bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Assay for Screening Inhibitors Targeting HIV Integrase LEDGF/p75 Interaction Based on Ni2+ Coated Magnetic Agarose Beads
Authors: Dawei Zhang , Hongqiu He , Mengmeng Liu , Zhixia Meng , Shunxing Guo 
Published: September 2016

AbstractHIV-1 integrase (IN) plays an essential role in viral replication and thus serves as an important target for chemotherapeutic intervention against HIV-1 infection. However, the current three clinical IN inhibitors, raltegravir, elvitegravir and dolutegravir share the same inhibitory mechanism, resulting in a common clinical resistance profile which have emerged in infected patients receiving treatment. Therefore, it is important to develop small molecule inhibitors that impair IN function with distinct mechanisms of action. In this work, a magnetic-beads based biochemical assay targeting the protein-protein interaction (PPI) between HIV IN and the cellular cofactor LEDGF/p75 was developed for identification of HIV-1 IN inhibitors. Furthermore, a library containing 1000 US. Food and Drug Administration (FDA)-approved drugs currently used for human medication was screened to identify inhibitors targeting the PPI. The assay was proved to be quite robust and with the novel assay we successfully identified dexlansoprazole (IC50 of 4.8 μM), a FDA-approved proton pump inhibitor, as a potential inhibitor for the PPI between IN and LEDGF/p75, which bound to the LEDGF/p75 partner with a kinetic dissociation (Kd) constant of 330 nM ± 2.6 nM.
Quantitative and combinatory determination of in situ phosphorylation of tau and its FTDP-17 mutants
Authors: Kimura Taeko , Hosokawa Tomohisa , Taoka Masato , Tsutsumi Koji , Ando Kanae , Ishiguro Koichi , Hosokawa Masato , Hasegawa Masato , Hisanaga Shin-ichi 
Published: September 2016

AbstractTau is hyperphosphorylated in the brains of patients with tauopathies, such as Alzheimer’s disease and frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17). However, neither the mechanism of hyperphosphorylation nor its contribution to pathogenesis is known. We applied Phos-tag SDS-PAGE, a phosphoaffinity electrophoresis, to the analysis of tau phosphorylation in vitro by Cdk5, in cultured cells and in mouse brain. Here, we found that Cdk5-p25 phosphorylated tau in vitro at Ser404, Ser235, Thr205 and Ser202 in this order. In contrast in cultured cells, Ser404 was preferentially phosphorylated by Cdk5-p35, whereas Thr205 was not phosphorylated. Ser202 and Ser235 were phosphorylated by endogenous kinases. Tau exhibited ~12 phosphorylation isotypes in COS-7 cells with different combinations of phosphorylation at Thr181, Ser202, Thr231, Ser235 and Ser404. These phosphorylation sites were similar to tau phosphorylated in mouse brains. FTDP-17 tau with a mutation in the C-terminal region had different banding patterns, indicating a different phosphorylation pattern. In particular, it was clear that the R406W mutation causes loss of Ser404 phosphorylation. These results demonstrate the usefulness of the Phos-tag technique in the quantitative analysis of site-specific in vivo phosphorylation of tau and provide detailed information on in situ combinatory phosphorylation of tau.
iRSpot-DACC: a computational predictor for recombination hot/cold spots identification based on dinucleotide-based auto-cross covariance
Authors: Liu Bingquan , Liu Yumeng , Jin Xiaopeng , Wang Xiaolong , Liu Bin 
Published: September 2016

AbstractMeiotic recombination presents an uneven distribution across the genome. Genomic regions that exhibit at relatively high frequencies of recombination are called hotspots, whereas those with relatively low frequencies of recombination are called coldspots. Therefore, hotspots and coldspots would provide useful information for the study of the mechanism of recombination. In this study, we proposed a computational predictor called iRSpot-DACC to predict hot/cold spots across the yeast genome. It combined Support Vector Machines (SVMs) and a feature called dinucleotide-based auto-cross covariance (DACC), which is able to incorporate the global sequence-order information and fifteen local DNA properties into the predictor. Combined with Principal Component Analysis (PCA), its performance was further improved. Experimental results on a benchmark dataset showed that iRSpot-DACC can achieve an accuracy of 82.7%, outperforming some highly related methods.
Lack of adrenomedullin in mouse endothelial cells results in defective angiogenesis, enhanced vascular permeability, less metastasis, and more brain damage
Authors: Ochoa-Callejero Laura , Pozo-Rodrigálvarez Andrea , Martínez-Murillo Ricardo , Martínez Alfredo 
Published: September 2016

