bluuebunny/crossref_metadata_2025 huggingface dataset:
Spring reproductive success influences autumnal malarial load in a passerine bird
Authors: Pigeault Romain , Cozzarolo Camille-Sophie , Wassef Jérôme , Gremion Jérémy , Bastardot Marc , Glaizot Olivier , Christe Philippe
Published: July 2023

Although avian haemosporidian parasites are widely used as model organisms to study fundamental questions in evolutionary and behavorial ecology of host-parasite interactions, some of their basic characteristics, such as seasonal variations in within-host density, are still mostly unknown. In addition, their interplay with host reproductive success in the wild seems to depend on the interaction of many factors, starting with host and parasite species and the temporal scale under study. Here, we monitored the parasitemia of two haemosporidian parasites –Plasmodium relictum(lineage SGS1) andP. homonucleophilum(lineage SW2) – in two wild populations of great tits (Parus major) in Switzerland over three years, to characterize their dynamics. We also collected data on birds’ reproductive output – laying date, clutch size, fledging success – to determine whether they were associated with parasitemia before (winter), during (spring) and after (autumn) breeding season. Parasitemia of both species dramatically increased in spring, in a way that was correlated to parasitemia in winter. Parasitemia before and during breeding season did not explain reproductive success. However, the birds which fledged the more chicks had higher parasitemia in autumn, which was not associated with their parasitemia in previous spring. Our results tend to indicate that high haemosporidian parasite loads do not impair reproduction in great tits, but high resource allocation into reproduction can leave birds less able to maintain low parasitemia over the following months.
Clinical prediction of wound re-epithelisation outcomes in non-severe burn injury using the plasma lipidome
Authors: Ryan Monique J. , Raby Edward , Masuda Reika , Lodge Samantha , Nitschke Philipp , Maker Garth L. , Wist Julien , Fear Mark W. , Holmes Elaine , Nicholson Jeremy K. , Gray Nicola , Whiley Luke , Wood Fiona M.
Published: July 2023

Whilst wound repair in severe burns has received substantial research attention, non-severe burns (<20% total body surface area) remain relatively understudied, despite causing considerable physiological impact and constituting most of the hospital admissions for burns. Early prediction of healing outcomes would decrease financial and patient burden, and aid in preventing long-term complications from poor wound healing. Lipids have been implicated in inflammation and tissue repair and may play essential roles in burn wound healing. In this study, plasma samples were collected from 20 non-severe burn patients over 6 weeks from admission, including surgery, and analysed by liquid chromatography-tandem mass spectrometry and nuclear magnetic resonance spectroscopy to detect 850 lipids and 112 lipoproteins. Orthogonal projections to latent structures-discriminant analysis was performed to identify changes associated with re-epithelialisation and delayed re-epithelisation.

We demonstrated that the lipid and lipoprotein profiles at admission could predict re-epithelisation outcomes at 2 weeks post-surgery, and that these discriminatory profiles were maintained up to 6 weeks post-burn. Inflammatory markers GlycB and C-reactive protein indicated divergent systemic responses to the burn injury at admission. Triacylglycerols, diacylglycerols and low-density lipoprotein subfractions were associated with delayed wound closure (p-value <0.02, Cliff’s delta >0.7), whilst high-density lipoprotein subfractions, phosphatidylinositols, phosphatidylcholines, and phosphatidylserines were associated with re-epithelisation at 2 weeks post-surgery (p-value <0.01, Cliff’s delta <-0.7). Further model validation will potentially lead to personalised intervention strategies to reduce the risk of chronic complications post-burn injury.
Targeted Photoconvertible BODIPYs Based on Directed Photooxidation Induced Conversion for Applications in Photoconversion and Live Super Resolution Imaging
Authors: Saladin Lazare , Breton Victor , Lequeu Thibault , Didier Pascal , Danglot Lydia , Collot Mayeul
Published: July 2023

Photomodulable fluorescent probes are drawing an increasing attention due to their applications in advanced bioimaging. Whereas photoconvertible probes can be advantageously used in tracking, photoswitchable probes constitute key tools for single molecule localization microscopy to perform super resolution imaging. Herein we shed light on a red and far-red BODIPY, namely BDP-576 and BDP-650 possessing both properties of conversion and switching. Our study demonstrates that theses pyrrolyl-BODIPYs respectively convert towards typical green- and red-emitting BODIPYs that are perfectly adapted to microscopy. We also showed that these pyrrolyl-BODIPYs undergo Directed Photooxidation Induced Conversion, a photoconversion mechanism that we recently introduced and where the pyrrole moiety plays a central role. These unique features were used to develop targeted photoconvertible probes towards different organelles or subcellular units (plasma membrane, mitochondria, nucleus, actin, Golgi apparatus,etc.) using chemical targeting moieties and Halo tag. We notably showed that BDP-650 could be used to track intracellular vesicles over more than 20 minutes in two color imaging with laser scanning confocal microscopy demonstrating its robustness. The switching properties of these photoconverters were studied at the single molecule level and were then successfully used in live Single Molecule Localization Microscopy in epithelial cells and neurons. Both membrane and mitochondria targeted probes could be used to decipher membrane 3D architecture and mitochondria dynamics at the nanoscale. This study builds a bridge between the photoconversion and photoswitching properties of probes undergoing directed photooxidation and shows the versatility and efficacy of this mechanism in live advanced imaging.
Earthworms and plants can decrease soil greenhouse gases emissions by modulating soil moisture fluctuations and soil macroporosity in a mesocosm experiment
Authors: Ganault Pierre , Nahmani Johanne , Capowiez Yvan , Fromin Nathalie , Shihan Ammar , Bertrand Isabelle , Buatois Bruno , Milcu Alexandru
Published: July 2023

