bluuebunny/crossref_metadata_2025 huggingface dataset:
“The Intestine is a Major Contributor to Circulating TCA Cycle Intermediates in Mice”
Authors: Tong Wenxin , Hannou Sarah A. , Wang You , Astapova Inna , Sargsyan Ashot , Monn Ruby , Thiriveedi Venkataramana , Li Diana , McCann Jessica R. , Rawls John F. , Roper Jatin , Zhang Guo-fang , Herman Mark A.
Published: January 2022

The tricarboxylic acid (TCA) cycle is the epicenter of cellular aerobic metabolism. TCA cycle intermediates facilitate energy production and provide anabolic precursors, but also function as intra- and extracellular metabolic signals regulating pleiotropic biological processes. Despite the importance of circulating TCA cycle metabolites as signaling molecules, the source of circulating TCA cycle intermediates remains uncertain. We observe that in mice, the concentration of TCA cycle intermediates in the portal blood exceeds that in tail blood indicating that the gut is a major contributor to circulating TCA cycle metabolites. With a focus on succinate as a representative of TCA cycle intermediate with signaling activities and using a combination of germ-free mice and isotopomer tracing, we demonstrate that intestinal microbiota are not major contributors to circulating TCA cycle metabolites. Moreover, we demonstrate that the endogenous succinate production is markedly higher than intestinal succinate absorption in normal physiological conditions. Altogether, these results indicate that endogenous succinate production within the intestinal tissue is a major physiological source of circulating succinate. These results provide a foundation for investigation into the role of intestine in regulating circulating TCA cycle metabolites and related signaling effects in health and disease.
The Retinal Basis of Light Aversion in Neonatal Mice
Authors: Caval-Holme Franklin S. , Aranda Marcos L. , Chen Andy Quaen , Tiriac Alexandre , Zhang Yizhen , Smith Benjamin , Birnbaumer Lutz , Schmidt Tiffany M. , Feller Marla B.
Published: January 2022

Aversive responses to bright light (photoaversion) require signaling from the eye to the brain. Melanopsin-expressing intrinsically photosensitive retinal ganglion cells (ipRGCs) encode absolute light intensity and are thought to provide the light signals for photoaversion. Consistent with this, neonatal mice exhibit photoaversion prior to the developmental onset of image vision, and melanopsin deletion abolishes photoaversion in neonates. It is not well understood how the population of ipRGCs, which constitutes multiple physiologically distinct types (denoted M1-M6 in mouse) encodes light stimuli to produce an aversive response. Here, we provide several lines of evidence that M1 ipRGCs that lack the Brn3b transcription factor drive photoaversion in neonatal mice. First, neonatal mice lacking TRPC6 and TRPC7 ion channels failed to turn away from bright light, while two photon Ca2+ imaging of their acutely isolated retinas revealed reduced photosensitivity in M1 ipRGCs, but not other ipRGC types. Second, mice in which all ipRGC types except for Brn3b-negative M1 ipRGCs are ablated, exhibited normal photoaversion. Third, pharmacological blockade or genetic knockout of gap junction channels expressed by ipRGCs, which reduces the light sensitivity of M2-M6 ipRGCs in the neonatal retina, had small effects on photoaversion only at the brightest light intensities. Finally, M1s were not strongly depolarized by spontaneous retinal waves, a robust source of activity in the developing retina that depolarizes all other ipRGC types. M1s therefore constitute a separate information channel between the neonatal retina and brain that could ensure behavioral responses to light but not spontaneous retinal waves.
GGDB: A Grameneae Genome Alignment Database of Homologous Genes Hierarchically Related to Evolutionary Events
Authors: Yang Qihang , Liu Tao , Wu Tong , Lei Tianyu , Li Yuxian , Wang Xiyin
Published: January 2022

Owing to their economic values, Gramineae plants have been preferentially sequenced their genomes. These genomes are often quite complex, e.g., harboring many duplicated genes, which were the main source of genetic innovation and often the results of recurrent polyploidization. Deciphering the complex genome structure and linking duplicated genes to specific polyploidization events are important to understand the biology and evolution of plants. However, the effort has been held back due to its high complexity in analyzing these genomes. Here, by hierarchically relating duplicated genes in colinearity to each polyploidization or speciation event, we analyzed 29 well-assembled and up-to-date Gramineae genome sequences, separated duplicated genes produced by each event, established lists of paralogous and orthologous genes, and eventually constructed an on-line database, GGDB (http://www.grassgenome.com/). Homologous gene lists from each plant and between them can be displayed, searched, and downloaded from the database. Interactive comparison tools were deployed to demonstrate homology among user-selected plants, to draw genome-scale or local alignment figures, phylogenetic trees of genes corrected by exploiting gene colinearity, etc. Using these tools and figures, users can easily observe genome structural changes, and explore the effects of paleo-polyploidy on crop genome structure and function. The GGDB will be a useful platform to improve understanding the genome changes and functional innovation of Gramineae plants.

Key points

GGDB is the only portal hosting Grameneae colinear homologous genes hierarchically related to evolutionary events, especially polyploidization, which have occurred recursively.

Allows systematic analysis of colinear gene relationships and function origination and/or divergence across Grameneae plants.

