bluuebunny/crossref_metadata_2025_split huggingface dataset:
Xanthomonas citri jumbo phage XacN1 exhibits a wide host range and high complement of tRNA genes
Authors: Yoshikawa Genki , Askora Ahmed , Blanc-Mathieu Romain , Kawasaki Takeru , Li Yanze , Nakano Miyako , Ogata Hiroyuki , Yamada Takashi 
Published: March 2018

AbstractXanthomonas virus (phage) XacN1 is a novel jumbo myovirus infecting Xanthomonas citri, the causative agent of Asian citrus canker. Its linear 384,670 bp double-stranded DNA genome encodes 592 proteins and presents the longest (66 kbp) direct terminal repeats (DTRs) among sequenced viral genomes. The DTRs harbor 56 tRNA genes, which correspond to all 20 amino acids and represent the largest number of tRNA genes reported in a viral genome. Codon usage analysis revealed a propensity for the phage encoded tRNAs to target codons that are highly used by the phage but less frequently by its host. The existence of these tRNA genes and seven additional translation-related genes as well as a chaperonin gene found in the XacN1 genome suggests a relative independence of phage replication on host molecular machinery, leading to a prediction of a wide host range for this jumbo phage. We confirmed the prediction by showing a wider host range of XacN1 than other X. citri phages in an infection test against a panel of host strains. Phylogenetic analyses revealed a clade of phages composed of XacN1 and ten other jumbo phages, indicating an evolutionary stable large genome size for this group of phages.
Constructing vesicle-based artificial cells with embedded living cells as organelle-like modules
Authors: Elani Yuval , Trantidou Tatiana , Wylie Douglas , Dekker Linda , Polizzi Karen , Law Robert V. , Ces Oscar 
Published: March 2018

AbstractThere is increasing interest in constructing artificial cells by functionalising lipid vesicles with biological and synthetic machinery. Due to their reduced complexity and lack of evolved biochemical pathways, the capabilities of artificial cells are limited in comparison to their biological counterparts. We show that encapsulating living cells in vesicles provides a means for artificial cells to leverage cellular biochemistry, with the encapsulated cells serving organelle-like functions as living modules inside a larger synthetic cell assembly. Using microfluidic technologies to construct such hybrid cellular bionic systems, we demonstrate that the vesicle host and the encapsulated cell operate in concert. The external architecture of the vesicle shields the cell from toxic surroundings, while the cell acts as a bioreactor module that processes encapsulated feedstock which is further processed by a synthetic enzymatic metabolism co-encapsulated in the vesicle.
Rapid histopathological imaging of skin and breast cancer surgical specimens using immersion microscopy with ultraviolet surface excitation
Authors: Yoshitake Tadayuki , Giacomelli Michael G. , Quintana Liza M. , Vardeh Hilde , Cahill Lucas C. , Faulkner-Jones Beverly E. , Connolly James L. , Do Daihung , Fujimoto James G. 
Published: March 2018

AbstractRapid histopathological evaluation of fresh, unfixed human tissue using optical sectioning microscopy would have applications to intraoperative surgical margin assessment. Microscopy with ultraviolet surface excitation (MUSE) is a low-cost optical sectioning technique using ultraviolet illumination which limits fluorescence excitation to the specimen surface. In this paper, we characterize MUSE using high incident angle, water immersion illumination to improve sectioning. Propidium iodide is used as a nuclear stain and eosin yellow as a counterstain. Histologic features of specimens using MUSE, nonlinear microscopy (NLM) and conventional hematoxylin and eosin (H&E) histology were evaluated by pathologists to assess potential application in Mohs surgery for skin cancer and lumpectomy for breast cancer. MUSE images of basal cell carcinoma showed high correspondence with frozen section H&E histology, suggesting that MUSE may be applicable to Mohs surgery. However, correspondence in breast tissue between MUSE and paraffin embedded H&E histology was limited due to the thicker optical sectioning in MUSE, suggesting that further development is needed for breast surgical applications. We further demonstrate that the transverse image resolution of MUSE is limited by the optical sectioning thickness and use co-registered NLM to quantify the improvement in MUSE optical sectioning from high incident angle water immersion illumination.
Identification and characterization of microRNAs in tree peony during chilling induced dormancy release by high-throughput sequencing
Authors: Zhang Yuxi , Wang Yanyan , Gao Xuekai , Liu Chunying , Gai Shupeng 
Published: March 2018

