bluuebunny/crossref_metadata_2025 huggingface dataset:
Future forest aboveground carbon dynamics in the central United States: the importance of forest demographic processes
Authors: Jin Wenchi , He Hong S. , Thompson Frank R. , Wang Wen J. , Fraser Jacob S. , Shifley Stephen R. , Hanberry Brice B. , Dijak William D.
Published: February 2017

The Central Hardwood Forest (CHF) in the United States is currently a major carbon sink, there are uncertainties in how long the current carbon sink will persist and if the CHF will eventually become a carbon source. We used a multi-model ensemble to investigate aboveground carbon density of the CHF from 2010 to 2300 under current climate. Simulations were done using one representative model for each of the simple, intermediate, and complex demographic approaches (ED2, LANDIS PRO, andLINKAGES, respectively). All approaches agreed that the current carbon sink would persist at least to 2100. However, carbon dynamics after current carbon sink diminishes to zero differ for different demographic modelling approaches. Both the simple and the complex demographic approaches predicted prolonged periods of relatively stable carbon densities after 2100, with minor declines, until the end of simulations in 2300. In contrast, the intermediate demographic approach predicted the CHF would become a carbon source between 2110 and 2260, followed by another carbon sink period. The disagreement between these patterns can be partly explained by differences in the capacity of models to simulate gross growth (both birth and subsequent growth) and mortality of short-lived, relatively shade-intolerant tree species.
Wnt7a Inhibits IL-1β Induced Catabolic Gene Expression and Prevents Articular Cartilage Damage in Experimental Osteoarthritis
Authors: Gibson Averi L. , Hui Mingalone Carrie K. , Foote Andrea T. , Uchimura Tomoya , Zhang Ming , Zeng Li
Published: February 2017

Wnt7a is a protein that plays a critical role in skeletal development. However, its effect on cartilage homeostasis under pathological conditions is not known. In this study, we found a unique inverse correlation between Wnt7a gene expression and that of MMP and IL-1β in individual human OA cartilage specimens. Upon ectopic expression in primary human articular chondrocytes, Wnt7a inhibited IL-1β-induced MMP and iNOS gene expression. Western blot analysis indicated that Wnt7a induced both canonical Wnt signaling and NFAT and Akt non-canonical signaling. Interestingly, inhibiting the canonical and Akt pathway did not affect Wnt7a activity. However, inhibiting the NFAT pathway impaired Wnt7a’s ability to inhibit MMP expression, suggesting that Wnt7a requires NFAT signaling to exert this function. In vivo, intraarticular injection of lentiviral Wnt7a strongly attenuated articular cartilage damage induced by destabilization of the medial meniscus (DMM) OA-inducing surgery in mice. Consistently, Wnt7a also inhibited the progressive increase of joint MMP activity in DMM animals. These results indicate that Wnt7a signaling inhibits inflammatory stimuli-induced catabolic gene expression in human articular chondrocytes and is sufficient to attenuate MMP activities and promote joint cartilage integrity in mouse experimental OA, demonstrating a novel effect of Wnt7a on regulating OA pathogenesis.
Anodically Grown Titania Nanotube Induced Cytotoxicity has Genotoxic Origins
Authors: Mohamed M. Sheikh , Torabi Aida , Paulose Maggie , Kumar D. Sakthi , Varghese Oomman K.
Published: February 2017

Nanoarchitectures of titania (TiO2) have been widely investigated for a number of medical applications including implants and drug delivery. Although titania is extensively used in the food, drug and cosmetic industries, biocompatibility of nanoscale titania is still under careful scrutiny due to the conflicting reports on its interaction with cellular matter. For an accurate insight, we performed in vitro studies on the response of human dermal fibroblast cells toward pristine titania nanotubes fabricated by anodic oxidation. The nanotubes at low concentrations were seen to induce toxicity to the cells, whereas at higher concentrations the cell vitality remained on par with controls. Further investigations revealed an increase in the G0 phase cell population depicting that majority of cells were in the resting rather than active phase. Though the mitochondrial set-up did not exhibit any signs of stress, significantly enhanced reactive oxygen species production in the nuclear compartment was noted. The TiO2 nanotubes were believed to have gained access to the nuclear machinery and caused increased stress leading to genotoxicity. This interesting property of the nanotubes could be utilized to kill cancer cells, especially if the nanotubes are functionalized for a specific target, thus eliminating the need for any chemotherapeutic agents.
Post-polyploidisation morphotype diversification associates with gene copy number variation
Authors: Schiessl Sarah , Huettel Bruno , Kuehn Diana , Reinhardt Richard , Snowdon Rod
Published: February 2017

Genetic models for polyploid crop adaptation provide important information relevant for future breeding prospects. A well-suited model is Brassica napus, a recent allopolyploid closely related to Arabidopsis thaliana. Flowering time is a major adaptation trait determining life cycle synchronization with the environment. Here we unravel natural genetic variation in B. napus flowering time regulators and investigate associations with evolutionary diversification into different life cycle morphotypes. Deep sequencing of 35 flowering regulators was performed in 280 diverse B. napus genotypes. High sequencing depth enabled high-quality calling of single-nucleotide polymorphisms (SNPs), insertion-deletions (InDels) and copy number variants (CNVs). By combining these data with genotyping data from the Brassica 60 K Illumina® Infinium SNP array, we performed a genome-wide marker distribution analysis across the 4 ecogeographical morphotypes. Twelve haplotypes, including Bna.FLC.A10, Bna.VIN3.A02 and the Bna.FT promoter on C02_random, were diagnostic for the diversification of winter and spring types. The subspecies split between oilseed/kale (B. napus ssp. napus) and swedes/rutabagas (B. napus ssp. napobrassica) was defined by 13 haplotypes, including genomic rearrangements encompassing copies of Bna.FLC, Bna.PHYA and Bna.GA3ox1. De novo variation in copies of important flowering-time genes in B. napus arose during allopolyploidisation, enabling sub-functionalisation that allowed different morphotypes to appropriately fine-tune their lifecycle.
Implementation of a method to visualize noise-induced hearing loss in mass stranded cetaceans
Authors: Morell Maria , Brownlow Andrew , McGovern Barry , Raverty Stephen A. , Shadwick Robert E. , André Michel
Published: February 2017

