bluuebunny/crossref_metadata_2025 huggingface dataset:
High abundance and expression of transposases in bacteria from the Baltic Sea
Authors: Vigil-Stenman Theoden , Ininbergs Karolina , Bergman Birgitta , Ekman Martin
Published: July 2017

Transposases are mobile genetic elements suggested to have an important role in bacterial genome plasticity and host adaptation but their transcriptional activity in natural bacterial communities is largely unexplored. Here we analyzed metagenomes and -transcriptomes of size fractionated (0.1–0.8, 0.8–3.0 and 3.0–200 μm) bacterial communities from the brackish Baltic Sea, and adjacent marine waters. The Baltic Sea transposase levels, up to 1.7% of bacterial genes and 2% of bacterial transcripts, were considerably higher than in marine waters and similar to levels reported for extreme environments. Large variations in expression were found between transposase families and groups of bacteria, with a two-fold higher transcription in Cyanobacteria than in any other phylum. The community-level results were corroborated at the genus level by Synechococcus transposases reaching up to 5.2% of genes and 6.9% of transcripts, which is in contrast to marine Synechococcus that largely lack these genes. Levels peaked in Synechococcus from the largest size fraction, suggesting high frequencies of lateral gene transfer and high genome plasticity in colony-forming picocyanobacteria. Together, the results support an elevated rate of transposition-based genome change and adaptation in bacterial populations of the Baltic Sea, and possibly also of other highly dynamic estuarine waters.
Changes in nutrient stoichiometry, elemental homeostasis and growth rate of aquatic litter-associated fungi in response to inorganic nutrient supply
Authors: Gulis Vladislav , Kuehn Kevin A , Schoettle Louie N , Leach Desiree , Benstead Jonathan P , Rosemond Amy D
Published: July 2017

Aquatic fungi mediate important energy and nutrient transfers in freshwater ecosystems, a role potentially altered by widespread eutrophication. We studied the effects of dissolved nitrogen (N) and phosphorus (P) concentrations and ratios on fungal stoichiometry, elemental homeostasis, nutrient uptake and growth rate in two experiments that used (1) liquid media and a relatively recalcitrant carbon (C) source and (2) fungi grown on leaf litter in microcosms. Two monospecific fungal cultures and a multi-species assemblage were assessed in each experiment. Combining a radioactive tracer to estimate fungal production (C accrual) with N and P uptake measurements provided an ecologically relevant estimate of mean fungal C:N:P of 107:9:1 in litter-associated fungi, similar to the 92:9:1 obtained from liquid cultures. Aquatic fungi were found to be relatively homeostatic with respect to their C:N ratio (~11:1), but non-homeostatic with respect to C:P and N:P. Dissolved N greatly affected fungal growth rate and production, with little effect on C:nutrient stoichiometry. Conversely, dissolved P did not affect fungal growth and production but controlled biomass C:P and N:P, probably via luxury P uptake and storage. The ability of fungi to immobilize and store excess P may alter nutrient flow through aquatic food webs and affect ecosystem functioning.
Nrp2 is sufficient to instruct circuit formation of mitral-cells to mediate odour-induced attractive social responses
Authors: Inokuchi Kasumi , Imamura Fumiaki , Takeuchi Haruki , Kim Ryang , Okuno Hiroyuki , Nishizumi Hirofumi , Bito Haruhiko , Kikusui Takefumi , Sakano Hitoshi
Published: July 2017

Odour information induces various innate responses that are critical to the survival of the individual and for the species. An axon guidance molecule, Neuropilin 2 (Nrp2), is known to mediate targeting of olfactory sensory neurons (primary neurons), to the posteroventral main olfactory bulb (PV MOB) in mice. Here we report that Nrp2-positive (Nrp2+) mitral cells (MCs, second-order neurons) play crucial roles in transmitting attractive social signals from the PV MOB to the anterior part of medial amygdala (MeA). Semaphorin 3F, a repulsive ligand to Nrp2, regulates both migration of Nrp2+ MCs to the PV MOB and their axonal projection to the anterior MeA. In the MC-specific Nrp2 knockout mice, circuit formation of Nrp2+ MCs and odour-induced attractive social responses are impaired. In utero, electroporation demonstrates that activation of the Nrp2 gene in MCs is sufficient to instruct their circuit formation from the PV MOB to the anterior MeA.
Chemical characterization of the adhesive secretions of the salamander Plethodon shermani (Caudata, Plethodontidae)
Authors: von Byern Janek , Grunwald Ingo , Kosok Max , Saporito Ralph A. , Dicke Ursula , Wetjen Oliver , Thiel Karsten , Borcherding Kai , Kowalik Thomas , Marchetti-Deschmann Martina
Published: July 2017

Salamanders have developed a wide variety of antipredator mechanisms, including tail autotomy, colour patterns, and noxious skin secretions. As an addition to these tactics, the red-legged salamander (Plethodon shermani) uses adhesive secretions as part of its defensive strategy. The high bonding strength, the fast-curing nature, and the composition of the biobased materials makes salamander adhesives interesting for practical applications in the medical sector. To understand the adhesive secretions ofP.shermani, its components were chemically analysed by energy dispersive X-ray spectroscopy (EDX), inductively coupled plasma mass spectrometry (ICP-MS), amino acid analysis, and spectroscopy (ATR-IR, Raman). In addition, proteins were separated by gel-electrophoresis and selected spots were characterised by peptide mass fingerprinting. The salamander secretion contains a high amount of water and predominantly proteins (around 77% in the dry stage). The gel-electrophoresis and peptide mass fingerprint analyses revealed ade novoset of peptides/proteins, largely with a pI between 5.0 and 8.0 and a molecular mass distribution between 10 and 170 kDa. Only low homologies with other proteins present in known databases could be identified. The results indicate that the secretions of the salamanderPlethodonclearly differ chemically from those shown for other glue-producing terrestrial or marine species and thus represent a unique glue system.
Synergistic blending of high-valued heterocycles inhibits growth of Plasmodium falciparum in culture and P. berghei infection in mouse model
Authors: Kumar Prashant , Achieng Angela O. , Rajendran Vinoth , Ghosh Prahlad C. , Singh Brajendra K. , Rawat Manmeet , Perkins Douglas J. , Kempaiah Prakasha , Rathi Brijesh
Published: July 2017

