bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of Commercial Thermo-sensitive Genic Male Sterile Rice Accelerates Hybrid Rice Breeding Using the CRISPR/Cas9-mediated TMS5 Editing System
Authors: Zhou Hai , He Ming , Li Jing , Chen Liang , Huang Zhifeng , Zheng Shaoyan , Zhu Liya , Ni Erdong , Jiang Dagang , Zhao Bingran , Zhuang Chuxiong 
Published: November 2016

AbstractHybrid rice breeding offers an important strategy to improve rice production, in which the cultivation of a male sterile line is the key to the success of cross-breeding. CRISPR/Cas9 systems have been widely used in target-site genome editing, whereas their application for crop genetic improvement has been rarely reported. Here, using the CRISPR/Cas9 system, we induced specific mutations in TMS5, which is the most widely applied thermo-sensitive genic male sterility (TGMS) gene in China, and developed new “transgene clean” TGMS lines. We designed 10 target sites in the coding region of TMS5 for targeted mutagenesis using the CRISPR/Cas9 system and assessed the potential rates of on- and off-target effects. Finally, we established the most efficient construct, the TMS5ab construct, for breeding potentially applicable “transgene clean” TGMS lines. We also discussed factors that affect the editing efficiency according to the characteristics of different target sequences. Notably, using the TMS5ab construct, we developed 11 new “transgene clean” TGMS lines with potential applications in hybrid breeding within only one year in both rice subspecies. The application of our system not only significantly accelerates the breeding of sterile lines but also facilitates the exploitation of heterosis.
Correlation analysis of the mRNA and miRNA expression profiles in the nascent synthetic allotetraploid Raphanobrassica
Authors: Ye Bingyuan , Wang Ruihua , Wang Jianbo 
Published: November 2016

AbstractRaphanobrassicais an allopolyploid species derived from inter-generic hybridization that combines the R genome fromR. sativusand the C genome fromB. oleraceavar.alboglabra. In the present study, we used a high-throughput sequencing method to identify the mRNA and miRNA profiles inRaphanobrassicaand its parents. A total of 33,561 mRNAs and 283 miRNAs were detected, 9,209 mRNAs and 134 miRNAs were differentially expressed respectively, 7,633 mRNAs and 39 miRNAs showed ELD expression, 5,219 mRNAs and 57 miRNAs were non-additively expressed inRaphanobrassica. Remarkably, differentially expressed genes (DEGs) were up-regulated and maternal bias was detected inRaphanobrassica. In addition, a miRNA-mRNA interaction network was constructed based on reverse regulated miRNA-mRNAs, which included 75 miRNAs and 178 mRNAs, 31 miRNAs were non-additively expressed target by 13 miRNAs. The related target genes were significantly enriched in the GO term ‘metabolic processes’. Non-additive related target genes regulation is involved in a range of biological pathways, like providing a driving force for variation and adaption in this allopolyploid. The integrative analysis of mRNA and miRNA profiling provides more information to elucidate gene expression mechanism and may supply a comprehensive and corresponding method to study genetic and transcription variation of allopolyploid.
Structural basis of TRPA1 inhibition by HC-030031 utilizing species-specific differences
Authors: Gupta Rupali , Saito Shigeru , Mori Yoshiharu , Itoh Satoru G. , Okumura Hisashi , Tominaga Makoto 
Published: November 2016

AbstractPain is a harmful sensation that arises from noxious stimuli. Transient receptor potential ankyrin 1 (TRPA1) is one target for studying pain mechanisms. TRPA1 is activated by various stimuli such as noxious cold, pungent natural products and environmental irritants. Since TRPA1 is an attractive target for pain therapy, a few TRPA1 antagonists have been developed and some function as analgesic agents. The responses of TRPA1 to agonists and antagonists vary among species and these species differences have been utilized to identify the structural basis of activation and inhibition mechanisms. The TRPA1 antagonist HC-030031 (HC) failed to inhibit frog TRPA1 (fTRPA1) and zebrafish TRPA1 activity induced by cinnamaldehyde (CA), but did inhibit human TRPA1 (hTRPA1) in a heterologous expression system. Chimeric studies between fTRPA1 and hTRPA1, as well as analyses using point mutants, revealed that a single amino acid residue (N855 in hTRPA1) significantly contributes to the inhibitory action of HC. Moreover, the N855 residue and the C-terminus region exhibited synergistic effects on the inhibition by HC. Molecular dynamics simulation suggested that HC stably binds to hTRPA1-N855. These findings provide novel insights into the structure-function relationship of TRPA1 and could lead to the development of more effective analgesics targeted to TRPA1.
Crosstalk among proteome, acetylome and succinylome in colon cancer HCT116 cell treated with sodium dichloroacetate
Authors: Zhu Danxi , Hou Lidan , Hu Bin , Zhao Hang , Sun Jie , Wang Jianhua , Meng Xiangjun 
Published: November 2016

