bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering Hidden Data in the AMNH Marine Invertebrate Collections
Authors: Wilkinson A. , Berniker L. , Johnson C. , Rodriguez E. 
Published: December 2023

AbstractAverage global sea surface temperatures have been consistently higher during the past thirty years than any other time since reliable temperature recordings in 1880. Marine life is sufficiently adaptable to survive in a range of temperatures, but extended periods of temperature extremes can have a profound effect on the biology and behavior of aquatic organisms. Historic baseline data is often critical to understanding these changes in biology, distribution, migration, and population dynamics. Data from museum specimens can provide such baselines, but are often an overlooked resource, in part because museum collection data are not readily available. The American Museum of Natural History’s invertebrate zoology collection is home to an estimated 7.5 million marine specimens dating back to the mid-1800s. Although many of the specimens have been catalogued in a public online database, data from a large number of these specimens are not yet in digital form and are therefore only accessible to staff and researchers visiting or borrowing from the collection. The Museum’s Crustacea collection contains around 19,400 specimen lots which hold significant historic value, including lots from the New York Zoological Society’s Bermuda Oceanographic Expeditions.The Bermuda Oceanographic Expeditions provide a rare opportunity to examine historic abundance and distribution of pelagic crustacea taxa that are currently experiencing extended periods of increased ocean temperatures. We synthesized data from the fluid-preserved specimens and from expedition field logs to compose a depth profile that compared the number of crustacean specimens, identified to family or lower taxonomic level, per depth. The results indicate that crustacean abundance and diversity was highest (4-7 families) between 500-1000 fathoms. Most of the specimens were diel-migratory shrimp from the family Sergestidae. We believe that this study provides a useful basis of historic sergestid distribution data that can be used to contextualize modern research in the warming Sargasso Sea.
NAD: Noise-augmented direct sequencing of target nucleic acids by augmenting with noise and selective sampling
Authors: Shim Hyunjin 
Published: December 2023

AbstractNext-generation sequencing necessitates a minimum quantity and concentration of DNA/RNA samples, typically achieved through amplification using the PCR technique. However, this amplification step introduces several drawbacks to biological insights, including PCR bias and the loss of epigenetic information. The advent of long-read sequencing technologies facilitates direct sequencing, with the primary constraint being the limited amount of DNA/RNA present in biological samples. Here, we present a novel method called Noise-Augmented Direct (NAD) sequencing that enables the direct sequencing of target DNA even when it falls below the minimum quantity and concentration required for long-read sequencing by augmenting with noise DNA and adaptive sampling. Adaptive sampling is an emerging technology of nanopore sequencing, allowing the enhanced sequencing of target DNA by selectively depleting noise DNA. In this study, we use the DNA standard of the Lambda phage genome as the noise DNA to augment samples containing low amounts of bacterial genomes (1 ng to 300 ng). The results with cost-effective flow cells indicate that NAD sequencing successfully detects the target DNA with an input quantity as low as 1 ng, and the bacterial genome ofSalmonella entericacan be assembled to 30% completion at an accuracy of 98% with an input quantity of 3 ng. With high throughput flow cells, the bacterial genome ofPseudonomas aeruginaswas assembled to near completion (99.9%) at an accuracy of 99.97% with an input quantity of 300 ng. This proof-of-concept study demonstrates the potential of NAD sequencing in enhancing the robustness of long-read sequencing with small input DNA/RNA samples with noise augmentation and adaptive sampling.
Engram Reactivation Mimics Cellular Signatures of Fear
Authors: Suthard Rebecca L. , Senne Ryan A. , Buzharsky Michelle D. , Diep Anh H. , Pyo Angela Y. , Ramirez Steve 
Published: December 2023

