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https://www.readbyqxmd.com/read/28550085/knockdown-of-sodium-calcium-exchanger-1-induces-epithelial-to-mesenchymal-transition-in-kidney-epithelial-cells
#1
Sona Lakshme Balasubramaniam, Anilkumar Gopalakrishnapillai, Nicholas J Petrelli, Sonali P Barwe
Mesenchymal to epithelial transition (MET) and epithelial to mesenchymal transition (EMT) are important processes in kidney development. Failure to undergo MET during development leads to the initiation of Wilms tumor (WT) whereas EMT contributes to the development of renal cell carcinomas (RCC). The role of calcium regulators in governing these processes is becoming evident. We demonstrated earlier that Na+/Ca2+ exchanger 1 (NCX1), a major calcium exporter in renal epithelial cells, regulates epithelial cell motility...
May 26, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28549531/targeting-the-akt-gsk-3-bcl-2-axis-in-acute-myeloid-leukemia
#2
REVIEW
Maria Rosaria Ricciardi, Simone Mirabilii, Roberto Licchetta, Monica Piedimonte, Agostino Tafuri
Over the last few decades, there has been significant progress in the understanding of the pathogenetic mechanisms of the Acute Myeloid Leukemia (AML). However, despite important advances in elucidating molecular mechanisms, the treatment of AML has not improved significantly, remaining anchored at the standard chemotherapy regimen "3 + 7", with the prognosis of patients remaining severe, especially for the elderly and for those not eligible for transplant procedures. The biological and clinical heterogeneity of AML represents the major obstacle that hinders the improvement of prognosis and the identification of new effective therapeutic approaches...
May 19, 2017: Advances in Biological Regulation
https://www.readbyqxmd.com/read/28548828/screening-of-pro-asp-sequences-exposed-on-bacteriophage-m13-as-an-ideal-anchor-for-gold-nanocubes
#3
Hwa Kyoung Lee, Yujean Lee, Hyori Kim, Hye-Eun Lee, Hyejin Chang, Ki Tae Nam, Dae Hong Jeong, Junho Chung
Bacteriophages are thought to be ideal vehicles for linking antibodies to nanoparticles. Here, we define the sequence of peptides exposed as a fusion protein on M13 bacteriophages to yield optimal binding of gold nanocubes and efficient bacteriophage amplification. We generated five helper bacteriophage libraries using AE(X)2DP, AE(X)3DP, AE(X)4DP, AE(X)5DP, and AE(X)6DP as the exposed portion of pVIII, in which X was a randomized amino acid residue encoded by the nucleotide sequence NNK. Efficient phage amplification was achievable only in the AE(X)2DP, AE(X)3DP, and AE(X)4DP libraries...
May 26, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28548821/turning-nonspecific-interference-into-signal-amplification-covalent-biosensing-nanoassembly-enabled-by-metal-catalyzed-cross-coupling
#4
Hao Li, Fang Wang, Shenguang Ge, Haiyun Liu, Mei Yan, Jinghua Yu
In this work, a new method of protein detection in complicated samples is proposed. This method employs probe-target recognition to induce cross-linking among the probe, the target, and the nonspecific proteins in the complicated sample as a means to convert interference into effective signal amplification. This also eliminates the necessity of multistep signal amplification in a separate solution system. On the basis of this strategy, a simple and robust assay for the activity of serum cathepsin B is established...
May 26, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28548485/clinically-relevant-detection-of-streptococcus-pneumoniae-with-dna-antibody-nanostructures
#5
Jinping Wang, May Ching Leong, Eric Zhewei Leong, Win Sen Kuan, David T Leong
Streptococcus pneumoniae (SP) is a pathogenic bacterium and a major cause of community-acquired pneumonia that could be fatal if left untreated. Therefore, rapid and sensitive detection of SP is crucial to enable targeted treatment during SP infections. In this study, DNA tetrahedron (DNA TH) with a hollow structure is anchored on gold electrodes to construct an electrochemical immunosensor for rapid detection of pneumococcal surface protein A (PspA) peptide and SP lysate from synthetic and actual human samples...
May 26, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28548292/hypertriglyceridemic-acute-pancreatitis-in-an-emergency-department-the-typical-clinical-features-and-genetic-variants
#6
Wan Jun Chen, Xiao Fan Sun, Rui Xue Zhang, Min Jie Xu, Tong Hai Dou, Xiao Bin Zhang, Min Zhong, Wei Qiang Yang, Li Liu, Xiao Ye Lu, Chang Qing Zhu
OBJECTIVE: To investigate the clinical characteristics of hypertriglyceridemic acute pancreatitis (HTGAP), and the molecular foundation contributing to the hypertriglyceridemia in this group of patients. METHODS: Clinical data from 329 patients with AP were collected and analyzed. All the patients were divided into 1) HTGAP group (n = 40), with fasting serum triglyceride ≥ 500 mg/dL; and 2) NHTGAP group (n = 289). Next, the targeted next-generation sequencing was applied in 11 HTGAP patients to detect the genetic mutation associated with hypertriglyceridemia that included apolipoprotein A-5 (APOA5), apolipoprotein C-3 (APOC3), apolipoprotein E (APOE), BLK proto-oncogene, lipoprotein lipase (LPL), apolipoprotein C-2 (APOC2), glycosylphosphatidylinositol anchored high density lipoprotein binding protein-1(GPIHBP1), and lipase maturation factor-1(LMF1)...
