bluuebunny/crossref_metadata_2025_split huggingface dataset:
GBF1 and Arf1 interact with Miro and regulate mitochondrial positioning within cells
Authors: Walch Laurence , Pellier Emilie , Leng Weihua , Lakisic Goran , Gautreau Alexis , Contremoulins Vincent , Verbavatz Jean-Marc , Jackson Catherine L. 
Published: November 2018

AbstractThe spatial organization of cells depends on coordination between cytoskeletal systems and intracellular organelles. The Arf1 small G protein and its activator GBF1 are important regulators of Golgi organization, maintaining its morphology and function. Here we show that GBF1 and its substrate Arf1 regulate the spatial organization of mitochondria in a microtubule-dependent manner. Miro is a mitochondrial membrane protein that interacts through adaptors with microtubule motor proteins such as cytoplasmic dynein, the major microtubule minus end directed motor. We demonstrate a physical interaction between GBF1 and Miro, and also between the active GTP-bound form of Arf1 and Miro. Inhibition of GBF1, inhibition of Arf1 activation, or overexpression of Miro, caused a collapse of the mitochondrial network towards the centrosome. The change in mitochondrial morphology upon GBF1 inhibition was due to a two-fold increase in the time engaged in retrograde movement compared to control conditions. Electron tomography revealed that GBF1 inhibition also resulted in larger mitochondria with more complex morphology. Miro silencing or drug inhibition of cytoplasmic dynein activity blocked the GBF1-dependent repositioning of mitochondria. Our results show that blocking GBF1 function promotes dynein- and Miro-dependent retrograde mitochondrial transport along microtubules towards the microtubule-organizing center, where they form an interconnected network.
Energy/Electron Transfer Switch for Controlling Optical Properties of Silicon Quantum Dots
Authors: Abdelhameed Mohammed , Aly Shawkat , Lant Jeremy T. , Zhang Xiaoran , Charpentier Paul 
Published: November 2018

AbstractThe superior optical properties of Silicon Quantum Dots (SQDs) have made them of increasing interest for a variety of biological and opto-electronic applications. The surface functionalization of the SQDs with aromatic ligands plays a key role in controlling their optical properties due to the interaction of the ligands with the electronic wave function of SQDs. However, there is limited reports in literature describing the impact of spacer groups connecting the aromatic chromophore to SQDs on the optical properties of the SQDs. Herein, we report the synthesis of two SQDs assemblies (1.6 nm average diameter) functionalized with perylene-3,4,9,10-tetracarboxylic acid diimide (PDI) chromophore through N-propylurea and propylamine spacers. Depending on the nature of the spacer, the photophysical measurements provide clear evidence for efficient energy and/or electron transfer between the SQDs and PDI. Energy transfer was confirmed to be the operative process when propylurea spacer was used, in which the rate was estimated to be ~2 × 109 s−1. On the other hand, the propylamine spacer was found to facilitate electron transfer process within the SQDs assembly. To illustrate functionality, the water soluble SQD-N-propylurea-PDI assembly was proven to be nontoxic and efficient for fluorescent imaging of embryonic kidney HEK293 cells and human bone cancerous U2OS cells.
Reconstructing charge-carrier dynamics in porous silicon membranes from time-resolved interferometric measurements
Authors: He Wei , Wu Rihan , Yurkevich Igor V. , Canham Leigh T. , Kaplan Andrey 
Published: November 2018

AbstractWe performed interferometric time-resolved simultaneous reflectance and transmittance measurements to investigate the carrier dynamics in pump-probe experiments on thin porous silicon membranes. The experimental data was analysed by using a method built on the Wentzel-Kramers-Brillouin approximation and the Drude model, allowing us to reconstruct the excited carriers’ non-uniform distribution in space and its evolution in time. The analysis revealed that the carrier dynamics in porous silicon, with ~50% porosity and native oxide chemistry, is governed by the Shockley-Read-Hall recombination process with a characteristic time constant of 375 picoseconds, whereas diffusion makes an insignificant contribution as it is suppressed by the high rate of scattering.
Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women
Authors: Dugas Lara R. , Bernabé Beatriz Peñalver , Priyadarshini Medha , Fei Na , Park Seo Jin , Brown Laquita , Plange-Rhule Jacob , Nelson David , Toh Evelyn C. , Gao Xiang , Dong Qunfeng , Sun Jun , Kliethermes Stephanie , Gottel Neil , Luke Amy , Gilbert Jack A. , Layden Brian T. 
Published: November 2018

