bluuebunny/crossref_metadata_2025 huggingface dataset:
Converging inputs compete at the lateral parabrachial nuclei to dictate the affective-motivational responses to cold pain
Authors: Reddy Prannay , Chaterji Shrivas , Varughese Austin , Yatika  , Sathyamurthy Anupama , Barik Arnab
Published: March 2024

The neural mechanisms of the affective-motivational symptoms of chronic pain are poorly understood. In chronic pain, our innate coping mechanisms fail to provide relief leading to heightened manifestation of these behaviors. In laboratory animals, such as mice and rats, licking the affected areas is a behavioral coping mechanism and it is sensitized in chronic pain. Hence, we have focused on delineating the brain circuits mediating licking in mice with chemotherapy-induced peripheral neuropathy (CIPN). Mice with CIPN develop intense cold hypersensitivity and lick their paws upon contact with cold stimuli. We studied how the lateral parabrachial nucleus (LPBN) neurons facilitate licking behavior when mice are exposed to noxious thermal stimuli. Taking advantage of transsynaptic viral, optogenetic, and chemogenetic strategies, we observed that the LPBN neurons become hypersensitive to cold in mice with CIPN and facilitate licks. Further, we found that the expression of licks depends on competing excitatory and inhibitory inputs from the spinal cord and lateral hypothalamus (LHA), respectively. We anatomically traced the post-synaptic targets of the spinal cord and LHA in the LPBN and found that they synapse onto overlapping populations. Activation of this LPBN population was sufficient to promote licking due to cold allodynia. In sum, our data indicate that the nociceptive inputs from the spinal cord and information on brain states from the hypothalamus impinge on overlapping LPBN populations to modulate their activity and, in turn, regulate the elevated affective-motivational responses in CIPN.
High resolution maps of chromatin reorganization through mouse meiosis reveal novel features of the 3D meiotic structure
Authors: Cheng Gang , Pratto Florencia , Brick Kevin , Li Xin , Alleva Benjamin , Huang Mini , Lam Gabriel , Camerini-Otero R. Daniel
Published: March 2024

When germ cells transition from the mitotic cycle into meiotic prophase I (MPI), chromosomes condense into an array of chromatin loops that are required to promote homolog pairing and genetic recombination. To identify the changes in chromosomal conformation, we isolated nuclei on a trajectory from spermatogonia to the end of MPI. At each stage along this trajectory, we built genomic interaction maps with the highest temporal and spatial resolution to date. The changes in chromatin folding coincided with a concurrent decline in mitotic cohesion and a rise in meiotic cohesin complexes. We found that the stereotypical large-scale A and B compartmentalization was lost during meiotic prophase I alongside the loss of topological associating domains (TADs). Still, local subcompartments were detected and maintained throughout meiosis. The enhanced Micro-C resolution revealed that, despite the loss of TADs, higher frequency contact sites between two loci were detectable during meiotic prophase I coinciding with CTCF bound sites. The pattern of interactions around these CTCF sites with their neighboring loci showed that CTCF sites were often anchoring the meiotic loops. Additionally, the localization of CTCF to the meiotic axes indicated that these anchors were at the base of loops. Strikingly, even in the face of the dramatic reconfiguration of interphase chromatin into a condensed loop-array, the interactions between regulatory elements remained well preserved. This establishes a potential mechanism for how the meiotic chromatin maintains active transcription within a highly structured genome. In summary, the high temporal and spatial resolution of these data revealed previously unappreciated aspects of mammalian meiotic chromatin organization.
Seamless, rapid and accurate analyses of outbreak genomic data using Split K-mer Analysis (SKA)
Authors: Derelle Romain , von Wachsmann Johanna , Mäklin Tommi , Hellewell Joel , Russell Timothy , Lalvani Ajit , Chindelevitch Leonid , Croucher Nicholas J. , Harris Simon R. , Lees John A.
Published: March 2024

Sequence variation observed in populations of pathogens can be used for important public health and evolution genomic analyses, especially outbreak analysis and transmission reconstruction. Identifying this variation is typically achieved by aligning sequence reads to a reference genome, but this approach is susceptible to reference biases and requires careful filtering of called genotypes. Additionally, while the volume of bacterial genomes continues to grow, tools which can accurately and quickly call genetic variation between sequences have not kept pace. There is a need for tools which can process this large volume of data, providing rapid results, but remain simple so they can be used without highly trained bioinformaticians, expensive data analysis, and long term storage and processing of large files.

Here we describe Split K-mer Analysis (SKA2), a method which supports both reference-free and reference-based mapping to quickly and accurately genotype populations of bacteria using sequencing reads or genome assemblies. SKA2 is highly accurate for closely related samples, and in outbreak simulations we show superior variant recall compared to reference-based methods, with no false positives. We also show that within bacterial strains, where it is possible to construct a clonal frame, SKA2 can also accurately map variants to a reference, and be used with recombination detection methods to rapidly reconstruct vertical evolutionary history. SKA2 is many times faster than comparable methods and can be used to add new genomes to an existing call set, allowing sequential use without the need to reanalyse entire collections. Given its robust implementation, inherent absence of reference bias and high accuracy, SKA2 has the potential to become the tool of choice for genotyping bacteria and can help expand the uses of genome data in evolutionary and epidemiological analyses. SKA2 is implemented in Rust and is freely available athttps://github.com/bacpop/ska.rust.
A NOVEL APPROACH TO RECOVERING OFF-TRACK ALIGNER TREATMENT THROUGH HYPER-ELASTIC POLYMER INNOVATION
Authors: Phan Loc X. , Mora Carla , Klucinska Agnieszka
Published: March 2024

Clear plastic aligners are becoming an increasingly popular choice for patients seeking orthodontic treatment. However, Industry Standard Aligners lack material properties that sustain tooth movement throughout the typical wear time for aligners.

