bluuebunny/crossref_metadata_2025 huggingface dataset:
A neomorphic cancer cell-specific role of MAGE-A4 in trans-lesion synthesis
Authors: Gao Yanzhe , Mutter-Rottmayer Elizabeth , Greenwalt Alicia M. , Goldfarb Dennis , Yan Feng , Yang Yang , Martinez-Chacin Raquel C. , Pearce Kenneth H. , Tateishi Satoshi , Major Michael B. , Vaziri Cyrus
Published: July 2016

Trans-lesion synthesis (TLS) is an important DNA-damage tolerance mechanism that permits ongoing DNA synthesis in cells harbouring damaged genomes. The E3 ubiquitin ligase RAD18 activates TLS by promoting recruitment of Y-family DNA polymerases to sites of DNA-damage-induced replication fork stalling. Here we identify the cancer/testes antigen melanoma antigen-A4 (MAGE-A4) as a tumour cell-specific RAD18-binding partner and an activator of TLS. MAGE-A4 depletion from MAGE-A4-expressing cancer cells destabilizes RAD18. Conversely, ectopic expression of MAGE-A4 (in cell lines lacking endogenous MAGE-A4) promotes RAD18 stability. DNA-damage-induced mono-ubiquitination of the RAD18 substrate PCNA is attenuated by MAGE-A4 silencing. MAGE-A4-depleted cells fail to resume DNA synthesis normally following ultraviolet irradiation and accumulate γH2AX, thereby recapitulating major hallmarks of TLS deficiency. Taken together, these results demonstrate a mechanism by which reprogramming of ubiquitin signalling in cancer cells can influence DNA damage tolerance and probably contribute to an altered genomic landscape.
Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila
Authors: Sysoev Vasiliy O. , Fischer Bernd , Frese Christian K. , Gupta Ishaan , Krijgsveld Jeroen , Hentze Matthias W. , Castello Alfredo , Ephrussi Anne
Published: July 2016

The maternal-to-zygotic transition (MZT) is a process that occurs in animal embryos at the earliest developmental stages, during which maternally deposited mRNAs and other molecules are degraded and replaced by products of the zygotic genome. The zygotic genome is not activated immediately upon fertilization, and in the pre-MZT embryo post-transcriptional control by RNA-binding proteins (RBPs) orchestrates the first steps of development. To identify relevant Drosophila RBPs organism-wide, we refined the RNA interactome capture method for comparative analysis of the pre- and post-MZT embryos. We determine 523 proteins as high-confidence RBPs, half of which were not previously reported to bind RNA. Comparison of the RNA interactomes of pre- and post-MZT embryos reveals high dynamicity of the RNA-bound proteome during early development, and suggests active regulation of RNA binding of some RBPs. This resource provides unprecedented insight into the system of RBPs that govern the earliest steps of Drosophila development.
Engineering biosynthesis of the anticancer alkaloid noscapine in yeast
Authors: Li Yanran , Smolke Christina D.
Published: July 2016

Noscapine is a potential anticancer drug isolated from the opium poppy Papaver somniferum, and genes encoding enzymes responsible for the synthesis of noscapine have been recently discovered to be clustered on the genome of P. somniferum. Here, we reconstitute the noscapine gene cluster in Saccharomyces cerevisiae to achieve the microbial production of noscapine and related pathway intermediates, complementing and extending previous in planta and in vitro investigations. Our work provides structural validation of the secoberberine intermediates and the description of the narcotoline-4′-O-methyltransferase, suggesting this activity is catalysed by a unique heterodimer. We also reconstitute a 14-step biosynthetic pathway of noscapine from the simple alkaloid norlaudanosoline by engineering a yeast strain expressing 16 heterologous plant enzymes, achieving reconstitution of a complex plant pathway in a microbial host. Other engineered yeasts produce previously inaccessible pathway intermediates and a novel derivative, thereby advancing protoberberine and noscapine related drug discovery.
Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses
Authors: Kapeli Katannya , Pratt Gabriel A. , Vu Anthony Q. , Hutt Kasey R. , Martinez Fernando J. , Sundararaman Balaji , Batra Ranjan , Freese Peter , Lambert Nicole J. , Huelga Stephanie C. , Chun Seung J. , Liang Tiffany Y. , Chang Jeremy , Donohue John P. , Shiue Lily , Zhang Jiayu , Zhu Haining , Cambi Franca , Kasarskis Edward , Hoon Shawn , Ares Manuel , Burge Christopher B. , Ravits John , Rigo Frank , Yeo Gene W.
Published: July 2016

The RNA-binding protein (RBP) TAF15 is implicated in amyotrophic lateral sclerosis (ALS). To compare TAF15 function to that of two ALS-associated RBPs, FUS and TDP-43, we integrate CLIP-seq and RNA Bind-N-Seq technologies, and show that TAF15 binds to ∼4,900 RNAs enriched for GGUA motifs in adult mouse brains. TAF15 and FUS exhibit similar binding patterns in introns, are enriched in 3′ untranslated regions and alter genes distinct from TDP-43. However, unlike FUS and TDP-43, TAF15 has a minimal role in alternative splicing. In human neural progenitors, TAF15 and FUS affect turnover of their RNA targets. In human stem cell-derived motor neurons, the RNA profile associated with concomitant loss of both TAF15 and FUS resembles that observed in the presence of the ALS-associated mutation FUS R521G, but contrasts with late-stage sporadic ALS patients. Taken together, our findings reveal convergent and divergent roles for FUS, TAF15 and TDP-43 in RNA metabolism.
Erratum: Embryonic transcription is controlled by maternally defined chromatin state
Authors: Hontelez Saartje , van Kruijsbergen Ila , Georgiou Georgios , van Heeringen Simon J. , Bogdanovic Ozren , Lister Ryan , Veenstra Gert Jan C.
Published: July 2016

