bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America
Authors: U’Ren Jana M. , Arnold A. Elizabeth 
Published: December 2016

BackgroundFungal endophytes inhabit symptomless, living tissues of all major plant lineages to form one of earth’s most prevalent groups of symbionts. Many reproduce from senesced and/or decomposing leaves and can produce extracellular leaf-degrading enzymes, blurring the line between symbiotrophy and saprotrophy. To better understand the endophyte–saprotroph continuum we compared fungal communities and functional traits of focal strains isolated from living leaves to those isolated from leaves after senescence and decomposition, with a focus on foliage of woody plants in five biogeographic provinces ranging from tundra to subtropical scrub forest.MethodsWe cultured fungi from the interior of surface-sterilized leaves that were living at the time of sampling (i.e., endophytes), leaves that were dead and were retained in plant canopies (dead leaf fungi, DLF), and fallen leaves (leaf litter fungi, LLF) from 3–4 species of woody plants in each of five sites in North America. Our sampling encompassed 18 plant species representing two families of Pinophyta and five families of Angiospermae. Diversity and composition of fungal communities within and among leaf life stages, hosts, and sites were compared using ITS-partial LSU rDNA data. We evaluated substrate use and enzyme activity by a subset of fungi isolated only from living tissues vs. fungi isolated only from non-living leaves.ResultsAcross the diverse biomes and plant taxa surveyed here, culturable fungi from living leaves were isolated less frequently and were less diverse than those isolated from non-living leaves. Fungal communities in living leaves also differed detectably in composition from communities in dead leaves and leaf litter within focal sites and host taxa, regardless of differential weighting of rare and abundant fungi. All focal isolates grew on cellulose, lignin, and pectin as sole carbon sources, but none displayed ligninolytic or pectinolytic activityin vitro. Cellulolytic activity differed among fungal classes. Within Dothideomycetes, activity differed significantly between fungi from living vs. non-living leaves, but such differences were not observed in Sordariomycetes.DiscussionAlthough some fungi with endophytic life stages clearly persist for periods of time in leaves after senescence and incorporation into leaf litter, our sampling across diverse biomes and host lineages detected consistent differences between fungal assemblages in living vs. non-living leaves, reflecting incursion by fungi from the leaf exterior after leaf death and as leaves begin to decompose. However, fungi found only in living leaves do not differ consistently in cellulolytic activity from those fungi detected thus far only in dead leaves. Future analyses should consider Basidiomycota in addition to the Ascomycota fungi evaluated here, and should explore more dimensions of functional traits and persistence to further define the endophytism-to-saprotrophy continuum.
One-year mortality after severe COPD exacerbation in Bulgaria
Authors: Mekov Evgeni , Slavova Yanina , Tsakova Adelina , Genova Marianka P. , Kostadinov Dimitar T. , Minchev Delcho , Marinova Dora , Boyanov Mihail A. 
Published: December 2016

Introduction
One-year mortality in COPD patients is reported to be between 4% and 43%, depending on the group examined.

Aim
To examine the one-year mortality in COPD patients after severe exacerbation and the correlation between mortality and patients’ characteristics and comorbidities.

Methods
A total of 152 COPD patients hospitalized for severe exacerbation were assessed for vitamin D status, diabetes mellitus (DM), arterial hypertension (AH), and metabolic syndrome (MS). Data were gathered about smoking status and number of exacerbations in previous year. CAT and mMRC questionnaires were completed by all patients. Pre- and post-bronchodilatory spirometry was performed. One-year mortality was established from national death register.

Results
One-year mortality is 7.2%. DM, MS, and VD are not predictors for one-year mortality. However there is a trend for increased mortality in patients with AH (9.5% vs. 2.1%, p = 0.107). There is increased mortality in patients with mMRC > 2 (11.1 vs. 0%, p = 0.013). The presence of severe exacerbation in the previous year is a risk factor for mortality (12.5% vs. 1.4%, p = 0.009). There is a trend for increased mortality in the group with FEV1 < 50% (11.5 vs. 4.4%, p = 0.094). Cox regression shows 3.7% increase in mortality rate for 1% decrease in FEV1, 5.2% for 1% decrease in PEF, 7.8% for one year age increase and 8.1% for 1 CAT point increase (all p < 0.05).

