bluuebunny/crossref_metadata_2025 huggingface dataset:
ESPressoscope: a small and powerful platform for in situ microscopy
Authors: Li Ethan , Saggiomo Vittorio , Ouyang Wei , Prakash Manu , Diederich Benedict
Published: January 2024

Microscopy is essential for detecting, identifying, analyzing, and measuring small objects. Access to modern microscopy equipment is crucial for scientific research, especially in the biomedical and analytical sciences. However, the high cost of equipment, limited availability of parts, and challenges associated with transporting equipment often limit the accessibility and operational capabilities of these tools, particularly in field sites and other remote or resource-limited settings. Thus, there is a need for affordable and accessible alternatives to traditional microscopy systems. We address this challenge by investigating the feasibility of using a simple microcontroller board not only as a portable and field-ready digital microscope, but furthermore as a versatile platform which can easily be adapted to a variety of imaging applications. By adding a few external components, we demonstrate that a low-cost ESP32 camera board can be used to build an autonomous in situ platform for digital time-lapse imaging of cells. This platform, which we call the ESPressoscope, can be adapted to applications ranging from monitoring incubator cell cultures in the lab to observing ecological phenomena in the sea, and it can be adapted for other techniques such as microfluidics or spectrophotometry. The ESPressoscope achieves a low power consumption and small size, which makes it ideal for field research in environments and applications where microscopy was previously infeasible. Its Wi-Fi connectivity enables integration with external image processing and storage systems, including on cloud platforms when internet access is available. Finally, we present several web browser-based tools to help users operate and manage the ESPressoscope’s software. Our findings demonstrate the potential for low-cost, portable microscopy solutions to enable new and more accessible experiments for biological and analytical applications.
nail: software for high-speed, high-sensitivity protein sequence annotation
Authors: Roddy Jack W. , Rich David H. , Wheeler Travis J.
Published: January 2024

“Fast is fine, but accuracy is final.”

-- Wyatt Earp

Background

The extreme diversity of newly sequenced organisms and considerable scale of modern sequence databases lead to a tension between competing needs for sensitivity and speed in sequence annotation, with multiple tools displacing the venerable BLAST software suite on one axis or another. Alignment based on profile hidden Markov models (pHMMs) has demonstrated state of art sensitivity, while recent algorithmic advances have resulted in hyper-fast annotation tools with sensitivity close to that of BLAST.

Results

Here, we introduce a new tool that bridges the gap between advances in these two directions, reaching speeds comparable to fast annotation methods such as MMseqs2 while retaining most of the sensitivity offered by pHMMs. The tool, callednail, implements a heuristic approximation of the pHMM Forward/Backward (FB) algorithm by identifying a sparse subset of the cells in the FB dynamic programming matrix that contains most of the probability mass. The method produces an accurate approximation of pHMM scores and E-values with high speed and small memory requirements. On a protein benchmark,nailrecovers the majority of recall difference between MMseqs2 and HMMER, with run time ∼26x faster than HMMER3 (only ∼2.4x slower than MMseqs2’s sensitive variant).nailis released under the open BSD-3-clause license and is available for download athttps://github.com/TravisWheelerLab/nail.
The MKK3 module integrates nitrate and light signals to modulate secondary dormancy inArabidopsis thaliana
Authors: Regnard Sarah , Otani Masahiko , Keruzore Marc , Teinturier Alizée , Blondel Marc , Kawakami Naoto , Krapp Anne , Colcombet Jean
Published: January 2024

Seed dormancy corresponds to a reversible blockage of germination. Primary dormancy is established during seed maturation while secondary dormancy is set up on the dispersed seed, following an exposure to unfavourable factors. Both dormancies are relieved in response to environmental factors, such as light, nitrate and coldness. QTL analyses for preharvest sprouting identified MKK3 kinase in cereals as a player in dormancy control. Here, we showed that MKK3 also plays a role in secondary dormancy in Arabidopsis within a signalling module composed of MAP3K13/14/19/20, MKK3 and clade-C MAPKs. Seeds impaired in this module acquired heat-induced secondary dormancy more rapidly than WT seeds and this dormancy is less sensitive to nitrate, a signal able to release dormancy. We also demonstrated that MPK7 was strongly activated in the seed during dormancy release, especially in response to light and nitrate. This activation was greatly reduced inmap3k13/14/19/20andmkk3mutants. Finally, we showed that the module was not regulated, and apparently did not regulate, the genes controlling ABA/GA hormone balance, one of the crucial mechanisms of seed dormancy control. Overall, our work identified a whole new MAPK module controlling seed germination and enlarged the panel of functions of the MKK3-related modules in plants.
Organic macromolecules transport a significant proportion of the calcium precursor for nacre formation
Authors: Macías-Sánchez Elena , Huang Xing , Willinger Marc G. , Rodríguez-Navarro Alejandro , Checa Antonio
Published: January 2024

