bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biomolecular regulation, composition and nanoarchitecture of bone mineral
Authors: Poundarik Atharva A. , Boskey Adele , Gundberg Caren , Vashishth Deepak 
Published: January 2018

AbstractTough natural nanocomposites like bone, nacre and sea sponges contain within their hierarchy, a mineral (phosphate, silicate or carbonate) phase that interacts with an organic phase. In bone, the role of mineral ultrastructure (organization, morphology, composition) is crucial to the mechanical and biological properties of the tissue. Better understanding of mineral interaction with the organic matrix, in particular non-collagenous proteins, osteocalcin (OC) and osteopontin (OPN), can lead to better design of biomimetic materials. Using small angle x-ray scattering (SAXS) and wavelength dispersive spectroscopy (WDS) on single (OC−/− and OPN−/−) and double (OC-OPN−/−;−/−) genetic knockout mice bones, we demonstrate that both osteocalcin and osteopontin have specific roles in the biomolecular regulation of mineral in bone and together they are major determinants of the quality of bone mineral. Specifically, for the first time, we show that proteins osteocalcin and osteopontin regulate bone mineral crystal size and organization in a codependent manner, while they independently determine crystal shape. We found that OC is more dominant in the regulation of the physical properties of bone mineral, while OPN is more dominant in the regulation of the mineral composition.
AV2 protein of tomato leaf curl Palampur virus promotes systemic necrosis in Nicotiana benthamiana and interacts with host Catalase2
Authors: Roshan Poonam , Kulshreshtha Aditya , Kumar Surender , Purohit Rituraj , Hallan Vipin 
Published: January 2018

AbstractTomato leaf curl Palampur virus (ToLCPalV) is a whitefly-transmitted, bipartite begomovirus. Here, we demonstrated that ectopic expression of AV2 from a Potato virus X (PVX)-based vector accelerated systemic necrosis and reactive oxygen species (ROS) accumulation in Nicotiana benthamiana. Furthermore, 10 amino acids from N-terminal region of AV2 were found to be associated with the systemic necrosis symptom/phenotype. Mutational studies of ToLCPalV infectious clones lacking the AV2 revealed that AV2 is essential for the systemic movement of DNA-A, symptom severity and viral DNA accumulation. In a yeast two-hybrid assay, Catalase2 (Cat2) was found to associate with AV2 protein. Further, silencing of Cat2 resulted in appearance of necrotic lesions on N. benthamiana and these plants were highly susceptible to ToLCPalV infection in comparison to control plants. Infection ToLCPalV on Solanum lycopersicum resulted in downregulation of Cat2 transcripts, followed by accumulation of ROS and stress marker transcripts. The AV2 protein also suppressed virus-induced gene silencing (VIGS) of the Phytoene desaturase (PDS) gene. Our results show that AV2 is essential for the pathogenicity, systemic movement and suppression of gene silencing in the host. Altogether, our findings suggest that interactions between AV2 and Cat2 might play a crucial role in the establishment of ToLCPalV infection.
Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach
Authors: Jacobs A. , De Noia M. , Praebel K. , Kanstad-Hanssen Ø. , Paterno M. , Jackson D. , McGinnity P. , Sturm A. , Elmer K. R. , Llewellyn M. S. 
Published: January 2018

AbstractCaligid sea lice represent a significant threat to salmonid aquaculture worldwide. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic Lepeophtheirus salmonis, frustrating efforts to track louse populations and improve targeted control measures. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among four L. salmonis populations from Ireland, Scotland and Northern Norway. Only weak global structure was observed based on the full SNP dataset. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment, increased global genetic structure and resulted in significant genetic population differentiation. A large proportion of SNPs found to be under directional selection were also identified to be highly discriminatory. Our data suggest that it is possible to discriminate between nearby L. salmonis populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.
Binder-free sheet-type all-solid-state batteries with enhanced rate capabilities and high energy densities
Authors: Yamamoto Mari , Terauchi Yoshihiro , Sakuda Atsushi , Takahashi Masanari 
Published: January 2018

