The increased availability of 3D image data requires improving the efficiency of digital segmentation, currently relying on manual labelling, especially when separating structures into multiple components. Automated and semi-automated methods to streamline segmentation have been developed, such as deep learning and smart interpolation, but require pre-labelled data, and specialized hardware and software. Deep learning models in particular often require the manual creation of extensive training data, particularly for complex multi-class segmentations. Here, we introduce SPROUT, a novel, semi-automated computer vision method providing a time-efficient and user-friendly pipeline for segmenting and parcellating image data. SPROUT generates seeds (representing parts of an object) based on specified density thresholds and erosion of connected components, to achieve element separation. Seeds are grown to obtain fully-parcellated segmentations. We compare SPROUT’s performance to that of smart interpolation and apply it to diverse datasets to demonstrate the utility and versatility of this open-source 3D segmentation method.
Receptor polarization through localized activity and global sensitization
Authors: Goetz Andrew , Dixit Purushottam D.
Published: November 2024

Eukaryotic cellschemosenseconcentration gradients of extracellular ligands using membrane-bound receptors that polarize their activity. Receptors from several chemosensing families are preferentially degraded after activation and undergo significant lateral diffusion, both of which may blunt their polarization. To explore the combined role of these two seemingly detrimental phenomena on active receptor polarization, we use a reaction/diffusion model. The model elucidates a counterintuitive principle that governs receptor polarization under external gradients: Localized Activity and Global Sensitization (LAGS). In LAGS, receptor activity is localized through receptor degradation or ligand unbinding. In contrast, uniform sensitivity to ligands is maintained over the plasma membrane through lateral receptor diffusion. Surprisingly, increasing preferential degradation of active receptors and increasing lateral diffusion of all receptors both sharpen active receptor polarization. Additionally, when combined with receptor oligomerization, an increase in preferential degradation allows cells to sense relative ligand gradients over a larger range of background ligand concentrations. An analytical model identifies parameter regimes that dictate which processes dominate receptor polarization. A survey of kinetic parameters suggests that receptor polarization in many mammalian pathways can be modeled using LAGS.
Pairwise interactions and serial bottlenecks help explain species composition in a multi-species microbial community
Authors: Lele Kasturi , Wolfe Benjamin E. , Uricchio Lawrence H.
Published: November 2024

Characterizing the processes that drive microbial community assembly remains a key challenge in ecology. Several recent studies have argued that pairwise interactions may be insufficient to explain co-occurrence patterns in complex microbial communities, but most such studies have focused on synthetic communities not found in nature or microbes grown in contexts that differ widely from their natural environment. Moreover, most models of pairwise interactions rely on equilibrium assumptions that are not relevant to all natural communities, such as gut microbiomes or species in fluctuating environments. Microbes from fermented foods can be cultured in their natural abiotic environment in the lab and typically have moderate species complexity, making them tractable systems for studying community assembly processes. In this study, we investigated whether multi-species co-occurrence patterns can be predicted from pairwise interactions for microbes isolated from sourdough starters. Interaction parameters inferred from pairwise growth trajectories were suggestive of widespread coexistence between pairs of microbes in our species’ pool. In communities of up to nine species, most species’ presence and relative abundance could be reliably predicted based on a model of pairwise interactions. The inclusion of nonequilibrium demography in our model further improved the accuracy of our pairwise model. Our work contributes to the broader debate on the processes underlying community assembly by showing that pairwise interactions are predictive of community structure in a system of moderate species complexity.
Laminin β4 is required for the development of human peripheral sensory neurons
Authors: Saito-Diaz Kenyi , Saini Tripti , Patel Archie Jayesh , James Christina , Thomas Kimata Safi , Knight Trinity Nora , Gogita Stephanie Beatrice , Zeltner Nadja
Published: November 2024