May 26, 2017: Journal of Digestive Diseases
https://www.readbyqxmd.com/read/28547747/deciphering-common-recognition-principles-of-nucleoside-mono-di-and-tri-phosphates-binding-in-diverse-proteins-via-structural-matching-of-their-binding-sites
#7
Raghu Bhagavat, Narayanaswamy Srinivasan, Nagasuma Chandra
Nucleoside triphosphate (NTP) ligands are of high biological importance and essential for all life forms. A pre-requisite for them to participate in diverse biochemical processes is their recognition by diverse proteins. It is thus of great interest to understand the basis for such recognition in different proteins. Towards this, we have employed a structural bioinformatics approach and analyse structures of 4677 NTP complexes available in PDB. Binding sites were extracted and compared exhaustively by using PocketMatch, a sensitive in-house site comparison algorithm, which resulted in grouping the entire dataset into 27 site-types...
May 25, 2017: Proteins
https://www.readbyqxmd.com/read/28546954/pleiotropic-cytotoxicity-of-vaca-toxin-in-host-cells-and-its-impact-on-immunotherapy
#8
REVIEW
Farnaz Fahimi, Mohammad Reza Tohidkia, Mehdi Fouladi, Reza Aghabeygi, Naser Samadi, Yadollah Omidi
Introduction: In the recent decades, a number of studies have highlighted the importance of Helicobacter pylori in the initiation and development of peptic ulcer and gastric cancer. Some potential virulence factors (e.g., urease, CagA, VacA, BabA) are exploited by this microorganism, facilitating its persistence through evading human defense mechanisms. Among these toxins and enzymes, vacuolating toxin A (VacA) is of a great importance in the pathogenesis of H. pylori. VacA toxin shows different pattern of cytotoxicity through binding to different cell surface receptors in various cells...
2017: BioImpacts: BI
https://www.readbyqxmd.com/read/28546514/the-nuclear-matrix-protein-ciz1-facilitates-localization-of-xist-rna-to-the-inactive-x-chromosome-territory
#9
Rebeca Ridings-Figueroa, Emma R Stewart, Tatyana B Nesterova, Heather Coker, Greta Pintacuda, Jonathan Godwin, Rose Wilson, Aidan Haslam, Fred Lilley, Renate Ruigrok, Sumia A Bageghni, Ghadeer Albadrani, William Mansfield, Jo-An Roulson, Neil Brockdorff, Justin F X Ainscough, Dawn Coverley
The nuclear matrix protein Cip1-interacting zinc finger protein 1 (CIZ1) promotes DNA replication in association with cyclins and has been linked to adult and pediatric cancers. Here we show that CIZ1 is highly enriched on the inactive X chromosome (Xi) in mouse and human female cells and is retained by interaction with the RNA-dependent nuclear matrix. CIZ1 is recruited to Xi in response to expression of X inactive-specific transcript (Xist) RNA during the earliest stages of X inactivation in embryonic stem cells and is dependent on the C-terminal nuclear matrix anchor domain of CIZ1 and the E repeats of Xist CIZ1-null mice, although viable, display fully penetrant female-specific lymphoproliferative disorder...
May 25, 2017: Genes & Development
https://www.readbyqxmd.com/read/28546512/wnt5a-promotes-frizzled-4-signalosome-assembly-by-stabilizing-cysteine-rich-domain-dimerization
#10
Zachary J DeBruine, Jiyuan Ke, Kaleeckal G Harikumar, Xin Gu, Peter Borowsky, Bart O Williams, Wenqing Xu, Laurence J Miller, H Eric Xu, Karsten Melcher
Wnt/β-catenin signaling is activated when extracellular Wnt ligands bind Frizzled (FZD) receptors at the cell membrane. Wnts bind FZD cysteine-rich domains (CRDs) with high affinity through a palmitoylated N-terminal "thumb" and a disulfide-stabilized C-terminal "index finger," yet how these binding events trigger receptor activation and intracellular signaling remains unclear. Here we report the crystal structure of the Frizzled-4 (FZD4) CRD in complex with palmitoleic acid, which reveals a CRD tetramer consisting of two cross-braced CRD dimers...
