bluuebunny/crossref_metadata_2025 huggingface dataset:
The Association of Racial Residential Segregation and Survival After Out-of-Hospital Cardiac Arrest in the United States
Authors: Abbott Ethan E , Buckler David G , Shekhar Aditya C , Landry Elizabeth , Abella Benjamin S , Richardson Lynne D , Zebrowski Alexis M ,   CARES Surveillance Group
Published: April 2024

Background

Residential segregation has been identified as drivers of disparities in health outcomes, but further work is needed to understand this association with clinical outcomes for out-of-hospital cardiac arrest (OHCA). We utilized Cardiac Arrest Registry to Enhance Survival (CARES) dataset to examine if there are differences in survival to discharge and survival with good neurological outcome, as well as likelihood of bystander CPR, using validated measures of racial, ethnic, and economic segregation.

Methods

We conducted a retrospective observational study using data from the Cardiac Arrest Registry to Enhance Survival (CARES) dataset to examine associations among adult OHCA patients. The primary predictor was the Index of Concentration at the Extremes (ICE), a validated measure that includes race, ethnicity, and income across three measures at the census tract level. The primary outcomes were survival to discharge and survival with good neurological status. A multivariable modified Poisson regression modeling approach with random effects at the EMS agency and hospital level was utilized.

Results

We identified 626,264 OHCA patients during the study period. The mean age was 62 years old (SD 17.2 years), and 35.7% (n =223,839) of the patients were female. In multivariable models, we observed an increased likelihood of survival to discharge and survival with good neurological outcome for those patients residing in predominately White population census tracts and higher income census tracts as compared to lower income Black and Hispanic/Latinx population census tracts (RR 1.24, CI 1.20-1.28) and a 32% increased likelihood of receiving bystander CPR in higher income census tracts as compared to reference (RR 1.32, CI 1.30-1.34).

Conclusions

In this study examining the association of measures of residential segregation and OHCA outcomes, there was an increased likelihood of survival to discharge, survival with good neurological status, and likelihood of receiving B-CPR for those patients residing in predominately White population and higher income census tracts when compared to predominately Black and/or Hispanic Latinx populations and lower income census tracts. This research suggests that areas impacted by residential and economic segregation are important targets for both public policy interventions as well as addressing disparities in care across the chain of survival for OHCA.
Analysis of Hypertension in Peru: Prevalence, Associated Factors, Knowledge, Management and Control, 2014-2022
Authors: Vera-Ponce Víctor Juan , Zuzunaga-Montoya Fiorella E. , Vásquez-Romero Luisa Erika Milagros , Loayza-Castro Joan A. , Iturregui Paucar Cori Raquel , Valladares-Garrido Mario J. , Vigil-Ventura Enrique
Published: April 2024

Introduction

Hypertension (HTN), prehypertension, and High Blood Pressure (HBP) represent a chronic medical condition of growing global concern. Highlighting the importance of Awareness, medication, and Control of HTN is essential. A significant proportion of hypertensive patients are unaware of their condition, hindering proper and early treatment. Among those diagnosed, not all receive or follow pharmacological treatment, and an even smaller percentage achieves effective blood pressure control.

Objective

The main objectives include determining the prevalence, trends, and associated factors of HTN, as well as investigating prehypertension and the variability in HBP levels during the same period. Special attention will be given to self-reported, medicated, and Controlled hypertension, analyzing its evolution and associated factors.

Methods

We conducted an analytical cross-sectional study using the National Survey of Demographic and Family Health database between 2014 and 2022. Our study included individuals aged 18 years and older, as the definitions of HTN apply to people from this age onwards.

Results

The study revealed an overall HTN, prehypertension, and HBP prevalence of 20.76%, 33.44%, and 33.44%, respectively, with annual variations. An increasing trend in the prevalence of known, medicated, and controlled HTN was observed, with factors such as gender, age, educational level, and geographical region significantly influencing it.

Conclusions

The investigation into HTN in Peru revealed an expanding occurrence of HTN, prehypertension, and HBP, emphasizing the necessity for early identification, suitable treatment, and effective management of HTN. A significant gap is observed between the condition’s awareness and effective management, highlighting the urgent need for public health strategies that address both the prevention and treatment of HTN in Peru.
Insights into Predicting Tooth Extraction from Panoramic Dental Images: Artificial Intelligence vs. Dentists
Authors: Motmaen Ila , Xie Kunpeng , Schönbrunn Leon , Berens Jeff , Grunert Kim , Plum Anna Maria , Raufeisen Johannes , Ferreira André , Hermans Alexander , Egger Jan , Hölzle Frank , Truhn Daniel , Puladi Behrus
Published: April 2024

Objectives

Tooth extraction is one of the most frequently performed medical procedures. The indication is based on the combination of clinical and radiological examination and individual patient parameters and should be made with great care. However, determining whether a tooth should be extracted is not always a straightforward decision. Moreover, visual and cognitive pitfalls in the analysis of radiographs may lead to incorrect decisions. Artificial intelligence (AI) could be used as a decision support tool to provide a score of tooth extractability.

Material and Methods

Using 26,956 single teeth images from 1,184 panoramic radiographs (PANs), we trained a ResNet50 network to classify teeth as either extraction-worthy or preservable. For this purpose, teeth were cropped with different margins from PANs and annotated. The usefulness of the AI-based classification as well that of dentists was evaluated on a test dataset. In addition, the explainability of the best AI model was visualized via a class activation mapping using CAMERAS.