A series of phthalimide analogues, novelized with high-valued bioactive scaffolds was synthesized by means of click-chemistry under non-conventional microwave heating and evaluated as noteworthy growth inhibitors of Plasmodium falciparum (3D7 and W2) in culture. Analogues 6a, 6h and 6 u showed highest activity to inhibit the growth of the parasite with IC50 values in submicromolar range. Structure-activity correlation indicated the necessity of unsubstituted triazoles and leucine linker to obtain maximal growth inhibition of the parasite. Notably, phthalimide 6a and 6u selectively inhibited the ring-stage growth and parasite maturation. On other hand, phthalimide 6h displayed selective schizonticidal activity. Besides, they displayed synergistic interactions with chloroquine and dihydroartemisinin against parasite. Additional in vivo experiments using P. berghei infected mice showed that administration of 6h and 6u alone, as well as in combination with dihydroartemisinin, substantially reduced the parasite load. The high antimalarial activity of 6h and 6u, coupled with low toxicity advocate their potential role as novel antimalarial agents, either as standalone or combination therapies.
High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci
Authors: Gloss Brian S. , Signal Bethany , Cheetham Seth W. , Gruhl Franziska , Kaczorowski Dominik C. , Perkins Andrew C. , Dinger Marcel E.
Published: July 2017

Cellular responses to stimuli are rapid and continuous and yet the vast majority of investigations of transcriptional responses during developmental transitions typically use long interval time courses; limiting the available interpretive power. Moreover, such experiments typically focus on protein-coding transcripts, ignoring the important impact of long noncoding RNAs. We therefore evaluated coding and noncoding expression dynamics at unprecedented temporal resolution (6-hourly) in differentiating mouse embryonic stem cells and report new insight into molecular processes and genome organization. We present a highly resolved differentiation cascade that exhibits coding and noncoding transcriptional alterations, transcription factor network interactions and alternative splicing events, little of which can be resolved by long-interval developmental time-courses. We describe novel short lived and cycling patterns of gene expression and dissect temporally ordered gene expression changes in response to transcription factors. We elucidate patterns in gene co-expression across the genome, describe asynchronous transcription at bidirectional promoters and functionally annotate known and novel regulatory lncRNAs. These findings highlight the complex and dynamic molecular events underlying mammalian differentiation that can only be observed though a temporally resolved time course.
Characterization and expression analysis of the WRKY gene family in moso bamboo
Authors: Li Long , Mu Shaohua , Cheng Zhanchao , Cheng Yuanwen , Zhang Ying , Miao Ying , Hou Chenglin , Li Xueping , Gao Jian
Published: July 2017

The WRKY family of transcription factors (TFs) is one of the ten largest families of TFs in higher plants and has been implicated in multiple biological processes. Here, we identified 121 WRKY TFs in moso bamboo, including five novel members that were not annotated in the Phyllostachys edulis genomic database. Estimation of the divergence time of paralogous gene pairs revealed an important role of the recent whole-genome duplication in the expansion of the WRKY family. Expression analysis based on quantitative reverse-transcription polymerase chain reaction (qRT-PCR) data revealed that a large number of PheWRKY genes varied significantly under cold or drought stress treatments, which could be defined as abiotic stress-responsive genes. The overexpression of PheWRKY72-2 in Arabidopsis resulted in a decreased sensitivity to drought stress during early seedling growth. PheWRKY72-2 may enhance plant tolerance to stress by functioning as a positive regulator of stoma closure. Our study provides a theoretical foundation and some experimental evidence for further functional verification of the PheWRKY family of TFs.
Selective dual-band metamaterial perfect absorber for infrared stealth technology
Authors: Kim Jagyeong , Han Kiwook , Hahn Jae W.
Published: July 2017

We propose a dual-band metamaterial perfect absorber with a metal–insulator–metal structure (MIM) for use in infrared (IR) stealth technology. We designed the MIM structure to have surface plasmon polariton (SPP) and magnetic polariton (MP) resonance peaks at 1.54 μm and 6.2 μm, respectively. One peak suppresses the scattering signals used by laser-guided missiles, and the other matches the atmospheric absorption band, thereby enabling the suppression of long-wavelength IR (LWIR) and mid-wavelength IR (MWIR) signals from objects as they propagate through the air. We analysed the spectral properties of the resonance peaks by comparing the wavelength of the MP peak calculated using the finite-difference time-domain method with that obtained by utilizing an inductor–capacitor circuit model. We evaluated the dependence of the performance of the dual-band metamaterial perfect absorber on the incident angle of light at the surface. The proposed absorber was able to reduce the scattering of 1.54 μm IR laser light by more than 90% and suppress the MWIR and LWIR signatures by more than 92%, as well as maintain MWIR and LWIR signal reduction rates greater than 90% across a wide temperature range from room temperature to 500 °C.
MiR-199a Inhibits Secondary Envelopment of Herpes Simplex Virus-1 Through the Downregulation of Cdc42-specific GTPase Activating Protein Localized in Golgi Apparatus
Authors: Kobayashi Kyousuke , Suemasa Fumiko , Sagara Hiroshi , Nakamura Shinya , Ino Yasushi , Kobayashi Kazuyoshi , Hiramatsu Hiroaki , Haraguchi Takeshi , Kurokawa Kazuo , Todo Tomoki , Nakano Akihiko , Iba Hideo
Published: July 2017