In a study compiling force data from existing Industry Standard Aligners and the OrthoFX Rescue Aligner, data points were plotted to compare the force profiles of each product. The Rescue Aligner aims to eliminate the mid-course correction process and provide consistent forces to improve treatment times and patient satisfaction.
Chilean brush-tailed mouse (Octodon degus): a diurnal precocial rodent as a new model to study visual receptive field properties of superior colliculus neurons
Authors: Márquez N.I. , Fernández-Aburto P.F. , Deichler A. , Perales I. , Letelier J.-C. , Marín G. J. , Mpodozis J. , Pallas S.L.
Published: March 2024

Lab rodent species used to study the visual system and its development (hamsters, rats, and mice) are nocturnal, altricial, and possess simpler visual systems than carnivores and primates. To widen the spectra of studied species, here we introduce an alternative model, the Chilean degu (Octodon degus), a diurnal, precocial Caviomorph rodent with a cone enriched, well-structured retina, and well-developed central visual projections. To assess degus’ visual physiological properties, we characterized the visual responses and receptive field (RF) properties of isolated neurons in the superficial layers of the superior colliculus (sSC). To facilitate comparison with studies in other rodent species, we used four types of stimuli: (1) a moving white square, (2) sinusoidal gratings, (3) an expanding black circle (looming), and (4) a stationary black circle. We found that as in other mammalian species, RF size increases from superficial to deeper SC layers. Interestingly, compared to other lab rodents, degus have smaller RF sizes, likely indicating higher acuity. sSC neurons displayed spatial frequency tuning to grating stimuli from 0.08 to 0.24 cycles/degree. Additionally, neurons from sSC showed transient ON, OFF, or ON-OFF responses to stationary stimuli but increased their firing rates as a looming object increased in size. Our results suggests that degus have higher visual acuity, higher frequency tuning, and lower contrast sensitivity than commonly used nocturnal lab rodents, positioning degus as a well-suited model for studies of diurnal vision that are more relevant to humans.
Comparative CNS Pharmacology of the Bruton’s Tyrosine Kinase (BTK) Inhibitor Tolebrutinib Versus Other BTK Inhibitor Candidates for Treating Multiple Sclerosis
Authors: Turner Timothy J. , Brun Priscilla , Gruber Ross , Ofengeim Dimitry
Published: March 2024

Tolebrutinib is a covalent BTK inhibitor designed and selected for potency and CNS exposure to optimize impact on BTK-dependent signaling in CNS-resident cells. We applied a translational approach to evaluate three BTK inhibitors in Phase 3 clinical development in MS with respect to their relative potency to block BTK-dependent signaling and exposure in the CNS, employingin vitrokinase, cellular activation assays, and pharmacokinetic sampling of cerebrospinal fluid (CSF) in the non-human primate cynomolgus to estimate the ability of these candidates (evobrutinib, fenebrutinib, and tolebrutinib) to block BTK-dependent signaling inside the CNS.In vitrokinase assays demonstrated that tolebrutinib reacted with BTK 65-times faster than evobrutinib, while fenebrutinib, a classical reversible antagonist with a Kivalue of 4.7 nM and slow off-rate (1.54 x 10−5s-1), also had an association rate 1760-fold slower (3.28 x 103M-1* s-1). Estimates of cellular potency were largely consistent with thein vitrokinase assays, with an estimated IC50 of 0.7 nM for tolebrutinib against 34.5 nM for evobrutinib and 2.9 nM for fenebrutinib. We then observed that evobrutinib, fenebrutinib, and tolebrutinib achieved similar levels of exposure in non-human primate CSF after oral doses of 10 mg/kg. However, tolebrutinib CSF exposure (4.8 ng/mL) (kp,uu CSF=0.40) exceeded the IC90 (the estimated concentration inhibiting 90% of kinase activity) value, while evobrutinib (3.2 ng/mL) (kp,uu CSF=0.13) and fenebrutinib (12.9 ng/mL) (kp,uu CSF=0.15) failed to reach the estimated IC90 values. We conclude that tolebrutinib is the only candidate that attained relevant CSF exposure in non-human primates.

DISCLOSURES

TT, PB, DO:Employees of Sanofi (may hold shares and/or stock options in the company).

RG

none.
Rationalizing diverse binding mechanisms to the same protein fold: insights for ligand recognition and biosensor design
Authors: Leonard Alison C. , Friedman Anika J. , Chayer Rachel , Petersen Brian M. , Kaar Joel , Shirts Michael R. , Whitehead Timothy A.
Published: March 2024