Serving the Grameneae research community, with new genomes, modules, tools, and analysis.
A chemical biology toolbox to investigate in-cell target engagement and specificity of PRMT5-inhibitors
Authors: Rothweiler Elisabeth M. , Stefaniak Jakub , Ward Jennifer A. , Rogers Catherine , Balikci Esra , Huber Kilian V. M.
Published: January 2022

Increasing evidence suggests the protein arginine methyltransferase PRMT5 as a contributor to tumorigenesis in various cancer types and several inhibitors have entered clinical trials. Robust assays to determine cellular target engagement and selectivity are an important asset for the optimisation of inhibitors and the design of relevant in vivo studies. Here we report a suite of chemical biology assays enabling quantitative assessment of PRMT5 inhibitor in-cell target engagement and global selectivity profiling using a representative set of inhibitors. With the help of a bespoke cellular probe, we assess inhibitor target occupancy in cells in relation to biochemical and functional cellular assays. Investigating the influence of SAM, the natural cofactor of PRMT5, our results support the hypothesis that SAM positively contributes to the engagement of substrate-competitive inhibitors via a PRMT5:SAM:inhibitor ternary complex. Extensive proteomic profiling studies by drug affinity chromatography and thermal profiling further indicate high specificity of the clinical PRMT5 inhibitor GSK3326595 (pemrametostat).

Graphical abstract
Heterosis counteracts hybrid breakdown to forestall speciation by parallel natural selection
Authors: Thompson Ken A. , Schluter Dolph
Published: January 2022

In contrast to ecological speciation, where reproductive isolation evolves as a consequence of divergent natural selection, speciation by parallel natural selection has been less thoroughly studied. To test whether parallel evolution drives speciation, we leveraged the repeated evolution of benthic and limnetic ecotypes of threespine stickleback fish and estimated fitness for pure crosses and within-ecotype hybrids in semi-natural ponds and in laboratory aquaria. In ponds, we detected hybrid breakdown in both ecotypes but this was counterbalanced by heterosis and the strength of post-zygotic isolation was nil. In aquaria, we detected heterosis only in limnetic crosses and breakdown in neither ecotype, suggesting that hybrid incompatibilities are environment-dependent for both ecotypes and that heterosis is environment-dependent in benthic crosses. Heterosis and breakdown were 3× greater in limnetic crosses than in benthic crosses, contrasting the prediction that the fitness consequences of hybridization should be greater in crosses among more derived ecotypes. Consistent with a primary role for stochastic processes, patterns differed among crosses between populations from different lakes. Yet, we observed qualitatively similar patterns of heterosis and hybrid breakdown in benthic crosses and limnetic crosses when averaging the lake pairs, suggesting that the outcome of hybridization is repeatable in a general sense.
Effects of Neonicotinoid Seed Treatments on Soil Microbial Gene Expression Vary with Time in an Agricultural Ecosystem
Authors: Parizadeh Mona , Mimee Benjamin , Kembel Steven W.
Published: January 2022

Neonicotinoids, a class of systemic insecticides, have been widely used for decades against various insect pests. Past studies have reported non-target effects of neonicotinoids on some beneficial macro- and micro-organisms. Given the crucial role that the soil microbiota plays in sustaining soil fertility, it is critical to understand how microbial taxonomic composition and gene expression respond to neonicotinoid exposure. To date, few studies have focused on this question, and these studies have evaluated the shifts in soil microbial taxonomic composition or used soil biochemical analyses to assess the changes in microbial functions. In this study, we have applied a metatranscriptomic approach to quantify the variability in soil microbial gene expression in a two-year soybean/corn crop rotation in Quebec, Canada. We identified weak and temporally inconsistent effects of neonicotinoid application on soil microbial gene expression, as well as a strong temporal variation in soil microbial gene expression among months and years. Neonicotinoid seed treatment altered the expression of a small number of microbial genes, including genes associated with heat shock proteins, regulatory functions, metabolic processes and DNA repair. These changes in gene expression varied during the growing season and between years. Overall, the composition of soil microbial expressed genes seems to be more resilient and less affected by neonicotinoid application than soil microbial taxonomic composition. Our study is among the first to document the effects of neonicotinoid seed treatment on microbial gene expression and highlights the strong temporal variability of soil microbial gene expression and its responses to neonicotinoid seed treatments.

IMPORTANCE

This work provides the first example of the impacts of neonicotinoid seed treatment on community-wide soil microbial gene expression in an experimental design representing real farming conditions. Neonicotinoid pesticides have attracted a great deal of attention in recent years due to their potential non-target impacts on ecological communities and their functions. Our paper represents the first use of metatranscriptomic sequencing to offer real-time and in-depth insights into the non-target effects of this pesticide on soil microbial gene expression and on potentially beneficial soil microorganisms.
B.1.617.2 SARS-CoV-2 (Delta) variant is associated with increased risk of hospitalization and death compared with B.1.1.7 SARS-CoV-2 (Alpha) variant
Authors: Rodrigues Eduardo Freire , Moreno Joana , Leite Pedro Pinto , Casaca Pedro , Nunes Baltazar , Gomes João Paulo , Ferreira Rita , Isidro Joana , Borges Vítor , Vieira Luís , Duarte Sílvia , Sousa Carlos , Almeida José Pedro , Menezes Luís , Vaz Dora , Leite Andreia , Peralta-Santos André
Published: January 2022

Introduction

The B.1.617.2 variant (Delta) was associated with increased transmissibility and lower vaccine effectiveness than the B.1.1.7 variant (Alpha). However, the effect of the B.1.617.2 variant on disease severity remains unclear. This study aims to assess whether infection with the B.1.617.2 variant was associated with a higher risk of serious illness, compared with other co-circulating variants, measured through hospitalization and death by COVID-19 in Portugal.

