Selective Passage Research Articles

Dual selection mechanisms drive efficient single-gene reverse genetics for rotavirus

Current methods for engineering the segmented double-stranded RNA genome of rotavirus (RV) are limited by inefficient recovery of the recombinant virus. In an effort to expand the utility of RV reverse genetics, we developed a method to recover recombinant viruses in which independent selection strategies are used to engineer single-gene replacements. We coupled a mutant SA11 RV encoding a temperature-sensitive (ts) defect in the NSP2 protein with RNAi-mediated degradation of NSP2 mRNAs to isolate a virus containing a single recombinant gene that evades both selection mechanisms. Recovery is rapid and simple; after two rounds of selective passage the recombinant virus reaches titers of ≥10(4) pfu/mL. We used this reverse genetics method to generate a panel of viruses with chimeric NSP2 genes. For one of the chimeric viruses, the introduced NSP2 sequence was obtained from a pathogenic, noncultivated human RV isolate, demonstrating that this reverse genetics system can be used to study the molecular biology of circulating RVs. Combining characterized RV ts mutants and validated siRNA targets should permit the extension of this "two-hit" reverse genetics methodology to other RV genes. Furthermore, application of a dual selection strategy to previously reported reverse genetics methods for RV may enhance the efficiency of recombinant virus recovery.

Origami in outer membrane mimetics: correlating the first detailed images of refolded VDAC with over 20 years of biochemical data

Mitochondrial porin forms an aqueous pore in the outer membrane, through which selective passage of small metabolites and ions occurs, thereby regulating both mitochondrial function and cellular respiration. Investigations of the structure and function of porin have been performed with whole mitochondria, membrane vesicles, artificial membranes, and in detergent solutions, resulting in numerous models of porin structure. The mechanisms by which this protein functions are undoubtedly linked to its structure, which remained elusive until 2008, with reports of 3 high-resolution structures of this voltage-dependent, anion-selective channel (VDAC). The barrel structure is relatively simple yet unique: it is arranged as 19 anti-parallel beta-strands, with beta-strands 1 and 19 aligned parallel to each other to close the barrel. The N-terminal helical component is located within the lumen of the channel, although its precise structure and location in the lumen varies. With the basic barrel structure in hand, the data obtained in attempts to model the structure and understand porin over the past 20 years can be re-evaluated. Herein, using the mammalian VDAC structures as templates, the amassed electrophysiological and biochemical information has been reassessed with respect to the functional mechanisms of VDAC activity, with a focus on voltage-dependent gating.

Charge as a Selection Criterion for Translocation through the Nuclear Pore Complex

Nuclear pore complexes (NPCs) are highly selective filters that control the exchange of material between nucleus and cytoplasm. The principles that govern selective filtering by NPCs are not fully understood. Previous studies find that cellular proteins capable of fast translocation through NPCs (transport receptors) are characterized by a high proportion of hydrophobic surface regions. Our analysis finds that transport receptors and their complexes are also highly negatively charged. Moreover, NPC components that constitute the permeability barrier are positively charged. We estimate that electrostatic interactions between a transport receptor and the NPC result in an energy gain of several k B T, which would enable significantly increased translocation rates of transport receptors relative to other cellular proteins. We suggest that negative charge is an essential criterion for selective passage through the NPC.

Abstract 582: Targeting the blood-brain barrier with a non-canonical iron-mimicry mechanism: A translational approach for the detection and treatment of human brain tumors

Abstract Treatment of central nervous system (CNS) diseases is limited by the blood-brain barrier (BBB), a selective vascular interface restricting passage of most molecules from blood into brain. Here we used the in vivo phage display technology to isolate peptide-targeted phage particles that can cross the BBB under normal and pathological conditions. We show that a non-canonical association of (i) transferrin, (ii) an iron-mimic ligand motif, and (iii) transferrin receptor mediates binding and transport of phage particles into the normal mouse brain through an allosteric mechanism. We also show that, in an orthotopic human glioma model, a combination of transferrin receptor overexpression plus extended vascular permeability and ligand retention results in remarkable brain tumor targeting. Such unique attributes enable molecular imaging and targeted therapy of intracranial tumors in a clinic-ready setting. Finally, we expand our data by analyzing a large panel of primary CNS tumors through comprehensive tissue microarrays. Together, our approach and results provide a translational avenue for the detection and treatment of brain tumors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 582.

