bluuebunny/crossref_metadata_2025 huggingface dataset:
Interplay between resource dynamics, network structure and spatial propagation of transient explosive synchronization in an adaptively coupled mouse brain network model
Authors: Ranjan Avinash , Gandhi Saurabh R.
Published: November 2023

Generalized epileptic attacks, which exhibit widespread disruption of brain activity, are characterized by recurrent, spontaneous and synchronized bursts of neural activity that self-initiate and self-terminate through critical transitions. Here we utilize the general framework of explosive synchronization (ES) from complex systems science to study the role of network structure and resource dynamics in the generation and propagation of seizures. We show that a combination of resource constraint and adaptive coupling in a Kuramoto network oscillator model can reliably generate seizure-like synchronization activity across different network topologies, including a biologically derived mesoscale mouse brain network. The model, coupled with a novel algorithm for tracking seizure propagation, provides mechanistic insight into the dynamics of transition to the synchronized state and its dependence on resources; and identifies key brain areas that may be involved in the initiation and spatial propagation of the seizure. The model, though minimal, efficiently recapitulates several experimental and theoretical predictions from more complex models, and makes novel experimentally testable predictions.

Significance statement / Author Summary

Understanding seizure dynamics at the whole-brain level is crucial for controlling abnormal hypersynchronous activity. Currently, complete brain coverage recordings are lacking in both patients and animal models. We employ network science tools to investigate epileptic seizure-like synchronization in a mouse whole brain network, leveraging network structure and supported dynamics as the basis for seizure evolution. Our results align with experimental findings, suggesting that seizure activity initiates in the cortico-thalamic circuit. Importantly, our novel analysis identifies key nodes, primarily in the cortex, driving this hypersynchronous activity. Our findings highlight network structure’s role in shaping seizure dynamics and the techniques developed here could enhance our control of generalized seizures when combined with patient-specific data.
Robust organ size in Arabidopsis is primarily governed by cell growth rather than cell division patterns
Authors: Burda Isabella , Li Chun-Biu , Clark Frances K. , Roeder Adrienne H. K.
Published: November 2023

Organ sizes and shapes are highly reproducible, or robust, within a species and individuals.Arabidopsis thalianasepals, which are the leaf-like organs that enclose flower buds, have consistent size and shape, which indicates robust development. Counterintuitively, variability in cell growth rate over time and between cells facilitates robust development because cumulative cell growth averages to a uniform rate. Here we investigate how sepal morphogenesis is robust to changes in cell division but not robust to changes in cell growth variability. We live image and quantitatively compare the development of sepals with increased or decreased cell division rate (lgomutant andLGOoverexpression, respectively), a mutant with altered cell growth variability (ftsh4), and double mutants combining these. We find that robustness is preserved when cell division rate changes because there is no change in the spatial pattern of growth. Meanwhile when robustness is lost inftsh4mutants, cell growth accumulates unevenly, and cells have disorganized growth directions. Thus, we demonstratein vivothat both cell growth rate and direction average in robust development, preserving robustness despite changes in cell division.

Summary statement

Robust sepal development is preserved despite changes in cell division rate and is characterized by spatiotemporal averaging of heterogeneity in cell growth rate and direction.
Impact of body image on the kinematics of gait initiation
Authors: Oku Kyosuke , Tanaka Shinsuke , Nishizaki Yukiko , Fukada Chie , Kida Noriyuki
Published: November 2023

In our daily lives, we walk naturally because we can consider our physical characteristics and formulate appropriate motor plans. However, the impact of changes in body image during motor planning on walking movements remains poorly understood. Therefore, in this study, we investigated how walking movements change when body image is altered. We included 26 participants (13 males, 13 females, aged 18.27±0.52) to perform walking movements under five conditions: open eyes (baseline), closed eyes, closed eyes while imagining their bodies becoming large, closed eyes again, and open eyes again. As a result, under the condition where participants imagined their bodies becoming large, their stride length, step completion time, and foot lift height increased. These results are attributed to the disparity between actual body size and body image, which affects motor planning. The results of this study have potential applications in rehabilitation and sports coaching settings.
Unraveling activation-related rearrangements and intrinsic divergence from ligand-induced conformational changes of the dopamine D3 and D2 receptors
Authors: Lee Kuo Hao , Shi Lei
Published: November 2023

