bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigating experimental storage methodologies for the understudied intermediate recalcitrant seed of Northern Wild Rice (Zizania palustrisL.)
Authors: Mickelson A. , McGilp L. , Kimball J.
Published: August 2023

The maintenance of plant genetic diversity is an essential target for conservation and breeding efforts. However, the ability to store seed varies between species with those that are more easily stored being overrepresented in seed banks. Northern Wild Rice (NWR;Zizania palustris) has intermediately recalcitrant seed which, along with its dormancy period, makes it more challenging to store long term. This study evaluated alternate storage treatments, including water changes, aeration, and the shift from submerged to moist seed, to extend the longevity of NWR seed in storage compared to current best management practices. Monthly water changes were the most effective storage treatment, maintaining greater than ∼ 50% viability for over 28 months. There was a negative correlation found between aerated treatments with high dissolved oxygen and seed viability. Submerged to moist storage was only effective for ∼16 months. Control treatments maintained relatively high viability (≥ 58%) through 21 months of storage. However, by 28 months, monthly water change seed had significantly higher viability (57.6%) compared to either the standard control (37.2%) or the bucket control (28.9%), suggesting that this treatment is more efficacious than standard storage conditions for maintaining seed viability of NWR.
An end-to-end workflow for non-destructive 3D pathology
Authors: Bishop Kevin W. , Barner Lindsey A. Erion , Han Qinghua , Baraznenok Elena , Lan Lydia , Poudel Chetan , Gao Gan , Serafin Robert B. , Chow Sarah S.L. , Glaser Adam K. , Janowczyk Andrew , Brenes David , Huang Hongyi , Miyasato Dominie , True Lawrence D. , Kang Soyoung , Vaughan Joshua C. , Liu Jonathan T.C.
Published: August 2023

Recent advances in 3D pathology offer the ability to image orders-of-magnitude more tissue than conventional pathology while providing a volumetric context that is lacking with 2D tissue sections, all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis is non-trivial, requiring careful attention to many details regarding tissue preparation, imaging, and data/image processing in an iterative process. Here we provide an end-to-end protocol covering all aspects of a 3D pathology workflow (using light-sheet microscopy as an illustrative imaging platform) with sufficient detail to perform well-controlled preclinical and clinical studies. While 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol will focus on a fluorescent analog of hematoxylin and eosin (H&E), which remains the most common stain for gold-standard diagnostic determinations. We present our guidelines for a broad range of end-users (e.g., biologists, clinical researchers, and engineers) in a simple tutorial format.
Spontaneous enteric nervous system activity precedes maturation of gastrointestinal motility
Authors: Dershowitz Lori B. , Garcia Hassler Bueno , Perley Andrew S. , Coleman Todd P. , Kaltschmidt Julia A.
Published: August 2023

Spontaneous neuronal network activity is essential in development of central and peripheral circuits, yet whether this is a feature of enteric nervous system development has yet to be established. Usingex vivogastrointestinal (GI) motility assays with unbiased computational analyses, we identify a previously unknown pattern of spontaneous neurogenic GI motility. We further show that this motility is driven by cholinergic signaling, which may inform GI pharmacology for preterm patients.
Decision-related activity and movement selection in primate visual cortex
Authors: Laamerad Pooya , Liu Liu D. , Pack Christopher C.
Published: August 2023

Fluctuations in the activity of sensory neurons often predict perceptual decisions. This connection can be quantified with a metric called choice probability (CP), and there has been a longstanding debate about whether CP reflects a causal influence on decisions, or an echo of decision-making activity elsewhere in the brain. Here we show that CP can actually reflect a third variable, namely the movement used to indicate the decision. In a standard visual motion discrimination task, neurons in the middle temporal (MT) area of the primate visual cortex responded more strongly during trials in which the animals executed a saccade toward their receptive fields, and less strongly for saccades directed away from the receptive fields. The resulting trial-to-trial variability accounted for much of the CP observed across the neuronal population, and it arose through training. Surprisingly, the learned association between MT activity and oculomotor selection was causal, as pharmacological inactivation of MT neurons biased behavioral responses away from the corresponding receptive field locations. These results demonstrate that training on a task with fixed sensorimotor contingencies introduces movement-related activity in sensory brain regions, and that this plasticity can shape the neural circuitry of perceptual decision-making.
Comparative study of thermal tolerance and other physiological characteristics inC. briggsaeandC. elegans
Authors: Jhaveri Nikita , Bhullar Harvir , Gupta Bhagwati P.
Published: August 2023

The nematodeCaenorhabditis briggsae(C. briggsae) is routinely used in genetic and evolutionary studies involving its well-known cousin,C. elegans. The two species are morphologically almost identical but exhibit significant developmental, genetic, and genomic differences. The AF16 isolate ofC. briggsaeis an established reference strain. We used additional wild isolates from tropical and temperate regions to perform a comparative study of phenotypic characters. The analysis revealed both intra (betweenC. briggsaeisolates) and inter (compared toC. elegansN2) species variability in dimensions and opacity. Our data also showed thatC. briggsaeisolates prefer higher temperatures for growth, reproduction, and survival thanC. elegansN2. The preference for higher temperatures further translated into a higher tolerance for heat stress, as evidenced by its survival at temperatures lethal to N2. Interestingly, we found that whileC. briggsaeis more resistant to heat and shows greater sensitivity to other forms of stress, namely oxidative and osmotic, compared toC. elegans. The heat resistance ofC. briggsaewas correlated with efficient upregulation of the cytosolic chaperonhsp-16.2. Overall, this work has revealed significant differences in stress sensitivities between the two nematodes and forms the basis to investigate changes in underlying mechanisms that affect their stress responses.
Impacts of early exposure to ethanol on adenosine functioning in zebrafish
Authors: Couto Giovanna Trevisan , da Silva Guilherme Pietro , Rockenbach Liliana , da Silva Jéssica Scheid , Roca Vianna Monica Ryff Moreira , Da Silva Rosane Souza
Published: August 2023