Nature Communications 6: Article number:10148 (2015); Published 18 December 2015; Updated 5 July 2016 This Article contains an error in Fig. 7 that was introduced during the production process. In panel a, the label ‘dx1’ should read ‘cdx1’. The correct version of the figure appears below. Figure 7
A systematic High-Content Screening microscopy approach reveals key roles for Rab33b, OATL1 and Myo6 in nanoparticle trafficking in HeLa cells
Authors: Panarella Angela , Bexiga Mariana G. , Galea George , O’ Neill Elaine D. , Salvati Anna , Dawson Kenneth A. , Simpson Jeremy C.
Published: July 2016

Synthetic nanoparticles are promising tools for imaging and drug delivery; however the molecular details of cellular internalization and trafficking await full characterization. Current knowledge suggests that following endocytosis most nanoparticles pass from endosomes to lysosomes. In order to design effective drug delivery strategies that can use the endocytic pathway, or by-pass lysosomal accumulation, a comprehensive understanding of nanoparticle uptake and trafficking mechanisms is therefore fundamental. Here we describe and apply an RNA interference-based high-content screening microscopy strategy to assess the intracellular trafficking of fluorescently-labeled polystyrene nanoparticles in HeLa cells. We screened a total of 408 genes involved in cytoskeleton and membrane function, revealing roles for myosin VI, Rab33b and OATL1 in this process. This work provides the first systematic large-scale quantitative assessment of the proteins responsible for nanoparticle trafficking in cells, paving the way for subsequent genome-wide studies.
A novel role for pigment genes in the stress response in rainbow trout (Oncorhynchus mykiss)
Authors: Khan Uniza Wahid , Øverli Øyvind , Hinkle Patricia M. , Pasha Farhan Ahmad , Johansen Ida Beitnes , Berget Ingunn , Silva Patricia I. M. , Kittilsen Silje , Höglund Erik , Omholt Stig W. , Våge Dag Inge
Published: July 2016

In many vertebrate species visible melanin-based pigmentation patterns correlate with high stress- and disease-resistance, but proximate mechanisms for this trait association remain enigmatic. Here we show that a missense mutation in a classical pigmentation gene, melanocyte stimulating hormone receptor (MC1R), is strongly associated with distinct differences in steroidogenic melanocortin 2 receptor (MC2R) mRNA expression between high- (HR) and low-responsive (LR) rainbow trout (Oncorhynchus mykiss). We also show experimentally that cortisol implants increase the expression of agouti signaling protein (ASIP) mRNA in skin, likely explaining the association between HR-traits and reduced skin melanin patterning. Molecular dynamics simulations predict that melanocortin 2 receptor accessory protein (MRAP), needed for MC2R function, binds differently to the two MC1R variants. Considering that mRNA for MC2R and the MC1R variants are present in head kidney cells, we hypothesized that MC2R activity is modulated in part by different binding affinities of the MC1R variants for MRAP. Experiments in mammalian cells confirmed that trout MRAP interacts with the two trout MC1R variants and MC2R, but failed to detect regulation of MC2R signaling, possibly due to high constitutive MC1R activity.
A Two-Year Treatment of Amnestic Mild Cognitive Impairment using a Compound Chinese Medicine: A Placebo Controlled Randomized Trial
Authors: Zhang Junying , Liu Zhen , Zhang Huamin , Yang Caishui , Li He , Li Xin , Chen Kewei , Zhang Zhanjun
Published: July 2016

We aimed to investigate the long-term therapeutic effects of a compound Chinese medicine, the Bushen capsule, on cognition and brain connectivity in patients with amnestic mild cognitive impairment (aMCI). Thus, sixty aMCI participants were recruited to this 24-month study and were randomly divided into treatment (30 with a Bushen capsule) and placebo (30 with a placebo capsule) groups. Neuropsychological tests with MMSE and episodic memory as the primary outcomes and resting-state functional magnetic resonance imaging (fMRI) were analyzed before and after the treatment over 24 month period. In contrast to the placebo group, the drug group presented improved or stable general cognitive function, memory, language and executive function especially the primary outcomes MMSE and episodic memory with Bushen capsule treatment. FMRI results showed increased connectivity in the right precuneus and the global connectivity indexed with goodness of fit (GOF) of the default mode network (DMN) in the drug group and decreased GOF in the placebo group. More importantly, we found the GOF change was positively correlated with changes in MMSE and memory scores after 24 months in the drug group. Over 24 months, treatment with the compound Chinese medicine Bushen capsule can improve multiple domains of cognition and increase the functional local (right precuneus) and global connectivity within the DMN, which are associated with better performance.
In vivo label-free measurement of lymph flow velocity and volumetric flow rates using Doppler optical coherence tomography
Authors: Blatter Cedric , Meijer Eelco F. J. , Nam Ahhyun S. , Jones Dennis , Bouma Brett E. , Padera Timothy P. , Vakoc Benjamin J.
Published: July 2016

Directin vivoimaging of lymph flow is key to understanding lymphatic system function in normal and disease states. Optical microscopy techniques provide the resolution required for these measurements, but existing optical techniques for measuring lymph flow require complex protocols and provide limited temporal resolution. Here, we describe a Doppler optical coherence tomography platform that allows direct, label-free quantification of lymph velocity and volumetric flow rates. We overcome the challenge of very low scattering by employing a Doppler algorithm that operates on low signal-to-noise measurements. We show that this technique can measure lymph velocity at sufficiently high temporal resolution to resolve the dynamic pulsatile flow in collecting lymphatic vessels.
Comparative genomic analysis of novel Acinetobacter symbionts: A combined systems biology and genomics approach
Authors: Gupta Vipin , Haider Shazia , Sood Utkarsh , Gilbert Jack A. , Ramjee Meenakshi , Forbes Ken , Singh Yogendra , Lopes Bruno S. , Lal Rup
Published: July 2016

