bluuebunny/crossref_metadata_2025_split huggingface dataset:
sept7b is required for the differentiation of pancreatic endocrine progenitors
Authors: Dash Surjya Narayan , Hakonen Elina , Ustinov Jarkko , Otonkoski Timo , Andersson Olov , Lehtonen Sanna 
Published: April 2016

AbstractProtection or restoration of pancreatic β-cell mass as a therapeutic treatment for type 1 diabetes requires understanding of the mechanisms that drive the specification and development of pancreatic endocrine cells. Septins are filamentous small GTPases that function in the regulation of cell division, cytoskeletal organization and membrane remodeling and are involved in various tissue-specific developmental processes. However, their role in pancreatic endocrine cell differentiation remains unknown. Here we show by functional manipulation techniques in transgenic zebrafish lines that suppression of sept7b, the zebrafish ortholog of human SEPT7, profoundly increases the number of endocrine progenitors but limits their differentiation, leading to reduction in β- and α-cell mass. Furthermore, we discovered that shh (sonic hedgehog) expression in the endoderm, essential for the development of pancreatic progenitors of the dorsal pancreatic bud, is absent in larvae depleted of sept7b. We also discovered that sept7b is important for the differentiation of ventral pancreatic bud-derived cells: sept7b-depleted larvae exhibit downregulation of Notch receptors notch1a and notch1b and show precocious differentiation of NeuroD-positive endocrine cells in the intrapancreatic duct and gut epithelium. Collectively, this study provides a novel insight into the development of pancreatic endocrine progenitors, revealing an essential role for sept7b in endocrine progenitor differentiation.
Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection
Authors: Sharma Garima , Sowpati Divya Tej , Singh Prakruti , Khan Mehak Zahoor , Ganji Rakesh , Upadhyay Sandeep , Banerjee Sharmistha , Nandicoori Vinay Kumar , Khosla Sanjeev 
Published: April 2016

AbstractA mammalian cell utilizes DNA methylation to modulate gene expression in response to environmental changes during development and differentiation. Aberrant DNA methylation changes as a correlate to diseased states like cancer, neurodegenerative conditions and cardiovascular diseases have been documented. Here we show genome-wide DNA methylation changes in macrophages infected with the pathogen M. tuberculosis. Majority of the affected genomic loci were hypermethylated in M. tuberculosis infected THP1 macrophages. Hotspots of differential DNA methylation were enriched in genes involved in immune response and chromatin reorganization. Importantly, DNA methylation changes were observed predominantly for cytosines present in non-CpG dinucleotide context. This observation was consistent with our previous finding that the mycobacterial DNA methyltransferase, Rv2966c, targets non-CpG dinucleotides in the host DNA during M. tuberculosis infection and reiterates the hypothesis that pathogenic bacteria use non-canonical epigenetic strategies during infection.
p58IPK suppresses NLRP3 inflammasome activation and IL-1β production via inhibition of PKR in macrophages
Authors: Boriushkin Evgenii , Wang Joshua J. , Li Junhua , Bhatta Maulasri , Zhang Sarah X. 
Published: April 2016

AbstractThe NLRP3 inflammasome activation is a key signaling event for activation and secretion of pro-inflammatory cytokines such as IL-1β from macrophages. p58IPK is a molecular chaperone that regulates protein homeostasis through inhibiting eIF-2α kinases including double-stranded RNA–dependent protein kinase (PKR), which has been recently implicated in inflammasome activation. Herein we investigate the role of p58IPK in TLR4 signaling and inflammasome activation in macrophages. Primary bone marrow-derived macrophages (BMDM) was isolated from p58IPK knockout (KO) and wildtype (WT) mice and treated with lipopolysaccharide (LPS) and ATP to activate TLR4 signaling and stimulate inflammasome activation. Compared to WT macrophages, p58IPK deficient cells demonstrated significantly stronger activation of PKR, NF-κB and JNK and higher expression of pro-inflammatory genes TNF-α and IL-1β. Coincidently, p58IPK deletion intensified NLRP3-inflammasome activation indicated by enhanced caspase 1 cleavage and increased IL-1β maturation and secretion. Pretreatment with specific PKR inhibitor or overexpression of p58IPK largely abolished the changes in inflammasome activation and IL-1β secretion in p58IPK null macrophages. Furthermore, immunoprecipitation assay confirmed the binding of p58IPK with PKR, but not other TLR4 downstream signaling molecules. Collectively, these results suggest a novel and crucial role of p58IPK in regulation of inflammasome activation and IL-1β secretion in macrophages.
Characterization of piRNAs across postnatal development in mouse brain
Authors: Ghosheh Yanal , Seridi Loqmane , Ryu Taewoo , Takahashi Hazuki , Orlando Valerio , Carninci Piero , Ravasi Timothy 
Published: April 2016