Assessment of the impact of noise over-exposure in stranded cetaceans is challenging, as the lesions that lead to hearing loss occur at the cellular level and inner ear cells are very sensitive to autolysis. Distinguishing ante-mortem pathology from post-mortem change has been a major constraint in diagnosing potential impact. Here, we outline a methodology applicable to the detection of noise-induced hearing loss in stranded cetaceans. Inner ears from two mass strandings of long-finned pilot whales in Scotland were processed for scanning electron microscopy observation. In one case, a juvenile animal, whose ears were fixed within 4 hours of death, revealed that many sensory cells at the apex of the cochlear spiral were missing. In this case, the absence of outer hair cells would be compatible with overexposure to underwater noise, affecting the region which transduces the lowest frequencies of the pilot whales hearing spectrum. Perfusion of cochlea with fixative greatly improved preservation and enabled diagnostic imaging of the organ of Corti, even 30 hours after death. This finding supports adopting a routine protocol to detect the pathological legacy of noise overexposure in mass stranded cetaceans as a key to understanding the complex processes and implications that lie behind such stranding events.
Modulation of Microglial Cell Fcγ Receptor Expression Following Viral Brain Infection
Authors: Chauhan Priyanka , Hu Shuxian , Sheng Wen S. , Prasad Sujata , Lokensgard James R.
Published: February 2017

Fcγ receptors (FcγRs) for IgG couple innate and adaptive immunity through activation of effector cells by antigen-antibody complexes. We investigated relative levels of activating and inhibitory FcγRs on brain-resident microglia following murine cytomegalovirus (MCMV) infection. Flow cytometric analysis of microglial cells obtained from infected brain tissue demonstrated that activating FcγRs were expressed maximally at 5 d post-infection (dpi), while the inhibitory receptor (FcγRIIB) remained highly elevated during both acute and chronic phases of infection. The highly induced expression of activating FcγRIV during the acute phase of infection was also noteworthy. Furthermore,in vitroanalysis using cultured primary microglia demonstrated the role of interferon (IFN)γ and interleukin (IL)-4 in polarizing these cells towards a M1 or M2 phenotype, respectively. Microglial cell-polarization correlated with maximal expression of either FcγRIV or FcγRIIB following stimulation with IFNγ or IL-4, respectively. Finally, we observed a significant delay in polarization of microglia towards an M2 phenotype in the absence of FcγRs in MCMV-infected Fcer1g and FcgR2b knockout mice. These studies demonstrate that neuro-inflammation following viral infection increases expression of activating FcγRs on M1-polarized microglia. In contrast, expression of the inhibitory FcγRIIB receptor promotes M2-polarization in order to shut-down deleterious immune responses and limit bystander brain damage.
Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity
Authors: Kuhn Benjamin M. , Nodzyński Tomasz , Errafi Sanae , Bucher Rahel , Gupta Shibu , Aryal Bibek , Dobrev Petre , Bigler Laurent , Geisler Markus , Zažímalová Eva , Friml Jiří , Ringli Christoph
Published: February 2017

The phytohormone auxin is a major determinant and regulatory component important for plant development. Auxin transport between cells is mediated by a complex system of transporters such as AUX1/LAX, PIN, and ABCB proteins, and their localization and activity is thought to be influenced by phosphatases and kinases. Flavonols have been shown to alter auxin transport activity and changes in flavonol accumulation in the Arabidopsis thaliana rol1-2 mutant cause defects in auxin transport and seedling development. A new mutation in ROOTS CURL IN NPA 1 (RCN1), encoding a regulatory subunit of the phosphatase PP2A, was found to suppress the growth defects of rol1-2 without changing the flavonol content. rol1-2 rcn1-3 double mutants show wild type-like auxin transport activity while levels of free auxin are not affected by rcn1-3. In the rol1-2 mutant, PIN2 shows a flavonol-induced basal-to-apical shift in polar localization which is reversed in the rol1-2 rcn1-3 to basal localization. In vivo analysis of PINOID action, a kinase known to influence PIN protein localization in a PP2A-antagonistic manner, revealed a negative impact of flavonols on PINOID activity. Together, these data suggest that flavonols affect auxin transport by modifying the antagonistic kinase/phosphatase equilibrium.
A Noise Trimming and Positional Significance of Transposon Insertion System to Identify Essential Genes in Yersinia pestis
Authors: Yang Zheng Rong , Bullifent Helen L. , Moore Karen , Paszkiewicz Konrad , Saint Richard J. , Southern Stephanie J. , Champion Olivia L. , Senior Nicola J. , Sarkar-Tyson Mitali , Oyston Petra C. F. , Atkins Timothy P. , Titball Richard W.
Published: February 2017

Massively parallel sequencing technology coupled with saturation mutagenesis has provided new and global insights into gene functions and roles. At a simplistic level, the frequency of mutations within genes can indicate the degree of essentiality. However, this approach neglects to take account of the positional significance of mutations - the function of a gene is less likely to be disrupted by a mutation close to the distal ends. Therefore, a systematic bioinformatics approach to improve the reliability of essential gene identification is desirable. We report here a parametric model which introduces a novel mutation feature together with a noise trimming approach to predict the biological significance of Tn5 mutations. We show improved performance of essential gene prediction in the bacterium Yersinia pestis, the causative agent of plague. This method would have broad applicability to other organisms and to the identification of genes which are essential for competitiveness or survival under a broad range of stresses.
High-throughput sequencing of multiple amplicons for barcoding and integrative taxonomy
Authors: Cruaud Perrine , Rasplus Jean-Yves , Rodriguez Lillian Jennifer , Cruaud Astrid
Published: February 2017

