bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic adaptation of mesenchymal stem cell physiology upon exposure to surface micropatterns
Authors: Beijer Nick R. M. , Nauryzgaliyeva Zarina M. , Arteaga Estela M. , Pieuchot Laurent , Anselme Karine , van de Peppel Jeroen , Vasilevich Aliaksei S. , Groen Nathalie , Roumans Nadia , Hebels Dennie G. A. J. , Boer Jan de 
Published: June 2019

AbstractHuman mesenchymal stem (hMSCs) are defined as multi-potent colony-forming cells expressing a specific subset of plasma membrane markers when grown on flat tissue culture polystyrene. However, as soon as hMSCs are used for transplantation, they are exposed to a 3D environment, which can strongly impact cell physiology and influence proliferation, differentiation and metabolism. Strategies to control in vivo hMSC behavior, for instance in stem cell transplantation or cancer treatment, are skewed by the un-physiological flatness of the standard well plates. Even though it is common knowledge that cells behave differently in vitro compared to in vivo, only little is known about the underlying adaptation processes. Here, we used micrometer-scale defined surface topographies as a model to describe the phenotype of hMSCs during this adaptation to their new environment. We used well established techniques to compare hMSCs cultured on flat and topographically enhanced polystyreneand observed dramatically changed cell morphologies accompanied by shrinkage of cytoplasm and nucleus, a decreased overall cellular metabolism, and slower cell cycle progression resulting in a lower proliferation rate in cells exposed to surface topographies. We hypothesized that this reduction in proliferation rate effects their sensitivity to certain cancer drugs, which was confirmed by higher survival rate of hMSCs cultured on topographies exposed to paclitaxel. Thus, micro-topographies can be used as a model system to mimic the natural cell micro-environment, and be a powerful tool to optimize cell treatment in vitro.
Towards understanding partial adaptation to the subterranean habitat in the European cave spider, Meta menardi: An ecocytological approach
Authors: Lipovšek Saška , Leitinger Gerd , Janžekovič Franc , Kozel Peter , Dariš Barbara , Perc Matjaž , Devetak Dušan , Weiland Nina , Novak Tone 
Published: June 2019

AbstractThe European cave spider, Meta menardi, is a representative of the troglophiles, i.e. non-strictly subterranean organisms. Our aim was to interpret the cytological results from an ecological perspective, and provide a synthesis of the hitherto knowledge about M. menardi into a theory of key features marking it a troglophile. We studied ultrastructural changes of the midgut epithelial cells in individuals spending winter under natural conditions in caves, using light microscopy and TEM. The midgut diverticula epithelium consisted of secretory cells, digestive cells and adipocytes. During winter, gradual vacuolization of some digestive cells appeared, and some necrotic digestive cells and necrotic adipocytes appeared. This cytological information completes previous studies on M. menardi starved under controlled conditions in the laboratory. In experimental starvation and natural winter conditions, M. menardi gradually exploit reserve compounds from spherites, protein granules and through autophagy, and energy-supplying lipids and glycogen, as do many overwintering arthropods. We found no special cellular response to living in the habitat. Features that make it partly adapted to the subterranean habitat include starvation hardiness as a possible preadaptation, an extremely opportunistic diet, a partly reduced orb, tracking and capturing prey on bare walls and partly reduced tolerance to below-zero temperatures.
Genome-wide identification of glutathione S-transferase gene family in pepper, its classification, and expression profiling under different anatomical and environmental conditions
Authors: Islam Shiful , Sajib Saikat Das , Jui Zakya Sultana , Arabia Shatil , Islam Tahmina , Ghosh Ajit 
Published: June 2019

