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https://www.readbyqxmd.com/read/28231512/the-impact-of-third-generation-genomic-technologies-on-plant-genome-assembly
#1
REVIEW
Wen-Biao Jiao, Korbinian Schneeberger
Since the introduction of next generation sequencing, plant genome assembly projects do not need to rely on dedicated research facilities or community-wide consortia anymore, even individual research groups can sequence and assemble the genomes they are interested in. However, such assemblies are typically not based on the entire breadth of genomic technologies including genetic and physical maps and their contiguities tend to be low compared to the full-length gold standard reference sequences. Recently emerging third generation genomic technologies like long-read sequencing or optical mapping promise to bridge this quality gap and enable simple and cost-effective solutions for chromosomal-level assemblies...
February 20, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28231467/synaptic-vesicle-endocytosis-occurs-on-multiple-timescales-and-is-mediated-by-formin-dependent-actin-assembly
#2
Tolga Soykan, Natalie Kaempf, Takeshi Sakaba, Dennis Vollweiter, Felix Goerdeler, Dmytro Puchkov, Natalia L Kononenko, Volker Haucke
Neurotransmission is based on the exocytic fusion of synaptic vesicles (SVs) followed by endocytic membrane retrieval and the reformation of SVs. Recent data suggest that at physiological temperature SVs are internalized via clathrin-independent ultrafast endocytosis (UFE) within hundreds of milliseconds, while other studies have postulated a key role for clathrin-mediated endocytosis (CME) of SV proteins on a timescale of seconds to tens of seconds. Here we demonstrate using cultured hippocampal neurons as a model that at physiological temperature SV endocytosis occurs on several timescales from less than a second to several seconds, yet, is largely independent of clathrin...
February 22, 2017: Neuron
https://www.readbyqxmd.com/read/28231430/combined-high-stretchability-and-gas-barrier-in-hydrogen-bonded-multilayer-nanobrick-wall-thin-films
#3
Shuang Qin, Yixuan Song, Michael Floto, Jaime C Grunlan
Hydrogen-bonded multilayer thin films are very stretchable, but their gas barrier properties are modest compared to more traditional ionically-bonded assemblies. In an effort to improve the gas barrier of poly(ethylene oxide) (PEO) - poly(acrylic acid) (PAA) multilayer films, without sacrificing stretchability, montmorillonite (MMT) clay platelets were combined with PAA and alternately deposited with PEO. A ten bilayer PEO/PAA+MMT film (432 nm thick), deposited on a 1 mm PU substrate, resulted in a 54X reduction in oxygen transmission rate after exposure to a 20% strain...
February 23, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28231426/engineering-of-anti-cd133-tri-specific-molecule-capable-of-inducing-nk-expansion-and-driving-antibody-dependent-cell-mediated-cytotoxicity-adcc
#4
Jörg U Schmohl, Martin Felices, Felix Oh, Alexander J Lenvik, Aaron M Lebeau, Jayanth Panyam, Jeffrey S Miller, Daniel A Vallera
Purpose: The selective elimination of cancer stem cells (CSCs) in tumor patients is a crucial goal because CSCs cause drug refractory relapse. To improve the current conventional bispecific immune-engager platform, a 16133 BiKE, consisting of scFvs binding FcγRIII (CD16) on NK cells and CD133 on carcinoma cells, was first synthesized and a modified IL-15 crosslinker capable of stimulating NK effector cells was introduced. Materials and Methods: DNA shuffling and ligation techniques were used to assemble and synthesize the 1615133 trispecific NK cell engager (TriKE)...
February 20, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28231383/the-pangenome-of-hexaploid-bread-wheat
#5
Juan D Montenegro, Agnieszka A Golicz, Philipp E Bayer, Bhavna Hurgobin, HueyTyng Lee, Chon-Kit Kenneth Chan, Paul Visendi, Kaitao Lai, Jaroslav Doležel, Jacqueline Batley, David Edwards
There is an increasing understanding that gene presence absence variation plays an important role in the heritability of agronomic traits, however there have been relatively few studies on gene presence absence variation in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic diversity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome diversity found in current modern elite cultivars...
February 23, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28231340/the-widely-used-nicotiana-benthamiana-16c-line-has-an-unusual-t-dna-integration-pattern-including-a-transposon-sequence
#6
Joshua G Philips, Fatima Naim, Michał T Lorenc, Kevin J Dudley, Roger P Hellens, Peter M Waterhouse
Nicotiana benthamiana is employed around the world for many types of research and one transgenic line has been used more extensively than any other. This line, 16c, expresses the Aequorea victoria green fluorescent protein (GFP), highly and constitutively, and has been a major resource for visualising the mobility and actions of small RNAs. Insights into the mechanisms studied at a molecular level in N. benthamiana 16c are likely to be deeper and more accurate with a greater knowledge of the GFP gene integration site...
