bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean
Authors: Patil Gunvant , Do Tuyen , Vuong Tri D. , Valliyodan Babu , Lee Jeong-Dong , Chaudhary Juhi , Shannon J. Grover , Nguyen Henry T. 
Published: January 2016

AbstractSoil salinity is a limiting factor of crop yield. The soybean is sensitive to soil salinity and a dominant gene,Glyma03g32900is primarily responsible for salt-tolerance. The identification of high throughput and robust markers as well as the deployment of salt-tolerant cultivars are effective approaches to minimize yield loss under saline conditions. We utilized high quality (15x) whole-genome resequencing (WGRS) on 106 diverse soybean lines and identified three major structural variants and allelic variation in the promoter and genic regions of theGmCHX1gene. The discovery of single nucleotide polymorphisms (SNPs) associated with structural variants facilitated the design of six KASPar assays. Additionally, haplotype analysis and pedigree tracking of 93 U.S. ancestral lines were performed using publically available WGRS datasets. Identified SNP markers were validated and a strong correlation was observed between the genotype and salt treatment phenotype (leaf scorch, chlorophyll content and Na+accumulation) using a panel of 104 soybean lines and, an interspecific bi-parental population (F8) from PI483463 x Hutcheson. These markers precisely identified salt-tolerant/sensitive genotypes (>91%) and different structural-variants (>98%). These SNP assays, supported by accurate phenotyping, haplotype analyses and pedigree tracking information, will accelerate marker-assisted selection programs to enhance the development of salt-tolerant soybean cultivars.
Plug-and-Display: decoration of Virus-Like Particles via isopeptide bonds for modular immunization
Authors: Brune Karl D. , Leneghan Darren B. , Brian Iona J. , Ishizuka Andrew S. , Bachmann Martin F. , Draper Simon J. , Biswas Sumi , Howarth Mark 
Published: January 2016

AbstractVirus-like particles (VLPs) are non-infectious self-assembling nanoparticles, useful in medicine and nanotechnology. Their repetitive molecularly-defined architecture is attractive for engineering multivalency, notably for vaccination. However, decorating VLPs with target-antigens by genetic fusion or chemical modification is time-consuming and often leads to capsid misassembly or antigen misfolding, hindering generation of protective immunity. Here we establish a platform for irreversibly decorating VLPs simply by mixing with protein antigen. SpyCatcher is a genetically-encoded protein designed to spontaneously form a covalent bond to its peptide-partner SpyTag. We expressed in E. coli VLPs from the bacteriophage AP205 genetically fused to SpyCatcher. We demonstrated quantitative covalent coupling to SpyCatcher-VLPs after mixing with SpyTag-linked to malaria antigens, including CIDR and Pfs25. In addition, we showed coupling to the VLPs for peptides relevant to cancer from epidermal growth factor receptor and telomerase. Injecting SpyCatcher-VLPs decorated with a malarial antigen efficiently induced antibody responses after only a single immunization. This simple, efficient and modular decoration of nanoparticles should accelerate vaccine development, as well as other applications of nanoparticle devices.
Possible introgression of the VRTN mutation increasing vertebral number, carcass length and teat number from Chinese pigs into European pigs
Authors: Yang Jie , Huang Lusheng , Yang Ming , Fan Yin , Li Lin , Fang Shaoming , Deng Wenjiang , Cui Leilei , Zhang Zhen , Ai Huashui , Wu Zhenfang , Gao Jun , Ren Jun 
Published: January 2016

AbstractVertnin (VRTN) variants have been associated with the number of thoracic vertebrae in European pigs, but the association has not been evidenced in Chinese indigenous pigs. In this study, we first performed a genome-wide association study in Chinese Erhualian pigs using one VRTN candidate causative mutation and the Illumina Porcine 60K SNP Beadchips. The VRTN mutation is significantly associated with thoracic vertebral number in this population. We further show that the VRTN mutation has pleiotropic and desirable effects on teat number and carcass (body) length across four diverse populations, including Erhualian, White Duroc × Erhualian F2 population, Duroc and Landrace pigs. No association was observed between VRTN genotype and growth and fatness traits in these populations. Therefore, testing for the VRTN mutation in pig breeding schemes would not only increase the number of vertebrae and nipples, but also enlarge body size without undesirable effects on growth and fatness traits, consequently improving pork production. Further, by using whole-genome sequence data, we show that the VRTN mutation was possibly introgressed from Chinese pigs into European pigs. Our results provide another example showing that introgressed Chinese genes greatly contributed to the development and production of modern European pig breeds.
Quantum speed limit and a signal of quantum criticality
Authors: Wei Yong-Bo , Zou Jian , Wang Zhao-Ming , Shao Bin 
Published: January 2016

