bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of protein supplementation, fumagillin treatment, and colony management on the productivity and long-term survival of honey bee (Apis mellifera) colonies in Canada
Authors: Peirson Michael , Ibrahim Abdullah , Ovinge Lynae P. , Hoover Shelley E. , Guarna M. Marta , Melathopoulos Andony , Pernal Stephen F.
Published: July 2023

In this study, we intensively measured the longitudinal productivity and survival of 362 commercially managed honey bee colonies in Canada, over a two-year period. A full factorial experimental design was used, whereby two treatments were repeated across apiaries situated in three distinct geographic regions: Northern Alberta, Southern Alberta and Prince Edward Island, each having unique bee management strategies. In the protein supplemented treatment, colonies were continuously provided a commercial protein supplement containing 25% w/w pollen, in addition to any feed normally provided by beekeepers in that region. In the fumagillin treatment, colonies were treated with the label dose of Fumagilin-B®each year during the fall. Our study shows that that neither treatment provided consistent benefits across all sites and dates. Fumagillin was associated with a large increase in honey production only at the Northern Alberta site, while protein supplementation produced an early season increase in brood production only at the Southern Alberta site. The protein supplement provided no long-lasting benefit at any site and was also associated with an increased risk of death and decreased colony size later in the study. Differences in colony survival and productivity among regions, and among colonies within beekeeping operations, were far larger than the effects of either treatment, suggesting that returns from extra feed supplements and fumagillin were highly contextually dependent. We conclude that use of fumagillin is safe and sometimes beneficial, but that beekeepers should only consider excess protein supplementation when natural forage is limiting.
An ACE2 decamer viral trap as a durable intervention solution for current and future SARS-CoV
Authors: Guo Hailong , Cho Bomsoo , Hinton Paul R , He Sijia , Yu Yongjun , Ramesh Ashwin Kumar , Sivaccumar Jwala Priyadarsini , Ku Zhiqiang , Campo Kristen , Holland Sarah , Sachdeva Sameer , Mensch Christopher , Dawod Mohamed , Whitaker Annalis , Eisenhauer Philip , Falcone Allison , Honce Rebekah , Botten Jason W. , Carroll Stephen F , Keyt Bruce A , Womack Andrew W , Strohl William R , Xu Kai , Zhang Ningyan , An Zhiqiang , Ha Sha , Shiver John W , Fu Tong-Ming
Published: July 2023

The capacity of SARS-CoV-2 to evolve poses challenges to conventional prevention and treatment options such as vaccination and monoclonal antibodies, as they rely on viral receptor binding domain (RBD) sequences from previous strains. Additionally, animal CoVs, especially those of the SARS family, are now appreciated as a constant pandemic threat. We present here a new antiviral approach featuring inhalation delivery of a recombinant viral trap composed of ten copies of angiotensin-converting enzyme 2 (ACE2) fused to the IgM Fc. This ACE2 decamer viral trap is designed to inhibit SARS-CoV-2 entry function, regardless of viral RBD sequence variations as shown by its high neutralization potency against all known SARS-CoV-2 variants, including Omicron BQ.1, BQ.1.1, XBB.1 and XBB.1.5. In addition, it demonstrates potency against SARS-CoV-1, human NL63, as well as bat and pangolin CoVs. The multivalent trap is effective in both prophylactic and therapeutic settings since a single intranasal dosing confers protection in human ACE2 transgenic mice against viral challenges. Lastly, this molecule is stable at ambient temperature for more than twelve weeks and can sustain physical stress from aerosolization. These results demonstrate the potential of a decameric ACE2 viral trap as an inhalation solution for ACE2-dependent coronaviruses of current and future pandemic concerns.
Physics-informed deep generative learning for quantitative assessment of the retina
Authors: Brown Emmeline , Guy Andrew , Holroyd Natalie , Sweeney Paul , Gourmet Lucie , Coleman Hannah , Walsh Claire , Markaki Athina , Shipley Rebecca , Rajendram Ranjan , Walker-Samuel Simon
Published: July 2023

Disruption of retinal vasculature is linked to various diseases, including diabetic retinopathy and macular degeneration, leading to vision loss. We present here a novel algorithmic approach that generates highly realistic digital models of human retinal blood vessels based on established biophysical principles, including fully-connected arterial and venous trees with a single inlet and outlet. This approach, using physics-informed generative adversarial networks (PI-GAN), enables the segmentation and reconstruction of blood vessel networks that requires no human input and out-performs human labelling. Our findings highlight the potential of PI-GAN for accurate retinal vasculature characterization, with implications for improving early disease detection, monitoring disease progression, and improving patient care.
Use of nanomaterials-modified carbon microfibre electrode material for superior electrochemical performance in lake sediment inoculated microbial fuel cells
Authors: Somasiri Maheshi , Amandani Tanusha , Basnayaka Charitha , Ahsan Ahmed , Dilangani Gayani P , Herath Ajith C. , Bandara Sampath , Nazeer Zumaira , Thilini Nirath , Kyazze Godfrey , Fernando Eustace Y.
Published: July 2023