AbstractAll-solid-state batteries using inorganic solid electrolytes are considered promising energy storage systems because of their safety and long life. Stackable and compact sheet-type all-solid-state batteries are urgently needed for industrial applications such as smart grids and electric vehicles. A binder is usually indispensable to the construction of sheet-type batteries; however, it can decrease the power and cycle performance of the battery. Here we report the first fabrication of a binder-free sheet-type battery. The key to this development is the use of volatile poly(propylene carbonate)-based binders; used to fabricate electrodes, solid electrolyte sheets, and a stacked three-layered sheet, these binders can also be removed by heat treatment. Binder removal leads to enhanced rate capability, excellent cycle stability, and a 2.6-fold increase in the cell-based-energy-density over previously reported sheet-type batteries. This achievement is the first step towards realizing sheet-type batteries with high energy and power density.
Magnetically sensitive nanodiamond-doped tellurite glass fibers
Authors: Ruan Yinlan , Simpson David A. , Jeske Jan , Ebendorff-Heidepriem Heike , Lau Desmond W. M. , Ji Hong , Johnson Brett C. , Ohshima Takeshi , Afshar V. Shahraam , Hollenberg Lloyd , Greentree Andrew D. , Monro Tanya M. , Gibson Brant C. 
Published: January 2018

AbstractTraditional optical fibers are insensitive to magnetic fields, however many applications would benefit from fiber-based magnetometry devices. In this work, we demonstrate a magnetically sensitive optical fiber by doping nanodiamonds containing nitrogen vacancy centers into tellurite glass fibers. The fabrication process provides a robust and isolated sensing platform as the magnetic sensors are fixed in the tellurite glass matrix. Using optically detected magnetic resonance from the doped nanodiamonds, we demonstrate detection of local magnetic fields via side excitation and longitudinal collection. This is a first step towards intrinsically magneto-sensitive fiber devices with future applications in medical magneto-endoscopy and remote mineral exploration sensing.
Compositional Bias in Naïve and Chemically-modified Phage-Displayed Libraries uncovered by Paired-end Deep Sequencing
Authors: He Bifang , Tjhung Katrina F. , Bennett Nicholas J. , Chou Ying , Rau Andrea , Huang Jian , Derda Ratmir 
Published: January 2018

AbstractUnderstanding the composition of a genetically-encoded (GE) library is instrumental to the success of ligand discovery. In this manuscript, we investigate the bias in GE-libraries of linear, macrocyclic and chemically post-translationally modified (cPTM) tetrapeptides displayed on the M13KE platform, which are produced via trinucleotide cassette synthesis (19 codons) and NNK-randomized codon. Differential enrichment of synthetic DNA {S}, ligated vector {L} (extension and ligation of synthetic DNA into the vector), naïve libraries {N} (transformation of the ligated vector into the bacteria followed by expression of the library for 4.5 hours to yield a “naïve” library), and libraries chemically modified by aldehyde ligation and cysteine macrocyclization {M} characterized by paired-end deep sequencing, detected a significant drop in diversity in {L} → {N}, but only a minor compositional difference in {S} → {L} and {N} → {M}. Libraries expressed at the N-terminus of phage protein pIII censored positively charged amino acids Arg and Lys; libraries expressed between pIII domains N1 and N2 overcame Arg/Lys-censorship but introduced new bias towards Gly and Ser. Interrogation of biases arising from cPTM by aldehyde ligation and cysteine macrocyclization unveiled censorship of sequences with Ser/Phe. Analogous analysis can be used to explore library diversity in new display platforms and optimize cPTM of these libraries.
Fabrication of multiple nanopores in a SiNx membrane via controlled breakdown
Authors: Wang Yunlong , Ying Cuifeng , Zhou Wenyuan , de Vreede Lennart , Liu Zhibo , Tian Jianguo 
Published: January 2018

