bluuebunny/crossref_metadata_2025 huggingface dataset:
Pathogenic soluble tau peptide disrupts endothelial calcium signaling and vasodilation in the brain microvasculature
Authors: Freeman Kalev , Sackheim Adrian M , Mughal Amreen , Koide Masayo , Bonson Grace , Ebner Grace , Hennig Grant , Lockette Warren , Nelson Mark T
Published: August 2023

The accumulation of the microtubule-associated tau protein in and around blood vessels contributes to brain microvascular dysfunction through mechanisms that are incompletely understood. Delivery of nutrients to active neurons in the brain relies on capillary inositol 1,4,5-triphosphate receptor (IP3R)–mediated calcium (Ca2+) signals to direct blood flow. The initiation and amplification of endothelial cell IP3R-mediated Ca2+signals requires an intact microtubule cytoskeleton. Since tau accumulation in endothelial cells disrupts native microtubule stability, we reasoned that tau-induced microtubule destabilization would impair endothelial IP3-evoked Ca2+signaling. We tested the hypothesis that tau disrupts the regulation of local cerebral blood flow by reducing endothelial cell Ca2+signals and endothelial-dependent vasodilation. We used a pathogenic soluble tau peptide (T-peptide) model of tau aggregation and mice with genetically encoded endothelial Ca2+sensors to measure cerebrovascular endothelial responses to tau exposure. T-peptide significantly attenuated endothelial Ca2+activity and cortical capillary blood flowin vivowithin 120 seconds. Further, T-peptide application constricted pressurized cerebral arteries and inhibited endothelium-dependent vasodilation. This study demonstrates that pathogenic tau alters cerebrovascular function through direct attenuation of endothelial Ca2+signaling and endothelium-dependent vasodilation.
The discovery of mixed colonies inTemnothoraxants supports the territoriality hypothesis of dulotic social parasite evolution in myrmicine ants
Authors: Bengston Sarah , Dornhaus Anna , Rabeling Christian
Published: August 2023

Social parasitism, where one social species parasitically depends on the other for survival and reproduction, is a highly successful life history strategy, especially in the eusocial Hymenoptera. In ants alone, more 400 species of socially parasitic species exist and multiple forms of social parasitism evolved independently and convergently. Yet disentangling the evolutionary history of obligate social parasitism is challenging. Identifying species that inform the transition from eusocial toward socially parasitic behavior is crucial for understanding the underlying co-evolutionary processes. Here, we report the first case of mixed colonies involving four predominantly free-livingTemnothoraxant species from the western United States. ThreeTemnothoraxspecies supplement their worker force with brood from the nests of their four congeners. We suggest, based on these observations and other published evidence, that this facultative dulotic behavior may have resulted from territorial contests due to limited nest sites. Socially parasitic behavior is not present in all populations across the species distribution ranges, however in populations where this behavior was observed, it is also associated with significant increases in interspecific aggression. These four species of Western USTemnothoraxants represent a particularly interesting case of social parasitism, because the presence of between-population behavioral variation provides a powerful system to test hypotheses about the ecological and behavioral conditions underlying the evolutionary transition from eusocial to socially parasitic behavior.
Aptamer-antibody chimera sensors for sensitive, rapid and reversible molecular detection in complex samples
Authors: Kong Dehui , Maganzini Nicolo , Thompson Ian A.P. , Eisenstein Michael , Soh H. Tom
Published: August 2023

The development of receptors suitable for the continuous detection of analytes in complex, interferent-rich samples remains challenging. Antibodies are highly sensitive but difficult to engineer in order to introduce signaling functionality, while aptamer switches are easy to construct but often yield only modest target sensitivity. We present here the programmable antibody and DNA aptamer switch (PANDAS), which combines the best features of both systems by using a nucleic acid tether to link an analyte-specific antibody to an internal strand-displacement (ISD)-based aptamer switch that recognizes the same target. The monoclonal antibody mediates initial analyte binding due to its higher affinity; the resulting increase in local analyte concentration then leads to cooperative binding and signaling by the ISD switch. We developed a PANDAS sensor for the clotting protein thrombin and show that this design achieves 100-fold enhanced sensitivity compared to using an aptamer alone. This design also exhibits reversible binding, enabling repeated measurements with temporal resolution of ∼10 minutes, and retains excellent sensitivity even in interferent-rich samples. With future development, this PANDAS approach could enable the adaptation of existing protein-binding aptamers with modest affinity into sensors that deliver excellent sensitivity and minute-scale resolution in minimally prepared biological specimens.
Generalization of procedural motor sequence learning after a single practice trial
Authors: Johnson B.P. , Iturrate I. , Fakhreddine R.Y. , Bönstrup M. , Buch E.R. , Robertson E.M. , Cohen L.G.
Published: August 2023