AbstractTree peony, one of the most valuable horticultural and medicinal plants in the world, has to go through winter to break dormancy. Growing studies from molecular aspects on dormancy release process have been reported, but inadequate study has been done on miRNA-guided regulation in tree peony. In this study, high-throughput sequencing was employed to identify and characterize miRNAs in three libraries (6 d, 18 d and 24 d chilling treatments). There were 7,122, 10,076 and 9,097 unique miRNA sequences belonging to 52, 87 and 68 miRNA families, respectively. A total of 32 conserved miRNAs and 17 putative novel miRNAs were identified during dormancy release. There were 771 unigenes as potential targets of 62 miRNA families. Total 112 known miRNAs were differentially expressed, of which 55 miRNAs were shared among three libraries and 28 miRNAs were only found in 18 d chilling duration library. The expression patterns of 15 conserved miRNAs were validated and classified into four types by RT-qPCR. Combining with our microarray data under same treatments, five miRNAs (miR156k, miR159a, miR167a, miR169a and miR172a) were inversely correlated to those of their target genes. Our results would provide new molecular basis about dormancy release in tree peony.
Computational Methods for Estimating Molecular System from Membrane Potential Recordings in Nerve Growth Cone
Authors: Yamada Tatsuya , Nishiyama Makoto , Oba Shigeyuki , Jimbo Henri Claver , Ikeda Kazushi , Ishii Shin , Hong Kyonsoo , Sakumura Yuichi 
Published: March 2018

AbstractBiological cells express intracellular biomolecular information to the extracellular environment as various physical responses. We show a novel computational approach to estimate intracellular biomolecular pathways from growth cone electrophysiological responses. Previously, it was shown that cGMP signaling regulates membrane potential (MP) shifts that control the growth cone turning direction during neuronal development. We present here an integrated deterministic mathematical model and Bayesian reversed-engineering framework that enables estimation of the molecular signaling pathway from electrical recordings and considers both the system uncertainty and cell-to-cell variability. Our computational method selects the most plausible molecular pathway from multiple candidates while satisfying model simplicity and considering all possible parameter ranges. The model quantitatively reproduces MP shifts depending on cGMP levels and MP variability potential in different experimental conditions. Lastly, our model predicts that chloride channel inhibition by cGMP-dependent protein kinase (PKG) is essential in the core system for regulation of the MP shifts.
Real-time size modulation and synchronization of a microfluidic dropmaker with pulsed surface acoustic waves (SAW)
Authors: Schmid Lothar , Franke Thomas 
Published: March 2018

AbstractWe show that a microfluidic flow focusing drop maker can be synchronized to a surface acoustic waves (SAW) triggered by an external electric signal. In this way droplet rate and volume can be controlled over a wide range of values in real time. Using SAW, the drop formation rate of a regularly operating water in oil drop maker without SAW can be increased by acoustically enforcing the drop pinch-off and thereby reducing the volume. Drop makers of square cross-sections (w = h = 30 µm, with width w and height h) that produce large drops of length l = 10 w can be triggered to produce drops as short as l ~ 2w, approaching the geometical limit l = w without changing the flow rates. Unlike devices that adjust drop size by changing the flow rates the acoustic dropmaker has very short transients allowing to adjust the size of every single drop. This allows us to produce custom made emulsions with a defined size distribution as demonstrated here not only for a monodisperse emulsion but also for binary emulsions with drops of alternating size. Moreover, we show that the robustness and monodispersity of our devices is enhanced compared to purely flow driven drop makers in the absence of acoustic synchronization.
Application of a Genetic Risk Score to Racially Diverse Type 1 Diabetes Populations Demonstrates the Need for Diversity in Risk-Modeling
Authors: Perry Daniel J. , Wasserfall Clive H. , Oram Richard A. , Williams MacKenzie D. , Posgai Amanda , Muir Andrew B. , Haller Michael J. , Schatz Desmond A. , Wallet Mark A. , Mathews Clayton E. , Atkinson Mark A. , Brusko Todd M. 
Published: March 2018