AbstractGlutathione S-transferases (GSTs) compose a family of multifunctional enzymes involved in the numerous aspects of regulating plant growth, development, and stress response. An in silico genome-wide analysis of pepper (Capsicum annuum L.) was performed to identify eighty-five GST genes that were annotated according to their chromosomal location. Segmental duplication contributed more than tandem duplication for the expansion of GST gene family in pepper. All the identified members belong to ten different classes which are highly conserved among Arabidopsis, rice, tomato and potato counterparts indicating the pre-dicot-monocot split diversification of GST classes. Gene structure, protein domain, and motif organization were found to be notably conserved over the distinct phylogenetic groups, which demonstrated the evolutionary significant role of each class. Expression of most of the CaGST transcripts as well as the total pepper GST activity was found to be significantly up-regulated in response to cold, heat, drought, salinity and osmotic stress conditions. Presence of various hormone and stress-responsive cis-elements on most of the putative CaGST promoter regions could be directly correlated with the alteration of their transcripts. All these findings might provide opportunities for future functional validation of this important gene family in pepper.
An Improved Method for Fabrication of Ag-GO Nanocomposite with Controlled Anti-Cancer and Anti-bacterial Behavior; A Comparative Study
Authors: Khorrami Sadegh , Abdollahi Zahra , Eshaghi Ghazaleh , Khosravi Arezoo , Bidram Elham , Zarrabi Ali 
Published: June 2019

AbstractIn this study, two green procedures for Silver-Graphene Oxide (Ag-GO) nanocomposite synthesis were investigated. As a common method, AgNO3 was first loaded on the GO surface and then was reduced and stabilized by walnut green husk extract, producing Ag-GO-І. As an innovative approach, GO was first exposed to the extract and then the AgNO3 was added as the second step, producing Ag-GO-П. Physicochemical properties, antibacterial and cytotoxicity activity of both nanocomposites were subsequently studied comparing with free silver nanoparticles (AgNPs) and pure GO. Based on the results, exposure of GO to the extract, as a reducing agent, at the first/last step of the synthesis process resulted in the fundamental differences in the final products. So that, high amounts of agglomerated silver nanoparticles were formed between the GO sheets, when using the common method, whereas in Ag-GO-П, small AgNPs were formed on the GO sheets without aggregation, entirely covering the sheets. Antibacterial and cytotoxic behavior of these nanomaterials could be compared as AgNPs > Ag-GO-П > Ag-GO-І. It is assumed that these differences are due to control of unwanted nucleation in the synthesis process that Ag nanoparticles are smaller with less agglomeration when the GO surfaces are pre-treated with reducing agent.
Soft culture substrates favor stem-like cellular phenotype and facilitate reprogramming of human mesenchymal stem/stromal cells (hMSCs) through mechanotransduction
Authors: Gerardo Heloísa , Lima Ana , Carvalho João , Ramos João R. D. , Couceiro Sofia , Travasso Rui D. M. , Pires das Neves Ricardo , Grãos Mário 
Published: June 2019

AbstractBiophysical cues influence many aspects of cell behavior. Stiffness of the extracellular matrix is probed by cells and transduced into biochemical signals through mechanotransduction protein networks, strongly influencing stem cell behavior. Cellular stemness is intimately related with mechanical properties of the cell, like intracellular contractility and stiffness, which in turn are influenced by the microenvironment. Pluripotency is associated with soft and low-contractility cells. Hence, we postulated that soft cell culture substrates, presumably inducing low cellular contractility and stiffness, increase the reprogramming efficiency of mesenchymal stem/stromal cells (MSCs) into induced pluripotent stem cells (iPSCs). We demonstrate that soft substrates (1.5 or 15 kPa polydimethylsiloxane – PDMS) caused modulation of several cellular features of MSCs into a phenotype closer to pluripotent stem cells (PSCs). MSCs cultured on soft substrates presented more relaxed nuclei, lower maturation of focal adhesions and F-actin assembling, more euchromatic and less heterochromatic nuclear DNA regions, and increased expression of pluripotency-related genes. These changes correlate with the reprogramming of MSCs, with a positive impact on the kinetics, robustness of colony formation and reprogramming efficiency. Additionally, substrate stiffness influences several phenotypic features of iPS cells and colonies, and data indicates that soft substrates favor full iPSC reprogramming.
A model of ganglion axon pathways accounts for percepts elicited by retinal implants
Authors: Beyeler Michael , Nanduri Devyani , Weiland James D. , Rokem Ariel , Boynton Geoffrey M. , Fine Ione 
Published: June 2019

