bluuebunny/crossref_metadata_2025 huggingface dataset:
Relationship Between Infection or Close Contact With COVID-19 and Workplace Mistreatment Among Japanese Workers
Authors: Sawamoto Naoya , Okawara Makoto , Muramatsu Keiji , Odagami Kiminori , Mafune Kosuke , Tateishi Seiichiro , Tsuji Mayumi , Ogami Akira , Fujino Yoshihisa
Published: January 2024

Objective

Discriminatory treatment against those with emerging infection is a long-standing problem. The present study investigates whether workers infected or in close contact with COVID-19 were susceptible to workplace mistreatment during the pandemic in Japan.

Methods

This Internet-based cross-sectional study analyzed a total of 18,170 workers aged 20 to 60 years in Japan in December 2020. Odds ratios (ORs) for workplace mistreatment were estimated.

Results

For workers with close contact or infection, ORs for workplace mistreatment in a model adjusted for socioeconomic factors were 7.64 (95% CI: 5.52–10.6,P< 0.001) and 10.7 (95% CI: 8.44–13.6,P< 0.001), respectively.

Conclusions

Workers with infection or close contact were significantly more likely to experience workplace mistreatment. Actions against workplace mistreatment for workers with emerging infection are still required.
A bird’s-eye view: exploration of the flavin-containing monooxygenase (FMO) superfamily in common wheat
Authors: Sun Sherry , Bakkeren Guus
Published: January 2024

The Flavin Monooxygenase (FMO) gene superfamily in plants is involved in various processes most widely documented for its involvement in auxin biosynthesis, specialized metabolite biosynthesis, and plant microbial defense signalling. The roles of FMOs in defense signaling and disease resistance have recently come into focus as they may present opportunities to increase immune responses in plants including leading to systemic acquired resistance, but are not well characterized. We present a comprehensive catalogue ofFMOs found in genomes across vascular plants and explore, in depth, 170 wheatTaFMOgenes for sequence architecture,cis-acting regulatory elements, and changes due to Transposable Element insertions. A molecular phylogeny separates TaFMOs into three clades (A, B, and C) for which we further report gene duplication patterns, and differential rates of homoeologue expansion and retention among TaFMO subclades. We discuss Clade B TaFMOs where gene expansion is similarly seen in other cereal genomes. Transcriptome data from various studies point towards involvement of subclade B2TaFMOs in disease responses against both biotrophic and necrotrophic pathogens, substantiated by promoter element analysis. We hypothesize that certain TaFMOs are responsive to both abiotic and biotic stresses, providing potential targets for enhancing disease resistance, plant yield and other important agronomic traits. Altogether, FMOs in wheat and other crop plants present an untapped resource to be exploited for improving the quality of crops.
Neurophysiological Correlates of Phase-Specific Enhancement of Motor Memory Consolidation via Slow-Wave Closed-Loop Targeted Memory Reactivation
Authors: Nicolas Judith , King Bradley R. , Levesque David , Lazzouni Latifa , Wang David , Grossman Nir , Swinnen Stephan P. , Doyon Julien , Carrier Julie , Albouy Geneviève
Published: January 2024

Memory consolidation can be enhanced during sleep using targeted memory reactivation (TMR) and closed-loop (CL) acoustic stimulation on the up-phase of slow oscillations (SOs). Here, we tested whether applying TMR at specific phases of the SOs (up vs. down vs. no reactivation) could influence the behavioral and neural correlates of motor memory consolidation in healthy young adults. Results showed that up- (as compared to down-) state cueing resulted in greater performance improvement. Sleep electrophysiological data indicated that up-stimulated SOs exhibited higher amplitude and greater peak-nested sigma power. Task-related functional magnetic resonance images revealed that up-state cueing strengthened activity in - and segregation of - striato-motor and hippocampal networks; and that these modulations were related to the beneficial effect of TMR on sleep features and performance. Overall, these findings highlight the potential of CL-TMR to induce phase-specific modulations of motor performance, sleep oscillations and brain responses during motor memory consolidation.
CXCR3-expressing myeloid cells recruited to the hypothalamus protect against diet-induced body mass gain and metabolic dysfunction
Authors: Mendes Natalia F. , Zanesco Ariane M. , Aguiar Cristhiane F. , Rodrigues-Luiz Gabriela F. , da Silva Dayana C. , Campos Jonathan F. , Câmara Niels O. S. , de Moraes-Vieira Pedro M. M. , de Araújo Eliana P. , Velloso Licio A.
Published: January 2024