High cathodic overpotential of the oxygen reduction reaction (ORR) in MFC carbon-based cathodes is one of the key barriers to the widespread adoption of the technology. Current Pt-based ORR catalysts are expensive. The use of novel and inexpensive catalysts as replacements for platinum is therefore desirable. In this study, nanomaterials were directly chemically synthesized on carbon microfiber electrodes to improve the performance of lake sediment inoculated MFCs. Nanomaterial of MnO2, MnO2/polyaniline (PANI), ZnO/NiO and ZnO/NiO/PANI attachments were directly chemically synthesized on the carbon material and used as cathode electrodes. The maximum power densities recorded for the different treatments were; MnO278.5 mW/m2, MnO2/PANI (Polyaniline) 141.6 mW/m2, ZnO/NiO 67.6 mW/m2, and ZnO/NiO/PANI 129.4 mW/m2. The current and poswer densities were more than six-fold higher in ZnO/NiO/PANI and MnO2/PANI nanoparticle modified cathodes compared to the control MFCs with no catalyst. Cyclic voltammetry (CV) and FTIR data and SEM images suggest that the nanoparticle attached carbon material is morphologically, chemically and electrochemically different from the controls with no nanomaterial attachment. The outcome of this study demonstrates that nanomaterials-incorporated carbon microfiber cathodes bring about significant enhancements to power densities and may potentially have applications in cost-effective MFCs.
Inherently reduced expression of ASC restricts caspase-1 processing in hepatocytes and promotesPlasmodiuminfection
Authors: Marques-da-Silva Camila , Baptista Rodrigo P. , Kurup Samarchith P.
Published: July 2023

Inflammasome-mediated caspase-1 activation facilitates innate immune control ofPlasmodiumin the liver, thereby limiting the incidence and severity of clinical malaria. However, caspase-1 processing occurs incompletely in the hepatocytes and precludes the generation of mature IL-1β or IL-18, unlike in other cells. Why this is so, or how it impactsPlasmodiumcontrol in the liver has remained unknown. We show that an inherently reduced expression of the inflammasome adaptor molecule ASC (apoptosis-associated speck-like protein containing CARD) is responsible for the incomplete proteolytic processing of caspase-1 in hepatocytes. Transgenically enhancing ASC expression in hepatocytes enabled complete caspase-1 processing, enhanced pyroptotic cell-death, maturation of the proinflammatory cytokines IL-1β and IL-18 that was otherwise absent, and resulted in better overall control ofPlasmodiuminfection in the liver mice. This however impeded the protection offered by live-attenuated anti-malarial vaccination. Tempering ASC expression in macrophages on the other hand resulted in incomplete processing of caspase-1. Our work shows how caspase-1 activation and function in host cells are fundamentally defined by ASC expression and offers a potential new pathway to create better disease and vaccination outcomes by modifying the latter.
NOTCH3 drives meningioma tumorigenesis and resistance to radiotherapy
Authors: Choudhury Abrar , Cady Martha A. , Lucas Calixto-Hope G. , Najem Hinda , Phillips Joanna J. , Palikuqi Brisa , Zakimi Naomi , Joseph Tara , Birrueta Janeth Ochoa , Chen William C. , Bush Nancy Ann Oberheim , Hervey-Jumper Shawn L. , Klein Ophir D. , Toedebusch Christine M. , Horbinski Craig M. , Magill Stephen T. , Bhaduri Aparna , Perry Arie , Dickinson Peter J. , Heimberger Amy B. , Ashworth Alan , Crouch Elizabeth E. , Raleigh David R.
Published: July 2023

Meningiomas are the most common primary intracranial tumors1–3. Treatments for patients with meningiomas are limited to surgery and radiotherapy, and systemic therapies remain ineffective or experimental4,5. Resistance to radiotherapy is common in high-grade meningiomas6, and the cell types and signaling mechanisms driving meningioma tumorigenesis or resistance to radiotherapy are incompletely understood. Here we report NOTCH3 drives meningioma tumorigenesis and resistance to radiotherapy and find NOTCH3+ meningioma mural cells are conserved across meningiomas from humans, dogs, and mice. NOTCH3+ cells are restricted to the perivascular niche during meningeal development and homeostasis and in low-grade meningiomas but are expressed throughout high-grade meningiomas that are resistant to radiotherapy. Integrating single-cell transcriptomics with lineage tracing and imaging approaches across mouse genetic and xenograft models, we show NOTCH3 drives tumor initiating capacity, cell proliferation, angiogenesis, and resistance to radiotherapy to increase meningioma growth and reduce survival. An antibody stabilizing the extracellular negative regulatory region of NOTCH37,8blocks meningioma tumorigenesis and sensitizes meningiomas to radiotherapy, reducing tumor growth and improving survival in preclinical models. In summary, our results identify a conserved cell type and signaling mechanism that underlie meningioma tumorigenesis and resistance to radiotherapy, revealing a new therapeutic vulnerability to treat meningiomas that are resistant to standard interventions.
Genomic Surveillance of SARS-CoV-2 Using Long-Range PCR Primers
Authors: Kandel Sangam , Hartzell Susanna L. , Ingold Ashton K. , Turner Grace A. , Kennedy Joshua L. , Ussery David W.
Published: July 2023

