Mechanisms of <i>CFTR</i> Functional Variants That Impair Regulated Bicarbonate Permeation and Increase Risk for Pancreatitis but Not for Cystic Fibrosis

LaRusch, Jessica,Jung, Jinsei,General, Ignacio J.,Lewis, Michele D.,Park, Hyun Woo,Brand, Randall E.,Gelrud, Andres,Anderson, Michelle A.,Banks, Peter A.,Conwell, Darwin,Lawrence, Christopher,Romagnuo Public Library of Science 2014 PLoS genetics Vol.10 No.7

<▼1><P>CFTR is a dynamically regulated anion channel. Intracellular WNK1-SPAK activation causes CFTR to change permeability and conductance characteristics from a chloride-preferring to bicarbonate-preferring channel through unknown mechanisms. Two severe CFTR mutations (<I>CFTR<SUP>sev</SUP></I>) cause complete loss of CFTR function and result in cystic fibrosis (CF), a severe genetic disorder affecting sweat glands, nasal sinuses, lungs, pancreas, liver, intestines, and male reproductive system. We hypothesize that those <I>CFTR</I> mutations that disrupt the WNK1-SPAK activation mechanisms cause a selective, bicarbonate defect in channel function (<I>CFTR<SUP>BD</SUP></I>) affecting organs that utilize CFTR for bicarbonate secretion (e.g. the pancreas, nasal sinus, vas deferens) but do not cause typical CF. To understand the structural and functional requirements of the CFTR bicarbonate-preferring channel, we (a) screened 984 well-phenotyped pancreatitis cases for candidate <I>CFTR<SUP>BD</SUP></I> mutations from among 81 previously described <I>CFTR</I> variants; (b) conducted electrophysiology studies on clones of variants found in pancreatitis but not CF; (c) computationally constructed a new, complete structural model of CFTR for molecular dynamics simulation of wild-type and mutant variants; and (d) tested the newly defined <I>CFTR<SUP>BD</SUP></I> variants for disease in non-pancreas organs utilizing CFTR for bicarbonate secretion. Nine variants (<I>CFTR</I> R74Q, R75Q, R117H, R170H, L967S, L997F, D1152H, S1235R, and D1270N) not associated with typical CF were associated with pancreatitis (OR 1.5, p = 0.002). Clones expressed in HEK 293T cells had normal chloride but not bicarbonate permeability and conductance with WNK1-SPAK activation. Molecular dynamics simulations suggest physical restriction of the CFTR channel and altered dynamic channel regulation. Comparing pancreatitis patients and controls, <I>CFTR<SUP>BD</SUP></I> increased risk for rhinosinusitis (OR 2.3, p<0.005) and male infertility (OR 395, p<<0.0001). WNK1-SPAK pathway-activated increases in CFTR bicarbonate permeability are altered by <I>CFTR<SUP>BD</SUP></I> variants through multiple mechanisms. <I>CFTR<SUP>BD</SUP></I> variants are associated with clinically significant disorders of the pancreas, sinuses, and male reproductive system.</P></▼1><▼2><P><B>Author Summary</B></P><P>Genetic disorders of ion channels can affect the body's ability to function properly in many ways. CFTR, an ion channel regulating movement of chloride and bicarbonate across cell membranes, is important for absorbing and secreting fluids. If the gene responsible for the CFTR channel is mutated severely, the result is cystic fibrosis, a hereditary disorder in which the patient develops thick mucus, especially in the lungs, as well as scarring (fibrosis) in the pancreas. Cystic fibrosis also affects the sweat glands, nasal sinuses, intestines, liver, and male reproductive system. Mutations to the CFTR gene that do not cause cystic fibrosis have been considered benign. However, we discovered 9 CFTR mutations that do not cause cystic fibrosis but do cause inflammation and scarring of the pancreas (chronic pancreatitis). These mutant CFTR channels secrete chloride, which is important in the sweat glands, lungs, and intestines, but not bicarbonate, which is important in the pancreas, sinuses, and male reproductive tract. We found patients with any of these 9 mutations had chronic pancreatitis, and often sinus infections, and male infertility, but not other symptoms of cystic fibrosis. Our computer models and data will help researchers develop better drugs and help physicians treating patients with chronic pancreatitis.</P></▼2>