Results

The ROC-AUC for the best AI model to discriminate teeth worthy of preservation was 0.901 with 2% margin on dental images. In contrast, the average ROC-AUC for dentists was only 0.797. With a 19.1% tooth extractions prevalence, the AI model’s PR-AUC was 0.749, while the human evaluation only reached 0.589.

Conclusion

AI models outperform dentists/specialists in predicting tooth extraction based solely on X-ray images, while the AI performance improves with increasing contextual information.

Clinical Relevance

AI could help monitor at-risk teeth and reduce errors in indications for extractions.
Association of aortic clamping time with systemic immune inflammation and systemic inflammatory response indexes in isolated coronary bypass surgery
Authors: Durmaz Duygu , Gündöner Sedat , Tekümit Hayrettin
Published: April 2024

Objective

Aortic clamping time during cardiopulmonary bypass (CPB) has been associated with inflammatory processes such as systemic inflammatory response syndrome. In this study, we evaluated the association of CPB and aortic cross-clamping (ACC) times with systemic inflammatory response index (SIRI) and systemic immune inflammation index (SIII) in isolated coronary artery bypass surgery (CABG).

Methods

96 patients who underwent isolated CABG at a single center between 2021 and 2023 were retrospectively analyzed. Patients were divided into below median aortic clamp time (group I; n=56) and above median aortic clamp time (group II; n=42) according to median aortic clamp time (66.2 minutes). Demographic data, preoperative and postoperative laboratory parameters were recorded. SIRI and SIII values were calculated.

Results

Baseline demographic data were similar between the groups. The duration of CPB and aortic clamping was significantly longer in group II (p<0.001). SIII and SIRI values were significantly increased in both groups in the postoperative period. However, there was no correlation between increased CPB and ACC durations and SIII and SIRI. However, no significant difference was observed in postoperative SIII and SIRI values between the groups. A weak correlation was found between SIII index and postoperative albumin levels.

Conclusions

There is no significant relationship between aortic clamping time and inflammatory indices in patients undergoing isolated CABG surgery. Increasing the duration of surgery does not affect the change in SIRI and SIII values.
Blood Pressure Control and Maintenance in a Prospective Cohort of Younger Veterans: Roles of Sex, Race, Ethnicity, and Social Determinants of Health
Authors: Gaffey Allison E. , Chang Tiffany E. , Brandt Cynthia A. , Haskell Sally G. , Dhruva Sanket S. , Bastian Lori A. , Levine Allison , Melissa Skanderson , Burg Matthew M.
Published: April 2024

Background

Proactive blood pressure (BP) management is particularly beneficial for younger Veterans, who have a greater prevalence and earlier onset of cardiovascular disease than non-Veterans. It is unknown what proportion of younger Veterans achieve and maintain BP control after hypertension onset and if BP control differs by demographics and social deprivation.

Methods

Electronic health records were merged from Veterans who enrolled in VA care 10/1/2001-9/30/2017 and met criteria for hypertension – first diagnosis or antihypertensive fill. BP control (140/90 mmHg), was estimated 1, 2, and 5 years post-hypertension documentation, and characterized by sex, race, and ethnicity. Adjusted logistic regressions assessed likelihood of BP control by these demographics and with the Social Deprivation Index (SDI).

Results

Overall, 17% patients met criteria for hypertension (n=198,367; 11% of women, median age 41). One year later, 59% of men and 65% of women achieved BP control. After adjustment, women had a 72% greater odds of BP control than men, with minimal change over 5 years. Black adults had a 22% lower odds of BP control than White adults. SDI did not significantly change these results.

Conclusions

In the largest study of hypertension in younger Veterans, 41% of men and 35% of women did not have BP control after 1 year, and BP control was consistently better for women through 5 years. Thus, the first year of hypertension management portends future, long-term BP control. As social deprivation did not affect BP control, the VA system may protect against disadvantages observed in the general U.S. population.
Facile detection of peptide-protein interactions using an electrophoretic crosslinking shift assay
Authors: Parker Benjamin W. , Weiss Eric L.
Published: April 2024

Protein-protein interactions with high specificity and low affinity are functionally important but are not comprehensively understood because they are difficult to identify. Particularly intriguing are the dynamic and specific interactions between folded protein domains and short unstructured peptides known as short linear motifs (SLiMs). Such domain-motif interactions (DMIs) are often difficult to identify and study because affinities are modest to weak. Here we describe “electrophoretic crosslinking shift assay” (ECSA), a simple in vitro approach that detects transient, low affinity interactions by covalently crosslinking a prey protein and a fluorescently labeled bait. We demonstrate this technique on the well characterized DMI between MAP kinases and unstructured D-motif peptide ligands. We show that ECSA detects sequence-specific micromolar interactions using less than a microgram of input prey protein per reaction, making it ideal for verifying candidate low-affinity DMIs of components that purify with low yield. We propose ECSA as an intermediate step in SLiM characterization that bridges the gap between high throughput techniques such as phage display and more resource-intensive biophysical and structural analysis.
Natural compound screening predicts novel GSK-3 isoform-specific inhibitors
Authors: Ahmad Firdos , Gupta Anamika , Marzook Hezlin , Woodgett James R. , Saleh Mohamed A. , Qaisar Rizwan
Published: April 2024

