bluuebunny/crossref_metadata_2025_split huggingface dataset:
The fragile X mental retardation protein regulates tumor invasiveness-related pathways in melanoma cells
Authors: Zalfa Francesca , Panasiti Vincenzo , Carotti Simone , Zingariello Maria , Perrone Giuseppe , Sancillo Laura , Pacini Laura , Luciani Flavie , Roberti Vincenzo , D'Amico Silvia , Coppola Rosa , Abate Simona Osella , Rana Rosa Alba , De Luca Anastasia , Fiers Mark , Melocchi Valentina , Bianchi Fabrizio , Farace Maria Giulia , Achsel Tilmann , Marine Jean-Christophe , Morini Sergio , Bagni Claudia 
Published: November 2017

AbstractThe fragile X mental retardation protein (FMRP) is lacking or mutated in patients with the fragile X syndrome (FXS), the most frequent form of inherited intellectual disability. FMRP affects metastasis formation in a mouse model for breast cancer. Here we show that FMRP is overexpressed in human melanoma with high Breslow thickness and high Clark level. Furthermore, meta-analysis of the TCGA melanoma data revealed that high levels of FMRP expression correlate significantly with metastatic tumor tissues, risk of relapsing and disease-free survival. Reduction of FMRP in metastatic melanoma cell lines impinges on cell migration, invasion and adhesion. Next-generation sequencing in human melanoma cells revealed that FMRP regulates a large number of mRNAs involved in relevant processes of melanoma progression. Our findings suggest an association between FMRP levels and the invasive phenotype in melanoma and might open new avenues towards the discovery of novel therapeutic targets.
Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system
Authors: Lian Jiazhang , HamediRad Mohammad , Hu Sumeng , Zhao Huimin 
Published: November 2017

AbstractDesigning an optimal microbial cell factory often requires overexpression, knock-down, and knock-out of multiple gene targets. Unfortunately, such rewiring of cellular metabolism is often carried out sequentially and with low throughput. Here, we report a combinatorial metabolic engineering strategy based on an orthogonal tri-functional CRISPR system that combines transcriptional activation, transcriptional interference, and gene deletion (CRISPR-AID) in the yeast Saccharomyces cerevisiae. This strategy enables perturbation of the metabolic and regulatory networks in a modular, parallel, and high-throughput manner. We demonstrate the application of CRISPR-AID not only to increase the production of β-carotene by 3-fold in a single step, but also to achieve 2.5-fold improvement in the display of an endoglucanase on the yeast surface by optimizing multiple metabolic engineering targets in a combinatorial manner.
Mussel larvae modify calcifying fluid carbonate chemistry to promote calcification
Authors: Ramesh Kirti , Hu Marian Y. , Thomsen Jörn , Bleich Markus , Melzner Frank 
Published: November 2017

AbstractUnderstanding mollusk calcification sensitivity to ocean acidification (OA) requires a better knowledge of calcification mechanisms. Especially in rapidly calcifying larval stages, mechanisms of shell formation are largely unexplored—yet these are the most vulnerable life stages. Here we find rapid generation of crystalline shell material in mussel larvae. We find no evidence for intracellular CaCO3 formation, indicating that mineral formation could be constrained to the calcifying space beneath the shell. Using microelectrodes we show that larvae can increase pH and [CO32−] beneath the growing shell, leading to a ~1.5-fold elevation in calcium carbonate saturation state (Ωarag). Larvae exposed to OA exhibit a drop in pH, [CO32−] and Ωarag at the site of calcification, which correlates with decreased shell growth, and, eventually, shell dissolution. Our findings help explain why bivalve larvae can form shells under moderate acidification scenarios and provide a direct link between ocean carbonate chemistry and larval calcification rate.
The genetic basis for the adaptation of E. coli to sugar synthesis from CO2
Authors: Herz Elad , Antonovsky Niv , Bar-On Yinon , Davidi Dan , Gleizer Shmuel , Prywes Noam , Noda-Garcia Lianet , Lyn Frisch Keren , Zohar Yehudit , Wernick David G. , Savidor Alon , Barenholz Uri , Milo Ron 
Published: November 2017