Exposure to ethanol at the beginning of development can impact the formation of the Nervous System. The set of symptoms resulting from ethanol consumption during pregnancy is called FASD (Fetal Alcohol Spectrum Disorders) and ranges from cognitive alterations to the most severe form called FAS (Fetal Alcohol Syndrome). The effect caused by ethanol on the formation of brain architecture directly affects the adenosine neuromodulation system. In this work, a single exposure regimen of 24 to 26 hpf to 1% ethanol transdermally was used as a model to assess adenosine signaling in the context of seizure susceptibility in zebrafish larvae and adults. To test sensitivity, a 2.5 mM subconvulsant dose of pentylenetetrazole (PTZ) was used, which was not able to increase seizure events in larvae or adults exposed to ethanol during embryonic phase. However, the duration of stage I was increased and the latency to reach stage II was decreased in larvae, showing a possible proconvulsant profile in these ethanol-treated animals. Also, the exposure of larvae to CPA (75 μM) was able to reverse the effect of embryonic ethanol treatment on the latency to reach stage II of seizure. Adenosine and ecto-5’-nucleotidase receptor mRNA expression did not show significant difference in both developmental stages. These results demonstrated that even a short and specific exposure to ethanol can promote, even if mild, effects on neuronal modulation, increasing susceptibility to seizures.
Extensive rewiring of the gene regulatory interactions between in vitro-produced conceptuses and endometrium during attachment
Authors: Biase Fernando H. , Moorey Sarah E. , Schnuelle Julie G. , Rodning Soren , Ortega Marta Sofia , Spencer Thomas E.
Published: August 2023

Pregnancy loss is a significant problem when embryos producedin vitroare transferred to a synchronized uterus. Currently, mechanisms that underlie losses ofin vitro-producedembryos during implantation are largely unknown. We investigated this problem using cattle as a model of conceptus attachment by analyzing transcriptome data of paired extraembryonic membrane and endometrial samples collected on gestation days 18 and 25, which spans the attachment window in cattle. We identified that the transfer of anin vitro-producedembryo caused a significant alteration in transcript abundance of hundreds of genes in extraembryonic and endometrial tissues on gestation days 18 and 25, when compared to pregnancies initiated by artificial insemination. Many of the genes with altered transcript abundance are associated with biological processes that are relevant to the establishment of pregnancy. An integrative analysis of transcriptome data from the conceptus and endometrium identified hundreds of putative ligand-receptor pairs. There was a limited variation of ligand-receptor pairs in pregnancies initiated byin vitro-producedembryos on gestation day 18, and no alteration was observed on gestation day 25. In parallel, we identified thatin vitroproduction of embryos caused an extensive alteration in the co-expression of genes expressed in the extraembryonic membranes and the corresponding endometrium on both gestation days. Both the transcriptional dysregulation that exists in the conceptus or endometrium independently, and the rewiring of gene transcription between the conceptus and endometrium are a potential component of the mechanisms that contribute to pregnancy losses caused by in vitro production of embryos.

SIGNIFICANCE STATEMENT

The successful establishment of pregnancies following the transfer of anin vitroproduced embryo is essential for cattle production and assisted human reproduction. Most of the pregnancies initiated by the transfer of anin vitroproduced embryo fail, in part because of dysfunctional interaction between the embryo and endometrium during pregnancy establishment. Our study identified that conceptuses producedin vitroand their corresponding endometrium have massive dysregulation in gene activity during the peri-implantation window, which affects crucial biological functions necessary for pregnancy. These gene expression alterations are a major contributor to the high rates of pregnancy loss following the transfer of anin vitroproduced embryo. Our findings have implications for improving assisted reproduction in both agriculture and biomedicine.
Non-target Analysis of Wastewater Treatment Plant Effluents: Chemical Fingerprinting as a Monitoring Tool
Authors: Aggerbeck Marie Rønne , Frøkjær Emil Egede , Johansen Anders , Ellegaard-Jensen Lea , Hansen Lars Hestbjerg , Hansen Martin
Published: August 2023

This study aims at discovering and characterizing the plethora of xenobiotic substances released into the environment with wastewater effluents. We present a novel non-targeted screening methodology based on ultra-high resolution Orbitrap mass spectrometry and nanoflow ultra-high performance liquid chromatography together with a new data-processing pipeline. This approach was applied to effluent samples from two state-of-the-art urban, and one small rural wastewater treatment facility. In total, 785 structures were obtained, of these 38 were identified as single compounds, while 480 structures were identified at a putative level. The vast majority of these were therapeutics and drugs, present as parent compounds and metabolites. Using the R packages Phyloseq and MetacodeR, we here present a novel way of visualizing LCMS data while showing significant difference in xenobiotic presence in the wastewater effluents between the three sites.

