bluuebunny/crossref_metadata_2025 huggingface dataset:
Rational improvement of gp41-targeting HIV-1 fusion inhibitors: an innovatively designed Ile-Asp-Leu tail with alternative conformations
Authors: Zhu Yun , Su Shan , Qin Lili , Wang Qian , Shi Lei , Ma Zhenxuan , Tang Jianchao , Jiang Shibo , Lu Lu , Ye Sheng , Zhang Rongguang
Published: September 2016

Peptides derived from the C-terminal heptad repeat (CHR) of HIV gp41 have been developed as effective fusion inhibitors against HIV-1, but facing the challenges of enhancing potency and stability. Here, we report a rationally designed novel HIV-1 fusion inhibitor derived from CHR-derived peptide (Trp628~Gln653, named CP), but with an innovative Ile-Asp-Leu tail (IDL) that dramatically increased the inhibitory activity by up to 100 folds. We also determined the crystal structures of artificial fusion peptides N36- and N43-L6-CP-IDL. Although the overall structures of both fusion peptides share the canonical six-helix bundle (6-HB) configuration, their IDL tails adopt two different conformations: a one-turn helix with the N36 and a hook-like structure with the longer N43. Structural comparison showed that the hook-like IDL tail possesses a larger interaction interface with NHR than the helical one. Further molecular dynamics simulations of the two 6-HBs and isolated CP-IDL peptides suggested that hook-like form of IDL tail can be stabilized by its binding to NHR trimer. Therefore, CP-IDL has potential for further development as a new HIV fusion inhibitor and this strategy could be widely used in developing artificial fusion inhibitors against HIV and other enveloped viruses.
Systemic blockade of ACVR2B ligands prevents chemotherapy-induced muscle wasting by restoring muscle protein synthesis without affecting oxidative capacity or atrogenes
Authors: Nissinen T. A. , Degerman J. , Räsänen M. , Poikonen A. R. , Koskinen S. , Mervaala E. , Pasternack A. , Ritvos O. , Kivelä R. , Hulmi J. J.
Published: September 2016

Doxorubicin is a widely used and effective chemotherapy drug. However, cardiac and skeletal muscle toxicity of doxorubicin limits its use. Inhibiting myostatin/activin signalling can prevent muscle atrophy, but its effects in chemotherapy-induced muscle wasting are unknown. In the present study we investigated the effects of doxorubicin administration alone or combined with activin receptor ligand pathway blockade by soluble activin receptor IIB (sACVR2B-Fc). Doxorubicin administration decreased body mass, muscle size and bone mineral density/content in mice. However, these effects were prevented by sACVR2B-Fc administration. Unlike in many other wasting situations, doxorubicin induced muscle atrophy without markedly increasing typical atrogenes or protein degradation pathways. Instead, doxorubicin decreased muscle protein synthesis which was completely restored by sACVR2B-Fc. Doxorubicin administration also resulted in impaired running performance without effects on skeletal muscle mitochondrial capacity/function or capillary density. Running performance and mitochondrial function were unaltered by sACVR2B-Fc administration. Tumour experiment using Lewis lung carcinoma cells demonstrated that sACVR2B-Fc decreased the cachectic effects of chemotherapy without affecting tumour growth. These results demonstrate that blocking ACVR2B signalling may be a promising strategy to counteract chemotherapy-induced muscle wasting without damage to skeletal muscle oxidative capacity or cancer treatment.
Identification and comparative analysis of the microRNA transcriptome in roots of two contrasting tobacco genotypes in response to cadmium stress
Authors: He Xiaoyan , Zheng Weite , Cao Fangbin , Wu Feibo
Published: September 2016

Tobacco (Nicotiana tabacumL.) is more acclimated to cadmium (Cd) uptake and preferentially enriches Cd in leaves than other crops. MicroRNAs (miRNAs) play crucial roles in regulating expression of various stress response genes in plants. However, genome-wide expression of miRNAs and their target genes in response to Cd stress in tobacco are still unknown. Here, miRNA high-throughput sequencing technology was performed using two contrasting tobacco genotypes Guiyan 1 and Yunyan 2 of Cd-sensitive and tolerance. Comprehensive analysis of miRNA expression profiles in control and Cd treated plants identified 72 known (27 families) and 14 novel differentially expressed miRNAs in the two genotypes. Among them, 28 known (14 families) and 5 novel miRNAs were considered as Cd tolerance associated miRNAs, which mainly involved in cell growth, ion homeostasis, stress defense, antioxidant and hormone signaling. Finally, a hypothetical model of Cd tolerance mechanism in Yunyan 2 was presented. Our findings suggest that some miRNAs and their target genes and pathways may play critical roles in Cd tolerance.
Identification and testing of oviposition attractant chemical compounds for Musca domestica
Authors: Tang Rui , Zhang Feng , Kone N’Golopé , Chen Jing-Hua , Zhu Fen , Han Ri-Chou , Lei Chao-Liang , Kenis Marc , Huang Ling-Qiao , Wang Chen-Zhu
Published: September 2016