Methods

We conducted a matched cohort study in adult individuals diagnosed with SARS-CoV-2/COVID-19 infection between March 29 and August 1, 2021. Cases were individuals with a positive PCR test notified to the surveillance system. SARS-CoV-2 variants were classified first by genomic sequencing (WGS) and, if this information was unavailable, by detecting the S gene target failure.

Delta (B.1.617.2) and Alpha (B.1.1.7) cases were matched on the week of diagnosis at a 1 to k ratio (k being the maximum number of unexposed available in that week) to maximize the inclusion of unexposed, using the nearest-neighbor algorithm. The hazard risk and 95% confidence intervals of hospitalization and death among those infected with the Delta (B.1.617.2) variant vs. Alpha (B.1.1.7) was estimated using a Cox proportional hazards model, adjusting for confounding for sex, age, and vaccination status.

Results

A total of 2,778 cases were included in the study. Of the total, 1 742 (68%) were identified as B.1.617.2 variant cases and 3 629 (32%) as B.1.1.7 variant. Within the B.1.1.7 variant cases 106 (2.9%) were hospitalized, and 110 (6.3%) within the B.1.617.2 variant cases. A total of 29 deaths were reported, 8 (0.2%) in patients infected with B.1.1.7 variant and 21 (1.2%) in patients with the B.1.617.2 variant. The confounding adjusted risk of hospitalization, in persons infected with the B.1.617.2 variant was 2.44 (95%CI 1.85; 3.20) times higher than the risk of hospitalization among B.1.1.7 variant cases, and the confounding-adjusted risk of death for B.1.617.2 variant cases was 5.20 (95%CI 2.20; 12.29) times higher than the risk of death in patients infected by B.1.1.7 variant.

Conclusion

The B.1.617.2 variant is associated with an increased risk of hospitalization and death compared with the B.1.1.7 variant.
Inflammation in children with chronic kidney disease linked to gut dysbiosis and metabolite imbalance
Authors: Holle Johannes , Bartolomaeus Hendrik , Löber Ulrike , Behrens Felix , Bartolomaeus Theda U. P. , Anandakumar Harithaa , Wimmer Moritz I. , Vu Dai Long , Kuhring Mathias , Maifeld Andras , Geisberger Sabrina , Kempa Stefan , Bufler Philip , Querfeld Uwe , Kitschke Stefanie , Engler Denise , Kuhrt Leonard D. , Drechsel Oliver , Eckardt Kai-Uwe , Forslund Sofia K. , Thürmer Andrea , McParland Victoria , Kirwan Jennifer A. , Wilck Nicola , Müller Dominik
Published: January 2022

Chronic kidney disease (CKD) is characterized by a sustained pro-inflammatory response. The underlying mechanisms are incompletely understood, but may be linked to gut dysbiosis. Dysbiosis has been described in adults with CKD; however, comorbidities limit CKD-specific conclusions. We analyzed the fecal microbiome, metabolites and immune phenotypes in children at three different CKD stages (G3-G4, G5 (hemodialysis), after kidney transplantation) and healthy controls. Serum TNF-α and sCD14 were stage-dependently elevated, indicating inflammation and gut barrier dysfunction. We observed microbiome alterations in CKD, including a diminished production of short-chain fatty acids. Bacterial tryptophan metabolites were increased in CKD. CKD serum activated the aryl hydrocarbon receptor and stimulated TNF-α production by monocytes, corresponding to a shift towards intermediate/non-classical monocytes. Unsupervised T cell analysis revealed pro-inflammatory shifts in MAIT and Treg cells. Thus, gut barrier dysfunction and microbial metabolites exacerbate inflammation and may therefore contribute to the increased cardiovascular burden in CKD.
The flavonoid nobiletin exhibits differential effects on cell viability in keratinocytes exposed to UVA versus UVB radiation
Authors: Cvammen William , Kemp Michael G.
Published: January 2022

The polymethoxylated flavonoid nobiletin has been shown to suppress inflammatory responses to UVB radiation and to enhance circadian rhythms. Because expression of the core nucleotide excision repair (NER) factor XPA and the rate of removal of UV photoproducts from DNA are regulated by the circadian clock, we investigated whether the beneficial effects of nobiletin in UVB-exposed cells could be due in part to enhanced NER. Though nobiletin limited UVB-irradiated human keratinocytes from undergoing cell death, we found that this enhanced survival was not associated with increased NER or XPA expression. Instead, nobiletin reduced initial UV photoproduct formation and promoted a G1 cell cycle arrest. We then examined the implications of this findings for exposures to solar radiation through use of a solar simulated light (SSL) source that contains primarily UVA radiation. In striking contrast to the results obtained with UVB radiation, nobiletin instead sensitized keratinocytes to both the SSL and a more defined UVA light source. This enhanced cell death was correlated with a photochemical change in nobiletin absorption spectrum in the UVA range. We conclude that nobiletin is unlikely to be a useful compound for protecting keratinocytes against the harmful effects of solar UV radiation.
Benchmark of Differential Gene Expression Analysis Methods for Inter-species RNA-Seq Data using a Phylogenetic Simulation Framework
Authors: Bastide Paul , Soneson Charlotte , Lespinet Olivier , Gallopin Mélina
Published: January 2022

