bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determining the inherent reaction-diffusion properties of actin-binding proteins in cells by incorporating genetic engineering to FRAP-based framework
Authors: Saito Takumi , Matsunaga Daiki , Matsui Tsubasa S. , Noi Kentaro , Deguchi Shinji 
Published: September 2020

AbstractProteins in cells undergo repeated association to other molecules, thereby reducing the apparent extent of their intracellular diffusion. While much effort has been made to analytically decouple these combined effects of pure diffusion and chemical reaction, it is difficult to attribute the measured quantities to the nature of specific domains of the probed proteins particularly if, as is often the case, the protein has multiple domains to independently interact with the same types but different molecules. Motivated by the common goal in cell signaling research aimed at identifying the protein domains responsible for particular intermolecular interactions, here we describe a new approach to determining the domain-level reaction and pure diffusion properties. To validate this methodology, we apply it to transgelin-2, an actin-binding protein whose intracellular dynamics remains elusive. We develop a fluorescence recovery after photobleaching (FRAP)-based framework, in which comprehensive combinations of domain-deletion mutants are created with genetic engineering, and the difference among the mutants in FRAP response is analyzed. We demonstrate that transgelin-2 in cells interacts with F-actin via two separate domains, and the chemical equilibrium constant of the interaction is determined at the individual domain levels. Its pure diffusion properties independent of the association to F-actin is also obtained. This approach requires some effort to construct the mutants, but instead enables in situ domain-level determination of the physicochemical properties, which will be useful, as specifically shown here for transgelin-2, in addressing the signaling mechanism of cellular proteins.
Overlapping activities of ELAV/Hu RNA binding proteins specify multiple neural alternative splicing programs
Authors: Lee Seungjae , Zhang Binglong , Wei Lu , Goering Raeann , Majumdar Sonali , Taliaferro J. Matthew , Lai Eric C. 
Published: September 2020

AbstractELAV/Hu factors are conserved RNA binding proteins that play diverse roles in mRNA processing and regulation. The founding member,DrosophilaElav, was recognized as a vital neural factor 35 years ago. Nevertheless, still little is known about its impacts on the transcriptome, and potential functional overlap with its paralogs. Building on our recent findings that neural-specific lengthened 3’ UTR isoforms are co-determined by ELAV/Hu factors, we address their impacts on splicing. In ectopic contexts, all three members (Elav, Fne and Rbp9) induce similar and broad changes to cassette exon and alternative last exon (ALE) splicing. Reciprocally, double mutants ofelav/fne, but notelavalone, have opposite effects on both types of mRNA processing events in the larval CNS. Accordingly, whilefnemutants are normal,fneloss strongly enhanceselavmutants with respect to neuronal differentiation. While manipulation ofDrosophilaELAV/Hu factors induces both exon skipping and inclusion, motif analysis indicates their major direct effects are to suppress cassette exon usage. Moreover, we find direct analogies in their roles in global promotion of distal ALE splicing and terminal 3’ UTR extension, since both involve local suppression of proximal polyadenylation signals via ELAV/Hu binding sites downstream of cleavage sites. Finally, we provide evidence for analogous co-implementation of distal ALE and APA lengthening programs in mammalian neurons, linked to ELAV/Hu motifs downstream of regulated polyadenylation sites. Overall, ELAV/Hu proteins orchestrate multiple conserved programs of neuronal mRNA processing by suppressing alternative exons and polyadenylation sites.
Antioxidant enriched fraction fromPueraria tuberosaalleviates ovariectomized-induced osteoporosis in rats, and inhibits growth of breast and ovarian cancer cell linesin vitro
Authors: Satpathy Swaha , Patra Arjun , Hussain Muhammad Delwar , Kazi Mohsin , Aldughaim Mohammed S , Ahirwar Bharti 
Published: September 2020

