bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of promoters and ribosome binding sites for biotechnological applications in the unicellular cyanobacterium Synechocystis sp. PCC 6803
Authors: Englund Elias , Liang Feiyan , Lindberg Pia 
Published: November 2016

AbstractFor effective metabolic engineering, a toolbox of genetic components that enables predictable control of gene expression is needed. Here we present a systematic study of promoters and ribosome binding sites in the unicellular cyanobacterium Synechocystis sp. PCC 6803. A set of metal ion inducible promoters from Synechocystis were compared to commonly used constitutive promoters, by measuring fluorescence of a reporter protein in a standardized setting to allow for accurate comparisons of promoter activity. The most versatile and useful promoter was found to be PnrsB, which from a relatively silent expression could be induced almost 40-fold, nearly up to the activity of the strong psbA2 promoter. By varying the concentrations of the two metal ion inducers Ni2+ and Co2+, expression from the promoter was highly tunable, results that were reproduced with PnrsB driving ethanol production. The activities of several ribosomal binding sites were also measured, and tested in parallel in Synechocystis and Escherichia coli. The results of the study add useful information to the Synechocystis genetic toolbox for biotechnological applications.
GR-independent down-modulation on GM-CSF bone marrow-derived dendritic cells by the selective glucocorticoid receptor modulator Compound A
Authors: Barcala Tabarrozzi Andres E. , Andreone Luz , Deckers Julie , Castro Carla N. , Gimeno María L. , Ariolfo Laura , Berguer Paula M. , Antunica-Noguerol María , Liberman Ana C. , Vettorazzi Sabine , Tuckermann Jan P. , De Bosscher Karolien , Perone Marcelo J. 
Published: November 2016

AbstractDendritic cells (DC) initiate the adaptive immune response. Glucocorticoids (GCs) down-modulate the function of DC. Compound A (CpdA, (2-(4-acetoxyphenyl)-2-chloro-N-methyl-ethylammonium chloride) is a plant-derived GR-ligand with marked dissociative properties. We investigated the effects of CpdA on in vitro generated GM-CSF-conditioned bone marrow-derived DC (BMDC). CpdA-exposed BMDC exhibited low expression of cell-surface molecules and diminution of the release of proinflammatory cytokines upon LPS stimulation; processes associated with BMDC maturation and activation. CpdA-treated BMDC were inefficient at Ag capture via mannose receptor-mediated endocytosis and displayed reduced T-cell priming. CpdA prevented the LPS-induced rise in pErk1/2 and pP38, kinases involved in TLR4 signaling. CpdA fully inhibited LPS-induced pAktSer473, a marker associated with the generation of tolerogenic DC. We used pharmacological blockade and selective genetic loss-of-function tools and demonstrated GR-independent inhibitory effects of CpdA in BMDC. Mechanistically, CpdA-mediated inactivation of the NF-κB intracellular signaling pathway was associated with a short-circuiting of pErk1/2 and pP38 upstream signaling. Assessment of the in vivo function of CpdA-treated BMDC pulsed with the hapten trinitrobenzenesulfonic acid showed impaired cell-mediated contact hypersensitivity. Collectively, we provide evidence that CpdA is an effective BMDC modulator that might have a benefit for immune disorders, even when GR is not directly targeted.
Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest
Authors: Purahong Witoon , Durka Walter , Fischer Markus , Dommert Sven , Schöps Ricardo , Buscot François , Wubet Tesfaye 
Published: November 2016

AbstractTree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.
Observation selection bias in contact prediction and its implications for structural bioinformatics
Authors: Orlando G. , Raimondi D. , Vranken W. F. 
Published: November 2016

