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https://www.readbyqxmd.com/read/28645155/features-of-genomic-organization-in-a-nucleotide-resolution-molecular-model-of-the-escherichia-coli-chromosome
#1
William C Hacker, Shuxiang Li, Adrian H Elcock
We describe structural models of the Escherichia coli chromosome in which the positions of all 4.6 million nucleotides of each DNA strand are resolved. Models consistent with two basic chromosomal orientations, differing in their positioning of the origin of replication, have been constructed. In both types of model, the chromosome is partitioned into plectoneme-abundant and plectoneme-free regions, with plectoneme lengths and branching patterns matching experimental distributions, and with spatial distributions of highly-transcribed chromosomal regions matching recent experimental measurements of the distribution of RNA polymerases...
June 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28644811/applying-pattern-recognition-to-high-resolution-images-to-determine-cellular-signaling-status
#2
Michael F Lohrer, Darrin M Hanna, Yang Liu, Kang-Hsin Wang, Fu-Tong Liu, Ted A Laurence, Gang-Yu Liu
Two frequently used tools to acquire high-resolution images of cells are scanning electron microscopy (SEM) and atomic force microscopy (AFM). The former provides a nanometer resolution view of cellular features rapidly and with high throughput, while the latter enables visualizing hydrated and living cells. In current practice, these images are viewed by eye to determine cellular status, e.g. activated versus resting. Automatic and quantitative data analysis is lacking. This work develops an algorithm of pattern recognition that works very effectively for AFM and SEM images...
June 21, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28644563/gas-phase-dissociation-study-of-erythrinian-alkaloids-by-electrospray-ionization-mass-spectrometry-and-computational-methods
#3
T Guaratini, L G P Feitosa, D B Silva, N P Lopes, J L C Lopes, R Vessecchi
Alkaloids from plants of the genus Erythrina display important biological activities, including anxiolytic action. Characterization of these alkaloids by mass spectrometry (MS) has contributed to the construction of a spectral library, has improved understanding of their structures, and has supported the proposal of fragmentation mechanisms in light of density functional calculations (DFT). In this study, we have used low- and high-resolution MS(n) analyses to investigate the fragmentation patterns of erythrinian alkaloids; we have employed the B3LYP/6-31+G(d,p) model to obtain their reactive sites...
June 23, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28644379/physical-forces-may-cause-the-hoxd-gene-cluster-elongation
#4
Spyros Papageorgiou
Hox gene collinearity was discovered be Edward B. Lewis in 1978. It consists of the Hox1, Hox2, Hox3 ordering of the Hox genes in the chromosome from the telomeric to the centromeric side of the chromosome. Surprisingly, the spatial activation of the Hox genes in the ontogenetic units of the embryo follows the same ordering along the anterior-posterior embryonic axis. The chromosome microscale differs from the embryo macroscale by 3 to 4 orders of magnitude. The traditional biomolecular mechanisms are not adequate to comprise phenomena at so divergent spatial domains...
June 23, 2017: Biology
https://www.readbyqxmd.com/read/28644020/the-underestimated-halogen-bonds-forming-with-protein-backbone-in-protein-data-bank
#5
Qian Zhang, Zhijian Xu, Jiye Shi, Weiliang Zhu
Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-Ray crystallography takes into account of XBs, which might result in the weakening or even vanishing of experimentally determined XBs in PDB. In our previous study, we showed that side-chain XBs forming with protein side chains are underestimated in PDB on the basis of the phenomenon that the proportion of side-chain XBs to overall XBs decreases as structural resolution becomes lower and lower...
June 23, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28643772/cryptic-indole-hydroxylation-by-a-non-canonical-terpenoid-cyclase-parallels-bacterial-xenobiotic-detoxification
#6
Susann Kugel, Martin Baunach, Philipp Baer, Mie Ishida-Ito, Srividhya Sundaram, Zhongli Xu, Michael Groll, Christian Hertweck
Terpenoid natural products comprise a wide range of molecular architectures that typically result from C-C bond formations catalysed by classical type I/II terpene cyclases. However, the molecular diversity of biologically active terpenoids is substantially increased by fully unrelated, non-canonical terpenoid cyclases. Their evolutionary origin has remained enigmatic. Here we report the in vitro reconstitution of an unusual flavin-dependent bacterial indoloterpenoid cyclase, XiaF, together with a designated flavoenzyme-reductase (XiaP) that mediates a key step in xiamycin biosynthesis...