AbstractProtein lysine acetylation and succinylation play important regulatory roles in cells, both of which or each other has a close relationship. Dichloroacetate (DCA), a well-known pyruvate dehydrogenase kinase (PDK) inhibitor, has the potential to be used as anti-cancer drugs for several tumors including colorectal cancer. However, little is known about the potential mechanism of DCA-based cancer therapy by protein posttranslational modifications (PTM) including global proteome, acetylome and succinylome. Here the combinations with stable isotope labeling (SILAC), antibody affinity enrichment and high resolution LC-MS/MS analysis were performed in human colon cancer HCT116 cells. The quantifiable proteome was annotated using bioinformatics. In total, 4,518 proteins, 1,436 acetylation sites, and 671 succinylation sites were quantified, respectively to DCA treatment. Among the quantified acetylated sites, 158 were with increased level (quantification ratio >1.5) and 145 with decreased level (quantification ratio <0.67). Meanwhile, 179 up-regulated and 114 down-regulated succinylated sites were identified. The bioinformatics analyses initially showed acetylation and succinylation were involved in a wide range of cellular functions upon DCA-based anti-cancer effects. Notably, protein-protein interaction network analyses demonstrated widespread interactions modulated by protein acetylation and succinylation. Taken together, this study may shed a light on understanding the mechanism of DCA-based cancer treatment.
Characterization of two distinct early post-entry blocks to HIV-1 in common marmoset lymphocytes
Authors: Pacheco Beatriz , Menéndez-Arias Luis , Sodroski Joseph 
Published: November 2016

AbstractIn nature, primate lentiviruses infect humans and several Old World monkeys and apes. However, to date, lentiviruses infecting New World monkeys have not been described. We studied the susceptibility of common marmoset cells to HIV-1 infection and observed the presence of post-entry blocks to the early phase of HIV-1 infection in peripheral blood lymphocytes (PBLs) and a B lymphocytic cell line (B-LCL). The blocks present in these cells are dominant and phenotypically different from each other. In PBLs, the block occurs at the level of reverse transcription, reducing the accumulation of early and late transcripts, similar to the block imposed by TRIM5α. However, we have found that marmoset TRIM5α does not block HIV-1. In contrast, the restriction factor present in B-LCLs blocks HIV-1 replication at a later step, after nuclear entry, and inhibits integration. Additionally, we have identified an HIV-1 capsid mutant, N74D, that is able to escape the restriction in the marmoset B-LCLs. Our results suggest that the factors responsible for the blocks present in marmoset PBLs and B-LCLs are different. We propose the existence of at least two new restriction factors able to block HIV-1 infection in marmoset lymphocytes.
The coordinated roles of miR-26a and miR-30c in regulating TGFβ1-induced epithelial-to-mesenchymal transition in diabetic nephropathy
Authors: Zheng Zongji , Guan Meiping , Jia Yijie , Wang Dan , Pang Ruoyu , Lv Fuping , Xiao Zhizhou , Wang Ling , Zhang Hongbin , Xue Yaoming 
Published: November 2016

AbstractMicroRNAs (miRNAs) play vital roles in the development of diabetic nephropathy. Here, we compared the protective efficacies of miR-26a and miR-30c in renal tubular epithelial cells (NRK-52E) and determined whether they demonstrated additive effects in the attenuation of renal fibrosis. TGFβ1 suppressed miR-26a and miR-30c expression but up-regulated pro-fibrotic markers in NRK-52E cells, and these changes were also found in the kidney cortex of 40-week-old diabetic Otsuka Long-Evans Tokushima fatty (OLETF) rats. Bioinformatic analyses and luciferase assays further demonstrated that both miR-26a and miR-30c targeted connective tissue growth factor (CTGF); additionally, Snail family zinc finger 1 (Snail1), a potent epithelial-to-mesenchymal transition (EMT) inducer, was targeted by miR-30c. Overexpression of miR-26a and miR-30c coordinately decreased CTGF protein levels and subsequently ameliorated TGFβ1-induced EMT in NRK-52E cells. Co-silencing of miR-26a and miR-30c exhibited the opposite effect. Moreover, miR-26a and miR-30c co-silenced CTGF to decrease ERK1/2 and p38 MAPK activation. Furthermore, miR-26a was up-regulated in urinary extracellular vesicles of diabetic nephropathy patients. Our study provides evidence for the cooperative roles of miR-26a and miR-30c in the pathogenesis of diabetic nephropathy, and the co-targeting of miR-26a and miR-30c could provide a new direction for diabetic nephropathy treatment.
Close relationship between a dry-wet transition and a bubble rearrangement in two-dimensional foam
Authors: Furuta Yujiro , Oikawa Noriko , Kurita Rei 
Published: November 2016

