bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell morphogenesis via self-propelled treadmilling actin waves
Authors: Yagami Kio , Baba Kentarou , Minegishi Takunori , Misu Shinji , Katsuno-Kambe Hiroko , Okano Kazunori , Sakumura Yuichi , Hosokawa Yoichiroh , Inagaki Naoyuki 
Published: February 2024

SUMMARYActin dynamics mediate cell morphogenesis. Actin filaments polymerize outward at cell protrusions such as the leading edge of migrating cells, thereby pushing the membrane to protrude. The current paradigm explains that actin dynamics are regulated by cell signaling. However, it is unclear how cells spontaneously form actin-based protrusions even without a specific local signaling cue. We found that arrays of treadmilling actin filaments emerge widely in migrating cells and move in the direction of polymerization as actin waves. Their arrival at the cell periphery pushes the plasma membrane to protrude. Furthermore, they accumulate at protrusions without local signaling cues, similar to self-propelled particles colliding with a boundary. This leads to further growth of protrusions, thereby promoting spontaneous formation of the leading edge for migration. We propose that the self-propelled actin waves drive robust formation of protrusions for cell morphogenesis, through their abilities to self-accumulate into protrusions and push the membrane.
Nanocarrier Drug Release and Blood-Brain Barrier Penetration at Post-Stroke Microthrombi Monitored by Real-Time Förster Resonance Energy Transfer-Based Detection System (FedEcs)
Authors: Khalin Igor , Adarsh Nagappanpillai , Schifferer Martina , Wehn Antonia , Boide-Trujillo Valeria J. , Mamrak Uta , Shrouder Joshua , Misgeld Thomas , Filser Severin , Klymchenko Andrey , Plesnila Nikolaus 
Published: February 2024

AbstractNanotechnology holds great promise for improving the delivery of therapeutics to the brain. However, current approaches often operate at the organ or tissue level and are limited by the lack of tools to dynamically monitor cargo deliveryin vivo. We have developed highly fluorescent lipid nanodroplets (LNDs) that enable tracking of nanocarrier behaviour at the subcellular level while also carrying a Förster resonance energy transfer (FRET)-based drug delivery detection system (FedEcs) capable of monitoring cargo releasein vivo. Using two-photon microscopy, we demonstrate that circulating LNDs in naïve mouse brain vasculature exhibit 3D real-time FRET changes, showing size-dependent stability over two hours in blood circulation. Further, in a novel nano-stroke model, dynamic intravital two-photon imaging revealed that LNDs accumulated within cerebral post-ischemic microthrombi, where they released their cargo significantly faster than in normal blood circulation. Furthermore, the blood-brain barrier (BBB) became permeable at the microclot sites thereby allowing accumulated FedEcs-LNDs to cross the BBB and deliver their cargo to the brain parenchyma. This microthrombi-associated translocation was confirmed at the ultrastructural level via volume correlative light-electron microscopy. Consequently, our FedEcs represents a novel tool to quantitatively study the biodistribution and cargo release of nanocarriers at high resolution in real time. By enabling us to resolve passive targeting mechanisms post-stroke, - specifically, accumulation, degradation and extravasation via post-stroke microthrombi - this system could significantly enhance the translational validation of nanocarriers for future treatments of brain diseases.
Mechanosensory cephalic bristles mediate rapid flight initiation in endothermic hawkmoths
Authors: Manjunath Maitri , Mukunda Chinmayee L. , Sane Sanjay P. 
Published: February 2024