The extracellular matrix (ECM) is a mixture of glycoproteins and fibrous proteins that provide the biophysical properties necessary to maintain cellular homeostasis. ECM integrity is of particular importance during development, where it allows proper migration and cellular differentiation. Laminins are ECM heterotrimeric proteins consisting of α, β, and γ chains. There are five known α chains, four β chains, and three γ chains. Thus, there are 60 potential combinations for laminin trimers, however only 16 laminin trimers have been identified to date. Furthermore, none of them contain laminin β4 and its function is unknown. Here, we sought to characterize the role ofLAMB4(the gene encoding laminin β4) during human embryonic development of the peripheral sensory nervous system. Using human pluripotent stem cells (hPSCs), we found thatLAMB4is expressed in the ectoderm in the early stages of sensory neuron (SN) specification. SNs, part of the peripheral nervous system, are specialized neurons that detect pain, temperature, and touch. Surprisingly, more than 20 million people in the US have some form of peripheral nerve damage (including SNs), however there are very few treatment options available. Learning about the biology of peripheral neurons will uncover potential new therapeutic targets, thus we focused on understanding the effects ofLAMB4in SNs. First, we knocked outLAMB4in hPSCs, using CRISPR/Cas9, and found that loss ofLAMB4impairs the migration of the SN progenitors neural crest cells (NCCs) and harms SN development and survival. To assess ifLAMB4has clinical relevance, we studied the genetic disorder Familial Dysautonomia (FD), which specifically affects the peripheral nervous system. FD is caused by a mutation inELP1(a component of the Elongator complex) leading to developmental and degenerative defects in SNs. A previous report showed that patients with severe FD harbor additional single nucleotide variants in LAMB4. We found that these variants sharply downregulate the expression ofLAMB4and laminin β4 levels in SNs differentiated from induced pluripotent stem cells (iPSCs) reprogramed from patients with severe FD. Moreover, a healthy ECM is sufficient to rescue the developmental phenotypes of FD, further confirming that ECM defects contribute significantly to the etiology of FD. Finally, we found that LAMB4/laminin β4 is necessary for actin filament accumulation and it interacts with laminin α4 and laminin γ3, forming the laminin-443, a previously unreported laminin trimer. Together, these results show thatLAMB4is a critical, but largely unknown gene required for SN development and survival.
Inositol-Requiring Enzyme 1 pathway and autophagy drive sequential response of endothelial cells to febrile range hyperthermia
Authors: Vorbe Julie , Massey Florence , Rocher Corinne , Morales Océane , Brikci Nihal , Le Borgne Marie , Caligiuri Giuseppina , Nicoletti Antonino , Franck Grégory , Illiano Stéphane
Published: November 2024

Context

Fever is an evolutionarily conserved and adaptive response during infections. However, prolonged fever has numerous systemic metabolic and functional side effects. In the heart, prolonged fever associated with infection is linked to fatal adverse effects, particularly involving impaired coronary circulation. Yet, the direct relationship between elevated temperature and coronary microcirculation dysfunction, remains to be fully demonstrated. In this study, we aimed to explore the specific responses of human coronary artery endothelial cells (HCAECs) to fever-range hyperthermia.

Method

HCAECs were cultured at either 37°C or 40°C for up to 24 hours. Transcriptomic and proteomic profiles were obtained through microarray and mass spectrometry after 6, 12, and 24 hours of exposure. Key signaling pathways, upstream regulators, and candidate mechanisms were identified and validated at the mRNA and protein levels using mechanistic approaches.

Results

Prolonged hyperthermia compromised HCAEC function, evidenced by cell detachment, loss of junctions, and increased permeability. HCAECs rapidly activated the unfolded protein response (UPR), including IRE1α activation andXBP1splicing. Additionally, autophagic flux was significantly elevated, participating in the degradation of junction proteins. Pharmacological inhibition of IRE1α reduced the autophagic burden, protected against cell detachment, and preserved junction integrity over time.

