bluuebunny/crossref_metadata_2025 huggingface dataset:
SuperMassive Blackholes grow from stellar BHs of star formation history?
Authors: Rocca-Volmerange Brigitte
Published: August 2016

The origin of the supermassive black hole masses MSMBH discovered at the highest redshifts is still actively debated. Moreover the statistically significant relation of MSMBH with bulge luminosities LV, extended on several magnitude orders, confirms a common physical process linking small (≤ 1pc) to large (kpcs) size scales. The Spectral Energy Distributions (SEDs) of two z=3.8 radio galaxies 4C41.17 and TN J2007-1316, best-fitted by evolved early type galaxy and starburst scenarios also imply masses of stellar remnants. Computed with the evolutionary code Pegase.3, the cumulated stellar black hole mass MsBH reach up to several 109M⊙, similar to MSMBH at same z. We propose the SMBH growth is due to the migration of the stellar dense residues (sBH) towards the galaxy core by dynamical friction. Discussed in terms of time-scales, this process which is linking AGN and star formation, also fully justifies the famous relation MSMBH-LV.
Galaxies at z ~ 6: physical properties at the edge of the cosmic reionization
Authors: de Barros Stephane , Vanzella Eros , Pentericci Laura , Fontana Adriano , Grazian Andrea , Castellano Marco
Published: August 2016

An important effort has been recently made to detect spectroscopically galaxies at z ~ 6 and higher where the cosmic reionization is thought to occur. The drop of the fraction of Lyman Alpha Emitters (LAEs) at z>6 is currently interpreted as an effect of the increasing neutral hydrogen density.

We present preliminary results from the latest VLT/FORS2 programs, combined with ESO archival data, to perform a large census of z ~ 6 galaxies. We derive their physical properties as stellar mass and dust attenuation with an SED fitting tool including nebular emission which is of primeval importance because IRAC channels are strongly contaminated by emission lines at those redshifts. We take a special care to derive with precision the redshift of non LAEs to perform a comparison of their properties with the LAE population and derive as accurately as possible the fraction of LAEs. In particular, we compare the UV beta slope with the Lyα equivalent width which are known to correlate at lower redshift.

We also report the detection of few peculiar z ~ 6 galaxies with extremely blue UV β slope (~−3), which can be a signature of unusual stellar populations (e.g., very hot and massive stars).
The VIMOS Ultra Deep Survey: Lyα Emission and Stellar Populations of Star-Forming Galaxies at 2 < z < 6
Authors: Hathi Nimish P. , Le Fèvre Olivier ,   the VUDS team
Published: August 2016

The extensive ground-based spectroscopy campaign from the VIMOS Ultra-Deep Survey (VUDS), and the deep multi-wavelength photometry in three very well observed extragalactic fields (ECDFS, COSMOS, VVDS), allow us to investigate physical properties of a large sample (~4000 galaxies) of spectroscopically confirmed faint (iAB ≲ 25 mag) SFGs, with and without Lyα in emission, at z ~ 2–6. The fraction of Lyα emitters (LAEs; equivalent width (EW) ≥ 20Å) increases from ~10% at z ~ 2 to ~40% at z ~ 5–6, which is consistent with previous studies that employ higher Lyα EW cut. This increase in the LAE fraction could be, in part, due to a decrease in the dust content of galaxies as redshift increases. When we compare best-fit SED estimated stellar parameters for LAEs and non-LAEs, we find that Es(B-V) is smaller for LAEs at all redshifts and the difference in the median Es(B-V) between LAEs and non-LAEs increases as redshift increases, from 0.05 at z ~ 2 to 0.1 at z ~ 3.5 to 0.2 at z ~ 5. For the luminosities probed here (~L*), we find that star formation rates (SFRs) and stellar masses of galaxies, with and without Lyα in emission, show small differences such that, LAEs have lower SFRs and stellar masses compared to non-LAEs. This result could be a direct consequence of the sample selection. Our sample of LAEs are selected based on their continuum magnitudes and they probe higher continuum luminosities compared to narrow-band/emission line selected LAEs. Based on our results, it is important to note that all LAEs are not universally similar and their properties are strongly dependent on the sample selection, and/or continuum luminosities.
Probabilistic Selection of High-redshift Quasars with Subaru/Hyper Suprime-Cam Survey
Authors: Onoue Masafusa
Published: August 2016

High-redshift quasars are an important probe of the distant Universe. They enable observational studies of the early growth of supermassive blackholes, cosmic reionization, chemical enrichment of host galaxies, and so on. Through pioneering optical and near-infrared wide-area surveys such as the SDSS and the VIKING Survey, about one hundred quasars have been found at z > 6 (e.g., Fan et al. (2006b), Venemans et al. (2013)). However, its current small sample size and the fact that most of them are the most luminous (M1450 ≲ −24) population in this epoch prevents one from constraining statistics on high-redshift quasars, namely quasar luminosity function (QLF), and redshift evolution of IGM neutral fraction. Thus, discovery of large number of z > 6 quasars, especially low-luminous or z > 7 quasars, is highly desired for further understanding of the early universe.

We are now starting a new ground-breaking survey of high-redshift (z > 6) quasars using the exquisite imaging data provided by the Hyper Suprime-Cam (HSC) Subaru Strategic Program (SSP) Survey. Thanks to its extremely wide coverage and its high sensitivity thorough five optical bands (1,400 deg2 to the depth of r ~ 26 in HSC-Wide layer), it is one of the most powerful contemporary surveys that makes it possible for us to increase the number of z > 6 quasars by almost an order of magnitude, i.e., 300 at z ~ 6 and 50 at z ~ 7, based on the current estimate of the QLF at z > 6 by Willott et al. (2010b).