Oviposition attractants for the house fly Musca domestica have been investigated using electrophysiological tests, behavioural assays and field tests. Volatiles were collected via head space absorption method from fermented wheat bran, fresh wheat bran, rearing substrate residue and house fly maggots. A Y-tube olfactometer assay showed that the odor of fermented wheat bran was a significant attractant for female house flies. Bioactive compounds from fermented wheat bran for house fly females were identified by electrophysiology and mass spectrophotometry and confirmed with standard chemicals. Four electrophysiologically active compounds including ethyl palmitate, ethyl linoleate, methyl linoleate, and linoleic acid were found at a proportion of 10:24:6:0.2. Functional imaging in the female antennal lobes revealed an overlapped active pattern for all chemicals. Further multiple-choice behavioural bioassays showed that these chemicals, as well as a mixture that mimicked the naturally occurring combination, increased the attractiveness of non-preferred rearing substrates of cotton and maize powder. Finally, a field demonstration test revealed that, by adding this mimic blend into a rearing substrate used to attract and breed house flies in West Africa, egg numbers laid by females were increased. These chemicals could be utilized to improve house fly production systems or considered for lure traps.
Design, Synthesis and Evaluation of Novel Isoxazolines/Oxime Sulfonates of 2′(2′,6′)-(Di)Chloropodophyllotoxins as Insecticidal Agents
Authors: Yu Mingqiao , Liu Guangci , Zhang Yuanyuan , Feng Tao , Xu Ming , Xu Hui
Published: September 2016

A series of 2′(2′,6′)-(di)halogeno-isoxazolopodophyllic acids-based esters, and oxime sulfonates of 2′(2′,6′)-(di)halogenopodophyllones were prepared by structural modifications of podophyllotoxin as insecticidal agents against Mythimna separata Walker. It was found that when 2′(2′,6′)-(di)halogenopodophyllones or 2′(2′,6′)-(di)chloropicropodophyllones reacted with hydroxylamine hydrochloride, the desired products were related with the configuration of their lactones. Three key single-crystal structures of Ie, IIe and IIIb were determined by X-ray diffraction. Especially compounds IIc and Vc showed the highest insecticidal activity. Moreover, some interesting results of structure-insecticidal activity relationships of tested compounds were also observed.
Exposure to Sound Vibrations Lead to Transcriptomic, Proteomic and Hormonal Changes in Arabidopsis
Authors: Ghosh Ritesh , Mishra Ratnesh Chandra , Choi Bosung , Kwon Young Sang , Bae Dong Won , Park Soo-Chul , Jeong Mi-Jeong , Bae Hanhong
Published: September 2016

Sound vibration (SV) is considered as an external mechanical force that modulates plant growth and development like other mechanical stimuli (e.g., wind, rain, touch and vibration). A number of previous and recent studies reported developmental responses in plants tailored against SV of varied frequencies. This strongly suggests the existence of sophisticated molecular mechanisms for SV perception and signal transduction. Despite this there exists a huge gap in our understanding regarding the SV-mediated molecular alterations, which is a prerequisite to gain insight into SV-mediated plant development. Herein, we investigated the global gene expression changes inArabidopsis thalianaupon treatment with five different single frequencies of SV at constant amplitude for 1 h. As a next step, we also studied the SV-mediated proteomic changes in Arabidopsis. Data suggested that like other stimuli, SV also activated signature cellular events, for example, scavenging of reactive oxygen species (ROS), alteration of primary metabolism, and hormonal signaling. Phytohormonal analysis indicated that SV-mediated responses were, in part, modulated by specific alterations in phytohormone levels; especially salicylic acid (SA). Notably, several touch regulated genes were also up-regulated by SV treatment suggesting a possible molecular crosstalk among the two mechanical stimuli, sound and touch. Overall, these results provide a molecular basis to SV triggered global transcriptomic, proteomic and hormonal changes in plant.
Electronic properties of MoS2/MoOx interfaces: Implications in Tunnel Field Effect Transistors and Hole Contacts
Authors: K. C. Santosh , Longo Roberto C. , Addou Rafik , Wallace Robert M. , Cho Kyeongjae
Published: September 2016

In an electronic device based on two dimensional (2D) transitional metal dichalcogenides (TMDs), finding a low resistance metal contact is critical in order to achieve the desired performance. However, due to the unusual Fermi level pinning in metal/2D TMD interface, the performance is limited. Here, we investigate the electronic properties of TMDs and transition metal oxide (TMO) interfaces (MoS2/MoO3) using density functional theory (DFT). Our results demonstrate that, due to the large work function of MoO3 and the relative band alignment with MoS2, together with small energy gap, the MoS2/MoO3 interface is a good candidate for a tunnel field effect (TFET)-type device. Moreover, if the interface is not stoichiometric because of the presence of oxygen vacancies in MoO3, the heterostructure is more suitable for p-type (hole) contacts, exhibiting an Ohmic electrical behavior as experimentally demonstrated for different TMO/TMD interfaces. Our results reveal that the defect state induced by an oxygen vacancy in the MoO3 aligns with the valance band of MoS2, showing an insignificant impact on the band gap of the TMD. This result highlights the role of oxygen vacancies in oxides on facilitating appropriate contacts at the MoS2 and MoOx (x < 3) interface, which consistently explains the available experimental observations.
MuSK Kinase Activity is Modulated By A Serine Phosphorylation Site in The Kinase Loop
Authors: Camurdanoglu B. Z. , Hrovat C. , Dürnberger G. , Madalinski M. , Mechtler K. , Herbst R.
Published: September 2016

The neuromuscular junction (NMJ) forms when a motor neuron contacts a muscle fibre. A reciprocal exchange of signals initiates a cascade of signalling events that result in pre- and postsynaptic differentiation. At the centre of these signalling events stands muscle specific kinase (MuSK). MuSK activation, kinase activity and subsequent downstream signalling are crucial for NMJ formation as well as maintenance. Therefore MuSK kinase activity is tightly regulated to ensure proper NMJ development. We have identified a novel serine phosphorylation site at position 751 in MuSK that is increasingly phosphorylated upon agrin stimulation. S751 is also phosphorylated in muscle tissue and its phosphorylation depends on MuSK kinase activity. A phosphomimetic mutant of S751 increases MuSK kinase activity in response to non-saturating agrin concentrations . In addition, basal MuSK and AChR phosphorylation as well as AChR cluster size are increased. We believe that the phosphorylation of S751 provides a novel mechanism to relief the autoinhibition of the MuSK activation loop. Such a lower autoinhibition could foster or stabilize MuSK kinase activation, especially during stages when no or low level of agrin are present. Phosphorylation of S751 might therefore represent a novel mechanism to modulate MuSK kinase activity during prepatterning or NMJ maintenance.
Development and characterisation of highly antibiotic resistant Bartonella bacilliformis mutants
Authors: Gomes Cláudia , Martínez-Puchol Sandra , Ruiz-Roldán Lidia , Pons Maria J. , del Valle Mendoza Juana , Ruiz Joaquim
Published: September 2016

