bluuebunny/crossref_metadata_2025 huggingface dataset:
Interplay between cohesin kinetics and polymer relaxation modulates chromatin-domain structure and dynamics
Authors: Kadam Sangram , Sahoo Soudamini , Kumar P. B. Sunil , Padinhateeri Ranjith
Published: May 2024

The three-dimensional organization of chromatin into domains and compartments leads to specific scaling of contact probability and compaction with genomic distance. However, chromatin is also dynamic, with active loop extrusion playing a crucial role. While extrusion ensures a specific spatial organization, how it affects the dynamic scaling of measurable quantities is an open question. In this work, using polymer simulations with active loop extrusion, we demonstrate that the interplay between the timescales of extrusion processes and polymer relaxation can influence the 3D organization of chromatin polymer. We point out this as a factor contributing to the experimentally observed non-trivial scaling of relaxation time with genomic separation and mean-square displacement with time. We show that the dynamic scaling exponents with loop extrusion are consistent with the experimental observations and can be very different from those predicted by existing fractal-globule models for chromatin.
MEK1/2 and ERK1/2 mediated lung endothelial injury and altered hemostasis promote diffuse alveolar hemorrhage in murine lupus
Authors: Zhuang Haoyang , Han Shuhong , Harris Neil S. , Reeves Westley H.
Published: May 2024

Objective

About 3% of lupus patients develop severe diffuse alveolar hemorrhage (DAH) with pulmonary vasculitis. B6 mice with pristane-induced lupus also develop DAH, but BALB/c mice are resistant. DAH is independent of TLR signaling and other inflammatory pathways. This study examined the role of the mitogen-activated protein kinase pathway (MEK1/2-ERK1/2, JNK, p38).

Methods

B6 and BALB/c mice were treated with pristane ± inhibitors of MEK1/2 (trametinib/GSK1120212, “GSK”), ERK1/2 (SCH772984, “SCH”), JNK, or p38. Effects on lung hemorrhage and hemostasis were determined.

Results

GSK and SCH abolished DAH, whereas JNK and p38 inhibitors were ineffective. Apoptotic cells were present in lung from pristane-treated mice, but not mice receiving pristane+GSK and endothelial dysfunction was normalized. Expression of the ERK1/2-regulated transcription factorEgr1increased in pristane-treated B6, but not BALB/c, mice and was normalized by GSK. Pristane also increased expression of the anticoagulant genesTfpi(tissue factor pathway inhibitor) andThbd(thrombomodulin) in B6 mice. The ratio of tissue factor (F3) toTfpiincreased in B6 (but not BALB/c) mice and was normalized by GSK. Circulating Thbd protein increased in B6 mice and returned to normal after GSK treatment. Consistent with augmented endothelial anticoagulant activity, pristane treatment increased tail bleeding in B6 mice.

Conclusion

Pristane treatment promotes lung endothelial injury and DAH in B6 mice by activating the MEK1/2-ERK1/2 pathway and impairing hemostasis. The hereditary factors determining susceptibility to lung injury and bleeding in pristane-induced lupus are relevant to the pathophysiology of life-threatening DAH in SLE and may help to optimize therapy.
Compartmental Differences in the Retinal Ganglion Cell Mitochondrial Proteome
Authors: Lewis Liam S.C. , Skiba Nikolai P. , Hao Ying , Bomze Howard M. , Arshavsky Vadim Y. , Cartoni Romain , Gospe Sidney M.
Published: May 2024

Among neurons, retinal ganglion cells (RGCs) are uniquely sensitive to mitochondrial dysfunction. The RGC is highly polarized, with a somatodendritic compartment in the inner retina and an axonal compartment projecting to targets in the brain. The drastically dissimilar functions of these compartments implies that mitochondria face different bioenergetic and other physiological demands. We hypothesized that compartmental differences in mitochondrial biology would be reflected by disparities in mitochondrial protein composition. Here, we describe a protocol to isolate intact mitochondria separately from mouse RGC somatodendritic and axonal compartments by immunoprecipitating labeled mitochondria from RGC MitoTag mice. Using mass spectrometry,471and357proteins were identified in RGC somatodendritic and axonal mitochondrial immunoprecipitates, respectively. We identified 10 mitochondrial proteins exclusively in the somatodendritic compartment and 19 enriched ≥2-fold there, while 3 proteins were exclusively identified and 18 enriched in the axonal compartment. Our observation of compartment-specific enrichment of mitochondrial proteins was validated through immunofluorescence analysis of the localization and relative abundance of superoxide dismutase (SOD2), sideroflexin-3 (SFXN3) and trifunctional enzyme subunit alpha (HADHA) in retina and optic nerve specimens. The identified compartmental differences in RGC mitochondrial composition may provide promising leads for uncovering physiologically relevant pathways amenable to therapeutic intervention for optic neuropathies.
The influence of calcific aortic stenosis on atrioventricular conduction: a prospective observational study and Mendelian randomization
Authors: Rao Karan , Ciofani Jonathan L , Han Daniel , Nazarzadeh Milad , Rahimi Kazem , Baer Alexandra , Saad Natasha , Litkouhi Princess Neila , Allahwala Usaid , Hansen Peter , Bhindi Ravinay
Published: May 2024

Background

Aortic stenosis (AS) may prolong atrioventricular (AV) conduction secondary to calcium infiltration of the atrioventricular-His-pathway, which is hypothesized to contribute to bradyarrhythmia and sudden cardiac death in this cohort. This study investigates the correlation between calcific AS and impaired AV conduction.