When humans begin learning new motor skills, they typically display early rapid performance improvements. It is not well understood how knowledge acquired during this early skill learning period generalizes to new, related skills. Here, we addressed this question by investigating factors influencing generalization of early learning from a skill A to a different, but related skill B. Early skill generalization was tested over four experiments (N = 2,095). Subjects successively learned two related motor sequence skills (skills A and B) over different practice schedules. Skill A and B sequences shared ordinal (i.e. – matching keypress locations), transitional (i.e. – ordered keypress pairs), parsing rule (i.e., distinct sequence events like repeated keypresses that can be used as a breakpoint for segmenting the sequence into smaller units) structures, or possessed no structure similarities. Results showed generalization for shared parsing rule structure between skills A and B after only a single 10-second practice trial of skill A. Manipulating the initial practice exposure to skill A (1 to 12 trials) and inter-practice rest interval (0 to 30s) between skills A and B had no impact on parsing rule structure generalization. Furthermore, this generalization was not explained by stronger sensorimotor mapping between individual keypress actions and their symbolic representations. In contrast, learning from skill A did not generalize to skill B during early learning when the sequences shared only ordinal or transitional structure features. These results document sequence structure that can be very rapidly generalized during initial learning to facilitate generalization of skill.
Interferon response and epigenetic modulation bySMARCA4mutations drive ovarian tumor immunogenicity
Authors: Brodeur Melica Nourmoussavi , Dopeso Higinio , Zhu Yingjie , Longhini Ana Leda F. , Gazzo Andrea , Sun Siyu , Koche Richard , Qu Rui , Hamard Pierre-Jacques , Bykov Yonina , Green Hunter , Chiappinelli Katherine B. , Ozsoy Melih Arda , Basili Thais , Gardner Rui , Walderich Sven , DeStanchina Elisa , Greenbaum Benjamin , Gönen Mithat , Weigelt Britta , Zamarin Dmitriy
Published: August 2023

Cell-intrinsic mechanisms of immunogenicity in ovarian cancer (OC) are not well understood. The presence of damaging mutations in the SWI/SNF chromatin remodeling complex, such as theSMARCA4(BRG1) catalytic subunit, has been associated with improved response to ICB, however the mechanism by which this occurs is unclear. The aim of this current study was to examine the alterations in tumor cell-intrinsic and extrinsic immune signaling caused bySMARCA4loss. Using OC models with loss-of-function mutations inSMARCA4, we found thatSMARCA4loss resulted in increased cancer cell-intrinsic immunogenicity, characterized by upregulation of long-terminal RNA repeats such as endogenous retroviruses, increased expression of interferon-stimulated genes, and upregulation of antigen presentation machinery. Notably, this response was dependent on IRF3 signaling, but was independent of the type I interferon receptor. Mice inoculated with cancer cells bearingSMARCA4loss demonstrated increased activation of cytotoxic T cells and NK cells in the tumor microenvironment as well as increased infiltration with activated dendritic cells. These results were recapitulated when animals bearingSMARCA4-proficient tumors were treated with a BRG1 inhibitor, suggesting that modulation of chromatin remodeling through targetingSMARCA4may serve as a strategy to reverse immune evasion in OC.
Parvalbumin and somatostatin: biomarkers for two parallel tectothalamic pathways in the auditory midbrain
Authors: Liu Mengting , Gao Yixiao , Xin Fengyuan , Hu Ying , Wang Tao , Xie Fenghua , Li Tianyu , Wang Ningyu , Yuan Kexin
Published: August 2023

The inferior colliculus (IC) represents a crucial relay station in the auditory pathway, located in the midbrain’s tectum and primarily projecting to the thalamus. Despite the identification of distinct cell types based on various biomarkers in the IC, their specific contributions to the organization of auditory tectothalamic pathways have remained poorly understood. In this study, we demonstrate that IC neurons expressing parvalbumin (ICPV+) or somatostatin (ICSOM+) represent major, non-overlapping cell types throughout the three IC subdivisions. Strikingly, regardless of their location within the IC, these neurons predominantly project to the primary and secondary auditory thalamic nuclei, respectively. Retrograde tracing data specific to cell types indicate that ICPV+neurons primarily receive auditory inputs, whereas ICSOM+neurons integrate polymodal inputs that hold behavioral significance. Furthermore, ICPV+neurons exhibit significant heterogeneity in both intrinsic electrophysiological properties and presynaptic terminal size compared to ICSOM+neurons. Notably, approximately one quarter of ICPV+neurons are inhibitory neurons, whereas all ICSOM+neurons are excitatory neurons. Collectively, our findings suggest that parvalbumin and somatostatin expression in the IC can serve as biomarkers for two functionally distinct, parallel tectothalamic pathways. This discovery challenges the conventional IC subdivision-based definition of tectothalamic pathways and calls for a reassessment of their functional roles.
COUP-TFII regulates early bipotential gonad signaling and commitment to ovarian progenitors
Authors: Ferreira Lucas G. A. , Kizys Marina M. L. , Gama Gabriel A. C. , Pachernegg Svenja , Robevska Gorjana , Sinclair Andrew H. , Ayers Katie L. , da Silva Magnus R. Dias
Published: August 2023

The absence of expression of the Y-chromosome linked testis-determining geneSRYin early supporting gonadal cells (ESGC) of bipotential gonads leads to ovarian development. However, genetic variants inNR2F2/COUP-TFII represent a novel cause ofSRY-negative 46,XX testicular/ovotesticular differences of sex development (T/OT-DSD). Thus, we hy-pothesized that COUP-TFII is part of the ovarian developmental network. We examinedNR2F2/COUP-TFII expression and the genetic network under its regulation in human gonadal cells by analyzing single cell RNA-sequencing datasets of fetal gonads, differentiating induced pluripotent stem cells into bipotential gonad-like cellsin vitro, and generating aNR2F2knockout (KO) in the human granulosa-like cell line COV434.NR2F2expression is highly upregulated during the bipotential gonad development, being detected in ESGCs. We identified thatNR2F2ablation in COV434 cells downregulated markers of ESGC and pre-granulosa cells, suggesting that COUP-TFII has a role in maintaining a multipotent state necessary for commitment to the ovarian development. We propose that impairment of COUP-TFII function may disrupt the transcriptional plasticity of ESGCs and instead drive them into commitment to the testicular pathway.
Characteristics and Attitudes of Wearable Device Users and Non-Users in a Large Healthcare System
Authors: Venn Rachael A. , Khurshid Shaan , Grayson Mia , Ashburner Jeffrey M. , Al-Alusi Mostafa A. , Chang Yuchiao , Foulkes Andrea , Ellinor Patrick T. , McManus David D. , Singer Daniel E. , Atlas Steven J. , Lubitz Steven A.
Published: August 2023

Introduction

Consumer wearable devices with health and wellness features are increasingly common and may enhance prevention and management of cardiovascular disease. However, the characteristics and attitudes of wearable device users versus non-users are poorly understood.