Because several studies have shown that exogenous miR-199a has antiviral effects against various viruses, including herpesviruses, we examined how miR-199a exerts its antiviral effects using epithelial tumour cell lines infected with herpes simplex virus-1 (HSV-1). We found that both miR-199a-5p and -3p impair the secondary envelopment of HSV-1 by suppressing their common target, ARHGAP21, a Golgi-localized GTPase-activating protein for Cdc42. We further found that the trans-cisternae of the Golgi apparatus are a potential membrane compartment for secondary envelopment. Exogenous expression of either pre-miR-199a or sh-ARHGAP21 exhibited shared phenotypes i.e. alteration of Golgi function in uninfected cells, inhibition of HSV-1 secondary envelopment, and reduction of trans-Golgi proteins upon HSV-1 infection. A constitutively active form of Cdc42 also inhibited HSV-1 secondary envelopment. Endogenous levels of miR-199a in epithelial tumour cell lines were negatively correlated with the efficiency of HSV-1 secondary envelopment within these cells. These results suggest that miR-199a is a crucial regulator of Cdc42 activity on Golgi membranes, which is important for the maintenance of Golgi function and for the secondary envelopment of HSV-1 upon its infection.
Global biogeography, cryptic species and systematic issues in the shrimp genus Hippolyte Leach, 1814 (Decapoda: Caridea: Hippolytidae) by multimarker analyses
Authors: Terossi Mariana , De Grave Sammy , Mantelatto Fernando L.
Published: July 2017

Hippolyteis a genus of small bodied marine shrimps, with a global distribution. Here, we studied the phylogenetic and biogeographic relationships amongst the species of this genus with two mitochondrial and two nuclear markers, using Bayesian Inference, Maximum Likelihood, genetic divergence, molecular clock and S-DIVA. In addition, the Indo-West Pacific genusAlcyonohippolytewas included. Based on sequences from 57 specimens of 27 species, we recovered a robust biogeographic scenario that shows the Indo-West Pacific as the probable ancestral area of the genusHippolyte, which emerged in the Paleocene, followed by dispersal in three general directions: (1) South Pacific, (2) eastern Atlantic and Mediterranean Sea and (3) Americas, the latter with a primary colonization in the eastern Pacific followed by a radiation into the western Atlantic. Our analysis reveals that the species of theH.ventricosagroup do not constitute a monophyletic group andAlcyonohippolytedoes not constitute a reciprocally monophyletic group toHippolyte, with both genera herein synonimised. The relationships and systematic status of several transisthmian and Atlantic species are clarified.
Targeted DNA methylation in human cells using engineered dCas9-methyltransferases
Authors: Xiong Tina , Meister Glenna E. , Workman Rachael E. , Kato Nathaniel C. , Spellberg Michael J. , Turker Fulya , Timp Winston , Ostermeier Marc , Novina Carl D.
Published: July 2017

Mammalian genomes exhibit complex patterns of gene expression regulated, in part, by DNA methylation. The advent of engineered DNA methyltransferases (MTases) to target DNA methylation to specific sites in the genome will accelerate many areas of biological research. However, targeted MTases require clear design rules to direct site-specific DNA methylation and minimize the unintended effects of off-target DNA methylation. Here we report a targeted MTase composed of an artificially split CpG MTase (sMTase) with one fragment fused to a catalytically-inactive Cas9 (dCas9) that directs the functional assembly of sMTase fragments at the targeted CpG site. We precisely map RNA-programmed DNA methylation to targeted CpG sites as a function of distance and orientation from the protospacer adjacent motif (PAM). Expression of the dCas9-sMTase in mammalian cells led to predictable and efficient (up to ~70%) DNA methylation at targeted sites. Multiplexing sgRNAs enabled targeting methylation to multiple sites in a single promoter and to multiple sites in multiple promoters. This programmable de novo MTase tool might be used for studying mechanisms of initiation, spreading and inheritance of DNA methylation, and for therapeutic gene silencing.
Soil microbial community structure and catabolic activity are significantly degenerated in successive rotations of Chinese fir plantations
Authors: Wu Zeyan , Li Jianjuan , Zheng Jie , Liu Jinfu , Liu Shuying , Lin Wenxiong , Wu Chengzhen
Published: July 2017

This study examined the hypotheses that soil microbial community composition and catabolic activity would significantly degenerated by consecutive monoculture in Chinese fir plantations. The phospholipid fatty acids (PLFA) and community level physiological profiles (CLPP) methods were used to assess the variations of soil microbial community among the first rotation Chinese fir plantation (FCP), the second rotation plantation (SCP) and the third rotation plantation (TCP). The total content of PLFA biomarkers was highest in FCP, followed by SCP, and TCP was the least detected. Conversely, the fungi/bacteria ratio significantly increased in the SCP and TCP soils. The average well-color development (AWCD) values significantly decreased (FCP > SCP > TCP). However, the sum of AWCD values of amino acids, carboxylic acids and phenolic compounds were higher significantly in the SCP and TCP soils than FCP soils, suggesting that the microflora feeding on acids gradually became predominant in the continuous monoculture plantation soils. Soil C/N ratio was one of the most important factors to soil microbial diversity. Both the PLFA and CLPP results illustrated the long-term pure plantation pattern exacerbated the microecological imbalance in the rhizospheric soils of Chinese fir, and markedly decreased the soil microbial community diversity and metabolic activity.
Tannic acid as a plant-derived polyphenol exerts vasoprotection via enhancing KLF2 expression in endothelial cells
Authors: Xu Yanni , Liu Peng , Xu Suowen , Koroleva Marina , Zhang Shuya , Si Shuyi , Jin Zheng Gen
Published: July 2017