SummaryEngrams, or the physical substrate of memory in the brain, recruit heterogeneous cell-types. Targeted reactivation of neurons processing discrete memories drives the behavioral expression of memory, though the underlying landscape of recruited cells and their real-time responses remain elusive. To understand how artificial stimulation of fear affects intra-hippocampal neuronal and astrocytic dynamics as well as their behavioral consequences, we expressed channelrhodopsin-2 in an activity-dependent manner in dentate gyrus neurons while performing fiber photometry of both cell types in ventral CA1 across learning and memory. Neurons and astrocytes were shock-responsive, while astrocytic calcium events were uniquely modulated by fear conditioning. Notably, optogenetic stimulation of a hippocampus-mediated engram recapitulated coordinated calcium signatures time-locked to freezing that were also observed during natural fear memory recall, suggesting that engram activation alters activity across different cell types within hippocampal circuits during the behavioral expression of fear. Together, our data reveals cell-type specific hippocampal dynamics during freezing behavior and points to neuronal-astrocytic coupling as a shared mechanism enabling the natural and artificial recall of a memory.HighlightsVentral hippocampal neurons and astrocytes are active during foot shockCalcium activity is time-locked to freezing during fear conditioning and recallOptogenetic reactivation of fear recapitulates cellular signatures seen during recallReactivation of a fear memory allows prediction of freezing behavior
HELZ promotes R loop resolution to facilitate DNA double-strand break repair by homologous recombination
Authors: Haji-Seyed-Javadi Ramona , Koyen Allyson E. , Rath Sandip K. , Madden Matthew Z. , Hou Yingzi , Song Boying S. , Kenney Anna M. , Lan Li , Yao Bing , Yu David S. 
Published: December 2023

AbstractR loops are RNA-DNA hybrid containing structures involved in diverse cellular processes, including DNA double-strand break (DSB) repair. R loop homeostasis involving the formation and resolution of R loops is critical for DSB repair, and its dysregulation leads to genome instability. Here we show that the HELZ helicase promotes R loop resolution to facilitate DSB repair by homologous recombination (HR). HELZ depletion causes hypersensitivity to DSB-inducing agents, and HELZ localizes and binds to DSBs. HELZ depletion further leads to genomic instability in a R loop dependent manner and the accumulation of R loops globally and at DSBs. HELZ binds to R loops in response to DSBs and promotes their resolution, thereby facilitating HR to promote genome integrity. Our findings thus define a role for HELZ in promoting the resolution of R loops critical for DSB repair by HR.
The Natural Products Discovery Center: Release of the First 8490 Sequenced Strains for Exploring Actinobacteria Biosynthetic Diversity
Authors: Kalkreuter Edward , Kautsar Satria A. , Yang Dong , Bader Chantal D. , Teijaro Christiana N. , Fluegel Lucas L. , Davis Christina M. , Simpson Johnathon R. , Lauterbach Lukas , Steele Andrew D. , Gui Chun , Meng Song , Li Gengnan , Viehrig Konrad , Ye Fei , Su Ping , Kiefer Alexander F. , Nichols Angela , Cepeda Alexis J. , Yan Wei , Fan Boyi , Jiang Yanlong , Adhikari Ajeeth , Zheng Cheng-Jian , Schuster Layla , Cowan Tyler M. , Smanski Michael J. , Chevrette Marc G. , de Carvalho Luiz P. S. , Shen Ben 
Published: December 2023

AbstractActinobacteria, the bacterial phylum most renowned for natural product discovery, has been established as a valuable source for drug discovery and biotechnology but is underrepresented within accessible genome and strain collections. Herein, we introduce the Natural Products Discovery Center (NPDC), featuring 122,449 strains assembled over eight decades, the genomes of the first 8490 NPDC strains (7142 Actinobacteria), and the online NPDC Portal making both strains and genomes publicly available. A comparative survey of RefSeq and NPDC Actinobacteria highlights the taxonomic and biosynthetic diversity within the NPDC collection, including three new genera, hundreds of new species, and ∼7000 new gene cluster families. Selected examples demonstrate how the NPDC Portal’s strain metadata, genomes, and biosynthetic gene clusters can be leveraged using genome mining approaches. Our findings underscore the ongoing significance of Actinobacteria in natural product discovery, and the NPDC serves as an unparalleled resource for both Actinobacteria strains and genomes.
Pan-azole- and multi-fungicide-resistantAspergillus fumigatusis widespread in the United States
Authors: Celia-Sanchez BN , Mangum B , Gómez Londoño LF , Wang C , Shuman B , Brewer MT , Momany M 
Published: December 2023