AbstractPueraria tuberosa(P. tuberosa), known as Indian Kudzu belongs to family Fabaceae and it is solicited as “Rasayana” drugs in Ayurveda. In the present study, we analyzed the efficacy an antioxidant enriched fraction (AEF) from the tuber extract ofP. tuberosaagainst menopausal osteoporosis and breast and ovarian cancer cell lines. The AEF fromP. tuberosawas identified by determining phenolic composition (total phenolic and flavonoid amount). Antioxidant property (in vitroassays) was also carried out followed by analysis of the AEF for its antiosteoporotic and anticancer potentials. Antiosteoporotic activity of AEF was investigated in ovariectomy-induced osteoporosis in rats andin vitroanticancer activity by MTT assay. Also, the GC/MS analysis of AEF was performed to determine various phytoconstituents. A docking analysis was performed to verify the interaction of bioactive molecules with estrogen receptors (ERs). Ethyl acetate fraction of the mother extract was proved as the AEF. AEF significantly improved various biomechanical and biochemical parameters in a dose dependent manner in the ovariectomized animals. AEF also controlled the increased body weight and decreased uterus weight following ovariectomy. Histopathology of femur revealed the restoration of typical bone structure and trabecular width in ovariectomized animals after AEF and raloxifene treatment. AEF also exhibitedin vitrocytotoxicity in breast (MCF-7 and MDA-MB-231) and ovarian (SKOV-3) cancer cells. Further, genistein and daidzein exhibited a high affinity towards both estrogen receptors (α and β) in docking study revealing the probable mechanism of the antiosteoporotic activity. GC/MS analysis confirmed the presence of bioactive molecules such as stigmasterol, β-sitosterol, and stigmasta-3,5-dien-7-one. The observations of this study vindicate the potency of AEF fromP. tuberosain the treatment of menopausal osteoporosis and cancer.
A comparative genomics and immunoinformatics approach to identify epitope-based peptide vaccine candidates against bovine hemoplasmosis
Authors: Quiroz-Castañeda Rosa Estela , Aguilar-Díaz Hugo , Flores-García Diana Laura , Martínez-Ocampo Fernando , Amaro-Estrada Itzel 
Published: September 2020

AbstractMycoplasma wenyoniiand ‘CandidatusMycoplasma haemobos’ have been described as major hemoplasmas that infect cattle worldwide. Currently, three bovine hemoplasma genomes are known. The aim of this work was to know the main genomic characteristics and the evolutionary relationships between hemoplasmas, as well as to provide a list of epitopes identified by immunoinformatics that could be used as vaccine candidates against bovine hemoplasmosis. So far, there is not a vaccine to prevent this disease that impact economically in cattle production around the world.In this work, we used comparative genomics to analyze the genomes of the hemoplasmas so far reported. As a result, we confirm that ‘Ca. M haemobos’ INIFAP01 is a divergent species fromM. wenyoniiINIFAP02 andM. wenyoniiMassachusetts. Although both strains ofM. wenyoniihave genomes with similar characteristics (length, G+C content, tRNAs and position of rRNAs) they have different structures (alignment coverage and identity of 51.58 and 79.37%, respectively).The correct genomic characterization of bovine hemoplasmas, never studied before, will allow to develop better molecular detection methods, to understand the possible pathogenic mechanisms of these bacteria and to identify epitopes sequences that could be used in the vaccine design.
Applications of spatial models to ordinal data
Authors: Xu Zhanyou , Cannon Steven B. , Beavis William D. 
Published: September 2020

AbstractModels have been developed to account for heterogeneous spatial variation in field trials. These spatial models have been shown to successfully increase the quality of phenotypic data resulting in improved effectiveness of selection by plant breeders. The models were developed for continuous data types such as grain yield and plant height, but data for most traits, such as in iron deficiency chlorosis (IDC), are recorded on ordinal scales. Is it reasonable to make spatial adjustments to ordinal data by simply applying methods developed for continuous data? The objective of the research described herein is to evaluate methods for spatial adjustment on ordinal data, using soybean IDC as an example. Spatial adjustment models are classified into three different groups: group I, moving average grid adjustment; group II, geospatial autoregressive regression (SAR) models; and group III, tensor product penalized P-splines. Comparisons of eight models sampled from these three classes demonstrate that spatial adjustments depend on severity of field heterogeneity, the irregularity of the spatial patterns, and the model used. SAR models generally produce better performance metrics than other classes of models. However, none of the eight evaluated models fully removed spatial patterns indicating that there is a need to either adjust existing models or develop novel models for spatial adjustments of ordinal data collected in fields exhibiting discontinuous transitions between heterogeneous patches.
Mecamylamine inhibits seizure-like activity in CA1-CA3 hippocampus through antagonism to nicotinic receptors
Authors: Zapukhliak Olha , Netsyk Olga , Romanov Artur , Maximyuk Oleksandr , Oz Murat , Holmes Gregory L. , Krishtal Oleg , Isaev Dmytro 
Published: September 2020

