bluuebunny/crossref_metadata_2025 huggingface dataset:
Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria
Authors: Eiler Alexander , Mondav Rhiannon , Sinclair Lucas , Fernandez-Vidal Leyden , Scofield Douglas G , Schwientek Patrick , Martinez-Garcia Manuel , Torrents David , McMahon Katherine D , Andersson Siv G E , Stepanauskas Ramunas , Woyke Tanja , Bertilsson Stefan
Published: January 2016

Most free-living planktonic cells are streamlined and in spite of their limitations in functional flexibility, their vast populations have radiated into a wide range of aquatic habitats. Here we compared the metabolic potential of subgroups in the Alphaproteobacteria lineage SAR11 adapted to marine and freshwater habitats. Our results suggest that the successful leap from marine to freshwaters in SAR11 was accompanied by a loss of several carbon degradation pathways and a rewiring of the central metabolism. Examples for these are C1 and methylated compounds degradation pathways, the Entner–Doudouroff pathway, the glyoxylate shunt and anapleuretic carbon fixation being absent from the freshwater genomes. Evolutionary reconstructions further suggest that the metabolic modules making up these important freshwater metabolic traits were already present in the gene pool of ancestral marine SAR11 populations. The loss of the glyoxylate shunt had already occurred in the common ancestor of the freshwater subgroup and its closest marine relatives, suggesting that the adaptation to freshwater was a gradual process. Furthermore, our results indicate rapid evolution of TRAP transporters in the freshwater clade involved in the uptake of low molecular weight carboxylic acids. We propose that such gradual tuning of metabolic pathways and transporters toward locally available organic substrates is linked to the formation of subgroups within the SAR11 clade and that this process was critical for the freshwater clade to find and fix an adaptive phenotype.
Autonomous beating rate adaptation in human stem cell-derived cardiomyocytes
Authors: Eng George , Lee Benjamin W. , Protas Lev , Gagliardi Mark , Brown Kristy , Kass Robert S. , Keller Gordon , Robinson Richard B. , Vunjak-Novakovic Gordana
Published: January 2016

The therapeutic success of human stem cell-derived cardiomyocytes critically depends on their ability to respond to and integrate with the surrounding electromechanical environment. Currently, the immaturity of human cardiomyocytes derived from stem cells limits their utility for regenerative medicine and biological research. We hypothesize that biomimetic electrical signals regulate the intrinsic beating properties of cardiomyocytes. Here we show that electrical conditioning of human stem cell-derived cardiomyocytes in three-dimensional culture promotes cardiomyocyte maturation, alters their automaticity and enhances connexin expression. Cardiomyocytes adapt their autonomous beating rate to the frequency at which they were stimulated, an effect mediated by the emergence of a rapidly depolarizing cell population, and the expression of hERG. This rate-adaptive behaviour is long lasting and transferable to the surrounding cardiomyocytes. Thus, electrical conditioning may be used to promote cardiomyocyte maturation and establish their automaticity, with implications for cell-based reduction of arrhythmia during heart regeneration.
Generalized Brewster effect in dielectric metasurfaces
Authors: Paniagua-Domínguez Ramón , Yu Ye Feng , Miroshnichenko Andrey E. , Krivitsky Leonid A. , Fu Yuan Hsing , Valuckas Vytautas , Gonzaga Leonard , Toh Yeow Teck , Kay Anthony Yew Seng , Luk’yanchuk Boris , Kuznetsov Arseniy I.
Published: January 2016

Polarization is a key property defining the state of light. It was discovered by Brewster, while studying light reflected from materials at different angles. This led to the first polarizers, based on Brewster’s effect. Now, one of the trends in photonics is the study of miniaturized devices exhibiting similar, or improved, functionalities compared with bulk optical elements. In this work, it is theoretically predicted that a properly designed all-dielectric metasurface exhibits a generalized Brewster’s effect potentially for any angle, wavelength and polarization of choice. The effect is experimentally demonstrated for an array of silicon nanodisks at visible wavelengths. The underlying physics is related to the suppressed scattering at certain angles due to the interference between the electric and magnetic dipole resonances excited in the nanoparticles. These findings open doors for Brewster phenomenon to new applications in photonics, which are not bonded to a specific polarization or angle of incidence.
Optimal metal domain size for photocatalysis with hybrid semiconductor-metal nanorods
Authors: Ben-Shahar Yuval , Scotognella Francesco , Kriegel Ilka , Moretti Luca , Cerullo Giulio , Rabani Eran , Banin Uri
Published: January 2016

