bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational preludes to the latency transition in PAI-1 as determined by atomistic computer simulations and hydrogen/deuterium-exchange mass spectrometry
Authors: Petersen Michael , Madsen Jeppe B. , Jørgensen Thomas J. D. , Trelle Morten B. 
Published: July 2017

AbstractBoth function and dysfunction of serine protease inhibitors (serpins) involve massive conformational change in their tertiary structure but the dynamics facilitating these events remain poorly understood. We have studied the dynamic preludes to conformational change in the serpin plasminogen activator inhibitor 1 (PAI-1). We report the first multi-microsecond atomistic molecular dynamics simulations of PAI-1 and compare the data with experimental hydrogen/deuterium-exchange data (HDXMS). The simulations reveal notable conformational flexibility of helices D, E and F and major fluctuations are observed in the W86-loop which occasionally leads to progressive detachment of β-strand 2 A from β-strand 3 A. An interesting correlation between Cα-RMSD values from simulations and experimental HDXMS data is observed. Helices D, E and F are known to be important for the overall stability of active PAI-1 as ligand binding in this region can accelerate or decelerate the conformational inactivation. Plasticity in this region may thus be mechanistically linked to the conformational change, possibly through facilitation of further unfolding of the hydrophobic core, as previously reported. This study provides a promising example of how computer simulations can help tether out mechanisms of serpin function and dysfunction at a spatial and temporal resolution that is far beyond the reach of any experiment.
Morpho-functional characterization of the systemic venous pole of the reptile heart
Authors: Jensen Bjarke , Vesterskov Signe , Boukens Bastiaan J. , Nielsen Jan M. , Moorman Antoon F. M. , Christoffels Vincent M. , Wang Tobias 
Published: July 2017

AbstractMammals evolved from reptile-like ancestors, and while the mammalian heart is driven by a distinct sinus node, a sinus node is not apparent in reptiles. We characterized the myocardial systemic venous pole, the sinus venosus, in reptiles to identify the dominant pacemaker and to assess whether the sinus venosus remodels and adopts an atrium-like phenotype as observed in mammals. Anolis lizards had an extensive sinus venosus of myocardium expressing Tbx18. A small sub-population of cells encircling the sinuatrial junction expressed Isl1, Bmp2, Tbx3, and Hcn4, homologues of genes marking the mammalian sinus node. Electrical mapping showed that hearts of Anolis lizards and Python snakes were driven from the sinuatrial junction. The electrical impulse was delayed between the sinus venosus and the right atrium, allowing the sinus venosus to contract and aid right atrial filling. In proximity of the systemic veins, the Anolis sinus venosus expressed markers of the atrial phenotype Nkx2-5 and Gja5. In conclusion, the reptile heart is driven by a pacemaker region with an expression signature similar to that of the immature sinus node of mammals. Unlike mammals, reptiles maintain a sinuatrial delay of the impulse, allowing the partly atrialized sinus venosus to function as a chamber.
Identification of non-activated lymphocytes using three-dimensional refractive index tomography and machine learning
Authors: Yoon Jonghee , Jo YoungJu , Kim Min-hyeok , Kim Kyoohyun , Lee SangYun , Kang Suk-Jo , Park YongKeun 
Published: July 2017

AbstractIdentification of lymphocyte cell types are crucial for understanding their pathophysiological roles in human diseases. Current methods for discriminating lymphocyte cell types primarily rely on labelling techniques with magnetic beads or fluorescence agents, which take time and have costs for sample preparation and may also have a potential risk of altering cellular functions. Here, we present the identification of non-activated lymphocyte cell types at the single-cell level using refractive index (RI) tomography and machine learning. From the measurements of three-dimensional RI maps of individual lymphocytes, the morphological and biochemical properties of the cells are quantitatively retrieved. To construct cell type classification models, various statistical classification algorithms are compared, and the k-NN (k = 4) algorithm was selected. The algorithm combines multiple quantitative characteristics of the lymphocyte to construct the cell type classifiers. After optimizing the feature sets via cross-validation, the trained classifiers enable identification of three lymphocyte cell types (B, CD4+ T, and CD8+ T cells) with high sensitivity and specificity. The present method, which combines RI tomography and machine learning for the first time to our knowledge, could be a versatile tool for investigating the pathophysiological roles of lymphocytes in various diseases including cancers, autoimmune diseases, and virus infections.
In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease
Authors: Yoshino Ryunosuke , Yasuo Nobuaki , Hagiwara Yohsuke , Ishida Takashi , Inaoka Daniel Ken , Amano Yasushi , Tateishi Yukihiro , Ohno Kazuki , Namatame Ichiji , Niimi Tatsuya , Orita Masaya , Kita Kiyoshi , Akiyama Yutaka , Sekijima Masakazu 
Published: July 2017

