bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanical coupling coordinates microtubule growth
Authors: Leeds Bonnibelle K. , Kostello Katelyn F. , Liu Yuna Y. , Nelson Christian R. , Biggins Sue , Asbury Charles L.
Published: July 2023

During mitosis, kinetochore-attached microtubules form bundles (k-fibers) in which many filaments grow and shorten in near-perfect unison to align and segregate each chromosome. However, individual microtubules grow at intrinsically variable rates, which must be tightly regulated for a k-fiber to behave as a single unit. This exquisite coordination might be achieved biochemically, via selective binding of polymerases and depolymerases, or mechanically, because k-fiber microtubules are coupled through a shared load that influences their growth. Here, we use a novel dual laser trap assay to show that microtubule pairs growingin vitroare coordinated by mechanical coupling. Kinetic analyses show that microtubule growth is interrupted by stochastic, force-dependent pauses and indicate persistent heterogeneity in growth speed during non-pauses. A simple model incorporating both force-dependent pausing and persistent growth speed heterogeneity explains the measured coordination of microtubule pairs without any free fit parameters. Our findings illustrate how microtubule growth may be synchronized during mitosis and provide a basis for modeling k-fiber bundles with three or more microtubules, as found in many eukaryotes.
Transcription factor Nrf1 regulates proteotoxic stress-induced autophagy
Authors: Kaya Hatem Elif Kamber , Ward Madison A. , Vangala Janakiram R. , Byers Holly A. , Diaz Antonio , Kaushik Susmita , Cuervo Ana Maria , Radhakrishnan Senthil K.
Published: July 2023

Cells exposed to proteotoxic stress invoke adaptive responses aimed at restoring proteostasis. Our previous studies have established a firm role for the transcription factor Nuclear factor erythroid derived 2-related factor 1 (Nrf1, also called NFE2L1) in responding to proteotoxic stress elicited by inhibition of cellular proteasome. Following proteasome inhibition, Nrf1 mediates new proteasome synthesis, thus enabling the cells to mitigate the proteotoxic stress. Here we report that under similar circumstances, multiple components of the autophagy lysosomal pathway (ALP) are transcriptionally upregulated in an Nrf1-dependent fashion, thus providing the cells with an additional route to cope with proteasome insufficiency. In response to proteasome inhibitors, Nrf1-deficient cells displayed profound defects in invoking autophagy and clearance of aggresomes. This phenomenon was also recapitulated in NGLY1 knockout cells (a model for NGLY1 disease) where Nrf1 is known to be non-functional. Overall, our results significantly expand the role of Nrf1 in shaping the cellular response to proteotoxic stress.
Retrovirus-derivedRTL9plays an important role in innate antifungal immunity in the eutherian brain
Authors: Ishino Fumitoshi , Itoh Johbu , Irie Masahito , Matsuzawa Ayumi , Naruse Mie , Suzuki Toru , Hiraoka Yuichi , Kaneko-Ishino Tomoko
Published: July 2023

Retrotransposon Gag-like (RTL) genes plays a variety of essential/important roles in the eutherian placenta and brain. It has recently been demonstrated thatRTL5andRTL6(akasushi-ichi retrotransposon homolog 8(SIRH8) andSIRH3) are microglial genes that play important roles in the brain’s innate immunity against viruses and bacteria by their removal of double-stranded RNA and lipopolysaccharide, respectively. Here we demonstrate thatRTL9(akaSIRH10) also plays an important role, degrading fungal zymosan in the brain. The RTL9 protein is localized in the microglial lysosomes where incorporated zymosan is digested. Interestingly, inRtl9knockout mice expressing RTL9ΔC protein lacking the C-terminus retroviral GAG-like region, the zymosan degrading activity was lost, demonstrating that RTL9 is essentially engaged in this reaction, presumably via its GAG-like region. Together with our previous study, this result highlights the importance of three retrovirus-derived microglial RTL genes as eutherian-specific constituents of the current brain innate immune system,RTL9,RTL5andRTL6responding to fungi, viruses and bacteria, respectively.

Author Summary

We have recently demonstrated thatRTL5andRTL6are microglial genes that play important roles in the brain’s innate immunity against viruses and bacteria. In this report, we demonstrate thatRTL9is functional in innate antifungal immunity in the brain becauseRtl9KO mice lose zymosan degradation activity. Fungi are one of the most dangerous infectious pathogens, along with viruses, bacteria and protozoa. Phagocytic cells, such as microglia/macrophages, are essential for mounting a defense against fungal infection. As defects in these cells reduce host resistance to fungal infection,RTL9is an antifungal therapy target as a newly identified member of innate antifungal immunity in eutherians.
Spatially resolved transcriptomic profiling for glomerular and tubulointerstitial gene expression in C3 glomerulopathy
Authors: Koh Jung Hun , Kang Minji , Park Sehoon , Cho Jeong Min , Cho Semin , Kim Yaerim , Lee Soojin , Lee Hajeong , Joo Kwon-Wook , Kim Yon Su , Moon Kyung Chul , Kim Hyun Je , Kim Dong Ki
Published: July 2023

Introduction

C3 glomerulopathy (C3G) is a rare but clinically significant glomerulopathy. However, little is known about its transcriptomic profile. We investigated the substructure-specific gene expression profile of C3G using the recently introduced spatial transcriptomics technology.