The mechanism of nacre formation in gastropods involves a vesicular system that transports organic and mineral precursors from the mantle epithelium to the mineralization chamber. Between them lies the surface membrane, a thick organic structure that covers the mineralization chamber and the forming nacre. The surface membrane is a dynamic structure that grows by the addition of vesicles on the outer side and recedes by the formation of interlamellar membranes on the inner side. By using a combination of electron microscopy imaging and spectroscopy, we have monitored the journey of the vesicles from the mantle epithelium to the mineralization chamber, focusing on the elemental composition of the organic structures at each stage. Our data reveal that transport occurs in lipid bilayer vesicles through exocytosis from the outer mantle epithelium. After release into the surface membrane, chitin undergoes a process of self-assembly and interaction with proteins, resulting in progressive changes of the internal structure of the surface membrane until the final structure of the interlamellar membranes is acquired. Finally, these detach from the inner side of the surface membrane. Elemental analysis revealed the transport of a considerable amount of calcium bound to proteins, likely forming calcium-protein complexes.
Unusual migratory strategy a key factor driving interactions at wind energy facilities in at-risk bats
Authors: Campbell Caitlin J. , Nelson David M. , Nagel Juliet , Clerc Jeff , Weller Theodore J. , Weiringa Jamin G. , Fraser Erin , Longstaffe Fred J. , Hale Amanda M. , Lout Meghan , Pruitt Lori , Guralnick Robert , Vander Zanden Hannah B.
Published: January 2024

Seasonal movement strategies are poorly understood for most animals, impeding broader understanding of processes underlying migration and limiting practical conservation needs. Here we develop and implement a framework for integrating multiple sources of endogenous markers, in particular stable hydrogen isotope data, that capture and scale dynamics from the movements of individuals to that of continental migration. We assembled and integrated thousands of new isotopic measurements from bat fur with existing datasets and applied this framework to reveal migratory patterns of three broadly distributed bat species most at risk for fatalities at wind energy facilities. Our findings show that the species comprising the lowest proportion of wind turbine fatalities (silver-haired bats) exhibits expected movements to lower latitudes in autumn and higher latitudes in spring. Surprisingly, the two species with higher wind turbine fatality rates (hoary and eastern red bats) have more complex movements, including significant movement to higher latitudes during autumn. We term this unique strategy “pell-mell” migration, during which some individuals are as likely to move to higher latitudes as lower latitudes, relative to their individual summering grounds, in early autumn, after which they move to similar or lower latitudes to overwinter. The pell-mell migratory period corresponds with peak fatalities at wind energy facilities, and bats moving northward during autumn are associated with mortality at those facilities. Our results provide direct support for the hypothesis that bat fatalities at wind energy facilities are related to migration and highlight the importance of migratory distance as an ultimate driver of increased interactions with wind energy facilities, which appears significantly greater for species that travel widely across latitudes in the autumn.
scGND: Graph neural diffusion model enhances single-cell RNA-seq analysis
Authors: Liu Yu-Chen , Zou Anqi , Lu Simon Liang , Lee Jou-Hsuan , Wang Juexin , Zhang Chao
Published: January 2024

Single-cell sequencing technologies have played a pivotal role in advancing biomedical research over the last decade. With the evolution of deep learning, a variety of models based on deep neural networks have been developed to improve the precision of single-cell RNA sequencing (scRNA-seq) analysis from multiple angles. However, deep learning models currently used in scRNA-seq analysis frequently suffer from a lack of interpretability. In this study, we present a novel physics-informed graph generative model, termed Single Cell Graph Neural Diffusion (scGND). This model is founded on solid mathematical concepts and provides enhanced interpretability. Unlike methods that focus solely on gene expression in individual cells, scGND concentrates on the cell-cell interaction graph, incorporating two key physical concepts: local and global equilibrium. We show that achieving a balance between local and global equilibrium significantly improves the geometric properties of the graph, aiding in the extraction of inherent biological insights from the cell-cell interaction graph at multiple scales. The effectiveness of scGND has been proven through benchmark tests involving five independent scRNA-seq datasets from various tissues and species. scGND consistently achieves better or comparable results comparing with several established competitors in both clustering and trajectory analysis. scGND represents a comprehensive generative model based on cell graph diffusion, demonstrating considerable promise for both theoretical and practical applications in scRNA-seq data analysis.
Novel mutation leading to splice donor loss in a conserved site ofDMDcauses cryptorchidism
Authors: Chen Jianhai , Jia Yangying , Zhong Jie , Zhang Kun , Dai Hongzheng , He Guanglin , Li Fuping , Zeng Li , Fan Chuanzhu , Xu Huayan
Published: January 2024

Background

As one of the most common congenital abnormalities in male births, cryptorchidism has been found to have a polygenic etiology according to previous studies of common variants. However, little is known about genetic predisposition of rare variants for cryptorchidism, since rare variants have larger effective size on diseases than common variants.

Methods

In this study, a cohort of 115 Chinese probands with cryptorchidism was analyzed using whole-genome sequencing (WGS), alongside 19 parental controls and 2136 unaffected men. Additionally, CRISPR-Cas9 editing of a conserved variant was performed in a mouse model, with MRI screening utilized to observe the phenotype.

Results

In 30 of 115 patients (26.1%), we identified four novel genes (ARSH,DMD,MAGEA4, andSHROOM2) affecting at least five unrelated patients and four known genes (USP9Y,UBA1,BCORL1, andKDM6A) with the candidate rare pathogenic variants affecting at least two cases. Burden tests of rare variants revealed the genome-wide significances for newly identified genes (p< 2.5×10-6) under the Bonferroni correction. Surprisingly, novel and known genes were mainly from X chromosome (seven on X and one on Y) and all rare X-chromosomal segregating variants exhibited a maternal inheritance rather thande novoorigin. CRISPR-Cas9 mouse modeling of a splice donor loss variant inDMD(NC_000023.11:g.32454661C>G), which resides in a conserved site across vertebrates, replicated bilateral cryptorchidism phenotypes, confirmed by Magnetic resonance imaging (MRI) at 4 and 10 weeks.