AbstractThis paper reports a controlled breakdown (CBD) method to fabricate multiple nanopores in a silicon nitride (SiNx) membrane with control over both nanopore count and nanopore diameter. Despite the stochastic process of the breakdown, we found that the nanopores created via CBD, tend to be of the same diameter. We propose a membrane resistance model to explain and control the multiple nanopores forming in the membrane. We prove that the membrane resistance can reflect the number of nanopores in the membrane and that the diameter of the nanopores is controlled by the exposure time and strength of the electric field. This controllable multiple nanopore formation via CBD avoids the utilization of complicated instruments and time-intensive manufacturing. We anticipate CBD has the potential to become a nanopore fabrication technique which, integrated into an optical setup, could be used as a high-throughput and multichannel characterization technique.
Tracking the Evolution of Transiently Transfected Individual Cells in a Microfluidic Platform
Authors: Vitor Micaela Tamara , Sart Sébastien , Barizien Antoine , Torre Lucimara Gaziola De La , Baroud Charles N. 
Published: January 2018

AbstractTransient gene expression (TGE) technology enables the rapid production of large amount of recombinant proteins, without the need of fastidious screening of the producing cells required for stable transfection (ST). However, several barriers must be overcome before reaching the production yields using ST. For optimizing the production yields from suspended cells using TGE, a better understanding of the transfection conditions at the single cell level are required. In this study, a universal droplet microfluidic platform was used to assess the heterogeneities of CHO-S population transiently transfected with cationic liposomes (CL) (lipoplexes) complexed with GFP-coding plasmid DNA (pDNA). A single cell analysis of GFP production kinetics revealed the presence of a subpopulation producing higher levels of GFP compared with the main population. The size of high producing (HP) cells, their relative abundance, and their specific productivity were dependent on the charge and the pDNA content of the different lipoplexes: HPs showed increased cell size in comparison to the average population, lipoplexes with positive charge produced more HPs, and lipoplexes carrying a larger amount of pDNA yielded a higher specific productivity of HPs. This study demonstrates the potential for time-resolved single-cell measurements to explain population dynamics from a microscopic point of view.
Molecular characterization of the grape seeds extract’s effect against chemically induced liver cancer: In vivo and in vitro analyses
Authors: Hamza Alaaeldin Ahmed , Heeba Gehan Hussein , Elwy Hanan Mohamed , Murali Chandraprabha , El-Awady Raafat , Amin Amr 
Published: January 2018

AbstractThe purpose of this study was to investigate the anti-cancer property of grape seed extract (GSE) during early stages of developing liver cancer using a two-stage carcinogenic model combining diethylnitrosamine (DEN) and 2-Acetyl Aminofluorene (2-AAF). Administration of GSE at doses 25, 50 and 100 mg/kg per day started at the beginning of promotion periods and continued for 14 weeks. GSE dramatically inhibited pre-neoplastic foci formation as well as significantly decreased the number and the area of placental glutathione-S-transferase in livers of DEN-2AAF-treated rats by approximately 4 & 10 fold deductions, respectively. GSE’s effects were associated with induced apoptosis, reduced cell proliferation, decreased oxidative stress and down regulation of histone deacetylase activity and inflammation makers, such as cyclooxygenase 2, inducible nitric oxide synthase, nuclear factor-kappa B-p65 and p- phosphorylated tumor necrosis factor receptor expressions in liver. GSE treatment also decreased the viability of HepG2 cells and induced early and late apoptosis through activating caspase-3 and Bax. Furthermore, GSE induced G2/M and G1/S cell cycle arrest. The present study provides evidence that the GSE’s anticancer effect is mediated through the inhibition of cell proliferation, induction of apoptosis, modulating oxidative damage and suppressing inflammatory response.
Pre-conception maternal erythrocyte saturated to unsaturated fatty acid ratio predicts pregnancy after natural cycle frozen embryo transfer
Authors: Onyiaodike Christopher C. , Murray Heather M. , Zhang Ruiqi , Meyer Barbara J. , Jordan Fiona , Brown E. Ann , Nibbs Robert J. B. , Lyall Helen , Sattar Naveed , Nelson Scott M. , Freeman Dilys J. 
Published: January 2018