Methods

We performed an observational study and Mendelian randomization (MR). The observational study was a sub-analysis on AS patients undergoing transcatheter aortic valve implantation2021-2023). Regression analyses were used to assess the association between aortic valve calcium volumes with electrophysiology study derived markers of AV conduction. The primary MR analyses used European-ancestry genome-wide association studies for AS (653,867 participants,13,765 cases) and PR interval (271,570 participants). The exposure outcome was the genetic liability for AS, whilst the outcome was prolonged PR interval or AV block.

Results

The mean age in the observational study (n=196) was 81.8 years, 64.8% were men, and 46(23.6%) had first-degree heart block. There was no significant association between total aortic valve complex calcium volume and first-degree heart block, or with PR, AH or HV intervals. On MR, no association was found between genetic liability for AS and PR interval (beta -0.41, 95%CI -1.33-0.51, p=0.38). Additional analyses evaluating genetic liability for AS and AV block suggested a significant association on IVW analysis (OR 1.15, 95%CI 1.02-1.30, p=0.02), but this was not supported by sensitivity analyses and thus interpreted with caution.

Conclusions

This study found no meaningful association between aortic valve calcification and PR, AH or HV interval, challenging the hypothesis that calcific AS impairs atrioventricular conduction.
Investigation and optimization the effect of electrical stimulation parameters on the differentiation of human adipose mesenchymal stem cells into neurons-like cells on carbon nanofibers
Authors: Nekounam Houra , Golmohammadi Hossein , Amini Seyed Mohammad , Shokrgozar Mohammad Ali , Faridi-Majid Reza
Published: May 2024

Background

Neurodegenerative diseases are among the most challenging diseases because neuron cells are not able to regenerate spontaneously. Tissue engineering is one of the most promising stem cell-based therapies. Controlling stem cell differentiation is a very crucial aspect of tissue engineering.

Methods

In this study, carbon nanofibers with an average diameter of 181±45 nm were prepared as a conductive scaffold based on the electrospinning method and subsequent thermal processing. Scaffold structure characterization were performed with XRD, Raman and Electrical conductivity tests. A homemade device was prepared to transmit electrical current to cells seeded on the scaffold in a culture plate. Various current parameters such as current intensity, frequency, waveform, daily shock duration, and shock period on adipose mesenchymal stem cells were examined for differentiation into neuronal cells. SPSS software and the one-way analysis of variance (ANOVA) was used as statistical analysis.

Results

Characterization tests confirmed the formation of the carbon and crystallite structure with the electrical conductivity . Current with 1500 uA intensity, 500Hz frequency, and square waveform were selected as the optimal current parameters. It was found that the daily and periodic increase in shock time leads to an increase in the expression of neural and glial genes. A comparison of groups with real-time PCR and immunofluorescence of nestin, Map2, TubB3, and GFAPgenes was evaluated.

Conclusions

There are a variety of chemical and physical methods to control cell behavior, one of which is electrical stimulation. Conductive scaffolding is required for direct electrical stimulation of cells. The results showed that the method based on electrical stimulation can well cause neural differentiation, and considering the problems in preparing and maintaining chemical differentiation agents, it can be used practically.Graphical abstract:

stages of scaffold preparation and electrical stimulation of stem cells
Unveiling genetic anchors in Saccharomyces cerevisiae: QTL mapping identifies IRA2 as a key player in ethanol tolerance and beyond
Authors: Tristão Larissa Escalfi , de Sousa Lara Isensee Saboya , Vargas Beatriz de Oliveira , José Juliana , Carazzolle Marcelo Falsarella , Silva Eduardo Menoti , Galhardo Juliana Pimentel , Pereira Gonçalo Amarante Guimarães , de Mello Fellipe da Silveira Bezerra
Published: May 2024

Ethanol stress inSaccharomyces cerevisiaeis a well-studied phenomenon, but pinpointing specific genes or polymorphisms governing ethanol tolerance remains a subject of ongoing debate. Naturally found in sugar-rich environments, this yeast has evolved to withstand high ethanol concentrations, primarily produced during fermentation in the presence of suitable oxygen or sugar levels. Originally a defense mechanism against competing microorganisms, yeast-produced ethanol is now a cornerstone of brewing and bioethanol industries, where customized yeasts require high ethanol resistance for economic viability. However, yeast strains exhibit varying degrees of ethanol tolerance, ranging from 8% to 20%, making the genetic architecture of this trait complex and challenging to decipher. In this study, we introduce a novel QTL mapping pipeline to investigate the genetic markers underlying ethanol tolerance in an industrial bioethanolS. cerevisiaestrain. By calculating missense mutation frequency in a prominent QTL region within a population of 1011S. cerevisiaestrains, we uncovered rare occurrences in geneIRA2. Following molecular validation, we confirmed the significant contribution of this gene to ethanol tolerance, particularly in concentrations exceeding 12% of ethanol.IRA2pivotal role in stress tolerance due to its participation in the Ras-cAMP pathway was further supported by its involvement in other tolerance responses, including thermotolerance, low pH tolerance, and resistance to acetic acid. Understanding the genetic basis of ethanol stress inS. cerevisiaeholds promise for developing robust yeast strains tailored for industrial applications.
Enhancing Transcriptome Mapping with Rapid PRO-seq Profiling of Nascent RNA
Authors: Cingaram Pradeep Reddy , Beckedorff Felipe , Yue Jingyin , Liu Fan , Dos Santos Helena Gomes , Shiekhattar Ramin
Published: May 2024