Inter-species RNA-Seq datasets are increasingly common, and have the potential to answer new questions on gene expression patterns across the evolution. Single species differential expression analysis is a now well studied problem, that benefits from sound statistical methods. Extensive reviews on biological or synthetic datasets have provided the community with a clear picture on the relative performances of the available tools in various settings. Such benchmarks are still missing in the inter-species gene expression context. In this work, we take a first step in this direction by developing and implementing a new simulation framework. This tool builds on both the RNA-Seq and the Phylogenetic Comparative Methods literatures to generate realistic count datasets, while taking into account the phylogenetic relationships between the samples. We illustrate the features of this new framework through a targeted simulation study, that reveals some of the strengths and weaknesses of both the classical and phylogenetic approaches for inter-species differential expression analysis. The tool has been integrated in the R package compcodeR freely available on Bioconductor.
Dissociation Protocols used for Sarcoma Tissues Bias the Transcriptome observed in Single-cell and Single-nucleus RNA sequencing
Authors: Truong Danh D. , Lamhamedi-Cherradi Salah-Eddine , Porter Robert W. , Krishnan Sandhya , Swaminathan Jyothishmathi , Gibson Amber , Lazar Alexander J. , Livingston John A. , Gopalakrishnan Vidya , Gordon Nancy , Daw Najat C. , Gorlick Richard , Ludwig Joseph A.
Published: January 2022

Background

Single-cell RNA-seq has emerged as an innovative technology used to study complex tissues and characterize cell types, states, and lineages at a single-cell level. Classification of bulk tumors by their individual cellular constituents has also created new opportunities to generate single-cell atlases for many organs, cancers, and developmental models. Despite the tremendous promise of this technology, recent evidence studying epithelial tissues and diverse carcinomas suggests the methods used for tissue processing, cell disaggregation, and preservation can significantly bias gene expression and alter the observed cell types. To determine whether sarcomas – tumors of mesenchymal origin – are subject to the same technical artifacts, we profiled patient-derived tumor explants (PDXs) propagated from three aggressive subtypes: osteosarcoma, Ewing sarcoma (ES), desmoplastic small round cell tumor (DSRCT). Given the rarity of these sarcoma subtypes, we explored whether single-nuclei RNA-seq from more widely available archival frozen specimens could accurately be identified by gene expression signatures linked to tissue phenotype or pathognomonic fusion proteins.

Results

We systematically assessed dissociation methods across different sarcoma subtypes. We compared gene expression from single-cell and single-nucleus RNA-sequencing of 125,831 whole-cells and nuclei from ES, DSRCT, and osteosarcoma PDXs. We detected warm dissociation artifacts in single-cell samples and gene length bias in single-nucleus samples. Classic sarcoma gene signatures were observed regardless of dissociation method. In addition, we showed that dissociation method biases can be computationally corrected.

Conclusions

We highlighted transcriptional biases, including warm dissociation and gene-length biases, introduced by the dissociation method for various sarcoma subtypes. This work is the first to characterize how the dissociation methods used for sc/snRNA-seq may affect the interpretation of the molecular features in sarcoma PDXs.
White matter connections of high-level visual areas predict cytoarchitecture better than category-selectivity in childhood, but not adulthood
Authors: Kubota Emily , Grotheer Mareike , Finzi Dawn , Natu Vaidehi S. , Gomez Jesse , Grill-Spector Kalanit
Published: January 2022

Ventral temporal cortex (VTC) consists of high-level visual regions that are arranged in consistent anatomical locations across individuals. This consistency has led to several hypotheses about the factors that constrain the functional organization of VTC. A prevailing theory is that white matter connections influence the organization of VTC, however, the nature of this constraint is unclear. Here, we test two hypotheses: (1) white matter tracts are specific for each category or (2) white matter tracts are specific to cytoarchitectonic areas of VTC. To test these hypotheses, we used diffusion magnetic resonance imaging (dMRI) to identify white matter tracts and functional magnetic resonance imaging (fMRI) to identify category-selective regions in VTC in children and adults. We find that in childhood, white matter connections are linked to cytoarchitecture rather than category-selectivity. In adulthood, however, white matter connections are linked to both cytoarchitecture and category-selectivity. These results suggest a rethinking of the view that category-selective regions in VTC have category-specific white matter connections early in development. Instead, these findings suggest that the neural hardware underlying the processing of categorical stimuli may be more domain-general than previously thought, particularly in childhood.
A draft genome assembly for the heterozygous wild tomato Solanum habrochaites highlights haplotypic structural variations of intracellular immune receptors
Authors: Seong Kyungyong , Shaw China Lunde , Seo Eunyoung , Li Meng , Krasileva Ksenia V , Staskawicz Brian
Published: January 2022