Conclusion

Our findings reveal that in response to fever-range hyperthermia, the IRE1α-autophagy axis regulates the survival and function of coronary endothelial cells. This mechanism could play a key role in modulating endothelial responses during infection and contribute to the pathological outcomes of fever. Furthermore, it may be relevant in local inflammatory conditions with elevated temperatures.
Structure-Based Design of Covalent Nanobody Binders for a Thermostable Green Fluorescence Protein
Authors: Yue Zhihao , Li Yanfang , Cai Hongmin , Yao Hebang , Li Dianfan , Ni Aimin , Li Tingting
Published: November 2024

Green fluorescence protein (GFP) lights up almost every aspects of life sciences. An ultra thermostable GFP (TGP), engineered from a coral GFP, offers potential advantages over traditional jellyfish-derived GFP due to its high stability. However, owing to its later discovery, TGP lacks the extensive toolsets available for GFP, such as heavy chain-only antibody binders known as nanobodies. In this study, we have structurally characterized TGP in complex with Sb92, a synthetic nanobody identified from a previous in vitro screening, revealing its precise three-dimensional epitope. This structural insight, alongside the previously characterized Sb44-TGP complex, have allowed us to rationally design disulfide bonds between antigen and antibody for tighter interactions. Using biochemical analyses, we identify two bridged complexes (TGP A18C-Sb44 V100C, TGP E118C-Sb92 S57C), with the TGP-Sb92 disulfide pair showing high resistance to reducing agents. Our study expands the toolkit available for TGP and should encourage its wider applications.
Novel endornaviruses infecting Phytophthora cactorum that attenuate vegetative growth, promote sporangia formation, and confer hypervirulence to the host oomycete.
Authors: Sakuta Kohei , Ito Aori , Sassa-OBrien Yukiko , Yoshida Tomohiro , Fukuhara Toshiyuki , Uematsu Seiji , Komatsu Ken , Moriyama Hiromitsu
Published: November 2024

Two novel endornaviruses were found in Phytophthora cactorum isolated from severe black lesions on Boehmeria nivea (B. nivea) var. nipononivea plants in a Japanese forest. These two endornaviruses were named Phytophthora cactorum alphaendornavirus 4 (PcAEV4) and Phytophthora cactorum alphaendornavirus 5 (PcAEV5), and have site-specific nick structures in their positive RNA strands, which are hallmarks of alphaendornaviruses. Ribavirin and cycloheximide treatment of the protoplasts effectively cured the host oomycete (Kara1) of the viruses. The resultant virus-free strain (Kara1-C) displayed luxuriant mycelial growth with less zoosporangia formation as compared to the Kara1 strain. Remarkably, the Kara1-C strain exhibited reduced ability to form black lesions on B. nivea leaves, suggesting that presence of PcAEV4 and PcAEV5 in the Kara1 strain led to enhanced virulence in host plants. Under osmotic pressure and cell wall synthesis inhibition, the Kara1 strain exhibited less growth inhibition compared with the Kara1-C strain. In contrast, the Kara1 strain showed more growth inhibition to membrane-permeable surfactant compared with the Kara1-C strain, indicating that these endornaviruses can alter the susceptibility of the host oomycete to abiotic stresses. Co-localization and cell fractionation analyses showed that PcAEV4 and PcAEV5 localized to intracellular membranes, particularly the ER membrane fraction. Further, infection with these 2 endornaviruses was found to affect the host's response to exogenous sterols, which enhanced vegetative growth and zoosporangia formation, as well as virulence of the host oomycete. These results provide deep insights into the effects of endornavirus infection in the Phytophthora spp. and also highlight protoplast-based methods in advancing Phytophthora virus studies.
Mechanics ofE. colicell width homeostasis and bulging dynamics from MreB and septum inhibition
Authors: Kale Tanvi , Dasgupta Ryth , Inamdar Mandar M. , Athale Chaitanya A.
Published: November 2024

