bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assembly of gut-derived bacterial communities follows “early-bird” resource utilization dynamics
Authors: Aranda-Díaz Andrés , Willis Lisa , Nguyen Taylor H. , Ho Po-Yi , Vila Jean , Thomsen Tani , Chavez Taylor , Yan Rose , Yu Feiqiao Brian , Neff Norma , Sanchez Alvaro , Estrela Sylvie , Huang Kerwyn Casey 
Published: January 2023

AbstractDiet can impact host health through changes to the gut microbiota, yet we lack mechanistic understanding linking nutrient availability and microbiota composition. Here, we use thousands of microbial communities culturedin vitrofrom human feces to uncover simple assembly rules and develop a predictive model of community composition upon addition of single nutrients from central carbon metabolism to a complex medium. Community membership was largely determined by the donor feces, whereas relative abundances were determined by the supplemental carbon source. The absolute abundance of most taxa was independent of the supplementing nutrient, due to the ability of fast-growing organisms to quickly exhaust their niche in the complex medium and then exploit and monopolize the supplemental carbon source. Relative abundances of dominant taxa could be predicted from the nutritional preferences and growth dynamics of species in isolation, and exceptions were consistent with strain-level variation in growth capabilities. Our study reveals that community assembly follows simple rules of nutrient utilization dynamics and provides a predictive framework for manipulating gut commensal communities through nutritional perturbations.
Activation of thePlasmodiumegress effector subtilisin-like protease 1 is achieved by plasmepsin X destruction of the propiece
Authors: Mukherjee Sumit , Nasamu Armiyaw S. , Rubiano Kelly , Goldberg Daniel E. 
Published: January 2023

AbstractFollowing each round of replication, daughter merozoites of the malaria parasitePlasmodium falciparumescape (egress) from the infected host red blood cell (RBC) by rupturing the parasitophorous vacuole membrane (PVM) and the RBC membrane (RBCM). A proteolytic cascade orchestrated by the parasite’s serine protease, subtilisin-like protease 1 (SUB1) regulates the membrane breakdown. SUB1 activation involves primary auto-processing of the 82 kDa zymogen to a 54 kDa (p54) intermediate that remains bound to its inhibitory propiece (p31) post cleavage. A second processing step converts p54 to the terminal 47 kDa (p47) form of SUB1. Although the aspartic protease plasmepsin X (PM X) has been implicated in the activation of SUB1, the mechanism remains unknown. Here, we show that upon knockdown of PM X the inhibitory p31/p54 complex of SUB1 accumulates in the parasites. Using recombinant PM X and SUB1, we show that PM X can directly cleave both p31 and p54. We have mapped the cleavage sites on recombinant p31. Furthermore, we demonstrate that the conversion of p54 to p47 can be effected by cleavage at either a SUB1 or PM X cleavage site that are adjacent to one another. Importantly once the p31 is removed, p54 is fully functional inside the parasites suggesting that the conversion to p47 is dispensable for SUB1 activity. Relief of propiece inhibition via a heterologous protease is a novel mechanism for subtilisin activation.Significance StatementMalaria parasites replicate inside a parasitophorous vacuole within the host red blood cells. Exit of mature progeny from the infected host cells is essential for further dissemination. Parasite exit is a highly regulated, explosive process that involves membrane breakdown. To do this, the parasite utilizes a serine protease, called the subtilisin-like protease 1 or SUB1 that proteolytically activates various effector proteins. SUB1 activity is dependent on an upstream protease, called plasmepsin X (PM X), although the mechanism was unknown. Here we describe the molecular basis for PM X mediated SUB1 activation. PM X proteolytically degrades the inhibitory segment of SUB1, thereby activating it. Involvement of a heterologous protease is a novel mechanism for subtilisin activation.
A nanoparticle priming agent reduces cellular uptake of cell-free DNA and enhances the sensitivity of liquid biopsies
Authors: Martin-Alonso Carmen , Tabrizi Shervin , Xiong Kan , Blewett Timothy , Patel Sahil , An Zhenyi , Sridhar Sainetra , Bekdemir Ahmet , Shea Douglas , Amini Ava P. , Wang Shih-Ting , Kirkpatrick Jesse , Rhoades Justin , Golub Todd R. , Love J. Christopher , Adalsteinsson Viktor A. , Bhatia Sangeeta N. 
Published: January 2023