The objective was to develop and characterise in vitro Bartonella bacilliformis antibiotic resistant mutants. Three B. bacilliformis strains were plated 35 or 40 times with azithromycin, chloramphenicol, ciprofloxacin or rifampicin discs. Resistance-stability was assessed performing 5 serial passages without antibiotic pressure. MICs were determined with/without Phe-Arg-β-Napthylamide and artesunate. Target alterations were screened in the 23S rRNA, rplD, rplV, gyrA, gyrB, parC, parE and rpoB genes. Chloramphenicol and ciprofloxacin resistance were the most difficult and easiest (>37.3 and 10.6 passages) to be selected, respectively. All mutants but one selected with chloramphenicol achieved high resistance levels. All rifampicin, one azithromycin and one ciprofloxacin mutants did not totally revert when cultured without antibiotic pressure. Azithromycin resistance was related to L4 substitutions Gln-66 → Lys or Gly-70 → Arg; L4 deletion Δ62–65 (Lys-Met-Tyr-Lys) or L22 insertion 83::Val-Ser-Glu-Ala-His-Val-Gly-Lys-Ser; in two chloramphenicol-resistant mutants the 23S rRNA mutation G2372A was detected. GyrA Ala-91 → Val and Asp-95 → Gly and GyrB Glu474 → Lys were detected in ciprofloxacin-resistant mutants. RpoB substitutions Gln-527 → Arg, His-540 → Tyr and Ser-545 → Phe plus Ser-588 → Tyr were detected in rifampicin-resistant mutants. In 5 mutants the effect of efflux pumps on resistance was observed. Antibiotic resistance was mainly related to target mutations and overexpression of efflux pumps, which might underlie microbiological failures during treatments.
Fast generations of tree-type three-dimensional entanglement via Lewis-Riesenfeld invariants and transitionless quantum driving
Authors: Wu Jin-Lei , Ji Xin , Zhang Shou
Published: September 2016

Recently, a novel three-dimensional entangled state called tree-type entanglement, which is likely to have applications for improving quantum communication security, was prepared via adiabatic passage by Songet al. Here we propose two schemes for fast generating tree-type three-dimensional entanglement among three spatially separated atoms via shortcuts to adiabatic passage. With the help of quantum Zeno dynamics, two kinds of different but equivalent methods, Lewis-Riesenfeld invariants and transitionless quantum driving, are applied to construct shortcuts to adiabatic passage. The comparisons between the two methods are discussed. The strict numerical simulations show that the tree-type three-dimensional entangled states can be fast prepared with quite high fidelities and the two schemes are both robust against the variations in the parameters, atomic spontaneous emissions and the cavity-fiber photon leakages.
Characterization of CD46 and β1 integrin dynamics during sperm acrosome reaction
Authors: Frolikova Michaela , Sebkova Natasa , Ded Lukas , Dvorakova-Hortova Katerina
Published: September 2016

The acrosome reaction (AR) is a process of membrane fusion and lytic enzyme release, which enables sperm to penetrate the egg surroundings. It is widely recognized that specific sperm proteins form an active network prior to fertilization and their dynamic relocation is crucial for the sperm-egg fusion. The unique presence of the membrane cofactor protein CD46 in the sperm acrosomal membrane was shown, however, its behaviour and connection with other sperm proteins has not been explored further. Using super resolution microscopy, we demonstrated a dynamic CD46 reorganisation over the sperm head during the AR and its interaction with transmembrane protein integrins, which was confirmed by proximity ligation assay. Furthermore, we propose their joint involvement in actin network rearrangement. Moreover, CD46 and β1 integrins with subunit α3, but not α6, are localized into the apical acrosome and are expected to be involved in signal transduction pathways directing the acrosome stability and essential protein network rearrangements prior to gamete fusion.
True Randomness from Big Data
Authors: Papakonstantinou Periklis A. , Woodruff David P. , Yang Guang
Published: September 2016

Generating random bits is a difficult task, which is important for physical systems simulation, cryptography, and many applications that rely on high-quality random bits. Our contribution is to show how to generate provably random bits from uncertain events whose outcomes are routinely recorded in the form of massive data sets. These include scientific data sets, such as in astronomics, genomics, as well as data produced by individuals, such as internet search logs, sensor networks, and social network feeds. We view the generation of such data as the sampling process from a big source, which is a random variable of size at least a few gigabytes. Our view initiates the study of big sources in the randomness extraction literature. Previous approaches for big sources rely on statistical assumptions about the samples. We introduce a general method that provably extracts almost-uniform random bits from big sources and extensively validate it empirically on real data sets. The experimental findings indicate that our method is efficient enough to handle large enough sources, while previous extractor constructions are not efficient enough to be practical. Quality-wise, our method at least matches quantum randomness expanders and classical world empirical extractors as measured by standardized tests.
Analysis of heterogeneous dengue transmission in Guangdong in 2014 with multivariate time series model
Authors: Cheng Qing , Lu Xin , Wu Joseph T. , Liu Zhong , Huang Jincai
Published: September 2016

