bluuebunny/crossref_metadata_2025 huggingface dataset:
Mutation of DNA Polymerase β R137Q Results in Retarded Embryo Development Due to Impaired DNA Base Excision Repair in Mice
Authors: Pan Feiyan , Zhao Jing , Zhou Ting , Kuang Zhihui , Dai Huifang , Wu Huan , Sun Hongfang , Zhou Xiaolong , Wu Xuping , Hu Zhigang , He Lingfeng , Shen Binghui , Guo Zhigang
Published: June 2016

DNA polymerase β (Pol β), a key enzyme in the DNA base excision repair (BER) pathway, is pivotal in maintaining the integrity and stability of genomes. One Pol β mutation that has been identified in tumors, R137Q (arginine to glutamine substitution), has been shown to lower polymerase activity and impair its DNA repair capacity. However, the exact functional deficiency associated with this polymorphism in living organisms is still unknown. Here, we constructed Pol β R137Q knock-in mice and found that homozygous knock-in mouse embryos were typically small in size and had a high mortality rate (21%). These embryonic abnormalities were caused by slow cell proliferation and increased apoptosis. In R137Q knock-in mouse embryos, the BER efficiency was severely impaired, which subsequently resulted in double-strand breaks (DSBs) and chromosomal aberrations. Furthermore, R137Q mouse embryo fibroblasts (MEFs) were more sensitive to DNA-damaging reagents, such as methyl methanesulfonate (MMS) and H2O2. They displayed a higher percentage of DSBs and were more likely to undergo apoptosis. Our results indicate that R137 is a key amino acid site that is essential for proper Pol β functioning in maintaining genomic stability and embryo development.
Growth of Co2FeAl Heusler alloy thin films on Si(100) having very small Gilbert damping by Ion beam sputtering
Authors: Husain Sajid , Akansel Serkan , Kumar Ankit , Svedlindh Peter , Chaudhary Sujeet
Published: June 2016

The influence of growth temperatureTs(300–773 K) on the structural phase ordering, static and dynamic magnetization behaviour has been investigated in ion beam sputtered full Heusler alloy Co2FeAl (CFA) thin films on industrially important Si(100) substrate. TheB2type magnetic ordering is established in these films based on the clear observation of the (200) diffraction peak. These ion beam sputtered CFA films possess very small surface roughness of the order of subatomic dimensions (<3 Å) as determined from the fitting of XRR spectra and also by AFM imaging. This is supported by the occurrence of distinct Kiessig fringes spanning over the whole scanning range (~4°) in the x-ray reflectivity (XRR) spectra. The Gilbert damping constant α and effective magnetization4πMeffare found to vary from 0.0053 ± 0.0002 to 0.0015 ± 0.0001 and 13.45 ± 00.03 kG to 14.03 ± 0.04 kG, respectively. These Co2FeAl films possess saturation magnetization ranging from 4.82 ± 0.09 to 5.22 ± 0.10 μB/f.u. consistent with the bulkL21-type ordering. A record low α-value of 0.0015 is obtained for Co2FeAl films deposited on Si substrate atTs ~ 573 K.
A high-resolution palaeoenvironmental record from carbonate deposits in the Roman aqueduct of Patara, SW Turkey, from the time of Nero
Authors: Passchier Cornelis , Sürmelihindi Gül , Spötl Christoph
Published: June 2016

An inscription on the supporting wall of the inverted siphon of the aqueduct of the ancient Roman city of Patara, SW Turkey, explains how the wall collapsed during an earthquake and was subsequently restored. Carbonate deposits formed inside the aqueduct channel show cyclic stable isotope changes representing 17 years of deposition. This sequence, together with the text of the inscription, allows dating the earthquake to 68 AD and the original inauguration of the aqueduct to the winter of 51/52 AD. Thus, the carbonate deposits represent a high-resolution record of palaeotemperature and precipitation for SW Turkey covering the complete reign of the Emperor Nero. The period shows a cooling and drying trend after an initial warm and more humid period, interrupted by a few anomalous years. These 2 cm of calcite highlight the significance of carbonate deposits in ancient water supply systems as a high-resolution archive for palaeoclimate, palaeoseismology and archaeology.
Spatially oriented plasmonic ‘nanograter’ structures
Authors: Liu Zhe , Cui Ajuan , Gong Zhijie , Li Hongqiang , Xia Xiaoxiang , Shen Tiehan H. , Li Junjie , Yang Haifang , Li Wuxia , Gu Changzhi
Published: June 2016

One of the key motivations in producing 3D structures has always been the realization of metamaterials with effective constituent properties that can be tuned in all propagation directions at various frequencies. Here, we report the investigation of spatially oriented “Nanograter” structures with orientation-dependent responses over a wide spectrum by focused-ion-beam based patterning and folding of thin film nanostructures. Au nano units of different shapes, standing along specifically designated orientations, were fabricated. Experimental measurements and simulation results show that such structures offer an additional degree of freedom for adjusting optical properties with the angle of inclination, in additional to the size of the structures. The response frequency can be varied in a wide range (8 μm–14 μm) by the spatial orientation (0°–180°) of the structures, transforming the response from magnetic into electric coupling. This may open up prospects for the fabrication of 3D nanostructures as optical interconnects, focusing elements and logic elements, moving toward the realization of 3D optical circuits.
One Step Quantum Key Distribution Based on EPR Entanglement
Authors: Li Jian , Li Na , Li Lei-Lei , Wang Tao
Published: June 2016