AbstractChagas disease results from infection by Trypanosoma cruzi and is a neglected tropical disease (NTD). Although some treatment drugs are available, their use is associated with severe problems, including adverse effects and limited effectiveness during the chronic disease phase. To develop a novel anti-Chagas drug, we virtually screened 4.8 million small molecules against spermidine synthase (SpdSyn) as the target protein using our super computer “TSUBAME2.5” and conducted in vitro enzyme assays to determine the half-maximal inhibitory concentration values. We identified four hit compounds that inhibit T. cruzi SpdSyn (TcSpdSyn) by in silico and in vitro screening. We also determined the TcSpdSyn–hit compound complex structure using X-ray crystallography, which shows that the hit compound binds to the putrescine-binding site and interacts with Asp171 through a salt bridge.
OsFH15, a class I formin, interacts with microfilaments and microtubules to regulate grain size via affecting cell expansion in rice
Authors: Sun Tiantian , Li Shanwei , Ren Haiyun 
Published: July 2017

AbstractGrain size is an important agronomic trait determining rice yield and is mainly restricted by spikelet hull size. However, it remains largely unknown how the spikelet hull size is regulated. In this study, OsFH15, a class I formin protein in Oryza sativa, was found to be able to regulate the size of cells and spikelet hull. OsFH15-Cas9 and OsFH15-RNAi mutants had decreased grain size with reduced cell length, cell width and cell area of inner epidermal cells of the lemma compared with wild-type plants. By contrast, OsFH15-overexpressed plants had increased grain size with larger cells, as well as more abundant microtubules (MTs) and actin filaments (AFs) arrays. OsFH15 was mainly expressed in shoot apical meristem (SAM), spikelets, spikelet hulls and seeds in rice. In vitro biochemical experiments showed that OsFH15 can efficiently nucleate actin polymerization with or without profilin, can cap the barbed end of AFs, and can bind and bundle both AFs and MTs. OsFH15 can also crosslink AFs with MTs, and preferentially bind MTs to AFs. These results demonstrated that OsFH15 played an important role in grain-size control by affecting cell expansion through regulating AFs and MTs.
In-vivo loss of carbapenem resistance by extensively drug-resistant Klebsiella pneumoniae during treatment via porin expression modification
Authors: Bialek-Davenet Suzanne , Mayer Noémie , Vergalli Julia , Duprilot Marion , Brisse Sylvain , Pagès Jean-Marie , Nicolas-Chanoine Marie-Hélène 
Published: July 2017

AbstractKlebsiella pneumoniae, an Enterobacteriaceae that mostly causes hospital-acquired infections, belongs to the recently published WHO’s list of antibiotic-resistant pathogens that pose the greatest threat to human health. Indeed, K. pneumoniae is the enterobacterial species most concerned by both resistance to extended-spectrum cephalosporins, due to extended-spectrum β-lactamase (ESBL) production, and resistance to carbapenems, i.e. the β-lactams with the broadest activity. Carbapenem resistance is related not only to carbapenemase production, but also the production of ESBL or AmpC and the loss of general porins. Here, we characterized the mechanisms that deprived a urinary ESBL-producing, porin-deficient K. pneumoniae isolate, isolated 13 days after the end of a 40-day course of imipenem treatment, of its carbapenem resistance. These mechanisms were observed in two in-vivo derivatives of this isolate and consisted of mutations in genes encoding molecules that participate in the downregulation of the synthesis of PhoE, a porin specialized in phosphate transport. We obtained three new derivatives from one of the two original derivatives, following in-vitro antibiotic pressure, in which the carbapenem resistance was restored because of mutations in genes encoding molecules that participate in the upregulation of PhoE synthesis. Thus, we uncovered novel mechanisms of carbapenem resistance/susceptibility switching in K. pneumoniae.
Activation of mitophagy leads to decline in Mfn2 and loss of mitochondrial mass in Fuchs endothelial corneal dystrophy
Authors: Benischke Anne-Sophie , Vasanth Shivakumar , Miyai Takashi , Katikireddy Kishore Reddy , White Tomas , Chen Yuming , Halilovic Adna , Price Marianne , Price Francis , Liton Paloma B. , Jurkunas Ula V. 
Published: July 2017