Semiconductor-metal hybrid nanostructures offer a highly controllable platform for light-induced charge separation, with direct relevance for their implementation in photocatalysis. Advances in the synthesis allow for control over the size, shape and morphology, providing tunability of the optical and electronic properties. A critical determining factor of the photocatalytic cycle is the metal domain characteristics and in particular its size, a subject that lacks deep understanding. Here, using a well-defined model system of cadmium sulfide-gold nanorods, we address the effect of the gold tip size on the photocatalytic function, including the charge transfer dynamics and hydrogen production efficiency. A combination of transient absorption, hydrogen evolution kinetics and theoretical modelling reveal a non-monotonic behaviour with size of the gold tip, leading to an optimal metal domain size for the most efficient photocatalysis. We show that this results from the size-dependent interplay of the metal domain charging, the relative band-alignments, and the resulting kinetics.
Direct measurement of large-scale quantum states via expectation values of non-Hermitian matrices
Authors: Bolduc Eliot , Gariepy Genevieve , Leach Jonathan
Published: January 2016

In quantum mechanics, predictions are made by way of calculating expectation values of observables, which take the form of Hermitian operators. Non-Hermitian operators, however, are not necessarily devoid of physical significance, and they can play a crucial role in the characterization of quantum states. Here we show that the expectation values of a particular set of non-Hermitian matrices, which we call column operators, directly yield the complex coefficients of a quantum state vector. We provide a definition of the state vector in terms of measurable quantities by decomposing these column operators into observables. The technique we propose renders very-large-scale quantum states significantly more accessible in the laboratory, as we demonstrate by experimentally characterizing a 100,000-dimensional entangled state. This represents an improvement of two orders of magnitude with respect to previous phase-and-amplitude characterizations of discrete entangled states.
The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts
Authors: Rinaldi Arlie J. , Lund Paul E. , Blanco Mario R. , Walter Nils G.
Published: January 2016

In response to intracellular signals in Gram-negative bacteria, translational riboswitches—commonly embedded in messenger RNAs (mRNAs)—regulate gene expression through inhibition of translation initiation. It is generally thought that this regulation originates from occlusion of the Shine-Dalgarno (SD) sequence upon ligand binding; however, little direct evidence exists. Here we develop Single Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) to investigate the ligand-dependent accessibility of the SD sequence of an mRNA hosting the 7-aminomethyl-7-deazaguanine (preQ1)-sensing riboswitch. Spike train analysis reveals that individual mRNA molecules alternate between two conformational states, distinguished by ‘bursts’ of probe binding associated with increased SD sequence accessibility. Addition of preQ1 decreases the lifetime of the SD’s high-accessibility (bursting) state and prolongs the time between bursts. In addition, ligand-jump experiments reveal imperfect riboswitching of single mRNA molecules. Such complex ligand sensing by individual mRNA molecules rationalizes the nuanced ligand response observed during bulk mRNA translation.
Tumor-associated macrophages: unwitting accomplices in breast cancer malignancy
Authors: Williams Carly Bess , Yeh Elizabeth S , Soloff Adam C
Published: January 2016

Deleterious inflammation is a primary feature of breast cancer. Accumulating evidence demonstrates that macrophages, the most abundant leukocyte population in mammary tumors, have a critical role at each stage of cancer progression. Such tumor-associated macrophages facilitate neoplastic transformation, tumor immune evasion and the subsequent metastatic cascade. Herein, we discuss the dynamic process whereby molecular and cellular features of the tumor microenvironment act to license tissue-repair mechanisms of macrophages, fostering angiogenesis, metastasis and the support of cancer stem cells. We illustrate how tumors induce, then exploit trophic macrophages to subvert innate and adaptive immune responses capable of destroying malignant cells. Finally, we discuss compelling evidence from murine models of cancer and early clinical trials in support of macrophage-targeted intervention strategies with the potential to dramatically reduce breast cancer morbidity and mortality.
Trading off stability against activity in extremophilic aldolases
Authors: Dick Markus , Weiergräber Oliver H. , Classen Thomas , Bisterfeld Carolin , Bramski Julia , Gohlke Holger , Pietruszka Jörg
Published: January 2016