Whole Genome Sequencing (WGS) of the SARS-CoV-2 virus is crucial in the surveillance of the COVID-19 pandemic. Several primer schemes have been developed to sequence the ∼30,000 nucleotide SARS-CoV-2 genome that use a multiplex PCR approach to amplify cDNA copies of the viral genomic RNA. Midnight primers and ARTIC V4.1 primers are the most popular primer schemes that can amplify segments of SARS-CoV-2 (400 bp and 1200 bp, respectively) tiled across the viral RNA genome. Mutations within primer binding sites and primer-primer interactions can result in amplicon dropouts and coverage bias, yielding low-quality genomes with ‘Ns’ inserted in the missing amplicon regions, causing inaccurate lineage assignments, and making it challenging to monitor lineage-specific mutations in Variants of Concern (VoCs). This study uses seven long-range PCR primers with an amplicon size of ∼4500 bp to tile across the complete SARS-CoV-2 genome. One of these regions includes the full-length S-gene by using a set of flanking primers. Using a small set of long-range primers to sequence SARS-CoV-2 genomes reduces the possibility of amplicon dropout and coverage bias.
Handling difficult cryo-ET samples: A study with primary neurons fromDrosophila melanogaster
Authors: Kim Joseph Y. , Yang Jie E. , Mitchell Josephine W. , English Lauren A. , Yang Sihui Z. , Tenpas Tanner , Dent Erik W. , Wildonger Jill , Wright Elizabeth R.
Published: July 2023

Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rdinstarDrosophila melanogasterlarval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishingDrosophilaneurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.
Expression status transition ofNOTCH1accompanies chromatin remodeling in human early retinal progenitor cells
Authors: Watabe Yoshitoku , Kobayashi Sakurako , Nakayama Takahiro , Takahashi Satoru , Yoshihara Masaharu
Published: July 2023

Objective

The regulation of receptor expression is crucial for fine-tuned signal transduction. Notch signaling is a key signaling pathway involved in retinal development. Although the involvement of this signaling pathway in the differentiation of retinal ganglion cells has been documented, less is known about its involvement in earlier stages of retinal progenitor cell differentiation. To clarify the timing of Notch receptor expression in undifferentiated retinal progenitor cells and elucidate the possible involvement of chromatin remodeling in the regulation of Notch receptor expressions, we re-analyzed publicly available human fetal retina single-cell RNA-seq and ATAC-seq data.

Results

On days 59, 74, and 78, we observedNOTCH1mRNA expression in early retinal progenitor cells, which diminished at later stages of differentiation. Integration of single-cell RNA-seq and ATAC-seq revealed that chromatin remodeling in part of theNOTCH1locus was accompanied by transitions in its mRNA expression. Importantly, chromatin accessibility in the region upstream ofNOTCH1depended on the differentiated cell types. These results suggest that chromatin remodeling may be involved in the differential expression ofNOTCH1, although another type of Notch mRNA expression regulation may exist.
Impact of genetic counselling strategy on diagnostic yield and workload for genome sequencing-based tumour diagnostics
Authors: Koster Roelof , Schipper Luuk J. , Giesbertz Noor A. A. , van Beek Daphne , Mendeville Matías , Samsom Kris G. , Rosenberg Efraim H. , Hogervorst Frans B.L. , Roepman Paul , Boelens Mirjam C. , Bosch Linda J.W. , van den Berg Jose G. , Meijer Gerrit A. , Voest Emile E. , Cuppen Edwin , Ruijs Marielle W.G. , van Wezel Tom , van der Kolk Lizet , Monkhorst Kim
Published: July 2023

Purpose

Genome sequencing (GS) enables comprehensive molecular analysis of tumours and identification of hereditary cancer predisposition. According to guidelines, directly determining pathogenic germline variants (PGVs) requires pre-test genetic counselling, which is cost-ineffective. Referral for genetic counselling based on tumour variants alone could miss relevant PGVs and/or result in unnecessary referrals.

Methods

We validated GS for detection of germline variants and simulated three strategies using paired tumour-normal genome sequencing data of 937 metastatic patients. In strategy-1 genetic counselling prior to tumour testing allowed direct PGV analysis. In strategy-2 and -3, germline testing and referral for post-test genetic counselling is based on tumour variants using Dutch (strategy-2) or ESMO-PMWG (strategy-3) guidelines.

Results

In strategy-1, PGVs would be detected in 50 patients (number-needed-to counsel; NTC=18.7). In strategy-2, 86 patients would have been referred for genetic counselling and 43 would have PGVs (NTC=2). In strategy-3, 94 patients would have been referred for genetic counselling and 32 would have PGVs (NTC=2.9). Hence, 43 and 62 patients, respectively, were unnecessarily referred based on a somatic variant.

Conclusion

Both post-tumour test counselling strategies (2 and 3) had significantly lower NTC, and strategy-2 had the highest PGV yield. Combining pre-tumour test mainstreaming and post-tumour test counselling may maximize the clinically relevant PGV yield and minimize unnecessary referrals.
Understanding Health Service Utilisation Patterns for Care Home Residents During the COVID-19 Pandemic using Routinely Collected Healthcare Data
Authors: Garner Alex , Preston Nancy , Caiado Camila , Stubington Emma , Hanratty Barbara , Limb James , Mason Suzanne , Knight Jo
Published: July 2023

Background

Healthcare in care homes during the COVID-19 pandemic required a balance, providing treatment while minimising exposure risk. Policy for how residents should receive care changed rapidly throughout the pandemic. A lack of accessible data on care home residents over this time meant policy decisions were difficult to make and verify. This study investigates common patterns of healthcare utilisation for care home residents in relation to COVID-19 testing events, and associations between utilisation patterns and resident characteristics.