Conclusions
This study finds relatively low one-year mortality in COPD patients after surviving severe exacerbation. Grade C and FEV1 > 80% may be factors for good prognosis. Risk factors for increased mortality are age, FEV1 value, severe exacerbation in previous year and reduced quality of life.
Sea ice thickness and recent Arctic warming
Authors: Lang Andreas , Yang Shuting , Kaas Eigil 
Published: December 2016

AbstractThe climatic impact of increased Arctic sea ice loss has received growing attention in the last years. However, little focus has been set on the role of sea ice thickness, although it strongly determines surface heat fluxes. Here ensembles of simulations using the EC‐Earth atmospheric model (Integrated Forecast System) are performed and analyzed to quantify the atmospheric impacts of Arctic sea ice thickness change since 1982 as revealed by the sea ice model assimilation Global Ice‐Ocean Modeling and Assimilation System. Results show that the recent sea ice thinning has significantly affected the Arctic climate, while remote atmospheric responses are less pronounced owing to a high internal atmospheric variability. Locally, the sea ice thinning results in enhancement of near‐surface warming of about 1°C per decade in winter, which is most pronounced over marginal sea ice areas with thin ice. This leads to an increase of the Arctic amplification factor by 37%.
A study of the dissociative recombination of CaO+ with electrons: Implications for Ca chemistry in the upper atmosphere
Authors: Bones D. L. , Gerding M. , Höffner J. , Martín Juan Carlos Gómez , Plane J. M. C. 
Published: December 2016

AbstractThe dissociative recombination of CaO+ ions with electrons has been studied in a flowing afterglow reactor. CaO+ was generated by the pulsed laser ablation of a Ca target, followed by entrainment in an Ar+ ion/electron plasma. A kinetic model describing the gas‐phase chemistry and diffusion to the reactor walls was fitted to the experimental data, yielding a rate coefficient of (3.0 ± 1.0) × 10−7 cm3 molecule−1 s−1 at 295 K. This result has two atmospheric implications. First, the surprising observation that the Ca+/Fe+ ratio is ~8 times larger than Ca/Fe between 90 and 100 km in the atmosphere can now be explained quantitatively by the known ion‐molecule chemistry of these two metals. Second, the rate of neutralization of Ca+ ions in a descending sporadic E layer is fast enough to explain the often explosive growth of sporadic neutral Ca layers.
In situ measurements of water uptake by black carbon‐containing aerosol in wildfire plumes
Authors: Perring Anne E. , Schwarz Joshua P. , Markovic Milos Z. , Fahey David W. , Jimenez Jose L. , Campuzano‐Jost Pedro , Palm Brett D. , Wisthaler Armin , Mikoviny Tomas , Diskin Glenn , Sachse Glen , Ziemba Luke , Anderson Bruce , Shingler Taylor , Crosbie Ewan , Sorooshian Armin , Yokelson Robert , Gao Ru‐Shan 
Published: December 2016

AbstractWater uptake by black carbon (BC)‐containing aerosol was quantified in North American wildfire plumes of varying age (1 to ~40 h old) sampled during the SEAC4RS mission (2013). A Humidified Dual SP2 (HD‐SP2) is used to optically size BC‐containing particles under dry and humid conditions from which we extract the hygroscopicity parameter, κ, of materials internally mixed with BC. Instrumental variability and the uncertainty of the technique are briefly discussed. An ensemble average κ of 0.04 is found for the set of plumes sampled, consistent with previous estimates of bulk aerosol hygroscopicity from biomass burning sources. The temporal evolution of κ in the Yosemite Rim Fire plume is explored to constrain the rate of conversion of BC‐containing aerosol from hydrophobic to more hydrophilic modes in these emissions. A BC‐specific κ increase of ~0.06 over 40 h is found, fit well with an exponential curve corresponding to a transition from a κ of 0 to a κ of ~0.09 with an e‐folding time of 29 h. Although only a few percent of wildfire particles contain BC, a similar κ increase is estimated for bulk aerosol and the measured aerosol composition is used to infer that the observed κ change is driven by a combination of incorporation of ammonium sulfate and oxidation of existing organic materials. Finally, a substantial fraction of wildfire‐generated BC‐containing aerosol is calculated to be active as cloud condensation nuclei shortly after emission likely indicating efficient wet removal. These results can constrain model treatment of BC from wildfire sources.
Polarization diversity in a long‐haul transequatorial HF link from Antarctica to Spain
Authors: Bergadà Pau , Alsina‐Pagès Rosa Ma , Hervás Marcos 
Published: December 2016