Earthworms can stimulate microbial activity and hence, greenhouse gas (GHG) emissions from soils. However, the extent of this effect in the presence of plants and soil moisture fluctuations, which are influenced by earthworm burrowing activity, remains uncertain. Here we report the effect of earthworms (without, anecic, endogeic, both) and plants (with, without) on GHG (CO2, N2O) emissions in a 3 month-greenhouse mesocosm experiment simulating a simplified agricultural context. The mesocosms allowed for water drainage at the bottom to account for the earthworm engineering effect on water flow during two drying-wetting cycles. N2O cumulative emissions were 34.6 and 44.8% lower when both earthworm species and only endogeic species were present, respectively, and 19.8% lower in presence of plants. The presence of the endogeic species alone or in combination with the anecic species slightly reduced CO2emissions by 5.9% and 11.4% respectively, and plants presence increased emissions by 6%. Earthworms, plants and soil water content interactively affected weekly N2O emissions, an effect controlled by increased soil dryness due to drainage via earthworm burrows and mesocosm evapotranspiration. Soil macroporosity (measured by X-ray tomography) was affected by earthworm species-specific burrowing activity. Both GHG emissions decreased with top soil macropore volume, presumably due to reduced moisture and microbial activity. N2O emissions decreased with macropore volume in the deepest layer, likely due to fewer anaerobic microsites. Our results indicate that, under experimental conditions allowing for plant and earthworm engineering effects on soil moisture, earthworms do not increase GHG emissions and that endogeic earthworms may even reduce N2O emissions.
The C-terminus of α-Synuclein regulates its dynamic cellular internalization by Neurexin 1β
Authors: Birol Melissa , Douzoglou Muñoz Isabella Ioana , Rhoades Elizabeth
Published: July 2023

The aggregation of the disordered neuronal protein, α-Synuclein (αS), is the primary pathological feature of Parkinson’s disease. Current hypotheses favor cell-to-cell spread of αS species as underlying disease progression, driving interest in identifying the molecular and cellular species involved in cellular internalization of αS. Prior work from our lab identified the chemically specific interaction between αS and the pre-synaptic adhesion protein neurexin 1β (N1β) to be capable of driving cellular internalization of both monomer and aggregated forms of αS. Here we explore the physical basis of N1β-driven internalization of αS. Specifically, we show that spontaneous internalization of αS by SH-SY5Y and HEK293 cells expressing N1β requires essentially all of the membrane-binding domain of αS; αS constructs truncated beyond residue 90 bind to N1β in the plasma membrane of HEK cells, but are not internalized. Interestingly, prior to internalization, αS and N1β co-diffuse rapidly in the plasma membrane. αS constructs that are not internalized show very slow mobility themselves, as well as slow N1β diffusion. Finally, we find that truncated αS is capable of blocking internalization of full-length αS. Our results draw attention to the potential therapeutic value of blocking αS-N1β interactions.
Single tyrosine mutation in VE-cadherin modulates gene lung expressions: evidence for FOXF1 mediated S1PR1 upregulation to stabilize vessels in mice
Authors: Garnier Olivia , Jeanneret Florian , Durand Aude , Fertin Arnold , Martin Donald , Berndt Sarah , Carpentier Gilles , Battail Christophe , Vilgrain Isabelle
Published: July 2023

Rationale

Phosphorylation-dephosphorylation are processes involved in the adhesion of endothelial cells (ECs) to maintain vascular integrity in adults. VE-cadherin is a target for Src-mediated Y685phosphorylation, identified in highly vascularized human glioblastoma where it is involved in the abnormal feature of tumor blood vessels.

Objective

We aimed at understanding the molecular mechanisms through which Y685F-VE-cadherin triggers S1PR1 gene expression and stabilizes lung vessels in adult mice.

Methods and Results

We compared lung ECs from a knock-in (KI) mouse carrying a point mutation in VE-cadherin (Tyr 685 to Phe) to Wild type. Analysis of EC parameters showed a difference in the migratory rate was between ECs from KI (22.45% ± 5.207) and WT (13.24% ± 5.17) (p-value=0.034). The direct adhesion of ECs from KI mice to fibronectin was significantly higher (37.625 ± 9.23) than that of the WT (26.8 ± 3.258, p-value=0.012). In the fibrin bead assay, ECs from KI showed a weaker angiogenic response. The transcriptome of mutated ECs showed that 884 genes were dysregulated of which 766 genes were downregulated and 118 genes were upregulated. The Gene Ontology Enrichment showed that most of the genes were related to cell-cell adhesion and angiogenesis. Focusing on angiogenic genes, we found that Sphingosine-1-phosphate-receptor was a gene upregulated in mutated ECs which was confirmed by RT-PCR and westernblotting. Mechanistically, chromatin immunoprecipitation assay (CHIPS) demonstrated that FOXF1 directly bound to the S1pr1 promoter 7 fold greater than WT. As a consequence, VE-cadherin at the membrane was higher in the mutant vs WT (100 ± 6.52 for WT vs 189.7 ± 21.06 for KI (p-value 0.0001). Finally, lung morphometric analysis showed less vessels and vascular remodeling with no fibrosis in mutated mice.