AbstractLiquid foams are classified into a dry foam and a wet foam, empirically judging from the liquid fraction or the shape of the gas bubbles. It is known that physical properties such as elasticity and diffusion are different between the dry foam and the wet foam. Nevertheless, definitions of those states have been vague and the dry-wet transition of foams has not been clarified yet. Here we show that the dry-wet transition is closely related to rearrangement of the gas bubbles, by simultaneously analysing the shape change of the bubbles and that of the entire foam in two dimensional foam. In addition, we also find a new state in quite low liquid fraction, which is named “superdry foam”. Whereas the shape change of the bubbles strongly depends on the change of the liquid fraction in the superdry foam, the shape of the bubbles does not change with changing the liquid fraction in the dry foam. Our results elucidate the relationship between the transitions and the macroscopic mechanical properties.
miR-706 inhibits the oxidative stress-induced activation of PKCα/TAOK1 in liver fibrogenesis
Authors: Yin Ruili , Guo Duo , Zhang Shuxian , Zhang Xiuying 
Published: November 2016

AbstractOxidative stress induces the activation of liver fibrogenic cells (myofibroblasts), thus promoting the expression of fibrosis-related genes, leading to hepatic fibrogenesis. MicroRNAs (miRNAs) are a new class of small RNAs ~18–25 nucleotides in length involved in post-transcriptional regulation of gene expression. Wound-healing and remodeling processes in liver fibrosis have been associated with changes in hepatic miRNA expression. However, the role of miR-706 in liver fibrogenesis is currently unknown. In the present study, we show that miR-706 is abundantly expressed in hepatocytes. Moreover, oxidative stress leads to a significant downregulation of miR-706, and the further reintroduction of miR-706 inhibits oxidative stress-induced expression of fibrosis-related markers such as α-SMA. Subsequent studies revealed that miR-706 directly inhibits PKCα and TAOK1 expression via binding to the 3′-untranslated region, preventing epithelial mesenchymal transition. In vivo studies showed that intravenous injection of miR-706 agomir successfully increases hepatic miR-706 and decreases α-SMA, PKCα, and TAOK1 protein levels in livers of carbon tetrachloride (CCl4)-treated mice. In summary, this study reveals a protective role for miR-706 by blocking the oxidative stress-induced activation of PKCα/TAOK1. Our results further identify a major implication for miR-706 in preventing hepatic fibrogenesis and suggest that miR-706 may be a suitable molecular target for anti-fibrosis therapy.
Inverse changes in L1 retrotransposons between blood and brain in major depressive disorder
Authors: Liu Shu , Du Tingfu , Liu Zeyue , Shen Yan , Xiu Jianbo , Xu Qi 
Published: November 2016

AbstractLong interspersed nuclear element-1 (LINE-1 or L1) is a type of retrotransposons comprising 17% of the human and mouse genome, and has been found to be associated with several types of neurological disorders. Previous post-mortem brain studies reveal increased L1 copy number in the prefrontal cortex from schizophrenia patients. However, whether L1 retrotransposition occurs similarly in major depressive disorder (MDD) is unknown. Here, L1 copy number was measured by quantitative PCR analysis in peripheral blood of MDD patients (n = 105) and healthy controls (n = 105). The results showed that L1 copy number was increased in MDD patients possibly due to its hypomethylation. Furthermore, L1 copy number in peripheral blood and five brain regions (prefrontal cortex, hippocampus, amygdala, nucleus accumbens and paraventricular hypothalamic nucleus) was measured in the chronic unpredictable mild stress (CUMS) model of depression in mice. Intriguingly, increased L1 copy number in blood and the decreased L1 copy number in the prefrontal cortex were observed in stressed mice, while no change was found in other brain regions. Our results suggest that the changes of L1 may be associated with the pathophysiology of MDD, but the biological mechanism behind dysfunction of L1 retrotransposition in MDD remains to be further investigated.
The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle
Authors: Rougon-Cardoso Alejandra , Flores-Ponce Mitzi , Ramos-Aboites Hilda Eréndira , Martínez-Guerrero Christian Eduardo , Hao You-Jin , Cunha Luis , Rodríguez-Martínez Jonathan Alejandro , Ovando-Vázquez Cesaré , Bermúdez-Barrientos José Roberto , Abreu-Goodger Cei , Chavarría-Hernández Norberto , Simões Nelson , Montiel Rafael 
Published: November 2016

