bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virtual staining from bright-field microscopy for label-free quantitative analysis of plant cell structures
Authors: Ichita Manami , Yamamichi Haruna , Higaki Takumi 
Published: October 2024

AbstractThe applicability of a deep learning model for the virtual staining of plant cell structures using bright-field microscopy was investigated. The training dataset consisted of microscopy images of tobacco BY-2 cells with the plasma membrane stained with the fluorescent dye PlasMem Bright Green and the cell nucleus labeled with Histone-red fluorescent protein. The trained models successfully detected the expansion of cell nuclei upon aphidicolin treatment and a decrease in the cell aspect ratio upon propyzamide treatment, demonstrating its utility in cell morphometry. The model also accurately documented the shape of Arabidopsis pavement cells in both wild type and thebpp125triple mutant, which has an altered pavement cell phenotype. Metrics such as cell area, circularity, and solidity obtained from virtual staining analyses were highly correlated with those obtained by manual measurements of cell features from microscopy images. Furthermore, the versatility of virtual staining was highlighted by its application to track chloroplast movement inEgeria densa. The method was also effective for classifying live and dead BY-2 cells using texture-based machine learning, suggesting that virtual staining can be applied beyond typical segmentation tasks. Although this method still has some limitations, its non-invasive nature and efficiency make it highly suitable for label-free, dynamic, and high-throughput analyses in quantitative plant cell biology.
Suregada multifloraRoot Fluro-PolyPhosphate-Glycoside (NU2) inhibits MDR Bacteria and Unicellular Parasites Targeting DNA Topoisomerase I
Authors: Chakraborty Asit Kumar 
Published: October 2024

AbstractBackgroundCommon antibiotics were useless now asmdrgenes were gradually accumulating in all environmental bacterial plasmids. Thus, development of alternate to synthetic antibiotics is great.ObjectivesPlants secrete ex-metabolites to prevent soil bacteria and thus a good source for new antibiotics. Our objective is to discover an abundant active phyto-chemical against MDR pathogens from household plants of West Bengal.MethodsSuregada multifloraplant was grown in clay pot. Root ethanol extract was made for overnight at RT and concentrated. Preparative TLC was performed to isolate major active component by UV-shadow method and was further purified by HPLC. NU2 Inhibitory assays on MDREscherichia coliKT-1,Leishmania donovanipromastigotes,Plasmodium falciparumin human RBC culture were performed as described previously. Biochemical assays, elementary and spectral analyses (MASS, FTIR, NMR) were performed to validate chemical nature of NU2. DNA Topoisomerase I, RNA polymerase and DNA polymerase assays were performed to find modes of action. The structures of NU2 were drawn using Stacher and NU2 binding to DNA topoisomerase I was performed using SwissDock server [Bugnon et al. 2024].ResultsWell cultivatedS. multifloraroot extract was 18fold active than bark extract and further enhanced 2.8fold in MS media root culture. The four times TLC purified active principle (NU2) was eluted at 10.2min in HPLC C18column. NU2 inhibits MDR bacteria as well as unicellular parasitesPlasmodium falciparum,Leishmania donovaniand Trypanosoma brucei. Spectral analyses suggested NU2 was a glycoside-polyphosphate with molecular mass 454mu and molecular formula C4H7P4O16F. FT-IR gave broad band at 3000-3600cm-1for -OH including at 1559cm-1 for -OH bending. The distinct phosphate -PO4-3group absorption was confirmed at 1021.4cm-1including 928.7cm-1for C-O-P and skeleton minor phosphate group vibration at 525cm-1. Proton-NMR demonstrated huge absorption at δ=2.16ppm for C-O-H, at δ=1.52ppm for -POH while Carbon-NMR at 30.1ppm for C-H and at 207.01ppm for -HC=O. NU2 actively inhibited the DNA topoisomerase I but DNA polymerase and RNA polymerase ofEscherichia coliwere not inhibited. The AI-guided computer simulation suggested that NU2.1, NU2.2 and NU2.3 were better inhibitors for topoIII than topoI ofE. coli,M. tuberculosisandL. donovani. We postulate that NU2 prevent the DNA nicking, strand passing and ligase activities after specific binding to the domain-2 active sites.ConclusionThus, NU2 cyclic glycoside-fluoropolyphosphate may be a versatile type-I DNA topoisomerase inhibitor and could be studied further for drug design against bacterial and parasite drug-resistant pathogenesis.Graphical Abstract
Gardenia duerrii(Gardenieae : Rubiaceae), a new species from India and Neotypification ofGardenia resiniferaRoth
Authors: Raja Kullayiswamy K , Sarojini Devi N 
Published: October 2024