Methods

We performed spatial transcriptomic profiling using GeoMx Digital Spatial Profiler with formalin-fixed paraffin-embedded kidney biopsy specimens of three C3G cases and seven controls from donor kidney biopsy. Additionally, 41 samples of other glomerulonephritis, including focal segmental glomerulosclerosis, membranous nephropathy, and minimal change disease, were included as disease controls. Gene expression levels were compared by DESeq2 method to identify differentially expressed genes (DEGs). We performed gene ontology (GO) annotation through the ToppGene suite and mapped interactions among the DEGs using the STRING database.

Results

We identified 229 and 157 highly expressed DEGs in the glomeruli of C3G compared to those of donor and disease controls, respectively, with consistently highest fold changes in POSTN, COL1A2, and IFI44L. Protease binding, structural molecule activity, and extracellular matrix structural constituent were among the top enriched GO terms in the glomeruli of C3G, with consistent features seen in the network analysis. In contrast, no significant GO enrichment was found among the 563 and 347 lowly expressed DEGs in the glomeruli of C3G compared to the controls. The tubulointerstitial transcriptomic profiles of C3G were similar to those of the controls.

Conclusion

In the glomerulus of C3G, genes related to the extracellular matrix and interferon activity were the most upregulated. Significant disease-specific transcriptomic alterations in C3G provide potential insights into the pathophysiology.
BOston Neonatal Brain Injury Dataset for Hypoxic Ischemic Encephalopathy (BONBID-HIE): Part I. MRI and Manual Lesion Annotation
Authors: Bao Rina , Song Ya’nan , Bates Sara V. , Weiss Rebecca J. , Foster Anna N. , Cobos Camilo Jaimes , Sotardi Susan , Zhang Yue , Gollub Randy L. , Grant P. Ellen , Ou Yangming
Published: July 2023

Hypoxic ischemic encephalopathy (HIE) is a brain injury that occurs in 1 ∼5/1000 term neonates. Accurate identification and segmentation of HIE-related lesions in neonatal brain magnetic resonance images (MRIs) is the first step toward predicting prognosis, identifying high-risk patients, and evaluating treatment effects. It will lead to a more accurate estimation of prognosis, a better understanding of neurological symptoms, and a timely prediction of response to therapy. We release the first public dataset containing neonatal brain diffusion MRI and expert annotation of lesions from 133 patients diagnosed with HIE. HIE-related lesions in brain MRI are often diffuse (i.e., multi-focal), and small (over half the patients in our data having lesions occupying <1% of brain volume). Segmentation for HIE MRI data is remarkably different from, and arguably more challenging than, other segmentation tasks such as brain tumors with focal and relatively large lesions. We hope that this dataset can help fuel the development of MRI lesion segmentation methods for HIE and small diffuse lesions in general.
A globally synthesised and flagged bee occurrence dataset and cleaning workflow
Authors: Dorey James B. , Fischer Erica E. , Chesshire Paige R. , Nava-Bolaños Angela , O’Reilly Robert L. , Bossert Silas , Collins Shannon M. , Lichtenberg Elinor M. , Tucker Erika M. , Smith-Pardo Allan , Falcon-Brindis Armando , Guevara Diego A. , Ribeiro Bruno , de Pedro Diego , Pickering John , Hung Keng-Lou James , Parys Katherine A. , McCabe Lindsie M. , Rogan Matthew S. , Minckley Robert L. , Velazco Santiago J.E. , Griswold Terry , Zarrillo Tracy A. , Jetz Walter , Sica Yanina V. , Orr Michael C. , Guzman Laura Melissa , Ascher John S. , Hughes Alice C. , Cobb Neil S.
Published: July 2023

Species occurrence data are foundational for research, conservation, and science communication, but the limited availability and accessibility of reliable data represents a major obstacle, particularly for insects, which face mounting pressures. We presentBeeBDC, a newRpackage, and a global bee occurrence dataset to address this issue. We combined >18.3 million bee occurrence records from multiple public repositories (GBIF, SCAN, iDigBio, USGS, ALA) and smaller datasets, then standardised, flagged, deduplicated, and cleaned the data using the reproducibleBeeBDC R-workflow. Specifically, we harmonised species names (following established global taxonomy), country names, and collection dates and we added record-level flags for a series of potential quality issues. These data are provided in two formats, “cleaned” and “flagged-but-uncleaned”. TheBeeBDCpackage with online documentation provides end users the ability to modify filtering parameters to address their research questions. By publishing reproducibleRworkflows and globally cleaned datasets, we can increase the accessibility and reliability of downstream analyses. This workflow can be implemented for other taxa to support research and conservation.
Morphological variability may limit single-cell specificity to electric field stimulation
Authors: Trotter Daniel , Pariz Aref , Hutt Axel , Lefebvre Jérémie
Published: July 2023

Non-invasive brain stimulation techniques are widely used for manipulating the behaviour of neuronal circuits and the excitability of the neurons therein. While the usage of these techniques is widely studied at the meso- and macroscopic scales, less is known about the specificity of such approaches at the level of individual cells. Here we use models based on the morphologies of real pyramidal and parvalbumin neurons from mouse primary visual cortex created by the Allen Institute for Brain Science to explore the variability and evoked response susceptibility of different morphologies to uniform electric fields. We devised a range of metrics quantifying various aspects of cellular morphology, ranging from whole cell attributes to net compartment length, branching, diameter to orientation. In supporting layer- and cell-type specific responses, none of these physical traits passed statistical significance tests. While electric fields can modulate somatic, dendritic and axonal compartments reliably and subtype-specific responses could be observed, the specificity of such stimuli was blurred by the variability in cellular morphology. These null results suggest that morphology alone may not account for the reported subtype specificity of brain stimulation paradigms, and question the extent to which such techniques may be used to probe and control neural circuitry.