One of the biggest challenges in z > 6 quasar candidate selection is contamination of Galactic brown dwarfs, which have the same point-like appearance as and similarly red colors to the quasars. To overcome this issue and maximize the selection efficiency, we apply a double-layered approach to the HSC survey products, namely combination of two probabilistic selections: SED-fitting and Bayesian selection. In particular, we have developed a template SED fitting method optimized to high-redshift quasars selection. Its application with 27 photometric bands to the COSMOS quasars at 3 < z < 5 have shown that almost all of the known quasars are correctly classified with small dispersion σ|Δz|/(1+z)=0.01 and as low as η=2.5% outlier rate. At present, the HSC survey have successfully covered ~100 deg2 of HSC-Wide area in full colors. From the first-year data products, we have already started z > 6 quasar selection, and it is expected that the first HSC quasar discovery will be in the near future.
Galaxy morphologies in the era of big-data surveys
Authors: Huertas-Company M.
Published: August 2016

Galaxy morphology is a first-order descriptor of a galaxy and a useful proxy to identify physical processes. The 100 years old Hubble fork describes the structural diversity of galaxies in the local universe. Unveiling the origins of this galaxy zoology is a key challenge in galaxy evolution. In this review talk, I first summarized some key advances in our understanding of the morphological evolution of galaxies from z ~ 0 to z ~ 3, thank you in particular to the SDSS and HST legacies. In the second part, I focused on the classification techniques. With the emergence in the last years of large surveys the samples of study have increased by several orders of magnitude going from a few tens to several millions of objects. This trend will clearly continue in the next decade with coming surveys/missions such as EUCLID and WFIRST. While galaxy classification is still a required step in any survey, visual inspection of galaxies is becoming prohibitively time-consuming. Under these circumstances, the techniques used to estimate galaxy morphologies need to be updated.
Minor mergers: fundamental but unexplored drivers of galaxy evolution
Authors: Kaviraj Sugata
Published: August 2016

We use the SDSS Stripe 82 to study the stellar-mass growth that is triggered by minor mergers in local disk galaxies. Since major mergers destroy disks and create spheroids, morphologically disturbed spirals are likely remnants of minor mergers (since the disk remains intact). Disturbed spirals exhibit enhanced specific star formation rates (SSFRs), with the enhancement increasing in galaxies with ‘later’ morphological type (that have larger gas reservoirs and smaller bulges). By combining the SSFR enhancements with the fraction of time spirals in various morphological classes spend in this ‘enhanced’ mode, we estimate that ~40% of the star formation activity in local spirals is directly triggered by minor mergers. Combining our results with the star formation in local early-type galaxies – which is almost completely driven by minor mergers – suggests that around half the star formation activity at the present day is likely to be triggered by the minor-merger process.
Public Choice barriers to efficient climate adaptation – theoretical insights and lessons learned from German flood disasters
Authors: GAWEL ERIK , LEHMANN PAUL , STRUNZ SEBASTIAN , HEUSON CLEMENS
Published: August 2016

In this paper, we take a Public Choice perspective to identify and categorise barriers to efficient public climate adaptation. Specifically, we distinguish three dimensions of public adaptation: extent, structure (form and timing) and organisation (coordination across territorial authorities and policy fields). Within each of these dimensions, we investigate how the self-interest of voters, pressure groups, bureaucrats and politicians may bias adaptation decisions. Thus, we indicate specific barriers to efficient public adaptation. Based on this framework, we illustrate how Germany's response to major flood disasters reflects the incentive structure of concerned stakeholders and their political interaction. The ad hoc character of some public adaptation measures implies a clear bias from the efficient benchmark. In conclusion, we argue that the propositions of Public Choice theory shed some light on how empirical public adaptation processes unfold.
Neural correlates of two different types of extinction learning in the amygdala central nucleus
Authors: Iordanova Mihaela D. , Deroche Mickael L. D. , Esber Guillem R. , Schoenbaum Geoffrey
Published: August 2016

Extinction is a fundamental form of memory updating in which one learns to stop expecting an event that no longer occurs. This learning ensues when one experiences a change in environmental contingencies, that is, when an expected outcome fails to occur (simple extinction), or when a novel inflated expectation of a double outcome (overexpectation) is in conflict with the real outcome, and is a process that has been linked to amygdala function. Here, we show that in rats, the same neuronal population in the amygdala central nucleus updates reward expectancies and behaviour in both types of extinction, and neural changes in one paradigm are reflected in the other. This work may have implications for the management of addiction and anxiety disorders that require treatments based on the outcome omission, and disorders such as obesity that could use overexpectation, but not omission strategies.
PARP3 is a sensor of nicked nucleosomes and monoribosylates histone H2BGlu2
Authors: Grundy Gabrielle J. , Polo Luis M. , Zeng Zhihong , Rulten Stuart L. , Hoch Nicolas C. , Paomephan Pathompong , Xu Yingqi , Sweet Steve M. , Thorne Alan W. , Oliver Antony W. , Matthews Steve J. , Pearl Laurence H. , Caldecott Keith W.
Published: August 2016