AbstractEndothermic insects including bees, butterflies, and moths need to warm up their flight muscles before taking flight. For instance, diurnal butterflies bask in the sun to heat their flight muscles, whereas nocturnal hawkmoths display a pre-flight shivering behavior in which small-amplitude wing movements cause flight muscles to warm up, eventually generating large-amplitude wing motion for flight. The time required for warm-up puts such insects at a considerable risk if they need to rapidly escape from predators. Here, we show that upon experiencing a sudden air-puff on the head, hawkmoths rapidly initiate flight bypassing the pre-flight shivering phase. This response is mediated by mechanosensory cephalic bristles that are buried under the scales on their head. Cephalic bristle mediated flight entails a stereotypic triggering of various flight-related reflexes including antennal positioning, foreleg extension, wing movement, and abdominal flexion. Some mechanosensory neurons underlying cephalic bristles arborize in the subesophageal zone (SEZ) and antennal motor and mechanonsensory center (AMMC), whereas most arborize in pro-, meso- and meta-thoracic ganglia which contain the motor circuitry for foreleg motion, flight, and abdominal flexion. Thermal recordings revealed that large-amplitude wing motion following cephalic bristle-stimulation occurs at lower thoracic temperatures than required for voluntary flight. Electromyogram recordings from steering and indirect flight muscles show significant variability in activation latency in response to cephalic bristle stimulus. The range of latency values among different muscles overlaps, suggesting that cephalic bristle stimulation activates steering muscles, thereby generating high-amplitude wing movement at lower thoracic temperatures. Concomitant activation of the indirect flight muscles initiates thoracic warm-up in preparation for longer flight. Thus, akin to locusts, the cephalic bristle system in hawkmoths rapidly triggers flight upon sensing danger, ensuring swift escape from potential threats.
The ER-resident Ras Inhibitor 1 (Eri1) ofCandida albicansinhibits hyphal morphogenesis via the Ras-independent cAMP-PKA pathway
Authors: Sethi Subhash Chandra , Bharati Monika , Yadav Usha , Kumar Yatin , Komath Sneha Sudha 
Published: February 2024

AbstractRas signaling and glycosylphosphatidylinositol (GPI) biosynthesis are mutually inhibitory inS. cerevisiae. The inhibition is mediated via an interaction of yeast Ras2 with the Eri1 subunit of its GPI-N-acetylglucosaminyl transferase (GPI-GnT), the enzyme catalyzing the very first GPI biosynthetic step. In contrast, Ras signaling and GPI biosynthesis inC. albicansare mutually activated and together control the virulence traits of the human fungal pathogen. What might be the role of Eri1 in this pathogen? The present manuscript addresses this question while simultaneously characterizing the cellular role of CaEri1. It is either non-essential or required at very low levels for cell viability inC. albicans. Severe depletion of CaEri1 results in reduced GPI biosynthesis and cell wall defects. It also produces hyperfilamentation phenotypes in Spider medium as well as in bicarbonate medium containing 5% CO2, suggesting that both the Ras-dependent and Ras-independent cAMP-PKA pathways for hyphal morphogenesis are activated in these cells. Pull-down and acceptor-photobleaching FRET experiments suggest that CaEri1 does not directly interact with CaRas1, but does so through CaGpi2, another GPI-GnT subunit. CaGpi2 is also downstream of CaEri1 in cross-talk with CaRas1 and control of hyphal growth in Spider medium. However, CaEri1 is downstream of all GPI-GnT subunits in inhibiting Ras-independent filamentation.CaERI1also participates in the inter-subunit transcriptional cross-talk within the GPI-GnT, a feature unique toC. albicans. Virulence studies usingG. mellonellalarvae show that a heterozygous strain ofCaERI1is better cleared by the host and is attenuated in virulence.
Attenuated replication and damaging effects of SARS-CoV-2 Omicron variants in an intestinal epithelial barrier model
Authors: Volcic Meta , Nchioua Rayhane , Pastorio Chiara , Zech Fabian , Read Clarissa , Walther Paul , Kirchhoff Frank 
Published: February 2024