AbstractPrior studies identified HLA class-II and 57 additional loci as contributors to genetic susceptibility for type 1 diabetes (T1D). We hypothesized that race and/or ethnicity would be contextually important for evaluating genetic risk markers previously identified from Caucasian/European cohorts. We determined the capacity for a combined genetic risk score (GRS) to discriminate disease-risk subgroups in a racially and ethnically diverse cohort from the southeastern U.S. including 637 T1D patients, 46 at-risk relatives having two or more T1D-related autoantibodies (≥2AAb+), 790 first-degree relatives (≤1AAb+), 68 second-degree relatives (≤1 AAb+), and 405 controls. GRS was higher among Caucasian T1D and at-risk subjects versus ≤ 1AAb+ relatives or controls (P < 0.001). GRS receiver operating characteristic AUC (AUROC) for T1D versus controls was 0.86 (P < 0.001, specificity = 73.9%, sensitivity = 83.3%) among all Caucasian subjects and 0.90 for Hispanic Caucasians (P < 0.001, specificity = 86.5%, sensitivity = 84.4%). Age-at-diagnosis negatively correlated with GRS (P < 0.001) and associated with HLA-DR3/DR4 diplotype. Conversely, GRS was less robust (AUROC = 0.75) and did not correlate with age-of-diagnosis for African Americans. Our findings confirm GRS should be further used in Caucasian populations to assign T1D risk for clinical trials designed for biomarker identification and development of personalized treatment strategies. We also highlight the need to develop a GRS model that accommodates racial diversity.
Grain Yield, Starch Content and Activities of Key Enzymes of Waxy and Non-waxy Wheat (Triticum aestivum L.)
Authors: Zi Yan , Ding Jinfeng , Song Jianmin , Humphreys Gavin , Peng Yongxin , Li Chunyan , Zhu Xinkai , Guo Wenshan 
Published: March 2018

AbstractWaxy wheat has unique end-use properties; however, its production is limited due mainly to its low grain yield compared with non-waxy wheat. In order to increase its grain yield, it is critical to understand the eco-physiological differences in grain filling between the waxy and non-waxy wheat. In this study, two waxy wheat and two non-waxy wheat cultivars were used to investigate the differences in starch-associated enzymes processes, sucrose and starch dynamics, yield components, and the final grain yield. The results indicated that the mean total grain starch and amylose content, the average 1000-kernel weight and grain yield of the waxy wheat were lower than those of the non-waxy wheat at maturity. The amylose content was significantly and positively correlated with the activity of GBSS (r = 0.80,p < 0.01). Significant positive correlation also exists among activities of AGPase, SSS, GBSS, and SBE, except for GBSS-SBE. In summary, our study has revealed that the reduced conversion of sucrose to starch in the late grain filling stage is the main cause for the low kernel weight and total starch accumulation of the waxy wheat. The reduced conversion also appears to be a factor contributing to the lower grain yield of the waxy wheat.
Fetal extracellular matrix nerve wraps locally improve peripheral nerve remodeling after complete transection and direct repair in rat
Authors: Ren Tanchen , Faust Anne , van der Merwe Yolandi , Xiao Bo , Johnson Scott , Kandakatla Apoorva , Gorantla Vijay S. , Badylak Stephen F. , Washington Kia M. , Steketee Michael B. 
Published: March 2018

AbstractIn peripheral nerve (PN) injuries requiring surgical repair, as in PN transection, cellular and ECM remodeling at PN epineurial repair sites is hypothesized to reduce PN functional outcomes by slowing, misdirecting, or preventing axons from regrowing appropriately across the repair site. Herein this study reports on deriving and analyzing fetal porcine urinary bladder extracellular matrix (fUB-ECM) by vacuum assisted decellularization, fabricating fUBM-ECM nerve wraps, and testing fUB-ECM nerve wrap biocompatibility and bioactivity in a trigeminal, infraorbital nerve (ION) branch transection and direct end-to-end repair model in rat. FUB-ECM nerve wraps significantly improved epi- and endoneurial organization and increased both neovascularization and growth associated protein-43 (GAP-43) expression at PN repair sites, 28-days post surgery. However, the number of neurofilament positive axons, remyelination, and whisker-evoked response properties of ION axons were unaltered, indicating improved tissue remodeling per se does not predict axon regrowth, remyelination, and the return of mechanoreceptor cortical signaling. This study shows fUB-ECM nerve wraps are biocompatible, bioactive, and good experimental and potentially clinical devices for treating epineurial repairs. Moreover, this study highlights the value provided by precise, analytic models, like the ION repair model, in understanding how PN tissue remodeling relates to axonal regrowth, remyelination, and axonal response properties.
Different vasodilatation characteristics among the main cerebral arteries in fetuses with congenital heart defects
Authors: Peng Qinghai , Zeng Shi , Zhou Qichang , Deng Wen , Wang Tao , Tan Ya , Liu Yushan 
Published: March 2018

