Observation of molecular level behavior in molecular electronic junction device

NASA Astrophysics Data System (ADS)

Maitani, Masato

In this dissertation, I utilize AFM based scanning probe measurement and surface enhanced Raman scattering based vibrational spectroscopic analysis to directly characterize topographic, electronic, and chemical properties of molecules confined in the local area of M3 junction to elucidate the molecular level behavior of molecular junction electronic devices. In the introduction, the characterization of molecular electronic devices with different types of metal-molecule-metal (M3) structures based upon self-assembled monolayers (SAMs) is reviewed. A background of the characterization methods I use in this dissertation, conducting probe atomic force microscopy (cp-AFM) and surface enhanced Raman spectroscopy (SERS), is provided in chapter 1. Several attempts are performed to create the ideal top metal contacts on SAMs by metal vapor phase deposition in order to prevent the metal penetration inducing critical defects of the molecular electronic devices. The scanning probe microscopy (SPM), such as cp-AFM, contact mode (c-) AFM and non-contact mode (nc-) AFM, in ultra high vacuum conditions are utilized to study the process of the metal-SAM interface construction in terms of the correlation between the morphological and electrical properties including the metal nucleation and filament generation as a function of the functionalization of long-chain alkane thiolate SAMs on Au. In chapter 2, the nascent condensation process of vapor phase Al deposition on inert and reactive SAMs are studied by SPM. The results of top deposition, penetration, and filament generation of deposited Al are discussed and compared to the results previously observed by spectroscopic measurements. Cp-AFM was shown to provide new insights into Al filament formation which has not been observed by conventional spectroscopic analysis. Additionally, the electronic characteristics of individual Al filaments are measured. Chapter 3 reveals SPM characterization of Au deposition onto --COOH terminated SAMs utilized with strong surface dipole-dipole intermolecular interaction based on hydrogen bonding and ionic bonding potentially preventing the metal penetration. The observed results are discussed with kinetic paths of metal atoms on each SAM including temporal vacancies controlled by the intermolecular interactions in SAM upon the comparison with the spectroscopic results previously reported. The results in chapter 2 and 3 strongly suggests that AFM based characterization technique is powerful tool especially for detecting molecular-size local phenomena in vapor phase metal deposition process, especially, the electric short-circuit filaments growing through SAMs, which may induce critical misinterpretation of M3 junction device properties. In Chapter 4, an altered metal deposition process on inert SAM with using a buffer layer is performed to diminish the kinetic energy of impinging metal atoms. SPM characterization reveals an abrupt metal-SAM interface without any metal penetration. Examined electric characteristics also revealed typical non-resonant tunneling characteristics of long chain alkane thiolate SAMs. In chapter 5, the buffer layer assisted growth process is used to prepare a nano particles-SAM pristine interface on SAMs to control the metal-SAM interaction in order to study the fundamental issue of chemical enhancement mechanism of SERS. Identical Au nanoparticles-SAM-Au M3 structures with different Au-SAM interactions reveal a large discrepancy of enhancement factors of ˜100 attributed to the chemical interaction. In chapter 6, Raman spectroscopy of M3 junction is applied to the characterization of molecular electronics devices. A crossed nanowire junction (X-nWJ) device is employed for in-situ electronic-spectroscopic simultaneous characterization using Raman spectroscopy. A detailed study reveals the multi-probe capability of X-nWJ for in-situ Raman and in-elastic electron tunneling spectroscopy (IETS) as vibrational spectroscopies to diagnose molecular electronic devices. In chapter 7, aniline oligomer (OAn) based redox SAMs are characterized by spectroscopic and microscopic methods under different chemical redox states by reflection absorption infrared spectroscopy (RAIRS), Raman, x-ray photoelectron spectroscopy (XPS), and AFM in order to elucidate the mechanism of electric switching molecular junctions previously reported. Obtained results are discussed in terms of the chemical and geometrical conformations of molecules in closely packed SAM domains. In chapter 8, in-situ Raman spectroscopy and cp-AFM microscopic techniques are applied to study the electric switching characteristics of X-nWJ incorporating OAn based SAM. The results of tunneling current and in-situ Raman spectroscopy are discussed with the conformational change of OAn component. The conductance switching mechanism associated with domain conformation change of OAn SAM is proposed and evaluated based on the results.

Antibody-controlled actuation of DNA-based molecular circuits.

PubMed

Engelen, Wouter; Meijer, Lenny H H; Somers, Bram; de Greef, Tom F A; Merkx, Maarten

2017-02-17

DNA-based molecular circuits allow autonomous signal processing, but their actuation has relied mostly on RNA/DNA-based inputs, limiting their application in synthetic biology, biomedicine and molecular diagnostics. Here we introduce a generic method to translate the presence of an antibody into a unique DNA strand, enabling the use of antibodies as specific inputs for DNA-based molecular computing. Our approach, antibody-templated strand exchange (ATSE), uses the characteristic bivalent architecture of antibodies to promote DNA-strand exchange reactions both thermodynamically and kinetically. Detailed characterization of the ATSE reaction allowed the establishment of a comprehensive model that describes the kinetics and thermodynamics of ATSE as a function of toehold length, antibody-epitope affinity and concentration. ATSE enables the introduction of complex signal processing in antibody-based diagnostics, as demonstrated here by constructing molecular circuits for multiplex antibody detection, integration of multiple antibody inputs using logic gates and actuation of enzymes and DNAzymes for signal amplification.

Antibody-controlled actuation of DNA-based molecular circuits

NASA Astrophysics Data System (ADS)

Engelen, Wouter; Meijer, Lenny H. H.; Somers, Bram; de Greef, Tom F. A.; Merkx, Maarten

2017-02-01

DNA-based molecular circuits allow autonomous signal processing, but their actuation has relied mostly on RNA/DNA-based inputs, limiting their application in synthetic biology, biomedicine and molecular diagnostics. Here we introduce a generic method to translate the presence of an antibody into a unique DNA strand, enabling the use of antibodies as specific inputs for DNA-based molecular computing. Our approach, antibody-templated strand exchange (ATSE), uses the characteristic bivalent architecture of antibodies to promote DNA-strand exchange reactions both thermodynamically and kinetically. Detailed characterization of the ATSE reaction allowed the establishment of a comprehensive model that describes the kinetics and thermodynamics of ATSE as a function of toehold length, antibody-epitope affinity and concentration. ATSE enables the introduction of complex signal processing in antibody-based diagnostics, as demonstrated here by constructing molecular circuits for multiplex antibody detection, integration of multiple antibody inputs using logic gates and actuation of enzymes and DNAzymes for signal amplification.

The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae.

PubMed

Diaz, Maureen H; Winchell, Jonas M

2016-01-01

Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.

Genetic variability among elite popcorn lines based on molecular and morphoagronomic characteristics.

PubMed

Dos Santos, J F; Mangolin, C A; Machado, M F P S; Scapim, C A; Giordani, W; Gonçalves, L S A

2017-06-29

Knowledge of genetic diversity among genotypes and relationships among elite lines is of great importance for the development of breeding programs. Therefore, the objective of this study was to evaluate genetic variability based on the morphoagronomic and molecular characterization of 18 elite popcorn (Zea mays var. everta) lines to be used by Universidade Estadual de Maringá breeding programs. We used 31 microsatellite primers (widely distributed in the genome), and 16 morphological descriptors (including the resistance to maize white spot, common rust, polysora rust of maize, cercospora and leaf blights). The molecular data revealed variability among the lines, which were divided into four groups that were partially concordant with unweighted pair group method with arithmetic mean (UPMGA) and Bayesian clusters. The lines G3, G4, G11, and G13 exhibited favorable morphological characters and low disease incidence rates. The four groups were confirmed using the Gower distance in the UPGMA cluster; however, there was no association with the dissimilarity patterns obtained using the molecular data. The absence of a correlation suggests that both characterizations (morphoagronomic and molecular) are important for discriminating among elite popcorn lines.

Ultrathin inorganic molecular nanowire based on polyoxometalates

PubMed Central

Zhang, Zhenxin; Murayama, Toru; Sadakane, Masahiro; Ariga, Hiroko; Yasuda, Nobuhiro; Sakaguchi, Norihito; Asakura, Kiyotaka; Ueda, Wataru

2015-01-01

The development of metal oxide-based molecular wires is important for fundamental research and potential practical applications. However, examples of these materials are rare. Here we report an all-inorganic transition metal oxide molecular wire prepared by disassembly of larger crystals. The wires are comprised of molybdenum(VI) with either tellurium(IV) or selenium(IV): {(NH4)2[XMo6O21]}n (X=tellurium(IV) or selenium(IV)). The ultrathin molecular nanowires with widths of 1.2 nm grow to micrometre-scale crystals and are characterized by single-crystal X-ray analysis, Rietveld analysis, scanning electron microscopy, X-ray photoelectron spectroscopy, ultraviolet–visible spectroscopy, thermal analysis and elemental analysis. The crystals can be disassembled into individual molecular wires through cation exchange and subsequent ultrasound treatment, as visualized by atomic force microscopy and transmission electron microscopy. The ultrathin molecular wire-based material exhibits high activity as an acid catalyst, and the band gap of the molecular wire-based crystal is tunable by heat treatment. PMID:26139011

Atomic force microscopy-based characterization and design of biointerfaces

NASA Astrophysics Data System (ADS)

Alsteens, David; Gaub, Hermann E.; Newton, Richard; Pfreundschuh, Moritz; Gerber, Christoph; Müller, Daniel J.

2017-03-01

Atomic force microscopy (AFM)-based methods have matured into a powerful nanoscopic platform, enabling the characterization of a wide range of biological and synthetic biointerfaces ranging from tissues, cells, membranes, proteins, nucleic acids and functional materials. Although the unprecedented signal-to-noise ratio of AFM enables the imaging of biological interfaces from the cellular to the molecular scale, AFM-based force spectroscopy allows their mechanical, chemical, conductive or electrostatic, and biological properties to be probed. The combination of AFM-based imaging and spectroscopy structurally maps these properties and allows their 3D manipulation with molecular precision. In this Review, we survey basic and advanced AFM-related approaches and evaluate their unique advantages and limitations in imaging, sensing, parameterizing and designing biointerfaces. It is anticipated that in the next decade these AFM-related techniques will have a profound influence on the way researchers view, characterize and construct biointerfaces, thereby helping to solve and address fundamental challenges that cannot be addressed with other techniques.

Computational and experimental characterization of a pyrrolidinium-based ionic liquid for electrolyte applications

NASA Astrophysics Data System (ADS)

Torabifard, Hedieh; Reed, Luke; Berry, Matthew T.; Hein, Jason E.; Menke, Erik; Cisneros, G. Andrés

2017-10-01

The development of Li-ion batteries for energy storage has received significant attention. The synthesis and characterization of electrolytes in these batteries are an important component of this development. Ionic liquids (ILs) have been proposed as possible electrolytes in these devices. Thus, the accurate determination of thermophysical properties for these solvents becomes important for determining their applicability as electrolytes. In this contribution, we present the synthesis and experimental/computational characterization of thermodynamic and transport properties of a pyrrolidinium based ionic liquid as a first step to investigate the possible applicability of this class of ILs for Li-ion batteries. A quantum mechanical-based force field with many-body polarizable interactions has been developed for the simulation of spirocyclic pyrrolidinium, [sPyr+], with BF4- and Li+. Molecular dynamics calculations employing intra-molecular polarization predicted larger heat of vaporization and self-diffusion coefficients and smaller densities in comparison with the model without intra-molecular polarization, indicating that the inclusion of this term can significantly effect the inter-ionic interactions. The calculated properties are in good agreement with available experimental data for similar IL pairs and isothermal titration calorimetry data for [sPyr+][BF4-].

The Effect of Molecular Diagnostics on the Treatment of Glioma.

PubMed

Bush, Nancy Ann Oberheim; Butowski, Nicholas

2017-04-01

This review summarizes the use of molecular diagnostics in glioma and its effect on the development of novel therapeutics and management decisions. Genomic and proteomic profiling of brain tumors has provided significant expansion of our understanding of oncogenesis, characterization, and prognostication of brain tumors. Molecular markers such as MGMT, EGFR, IDH, 1p19q, ATRX, TERT, FGFR-TACC, and BRAF are now being used to classify brain tumors as well as influence management decisions. Several of these markers are also being used as therapeutic targets. We review the use of several molecular diagnostics in gliomas and discuss their impact on drug development and clinical trial design. In the future, molecular characterization based on a specific genomic, proteomic as well as transcriptomes for bioformatics analysis will provide clinicians the ability to rationally select drugs with actionable targets for each patient.

Synthesis and molecular characterization of chitosan based polyurethane elastomers using aromatic diisocyanate.

PubMed

Zia, Khalid Mahmood; Anjum, Sohail; Zuber, Mohammad; Mujahid, Muhammad; Jamil, Tahir

2014-05-01

The present research work was performed to synthesize a new series of chitosan based polyurethane elastomers (PUEs) using poly(ɛ-caprolactone) (PCL). The chitosan based PUEs were prepared by step-growth polymerization technique using poly(ɛ-caprolactone) (PCL) and 2,4-toluene diisocyanate (TDI). In the second step the PU prepolymer was extended with different mole ratios of chitosan and 1,4-butane diol (BDO). Molecular engineering was carried out during the synthesis. The conventional spectroscopic characterization of the synthesized samples using FT-IR confirms the existence of the proposed chitosan based PUEs structure. Internal morphology of the prepared PUEs was studied using SEM analysis. The SEM images confirmed the incorporation of chitosan molecules into the PU backbone. Copyright © 2014 Elsevier B.V. All rights reserved.

Enhanced Molecular Sieve CO2 Removal Evaluation

NASA Technical Reports Server (NTRS)

Rose, Susan; ElSherif, Dina; MacKnight, Allen

1996-01-01

The objective of this research is to quantitatively characterize the performance of two major types of molecular sieves for two-bed regenerative carbon dioxide removal at the conditions compatible with both a spacesuit and station application. One sorbent is a zeolite-based molecular sieve that has been substantially improved over the materials used in Skylab. The second sorbent is a recently developed carbon-based molecular sieve. Both molecular sieves offer the potential of high payoff for future manned missions by reducing system complexity, weight (including consumables), and power consumption in comparison with competing concepts. The research reported here provides the technical data required to improve CO2 removal systems for regenerative life support systems for future IVA and EVA missions.

Molecular Characterization of Epithelial Ovarian Cancer: Implications for Diagnosis and Treatment.

PubMed

Rojas, Veronica; Hirshfield, Kim M; Ganesan, Shridar; Rodriguez-Rodriguez, Lorna

2016-12-15

Epithelial ovarian cancer is a highly heterogeneous disease characterized by multiple histological subtypes. Molecular diversity has been shown to occur within specific histological subtypes of epithelial ovarian cancer, between different tumors of an individual patient, as well as within individual tumors. Recent advances in the molecular characterization of epithelial ovarian cancer tumors have provided the basis for a simplified classification scheme in which these cancers are classified as either type I or type II tumors, and these two categories have implications regarding disease pathogenesis and prognosis. Molecular analyses, primarily based on next-generation sequencing, otherwise known as high-throughput sequencing, are allowing for further refinement of ovarian cancer classification, facilitating the elucidation of the site(s) of precursor lesions of high-grade serous ovarian cancer, and providing insight into the processes of clonal selection and evolution that may be associated with development of chemoresistance. Potential therapeutic targets have been identified from recent molecular profiling studies of these tumors, and the effectiveness and safety of a number of specific targeted therapies have been evaluated or are currently being studied for the treatment of women with this disease.