A novel quantum key distribution protocol is presented, based on entanglement and dense coding and allowing asymptotically secure key distribution. Considering the storage time limit of quantum bits, a grouping quantum key distribution protocol is proposed, which overcomes the vulnerability of first protocol and improves the maneuverability. Moreover, a security analysis is given and a simple type of eavesdropper’s attack would introduce at least an error rate of 46.875%. Compared with the “Ping-pong” protocol involving two steps, the proposed protocol does not need to store the qubit and only involves one step.
Responsive Guest Encapsulation of Dynamic Conjugated Microporous Polymers
Authors: Xu Lai , Li Youyong
Published: June 2016

The host-guest complexes of conjugated microporous polymers encapsulating C60 and dye molecules have been investigated systematically. The orientation of guest molecules inside the cavities, have different terms: inside the open cavities of the polymer, or inside the cavities formed by packing different polymers. The host backbone shows responsive dynamic behavior in order to accommodate the size and shape of incoming guest molecule or guest aggregates. Simulations show that the host-guest binding of conjugated polymers is stronger than that of non-conjugated polymers. This detailed study could provide a clear picture for the host-guest interaction for dynamic conjugated microporous polymers. The mechanism obtained could guide designing new conjugated microporous polymers.
Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions
Authors: Upadhyaya Bijaya , McCormack Lacey , Fardin-Kia Ali Reza , Juenemann Robert , Nichenametla Sailendra , Clapper Jeffrey , Specker Bonny , Dey Moul
Published: June 2016

Dietary modulation of the gut microbiota impacts human health. Here we investigated the hitherto unknown effects of resistant starch type 4 (RS4) enriched diet on gut microbiota composition and short-chain fatty acid (SCFA) concentrations in parallel with host immunometabolic functions in twenty individuals with signs of metabolic syndrome (MetS). Cholesterols, fasting glucose, glycosylated haemoglobin and proinflammatory markers in the blood as well as waist circumference and % body fat were lower post intervention in the RS4 group compared with the control group. 16S-rRNA gene sequencing revealed a differential abundance of 71 bacterial operational taxonomic units, including the enrichment of three Bacteroides species and one each of Parabacteroides, Oscillospira, Blautia, Ruminococcus, Eubacterium and Christensenella species in the RS4 group. Gas chromatography–mass spectrometry revealed higher faecal SCFAs, including butyrate, propionate, valerate, isovalerate and hexanoate after RS4-intake. Bivariate analyses showed RS4-specific associations of the gut microbiota with the host metabolic functions and SCFA levels. Here we show that dietary RS4 induced changes in the gut microbiota are linked to its biological activity in individuals with signs of MetS. These findings have potential implications for dietary guidelines in metabolic health management.
Quantifying cadherin mechanotransduction machinery assembly/disassembly dynamics using fluorescence covariance analysis
Authors: Vedula Pavan , Cruz Lissette A. , Gutierrez Natasha , Davis Justin , Ayee Brian , Abramczyk Rachel , Rodriguez Alexis J.
Published: June 2016

Quantifying multi-molecular complex assembly in specific cytoplasmic compartments is crucial to understand how cells use assembly/disassembly of these complexes to control function. Currently, biophysical methods like Fluorescence Resonance Energy Transfer and Fluorescence Correlation Spectroscopy provide quantitative measurements of direct protein-protein interactions, while traditional biochemical approaches such as sub-cellular fractionation and immunoprecipitation remain the main approaches used to study multi-protein complex assembly/disassembly dynamics. In this article, we validate and quantify multi-protein adherens junction complex assembly in situ using light microscopy and Fluorescence Covariance Analysis. Utilizing specific fluorescently-labeled protein pairs, we quantified various stages of adherens junction complex assembly, the multiprotein complex regulating epithelial tissue structure and function following de novo cell-cell contact. We demonstrate: minimal cadherin-catenin complex assembly in the perinuclear cytoplasm and subsequent localization to the cell-cell contact zone, assembly of adherens junction complexes, acto-myosin tension-mediated anchoring and adherens junction maturation following de novo cell-cell contact. Finally applying Fluorescence Covariance Analysis in live cells expressing fluorescently tagged adherens junction complex proteins, we also quantified adherens junction complex assembly dynamics during epithelial monolayer formation.
Microfluidics-based side view flow chamber reveals tether-to-sling transition in rolling neutrophils
Authors: Marki Alex , Gutierrez Edgar , Mikulski Zbigniew , Groisman Alex , Ley Klaus
Published: June 2016

Neutrophils rolling at high shear stress (above 6 dyn/cm2) form tethers in the rear and slings in the front. Here, we developed a novel photo-lithographically fabricated, silicone(PDMS)-based side-view flow chamber to dynamically visualize tether and sling formation. Fluorescently membrane-labeled mouse neutrophils rolled on P-selectin substrate at 10 dyn/cm2. Most rolling cells formed 5 tethers that were 2–30 μm long. Breaking of a single tether caused a reproducible forward microjump of the cell, showing that the tether was load-bearing. About 15% of all tether-breaking events resulted in slings. The tether-to-sling transition was fast (<100 ms) with no visible material extending above the rolling cell, suggesting a very low bending modulus of the tether. The sling downstream of the rolling cell aligned according to the streamlines before landing on the flow chamber. These new observations explain how slings form from tethers and provide insight into their biomechanical properties.
Temporal Lobe Epilepsy Alters Auditory-motor Integration For Voice Control
Authors: Li Weifeng , Chen Ziyi , Yan Nan , Jones Jeffery A. , Guo Zhiqiang , Huang Xiyan , Chen Shaozhen , Liu Peng , Liu Hanjun
Published: June 2016

