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https://www.readbyqxmd.com/read/29154869/evaluating-different-dna-binding-domains-to-modulate-l1-orf2p-driven-site-specific-retrotransposition-events-in-human-cells
#1
Catherine M Ade, Rebecca S Derbes, Bradley J Wagstaff, Sara B Linker, Travis B White, Dawn Deharo, Victoria P Belancio, Zoltán Ivics, Astrid M Roy-Engel
DNA binding domains (DBDs) have been used with great success to impart targeting capabilities to a variety of proteins creating highly useful genomic tools. We evaluated the ability of five types of DBDs and strategies (AAV Rep proteins, Cre, TAL effectors, zinc finger proteins, and Cas9/gRNA system) to target the L1 ORF2 protein to drive retrotransposition of Alu inserts to specific sequences in the human genome. First, we find that the L1 ORF2 protein tolerates the addition of protein domains both at the amino- and carboxy-terminus...
November 14, 2017: Gene
https://www.readbyqxmd.com/read/29149973/hepatitis-c-virus-recurrence-occurs-earlier-in-patients-receiving-donation-after-circulatory-death-liver-transplant-grafts-compared-with-those-receiving-donation-after-brainstem-death-grafts
#2
S A Townsend, M A Monga, P Nightingale, D Mutimer, A M Elsharkawy, A Holt
INTRODUCTION: Hepatitis C virus (HCV)-related cirrhosis remains the commonest indication for liver transplantation worldwide, yet few studies have investigated the impact of donation after circulatory death (DCD) graft use on HCV recurrence and patient outcomes. DCD grafts have augmented the limited donor organ pool and reduced wait-list mortality, although concerns regarding graft longevity and patient outcome persist. METHODS: This was a single-center study of all HCV + adults who underwent DCD liver transplantation between 2004 and 2014...
November 2017: Transplantation Proceedings
https://www.readbyqxmd.com/read/29135372/first-study-on-interferon-regulatory-factor-in-sturgeon-expression-pattern-of-interferon-regulatory-factor-in-dabry-s-sturgeon-acipenser-dabryanus
#3
Youshen Li, Shuhuan Zhang, Kai Luo, Lihai Xia, Wei Hu, Guangming Tian, Zhitao Qi, Qiaoqing Xu, Qiwei Wei
Interferon regulatory factors (IRFs) are crucial regulators in initiating the host innate immune response against pathogen invasions. Dabry's sturgeon (Acipenser dabryanus) is particularly a valuable fish species found in the Yangtze River, China for which there is scarce immunological data. In the present study, we investigated the expression profile of sturgeon IRF genes. All adIRFs were composed of 8 exons and 7 introns, except adIRF1, which possessed 9 exons interrupted by 8 introns. Moreover, the predicted protein sequence has a DNA-binding domain (DBD) sharing high identity with spotted gar (Lepisosteus oculatus)...
November 2017: Journal of Interferon & Cytokine Research
https://www.readbyqxmd.com/read/29133527/interaction-of-the-phosphorylated-dna-binding-domain-in-nuclear-receptor-car-with-its-ligand-binding-domain-regulates-car-activation
#4
Ryota Shizu, Jungki Min, Mack Sobhany, Lars C Pedersen, Shingo Mutoh, Masahiko Negishi
The nuclear protein constitutive active/androstane receptor (CAR or NR1I3) regulates several liver functions such as drug and energy metabolism and cell growth or death, which are often involved in the development of diseases such as diabetes and hepatocellular carcinoma. CAR undergoes a conversion from inactive homodimers to active heterodimers with retinoid X receptor alpha (RXRα), and phosphorylation of the DNA-binding domain (DBD) at Thr-38 in CAR regulates this conversion. Here, we uncovered the molecular mechanism by which this phosphorylation regulates the intramolecular interaction between CARs DBD and ligand-binding domain (LBD), enabling the homodimer-heterodimer conversion...
November 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29100756/trpv1-alterations-in-urinary-bladder-dysfunction-in-a-rat-model-of-stz-induced-diabetes
#5
Bizhan R Sharopov, Kseniya L Gulak, Igor B Philyppov, Anna V Sotkis, Yaroslav M Shuba
AIMS: More than half of diabetic patients experience voiding disorder termed diabetic urinary bladder dysfunction (DBD). Here we have investigated how the alterations in transient receptor potential vanilloid 1 (TRPV1) ion channel expressed in bladder-innervating afferents may contribute to DBD pathogenesis. MAIN METHODS: The rat model of streptozotocin (STZ)-induced diabetes was used. The functional profile of TRPV1 in retrogradely labeled afferent, bladder-innervating dorsal root ganglia (DRG) neurons was examined using patch clamp...