Conclusions

These data extend our knowledge on pY-VE-cadherin mediated pathological angiogenesis and provide new therapeutic opportunities to vascular normalization through pharmacological inhibition of the Y685-VE-cadherin phosphorylation.
Birth of an organelle: molecular mechanism of lipid droplet biogenesis
Authors: Nieto Vincent , Crowley Jackson , Santos Denys , Monticelli Luca
Published: July 2023

Lipid droplets (LDs) are cellular organelles regulating energy and lipid metabolism. Generated in the endoplasmic reticulum (ER) by phase separation of neutral lipids (e.g., triglycerides), nascent LDs resemble lens-shaped blisters, grow into spherical droplets, and eventually emerge from the ER membrane, generally towards the cytosol – a process known as budding. Images of both nascent and mature LDs are available, but the mechanism of biogenesis has never been observed experimentally.

Here we identify the mechanism of the initial steps in LD biogenesis using computer simulations at the molecular level, emulating LD growth in ER-mimicking membranes. We find that LDs bud towards the cytosol only when sufficient asymmetry is generated between the two membrane leaflets: the budding transition is independent of membrane morphology, lipid composition, and LD size. Seipin, a protein essential for correct LD biogenesis, isper senot sufficient to promote budding, but it stabilizes LD-ER contact sites. Localization of triglyceride synthesis in the proximity of seipin is necessary to avoid nucleation of multiple LDs – a possible cause of aberrant phenotypes. In contrast, localization of phospholipid synthesis has no effect on the mechanism of budding. Our new methodology paves the way to simulations of organelle and cell biogenesis.
Mitochondrial Genome Diversity across the Subphylum Saccharomycotina
Authors: Wolters John F. , LaBella Abigail L. , Opulente Dana A. , Rokas Antonis , Hittinger Chris Todd
Published: July 2023

Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeastSaccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the generaMetschnikowiaandSaccharomycestrended larger, while several species in the order Saccharomycetales, which includesS. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.
Low-barrier hydrogen bond determines target-binding affinity and specificity of the antitubercular drug bedaquiline
Authors: Słabońska Joanna , Sappati Subrahmanyam , Marciniak Antoni , Czub Jacek
Published: July 2023

The role of short strong hydrogen bonds (SSHB) in ligand-target binding remains largely unexplored, thereby hindering a potentially important avenue in the rational drug design. Here, we investigate the interaction between bedaquiline (Bq), a potent anti-tuberculosis drug, and the mycobacterial ATP synthase, to unravel the role of a specific hydrogen bond to a conserved acidic residue in the target affinity and specificity. Our ab initio molecular dynamics simulations reveal that this bond belongs to the SSHB category and accounts for a substantial fraction of the target binding energy. We also demonstrate that the presence of an extra acidic residue (D32), found exclusively in mycobacteria, cooperatively enhances the HB strength ensuring the specificity for the mycobacterial target. Consistently, we show that the removal of D32 markedly weakens the affinity, leading to Bq resistance associated with mutations of D32 to non-acidic residues. By designing simple Bq analogs, we then explore the possibility to overcome the resistance and potentially broaden the Bq antimicrobial spectrum by making the SSHB independent on the presence of the extra acidic residue.
Barriers to and enablers of quality improvement in primary health care in low- and middle-income countries: a systematic review
Authors: Odhus¹ Camlus , Kapanga² Ruth , Oele³ Elizabeth
Published: July 2023