Temporal lobe epilepsy (TLE) is the most common drug-refractory focal epilepsy in adults. Previous research has shown that patients with TLE exhibit decreased performance in listening to speech sounds and deficits in the cortical processing of auditory information. Whether TLE compromises auditory-motor integration for voice control, however, remains largely unknown. To address this question, event-related potentials (ERPs) and vocal responses to vocal pitch errors (1/2 or 2 semitones upward) heard in auditory feedback were compared across 28 patients with TLE and 28 healthy controls. Patients with TLE produced significantly larger vocal responses but smaller P2 responses than healthy controls. Moreover, patients with TLE exhibited a positive correlation between vocal response magnitude and baseline voice variability and a negative correlation between P2 amplitude and disease duration. Graphical network analyses revealed a disrupted neuronal network for patients with TLE with a significant increase of clustering coefficients and path lengths as compared to healthy controls. These findings provide strong evidence that TLE is associated with an atypical integration of the auditory and motor systems for vocal pitch regulation and that the functional networks that support the auditory-motor processing of pitch feedback errors differ between patients with TLE and healthy controls.
Multiple cone pathways are involved in photic regulation of retinal dopamine
Authors: Qiao Sheng-Nan , Zhang Zhijing , Ribelayga Christophe P. , Zhong Yong-Mei , Zhang Dao-Qi
Published: June 2016

Dopamine is a key neurotransmitter in the retina and plays a central role in the light adaptive processes of the visual system. The sole source of retinal dopamine is dopaminergic amacrine cells (DACs). We and others have previously demonstrated that DACs are activated by rods, cones and intrinsically photosensitive retinal ganglion cells (ipRGCs) upon illumination. However, it is still not clear how each class of photosensitive cells generates light responses in DACs. We genetically isolated cone function in mice to specifically examine the cone-mediated responses of DACs and their neural pathways. In addition to the reported excitatory input to DACs from light-increment (ON) bipolar cells, we found that cones alternatively signal to DACs via a retrograde signalling pathway from ipRGCs. Cones also produce ON and light-decrement (OFF) inhibitory responses in DACs, which are mediated by other amacrine cells, likely driven by type 1 and type 2/3a OFF bipolar cells, respectively. Dye injections indicated that DACs had similar morphological profiles with or without ON/OFF inhibition. Our data demonstrate that cones utilize specific parallel excitatory and inhibitory circuits to modulate DAC activity and efficiently regulate dopamine release and the light-adaptive state of the retina.
Lipidomic Signatures and Associated Transcriptomic Profiles of Clear Cell Renal Cell Carcinoma
Authors: Saito Kosuke , Arai Eri , Maekawa Keiko , Ishikawa Masaki , Fujimoto Hiroyuki , Taguchi Ryo , Matsumoto Kenji , Kanai Yae , Saito Yoshiro
Published: June 2016

Renal cell carcinoma (RCC) is the most common histological type of adult kidney cancer. In this study, we obtained lipidomic profiles of clear cell RCC (ccRCC), a major RCC subtype, by performing a lipidomic analysis of specimens of cancerous tissue and the surrounding normal renal cortex obtained from the same patients (N = 49). We also compared the lipidomic profiles with the lipogenic transcriptome of specimens of cancerous tissue and the surrounding normal renal cortex for an additional set of patient samples (N = 95). Overall, we detected 326 lipids, including phospholipids, sphingolipids, neutral lipids, and eicosanoids. The levels of more than 70% of the detected lipids were significantly different (P < 0.01, corrected by the false discovery rate). The cancerous tissue was distinguished by higher levels of ether-type phospholipids, cholesterol esters, and triacylglycerols, as well as by lower levels of phospholipids (except for phosphatidylcholines) and polyunsaturated fatty acids. Characteristic changes in the levels of mRNAs and metabolites suggested that the phosphatidylethanolamine (PE) synthesis pathway is suppressed in ccRCC and associated with cell proliferation. The present study represents the lipidomic profiles of ccRCC, which provides novel information about the metabolic changes in renal cancerous tissue and RCC pathophysiology.
The first characterization of multidrug and toxin extrusion (MATE/SLC47) proteins in zebrafish (Danio rerio)
Authors: Lončar Jovica , Popović Marta , Krznar Petra , Zaja Roko , Smital Tvrtko
Published: June 2016

Multidrug and toxin extrusion (MATE) proteins are involved in the extrusion of endogenous compounds and xenobiotics across the plasma membrane. They are conserved from bacteria to mammals, with different numbers of genes within groups. Here, we present the first data on identification and functional characterization of Mate proteins in zebrafish (Danio rerio). Phylogenetic analysis revealed six Mates in teleost fish, annotated as Mate3–8, which form a distinct cluster separated from the tetrapod MATEs/Mates. Synteny analysis showed that zebrafish mate genes are orthologous to human MATEs. Gene expression analysis revealed that all the mate transcripts were constitutively and differentially expressed during embryonic development, followed by pronounced and tissue-specific expression in adults. Functional analyses were performed using transport activity assays with model substrates after heterologous overexpression of five zebrafish Mates in HEK293T cells. The results showed that zebrafish Mates interact with both physiological and xenobiotic substances but also substantially differ with respect to the interacting compounds and interaction strength in comparison to mammalian MATEs/Mates. Taken together, our data clearly indicate a potentially important role for zebrafish Mate transporters in zebrafish embryos and adults and provide a basis for detailed functional characterizations of single zebrafish Mate transporters.
Quantitative and compositional responses of ammonia-oxidizing archaea and bacteria to long-term field fertilization
Authors: Xue Chao , Zhang Xu , Zhu Chen , Zhao Jun , Zhu Ping , Peng Chang , Ling Ning , Shen Qirong
Published: June 2016

Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM) and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.
Loss of cortactin causes endothelial barrier dysfunction via disturbed adrenomedullin secretion and actomyosin contractility
Authors: García Ponce Alexander , Citalán Madrid Alí F. , Vargas Robles Hilda , Chánez Paredes Sandra , Nava Porfirio , Betanzos Abigail , Zarbock Alexander , Rottner Klemens , Vestweber Dietmar , Schnoor Michael
Published: June 2016

Changes in vascular permeability occur during inflammation and the actin cytoskeleton plays a crucial role in regulating endothelial cell contacts and permeability. We demonstrated recently that the actin-binding protein cortactin regulates vascular permeability via Rap1. However, it is unknown if the actin cytoskeleton contributes to increased vascular permeability without cortactin. As we consistently observed more actin fibres in cortactin-depleted endothelial cells, we hypothesised that cortactin depletion results in increased stress fibre contractility and endothelial barrier destabilisation. Analysing the contractile machinery, we found increased ROCK1 protein levels in cortactin-depleted endothelium. Concomitantly, myosin light chain phosphorylation was increased while cofilin, mDia and ERM were unaffected. Secretion of the barrier-stabilising hormone adrenomedullin, which activates Rap1 and counteracts actomyosin contractility, was reduced in plasma from cortactin-deficient mice and in supernatants of cortactin-depleted endothelium. Importantly, adrenomedullin administration and ROCK1 inhibition reduced actomyosin contractility and rescued the effect on permeability provoked by cortactin deficiency in vitro and in vivo. Our data suggest a new role for cortactin in controlling actomyosin contractility with consequences for endothelial barrier integrity.
Transcriptome sequencing and marker development in winged bean (Psophocarpus tetragonolobus; Leguminosae)
Authors: Vatanparast Mohammad , Shetty Prateek , Chopra Ratan , Doyle Jeff J. , Sathyanarayana N. , Egan Ashley N.
Published: June 2016

Winged bean, Psophocarpus tetragonolobus (L.) DC., is similar to soybean in yield and nutritional value but more viable in tropical conditions. Here, we strengthen genetic resources for this orphan crop by producing a de novo transcriptome assembly and annotation of two Sri Lankan accessions (denoted herein as CPP34 [PI 491423] and CPP37 [PI 639033]), developing simple sequence repeat (SSR) markers and identifying single nucleotide polymorphisms (SNPs) between geographically separated genotypes. A combined assembly based on 804,757 reads from two accessions produced 16,115 contigs with an N50 of 889 bp, over 90% of which has significant sequence similarity to other legumes. Combining contigs with singletons produced 97,241 transcripts. We identified 12,956 SSRs, including 2,594 repeats for which primers were designed and 5,190 high-confidence SNPs between Sri Lankan and Nigerian genotypes. The transcriptomic data sets generated here provide new resources for gene discovery and marker development in this orphan crop and will be vital for future plant breeding efforts. We also analyzed the soybean trypsin inhibitor (STI) gene family, important plant defense genes, in the context of related legumes and found evidence for radiation of the Kunitz trypsin inhibitor (KTI) gene family within winged bean.
Temporal tuning in the bat auditory cortex is sharper when studied with natural echolocation sequences
Authors: Beetz M. Jerome , Hechavarría Julio C. , Kössl Manfred
Published: June 2016

Precise temporal coding is necessary for proper acoustic analysis. However, at cortical level, forward suppression appears to limit the ability of neurons to extract temporal information from natural sound sequences. Here we studied how temporal processing can be maintained in the bats’ cortex in the presence of suppression evoked by natural echolocation streams that are relevant to the bats’ behavior. We show that cortical neurons tuned to target-distance actually profit from forward suppression induced by natural echolocation sequences. These neurons can more precisely extract target distance information when they are stimulated with natural echolocation sequences than during stimulation with isolated call-echo pairs. We conclude that forward suppression does for time domain tuning what lateral inhibition does for selectivity forms such as auditory frequency tuning and visual orientation tuning. When talking about cortical processing, suppression should be seen as a mechanistic tool rather than a limiting element.
Tunnelling current-voltage characteristics of Angstrom gaps measured with terahertz time-domain spectroscopy
Authors: Kim Joon-Yeon , Kang Bong Joo , Bahk Young-Mi , Kim Yong Seung , Park Joohyun , Kim Won Tae , Rhie Jiyeah , Han Sanghoon , Jeon Hyeongtag , Park Cheol-Hwan , Rotermund Fabian , Kim Dai-Sik
Published: June 2016

Quantum tunnelling becomes inevitable as gap dimensions in metal structures approach the atomic length scale, and light passing through these gaps can be used to examine the quantum processes at optical frequencies. Here, we report on the measurement of the tunnelling current through a 3-Å-wide metal-graphene-metal gap using terahertz time-domain spectroscopy. By analysing the waveforms of the incident and transmitted terahertz pulses, we obtain the tunnelling resistivity and the time evolution of the induced current and electric fields in the gap and show that the ratio of the applied voltage to the tunnelling current is constant, i.e., the gap shows ohmic behaviour for the strength of the incident electric field up to 30 kV/cm. We further show that our method can be extended and applied to different types of nanogap tunnel junctions using suitable equivalent RLC circuits for the corresponding structures by taking an array of ring-shaped nanoslots as an example.
Iron overload by Superparamagnetic Iron Oxide Nanoparticles is a High Risk Factor in Cirrhosis by a Systems Toxicology Assessment
Authors: Wei Yushuang , Zhao Mengzhu , Yang Fang , Mao Yang , Xie Hang , Zhou Qibing
Published: June 2016