Methods

Wearable Activity Tracking for Comprehensive Healthcare-Integrated Technology (WATCH-IT) was a prospective study of adults aged ≥18 years receiving longitudinal primary or ambulatory cardiovascular care at one of eleven hospitals within the Mass General Brigham multi-institutional healthcare system between January 2010-July 2021. We invited patients, including wearable users and non-users, to participate via an electronic patient portal. Participants were asked to complete a 20-question survey regarding perceptions and use of consumer wearable devices. Responses were linked to electronic health record data. Multivariable logistic regression was used to identify factors associated with device use.

Results

Among 280,834 individuals receiving longitudinal primary or cardiovascular care, 65,842 did not have an active electronic portal or opted out of research contact. Of the 214,992 individuals sent a survey link, 11,121 responded (5.2%), comprising the WATCH-IT patient sample. Most respondents (55.8%) reported current use of a wearable device, and most non-users (95.3%) reported they would use a wearable device if provided at no cost. Although most users (70.2%) had not shared device data with their doctor previously, the majority believed it would be very (20.4%) or moderately (34.4%) important to share device-related health information with providers. In multivariable models, older age (odds ratio [OR] 0.80 per 10-year increase, 95% CI 0.77-0.82), male sex (0.87, 95% CI 0.80-0.95), and heart failure (0.75, 95% CI 0.63-0.89) were associated with lower odds of wearable device use, whereas higher median zip code income (1.08 per 1-quartile increase, 95% CI 1.04-1.12) and care in a cardiovascular medicine clinic (1.17, 95% CI 1.05-1.30) were associated with greater odds of device use. Nearly all respondents (98%) stated they would share device data with researchers studying health outcomes.

Conclusions

Within an electronically assembled cohort of patients in primary and cardiovascular medicine clinics with linkage to detailed health records, wearable device use is common. Most users perceive value in wearable data. Our platform may enable future study of the relationships between wearable technology and resource utilization, clinical outcomes, and health disparities.
Deviation from Personalized Blood Pressure Targets Correlates with Worse Outcome after Successful Recanalization
Authors: Zhang Zhe , Pu Yuehua , Yu Lei , Bai Haiwei , Duan Wanying , Liu Xin , Liu Jingyi , Zheng Lina , Hu Xiao , Leng Xinyi , Pan Yuesong , Petersen Nils H. , Liu Liping
Published: August 2023

Background

Personalized blood pressure (BP) management for acute ischemic stroke patients after successful recanalization lacks evidence. Our study aimed to investigate whether the deviation of BP from cerebral autoregulation (CA) limits, either in duration or burden, is associated with worse outcomes.

Methods

We prospectively enrolled patients with acute large anterior circulation artery occlusive stroke who had achieved successful recanalization (mTICI 2b-3). CA was determined by measuring mean velocity index (Mx) using transcranial Doppler sonography (TCD). We calculated the percent time and the burden (defined as the time-BP area) with BP outside the CA limits of each subject within 48 hours after recanalization. The outcomes included unfavorable functional outcome (mRS scored 3-6) at 90 days, early neurological deterioration (END), infarct volume growth at 7 days, and symptomatic intracranial hemorrhage (sICH) within 48 hours.

Results

A total of 91 patients were enrolled. Entire failure of autoregulation was found in 31.9% (29 / 91) of patients. The burden with BP outside the CA limits was associated with poor functional outcome at 90 days (aORper 100 h·mmHg 1.29 [95% CI, 1.05 – 1.59]P=0.018). Both the percent time and the burden with BP out of the CA limits was correlated with END (aORper 10% time 1.38 [95% CI, 1.05 – 1.83]P=0.022, aORper 100h·mmHg 1.22 [95% CI, 1.01 – 1.48]P=0.039). The burden of BP that decreased below the CA lower limit was associated with infarct volume growth (adjustedβper 100 h·mmHg 5.47 [95% CI, 0.13 – 10.80]P=0.045). The percent time that BP exceeded the CA upper limit was associated with sICH (aORper 10% time 1.45 [95% CI, 1.01 – 2.07]P=0.043).

Conclusions

Both the percent time and burden of BP that deviates from the autoregulation-preserved range correlate with worse outcomes after successful recanalization. Further randomized control trials are warranted to examine the effectiveness of autoregulation-guided BP targets.
Comparative Immunogenicity, Safety and Efficacy Profiles of four COVID-19 Vaccine types in healthy adults: Systematic Review cum Meta-analysis of Clinical Trial data
Authors: Yoong Si Qi , Bhowmik Priyanka , Dutta Debprasad
Published: August 2023