The increasing trend of antibiotic resistance in Acinetobacter drastically limits the range of therapeutic agents required to treat multidrug resistant (MDR) infections. This study focused on analysis of novel Acinetobacter strains using a genomics and systems biology approach. Here we used a network theory method for pathogenic and non-pathogenic Acinetobacter spp. to identify the key regulatory proteins (hubs) in each strain. We identified nine key regulatory proteins, guaA, guaB, rpsB, rpsI, rpsL, rpsE, rpsC, rplM and trmD, which have functional roles as hubs in a hierarchical scale-free fractal protein-protein interaction network. Two key hubs (guaA and guaB) were important for insect-associated strains, and comparative analysis identified guaA as more important than guaB due to its role in effective module regulation. rpsI played a significant role in all the novel strains, while rplM was unique to sheep-associated strains. rpsM, rpsB and rpsI were involved in the regulation of overall network topology across all Acinetobacter strains analyzed in this study. Future analysis will investigate whether these hubs are useful as drug targets for treating Acinetobacter infections.
Glycogen synthase kinase 3β suppresses polyglutamine aggregation by inhibiting Vaccinia-related kinase 2 activity
Authors: Lee Eunju , Ryu Hye Guk , Kim Sangjune , Lee Dohyun , Jeong Young-Hun , Kim Kyong-Tai
Published: July 2016

Huntington’s disease (HD) is a neurodegenerative disorder caused by an abnormal expansion of polyglutamine repeats in the N-terminal of huntingtin. The amount of aggregate-prone protein is controlled by various mechanisms, including molecular chaperones. Vaccinia-related kinase 2 (VRK2) is known to negatively regulate chaperonin TRiC, and VRK2-facilitated degradation of TRiC increases polyQ protein aggregation, which is involved in HD. We found that VRK2 activity was negatively controlled by glycogen synthase kinase 3β (GSK3β). GSK3β directly bound to VRK2 and inhibited the catalytic activity of VRK2 in a kinase activity-independent manner. Furthermore, GSK3β increased the stability of TRiC and decreased the formation of HttQ103-GFP aggregates by inhibiting VRK2. These results indicate that GSK3β signaling may be a regulatory mechanism of HD progression and suggest targets for further therapeutic trials for HD.
Exotic skyrmion crystals in chiral magnets with compass anisotropy
Authors: Chen J. P. , Zhang Dan-Wei , Liu J. -M.
Published: July 2016

The compass-type anisotropy appears naturally in diverse physical contexts with strong spin-orbit coupling (SOC) such as transition metal oxides and cold atomic gases etc and it has been receiving substantial attention. Motivated by recent studies and particularly recent experimental observations on helimagnet MnGe, we investigate the critical roles of this compass-type anisotropy in modulating various spin textures of chiral magnets with strong SOC, by Monte Carlo simulations based on a classical Heisenberg spin model with Dzyaloshinsky-Moriya interaction and compass anisotropy. A phase diagram with emergent spin orders in the space of compass anisotropy and out-of-plane magnetic field is presented. In this phase diagram, we propose that a hybrid super-crystal structure consisting of alternating half-skyrmion and half-anti-skyrmion is the possible zero-field ground state of MnGe. The simulated evolution of the spin structure driven by magnetic field is in good accordance with experimental observations on MnGe. Therefore, this Heisenberg spin model successfully captures the main physics responsible for the magnetic structures in MnGe and the present work may also be instructive to research on the magnetic states in other systems with strong SOC.
Sharp temporal tuning in the bat auditory midbrain overcomes spectral-temporal trade-off imposed by cochlear mechanics
Authors: Macías Silvio , Hechavarría Julio C. , Kössl Manfred
Published: July 2016

In the cochlea of the mustached bat, cochlear resonance produces extremely sharp frequency tuning to the dominant frequency of the echolocation calls, around 61 kHz. Such high frequency resolution in the cochlea is accomplished at the expense of losing temporal resolution because of cochlear ringing, an effect that is observable not only in the cochlea but also in the cochlear nucleus. In the midbrain, the duration of sounds is thought to be analyzed by duration-tuned neurons, which are selective to both stimulus duration and frequency. We recorded from 57 DTNs in the auditory midbrain of the mustached bat to assess if a spectral-temporal trade-off is present. Such spectral-temporal trade-off is known to occur as sharp tuning in the frequency domain which results in poorer resolution in the time domain, and vice versa. We found that a specialized sub-population of midbrain DTNs tuned to the bat’s mechanical cochlear resonance frequency escape the cochlear spectral-temporal trade-off. We also show evidence that points towards an underlying neuronal inhibition that appears to be specific only at the resonance frequency.
Overexpression of Bmi1 in Lymphocytes Stimulates Skeletogenesis by Improving the Osteogenic Microenvironment
Authors: Zhou Xichao , Dai Xiuliang , Wu Xuan , Ji Ji , Karaplis Andrew , Goltzman David , Yang Xiangjiao , Miao Dengshun
Published: July 2016

To investigate whether overexpression of Bmi1 in lymphocytes can stimulate skeletogenesis by improving the osteogenic microenvironment, we examined the skeletal phenotype of EμBmi1 transgenic mice with overexpression of Bmi1 in lymphocytes. The size of the skeleton, trabecular bone volume and osteoblast number, indices of proliferation and differentiation of bone marrow mesenchymal stem cells (BM-MSCs) were increased significantly, ROS levels were reduced and antioxidative capacity was enhanced in EμBmi1 mice compared to WT mice. In PTHrP1–84 knockin (PthrpKI/KI) mice, the expression levels of Bmi1 are reduced and potentially can mediate the premature osteoporosis observed. We therefore generated a PthrpKI/KI mice overexpressing Bmi1 in lymphocytes and compared them with PthrpKI/KI and WT littermates. Overexpression of Bmi1 in PthrpKI/KI mice resulted in a longer lifespan, increased body weight and improvement in skeletal growth and parameters of osteoblastic bone formation with reduced ROS levels and DNA damage response parameters. Our results demonstrate that overexpression of Bmi1 in lymphocytes can stimulate osteogenesis in vivo and partially rescue defects in skeletal growth and osteogenesis in PthrpKI/KI mice. These studies therefore indicate that overexpression of Bmi1 in lymphocytes can stimulate skeletogenesis by inhibiting oxidative stress and improving the osteogenic microenvironment.
Monolayer MoS2 Bandgap Modulation by Dielectric Environments and Tunable Bandgap Transistors
Authors: Ryou Junga , Kim Yong-Sung , KC Santosh , Cho Kyeongjae
Published: July 2016