Molecular Characterization of Epithelial Ovarian Cancer: Implications for Diagnosis and Treatment

PubMed Central

Rojas, Veronica; Hirshfield, Kim M.; Ganesan, Shridar; Rodriguez-Rodriguez, Lorna

2016-01-01

Epithelial ovarian cancer is a highly heterogeneous disease characterized by multiple histological subtypes. Molecular diversity has been shown to occur within specific histological subtypes of epithelial ovarian cancer, between different tumors of an individual patient, as well as within individual tumors. Recent advances in the molecular characterization of epithelial ovarian cancer tumors have provided the basis for a simplified classification scheme in which these cancers are classified as either type I or type II tumors, and these two categories have implications regarding disease pathogenesis and prognosis. Molecular analyses, primarily based on next-generation sequencing, otherwise known as high-throughput sequencing, are allowing for further refinement of ovarian cancer classification, facilitating the elucidation of the site(s) of precursor lesions of high-grade serous ovarian cancer, and providing insight into the processes of clonal selection and evolution that may be associated with development of chemoresistance. Potential therapeutic targets have been identified from recent molecular profiling studies of these tumors, and the effectiveness and safety of a number of specific targeted therapies have been evaluated or are currently being studied for the treatment of women with this disease. PMID:27983698

Comprehensive Molecular Characterization of Papillary Renal Cell Carcinoma

PubMed Central

Linehan, W. Marston; Spellman, Paul T.; Ricketts, Christopher J.; Creighton, Chad J.; Fei, Suzanne S.; Davis, Caleb; Wheeler, David A.; Murray, Bradley A.; Schmidt, Laura; Vocke, Cathy D.; Peto, Myron; Al Mamun, Abu Amar M.; Shinbrot, Eve; Sethi, Anurag; Brooks, Samira; Rathmell, W. Kimryn; Brooks, Angela N.; Hoadley, Katherine A.; Robertson, A. Gordon; Brooks, Denise; Bowlby, Reanne; Sadeghi, Sara; Shen, Hui; Weisenberger, Daniel J.; Bootwalla, Moiz; Baylin, Stephen B.; Laird, Peter W.; Cherniack, Andrew D.; Saksena, Gordon; Haake, Scott; Li, Jun; Liang, Han; Lu, Yiling; Mills, Gordon B.; Akbani, Rehan; Leiserson, Mark D.M.; Raphael, Benjamin J.; Anur, Pavana; Bottaro, Donald; Albiges, Laurence; Barnabas, Nandita; Choueiri, Toni K.; Czerniak, Bogdan; Godwin, Andrew K.; Hakimi, A. Ari; Ho, Thai; Hsieh, James; Ittmann, Michael; Kim, William Y.; Krishnan, Bhavani; Merino, Maria J.; Mills Shaw, Kenna R.; Reuter, Victor E.; Reznik, Ed; Shelley, Carl Simon; Shuch, Brian; Signoretti, Sabina; Srinivasan, Ramaprasad; Tamboli, Pheroze; Thomas, George; Tickoo, Satish; Burnett, Kenneth; Crain, Daniel; Gardner, Johanna; Lau, Kevin; Mallery, David; Morris, Scott; Paulauskis, Joseph D.; Penny, Robert J.; Shelton, Candace; Shelton, W. Troy; Sherman, Mark; Thompson, Eric; Yena, Peggy; Avedon, Melissa T.; Bowen, Jay; Gastier-Foster, Julie M.; Gerken, Mark; Leraas, Kristen M.; Lichtenberg, Tara M.; Ramirez, Nilsa C.; Santos, Tracie; Wise, Lisa; Zmuda, Erik; Demchok, John A.; Felau, Ina; Hutter, Carolyn M.; Sheth, Margi; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Ayala, Brenda; Baboud, Julien; Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; Wan, Yunhu; Wu, Ye; Ally, Adrian; Balasundaram, Miruna; Balu, Saianand; Beroukhim, Rameen; Bodenheimer, Tom; Buhay, Christian; Butterfield, Yaron S.N.; Carlsen, Rebecca; Carter, Scott L.; Chao, Hsu; Chuah, Eric; Clarke, Amanda; Covington, Kyle R.; Dahdouli, Mahmoud; Dewal, Ninad; Dhalla, Noreen; Doddapaneni, HarshaVardhan; Drummond, Jennifer; Gabriel, Stacey B.; Gibbs, Richard A.; Guin, Ranabir; Hale, Walker; Hawes, Alicia; Hayes, D. Neil; Holt, Robert A.; Hoyle, Alan P.; Jefferys, Stuart R.; Jones, Steven J.M.; Jones, Corbin D.; Kalra, Divya; Kovar, Christie; Lewis, Lora; Li, Jie; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Meng, Shaowu; Meyerson, Matthew; Mieczkowski, Piotr A.; Moore, Richard A.; Morton, Donna; Mose, Lisle E.; Mungall, Andrew J.; Muzny, Donna; Parker, Joel S.; Perou, Charles M.; Roach, Jeffrey; Schein, Jacqueline E.; Schumacher, Steven E.; Shi, Yan; Simons, Janae V.; Sipahimalani, Payal; Skelly, Tara; Soloway, Matthew G.; Sougnez, Carrie; Tam, Angela; Tan, Donghui; Thiessen, Nina; Veluvolu, Umadevi; Wang, Min; Wilkerson, Matthew D.; Wong, Tina; Wu, Junyuan; Xi, Liu; Zhou, Jane; Bedford, Jason; Chen, Fengju; Fu, Yao; Gerstein, Mark; Haussler, David; Kasaian, Katayoon; Lai, Phillip; Ling, Shiyun; Radenbaugh, Amie; Van Den Berg, David; Weinstein, John N.; Zhu, Jingchun; Albert, Monique; Alexopoulou, Iakovina; Andersen, Jeremiah J; Auman, J. Todd; Bartlett, John; Bastacky, Sheldon; Bergsten, Julie; Blute, Michael L.; Boice, Lori; Bollag, Roni J.; Boyd, Jeff; Castle, Erik; Chen, Ying-Bei; Cheville, John C.; Curley, Erin; Davies, Benjamin; DeVolk, April; Dhir, Rajiv; Dike, Laura; Eckman, John; Engel, Jay; Harr, Jodi; Hrebinko, Ronald; Huang, Mei; Huelsenbeck-Dill, Lori; Iacocca, Mary; Jacobs, Bruce; Lobis, Michael; Maranchie, Jodi K.; McMeekin, Scott; Myers, Jerome; Nelson, Joel; Parfitt, Jeremy; Parwani, Anil; Petrelli, Nicholas; Rabeno, Brenda; Roy, Somak; Salner, Andrew L.; Slaton, Joel; Stanton, Melissa; Thompson, R. Houston; Thorne, Leigh; Tucker, Kelinda; Weinberger, Paul M.; Winemiller, Cythnia; Zach, Leigh Anne; Zuna, Rosemary

2016-01-01

Background Papillary renal cell carcinoma, accounting for 15% of renal cell carcinoma, is a heterogeneous disease consisting of different types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal cell carcinoma; no effective forms of therapy for advanced disease exist. Methods We performed comprehensive molecular characterization utilizing whole-exome sequencing, copy number, mRNA, microRNA, methylation and proteomic analyses of 161 primary papillary renal cell carcinomas. Results Type 1 and Type 2 papillary renal cell carcinomas were found to be different types of renal cancer characterized by specific genetic alterations, with Type 2 further classified into three individual subgroups based on molecular differences that influenced patient survival. MET alterations were associated with Type 1 tumors, whereas Type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-ARE pathway. A CpG island methylator phenotype (CIMP) was found in a distinct subset of Type 2 papillary renal cell carcinoma characterized by poor survival and mutation of the fumarate hydratase (FH) gene. Conclusions Type 1 and Type 2 papillary renal cell carcinomas are clinically and biologically distinct. Alterations in the MET pathway are associated with Type 1 and activation of the NRF2-ARE pathway with Type 2; CDKN2A loss and CIMP in Type 2 convey a poor prognosis. Furthermore, Type 2 papillary renal cell carcinoma consists of at least 3 subtypes based upon molecular and phenotypic features. PMID:26536169

Description of three new species of Hepatozoon (Apicomplexa, Hepatozoidae) from Rattlesnakes (Crotalus durissus terrificus) based on molecular, morphometric and morphologic characters.

PubMed

O'Dwyer, Lucia Helena; Moço, Tatiana Cristina; Paduan, Karina dos Santos; Spenassatto, Carine; da Silva, Reinaldo José; Ribolla, Paulo Eduardo Martins

2013-10-01

Hepatozoon spp. are commonly found infecting snakes. Since the latter are parasitized by diverse forms and data in the literature show divergence, we studied Hepatozoon spp. diversity on Crotalus durissus terrificus snakes using both molecular and morphological approaches. Naturally infected animals were employed. Blood was collected, blood smears were prepared and an aliquot was stored at -20°C for DNA extraction. Five specimens of C. durissus terrificus were selected, each of them infected with one gamont type. Morphological and morphometric analyses of the found gamonts led to their grouping into three populations. For molecular characterization, seven oligonucleotide pairs that amplify distinct regions of rDNA gene were tested by adopting the PCR technique. Only the oligonucleotide pairs HepF300/Hep900 and HEMO1/HEMO2 were efficient in amplifying and distinguishing different isolates of Hepatozoon spp. from snakes. The better results were obtained when both oligonucleotide pairs were used in association. Based on the molecular and morphologic differences, three new species were proposed: Hepatozoon cuestensis sp. nov.; Hepatozoon cevapii sp. nov. and Hepatozoon massardii sp. nov. This is the first description of new Hepatozoon species from snakes, based on molecular characterization and morphological data, in South America. Copyright © 2013 Elsevier Inc. All rights reserved.

Morphological and molecular characterization of Cladosporium cladosporioides species complex causing pecan tree leaf spot.

PubMed

Walker, C; Muniz, M F B; Rolim, J M; Martins, R R O; Rosenthal, V C; Maciel, C G; Mezzomo, R; Reiniger, L R S

2016-09-16

The objective of this study was to characterize species of the Cladosporium cladosporioides complex isolated from pecan trees (Carya illinoinensis) with symptoms of leaf spot, based on morphological and molecular approaches. Morphological attributes were assessed using monosporic cultures on potato dextrose agar medium, which were examined for mycelial growth, sporulation, color, and conidia and ramoconidia size. Molecular characterization comprised isolation of DNA and subsequent amplification of the translation elongation factor 1α (TEF-1α) region. Three species of the C. cladosporioides complex were identified: C. cladosporioides, Cladosporium pseudocladosporioides, and Cladosporium subuliforme. Sporulation was the most important characteristic differentiating species of this genus. However, morphological features must be considered together with molecular analysis, as certain characters are indistinguishable between species. TEF-1αcan be effectively used to identify and group isolates belonging to the C. cladosporioides complex. The present study provides an important example of a methodology to ascertain similarity between isolates of this complex causing leaf spot in pecan trees, which should facilitate future pathogenicity studies.

Has the use of molecular methods for the characterization of the human oral microbiome changed our understanding of the role of bacteria in the pathogenesis of periodontal disease?

PubMed

Wade, William Geoffrey

2011-03-01

Only around half of oral bacteria can be grown in the laboratory using conventional culture methods. Molecular methods based on 16S rRNA gene sequence are now available and are being used to characterize the periodontal microbiota in its entirety. This review describes the cultural characterization of the oral and periodontal microbiotas and explores the influence of the additional data now available from culture-independent molecular analyses on current thinking on the role of bacteria in periodontitis. Culture-independent molecular analysis of the periodontal microbiota has shown it to be far more diverse than previously thought. A number of species including some that have yet to be cultured are as strongly associated with disease as those organisms traditionally regarded as periodontal pathogens. Sequencing of bacterial genomes has revealed a high degree of intra-specific genetic diversity. The use of molecular methods for the characterization of the periodontal microbiome has greatly expanded the range of bacterial species known to colonize this habitat. Understanding the interactions between the human host and its commensal bacterial community at the functional level is a priority. © 2011 John Wiley & Sons A/S.

Molecular characterization of canine parvovirus (CPV) infection in dogs in Turkey.

PubMed

Timurkan, Mehmet; Oğuzoğlu, Tuba

2015-01-01

This study provides data about canine parvovirus (CPV) types circulating among dogs in Turkey. Sixty-five samples from dogs with and without clinical signs of parvovirus infection were collected between April 2009 and February 2010. The samples were subsequently tested for CPV using polymerase chain reaction (PCR). Twenty-five samples (38.4%) were positive; when positive samples were characterized by sequence analysis, results showed that both CPV-2a (17/25, 68%) and CPV-2b (8/25, 32%) strains are circulating among domestic dogs in Turkey. This is the first molecular characterization study of CPVs from dogs based on partial VP2 gene sequences in Turkey.

Molecular design and theoretical characterization of benzodithiophene based organic photovoltaic materials

NASA Astrophysics Data System (ADS)

Bhattacharya, Labanya; Sahu, Sridhar

2018-05-01

Two different oligomers, containing methyl substituted Benzodithiophene (BDT) as donor unit, fluorinated thiophene as the π-bridge unit and two different kinds of acceptors based on fluorinated benzothiadiazole, fluorinated benzoselenadiazole units are designed for bulk heterojunction (BHJ) organic solar cell (OSC). The ground and excited state properties of those donor-π-acceptor-π-donor (D-π-A-π-D) oligomeric configurations are characterized via density functional (DFT) and time dependent density functional theory (TD-DFT). The parameters such as dipole moment (ρ), chemical potential (µ), electronegativity (χ), frontier molecular orbital (FMO) analysis, HOMO-LUMO gap, open circuit voltage (Voc) and driving force (ΔE) are calculated to analyze geometrical, electronic structural, quantum chemical and photovoltaic properties of the compounds. In addition, optical absorption spectra are also presented for the optical characterization of the compounds.

Molecular and phylogenetic characterizations of an Eimeria krijgsmanni Yakimoff & Gouseff, 1938 (Apicomplexa: Eimeriidae) mouse intestinal protozoan parasite by partial 18S ribosomal RNA gene sequence analysis.

PubMed

Takeo, Toshinori; Tanaka, Tetsuya; Matsubayashi, Makoto; Maeda, Hiroki; Kusakisako, Kodai; Matsui, Toshihiro; Mochizuki, Masami; Matsuo, Tomohide

2014-08-01

Previously, we characterized an undocumented strain of Eimeria krijgsmanni by morphological and biological features. Here, we present a detailed molecular phylogenetic analysis of this organism. Namely, 18S ribosomal RNA gene (rDNA) sequences of E. krijgsmanni were analyzed to incorporate this species into a comprehensive Eimeria phylogeny. As a result, partial 18S rDNA sequence from E. krijgsmanni was successfully determined, and two different types, Type A and Type B, that differed by 1 base pair were identified. E. krijgsmanni was originally isolated from a single oocyst, and thus the result show that the two types might have allelic sequence heterogeneity in the 18S rDNA. Based on phylogenetic analyses, the two types of E. krijgsmanni 18S rDNA formed one of two clades among murine Eimeria spp.; these Eimeria clades reflected morphological similarity among the Eimeria spp. This is the third molecular phylogenetic characterization of a murine Eimeria spp. in addition to E. falciformis and E. papillata. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Towards a unifying theory for the first-, second-, and third-order molecular (non)linear optical response

NASA Astrophysics Data System (ADS)

Pérez-Moreno, Javier; Clays, Koen; Kuzyk, Mark G.