Author summary

Over the last several decades there has been increased interest in the efficacy of non-invasive brain stimulation, particularly in determining the limits of specificity of such techniques. Despite this growing area of research, much remains unknown about the interactions of non-invasive techniques with neurons at the single-cell level, notably the importance of morphology to these interactions. We make use of detailed single-neuron models and simulate them in a uniform electric field and demonstrate that the high variability in neuron morphologies may limit how specifically single neurons can be targeted non-invasively. We confirmed this for neuron morphology characteristics at macro- and meso- scales and at varied orientations. Our work suggests that previously reported subtype specificities in non-invasive frameworks are not accounted for by considering only morphological factors.
Unbiased phosphoproteomics analysis unveils modulation of insulin signaling by extramitotic CDK1 kinase activity in human myotubes
Authors: Han Bitnara , Li Ginny X. , Liew Wei Lin , Chan Edmund , Huang Shiqi , Khoo Chin Meng , Leow Melvin Khee-Shing , Lee Yung Seng , Zhao Tianyun , Wang Loo Chien , Sobota Radoslaw , Choi Hyungwon , Liu Mei Hui , Kim Kwang Pyo , Tai E Shyong
Published: July 2023

Sensitivity and plasticity of insulin signaling and glucose uptake in skeletal muscle depends on determinants such as genetic variation and obesity. We collected muscle biopsies and isolated myoblasts from a multi-ethnic cohort of lean South Asians (N=10), lean Chinese (N=10), and obese Chinese (N=10), and analysed the proteome and phosphoproteome dynamics in terminally differentiated myotubes after a low-dose insulin stimulation (10nM at 0, 5, 30 min). The myotubes initially responded with increased abundance and phosphorylation level changes along the PI3K/AKT/mTOR axis, decreased abundance of translation initiation factors, and increased phosphorylation levels on proteins involved in mRNA processing at 5 min. After the acute response, protein abundance returned to baseline at 30 min, while phosphorylation changes persisted in proteins including AKT, RPS6 and AS160 (TBC1D4). A joint kinase-substrate statistical analysis revealed that protein abundance changes of AKT, PAK1 and CDK1 showed concordant phosphorylation changes in their respective substrates upon insulin stimulation. We also observed increased phosphorylation of some substrates uniquely in each group, particularly the substrates of CDKs showing stronger changes in South Asians than in Chinese. Pharmacological inhibition and siRNA knockdown of CDK1, a non-myogenic kinase, in terminally differentiated myotubes reduced glucose uptake and desensitized several phosphorylation-mediated signaling on protein translation initiation factors, IRS1, and AS160. Our data suggest that basal extramitotic activity of CDK1 is required for PI3K/AKT/mTORC1 signaling cascade and glucose uptake in insulin-stimulated myotubes. The data also provide a rich resource for studying the role of other kinases in the mechanism of insulin resistance in human myotubes.
Intra-Articular Sprouting Of Nociceptors Accompanies Progressive Osteoarthritis: Comparative Evidence In Four Murine Models
Authors: Obeidat Alia M. , Ishihara Shingo , Li Jun , Lammlin Lindsey , Junginger Lucas , Maerz Tristan , Miller Richard J. , Miller Rachel E. , Malfait Anne-Marie
Published: July 2023

Objective

Knee joints are densely innervated by nociceptors. Sprouting of nociceptors has been reported in late-stage osteoarthritis (OA), both in human knees and in rodent models. Here, we sought to describe progressive nociceptor remodeling in four mouse models of knee OA, capturing early and late-stage disease.

Methods

Sham surgery, destabilization of the medial meniscus (DMM), partial meniscectomy (PMX), or non-invasive anterior cruciate ligament rupture (ACLR) was performed in the right knee of 10-12-week old male C57BL/6 NaV1.8-tdTomato mice. Mice were euthanized (1) 4, 8 or 16 weeks after DMM or sham surgery; (2) 4 or 12 weeks after PMX or sham; (3) 1 or 4 weeks after ACLR injury or sham. Additionally, a cohort of naïve male wildtype mice was evaluated at 6 and 24 months. Twenty-μm thick mid-joint cryosections were assessed qualitatively and quantitatively for NaV1.8+ and PGP9.5+ innervation. Cartilage damage (using a modified OARSI score), synovitis, and osteophytes were assessed blindly.

Results

Progressive OA developed in the medial compartment after DMM, PMX, and ACLR. Synovitis and associated neo-innervation by nociceptors peaked in early-stage OA. In the subchondral bone, channels containing sprouting nociceptors appeared early, and progressed with worsening joint damage. Two-year old mice developed primary OA in both the medial and the lateral compartment, accompanied with neuroplasticity in the synovium and the subchondral bone. All 4 models had an increased nerve signal in osteophytes.