AbstractUnderstanding the evolution of a new metabolic capability in full mechanistic detail is challenging, as causative mutations may be masked by non-essential "hitchhiking" mutations accumulated during the evolutionary trajectory. We have previously used adaptive laboratory evolution of a rationally engineered ancestor to generate an Escherichia coli strain able to utilize CO2 fixation for sugar synthesis. Here, we reveal the genetic basis underlying this metabolic transition. Five mutations are sufficient to enable robust growth when a non-native Calvin–Benson–Bassham cycle provides all the sugar-derived metabolic building blocks. These mutations are found either in enzymes that affect the efflux of intermediates from the autocatalytic CO2 fixation cycle toward biomass (prs, serA, and pgi), or in key regulators of carbon metabolism (crp and ppsR). Using suppressor analysis, we show that a decrease in catalytic capacity is a common feature of all mutations found in enzymes. These findings highlight the enzymatic constraints that are essential to the metabolic stability of autocatalytic cycles and are relevant to future efforts in constructing non-native carbon fixation pathways.
Eroded telomeres are rearranged in quiescent fission yeast cells through duplications of subtelomeric sequences
Authors: Maestroni Laetitia , Audry Julien , Matmati Samah , Arcangioli Benoit , Géli Vincent , Coulon Stéphane 
Published: November 2017

AbstractWhile the mechanisms of telomere maintenance has been investigated in dividing cells, little is known about the stability of telomeres in quiescent cells and how dysfunctional telomeres are processed in non-proliferating cells. Here we examine the stability of telomeres in quiescent cells using fission yeast. While wild type telomeres are stable in quiescence, we observe that eroded telomeres were highly rearranged during quiescence in telomerase minus cells. These rearrangements depend on homologous recombination (HR) and correspond to duplications of subtelomeric regions. HR is initiated at newly identified subtelomeric homologous repeated sequences (HRS). We further show that TERRA (Telomeric Repeat-containing RNA) is increased in post-mitotic cells with short telomeres and correlates with telomere rearrangements. Finally, we demonstrate that rearranged telomeres prevent cells to exit properly from quiescence. Taken together, we describe in fission yeast a mode of telomere repair mechanism specific to post-mitotic cells that is likely promoted by transcription.
Manufacture of highly loaded silica-supported cobalt Fischer–Tropsch catalysts from a metal organic framework
Authors: Sun Xiaohui , Suarez Alma I. Olivos , Meijerink Mark , van Deelen Tom , Ould-Chikh Samy , Zečević Jovana , de Jong Krijn P. , Kapteijn Freek , Gascon Jorge 
Published: November 2017

AbstractThe development of synthetic protocols for the preparation of highly loaded metal nanoparticle-supported catalysts has received a great deal of attention over the last few decades. Independently controlling metal loading, nanoparticle size, distribution, and accessibility has proven challenging because of the clear interdependence between these crucial performance parameters. Here we present a stepwise methodology that, making use of a cobalt-containing metal organic framework as hard template (ZIF-67), allows addressing this long-standing challenge. Condensation of silica in the Co-metal organic framework pore space followed by pyrolysis and subsequent calcination of these composites renders highly loaded cobalt nanocomposites (~ 50 wt.% Co), with cobalt oxide reducibility in the order of 80% and a good particle dispersion, that exhibit high activity, C5 + selectivity and stability in Fischer–Tropsch synthesis.
Functional germline variants as potential co-oncogenes
Authors: Agarwal Divyansh , Nowak Christoph , Zhang Nancy R. , Pusztai Lajos , Hatzis Christos 
Published: November 2017

AbstractGermline variants that affect the expression or function of proteins contribute to phenotypic variation in humans and likely determine individual characteristics and susceptibility to diseases including cancer. A number of high penetrance germline variants that increase cancer risk have been identified and studied, but germline functional polymorphisms are not typically considered in the context of cancer biology, where the focus is primarily on somatic mutations. Yet, there is evidence from familial cancers indicating that specific cancer subtypes tend to arise in carriers of high-risk germline variants (e.g., triple negative breast cancers in mutated BRCA carriers), which suggests that pre-existing germline variants may determine which complementary somatic driver mutations are needed to drive tumorigenesis. Recent genome sequencing studies of large breast cancer cohorts reported only a handful of highly recurrent driver mutations, suggesting that different oncogenic events drive individual cancers. Here, we propose that germline polymorphisms can function as oncogenic modifiers, or co-oncogenes, and these determine what complementary subsequent somatic events are required for full malignant transformation. Therefore, we propose that germline aberrations should be considered together with somatic mutations to determine what genes drive cancer and how they may be targeted.
Advances in malaria vaccine development: report from the 2017 malaria vaccine symposium
Authors: Coelho Camila Henriques , Doritchamou Justin Yai Alamou , Zaidi Irfan , Duffy Patrick E. 
Published: November 2017