1.

Significance

We characterized a wide spectrum of xenobiotic substances using ultra-high performance liquid chromatography, and analysed the data with a new data-processing pipeline using microbial ecological tools to visualize and perform statistical testing of the chemical data to reveal trends in compound composition at the three WWTPs. This approach was applied to obtain and analyse data from effluent samples collected at three wastewater treatment facilities. In total, 785 chemical structures were achieved, with a majority identified as therapeutics and drugs. Several of the compounds are suspected endocrine disruptors. The data reveal a significant difference in compound diversity persisting in the wastewater effluents at the three sites. Our findings reveal the presence of undesirable compounds in effluent released into waterways, and address the greatest challenge in environmental chemistry – pinpointing single compounds of interest from masses of data produced.
Investigating the phylogenetic history of toxin tolerance in mushroom-feedingDrosophila
Authors: Erlenbach Theresa , Haynes Lauren , Fish Olivia , Beveridge Jordan , Bingolo Eunice , Giambrone Sarah-Ashley , Kropelin Grace , Rudisill Stephanie , Chialvo Pablo , Reed Laura K. , Dyer Kelly A. , Chialvo Clare Scott
Published: August 2023

Understanding how and when key novel adaptations evolved is a central goal of evolutionary biology. Within theimmigrans-tripunctataradiation ofDrosophila, many mushroom-feeding species are tolerant of host toxins, such as cyclopeptides, that are lethal to nearly all other eukaryotes. In this study, we used phylogenetic and functional approaches to investigate the evolution of cyclopeptide tolerance in theimmigrans-tripunctataradiation ofDrosophila. We first inferred the evolutionary relationships among 48 species in this radiation using 978 single copy orthologs. Our results resolved previous incongruities within species groups across the phylogeny. Second, we expanded on previous studies of toxin tolerance by assaying 16 of these species for tolerance to α-amanitin and found that six of these species could develop on diet with toxin. Third, we examined fly development on a diet containing a natural mix of toxins extracted from the Death CapAmanita phalloidesmushroom. Both tolerant and susceptible species developed on diet with this mix, though tolerant species survived at significantly higher concentrations. Finally, we asked how cyclopeptide tolerance might have evolved across theimmigrans-tripunctataradiation and inferred that toxin tolerance was ancestral and subsequently lost multiple times. Our results suggest the evolutionary history of cyclopeptide tolerance is complex, and simply describing this trait as present or absent does not fully capture the occurrence or impact on this adaptive radiation. More broadly, the evolution of novelty can be more complex than previously thought, and that accurate descriptions of such novelties are critical in studies examining their evolution.
Functional dissection of KATP channel structures reveals the importance of a conserved interface
Authors: Yang Yaxiong , Chen Lei
Published: August 2023

ATP-sensitive potassium channels (KATP) are inhibited by ATP but activated by Mg-ADP, coupling the intracellular ATP/ADP ratio to the potassium conductance of the plasma membrane. Although there has been progress in determining the structure of KATP channels, the functional significance of the domain-domain interface in the gating properties of KATP channels is not fully understood. In this study, we propose a new two-module assembly model for the KATP channel. Our mutagenesis experiments, based on this model, indicate that deleting ECL3 on the SUR1 subunit impairs KNtp-independent Mg-ADP activation. This finding demonstrates the essential role of intramolecular interactions between KATPcoreand SURABCin Mg-ADP activation. Notably, this interface is functionally conserved between SUR1 and SUR2. Additionally, the hydrophobic residue F351 on ECL3 of SUR1 is crucial for maintaining the stability of this interface.
RPRM as a potential preventive and therapeutic target for radiation-induced brain injury via multiple mechanisms
Authors: Ye Zhujing , Wang Jin , Shi Wenyu , Zhou Zhou , Zhang Yarui , Wang Jingdong , Yang Hongying
Published: August 2023

Patients receiving cranial radiotherapy for primary and metastatic brain tumors may experience radiation-induced brain injury (RIBI). So far there is a lack of effective preventive and therapeutic strategies for RIBI. Due to its complicated underlying pathogenic mechanisms, it is rather difficult to develop a single approach to target them simultaneously. We have recently reported that Reprimo (RPRM), a tumor suppressor gene, is a critical player in DNA damage repair, and RPRM deletion significantly confers radioresistance to mice. Here in this study, by using RPRM knockout (KO) mouse model established in our laboratory, we found that RPRM deletion alleviated RIBI in mice via targeting its multiple underlying mechanisms. Specifically, RPRM knockout significantly reduced hippocampal DNA damage and apoptosis shortly after mice were exposed to whole brain irradiation (WBI). For the late-delayed effect of WBI, RPRM knockout obviously ameliorated radiation-induced decline in neurocognitive function and dramatically diminished WBI-induced neurogenesis inhibition. Moreover, RPRM KO mice exhibited a significantly lower level of acute and chronic inflammation response and microglial activation than wild type (WT) mice did post WBI. Finally, we uncovered that RPRM knockout not only protected microglia against radiation-induced damage, thus prevented microglial activation, but also protected neurons and decreased the induction of CCL2 in neurons after irradiation, in turn attenuating the activation of microglial cells nearby through paracrine CCL2. Taken together, Our results indicate that RPRM plays a crucial role in the occurrence of RIBI, suggesting that RPRM may serve as a novel potential target for the prevention and treatment of RIBI.
SiCR: Web application for single-cell repertoire analysis and immune profiling
Authors: Ishikawa Masakazu , Matsumoto Kaoru , Okuzaki Daisuke
Published: August 2023

Background

Single-cell RNA sequencing (scRNA-seq) allows analysis of complete sequences of antigen receptors in individual cells. However, it is a complex technique that requires multiple analyses to obtain accurate results. Although several user-friendly tools for scRNA-seq are available, none are specifically designed for immune profiling.