2017: PloS One
https://www.readbyqxmd.com/read/28231333/molecular-mechanisms-of-cooperative-binding-of-transcription-factors-runx1-cbf%C3%AE-ets1-on-the-tcr%C3%AE-gene-enhancer
#7
Kota Kasahara, Masaaki Shiina, Ikuo Fukuda, Kazuhiro Ogata, Haruki Nakamura
Ets1 is an essential transcription factor (TF) for several important physiological processes, including cell proliferation and differentiation. Its recognition of the enhancer region of the TCRα gene is enhanced by the cooperative binding of the Runx1-CBFβ heterodimer, with the cancelation of phosphorylation-dependent autoinhibition. The detailed mechanism of this interesting cooperativity between Ets1 and the Runx1-CBFβ heterodimer is still largely unclear. Here, we investigated the molecular mechanisms of this cooperativity, by using molecular dynamics simulations...
2017: PloS One
https://www.readbyqxmd.com/read/28231302/bioinformatic-prediction-of-g-protein-coupled-receptor-encoding-sequences-from-the-transcriptome-of-the-foreleg-including-the-haller-s-organ-of-the-cattle-tick-rhipicephalus-australis
#8
Sergio Munoz, Felix D Guerrero, Anastasia Kellogg, Andrew M Heekin, Ming-Ying Leung
The cattle tick of Australia, Rhipicephalus australis, is a vector for microbial parasites that cause serious bovine diseases. The Haller's organ, located in the tick's forelegs, is crucial for host detection and mating. To facilitate the development of new technologies for better control of this agricultural pest, we aimed to sequence and annotate the transcriptome of the R. australis forelegs and associated tissues, including the Haller's organ. As G protein-coupled receptors (GPCRs) are an important family of eukaryotic proteins studied as pharmaceutical targets in humans, we prioritized the identification and classification of the GPCRs expressed in the foreleg tissues...
2017: PloS One
https://www.readbyqxmd.com/read/28231281/the-intron-in-centromeric-noncoding-rna-facilitates-rnai-mediated-formation-of-heterochromatin
#9
Masatoshi Mutazono, Misato Morita, Chihiro Tsukahara, Madoka Chinen, Shiori Nishioka, Tatsuhiro Yumikake, Kohei Dohke, Misuzu Sakamoto, Takashi Ideue, Jun-Ichi Nakayama, Kojiro Ishii, Tokio Tani
In fission yeast, the formation of centromeric heterochromatin is induced through the RNA interference (RNAi)-mediated pathway. Some pre-mRNA splicing mutants (prp) exhibit defective formation of centromeric heterochromatin, suggesting that splicing factors play roles in the formation of heterochromatin, or alternatively that the defect is caused by impaired splicing of pre-mRNAs encoding RNAi factors. Herein, we demonstrate that the splicing factor spPrp16p is enriched at the centromere, and associates with Cid12p (a factor in the RNAi pathway) and the intron-containing dg ncRNA...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28231023/increasing-nocardia-incidence-associated-with-bronchiectasis-at-a-tertiary-care-center
#10
Michael H Woodworth, Jennifer L Saullo, Paul M Lantos, Gary M Cox, Jason E Stout
RATIONALE: Nocardia is a genus of pathogens that most commonly afflicts immunocompromised hosts, but may be an emerging infection among persons with bronchiectasis. OBJECTIVES: To examine the epidemiology and clinical presentation of adult patients with Nocardia and bronchiectasis relative to other patient groups. METHODS: We examined a retrospectively-assembled cohort of adults at Duke University Hospital in Durham, North Carolina with at least one positive culture from a bodily fluid or tissue specimen for Nocardia between January 1996 and December 2013...