AbstractPIWI-interacting RNAs (piRNAs) are responsible for maintaining the genome stability by silencing retrotransposons in germline tissues– where piRNAs were first discovered and thought to be restricted. Recently, novel functions were reported for piRNAs in germline and somatic cells. Using deep sequencing of small RNAs and CAGE of postnatal development of mouse brain, we identified piRNAs only in adult mouse brain. These piRNAs have similar sequence length as those of MILI-bound piRNAs. In addition, we predicted novel candidate regulators and putative targets of adult brain piRNAs.
Optical polarization and intervalley scattering in single layers of MoS2 and MoSe2
Authors: Kioseoglou G. , Hanbicki A. T. , Currie M. , Friedman A. L. , Jonker B. T. 
Published: April 2016

AbstractSingle layers of MoS2 and MoSe2 were optically pumped with circularly polarized light and an appreciable polarization was initialized as the pump energy was varied. The circular polarization of the emitted photoluminescence was monitored as a function of the difference between the excitation energy and the A-exciton emission at the K-point of the Brillouin zone. Our results show a threshold of twice the LA phonon energy, specific to the material, above which phonon-assisted intervalley scattering causes depolarization. In both materials this leads to almost complete depolarization within ~100 meV above the threshold energy. We identify the extra kinetic energy of the exciton (independent of whether it is neutral or charged) as the key parameter for presenting a unifying picture of the depolarization process.
Evaluation of tobacco specific nitrosamines exposure by quantification of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in human hair of non-smokers
Authors: Pérez-Ortuño Raúl , Martínez-Sánchez Jose M. , Fu Marcela , Fernández Esteve , Pascual José A. 
Published: April 2016

AbstractChronic exposure to specific carcinogens present in secondhand smoke has been associated with different types of cancers. Hair is an ideal matrix to develop a proper biomarker as it absorbs substances in circulation and allows measuring their average concentration over long periods of time. A method was developed for the simultaneous quantification of nicotine, cotinine, NNN, NNK and NNAL in 20 mg human hair samples. Concentrations were significantly different depending on the declared exposure. This study shows for the first time that NNK is present in hair samples from non-smokers in concentrations much higher than any other tobacco specific nitrosamine. NNN could also be detected in samples from the most exposed non-smokers while, as previously reported, NNAL was undetectable. NNK correlates well with nicotine and cotinine (rsp = 0.774 and rsp = 0.792 respectively, p < 0.001 in both cases). However, NNN concentrations did not correlate with any of the other analytes. Ratios between NNK and nicotine show variability with different concentrations of NNK present in samples with similar nicotine values. NNK has proven to be the best marker of tobacco specific nitrosamines in hair. Monitoring NNK may provide a good estimation of cancer risk associated with exposure to secondhand smoke.
Plasmacytoid dendritic cells are short-lived: reappraising the influence of migration, genetic factors and activation on estimation of lifespan
Authors: Zhan Yifan , Chow Kevin V. , Soo Priscilla , Xu Zhen , Brady Jamie L. , Lawlor Kate E. , Masters Seth L. , O’keeffe Meredith , Shortman Ken , Zhang Jian-Guo , Lew Andrew M. 
Published: April 2016