Results

We developed a web application called SiCR that is based on the Shiny framework of the R package and specializes in single-cell immune profiling. SiCR allows clustering and cell typing required for both general single-cell and immune profiling analyses, such as predicting whether the chronotype is expanding in each group and the antigen the expanding chronotype targets. These analyses can be performed using a cursor control. SiCR also allows for detailed figure settings, enabling immediate publication of results.

Conclusions

SiCR is a comprehensive workbench that can be used by biologists for single-cell immune profiling. Currently, it is the only web application that allows single-cell repertoire analysis using both raw and preprocessed data. Moreover, SiCR significantly reduces the time and effort required to analyze and interpret information in single-cell immune profiling. Therefore, SiCR is a potential reference application for interactive analysis and investigation of biological data, especially for immune profiling.
Methods for constructing and evaluating consensus genomic interval sets
Authors: Rymuza Julia , Sun Yuchen , Zheng Guangtao , LeRoy Nathan J. , Murach Maria , Phan Neil , Zhang Aidong , Sheffield Nathan C.
Published: August 2023

The amount of genomic region data continues to increase. Integrating across diverse genomic region sets requires consensus regions, which enable comparing regions across experiments, but also by necessity lose precision in region definitions. We require methods to assess this loss of precision and build optimal consensus region sets. Here, we introduce the concept offlexible intervalsand propose 3 novel methods for building consensus region sets, or universes: a coverage cutoff method, a likelihood method, and a Hidden Markov Model. We then propose 3 novel measures for evaluating how well a proposed universe fits a collection of region sets: a base-level overlap score, a region boundary distance score, and a likelihood score. We apply our methods and evaluation approaches to several collections of region sets and show how these methods can be used to evaluate fit of universes and build optimal universes. We describe scenarios where the common approach of merging regions to create consensus leads to undesirable outcomes and provide principled alternatives that provide interoperability of interval data while minimizing loss of resolution. Software is available athttps://github.com/databio/geniml.
Learning produces a hippocampal cognitive map in the form of an orthogonalized state machine
Authors: Sun Weinan , Winnubst Johan , Natrajan Maanasa , Lai Chongxi , Kajikawa Koichiro , Michaelos Michalis , Gattoni Rachel , Stringer Carsen , Flickinger Daniel , Fitzgerald James E. , Spruston Nelson
Published: August 2023

Cognitive maps confer animals with flexible intelligence by representing spatial, temporal, and abstract relationships that can be used to shape thought, planning, and behavior. Cognitive maps have been observed in the hippocampus, but their algorithmic form and the processes by which they are learned remain obscure. Here, we employed large-scale, longitudinal two-photon calcium imaging to record activity from thousands of neurons in the CA1 region of the hippocampus while mice learned to efficiently collect rewards from two subtly different versions of linear tracks in virtual reality. The results provide a detailed view of the formation of a cognitive map in the hippocampus. Throughout learning, both the animal behavior and hippocampal neural activity progressed through multiple intermediate stages, gradually revealing improved task representation that mirrored improved behavioral efficiency. The learning process led to progressive decorrelations in initially similar hippocampal neural activity within and across tracks, ultimately resulting in orthogonalized representations resembling a state machine capturing the inherent structure of the task. We show that a Hidden Markov Model (HMM) and a biologically plausible recurrent neural network trained using Hebbian learning can both capture core aspects of the learning dynamics and the orthogonalized representational structure in neural activity. In contrast, we show that gradient-based learning of sequence models such as Long Short-Term Memory networks (LSTMs) and Transformers do not naturally produce such orthogonalized representations. We further demonstrate that mice exhibited adaptive behavior in novel task settings, with neural activity reflecting flexible deployment of the state machine. These findings shed light on the mathematical form of cognitive maps, the learning rules that sculpt them, and the algorithms that promote adaptive behavior in animals. The work thus charts a course toward a deeper understanding of biological intelligence and offers insights toward developing more robust learning algorithms in artificial intelligence.
Mechanism of Phosphate Release from Actin Filaments
Authors: Wang Yihang , Wu Jiangbo , Zsolnay Vilmos , Pollard Thomas D. , Voth Gregory A.
Published: August 2023

After ATP-actin monomers assemble filaments, the ATP’s γ-phosphate is hydrolyzed within seconds and dissociates over minutes. We used all-atom molecular dynamics simulations to sample the release of phosphate from filaments and study residues that gate release. Dissociation of phosphate from Mg2+is rate limiting and associated with an energy barrier of 20 kcal/mol, consistent with experimental rates of phosphate release. Phosphate then diffuses in an internal cavity toward a gate formed by R177 suggested in prior computational studies and cryo-EM structures. The gate is closed when R177 hydrogen bonds with N111 and is open when R177 forms a salt bridge with D179. Most of the time interactions of R177 with other residues occludes the phosphate release pathway. Machine learning analysis reveals that the occluding interactions fluctuate rapidly, underscoring the secondary role of backdoor gate opening in Pirelease, in contrast with the previous hypothesis that gate opening is the primary event.