Effective rational drug discovery targeting a specific protein hinges on understanding their functional states and distinguishing it from homologs. However, for the G protein coupled receptors, both the activation-related conformational changes (ACCs) and the intrinsic divergence among receptors can be misled or obscured by ligand-induced conformational changes (LCCs). Here, we unraveled ACCs and intrinsic divergence from LCCs of the dopamine D3 and D2 receptors (D3R and D2R), by analyzing their experimentally determined structures and the molecular dynamics simulation results of the receptors bound with different ligands. In addition to the ACCs common to other aminergic receptors, we revealed unique ACCs for these two receptors including TM5e and TM6e shifting away from TM2e and TM3e, with a subtle rotation of TM5e. In identifying intrinsic divergence, we found pronounced outward tilting of TM6e in the D2R compared to the D3R in both experimental structures and simulations with ligands in different scaffolds. This tilting was drastically reduced in the simulations of the receptors bound with nonselective full agonist quinpirole, suggesting a misleading impact of LCCs. Further, in the quinpirole-bound simulations, TM1 showed a greater disparity between these receptors, indicating that LCCs may obscure intrinsic divergence. In addition, our analysis showed that the impact of the nonconserved TM1 propagated to conserved Trp7.40and Glu2.65, both are ligand binding residues. We also found that the D2R exhibited heightened flexibility compared to the D3R in the extracellular portions of TMs 5, 6, and 7, potentially associated with its greater ligand binding site plasticity. Our results lay the groundwork for crafting ligands specifically targeting D2R or D3R with more precise pharmacological profiles.
Joint representation and visualization of derailed cell states with Decipher
Authors: Nazaret Achille , Fan Joy Linyue , Lavallée Vincent-Philippe , Burdziak Cassandra , Cornish Andrew E. , Kiseliovas Vaidotas , Bowman Robert L. , Masilionis Ignas , Chun Jaeyoung , Eisman Shira E. , Wang James , Hong Justin , Shi Lingting , Levine Ross L. , Mazutis Linas , Blei David , Pe’er Dana , Azizi Elham
Published: November 2023

Biological insights often depend on comparing conditions such as disease and health, yet we lack effective computational tools for integrating single-cell genomics data across conditions or characterizing transitions from normal to deviant cell states. Here, we present Decipher, a deep generative model that characterizes derailed cell-state trajectories. Decipher jointly models and visualizes gene expression and cell state from normal and perturbed single-cell RNA-seq data, revealing shared and disrupted dynamics. We demonstrate its superior performance across diverse contexts, including in pancreatitis with oncogene mutation, acute myeloid leukemia, and gastric cancer.
GexMolGen: Cross-modal Generation of Hit-like Molecules via Large Language Model Encoding of Gene Expression Signatures
Authors: Cheng Jiabei , Pan Xiaoyong , Fang Yi , Yang Kaiyuan , Xue Yiming , Yan Qingran , Yuan Ye
Published: November 2023

Designing de novo molecules with specific biological activity is an essential task since it holds the potential to bypass the exploration of target genes, which is an initial step in the modern drug discovery paradigm. However, traditional methods mainly screen molecules by comparing the desired molecular effects within the documented experimental results. The data set limits this process, and it is hard to conduct direct cross-modal comparisons. Therefore, we propose a solution based on cross-modal generation called GexMolGen (Gene Expression-based Molecule Generator), which generates hit-like molecules using gene expression signatures alone. These signatures are calculated by inputting control and desired gene expression states. Our model GexMolGen adopts a “first-align-then-generate” strategy, aligning the gene expression signatures and molecules within a mapping space, ensuring a smooth cross-modal transition. The transformed molecular embeddings are then decoded into molecular graphs. In addition, we employ an advanced single-cell large language model for input flexibility and pre-train a scaffold-based molecular model to ensure that all generated molecules are 100% valid. Empirical results show that our model can produce molecules highly similar to known references, whether feeding in- or out-of-domain transcriptome data. Furthermore, it can also serve as a reliable tool for cross-modal screening.
Control of a gene transfer agent cluster inCaulobacter crescentusby transcriptional activation and anti-termination
Authors: Tran Ngat T. , Le Tung B.K.
Published: November 2023

Gene Transfer Agents (GTAs) are domesticated prophages that cannot self-multiply and be infectious but might have been co-opted to perform biological functions for the host bacteria.Caulobacter crescentus, a bacterium best known as a model organism to study bacterial cell biology and cell cycle regulation, has recently been demonstrated to producebona fideGTA particles (CcGTA). Two direct activators of the CcGTA biosynthetic gene cluster, GafY and GafZ, have been identified, however, it is unknown how GafYZ controls transcription mechanistically or how they coordinate gene expression of the CcGTA gene cluster with other accessory genes elsewhere on the genome for complete CcGTA production. Here, we show that the CcGTA gene cluster is transcriptionally co-activated by GafY, integration host factor (IHF), and by GafZ-mediated transcription anti-termination. We present evidence that GafZ is a novel transcription anti-terminator that likely forms an anti-termination complex with RNA polymerase, NusA, NusG, and NusE to bypass transcription terminators within the 14 kb CcGTA cluster. Overall, we reveal a two-tier regulation that coordinates the synthesis of GTA particles inC. crescentus.
Nutritional value of extracted soybean, full fat soya and maize gluten meal proteins in comparison to a fish meal based reference diet for fingerling tilapia (Oreochromis mossambicus)
Authors: Bell M. E. , Davies S. J.
Published: November 2023

A two-month investigation evaluated potential selected plant protein sources compared to fish meal protein in scientifically formulated diets for fingerling tilapia (Oreochromis mossambicus). Six nutritionally balanced diets: one reference (control) diet (fish-meal-based diet), three selected plant proteins (solvent extracted soybean, full fat soybean, and maize gluten) were substituted in the LT (Low Temperature dried) fish-meal-based control diet protein at 50% respectively, and the remaining diets were replaced with 75% inclusion of solvent extracted soybean and maize gluten meals. Results showed that SESB50, FFSB50 and MG50 fed tilapia did not appreciably differ in their growthperformance (final mean weights of 12.07, 10.75 and 9.18% respectively) with a final mean weight of 14.95g being significantly superior for the fish meal control (CO) group. Substitution of fish meal diet with solvent-extracted soybean and maize gluten at levels of 75% gave the poorest growth performance and Feed Efficiency (FE) (7.01g final weight, 51% FE). However, the MG50 diet also showed some inferior feed utilisation performance. However, tilapia fed on a full fat soybean diet (FFSB50) did not vary significantly from the control (CON) diet in terms of Apparent Net Protein Utilisation (ANPU) at 34.20 and 37.53% respectively. Whilst this preliminary study concluded that limitations on the use of the selected plant proteins in diets for tilapia are apparent, several approaches that could result in the future improvement of the nutritional value of soybean and maize gluten products for use in fish diets are also stated.