The engineering of novel protein-ligand binding interactions, particularly for complex drug-like molecules, is an unsolved problem which could enable many practical applications of protein biosensors. In this work, we analyzed two engineer ed biosensors, derived from the plant hormone sensor PYR1, to recognize either the agrochemical mandipropamid or the synthetic cannabinoid WIN55,212-2. Using a combination of quantitative deep mutational scanning experiments and molecular dynamics simulations, we demonstrated that mutations at common positions can promote protein-ligand shape complementarity and revealed prominent differences in the electrostatic networks needed to complement diverse ligands. MD simulations indicate that both PYR1 protein-ligand complexes bind a single conformer of their target ligand that is close to the lowest free energy conformer. Computational design using a fixed conformer and rigid body orientation led to new WIN55,212-2 sensors with nanomolar limits of detection. This work reveals mechanisms by which the versatile PYR1 biosensor scaffold can bind diverse ligands. This work also provides computational methods to sample realistic ligand conformers and rigid body alignments that simplify the computational design of biosensors for novel ligands of interest.
GenoTools: An Open-Source Python Package for Efficient Genotype Data Quality Control and Analysis
Authors: Vitale Dan , Koretsky Mathew , Kuznetsov Nicole , Hong Samantha , Martin Jessica , James Mikayla , Makarious Mary B , Leonard Hampton , Iwaki Hirotaka , Faghri Faraz , Blauwendraat Cornelis , Singleton Andrew B. , Song Yeajin , Levine Kristin , Sreelatha Ashwin Ashok Kumar , Fang Zih-Hua , Nalls Mike
Published: March 2024

GenoTools, a Python package, streamlines population genetics research by integrating ancestry estimation, quality control (QC), and genome-wide association studies (GWAS) capabilities into efficient pipelines. By tracking samples, variants, and quality-specific measures throughout fully customizable pipelines, users can easily manage genetics data for large and small studies. GenoTools’ “Ancestry” module renders highly accurate predictions, allowing for high-quality ancestry-specific studies, and enables custom ancestry model training and serialization, specified to the user’s genotyping or sequencing platform. As the genotype processing engine that powers several large initiatives, including the NIH’s Center for Alzheimer’s and Related Dementias (CARD) and the Global Parkinson’s Genetics Program (GP2). GenoTools was used to process and analyze the UK Biobank and major Alzheimer’s Disease (AD) and Parkinson’s Disease (PD) datasets with over 400,000 genotypes from arrays and 5000 sequences and has led to novel discoveries in diverse populations. It has provided replicable ancestry predictions, implemented rigorous QC, and conducted genetic ancestry-specific GWAS to identify systematic errors or biases through a single command. GenoTools is a customizable tool that enables users to efficiently analyze and scale genotype data with reproducible and scalable ancestry, QC, and GWAS pipelines.
Impaired AMPK Control of Alveolar Epithelial Cell Metabolism Promotes Pulmonary Fibrosis
Authors: Rodriguez Luis R , Alysandratos Konstantinos-Dionysios , Katzen Jeremy , Murthy Aditi , Barboza Willy Roque , Tomer Yaniv , Acin-Perez Rebeca , Petcherski Anton , Minakin Kasey , Carson Paige , Iyer Swati , Chavez Katrina , Cooper Charlotte H , Babu Apoorva , Weiner Aaron I , Vaughan Andrew E , Arany Zoltan , Shirihai Orian S , Kotton Darrell N , Beers Michael F
Published: March 2024

Alveolar epithelial type II (AT2) cell dysfunction is implicated in the pathogenesis of familial and sporadic idiopathic pulmonary fibrosis (IPF). We previously described that expression of an AT2 cell exclusive disease-associated protein isoform (SP-CI73T) in murine and patient-specific induced pluripotent stem cell (iPSC)-derived AT2 cells leads to a block in late macroautophagy and promotes time-dependent mitochondrial impairments; however, how a metabolically dysfunctional AT2 cell results in fibrosis remains elusive. Here using murine and human iPSC-derived AT2 cell models expressing SP-CI73T, we characterize the molecular mechanisms governing alterations in AT2 cell metabolism that lead to increased glycolysis, decreased mitochondrial biogenesis, disrupted fatty acid oxidation, accumulation of impaired mitochondria, and diminished AT2 cell progenitor capacity manifesting as reduced AT2 self-renewal and accumulation of transitional epithelial cells. We identify deficient AMP-kinase signaling as a key upstream signaling hub driving disease in these dysfunctional AT2 cells and augment this pathway to restore alveolar epithelial metabolic function, thus successfully alleviating lung fibrosis in vivo.
Conserved DNA Methylation Signatures in The Prefrontal Cortex of Newborn and Juvenile Guinea Pigs Following Antenatal Corticosteroid Exposure
Authors: Kim Bona , Kostaki Alisa , Matthews Stephen G.
Published: March 2024

Antenatal corticosteroids (ACS) are provided to improve perinatal survival when there is risk of preterm birth. Though evidence suggests increased risk of developing neurobehavioural disorders in exposed offspring, the mechanisms that mediate this relationship remain largely unknown. Here, we investigated the DNA methylation patterns in the prefrontal cortex (PFC) of exposed offspring. We hypothesized that differential methylation will be evident at both newborn and juvenile ages.

Pregnant guinea pigs were administered saline or betamethasone (1mg/kg) on gestational days 50/51 to mimic a single course of ACS. gDNA was isolated from the PFC of term-born offspring on postnatal day 1 (PND1) and PND14 to identify differentially methylated CpG sites (DMCs) using reduced representative bisulfite sequencing.

In the PND1 PFC, 1521 DMCs, annotating to 145 genes were identified following ACS. Identified genes were involved in pathways regulating ‘developmental cellular process’. In the PND14 PFC, 776 DMCs representing 46 genes were identified, and were enriched in ‘synaptic signalling’ pathways. Though no individual DMCs were identified at both PND1 and PND14, differential methylation was consistently observed at the binding sites of transcription factors PLAGL1, TFAP2C, ZNF263, and SP1 at both ages.