2010-05-01

We present a procedure for the modeling of the dispersion of the nonlinear optical response of complex molecular structures that is based strictly on the results from experimental characterization. We show how under some general conditions, the use of the Thomas-Kuhn sum-rules leads to a successful modeling of the nonlinear response of complex molecular structures.

Materials and Manufacturing Technology Directorate Thermal Sciences and Materials Branch (Overview)

DTIC Science & Technology

2010-09-01

Molecular Mechanics for thermo-mechanical response Materials Characterization • CNT modified durable thermal interface ( DTI ) • MEMS-based RTD micro...stabilization. Surface Characterization by Atomic Force Microscopy: Probing Thermal, Electrical, and Mechanical Properties Heater Current Path Anchor Leg 50 µm

Characterization of Capsicum species using anatomical and molecular data.

PubMed

Dias, G B; Gomes, V M; Moraes, T M S; Zottich, U P; Rabelo, G R; Carvalho, A O; Moulin, M; Gonçalves, L S A; Rodrigues, R; Da Cunha, M

2013-02-28

Capsicum species are frequently described in terms of genetic divergence, considering morphological, agronomic, and molecular databases. However, descriptions of genetic differences based on anatomical characters are rare. We examined the anatomy and the micromorphology of vegetative and reproductive organs of several Capsicum species. Four Capsicum accessions representing the species C. annuum var. annuum, C. baccatum var. pendulum, C. chinense, and C. frutescens were cultivated in a greenhouse; leaves, fruits and seeds were sampled and their organ structure analyzed by light and scanning electronic microscopy. Molecular accession characterization was made using ISSR markers. Polymorphism was observed among tector trichomes and also in fruit color and shape. High variability among accessions was detected by ISSR markers. Despite the species studied present a wide morphological and molecular variability that was not reflected by anatomical features.

Genomic Classification of Tumors | Center for Cancer Research

Cancer.gov

CCR investigators were among the first to classify tumors based on genetics, laying the groundwork for today’s common practice to molecularly characterize tumors based on their genetic fingerprints for personalized treatments.

Characterizing the heterogeneity of tumor tissues from spatially resolved molecular measures

PubMed Central

Zavodszky, Maria I.

2017-01-01

Background Tumor heterogeneity can manifest itself by sub-populations of cells having distinct phenotypic profiles expressed as diverse molecular, morphological and spatial distributions. This inherent heterogeneity poses challenges in terms of diagnosis, prognosis and efficient treatment. Consequently, tools and techniques are being developed to properly characterize and quantify tumor heterogeneity. Multiplexed immunofluorescence (MxIF) is one such technology that offers molecular insight into both inter-individual and intratumor heterogeneity. It enables the quantification of both the concentration and spatial distribution of 60+ proteins across a tissue section. Upon bioimage processing, protein expression data can be generated for each cell from a tissue field of view. Results The Multi-Omics Heterogeneity Analysis (MOHA) tool was developed to compute tissue heterogeneity metrics from MxIF spatially resolved tissue imaging data. This technique computes the molecular state of each cell in a sample based on a pathway or gene set. Spatial states are then computed based on the spatial arrangements of the cells as distinguished by their respective molecular states. MOHA computes tissue heterogeneity metrics from the distributions of these molecular and spatially defined states. A colorectal cancer cohort of approximately 700 subjects with MxIF data is presented to demonstrate the MOHA methodology. Within this dataset, statistically significant correlations were found between the intratumor AKT pathway state diversity and cancer stage and histological tumor grade. Furthermore, intratumor spatial diversity metrics were found to correlate with cancer recurrence. Conclusions MOHA provides a simple and robust approach to characterize molecular and spatial heterogeneity of tissues. Research projects that generate spatially resolved tissue imaging data can take full advantage of this useful technique. The MOHA algorithm is implemented as a freely available R script (see supplementary information). PMID:29190747

Computational Nanotechnology at NASA Ames Research Center, 1996

NASA Technical Reports Server (NTRS)

Globus, Al; Bailey, David; Langhoff, Steve; Pohorille, Andrew; Levit, Creon; Chancellor, Marisa K. (Technical Monitor)

1996-01-01

Some forms of nanotechnology appear to have enormous potential to improve aerospace and computer systems; computational nanotechnology, the design and simulation of programmable molecular machines, is crucial to progress. NASA Ames Research Center has begun a computational nanotechnology program including in-house work, external research grants, and grants of supercomputer time. Four goals have been established: (1) Simulate a hypothetical programmable molecular machine replicating itself and building other products. (2) Develop molecular manufacturing CAD (computer aided design) software and use it to design molecular manufacturing systems and products of aerospace interest, including computer components. (3) Characterize nanotechnologically accessible materials of aerospace interest. Such materials may have excellent strength and thermal properties. (4) Collaborate with experimentalists. Current in-house activities include: (1) Development of NanoDesign, software to design and simulate a nanotechnology based on functionalized fullerenes. Early work focuses on gears. (2) A design for high density atomically precise memory. (3) Design of nanotechnology systems based on biology. (4) Characterization of diamonoid mechanosynthetic pathways. (5) Studies of the laplacian of the electronic charge density to understand molecular structure and reactivity. (6) Studies of entropic effects during self-assembly. Characterization of properties of matter for clusters up to sizes exhibiting bulk properties. In addition, the NAS (NASA Advanced Supercomputing) supercomputer division sponsored a workshop on computational molecular nanotechnology on March 4-5, 1996 held at NASA Ames Research Center. Finally, collaborations with Bill Goddard at CalTech, Ralph Merkle at Xerox Parc, Don Brenner at NCSU (North Carolina State University), Tom McKendree at Hughes, and Todd Wipke at UCSC are underway.

Pediatric Glioblastoma Therapies Based on Patient-Derived Stem Cell Resources

DTIC Science & Technology

2012-09-01

cells, to evaluate whether pediatric tumor will have fundamental different responses to the new therapeutic regimes. Since glioma stem cell lines have...glioma stem cell lines and has begun molecular and phenotypic characterization of these lines. This characterization has included analysis of gene

On-wire lithography-generated molecule-based transport junctions: a new testbed for molecular electronics.

PubMed

Chen, Xiaodong; Jeon, You-Moon; Jang, Jae-Won; Qin, Lidong; Huo, Fengwei; Wei, Wei; Mirkin, Chad A

2008-07-02

On-wire lithography (OWL) fabricated nanogaps are used as a new testbed to construct molecular transport junctions (MTJs) through the assembly of thiolated molecular wires across a nanogap formed between two Au electrodes. In addition, we show that one can use OWL to rapidly characterize a MTJ and optimize gap size for two molecular wires of different dimensions. Finally, we have used this new testbed to identify unusual temperature-dependent transport mechanisms for alpha,omega-dithiol terminated oligo(phenylene ethynylene).

Paper-Based MicroRNA Expression Profiling from Plasma and Circulating Tumor Cells.

PubMed

Leong, Sai Mun; Tan, Karen Mei-Ling; Chua, Hui Wen; Huang, Mo-Chao; Cheong, Wai Chye; Li, Mo-Huang; Tucker, Steven; Koay, Evelyn Siew-Chuan

2017-03-01

Molecular characterization of circulating tumor cells (CTCs) holds great promise for monitoring metastatic progression and characterizing metastatic disease. However, leukocyte and red blood cell contamination of routinely isolated CTCs makes CTC-specific molecular characterization extremely challenging. Here we report the use of a paper-based medium for efficient extraction of microRNAs (miRNAs) from limited amounts of biological samples such as rare CTCs harvested from cancer patient blood. Specifically, we devised a workflow involving the use of Flinders Technology Associates (FTA) ® Elute Card with a digital PCR-inspired "partitioning" method to extract and purify miRNAs from plasma and CTCs. We demonstrated the sensitivity of this method to detect miRNA expression from as few as 3 cancer cells spiked into human blood. Using this method, background miRNA expression was excluded from contaminating blood cells, and CTC-specific miRNA expression profiles were derived from breast and colorectal cancer patients. Plasma separated out during purification of CTCs could likewise be processed using the same paper-based method for miRNA detection, thereby maximizing the amount of patient-specific information that can be derived from a single blood draw. Overall, this paper-based extraction method enables an efficient, cost-effective workflow for maximized recovery of small RNAs from limited biological samples for downstream molecular analyses. © 2016 American Association for Clinical Chemistry.

Synthesis, Characterization, and Multimillion-Atom Simulation of Halogen-Based Energetic Materials for Agent Defeat

DTIC Science & Technology

2013-04-01

DTRA-TR-13-23 Synthesis, Characterization, and Multimillion -Atom Simulation of Halogen-Based Energetic Materials for Agent Defeat Approved for...reagents for the destruction of biologically active materials and a simulation of their reactions on a multimillion atom scale with quantum...explosives for destruction of chemical & biological agents. Multimillion -atom molecular dynamics simulations with quantum mechanical accuracy were

[Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)].

PubMed

Zakhia, Frédéric; de Lajudie, Philippe

2006-03-01

Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.

Molecular and morphological characterization of the cercariae of Lecithodendrium linstowi (Dollfus, 1931), a trematode of bats, and incrimination of the first intermediate snail host, Radix balthica.

PubMed

Enabulele, Egie E; Lawton, Scott P; Walker, Anthony J; Kirk, Ruth S

2018-03-01

Lecithodendrium linstowi is one of the most prevalent and abundant trematodes of bats, but the larval stages and intermediate hosts have not been identified. We present the first molecular and morphological characterization of the cercariae of L. linstowi based on a phylogenetic analysis of partial fragments of LSU and ITS2 rDNA. The first intermediate host was incriminated as Radix balthica by DNA barcoding using cox1 and ITS2 sequences, although the snail morphologically resembled Radix peregra, emphasizing the requirement for molecular identification of lymnaeids as important intermediate hosts of medical and veterinary impact. The application of molecular data in this study has enabled linkage of life cycle stages and accurate incrimination of the first intermediate host.

A systematic investigation of the preparation and properties of composite carbon molecular sieves containing inorganic oxides

NASA Technical Reports Server (NTRS)

Foley, Henry C.

1990-01-01

The objective of this research is to define the methodology for the preparation and characterization of new carbon-based molecular sieves with composite structures. Carbon molecular sieves have found increasing application in the field of separation and purification of gases. These materials are relatively easy to prepare and their surfaces can be modified to some extent. It is expected that by combining inorganic oxides with the carbonaceous structure one can begin to design composite materials with a wider range of possible chemical and physical properties. In this way, the IOM-CMS materials may confer distinct advantages over pure carbon molecular sieves, not just for separation, but also for catalysis. The most recent results in the design and characterization of these IOM-CMS materials are reviewed and summarized. Directions for further research are also presented.

Identification of the Molecular Clockwork of the Oyster Crassostrea gigas

PubMed Central

Perrigault, Mickael; Tran, Damien

2017-01-01

Molecular clock system constitutes the origin of biological rhythms that allow organisms to anticipate cyclic environmental changes and adapt their behavior and physiology. Components of the molecular clock are largely conserved across a broad range of species but appreciable diversity in clock structure and function is also present especially in invertebrates. The present work aimed at identify and characterize molecular clockwork components in relationship with the monitoring of valve activity behavior in the oyster Crassostrea gigas. Results provided the characterization of most of canonical clock gene including clock, bmal/cycle, period, timeless, vertebrate-type cry, rev-erb, ror as well as other members of the cryptochrome/photolyase family (plant-like cry, 6–4 photolyase). Analyses of transcriptional variations of clock candidates in oysters exposed to light / dark regime and to constant darkness led to the generation of a putative and original clockwork model in C. gigas, intermediate of described systems in vertebrates and insects. This study is the first characterization of a mollusk clockwork. It constitutes essential bases to understand interactions of the different components of the molecular clock in C. gigas as well as the global mechanisms associated to the generation and the synchronization of biological rhythms in oysters. PMID:28072861

Application of multiplex PCR, pulsed-field gel electrophoresis (PFGE), and BOX-PCR for molecular analysis of enterococci

USDA-ARS?s Scientific Manuscript database

The objective of the study was to use band-based molecular methods including BOX-PCR (Polymerase Chain Reaction) and Pulsed-Field Gel Electrophoresis (PFGE) to determine if genetically related enterococci were found among different stores, food types, or years. Enterococci were also characterized f...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, Guanguang; Chen, Baowei; Zhang, Rui

In this work, new strategies involving organic bases were evaluated to depolymerize lignin to reduced molecular fragments in aqueous medium. NaOH as an inorganic base was also investigated as a reference. Full nature lignin samples are used for the study. As research tools to unravel the complexity of the macro lignin structure and bulky molecular size under this study, size exclusion chromatography and high resolution mass spectrometric analysis, typically used for protein characterizations, were used to follow the progress of lignin depolymerisation by measuring the molecular weight distribution of the products and determining the key molecular fingerprints, respectively. The resultsmore » show that sodium phenoxide and guanidine carbonate are effective catalysts for lignin depolymerization. It is observed that there exists a synergism between H2O2 and the organic base, which is strongest with guanidine carbonate.« less

A Cobalt Supramolecular Triple-Stranded Helicate-based Discrete Molecular Cage

PubMed Central

Mai, Hien Duy; Kang, Philjae; Kim, Jin Kyung; Yoo, Hyojong

2017-01-01

We report a strategy to achieve a discrete cage molecule featuring a high level of structural hierarchy through a multiple-assembly process. A cobalt (Co) supramolecular triple-stranded helicate (Co-TSH)-based discrete molecular cage (1) is successfully synthesized and fully characterized. The solid-state structure of 1 shows that it is composed of six triple-stranded helicates interconnected by four linking cobalt species. This is an unusual example of a highly symmetric cage architecture resulting from the coordination-driven assembly of metallosupramolecular modules. The molecular cage 1 shows much higher CO2 uptake properties and selectivity compared with the separate supramolecular modules (Co-TSH, complex 2) and other molecular platforms. PMID:28262690

Structural characterization/correlation of calorimetric properties of coal fluids: Final report, September 1, 1985--August 31, 1988

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, IR, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined. 8 refs.« less

Structural characterization/correlation of calorimetric properties of coal fluids: Second annual report, September 1, 1986-August 31, 1987

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, ir, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined.« less

Structural characterization/correlation of calorimetric properties of coal fluids. First annual report, September 1, 1985-August 31, 1986

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal liquids and their molecular functional group composition. Coal liquid samples which have had their calorimetric properties measured are characterized using proton NMR, ir and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal liquid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for heat capacities will then be examined within anmore » existing equation of state methodology to determine an optimal correlation. Also, the optimal recipe for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model will be examined and determined. 7 refs.« less

Physiological and molecular characterization of drought responses and identification of candidate tolerance genes in cassava

PubMed Central

Turyagyenda, Laban F.; Kizito, Elizabeth B.; Ferguson, Morag; Baguma, Yona; Agaba, Morris; Harvey, Jagger J. W.; Osiru, David S. O.

