bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic stem cell states: naïve to primed pluripotency in rodents and humans
Authors: Weinberger Leehee , Ayyash Muneef , Novershtern Noa , Hanna Jacob H. 
Published: November 2015

PrefaceThe molecular mechanisms and signalling pathways that regulate thein vitropreservation of distinct pluripotent stem cell configurations, and their induction in somatic cells via direct reprogramming approaches, continue to constitute a highly exciting area of research. In this review, we provide an integrative synthesis on recent discoveries related to isolating unique naïve and primed pluripotent stem cell states with altered functional and molecular characteristics, and from different species. We overview pathways underlying pluripotent state transitions and interconversionin vitroandin vivo.We conclude by highlighting unresolved key questions, future directions and potential novel applications of such dynamic pluripotent cell states.
Fitness costs of herbicide resistance across natural populations of the common morning glory,Ipomoea purpurea
Authors: van Etten Megan L. , Kuester Adam , Chang Shu-Mei , Baucom Regina S 
Published: November 2015

AbstractAlthough fitness costs associated with plant defensive traits are widely expected, they are not universally detected, calling into question their generality. Here we examine the potential for life history trade-offs associated with herbicide resistance by examining seed germination, root growth, and above-ground growth across 43 naturally occurring populations ofIpomoea purpureathat vary in their resistance to RoundUp®, the most commonly used herbicide worldwide. We find evidence for life history trade-offs associated with all three traits; highly resistant populations had lower germination rates, shorter roots and smaller above-ground size. A visual exploration of the data indicated that the type of trade-off may differ among populations. Our results demonstrate that costs of adaptation may be present at stages other than simply the production of progeny in this agricultural weed. Additionally, the cumulative effect of costs at multiple life cycle stages can result in severe consequences to fitness when adapting to novel environments.
Adaptation to an invasive host is collapsing a native ecotype
Authors: Cenzer M L 
Published: November 2015

AbstractLocally adapted populations are often used as model systems for the early stages of ecological speciation, but most of these young divergent lineages will never become complete species. While the collapse of incipient species is theoretically common, very few examples have been documented in nature. Here I show that soapberry bugs (Jadera haematoloma) have lost adaptations to their native host plant (Cardiospermum corindum) and are regionally specializing on an invasive host plant (Koelreuteria elegans), collapsing a classic and well-documented example of local adaptation. All populations that were adapted to the native host - including those still found on that host today - are now better adapted to the invasive in multiple phenotypes. Weak differentiation remains in two traits, suggesting that homogenization across the region is incomplete. This study highlights the potential for adaptation to invasive species to disrupt native communities by swamping adaptation to native conditions through maladaptive gene flow.
A pan-cancer analysis of prognostic genes
Authors: Anaya Jordan , Reon Brian J. , Chen Wei-Min , Bekiranov Stefan , Dutta Anindya 
Published: November 2015

AbstractNumerous studies have identified prognostic genes in individual cancers, but a thorough pan-cancer analysis has not been performed. In addition, previous studies have mostly used microarray data instead of RNA-SEQ, and have not published comprehensive lists of associations with survival. Using recently available RNA-SEQ and clinical data from the The Cancer Genome Atlas for 6,495 patients, we have investigated every annotated and expressed gene’s association with survival across 16 cancer types. The most statistically significant harmful and protective genes were not shared across cancers, but were enriched in distinct gene sets which were shared across certain groups of cancers. These groups of cancers were independently reconstructed by unsupervised clustering of Cox coefficients (a measure of association with survival) for individual genes or for gene programs. This analysis has revealed unappreciated commonalities among cancers which may provide insights into cancer pathogenesis and rationales for co-opting treatments between cancers.
Assisted reproduction causes intrauterus growth restriction by disrupting placental lipid metabolism
Authors: Wei Yubao , Chen Shuqiang , Huang Xiuying , Lam Sin Man , Shui Guanghou , Sun Fangzhen 
Published: November 2015

