bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation and characterization of three lytic podo-bacteriophages with two receptor recognition modules against multidrug-resistantKlebsiella pneumoniae
Authors: Huang Liang , Huang Xueting , Zhao Tongfei , Zhang Jingren , Xiang Ye
Published: May 2024

The multidrug-resistant nosocomial pathogenKlebsiella pneumoniaeis considered as one of the major threats to public health. Recent studies showed that bacteriophages could be used as an alternative to antibiotics for treating infections caused by multidrug-resistantK. pneumoniae.Here we isolated and characterized three lytic bacteriophages Kp7, Kp9 and Kp11 ofK. pneumoniae. Transmission electron microscopy analysis showed that all three phages have an isometric head of approximately 60 nm in diameter and a short noncontractile tail. Host specificity, one-step growth curve, tolerance to pH and temperature changes were characterized for Kp7, Kp9, and Kp11. Mass-spectrum and bioinformatical analysis identified two different types of tail fibers in each phage. The tail fiber proteins gp52 of Kp7, gp43 of Kp9 and gp46 of Kp11 are homologous and have robust enzymatic activity in digesting purified serotype K2 capsule ofK. pneumoniae. However, tail fiber proteins gp51 of Kp7, gp42 of Kp9 and gp45 of Kp11 have diverse sequences and show weak or no enzyme activity in digesting purified serotype K2 capsule. Genetic knockout and biochemical assays indicated that the capsule is essential for the infection of Kp7, Kp9 and Kp11. Spot tests showed that 15 clinical isolates of drug-resistantK. pneumoniaewith the serotype K2 capsule can all be infected by Kp7, Kp9 and Kp11 but with different susceptibility. Further mechanistic studies showed that transcriptional inhibition at the early stage of phage infection determines the susceptibility of differentK. pneumoniaeisolates.
Seizures may worsen outcomes of neonatal hypoxic ischemic encephalopathy: a longitudinal serum biomarkers study
Authors: Aziz Khyzer B , Kuiper Jordan , Kilborn Alison , Kambli Hrishikesh , Jayakumar Srishti , Gerner Gwendolyn J , Tekes Aylin , Parkinson Charlamaine , Graham Ernest M. , Stafstrom Carl E. , Campbell Christopher , Demos Catherine , Stengelin Martin , Sigal George , Wohlstadter Jacob , Everett Allen D. , Northington Frances J. , Chavez-Valdez Raul
Published: May 2024

Introduction

Screening and treatment of seizures (Sz) in neonates suffering from hypoxic-ischemic encephalopathy (HIE) is routine. Understanding if Sz worsen brain injury and outcomes would optimize treatment decisions, recognizing risks and benefits. We hypothesized that serum central nervous system (CNS)-specific biomarkers would discriminate neonates with Sz and relate to outcomes.

Methods

This retrospective cohort study was conducted between April 28, 2009 and November 15, 2019, including neonates diagnosed with seizures (Sz) and/or HIE treated with therapeutic hypothermia (TH), who had sufficient remnant serum for biomarker analysis. Neonates were grouped in i) only Sz without HIE (Sz-no HIE), ii) HIE with Sz (Sz-HIE) and iii) HIE without Sz (no Sz-HIE). Levels of glial fibrillary acidic protein (GFAP, astrocytic reactivity), Tau (neuronal injury) and neurofilament light chain (NF-L, axonal degeneration) were studied at admission, <72h and 72-144h of life against time to full oral feeds and brain injury in MRI.

Results

After exclusions 145 neonates were included (61% male; 33% Black). Admission GFAP levels were higher in Sz-HIE than in no Sz-HIE neonates. During the first 72h of life, levels of all 3 biomarkers were similar between Sz groups (Sz-no HIE & Sz-HIE), but higher than in no Sz-HIE. After 72h, NF-L and Tau remained higher in both Sz groups vs. no Sz-HIE. Stroke diagnosed in 31% (Sz-no HIE), 8% (Sz-HIE) and 11% (no Sz-HIE) of neonates had no effect in biomarkers levels. In adjusted regression models higher Tau and NF-L percentiles related to longer time to reach full oral feeding and higher odds of significant brain injury in MRI in both Sz groups.

Conclusions

In this study, Tau and NF-L levels are higher in those neonates developing Sz, irrespective of their HIE diagnosis. These results provide additional support for the notion that Sz may worsen brain injury and outcomes in neonates with HIE even with TH.
Connectome-based predictive modeling of early and chronic psychosis symptoms
Authors: Foster Maya L. , Ye Jean , Powers Albert , Dvornek Nicha , Scheinost Dustin
Published: May 2024