Methods

Linked datasets including secondary care, community care and a care home telehealth app are used to define daily healthcare utilisation sequences for care home residents. We derive four 10-day sets of sequences related to Pillar 1 COVID-19 testing; before [1] and after [2] a resident’s first positive test and before [3] and after [4] a resident’s first test. These sequences are clustered, grouping residents with similar healthcare patterns in each set. Association of individual characteristics (e.g. health conditions such as diabetes and dementia) with healthcare patterns are investigated.

Results

We demonstrate how routinely collected health data can be used to produce longitudinal descriptions of patient care. Clustered sequences [1,2,3,4] are produced for 3,471 care home residents tested between 01/03/2020–01/09/2021. Clusters characterised by higher levels of utilisation were significantly associated with higher prevalence of diabetes. Dementia is associated with higher levels of care after a testing event, and appears to be correlated with a hospital discharge after a first test. Residents discharged from inpatient care within 10 days of their first test had the same mortality rate as those who stayed in hospital.

Conclusion

We provide longitudinal, resident-level data on care home resident healthcare during the COVID-19 pandemic. We find that vulnerable residents were associated with higher levels of healthcare usage despite the additional risks. Implications of findings are limited by the challenges of routinely collected data. However, this study demonstrates the potential for further research into healthcare pathways using linked, routinely collected datasets.
Genomic characterization ofPseudomonas syringaepv.syringaefrom Callery pear and the efficiency of associated phages in disease protection
Authors: Holtappels D. , Abelson S.A. , Nouth S.C. , Rickus G.E.J. , Giller J.P. , Koskella B.
Published: July 2023

Pseudomonas syringaeis a heterogeneous species complex of plant pathogenic bacteria associated with a wide distribution of plant species. Advances in genomics are revealing the complex evolutionary history of this species complex and the wide array of genetic adaptations underpinning their diverse lifestyles. Here, we genomically characterize twoP. syringaeisolates collected from diseased Callery pears (Pyrus calleryana) in Berkeley, California in 2019 and 2022. We also isolated a lytic bacteriophage, which we characterized and evaluated for biocontrol efficiency. Using a multilocus sequence analysis and core genome alignment, we classified theP. syringaeisolates as members of phylogroup two, related to other strains previously isolated fromPyrusandPrunus. An analysis of effector proteins demonstrated an evolutionary conservation of effectoromes across isolates classified in PG2, and yet uncovered unique effector profiles for each, including the two newly identified isolates. Whole genome sequencing of the associated phage uncovered a novel phage genus related to Psa phage PHB09 and theFlaundravirusgenus. Finally, using in planta infection assays, we demonstrate that the phage was equally useful in symptom mitigation of immature pear fruit regardless of the Pss strain tested. Overall, this study demonstrates the diversity ofP. syringaeand their viruses associated with ornamental pear trees, posing spill-over risks to commercial pear trees and the possibility of using phages as biocontrol agents to reduce the impact of disease.
Non-canonical functions of UHRF1 maintain DNA methylation homeostasis in cancer cells
Authors: Yamaguchi Kosuke , Chen Xiaoying , Rodgers Brianna , Miura Fumihito , Bashtrykov Pavel , Ferry Laure , Kirsh Olivier , Laisné Marthe , Bonhomme Frédéric , Salinas-Luypaert Catalina , Scelfo Andrea , Ugur Enes , Arimondo Paola B. , Leonhardt Heinrich , Kanemaki Masato T. , Fachinetti Daniele , Jeltsch Albert , Ito Takashi , Defossez Pierre-Antoine
Published: July 2023

DNA methylation is an essential epigenetic chromatin modification, and its maintenance in mammals requires the protein UHRF1. It is yet unclear if UHRF1 functions solely by stimulating DNA methylation maintenance by DNMT1, or if it has important additional functions. Using degron alleles, we show that UHRF1 depletion causes a much greater loss of DNA methylation than DNMT1 depletion. This is not caused by passive demethylation as UHRF1-depleted cells proliferate more slowly than DNMT1-depleted cells. Instead, bioinformatics, proteomics and genetics experiments establish that UHRF1, besides activating DNMT1, interacts with DNMT3A and DNMT3B and promotes their activity. In addition, we show that UHRF1 antagonizes active DNA demethylation by TET2. Therefore, UHRF1 has non-canonical roles that contribute importantly to DNA methylation homeostasis; these findings have practical implications for epigenetics in health and disease.
Treatment with furosemide indirectly increases inhibitory transmission in the developing hippocampus
Authors: Peerboom C. , Wijne T. , Wierenga C.J.
Published: July 2023