PARP3 is a member of the ADP-ribosyl transferase superfamily that we show accelerates the repair of chromosomal DNA single-strand breaks in avian DT40 cells. Two-dimensional nuclear magnetic resonance experiments reveal that PARP3 employs a conserved DNA-binding interface to detect and stably bind DNA breaks and to accumulate at sites of chromosome damage. PARP3 preferentially binds to and is activated by mononucleosomes containing nicked DNA and which target PARP3 trans-ribosylation activity to a single-histone substrate. Although nicks in naked DNA stimulate PARP3 autoribosylation, nicks in mononucleosomes promote the trans-ribosylation of histone H2B specifically at Glu2. These data identify PARP3 as a molecular sensor of nicked nucleosomes and demonstrate, for the first time, the ribosylation of chromatin at a site-specific DNA single-strand break.
Rapid α-oligomer formation mediated by the Aβ C terminus initiates an amyloid assembly pathway
Authors: Misra Pinaki , Kodali Ravindra , Chemuru Saketh , Kar Karunakar , Wetzel Ronald
Published: August 2016

Since early oligomeric intermediates in amyloid assembly are often transient and difficult to distinguish, characterize and quantify, the mechanistic basis of the initiation of spontaneous amyloid growth is often opaque. We describe here an approach to the analysis of the Aβ aggregation mechanism that uses Aβ-polyglutamine hybrid peptides designed to retard amyloid maturation and an adjusted thioflavin intensity scale that reveals structural features of aggregation intermediates. The results support an aggregation initiation mechanism for Aβ-polyQ hybrids, and by extension for full-length Aβ peptides, in which a modular Aβ C-terminal segment mediates rapid, non-nucleated formation of α-helical oligomers. The resulting high local concentration of tethered amyloidogenic segments within these α-oligomers facilitates transition to a β-oligomer population that, via further remodelling and/or elongation steps, ultimately generates mature amyloid. Consistent with this mechanism, an engineered Aβ C-terminal fragment delays aggregation onset by Aβ-polyglutamine peptides and redirects assembly of Aβ42 fibrils.
Asymmetric counteranion-directed Lewis acid organocatalysis for the scalable cyanosilylation of aldehydes
Authors: Zhang Zhipeng , Bae Han Yong , Guin Joyram , Rabalakos Constantinos , van Gemmeren Manuel , Leutzsch Markus , Klussmann Martin , List Benjamin
Published: August 2016

Due to the high versatility of chiral cyanohydrins, the catalytic asymmetric cyanation reaction of carbonyl compounds has attracted widespread interest. However, efficient protocols that function at a preparative scale with low catalyst loading are still rare. Here, asymmetric counteranion-directed Lewis acid organocatalysis proves to be remarkably successful in addressing this problem and enabled a molar-scale cyanosilylation in quantitative yield and with excellent enantioselectivity. Also, the catalyst loading could be lowered to a part-per-million level (50 ppm: 0.005 mol%). A readily accessible chiral disulfonimide was used, which in combination with trimethylsilyl cyanide, turned into the active silylium Lewis acid organocatalyst. The nature of a peculiar phenomenon referred to as a “dormant period”, which is mainly induced by water, was systematically investigated by means of in situ Fourier transform infrared analysis.
Core-shell nanoscale coordination polymers combine chemotherapy and photodynamic therapy to potentiate checkpoint blockade cancer immunotherapy
Authors: He Chunbai , Duan Xiaopin , Guo Nining , Chan Christina , Poon Christopher , Weichselbaum Ralph R. , Lin Wenbin
Published: August 2016

Advanced colorectal cancer is one of the deadliest cancers, with a 5-year survival rate of only 12% for patients with the metastatic disease. Checkpoint inhibitors, such as the antibodies inhibiting the PD-1/PD-L1 axis, are among the most promising immunotherapies for patients with advanced colon cancer, but their durable response rate remains low. We herein report the use of immunogenic nanoparticles to augment the antitumour efficacy of PD-L1 antibody-mediated cancer immunotherapy. Nanoscale coordination polymer (NCP) core-shell nanoparticles carry oxaliplatin in the core and the photosensitizer pyropheophorbide-lipid conjugate (pyrolipid) in the shell (NCP@pyrolipid) for effective chemotherapy and photodynamic therapy (PDT). Synergy between oxaliplatin and pyrolipid-induced PDT kills tumour cells and provokes an immune response, resulting in calreticulin exposure on the cell surface, antitumour vaccination and an abscopal effect. When combined with anti-PD-L1 therapy, NCP@pyrolipid mediates regression of both light-irradiated primary tumours and non-irradiated distant tumours by inducing a strong tumour-specific immune response.
Mid-Holocene pulse of thinning in the Weddell Sea sector of the West Antarctic ice sheet
Authors: Hein Andrew S. , Marrero Shasta M. , Woodward John , Dunning Stuart A. , Winter Kate , Westoby Matthew J. , Freeman Stewart P. H. T. , Shanks Richard P. , Sugden David E.
Published: August 2016