AbstractGardenia duerriisp. nov. is described and illustrated from middle parts of Central Peninsula Plateau, India. This new species is allied toGardenia resiniferain flower (corolla tube, lobes and anther) and somewhat in leaf and stipule, but it differs in leaf texture, venation, fruit and calyx nature. Distribution of the new species is under the canopy of dry deciduous forests of Telangana, Andhra Pradesh, Odisha and Maharashtra states of India. Allied speciesGardenia resiniferaRoth type specimen is missing or likely destroyed during WW-II at the Botanic Garden and Botanical Museum Berlin, Germany. Consequently, we designate herein a neotype forGardenia resinifera.
Biomimic opto-nanobiointerface enables multiscale biomodulation
Authors: Müller Christoph Alexander , Zhang Yuge , Meng Lingyuan , Kalatanova Anna , Madsen Jesper Guldsmed , Klompmaker Kjeld Kaj , Jakobsen Thomas Stax , Jørgensen Asbjørn C. , Askou Anne Louise , Huang Ge , Li Wen , Davidsen Rasmus Schmidt , Bek Toke , Hatzakis Nikos S. , Corydon Thomas J. , Leinonen Henri , Tian Bozhi , Dong Mingdong , Chen Menglin 
Published: October 2024

AbstractVirtually all organic material on Earth has been produced converting solar energy through photosynthesis in chloroplasts, a sack-like, double membrane organelle in plants and algae, where transmembrane electron transfer occurs from lumen to stroma. Although animals hardly harness the power of photosynthesis, their bioelectrical signals extensively regulate complex electrophysiological behaviors, rendering it a superior target for biomedical innovation. Here a crude structural mimicry of chloroplast has led us to discover that hollow sphere graphitic carbon nitride nanoparticles (hg-C3N4NPs) endowed non-genetic, subcellular and intercellular photo-modulation of various excitable and non-excitable cells, accumulatively achieving modulation at tissue/organ function level. The homogeneous hg-C3N4NPs showed photo-responsiveness via photoelectrochemical and photothermal mechanisms under photocurrent measurement. The hg-C3N4NPs can be spontaneously internalized with excellent cytocompatibility. Using a focusing laser, the hg-C3N4NPs enable intracellular optical stimulation with subcellular resolution, inducing calcium transient release in multiple cells and propagation in primary cardiomyocytes and cardiac fibroblasts. At multicellular scale, optical pacing and synchronization of cardiomyocyte beating is achieved facilely by LED. Further, we demonstrate that hg-C3N4NPs can be safely injected into mouse eyes, restoring light sensitivity in blind mice. Finally, application of hg-C3N4NPs to porcine retinal tissueex vivoconfirmed their modulation capability to reactivate RGCs activity under LED photostimulation. Taken together, these nanostructured biomimic semiconductor NPs offer high resolution, leadless optical probing, non-invasive delivery and great biocompatibility, serving as a versatile tool for addressing a range of complex biomedical challenges through subcellular, intercellular and tissue-level photo-modulation across a broad spectrum of scales.
Getting Started with Machine Learning for Experimental Biochemists and Other Molecular Scientists
Authors: Vince Matthew J. K. , Hughes Kristin A. , Buzuk Anastasiya , Perlstein Deborah L. , Viarengo-Baker Lauren A. , Whitty Adrian 
Published: October 2024