Conclusion

Our results revealed the role of theDMDgene mutation in causing cryptorchidism. The results also suggest that maternal-X inheritance of pathogenic defects could have a predominant role in the development of cryptorchidism.
Exploring Beauty Product Accessibility for Individuals with Upper Extremity Disabilities
Authors: Fullmer Niko , Cone Hannah , Gumarang Jeanette , Kieffer Emily , Bae Soyoung Esther , Rosario Emily R
Published: January 2024

Objective

This study explores the accessibility of beauty products for individuals with upper extremity disabilities.

Methods

Participants with varied upper extremity impairments used Rare Beauty makeup products over two weeks. Assessments of hand function and questionnaires evaluated usability and satisfaction.

Results

Product features like bottle shape, cap design, and texture significantly influenced usability for those with hand and arm impairments. Notably, individuals with fine motor skill impairments reported easier gripping with larger bottle sizes and ease of opening with cap enhancements. The unique product shape and enhanced caps were also found to be more accessible for participants across all ability levels. Overall, the products were well-received, with most participants finding them comfortable and user-friendly.

Conclusions

The study emphasizes the need for inclusive design in the beauty industry, catering to those with upper extremity disabilities. It reveals the importance of ergonomic and adaptable product features to enhance usability and accessibility.

Plain Language summary

This study investigated the use of beauty products by people with upper extremity disabilities. Participants tried Rare Beauty makeup for two weeks and provided feedback. Results showed that product design, like bottle shape and cap ease, significantly impacts usability for those with hand and arm function impairments. Key findings included better grip on certain products for those with fine motor skill challenges. Overall, participants found the products comfortable and easy to use, highlighting the importance of inclusive design in beauty products for people with disabilities.
Transient peripheral blood transcriptomic response to ketamine treatment in children with ADNP syndrome
Authors: Buxbaum Grice Ariela S. , Sloofman Laura , Levy Tess , Walker Hannah , Ganesh Gauri , Rodriguez de los Santos Miguel , Armini Pardis , Buxbaum Joseph D. , Kolevzon Alexander , Kostic Ana , Breen Michael S.
Published: January 2024

Activity-dependent neuroprotective protein (ADNP) syndrome is a rare neurodevelopmental disorder resulting in intellectual disability, developmental delay and autism spectrum disorder (ASD) and is due to mutations in theADNPgene. Ketamine treatment has emerged as a promising therapeutic option for ADNP syndrome, showing safety and apparent behavioral improvements in a first open label study. However, the molecular perturbations induced by ketamine remain poorly understood. Here, we investigated the longitudinal effect of ketamine on the blood transcriptome of 10 individuals with ADNP syndrome. Transcriptomic profiling was performed before and at multiple time points after a single low-dose intravenous ketamine infusion (0.5mg/kg). We show that ketamine triggers immediate and profound gene expression alterations, with specific enrichment of monocyte-related expression patterns. These acute alterations encompass diverse signaling pathways and co-expression networks, implicating up-regulation of immune and inflammatory-related processes and down-regulation of RNA processing mechanisms and metabolism. Notably, these changes exhibit a transient nature, returning to baseline levels 24 hours to 1 week after treatment. These findings enhance our understanding of ketamine’s molecular effects and lay the groundwork for further research elucidating its specific cellular and molecular targets. Moreover, they contribute to the development of therapeutic strategies for ADNP syndrome and potentially, ASD more broadly.
Impact of Pre-reperfusion Left Ventricle Unloading on ST-segment-elevation Myocardial Infarction According to the Onset-to-Unloading Time
Authors: Okamoto Naotaka , Egami Yasuyuki , Abe Masaru , Osuga Mizuki , Nohara Hiroaki , Kawanami Shodai , Kawamura Akito , Ukita Kohei , Yasumoto Koji , Tsuda Masaki , Matsunaga-Lee Yasuharu , Yano Masamichi , Nishino Masami ,   J-PVAD investigators
Published: January 2024

Background

Impella in the left ventricle (LV) with delaying reperfusion reduces the infarction size in animal models. However, the onset-to-unloading time in real-world practice can frequently be longer than that in animal experiments. It is unclear whether the impact of pre-reperfusion Impella use is sustained throughout all periods from the onset. This study aimed to evaluate the association between the onset-to-unloading time and the effect of pre-reperfusion Impella on the survival of patients with ST-segment-elevation myocardial infarction (STEMI).

Methods

This study is a post-hoc analysis of the J-PVAD registry. Among all patients registered in J-PVAD between February 2020 and December 2021, patients with STEMI and treated with Impella alone support were selected. Two cohorts were provided based on whether the onset-to-unloading time was less than 6 hours. The patients were divided into two groups according to pre- or post-reperfusion use of Impella in each cohort. The primary outcome was an 80-day survival rate. The independent factors of survival were identified with a multivariable Cox proportional hazard regression analysis after adjusting for the variables that were statistically significant in the univariable analysis.

Results

Patients with pre-reperfusion unloading had a significantly higher 80-day survival rate than patients with post-reperfusion unloading (81.6% vs. 59.5%, p=0.02) in the cohort with an onset-to-unloading time ≥6 hours, while patients with pre- and post-reperfusion unloading had similar 80-day survival rates (85.3% vs. 91.2%, p=0.38) in the cohort with an onset-to-unloading time <6 hours. A multivariable analysis revealed that pre-reperfusion use of Impella was an independent factor of survival (hazard ratio 0.184 [95% confidence interval 0.045-0.746], p=0.02) in the onset-to-unloading time ≥6 hours cohort.