Until now, the potential of NGS for the construction of barcode libraries or integrative taxonomy has been seldom realised. Here, we amplified (two-step PCR) and simultaneously sequenced (MiSeq) multiple markers from hundreds of fig wasp specimens. We also developed a workflow for quality control of the data. Illumina and Sanger sequences accumulated in the past years were compared. Interestingly, primers and PCR conditions used for the Sanger approach did not require optimisation to construct the MiSeq library. After quality controls, 87% of the species (76% of the specimens) had a valid MiSeq sequence for each marker. Importantly, major clusters did not always correspond to the targeted loci. Nine specimens exhibited two divergent sequences (up to 10%). In 95% of the species, MiSeq and Sanger sequences obtained from the same sampling were similar. For the remaining 5%, species were paraphyletic or the sequences clustered into divergent groups on the Sanger + MiSeq trees (>7%). These problematic cases may represent coding NUMTS or heteroplasms. Our results illustrate that Illumina approaches are not artefact-free and confirm that Sanger databases can contain non-target genes. This highlights the importance of quality controls, working with taxonomists and using multiple markers for DNA-taxonomy or species diversity assessment.
Lead-free piezoelectrics: V3+ to V5+ ion conversion promoting the performances of V-doped Zinc Oxide
Authors: Laurenti M. , Castellino M. , Perrone D. , Asvarov A. , Canavese G. , Chiolerio A.
Published: February 2017

Vanadium doped ZnO (VZO) thin films were grown by RF magnetron sputtering, starting from a ZnO:V ceramic target. The crystal structure, chemical composition, electric and piezoelectric properties of the films were investigated either on the as-grown thin films or after a post-deposition rapid thermal annealing (RTA) treatment performed at 600 °C for different lengths of time (1 and 5 min) in an oxygen atmosphere. Substitutional doping of Zn2+ with V3+ and V5+ ions strongly deteriorated the hexagonal wurtzite ZnO structure of the as-grown thin films due to lattice distortion. The resulting slight amorphization led to a poor piezoelectric response and higher resistivity. After the RTA treatment, strong c-axis oriented VZO thin films were obtained, together with a partial conversion of the starting V3+ ions into V5+. The improvement of the crystal structure and the stronger polarity of both V3+ – O and V5+ – O chemical bonds, together with the corresponding easier rotation under the application of an external electric field, positively affected the piezoelectric response and increased conductivity. This was confirmed by closed-loop butterfly piezoelectric curves, by a maximum d33 piezoelectric coefficient of 85 pm·V−1, and also by ferroelectric switching domains with a well-defined polarization hysteresis curve, featuring a residual polarization of 12.5 μC∙cm−2.
Expression of human endogenous retrovirus-K is strongly associated with the basal-like breast cancer phenotype
Authors: Johanning Gary L. , Malouf Gabriel G. , Zheng Xiaofeng , Esteva Francisco J. , Weinstein John N. , Wang-Johanning Feng , Su Xiaoping
Published: February 2017

Human endogenous retroviruses (HERVs), which make up approximately 8% of the human genome, are overexpressed in some breast cancer cells and tissues but without regard to cancer subtype. We, therefore, analyzed TCGA RNA-Seq data to evaluate differences in expression of the HERV-K family in breast cancers of the various subtypes. Four HERV-K loci on different chromosomes were analyzed in basal, Her2E, LumA, and LumB breast cancer subtypes of 512 breast cancer patients with invasive ductal carcinoma (IDC). The results for all four loci showed higher HERV-K expression in the basal subtype, suggesting similar mechanisms of regulation regardless of locus. Expression of the HERV-K envelope gene (env) was highly significantly increased in basal tumors in comparison with the also-upregulated expression of other HERV-K genes. Analysis of reverse-phase protein array data indicated that increased expression of HERV-K is associated with decreased mutation of H-Ras (wild-type). Our results show elevation of HERV-K expression exclusively in the basal subtype of IDC breast cancer (as opposed to the other subtypes) and suggest HERV-K as a possible target for cancer vaccines or immunotherapy against this highly aggressive form of breast cancer.
Electromagnetic Tunneling and Resonances in Pseudochiral Omega Slabs
Authors: Razzaz Faroq , Alkanhal Majeed A. S.
Published: February 2017

This paper presents theoretical investigation of the electromagnetic wave tunneling and anomalous transmission around the trapped modes in a pseudochiral omega slab. The dispersion relation, the conditions of the trapped modes, and the evanescent wave coupling and tunneling in two different reciprocal pseudochiral omega slab structures are derived. The Berreman’s matrix method is applied to obtain the transmission coefficients across the pseudochiral omega slab. When the structure is perturbed, a resonance phenomenon is detected around the trapped modes. This resonance results in transmission anomalies (total transmission and total reflection) and dramatic field amplifications around the trapped modes. The number of the discrete trapped modes and then the resonance frequencies are prescribed by the parameters of the pseudochiral omega slab such as the value of the omega parameter and its orientation and the slab thickness.
Micheliolide provides protection of mice against Staphylococcus aureus and MRSA infection by down-regulating inflammatory response
Authors: Jiang Xinru , Wang Yuli , Qin Yifei , He Weigang , Benlahrech Adel , Zhang Qingwen , Jiang Xin , Lu Zhenhui , Ji Guang , Zheng Yuejuan
Published: February 2017