The mechanobiology of cytoskeleton and cell envelope play a vital role in cell shape homeostasis. In the gram-negative model rod-shaped bacteriumEscherichia coliantibiotics that weaken the cell envelope are seen to result in bulges that eventually lead to lysis. Here, we quantify the shape dynamics ofE. colitreated with cephalexin, a PBP3 inhibitor and A22, an MreB polymerization inhibitor from single cell microscopy. We find low concentrations of both inhibitors result in bulge formation with multiple cell shapes observed: rugby, large bacilli and rods with two and three bulges. We quantify the parameters of cell envelope rigidity, pressure and fluidity obtained from fitting a computational model of shell-mechanics to length and width dynamics from experiment. Using this optimized model we estimate the turgor and growth pressures of untreated growing cells as ≈0.15 MPa and ≈0.4 MPa. The bulge expansion dynamics correlate most prominently with a change in bending rigidity of the cell wall and cytoskeleton. Simulations predict a threshold behavior in response to envelope bending rigidity that is validated by comparison with experiments ofE. colitreated with A22 either in isolation or in combination, resulting in loss of width control and cell shape change.
In situMembrane Protein Expression by Efficient Recruitment of mRNA to the Membranes of Synthetic Cells
Authors: Fu Hang , Ma Lijuan , Xu Chunhua , Li Jinghua , Sun Yunhai , Tao Yuanxiao , Wang Hao , Hu Shuxin , Fu Meifang , Zheng Hai , Liu Chenli , Ye Fangfu , Qiao Yan , Li Ming , Lu Ying
Published: November 2024

The synthesis of artificial cells is crucial for understanding the origins of life. In synthetic cells, however, the absence of membrane-bound organelles and auxiliary proteins severely limits the efficient expression and precise localization of membrane proteins using cell-free expression systems. Here we introduce a robust method that significantly enhances membrane protein synthesis by recruiting mRNA to phospholipid membranes. This is achieved through the use of cholesterol-modified, single-stranded DNA that anchors to the membrane and pairs with the mRNA’s untranslated region. This strategic placement facilitates the assembly of protein expression machinery, promoting direct co-translational folding at the membrane. Our approach not only ensures correct protein topology and functionality but also demonstrates broad applicability for thein situexpression of various membrane proteins. It effectively addresses the challenges of membrane protein localization and assembly in synthetic cells, showcasing its versatility for synthesizing a wide array of membrane proteins.
Mapping enhancer-gene regulatory interactions from single-cell data
Authors: Sheth Maya U. , Qiu Wei-Lin , Rosa Ma X. , Gschwind Andreas R. , Jagoda Evelyn , Tan Anthony S. , Einarsson Hjörleifur , Gorissen Bram L. , Dubocanin Danilo , McGinnis Christopher S. , Amgalan Dulguun , Satpathy Ansuman T. , Jones Thouis R. , Steinmetz Lars M. , Kundaje Anshul , Ustun Berk , Engreitz Jesse M. , Andersson Robin
Published: November 2024

Mapping enhancers and their target genes in specific cell types is crucial for understanding gene regulation and human disease genetics. However, accurately predicting enhancer-gene regulatory interactions from single-cell datasets has been challenging. Here, we introduce a new family of classification models, scE2G, to predict enhancer-gene regulation. These models use features from single-cell ATAC-seq or multiomic RNA and ATAC-seq data and are trained on a CRISPR perturbation dataset including >10,000 evaluated element-gene pairs. We benchmark scE2G models against CRISPR perturbations, fine-mapped eQTLs, and GWAS variant-gene associations and demonstrate state-of-the-art performance at prediction tasks across multiple cell types and categories of perturbations. We apply scE2G to build maps of enhancer-gene regulatory interactions in heterogeneous tissues and interpret noncoding variants associated with complex traits, nominating regulatory interactions linkingINPP4BandIL15to lymphocyte counts. The scE2G models will enable accurate mapping of enhancer-gene regulatory interactions across thousands of diverse human cell types.
The dark side of fluorescent protein tagging – the impact of protein tags on biomolecular condensation
Authors: Fatti Edoardo , Khawaja Sarah , Weis Karsten
Published: November 2024

Biomolecular condensation has emerged as an important mechanism to control various cellular processes through the formation of membraneless organelles. Fluorescent protein tags have been extensively used to study the formation and the properties of condensatesin vitroandin vivo, but there is evidence that tags may perturb the condensation properties of proteins. In this study, we carefully assess the effects of protein tags on the yeast DEAD-box ATPase Dhh1, a central regulator of processing bodies (P-bodies), which are biomolecular condensates involved in mRNA metabolism. We show that fluorescent tags as well as a poly-histidine tag greatly affect Dhh1 condensationin vitroand lead to condensates with different dynamic properties. Tagging of Dhh1 with various fluorescent proteinsin vivoalters the number of P-bodies upon glucose starvation and some tags even show constitutive P-bodies in non-stressed cells. These data raise concerns about the accuracy of tagged protein condensation experiments, highlighting the need for caution when interpreting the results.