AbstractAdrenomedullin (AM) is a vasodilating peptide involved in the regulation of circulatory homeostasis and in the pathophysiology of certain cardiovascular diseases. AM plays critical roles in blood vessels, including regulation of vascular stability and permeability. To elucidate the autocrine/paracrine function of AM in endothelial cells (EC) in vivo, a conditional knockout of AM in EC (AMEC-KO) was used. The amount of vascularization of the matrigel implants was lower in AMEC-KO mice indicating a defective angiogenesis. Moreover, ablation of AM in EC revealed increased vascular permeability in comparison with wild type (WT) littermates. In addition, AMEC-KO lungs exhibited significantly less tumor growth than littermate WT mice using a syngeneic model of metastasis. Furthermore, following middle cerebral artery permanent occlusion, there was a significant infarct size decrease in animals lacking endothelial AM when compared to their WT counterparts. AM is an important regulator of EC function, angiogenesis, tumorigenesis, and brain response to ischemia. Studies of AM should bring novel approaches to the treatment of vascular diseases.
SCOP/PHLPP1β in the basolateral amygdala regulates circadian expression of mouse anxiety-like behavior
Authors: Nakano Jun J. , Shimizu Kimiko , Shimba Shigeki , Fukada Yoshitaka 
Published: September 2016

AbstractWhile disruption of the circadian clock triggers a spectrum of affective abnormalities, how the clock regulates mammalian emotionality remains unclear. Here, we characterized the time-of-day-dependent regulation of mouse anxiety-like behaviors. We show that anxiety-like behaviors are expressed in a circadian manner in mice and demonstrate that the clock machineries in the dorsal telencephalon (dTel) are required for the time-of-day-dependent regulation of anxiety-like behaviors. We identify suprachiasmatic nucleus circadian oscillatory protein (SCOP/PHLPP1β) as an essential intracellular signaling molecule mediating this temporal regulation downstream of the clock. Using viral-mediated, basolateral amygdala (BLA)-specific knockout of Scop, we demonstrate that deletion of SCOP in the BLA exerts anxiolytic effects on the elevated plus maze at early subjective night, thereby blunting the circadian variation in the anxiety-like behavior. We conclude that the circadian expression of SCOP in the BLA plays a key role in generating circadian rhythmicity in the anxiety-like behavior. Our results demonstrate SCOP as a regulator of anxiety-like behaviors and reveal its key roles in the anxiogenic functions of the BLA.
TSPO ligands stimulate ZnPPIX transport and ROS accumulation leading to the inhibition of P. falciparum growth in human blood
Authors: Marginedas-Freixa I. , Hattab C. , Bouyer G. , Halle F. , Chene A. , Lefevre S. D. , Cambot M. , Cueff A. , Schmitt M. , Gamain B. , Lacapere J. J. , Egee S. , Bihel F. , Le Van Kim C. , Ostuni M. A. 
Published: September 2016

AbstractAfter invading red blood cells (RBCs), Plasmodium falciparum (Pf) can export its own proteins to the host membrane and activate endogenous channels that are present in the membrane of RBCs. This transport pathway involves the Voltage Dependent Anion Channel (VDAC). Moreover, ligands of the VDAC partner TranSlocator PrOtein (TSPO) were demonstrated to inhibit the growth of the parasite. We studied the expression of TSPO and VDAC isoforms in late erythroid precursors, examined the presence of these proteins in membranes of non-infected and infected human RBCs, and evaluated the efficiency of TSPO ligands in inhibiting plasmodium growth, transporting the haem analogue Zn-protoporphyrin-IX (ZnPPIX) and enhancing the accumulation of reactive oxygen species (ROS). TSPO and VDAC isoforms are differentially expressed on erythroid cells in late differentiation states. TSPO2 and VDAC are present in the membranes of mature RBCs in a unique protein complex that changes the affinity of TSPO ligands after Pf infection. TSPO ligands dose-dependently inhibited parasite growth, and this inhibition was correlated to ZnPPIX uptake and ROS accumulation in the infected RBCs. Our results demonstrate that TSPO ligands can induce Pf death by increasing the uptake of porphyrins through a TSPO2–VDAC complex, which leads to an accumulation of ROS.
Automatic Bayesian single molecule identification for localization microscopy
Authors: Tang Yunqing , Hendriks Johnny , Gensch Thomas , Dai Luru , Li Junbai 
Published: September 2016

