bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating SANS and fluid-invasion methods to characterize pore structure of typical American shale oil reservoirs
Authors: Zhao Jianhua , Jin Zhijun , Hu Qinhong , Jin Zhenkui , Barber Troy. J. , Zhang Yuxiang , Bleuel Markus 
Published: November 2017

AbstractAn integration of small-angle neutron scattering (SANS), low-pressure N2 physisorption (LPNP), and mercury injection capillary pressure (MICP) methods was employed to study the pore structure of four oil shale samples from leading Niobrara, Wolfcamp, Bakken, and Utica Formations in USA. Porosity values obtained from SANS are higher than those from two fluid-invasion methods, due to the ability of neutrons to probe pore spaces inaccessible to N2 and mercury. However, SANS and LPNP methods exhibit a similar pore-size distribution, and both methods (in measuring total pore volume) show different results of porosity and pore-size distribution obtained from the MICP method (quantifying pore throats). Multi-scale (five pore-diameter intervals) inaccessible porosity to N2 was determined using SANS and LPNP data. Overall, a large value of inaccessible porosity occurs at pore diameters <10 nm, which we attribute to low connectivity of organic matter-hosted and clay-associated pores in these shales. While each method probes a unique aspect of complex pore structure of shale, the discrepancy between pore structure results from different methods is explained with respect to their difference in measurable ranges of pore diameter, pore space, pore type, sample size and associated pore connectivity, as well as theoretical base and interpretation.
Effect of soy on bone turn-over markers in men with type 2 diabetes and hypogonadism – a randomised controlled study
Authors: Sathyapalan T. , Aye M. , Rigby A. S. , Fraser W. D. , Kilpatrick E. S. , Atkin S. L. 
Published: November 2017

AbstractType 2 diabetes (T2DM) is associated with increased risk of fractures. Soy supplementation has been shown to have a beneficial effect on bone turnover markers (BTM) in postmenopausal women. However, the effect of soy supplementation on BTM in T2DM and particularly in men is unclear. We performed an analysis of a randomized double blind parallel study of 200 men with T2DM treated with soy, either with or without isoflavones. Outcome measures were type I collagen crosslinked beta C-telopeptide (βCTX), and type 1 procollagen-N-propeptide (P1NP). The men, with a total testosterone <12 nmol/L, were treated with 15 g soy protein containing 66 mg of isoflavones (SPI) or 15 g soy protein alone without isoflavones (SP) daily for three months. There was a 15% reduction in βCTX after three months of SPI compared to SP supplementation. There was no significant difference in P1NP with either SPI or SP supplementation. There was a significant linear correlation between the reduction in βCTX in the SPI group with the reduction in HbA1c (r2 = 0.42; p = 0.04) and HOMA-IR (r2 = 0.54; p = 0.02). Our study indicates that there was a significant reduction in bone resorption following 3 months of SPI supplementation that correlated with an improvement of glycemic control in men with T2DM.
Antennal transcriptome analysis and expression profiles of olfactory genes in Anoplophora chinensis
Authors: Wang Jingzhen , Hu Ping , Gao Peng , Tao Jing , Luo Youqing 
Published: November 2017

AbstractOlfaction in insects is essential for host identification, mating and oviposition, in which olfactory proteins are responsible for chemical signaling. Here, we determined the transcriptomes of male and female adult antennae of Anoplophora chinensis, the citrus longhorned beetle. Among 59,357 unigenes in the antennal assembly, we identified 46 odorant-binding proteins, 16 chemosensory proteins (CSPs), 44 odorant receptors, 19 gustatory receptors, 23 ionotropic receptors, and 3 sensory neuron membrane proteins. Among CSPs, AchiCSP10 was predominantly expressed in antennae (compared with legs or maxillary palps), at a significantly higher level in males than in females, suggesting that AchiCSP10 has a role in reception of female sex pheromones. Many highly expressed genes encoding CSPs are orthologue genes of A. chinensis and Anoplophora glabripennis. Notably, AchiPBP1 and AchiPBP2 showed 100% and 96% identity with AglaPBP1 and AglaPBP2 from A. glabripennis, with similar expression profiles in the two species; PBP2 was highly expressed in male antennae, whereas PBP1 was expressed in all three tissues in both males and females. These results provide a basis for further studies on the molecular chemoreception mechanisms of A. chinensis, and suggest novel targets for control of A. chinensis.
A conserved stem of the Myxococcus xanthus sRNA Pxr controls sRNA accumulation and multicellular development
Authors: Yu Yuen-Tsu N. , Cooper Elizabeth , Velicer Gregory J. 
Published: November 2017