A major obstacle to therapy in intensive care units is sepsis caused by severe infection. In recent years gram-positive (G+) bacteria, most commonly staphylococci, are thought to be the main pathogens. Micheliolide (MCL) was demonstrated to provide a therapeutic role in rheumatoid arthritis, inflammatory intestinal disease, colitis-associated cancer, and lipopolysaccharide (LPS, the main component of G−bacterial cell wall) induced septic shock. We proved here that MCL played an anti-inflammatory role inStaphylococcus aureus (S. aureus) and methicillin-resistantS. aureus(MRSA) induced peritonitis. It inhibited the expression of inflammatory cytokines and chemokines in macrophages and dendritic cells upon stimulation with peptidoglycan (PGN, the main cell wall composition of G+bacteria). PI3K/Akt and NF-κB pathways account for the anti-inflammatory role of MCL after PGN stimulation. MCL reduced IL-6 secretion through down-regulating NF-κB activation and improved the survival status in mice challenged with a lethal dose ofS. aureus. In MRSA infection mouse model, MCL down-regulated the expression of IL-6, TNF-α, MCP-1/CCL2 and IFN-γ in sera, and ameliorated the organ damage of liver and kidney. In conclusion, MCL can help maintain immune equilibrium and decrease PGN,S. aureusand MRSA-triggered inflammatory response. These provide the rationality for the potential usage of MCL in sepsis caused by G+bacteria (e.g.,S. aureus) and antibiotic-resistant bacteria (e.g., MRSA).
Magnetic Lifshitz transition and its consequences in multi-band iron-based superconductors
Authors: Ptok Andrzej , Kapcia Konrad J. , Cichy Agnieszka , Oleś Andrzej M. , Piekarz Przemysław
Published: February 2017

In this paper we address Lifshitz transition induced by applied external magnetic field in a case of iron-based superconductors, in which a difference between the Fermi level and the edges of the bands is relatively small. We introduce and investigate a two-band model with intra-band pairing in the relevant parameters regime to address a generic behaviour of a system with hole-like and electron-like bands in external magnetic field. Our results show that two Lifshitz transitions can develop in analysed systems and the first one occurs in the superconducting phase and takes place at approximately constant magnetic field. The chosen sets of the model parameters can describe characteristic band structure of iron-based superconductors and thus the obtained results can explain the experimental observations in FeSe and Co-doped BaFe2As2 compounds.
Insights into structure and activity of natural compound inhibitors of pneumolysin
Authors: Li Hongen , Zhao Xiaoran , Deng Xuming , Wang Jianfeng , Song Meng , Niu Xiaodi , Peng Liping
Published: February 2017

Pneumolysin is the one of the major virulence factor of the bacterium Streptococcus pneumoniae. In previous report, it is shown that β-sitosterol, a natural compound without antimicrobial activity, is a potent antagonist of pneumolysin. Here, two new pneumolysin natural compound inhibitors, with differential activity, were discovered via haemolysis assay. To explore the key factor of the conformation for the inhibition activity, the interactions between five natural compound inhibitors with differential activity and pneumolysin were reported using molecular modelling, the potential of mean force profiles. Interestingly, it is found that incorporation of the single bond (C22-C23-C24-C25) to replace the double bond (hydrocarbon sidechain) improved the anti-haemolytic activity. In view of the molecular modelling, binding of the five inhibitors to the conserved loop region (Val372, Leu460, and Tyr461) of the cholesterol binding sites led to stable complex systems, which was consistent with the result of β-sitosterol. Owing to the single bond (C22-C23-C24-C25), campesterol and brassicasterol could form strong interactions with Val372 and show higher anti-haemolytic activity, which indicated that the single bond (C22-C23-C24-C25) in inhibitors was required for the anti-haemolytic activity. Overall, the current molecular modelling work provides a starting point for the development of rational design and higher activity pneumolysin inhibitors.
Microbial nitrification, denitrification and respiration in the leached cinnamon soil of the upper basin of Miyun Reservoir
Authors: Xu Wen , Cai Yan-Peng , Yang Zhi-Feng , Yin Xin-An , Tan Qian
Published: February 2017

Leached cinnamon soil is the main agricultural soil distributed in the North China Plain. In this research, leached cinnamon soil samples were collected in the upper basin of Miyun Reservoir (northeast of Beijing, China). The BaPS method (Barometric Process Separation) was applied to measure nitrification, denitrification and respiration rates. The rates of nitrification, denitrification and respiration were 0–120.35 μg N/kg SDW h, 0–246.86 μg N/kg SDW h and 0.17–225.85 μg C/kg SDW h (Soil Dry Weight, SDW), respectively. The emission rates of CO2 and NxOy through nitrification, denitrification and respiration were 1.00–547.80 and 6.00–4850.65 μmol/h, respectively. The analysis of relationships between nitrification, denitrification and respiration rates indicated that these three microbial processes were interacted, which posed impacts on soil nitrogen availability. As indicated by the results, C:N ratio coupled with "Equation missing" content could be taken as the indicators of "Equation missing" content, which is usually the predominant form of N available to plants growing in soil. Results showed that "Equation missing" content was the highest (i.e., >62.4 mg/kg) when C:N ratio was 5.30–8.40, meanwhile "Equation missing" content was 3.71–4.39 mg/kg. Nevertheless, "Equation missing" content was the lowest (i.e., <6.40 mg/kg) when C:N ratio was 9.2–12.10, meanwhile "Equation missing" content was 3.41–4.35 mg/kg.
The Demographic Features, Clinicopathological Characteristics and Cancer-specific Outcomes for Patients with Microinvasive Breast Cancer: A SEER Database Analysis
Authors: Wang Wenna , Zhu Wenjie , Du Feng , Luo Yang , Xu Binghe
Published: February 2017

