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https://www.readbyqxmd.com/read/29784784/uncovering-universal-rules-governing-the-selectivity-of-the-archetypal-dna-glycosylase-tdg
#1
Thomas Dodd, Chunli Yan, Bradley R Kossmann, Kurt Martin, Ivaylo Ivanov
Thymine DNA glycosylase (TDG) is a pivotal enzyme with dual roles in both genome maintenance and epigenetic regulation. TDG is involved in cytosine demethylation at CpG sites in DNA. Here we have used molecular modeling to delineate the lesion search and DNA base interrogation mechanisms of TDG. First, we examined the capacity of TDG to interrogate not only DNA substrates with 5-carboxyl cytosine modifications but also G:T mismatches and nonmismatched (A:T) base pairs using classical and accelerated molecular dynamics...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29783174/facile-isolation-of-%C3%AE-ribazole-from-vitamin-b-12-hydrolysates-using-boronate-affinity-chromatography
#2
Theodoric A Mattes, Jorge C Escalante-Semerena
Alpha-ribazole (α-R) is a unique riboside found in the nucleotide loop of coenzyme B12 (CoB12 ). α-R is not an intermediate of the de novo biosynthetic pathway of coenzyme B12 , but some bacteria of the phylum Firmicutes have evolved a two-protein system (transporter, kinase) that scavenges α-R from the environment and converts it to the pathway intermediate α-RP. Since α-R is not commercially available, one must either synthesize α-R, or isolate it from hydrolysates of vitamin B12 (cyano-B12 , CNB12 ), so the function of the above-mentioned proteins can be studied...
May 16, 2018: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/29782551/structural-insights-on-the-efficient-catalysis-of-hydroperoxide-reduction-by-ohr-crystallographic-and-molecular-dynamics-approaches
#3
Erika Piccirillo, Thiago G P Alegria, Karen F Discola, José R R Cussiol, Renato M Domingos, Marcos A de Oliveira, Leandro de Rezende, Luis E S Netto, Antonia T-do Amaral
Organic hydroperoxide resistance (Ohr) enzymes are highly efficient Cys-based peroxidases that play central roles in bacterial response to fatty acid hydroperoxides and peroxynitrite, two oxidants that are generated during host-pathogen interactions. In the active site of Ohr proteins, the conserved Arg (Arg19 in Ohr from Xylella fastidiosa) and Glu (Glu51 in Ohr from Xylella fastidiosa) residues, among other factors, are involved in the extremely high reactivity of the peroxidatic Cys (Cp) toward hydroperoxides...
2018: PloS One
https://www.readbyqxmd.com/read/29782346/claudins-and-nephrolithiasis
#4
Allein Plain, R Todd Alexander
PURPOSE OF REVIEW: The greatest risk factor for kidney stone formation is increased urinary calcium excretion. Most filtered calcium is reabsorbed from the proximal tubule and the thick ascending limb (TAL) of Henle's loop via a paracellular pathway. Claudins are tight junction proteins that confer the permeability properties of an epithelium. We review the contribution of renal claudins to nephron calcium permeability and how perturbations in these pathways cause alterations in tubular calcium transport, hypercalciuria, nephrocalcinosis, or nephrolithiasis...
May 17, 2018: Current Opinion in Nephrology and Hypertension
https://www.readbyqxmd.com/read/29781659/nicotine-deprivation-increases-pain-intensity-neurogenic-inflammation-and-mechanical-hyperalgesia-among-daily-tobacco-smokers
#5
Joseph W Ditre, Emily L Zale, Lisa R LaRowe, Jesse D Kosiba, Martin J De Vita
An evolving reciprocal model posits that pain and tobacco smoking behavior interact in the manner of a positive feedback loop, resulting in greater pain and the maintenance of nicotine dependence. There is also reason to believe that abstaining from smoking may increase pain during the early stages of smoking cessation. The goal of this study was to test the effects of nicotine deprivation on experimental pain reactivity. Daily tobacco cigarette smokers (N = 165; 43% female) were randomized to either extended nicotine deprivation (12-24 hr smoking abstinence), minimal deprivation (2 hr smoking abstinence), or continued smoking conditions, prior to undergoing pain induction via topical capsaicin...
