bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chronic dysfunction of Stromal interaction molecule by pulsed RNAi induction in fat tissue impairs organismal energy homeostasis in Drosophila
Authors: Xu Yanjun , Borcherding Annika F. , Heier Christoph , Tian Gu , Roeder Thomas , Kühnlein Ronald P. 
Published: May 2019

AbstractObesity is a progressive, chronic disease, which can be caused by long-term miscommunication between organs. It remains challenging to understand how chronic dysfunction in a particular tissue remotely impairs other organs to eventually imbalance organismal energy homeostasis. Here we introduce RNAi Pulse Induction (RiPI) mediated by short hairpin RNA (shRiPI) or double-stranded RNA (dsRiPI) to generate chronic, organ-specific gene knockdown in the adult Drosophila fat tissue. We show that organ-restricted RiPI targeting Stromal interaction molecule (Stim), an essential factor of store-operated calcium entry (SOCE), results in progressive fat accumulation in fly adipose tissue. Chronic SOCE-dependent adipose tissue dysfunction manifests in considerable changes of the fat cell transcriptome profile, and in resistance to the glucagon-like Adipokinetic hormone (Akh) signaling. Remotely, the adipose tissue dysfunction promotes hyperphagia likely via increased secretion of Akh from the neuroendocrine system. Collectively, our study presents a novel in vivo paradigm in the fly, which is widely applicable to model and functionally analyze inter-organ communication processes in chronic diseases.
The structural arrangement at intersubunit interfaces in homomeric kainate receptors
Authors: Litwin Douglas B. , Carrillo Elisa , Shaikh Sana A. , Berka Vladimir , Jayaraman Vasanthi 
Published: May 2019

AbstractKainate receptors are glutamate-gated cation-selective channels involved in excitatory synaptic signaling and are known to be modulated by ions. Prior functional and structural studies suggest that the dimer interface at the agonist-binding domain plays a key role in activation, desensitization, and ion modulation in kainate receptors. Here we have used fluorescence-based methods to investigate the changes and conformational heterogeneity at these interfaces associated with the resting, antagonist-bound, active, desensitized, and ion-modulated states of the receptor. These studies show that in the presence of Na+ ions the interfaces exist primarily in the coupled state in the apo, antagonist-bound and activated (open channel) states. Under desensitizing conditions, the largely decoupled dimer interface at the agonist-binding domain as seen in the cryo-EM structure is one of the states observed. However, in addition to this state there are several additional states with lower levels of decoupling. Replacing Na+ with Cs+ does not alter the FRET efficiencies of the states significantly, but shifts the population to the more decoupled states in both resting and desensitized states, which can be correlated with the lower activation seen in the presence of Cs+.
A practical adaptive moving-mesh algorithm for solving unconfined seepage problem with Galerkin finite element method
Authors: Dai Qianwei , Lei Yi , Zhang Bin , Feng Deshan , Wang Xun , Yin Xiaobo 
Published: May 2019

AbstractOne of the great challenges of unconfined seepage through a dam lies in the accurate determination of free surface that depends on the complexity of the seepage model, especially if the model is characterized with complex geometry and sharp variations in permeability distribution. This study presents a practical methodology that combines the adaptive moving-mesh algorithm and the Galerkin finite element method (FEM) to solve an unconfined seepage problem with high efficiency and precision. The methodology employs a set of improvement terms, such as remainder factor, step-size parameter and termination condition, all of which guarantee that the simulation and the refinement fitting can be implemented efficiently until the free surface converges within a given allowable error. In particular, a specialized discussion is presented for the significant relation between the location of the exit point and the corresponding grid fineness. To validate the practicability of the proposed method, a series of examples are performed. Comparing the result with those of other numerical approaches, we conclude that even though the unconfined seepage model may be complicated with arbitrary complex geometry and sharp variations in permeability distribution, the proposed algorithm provides a great improvement in efficiency and accuracy in free-surface searching.
Proteomic and structural differences in lumpfish skin among the dorsal, caudal and ventral regions
Authors: Patel Deepti M. , Bhide Katarina , Bhide Mangesh , Iversen Martin H. , Brinchmann Monica F. 
Published: May 2019