The symptoms of psychosis-spectrum disorders, which include positive symptoms (e.g., hallucinations and delusions) and negative symptoms (e.g., memory impairment and disorganized thinking), can cause significant distress and disability. Despite shared symptomatology and converging brain correlates, early (EP) and chronic (CP) psychosis differ in their symptom-related treatment response. At present, the mechanism underlying these differences is unknown, in large part because EP and CP have predominantly been studied and characterized independently or in comparison to control populations. To answer this question, we use connectome-based predictive modeling (CPM) and resting-state functional magnetic resonance imaging to identify biologically-based early (EP, n=107) and chronic (CP, n=123) psychosis symptom networks. We predicted both samples’ total, positive, and negative symptoms from the PANSS. Virtual lesioning analyses highlight the frontoparietal network as a critical component of EP and CP symptom networks, but the specific functional connections used for prediction differ. Finally, group differences compared to healthy controls (n=150) were observed for CP but not EP. These differences broadly overlapped with the symptom model for both EP and CP. Our results encourage using longitudinal studies to track connectivity changes in putative symptom networks during the progression of psychosis, as they may be explicative of EP-CP treatment differences.
Polygenic and transcriptional risk scores identify chronic obstructive pulmonary disease subtypes
Authors: Moll Matthew , Hecker Julian , Platig John , Zhang Jingzhou , Ghosh Auyon J. , Pratte Katherine A. , Wang Rui-Sheng , Hill Davin , Konigsberg Iain R. , Chiles Joe W. , Hersh Craig P. , Castaldi Peter J. , Glass Kimberly , Dy Jennifer G. , Sin Don D. , Tal-Singer Ruth , Mouded Majd , Rennard Stephen I. , Anderson Gary P. , Kinney Gregory L. , Bowler Russell P. , Curtis Jeffrey L. , McDonald Merry-Lynn , Silverman Edwin K. , Hobbs Brian D. , Cho Michael H.
Published: May 2024

Rationale

Genetic variants and gene expression predict risk of chronic obstructive pulmonary disease (COPD), but their effect on COPD heterogeneity is unclear.

Objectives

Define high-risk COPD subtypes using both genetics (polygenic risk score, PRS) and blood gene expression (transcriptional risk score, TRS) and assess differences in clinical and molecular characteristics.

Methods

We defined high-risk groups based on PRS and TRS quantiles by maximizing differences in protein biomarkers in a COPDGene training set and identified these groups in COPDGene and ECLIPSE test sets. We tested multivariable associations of subgroups with clinical outcomes and compared protein-protein interaction networks and drug repurposing analyses between high-risk groups.

Measurements and Main Results

We examined two high-risk omics-defined groups in non-overlapping test sets (n=1,133 NHW COPDGene, n=299 African American (AA) COPDGene, n=468 ECLIPSE). We defined “High activity” (low PRS/high TRS) and “severe risk” (high PRS/high TRS) subgroups. Participants in both subgroups had lower body-mass index (BMI), lower lung function, and alterations in metabolic, growth, and immune signaling processes compared to a low-risk (low PRS, low TRS) reference subgroup. “High activity” but not “severe risk” participants had greater prospective FEV1decline (COPDGene: -51 mL/year; ECLIPSE: - 40 mL/year) and their proteomic profiles were enriched in gene sets perturbed by treatment with 5-lipoxygenase inhibitors and angiotensin-converting enzyme (ACE) inhibitors.

Conclusions

Concomitant use of polygenic and transcriptional risk scores identified clinical and molecular heterogeneity amongst high-risk individuals. Proteomic and drug repurposing analysis identified subtype-specific enrichment for therapies and suggest prior drug repurposing failures may be explained by patient selection.
Hyperdisordered cell packing on a growing surface
Authors: Ross R. J. H. , Masucci Giovanni D. , Lin Chun Yen , Iglesias Teresa L. , Reiter Sam , Pigolotti Simone
Published: May 2024

While the physics of disordered packing in non-growing systems is well understood, unexplored phenomena can emerge when packing takes place in growing domains. We study the arrangements of pigment cells (chromatophores) on squid skin as a biological example of a packed system on an expanding surface. We find that relative density fluctuations in cell numbers grow with spatial scale. We term this behavior “hyperdisordered”, in contrast with hyperuniform behavior in which relative fluctuations tend to zero at large scale. We find that hyperdisordered scaling, akin to that of a critical system, is quantitatively reproduced by a model in which hard disks are randomly inserted in a homogeneously growing surface. In addition, we find that chromatophores increase in size during animal development, but maintain a stationary size distribution. The physical mechanisms described in our work may apply to a broad class of growing dense systems.
Adhesion-driven vesicle translocation through membrane-covered pores
Authors: Baruah Nishant , Midya Jiarul , Gompper Gerhard , Dasanna Anil Kumar , Auth Thorsten
Published: May 2024

Translocation across barriers and through constrictions is a mechanism that is often used in vivo for transporting material between compartments. A specific example is apicomplexan parasites invading host cells through the tight junction that acts as a pore, and a similar barrier crossing is involved in drug delivery using lipid vesicles on the skin. Here, we use triangulated membranes and energy minimization to study the translocation of vesicles through pores with fixed radii. The vesicles bind to a lipid bilayer spanning the pore, and the adhesion-energy gain drives the translocation; the vesicle deformation while squeezing through leads to an energy barrier. In addition, the deformation-energy cost for deforming the pore-spanning membrane hinders translocation. Increasing the bending rigidity of the pore-spanning membrane and decreasing the pore size both increase the barrier height and shift the maximum to smaller translocation fractions. We compare the translocation of initially spherical vesicles with fixed membrane area and freely adjustable volume to that of initially prolate vesicles with fixed membrane area and volume. In the latter case, translocation can be entirely suppressed. Our predictions may help rationalize the invasion of apicomplexan parasites into host cells and design measures to combat the diseases they transmit.
Competitor Displacement by an Herbivore that Manipulates Plant Defences
Authors: Chafi Rachid , Ataide Livia M. S. , Scala Alessandra , Villacis-Perez Ernesto , Alba Juan M. , Schimmel Bernardus C. J. , Kant Merijn R.
Published: May 2024