AbstractHuman corneal endothelial cells (HCEnCs) are terminally differentiated cells that have limited regenerative potential. The large numbers of mitochondria in HCEnCs are critical for pump and barrier function required for corneal hydration and transparency. Fuchs Endothelial Corneal Dystrophy (FECD) is a highly prevalent late-onset oxidative stress disorder characterized by progressive loss of HCEnCs. We previously reported increased mitochondrial fragmentation and reduced ATP and mtDNA copy number in FECD. Herein, carbonyl cyanide m-chlorophenyl hydrazone (CCCP)-induced mitochondrial depolarization decreased mitochondrial mass and Mfn2 levels, which were rescued with mitophagy blocker, bafilomycin, in FECD. Moreover, electron transport chain complex (I, V) decrease in FECD indicated deficient mitochondrial bioenergetics. Transmission electron microscopy of FECD tissues displayed an increased number of autophagic vacuoles containing degenerated and swollen mitochondria with cristolysis. An elevation of LC3-II and LAMP1 and downregulation of Mfn2 in mitochondrial fractions suggested that loss of fusion capacity targets fragmented mitochondria to the pre-autophagic pool and upregulates mitophagy. CCCP-induced mitochondrial fragmentation leads to Mfn2 and LC3 co-localization without activation of proteosome, suggesting a novel Mfn2 degradation pathway via mitophagy. These data indicate constitutive activation of mitophagy results in reduction of mitochondrial mass and abrogates cellular bioenergetics during degeneration of post-mitotic cells of ocular tissue.
Predicting trend of early childhood caries in mainland China: a combined meta-analytic and mathematical modelling approach based on epidemiological surveys
Authors: Zhang Xiaonan , Zhang Lei , Zhang Yonghong , Liao Zhaoying , Song Jinlin 
Published: July 2017

AbstractEarly childhood caries (ECC) is the most common chronic disease in young children. A reliable predictive model for ECC prevalence is needed in China as a decision supportive tool for planning health resources. In this study, we first established the autoregressive integrated moving average (ARIMA) model and grey predictive model (GM) based on the estimated national prevalence of ECC with meta-analysis from the published articles. The pooled data from 1988 to 2010 were used to establish the model, while the data from 2011 to 2013 were used to validate the models. The fitting and prediction accuracy of the two models were evaluated by mean absolute error (MAE) and mean absolute percentage error (MAPE). Then, we forecasted the annual prevalence from 2014 to 2018, which was 55.8%, 53.5%, 54.0%, 52.9%, 51.2% by ARIMA model and 52.8%, 52.0%, 51.2%, 50.4%, 49.6% by GM. The declining trend in ECC prevalence may be attributed to the socioeconomic developments and improved public health service in China. In conclusion, both ARIMA and GM models can be well applied to forecast and analyze the trend of ECC; the fitting and testing errors generated by the ARIMA model were lower than those obtained from GM.
Comparative Analysis of Four Buckwheat Species Based on Morphology and Complete Chloroplast Genome Sequences
Authors: Wang Cheng-Long , Ding Meng-Qi , Zou Chen-Yan , Zhu Xue-Mei , Tang Yu , Zhou Mei-Liang , Shao Ji-Rong 
Published: July 2017