2013-01-01

Cassava is an important root crop to resource-poor farmers in marginal areas, where its production faces drought stress constraints. Given the difficulties associated with cassava breeding, a molecular understanding of drought tolerance in cassava will help in the identification of markers for use in marker-assisted selection and genes for transgenic improvement of drought tolerance. This study was carried out to identify candidate drought-tolerance genes and expression-based markers of drought stress in cassava. One drought-tolerant (improved variety) and one drought-susceptible (farmer-preferred) cassava landrace were grown in the glasshouse under well-watered and water-stressed conditions. Their morphological, physiological and molecular responses to drought were characterized. Morphological and physiological measurements indicate that the tolerance of the improved variety is based on drought avoidance, through reduction of water loss via partial stomatal closure. Ten genes that have previously been biologically validated as conferring or being associated with drought tolerance in other plant species were confirmed as being drought responsive in cassava. Four genes (MeALDH, MeZFP, MeMSD and MeRD28) were identified as candidate cassava drought-tolerance genes, as they were exclusively up-regulated in the drought-tolerant genotype to comparable levels known to confer drought tolerance in other species. Based on these genes, we hypothesize that the basis of the tolerance at the cellular level is probably through mitigation of the oxidative burst and osmotic adjustment. This study provides an initial characterization of the molecular response of cassava to drought stress resembling field conditions. The drought-responsive genes can now be used as expression-based markers of drought stress tolerance in cassava, and the candidate tolerance genes tested in the context of breeding (as possible quantitative trait loci) and engineering drought tolerance in transgenics. PMID:23519782

Application of single-cell sequencing in human cancer.

PubMed

Rantalainen, Mattias

2017-11-02

Precision medicine is emerging as a cornerstone of future cancer care with the objective of providing targeted therapies based on the molecular phenotype of each individual patient. Traditional bulk-level molecular phenotyping of tumours leads to significant information loss, as the molecular profile represents an average phenotype over large numbers of cells, while cancer is a disease with inherent intra-tumour heterogeneity at the cellular level caused by several factors, including clonal evolution, tissue hierarchies, rare cells and dynamic cell states. Single-cell sequencing provides means to characterize heterogeneity in a large population of cells and opens up opportunity to determine key molecular properties that influence clinical outcomes, including prognosis and probability of treatment response. Single-cell sequencing methods are now reliable enough to be used in many research laboratories, and we are starting to see applications of these technologies for characterization of human primary cancer cells. In this review, we provide an overview of studies that have applied single-cell sequencing to characterize human cancers at the single-cell level, and we discuss some of the current challenges in the field. © The Author 2017. Published by Oxford University Press.

Characterization of the Host Response to Pichinde Virus Infection in the Syrian Golden Hamster by Species-Specific Kinome Analysis*

PubMed Central

Falcinelli, Shane; Gowen, Brian B.; Trost, Brett; Napper, Scott; Kusalik, Anthony; Johnson, Reed F.; Safronetz, David; Prescott, Joseph; Wahl-Jensen, Victoria; Jahrling, Peter B.; Kindrachuk, Jason

2015-01-01

The Syrian golden hamster has been increasingly used to study viral hemorrhagic fever (VHF) pathogenesis and countermeasure efficacy. As VHFs are a global health concern, well-characterized animal models are essential for both the development of therapeutics and vaccines as well as for increasing our understanding of the molecular events that underlie viral pathogenesis. However, the paucity of reagents or platforms that are available for studying hamsters at a molecular level limits the ability to extract biological information from this important animal model. As such, there is a need to develop platforms/technologies for characterizing host responses of hamsters at a molecular level. To this end, we developed hamster-specific kinome peptide arrays to characterize the molecular host response of the Syrian golden hamster. After validating the functionality of the arrays using immune agonists of defined signaling mechanisms (lipopolysaccharide (LPS) and tumor necrosis factor (TNF)-α), we characterized the host response in a hamster model of VHF based on Pichinde virus (PICV1) infection by performing temporal kinome analysis of lung tissue. Our analysis revealed key roles for vascular endothelial growth factor (VEGF), interleukin (IL) responses, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling, and Toll-like receptor (TLR) signaling in the response to PICV infection. These findings were validated through phosphorylation-specific Western blot analysis. Overall, we have demonstrated that hamster-specific kinome arrays are a robust tool for characterizing the species-specific molecular host response in a VHF model. Further, our results provide key insights into the hamster host response to PICV infection and will inform future studies with high-consequence VHF pathogens. PMID:25573744

Molecular imaging with bioconjugates in mouse models of cancer.

PubMed

Mather, Stephen

2009-04-01

The definition of molecular imaging provided by the Society of Nuclear Medicine is "the visualization, characterization and measurement of biological processes at the molecular and cellular levels in humans and other living systems". This review gives an overview of the technologies available for and the potential benefits from molecular imaging at the preclinical stage. It focuses on the use of imaging probes based on bioconjugates and for reasons of brevity confines itself to discussion of applications in the field of oncology, although molecular imaging can be equally useful in many fields including cardiovascular medicine, neurosciences, infection, and others.

Morphological and molecular characterization of Fusarium spp pathogenic to pecan tree in Brazil.

PubMed

Lazarotto, M; Milanesi, P M; Muniz, M F B; Reiniger, L R S; Beltrame, R; Harakava, R; Blume, E

2014-11-11

The occurrence of Fusarium spp associated with pecan tree (Carya illinoinensis) diseases in Brazil has been observed in recent laboratory analyses in Rio Grande do Sul State. Thus, in this study, we i) obtained Fusarium isolates from plants with disease symptoms; ii) tested the pathogenicity of these Fusarium isolates to pecan; iii) characterized and grouped Fusarium isolates that were pathogenic to the pecan tree based on morphological characteristics; iv) identified Fusarium spp to the species complex level through TEF-1α sequencing; and v) compared the identification methods used in the study. Fifteen isolates collected from the inflorescences, roots, and seeds of symptomatic plants (leaf necrosis or root rot) were used for pathogenicity tests. Morphological characterization was conducted using only pathogenic isolates, for a total of 11 isolates, based on the mycelial growth rate, sporulation, colony pigmentation, and conidial length and width variables. Pathogenic isolates were grouped based on morphological characteristics, and molecular characterization was performed by sequencing TEF-1α genes. Pathogenic isolates belonging to the Fusarium chlamydosporum species complex, Fusarium graminearum species complex, Fusarium proliferatum, and Fusarium oxysporum were identified based on the TEF-1α region. Morphological characteristics were used to effectively differentiate isolates and group the isolates according to genetic similarity, particularly conidial width, which emerged as a key morphological descriptor in this study.

Combining differential expression, chromosomal and pathway analyses for the molecular characterization of renal cell carcinoma

PubMed Central

Furge, Kyle A; Dykema, Karl; Petillo, David; Westphal, Michael; Zhang, Zhongfa; Kort, Eric J; Teh, Bin Tean

2007-01-01

Using high-throughput gene-expression profiling technology, we can now gain a better understanding of the complex biology that is taking place in cancer cells. This complexity is largely dictated by the abnormal genetic makeup of the cancer cells. This abnormal genetic makeup can have profound effects on cellular activities such as cell growth, cell survival and other regulatory processes. Based on the pattern of gene expression, or molecular signatures of the tumours, we can distinguish or subclassify different types of cancers according to their cell of origin, behaviour, and the way they respond to therapeutic agents and radiation. These approaches will lead to better molecular subclassification of tumours, the basis of personalized medicine. We have, to date, done whole-genome microarray gene-expression profiling on several hundreds of kidney tumours. We adopt a combined bioinformatic approach, based on an integrative analysis of the gene-expression data. These data are used to identify both cytogenetic abnormalities and molecular pathways that are deregulated in renal cell carcinoma (RCC). For example, we have identified the deregulation of the VHL-hypoxia pathway in clear-cell RCC, as previously known, and the c-Myc pathway in aggressive papillary RCC. Besides the more common clear-cell, papillary and chromophobe RCCs, we are currently characterizing the molecular signatures of rarer forms of renal neoplasia such as carcinoma of the collecting ducts, mixed epithelial and stromal tumours, chromosome Xp11 translocations associated with papillary RCC, renal medullary carcinoma, mucinous tubular and spindle-cell carcinoma, and a group of unclassified tumours. Continued development and improvement in the field of molecular profiling will better characterize cancer and provide more accurate diagnosis, prognosis and prediction of drug response. PMID:18542781

The spectroscopic characterization of newly developed emissive materials and the effects of environment on their photophysical properties

NASA Astrophysics Data System (ADS)

McNamara, Louis Edward, III

The development of new materials capable of efficient charge transfer and energy storage has become increasingly important in many areas of modern chemical research. This is especially true for the development of emissive optoelectronic devices and in the field of solar to electric energy conversion. The characterization of the photophysical properties of new molecular systems for these applications has become critical in the design and development of these materials. Many molecular building blocks have been developed and understanding the properties of these molecules at a fundamental level is essential for their successful implementation and future engineering. This dissertation focuses on the characterization of some of these newly-developed molecular systems. The spectroscopic studies focus on the characterization of newly-developed molecules based on perylene and indolizine derivatives for solar to electric energy conversion, thienopyrazine derivatives for near infrared (NIR) emissive applications, an SCS pincer complex for blue emissive materials and a fluorescent probe for medical applications. The effects of noncovalent interactions are also investigated on these systems and a benchmark biological molecule trimethylamine N-oxide (TMAO).

Synthesis and characterization of MAA-based molecularly-imprinted polymer (MIP) with D-glucose template

NASA Astrophysics Data System (ADS)

Yanti; Nurhayati, T.; Royani, I.; Widayani; Khairurrijal

2016-08-01

In this study, molecularly-imprinted polymer (MIP) was prepared by using a D-glucose template and a methacrylic acid (MAA) functional monomer. The obtained MIP was characterized using X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy techniques to study the template imprinting results. For comparison, similar characterizations were also carried out for the respective non imprinted polymer (NIP). It was found that the polymer has semicrystalline structure, with crystallinity degree of the unleached- polymer, the NIP, and the MIP is 62.40%, 62.97%, and 63.47%, respectively. XRD patterns showed that the intensity peaks increases as D-glucose content decreases. The FTIR spectra of the MIP indicate the detail interaction of template and functional monomer.

Molecular characterization of Peruvian Citrus tristeza virus isolates based on 3’UTR sequences

USDA-ARS?s Scientific Manuscript database

Citrus in Peru was decimated by quick decline and stem pitting strains of Citrus tristeza virus (CTV). Commercial citrus production in Peru is being restored by use of CTV cross-protection. To characterize the predominant CTV strains involved, Peruvian CTV isolates from “protected” and “non-protecti...

A critical review on characterization strategies of organic matter for wastewater and water treatment processes.

PubMed

Tran, Ngoc Han; Ngo, Huu Hao; Urase, Taro; Gin, Karina Yew-Hoong

2015-10-01

The presence of organic matter (OM) in raw wastewater, treated wastewater effluents, and natural water samples has been known to cause many problems in wastewater treatment and water reclamation processes, such as treatability, membrane fouling, and the formation of potentially toxic by-products during wastewater treatment. This paper summarizes the current knowledge on the methods for characterization and quantification of OM in water samples in relation to wastewater and water treatment processes including: (i) characterization based on the biodegradability; (ii) characterization based on particle size distribution; (iii) fractionation based on the hydrophilic/hydrophobic properties; (iv) characterization based on the molecular weight (MW) size distribution; and (v) characterization based on fluorescence excitation emission matrix. In addition, the advantages, disadvantages and applications of these methods are discussed in detail. The establishment of correlations among biodegradability, hydrophobic/hydrophilic fractions, MW size distribution of OM, membrane fouling and formation of toxic by-products potential is highly recommended for further studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Strategies for Characterization of Low-Abundant Intact or Truncated Low-Molecular-Weight Proteins From Human Plasma.

PubMed

Cai, Tanxi; Yang, Fuquan

2017-01-01

Low-molecular-weight region (LMW, MW≤30kDa) of human serum/plasma proteins, including small intact proteins, truncated fragments of larger proteins, along with some other small components, has been associated with the ongoing physiological and pathological events, and thereby represent a treasure trove of diagnostic molecules. Great progress in the mining of novel biomarkers from this diagnostic treasure trove for disease diagnosis and health monitoring has been achieved based on serum samples from healthy individuals and patients and powerful new approaches in biochemistry and systems biology. However, cumulative evidence indicates that many potential LMW protein biomarkers might still have escaped from detection due to their low abundance, the dynamic complexity of serum/plasma, and the limited efficiency of characterization approaches. Here, we provide an overview of the current state of knowledge with respect to strategies for the characterization of low-abundant LMW proteins (small intact or truncated proteins) from human serum/plasma, involving prefractionation or enrichment methods to reduce dynamic range and mass spectrometry-based characterization of low-abundant LMW proteins. © 2017 Elsevier Inc. All rights reserved.

Hydrodynamic size-based separation and characterization of protein aggregates from total cell lysates

PubMed Central

Tanase, Maya; Zolla, Valerio; Clement, Cristina C; Borghi, Francesco; Urbanska, Aleksandra M; Rodriguez-Navarro, Jose Antonio; Roda, Barbara; Zattoni, Andrea; Reschiglian, Pierluigi; Cuervo, Ana Maria; Santambrogio, Laura

2016-01-01

Herein we describe a protocol that uses hollow-fiber flow field-flow fractionation (FFF) coupled with multiangle light scattering (MALS) for hydrodynamic size-based separation and characterization of complex protein aggregates. The fractionation method, which requires 1.5 h to run, was successfully modified from the analysis of protein aggregates, as found in simple protein mixtures, to complex aggregates, as found in total cell lysates. In contrast to other related methods (filter assay, analytical ultracentrifugation, gel electrophoresis and size-exclusion chromatography), hollow-fiber flow FFF coupled with MALS allows a flow-based fractionation of highly purified protein aggregates and simultaneous measurement of their molecular weight, r.m.s. radius and molecular conformation (e.g., round, rod-shaped, compact or relaxed). The polyethersulfone hollow fibers used, which have a 0.8-mm inner diameter, allow separation of as little as 20 μg of total cell lysates. In addition, the ability to run the samples in different denaturing and nondenaturing buffer allows defining true aggregates from artifacts, which can form during sample preparation. The protocol was set up using Paraquat-induced carbonylation, a model that induces protein aggregation in cultured cells. This technique will advance the biochemical, proteomic and biophysical characterization of molecular-weight aggregates associated with protein mutations, as found in many CNS degenerative diseases, or chronic oxidative stress, as found in aging, and chronic metabolic and inflammatory conditions. PMID:25521790

Characterization of some bread wheat genotypes using molecular markers for drought tolerance.

PubMed

Ateş Sönmezoğlu, Özlem; Terzi, Begüm

2018-02-01

Because of its wide geographical adaptation and importance in human nutrition, wheat is one of the most important crops in the world. However, wheat yield has reduced due to drought stress posing threat to sustainability and world food security in agricultural production. The first stage of drought tolerant variety breeding occurs on the molecular and biochemical characterization and classification of wheat genotypes. The aim of the present study is characterization of widely grown bread wheat cultivars and breeding lines for drought tolerance so as to be adapted to different regions in Turkey. The genotypes were screened with molecular markers for the presence of QTLs mapped to different chromosomes. Results of the molecular studies identified and detected 15 polymorphic SSR markers which gave the clearest PCR bands among the control genotypes. At the end of the research, bread wheat genotypes which were classified for tolerance or sensitivity to drought and the genetic similarity within control varieties were determined by molecular markers. According to SSR based dendrogram, two main groups were obtained for drought tolerance. At end of the molecular screening with SSR primers, genetic similarity coefficients were obtained that ranged from 0.14 to 0.71. The ones numbered 8 and 11 were the closest genotypes to drought tolerant cultivar Gerek 79 and the furthest genotypes from this cultivar were number 16 and to drought sensitive cultivar Sultan 95. The genotypes as drought tolerance due to their SSR markers scores are expected to provide useful information for drought related molecular breeding studies.