To investigate the clinicopathological characteristics and survival outcomes of microinvasive breast cancer, we conducted an observational study of female diagnosed with DCIS or DCIS with microinvasion (DCISM) from 1990 to 2012 using the Surveillance, Epidemiology, and End Results (SEER) database. There were 87695 DCIS and 8863 DCISM identified. In DCISM group, patients appeared to be younger and more black patients were identified in comparison with DCIS group. Furthermore, DCISM was associated with more aggressive tumor characteristics like higher rates of oestrogen receptor (ER) and progesterone receptor (PR) negativity, HER2 positivity, and lymph node metastasis. With a median follow-up of 91 months, patients with DCISM had worse cancer-specific survival (CSS) (hazard ratio [HR], 2.475; P < 0.001) and overall survival (OS) (HR, 1.263; P < 0.001). In the multivariable analysis, microinvasion was an independent prognostic factor for worse CSS (HR, 1.919; P < 0.001) and OS (HR, 1.184; P < 0.001). The 10-year cancer-specific mortality rate was 1.49% in DCIS and 4.08% in DCISM (HR, 2.771; P < 0.001). The 20-year cancer-specific mortality rate was 4.00% in DCIS and 9.65% in DCISM (HR, 2.482; P < 0.001). Deepening understanding of the nature of microinvasive breast cancer will be valuable for clinical treatment recommendations.
A universal computational model for predicting antigenic variants of influenza A virus based on conserved antigenic structures
Authors: Peng Yousong , Wang Dayan , Wang Jianhong , Li Kenli , Tan Zhongyang , Shu Yuelong , Jiang Taijiao
Published: February 2017

Rapid determination of the antigenicity of influenza A virus could help identify the antigenic variants in time. Currently, there is a lack of computational models for predicting antigenic variants of some common hemagglutinin (HA) subtypes of influenza A viruses. By means of sequence analysis, we demonstrate here that multiple HA subtypes of influenza A virus undergo similar mutation patterns of HA1 protein (the immunogenic part of HA). Further analysis on the antigenic variation of influenza A virus H1N1, H3N2 and H5N1 showed that the amino acid residues’ contribution to antigenic variation highly differed in these subtypes, while the regional bands, defined based on their distance to the top of HA1, played conserved roles in antigenic variation of these subtypes. Moreover, the computational models for predicting antigenic variants based on regional bands performed much better in the testing HA subtype than those did based on amino acid residues. Therefore, a universal computational model, named PREDAV-FluA, was built based on the regional bands to predict the antigenic variants for all HA subtypes of influenza A viruses. The model achieved an accuracy of 0.77 when tested with avian influenza H9N2 viruses. It may help for rapid identification of antigenic variants in influenza surveillance.
Bet-hedging in bacteriocin producing Escherichia coli populations: the single cell perspective
Authors: Bayramoglu Bihter , Toubiana David , van Vliet Simon , Inglis R. Fredrik , Shnerb Nadav , Gillor Osnat
Published: February 2017

Production of public goods in biological systems is often a collaborative effort that may be detrimental to the producers. It is therefore sustainable only if a small fraction of the population shoulders the cost while the majority reap the benefits. We modelled this scenario using Escherichia coli populations producing colicins, an antibiotic that kills producer cells’ close relatives. Colicin expression is a costly trait, and it has been proposed that only a small fraction of the population actively expresses the antibiotic. Colicinogenic populations were followed at the single-cell level using time-lapse microscopy, and showed two distinct, albeit dynamic, subpopulations: the majority silenced colicin expression, while a small fraction of elongated, slow-growing cells formed colicin-expressing hotspots, placing a significant burden on expressers. Moreover, monitoring lineages of individual colicinogenic cells showed stochastic switching between expressers and non-expressers. Hence, colicin expressers may be engaged in risk-reducing strategies—or bet-hedging—as they balance the cost of colicin production with the need to repel competitors. To test the bet-hedging strategy in colicin-mediated interactions, competitions between colicin-sensitive and producer cells were simulated using a numerical model, demonstrating a finely balanced expression range that is essential to sustaining the colicinogenic population.
Dissociation and Ionization of Quasi-Periodically Vibrating H2+ in Intense Few-Cycle Mid-Infrared Laser Fields
Authors: Jiang Shicheng , Yu Chao , Yuan Guanglu , Wu Tong , Lu Ruifeng
Published: February 2017

Using quantum mechanics calculations, we theoretically study the dissociation and ionization dynamics of the hydrogen-molecule ion in strong laser fields. Having prepared the nuclear wave packet of H2+ in a specific vibrational state, a pump laser is used to produce a vibrational excitation, leading to quasi-periodical vibration without ionization. Then, a time-delayed few-cycle laser is applied to trigger the dissociation or ionization of H2+. Both the time delay and the intensity of the probe laser alter the competition between dissociation and ionization. We also explore the dependence of kinetic-energy release spectra of fragments on the time delay, showing that the channels of above-threshold dissociation and below-threshold dissociation are opened and closed periodically. Also, dissociation from different channels is influenced by nuclear motion. The dissociation mechanism has been described in detail using the Floquet picture. This work provides a useful method for steering the electronic and nuclear dynamics of diatomic molecules in intense laser fields.
Combined analysis of mRNA and miRNA identifies dehydration and salinity responsive key molecular players in citrus roots
Authors: Xie Rangjin , Zhang Jin , Ma Yanyan , Pan Xiaoting , Dong Cuicui , Pang Shaoping , He Shaolan , Deng Lie , Yi Shilai , Zheng Yongqiang , Lv Qiang
Published: February 2017