During the first two postnatal weeks intraneuronal chloride concentrations in rodents gradually decrease, causing a shift from depolarizing to hyperpolarizing γ-aminobutyric acid (GABA) responses. GABAergic depolarization in the immature brain is crucial for the formation and maturation of excitatory synapses, but when GABAergic signaling becomes inhibitory it no longer promotes synapse formation. Here we examined the role of chloride transporters in developing postnatal hippocampal neurons using furosemide, an inhibitor of the chloride importer NKCC1 and chloride exporter KCC2 with reported anticonvulsant effects. We treated organotypic hippocampal cultures made from 6 to 7-day old mice with 200 μM furosemide from DIV1 to DIV8. Using perforated patch clamp recordings we observed that the GABA reversal potential was depolarized after acute furosemide application, but after a week of furosemide treatment the GABA reversal potential but was more hyperpolarized compared to control. Expression levels of the chloride cotransporters were unaffected after one week furosemide treatment. This suggests that furosemide inhibited KCC2 acutely, while prolonged treatment resulted in (additional) inhibition of NKCC1, but we cannot exclude changes in HCO3-. We assessed the effects of accelerating the GABA shift by furosemide treatment on inhibitory synapses onto CA1 pyramidal cells. Directly after cessation of furosemide treatment at DIV9, inhibitory synapses were not affected. However at DIV21, two weeks after ending the treatment, we found that the frequency of inhibitory currents was increased, and VGAT puncta density instratum Radiatumwas increased. In addition, cell capacitance of CA1 pyramidal neurons was reduced in furosemide-treated slices at DIV21 in an activity-dependent manner. Our results suggest that furosemide treatment indirectly promoted inhibitory transmission, possibly by increasing activity-independent GABA release.
FAST: a fast and scalable factor analysis for spatially aware dimension reduction of multi-section spatial transcriptomics data
Authors: Liu Wei , Zhang Xiao , Chai Xiaoran , Fan Zhenqian , Lin Huazhen , Chen Jinmiao , Sun Lei , Yu Tianwei , Yeong Joe , Liu Jin
Published: July 2023

Biological techniques for spatially resolved transcriptomics (SRT) have advanced rapidly in both throughput and spatial resolution for a single spatial location. This progress necessitates the development of efficient and scalable spatial dimension reduction methods that can handle large-scale SRT data from multiple sections. Here, we developed FAST as a fast and efficient generalized probabilistic factor analysis for spatially aware dimension reduction, which simultaneously accounts for the count nature of SRT data and extracts a low-dimensional representation of SRT data across multiple sections, while preserving biological effects with consideration of spatial smoothness among nearby locations. Compared with existing methods, FAST uniquely models the count data across multiple sections while using a local spatial dependence with scalable computational complexity. Using both simulated and real datasets, we demonstrated the improved correlation between FAST estimated embeddings and annotated cell/domain types. Furthermore, FAST exhibits remarkable speed, with only FAST being applicable to analyze a mouse embryo Stereo-seq dataset with >2.3 million locations in only 2 hours. More importantly, FAST identified the differential activities of immune-related transcription factors between tumor and non-tumor clusters and also predicted a carcinogenesis factorCCNHas the upstream regulator of differentially expressed genes in a breast cancer Xenium dataset.
Low concentrations of ethylene bisdithiocarbamate pesticides maneb and mancozeb impair manganese and zinc homeostasis to induce oxidative stress and caspase-dependent apoptosis in human hepatocytes
Authors: Petitjean Kilian , Verres Yann , Bristeau Sébastien , Ribault Catherine , Aninat Caroline , Olivier Christophe , Leroyer Patricia , Ropert Martine , Loreal Olivier , Herault Olivier , Amalric Laurence , Baran Nicole , Fromenty Bernard , Corlu Anne , Loyer Pascal
Published: July 2023

The worldwide and intensive use of phytosanitary compounds results in environmental and food contamination by chemical residues. Human exposure to multiple pesticide residues is a major health issue. Considering that the liver is not only the main organ for metabolizing pesticides but also a major target of toxicities induced by xenobiotics, we studied the effects of a mixture of 7 pesticides (chlorpyrifos-ethyl, dimethoate, diazinon, iprodione, imazalil, maneb, mancozeb) often detected in food samples. Effects of the mixture was investigated using metabolically competent HepaRG cells and human hepatocytes in primary culture. We report the strong cytotoxicity of the pesticide mixture towards hepatocytes-like HepaRG cells and human hepatocytes upon acute and chronic exposures at low concentrations extrapolated from the Acceptable Daily Intake (ADI) of each compound. Unexpectedly, we demonstrated that the manganese (Mn)-containing dithiocarbamates (DTCs) maneb and mancozeb were solely responsible for the cytotoxicity induced by the mixture. The mechanism of cell death involved the induction of oxidative stress, which led to cell death by intrinsic apoptosis involving caspases 3 and 9. Importantly, this cytotoxic effect was found only in cells metabolizing these pesticides. Herein, we unveil a novel mechanism of toxicity of the Mn-containing DTCs maneb and mancozeb through their metabolization in hepatocytes generating the main metabolite ethylene thiourea (ETU) and the release of Mn leading to intracellular Mn overload and depletion in zinc (Zn). Alteration of the Mn and Zn homeostasis provokes the oxidative stress and the induction of apoptosis, which can be prevented by Zn supplementation. Our data demonstrate the hepatotoxicity of Mn-containing fungicides at very low doses and unveil their adverse effect in disrupting Mn and Zn homeostasis and triggering oxidative stress in human hepatocytes.
Detecting subtle transcriptomic perturbations induced by lncRNAs Knock-Down in single-cell CRISPRi screening using a new sparse supervised autoencoder neural network
Authors: Truchi Marin , Lacoux Caroline , Gille Cyprien , Fassy Julien , Magnone Virginie , Lopez-Goncalvez Rafael , Girard-Riboulleau Cédric , Manosalva-Pena Iris , Gautier-Isola Marine , Lebrigand Kevin , Barbry Pascal , Spicuglia Salvatore , Vassaux Georges , Rezzonico Roger , Barlaud Michel , Mari Bernard
Published: July 2023