Four principal types of authorised COVID-19 vaccines include inactivated whole-virus vaccines, protein subunit vaccines, viral-vector vaccines and nucleic acid (mRNA and DNA) vaccines. Despite numerous Randomised Controlled Trials (RCTs), comprehensive systematic review and comparative meta-analysis have not been performed to validate the immunogenicity, safety and efficacy of COVID-19 vaccines in the healthy adult population. We aim to fulfil this unmet void. We searched for peer-reviewed articles about RCTs of the COVID-19 vaccines on healthy adults (18-64 years) available in eight major bibliographic databases (PubMed, EMBASE, Web of Science, Cochrane Library, Scopus, ScienceDirect, POPLINE, HINARI) till August 28, 2022. The Risk of Bias (RoB) was assessed using the Cochrane RoB-2. Random effects meta-analysis was conducted by pooling dichotomous outcomes using risk ratios (safety outcomes) and continuous outcomes using standardised mean differences (immunogenicity outcomes). Efficacy outcomes were summarised narratively. Moderate to high-quality evidence suggests that those receiving COVID-19 vaccines had significantly higher immune responses compared to placebo. Serious adverse events were rare, confirming that COVID-19 vaccines were safe and immunogenic for the healthy adult population. Remarkably, adverse events were the least common in inactivated vaccines, and nucleic acid vaccines were the most immunogenic. The efficacies of COVID-19 vaccines ranged from 21.9% to 95.9% in preventing COVID-19. We endorse all four types of COVID-19 vaccines for public health policy implementing taskforces. Yet, meta-analyses based on individual patient data are warranted for more extensive measurement of differential impacts of COVID-19 vaccines on different genders, ethnicities, comorbidities and types of vaccine jabbed.
Computational inference of eIF4F complex function and structure in human cancers
Authors: Wu Su , Wagner Gerhard
Published: August 2023

The canonical eukaryotic initiation factor 4F (eIF4F) complex, composed of eIF4G1, eIF4A1, and the cap-binding protein eIF4E, plays a crucial role in cap-dependent translation initiation in eukaryotic cells (1). However, cap-independent initiation can occur through internal ribosomal entry sites (IRESs), involving only eIF4G1 and eIF4A1 present, which is considered to be a complementary process to cap-dependent initiation in tumors under stress conditions (2). The selection and molecular mechanism of specific translation initiation in human cancers remains poorly understood. Thus, we analyzed gene copy number variations (CNVs) in TCGA tumor samples and found frequent amplification of genes involved in translation initiation. Copy number gains inEIF4G1andEIF3Efrequently co-occur across human cancers. Additionally,EIF4G1expression strongly correlates with genes from cancer cell survival pathways including cell cycle and lipogenesis, in tumors withEIF4G1amplification or duplication. Furthermore, we revealed that eIF4G1 and eIF4A1 protein levels strongly co-regulate with ribosomal subunits, eIF2, and eIF3 complexes, while eIF4E co-regulates with 4E-BP1, ubiquitination, and ESCRT proteins. Using Alphafold predictions, we modeled the eIF4F structure with and without eIF4G1-eIF4E binding. The modeling for cap-dependent initiation suggests that eIF4G1 interacts with eIF4E through its N-terminal eIF4E-binding domain, bringing eIF4E near the eIF4A1 mRNA binding cavity and closing the cavity with both eIF4G1 HEAT-2 domain and eIF4E. In the cap-independent mechanism, α-helix5of eIF4G1 HEAT-2 domain instead directly interacts with the eIF4A1 N-terminal domain to close the mRNA binding cavity without eIF4E involvement, resulting in a stronger interaction between eIF4G1 and eIF4A1.

Significance Statement

Translation initiation is primarily governed by eIF4F, employing a “cap-dependent” mechanism, but eIF4F dysregulation may lead to a “cap-independent” mechanism in stressed cancer cells. We found frequent amplification of translation initiation genes, and co-occurring copy number gains ofEIF4G1andEIF3Egenes in human cancers.EIF4G1amplification or duplication may be positively selected for its beneficial impact on the overexpression of cancer survival genes. The co-regulation of eIF4G1 and eIF4A1, distinctly from eIF4E, reveals eIF4F dysregulation favoring cap-independent initiation. Alphafold predicts changes in the eIF4F complex assembly to accommodate both initiation mechanisms. These findings have significant implications for evaluating cancer cell vulnerability to eIF4F inhibition and developing treatments that target cancer cells with dependency on the translation initiation mechanism.
Additive Manufacturing Leveraged Microfluidic Setup for Sample to Answer Colorimetric Detection of Pathogens
Authors: Yedire Sripadh Guptha , Hosseini Imman Isaac , Shieh Hamed , Jahromi Arash Khorrami , AbdelFatah Tamer , Jalali Mahsa , Mahshid Sara
Published: August 2023

Colorimetric readout for the detection of infectious diseases is gaining traction at the point of care/need owing to its ease of analysis and interpretation, and integration potential with highly specific Loop-mediated amplification (LAMP) assays. However, coupling colorimetric readout with LAMP is rife with challenges including, rapidity, inter-user variability, colorimetric signal quantification, and user involvement in sequential steps of the LAMP assay, hindering its application. To address these challenges, for the first time, we propose a remotely smartphone-operated automated setup consisting of (i) an additively manufactured microfluidic cartridge, (ii) a portable reflected-light imaging setup with controlled epi-illumination (PRICE) module, and (iii) a control and data analysis module. The microfluidic cartridge facilitates sample collection, lysis, mixing of amplification reagents stored on-chip, and subsequent isothermal heating for initiation of amplification in a novel way by employing tunable elastomeric chambers and auxiliary components (heaters and linear actuators). PRICE offers a new imaging setup that captures the colorimetric change of the amplification media over a plasmonic nanostructured substrate in a controlled and noise-free environment for rapid minute-scale nucleic acid detection. The control and data analysis module employs microprocessors to automate cartridge operation in tandem with the imaging module. The different device components were characterized individually and finally, as a proof of concept, SARS-CoV-2 wild-type RNA was detected with a turnaround time of 13 minutes, showing the device’s clinical feasibility. The suggested automated device can be adopted in future iterations for other detection and molecular assays that require sequential fluid handling steps.
Spontaneous Mutation in2310061I04RikResults in Reduced Expression of Mitochondrial Genes and Impaired Brain Myelination
Authors: Tsitsikov Erdyni N. , Phan Khanh P. , Liu Yufeng , Tsytsykova Alla V. , Paterno Rosalia , Sherry David M. , Johnson Anthony C. , Dunn Ian F.
Published: August 2023