Electricity Generation by Microbial Fuel Cell Using Microorganisms as Catalyst in Cathode

( Jae Kyung Jang ),( Jin Jun Kan ),( Orianna Bretschger ),( Yuri A Gorby ),( Lewis Hsu ),( Byung Hong Kim ),( Kenneth H Nealson ) 한국미생물 · 생명공학회 2013 Journal of microbiology and biotechnology Vol.23 No.12

The cathode reaction is one of the most seriously limiting factors in a microbial fuel cell (MFC). The critical dissolved oxygen (DO) concentration of a platinum-loaded graphite electrode was reported as 2.2 mg/l, about 10-fold higher than an aerobic bacterium. A series of MFCs were run with the cathode compartment inoculated with activated sludge (biotic) or not (abiotic) on platinum-loaded or bare graphite electrodes. At the beginning of the operation, the current values from MFCs with a biocathode and abiotic cathode were 2.3 ± 0.1 and 2.6 ± 0.2 mA, respectively, at the air-saturated water supply in the cathode. The current from MFCs with an abiotic cathode did not change, but that of MFCs with a biotic cathode increased to 3.0 mA after 8 weeks. The coulomb efficiency was 59.6% in the MFCs with a biotic cathode, much higher than the value of 15.6% of the abiotic cathode. When the DO supply was reduced, the current from MFCs with an abiotic cathode decreased more sharply than in those with a biotic cathode. When the respiratory inhibitor azide was added to the catholyte, the current decreased in MFCs with a biotic cathode but did not change in MFCs with an abiotic cathode. The power density was higher in MFCs with a biotic cathode (430 W/m3 cathode compartment) than the abiotic cathode MFC (257 W/m3 cathode compartment). Electron microscopic observation revealed nanowire structures in biofilms that developed on both the anode and on the biocathode. These results show that an electron-consuming bacterial consortium can be used as a cathode catalyst to improve the cathode reaction.

The Brassica/Arabidopsis Comparative Genome Browser A Novel Approach to Genome Browsing

Lewis Christopher T.,Sharpe Andrew G.,Lydiate Derek J.,Parkin Isobel A.P. The Korean Society of Plant Biotechnology 2003 Plant molecular biology and biotechnology research Vol.5 No.4

Scalable Vector Graphics (SVG) has enabled a visually appealing, browser-based application for the display of Brassica sequences relative to Arabidopsis thaliana, and there are currently more than 70,000 B. napus Expressed Sequence Tags (ESTs) displayed. The client side of this browser is based on a Custom Graphical User Interface (CGUI) library which uses SVG, a new web graphics standard, to provide windowing functionality inside the web browser. This windowing functionality, combined with asynchronous data retrieval and client side rendering overcomes two of the key technology imposed drawbacks of current web based browsers: Fixed displays and frequent page reloads. The end result is an intuitive and enjoyable browsing experience. The browser is accessible online from the Brassica / Arabidopsis Genomics Initiative (http://brassica.agr.gc.ca). Inquiries about the browser should be directed to LewisCT@agr.gc.ca.

A human mitochondrial poly(A) polymerase mutation reveals the complexities of post-transcriptional mitochondrial gene expression

Wilson, William C.,Hornig-Do, Hue-Tran,Bruni, Francesco,Chang, Jeong Ho,Jourdain, Alexis A.,Martinou, Jean-Claude,Falkenberg, Maria,Spå,hr, Henrik,Larsson, Nils-Gö,ran,Lewis, Richard J.,Hewit Oxford University Press 2014 Human Molecular Genetics Vol.23 No.23