The quality of health care remains generally poor across primary health care settings, especially in low- and middle-income countries where tertiary care tends to take up much of the limited resources despite primary health care being the first (and often the only) point of contact with the health system for nearly 80 per cent of people in these countries. Evidence is needed on barriers and enablers of quality improvement initiatives. This systematic review sought to answer the question: What are the enablers of and barriers to quality improvement in primary health care in low- and middle-income countries? It adopted an integrative review approach with narrative evidence synthesis, which combined qualitative and mixed methods research studies systematically. Using a customized geographic search filter for LMICs developed by the Cochrane Collaboration, Scopus, Academic Search Ultimate, MEDLINE, CINAHL, PSYCHINFO, EMBASE, ProQuest Dissertations and Overton.io (a new database for LMIC literature) were searched in January and February 2023, as were selected websites and journals. 7,077 reports were retrieved. After removing duplicates, four reviewers screened titles, abstracts, and full texts, and performed quality appraisal and data extraction and synthesis. 50 reports from 47 studies were included, covering 52 LMIC settings. Six themes related to barriers and enablers of quality improvement were identified and organized using the model for understanding success in quality (MUSIQ) and the consolidated framework for implementation research (CFIR). These were: microsystem of quality improvement, intervention attributes, implementing organization and team, health systems support and capacity, external environment and structural factors, and execution. Decision makers, practitioners, funders, implementers, and other stakeholders can use the evidence from this systematic review to minimize barriers and amplify enablers to better the chances that quality improvement initiatives will be successful in resource-limited settings. PROSPERO registration: CRD42023395166.
Conserved long noncoding RNATILAMpromotes liver fibrosis through interaction with PML in hepatic stellate cells
Authors: Sun Cheng , Zhou Chan , Daneshvar Kaveh , Kratkiewicz Arcadia J. , Saad Amel Ben , Hess Anja , Chen Jennifer Y. , Pondick Joshua V. , York Samuel R. , Li Wenyang , Moran Sean , Gentile Stefan , Rahman Raza Ur , Li Zixiu , Sparks Robert , Habboub Tim , Kim Byeong-Moo , Choi Michael Y. , Affo Silvia , Schwabe Robert F. , Popov Yury V. , Mullen Alan C.
Published: July 2023

Background & Aims

Fibrosis is the common endpoint for all forms of chronic liver injury, and progression of fibrosis leads to the development of end-stage liver disease. Activation of hepatic stellate cells (HSCs) and their transdifferentiation to myofibroblasts results in the accumulation of extracellular matrix (ECM) proteins that form the fibrotic scar. Long noncoding (lnc) RNAs regulate the activity of HSCs and may provide targets for fibrotic therapies.

Methods

We identified lncRNATILAMas expressed nearCOL1A1in human HSCs and performed loss-of-function studies in human HSCs and liver organoids. Transcriptomic analyses of HSCs isolated from mice defined the murine ortholog ofTILAM. We then generatedTilam-deficient GFP reporter mice and quantified fibrotic responses to carbon tetrachloride (CCl4) and choline-deficient L-amino acid defined high fat diet (CDA-HFD). Co-precipitation studies, mass spectrometry, and gene expression analyses identified protein partners ofTILAM.

Results

TILAMis conserved between human and mouse HSCs and regulates expression of ECM proteins, including collagen.Tilamis selectively induced in HSCs during the development of fibrosisin vivo. In both male and female mice, loss ofTilamresults in reduced fibrosis in the setting of CCl4and CDA-HFD injury models.TILAMinteracts with promyelocytic leukemia protein (PML) to stabilize PML protein levels and promote the fibrotic activity of HSCs.

Conclusion

TILAMis activated in HSCs and interacts with PML to drive the development of liver fibrosis. Depletion ofTILAMmay serve as a therapeutic approach to combat the development of end stage liver disease.
Neural division of labor: the gastropodBerghiadefends against attack using its PNS to retaliate and its CNS to erect a defensive screen
Authors: Brown Jeffrey W. , Berg Ondine H. , Boutko Anastasiya , Stoerck Cody , Boersma Margaret A. , Frost William N.
Published: July 2023

Relatively little is known about how the peripheral nervous system (PNS) contributes to the patterning of behavior, in which its role transcends the simple execution of central motor commands or mediation of reflexes. We sought to draw inferences to this end in the aeolid nudibranchBerghia stephanieae, which generates a rapid, dramatic defense behavior, “bristling.” This behavior involves the coordinated movement of cerata, dozens of venomous appendages emerging from the animal’s mantle. Our investigations revealed that bristling constitutes a stereotyped but non-reflexive two-stage behavior: an initial adduction of proximate cerata to sting the offending stimulus (Stage 1), followed by a coordinated radial extension of remaining cerata to create a pincushion-like defensive screen around the animal (Stage 2). In decerebrated specimens, Stage 1 bristling was preserved, while Stage 2 bristling was replaced by slower, uncoordinated, and ultimately maladaptive ceratal movements. We conclude from these observations that 1) the PNS and central nervous system (CNS) mediate Stages 1 and 2 of bristling, respectively; 2) the behavior propagates through the body utilizing both peripheral- and central-origin nerve networks that support different signaling kinetics; and 3) the former network inhibits the latter in the body region being stimulated. These findings extend our understanding of the PNS’s computational capacity and provide insight into a neuroethological scheme that may generalize across cephalized animals, in which the CNS and PNS both independently and interactively pattern different aspects of non-reflexive behavior.
Fish on the platter! Investigating the dietary habits of fishing cats (Prionailurus viverrinus) in the Godavari Delta, India
Authors: Malla Giridhar , Ray Paromita , Srinivas Yellapu , Malla Sudhakar , Reddy Byragi T. , Hayward Matt , Sivakumar Kuppusamy
Published: July 2023