AbstractSingle molecule localization microscopy (SMLM) is on its way to become a mainstream imaging technique in the life sciences. However, analysis of SMLM data is biased by user provided subjective parameters required by the analysis software. To remove this human bias we introduce here the Auto-Bayes method that executes the analysis of SMLM data automatically. We demonstrate the success of the method using the photoelectron count of an emitter as selection characteristic. Moreover, the principle can be used for any characteristic that is bimodally distributed with respect to false and true emitters. The method also allows generation of an emitter reliability map for estimating quality of SMLM-based structures. The potential of the Auto-Bayes method is shown by the fact that our first basic implementation was able to outperform all software packages that were compared in the ISBI online challenge in 2015, with respect to molecule detection (Jaccard index).
Olive and grape seed extract prevents post-traumatic osteoarthritis damages and exhibits in vitro anti IL-1β activities before and after oral consumption
Authors: Mével Elsa , Merceron Christophe , Vinatier Claire , Krisa Stéphanie , Richard Tristan , Masson Martial , Lesoeur Julie , Hivernaud Vincent , Gauthier Olivier , Abadie Jérôme , Nourissat Geoffroy , Houard Xavier , Wittrant Yohann , Urban Nelly , Beck Laurent , Guicheux Jérôme 
Published: September 2016

AbstractPolyphenols exert a large range of beneficial effects in the prevention of age-related diseases. We sought to determine whether an extract of olive and grape seed standardized according to hydroxytyrosol (HT) and procyanidins (PCy) content, exerts preventive anti-osteoathritic effects. To this aim, we evaluated whether the HT/PCy mix could (i) have in vitro anti-inflammatory and chondroprotective actions, (ii) exert anti-osteoarthritis effects in two post-traumatic animal models and (iii) retain its bioactivity after oral administration. Anti-inflammatory and chondroprotective actions of HT/PCy were tested on primary cultured rabbit chondrocytes stimulated by interleukin-1 beta (IL-1β). The results showed that HT/PCy exerts anti-inflammatory and chondroprotective actions in vitro. The preventive effect of HT/PCy association was assessed in two animal models of post-traumatic OA in mice and rabbits. Diet supplementation with HT/PCy significantly decreased the severity of post-traumatic osteoarthritis in two complementary mice and rabbit models. The bioavailability and bioactivity was evaluated following gavage with HT/PCy in rabbits. Regular metabolites from HT/PCy extract were found in sera from rabbits following oral intake. Finally, sera from rabbits force-fed with HT/PCy conserved anti-IL-1β effect, suggesting the bioactivity of this extract. To conclude, HT/PCy extract may be of clinical significance for the preventive treatment of osteoarthritis.
Highly efficient removal of lead and cadmium during wastewater irrigation using a polyethylenimine-grafted gelatin sponge
Authors: Li Bingbing , Zhou Feng , Huang Kai , Wang Yipei , Mei Surong , Zhou Yikai , Jing Tao 
Published: September 2016

AbstractWastewater irrigation is a very important resource for heavy metal pollution in soil and then accumulation in vegetable crops. In this study, a polyethylenimine (PEI)-grafted gelatin sponge was prepared to effectively adsorb heavy metals during wastewater irrigation. Based on the strong water adsorption ability, wastewater remained in the PEI-grafted gelatin sponge for a sufficient time for the heavy metals to interact with the sorbents. The binding capacities of Pb(II) ions and Cd(II) ions on the PEI-grafted gelatin sponge were 66 mg g−1 and 65 mg g−1, which were much more than those on the gelatin sponge (9.75 mg g−1 and 9.35 mg g−1). Subsequently, the PEI-grafted gelatin sponge was spread on the surface of soil planted with garlic and then sprayed with synthetic wastewater. The concentrations of cadmium and lead in the garlic leaves were 1.59 mg kg−1 and 5.69 mg kg−1, respectively, which were much lower than those (15.78 mg kg−1 and 27.98 mg kg−1) without the gelatin sponge and the removal efficiencies were 89.9% and 79.7%. The PEI-grafting gelatin sponge could effectively remove heavy metals during wastewater irrigation, which improved the soil environment and reduced human exposure to heavy metals.
The N-terminal domain plays a crucial role in the structure of a full-length human mitochondrial Lon protease
Authors: Kereïche Sami , Kováčik Lubomír , Bednár Jan , Pevala Vladimír , Kunová Nina , Ondrovičová Gabriela , Bauer Jacob , Ambro Ľuboš , Bellová Jana , Kutejová Eva , Raška Ivan 
Published: September 2016