The transcription factor Kruppel-like factor 2 (KLF2) is a critical anti-inflammatory and anti-atherogenic molecule in vascular endothelium. Enhancing KLF2 expression and activity improves endothelial function and prevents atherosclerosis. However, the pharmacological and molecular regulators for KLF2 are scarce. Using high-throughput luciferase reporter assay to screen for KLF2 activators, we have identified tannic acid (TA), a polyphenolic compound, as a potent KLF2 activator that attenuates endothelial inflammation. Mechanistic studies suggested that TA induced KLF2 expression in part through the ERK5/MEF2 pathway. Functionally, TA markedly decreased monocyte adhesion to ECs by reducing expression of adhesion molecule VCAM1. Using lung ECs isolated from Klf2+/+ and Klf2+/− mice, we showed that the anti-inflammatory effect of TA is dependent on KLF2. Collectively, our results demonstrate that TA is a potent KLF2 activator and TA attenuated endothelial inflammation through upregulation of KLF2. Our findings provide a novel mechanism for the well-established beneficial cardiovascular effects of TA and suggest that KLF2 could be a novel therapeutic target for atherosclerotic vascular disease.
Visual adaptation alters the apparent speed of real-world actions
Authors: Mather George , Sharman Rebecca J. , Parsons Todd
Published: July 2017

The apparent physical speed of an object in the field of view remains constant despite variations in retinal velocity due to viewing conditions (velocity constancy). For example, people and cars appear to move across the field of view at the same objective speed regardless of distance. In this study a series of experiments investigated the visual processes underpinning judgements of objective speed using an adaptation paradigm and video recordings of natural human locomotion. Viewing a video played in slow-motion for 30 seconds caused participants to perceive subsequently viewed clips played at standard speed as too fast, so playback had to be slowed down in order for it to appear natural; conversely after viewing fast-forward videos for 30 seconds, playback had to be speeded up in order to appear natural. The perceived speed of locomotion shifted towards the speed depicted in the adapting video (‘re-normalisation’). Results were qualitatively different from those obtained in previously reported studies of retinal velocity adaptation. Adapting videos that were scrambled to remove recognizable human figures or coherent motion caused significant, though smaller shifts in apparent locomotion speed, indicating that both low-level and high-level visual properties of the adapting stimulus contributed to the changes in apparent speed.
A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis
Authors: Fouhy F. , Ronan N. J. , O’Sullivan O. , McCarthy Y. , Walsh A. M. , Murphy D. M. , Daly M. , Flanagan E. T. , Fleming C. , McCarthy M. , Shortt C. , Eustace J. A. , Shanahan F. , Rea M. C. , Ross R. P. , Stanton C. , Plant B. J.
Published: July 2017

Cystic Fibrosis (CF) and its treatment result in an altered gut microbiota composition compared to non-CF controls. However, the impact of this on gut microbiota functionality has not been extensively characterised. Our aim was to conduct a proof-of-principle study to investigate if measurable changes in gut microbiota functionality occur in adult CF patients compared to controls. Metagenomic DNA was extracted from faecal samples from six CF patients and six non-CF controls and shotgun metagenomic sequencing was performed on the MiSeq platform. Metabolomic analysis using gas chromatography-mass spectrometry was conducted on faecal water. The gut microbiota of the CF group was significantly different compared to the non-CF controls, with significantly increased Firmicutes and decreased Bacteroidetes. Functionality was altered, with higher pathway abundances and gene families involved in lipid (e.g. PWY 6284 unsaturated fatty acid biosynthesis (p = 0.016)) and xenobiotic metabolism (e.g. PWY-5430 meta-cleavage pathway of aromatic compounds (p = 0.004)) in CF patients compared to the controls. Significant differences in metabolites occurred between the two groups. This proof-of-principle study demonstrates that measurable changes in gut microbiota functionality occur in CF patients compared to controls. Larger studies are thus needed to interrogate this further.
Establishment of patient derived xenografts as functional testing of lung cancer aggressiveness
Authors: Moro Massimo , Bertolini Giulia , Caserini Roberto , Borzi Cristina , Boeri Mattia , Fabbri Alessandra , Leone Giorgia , Gasparini Patrizia , Galeone Carlotta , Pelosi Giuseppe , Roz Luca , Sozzi Gabriella , Pastorino Ugo
Published: July 2017

Despite many years of research efforts, lung cancer still remains the leading cause of cancer deaths worldwide. Objective of this study was to set up a platform of non-small cell lung cancer patient derived xenografts (PDXs) faithfully representing primary tumour characteristics and offering a unique tool for studying effectiveness of therapies at a preclinical level. We established 38 PDXs with a successful take rate of 39.2%. All models closely mirrored parental tumour characteristics although a selective pressure for solid patterns, vimentin expression and EMT was observed in several models. An increased grafting rate for tumours derived from patients with worse outcome (p = 0.006), higher stage (p = 0.038) and higher CD133+/CXCR4+/EpCAM− stem cell content (p = 0.019) was observed whereas a trend towards an association with SUVmax higher than 8 (p = 0.084) was detected. Kaplan Meier analyses showed a significantly worse (p = 0.0008) overall survival at 5 years in patients with grafted vs not grafted PDXs also after adjusting for tumour stage. Moreover, for 63.2% models, grafting was reached before clinical recurrence occurred. Our findings strengthen the relevance of PDXs as useful preclinical models closely reflecting parental patients tumours and highlight PDXs establishment as a functional testing of lung cancer aggressiveness and personalized therapies.
High-performance nanoscale topological energy transduction
Authors: Philip Timothy M. , Gilbert Matthew J.
Published: July 2017