Semiconductors with a moderate bandgap have enabled modern electronic device technology, and the current scaling trends down to nanometer scale have introduced two-dimensional (2D) semiconductors. The bandgap of a semiconductor has been an intrinsic property independent of the environments and determined fundamental semiconductor device characteristics. In contrast to bulk semiconductors, we demonstrate that an atomically thin two-dimensional semiconductor has a bandgap with strong dependence on dielectric environments. Specifically, monolayer MoS2 bandgap is shown to change from 2.8 eV to 1.9 eV by dielectric environment. Utilizing the bandgap modulation property, a tunable bandgap transistor, which can be in general made of a two-dimensional semiconductor, is proposed.
Soft magnetic memory of silk cocoon membrane
Authors: Roy Manas , Dubey Amarish , Singh Sushil Kumar , Bhargava Kalpana , Sethy Niroj Kumar , Philip Deepu , Sarkar Sabyasachi , Bajpai Alok , Das Mainak
Published: July 2016

Silk cocoon membrane (SCM), a solid matrix of protein fiber, responds to light, heat and moisture and converts these energies to electrical signals. Essentially it exhibits photo-electric and thermo-electric properties; making it a natural electro-magnetic sensor, which may influence the pupal development. This raises the question: ‘is it only electricity?’, or ‘it also posses some kind of magnetic memory?’ This work attempted to explore the magnetic memory of SCM and confirm its soft magnetism. Fe, Co, Ni, Mn, Gd were found in SCM, in traces, through energy dispersive X-ray analysis (EDX), X-ray photoelectron spectroscopy (XPS) and inductively coupled plasma mass spectrometry (ICP-MS). Presence of iron was ascertained by electron paramagnetic resonance (EPR). In addition, EPR-spectra showed the presence of a stable pool of carbon-centric free radical in the cocoon structure. Carbon-centric free radicals behaves as a soft magnet inherently. Magnetic-Hysteresis (M-H) of SCM confirmed its soft magnetism. It can be concluded that the soft bio-magnetic feature of SCM is due to the entrapment of ferromagnetic elements in a stable pool of carbon centric radicals occurring on the super-coiled protein structure. Natural soft magnets like SCM provide us with models for developing eco-friendly, protein-based biological soft magnets.
HANDS2: accurate assignment of homoeallelic base-identity in allopolyploids despite missing data
Authors: Khan Amina , Belfield Eric J. , Harberd Nicholas P. , Mithani Aziz
Published: July 2016

Characterization of homoeallelic base-identity in allopolyploids is difficult since homeologous subgenomes are closely related and becomes further challenging if diploid-progenitor data is missing. We present HANDS2, a next-generation sequencing-based tool that enables highly accurate (>90%) genome-wide discovery of homeolog-specific base-identity in allopolyploids even in the absence of a diploid-progenitor. We applied HANDS2 to the transcriptomes of various cruciferous plants belonging to genus Brassica. Our results suggest that the three C genomes in Brassica are more similar to each other than the three A genomes, and provide important insights into the relationships between various Brassica tetraploids and their diploid-progenitors at a single-base resolution.
The modification of the thrombin generation test for the clinical assessment of dabigatran etexilate efficiency
Authors: Gribkova Irina V. , Lipets Elena N. , Rekhtina Irina G. , Bernakevich Alex I. , Ayusheev Dorzho B. , Ovsepyan Ruzanna A. , Ataullakhanov Fazoil I. , Sinauridze Elena I.
Published: July 2016

A new oral anticoagulant, dabigatran etexilate (DE, a prodrug of direct thrombin inhibitor (DTI) dabigatran), has been used clinically to prevent thrombosis. The assessment of dabigatran efficiency is necessary in some clinical cases, such as renal insufficiency, risk of bleeding, and drug interactions. However, a specific thrombin generation test (TGT) that is one of the most informative and sensitive to anticoagulant therapy (calibrated automated thrombinography (САТ)) shows a paradoxical increase of test parameters, such as endogenous thrombin potential (ETP) and peak thrombin, in patients receiving DE. The paradoxical behaviour of ETP and peak thrombin in these patients in the presence of DTIs is mostly caused by a decrease in the activity of thrombin in the α2-macroglobulin-thrombin complex that is used as a calibrator in CAT. For a correct estimation of the TGT parameters in patient’s plasma containing DTIs we proposed to use our previously described alternative calibration method that is based on the measurement of the fluorescence signal of a well-known concentration of the reaction product (7-amino-4-methylcoumarin). In this study, the validity of such approach was demonstrated in an ex vivo study in patients with knee replacement and two special patients with multiple myeloma, who received DE for thrombosis prophylaxis.
Conformational stability of digestion-resistant peptides of peanut conglutins reveals the molecular basis of their allergenicity
Authors: Apostolovic Danijela , Stanic-Vucinic Dragana , de Jongh Harmen H. J. , de Jong Govardus A. H. , Mihailovic Jelena , Radosavljevic Jelena , Radibratovic Milica , Nordlee Julie A. , Baumert Joseph L. , Milcic Milos , Taylor Steve L. , Garrido Clua Nuria , Cirkovic Velickovic Tanja , Koppelman Stef J.
Published: July 2016