Solanum habrochaites LA1353 is a self-incompatible, highly heterozygous wild tomato that is a useful germplasm resource for the study of metabolism, reproduction and disease resistance. We generated a draft genome assembly with PacBio HiFi reads and genome annotations, which underscored the expansion of gene families associated with metabolite-production, self-incompatibility, DNA regulation and immunity. After manually curating intracellular nucleotide-binding leucine-rich repeat immune receptors (NLRs), we found that S. habrochaites LA1353 has a larger NLR inventory than other wild tomato species. A great number of heterozygous local copy number variations (CNVs) driven by haplotypic structural variations further expands the inventory, both enhancing NLR diversity and providing more opportunities for sequence evolution. The NLRs associated with local CNVs predominantly appear in the helper NLR (NRC)-related phylogenetic clades and are concentrated in a few physical NLR gene clusters. Synteny analysis points out that these genomic regions correspond to the known NLR clusters from which experimentally validated, functional NLRs, such as Hero, Mi-1.2 and Rpi-amr1, have been identified. Producing and incorporating Resistance Gene Enrichment Sequencing (RenSeq) data across wild tomato species, we reveal that the regions with local CNVs might have been shaped nearly equally by recent NLR gains and losses, along with enhanced sequence diversification that diminishes one-to-one orthology between heterozygous alleles. Our analysis suggests that these genomic regions may have accelerated evolutionary dynamics for NLR diversity generation in S. habrochaites LA1353.
Pharmacological inhibition of HDAC6 downregulates TGF-β via Smad2/3 acetylation and improves dystrophin-deficient muscles
Authors: Osseni Alexis , Ravel-Chapuis Aymeric , Scionti Isabella , Gangloff Yann-Gaël , Moncollin Vincent , Mounier Remi , Leblanc Pascal , Jasmin Bernard J. , Schaeffer Laurent
Published: January 2022

Abstract / Summary

The absence of dystrophin in Duchenne muscular dystrophy (DMD) disrupts the dystrophin dystroglycan glycoprotein complex (DGC) resulting in fibers fragility and atrophy, associated with fibrosis and microtubules and neuromuscular junction (NMJ) disorganization. The specific non-conventional cytoplasmic histone deacetylase 6 (HDAC6) was previously shown to regulate acetylcholine receptor distribution and muscle atrophy. Here we show that administration of the HDAC6 specific inhibitor tubastatin A to the DMD mouse model mdx improves muscle strength, restores microtubules, NMJ and DGC organization, and reduces muscle atrophy and fibrosis. These effects involve the known action of HDAC6 on microtubules acetylation and muscle atrophy but also involve a yet undiscovered action of HDAC6 on transforming growth factor beta (TGF-β) signaling. Conversely, to inhibitors of nuclear HDACs that regulate TGF-β signaling via the activation of Follistatin expression, HDAC6 inhibition acts downstream of TGF-β ligands and receptors by increasing Smad2/3 acetylation in the cytoplasm which in turn inhibits its phosphorylation and transcriptional activity.
Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes
Authors: Vigué Lucile , Croce Giancarlo , Petitjean Marie , Ruppé Etienne , Tenaillon Olivier , Weigt Martin
Published: January 2022

Characterizing the effect of mutations is key to understand the evolution of protein sequences and to separate neutral amino-acid changes from deleterious ones. Epistatic interactions between residues can lead to a context dependence of mutation effect. Context dependence constrains the amino-acid changes that can contribute to polymorphism in the short term, and the ones that can accumulate between species in the long term. We use computational approaches to accurately predict the polymorphisms segregating in a panel of 61,157 Escherichia coli genomes from the analysis of distant homologues. By comparing a context-aware Direct-Coupling Analysis modelling to a non-epistatic approach, we show that the genetic context strongly constrains the tolerable amino acids in 30% to 50% of amino-acid sites. The study of more distant species suggests the gradual build-up of genetic context over long evolutionary timescales by the accumulation of small epistatic contributions.
Can double PPO mutations exist in a same allele and are such mutants functional?
Authors: Porri Aimone , Noguera Matheus M. , Betz Michael , Sälinger Daniel , Brändle Frank , Bowe Steven J. , Lerchl Jens , Meyer Lucie , Knapp Michael , Roma-Burgos Nilda
Published: January 2022

Background

Resistance to PPO-inhibiting herbicides is primarily endowed by target site mutations at thePPO2gene that compromise binding of the herbicide to the catalytic domain. InAmaranthusssp.PPO2, the most prevalent target mutations are deletion of the G210 codon and the R128G and G339A substitutions. These mutations strongly affect the dynamic of the PPO2 binding pocket resulting in reduced affinity with the ligand. Here we investigated the likelihood of co-occurrence of the most widespread target site mutations in the sameppo2allele.

Results

Plants carrying R128G+/+ ΔG210+/-, where + indicates presence of the mutation, were crossed with each other. Theppo2of the offspring was subjected to pyrosequencing andE. coli-based Sanger sequencing to determine mutation frequencies and allele co-occurrence. The data show that R128G ΔG210 can occur only in one allele; the second allele carries only one mutation. Double mutation in both alleles is less likely because of significant loss of enzyme activity. The segregation of offspring populations derived from a cross between heterozygous plants carrying ΔG210 G399A also showed no co-occurrence in the same allele. The offspring exhibited the expected mutation distribution patterns with few exceptions.

Conclusions

Homozygous double-mutants are not physiologically viable. Double-mutant plants can only exist in a heterozygous state. Alternatively, if two mutations are detected in one plant, each mutation would occur in a separate allele.