FlyBase: genes and gene models

PubMed Central

Drysdale, Rachel A.; Crosby, Madeline A.

2005-01-01

FlyBase (http://flybase.org) is the primary repository of genetic and molecular data of the insect family Drosophilidae. For the most extensively studied species, Drosophila melanogaster, a wide range of data are presented in integrated formats. Data types include mutant phenotypes, molecular characterization of mutant alleles and aberrations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models and molecular classification of gene product functions. There is a growing body of data for other Drosophila species; this is expected to increase dramatically over the next year, with the completion of draft-quality genomic sequences of an additional 11 Drosphila species. PMID:15608223

Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

PubMed Central

Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

2015-01-01

Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold Q and its tangent space Q at the current configuration q. In contrast to methods based on combinatorial constraint counting, our method is valid for both generic and non-generic, e.g., singular configurations. Importantly, our geometric approach provides an explicit basis for collective motions along floppy modes, resulting in an efficient procedure to probe conformational space. An atomically detailed structural characterization of coordinated, collective motions would allow us to engineer or allosterically modulate biomolecules by selectively stabilizing conformations that enhance or inhibit function with broad implications for human health. PMID:26213417

Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

NASA Astrophysics Data System (ADS)

Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

2015-10-01

Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold Q and its tangent space Tq Q at the current configuration q. In contrast to methods based on combinatorial constraint counting, our method is valid for both generic and non-generic, e.g., singular configurations. Importantly, our geometric approach provides an explicit basis for collective motions along floppy modes, resulting in an efficient procedure to probe conformational space. An atomically detailed structural characterization of coordinated, collective motions would allow us to engineer or allosterically modulate biomolecules by selectively stabilizing conformations that enhance or inhibit function with broad implications for human health.

[Molecular biology in clinical cancer research: the example of digestive cancers].

PubMed

Lièvre, A; Laurent-Puig, P

2005-06-01

Cancer is a DNA disease characterized by uncontrolled cell proliferation due to the accumulation of genetic alterations. Recent progress in molecular biology allowed the identification of markers potentially usefull for patients management through the identification of these genetic alterations and a best understanding of chemotherapy molecular targets. Several examples in digestive oncology underline the relevance of molecular biology in clinical research. If almost all colorectal cancers (CRC) correspond to the same histopathological type (adenocarcinoma), molecular biology allowed the identification of two different molecular mechanisms of colorectal carcinogenesis: chromosomal instability characterized by recurrent allelic losses on chromosomes 17, 5, 18, 8 and 22 that contribute to the inactivation of tumor suppressor genes, and genetic instability characterized by the instability of microsatellite loci due to an alteration of DNA mismatch repair leading to the accumulation of mutations in genes involved in the control of cell cycle and apoptosis. These data are potentially interesting for the management of CRC patients. Indeed, microsatellite instability seems not only to be a good prognostic factor but also a molecular factor that can predict response to adjuvant 5-fluorouracil based chemotherapy. Therapeutic clinical trials taking into account these molecular parameters are still going on. DNA microarray-based gene expression profiling technology that allows the simultaneous analysis of thousand of tumor genes represents also an interesting approach in oncology with the recent identification of a "genetic signature" as a risk factor of tumor recurrence in stage II CRC, a setting in which the benefit of adjuvant chemotherapy remains on debate. At last, a best understanding of chemotherapy molecular targets allowed the identification of genetic markers that can predict the response and/or the toxicity of anti-cancer drugs used in gastrointestinal cancers, which could be helpful in the future to propose for each patient a personalized treatment. Mutations that can predict the response of new target therapies such as the inhibitors of the c-KIT tyrosine kinase activity in gastrointestinal stromal tumors have also been found and will allow the selection of patients who can have benefit from these new therapeutic drugs.

Molecular Weights of Bovine and Porcine Heparin Samples: Comparison of Chromatographic Methods and Results of a Collaborative Survey.

PubMed

Bertini, Sabrina; Risi, Giulia; Guerrini, Marco; Carrick, Kevin; Szajek, Anita Y; Mulloy, Barbara

2017-07-19

In a collaborative study involving six laboratories in the USA, Europe, and India the molecular weight distributions of a panel of heparin sodium samples were determined, in order to compare heparin sodium of bovine intestinal origin with that of bovine lung and porcine intestinal origin. Porcine samples met the current criteria as laid out in the USP Heparin Sodium monograph. Bovine lung heparin samples had consistently lower average molecular weights. Bovine intestinal heparin was variable in molecular weight; some samples fell below the USP limits, some fell within these limits and others fell above the upper limits. These data will inform the establishment of pharmacopeial acceptance criteria for heparin sodium derived from bovine intestinal mucosa. The method for MW determination as described in the USP monograph uses a single, broad standard calibrant to characterize the chromatographic profile of heparin sodium on high-resolution silica-based GPC columns. These columns may be short-lived in some laboratories. Using the panel of samples described above, methods based on the use of robust polymer-based columns have been developed. In addition to the use of the USP's broad standard calibrant for heparin sodium with these columns, a set of conditions have been devised that allow light-scattering detected molecular weight characterization of heparin sodium, giving results that agree well with the monograph method. These findings may facilitate the validation of variant chromatographic methods with some practical advantages over the USP monograph method.

Physiological and Molecular Characterization of Cephaleuros virescens Occurring in Mango Trees.

PubMed

Vasconcelos, Camila Vilela; Pereira, Fabíola Teodoro; Duarte, Elizabeth Amélia Alves; de Oliveira, Thiago Alves Santos; Peixoto, Nei; Carvalho, Daniel Diego Costa

2018-06-01

The objective of this work was to accomplish the isolation, molecular identification and characterizing the physiology of the causal agent of the algal spot in mango trees. For this purpose, the pathogen growth was assessed in different culture media, with subsequent observation and measurements of the filamentous cells. The molecular identification was made using mycelium obtained from leaf lesions and pure algae colonies grown in culture medium. Descriptions based on DNA sequencing indicated that the algae is Cephaleuros virescens . The algae must be isolated primarily in liquid medium for further pricking into agar medium. The highest mycelial growth average in Petri dishes occurred when the algae were grown in Trebouxia and BBM. Trebouxia enabled larger cells in the filamentous cells when compared to other culture media.

A perspective on extracellular vesicles proteomics

NASA Astrophysics Data System (ADS)

Rosa-Fernandes, Livia; Rocha, Victória Bombarda; Carregari, Victor Corasolla; Urbani, Andrea; Palmisano, Giuseppe

2017-11-01

Increasing attention has been given to secreted extracellular vesicles (EVs) in the past decades, especially in the portrayal of their molecular cargo and role as messengers in both homeostasis and pathophysiological conditions. This review presents the state-of-the-art proteomic technologies to identify and quantify EVs proteins along with their PTMs, interacting partners and structural details. The rapid growth of mass spectrometry-based analytical strategies for protein sequencing, PTMs and structural characterization has improved the level of molecular details that can be achieve from limited amount of EVs isolated from different biological sources. Here we will provide a perspective view on the achievements and challenges on EVs proteome characterization using mass spectrometry. A detailed bioinformatics approach will help us to picture the molecular fingerprint of EVs and understand better their pathophysiological function.

Synthesis and characterization of a helicene-based imidazolium salt and its application in organic molecular electronics.

PubMed

Storch, Jan; Zadny, Jaroslav; Strasak, Tomas; Kubala, Martin; Sykora, Jan; Dusek, Michal; Cirkva, Vladimir; Matejka, Pavel; Krbal, Milos; Vacek, Jan

2015-02-02

Herein we demonstrate the synthesis of a helicene-based imidazolium salt. The salt was prepared by starting from racemic 2-methyl[6]helicene, which undergoes radical bromination to yield 2-(bromomethyl)[6]helicene. Subsequent treatment with 1-butylimidazole leads to the corresponding salt 1-butyl-3-(2-methyl[6]helicenyl)-imidazolium bromide. The prepared salt was subsequently characterized by using NMR spectroscopy and X-ray analysis, various optical spectrometric techniques, and computational chemistry tools. Finally, the imidazolium salt was immobilized onto a SiO2 substrate as a crystalline or amorphous deposit. The deposited layers were used for the development of organic molecular semiconductor devices and the construction of a fully reversible humidity sensor. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Portraying the Expression Landscapes of B-Cell Lymphoma-Intuitive Detection of Outlier Samples and of Molecular Subtypes

PubMed Central

Hopp, Lydia; Lembcke, Kathrin; Binder, Hans; Wirth, Henry

2013-01-01

We present an analytic framework based on Self-Organizing Map (SOM) machine learning to study large scale patient data sets. The potency of the approach is demonstrated in a case study using gene expression data of more than 200 mature aggressive B-cell lymphoma patients. The method portrays each sample with individual resolution, characterizes the subtypes, disentangles the expression patterns into distinct modules, extracts their functional context using enrichment techniques and enables investigation of the similarity relations between the samples. The method also allows to detect and to correct outliers caused by contaminations. Based on our analysis, we propose a refined classification of B-cell Lymphoma into four molecular subtypes which are characterized by differential functional and clinical characteristics. PMID:24833231

Morphological and molecular characterization of a novel myxosporean parasite Myxobolus bejeranoi n. sp. (Cnidaria: Myxosporea) from hybrid tilapia in Israel.

PubMed

Lövy, Alena; Smirnov, Margarita; Brekhman, Vera; Ofek, Tamir; Lotan, Tamar

2018-02-01

Myxosporean infections can cause severe damage to commercially grown tilapia. Here, we report a novel myxosporean that was found in gills of Oreochromis aureus male × Oreochromis niloticus female, which is an important aquaculture tilapia hybrid in Israel. Three-month-old fish were found to have cysts located in gill muscle tissue, which were filled with both immature and mature spores. Affected fish displayed higher mortality rate. Spore dimensions (10.8 ± 0.7 μm length × 6.8 ± 0.6 μm width) and molecular characterization using 18S ribosomal DNA revealed that the unknown parasite belongs in the Myxobolus clade. Based on the infection site, spore morphology and molecular characterization, we describe this parasite as Myxobolus bejeranoi n. sp. (MF401455). Phylogenetic analysis showed that the new species is most closely related to two Myxobolus spp. from O. niloticus in Egypt and Ghana.

Molecular subgroups of medulloblastoma

PubMed Central

Northcott, Paul A; Dubuc, Adrian M; Pfister, Stefan; Taylor, Michael D

2014-01-01

Recent efforts at stratifying medulloblastomas based on their molecular features have revolutionized our understanding of this morbidity. Collective efforts by multiple independent groups have subdivided medulloblastoma from a single disease into four distinct molecular subgroups characterized by disparate transcriptional signatures, mutational spectra, copy number profiles and, most importantly, clinical features. We present a summary of recent studies that have contributed to our understanding of the core medulloblastoma subgroups, focusing largely on clinically relevant discoveries that have already, and will continue to, shape research. PMID:22853794

Analysis of Physical and Numerical Factors for Prediction of UV Radiation from High Altitude Two-Phase Plumes

DTIC Science & Technology

2008-05-30

varies from continuum inside the nozzle, to transitional in the near field, to free molecular in the far field of the plume. The scales of interest vary...unity based on the rocket length. This results in the formation of a viscous shock layer characterized by a bimodal molecular velocity distribution. The...transfer model. Previous analysis21 have shown that the heat transfer model implemented in CFD++ is reproduced closely by the free molecular model

Formulation and Solid State Characterization of Nicotinamide-based Co-crystals of Fenofibrate

PubMed Central

Shewale, Sheetal; Shete, A. S.; Doijad, R. C.; Kadam, S. S.; Patil, V. A.; Yadav, A. V.

2015-01-01

The present investigation deals with formulation of nicotinamide-based co-crystals of fenofibrate by different methods and solid-state characterization of the prepared co-crystals. Fenofibrate and nicotinamide as a coformer in 1:1 molar ratio were used to formulate molecular complexes by kneading, solution crystallization, antisolvent addition and solvent drop grinding methods. The prepared molecular complexes were characterized by powder X-ray diffractometry, differential scanning calorimetry, Fourier transform infrared spectroscopy, nuclear magnetic resonance spectroscopy and in vitro dissolution study. Considerable improvement in the dissolution rate of fenofibrate from optimized co-crystal formulation was due to an increased solubility that is attributed to the super saturation from the fine co-crystals is faster because of large specific surface area of small particles and prevention of phase transformation to pure fenofibrate. In vitro dissolution study showed that the formation of co-crystals improves the dissolution rate of fenofibrate. Nicotinamide forms the co-crystals with fenofibrate, theoretically and practically. PMID:26180279

Gas solubility in dilute solutions: A novel molecular thermodynamic perspective

NASA Astrophysics Data System (ADS)

Chialvo, Ariel A.

2018-05-01

We present an explicit molecular-based interpretation of the thermodynamic phase equilibrium underlying gas solubility in liquids, through rigorous links between the microstructure of the dilute systems and the relevant macroscopic quantities that characterize their solution thermodynamics. We apply the formal analysis to unravel and highlight the molecular-level nature of the approximations behind the widely used Krichevsky-Kasarnovsky [J. Am. Chem. Soc. 57, 2168 (1935)] and Krichevsky-Ilinskaya [Acta Physicochim. 20, 327 (1945)] equations for the modeling of gas solubility. Then, we implement a general molecular-based approach to gas solubility and illustrate it by studying Lennard-Jones binary systems whose microstructure and thermodynamic properties were consistently generated via integral equation calculations. Furthermore, guided by the molecular-based analysis, we propose a novel macroscopic modeling approach to gas solubility, emphasize some usually overlook modeling subtleties, and identify novel interdependences among relevant solubility quantities that can be used as either handy modeling constraints or tools for consistency tests.

Gas solubility in dilute solutions: A novel molecular thermodynamic perspective.

PubMed

Chialvo, Ariel A

2018-05-07

We present an explicit molecular-based interpretation of the thermodynamic phase equilibrium underlying gas solubility in liquids, through rigorous links between the microstructure of the dilute systems and the relevant macroscopic quantities that characterize their solution thermodynamics. We apply the formal analysis to unravel and highlight the molecular-level nature of the approximations behind the widely used Krichevsky-Kasarnovsky [J. Am. Chem. Soc. 57, 2168 (1935)] and Krichevsky-Ilinskaya [Acta Physicochim. 20, 327 (1945)] equations for the modeling of gas solubility. Then, we implement a general molecular-based approach to gas solubility and illustrate it by studying Lennard-Jones binary systems whose microstructure and thermodynamic properties were consistently generated via integral equation calculations. Furthermore, guided by the molecular-based analysis, we propose a novel macroscopic modeling approach to gas solubility, emphasize some usually overlook modeling subtleties, and identify novel interdependences among relevant solubility quantities that can be used as either handy modeling constraints or tools for consistency tests.