Conclusion

Anatomical neuroplasticity of nociceptors was observed in association with joint damage in 4 distinct mouse models, suggesting that it is intrinsic to OA pathology.
Free energy surface and molecular characterization of slow structural transitions in lipid bilayers
Authors: Punia Rajat , Goel Gaurav
Published: July 2023

The need to incorporate specific molecular-scale features for largescale structural changes in biological membranes necessitate use of a multi-scale computational approach. Here, this comprises of Langevin dynamics in a normal mode space determined from an elastic network model (ENM) representation for lipid-water Hamiltonian. All atom (AA) MD simulations are used to determine model parameters, and Langevin dynamics predictions for an extensive set of bilayer properties, such as, undulation spectra, undulation relaxation rates, dynamic structure factor, and mechanical properties are validated against the data from MD simulations and experiments. The transferability of model parameters to describe dynamics of a larger lipid bilayer and a heterogeneous membrane-protein system is assessed. The developed model is coupled to the energy landscape for membrane deformations to obtain a set of generic reaction coordinates (RCs) for pore formation in two tensionless, single lipid-type bilayers, namely, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). Structure evolution is carried in an AA MD simulation wherein the generic RCs are used in a path metadynamics or an umbrella sampling simulation to investigate thermodynamics of pore formation and its molecular determinants. The transition state is characterized extensively to bring out the interplay between various bilayer motions (undulations, lateral density fluctuations, thinning, lipid tilt), lipid solvation, and lipid packing.
FADS1/2-mediated lipid metabolic reprogramming drives ferroptosis sensitivity in triple-negative breast cancer
Authors: Lorito Nicla , Subbiani Angela , Smiriglia Alfredo , Bacci Marina , Bonechi Francesca , Tronci Laura , Corrado Alessia , Longo Dario Livio , Iozzo Marta , Ippolito Luigi , Comito Giuseppina , Giannoni Elisa , Meattini Icro , Avgustinova Alexandra , Chiarugi Paola , Bachi Angela , Morandi Andrea
Published: July 2023

Triple-negative breast cancer (TNBC) has limited therapeutic options, is highly metastatic and characterized by early recurrence. Lipid metabolism is generally deregulated in TNBC and might reveal vulnerabilities to be targeted or used as biomarkers with clinical value.

Ferroptosis is a type of cell death caused by iron-dependent lipid peroxidation which is facilitated by the presence of polyunsaturated fatty acids (PUFA).

Here we identify fatty acid desaturases 1 and 2 (FADS1/2), which are responsible for PUFA biosynthesis, lipid susceptible to peroxidation, to be highly expressed in a subset of TNBC with a poorer prognosis. Lipidomic analysis, coupled with functional metabolic assays, showed that FADS1/2 high-expressing TNBC are susceptible to ferroptosis-inducing agents and that targeting FADS1/2 renders those tumors ferroptosis-resistant. These findings were validatedin vitroandin vivoin mouse and human-derived clinically relevant models and in a retrospective cohort of TNBC patients.

One sentence summary

The availability of intracellular PUFA depends on FADS1/2 desaturases, expressed at higher levels in aggressive triple-negative breast cancers highly susceptible to ferroptosis.
Differentiation of hypervirulent and classicalKlebsiella pneumoniaewith acquired drug resistance
Authors: Russo Thomas A. , Alvarado Cassandra L. , Davies Connor J. , Drayer Zachary J. , Carlino-MacDonald Ulrike , Hutson Alan , Luo Ting L. , Martin Melissa J. , Corey Brendan W. , Moser Kara A. , Rasheed J. Kamile , Halpin Alison L. , McGann Patrick T. , Lebreton Francois
Published: July 2023

Distinguishing hypervirulent (hvKp) from classicalKlebsiella pneumoniae(cKp) strains is important for clinical care, surveillance, and research. Some combination ofiucA, iroB, peg-344, rmpA,andrmpA2are most commonly used, but it is unclear what combination of genotypic or phenotypic markers (e.g. siderophore concentration, mucoviscosity) most accurately predicts the hypervirulent phenotype. Further, acquisition of antimicrobial resistance may affect virulence and confound identification. Therefore, 49K. pneumoniaestrains that possessed some combination ofiucA, iroB, peg-344, rmpA,andrmpA2and had acquired resistance were assembled and categorized as hypervirulent hvKp (hvKp) (N=16) or cKp (N=33) via a murine infection model. Biomarker number, siderophore production, mucoviscosity, virulence plasmid’s Mash/Jaccard distances to the canonical pLVPK, and Kleborate virulence score were measured and evaluated to accurately differentiate these pathotypes. Both stepwise logistic regression and a CART model were used to determine which variable was most predictive of the strain cohorts. The biomarker count alone was the strongest predictor for both analyses. For logistic regression the area under the curve for biomarker count was 0.962 (P = 0.004). The CART model generated the classification rule that a biomarker count = 5 would classify the strain as hvKP, resulting in a sensitivity for predicting hvKP of 94% (15/16), a specificity of 94% (31/33), and an overall accuracy of 94% (46/49). Although a count of ≥ 4 was 100% (16/16) sensitive for predicting hvKP, the specificity and accuracy decreased to 76% (25/33) and 84% (41/49) respectively. These findings can be used to inform the identification of hvKp.