AbstractLiquid biopsies are enabling minimally invasive monitoring and molecular profiling of diseases across medicine, but their sensitivity remains limited by the scarcity of cell-free DNA (cfDNA) in blood. Here, we report an intravenous priming agent that is given prior to a blood draw to increase the abundance of cfDNA in circulation. Our priming agent consists of nanoparticles that act on the cells responsible for cfDNA clearance to slow down cfDNA uptake. In tumor-bearing mice, this agent increases the recovery of circulating tumor DNA (ctDNA) by up to 60-fold and improves the sensitivity of a ctDNA diagnostic assay from 0% to 75% at low tumor burden. We envision that this priming approach will significantly improve the performance of liquid biopsies across a wide range of clinical applications in oncology and beyond.
DBDA matrix increases ion abundance of fatty acids and sulfatides in MALDI-TOF and mass spectrometry imaging studies
Authors: Khamidova Nigina , Pergande Melissa R. , Pathmasiri Koralege C. , Khan Rida , Mohr Justin T. , Cologna Stephanie M. 
Published: January 2023

AbstractMALDI-TOF MS is a powerful tool to analyze biomolecules owing to its soft ionization nature and generally results in simple spectra of singly charged ions. Moreover, implementation of the technology in imaging mode provides a means to spatially map analytes in situ. Recently, a new matrix, DBDA (N1,N4-dibenzylidenebenzene-1,4-diamine) was reported to facilitate the ionization of free fatty acids in the negative ion mode. Building on this finding, we sought to implement DBDA for MALDI mass spectrometry imaging studies in brain tissue and successfully map oleic acid, palmitic acid, stearic acid, docosahexaenoic acid and arachidonic acid using mouse brain sections. Moreover, we hypothesized that DBDA would provide superior ionization for sulfatides, a class of sulfolipids, with multiple biological functions. Herein we also demonstrate that DBDA is ideal for MALDI mass spectrometry imaging of fatty acids and sulfatides in brain tissue sections. Additionally, we show enhanced ionization of sulfatides using DBDA compared to three different traditionally used MALDI matrices. Together these results provide new opportunities for studies to measure sulfatides by MALDI-TOF MS including in imaging modes.
Neuronal expression of herpes simplex virus type-1 VP16 protein induces pseudorabies virus escape from silencing and reactivation by activating Jun
Authors: Hsu Zhi-Shan , Engel Esteban A. , Enquist Lynn W. , Koyuncu Orkide O. 
Published: January 2023

AbstractAlpha herpesvirus (α-HV) particles enter their hosts from mucosal surfaces and efficiently maintain fast transport in peripheral nervous system (PNS) axons to establish infections in the peripheral ganglia. The path from axons to distant neuronal nuclei is challenging to dissect due to the difficulty of monitoring early events in a dispersed neuron culture model. We have established well-controlled, reproducible, and reactivateable latent infections in compartmented rodent neurons by infecting physically isolated axons with a small number of viral particles. This system not only recapitulates the physiological infection route, but also facilitates independent treatment of isolated cell bodies or axons. Consequently, this system enables study not only of the stimuli that promote reactivation, but also the factors that regulate the initial switch from productive to latent infection. Adeno associated virus (AAV) mediated expression of herpes simplex type 1 (HSV-1) VP16 alone in neuronal cell bodies enabled the escape from silencing of incoming pseudorabies virus (PRV) genomes. Furthermore, expression of HSV VP16 alone reactivated a latent PRV infection in this system. Surprisingly, expression of PRV VP16 protein supported neither PRV escape from silencing nor reactivation. We compared transcription transactivation activity of both VP16 proteins in primary neurons by RNA sequencing and found that these homolog viral proteins produce different gene expression profiles. AAV transduced HSV VP16 specifically induced expression of proto-oncogenes including Jun and Pim2. In addition, HSV VP16 induces phosphorylation of Jun in neurons, and when this activity is inhibited, escape of PRV silencing is dramatically reduced.
Contrasting patterns of somatic mutations in neurons and glia reveal differential predisposition to disease in the aging human brain
Authors: Ganz Javier , Luquette Lovelace J. , Bizzotto Sara , Bohrson Craig L. , Jin Hu , Miller Michael B. , Zhou Zinan , Galor Alon , Park Peter J. , Walsh Christopher A. 
Published: January 2023