AbstractThe small RNA (sRNA) Pxr negatively controls multicellular fruiting body formation in the bacterium Myxococcus xanthus, inhibiting the transition from growth to development when nutrients are abundant. Like many other prokaryotic sRNAs, Pxr is predicted to fold into three stem loops (SL1-SL3). SL1 and SL2 are highly conserved across the myxobacteria, whereas SL3 is much more variable. SL1 is necessary for the regulatory function of Pxr but the importance of SL3 in this regard is unknown. To test for cis genetic elements required for Pxr function, we deleted the entire pxr gene from a developmentally defective strain that fails to remove Pxr-mediated blockage of development and reintroduced variably truncated fragments of the pxr region to test for their ability to block development. These truncations demonstrated that SL3 is necessary for Pxr function in the defective strain. We further show that a highly conserved eight-base-pair segment of SL3 is not only necessary for Pxr to block development in the defective strain under starvation conditions, but is also required for Pxr to prevent fruiting body development by a developmentally proficient wild-type strain under high-nutrient conditions. This conserved segment of SL3 is also necessary for detectable levels of Pxr to accumulate, suggesting that this segment either stabilizes Pxr against premature degradation during vegetative growth or positively regulates its transcription.
Identification of miRNA-mediated drought responsive multi-tiered regulatory network in drought tolerant rice, Nagina 22
Authors: Balyan Sonia , Kumar Mukesh , Mutum Roseeta Devi , Raghuvanshi Utkarsh , Agarwal Priyanka , Mathur Saloni , Raghuvanshi Saurabh 
Published: November 2017

AbstractComparative characterization of microRNA-mediated stress regulatory networks in contrasting rice cultivars is critical to decipher plant stress response. Consequently, a multi-level comparative analysis, using sRNA sequencing, degradome analysis, enzymatic and metabolite assays and metal ion analysis, in drought tolerant and sensitive rice cultivars was conducted. The study identified a group of miRNAs “Cultivar-specific drought responsive” (CSDR)-miRNAs (osa-miR159f, osa-miR1871, osa-miR398b, osa-miR408-3p, osa-miR2878-5p, osa-miR528-5p and osa-miR397a) that were up-regulated in the flag-leaves of tolerant cultivar, Nagina 22 (N22) and Vandana, but down-regulated in the sensitive cultivar, Pusa Basmati 1 (PB1) and IR64, during drought. Interestingly, CSDR-miRNAs target several copper-protein coding transcripts like plantacyanins, laccases and Copper/Zinc superoxide dismutases (Cu/Zn SODs) and are themselves found to be similarly induced under simulated copper-starvation in both N22 and PB1. Transcription factor OsSPL9, implicated in Cu-homeostasis also interacted with osa-miR408-3p and osa-miR528-5p promoters. Further, N22 flag leaves showed lower SOD activity, accumulated ROS and had a higher stomata closure. Interestingly, compared to PB1, internal Cu levels significantly decreased in the N22 flag-leaves, during drought. Thus, the study identifies the unique drought mediated dynamism and interplay of Cu and ROS homeostasis, in the flag leaves of drought tolerant rice, wherein CSDR-miRNAs play a pivotal role.
A novel cytotherapy device for rapid screening, enriching and combining mesenchymal stem cells into a biomaterial for promoting bone regeneration
Authors: Zhuang Yifu , Gan Yaokai , Shi Dingwei , Zhao Jie , Tang Tingting , Dai Kerong 
Published: November 2017

AbstractBone defects are a common challenge in clinic, usually warranting bone grafts. However, current strategies to obtain effective graft materials have many drawbacks. Mesenchymal stem cell (MSC)-based therapy is a promising alternative. We designed an innovative appliance named the stem cell screen–enrich–combine(-biomaterials) circulating system (SECCS). In this study, 42 patients who required bone graft underwent SECCS-based treatment. Their bone marrow samples and beta-tricalcium phosphate (β-TCP) granules were processed in the SECCS for 10–15 minutes, to produce MSC/β-TCP composites. These composites were grafted back into bone defect sites. The results showed 85.53% ± 7.95% autologous MSCs were successfully screened, enriched, and seeded on the β-TCP scaffolds synchronously. The cell viability remained unchanged after SECCS processing. Clinically, all patients obtained satisfactory bone healing. Thus, without in vitro culture, the SECCS can produce bioactive MSC/β-TCP composites for bone regeneration during surgery. The SECCS represents a convenient, rapid, low-cost, and safe method for bone regeneration.
Differential responses of body growth to artificial warming between parasitoids and hosts and the consequences for plant seed damage
Authors: Xi Xinqiang , Yang Yangheshan , Yang Xiaocheng , Nylin Sören , Eisenhauer Nico , Sun Shucun 
Published: November 2017