Tetranychus evansiis an herbivorous mite specialised on solanaceous hosts, although it has also been observed to colonise non-solanaceous species. It has the ability to suppress the defences of tomato (Solanum lycopersicum), and it can displace competitors from this host using a diverse array of traits.T. evansiis an invasive species in Africa and Europe, where it often displaces native species. While recent evidence suggests thatT. evansican also suppress defences of non-solanaceous hosts, there is a lack of understanding of the molecular changes induced upon mite infestation on hosts other than tomato, as well as how these changes may impact populations of competing herbivores. Here, we investigate the transcriptomic and metabolomic responses of bean (Phaseolus vulgaris) toT. evansiinfestation and toT. urticaeinfestation, a cosmopolitan congeneric that often competes withT. evansifor hosts in areas of co-occurrence. We ask whether the presence ofT. evansifacilitates bean colonization forT. urticae,and whether the spatial distribution of mite feeding sites depends on the presence of competitors on bean leaves. We examine whether this facilitation is attributed to jasmonic acid (JA) or salicylic acid (SA) defences by treating plants with exogenous SA and JA and comparing the transcriptomes and metabolomes of bean exposed to either phytohormones or to mite feeding. Finally, we measure phytohormone concentrations and the expression of JA- and SA-responsive genes in plants infested with either mite species or co-infested with both, at different spatial scales. We found that, as previously observed on tomato,T. urticaebenefits from the suppression of bean defences when sharing a leaf withT. evansi.Phytohormone treatments revealed that the reproductive performance of both species decreases with artificially induced JA defences, irrespective of the presence of SA. We found that the molecular suppression and induction of defences is mostly, but not exclusively restricted to the leaf area from where the mites feed. In full leaves co-infested with both mites, levels of marker gene induction were comparable to the inducer miteT. urticae, although not as prominent, while in smaller feeding arenas where both species fed closely to each other, the expression of a JA-responsive proteinase inhibitor was suppressed. When residing alone on a leaf, both mites had distinct preferred feeding sites with only partial overlap, but when sharing a leaf,T. evansiretained its preferred feeding site andT. urticaemoved away from its own. We argue that the suppression of defences byT. evansiis mostly, although not exclusively, locally restricted, and thus the spatial distribution of individuals on the leaf is a strong determinant of competitor facilitation. This suggests that traits that displace competitors from plant tissues with suppressed defences would be under selection to co-evolve together with defence suppression.
The ontogeny of immune tolerance: a model of early-life secretory IgA - gut microbiome interactions
Authors: Tepekule Burcu , Lim Ai Ing , Metcalf C. Jessica E.
Published: May 2024

Abstract

To achieve immune and microbial homeostasis during adulthood, the developing immune system must learn to identify which microbes to tolerate and which to defend against. How such ‘immune education’ unfolds remains a major knowledge gap. We address this gap by synthesizing existing literature to develop a mechanistic mathematical model representing the interplay between gut ecology and adaptive immunity in early life. Our results indicate that the inflammatory tone of the microenvironment is the mediator of information flow from pre- to post- weaning periods. We evaluate the power of postnatal fecal samples for predicting immunological trajectories, and explore breastfeeding scenarios when maternal immunological conditions affect breastmilk composition. Our work establishes a quantitative basis for ’immune education’, yielding insights into questions of applied relevance.
Control of Physiologic Glucose Homeostasis via the Hypothalamic Modulation of Gluconeogenic Substrate Availability
Authors: Hashsham Abdullah , Kodur Nandan , Su Jiaao , Tomlinson Abigail J. , Yacawych Warren T. , Flak Jon N. , Lewis Kenneth T. , Oles Lily R. , Mori Hiroyuki , Bozadjieva-Kramer Nadejda , Turcu Adina F. , MacDougald Ormond A. , Myers Martin G. , Affinati Alison H.
Published: May 2024

The brain augments glucose production during fasting, but the mechanisms are poorly understood. Here, we show thatCckbr-expressing neurons in the ventromedial hypothalamic nucleus (VMNCckbrcells) prevent low blood glucose during fasting through sympathetic nervous system (SNS)-mediated augmentation of adipose tissue lipolysis and substrate release. Activating VMNCckbrneurons mobilized gluconeogenic substrates without altering glycogenolysis or gluconeogenic enzyme expression. Silencing these cells (CckbrTetToxanimals) reduced fasting blood glucose, impaired lipolysis, and decreased circulating glycerol (but not other gluconeogenic substrates) despite normal insulin, counterregulatory hormones, liver glycogen, and liver gluconeogenic gene expression. Furthermore, β3-adrenergic adipose tissue stimulation in CckbrTetToxanimals restored lipolysis and blood glucose. Hence, VMNCckbrneurons impact blood glucose not by controlling islet or liver physiology, but rather by mobilizing gluconeogenic substrates. These findings establish a central role for hypothalamic and SNS signaling during normal glucose homeostasis and highlight the importance of gluconeogenic substrate mobilization during physiologic fasting.
Live-cell imaging and CLEM reveal the existence of ACTN4-dependent ruffle-edge lamellipodia acting as a novel mode of cell migration
Authors: Morishita Haruka , Kawai Katsuhisa , Egami Youhei , Honda Kazufumi , Araki Nobukazu
Published: May 2024