AbstractIVF related intrauterus growth restriction or low birth weight (LBW) is very common in ART clinic. This study is focus on the aberrant lipid metabolism induced by in vitro fertilization and its mechanism. Firstly, we investigated the effect of IVF on fetal weight and placenta efficiency at E18.5 (at birth) and E14.5 (middle gestation). Data shows that IVF caused LBW and low placenta efficiency. Then we studied the lipidomics of E18.5 placenta and E14.5 placenta. The IVF group has an eccentric lipid content compared toin vivogroup. All the 15 lipid classes are largely accumulated in E18.5 IVF placenta and are deficient in E14.5 IVF placenta. In detail, most of the 287 lipid species is accumulated at E18.5 and went short at E14.5. Using qRT-PCR we detected the expression level of genes related to lipid uptake, transport and metabolism. Most of these genes are down-regulated which indicated the metabolism function of placenta is disrupted seriously. To the imprinted genes for lipid metabolism regulation asGNASandGrb10, IVF not only disrupt their imprinting status (methylation level) but also disrupt their gene expression. The expression ofDNMTsandTetsare also disrupted in the placenta. These data demonstrate that IVF impaired the regulation network of lipid metabolism. These results prove the hypothesis: imperfect IVF condition of fertilization jeopardize the expressionDNMTs,Tetsand imprinting status of imprinted genes for lipid metabolism regulation. Then it causes to abnormal expression of genes for lipid metabolism and regulation. This leads to the significant differences in lipid species quantification and lipid metabolism. So it contributed to low lipid transport efficiency, restricted fetal growth and LBW. This study provides a renewed knowledge of lipid metabolism in placenta and its relation to imprinted genes and gave some clinical aware for optimizing the ART practice.FundingThis work was supported by grants from the National Basic Research Program of China (973 Program) and National Natural Science Foundation of China.Competing InterestsThe authors have declared that no competing interests exist.AbbreviationsARTartificial reproductive technologyIVFin vitro fertilizationLBWlow birth weightGNASGuanine Nucleotide Binding Protein AlphaGrb10Growth factor receptor-bound protein 10
Depolarized Dynamic Light Scattering a method to analyse Particle Shape and Size
Authors: Meyer Arne , Dierks Karsten , Betzel Christian 
Published: November 2015

Dynamic Light Scattering (DLS) is already a widely used method for small particle size distribution analysis [1]. The main purpose of this method is the determination of particle sizes, respectively the hydrodynamic radius in the sub-microscopic range, i.e. 1 nm up to few µm. It is based on the Brownian motion of those particles. Light scattering methods are non-invasive and therefore a great advantage in the field of particle analysis [2a]. The next generation of Dynamic Light Scattering devices will apply depolarized dynamic light scattering (DDLS) [2b]. This technique allows to obtain beside radius distributions also information about the particle shape. However, for some time technical drawbacks made it almost unfeasible to use it for biological samples. In cooperation with the University of Hamburg we developed the first experimental set-up of a DDLS system to be used in the laboratory to analyze and characterize protein solutions as well as suspensions of nano crystals, suitable for Free-Electron-Laser applications. The fundamental difference to so far known "standard" DLS is that the scattered light is separated into two signal pathways, a vertically and a horizontally polarized component, applying a special designed beam splitter. DDLS allows to measure the translational diffusion and the rotational constants simultaneously. Both constants are derived from the decay times of the autocorrelation functions. With the equations of Perrin the system is capable of calculating the axis ratio of the particles, approximating the real particle shape as a rotational ellipsoid. For calibration and tests gold rod particles of 575 nm in length and 25 nm diameter were applied. The first biological sample, which was analyzed by DDLS was hemocyanin from Limulus polyphemus hemolymph [3a], which occurrs predominantly as hexamers, dodecamers and traces of higher aggregates occur at high pH. In summary, together with additional advantages like viscosity independent measurements and ten times higher resolution compared to DLS, the DDLS-technique is optimal to characterize biological samples to be used for crystallization experiments and to score solutions and suspensions of nano-crystals to be used for Free-Electron Laser applications [3b].
Modeling molecular crystals with fragment-based electronic structure techniques
Authors: Beran Gregory 
Published: November 2015

A proper theoretical description of molecular crystal packing requires a uniformly high-quality treatment of the diverse intra- and intermolecular interactions. Fragment-based electronic structure methods enable the application of accurate electronic structure approaches to chemically interesting molecular crystals by decomposing the total crystal energy into the sum of many smaller "fragment" calculations. In this talk, we will discuss (1) the hybrid quantum/classical fragment based approach we have developed for molecular crystal problems, (2) state-of-the-art electronic structure approaches for treating the individual fragments with the requisite accuracy and acceptable computational effort, and (3) applications of these techniques to interesting molecular crystal problems.
Crystal Structure of AcrB Complexed with Linezolid at 3.5Å Resolution
Authors: Hung Li-Wei , Kim Heungbok , Murakami Satoshi , Gupta Goutam , Kim Chang-Yub , Terwilliger Thomas 
Published: November 2015