In this study, we identified an altered DNA methylome in the PFC of ACS-exposed guinea pig offspring at both newborn and juvenile ages. Notably, a unique methylation signature was consistently observed at four key transcription factor binding sites at multiple post-natal time points, indicating a persistent change which may predispose the development of altered neurobehavioural phenotypes that have been described in exposed offspring.
Emergent Collective Behavior Evolves More Rapidly Than Individual Behavior Among Ant Species
Authors: Doering Grant Navid , Prebus Matthew M. , Suresh Sachin , Greer Jordan N. , Bowden Reilly , Linksvayer Timothy A.
Published: March 2024

Emergence is a fundamental concept in biology and other disciplines, but whether emergent phenotypes evolve similarly to non-emergent phenotypes is unclear. The hypothesized process ofemergent evolutionposits that evolutionary change in collective behavior is irreducible to evolutionary change in the intrinsic behaviors of isolated individuals. As a result, collective behavior might evolve more rapidly and diversify more between populations compared to individual behavior. To test if collective behavior evolves emergently, we conducted a large comparative study using 22 ant species and gathered over 1,500 behavioral rhythm time series from hundreds of colonies and isolated individuals, totaling over 1.5 years of behavioral data. We show that analogous traits measured at individual and collective levels exhibit distinct evolutionary patterns. The estimated rates of phenotypic evolution for the rhythmicity of activity in ant colonies were faster than the evolutionary rates of the same behavior measured in isolated individual ants, and total variation across species in collective behavior was higher than variation in individual behavior. We hypothesize that more rapid evolution and higher variation is a general feature of emergent phenotypes relative to lower-level phenotypes across complex biological systems.
Complement activation by IgG subclasses is governed by their ability to oligomerize upon antigen binding
Authors: Frischauf Nikolaus , Strasser Jürgen , Borg Ellen G.F. , Labrijn Aran F. , Beurskens Frank J. , Preiner Johannes
Published: March 2024

Complement activation through antibody-antigen complexes is crucial in various pathophysiological processes such as infections, inflammation, and autoimmunity, but is also utilized in immunotherapies to eliminate infectious agents, regulatory immune cells, or cancer cells. Although the tertiary structures of the four IgG antibody subclasses are largely identical, complement recruitment and further activation depend strongly on subclass, which is commonly explained by the respective affinity for C1, the first component of the classical complement pathway. Contradicting this established view, we here demonstrate that complement activation by different IgG subclasses is determined by their varying ability to form IgG oligomers on antigenic surfaces large enough to multivalently bind and activate C1. We directly visualize the resulting IgG oligomer structures and characterize their distribution by means of high-speed atomic force microscopy (HS-AFM), quantify their complement recruitment efficiency from quartz crystal microbalance (QCM) experiments, and characterize their ability to activate complement on tumor cell lines as well as in vesicle-based complement lysis assays. We present a mechanistic model of the multivalent interactions that govern C1 binding to IgG oligomers and use this model to extract affinities and kinetic rate constants from real-time interaction QCM data. Together, our detailed characterization yields a comprehensive view on the parameters that govern complement activation by the different IgG subclasses, which may inform the design of future antibody therapies.
Thalamic blood flow and EEG frequency band power during hyperventilation in idiopathic generalized epilepsy
Authors: Debatisse Justine , Yaakub Siti N , De Vita Enrico , Charles-Edwards Geoff , Jeljeli Sami , Stirling James , Flaus Anthime , Dunn Joel , Koutroumanidis Michalis , Hammers Alexander , McGinnity Colm J
Published: March 2024

Absence seizures in idiopathic generalised epilepsy (IGE) involve thalamo-cortical circuits. Hyperventilation (HV) is a standard technique to trigger epileptiform discharges and absence seizures in IGE. HV also increases electroencephalography (EEG) delta band power and decreases global cerebral blood flow (CBF). The relationships between HV, EEG band power, and regional CBF have not been investigated in the same patients at the same time.

We compared the effects of hyperventilation between 13 individuals with IGE and 18 healthy controls on thalamic CBF assessed with pseudo-continuous Arterial Spin Labelling (pCASL) simultaneously to EEG frequency band power during three periods of hyperventilation interleaved with three periods of rest, normalised to each participant’s pre-HV values.

Pre-HV, there were no differences between patients and controls. During the three rest periods combined, patients had higher normalised respiratory rates but no difference in CBF or EEG band power compared with controls.

During HV, CBF decreases were similar in controls and IGE patients in cortical gray matter (37.1±1.3% in controls, 37.9±2.0% in patients) and basal ganglia (35.6±2.0% in controls, 33.3±2.3% in patients). In the thalamus, CBF decreased by 35.5±1.9% in controls, but only by 27.1±2.5% in patients (p=0.011). Delta band power increased by 42% in patients, but only by 27% in patients (p<0.045).

Both controls’ and patients’ thalamic CBF significantly decreased as a function of respiratory rate, but the relationship was weaker in patients (rho –0.38 [0.95 confidence interval lower limit −0.629; upper limit −0.059] vs –0.51 [-0.698; −0.255] in controls). Delta power correlated with thalamic CBF only in controls (rho −0.21 [-0.388; −0.017]) but not in patients (rho −0.1 [-0.345; 0.157]). EEG power and respiratory rate were not significantly correlated in either group.

This first study of the interrelationships between HV, blood flow, and EEG band power suggests that regional thalamic abnormalities of blood flow regulation, or a neurophysiological abnormality leading to smaller reactive blood flow changes, may underlie HV-associated EEG activation.