Glycogen synthase kinase-3 (GSK-3) plays important roles in the pathogenesis of cardiovascular, metabolic, neurological disorders and cancer. Isoform-specific loss of either GSK-3α or GSK-3β often provides cytoprotective effects under such clinical conditions. However, available synthetic small molecule inhibitors are relatively non-specific, and their chronic use may lead to adverse effects. Therefore, screening for natural compound inhibitors to identify the isoform-specific inhibitors may provide improved clinical utility. Here, we screened 70 natural compounds to identify novel natural GSK-3 inhibitors employing comprehensivein silicoand biochemical approaches. Molecular docking and pharmacokinetics analysis identified two natural compounds Psoralidin and Rosmarinic acid as potential GSK-3 inhibitors. Specifically, Psoralidin and Rosmarinic acid exhibited the highest binding affinities for GSK-3α and GSK-3β, respectively. Consistent within silicofindings, the kinase assay-driven IC50 revealed superior inhibitory effects of Psoralidin against GSK-3α (IC50=2.26 µM) vs. GSK-3β (IC50=4.23 µM) while Rosmarinic acid was found to be more potent against GSK-3β (IC50=2.24 µM) than GSK-3α (IC50=5.14 µM). Taken together, these studies show that the identified natural compounds may serve as GSK-3 inhibitors with Psoralidin serving as a better inhibitor for GSK-3α and Rosmarinic for GSK-3β isoform, respectively. Further characterization employingin vitroand preclinical models will be required to test the utility of these compounds as GSK-3 inhibitors for cardiometabolic and neurological disorders and cancers.

Highlights

Current GSK-3 inhibitors lack specificity and cause side effects.

This study identifies potential GSK-3 isoform-specific natural compounds.

Psoralidin is likely a better inhibitor for GSK-3α while Rosmarinic for GSK-3β.

These natural compounds may be promising future treatments.
Identification of a non-canonical function of prefoldin subunit 5 in proteasome assembly
Authors: Shahmoradi Ghahe Somayeh , Drabikowski Krzysztof , Topf Ulrike
Published: April 2024

The prefoldin complex is a heterohexameric, evolutionarily conserved co-chaperone that assists in the folding of polypeptides downstream of the protein translation machinery. Loss of prefoldin function leads to impaired solubility of cellular proteins. The degradation of proteins by the proteasome is an integral part of protein homeostasis. Failure of regulated protein degradation can lead to the accumulation of misfolded and defective proteins. We show that prefoldin subunit 5 is required for proteasome activity by contributing to the assembly of the 26S proteasome. In particular, we found that the absence of prefoldin subunit 5 impairs the formation of the Rpt ring subcomplex of the proteasome. Concomitant deletion ofPFD5andHSM3, a chaperone for assembly of the ATPase subunits comprising the Rpt ring, exacerbates this effect, suggesting a synergistic relationship between the two factors in proteasome assembly. Thus, our findings reveal a regulatory mechanism wherein prefoldin subunit 5 plays a crucial role in maintaining proteasome integrity, thereby influencing the degradation of proteins.
Re-examination of the taxonomic status of the AntarcticPseudomonas syringaeLz4W isolate and proposal to rename it as a novel speciesPseudomonas cryophilasp. nov
Authors: Ray Malay K , Pandiyan Apuratha , Sahu Bhubanananda
Published: April 2024

A taxonomic re-evaluation of the Antarctic psychrotrophic bacteriumPseudomonas syringaeLz4W was performed in the light of its available genome sequence and due to a revision in the key phenotypic characteristics that are in conflict with the “syringae” group of Pseudomonads. A 16S rRNA gene sequence based phylogenetic analysis suggested that Lz4WTstrain belongs to “fragi” cluster ofPseudomonasspecies, with closest similarity (99.72%) to the type strainP. deceptionensisM1T. However,in silicoanalysis of the Lz4W genome sequence using SpecI (species identification tools), ANI (average nucleotide identity), and GBDP (Genome Blast Distance phylogeny) methods suggest that Lz4WTstrain cannot be delineated with any of the type strains of “fragi” cluster of species. Based on predictive low DNA-DNA hybridization value (<29.9%) and differences in phenotypic features with the related species we suggest that Lz4WTis a novel species under thePseudomonasgenus, and we propose that the strain be named asPseudomonas cryophilasp. nov. The type strain is Lz4WT(=CFBP 8403T=KCTC 42933T=LMG 29591T=MTCC 673T).
Characterization of novel and essential kinetoplast-associated proteins inTrypanosoma brucei
Authors: Cadena Lawrence Rudy , Svobodová Michaela , Benz Corinna , Rašková Vendula , Chmelová Ľubomíra , Škodová-Sveráková Ingrid , Yurchenko Vyacheslav , Lukeš Julius , Hammond Michael , Durante Ignacio Miguel
Published: April 2024