We present the crystal structure of AcrB in complex with Linezolid[1]. AcrB is an inner-membrane Resistance-Nodulation-Division efflux pump and is part of the AcrAB-TolC multidrug-resistance tripartite efflux system in E. Coli. Crystal structures of AcrB by itself as well as several drug-bound complexes have been structurally characterized. Linezolid is an approved oxazolidinone antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to other antibiotics, and has been called a "reserve antibiotic", a drug of last resort against potentially intractable infections. This antibiotic inhibits bacterial protein synthesis by specifically binding to the 50S ribosomal subunit. Linezolid has no clinically significant effect on most Gram-negative bacteria. This is thought to be a result of relatively low intracellular concentration of Linezolid due to efflux, but there is no direct evidence yet to support this hypothesis. This membrane protein-drug complex shows that an antibiotic specific to Gram-positive bacteria can also bind an efflux pump from E. coli, a Gram-negative bacterium. The crystal structure of AcrB and Linezolid complex reveals that Linezolid binds to the A385/F386 loops of the symmetric trimers of AcrB in the same fashion as several other antibiotics that are extruded by efflux pumps. A conformational change of a loop in the bottom of the periplasmic cleft is also observed.
High-performance, quantum mechanics-based macromolecular x-ray refinement
Authors: Borbulevych Oleg , Westerhoff Lance 
Published: November 2015

Modern, structure based drug discovery (SBDD) is dependent upon accurate protein:ligand structure determination and characterization. In conventional x-ray refinement, the geometry of the ligand within the active site is modeled according to the practitioner's beliefs as expressed in the form of stereochemical restraints provided by the ligand library or CIF file. Further, metal centers, bound species, and so on can be difficult to refine correctly without significant human intervention. Our work has addressed this problem through the integration of DivCon6 - a linear scaling, semiempirical, quantum mechanics (SE-QM) functional - with the Phenix refinement package. With Phenix/DivCon[1], SE-QM is used in "real-time" during each microcycle over the course of the refinement. With its inclusion of electrostatics, charge transfer, polarization, dispersion, hydrogen bonds, etcetera, this method is a much more rigorous, robust alternative to conventional stereochemical restraints and is better able to accurately model protein:ligand structures without "tweaking" any restraints. We report PM6 refinement results for several key examples including structures with metal coordination spheres, covalent bonds, and other exotic protein:ligand chemistry situations. When compared with the originally deposited PDB structures, we found in all cases that QM refinement leads to ligand structures with much lower strain, and in some cases, the improvement is dramatic and as much 10+ fold. At the same time, SE-QM methods are better able to capture the influence of the surrounding structure (e.g. active site) on the ligand. These interactions are particularly interesting in SBDD as they are often the targets for lead design and optimization, and examples that illustrate how these interactions are captured with SE-QM will also be discussed.
Aperiodic 3D tiling by self-similar substitution method using solid unit
Authors: Watanabe Yasunari 
Published: November 2015

There are two important aperiodic tiling methods. One is a projection method and the other is self-similar substitution method. Author applied projection and substitution method to several quasi-periodic tiling [1a] [1b] [1c] [2a] [2b] [2c]. Quantity of the information for research of aperiodic tiling except quasi-periodic tiling is not so large as that of quasi-periodic tiling. Author shows one of the substitution example. that is a "pentomino tile" which is made of five unit squares. First generation of a "pentomino tile" is composed of two original pentominos and chiral two original pentominos [3]. Author considered 3D solid body unit similar to exterior view of car-body as shown in figure, then succeeded in first generation tile using the body unit. In this study, author consider a relation between substitution and crystallographic rotation matrix and translation matrix and discuss general formulation of self-similar substitution. Caption of Figure: (left-hand) original generation, (center) First generation, (right-hand) Second generation
Agilent Technologies: Proud Global Sponsors of the IYCr2014
Authors: Presly Oliver 
Published: November 2015

The International Year of Crystallography 2014 represents a unique chance to highlight crystallography to a wide audience of researchers, students, school children and members of the public. It also offers a platform for boosting the capabilities of research laboratories in less well developed parts of the world, with instruments and expertise helping a new generation of scientists to learn theory and techniques, to generate data and to form collaborations with experts in various crystallographic fields. Agilent is proud to support IYCr2014, to assist the International Union of Crystallography (IUCr) and its partners in achieving some of the key goals of the project. To this end, Agilent has teamed up with the IUCr in the IYCr2014 "Crystallography in Everyday Life" photo contest. A highlight of the IUCr Congress, this contest has been open throughout 2014, inviting all amateur and professional photographers to submit stunning images that capture the spirit of crystallography in the places, objects and experiences of everyday life. Entries have been submitted from across the world from both scientists and non-scientists alike. Two winning entries will each receive bursaries to attend the IUCr Congress, and their entries will be on display in the main exhibition area. These and 14 further notable entries will make up the Agilent-IUCr IYCr2014 academic calendar (2014-15), and copies will be available from the Agilent booth in Montreal. Agilent is also proudly supporting the IUCr-UNESCO OpenLab initiative; aiming to provide facilities and teaching to young scientists without access to their own instrumentation. Agilent and the IUCr have been working with a number of Agilent system users, specifically in Argentina, Hong Kong and Turkey, to develop OpenLab workshops organized by local researchers and supported by Agilent sponsorship and Application Scientists. This poster will highlight Agilent's IYCr participation, focusing on these initiatives.
UNESCO activities in Africa for the 2014 International Year of Crystallography (IYCr)
Authors: Ngome Abiaga Jean-Paul 
Published: November 2015