AbstractPlasmacytoid dendritic cells (pDCs) play an important role in immunity to certain pathogens and immunopathology in some autoimmune diseases. They are thought to have a longer lifespan than conventional DCs (cDCs), largely based on a slower rate of BrdU labeling by splenic pDCs. Here we demonstrated that pDC expansion and therefore BrdU labeling by pDCs occurs in bone marrow (BM). The rate of labeling was similar between BM pDCs and spleen cDCs. Therefore, slower BrdU labeling of spleen pDCs likely reflects the “migration time” (∼2 days) for BrdU labeled pDCs to traffic to the spleen, not necessarily reflecting longer life span. Tracking the decay of differentiated DCs showed that splenic pDCs and cDCs decayed at a similar rate. We suggest that spleen pDCs have a shorter in vivo lifespan than estimated utilizing some of the previous approaches. Nevertheless, pDC lifespan varies between mouse strains. pDCs from lupus-prone NZB mice survived longer than C57BL/6 pDCs. We also demonstrated that activation either positively or negatively impacted on the survival of pDCs via different cell-death mechanisms. Thus, pDCs are also short-lived. However, the pDC lifespan is regulated by genetic and environmental factors that may have pathological consequence.
AutA and AutR, Two Novel Global Transcriptional Regulators, Facilitate Avian Pathogenic Escherichia coli Infection
Authors: Zhuge Xiangkai , Tang Fang , Zhu Hongfei , Mao Xiang , Wang Shaohui , Wu Zongfu , Lu Chengping , Dai Jianjun , Fan Hongjie 
Published: April 2016

AbstractBacteria can change its lifestyle during inhabiting in host niches where they survive and replicate by rapidly altering gene expression pattern to accommodate the new environment. In this study, two novel regulators in avian pathogenicEscherichia coli(APEC) were identified and designated as AutA and AutR. RT-PCR and β-galactosidase assay results showed that AutA and AutR co-regulated the expression of adhesin UpaB in APEC strain DE205B. Electrophoretic mobility shift assay showed that AutA and AutR could directly bind theupaBpromoter DNA.In vitrotranscription assay indicated that AutA could activate theupaBtranscription, while AutR inhibited theupaBtranscription due to directly suppressing the activating effect of AutA on UpaB expression. Transcriptome analysis showed that AutA and AutR coherently affected the expression of hundreds of genes. Our study confirmed that AutA and AutR co-regulated the expression of DE205B K1 capsule and acid resistance systems inE. coliacid fitness island (AFI). Moreover, phenotypic heterogeneity in expression of K1 capsule and acid resistance systems in AFI during host–pathogen interaction was associated with the regulation of AutA and AutR. Collectively speaking, our studies presented that AutA and AutR are involved in APEC adaptive lifestyle change to facilitate its infection.
Significant accumulation of nitrate in Chinese semi-humid croplands
Authors: Zhou Junyu , Gu Baojing , Schlesinger William H. , Ju Xiaotang 
Published: April 2016

AbstractSoil nitrate is important for crop growth, but it can also leach to groundwater causing nitrate contamination, a threat to human health. Here, we report a significant accumulation of soil nitrate in Chinese semi-humid croplands based upon more than 7000 samples from 141 sites collected from 1994 to 2015. In the 0–4 meters depth of soil, total nitrate accumulation reaches 453 ± 39, 749 ± 75, 1191 ± 89, 1269 ± 114, 2155 ± 330 kg N ha−1 on average in wheat, maize, open-field vegetables (OFV), solar plastic-roofed greenhouse vegetables (GHV) and orchard fields, respectively. Surprisingly, there is also a comparable amount of nitrate accumulated in the vadose-zone deeper than 4 meters. Over-use of N fertilizer (and/or manure) and a declining groundwater table are the major causes for this huge nitrate reservoir in the vadose-zone of semi-humid croplands, where the nitrate cannot be denitrified due to the presence of oxygen and lack of carbon sources. Future climatic change with more extreme rainfall events would increase the risk of accumulated nitrate moving downwards and threatening groundwater nitrate contamination.
Disordered array of Au covered Silicon nanowires for SERS biosensing combined with electrochemical detection
Authors: Convertino Annalisa , Mussi Valentina , Maiolo Luca 
Published: April 2016

AbstractWe report on highly disordered array of Au coated silicon nanowires (Au/SiNWs) as surface enhanced Raman scattering (SERS) probe combined with electrochemical detection for biosensing applications. SiNWs, few microns long, were grown by plasma enhanced chemical vapor deposition on common microscope slides and covered by Au evaporated film, 150 nm thick. The capability of the resulting composite structure to act as SERS biosensor was studied via the biotin-avidin interaction: the Raman signal obtained from this structure allowed to follow each surface modification step as well as to detect efficiently avidin molecules over a broad range of concentrations from micromolar down to the nanomolar values. The metallic coverage wrapping SiNWs was exploited also to obtain a dual detection of the same bioanalyte by electrochemical impedance spectroscopy (EIS). Indeed, the SERS signal and impedance modifications induced by the biomolecule perturbations on the metalized surface of the NWs were monitored on the very same three-electrode device with the Au/SiNWs acting as both working electrode and SERS probe.
Odorant receptors of Drosophila are sensitive to the molecular volume of odorants
Authors: Saberi Majid , Seyed-allaei Hamed 
Published: April 2016