AbstractLon is an essential, multitasking AAA+protease regulating many cellular processes in species across all kingdoms of life. Altered expression levels of the human mitochondrial Lon protease (hLon) are linked to serious diseases including myopathies, paraplegia, and cancer. Here, we present the first 3D structure of full-lengthhLon using cryo-electron microscopy.hLon has a unique three-dimensional structure, in which the proteolytic and ATP-binding domains (AP-domain) form a hexameric chamber, while the N-terminal domain is arranged as a trimer of dimers. These two domains are linked by a narrow trimeric channel composed likely of coiled-coil helices. In the presence of AMP-PNP, the AP-domain has a closed-ring conformation and its N-terminal entry gate appears closed, but in ADP binding, it switches to a lock-washer conformation and its N-terminal gate opens, which is accompanied by a rearrangement of the N-terminal domain. We have also found that both the enzymatic activities and the 3D structure of ahLon mutant lacking the first 156 amino acids are severely disturbed, showing thathLon’s N-terminal domains are crucial for the overall structure of thehLon, maintaining a conformation allowing its proper functioning.
Full-length model of the human galectin-4 and insights into dynamics of inter-domain communication
Authors: Rustiguel Joane K. , Soares Ricardo O. S. , Meisburger Steve P. , Davis Katherine M. , Malzbender Kristina L. , Ando Nozomi , Dias-Baruffi Marcelo , Nonato Maria Cristina 
Published: September 2016

AbstractGalectins are proteins involved in diverse cellular contexts due to their capacity to decipher and respond to the information encoded by β-galactoside sugars. In particular, human galectin-4, normally expressed in the healthy gastrointestinal tract, displays differential expression in cancerous tissues and is considered a potential drug target for liver and lung cancer. Galectin-4 is a tandem-repeat galectin characterized by two carbohydrate recognition domains connected by a linker-peptide. Despite their relevance to cell function and pathogenesis, structural characterization of full-length tandem-repeat galectins has remained elusive. Here, we investigate galectin-4 using X-ray crystallography, small- and wide-angle X-ray scattering, molecular modelling, molecular dynamics simulations and differential scanning fluorimetry assays and describe for the first time a structural model for human galectin-4. Our results provide insight into the structural role of the linker-peptide and shed light on the dynamic characteristics of the mechanism of carbohydrate recognition among tandem-repeat galectins.
In Situ Anabolic Activity of Periodontal Pathogens Porphyromonas gingivalis and Filifactor alocis in Chronic Periodontitis
Authors: Spooner Ralee , Weigel Kris M. , Harrison Peter L. , Lee KyuLim , Cangelosi Gerard A. , Yilmaz Özlem 
Published: September 2016

AbstractPorphyromonas gingivalis and Filifactor alocis are fastidious anaerobic bacteria strongly associated with chronic forms of periodontitis. Our understanding of the growth activities of these microorganisms in situ is very limited. Previous studies have shown that copy numbers of ribosomal-RNA precursor (pre-rRNA) of specific pathogen species relative to genomic-DNA (gDNA) of the same species (P:G ratios) are greater in actively growing bacterial cells than in resting cells. The method, so-called steady-state pre-rRNA-analysis, represents a novel culture-independent approach to study bacteria. This study employed this technique to examine the in situ growth activities of oral bacteria in periodontitis before and after non-surgical periodontal therapy. Sub-gingival paper-point samples were taken at initial and re-evaluation appointments. Pre-rRNA and gDNA levels of P. gingivalis and F. alocis were quantified and compared using reverse-transcriptase qPCR. The results indicate significantly reduced growth activity of P. gingivalis, but not F. alocis, after therapy. The P:G ratios of P. gingivalis and F. alocis were compared and a low-strength, but statistically significant inter-species correlation was detected. Our study demonstrates that steady-state pre-rRNA-analysis can be a valuable culture-independent approach to studying opportunistic bacteria in periodontitis.
Size-Exclusion Chromatography-based isolation minimally alters Extracellular Vesicles’ characteristics compared to precipitating agents
Authors: Gámez-Valero Ana , Monguió-Tortajada Marta , Carreras-Planella Laura , Franquesa Marcel·la , Beyer Katrin , Borràs Francesc E. 
Published: September 2016