June 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28643359/an-open-8-channel-parallel-transmission-coil-for-static-and-dynamic-7t-mri-of-the-knee-and-ankle-joints-at-multiple-postures
#7
Jin Jin, Ewald Weber, Aurelien Destruel, Kieran O'Brien, Bassem Henin, Craig Engstrom, Stuart Crozier
PURPOSE: We present the initial in vivo imaging results of an open architecture eight-channel parallel transmission (pTx) transceive radiofrequency (RF) coil array that was designed and constructed for static and dynamic 7T MRI of the knee and ankle joints. METHODS: The pTx coil has a U-shaped dual-row configuration (200 mm overall length longitudinally) that allows static and dynamic imaging of the knee and ankle joints at various postures and during active movements...
June 22, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28643349/a-qm-mm-study-of-the-catalytic-mechanism-of-sam-methyltransferase-rlmn-from-escherichia-coli
#8
Chenxiao Zhao, Lihua Dong, Yongjun Liu
RlmN is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the C2 methylation of adenosine 2503 (A2503) in 23S rRNA and adenosine 37 (A37) in several Escherichia coli transfer RNAs (tRNA). The catalytic reaction of RlmN is distinctly different from that of typical SAM-dependent methyltransferases that employs an SN 2 mechanism, but follows a ping-pong mechanism which involves the intermediate methylation of a conserved cysteine residue. Recently, the x-ray structure of a key intermediate in the RlmN reaction has been reported, allowing us to perform combined quantum mechanics and molecular mechanics (QM/MM) calculations to delineate the reaction details of RlmN at atomic level...
June 23, 2017: Proteins
https://www.readbyqxmd.com/read/28643319/-progress-of-the-application-of-optical-coherence-tomography-in-gastrointestinal-tumor-surgery
#9
Yongsheng Li, Hao Liu, Haipeng Huang, Yu Zhu, Haijun Deng, Jiang Yu, Site Luo, Li Huo, Li Lin, Huikai Xie, Guoxin Li
Optical coherence tomography (OCT) is a real-time, cross-sectional optical imaging technology. It is analogous to ultrasonography, except that OCT uses light waves instead of sound waves, and can provide three-dimensional morphological images of living tissues with a micrometer resolution. Through the use of endoscopes, needles, catheters and laparoscopes, OCT has demonstrated tremendous imaging potential in tumor surgery. The current studies suggest that OCT has potential for clinical applications in the following fields of gastrointestinal tumor surgery: (1) Early tumor detection and diagnosis: OCT can distinguish differences between polyp tissue, normal tissue and malignant tissue...
June 25, 2017: Zhonghua Wei Chang Wai Ke za Zhi, Chinese Journal of Gastrointestinal Surgery
https://www.readbyqxmd.com/read/28643003/recent-developments-in-solution-nuclear-magnetic-resonance-nmr-based-molecular-biology
#10
REVIEW
Joshua J Ziarek, Diego Baptista, Gerhard Wagner
Visualizing post-translational modifications, conformations, and interaction surfaces of protein structures at atomic resolution underpins the development of novel therapeutics to combat disease. As computational resources expand, in silico calculations coupled with experimentally derived structures and functional assays have led to an explosion in structure-based drug design (SBDD) with several compounds in clinical trials. It is increasingly clear that "hidden" transition-state structures along activation trajectories can be harnessed to develop novel classes of allosteric inhibitors...