Citrus is one of the most economically important fruit crops around world. Drought and salinity stresses adversely affected its productivity and fruit quality. However, the genetic regulatory networks and signaling pathways involved in drought and salinity remain to be elucidated. With RNA-seq and sRNA-seq, an integrative analysis of miRNA and mRNA expression profiling and their regulatory networks were conducted using citrus roots subjected to dehydration and salt treatment. Differentially expressed (DE) mRNA and miRNA profiles were obtained according to fold change analysis and the relationships between miRNAs and target mRNAs were found to be coherent and incoherent in the regulatory networks. GO enrichment analysis revealed that some crucial biological processes related to signal transduction (e.g. ‘MAPK cascade’), hormone-mediated signaling pathways (e.g. abscisic acid- activated signaling pathway’), reactive oxygen species (ROS) metabolic process (e.g. ‘hydrogen peroxide catabolic process’) and transcription factors (e.g., ‘MYB, ZFP and bZIP’) were involved in dehydration and/or salt treatment. The molecular players in response to dehydration and salt treatment were partially overlapping. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-seq and sRNA-seq analysis. This study provides new insights into the molecular mechanisms how citrus roots respond to dehydration and salt treatment.
Microbial Typing by Machine Learned DNA Melt Signatures
Authors: Andini Nadya , Wang Bo , Athamanolap Pornpat , Hardick Justin , Masek Billie J. , Thair Simone , Hu Anne , Avornu Gideon , Peterson Stephen , Cogill Steven , Rothman Richard E. , Carroll Karen C. , Gaydos Charlotte A. , Wang Jeff Tza-Huei , Batzoglou Serafim , Yang Samuel
Published: February 2017

There is still an ongoing demand for a simple broad-spectrum molecular diagnostic assay for pathogenic bacteria. For this purpose, we developed a single-plex High Resolution Melt (HRM) assay that generates complex melt curves for bacterial identification. Using internal transcribed spacer (ITS) region as the phylogenetic marker for HRM, we observed complex melt curve signatures as compared to 16S rDNA amplicons with enhanced interspecies discrimination. We also developed a novel Naïve Bayes curve classification algorithm with statistical interpretation and achieved 95% accuracy in differentiating 89 bacterial species in our library using leave-one-out cross-validation. Pilot clinical validation of our method correctly identified the etiologic organisms at the species-level in 59 culture-positive mono-bacterial blood culture samples with 90% accuracy. Our findings suggest that broad bacterial sequences may be simply, reliably and automatically profiled by ITS HRM assay for clinical adoption.
Light-sheet fluorescence imaging to localize cardiac lineage and protein distribution
Authors: Ding Yichen , Lee Juhyun , Ma Jianguo , Sung Kevin , Yokota Tomohiro , Singh Neha , Dooraghi Mojdeh , Abiri Parinaz , Wang Yibin , Kulkarni Rajan P. , Nakano Atsushi , Nguyen Thao P. , Fei Peng , Hsiai Tzung K.
Published: February 2017

Light-sheet fluorescence microscopy (LSFM) serves to advance developmental research and regenerative medicine. Coupled with the paralleled advances in fluorescence-friendly tissue clearing technique, our cardiac LSFM enables dual-sided illumination to rapidly uncover the architecture of murine hearts over 10 by 10 by 10 mm3 in volume; thereby allowing for localizing progenitor differentiation to the cardiomyocyte lineage and AAV9-mediated expression of exogenous transmembrane potassium channels with high contrast and resolution. Without the steps of stitching image columns, pivoting the light-sheet and sectioning the heart mechanically, we establish a holistic strategy for 3-dimentional reconstruction of the “digital murine heart” to assess aberrant cardiac structures as well as the spatial distribution of the cardiac lineages in neonates and ion-channels in adults.
Novel flow cytometry approach to identify bronchial epithelial cells from healthy human airways
Authors: Maestre-Batlle Danay , Pena Olga M. , Hirota Jeremy A. , Gunawan Evelyn , Rider Christopher F. , Sutherland Darren , Alexis Neil E. , Carlsten Chris
Published: February 2017

Sampling various compartments within the lower airways to examine human bronchial epithelial cells (HBEC) is essential for understanding numerous lung diseases. Conventional methods to identify HBEC in bronchoalveolar lavage (BAL) and wash (BW) have throughput limitations in terms of efficiency and ensuring adequate cell numbers for quantification. Flow cytometry can provide high-throughput quantification of cell number and function in BAL and BW samples, while requiring low cell numbers. To date, a flow cytometric method to identify HBEC recovered from lower human airway samples is unavailable. In this study we present a flow cytometric method identifying HBEC as CD45 negative, EpCAM/pan-cytokeratin (pan-CK) double-positive population after excluding debris, doublets and dead cells from the analysis. For validation, the HBEC panel was applied to primary HBEC resulting in 98.6% of live cells. In healthy volunteers, HBEC recovered from BAL (2.3% of live cells), BW (32.5%) and bronchial brushing samples (88.9%) correlated significantly (p = 0.0001) with the manual microscopy counts with an overall Pearson correlation of 0.96 across the three sample types. We therefore have developed, validated, and applied a flow cytometric method that will be useful to interrogate the role of the respiratory epithelium in multiple lung diseases.
β1- and β2-adrenergic stimulation-induced electrogenic transport by human endolymphatic sac epithelium and its clinical implications
Authors: Kim Bo Gyung , Kim Jin Young , Jung JinSei , Moon In Seok , Yoon Joo-Heon , Choi Jae Young , Kim Sung Huhn
Published: February 2017

The endolymphatic sac (ES) is a cystic structure of the inner ear connected to the cochlea and vestibule, which plays a role in regulating ion homeostasis in inner ear fluid. Disruption of ion homeostasis can cause inner ear disorders with hearing loss and dizziness, such as Meniere’s disease. Herein, we found, for the first time, functional evidence for the involvement of β1- and β2-adrenergic receptors in apical electrogenic ion transport by human ES epithelium by using electrophysiological/pharmacological and molecular biological methods, which were dependent on K+ and Cl− ion transport. The apical electrogenic transport was absent or very weak in ES epithelia of patients with Meniere’s disease. These results suggested that adrenergic stimulation via β1- and β2-adrenergic receptors in the human ES was involved in regulation of inner ear fluid ion homeostasis and impairment of this response could be a pathological mechanism of Meniere’s disease.
Relationship between auxiliary gamma subunits and mallotoxin on BK channel modulation
Authors: Guan Xin , Li Qin , Yan Jiusheng
Published: February 2017