Importance

HypervirulentKlebsiella pneumoniae(hvKp) is a concerning pathogen that can cause life-threatening infections in otherwise healthy individuals. Importantly, although strains of hvKp have been acquiring antimicrobial resistance, the effect on virulence is unclear. Therefore, it is of critical importance to determine whether a given antimicrobial resistantK. pneumoniaeisolate is hypervirulent. This report determined which combination of genotypic and phenotypic markers could most accurately identify hvKp strains with acquired resistance. Both logistic regression and a machine-learning prediction model demonstrated that biomarker count alone was the strongest predictor. The presence of all 5 of the biomarkersiucA, iroB, peg-344, rmpA,andrmpA2was most accurate (94%); the presence of ≥ 4 of these biomarkers was most sensitive (100%). Accurately identifying hvKp is vital for surveillance and research, and the availability of biomarker data could alert the clinician that hvKp is a consideration, which in turn would assist in optimizing patient care.
Direction-Specific Effects of Artificial Skin-Stretch on Stiffness Perception and Grip Force Control
Authors: Farajian Mor , Leib Raz , Kossowsky Hanna , Nisky Ilana
Published: July 2023

When interacting with an object, we use kinesthetic and tactile information to create our perception of the object’s properties and to prevent its slippage using grip force control. We previously showed that applying artificial skin-stretch together with, and in the same direction as, kinesthetic force increases the perceived stiffness. Here, we investigated the effect of the direction of the artificial stretch on stiffness perception and grip force control. We presented participants with kinesthetic force together with negative or positive artificial stretch, in the opposite or the same direction of the natural stretch due to the kinesthetic force, respectively. Our results showed that artificial skin-stretch in both directions augmented the perceived stiffness; however, the augmentation caused by the negative stretch was consistently lower than that caused by the positive stretch. Additionally, we proposed a computational model that predicts the perceptual effects based on the preferred directions of the stimulated mechanoreceptors. When examining the grip force, we found that participants applied higher grip forces during the interactions with positive skin-stretch in comparison to the negative skin-stretch, which is consistent with the perceptual results. These results may be useful in tactile technologies for wearable haptic devices, teleoperation, and robot-assisted surgery.
A Cardiac Transcriptional Enhancer is Repurposed During Regeneration to Activate an Anti-proliferative Program
Authors: Rao Anupama , Russell Andrew , Segura-Bermudez Jose , Franz Charles , Dockery Rejenae , Blatnik Anton , Panten Jacob , Zevallos Mateo , McNulty Carson , Pietrzak Maciej , Goldman Joseph Aaron
Published: July 2023

Zebrafish have a high capacity to regenerate their hearts. Several studies have surveyed transcriptional enhancers to understand how gene expression is controlled during heart regeneration. We have identifiedRENor therunx1enhancer that during regeneration regulates the expression of the nearbyrunx1gene. We show thatrunx1mRNA is reduced with deletion ofREN(ΔREN)and cardiomyocyte proliferation is enhanced in both ΔRENand Δrunx1mutants only during regeneration. Interestingly, in uninjured hearts, ΔRENmutants have reduced expression ofadamts1, a nearby gene that encodes a Collagen protease. This results in excess Collagen within cardiac valves of uninjured hearts. The ΔRENCollagen phenotype is rescued even by Δrunx1mutations, suggesting that in uninjured heartsRENregulatesadamts1independently ofrunx1. Taken together, this suggests thatRENis rewired fromadamts1in uninjured hearts to stimulaterunx1transcription during regeneration. Our data point to a previously unappreciated mechanism for gene regulation during zebrafish heart regeneration. We report that an enhancer is rewired from expression in a distal cardiac domain to activate a different gene in regenerating tissue.
Preferential transport of synaptic vesicles across neuronal branches is regulated by the levels of the anterograde motor UNC-104/KIF1A
Authors: Vasudevan Amruta , Ratnakaran Neena , Murthy Kausalya , Ahlawat Shikha , Koushika Sandhya P.
Published: July 2023

Asymmetric transport of cargo across axonal branches is a field of active research. Mechanisms contributing to preferential cargo transport along specific branchesin vivoin wild type neurons are poorly understood. We find that anterograde synaptic vesicles preferentially enter the synaptic branch or pause at the branch point inC. elegansPLM neurons. The anterograde motor UNC-104/KIF1A regulates this vesicle behaviour at the branch point. Reduced levels of functional UNC-104 cause vesicles to predominantly pause at the branch point and lose their preference for turning into the synaptic branch. SAM- 4/Myrlysin, which aids in recruitment/activation of UNC-104 on synaptic vesicles, regulates vesicle behaviour at the branch point similar to UNC-104. Increasing the levels of UNC-104 increases the preference of vesicles to go straight towards the asynaptic end. This suggests that the neuron optimises UNC-104 levels on the cargo surface to maximise the fraction of vesicles entering the branch and minimise the fraction going to the asynaptic end.
Topology-dependent DNA binding
Authors: Kolbeck Pauline J. , Tišma Miloš , Analikwu Brian T. , Vanderlinden Willem , Dekker Cees , Lipfert Jan
Published: July 2023

DNA stores our genetic information and is ubiquitous in biological and biotechnological applications, where it interacts with binding partners ranging from small molecules to large macromolecular complexes. Binding is modulated by mechanical strains in the molecule and, in turn, can change the local DNA structure. Frequently, DNA occurs in closed topological forms where topology and supercoiling add a global constraint to the interplay of binding-induced deformations and strain-modulated binding. Here, we present a quantitative model of how the global constraints introduced by DNA topology modulate binding and create a complex interplay between topology and affinity. We focus on fluorescent intercalators, which unwind DNA and enable direct quantification via fluorescence detection. Using bulk measurements, we show that DNA supercoiling can increase or decrease intercalation relative to an open topology depending on ligand concentration and the initial topology. Our model quantitatively accounts for observations obtained using psoralen for UV-induced DNA crosslinking, which is frequently used to quantify supercoilingin vivo. Finally, we observe topology-dependent binding in a single-molecule assay, which provides direct access to binding kinetics and DNA supercoil dynamics. Our results have broad implications for the detection and quantification of DNA and for the modulation of DNA binding in cellular contexts.
The leptin receptor has no role in delta-cell control of beta-cell function in the mouse
Authors: Zhang Jia , Katada Kay , Mosleh Elham , Yuhas Andrew , Peng Guihong , Golson Maria L.
Published: July 2023