AbstractWe compared the gut microbial populations in 100 women, from rural Ghana and urban US [50% lean (BMI < 25 kg/m2) and 50% obese (BMI ≥ 30 kg/m2)] to examine the ecological co-occurrence network topology of the gut microbiota as well as the relationship of short chain fatty acids (SCFAs) with obesity. Ghanaians consumed significantly more dietary fiber, had greater microbial alpha-diversity, different beta-diversity, and had a greater concentration of total fecal SCFAs (p-value < 0.002). Lean Ghanaians had significantly greater network density, connectivity and stability than either obese Ghanaians, or lean and obese US participants (false discovery rate (FDR) corrected p-value ≤ 0.01).Bacteroides uniformiswas significantly more abundant in lean women, irrespective of country (FDR corrected p < 0.001), while lean Ghanaians had a significantly greater proportion ofRuminococcus callidus,Prevotella copri, andEscherichia coli, and smaller proportions of Lachnospiraceae,BacteroidesandParabacteroides. Lean Ghanaians had a significantly greater abundance of predicted microbial genes that catalyzed the production of butyric acid via the fermentation of pyruvate or branched amino-acids, while obese Ghanaians and US women (irrespective of BMI) had a significantly greater abundance of predicted microbial genes that encoded for enzymes associated with the fermentation of amino-acids such as alanine, aspartate, lysine and glutamate. Similar to lean Ghanaian women, mice humanized with stool from the lean Ghanaian participant had a significantly lower abundance of family Lachnospiraceae and genusBacteroidesandParabacteroides, and were resistant to obesity following 6-weeks of high fat feeding (p-value < 0.01). Obesity-resistant mice also showed increased intestinal transcriptional expression of the free fatty acid (Ffa) receptorFfa2, in spite of similar fecal SCFAs concentrations. We demonstrate that the association between obesity resistance and increased predicted ecological connectivity and stability of the lean Ghanaian microbiota, as well as increased local SCFA receptor level, provides evidence of the importance of robust gut ecologic network in obesity.
The discovered chimeric protein plays the cohesive role to maintain scallop byssal root structural integrity
Authors: Xu Pingping , Dai Xiaoting , Wang Dandan , Miao Yan , Zhang Xiaokang , Wang Shuoshuo , Teng Luyao , Dong Bo , Bao Zhenmin , Wang Shi , Lyu Qianqian , Liu Weizhi 
Published: November 2018

AbstractAdhesion is essential for many marine sessile organisms. Unraveling the compositions and assembly of marine bioadheisves is the fundamental to understand their physiological roles. Despite the remarkable diversity of animal bioadhesion, our understanding of this biological process remains limited to only a few animal lineages, leaving the majority of lineages remain enigmatic. Our previous study demonstrated that scallop byssus had distinct protein composition and unusual assembly mechanism apart from mussels. Here a novel protein (Sbp9) was discovered from the key part of the byssus (byssal root), which contains two Calcium Binding Domain (CBD) and 49 tandem Epidermal Growth Factor-Like (EGFL) domain repeats. Modular architecture of Sbp9 represents a novel chimeric gene family resulting from a gene fusion event through the acquisition of CBD2 domain by tenascin like (TNL) gene from Na+/Ca2+exchanger 1 (NCX1) gene. Finally, free thiols are present in Sbp9 and the results of a rescue assay indicated that Sbp9 likely plays the cohesive role for byssal root integrity. This study not only aids our understanding of byssus assembly but will also inspire biomimetic material design.
Superdislocations and point defects in pyrochlore Yb2Ti2O7 single crystals and implication on magnetic ground states
Authors: Shafieizadeh Zahra , Xin Yan , Koohpayeh Seyed M. , Huang Qing , Zhou Haidong 
Published: November 2018

AbstractThis study reports atomic-scale characterization of structural defects in Yb2Ti2O7, a pyrochlore oxide whose subtle magnetic interactions is prone to small perturbations. Due to discrepancies in the reported magnetic ground states, it has become a pressing issue to determine the nature of defects in this system. In the present study, we use atomic resolution scanning transmission electron microscopy techniques to identify the type of defects in the ytterbium titanate single crystals grown by the conventional optical floating zone (FZ) method. In addition to the known point defects of substitution Yb on Ti B-sites, extended defects such as dissociated superdislocations and anti-phase boundaries were discovered for the first time in this material. Such defects were prevalently observed in the FZ grown single crystals (of a darker color), in contrast to the stoichiometric white polycrystalline powders or high quality colorless single crystals grown by the traveling solvent floating zone technique. The lattice strains from these extended defects result in distortions of Yb-tetrahedron. A change of Ti valance was not detected at the defects. Our findings provide new insights into understanding the nature of defects that are of great importance for the physical property studies of geometrically frustrated compounds. Furthermore, this work sheds light on the complicated core structure of superdislocations that have large Burgers vectors in oxides with complex unit cells.
Transcriptome analysis provides insight into prickle development and its link to defense and secondary metabolism in Solanum viarum Dunal
Authors: Pandey Shatrujeet , Goel Ridhi , Bhardwaj Archana , Asif Mehar H. , Sawant Samir V. , Misra Pratibha 
Published: November 2018