The large-conductance, calcium- and voltage-activated K+(BK) channel consists of the pore-forming α subunits (BKα) and auxiliary subunits. The auxiliary γ1-3 subunits potently modulate the BK channel by shifting its voltage-dependence of channel activation toward the hyperpolarizing direction by approximately 145 mV (γ1), 100 mV (γ2), and 50 mV (γ3). Mallotoxin is a potent small-molecule BK channel activator. We analyzed the relationship between mallotoxin and the γ subunits in their BK channel-activating effects in membrane patches excised from HEK-293 cells. We found that mallotoxin, when applied extracellularly, shifted the half-activation voltage (V1/2) of BKα channels by −72 mV. The channel-activating effect of mallotoxin was greatly attenuated in the presence of the γ1, γ2, or γ3 subunit, with resultant ΔV1/2 (+/− mallotoxin) values of −9, −28, or −15 mV, respectively. Most examined γ1 mutant subunits antagonized mallotoxin’s channel-activating effect in a manner that was largely dependent on its own modulatory function. However, mallotoxin caused an irreversible functional and structural disengagement of the γ1-F273S mutant from BK channels. We infer that the auxiliary γ subunit effectively interferes with mallotoxin on BK channel modulation via either a direct steric competition or an indirect allosteric influence on mallotoxin’s binding and action on BKα.
Highly branched photomechanical crystals
Authors: Al-Kaysi Rabih O. , Tong Fei , Al-Haidar Maram , Zhu Lingyan , Bardeen Christopher J.
Published: February 2017

Ultraviolet light exposure causes highly branched microcrystals of 4-fluoroanthracene-9-carboxylic acid to reversibly deform and manipulate objects on a surface.
Comparative analysis of triarylamine and phenothiazine sensitizer donor units in dye-sensitized solar cells
Authors: Chiykowski Valerie A. , Lam Brian , Du Chuan , Berlinguette Curtis P.
Published: February 2017

The performance of a homologous set of dyes that differ only in the donor fragments, namely phenothiazine (PTZ) and triarylamine (TPA) units, was evaluated in dye-sensitized solar cells (DSSCs).
Fast and slow excited-state intramolecular proton transfer in 3-hydroxychromone: a two-state story?
Authors: Perveaux Aurelie , Lorphelin Maxime , Lasorne Benjamin , Lauvergnat David
Published: February 2017

The photodynamics of 3-hydroxychromone in its first-excited singlet electronic state (bright state of ππ* character) is investigated with special emphasis given to two types of reaction pathways: the excited-state intramolecular-proton-transfer coordinate and the hydrogen-torsion coordinate linking the excitedcisandtransisomers.
Direct dual-template synthesis of HZSM-5 zeolite for enhanced p-xylene selectivity in toluene methylation with CH3Br
Authors: Xie Jun , Chen Lang , Wang Wu-Hui , Wang Peng , Au Chak-Tong , Yin Shuang-Feng
Published: February 2017

HZSM-5 catalysts of different crystal sizes directly synthesized by a single-step method using TPAOH and TEA as templates were characterized by XRD, SEM, N2 adsorption–desorption and NH3-TPD techniques.
The effect of collagen hydrolysates from silver carp (Hypophthalmichthys molitrix) skin on UV-induced photoaging in mice: molecular weight affects skin repair
Authors: Song Hongdong , Meng Mengfei , Cheng Xiaofeng , Li Bo , Wang Chengtao
Published: February 2017

LMCH exerted stronger beneficial effects on photoaging skin than HMCH and gelatin.
Determination of the temperature-dependent cell membrane permeabilities using microfluidics with integrated flow and temperature control
Authors: Fang Cifeng , Ji Fujun , Shu Zhiquan , Gao Dayong
Published: February 2017

We developed an integrated microfluidic platform for instantaneous flow and localized temperature control.
Disposable cartridge platform for rapid detection of viral hemorrhagic fever viruses
Authors: Scherr Steven M. , Freedman David S. , Agans Krystle N. , Rosca Alexandru , Carter Erik , Kuroda Melody , Fawcett Helen E. , Mire Chad E. , Geisbert Thomas W. , Ünlü M. Selim , Connor John H.
Published: February 2017

A capillary-flow based automated microfluidic system for multiplexed visualization of single viruses in serum.
A 3D microblade structure for precise and parallel droplet splitting on digital microfluidic chips
Authors: Dong Cheng , Jia Yanwei , Gao Jie , Chen Tianlan , Mak Pui-In , Vai Mang-I , Martins Rui P.
Published: February 2017

3D microblade structures were fabricated on digital microfluidic chips for precise and parallel droplet splitting of biological samples for disease diagnostics.
Significantly improving the efficiency of polymer solar cells through incorporating noncovalent conformational locks
Authors: Lv Lei , Wang Xiaofen , Dong Tao , Wang Xinlong , Wu Xiaoxi , Yang Lei , Huang Hui
Published: February 2017

The power conversion efficiency of polymer solar cells was significantly enhanced through introducing conformational locks into the backbone of polymers.
Green light-emitting 2-(1H-indol-3-yl)acetonitrile-based D–A fluorophores – a combined theoretical and experimental study
Authors: Muruganantham Subramanian , Nagarajan Natarajan , Velmurugan Gunasekaran , Prakash Asit , Katiyar Monica , Venuvanalingam Ponnambalam , Renganathan Rajalingam
Published: February 2017

