ALBERT

Description: We present an anisotropic analysis of the baryon acoustic oscillation (BAO) scale in the twelfth and final data release of the Baryon Oscillation Spectroscopic Survey (BOSS). We independently analyse the LOWZ and CMASS galaxy samples: the LOWZ sample contains 361 762 galaxies with an effective redshift of z LOWZ = 0.32; the CMASS sample consists of 777 202 galaxies with an effective redshift of z CMASS = 0.57. We extract the BAO peak position from the monopole power-spectrum moment, α 0 , and from the μ 2 moment, α 2 , where μ is the cosine of the angle to the line of sight. The μ 2 -moment provides equivalent information to that available in the quadrupole but is simpler to analyse. After applying a reconstruction algorithm to reduce the BAO suppression by bulk motions, we measure the BAO peak position in the monopole and μ 2 -moment, which are related to radial and angular shifts in scale. We report H ( z LOWZ ) r s ( z d ) = (11.60 ± 0.60) x 10 3 km s –1 and D A ( z LOWZ )/ r s ( z d ) = 6.66 ± 0.16 with a cross-correlation coefficient of $r_{HD_{\rm A}}=0.41$ , for the LOWZ sample; and H ( z CMASS ) r s ( z d ) = (14.56 ± 0.37) x 10 3 km s –1 and D A ( z CMASS )/ r s ( z d ) = 9.42 ± 0.13 with a cross-correlation coefficient of $r_{HD_{\rm A}}=0.47$ , for the CMASS sample. We demonstrate that our results are not affected by the fiducial cosmology assumed for the analysis. We combine these results with the measurements of the BAO peak position in the monopole and quadrupole correlation function of the same data set (Cuesta et al. 2016 , companion paper) and report the consensus values: H ( z LOWZ ) r s ( z d ) = (11.63 ± 0.69) x 10 3 km s –1 and D A ( z LOWZ )/ r s ( z d ) = 6.67 ± 0.15 with $r_{HD_{\rm A}}=0.35$ for the LOWZ sample; H ( z CMASS ) r s ( z d ) = (14.67 ± 0.42) x 10 3 km s –1 and D A ( z CMASS )/ r s ( z d ) = 9.47 ± 0.12 with $r_{HD_{\rm A}}=0.52$ for the CMASS sample.

Description: A renewed interest in non-coding RNA (ncRNA) has led to the discovery of novel RNA species and post-transcriptional ribonucleoside modifications, and an emerging appreciation for the role of ncRNA in RNA epigenetics. Although much can be learned by amplification-based analysis of ncRNA sequence and quantity, there is a significant need for direct analysis of RNA, which has led to numerous methods for purification of specific ncRNA molecules. However, no single method allows purification of the full range of cellular ncRNA species. To this end, we developed a multidimensional chromatographic platform to resolve, isolate and quantify all canonical ncRNAs in a single sample of cells or tissue, as well as novel ncRNA species. The applicability of the platform is demonstrated in analyses of ncRNA from bacteria, human cells and plasmodium-infected reticulocytes, as well as a viral RNA genome. Among the many potential applications of this platform are a system-level analysis of the dozens of modified ribonucleosides in ncRNA, characterization of novel long ncRNA species, enhanced detection of rare transcript variants and analysis of viral genomes.

Description: The dominant cause of malaria in Malaysia is now Plasmodium knowlesi, a zoonotic parasite of cynomolgus macaque monkeys found throughout South East Asia. Comparative genomic analysis of parasites adapted to in vitro growth in either cynomolgus or human RBCs identified a genomic deletion that includes the gene encoding normocyte-binding protein...