Conclusions

Pre-reperfusion LV unloading could be a crucial treatment to improve the short-term survival rate when the onset-to-LV unloading was more than 6 hours.
A CRISPR-Nonhomologous End-Joining-based strategy for rapid and efficient gene disruption inMycobacterium abscessus
Authors: Zeng Sanshan , Ju Yanan , Alam Md Shah , Lu Ziwen , Hameed H.M. Adnan , Li Lijie , Tian Xirong , Fang Cuiting , Fang Xiange , Ding Jie , Wang Xinyue , Hu Jinxing , Wang Shuai , Zhang Tianyu
Published: January 2024

Mycobacterium abscessus, a fast-growing, non-tuberculous mycobacterium resistant to most antimicrobial drugs, causes many types of serious infections in humans, posing a significant public health challenge. Currently, effective genetic manipulation tools forM. abscessusare still being developed, which hampers research and therapeutic development. However, the clustered regularly interspaced short palindromic repeats (CRISPR) - associated protein (Cas) systems have emerged as promising methods for generating highly specific double-strand breaks (DSBs) in its genome. These DSBs can be repaired by the error-prone nonhomologous end joining (NHEJ) mechanism, facilitating targeted gene editing. Here, our study marks a pioneering application of the CRISPR-NHEJ strategy inM. abscessus. Additionally, we discovered that NrgA fromMycobacterium marinumis crucial for the repair of DSBs caused by the CRISPR-Cas system inM. abscessus. Finally, contrary to previous findings, our study also indicates that inhibiting or overexpressing homologous recombination/single-strand annealing significantly decreases the efficiency of NHEJ repair inM. abscessus. This discovery challenges established perspectives and suggests that the NHEJ repair inM. abscessusmay require the involvement of components from homologous recombination and single-strand annealing, demonstrating the complex interactions among the three DSB repair pathways inM. abscessus.

Impact statement

There are still very few genetic manipulation tools available forMycobacterium abscessus. Here we report the successful application of CRISPR-Cas12a-assisted nonhomologous end joining (NHEJ) in efficient gene editing inM. abscessus. Contrary to previous research suggesting that homologous recombination (HR) inhibition may enhance such editing efficiency in other Mycobacterium species, our results showed that disruption or overexpression of either HR or single-strand annealing not only failed to enhance but also significantly reduced the gene editing efficiency inM. abscessus. This suggests that NHEJ repair inM. abscessusmay require components from both HR and single-strand annealing, highlighting a complex interaction among the DSB repair pathways inM. abscessus.
In-silicoDrug Repurposing Pipeline for Epilepsy: Integrating Deep Learning and Structure-based Approaches
Authors: Lv Xiaoying , Wang Jia , Yuan Ying , Pan Lurong , Guo Jinjiang
Published: January 2024

Due to considerable global prevalence and high recurrence rate, the pursuit of effective new medication for epilepsy treatment remains an urgent and significant challenge. Drug repurposing emerges as a cost-effective and efficient strategy to combat this disorder. This study leverages the transformer-based deep learning methods coupled with molecular binding affinity calculation to develop a novelin-silicodrug repurposing pipeline for epilepsy. The number of candidate inhibitors against 24 target proteins encoded by gain-of-function (GOF) genes implicated in epileptogenesis ranged from zero to several hundreds. Our pipeline has repurposed the medications with most anti-epileptic drugs (AEDs) and nearly half psychiatric medications, highlighting the effectiveness of our pipeline. Furthermore, Lomitapide, a cholesterol-lowering drug, first emerged as particularly noteworthy, exhibiting high binding affinity for 10 targets and verified by molecular dynamics (MD) simulation and mechanism analysis. These findings provided a novel perspective on therapeutic strategies for other central nervous system (CNS) disease.
Disease resistance ofBrassica junceatoSclerotinia sclerotiorumis established through the induction of indole glucosinolate biosynthesis
Authors: Zhang Jinze , Yang Xu , Jiang Yingfen , Jin Hairun , Yu Kunjiang , Xiao Lijing , Ouyang Qingjing , Tian Entang
Published: January 2024

Sclerotinia stem rot (SSR), caused bySclerotinia sclerotiorum, is the main disease threat to oilseeds in Brassiceae, causing significant yield losses and reduction in oil content and quality. The studies onS. sclerotiorumrequire a great focus and extensive research onB. junceacompared to those onB. napusandB. oleracea. Transcriptome analysis revealed a large number of defense-related genes and response processes inB. napusandB. oleracea. However, similarities and differences in the defense responses toS. sclerotiorumonB. junceaare rarely reported. In the present study, we reported aB. junceabreeding line of H83 with highS. sclerotiorumresistance, which was used for transcriptome analysis compared to L36 with low resistance. A novel regulatory network was proposed to defend againstS. sclerotioruminvasion inB. juncea. Upon infection ofS. sclerotiorum, a series of auxin and MAPK signaling pathways were initiated within 12 h, and then defenses were activated to restrict the development and spread ofS. sclerotiorumby inducing the massive synthesis of indole glucosinolates after 24 h. Twelve hub genes involved in the network were identified by the weighted gene co-expression network (WGCNA), which are involved in plant-pathogen interaction, signaling pathway genes, indole glucosinolate biosynthesis and cell wall formation. The hub genes were further validated by qRT-PCR. The research revealed a new resistant line of H83 againstS. sclerotiorumand a different regulatory network inB. juncea, which would be beneficial for the future effective breeding of Sclerotinia-resistant varieties.
The usefulness of Nanopore Sequencing in Whole-Genome Sequencing-Based Genotyping ofListeria monocytogenesandSalmonella entericaserovar Enteritidis
Authors: Hong Yu-Ping , Chen Bo-Han , Wang You-Wun , Teng Ru-Hsiou , Wei Hsiao Lun , Chiou Chien-Shun
Published: January 2024