The realization of high-performance, small-footprint, on-chip inductors remains a challenge in radio-frequency and power microelectronics, where they perform vital energy transduction in filters and power converters. Modern planar inductors consist of metallic spirals that consume significant chip area, resulting in low inductance densities. We present a novel method for magnetic energy transduction that utilizes ferromagnetic islands (FIs) on the surface of a 3D time-reversal-invariant topological insulator (TI) to produce paradigmatically different inductors. Depending on the chemical potential, the FIs induce either an anomalous or quantum anomalous Hall effect in the topological surface states. These Hall effects direct current around the FIs, concentrating magnetic flux and producing a highly inductive device. Using a novel self-consistent simulation that couples AC non-equilibrium Green functions to fully electrodynamic solutions of Maxwell’s equations, we demonstrate excellent inductance densities up to terahertz frequencies, thus harnessing the unique properties of topological materials for practical device applications.
Rapid ILs-polishing Processes Toward Flexible Nanostructured Paper with Dually High Transparency and Haze
Authors: Ou Yanghao , Chen Jinbo , Lu Pengbo , Cheng Fan , Lin Meiyan , Su Lingfeng , Li Jun , Liu Detao
Published: July 2017

Biodegradable highly nanostructured paper has received great interest in past years due to its excellent optical properties which facilitate its wide applications in green flexible electronics and devices. However, energy and/or time-consuming procedure during the process of fabricating most nanostructured transparent paper are presently the main obstacle to their scalable production. In this work, we demonstrated a novel nanostructured paper with dually high transparency (∼91%) and high haze (∼89%) that was directly fabricated from original paper with rapid ILs-polishing processes. The whole fabricating time only requires 10 min. Compared to the previously reported nanopaper made of the isolated cellulose nanofibers by pure mechanical and/or chemical approaches, this work presented herein is devoted to use green ILs to polish directly the micrometer-sized fibrous paper into the nanostructured paper. This new method brings a rapid fabrication of transparent nanostructured paper while also retaining dual intriguing properties both in optical transmittance and haze. This work is capable of fabricating next-generation flexible and highly transparent and haze paper by a high-speed roll-to-roll manufacturing process with a much lower cost.
A deletion affecting an LRR-RLK gene co-segregates with the fruit flat shape trait in peach
Authors: López-Girona Elena , Zhang Yu , Eduardo Iban , Mora José Ramón Hernández , Alexiou Konstantinos G. , Arús Pere , Aranzana María José
Published: July 2017

In peach, the flat phenotype is caused by a partially dominant allele in heterozygosis (Ss), fruits from homozygous trees (SS) abort a few weeks after fruit setting. Previous research has identified a SSR marker (UDP98–412) highly associated with the trait, found suitable for marker assisted selection (MAS). Here we report a ∼10 Kb deletion affecting the gene PRUPE.6G281100, 400 Kb upstream of UDP98-412, co-segregating with the trait. This gene is a leucine-rich repeat receptor-like kinase (LRR-RLK) orthologous to the Brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1) group. PCR markers suitable for MAS confirmed its strong association with the trait in a collection of 246 cultivars. They were used to evaluate the DNA from a round fruit derived from a somatic mutation of the flat variety ‘UFO-4’, revealing that the mutation affected the flat associated allele (S). Protein BLAST alignment identified significant hits with genes involved in different biological processes. Best protein hit occurred with AtRLP12, which may functionally complement CLAVATA2, a key regulator that controls the stem cell population size. RT-PCR analysis revealed the absence of transcription of the partially deleted allele. The data support PRUPE.6G281100 as a candidate gene for flat shape in peach.
Controlling bi-anisotropy in infrared metamaterials using three-dimensional split-ring-resonators for purely magnetic resonance
Authors: Moritake Yuto , Tanaka Takuo
Published: July 2017

We propose and demonstrate the strategy to control bi-anisotropic response in three-dimensional split-ring-resonators (3D-SRRs) array for purely magnetic resonance in the mid-infrared region. By using a metal-stress-driven self-folding method, inversion symmetry along a propagation axis of 3D-SRRs was controlled. The inversion symmetry of 3D-SRRs realized non-bi-anisotropic response of a magnetic resonant mode at around 10 μm in wavelength resulting in purely magnetic resonance with high transmission of 70%. Highly transparent purely magnetic artificial elements demonstrated in this study will be a key component for functional applications using artificial magnetism at the optical frequencies.
A First Phylogeny of the Genus Dimocarpus and Suggestions for Revision of Some Taxa Based on Molecular and Morphological Evidence
Authors: Lithanatudom Suparat K. , Chaowasku Tanawat , Nantarat Nattawadee , Jaroenkit Theeranuch , Smith Duncan R. , Lithanatudom Pathrapol
Published: July 2017