Nomenclature

Palmer amaranth,Amaranthus palmeriS. Wats.; protoporphyrinogen oxidase, PPO; tall waterhemp,Amaranthus tuberculatus(Moq.) J.D.Sauer
Deep learning can predict multi-omic biomarkers from routine pathology images: A systematic large-scale study
Authors: Arslan Salim , Mehrotra Debapriya , Schmidt Julian , Geraldes Andre , Singhal Shikha , Hense Julius , Li Xiusi , Bass Cher , Kather Jakob Nikolas , Pandya Pahini , Raharja-Liu Pandu
Published: January 2022

We assessed the pan-cancer predictability of multi-omic biomarkers from haematoxylin and eosin (H&E)-stained whole slide images (WSI) using deep learning (DL) throughout a systematic study. A total of 13,443 DL models predicting 4,481 multi-omic biomarkers across 32 cancer types were trained and validated. The investigated biomarkers included a broad range of genetic, transcriptomic, proteomic, and metabolic alterations, as well as established markers relevant for prognosis, molecular subtypes and clinical outcomes. Overall, we found that DL can predict multi-omic biomarkers directly from routine histology images across solid cancer types, with 50% of the models performing at an area under the curve (AUC) of more than 0.633 (with 25% of the models having an AUC larger than 0.711). A wide range of biomarkers were detectable from routine histology images across all investigated cancer types, with a mean AUC of at least 0.62 in almost all malignancies. Strikingly, we observed that biomarker predictability was mostly consistent and not dependent on sample size and class ratio, suggesting a degree of true predictability inherent in histomorphology. Together, the results of our study show the potential of DL to predict a multitude of biomarkers across the omics spectrum using only routine slides. This paves the way for accelerating diagnosis and developing more precise treatments for cancer patients.
Butterfly wings exhibit spatial variation in chromatin accessibility
Authors: Connahs Heidi , das Gupta Mainak , Monteiro Antónia
Published: January 2022

Butterfly wings exhibit a diversity of patterns which can vary between forewings and hindwings and spatially across the same wing. Regulation of morphological variation involves changes in how genes are expressed across different spatial scales which is driven by chromatin dynamics during development. How patterns of chromatin dynamics correspond to morphological variation remains unclear. Here we compared the chromatin landscape between forewings and hindwings and also across the proximal and distal regions of the hindwings in two butterfly species, Bicyclus anynana and Danaus plexippus. We found that the chromatin profile varied significantly between the different wing regions, however, there was no clear correspondence between the chromatin profile and the wing patterns. In some cases, wing regions with different phenotypes shared the same chromatin profile whereas those with a similar phenotype had a different profile. We also found that in the forewing, open chromatin regions (OCRs) were AT rich whereas those in the hindwing were GC rich. GC content of the OCRs also varied between the proximal and hindwing regions. These differences in GC content were also reflected in the transcription factor binding motifs that were differentially enriched between the wings and wing regions. Our results suggest that distinct wing patterns may result from the interaction of pioneer factors, including Hox genes, differentially opening chromatin in different wings and wing regions and cooperating with other transcriptions factors, that show preferences for specific GC content, to function either as activator or repressors of nearby genes.
Prostaglandin E1 as therapeutic molecule for Nephronophthisis and related ciliopathies
Authors: Garcia Hugo , Serafin Alice , Silbermann Flora , Poree Esther , Mahaut Clémentine , Viau Amandine , Billot Katy , Birgy Éléonore , Garfa-Traore Meriem , Roy Stéphanie , Cecarelli Salomé , Mehraz Manon , Rodriguez Pamela C. , Deleglise Bérangère , Furio Laetitia , Jabot-Hanin Fabienne , Cagnard Nicolas , Del Nery Elaine , Fila Marc , Sin-Monnot Soraya , Antignac Corinne , Lyonnet Stanislas , Krug Pauline , Salomon Rémi , Annereau Jean-Philippe , Benmerah Alexandre , Delous Marion , Briseño-Roa Luis , Saunier Sophie
Published: January 2022

Nephronophthisis (NPH) is an autosomal recessive tubulointerstitial nephropathy belonging to the ciliopathy disorders and known as the most common cause of hereditary end-stage renal disease in children. Yet, no curative treatment is available. The major gene, NPHP1, encodes a protein playing key functions at the primary cilium and cellular junctions. Using an in cellulo medium-throughput drug-screen, we identified 51 FDA-approved compounds and selected 11 for their physicochemical properties, including prostaglandin E1 (PGE1). PGE1 was further validated to rescue ciliogenesis in immortalized patient NPHP1-/- urine-derived renal tubular cells and corroborated by the effects of its analog PGE2. The two molecules reduced pronephric cyst occurrence in vivo in nphp4 zebrafish model, and PGE1 treatment in Nphp1-/- mice led to a significant reduction of renal tubular dilatations, partially restoring cilia length within tubules. Finally, comparative transcriptomics allowed identification of key molecules downstream PGE1. Altogether, our drug-screen strategy led to the identification of PGE1 as the first potential therapeutic molecule for NPH-associated ciliopathies.