Conglutins represent the major peanut allergens and are renowned for their resistance to gastro-intestinal digestion. Our aim was to characterize the digestion-resistant peptides (DRPs) of conglutins by biochemical and biophysical methods followed by a molecular dynamics simulation in order to better understand the molecular basis of food protein allergenicity. We have mapped proteolysis sites at the N- and C-termini and at a limited internal segment, while other potential proteolysis sites remained unaffected. Molecular dynamics simulation showed that proteolysis only occurred in the vibrant regions of the proteins. DRPs appeared to be conformationally stable as intact conglutins. Also, the overall secondary structure and IgE-binding potency of DRPs was comparable to that of intact conglutins. The stability of conglutins toward gastro-intestinal digestion, combined with the conformational stability of the resulting DRPs provide conditions for optimal exposure to the intestinal immune system, providing an explanation for the extraordinary allergenicity of peanut conglutins.
Transition of differential histone H3 methylation in photoreceptors and other retinal cells during retinal differentiation
Authors: Ueno Kazuko , Iwagawa Toshiro , Kuribayashi Hiroshi , Baba Yukihiro , Nakauchi Hiromitsu , Murakami Akira , Nagasaki Masao , Suzuki Yutaka , Watanabe Sumiko
Published: July 2016

To analyze cell lineage-specific transitions in global transcriptional and epigenetic changes during retinogenesis, we purified retinal cells from normal mice during postnatal development into two fractions, namely, photoreceptors and other retinal cells, based on Cd73 expression, and performed RNA sequencing and ChIP sequencing of H3K27me3 and H3K4me3. Genes expressed in the photoreceptor lineage were marked with H3K4me3 in the Cd73-positive cell fraction; however, the level of H3K27me3 was very low in both Cd73-positive and -negative populations. H3K27me3 may be involved in spatio-temporal onset of a subset of bipolar-related genes. Subsets of genes expressed in amacrine and retinal ganglion cells, which are early-born retinal cell types, were suggested to be maintained in a silent state by H3K27me3 during late-stage retinogenesis. In the outer nuclear layer, upregulation of Rho and rod-related genes were observed in Ezh2-ablated retina, suggesting a role for H3K27me3 in the maintenance of proper expression levels. Taken together, our data on the transition of lineage-specific molecular signatures during development suggest that histone methylation is involved in retinal differentiation and maintenance through cell lineage-specific mechanisms.
The normal modes of lattice vibrations of ice XI
Authors: Zhang Peng , Wang Zhe , Lu Ying-Bo , Ding Zheng-Wen
Published: July 2016

The vibrational spectrum of ice XI at thermal wavelengths using the CASTEP code, a first-principles simulation method, is investigated. A dual-track approach is constructed to verify the validity for the computational phonon spectrum: collate the simulated spectrum with inelastic neutron scattering experiments and assign the photon scattering peaks according to the calculated normal vibration frequencies. The 33 optical normal vibrations at the Brillouin center are illustrated definitely from the ab initio outcomes. The depolarizing field effect of the hydrogen bond vibrations at frequencies of 229 cm−1 and 310 cm−1 is found to agree well with the LST relationship. It is a convincing evidence to manifest the LO-TO splitting of hydrogen bonds in ice crystal. We attribute the two hydrogen bond peaks to the depolarization effect and apply this viewpoint to ordinary ice phase, ice Ih, which is difficult to analyse their vibration modes due to proton disorder.
Optimal processes for probabilistic work extraction beyond the second law
Authors: Cavina Vasco , Mari Andrea , Giovannetti Vittorio
Published: July 2016

According to the second law of thermodynamics, for every transformation performed on a system which is in contact with an environment of fixed temperature, the average extracted work is bounded by the decrease of the free energy of the system. However, in a single realization of a generic process, the extracted work is subject to statistical fluctuations which may allow for probabilistic violations of the previous bound. We are interested in enhancing this effect, i.e. we look for thermodynamic processes that maximize the probability of extracting work above a given arbitrary threshold. For any process obeying the Jarzynski identity, we determine an upper bound for the work extraction probability that depends also on the minimum amount of work that we are willing to extract in case of failure, or on the average work we wish to extract from the system. Then we show that this bound can be saturated within the thermodynamic formalism of quantum discrete processes composed by sequences of unitary quenches and complete thermalizations. We explicitly determine the optimal protocol which is given by two quasi-static isothermal transformations separated by a finite unitary quench.
p66Shc: A novel biomarker of tubular oxidative injury in patients with diabetic nephropathy
Authors: Xu Xiaoxuan , Zhu Xuejing , Ma Mingming , Han Yachun , Hu Chun , Yuan Shuguang , Yang Yuan , Xiao Li , Liu Fuyou , Kanwar Yashpal S. , Sun Lin
Published: July 2016

Increased p66Shc expression has been associated with diabetic nephropathy (DN). However, whether p66Shc can serve as a potential biomarker for tubular oxidative injury in DN is unknown. We measured the expression of p66Shc in peripheral blood monocytes (PBMs) and renal biopsy tissues from DN patients and then analysed the relationship between p66Shc expression and the clinical characteristics of patients with DN. Patients were divided into 4 groups (class IIa, class IIb, class III and the control group). qPCR, Western blotting and immunohistochemistry were performed. The results showed that both p66Shc and p-p66Shc expression significantly increased in PBMs and kidney tissues of DN patients. Moreover, Spearman’s correlation and multiple regression analyses were carried out. A positive relationship between the p66Shc expression and oxidative stress was found. p66Shc and oxidative stress were significant predictors of the degree of tubular damage. In addition, p66Shc expression was positively correlated with the concentrations of β-NAG, UACR and 8-OHdG, low-density lipoprotein and blood glucose levels, and duration of diabetes in patients with DN from class IIa to class III. These data indicated that increased expression of p66Shc may serve as a therapeutic target and a novel biomarker of DN.
Novel multifunctional pH-sensitive nanoparticles loaded into microbubbles as drug delivery vehicles for enhanced tumor targeting
Authors: Lv Yongjiu , Hao Lan , Hu Wenjing , Ran Ya , Bai Yan , Zhang Liangke
Published: July 2016