Single-cell CRISPR-based transcriptome screens are potent genetic tools for concomitantly assessing the expression profiles of cells targeted by a set of guides RNA (gRNA), and inferring target gene functions from the observed perturbations. However, due to various limitations, this approach lacks sensitivity in detecting weak perturbations and is essentially reliable when studying master regulators such as transcription factors. To overcome the challenge of detecting subtle gRNA induced transcriptomic perturbations and classifying the most responsive cells, we developed a new supervised autoencoder neural network method. Our Sparse supervised autoencoder (SSAE) neural network provides selection of both relevant features (genes) and actual perturbed cells. We applied this method on an in-house single-cell CRISPR-interference-based (CRISPRi) transcriptome screening (CROP-Seq) focusing on a subset of long non-coding RNAs (lncRNAs) regulated by hypoxia, a condition that promote tumor aggressiveness and drug resistance, in the context of lung adenocarcinoma (LUAD). The CROP-seq library of validated gRNA against a subset of lncRNAs and, as positive controls, HIF1A and HIF2A, the 2 main transcription factors of the hypoxic response, was transduced in A549 LUAD cells cultured in normoxia or exposed to hypoxic conditions during 3, 6 or 24 hours. We first validated the SSAE approach on HIF1A and HIF2 by confirming the specific effect of their knock-down during the temporal switch of the hypoxic response. Next, the SSAE method was able to detect stable short hypoxia-dependent transcriptomic signatures induced by the knock-down of some lncRNAs candidates, outperforming previously published machine learning approaches. This proof of concept demonstrates the relevance of the SSAE approach for deciphering weak perturbations in single-cell transcriptomic data readout as part of CRISPR-based screening.
The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome
Authors: Lasne Clementine , Elkrewi Marwan , Toups Melissa A. , Layana Lorena , Macon Ariana , Vicoso Beatriz
Published: July 2023

Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionflyPanorpa cognataX-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.
Brain network interconnectivity dynamics explain metacognitive differences in listening behavior
Authors: Alavash Mohsen , Obleser Jonas
Published: July 2023

Complex auditory scenes pose a challenge to attentive listening, rendering listeners slower and more uncertain in their perceptual decisions. How can we explain such behaviors from the dynamics of cortical networks that pertain to the control of listening behavior? We here follow up on the hypothesis that human adaptive perception in challenging listening situations is supported by modular reconfiguration of auditory-control networks in a sample of N=40 participants (13 males) who underwent resting-state and task functional magnetic resonance imaging (fMRI). Individual titration of a spatial selective auditory attention task maintained an average accuracy of∼ 70% but yielded considerable inter-individual differences in listeners’ response speed and reported confidence in their own perceptual decisions. Whole-brain network modularity increased from rest to task by reconfiguring auditory, cinguloopercular, and dorsal attention networks. Specifically, interconnectivity between the auditory network and cinguloopercular network decreased during the task relative to the resting state. Additionally, interconnectivity between the dorsal attention network and cinguloopercular network increased. These interconnectivity dynamics were predictive of individual differences in response confidence, the degree of which was more pronounced after incorrect judgments. Our findings uncover the behavioral relevance of functional crosstalk between auditory and attentional-control networks during metacognitive assessment of one’s own perception in challenging listening situations and suggest two functionally dissociable cortical networked systems that shape the considerable metacognitive differences between individuals in adaptive listening behavior.

Significance Statement

The ability to communicate in challenging listening situations varies not only objectively between individuals but also in terms of their subjective perceptual confidence. Using fMRI and a challenging auditory task, we demonstrate that this variability in the metacognitive aspect of listening behavior is reflected on a cortical level through the modular reconfiguration of brain networks. Importantly, task-related modulation of interconnectivity between the cinguolopercular network and each auditory and dorsal attention network can explain for individuals’ differences in response confidence. This suggests two dissociable cortical networked systems that shape the individual evaluation of one’s own perception during listening, promising new opportunities to better understand and intervene in deficits of auditory perception such as age-related hearing loss or auditory hallucinations.
Experimental drought reduces the productivity and stability of a recovering calcareous grassland
Authors: Jackson J. , Middleton S.L , Lawson C. S. , Jardine E. , Hawes N. , Maseyk K. , Salguero-Gómez R , Hector A.
Published: July 2023

Grasslands comprise 40% of terrestrial ecosystems and are globally important for food production, carbon storage, and other ecosystem services. However, grasslands in many areas are becoming increasingly exposed to extreme wet and dry periods resulting from global temperature increases.