May 25, 2017: Genes & Development
https://www.readbyqxmd.com/read/28542831/machine-learning-reveals-a-non-canonical-mode-of-peptide-binding-to-mhc-class-ii-molecules
#11
Massimo Andreatta, Vanessa Isabell Jurtz, Thomas Kaever, Alessandro Sette, Bjoern Peters, Morten Nielsen
MHC class II molecules play a fundamental role in the cellular immune system: they load short peptide fragments derived from extracellular proteins and present them on the cell surface. It is currently thought that the peptide binds lying more or less flat in the MHC groove, with a fixed distance of nine amino acids between the first and last residue in contact with the MHCII. While confirming that the great majority of peptides bind to the MHC using this canonical mode, we report evidence for an alternative, less common mode of interaction...
May 24, 2017: Immunology
https://www.readbyqxmd.com/read/28542301/electronic-cigarette-aerosols-suppress-cellular-antioxidant-defenses-and-induce-significant-oxidative-dna-damage
#12
Vengatesh Ganapathy, Jimmy Manyanga, Lacy Brame, Dehra McGuire, Balaji Sadhasivam, Evan Floyd, David A Rubenstein, Ilangovan Ramachandran, Theodore Wagener, Lurdes Queimado
BACKGROUND: Electronic cigarette (EC) aerosols contain unique compounds in addition to toxicants and carcinogens traditionally found in tobacco smoke. Studies are warranted to understand the public health risks of ECs. OBJECTIVE: The aim of this study was to determine the genotoxicity and the mechanisms induced by EC aerosol extracts on human oral and lung epithelial cells. METHODS: Cells were exposed to EC aerosol or mainstream smoke extracts and DNA damage was measured using the primer anchored DNA damage detection assay (q-PADDA) and 8-oxo-dG ELISA assay...
2017: PloS One
https://www.readbyqxmd.com/read/28540724/pde%C3%AE-binding-to-ras-isoforms-provides-a-route-to-proper-membrane-localization
#13
Serena Muratcioglu, Hyunbum Jang, Attila Gursoy, Ozlem Keskin, Ruth Nussinov
To signal, Ras isoforms must be enriched at the plasma membrane (PM). It was suggested that phosphodiesterase-δ (PDEδ) can bind and shuttle some farnesylated Ras isoforms to the PM - but not all. Among these, interest focused on K-Ras4B, the most abundant oncogenic Ras isoform. To study PDEδ/Ras interactions, we modeled and simulated the PDEδ/K-Ras4B complex. We obtained structures which were similar to two subsequently determined crystal structures. We next modeled and simulated complexes of PDEδ with the farnesylated hypervariable regions (HVRs) of K-Ras4A and N-Ras...
May 25, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28540183/the-draft-genome-of-corchorus-olitorius-cv-jro-524-navin
#14
Debabrata Sarkar, Ajay Kumar Mahato, Pratik Satya, Avijit Kundu, Sangeeta Singh, Pawan Kumar Jayaswal, Akshay Singh, Kaushlendra Bahadur, Sasmita Pattnaik, Nisha Singh, Avrajit Chakraborty, Nur Alam Mandal, Debajeet Das, Tista Basu, Amitha Mithra Sevanthi, Dipnarayan Saha, Subhojit Datta, Chandan Sourav Kar, Jiban Mitra, Karabi Datta, Pran Gobinda Karmakar, Tilak Raj Sharma, Trilochan Mohapatra, Nagendra Kumar Singh
Here, we present the draft genome (377.3 Mbp) of Corchorus olitorious cv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv. Sudan Green) and indigenous (cv. JRO-632) types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of Theobroma cacao followed by Gossypium raimondii...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28539360/a-dock-and-coalesce-mechanism-driven-by-hydrophobic-interactions-governs-cdc42-binding-with-its-effector-protein-ack
#15
George J N Tetley, Helen R Mott, R Neil Cooley, Darerca Owen
Cdc42 is a Rho-family small G protein that has been widely studied for its role in controlling the actin cytoskeleton and plays a part in several potentially oncogenic signalling networks. Similar to most other small G proteins, Cdc42 binds to many downstream effector proteins to elicit its cellular effects. These effector proteins all engage the same face of Cdc42, the conformation of which is governed by the activation state of the G protein. Previously, the importance of individual residues in conferring binding affinity has been explored for residues within Cdc42 for three of its CRIB effectors, activated Cdc42 kinase (ACK), p21-activated kinase (PAK), and Wiskott-Aldrich syndrome protein (WASP)...