Guangdong experienced the largest dengue epidemic in recent history. In 2014, the number of dengue cases was the highest in the previous 10 years and comprised more than 90% of all cases. In order to analyze heterogeneous transmission of dengue, a multivariate time series model decomposing dengue risk additively into endemic, autoregressive and spatiotemporal components was used to model dengue transmission. Moreover, random effects were introduced in the model to deal with heterogeneous dengue transmission and incidence levels and power law approach was embedded into the model to account for spatial interaction. There was little spatial variation in the autoregressive component. In contrast, for the endemic component, there was a pronounced heterogeneity between the Pearl River Delta area and the remaining districts. For the spatiotemporal component, there was considerable heterogeneity across districts with highest values in some western and eastern department. The results showed that the patterns driving dengue transmission were found by using clustering analysis. And endemic component contribution seems to be important in the Pearl River Delta area, where the incidence is high (95 per 100,000), while areas with relatively low incidence (4 per 100,000) are highly dependent on spatiotemporal spread and local autoregression.
Endothelial Antioxidant-1: a Key Mediator of Copper-dependent Wound Healing in vivo
Authors: Das Archita , Sudhahar Varadarajan , Chen Gin-Fu , Kim Ha Won , Youn Seock-Won , Finney Lydia , Vogt Stefan , Yang Jay , Kweon Junghun , Surenkhuu Bayasgalan , Ushio-Fukai Masuko , Fukai Tohru
Published: September 2016

Copper (Cu), an essential nutrient, promotes wound healing, however, target of Cu action and underlying mechanisms remain elusive. Cu chaperone Antioxidant-1 (Atox1) in the cytosol supplies Cu to the secretory enzymes such as lysyl oxidase (LOX), while Atox1 in the nucleus functions as a Cu-dependent transcription factor. Using mouse cutaneous wound healing model, here we show that Cu content (by X-ray Fluorescence Microscopy) and nuclear Atox1 are increased after wounding, and that wound healing with and without Cu treatment is impaired in Atox1−/− mice. Endothelial cell (EC)-specific Atox1−/− mice and gene transfer of nuclear-target Atox1 in Atox1−/− mice reveal that Atox1 in ECs as well as transcription factor function of Atox1 are required for wound healing. Mechanistically, Atox1−/− mice show reduced Atox1 target proteins such as p47phox NADPH oxidase and cyclin D1 as well as extracellular matrix Cu enzyme LOX activity in wound tissues. This in turn results in reducing O2− production in ECs, NFkB activity, cell proliferation and collagen formation, thereby inhibiting angiogenesis, macrophage recruitment and extracellular matrix maturation. Our findings suggest that Cu-dependent transcription factor/Cu chaperone Atox1 in ECs plays an important role to sense Cu to accelerate wound angiogenesis and healing.
Migratory blackcaps can use their magnetic compass at 5 degrees inclination, but are completely random at 0 degrees inclination
Authors: Schwarze Susanne , Steenken Friederike , Thiele Nadine , Kobylkov Dmitry , Lefeldt Nele , Dreyer David , Schneider Nils-Lasse , Mouritsen Henrik
Published: September 2016

It is known that night-migratory songbirds use a magnetic compass measuring the magnetic inclination angle, i.e. the angle between the Earth’s surface and the magnetic field lines, but how do such birds orient at the magnetic equator? A previous study reported that birds are completely randomly oriented in a horizontal north-south magnetic field with 0° inclination angle. This seems counter-intuitive, because birds using an inclination compass should be able to separate the north-south axis from the east-west axis, so that bimodal orientation might be expected in a horizontal field. Furthermore, little is known about how shallow inclination angles migratory birds can still use for orientation. In this study, we tested the magnetic compass orientation of night-migratory Eurasian blackcaps (Sylvia atricapilla) in magnetic fields with 5° and 0° inclination. At 5° inclination, the birds oriented as well as they did in the normal 67° inclined field in Oldenburg. In contrast, they were completely randomly oriented in the horizontal field, showing no sign of bimodality. Our results indicate that the inclination limit for the magnetic compass of the blackcap is below 5° and that these birds indeed seem completely unable to use their magnetic compass for orientation in a horizontal magnetic field.
Anomalous Enhancement of Mechanical Properties in the Ammonia Adsorbed Defective Graphene
Authors: Ma Fengxian , Jiao Yalong , Gu Yuantong , Bilic Ante , Chen Ying , Chen Zhongfang , Du Aijun
Published: September 2016

Pure graphene is known as the strongest material ever discovered. However, the unavoidable defect formation in the fabrication process renders the strength of defective graphene much lower (~14%) than that of its perfect counterpart. By means of density functional theory computations, we systematically explored the effect of gas molecules (H2, N2, NH3, CO, CO2 and O2) adsorption on the mechanical strength of perfect/defective graphene. The NH3 molecule is found to play a dominant role in enhancing the strength of defective graphene by up to ~15.6%, while other gas molecules decrease the strength of graphene with varying degrees. The remarkable strength enhancement can be interpreted by the decomposition of NH3, which saturates the dangling bond and leads to charge redistribution at the defect site. The present work provides basic information for the mechanical failure of gas-adsorbed graphene and guidance for manufacturing graphene-based electromechanical devices.
MicroRNA-122 as a predictor of HBsAg seroclearance in hepatitis B and C dual infected patients treated with interferon and ribavirin
Authors: Yen Yi-Hao , Huang Chao-Min , Wei Kuo-Liang , Wang Jing-Houng , Lu Sheng-Nan , Lee Chuan-Mo , Hung Chao-Hung , Chen Chien-Hung , Tseng Po-Lin , Chang Kuo-Chin , Tsai Ming-Chao , Lin Ming-Tsung , Wu Cheng-Kun , Yang Cheng-Hong , Moi Sin-Hua , Cho Chung-Lung , Hu Tsung-Hui
Published: September 2016

