bluuebunny/crossref_metadata_2025 huggingface dataset:
The chemopreventive potential of lycopene against atrazine-induced cardiotoxicity: modulation of ionic homeostasis
Authors: Lin Jia , Li Hui-Xin , Xia Jun , Li Xue-Nan , Jiang Xiu-Qing , Zhu Shi-Yong , Ge Jing , Li Jin-Long
Published: April 2016

People who drink water contaminated with atrazine (ATR) over many years can experience problems with their cardiovascular system. Lycopene (LYC) has been shown to exhibit cardiovascular disease preventive effects. However, chemopreventive potential of LYC against ATR-induced cardiotoxicity remains unclear. To determine the effects of ATR and/or LYC on heart, mice were treated with ATR (50 mg/kg or 200 mg/kg) and/or LYC (5 mg/kg) by intragastric administration for 21 days. Histopathological and biochemical analyses, including analysis of ion concentrations (Na+, K+, Ca2+ and Mg2+), ATPases (Na+-K+-ATPase, Ca2+-ATPase, Mg2+-ATPase and Ca2+-Mg2+-ATPase) activities and the transcription of their subunits, were performed on heart. The results revealed that ATR led to decreased Creative Kinase (CK) activity and increased histological alterations. Furthermore, a significant change in Na+, K+ and Ca2+ content and the down-regulation of Na+-K+-ATPase and Ca2+-ATPase activities and the mRNA expression of their subunits were observed in ATR-exposed mice. Notably, supplementary LYC significantly protected the heart against ATR-induced damage. In conclusion, ATR induced cardiotoxicity by modulating cardiac ATPase activity and the transcription of its subunits, thereby triggering ionic disturbances. However, supplementary LYC significantly combated ATR-induced cardiotoxicity via the regulation of ATPase activity and subunit transcription. Thus, LYC exhibited a significant chemopreventive potential against ATR-induced cardiotoxicity.
A New Figure of Merit for Organic Solar Cells with Transport-limited Photocurrents
Authors: Neher Dieter , Kniepert Juliane , Elimelech Arik , Koster L. Jan Anton
Published: April 2016

Compared to their inorganic counterparts, organic semiconductors suffer from relatively low charge carrier mobilities. Therefore, expressions derived for inorganic solar cells to correlate characteristic performance parameters to material properties are prone to fail when applied to organic devices. This is especially true for the classical Shockley-equation commonly used to describe current-voltage (JV)-curves, as it assumes a high electrical conductivity of the charge transporting material. Here, an analytical expression for the JV-curves of organic solar cells is derived based on a previously published analytical model. This expression, bearing a similar functional dependence as the Shockley-equation, delivers a new figure of merit α to express the balance between free charge recombination and extraction in low mobility photoactive materials. This figure of merit is shown to determine critical device parameters such as the apparent series resistance and the fill factor.
Functional characterization of electron-transferring flavoprotein and its dehydrogenase required for fungal development and plant infection by the rice blast fungus
Authors: Li Ya , Zhu Jindong , Hu Jiexiong , Meng Xiuli , Zhang Qi , Zhu Kunpeng , Chen Xiaomin , Chen Xuehang , Li Guangpu , Wang Zonghua , Lu Guodong
Published: April 2016

Electron-transferring flavoprotein (ETF) and its dehydrogenase (ETFDH) are highly conserved electron carriers which mainly function in mitochondrial fatty acid β oxidation. Here, we report the identification and characterization of ETF α and β subunit encoding genes (ETFA and ETFB) and ETFDH encoding gene (ETFDH) in the rice blast fungus Magnaporthe oryzae. It was demonstrated that, by impacting fatty acid metabolism, ETF and ETFDH mutations led to severe growth and conidiation defects, which could be largely rescued by exogenous acetate or carbonate. Furthermore, although conidium germination and appressorium formation appeared to be normal in ETF and ETFDH mutants, most appressoria failed to penetrate the host epidermis due to low turgor pressure. The few appressoria that succeeded in penetration were severely restricted in invasive growth and consequently failed to cause disease. Moreover, ETF mutant etfb− induced ROS accumulation in infected host cells and exogenous antioxidant GSH accelerated mutant invading growth without increasing the penetration rate. In addition, mutant etfb− displayed elevated lipid body accumulation and reduced ATP synthesis. Taken together, ETF and ETFDH play an important role in fungal development and plant infection in M. oryzae by regulation of fatty acid metabolism, turgor establishment and induction of host ROS accumulation.
Amphiregulin mediates hCG-induced StAR expression and progesterone production in human granulosa cells
Authors: Fang Lanlan , Yu Yiping , Zhang Ruizhe , He Jingyan , Sun Ying-Pu
Published: April 2016