AbstractCholinergic modulation of hippocampal network function is implicated in multiple behavioral and cognitive states. Activation of nicotinic and muscarinic acetylcholine receptors affects neuronal excitability, synaptic transmission and rhythmic oscillations in the hippocampus. In this work, we study the ability of the cholinergic system to sustain hippocampal epileptiform activity independently from glutamate and GABA transmission. Simultaneous CA3 and CA1 field potential recordings were obtained during the perfusion of hippocampal slices with the aCSF containing AMPA, NMDA and GABA receptor antagonists. Under these conditions, recurrent field discharges synchronous between CA3 and CA1 were recorded. Field discharges were blocked by addition of calcium-channel blocker Cd2+and disappeared in CA1 after a surgical cut between CA3 and CA1. Cholinergic antagonist mecamylamine abolished CA3-CA1 synchronous field discharges, while antagonists of α7 and α4β2 nAChRs – MLA and DhβE had no effect. Our results suggest that activation of nicotinic acetylcholine receptors is able to sustain CA3-CA1 synchronous epileptiform activity independently from AMPA NMDA and GABA transmission. In addition, mecamylamine but not α7 and α4β2 nAChRs antagonists reduce bicuculline-induced seizure-like activity. The ability of mecamylamine to decrease hippocampal network synchronization might be associated with its therapeutic effects in a wide variety of CNS disorders including addiction, depression and anxiety.
Temporal scaling inC. eleganslarval development
Authors: Filina Olga , Haagmans Rik , van Zon Jeroen S. 
Published: September 2020

AbstractIt is essential that correct temporal order of cellular events is maintained during animal development. During post-embryonic development, the rate of development depends on external conditions, such as food availability, diet and temperature. How timing of cellular events is impacted when the rate of development is changed at the organism-level is not known. We used a novel time-lapse microscopy approach to simultaneously measure timing of oscillatory gene expression, hypodermal stem cell divisions and cuticle shedding in individual animals, duringC. eleganslarval development from hatching to adulthood. This revealed strong variability in timing between isogenic individuals under the same conditions. However, this variability obeyed ‘temporal scaling’, meaning that events occurred at the same time when measured relative to the duration of development in each individual. We also observed pervasive changes in population-averaged timing when temperature, diet or genotype were varied, but with larval development divided in ‘epochs’ that differed in how the timing of events was impacted. Yet, these variations in timing were still explained by temporal scaling when timing was rescaled by the duration of the respective epochs in each individual. Surprisingly, timing obeyed temporal scaling even in mutants lackinglin-42/Period, presumed a core regulator of timing of larval development, that exhibited strongly delayed, heterogeneous timing and growth arrest. Timing of larval development is likely controlled by timers based on protein degradation or protein oscillations, but such mechanisms do not inherently generate temporal scaling. Hence, our observations will put strong constraints on models to explain timing of larval development.
CD8+T cell priming in oral mucosa-draining lymph nodes supports systemic immunity
Authors: de Albuquerque Juliana Barreto , von Werdt Diego , Francisco David , van Geest Geert , Altenburger Lukas M. , Abe Jun , Ficht Xenia , Iannacone Matteo , Bruggmann Remy , Mueller Christoph , Stein Jens V. 
Published: September 2020