Bacterial genotyping through whole-genome sequencing plays a crucial role in disease surveillance and outbreak investigations in public health laboratories. This study assessed the effectiveness of Nanopore Oxford Technologies (ONT) sequencing in the genotyping ofListeria monocytogenesandSalmonella entericaserovar Enteritidis. Our results indicated that ONT sequences, generated with the R10.4.1 flow cell and basecalled using the Dorado 0.5.0 Super Accurate 4.3 model, exhibited comparable accuracy to Illumina sequences, effectively discriminating among bacterial strains from outbreaks. These findings suggest that ONT sequencing has the potential to be a promising tool for rapid whole-genome sequencing of bacterial pathogens in public health laboratories for epidemiological investigations.
In turkeys, unlike chickens, the non-structural NS1 protein does not play a significant role in the replication and tissue tropism of the H7N1 avian influenza virus
Authors: Kuryshko Maryna , Landmann Maria , Luttermann Christine , Ulrich Reiner , Abdelwhab Elsayed M.
Published: January 2024

The economic losses caused by high pathogenicity (HP) avian influenza viruses (AIV) in poultry industry worldwide are enormous. Although chickens and turkeys are two closely related Galliformes, turkeys are thought to be a bridging host for the adaptation of AIV from wild birds to poultry because of their high susceptibility to AIV infections. HPAIV evolve from low pathogenicity (LP) AIV after circulation in poultry through mutations in different viral proteins, including the non-structural protein (NS1), a major interferon (IFN) antagonist of AIV. At present, it is largely unknown whether the virulence determinants of HPAIV are the same in turkeys and chickens. Previously, we showed that mutations in the NS1 of HPAIV H7N1 significantly reduced viral replication in chickens in vitro and in vivo. Here, we investigated the effect of NS1 on the replication and virulence of HPAIV H7N1 in turkeys after inoculation with recombinant H7N1 carrying a naturally truncated wild-type NS1 (with 224 amino-acid “aa” in length) or an extended NS1 with 230-aa similar to the LP H7N1 ancestor. There were no significant differences in multiple-cycle viral replication or in the efficiency of NS1 to block IFN induction in cell culture. Similarly, all viruses were highly virulent in turkeys and replicated at similar levels in various organs and swabs collected from inoculated turkeys. These results suggest that NS1 does not play a role in the virulence or replication of HPAIV H7N1 in turkeys and further indicate that the genetic determinants of HPAIV differ in these two closely related galliform species.
miR-26 deficiency causes alterations in lens transcriptome and results in adult-onset cataract
Authors: Upreti Anil , Hoang Thanh V. , Li Minghua , Tangeman Jared A. , Dierker David S. , Wagner Brad D. , Tsonis Panagiotis A. , Liang Chun , Lachke Salil A. , Robinson Michael L.
Published: January 2024

Purpose

Despite strong evidence demonstrating that normal lens development requires regulation governed by miRNAs, the functional role of specific miRNAs in mammalian lens development remains largely unexplored.

Methods

A comprehensive analysis of miRNA transcripts in the newborn mouse lens, exploring both differential expression between lens epithelial cells and lens fiber cells and overall miRNA abundance was conducted by miRNA-seq. Mouse lenses lacking each of three abundantly expressed lens miRNAs: miR-184, miR-26 and miR-1 were analyzed to explore the role of these miRNAs in lens development.

Results

Mice lacking all three copies ofmiR-26(miR-26TKO) developed postnatal cataracts as early as 4-6 weeks of age. RNA-seq analysis of neonatal lenses frommiR-26TKOmice exhibited abnormal reduced expression of a cohort of genes found to be lens-enriched and linked to cataract (e.g. Foxe3,Hsf4,Mip,Tdrd7,and numerous crystallin genes), and abnormal elevated expression of genes related to neural development (Lhx3, Neurod4, Shisa7, Elavl3), inflammation (Ccr1, Tnfrsf12a, Csf2ra), the complement pathway, and epithelial to mesenchymal transition (Tnfrsf1a, Ccl7, Stat3, Cntfr).

Conclusion

miR-1, miR-184 and miR-26 are each dispensable for normal embryonic lens development. However, loss of miR-26 causes lens transcriptome changes and drives cataract formation.
Mitochondrial DNA copy number reduction viain vitro TFAMknockout remodels the nuclear epigenome and transcriptome
Authors: Nguyen Julia , Win Phyo W. , Nagano Tyler Shin , Shin Elly H. , Newcomb Charles , Arking Dan E. , Castellani Christina A.
Published: January 2024