February 23, 2017: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/28231012/quantum-percolation-and-magnetic-nano-droplet-states-in-electronically-phase-separated-manganite-nanowires
#11
Kaixuan Zhang, Lin Li, Hui Li, Qiyuan Feng, Nan Zhang, Long Cheng, Xiaodong Fan, Yubin Hou, Qingyou Lu, Zhenyu Zhang, Changgan Zeng
One-dimensional (1D) confinement has been revealed to effectively tune the properties of materials in homogeneous states. The 1D physics can be further enriched by electronic inhomogeneity, which unfortunately remains largely unknown. Here we demonstrate the ultra-high sensitivity to magnetic fluctuations and the tunability of phase stability in the electronic transport properties of self-assembled electronically phase-separated manganite nanowires with extreme aspect ratio. The onset of magnetic nano-droplet state, a precursor to the ferromagnetic metallic state, is unambiguously revealed, which is attributed to the small lateral size of the nanowires that is comparable to the droplet size...
February 23, 2017: Nano Letters
https://www.readbyqxmd.com/read/28231010/generation-of-anisotropic-massless-dirac-fermions-and-asymmetric-klein-tunneling-in-few-layer-black-phosphorus-superlattices
#12
Zhenglu Li, Ting Cao, Meng Wu, Steven G Louie
Artificial lattices have been employed in a broad range of two-dimensional systems, including those with electrons, atoms and photons, in the quest for massless Dirac fermions with high flexibility and controllability. Establishing triangular or hexagonal symmetry, from periodically patterned molecule assembly or electrostatic gating as well as from moiré pattern induced by substrate, has produced electronic states with linear dispersions from two-dimensional electron gas (2DEG) residing in semiconductors, metals and graphene...
February 23, 2017: Nano Letters
https://www.readbyqxmd.com/read/28231002/mid-infrared-photoluminescence-up-to-290-k-reveals-radiative-mechanisms-and-substrate-doping-type-effects-of-inas-nanowires
#13
Xiren Chen, Qiandong Zhuang, Hayfaa Alradhi, ZhiMing Jin, Liangqing Zhu, Xin Chen, Jun Shao
Photoluminescence (PL) as a conventional yet powerful optical spectroscopy may provide crucial insight into the mechanism of carrier recombination and bandedge structure in semiconductors. In this study, mid-infrared PL measurements on vertically aligned InAs nanowires (NWs) are realized for the first time in a wide temperature range of up to 290 K, by which the radiative recombinations are clarified in the NWs grown on n- and p-type Si substrates, respectively. A dominant PL feature is identified to be from the type-II optical transition across the interfaces between the zinc-blend (ZB) and the wurtzite (WZ) InAs, a lower-energy feature at low temperatures is ascribed to impurity-related transition, and a higher-energy feature at high temperatures originates in the interband transition of the WZ InAs being activated by thermal-induced electron transfer...
February 23, 2017: Nano Letters
https://www.readbyqxmd.com/read/28230982/synthesis-of-%C3%AE-1-2-linked-6-deoxy-l-altropyranose-oligosaccharides-via-gold-i-catalyzed-glycosylation-of-a-ortho-hexynylbenzoate-donor
#14
Zhengnan Shen, Hani Mobarak, Wei Li, Göran Widmalm, Biao Yu
The β-(1-2)-linked 6-deoxy-L-altropyranose di- to penta-saccharides 2-5, relevant to the O-antigen of the infectious Yersinia enterocolitica O:3, were synthesized for the first time. The challenging 1,2-cis-altropyranosyl linkage was assembled effectively via glycosylation with 2-O-benzyl-3,4-di-O-benzoyl-6-deoxy-L-altropyranosyl ortho-hexynylbenzoate (7) under the catalysis of PPh3AuNTf2. NMR and molecular modeling studies showed that the pentasaccharide (5) adopted a left-handed helical conformation.
February 23, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28230977/extracellular-self-assembly-of-functional-and-tunable-protein-conjugates-from-bacillus-subtilis
#15
Charlie Gilbert, Mark Howarth, Colin R Harwood, Tom Ellis
The ability to stably and specifically conjugate recombinant proteins to one another is a powerful approach for engineering multifunctional enzymes, protein therapeutics and novel biological materials. While many of these applications have been illustrated through in vitro and in vivo intracellular protein conjugation methods, extracellular self-assembly of protein conjugates offers unique advantages: simplifying purification, reducing toxicity and burden, and enabling tunability. Exploiting the recently described SpyTag-SpyCatcher system, we describe here how enzymes and structural proteins can be genetically-encoded to covalently conjugate in culture media following programmable secretion from Bacillus subtilis...