Local site preference rationalizes disentangling by DNA topoisomerases

To rationalize the disentangling action of type II topoisomerases, an improved wormlike DNA model was used to delineate the degree of unknotting and decatenating achievable by selective segment passage at specific juxtaposition geometries and to determine how these activities were affected by DNA circle size and solution ionic strength. We found that segment passage at hooked geometries can reduce knot populations as dramatically as seen in experiments. Selective segment passage also provided theoretical underpinning for an intriguing empirical scaling relation between unknotting and decatenating potentials.

Highly metastatic nude mouse model of human primary gastric lymphoma constructed by surgical orthotopic transplantation and in vivo continuous screening method

To develop a series of high metastatic models of human gastric malignant lymphoma in nude mice by orthotopic transplantation. Two histologically intact primary and hepatic metastatic fragments derived from surgical specimen of a patient with primary gastric lymphoma were implanted into the submucosa of stomach in nude mice. Highly metastatic and specific organ metastatic models were screened by selective orthotopic passage in nude mice. Transplantability, invasion, metastasis, morphological characteristics (light microscopy, electron microscopy and immunohistochemistry), karyotypic analysis and DNA content of orthotopically transplanted tumors were studied. Primary and hepatic metastatic fragments of primary gastric lymphoma were successfully transplanted in nude mice. Two nude mouse models of human primary gastric lymphoma, termed HGBL-0304 (hepatic metastasis model) and HGBL-0305 (high metastasis model), were developed, exhibiting different metastasis biology. Histopathology of transplanted tumors showed primary gastric diffuse large B cell lymphoma. Two models have been maintained for 45 generations by orthotopic passage in nude mice. A total of 419 nude mice were used for transplantation. The growth rate and resuscitation rate of liquid nitrogen cryopreservation of transplanted tumors were both 100%. Significant difference in metastasis biology was exhibited in four aspects of metastasis time, organ metastatic rate, the extent of hepatic metastasis and survival of cancer-bearing mice. The metastatic rates of liver, spleen, lymph nodes and peritoneal seeding in HGBL-0304 and HGBL-0305 models were 100% and 69.5%, 94.3% and 55.6%, 62.6% and 45.7%, and 43.5% and 30.5%. The onset time for metastases of liver, spleen, lymph nodes and peritoneal seeding was 2 w and 5 w, 3 w and 6 w, 2 w and 3 w, 3 w and 6 w respectively. The extent of hepatic metastasis in HGBL-0304 and HGBL-0305 models displayed diffuse involvement of the whole liver and mainly right lobe invasion of liver respectively. The mean survival time of HGBL-0304 and HGBL-0305 models was 54.3d and 106.9 d respectively. Surgical orthotopic implantation combined with in vivo selective passage screening is an effective method for establishing highly metastatic and specific organ metastatic models of human malignant lymphoma in nude mice. The study is the first time to establish hepatic metastasis and high metastasis nude mouse models of human primary gastric lymphoma with the same original patient and different potentials of invasion and metastasis.

Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima. 2. Molecular organization and structural stability

ABC transport systems provide selective passage of metabolites across cell membranes and typically require the presence of a soluble binding protein with high specificity to a specific ligand. In addition to their primary role in nutrient gathering, the binding proteins associated with bacterial transport systems have been studied for their potential to serve as design scaffolds for the development of fluorescent protein biosensors. In this work, we used Fourier transform infrared spectroscopy and molecular dynamics simulations to investigate the physicochemical properties of a hyperthermophilic binding protein from Thermotoga maritima. We demonstrated preferential binding for the polar amino acid arginine and experimentally monitored the significant stabilization achieved upon binding of ligand to protein. The effect of temperature, pH, and detergent was also studied to provide a more complete picture of the protein dynamics. A protein structure model was obtained and molecular dynamic experiments were performed to investigate and couple the spectroscopic observations with specific secondary structural elements. The data determined the presence of a buried beta-sheet providing significant stability to the protein under all conditions investigated. The specific amino acid residues responsible for arginine binding were also identified. Our data on dynamics and stability will contribute to our understanding of bacterial binding protein family members and their potential biotechnological applications.

Selective Ion Passage through Functionalized Graphene Nanopores

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionSelective Ion Passage through Functionalized Graphene NanoporesKyaw Sint, Boyang Wang, and Petr Král*Cite this: J. Am. Chem. Soc. 2009, 131, 27, 9600Publication Date (Web):June 1, 2009Publication History Published online1 June 2009Published inissue 15 July 2009https://doi.org/10.1021/ja903655uCopyright © 2009 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views3041Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (53 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Functionalization,Ions,Nanopores,Two dimensional materials Get e-Alerts

Adhesion and transcellular migration of neutrophils and B lymphocytes on fibroblasts

During tissue inflammation, infiltrated leukocytes may have physical contacts with fibroblasts. We observed that neutrophils and B lymphocytes adhered in a larger proportion than T cells on cultured fibroblasts. Microscopy showed that adhesion was also characterized by leukocyte engulfment by the fibroblasts. In migration assays, only neutrophils and B lymphocytes were selectively able to migrate through a fibroblast barrier. Adhesion and migration were increased by stimulation with tumor necrosis factor-α (TNF-α) and phorbol-12-myristate-13-acetate (PMA). Antibodies against ICAM-1/β2 integrin blocked the interaction of neutrophils to fibroblasts. For B lymphocytes the couple VCAM-1/α4 integrin was also involved in this interaction. Human skin fibroblasts presented similar adhesion characteristics as rat cardiac fibroblasts. By measuring the distance between the border of migration holes and cadherin-positive adherens junctions, more than 65% of the holes correspond to the transcellular route over the paracellular route. Furthermore, vimentin staining revealed that the migration holes were highly nested by intermediate filaments in accordance with the transcellular route. Our results demonstrated that engulfment of neutrophils and B lymphocytes by fibroblasts resulted in selective passage by a transcellular route.

A reverse genetic screen in the zebrafish identifies crb2b as a regulator of the glomerular filtration barrier

The glomerular filtration barrier is necessary for the selective passage of low molecular weight waste products and the retention of blood plasma proteins. Damage to the filter results in proteinuria. The filtration barrier is the major pathogenic site in almost all glomerular diseases and its study is therefore of clinical significance. We have taken advantage of the zebrafish pronephros as a system for studying glomerular filtration. In order to identify new regulators of filtration barrier assembly, we have performed a reverse genetic screen in the zebrafish testing a group of genes which are enriched in their expression within the mammalian glomerulus. In this novel screen, we have coupled gene knockdown using morpholinos with a physiological glomerular dye filtration assay to test for selective glomerular permeability in living zebrafish larvae. Screening 20 genes resulted in the identification of ralgps1, rapgef2, rabgef1, and crb2b. The crumbs (crb) genes encode a family of evolutionarily conserved proteins important for apical-basal polarity within epithelia. The crb2b gene is expressed in zebrafish podocytes. Electron microscopic analysis of crb2b morphants reveals a gross disorganization of podocyte foot process architecture and loss of slit diaphragms while overall polarity is maintained. Nephrin, a major component of the slit diaphragm, is apically mis-localized in podocytes from crb2b morphants suggesting that crb2b is required for the proper protein trafficking of Nephrin. This report is the first to show a role for crb function in podocyte differentiation. Furthermore, these results suggest a novel link between epithelial polarization and the maintenance of a functional filtration barrier.