AbstractTo observe Doppler changes in the three main cerebral arteries in fetuses with congenital heart defects (CHDs). The pulsatility index (PI) values of the anterior cerebral artery (ACA), middle cerebral artery (MCA), and posterior cerebral artery (PCA) were prospectively compared in 78 CHD fetuses and 78 normal control fetuses. Correlations between the cerebral artery PIs and the neurodevelopment scores (psychomotor development index [PDI] and mental development index [MDI]) were assessed. The MCA-PI was decreased significantly in fetuses with hypoplastic left heart syndrome (HLHS). The ACA-PI was reduced significantly in fetuses with HLHS, fetuses with left-sided obstructive lesions (LSOLs) and fetuses with transposition of the great arteries. The PCA-PI was significantly smaller in fetuses with HLHS and fetuses with LSOLs. More fetuses presented signs of cerebral vasodilatation of the ACA than the MCA for certain types of CHD (P < 0.05). The ACA-PI was positively correlated with the PDI and MDI scores in fetuses with CHDs (r2 = 0.26, 0.20, P < 0.01). The MCA-PI was only positively correlated with the PDI scores (r2 = 0.15, P < 0.01). The ACA exhibited signs of vasodilatation more frequently and severely than the MCA. The ACA-PI appears to be more sensitive for predicting abnormal neurodevelopmental outcomes than the MCA-PI.
Reduced background autofluorescence for cell imaging using nanodiamonds and lanthanide chelates
Authors: Cordina Nicole M. , Sayyadi Nima , Parker Lindsay M. , Everest-Dass Arun , Brown Louise J. , Packer Nicolle H. 
Published: March 2018

AbstractBio-imaging is a key technique in tracking and monitoring important biological processes and fundamental biomolecular interactions, however the interference of background autofluorescence with targeted fluorophores is problematic for many bio-imaging applications. This study reports on two novel methods for reducing interference with cellular autofluorescence for bio-imaging. The first method uses fluorescent nanodiamonds (FNDs), containing nitrogen vacancy centers. FNDs emit at near-infrared wavelengths typically higher than most cellular autofluorescence; and when appropriately functionalized, can be used for background-free imaging of targeted biomolecules. The second method uses europium-chelating tags with long fluorescence lifetimes. These europium-chelating tags enhance background-free imaging due to the short fluorescent lifetimes of cellular autofluorescence. In this study, we used both methods to target E-selectin, a transmembrane glycoprotein that is activated by inflammation, to demonstrate background-free fluorescent staining in fixed endothelial cells. Our findings indicate that both FND and Europium based staining can improve fluorescent bio-imaging capabilities by reducing competition with cellular autofluorescence. 30 nm nanodiamonds coated with the E-selectin antibody was found to enable the most sensitive detective of E-selectin in inflamed cells, with a 40-fold increase in intensity detected.
The voltage-gated sodium channel EF-hands form an interaction with the III-IV linker that is disturbed by disease-causing mutations
Authors: Gardill Bernd R. , Rivera-Acevedo Ricardo E. , Tung Ching-Chieh , Okon Mark , McIntosh Lawrence P. , Van Petegem Filip 
Published: March 2018

AbstractVoltage-gated sodium channels (NaV) are responsible for the rapid depolarization of many excitable cells. They readily inactivate, a process where currents diminish after milliseconds of channel opening. They are also targets for a multitude of disease-causing mutations, many of which have been shown to affect inactivation. A cluster of disease mutations, linked to Long-QT and Brugada syndromes, is located in a C-terminal EF-hand like domain of NaV1.5, the predominant cardiac sodium channel isoform. Previous studies have suggested interactions with the III-IV linker, a cytosolic element directly involved in inactivation. Here we validate and map the interaction interface using isothermal titration calorimetry (ITC) and NMR spectroscopy. We investigated the impact of various disease mutations on the stability of the domain, and found that mutations that cause misfolding of the EF-hand domain result in hyperpolarizing shifts in the steady-state inactivation curve. Conversely, mutations in the III-IV linker that disrupt the interaction with the EF-hand domain also result in large hyperpolarization shifts, supporting the interaction between both elements in intact channels. Disrupting the interaction also causes large late currents, pointing to a dual role of the interaction in reducing the population of channels entering inactivation and in stabilizing the inactivated state.
Defects in Quantum Computers
Authors: Gardas Bartłomiej , Dziarmaga Jacek , Zurek Wojciech H. , Zwolak Michael 
Published: March 2018