Mitochondrial DNA copy number (mtDNA-CN) is associated with several age-related chronic diseases and is a predictor of all-cause mortality. Here, we examine site-specific differential nuclear DNA (nDNA) methylation and differential gene expression resulting fromin vitroreduction of mtDNA-CN to uncover shared genes and biological pathways mediating the effect of mtDNA-CN on disease. Epigenome and transcriptome profiles were generated for three independent human embryonic kidney (HEK293T) cell lines harbouring a mitochondrial transcription factor A (TFAM) heterozygous knockout generated via CRISPR-Cas9, and matched control lines. We identified 4,242 differentially methylated sites, 228 differentially methylated regions, and 179 differentially expressed genes associated with mtDNA-CN. Integrated analysis uncovered 381 Gene-CpG pairs. GABAAreceptor genes and related pathways, the neuroactive ligand receptor interaction pathway, ABCD1/2 gene activity, and cell signalling processes were overrepresented, providing insight into the underlying biological mechanisms facilitating these associations. We also report evidence implicating chromatin state regulatory mechanisms as modulators of mtDNA-CN effect on gene expression. We demonstrate that mitochondrial DNA variation signals to the nuclear DNA epigenome and transcriptome and may lead to nuclear remodelling relevant to development, aging, and complex disease.
The human claustrum tracks slow waves during sleep
Authors: Lamsam Layton , Liang Mingli , Gu Brett , Sun George , Hirsch Lawrence J. , Pittenger Christopher , Kaye Alfred P. , Krystal John H. , Damisah Eyiyemisi C.
Published: January 2024

Slow waves are a distinguishing feature of non-rapid-eye-movement (NREM) sleep, an evolutionarily conserved process critical for brain function. Non-human studies posit that the claustrum, a small subcortical nucleus, coordinates slow waves. We recorded claustrum neurons in humans during sleep. In contrast to neurons from other brain regions, claustrum neurons increased their activity and tracked slow waves during NREM sleep suggesting that the claustrum plays a role in human sleep architecture.
Effects of APOE e4 and Neuropathological Diagnoses on Neuropsychiatric Symptoms: Mediation Analyses and Likely Causation in an Integrated NACC Database
Authors: Goldberg Terry E. , Devanand D.P. , Fang Zhiqian , Kim Hyun , Rueppel Elizabeth , Tucker Aren , Carlson Scott , Lee Seonjoo
Published: January 2024

Background

Our goal in this study was to identify paths from APOE e4 to neurobehaviors itemized on a neuropsychiatric inventory that involved neuropathologies associated with e4 (amyloid, tau, cerebral amyloid angiopathy, and Lewy bodies) or cognition mediators (memory or global cognitive status), as well as direct paths from e4 to cognition or neurobehaviors.

Methods

A total of 1199 cases with available neurobehavioral, cognition and neuropathological data were included. We then conducted a series of causal mediation analyses in R in which e4 always served as the independent variable and Neuropsychiatric Inventory (NPI) neurobehavioral items, when included in the mediation, the outcome. Neuropathologies or cognition served as mediators.

Results

Multiple significant indirect paths from e4 through neuropathologies to neurobehaviors were identified. More refined analyses indicated that neuritic plaques and Braak stage, but not extent of diffuse amyloid plaques, drove the findings. A significant direct effect of e4 to memory was also identified. Additionally, Lewy body disease, when treated as an exposure, had a direct effect on hallucinations in keeping with known features of the disease.

Conclusions

We found strong evidence for partial mediation of NPI symptoms by cognition, suggesting that cognitive limitations that may have influenced understanding (or misunderstanding) the environment with impacts on maladaptive behavior. In addition, neuritic amyloid plaque levels and Braak stage, but not diffuse amyloid plaque extent, were key in NPI mediated associations suggesting the possibility that synaptic failure play an important role in multiple neurobehavioral symptoms in dementia, including psychosis. Last, we found strong evidence that e4 may have direct effects on cognition when we used verbal episodic memory as an outcome, suggesting that medial temporal regions that support memory may be sensitive to non-amyloidogenic and non-tau related pathophysiological processes.
Assessing the Impact of Non-exhaust Emissions on the Asthmatic Airway (IONA) Protocol for a randomised three exposure crossover study
Authors: Scales James , Hajmohammadi Hajar , Priestman Max , McIlvenna Luke C. , de Boer Ingrid E. , Hassan Haneen , Tremper Anja H. , Chen Gang , Wood Helen E. , Green David C. , Katsouyanni Klea , Mudway Ian S. , Griffiths Christopher
Published: January 2024

Background

People living with asthma are disproportionately affected by air pollution, with increased symptoms, medication usage, hospital admissions and the risk of death. To date there has been a focus on exhaust emissions, but traffic-related air pollution (TRAP) can also arise from the mechanical abrasion of tyres, brakes, and road surfaces. Non-exhaust emissions (NEE) currently make up a greater proportion of TRAP by mass than exhaust emissions. With the increasing weight of vehicle fleets due to electrification, and increasing uptake of larger vehicles, it is likely that NEE will continue to be an increasing health challenge.

These NEE remain unregulated and underexplored in terms of their health impacts, particularly in vulnerable groups such as people living with asthma. To date, few real-world studies have attempted to explore the impacts of non-exhaust emissions on human health. We therefore created a study with the aim of investigating the acute impacts of NEE on the lung function and airway immune status of asthmatic adults.

Methods

The IONA study will expose adults with asthma in random order at three locations in London selected to provide the greatest contrast in the NEE components within TRAP. Health responses will be assessed before and after each exposure, with lung function measured by spirometry as the primary outcome variable.

Discussion

Collectively this study will provide us with valuable information on the health effects of NEE components within ambient PM2.5and PM10, whilst establishing a biological mechanism to help contextualise current epidemiological observations.

Trial registration

IRAS Number 320784 athttps://clinicaltrials.gov/
Using routine primary care data to assess Sudden Cardiac Arrest risk in people with type 2 diabetes: a proof-of-concept case-control study
Authors: Harms Peter P. , van Dongen Laura H , Oosterbaan Nicky I.C. , Bennis Frank C. , Beulens Joline WJ , Swart Karin M.A. , Hoogendoorn Mark , Tan Hanno L. , Elders Petra P.J.M. , Blom Marieke T.
Published: January 2024

Background

Approximately 50% of out-of-hospital Sudden Cardiac Arrest (SCA) occurs in people with unrecognized SCA-risk and no preceding cardiologic care records. General practitioner (GP) records include these people, specifically people with type 2 diabetes (T2D) with increased SCA-risk. We aimed to provide a proof-of-concept for using routine primary care data to study SCA-risk in people with T2D.