Superparamagnetic iron oxide nanoparticles (SPIONs) as a contrast agent have been widely used in magnetic resonance imaging for tumor diagnosis and theranostics. However, there has been safety concern of SPIONs with cirrhosis related to excess iron-induced oxidative stress. In this study, the impact of iron overload by SPIONs was assessed on a mouse cirrhosis model. A single dose of SPION injection at 0.5 or 5 mg Fe/kg in the cirrhosis group induced a septic shock response at 24 h with elevated serum levels of liver and kidney function markers and extended impacts over 14 days including high levels of serum cholesterols and persistent low serum iron level. In contrast, full restoration of liver functions was found in the normal group with the same dosages over time. Analysis with PCR array of the toxicity pathways revealed the high dose of SPIONs induced significant expression changes of a distinct subset of genes in the cirrhosis liver. All these results suggested that excess iron of the high dose of SPIONs might be a risk factor for cirrhosis because of the marked impacts of elevated lipid metabolism, disruption of iron homeostasis and possibly, aggravated loss of liver functions.
PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets
Authors: Dabdoub Shareef M. , Fellows Megan L. , Paropkari Akshay D. , Mason Matthew R. , Huja Sarandeep S. , Tsigarida Alexandra A. , Kumar Purnima S.
Published: June 2016

The 16S rRNA gene is widely used for taxonomic profiling of microbial ecosystems; and recent advances in sequencing chemistry have allowed extremely large numbers of sequences to be generated from minimal amounts of biological samples. Analysis speed and resolution of data to species-level taxa are two important factors in large-scale explorations of complex microbiomes using 16S sequencing. We present here new software, Phylogenetic Tools for Analysis of Species-level Taxa (PhyloToAST), that completely integrates with the QIIME pipeline to improve analysis speed, reduce primer bias (requiring two sequencing primers), enhance species-level analysis and add new visualization tools. The code is free and open source and can be accessed at http://phylotoast.org.
Determination of GLUT1 Oligomerization Parameters using Bioluminescent Förster Resonance Energy Transfer
Authors: Looyenga Brendan , VanOpstall Calvin , Lee Zion , Bell Jed , Lodge Evans , Wrobel Katherine , Arnoys Eric , Louters Larry
Published: June 2016

The facilitated glucose transporter GLUT1 (SLC2A1) is an important mediator of glucose homeostasis in humans. Though it is found in most cell types to some extent, the level of GLUT1 expression across different cell types can vary dramatically. Prior studies in erythrocytes—which express particularly high levels of GLUT1—have suggested that GLUT1 is able to form tetrameric complexes with enhanced transport activity. Whether dynamic aggregation of GLUT1 also occurs in cell types with more modest expression of GLUT1, however, is unclear. To address this question, we developed a genetically encoded bioluminescent Förster resonance energy transfer (BRET) assay using the luminescent donor Nanoluciferase and fluorescent acceptor mCherry. By tethering these proteins to the N-terminus of GLUT1 and performing saturation BRET analysis, we were able to demonstrate the formation of multimeric complexes in live cells. Parallel use of flow cytometry and immunoblotting further enabled us to estimate the density of GLUT1 proteins required for spontaneous oligomerization. These data provide new insights into the physiological relevance of GLUT1 multimerization as well as a new variant of BRET assay that is useful for measuring the interactions among other cell membrane proteins in live cells.
A HIV-Tat/C4-binding protein chimera encoded by a DNA vaccine is highly immunogenic and contains acute EcoHIV infection in mice
Authors: Tomusange Khamis , Wijesundara Danushka , Gummow Jason , Garrod Tamsin , Li Yanrui , Gray Lachlan , Churchill Melissa , Grubor-Bauk Branka , Gowans Eric J.
Published: June 2016

DNA vaccines are cost-effective to manufacture on a global scale and Tat-based DNA vaccines have yielded protective outcomes in preclinical and clinical models of human immunodeficiency virus (HIV), highlighting the potential of such vaccines. However, Tat-based DNA vaccines have been poorly immunogenic and despite the administration of multiple doses and/or the addition of adjuvants, these vaccines are not in general use. In this study, we improved Tat immunogenicity by fusing it with the oligomerisation domain of a chimeric C4-binding protein (C4b-p), termed IMX313, resulting in Tat heptamerisation and linked Tat to the leader sequence of tissue plasminogen activator (TPA) to ensure that the bulk of heptamerised Tat is secreted. Mice vaccinated with secreted Tat fused to IMX313 (pVAX-sTat-IMX313) developed higher titres of Tat-specific serum IgG, mucosal sIgA and cell-mediated immune (CMI) responses and showed superior control of EcoHIV infection, a surrogate murine HIV challenge model, compared with animals vaccinated with other test vaccines. Given the crucial contribution of Tat to HIV-1 pathogenesis and the precedent of Tat-based DNA vaccines in conferring some level of protection in animal models, we believe that the virologic control demonstrated with this novel multimerised Tat vaccine highlights the promise of this vaccine candidate for humans.
Graphene quantum dots decorated with Fe3O4 nanoparticles/functionalized multiwalled carbon nanotubes as a new sensing platform for electrochemical determination of l-DOPA in agricultural products
Authors: Arvand M. , Abbasnejad S. , Ghodsi N.
Published: June 2016