This study fabricated novel multifunctional pH-sensitive nanoparticles loaded into microbubbles (PNP-MB) with the combined advantages of two excellent drug delivery vehicles, namely, pH-sensitive nanoparticles and microbubbles. As an antitumor drug, resveratrol (RES) was loaded into acetylated β-cyclodextrin nanoparticles (RES-PNP). The drug-loaded nanoparticles were then encapsulated into the internal space of the microbubbles. The characterization and morphology of this vehicle were investigated through dynamic light scattering and confocal laser scanning microscopy, respectively. In vitro drug release was performed to investigate the pH sensitivity of RES-PNP. The antitumor property of RES-loaded PNP-MB (RES-PNP-MB) was also analyzed in vivo to evaluate the antitumor effect of RES-PNP-MB. Results suggested that PNP exhibited pH sensitivity, and was successfully encapsulated into the microbubbles. RES-PNP-MB exhibit effective tumor growth suppressing in vivo. Therefore, such drug delivery vehicle should be of great attention in tumor therapy.
Micro-motors: A motile bacteria based system for liposome cargo transport
Authors: Dogra Navneet , Izadi Hadi , Vanderlick T. Kyle
Published: July 2016

Biological micro-motors (microorganisms) have potential applications in energy utilization and nanotechnology. However, harnessing the power generated by such motors to execute desired work is extremely difficult. Here, we employ the power of motile bacteria to transport small, large and giant unilamellar vesicles (SUVs, LUVs and GUVs). Furthermore, we demonstrate bacteria–bilayer interactions by probing glycolipids inside the model membrane scaffold. Fluorescence Resonance Energy Transfer (FRET) spectroscopic and microscopic methods were utilized for understanding these interactions. We found that motile bacteria could successfully propel SUVs and LUVs with a velocity of 28 μm s−1 and 13 μm s−1, respectively. GUVs, however, displayed Brownian motion and could not be propelled by attached bacteria. Bacterial velocity decreased with the larger loaded cargo, which agrees with our calculations of loaded bacteria swimming at low Reynolds number.
Self-assembled targeted nanoparticles based on transferrin-modified eight-arm-polyethylene glycol–dihydroartemisinin conjugate
Authors: Liu Kefeng , Dai Lin , Li Chunxiao , Liu Jing , Wang Luying , Lei Jiandu
Published: July 2016

Poor delivery of insoluble anticancer drugs has so far precluded their clinical application. In this study, an efficient tumor targeted-nanoparticle delivery system, transferrin-eight-arm-polyethylene glycol–dihydroartemisinin nanoparticles (TF-8arm-PEG-DHA NPs) for the vehiculation of dihydroartemisinin (DHA) was first prepared and evaluated for its targeting efficiency and cytotoxicity in vitro and in vivo to Lewis lung carcinoma (LLC) cells, which overexpress transferrin receptors (TFRs). The synthesized TF-8arm-PEG–DHA NPs had high solubility (~102 fold of free DHA), relatively high drug loading (~10 wt% DHA), long circulating half-life and moderate particle size (~147 nm). The in vitro cytotoxicity and in vivo tumor growth inhibition studies in LLC-tumor bearing mice confirmed the enhanced efficacy of TF-modified 8arm-PEG-DHA NPs compared to free DHA and non-modified 8arm-PEG-DHA NPs. All these results together supported that the formulation developed in this work exhibited great potential as an effective tumor targeting delivery system for insoluble anticancer drugs.
Genetic optimization of a bacteriophage-delivered alkaline phosphatase reporter to detect Escherichia coli
Authors: Jackson Angelyca A. , Hinkley Troy C. , Talbert Joey N. , Nugen Sam R. , Sela David A.
Published: July 2016

A large fraction of foodborne illnesses are linked to (∼46%) leafy green vegetables contaminated by pathogens harbored in agricultural water.
High throughput LSPR and SERS analysis of aminoglycoside antibiotics
Authors: McKeating Kristy S. , Couture Maxime , Dinel Marie-Pier , Garneau-Tsodikova Sylvie , Masson Jean-Francois
Published: July 2016

Aminoglycoside antibiotics are used in the treatment of infections caused by Gram-negative bacteria, and are often dispensed only in severe cases due to their adverse side effects.
Reliable SERS detection of nitrite based on pH and laser irradiance-dependent diazotization through a convenient sampling micro-chamber
Authors: Gao Mengyue , Fang Wei , Ren Jiaqiang , Shen Aiguo , Hu Jiming
Published: July 2016

A SERS-enabled micro-chamber was constructed for reliable and pretreatment-free detection of NO2−based on a pH and laser irradiance-dependent diazotization.
In situ monitoring of additives during CO2gas hydrate formation
Authors: Schwenk M. , Katzir A. , Mizaikoff B.
Published: July 2016

The combination of pressure/temperature traces within situmid-infrared fiberoptic evanescent field spectroscopy as advanced sensing concept for CO2gas hydrate analysis.
Production of a sensitive antibody against sirolimus for chemiluminescence immunoassay potential in its therapeutic drug monitoring
Authors: Zhang Lisha , Long Hao , Li Xiaogang , Xu Kun , Meng Meng , Yin Yongmei , Xi Rimo
Published: July 2016

A competitive chemiluminescence immunoassay is established and applied to the TDM of sirolimus.
Mechanically robust, chemically inert superhydrophobic charcoal surfaces
Authors: Xie Jian-Bo , Li Liang , Knyazeva Anastassiya , Weston James , Naumov Panče
Published: July 2016

Superhydrophobic composite was prepared by paving adhesive tape with active charcoal which is endowed with mechanical robustness and chemical resistivity.
Insight into the formation of the tert-butyl cation confined inside H-ZSM-5 zeolite from NMR spectroscopy and DFT calculations
Authors: Huang Mengdi , Wang Qiang , Yi Xianfeng , Chu Yueying , Dai Weili , Li Landong , Zheng Anmin , Deng Feng
Published: July 2016