AbstractAspergillus fumigatusis an important global fungal pathogen of humans. Azole drugs are among the most effective treatments forA. fumigatusinfection. Azoles are also widely used in agriculture as fungicides against fungal pathogens of crops. Azole-resistantA. fumigatushas been increasing in Europe and Asia for two decades where clinical resistance is thought to be driven by agricultural use of azole fungicides. The most prevalent mechanisms of azole resistance inA. fumigatusare tandem repeats (TR) in thecyp51Apromoter coupled with mutations in the coding region which result in resistance to multiple azole drugs (pan-azole resistance). Azole-resistantA. fumigatushas been isolated from patients in the United States (U.S.), but little is known about its environmental distribution. To better understand the distribution of azole-resistantA. fumigatusin the U.S., we collected isolates from agricultural sites in 8 states and tested 202 isolates for sensitivity to azoles. We found azole-resistantA. fumigatusin agricultural environments in 7 states showing that it is widespread in the U.S. We sequenced environmental isolates representing the range of U.S. sample sites and compared them with publicly available environmental worldwide isolates in phylogenetic, principal component, and ADMIXTURE analyses. We found worldwide isolates fell into three clades and that TR-based pan-azole resistance was largely in a single clade that was strongly associated with resistance to multiple agricultural fungicides. We also found high levels of gene flow with clear recombination between two clades highlighting the potential for azole-resistance to continue spreading in the U.S.ImportanceAspergillus fumigatusis a fungal pathogen of humans that causes over 250,000 invasive infections each year. It is found in soils, plant debris and compost. Azoles are the first line of defense antifungal drugs againstA. fumigatus. Azoles are also used as agricultural fungicides to combat other fungi that attack plants. Azole-resistantA. fumigatushas been a problem in Europe and Asia for twenty years and has recently been reported in patients in the U.S. Until this study we didn’t know much about azole-resistantA. fumigatusin agricultural settings in the U.S. In this study we isolated azole-resistantA. fumigatusfrom multiple states and compared it to isolates from around the world. We show thatA. fumigatusthat is resistant to azoles and to other strictly agricultural fungicides is widespread in the U.S.
In-vivoTherapeutic Evaluation of the Wound Healing: Potential of Ethanolic Extract ofTrichilia heudelotiiLeaves in Wistar Rats
Authors: Victoria Awolola Gbonjubola , Hassan Jinadu Taiwo , Toyin Yakubu Musa , Oyetunji Oyewopo Adeoye , Aborode Abdullahi Tunde , Ayobami Onifade Isreal 
Published: December 2023

AbstractBackgroundTrichilia heudelotiibelongs to theMeliaceaefamily and is commonly used in indigenous African medicine to prevent and treat various microbial ailments.MethodsTrichilia heudelotii’sethanolic leaf extracts contains phytochemicals which was studied to demonstrate its wound-healing properties. Phytochemical screening of leaf extracts contains flavonoids, phenolics, tannins, terpenoids, saponins, and alkaloids, which play a vital part in the healing process. Overall, quantitative, and qualitative screening were performed to evaluate the therapeutic efficacy ofTrichilia heudelotii’sphytochemicals for wound treatment.ResultsThe wound-healing potency was evaluated using different concentrations of formulated oil extracts (0.5, 1.0, and 2.0g/10g) on fresh wounds inflicted on Wistar rats using the excision model. Healing capacity was assessed based on rate of wound contracting ability, time of wound closure, and epithelisation period. The results shows that leaf extract oils exhibited significant wound healing capacity (p<0.05) compared with controls. On the 18th day in the infected group using 2.0/10g extract formulated ointment, 100% wound closure was observed. On day 21, using 0.5/10g and 1.0/ 10g, extract formulated ointment compared with controls which exhibited 79% and 89%, respectively. In addition, histopathological characteristics show increased and well-organized new bands of collagen and fibroblasts in the extract formulated treatment than in the controls, which supports the wounding healing potential of the plant. This is the first report providing therapeutic evidence for the wound healing activity of ethanolic leaf extract on Wistar rats.ConclusionThis indicate the evidence that establish the traditional use ofTrichilia heudelotiiextract for treating skin infections and wounds. The results also raise the possibility of developing a commercialized medicinal product-based venture based on this extract.Graphical Abstract
Ecological and spatial overlap indicate interspecific competition during North American Canid radiation
Authors: Graciotti Rodolfo P. , Porto Lucas , Quental Tiago B. 
Published: December 2023