ABSTRACTMany COVID-19 patients suffer from gastrointestinal symptoms and impaired intestinal barrier function may play a key role in Long COVID. Despite its importance, the impact of SARS-CoV-2 on intestinal epithelia is poorly understood. To address this, we established an intestinal barrier model integrating epithelial Caco-2 cells, mucus-secreting HT29 cells and human Raji cells. This gut epithelial model allows efficient differentiation of Caco-2 cells into microfold-like cells, faithfully mimics intestinal barrier function, and is highly permissive to SARS-CoV-2 infection. Early strains of SARS-CoV-2 and the Delta variant replicated with high efficiency, severely disrupted barrier function, and depleted tight junction proteins, such as claudin-1, occludin and ZO-1. In comparison, Omicron subvariants also depleted ZO-1 from tight junctions but had fewer damaging effects on mucosal integrity and barrier function. Remdesivir and the TMPRSS2 inhibitor Camostat prevented SARS-CoV-2 replication and thus epithelial barrier damage, while the Cathepsin inhibitor E64d was ineffective. Our results support that SARS-CoV-2 disrupts intestinal barrier function but further suggest that circulating Omicron variants are less damaging than earlier viral strains.
Iterative Bleaching Extends Multiplexity (IBEX) imaging facilitates simultaneous identification of all cell types in the vertebrate retina
Authors: Kothurkar Aanandita , Patient Gregory S. , Noel Nicole C. L. , Krzywańska Aleksandra M , Carr Brittany J. , Chu Colin J. , MacDonald Ryan B. 
Published: February 2024

ABSTRACTThe vertebrate retina is a complex multicellular tissue made up of distinct neuron types and glia, arranged in a stereotypic layered organisation to facilitate vision. Understanding how these cell types come together to form precise circuits during development requires the ability to simultaneously discriminate between multiple cell types and their spatial position in the same tissue. Currently, we have a limited capacity to resolve all constitutive cell types and their relationships to one another due to our limited ability to combine multiple cellular markers. To extend this capacity, we have adapted a highly multiplexed immunohistochemistry technique known as Iterative Bleaching Extends Multiplexity (IBEX) and applied it to the development of the zebrafish (Danio rerio)retina. IBEX allows for multiple rounds of cellular labelling to be performed, before imaging and integration of data, resulting in the ability to visualise multiple markers on the same tissue. We have optimised IBEX in zebrafish using fluorescent micro-conjugation of known antibody markers to label the complete retina with up to 11 cell-specific antibodies. We have further adapted the IBEX technique to be compatible with fluorescent transgenic reporter lines,in situhybridisation chain reaction (HCR), and wholemount immunohistochemistry (WMIHC). We then took advantage of IBEX to explore the multicellular relationships in the developing retina between glial cells and neurons and photoreceptor subtypes. Finally, we tested IBEX on retinas from the emerging ageing model, the killifish (Nothobranchius furzeri), and developmental model, the African clawed frog (Xenopus laevis),demonstrating the usefulness of the technique across multiple species. The techniques described here can be applied to any tissue in any organism where antibodies are readily available to efficiently explore cellular relationships in the context of development, ageing or disease.
Linking Neural Manifolds to Circuit Structure in Recurrent Networks
Authors: Pezon Louis , Schmutz Valentin , Gerstner Wulfram 
Published: February 2024

AbstractThe classic view of cortical circuits composed of precisely tuned neurons hardly accounts for large-scale recordings indicating that neuronal populations are heterogeneous and exhibit activity patterns evolving on low-dimensional manifolds. Using a modelling approach, we connect these two contrasting views. Our recurrent spiking network models explicitly link the circuit structure with the low-dimensional dynamics of the population activity. Importantly, we show that different circuit models can lead to equivalent low-dimensional dynamics. Nevertheless, we design a method for retrieving the circuit structure from large-scale recordings and test it on simulated data. Our approach not only unifies cortical circuit models with established models of collective neuronal dynamics, but also paves the way for identifying elements of circuit structure from large-scale experimental recordings.
Post-transcriptional regulation of the MiaA prenyl transferase by CsrA and the small RNA CsrB inE. coli
Authors: Aubee Joseph I , Williams Kinlyn , Adigun Alexandria , Olusanya Olufolakemi , Nurse Jalisa , Thompson Karl M 
Published: February 2024