Here, we describe a spontaneous mouse mutant with a deletion in a predicted gene2310061I04Rik(Rik) of unknown function located on chromosome 17. A 59 base pair long deletion occurred in the first intron of theRikgene and disrupted its expression.Riknullmice were born healthy and appeared anatomically normal up to two weeks of age. After that, these mice showed inhibited growth, ataxic gait, and died shortly after postnatal day 24 (P24). Transcriptome analysis at P14 and P23 revealed significantly reduced expression of mitochondrial genes inRiknullbrains compared to wild type controls includingmt-Nd4,mt-Cytb,mt-Nd2,mt-Co1,mt-Atp6,and others. Similarly, genes specific for myelinating oligodendrocytes also showed reduced expression in P23Riknullbrains compared to controls. Histological examination of anterior thalamic nuclei demonstrated decreased myelination of anteroventral nuclei but not of anterodorsal nuclei in P23Riknullmice. Myelination of the anterior commissure was also impaired and displayed extensive vacuolation. Consistent with these findings, immunohistochemistry showed reduced expression of Opalin, a glycoprotein expressed in differentiated oligodendrocytes. Taken together, these results suggest that RIK is important for oligodendrocyte maturation, and myelination in the developing brain.
One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes
Authors: Ye Zilu , Sabatier Pierre , Martin-Gonzalez Javier , Eguchi Akihiro , Bekker-Jensen Dorte B. , Bache Nicolai , Olsen Jesper V.
Published: August 2023

We present One-Tip, a lossless proteomics methodology that seamlessly combines swift, one-pot sample preparation with narrow-window data-independent acquisition mass spectrometric analysis. With simplest sample processing, One-Tip reproducibly identifies > 9,000 proteins from ∼1000 cells and ∼ 6,000 proteins in a single mouse zygote with a throughput of 40 samples-per-day. This easy-to-use method expands capabilities of proteomics research by enabling greater depth, scalability and throughput covering low to high input samples.
DNA end sensing and cleavage by the Shedu anti-phage defense system
Authors: Loeff Luuk , Walter Alexander , Rosalen Gian Tizio , Jinek Martin
Published: August 2023

The detection of molecular patterns associated with invading pathogens is a hallmark of innate immune systems. Prokaryotes deploy sophisticated host-defense mechanisms in innate anti-phage immunity. Shedu is a single-component defense system comprising a putative nuclease SduA. Here we report cryo-EM structures of apo- and dsDNA-bound tetrameric SduA assemblies, revealing that the N-terminal domains of SduA form a clamp that recognizes free DNA ends. End binding positions the DNA over the PD/ExK nuclease domain, resulting in dsDNA nicking at a fixed distance from the 5’ end. The end-directed DNA nicking activity of Shedu prevents propagation of linear DNAin vivo. Finally, we show that phages escape Shedu immunity by suppressing their recombination-dependent DNA replication pathway. Taken together, these results define the antiviral mechanism of Shedu systems, underlining the paradigm that recognition of pathogen-specific nucleic acid structures is a conserved feature of innate immunity across all domains of life.
Sphingolipid metabolism is spatially regulated in the developing embryo bySOXEgenes
Authors: Piacentino Michael L. , Fasse Aria J. , Camacho-Avila Alexis , Grabylnikov Ilya , Bronner Marianne E.
Published: August 2023

During epithelial-to-mesenchymal transition (EMT), significant rearrangements occur in plasma membrane protein and lipid content that are important for membrane function and acquisition of cell motility. To gain insight into how neural crest cells regulate their lipid content at the transcriptional level during EMT, here we identify critical enhancer sequences that regulate the expression ofSMPD3, a gene responsible for sphingomyelin hydrolysis to produce ceramide, which is necessary for neural crest EMT. We uncovered three enhancer regions within the first intron of theSMPD3locus that drive reporter expression in distinct spatial and temporal domains, together collectively recapitulating the expression domains of endogenousSMPD3within the ectodermal lineages. We further dissected one enhancer that is specifically active in the migrating neural crest. By mutating putative transcriptional input sites or knocking down upstream regulators, we find that the SoxE-family transcription factors Sox9 and Sox10 regulate the expression ofSMPD3in migrating neural crest cells. Together these results shed light on how core components of developmental gene regulatory networks interact with metabolic effector genes to control changes in membrane lipid content.