SUMMARYCharacterizing the mechanisms of somatic mutations in the brain is important for understanding aging and disease, but little is known about the mutational patterns of different cell types. We performed whole-genome sequencing of 71 oligodendrocytes and 51 neurons from neurotypical individuals (0.4 to 104 years old) and identified >67,000 somatic single nucleotide variants (sSNVs) and small insertions and deletions (indels). While both cell types accumulate mutations with age, oligodendrocytes accumulate sSNVs 69% faster than neurons (27/year versus 16/year) whereas indels accumulate 42% slower (1.8/year versus 3.1/year). Correlation with single-cell RNA and chromatin accessibility from the same brains revealed that oligodendrocyte mutations are enriched in inactive genomic regions and are distributed similarly to mutations in brain cancers. In contrast, neuronal mutations are enriched in open, transcriptionally active chromatin. These patterns highlight differences in the mutagenic processes in glia and neurons and suggest cell type-specific, age-related contributions to neurodegeneration and oncogenesis.
SMIM36, a novel and conserved microprotein, is involved in retinal lamination in zebrafish
Authors: Sharma Surbhi , Ramasamy Soundhar , Khan Yasmeen , Joshi Dheeraj Chandra , Pillai Beena 
Published: January 2023

AbstractMicroproteins are small proteins comprising 2 to 200 amino acids, arising from small Open Reading Frames (smORFs). They are found in different parts of the cell and regulate basic molecular processes like DNA replication, repair, transcription and recombination. SMIM or SMall Integral Membrane proteins are novel, largely uncharacterized, members to the class of microproteins defined by the presence of a transmembrane domain. The retinal transcriptome of zebrafish, reported previously by our group, revealed several novel mRNA transcripts that show oscillating expression in a diurnal manner. Here, we show that one of these transcripts encodes the zebrafish homolog of the human SMIM36 protein, which has not been functionally characterised. This highly conserved microprotein is expressed in the human and zebrafish retina, and efficiently translated in cell lines. Using single-cell RNA-seq datasets, we found that it is expressed in the bipolar cells, rods and Muller glia in the human retina. The knockdown of SMIM36 using splice-block morpholino caused microphthalmia and defects in the retinal layers in zebrafish. Therefore, we show the role of a microprotein in the neural retina thus paving the way for future studies on the role of SMIM proteins in retinal disorders.
At-home saliva sampling in healthy adults using CandyCollect, a lollipop-inspired device
Authors: Tu Wan-chen , McManamen Anika M. , Su Xiaojing , Jeacopello Ingrid , Takezawa Meg G. , Hieber Damielle L. , Hassan Grant W. , Lee Ulri N. , Anana Eden V. , Locknane Mason P. , Stephenson Molly W. , Shinkawa Victoria A. M. , Wald Ellen R. , DeMuri Gregory P. , Adams Karen , Berthier Erwin , Thongpang Sanitta , Theberge Ashleigh B. 
Published: January 2023

ABSTRACTRespiratory infections are common in children, and there is a need for user-friendly collection methods. Here, we performed the first human subjects study using the CandyCollect device, a lollipop inspired saliva collection device.1We showed the CandyCollect device can be used to collect salivary bacteria from healthy adults usingStreptococcus mutansandStaphylococcus aureusas proof-of-concept commensal bacteria. We enrolled healthy adults in a nationwide (USA) remote study in which participants were sent study packages containing CandyCollect devices and traditional commercially available oral swabs and spit tubes. Participants sampled themselves at home, completed usability and user preference surveys, and mailed the samples back to our laboratory for analysis by qPCR. Our results showed that for participants in which a given bacterium (S. mutansorS. aureus) was detected in one or both of the commercially available methods (oral swab and/or spit tubes), CandyCollect devices had a 100% concordance with the positive result (n=14 participants). Furthermore, the CandyCollect device was ranked the highest preference sampling method among the three sampling methods by 26 participants surveyed (combining survey results across two enrollment groups). We also showed that the CandyCollect device has a shelf life of up to 1 year at room temperature, a storage period that is convenient for clinics or patients to keep the CandyCollect device and use it any time. Taken together, we have demonstrated that the CandyCollect is a user-friendly saliva collection tool that has the potential to be incorporated into diagnostic assays in clinic visits and telemedicine.For Table of Contents Only
Insm1 regulates the development of mTECs and immune tolerance
Authors: Tao Wehuai , Wei Yiqiu , Ye Zhihuan , Wang Jianxue , Yang Weixin , Yu Guoxing , Xiong Jieyi , Jia Shiqi 
Published: January 2023