Graphical abstract text

In this first investigation of combined hyperventilation, blood flow and EEG band power measurements in idiopathic generalised epileptic patients and healthy subjects, we revealed that localized thalamic blood flow regulatory problems or neurophysiological disorders caused minor reactive blood flow variations and may cause hyperventilation-associated EEG activation.
Crude extract ofRuellia tuberosaL. flower induces intracellular ROS, promotes DNA damage and apoptosis in Triple Negative Breast Cancer Cells
Authors: Guha Subhabrata , Talukdar Debojit , Mandal Gautam Kumar , Mukherjee Rimi , Ghosh Srestha , Naskar Rahul , Saha Prosenjit , Murmu Nabendu , Das Gaurav
Published: March 2024

Ethnophamacological relevance

In the traditional folklore medicine system, the primary uses ofRuellia tuberosaL. include as a diuretic, anti-hypertensive, antipyretic, anti-diabetic, analgesic, and gastroprotective agent. Some reports also demonstrated that it has been used to treat gonorrhea-like diseases.

Purpose

Exploring the anti-cancer potential of the methanolic extract ofRuellia tuberosaL. flower (RTME) with special emphasis on human triple-negative breast cancer (TNBC) and investigating the possible signaling networks and regulatory pathways underlying it.

Methods

Preparation of RTME and identifying the possible phytochemicals through GC-MS analysis. The anti-cancer potential of RTME was executed throughin-vitrocytotoxicity assay, clonogenic assay, wound healing assay, ROS generation assay, cell cycle arrest, apoptotic nuclear morphology study, cellular apoptosis study, mitochondrial membrane potential (MMP) alteration study, protein and gene expressions alteration study. Apart from this, toxicological status andin-silicomolecular docking studies were also conducted.

Results

From this study, it was obvious that several phytochemicals within RTME have the potential to act as anti-cancerous agents. RTME was found to exhibit significantin-vitrocytotoxicity along with a reduction in colony formation and inhibition of cell migratory potential in MDA-MB-231 cells. RTME also induced intracellular ROS, promoted G0/G1 cell cycle arrest, caused mitochondrial membrane potential (MMP) alteration, and promoted cell death. From the pro- and anti-apoptotic marker study through the western blot and the qRT-PCR analysis, it was revealed that RTME promoted the intrinsic pathway of apoptosis. Furthermore, blood parameters and histological analysis revealed that RTME doesn’t exhibit any toxic effect on female Balb/C mice. Finally, anin-silicomolecular docking study revealed that the three identified lead phytochemicals in RTME show strong receptor-ligand interactions with the anti-apoptotic Bcl-2 and give a clue to the possible molecular mechanism of the RTME extract.

Conclusion

From the findings, it was concluded that RTME has a significant therapeutic potential against TNBC which could be an alternative option for anti-cancer drug development.

Graphical Abstract

Highlights

Preparation of methanolic extract ofRuellia tuberosaL. flower,

Identification of phytochemicals from the methanolic extract ofRuellia tuberosaL. flower,

Methanolic extract ofRuellia tuberosaL. (RTME) flower exhibited significant anti-cancer potential in triple-negative breast cancer (TNBC) cells, MDA-MB-231 through induction of intracellular ROS, G0/G1 cell cycle arrest, and apoptosis,

Toxicological assessments of RTME on female Balb/C mice,

In-silicoassessments of lead phytochemicals with the target anti-apoptotic protein, bcl-2
Holding glycolysis in check though Alox15 activity is required for macrophage M2 commitment and function in tissue repair and anti-helminth immunity
Authors: Doolan R. , Moyat M. , Coakley G. , Wickramasinghe L. , Daunt C. , Volpe B.. , Henkel F. , Trefzer V. , Ubags N. , Butler A. , Chatzis R. , Marsland B. , Smith A. , Deveson Lucas D. , McGowan E.N.S. , Binger K.J. , Esser-von-Bieren J. , Bouchery T. , Harris N.
Published: March 2024

Macrophage polarization by type-2 cytokines is central to anti-helminth immunity and tissue repair. While some hallmark changes in macrophages are well-characterized and associated with protection against helminths, it is still unclear how macrophages exert their anti-helminth effects. In this context, we investigated Arachidonate 15-lipoxygenase (Alox15), a lipoxygenase well known for its role in macrophage polarization in the context of metabolic diseases, and a hallmark of type-2 macrophage (M2) human polarization. We show that in the absence of Alox15, M2 cannot trap and kill helminths. Surprisingly, expression of M2 markers was normal despite a loss of function. Instead, we found a concomitant increase in pro-inflammatory responses due to an uncontrolled activation of glycolysis. We further show that activation of Peroxisome proliferator-activated receptor-delta (PPAR-δ) by lipids downstream of Docosapentaenoic acid (DPA) can restore normal glycolysis control, highlighting a novel role for lipids in the fine-tuning of the metabolic support required for optimal macrophage polarization.
The immune profile of circulating autoreactive CD4 T cells is imprinted through tissue activation during autoimmune liver diseases
Authors: Cardon Anaïs , Guinebretière Thomas , Dong Chuang , Gil Laurine , Ado Sakina , Gavlovsky Pierre-jean , Braud Martin , Danger Richard , Schultheiß Christoph , Doméné Aurélie , Paul-Gilloteaux Perrine , Chevalier Caroline , Bernier Laura , Judor Jean-Paul , Fourgeux Cynthia , Imbert Astrid , Khaldi Marion , Bardou-Jacquet Edouard , Elkrief Laure , Lannes Adrien , Silvain Christine , Schnee Matthieu , Tanne Florence , Vavasseur Fabienne , Brusselle Lucas , Brouard Sophie , Kwok William W , Mosnier Jean-François , Lohse Ansgar , Poschmann Jeremie , Binder Mascha , Gournay Jérôme , Conchon Sophie , Milpied Pierre , Renand Amédée
Published: March 2024