Highlights

A scientifically formulated reference diet using a Low Temperature dried (LT) fish meal produced superior growth performance for fingerling tilapia compared to selected oilseed (soybean) and grain (maize gluten) derived protein concentrates.

Soybean and full fat soybean meals were effective in contributing to 50% inclusion in experimental diets, but 75% of soybean and maize gluten meal was not able to support similar growth of tilapia over eight weeks.

Feed utilisation parameters such as Protein Efficiency Ratio (PER), Apparent Net Protein Utilisation (ANPU), Net Energy Utilisation (NEU) and Feed Efficiency (FE) gave supporting evidence and conclusions for optimal threshold inclusions of the test plant ingredients for tilapia.
A note on predator-prey dynamics in radiocarbon datasets
Authors: Marom Nimrod , Wolkowski Uri
Published: November 2023

Abstract

Predator-prey interactions have been a central theme in population ecology for the past century, but real-world data sets only exist for recent, relatively short (<100 years) time spans. This limits our ability to study centennial/millennial-scale predator-prey dynamics. We propose that regional radiocarbon databases can be used to reconstruct a signal of predator-prey population dynamics in deep time, overcoming this limitation. We support our argument with examples from Pleistocene Beringia and the Holocene Judean Desert.
A transcriptomic dataset for investigating the Arabidopsis Unfolded Protein Response under chronic, proteotoxic endoplasmic reticulum stress
Authors: Ducloy Amélie , Azzopardi Marianne , Ivsic Caroline , Cueff Gwendal , Sourdeval Delphine , Charif Delphine , Cacas Jean-Luc
Published: November 2023

The Unfolded Protein Response (UPR) is a retrograde, ER-to-nucleus, signalling pathway which is conserved across kingdoms. In plants, it contributes to development, reproduction, immunity and tolerance to abiotic stress. This RNA sequencing dataset was produced from 14-day-oldArabidopsis thalianaseedlings challenged by tunicamycin (Tm), an antibiotic inhibiting Asn-linked glycosylation in the endoplasmic reticulum (ER), causing an ER stress and eventually activating the UPR. Wild-type (WT) and a double mutant deficient for two main actors of the UPR (INOSITOL-REQUIRING ENZYME 1AandINOSITOL-REQUIRING ENZYME 1B) were used as genetic backgrounds in our experimental setup, allowing to distinguish among differentially-expressed genes (DEGs) which ones are dependent on or independent on IRE1s. Also, shoots and roots were harvested separately to determine organ-specific transcriptomic responses to Tm. Library and sequencing were performed using DNBseq™ technology by the Beijing Genomics Institute. Reads were mapped and quantified against the Arabidopsis genome. Differentially-expressed genes were identified using Rflomics upon filtering and normalization by the Trimmed Mean of M-value (TMM) method. While the genotype effect was weak under mock conditions (with a total of 182 DEGs in shoots and 195 DEGs in roots), the tunicamycin effect on each genotype was characterized by several hundred of DEGs in both shoots and roots. Among these genes, 872 and 563 genes were statistically up- and down-regulated in the shoot tissues of the double mutant when compared to those of WT, respectively. In roots of Tm-challenged seedlings, 425 and 439 genes were significantly up- and down-regulated in mutants with respect to WT. We believe that our dataset could be reused for investigating any biological questions linked to ER homeostasis and its role in plant physiology.

SPECIFICATIONS TABLE
Single cell RNA-sequencing suggests a novel lipid associated mast cell population following weight cycling
Authors: Caslin Heather L. , Cottam Matthew A. , Betjemann Alexa M. , Mashayekhi Mona , Silver Heidi J , Hasty Alyssa H.
Published: November 2023

Our recent study showed weight cycled mice have increased adipose mast cells compared to obese mice by single cell RNA-sequencing. Here, we aimed to confirm and elucidate these changes. Further analysis of our dataset showed that our initial mast cell cluster could subcluster into two unique populations: one with very high expression of classical mast cell markers and another with elevated lipid handling and antigen presentation genes. This new mast cell cluster accounted for most of the mast cells in the weight cycled group although it was not possible to detect the different populations by new studies with flow cytometry or Toluidine blue staining in mice, possibly due to a downregulation in classical mast cell genes. Interestingly, a pilot study in humans did suggest the existence of two mast cell populations in subcutaneous adipose tissue from obese women that appear similar to the murine populations detected by sequencing; one of which was significantly correlated with weight variance. Together, these data suggest that weight cycling may induce a unique population of mast cells similar to lipid associated macrophages. Future studies will focus on isolation of these cells to better determine their lineage, differentiation, and functional roles.
Sclerostin modulates the degree of mineralization and the stiffness profile of the fibrocartilaginous enthesis for mechanical tissue integrity
Authors: Yambe Shinsei , Yoshimoto Yuki , Ikeda Kazutaka , Maki Koichiro , Takimoto Aki , Higuchi Shinnosuke , Yu Xinyi , Uchibe Kenta , Miura Shigenori , Watanabe Hitomi , Sakuma Tetsushi , Yamamoto Takashi , Tanimoto Kotaro , Kondoh Gen , Docheva Denitsa , Adachi Taiji , Shukunami Chisa
Published: November 2023