Significance Statement

The protein actin assembles into filaments that participate in muscle contraction and cellular movements. An ATP bound to the actin monomer is hydrolyzed rapidly during filament assembly, but the γ-phosphate dissociates slowly from the filament. We identified phosphate dissociation from Mg2+as the rate-limiting step in phosphate release from actin based on an energy barrier that aligns with the experimentally determined release rate. The release of phosphate from the protein requires opening a gate in the actin molecule formed by the interaction between sidechains of arginine 177 and asparagine 111. Surprisingly, simulations revealed other interactions of the sidechain of arginine 177 that occlude the release pathway most of the time but have not been observed in low-temperature cryo-EM structures.
Comprehensive Assessment of Isoform Detection Methods for Third-Generation Sequencing Data
Authors: Su Yaqi , Yu Zhejian , Jin Siqian , Ai Zhipeng , Yuan Ruihong , Chen Xinyi , Xue Ziwei , Guo Yixin , Chen Di , Liang Hongqing , Liu Zuozhu , Liu Wanlu
Published: August 2023

The advancement of Third-Generation Sequencing (TGS) techniques has significantly increased the length of sequencing to several kilobases, thereby facilitating the identification of alternative splicing (AS) events and isoform expressions. Recently, numerous computational methods for isoform detection using long-read sequencing data have been developed. However, there is lack of prior comparative studies that systemically evaluates the performance of these software tools, implemented with different algorithms, under various simulations that encompass potential influencing factors. In this study, we conducted a benchmarking analysis of eleven methods implemented in eight computational tools capable of identifying isoform structures from TGS RNA sequencing data. We evaluated their performances using simulated data, which represented diverse sequencing platforms generated by an in-house simulator, as well as experimental data. Our comprehensive results demonstrate the guided mode of StringTie2 and Bambu achieved the best performance in sensitivity and precision, respectively. This study provides valuable guidance for future research on AS analysis and the ongoing improvement of tools for isoform detection using TGS data.
Dynamic Regulation of Vesicle Pools in a Detailed Spatial Model of the Complete Synaptic Vesicle Cycle
Authors: Gallimore Andrew R. , Hepburn Iain , Rizzoli Silvio , Schutter Erik De
Published: August 2023

Synaptic transmission is driven by a complex cycle of synaptic vesicle docking, release, and recycling, and maintained by distinct vesicle pools with differing propensities for docking and release. However, the partitioning of vesicles into distinct pools and the conditions under which they are recruited from the reserve to the recycling pool remain poorly understood. Whilst computational modeling at the molecular level has progressed massively in recent years, modeling voluminous, dynamic, and heterogenous structures such as synaptic vesicles remains an unsolved problem. Here, we use a novel vesicle modeling technology to model the complete synaptic vesicle cycle in unprecedented molecular and spatial detail at a hippocampal en passant synapse, incorporating vesicle diffusion, the accumulation and diffusion of proteins on the vesicle surface, vesicle clustering, tethering, and docking, and regulated vesicle fusion and recycling. Our model demonstrates highly dynamic and robust recycling of synaptic vesicles able to maintain stable and consistent synaptic release over time, even during high frequency and sustained firing. We also reveal how the cytosolic proteins synapsin-1 and tomosyn-1 can cooperate to regulate the recruitment of vesicles from the reserve pool during sustained periods of synaptic activity in order to maintain transmission, as well as the potential of selective vesicle tethering close to the active zone to ensure rapid vesicle replenishment and enhance the efficiency of the vesicle cycle by minimizing the recruitment of vesicles from the reserve pool.
SpaRx: Elucidate single-cell spatial heterogeneity of drug responses for personalized treatment
Authors: Tang Ziyang , Liu Xiang , Li Zuotian , Zhang Tonglin , Yang Baijian , Su Jing , Song Qianqian
Published: August 2023

Spatial cellular heterogeneity contributes to differential drug responses in a tumor lesion and potential therapeutic resistance. Recent emerging spatial technologies such as CosMx SMI, MERSCOPE, and Xenium delineate the spatial gene expression patterns at the single cell resolution. This provides unprecedented opportunities to identify spatially localized cellular resistance and to optimize the treatment for individual patients. In this work, we present a graph-based domain adaptation model, SpaRx, to reveal the heterogeneity of spatial cellular response to drugs. SpaRx transfers the knowledge from pharmacogenomics profiles to single-cell spatial transcriptomics data, through hybrid learning with dynamic adversarial adaption. Comprehensive benchmarking demonstrates the superior and robust performance of SpaRx at different dropout rates, noise levels, and transcriptomics coverage. Further application of SpaRx to the state-of-art single-cell spatial transcriptomics data reveals that tumor cells in different locations of a tumor lesion present heterogenous sensitivity or resistance to drugs. Moreover, resistant tumor cells interact with themselves or the surrounding constituents to form an ecosystem for drug resistance. Collectively, SpaRx characterizes the spatial therapeutic variability, unveils the molecular mechanisms underpinning drug resistance, and identifies personalized drug targets and effective drug combinations.