AbstractFish skin is a vital organ that serves a multitude of functions including mechanical protection, homeostasis, osmoregulation and protection against diseases. The expression of skin proteins changes under different physiological conditions. However, little is known about differences in protein expression among various body sites in naïve fish. The objectives of this work is to study potential differences in protein and gene expression among dorsal, caudal and ventral regions of lumpfish skin employing 2D gel based proteomics and real-time PCR and to assess structural differences between these regions by using Alcian blue and Periodic acid Schiff stained skin sections. The proteins collagen alfa-1, collagen alfa-2, heat shock cognate 71 kDa, histone H4, parvalbumin, natterin-2, 40S ribosomal protein S12, topoisomerase A and topoisomerase B were differentially expressed among the three regions. mRNA expression of apoa1, hspa8 and hist1h2b showed significant differences between regions. Skin photomicrographs showed differences in epidermal thickness and goblet cell counts. The ventral region showed relatively high protein expression, goblet cell count and epidermal thickness compared to dorsal and caudal regions. Overall, this study provides an important benchmark for comparative analysis of skin proteins and structure between different parts of the lumpfish body.
Genotyping by sequencing provides new insights into the diversity of Napier grass (Cenchrus purpureus) and reveals variation in genome-wide LD patterns between collections
Authors: Muktar Meki S. , Teshome Abel , Hanson Jean , Negawo Alemayehu T. , Habte Ermias , Domelevo Entfellner Jean-Baka , Lee Ki-Won , Jones Chris S. 
Published: May 2019

AbstractNapier grass is an important tropical forage-grass and of growing potential as an energy crop. One-hundred-five Napier grass accessions, encompassing two independent collections, were subjected to genotyping by sequencing which generated a set of high-density genome-wide markers together with short sequence reads. The reads, averaging 54 nucleotides, were mapped to the pearl millet genome and the closest genes and annotation information were used to select candidate genes linked to key forage traits. 980 highly polymorphic SNP markers, distributed across the genome, were used to assess population structure and diversity with seven-subgroups identified. A few representative accessions were selected with the objective of distributing subsets of a manageable size for further evaluation. Genome-wide linkage disequilibrium (LD) analyses revealed a fast LD-decay, on average 2.54 kbp, in the combined population with a slower LD-decay in the ILRI collection compared with the EMBRAPA collection, the significance of which is discussed. This initiative generated high-density markers with a good distribution across the genome. The diversity analysis revealed the existence of a substantial amount of variation in the ILRI collection and identified some unique materials from the EMBRAPA collection, demonstrating the potential of the overall population for further genetic and marker-trait-association studies.
Enhancement of HIFU ablation by sonosensitizer-loading liquid fluorocarbon nanoparticles with pre-targeting in a mouse model
Authors: Zhang Yong , Yong Lijun , Luo Yong , Ding Xiaoya , Xu Die , Gao Xuan , Yan Sijing , Wang Qi , Luo Jie , Pu Darong , Zou Jianzhong 
Published: May 2019

AbstractHigh intensity focused ultrasound (HIFU) is a noninvasive thermal ablation technique for the treatment of benign and malignant solid masses. To improve the efficacy of HIFU ablation, we developed poly (lactide-co-glycolide) (PLGA) nanoparticles encapsulating perfluoropentane (PFP) and hematoporphyrin monomethyl ether (HMME) as synergistic agents (HMME+PFP/PLGA). Two-step biotin-avidin pre-targeting technique was applied for the HIFU ablation. We further modified the nanoparticles with streptavidin (HMME+PFP/PLGA-SA). HMME+PFP/PLGA-SA were highly dispersed with spherical morphology (477.8 ± 81.8 nm in diameter). The encapsulation efficiency of HMME and PFP were 46.6 ± 3.3% and 40.1 ± 2.6%, respectively. The binding efficiency of nanoparticles to streptavidin was 95.5 ± 2.5%. The targeting ability of the HMME+PFP/PLGA-SA nanoparticles was tested by parallel plate flow chamber in vitro. In the pre-targeting group (HMME+PFP/PLGA-SA), a large number of nanoparticles bound to the peripheral and surface of the cell. In the HIFU ablation experiment in vivo, compared with the other groups, the largest gray-scale changes and coagulation necrosis areas were observed in the pre-targeting (HMME+PFP/PLGA-SA) group, with the lowest energy efficiency factor value. Moreover, the microvessel density and proliferation index declined, while the apoptotic index increased, in the tumor tissue surrounding the coagulation necrosis area in the pre-targeting group. Meanwhile, the survival time of the tumor-bearing nude mice in the pre-targeting group was significantly longer than that in the HIFU treatment group. These results suggest that HMME+PFP/PLGA-SA have high potential to act as synergistic agents in HIFU ablation.
In vitro evolution of enhanced RNA replicons for immunotherapy
Authors: Li Yingzhong , Teague Brian , Zhang Yuan , Su Zhijun , Porter Ely , Dobosh Brian , Wagner Tyler , Irvine Darrell J. , Weiss Ron 
Published: May 2019