The kinetoplast is one of the defining features of kinetoplastid protists and represents a unique concentration of mitochondrial DNA. This subcellular structure is a highly complex assembly of thousands of mutually catenated, circular DNA molecules as well as up to one hundred dedicated proteins. These components work in tandem to replicate and segregate the mitochondrial genome during cellular division, additionally coordinating with the basal body and flagellum through the tripartite attachment complex (TAC) superstructure. Here, we screened the MitoTag localization repository and identified a number of previously undescribed hypothetical proteins exhibiting putative signals within the kinetoplast ofTrypanosoma brucei. Through endogenous tagging we verify their association with the kinetoplast or TAC. The essentiality for several of these kinetoplast proteins (KP) was assessed by RNAi knock-downs, revealing that the newly characterized KP56, KP84 and KP86 are indispensable for growth of the procyclic stage. Additionally, KP37, KP56, and KP84 displayed alterations in the abundance of maxicircles or minicircles, while the depletion of KP84 and KP86 resulted in cell cycle alternations. Pulldown assays using the endogenously V5-tagged cell lines identified novel interactors, which were additionally subjected to endogenous tagging for subcellular localization, revealing two additional proteins (KP45 and KP66) with dual localization to the kinetoplast and throughout the mitochondrial lumen. This work represents the most extensive identification of novel KPs to date and provides a methodological pipeline for the characterization of remaining KPs to further understand this intricate molecular structure.
Cell-free assays reveal that the HIV-1 capsid protects reverse transcripts from cGAS
Authors: Scott Tiana M. , Arnold Lydia M. , Powers Jordan A. , McCann Delaney A. , Rowe Ana B. , Christensen Devin E. , Pereira Miguel J. , Zhou Wen , Torrez Rachel M. , Iwasa Janet H. , Kranzusch Philip J. , Sundquist Wesley I. , Johnson Jarrod S.
Published: April 2024

Retroviruses can be detected by the innate immune sensor cyclic GMP-AMP synthase (cGAS), which recognizes reverse-transcribed DNA and activates an antiviral response.

However, the extent to which HIV-1 shields its genome from cGAS recognition remains unclear. To study this process in mechanistic detail, we reconstituted reverse transcription, genome release, and innate immune sensing of HIV-1 in a cell-free system. We found that wild-type HIV-1 capsids protect viral genomes from cGAS even after completing reverse transcription. Viral DNA could be “deprotected” by thermal stress, capsid mutations, or reduced concentrations of inositol hexakisphosphate (IP6) that destabilize the capsid. Strikingly, the capsid inhibitor lenacapavir also disrupted viral cores and dramatically potentiated cGAS activity, both in vitro and in cellular infections. Our results provide biochemical evidence that the HIV-1 capsid lattice conceals the genome from cGAS and that chemical or physical disruption of the viral core can expose HIV-1 DNA and activate innate immune signaling.
How distributed subcortical integration of reward and threat may inform subsequent approach-avoidance decisions
Authors: Hulsman Anneloes M. , Klaassen Felix H. , de Voogd Lycia D. , Roelofs Karin , Klumpers Floris
Published: April 2024

Healthy and successful living involves carefully navigating rewarding and threatening situations by balancing approach and avoidance behaviours. Excessive avoidance to evade potential threats often leads to forfeiting potential rewards. However, little is known about how reward and threat information is integrated neurally to inform approach or avoidance decisions. In this preregistered study, participants (Nbehaviour=31, 17F; NMRI=28, 15F) made approach-avoidance decisions under varying reward (monetary gains) and threat (electrical stimulations) prospects during functional MRI scanning. In contrast to theorizedparallel subcorticalprocessing of reward and threat information before cortical integration, Bayesian Multivariate Multilevel analyses revealed subcortical reward and threatintegrationprior to indicating approach-avoidance decisions. This integration occurred in the ventral striatum, thalamus, and bed nucleus of the stria terminalis (BNST). When reward was low, risk-diminishing avoidance decisions dominated, which was linked to more positive tracking of threat magnitude prior to indicating avoidance than approach decisions across these regions. In contrast, the amygdala exhibited dual sensitivity to reward and threat. While anticipating outcomes of risky approach decisions, we observed positive tracking of threat magnitude within the salience network (dorsal anterior cingulate cortex, thalamus, periaqueductal gray, BNST). Conversely, after risk-diminishing avoidance, characterized by reduced reward prospects, we observed more negative tracking of reward magnitude in the ventromedial prefrontal cortex and ventral striatum. These findings shed light on the temporal dynamics of approach-avoidance decision-making. Importantly, they demonstrate the role of subcortical integration of reward and threat information in balancing approach and avoidance, challenging theories positing predominantly separate subcortical processing prior to cortical integration.
SETDB1 activity is globally directed by H3K14 acetylation via its Triple Tudor Domain
Authors: Chandrasekaran Thyagarajan T. , Choudalakis Michel , Bröhm Alexander , Weirich Sara , Kouroukli Alexandra G , Ammerpohl Ole , Rathert Philipp , Bashtrykov Pavel , Jeltsch Albert
Published: April 2024