AbstractWe study the quantum speed limit time (QSLT) of a coupled system consisting of a central spin and its surrounding environment and the environment is described by a general XY spin-chain model. For initial pure state, we find that the local anomalous enhancement of the QSLT occurs near the critical point. In addition, we investigate the QSLT for arbitrary time-evolution state in the whole dynamics process and find that the QSLT will decay monotonously and rapidly at a large size of environment near the quantum critical point. These anomalous behaviors in the critical vicinity of XY spin-chain environment can be used to indicate the quantum phase transition point. Especially for the XX spin-chain environment, we find that the QSLT displays a sudden transition from discontinuous segmented values to a steady value at the critical point. In this case, the non-Makovianity and the Loschmidt echo are incapable of signaling the critical value of the transverse field, while the QSLT can still witness the quantum phase transition. So, the QSLT provides a further insight and sharper identification of quantum criticality.
The RNA chaperone activity of the Trypanosoma brucei editosome raises the dynamic of bound pre-mRNAs
Authors: Leeder W.-Matthias , Voigt Christin , Brecht Michael , Göringer H. Ulrich 
Published: January 2016

AbstractMitochondrial transcript maturation in African trypanosomes requires an RNA editing reaction that is characterized by the insertion and deletion of U-nucleotides into otherwise non-functional mRNAs. The reaction is catalyzed by editosomes and requires guide (g)RNAs as templates. Recent data demonstrate that the binding of pre-edited mRNAs to editosomes is followed by a chaperone-type RNA remodeling reaction. Here we map the changes in RNA folding using selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). We demonstrate that pre-mRNAs in their free state adopt intricately folded, highly stable 2D-structures. Editosome binding renders the pre-mRNAs to adopt 2D-conformations of reduced stabilities. On average about 30% of the nucleotides in every pre-mRNA are affected with a prevalence for U-nucleotides. The data demonstrate that the chaperone activity acts by increasing the flexibility of U-residues to lower their base-pairing probability. This results in a simplified RNA folding landscape with a reduced energy barrier to facilitate the binding of gRNAs. The data provide a first rational for the enigmatic U-specificity of the editing reaction.
Site-specific scFv labelling with invertase via Sortase A mechanism as a platform for antibody-antigen detection using the personal glucose meter
Authors: Ismail Nur Faezee , Lim Theam Soon 
Published: January 2016

AbstractAntibody labelling to reporter molecules is gaining popularity due to its many potential applications for diagnostics and therapeutics. However, non-directional bioconjugation methods which are commonly used often results in the loss of target binding capabilities. Therefore, a site-specific enzymatic based bioconjugation such as sortase-mediated transpeptidation allows for a more rapid and efficient method of antibody conjugation for diagnostic applications. Here we describe the utilization of sortase A bioconjugation to conjugate a single chain fragment variable (scFv) to the extracellular invertase (invB) from Zymomonas mobilis with the aim of developing an invertase based immunoassay. In addition, conjugation to enhanced green fluorescent protein (eGFP) was also validated to show the flexibility of the method. The invertase conjugated complex was successfully applied for the detection of antibody-antigen interaction using a personal glucose meter (PGM) for assay readout. The setup was used in both a direct and competitive assay highlighting the robustness of the conjugate for assay development. The method provides an alternative conjugation process to allow easy exchange of antibodies to facilitate rapid development of diagnostic assays for various diseases on the PGM platform.
Selective effect of cell membrane on synaptic neurotransmission
Authors: Postila Pekka A. , Vattulainen Ilpo , Róg Tomasz 
Published: January 2016