AbstractDegenerative retinal diseases such as retinitis pigmentosa and macular degeneration cause irreversible vision loss in more than 10 million people worldwide. Retinal prostheses, now implanted in over 250 patients worldwide, electrically stimulate surviving cells in order to evoke neuronal responses that are interpreted by the brain as visual percepts (‘phosphenes’). However, instead of seeing focal spots of light, current implant users perceive highly distorted phosphenes that vary in shape both across subjects and electrodes. We characterized these distortions by asking users of the Argus retinal prosthesis system (Second Sight Medical Products Inc.) to draw electrically elicited percepts on a touchscreen. Using ophthalmic fundus imaging and computational modeling, we show that elicited percepts can be accurately predicted by the topographic organization of optic nerve fiber bundles in each subject’s retina, successfully replicating visual percepts ranging from ‘blobs’ to oriented ‘streaks’ and ‘wedges’ depending on the retinal location of the stimulating electrode. This provides the first evidence that activation of passing axon fibers accounts for the rich repertoire of phosphene shape commonly reported in psychophysical experiments, which can severely distort the quality of the generated visual experience. Overall our findings argue for more detailed modeling of biological detail across neural engineering applications.
Paired Box-1 (PAX1) Activates Multiple Phosphatases and Inhibits Kinase Cascades in Cervical Cancer
Authors: Su Po-Hsuan , Lai Hung-Cheng , Huang Rui-Lan , Chen Lin-Yu , Wang Yu-Chi , Wu Tzu-I , Chan Michael W. Y. , Liao Chi-Chun , Chen Chien‐Wen , Lin Wei-Yu , Chang Cheng-Chang 
Published: June 2019

AbstractDNA methylation alteration, such as global hypomethylation and localized hypermethylation, within the promoters of tumor suppressor genes, is an important risk factor in cervical cancer. The potential use of DNA methylation detection, in cervical cancer screening or triage of mildly abnormal cytology, has recently been demonstrated. In particular, PAX1 DNA methylation testing was approved as an adjunct to cytology, in Taiwan, and is now undergoing registration trials in China. However, the function of PAX1 in cancer biology remains largely unknown. Here, we show that PAX1 inhibits malignant phenotypes upon oncogenic stress. Specifically, PAX1 expression inhibited the phosphorylation of multiple kinases, after challenges with oncogenic growth factors such as EGF and IL-6. Analogously, PAX1 activated a panel of phosphatases, including DUSP1, 5, and 6, and inhibited EGF/MAPK signaling. PAX1 also interacted with SET1B, increasing histone H3K4 methylation and DNA demethylation of numerous phosphatase-encoding genes. Furthermore, hypermethylated PAX1 associated with poor prognosis in cervical cancer. Taken together, this study reveals, for the first time, the functional relevance of PAX1 in cancer biology, and further supports the prospect of targeting multifold oncogenic kinase cascades, which jointly contribute to multiresistance, via epigenetic reactivation of PAX1.
Early pregnancy serum levels of perfluoroalkyl substances and risk of preeclampsia in Swedish women
Authors: Wikström Sverre , Lindh Christian H. , Shu Huan , Bornehag Carl-Gustaf 
Published: June 2019

AbstractPreeclampsia is a major cause of maternal and fetal morbidity. Emerging research shows an association with environmental exposures. The present aim was to investigate associations between early pregnancy serum levels of perfluoroalkyl substances (PFAS) and preeclampsia. Within the Swedish SELMA study, eight PFAS were measured at median 10 gestational weeks and cases of preeclampsia were postnatally identified from registers. Associations between individual PFAS and preeclampsia were assessed, adjusting for parity, age, weight and smoking. Out of 1,773 women in the study group, 64 (3.6%), developed preeclampsia. A doubling of PFOS and PFNA exposure, corresponding to an inter-quartile increase, was associated with an increased risk for preeclampsia of about 38–53% respectively. Serum PFOS within the highest quartile was associated with an odds ratio of 2.68 (CI 95%: 1.17–6.12), equal to the increased risk associated with nulliparity, when compared to exposure in the first quartile. The same associations were identified, although with higher risk estimates, in analyses restricted to nulliparous women. For other PFAS, there were no associations. In conclusion and consistent with limited previous research only on PFOS, increasing serum levels of PFOS and PFNA during early pregnancy were associated with a clinically relevant risk of preeclampsia, adjusting for established confounders.
Simultaneous gains in grain yield and nitrogen efficiency over 70 years of maize genetic improvement
Authors: Mueller Sarah M. , Messina Carlos D. , Vyn Tony J. 
Published: June 2019