May 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28536260/functional-role-of-the-three-conserved-cysteines-in-the-n-domain-of-visual-arrestin-1
#16
Sergey A Vishnivetskiy, Regina J Lee, X Edward Zhou, Andreas Franz, Qiuyi Xu, H Eric Xu, Vsevolod V Gurevich
Arrestins specifically bind active and phosphorylated forms of their cognate G protein-coupled receptors, blocking G protein coupling and often redirecting the signaling to alternative pathways. High-affinity receptor binding is accompanied by the two major structural changes in arrestin: the release of the C-tail and rotation of the two domains relative to each other. The first requires the detachment of the arrestin C-tail from the body of the molecule, whereas the second requires the disruption of the network of charge-charge interactions at the interdomain interface, termed the polar core...
May 23, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28536180/yy1-and-ctcf-orchestrate-a-3d-chromatin-looping-switch-during-early-neural-lineage-commitment
#17
Jonathan A Beagan, Michael T Duong, Katelyn R Titus, Linda Zhou, Zhendong Cao, Jingjing Ma, Caroline V Lachanski, Daniel R Gillis, Jennifer E Phillips-Cremins
CTCF is an architectural protein with a critical role in connecting higher-order chromatin folding in pluripotent stem cells. Recent reports have suggested that CTCF binding is more dynamic during development than previously appreciated. Here we set out to understand the extent to which shifts in genome-wide CTCF occupancy contribute to the 3-D reconfiguration of fine-scale chromatin folding during early neural lineage commitment. Unexpectedly, we observe a sharp decrease in CTCF occupancy during the transition from naive/primed pluripotency to multipotent primary neural progenitor cells (NPCs)...
May 23, 2017: Genome Research
https://www.readbyqxmd.com/read/28535907/suppression-of-epithelial-restitution-using-an-inhibitor-against-rho-associated-coiled-coil-containing-protein-kinase-aggravates-colitis-through-reduced-epithelial-expression-of-a-kinase-anchor-protein-13
#18
Yumi Kangawa, Toshinori Yoshida, Yutaka Yonezawa, Kiyoshi Maruyama, Shim-Mo Hayashi, Makoto Shibutani
In the gastrointestinal tract, the immediate healing response to mucosal damage is critical to sustain mucosal homeostasis. The migration of surrounding epithelial cells to cover the denuded area without proliferation is termed restitution, followed by early reparation of the damage. In this study, we determined the role of A-kinase anchor protein 13 (AKAP13) in mice with dextran sulphate sodium (DSS)-induced colitis upon mucosal injury and restitution, and investigated whether inhibition of Rho-associated coiled-coil containing protein kinase (ROCK), downstream effector of AKAP13, affects these mucosal responses...
May 20, 2017: Experimental and Toxicologic Pathology: Official Journal of the Gesellschaft Für Toxikologische Pathologie
https://www.readbyqxmd.com/read/28535337/overall-structural-model-of-ns5a-protein-from-hepatitis-c-virus-and-modulation-by-mutations-confering-resistance-of-virus-replication-to-cyclosporin-a
#19
Aurelie Badillo, Veronique Brechot, Stephane Sarrazin, François-Xavier Cantrelle, Frederic Delolme, Marie-Laure Fogeron, Jennifer Molle, Roland Montserret, Anja Bockmann, Ralf Bartenschlager, Volker Lohmann, Guy Lippens, Sylvie Ricard-Blum, Xavier Hanoulle, Francois Penin
Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is a RNA-binding phosphoprotein composed of a N-terminal membrane anchor (AH), a structured domain 1 (D1) and two intrinsically disordered domains (D2 and D3). The knowledge of the functional architecture of this multifunctional protein remains limited. We report here that NS5A-D1D2D3 produced in a wheat germ cell-free system is obtained under a highly phosphorylated state. Its NMR analysis revealed that these phosphorylations do not change the disordered nature of D2 and D3 domains but increase the number of conformers due to partial phosphorylations...
May 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28534112/decolorization-of-textile-dye-rb19-using-volcanic-rock-matrix-immobilized-bacillus-thuringiensis-cells-with-surface-displayed-laccase
#20
Juan Wan, Xiaowen Sun, Cheng Liu, Mengjun Tang, Lin Li, Hong Ni
A triplicate volcanic rock matrix-Bacillus thuringiensis-laccase WlacD (VRMs-Bt-WlacD) dye decolorization system was developed. WlacD was displayed on the B. thuringiensis MB174 cell surface to prepare a whole-cell laccase biocatalyst by using two repeat N-terminal domains of autolysin Mbg (Mbgn)2 as the anchoring motif. Immunofluorescence microscopic assays confirmed that the fusion protein (Mbgn)2-WlacD was anchored on the surface of the recombinant B. thuringiensis MB174. After optimization by a single factor test, L 9(3(4))-orthogonal test, Plackett-Burman test, steepest ascent method, and Box-Behnken response surface methodology, the whole-cell specific laccase activity of B...
June 2017: World Journal of Microbiology & Biotechnology
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