SETDB1 is a major H3K9 methyltransferase involved in heterochromatin formation and silencing of repeat elements. It contains a unique Triple Tudor Domain (3TD) which specifically binds the dual modification of H3K14ac in the presence of H3K9me1/2/3. Here, we explored the role of the 3TD H3-tail interaction for the H3K9 methylation activity of SETDB1. We generated a binding reduced 3TD mutant and demonstrate in biochemical methylation assays on peptides and recombinant nucleosomes containing H3K14ac analogs, that H3K14 acetylation is crucial for the 3TD mediated recruitment of SETDB1. We also observe this effect in cells where SETDB1 binding and activity is globally correlated with H3K14ac, and KO of the H3K14 acetyltransferase HBO1 causes a drastic reduction in H3K9me3 levels at SETDB1 dependent sites. Further analyses revealed that 3TD particularly important at specific target regions like L1M repeat elements, where SETDB1 KO cannot be efficiently reconstituted by the 3TD mutant of SETDB1. In summary, our data demonstrate that the H3K9me3 and H3K14ac are not antagonistic marks but rather the presence of H3K14ac is required for SETDB1 recruitment via 3TD binding to H3K9me1/2/3-K14ac and establishment of H3K9me3.
Deep sequencing of 16Ixodes ricinusticks unveils insights into their interactions with endosymbionts
Authors: Lesiczka Paulina M. , Azagi Tal , Krawczyk Aleksandra I. , Scott William T. , Dirks Ron P. , Šimo Ladislav , Dobler Gerhard , Nijsse Bart , Schaap Peter J. , Sprong Hein , Koehorst Jasper J.
Published: April 2024

Background

Ixodes ricinusticks act as vectors for numerous pathogens that present substantial health threats. Additionally, they harbour vertically transmitted symbionts, some of which have been linked to diseases. The difficulty of isolating and cultivating these symbionts has hampered our understanding of their biological role, their potential to cause disease, and their modes of transmission. To expand our understanding on the tick symbiontMidichloria mitochondriiand onRickettsia helvetica, which has been linked to disease in humans, we utilized deep sequencing on sixteen individual adult female ticks collected from coastal dune and forested areas in the Netherlands.

Results

By employing a combination of second and third-generation sequencing techniques, we successfully reconstructed the complete genomes ofM. mitochondriifrom eleven individuals,R. helveticafrom eight individuals and the mitochondrial genome from all ticks. Additionally, we visualised the location ofR. helveticain tick organs and constructed genome-scale metabolic models (GEMs) of both symbionts to study their environmental dependencies.

Our analysis revealed a strong cophylogeny between M. mitochondrii and mitochondrial genomes, suggesting frequent maternal transmission. In contrast, the absence of cophylogeny between R. helvetica and the mitochondrial genomes, coupled with its presence in the receptaculum seminis of I. ricinus females, raises the possibility of paternal transmission of R. helvetica. Notably, the genetic diversity of R. helvetica was found to be very low, except for the rickA virulence gene, where the presence of up to thirteen insertions of a33nt-long repeat led to significant variability. However, this variation could not account for the differences in infection prevalence observed across eight distinct locations in the Netherlands.

Conclusions

By employing deep sequencing, it becomes feasible to extract complete genomes and genetic data of symbionts directly from their host organisms. This methodology serves as a robust means to gain fresh insights into their interactions. Our observations, which suggest paternal transmission ofR. helvetica, a relatively unexplored mode of transmission in ticks, require validation through experimental investigations. The genetic variations identified in therickA virulence gene ofR. helveticahave the potential to influence the infectivity and transmission dynamics ofR. helvetica
A key residue of the extracellular gate provides quality control contributing to ABCG substrate specificity
Authors: Xia Jian , Siffert Alexandra , Torres Odalys , Banasiak Joanna , Pakuła Konrad , Ziegler Jörg , Rosahl Sabine , Ferro Noel , Jasiński Michał , Hegedűs Tamás , Geisler Markus M.
Published: April 2024

For G-type ATP-binding cassette (ABC) transporters, a hydrophobic “di-leucine motif” as part of a hydrophobic extracellular gate has been described to separate a large substrate-binding cavity from a smaller upper cavity and proposed to act as a valve controlling drug extrusion.

Here, we show that an L704F mutation in the hydrophobic extracellular gate of Arabidopsis ABCG36/PDR8/PEN3 uncouples the export of the auxin precursor indole-3-butyric acid (IBA) from that of the defense compound camalexin (CLX). Molecular dynamics simulations reveal an increase in free energy and pulling forces for CLX at both the entrance and exit sites of ABCG36L704F, respectively, providing a mechanistic rationale for the transport discrimination of CLX. Mutagenesis of L704 to tyrosine allows export of structurally related non-ABCG36 substrates, indole-3-acetic acid (IAA) and indole, suggesting an allosteric communication between the extracellular gate and the central substrate binding pocket.

In summary, our work supports the conclusion that L704 is a key residue of the extracellular gate that provides a final quality control contributing to ABCG substrate specificity.
A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread
Authors: Boyd Caroline M. , Seed Kimberley D.
Published: April 2024