Significance Statement

Fluorescent tags are extensively used in protein condensation studies although their effect in condensate dynamics has not been carefully investigated.

Tags affect the condensation propensity and dynamics of Dhh1in vitroand P-body numbersin vivo.

Tags may generally alter the behavior of proteins in biomolecular condensates and their use needs to be carefully evaluated and controlled.
Measuring regulatory network inheritance in dividing yeast cells using ordinary differential equations
Authors: Wu Wenbin , Kennedy Taylor , Arguello-Miranda Orlando , Lin Kevin Z.
Published: November 2024

Quantifying the inheritance of regulatory networks among proteins during asymmetric cell division remains a challenge due to the complexity of these systems and the lack of robust mathematical definitions for inheritance. We propose a novel statistical framework called ODEinherit to measure how much a mother cell’s regulatory network explains its daughter’s trajectories, addressing this gap. Using time-lapse microscopy, we tracked the expression dynamics of six proteins across 85 dividingS. cerevisiaecells, observed over eight hours at 12-minute intervals. Our framework employs a two-step approach. First, we estimate an ordinary differential equation (ODE) system for each cell to characterize protein interactions, introducing novel adjustments for non-oscillatory time series and leveraging multi-cell data. Second, we assess inheritance by clustering cells based on cycling markers and quantifying how well a mother’s regulatory network predicts her daughter’s. Preliminary findings suggest stage-dependent differences in inheritance rates, paving the way for applications in cellular stress response and cell-fate prediction studies across generations.
The 1.3 Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1
Authors: Bragagnolo Nicholas , Audette Gerald F.
Published: November 2024

The type IV pilus is a diverse molecular machine capable of conferring a variety of functions and is produced by a wide range of bacterial species. The ability of the pilus to perform host-cell adherence makes it a viable target for the development of vaccines against infection by human pathogens such as Pseudomonas aeruginosa. Here, the 1.3 Å resolution crystal structure of the N-terminally truncated type IV pilin from P. aeruginosa strain P1 (ΔP1) is reported, the first structure of its phylogenetically linked group (group I) to be discussed in the literature. The structure was solved from X-ray diffraction data that were collected 20 years ago with a molecular-replacement search model generated using AlphaFold; the effectiveness of other search models was analyzed. Examination of the high-resolution ΔP1 structure revealed a solvent network that aids in maintaining the fold of the protein. On comparing the sequence and structure of P1 with a variety of type IV pilins, it was observed that there are cases of higher structural similarities between the phylogenetic groups of P. aeruginosa than there are between the same phylogenetic group, indicating that a structural grouping of pilins may be necessary in developing antivirulence drugs and vaccines. These analyses also identified the α–β loop as the most structurally diverse domain of the pilins, which could allow it to serve a role in pilus recognition. Studies of ΔP1 in vitro polymerization demonstrate that the optimal hydrophobic catalyst for the oligomerization of the pilus from strain K122 is not conducive for pilus formation of ΔP1; a model of a three-start helical assembly using the ΔP1 structure indicates that the α–β loop and the D-loop prevent in vitro polymerization.
Management excellence practices in small- and medium-sized industries: proposition of an evaluation approach and application in an emerging country
Authors: Pacheco Junior Marco Antonio , Sigahi Tiago F.A.C. , Rampasso Izabela Simon , Zanon Lucas Gabriel , Leal Filho Walter , Anholon Rosley
Published: November 2024

Purpose

This paper proposes an evaluation approach for analyzing excellence management practices at a regional level based on experts’ assessment.