A series of new fluorophores based on 2-(1H-indol-3-yl)acetonitrile incorporated with various polycyclic aromatic hydrocarbons, carbazole, pyridine, triphenylamine was synthesised and their optical, thermal, electrochemical properties were evaluated.
Downsizing metal–organic frameworks with distinct morphologies as cathode materials for high-capacity Li–O2 batteries
Authors: Yan Wenjuan , Guo Ziyang , Xu Huoshu , Lou Yongbing , Chen Jinxi , Li Qiaowei
Published: February 2017

By downsizing Co-MOF-74 crystals with distinct morphologies, high capacities were achieved when they were employed in Li–O2 batteries.
Microwave-assisted synthesis of chitosan biguanidine hydrochloride and its regulation on InsR and GLUT2 in insulin resistant HepG2 cells
Authors: Zhang Shengsheng , Zhang Hai , Wang Li , Liu Xiaofei , Wu Yuntang
Published: February 2017

CSGH increased glucose consumption of HepG2 cells by accelerating the expression of InsR and inhibiting the high-insulin-induced over-expression of GLUT2.
Fabrication of a silver octahedral nanoparticle-containing polycaprolactone nanocomposite for antibacterial bone scaffolds
Authors: Gao Yu , Hassanbhai Ammar Mansoor , Lim Jing , Wang Lianhui , Xu Chenjie
Published: February 2017

Ag octahedral nanoparticle-containing PCL nanocomposite scaffolds exhibit successful osteogenic differentiation of stem cells and localized antibacterial effects.
Conformational stabilization of isatin Schiff bases – biologically active chemical probes
Authors: Smirnov Andrey S. , Nikolaev Dmitriy N. , Gurzhiy Vlad V. , Smirnov Sergey N. , Suslonov Vitaliy S. , Garabadzhiu Alexander V. , Davidovich Pavel B.
Published: February 2017

Two ways of conformation stabilization for isatin Schiff bases (group of biologically active compounds) are reported here: complexation with metals that stabilize E-conformer and substitution in the 4th position of isatin core stabilizing Z-form.
Continuous synthesis of CuInS2 quantum dots
Authors: Akdas T. , Haderlein M. , Walter J. , Apeleo Zubiri B. , Spiecker E. , Peukert W.
Published: February 2017

The impact of reactor type on synthesis parameters and disperse properties.
Solution copolymerization of ethylene and propylene by salicylaldiminato-derived [O-NS]TiCl3/MAO catalysts: synthesis, characterization and reactivity ratio estimation
Authors: Yao Zhen , Ma Da-Feng , Xiao Zhi-xian , Yang Wen-long , Tu Yu-Xia , Cao Kun
Published: February 2017

Salicylaldiminato-derived [O-NS]TiCl3 is used in the copolymerization of ethylene and propylene in toluene solution with methylaluminoxane as the co-catalyst.
Magnetic Fe3O4@poly(propylene fumarate-co-ethylene glycol) core–shell biomaterials
Authors: Díez-Pascual Ana M. , Díez-Vicente Angel L.
Published: February 2017

MagP®-NH2/(P(PF-co-EG)) core–shell biocomposites show antibacterial activity and magnetic-field tunable mechanical properties, hence they could be used as scaffolds for soft-tissue replacement.
Solvent co-mediated synthesis of ultrathin BiOCl nanosheets with highly efficient visible-light photocatalytic activity
Authors: Li Xiaoyu , Zhu Chengzhou , Song Yang , Du Dan , Lin Yuehe
Published: February 2017

Ultrathin BiOCl nanosheets exhibit outstanding photocatalytic degradation of RhB solution under visible-light irradiation.
Terbium and holmium codoped yttrium phosphate as non-contact optical temperature sensors
Authors: Fang Hongwei , Wei Xiantao , Zhou Shaoshuai , Li Xinyue , Chen Yonghu , Duan Chang-Kui , Yin Min
Published: February 2017

A new sensing mechanism is presented and a high relative sensitivity is achieved in our sample YPO4:3.2%Tb3+,0.8%Ho3+.
Polypyrrole-modified CuS nanoprisms for efficient near-infrared photothermal therapy
Authors: Zhao Ruiyang , Sun Xiaoxia , Sun Jing , Wang Lei , Han Jishu
Published: February 2017

PPy-Modified CuS nanoprisms with intense near-infrared absorption, excellent biocompatibility and photothermal conversion performance, were applied to in vivo photothermal therapy.
Vertical Al2Se3/MoSe2 heterojunction on sapphire synthesized using ion beam
Authors: Tsai Hsu-Sheng , Liou Jhe-Wei , Wang Yi-Chung , Chen Chia-Wei , Chueh Yu-Lun , Hsiao Ching-Hung , Ouyang Hao , Woon Wei-Yen , Liang Jenq-Horng
Published: February 2017

The vertical Al2Se3/MoSe2 heterojunction on sapphire was first fabricated via an ion beam-assisted process.
Dispersion and soap-free emulsion polymerization of tert-butyl acrylate with the living character and controlled particle size mediated by cobalt porphyrin
Authors: Zhao Huanqin , Wang Baolong , Li Qingpan , Wang Liying , Sun Junmin , Zhang Yongfeng , Ji Lichun , Cao Zhenzhu
Published: February 2017

Living radical polymerization (LRP) oftert-butyl acrylate (tBA) was carried outviathe dispersion and soap-free emulsion polymerization mediated by cobalt porphyrin [cobalt tetramethoxyphenylporphyrin, (TMOP)Co(ii)].
Lithiation mechanisms and lithium storage capacity of reduced graphene oxide nanoribbons: a first-principles study
Authors: Lin Kun-Han , Kuo Chin-Lung
Published: February 2017

New findings on the lithiation mechanisms and the achievable Li capacity limits of various types of functional groups on the basal plane and those terminating the edge sites of graphene nanomaterials based on first-principles density functional theory calculations.