The threatened fishing cat (Prionailurus viverrinus) is an elusive and medium-sized cat that is adapted to mangroves, swamps, wetlands, and riverine habitats. A close look at the literature indicates that fishing cats are piscivorous, however this is based on very few studies. Understanding the patterns of resource utilisation by species is crucial for assessing their role in ecosystems and in ensuring their conservation. Therefore, our study presents insights into fishing cat feeding patterns from mangroves of the Godavari delta, Andhra Pradesh, India. We collected 303 putative fishing cat scats and conducted analysis using 120 genetically identified scats. Our analysis revealed that fish was the most important prey by fishing cats in the study area, followed by crabs and rodents. The prey composition did not vary significantly between the three seasons but there were differences between the survey years. The niche breadth also varied across the three seasons, from being a generalist in winters to a specialist in summers. Our results suggest that long term conservation and survival of the fishing cats depends on fish populations, which are the main prey of the species and thus recommend the need to protect the fish populations in the Godavari delta and the surrounding riverine habitats. Given the importance of fish to the diet of the fishing cat, the health of waterways throughout their distribution must be one of the focal strategies of conservation action.
Investigating the mechanisms underlying Bortezomib resistance
Authors: Zafeiropoulou Kalliopi , Kalampounias Georgios , Alexis Spyridon , Anastasopoulos Daniel , Symeonidis Argiris , Katsoris Panagiotis
Published: July 2023

Proteasome inhibitors such as Bortezomib, represent an established type of targeted treatment for several types of hematological malignancies, including multiple myeloma, Waldenstrom’s macroglobulinemia and mantle cell lymphoma, based on the cancer cell’s susceptibility upon impairment of the proteasome-ubiquitin system. However, a major problem limiting their efficacy is the emergence of resistance. Their application on solid tumors is currently being studied, while simultaneously, a wide spectrum of hematological cancers, such as Myelodysplastic Syndromes show minimal or no response to Bortezomib treatment. In this study, we utilize the prostate cancer cell line DU-145 to establish a model of Bortezomib resistance, studying the underlying mechanisms. Evaluating the resulting resistant cell line, we observed restoration of proteasome chymotrypsin-like activity, regardless of drug presence, an induction of pro-survival pathways, and the substitution of the Ubiquitin-Proteasome System role in proteostasis by induction of autophagy. Finally, an estimation of the oxidative condition of the cells, indicated that the resistant clones reduce the generation of reactive oxygen species induced by Bortezomib, to levels even lower than those induced in non-resistant cells. Our findings elucidate key proteins of survival and stress regulation pathways as potential pharmaceutical targets, which could increase the efficiency of the proteasome-targeting therapies, thus expanding the group of molecular targets for neoplastic disorders.
A developmentally-inspired hypoxia condition promotes kidney organoid differentiation from human pluripotent stem cells
Authors: Lim Hyeonji , Kim Dohui , Yoon Haejin , Kang Joo H. , Kim Dong Sung , Park Tae-Eun
Published: July 2023

Kidney organoids derived from human pluripotent stem cells (hPSCs) lack a contiguous network of collecting ducts, which limits their utility in modeling kidney development and disease. Here, we report the generation of kidney organoids containing ureteric bud (UB)-derived collecting ducts connected to metanephric mesenchyme (MM)-derived nephrons using developmentally-inspired hypoxic differentiation conditions. Hypoxia promotes a reiterative process of branching morphogenesis and nephron induction through reciprocal interactions between co-induced MM and UB, which lead to a higher-order kidney organogenesisin vitro. The resulting kidney organoids demonstrate greater maturity, as indicated by higher levels of functional markers and more realistic micro-anatomy of the tubules and collecting ducts. Additionally, these hypoxic-enhanced kidney organoids show a great potential asin vitromodels for renal cystic diseases, as they efficiently generate cystic formations and display high sensitivity to drugs. This hypoxia approach may open new avenues for an enhanced understanding of kidney development and diseases.
Improved modeling of human vision by incorporating robustness to blur in convolutional neural networks
Authors: Jang Hojin , Tong Frank
Published: July 2023

Whenever a visual scene is cast onto the retina, much of it will appear degraded due to poor resolution in the periphery; moreover, optical defocus can cause blur in central vision. However, the pervasiveness of blurry or degraded input is typically overlooked in the training of convolutional neural networks (CNNs). We hypothesized that the absence of blurry training inputs may cause CNNs to rely excessively on high spatial frequency information for object recognition, thereby causing systematic deviations from biological vision. We evaluated this hypothesis by comparing standard CNNs with CNNs trained on a combination of clear and blurry images. We show that blur-trained CNNs outperform standard CNNs at predicting neural responses to objects across a variety of viewing conditions. Moreover, blur-trained CNNs acquire increased sensitivity to shape information and greater robustness to multiple forms of visual noise, leading to improved correspondence with human perception. Our results provide novel neurocomputational evidence that blurry visual experiences are very important for conferring robustness to biological visual systems.
Square beams for optimal tiling in TEM
Authors: Chua Eugene YD , Alink Lambertus M , Kopylov Mykhailo , Johnston Jake , Eisenstein Fabian , de Marco Alex
Published: July 2023

Imaging large fields of view at a high magnification requires tiling. Transmission electron microscopes typically have round beam profiles; therefore, tiling across a large area is either imperfect or results in uneven exposures, a problem on dose-sensitive samples. Here, we introduce a square electron beam that can be easily retrofitted in existing microscopes and demonstrate its application, showing it can tile nearly perfectly and deliver cryo-EM imaging with a resolution comparable to conventional setups.
Assessing the Generalization Capabilities of TCR Binding Predictors via Peptide Distance Analysis
Authors: Castorina Leonardo V. , Grazioli Filippo , Machart Pierre , Mösch Anja , Errica Federico
Published: July 2023

Understanding the interaction between T Cell Receptors (TCRs) and peptide-bound Major Histocompatibility Complexes (pMHCs) is crucial for comprehending immune responses and developing targeted immunotherapies. While recent machine learning (ML) models show remarkable success in predicting TCR-pMHC binding within training data, these models often fail to generalize to peptides outside of their training distributions, raising concerns about their applicability in therapeutic settings. Understanding and improving the generalization of these models is therefore critical to ensure real-world applications.