α-Actinin-4 (ACTN4) expression levels are correlated with the invasive and metastatic potential of cancer cells; however, the underlying mechanism remains unclear. Here, we identified ACTN4-localized ruffle-edge lamellipodia using live-cell imaging and correlative light and electron microscopy (CLEM). BSC-1 cells expressing EGFP-ACTN4 showed that ACTN4 was most abundant in the leading edges of lamellipodia, although it was also present in stress fibers and focal adhesions. ACTN4 localization in lamellipodia was markedly diminished by phosphoinositide 3-kinase inhibition, whereas its localization in stress fibers and focal adhesions remained. Furthermore, overexpression of ACTN4, but not ACTN1, promoted lamellipodial formation. Live-cell analysis demonstrated that ACTN4-enriched lamellipodia are highly dynamic and associated with cell migration. CLEM revealed that ACTN4-enriched lamellipodia exhibit a characteristic morphology of multilayered ruffle-edges that differs from canonical flat lamellipodia. Similar ruffle-edge lamellipodia were observed in A549 and MBA-MD-231 invasive cancer cells. ACTN4 knockdown suppressed the formation of ruffle-edge lamellipodia and cell migration during wound healing in A549 monolayer cultures. Additionally, membrane-type 1 matrix metalloproteinase was observed in the membrane ruffles, suggesting that ruffle-edge lamellipodia have the ability to degrade the extracellular matrix and may contribute to active cell migration/invasion in certain cancer cell types.
IP3R1 is required for meiotic progression and embryonic development by regulating mitochondrial calcium and oxidative damage
Authors: Zhang Chang , Sun Xiaoqing , Wu Deyi , Wang Guoxia , Lan Hainan , Zheng Xin , Li Suo
Published: May 2024

Calcium ions (Ca2+) regulate cell proliferation and differentiation and participate in various physiological activities of cells. The calcium transfer protein inositol 1,4,5-triphosphate receptor (IP3R), located between the endoplasmic reticulum (ER) and mitochondria, plays an important role in regulating Ca2+levels. However, the mechanism by which IP3R1 affects porcine meiotic progression and embryonic development remains unclear. We established a model in porcine oocytes using siRNA-mediated knockdown of IP3R1 to investigate the effects of IP3R1 on porcine oocyte meiotic progression and embryonic development. The results indicated that a decrease in IP3R1 expression significantly enhanced the interaction between the ER and mitochondria. Additionally, the interaction between the ER and the mitochondrial Ca2+([Ca2+]m) transport network protein IP3R1-GRP75-VDAC1 was disrupted. PLA decreased IP3R1, weakened the pairwise interaction between IP3R1-GRP75 and VDAC1 and significantly enhanced the interaction between GRP75 and VDAC1, resulting in the accumulation of large amounts of [Ca2+]m. These changes led to mitochondrial oxidative stress and reduced ATP production, which hindered the maturation and late development of porcine oocytes and caused apoptosis.
Personalized stimulation therapies for disorders of consciousness: a computational approach to inducing healthy-like brain activity based on neural field theory
Authors: Polyakov Daniel , Robinson P.A. , Müller Eli J. , van der Lande Glenn , Nunez Pablo , Annen Jitka , Gosseries Olivia , Shriki Oren
Published: May 2024

Disorders of consciousness (DoC) pose significant challenges in neurology. Conventional neuromodulation therapies for DoC have exhibited limited success, with varying effectiveness among patients. In this study, we introduce a computational approach for constructing personalized stimulus signals capable of inducing healthy-like neural activity patterns in DoC patients.

Leveraging a simplified brain model based on neural field theory, we fit this model to the power spectrum of a patient with DoC and derive a personalized stimulus time series to induce a healthy-like power spectrum. By applying this stimulus to brain regions typically targeted by stimulation therapies such as deep brain stimulation and repetitive transcranial magnetic stimulation, we demonstratein silicothe ability of our method to elicit EEG power spectra resembling those of healthy individuals.

We speculate that in the course of a long-term treatment, when the brain produces healthy-like activity, it may trigger intrinsic plasticity mechanisms, potentially leading to sustained improvements in the patient’s condition. While further clinical adjustments and validation are needed, this novel approach offers promise in tailoring brain stimulation therapies for DoC patients. Moreover, it presents potential extensions to other conditions that could also benefit from brain stimulation therapies.

Author summary

In this research, we tackled a challenging issue in the field of neurology - disorders of consciousness (DoC). These conditions, which include states like coma and the minimally consciousness state, have been difficult to treat effectively. While traditional brain stimulation treatments have been tried, they do not always work well, and their effects can vary greatly from one person to another. Thus, we set out to find a new way to help these patients. Our approach involves using computer models of the brain to design personalized treatments. We designed a method to generate stimulation signals tailored to individual DoC patients. These signals aim to trigger healthier brain activity patterns, similar to those found in individuals without consciousness disorders. What is exciting is that if the brain begins to produce these healthy-like patterns, it could potentially lead to lasting improvements in the patient’s consciousness level. We show that this approach works in different simulations, and can be applied in multiple neuromodulation techniques like deep brain stimulation and transcranial magnetic stimulation. This research opens up new possibilities for more effective treatments for people dealing with these challenging disorders. Plus, it might work for other conditions treated with similar brain stimulation therapies.
Personality and MB-COMT gene: molecular-genetic and epigenetic associations with NEO-PI-R personality domains and facets in monozygotic twins
Authors: Mitrović Dušanka , Smederevac Snežana , Delgado-Cruzata Lissette , Sadiković Selka , Pajić Dejan , Prinz Mechthild , Budimlija Zoran , Oljača Milan , Kušić-Tišma Jelena , Vučinić Nataša , Milutinović Aleksandra
Published: May 2024