It has been demonstrated that microRNA-122 (miR-122) plays key roles in the modulation of hepatitis B virus (HBV) replication. This study examined the role of miR-122 in patients with hepatitis C virus (HCV)-HBV dual infection with active hepatitis C who received pegylated interferon-α and ribavirin dual therapy. We enrolled 121 patients with HCV-HBV dual infection after dual therapy. Stored serum was collected before treatment. RT-PCR was used to analyze miR-122. HBsAg seroclearance was noted in 37 (30.1%) cases during a median follow-up period of 5.4 years. miR-122 was significantly lower in HBsAg seroclearance patients than in non-HBsAg seroclearance patients (P < 0.014). Multivariate analysis showed that miR-122 was an independent factor of HBsAg seroclearance (OR: 0.30, 95% CI: 0.09–0.98, P = 0.046). miR-122 was significantly higher in patients who were qHBsAg > 100 IU/mL versus ≤100 IU/mL (P < 0.001). We concluded that in patients with HBV-HCV dual infection with active hepatitis C, miR-122 was associated with HBsAg seroclearance after therapy and qHBsAg level before therapy, indicating that miR-122 plays key roles in modulating HBV replication.
Automated Internal Classification of Beadless Chinese ZhuJi Freshwater Pearls based on Optical Coherence Tomography Images
Authors: Zhou Yang , Liu Tiebing , Shi Yang , Chen Zhengwei , Mao Jianwei , Zhou Wujie
Published: September 2016

Optical coherence tomography (OCT) has been applied to inspect the internal defect of beadless Chinese ZhuJi freshwater pearls. A novel fully automated algorithm is proposed to classify between normal and defective sub-layer in nacre layer. Our algorithm utilizes the graph segmentation approach to estimate the up and down boundaries of defect sub-layers from flattened and cropped image, and also proposes the strategy for edge and weight construction in segmentation process. The vertical gradients of boundary pixels are used to make grading decision. The algorithm is tested by typical pearl samples, and achieves 100% classification accuracy. The experiment result shows the feasibility and adaptability of the proposed approach, and proves that the OCT technique combined with proposed algorithm is a potential tool for fast and non-destructive diagnosis of internal structure of beadless pearl.
The H2/CH4 ratio during serpentinization cannot reliably identify biological signatures
Authors: Huang Ruifang , Sun Weidong , Liu Jinzhong , Ding Xing , Peng Shaobang , Zhan Wenhuan
Published: September 2016

Serpentinization potentially contributes to the origin and evolution of life during early history of the Earth. Serpentinization produces molecular hydrogen (H2) that can be utilized by microorganisms to gain metabolic energy. Methane can be formed through reactions between molecular hydrogen and oxidized carbon (e.g., carbon dioxide) or through biotic processes. A simple criterion, the H2/CH4 ratio, has been proposed to differentiate abiotic from biotic methane, with values approximately larger than 40 for abiotic methane and values of <40 for biotic methane. The definition of the criterion was based on two serpentinization experiments at 200 °C and 0.3 kbar. However, it is not clear whether the criterion is applicable at a wider range of temperatures. In this study, we performed sixteen experiments at 311–500 °C and 3.0 kbar using natural ground peridotite. Our results demonstrate that the H2/CH4 ratios strongly depend on temperature. At 311 °C and 3.0 kbar, the H2/CH4 ratios ranged from 58 to 2,120, much greater than the critical value of 40. By contrast, at 400–500 °C, the H2/CH4 ratios were much lower, ranging from 0.1 to 8.2. The results of this study suggest that the H2/CH4 ratios cannot reliably discriminate abiotic from biotic methane.
Integrating occurrence and detectability patterns based on interview data: a case study for threatened mammals in Equatorial Guinea
Authors: Martínez-Martí Chele , Jiménez-Franco María V. , Royle J. Andrew , Palazón José A. , Calvo José F.
Published: September 2016

Occurrence models that account for imperfect detection of species are increasingly used for estimating geographical range, for determining species-landscape relations and to prioritize conservation actions worldwide. In 2010, we conducted a large-scale survey in Río Muni, the mainland territory of Equatorial Guinea, which aimed to estimate the probabilities of occurrence and detection of threatened mammals based on environmental covariates, and to identify priority areas for conservation. Interviews with hunters were designed to record presence/absence data of seven species (golden cat, leopard, forest elephant, forest buffalo, western gorilla, chimpanzee and mandrill) in 225 sites throughout the region. We fitted single season occupancy models and recently developed models which also include false positive errors (i.e. species detected in places where it actually does not occur), which should provide more accurate estimates for most species, which are susceptible to mis-identification. Golden cat and leopard had the lowest occurrence rates in the region, whereas primates had the highest rates. All species, except gorilla, were affected negatively by human settlements. The southern half of Río Muni showed the highest occurrence of the species studied, and conservation strategies for ensuring the persistence of threatened mammals should be focused on this area.
RbTiOPO4 cascaded Raman operation with multiple Raman frequency shifts derived by Q-switched Nd:YAlO3 laser
Authors: Duan Yanmin , Zhu Haiyong , Zhang Yaoju , Zhang Ge , Zhang Jian , Tang Dingyuan , Kaminskii A. A.
Published: September 2016