This paper describes the development and utilization of a new nanocomposite consisting of graphene quantum dots, magnetic nanoparticles and carboxylated multiwalled carbon nanotubes for glassy carbon electrode surface modification.
Facile construction of pyrrolo[1,2-b]isoquinolin-10(5H)-ones via a redox-amination–aromatization–Friedel–Crafts acylation cascade reaction and discovery of novel topoisomerase inhibitors
Authors: Wu Shanchao , Liu Na , Dong Guoqiang , Ma Lin , Wang Shengzheng , Shi Wencai , Fang Kun , Chen Shuqiang , Li Jian , Zhang Wannian , Sheng Chunquan , Wang Wei
Published: June 2016

The new title compounds with uncovered topoisomerase inhibitory activities are efficiently constructed via a redox-amination–aromatization–Friedel–Crafts acylation cascade reaction.
Exploring structural features of folded peptide architectures in the construction of nanomaterials
Authors: Misra Rajkumar , Reja Rahi M. , Narendra Lagumaddepalli V. , George Gijo , Raghothama Srinivasarao , Gopi Hosahudya N.
Published: June 2016

Supramolecular assemblies of conformationally biased α,γ-hybrid peptides composed of alternating α-Phe and 4,4-dimethyl substituted γ-amino acids are investigated.
A direct and sustainable synthesis of tertiary butyl esters enabled by flow microreactors
Authors: Degennaro Leonardo , Maggiulli Daniela , Carlucci Claudia , Fanelli Flavio , Romanazzi Giuseppe , Luisi Renzo
Published: June 2016

A straightforward synthesis of tertiary butyl esters enabled by flow microreactors is reported.
Trehalose-based Janus cyclooligosaccharides: the “Click” synthesis and DNA-directed assembly into pH-sensitive transfectious nanoparticles
Authors: Jiménez Blanco J. L. , Ortega-Caballero F. , Blanco-Fernández L. , Carmona T. , Marcelo G. , Martínez-Negro M. , Aicart E. , Junquera E. , Mendicuti F. , Tros de Ilarduya C. , Ortiz Mellet C. , García Fernández J. M.
Published: June 2016

Trehalose-based Janus cyclooligosaccharides undergo DNA-promoted self-assembling.
Three-dimensional nanotubes composed of carbon-anchored ultrathin MoS2 nanosheets with enhanced lithium storage
Authors: Yi Fenglian , Niu Yubin , Liu Sangui , Hou Junke , Bao Shujuan , Xu Maowen
Published: June 2016

MoS2 nanotubes (denoted as MoS2 NTs) assembled from well-aligned amorphous carbon-modified ultrathin MoS2 nanosheets (denoted as MoS2 NT@C) were successfully fabricated via a facile solvothermal method combined with subsequent annealing treatment.
Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure
Authors: Timoshenko Janis , Shivhare Atal , Scott Robert W. J. , Lu Deyu , Frenkel Anatoly I.
Published: June 2016

XANES analysis guided by ab initio modeling is proposed for refinement of local environments around metal impurities in heterogeneous catalysts.
Molecular design of light-harvesting photosensitizers: effect of varied linker conjugation on interfacial electron transfer
Authors: Jiang Jianbing , Swierk John R. , Hedström Svante , Matula Adam J. , Crabtree Robert H. , Batista Victor S. , Schmuttenmaer Charles A. , Brudvig Gary W.
Published: June 2016

Interfacial electron transfer dynamics of a series of photosensitizers bound to TiO2via linkers of varying conjugation strength are explored by spectroscopic and computational techniques.
A DFT study of molecular adsorption on Au–Rh nanoalloys
Authors: Demiroglu Ilker , Li Z. Y. , Piccolo Laurent , Johnston Roy L.
Published: June 2016

Density functional theory calculations are performed to investigate both mixing and adsorption properties of 38-atom and 79-atom Au–Rh nanoalloys at the nanoscale.
Understanding the hydrologic impacts of wastewater treatment plant discharge to shallow groundwater: before and after plant shutdown
Authors: Hubbard Laura E. , Keefe Steffanie H. , Kolpin Dana W. , Barber Larry B. , Duris Joseph W. , Hutchinson Kasey J. , Bradley Paul M.
Published: June 2016

WWTP cessation is a rare environmental event with far-ranging hydrologic effects. Results have implications for shallow-groundwater recharge and WWTP-derived contamination kilometers downstream from the outfall.
Malondialdehyde and 4-hydroxy-2-hexenal are formed during dynamic gastrointestinal in vitro digestion of cod liver oils
Authors: Larsson Karin , Tullberg Cecilia , Alminger Marie , Havenaar Robert , Undeland Ingrid
Published: June 2016

Lipid oxidation products are formed during dynamicin vitrodigestion of cod liver oil.
Novel triterpenoids isolated from raisins exert potent antiproliferative activities by targeting mitochondrial and Ras/Raf/ERK signaling in human breast cancer cells
Authors: Liu Juan , Wang Yihai , Liu Rui Hai , He Xiangjiu
Published: June 2016

Raisins are produced in many regions of the world and may be eaten raw or used in cooking, baking and brewing.
Membrane activity of a supramolecular peptide-based chemotherapeutic enhancer
Authors: Xu Dawei , Jiang Linhai , DeRidder Louis , Elmore Brendan , Bukhari Maurish , Wei Qiang , Samways Damien S. K. , Dong He
Published: June 2016