Microgliosis is an important component of diet-induced hypothalamic inflammation in obesity. A few hours after the introduction of a high-fat diet, the mediobasal hypothalamus resident microglia undergo morphological and functional changes toward an inflammatory phenotype. If the consumption of large amounts of dietary fats persists for long periods, bone marrow- derived myeloid cells are recruited and integrated into a new landscape of hypothalamic microglia. However, it is currently unknown what are the transcriptional signatures and specific functions exerted by either resident or recruited subsets of hypothalamic microglia. Here, the elucidation of the transcriptional signatures revealed that resident microglia undergo only minor changes in response to dietary fats; however, under the consumption of a high-fat diet, there are major transcriptional differences between resident and recruited immune cells with major impact on chemotaxis. In addition, in CCR2+ recruited peripheral immune cells, there are major transcriptional differences between females and males with important impact on transcripts involved in neurodegeneration and thermogenesis. The chemokine receptor CXCR3 emerged as one of the components of chemotaxis with the greatest difference between recruited and resident microglia, and thus, was elected for further intervention. The hypothalamic immunoneutralization of CXCL10, one of the ligands for CXCR3, resulted in increased body mass gain and reduced energy expenditure, particularly in females. Furthermore, the chemical inhibition of CXCR3 resulted in a much greater change in phenotype with increased body mass gain, reduced energy expenditure, increased blood leptin, glucose intolerance, and reduced insulin. Thus, this study has elucidated the transcriptional differences between resident microglia and recruited immune cells in diet-induced obesity, identifying chemokines as a relevant subset of genes undergoing regulation. In addition, we showed that a subset of recruited immune cells expressing CXCR3 has a protective, rather than a detrimental role in the metabolic outcomes promoted by the consumption of a high-fat diet, thus, establishing a new concept in obesity-associated hypothalamic inflammation.
Advancing Transcription Factor Binding Site Prediction Using DNA Breathing Dynamics and Sequence Transformers via Cross Attention
Authors: Kabir Anowarul , Bhattarai Manish , Rasmussen Kim Ø. , Shehu Amarda , Bishop Alan R , Alexandrov Boian , Usheva Anny
Published: January 2024

Understanding the impact of genomic variants on transcription factor binding and gene regulation remains a key area of research, with implications for unraveling the complex mechanisms underlying various functional effects. Our study delves into the role of DNA’s biophysical properties, including thermodynamic stability, shape, and flexibility in transcription factor (TF) binding. We developed a multi-modal deep learning model integrating these properties with DNA sequence data. Trained on ChIP-Seq (chromatin immunoprecipitation sequencing) datain vivoinvolving 690 TF-DNA binding events in human genome, our model significantly improves prediction performance in over 660 binding events, with up to 9.6% increase in AUROC metric compared to the baseline model when using no DNA biophysical properties explicitly. Further, we expanded our analysis toin vitrohigh-throughput Systematic Evolution of Ligands by Exponential enrichment (SELEX) and Protein Binding Microarray (PBM) datasets, comparing our model with established frameworks. The inclusion of DNA breathing features consistently improved TF binding predictions across different cell lines in these datasets. Notably, for complex ChIP-Seq datasets, integrating DNABERT2 with a cross-attention mechanism provided greater predictive capabilities and insights into the mechanisms of disease-related non-coding variants found in genome-wide association studies. This work highlights the importance of DNA biophysical characteristics in TF binding and the effectiveness of multi-modal deep learning models in gene regulation studies.
Characterization of non-monotonic relationships between tumor mutational burden and clinical outcomes
Authors: Anaya Jordan , Kung Julia , Baras Alexander S.
Published: January 2024

Potential clinical biomarkers are often assessed with Cox regressions or their ability to differentiate two groups of patients based on a single cutoff. However, both of these approaches assume a monotonic relationship between the potential biomarker and survival. Tumor mutational burden (TMB) is currently being studied as a predictive biomarker for immunotherapy, and a single cutoff is often used to divide patients. In this study we introduce a two-cutoff approach that allows splitting of patients when a non-monotonic relationship is present, and explore the use of neural networks to model more complex relationships of TMB to outcome data. Using real-world data we find that while in most cases the true relationship between TMB and survival appears monotonic, that is not always the case and researchers should be made aware of this possibility.

Significance

When a non-monotonic relationship to survival is present it is not possible to divide patients by a single value of a predictor. Neural networks allow for complex transformations and can be used to correctly split patients when a non-monotonic relationship is present.
Cell polarity proteins promote macropinocytosis in response to metabolic stress
Authors: Lambies Guillem , Lee Szu-Wei , Duong-Polk Karen , Aza-Blanc Pedro , Maganti Swetha , Dawson David W. , Commisso Cosimo
Published: January 2024

Macropinocytosis has emerged as a nutrient-scavenging pathway that cancer cells exploit to survive the nutrient-deprived conditions of the tumor microenvironment. Cancer cells are especially reliant on glutamine for their survival, and in pancreatic ductal adenocarcinoma (PDAC) cells, glutamine deficiency can enhance the stimulation of macropinocytosis, allowing the cells to escape metabolic stress through the production of extracellular-protein-derived amino acids. Here, we identify the atypical protein kinase C (aPKC) enzymes, PKCζ and PKCι, as novel regulators of macropinocytosis. In normal epithelial cells, aPKCs are known to regulate cell polarity in association with the scaffold proteins Par3 and Par6, controlling the function of several targets, including the Par1 kinases. In PDAC cells, we identify that each of these cell polarity proteins are required for glutamine stress-induced macropinocytosis. Mechanistically, we find that the aPKCs are regulated by EGFR signaling or by the transcription factor CREM to promote the relocation of Par3 to microtubules, facilitating macropinocytosis in a dynein-dependent manner. Importantly, we determine that cell fitness impairment caused by aPKC depletion is rescued by the restoration of macropinocytosis and that aPKCs support PDAC growthin vivo. These results identify a previously unappreciated role for cell polarity proteins in the regulation of macropinocytosis and provide a better understanding of the mechanistic underpinnings that control macropinocytic uptake in the context of metabolic stress.
A dynamicWUSCHEL/ Layer 1 interplay directs shoot apical meristem formation during regeneration
Authors: Kumar Manoj , Ayzenshtat Dana , Zemach Hanita , Belausov Eduard , Williams Leor Eshed , Bocobza Samuel
Published: January 2024