Solid-state NMR experiments and DFT calculations have been carried out to determine the complex structures of coadsorbed13C-labeledtert-butanol and NH3in acidic H-ZSM-5 zeolite.
Reaction rate of a composite core–shell nanoreactor with multiple nanocatalysts
Authors: Galanti Marta , Fanelli Duccio , Angioletti-Uberti Stefano , Ballauff Matthias , Dzubiella Joachim , Piazza Francesco
Published: July 2016

We present a detailed theory for the reaction rate constant of a core–shell nanoreactor, consisting of a solid core surrounded by a hydrogel layer with several small embedded nanocatalysts.
Smart windows application of carbazole and triazine based star shaped architecture
Authors: Guzel Merve , Soganci Tugba , Ayranci Rukiye , Ak Metin
Published: July 2016

Triazine-based, star shape and electroactive monomer was successfully synthesized and electropolymerized. The polymer showed superior optoelectronic and thermal properties. Due to the fact that the redox color characteristics of the polymer are indispensable for smart windows, PTCZ-based electrochromic device was constructed.
An efficient perovskite solar cell with symmetrical Zn(ii) phthalocyanine infiltrated buffering porous Al2O3 as the hybrid interfacial hole-transporting layer
Authors: Gao P. , Cho K. T. , Abate A. , Grancini G. , Reddy P. Y. , Srivasu M. , Adachi M. , Suzuki A. , Tsuchimoto K. , Grätzel M. , Nazeeruddin Mohammad Khaja
Published: July 2016

An interfacial buffer layer made of Al2O3 and sym-HTPcH facilitates perovskite solar cells with an average PCE value of 12.3%.
Decoupling the effects of confinement and passivation on semiconductor quantum dots
Authors: Rudd Roya , Hall Colin , Murphy Peter J. , Reece Peter J. , Charrault Eric , Evans Drew
Published: July 2016

Plasma synthesised Si QDs are deposited in liquids to decouple confinement and passivation effects on their optical properties.
First-principles study of photovoltaics and carrier mobility for non-toxic halide perovskite CH3NH3SnCl3: theoretical prediction
Authors: Wang Lin-Zhi , Zhao Yu-Qing , Liu Biao , Wu Li-Juan , Cai Meng-Qiu
Published: July 2016

The crystal structures, optical properties and carrier mobility for three phases of non-toxic perovskite halide CH3NH3SnCl3 are calculated by applying density functional theory with the nonlocal van der Waals (vdW) correlation.
A facile synthesis of three dimensional graphene sponge composited with sulfur nanoparticles for flexible Li–S cathodes
Authors: Lin Chao , Niu Chaojiang , Xu Xu , Li Ke , Cai Zhengyang , Zhang Yonglai , Wang Xuanpeng , Qu Longbing , Xu Yuxi , Mai Liqiang
Published: July 2016

A novel 3DGS was fabricatedviaa reduction induced self-assembly method. When used as a sulfur cathode, it shows high rate discharge capacity retention up to 500 cycles.
Reverse solvatochromism in solvent binary mixtures: a case study using a 4-(nitrostyryl)phenolate as a probe
Authors: Stock Rafaela I. , Schramm Adriana D. S. , Rezende Marcos C. , Machado Vanderlei G.
Published: July 2016

A 4-(nitrostyryl)phenolate was synthesized and its use in pure solvents revealed a reversion in solvatochromism.
Magnetism, structures and stabilities of cluster assembled TM@Si nanotubes (TM = Cr, Mn and Fe): a density functional study
Authors: Dhaka Kapil , Bandyopadhyay Debashis
Published: July 2016

Four different types (Type 1 to Type 4) of empty and transition metal (Cr, Mn and Fe) doped silicon nanotubes have been studied. The calculated band structures and DOS assigned them as metallic, semiconductor, semi-metallic and half-metallic depending upon the combination of the type of nanotube and the transition metal doping.
An upconversion nanoplatform for simultaneous photodynamic therapy and Pt chemotherapy to combat cisplatin resistance
Authors: Ai Fujin , Sun Tianying , Xu Zoufeng , Wang Zhigang , Kong Wei , To Man Wai , Wang Feng , Zhu Guangyu
Published: July 2016

Combined photodynamic therapy and Pt chemotherapy based on upconversion nanoparticles are very effective in killing cisplatin-resistant cancer cells.
Metal ion binding by pyridylethyl-containing polymers: experimental and theoretical study
Authors: Bratskaya Svetlana , Voit Alexey , Privar Yuliya , Ziatdinov Albert , Ustinov Alexander , Marinin Dmitry , Pestov Alexander
Published: July 2016

Structure of polymer precursors significantly affects binding efficiency of their pyridylethylated derivatives toward Cu2+, Ni2+, and Ag+ ions.
Near-infrared light triggered superior photocatalytic activity from MoS2–NaYF4:Yb3+/Er3+ nanocomposites
Authors: Chatti Manjunath , Adusumalli Venkata N. K. B. , Ganguli Sagar , Mahalingam Venkataramanan
Published: July 2016

A near infrared (NIR) responsive photocatalyst, composed of a narrow band gap semiconductor (i.e. MoS2) and an optical material possessing upconverting ability (i.e. NaYF4:Yb3+/Er3+) has been successfully prepared via a simple hydrothermal method.
Correction: Dynamic ruffling distortion of the heme substrate in non-canonical heme oxygenase enzymes
Authors: Graves Amanda B. , Horak Erik H. , Liptak Matthew D.
Published: July 2016

Correction for ‘Dynamic ruffling distortion of the heme substrate in non-canonical heme oxygenase enzymes’ by Amanda B. Graves et al., Dalton Trans., 2016, 45, 10058–10067.
TiO2/graphene/NiFe-layered double hydroxide nanorod array photoanodes for efficient photoelectrochemical water splitting
Authors: Ning Fanyu , Shao Mingfei , Xu Simin , Fu Yi , Zhang Ruikang , Wei Min , Evans David G. , Duan Xue
Published: July 2016