AbstractThe entomopathogenic nematode Steinernema carpocapsae has been widely used for the biological control of insect pests. It shares a symbiotic relationship with the bacterium Xenorhabdus nematophila, and is emerging as a genetic model to study symbiosis and pathogenesis. We obtained a high-quality draft of the nematode’s genome comprising 84,613,633 bp in 347 scaffolds, with an N50 of 1.24 Mb. To improve annotation, we sequenced both short and long RNA and conducted shotgun proteomic analyses. S. carpocapsae shares orthologous genes with other parasitic nematodes that are absent in the free-living nematode C. elegans, it has ncRNA families that are enriched in parasites, and expresses proteins putatively associated with parasitism and pathogenesis, suggesting an active role for the nematode during the pathogenic process. Host and parasites might engage in a co-evolutionary arms-race dynamic with genes participating in their interaction showing signatures of positive selection. Our analyses indicate that the consequence of this arms race is better characterized by positive selection altering specific functions instead of just increasing the number of positively selected genes, adding a new perspective to these co-evolutionary theories. We identified a protein, ATAD-3, that suggests a relevant role for mitochondrial function in the evolution and mechanisms of nematode parasitism.
Navigation by anomalous random walks on complex networks
Authors: Weng Tongfeng , Zhang Jie , Khajehnejad Moein , Small Michael , Zheng Rui , Hui Pan 
Published: November 2016

AbstractAnomalous random walks having long-range jumps are a critical branch of dynamical processes on networks, which can model a number of search and transport processes. However, traditional measurements based on mean first passage time are not useful as they fail to characterize the cost associated with each jump. Here we introduce a new concept of mean first traverse distance (MFTD) to characterize anomalous random walks that represents the expected traverse distance taken by walkers searching from source node to target node, and we provide a procedure for calculating the MFTD between two nodes. We use Lévy walks on networks as an example, and demonstrate that the proposed approach can unravel the interplay between diffusion dynamics of Lévy walks and the underlying network structure. Moreover, applying our framework to the famous PageRank search, we show how to inform the optimality of the PageRank search. The framework for analyzing anomalous random walks on complex networks offers a useful new paradigm to understand the dynamics of anomalous diffusion processes, and provides a unified scheme to characterize search and transport processes on networks.
The Mediterranean Plastic Soup: synthetic polymers in Mediterranean surface waters
Authors: Suaria Giuseppe , Avio Carlo G. , Mineo Annabella , Lattin Gwendolyn L. , Magaldi Marcello G. , Belmonte Genuario , Moore Charles J. , Regoli Francesco , Aliani Stefano 
Published: November 2016

AbstractThe Mediterranean Sea has been recently proposed as one of the most impacted regions of the world with regards to microplastics, however the polymeric composition of these floating particles is still largely unknown. Here we present the results of a large-scale survey of neustonic micro- and meso-plastics floating in Mediterranean waters, providing the first extensive characterization of their chemical identity as well as detailed information on their abundance and geographical distribution. All particles >700 μm collected in our samples were identified through FT-IR analysis (n = 4050 particles), shedding for the first time light on the polymeric diversity of this emerging pollutant. Sixteen different classes of synthetic materials were identified. Low-density polymers such as polyethylene and polypropylene were the most abundant compounds, followed by polyamides, plastic-based paints, polyvinyl chloride, polystyrene and polyvinyl alcohol. Less frequent polymers included polyethylene terephthalate, polyisoprene, poly(vinyl stearate), ethylene-vinyl acetate, polyepoxide, paraffin wax and polycaprolactone, a biodegradable polyester reported for the first time floating in off-shore waters. Geographical differences in sample composition were also observed, demonstrating sub-basin scale heterogeneity in plastics distribution and likely reflecting a complex interplay between pollution sources, sinks and residence times of different polymers at sea.
Growth Mechanisms of Inductively-Coupled Plasma Torch Synthesized Silicon Nanowires and their associated photoluminescence properties
Authors: Agati M. , Amiard G. , Le Borgne V. , Castrucci P. , Dolbec R. , De Crescenzi M. , El Khakani M. A. , Boninelli S. 
Published: November 2016