To address this issue, we evaluate the effect of the distance between training and testing peptide distributions on ML model empirical risk assessments, using sequence-based and 3D structure-based distance metrics. In our analysis we use several state-of-the-art models for TCR-peptide binding prediction: Attentive Variational Information Bottleneck (AVIB), NetTCR-2.0 and -2.2, and ERGO II (pre-trained autoencoder) and ERGO II (LSTM).

In this work, we introduce a novel approach for assessing the generalization capabilities of TCR binding predictors: the Distance Split (DS) algorithm. The DS algorithm controls the distance between training and testing peptides based on both sequence and structure, allowing for a more nuanced evaluation of model performance. We show that lower 3D shape similarity between training and test peptides is associated with a harder out-of-distribution task definition, which is more interesting when measuring the ability to generalize to unseen peptides. However, we observe the opposite effect when splitting using sequence-based similarity. These findings highlight the importance of using a distance-based splitting approach to benchmark models. This could then be used to estimate a confidence score on predictions on novel and unseen peptides, based on how different they are from the training ones. Additionally, our results may hint that employing 3D shape to complement sequence information could improve the accuracy of TCR-pMHC binding predictors.
Identification of 5-HT2AReceptor Signaling Pathways Responsible for Psychedelic Potential
Authors: Wallach Jason , Cao Andrew B. , Calkins Maggie M. , Heim Andrew J. , Lanham Janelle K. , Bonniwell Emma M. , Hennessey Joseph J. , Bock Hailey A. , Anderson Emilie I. , Sherwood Alexander M. , Morris Hamilton , de Klein Robbin , Klein Adam K. , Cuccurazzu Bruna , Gamrat James , Fannana Tilka , Zauhar Randy , Halberstadt Adam L. , McCorvy John D.
Published: July 2023

Serotonergic psychedelics possess considerable therapeutic potential. Although 5-HT2Areceptor activation mediates psychedelic effects, prototypical psychedelics activate both 5-HT2A-Gq/11 and β-arrestin2 signaling, making their respective roles unclear. To elucidate this, we developed a series of 5-HT2A-selective ligands with varying Gq efficacies, including β-arrestin-biased ligands. We show that 5-HT2A-Gq but not 5-HT2A-β-arrestin2 efficacy predicts psychedelic potential, assessed using head-twitch response (HTR) magnitude in male mice. We further show that disrupting Gq-PLC signaling attenuates the HTR and a threshold level of Gq activation is required to induce psychedelic-like effects, consistent with the fact that certain 5-HT2Apartial agonists (e.g., lisuride) are non-psychedelic. Understanding the role of 5-HT2A-Gq efficacy in psychedelic-like psychopharmacology permits rational development of non-psychedelic 5-HT2Aagonists. We also demonstrate that β-arrestin-biased 5-HT2Areceptor agonists induce receptor downregulation and tachyphylaxis, and have an anti-psychotic-like behavioral profile. Overall, 5-HT2Areceptor signaling can be fine-tuned to generate ligands with properties distinct from classical psychedelics.
Quantifying the large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition of cell cycle
Authors: Chu Xiakun , Wang Jin
Published: July 2023

Cell cycle, essential for various cellular processes, is known to be precisely regulated by the underlying gene network. Accumulating evidence has revealed that the chromosome, which serves as the scaffold for the gene expressions, undergoes significant structural reorganizations during mitosis. Understanding the mechanism of the cell cycle from the molecular chromosome structural perspective remains a grand challenge. In this study, we applied an integrated approach using a data-driven model combined with a nonequilibrium landscape-switching model to investigate large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition. We generated 3D chromosome structural ensembles for the five critical stages in the process. We observed that the chromosome structural expansion and adaptation of the structural asphericity do not occur synchronously. We attributed this asynchronous adaptation behavior in the chromosome structural geometry to the unique unloading sequence of the two types of condensins. Furthermore, we observed that the coherent motions between the chromosomal loci are primarily enhanced within the topologically associating domains (TADs) as cells progress to the G1 phase, suggesting that TADs can be considered as both structural and dynamical units for organizing the 3D chromosome. Our analysis also reveals that the quantified pathways of chromosome structural reorganizations during the mitosis-to-G1 phase transition exhibit high stochasticity at the single-cell level and show non-linear behaviors in changing TADs and contacts formed at the long-range regions. These features underscore the complex nature of the cell-cycle processes. Our findings, which are consistent with the experiments in many aspects, offer valuable insights into the large-scale chromosome structural dynamics after mitosis and contribute to the molecular-level understanding of the cell-cycle process.
Intersubject representational similarity analysis uncovers the impact of state anxiety on brain activation patterns in the human extrastriate cortex
Authors: Hsiao Po-Yuan A. , Kim M. Justin , Chou Feng-Chun B. , Chen Pin-Hao A.
Published: July 2023