An intra-cavity RbTiOPO4 (RTP) cascade Raman laser was demonstrated for efficient multi-order Stokes emission. An acousto-optic Q-switched Nd:YAlO3 laser at 1.08 μm was used as the pump source and a 20-mm-long x-cut RTP crystal was used as the Raman medium to meet the X(Z,Z)X Raman configuration. Multi-order Stokes with multiple Raman shifts (~271, ~559 and ~687 cm−1) were achieved in the output. Under an incident pump power of 9.5 W, a total average output power of 580 mW with a pulse repetition frequency of 10 kHz was obtained. The optical conversion efficiency is 6.1%. The results show that the RTP crystal can enrich laser spectral lines and generate high order Stokes light.
Enhanced cardiac TBC1D10C expression lowers heart rate and enhances exercise capacity and survival
Authors: Volland Cornelia , Bremer Sebastian , Hellenkamp Kristian , Hartmann Nico , Dybkova Nataliya , Khadjeh Sara , Kutschenko Anna , Liebetanz David , Wagner Stefan , Unsöld Bernhard , Didié Michael , Toischer Karl , Sossalla Samuel , Hasenfuß Gerd , Seidler Tim
Published: September 2016

TBC1D10C is a protein previously demonstrated to bind and inhibit Ras and Calcineurin. In cardiomyocytes, also CaMKII is inhibited and all three targeted enzymes are known to promote maladaptive cardiomyocyte hypertrophy. Here, in accordance with lack of Calcineurin inhibition in vivo, we did not observe a relevant anti-hypertrophic effect despite inhibition of Ras and CaMKII. However, cardiomyocyte-specific TBC1D10C overexpressing transgenic mice exhibited enhanced longevity. Ejection fraction and exercise capacity were enhanced in transgenic mice, but shortening of isolated cardiomyocytes was not increased. This suggests longevity resulted from enhanced cardiac performance but independent of cardiomyocyte contractile force. In further search for mechanisms, a transcriptome-wide analysis revealed expressional changes in several genes pertinent to control of heart rate (HR) including Hcn4, Scn10a, Sema3a and Cacna2d2. Indeed, telemetric holter recordings demonstrated slower atrial conduction and significantly lower HR. Pharmacological reduction of HR was previously demonstrated to enhance survival in mice. Thus, in addition to inhibition of stress signaling, TBC1D10C economizes generation of cardiac output via HR reduction, enhancing exercise capacity and survival. TBC1D10C may be a new target for HR reduction and longevity.
Proteomic Analysis of Non-depleted Serum Proteins from Bottlenose Dolphins Uncovers a High Vanin-1 Phenotype
Authors: Sobolesky Philip , Parry Celeste , Boxall Baylye , Wells Randall , Venn-Watson Stephanie , Janech Michael G.
Published: September 2016

Targeted approaches have been widely used to help explain physiological adaptations, but few studies have used non-targeted omics approaches to explore differences between diving marine mammals and terrestrial mammals. A rank comparison of undepleted serum proteins from common bottlenose dolphins (Tursiops truncatus) and pooled normal human serum led to the discovery of 11 proteins that appeared exclusive to dolphin serum. Compared to the comprehensive human plasma proteome, 5 of 11 serum proteins had a differential rank greater than 200. One of these proteins, Vanin-1, was quantified using parallel reaction monitoring in dolphins under human care and free-ranging dolphins. Dolphin serum Vanin-1 ranged between 31–106 μg/ml, which is 20–1000 times higher than concentrations reported for healthy humans. Serum Vanin-1 was also higher in dolphins under human care compared to free-ranging dolphins (64 ± 16 vs. 47 ± 12 μg/ml P < 0.05). Vanin-1 levels positively correlated with liver enzymes AST and ALT and negatively correlated with white blood cell counts and fibrinogen in free-ranging dolphins. Major differences exist in the circulating blood proteome of the bottlenose dolphin compared to terrestrial mammals and exploration of these differences in bottlenose dolphins and other marine mammals may identify veiled protective strategies to counter physiological stress.
Computational understanding and experimental characterization of twice-as-smart quadruplex ligands as chemical sensors of bacterial nucleotide second messengers
Authors: Zhou Jie , Roembke Benjamin T. , Paragi Gabor , Laguerre Aurélien , Sintim Herman O. , Fonseca Guerra Célia , Monchaud David
Published: September 2016

A twice-as-smart ligand is a small molecule that experiences a structural switch upon interaction with its target (i.e., smart ligand) that concomitantly triggers its fluorescence (i.e., smart probe). Prototypes of twice-as-smart ligands were recently developed to track and label G-quadruplexes: these higher-order nucleic acid structures originate in the assembly of four guanine(G)-rich DNA or RNA strands, whose stability is imparted by the formation and the self-assembly of G-quartets. The first prototypes of twice-as-smart quadruplex ligands were designed to exploit the self-association of quartets, being themselves synthetic G-quartets. While their quadruplex recognition capability has been thoroughly documented, some doubts remain about the precise photophysical mechanism that underlies their peculiar spectroscopic properties. Here, we uncovered this mechanism via complete theoretical calculations. Collected information was then used to develop a novel application of twice-as-smart ligands, as efficient chemical sensors of bacterial signaling pathways via the fluorescent detection of naturally occurring extracellular quadruplexes formed by cyclic dimeric guanosine monophosphate (c-di-GMP).
Structural and histone binding ability characterization of the ARB2 domain of a histone deacetylase Hda1 from Saccharomyces cerevisiae
Authors: Shen Hui , Zhu Yuwei , Wang Chongyuan , Yan Hui , Teng Maikun , Li Xu
Published: September 2016