AbstractBuckwheat is a nutritional and economically crop belonging to Polygonaceae, Fagopyrum. To better understand the mutation patterns and evolution trend in the chloroplast (cp) genome of buckwheat, and found sufficient number of variable regions to explore the phylogenetic relationships of this genus, two complete cp genomes of buckwheat including Fagopyrum dibotrys (F. dibotrys) and Fagopyrum luojishanense (F. luojishanense) were sequenced, and other two Fagopyrum cp genomes were used for comparative analysis. After morphological analysis, the main difference among these buckwheat were height, leaf shape, seeds and flower type. F. luojishanense was distinguishable from the cultivated species easily. Although the F. dibotrys and two cultivated species has some similarity, they different in habit and component contents. The cp genome of F. dibotrys was 159,320 bp while the F. luojishanense was 159,265 bp. 48 and 61 SSRs were found in F. dibotrys and F. luojishanense respectively. Meanwhile, 10 highly variable regions among these buckwheat species were located precisely. The phylogenetic relationships among four Fagopyrum species based on complete cp genomes was showed. The results suggested that F. dibotrys is more closely related to Fagopyrum tataricum. These data provided valuable genetic information for Fagopyrum species identification, taxonomy, phylogenetic study and molecular breeding.
Molecular Characterization of Viral Responsive Protein 15 and Its Possible Role in Nuclear Export of Virus in Black Tiger Shrimp Penaeus monodon
Authors: Jaturontakul Krisadaporn , Jatuyosporn Thapanan , Laohawutthichai Pasunee , Kim Sun-Yong , Mori Tomoyuki , Supungul Premruethai , Hakoshima Toshio , Tassanakajon Anchalee , Krusong Kuakarun 
Published: July 2017

AbstractA viral responsive protein 15 from Penaeus monodon (PmVRP15) has been reported to be important for white spot syndrome virus (WSSV) infection in vivo. This work aims to characterize PmVRP15 and investigate its possible role in nuclear import/export of the virus. Circular dichroism spectra showed that PmVRP15 contains high helical contents (82%). Analytical ultracentrifugation suggested that PmVRP15 could possibly form oligomers in solution. A subcellular fractionation study showed that PmVRP15 was found in heavy and light membrane fractions, indicating that PmVRP15 may be associated with endoplasmic reticulum. Double-stranded RNAi-mediated knockdown of PmVRP15 gene expression in vitro showed no effect on WSSV copy number in whole hemocyte cells. However, PmVRP15 silencing resulted in an accumulation of WSSV DNA in the nucleus of PmVRP15-silenced hemocytes. Immunofluorescence confocal microscopy showed that PmVRP15 knockdown hemocytes had a much lower level of VP28 (WSSV envelope protein), in comparison to that in the control. It is likely that PmVRP15 may play a role in viral nuclear egress.
Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
Authors: Tessler Michael , Neumann Johannes S. , Afshinnekoo Ebrahim , Pineda Michael , Hersch Rebecca , Velho Luiz Felipe M. , Segovia Bianca T. , Lansac-Toha Fabio A. , Lemke Michael , DeSalle Rob , Mason Christopher E. , Brugler Mercer R. 
Published: July 2017

AbstractModern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques – amplicon and shotgun – on water samples across four of Brazil’s major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles the sampling size in similar environmental studies, and novelly integrates environmental data (e.g., pH, temperature, nutrients) from each site, revealing divergent correlations depending on which data are used. While myriad variants on NGS techniques and bioinformatic pipelines are available, our results point to core differences that have not been highlighted in any studies to date. Given the low number of taxa identified when coupling shotgun data with clade-based taxonomic algorithms, previous studies that quantified biodiversity using such bioinformatic tools should be viewed cautiously or re-analyzed. Nonetheless, shotgun has complementary advantages that should be weighed when designing projects.
Glycoengineering of EphA4 Fc leads to a unique, long-acting and broad spectrum, Eph receptor therapeutic antagonist
Authors: Pegg Cassandra L. , Cooper Leanne T. , Zhao Jing , Gerometta Michael , Smith Fiona M. , Yeh Michael , Bartlett Perry F. , Gorman Jeffrey J. , Boyd Andrew W. 
Published: July 2017

AbstractEph receptors have emerged as targets for therapy in both neoplastic and non-neoplastic disease, however, particularly in non-neoplastic diseases, redundancy of function limits the effectiveness of targeting individual Eph proteins. We have shown previously that a soluble fusion protein, where the EphA4 ectodomain was fused to IgG Fc (EphA4 Fc), was an effective therapy in acute injuries and demonstrated that EphA4 Fc was a broad spectrum Eph/ephrin antagonist. However, a very short in vivo half-life effectively limited its therapeutic development. We report a unique glycoengineering approach to enhance the half-life of EphA4 Fc. Progressive deletion of three demonstrated N-linked sites in EphA4 progressively increased in vivo half-life such that the triple mutant protein showed dramatically improved pharmacokinetic characteristics. Importantly, protein stability, affinity for ephrin ligands and antagonism of cell expressed EphA4 was fully preserved, enabling it to be developed as a broad spectrum Eph/ephrin antagonist for use in both acute and chronic diseases.
Fractal scaling of particle-size distribution and associations with soil properties of Mongolian pine plantations in the Mu Us Desert, China
Authors: Deng Jifeng , Li Jinghao , Deng Ge , Zhu Hangyong , Zhang Ruohan 
Published: July 2017