AbstractThe competing demands of increasing grain yields to feed a growing population and decreasing nitrogen (N) fertilizer use and loss to the environment poses a grand challenge to farmers and society, and necessitates achieving improved N use efficiency (NUE) in cereal crops. Although selection for increased yield in maize has improved NUE over time, the present understanding of the physiological determinants of NUE and its key components hampers the design of more effective breeding strategies conducive to accelerating genetic gain for this trait. We show that maize NUE gains have been supported by more efficient allocation of N among plant organs during the grain filling period. Comparing seven maize hybrids commercialized between 1946 and 2015 from a single seed company in multiple N fertilizer treatments, we demonstrate that modern hybrids produced more grain per unit of accumulated N by more efficiently remobilizing N stored in stems than in leaves to support kernel growth. Increases in N fertilizer recovery and N harvest index at maturity were mirrored by a steady decrease in stem N allocation in this era study. These insights can inform future breeding strategies for continued NUE gains through improved conversion efficiency of accumulated plant N into grain yield.
Oral administration of EPA-rich oil impairs collagen reorganization due to elevated production of IL-10 during skin wound healing in mice
Authors: Burger Beatriz , Kühl Carolina M. C. , Candreva Thamiris , Cardoso Renato da S. , Silva Jéssica R. , Castelucci Bianca G. , Consonni Sílvio R. , Fisk Helena L. , Calder Philip C. , Vinolo Marco Aurélio R. , Rodrigues Hosana G. 
Published: June 2019

AbstractWound healing is an essential process for organism survival. Some fatty acids have been described as modulators of wound healing. However, the role of omega-3 fatty acids is unclear. In the present work, we investigate the effects of oral administration of eicosapentaenoic acid (EPA)-rich oil on wound healing in mice. After 4 weeks of EPA-rich oil supplementation (2 g/kg of body weight), mice had increased serum concentrations of EPA (20:5ω-3) (6-fold) and docosahexaenoic acid (DHA; 22:6ω-3) (33%) in relation to control mice. Omega-3 fatty acids were also incorporated into skin in the EPA fed mice. The wound healing process was delayed at the 3rd and 7th days after wounding in mice that received EPA-rich oil when compared to control mice but there was no effect on the total time required for wound closure. Collagen reorganization, that impacts the quality of the wound tissue, was impaired after EPA-rich oil supplementation. These effects were associated with an increase of M2 macrophages (twice in relation to control animals) and interleukin-10 (IL-10) concentrations in tissue in the initial stages of wound healing. In the absence of IL-10 (IL-10−/− mice), wound closure and organization of collagen were normalized even when EPA was fed, supporting that the deleterious effects of EPA-rich oil supplementation were due to the excessive production of IL-10. In conclusion, oral administration of EPA-rich oil impairs the quality of wound healing without affecting the wound closure time likely due to an elevation of the anti-inflammatory cytokine IL-10.
In vivo measurements reveal a single 5′-intron is sufficient to increase protein expression level in Caenorhabditis elegans
Authors: Crane Matthew M. , Sands Bryan , Battaglia Christian , Johnson Brock , Yun Soo , Kaeberlein Matt , Brent Roger , Mendenhall Alex 
Published: June 2019

AbstractIntrons can increase gene expression levels using a variety of mechanisms collectively referred to as Intron Mediated Enhancement (IME). IME has been measured in cell culture and plant models by quantifying expression of intronless and intron-bearing reporter genes in vitro. We developed hardware and software to implement microfluidic chip-based gene expression quantification in vivo. We altered position, number and sequence of introns in reporter genes controlled by the hsp-90 promoter. Consistent with plant and mammalian studies, we determined a single, natural or synthetic, 5′-intron is sufficient for the full IME effect conferred by three synthetic introns, while a 3′-intron is not. We found coding sequence can affect IME; the same three synthetic introns that increase mcherry protein concentration by approximately 50%, increase mEGFP by 80%. We determined IME effect size is not greatly affected by the stronger vit-2 promoter. Our microfluidic imaging approach should facilitate screens for factors affecting IME and other intron-dependent processes.
Discovery and characterization of functional modules associated with body weight in broilers
Authors: Tarsani Eirini , Kranis Andreas , Maniatis Gerasimos , Avendano Santiago , Hager-Theodorides Ariadne L. , Kominakis Antonios 
Published: June 2019