AbstractThe environment for embryo implantation and fetal growth and development is affected by maternal nutritional, metabolic and health status. The aim of this prospective, cohort study was to test whether plasma metabolic and inflammatory biomarkers can predict pregnancy resulting from in vitro fertilisation (IVF). Women with a natural menstrual cycle undergoing frozen embryo transfer (FET) were recruited and fasting baseline blood samples were collected a mean of 3.4 days prior to the luteinising hormone (LH) surge and a non-fasting blood sample was taken on the day of FET. Ongoing pregnancy was defined by positive fetal heartbeat on ultrasound scan at day 45 post LH surge. Thirty-six pregnancies resulted from FET in 143 women. In an overall stepwise multivariable analysis, erythrocyte saturated to unsaturated fatty acid ratio was positively associated with ongoing pregnancy. A similar model incorporating day of FET covariates found that erythrocyte saturated to unsaturated fatty acid ratio, erythrocyte fatty acid average chain length and plasma log-triglycerides predicted ongoing pregnancy. In conclusion, a higher peri-conceptional saturated to unsaturated fatty acid ratio predicted ongoing pregnancy after natural cycle frozen embryo transfer and may reflect a maternal nutritional status that facilitates pregnancy success in this assisted conception scenario.
Mechanical behavior of a soft hydrogel reinforced with three-dimensional printed microfibre scaffolds
Authors: Castilho Miguel , Hochleitner Gernot , Wilson Wouter , van Rietbergen Bert , Dalton Paul D. , Groll Jürgen , Malda Jos , Ito Keita 
Published: January 2018

AbstractReinforcing hydrogels with micro-fibre scaffolds obtained by a Melt-Electrospinning Writing (MEW) process has demonstrated great promise for developing tissue engineered (TE) constructs with mechanical properties compatible to native tissues. However, the mechanical performance and reinforcement mechanism of the micro-fibre reinforced hydrogels is not yet fully understood. In this study, FE models, implementing material properties measured experimentally, were used to explore the reinforcement mechanism of fibre-hydrogel composites. First, a continuum FE model based on idealized scaffold geometry was used to capture reinforcement effects related to the suppression of lateral gel expansion by the scaffold, while a second micro-FE model based on micro-CT images of the real construct geometry during compaction captured the effects of load transfer through the scaffold interconnections. Results demonstrate that the reinforcement mechanism at higher scaffold volume fractions was dominated by the load carrying-ability of the fibre scaffold interconnections, which was much higher than expected based on testing scaffolds alone because the hydrogel provides resistance against buckling of the scaffold. We propose that the theoretical understanding presented in this work will assist the design of more effective composite constructs with potential applications in a wide range of TE conditions.
Cucumber mosaic virus coat protein induces the development of chlorotic symptoms through interacting with the chloroplast ferredoxin I protein
Authors: Qiu Yanhong , Zhang Yongjiang , Wang Chaonan , Lei Rong , Wu Yupin , Li Xinshi , Zhu Shuifang 
Published: January 2018

AbstractCucumber mosaic virus (CMV) infection could induce mosaic symptoms on a wide-range of host plants. However, there is still limited information regarding the molecular mechanism underlying the development of the symptoms. In this study, the coat protein (CP) was confirmed as the symptom determinant by exchanging the CP between a chlorosis inducing CMV-M strain and a green-mosaic inducing CMV-Q strain. A yeast two-hybrid analysis and bimolecular fluorescence complementation revealed that the chloroplast ferredoxin I (Fd I) protein interacted with the CP of CMV-M both in vitro and in vivo, but not with the CP of CMV-Q. The severity of chlorosis was directly related to the expression of Fd1, that was down-regulated in CMV-M but not in CMV-Q. Moreover, the silencing of Fd I induced chlorosis symptoms that were similar to those elicited by CMV-M. Subsequent analyses indicated that the CP of CMV-M interacted with the precursor of Fd I in the cytoplasm and disrupted the transport of Fd I into chloroplasts, leading to the suppression of Fd I functions during a viral infection. Collectively, our findings accentuate that the interaction between the CP of CMV and Fd I is the primary determinant for the induction of chlorosis in tobacco.
High content analysis identifies unique morphological features of reprogrammed cardiomyocytes
Authors: Sutcliffe Matthew D. , Tan Philip M. , Fernandez-Perez Antonio , Nam Young-Jae , Munshi Nikhil V. , Saucerman Jeffrey J. 
Published: January 2018