Autoimmune liver diseases (AILD) are immune-mediated disorders in which CD4 T cells play a central role. However, the link between circulating self-antigen-specific CD4 T cells and the targeted tissue has not been extensively studied in AILD. We hypothesized that circulating autoreactive CD4 T cells were clonally and functionally related to dominant intra-hepatic pathogenic CD4 T cell clones. Single cell transcriptomic analysis of circulating self-antigen-specific CD4 T cells revealed a specific B-helper and immuno-exhausted transcriptional profile, which was conserved for different autoantigens, but distinct from several other types of foreign antigen specificities. In the blood, the dominant hepatic CD4 T cell clones had a similar transcriptomic signature and were enriched in the PD-1+TIGIT+HLA-DR+CD4 T cell subset. In a mouse model, antigen-specific CD4 T cells acquired the immuno-exhausted transcriptional profile when they accumulated in the liver after local antigen reactivity. Locally, immune checkpoint molecules controlled the response of antigen-specific CD4 T cells responsible for liver damage. Our study reveals the origin and biology of liver-derived autoreactive CD4 T cells in the blood of AILD patients that are imprinted by the liver environment, and suggest a dysregulation of the immune checkpoint molecules pathways. Our study enables tracking and isolating circulating autoreactive CD4 T cells for future diagnostic and therapeutic purposes.
Cellects, a software to quantify cell expansion and motion
Authors: Boussard Aurèle , Arrufat Patrick , Dussutour Audrey , Pérez-Escudero Alfonso
Published: March 2024

Motivation

Growth and motion quantification is a crucial step in studying the evolution, growth and behavior of many species. However, there is no free and easy to use software to automatically quantify the growth of an organism, and that works across a wide range of species. To fill this gap, we developed Cellects, an open-source software that quantifies growth and motion under any conditions and for any species.

Automated quantification offers unique opportunities to study biological phenomena, increasing reproducibility, replicability, accuracy, and throughput, while reducing observer biases. We present Cellects, a tool to quantify growth and motion in 2D. This software operates with image sequences containing specimens growing and moving on an immobile flat surface. Its user-friendly interface makes it easy to adjust the quantification parameters to cover a wide range of species and conditions, and includes tools to validate the results and correct mistakes if necessary. The software provides the region covered by the specimens at each point of time, as well as many geometrical descriptors that characterize it. We validated Cellects withPhysarum polycephalum, which is particularly difficult to detect because of its complex shape and internal heterogeneity. This validation covered five different conditions with different background and lighting, and found Cellects to be highly accurate in all cases. Cellects’ main strengths are its broad scope of action, automated computation of a variety of geometrical descriptors, easy installation and user-friendly interface.

github link:https://github.com/Aurele-B/Cellects

Highlights

We present Cellects, a tool to quantify growth and motion of organisms automatically.

Cellects is easy to install and use thanks to its user-friendly interface.

It works with a wide range of organisms, providing many geometrical descriptors.

Our validation showed high accuracy even in challenging experimental conditions.
Airway succinate chemosensing induces CFTR-dependent anion secretion and mucus clearance which is impaired in cystic fibrosis
Authors: Apablaza Tábata , Barros-Poblete Marisol , Delpiano Livia , Villanueva Sandra , Guequen Anita , Tapia-Balladares Bárbara , Haq Iram , Tribiños Felipe , Hernández-Rivas Sebastián , Verdon Bernard , Biggart Matthew G.S. , Sánchez Yenniffer , Ward Christopher , Baxter B Dnate’ , Restrepo Diego , Cornejo Isabel , Tarran Robert , Catalán Marcelo A. , Gray Michael A. , Flores Carlos A.
Published: March 2024

The respiratory tract possesses a highly regulated innate defense system which includes efficient cilia-mediated mucus transport or mucociliary clearance (MCC). This essential process relies on appropriate hydration of airway surfaces which is controlled by a blend of transepithelial sodium and liquid absorption via the epithelial sodium channel (ENaC), and anion and liquid secretion, primarily regulated by the cystic fibrosis transmembrane conductance regulator (CFTR) channel. MCC is tightly regulated by second messenger signalling pathways. Succinate is derived from parasites, microorganisms and inflammatory cells, and its concentration increases in the airway surface liquid (ASL) during infections. Increases in ASL succinate activates the G-protein coupled succinate receptor (SUCNR1), which acts as a succinate sensor. Here, we tested the hypothesis that succinate signalling was linked to CFTR activity, ASL hydration and increased MCC.