AbstractSelf-replicating (replicon) RNA is a promising new platform for gene therapy, but applications are still limited by short persistence of expression in most cell types and low levels of transgene expression in vivo. To address these shortcomings, we developed an in vitro evolution strategy and identified six mutations in nonstructural proteins (nsPs) of Venezuelan equine encephalitis (VEE) replicon that promoted subgenome expression in cells. Two mutations in nsP2 and nsP3 enhanced transgene expression, while three mutations in nsP3 regulated this expression. Replicons containing the most effective mutation combinations showed enhanced duration and cargo gene expression in vivo. In comparison to wildtype replicon, mutants expressing IL-2 injected into murine B16F10 melanoma showed 5.5-fold increase in intratumoral IL-2 and 2.1-fold increase in infiltrating CD8 T cells, resulting in significantly slowed tumor growth. Thus, these mutant replicons may be useful for improving RNA therapeutics for vaccination, cancer immunotherapy, and gene therapy.
TickPath Layerplex: adaptation of a real-time PCR methodology for the simultaneous detection and molecular surveillance of tick-borne pathogens
Authors: Modarelli Joseph J. , Ferro Pamela J. , de León Adalberto A. Pérez , Esteve-Gasent Maria D. 
Published: May 2019

AbstractTick-borne diseases (TBD) are common across the United States and can result in critical and chronic diseases in a variety of veterinary patients. Moreover, borreliosis, anaplasmosis, rickettsiosis, ehrlichiosis, and babesiosis are zoonotic and have been cited as the most common TBDs. Molecular diagnostic methodologies utilized for screening domestic dogs for these causative agents include real-time PCR (qPCR) assays in both singleplex and multiplex formats. However, current limitations of qPCR instruments restrict the number of fluorogenic labels that can be differentiated by the instrument for a given reaction. This study describes the development of the TickPath Layerplex, a diagnostic assay based on qPCR methodology that was adapted for the simultaneous detection and characterization of 11 pathogens responsible for causing 5 common TBDs in domestic dogs. The analytical and diagnostic performance of the layerplex assay was evaluated and shown to be compatible with common instruments utilized in molecular diagnostic laboratories. Test results revealed no inhibition or reduction in sensitivity during validation of the layerplex assay, and the limit of detection was determined to be near 16 genome copy equivalents per microliter. Overall, the high sensitivity, specificity, and screening capability of the assay demonstrate its utility for broadly screening dogs for common TBDs.
Stability Mechanism of Two Soybean Protein-Phosphatidylcholine Nanoemulsion Preparation Methods from a Structural Perspective: A Raman Spectroscopy Analysis
Authors: Zhu Ying , Li Yang , Wu Changling , Teng Fei , Qi Baokun , Zhang Xiaonan , Zhou Linyi , Yu Guoping , Wang Huan , Zhang Shuang , Wang Zhongjiang , Jiang Lianzhou 
Published: May 2019