[Pancreatic acinar neoplasms : Comparative molecular characterization].

PubMed

Bergmann, F

2016-11-01

Pancreatic acinar cell carcinomas are biologically aggressive neoplasms for which treatment options are very limited. The molecular mechanisms of tumor initiation and progression are largely not understood and precursor lesions have not yet been identified. In this study, pancreatic acinar cell carcinomas were cytogenetically characterized as well as by molecular and immunohistochemical analyses. Corresponding investigations were carried out on pancreatic ductal adenocarcinomas and pancreatic neuroendocrine neoplasms augmented by functional analyses. We show that pancreatic acinar cell carcinomas display a microsatellite stable, chromosomal unstable genotype, characterized by recurrent chromosomal imbalances that clearly discriminate them from pancreatic ductal adenocarcinomas and neuroendocrine neoplasms. Based on findings obtained from comparative genomic hybridization, candidate genes could be identified, such as deleted in colorectal cancer (DCC) and c-MYC. Furthermore, several therapeutic targets were identified in acinar cell carcinomas and other pancreatic neoplasms, including epidermal growth factor receptor (EGFR), L1 cell adhesion molecule (L1CAM) and heat shock protein 90 (HSP90). Moreover, L1CAM was shown to play a significant role in the tumorigenesis of pancreatic ductal adenocarcinoma. Functional analyses in cell lines derived from pancreatic neuroendocrine neoplasms revealed promising anti-tumorigenic effects using EGFR and HSP90 inhibitors affecting the cell cycle and in the case of HSP90, regulating several other oncogenes. Finally, based on mutational analyses of mitochondrial DNA, molecular evidence is provided that acinar cell cystadenomas (or better cystic acinar transformation) represent non-clonal lesions, suggesting an inflammatory reactive non-neoplastic nature.

Conducting Reflective, Hands-On Research with Advanced Characterization Instruments: A High-Level Undergraduate Practical Exploring Solid-State Polymorphism

ERIC Educational Resources Information Center

Coles, S. J.; Mapp, L. K.

2016-01-01

An undergraduate practical exercise has been designed to provide hands-on, instrument-based experience of advanced characterization techniques. A research experience approach is taken, centered around the concept of solid-state polymorphism, which requires a detailed knowledge of molecular and crystal structure to be gained by advanced analytical…

Molecular and cellular alterations in Down syndrome: toward the identification of targets for therapeutics.

PubMed

Créau, Nicole

2012-01-01

Down syndrome is a complex disease that has challenged molecular and cellular research for more than 50 years. Understanding the molecular bases of morphological, cellular, and functional alterations resulting from the presence of an additional complete chromosome 21 would aid in targeting specific genes and pathways for rescuing some phenotypes. Recently, progress has been made by characterization of brain alterations in mouse models of Down syndrome. This review will highlight the main molecular and cellular findings recently described for these models, particularly with respect to their relationship to Down syndrome phenotypes.

Molecular characterization of Hepatozoon sp. in cats from São Luís Island, Maranhão, Northeastern Brazil.

PubMed

de Bortoli, Caroline P; André, Marcos R; Braga, Maria do Socorro C; Machado, Rosangela Zacarias

2011-10-01

Few molecular studies have been done concerning the molecular characterization of Hepatozoon species among domestic and wild felids. The present work aimed to characterize molecularly the presence of Hepatozoon sp. DNA in cat blood samples from São Luís Island, Maranhão state, Northeastern Brazil. EDTA-whole blood samples were collected from 200 domestic cats with outdoor and wood areas access from São Luís, Maranhão, Brazil. Each sample of extracted DNA was used as a template in PCR reactions aiming to amplify a partial sequence of 18S rRNA of Hepatozoon spp. We also performed sequence alignment to establish the identity of the parasite species infecting these animals using DNA sequences based on 18S rRNA. From 200 sampled cats, Hepatozoon DNA was only found in one animal (0.5%). The found Hepatozoon DNA showed 97% of identity with Hemobartonella felis isolates 1 and 2 from Spain. When analyzing the phylogenetic tree, the found Hepatozoon DNA was in the same clade than H. felis isolates. Our findings suggest that more than one species of Hepatozoon could infect felids in Brazil.

A novel microfluidic platform for size and deformability based separation and the subsequent molecular characterization of viable circulating tumor cells.

PubMed

Hvichia, G E; Parveen, Z; Wagner, C; Janning, M; Quidde, J; Stein, A; Müller, V; Loges, S; Neves, R P L; Stoecklein, N H; Wikman, H; Riethdorf, S; Pantel, K; Gorges, T M

2016-06-15

Circulating tumor cells (CTCs) were introduced as biomarkers more than 10 years ago, but capture of viable CTCs at high purity from peripheral blood of cancer patients is still a major technical challenge. Here, we report a novel microfluidic platform designed for marker independent capture of CTCs. The Parsortix™ cell separation system provides size and deformability-based enrichment with automated staining for cell identification, and subsequent recovery (harvesting) of cells from the device. Using the Parsortix™ system, average cell capture inside the device ranged between 42% and 70%. Subsequent harvest of cells from the device ranged between 54% and 69% of cells captured. Most importantly, 99% of the isolated tumor cells were viable after processing in spiking experiments as well as after harvesting from patient samples and still functional for downstream molecular analysis as demonstrated by mRNA characterization and array-based comparative genomic hybridization. Analyzing clinical blood samples from metastatic (n = 20) and nonmetastatic (n = 6) cancer patients in parallel with CellSearch(®) system, we found that there was no statistically significant difference between the quantitative behavior of the two systems in this set of twenty six paired separations. In conclusion, the epitope independent Parsortix™ system enables the isolation of viable CTCs at a very high purity. Using this system, viable tumor cells are easily accessible and ready for molecular and functional analysis. The system's ability for enumeration and molecular characterization of EpCAM-negative CTCs will help to broaden research into the mechanisms of cancer as well as facilitating the use of CTCs as "liquid biopsies." © 2016 The Authors International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UICC.

Isatin based Schiff bases as inhibitors of α-glucosidase: Synthesis, characterization, in vitro evaluation and molecular docking studies.

PubMed

Rahim, Fazal; Malik, Fazal; Ullah, Hayat; Wadood, Abdul; Khan, Fahad; Javid, Muhammad Tariq; Taha, Muhammad; Rehman, Wajid; Ur Rehman, Ashfaq; Khan, Khalid Mohammed

2015-06-01

Isatin base Schiff bases (1-20) were synthesized, characterized by (1)H NMR and EI/MS and evaluated for α-glucosidase inhibitory potential. Out of these twenty (20) compounds only six analogs showed potent α-glucosidase inhibitory potential with IC50 value ranging in between 2.2±0.25 and 83.5±1.0μM when compared with the standard acarbose (IC50=840±1.73μM). Among the series compound 2 having IC50 value (18.3±0.56μM), 9 (83.5±1.0μM), 11 (3.3±0.25μM), 12 (2.2±0.25μM), 14 (11.8±0.15μM), and 20 (3.0±0.15μM) showed excellent inhibitory potential many fold better than the standard acarbose. The binding interactions of these active analogs were confirmed through molecular docking. Copyright © 2015 Elsevier Inc. All rights reserved.

Morphological variability in leaves and molecular characterization of novel table grape candidate cultivars (Vitis vinifera L.).

PubMed

Alba, Vittorio; Bergamini, Carlo; Cardone, Maria Francesca; Gasparro, Marica; Perniola, Rocco; Genghi, Rosalinda; Antonacci, Donato

2014-06-01

The present work report the characterization of twenty-one table grapes candidate cultivars plus five registered ones included as reference, by means of 47 ampelographic traits, 23 ampelometric measurements and six microsatellite loci. The final goal of the research was to analyse the possibility of reducing the number of morphological and molecular tools required for a precise and effective description of a grape genotype or cultivar. This would be of great help for future biodiversity description on a larger sample of more than 300 table grapes accessions today grown at the 'Consiglio per la Ricerca e la sperimentazione in Agricoltura (C.R.A.)-Unità di ricerca per l'uva da tavola e la vitivinicoltura in ambiente mediterraneo (Bari-Italy)'. OIV ampelographic traits showed a clear distinction among all twenty-six genotypes analysed, suggesting the relevant morphological variability investigated. Principal component analysis based on ampelometric traits revealed main veins ON(3), ON(4) and O(3)N(4); ratios between main veins; angles between main veins and of petiolar sinus, to be the most effective records in differentiating cultivars, for a total variation of 69.9 % described by the first three components. Molecular analysis based on six microsatellite loci was performed on all genotypes, providing a detailed molecular profile and a dendrogram of genetic similarity, in which all genotypes were clearly distinguishable. Finally, with the goal of using the minimum possible number of markers to differentiate genotypes, microsatellites VVMD5 and VVMD27 were selected to be sufficient to distinguish among all the candidate cultivars included in the analysis, representing a possible 'step by step' approach when a molecular characterization has to be undertaken on a large number of genotypes, by first testing few markers and increasing their number only if necessary.

Dipolar filtered magic-sandwich-echoes as a tool for probing molecular motions using time domain NMR

NASA Astrophysics Data System (ADS)

Filgueiras, Jefferson G.; da Silva, Uilson B.; Paro, Giovanni; d'Eurydice, Marcel N.; Cobo, Márcio F.; deAzevedo, Eduardo R.

2017-12-01

We present a simple 1 H NMR approach for characterizing intermediate to fast regime molecular motions using 1 H time-domain NMR at low magnetic field. The method is based on a Goldmann Shen dipolar filter (DF) followed by a Mixed Magic Sandwich Echo (MSE). The dipolar filter suppresses the signals arising from molecular segments presenting sub kHz mobility, so only signals from mobile segments are detected. Thus, the temperature dependence of the signal intensities directly evidences the onset of molecular motions with rates higher than kHz. The DF-MSE signal intensity is described by an analytical function based on the Anderson Weiss theory, from where parameters related to the molecular motion (e.g. correlation times and activation energy) can be estimated when performing experiments as function of the temperature. Furthermore, we propose the use of the Tikhonov regularization for estimating the width of the distribution of correlation times.

Morphological, molecular and phylogenetic analyses of Diplotriaena bargusinica Skrjabin, 1917 (Nematoda: Diplotriaenidae).

PubMed

Dutra Vieira, Thainá; Pegoraro de Macedo, Marcia Raquel; Fedatto Bernardon, Fabiana; Müller, Gertrud

2017-10-01

The nematode Diplotriaena bargusinica is a bird air sac parasite, and its taxonomy is based mainly on morphological and morphometric characteristics. Increasing knowledge of genetic information variability has spurred the use of DNA markers in conjunction with morphological data for inferring phylogenetic relationships in different taxa. Considering the potential of molecular biology in taxonomy, this study presents the morphological and molecular characterization of D. bargusinica, and establishes the phylogenetic position of the nematode in Spirurina. Twenty partial sequences of the 18S region of D. bargusinica rDNA were generated. Phylogenetic trees were obtained through the Maximum Likelihood and Bayesian Inference methods where both had similar topology. The group Diplotriaenoidea is monophyletic and the topologies generated corroborate the phylogenetic studies based on traditional and previously performed molecular taxonomy. This study is the first to generate molecular data associated with the morphology of the species. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular recognition of microbial lipid-based antigens by T cells.

PubMed

Gras, Stephanie; Van Rhijn, Ildiko; Shahine, Adam; Le Nours, Jérôme

2018-05-01

The immune system has evolved to protect hosts from pathogens. T cells represent a critical component of the immune system by their engagement in host defence mechanisms against microbial infections. Our knowledge of the molecular recognition by T cells of pathogen-derived peptidic antigens that are presented by the major histocompatibility complex glycoproteins is now well established. However, lipids represent an additional, distinct chemical class of molecules that when presented by the family of CD1 antigen-presenting molecules can serve as antigens, and be recognized by specialized subsets of T cells leading to antigen-specific activation. Over the past decades, numerous CD1-presented self- and bacterial lipid-based antigens have been isolated and characterized. However, our understanding at the molecular level of T cell immunity to CD1 molecules presenting microbial lipid-based antigens is still largely unexplored. Here, we review the insights and the molecular basis underpinning the recognition of microbial lipid-based antigens by T cells.

Phase computations and phase models for discrete molecular oscillators.

PubMed

Suvak, Onder; Demir, Alper

2012-06-11

Biochemical oscillators perform crucial functions in cells, e.g., they set up circadian clocks. The dynamical behavior of oscillators is best described and analyzed in terms of the scalar quantity, phase. A rigorous and useful definition for phase is based on the so-called isochrons of oscillators. Phase computation techniques for continuous oscillators that are based on isochrons have been used for characterizing the behavior of various types of oscillators under the influence of perturbations such as noise. In this article, we extend the applicability of these phase computation methods to biochemical oscillators as discrete molecular systems, upon the information obtained from a continuous-state approximation of such oscillators. In particular, we describe techniques for computing the instantaneous phase of discrete, molecular oscillators for stochastic simulation algorithm generated sample paths. We comment on the accuracies and derive certain measures for assessing the feasibilities of the proposed phase computation methods. Phase computation experiments on the sample paths of well-known biological oscillators validate our analyses. The impact of noise that arises from the discrete and random nature of the mechanisms that make up molecular oscillators can be characterized based on the phase computation techniques proposed in this article. The concept of isochrons is the natural choice upon which the phase notion of oscillators can be founded. The isochron-theoretic phase computation methods that we propose can be applied to discrete molecular oscillators of any dimension, provided that the oscillatory behavior observed in discrete-state does not vanish in a continuous-state approximation. Analysis of the full versatility of phase noise phenomena in molecular oscillators will be possible if a proper phase model theory is developed, without resorting to such approximations.

Phase computations and phase models for discrete molecular oscillators

PubMed Central

2012-01-01

Background Biochemical oscillators perform crucial functions in cells, e.g., they set up circadian clocks. The dynamical behavior of oscillators is best described and analyzed in terms of the scalar quantity, phase. A rigorous and useful definition for phase is based on the so-called isochrons of oscillators. Phase computation techniques for continuous oscillators that are based on isochrons have been used for characterizing the behavior of various types of oscillators under the influence of perturbations such as noise. Results In this article, we extend the applicability of these phase computation methods to biochemical oscillators as discrete molecular systems, upon the information obtained from a continuous-state approximation of such oscillators. In particular, we describe techniques for computing the instantaneous phase of discrete, molecular oscillators for stochastic simulation algorithm generated sample paths. We comment on the accuracies and derive certain measures for assessing the feasibilities of the proposed phase computation methods. Phase computation experiments on the sample paths of well-known biological oscillators validate our analyses. Conclusions The impact of noise that arises from the discrete and random nature of the mechanisms that make up molecular oscillators can be characterized based on the phase computation techniques proposed in this article. The concept of isochrons is the natural choice upon which the phase notion of oscillators can be founded. The isochron-theoretic phase computation methods that we propose can be applied to discrete molecular oscillators of any dimension, provided that the oscillatory behavior observed in discrete-state does not vanish in a continuous-state approximation. Analysis of the full versatility of phase noise phenomena in molecular oscillators will be possible if a proper phase model theory is developed, without resorting to such approximations. PMID:22687330

Characterization of the low-molecular-weight glutenin subunit gene family members using a PCR-based marker approach

USDA-ARS?s Scientific Manuscript database

Low-molecular-weight glutenin subunits (LMW-GS) are a class of seed storage proteins that play a major role in the determination of the processing quality of wheat flour. The LMW-GS are encoded by multi-gene families located on the short arms of the homoeologous group 1 chromosomes, at the Glu-A3, G...