AbstractThis paper describes a set of experiments which examine the feasibility of applying polarization diversity to a 12,760 km ionospheric link from Livingston Island (62.6°S, 60.4°W), South Shetlands, to Cambrils (41.0°N, 1.0°E), Spain. A transmitting monopole and both a monopole and a dipole (inverted‐V) at reception are the antennas used in this measurement campaign. Receiving antennas are orthogonal polarized to check whether wave polarization rotation causes differences between simultaneous signals. The results gathered in the paper indicate that there is a marked difference between simultaneous signals at vertical and horizontal polarized antennas, which depends on the hour of the day and the signal frequency. In this low‐throughput HF data link, polarization diversity could be used to increase SNR and performance through smart combination of receiving signals, due to the low cross‐correlation factor between them.
Synthetische Biologie – die Synthese der Biologie
Authors: Ausländer Simon , Ausländer David , Fussenegger Martin 
Published: December 2016

AbstractDie synthetische Biologie befasst sich mit der gezielten Konstruktion von lebenden Biomaschinen aus standardisierten Komponenten, die vordefinierte Aufgaben in einer (selbst‐)kontrollierten Weise ausführen können. Unterschiedliche Forschungsstrategien und interdisziplinäre Ansätze werden verfolgt, um technische Prinzipien in die Biologie zu implementieren. Die “top‐down”‐Strategie greift auf die enorme Diversität der Natur zurück, um natürliche Komponenten künstlich in genetischen, metabolischen oder signalweiterleitenden Netzwerken mit vorhersehbaren und kontrollierbaren Eigenschaften zusammenzuführen. Dieser hauptsächlich von der Anwendung her gedachte Ansatz bringt lebende Fabriken hervor, die Wirkstoffe, Treibstoffe, Biomaterialien und Feinchemikalien produzieren. Man bekommt lebende Pillen an die Hand, bestehend aus konstruierten Zellen mit der Fähigkeit, Krankheiten in vivo autonom zu entdecken und zu behandeln. Im Gegensatz dazu versucht man in der “bottom‐up”‐Strategie, sich von bestehenden lebenden Systemen unabhängig zu machen und biologische Systeme von Grund auf neu zu entwerfen. So sollen künstliche biologische Gebilde synthetisiert werden, die es in der Natur nicht gibt. Dieser eher wissensgetriebene Ansatz untersucht die Rekonstruktion minimaler biologischer Systeme, die grundlegende biologische Phänomene wie Selbstorganisation, Selbstreplikation und Selbsterhaltung hervorbringen können. Die Synthese künstlicher biologischer Einheiten wie synthetischer Nucleotide oder Aminosäuren und ihr Einbau in Polymere im Inneren lebender Zellen stellt gegenwärtig die Grenze zwischen natürlichen und künstlichen biologischen Systemen dar. Insbesondere Entwurf und Synthese ganzer Genome in vitro und ihre Übertragung in Wirtzellen sowie die Anwendung effizienter genomweiter Manipulationstechniken deuten auf die Zukunft der synthetischen Biologie: die Erschaffung lebender Designerzellen mit maßgeschneiderten erwünschten Eigenschaften für Biomedizin und Biotechnologie.
Synthetic Biology—The Synthesis of Biology
Authors: Ausländer Simon , Ausländer David , Fussenegger Martin 
Published: December 2016

AbstractSynthetic biology concerns the engineering of man‐made living biomachines from standardized components that can perform predefined functions in a (self‐)controlled manner. Different research strategies and interdisciplinary efforts are pursued to implement engineering principles to biology. The “top‐down” strategy exploits nature's incredible diversity of existing, natural parts to construct synthetic compositions of genetic, metabolic, or signaling networks with predictable and controllable properties. This mainly application‐driven approach results in living factories that produce drugs, biofuels, biomaterials, and fine chemicals, and results in living pills that are based on engineered cells with the capacity to autonomously detect and treat disease states in vivo. In contrast, the “bottom‐up” strategy seeks to be independent of existing living systems by designing biological systems from scratch and synthesizing artificial biological entities not found in nature. This more knowledge‐driven approach investigates the reconstruction of minimal biological systems that are capable of performing basic biological phenomena, such as self‐organization, self‐replication, and self‐sustainability. Moreover, the syntheses of artificial biological units, such as synthetic nucleotides or amino acids, and their implementation into polymers inside living cells currently set the boundaries between natural and artificial biological systems. In particular, the in vitro design, synthesis, and transfer of complete genomes into host cells point to the future of synthetic biology: the creation of designer cells with tailored desirable properties for biomedicine and biotechnology.
Integrated Genome and Protein Editing Swaps α‐2,6 Sialylation for α‐2,3 Sialic Acid on Recombinant Antibodies from CHO
Authors: Chung Cheng‐yu , Wang Qiong , Yang Shuang , Yin Bojiao , Zhang Hui , Betenbaugh Michael 
Published: December 2016