AbstractAtomistic molecular dynamics simulations were performed with 13 non-peptidic neurotransmitters (NTs) in three different membrane environments. The results provide compelling evidence that NTs are divided into membrane-binding and membrane-nonbinding molecules. NTs adhere to the postsynaptic membrane surface whenever the ligand-binding sites of their synaptic receptors are buried in the lipid bilayer. In contrast, NTs that have extracellular ligand-binding sites do not have a similar tendency to adhere to the membrane surface. This finding is a seemingly simple yet important addition to the paradigm of neurotransmission, essentially dividing it into membrane-independent and membrane-dependent mechanisms. Moreover, the simulations also indicate that the lipid composition especially in terms of charged lipids can affect the membrane partitioning of NTs. The revised paradigm, highlighting the importance of cell membrane and specific lipids for neurotransmission, should to be of interest to neuroscientists, drug industry and the general public alike.
Downregulation of miR-522 suppresses proliferation and metastasis of non-small cell lung cancer cells by directly targeting DENN/MADD domain containing 2D
Authors: Zhang Tianze , Hu Yingying , Ju Jin , Hou Liangyu , Li Zhange , Xiao Dan , Li Yongchao , Yao Jianyu , Wang Chao , Zhang Yong , Zhang Linyou 
Published: January 2016

AbstractNon-small cell lung cancer (NSCLC), one of the most common causes of cancer-related death, is a worldwide public health problem. MicroRNAs (miRNAs) have recently been identified as a novel class of regulators of carcinogenesis and tumor progression, including miRNAs associated with NSCLC. This study aimed to explore the role of miR-522 in NSCLC and the mechanisms underlying this role. We report here that miR-522 expression was significantly increased in both human NSCLC tissues and cell lines. Furthermore, an MTT assay, 5-Ethynyl-2′-deoxyuridine (EdU) assay kit and flow cytometry confirmed that the inhibition of miR-522 suppressed NSCLC cells proliferation and induced apoptosis. Compared with miR-522 overexpression, miR-522 inhibitor markedly reduced cells migration and invasion, as indicated by wound-healing and transwell assays. In addition, a luciferase assay identified DENN/MADD domain containing 2D (DENND2D) as a direct target of miR-522. qRT-PCR and western blot analyses indicated the reciprocal expression of miR-522 and DENND2D in NSCLC tissue samples. DENND2D was involved in miR-522 induced proliferation and metastasis of NSCLC cells by a miRNA-masking antisense oligonucleotides (miR-mask) technology. These data highlight a novel molecular interaction between miR-522 and DENND2D, which indicates that targeting miR-522 may constitute a potential therapy for NSCLC.
Cue properties change timing strategies in group movement synchronisation
Authors: Honisch Juliane J. , Elliott Mark T. , Jacoby Nori , Wing Alan M. 
Published: January 2016

AbstractTo maintain synchrony in group activities, each individual within the group must continuously correct their movements to remain in time with the temporal cues available. Cues might originate from one or more members of the group. Current research suggests that when synchronising movements, individuals optimise their performance in terms of minimising variability of timing errors (asynchronies) between external cues and their own movements. However, the cost of this is an increase in the timing variability of their own movements. Here we investigate whether an individual’s timing strategy changes according to the task, in a group scenario. To investigate this, we employed a novel paradigm that positioned six individuals to form two chains with common origin and termination on the circumference of a circle. We found that participants with access to timing cues from only one other member used a strategy to minimise their asynchrony variance. In contrast, the participant at the common termination of the two chains, who was required to integrate timing cues from two members, used a strategy that minimised movement variability. We conclude that humans are able to flexibly switch timekeeping strategies to maintain task demands and thus optimise the temporal performance of their movements.
Transcriptional regulation of PRPF31 gene expression by MSR1 repeat elements causes incomplete penetrance in retinitis pigmentosa
Authors: Rose Anna M. , Shah Amna Z. , Venturini Giulia , Krishna Abhay , Chakravarti Aravinda , Rivolta Carlo , Bhattacharya Shomi S. 
Published: January 2016