AbstractUltra-thin Silicon Nanowires (SiNWs) were produced by means of an industrial inductively-coupled plasma (ICP) based process. Two families of SiNWs have been identified, namely long SiNWs (up to 2–3 micron in length) and shorter ones (~100 nm). SiNWs were found to consist of a Si core (with diameter as thin as 2 nm) and a silica shell, of which the thickness varies from 5 to 20 nm. By combining advanced transmission electron microscopy (TEM) techniques, we demonstrate that the growth of the long SiNWs occurred via the Oxide Assisted Growth (OAG) mechanism, while the Vapor Liquid Solid (VLS) mechanism is responsible for the growth of shorter ones. Energy filtered TEM analyses revealed, in some cases, the existence of chapelet-like Si nanocrystals embedded in an otherwise silica nanowire. Such nanostructures are believed to result from the exposure of some OAG SiNWs to high temperatures prevailing inside the reactor. Finally, the intense photoluminescence (PL) of these ICP-grown SiNWs in the 620–950 nm spectral range is a clear indication of the occurrence of quantum confinement. Such a PL emission is in accordance with the TEM results which revealed that the size of nanostructures are indeed below the exciton Bohr radius of silicon.
Experimental investigation into the oxidation reactivity and nanostructure of particulate matter from diesel engine fuelled with diesel/polyoxymethylene dimethyl ethers blends
Authors: Yang Hao , Li Xinghu , Wang Yan , Mu Mingfei , Li Xuehao , Kou Guiyue 
Published: November 2016

AbstractThis paper focuses on oxidation reactivity and nanostructural characteristics of particulate matter (PM) emitted from diesel engine fuelled with different volume proportions of diesel/polyoxymethylene dimethyl ethers (PODEn) blends (P0, P10 and P20). PM was collected using a metal filter from the exhaust manifold. The collected PM samples were characterized using thermogravimetric analysis (TGA), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and Raman spectroscopy. The TGA results indicated that the PM produced by P20 had the highest moisture and volatility contents and the fastest oxidation rate of solid carbon followed by P10 and P0 derived PM. SEM analysis showed that PM generated from P20 was looser with a lower mean value than PM emitted from P10 and P0. Quantitative analysis of high-resolution TEM images presented that fringe length was reduced along with increased separation distance and tortuosity with an increase in PODEnconcentration. These trends improved the oxidation reactivity. According to Raman spectroscopy data, the intensity, full width at half-maximum and intensity ratio of the bands also changed demonstrating that PM nanostructure disorder was correlated with a faster oxidation rate. The results show the use of PODEnaffects the oxidation reactivity and nanostructure of PM that is easier to oxidize.
High-Acquisition-Rate Single-Shot Pump-Probe Measurements Using Time-Stretching Method
Authors: Kobayashi Masataka , Minami Yasuo , Johnson Courtney L. , Salmans Parker D. , Ellsworth Nicholas R. , Takeda Jun , Johnson Jeremy A. , Katayama Ikufumi 
Published: November 2016

AbstractRecent advances of ultrafast spectroscopy allow the capture of an entire ultrafast signal waveform in a single probe shot, which greatly reduces the measurement time and opens the door for the spectroscopy of unrepeatable phenomena. However, most single-shot detection schemes rely on two-dimensional detectors, which limit the repetition rate of the measurement and can hinder real-time visualization and manipulation of signal waveforms. Here, we demonstrate a new method to circumvent these difficulties and to greatly simplify the detection setup by using a long, single-mode optical fiber and a fast photodiode. Initially, a probe pulse is linearly chirped (the optical frequency varies linearly across the pulse in time), and the temporal profile of an ultrafast signal is then encoded in the probe spectrum. The probe pulse and encoded temporal dynamics are further chirped to nanosecond time scales using the dispersion in the optical fiber, thus, slowing down the ultrafast signal to time scales easily recorded with fast detectors and high-bandwidth electronics. We apply this method to three distinct ultrafast experiments: investigating the power dependence of the Kerr signal in LiNbO3, observing an irreversible transmission change of a phase change material, and capturing terahertz waveforms.