AbstractUltrasound treatment and high-pressure homogenization were used to prepare soybean protein (SP)-phosphatidylcholine (PC) nanoemulsions in this study. Nanoemulsions prepared by high-pressure homogenization were more stable. The structural changes of SP and PC under ultrasound treatment and high-pressure homogenization treatment were investigated by Raman spectroscopy. It could be concluded that ultrasound and high-pressure homogenization treatments increased both the content of α-helix and unordered structure but decreased that of β-structures of SP, while the interaction between SP and PC decreased α-helix content and also reduced unordered structure and β-sheet structure. Ultrasound treatment and high-pressure homogenization exposed more tryptophan and tyrosine residues to promote hydrophobic interaction between SP and PC, which was beneficial for stabilizing the nanoemulsion. The SP-PC interaction exerted a more significant effect on side chain structure than those observed under ultrasound treatment and high-pressure homogenization. The dominantg-g-tvibrational mode of the disulfide bond of soybean protein was not appreciably changed by the two preparations. High-pressure homogenization increased the disorder of lipid chains of PC, promoting SP-PC interaction and thereby increasing the stability of the nanoemulsion. The structural change provided a theoretical basis for preparation of two nanoemulsions.
Average firing rate rather than temporal pattern determines metabolic cost of activity in thalamocortical relay neurons
Authors: Yi Guosheng , Grill Warren M. 
Published: May 2019

AbstractThalamocortical (TC) relay cells exhibit different temporal patterns of activity, including tonic mode and burst mode, to transmit sensory information to the cortex. Our aim was to quantify the metabolic cost of different temporal patterns of neural activity across a range of average firing rates. We used a biophysically-realistic model of a TC relay neuron to simulate tonic and burst patterns of firing. We calculated the metabolic cost by converting the calculated ion fluxes into the demand for ATP to maintain homeostasis of intracellular ion concentrations. Most energy was expended on reversing Na+ entry during action potentials and pumping Ca2+ out of the cell. Average firing rate determined the ATP cost across firing patterns by controlling the overall number of spikes. Varying intraburst frequency or spike number in each burst influenced the metabolic cost by altering the interactions of inward and outward currents on multiple timescales, but temporal pattern contributed substantially less to the metabolic demand of neural activity as compared to average firing rate. These predictions should be considered when interpreting findings of functional imaging studies that rely of estimates of neuronal metabolic demand, e.g., functional magnetic resonance imaging.
Yield instability of winter oilseed rape modulated by early winter temperature
Authors: Brown James K. M. , Beeby Rebecca , Penfield Steven 
Published: May 2019

AbstractYield stability is a major problem in oilseed rape with inter-annual variation accounting for between 30–50% of the crop value among the major global rapeseed producers. The United Kingdom has persistent problems with yield instability, but the underlying causes remain unclear. We tested whether temperature plays a role in UK winter oilseed rape (WOSR) yield variation through analysis of aggregated country-wide on-farm yield data and in annual Recommended List variety trial data run by the UK Agriculture and Horticulture Development Board (AHDB). Our analyses of the two independent datasets both show that mean temperature in early winter is strongly and uniquely linked to variation in WOSR yield, with a rise in mean temperature of 1 °C associated with an average reduction of 113 (+−21) kg ha−1 in yield. We propose that understanding the mechanism by which early winter chilling affects WOSR yield will enable the breeding of varieties with a more stable and resilient yield in Western Europe as climatic variation increases.
Short-term mindfulness practice attenuates reward prediction errors signals in the brain
Authors: Kirk Ulrich , Pagnoni Giuseppe , Hétu Sébastien , Montague Read 
Published: May 2019

AbstractActivity changes in dopaminergic neurons encode the ongoing discrepancy between expected and actual value of a stimulus, providing a teaching signal for a reward prediction process. Previous work comparing a cohort of long-term Zen meditators to controls demonstrated an attenuation of reward prediction signals to appetitive reward in the striatum. Using a cross-commodity design encompassing primary- and secondary-reward conditioning experiments, the present study asks the question of whether reward prediction signals are causally altered by mindfulness training in naïve subjects. Volunteers were randomly assigned to 8 weeks of mindfulness training (MT), active control training (CT), or a one-time mindfulness induction group (MI). We observed a decreased response to positive prediction errors in the putamen in the MT group compared to CT using both a primary and a secondary-reward experiment. Furthermore, the posterior insula showed greater activation to primary rewards, independently of their predictability, in the MT group, relative to CT and MI group. These results support the notion that increased attention to the present moment and its interoceptive features - a core component of mindfulness practice - may reduce predictability effects in reward processing, without dampening (in fact, enhancing) the response to the actual delivery of the stimulus.
Immunohistochemical and ultrastructural analysis of the maturing larval zebrafish enteric nervous system reveals the formation of a neuropil pattern
Authors: Baker Phillip A. , Meyer Matthew D. , Tsang Ashley , Uribe Rosa A. 
Published: May 2019