May 21, 2018: Journal of Abnormal Psychology
https://www.readbyqxmd.com/read/29781036/correlation-between-hgf-c-met-and-notch1-signaling-pathways-in-human-gastric-cancer-cells
#6
Kuo-Hung Huang, I-Cheng Sung, Wen-Liang Fang, Chin-Wen Chi, Tien-Shun Yeh, Hsin-Chen Lee, Pen-Hui Yin, Anna Fen-Yau Li, Chew-Wun Wu, Yi-Ming Shyr, Muh-Hwa Yang
In recent decades, research concerning gastric carcinogenesis has rapidly progressed. It is evident that hepatocyte growth factor (HGF) is clinically related to gastric cancer progression and metastasis. In addition, previous studies have found that expression of Notch ligand Jagged1 is correlated with the poor prognosis of gastric cancer. However, the interaction between the HGF/c-Met and Notch1 signaling pathways remains unknown. In the present study, we found that gastric cancer patients with positive c-Met expression exhibited poorer overall survival than patients without c-Met expression (P=0...
May 16, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29780979/entropy-connects-water-structure-and-dynamics-in-protein-hydration-layer
#7
Jayangika N Dahanayake, Katie R Mitchell-Koch
The enzyme Candida Antarctica lipase B (CALB) serves here as a model for understanding connections among hydration layer dynamics, solvation shell structure, and protein surface structure. The structure and dynamics of water molecules in the hydration layer were characterized for regions of the CALB surface, divided around each α-helix, β-sheet, and loop structure. Heterogeneous hydration dynamics were observed around the surface of the enzyme, in line with spectroscopic observations of other proteins. Regional differences in the structure of the biomolecular hydration layer were found to be concomitant with variations in dynamics...
May 21, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29780034/improving-predictive-asthma-algorithms-with-modelled-environment-data-for-scotland-an-observational-cohort-study-protocol
#8
Ireneous N Soyiri, Aziz Sheikh, Stefan Reis, Kimberly Kavanagh, Massimo Vieno, Tom Clemens, Edward J Carnell, Jiafeng Pan, Abby King, Rachel C Beck, Hester J T Ward, Chris Dibben, Chris Robertson, Colin R Simpson
INTRODUCTION: Asthma has a considerable, but potentially, avoidable burden on many populations globally. Scotland has some of the poorest health outcomes from asthma. Although ambient pollution, weather changes and sociodemographic factors have been associated with asthma attacks, it remains unclear whether modelled environment data and geospatial information can improve population-based asthma predictive algorithms. We aim to create the afferent loop of a national learning health system for asthma in Scotland...
May 20, 2018: BMJ Open
https://www.readbyqxmd.com/read/29775653/atomic-structure-of-a-rationally-engineered-gene-delivery-vector-aav2-5
#9
Matthew Burg, Claire Rosebrough, Lauren M Drouin, Antonette Bennett, Mario Mietzsch, Paul Chipman, Robert McKenna, Duncan Sousa, Mark Potter, Barry Byrne, R Jude Samulski, Mavis Agbandje-McKenna
AAV2.5 represents the first structure-guided in-silico designed Adeno-associated virus (AAV) gene delivery vector. This engineered vector combined the receptor attachment properties of AAV serotype 2 (AAV2) with the muscle tropic properties of AAV1, and exhibited an antibody escape phenotype because of a modified antigenic epitope. To confirm the design, the structure of the vector was determined to a resolution of 2.78 Å using cryo-electron microscopy and image reconstruction. The structure of the major viral protein (VP), VP3, was ordered from residue 219 to 736, as reported for other AAV structures, and the five AAV2...
May 15, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29773644/bhlhe40-is-an-essential-repressor-of-il-10-during-mycobacterium-tuberculosis-infection
#10
Jeremy P Huynh, Chih-Chung Lin, Jacqueline M Kimmey, Nicholas N Jarjour, Elizabeth A Schwarzkopf, Tara R Bradstreet, Irina Shchukina, Oleg Shpynov, Casey T Weaver, Reshma Taneja, Maxim N Artyomov, Brian T Edelson, Christina L Stallings
The cytokine IL-10 antagonizes pathways that control Mycobacterium tuberculosis ( Mtb ) infection. Nevertheless, the impact of IL-10 during Mtb infection has been difficult to decipher because loss-of-function studies in animal models have yielded only mild phenotypes. We have discovered that the transcription factor basic helix-loop-helix family member e40 (Bhlhe40) is required to repress Il10 expression during Mtb infection. Loss of Bhlhe40 in mice results in higher Il10 expression, higher bacterial burden, and early susceptibility similar to that observed in mice lacking IFN-γ...