AbstractThe Malaria Vaccine Symposium occurred at Johns Hopkins University in Baltimore, MD, USA on April 25th, 2017, coinciding with World Malaria Day and the WHO announcement that the RTS,S malaria vaccine would begin pilot implementation programs in Ghana, Kenya, and Malawi in 2018. Scientists from several disciplines reported progress on an array of malaria vaccine concepts and product candidates, including pre-erythrocytic vaccines that prevent infection, blood-stage vaccines that limit infection and disease, and transmission-blocking vaccines that interrupt the spread of infection. Other speakers highlighted the immunological and genetic considerations that must be addressed by vaccinologists to yield the most efficacious vaccines. Here, we highlight the advances in malaria vaccinology that were reported at the symposium.
Taxonomy and Identification of the Genus Scolopendra in China Using Integrated Methods of External Morphology and Molecular Phylogenetics
Authors: Kang Sihe , Liu Yimei , Zeng Xiaoxuan , Deng Haiying , Luo Ying , Chen Keli , Chen Shilin 
Published: November 2017

Abstract
The centipede Scolopendra has important medicinal value and high toxicity, making it to be an interesting subject for evolutionary studies. However, species identification in China is difficult because of limited resource exploration and lack of recent taxonomic revision. To improve the identification and taxonomy of the genus Scolopendra in China, an in-depth investigation was conducted, and an integrated method that combined morphological characteristics with molecular data was applied. The identification key was revised to show the main difference among species. Our results indicated that morphologically-delimited species were consistent with the molecular analysis inferred from the COI sequences with genetic distances and phylogenetic trees. Additional morphometrics of four characteristics provided criteria for shape variation. These results suggested that the members of the genus Scolopendra in China could be delineated as 14 separate species. A new species from Lufeng county, Yunnan province, was proposed according to its characteristics, which was named as S. lufengia sp. nov. Our results comprehensively ascertained the taxonomic status of Scolopendra species in China, explored their phylogenetic relationships, showed a high success in the identification of medicinal centipedes.
Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis)
Authors: Ali Mohammed , Li Penghui , She Guangbiao , Chen Daofu , Wan Xiaochun , Zhao Jian 
Published: November 2017

AbstractA large number of terpenoid compounds have been extracted from different tissues of S. officinalis. However, the molecular genetic basis of terpene biosynthesis pathways is virtually unknown. In this study, approximately 6.6 Gb of raw data were generated from the transcriptome of S. officinalis leaves using Illumina HiSeq 2000 sequencing. After filtering and removing the adapter sequences from the raw data, the number of reads reached 21 million, comprising 98 million of high-quality nucleotide bases. 48,671 unigenes were assembled de novo and annotated for establishing a valid database for studying terpenoid biosynthesis. We identified 135 unigenes that are putatively involved in terpenoid metabolism, including 70 mevalonate and methyl-erythritol phosphate pathways, terpenoid backbone biosynthesis genes, and 65 terpene synthase genes. Moreover, five terpene synthase genes were studied for their functions in terpenoid biosynthesis by using transgenic tobacco; most transgenic tobacco plants expressing these terpene synthetic genes produced increased amounts of terpenoids compared with wild-type control. The combined data analyses from the transcriptome and metabolome provide new insights into our understanding of the complex metabolic genes in terpenoid-rich sage, and our study paves the way for the future metabolic engineering of the biosynthesis of useful terpene compounds in S. officinalis.
Band gap engineering of In(Ga)N/GaN short period superlattices
Authors: Gorczyca I. , Suski T. , Strak P. , Staszczak G. , Christensen N. E. 
Published: November 2017