AbstractWhich properties of a molecule define its odor? This is a basic yet unanswered question regarding the olfactory system. The olfactory system ofDrosophilahas a repertoire of approximately 60 odorant receptors. Molecules bind to odorant receptors with different affinities and activate them with different efficacies, thus providing a combinatorial code that identifies odorants. We hypothesized that the binding affinity of an odorant-receptor pair is affected by their relative sizes. The maximum affinity can be attained when the molecular volume of an odorant matches the volume of the binding pocket. The affinity drops to zero when the sizes are too different, thus obscuring the effects of other molecular properties. We developed a mathematical formulation of this hypothesis and verified it usingDrosophiladata. We also predicted the volume and structural flexibility of the binding site of each odorant receptor; these features significantly differ between odorant receptors. The differences in the volumes and structural flexibilities of different odorant receptor binding sites may explain the difference in the scents of similar molecules with different sizes.
Comprehensive analysis of the polygalacturonase and pectin methylesterase genes in Brassica rapa shed light on their different evolutionary patterns
Authors: Duan Weike , Huang Zhinan , Song Xiaoming , Liu Tongkun , Liu Hailong , Hou Xilin , Li Ying 
Published: April 2016

AbstractPectins are fundamental polysaccharides in the plant primary cell wall. Polygalacturonases (PGs) and pectin methylesterases (PMEs), major components of the pectin remodeling and disassembly network, are involved in cell separation processes during many stages of plant development. A comprehensive study of these genes in plants could shed light on the evolution patterns of their structural development. In this study, we conducted whole-genome annotation, molecular evolution and gene expression analyses of PGs and PMEs in Brassica rapa and 8 other plant species. A total of 100 PGs and 110 PMEs were identified in B. rapa; they primarily diverged from 12–18 MYA and PMEs were retained more than PGs. Along with another 305 PGs and 348 PMEs in the 8 species, two different expansion or evolution types were discovered: a new branch of class A PGs appeared after the split of gymnosperms and angiosperms, which led to the rapid expansion of PGs; the pro domain was obtained or lost in the proPMEs through comprehensive analyses among PME genes. In addition, the PGs and PMEs exhibit diverged expression patterns. These findings will lead to novel insight regarding functional divergence and conservation in the gene families and provide more support for molecular evolution analyses.
Biochar affects carbon composition and stability in soil: a combined spectroscopy-microscopy study
Authors: Hernandez-Soriano Maria C. , Kerré Bart , Kopittke Peter M. , Horemans Benjamin , Smolders Erik 
Published: April 2016

AbstractThe use of biochar can contribute to carbon (C) storage in soil. Upon addition of biochar, there is a spatial reorganization of C within soil particles, but the mechanisms remain unclear. Here, we used Fourier transformed infrared-microscopy and confocal laser scanning microscopy to examine this reorganization. A silty-loam soil was amended with three different organic residues and with the biochar produced from these residues and incubated for 237 d. Soil respiration was lower in biochar-amended soils than in residue-amended soils. Fluorescence analysis of the dissolved organic matter revealed that biochar application increased a humic-like fluorescent component, likely associated with biochar-C in solution. The combined spectroscopy-microscopy approach revealed the accumulation of aromatic-C in discrete spots in the solid-phase of microaggregates and its co-localization with clay minerals for soil amended with raw residue or biochar.The co-localization of aromatic-C:polysaccharides-C was consistently reduced upon biochar application. We conclude that reduced C metabolism is an important mechanism for C stabilization in biochar-amended soils.
Maximizing Photoluminescence Extraction in Silicon Photonic Crystal Slabs
Authors: Mahdavi Ali , Sarau George , Xavier Jolly , Paraïso Taofiq K. , Christiansen Silke , Vollmer Frank 
Published: April 2016