AbstractTemperature increase may disrupt trophic interactions by differentially changing body growth of the species involved. In this study, we tested whether the response of body growth to artificial warming (~2.2 °C) of a solitary koinobiont endo-parasitoid wasp (Pteromalus albipennis, Hymenoptera: Pteromalidae) differed from its main host tephritid fly (Tephritis femoralis, Diptera: Tephritidae; pre-dispersal seed predator), and whether the plant seed damage caused by wasp-parasitized and unparasitized maggots (larval flies) were altered by warming. In contrast to the significant and season-dependent effects of warming on body growth of the host tephritid fly reported in one of our previous studies, the effect of artificial warming on body growth was non-significant on the studied wasp. Moreover, the warming effect on seed damage due to unparasitized maggots was significant and varied with season, but the damage by parasitized maggots was not altered by warming. Distinct responses of body growth to warming between parasitoids studied here and hosts assessed in a previous study indicate that temperature increase may differentially affect life history traits of animals along food chains, which is likely to affect trophic interactions.
Exploration of Antifungal and Immunomodulatory Potentials of a Furanone Derivative to Rescue Disseminated Cryptococosis in Mice
Authors: Rathore Sudarshan Singh , Isravel Muthukrishnan , Vellaisamy Sridharan , Chellappan David Raj , Cheepurupalli Lalitha , Raman Thiagarajan , Ramakrishnan Jayapradha 
Published: November 2017

AbstractCryptococcus neoformans infection is quite complex with both host-pathogen interaction and host immune profile determining disease progress and therapeutic outcome. Hence in the present study, the potential utility of (E)-5-benzylidenedihydrofuran-2(3 H)-one (compound-6) was explored as an effective anticryptococcal compound with immunomodulatory potential. The efficacy of compound-6 in pulmonary cryptococosis model using H99 strain was investigated. The effective dose was found to provide 100% survival, with a significant reduction of yeast burden in lungs and brain. The biodistribution analysis provided evidence for the presence of higher concentration of compound-6 in major organs including lungs and brain. In addition, compound-6 treated mice had significantly higher expression of IL-6, IL-4 and IFN-γ in lung and brain. Similarly, elevated expression of TNF-α, IL-β1 and IL-12 were observed in lungs, suggesting the protective host response against C. neoformans. The reduction and clearance of fungal load in systemic organs and mouse survival are notable results to confirm the ability of compound-6 to treat cryptococcosis. In conclusion, the low molecular weight (174 Da), lipophilicity, its ability to cross blood brain barrier, and facilitating modulation of cytokine expression are the added advantages of compound-6 to combat against disseminated cryptococosis.
Stromatolites on the rise in peat-bound karstic wetlands
Authors: Proemse Bernadette C. , Eberhard Rolan S. , Sharples Chris , Bowman John P. , Richards Karen , Comfort Michael , Barmuta Leon A. 
Published: November 2017

AbstractStromatolites are the oldest evidence for life on Earth, but modern living examples are rare and predominantly occur in shallow marine or (hyper-) saline lacustrine environments, subject to exotic physico-chemical conditions. Here we report the discovery of living freshwater stromatolites in cool-temperate karstic wetlands in the Giblin River catchment of the UNESCO-listed Tasmanian Wilderness World Heritage Area, Australia. These stromatolites colonize the slopes of karstic spring mounds which create mildly alkaline (pH of 7.0-7.9) enclaves within an otherwise uniformly acidic organosol terrain. The freshwater emerging from the springs is Ca-HCO3 dominated and water temperatures show no evidence of geothermal heating. Using 16 S rRNA gene clone library analysis we revealed that the bacterial community is dominated by Cyanobacteria, Alphaproteobacteria and an unusually high proportion of Chloroflexi, followed by Armatimonadetes and Planctomycetes, and is therefore unique compared to other living examples. Macroinvertebrates are sparse and snails in particular are disadvantaged by the development of debilitating accumulations of carbonate on their shells, corroborating evidence that stromatolites flourish under conditions where predation by metazoans is suppressed. Our findings constitute a novel habitat for stromatolites because cool-temperate freshwater wetlands are not a conventional stromatolite niche, suggesting that stromatolites may be more common than previously thought.
Gastric microbiome of Indian patients with Helicobacter pylori infection, and their interaction networks
Authors: Das Anubhav , Pereira Verima , Saxena Shruti , Ghosh Tarini Shankar , Anbumani D. , Bag Satyabrata , Das Bhabatosh , Nair G. Balakrish , Abraham Philip , Mande Sharmila S. 
Published: November 2017