Methods

This case-control study, identified SCA cases through the AmsteRdam REsuscitation STudies (ARREST) registry of out-of-hospital SCA in the Dutch region of Noord-Holland (2005-2019). We included cases with presumed cardiac cause and T2D registered at participating GP practices from the PHARMO Data Network and the academic network of general practice Amsterdam UMC (ANHA). Cases were matched (age, sex, T2D, GP-practice) with up to five non-SCA controls. From their GP files, we collected clinical measurements, medication use and medical history. Associations with SCA were analysed using univariable and multivariable conditional logistic regression (Odds Ratios, 95% confidence intervals).

Results

We included 247 cases and 1,143 controls. In the multivariable model, high fasting glucose (1.08 (1.01-1.16) per 1 mmol/L), high cholesterol ratio (1.17 (1.03-1.34)), moderate albuminuria (2.77 (1.84-4.16)), severe albuminuria (2.96 (1.44-6.08)), dyslipidaemia (0.53 (0.33-0.86)) and a history of cardiovascular disease (1.72 (1.23-2.17)) were significantly associated with SCA. Current smoking behaviour, decreased eGFR, insulin use, hypertension and microvascular complications were close to significantly associated with SCA.

Conclusions

The relatively strong associations in our small sample are consistent with those found in cardiologic care populations, indicating that GP file data can be useful to study SCA-risk.
AI-Enhanced Reconstruction of the 12-Lead Electrocardiogram via 3-Leads with Accurate Clinical Assessment
Authors: Mason Federico , Pandey Amitabh C. , Gadaleta Matteo , Topol Eric J. , Muse Evan D. , Quer Giorgio
Published: January 2024

The 12-lead electrocardiogram (ECG) is an integral component to the diagnosis of a multitude of cardiovascular conditions. It is performed using a complex set of skin surface electrodes, limiting its use outside traditional clinical settings. We developed an artificial intelligence algorithm, trained over 600,000 clinically acquired ECGs, to explore whether fewer leads as input are sufficient to reconstruct a full 12-lead ECG. Two limb leads (I and II) and one precordial lead (V3) were required to generate a reconstructed synthetic 12-lead ECG highly correlated with the original ECG. An automatic algorithm for detection of acute myocardial infarction (MI) performed similarly for original and reconstructed ECGs (AUC=0.94). When interpreted by cardiologists, reconstructed ECGs achieved an accuracy of 81.4±5.0% in identifying ST elevation MI, comparable with the original 12-lead ECGs (accuracy 84.6±4.6%). These results will impact development efforts to innovate ECG acquisition methods with simplified tools in non-specialized settings.
SAR324 and related lineages are associated with the evolutionary history and origins of dsr-mediated sulfur oxidation
Authors: Klier Katherine M. , Martin Cody , Langwig Marguerite V. , Anantharaman Karthik
Published: January 2024

Microorganisms play vital roles in sulfur cycling through the oxidation of elemental sulfur and reduction of sulfite. These metabolisms are catalyzed by dissimilatory sulfite reductases (dsr) which function in the reductive (dsr) or reverse, oxidative direction (rdsr). Dsr-based sulfite reduction is an ancient metabolism and has been proposed to fuel energy metabolism in some of Earth’s earliest microorganisms. Conversely, sulfur oxidation is believed to have evolved later in association with the widespread availability of oxygen on Earth. Organisms are generally believed to carry out either the reductiveoroxidative pathway, yet a subset of bacterial phyla have recently been discovered with gene combinations that implicate them in both pathways. A comprehensive global investigation into the metabolisms of these phyla regarding dsr can shed light on the evolutionary underpinnings of sulfur metabolism but is currently lacking. In this study, we selected one of these phyla, the abundant and metabolically versatile candidate phylum SAR324, to study the ecology and evolution of dsr and rdsr. We confirmed that phylogenetically, environmentally, and geographically diverse SAR324 contained dsr, rdsr, or both. Comprehensive phylogenetic analyses with other dsr-encoding bacterial and archaeal phyla revealed that organisms encoding both dsr and rdsr genes are constrained to a few phyla, which we term “transitionary clades for sulfur oxidation”, and these phyla are phylogenetically positioned at the interface between well-defined oxidative and reductive bacterial clades. Together, this research suggests that SAR324 and other transitionary clades are associated with the evolutionary history and origins of the reverse dsr pathway in bacteria.
The Fanconi anemia pathway repairs colibactin-induced DNA interstrand cross-links
Authors: Altshuller Maria , He Xu , MacKrell Elliot J. , Wernke Kevin M. , Wong Joel W. H. , Sellés-Baiget Selene , Wang Ting-Yu , Chou Tsui-Fen , Duxin Julien P. , Balskus Emily P. , Herzon Seth B. , Semlow Daniel R.
Published: January 2024