Understanding enzyme stability and activity in extremophilic organisms is of great biotechnological interest, but many questions are still unsolved. Using 2-deoxy-D-ribose-5-phosphate aldolase (DERA) as model enzyme, we have evaluated structural and functional characteristics of different orthologs from psychrophilic, mesophilic and hyperthermophilic organisms. We present the first crystal structures of psychrophilic DERAs, revealing a dimeric organization resembling their mesophilic but not their thermophilic counterparts. Conversion into monomeric proteins showed that the native dimer interface contributes to stability only in the hyperthermophilic enzymes. Nevertheless, introduction of a disulfide bridge in the interface of a psychrophilic DERA did confer increased thermostability, suggesting a strategy for rational design of more durable enzyme variants. Constraint network analysis revealed particularly sparse interactions between the substrate pocket and its surrounding α-helices in psychrophilic DERAs, which indicates that a more flexible active center underlies their high turnover numbers.
Effects of veridical expectations on syntax processing in music: Event-related potential evidence
Authors: Guo Shuang , Koelsch Stefan
Published: January 2016

Numerous past studies have investigated neurophysiological correlates of music-syntactic processing. However, only little is known about how prior knowledge about an upcoming syntactically irregular event modulates brain correlates of music-syntactic processing. Two versions of a short chord sequence were presented repeatedly to non-musicians (n = 20) and musicians (n = 20). One sequence version ended on a syntactically regular chord and the other one ended on a syntactically irregular chord. Participants were either informed (cued condition), or not informed (non-cued condition) about whether the sequence would end on the regular or the irregular chord. Results indicate that in the cued condition (compared to the non-cued condition) the peak latency of the early right anterior negativity (ERAN), elicited by irregular chords, was earlier in both non-musicians and musicians. However, the expectations due to the knowledge about the upcoming event (veridical expectations) did not influence the amplitude of the ERAN. These results suggest that veridical expectations modulate only the speed, but not the principle mechanisms, of music-syntactic processing.
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

Soil 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

Virus-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

Vertnin (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

We 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

Mitochondrial 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

Antibody 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

Atomistic 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

Non-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.
Correction: Corrigendum: Circulating HIV DNA Correlates With Neurocognitive Impairment in Older HIV-infected Adults on Suppressive ART
Authors: de Oliveira Michelli Faria , Murrell Ben , Pérez-Santiago Josué , Vargas Milenka , Ellis Ronald J. , Letendre Scott , Grant Igor , Smith Davey M. , Woods Steven Paul , Gianella Sara
Published: January 2016

Older HIV-infected adults have a higher risk of neurocognitive impairment, but the underlying mechanisms are poorly understood. Here, we investigated the associations between levels of HIV DNA in peripheral blood, soluble markers of inflammation and cellular trafficking in blood and cerebrospinal fluid (CSF) and neurocognitive functioning among 18 younger (22–40 years) and 26 older (50–71 years) HIV-infected subjects, who were administered a comprehensive neurocognitive battery. Older HIV-infected individuals presented higher levels of inflammation in CSF and blood compared to younger individuals, but no difference was observed in HIV DNA levels. Among older participants, higher HIV DNA levels were significantly associated with more severe neurocognitive impairment (p = 0.005), particularly in the Executive Functions domain (p = 0.004). No association was observed between HIV DNA and neurocognition among younger individuals. Despite significantly increased inflammation observed in the older group, none of the inflammatory markers were associated with neurocognitive impairment among older HIV+ individuals (p > 0.05). Our study supports the involvement of peripheral HIV DNA reservoir in the pathogenesis of neurocognitive disorder during suppressive ART. Correlates of neurocognitive impairment might differ between younger and older adults, suggesting that future treatment and prevention strategies for HIV-associated neurocognitive disorders likely need to be tailored based on age.
Cue properties change timing strategies in group movement synchronisation
Authors: Honisch Juliane J. , Elliott Mark T. , Jacoby Nori , Wing Alan M.
Published: January 2016

To 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

PRPF31-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

The 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

Anomalous 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

Owing 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

Hyperentangled 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

We 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

Enhancing 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

Building 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.
How Do the Size, Charge and Shape of Nanoparticles Affect Amyloid β Aggregation on Brain Lipid Bilayer?
Authors: Kim Yuna , Park Ji-Hyun , Lee Hyojin , Nam Jwa-Min
Published: January 2016