AbstractUnderstanding biodiversity patterns and the processes that generate them are key goals in ecology and macroevolutionary studies. Diversity-dependent models of diversification have been used to indirectly infer the relevance of interspecific competition on driving speciation and extinction dynamics. In this study, we develop a new approach that more explicitly incorporated spatial and eco-morphological overlap among species to test how interspecific competition my affect diversification dynamics at deep time. We built different metrics that capture not only species temporal coexistence, but also their coexistence in space and morphospace to test the hypothesis that an increase in the intensity of competition would result in both a decrease in speciation rate and an increase in extinction rate. We tested our predictions using the North American fossil record of the family Canidae, a group that has been extensively studied and well characterized both from the eco-morphological and paleontological points of view. We found that interspecific competition only affected diversification dynamics during the early stages of Canidae radiation, resulting only in the suppression of speciation rate at the time the clade was expanding in diversity. We found no association between the intensity of the competition and extinction dynamics as expected by a competitive model, nor an association between changes in speciation and extinction rates and changes in global temperature, suggesting that extinction dynamics might be more related to external factors, such as clade-competition. We discuss the relevance of different factors on driving diversification dynamics changes over time and how evaluating the role of interspecific competition using different metrics that better capture the intensity of competition (as opposed to diversity dependent models), might be a way forward to investigate the role of biotic interactions at deep time.
Smart Parallel Automated Cryo Electron tomography
Authors: Eisenstein Fabian , Fukuda Yoshiyuki , Danev Radostin 
Published: December 2023

AbstractIn situcryo electron tomography enables investigation of macromolecules in their native cellular environment. Data collection, however, requires an experienced operator and valuable microscope time to carefully select targets for tilt series acquisition. Here, we developed a workflow using machine learning approaches to fully automate the entire process, including lamella detection, biological feature segmentation, target selection, and tilt series acquisition, all without the need for human intervention.
ORP9-PH domain-based fluorescent reporters for visualizing phosphatidylinositol 4-phosphate dynamics in living cells
Authors: Ajiki Moeka , Yoshikawa Masaru , Miyazaki Tomoki , Kawasaki Asami , Aoki Kazuhiro , Nakatsu Fubito , Tsukiji Shinya 
Published: December 2023

AbstractFluorescent reporters that visualize phosphatidylinositol 4-phosphate (PI4P) in living cells are indispensable to elucidate the roles of this fundamental lipid in cell physiology. However, currently available PI4P reporters have limitations, such as Golgi-biased localization and low detection sensitivity. Here, we present a series of fluorescent PI4P reporters based on the pleckstrin homology (PH) domain of oxysterol-binding protein-related protein 9 (ORP9). We show that the green fluorescent protein AcGFP1-tagged ORP9-PH domain can be used as a fluorescent PI4P reporter to detect cellular PI4P across its wide distribution at multiple cellular locations, including the plasma membrane (PM), Golgi, endosomes, and lysosomes with high specificity and contrast. We also developed blue, red, and near-infrared fluorescent PI4P reporters suitable for multicolor fluorescence imaging experiments. Finally, we demonstrate the utility of the ORP9-PH domain-based reporter to visualize dynamic changes in the PI4P distribution and level in living cells upon synthetic ER–PM membrane contact manipulation and GPCR stimulation. This work offers a new set of genetically encoded fluorescent PI4P reporters that are practically useful for the study of PI4P biology.
MFSD1 in complex with its accessory subunit GLMP functions as a general dipeptide uniporter in lysosomes
Authors: Jungnickel Katharina Esther Julia , Guelle Océane , Iguchi Miharu , Dong Wentao , Kotov Vadim , Gabriel Florian , Debacker Cécile , Dairou Julien , McCort-Tranchepain Isabelle , Laqtom Nouf N. , Chan Sze Ham , Ejima Akika , Sato Kenji , Massa López David , Saftig Paul , Mehdipour Ahmad Reza , Abu-Remaileh Monther , Gasnier Bruno , Löw Christian , Damme Markus 
Published: December 2023