Hda1 is the catalytic core component of the H2B- and H3- specific histone deacetylase (HDAC) complex from Saccharomyces cerevisiae, which is involved in the epigenetic repression and plays a crucial role in transcriptional regulation and developmental events. Though the N-terminal catalytic HDAC domain of Hda1 is well characterized, the function of the C-terminal ARB2 domain remains unknown. In this study, we determine the crystal structure of the ARB2 domain from S. cerevisiae Hda1 at a resolution of 2.7 Å. The ARB2 domain displays an α/β sandwich architecture with an arm protruding outside. Two ARB2 domain molecules form a compact homo-dimer via the arm elements, and assemble as an inverse “V” shape. The pull-down and ITC results reveal that the ARB2 domain possesses the histone binding ability, recognizing both the H2A-H2B dimer and H3-H4 tetramer. Perturbation of the dimer interface abolishes the histone binding ability of the ARB2 domain, indicating that the unique dimer architecture of the ARB2 domain coincides with the function for anchoring to histone. Collectively, our data report the first structure of the ARB2 domain and disclose its histone binding ability, which is of benefit for understanding the deacetylation reaction catalyzed by the class II Hda1 HDAC complex.
Smoothing a rugged protein folding landscape by sequence-based redesign
Authors: Porebski Benjamin T. , Keleher Shani , Hollins Jeffrey J. , Nickson Adrian A. , Marijanovic Emilia M. , Borg Natalie A. , Costa Mauricio G. S. , Pearce Mary A. , Dai Weiwen , Zhu Liguang , Irving James A. , Hoke David E. , Kass Itamar , Whisstock James C. , Bottomley Stephen P. , Webb Geoffrey I. , McGowan Sheena , Buckle Ashley M.
Published: September 2016

The rugged folding landscapes of functional proteins puts them at risk of misfolding and aggregation. Serine protease inhibitors, or serpins, are paradigms for this delicate balance between function and misfolding. Serpins exist in a metastable state that undergoes a major conformational change in order to inhibit proteases. However, conformational labiality of the native serpin fold renders them susceptible to misfolding, which underlies misfolding diseases such as α1-antitrypsin deficiency. To investigate how serpins balance function and folding, we used consensus design to create conserpin, a synthetic serpin that folds reversibly, is functional, thermostable and polymerization resistant. Characterization of its structure, folding and dynamics suggest that consensus design has remodeled the folding landscape to reconcile competing requirements for stability and function. This approach may offer general benefits for engineering functional proteins that have risky folding landscapes, including the removal of aggregation-prone intermediates and modifying scaffolds for use as protein therapeutics.
Using fluorescent dissolved organic matter to trace and distinguish the origin of Arctic surface waters
Authors: Gonçalves-Araujo Rafael , Granskog Mats A. , Bracher Astrid , Azetsu-Scott Kumiko , Dodd Paul A. , Stedmon Colin A.
Published: September 2016

Climate change affects the Arctic with regards to permafrost thaw, sea-ice melt, alterations to the freshwater budget and increased export of terrestrial material to the Arctic Ocean. The Fram and Davis Straits represent the major gateways connecting the Arctic and Atlantic. Oceanographic surveys were performed in the Fram and Davis Straits and on the east Greenland Shelf (EGS), in late summer 2012/2013. Meteoric (fmw), sea-ice melt, Atlantic and Pacific water fractions were determined and the fluorescence properties of dissolved organic matter (FDOM) were characterized. In Fram Strait and EGS, a robust correlation between visible wavelength fluorescence andfmwwas apparent, suggesting it as a reliable tracer of polar waters. However, a pattern was observed which linked the organic matter characteristics to the origin of polar waters. At depth in Davis Strait, visible wavelength FDOM was correlated to apparent oxygen utilization (AOU) and traced deep-water DOM turnover. In surface waters FDOM characteristics could distinguish between surface waters from eastern (Atlantic + modified polar waters) and western (Canada-basin polar waters) Arctic sectors. The findings highlight the potential of designingin situmulti-channel DOM fluorometers to trace the freshwater origins and decipher water mass mixing dynamics in the region without laborious samples analyses.
TDP-43 aggregation mirrors TDP-43 knockdown, affecting the expression levels of a common set of proteins
Authors: Prpar Mihevc S. , Baralle Marco , Buratti Emanuele , Rogelj Boris
Published: September 2016

TDP-43 protein plays an important role in regulating transcriptional repression, RNA metabolism and splicing. Typically it shuttles between the nucleus and the cytoplasm to perform its functions, while abnormal cytoplasmic aggregation of TDP-43 has been associated with neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). For the purpose of this study we selected a set of proteins that were misregulated following silencing of TDP-43 and analysed their expression in a TDP-43-aggregation model cell line HEK293 Flp-in Flag-TDP-43-12x-Q/N F4L. Following TDP-43 sequestration in insoluble aggregates, we observed higher nuclear levels of EIF4A3 and POLDIP3β, whereas nuclear levels of DNMT3A, HNRNPA3, PABPC1 and POLDIP3α dropped and cytoplasmic levels of RANBP1 dropped. In addition, immunofluorescence signal intensity quantifications showed increased nuclear expression of HNRNPL and YARS and downregulation of cytoplasmic DPCD. Furthermore, cytoplasmic levels of predominantly nuclear protein ALYREF increased. In conclusion, by identifying a common set of proteins that are differentially expressed in a similar manner in these two different conditions, we show that TDP-43 aggregation has a comparable effect to TDP-43 knockdown.
Integrating Multi-omics Data to Dissect Mechanisms of DNA repair Dysregulation in Breast Cancer
Authors: Liu Chao , Rohart Florian , Simpson Peter T. , Khanna Kum Kum , Ragan Mark A. , Lê Cao Kim-Anh
Published: September 2016