Highlights

SMPD3is expressed in the neural tube, neural crest, and notochord during early development

SMPD3expression is regulated by at least three intronic enhancers

Sox10 and its binding sites are required for expression by a migratory neural crest-specificSMPD3enhancer

Sox10 is a positive regulator of endogenousSMPD3expression during neural crest migration
Metal Ions Guide the Production of Silkworm Fibers
Authors: Brookstein Ori , Shimoni Eyal , Eliaz Dror , Kaplan-Ashiri Ifat , Carmel Itay , Shimanovich Ulyana
Published: August 2023

Silk fibers’ unique mechanical properties have made them a desirable material for various applications, from medical to optical materials and even in sensing. Yet, to date, no synthetic method has come close to reproducing this remarkably strong biomaterial due to the complexity and insufficient understanding of the mechanism of silk fiber formation. While ions are known to play a key role in the production of natural silk fiber, how they do so has thus far eluded discovery. Here we report that a broad composition of metal ions guides structural transformations in the silk fibroin protein inside the silkworm silk gland. By using a combination of cryo-electron microscopy techniques coupled with elemental analysis, we followed the changes in the composition and spatial localization of metal ions inside the silk gland. We observed that ions are homogenously dispersed during the initial stages of silk secretion and storage inside the silk gland, but once the fibers are spun, the ions delocalize from the silk fibroin fiber core to the sericin coating gum layer. This shift in ion localization is accompanied by the alignment of protein chains and an increase in silk feedstock viscosity inside the silk gland - changes that make the protein more sensitive to shear and enable the initiation of the liquid-to-solid transition in the silk. Moreover, the selective doping of the spun silk fibers with metal ions modifies their mechanical performance. These findings highlight the importance and the dynamic role of metal ions in the evolution of silk fibers’ mechanical properties, enhance our understanding of the mechanism of silk fiber formation, and lay the foundations for developing new concepts in biomaterial design.
The PP1 phosphatase exhibits pleiotropic roles controlling both the tachyzoite cell cycle and amylopectin-steady state levels inToxoplasma gondii
Authors: Khelifa Asma Sarah , Boissavy Tom , Mouveaux Thomas , Araujo Silva Tatiana , Chhuon Cerina , Attias Marcia , Guerrera Ida Chiara , De Souza Wanderley , Dauvillee David , Roger Emmanuel , Gissot Mathieu
Published: August 2023

Virulence of apicomplexan parasites is based on their ability to divide rapidly to produce significant biomass. The regulation of their cell-cycle is therefore key to their pathogenesis. Phosphorylation is a crucial post-transcriptional modification that regulates many aspects of the eucaryotic cell cycle. The phosphatase PP1 is known to play a major role in the phosphorylation balance in eukaryotes. We explored the role of TgPP1 during the cell cycle of the tachyzoite form of the apicomplexan parasiteToxoplasma gondii. Using a conditional mutant strain, we show that TgPP1 regulates many aspects of the cell cycle including the proper assembly of the daughter cells inner membrane complex (IMC), the segregation of organelles and nuclear division. Unexpectedly, depletion of TgPP1 also results in the accumulation of amylopectin, a storage polysaccharide that is normally found in the latent bradyzoite form of the parasite. Using transcriptomics and phosphoproteomics, we show that TgPP1 mainly acts through post-transcriptional mechanisms by dephosphorylating target proteins including IMC proteins. TgPP1 also dephosphorylate a protein bearing a starch binding domain. Mutagenesis analysis reveals that the targeted phospho-sites are linked to the ability of the parasite to regulate amylopectin steady-state levels. Therefore, we show that TgPP1 has pleiotropic roles during the tachyzoite cell cycle regulation, but also regulates amylopectin accumulation.
Nucleolar stress caused by arginine-rich peptides triggers a ribosomopathy and accelerates ageing in mice
Authors: Sirozh Oleksandra , Jung Bomi , Sanchez-Burgos Laura , Ventoso Ivan , Lafarga Vanesa , Fernández-Capetillo Oscar
Published: August 2023

Nucleolar stress (NS) has been associated to several age-related diseases such as cancer or neurodegeneration. To investigate the mechanisms of toxicity triggered by NS, we here used (PR)n arginine-rich peptides that are found in patients of some neurodegenerative diseases. Although these peptides accumulate at nucleoli and generate NS, how this translates into cellular toxicity is poorly understood. We here reveal that whereas (PR)n expression leads to an overall decrease in protein abundance, this occurs concomitant with an accumulation of free ribosomal (r) proteins in the cytoplasm, a hallmark of ribosomopathies. Conversely, cells with acquired resistance to (PR)n peptides present global downregulation of r-proteins and low levels of mTOR signaling. In mice, systemic expression of (PR)97drives widespread NS and accelerated ageing, which is associated to an increased expression of r-proteins and mTOR hyperactivation. Furthermore, the reduced lifespan of (PR)97-expressing mice was alleviated by the mTOR inhibitor rapamycin. Importantly, we show that the generalised accumulation of free r-proteins is a common outcome in response to chemical or genetic perturbations that trigger NS, such as Actinomycin D, TIF-IA depletion, or the expression of mutant HMGB1 variants recently associated to rare human diseases. Together, our study presentsin vivoevidence supporting the role of NS as a driver of ageing, and provides a general framework to explain the toxicity caused by NS in mammalian cells.
Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors
Authors: Hu Qing , Espejo Valle-Inclan Jose , Dahiya Rashmi , Guyer Alison , Mazzagatti Alice , Maurais Elizabeth G. , Engel Justin L. , Cortés-Ciriano Isidro , Ly Peter
Published: August 2023