Dimocarpus longan, commonly known as the longan, belongs to the family Sapindaceae, and is one of the most economically important fruits commonly cultivated in several regions in Asia. There are various cultivars of longan throughout the Thai-Malay peninsula region, but until now no phylogenetic analysis has been undertaken to determine the genetic relatedness of these cultivars. To address this issue, 6 loci, namely ITS2, matK, rbcL, trnH-psbA, trnL-I and trnL-trnF were amplified and sequenced from 40 individuals consisting of 26 longan cultivars 2 types of lychee and 8 herbarium samples. The sequencing results were used to construct a phylogenetic tree using the neighbor-joining (NJ), maximum likelihood (ML) and Bayesian inference (BI) criteria. The tree showed cryptic groups of D. longan from the Thailand-Malaysia region (Dimocarpus longan spp.). This is the first report of the genetic relationship of Dimocarpus based on multi-locus molecular markers and morphological characteristics. Multiple sequence alignments, phylogenetic trees and species delimitation support that Dimocarpus longan spp. longan var. obtusus and Dimocarpus longan spp. malesianus var. malesianus should be placed into a higher order and are two additional species in the genus Dimocarpus. Therefore these two species require nomenclatural changes as Dimocarpus malesianus and Dimocarpus obtusus, respectively.
Evolution, expression and association of the chemosensory protein genes with the outbreak phase of the two main pest locusts
Authors: Martín-Blázquez R. , Chen B. , Kang L. , Bakkali M.
Published: July 2017

We analyze the evolutionary relationships and expression patterns of the large set of genes for chemosensory proteins (CSPs) in the two main pest locusts. We used the available transcriptome and genome data to infer the number of genes using BLAST searches and sequence similarity matrices. Maximum likelihood phylogenies revealed the relationships between these CSPs and CSPs from several arthropods. RNAseq and qPCR allowed associating CSPs to locust phases. Crossing the phylogenetic and expression data allowed us to deduce homologies and conservation of the involvement in the phase change. We confirm that Locusta migratoria has at least 58 CSP gene copies, only five of which lack evidence of expression, and we reveal that Schistocerca gregaria has at least 42 expressed CSP genes. Both species share 21 orthologs, whereas 33 L. migratoria and 15 S. gregaria CSPs seem species-specific. Additional six S. gregaria and four L. migratoria CSPs seem duplications. Although the expression profiles are not especially conserved, seven orthologous CSP pairs share a gregarious over-expression pattern in adult locusts. We thus confirm that the number of locusts’ CSPs is large, due to gene duplications during the evolution of Orthoptera, we establish sequence and potential functional homologies, and we highlight specific CSPs that appear to be involved in locust gregariousness either in general or in a species-specific manner.
Evidence for a role of TRIB3 in the regulation of megakaryocytopoiesis
Authors: Butcher Lee , Ahluwalia Maninder , Örd Tiit , Johnston Jessica , Morris Roger H. , Kiss-Toth Endre , Örd Tõnis , Erusalimsky Jorge D.
Published: July 2017

Megakaryocytopoiesis is a complex differentiation process driven by the hormone thrombopoietin by which haematopoietic progenitor cells give rise to megakaryocytes, the giant bone marrow cells that in turn break down to form blood platelets. The Tribbles Pseudokinase 3 gene (TRIB3) encodes a pleiotropic protein increasingly implicated in the regulation of cellular differentiation programmes. Previous studies have hinted that TRIB3 could be also involved in megakaryocytopoiesis but its role in this process has so far not been investigated. Using cellular model systems of haematopoietic lineage differentiation here we demonstrate that TRIB3 is a negative modulator of megakaryocytopoiesis. We found that in primary cultures derived from human haematopoietic progenitor cells, thrombopoietin-induced megakaryocytic differentiation led to a time and dose-dependent decrease in TRIB3 mRNA levels. In the haematopoietic cell line UT7/mpl, silencing of TRIB3 increased basal and thrombopoietin-stimulated megakaryocyte antigen expression, as well as basal levels of ERK1/2 phosphorylation. In primary haematopoietic cell cultures, silencing of TRIB3 facilitated megakaryocyte differentiation. In contrast, over-expression of TRIB3 in these cells inhibited the differentiation process. The in-vitro identification of TRIB3 as a negative regulator of megakaryocytopoiesis suggests that in-vivo this gene could be important for the regulation of platelet production.
Construction of porous CuCo2S4 nanorod arrays via anion exchange for high-performance asymmetric supercapacitor
Authors: Cheng Siyi , Shi Tielin , Chen Chen , Zhong Yan , Huang Yuanyuan , Tao Xiangxu , Li Junjie , Liao Guanglan , Tang Zirong
Published: July 2017

To push the energy density limit of supercapacitors, proper pseudocapacitive materials with favorable nanostructures are urgently pursued. Ternary transition metal sulfides are promising electrode materials due to the better conductivity and higher electrochemical activity in comparison to the single element sulfides and transition metal oxides. In this work, we have successfully synthesized porous CuCo2S4 nanorod array (NRAs) on carbon textile through a stepwise hydrothermal method, including the growth of the Cu-Co precursor nanowire arrays and subsequent conversion into CuCo2S4 NRAs via anion exchange reaction. The CuCo2S4 NRAs electrode exhibits a greatly enhanced specific capacitance and an outstanding cycling stability. Moreover, an asymmetric supercapacitor using the CuCo2S4 NRAs as positive electrode and activated carbon as negative electrode delivers a high energy density of 56.96 W h kg−1. Such superior performance demonstrate that the CuCo2S4 NRAs are promising materials for future energy storage applications.
Si Wire Supported MnO2/Al/Fluorocarbon 3D Core/Shell Nanoenergetic Arrays with Long-Term Storage Stability
Authors: Zhu Ying , Zhou Xiang , Wu Chun , Cheng Hua , Lu Zhouguang , Zhang Kaili
Published: July 2017