AbstractThe gastric microbiome is suspected to have a role in the causation of diseases by Helicobacter pylori. Reports on their relative abundance vis-à-vis H. pylori are available from various ethnic and geographic groups, but little is known about their interaction patterns. Endoscopic mucosal biopsy samples from the gastric antrum and corpus of 39 patients with suspected H. pylori infection were collected and microbiomes were analyzed by 16S rDNA profiling. Four groups of samples were identified, which harbored Helicobacter as well as a diverse group of bacteria including Lactobacillus, Halomonas and Prevotella. There was a negative association between the microbiome diversity and Helicobacter abundance. Network analyses showed that Helicobacter had negative interactions with members of the gastric microbiome, while other microbes interacted positively with each other, showing a higher tendency towards intra-cluster co-occurrence/co-operation. Cross-geographic comparisons suggested the presence of region-specific microbial abundance profiles. We report the microbial diversity, abundance variation and interaction patterns of the gastric microbiota of Indian patients with H. pylori infection and present a comparison of the same with the gastric microbial ecology in samples from different geographic regions. Such microbial abundance profiles and microbial interactions can help in understanding the pathophysiology of gastric ailments and can thus help in development of new strategies to curb it.
Site-specific phosphorylation regulates the structure and function of an intrinsically disordered domain of the glucocorticoid receptor
Authors: Khan Shagufta H. , McLaughlin William A. , Kumar Raj 
Published: November 2017

AbstractIntrinsically disordered (ID) regions of the transcription factor proteins have much larger frequency of phosphorylation sites than ordered regions, suggesting an important role in their regulatory capacity. Consistent with this phenomenon, most of the functionally known phosphorylation sites in the steroid receptor family of transcription factors are located in the ID N-terminal domain that contains a powerful activation function (AF1) region. In this study, we determined the structural and functional consequences of functionally known phosphorylation residues (Ser203, 211, and 226) located in the human glucocorticoid receptor’s (GR’s) ID AF1 domain. We report the relative importance of each phosphorylation site in inducing a functionally active ordered conformation in GR’s ID AF1 domain. Our data demonstrate a mechanism through which ID domain of the steroid receptors and other similar transcription factors may adopt a functionally active conformation under physiological conditions.
Animal multicellularity and polarity without Wnt signaling
Authors: Schenkelaars Quentin , Pratlong Marine , Kodjabachian Laurent , Fierro-Constain Laura , Vacelet Jean , Le Bivic André , Renard Emmanuelle , Borchiellini Carole 
Published: November 2017

AbstractAcquisition of multicellularity is a central event in the evolution of Eukaryota. Strikingly, animal multicellularity coincides with the emergence of three intercellular communication pathways – Notch, TGF-β and Wnt – all considered as hallmarks of metazoan development. By investigating Oopsacas minuta and Aphrocallistes vastus, we show here that the emergence of a syncytium and plugged junctions in glass sponges coincides with the loss of essential components of the Wnt signaling (i.e. Wntless, Wnt ligands and Disheveled), whereas core components of the TGF-β and Notch modules appear unaffected. This suggests that Wnt signaling is not essential for cell differentiation, polarity and morphogenesis in glass sponges. Beyond providing a comparative study of key developmental toolkits, we define here the first case of a metazoan phylum that maintained a level of complexity similar to its relatives despite molecular degeneration of Wnt pathways.
Copper (II) binding of NAD(P)H- flavin oxidoreductase (NfoR) enhances its Cr (VI)-reducing ability
Authors: Han Huawen , Ling Zhenmin , Zhou Tuoyu , Xu Rong , He Yongxing , Liu Pu , Li Xiangkai 
Published: November 2017