Progesterone plays critical roles in maintaining a successful pregnancy at the early embryonic stage. Human chorionic gonadotropin (hCG) rapidly induces amphiregulin (AREG) expression. However, it remains unknown whether AREG mediates hCG-induced progesterone production. Thus, the objective of this study was to investigate the role of AREG in hCG-induced progesterone production and the underlying molecular mechanism in human granulosa cells; primary cells were used as the experimental model. We demonstrated that the inhibition of EGFR and the knockdown of AREG abolished hCG-induced steroidogenic acute regulatory protein (StAR) expression and progesterone production. Importantly, follicular fluid AREG levels were positively correlated with progesterone levels in the follicular fluid and serum. Treatment with AREG increased StAR expression and progesterone production and these stimulatory effects were abolished by EGFR inhibition. Moreover, activation of ERK1/2, but not PI3K/Akt, signaling was required for the AREG-induced up-regulation of StAR expression and progesterone production. Our results demonstrate that AREG mediates hCG-induced StAR expression and progesterone production in human granulosa cells, providing novel evidence for the role of AREG in the regulation of steroidogenesis.
Using Wannier functions to improve solid band gap predictions in density functional theory
Authors: Ma Jie , Wang Lin-Wang
Published: April 2016

Enforcing a straight-line condition of the total energy upon removal/addition of fractional electrons on eigen states has been successfully applied to atoms and molecules for calculating ionization potentials and electron affinities, but fails for solids due to the extended nature of the eigen orbitals. Here we have extended the straight-line condition to the removal/addition of fractional electrons on Wannier functions constructed within the occupied/unoccupied subspaces. It removes the self-interaction energies of those Wannier functions, and yields accurate band gaps for solids compared to experiments. It does not have any adjustable parameters and the computational cost is at the DFT level. This method can also work for molecules, providing eigen energies in good agreement with experimental ionization potentials and electron affinities. Our approach can be viewed as an alternative approach of the standard LDA+U procedure.
Scaling in topological properties of brain networks
Authors: Singh Soibam Shyamchand , Khundrakpam Budhachandra , Reid Andrew T. , Lewis John D. , Evans Alan C. , Ishrat Romana , Sharma B. Indrajit , Singh R. K. Brojen
Published: April 2016

The organization in brain networks shows highly modular features with weak inter-modular interaction. The topology of the networks involves emergence of modules and sub-modules at different levels of constitution governed by fractal laws that are signatures of self-organization in complex networks. The modular organization, in terms of modular mass, inter-modular, and intra-modular interaction, also obeys fractal nature. The parameters which characterize topological properties of brain networks follow one parameter scaling theory in all levels of network structure, which reveals the self-similar rules governing the network structure. Further, the calculated fractal dimensions of brain networks of different species are found to decrease when one goes from lower to higher level species which implicates the more ordered and self-organized topography at higher level species. The sparsely distributed hubs in brain networks may be most influencing nodes but their absence may not cause network breakdown, and centrality parameters characterizing them also follow one parameter scaling law indicating self-similar roles of these hubs at different levels of organization in brain networks. The local-community-paradigm decomposition plot and calculated local-community-paradigm-correlation co-efficient of brain networks also shows the evidence for self-organization in these networks.
MEMS Based Broadband Piezoelectric Ultrasonic Energy Harvester (PUEH) for Enabling Self-Powered Implantable Biomedical Devices
Authors: Shi Qiongfeng , Wang Tao , Lee Chengkuo
Published: April 2016

Acoustic energy transfer is a promising energy harvesting technology candidate for implantable biomedical devices. However, it does not show competitive strength for enabling self-powered implantable biomedical devices due to two issues – large size of bulk piezoelectric ultrasound transducers and output power fluctuation with transferred distance due to standing wave. Here we report a microelectromechanical systems (MEMS) based broadband piezoelectric ultrasonic energy harvester (PUEH) to enable self-powered implantable biomedical devices. The PUEH is a microfabricated lead zirconate titanate (PZT) diaphragm array and has wide operation bandwidth. By adjusting frequency of the input ultrasound wave within the operation bandwidth, standing wave effect can be minimized for any given distances. For example, at 1 cm distance, power density can be increased from 0.59 μW/cm2 to 3.75 μW/cm2 at input ultrasound intensity of 1 mW/cm2 when frequency changes from 250 to 240 kHz. Due to the difference of human body and manual surgical process, distance fluctuation for implantable biomedical devices is unavoidable and it strongly affects the coupling efficiency. This issue can be overcome by performing frequency adjustment of the PUEH. The proposed PUEH shows great potential to be integrated on an implanted biomedical device chip as power source for various applications.
A biofidelic 3D culture model to study the development of brain cellular systems
Authors: Ren M. , Du C. , Herrero Acero E. , Tang-Schomer M. D. , Özkucur N.
Published: April 2016