TiO2/graphene/NiFe-layered double hydroxide nanorod arrays were fabricated as highly efficient photoanodes for photoelectrochemical water splitting with simultaneously enhanced charge separation and water oxidation efficiency.
Sticking to (first) principles: quantum molecular dynamics and Bayesian probabilistic methods to simulate aquatic pollutant absorption spectra
Authors: Trerayapiwat Kasidet , Ricke Nathan , Cohen Peter , Poblete Alex , Rudel Holly , Eustis Soren N.
Published: July 2016

This work explores the relationship between theoretically predicted excitation energies and experimental molar absorption spectra as they pertain to environmental aquatic photochemistry.
Role of tunnel ionization in high harmonic generation from substituted benzenes
Authors: Austin Dane R. , McGrath Felicity , Miseikis Lukas , Wood David , Hawkins Peter , Johnson Allan S. , Vacher Morgane , Mašín Zdeněk , Harvey Alex , Ivanov Misha , Smirnova Olga , Marangos Jon P.
Published: July 2016

We theoretically study high-harmonic generation in toluene, ortho-xylene and fluorobenzene driven by a 1.8 μm ultrashort pulse. We find that the chemical substitutions have a strong influence on the amplitude and phase of the emission from the highest occupied molecular orbital, despite having a small influence on the orbital itself. We show that this influence is due to the tunnel ionization step, which depends critically on the sign and amplitude of the asymptotic part of the wave function. We discuss how these effects would manifest in phase-sensitive high-harmonic generation spectroscopy experiments.
Milk digesta and milk protein fractions influence the adherence of Lactobacillus gasseri R and Lactobacillus casei FMP to human cultured cells
Authors: Volstatova Tereza , Havlik Jaroslav , Potuckova Miroslava , Geigerova Martina
Published: July 2016

Adhesion to the intestinal epithelium is considered an important feature of probiotic bacteria, which may increase their persistence in the intestine, allowing them to exert their beneficial health effect or promote the colonisation process.
Probabilistic diagram for designing chemicals with reduced potency to incur cytotoxicity
Authors: Shen Longzhu Q. , Judson Richard S. , Melnikov Fjodor , Roethle John , Gudibanda Aditya , Zimmerman Julie B. , Anastas Paul T.
Published: July 2016

A probabilistic diagram presenting the complete solution in the variable space to guide safer chemical design against cytotoxicity.
Tunable superomniphobic surfaces for sorting droplets by surface tension
Authors: Movafaghi S. , Wang W. , Metzger A. , Williams D. D. , Williams J. D. , Kota A. K.
Published: July 2016

Utilizing tunable superomniphobic surfaces with flower-like TiO2 nanostructures, we fabricated a simple device that can sort droplets by surface tension.
Small-molecule binding sites to explore protein–protein interactions in the cancer proteome
Authors: Xu David , Jalal Shadia I. , Sledge George W. , Meroueh Samy O.
Published: July 2016

The Cancer Genome Atlas (TCGA) offers an unprecedented opportunity to identify small-molecule binding sites on proteins with overexpressed mRNA levels that correlate with poor survival.
2015 First Boston Symposium of Encoded Library Platforms
Authors: Goodnow Jr. Robert A. , Davie Christopher P.
Published: July 2016

Guest Editors Robert Goodnow and Christopher Davie recap the first Boston Symposium of Encoded Library Platforms and introduce the MedChemComm web collection on ‘DNA Encoded Libraries’.
Synthesis of 1,3-dibromo-2-aryl-1H-indenes via NBS mediated unusual bromination of 2-alkynylbenzaldoximes
Authors: Singha Raju , Ghosh Munmun , Das Saikat , Das Dhiraj , Ray Jayanta K.
Published: July 2016

An interesting side-pathway leading to 1,3-dibromo-2-aryl-1H-indenes as opposed to isoquinoline N-oxides via NBS mediated bromination of 2-alkynylbenzaldoximes.
Optimizing the electric field around solid and core–shell alloy nanostructures for near-field applications
Authors: Montaño-Priede Luis , Peña-Rodríguez Ovidio , Rivera Antonio , Guerrero-Martínez Andrés , Pal Umapada
Published: July 2016

Understanding the variations of the near electric field around plasmonic nanoparticles is very important for several applications where the interactions occur close to the surface of the nanoparticle.
Thin film synthesis of SbSI micro-crystals for self-powered photodetectors with rapid time response
Authors: Gödel Karl C. , Steiner Ullrich
Published: July 2016

We describe a new thin film deposition method for the growth of crystalline SbSI micro-needles via the conversion of Sb2S3 using SbI3 vapour, in a facile process that takes less than 15 minutes.
Recent developments in free-radical-promoted C–Si formation via selective C–H/Si–H functionalization
Authors: Shang Xiaojie , Liu Zhong-Quan
Published: July 2016

As important and valuable alternatives to transition-metal-catalysis, free-radical strategies for C–Si bond construction via selective C–H/Si–H functionalization have been developed recently. These new reactions along with their suggested mechanisms are summarized and discussed here.
A novel bis(pinacolato)diboron-mediated N–O bond deoxygenative route to C6 benzotriazolyl purine nucleoside derivatives
Authors: Basava Vikram , Yang Lijia , Pradhan Padmanava , Lakshman Mahesh K.
Published: July 2016

O6-(Benzotriazol-1-yl)purine nucleosides, containing a C–O–N bond, undergo facile reduction of the N–O bond with (pinB)2and Cs2CO3.Viathis approach a series of 6-(benzotriazol-1-yl)purine nucleosides were synthesized and the mechanism has been investigated.
Synthesis and polymerization of boronic acid containing monomers
Authors: Vancoillie Gertjan , Hoogenboom Richard
Published: July 2016

This mini-review summarizes the most commonly used methods for the synthesis of phenylboronic acid-(co)polymers ranging from simple straightforward polymerization to complex post-polymerization modification.