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https://www.readbyqxmd.com/read/28106396/tetrel-bonds-in-infinite-molecular-chains-by-electronic-structure-theory-and-their-role-for-crystal-stabilization
#1
Janine George, Richard Dronskowski
Intermolecular bonds play a crucial role in the rational design of crystal structures, dubbed crystal engineering. The relatively new term tetrel bonds (TBs) describes a long-known type of such interactions presently in the focus of quantum-chemical cluster calculations. Here, we energetically explore the strengths and cooperativity of these interactions in infinite chains, a possible arrangement of such tetrel bonds in extended crystals, by periodic density-functional theory. In the chains, the TBs are amplified due to cooperativity by up to 60%...
January 20, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28096488/novel-superspreader-bacteriophages-promote-horizontal-gene-transfer-by-transformation
#2
Eric C Keen, Valery V Bliskovsky, Francisco Malagon, James D Baker, Jeffrey S Prince, James S Klaus, Sankar L Adhya
: Bacteriophages infect an estimated 10(23) to 10(25) bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub "superspreaders," releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096485/murine-cytomegalovirus-deubiquitinase-regulates-viral-chemokine-levels-to-control-inflammation-and-pathogenesis
#3
Adam T Hilterbrand, Daniel R Boutz, Edward M Marcotte, Jason W Upton
: Maintaining control over inflammatory processes represents a paradox for viral pathogens. Although many viruses induce host inflammatory responses to facilitate infection, control is necessary to avoid overactivation. One way is through the manipulation of proinflammatory chemokine levels, both host and viral. Murine cytomegalovirus (MCMV), a model betaherpesvirus, encodes a viral C-C chemokine, MCK2, which promotes host inflammatory responses and incorporates into virions to facilitate viral dissemination...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28094850/discriminating-solitary-cysts-from-soft-tissue-lesions-in-mammography-using-a-pretrained-deep-convolutional-neural-network
#4
Thijs Kooi, Bram van Ginneken, Nico Karssemeijer, Ard den Heeten
PURPOSE: It is estimated that 7% of women in the western world will develop palpable breast cysts in their lifetime. Even though cysts have been correlated with risk of developing breast cancer, many of them are benign and do not require follow-up. We develop a method to discriminate benign solitary cysts from malignant masses in digital mammography. We think a system like this can have merit in the clinic as a decision aid or complementary to specialised modalities. METHODS: We employ a deep Convolutional Neural Network (CNN) to classify cyst and mass patches...
January 17, 2017: Medical Physics
https://www.readbyqxmd.com/read/28092528/low-rank-and-adaptive-sparse-signal-lassi-models-for-highly-accelerated-dynamic-imaging
#5
Saiprasad Ravishankar, Brian Moore, Raj Nadakuditi, Jeffrey Fessler
Sparsity-based approaches have been popular in many applications in image processing and imaging. Compressed sensing exploits the sparsity of images in a transform domain or dictionary to improve image recovery from undersampled measurements. In the context of inverse problems in dynamic imaging, recent research has demonstrated the promise of sparsity and low-rank techniques. For example, the patches of the underlying data are modeled as sparse in an adaptive dictionary domain, and the resulting image and dictionary estimation from undersampled measurements is called dictionary-blind compressed sensing, or the dynamic image sequence is modeled as a sum of low-rank and sparse (in some transform domain) components (L+S model) that are estimated from limited measurements...