AbstractDiscussion of band gap behavior based on first principles calculations of the electronic band structures for several InN/GaN superlattices (SLs) (free-standing and pseudomorphic) grown along different directions (polar and nonpolar) is presented. Taking into account the dependence on internal strain and lattice geometry mainly two factors influence the dependence of the band gap, E
g
on the layer thickness: the internal electric field and the hyb wells) is more important. We also consider mIn ridization of well and barrier wave functions. We illustrate their influence on the band gap engineering by calculating the strength of built-in electric field and the oscillator strength. It appears that there are two interesting ranges of layer thicknesses. In one the influence of the electric field on the gaps is dominant (wider wells), whereas in the other the wave function hybridization (narrow wells) is more important. We also consider mIn
0.33
Ga
0.67
N/nGaN SLs, which seem to be easier to fabricate than high In content quantum wells. The calculated band gaps are compared with recent experimental data. It is shown that for In(Ga)N/GaN superlattices it is possible to exceed by far the range of band gap values, which can be realized in ternary InGaN alloys.
Micromechanical Resonator Driven by Radiation Pressure Force
Authors: Boales Joseph A. , Mateen Farrukh , Mohanty Pritiraj 
Published: November 2017

AbstractRadiation pressure exerted by light on any surface is the pressure generated by the momentum of impinging photons. The associated force – fundamentally, a quantum mechanical aspect of light – is usually too small to be useful, except in large-scale problems in astronomy and astrodynamics. In atomic and molecular optics, radiation pressure can be used to trap or cool atoms and ions. Use of radiation pressure on larger objects such as micromechanical resonators has been so far limited to its coupling to an acoustic mode, sideband cooling, or levitation of microscopic objects. In this Letter, we demonstrate direct actuation of a radio-frequency micromechanical plate-type resonator by the radiation pressure force generated by a standard laser diode at room temperature. Using two independent methods, the magnitude of the resonator’s response to forcing by radiation pressure is found to be proportional to the intensity of the incident light.
Symmetry breaking, Josephson oscillation and self-trapping in a self-bound three-dimensional quantum ball
Authors: Adhikari S. K. 
Published: November 2017

AbstractWe study spontaneous symmetry breaking (SSB), Josephson oscillation, and self-trapping in a stable, mobile, three-dimensional matter-wave spherical quantum ball self-bound by attractive two-body and repulsive three-body interactions. The SSB is realized by a parity-symmetric (a) one-dimensional (1D) double-well potential or (b) a 1D Gaussian potential, both along the z axis and no potential along the x and y axes. In the presence of each of these potentials, the symmetric ground state dynamically evolves into a doubly-degenerate SSB ground state. If the SSB ground state in the double well, predominantly located in the first well (z > 0), is given a small displacement, the quantum ball oscillates with a self-trapping in the first well. For a medium displacement one encounters an asymmetric Josephson oscillation. The asymmetric oscillation is a consequence of SSB. The study is performed by a variational and a numerical solution of a non-linear mean-field model with 1D parity-symmetric perturbations.
Long-Read Sequencing of Human Cytomegalovirus Transcriptome Reveals RNA Isoforms Carrying Distinct Coding Potentials
Authors: Balázs Zsolt , Tombácz Dóra , Szűcs Attila , Csabai Zsolt , Megyeri Klára , Petrov Alexey N. , Snyder Michael , Boldogkői Zsolt 
Published: November 2017

AbstractThe human cytomegalovirus (HCMV) is a ubiquitous, human pathogenic herpesvirus. The complete viral genome is transcriptionally active during infection; however, a large part of its transcriptome has yet to be annotated. In this work, we applied the amplified isoform sequencing technique from Pacific Biosciences to characterize the lytic transcriptome of HCMV strain Towne varS. We developed a pipeline for transcript annotation using long-read sequencing data. We identified 248 transcriptional start sites, 116 transcriptional termination sites and 80 splicing events. Using this information, we have annotated 291 previously undescribed or only partially annotated transcript isoforms, including eight novel antisense transcripts and their isoforms, as well as a novel transcript (RS2) in the short repeat region, partially antisense to RS1. Similarly to other organisms, we discovered a high transcriptional diversity in HCMV, with many transcripts only slightly differing from one another. Comparing our transcriptome profiling results to an earlier ribosome footprint analysis, we have concluded that the majority of the transcripts contain multiple translationally active ORFs, and also that most isoforms contain unique combinations of ORFs. Based on these results, we propose that one important function of this transcriptional diversity may be to provide a regulatory mechanism at the level of translation.
Structural analyses of adenylate kinases from Antarctic and tropical fishes for understanding cold adaptation of enzymes
Authors: Moon Sojin , Kim Junhyung , Bae Euiyoung 
Published: November 2017