Key Points

We have developed a novel graph-based domain adaption model named SpaRx, to reveal the heterogeneity of spatial cellular response to different types of drugs, which bridges the gap between pharmacogenomics knowledgebase and single-cell spatial transcriptomics data.

SpaRx is developed tailored for single-cell spatial transcriptomics data and is provided available as a ready-to-use open-source software, which demonstrates high accuracy and robust performance.

SpaRx uncovers that tumor cells located in different areas within tumor lesion exhibit varying levels of sensitivity or resistance to drugs. Moreover, SpaRx reveals that tumor cells interact with themselves and the surrounding microenvironment to form an ecosystem capable of drug resistance.
Revealing Shared Proteins and Pathways in Cardiovascular and Cognitive Diseases Using Protein Interaction Network Analysis
Authors: Zeylan Melisa E. , Senyuz Simge , Picón-Pagès Pol , García-Elías Anna , Tajes Marta , Muñoz Francisco J. , Oliva Baldo , Garcia-Ojalvo Jordi , Barbu Eduard , Vicente Raul , Nattel Stanley , Ois-Santiago Angel J. , Puig-Pijoan Albert , Keskin Ozlem , Gursoy Attila
Published: August 2023

One of the primary goals of systems medicine is detecting putative proteins and pathways involved in disease progression and pathological phenotypes. Vascular Cognitive Impairment (VCI) is a heterogeneous condition manifesting as cognitive impairment resulting from vascular factors. The precise mechanisms underlying this relationship remain unclear, which poses challenges for experimental research. Here, we applied computational approaches like systems biology to unveil and select relevant proteins and pathways related to VCI by studying the crosstalk between cardiovascular and cognitive diseases. In addition, we specifically included signals related to oxidative stress, a common etiologic factor tightly linked to aging, a major determinant of VCI. Our results show that pathways associated with oxidative stress are quite relevant, as most of the prioritized vascular-cognitive genes/proteins were enriched in these pathways. Our analysis provided a short list of proteins that could be contributing to VCI: DOLK, TSC1, ATP1A1, MAPK14, YWHAZ, CREB3, HSPB1, PRDX6, and LMNA. Moreover, our experimental results suggest a high implication of glycative stress, generating oxidative processes and post-translational protein modifications through advanced glycation end-products (AGEs). We propose that these products interact with their specific receptors (RAGE) and Notch signaling to contribute to the etiology of VCI.
Phenotype-based targeted treatment of SGLT2 inhibitors and GLP-1 receptor agonists in type 2 diabetes
Authors: Cardoso Pedro , Young Katie G. , Nair Anand T.N. , Hopkins Rhian , McGovern Andrew P , Haider Eram , Karunaratne Piyumanga , Donnelly Louise , Mateen Bilal A. , Sattar Naveed , Holman Rury R. , Bowden Jack , Hattersley Andrew T. , Pearson Ewan R. , Jones Angus G. , Shields Beverley M. , McKinley Trevelyan J. , Dennis John M.
Published: August 2023

A precision medicine approach in type 2 diabetes (T2D) could enhance targeting specific glucose-lowering therapies to individual patients most likely to benefit. We utilised Bayesian non-parametric modelling to develop and validate an individualised treatment selection algorithm for two major T2D drug classes, SGLT2-inhibitors (SGLT2i) and GLP1-receptor agonists (GLP1-RA). The algorithm is designed to predict differences in 12-month glycaemic outcome (HbA1c) between the 2 therapies, based on routine clinical features of 46,394 people with T2D in England (27,319 for model development, 19,075 for hold-out validation), with additional external validation in 2,252 people with T2D from Scotland. Routine clinical features, including sex (with females markedly more responsive to GLP1-RA), were associated with differences in glycaemic outcomes. Our algorithm identifies clearly delineable subgroups with reproducible ≥5mmol/mol HbA1cbenefits associated with each drug class. Moreover, we demonstrate that targeting the therapies based on predicted glycaemic response is associated with improvements in short-term tolerability and long-term risk of new-onset microvascular complications. These results show that precision medicine approaches to T2D can facilitate effective individualised treatment selection, and that use of routinely collected clinical features could support low-cost deployment in many countries.
Exploring pleiotropy in Mendelian randomisation analyses: What are genetic variants associated with “cigarette smoking initiation” really capturing?
Authors: Reed Zoe E. , Wootton Robyn E. , Khouja Jasmine N. , Richardson Tom G. , Sanderson Eleanor , Smith George Davey , Munafò Marcus R
Published: August 2023

Background

Genetic variants used as instruments for exposures in Mendelian randomisation (MR) analyses may also have horizontal pleiotropic effects (i.e., influence outcomes via pathways other than through the exposure), which can undermine the validity of results. We examined the extent to which horizontal pleiotropy may be present, using smoking behaviours as an example.

Methods

We first ran a phenome-wide association study in UK Biobank, using a genetic instrument for smoking initiation. From the most strongly associated phenotypes, we selected those that we considered could either plausibly or not plausibly be caused by smoking. We next examined the association between genetic instruments for smoking initiation, smoking heaviness and lifetime smoking and these phenotypes in both UK Biobank and the Avon Longitudinal Study of Parents and Children (ALSPAC). We conducted negative control analyses among never smokers, including children in ALSPAC.