Leptin inhibits insulin secretion from isolated islets from multiple species, but the cell type that mediates this process remains elusive. Mouse models have been used to explore this question. Ablation of the leptin receptor (Lepr) throughout the pancreatic epithelium results in altered glucose homeostasis, ex vivo insulin secretion, and calcium dynamics. However, the removal of Lepr from neither alpha nor beta cells mimics these results. Because Lepr is enriched in the delta cells of human islets, we used a mouse model to test whether delta cells mediate the diminished glucose-stimulated insulin secretion in response to leptin. However, ablation of Lepr within mouse delta cells had no impact on glucose homeostasis or insulin secretion. We further demonstrate that Lepr is not appreciably expressed within mouse delta cells.
Robustness of biomolecular networks suggests functional modules far from the edge of chaos
Authors: Park Kyu Hyong , Costa Felipe Xavier , Rocha Luis M , Albert Réka , Rozum Jordan C
Published: July 2023

A common feature of complex systems is their ability to balance the flexibility needed to adapt to their environment with the rigidity required for robust function. It has been conjectured that living systems accomplish this by existing at the “edge of chaos”, i.e., the critical boundary between ordered and disordered dynamics. Simple toy models of gene regulatory networks lend support to this idea, and mathematical tools developed for these toy models yield similar results when applied to experimentally-supported models of specific cellular regulatory mechanisms (functional modules). Here, however, we demonstrate that a deeper inspection of 72 experimentally-supported discrete dynamical models of functional modules reveals previously unobserved order in these systems on long time scales, suggesting greater rigidity in these systems than was previously conjectured. Our analysis relies on new measures that quantify the tendency of perturbations to spread through a discrete dynamical system. A benefit of our new approach is that it accounts for how system trajectories are mapped to phenotypes in practice. Because these measures are computationally expensive to estimate, existing tools were insufficient for the ensemble of models considered here. To simulate the tens of millions of trajectories required for convergence, we developed a multipurpose CUDA-based simulation tool, which we have made available as the open-source Python library cubewalkers. We find that in experimentally-supported models of biomolecular functional modules, perturbation propagation is more transitory than previously thought, and that even in cases where large perturbation cascades persist, their phenotypic effects are often minimal. Moreover, by examining the impact of update scheme on experimentally-supported models, we find evidence that stochasticity and desynchronization can lead to increased recovery from regulatory perturbation cascades in functional modules and uncover previously unreported population-level robustness to even timing perturbations in these systems. We identify specific biological mechanisms underlying these dynamical behaviors and highlight them in experimentally-supported regulatory networks from the systems biology literature. Based on novel measures and simulations, our results suggest that–contrary to current theory–functional modules of biological systems are ordered and far from the edge of chaos.
Reverse engineering of a pathogenic antibody reveals the molecular mechanism of vaccine-induced immune thrombotic thrombocytopenia
Authors: Ivanov Daniil G. , Ivetic Nikola , Du Yi , Nguyen Son N. , Le S. Hung , Favre Daniel , Nazy Ishac , Kaltashov Igor A.
Published: July 2023

The massive COVID-19 vaccine roll-out campaign illuminated a range of rare side effects, the most dangerous of which – vaccine-induced immune thrombotic thrombocytopenia (VITT) – is caused by adenoviral (Ad)-vectored vaccines. VITT occurrence had been linked to production of pathogenic antibodies that recognize an endogenous chemokine, platelet factor 4 (PF4). Mass spectrometry (MS)-based evaluation of the ensemble of anti-PF4 antibodies obtained from a VITT patient’s blood indicates that its major component is a monoclonal antibody. Structural characterization of this antibody reveals several unusual characteristics, such as the presence of anN-glycan in the Fab segment and high density of acidic amino acid residues in the CDR regions. A recombinant version of this antibody (RVT1) was generated by transient expression in mammalian cells based on the newly determined sequence. It captures the key properties of VITT antibodies, such as their ability to activate platelets in a PF4-dependent fashion. Homology modeling of the Fab segment reveals a well-defined polyanionic paratope, and the docking studies indicate that the polycationic segment of PF4 readily accommodates two Fab segments, cross-linking the antibodies to yield polymerized immune complexes. Their existence was verified with native MS by detecting assemblies as large as (RVT1)3(PF4)2, pointing out at FcγRIIa-mediated platelet activation as the molecular mechanism underlying VITT clinical manifestations. In addition to high PF4 affinity, RVT1 readily binds other polycationic targets, indicating a polyreactive nature of this antibody. This surprising polyspecificity not only sheds light on VITT etiology, but also opens up a range of opportunities to manage this pathology.