Little is known about how cells assemble as systems during corticogenesis to generate collective functions. We built a neurobiology platform that consists of fetal rat cerebral cortical cells grown within 3D silk scaffolds (SF). Ivermectin (Ivm), a glycine receptor (GLR) agonist, was used to modulate cell resting membrane potential (Vmem) according to methods described in a previous work that implicated Ivm in the arrangement and connectivity of cortical cell assemblies. The cells developed into distinct populations of neuroglial stem/progenitor cells, mature neurons or epithelial-mesenchymal cells. Importantly, the synchronized electrical activity in the newly developed cortical assemblies could be recorded as local field potential (LFP) measurements. This study therefore describes the first example of the development of a biologically relevant cortical plate assembly outside of the body. This model provides i) a preclinical basis for engineering cerebral cortex tissue autografts and ii) a biofidelic 3D culture model for investigating biologically relevant processes during the functional development of cerebral cortical cellular systems.
Human somatic cells subjected to genetic induction with six germ line-related factors display meiotic germ cell-like features
Authors: Medrano Jose V. , Martínez-Arroyo Ana M. , Míguez Jose M. , Moreno Inmaculada , Martínez Sebastián , Quiñonero Alicia , Díaz-Gimeno Patricia , Marqués-Marí Ana I. , Pellicer Antonio , Remohí Jose , Simón Carlos
Published: April 2016

The in vitro derivation of human germ cells has attracted interest in the last years, but their direct conversion from human somatic cells has not yet been reported. Here we tested the ability of human male somatic cells to directly convert into a meiotic germ cell-like phenotype by inducing them with a combination of selected key germ cell developmental factors. We started with a pool of 12 candidates that were reduced to 6, demonstrating that ectopic expression of the germ line-related genes PRDM1, PRDM14, LIN28A, DAZL, VASA and SYCP3 induced direct conversion of somatic cells (hFSK (46, XY) and hMSC (46, XY)) into a germ cell-like phenotype in vitro. Induced germ cell-like cells showed a marked switch in their transcriptomic profile and expressed several post-meiotic germ line related markers, showed meiotic progression, evidence of epigenetic reprogramming and approximately 1% were able to complete meiosis as demonstrated by their haploid status and the expression of several post-meiotic markers. Furthermore, xenotransplantation assays demonstrated that a subset of induced cells properly colonize the spermatogonial niche. Knowledge obtained from this work can be used to create in vitro models to study gamete-related diseases in humans.
Model-based genotype-phenotype mapping used to investigate gene signatures of immune sensitivity and resistance in melanoma micrometastasis
Authors: Santos Guido , Nikolov Svetoslav , Lai Xin , Eberhardt Martin , Dreyer Florian S. , Paul Sushmita , Schuler Gerold , Vera Julio
Published: April 2016

In this paper, we combine kinetic modelling and patient gene expression data analysis to elucidate biological mechanisms by which melanoma becomes resistant to the immune system and to immunotherapy. To this end, we systematically perturbed the parameters in a kinetic model and performed a mathematical analysis of their impact, thereby obtaining signatures associated with the emergence of phenotypes of melanoma immune sensitivity and resistance. Our phenotypic signatures were compared with published clinical data on pretreatment tumor gene expression in patients subjected to immunotherapy against metastatic melanoma. To this end, the differentially expressed genes were annotated with standard gene ontology terms and aggregated into metagenes. Our method sheds light on putative mechanisms by which melanoma may develop immunoresistance. Precisely, our results and the clinical data point to the existence of a signature of intermediate expression levels for genes related to antigen presentation that constitutes an intriguing resistance mechanism, whereby micrometastases are able to minimize the combined anti-tumor activity of complementary responses mediated by cytotoxic T cells and natural killer cells, respectively. Finally, we computationally explored the efficacy of cytokines used as low-dose co-adjuvants for the therapeutic anticancer vaccine to overcome tumor immunoresistance.
Smad6 determines BMP-regulated invasive behaviour of breast cancer cells in a zebrafish xenograft model
Authors: de Boeck Miriam , Cui Chao , Mulder Aat A , Jost Carolina R , Ikeno Souichi , ten Dijke Peter
Published: April 2016