Therefore, understanding how grasslands will respond to climate change is a pressing issue for managing changes to biodiversity and ecosystem service provision.

Here, we use experimental manipulations of precipitation (50% increase and 50% decrease of growing-season precipitation) to investigate the resistance of the diversity and productivity of a calcareous grassland community recovering from historical agricultural conversion.

We found that decreasing growing season precipitation led to reductions of mean productivity (25 % decrease in peak above-ground biomass) and its temporal stability (54 % increase in biomass variance across years). However, the grassland community composition was resistant to the precipitation manipulations, with no clear difference in community compositional turnover, dissimilarity, or biodiversity indices. Furthermore, the precipitation manipulations had no effect on the path of ongoing (30 year) recovery of grassland plant diversity from the period of previous agricultural conversion.

While the diversity of this calcareous grassland was resistant to precipitation extremes (at least in the short term), sustained reductions in growing-season precipitation reduced productivity and its temporal stability demonstrating that different properties of grasslands can vary in their responses to changes in precipitation.
A side-by-side comparison of peptide-delivered antisense antibiotics employing different nucleotide mimics
Authors: Ghosh Chandradhish , Popella Linda , Dhamodharan V. , Jung Jakob , Barquist Lars , Höbartner Claudia , Vogel Jörg
Published: July 2023

Antisense oligomer (ASO)-based antibiotics that target mRNAs of essential bacterial genes have great potential for counteracting antimicrobial resistance and for precision microbiome editing. To date, the development of such antisense antibiotics has primarily focused on using phosphorodiamidate morpholino (PMO) and peptide nucleic acid (PNA) backbones, largely ignoring the growing number of chemical modalities that have spurred the success of ASO-based human therapy. Here, we directly compare the activities of seven chemically distinct 10mer ASOs, all designed to target the essential geneacpPupon delivery with a KFF-peptide carrier intoSalmonella.Our systematic analysis of PNA, PMO, phosphorothioate-modified DNA (PTO), 2’-methylated RNA (RNA-OMe), 2’-methoxyethylated RNA (RNA-MOE), 2’-fluorinated RNA (RNA-F) and 2’-4’-locked RNA (LNA) is based on a variety ofin vitroandin vivomethods to evaluate ASO uptake, target pairing and inhibition of bacterial growth. Our data show that only PNA and PMO are efficiently delivered by the KFF peptide intoSalmonellato inhibit bacterial growth. Nevertheless, the strong target binding affinity andin vitrotranslational repression activity of LNA and RNA-MOE make them promising modalities for antisense antibiotics that will require the identification of an effective carrier.
Neural entrainment to speech in theta range is affected by language properties but not by the native language of the listeners
Authors: Özer Ege Ekin , Silva Pereira Silvana , Sebastian-Galles Nuria
Published: July 2023

A universal speech rhythm around 5 Hz, corresponding to syllable beats, is captured by neural oscillations in the human brain. However, there is significant variability in syllabic complexity across languages: some languages allow only simple syllables, while some allow more variation (a variation related to linguistic rhythm). Behavioral evidence suggests that humans show different patterns of speech segmentation depending on the linguistic rhythm of their native language. Here, we tested if the entrainment of neural oscillations in the theta range (3–8 Hz) to sentences of languages representative of different linguistic rhythms depends on participants’ native language rhythm or rather reflects language-specific rhythmic properties. We recorded EEG in two groups of participants: native speakers of English (stress-timed, Experiment 1) and native speakers of Spanish (syllable-timed, Experiment 2). Both groups listened tosaltanajresynthesized sentences from English (stress-timed), Spanish (syllable-timed) and Japanese (mora-timed), a procedure that removes comprehension but keeps language-specific phonological properties. Phase locking value between sentence envelopes and EEG showed the same pattern regardless of participants’ native language: lowest for English, intermediate for Spanish, and highest for Japanese. Our results suggest that entrainment to speech in the theta frequency range is sensitive to differences in variation in syllabic complexity across languages.
Bacterial sepsis triggers stronger transcriptomic immune responses in larger primates
Authors: McMinds Ryan , Jiang Rays H.Y. , Adapa Swamy R. , Cornelius Ruhs Emily , Munds Rachel A. , Leiding Jennifer W. , Downs Cynthia J. , Martin Lynn B.
Published: July 2023

Empirical data relating body mass to immune defense against infections remain limited. Although the Metabolic Theory of Ecology predicts that larger organisms would have weaker immune responses, recent studies have suggested that the opposite may be true. These discoveries have led to the Safety Factor hypothesis, which proposes that larger organisms have evolved stronger immune defenses because they carry greater risks of exposure to pathogens and parasites. In this study, we simulated sepsis by exposing blood from nine primate species to a bacterial lipopolysaccharide (LPS), measured the relative expression of immune and other genes using RNAseq, and fit phylogenetic models to determine how gene expression was related to body mass. In contrast to non-immune-annotated genes, we discovered hypermetric scaling in the LPS-induced expression of innate immune genes, such that large primates had a disproportionately greater increase in gene expression of immune genes compared to small primates. Hypermetric immune gene expression appears to support the Safety Factor hypothesis, though this pattern may represent a balanced evolutionary mechanism to compensate for lower per-transcript immunological effectiveness. This study contributes to the growing body of immune allometry research, highlighting its importance in understanding the complex interplay between body size and immunity over evolutionary timescales.