AbstractThe gastrointestinal (GI) tract constitutes an essential barrier against ingested pathogens. While immune reactions are well-studied in the lower GI tract, it remains unclear how adaptive immune responses are initiated during microbial challenge of the oral mucosa, the primary site of pathogen encounter in the upper GI tract. Here, we identify mandibular lymph nodes (mandLN) as sentinel lymphoid organs that collect orally administeredListeria monocytogenes(Lm), leading to local CD8+T cell activation. In contrast to CD8+T effector cells (TEFF) generated in mesenteric lymph nodes, mandLN CD8+TEFFlacked a gut-seeking phenotype but contributed to systemic host protection. Accordingly, mandLN stromal and dendritic cells expressed low levels of enzymes required for gut homing imprinting. Our findings extend the concept of regional specialization of immune responses along the length of the GI tract, with mandLN acting as oral lymph-draining counterparts of intestinal lymph-draining LN of the lower GI tract.SummaryListeria monocytogenesingestion leads to priming of cytotoxic T cells in oral mucosa draining mandibular lymph nodes, which contribute to systemic host protection.
The gut microbiome stability of a butterflyfish is disrupted on severely degraded Caribbean coral reefs
Authors: Clever Friederike , Sourisse Jade M. , Preziosi Richard F. , Eisen Jonathan A. , Guerra E. Catalina Rodriguez , Scott Jarrod J. , Wilkins Laetitia G.E. , Altieri Andrew H. , McMillan W. Owen , Leray Matthieu 
Published: September 2020

AbstractEnvironmental degradation has the potential to alter key mutualisms that underline the structure and function of ecological communities. While it is well recognized that the global loss of coral reefs alters fish communities, the effects of habitat degradation on microbial communities associated with fishes remain largely unknown despite their fundamental roles in host nutrition and immunity. Using a gradient of reef degradation, we show that the gut microbiome of a facultative, coral-feeding butterflyfish (Chaetodon capistratus) is significantly more variable among individuals at degraded reefs with very low live coral cover (~0%) than reefs with higher coral cover (~30%), mirroring a known pattern of microbial imbalance observed in immunodeficient humans and other stressed or diseased animals. We demonstrate that fish gut microbiomes on severely degraded reefs have a lower abundance of Endozoicomonas and a higher diversity of anaerobic fermentative bacteria, which suggests a broader and less coral dominated diet. The observed shifts in fish gut bacterial communities across the habitat gradient extend to a small set of potentially beneficial host associated bacteria (i.e., the core microbiome) suggesting essential fish-microbiome interactions are vulnerable to severe coral degradation.
Integrative systems approach reveals dynamics of microbiome-metal-ion axis in mesocosms representing tropical urban freshwater canal ecosystem
Authors: Saxena Gourvendu , Hill Eric Dubois , Marzinelli Ezequiel M. , Umashankar Shivshankar , Wei Toh Jun , Yissue Wei Woo , Steinberg Peter D. , Rajal Verónica B. , Kjelleberg Staffan , Williams Rohan B. H. , Wuertz Stefan , Swarup Sanjay 
Published: September 2020

AbstractFreshwater ecosystems oftropicalurbancanalssystems (TrUCS), are highly dynamic and experience constant pressures from interspersed effects of land-use and rain. The dynamic nature of TrUCS ecosystems presents a unique opportunity to unravel the signature interactions between the macro-organisms (top-down),sedimentarymicrobialcommunities (SedMICs), their functioning and the geochemical environment (bottom-up). A systems level understanding of the molecular and mechanistic basis of the highly dynamic behaviour that leads to specific ecosystem outcomes, is currently lacking. Therefore, a research framework to identify the direct link between top-down and bottom-up ecological effects on SedMICs in a highly dynamic urban canal sedimentary system is needed. Here, we present a framework of integrated multi-dimensional data across system-level biotic and abiotic ecological descriptors, such as environmental variables and active SedMICs. We followed the ecosystem shifts after a natural disturbance (rain) in two different anthropogenic disturbance (land-use) regimes. Shifts in profiles of metabolically active community were conserved across different land-use types, indicating resilience to perturbation is an intrinsic property of the TrUCs ecosystem. Three distinct phases, which were dominated sequentially by autotrophy, anoxic-heterotrophy and oxic-heterotrophy, were identified within these shifts. The first two phases were influenced by the bottom-up effects of specific metal-ion combinations of nitrates and sulfates with magnesium, aluminum and iron, and the third phase was triggered by top-down influences of bioturbation. This generalized systems-level approach, which provides an ecosystem-centric understanding of TrUCS and integrates them in sustainable management practices, can also be extended to other freshwater ecosystems.
Ablation of endogenously cycling adult cardiomyocytes worsens myocardial function after injury
Authors: Bradley Leigh A. , Young Alexander , Billcheck Helen O. , Wolf Matthew J. 
Published: September 2020