AbstractMachine learning (ML) is rapidly gaining traction in many areas of experimental molecular science for elucidating relationships and patterns in large or complex data sets. Historically, ML was largely the preserve of those with specialized training in fields such as statistics or cheminformatics. Increasingly, however, ML methodologies are becoming part of the standard toolkit for experimental scientists across a range of disciplines. Lowering the barrier of entry to these ML techniques, for scientists without a significant background in computer science or statistics, is important to broadening access to these powerful methods. Here we provide detailed, step by step tutorials for performing four ML methods that are particularly useful for applications in biochemistry, cell biology, and drug discovery: hierarchical clustering, Principal Component Analysis (PCA), Partial Least-Squares Discriminant Analysis (PLSDA), and Partial Least-Squares Regression (PLSR). The protocols are written for the widely used software MATLAB, but no prior experience with MATLAB is required to use them. We include an explanation of each step, pitched at a level to be understood by investigators without any prior experience with ML, MATLAB, or any kind of coding. We also highlight the scientific issues pertaining to selecting and scaling the data to be analyzed, and describe controls to test the validity of the results obtained. Throughout, we emphasize the relationship between the scientific question and how to choose data and methods that will allow it to be addressed in a meaningful way. Our aim is to provide a basic introduction that will equip experimental chemical biologists and other chemical and biomedical scientists with the knowledge required to use ML to aid in the design of experiments, the formulation and data-driven testing of hypotheses, and the analysis of experimental data.Basic Protocol 1ClusteringBasic Protocol 2Principal Component Analysis (PCA)Basic Protocol 3Partial Least Squares Discriminant Analysis (PLSDA)Basic Protocol 4Partial Least Squares Regression (PLSR)
Grey Matter Volume and Fractional Anisotropy as Correlates of Cognitive Improvement in Traumatic Brain Injury Over a 6-Month Period
Authors: Zhang Ben , Fulmer Niko , Dunn Sarah , Zheng Zhong Sheng , Schnakers Caroline , Rosario Emily R. 
Published: October 2024

AbstractObjectiveIn this study we explored how neuroimaging and blood biomarkers relate to cognitive recovery in traumatic brain injury (TBI) patients.MethodsSixteen participants with moderate to severe traumatic brain injury (TBI) were enrolled, with blood samples, MRI, and diffusion tensor imaging (DTI) collected at enrollment and six months. The Repeatable Battery for the Assessment of Neuropsychological Status (RBANS), Disability Rating Scale, and Montreal Cognitive Assessment (MoCA) were also administered at both time points to evaluate neuropsychological and functional outcomes.ResultsFractional anisotropy (FA) in the genu (rs= 0.937, p = 0.002) and splenium of the corpus callosum (rs= 0.955, p < 0.001) was strongly correlated with changes in RBANS - Attention scores. Fornix FA was correlated with changes in RBANS - Total (rs= 0.928, p = 0.008), and left tapetum FA was correlated with changes in RBANS - Visuospatial scores (rs= 0.964, p < 0.001). Right temporal fusiform cortex grey matter (GM) volume was correlated with changes in RBANS - Attention scores (rs= 0.975, p = 0.005). Blood biomarkers did not show significance.ConclusionImaging markers like FA and GM volume appear to help predict cognitive recovery in TBI, supporting the potential use of neuroimaging to guide rehabilitation strategies.
The global burden of chikungunya virus and the potential benefit of vaccines
Authors: Ribeiro dos Santos Gabriel , Jawed Fariha , Mukandavire Christinah , Deol Arminder , Scarponi Danny , Mboera Leonard E.G. , Seruyange Eric , Poirier Mathieu J.P. , Bosomprah Samuel , Udeze Augustine O. , Dellagi Koussay , Hozé Nathanael , Chilongola Jaffu , Nasrallah Gheyath K. , Saathof Elmar , Cauchemez Simon , Salje Henrik 
Published: October 2024