This study investigates the relationship betweenMB-COMTDNA methylation (DNAm) and the personality traits outlined in the NEO-PI-R model through an epigenetic study of monozygotic twins. DNAm, a critical epigenetic mechanism, regulates gene expression and has been linked to various biological processes and disorders. By leveraging the genetic similarities of monozygotic twins, this research explores how epigenetic variations influenced by environmental factors correlate with personality differences. The study utilized the Five-Factor Model (FFM) to categorize personality traits into five domains: Neuroticism, Extraversion, Conscientiousness, Agreeableness, and Openness to Experience. Each domain comprises six facets, providing a granular view of personality. The research centered on the catechol-O-methyltransferase (COMT) gene, focusing on its role in dopamine metabolism, which is hypothesized to influence personality traits through the dopaminergic system. DNAm status in the promoter region of theMB-COMTgene, was examined to determine its association with personality facets. Preliminary findings suggest a complex interaction betweenMB-COMTDNAm patterns and personality traits. Specific methylation patterns at different CpG sites were linked to varying expressions of traits such as impulsivity and aggression, highlighting the nuanced impact of epigenetics on personality. This study underscores the potential of integrating genetic, epigenetic, and environmental data to enhance our understanding of personality formation. The results contribute to a broader understanding of how genetic predispositions shaped by environmental factors manifest in complex trait differences, paving the way for future research in genetic psychiatry and personalized medicine.
The long-term effects of chemotherapy on normal blood cells
Authors: Mitchell Emily , Pham My H. , Clay Anna , Sanghvi Rashesh , Pietsch Sandra , Hsu Joanne I. , Jung Hyunchul , Vedi Aditi , Moody Sarah , Wang Jingwei , Leonganmornlert Daniel , Chapman Michael Spencer , Williams Nicholas , Dunstone Ellie , Santarsieri Anna , Cagan Alex , Machado Heather E. , Baxter Joanna , Follows George , Hodson Daniel J , McDermott Ultan , Doherty Gary J. , Martincorena Inigo , Humphreys Laura , Mahbubani Krishnaa , Parsy Kourosh Saeb , Takahashi Koichi , Goodell Margaret A. , Kent David , Laurenti Elisa , Campbell Peter J. , Rahbari Raheleh , Nangalia Jyoti , Stratton Michael R.
Published: May 2024

In developed countries, ∼10% of individuals are exposed to systemic chemotherapy for cancer and other diseases. Many chemotherapeutic agents act by increasing DNA damage in cancer cells, triggering cell death. However, there is limited understanding of the extent and long-term consequences of collateral DNA damage to normal tissues. To investigate the impact of chemotherapy on mutation burdens and cell population structure of a normal tissue we sequenced blood cell genomes from 23 individuals, aged 3–80 years, treated with a range of chemotherapy regimens. Substantial additional mutation loads with characteristic mutational signatures were imposed by some chemotherapeutic agents, but there were differences in burden between different classes of agent, different agents of the same class and different blood cell types. Chemotherapy also induced premature changes in the cell population structure of normal blood, similar to those of normal ageing. The results constitute an initial survey of the long-term biological consequences of cytotoxic agents to which a substantial fraction of the population is exposed during the course of their disease management, raising mechanistic questions and highlighting opportunities for mitigation of adverse effects.
Spatial omics of acute myocardial infarction reveals a novel mode of immune cell infiltration
Authors: Wünnemann Florian , Sicklinger Florian , Bestak Kresimir , Nimo Jose , Thiemann Tobias , Amrute Junedh , Nordbeck Mathias , Hartmann Niklas , Ibarra-Arellano Miguel A. , Tanevski Jovan , Heine Clara , Frey Norbert , Lavine Kory J. , Coscia Fabian , Saez-Rodriguez Julio , Leuschner Florian , Schapiro Denis
Published: May 2024

Myocardial infarction (MI) continues to be a leading cause of death worldwide. Even though it is well-established that the complex interplay between different cell types determines the overall healing response after MI, the precise changes in the tissue architecture are still poorly understood. Here we generated an integrative cellular map of the acute phase after murine MI using a combination of imaging-based transcriptomics (Molecular Cartography) and antibody-based highly multiplexed imaging (Sequential Immunofluorescence), which enabled us to evaluate cell-type compositions and changes at subcellular resolution over time. One striking finding of these analyses was the identification of a novel mode of leukocyte accumulation to the infarcted heart via the endocardium - the inner layer of the heart. To investigate the underlying mechanisms driving this previously unknown infiltration route, we performed unbiased spatial proteomic analysis using Deep Visual Proteomics (DVP). When comparing endocardial cells of homeostatic hearts and infarcted hearts, DVP identified von Willebrand Factor (vWF) as an upregulated mediator of inflammation 24 hours post-MI. To further explore the immune mediating capabilities of vWF and its effect on tissue repair, we performed functional blocking of vWF during acute murine MI. This resulted in a reduced amount of infiltration by CCR2+monocytes and worse cardiac function post-MI. Our study provides the first spatial map of acute murine MI with subcellular resolution and subsequently discovers a novel route of immune infiltration. Furthermore, we identified vWF as a critical immune mediating agent for endocardial immune cell infiltration.
Predicted Future Changes in the Mean Seasonal Carbon Cycle Due to Climate Change
Authors: Morichetti Mauro , Vangi Elia , Collalti Alessio
Published: May 2024