Ultrafast photodissociation assisted by strong non-resonant Stark effect: the ‘straddling’ control pulse

Control of the ultrashort photodissociation dynamics of a diatomic molecule on different excitation channels is investigated by Stark shift with a strong and approximately constant electric pulse, that ‘straddles’ the pump pulse excitation. The scheme implies first the creation of the light-induced potentials (LIP) in the presence of the control field, then the selective crossing to a single excited LIP by the ultrashort pump pulse, and finally the turn-off of the control field. We observe: (1) blue-shifting of the photospectra controlled by the field amplitude; (2) non-selective photodissociation of a single exit channel in all the interval of energies despite selective adiabatic passage of the wave packet and some control of the branching ratio; (3) high yields of population transfer to weakly bonded states in the excited potentials with ultrashort pulses and no frequency tuning.

Liquid–liquid phase separation: characterisation of a novel device capable of separating particle carrying multiphase flows

Capillary forces on the microscale are exploited to create a continuous flow liquid-liquid phase separator. Segmented flow regimes of immiscible fluids are generated and subsequently separated into their component phases through an array of high aspect ratio, laser machined, separation ducts (36 microm wide, 130 microm deep) in a planar, integrated, polytetrafluoroethylene (PTFE) microdevice. A controlled pressure differential across the phase separator architecture facilitates the selective passage of the wetting, organic, phase through the separator ducts, enabling separation of microfluidic multiphase flow streams. The reported device is demonstrated to separate water and chloroform segmented flow regimes at flow rates up to 0.4 ml min(-1). Separation efficiency is quantified over a range of flow rates and applied pressure differentials, characterising device behaviour and limits of operation. Experimental measurements and observations are supported by theoretical hydrodynamic and capillary pressure modelling. The influence of material properties and geometric design parameters on phase separation is quantified and optimisation strategies proposed. The novel ability of the membrane free device to separate an organic phase containing suspended microparticulates, from an aqueous phase, is also demonstrated.

Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima

Members of the periplasmic binding protein superfamily are involved in the selective passage of ligands through bacterial cell membranes. The hyperthermophilic eubacterium Thermotoga maritima was found to encode a highly stable and specific periplasmic arginine-binding protein (TM0593). Following signal sequence removal and overexpression in Escherichia coli, TM0593 was purified by thermoprecipitation and affinity chromatography. The ultra-stable protein with a monomeric molecular weight of 27.7 kDa was found to exist as both a homodimer and homotrimer at appreciable concentrations even under strongly denaturing conditions, with an estimated transition temperature of 116 degrees C. Its multimeric structure may provide further evidence of the importance of quaternary structure in the movement of nutrients across bacterial membranes. Purified and refolded TM0593 was further characterized by fluorescence spectroscopy, mass spectrometry, and circular dichroism to demonstrate the specificity of the protein for arginine and to elucidate structural changes associated with arginine binding. The protein binds arginine with a dissociation constant of 20 muM as determined by surface plasmon resonance measurements. Due to its high thermodynamic stability, TM0593 may serve as a scaffold for the creation of a robust fluorescent biosensor.

Selective Ion Passage through Functionalized Graphene Nanopores

We design functionalized nanopores in graphene monolayers and show by molecular dynamics simulations that they provide highly selective passage of hydrated ions. Only ions that can be partly stripped of their hydration shells can pass through these ultrasmall pores with diameters of ∼5 A. For example, a fluorine−nitrogen-terminated pore allows the passage of Li+, Na+, and K+ cations with the ratio 9:14:33, but it blocks the passage of anions. The hydrogen-terminated pore allows the passage of F−, Cl−, and Br− anions with the ratio 0:17:33, but it blocks the passage of cations. These nanopores could have potential applications in molecular separation, desalination, and energy storage systems.