October 31, 2017: Life Sciences
https://www.readbyqxmd.com/read/29084380/a-combinatorial-approach-to-synthetic-transcription-factor-promoter-combinations-for-yeast-strain-engineering
#6
Zain Y Dossani, Amanda Reider Apel, Heather S Middleton, Nathan J Hillson, Samuel Deutch, Jay D Keasling, Aindrila Mukhopadhyay
Despite the need for inducible promoters in strain development efforts, the majority of engineering in Saccharomyces cerevisiae continues to rely on a few constitutively active or inducible promoters. Building on advances that use the modular nature of both transcription factors and promoter regions, we have built a library of hybrid promoters that are regulated by a synthetic transcription factor. The hybrid promoters consist of native S. cerevisiae promoters, in which the operator regions have been replaced with sequences that are recognized by the bacterial LexA DNA binding protein...
October 30, 2017: Yeast
https://www.readbyqxmd.com/read/29083935/tri-nucleotide-consortium-of-androgen-receptor-is-associated-with-low-serum-fsh-and-testosterone-in-asthenospermic-men
#7
Haroon Latif Khan, Shahzad Bhatti, Sana Abbas, Yousaf Latif Khan, Muhammad Aslamkhan, Rosa Maria Marquez Gonzalez, Gerardo Rodriguez Gonzalez, Hikmet Hakan Aydin, Magali Segundo Trinidad
Androgen mediating signaling is implicated in regulating the expression of reproductive related genes. Any deviation in the gene expression might be the ignitable precursor for genomic instability that inflames the genomic rearrangements and a leading cause of cancer. The main goal of this study was to determine the relationships between trinucleotide repeats of androgen receptor (AR), sex steroids, and sexual function in men presenting with reduced sperm motility. We investigated the singleton or combinatorial effects of the length of trinucleotide repeats of AR on reproductive hormones, clinical parameters, semen analyses, as well as sexual assessment function of 210 asthenospermic outpatients along with 125 normal subjects...
October 30, 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/29080685/functional-characterization-of-interferon-regulatory-factor-5-and-its-role-in-the-innate-antiviral-immune-response
#8
Kete Ai, Kai Luo, Lihai Xia, Weihua Gao, Wei Hu, Zhitao Qi, Qiaoqing Xu
In mammals, type I interferons (IFNs) are primarily regulated by transcription factors of the IFN regulatory (IRF) family. Interferon regulatory factor 5 (IRF-5) plays pivotal roles in antiviral and inflammatory responses. In the present study, we found that zebrafish (Danio rerio) IRF5 is a key player in the regulation of the expression of type I IFN and its antiviral immune response. IRF5 was upregulated in zebrafish embryonic fibroblast cells (ZF4) when challenged with grass carp reovirus (GCRV). Moreover, the expression profiles of Mx, IFN, Viperin, and IRF7, but not IRF3, were upregulated by overexpression of IRF5 in Epithelioma papulosum cyprinid cells (EPCs)...
October 28, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29076552/an-experimental-investigation-of-antisocial-lie-telling-among-children-with-disruptive-behavior-disorders-and-typically-developing-children
#9
Allison P Mugno, Lindsay C Malloy, Daniel A Waschbusch, William E Pelham, Victoria Talwar
Children's lie-telling is surprisingly understudied among children with significant behavioral problems. In the present study, experimental paradigms were used to examine antisocial lie-telling among ethnically diverse 5- to 10-year-old children with disruptive behavior disorders (DBD; n = 71) and a typically developing (TD) comparison sample (n = 50) recruited from a southeastern state from 2013 to 2014. Children completed two games that measured the prevalence and skill of their lies: (a) for personal gain and (b) to conceal wrongdoing...
October 27, 2017: Child Development
https://www.readbyqxmd.com/read/29059560/simultaneous-removal-of-cr-vi-and-acid-orange-7-from-water-solution-by-dielectric-barrier-discharge-plasma
#10
Chunxiao Zhang, Yabing Sun, Zhongqing Yu, Guyu Zhang, Jingwei Feng
A feasibility study was conducted for simultaneous removal of hexavalent chromium (Cr(VI)) and azo dye acid orange 7 (AO7) by the dielectric barrier discharge (DBD) plasma. The results showed that there was a synergistic effect between Cr(VI) reduction and AO7 degradation. The presence of Cr(VI) enhanced the degradation efficiency of AO7. Meanwhile, the removal efficiency of Cr(VI) also increased in the presence of AO7. Under acidic conditions (pH = 3.0), the reduction efficiency of Cr(VI) was higher (approximately 94%)...