Here, we studied the effect of the size, shape and surface charge of Au nanoparticles (AuNPs) on amyloid beta (Aβ) aggregation on a total brain lipid-based supported lipid bilayer (brain SLB), a fluid platform that facilitates Aβ-AuNP aggregation process. We found that larger AuNPs induce large and amorphous aggregates on the brain SLB, whereas smaller AuNPs induce protofibrillar Aβ structures. Positively charged AuNPs were more strongly attracted to Aβ than negatively charged AuNPs and the stronger interactions between AuNPs and Aβ resulted in fewer β-sheets and more random coil structures. We also compared spherical AuNPs, gold nanorods (AuNRs) and gold nanocubes (AuNCs) to study the effect of nanoparticle shape on Aβ aggregation on the brain SLB. Aβ was preferentially bound to the long axis of AuNRs and fewer fibrils were formed whereas all the facets of AuNCs interacted with Aβ to produce the fibril networks. Finally, it was revealed that different nanostructures induce different cytotoxicity on neuroblastoma cells, and, overall, smaller Aβ aggregates induce higher cytotoxicity. The results offer insight into the roles of NPs and brain SLB in Aβ aggregation on the cell membrane and can facilitate the understanding of Aβ-nanostructure co-aggregation mechanism and tuning Aβ aggregate structures.
Immunization against an IL-6 peptide induces anti-IL-6 antibodies and modulates the Delayed-Type Hypersensitivity reaction in cynomolgus monkeys
Authors: Desallais Lucille , Bouchez Caroline , Mouhsine Hadley , Moreau Gabriel , Ratsimandresy Rojo , Montes Matthieu , Do Hervé , Quintin-Colonna Françoise , Zagury Jean-François
Published: January 2016

Interleukin-6 (IL-6) overproduction has been involved in the pathogenesis of several chronic inflammatory diseases and the administration of an anti-IL-6 receptor monoclonal antibody has been proven clinically efficient to treat them. However, the drawbacks of monoclonal antibodies have led our group to develop an innovative anti-IL-6 strategy using a peptide-based active immunization. This approach has previously shown its efficacy in a mouse model of systemic sclerosis. Here the safety, immunogenicity and efficacy of this strategy was assessed in non human primates. No unscheduled death and clinical signs of toxicity was observed during the study. Furthermore, the cynomolgus monkeys immunized against the IL-6 peptide produced high levels of anti-IL-6 antibodies as well as neutralizing antibodies compared to control groups. They also showed an important decrease of the cumulative inflammatory score following a delayed-type hypersensitivity reaction induced by the Tetanus vaccine compared to control groups (minus 57,9%,P = 0.014). These findings are highly significant because the immunizing IL-6 peptide used in this study is identical in humans and in monkeys and this novel anti-IL-6 strategy could thus represent a promising alternative to monoclonal antibodies.
Optically induced mode splitting in self-assembled, high quality-factor conjugated polymer microcavities
Authors: Braam Daniel , Kushida Soh , Niemöller Robert , Prinz Günther M. , Saito Hitoshi , Kanbara Takaki , Kuwabara Junpei , Yamamoto Yohei , Lorke Axel
Published: January 2016

We investigate the whispering gallery modes (WGMs) of self-assembled single microspheres. They consist of a recently developed highly fluorescent π-conjugated copolymer and exhibit excellent optical properties with Q-factors up to 104. Under continuous laser irradiation, we observe a splitting of the highly degenerate spherical WGMs into a multiplet of lines. Comparison with the calculated spectral response of a weakly distorted sphere shows that the optical excitation induces a change of the optical path length in the microcavity so that it resembles a prolate spheroid. The separation of the lines is given by the ellipticity and the azimuthal mode number. Measurements in various gaseous environments suggest that the distortion is caused by light induced oxidation of the polymer. Our findings show that photooxidation can be a beneficial mechanism for in-situ tuning of optically active polymer structures.
Pre-sowing Seed Treatments in Direct-seeded Early Rice: Consequences for Emergence, Seedling Growth and Associated Metabolic Events under Chilling Stress
Authors: Wang Weiqin , Chen Qian , Hussain Saddam , Mei Junhao , Dong Huanglin , Peng Shaobing , Huang Jianliang , Cui Kehui , Nie Lixiao
Published: January 2016