DNA repair genes and pathways that are transcriptionally dysregulated in cancer provide the first line of evidence for the altered DNA repair status in tumours and hence have been explored intensively as a source for biomarker discovery. The molecular mechanisms underlying DNA repair dysregulation, however, have not been systematically investigated in any cancer type. In this study, we performed a statistical analysis to dissect the roles of DNA copy number alteration (CNA), DNA methylation (DM) at gene promoter regions and the expression changes of transcription factors (TFs) in the differential expression of individual DNA repair genes in normal versus tumour breast samples. These gene-level results were summarised at pathway level to assess whether different DNA repair pathways are affected in distinct manners. Our results suggest that CNA and expression changes of TFs are major causes of DNA repair dysregulation in breast cancer and that a subset of the identified TFs may exert global impacts on the dysregulation of multiple repair pathways. Our work hence provides novel insights into DNA repair dysregulation in breast cancer. These insights improve our understanding of the molecular basis of the DNA repair biomarkers identified thus far and have potential to inform future biomarker discovery.
Parametric analysis of colony morphology of non-labelled live human pluripotent stem cells for cell quality control
Authors: Kato Ryuji , Matsumoto Megumi , Sasaki Hiroto , Joto Risako , Okada Mai , Ikeda Yurika , Kanie Kei , Suga Mika , Kinehara Masaki , Yanagihara Kana , Liu Yujung , Uchio-Yamada Kozue , Fukuda Takayuki , Kii Hiroaki , Uozumi Takayuki , Honda Hiroyuki , Kiyota Yasujiro , Furue Miho K
Published: September 2016

Given the difficulties inherent in maintaining human pluripotent stem cells (hPSCs) in a healthy state, hPSCs should be routinely characterized using several established standard criteria during expansion for research or therapeutic purposes. hPSC colony morphology is typically considered an important criterion, but it is not evaluated quantitatively. Thus, we designed an unbiased method to evaluate hPSC colony morphology. This method involves a combination of automated non-labelled live-cell imaging and the implementation of morphological colony analysis algorithms with multiple parameters. To validate the utility of the quantitative evaluation method, a parent cell line exhibiting typical embryonic stem cell (ESC)-like morphology and an aberrant hPSC subclone demonstrating unusual colony morphology were used as models. According to statistical colony classification based on morphological parameters, colonies containing readily discernible areas of differentiation constituted a major classification cluster and were distinguishable from typical ESC-like colonies; similar results were obtained via classification based on global gene expression profiles. Thus, the morphological features of hPSC colonies are closely associated with cellular characteristics. Our quantitative evaluation method provides a biological definition of ‘hPSC colony morphology’, permits the non-invasive monitoring of hPSC conditions and is particularly useful for detecting variations in hPSC heterogeneity.
Ska3 Ensures Timely Mitotic Progression by Interacting Directly With Microtubules and Ska1 Microtubule Binding Domain
Authors: Abad Maria Alba , Zou Juan , Medina-Pritchard Bethan , Nigg Erich A. , Rappsilber Juri , Santamaria Anna , Jeyaprakash A. Arockia
Published: September 2016

The establishment of physical attachment between the kinetochore and dynamic spindle microtubules, which undergo cycles of polymerization and depolymerization generating straight and curved microtubule structures, is essential for accurate chromosome segregation. The Ndc80 and Ska complexes are the major microtubule-binding factors of the kinetochore responsible for maintaining chromosome-microtubule coupling during chromosome segregation. We previously showed that the Ska1 subunit of the Ska complex binds dynamic microtubules using multiple contact sites in a mode that allows conformation-independent binding. Here, we show that the Ska3 subunit is required to modulate the microtubule binding capability of the Ska complex (i) by directly interacting with tubulin monomers and (ii) indirectly by interacting with tubulin contacting regions of Ska1 suggesting an allosteric regulation. Perturbing either the Ska3-microtubule interaction or the Ska3-Ska1 interactions negatively influences microtubule binding by the Ska complex in vitro and affects the timely onset of anaphase in cells. Thus, Ska3 employs additional modulatory elements within the Ska complex to ensure robust kinetochore-microtubule attachments and timely progression of mitosis.
Etoposide induced cytotoxicity mediated by ROS and ERK in human kidney proximal tubule cells
Authors: Shin Hyeon-Jun , Kwon Hyuk-Kwon , Lee Jae-Hyeok , Anwar Muhammad Ayaz , Choi Sangdun
Published: September 2016

Etoposide (ETO) is a commonly used chemotherapeutic drug that inhibits topoisomerase II activity, thereby leading to genotoxicity and cytotoxicity. However, ETO has limited application due to its side effects on normal organs, especially the kidney. Here, we report the mechanism of ETO-induced cytotoxicity progression in human kidney proximal tubule (HK-2) cells. Our results show that ETO perpetuates DNA damage, activates mitogen-activated protein kinase (MAPK), and triggers morphological changes, such as cell and nuclear swelling. When NAC, a well-known reactive oxygen species (ROS) scavenger, is co-treated with ETO, it inhibits an ETO-induced increase in mitochondrial mass, mitochondrial DNA (ND1 and ND4) copy number, intracellular ATP level, and mitochondrial biogenesis activators (TFAM, PGC-1α and PGC-1β). Moreover, co-treatment with ETO and NAC inhibits ETO-induced necrosis and cell swelling, but not apoptosis. Studies using MAPK inhibitors reveal that inhibition of extracellular signal regulated kinase (ERK) protects ETO-induced cytotoxicity by inhibiting DNA damage and caspase 3/7 activity. Eventually, ERK inhibitor treated cells are protected from ETO-induced nuclear envelope (NE) rupture and DNA leakage through inhibition of caspase activity. Taken together, these data suggest that ETO mediates cytotoxicity in HK-2 cells through ROS and ERK pathways, which highlight the preventive avenues in ETO-induced cytotoxicity in kidney.