October 16, 2017: Chemosphere
https://www.readbyqxmd.com/read/29054828/cloning-and-expression-study-of-an-irf4a-gene-and-its-two-transcript-variants-in-turbot-scophthalmus-maximus
#11
Song Li, Guobin Hu, Zhipeng Chen, Lianfei Song, Guanjie Wang, Dahai Liu, Qiuming Liu
Interferon regulatory factor 4 (IRF4) is known to be involved in antiviral response as well as regulation of functional and developmental processes in lymphomyeloid cell lineages in mammals. In this study, the gene of IRF4a and its two transcript variants (named IRF4a1 and -2) were cloned from turbot, Scophthalmus maximus, the tissue distributions and in vivo immune responsive expression patterns of the two transcripts were subsequently examined. The Scophthalmus maximus (Sm)IRF4a gene is 8367 nucleotide (nt) in length, consisting of eight exons and seven introns...
October 18, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29054521/computational-simulations-and-experimental-validation-of-structure-physicochemical-properties-of-pristine-and-functionalized-graphene-implications-for-adverse-effects-on-p53-mediated-dna-damage-response
#12
Faiza Basheer, Anu R Melge, Abhilash Sasidharan, Shantikumar V Nair, K Manzoor, C Gopi Mohan
Recent reports indicated DNA damaging potential of few-layer graphene in human cell systems. Here, we used computational technique to understand the interaction of both pristine (pG) or carboxyl functionalized graphene (fG) of different sizes (1, 6, and 10nm) with an important DNA repair protein p53. The molecular docking study revealed strong interaction between pG and DNA binding domains (DBD) of p53 with binding free energies (BE) varying from -12.0 (1nm) to -34 (6nm)kcal/mol, while fG showed relatively less interaction with BE varying from -6...
October 17, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29042652/computational-analysis-of-the-molecular-mechanism-of-ramr-mutations-contributing-to-antimicrobial-resistance-in-salmonella-enterica
#13
Yen-Yi Liu, Chih-Chieh Chen
Antimicrobial resistance (AMR) in pathogenic microorganisms with multidrug resistance (MDR) constitutes a severe threat to human health. A major causative mechanism of AMR is mediated through the multidrug efflux pump (MEP). The resistance-nodulation-division superfamily (RND family) of Gram-negative bacteria is usually the major cause of MDR in clinical studies. In Salmonella enterica, the RND pump is translated from the arcAB gene, which is regulated by the activator RamA. Many MEP-caused AMR strains have high ramA gene expression due to mutations in RamR, which has a homodimeric structure comprising the dimerization domain and DNA-binding domain (DBD)...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29036376/the-mechanism-and-high-free-energy-transition-state-of-lac-repressor-lac-operator-interaction
#14
Rituparna Sengupta, Michael W Capp, Irina A Shkel, M Thomas Record
Significant, otherwise-unavailable information about mechanisms and transition states (TS) of protein folding and binding is obtained from solute effects on rate constants. Here we characterize TS for lac repressor(R)-lac operator(O) binding by analyzing effects of RO-stabilizing and RO-destabilizing solutes on association (ka) and dissociation (kd) rate constants. RO-destabilizing solutes (urea, KCl) reduce ka comparably (urea) or more than (KCl) they increase kd, demonstrating that they destabilize TS relative to reactants and RO, and that TS exhibits most of the Coulombic interactions between R and O...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29033191/effect-of-the-ultraviolet-light-treatment-and-storage-methods-on-the-biological-activity-of-a-titanium-implant-surface
#15
Sung-Hwan Choi, Won-Seok Jeong, Jung-Yul Cha, Jae-Hoon Lee, Kee-Joon Lee, Hyung-Seog Yu, Eun-Ha Choi, Kwang-Mahn Kim, Chung-Ju Hwang
OBJECTIVE: We evaluated whether the biological activity of the surface of titanium, when stored in an aqueous solution, in low vacuum, and under ambient conditions after ultraviolet light (UV) treatment is comparable to that of the surface immediately after UV treatment for 15min and that after dielectric barrier discharge (DBD) plasma treatment for 15min. METHODS: Grade IV titanium discs with machined surfaces were irradiated with UV and their surface properties were evaluated immediately and after storage for 28days in distilled H2O (dH2O), a vacuum desiccator (31...