Fibrocartilaginous entheses consist of four graded tissue layers including tendon, the unmineralized and mineralized fibrocartilage, and subchondral bone with varying degrees of stiffness. Here we examined the functional role of sclerostin that is expressed in mature mineralized fibrochondrocytes. Following rapid mineralization of the unmineralized fibrocartilage and parallel replacement of epiphyseal hyaline cartilage by bone, the unmineralized fibrocartilage re-expanded after a decline in alkaline phosphatase activity at the mineralization front. Sclerostin was co-expressed with osteocalcin in the bottom of the mineralized fibrocartilage adjacent to subchondral bone. InScxdeficient mice with less mechanical loading due to defects of the Achilles tendon, the number of sclerostin+fibrochondrocytes was significantly reduced in the defective enthesis where chondrocyte maturation was markedly impaired in both fibrocartilage and hyaline cartilage. Loss of theSostgene, coding for sclerostin, caused increased mineral density in the mineralized zones of the fibrocartilaginous enthesis. Atomic force microscopy analysis revealed the higher stiffness of fibrocartilage. These lines of evidence suggest that sclerostin in mature mineralized fibrochondrocytes acts as a modulator for mechanical tissue integrity of the fibrocartilaginous enthesis.
cellstruct: Metrics scores to quantify the biological preservation between two embeddings
Authors: Loh Jui Wan , Ouyang John F.
Published: November 2023

Single-cell transcriptomics (scRNA-seq) is extensively applied in uncovering biological heterogeneity. There are different dimensionality reduction techniques, but it is unclear which method works best in preserving biological information when creating a two-dimensional embedding. Therefore, we implemented cellstruct, which calculates three metrics scores to quantify the global or local biological similarity between a two-dimensional and its corresponding higher-dimensional PCA embeddings at either single-cell or cluster level. These scores pinpoint cell populations with low biological information preservation, in addition to visualizing the cell-cell or cluster-cluster relationships in the PCA embedding. Two study cases illustrate the usefulness of cellstruct in exploratory data analysis.
Cyld aborts hyperactivation of synovial fibroblasts in inflammatory arthritis by regulating the TAK1/IKK2 signaling axis
Authors: Rinotas Vagelis , Iliaki Kalliopi , Pavlidi Lydia , Meletakos Theodore , Mosialos George , Armaka Marietta
Published: November 2023

TNF is a potent cytokine known for its involvement in physiology and pathology. In Rheumatoid Arthritis (RA), persistent TNF signals cause aberrant activation of synovial fibroblasts (SFs), the resident cells crucially involved in the inflammatory and destructive responses of the affected synovial membrane. However, the molecular switches that control the pathogenic activation of SFs remain poorly defined. Cyld is a major component of deubiquitination (DUB) machinery regulating the signaling responses towards survival/inflammation and programmed necrosis that induced by cytokines, growth factors and microbial products. Here we follow functional genetic approaches to understand how Cyld affects arthritogenic TNF signaling in SFs. We demonstrate that in spontaneous and induced RA models, SF-Cyld DUB deficiency deteriorates arthritic phenotypes due to increased levels of chemokines, adhesion receptors and bone-degrading enzymes generated by mutant SFs. Mechanistically, Cyld serves to restrict the TNF-induced hyperactivation of SFs by limiting Tak1-mediated signaling, and, therefore, leading to supervised NFkB and JNK activity. However, Cyld is not critically involved in the regulation of TNF-induced death of SFs. Our results identify SF-Cyld as a regulator of TNF-mediated arthritis and inform the signaling landscape underpinning the SF responses.
The helminth TGF-β mimic TGM4 is a modular ligand that binds CD44, CD49d and TGF-β receptors to preferentially target myeloid cells
Authors: Singh Shashi P. , Smyth Danielle J. , Cunningham Kyle , Mukundan Ananya , Byeon Chang-Hyeock , Hinck Cynthia S. , White Madeleine P. J. , Ciancia Claire , Wosowska Nątalia , Sanders Anna , Jin Regina , Lilla Sergio , Zanivan Sara , Schoenherr Christina , Inman Gareth , van Dinther Maarten , ten Dijke Peter , Hinck Andrew P. , Maizels Rick M.
Published: November 2023