Precision nuclear run-on (PRO) sequencing (PRO-seq) is a powerful technique for mapping polymerase active sites with nucleotide resolution and measuring newly synthesized transcripts at both promoters and enhancer elements. The current PRO-seq protocol is time-intensive, technically challenging, and requires a large amount of starting material. To overcome these limitations, we developed rapid PRO-seq (rPRO-seq) which utilizes pre-adenylated single-stranded DNAs (AppDNA), a dimer blocking oligonucleotide (DBO), on-bead 5’ RNA end repair, and column-based purification. These modifications enabled efficient transcriptome mapping within a single day (∼12 hours) increasing ligation efficiency, abolished adapter dimers, and reduced sample loss and RNA degradation. We demonstrate the reproducibility of rPRO-seq in measuring polymerases at promoters, gene bodies, and enhancers as compared to original PRO-seq protocols. Additionally, rPRO-seq is scalable, allowing for transcriptome mapping with as little as 25,000 cells. We apply rPRO-seq to study the role of Integrator in mouse hematopoietic stem and progenitor cell (mHSPC) homeostasis, identifyingInts11as an essential component of transcriptional regulation and RNA processing in mHSPC homeostasis. Overall, rPRO-seq represents a significant advance in the field of nascent transcript analyses and will be a valuable tool for generating patient-specific genome-wide transcription profiles with minimal sample requirements.
Environment by environment interactions (ExE) differ across genetic backgrounds (ExExG)
Authors: Schmidlin Kara , Ogbunugafor C. Brandon , Sastokas Alexander , Geiler-Samerotte Kerry
Published: May 2024

While the terms “gene-by-gene interaction” (GxG) and “gene-by-environment interaction” (GxE) are widely recognized in the fields of quantitative and evolutionary genetics, “environment-byenvironment interaction” (ExE) is a term used less often. In this study, we find that environmentby-environment interactions are a meaningful driver of phenotypes, and moreover, that they differ across different genotypes (suggestive of ExExG). To support this conclusion, we analyzed a large dataset of roughly 1,000 mutant yeast strains with varying degrees of resistance to different antifungal drugs. Our findings reveal that the effectiveness of a drug combination, relative to single drugs, often differs across drug resistant mutants. Remarkably, even mutants that differ by only a single nucleotide change can have dramatically different drug x drug (ExE) interactions. We also introduce a new framework that more accurately predicts the direction and magnitude of ExE interactions for some mutants. Understanding how ExE interactions change across genotypes (ExExG) is crucial not only for modeling the evolution of pathogenic microbes, but also for enhancing our knowledge of the underlying cell biology and the sources of phenotypic variance within populations. While the significance of ExExG interactions has been overlooked in evolutionary and population genetics, these fields and others stand to benefit from understanding how these interactions shape the complex behavior of living systems.
De novogenome assembly for an endangered lemur using portable nanopore sequencing in rural Madagascar
Authors: Hauff Lindsey , Rasoanaivo Noa Elosmie , Razafindrakoto Andriamahery , Ravelonjanahary Hajanirina , Wright Patricia C. , Rakotoarivony Rindra , Bergey Christina M.
Published: May 2024

As one of the most threatened mammalian taxa, lemurs of Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on conservation genomics to identify populations of particular concern. However, many of these genomic approaches necessitate high-quality genomes. While the advent of next generation sequencing technologies and the resulting reduction of associated costs have led to the proliferation of genomic data and high-quality reference genomes, global discrepancies in genomic sequencing capabilities often result in biological samples from biodiverse host countries being exported to facilities in the Global North, creating inequalities in access and training within genomic research. Here, we present the first reference genome for the endangered red-fronted brown lemur (Eulemur rufifrons) from sequencing efforts conducted entirely within the host country using portable Oxford Nanopore sequencing. Using an archivedE. rufifronsspecimen, we conducted long-read, nanopore sequencing at the Centre ValBio Research Station near Ranomafana National Park, in rural Madagascar, generating over 750 Gb of sequencing data from 10 MinION flow cells. Exclusively using this long-read data, we assembled 2.21 gigabase, 20,330-contig nuclear assembly with an N50 of 98.9 Mb and a 17,108 bp mitogenome. The nuclear assembly had 31x average coverage and was comparable in completeness to other primate reference genomes, with a 95.47% BUSCO completeness score for primate-specific genes. As the first reference genome forE. rufifronsand the only annotated genome available for the specioseEulemurgenus, this resource will prove vital for conservation genomic studies while our efforts exhibit the potential of this protocol to address research inequalities and build genomic capacity.
In Utero Hematopoietic Stem Cell Transplant for Fanconi Anemia
Authors: Swartzrock Leah , Dib Carla , Denis Morgane , Willner Hana , Ho Katie , Haslett Ethan , Krampf Mark R. , Girsen Anna , Blumenfeld Yair J. , El-Sayed Yasser Y. , Roncarolo Maria G , MacKenzie Tippi C. , Czechowicz Agnieszka D.
Published: May 2024