Following the United Nations General Assembly (Decision A/66/L.51) declaration of 2014 as the International Year of Crystallography (IYCr2014), UNESCO and IUCr received a strong mandate to coordinate the activities of the Year in order to tackle the global disaffection from science and scientific careers, namely in crystallography, that threatens scientific enterprise innovation and sustainability and, consequently, the prospects for using science for development, especially in Africa. In addition, the crystallography capacity-gap between the wealthiest and the poorest regions of the world is increasing due to brain drain, the weakness of local expertise, the absence of linkage between science policy and the regional community of crystallographers, as well as the lack of inclusion of Africa in international scientific cooperation. For developing countries in Africa, it is therefore vital to be in a position to exploit the opportunities that crystallography and the IYCr2014 offer in terms of building, nurturing and maintaining a critical mass of highly qualified, innovative scientists, students and engineers in crystallography-related fields. For all those reasons, UNESCO seizes the opportunities presented by the International Year to foster crystallography education, research and cooperation and its use and applications, which are providing solutions to some of the developmental challenges that Africa is facing today. Some of the UNESCO/IUCr flagships initiatives echoing to this strategy are both the IUCr-UNESCO OpenLabs (a network of operational crystallographic laboratories) in Africa and the Regional Summit meeting in Bloemfontein, South Africa.
High pressure studies of L-Serine-L-Ascorbic acid co-crystal
Authors: Arkhipov Sergey , Zakharov Boris , Boldyreva Elena 
Published: November 2015

Experiments for studying crystalline materials under extreme conditions are a powerful tool for investigating "structure-property" relationships. They also give information on the behavior of hydrogen bonds and are important both for materials science and crystal engineering. In addition, many processes in the living organisms are also related to mechanical stress. One of the most interesting tasks is to identify factors which influence the stability of a structure, or a part of the structure, at high pressure. Experiments on the systematic study of compounds in a wide range of pressures allow us to accumulate data that can be used to solve this problem. For a more complete picture, the mixed crystals of the selected compound are studied. Investigation of mixed crystals and cocrystals of interest can be compared with the crystals of individual compounds. We have chosen the structure of L-serine - L-ascorbic acid to be compared with those of L-serine and L-ascorbic acids for such a study. Phase transitions were previously reported to be induced by increasing pressure in both L-serine [1] and L-ascorbic acid [2]; moreover, the structure of L-serine was followed at multiple pressures by single-crystal and powder X-ray diffraction[3]. L-serine – L-ascorbic acid co-crystal was studied in the pressure range 0-5.4 GPa (at multiple points at every 0.5-0.7 GPa) by single-crystal X-ray diffraction and Raman spectroscopy. A phase transition has been detected and some rearrangement in the network of hydrogen bonds was observed. The high pressure data were compared with those for the individual structures of the L-serine and L-ascorbic acid. This work was supported by RFBR (grants 12–03-31541, 14-03-31866, 13-03-92704, 14-03-00902 ), Ministry of Science and Education of Russia and Russian Academy of Sciences.
Solid-state assembly of metal-organic architectures
Authors: Friscic Tomislav 
Published: November 2015

Chemical reactions induced or sustained by mechanical force (mechanochemistry) have attracted considerable interest as a means to achieve cleaner and "greener" solvent-free synthesis of molecules and materials. Such reactions also provide an opportunity to explore molecular recognition and self-assembly without the interfering effects of bulk solvents, such as solubility, complexation with solvent, or solvolysis.[1] This presentation will highlight our recent exploration of solvent-free chemistry as a means to understand the assembly, templating and the collapse of porous metal-organic structures. First, the recently developed methodology for real-time, in situ monitoring of mechanochemical reactions will be presented,[2] which uses highly penetrating synchrotron radiation to directly observe chemical and structural transformations during mechanical milling. By using this methodology it was possible, for the first time, to illuminate the mechanisms of metal-organic framework formation by milling, and observe new, fleeting intermediate phases. The second part of the presentation will focus on 'accelerated aging", a simple, diffusion-controlled and catalytically-accelerated methodology for the transformation of inert metal oxides into metal-organic architectures under the conditions mimicking those of geological mineral "weathering".[3] This solvent-free and low-energy technique provides reactant generality not yet demonstrated in mechanosynthesis, and allows the transformations of diverse transition, main group and lanthanide metal oxides, into 2- and 3-dimensional metal-organic architectures. The applications of accelerated aging in the clean synthesis of metal-organic frameworks and low-energy, solvent-free mineral separation will be discussed.