AbstractThe shift of interest from general purpose quantum computers to adiabatic quantum computing or quantum annealing calls for a broadly applicable and easy to implement test to assess how quantum or adiabatic is a specific hardware. Here we propose such a test based on an exactly solvable many body system–the quantum Ising chain in transverse field–and implement it on the D-Wave machine. An ideal adiabatic quench of the quantum Ising chain should lead to an ordered broken symmetry ground state with all spins aligned in the same direction. An actual quench can be imperfect due to decoherence, noise, flaws in the implemented Hamiltonian, or simply too fast to be adiabatic. Imperfections result in topological defects: Spins change orientation, kinks punctuating ordered sections of the chain. The number of such defects quantifies the extent by which the quantum computer misses the ground state, and is, therefore, imperfect.
Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A
Authors: Shahid Muhammad , Gull Nicole , Yeon Austin , Cho Eunho , Bae Jooeun , Yoon Hyun Seok , You Sungyong , Yoon Hana , Kim Minjung , Berman Benjamin P. , Kim Jayoung 
Published: March 2018

AbstractInterstitial cystitis (IC) is a chronic urinary tract disease that is characterized by unpleasant sensations, such as persistent pelvic pain, in the absence of infection or other identifiable causes. We previously performed comprehensive metabolomics profiling of urine samples from IC patients using nuclear magnetic resonance and gas-chromatography/mass spectrometry and found that urinary α-oxoglutarate (α-OG), was significantly elevated. α-OG, a tricarboxylic acid (TCA) cycle intermediate, reportedly functions to suppress the proliferation of immortalized normal human bladder epithelial cells. Here, we identified AT-rich interactive domain 1 A (ARID1A), a key chromatin remodeler, as being hypomethylated and upregulated by α-OG treatment. This was done through EPIC DNA methylation profiling and subsequent biochemical approaches, including quantitative RT-PCR and western blot analyses. Furthermore, we found that α-OG almost completely suppresses ten-eleven translocation (TET) activity, but does not affect DNA methyltransferase (DNMT) activity. Altogether, our studies reveal the potential role of α-OG in epigenetic remodeling through its effects on ARID1A and TET expression in the bladder. This may provide a new possible therapeutic strategy in treating IC.
Microcirculatory Disorders and Protective Role of Xuebijing in Severe Heat Stroke
Authors: Jin Hui , Chen Yi , Ding Chengjia , Lin Youping , Chen Yulan , Jiang Dongxin , Su Lei 
Published: March 2018

AbstractThis study was conducted to explore underlying mechanism of microcirculation dysfunction and protectiverole of Xuebijing in heat stroke. Forty rats were divided into: control, vehicle + heat stress (HS), superoxide dismutase (SOD) + HS, and Xuebijing + HS groups. Rats in heat stress groups were subjected to continuous heat stress in infant incubator 1 h after tail vein injection of the tested compound and spinotrapezius preparation. Velocity of blood flow through micro-vessels and vascular diameter were detected in real time. Another 27 rats were divided into: vehicle, SOD, and Xuebijing groups, then further divided into three subgroups each: control, Tcore = 38 °C, Tcore = 41 °C. Rats were sacrificed, and spinotrapezius single-cell suspensions were prepared for detecting SOD and reactive oxygen species (ROS). The results showed that heat stress decreased SOD activity, increased ROS levels, and reduced the blood flow rate. Xuebijing increased SOD activity, decreased ROS levels and exhibited a protective effect in terms of blood flow rate but was less protective than SOD. The survival time in Xuebijing + HS group was longer than that in vehicle group but shorter than that in SOD + HS group. The results suggested Xuebijing could decrease ROS levels and have protective effects in severe heat stroke.