A toolbox facilitating stable transfection of Eimeria species

Stable transfection of Eimeria species has been difficult to achieve because of the obligate requirement for in vivo amplification and selection of the parasites. Strategies to generate and stabilise populations of transfected Eimeria tenella are described here, together with the identification of optimal parameters for the transfection process. A series of plasmids expressing selectable markers, including a panel of fluorescent reporter genes and a mutant Toxoplasma gondii dihydrofolate reductase–thymidylate synthase (DHFR-TSm2m3) gene that confers resistance to pyrimethamine, were electroporated into sporozoites of the E. tenella Wisconsin strain and stabilised by selective passage through chickens. Very high transfection efficiencies of up to 25% sporozoites in transient transfection and up to 9% oocysts following a single round of in vivo selection were achieved. Crucial factors include the use of very freshly harvested parasites with the AMAXA nucleofection system (program U33 in a cytomix-buffered reaction) and linearised plasmid DNA. The use of a restriction enzyme mediated integration (REMI) protocol boosted overall efficiency and elevated insertion rate per genome. Successful development of methods to generate and isolate stable populations of transfected Eimeria parasites will now stimulate rapid expansion of reverse genetic studies in this important coccidian.

Gap Junction Channels Exhibit Connexin-specific Permeability to Cyclic Nucleotides

Gap junction channels exhibit connexin dependent biophysical properties, including selective intercellular passage of larger solutes, such as second messengers and siRNA. Here, we report the determination of cyclic nucleotide (cAMP) permeability through gap junction channels composed of Cx43, Cx40, or Cx26 using simultaneous measurements of junctional conductance and intercellular transfer of cAMP. For cAMP detection the recipient cells were transfected with a reporter gene, the cyclic nucleotide-modulated channel from sea urchin sperm (SpIH). cAMP was introduced via patch pipette into the cell of the pair that did not express SpIH. SpIH-derived currents (I h) were recorded from the other cell of a pair that expressed SpIH. cAMP diffusion through gap junction channels to the neighboring SpIH-transfected cell resulted in a five to sixfold increase in I h current over time. Cyclic AMP transfer was observed for homotypic Cx43 channels over a wide range of conductances. However, homotypic Cx40 and homotypic Cx26 exhibited reduced cAMP permeability in comparison to Cx43. The cAMP/K+ permeability ratios were 0.18, 0.027, and 0.018 for Cx43, Cx26, and Cx40, respectively. Cx43 channels were ∼10 to 7 times more permeable to cAMP than Cx40 or Cx26 (Cx43 > Cx26 ≥ Cx40), suggesting that these channels have distinctly different selectivity for negatively charged larger solutes involved in metabolic/biochemical coupling. These data suggest that Cx43 permeability to cAMP results in a rapid delivery of cAMP from cell to cell in sufficient quantity before degradation by phosphodiesterase to trigger relevant intracellular responses. The data also suggest that the reduced permeability of Cx26 and Cx40 might compromise their ability to deliver cAMP rapidly enough to cause functional changes in a recipient cell.