AbstractThe gastrointestinal tract is constructed with an intrinsic series of interconnected ganglia that span its entire length, called the enteric nervous system (ENS). The ENS exerts critical local reflex control over many essential gut functions; including peristalsis, water balance, hormone secretions and intestinal barrier homeostasis. ENS ganglia exist as a collection of neurons and glia that are arranged in a series of plexuses throughout the gut: the myenteric plexus and submucosal plexus. While it is known that enteric ganglia are derived from a stem cell population called the neural crest, mechanisms that dictate final neuropil plexus organization remain obscure. Recently, the vertebrate animal, zebrafish, has emerged as a useful model to understand ENS development, however knowledge of its developing myenteric plexus architecture was unknown. Here, we examine myenteric plexus of the maturing zebrafish larval fish histologically over time and find that it consists of a series of tight axon layers and long glial cell processes that wrap the circumference of the gut tube to completely encapsulate it, along all levels of the gut. By late larval stages, complexity of the myenteric plexus increases such that a layer of axons is juxtaposed to concentric layers of glial cells. Ultrastructurally, glial cells contain glial filaments and make intimate contacts with one another in long, thread-like projections. Conserved indicators of vesicular axon profiles are readily abundant throughout the larval plexus neuropil. Together, these data extend our understanding of myenteric plexus architecture in maturing zebrafish, thereby enabling functional studies of its formation in the future.
Two-dimensional transition metal dichalcogenides assisted biofunctionalized optical fiber SPR biosensor for efficient and rapid detection of bovine serum albumin
Authors: Kaushik Siddharth , Tiwari Umesh K. , Deep Akash , Sinha Ravindra K. 
Published: May 2019

AbstractThe present study reports an alternative method of functionalizing the optical fiber Surface Plasmon Resonance (SPR) sensing probe with antibodies for label-free detection of bovine serum albumin (BSA) protein. In this novel approach, the gold coated fiber was first modified with Molybdenum disulfide (MoS2) nanosheets followed by its bio-functionalization with Anti-BSA antibodies. The developed technique not only allowed the amplification of the SPR signals by synergic effects of MoS2 and gold metallic thin film but also enabled a direct and chemical-free attachment of representative antibodies through hydrophobic interactions. The sensitivity of the MoS2 modified sensing probe with detection limit of 0.29 µg/mL was improved as compared to the fiber optic SPR biosensor without MoS2 overlayer (Detection limit for BSA was 0.45 μg/mL). The developed biosensor has good specificity, and environmental stability. Accordingly, the proposed design of the MoS2 based SPR optical biosensor can offer the development of a simplified optical device for the monitoring of various biomedical and environmental parameters.
Screening substrate-binding positions by rolling circle amplification suggesting a binding model of Nt.BstNBI
Authors: Wei Hua , Tang Suming , Duan Xuying , Guan Yifu , Zhao Guojie 
Published: May 2019

Abstract
Nicking endonucleases (NEs) become increasingly attractive for their promising applications in isothermal amplification. Unfortunately, in comparison with their applications, their catalytic mechanism studies have relatively lagged behind due to a paucity of crystal structure information. Nt.BstNBI is one of those widely used NEs. However, many aspects of its catalytic mechanism still remained to be explored. Herein, we employed only rolling circle amplification (RCA) assay as a major analytic tool and succeeded in identifying the potential binding positions and regions of the DNA substrate based on locked nucleic acid modification, DNA duplex length of substrate, and substrate mismatch designs. Based on these data, we, for the first time, revealed that Nt.BstNBI was likely to recognize six adjacent positions of the recognition sequence (G1rt, A2rt, G3rt, A2rb, C3rb, and T4rb) in the major groove and hold three positions of the cleavage sequence (N3ct, N4ct, and N7cb) in the minor groove of DNA duplex for nicking. Moreover, this work also demonstrated the unexpected efficiency of RCA to study the macromolecular interaction for certain kind of nucleases in an easy and high-throughput way.