AbstractNext Generation Sequencing is dramatically increasing the number of known protein sequences, with related experimentally determined protein structures lagging behind. Structural bioinformatics is attempting to close this gap by developing approaches that predict structure-level characteristics for uncharacterized protein sequences, with most of the developed methods relying heavily on evolutionary information collected from homologous sequences. Here we show that there is a substantial observational selection bias in this approach: the predictions are validated on proteins with known structures from the PDB, but exactly for those proteins significantly more homologs are available compared to less studied sequences randomly extracted from Uniprot. Structural bioinformatics methods that were developed this way are thus likely to have over-estimated performances; we demonstrate this for two contact prediction methods, where performances drop up to 60% when taking into account a more realistic amount of evolutionary information. We provide a bias-free dataset for the validation for contact prediction methods called NOUMENON.
Principles of proteome allocation are revealed using proteomic data and genome-scale models
Authors: Yang Laurence , Yurkovich James T. , Lloyd Colton J. , Ebrahim Ali , Saunders Michael A. , Palsson Bernhard O. 
Published: November 2016

AbstractIntegrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the “generalist” (wild-type) E. coli proteome and phenotype across diverse growth environments. Across 15 growth conditions, prediction errors for growth rate and metabolic fluxes were 69% and 14% lower, respectively. The sector-constrained ME model thus represents a generalist ME model reflecting both growth rate maximization and “hedging” against uncertain environments and stresses, as indicated by significant enrichment of these sectors for the general stress response sigma factor σS. Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally-related protein groups) as demonstrated here. This flexible formalism provides an accessible approach for narrowing the gap between the complexity captured by omics data and governing principles of proteome allocation described by systems-level models.
Synthesis of (3R)-acetoin and 2,3-butanediol isomers by metabolically engineered Lactococcus lactis
Authors: Kandasamy Vijayalakshmi , Liu Jianming , Dantoft Shruti Harnal , Solem Christian , Jensen Peter Ruhdal 
Published: November 2016

AbstractThe potential that lies in harnessing the chemical synthesis capabilities inherent in living organisms is immense. Here we demonstrate how the biosynthetic machinery of Lactococcus lactis, can be diverted to make (3R)-acetoin and the derived 2,3-butanediol isomers meso-(2,3)-butanediol (m-BDO) and (2R,3R)-butanediol (R-BDO). Efficient production of (3R)-acetoin was accomplished using a strain where the competing lactate, acetate and ethanol forming pathways had been blocked. By introducing different alcohol dehydrogenases into this strain, either EcBDH from Enterobacter cloacae or SadB from Achromobacter xylosooxidans, it was possible to achieve high-yield production of m-BDO or R-BDO respectively. To achieve biosustainable production of these chemicals from dairy waste, we transformed the above strains with the lactose plasmid pLP712. This enabled efficient production of (3R)-acetoin, m-BDO and R-BDO from processed whey waste, with titers of 27, 51, and 32 g/L respectively. The corresponding yields obtained were 0.42, 0.47 and 0.40 g/g lactose, which is 82%, 89%, and 76% of maximum theoretical yield respectively. These results clearly demonstrate that L. lactis is an excellent choice as a cell factory for transforming lactose containing dairy waste into value added chemicals.
Osteogenic and bactericidal surfaces from hydrothermal titania nanowires on titanium substrates
Authors: Tsimbouri P. M. , Fisher L. , Holloway N. , Sjostrom T. , Nobbs A. H. , Meek R. M. D , Su B. , Dalby M. J. 
Published: November 2016

AbstractNanotopographical cues on Ti have been shown to elicit different cell responses such as cell differentiation and selective growth. Bone remodelling is a constant process requiring specific cues for optimal bone growth and implant fixation. Moreover, biofilm formation and the resulting infection on surgical implants is a major issue. Our aim is to identify nanopatterns on Ti surfaces that would be optimal for both bone remodelling and for reducing risk of bacterial infection. Primary human osteoblast/osteoclast co-cultures were seeded onto Ti substrates with TiO2 nanowires grown under alkaline conditions at 240 °C for different times (2, 2.5 or 3 h). Cell growth and behaviour was assessed by scanning electron microscopy (SEM), immunofluorescence microscopy, histochemistry and quantitative RT-PCR methods. Bacterial colonisation of the nanowire surfaces was also assessed by confocal microscopy and SEM. From the three surfaces tested the 2 h nanowire surface supported osteoblast and to a lesser extent osteoclast growth and differentiation. At the same time bacterial viability was reduced. Hence the 2 h surface provided optimal bone remodeling in vitro conditions while reducing infection risk, making it a favourable candidate for future implant surfaces.
Low-voltage scanning electron microscopy study of lampbrush chromosomes and nuclear bodies in avian and amphibian oocytes
Authors: Kulikova Tatiana , Khodyuchenko Tatiana , Petrov Yuri , Krasikova Alla 
Published: November 2016