AbstractPrickles are epidermal outgrowth found on the aerial surface of several terrestrial plants. Microscopic studies on prickles ofS.viarumDunal indicated a crucial role of glandular trichomes (GTs) in their development. A spontaneously obtained prickleless mutant showed normal epidermal GTs, but its downstream developmental process to prickle was perturbed. Thus, prickleless mutant offers an ideal opportunity to unveil molecular regulators working downstream to GTs in the prickle formation. Differential transcriptome analysis of epidermis of prickly and prickleless mutant revealed that expression of several defense regulators like ethylene, salicylic acid, PR-proteins, etc. were significantly down-regulated in prickleless mutant, provide an important link between defense and prickle development. It was also noteworthy that the expression of few essential development related TFs like MADS-box, R2R3-MYB, REM, DRL1, were also down-regulated in the stem, petioles, and leaves of prickleless mutant indicating their potential role in prickle development. Interestingly, the gene expression of terpenoid, steroid, flavonoid, glucosinolate, and lignin biosynthesis pathways were up-regulated in prickleless mutant. The biochemical and qRT-PCR analysis also confirmed metabolite elevation. These results indicated that the loss of prickle was compensated by elevated secondary metabolism in the prickleless mutant which played important role in the biotic and abiotic stress management.
An integrative transcriptome analysis indicates regulatory mRNA-miRNA networks for residual feed intake in Nelore cattle
Authors: De Oliveira Priscila S. N. , Coutinho Luiz L. , Tizioto Polyana C. , Cesar Aline S. M. , de Oliveira Gabriella B. , Diniz Wellison J. da S. , De Lima Andressa O. , Reecy James M. , Mourão Gerson B. , Zerlotini Adhemar , Regitano Luciana C. A. 
Published: November 2018

AbstractResidual Feed Intake (RFI) is an economically relevant trait in beef cattle. Among the molecular regulatory mechanisms, microRNAs (miRNAs) are an important dimension in post-transcriptional regulation and have been associated with different biological pathways. Here, we performed differential miRNAs expression and weighted gene co-expression network analyses (WGCNA) to better understand the complex interactions between miRNAs and mRNAs expressed in bovine skeletal muscle and liver. MiRNA and mRNA expression data were obtained from Nelore steers that were genetically divergent for RFI (N = 10 [low RFI or feed efficient]; N = 10 [high RFI or feed inefficient]). Differentially expressed and hub miRNAs such as bta-miR-486, bta-miR-7, bta-miR15a, bta-miR-21, bta-miR 29, bta- miR-30b, bta-miR-106b, bta-miR-199a-3p, bta-miR-204, and bta-miR 296 may have a potential role in variation of RFI. Functional enrichment analysis of differentially expressed (DE) miRNA’s target genes and miRNA–mRNA correlated modules revealed that insulin, lipid, immune system, oxidative stress and muscle development signaling pathways might potentially be involved in RFI in this population. Our study identified DE miRNAs, miRNA - mRNA regulatory networks and hub miRNAs related to RFI. These findings suggest a possible role of miRNAs in regulation of RFI, providing new insights into the potential molecular mechanisms that control feed efficiency in Nelore cattle.
Genome sequences identify three families of Coleoptera as morphologically derived click beetles (Elateridae)
Authors: Kusy Dominik , Motyka Michal , Bocek Matej , Vogler Alfried P. , Bocak Ladislav 
Published: November 2018