Establishing the trajectory of thinning of the West Antarctic ice sheet (WAIS) since the last glacial maximum (LGM) is important for addressing questions concerning ice sheet (in)stability and changes in global sea level. Here we present detailed geomorphological and cosmogenic nuclide data from the southern Ellsworth Mountains in the heart of the Weddell Sea embayment that suggest the ice sheet, nourished by increased snowfall until the early Holocene, was close to its LGM thickness at 10 ka. A pulse of rapid thinning caused the ice elevation to fall ∼400 m to the present level at 6.5–3.5 ka, and could have contributed 1.4–2 m to global sea-level rise. These results imply that the Weddell Sea sector of the WAIS contributed little to late-glacial pulses in sea-level rise but was involved in mid-Holocene rises. The stepped decline is argued to reflect marine downdraw triggered by grounding line retreat into Hercules Inlet.
reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T cells
Authors: Kinkley Sarah , Helmuth Johannes , Polansky Julia K. , Dunkel Ilona , Gasparoni Gilles , Fröhler Sebastian , Chen Wei , Walter Jörn , Hamann Alf , Chung Ho-Ryun
Published: August 2016

The combinatorial action of co-localizing chromatin modifications and regulators determines chromatin structure and function. However, identifying co-localizing chromatin features in a high-throughput manner remains a technical challenge. Here we describe a novel reChIP-seq approach and tailored bioinformatic analysis tool, normR that allows for the sequential enrichment and detection of co-localizing DNA-associated proteins in an unbiased and genome-wide manner. We illustrate the utility of the reChIP-seq method and normR by identifying H3K4me3 or H3K27me3 bivalently modified nucleosomes in primary human CD4+ memory T cells. We unravel widespread bivalency at hypomethylated CpG-islands coinciding with inactive promoters of developmental regulators. reChIP-seq additionally uncovered heterogeneous bivalency in the population, which was undetectable by intersecting H3K4me3 and H3K27me3 ChIP-seq tracks. Finally, we provide evidence that bivalency is established and stabilized by an interplay between the genome and epigenome. Our reChIP-seq approach augments conventional ChIP-seq and is broadly applicable to unravel combinatorial modes of action.
Pathogenic landscape of idiopathic male infertility: new insight towards its regulatory networks
Authors: Kothandaraman Narasimhan , Agarwal Ashok , Abu-Elmagd Muhammad , Al-Qahtani Mohammed H
Published: August 2016

Idiopathic male infertility (IMI) affects nearly 10−15% of men in their prime reproductive age. More than 500 target genes were postulated to be associated with this disease condition through various genomic studies. The challenge is to determine the functional role of these genes and proteins that form part of a larger network leading to pathogenesis of the IMI phenotype in humans. In the current study, we have catalogued all of the genes associated with IMI from published studies, as well as looked at reactive oxygen species and antioxidant genes, the two key physiological determinants essential for normal spermatogenesis. Any imbalance in these genes through mutation, single-nucleotide polymorphisms (SNPs) or other forms could result in abnormal regulation of genes leading to infertility. SNPs catalogued in the current study, representing a third of the IMI genes, could possibly explain the various hidden factors associated with this condition. The enriched biological functions in SNPs, as well as functional analysis of IMI genes, resulted in the identification of novel gene pairs, from which we proposed new models to describe the underlying pathogenesis of this disease condition. The outcome of this study will give a new set of genes and proteins that could help explain the disease from a global perspective previously not addressed using standard approaches. Genes corresponding to proteins identified from the current study for spermatozoa and seminal plasma showed functional correlation based on their localization, which gave further confirmation of their roles in defective spermatogenesis as seen in IMI.
Towards human exploration of space: the THESEUS review series on neurophysiology research priorities
Authors: White Olivier , Clément Gilles , Fortrat Jacques-Olivier , Pavy-LeTraon Anne , Thonnard Jean-Louis , Blanc Stéphane , Wuyts Floris L , Paloski William H
Published: August 2016

The THESEUS project (Towards Human Exploration of Space: a European Strategy), initiated within the seventh Framework Programme by the European Commission, aimed at providing a cross-cutting, life-science-based roadmap for Europe’s strategy towards human exploration of long space missions, and its relevance to applications on Earth. This topic was investigated by experts in the field, in the framework of the THESEUS project whose aim was to develop an integrated life sciences research roadmap regarding human space exploration. In particular, decades of research have shown that altered gravity impairs neurological responses at large, such as perception, sleep, motor control, and cognitive factors. International experts established a list of key issues that should be addressed in that context and provided several recommendations such as a maximal exploitation of currently available resources on Earth and in space.
Towards human exploration of space: The THESEUS review series on nutrition and metabolism research priorities
Authors: Bergouignan Audrey , Stein T Peter , Habold Caroline , Coxam Veronique , O’ Gorman Donal , Blanc Stéphane
Published: August 2016

Nutrition has multiple roles during space flight from providing sufficient nutrients to meet the metabolic needs of the body and to maintain good health, to the beneficial psychosocial aspects related to the meals. Nutrition is central to the functioning of the body; poor nutrition compromises all the physiological systems. Nutrition is therefore likely to have a key role in counteracting the negative effects of space flight (e.g., radiation, immune deficits, oxidative stress, and bone and muscle loss). As missions increase in duration, any dietary/nutritional deficiencies will become progressively more detrimental. Moreover, it has been recognized that the human diet contains, in addition to essential macronutrients, a complex array of naturally occurring bioactive micronutrients that may confer significant long-term health benefits. It is therefore critical that astronauts be adequately nourished during missions. Problems of nutritional origin are often treatable by simply providing the appropriate nutrients and adequate recommendations. This review highlights six key issues that have been identified as space research priorities in nutrition field: in-flight energy balance; altered feeding behavior; development of metabolic stress; micronutrient deficiency; alteration of gut microflora; and altered fluid and electrolytes balance. For each of these topics, relevance for space exploration, knowledge gaps and proposed investigations are described. Finally, the nutritional questions related to bioastronautics research are very relevant to multiple ground-based-related health issues. The potential spin-offs are both interesting scientifically and potentially of great clinical importance.
DNMT1-PPARγ pathway in macrophages regulates chronic inflammation and atherosclerosis development in mice
Authors: Yu Jie , Qiu Youzhu , Yang Jie , Bian Shizhu , Chen Guozhu , Deng Mengyang , Kang Huali , Huang Lan
Published: August 2016