ABSTRACTTo determine the role of small RNAs (sRNAs) in the regulation ofmiaA, we constructed a chromosomalmiaA-lacZtranslational fusion driven by the arabinose responsive PBADpromoter and used it to screen against anEscherichia colismall RNA library (containing small RNAs driven by the IPTG inducible PLacpromoter). Our genetic screen and quantitative β-galactosidase assays identified CsrB and its cognate protein CsrA as potential regulators ofmiaAexpression inEscherichia coli. Consistent with our hypothesis that CsrA regulates MiaA post-transcriptional gene expression through binding to the MiaA mRNA 5’ UTR, and CsrB binds and regulates MiaA post-transcriptional gene expression through sequestration of CsrA levels, a deletion ofcsrAsignificantly reduced expression of the reporter fusion as well as reducingmiaAmRNA levels. These results suggest under conditions where CsrA is inhibited, MiaA translation and thus MiaA-dependent tRNA modification may be limiting.IMPORTANCEWe previously demonstrated a role for the i6A modification in the tuning of transcripts for several stress response genes inE. coli. The i6A tRNA modification is catalyzed by the tRNA prenyl transferase encoded by themiaAgene. We set out to identify posttranscriptional regulators of the enzyme necessary for the catalysis of i6A, MiaA, to further understand factors influencing i6A levels in the cell. We identified the CsrA RNA Binding Protein, the CsrB Small RNA, and RNA Degradosome enzymes: RNaseE and PNPase as regulators ofmiaAexpressioin at the post-transcriptional level. Identifying these post-transcripitonal regulators ofmiaAwill help us understand factors influencing i6A levels and may guide future investigations into RNA modifications with regulatory effects on the transcriptome.
Accelerating Single-Cell Sequencing Data Analysis with SciDAP: A User-Friendly Approach
Authors: Kotliar Michael , Kartashov Andrey , Barski Artem 
Published: February 2024

AbstractSingle-cell (sc) RNA, ATAC and Multiome sequencing became powerful tools for uncovering biological and disease mechanisms. Unfortunately, manual analysis of sc data presents multiple challenges due to large data volumes and complexity of configuration parameters. This complexity, as well as not being able to reproduce a computational environment, affects the reproducibility of analysis results. The Scientific Data Analysis Platform (https://SciDAP.com) allows biologists without computational expertise to analyze sequencing-based data using portable and reproducible pipelines written in Common Workflow Language (CWL). Our suite of computational pipelines addresses the most common needs in scRNA-Seq, scATAC-Seq and scMultiome data analysis. When executed on SciDAP, it offers a user-friendly alternative to manual data processing, eliminating the need for coding expertise. In this protocol, we describe the use of SciDAP to analyze scMultiome data. Similar approaches can be used for analysis of scRNA-Seq, scATAC-Seq and scVDJ-Seq datasets.
Long COVID and kidney function: A scoping review protocol
Authors: Frediani Marcella M. , Ribeiro Heitor S. , Busatto Geraldo F. , Carvalho Carlos Roberto Ribeiro , Burdmann Emmanuel A. 
Published: February 2024

AbstractIntroductionThe coronavirus disease 2019 (COVID-19) pandemic had catastrophic repercussions worldwide, including short- and long-term effects on multiple organs. The term “long COVID” encompasses signs and symptoms associated with COVID that persist for more than two months. However, the effects of long COVID on kidney function remain poorly understood.ObjectiveThis scoping review aims to describe the effects of long COVID on kidney function and/or kidney-related outcomes.MethodsWe will follow the Joanna Briggs Institute methodology and Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews. Based on the PCC framework, we will include studies that investigated long COVID survivors (Participants); describing kidney function and/or kidney-related outcomes (Concept); in all settings and designs (Context). A comprehensive literature search was performed using the MEDLINE, Embase, and LILACS databases without date or language restrictions from inception until August 2023. Websites, books, and guidelines will also be searched. Observational studies with retrospective, prospective, and case-control designs will be considered. Two independent reviewers will screen titles and abstracts and perform the full-text review. Data extraction will be done by the main reviewer and checked by a second one. Data about the diagnosis of COVID, follow-up time for long symptoms, and kidney function assessment and outcomes will be extracted from selected evidence. The quantitative results will be synthesized and presented in tables and figures along with a narrative summary.Ethics and disseminationThere is no requirement for ethical approval for this scoping review. On completion, it will be published in a peer-reviewed academic journal and presented at a conference.
Characterisation of prophages inClostridium clostridioforme: an understudied component of the intestinal microbiome
Authors: Humphrey Suzanne , Marouli Angeliki , Thümmler Katja , Mullin Margaret , Wall Daniel M. 
Published: February 2024