Through photosynthesis, forests absorb annually large amounts of atmospheric CO2. However, they also release CO2back through respiration. These two, opposite in sign, large fluxes determine, much of the carbon that is stored or released back to the atmosphere. The mean seasonal cycle (MSC) is an interesting metric that associates phenology and carbon (C) partitioning-allocation analysis within forest stands. Here we applied the 3D-CMCC-FEM model and analyzed its capability to represent the main C-fluxes, by validating the model against observed data, questioning if the sink/source mean seasonality is influenced under two scenarios of climate change, in five contrasting European forest sites. We found the model has, under current climate conditions, robust predictive abilities in estimating NEE. Model results also predict a consistent reduction of the forest’s capabilities to act as a C-sink under climate change and stand-ageing at all sites. Such a reduction is predicted despite the number of annual days of C-sink in evergreen forests increasing over the years, indicating a consistent downward trend. Similarly, deciduous forests, despite maintaining a relatively stable number of C-sink days throughout the year and over the century, show a reduction in their overall annual C-sink capacity. Overall, both types of forests at all sites show a consistent reduction in their future mitigating potential.
One-day phenotypic drug susceptibility testing forMycobacterium tuberculosisvariantbovisBCG using single-cell imaging and a deep neural network
Authors: Tran Buu Minh , Larsson Jimmy , Grip Anastasia , Karempudi Praneeth , Elf Johan
Published: May 2024

Drug-resistant tuberculosis (TB) kills approximately 200,000 people every year. A contributing factor is the slow turnaround time associated with anti-tuberculosis drug susceptibility diagnostics. The prevailing gold standard for phenotypic drug susceptibility testing (pDST) takes at least two weeks. In this study, we usedMycobacterium tuberculosisvariantbovisBCG (M. bovisBCG) andMycobacterium smegmatisas models for tuberculous and nontuberculous pathogens. The bacteria were loaded into a microfluidic chip, trapping them in microchambers, and allowing simultaneous tracking of single-cell growth with and without antibiotic exposure. A deep neural network image-segmentation algorithm was employed to quantify the growth rate over time and determine how the strains responded to the drugs compared to the untreated reference. We determined that the response time of the susceptible strains to isoniazid (INH), ethambutol (EMB), and linezolid (LZD) at MIC was within 3 hours and 1.5 hours forM. bovisBCG andM. smegmatis, respectively. Resistant strains ofM. smegmatiswere identifiable within 3 hours, suggesting that growth-based pDST can be conducted in less than 12 hours for slow-growingM. bovisBCG. The results obtained forM. bovisBCG are most likely comparable to what we expect forM. tuberculosisas these strains share 99.96% genetic identity.
p53 and TIGAR promote redox control to protect against metabolic dysfunction-associated steatohepatitis
Authors: Wittke Celine I , Cheung Eric C , Athineos Dimitris , Clements Nicola , Butler Liam , Hughes Mark , Morrison Vivienne , Watt Dale M , Blyth Karen , Vousden Karen H , Humpton Timothy J
Published: May 2024

TP53is a potent tumour suppressor that coordinates diverse stress response programmes within the cell. The activity of p53 is frequently context and cell type-dependent, and ranges from pro-survival activities, including the implementation of transient cell cycle arrest and metabolic rewiring, through to cell death. In addition to tumour suppressor functions, p53 also has established roles in the pathological response to stress that occurs during tissue damage and repair, including within the liver. Metabolic dysfunction-associated steatohepatitis (MASH) is a major driver of hepatocellular carcinoma (HCC), but our understanding of the molecular determinants of MASH development remains incomplete.

Here, using a p53 reporter mouse, we report early and sustained activation of hepatic p53 in response to an obesogenic high fat and high sugar diet. In this context, liver-specific loss of p53 accelerates the progression of benign fatty liver disease to MASH that is characterised by high levels of reactive oxygen species (ROS), extensive fibrosis, and chronic inflammation. Using anin vitroculture system, we show that p53 functions to control ROS and protect against the development of MASH, in part through induction of the antioxidant gene TP53-induced glycolysis and apoptosis regulator (TIGAR). Our work demonstrates an important role for the p53-TIGAR axis in protecting against MASH, and identifies redox control as an essential barrier against liver disease progression.
Aligning protein generative models with experimental fitness via Direct Preference Optimization
Authors: Widatalla Talal , Rafailov Rafael , Hie Brian
Published: May 2024

Generative models trained on unlabeled protein datasets have demonstrated a remarkable ability to predict some biological functions without any task-specific training data. However, this capability does not extend to all relevant functions and, in many cases, the unsupervised model still underperforms task-specific, supervised baselines. We hypothesize that this is due to a fundamental “alignment gap” in which the rules learned during unsupervised training are not guaranteed to be related to the function of interest. Here, we demonstrate how to provide protein generative models with useful task-specific information without losing the rich, general knowledge learned during pretraining. Using an optimization task called Direct Preference Optimization (DPO), we align a structure-conditioned language model to generate stable protein sequences by encouraging the model to prefer stabilizing over destabilizing variants given a protein backbone structure. Our resulting model, ProteinDPO, is the first structure-conditioned language model preference-optimized to experimental data. ProteinDPO achieves competitive stability prediction and consistently outperforms both unsupervised and finetuned versions of the model. Notably, the aligned model also performs well in domains beyond its training data to enable absolute stability prediction of large proteins and binding affinity prediction of multi-chain complexes, while also enabling single-step stabilization of diverse backbones. These results indicate that ProteinDPO has learned generalizable information from its biophysical alignment data.
Sexual dimorphism in histamine regulation of striatal dopamine
Authors: Van Zandt Meghan , Pittenger Christopher
Published: May 2024