AbstractExtracellular vesicles (EVs) have become an attractive field among the scientific community. Yet, a major challenge is to define a consensus method for EVs isolation. Ultracentrifugation has been the most widely used methodology but rapid methods, including Size Exclusion Chromatography (SEC) and/or precipitating agents such as Polyethylene glycol (PEG) or PRotein Organic Solvent PRecipitation (PROSPR) have emerged. To evaluate the impact of these different methods on the resulting EV preparations, plasma EVs were isolated using SEC, PEG and PROSPR and their total protein content, NTA and Cryo-electron microscopy profiles and EV-markers were compared. Also, their effect on recipient cells was tested. Low protein content and Cryo-EM analysis showed that SEC removed most of the overabundant soluble plasma proteins, which were not removed using PEG and partially by PROSPR. Moreover, only SEC allowed the detection of the EV-markers CD9, CD63 and CD81, LGALS3BP and CD5L, suggesting a putative interference of the precipitating agents in the structure/composition of the EVs. Furthermore, PEG and PROSPR-based EV isolation resulted in reduced cell viability in vitro. These results stress that appropriate EV-isolation method should be considered depending on the forthcoming application of the purified EVs.
Thermal stress depletes energy reserves in Drosophila
Authors: Klepsatel Peter , Gáliková Martina , Xu Yanjun , Kühnlein Ronald P. 
Published: September 2016

AbstractUnderstanding how environmental temperature affects metabolic and physiological functions is of crucial importance to assess the impacts of climate change on organisms. Here, we used different laboratory strains and a wild-caught population of the fruit flyDrosophila melanogasterto examine the effect of temperature on the body energy reserves of an ectothermic organism. We found that permanent ambient temperature elevation or transient thermal stress causes significant depletion of body fat stores. Surprisingly, transient thermal stress induces a lasting “memory effect” on body fat storage, which also reduces survivorship of the flies upon food deprivation later after stress exposure. Functional analyses revealed that an intact heat-shock response is essential to protect flies from temperature-dependent body fat decline. Moreover, we found that the temperature-dependent body fat reduction is caused at least in part by apoptosis of fat body cells, which might irreversibly compromise the fat storage capacity of the flies. Altogether, our results provide evidence that thermal stress has a significant negative impact on organismal energy reserves, which in turn might affect individual fitness.
RETRACTED ARTICLE: Silencing of Histone Deacetylase 9 Expression in Podocytes Attenuates Kidney Injury in Diabetic Nephropathy
Authors: Liu Feng , Zong Ming , Wen Xiaofei , Li Xuezhu , Wang Jun , Wang Yi , Jiang Wei , Li Xiaojun , Guo Zhongliang , Qi Hualin 
Published: September 2016

AbstractPodocyte dysfunction is important in the onset and development of diabetic nephropathy (DN). Histone deacetylases (HDACs) have been recently proved to play critical roles in the pathogenesis of DN. As one subtype of the class IIa HDACs, HDAC9 is capable to repress/de-repress their target genes in tumor, inflammation, atherosclerosis and metabolic diseases. In the present study, we investigate whether HDAC9 is involved in the pathophysiologic process of DN, especially the podocyte injury. Firstly, we explored the expression patterns and localization of HDAC9 and found that HDAC9 expression was significantly up-regulated in high glucose (HG)-treated mouse podocytes, as well as kidney tissues from diabetic db/db mice and patients with DN. Secondly, knockdown of HDAC9 in mouse podocytes significantly suppressed HG-induced reactive oxygen species (ROS) generation, cell apoptosis and inflammation through JAK2/STAT3 pathway and reduced the podocytes injury by decreasing the expression levels of Nephrin and Podocin. Moreover, in diabetic db/db mice, silencing of HDAC9 attenuated the glomerulosclerosis, inflammatory cytokine release, podocyte apoptosis and renal injury. Collectively, these data indicate that HDAC9 may be involved in the process of DN, especially podocyte injury. Our study suggest that inhibition of HDAC9 may have a therapeutic potential in DN treatment.
Suture pattern formation in ammonites and the unknown rear mantle structure
Authors: Inoue Shinya , Kondo Shigeru 
Published: September 2016

AbstractAmmonite shells have complex patterns of suture lines that vary across species. The lines are formed at the intersection of the outer shell wall and the septa. The wavy septa can form if the rear mantle of the ammonite, which functions as the template, has a complex shape. Previous hypotheses assumed that the rear mantle is like a flexible membrane that can be folded by some physical force. The elucidation of the mechanism of septa formation requires that the detailed shape of the septa should be known. We developed a new protocol of X-ray micro-computed tomography (CT) and obtained high-resolution three-dimensional (3D) images of the septa of the Upper Cretaceous ammoniteDamesitescf.damesi. The obtained image suggested that the wavy and branched structures of the rear mantle grew autonomously. We found that some extant sea slugs have branched structures and showed similar shape and growth sequence as those in fossils, suggesting that the mantle of molluscs basically has the potential to form branched projections. Based on the characteristics of the obtained 3D structure, we explain how ammonites might have formed the complex suture patterns.