AbstractPhotonic crystal modes can be tailored for increasing light matter interactions and light extraction efficiencies. These PhC properties have been explored for improving the device performance of LEDs, solar cells and precision biosensors. Tuning the extended band structure of 2D PhC provides a means for increasing light extraction throughout a planar device. This requires careful design and fabrication of PhC with a desirable mode structure overlapping with the spectral region of emission. We show a method for predicting and maximizing light extraction from 2D photonic crystal slabs, exemplified by maximizing silicon photoluminescence (PL). Systematically varying the lattice constant and filling factor, we predict the increases in PL intensity from band structure calculations and confirm predictions in micro-PL experiments. With the near optimal design parameters of PhC, we demonstrate more than 500-fold increase in PL intensity, measured near band edge of silicon at room temperature, an enhancement by an order of magnitude more than what has been reported.
Folding and Stabilization of Native-Sequence-Reversed Proteins
Authors: Zhang Yuanzhao , Weber Jeffrey K , Zhou Ruhong 
Published: April 2016

AbstractThough the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we investigate how the reverse-sequences of native proteins might fold by examining a series of small proteins of increasing structural complexity (α-helix, β-hairpin, α-helix bundle and α/β-protein). Employing a tandem protein structure prediction algorithmic and molecular dynamics simulation approach, we find that the ability of reverse sequences to adopt native-like folds is strongly influenced by protein size and the flexibility of the native hydrophobic core. For β-hairpins with reverse-sequences that fail to fold, we employ a simple mutational strategy for guiding stable hairpin formation that involves the insertion of amino acids into the β-turn region. This systematic look at reverse sequence duality sheds new light on the problem of protein sequence-structure mapping and may serve to inspire new protein design and protein structure prediction protocols.
Disease-emergence dynamics and control in a socially-structured wildlife species
Authors: Pepin Kim M. , VerCauteren Kurt C. 
Published: April 2016

AbstractOnce a pathogen is introduced in a population, key factors governing rate of spread include contact structure, supply of susceptible individuals and pathogen life-history. We examined the interplay of these factors on emergence dynamics and efficacy of disease prevention and response. We contrasted transmission dynamics of livestock viruses with different life-histories in hypothetical populations of feral swine with different contact structures (homogenous, metapopulation, spatial and network). Persistence probability was near 0 for the FMDV-like case under a wide range of parameter values and contact structures, while persistence was probable for the CSFV-like case. There were no sets of conditions where the FMDV-like pathogen persisted in every stochastic simulation. Even when population growth rates were up to 300% annually, the FMDV-like pathogen persisted in <25% of simulations regardless of transmission probabilities and contact structure. For networks and spatial contact structure, persistence probability of the FMDV-like pathogen was always <10%. Because of its low persistence probability, even very early response to the FMDV-like pathogen in feral swine was unwarranted while response to the CSFV-like pathogen was generally effective. When pre-emergence culling of feral swine caused population declines, it was effective at decreasing outbreak size of both diseases by ≥80%.
Endophilin B2 promotes inner mitochondrial membrane degradation by forming heterodimers with Endophilin B1 during mitophagy
Authors: Wang Yi-Han , Wang Jiu-Qiang , Wang Qiaochu , Wang Yun , Guo Caixia , Chen Quan , Chai Tuanyao , Tang Tie-Shan 
Published: April 2016

AbstractMitochondrial sequestration by autophagosomes is a key step in mitophagy while the mechanisms mediating this process are not fully understood. It has been reported that Endophilin B1 (EB1) promotes mitochondrial sequestration by binding and shaping membrane. However, the role of EB1 homolog Endophilin B2 (EB2) in mitophagy remains unclear. Here we report that EB2 plays an indispensable role in mitochondria sequestration and inner mitochondrial membrane (IMM) protein degradation during mitophagy. Similar to EB1, EB2 aggregates into foci and then translocates to damaged mitochondria. Loss of either EB2 and/or EB1 significantly enervates the foci translocation to fragmented mitochondria and IMM degradation and the EB1/EB2 heterodimer formed by EB1/EB2 interaction promotes the above process. We noticed that, it is the dimer domain of EB2 but not that of EB1 mediating the heterodimer formation, manifesting the importance of EB2 in mitophagy. Furthermore, we demonstrate that the EB foci formation is closely regulated by the PINK1-Parkin signaling pathway. From these results, we propose that EB1/EB2 heterodimers may serve as linkers between damaged mitochondria and phagophores during mitophagy.