Fanconi Anemia (FA) is an inherited DNA-repair deficiency caused by mutations in diverseFancgenes that leads to bone marrow failure and malignancies. FA disease begins at early embryonic stages, and while FA prenatal testing has long been available, no fetal therapies for FA currently exist. Postnatally, FA hematologic disease can be cured through allogeneic hematopoietic stem cell transplantation (HSCT); however, this requires chemotherapy and/or irradiation-based conditioning which amongst various side-effects also increases likelihood of malignancies later in life in these fragile patients. Given fetal immune tolerance and the competitive advantage of healthy hematopoietic stem and progenitor cells (HSPCs) over failing FA HSPCs, in utero HSCT without conditioning may be an alternative approach to stabilization of the hematopoietic system without conventional toxicities. We performed in utero HSCT using HSPCs from wildtype (WT) donors into two FA mouse models (Fancd2−/−,Fanca−/−) and observed robust multi-lineage hematopoietic donor engraftment in homozygous FA mice compared to both heterozygous FA and WT littermates. Upon serial assessments, we also observed increasing donor chimerism up to 94.1%, showcasing the competitive advantage of WT donor HSPCs over FA HSPCs. Given that 1% donor chimerism is predicted to stabilize FA BM, in utero HSCT may be a safe and curative prenatal treatment for all subtypes of FA.
Cell-type specific auditory responses in the striatum are shaped by feed forward inhibition
Authors: Druart Mélanie , Kori Megha , Chaimowitz Corryn , Fan Catherine , Sippy Tanya
Published: May 2024

Summary/Abstract

The posterior “tail” region of the striatum receives dense innervation from sensory brain regions and has been demonstrated to play a role in behaviors that require sensorimotor integration including discrimination1,2, avoidance3and defense4responses. The output neurons of the striatum, the D1 and D2 striatal projection neurons (SPNs) that make up the direct and indirect pathways, respectively, are thought to play differential roles in these behavioral responses, although it remains unclear if or how these neurons display differential responsivity to sensory stimuli. Here, we used whole-cell recordings in vivo and ex vivo to examine the strength of excitatory and inhibitory synaptic inputs onto D1 and D2 SPNs following the stimulation of upstream auditory pathways. While D1 and D2 SPNs both displayed stimulus-evoked depolarizations, D1 SPN responses were stronger and faster for all stimuli tested in vivo as well as in brain slices. This difference did not arise from differences in the strength of excitatory inputs but from differences in the strength of feed forward inhibition. Indeed, fast spiking interneurons, which are readily engaged by auditory afferents exerted stronger inhibition onto D2 SPNs compared to D1 SPNs. Our results support a model in which differences in feed forward inhibition enable the preferential recruitment of the direct pathway in response to auditory stimuli, positioning this pathway to initiate sound-driven actions.
Depression in Parkinson’s disease is associated with dopamine unresponsive reduced reward sensitivity during effort-based decision making
Authors: Costello Harry , Yamamori Yumeya , Kieslich Karel , Murphy Mackenzie , Bobyreva Kamilla , Schrag Anette-Eleonore , Howard Robert , Roiser Jonathan P
Published: May 2024

Willingness to exert effort for a given goal is dependent on the magnitude of the potential rewards and effort costs of an action. Such effort-based decision making is an essential component of motivation, in which the dopaminergic system plays a key role. Depression in Parkinson’s disease (PD) is common, disabling and has poor outcomes. Motivational symptoms such as apathy and anhedonia, are prominent in PD depression and related to dopaminergic loss. We hypothesised that dopamine-dependent disruption in effort-based decision-making contributes to depression in PD.

In the present study, an effort-based decision-making task was administered to 62 patients with PD, with and without depression, ON and OFF their dopaminergic medication across two sessions, as well as to 34 patients with depression and 29 matched controls on a single occasion. During the task, on each trial, participants decided whether to accept or reject offers of different levels of monetary reward in return for exerting varying levels of physical effort via grip force, measured using individually calibrated dynamometers. The primary outcome variable was choice (accept/decline offer), analysed using both logistic mixed-effects modelling and a computational model which dissected the individual contributions of reward and effort on depression and dopamine state in PD.

We found PD depression was characterised by lower acceptance of offers, driven by markedly lower incentivisation by reward (reward sensitivity), compared to all other groups. Within-subjects analysis of the effect of dopamine medication revealed that, although dopamine treatment improves reward sensitivity in non-depressed PD patients, this therapeutic effect is not present in PD patients with depression.

These findings suggest that disrupted effort-based decision-making, unresponsive to dopamine, contributes to PD depression. This highlights reward sensitivity as a key mechanism and treatment target for PD depression that potentially requires non-dopaminergic therapies.
Mitochondrial Phosphopantetheinylation is Required for Oxidative Function
Authors: Norden Pieter R. , Wedan Riley J. , Longenecker Jacob Z. , Preston Samuel E. J. , Graber Naomi , Pentecost Olivia A. , Canfield Morgan , McLaughlin Elizabeth , Nowinski Sara M.
Published: May 2024

4’-phosphopantetheinyl (4’PP) groups are essential co-factors added to target proteins byphosphopantetheinyl transferase (PPTase) enzymes. Although mitochondrial 4’PP-modified proteins have been described for decades, a mitochondrially-localized PPTase has never been found in mammals. We discovered that the cytoplasmic PPTaseaminoadipatesemialdehydedehydrogenasephosphopantetheinyltransferase (AASDHPPT) is required for mitochondrial respiration and oxidative metabolism. Loss of AASDHPPT results in failed 4’-PP modification of the mitochondrial acyl carrier protein and blunted activity of the mitochondrial fatty acid synthesis (mtFAS) pathway. We found that in addition to its cytoplasmic localization, AASDHPPT localizes to the mitochondrial matrix via an N-terminal mitochondrial targeting sequence contained within the first 13 amino acids of the protein. Our data show that this novel mitochondrial localization of AASDHPPT is required to support mtFAS activity and oxidative function. We further identify two variants of uncertain significance inAASDHPPTthat are likely pathogenic in humans due to loss of mtFAS activity.
Yes Associated Transcriptional Regulator 1 (YAP1) and WW Domain Containing Transcription Regulator (WWTR1) are required for murine pregnancy initiation
Authors: Moldovan Genna E. , Massri Noura , Vegter Erin , Pauneto-Delgado Ivonne L , Burns Gregory W. , Joshi Niraj , Gu Bin , Arora Ripla , Fazleabas Asgerally T.
Published: May 2024