The DNA methyltransferase-mediated proinflammatory activation of macrophages is causally linked to the development of atherosclerosis (AS). However, the role of DNMT1, a DNA methylation maintenance enzyme, in macrophage polarization and AS development remains obscure. Here, we established transgenic mice with macrophage-specific overexpression of DNMT1 (TgDNMT1) or PPAR-γ (TgPPAR-γ) to investigate their effects on AS progression in ApoE-knockout mice fed an atherogenic diet. Primary macrophages were extracted to study the role of the DNMT1/PPAR-γ pathway in regulating inflammatory cytokine production. We demonstrated that TgDNMT1 significantly increased proinflammatory cytokine production in macrophages and plasma and it accelerated the progression of AS in the atherogenic diet-treated ApoE-knockout mice. Further, we found that the DNA methylation status of the proximal PPAR-γ promoter was regulated by DNMT1 in macrophages. Notably, additional TgPPAR-γ or pharmacological activation of PPAR-γ effectively prevented TgDNMT1-induced proinflammatory cytokine production in macrophages and AS development in the mouse model. Finally, we demonstrated that elevated DNMT1 was correlated with decreased PPAR-γ and increased proinflammatory cytokine production in the peripheral blood monocytes isolated from the patients with AS, compared to those of healthy donors. Our findings shed light on a novel strategy for the prevention and therapy of AS.
CRISPR-PCS: a powerful new approach to inducing multiple chromosome splitting in Saccharomyces cerevisiae
Authors: Sasano Yu , Nagasawa Koki , Kaboli Saeed , Sugiyama Minetaka , Harashima Satoshi
Published: August 2016

PCR-mediated chromosome splitting (PCS) was developed in the yeast Saccharomyces cerevisiae. It is based on homologous recombination and enables division of a chromosome at any point to form two derived and functional chromosomes. However, because of low homologous recombination activity, PCS is limited to a single site at a time, which makes the splitting of multiple loci laborious and time-consuming. Here we have developed a highly efficient and versatile chromosome engineering technology named CRISPR-PCS that integrates PCS with the novel genome editing CRISPR/Cas9 system. This integration allows PCS to utilize induced double strand breaks to activate homologous recombination. CRISPR-PCS enhances the efficiency of chromosome splitting approximately 200-fold and enables generation of simultaneous multiple chromosome splits. We propose that CRISPR-PCS will be a powerful tool for breeding novel yeast strains with desirable traits for specific industrial applications and for investigating genome function.
Ocean acidification changes the male fitness landscape
Authors: Campbell Anna L. , Levitan Don R. , Hosken David J. , Lewis Ceri
Published: August 2016

Sperm competition is extremely common in many ecologically important marine taxa. Ocean acidification (OA) is driving rapid changes to the marine environments in which freely spawned sperm operate, yet the consequences of OA on sperm performance are poorly understood in the context of sperm competition. Here, we investigated the impacts of OA (+1000 μatm pCO2) on sperm competitiveness for the sea urchin Paracentrotus lividus. Males with faster sperm had greater competitive fertilisation success in both seawater conditions. Similarly, males with more motile sperm had greater sperm competitiveness, but only under current pCO2 levels. Under OA the strength of this association was significantly reduced and there were male sperm performance rank changes under OA, such that the best males in current conditions are not necessarily best under OA. Therefore OA will likely change the male fitness landscape, providing a mechanism by which environmental change alters the genetic landscape of marine species.
Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions
Authors: Li Lin , Alper Joshua , Alexov Emil
Published: August 2016

Dyneins are important molecular motors involved in many essential biological processes, including cargo transport along microtubules, mitosis, and in cilia. Dynein motility involves the coupling of microtubule binding and unbinding to a change in the configuration of the linker domain induced by ATP hydrolysis, which occur some 25 nm apart. This leaves the accuracy of dynein stepping relatively inaccurate and susceptible to thermal noise. Using multi-scale modeling with a computational focusing technique, we demonstrate that the microtubule forms an electrostatic funnel that guides the dynein’s microtubule binding domain (MTBD) as it finally docks to the precise, keyed binding location on the microtubule. Furthermore, we demonstrate that electrostatic component of the MTBD’s binding free energy is linearly correlated with the velocity and run length of dynein, and we use this linearity to predict the effect of mutating each glutamic and aspartic acid located in MTBD domain to alanine. Lastly, we show that the binding of dynein to the microtubule is associated with conformational changes involving several helices, and we localize flexible hinge points within the stalk helices. Taken all together, we demonstrate that long range electrostatic interactions bring a level of precision to an otherwise noisy dynein stepping process.
The two chromosomes of the mitochondrial genome of a sugarcane cultivar: assembly and recombination analysis using long PacBio reads
Authors: Shearman Jeremy R. , Sonthirod Chutima , Naktang Chaiwat , Pootakham Wirulda , Yoocha Thippawan , Sangsrakru Duangjai , Jomchai Nukoon , Tragoonrung Somvong , Tangphatsornruang Sithichoke
Published: August 2016