AbstractNucleus is a highly compartmentalized part of the cell where the key processes of genome functionality are realized through the formation of non-membranous nuclear domains. Physically nuclear domains appear as liquid droplets with different viscosity stably maintained throughout the interphase or during the long diplotene stage of meiosis. Since nuclear body surface represents boundary between two liquid phases, the ultrastructural surface topography of nuclear domains is of an outstanding interest. The aim of this study was to examine ultrathin surface topography of the amphibian and avian oocyte nuclear structures such as lampbrush chromosomes, nucleoli, histone-locus bodies, Cajal body-like bodies, and the interchromatin granule clusters via low-voltage scanning electron microscopy. Our results demonstrate that nuclear bodies with similar molecular composition may differ dramatically in the surface topography and vice versa, nuclear bodies that do not share common molecular components may possess similar topographical characteristics. We also have analyzed surface distribution of particular nuclear antigens (double stranded DNA, coilin and splicing snRNA) using indirect immunogold labeling with subsequent secondary electron detection of gold nanoparticles. We suggest that ultrastructural surface morphology reflects functional status of a nuclear body.
A Direct Mapping of Max k-SAT and High Order Parity Checks to a Chimera Graph
Authors: Chancellor N. , Zohren S. , Warburton P. A. , Benjamin S. C. , Roberts S. 
Published: November 2016

AbstractWe demonstrate a direct mapping of max k-SAT problems (and weighted max k-SAT) to a Chimera graph, which is the non-planar hardware graph of the devices built by D-Wave Systems Inc. We further show that this mapping can be used to map a similar class of maximum satisfiability problems where the clauses are replaced by parity checks over potentially large numbers of bits. The latter is of specific interest for applications in decoding for communication. We discuss an example in which the decoding of a turbo code, which has been demonstrated to perform near the Shannon limit, can be mapped to a Chimera graph. The weighted max k-SAT problem is the most general class of satisfiability problems, so our result effectively demonstrates how any satisfiability problem may be directly mapped to a Chimera graph. Our methods faithfully reproduce the low energy spectrum of the target problems, so therefore may also be used for maximum entropy inference.
FPA-FTIR Microspectroscopy for Monitoring Chemotherapy Efficacy in Triple-Negative Breast Cancer
Authors: Zawlik Izabela , Kaznowska Ewa , Cebulski Jozef , Kolodziej Magdalena , Depciuch Joanna , Vongsvivut Jitraporn , Cholewa Marian 
Published: November 2016

AbstractTriple-negative breast cancer is the most aggressive breast cancer subtype with limited treatment options and a poor prognosis. Approximately 70% of triple-negative breast cancer patients fail to achieve a pathologic complete response (pCR) after chemotherapy due to the lack of targeted therapies for this subtype. We report here the development of a focal-plane-array Fourier transform infrared (FPA-FTIR) microspectroscopic technique combined with principal component analysis (PCA) for monitoring chemotherapy effects in triple-negative breast cancer patients. The PCA results obtained using the FPA-FTIR spectral data collected from the same patients before and after the chemotherapy revealed discriminatory features that were consistent with the pathologic and clinical responses to chemotherapy, indicating the potential of the technique as a monitoring tool for observing chemotherapy efficacy.
Simulated ischemia/reperfusion-induced p65-Beclin 1-dependent autophagic cell death in human umbilical vein endothelial cells
Authors: Zeng Min , Wei Xin , Wu Zhiyong , Li Wei , Zheng Yin , Li Bing , Meng Xuqing , Fu Xiuhong , Fei Yi 
Published: November 2016