Results

We found evidence that smoking-related genetic instruments (mainly for smoking initiation and lifetime smoking) were associated with phenotypes not plausibly caused by smoking in UK Biobank and (to a lesser extent) ALSPAC, although this may reflect the much smaller sample size in ALSPAC. We also observed associations with several phenotypes among never smokers.

Conclusion

Our results suggest that genetic instruments for smoking-related phenotypes demonstrate horizontal pleiotropy. When using genetic variants – particularly those for complex behavioural exposures – in genetically-informed causal inference analyses (e.g., MR) it is important to include negative control outcomes where possible, and other triangulation approaches, to avoid arriving at incorrect conclusions.
Recent UK type 2 diabetes treatment guidance represents a near whole population indication for SGLT2-inhibitor therapy
Authors: Young Katherine G , Hopkins Rhian , Shields Beverley M , Thomas Nicholas J , McGovern Andrew P , Dennis John M
Published: August 2023

Recent type 2 diabetes guidance from the UK’s National Institute for Health and Care Excellence (NICE) proposes offering SGLT2-inhibitor therapy to people with established atherosclerotic cardiovascular disease (ASCVD) or heart failure, or at high-risk of cardiovascular disease defined as a 10-year cardiovascular risk of >10% using the QRISK2 algorithm.

We used a contemporary population-representative UK cohort of people with type 2 diabetes to assess the implications of this guidance. 93.1% of people currently on anti-hyperglycaemic treatment are now recommended or considered for SGLT2-inhibitor therapy, with the majority (59.6%) eligible on the basis of QRISK2 rather than established ASCVD or heart failure (33.6%). Applying these results to the approximately 2.20 million people in England currently on anti-hyperglycaemic medication suggests 1.75 million people will now be considered for additional SGLT2-inhibitor therapy.

Given older people, those of non-white ethnic groups, and those at lower cardiovascular disease risk were underrepresented in the clinical trials upon which this guidance was based, careful evaluation of the impact and safety of increased SGLT2-inhibitor prescribing across different populations is urgently required. Evidence of benefit should be weighed against the major cost implications for the NHS.
Efficient and accurate sequence generation with small-scale protein language models
Authors: Serrano Yaiza , Roda Sergi , Guallar Victor , Molina Alexis
Published: August 2023

Large Language Models (LLMs) have demonstrated exceptional capabilities in understanding contextual relationships, outperforming traditional methodologies in downstream tasks such as text generation and sentence classification. This success has been mirrored in the realm of protein language models (pLMs), where proteins are encoded as text via their amino acid sequences. However, the training of pLMs, which involves tens to hundreds of millions of sequences and hundreds of millions to billions of parameters, poses a significant computational challenge.

In this study, we introduce a Small-Scale Protein Language Model (SS-pLM), a more accessible approach that requires training on merely millions of representative sequences, reducing the number of trainable parameters to 14.8M. This model significantly reduces the computational load, thereby democratizing the use of foundational models in protein studies. We demonstrate that the performance of our model, when fine-tuned to a specific set of sequences for generation, is comparable to that of larger, more computationally demanding pLM.
Molecular modeling of apoE in complexes with Alzheimer’s amyloid-β fibrils from human brain suggests a structural basis for apolipoprotein co-deposition with amyloids
Authors: Lewkowicz Emily , Nakamura Mari N. , Rynkiewicz Michael J. , Gursky Olga
Published: August 2023

Apolipoproteins co-deposit with amyloids, yet apolipoprotein-amyloid interactions are enigmatic. To understand how apoE interacts with Alzheimer’s amyloid-β(Aβ) peptide in fibrillary deposits, the NMR structure of full-length human apoE was docked to four structures of patient-derived Aβ1-40and Aβ1-42fibrils determined previously using cryo-electron microscopy or solid-state NMR. Similar docking was done using the NMR structure of human apoC-III. In all complexes, conformational changes in apolipoproteins were required to expose large hydrophobic faces of their amphipathicα-helices for sub-stoichiometric binding to hydrophobic surfaces on sides or ends of fibrils. Basic residues flanking the hydrophobic helical faces in apolipoproteins interacted favorably with acidic residue ladders in some amyloid polymorphs. Molecular dynamics simulations of selected apoE-fibril complexes confirmed their stability. Amyloid bindingviacryptic sites, which became available upon opening of flexibly linked apolipoproteinα-helices, resembled apolipoprotein-lipid binding. This mechanism probably extends to other apolipoprotein-amyloid interactions. Apolipoprotein binding alongside fibrils could interfere with fibril fragmentation and secondary nucleation, while binding at the fibril ends could halt amyloid elongation and dissolution in a polymorph-specific manner. The proposed mechanism is supported by extensive prior experimental evidence and helps reconcile disparate reports on apoE’s role in Aβaggregation. Furthermore, apoE domain opening and direct interaction of Arg/Cys158 with amyloid potentially contributes to isoform-specific effects in Alzheimer’s disease. In summary, current modeling supported by prior experimental studies suggests similar mechanisms for apolipoprotein-amyloid and apolipoprotein-lipid interactions; explains why apolipoproteins co-deposit with amyloids; and helps reconcile conflicting reports on the chaperone-like apoE action in Aβaggregation.
Unilateral ephaptic program underlying sweetness dominance
Authors: Lee MinHyuk , Kim Seon Yeong , Park Taeim , Joo Kyeung Min , Kwon Jae Young , Kim Kyuhyung , Kang KyeongJin
Published: August 2023