AbstractPsychrophiles are extremophilic organisms capable of thriving in cold environments. Proteins from these cold-adapted organisms can remain physiologically functional at low temperatures, but are structurally unstable even at moderate temperatures. Here, we report the crystal structure of adenylate kinase (AK) from the Antarctic fish Notothenia coriiceps, and identify the structural basis of cold adaptation by comparison with homologues from tropical fishes including Danio rerio. The structure of N. coriiceps AK (AKNc) revealed suboptimal hydrophobic packing around three Val residues in its central CORE domain, which are replaced with Ile residues in D. rerio AK (AKDr). The Val-to-Ile mutations that improve hydrophobic CORE packing in AKNc increased stability at high temperatures but decreased activity at low temperatures, suggesting that the suboptimal hydrophobic CORE packing is important for cold adaptation. Such linkage between stability and activity was also observed in AKDr. Ile-to-Val mutations that destabilized the tropical AK resulted in increased activity at low temperatures. Our results provide the structural basis of cold adaptation of a psychrophilic enzyme from a multicellular, eukaryotic organism, and highlight the similarities and differences in the structural adjustment of vertebrate and bacterial psychrophilic AKs during cold adaptation.
Development and validation of scFv-conjugated affinity silk protein for specific detection of carcinoembryonic antigen
Authors: Sato Mitsuru , Kitani Hiroshi , Kojima Katsura 
Published: November 2017

AbstractThe production costs for monoclonal antibodies (MAbs) utilized in medical diagnostic kits are inevitably high because the MAbs are mostly obtained from hybridoma cell culture. Here, we report the development and validation of a novel affinity silk protein produced by transgenic silkworm technology as a possible alternative diagnostic tool for cancers. We generated a transgenic silkworm expressing a cDNA construct containing fibroin L-chain fused to a single-chain variable fragment (scFv) derived from a MAb against carcinoembryonic antigen (CEA). The transgenic cocoons were dissolved in aqueous lithium bromide solution, applied to 96-well plates, and analysed by enzyme-linked immunosorbent assay. The scFv-conjugated affinity silk protein specifically recognized CEA as well as the parental MAb. The binding activity was retained after several months of storage in coated plates or concentrated solution. Thus, the scFv-conjugated affinity silk protein provides a potentially useful alternative to conventional MAbs in medical diagnostic kits.
Creation and Annihilation of Skyrmions in the Frustrated Magnets with Competing Exchange Interactions
Authors: Hu Yong , Chi Xiaodan , Li Xuesi , Liu Yan , Du An 
Published: November 2017

AbstractIn triangular-lattice magnets, the coexistence of third-neighbor antiferromagnetic and nearest-neighbor ferromagnetic exchange interactions can induce rich magnetic phases including noncoplanar skyrmion crystals. Based on Monte Carlo simulation, we studied the dependence of magnetic phase transition on exchange interaction strength. Under the consideration of uniaxial anisotropy and magnetic field both perpendicular to the film plane, a large antiferromagnetic exchange interaction induces a high frustration. When the value of antiferromagnetic exchange interaction is one and a half times larger than the ferromagnetic one, a magnetic phase composed of canting spin stripes, never observed in the chiral magnets, forms. Interestingly, different canting spin stripes along three 120 degree propagation directions may coexist randomly in a magnetic phase, attesting that the canting spin stripes are three-fold degenerate states akin to helices and the multiple state of canting spin stripes is a circular configuration with zero skyrmion charge number. Moreover, skyrmions and antiskyrmions can be observed simultaneously in the configuration at the low temperature nearly close to 0 K, and their configuration and diameter properties are discussed. Finally, the mechanisms of skyrmion creation and annihilation are properly interpreted by comparing exchange and Zeeman energy terms.