AbstractImmunoglobin G with α‐2,6 sialylation has been reported to have an impact on antibody‐dependent cellular cytotoxicity and anti‐inflammatory efficacy. However, production of antibodies with α‐2,6 sialylation from Chinese hamster ovary cells is challenging due to the inaccessibility of sialyltransferases for the heavy chain N‐glycan site and the presence of exclusively α‐2,3 sialyltransferases. In this study, combining mutations on the Fc regions to allow sialyltransferase accessibility with overexpression of α‐2,6 sialyltransferase produced IgG with significant levels of both α‐2,6 and α‐2,3 sialylation. Therefore, ST3GAL4 and ST3GAL6 genes were disrupted by CRISPR/Cas9 to minimize the α‐2,3 sialylation. Sialidase treatment and SNA lectin blot indicated greatly increased α‐2,6 sialylation level relative to α‐2,3 sialylation for the α‐2,3 sialyltransferase knockouts when combined with α‐2,6 sialyltransferase overexpression. Indeed, α‐2,3 linked sialic acids were not detected on IgG produced from the α‐2,3 sialyltransferase knockout‐α‐2,6 sialyltransferase overexpression pools. Finally, glycoprofiling of IgG with four amino acid substitutions expressed from an α‐2,3 sialyltransferase knockout‐α‐2,6 sialyltransferase stable clone resulted in more than 77% sialylated glycans and more than 62% biantennary disialylated glycans as indicated by both MALDI‐TOF and LC‐ESI‐MS. Engineered antibodies from these modified Chinese hamster ovary cell lines will provide biotechnologists with IgGs containing N‐glycans with different structural variations for examining the role of glycosylation on protein performance.
Metabolic engineering of fatty alcohol production in transgenic hairy roots of Crambe abyssinica
Authors: Miklaszewska Magdalena , Banaś Antoni , Królicka Aleksandra 
Published: December 2016

ABSTRACTBiotechnological production of fatty alcohols, important raw materials in the chemical industry, has been receiving considerable attention in recent years. Fatty alcohols are formed by the reduction of fatty acyl‐CoAs or fatty acyl‐ACPs catalyzed by a fatty acyl reductase (FAR). In this study, we introduced genes encoding FARs from Arabidopsis thaliana (AtFAR5) and Simmondsia chinensis (ScFAR) into Crambe abyssinica hairy roots via Agrobacterium rhizogenes‐mediated transformation. The efficiency of the transformation ranged between 30 and 45%. The fatty alcohols were only detected in the transgenic hairy root lines expressing ScFAR gene. In all tested lines stearyl alcohol (18:0‐OH), arachidyl alcohol (20:0‐OH), and behenyl alcohol (22:0‐OH) were produced. The content of 18:0‐OH varied from 1 to 3% of total fatty acids and fatty alcohols, while the amount of either 20:0‐OH and 22:0‐OH did not exceed 2%. The transgenic hairy root lines produced from 0.98 to 2.59 nmol of fatty alcohols per mg of dry weight. Very low activity of ScFAR was detected in the microsomal fractions isolated from the selected hairy root lines. To our knowledge, this is the first report on the fatty alcohol production in the hairy root cultures. Biotechnol. Bioeng. 2017;114: 1275–1282. © 2016 Wiley Periodicals, Inc.
Enhancing functional expression of codon‐optimized heterologous enzymes in Escherichia coli BL21(DE3) by selective introduction of synonymous rare codons
Authors: Zhong Chao , Wei Ping , Zhang Yi‐Heng Percival 
Published: December 2016