Significance Statement

Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a dangerous side effect of adenoviral-vectored vaccines that is linked to the emergence of autoantibodies recognizing platelet factor 4 (PF4). We have engineered a recombinant VITT antibody by sequencing a VITT patient-derived anti-PF4 monoclonal antibody that causes platelet activation and triggers thrombosis. This antibody was used to characterize architecture of the pathogenic immune complexes with a combination of biophysical and computational approaches, revealing the molecular mechanism of VITT. The results of this work demonstrate the critical role of electrostatics in PF4 recognition by the pathogenic antibody and the polyspecificity of the latter. Availability of the engineered VITT antibody will be invaluable for future studies aiming at understanding the general mechanistic features of autoimmune pathologies.
Inclusion Criteria for Extracorporeal Membrane Oxygenation (ECMO) in Patients with Acute Respiratory Distress Syndrome (ARDS) Due to COVID-19: A Systematic Review
Authors: Triantafyllaki Panagiota , Charalampopoulos Marios , Sampani Christina-Athanasia , Triantafyllou Christos , Papageorgiou Dimitrios
Published: July 2023

Introduction

At the end of 2019, in the city of Wuhan, China, a virus of the family of coronaviruses first appeared, mainly affecting the respiratory system, which was called SARS-COV-2 and causes COVID-19. Although in most patients, it occurs with mild symptomatology, however, a significant percentage (15-30%) will develop acute respiratory distress syndrome (ARDS) with increased chances of intubation and mechanical ventilation. In special cases of severe disease, where the oxygenation of the patient is not improved by the use of the ventilator, extracorporeal membrane oxygenation (ECMO) can be applied, a technique that has been used in previous pandemics that affected the respiratory system.

Aim

To investigate the evidence of the appliance of the ECMO, based on international literature, of the extracorporeal membrane oxygenator in patients with severe respiratory failure due to Covid-19 disease.

Method

Articles were searched on the international bases of scientific studies PubMed, Cochrane Library, and Google Scholar. This review was carried out using meta-analysis and international guidelines.

Results

Four articles were included where there was an agreement on the basic characteristics of patients, which can be considered as selection criteria. The primary criteria indicate the age, where the patient must be under 65 years old, and the body mass index (BMI) should be below 40. In addition, it is very important that there is no serious underlying pathology such as multi-organ failure syndrome. Also, the mechanical ventilation should not exceed seven (7) days until the placement of the ECMO, while all the other therapeutic methods, such as the prone position, neuromuscular blockers, and the appropriate positive end-expiratory pressure of the airways (Positive end-expiratory pressure - PEEP) should be already applied.

Conclusions

The application of ECMO is widely used as a treatment for patients with severe COVID-19 disease. However, in order to have the best therapeutic results while reducing hospitalization costs, it is necessary to follow the guidelines regarding the selection of patients who will benefit substantially.
Assessing Radiotherapy Responses in Low-Risk Prostate Cancer: A Longitudinal Analysis of T2 Relaxation Times
Authors: Hanzlikova Pavla , Vilimek Dominik , Vilimkova Kahankova Radana , Ladrova Martina , Skopelidou Valeria , Ruzickova Zuzana , Martinek Radek , Cvek Jakub
Published: July 2023

Rationale and Objectives

To evaluate short and long-term changes inT2relaxation as a response to radiotherapy in patients with low and intermediate risk localized prostate cancer.

Materials and Methods

A total of 24 patients were selected for this retrospective study. Each participant underwent 1.5T magnetic resonance imaging on seven separate occasions: initially after the implantation of gold fiducials, the required step for Cyberknife therapy guidance, followed by MRI scans two weeks post-therapy and monthly thereafter. As part of each MRI scan, the prostate region was manually delineated, and theT2relaxation times were calculated for quantitative analysis. TheT2relaxation times between individual follow-ups were analyzed using Repeated Measures Analysis of Variance.

Results

Repeated Measures Analysis of Variance (RM-ANOVA) revealed a significant difference across all measurements (F (6, 120) = 0.611, p<<0.001). A Bonferroni post hoc test revealed significant differences in medianT2values between the baseline and subsequent measurements, particularly between pre-therapy (M0) and two weeks post-therapy (M1), as well as during the monthly interval checks (M2-M6). Some cases showed a delayed decrease in relaxation times, indicating the prolonged effects of therapy.

Conclusion

The changes inT2values during the course of radiotherapy can help in monitoring radiotherapy response in unconfirmed patients, quantifying the scarring process, and recognizing the therapy failure.
A quantitative systems pharmacology workflow towards optimal design and biomarker stratification of atopic dermatitis clinical trials
Authors: Go Natacha , Arsène Simon , Faddeenkov Igor , Galland Théo , Martis B. Shiny , Lefaudeux Diane , Wang Yishu , Etheve Loic , Jacob Evgueni , Monteiro Claudio , Bosley Jim , Sansone Caterina , Pasquali Christian , Lehr Lorenz , Kulesza Alexander
Published: July 2023

Background

The development of atopic dermatitis (AD) drugs is confronted by many disease phenotypes and trial design options, which are hard to explore experimentally.

Objective

Optimize AD trial design using simulations.

Methods

We constructed a quantitative systems pharmacology (QSP) model of AD and standard of care (SoC) treatments and generated a phenotypically diverse virtual population whose parameter distribution is derived from known relationships between AD biomarkers and disease severity and b) calibrated using disease severity evolution under SoC regimens.

Results

We applied this workflow to the immunomodulator OM-85, currently being investigated for its potential use in AD, and calibrated investigational treatment model with the efficacy profile of an existing trial (thereby enriching it with plausible marker levels and dynamics). We assessed the sensitivity of trial outcomes to trial protocol and found that for this particular example, a) the choice of endpoint is more important than the choice of dosing-regimen and b) patient selection by model-based responder enrichment could increase the expected effect size. A global sensitivity analysis reveals that only a limited subset of baseline biomarkers is needed to predict the drug response of the full virtual population

Conclusion

This AD QSP workflow built around knowledge of marker-severity relationships as well as SoC efficacy can be tailored to specific development cases so as to optimize several trial protocol parameters and biomarker-stratificaiton and therefore holds promise to become a powerful model-informed drug development tool.