Colibactin is a secondary metabolite produced by bacteria present in the human gut and is implicated in the progression of colorectal cancer and inflammatory bowel disease. This genotoxin alkylates deoxyadenosines on opposite strands of host cell DNA to produce DNA interstrand cross-links (ICLs) that block DNA replication. While cells have evolved multiple mechanisms to resolve (“unhook”) ICLs encountered by the replication machinery, little is known about which of these pathways promote resistance to colibactin-induced ICLs. Here, we useXenopusegg extracts to investigate replication-coupled repair of plasmids engineered to contain site-specific colibactin-ICLs. We show that replication fork stalling at a colibactin-ICL leads to replisome disassembly and activation of the Fanconi anemia ICL repair pathway, which unhooks the colibactin-ICL through nucleolytic incisions. These incisions generate a DNA double-strand break intermediate in one sister chromatid, which can be repaired by homologous recombination, and a monoadduct (“ICL remnant”) in the other. Our data indicate that translesion synthesis past the colibactin-ICL remnant depends on Polη and a Polκ-REV1-Polζ polymerase complex. Although translesion synthesis past colibactin-induced DNA damage is frequently error-free, it can introduce T>N point mutations that partially recapitulate the mutation signature associated with colibactin exposurein vivo. Taken together, our work provides a biochemical framework for understanding how cells tolerate a naturally-occurring and clinically-relevant ICL.
Detailing organelle division and segregation inPlasmodium falciparum
Authors: Verhoef Julie M.J. , Boshoven Cas , Evers Felix , Akkerman Laura J. , Gijsbrechts Barend C.A. , van de Vegte-Bolmer Marga , van Gemert Geert-Jan , Vaidya Akhil B. , Kooij Taco W.A.
Published: January 2024

The malaria causing parasite,Plasmodium falciparum, replicates through a tightly orchestrated process termed schizogony, where approximately 32 daughter parasites are formed in a single infected red blood cell and thousands of daughter cells in mosquito or liver stages. One-per-cell organelles, such as the mitochondrion and apicoplast, need to be properly divided and segregated to ensure a complete set of organelles per daughter parasites. Although this is highly essential, details about the processes and mechanisms involved remain unknown. We developed a new reporter parasite line that allows visualization of the mitochondrion in blood and mosquito stages. Using high-resolution 3D-imaging, we found that the mitochondrion orients in a cartwheel structure, prior to stepwise, non-geometric division during the last stage of schizogony. Analysis of focused ion beam scanning electron microscopy (FIB-SEM) data confirmed these mitochondrial division stages. Furthermore, these data allowed us to elucidate apicoplast division steps, highlighted its close association with the mitochondrion, and showed putative roles of the centriolar plaques (CPs) in apicoplast segregation. These observations form the foundation for a new detailed mechanistic model of mitochondrial and apicoplast division and segregation duringP. falciparumschizogony and pave the way for future studies into the proteins and protein complexes involved in organelle division and segregation.
Metabolic fingerprinting reveals roles ofArabidopsis thalianaBGLU1, BGLU3 and BGLU4 in glycosylation of various flavonoids
Authors: Frommann Jana-Freja , Pucker Boas , Sielmann Lennart Malte , Müller Caroline , Weisshaar Bernd , Stracke Ralf , Schweiger Rabea
Published: January 2024

Flavonoids are specialized metabolites that play important roles in plants, including interactions with the environment. The high structural diversity of this metabolite group is largely due to enzyme-mediated modifications of flavonoid core skeletons. In particular, glycosylation with different sugars is very common. In this study, the functions of theArabidopsis thalianaglycoside hydrolase family 1-type glycosyltransferase proteins BGLU1, BGLU3 and BGLU4 were investigated, using a reverse genetics approach and untargeted metabolic fingerprinting. We screened for metabolic differences betweenA. thalianawild type, loss-of-function mutants and overexpression lines and partially identified differentially accumulating metabolites, which are putative products and/or substrates of the BGLU enzymes. Our study revealed that the investigated BGLU proteins are glycosyltransferases involved in the glycosylation of already glycosylated flavonoids using different substrates. While BGLU1 appears to be involved in the rhamnosylation of a kaempferol diglycoside in leaves, BGLU3 and BGLU4 are likely involved in the glycosylation of quercetin glycosides inA. thalianaseeds. In addition, we present evidence that BGLU3 is a multifunctional enzyme that catalyzes other metabolic reactions with more complex substrates. This study deepens our understanding of the metabolic pathways and enzymes that contribute to the high structural diversity of flavonoids.

Highlight

The proteins BGLU1, BGLU3 and BGLU4 are involved in glycosylations of different, already glycosylated flavonoids inArabidopsis thaliana. BGLU3 appears to be multifunctional, acting on several complex substrates.
Endocannabinoid-mediated rescue of somatosensory cortex activity, plasticity and related behaviors following an early in life concussion
Authors: Badaut J. , Hippauf L. , Malinconi M. , Noarbe B.P. , Obenaus A. , Dubois C. J.
Published: January 2024

Due to the assumed plasticity of immature brain, early in life brain alterations are thought to lead to better recoveries in comparison to the mature brain. Despite clinical needs, how neuronal networks and associated behaviors are affected by early in life brain stresses, such as pediatric concussions, have been overlooked. Here we provide first evidence in mice that a single early in life concussion durably increases neuronal activity in the somatosensory cortex into adulthood, disrupting neuronal integration while the animal is performing sensory-related tasks. This represents a previously unappreciated clinically relevant mechanism for the impairment of sensory-related behavior performance. Furthermore, we demonstrate that pharmacological modulation of the endocannabinoid system a year post-concussion is well-suited to rescue neuronal activity and plasticity, and to normalize sensory-related behavioral performance, addressing the fundamental question of whether a treatment is still possible once post-concussive symptoms have developed, a time-window compatible with clinical treatment.