January 10, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28092036/creation-of-phosphotyrosine-superbinders-by-directed-evolution-of-an-sh2-domain
#6
Haiming Huang, Tomonori Kaneko, Sachdev S Sidhu, Shawn S C Li
Commercial antibodies raised against phosphotyrosine have been widely used as reagents to detect or isolate tyrosine-phosphorylated proteins from cellular samples. However, these antibodies are costly and are not amenable to in-house production in an academic lab setting. In this chapter, we describe a method to generate super-high affinity SH2 domains, dubbed the phosphotyrosine superbinders, by evolving a natural SH2 domain using the phage display technology. The superbinders are stable and can be easily produced in Escherichia coli in large quantities...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28088524/possible-roles-of-the-transcription-factor-nrf1-nfe2l1-in-neural-homeostasis-by-regulating-the-gene-expression-of-deubiquitinating-enzymes
#7
Hiroaki Taniguchi, Shota Okamuro, Misaki Kohji, Tsuyoshi Waku, Kaori Kubo, Atsushi Hatanaka, Yimeng Sun, A M Masudul Azad Chowdhury, Akiyoshi Fukamizu, Akira Kobayashi
The transcription factor Nrf1 (NFE2L1) maintains protein homeostasis (proteostasis) by regulating the gene expression of proteasome subunits in response to proteasome inhibition. The deletion of the Nrf1 gene in neural stem/progenitor cells causes severe neurodegeneration due to the accumulation of ubiquitinated proteins in Purkinje cells and motor neurons (Nrf1 NKO mice). However, the molecular mechanisms governing this neurodegenerative process remain unclear. We demonstrate herein that the loss of Nrf1 leads to the reduced gene expression of the deubiquitinating enzymes (DUBs) but not proteasome subunits in Nrf1 NKO mice between P7 and P18...
January 11, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28076680/regulating-the-master-regulator-controlling-ubiquitination-by-thinking-outside-the-active-site
#8
Stacey-Lynn Paiva, Sara R da Silva, Elvin D de Araujo, Patrick Thomas Gunning
The labeling of proteins with ubiquitin/ubiquitin-like (Ubl) proteins is crucial for several physiological processes and in the onset of various diseases. Recently, targeting ubiquitin protein labeling has shifted towards the use of allosteric mechanisms over classical activity-based approaches. Allosteric enzyme regulation offers the potential for greater selectivity and has demonstrated less susceptibility to acquired resistance often associated with active site inhibitors. Furthermore, the isoform diversity among E1 activating, E2 conjugating, E3 ligase and deubiquitinating (DUB) enzymes offers an ideal platform for modulating activity via allostery...
January 11, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28074857/deubiquitylation-of-hepatitis-b-virus-x-protein-hbx-by-ubiquitin-specific-peptidase-15-usp15-increases-hbx-stability-and-its-transactivation-activity
#9
Zhi-Jun Su, Jia-Shou Cao, Yan-Fang Wu, Wan-Nan Chen, Xinjian Lin, Yun-Li Wu, Xu Lin
Hepatitis B virus X protein (HBx) plays important roles in viral replication and the development of hepatocellular carcinoma. HBx is a rapid turnover protein and ubiquitin-proteasome pathway has been suggested to influence HBx stability as treatment with proteasome inhibitors increases the levels of HBx protein and causes accumulation of the polyubiquitinated forms of HBx. Deubiquitinases (DUBs) are known to act by removing ubiquitin moieties from proteins and thereby reverse their stability and/or activity...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28073898/two-stage-isothermal-enzymatic-amplification-for-concurrent-multiplex-molecular-detection
#10
Jinzhao Song, Changchun Liu, Michael G Mauk, Shelley C Rankin, James B Lok, Robert M Greenberg, Haim H Bau
BACKGROUND: The wide array of pathogens responsible for infectious diseases makes it difficult to identify causative pathogens with single-plex tests. Although multiplex PCR detects multiple targets, it is restricted to centralized laboratories, which delays test results or makes multiplexing unavailable, depriving healthcare providers of critical, real-time information. METHODS: To address the need for point-of-care (POC) highly multiplexed tests, we propose the 2-stage, nested-like, rapid (<40 min) isothermal amplification assay, dubbed rapid amplification (RAMP)...
January 10, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28066899/a-role-for-the-histone-h2a-deubiquitinase-mysm1-in-maintenance-of-cd8-t-cells
#11
Michael Förster, Rupinder K Boora, Jessica C Petrov, Nassima Fodil, Isabella Albanese, Jamie Kim, Philippe Gros, Anastasia Nijnik
Several previous studies outlined the importance of the histone H2A deubiquitinase (H2A-DUB) MYSM1 in the regulation of stem cell quiescence and hematopoiesis. In this study we investigated the role of MYSM1 in T cell development. Using mouse models that allow conditional Mysm1 ablation at late stages of thymic development, we found that MYSM1 is intricately involved in the maintenance, activation, and survival of CD8+ T cells. Mysm1 ablation resulted in a 2-fold reduction in CD8+ T cell numbers, and also led to a hyperactivated CD8+ T cell state accompanied by impaired proliferation and increased proinflammatory cytokine production after ex vivo stimulation...