Errors in mitosis can generate micronuclei that entrap mis-segregated chromosomes, which are susceptible to catastrophic fragmentation through a process termed chromothripsis. The reassembly of fragmented chromosomes by error-prone DNA double-strand break (DSB) repair generates a spectrum of simple and complex genomic rearrangements that are associated with human cancers and disorders. How specific DSB repair pathways recognize and process these lesions remains poorly understood. Here we used CRISPR/Cas9 to systematically inactivate distinct DSB processing or repair pathways and interrogated the rearrangement landscape of fragmented chromosomes from micronuclei. Deletion of canonical non-homologous end joining (NHEJ) components, including DNA-PKcs, LIG4, and XLF, substantially reduced the formation of complex rearrangements and shifted the rearrangement landscape toward simple alterations without the characteristic patterns of cancer-associated chromothripsis. Following reincorporation into the nucleus, fragmented chromosomes localize within micronuclei bodies (MN bodies) and undergo successful ligation by NHEJ within a single cell cycle. In the absence of NHEJ, chromosome fragments were rarely engaged by polymerase theta-mediated alternative end-joining or recombination-based mechanisms, resulting in delayed repair kinetics and persistent 53BP1-labeled MN bodies in the interphase nucleus. Prolonged DNA damage signaling from unrepaired fragments ultimately triggered cell cycle arrest. Thus, we provide evidence supporting NHEJ as the exclusive DSB repair pathway generating complex rearrangements following chromothripsis from mitotic errors.
Spatiotemporal optical control of Gαq-PLCβ interactions
Authors: Ubeysinghe Sithurandi , Kankanamge Dinesh , Thotamune Waruna , Wijayaratna Dhanushan , Mohan Thomas M. , Karunarathne Ajith
Published: August 2023

Cells experience time-varying and spatially heterogeneous chemokine signals in vivo, activating cell surface proteins, including G protein-coupled receptors (GPCRs). The Gαq pathway activation by GPCRs is a major signaling axis with a broad physiological and pathological significance. Compared to other Gα members, GαqGTP activates many crucial effectors, including PLCβ (Phospholipase Cβ) and Rho GEFs (Rho guanine nucleotide exchange factors). PLCβ regulates many key processes, such as hematopoiesis, synaptogenesis, and cell cycle, and is therefore implicated in terminal - debilitating diseases, including cancer, epilepsy, Huntington’s Disease, and Alzheimer’s Disease. However, due to a lack of genetic and pharmacological tools, examining how the dynamic regulation of PLCβ signaling controls cellular physiology has been difficult. Since activated PLCβ induces several abrupt cellular changes, including cell morphology, examining how the other pathways downstream of Gq-GPCRs contribute to the overall signaling has also been difficult. Here we show the engineering, validation, and application of a highly selective and efficient optogenetic inhibitor (Opto-dHTH) to completely disrupt GαqGTP-PLCβ interactions reversibly in user-defined cellular-subcellular regions on optical command. Using this newly gained PLCβ signaling control, our data indicate that the molecular competition between RhoGEFs and PLCβ for GαqGTP determines the potency of Gq-GPCR-governed directional cell migration.
Mesoscopic Oblique Plane Microscopy via Light-sheet Mirroring
Authors: Daetwyler Stephan , Chang Bo-Jui , Chen Bingying , Zhou Felix , Fiolka Reto
Published: August 2023

Understanding the intricate interplay and inter-connectivity of biological processes across an entire organism is important in various fields of biology, including cardiovascular research, neuroscience, and developmental biology. Here, we present a mesoscopic oblique plane microscope (OPM) that enables whole organism imaging with high speed and subcellular resolution. A microprism underneath the sample enhances the axial resolution and optical sectioning through total internal reflection of the light-sheet. Through rapid refocusing of the light-sheet, the imaging depth is extended up to threefold while keeping the axial resolution constant. Using low magnification objectives with a large field of view, we realize mesoscopic imaging over a volume of 3.7×1.5×1 mm3with ∼2.3 microns lateral and ∼9.2 microns axial resolution. Applying the mesoscopic OPM, we demonstratein vivoandin totowhole organism imaging of the zebrafish vasculature and its endothelial nuclei, and blood flow dynamics at 12 Hz acquisition rate, resulting in a quantitative map of blood flow across the entire organism.
Pretrainable Geometric Graph Neural Network for Antibody Affinity Maturation
Authors: Cai Huiyu , Zhang Zuobai , Wang Mingkai , Zhong Bozitao , Li Quanxiao , Zhong Yuxuan , Wu Yanling , Ying Tianlei , Tang Jian
Published: August 2023

Increasing the binding affinity of an antibody to its target antigen is a crucial task in antibody therapeutics development. This paper presents a pretrainable geometric graph neural network, GearBind, and explores its potential inin silicoaffinity maturation. Leveraging multi-relational graph construction, multi-level geometric message passing and contrastive pretraining on mass-scale, unlabeled protein structural data, GearBind outperforms previous state-of-the-art approaches on SKEMPI and an independent test set. A powerful ensemble model based on GearBind is then derived and used to successfully enhance the binding of two antibodies with distinct formats and target antigens. ELISA EC50values of the designed antibody mutants are decreased by up to 17 fold, andKDvalues by up to 6.1 fold. These promising results underscore the utility of geometric deep learning and effective pretraining in macromolecule interaction modeling tasks.
Bioluminescence Assay of Lysine Deacylase Sirtuin Activity
Authors: Van Scoyk Alexandria N. , Antelope Orlando , Franzini Anca , Ayer Donald E. , Peterson Randall T. , Pomicter Anthony D. , Owen Shawn C. , Deininger Michael W.
Published: August 2023