Three-dimensional MnO2/Al/fluorocarbon core/shell nanoenergetic arrays are prepared on silicon substrate that is with silicon wires on top. Silicon wires are first prepared as the scaffolds by maskless deep reactive ion etching of silicon wafer, which is followed by the hydrothermal growth of MnO2. Al and fluorocarbon are then deposited sequentially around the silicon wire (Si-W) supported MnO2 arrays by magnetron sputtering to realize the core/shell nanoenergetic composite. Several characterization techniques are used to investigate the prepared Si-W/MnO2/Al/fluorocarbon arrays, including the scanning electron microscopy, transmission electron microscopy, energy dispersive spectroscopy, X-ray photoelectron spectroscopy, and thermal analysis. 3D upright aligned core/shell structure with an intimate contact between MnO2 and Al is confirmed from the morphological characterization. Superhydrophobicity is achieved after the fluorocarbon coating. Most importantly, the Si-W/MnO2/Al/fluorocarbon nanoenergetic arrays show no decay of energy density after 9 months of storage, indicating potential applications in nanoenergetics-on-a-chip when long-term storage is needed.
Lower mean platelet volume predicts poor prognosis in renal cell carcinoma
Authors: Yun Zhi-yuan , Zhang Xin , Liu Yan-song , Liu Tiemin , Liu Zhi-ping , Wang Rui-tao , Yu Kai-jiang
Published: July 2017

Altered mean platelet volume (MPV) is found in several malignancies. Remarkably, there is little consensus on using the value of MPV in the prognostic evaluations of renal cell carcinoma (RCC). The aim of this study is to examine the feasibility of MPV value as a prognostic indicator of RCC. The retrospective study recruited 306 consecutive RCC patients between January 2009 and December 2009. The relationships between MPV and clinicopathological characteristics were analyzed. Kaplan-Meier method and Cox regression were used to evaluate the prognostic impact of MPV. Of the 306 RCC patients, low MPV levels were detected in 61 (19.9%) patients. Reduced MPV was associated with histology types, T classification, UCLA Integrated Scoring System (UISS) category, and Mayo clinic stage, size, grade, and necrosis score (SSIGN) category (P < 0.05). Patients with decreased MPV had significantly shorter survival time than patients with normal MPV (P < 0.001). Cox regression analysis revealed that reduced MPV was an independent prognostic factor for overall survival (hazard ratio, 1.758; 95% confidence interval [CI], 1.083–2.855, P = 0.023). Moreover, the prognostic accuracy of TNM stage, UISS, and SSIGN prognostic models were improved when MPV was added. In conclusion, reduced MPV is identified as an independent predictor of adverse clinical outcome in RCC.
Increased functional connectivity after stroke correlates with behavioral scores in non-human primate model
Authors: Hernandez-Castillo Carlos R. , Nashed Joseph Y. , Fernandez-Ruiz Juan , Wang Justin , Gallivan Jason , Cook Douglas J.
Published: July 2017

Here we characterized the functional connectivity (FC) changes occurring after a controlled MCA stroke in a primate model. We hypothesize that if FC can inform about the neural changes after a stroke in the non-human primate (NHP) stroke model, then significant FC changes after the stroke would have to correlate with the remaining behavioral capacities. Eleven cynomolgus monkeys underwent an experimental middle cerebral artery occlusion while five monkeys remained as the control group. One month later the neurological function was assessed with a set of fine motor tasks and the Nonhuman Primate Stroke Scale (NHPSS). Structural and functional connectivity analyses were done to compare both groups. Three FC changes showed significant behavioral correlations: right sensorimotor-right lateral intraparietal FC with the six-well task; left posterior intraparietal-left dorsal premotor FC with the hill task; and right visual-left primary motor FC with the NHPSS. In the three instances, stronger FC correlated with better behavioral outcome. The results show that the functional changes correlating with behavioral outcomes involved sensorimotor cortices that were not restricted to the affected hemisphere. These results show that the FC analysis in NHP stroke model is a relevant methodology suitable to inform the neural changes occurring after a stroke.
Large nonlinear dielectric behavior in BaTi1−xSnxO3
Authors: Ren Pengrong , Liu Zicheng , Wang Qian , Peng Biaolin , Ke Shanming , Fan Huiqing , Zhao Gaoyang
Published: July 2017

BaTi1−xSnxO3 (BTSn, 0 ≤ x ≤ 0.30) ceramics were prepared by both the conventional sintering (CS) and sparking plasma sintering (SPS). Composition, temperature and grain size dependences of the nonlinear dielectric behaviors were systematically studied. BTSn was found to have especially large tunability (≥90%), which is larger than most other Pb-free systems, and is comparable to Pb-based relaxors. The high dielectric tunability in BTSn is attributed to its specific domain structures. Besides, temperature dependent tunability of BTSn presents a dispersed behavior and the dispersion is enhanced with the increase of Sn4+ concentrations, which is explained by the compositional fluctuation model.
Etiology and Pathogenesis of Parkinson’s Disease
Authors: de Miranda Briana R. , Greenamyre J. Timothy
Published: July 2017

Parkinson’s disease (PD) is a common neurodegenerative disease, affecting an estimated 7 million adults worldwide. The defining features of PD are a set of motor deficits that progressively impair voluntary movement, coupled with non-motor manifestations ranging from olfactory and gastrointestinal dysfunction to dementia. Underlying the motor symptoms is a loss of dopamine input into the basal ganglia, caused by the progressive death of dopamine neurons within the substantia nigra. In addition to dopamine neuron loss, a hallmark pathology of PD is the appearance of proteinaceous Lewy body inclusions in surviving neurons, of which, α-synuclein is a key component. While several genetic mutations have been implicated in the pathology of dopamine neuron death, the majority of PD cases remain idiopathic with no direct link to either genetic mutations or environmental exposures. The newest data connecting etiological risk factors to PD suggest multiple types of cellular dysfunction, as well as a central role of oxidative stress. This chapter examines potential links between highly penetrant monogenic causes of inherited PD and less apparent susceptibility genes that may predispose an individual to developing the disorder. In addition, it considers epidemiological data about exposures to environmental toxins and pathogens and how these relate to research models of PD.
Glutathione and Thiol Redox Signalling in Parkinson’s Disease
Authors: Smeyne Michelle , Smeyne Richard Jay
Published: July 2017