Dopamine modulation of the basal ganglia differs in males and females and is implicated in numerous neuropsychiatric conditions, including some, like Tourette Syndrome (TS) and attention deficit hyperactivity disorder (ADHD), that have marked sex differences in prevalence. Genetic studies in TS and subsequent work in animals suggest that a loss of histamine may contribute to dysregulation of dopamine. Motivated by this, we characterized the modulation of striatal dopamine by histamine, using microdialysis, targeted pharmacology, and siRNA knockdown of histamine receptors. Intracerebroventricular (ICV) histamine reduced striatal dopamine in male mice, replicating previous work. In contrast, and unexpectedly, ICV histamine increased striatal dopamine in females. ICV or targeted infusion of agonists revealed that the effect in males depends on H2R receptors in the substantia nigra pars compacta (SNc). Knockdown of H2R in SNc GABAergic neurons abrogated the effect, identifying these cells as a key locus of histamine’s regulation of dopamine in males. In females, however, H2R had no discernible role; instead, H3R agonists in the striatum increased striatal dopamine. Strikingly, the effect of histamine on dopamine in females was modulated by the estrous cycle, appearing only in estrus/proestrus, when estrogen levels are high. These findings confirm the regulation of striatal dopamine by histamine but identify marked sexual dimorphism in and estrous modulation of this effect. These findings may shed light on the mechanistic underpinnings of sex differences in the striatal circuitry, and in several neuropsychiatric conditions.

Significance Statement

Dysregulation of the basal ganglia contributes to the pathophysiology of numerous neuropsychiatric diseases, including several, such as Tourette syndrome (TS), that are characterized by sex differences. Previous genetic studies in humans identified histamine dysregulation as a potential to the development of TS; follow-up work in mice highlighted the role of histamine in regulating striatal dopamine tone. Striatal dopamine dysregulation has been implicated in numerous neuropsychiatric disorders, including TS, schizophrenia, and attention deficit-hyperactivity disorder. Here, we uncover novel and significant sex differences in histamine regulation of dopaminergic modulation of circuitry in the striatum. A better understanding of these inherent differences can provide insight into the mechanisms underlying sex-dependent outcomes in neuropsychiatric disease.
Compaction of Active Chromatin Domains and Promoters by H3S10 Phosphorylation during Mitosis Preserves Interphase-Specific Chromatin Structure and Function
Authors: Meel Sweety , Mishra Sachin , Mann Rajat , Najar Arif Hussain , Singh Anurag Kumar , Notani Dimple
Published: May 2024

Mitotic chromosomes lose interphase-specific genome organization and transcription but gain histone phosphorylation, specifically H3S10p. This phosphorylation event compacts chromosomes in early mitosis by reducing inter-nucleosomal distance before the loading of condensins. However, it is unclear if H3S10p in mitosis preserves the identity of lost chromatin domains and promoters, both physically and functionally. Here, using the pre- mitotic expression of histone H3S10 and its mutants H3S10A and H3S10D, we show that H3S10p hyper-phosphorylates active promoters and spreads into super-domains A in mitosis, causing compaction of these regions. By spreading into active domains in the absence of genome organization, H3S10p retains their identity physically. Functionally, H3S10p ensures optimal closing of promoters by stabilizing the nucleosomes, thereby protecting them from excess loading of transcription machinery post-mitosis. In the H3S10p phospho-mutants, these chromatin regions fail to condense properly during mitosis. As a result, they exhibit enhanced accessibility and transcription of active genes in the next interphase. We propose that the spreading of mitotic H3S10p into active domains preserves their identity during mitosis and, in subsequent interphase, acts as a rheostat to fine-tune transcription and chromatin domain re-formation.
MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge
Authors: Wade Kristen J. , Suseno Rayo , Kizer Kerry , Williams Jacqueline , Boquett Juliano , Caillier Stacy , Pollock Nicholas R. , Renschen Adam , Santaniello Adam , Oksenberg Jorge R. , Norman Paul J. , Augusto Danillo G. , Hollenbach Jill A.
Published: May 2024

The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short readde novoassembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target-capture short read data in large, population cohorts. To-date, no other self-contained tool exists for the generation ofde novoMHC assemblies from short read data. MHConstructor facilitates wide-spread access to high quality, alignment-free MHC sequence analysis.
Profiling Antibiotic Resistance Determinants in Ancient Permafrost Microbiomes
Authors: Gomathinayagam Sankaranarayanan , Muthukaliannan Gothandam Kodiveri
Published: May 2024