AbstractThe first chikungunya virus (CHIKV) vaccine has now been licensed, however, its potential to reduce disease burden remains unknown due to a poor knowledge of the underlying global burden. We use data from seroprevalence studies, observed cases and mosquito distributions to quantify the underlying burden in 190 countries and territories, and explore the potential impact of the vaccine. We estimate that 104 countries have experienced transmission, covering 2.8 billion individuals and that in epidemic settings, the mean duration between outbreaks is 6.2 years, with 8.4% of the susceptible population infected per outbreak. Globally there are 33.7 million annual infections, driven by countries in Southeast Asia, Africa and the Americas. Assuming a vaccine efficacy against disease of 70% a protection against infection of 40%, vaccinating 50% of individuals over 12 years old in places and times where the virus circulates would avert 3,718 infections, 2.8 deaths and 158 DALYs per 100,000 doses used. These findings highlight the global burden and the significant potential of the vaccine.
Predicting the 10-year risk of cardiomyopathy in long-term survivors of childhood cancer: a report from the St. Jude Lifetime Cohort and the Childhood Cancer Survivor Study
Authors: Petrykey Kateryna , Chen Yan , Neupane Achal , French Jennifer , Wang Huiqi , Xiang Haoxue , Dixon Stephanie B. , Vukadinovich Chris , Im Cindy , Ehrhardt Matthew J. , Mulrooney Daniel A. , Sharafeldin Noha , Wang Xuexia , Howell Rebecca M. , Jefferies John L. , Burridge Paul W. , Oeffinger Kevin C. , Gramatges M. Monica , Bhatia Smita , Robison Leslie L. , Ness Kirsten K. , Hudson Melissa M. , Chow Eric J. , Armstrong Gregory T. , Yasui Yutaka , Sapkota Yadav 
Published: October 2024

ABSTRACTPurposeConsidering the heightened risk of cancer treatment-related cardiomyopathy and cardiac death in long-term survivors of childhood cancer, we aimed to develop and validate a clinically-applicable risk prediction model for cardiomyopathy.Patients and MethodsChildhood cancer survivors from St. Jude Lifetime Cohort, (SJLIFE, model-development; n=3,479; median age 32.3 years, IQR 24.4-40.9) and Childhood Cancer Survivor Study (CCSS, model-validation; n=6,875; median age 33.2 years, IQR 27.9-38.9) were assessed for demographic and cardiovascular risk factors, treatment exposures, and polygenic risk scores (PRSs) for cardiomyopathy, heart failure, cardiac structure and function, and anthracycline-related cardiomyopathy risk. Multivariable Poisson regression predicted the 10-year risk of cardiomyopathy (CTCAE grade ≥3: requiring heart failure medications or heart transplantation or leading to death) following baseline visit/survey. Model performance was assessed by area under the receiver operating characteristic curve (AUC).ResultsCardiomyopathy was clinically identified in 75 (2.2%, SJLIFE) and self-reported in 87 (1.3%, CCSS) survivors within 10 years of the baseline assessment. AUC of a clinical model with sex, age at cancer diagnosis, cumulative anthracycline and mean heart radiation doses was 0.833 (SJLIFE) and 0.812 (CCSS). Age at baseline, hypertension and genetic ancestry showed associations with higher cardiomyopathy rates in SJLIFE but did not increase AUC in CCSS (0.812). Adding PRSs for hypertrophic cardiomyopathy and left ventricular end-systolic volume improved AUC in CCSS (0.822;P=0.016). Compared to existing survivorship-care guidelines, the PRS model classified fewer survivors as high-risk or moderate-risk, while identifying survivors in those categories as having 1.5-times greater risk.ConclusionWe developed and validated a model with highest-to-date performance for estimating the 10-year risk of cardiomyopathy in survivors of childhood cancer. Results could enhance identification of at-risk survivors beyond current guidelines.
Construction of a macrophage-tropic subtype C HIV-1 mGreenLantern reporter virus for studies on HIV-1 replication and the impact of methamphetamine
Authors: Mofed Dina , Mandarino Angelo , Wu Xuhong , Lang Yuekun , Gowripalan Anjali , Kalpana Ganjam V. , Prasad Vinayaka R. 
Published: October 2024