The murine helminth parasiteHeligmosomoides polygyrusexpresses a family of modular proteins which, replicating the functional activity of the immunomodulatory cytokine TGF-β, have been named TGM (TGF-β Μimic). Multiple domains bind to different receptors, including TGF-β receptors TβRI (ALK5) and TβRII through domains 1-3, and prototypic family member TGM1 binds the cell surface co-receptor CD44 through domains 4-5. This allows TGM1 to induce T lymphocyte Foxp3 expression, characteristic of regulatory (Treg) cells, and to activate a range of TGF-β-responsive cell types. In contrast, a related protein, TGM4, targets a much more restricted cell repertoire, primarily acting on myeloid cells, with less potent effects on T cells and lacking activity on other TGF-β-responsive cell types. TGM4 binds avidly to myeloid cells by flow cytometry, and can outcompete TGM1 for cell binding. Analysis of receptor binding in comparison to TGM1 reveals a 10-fold higher affinity than TGM1 for TGFβR-I (TβRI), but a 100-fold lower affinity for TβRII through Domain 3. Consequently, TGM4 is more dependent on co-receptor binding; in addition to CD44, TGM4 also engages CD49d (Itga4) through Domains 1-3, as well as CD206 and Neuropilin-1 through Domains 4 and 5. TGM4 was found to effectively modulate macrophage populations, inhibiting lipopolysaccharide-driven inflammatory cytokine production and boosting interleukin (IL)-4-stimulated responses such as Arginase-1in vitroandin vivo. These results reveal that the modular nature of TGMs has allowed the fine tuning of the binding affinities of the TβR- and co-receptor binding domains to establish cell specificity for TGF-β signalling in a manner that cannot be attained by the mammalian cytokine.
Enhancing CAR-T Cell Metabolism to Overcome Hypoxic Conditions in the Brain Tumor Microenvironment
Authors: Hatae Ryusuke , Kyewalabye Keith , Yamamichi Akane , Chen Tiffany , Phyu Su , Chuntova Pavlina , Nejo Takahide , Levine Lauren S. , Spitzer Matthew H. , Okada Hideho
Published: November 2023

The efficacy of chimeric antigen receptor (CAR)-T therapy has been limited against brain tumors to date. CAR-T cells infiltrating syngeneic intracerebral SB28-EGFRvIII glioma revealed impaired mitochondrial ATP production and a markedly hypoxic status compared to ones migrating to subcutaneous tumors. Drug screenings to improve metabolic states of T cells under hypoxic conditions led us to evaluate the combination of AMPK activator Metformin and the mTOR inhibitor Rapamycin (Met+Rap). Met+Rap-pretreated mouse CAR-T cells showed activated PPAR-gamma coactivator 1α (PGC-1α) through mTOR inhibition and AMPK activation, and a higher level of mitochondrial spare respiratory capacity than those pretreated with individual drugs or without pretreatment. Moreover, Met+Rap-pretreated CAR-T cells demonstrated persistent and effective anti-glioma cytotoxic activities in the hypoxic condition. Furthermore, a single intravenous infusion of Met+Rap-pretreated CAR-T cells significantly extended the survival of mice bearing intracerebral SB28-EGFRvIII gliomas. Mass cytometric analyses highlighted increased glioma-infiltrating CAR-T cells in the Met+Rap group with fewer Ly6c+ CD11b+ monocytic myeloid-derived suppressor cells in the tumors. Finally, human CAR-T cells pretreated with Met+Rap recapitulated the observations with murine CAR-T cells, demonstrating improved functions in vitro hypoxic conditions. These findings advocate for translational and clinical exploration of Met+Rap-pretreated CAR-T cells in human trials.
Multi-genome comparisons reveal gain-and-loss evolution of theanti-Mullerian hormone receptor type 2gene, an old master sex determining gene, in Percidae
Authors: Kuhl Heiner , Euclide Peter T , Klopp Christophe , Cabau Cedric , Zahm Margot , Roques Céline , Iampietro Carole , Kuchly Claire , Donnadieu Cécile , Feron Romain , Parrinello Hugues , Poncet Charles , Jaffrelo Lydia , Confolent Carole , Wen Ming , Herpin Amaury , Jouanno Elodie , Bestin Anastasia , Haffray Pierrick , Morvezen Romain , de Almeida Taina Rocha , Lecocq Thomas , Schaerlinger Bérénice , Chardard Dominique , Żarski Daniel , Larson Wes , Postlethwait John H. , Timirkhanov Serik , Kloas Werner , Wuertz Sven , Stöck Matthias , Guiguen Yann
Published: November 2023

The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies inPerca fluviatilis,Perca schrenkiiandSander vitreusalong with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex determining (MSD) gene inP. flavescens. Phylogenetically related and structurally similar amhr2duplications (amhr2b) were found inP. schrenkiiandSander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. InP. fluviatilisandS. vitreus, thisamhr2bduplicate has been lost while it was subject to amplification inS. lucioperca. Analyses of theamhr2blocus inP. schrenkiisuggest that this duplication could be also male-specific as it is inP. flavescens. InP. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting thatP. fluviatilishas a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198,hsdl1,tbc1d32) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three knownPercaspecies.
Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HT3Areceptor
Authors: Haloi Nandan , Karlsson Emelia , Delarue Marc , Howard Rebecca J. , Lindahl Erik
Published: November 2023