Antimicrobial resistance presents a formidable challenge, yet its existence predates the introduction of antibiotics. Our study delves into the presence of antimicrobial resistance determinants (ARDs) in ancient permafrost microbiomes, comparing them with contemporary soil and pristine environments. Majority of the samples are from regions around Beringia, encompassing parts of Russia and Alaska, with only one sample originating from the Tien Shan Mountain range in Kyrgyzstan. From over 2.3 tera base pairs of raw metagenomic data, we assembled about 1.3 billion metagenomic contigs and explored the prevalence of ARDs in them. Our findings reveal a diverse array of ARDs in ancient microbiomes, akin to contemporary counterparts. On average, we identified 2 ARDs per ribosomal protein gene in ancient samples.Actinomycetota, Bacillota, and several thermophiles were prominent carriers of ARDs in Chukochi and Kamchatkan samples. Conversely, ancient permafrost from the Tien Shan Mountain range exhibited no Thermophiles orActinomycetotacarrying ARDs. Both ancient and contemporary microbiomes showcased numerous divergent ARDs, with approximately 40% identity to genes in antibiotic resistance gene databases. Antibiotic inactivation-type ARDs exhibited purifying selection with contemporary resistance genes, as estimated by dN/dS ratio. Importantly, we retrieved 359 putative complete viruses from ancient microbiomes and none of them harboured any ARDs.
Cellular cruise control: energy expenditure as a regulator of collective migration in epithelia
Authors: Breinyn Isaac B. , Martina-Perez Simon F. , Baker Ruth E. , Cohen Daniel J.
Published: May 2024

Epithelial migration is implicit in processes ranging from gastrula development to the healing of skin, and involves the coordinated motion, force production, and resulting energy expenditure of thousands of constitutive cells. However, the spatiotemporal patterning and regulation of energy expenditure during epithelial migration remains poorly understood. Here, we propose a continuum mechan-ics framework and use it to explore how energy expenditure regulates epithelial migration. We use canonical mechanical metrics such as force, work and power to define what it means for a tissue to migrate ‘efficiently’ and show that freely expanding epithelia actively regulate themselves to operate within a maximally efficient regime. We then leverage electrotaxis (directed motion in response to an externally applied electric field) as a tool to study non-homeostatic migra-tion using this new framework. We show that regulation of migration is robust to external cues and acts to to attenuate a tissues response to stimuli.
Label-Free Electrochemical Imaging of Single Extracellular Vesicles
Authors: Zhang Yuanxin , Hong Zichen , Fu Xuan , Yao Bo , Ma Guangzhong
Published: May 2024

Extracellular vesicles (EVs) are pivotal in various biological processes and diseases, yet their small size and heterogeneity pose challenges for single EV quantification. We introduce interferometric electrochemical microscopy (iECM), a sensitive label-free technique that combines interferometric scattering and electrochemical impedance imaging. This method enables the quantification of the impedance of single EVs, providing unique insights into their electrochemical properties, and allows for the simultaneous measurement of size and real-time monitoring of antibody binding. Notably, we discovered that the impedance spectra of EVs can serve as unique fingerprints to differentiate EVs from cancerous and healthy cells, offering potential advancements in clinical diagnostics and the profiling of extracellular biomarkers.
IK channel confers fine-tuning of rod bipolar cell excitation and synaptic transmission in the retina
Authors: Park Yong Soo , Sung Ki-Wug , Kim In-Beom
Published: May 2024

During retinal visual processing, rod bipolar cells (RBCs) transfer scotopic signals from rods to AII amacrine cells as second-order neurons. Elucidation of the RBC excitation/inhibition is essential for understanding the visual signal transmission. Although excitation and extrinsic inhibitory mechanisms have been studied, intrinsic inhibitory mechanisms remain unclear. We focused on RBC’s prominent K+current, which exhibits voltage and Ca2+dependence. We isolated and confirmed intermediate-conductance Ca2+-activated K+channels (IK) and in RBCs using the patch-clamp method with IK inhibitors (clotrimazole and TRAM34). The regulation of the IK current primarily relies on Ca2+influx via low-threshold Ca2+channels during RBC excitation. It mediates RBC repolarization and oscillation, enabling fast and transient synaptic transmission to AII amacrine cells. Our findings highlight the unique role of the IK channel in RBC, suggesting that it plays a critical role in the scotopic pathway by fine-tuning RBC activity.
Developmental regulators drive DUX4 expression in facioscapulohumeral muscular dystrophy
Authors: Fox Amelia , Oliva Jonathan , Vangipurapu Rajanikanth , Sverdrup Francis M.
Published: May 2024

Facioscapulohumeral muscular dystrophy (FSHD) is a progressive muscle wasting disease caused by misexpression of the Double Homeobox 4 (DUX4) transcription factor in skeletal muscle. While epigenetic derepression of D4Z4 macrosatellite repeats is recognized to cause DUX4 misexpression in FSHD, the factors promotingDUX4transcription are unknown. Here, we show that SIX (sine oculis) transcription factors, critical during embryonic development, muscle differentiation, regeneration and homeostasis, are key regulators ofDUX4expression in FSHD muscle cells. In this study, we demonstrate SIX1, SIX2, and SIX4 to be necessary for induction ofDUX4transcription in differentiating FSHD myotubesin vitro, with SIX1 and SIX2 being the most critical in drivingDUX4expression. Interestingly, DUX4 downregulatesSIXRNA levels, suggesting negative feedback regulation. Our findings highlight the involvement of SIX transcription factors in driving the pathogenesis of FSHD by promotingDUX4and DUX4 target gene expression.

Teaser

We identified a family of developmental regulators that promote aberrantDUX4expression in FSHD differentiating muscle cells.