AbstractHIV-1 subtype C viruses are responsible for 50% of global HIV burden. However, nearly all currently available reporter viruses widely used in HIV research are based on subtype B. We constructed and characterized a replication competent HIV-1 subtype C reporter virus expressing mGreenLantern. mGreenLantern sequences were inserted in-frame withnefATG in HIV-1IndieC1. As controls, we employed HIV-1IndieC1, HIV-1ADA,and HIV-1NLAD8-GFP-Nefviruses. HIV-1IndieC1-mGreenLantern(HIV-1IndieC1-mGL) exhibited characteristics of the parental HIV-1IndieC1virus, including its infectivity in TZMbl reporter cells and replication competence in macrophages. To further characterize HIV-1IndieC1-mGLvirus, we tested its responsiveness to CCL2 levels, a characteristic feature of subtype B HIV-1 that is missing in subtype C. CCL2 immunodepletion inhibited the production of HIV-1ADAand HIV-1NLAD8-GFP-Nefas expected, but not that of HIV-1IndieC1-mGLas previously reported. We also tested the effect of Methamphetamine, as its effect is mediated by NF-κB and since subtype C viruses carry an additional copy of NFκB. We found that methamphetamine increased the replication of all viruses tested in macrophages, however, its effect was much more robust for HIV-1IndieC1and HIV-1IndieC1-mGL. Our studies established that HIV-1IndieC1-mGLretains all the characteristics of the parental HIV-1IndieC1and can be a useful tool for HIV-1 subtype C investigations.
Optical control of sphingolipid biosynthesis using photoswitchable sphingosines
Authors: Kol Matthijs , Novak Alexander J.E. , Morstein Johannes , Schröer Christian , Sokoya Tolulope , Mensing Svenja , Korneev Sergei M. , Trauner Dirk , Holthuis Joost C.M. 
Published: October 2024

ABSTRACTSphingolipid metabolism comprises a complex interconnected web of enzymes, metabolites and modes of regulation that influence a wide range of cellular and physiological processes. Deciphering the biological relevance of this network is challenging as numerous intermediates of sphingolipid metabolism are short-lived molecules with often opposing biological activities. Here, we introduce clickable, azobenzene-containing sphingosines, termedcaSphs, as light-sensitive substrates for sphingolipid biosynthesis. Photo-isomerization of the azobenzene moiety enables reversible switching between a straighttrans- and curvedcis-form of the lipid’s hydrocarbon tail. Combiningin vitroenzyme assays with metabolic labeling studies, we demonstrate thattrans-to-cisisomerization ofcaSphs profoundly stimulates their metabolic conversion by ceramide synthases and downstream sphingomyelin synthases. These light-induced changes in sphingolipid production rates are acute, reversible, and can be implemented with great efficiency in living cells. Our findings establishcaSphs as versatile tools with unprecedented opportunities to manipulate sphingolipid biosynthesis and function with the spatiotemporal precision of light.
Cortical norepinephrine-astrocyte signaling critically mediates learned behavior
Authors: Drummond Gabrielle T. , Natesan Arundhati , Celotto Marco , Shih Jennifer , Ojha Prachi , Osako Yuma , Park Jiho , Sipe Grayson O. , Jenks Kyle R. , Breton-Provencher Vincent , Simpson Paul C. , Panzeri Stefano , Sur Mriganka 
Published: October 2024