Filtered Rayleigh Scattering Measurements in a Buoyant Flow Field

DTIC Science & Technology

2008-03-01

ENY/08-M22 Abstract Filtered Rayleigh Scattering (FRS) is a non-intrusive, laser -based flow characterization technique that consists of a narrow...linewidth laser , a molecular absorption filter, and a high resolution camera behind the filter to record images. Gases of different species have...different molecular scattering cross-sections that become apparent as they pass through the interrogating laser light source, and this difference is

A perspective on slow-relaxing molecular magnets built from rare-earths and nitronyl-nitroxide building blocks (invited)

NASA Astrophysics Data System (ADS)

Bogani, Lapo

2011-04-01

We offer a perspective, accessible to both chemists and physicists, of recent developments in the synthesis and characterization of molecular magnetic materials based on rare-earths and nitronyl-nitroxide radicals. We show both the rationale of the synthetic strategies and the observed behaviors. We highlight the relevance of these findings for synthetic chemists, material scientists, and physicists.

Lab Plays Central Role in Groundbreaking National Clinical Trial in Precision Medicine | Poster

Cancer.gov

The Molecular Characterization Laboratory lies at the heart of an ambitious new approach for testing cancer drugs that will use the newest tools of precision medicine to select the best treatment for individual patients based on the genetic makeup of their tumors. The protocol, called NCI-Molecular Analysis for Therapy Choice (NCI-MATCH), will start with tumor biopsies from as

Mass spectrometric techniques for characterizing low-molecular-weight resins used as paint varnishes.

PubMed

Bonaduce, I; Colombini, M P; Degano, I; Di Girolamo, F; La Nasa, J; Modugno, F; Orsini, S

2013-01-01

The molecular structure of three low-molecular-weight resins used as paint varnishes has been characterized by use of an approach based on three different mass spectrometric techniques. We investigated the ketone resin MS2A, the aldehyde resin Laropal A81, and the hydrocarbon resin Regalrez 1094, now commonly used in restoration. To date, the molecular structures of these resins have not been completely elucidated. To improve current knowledge of the chemical composition of these materials, information obtained by gas chromatography-mass spectrometry (GC/MS), pyrolysis-gas chromatography-mass spectrometry (Py/GC/MS), and electrospray ionization mass spectrometry (ESI-Q-ToF) was combined. Analysis, in solution, of the whole polymeric fraction of the resins by flow-injection ESI-Q-ToF, and of the non-polymeric fraction by GC-MS, enabled us to identify previously unreported features of the polymer structures. In addition, the Py-GC/MS profiles that we obtained will help to enhance the databases currently available in the literature. The proposed approach can be extended to other low-molecular-weight resins used as varnishes in conservation.

Fractionation and characterization of dissolved organic matter (DOM) in refinery wastewater by revised phase retention and ion-exchange adsorption solid phase extraction followed by ESI FT-ICR MS.

PubMed

Fang, Zhi; He, Chen; Li, Yongyong; Chung, Keng H; Xu, Chunming; Shi, Quan

2017-01-01

Although the progress of high resolution mass spectrometry in the past decade has enabled the molecular characterization of dissolved organic matter (DOM) in water as a whole, fractionation of DOM is necessary for a comprehensive characterization due to its super-complex nature. Here we proposed a method for the fractionation of DOM in a wastewater based on solubility and acidic-basic properties. Solid phase extraction (SPE) cartridges with reversed phase retention and ion-exchange adsorption capacities, namely MAX and MCX, were used in succession to fractionate a petroleum refinery wastewater into four fractions: hydrophobic acid (HOA), hydrophobic neutral (HON), hydrophobic base (HOB), and hydrophilic substance (HIS) fractions. According to the total organic carbon (TOC) analysis, 72.6% (in term of TOC) of DOM was extracted in hydrophobic fractions, in which HON was the most abundant. Hydrophobic extracts were characterized by negative and positive ion electrospray (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), respectively. Compounds with multiple oxygen atoms were predominant in the HOA, which were responded strongly in the negative ESI MS. Nitrogen containing compounds were the major detected species by positive ion ESI in all hydrophobic fractions. The molecular composition of the DOM were discussed based on the FT-ICR MS results. The fractionation provided salt free samples which enables the direct analysis of the fractions by ESI and a deep insight into the molecular composition of DOM in the wastewater. The method is potential for routine evaluation of DOM in industry wastewaters, as well as environmental water samples. Copyright © 2016. Published by Elsevier B.V.

Ni-O4 species anchored on N-doped graphene-based materials as molecular entities and electrocatalytic performances for oxygen reduction reaction

NASA Astrophysics Data System (ADS)

Jang, Dawoon; Lee, Seungjun; Shin, Yunseok; Ohn, Saerom; Park, Sunghee; Lim, Donggyu; Park, Gilsoo; Park, Sungjin

2017-12-01

The generation of molecular active species on the surface of nano-materials has become promising routes to produce efficient electrocatalysts. Development of cost-effective catalysts with high performances for oxygen reduction reaction (ORR) is an important challenge for fuel cell and metal-air battery applications. In this work, we report a novel hybrid produced by room-temperature solution processes using Ni-based organometallic molecules and N-doped graphene-based materials. Chemical and structural characterizations reveal that Ni-containing species are well-dispersed on the surface of graphene network as molecular entity. The hybrid shows excellent electrocatalytic performances for ORR in basic medium with an onset potential of 0.87 V (vs. RHE), superior durability and good methanol tolerance.

Molecular Diode Studies Based on a Highly Sensitive Molecular Measurement Technique.

PubMed

Iwane, Madoka; Fujii, Shintaro; Kiguchi, Manabu

2017-04-26

In 1974, molecular electronics pioneers Mark Ratner and Arieh Aviram predicted that a single molecule could act as a diode, in which electronic current can be rectified. The electronic rectification property of the diode is one of basic functions of electronic components and since then, the molecular diode has been investigated as a first single-molecule device that would have a practical application. In this review, we first describe the experimental fabrication and electronic characterization techniques of molecular diodes consisting of a small number of molecules or a single molecule. Then, two main mechanisms of the rectification property of the molecular diode are discussed. Finally, representative results for the molecular diode are reviewed and a brief outlook on crucial issues that need to be addressed in future research is discussed.

Molecular Diode Studies Based on a Highly Sensitive Molecular Measurement Technique

PubMed Central

Iwane, Madoka; Fujii, Shintaro; Kiguchi, Manabu

2017-01-01

In 1974, molecular electronics pioneers Mark Ratner and Arieh Aviram predicted that a single molecule could act as a diode, in which electronic current can be rectified. The electronic rectification property of the diode is one of basic functions of electronic components and since then, the molecular diode has been investigated as a first single-molecule device that would have a practical application. In this review, we first describe the experimental fabrication and electronic characterization techniques of molecular diodes consisting of a small number of molecules or a single molecule. Then, two main mechanisms of the rectification property of the molecular diode are discussed. Finally, representative results for the molecular diode are reviewed and a brief outlook on crucial issues that need to be addressed in future research is discussed. PMID:28445393

Molecular Detection of Rickettsia africae in Amblyomma variegatum Collected from Sudan.

PubMed

Nakao, Ryo; Qiu, Yongjin; Salim, Bashir; Hassan, Shawgi Mohamed; Sugimoto, Chihiro

2015-05-01

Despite the increasing awareness of the importance of emerging vector-borne diseases, human tick-borne diseases, particularly rickettsial infections, are overlooked, especially in the countries such as Sudan with limited resources to perform molecular-based surveys. This study aimed at detection and genetic characterization of Rickettsia spp. in ticks collected from Sudan. The samples were first screened for the presence of rickettsial agents by gltA real-time PCR and subsequently characterized by gltA and ompA PCR and size-based multispacer typing. The results demonstrated the wide distribution of Rickettsia africae and/or closely related species across Sudan. The results of this report highlight the need for careful consideration of rickettsial infections in patients with nonmalarial febrile illness in this country. Nationwide surveillance on ticks associated with human rickettsial infections in Sudan is warranted.

Preparation and characterization of fusion processed solid dispersions containing a viscous thermally labile polymeric carrier.

PubMed

Hughey, Justin R; Keen, Justin M; Miller, Dave A; Brough, Chris; McGinity, James W

2012-11-15

The primary aim of the present study was to investigate the ability of hydroxypropyl and methoxyl substituted cellulose ethers to stabilize supersaturated concentrations of itraconazole (ITZ), a poorly water-soluble weak base, after an acid-to-neutral pH transition. A secondary aim of the study was to evaluate the effect of fusion processes on polymer stability and molecular weight. Polymer screening studies showed that stabilization of ITZ supersaturation was related to the molecular weight of the polymer and levels of hydroxypropyl and methoxyl substitution. METHOCEL E50LV (E50LV), which is characterized as having a high melt viscosity, was selected for solid dispersion formulation studies. Hot-melt extrusion processing of E50LV based compositions resulted in high torque loads, low material throughput and polymer degradation. KinetiSol Dispersing, a novel fusion based processing technique, was evaluated as a method to prepare the solid dispersions with reduced levels of polymer degradation. An experimental design revealed that polymer molecular weight was sensitive to shearing forces and high temperatures. However, optimal processing conditions resulted in significantly reduced E50LV degradation relative to HME processing. The technique was effectively utilized to prepare homogenous solid solutions of E50LV and ITZ, characterized as having a single glass transition temperature over a wide range of drug loadings. All prepared compositions provided for a high degree of ITZ supersaturation stabilization. Copyright © 2012 Elsevier B.V. All rights reserved.

New Researches and Application Progress of Commonly Used Optical Molecular Imaging Technology

PubMed Central

Chen, Zhi-Yi; Yang, Feng; Lin, Yan; Zhou, Qiu-Lan; Liao, Yang-Ying

2014-01-01

Optical molecular imaging, a new medical imaging technique, is developed based on genomics, proteomics and modern optical imaging technique, characterized by non-invasiveness, non-radiativity, high cost-effectiveness, high resolution, high sensitivity and simple operation in comparison with conventional imaging modalities. Currently, it has become one of the most widely used molecular imaging techniques and has been applied in gene expression regulation and activity detection, biological development and cytological detection, drug research and development, pathogenesis research, pharmaceutical effect evaluation and therapeutic effect evaluation, and so forth, This paper will review the latest researches and application progresses of commonly used optical molecular imaging techniques such as bioluminescence imaging and fluorescence molecular imaging. PMID:24696850

Detectable states, cycle fluxes, and motility scaling of molecular motor kinesin: An integrative kinetic graph theory analysis

NASA Astrophysics Data System (ADS)

Ren, Jie

2017-12-01

The process by which a kinesin motor couples its ATPase activity with concerted mechanical hand-over-hand steps is a foremost topic of molecular motor physics. Two major routes toward elucidating kinesin mechanisms are the motility performance characterization of velocity and run length, and single-molecular state detection experiments. However, these two sets of experimental approaches are largely uncoupled to date. Here, we introduce an integrative motility state analysis based on a theorized kinetic graph theory for kinesin, which, on one hand, is validated by a wealth of accumulated motility data, and, on the other hand, allows for rigorous quantification of state occurrences and chemomechanical cycling probabilities. An interesting linear scaling for kinesin motility performance across species is discussed as well. An integrative kinetic graph theory analysis provides a powerful tool to bridge motility and state characterization experiments, so as to forge a unified effort for the elucidation of the working mechanisms of molecular motors.

Molecular rheology of branched polymers: decoding and exploring the role of architectural dispersity through a synergy of anionic synthesis, interaction chromatography, rheometry and modeling.

PubMed

van Ruymbeke, E; Lee, H; Chang, T; Nikopoulou, A; Hadjichristidis, N; Snijkers, F; Vlassopoulos, D

2014-07-21

An emerging challenge in polymer physics is the quantitative understanding of the influence of a macromolecular architecture (i.e., branching) on the rheological response of entangled complex polymers. Recent investigations of the rheology of well-defined architecturally complex polymers have determined the composition in the molecular structure and identified the role of side-products in the measured samples. The combination of different characterization techniques, experimental and/or theoretical, represents the current state-of-the-art. Here we review this interdisciplinary approach to molecular rheology of complex polymers, and show the importance of confronting these different tools for ensuring an accurate characterization of a given polymeric sample. We use statistical tools in order to relate the information available from the synthesis protocols of a sample and its experimental molar mass distribution (typically obtained from size exclusion chromatography), and hence obtain precise information about its structural composition, i.e. enhance the existing sensitivity limit. We critically discuss the use of linear rheology as a reliable quantitative characterization tool, along with the recently developed temperature gradient interaction chromatography. The latter, which has emerged as an indispensable characterization tool for branched architectures, offers unprecedented sensitivity in detecting the presence of different molecular structures in a sample. Combining these techniques is imperative in order to quantify the molecular composition of a polymer and its consequences on the macroscopic properties. We validate this approach by means of a new model asymmetric comb polymer which was synthesized anionically. It was thoroughly characterized and its rheology was carefully analyzed. The main result is that the rheological signal reveals fine molecular details, which must be taken into account to fully elucidate the viscoelastic response of entangled branched polymers. It is important to appreciate that, even optimal model systems, i.e., those synthesized with high-vacuum anionic methods, need thorough characterization via a combination of techniques. Besides helping to improve synthetic techniques, this methodology will be significant in fine-tuning mesoscopic tube-based models and addressing outstanding issues such as the quantitative description of the constraint release mechanism.

Detection and Characterization of Circulating Tumor Associated Cells in Metastatic Breast Cancer.

PubMed

Mu, Zhaomei; Benali-Furet, Naoual; Uzan, Georges; Znaty, Anaëlle; Ye, Zhong; Paolillo, Carmela; Wang, Chun; Austin, Laura; Rossi, Giovanna; Fortina, Paolo; Yang, Hushan; Cristofanilli, Massimo

2016-09-30

The availability of blood-based diagnostic testing using a non-invasive technique holds promise for real-time monitoring of disease progression and treatment selection. Circulating tumor cells (CTCs) have been used as a prognostic biomarker for the metastatic breast cancer (MBC). The molecular characterization of CTCs is fundamental to the phenotypic identification of malignant cells and description of the relevant genetic alterations that may change according to disease progression and therapy resistance. However, the molecular characterization of CTCs remains a challenge because of the rarity and heterogeneity of CTCs and technological difficulties in the enrichment, isolation and molecular characterization of CTCs. In this pilot study, we evaluated circulating tumor associated cells in one blood draw by size exclusion technology and cytological analysis. Among 30 prospectively enrolled MBC patients, CTCs, circulating tumor cell clusters (CTC clusters), CTCs of epithelial-mesenchymal transition (EMT) and cancer associated macrophage-like cells (CAMLs) were detected and analyzed. For molecular characterization of CTCs, size-exclusion method for CTC enrichment was tested in combination with DEPArray™ technology, which allows the recovery of single CTCs or pools of CTCs as a pure CTC sample for mutation analysis. Genomic mutations of TP53 and ESR1 were analyzed by targeted sequencing on isolated 7 CTCs from a patient with MBC. The results of genomic analysis showed heterozygous TP53 R248W mutation from one single CTC and pools of three CTCs, and homozygous TP53 R248W mutation from one single CTC and pools of two CTCs. Wild-type ESR1 was detected in the same isolated CTCs. The results of this study reveal that size-exclusion method can be used to enrich and identify circulating tumor associated cells, and enriched CTCs were characterized for genetic alterations in MBC patients, respectively.