We observed that SUCNR1 activation stimulated anion secretion, increased mucus transport and induced bronchoconstriction in mouse airways. In parallel, stimulation of human bronchial epithelial cells (HBEC) with succinate activated anion secretion and increased ASL height. All functions activated by succinate/SUCNR1 were impeded when working with tissues and cells isolated from animal models or individuals affected cystic fibrosis (CF) or when CFTR was inhibited. Moreover, when HBECs derived from ΔF508 individuals were incubated with the triple drug combination of elexacaftor/tezacaftor/ivacaftor (ETI), succinate-induced anion secretion was restored, confirming the tight relationship between SUCNR1 signalling and CFTR function. Our results identify a novel activation pathway for CFTR that participates in the defence response of the airways, which is defective in CF. We propose that succinate acts as a danger molecule that alerts the airways to the presence of pathogens leading to a flushing out of the airways.
KAT6A deficiency impairs cognitive functions through suppressing RSPO2/Wnt signaling in hippocampal CA3
Authors: Liu Yongqing , Fan Minghua , Yang Junhua , Mihaljević Ljubica , Chen Kevin Hong , Ye Yingzhi , Sun Shuying , Qiu Zhaozhu
Published: March 2024

Intellectual disability (ID) affects ∼2% of the general population and is often genetic in origin. ID-associated genes are enriched for epigenetic factors, including those encoding the largest family of histone lysine acetyltransferases (KAT5-KAT8). Among them isKAT6A, whosede novoheterozygous mutations cause KAT6A Syndrome (or Arboleda-Tham Syndrome), with ID as a common clinical feature. However, the underlying molecular mechanisms remain elusive. Here, we show that haploinsufficiency ofKat6aimpairs learning and memory in mice, and specific deletion ofKat6ain excitatory neurons recapitulates the hippocampus-dependent memory deficits. Unexpectedly, KAT6A deficiency results in impaired synaptic structure and plasticity in hippocampal CA3, but not in CA1 region. Combining single-nucleus RNA-sequencing and chromatin analysis, we identify a CA3-enriched geneRspo2, encoding a Wnt activator R-spondin 2, as a key transcriptional target of KAT6A. Moreover, deletion ofRspo2in excitatory neurons phenocopies the loss ofKat6a, resulting in defective Wnt/β-catenin signaling and synaptic plasticity in CA3, and abnormal cognitive behaviors in mice. Importantly, restoring RSPO2 expression in CA3 pyramidal neurons rescues the deficits in Wnt signaling and learning-associated behaviors inKat6amutant mice. Collectively, our results demonstrate that KAT6A plays a critical role in regulating synaptic plasticity and memory formation through RSPO2-mediated Wnt signaling in hippocampal CA3, shedding new light on the fundamental mechanisms of ID and providing potential therapeutic targets for the treatment of KAT6A Syndrome and related neurodevelopmental diseases.
Evaluating Species at Risk in Data-Limited Fisheries: A Comprehensive Productivity-Susceptibility Analysis of the Most Traded Marine Aquarium Fish
Authors: Baillargeon Gabrielle A. , Wynn Alice A. , Baldisimo Jemelyn Grace P. , Tlusty Michael F. , Rhyne Andrew
Published: March 2024

The marine aquarium trade is a significant global industry harvesting millions of live coral reef fishes annually. Wild-caught fish dominate public and private aquaria markets in the USA and Europe, supporting fisher livelihoods in the Indo-Pacific. This diverse and species-rich trade is considered data-limited, creating barriers to quantify the sustainability of this fishery to the net benefit of the coral reef socio-ecological system. We present a revised and expanded productivity-susceptibility analysis (PSA) framework to assess the vulnerability to overharvesting of the top 258 traded species, an estimated 92.5% of all import volume into the USA in 2011. Vulnerability was calculated based on various productivity and susceptibility factors, tailored to the unique life-history and fishery selectivity characteristics of the marine aquarium trade. We present novel factors that improve model accuracy, methods to overcome missing data for individual factors, and apply an improved Gaussian mixture model clustering algorithm to objectively classify species as least, moderately, or most vulnerable. Our results show that an overwhelming 85% of species evaluated fall into the least or moderately vulnerable classification, with the remaining species designated as high priority for localized assessment and management initiatives. A comparative case study between our PSA and the popular FishBase Vulnerability assessment illustrates how it is ill-suited to handle data limitations of non-food fishes. The results of our PSA, at a species and family level, provide useful information to stakeholders and serves as a robust and accessible risk assessment tool to prioritize species for management based on their vulnerability scores.
Comprehensive prediction and analysis of human protein essentiality based on a pre-trained protein large language model
Authors: Kang Boming , Fan Rui , Cui Chunmei , Cui Qinghua
Published: March 2024

Human essential genes and their protein products are indispensable for the viability and development of the individuals. Thus, it is quite important to decipher the essential proteins and up to now numerous computational methods have been developed for the above purpose. However, the current methods failed to comprehensively measure human protein essentiality at levels of humans, human cell lines, and mice orthologues. For doing so, here we developed Protein Importance Calculator (PIC), a sequence-based deep learning model, which was built by fine-tuning a pre-trained protein language model. As a result, PIC outperformed existing methods by increasing 5.13%-12.10% AUROC for predicting essential proteins at human cell-line level. In addition, it improved an average of 9.64% AUROC on 323 human cell lines compared to the only existing cell line-specific method, DeepCellEss. Moreover, we defined Protein Essential Score (PES) to quantify protein essentiality based on PIC and confirmed its power of measuring human protein essentiality and functional divergence across the above three levels. Finally, we successfully used PES to identify prognostic biomarkers of breast cancer and at the first time to quantify the essentiality of 617462 human microproteins.

Key Points

PIC outperformed existing computational methods for predicting essential proteins.

PIC could comprehensively predict human protein essentiality at levels of human, human cell lines and mice orthologues at the same time.