AbstractUpdating behavior based on feedback from the environment is a crucial means by which organisms learn and develop optimal behavioral strategies1–3. Norepinephrine (NE) release from the locus coeruleus (LC) has been shown to mediate learned behaviors4–6such that in a task with graded stimulus uncertainty and performance, a high level of NE released after an unexpected outcome causes improvement in subsequent behavior7. Yet, how the transient activity of LC-NE neurons, lasting tens of milliseconds, influences behavior several seconds later, is unclear. Here, we show that NE acts directly on cortical astrocytes via Adra1a adrenergic receptors to elicit sustained increases in intracellular calcium. Chemogenetic blockade of astrocytic calcium elevation prevents the improvement in behavioral performance. NE-activated calcium invokes purinergic pathways in cortical astrocytes that signal to neurons; pathway-specific astrocyte gene expression is altered in mice trained on the task, and blocking neuronal adenosine-sensitive A1 receptors also prevents post-reinforcement behavioral gain. Finally, blocking either astrocyte calcium dynamics or A1 receptors alters encoding of the task in prefrontal cortex neurons, preventing the post-reinforcement change in discriminability of rewarded and unrewarded stimuli underlying behavioral improvement. Together, these data demonstrate that astrocytes, rather than indirectly reflecting neuronal drive, play a direct, instrumental role in representing task-relevant information and signaling to neurons to mediate a fundamental component of learning in the brain.
Surface display of proximity labeling enzymes on extracellular vesicles for surfaceome and target cell mapping
Authors: Zheng Wenyi , Mowoe Metoboroghene , Hou Wenqing , Hagey Daniel W. , Imami Koshi , Andaloussi Samir EL 
Published: October 2024

ABSTRACTExtracellular vesicles (EV) surface proteins have important extracellular functions and determine cellular tropism; however, characterizing the EV surfaceome remains challenging with available methods. EV-mediated intercellular communication takes place primarily through interactions at the recipient cell membrane, underscoring the importance of methodological advances to map this interplay. Here, we leverage the proximity labeling enzyme APEX2 (Apurinic/Apyrimidinic Endodeoxyribonuclease 2) for high-fidelity analysis of the EV surfaceome and cellular tropism. Surface display of APEX2 on EVs is achieved through its genetic fusion with EV-sorting domains, such as CD63 and TSPAN2. Upon adding the substrates biotin-phenol and hydrogen peroxide, vesicle surface APEX2 enables biotinylation of EV integral and corona proteins as well as target cells in vitro. Further data mining of the EV surfaceome reveals potential scaffolds for the bioengineering of EVs. Altogether, we introduce a robust tool for EV surfaceome and target cell mapping and uncover novel EV-sorting domains for bioengineering.
Topological rearrangements activate the HerA-DUF anti-phage defense system
Authors: Rish Anthony D. , Fosuah Elizabeth , Shen Zhangfei , Marathe Ila A. , Wysocki Vicki H. , Fu Tian-Min 
Published: October 2024

SummaryLeveraging the rich structural information provided by AlphaFold, we used integrated experimental approaches to characterize the HerA-DUF4297 (DUF) anti-phage defense system, in which DUF is of unknown function. To infer the function of DUF, we performed structure-guided genomic analysis and found that DUF homologs are universally present in bacterial immune defense systems. One notable homolog of DUF is Cap4, a universal effector with nuclease activity in CBASS, the most prevalent anti-phage system in bacteria. To test the inferred nuclease function of DUF, we performed biochemical experiments and discovered that the DUF only exhibits activity against DNA substrates when it is bound by HerA. To understand how HerA activates DUF, we determined the structures of DUF and the HerA-DUF complex. DUF forms large oligomeric assemblies with or without HerA, suggesting that oligomerization per se is not sufficient for DUF activation. Instead, DUF activation requires dramatic topological rearrangements that propagate from HerA to the entire HerA-DUF complex, leading to reorganization of DUF for effective DNA cleavage. We further validated these structural insights by structure- guided mutagenesis. Together, these findings reveal dramatic topological rearrangements throughout the HerA-DUF complex, challenge the long-standing dogma that protein oligomerization alone activates immune signaling, and may inform the activation mechanism of CBASS.