Endometrial stromal cell decidualization is required for pregnancy success. Although this process is integral to fertility, many of the intricate molecular mechanisms contributing to decidualization remain undefined. One pathway that has been implicated in endometrial stromal cell decidualization in humansin vitrois the Hippo signaling pathway. Two previously conducted studies showed that the effectors of the Hippo signaling pathway, YAP1 and WWTR1, were required for decidualization of primary stromal cells in culture. To investigate thein vivorole of YAP1 and WWTR1 in decidualization and pregnancy initiation, we generated aProgesterone Cremediated partial double knockout (pdKO) ofYap1andWwtr1. Female pdKOs exhibited subfertility, a compromised decidualization response, partial interruption in embryo transport, blunted endometrial receptivity, delayed implantation and subsequent embryonic development, and a unique transcriptional profile. Bulk mRNA sequencing revealed aberrant maternal remodeling evidenced by significant alterations in extracellular matrix proteins at 7.5 days post-coitus in pdKO dams and enrichment for terms associated with fertility-compromising diseases like pre-eclampsia and endometriosis. Our results indicate a required role for YAP1 and WWTR1 for successful mammalian uterine function and pregnancy success.
Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat
Authors: Li Yichen , Chen Enlian , Xu Jialu , Zhang Wenhai , Zeng Xiangxiang , Liu Yuansheng , Luo Xiao
Published: May 2024

Error self-correction is a pivotal first step in the analysis of long-read sequencing data. However, most existing methods for this purpose are primarily tailored for noisy sequencing data with error rates exceeding 5%, often collapsing true variants in repeats and haplotypes. Alternatively, some methods are heavily optimized for PacBio HiFi reads, leaving a gap in methods specifically designed for Nanopore R10 reads basecalled with high accuracy or super accuracy models, which typically have error rates below 2%. Here, we introduce DeChat, a novel approach specifically designed for Nanopore R10 reads. DeChat enables repeat- and haplotype-aware error correction, leveraging the strengths of both de Bruijn graphs and variant-aware multiple sequence alignment to create a synergistic approach. This approach avoids read overcorrection, ensuring that variants in repeats and haplotypes are preserved while sequencing errors are accurately corrected. Benchmarking experiments reveal that reads corrected using DeChat exhibit substantially fewer errors, ranging from several times to two orders of magnitude lower, compared to the current state-of-the-art approaches. Furthermore, the application of DeChat for error correction significantly improves genome assembly across various aspects. DeChat is implemented as a highly efficient, standalone, and user-friendly software and is publicly available at https://github.com/LuoGroup2023/DeChat.
Experimental parkinsonism induced by tetanus toxin injected into basal ganglia
Authors: Meglić Patrik , Šoštarić Petra , Habek Nikola , Virag Davor , Knezović Ana , Matak Ivica
Published: May 2024

Background and Objectives

Local inhibitory circuits and long-range inhibitory projections within the interconnected basal ganglia nuclei are critical for control of voluntary movement and pathophysiology of different extrapyramidal movement disorders. Herein, we examined the major motor effects of tetanus neurotoxin (TeNT), a presynaptic neurotoxin that selectively targets the GABA-ergic synaptic transmission, when injected into individual basal ganglia nuclei.

Methods

The rats were injected with low-dose TeNT (0.4-0.8 ng) unilaterally into globus pallidus internus (GPi), substantia nigra (SN), or caudate putamen (CPu). The effects of TeNT-induced disinhibition were characterized by repeated assessments of motor coordination, gait, and rotational behavior, followed by measurement of regional protein content of major neuronal monoaminergic, GABA-ergic and glutamatergic population markers.

Results

In the beamwalk test, the CPu injection of TeNT induced contralateral plantar misplacement. TeNT injections into GPi and CPu were associated with decreased stride length and increased duration of step cycle and induced a slight ipsiversive circling during open field observation, and more intensive rotational behavior during swimming, differentially affected by D-amphetamine. Unlike rotational behavior, the gait and motor control deficits during beamwalk recovered promptly by day 14 post TeNT, which, along with the lack of reduced neuronal marker protein contents, suggested the reversibility and lack of neuronal degeneration.