The transforming growth factor-β (TGF-β) family is known to play critical roles in cancer progression. While the dual role of TGF-β is well described, the function of bone morphogenetic proteins (BMPs) is unclear. In this study, we established the involvement of Smad6, a BMP-specific inhibitory Smad, in breast cancer cell invasion. We show that stable overexpression of Smad6 in breast cancer MCF10A M2 cells inhibits BMP signalling, thereby mitigating BMP6-induced suppression of mesenchymal marker expression. Using a zebrafish xenograft model, we demonstrate that overexpression of Smad6 potentiates invasion of MCF10A M2 cells and enhances the aggressiveness of breast cancer MDA-MB-231 cells in vivo, whereas a reversed phenotype is observed after Smad6 knockdown. Interestingly, BMP6 pre-treatment of MDA-MB-231 cells induced cluster formation at the invasive site in the zebrafish. BMP6 also stimulated cluster formation of MDA-MB-231 cells co-cultured on Human Microvascular Endothelial Cells (HMEC)-1 in vitro. Electron microscopy illustrated an induction of cell-cell contact by BMP6. The clinical relevance of our findings is highlighted by a correlation of high Smad6 expression with poor distant metastasis free survival in ER-negative cancer patients. Collectively, our data strongly indicates the involvement of Smad6 and BMP signalling in breast cancer cell invasion in vivo.
MiR-142-3p is a RANKL-dependent inducer of cell death in osteoclasts
Authors: Fordham Jezrom B. , Guilfoyle Katherine , Naqvi Afsar Raza , Nares Salvador
Published: April 2016

MicroRNA are small, non-coding, single-stranded RNAs that are estimated to regulate ~60% of the human genome. MiRNA profiling of monocyte-to-osteoclast differentiation identified miR-142-3p as a miRNA that is significantly, differentially expressed throughout osteoclastogenesis. Enforced expression of miR-142-3p via transient transfection with miR-142-3p mimic inhibited cell-to-cell contact and fusion, decreased protein kinase C alpha expression, and ultimately reduced cell viability. miR-142-3p was also identified as significantly differentially expressed during monocyte-to-macrophage differentiation and overexpression of miR-142-3p prevented their conversion to osteoclasts. Furthermore, the inhibitory effect of miR-142-3p on osteoclastogenesis extended to the conversion of a third osteoclast precursor cell type- dendritic cells. These results demonstrate miR-142-3p to be a negative regulator of osteoclastogenesis from the 3 main precursor cell types: monocytes, macrophages and dendritic cells. Importantly, decreased survival was dependent upon both miR-142-3p expression and RANK-signaling, with no harmful effects detected in the absence of this combination. As such, miR-142-3p represents a novel target for the selective removal of osteoclasts by targeting of osteoclastogenic pathways.
Partial Oxidized Arsenene: Emerging Tunable Direct Bandgap Semiconductor
Authors: Wang Yu-Jiao , Zhou Kai-Ge , Yu Geliang , Zhong Xing , Zhang Hao-Li
Published: April 2016

Arsenene, as a member of the Group V elemental two-dimensional materials appears on the horizon, has shown great prospects. However, its indirect bandgap limits the applications in optoelectronics. In this theoretical work, we reported that partial oxidation can tune the indirect bandgap of arsenene into the direct one. Attributed to the enthalpy decreasing linear to the oxygen ratio, partial oxidized arsenene can be controllably produced by the progressive oxidation under low temperature. Importantly, by increasing the oxygen content from 1O/18As to 18O/18As, the oxidation can narrow the direct bandgap of oxidized arsenene from 1.29 to 0.02 eV. The bandgap of partial oxidized arsenene is proportional to the oxygen content. Consequently, the partial oxidized arsenene with tunable direct bandgap has great potentials in the high efficient infra light emitter and photo-voltaic devices.
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