In ephaptic coupling, physically adjacent neurons influence one another’s activity via the electric fields they generate. To date, the molecular mechanisms that mediate and modulate ephaptic coupling’s effects remain poorly understood. Here, we show that the hyperpolarization-activated cyclic nucleotide-gated (HCN) channel lateralizes the potentially mutual ephaptic inhibition betweenDrosophilagustatory receptor neurons (GRNs). While sweet-sensing GRNs (sGRNs) engage in ephaptic suppression of the adjacent bitter-sensing GRNs (bGRNs), HCN expression in sGRNs enables them to resist ephaptic suppression from the bGRNs. Such one-sided ephaptic inhibition confers sweetness dominance, facilitating ingestion of bitter-laced sweets. Flies with HCN-deficient sGRNs exhibited dramatically decreased attraction to sucrose mixed with moderate levels of caffeine, highlighting the behavioral significance that gustatory ephaptic inhibition promotes ingestion of carbohydrates buried in bitterness. Our findings indicate a role for the gating of ephaptic coding to ensure the intake of the essential nutrient despite bitter contaminants present in the feeding niche ofDrosophila, as the gating establishes a hierarchy of gustatory neuron excitation. Such refinement provides a previously unappreciated mechanism for controlling the activity of a neuronal network with potential implications in the mammalian brain, given the evolutionary conservation of the HCN genes.
TGFß/activin-dependent activation of Torso controls the timing of the metamorphic transition in the red flour beetleTribolium castaneum
Authors: Chafino Sílvia , Salvia Roser , Martín David , Franch-Marro Xavier
Published: August 2023

Understanding the mechanisms governing body size attainment during animal development is of paramount importance in biology. In insects, a crucial phase in determining body size occurs at the larva-pupa transition, marking the end of the larval growth period. Central to this process is the attainment of the threshold size (TS), a critical developmental checkpoint that must be reached before the larva can undergo metamorphosis. However, the intricate molecular mechanisms by which the TS orchestrates this transition remain poor understood. In this study, we investigate the role of the interaction between the Torso and TGFß/activin signaling pathways in regulating metamorphic timing in the red flour beetle,Tribolium castaneum. Our results show that Torso signaling is required specifically during the last larval instar and that its activation is mediated not only by the prothoracicotropic hormone (Tc-Ptth) but also by Trunk (Tc-Trk), another ligand of the Tc-Torso receptor. Interestingly, we show that while Torso activation by Tc-Ptth determines the onset of metamorphosis, Tc-Trk promotes growth during the last larval stage. In addition, we found that the expression ofTc-torsocorrelates with the attainment of the TS and the decay of juvenile hormone (JH) levels, at the onset of the last larval instar. Notably, our data reveals that activation of TGFß/activin signaling pathway at the TS is responsible for repressing the JH synthesis and inducingTc-torsoexpression, initiating metamorphosis. Altogether, these findings shed light on the pivotal involvement of the Ptth/Trunk/Torso and TGFß/activin signaling pathways as critical regulatory components orchestrating the TS-driven metamorphic initiation, offering valuable insights into the mechanisms underlying body size determination in insects.
Identification of glucose-independent metabolic pathways associated with anti-proliferative effect of metformin, their coordinate derangement with cMyc downregulation and reversibility in liver cancer cells
Authors: Islam Sk Ramiz , Manna Soumen Kanti
Published: August 2023

Several studies indicated anti-cancer effects of metformin in liver cancer. This was attributed to the activation of LKB-AMPK axis, which is associated with anti-hyperglycaemic effect and cytotoxicity. However, despite lack of evidence on cytotoxic effect of physiological metformin concentrations and ability of cancer cells to survive under glucose-deprivation, no study has examined the glucose-independent effect of non-cytotoxic metformin or metabolic reprogramming associated with it. In addition, no study has ever been conducted on reversibility of anti-cancer effects of metformin. Here, the dose-dependent effects of metformin on HepG2 cells were examined in presence and absence of glucose. The longitudinal evolution of metabolome was analyzed along with gene and protein expression as well as their correlations with and reversibility of cellular phenotype and metabolic signatures. Metformin concentrations up to 2.5mM were found to be non-cytotoxic but anti-proliferative irrespective of presence of glucose. Apart from mitochondrial impairment, derangement of fatty acid desaturation, one-carbon, glutathione and polyamine metabolism were associated with non-cytotoxic metformin treatment irrespective of glucose supplementation. Depletion of pantothenic acid, downregulation of essential amino acid uptake, metabolism and purine salvage were identified as novel glucose-independent effects of metformin. These were significantly correlated withcMycexpression and reduction in proliferation. Rescue experiments established reversibility upon metformin withdrawal and tight association between proliferation, metabotype andcMycexpression. Taken together, derangement of novel glucose-independent metabolic pathways and concomitant cMyc downregulation co-ordinately contribute to anti-proliferative effect of metformin even at non-cytotoxic concentrations, which is reversible and may influence its therapeutic utility.