Conclusion and Implications

Tetanus toxin injected into basal ganglia evokes transient hypokinetic motor dysfunctions consistent with experimental parkinsonism, with differential occurrence of individual motor symptoms depending on the region targeted. These results suggest that TeNT might be a useful non-neurodegenerative pharmacological agent for investigating the motor control abnormalities involving GABA-ergic basal ganglia circuits.
Evolutionary Insights from the Mitochondrial Genome ofOikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss
Authors: Klirs Yael , Novosolov Maria , Gissi Carmela , Garic Rade , Pupko Tal , Stach Thomas , Huchon Dorothée
Published: May 2024

Sequencing the mitochondrial genome of the tunicateOikopleura dioicais a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation of the majority of the mitochondrial genome ofO. dioicaby means of combining several DNA and amplicon reads obtained by Illumina and MinIon Oxford Nanopore Technologies (ONT) with public RNA sequences. We document extensive RNA editing, since all homopolymer stretches present in the mitochondrial DNA correspond to 6U-regions in the mitochondrial RNA. Out of the 13 canonical protein-coding genes, we were able to detect eight, plus an unassigned ORF that lacked sequence similarity to canonical mitochondrial protein-coding genes. We show that thenad3gene has been transferred to the nucleus and acquired a mitochondria-targeting signal. In addition to two very short rRNAs, we could only identify a single tRNA (tRNA-Met), suggesting multiple losses of tRNA genes, supported by a corresponding loss of mitochondrial aminoacyl-tRNA synthetases in the nuclear genome. Based on the eight canonical protein-coding genes identified, we reconstructed maximum likelihood and Bayesian phylogenetic trees and inferred an extreme evolutionary rate of this mitochondrial genome. The phylogenetic position of appendicularians among tunicates, however, could not be accurately determined.

Significance

Sequencing and annotating the mitochondrial genome of fast-evolving organisms is difficult because they often present unusual characteristics. The tunicateOikopleura dioicais a model species for understanding tunicate and chordate genome evolution. However, no complete annotated mitochondrial genome for this species has been published to date. Here, we determined the major part of the mitochondrial genome ofO. dioica. Our results indicate the presence of highly modified rRNA genes and the absence of all tRNAs except tRNA-Met. Moreover, we show that the mitochondrial genome undergoes editing at the RNA level. Our study demonstrates that utilizing a combination of public RNA data and DNA from long-and short-read sequencing platforms significantly improves our ability to study mitochondrial genomes with atypical characteristics.
Histone Modifications and miRNA Perturbations Contribute to Transcriptional Dysregulation of Hypertrophy in Obstructive Hypertrophic Cardiomyopathy
Authors: Garmany Ramin , Dasari Surendra , Bos J. Martijn , Kim Evelyn T. , Tester David J. , Remedios Cristobal dos , Maleszewski Joseph J. , Robertson Keith D. , Dearani Joseph A. , Ommen Steve R. , Giudicessi John R. , Ackerman Michael J.
Published: May 2024

Abstract

Background

Recently, we demonstrated transcriptional downregulation of hypertrophy pathways in myectomy tissue derived from patients with obstructive hypertrophic cardiomyopathy (HCM) despite translational activation of hypertrophy pathways. The mechanisms and modifiers of this transcriptional dysregulation in HCM remain unexplored. We hypothesized that miRNA and post-translational modifications of histones contribute to transcriptional dysregulation in HCM.

Methods

First, miRNA-sequencing and chromatin immunoprecipitation sequencing (ChIP-seq) were performed on HCM myectomy tissue and control donor hearts to characterize miRNA and differential histone marks across the genome. Next, the differential miRNA and histone marks were integrated with RNA-sequencing (RNA-seq) data. Finally, the effects of miRNA and histones were removedin silicoto determine their necessity for transcriptional dysregulation of pathways.

Results

miRNA-analysis identified 19 differentially expressed miRNA. ChIP-seq analysis identified 2,912 (7%) differential H3K4me3 peaks, 23,339 (21%) differential H3K9ac peaks, 33 (0.05%) differential H3K9me3 peaks, 58,837 (42%) differential H3K27ac peaks, and 853 (3%) differential H3K27me3 peaks. Univariate analysis of concordance between H3K9ac with RNA-seq data showed activation of cardiac hypertrophy signaling, while H3K27me showed downregulation of cardiac hypertrophy signaling. Similarly, miRNAs were predicted to result in downregulation of cardiac hypertrophy signaling.In silicoknock-out that effects either miRNA or histones attenuated transcriptional downregulation while knocking out both abolished downregulation of hypertrophy pathways completely.

Conclusion

Myectomy tissue from patients with obstructive HCM shows transcriptional dysregulation, including transcriptional downregulation of hypertrophy pathways mediated by miRNA and post-translational modifications of histones. Cardiac hypertrophy loci showed activation via changes in H3K9ac and a mix of activation and repression via H3K27ac.
Passive shaping of intra- and intercellular m6A dynamics via mRNA metabolism
Authors: Dierks David , Shachar Ran , Nir Ronit , Garcia-Campos Miguel Angel , Uzonyi Anna , Wiener David , Toth Ursula , Rossmanith Walter , Lasman Lior , Slobodin Boris , Hanna Jacob H. , Antebi Yaron , Scherz-Shouval Ruth , Schwartz Schraga
Published: May 2024