Sugarcane accounts for a large portion of the worlds sugar production. Modern commercial cultivars are complex hybrids of S. officinarum and several other Saccharum species. Historical records identify New Guinea as the origin of S. officinarum and that a small number of plants originating from there were used to generate all modern commercial cultivars. The mitochondrial genome can be a useful way to identify the maternal origin of commercial cultivars. We have used the PacBio RSII to sequence and assemble the mitochondrial genome of a South East Asian commercial cultivar, known as Khon Kaen 3. The long read length of this sequencing technology allowed for the mitochondrial genome to be assembled into two distinct circular chromosomes with all repeat sequences spanned by individual reads. Comparison of five commercial hybrids, two S. officinarum and one S. spontaneum to our assembly reveals no structural rearrangements between our assembly, the commercial hybrids and an S. officinarum from New Guinea. The S. spontaneum, from India and one sample of S. officinarum (unknown origin) are substantially rearranged and have a large number of homozygous variants. This supports the record that S. officinarum plants from New Guinea are the maternal source of all modern commercial hybrids.
Recombinant adenovirus of human p66Shc inhibits MCF-7 cell proliferation
Authors: Yang Xiaoshan , Xu Rong , Lin Yajun , Zhen Yongzhan , Wei Jie , Hu Gang , Sun Hongfan
Published: August 2016

The aim of this work was to construct a human recombinant p66Shc adenovirus and to investigate the inhibition of recombinant p66Shc adenovirus on MCF-7 cells. The recombinant adenovirus expression vector was constructed using the Adeno-X Adenoviral System 3. Inhibition of MCF-7 cell proliferation was determined by MTT. Intracellular ROS was measured by DCFH-DA fluorescent probes and 8-OHdG was detected by ELISA. Cell apoptosis and the cell cycle were assayed by flow cytometry. Western blot were used to observe protein expression. p66Shc expression was upregulated in 4 cell lines after infection. The inhibitory effect of p66Shc recombinant adenovirus on MCF-7 cells was accompanied by enhanced ROS and 8-OHdG. However, no significant differences were observed in the cell apoptosis rate. The ratio of the cell cycle G2/M phase showed a significant increase. Follow-up experiments demonstrated that the expressions of p53, p-p53, cyclin B1 and CDK1 were upregulated with the overexpression of p66Shc. The Adeno-X Adenoviral System 3 can be used to efficiently construct recombinant adenovirus containing p66Shc gene and the Adeno-X can inhibit the proliferation of MCF-7 cells by inducing cell cycle arrest at the G2/M phase. These results suggested that p66Shc may be a key target for clinical cancer therapy.
Inhibition of cytochrome P450 3A by acetoxylated analogues of resveratrol in in vitro and in silico models
Authors: Basheer Loai , Schultz Keren , Kerem Zohar
Published: August 2016

Many dietary compounds, including resveratrol, are potent inhibitors of CYP3A4. Here we examined the potential to predict inhibition capacity of dietary polyphenolics using an in silico and in vitro approaches and synthetic model compounds. Mono, di and tri-acetoxy resveratrol were synthesized, a cell line of human intestine origin and microsomes from rat liver served to determine their in vitro inhibition of CYP3A4 and compared to that of resveratrol. Docking simulation served to predict the affinity of the synthetic model compounds to the enzyme. Modelling of the enzyme’s binding site revealed three types of interaction: hydrophobic, electrostatic and H-bonding. The simulation revealed that each of the examined acetylations of resveratrol led to the loss of important interactions of all types. Tri-acetoxy resveratrol was the weakest inhibitor in vitro despite being the more lipophilic and having the highest affinity for the binding site. The simulation demonstrated exclusion of all interactions between tri-acetoxy resveratrol and the heme due to distal binding, highlighting the complexity of the CYP3A4 binding site, which may allow simultaneous accommodation of two molecules. Finally, the use of computational modelling may serve as a quick predictive tool to identify potential harmful interactions between dietary compounds and prescribed drugs.
Photo Initiated Chemical Vapour Deposition To Increase Polymer Hydrophobicity
Authors: Bérard Ariane , Patience Gregory S. , Chouinard Gérald , Tavares Jason R.
Published: August 2016

Apple growers face new challenges to produce organic apples and now many cover orchards with high-density polyethylene (HDPE) nets to exclude insects, rather than spraying insecticides. However, rainwater- associated wetness favours the development of apple scabs,Venturia inaequalis, whose lesions accumulate on the leaves and fruit causing unsightly spots. Treating the nets with a superhydrophobic coating should reduce the amount of water that passes through the net. Here we treat HDPE and polyethylene terephthalate using photo-initiated chemical vapour deposition (PICVD). We placed polymer samples in a quartz tube and passed a mixture of H2and CO through it while a UVC lamp (254 nm) illuminated the surface. After the treatment, the contact angle between water droplets and the surface increased by an average of 20°. The contact angle of samples placed 70 cm from the entrance of the tube was higher than those at 45 cm and 20 cm. The PICVD-treated HDPE achieved a contact angle of 124°. Nets spray coated with a solvent-based commercial product achieved 180° but water ingress was, surprisingly, higher than that for nets with a lower contact angle.
Frequency shift of the Bragg and Non-Bragg backscattering from periodic water wave
Authors: Wen Biyang , Li Ke
Published: August 2016