<P>The p.N478D missense mutation in human mitochondrial poly(A) polymerase (mtPAP) has previously been implicated in a form of spastic ataxia with optic atrophy. In this study, we have investigated fibroblast cell lines established from family members. The homozygous mutation resulted in the loss of polyadenylation of all mitochondrial transcripts assessed; however, oligoadenylation was retained. Interestingly, this had differential effects on transcript stability that were dependent on the particular species of transcript. These changes were accompanied by a severe loss of oxidative phosphorylation complexes I and IV, and perturbation of <I>de novo</I> mitochondrial protein synthesis. Decreases in transcript polyadenylation and in respiratory chain complexes were effectively rescued by overexpression of wild-type mtPAP. Both mutated and wild-type mtPAP localized to the mitochondrial RNA-processing granules thereby eliminating mislocalization as a cause of defective polyadenylation. <I>In vitro</I> polyadenylation assays revealed severely compromised activity by the mutated protein, which generated only short oligo(A) extensions on RNA substrates, irrespective of RNA secondary structure. The addition of LRPPRC/SLIRP, a mitochondrial RNA-binding complex, enhanced activity of the wild-type mtPAP resulting in increased overall tail length. The LRPPRC/SLIRP effect although present was less marked with mutated mtPAP, independent of RNA secondary structure. We conclude that (i) the polymerase activity of mtPAP can be modulated by the presence of LRPPRC/SLIRP, (ii) N478D mtPAP mutation decreases polymerase activity and (iii) the alteration in poly(A) length is sufficient to cause dysregulation of post-transcriptional expression and the pathogenic lack of respiratory chain complexes.</P>

Peristaltic flow of a Casson fluid in an annulus

P. Nagarani,A. Lewis 한국유변학회 2012 Korea-Australia rheology journal Vol.24 No.1

Peristaltic transport of a non-Newtonian fluid through the annular gap between two coaxial tubes is studied. We assumed that the inner tube is rigid whereas the outer tube has sinusoidal wave travelling down its wall. We modelled the flowing fluid as a Casson fluid to study the combined effects of yield stress (plug width) and annular gap on peristaltic transport. The flow is investigated in a wave frame of reference moving with velocity of the wave under long wavelength and low Reynolds number assumption. The expressions for velocity, stream function, pressure rise, flow rate and frictional force on inner and outer wall are obtained. Results are shown graphically and discussed in the results and discussion section. It is observed that yield stress and annular gap both have significant impact on the pressure rise, frictional resistance on the walls and on the formation and variation of trapped bolus.

Inhibition of Pathogenic Bacteria and Fungi by Natural Phenoxazinone from Octopus Ommochrome Pigments

Luján Lidianys María Lewis,Rosas-Burgos Ema Carina,Brauer Josafat Marina Ezquerra,Burboa-Zazueta María Guadalupe,Assanga Simon Bernard Iloki,Castro Teresa del Castillo,Penton Giselle,Plascencia-Jatome 한국미생물·생명공학회 2022 Journal of microbiology and biotechnology Vol.32 No.8

Cephalopods, in particular octopus (Octopus vulgaris), have the ability to alter their appearance or body pattern by showing a wide range of camouflage by virtue of their chromatophores, which contain nanostructured granules of ommochrome pigments. Recently, the antioxidant and antimicrobial activities of ommochromes have become of great interest; therefore, in this study, the pH-dependent redox effect of the extraction solvent on the antioxidant potential and the structural characterization of the pigments were evaluated. Cell viability was determined by the microdilution method in broth by turbidity, MTT, resazurin, as well as fluorescence microscopy kit assays. A Live/ Dead Double Staining Kit and an ROS Kit were used to elucidate the possible inhibitory mechanisms of ommochromes against bacterial and fungal strains. The results obtained revealed that the redox state alters the color changes of the ommochromes and is dependent on the pH in the extraction solvent. Natural phenoxazinone (ommochromes) is moderately toxic to the pathogens Staphylococcus aureus, Bacillus subtilis, Salmonella Typhimurium and Candida albicans, while the species Pseudomonas aeruginosa and Pseudomonas fluorescens, and the filamentous fungi Aspergillus parasiticus, Alternaria spp. and Fusarium verticillioides, were tolerant to these pigments. UV/visible spectral scanning and Fourier- transform infrared spectroscopy (FTIR) suggest the presence of reduced ommatin in methanol/ HCl extract with high intrinsic fluorescence.

Amorphous calcium silicate as a chemisorbent for phosphate

T. W. Lewis,D. C. Southam,A. J. McFarlane,J. H. Johnston 한국물리학회 2004 Current Applied Physics Vol.4 No.2-4

Amorphous calcium silicate (ACS), a novel silicate material developed as ller for use in paper manufacture, has shown ananity for the chemisorption of orthophosphate from an aqueous solution obeying a Freundlich isotherm. Removal eciencies ofup to 100% were achieved at environmental- and waste-scale concentrations of phosphate of between 0.01 and 100 mg P l. 1.Chemisorption studies indicated loadings up to 1.9 mmol HxPOð3. xÞ.4 g. 1 ACS were achievable. Kinetics studies comparing the rateof consumption of phosphate have shown that H2PO.4 is kinetically favoured and chemisorbed with higher loadings, and hencegreater eciency. This is a signicant improvement on other adsorbent-based methods for the removal of phosphate.