Design/methodology/approach

Using the National Quality Foundation’s Management Excellence Model (MEG), 19 management excellence practices were identified and tailored for small- and medium-sized industries (SMIs). Data were collected through a survey with 25 experts who assessed these practices in the context of Brazilian manufacturing SMIs. The analysis utilized Fuzzy TOPSIS Class (FTC), and a sensitivity analysis was also conducted.

Findings

The proposed evaluation approach integrates a reference model for management excellence (MEG), an analysis method incorporating uncertainty (FTC), and results that enable decision-makers to make well-informed choices. Of the 19 practices assessed, 15 were classified as “unacceptable,” while four were rated as “regular,” and none as “expected.” Key challenges relate to practices in information security, knowledge, innovation and change management.

Research limitations/implications

The study’s primary limitation is the use of non-probabilistic sampling and its focus on the Brazilian context. However, the extensive knowledge and experience of the experts in manufacturing SMIs and the need for studies addressing specific regional contexts should be noted.

Practical implications

The findings reveal a significant gap between ideal management practices and the actual state of SMIs, especially in emerging markets.

Originality/value

This research introduces a novel approach that combines a reference model tailored for SMIs with a multicriteria decision-making method, offering valuable insights for decision-makers and guiding future research.
Digitization and radical innovation: the serial mediation effect of absorptive capacity
Authors: Liu Yexin , Gao Bohan , Wu Weiwei
Published: November 2024

Purpose

Radical innovation involves significant technological advances that have a critical impact on both firm growth and society development. Therefore, there is a growing need to understand how to achieve radical innovation. While previous studies have examined the direct effect of digitization on firm innovation, there is still limited knowledge of how digitization affects radical innovation. This paper aims to contribute to further exploring the underlying mechanism of how digitization affects radical innovation by incorporating the serial mediation effect of absorptive capacity.

Design/methodology/approach

This paper collected data from Chinese-listed manufacturing firms from 2015 to 2021 and analyzed the data using bootstrap analysis.

Findings

The research results show that digitization has a positive impact on radical innovation. Furthermore, digitization can influence radical innovation through potential absorptive capacity and realized absorptive capacity, and the mediation effect of potential absorptive capacity and realized absorptive capacity can occur sequentially. These research results are validated by a range of robustness tests.

Originality/value

This paper contributes to the literature on digitization and radical innovation by validating a model that links digitization through absorptive capacity to radical innovation. This model helps to explain the relationship between digitization and radical innovation, which has previously been a topic of debate. This paper also contributes to the absorptive capacity literature by unpacking the asymmetric roles of the potential absorptive capacity and the realized absorptive capacity. This paper also provides valuable implications for practices.
Identifying leadership competencies for Indian public health leaders using LEADS framework
Authors: Panchamia Jallavi , Iyer Veena , Bhakare Shilpa , Sharma Bharati
Published: November 2024

Purpose

There are few studies exploring leadership competencies for public health leaders in low-middle-income countries, including India. The purpose of this study is to discern the leadership competencies the public health leaders might need by adapting the LEADS framework of leadership competencies and understanding the characteristics of the Indian public health system that influence the practice of these competencies.

Design/methodology/approach

The authors followed a sequential multiphase mixed-method design. Phase I included a concurrent literature review and in-depth interviews of senior public health leaders in western India. Phase II was an online leadership competency survey (10 statements each for knowledge, skills and behaviors) of 88 district-level public health leaders. Phase III included focus group discussions with 33 district-level public health leaders to better understand survey results.

Findings

The practice of leadership competencies was determined by health system characteristics, governance and managerial processes, health system culture and sociopolitical environment in which the health system shared an interface. In total, 20 out of 30 competencies were categorized under the first two LEADS domains of “Leading self” and “Engaging others.” “Achieving results” was affected by the centralized nature of health programs’ planning and monitoring. The health systems context provided limited scope to practice competencies under the “Developing coalitions” and “Systems transformation” domains.

Practical implications

Findings from this study can help address gaps in leadership competencies and tailor leadership development programs.

Originality/value

Past research on leadership competencies in India has used Western frameworks without adaptation. Through this study, the authors tried to conceptualize and contextualize competencies for Indian public health leaders adapting the LEADS framework.