Lysine acylation can direct protein function, localization, and interactions. Sirtuins deacylate lysine towards maintaining cellular homeostasis, and their aberrant expression contributes to the pathogenesis of multiple pathological conditions, including cancer. Measuring sirtuins’ activity is essential to exploring their potential as therapeutic targets, but accurate quantification is challenging. We developed ‘SIRTify’, a high-sensitivity assay for measuring sirtuin activityin vitroandin vivo. SIRTifyis based on a split-version of the NanoLuc® luciferase consisting of a truncated, catalytically inactive N-terminal moiety (LgBiT) that complements with a high-affinity C-terminal peptide (p86) to form active luciferase. Acylation of two lysines within p86 disrupts binding to LgBiT and abates luminescence. Deacylation by sirtuins reestablishes p86 and restores binding, generating a luminescence signal proportional to sirtuin activity. Measurements accurately reflect reported sirtuin specificity for lysine acylations and confirm the effects of sirtuin modulators. SIRTifyeffectively quantifies lysine deacylation dynamics and may be adaptable to monitoring additional post-translational modifications.
Aging and senescence-associated analysis of the aged kidney glomerulus highlights the role of mesangial cells in renal aging
Authors: Korin Ben , Avraham Shimrit , McKay Andrew , Durinck Steffen , Moncada Reuben , Menon Hari , Darmanis Spyros , Liang Yuxin , Modrusan Zora , Webster Joshua D. , Shaw Andrey S
Published: August 2023

Most causes of chronic kidney disease begin with injury to the glomerulus and involve progressive loss of kidney function. The glomerulus is a capillary bed where blood filtration to produce urine in the kidney occurs. During aging, there is progressive loss of glomeruli and filtration capacity of the kidney because podocytes, the glomerular epithelial cell, are lost with aging and after injury. Podocytes cannot divide and therefore cannot be replaced. Our histological analysis confirmed the presence of glomerulosclerosis, generalized interstitial fibrosis and glomerular hypertrophy in the aged mouse kidney. One barrier to studies of glomeruli is their low frequency in the kidney, less than 1.5% of the cells, and as such, they are often underrepresented in whole kidney analyses. To address this challenge, we used both bulk and single cell RNA sequencing (scRNA-Seq) to characterize purified glomeruli from young and aged mice. Aged glomeruli displayed increased inflammation and expressed a variety of injury and senescence-associated markers, most notably in mesangial cells and macrophages. This increased expression of senescence markers in mesangial cells of aged kidneys suggests a potential cellular target to address age-related renal dysfunction and chronic kidney disease (CKD), which represent a tremendous unmet medical need.
Flow cytometry methods for targeted isolation of ctenophore cells
Authors: Dieter Abigail C , True Aliyah BK , Gilbertson Emily , Snyder Grace , Lacy-Hulbert Adam , Traylor-Knowles Nikki , Browne William E , Vandepas Lauren E
Published: August 2023

Cell suspension fluidics, such as flow cytometry (FCS) and fluorescence-activated cell sorting (FACS), facilitates the identification and precise separation of individual cells based on phenotype. Since its introduction, flow cytometry has been used to analyze cell types and cellular processes in diverse non-vertebrate taxa, including cnidarians, molluscs, and arthropods. Ctenophores, which diverged very early from the metazoan stem lineage, have emerged as an informative clade for the study of metazoan cell type evolution. We present standardized methodologies for flow cytometry-mediated identification and analyses of cells from the model ctenophoreMnemiopsis leidyithat can also be applied to isolate targeted cell populations. Here we focus on the identification and isolation of ctenophore phagocytes. Implementing flow cytometry methods in ctenophores allows for fine scale analyses of fundamental cellular processes conserved broadly across animals, as well as potentially revealing novel cellular phenotypes and behaviors restricted to the ctenophore lineage.
A trait-based understanding of the vulnerability of a paleotropical moth community to predation by a sympatric bat with flexible foraging strategies
Authors: Dey Pritha , Balakrishnan Rohini
Published: August 2023

Prey profitability for a predator hunting diverse prey varies with species and seasons. Whereas prey selection by aerial-hawking or gleaning bats is well established, this is challenging to establish in species that adopt both these strategies flexibly. Measurable prey traits coupled with availability in the foraging grounds help characterize the vulnerability of prey species to predation.

In the Western Ghats of India, a global biodiversity hotspot, we studied an anthropogenic landscape, where insectivorous bats are abundant and diverse, but their impact on moth communities is little understood. We investigated the morphological traits of a sympatric moth community that make them more vulnerable to predation byMegaderma spasma, a bat with flexible foraging strategies. We also established the seasonal composition of moth prey in the diet of the bat.

We analyzed the discarded prey remains from several roosts, collected over three years, for seasonal patterns in the diet and selective hunting. Through light-trapping, we collected moth specimens in different seasons to assess the morphological traits of the moth community available in the foraging area of the bat.

The traits likely to affect the profitability of prey moths were measured: forewing length, hindwing length, wingspan, and body length (a proxy for body size); forewing area, hindwing area, maneuverability, and wing loading (as a proxy for evasive flight capability), and forewing aspect ratio (as a proxy for wing shape).

Our results showed that consumed moth prey diversity varies seasonally, with moths belonging to the Hepialidae family being preferred in the wet season. Moths belonging to the Sphingidae family were the most abundant in the diet, followed by Erebidae and Hepialidae. Sphingid moths have the lowest maneuverability, and highest forewing aspect ratio; the Hepialidae moths have the maximum body size followed by Sphingids thus confirming our hypothesis that larger moths with low evasive capabilities are more vulnerable to predation.

Assessing vulnerability at the prey community level, we establish a framework for future research on moth-bat interactions from the diverse and less-explored paleotropical communities. Additionally, the study reiterates the usefulness of trait-based approaches to understanding prey-predator dynamics.