Peristaltic flow of a Casson fluid in an annulus

Nagarani, P.,Lewis, A. 한국유변학회 2012 Korea-Australia rheology journal Vol.24 No.1

Peristaltic transport of a non-Newtonian fluid through the annular gap between two coaxial tubes is studied. We assumed that the inner tube is rigid whereas the outer tube has sinusoidal wave travelling down its wall. We modelled the flowing fluid as a Casson fluid to study the combined effects of yield stress (plug width) and annular gap on peristaltic transport. The flow is investigated in a wave frame of reference moving with velocity of the wave under long wavelength and low Reynolds number assumption. The expressions for velocity, stream function, pressure rise, flow rate and frictional force on inner and outer wall are obtained. Results are shown graphically and discussed in the results and discussion section. It is observed that yield stress and annular gap both have significant impact on the pressure rise, frictional resistance on the walls and on the formation and variation of trapped bolus.

Model to estimate survival in ambulatory patients with hepatocellular carcinoma

Yang, Ju Dong,Kim, W. Ray,Park, Kyung Woo,Chaiteerakij, Roongruedee,Kim, Bohyun,Sanderson, Schuyler O.,Larson, Joseph J.,Pedersen, Rachel A.,Therneau, Terry M.,Gores, Gregory J.,Roberts, Lewis R.,Park Wiley Subscription Services, Inc., A Wiley Company 2012 Hepatology Vol.56 No.2

<P><B>Abstract</B></P><P>Survival of patients with hepatocellular carcinoma (HCC) is determined by the extent of the tumor and the underlying liver function. We aimed to develop a survival model for HCC based on objective parameters including the Model for Endstage Liver Disease (MELD) as a gauge of liver dysfunction. This analysis is based on 477 patients with HCC seen at Mayo Clinic Rochester between 1994 and 2008 (derivation cohort) and 904 patients at the Korean National Cancer Center between 2000 and 2003 (validation cohort). Multivariate proportional hazards models and corresponding risk score were created based on baseline demographic, clinical, and tumor characteristics. Internal and external validation of the model was performed. Discrimination and calibration of this new model were compared against existing models including Barcelona Clinic Liver Cancer (BCLC), Cancer of the Liver Italian Program (CLIP), and Japan Integrated Staging (JIS) scores. The majority of the patients had viral hepatitis as the underlying liver disease (100% in the derivation cohort and 85% in the validation cohort). The survival model incorporated MELD, age, number of tumor nodules, size of the largest nodule, vascular invasion, metastasis, serum albumin, and alpha‐fetoprotein. In cross‐validation, the coefficients remained largely unchanged between iterations. Observed survival in the validation cohort matched closely with what was predicted by the model. The concordance (c)‐statistic for this model (0.77) was superior to that for BCLC (0.71), CLIP (0.70), or JIS (0.70). The score was able to further classify patient survival within each stage of the BCLC classification. <I>Conclusion</I>: A new model to predict survival of HCC patients based on objective parameters provides refined prognostication and supplements the BCLC classification. (H<SMALL>EPATOLOGY</SMALL> 2012)</P>

Printed Origami Structures (Adv. Mater. 20/2010)

Ahn, Bok Yeop,Shoji, Daisuke,Hansen, Christopher J.,Hong, Eunji,Dunand, David C.,Lewis, Jennifer A. WILEY-VCH Verlag 2010 Advanced Materials Vol.22 No.20

<B>Graphic Abstract</B> <P>Bok Y. Ahn, Jennifer Lewis, and co-workers report on p. 2251 a new method for creating complex 3D structures that combines direct-write assembly with a wet-folding origami technique. Planar lattices composed of a titanium hydride ink are printed, and then folded, rolled, or molded into the desired shape. These 3D objects are then transformed into metallic or ceramic structures by thermal annealing. <img src='wiley_img_2010/09359648-2010-22-20-ADMA201090069-content.gif' alt='wiley_img_2010/09359648-2010-22-20-ADMA201090069-content'> </P>