May 17, 2018: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/29772275/5c-id-increased-resolution-chromosome-conformation-capture-carbon-copy-with-in-situ-3c-and-double-alternating-primer-design
#11
Ji Hun Kim, Katelyn R Titus, Wanfeng Gong, Jonathan A Beagan, Zhendong Cao, Jennifer E Phillips-Cremins
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library...
May 14, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29771603/negative-feedback-loop-of-autophagy-and-endoplasmic-reticulum-stress-in-rapamycin-protection-against-renal-ischemia-reperfusion-injury-during-initial-reperfusion-phase
#12
Xinyuan Li, Gongmin Zhu, Xin Gou, Weiyang He, Hubin Yin, Xiaoyu Yang, Jie Li
Rapamycin, an immunosuppressant, is widely used in patients with kidney transplant. However, the therapeutic effects of rapamycin remain controversial. Additionally, previous studies have revealed deleterious effects of rapamycin predominantly when administered for ≥24 h. Few studies, however, have focused on the short-term effects of rapamycin administered only during the initial reperfusion phase. As such, we designed this study to explore the potential effects and mechanisms of rapamycin under a specific therapeutic regimen in which rapamycin is mixed in the perfusate during the initial reperfusion phase (within 24 h)...
May 17, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29769321/lectin-mediated-binding-and-sialoglycans-of-porcine-surfactant-protein-d-synergistically-neutralize-influenza-a-virus
#13
Martin van Eijk, Michael J Rynkiewicz, Kshitij Khatri, Nancy Leymarie, Joseph Zaia, Mitchell R White, Kevan L Hartshorn, Tanya R Cafarella, Irma Van Die, Martin Hessing, Barbara A Seaton, Henk P Haagsman
Innate immunity is critical in the early containment of influenza A virus (IAV) infection, and surfactant protein D (SP-D) plays a crucial role in the pulmonary defense against IAV. In pigs, which are important intermediate hosts during the generation of pandemic IAVs, SP-D uses its unique carbohydrate recognition domain (CRD) to interact with IAV. An N-linked CRD-glycosylation provides interactions with the sialic acid binding site of IAV, and a tripeptide loop at the lectin binding site facilitates enhanced interactions with IAV glycans...
May 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29769197/cancer-associated-fibroblasts-drive-glycolysis-in-a-targetable-signaling-loop-implicated-in-head-and-neck-squamous-cell-carcinoma-progression
#14
Dhruv Kumar, Jacob New, Vikalp Vishwakarma, Radhika Joshi, Jonathan Enders, Fangchen Lin, Sumana Dasari, Wade R Gutierrez, George Leef, Sivapriya Ponnurangam, Hemantkumar Chavan, Lydia Ganaden, Mackenzie M Thornton, Hongying Dai, Ossama Tawfik, Jeffrey Straub, Yelizaveta Shnayder, Kiran Kakarala, Terance Ted Tsue, Douglas A Girod, Bennett Van Houten, Shrikant Anant, Partha Krishnamurthy, Sufi Mary Thomas
Despite aggressive therapies, head and neck squamous cell carcinoma (HNSCC) is associated with a less than 50% 5-year survival rate. Late stage HNSCC frequently consists of up to 80% cancer-associated fibroblasts (CAF). We previously reported that CAF-secreted hepatocyte growth factor (HGF) facilitates HNSCC progression, however very little is known about the role of CAFs in HNSCC metabolism. Here we demonstrate that CAF-secreted HGF increases extracellular lactate levels in HNSCC via upregulation of glycolysis...
May 16, 2018: Cancer Research
https://www.readbyqxmd.com/read/29768115/three-dimensional-printing-of-vitrification-loop-prototypes-for-aquatic-species
#15
Nolan J Tiersch, William M Childress, Terrence R Tiersch
Vitrification is a method of cryopreservation that freezes samples rapidly, while forming an amorphous solid ("glass"), typically in small (μL) volumes. The goal of this project was to create, by three-dimensional (3D) printing, open vitrification devices based on an elliptical loop that could be efficiently used and stored. Vitrification efforts can benefit from the application of 3D printing, and to begin integration of this technology, we addressed four main variables: thermoplastic filament type, loop length, loop height, and method of loading...