Significant statement

Juvenile nephronophthisis (NPH) is a renal ciliopathy due to a dysfunction of primary cilia and a common genetic cause of end-stage renal disease in children and young adults. No curative treatment is available. This paper describes the identification of Prostaglandin E1 (PGE1) as the first potential therapeutic molecule for NPH-associated ciliopathies. We demonstrated that PGE1 rescues defective ciliogenesis and ciliary composition in NPHP1-/- patient urine-derived renal tubular cells. Furthermore, PGE1 improves ciliary and kidney phenotypes in our NPH zebrafish and Nphp1-/- mouse models. Finally, in vitro experiments as well as transcriptomic analyses pointed out several pathways downstream PGE1 as cAMP, cell-cell/cell-matrix adhesion or actin cytoskeleton. Altogether, our findings provide a new alternative for treatment of NPH.
Microglia integration into human midbrain organoids leads to increased neuronal maturation and functionality
Authors: Sabate-Soler Sonia , Nickels Sarah Louise , Saraiva Cláudia , Berger Emanuel , Dubonyte Ugne , Barmpa Kyriaki , Lan Yan Jun , Kouno Tsukasa , Jarazo Javier , Robertson Graham , Sharif Jafar , Koseki Haruhiko , Thome Christian , Shin Jay W. , Cowley Sally A. , Schwamborn Jens C.
Published: January 2022

The human brain is a complex, three-dimensional structure. To better recapitulate brain complexity, recent efforts have focused on the development of human specific midbrain organoids. Human iPSC-derived midbrain organoids consist of differentiated and functional neurons, which contain active synapses, as well as astrocytes and oligodendrocytes. However, the absence of microglia, with their ability to remodel neuronal networks and phagocytose apoptotic cells and debris, represents a major disadvantage for the current midbrain organoid systems. Additionally, neuro-inflammation related disease modeling is not possible in the absence of microglia. So far, no studies about the effects of human iPSC-derived microglia on midbrain organoid neural cells have been published. Here we describe an approach to derive microglia from human iPSCs and integrate them into iPSC-derived midbrain organoids. Using single nuclear RNA Sequencing, we provide a detailed characterization of microglia in midbrain organoids as well as the influence of their presence on the other cells of the organoids. Furthermore, we describe the effects that microglia have on cell death and oxidative stress- related gene expression. Finally, we show that microglia in midbrain organoids affect synaptic remodeling and increase neuronal excitability. Altogether, we show a more suitable system to further investigate brain development, as well as neurodegenerative diseases and neuro- inflammation.

Main Points

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Macrophage precursors can be efficiently co-cultured with midbrain organoids, they integrate into the tissue and differentiate into microglia in 3D.

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Organoids containing microglia have a smaller size and show a down-regulation of oxidative stress-related genes.

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Organoids co-cultured with microglia show differences in genes related to synaptic remodeling and action potential, as well as a more spontaneous action potential firing.
Histochemical Examination of Changes In Testis After Vasectomy In Rats And Qualitative Analysis Of Tissue Zinc Content
Authors: Ozcinar Emine , Ersoy Canillioglu Yasemin , Cetinel Sule
Published: January 2022

It is claimed that around 100 million men worldwide have undergone vasectomy for birth control. Vasectomy is an operation to prevent the transfer of sperm by preventing the luminal continuity of the vas deferens. Degenerative changes after vasectomy usually start with loss of spermatogenic cells in the germinal epithelium, while Sertoli cells are affected later. There is no change in Leydig cells. Zinc, which is found at high rates in the male reproductive system, is an element in the structure of many enzymes necessary for cell membrane integrity, growth and sexual maturity.

In this study, bilateral vasectomy was performed on 18 young adult male rats and control operation was performed on 18 rats. Afterwards, 6 animals from each group were sacrificed after 6 weeks, 12 weeks and 12 months. Germinal epithelium, tubule structure, basement membrane, interstitium and collagen fiber changes were examined at microscope and transmission electron microscope level. On the other hand, zinc content in testicular tissue was measured by Energy-dispersive X-ray spectroscopy (EDS). Six weeks after vasectomy, localized losses in the germinal epithelium and disorganization of spermatogenic cells were observed. In addition to the loss of spermatogenic cells at the 12th week, separations, thickening and an increase in the collagen fiber in the peritubular area were observed in the interstitium and perinuclear area. Tissue zinc content was also found to be the lowest in the 12 months group.

In conclusion, our study showed that the degenerative changes in the rat testis that increased with time after vasectomy were parallel to the decrease in tissue zinc content.
A common venomous ancestor? Prevalent bee venom genes evolved before the aculeate stinger while few major toxins are bee-specific
Authors: Koludarov Ivan , Velasque Mariana , Timm Thomas , Greve Carola , Ben Hamadou Alexander , Gupta Deepak Kumar , Lochnit Günter , Heinzinger Michael , Vilcinskas Andreas , Gloag Rosalyn , Harpur Brock A. , Podsiadlowski Lars , Rost Burkhard , Jackson Timothy N. W. , Dutertre Sebastien , Stolle Eckart , von Reumont Björn M
Published: January 2022