AbstractPlastoceridae Crowson, 1972, Drilidae Blanchard, 1845 and Omalisidae Lacordaire, 1857 (Elateroidea) are families of the Coleoptera with obscure phylogenetic relationships and modified morphology showing neotenic traits such as soft bodies, reduced wing cases and larviform females. We shotgun sequenced genomes ofPlastocerus,DrilusandOmalisusand incorporated them into data matrices of 66 and 4202 single-copy nuclear genes representing Elateroidea. Phylogenetic analyses indicate their terminal positions within the broadly defined well-sclerotized and fully metamorphosed Elateridae and thus Omalisidae should now be considered as Omalisinae stat. nov. in Elateridae Leach, 1815. The results support multiple independent origins of incomplete metamorphosis in Elateridae and indicate the parallel evolution of morphological and ecological traits. Unlike other neotenic elateroids derived from the supposedly pre-adapted aposematically coloured and unpalatable soft-bodied elateroids, such as fireflies (Lampyridae) and net-winged beetles (Lycidae), omalisids and drilids evolved from well-sclerotized click beetles. These findings suggest sudden morphological shifts through incomplete metamorphosis, with important implications for macroevolution, including reduced speciation rate and high extinction risk in unstable habitats. Precise phylogenetic placement is necessary for studies of the molecular mechanisms of ontogenetic shifts leading to profoundly changed morphology.
Strengthening long-lasting insecticidal nets effectiveness monitoring using retrospective analysis of cross-sectional, population-based surveys across sub-Saharan Africa
Authors: Janko Mark M. , Churcher Thomas S. , Emch Michael E. , Meshnick Steven R. 
Published: November 2018

AbstractBed nets averted 68% of malaria cases in Africa between 2000 and 2015. However, concerns over insecticide resistance, bed net durability and the effectiveness of long-lasting insecticidal nets (LLIN) are growing. To assess the effectiveness of LLINs of different ages and insecticides against malaria, we conducted a population-based, cross-sectional study using data from 162,963 children younger than 5 years of age participating in 33 Demographic and Health and Malaria Indicator Surveys conducted in 21 countries between 2009 and 2016. We used Bayesian logistic regression to estimate associations between LLIN age, insecticide type, and malaria. Children sleeping under LLINs the previous night experienced 21% lower odds of malaria infection than children who did not (odds ratio [OR] 0.79; 95% Uncertainty Interval [UI] 0.76–0.82). Nets less than one year of age exhibited the strongest protective effect (OR 0.75; 95% UI 0.72–0.79), and protection weakened as net age increased. LLINs containing different insecticides exhibited similar protection (ORdeltamethrin 0.78 [0.75–0.82]; ORpermethrin 0.79 [0.75–0.83]; ORalphacypermethrin 0.85 [0.76–0.94]). Freely-available, population-based surveys can enhance and guide current entomological monitoring amid concerns of insecticide resistance and bed net durability, and be used with locally-collected data to support decisions on LLIN redistribution campaign timing which insecticide to use.
Metabolomics and transcriptomics pathway approach reveals outcome-specific perturbations in COPD
Authors: Cruickshank-Quinn Charmion I. , Jacobson Sean , Hughes Grant , Powell Roger L. , Petrache Irina , Kechris Katerina , Bowler Russell , Reisdorph Nichole 
Published: November 2018

AbstractChronic obstructive pulmonary disease (COPD) comprises multiple phenotypes such as airflow obstruction, emphysema, and frequent episodes of acute worsening of respiratory symptoms, known as exacerbations. The goal of this pilot study was to test the usefulness of unbiased metabolomics and transcriptomics approaches to delineate biological pathways associated with COPD phenotypes and outcomes. Blood was collected from 149 current or former smokers with or without COPD and separated into peripheral blood mononuclear cells (PBMC) and plasma. PBMCs and plasma were analyzed using microarray and liquid chromatography mass spectrometry, respectively. Statistically significant transcripts and compounds were mapped to pathways using IMPaLA. Results showed that glycerophospholipid metabolism was associated with worse airflow obstruction and more COPD exacerbations. Sphingolipid metabolism was associated with worse lung function outcomes and exacerbation severity requiring hospitalizations. The strongest associations between a pathway and a certain COPD outcome were: fat digestion and absorption and T cell receptor signaling with lung function outcomes; antigen processing with exacerbation frequency; arginine and proline metabolism with exacerbation severity; and oxidative phosphorylation with emphysema. Overlaying transcriptomic and metabolomics datasets across pathways enabled outcome and phenotypic differences to be determined. Findings are relevant for identifying molecular targets for animal intervention studies and early intervention markers in human cohorts.
Understanding the Thalidomide Chirality in Biological Processes by the Self-disproportionation of Enantiomers
Authors: Tokunaga Etsuko , Yamamoto Takeshi , Ito Emi , Shibata Norio 
Published: November 2018