Description: Author(s): S. Horzum, D. Çakır, J. Suh, S. Tongay, Y.-S. Huang, C.-H. Ho, J. Wu, H. Sahin, and F. M. Peeters Recently, rhenium disulfide (ReS2) monolayers were experimentally extracted by conventional mechanical exfoliation technique from as-grown ReS2 crystals. Unlike the well-known members of transition metal dichalcogenides (TMDs), ReS2 crystallizes in a stable distorted-1T structure and lacks an indire... [Phys. Rev. B 89, 155433] Published Mon Apr 28, 2014

Description: The electronic transport properties in individual niobium disulphide (NbS 2 ) nanoflakes mechanically exfoliated from the bulk crystal with three rhombohedral (3R) structure grown by chemical vapor transport were investigated. It is found that the conductivity values of the single-crystalline nanoflakes are approximately two orders of magnitude lower than that of their bulk counterparts. Temperature-dependent conductivity measurements show that the 3R-NbS 2 nanoflakes exhibit semiconducting transport behavior, which is also different from the metallic character in the bulk crystals. In addition, the noncontinuous conductivity variations were observed at the temperature below 180 K for both the nanoflakes and the bulks, which is attributed to the probable charge density wave transition. The photoconductivities in the semiconducting nanoflakes were also observed under the excitation at 532 nm wavelength. The probable mechanisms resulting in the different transport behaviors between the NbS 2 nanostructure and bulk were discussed.

Description: 2-Oxoglutarate (2OG)-dependent oxygenases have important roles in the regulation of gene expression via demethylation of N-methylated chromatin components and in the hydroxylation of transcription factors and splicing factor proteins. Recently, 2OG-dependent oxygenases that catalyse hydroxylation of transfer RNA and ribosomal proteins have been shown to be important in translation relating to cellular growth, TH17-cell differentiation and translational accuracy. The finding that ribosomal oxygenases (ROXs) occur in organisms ranging from prokaryotes to humans raises questions as to their structural and evolutionary relationships. In Escherichia coli, YcfD catalyses arginine hydroxylation in the ribosomal protein L16; in humans, MYC-induced nuclear antigen (MINA53; also known as MINA) and nucleolar protein 66 (NO66) catalyse histidine hydroxylation in the ribosomal proteins RPL27A and RPL8, respectively. The functional assignments of ROXs open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in the residue and protein selectivities of prokaryotic and eukaryotic ROXs, comparison of the crystal structures of E. coli YcfD and Rhodothermus marinus YcfD with those of human MINA53 and NO66 reveals highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-dependent oxygenases. ROX structures with and without their substrates support their functional assignments as hydroxylases but not demethylases, and reveal how the subfamily has evolved to catalyse the hydroxylation of different residue side chains of ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-domain-containing hydroxylases, including the hypoxia-inducible factor asparaginyl hydroxylase FIH and histone N(epsilon)-methyl lysine demethylases, identifies branch points in 2OG-dependent oxygenase evolution and distinguishes between JmjC-containing hydroxylases and demethylases catalysing modifications of translational and transcriptional machinery. The structures reveal that new protein hydroxylation activities can evolve by changing the coordination position from which the iron-bound substrate-oxidizing species reacts. This coordination flexibility has probably contributed to the evolution of the wide range of reactions catalysed by oxygenases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066111/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066111/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chowdhury, Rasheduzzaman -- Sekirnik, Rok -- Brissett, Nigel C -- Krojer, Tobias -- Ho, Chia-Hua -- Ng, Stanley S -- Clifton, Ian J -- Ge, Wei -- Kershaw, Nadia J -- Fox, Gavin C -- Muniz, Joao R C -- Vollmar, Melanie -- Phillips, Claire -- Pilka, Ewa S -- Kavanagh, Kathryn L -- von Delft, Frank -- Oppermann, Udo -- McDonough, Michael A -- Doherty, Aidan J -- Schofield, Christopher J -- 092809/Wellcome Trust/United Kingdom -- 6947/Cancer Research UK/United Kingdom -- BB/C518230/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/L009846/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Arthritis Research UK/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Cancer Research UK/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2014 Jun 19;510(7505):422-6. doi: 10.1038/nature13263. Epub 2014 May 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK. ; 1] The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK [2]. ; 1] Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK [2]. ; Structural Genomics Consortium, University of Oxford, Headington, Oxford OX3 7DQ, UK. ; Synchrotron SOLEIL, Saint Aubin, 91192 Gif-sur-Yvette Cedex, France. ; 1] Structural Genomics Consortium, University of Oxford, Headington, Oxford OX3 7DQ, UK [2] NIHR Oxford Biomedical Research Unit, Botnar Research Centre, Oxford OX3 7LD, UK. ; Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24814345" target="_blank"〉PubMed〈/a〉

Description: Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome, Published online: 22 May 2018; doi:10.1038/s41467-018-03143-w The Sc2.0 project has built the Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system into their synthetic chromosomes. Here the authors use SCRaMbLE to rapidly develop, diversify and screen strains for diverse production and growth characteristics.