This work explored the membrane activity of filamentous supramolecular peptides and their great potential as a supramolecular peptide-based chemotherapeutic enhancer.
Two dpa-based zinc(ii) complexes as potential anticancer agents: nuclease activity, cytotoxicity and apoptosis studies
Authors: Zhang Yong-Po , Ma Zhong-Ying , Gao Chun-Yan , Qiao Xin , Tian Jin-Lei , Gu Wen , Liu Xin , Xu Jing-Yuan , Zhao Jin-Zhong , Yan Shi-Ping
Published: June 2016

Two new mononuclear Zn(ii)-PhMe-dpa complexes have been synthesized and the apoptosis-inducing activity of1was assessed by Hoechst 33342 staining, Annexin V binding and cell cycle experiments.
Silanated nano ZnO hybrid embedded PMMA polymer coatings on cotton fabrics for near-IR reflective, antifungal cool-textiles
Authors: Soumya S. , Kumar S. Nishanth , Mohamed A. Peer , Ananthakumar S.
Published: June 2016

Silanated nano ZnO hybrid embedded PMMA polymer coatings for cotton fabrics are developed to produce near-IR reflective, antifungal cool-textiles.
Metal-free homolytic hydrogen activation: a quest through density functional theory computations
Authors: Zhang Chenggen , Lv Xiangying , Lu Gang , Wang Zhi-Xiang
Published: June 2016

DFT computations reveal that heavier analogs of 1,3-butadiene could activate H2homolyticallyvia1,4-addition.
Structure–function relationships in single molecule rectification by N-phenylbenzamide derivatives
Authors: Koenigsmann Christopher , Ding Wendu , Koepf Matthieu , Batra Arunabh , Venkataraman Latha , Negre Christian F. A. , Brudvig Gary W. , Crabtree Robert H. , Batista Victor S. , Schmuttenmaer Charles A.
Published: June 2016

The trend in measured rectification ratios suggests that there is a strong correlation between rectification and the energy of the transmission state relative to the Fermi level.
Correction: Mutagenicity of N-acyloxy-N-alkoxyamides as an indicator of DNA intercalation part 1: evidence for naphthalene as a DNA intercalator
Authors: Banks Tony M. , Clay Samuel F. , Glover Stephen A. , Schumacher Rhiannon R.
Published: June 2016

Correction for ‘Mutagenicity of N-acyloxy-N-alkoxyamides as an indicator of DNA intercalation part 1: evidence for naphthalene as a DNA intercalator’ by Tony M. Banks, et al., Org. Biomol. Chem., 2016, 14, 3699–3714.
1,10-Phenanthroline-2,9-dicarboxamides as ligands for separation and sensing of hazardous metals
Authors: Alyapyshev M. , Ashina J. , Dar’in D. , Kenf E. , Kirsanov D. , Tkachenko L. , Legin A. , Starova G. , Babain V.
Published: June 2016

1,10-Phenanthroline-2,9-dicarboxamides of various structures were synthesized and studied as ligands for separation and sensing of d- and f-metals.
Gold nanoparticles as potent anticancer agent: green synthesis, characterization, and in vitro study
Authors: Kajani Abolghasem Abbasi , Bordbar Abdol-Khalegh , Zarkesh Esfahani Sayyed Hamid , Razmjou Amir
Published: June 2016

High quality colloidal gold nanoparticles with promising anticancer activity were synthesized using Taxus baccata extracts.
Nanoporous ZnO nanostructure synthesis by a facile method for superior sensitivity ethanol sensor applications
Authors: Phuong Nhung Nguyen Thi , Van Tong Pham , Hung Chu Manh , Van Duy Nguyen , Chien Nguyen Viet , Van Vinh Nguyen , Tuyen Nguyen Thai , Hoa Nguyen Duc
Published: June 2016

Nanoporous ZnO nanostructures prepared by thermal decomposition of plate-like hydrozincite showed superior sensitivity to ethanol for lung cancer diagnosis.
Core–shell composite of wood-derived biochar supported MnO2nanosheets for supercapacitor applications
Authors: Wan Caichao , Jiao Yue , Li Jian
Published: June 2016

Eco-friendly wood-derived biochar (WDB) was used as a substrate material to support sheet-like nano-MnO2viaan easily-operatedin situredox reaction between the biochar and KMnO4.
Hard-template synthesis of three-dimensional mesoporous Cu–Ce based catalysts with tunable architectures and their application in the CO catalytic oxidation
Authors: Li Liyan , Han Weiliang , Tang Zhicheng , Zhang Jiyi , Lu Gongxuan
Published: June 2016

In this paper, 3D Cu–Ce-Ox catalysts with different pores were synthesized by controlling the calcination temperaturre. The CeCu20-600 showed the highest catalytic activity, where CO can be fully oxidized at 55 °C and expressed good stability.
Molecular modeling of structural and functional variance in the SAGA deubiquitinating module caused by Sgf73 Y57A mutation
Authors: Chen Ya-Jyun , Yang Chia-Ning
Published: June 2016

Summary of the structural and dynamic impact caused by Sgf73 Y57A mutation.
Determining the substrate permeability through the bilayer of large unilamellar vesicles of DOPC. A kinetic study
Authors: Luna Maria Alejandra , Silber Juana J. , Sereno Leonides , Correa N. Mariano , Moyano Fernando
Published: June 2016

In this work we determine the permeability of DOPC vesicles in the presence of different cholesterol contents, by using the enzymatic hydrolysis of N-benzoyl-l-tyrosine p-nitroanilide catalyzed by α-chymotrypsin.
A novel nano-energetic system based on bismuth hydroxide
Authors: Hobosyan Mkhitar A. , Yolchinyan Srbuhi A. , Martirosyan Karen S.
Published: June 2016