June 23, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/28642465/structural-basis-for-biologically-relevant-mechanical-stiffening-of-a-virus-capsid-by-cavity-creating-or-spacefilling-mutations
#11
Pablo Guerra, Alejandro Valbuena, Jordi Querol-Audí, Cristina Silva, Milagros Castellanos, Alicia Rodríguez-Huete, Damià Garriga, Mauricio G Mateu, Nuria Verdaguer
Recent studies reveal that the mechanical properties of virus particles may have been shaped by evolution to facilitate virus survival. Manipulation of the mechanical behavior of virus capsids is leading to a better understanding of viral infection, and to the development of virus-based nanoparticles with improved mechanical properties for nanotechnological applications. In the minute virus of mice (MVM), deleterious mutations around capsid pores involved in infection-related translocation events invariably increased local mechanical stiffness and interfered with pore-associated dynamics...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642263/volumetric-analysis-from-a-harmonized-multisite-brain-mri-study-of-a-single-subject-with-multiple-sclerosis
#12
R T Shinohara, J Oh, G Nair, P A Calabresi, C Davatzikos, J Doshi, R G Henry, G Kim, K A Linn, N Papinutto, D Pelletier, D L Pham, D S Reich, W Rooney, S Roy, W Stern, S Tummala, F Yousuf, A Zhu, N L Sicotte, R Bakshi
BACKGROUND AND PURPOSE: MR imaging can be used to measure structural changes in the brains of individuals with multiple sclerosis and is essential for diagnosis, longitudinal monitoring, and therapy evaluation. The North American Imaging in Multiple Sclerosis Cooperative steering committee developed a uniform high-resolution 3T MR imaging protocol relevant to the quantification of cerebral lesions and atrophy and implemented it at 7 sites across the United States. To assess intersite variability in scan data, we imaged a volunteer with relapsing-remitting MS with a scan-rescan at each site...
June 22, 2017: AJNR. American Journal of Neuroradiology
https://www.readbyqxmd.com/read/28642073/synthesis-of-biogenic-ag-pd-core-shell-nanoparticles-having-anti-cancer-anti-microbial-functions
#13
Wafa I Abdel-Fattah, M M Eid, Sh I Abd El-Moez, E Mohamed, Ghareib W Ali
Biogenic Ag@Pd core-shell nanoparticles were greenly synthesized within two plant extracts aiming at enhanced anticancer/bactericidal functions. These functions were verified for the two Pd@Ag biogenic core-shell nanoparticles (BCSnp) with constant Pd to several Ag contents. BCSnp were synthesized within two extracts of Almond nuts and Black Berry fruits, four samples each, through simple, low cost and echo friendly microwave route. The BCSnp Surface Plasmon Resonance (SPR) was detected via UV/visible spectrophotometer...
June 19, 2017: Life Sciences
https://www.readbyqxmd.com/read/28641399/compannotate-a-comparative-approach-to-annotate-base-pairing-interactions-in-rna-3d-structures
#14
Shahidul Islam, Ping Ge, Shaojie Zhang
The analysis of RNA tertiary structure is hindered by the fact that not too many structural data are available and a significant amount of them are in low resolution. Due to the atomic coordinate errors posed by the limitations of low-resolution RNA three-dimensional structures, it becomes a critical challenge to extract key geometric characteristics of RNA, particularly, the interaction of bases. To address this issue, we have devised a comparative method, named CompAnnotate, that utilizes more precise structural information of high-resolution homologs to annotate the base-pairing interactions in the low-resolution structures, by aligning and making comparative geometric assessments...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28641259/face-hallucination-using-linear-models-of-coupled-sparse-support
#15
Reuben A Farrugia, Christine Guillemot
Most face super-resolution methods assume that low- and high-resolution manifolds have similar local geometrical structure, hence learn local models on the low-resolution manifold (e.g. sparse or locally linear embedding models), which are then applied on the high- resolution manifold. However, the low-resolution manifold is distorted by the one-to-many relationship between low- and high- resolution patches. This paper presents the Linear Model of Coupled Sparse Support (LM-CSS) method which learns linear models based on the local geometrical structure on the high-resolution manifold rather than on the low-resolution manifold...