May 16, 2018: Zebrafish
https://www.readbyqxmd.com/read/29765713/different-packing-motifs-of-isomeric-e-n-halo-phenyl-methyl-idene-n-methyl-2-thio-phen-2-yl-acetohydrazides-controlled-by-c-h%C3%A2-o-inter-actions
#16
Laura N F Cardoso, Thais C M Noguiera, James L Wardell, Marcus V N de Souza, William T A Harrison
The crystal structures of three isomeric ( E )- N '-(chloro-phenyl-methyl-idene)- N -methyl-2-(thio-phen-2-yl)acetohydrazides (C14 H13 ClN2 OS) are described, with the Cl atom in ortho (I), meta (III) and para (IV) positions in the benzene ring. The ortho -bromo derivative (II) (C14 H13 BrN2 OS), which is isostructural with its chloro congener (I), is also reported. Mol-ecules (I)-(III) have similar conformations, which approximate to l-shapes, as indicated by their N-C-C-Ct (t = thio-phene) torsion angles of -90...
March 1, 2018: Acta Crystallographica. Section E, Crystallographic Communications
https://www.readbyqxmd.com/read/29758717/biaxial-potential-of-surface-stabilized-ferroelectric-liquid-crystals
#17
Anatoly Kaznacheev, Evgeny Pozhidaev, Vladimir Rudyak, Alexander V Emelyanenko, Alexei Khokhlov
A biaxial surface potential Φ_{s} of smectic-C^{*} surface-stabilized ferroelectric liquid crystals (SSFLCs) is introduced in this paper to explain the experimentally observed electric-field dependence of polarization P[over ̃]_{cell}(E), in particular the shape of the static hysteresis loops. Our potential consists of three independent parts. The first nonpolar part Φ_{n} describes the deviation of the prime director n (which is the most probable orientation of the long molecular axes) from the easy alignment axis R, which is located in the boundary surface plane...
April 2018: Physical Review. E
https://www.readbyqxmd.com/read/29758107/locking-the-non-template-dna-to-control-transcription
#18
Yuri Nedialkov, Dmitri Svetlov, Georgiy A Belogurov, Irina Artsimovitch
Universally conserved NusG/Spt5 factors reduce RNA polymerase pausing and arrest. In a widely accepted model, these proteins bridge the RNA polymerase clamp and lobe domains across the DNA channel, inhibiting the clamp opening to promote pause-free RNA synthesis. However, recent structures of paused transcription elongation complexes show that the clamp does not open and suggest alternative mechanisms of antipausing. Among these mechanisms, direct contacts of NusG/Spt5 proteins with the nontemplate DNA in the transcription bubble have been proposed to prevent unproductive DNA conformations and thus inhibit arrest...
May 14, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29757445/lessons-learned-from-merging-wet-lab-experiments-with-molecular-simulation-to-improve-mab-humanization
#19
L Schwaigerlehner, M Pechlaner, P Mayrhofer, C Oostenbrink, R Kunert
Humanized monoclonal antibodies (mAbs) are among the most promising modern therapeutics, but defined engineering strategies are still not available. Antibody humanization often leads to a loss of affinity, as it is the case for our model antibody Ab2/3H6 (PDB entry 3BQU). Identifying appropriate back-to-mouse mutations is needed to restore binding affinity, but highly challenging. In order to get more insight, we have applied molecular dynamics simulations and correlated them to antibody binding and expression in wet lab experiments...
May 11, 2018: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/29754213/pathogenesis-of-alzheimer-s-disease-examined-using-a-modified-puri-li-model-that-incorporates-calcium-ion-homeostasis
#20
R A Thuraisingham
The Puri-Li kinetic model is modified to include neuronal calcium ion homeostasis to study the effect of calcium ions on the production of amyloid-β peptides (Aβ), microglia, and astroglia during the pathogenesis of Alzheimer's disease (AD). This is carried out by solving the modified Puri-Li model under steady-state conditions. The derived expressions show that the inclusion of calcium ions has altered the steady-state populations of Aβ, microglia, and astroglia. The calcium ions activate the synthesis of Aβ which in turn increases the calcium ions entering the cytoplasm of the neuronal cells, thus creating a positive loop...
May 13, 2018: Journal of Molecular Neuroscience: MN
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