AbstractMyocardial ischemia/reperfusion (I/R) injury detrimentally alters the prognosis of patients undergoing revascularization after acute myocardial infarction. Our previous study demonstrated that NF-κB-induced autophagy plays a detrimental role in cardiac I/R injury using a rabbit myocardial I/R model. In this study, we sought to explore the specific mechanism of this autophagy-mediated cell damage in an in vitro simulated ischemia/reperfusion (sI/R) model using human umbilical vein endothelial cells. Our current study demonstrates that simulated I/R induces autophagy in a p65-Beclin 1-dependent manner, which can be suppressed with the inhibition of NF-κB. Furthermore, rapamycin which promotes autophagy, exacerbates sI/R-induced cell death. While 3-methyladenine rescues cell damage. Our data thus suggest that I/R promotes NF-κB p65 activity mediated Beclin 1-mediated autophagic flux, thereby exacerbating myocardial injury.
Quantitative identification of dynamical transitions in a semiconductor laser with optical feedback
Authors: Quintero-Quiroz C. , Tiana-Alsina J. , Romà J. , Torrent M. C. , Masoller C. 
Published: November 2016

AbstractIdentifying transitions to complex dynamical regimes is a fundamental open problem with many practical applications. Semi- conductor lasers with optical feedback are excellent testbeds for studying such transitions, as they can generate a rich variety of output signals. Here we apply three analysis tools to quantify various aspects of the dynamical transitions that occur as the laser pump current increases. These tools allow to quantitatively detect the onset of two different regimes, low-frequency fluctuations and coherence collapse, and can be used for identifying the operating conditions that result in specific dynamical properties of the laser output. These tools can also be valuable for analyzing regime transitions in other complex systems.
Evaluating renewable natural resources flow and net primary productivity with a GIS-Emergy approach: A case study of Hokkaido, Japan
Authors: Wang Chengdong , Zhang Shenyan , Yan Wanglin , Wang Renqing , Liu Jian , Wang Yutao 
Published: November 2016

AbstractRenewable natural resources, such as solar radiation, rainfall, wind, and geothermal heat, together with ecosystem services, provide the elementary supports for the sustainable development of human society. To improve regional sustainability, we studied the spatial distributions and quantities of renewable natural resources and net primary productivity (NPP) in Hokkaido, which is the second largest island of Japan. With the help of Geographic Information System (GIS) software, distribution maps for each type of renewable natural resource were generated by kriging interpolation based on statistical records. A composite map of the flow of all types of renewable natural resources was also generated by map layer overlapping. Additionally, we utilized emergy analysis to convert each renewable flow with different attributes into a unified unit (i.e., solar equivalent joules [sej]). As a result, the spatial distributions of the flow of renewable natural resources of the Hokkaido region are presented in the form of thematic emergy maps. Thus, the areas with higher renewable emergy can be easily visualized and identified. The dominant renewable flow in certain areas can also be directly distinguished. The results can provide useful information for regional sustainable development, environmental conservation and ecological management.
Charge storage mechanisms of manganese oxide nanosheets and N-doped reduced graphene oxide aerogel for high-performance asymmetric supercapacitors
Authors: Iamprasertkun Pawin , Krittayavathananon Atiweena , Seubsai Anusorn , Chanlek Narong , Kidkhunthod Pinit , Sangthong Winyoo , Maensiri Santi , Yimnirun Rattikorn , Nilmoung Sukanya , Pannopard Panvika , Ittisanronnachai Somlak , Kongpatpanich Kanokwan , Limtrakul Jumras , Sawangphruk Montree 
Published: November 2016