AbstractDirect reprogramming of fibroblasts into cardiomyocytes is a promising approach for cardiac regeneration but still faces challenges in efficiently generating mature cardiomyocytes. Systematic optimization of reprogramming protocols requires scalable, objective methods to assess cellular phenotype beyond what is captured by transcriptional signatures alone. To address this question, we automatically segmented reprogrammed cardiomyocytes from immunofluorescence images and analyzed cell morphology. We also introduce a method to quantify sarcomere structure using Haralick texture features, called SarcOmere Texture Analysis (SOTA). We show that induced cardiac-like myocytes (iCLMs) are highly variable in expression of cardiomyocyte markers, producing subtypes that are not typically seen in vivo. Compared to neonatal mouse cardiomyocytes, iCLMs have more variable cell size and shape, have less organized sarcomere structure, and demonstrate reduced sarcomere length. Taken together, these results indicate that traditional methods of assessing cardiomyocyte reprogramming by quantifying induction of cardiomyocyte marker proteins may not be sufficient to predict functionality. The automated image analysis methods described in this study may enable more systematic approaches for improving reprogramming techniques above and beyond existing algorithms that rely heavily on transcriptome profiling.
Mechanical phenotyping of K562 cells by the Micropipette Aspiration Technique allows identifying mechanical changes induced by drugs
Authors: Di Cerbo Alessandro , Rubino Valentina , Morelli Francesca , Ruggiero Giuseppina , Landi Rosaria , Guidetti Gianandrea , Canello Sergio , Terrazzano Giuseppe , Alessandrini Andrea 
Published: January 2018

AbstractMechanical properties of living cells can be used as reliable markers of their state, such as the presence of a pathological state or their differentiation phase. The mechanical behavior of cells depends on the organization of their cytoskeletal network and the main contribution typically comes from the actomyosin contractile system, in both suspended and adherent cells. In the present study, we investigated the effect of a pharmaceutical formulation (OTC – Ossitetraciclina liquida 20%) used as antibiotic, on the mechanical properties of K562 cells by using the Micropipette Aspiration Technique (MAT). This formulation has been shown to increase in a time dependent way the inflammation and toxicity in terms of apoptosis inin vitroexperiments on K562 and other types of cells. Here we show that by measuring the mechanical properties of cells exposed to OTC for different incubation times, it is possible to infer modifications induced by the formulation to the actomyosin contractile system. We emphasize that this system is involved in the first stages of the apoptotic process where an increase of the cortical tension leads to the formation of blebs. We discuss the possible relation between the observed mechanical behavior of cells aspirated inside a micropipette and apoptosis.
Towards an experimental classification system for membrane active peptides
Authors: Brand G. D. , Ramada M. H. S. , Genaro-Mattos T. C. , Bloch C. 
Published: January 2018

AbstractMature proteins can act as potential sources of encrypted bioactive peptides that, once released from their parent proteins, might interact with diverse biomolecular targets. In recent work we introduced a systematic methodology to uncover encrypted intragenic antimicrobial peptides (IAPs) within large protein sequence libraries. Given that such peptides may interact with membranes in different ways, resulting in distinct observable outcomes, it is desirable to develop a predictive methodology to categorize membrane active peptides and establish a link to their physicochemical properties. Building upon previous work, we explored the interaction of a range of IAPs with model membranes probed by differential scanning calorimetry (DSC) and circular dichroism (CD) techniques. The biophysical data were submitted to multivariate statistical methods and resulting peptide clusters were correlated to peptide structure and to their antimicrobial activity. A re-evaluation of the physicochemical properties of the peptides was conducted based on peptide cluster memberships. Our data indicate that membranolytic peptides produce characteristic thermal transition (DSC) profiles in model vesicles and that this can be used to categorize novel molecules with unknown biological activity. Incremental expansion of the model presented here might result in a unified experimental framework for the prediction of novel classes of membrane active peptides.