bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractEstablishing 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

AbstractThe 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

AbstractIdiopathic 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

AbstractThe 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

AbstractNutrition 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

AbstractThe 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

AbstractPCR-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

AbstractSperm 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

AbstractDyneins 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

AbstractSugarcane 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

AbstractThe 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

AbstractMany 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

AbstractApple 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

AbstractDoppler 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

AbstractChirality 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

AbstractWe 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.