Double direct-seeding for double rice cropping is a simplified, labor saving and efficient cropping system to improve multiple-crop index and total rice production in central China. However, poor crop establishment of direct-seeded early rice due to chilling stress is the main obstacle to wide spread of this system. A series of experiments were conducted to unravel the effects of pre-sowing seed treatments on emergence, seedling growth and associated metabolic events of direct-seeded early rice under chilling stress. Two seed priming treatments and two seed coating treatments were used in all the experiments. A non-treated control treatment was also maintained for comparison. In both the field and growth chamber studies, seed priming with selenium or salicylic acid significantly enhanced the emergence and seedling growth of rice compared with non-treated control. Nevertheless, such positive effects were not apparent for seed coating treatments. Better emergence and vigorous seedling growth of rice after seed priming was associated with enhanced α-amylase activity, higher soluble sugars contents and greater respiration rate in primed rice seedlings under chilling stress. Taking together, these findings may provide new avenues for understanding and advancing priming-induced chilling tolerance in direct-seeded early rice in double rice cropping system.
Effects of K-115 (Ripasudil), a novel ROCK inhibitor, on trabecular meshwork and Schlemm’s canal endothelial cells
Authors: Kaneko Yoshio , Ohta Masayuki , Inoue Toshihiro , Mizuno Ken , Isobe Tomoyuki , Tanabe Sohei , Tanihara Hidenobu
Published: January 2016

Ripasudil hydrochloride hydrate (K-115), a specific Rho-associated coiled-coil containing protein kinase (ROCK) inhibitor, was the first ophthalmic solution developed for the treatment of glaucoma and ocular hypertension in Japan. Topical administration of K-115 decreased intraocular pressure (IOP) and increased outflow facility in rabbits. This study evaluated the effect of K-115 on monkey trabecular meshwork (TM) cells and Schlemm’s canal endothelial (SCE) cells. K-115 induced retraction and rounding of cell bodies as well as disruption of actin bundles in TM cells. In SCE-cell monolayer permeability studies, K-115 significantly decreased transendothelial electrical resistance (TEER) and increased the transendothelial flux of FITC-dextran. Further, K-115 disrupted cellular localization of ZO-1 expression in SCE-cell monolayers. These results indicate that K-115 decreases IOP by increasing outflow facility in association with the modulation of TM cell behavior and SCE cell permeability in association with disruption of tight junction.
Dual Ionic and Organic Nature of Ionic Liquids
Authors: Shi Rui , Wang Yanting
Published: January 2016

Inherited the advantages of inorganic salts and organic solvents, ionic liquids (ILs) exhibit many superior properties allowing them promising green solvents for the future. Although it has been widely acknowledged that the unique features of ILs originate from their dual ionic and organic nature, its microscopic physical origin still remains blurry. In this work, by comparing the ion/molecule cage structures obtained from molecular dynamics simulations for seven prototypic liquids—a molten inorganic salt, four ILs, a strongly polar organic solvent and a weakly polar organic solvent, we have revealed that the depth of the cage energy landscape characterizes the ionic nature of ILs, whereas the slope and curvature of its mimimum determine the organic nature of ILs. This finding advances our understanding of ILs and thus will help their efficient utilization as well as the systematic design of novel functionalized ILs.
Characterization of the promoter region of the bovine long-chain acyl-CoA synthetase 1 gene: Roles of E2F1, Sp1, KLF15 and E2F4
Authors: Zhao Zhi-Dong , Zan Lin-Sen , Li An-Ning , Cheng Gong , Li Shi-Jun , Zhang Ya-Ran , Wang Xiao-Yu , Zhang Ying-Ying
Published: January 2016

The nutritional value and eating qualities of beef are enhanced when the unsaturated fatty acid content of fat is increased. Long-chain acyl-CoA synthetase 1 (ACSL1) plays key roles in fatty acid transport and degradation, as well as lipid synthesis. It has been identified as a plausible functional and positional candidate gene for manipulations of fatty acid composition in bovine skeletal muscle. In the present study, we determined that bovine ACSL1was highly expressed in subcutaneous adipose tissue and longissimus thoracis. To elucidate the molecular mechanisms involved in bovine ACSL1 regulation, we cloned and characterized the promoter region of ACSL1. Applying 5′-rapid amplification of cDNA end analysis (RACE), we identified multiple transcriptional start sites (TSSs) in its promoter region. Using a series of 5′ deletion promoter plasmids in luciferase reporter assays, we found that the proximal minimal promoter of ACSL1 was located within the region −325/−141 relative to the TSS and it was also located in the predicted CpG island. Mutational analysis and electrophoretic mobility shift assays demonstrated that E2F1, Sp1, KLF15 and E2F4 binding to the promoter region drives ACSL1 transcription. Together these interactions integrate and frame a key functional role for ACSL1 in mediating the lipid composition of beef.