January 9, 2017: Immunology
https://www.readbyqxmd.com/read/28058436/pentagonal-five-center-four-electron-%C3%AF-bond-in-ternary-b3n2h5-cluster-an-extension-of-the-concept-of-three-center-four-electron-%C3%AF-bond
#12
Da-Zhi Li, Lin-Yan Feng, Ling Pei, Li-Juan Zhang, Shu-Guo Wu, Hua-Jin Zhai
Boron-based heteroatomic rings can have exotic chemical bonding, in which the p lone-pairs of heteroatoms manage to participate in delocalized π bonding, compensating for boron's electron-deficiency. We explore herein the bonding properties of ternary B-N-H systems with a pentagonal ring, using the B3N2H5(0/-/2-) clusters as examples. Computational structural searches lead to perfectly planar C2v B3N2H5 (1, (1)A1) and C2v B3N2H5(-) (2, (2)B1) as global minima for the neutral species and monoanion, which feature a pentagonal B3N2 ring...
January 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28045260/why-does-alkylation-of-the-n-h-functionality-within-m-nh-bifunctional-noyori-type-catalysts-lead-to-turnover
#13
Pavel A Dub, Brian L Scott, John C Gordon
Molecular metal/NH bifunctional Noyori-type catalysts are remarkable in that they are among the most efficient artificial catalysts developed to date for the hydrogenation of carbonyl functionalities (loadings up to ∼10(-5) mol %). In addition, these catalysts typically exhibit high C═O/C═C chemo- and enantioselectivities. This unique set of properties is traditionally associated with the operation of an unconventional mechanism for homogeneous catalysts in which the chelating ligand plays a key role in facilitating the catalytic reaction and enabling the aforementioned selectivities by delivering/accepting a proton (H(+)) via its N-H bond cleavage/formation...
January 3, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28040451/regulation-of-xiap-turnover-reveals-a-role-for-usp11-in-promotion-of-tumorigenesis
#14
Zhuan Zhou, Aiping Luo, Indira Shrivastava, Mingjing He, Yi Huang, Ivet Bahar, Zhihua Liu, Yong Wan
The emerging regulatory role of deubiquitinases (DUBs) has been implicated in various fundamental processes and pathogenesis. To determine the pivotal role that DUBs play in mediating tumorigenesis, we have performed a non-biased screen of 67 human DUBs based on a mammary cell transformation assay. This led to the identification of USP11 as a critical determinant of mammary tumor initiation and progression. Using an approach of protein complex purification coupled with mass spectrometry, we further identified XIAP to be a target for USP11...
February 2017: EBioMedicine
https://www.readbyqxmd.com/read/28039431/data-integration-in-physiology-using-bayes-rule-and-minimum-bayes-factors-deubiquitylating-enzymes-in-the-renal-collecting-duct
#15
Zhe Xue, Jia-Xu Chen, Yue Zhao, Barbara Medvar, Mark A Knepper
A major challenge in physiology is to exploit the many large-scale datasets available from "-omic" studies in order to seek answers to key physiological questions. In previous studies, Bayes' Theorem has been used for this purpose. This approach requires a means to map continuously distributed experimental data to probabilities (likelihood values) in order to derive posterior probabilities from the combination of prior probabilities and new data. Here, we introduce the use of Minimum Bayes' Factors for this purpose and illustrate the approach by addressing a physiological question, "Which deubiquitylating enzymes (DUBs) encoded by mammalian genomes are most likely to regulate plasma membrane transport processes in renal cortical collecting duct principal cells?" To do this, we have created a comprehensive online database of 110 DUBs present in the mammalian genome (https://hpcwebapps...