De novoshoot apical meristem (SAM) organogenesis during regeneration in tissue culture has been investigated for several decades, but the precise mechanisms governing early-stage cell fate specification remain elusive. In contrast to SAM establishment during embryogenesis,in vitroSAM formation occurs without positional cues, and is characterized by spontaneous cellular patterning. Here, we have elucidated the initial stages of SAM organogenesis and the molecular mechanisms that orchestrate gene patterning to establish SAM homeostasis. We found that SAM organogenesis in tobacco calli initiates with protuberance formation followed by the formation of an intact L1 layer covering the nascent protuberance. Acquisition of L1 cellular identity is indispensable for de novo SAM formation, which also requiresWUSCHEL(WUS) and the cellular capacity to direct anticlinal cell divisions. An intriguing finding is thatTONNEAU1silencing prevents the exclusive occurrence of anticlinal divisions in the outermost layer of the protuberances and suppresses the acquisition of L1 cellular identity, ultimately impeding regeneration. This study exposes an intricate interplay between L1 andWUSexpression and that any disruption in this interplay compromises shoot formation. It further provides a novel molecular framework for the characterization ofWUS/L1 interplay-mediated shoot apical meristem formation during regeneration.
Neural space-time model for dynamic scene recovery in multi-shot computational imaging systems
Authors: Cao Ruiming , Divekar Nikita , Nuñez James , Upadhyayula Srigokul , Waller Laura
Published: January 2024

Computational imaging reconstructions from multiple measurements that are captured sequentially often suffer from motion artifacts if the scene is dynamic. We propose a neural space-time model (NSTM) that jointly estimates the scene and its motion dynamics. Hence, we can both remove motion artifacts and resolve sample dynamics. We demonstrate NSTM in three computational imaging systems: differential phase contrast microscopy, 3D structured illumination microscopy, and rolling-shutter DiffuserCam. We show that NSTM can recover subcellular motion dynamics and thus reduce the misinterpretation of living systems caused by motion artifacts.
Pharmacogenomics Guided Spaceflight: the intersection between space-flown drugs and space genes
Authors: Nelson Theodore M. , Rose Julianna K. , Walter Claire E. , Cervantes-Navarro Gresia L. , Schmidt Caleb M. , Lin Richard , Alexander Emma , Zheng Jiang Tao , Glicksberg Benjamin S. , Schmidt Julian C. , Overbey Eliah , Rana Brinda , Patel Hemal , Schmidt Michael A. , Mason Christopher E.
Published: January 2024

Ten years ago, it was predicted that the multi-omics revolution would also revolutionize space pharmacogenomics. Current barriers related to the findable, accessible, interoperable, and reproducible use of space-flown pharmaceutical data have contributed to a lack of progress beyond application of earth-based principles. To directly tackle these challenges, we have produced a novel database of all the drugs flown into space, compiled from publicly available ontological and spaceflight-related datasets, to exemplify analyses for describing significant spaceflight-related targets. By focusing on mechanisms perturbed by spaceflight, we have provided a novel avenue for identifying the most relevant changes within the drug absorption, distribution, metabolism, and excretion pathways. We suggest a set of space genes, by necessity limited to available tissue types, that can be expanded and modified based on future tissue-specific and mechanistic-specific high-throughput assays. In sum, we provide the justification and a definitive starting point for pharmacogenomics guided spaceflight as a foundation of precision medicine, which will enable long-term human habitation of the Moon, Mars, and beyond.

Graphical Abstract
Mountain pine beetle spread in forests with varying host resistance
Authors: Brush Micah , Lewis Mark A.
Published: January 2024

In the last few decades, mountain pine beetle (MPB) have spread into novel regions in Canada. An important aspect seldom captured in models of MPB spread is host resistance. Lodgepole pine, the predominant host of MPB, varies in resistance across the landscape. There is evidence for a genetic component of resistance, as well as evidence that hosts in areas where MPB has not been present historically are at risk of increased susceptibility. In addition to the spatially varying resistance of the primary host species, the eastward spread of MPB has brought them into jack pine forests. Host resistance in jack pine remains uncertain, but experiments indicate jack pine could be a suitable host. We develop a model of pine beetle spread that links pine beetle population dynamics and forest structure and resistance. We find that beetle outbreaks in the model are characterized by large transient outbreaks that move through the forest. We show how the speed of these outbreaks changes with host resistance and find that biologically plausible values for host resistance are able to stop the wave from advancing. We also find that near the threshold of resistance where the wave is able to advance, small changes in host resistance dramatically decrease the severity of the outbreak. These results indicate that planting trees selected for higher MPB resistance on the landscape may be able to slow or even stop the local spread of MPB. In terms of further eastward spread, our results indicate future outbreaks may move more quickly and be more severe if novel lodgepole pine hosts are indeed more susceptible to beetle attacks, although more research is needed into the susceptibility of jack pine.
Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders
Authors: Kroupova Alena , Spiteri Valentina A. , Furihata Hirotake , Darren Darren , Ramachandran Sarath , Rutter Zoe J. , Chakraborti Sohini , Haubrich Kevin , Pethe Julie , Gonzales Denzel , Wijaya Andre , Rodriguez-Rios Maria , Lynch Dylan M. , Farnaby William , Nakasone Mark A. , Zollman David , Ciulli Alessio
Published: January 2024