ICP1, a lytic bacteriophage ofVibrio cholerae, is parasitized by phage satellites, PLEs, which hijack ICP1 proteins for their own horizontal spread. PLEs’ dependence on ICP1’s DNA replication machinery, and virion components results in inhibition of ICP1’s lifecycle. PLEs’ are expected to depend on ICP1 factors for genome packaging, but the mechanism(s) PLEs use to inhibit ICP1 genome packaging is currently unknown. Here, we identify and characterize Gpi, PLE’s indiscriminate genome packaging inhibitor. Gpi binds to ICP1’s large terminase (TerL), the packaging motor, and blocks genome packaging. To overcome Gpi’s negative effect on TerL, a component PLE also requires, PLE uses two genome packaging specifiers, GpsA and GpsB, that specifically allow packaging of PLE genomes. Surprisingly, PLE also uses mimicry of ICP1’spacsite as a backup strategy to ensure genome packaging. PLE’spacsite mimicry, however, is only sufficient if PLE can inhibit ICP1 at other stages of its lifecycle, suggesting an advantage to maintaining Gpi, GpsA, and GpsB. Collectively, these results provide mechanistic insights into another stage of ICP1’s lifecycle that is inhibited by PLE, which is currently the most inhibitory of the documented phage satellites. More broadly, Gpi represents the first satellite-encoded inhibitor of a phage TerL.
Perpetual step-like restructuring of hippocampal circuit dynamics
Authors: Zheng Zheyang (Sam) , Huszár Roman , Hainmueller Thomas , Bartos Marlene , Williams Alex , Buzsáki György
Published: April 2024

Representation of the environment by hippocampal populations is known to drift even within a familiar environment, which could reflect gradual changes in single cell activity or result from averaging across discrete switches of single neurons. Disambiguating these possibilities is crucial, as they each imply distinct mechanisms. Leveraging change point detection and model comparison, we found that CA1 population vectors decorrelated gradually within a session. In contrast, individual neurons exhibited predominantly step-like emergence and disappearance of place fields or sustained change in within-field firing. The changes were not restricted to particular parts of the maze or trials and did not require apparent behavioral changes. The same place fields emerged, disappeared, and reappeared across days, suggesting that the hippocampus reuses pre-existing assemblies, rather than forming new fieldsde novo. Our results suggest an internally-driven perpetual step-like reorganization of the neuronal assemblies.
Chimeric origin of eukaryotes from Asgard archaea and ancestral giant viruses
Authors: Karki Sangita , Barth Zachary K. , Aylward Frank O.
Published: April 2024

The details surrounding the evolution of complex cells remain some of the most enduring mysteries in biology. Recent evidence has demonstrated that Asgard archaea are the closest cellular relatives of eukaryotes, but several eukaryotic enzymes involved in key cellular processes lack phylogenetic affinity with archaea. In particular, phylogenies of eukaryotic DNA and RNA polymerases often support a 3-domain topology that is not consistent with an archaeal origin. Here we present comprehensive phylogenetic analysis of eukaryotic family B DNA polymerases and multimeric RNA polymerases and show that these core subunits of these enzymes are derived from the ancestors of modern giant viruses (phylumNucleocytoviricota). Specifically, we show that the eukaryotic delta polymerase (Polδ), a key processive polymerase required for genome replication in all eukaryotes, clusters within an ancient viral clade, strongly supporting a viral origin. By contrast, the other eukaryotic processive polymerase (Polε), clusters within an Asgard archaeal clade. Together, these observations provide a strong and direct link between early eukaryotes, Asgard archaea, and giant viruses. Lastly, we provide a comprehensive phylogenetic analysis of eukaryotic multimeric RNA polymerases to confirm that RNA polymerase II, which is responsible for mRNA transcription in eukaryotes, is also derived from the ancestors of modern giant viruses. In total, our results support a model of eukaryogenesis in which complex cells emerged from a genomic chimera of Asgard archaea and an ancient viral lineage.
Asymptomatic neonatal herpes simplex virus infection in mice leads to long-term cognitive impairment
Authors: Dutton A , Patel CD , Taylor SA , Garland CR , Turnbaugh EM , Alers-Velazquez R , Mehrbach J , Nautiyal KM , Leib DA
Published: April 2024

Neonatal herpes simplex virus (nHSV) is a devastating infection impacting approximately 14,000 newborns globally each year. Infection is associated with high neurologic morbidity and mortality, making early intervention and treatment critical. Clinical outcomes of symptomatic nHSV infections are well-studied, but little is known about the frequency of, or outcomes following, sub-clinical or asymptomatic nHSV. Given the ubiquitous nature of HSV infection and frequency of asymptomatic shedding in adults, subclinical infections are underreported, yet could contribute to long-term neurological damage. To assess potential neurological morbidity associated with subclinical nHSV infection, we developed a low-dose (100 PFU) HSV infection protocol in neonatal C57BL/6 mice. At this dose, HSV DNA was detected in the brain by PCR but was not associated with acute clinical symptoms. However, months after initial inoculation with 100 PFU of HSV, we observed impaired mouse performance on a range of cognitive and memory performance tasks. Memory impairment was induced by infection with either HSV-1 or HSV-2 wild-type viruses, but not by a viral mutant lacking the autophagy-modulating Beclin-binding domain of the neurovirulence gene γ34.5. Retroviral expression of wild type γ34.5 gene led to behavioral pathology in mice, suggesting that γ34.5 expression may be sufficient to cause cognitive impairment. Maternal immunization and HSV-specific antibody treatment prevented offspring from developing neurological sequelae following nHSV-1 infection. Altogether, these results support the idea that subclinical neonatal infections may lead to cognitive decline in adulthood, with possible profound implications for research on human neurodegenerative disorders such as Alzheimer’s Disease.
Conserved domains and structural motifs that differentiate closely related Rex1 and Rex3 DEDDh Exoribonuclease families are required for their function in yeast
Authors: Daniels Peter W. , Kelly Sophie , Tebbs Iwan J. , Mitchell Phil
Published: April 2024