AbstractGenome sequencing ofClostridium clostridioformestrain LM41 revealed the presence of an atypically high proportion of mobile genetic elements for this species, with a particularly high abundance of prophages. Bioinformatic analysis of prophage sequences sought to characterise these elements and identify prophage-linked genes contributing to enhanced fitness of the host bacteria in the dysbiotic gut. This work has identified 15 prophages, of which 4 are predicted to be intact, 2 are predicted to be defective, and 9 are unclassified. qPCR analysis revealed spontaneous release of four of the LM41 prophages into the culture supernatant, the majority of which had morphology akin to podoviruses when visualised using Transmission Electron Microscopy. We observed diversity in the lysogeny mechanisms utilised by the prophages, with examples of the classical λ-like CI/Cro system, the ICEBs1 ImmR/ImmA-like system, and the Mu-like C/Ner system. Classical morons, such as toxins or immune evasion factors, were not observed. We did, however, identify a variety of genes with roles in mediating restriction modification and genetic diversity, as well as some candidate genes with potential roles in host adaptation. Despite being the most abundant entities in the intestine, there is a dearth of information about phages associated with members of the microbiome. This work begins to shed light on the contribution of these elements to the lifestyle ofC. clostridioformeLM41.
Failure of the Baym-Kadanoff construction to consistently match quantum dynamics with thermodynamic critical behavior
Authors: Janiš Václav , Pokorný Vladislav , Kos Šimon 
Published: February 2024

We disclose a serious deficiency of the Baym-Kadanoff construction of thermodynamically consistent conserving approximations. There are two vertices in this scheme: dynamical and conserving. The divergence of each indicates a phase instability. We show that each leads to incomplete and qualitatively different behavior at different critical points. The diagrammatically controlled dynamical vertex from the Schwinger-Dyson equation does not obey the Ward identity and cannot be continued beyond its singularity. The standardly used dynamical vertex alone cannot, hence, conclusively decide about the stability of the high-temperature phase. On the other hand, the divergence in the conserving vertex, obeying the conservation laws, does not invoke critical behavior of the spectral function and the specific heat. Moreover, the critical behavior of the conserving vertex may become spurious in low-dimensional systems. Consequently, the description of the critical behavior of correlated electrons becomes consistent and reliable only if the fluctuations of the order parameter in the conserving vertex lead to a divergence coinciding with that of the dynamical one.

Published by the American Physical Society
2024
One-loop electroweak radiative corrections to polarized
e+e−→ZZ
process
Authors: Bondarenko S. , Dydyshka Ya. , Kalinovskaya L. , Sadykov R. , Yermolchyk V. 
Published: February 2024

In the paper we recalculate and discuss high-precision theoretical predictions for cross sections of the process e+e−→ZZ. We assume a complete one-loop implementation and a possibility of estimating the initial state polarizations, as well as the full-phase calculation. Numerical results are provided by our Monte Carlo tools integrator and generator for typical energies and degrees of polarization of ILC and CLIC projects in two α(0) and Gμ electroweak schemes.

Published by the American Physical Society
2024
Molecular-type
QQsss¯
pentaquarks predicted by an extended hidden gauge symmetry approach
Authors: Wang Zhong-Yu , Xiao Chu-Wen , Sun Zhi-Feng , Liu Xiang 
Published: February 2024

In this work, we investigate the double-heavy molecular pentaquark states with the quark contents ccsss¯, bbsss¯, and bcsss¯ by using the coupled channel approach. The extended local hidden gauge Lagrangians are used to obtain the meson-baryon interactions by exchanging the vector mesons. We predict some candidates for the molecular states with the quantum numbers I(JP)=0(1/2−,3/2−,5/2−), whose binding energies are of the order of 20–30 MeV and whose widths are all less than 8 MeV. These predicted exotic double-heavy molecular pentaquark states may be accessible in future experiments such as LHCb.

Published by the American Physical Society
2024