Author Summary

Understanding the relationship between an animal’s size and its ability to defend against disease can inform predictions about evolutionary tradeoffs and susceptibility to infection. Two major theories – the Metabolic Theory of Ecology (MTE) and the Safety Factor hypothesis – offer opposing views on how body size influences it immune defenses. In this study, we compared the immune gene expression of nine primate species to a simulated bacterial infection. We found that larger species mounted a stronger transcriptional immune response, consistent with either the Safety Factor hypothesis or an evolutionary pressure to compensate for and balance the effects expected in the context of the MTE.
The ADNEX risk prediction model for ovarian cancer diagnosis: A systematic review and meta-analysis of external validation studies
Authors: BARREÑADA Lasai , LEDGER Ashleigh , DHIMAN Paula , COLLINS Gary S. , WYNANTS Laure , VERBAKEL Jan Y. , TIMMERMAN Dirk , VALENTIN Lil , VAN CALSTER Ben
Published: July 2023

Objectives: To conduct a systematic review of studies externally validating the ADNEX model for ovarian cancer diagnosis and perform a meta-analysis of its performance. Design: Systematic review, meta-analysis Data sources: Medline, EMBASE, WOS, Scopus, and EuropePMC up to 15/05/2023. Review methods: We included external validation studies of the performance of ADNEX using any study design and any study population comprising patients with an adnexal mass. Two independent reviewers extracted data. Disagreements were resolved through discussion. Reporting quality of the studies was scored using the TRIPOD reporting guideline and methodological conduct and risk of bias using the PROBAST tool. We performed random effects meta-analysis of the AUC, sensitivity and specificity at the 10% risk of malignancy threshold, and Net Benefit and Relative Utility at the 10% risk of malignancy threshold. Results: We included 47 studies (17,007 tumours) with median study sample size 261 (range 24-4905). On average, 61% of TRIPOD items were reported. Handling of missing data, sample size justification, and model calibration were rarely described. 91% of validations were at high risk of bias, mainly due to the unexplained exclusion of incomplete cases, low sample size, or absent calibration assessment. The summary AUC to distinguish benign from malignant tumours in operated patients was 0.93 (95% CI 0.92-0.94, 95% prediction interval 0.85-0.98) for ADNEX with CA125 as a predictor (9202 tumours, 43 centres, 18 countries, 21 studies) and 0.93 (95% CI 0.91-0.94, 95% prediction interval 0.85-0.98) for ADNEX without CA125 (6309 tumours, 31 centres, 13 countries, 12 studies). The estimated probability that the model has clinical utility in a new centre was 95% (with CA125) and 91% (without CA125). When restricting analysis to studies at low risk of bias, summary AUCs were 0.93 (with CA125) and 0.91 (without CA125), and estimated probabilities that the model has clinical utility were 89% (with CA125) and 87% (without CA125). Discussion: ADNEX performed well to distinguish benign from malignant tumours in populations from different countries and settings regardless of whether CA125 was used or not. A key limitation is that calibration was rarely assessed. Review registration: PROSPERO, CRD42022373182
Association of Genetic Ancestry with Molecular Tumor Profiles in Colorectal Cancer
Authors: Rhead Brooke , Hein David M. , Pouliot Yannick , Guinney Justin , De La Vega Francisco M. , Sanford Nina N.
Published: July 2023

Background

Prior research on molecular correlates of disparities in incidence and outcomes of colorectal cancer (CRC) have typically used self-reported or observed categories of race and ethnicity, which can be missing or inaccurate. Furthermore, race and ethnicity do not always capture genetic similarity well, particularly in admixed populations. To overcome these limitations, we examined associations of CRC tumor molecular profiles using genetic ancestry.

Methods

Sequencing was performed with the Tempus xT NGS 648-gene panel and whole exome capture RNA-Seq for 8,454 CRC patients. Genetic ancestry proportions were estimated for five continental groups, Africa (AFR), Americas (AMR), East Asia (EAS), Europe (EUR), and South Asia (SAS), using ancestry informative markers. We assessed association of genetic ancestry proportions and genetic ancestry-imputed race and ethnicity categories with somatic mutations in relevant CRC genes and in expression profiles, including consensus molecular subtypes (CMS).

Results

Increased AFR ancestry was associated with higher odds of somatic mutations inAPC,KRASandPIK3CAand lower odds ofBRAFmutations. Additionally, increased EAS ancestry was associated with lower odds of mutations inKRAS, EUR with higher odds inBRAF, and the Hispanic/Latino category with lower odds inBRAF. Greater AFR ancestry and the non-Hispanic Black category were associated with higher rates of CMS3, while patients in the Hispanic/Latino category had more indeterminate CMS.

Conclusions

Use of genetic ancestry enables identification of molecular differences in CRC tumor mutation frequencies and gene expression that may underlie observed differences by race and ethnicity, and suggests that subtype classifications such as CMS may benefit from greater patient diversity.