AbstractTwenty years after the thalidomide disaster in the late 1950s, Blaschkeet al. reported that only the (S)-enantiomer of thalidomide is teratogenic. However, other work has shown that the enantiomers of thalidomide interconvertin vivo, which begs the question: why is teratogen activity not observed in animal experiments that use (R)-thalidomide given the readyin vivoracemization (“thalidomide paradox”)? Herein, we disclose a hypothesis to explain this “thalidomide paradox” through thein-vivoself-disproportionation of enantiomers. Upon stirring a 20% ee solution of thalidomide in a given solvent, significant enantiomeric enrichment of up to 98% ee was observed reproducibly in solution. We hypothesize that a fraction of thalidomide enantiomers epimerizesin vivo, followed by precipitation of racemic thalidomide in (R/S)-heterodimeric form. Thus, racemic thalidomide is most likely removed from biological processes upon racemic precipitation in (R/S)-heterodimeric form. On the other hand, enantiomerically pure thalidomide remains in solution, affording the observed biological experimental results: the (S)-enantiomer is teratogenic, while the (R)-enantiomer is not.
Photobiomodulation (PBM) promotes angiogenesis in-vitro and in chick embryo chorioallantoic membrane model
Authors: Winter Raimund , Dungel Peter , Reischies Frederike Marie Josephine , Rohringer Sabrina , Slezak Paul , Smolle Christian , Spendel Stephan , Kamolz Lars-Peter , Ghaffari-Tabrizi-Wizsy Nassim , Schicho Kurt 
Published: November 2018

AbstractThe application of light in various therapeutic settings known as Photobiomodulation (PBM) is well established. Indications are the improvement of wound healing and tissue regeneration, scarring, and perfusion as well as pain therapy. Tissue perfusion is mandatory for successful wound healing. Nevertheless, there is a lack of mechanistic studies. We investigate the potential effect of PBM from light emitting diodes (LED) at 635 nm, 80 mW/cm2, 24 J/cm2 on angiogenesis in a two-part study: 1.) Investigation of the effect of PBM on the proliferation of endothelial cells and on vasculogenesis in a co-culture model of endothelial cells and stem cells. 2.) Investigation of the influence of PBM at chick egg chorioallantoic membrane (CAM) assays with fresh human skin xenografts. In both study phases, we observed a stimulating effect of PBM at 635 nm; in part 1: for proliferation of HUVEC (human umbilical vein endothelial cells) (25833 ± 12859 versus 63002 ± 35760 cells/well, p < 0.05, for cellular network formation (2.1 ± 2.1 versus 4.6 ± 3.5, p < 0.05) and for less cell compactness p = 0.01; in part 2: for the increase of number of vessel junctions per ROI (region of interest) (15.9 ± 2.6 versus 20.8 ± 5.4, p < 0.05). Our results suggest significant promotion of angiogenesis by PBM at 635 nm in vitro and in vivo.
Pendimethalin-induced oxidative stress, DNA damage and activation of anti-inflammatory and apoptotic markers in male rats
Authors: Ahmad Md. Irshad , Zafeer Mohd Faraz , Javed Mehjbeen , Ahmad Masood 
Published: November 2018

AbstractMale Wistar rats were exposed to herbicide, pendimethalin (PND) at varying oral doses of 62.5, 125 and 250 mg/kg b.w. for 14 days. Toxiological effects were assessed in terms of oxidative stress, DNA damage, histopathological alterations and induction of anti-inflammatory and apoptotic responses linked Bax, Bcl-2, IFN-γ, TNF-α and caspase-3 gene expression. In comparison with respective untreated controls, all exposure groups of PND exhibited significant changes in the oxidative stress markers (protein carbonylation and lipid peroxidation) and antioxidant defenses (GSH, SOD, CAT and GST) in liver and kidney tissues. The histopathological changes including leucocyte infiltration, pyknotic nuclei, necrosis, large bowman’s space, shrinked renal cortex, were observed in the liver and kidney tissues of PND exposed rats. Significant DNA damage was recorded through comet assay in liver and kidney cells of treated animals as compared to control. Alteration in anti-inflammatory and apoptotic genes expression determined by RT-PCR, revealed the activation of intrinsic apoptotic pathway(s) under the PND induced cellular stress. A pronounced increase in Bax expression, caspase-3 activities and decreased Bcl-2 expressions were also associated with PND-induced apoptosis. Data from this study suggests that PND induces cellular toxicity and genetic perturbations which can alter the normal cellular and physiological functioning in rats.