Ligand-gated ion channels propagate electrochemical signals in the nervous system. A diverse set of modulators including stimulants, anesthetics, and lipids regulate their function; however, structures of ligand-bound complexes can be difficult to capture by experimental methods, particularly when binding is dynamic or transient. Here, we used computational methods and electrophysiology to identify a possible bound state of a modulatory stimulant derivative in a cryptic vestibular pocket, distinct from the orthosteric neurotransmitter binding site, of a mammalian serotonin-3A receptor. Starting from a closed-pocket experimental structure, we first applied a molecular dynamics simulations-based goal-oriented adaptive sampling method to identify possible open-pocket conformations. To find plausible ligand-binding poses, we performed Boltzmann docking, which combines traditional docking with Markov state modeling, of the newly sampled conformations. Clustering and analysis of stability and accessibility of docked poses supported a preferred binding site; we further validated this site by mutagenesis and electrophysiology, suggesting a mechanism of potentiation by stabilizing intersubunit contacts. Given the pharmaceutical relevance of serotonin-3 receptors in emesis, psychiatric and gastrointestinal diseases, characterizing relatively unexplored modulatory sites such as these could open valuable avenues to understanding conformational cycling and designing state-dependent drugs.

Significance

5-HT3Areceptors receive the chemical signals of excitatory neurotransmission across the synapse in the central and peripheral nervous systems, and are involved in conditions including emesis, pain, psychiatric disorders, drug abuse, and irritable bowel syndrome. Given their pharmaceutical importance, there is great interest in understanding how and where ligands interact with these receptors. A pocket facing the extracellular vestibule of this membrane protein has been proposed as a modulatory site, but it remains largely uncharacterized in the context of structural modeling or pharmacologically relevant ligands. Here, we are able to identify and investigate binding of a stimulant derivative, 4-bromoamphetamine, in this site by using an integrative computational and experimental approach that is able to account for conformational flexibility.
ROS-mediated TNFR Wengen activation in response to apoptosis
Authors: Esteban-Collado José , Fernàndez-Mañas Mar , Fernández-Moreno Manuel , Maeso Ignacio , Corominas Montserrat , Serras Florenci
Published: November 2023

The activation of tumor necrosis factor receptors (TNFR) controls pleiotropic pro-inflammatory functions ranging from apoptosis to survival. The ability to trigger a particular function will depend on the upstream activation, association with regulatory complexes and downstream pathways. InDrosophila,two TNFRs have been identified, Wengen (Wgn) and Grindelwald (Grnd). Although several reports associate these receptors with JNK-dependent apoptosis, it has recently been found that Wgn activates a variety of functions. We demonstrate that Wgn is required for survival by protecting cells from apoptosis. This is mediated by the signaling molecule dTRAF1 and results in the activation of the p38 MAP kinase signaling pathway. Remarkably, Wgn is required for apoptosis-induced regeneration and is activated by the reactive oxygen species (ROS) produced following apoptosis. This ROS activation is exclusive for Wgn, but not for Grnd, and occurs in the absence of the ligand Eiger/TNFα. Furthermore, based on protein sequence conservation, the extracellular Cys-rich domain of Grnd is much more divergent and phylogenetically restricted than that of Wgn, which is more similar to TNFR families from other animals, including those of human TNFRs. Taken together, our results show a novel function for a TNFR that responds to cellular damage by ensuring the cell survival required for the response to damage.
The yeast ribosomal protein Rpl1b is not required for respiration
Authors: Futcher B.
Published: November 2023

Previously, Segev and Gerst found that mutants in any of the four ribosomal protein genesrpl1b, rpl2b, rps11a, orrps26bhad a petite phenotype—i.e., the mutants were deficient in respiration. Strikingly, mutants of their paralogsrpl1a, rpl2a, rps11b, andrps26awere grande—i.e., competent for respiration. It is remarkable that these paralogs should have opposite phenotypes, because three of the paralog pairs (Rpl1a/Rpl1b, Rpl2a/Rpl2b, Rps11a/Rps11b) are 100% identical to each other in amino acid sequence, while Rps26a and Rps26b differ in 2 amino acids out of 119. However, while attempting to use this paralog-specific petite phenotype in an unrelated experiment, I found that therpl1b, rpl2b, rps11a, andrps26bdeletion mutants are competent for respiration, contrary to Segev and Gerst.
MicrobeMod: A computational toolkit for identifying prokaryotic methylation and restriction-modification with nanopore sequencing
Authors: Crits-Christoph Alexander , Kang Shinyoung Clair , Lee Henry H. , Ostrov Nili
Published: November 2023

Bacteria and archaea use restriction-modification (R-M) systems to distinguish self from foreign DNA by methylating their genomes with DNA methyltransferases with diverse sequence specificities, and these immunity systems often vary at the strain level. Identifying active methylation patterns and R-M systems can reveal barriers to the introduction of recombinant DNA or phage infection. Here, we present the computational MicrobeMod toolkit for identifying 5mC and 6mA methylation sequence motifs and R-M systems in bacterial genomes using nanopore sequencing of native DNA. We benchmark this approach on a set of referenceE. colistrains expressing methyltransferases with known specificities. We then applied these analyses to 31 diverse bacterial and archaeal organisms to reveal the methylation patterns of strains with previously unexplored epigenetics, finding that prokaryotic 5-methylcytosine may be more common than previously reported. In summary, MicrobeMod can rapidly reveal new epigenetics within a prokaryotic genome sequenced with Oxford Nanopore R10.4.1 flow cells at sequencing depths as low as 10x and only requires native DNA. This toolkit can be used to advance fundamental knowledge of bacterial methylation and guide strategies to overcome R-M barriers of genetic tractability in non-model microbes.
Does stomatal patterning in amphistomatous leaves minimize the CO2diffusion path length within leaves?
Authors: Watts Jacob L. , Dow Graham J. , Buckley Thomas N. , Muir Christopher D.
Published: November 2023