The DEDD family of exonucleases has expanded through evolution whilst retaining a well conserved catalytic domain. One subgroup of DEDD exoribonucleases with very closely related catalytic domain sequences includes the yeast enzymes Rex1 (RNA exonuclease 1) and Rex3, the metazoan REXO1 (RNA exonuclease 1 homologue) and Rexo5 proteins, and the plant protein Sdn5 (small RNA degrading nuclease). Comparison of Alphafold models for these proteins reveals that Rex1, Rexo5 and Sdn5 are structural homologues, consisting of a central catalytic domain inserted within a discontinuous alkaline phosphatase (AlkP) domain. The core AlkP domain of Rex1-related proteins contains distinct surface insertions in different eukaryotic lineages. Yeast Rex1 contains three loops that are modelled to be directed towards the DEDD domain, one of which forms an extended helical arch that is conserved across fungi and plants but absent in metazoan homologues. We show that the arch and an adjacent loop are required for Rex1-mediated processing of 5S rRNA and tRNA inSaccharomyces cerevisiae. Rex3 structural homologues, including REXO1, contain a KIX domain (CREB kinase-inducible domain (KID) interacting domain) and a cysteine- and histidine-rich domain (CHORD) adjacent to a C-terminal DEDD domain. In contrast to Rex1, Rex3 proteins are found in metazoans and fungi but not in plants or algae. Deletion of the KIX domain within yeast Rex3 blocked its function in RNase MRP processing. Taken together, this work identifies evolutionarily conserved structural hallmarks of Rex1 and Rex3 enzymes and demonstrates that these features are required for Rex1- and Rex3-mediated RNA processing pathwaysin vivo.
Sex differences in the functional network underpinnings of psychotic-like experiences in children
Authors: Dhamala Elvisha , Chopra Sidhant , Ooi Leon Qi Rong , Rubio Jose M , Yeo B.T. Thomas , Malhotra Anil K , Holmes Avram J
Published: April 2024

Psychotic-like experiences (PLEs) include a range of sub-threshold symptoms that resemble aspects of psychosis but do not necessarily indicate the presence of psychiatric illness. These experiences are highly prevalent in youth and are associated with developmental disruptions across social, academic, and emotional domains. While not all youth who report PLEs develop psychosis, many develop other psychiatric illnesses during adolescence and adulthood. As such, PLEs are theorized to represent early markers of poor mental health. Here, we characterized the similarities and differences in the neurobiological underpinnings of childhood PLEs across the sexes using a large sample from the ABCD Study (n=5,260), revealing sex-specific associations between functional networks connectivity and PLEs. We find that although the networks associated with PLEs overlap to some extent across the sexes, there are also crucial differences. In females, PLEs are associated with dispersed cortical and non-cortical connections, whereas in males, they are primarily associated with functional connections within limbic, temporal parietal, somato/motor, and visual networks. These results suggest that early transdiagnostic markers of psychopathology may be distinct across the sexes, further emphasizing the need to consider sex in psychiatric research as well as clinical practice.
Quantitative bias analysis methods for summary level epidemiologic data in the peer-reviewed literature: a systematic review
Authors: Shi Xiaoting , Liu Ziang , Zhang Mingfeng , Hua Wei , Li Jie , Lee Joo-Yeon , Dharmarajan Sai , Nyhan Kate , Naimi Ashley , Lash Timothy L. , Jeffery Molly M. , Ross Joseph S. , Liew Zeyan , Wallach Joshua D.
Published: April 2024

Objective

Quantitative bias analysis (QBA) methods evaluate the impact of biases arising from systematic errors on observational study results. This systematic review aimed to summarize the range and characteristics of quantitative bias analysis (QBA) methods for summary level data published in the peer-reviewed literature.

Study Design and Setting

We searched MEDLINE, Embase, Scopus, and Web of Science for English-language articles describing QBA methods. For each QBA method, we recorded key characteristics, including applicable study designs, bias(es) addressed; bias parameters, and publicly available software. The study protocol was pre-registered on the Open Science Framework (https://osf.io/ue6vm/).

Results

Our search identified 10,249 records, of which 53 were articles describing 57 QBA methods for summary level data. Of the 57 QBA methods, 51 (89%) were explicitly designed for observational studies, 2 (4%) for non-randomized interventional studies, and 4 (7%) for meta-analyses. There were 29 (51%) QBA methods that addressed unmeasured confounding, 20 (35%) misclassification bias, 5 (9%) selection bias, and 3 (5%) multiple biases. 38 (67%) QBA methods were designed to generate bias-adjusted effect estimates and 18 (32%) were designed to describe how bias could explain away observed findings. 22 (39%) articles provided code or online tools to implement the QBA methods.

Conclusion

In this systematic review, we identified a total of 57 QBA methods for summary level epidemiologic data published in the peer-reviewed literature. Future investigators can use this systematic review to identify different QBA methods for summary level epidemiologic data.

What is New?

Key findings

This systematic review identified 57 quantitative bias analysis (QBA) methods for summary level data from observational and non-randomized interventional studies.