The current study used functional magnetic resonance imaging (fMRI) and showed that state anxiety modulated extrastriate cortex activity in response to emotionally-charged visual images. State anxiety and neuroimaging data from 53 individuals were subjected to an intersubject representational similarity analysis (ISRSA), wherein the geometries between neural and behavioral data were compared. This analysis identified the extrastriate cortex (fusiform gyrus and area MT) to be the sole regions whose activity patterns covaried with state anxiety. Importantly, we show that this brain-behavior association is revealed when treating state anxiety data as a multidimensional response pattern, rather than a single composite score. This suggests that ISRSA using multivariate distances may be more sensitive in identifying the shared geometries between self-report questionnaires and brain imaging data. Overall, our findings demonstrate that a transient state of anxiety may influence how visual information – especially those relevant to the valence dimension – is processed in the extrastriate cortex.
Multiple Receptor Tyrosine Kinases Regulate Dengue Infection of Hepatocytes
Authors: Bourgeois Natasha M. , Wei Ling , Ho Nhi N. T. , Neal Maxwell L. , Seferos Denali , Tongogara Tinotenda , Mast Fred D. , Aitchison John D. , Kaushansky Alexis
Published: July 2023

Dengue is an arboviral disease causing severe illness in over 500,000 people each year. Currently, there is no way to constrain dengue in the clinic. Host kinase regulators of dengue virus (DENV) infection have the potential to be disrupted by existing therapeutics to prevent infection and/or disease progression. To evaluate kinase regulation of DENV infection, we performed kinase regression (KiR), a machine learning approach that predicts kinase regulators of infection using existing drug-target information and a small drug screen. We infected hepatocytes with DENVin vitroin the presence of a panel of 38 kinase inhibitors then quantified the effect of each inhibitor on infection rate. We employed elastic net regularization on these data to obtain predictions of which of 300 kinases are regulating DENV infection. Thirty-six kinases were predicted to have a functional role. Intriguingly, seven of the predicted kinases – EPH receptor A4 (EPHA4), EPH receptor B3 (EPHB3), EPH receptor B4 (EPHB4), erb-b2 receptor tyrosine kinase 2 (ERBB2), fibroblast growth factor receptor 2 (FGFR2), Insulin like growth factor 1 receptor (IGF1R), and ret proto-oncogene (RET) – belong to the receptor tyrosine kinase (RTK) family, which are already therapeutic targets in the clinic. We demonstrate that predicted RTKs are expressed at higher levels in DENV infected cells. Knockdown of ERBB2, FGFR2 and IGF1R reduces DENV infection in hepatocytes. Finally, we observe differential temporal induction of ERBB2 and IGF1R following DENV infection, highlighting their unique roles in regulating DENV. Collectively, our findings underscore the significance of multiple RTKs in DENV infection and advocate further exploration of RTK-oriented interventions against dengue.
A test of time-resolved functional MRI with sub-second event durations
Authors: Wong Alvin P.H. , Wu Esther X.W. , Rogers Baxter P. , Asplund Christopher L.
Published: July 2023

Functional neuroimaging (fMRI) signals are famously sluggish, unfolding over several seconds after even brief sensory (and neural) events. Relative timing differences between different evoking conditions, however, can distinguish between changes in the duration or intensity of neural activity (Henson et al., 2002). Specifically, increases in stimulus duration cause a delayed response peak with a greater amplitude, whereas increases in stimulus intensity affect the peak magnitude alone. These relationships have been empirically demonstrated using stimulus durations of several seconds (Friston, 2005), but many processes relevant to cognitive psychology occur on sub-second timescales. Here we tested whether the predicted relationship between stimulus properties and the hemodynamic response held for sub-second stimuli and sub-second changes in stimulus duration. In Experiment 1 (n=15), we presented visual and auditory stimuli at three durations (100, 300, and 900 ms) and three intensities in a slow event-related design with a rapid TR (625 ms). In Experiment 2 (n=14), the stimulus durations were extended (1000, 1200, and 1800 ms) to increase the evoked signal. By fitting the observed fMRI signals to parameterised hemodynamic response functions, we found that changes in stimulus duration caused differences in peak latency and magnitude, whereas changes in stimulus intensity affected only peak magnitude. Significant effects were found for duration differences as small as 200 ms, with clearer results when a sufficiently large base signal was evoked and when a bootstrap resampling technique was used. Our results support the validity of existing models of the hemodynamic response. They also support the use of time-resolved fMRI for mental chronometry in cognitive neuroscience, thereby allowing researchers to draw additional inferences about brief mental events.
Highly effective gene inactivation in tetraploidXenopus laeviswith low-temperature-active engineered Cas12a
Authors: Yun Seongmin , Kim Seohyun , Hong Juyeon , Choi Jiwon , Shin Jeong-Sik , Choi Subin , Lee Hyun-Shik , Cho Seung Woo , Park Tae Joo , Kwon Taejoon
Published: July 2023