Photosynthesis is co-limited by multiple factors depending on the plant and its environment. These include biochemical rate limitations, internal and external water potentials, temperature, irradiance, and carbon dioxide (CO2). Amphistomatous leaves have stomata on both abaxial and adaxial leaf surfaces. This feature is considered an adaptation to alleviate CO2diffusion limitations in productive environments where other factors are not limiting as the diffusion path length from stomate to chloroplast is effectively halved. Plants can also reduce CO2limitations through other aspects of optimal stomatal anatomy: stomatal density, distribution, patterning, and size. A number of studies have demonstrated that stomata are overdispersed on a single leaf surface; however, much less is known about stomatal anatomy in amphistomatous leaves, especially the coordination between leaf surfaces, despite their prevelance in nature and near ubiquity among crop species. Here we use novel spatial statistics based on simulations and photosynthesis modeling to test hypotheses about how amphistomatous plants may optimize CO2limitations in the model angiospermArabidopsis thalianagrown in different light environments. We find that 1) stomata are overdispersed, but not ideally dispersed, on both leaf surfaces across all light treatments; 2) abaxial and adaxial leaf surface patterning are independent; and 3) the theoretical improvements to photosynthesis from abaxial-adaxial stomatal coordination are miniscule (≪ 1%) across the range of feasible parameter space. However, we also find that 4) stomatal size is correlated with the mesophyll volume that it supplies with CO2, suggesting that plants may optimize CO2diffusion limitations through alternative pathways other than ideal, uniform stomatal spacing. We discuss the developmental, physical, and evolutionary constraits which may prohibit plants from reaching the theoretical adaptive peak of uniform stomatal spacing and inter-surface stomatal coordination. These findings contribute to our understanding of variation in the anatomy of amphistomatous leaves.
CRISPR-based editing strategies to rectifyEYA1complex genomic rearrangement linked to haploinsufficiency
Authors: Hwalin Yi , Yun Yejin , Choi Won Hoon , Hwang Hye-Yeon , Cha Ju Hyuen , Seok Heeyoung , Song Jae-Jin , Lee Jun Ho , Oh Seung Ha , Lee Sang-Yeon , Kim Daesik
Published: November 2023

Pathogenic structure variations (SVs) and genomic rearrangements are associated with various types of cancer and rare genetic diseases. Recent studies have used Cas9 nuclease with paired guide RNAs (gRNAs) to generate targeted chromosomal rearrangements. Studies on Cas9-mediated translocations and inversions have mainly focused on producing fusion proteins that cause cancer, whereas research on precision genome editing for rectifying SVs is limited. In this study, through whole- genome sequencing, we identified a novel complex genomic rearrangement (CGR), specifically anEYA1inversion with a deletion, implicated in branchio-oto- renal/branchio-oto (BOR/BO) syndrome. The CGR results in a loss-of-function allele, leading to haploinsufficiency. To address this, two CRISPR-based editing approaches were tested. First, we engineered Cas9 nuclease and paired gRNAs tailored to the patient’s genome. The dual CRISPR/Cas9 system induced efficient editing at sites with paracentric inversion in patient-derived fibroblasts (up to 1.6%), and effectively restored the expression levels of theEYA1gene and its downstream targets, restoring overall transcriptional functionality. Additionally, we engineered gene-activating CRISPR-Cas modules (CRISPRa), which increasedEYA1mRNA and protein expression to wild-type levels in humanEYA1monoallelic knockout cells that mimic the haploinsufficiency. Moreover, CRISPRa significantly improved transcriptional activity essential for target gene expression. This suggests that CRISPRa-based gene therapies may offer substantial translational potential for approximately 70% of disease-causingEYA1variants responsible for haploinsufficiency. In parallel to deciphering the complexities of the genomic landscape related to human genetic disorders, our findings demonstrate the potential of CIRSPR-guided genome editing for correcting SVs, including those withEYA1CGR linked to haploinsufficiency.
Wastewater surveillance pilot at US military installations: a cost model analysis
Authors: Sanjak Jaleal , McAuley Erin M , Pinkham Richard , Tarnowski Jacob , Miko Nicole , Rasmussen Bridgette , Manalo Christian , Goodson Michael , Stamps Blake , Necciai Bryan D , Sozhamannan Shanmuga , Maier Ezekiel J
Published: November 2023

Background

The coronavirus disease 2019 (COVID-19) pandemic highlighted the need for pathogen surveillance systems to augment both early warning and outbreak monitoring/control efforts. Wastewater samples provide a rapid and accurate source of environmental surveillance data to complement direct patient sampling. Due to its global presence and critical missions, the US military is a leader in global pandemic preparedness efforts. Clinical testing for COVID-19 on US Air Force (USAF) bases (AFBs) was effective, but costly with respect to direct costs and indirect costs of lost time. To remain operating at peak capacity such bases sought a more passive surveillance option and piloted wastewater surveillance (WWS) at 17 AFBs to demonstrate feasibility, safety, and utility from May 2021 to January 2022.