PES could serve as a potential metric to quantify the essentiality of both human proteins and human microproteins.
Modeling the time-resolved modulations of cardiac activity in rats: A study on pharmacological autonomic stimulation
Authors: Candia-Rivera Diego , Carrion-Falgarona Sofia , De Vico Fallani Fabrizio , Chavez Mario
Published: March 2024

Assessing cardiac dynamics over time is essential for understanding cardiovascular health and its parallel patterns of activity with the brain. We present a methodology to estimate the time-resolved sympathetic and parasympathetic modulations of cardiac dynamics, specifically tailored for the rat heart. To evaluate the performance of our method, we study a dataset comprising spontaneously hypertensive rats and Wistar-Kyoto rats. These rats were administered dobutamine to elicit autonomic dynamics. The results obtained from our method demonstrated accurate time-resolved depiction of sympathetic reactivity induced by dobutamine administration. These responses closely resembled the expected autonomic alterations observed during physical exercise conditions, albeit emulated pharmacologically. We further compared our method with standard measures of low-frequency (LF) and high-frequency (HF) components, which are commonly used, although debated, for sympathetic and parasympathetic activity estimation. The comparisons with LF and HF measures further confirmed the effectiveness of our method in better capturing autonomic changes in rat cardiac dynamics. Our findings highlight the potential of our adapted method for time-resolved analysis in future clinical and translational studies involving rodents' models. The validation of our approach in animal models opens new avenues for investigating the relationship between ongoing changes in cardiac activity and parallel changes in brain dynamics. Such investigations are crucial for advancing our understanding of the brain-heart connection, particularly in cases involving neurodegeneration, brain injuries, and cardiovascular conditions.
Local nutrient addition drives plant diversity losses but not biotic homogenization in global grasslands
Authors: Chen Qingqing , Blowes Shane A. , Harpole W. Stanley , Ladouceur Emma , Borer Elizabeth T. , MacDougall Andrew , Martina Jason P. , Bakker Jonathan D. , Tognetti Pedro M. , Seabloom Eric W. , Daleo Pedro , Power Sally A. , Roscher Christiane , Adler Peter , Donohue Ian , Wheeler George , Stevens Carly , Veen Ciska , Risch Anita C. , Wardle Glenda M. , Hautier Yann , Estrada Catalina , Hersch-Green Erika , Niu Yujie , Peri Pablo L. , Eskelinen Anu , Gruner Daniel S , Olde Venterink Harry , D’Antonio Carla , Cadotte Marc W. , Haider Sylvia , Eisenhauer Nico , Catford Jane , Virtanen Risto , Morgan John W. , Tedder Michelle , Bagchi Sumanta , Caldeira Maria C. , Bugalho Miguel , Knops Johannes M. H. , Dickman Chris R. , Hagenah Nicole , Jentsch Anke , Macek Petr , Osborne Brooke B. , Laanisto Lauri , Chase Jonathan M.
Published: March 2024

Nutrient enrichment typically causes local plant diversity decline. A common but untested expectation is that it reduces variation in nutrient conditions among localities and selects for a smaller pool of species, causing greater diversity declines at larger scales and biotic homogenization. We apply a topology linking changes in species richness across scales that characterizes changes in the numbers of spatially restricted and widespread species to a standardized experiment adding nutrients across 72 grasslands on six continents. Overall, we found similar declines of spatially restricted and widespread species, and proportional species loss at local and larger scales, and no biotic homogenization after 4 years and up to 14 years of treatment. These patterns of diversity changes were generally consistent across species groups (e.g., native species, graminoids and legume species). Thus, nutrient enrichment poses threats to plant diversity that includes widespread species that are often critical for ecosystem functions.
An EEG Signature of MCH Neuron Activities Predicts Cocaine Seeking
Authors: Wang Yao , Li Danyang , Widjaja Joseph , Guo Rong , Cai Li , Yan Rongzhen , Ozsoy Sahin , Allocca Giancarlo , Fang Jidong , Dong Yan , Tseng George C. , Huang Chengcheng , Huang Yanhua H.
Published: March 2024

Background

Identifying biomarkers that predict substance use disorder (SUD) propensity may better strategize anti-addiction treatment. The melanin-concentrating hormone (MCH) neurons in the lateral hypothalamus (LH) critically mediates interactions between sleep and substance use; however, their activities are largely obscured in surface electroencephalogram (EEG) measures, hindering the development of biomarkers.

Methods

Surface EEG signals and real-time Ca2+activities of LH MCH neurons (Ca2+MCH) were simultaneously recorded in male and female adult rats. Mathematical modeling and machine learning were then applied to predict Ca2+MCHusing EEG derivatives. The robustness of the predictions was tested across sex and treatment conditions. Finally, features extracted from the EEG-predicted Ca2+MCHeither before or after cocaine experience were used to predict future drug-seeking behaviors.

Results

An EEG waveform derivative – a modified theta-to-delta ratio (EEG Ratio) – accurately tracks real-time Ca2+MCHin rats. The prediction was robust during rapid eye movement sleep (REMS), persisted through REMS manipulations, wakefulness, circadian phases, and was consistent across sex. Moreover, cocaine self-administration and long-term withdrawal altered EEG Ratio suggesting shortening and circadian redistribution of synchronous MCH neuron activities. In addition, features of EEG Ratio indicative of prolonged synchronous MCH neuron activities predicted lower subsequent cocaine seeking. EEG Ratio also exhibited advantages over conventional REMS measures for the predictions.

Conclusions

The identified EEG Ratio may serve as a non-invasive measure for assessing MCH neuron activitiesin vivoand evaluating REMS; it may also serve as a potential biomarker predicting drug use propensity.