The ubiquitin E3 ligase cereblon (CRBN) is the target of therapeutic drugs thalidomide and lenalidomide and is recruited by most targeted protein degraders (PROTACs and molecular glues) in clinical development. Biophysical and structural investigation of CRBN has been limited by current constructs that either require co-expression with the adaptor DDB1 or inadequately represent full-length protein, with high-resolution structures of degraders ternary complexes remaining rare. We present the design of CRBNmidi, a construct that readily expresses fromE. coliwith high yields as soluble, stable protein without DDB1. We benchmark CRBNmidifor wild-type functionality through a suite of biophysical techniques and solve high-resolution co-crystal structures of its binary and ternary complexes with degraders. We qualify CRBNmidias an enabling tool to accelerate structure-based discovery of the next generation of CRBN based therapeutics.

One sentence summary

A novel Cereblon construct (CRBNmidi) allows structural and biophysical enablement of ligand and degrader design
Effects of local and landscape factors on paddy field arthropod diversity: from species to communities
Authors: Ou Jia-Ang , Huang Chi-Lun , Tsai Chi-Wei , Ho Chuan-Kai
Published: January 2024

Agricultural landscapes are dynamic mosaics where environmental conditions vary across spatial scales. Identifying the spatial scales of environmental variables relevant to biodiversity is therefore essential for safeguarding biodiversity and the ecosystem services they provide. Although species richness is a useful aggregate metric the captures the responses of biodiversity as a whole, few studies have examined how species-specific responses to environmental variables give rise to community-level patterns. Failure to account for the heterogeneity in species responses may undermine potential processes that structure biodiversity. In this study, we sampled paddy-field inhabiting arthropods across the first growing season and examined how local (organic farming, water depth, and crop height) and landscape factors (forest cover and connectivity) affect their abundance and distribution. We built a spatio-temporally explicit joint species distribution model (JSDM) to answer three main questions. 1) How do species differ in their response to local and landscapes factors. 2) Can trophic guild explain the variation in species responses to environmental covariates, and 3) How do species-specific responses scale-up to structure species richness at the community-level? Our results show that the mean importance of environmental covariates was low overall (mean R2= 0.21), suggesting the prevalence of stochasticity in structuring species abundances. However, environmental importance varied substantially across species (highest R2= 0.87 and lowest R2= 0.01) and that trophic guild explained only approximately 15% of species responses, which indicates high idiosyncrasy in species responses both within and among guilds. At the community-level, we found that species richness responds negligibly to local factors while increasing with forest cover at the landscape scale. The importance of each environmental covariate was reflected by the variability of species responses. Lastly, we found no evidence of dispersal limitation in structuring species abundances. Taken together, our study suggests that many paddy field arthropods exhibit transient dynamics and that environmental effects are highly species-specific, even within the same trophic guild. Most importantly, our study highlights the need to understand biodiversity from the species level to understand the processes that structure them in dynamic mosaic landscapes.
Dynamic Visualization of DNA Methylation in Cell Cycle Genes during iPSC Cardiac Differentiation
Authors: Li Ning , Nguyen Ba Thong , Zhang Zhenhe , MacLellan W. Robb , Zhang Yiqiang
Published: January 2024

Background

Epigenetic DNA methylation is an essential mechanism controlling gene expression and cellular function. Existing analyses with conventional assays have generated significant insights into static states of DNA methylation, but were unable to visualize the dynamics of epigenetic regulation.

Aim

We utilized a genomic DNA methylation reporter (GMR) system to track changes in DNA methylation during cardiac differentiation.

Methods and Results

The promoter region ofCdk1(Cyclin-dependent kinase 1) orSox2(SRY-Box Transcription Factor 2) gene was cloned upstream of the small nuclear ribonucleoprotein polypeptide N (Snrpn) minimal promoter followed by a fluorescent reporter gene. Mouse induced pluripotent stem cells (iPSCs) carrying Sox2 GMR rapidly lost fluorescent reporter signal upon the induction of differentiation. Cdk1 GMR reporter signal was strong in undifferentiated iPSCs, and gradually decreased during directed cardiomyocyte (CM) differentiation. RT-qPCR and pyrosequencing demonstrated that the reduction ofSox2andCdk1was regulated by hypermethylation of their CpG regions during cardiac differentiation. The present study demonstrated the dynamic DNA methylation along the course of cell cycle withdrawal during CM differentiation.