AbstractPRPF31-associated retinitis pigmentosa presents a fascinating enigma: some mutation carriers are blind, while others are asymptomatic. We identify the major molecular cause of this incomplete penetrance through three cardinal features: (1) there is population variation in the number (3 or 4) of a minisatellite repeat element (MSR1) adjacent to the PRPF31 core promoter; (2) in vitro, 3-copies of the MSR1 element can repress gene transcription by 50 to 115-fold; (3) the higher-expressing 4-copy allele is not observed among symptomatic PRPF31 mutation carriers and correlates with the rate of asymptomatic carriers in different populations. Thus, a linked transcriptional modifier decreases PRPF31 gene expression that leads to haploinsufficiency. This result, taken with other identified risk alleles, allows precise genetic counseling for the first time. We also demonstrate that across the human genome, the presence of MSR1 repeats in the promoters or first introns of genes is associated with greater population variability in gene expression indicating that copy number variation of MSR1s is a generic controller of gene expression and promises to provide new insights into our understanding of gene expression regulation.
High survival of mouse oocytes using an optimized vitrification protocol
Authors: Zhou Cheng-Jie , Wang Dong-Hui , Niu Xin-Xin , Kong Xiang-Wei , Li Yan-Jiao , Ren Jing , Zhou Hong-Xia , Lu Angeleem , Zhao Yue-Fang , Liang Cheng-Guang 
Published: January 2016

AbstractThe method of vitrification has been widely used for cryopreservation. However, the effectiveness of this method for mammalian oocytes could be improved by optimizing each step of the process. In the present study, we tested the effects of varying several key parameters to determine the most effective protocol for mouse oocyte vitrification. We found that cryoprotectant containing ethylene glycol and dimethylsulfoxide plus 20% fetal calf serum produced the highest rates of oocyte survival, fertilization and blastocyst formation. The duration and temperature of oocyte exposure to vitrification and thawing solutions influenced survival rate. The presence of cumulus cells surrounding oocytes and the incubation of thawed oocytes in Toyoda-Yokoyama-Hosoki medium also increased oocyte survival. Open pulled straw and nylon loop methods were more effective than the mini-drop method. Finally, the combination of these improved methods resulted in better spindle morphology when compared to the unimproved methods. These results demonstrate that the outcomes of mouse oocyte vitrification can be improved by a suitable combination of cryopreservation methods, which could be applied to future clinical research with human oocytes.
Anomalous anti-damping in sputtered β-Ta/Py bilayer system
Authors: Behera Nilamani , Chaudhary Sujeet , Pandya Dinesh K. 
Published: January 2016

AbstractAnomalous decrease in effective damping parameter αeff in sputtered Ni81Fe19 (Py) thin films in contact with a very thin β-Ta layer without necessitating the flow of DC-current is observed. This reduction in αeff, which is also referred to as anti-damping effect, is found to be critically dependent on the thickness of β-Ta layer; αeff being highest, i.e., 0.0093 ± 0.0003 for bare Ni81Fe19(18 nm)/SiO2/Si compared to the smallest value of 0.0077 ± 0.0001 for β-Ta(6 nm)/Py(18 nm)/SiO2/Si. This anomalous anti-damping effect is understood in terms of interfacial Rashba effect associated with the formation of a thin protective Ta2O5 barrier layer and also the spin pumping induced non-equilibrium diffusive spin-accumulation effect in β-Ta layer near the Ta/Py interface which induces additional spin orbit torque (SOT) on the moments in Py leading to reduction in "Equation missing". The fitting of "Equation missing" (tTa) revealed an anomalous negative interfacial spin mixing conductance, "Equation missing"and spin diffusion length,"Equation missing". The increase in αeff observed above tTa = 6 nm is attributed to the weakening of SOT at higher tTa. The study highlights the potential of employing β-Ta based nanostructures in developing low power spintronic devices having tunable as well as low value of α.
Broadband nanophotonic wireless links and networks using on-chip integrated plasmonic antennas
Authors: Yang Yuanqing , Li Qiang , Qiu Min 
Published: January 2016

AbstractOwing to their high capacity and flexibility, broadband wireless communications have been widely employed in radio and microwave regimes, playing indispensable roles in our daily life. Their optical analogs, however, have not been demonstrated at the nanoscale. In this paper, by exploiting plasmonic nanoantennas, we demonstrate the complete design of broadband wireless links and networks in the realm of nanophotonics. With a 100-fold enhancement in power transfer superior to previous designs as well as an ultrawide bandwidth that covers the entire telecommunication wavelength range, such broadband nanolinks and networks are expected to pave the way for future optical integrated nanocircuits.
Complete hyperentangled-Bell-state analysis for photonic qubits assisted by a three-level Λ-type system
Authors: Wang Tie-Jun , Wang Chuan 
Published: January 2016