AbstractTheInsm1gene encodes a zinc finger protein with known functions in neuroendocrine cells and neurons. Here we characterized the expression and function ofInsm1in medullary thymic epithelial cells (mTECs).Insm1is co-expressed with Aire in majority of Insm1 or Aire positive cells, while a few Insm1 positive cells did not express Aire. Mutation ofInsm1impair the expression ofAireand the generation of normal numbers of Aire-expressing mTECs during development. We detected downregulation of genes that expressed specifically in Aire-expressing mTEC and mimetic cells inInsm1mutant mTECs. Conversely, whenInsm1was overexpressed in thymic epithelial cellsin vivo, the size of the mTECs compartment was enlarged and the expression ofAireand genes expressed specifically in the neuroendocrine mimetic cells were increased. Mechanistically, Insm1 bound DNA in mTECs and the majority of the Insm1 binding sites were co-occupied by Aire. These Insm1 binding sites were enriched on super-enhancer regions and thus may contributed to remoted regulation. Both, mice with a thymus-specific mutation inInsm1or nude mice transplanted withInsm1mutant thymus, displayed autoimmune responses in multiple peripheral tissues. Together, our data demonstrate a role of Insm1 in development of mTECs and immune tolerance.
PIF transcriptional regulators are required for rhythmic stomatal movements
Authors: Rovira Arnau , Veciana Nil , Locascio Antonella , Yenush Lynne , Leivar Pablo , Monte Elena 
Published: January 2023

AbstractStomata govern the gaseous exchange between the leaf and the external atmosphere, and their function is essential for photosynthesis and the global carbon and oxygen cycles. Rhythmic stomata movements in daily dark/light cycles prevent water loss at night and allow CO2uptake during the day. How the actors involved are transcriptionally regulated and how this might contribute to rhythmicity is largely unknown. Here, we show that morning stomata opening depends on the previous night period. The transcription factors PHYTOCHROMEINTERACTING FACTORS (PIFs) accumulate at the end of the night and directly induce the guard cell-specific K+channelKAT1. Remarkably, PIFs and KAT1 are required for blue light-induced stomata opening. Together, our data establish a molecular framework for daily rhythmic stomatal movements under well-water conditions, whereby PIFs are required for accumulation of KAT1 at night, which upon activation by blue light in the morning leads to the K+intake driving stomata opening.
A temporal atlas and response to nitrate availability of 3D root system architecture in diverse pennycress (Thlaspi arvenseL.) accessions
Authors: Griffiths Marcus , Liu Alexander E , Gunn Shayla L , Mutan Nida M , Morales Elisa Y , Topp Christopher N 
Published: January 2023

1AbstractRoots have a central role in plant resource capture and are the interface between the plant and the soil that affect multiple ecosystem processes. Field pennycress (Thlaspi arvenseL.) is a diploid annual cover crop species that has potential utility for reducing soil erosion and nutrient losses; and has rich seeds (30-35% oil) amenable to biofuel production and as a protein animal feed. The objective of this research was to (1) precisely characterize root system architecture and development, (2) understand adaptive responses of pennycress roots to nitrate nutrition, (3) and determine genotypic variance available in root development and nitrate plasticity. Using a root imaging and analysis pipeline, 4D pennycress root system architecture was characterized under four nitrate regimes (from zero to high nitrate concentration) across four time points (days 5, 9, 13, and 17 after sowing). Significant nitrate condition response and genotype interactions were identified for many root traits with greatest impact on lateral root traits. In trace nitrate conditions a greater lateral root count, length, interbranch density, and a steeper lateral root angle was observed compared to high nitrate conditions. Genotype-by-nitrate condition interaction was observed for root width, width:depth ratio, mean lateral root length, and lateral root density. These results illustrate root trait variance available in pennycress accessions that could be useful targets for breeding of improved nitrate responsive cover crops for greater productivity, resilience, and ecosystem service.
Hypometabolism to survive the long polar night in the diatomFragilariopsis cylindrus
Authors: Joli Nathalie , Concia Lorenzo , Mocaer Karel , Guterman Julie , Laude Juliette , Guerin Sebastien , Sciandra Theo , Bruyant Flavienne , Ait-Mohamed Ouardia , Beguin Marine , Forget Marie-Helene , Bourbousse Clara , Lacour Thomas , Bailleul Benjamin , Tremblay Jean-Eric , Campbell Douglas , Lavaud Johan , Schwab Yannick , Babin Marcel , Bowler Chris 
Published: January 2023