We report the first study of gas generation and thermal wave behavior during the performance of a novel nano-energetic system based on aluminum and bismuth hydroxide Al–Bi(OH)3.
NaHS inhibits NF-κB signal against inflammation and oxidative stress in post-infectious irritable bowel syndrome
Authors: Yang Shenglan , Deng Danfang , Luo Yingying , Wu Yanran , Zhu Rui , Xue Kaming , Zhou Yanping
Published: June 2016

In this study, the alleviating role of hydrogen sulfide (H2S) was investigated in a Post-Infectious Irritable Bowel Syndrome (PI-IBS) murine model and Caco-2 cells.
Normal and reverse base pairing of Iz and Oz lesions in DNA: structural implications for mutagenesis
Authors: Jena N. R. , Mishra P. C.
Published: June 2016

During replication, incorporation of G opposite Oz lesion is mainly responsible for G to C mutations in DNA.
Ferrocenyl chiral bisphosphorus ligands for highly enantioselective asymmetric hydrogenation via noncovalent ion pair interaction
Authors: Chen Caiyou , Wang Heng , Zhang Zhefan , Jin Shicheng , Wen Songwei , Ji Jianjian , Chung Lung Wa , Dong Xiu-Qin , Zhang Xumu
Published: June 2016

The new ferrocenyl bisphosphorus ligand, Wudaphos, was developed for highly enantioselective asymmetric hydrogenation based on noncovalent ion pair interaction.
Precision targeted ruthenium(ii) luminophores; highly effective probes for cell imaging by stimulated emission depletion (STED) microscopy
Authors: Byrne Aisling , Burke Christopher S. , Keyes Tia E.
Published: June 2016

Using precision peptide targeting to discrete cell organelles, it is demonstrated that Ru(ii) polypyridyl complexes are highly effective probes for stimulated emission depletion microscopy.
Poly(anthraquinonyl imide) as a high capacity organic cathode material for Na-ion batteries
Authors: Xu Fei , Wang Hongtao , Lin Jianghui , Luo Xiao , Cao Shun-an , Yang Hanxi
Published: June 2016

Poly(anthraquinonyl imide) (PAQI) exhibits a capacity of 190 mA h g−1 and a stable cyclability as an organic Na-ion battery cathode.
Twisted yarns for fiber-shaped supercapacitors based on wetspun PEDOT:PSS fibers from aqueous coagulation
Authors: Yuan Demao , Li Bo , Cheng Jianli , Guan Qun , Wang Zhuanpei , Ni Wei , Li Chun , Liu Heng , Wang Bin
Published: June 2016

Twisted yarns of wetspun PEDOT:PSS fibers from aqueous coagulation are prepared and used for fiber-shaped supercapacitors with excellent performances.
Gender specific differences in the liver proteome of rats exposed to short term and low-concentration hexabromocyclododecane (HBCD)
Authors: Miller I. , Diepenbroek C. , Rijntjes E. , Renaut J. , Teerds K. J. , Kwadijk C. , Cambier S. , Murk A. J. , Gutleb A. C. , Serchi T.
Published: June 2016

Gender specific impact of HBCD on rat liver proteome, determined by 2D-DIGE.
Non-antibody protein-based biosensors
Authors: Ferrigno Paul Ko
Published: June 2016

Biosensors that depend on a physical or chemical measurement can be adversely affected by non-specific interactions. For example, a biosensor designed to measure specifically the levels of a rare analyte can give false positive results if there is even a small amount of interaction with a highly abundant but irrelevant molecule. To overcome this limitation, the biosensor community has frequently turned to antibody molecules as recognition elements because they are renowned for their exquisite specificity. Unfortunately antibodies can often fail when immobilised on inorganic surfaces, and alternative biological recognition elements are needed. This article reviews the available non-antibody-binding proteins that have been successfully used in electrical and micro-mechanical biosensor platforms.
Oligonucleotide-based systems: DNA, microRNAs, DNA/RNA aptamers
Authors: Jolly Pawan , Estrela Pedro , Ladomery Michael
Published: June 2016

There are an increasing number of applications that have been developed for oligonucleotide-based biosensing systems in genetics and biomedicine. Oligonucleotide-based biosensors are those where the probe to capture the analyte is a strand of deoxyribonucleic acid (DNA), ribonucleic acid (RNA) or a synthetic analogue of naturally occurring nucleic acids. This review will shed light on various types of nucleic acids such as DNA and RNA (particularly microRNAs), their role and their application in biosensing. It will also cover DNA/RNA aptamers, which can be used as bioreceptors for a wide range of targets such as proteins, small molecules, bacteria and even cells. It will also highlight how the invention of synthetic oligonucleotides such as peptide nucleic acid (PNA) or locked nucleic acid (LNA) has pushed the limits of molecular biology and biosensor development to new perspectives. These technologies are very promising albeit still in need of development in order to bridge the gap between the laboratory-based status and the reality of biomedical applications.
Glycan and lectin biosensors
Authors: Belický Štefan , Katrlík Jaroslav , Tkáč Ján
Published: June 2016

A short description about the importance of glycan biorecognition in physiological (blood cell type) and pathological processes (infections by human and avian influenza viruses) is provided in this review. Glycans are described as much better information storage media, compared to proteins or DNA, due to the extensive variability of glycan structures. Techniques able to detect an exact glycan structure are briefly discussed with the main focus on the application of lectins (glycan-recognising proteins) in the specific analysis of glycans still attached to proteins or cells/viruses. Optical, electrochemical, piezoelectric and micromechanical biosensors with immobilised lectins or glycans able to detect a wide range of analytes including whole cells/viruses are also discussed.