ABSTRACTRare codon in a heterologous gene may cause premature termination of protein synthesis, misincorporation of amino acids, and/or slow translation of mRNA, decreasing the heterologous protein expression. However, its hypothetical function pertaining to functional protein folding has been barely reported. Here, we investigated the effects of selective introduction of synonymous rare codons (SRCs) to two codon‐optimized (i.e., rare codon‐free) genes sucrose phosphorylase (SP) gene from Thermoanaerobacterium thermosaccharolyticum and amidohydrolase gene from Streptomyces caatingaensis on their expression levels in Escherichia coli BL21(DE3). We investigated the introduction of a single SRC to the coding regions of alpha‐helix, beta‐strand, or linker in the first half of rare codon‐free sp and ah gene. The introduction of a single SRC in the beginning of the coding regions of beta‐strand greatly enhanced their soluble expression levels as compared to the other regions. Also, we applied directed evolution to test multi‐SRC‐containing sp gene mutants for enhanced soluble SP expression levels. To easily identify the soluble SP expression level of colonies growing on Petri dishes, mCherry fluorescent protein was used as a SP‐folding reporter when it was fused to the 3′ end of the sp gene mutant libraries. After three rounds of screening, the best sp gene mutant containing nine SRCs exhibited an approximately six‐fold enhancement in soluble protein expression level as compared to the wild‐type and rare codon‐free sp control. This study suggests that the selective introduction of SRCs can attenuate translation at specific points and such discontinuous attenuation can temporally separate the translation of segments of the peptide chains and actively coordinates their co‐translational folding, resulting in enhanced functional protein expression. Biotechnol. Bioeng. 2017;114: 1054–1064. © 2016 Wiley Periodicals, Inc.
Reverse Biosynthesis: Generating Combinatorial Pools of Drug Leads from Enzyme‐Mediated Fragmentation of Natural Products
Authors: Richardson‐Sanchez Tomas , Tieu William , Codd Rachel 
Published: December 2016

AbstractA combinatorial pool of hydroxamic acid fragments as potential metalloprotein drug leads was generated from the enzymatic hydrolysis of the natural product desferrioxamine B (DFOB). DFOB is a metabolite produced by Streptomyces pilosus for iron acquisition, and can be selectively catabolised by Niveispirillum irakense to access carbon for growth. The supernatant of a DFOB‐supplemented culture of N. irakense was analysed by LC‐MS at intervals over 168 h. This identified a mixture of endo‐hydroxamic acid fragments that contained reactive terminal groups. The supernatants from two cultures (at 48 h and 168 h) were reacted with 1,8‐naphthalic anhydride in a microwave synthesiser to generate pools of scriptaid analogues, which were screened against ZnII‐containing histone deacetylases (HDACs) and FeIII‐containing 5‐lipoxygenase (5‐LO). Compound S2 showed relative potency against 5‐LO (IC50=59 μm; BWA4C, 17 μm); it was 28‐fold more selective towards 5‐LO than HDAC1. Compound S1 inhibited HDAC1 but not 5‐LO. Enzyme‐mediated reverse biosynthesis could yield new benefits from structurally complex natural products in drug design.
Perylene Bisimide Cyclophanes with High Binding Affinity for Large Planar Polycyclic Aromatic Hydrocarbons: Host–Guest Complexation versus Self‐Encapsulation of Side Arms
Authors: Spenst Peter , Sieblist Andreas , Würthner Frank 
Published: December 2016

AbstractBinding of guest molecules with high affinity and selectivity requires well‐designed hosts to provide optimized interactions in the host–guest complexes. Herein we report the design and synthesis of new cyclophanes 2PBI(2,6‐iPr)2 and 2PBI(2,6‐Ph)2 based on core‐disubstituted perylene bisimide (PBI) chromophores bearing two phenoxy bay‐substituents that evoke almost planar PBI scaffolds. This strategy afforded the new cyclophanes with conformationally rigid cavities to ensure strong binding to stiff planar polycyclic aromatic hydrocarbons (PAHs). Our detailed host–guest binding studies with different PAHs by UV/Vis and fluorescence titration experiments revealed record binding strengths for PAHs with binding constants of up to 1.6×106 m−1 in chloroform at room temperature. One‐ and two‐dimensional NMR experiments and solvent‐dependent titration studies revealed self‐encapsulation of the side arms of PBI bay‐substituents into the cavities that attained high fluorescence quantum yields of these cyclophanes close to unity by preventing the interaction of PBI subunits in the excited states. The binding constants and Gibbs free energies of host–guest complexations disclosed significant effects of PBI bay‐substituents and core twist on the binding affinity of the cyclophanes.
Free‐Radical Carbo‐Alkenylation of Olefins: Scope, Limitations and Mechanistic Insights
Authors: Beniazza Redouane , Liautard Virginie , Poittevin Clément , Ovadia Benjamin , Mohammed Shireen , Robert Frédéric , Landais Yannick 
Published: December 2016

AbstractThe three‐component free‐radical carbo‐alkenylation of electron‐rich olefins has been studied, varying the substitution pattern in the alkene, in the radical precursor and in the final acceptor. New vinylsulfones were also prepared and their reactivity investigated. The scope and limitations of the process was established, and the reaction mechanism clarified using selected dienes as radical clocks. It was thus recognised that the reversible addition onto the olefin of the released sulfonyl group is an important event, which should not be overlooked when using such multicomponent carbo‐alkenylation reactions.