m6A is the most widespread mRNA modification and is primarily implicated in controlling mRNA stability. Fundamental questions pertaining to m6A are the extent to which it is dynamically modulated within cells and across stimuli, and the forces underlying such modulation. Prior work has focused on investigatingactivemechanisms governing m6A levels, such as recruitment of m6A writers or erasers leading to either ‘global’ or ‘site-specific’ modulation. Here, we propose that changes in m6A levels across subcellular compartments and biological trajectories may result frompassivechanges in gene-level mRNA metabolism. To predict the intricate interdependencies between m6A levels, mRNA localization, and mRNA decay, we establish a differential model ‘m6ADyn’ encompassing mRNA transcription, methylation, export, and m6A-dependent and independent degradation. We validate the predictions of m6ADyn in the context of intracellular m6A dynamics, where m6ADyn predicts associations between relative mRNA localization and m6A levels, which we experimentally confirm. We further explore m6ADyn predictions pertaining to changes in m6A levels upon controlled perturbations of mRNA metabolism, which we also experimentally confirm. Finally, we demonstrate the relevance of m6ADyn in the context of cellular heat stress response, where genes subjected to altered mRNA product and export also display predictable changes in m6A levels, consistent with m6ADyn predictions. Our findings establish a framework for dissecting m6A dynamics and suggest the role of passive dynamics in shaping m6A levels in mammalian systems.
Mammalian RNAi represses pericentromeric lncRNAs to maintain genome stability
Authors: Sandoval Rafael , Dilsavor Corinne N. , Grishanina Nadia R. , Patel Vandan , Zamudio Jesse R.
Published: May 2024

Mammalian pericentromeric tandem repeats produce long noncoding RNAs (lncRNAs) that are dysregulated in cancer and linked to genomic instability. Identifying the basic molecular characteristics of these lncRNAs and their regulation is important to understanding their biological function. Here, we determine that the Argonaute (Ago) proteins of the RNA interference (RNAi) pathway directly and uniformly repress bidirectional pericentromeric lncRNAs in a Dicer-dependent manner in mouse embryonic and adult stem cells. Ago-dependent and Dicer-dependent autoregulatory small RNAs were identified within pericentromeric lncRNA degradation intermediates. We develop an RNase H cleavage assay to determine the relative proportions and lengths of the pericentromeric lncRNA targets. We find that 5’-phosphate and non-polyadenylated bidirectional pericentromeric lncRNAs are expressed at similar proportions. These lncRNAs can span up to 9 repeats, with transcription from the reverse strand template yielding the longer products. Using pericentromeric repeat RNA reporters, we determine that Ago represses pericentromeric lncRNAs after S phase transcription. Upon loss of Ago, pericentromeric lncRNA dysregulation results in delayed cell cycle progression, a defective mitotic spindle assembly checkpoint (SAC) and genomic instability. These results show that an evolutionarily conserved Ago activity at pericentromeres contributes to mammalian genome stability.
Assessing the Impact of Valve Sizing and Orientation on Bioprosthetic Pulmonary Valve Hemodynamics Using In Vitro 4D-Flow MRI
Authors: Schiavone Nicole K. , Nair Priya J. , Elkins Christopher J. , McElhinney Doff B. , Ennis Daniel B. , Eaton John K. , Marsden Alison L.
Published: May 2024

Purpose

Pulmonary valve replacement (PVR) using bioprosthetic valves is a common procedure performed in patients with repaired Tetralogy of Fallot and other conditions, but these valves frequently become dysfunctional within 15 years of implantation. Since PVR is often performed in adolescence, valves are typically oversized to account for somatic growth. However, the contribution of oversizing to early valve failure are not clearly understood. The purpose of this study was to explore the impact of valve sizing and orientation on local hemodynamics and valve performance.

Methods

Different valve sizes were represented by changing the cardiac output through a 25 mm bioprosthetic valve implanted in an idealized 3D-printed model of the right ventricular outflow tract (RVOT). The local hemodynamics at three valve sizes and two valve orientations were assessed using 4D-Flow MRI and high-speed camera imaging.

Results

Noticeable differences in jet asymmetry, the amount of recirculation, leaflet opening patterns, as well as the size and location of reversed flow regions were observed with varying valve sizes. Rotation of the valve resulted in drastic differences in reversed flow regions, but not forward flow.

Conclusion

Flow features observed in the oversized valve in this study have previously been correlated with calcification, hemolysis, and leaflet fatigue. Therefore, valve oversizing can negatively impact local hemodynamics and leaflet performance.
Oxysterol accumulation in aging cells alters GPCR signalling
Authors: Asthana Suramya , Verma Anant , Bhattacharya Baivabi , Nath Arnab , Sajeev Nithin , Maan Kiran , Nair Raji R. , Ayappa K. Ganapathy , Saini Deepak K.
Published: May 2024

Organismal aging is accompanied by the accumulation of senescent cells in the body, which drives tissue dysfunction. Senescent cells have a distinctive profile, including proliferation arrest, resistance to apoptosis, altered gene expression, and high inflammation. Despite global signalling and metabolic dysregulation during senescence, the underlying reasons for changes in signalling remain unclear. GPCRs are pivotal in cellular signalling, dynamically mediating the complex interplay between cells and their surrounding environment to maintain cellular homeostasis. The chemokine receptor CXCR4 plays a crucial role in modulating immune responses and inflammation. It has been shown that expression of CXCR4 increases in cells undergoing senescence, which enhances inflammation post-activation. Here we examine CXCR4 signalling in deeply senescent cells, where cholesterol and its oxidized derivatives, oxysterols, affect receptor function. We report elevated oxysterol levels in senescent cells, which altered classical CXCL12-mediated CXCR4 signalling. Tail-oxidized sterols disrupted signalling more than ring-oxidized counterparts. Molecular dynamics simulations revealed that 27-hydroxycholesterol displaces cholesterol and binds strongly to alter the conformation of critical signalling residues to modify the sterol-CXCR4 interaction landscape. Our study provides a molecular view of the observed mitigated GPCR signalling in the presence of oxysterols, which switched G-protein signalling from Gαi/oto Gαsclass. Overall, we present an altered paradigm of GPCR signalling where cholesterol oxidation alters the signalling outcome in aged cells.