AbstractHyperentangled Bell-state analysis (HBSA) is an essential method in high-capacity quantum communication and quantum information processing. Here by replacing the two-qubit controlled-phase gate with the two-qubit SWAP gate, we propose a scheme to distinguish the 16 hyperentangled Bell states completely in both the polarization and the spatial-mode degrees of freedom (DOFs) of two-photon systems. The proposed scheme reduces the use of two-qubit interaction which is fragile and cumbersome and only one auxiliary particle is required. Meanwhile, it reduces the requirement for initializing the auxiliary particle which works as a temporary quantum memory and does not have to be actively controlled or measured. Moreover, the state of the auxiliary particle remains unchanged after the HBSA operation and within the coherence time, the auxiliary particle can be repeatedly used in the next HBSA operation. Therefore, the engineering complexity of our HBSA operation is greatly simplified. Finally, we discuss the feasibility of our scheme with current technologies.
Regenerative memory in time-delayed neuromorphic photonic resonators
Authors: Romeira B. , Avó R. , Figueiredo José M. L. , Barland S. , Javaloyes J. 
Published: January 2016

AbstractWe investigate a photonic regenerative memory based upon a neuromorphic oscillator with a delayed self-feedback (autaptic) connection. We disclose the existence of a unique temporal response characteristic of localized structures enabling an ideal support for bits in an optical buffer memory for storage and reshaping of data information. We link our experimental implementation, based upon a nanoscale nonlinear resonant tunneling diode driving a laser, to the paradigm of neuronal activity, the FitzHugh-Nagumo model with delayed feedback. This proof-of-concept photonic regenerative memory might constitute a building block for a new class of neuron-inspired photonic memories that can handle high bit-rate optical signals.
Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae
Authors: Reider Apel Amanda , Ouellet Mario , Szmidt-Middleton Heather , Keasling Jay D. , Mukhopadhyay Aindrila 
Published: January 2016

AbstractEnhancing xylose utilization has been a major focus in Saccharomyces cerevisiae strain-engineering efforts. The incentive for these studies arises from the need to use all sugars in the typical carbon mixtures that comprise standard renewable plant-biomass-based carbon sources. While major advances have been made in developing utilization pathways, the efficient import of five carbon sugars into the cell remains an important bottleneck in this endeavor. Here we use an engineered S. cerevisiae BY4742 strain, containing an established heterologous xylose utilization pathway and imposed a laboratory evolution regime with xylose as the sole carbon source. We obtained several evolved strains with improved growth phenotypes and evaluated the best candidate using genome resequencing. We observed remarkably few single nucleotide polymorphisms in the evolved strain, among which we confirmed a single amino acid change in the hexose transporter HXT7 coding sequence to be responsible for the evolved phenotype. The mutant HXT7(F79S) shows improved xylose uptake rates (Vmax = 186.4 ± 20.1 nmol•min−1•mg−1) that allows the S. cerevisiae strain to show significant growth with xylose as the sole carbon source, as well as partial co-utilization of glucose and xylose in a mixed sugar cultivation.
Operational resilience: concepts, design and analysis
Authors: Ganin Alexander A. , Massaro Emanuele , Gutfraind Alexander , Steen Nicolas , Keisler Jeffrey M. , Kott Alexander , Mangoubi Rami , Linkov Igor 
Published: January 2016

AbstractBuilding resilience into today’s complex infrastructures is critical to the daily functioning of society and its ability to withstand and recover from natural disasters, epidemics and cyber-threats. This study proposes quantitative measures that capture and implement the definition of engineering resilience advanced by the National Academy of Sciences. The approach is applicable across physical, information and social domains. It evaluates the critical functionality, defined as a performance function of time set by the stakeholders. Critical functionality is a source of valuable information, such as the integrated system resilience over a time interval and its robustness. The paper demonstrates the formulation on two classes of models: 1) multi-level directed acyclic graphs and 2) interdependent coupled networks. For both models synthetic case studies are used to explore trends. For the first class, the approach is also applied to the Linux operating system. Results indicate that desired resilience and robustness levels are achievable by trading off different design parameters, such as redundancy, node recovery time and backup supply available. The nonlinear relationship between network parameters and resilience levels confirms the utility of the proposed approach, which is of benefit to analysts and designers of complex systems and networks.