AbstractAim of the present study was to investigate whether body weight (BW) in broilers is associated with functional modular genes. To this end, first a GWAS for BW was conducted using 6,598 broilers and the high density SNP array. The next step was to search for positional candidate genes and QTLs within strong LD genomic regions around the significant SNPs. Using all positional candidate genes, a network was then constructed and community structure analysis was performed. Finally, functional enrichment analysis was applied to infer the functional relevance of modular genes. A total number of 645 positional candidate genes were identified in strong LD genomic regions around 11 genome-wide significant markers. 428 of the positional candidate genes were located within growth related QTLs. Community structure analysis detected 5 modules while functional enrichment analysis showed that 52 modular genes participated in developmental processes such as skeletal system development. An additional number of 14 modular genes (GABRG1, NGF, APOBEC2, STAT5B, STAT3, SMAD4, MED1, CACNB1, SLAIN2, LEMD2, ZC3H18, TMEM132D, FRYL and SGCB) were also identified as related to body weight. Taken together, current results suggested a total number of 66 genes as most plausible functional candidates for the trait examined.
Investigating the properties of TBA variants with twin thrombin binding domains
Authors: Amato Teresa , Virgilio Antonella , Pirone Luciano , Vellecco Valentina , Bucci Mariarosaria , Pedone Emilia , Esposito Veronica , Galeone Aldo 
Published: June 2019

AbstractIn this paper, we report studies concerning thrombin binding aptamer (TBA) dimeric derivatives in which the 3′-ends of two TBA sequences have been joined by means of linkers containing adenosine or thymidine residues and/or a glycerol moiety. CD and electrophoretic investigations indicate that all modified aptamers are able to form G-quadruplex domains resembling that of the parent TBA structure. However, isothermal titration calorimetry measurements of the aptamer/thrombin interaction point to different affinities to the target protein, depending on the type of linker. Consistently, the best ligands for thrombin show anticoagulant activities higher than TBA. Interestingly, two dimeric aptamers with the most promising properties also show far higher resistances in biological environment than TBA.
Century-long Taylor-Quinney interpretation of plasticity-induced heating reexamined
Authors: Zubelewicz Aleksander 
Published: June 2019

AbstractIn thermomechanics, the Taylor–Quinney coefficient specifies fraction of plastic work converted to heat. We challenge the nearly century-long interpretation. We postulate that some fraction of energy delivered to the plastically deformed material is responsible for readjustments of deformation pathways making the plastic flow a kinematically admissible process. The rerouting triggers mesoscale dynamic excitations and activates plasticity-induced heat. Another part of the energy is stored in lattice, while the rest of it contributes to the development of dislocation structures. According to this interpretation, plastic work is not converted to heat, but increases probability of the microstructural adaptiveness and, in this manner, contributes to configurational entropy of the system.
Impact of carbon inputs on soil carbon fractionation, sequestration and biological responses under major nutrient management practices for rice-wheat cropping systems
Authors: Bhardwaj Ajay Kumar , Rajwar Deepika , Mandal Uttam Kumar , Ahamad Sharif , Kaphaliya Bhumija , Minhas Paramjit Singh , Prabhakar Mathyam , Banyal Rakesh , Singh Ranbir , Chaudhari Suresh Kumar , Sharma Parbodh Chander 
Published: June 2019

AbstractMajor nutrient management systems for rice-wheat cropping were compared for their potential to credit organic carbon (C) to the soil, its fractionation into active (very labile, VLc; labile, Lc) and passive (less labile, LLc; non-labile, NLc) pools, and crop yield responses. A ten-year long experiment was used to study effects of: (i) no inputs (Control, O), (ii) 100% inorganic fertilizers (F) compared to reduced fertilizers inputs (55%) supplemented with biomass incorporation from (iii) opportunity legume crop (Vigna radiata) (LE), (iv) green manure (Sesbania aculeata) (GM), (v) farmyard manure (FYM), (vi) wheat stubble (WS), and (vii) rice stubble (RS). Maximum C input to soil (as the percentage of C assimilated in the system) was in GM (36%) followed by RS (34%), WS (33%), LE (24%), and FYM (21%) compared to O (15%) and F (15%). Total C input to soil had a direct effect on soil C stock, soil C fractions (maximum in VLc and LLc), yet the responses in terms of biological yield were controlled by the quality of the biomass (C:N ratio, decomposition, etc.) incorporated. Legume-based biomass inputs accrued most benefits for soil C sequestration and biological productivity.