October 12, 2017: Dental Materials: Official Publication of the Academy of Dental Materials
https://www.readbyqxmd.com/read/29027733/improvement-of-wheat-seed-vitality-by-dielectric-barrier-discharge-plasma-treatment
#16
Qiao Guo, Yiran Meng, Guangzhou Qu, Tiecheng Wang, Fengning Yang, Dongli Liang, Shibin Hu
Influences of discharge voltage on wheat seed vitality were investigated in a dielectric barrier discharge (DBD) plasma system at atmospheric pressure and temperature. Six different treatments were designed, and their discharge voltages were 0.0, 9.0, 11.0, 13.0, 15.0, and 17.0 kV, respectively. Fifty seeds were exposed to the DBD plasma atmosphere with an air flow rate of 1.5 L min(-1) for 4 min in each treatment, and then the DBD plasma-treated seeds were prepared for germination in several Petri dishes...
October 13, 2017: Bioelectromagnetics
https://www.readbyqxmd.com/read/29021580/the-quaternary-architecture-of-rar%C3%AE-rxr%C3%AE-heterodimer-facilitates-domain-domain-signal-transmission
#17
Vikas Chandra, Dalei Wu, Sheng Li, Nalini Potluri, Youngchang Kim, Fraydoon Rastinejad
Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor β-retinoic X receptor α (RARβ-RXRα) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies...
October 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/29018070/hypothermic-oxygenated-machine-perfusion-hope-for-orthotopic-liver-transplantation-of-human-liver-allografts-from-extended-criteria-donors-ecd-in-donation-after-brain-death-dbd-a-prospective-multicentre-randomised-controlled-trial-hope-ecd-dbd
#18
Zoltan Czigany, Wenzel Schöning, Tom Florian Ulmer, Jan Bednarsch, Iakovos Amygdalos, Thorsten Cramer, Xavier Rogiers, Irinel Popescu, Florin Botea, Jiří Froněk, Daniela Kroy, Alexander Koch, Frank Tacke, Christian Trautwein, Rene H Tolba, Marc Hein, Ger H Koek, Cornelis H C Dejong, Ulf Peter Neumann, Georg Lurje
INTRODUCTION: Orthotopic liver transplantation (OLT) has emerged as the mainstay of treatment for end-stage liver disease. In an attempt to improve the availability of donor allografts and reduce waiting list mortality, graft acceptance criteria were extended increasingly over the decades. The use of extended criteria donor (ECD) allografts is associated with a higher incidence of primary graft non-function and/or delayed graft function. As such, several strategies have been developed aiming at reconditioning poor quality ECD liver allografts...
October 10, 2017: BMJ Open
https://www.readbyqxmd.com/read/28986805/engineered-zinc-finger-dna-binding-domains-synthesis-assessment-of-dna-binding-affinity-and-direct-protein-delivery-to-mammalian-cells
#19
Mir A Hossain, Isaac J Knudson, Shaleen Thakur, Yong Shen, Jared R Stees, Joeva J Barrow, Jörg Bungert
Zinc finger proteins are the most common among families of DNA-binding transcription factors. Designer transcription factors generated by the fusion of engineered zinc finger DNA-binding domains (ZF-DBDs) to effector domains have been valuable tools for the modulation of gene expression and for targeted genome editing. However, ZF-DBDs without effector domains have also been shown to effectively modulate gene expression by competing with sequence-specific DNA-binding transcription factors. Here, we describe the methodology and provide a detailed workflow for the cloning, expression, purification, and direct cell delivery of engineered ZF-DBDs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28980391/the-duration-of-asystolic-ischemia-time-determines-the-risk-of-graft-failure-after-circulatory-dead-donor-kidney-transplantation-a-eurotransplant-cohort-study
#20
L Heylen, I Jochmans, U Samuel, I Tieken, M Naesens, J Pirenne, B Sprangers
Circulatory death donor (DCD) kidney transplantations are steadily increasing. Consensus reports recommend to limit donor warm ischemia time (DWIT) in DCD donation, although an independent effect on graft outcome has not been demonstrated. We investigated death-censored graft survival in 18,065 recipients of deceased-donor kidney transplants in the Eurotransplant region: 1,059 DCD and 17,006 brain-dead donor (DBD) kidney recipients. DWIT was defined as time from circulatory arrest until cold flush. DCD donation was an independent risk factor for graft failure (adjusted HR 1...
October 5, 2017: American Journal of Transplantation
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