Objective

Here we model the costs of a wastewater program for pathogens of pandemic potential within the specific context of US military installations using assumptions based on the results of the USAF and Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND) pilot program. The objective was to determine the cost of deploying WWS to all AFBs, relative to clinical swab testing surveillance regimes.

Methods

A simple WWS cost projection model was built based on subject matter expert input and actual costs incurred during a WWS pilot program at USAF AFBs. Several SARS-CoV-2 circulation scenarios were considered and costs of both WWS and clinical swab testing were projected. Break even analysis was conducted to determine how reduction in swab testing could open up space to enable WWS to occur in complement.

Results

Our model confirms that wastewater surveillance is complementary and highly cost-effective when compared to existing alternative forms of biosurveillance. We find that the cost of WWS was between $10.5 - $18.5 million less expensive annually in direct costs as compared to clinical swab testing surveillance. When indirect cost of lost work is incorporated, including assumed lost work required to go obtain a clinical swab test, we estimate that over two thirds of clinical swab testing could be maintained with no additional costs upon implementation of WWS.

Conclusions

Our results support adoption of wastewater surveillance across US military installations as part of a more comprehensive and early warning system that will enable adaptive monitoring during disease outbreaks.
Scalable Approach to Medical Wearable Post-Market Surveillance
Authors: Yoo Richard M. , Viggiano Ben T. , Pundi Krishna N. , Fries Jason A. , Zahedivash Aydin , Podchiyska Tanya , Din Natasha , Shah Nigam H.
Published: November 2023

Objective

We sought to develop a weak supervision-based approach to demonstrate feasibility of post-market surveillance of wearable devices that render AF pre-diagnosis.

Materials and Methods

Two approaches were evaluated to reduce clinical note labeling overhead for creating a training set for a classifier: one using programmatic codes, and the other using prompts to large language models (LLMs). Probabilistically labeled notes were then used to fine-tune a classifier, which identified patients with AF pre-diagnosis mentions in a note. A retrospective cohort study was conducted, where the baseline characteristics and subsequent care patterns of patients identified by the classifier were compared against those who did not receive pre-diagnosis.

Results

Label model derived from prompt-based labeling heuristics using LLMs (precision = 0.67, recall = 0.83, F1 = 0.74) nearly achieved the performance of code-based heuristics (precision = 0.84, recall = 0.72, F1 = 0.77), while cutting down the cost to create a labeled training set. The classifier learned on the labeled notes accurately identified patients with AF pre-diagnosis (precision = 0.85, recall = 0.81, F1 = 0.83). Those patients who received pre-diagnosis exhibited different demographic and comorbidity characteristics, and were enriched for anticoagulation and eventual diagnosis of AF. At the index diagnosis, existence of pre-diagnosis did not stratify patients on clinical characteristics, but did correlate with anticoagulant prescription.

Discussion and Conclusion

Our work establishes the feasibility of an EHR-based surveillance system for wearable devices that render AF pre-diagnosis. Further work is necessary to generalize these findings for patient populations at other sites.
Barriers and Facilitators to Equitable Implementation of Long-Acting ART for Adolescents and Youth with HIV in Low- and Middle-Income Settings
Authors: Sam-Agudu Nadia A. , Adirieje Chibueze , Agwu Allison L. , Rakhmanina Natella
Published: November 2023

Recent approvals of long-acting (LA) antiretroviral treatment (ART) support an innovative alternative to daily oral pills that can improve adherence and treatment outcomes among adolescents and youth (AY) with HIV. We solicited stakeholder feedback on the implementation of LA ART for AY in low-and middle-income countries (LMICs) through a consensus-building forum at the 2022 International Workshop on HIV and Adolescence.

We used the nominal group technique to generate, record, discuss, vote on, and rank perceived barriers and facilitators to implementing LA ART for AY. All in-person attendees were invited to participate and were assigned to six groups, each representing an intentional mix of AY, clinicians, researchers, program implementers and policymakers. We collected self-reported de-identified demographics and group rankings of barriers and facilitators. Responses were coded and categorized using the social-ecological model’s five levels of influence.

137 Workshop delegates (67.9% male, 27.7% female; 0.7% non-binary and 46.7% less than 35 years old) participated in the group discussions. A large proportion of participants (51.9%) reported working in public health/program implementation. Most participants (88.4%) were from and/or worked in the African region. We identified 55 barriers and 48 facilitators of LA ART implementation and ranked them in social-ecological model categories of public policy, community, institutional/organizational, interpersonal, and individual levels. The highest number of ranked barriers was at the institutional/organizational level. The themes of “equitable access” and “choices of ART” were cross-cutting across individual and interpersonal levels. Other cross-cutting themes were “cost of LA ART” and “need for funding and sustainability of LA ART programs”. Proposed facilitators addressed identified barriers at each social-ecological level of influence and emphasized peer engagement.

Our nominal groups identified key barriers and proposed facilitators at five different social ecological levels, which can inform implementation science-guided design and equitable implementation of youth centered LA ART in LMICs and globally.