AbstractAlthough manganese oxide- and graphene-based supercapacitors have been widely studied, their charge storage mechanisms are not yet fully investigated. In this work, we have studied the charge storage mechanisms of K-birnassite MnO2 nanosheets and N-doped reduced graphene oxide aerogel (N-rGOae) using an in situ X-ray absorption spectroscopy (XAS) and an electrochemical quart crystal microbalance (EQCM). The oxidation number of Mn at the MnO2 electrode is +3.01 at 0 V vs. SCE for the charging process and gets oxidized to +3.12 at +0.8 V vs. SCE and then reduced back to +3.01 at 0 V vs. SCE for the discharging process. The mass change of solvated ions, inserted to the layers of MnO2 during the charging process is 7.4 μg cm−2. Whilst, the mass change of the solvated ions at the N-rGOae electrode is 8.4 μg cm−2. An asymmetric supercapacitor of MnO2//N-rGOae (CR2016) provides a maximum specific capacitance of ca. 467 F g−1 at 1 A g−1, a maximum specific power of 39 kW kg−1 and a specific energy of 40 Wh kg−1 with a wide working potential of 1.6 V and 93.2% capacity retention after 7,500 cycles. The MnO2//N-rGOae supercapacitor may be practically used in high power and energy applications.
Effects of climate and fire on short-term vegetation recovery in the boreal larch forests of Northeastern China
Authors: Liu Zhihua 
Published: November 2016

AbstractUnderstanding the influence of climate variability and fire characteristics in shaping postfire vegetation recovery will help to predict future ecosystem trajectories in boreal forests. In this study, I asked: (1) which remotely-sensed vegetation index (VI) is a good proxy for vegetation recovery? and (2) what are the relative influences of climate and fire in controlling postfire vegetation recovery in a Siberian larch forest, a globally important but poorly understood ecosystem type? Analysis showed that the shortwave infrared (SWIR) VI is a good indicator of postfire vegetation recovery in boreal larch forests. A boosted regression tree analysis showed that postfire recovery was collectively controlled by processes that controlled seed availability, as well as by site conditions and climate variability. Fire severity and its spatial variability played a dominant role in determining vegetation recovery, indicating seed availability as the primary mechanism affecting postfire forest resilience. Environmental and immediate postfire climatic conditions appear to be less important, but interact strongly with fire severity to influence postfire recovery. If future warming and fire regimes manifest as expected in this region, seed limitation and climate-induced regeneration failure will become more prevalent and severe, which may cause forests to shift to alternative stable states.
The Pharyngostomy Tube: Indications, Technique, Efficacy, and Safety in Modern Surgical Practice
Authors: Berger Jonathan , Andrade Rafael , Podgaetz Eitan , Garza-Castillon Rafael 
Published: November 2016

Background Long-term nasogastric tubes are uncomfortable and associated with complications such as impairment with speech and swallowing, septum trauma, epistaxis, alar necrosis, and intubation of the trachea among others. Pharyngostomy tubes (PTs) are an alternative for prolonged enteral feeding, transluminal drainage of collections, and gastric decompression in patients with an intestinal obstruction and an inoperable abdomen.
Patients and Methods This is a retrospective analysis of patients who had a PT placed at our institution from May 2005 to March 2015. The primary end point of the study was to establish the type and rate of complications and aspiration events related to PT use.
Results During the specified period, a total of 84 PTs were placed. The most common indication for PT placement was enteric decompression in 65 (77.4%), followed by transluminal collection drainage in 12 (14.3%), and enteral access for nutrition in 7 (8.3%) patients. The mean time to tube removal was 17.8 days ± 17.1 (range, 2–119). We encountered 10 (11.2%) complications related to PT placement, including 7 cases of cellulitis, 2 superficial abscesses, and 1 patient with pharyngeal hemorrhage.
Conclusion PTs are a relatively simple, safe, and straightforward approach to achieve long-term enteral decompression, access for feeding or transluminal drainage, avoiding the complications associated with prolonged nasogastric tube placement. The complication rate is low and patient satisfaction and compliance appear to be higher than with nasogastric tubes. Modern surgeons should be familiar with the procedure and technique. PTs should be part of every surgeon's armamentarium.