Conclusion

The GMR reporter system can be a useful tool to monitor real-time epigenetic DNA modification at single-cell resolution.
The neocortical infrastructure for language involves region-specific patterns of laminar gene expression
Authors: Wong Maggie M.K. , Sha Zhiqiang , Lütje Lukas , Kong Xiang-Zhen , Velthuijs Niels , van Heukelum Sabrina , van de Berg Wilma D.J. , Jonkman Laura E. , Fisher Simon E. , Francks Clyde
Published: January 2024

The language network of the human brain has core components in the inferior frontal cortex and superior/middle temporal cortex, with left-hemisphere dominance in most people. Functional specialization and interconnectivity of these neocortical regions is likely to be reflected in their molecular and cellular profiles. Excitatory connections between cortical regions arise and innervate according to layer-specific patterns. Here we generated a new gene expression dataset from human postmortem cortical tissue samples from core language network regions, using spatial transcriptomics to discriminate gene expression across cortical layers. Integration of these data with existing single-cell expression data identified 56 genes that showed differences in laminar expression profiles between frontal and temporal language cortex together with upregulation in layer II/III and/or layer V/VI excitatory neurons. Based on data from large-scale genome-wide screening in the population, DNA variants within these 56 genes showed set-level associations with inter-individual variation in structural connectivity between left-hemisphere frontal and temporal language cortex, and with predisposition to dyslexia. The axon guidance genesSLIT1andSLIT2were consistently implicated. These findings identify region-specific patterns of laminar gene expression as a feature of the brain’s language network.
Signatures of adaptation at key insecticide resistance loci inAnopheles gambiaein Southern Ghana revealed by low-coverage WGS
Authors: Dennis Tristan P.W. , Essandoh John , Mable Barbara K. , Viana Mafalda S. , Yawson Alexander E. , Weetman David.
Published: January 2024

Resistance to insecticides and adaptation to a diverse range of environments present challenges toAnopheles gambiae s.l.mosquito control efforts in sub-Saharan Africa. Whole-genome-sequencing is often employed for identifying the genomic basis underlying adaptation inAnopheles, but remains expensive for large-scale surveys. Low-coverage whole-genome-sequencing (lcWGS) can identify regions of the genome involved in adaptation at a lower cost, but is currently untested inAnophelesmosquitoes. Here, we use lcWGS to investigate population genetic structure and identify signatures of local adaptation inAnophelesmosquitoes across southern Ghana. In contrast to previous analyses, we find no structuring by ecoregion, withAnopheles coluzziiandAnopheles gambiaepopulations largely displaying the hallmarks of large, unstructured populations. However, we find signatures of selection at insecticide resistance (IR) loci that appear ubiquitous across ecoregions inAn. coluzzii,and strongest in forest ecoregions inAn. gambiae. In the IR geneCyp9k1, we find species-specific alleles under selection, suggesting interspecific variation in the precise mechanism of resistance conferred byCyp9k1. Our study highlights resistance candidate genes in this region, and validates lcWGS, potentially to very low coverage levels, for population genomics and exploratory surveys for adaptation inAnophelestaxa.
Mappingin silicogenetic networks of theKMT2Dtumour suppressor gene to uncover novel functional associations and cancer cell vulnerabilities
Authors: Takemon Yuka , Pleasance Erin D. , Gagliardi Alessia , Hughes Christopher S. , Csizmok Veronika , Wee Kathleen , Trinh Diane L. , Huff Ryan D. , Mungall Andrew J. , Moore Richard A. , Chuah Eric , Mungall Karen L. , Lewis Eleanor , Nelson Jessica , Lim Howard J. , Renouf Daniel J. , Jones Steven JM. , Laskin Janessa , Marra Marco A.
Published: January 2024

Loss-of-function (LOF) alterations in tumour suppressor genes cannot be directly targeted. Approaches characterising gene function and vulnerabilities conferred by such mutations are required. Here, we computationally map genetic networks ofKMT2D, a tumour suppressor gene frequently mutated in several cancer types. UsingKMT2Dloss-of-function (KMT2DLOF) mutations as a model, we illustrate the utility ofin silicogenetic networks in uncovering novel functional associations and vulnerabilities in cancer cells with LOF alterations affecting tumour suppressor genes. We revealed genetic interactors with functions in histone modification, metabolism, and immune response, and synthetic lethal (SL) candidates, including some encoding existing therapeutic targets. Analysing patient data from The Cancer Genome Atlas and the Personalized OncoGenomics Project, we showed, for example, elevated immune checkpoint response markers inKMT2DLOFcases, possibly supportingKMT2DLOFas an immune checkpoint inhibitor biomarker. Our study illustrates how tumour suppressor gene LOF alterations can be exploited to reveal potentially targetable cancer cell vulnerabilities.
Development of immobilized antibody-based affinity grid strategy and application in on-grid purification of target proteins for high-resolution cryo-EM
Authors: Zhao Qiaoyu , Hong Xiaoyu , Wang Yanxing , Zhang Shaoning , Ding Zhanyu , Meng Xueming , Song Qianqian , Hong Qin , Jiang Wanying , Shi Xiangyi , Cai Tianxun , Cong Yao
Published: January 2024