Overall, there were 29 QBA methods that addressed unmeasured confounding, 20 that addressed misclassification bias, 5 that addressed selection bias, and 3 that addressed multiple biases.

What this adds to what is known related to methods research within the field of clinical epidemiology?

This systematic review provides an overview of the range and characteristics of QBA methods for summary level epidemiologic that are published in the peer-reviewed literature and that can be used by researchers within the field of clinical epidemiology.

What is the implication, what should change now?

This systematic review may help future investigators identify different QBA methods for summary level data. However, investigators should carefully review the original manuscripts to ensure that any assumptions are fulfilled, that the necessary bias parameters are available and accurate, and that all interpretations and conclusions are made with caution.
Age-patterns of severity of clade I mpox in historically endemic countries
Authors: Whittles Lilith K , Mbala-Kingebeni Placide , Ferguson Neil M
Published: April 2024

Background

The last two years have seen mpox emerge as a notable pandemic threat. The global 2022-23 outbreak of clade II mpox caused over 93,000 cases worldwide, while the 2023-24 epidemic of the more severe clade I virus in the Democratic Republic of Congo (DRC) has caused over 14,000 cases and over 650 deaths thus far. Of particular concern is that both case incidence and mortality in the DRC outbreak are concentrated in children.

However, quantification of age variation in severity for clade I infections has been lacking to date.

Methods

Using Bayesian binomial regression models, we analysed data from systematically reviewed clade I outbreaks to estimate case fatality ratios (CFR) by age, smallpox vaccination status and over time. We compared model predictive performance using leave-one-out cross-validation and compared our findings to the ongoing DRC outbreak.

Findings

The CFR had a near-reciprocal relationship with age, declining from 9.7% (95% credible interval: 6.9%-13.0%) among 5-year-olds to 1.2% (95%CrI: 0.3%-3.7%) by age 30. Accounting for vaccination status in addition to age did not improve model fit, but posterior parameter estimates suggest substantial vaccine-protection against death. Reanalysis incorporating cases from the ongoing DRC outbreak suggested less steep declines in severity with age and a protective effect of vaccination against death of 64% (95%CrI: - 3.4%-95.6%) and reduction in severity over time.

Interpretation

We provide estimates of the mpox clade I CFR in historically endemic settings by vaccine status, and find the highest risk of death in the youngest children.

Funding

Wellcome, NIHR, MRC, Community Jameel
JNK and PI3K signaling pathways mediate synapse formation and network spontaneous activities in primary neurons
Authors: Jia Xiaoli , Zhu Qiuyan , Wu Shaohua , Zhou Zhihong , Jiang Xian
Published: April 2024

Background

Cellular signals orchestrating synapse formation and neuronal network function remain poorly understood. To explore the critical signaling pathways in neurons and their influence on network development, pharmacological assays were employed to inhibit multiple signaling pathways in cultured neurons.

Methods

Immunofluorescence and western blotting are applied to identify the expression of synapse-related proteins within neurons. micro-electrode arrays (MEAs) are employed to study the developmental characteristics of neuronal networks. RNA sequencing is utilized to determine the gene expression profiles pertaining to multiple signaling pathways.

Results

Canonical c-jun N-terminal kinases (JNK) pathway is necessary for pre- and post-synaptic specializations, while phosphatidylinositide3-kinases (PI3K) is a key to postsynaptic specialization and affects the puncta sizes of presynaptic marker. Unexpectedly, pharmacological inhibition of JNK pathway significantly suppressed the mean firing rate (MFR), network burst frequency (NBF) and regularity of network firing after 4 weeks, but did not alter the synchrony of the network. During network development, PI3K pathway regulates the longer burst duration and lower network synchrony. Gene sets associated with neurodevelopmental processes and myelination was disturbed during restraining these signal pathways. Furthermore, inhibition of the PI3K signaling pathway obviously transformed voltage-gated ion channel activity, synaptic transmission and synaptic plasticity of neurons.

Conclusion

This study reveals that JNK and PI3K signaling pathways play different roles during synapse formation, and these signaling pathways have a lasting impact on the development of neuronal networks. Thus, this study provides further insights into the intracellular signaling pathways associated with synapse formation in the development of neuronal networks.
Quantitative single cell mass spectrometry reveals the dynamics of plant natural product biosynthesis
Authors: Vu Anh Hai , Kang Moonyoung , Wurlitzer Jens , Heinicke Sarah , Li Chenxin , Wood Joshua C. , Grabe Veit , Buell C. Robin , Caputi Lorenzo , O’Connor Sarah E.
Published: April 2024

Plants produce an extraordinary array of complex natural products (specialized metabolites). Since the biosynthetic genes that are responsible for synthesis of these molecules are often localized to rare or distinct cell types, recently developed single cell RNA-sequencing (scRNA-seq) approaches have tremendous potential to resolve these complex pathways. In contrast, detection, identification, and quantification of metabolites in single cells has remained challenging. Here, we report a robust method for single cell mass spectrometry in which we rigorously characterize and quantify the concentrations of four classes of natural products in individual cells of leaf, root, and petal of the medicinal plantCatharanthus roseus. These single cell mass spectrometry datasets reveal information about the biosynthetic processes that cannot be determined from the corresponding scRNA-seq data alone, providing a highly resolved picture of natural product biosynthesis at cell-specific resolution.