Protection 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

A 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

The 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

PIWI-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

Single 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

Chronic 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

Plasmacytoid 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

Bacteria 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

Soil 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

We 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

Which 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

Pectins 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

The 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

Photonic 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

Though 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

Once 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

Mitochondrial 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.
Role of the ESAT-6 secretion system in virulence of the emerging community-associated Staphylococcus aureus lineage ST398
Authors: Wang Yanan , Hu Mo , Liu Qian , Qin Juanxiu , Dai Yingxin , He Lei , Li Tianming , Zheng Bing , Zhou Fan , Yu Kaiwen , Fang Jingyuan , Liu Xiaoyun , Otto Michael , Li Min
Published: April 2016

Novel Staphylococcus aureus clones continue to emerge that cause infections in otherwise healthy people. One example is the sequence type (ST) 398 lineage, which we show here is increasing in importance as a significant cause of community-associated (CA) human infections in China. We have a profound lack of understanding about what determines the considerable virulence potential of such newly emerging clones. Information about the contribution to virulence of the more recently discovered ESAT-6 secretion system (ESS) has remained particularly scarce. The Chinese ST398 isolates exhibited significantly increased expression of ESS genes as compared to predominant hospital-associated clones, which we found is likely due to increased expression of the accessory gene regulator (Agr) system and control of ESS by Agr. Importantly, deletion of essB in ST398 resulted in significantly reduced resistance to neutrophil killing and decreased virulence in murine skin and blood infection models. Our results demonstrate a key function of ESS in promoting virulence and mechanisms of resistance to innate host defense in an important emerging CA-S. aureus lineage. They suggest that ESS has a so far underestimated role in promoting aggressive virulence and epidemiological success of S. aureus.
Tick receptor for outer surface protein A from Ixodes ricinus — the first intrinsically disordered protein involved in vector-microbe recognition
Authors: Urbanowicz Anna , Lewandowski Dominik , Szpotkowski Kamil , Figlerowicz Marek
Published: April 2016

The tick receptor for outer surface protein A (TROSPA) is the only identified factor involved in tick gut colonization by various Borrelia species. TROSPA is localized in the gut epithelium and can recognize and bind the outer surface bacterial protein OspA via an unknown mechanism. Based on earlier reports and our latest observations, we considered that TROSPA would be the first identified intrinsically disordered protein (IDP) involved in the interaction between a vector and a pathogenic microbe. To verify this hypothesis, we performed structural studies of a TROSPA mutant from Ixodes ricinus using both computational and experimental approaches. Irrespective of the method used, we observed that the secondary structure content of the TROSPA polypeptide chain is low. In addition, the collected SAXS data indicated that this protein is highly extended and exists in solution as a set of numerous conformers. These features are all commonly considered hallmarks of IDPs. Taking advantage of our SAXS data, we created structural models of TROSPA and proposed a putative mechanism for the TROSPA-OspA interaction. The disordered nature of TROSPA may explain the ability of a wide spectrum of Borrelia species to colonize the tick gut.
Subgenual cingulate cortical activity predicts the efficacy of electroconvulsive therapy
Authors: Argyelan M , Lencz T , Kaliora S , Sarpal D K , Weissman N , Kingsley P B , Malhotra A K , Petrides G
Published: April 2016

Electroconvulsive therapy (ECT) is the most effective treatment for depression, yet its mechanism of action is unknown. Our goal was to investigate the neurobiological underpinnings of ECT response using longitudinally collected resting-state functional magnetic resonance imaging (rs-fMRI) in 16 patients with treatment-resistant depression and 10 healthy controls. Patients received bifrontal ECT 3 times a week under general anesthesia. We acquired rs-fMRI at three time points: at baseline, after the 1st ECT administration and after the course of the ECT treatment; depression was assessed with the Hamilton Depression Rating Scale (HAM-D). The primary measure derived from rs-fMRI was fractional amplitude of low frequency fluctuation (fALFF), which provides an unbiased voxel-wise estimation of brain activity. We also conducted seed-based functional connectivity analysis based on our primary findings. We compared treatment-related changes in HAM-D scores with pre- and post-treatment fALFF and connectivity measures. Subcallosal cingulate cortex (SCC) demonstrated higher BOLD signal fluctuations (fALFF) at baseline in depressed patients, and SCC fALFF decreased over the course of treatment. The baseline level of fALFF of SCC predicted response to ECT. In addition, connectivity of SCC with bilateral hippocampus, bilateral temporal pole, and ventromedial prefrontal cortex was significantly reduced over the course of treatment. These results suggest that the antidepressant effect of ECT may be mediated by downregulation of SCC activity and connectivity. SCC function may serve as an important biomarker of target engagement in the development of novel therapies for depression that is resistant to treatment with standard medications.