Doppler effect is used to measure the relative speed of a moving target with respect to the radar and is also used to interpret the frequency shift of the backscattering from the ocean wave according to the water-wave phase velocity. The widely known relationship between the Doppler shift and the water-wave phase velocity was deduced from the scattering measurements data collected from actual sea surface and has not been verified under man-made conditions. Here we show that this ob- served frequency shift of the scattering data from the Bragg and Non-Bragg water wave is not the Doppler shift corresponding to the water-wave phase velocity as commonly believed, but is the water-wave frequency and its integral multiple frequency. The power spectrum of the backscatter from the periodic water wave consists of serials discrete peaks, which is equally spaced by water wave frequency. Only when the water-wave length is the integer multiples of the Bragg wave and the radar range resolution is infinite, does the frequency shift of the backscattering mathematically equal the Doppler shift according to the water-wave phase velocity.
Surface-anchored poly(acryloyl-L(D)-valine) with enhanced chirality-selective effect on cellular uptake of gold nanoparticles
Authors: Deng Jun , Wu Sai , Yao Mengyun , Gao Changyou
Published: August 2016

Chirality is one of the ubiquitous phenomena in biological systems. The left handed (L-) amino acids and right handed (D-) sugars are normally found in proteins and in RNAs and DNAs, respectively. The effect of chiral surfaces at the nanoscale on cellular uptake has, however, not been explored. This study reveals for the first time the molecular chirality on gold nanoparticles (AuNPs) functions as a direct regulator for cellular uptake. Monolayers of 2-mercaptoacetyl-L(D)-valine (L(D)-MAV) and poly(acryloyl-L(D)-valine (L(D)-PAV) chiral molecules were formed on AuNPs surface, respectively. The internalized amount of PAV-AuNPs was several times larger than that of MAV-AuNPs by A549 and HepG2 cells, regardless of the chirality difference. However, the D-PAV-AuNPs were internalized with significantly larger amount than the L-PAV-AuNPs. This chirality-dependent uptake effect is likely attributed to the preferable interaction between the L-phospholipid-based cell membrane and the D-enantiomers.
High Pressure Experimental Studies on CuO: Indication of Re-entrant Multiferroicity at Room Temperature
Authors: Jana Rajesh , Saha Pinku , Pareek Vivek , Basu Abhisek , Kapri Sutanu , Bhattacharyya Sayan , Mukherjee Goutam Dev
Published: August 2016

We have carried out detailed experimental investigations on polycrystalline CuO using dielectric constant, dc resistance, Raman spectroscopy and X-ray diffraction measurements at high pressures. Observation of anomalous changes both in dielectric constant and dielectric loss in the pressure range 3.7–4.4 GPa and reversal of piezoelectric current with reversal of poling field direction indicate to a change in ferroelectric order in CuO at high pressures. A sudden jump in Raman integrated intensity of Ag mode at 3.4 GPa and observation of Curie-Weiss type behaviour in dielectric constant below 3.7 GPa lends credibility to above ferroelectric transition. A slope change in the linear behaviour of the Ag mode and a minimum in the FWHM of the same indicate indirectly to a change in magnetic ordering. Since all the previous studies show a strong spin-lattice interaction in CuO, observed change in ferroic behaviour at high pressures can be related to a reentrant multiferroic ordering in the range 3.4 to 4.4 GPa, much earlier than predicted by theoretical studies. We argue that enhancement of spin frustration due to anisotropic compression that leads to change in internal lattice strain brings the multiferroic ordering to room temperature at high pressures.
Microgravity Level Measurement of the Beijing Drop Tower Using a Sensitive Accelerometer
Authors: Liu T. Y. , Wu Q. P. , Sun B. Q. , Han F. T.
Published: August 2016

Drop tower is the most common ground-based facility to provide microgravity environment and widely used in many science experiments. A differential space accelerometer has been proposed to test the spin-gravity interaction between rotating extended bodies onboard a drag-free satellite. In order to assist design and test of this inertial sensor in a series of ground- based pre-flight experiments, it is very important to know accurately the residual acceleration of drop towers. In this report, a sensitive instrument for this purpose was built with a high-performance servo quartz accelerometer and the dedicated interface electronics design providing small full-scale range and high sensitivity, up to 136.8 V/g0. The residual acceleration at the Beijing drop tower was measured using two different drop capsules. The experimental result shows that the microgravity level of the free-falling double capsule is better than 2 × 10−4g0 (Earth’s gravity). The measured data in this report provides critical microgravity information for design of the following ground experiments.
Antiproliferative and anti-inflammatory polyhydroxylated spirostanol saponins from Tupistra chinensis
Authors: Xiang Limin , Yi Xiaomin , Wang Yihai , He Xiangjiu
Published: August 2016