AbstractMicrobes can reduce hexavalent chromium Cr (VI) to the less toxic and soluble trivalent Cr (III). Copper stimulates microbial reduction of Cr (VI) by the Bacillus, Ochrobactrum, and Gluconobacter species; however, the mechanism remains unclear. In our study, the rate of Cr (VI) reduction by Staphylococcus aureus LZ-01 was increased by 210 % when supplemented with 60 μM Cu (II). A putative NAD(P)H-flavin oxidoreductase gene (nfoR) was upregulated under Cr (VI) stress. NfoR-knockout mutant displayed impaired reduction of Cr (VI) and Cu (II)-enhanced Cr (VI) reduction by nfoR isogenic mutant was attenuated in the presence of Cu (II). In vitro tests showed an increased V
max
value of 25.22 μM min−1 mg−1 NfoR in the presence of Cu (II). Together, these results indicate that NfoR is responsible for Cu (II) enhancement. Isothermal titration calorimetry (ITC) assays confirmed the interaction of NfoR with Cu (II) at the dissociation constant of 85.5 μM. Site-directed mutagenesis indicates that His100, His128, and Met165 residues may be important for Cu (II) binding, while Cys163 is necessary for the FMN binding of NfoR. These findings show that Cu (II)-enhanced NfoR belongs to a new branch of Cr (VI) reductases and profoundly influences Cr (VI) reduction.
Innate Cell-Mediated Cytotoxic Activity of European Sea Bass Leucocytes Against Nodavirus-Infected Cells: A Functional and RNA-seq Study
Authors: Chaves-Pozo Elena , Valero Yulema , Esteve-Codina Anna , Gómez-Garrido Jèssica , Dabad Marc , Alioto Tyler , Meseguer José , Esteban M. Ángeles , Cuesta Alberto 
Published: November 2017

AbstractNervous necrosis virus (NNV) causes high mortalities in several marine species. We aimed to evaluate the innate cell-mediated cytotoxic (CMC) activity of head-kidney leucocytes (HKLs) isolated from naïve European sea bass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata), a very susceptible and resistant fish species to NNV, respectively, against fish cell lines infected with NNV. Seabream HKLs showed significantly increased innate CMC activity against NNV-infected cells, compared to those uninfected, while sea bass HKLs failed to do so. Thus, we performed a RNA-seq study to identify genes related to the CMC activity of sea bass leucocytes. Thus, we found that sea bass HKLs incubated with DLB-1 cells alone (CMC_DLB1) or with NNV-infected DLB-1 cells (CMC_DLB1-NNV) showed very similar transcriptomic profiles and the GO analysis revealed that most of the up-regulated genes were related to immunity. Strikingly, when the CMC samples with and without NNV were compared, GO analysis revealed that most of the up-regulated genes in CMC_DLB1-NNV samples were related to metabolism and very few to immunity. This is also in agreement with the functional data. These data point to the escape of CMC activity by NNV infection as an important factor involved in the high susceptibility to nodavirus infections of European sea bass.
Random protein sequences can form defined secondary structures and are well-tolerated in vivo
Authors: Tretyachenko Vyacheslav , Vymětal Jiří , Bednárová Lucie , Kopecký Vladimír , Hofbauerová Kateřina , Jindrová Helena , Hubálek Martin , Souček Radko , Konvalinka Jan , Vondrášek Jiří , Hlouchová Klára 
Published: November 2017

AbstractThe protein sequences found in nature represent a tiny fraction of the potential sequences that could be constructed from the 20-amino-acid alphabet. To help define the properties that shaped proteins to stand out from the space of possible alternatives, we conducted a systematic computational and experimental exploration of random (unevolved) sequences in comparison with biological proteins. In our study, combinations of secondary structure, disorder, and aggregation predictions are accompanied by experimental characterization of selected proteins. We found that the overall secondary structure and physicochemical properties of random and biological sequences are very similar. Moreover, random sequences can be well-tolerated by living cells. Contrary to early hypotheses about the toxicity of random and disordered proteins, we found that random sequences with high disorder have low aggregation propensity (unlike random sequences with high structural content) and were particularly well-tolerated. This direct structure content/aggregation propensity dependence differentiates random and biological proteins. Our study indicates that while random sequences can be both structured and disordered, the properties of the latter make them better suited as progenitors (in both in vivo and in vitro settings) for further evolution of complex, soluble, three-dimensional scaffolds that can perform specific biochemical tasks.