Background

Gene knockout using the CRISPR/Cas (clustered regulatory interspaced short palindromic repeats/CRISPR-associated protein) system revolutionized reverse genetic (or targeted mutagenesis) studies in model and non-model organisms because almost all genetic elements can be targeted with few limitations. Although the CRISPR/Cas system incorporating SpCas9 (Cas9 derived fromStreptococcus pyogenes) remains the most popular for genome editing, another CRISPR/Cas system with Cas12a (Cpf1) has expanded its application. However, Cas12a is difficult to use in some aquatic model organisms, such asXenopus, because of its low activity at the temperatureXenopusis normally raised (lower than 25°C). Recently, an engineered Cas12a called Cas12a-Ultra was developed, which has improvedin vivoendonuclease activity with less temperature dependency, and several commercial products were introduced to the market.

Results

We evaluated the performance of these engineered Cas12a enzymes inXenopusembryos. We first confirmed that they were more active than SpCas9 at the low temperature thatX. laevisembryos are mostly raised (20–22°C) based onin vitrodigestion experiments. Then, we evaluated theirin vivoactivities by disrupting the tyrosinase enzyme (tyr), which induces albino-like phenotypes. LbCpf1 (Cpf1 derived fromLachnospiraceaebacterium)-Ultra outperformed the other enzymes, producing more than 80% of embryos with severely defective phenotypes even in low-temperature conditions. In addition, duplicated copies of two paralogous lysine demethylases (kdm5bandkdm5c) were successfully disrupted, which recapitulated the previously reported phenotypes observed upon morpholino-mediated knockdown.

Conclusions

Newly engineered Cas12a is valuable for gene function studies inXenopusand other model organisms with low growth temperatures.
Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress
Authors: Taylor Bethany C. , Steinthal Loic H. , Dias Michelle , Yalamanchili Hari K. , Ochsner Scott A. , Zapata Gladys E. , Mehta Nitesh R. , McKenna Neil J. , Young Nicolas L. , Nuotio-Antar Alli M.
Published: July 2023

Regulation of the thermogenic response by brown adipose tissue (BAT) is an important component of energy homeostasis with implications for the treatment of obesity and diabetes. Our preliminary analyses uncovered many nodes representing epigenetic modifiers that are altered in BAT in response to chronic thermogenic activation. Thus, we hypothesized that chronic thermogenic activation broadly alters epigenetic modifications of DNA and histones in BAT. Motivated to understand how BAT function is regulated epigenetically, we developed a novel method for the first-ever unbiased top- down proteomic quantitation of histone modifications in BAT and validated our results with a multi-omic approach. To test our hypothesis, wildtype male C57BL/6J mice were housed under chronic conditions of thermoneutral temperature (TN, 28.8°C), mild cold/room temperature (RT, 22°C), or severe cold (SC, 8°C) and BAT was analyzed for DNA methylation and histone modifications. Methylation of promoters and intragenic regions in genomic DNA decrease in response to chronic cold exposure. Integration of DNA methylation and RNA expression data suggest a role for epigenetic modification of DNA in gene regulation in response to cold. In response to cold housing, we observe increased bulk acetylation of histones H3.2 and H4, increased histone H3.2 proteoforms with di- and trimethylation of lysine 9 (K9me2 and K9me3), and increased histone H4 proteoforms with acetylation of lysine 16 (K16ac) in BAT. Taken together, our results reveal global epigenetically-regulated transcriptional “on” and “off” signals in murine BAT in response to varying degrees of chronic cold stimuli and establish a novel methodology to quantitatively study histones in BAT, allowing for direct comparisons to decipher mechanistic changes during the thermogenic response. Additionally, we make histone PTM and proteoform quantitation, RNA splicing, RRBS, and transcriptional footprint datasets available as a resource for future research.
PACS allows comprehensive dissection of multiple factors governing chromatin accessibility from snATAC-seq data
Authors: Miao Zhen , Wang Jianqiao , Park Kernyu , Kuang Da , Kim Junhyong
Published: July 2023

Single nucleus ATAC-seq (snATAC-seq) experimental designs have become increasingly complex with multiple factors that might affect chromatin accessibility, including genotype, cell type, tissue of origin, sample location, batch, etc., whose compound effects are difficult to test by existing methods. In addition, current snATAC-seq data present statistical difficulties due to their sparsity and variations in individual sequence capture. To address these problems, we present a zero-adjusted statistical model, Probability model of Accessible Chromatin of Single cells (PACS), that can allow complex hypothesis testing of factors that affect accessibility while accounting for sparse and incomplete data. For differential accessibility analysis, PACS controls the false positive rate and achieves on average a 17% to 122% higher power than existing tools. We demonstrate the effectiveness of PACS through several analysis tasks including supervised cell type annotation, compound hypothesis testing, batch effect correction, and spatiotemporal modeling. We apply PACS to several datasets from a variety of tissues and show its ability to reveal previously undiscovered insights in snATAC-seq data.