Tupistra chinensis is widely distributed in southwestern China and its rhizome is a famous folk medicine for the treatment of carbuncles and pharyngitis. Its chemical identity of potent antiproliferative and anti-inflammatory constituents has been carried out in this study. Twenty-three polyhydroxylated spirostanol saponins, including nine novels, were isolated and identified. The new spirostanol saponins were elucidated as spirost-25(27)-en-1β,2β,3β,4β,5β-pentol-2-O-β-D-xylopyranoside (1), spirost-25(27)- en-1β,2β,3β,4β,5β-pentol-2-O-α-L-arabinopyranoside (2), spirost-25(27)-en- 1β,3α,5β-triol (12), spirost-25(27)-en-1β,3α,4β,5β,6β-pentol (13), spirost-25(27)-en- 1β,2β,3β,5β-tetraol-5-O-β-D-glucopyranoside (16), 5β-spirost-25(27)-en-1β,3β-diol- 3-O-β-D-glucopyranosyl-(1 → 4)-β-D-glucopyranoside (17), (25R)-5β-spirostan- 1β,3β-diol-3-O-β-D-glucopyranosyl-(1 → 6)-β-D-glucopyranoside (18), (25R)-5β- spirostan-1β,3β-diol-3-O-β-D-fructofuranosyl-(2 → 6)-β-D-glucopyranoside (19), 5β-spirost-25(27)-en-3β-ol-3-O-β-D-glucopyranosyl-(1 → 4)-β-D-glucopyranoside (20). The antiproliferative effects against seven human cancer cell lines and inhibitory activities on nitric oxide (NO) production induced by lipopolysaccharide (LPS) in a macrophage cell line RAW 264.7 were assayed for all the isolated compounds. Compounds 17, 19 and 21 exhibited potential antiproliferative activities against all of human cancer cell lines tested. Compounds 21 showed significant inhibition on NO production with IC50 values of 11.5 μM. These results showed that the spirostanol saponins isolated from the dried rhizomes of T. chinensis have potent antiproliferative and anti-inflammatory activities and T. chinensis might be used as anticancer and.anti-inflammatory supplement.
Simultaneous Evaluation of Life Cycle Dynamics between a Host Paramecium and the Endosymbionts of Paramecium bursaria Using Capillary Flow Cytometry
Authors: Takahashi Toshiyuki
Published: August 2016

Endosymbioses are driving forces underlying cell evolution. The endosymbiosis exhibited by Paramecium bursaria is an excellent model with which to study symbiosis. A single-cell microscopic analysis of P. bursaria reveals that endosymbiont numbers double when the host is in the division phase. Consequently, endosymbionts must arrange their cell cycle schedule if the culture-condition-dependent change delays the generation time of P. bursaria. However, it remains poorly understood whether endosymbionts keep pace with the culture-condition-dependent behaviors of P. bursaria, or not. Using microscopy and flow cytometry, this study investigated the life cycle behaviors occurring between endosymbionts and the host. To establish a connection between the host cell cycle and endosymbionts comprehensively, multivariate analysis was applied. The multivariate analysis revealed important information related to regulation between the host and endosymbionts. Results show that dividing endosymbionts underwent transition smoothly from the division phase to interphase, when the host was in the logarithmic phase. In contrast, endosymbiont division stagnated when the host was in the stationary phase. This paper explains that endosymbionts fine-tune their cell cycle pace with their host and that a synchronous life cycle between the endosymbionts and the host is guaranteed in the symbiosis of P. bursaria.
Understanding the growth mechanism of graphene on Ge/Si(001) surfaces
Authors: Dabrowski J. , Lippert G. , Avila J. , Baringhaus J. , Colambo I. , Dedkov Yu S. , Herziger F. , Lupina G. , Maultzsch J. , Schaffus T. , Schroeder T. , Kot M. , Tegenkamp C. , Vignaud D. , Asensio M.-C.
Published: August 2016

The practical difficulties to use graphene in microelectronics and optoelectronics is that the available methods to grow graphene are not easily integrated in the mainstream technologies. A growth method that could overcome at least some of these problems is chemical vapour deposition (CVD) of graphene directly on semiconducting (Si or Ge) substrates. Here we report on the comparison of the CVD and molecular beam epitaxy (MBE) growth of graphene on the technologically relevant Ge(001)/Si(001) substrate from ethene (C2H4) precursor and describe the physical properties of the films as well as we discuss the surface reaction and diffusion processes that may be responsible for the observed behavior. Using nano angle resolved photoemission (nanoARPES) complemented by transport studies and Raman spectroscopy as well as density functional theory (DFT) calculations, we report the direct observation of massless Dirac particles in monolayer graphene, providing a comprehensive mapping of their low-hole doped Dirac electron bands. The micrometric graphene flakes are oriented along two predominant directions rotated by 30° with respect to each other. The growth mode is attributed to the mechanism when small graphene “molecules” nucleate on the Ge(001) surface and it is found that hydrogen plays a significant role in this process.
Label-free detection of real-time DNA amplification using a nanofluidic diffraction grating
Authors: Yasui Takao , Ogawa Kensuke , Kaji Noritada , Nilsson Mats , Ajiri Taiga , Tokeshi Manabu , Horiike Yasuhiro , Baba Yoshinobu
Published: August 2016

Quantitative DNA amplification using fluorescence labeling has played an important role in the recent, rapid progress of basic medical and molecular biological research. Here we report a label-free detection of real-time DNA amplification using a nanofluidic diffraction grating. Our detection system observed intensity changes during DNA amplification of diffracted light derived from the passage of a laser beam through nanochannels embedded in a microchannel. Numerical simulations revealed that the diffracted light intensity change in the nanofluidic diffraction grating was attributed to the change of refractive index. We showed the first case reported to date for label-free detection of real-time DNA amplification, such as specific DNA sequences from tubercle bacilli (TB) and human papillomavirus (HPV). Since our developed system allows quantification of the initial concentration of amplified DNA molecules ranging from 1 fM to 1 pM, we expect that it will offer a new strategy for developing fundamental techniques of medical applications.