AbstractRationaleEndogenously cycling adult cardiomyocytes (CMs) increase after myocardial infarction (MI) but remain scare, and are generally thought not to contribute to myocardial function. However, this broadly held assumption has not been tested, mainly because of the lack of transgenic reporters that restrict Cre expression to adult CMs that reenter the cell cycle.ObjectiveWe created and validated a new transgenic mouse,αMHC-MerDreMer-Ki67p-RoxedCre::Rox-Lox-tdTomato-eGFP(denotedαDKRC) that restricts Cre expression to cycling adult CMs and uniquely integrates spatial and temporal adult CM cycling events based on the DNA specificities of orthologous Dre- and Cre recombinases. We then created mice that expressed an inducible Diphtheria toxin (DTA),αDKRC::DTAmice, in adult cycling CMs and examined the effects of ablating these endogenously cycling CMs on myocardial function after Ischemic-Reperfusion (I/R) MI.Methods and ResultsA tandemαDKRCtransgene was designed, validated in cultured cells, and used to make transgenic mice. TheαDKRCtransgene integrated betweenMYH6andMYH7and did not disrupt expression of the surrounding genes. Compared to controls,αDKRC::RLTGmice treated with Tamoxifen expressed tdTomato+ in CMs with rare Bromodeoxyuridine (BrdU)+, eGFP+CMs, consistent with reentry of the cell cycle. We then pre- treatedαDKRC::RLTGmice with Tamoxifen to activate the reporter before sham or reperfusion (I/R) myocardial infarction (MI) surgeries. Compared to Sham surgery, the I/R MI group had increased single and paired eGFP+ CMs predominantly in the border zones (5.8 ± 0.5 vs. 3.3 ± 0.3 CMs per ten-micron section, N = 8 mice, n = 16 sections per mouse), indicative of cycled CMs. The single to paired eGFP+ CM ratio was ∼9 to 1 (5.2 ± 0.4 single vs. 0.6 ± 0.2 paired CMs) in the I/R MI group after MI, suggesting that cycling CMs were more likely to undergo polyploidy than replication. The ablation of endogenously cycling adult CMs inαDKRC::DTAmice caused progressive worsening left ventricular chamber size and function after I/R MI, compared to controls.ConclusionsAlthough scarce, endogenously cycling adult CMs contribute to myocardial function after injury, suggesting that these cells may be physiologically relevant.
Age-dependent impairment of disease tolerance is associated with a robust transcriptional response following RNA virus infection inDrosophila
Authors: Sheffield Lakbira , Sciambra Noah , Evans Alysa , Hagedorn Eli , Delfeld Megan , Goltz Casey , Fierst Janna L. , Chtarbanova Stanislava 
Published: September 2020

SummaryAdvanced age in humans is associated with greater susceptibility to and higher mortality rates from infections, including infections with some RNA viruses. The underlying innate immune mechanisms, which represent the first line of defense against pathogens, remain incompletely understood.Drosophila melanogasteris able to mount potent and evolutionarily conserved innate immune defenses against a variety of microorganisms including viruses and serves as an excellent model organism for studying host-pathogen interactions. With its relatively short lifespan,Drosophilaalso is an organism of choice for aging studies. Despite numerous advantages that this model offers,Drosophilahas not been used to its potential to investigate the response of the aged host to viral infection. Here we show that in comparison to younger flies, agedDrosophilasuccumb more rapidly to infection with the RNA-containing Flock House Virus (FHV) due to an age-dependent defect in disease tolerance. In comparison to younger individuals, we find that olderDrosophilamount larger transcriptional responses characterized by differential regulation of more genes and genes regulated to a greater extent. Our results indicate that loss of disease tolerance to FHV with age possibly results from a stronger regulation of genes involved in apoptosis, activation of theDrosophilaImmune deficiency (IMD) NF-kB pathway or from downregulation of genes whose products function in mitochondria and mitochondrial respiration. Our work shows thatDrosophilacan serve as a model to investigate host-virus interactions during aging and sets the stage for future analysis of the age-dependent mechanisms that govern survival and control of virus infections at older age.