Venoms, which have evolved numerous times in animals, are ideal models of convergent trait evolution. However, detailed genomic studies of toxin-encoding genes exist for only a few animal groups. The hyper-diverse hymenopteran insects are the most speciose venomous clade, but investigation of the origin of their venom genes has been largely neglected. Utilising a combination of genomic and proteo-transcriptomic data, we investigated the origin of 11 toxin genes in 29 published and three new hymenopteran genomes and compiled an up-to-date list of prevalent bee venom proteins. Observed patterns indicate that bee venom genes predominantly originate through single gene co-option with gene duplication contributing to subsequent diversification. Most Hymenoptera venom genes are shared by all members of the clade and only melittin and the new venom protein family anthophilin1 appear unique to the bee lineage. Most venom proteins thus predate the mega-radiation of hymenopterans and the evolution of the aculeate stinger.
FOXO dictate initiation of B cell development and myeloid restriction in common lymphoid progenitors
Authors: Peña-Pérez Lucía , Kharazi Shabnam , Frengen Nicolai , Krstic Aleksandra , Bouderlique Thibault , Hauenstein Julia , He Minghui , Somuncular Ece , Li Wang Xiaoze , Dahlberg Carin , Gustafsson Charlotte , Johansson Ann-Sofie , Walfridsson Julian , Kadri Nadir , Woll Petter , Kierczak Marcin , Qian Hong , Westerberg Lisa , Luc Sidinh , Månsson Robert
Published: January 2022

The development of B cells relies on an intricate network of transcription factors critical for developmental progression and lineage commitment. In the B cell developmental trajectory, a temporal switch from predominant Foxo3 to Foxo1 expression occurs at the CLP stage. Utilizing VAV-iCre mediated conditional deletion, we found that the loss of FOXO3 impaired B cell development from LMPP down to B cell precursors, while the loss of FOXO1 impaired B cell commitment and resulted in a complete developmental block at the CD25 negative proB cell stage. Strikingly, the combined loss of FOXO1 and FOXO3 resulted in the failure to restrict the myeloid potential of CLPs and the complete loss of the B cell lineage. This is underpinned by the failure to enforce the early B-lineage gene regulatory circuitry upon a predominantly pre-established open chromatin landscape. Altogether, this demonstrates that FOXO3 and FOXO1 cooperatively govern early lineage restriction and initiation of B-lineage commitment in CLPs.

Common lymphoid progenitors co-express the transcription factors FOXO1 and FOXO3. Removing FOXO1 and FOXO3 at this developmental stage results in regained myeloid potential, failed establishment of the early B cell gene regulatory program, and the complete loss of the B cell lineage.
Impact of neonatal activation of nuclear receptor CAR (Nr1i3) on Cyp2 gene expression in adult mouse liver
Authors: Shin Aram , Waxman David J.
Published: January 2022

Perinatal exposure to environmental chemicals is proposed to reprogram development and alter disease susceptibility later in life. Supporting this, neonatal activation of the nuclear receptor CAR (Nr1i3) by TCPOBOP induces persistent expression of mouse hepatic Cyp2 genes into adulthood, attributed to long-term epigenetic memory of the early life exposure [Hepatology (2012) 56:1499-1509]. Here, we confirm that the same high-dose (15x ED50) neonatal TCPOBOP exposure used in that work induces prolonged (12 weeks) increases in hepatic Cyp2 expression; however, we show that the persistence of expression can be fully explained by the persistence of residual TCPOBOP in liver tissue. When the long-term presence of TCPOBOP in tissue was eliminated by decreasing the neonatal TCPOBOP dose 22-fold (0.67x ED50), strong neonatal increases in hepatic Cyp2 expression were still obtained but did not persist into adulthood. Furthermore, the neonatal ED50-range TCPOBOP exposure did not sensitize mice to a subsequent, low-dose TCPOBOP treatment. In contrast, neonatal treatment with phenobarbital, a short half-life (t1/2=8 h) agonist of CAR and of PXR (Nr1i2), induced high-level neonatal activation of Cyp2 genes and also altered their responsiveness to low-dose phenobarbital exposure at adulthood by either increasing (Cyp2b10) or decreasing (Cyp2c55) expression. Thus, neonatal xenobiotic exposure can reprogram hepatic Cyp2 genes and alter their responsiveness to exposures later in life. These findings highlight the need to carefully consider xenobiotic dose, half-life and persistence in tissue when evaluating the long-term effects of early life environmental chemical exposures.
GM1 asymmetry in the membrane stabilizes pores
Authors: Aleksanyan Mina , Lira Rafael B. , Steinkühler Jan , Dimova Rumiana
Published: January 2022

Cell membranes are highly asymmetric and their stability against poration is crucial for survival. We investigated the influence of membrane asymmetry on electroporation of giant unilamellar vesicles with membranes doped with GM1, a ganglioside asymmetrically enriched in the outer leaflet of neuronal cell membranes. Compared to symmetric membranes, the lifetimes of micronsized pores are about an order of magnitude longer suggesting that pores are stabilized by GM1. Internal membrane nanotubes caused by the GM1 asymmetry, obstruct and additionally slow down pore closure, effectively reducing pore edge tension and leading to leaky membranes. Our results point to the drastic effects this ganglioside can have on pore resealing in biotechnology applications based on poration as well as on membrane repair processes.

SIGNIFICANCE

Membrane pore closure is crucial for cell survival and is important for biotechnological and medicine applications based on transfer of material, e.g. drugs, genes, through pores. Electroporation is widely used as means to perforate the membrane but factors governing membrane resealing are still a matter of debate, in particular the large variations of pore lifetimes. Here, we probed the effect of bilayer asymmetry on pore dynamics employing cell-sized giant unilamellar vesicles doped with the ganglioside GM1 (asymmetrically enriched in neurons). We find that the presence of GM1 and its asymmetric distribution in the bilayer dramatically slows down pore resealing, not only by mere molecular stabilization of the pore rim, but also by generating membrane nanotubes.