In cryo-electron microscopy (cryo-EM), sample preparation, especially for rare or fragile macromolecular assemblies and those suffering from air-water interface denaturation and particle orientation distribution problems, is a major bottleneck. Here, we developed and characterized an immobilized antibody-based affinity grid (IAAG) strategy based on the high-affinity PA tag/NZ-1 antibody epitope tag system. We used Pyr-NHS as a linker to immobilize NZ-1 Fab on the graphene oxide or carbon covered grid surface. We showed that the IAAG grid can enrich the PA-tagged target proteins, and overcome preferred orientation problems. Furthermore, we demonstrated that our IAAG strategy can be utilized for on-grid purification of low-abundance target complexes from cell lysates and enables atomic resolution cryo-EM. This approach greatly streamlines the purification process, reduces the need for large quantities of biological samples, and addresses common challenges encountered in cryo-EM sample preparation. Collectively, our IAAG strategy provides an efficient and robust means for combined sample purification and vitrification feasible for high-resolution cryo-EM. This approach also has the potential for broader applicability in cryo-EM and cryo-ET.
The mitochondrialorf117Shagene desynchronizes pollen development and causes pollen abortion in the Arabidopsis Sha CMS
Authors: Dehaene Noémie , Boussardon Clément , Andrey Philippe , Charif Delphine , Brandt Dennis , Gilouppe Taillefer Clémence , Nietzel Thomas , Ricou Anthony , Simon Matthieu , Tran Joseph , Vezon Daniel , Camilleri Christine , Arimura Shin-ichi , Schwarzländer Markus , Budar Françoise
Published: January 2024

Cytoplasmic male sterility (CMS) is of major agronomical relevance in hybrid breeding. In gametophytic CMS, abortion of pollen is determined by the grain genotype, while in sporophytic CMS, it is determined by the mother plant genotype. While several CMS mechanisms have been dissected at the molecular level, gametophytic CMS has not been straightforwardly accessible. We used the gametophytic Sha-CMS in Arabidopsis to characterize the cause and process of pollen abortion by implementingin vivobiosensing in single pollen and mitoTALEN mutagenesis. We obtained conclusive evidence thatorf117Shais the CMS-causing gene, despite distinct characteristics from other CMS-genes. We measured thein vivocytosolic ATP content in single pollen, followed pollen development and analyzed pollen mitochondrial volume in two genotypes that differed only by the presence of theorf117Shalocus. Our results show that the Sha-CMS is not triggered by ATP deficiency. Instead, we observed desynchronization of a pollen developmental program. Pollen death occurred independently in pollen grains at diverse stages and was preceded by mitochondrial swelling. We conclude that pollen death is grain-autonomous in Sha-CMS and propose that mitochondrial permeability transition, which was previously described as a hallmark of developmental and environmental-triggered cell death programs, precedes pollen death in Sha-CMS.

Highlight

The Arabidopsis CMS-causing geneorf117Shadoes not limit pollen ATP supply. Pollen-centered approaches show desynchronization of development and mitochondrial swelling before pollen death, which occurred at diverse stages.
A general model unifying the adaptive, transient and sustained properties of ON and OFF auditory neural responses
Authors: Rançon Ulysse , Masquelier Timothée , Cottereau Benoit R.
Published: January 2024

Sounds are temporal stimuli decomposed into numerous elementary components by the auditory nervous system. For instance, a temporal to spectro-temporal transformation modelling the frequency decomposition performed by the cochlea is a widely adopted first processing step in today’s computational models of auditory neural responses. Similarly, increments and decrements in sound intensity (i.e., of the raw waveform itself or of its spectral bands) constitute critical features of the neural code, with high behavioural significance. However, despite the growing attention of the scientific community on auditory OFF responses, their relationship with transient ON, sustained responses and adaptation remains unclear. In this context, we propose a new general model, based on a pair of linear filters, namedAdapTrans, that captures both sustained and transient ON and OFF responses into a unifying and easy to expand framework. We demonstrate that filtering audio cochleagrams with AdapTrans permits to accurately render known properties of neural responses measured in different mammal species such as the dependence of OFF responses on the stimulus fall time and on the preceding sound duration. Furthermore, by integrating our framework into gold standard and state-of-the-art machine learning models that predict neural responses from audio stimuli, following a supervised training on a large compilation of electrophysiology datasets (ready-to-deploy PyTorch models and pre-processed datasets shared publicly), we show that AdapTrans systematically improves the prediction accuracy of estimated responses within different cortical areas of the rat and ferret auditory brain. Together, these results motivate the use of our framework for computational and systems neuroscientists willing to increase the plausibility and performances of their models of audition.
PI3 kinase inhibitor PI828 uncouples aminergic GPCRs and Ca2+mobilization irrespectively of its primary target
Authors: Kotova Polina D. , Dymova Ekaterina A. , Lyamin Oleg O. , Rogachevskaja Olga A. , Kolesnikov Stanislav S.
Published: January 2024