New generation of low fouling nanofiltration membranes

The nanofiltration (NF) membranes and their properties are quite diverse, but can generally be described as having rejection characteristics that range from “loose” RO to “tight” ultrafiltration. The uniqueness of these membranes is highlighted by their ability to selectively reject different dissolved salts, and have high rejection of low molecular weight, dissolved components. Nanofiltration membranes are mainly used to partially soften potable water, allowing some minerals to pass into the product water and thus increase the stability of the water and prevent if from being aggressive to distribution piping material. Additionally, NF membranes are finding increasing use for purifying industrial effluents, and minimizing waste discharge. The key to using NF membranes for particular application is the selection of a membrane with appropriate rejection characteristic and the design of a suitable process. NF membranes are generally characterized by a high charge density and pore sizes in the range of nanometers. The surface charge is most often negative and has the greatest effect on the selective passage nature of these membranes. The design of a NF system can often be more complex than a RO system. Because the required transmembrane pressure is so low, a system design that will result in balanced flux throughout the array is difficult to achieve. One common approach is to design NF systems with multiple element types. Such so called “hybrid” designs can help more finely control flow in the NF system. Also, membrane fouling can cause a change of rejection selectivity and/or reduction of membrane permeability that could affect both the water quality and operating cost due to increased energy requirement and higher consumption of chemicals needed for stabilization of permeate. The rejection characteristics of NF membranes depend on chemistry and surface charges of the separating barrier layer, ionic composition and concentration of feedwater and operating parameters of the NF system: recovery rate and permeate flux. Although, theoretical models have been developed to calculate selective ion rejection of NF membranes, they are mostly adequate only for simple water systems in limited range of water compositions and concentrations. In algorithms applied for projection of permeate composition in commercial NF systems, the theoretical models are augmented by empirical correction coefficients developed from field results. Selection of proper NF membrane type and prediction of performance is further complicated by membrane fouling. In NF projects involving treatment of feedwater with high concentration of dissolved organics the membrane selection process usually include pilot unit operation to evaluate stability of salt rejection and water permeability of candidate membrane elements. The paper will discuss present offering of commercial NF membranes, case studies and models applied to calculate their performance. This will also include information on recently developed NF membranes with low fouling characteristic that are successfully applied in the world largest (150,000 m 3/d, 40 mgd) NF plant in Boca Raton, FL. The process of extensive field testing and parallel membrane performance optimization that led to selection of these nanofiltration elements for the Boca Raton plant will be described as well.

Transpath: A computational method for locating ion transit pathways through membrane proteins

The finely tuned structures of membrane channel proteins allow selective passage of ions through the available aqueous pores. To understand channel function, it is crucial to locate the pores and study their physical and chemical properties. Here, we propose a new pore-searching algorithm (TransPath), which uses the Configurational Bias Monte Carlo (CBMC) method to generate transmembrane trajectories driven by both geometric and electrostatic features. The trajectories are binned into groups determined by a vector distance criterion. From each group, a representative trajectory is selected based on the Rosenbluth weight, and the geometrically optimal path is obtained by simulated annealing. Candidate ion pathways can then be determined by analysis of the radius and potential profiles. The proposed method and its implementation are illustrated using the bacterial KcsA potassium channel as an example. The procedure is then applied to the more complex structures of the bacterial E. coli chloride channel homolog and a homology model of the ClC-0 channel.

Coxsackievirus Entry across Epithelial Tight Junctions Requires Occludin and the Small GTPases Rab34 and Rab5

The major group B coxsackievirus (CVB) receptor is a component of the epithelial tight junction (TJ), a protein complex that regulates the selective passage of ions and molecules across the epithelium. CVB enters polarized epithelial cells from the TJ, causing a transient disruption of TJ integrity. Here we show that CVB does not induce major reorganization of the TJ, but stimulates the specific internalization of occludin-a TJ integral membrane component-within macropinosomes. Although occludin does not interact directly with virus, depletion of occludin prevents CVB entry into the cytoplasm and inhibits infection. Both occludin internalization and CVB entry require caveolin but not dynamin; both are blocked by inhibitors of macropinocytosis and require the activity of Rab34, Ras, and Rab5, GTPases known to regulate macropinocytosis. Thus, CVB entry depends on occludin and occurs by a process that combines aspects of caveolar endocytosis with features characteristic of macropinocytosis.

Endothelial cells are a target of both complement and kinin system

The endothelium is a continuous physical barrier that regulates coagulation and selective passage of soluble molecules and circulating cells through the vessel wall into the tissue. Endothelial cells may contact components of the complement, the kinin and the coagulation systems and their functional activity can be influenced by these interactions. Therefore, complement activation products can induce pro-inflammatory and pro-coagulant responses by endothelial cells. Moreover complement can regulate the release of kinins on the endothelial cell surface influencing the vascular leakage. The aim of this review is to discuss the complex interplay that can be established among the endothelium, the complement proteins or its activation products, and the kinin system.