Significance Statement

Our study brings to light a novel and significant discovery in aged cells: the accumulation of oxysterols, oxidized forms of cholesterol, critically impairs CXCR4-dependent signalling and alters G-protein coupling specificity. This effect of oxysterols is demonstrated for the first time in aged cellular models, providing a molecular basis for a multitude of observed alterations in senescence, such as compromised immune functions and a decline in cellular responsiveness with age. Our research not only fills a crucial gap in understanding the aging process at the molecular level but also identifies potential targets for therapeutic interventions aimed at mitigating age-related cellular dysfunctions and diseases.
Efficacy and Safety of Nasal High-Frequency Oscillation in Preventing Intubation in Very-Low-Birth-Weight Infants with Respiratory Distress Syndrome
Authors: Dang Buu Quoc , Pham Tam Thi Thanh , Nguyen Duc Ninh , Long Nguyen Phuoc , Nguyen Tinh Thu
Published: May 2024

Background

Invasive mechanical ventilation in very-low-birth-weight infants (VLBWI) was associated with immediate and long-term complications. Nasal high-frequency oscillation (nHFO) has recently become a new non-invasive ventilation (NIV) mode for treating respiratory failure in VLBWI. This study aimed to investigate the safety and efficacy of nHFO as an alternative respiratory support to prevent intubation in VLBWI.

Methods

A retrospective analysis was conducted using the clinical data of 42 VLBWIs with respiratory distress syndrome (RDS) who were treated in our department from August 2018 to August 2020 and met the selection criteria.

Results

nHFO was used as a rescue strategy in 32 infants and a prophylactic strategy in 10 infants. It was observed that out of 42 cases, 30 cases (71.4%) were able to avoid intubation within 72 hours, while 23 cases (54.8%) were successfully switched to another NIV mode from nHFO. There was a significant decrease in pCO2 and an increase in pH one hour after using nHFO in the success group. Two cases (4.8%) of feeding intolerance associated with nHFO were noted.

Conclusion

This study showed that nHFO as alternative respiratory support for preterm infants with RDS might be safe and effective in reducing the need for intubation.

Highlights

Invasive mechanical ventilation in very low-birth-weight infants (VLBWI) was associated with immediate and long-term complications. As a result, there is an increasing focus on researching and applying non-invasive ventilation (NIV).

In this study, Nasal high-frequency oscillation (nHFO) in VLBWI with respiratory distress syndrome showed promising efficacy and safety, with 71.4% of cases avoiding intubation within 72 hours. Further, 54.8% of cases were successfully transitioned to another NIV mode from nHFO.

Further randomized controlled trials with adequately powered sample sizes are warranted to assess the overall safety and efficacy of nHFO.
Identification of a divalent metal transporter required for cellular iron metabolism in malaria parasites
Authors: Loveridge Kade M. , Sigala Paul A.
Published: May 2024

Plasmodium falciparummalaria parasites invade and multiply inside red blood cells (RBCs), the most iron-rich compartment in humans. Like all cells,P. falciparumrequires nutritional iron to support essential metabolic pathways, but the critical mechanisms of iron acquisition and trafficking during RBC infection have remained obscure. Parasites internalize and liberate massive amounts of heme during large-scale digestion of RBC hemoglobin within an acidic food vacuole (FV) but lack a heme oxygenase to release porphyrin-bound iron. Although most FV heme is sequestered into inert hemozoin crystals, prior studies indicate that trace heme escapes biomineralization and is susceptible to non-enzymatic degradation within the oxidizing FV environment to release labile iron. Parasites retain a homolog of divalent metal transporter 1 (DMT1), a known mammalian iron transporter, but its role inP. falciparumiron acquisition has not been tested. Our phylogenetic studies indicate thatP. falciparumDMT1 (PfDMT1) retains conserved molecular features critical for metal transport. We localized this protein to the FV membrane and defined its orientation in an export-competent topology. Conditional knockdown of PfDMT1 expression is lethal to parasites, which display broad cellular defects in iron-dependent functions, including impaired apicoplast biogenesis and mitochondrial polarization. Parasites are selectively rescued from partial PfDMT1 knockdown by supplementation with exogenous iron, but not other metals. These results support a cellular paradigm whereby PfDMT1 is the molecular gatekeeper to essential iron acquisition by blood-stage malaria parasites and suggest that therapeutic targeting of PfDMT1 may be a potent antimalarial strategy.
Two Separated Worlds: on the Preference of Influence in Life Science and Biomedical Research
Authors: Gu Zuguang
Published: May 2024

We introduced a new metric, “citation enrichment”, to measure country-to-country influence using citation data. This metric evaluates the degree to which a country prefers to cite another country compared to a random citation process. We applied the citation enrichment method to over 12 million publications in the life science and biomedical fields and we have the following key findings: 1) The global scientific landscape is divided into two separated worlds where developed Western countries exhibit an overall mutual under-influence with the rest of the world; 2) Within each world, countries form clusters based on their mutual citation preferences, with these groupings strongly associated with their geographical and cultural proximity; 3) The two worlds exhibit distinct patterns of the influence balance among countries, revealing underlying mechanisms that drive influence dynamics. We have constructed a comprehensive world map of scientific influence which greatly enhances the deep understanding of the international exchange of scientific knowledge. The citation enrichment metric is developed under a well-defined statistical framework and has the potential to be extended into a versatile and powerful tool for bibliometrics and related research fields.