Glutathione (GSH) and thiol redox signalling are at the most basic level of cellular redox reactions and responses to oxidative stress. Oxidative stress plays a major role in the etiology of Parkinson’s disease. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) that cause this stress may be generated by a number of factors, including byproducts generated by oxidative phosphorylation in the mitochondrial production of ATP, exposure to toxic environmental agents, inflammation and secondary effects of genetic mutations. The known characteristics of dopaminergic (DA) neurons combined with the permissive cytoarchitecture of the substantia nigra pars compacta (SNpc) provide an environment that makes these cells particularly vulnerable in the event of oxidative stress. The antioxidant tripeptide GSH, cysteine residues, and the thiol redox reactions in which they participate, function to reduce oxidative stress and protect cells from their sequelae. In this chapter, we discuss the factors that contribute to oxidative stress in the SNpc and Parkinson’s disease, as well as mechanisms by which GSH synthesis, thiol-disulfide exchange and thiol-modulated enzymes can modulate gene transcription during oxidative stress.
At the Intersection Between Mitochondrial Dysfunction and Lysosomal Autophagy: Role of PD-Related Neurotoxins and Gene Products
Authors: Asiago Josephat M. , Doyle Trevor B. , Mishra Vartika , Jacquet Aurélie de Rus , Rochet Jean-Christophe
Published: July 2017

Parkinson’s disease (PD) is a complex neurodegenerative disorder that involves a constellation of motor and nonmotor symptoms. Although several medications are moderately effective in attenuating motor symptoms during the early stages of PD, there are currently no therapies available to slow the underlying neurodegeneration, in large part because the molecular underpinnings of the disease are incompletely understood. In this chapter, we review neuropathological, toxicological, and genetic data supporting the premise that mitochondrial dysfunction and autophagic impairment play a central role in PD pathogenesis. Moreover, we examine findings suggesting that the interplay between these two toxic phenomena contributes to neurodegeneration in the brains of PD patients. Finally, we discuss how insights into the roles of mitochondrial and autophagic impairment in PD can set the stage for developing disease-modifying therapies.
Design, synthesis and pharmacological studies of some new quinoline Schiff bases and 2,5-(disubstituted-[1,3,4])-oxadiazoles
Authors: Bharadwaj S. Shashidhar , Poojary Boja , Madan Kumar S. , Byrappa K. , Nagananda Govinahalli Shivashankara , Chaitanya Amajala Krishna , Zaveri Kunal , Yarla Nagendra Sastry , Shiralgi Yallappa , Kudva Avinash K. , Dhananjaya B. L.
Published: July 2017

G6P-Ligand (4f) and (5b) interactions as visualized using Chimera (Version 1.8).
Direct quantitative analysis of the natural moisturizing factor (NMF) in the stratum corneum by direct analysis in real time mass spectrometry (DART-MS)
Authors: Maeno Katsuyuki , Shida Yasuo , Shimada Haruo
Published: July 2017

Analyzing the natural moisturizing factor (NMF) in the stratum corneum (SC), such as amino acids, pyrrolidone carboxylic acid, and urocanic acid, is important in dermatology research.
Induction time of a polymorphic transformation
Authors: Sun Wenhao , Ceder Gerbrand
Published: July 2017

We analyze the processes governing the lifetimes of transient metastable polymorphs, within the context of classical nucleation theory.
Controlling the distance between hydrogen-bonded chloro-s-triazine tapes: crystal engineering using N-alkyl chains and the influence of temperature
Authors: Aldilla Vina R. , Bhadbhade Mohan , Bhattacharyya Saroj , Kumar Naresh , Rich Anne M. , Marjo Christopher E.
Published: July 2017

Precise control of tape spacing in hydrogen-bonded alkyl-chain substituted chloro-s-triazines is demonstrated at 150–298 K, with some unexpected behaviour from the odd-number carbon derivatives.
The effect of potassium on steam-methane reforming on the Ni4/Al2O3 surface: a DFT study
Authors: Li Meng-Ru , Lu Zhe , Wang Gui-Chang
Published: July 2017

Steam-methane reforming is a method of converting natural gas to syngas, and the additive K could affect the activity of steam-methane reforming on Ni catalyst supported by Al2O3.
Ligand effect on the rhodium porphyrin catalyzed hydrogenation of [2.2]paracyclophane with water: key bimetallic hydrogenation
Authors: Tam Chun Meng , To Ching Tat , Chan Kin Shing
Published: July 2017

Rhodium porphyrin catalyzed hydrogenation of the aliphatic carbon–carbon σ-bond of [2.2]paracyclophane with water has been examined with a variety of tetraarylporphyrins and axial ligands.
Urchin-like hierarchical H-Nb2O5 microspheres: synthesis, formation mechanism and their applications in lithium ion batteries
Authors: Liu Xiaodi , Liu Guangyin , Liu Ying , Sun Ruixue , Ma Jianmin , Guo Jiali , Hu Min
Published: July 2017

Urchin-like hierarchical Nb2O5 microspheres are successfully synthesized through a facile solvothermal method in glycerol–isopropanol mixed medium followed by thermal treatment.