June 19, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28641108/high-speed-and-scalable-whole-brain-imaging-in-rodents-and-primates
#16
Kaoru Seiriki, Atsushi Kasai, Takeshi Hashimoto, Wiebke Schulze, Misaki Niu, Shun Yamaguchi, Takanobu Nakazawa, Ken-Ichi Inoue, Shiori Uezono, Masahiko Takada, Yuichiro Naka, Hisato Igarashi, Masato Tanuma, James A Waschek, Yukio Ago, Kenji F Tanaka, Atsuko Hayata-Takano, Kazuki Nagayasu, Norihito Shintani, Ryota Hashimoto, Yasuto Kunii, Mizuki Hino, Junya Matsumoto, Hirooki Yabe, Takeharu Nagai, Katsumasa Fujita, Toshio Matsuda, Kazuhiro Takuma, Akemichi Baba, Hitoshi Hashimoto
Subcellular resolution imaging of the whole brain and subsequent image analysis are prerequisites for understanding anatomical and functional brain networks. Here, we have developed a very high-speed serial-sectioning imaging system named FAST (block-face serial microscopy tomography), which acquires high-resolution images of a whole mouse brain in a speed range comparable to that of light-sheet fluorescence microscopy. FAST enables complete visualization of the brain at a resolution sufficient to resolve all cells and their subcellular structures...
June 21, 2017: Neuron
https://www.readbyqxmd.com/read/28640598/structural-and-light-absorption-characteristics-of-complex-water-insoluble-organic-mixtures-in-urban-submicron-aerosols
#17
Qingcai Chen, Fumikazu Ikemori, Yuua Nakamura, Petr Vodicka, Kimitaka Kawamura, Michihiro Mochida
Submicrometer aerosols in the urban atmosphere of Nagoya, Japan, were collected in late winter and early spring, and the water-insoluble organic matter (WISOM) in the samples were fractionated into six subfractions based on their polarities by using solvent and normal-phase solid-phase extractions: non-polar (F1), low-polar (F2 and F3), and medium-polar (F4, F5, and F6) fractions. The overall structural characteristics of these subfractions were then analyzed using Fourier transform infrared spectroscopy, nuclear magnetic resonance spectroscopy, and high-resolution aerosol mass spectrometry...
June 22, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28640495/control-of-mus81-nuclease-during-the-cell-cycle
#18
REVIEW
Boris Pfander, Joao Matos
DNA replication and homologous recombination rely on the formation of branched DNA structures that physically link chromosomes. Such DNA-based connections, which arise during S phase, are typically disengaged prior to entry into mitosis, in order to ensure proper chromosome segregation. Exceptions can, however, occur: replication stress, or elevated levels of DNA damage, may cause cells to enter mitosis with unfinished replication as well as carrying recombination intermediates, such as Holliday junctions. Hence, cells are equipped with pathways that recognize and process branched DNA structures, and evolved mechanisms to enhance their function when on the verge of undergoing cell division...
June 22, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28640306/tip-enhanced-raman-spectroscopy-from-early-developments-to-recent-advances
#19
REVIEW
Tanja Deckert-Gaudig, Atsushi Taguchi, Satoshi Kawata, Volker Deckert
An analytical technique operating at the nanoscale must be flexible regarding variable experimental conditions while ideally also being highly specific, extremely sensitive, and spatially confined. In this respect, tip-enhanced Raman scattering (TERS) has been demonstrated to be ideally suited to, e.g., elucidating chemical reaction mechanisms, determining the distribution of components and identifying and localizing specific molecular structures at the nanometre scale. TERS combines the specificity of Raman spectroscopy with the high spatial resolution of scanning probe microscopies by utilizing plasmonic nanostructures to confine the incident electromagnetic field and increase it by many orders of magnitude...
June 22, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28640271/a-massive-dead-disk-galaxy-in-the-early-universe
#20
Sune Toft, Johannes Zabl, Johan Richard, Anna Gallazzi, Stefano Zibetti, Moire Prescott, Claudio Grillo, Allison W S Man, Nicholas Y Lee, Carlos Gómez-Guijarro, Mikkel Stockmann, Georgios Magdis, Charles L Steinhardt
At redshift z = 2, when the Universe was just three billion years old, half of the most massive galaxies were extremely compact and had already exhausted their fuel for star formation. It is believed that they were formed in intense nuclear starbursts and that they ultimately grew into the most massive local elliptical galaxies seen today, through mergers with minor companions, but validating this picture requires higher-resolution observations of their centres than is currently possible. Magnification from gravitational lensing offers an opportunity to resolve the inner regions of galaxies...
June 21, 2017: Nature
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