February 23, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28230967/live-cell-pyrophosphate-imaging-by-in-situ-hot-spot-generation
#16
Mingmin Li, Jin Li, Huixia Di, Huiqiao Liu, Dingbin Liu
Controlling the electromagnetic hot-spot generation is essential for surface-enhanced Raman scattering (SERS) assays. Current hot spot-based SERS assays have been extensively studied in solutions or on substrates. However, probing biospecies by controlling the hot-spot assembly in living systems has not been demonstrated thus far. Herein, we report a background-free SERS probe for imag-ing pyrophosphate (PPi), a biochemically significant anion, in living cells. Intracellular PPi is able to induce the nanoparticle dimeri-zation, thus creating an intense electromagnetic hot spot and dramatically enhancing the signal of the Raman reporters residing in the hot spot...
February 23, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28230931/spatially-assembled-bilayer-cell-sheets-of-stem-cells-and-endothelial-cells-using-thermosensitive-hydrogels-for-therapeutic-angiogenesis
#17
Indong Jun, Taufiq Ahmad, Seongwoo Bak, Joong-Yup Lee, Eun Mi Kim, Jinkyu Lee, Yu Bin Lee, Hongsoo Jeong, Hojeong Jeon, Heungsoo Shin
Although the coculture of multiple cell types has been widely employed in regenerative medicine, in vivo transplantation of cocultured cells while maintaining the hierarchical structure remains challenging. Here, a spatially assembled bilayer cell sheet of human mesenchymal stem cells and human umbilical vein endothelial cells on a thermally expandable hydrogel containing fibronectin is prepared and its effect on in vitro proangiogenic functions and in vivo ischemic injury is investigated. The expansion of hydrogels in response to a temperature change from 37 to 4 °C allows rapid harvest and delivery of the bilayer cell sheet to two different targets (an in vitro model glass surface and in vivo tissue)...
February 23, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28230915/a-singlet-oxygen-generating-agent-by-chirality-dependent-plasmonic-shell-satellite-nanoassembly
#18
Fengli Gao, Maozhong Sun, Wei Ma, Xiaoling Wu, Liqiang Liu, Hua Kuang, Chuanlai Xu
Photodynamic therapy (PDT) agent, which generates singlet oxygen ((1) O2 ) under light, has attracted significant attention for its broad biological and medical applications. Here, DNA-driven shell-satellite (SS) gold assemblies as chiral photosensitizers are first fabricated. The chiral plasmonic nanostructure, coupling with cysteine enantiomers on its surface, exhibits intense chiroplasmonic activities (-40.2 ± 2.6 mdeg) in the visible region. These chiral SS nanoassemblies have high reactive oxygen species generating efficiency under circular polarized light illumination, resulting in a (1) O2 quantum yield of 1...
February 23, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28230870/colloidal-capsules-nano-and-microcapsules-with-colloidal-particle-shells
#19
REVIEW
Tobias Bollhorst, Kurosch Rezwan, Michael Maas
Utilizing colloidal particles for the assembly of the shell of nano- and microcapsules holds great promise for the tailor-made design of new functional materials. Increasing research efforts are devoted to the synthesis of such colloidal capsules, by which the integration of modular building blocks with distinct physical, chemical, or morphological characteristics in a capsule's shell can result in novel properties, not present in previous encapsulation structures. This review will provide a comprehensive overview of the synthesis strategies and the progress made so far of bringing nano- and microcapsules with shells of densely packed colloidal particles closer to application in fields such as chemical engineering, materials science, or pharmaceutical and life science...
February 23, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28230808/genome-sequence-of-rhodoferax-antarcticus-ant-br-t-a-psychrophilic-purple-nonsulfur-bacterium-from-an-antarctic-microbial-mat
#20
Jennifer M Baker, Carli J Riester, Blair M Skinner, Austin W Newell, Wesley D Swingley, Michael T Madigan, Deborah O Jung, Marie Asao, Min Chen, Patrick C Loughlin, Hao Pan, Yuankui Lin, Yaqiong Li, Jacob Shaw, Mindy Prado, Chris Sherman, Joseph Kuo-Hsiang Tang, Robert E Blankenship, Tingting Zhao, Jeffrey W Touchman, W Matthew Sattley
Rhodoferax antarcticus is an Antarctic purple nonsulfur bacterium and the only characterized anoxygenic phototroph that grows best below 20 °C. We present here a high-quality draft genome of Rfx. antarcticus strain ANT.BR(T), isolated from an Antarctic microbial mat. The circular chromosome (3.8 Mbp) of Rfx. antarcticus has a 59.1% guanine + cytosine (GC) content and contains 4036 open reading frames. In addition, the bacterium contains a sizable plasmid (198.6 kbp, 48.4% GC with 226 open reading frames) that comprises about 5% of the total genetic content...
February 21, 2017: Microorganisms
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