The phosphoinositide 3-kinase (PI3K) is involved in regulation of multiple intracellular processes. Although the inhibitory analysis is generally employed for validating a physiological role of PI3K, increasing body of evidence suggests that PI3K inhibitors can exhibit PI3K-unrelated activity as well. Here we studied Ca2+signaling initiated by aminergic agonists in a variety of different cells and analyzed effects of the PI3K inhibitor PI828 on cell responsiveness. It turned out that PI828 inhibited Ca2+transients elicited by acetylcholine (ACh), histamine, and serotonin, but did not affect Ca2+responses to norepinephrine and ATP. Another PI3K inhibitor wortmannin negligibly affected Ca2+signaling initiated by any one of the tested agonists. Using the genetically encoded PIP3sensor PH(Akt)-Venus, we confirmed that both PI828 and wortmannin effectively inhibited PI3K and ascertained that this kinase negligibly contributed to ACh transduction. These findings suggested that PI828 inhibited Ca2+responses to aminergic agonists tested, involving an unknown cellular mechanism unrelated to the PI3K inhibition. Complementary physiological experiments provided evidence that PI828 could inhibit Ca2+signals induced by certain agonists, by acting extracellularly, presumably, through their surface receptors. For the muscarinic M3 receptor, this possibility was verified with molecular docking and molecular dynamics. As demonstrated with these tools, wortmannin could be bound in the extracellular vestibule at the muscarinic M3 receptor but this did not preclude binding of ACh to the M3 receptor followed by its activation. In contrast, PI828 could sterically block the passage of ACh into the allosteric site, preventing activation of the muscarinic M3 receptor.
Acute exercise increases systemic kynurenine pathway metabolites and activates the AHR in human PBMCs
Authors: Joisten Niklas , Walzik David , Schenk Alexander , Metcalfe Alan J , Belen Sergen , Schaaf Kirill , Gehlert Sebastian , Spiliopoulou Polyxeni , Garzinsky Ann-Marie , Thevis Mario , Rappelt Ludwig , Donath Lars , Meuth Sven G , Bloch Wilhelm , Zimmer Philipp
Published: January 2024

The kynurenine pathway of tryptophan degradation generates several metabolites such as kynurenine or kynurenic acid that serve as endogenous ligands of the aryl hydrocarbon receptor (AHR). Due to its distinct biological roles particularly modulating the immune system, the AHR is a current therapeutic target across different inflammation-related diseases. Here, we show an exercise-induced increase in AHR ligand availability on a systemic level and a kynurenine pathway activation in peripheral mononuclear blood cells (PBMCs). Concurrently, the AHR is activated in PBMCs following acute exercise, with effects being dependent on exercise intensity. In conclusion, these data indicate a novel mechanistic link how exercise modulates the immune system through the kynurenine pathway-AHR axis, potentially underlying exercise-induced benefits in various chronic diseases.
cis-MoO2(BHAN)2Complex: Its Role in the Protection of Radiation-Induced DNA Damage
Authors: Deb Priyangana
Published: January 2024

The synthesized molybdenum complex, [cis-MoO2(BHAN)2] (BHAN=β-hydroxy-α-naphthaldehyde), exhibits remarkable efficacy in safeguarding DNA against radiation-induced damage. Comparative studies reveal that the complex offers superior protection to radiolysed DNA compared to the ligand (BHAN). Notably, at a concentration of 2 mM, the complex demonstrates the capability to shield 90% of damaged plasmid DNA from a 20 Gy radiation exposure. Additionally, it also affords significant protection against radiation-induced damage to cellular DNA (CTDNA) from gamma rays. These findings underscore the significant potential of cis-MoO2(BHAN)2as an effective radioprotector for normal tissues in the context of radiotherapy. The results of this study contribute valuable insights into the advancement of radioprotective strategies, presenting a noteworthy breakthrough with implications for future medical advancements.
Drugs Form Ternary Complexes with Human Liver Fatty Acid Binding Protein (FABP1) and FABP1 Binding Alters Drug Metabolism
Authors: Yabut King Clyde B. , Martynova Alice , Nath Abhinav , Zercher Benjamin P. , Bush Matthew F. , Isoherranen Nina
Published: January 2024

Liver fatty acid binding protein (FABP1) binds diverse endogenous lipids and is highly expressed in the human liver. Binding to FABP1 alters the metabolism and homeostasis of endogenous lipids in the liver. Drugs have also been shown to bind to rat FABP1, but limited data is available for human FABP1 (hFABP1). FABP1 has a large binding pocket and multiple fatty acids can bind to FABP1 simultaneously. We hypothesized that drug binding to hFABP1 results in formation of ternary complexes and that FABP1 binding alters drug metabolism. To test these hypotheses native protein mass spectrometry (MS) and fluorescent 11-(dansylamino)undecanoic acid (DAUDA) displacement assays were used to characterize drug binding to hFABP1 and diclofenac oxidation by cytochrome P450 2C9 (CYP2C9) was studied in the presence and absence of hFABP1. DAUDA binding to hFABP1 involved high (Kd,1=0.2 µM) and low affinity (Kd,2>10 µM) binding sites. Nine drugs bound to hFABP1 with Kdvalues ranging from 1 to 20 µM. None of the tested drugs completely displaced DAUDA from hFABP1 and fluorescence spectra showed evidence of ternary complex formation. Formation of DAUDA-diclofenac-hFABP1 ternary complex was verified with native MS. Docking placed diclofenac in the portal region of FABP1 with DAUDA in the binding cavity. Presence of hFABP1 decreased the kcatand Km,uof diclofenac with CYP2C9 by ∼50% suggesting that hFABP1 binding in the liver will alter drug metabolism and clearance. Together, these results suggest that drugs form ternary complexes with hFABP1 and that hFABP1 interacts with CYP2C9.