SummaryLysosomal degradation of macromolecules in lysosomes produces diverse small metabolites exported by specific transporters for reuse in biosynthetic pathways. Here, we deorphanized the Major Facilitator Superfamily Domain Containing 1 (MFSD1) protein, which forms a tight complex with the Glycosylated Lysosomal Membrane Protein (GLMP) in the lysosomal membrane. Untargeted metabolomics analysis of MFSD1-deficient mouse lysosomes revealed an increase in cationic dipeptides. Purified MFSD1 selectively bound diverse dipeptides, while electrophysiological, isotope tracer, and fluorescence-based studies inXenopusoocytes and proteoliposomes showed that MFSD1/GLMP acts as a uniporter for cationic and neutral dipeptides. Cryo-EM structure of the dipeptide-bound MFSD1/GLMP complex in outward-open conformation characterized the heterodimer interface and, in combination with molecular dynamics simulations, provided a structural basis for its selectivity towards diverse dipeptides. Together, our data identify MFSD1 as a general lysosomal dipeptide uniporter, providing an alternative route to recycle lysosomal proteolysis products when lysosomal amino acid exporters are overloaded.
Systematic review and meta-analysis on the effects of chronic peri-adolescent cannabinoid exposure on schizophrenia-like behaviour in rodents
Authors: Li Zhikun , Mukherjee Diptendu , Duric Bea , Austin-Zimmerman Isabelle , Trotta Giulia , Spinazzola Edoardo , Quattrone Diego , Murray Robin M , Di Forti Marta 
Published: December 2023

AbstractBackgroundThe link between cannabis use and schizophrenia is well-established in epidemiological studies, especially among adolescents with early-onset use. However, this association in rodent models is less clear. This meta-analysis examined the effects of adolescent cannabinoid exposure on distinct schizophrenia-like behaviours in rodents and how experimental variations influence outcomes.MethodsFollowing a pre-registered protocol (CRD42022338761), we searched PubMed, Ovid Medline, Embse and APA PsychInfo for English-language original studies until 2022. We synthesised data from experiments on schizophrenia-like behaviour in rats and mice after repeated peri-pubertal (onset between P23-P45) cannabinoid exposure. Risk of bias was assessed using the SYRCLE’s tool.ResultsWe included 291 experiments from 91 articles across 9 behavioural tests. We found meta-analytic evidence supporting that CB1R agonists, both natural and synthetic, elicited broad schizophrenia-like behavioural alterations, including impaired working memory (g =-0.58 [CI: -1.00,-0.16]), novel object recognition (g=-0.63 [CI: -0.97,-0.30]), novel object location recognition (g=-0.70 [CI: -1.22,-0.28]), social motivation (g=-0.40 [CI: -0.63, -0.16]), pre-pulse inhibition (g=-0.48 [CI: -0.89, -0.08]), and sucrose preference (g=-0.92 [CI: -1.87,0.04]). By contrast, effects on novelty-induced locomotion were negligible. Subgroup analyses revealed similar effects across sexes and species. Substantial variance in the protocols and moderate-to-high heterogeneity in behavioural outcomes were observed. We found CBD may attenuate novelty-induced locomotion in an open field and enhance fear memory recall, but data was limited.DiscussionThis is the first meta-analysis to comprehensively assess the link between cannabinoids and schizophrenia-like behaviours in rodents. Our results support epidemiological links between early cannabis use and schizophrenia-like phenotypes, confirming the utility of animal models. Standardising protocols will optimise models to strengthen reproducibility and comparisons, our work provides a framework for refining rodent models to elucidate biological pathways linking cannabis and schizophrenia.