December 30, 2016: Physiological Genomics
https://www.readbyqxmd.com/read/28032953/ultrasmall-yig-nanoparticles-with-high-coercivity-at-low-temperature-synthesized-by-laser-ablation-and-fragmentation-of-pressed-powders
#16
Tim Schmitz, Ulf Wiedwald, Carsten Dubs, Bilal Gökce
Pulsed laser ablation of pressed yttrium-ion-garnet powders in water is studied and compared to the ablation of a single crystal target. We find that target porosity is a crucial factor which has far-reaching implications on nanoparticle productivity. Although nanoparticle size distributions obtained by analytical disc centrifugation and transmission electron microscopy (TEM) are in agreement, X-ray diffraction and energy dispersive X-ray analysis show that only nanoparticles obtained from targets with densities close to that of a bulk target lead to comparable properties...
December 29, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28031360/herpes-simplex-virus-type-1-ubiquitin-specific-protease-ul36-abrogates-nf-%C3%AE%C2%BAb-activation-in-dna-sensing-signal-pathway
#17
Ruijie Ye, Chenhe Su, Haiyan Xu, Chunfu Zheng
: The DNA sensing pathway triggers innate immune responses against DNA virus infection and the NF-κB signaling plays a critical role in establishing the innate immunity. Here we report that the herpes simplex virus type 1 (HSV-1) ubiquitin-specific protease (UL36USP), which is a deubiquitinase (DUB), antagonizes the NF-κB activation, depending on its DUB activity. In this study, ectopically expressed UL36USP blocked promoter activation of interferon (IFN)-β and NF-κB induced by cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING)...
December 28, 2016: Journal of Virology
https://www.readbyqxmd.com/read/28029679/usp14-inhibitor-attenuates-cerebral-ischemia-reperfusion-induced-neuronal-injury-in-mice
#18
Jia-Wei Min, Lanhai Lü, Jessica Freeling, Doug Martin, Hongmin Wang
Stroke is associated with over-production of misfolded and aggregating proteins. However, it remains largely unclear whether enhanced removal of protein aggregates following ischemic stroke is neuroprotective. Deubiquitinating enzymes (DUBs) are a large group of proteases that regulate protein degradation. The ubiquitin-specific protease 14 (USP14) is a DUB that is associated with the proteasome and negatively regulates proteasome activity. In this study, we examined the effect of IU1, a specific small molecule inhibitor of USP14, on mouse focal cerebral ischemic stroke-induced neuronal injury in mice...
December 28, 2016: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28009202/quasi-many-body-localization-in-translation-invariant-systems
#19
N Y Yao, C R Laumann, J I Cirac, M D Lukin, J E Moore
We examine localization phenomena associated with generic, high entropy, states of a translation-invariant, one-dimensional spin ladder. At early times, we find slow growth of entanglement entropy consistent with the known phenomenology of many-body localization in disordered, interacting systems. At intermediate times, however, anomalous diffusion sets in, leading to full spin polarization decay on an exponentially activated time scale. We identify a single length scale which parametrically controls both the spin transport times and the apparent divergence of the susceptibility to spin glass ordering...
December 9, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/28008672/the-angulata7-gene-encodes-a-dnaj-like-zinc-finger-domain-protein-involved-in-chloroplast-function-and-leaf-development-in-arabidopsis
#20
Tamara Muñoz-Nortes, José Manuel Pérez-Pérez, María Rosa Ponce, Héctor Candela, José Luis Micol
The characterization of mutants with altered leaf shape and pigmentation has previously allowed the identification of nuclear genes that encode plastid-localized proteins that perform essential functions in leaf growth and development. A large-scale screen previously allowed us to isolate ethyl methanesulfonate-induced mutants with small rosettes and pale green leaves with prominent marginal teeth, which were assigned to a phenotypic class that we dubbed Angulata. The molecular characterization of the twelve genes assigned to this phenotypic class should help us to advance our understanding of the still poorly understood relationship between chloroplast biogenesis and leaf morphogenesis...
December 23, 2016: Plant Journal: for Cell and Molecular Biology
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