Description: Cellular membranes act as signaling platforms and control solute transport. Membrane receptors, transporters, and enzymes communicate with intracellular processes through protein-protein interactions. Using a split-ubiquitin yeast two-hybrid screen that covers a test-space of 6.4 x 10(6) pairs, we identified 12,102 membrane/signaling protein interactions from Arabidopsis. Besides confirmation of expected interactions such as heterotrimeric G protein subunit interactions and aquaporin oligomerization, 〉99% of the interactions were previously unknown. Interactions were confirmed at a rate of 32% in orthogonal in planta split-green flourescent protein interaction assays, which was statistically indistinguishable from the confirmation rate for known interactions collected from literature (38%). Regulatory associations in membrane protein trafficking, turnover, and phosphorylation include regulation of potassium channel activity through abscisic acid signaling, transporter activity by a WNK kinase, and a brassinolide receptor kinase by trafficking-related proteins. These examples underscore the utility of the membrane/signaling protein interaction network for gene discovery and hypothesis generation in plants and other organisms.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jones, Alexander M -- Xuan, Yuanhu -- Xu, Meng -- Wang, Rui-Sheng -- Ho, Cheng-Hsun -- Lalonde, Sylvie -- You, Chang Hun -- Sardi, Maria I -- Parsa, Saman A -- Smith-Valle, Erika -- Su, Tianying -- Frazer, Keith A -- Pilot, Guillaume -- Pratelli, Rejane -- Grossmann, Guido -- Acharya, Biswa R -- Hu, Heng-Cheng -- Engineer, Cawas -- Villiers, Florent -- Ju, Chuanli -- Takeda, Kouji -- Su, Zhao -- Dong, Qunfeng -- Assmann, Sarah M -- Chen, Jin -- Kwak, June M -- Schroeder, Julian I -- Albert, Reka -- Rhee, Seung Y -- Frommer, Wolf B -- New York, N.Y. -- Science. 2014 May 16;344(6185):711-6. doi: 10.1126/science.1251358.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Biology, Carnegie Institution for Science, CA 94305, USA. ; Department of Physics, Pennsylvania State University, University Park, PA 16802, USA. ; Department of Plant Biology, Carnegie Institution for Science, CA 94305, USA. Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic University and State University, Blacksburg, VA 24061, USA. ; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA. ; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA. ; Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA. ; Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA. ; Department of Plant Biology, Carnegie Institution for Science, CA 94305, USA. Michigan State University-U.S. Department of Energy (MSU-DOE) Plant Research Laboratory and Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA. ; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA. Center for Plant Aging Research, Institute for Basic Science, Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 711-873, Republic of Korea. ; Department of Plant Biology, Carnegie Institution for Science, CA 94305, USA. wfrommer@stanford.edu srhee@carnegiescience.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24833385" target="_blank"〉PubMed〈/a〉

Description: The temperature dependence of the spectral features in the vicinity of the direct band edge of mixed-crystals Mo(S x Se 1-x ) 2 solid solutions is measured in the temperature range of 25–295 K by using piezoreflectance (PzR). The near band-edge excitonic transition energies of Mo(S x Se 1-x ) 2 solid solutions were determined accurately from a detailed line-shape fit of the PzR spectra. The near band-edge excitonic transition energies were found to vary smoothly with the increase of S content x, indicating that the natures of the direct band edges of Mo(S x Se 1-x ) 2 solid solutions are similar. The temperature dependences of near band edge transition energies were analyzed using Bose-Einstein expressions in the temperature range from 25 to 295 K. The parameters that described the temperature variation of the energies and broadening function of the excitonic transitions were evaluated and discussed.

Description: Carbohydrate-based vaccines have shown therapeutic efficacy for infectious disease and cancer. The mushroom Ganoderma lucidum (Reishi) containing complex polysaccharides has been used as antitumor supplement, but the mechanism of immune response has rarely been studied. Here, we show that the mice immunized with a l-fucose (Fuc)-enriched Reishi polysaccharide fraction (designated...