AbstractDiatoms, the major eukaryotic phytoplankton in polar regions, are essential to sustain Arctic and Antarctic ecosystems. As such, it is fundamental to understand the physiological mechanisms and associated molecular basis of their resilience to the long polar night. Here, we report an integrative approach revealing that in prolonged darkness, diatom cells enter a state of quiescence associated with reduced metabolic and transcriptional activity during which no cell division occurs. We propose that minimal energy is provided by respiration and degradation of protein, carbohydrate, and lipid stores and that homeostasis is maintained by autophagy in prolonged darkness. We also report internal structural changes that manifest the morphological acclimation of cells to darkness. Our results further indicate that immediately following a return to light, diatom cells are able to use photoprotective mechanisms and rapidly resume photosynthesis. Cell division resumed rates similar to those before darkness. Our study demonstrates the remarkable robustness of polar diatoms to prolonged darkness at low temperatures.Graphical abstractTeaserTo survive the long winter, polar diatoms slow down metabolism and express genes to assure survival following return to light.
Bioorthogonal chemical labelling of endogenous neurotransmitter receptors in living mouse brains
Authors: Nonaka Hiroshi , Sakamoto Seiji , Shiraiwa Kazuki , Ishikawa Mamoru , Tamura Tomonori , Okuno Kyohei , Kiyonaka Shigeki , Susaki Etsuo A. , Shimizu Chika , Ueda Hiroki R. , Kakegawa Wataru , Arai Itaru , Yuzaki Michisuke , Hamachi Itaru 
Published: January 2023

AbstractNeurotransmitter receptors are essential components of synapses for communication between neurons in the brain. Because the spatiotemporal expression profiles and dynamics of neurotransmitter receptors involved in many functions are delicately governed in the brain,in vivoresearch tools with high spatiotemporal resolution for receptors in intact brains are highly desirable. Covalent chemical labelling of proteins without genetic manipulation is now a powerful method for analyzing receptorsin vitro. However, selective target receptor labelling in the brain has not yet been achieved. This study shows that ligand-directed alkoxyacylimidazole (LDAI) chemistry can be used to selectively tether synthetic probes to target endogenous receptors in living mouse brains. The reactive LDAI reagents with negative charges were found to diffuse well over the whole brain and could selectively label target endogenous receptors, including AMPAR, NMDAR, mGlu1, and GABAAR. This simple and robust labelling protocol was then used for various applications: three-dimensional spatial mapping of endogenous receptors in the brains of healthy and disease-model mice; multi-colour receptor imaging; and pulse-chase analysis of the receptor dynamics in postnatal mouse brains. Here, results demonstrated that bioorthogonal receptor modification in living animal brains may provide innovative molecular tools that contribute to the in-depth understanding of complicated brain functions.
Alternative equations and “pseudo-statistical” approaches that enhance the precision of initial rates for the determination of kinetic parameters
Authors: Udema Ikechukwu I. 
Published: January 2023

AbstractA burning concern among researchers studying enzyme kinetics has been ways of improving the accuracy of initial rates (v) with much greater precision. The goal of this study was to establish a formal (mathematical) way of achieving more accuratevvalues in enzyme assay. By adopting Bernfeld method of assay, thevvalues generated and other values in the literature were explored with two main objectives:1) to derive equations for a correctional calculation of initial rates and for the calculation of Michaelis-Menten (MM) parameters and 2) to evaluate the derived equations. The results of study showed that the maximum velocity (Vmax) and the MM constant (KM) obtained from a robust nonlinear regression (RNR) usingvvalues in the literature were respectively between 21 and 26-fold and 6.56 to 61.2-fold greater than values generated from other method such as double reciprocal plot (drp), reciprocal variant of direct linear plot (RVDLP), and new method (z-model) derived based on MM equation; theVmaxandKMvalues (for alpha-amylase) calculated based on the RVDLP using the uncorrectedvvalues were respectively 1.26- and 1.264-fold greater than the values using correctedvvalues; based on thezmethod, theVmaxandKMvalues using the uncorrectedvvalues were 179.8- and 9.35-fold greater than the values using their corrected counterparts. In conclusion, the erroneous initial rates can be corrected using new equations before fitting RNR, RVDLP, drp, and any other equation to the correctedvvalues for the determination of MM parameters.Graphical Abstract figureThe implication of the result in b (i) is that theVmaxandKMshould either be a negative value or infinite value according to the equations unlike b (ii).