Significance statement

Many commonly prescribed drugs bind FABP1 forming ternary complexes with FABP1 and the fluorescent fatty acid DAUDA. This suggests that in the human liver drugs will bind to apo-FABP1 and fatty acid bound FABP1. The high expression of FABP1 in the liver and binding of drugs to FABP1 will alter rates of drug metabolism in the liver.
Neutrophil immune profile controls spinal cord regeneration in zebrafish
Authors: de Sena-Tomás Carmen , Lameira Leonor Rebola , Taborda Patrícia Naique , Laborde Alexandre , Orger Michael , de Oliveira Sofia , Saúde Leonor
Published: January 2024

Spinal cord injury triggers a strong innate inflammatory response in both non-regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet, their role in the repair process, particularly in a regenerative context, remains largely unknown. Here, we show that, following rapid recruitment to the injured spinal cord, neutrophils mostly reverse migrate throughout the zebrafish body. In addition, promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil-specific RNA-seq analysis reveals an enhanced activation state that correlates with a transient increase intnf-αexpression in macrophage/microglia populations. Conversely, blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether, these findings provide new insights into the role of neutrophils in spinal cord regeneration, emphasizing the significant impact of their immune profile on the outcome of the repair process.

Graphical Abstract
Efficient 3D cone trajectory design for improved combined angiographic and perfusion imaging using arterial spin labeling
Authors: Shen Qijia , Wu Wenchuan , Chiew Mark , Ji Yang , Woods Joseph , Okell Thomas W
Published: January 2024

Purpose

To improve the spatial resolution and repeatability of a non-contrast MRI technique for simultaneous time resolved 3D angiography and perfusion imaging by developing an efficient 3D cone trajectory design.

Methods

A novel parameterized 3D cone trajectory design incorporating the 3D Golden Angle was integrated into 4D combined angiography and perfusion using radial imaging and arterial spin labeling (CAPRIA) to achieve higher spatial resolution and sampling efficiency for both dynamic angiography and perfusion imaging with flexible spatiotemporal resolution. Numerical simulations and physical phantom scanning were used to optimize the cone design. Eight healthy volunteers were scanned to compare the original radial trajectory in 4D CAPRIA with our newly designed cone trajectory. A locally low rank reconstruction method was used to leverage the complementary k-space sampling across time.

Results

The improved sampling in the periphery of k-space obtained with the optimized 3D cone trajectory resulted in improved spatial resolution compared with the radial trajectory in phantom scans. Improved vessel sharpness and perfusion visualization were also achieved in vivo. Less dephasing was observed in the angiograms due to the short echo time of our cone trajectory and the improved k-space sampling efficiency also resulted in higher repeatability compared to the original radial approach.

Conclusion

The proposed 3D cone trajectory combined with 3D Golden Angle ordering resulted in improved spatial resolution and image quality for both angiography and perfusion imaging and could potentially benefit other applications that require an efficient sampling scheme with flexible spatial and temporal resolution.
Spatially targeted inhibitory rhythms differentially affect neuronal integration
Authors: Headley Drew B. , Latimer Benjamin , Aberbach Adin , Nair Satish S.
Published: January 2024

Pyramidal neurons form dense recurrently connected networks with multiple types of inhibitory interneurons. A major differentiator between interneuron subtypes is whether they synapse onto perisomatic or dendritic regions. They can also engender local inhibitory rhythms, beta (12-35 Hz) and gamma (40-80 Hz). The interaction between the rhythmicity of inhibition and its spatial targeting on the neuron may determine how it regulates neuronal integration. Thus, we sought to understand how rhythmic perisomatic and distal dendritic inhibition impacted integration in a layer 5 pyramidal neuron model with elaborate dendrites and Na+, NMDA, and Ca2+dendritic spikes. We found that inhibition regulated the coupling between dendritic spikes and action potentials in a location and rhythm-dependent manner. Perisomatic inhibition principally regulated action potential generation, while distal dendritic inhibition regulated the incidence of dendritic spikes and their temporal coupling with action potentials. Perisomatic inhibition was most effective when provided at gamma frequencies, while distal dendritic inhibition functioned best at beta. Moreover, beta modulated responsiveness to apical inputs in a phase-dependent manner, while gamma did so for basal inputs. These results may provide a functional interpretation for the reported association of soma-targeting parvalbumin positive interneurons with gamma, and dendrite-targeting somatostatin interneurons with beta.
Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae
Authors: Thureborn Olle , Wikström Niklas , Razafimandimbison Sylvain G. , Rydin Catarina
Published: January 2024

In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.