AbstractMongolian pine plantations (MPPs) composed of Pinus sylvestris var. mongolica (P. sylvestris) are used for desertification control and restoration of degraded land in arid and semi-arid regions. We studied soil changes associated with P. sylvestris by comparing top (0–20 cm) and sub-top (20–40 cm) soil properties across 8 stand density gradients of MPPs ranging from 900 ± 5–2700 ± 50 trees ha–1. The study was conducted in the uncovered Sandy Land in the southern Mu Us Desert, China. The relationships between the volume fractal dimensions (D) of soil particle size distribution and soil physicochemical properties were evaluated. D was determined using a laser diffraction technique and soil properties were measured. In the top layer, P. sylvestris significantly positively affected soil physicochemical properties except for bulk density and total nitrogen. These effects were not observed in the sub-top soil layer. D values ranged from 1.52 ± 0.29–2.08 ± 0.06 and were significantly correlated with stand density. Significant correlations were observed between D and soil properties (except total nitrogen) in the top soil layer. Given these results, we concluded that D is a sensitive and useful index because it quantifies changes in soil properties that additionally implies desertification in the studied area.
Easily Regenerated Readily Deployable Absorbent for Heavy Metal Removal from Contaminated Water
Authors: Alagappan Perry N. , Heimann Jessica , Morrow Lauren , Andreoli Enrico , Barron Andrew R. 
Published: July 2017

AbstractAlthough clean and abundant water is the keystone of thriving communities, increasing demand and volatile climate patterns are depleting rivers and aquifers. Moreover, the quality of such water sources is threatened by noxious contaminants, of which heavy metals represents an area of growing concern. Recently, graphene oxide (GO) has been suggested as an adsorbent; however, a support is desirable to ensure a high surface area and an immobile phase. Herein, we described the preparation and characterization of a supported-epoxidized carbon nanotube (SENT) via the growth of multi walled carbon nanotubes (MWNTs) onto a quartz substrate. Subsequent epoxidation provides sufficient functionality to enable adsorbent of heavy metals (Cd2+, Co2+, Cu2+, Hg2+, Ni2+, and Pb2+) from aqueous solution with initial concentrations (60–6000 ppm) chosen to simulate high industrial wastewater contamination. The SENT adsorption efficiency is >99.4% for all metals and the saturation concentration is significantly greater than observed for either GO or acid treated MWNTs. The SENT adsorbent may be readily regenerated under mild conditions using a globally available household chemical, vinegar. 1 g of SENT has the potential to treat 83,000 L of contaminated water down to WHO limits which would be sufficient for 11,000 people.
Small fire refugia in the grassy matrix and the persistence of Afrotemperate forest in the Drakensberg mountains
Authors: Adie Hylton , Kotze D. Johan , Lawes Michael J. 
Published: July 2017

AbstractAfrotemperate forests situated in the Drakensberg mountains of South Africa are characteristically small (1–10 s ha) and widely dispersed in a vast fire-prone grassland. Compared with lowland forests, they are typically species poor with low levels of endemism and species turnover, patterns that are to date unexplained. Here we show that the richness, composition and functional traits of tree species distributed on extremely small (10–100 s m2) rocky fire-refugia situated in grassland are indistinguishable from that in forest. Afrotemperate forest tree species in the Drakensberg are widely dispersed and conform to the habitat generalist strategy. Most forest trees are bird dispersed; wind dispersal is rare and is associated only with species that resprout in response to fire. We present the ‘matrix refuge hypothesis’, which proposes that fire and extreme conditions associated with exposed rocky outcrops have filtered the Afrotemperate forest tree composition resulting in convergence in functional traits essential for trees to arrive, establish and persist on fire refugia in the grassland matrix. Most Afrotemperate forest tree diversity in the Drakensberg thus resides in the matrix where it may function as a recolonisation reservoir during climatic bottlenecks.