Key Messages

Disease and treatment models can quantify pre-existing knowledge about complex immune diseases such as atopic dermatitis and drug’s efficacy data under one common umbrella.

Embedding QSP models into trial simulation setup can give insight into clinical trial optimization.

Complex QSP models can help with patient selection and biomarker identification.

Capsule Summary

This study shows the relevance of QSP model and computer simulations in assisting clinical development in the field of atopic dermatitis by assessing the impact of trial protocol on treatment effect and guiding biomarker programs.
Assessing above and belowground recovery from ammonium sulfate addition and wildfire in a lowland heath: mycorrhizal fungi as potential indicators
Authors: Kowal Jill , Pino-Bodas Raquel , Arrigoni Elena , Delhaye Guillaume , Suz Laura M. , Duckett Jeffrey G. , Bidartondo Martin I. , Pressel Silvia
Published: July 2023

Atmospheric pollution containing soil-nitrifying ammonium sulphate is affecting semi-natural ecosystems worldwide. Long-term additions of ammonium sulphate on nitrogen (N)-limited habitats such as heathlands increase climate stress affecting recovery from wildfires. Yet although heathland vegetation largely depends on ericoid mycorrhizal fungi (ErM) to access soil N, we lack a detailed understanding of how prolonged exposure to ammonium sulphate may alter ErM community composition and host plants’ reliance on fungal partners following wildfire and substantial reductions in ammonium sulphate pollution. Effects on ecosystem processes, particularly carbon stores, also remain uncertain. Ammonium sulphate additions occurred bi-weekly for five years after a 2006 wildfire burnt a UK heathland. Ten years after the treatments ceased (2021), we measured vegetation structure, lichen and lichen photobiont composition, soil characteristics, ErM colonisation, ErM diversity in roots and soil, and assessed their potential as recovery indicators. We found heather height and density, and moss groundcover, were greater in N-enriched plots. Lichen community indices showed significant treatment effects without photobiont differences. Soil pH and Mg, and the proportion of putative ErM fungi in soil were significantly lower in treated plots while soil cation exchange capacity was significantly higher. Increases in soil pH were positively correlated to soil ErM abundance. Soil carbon stock measures were variable and negatively related with soil ErM. Our results indicate that atmospheric pollution following fire can have significant lingering effects and mycorrhizal fungi diversity are a novel and effective ecological tool to assess ecosystem recovery on heathlands.

IMPLICATIONS FOR PRACTICE

Recovery of heathlands from wildfire and atmospheric pollution may require decadal scales. Conventional restoration assessment tools lack critical understanding of belowground soil and mycorrhizal fungi interactions and nutritional feedback loops with aboveground hosts.

Given that ericoid mycorrhizal fungi (ErM) communities are key nutrient regulators of resilient heathlands, we recommend baseline measurements of ErM diversity and abundance in both soil and dominant plant roots be added to the recovery assessment toolkit prior to commencing restoration or management plans.

What defines ErM recovery, and disentangling effects of ammonium sulphate pollution and fire, remain open questions which only long-term field experiments across pollution gradients will address.
Uncovering the regulatory landscape of early human B-cell lymphopoiesis and its implications in the pathogenesis of B-cell acute lymphoblastic leukemia
Authors: Planell Núria , Martínez-de-Morentin Xabier , Mouzo Daniel , Lara-Astiaso David , Vilas-Zornoza Amaia , Martín-Uriz Patxi San , Alignani Diego , Paiva Bruno , Maillo Alberto , Kurowska Aleksandra , Berastegui Nerea , Garcia-Olloqui Paula , Urdangarin Arantxa , Noori Peri , Ortega-Legarreta Asier , Hernaez Mikel , Lagani Vincenzo , Kiani Narsis , Merkenschlager Matthias , Ezponda Teresa , Martín-Subero José I. , Ramírez Ricardo N. , Tegner Jesper , Prosper Felipe , Gomez-Cabrero David
Published: July 2023

Dysregulation of the early stages of B-cell lymphopoiesis, orchestrating the development of cellular immunity, may induce malignant transformations. Therefore, it is essential to characterize the gene regulatory network (GRN) driving B-cell lymphopoiesis in healthy individuals to uncover malignancy mechanisms. To this end, we generated a dataset that included paired human data for chromatin accessibility and gene expression in eight B-cell precursor stages, providing the first deep characterization of early B-cell lymphopoiesis, including the identification of regulatory elements and the reconstruction of the GRN. Using this data, we recapitulated well-known regulatory elements and revealed new regulons, such as ELK3, enriched in pro-B cells with a putative role in cell cycle progression. Moreover, a single-cell multi-omics analysis validated and enhanced the resolution of the regulatory landscape recovered by bulk data, revealing MYBL2 and ZNF367 as specific regulons of cycling cell states, and CEBPA associated with lymphoid multipotent progenitors (LMPPs). Importantly, this dataset enabled us to uncover B-cell acute lymphoblastic leukemia (B-ALL) triggers. We identified different cellular origins of malignant transformation depending on the B-ALL subtype, including the association of the ETV6-RUNX1 with pro-B cells and the increased expression ofELK3in this ALL subtype. Overall, our dataset provides the most comprehensive atlas to date of early human B-cell regulation (B-rex;https://translationalbio.shinyapps.io/brex/), facilitating further understanding of B-cell differentiation in health and disease.