Data on the synthesis and mechanical characterization of polysiloxane-based urea-elastomers prepared from amino-terminated polydimethylsiloxanes and polydimethyl-methyl-phenyl-siloxane-copolymers.

PubMed

Riehle, Natascha; Götz, Tobias; Kandelbauer, Andreas; Tovar, Günter E M; Lorenz, Günter

2018-06-01

This article contains data on the synthesis and mechanical characterization of polysiloxane-based urea-elastomers (PSUs) and is related to the research article entitled "Influence of PDMS molecular weight on transparency and mechanical properties of soft polysiloxane-urea-elastomers for intraocular lens application" (Riehle et al., 2018) [1]. These elastomers were prepared by a two-step polyaddition using the aliphatic diisocyanate 4,4'-Methylenbis(cyclohexylisocyanate) (H 12 MDI), a siloxane-based chain extender 1,3-Bis(3-aminopropyl)-1,1,3,3-tetramethyldisiloxane (APTMDS) and amino-terminated polydimethylsiloxanes (PDMS) or polydimethyl-methyl-phenyl-siloxane-copolymers (PDMS-Me,Ph), respectively. (More details about the synthesis procedure and the reaction scheme can be found in the related research article (Riehle et al., 2018) [1]). Amino-terminated polydimethylsiloxanes with varying molecular weights and PDMS-Me,Ph-copolymers were prepared prior by a base-catalyzed ring-chain equilibration of a cyclic siloxane and the endblocker APTMDS. This DiB article contains a procedure for the synthesis of the base catalyst tetramethylammonium-3-aminopropyl-dimethylsilanolate and a generic synthesis procedure for the preparation of a PDMS having a targeted number average molecular weight M ¯ n of 3000 g mol -1 . Molecular weights and the amount of methyl-phenyl-siloxane within the polysiloxane-copolymers were determined by 1 H NMR and 29 Si NMR spectroscopy. The corresponding NMR spectra and data are described in this article. Additionally, this DiB article contains processed data on in line and off line FTIR-ATR spectroscopy, which was used to follow the reaction progress of the polyaddition by showing the conversion of the diisocyanate. All relevant IR band assignments of a polydimethylsiloxane-urea spectrum are described in this article. Finally, data on the tensile properties and the mechanical hysteresis-behaviour at 100% elongation of PDMS-based polyurea-elastomers are shown in dependence to the PDMS molecular weight.

'Ogura'-based 'CMS' lines with different nuclear backgrounds of cabbage revealed substantial diversity at morphological and molecular levels.

PubMed

Parkash, Chander; Kumar, Sandeep; Singh, Rajender; Kumar, Ajay; Kumar, Satish; Dey, Shyam Sundar; Bhatia, Reeta; Kumar, Raj

2018-01-01

A comprehensive study on characterization and genetic diversity analysis was carried out in 16 'Ogura'-based 'CMS' lines of cabbage using 14 agro-morphological traits and 29 SSR markers. Agro-morphological characterization depicted considerable variations for different horticultural traits studied. The genotype, ZHA-2, performed better for most of the economically important quantitative traits. Further, gross head weight (0.76), head length (0.60) and head width (0.83) revealed significant positive correlation with net head weight. Dendrogram based on 10 quantitative traits exhibited considerable diversity among different CMS lines and principle component analysis (PCA) indicated that net and gross head weight, and head length and width are the main components of divergence between 16 CMS lines of cabbage. In molecular study, a total of 58 alleles were amplified by 29 SSR primers, averaging to 2.0 alleles in each locus. High mean values of Shannon's Information index (0.62), expected (0.45) and observed (0.32) heterozygosity and polymorphic information content (0.35) depicted substantial polymorphism. Dendrogram based on Jaccard's similarity coefficient constructed two major groups and eight sub-groups, which revealed substantial diversity among different CMS lines. In overall, based on agro-morphological and molecular studies genotype RRMA, ZHA-2 and RCA were found most divergent. Hence, they have immense potential in future breeding programs for the high-yielding hybrid development in cabbage.

Solvent-based and solvent-free characterization of low solubility and low molecular weight polyamides by mass spectrometry: a complementary approach.

PubMed

Barrère, Caroline; Hubert-Roux, Marie; Lange, Catherine M; Rejaibi, Majed; Kebir, Nasreddine; Désilles, Nicolas; Lecamp, Laurence; Burel, Fabrice; Loutelier-Bourhis, Corinne

2012-06-15

Polyamides (PA) belong to the most used classes of polymers because of their attractive chemical and mechanical properties. In order to monitor original PA design, it is essential to develop analytical methods for the characterization of these compounds that are mostly insoluble in usual solvents. A low molecular weight polyamide (PA11), synthesized with a chain limiter, has been used as a model compound and characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). In the solvent-based approach, specific solvents for PA, i.e. trifluoroacetic acid (TFA) and hexafluoroisopropanol (HFIP), were tested. Solvent-based sample preparation methods, dried-droplet and thin layer, were optimized through the choice of matrix and salt. Solvent-based (thin layer) and solvent-free methods were then compared for this low solubility polymer. Ultra-high-performance liquid chromatography/electrospray ionization (UHPLC/ESI)-TOF-MS analyses were then used to confirm elemental compositions through accurate mass measurement. Sodium iodide (NaI) and 2,5-dihydroxybenzoic acid (2,5-DHB) are, respectively, the best cationizing agent and matrix. The dried-droplet sample preparation method led to inhomogeneous deposits, but the thin-layer method could overcome this problem. Moreover, the solvent-free approach was the easiest and safest sample preparation method giving equivalent results to solvent-based methods. Linear as well as cyclic oligomers were observed. Although the PA molecular weights obtained by MALDI-TOF-MS were lower than those obtained by (1)H NMR and acido-basic titration, this technique allowed us to determine the presence of cyclic and linear species, not differentiated by the other techniques. TFA was shown to induce modification of linear oligomers that permitted cyclic and linear oligomers to be clearly highlighted in spectra. Optimal sample preparation conditions were determined for the MALDI-TOF-MS analysis of PA11, a model of polyamide analogues. The advantages of the solvent-free and solvent-based approaches were shown. Molecular weight determination using MALDI was discussed. Copyright © 2012 John Wiley & Sons, Ltd.

How to detect carbapenemase producers? A literature review of phenotypic and molecular methods.

PubMed

Hammoudi, D; Moubareck, C Ayoub; Sarkis, D Karam

2014-12-01

This review describes the current state-of-art of carbapenemase detection methods. Identification of carbapenemases is first based on conventional phenotypic tests including antimicrobial susceptibility testing, modified-Hodge test and carbapenemase-inhibitor culture tests. Second, molecular characterization of carbapenemase genes by PCR sequencing is essential. Third, innovative biochemical and spectrometric detection may be applied. Copyright © 2014 Elsevier B.V. All rights reserved.

Smoothed-particle hydrodynamics and nonequilibrium molecular dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hoover, W. G.; Hoover, C. G.

1993-08-01

Gingold, Lucy, and Monaghan invented a grid-free version of continuum mechanics ``smoothed-particle hydrodynamics,`` in 1977. It is a likely contributor to ``hybrid`` simulations combining atomistic and continuum simulations. We describe applications of this particle-based continuum technique from the closely-related standpoint of nonequilibrium molecular dynamics. We compare chaotic Lyapunov spectra for atomistic solids and fluids with those which characterize a two-dimensional smoothed-particle fluid system.

Occurrence of Cryptosporidium and Giardia in recycled waters used for irrigation and first description of Cryptosporidium parvum and C. muris in Greece.

PubMed

Spanakos, Gregory; Biba, Anastasia; Mavridou, Athena; Karanis, Panagiotis

2015-05-01

Here, we present the first time findings regarding the occurrence of Cryptosporidium and Giardia in sewage waters and the first molecular characterization of Cryptosporidium species in Greece. Biological treatment plants from three regions in Greece have been investigated. The detection of Cryptosporidium oocysts was by modified Ziehl-Neelsen acid fast (MZN-AF) and by immunofluorescence microscopy (IFT) for Cryptosporidium and Giardia (oo)cysts, whereas nested PCR based on the SSU rDNA assay was used for molecular detection of Cryptosporidium followed by sequencing for the genetic characterization of the species. In total, 73 samples (37 raw sewage samples and 38 of treated water samples) were collected and analyzed. Of the 73 water samples, 4 samples were Cryptosporidium-positive by IFT and staining, 12 samples were Cryptosporidium-positive by nested PCR; 9 samples were Giardia-positive by IFT. We showed that Cryptosporidium cysts are found both in the input and the discharge of the biological treatment plants. Molecular characterization of Cryptosporidium based on the small subunit ribosomal DNA gene resulted in the determination of Cryptosporidium parvum and Cryptosporidium muris Greek isolates. This is the first report of Cryptosporidium and Giardia occurrence in wastewaters and the first molecular identification of Cryptosporidium species in Greek environments. As the treated water is used for irrigation, or it is discharged into the sea, our findings indicate that biological treatment facilities constitute a possible risk for public health because the related species are prevalent in humans; the results invite for further epidemiological investigations to evaluate the real public health risk in Greece.

Molecular Characterization of Hypoderma SPP. in Domestic Ruminants from Turkey and Pakistan.

PubMed

Ahmed, Haroon; Simsek, Sami; Saki, Cem Ecmel; Kesik, Harun Kaya; Kilinc, Seyma Gunyakti

2017-08-01

The aim of this study was to determine the morphological and molecular characterization of Hypoderma spp. in cattle and yak from provinces in Turkey and Pakistan. In total, 78 Hypoderma larvae were collected from slaughtered animals in Turkey and Pakistan from October 2015 to January 2016. Thirty-eight of these 78 Hypoderma larvae were morphologically classified as third instar larvae (L3s) of Hypoderma bovis, 37 were classified as Hypoderma lineatum, and 3 were classified as suspected or unidentified. The restriction enzyme TaqI was used to differentiate the Hypoderma spp. by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP). According to the sequences and the PCR-RFLP results, all larval samples from cattle from Turkey were classified as H. bovis, except for 1 sample classified as H. lineatum. All Hypoderma larvae from Pakistan were classified as H. lineatum from cattle and as Hypoderma sinense from yak. This study provides the first molecular characterization of H. lineatum (cattle) and H. sinense (yak) in Pakistan based on PCR-RFLP and sequencing results.

Turning Defense into Offense: Defensin Mimetics as Novel Antibiotics Targeting Lipid II

PubMed Central

Ateh, Eugene; Oashi, Taiji; Lu, Wuyuan; Huang, Jing; Diepeveen-de Buin, Marlies; Bryant, Joseph; Breukink, Eefjan; MacKerell, Alexander D.; de Leeuw, Erik P. H.

2013-01-01

We have previously reported on the functional interaction of Lipid II with human alpha-defensins, a class of antimicrobial peptides. Lipid II is an essential precursor for bacterial cell wall biosynthesis and an ideal and validated target for natural antibiotic compounds. Using a combination of structural, functional and in silico analyses, we present here the molecular basis for defensin-Lipid II binding. Based on the complex of Lipid II with Human Neutrophil peptide-1, we could identify and characterize chemically diverse low-molecular weight compounds that mimic the interactions between HNP-1 and Lipid II. Lead compound BAS00127538 was further characterized structurally and functionally; it specifically interacts with the N-acetyl muramic acid moiety and isoprenyl tail of Lipid II, targets cell wall synthesis and was protective in an in vivo model for sepsis. For the first time, we have identified and characterized low molecular weight synthetic compounds that target Lipid II with high specificity and affinity. Optimization of these compounds may allow for their development as novel, next generation therapeutic agents for the treatment of Gram-positive pathogenic infections. PMID:24244161

Ferrocene-Alkynyl Conjugated Molecular Wires: Synthesis, Characterization, and Conductance Properties.

PubMed

Yuan, Ye; Yan, Jian-Feng; Lin, Da-Qiang; Mao, Bing-Wei; Yuan, Yao-Feng

2018-03-07

A novel series of 1,2,3-substituted ferrocene-based wires a1-a2 and b4-b5 have been synthesized by using an iterative Pd-mediated Sonogashira cross-coupling methodology. The molecular structures of a2 and b3 were determined by single-crystal X-ray analysis. Electrochemical data showed that there was a strong electronic communication among the ferrocenyl moieties in b1-b5. The UV absorption spectra indicated that replacing the 1,1'-substituted ferrocene unit with a 1,2,3-substituted ferrocene moiety causes delocalization of electrons in the extended π orbitals. The self-assembled monolayers of wire a1 and a2 on Au surfaces have been comprehensively characterized by electrochemistry and scanning tunneling microscopy break junction. The data demonstrated that 1,2,3-substituted ferrocene-based wires reduced the intermolecular π-π stacking, and furthermore solved the rotation problem in the 1,1'-substituted ferrocene-based wires. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

High Resolution PET Imaging Probe for the Detection, Molecular Characterization and Treatment Monitoring of Prostate Cancer

DTIC Science & Technology

2010-07-01

W81XWH-09-1-0420 TITLE: High Resolution PET Imaging Probe for the Detection, Molecular Characterization and Treatment Monitoring of Prostate Cancer...4. TITLE AND SUBTITLE High-Resolution PET Imaging Probe for the Detection, Molecular Characterization and Treatment of Prostate Cancer... molecular imaging for diagnosis as well as treatment planning and monitoring in prostate cancer. This investigation hypothesizes that a dedicated

Pediatric Glioblastoma Therapies Based on Patient-Derived Stem Cell Resources

DTIC Science & Technology

2013-10-01

stem cell lines have been successfully isolated from adults, in this proposal we aim to isolate and characterize GSC populations from pediatric patients. In the past two years we have successfully derived and cultured eight patient-derived pediatric glioma stem cell lines. In the past year we have continued molecular and phenotypic characterization of these lines. This characterization included analysis of gene expression and patient-specific gene mutations, and also proof-of-concept shRNA screens. In addition we have begun to identify candidate

Characterization of buried metal-molecule-metal junctions using Fourier transform infrared microspectroscopy

NASA Astrophysics Data System (ADS)

Babayco, Christopher B.; Land, Donald P.; Parikh, Atul N.; Kiehl, Richard A.

2014-09-01

We have devised an infrared spectromicroscopy based experimental configuration to enable structural characterization of buried molecular junctions. Our design utilizes a small mercury drop at the focal point of an infrared microscope to act as a mirror in studying metal-molecule-metal (MmM) junctions. An organic molecular monolayer is formed either directly on the mercury drop or on a thin, infrared (IR) semi-transparent layer of Au deposited onto an IR transparent, undoped silicon substrate. Following the formation of the monolayer, films on either metal can be examined independently using specular reflection spectroscopy. Furthermore, by bringing together the two monolayers, a buried molecular bilayer within the MmM junction can be characterized. Independent examination of each half of the junction prior to junction formation also allows probing any structural and/or conformational changes that occur as a result of forming the bilayer. Because our approach allows assembling and disassembling microscopic junctions by forming and withdrawing Hg drops onto the monolayer covered metal, spatial mapping of junctions can be performed simply by translating the location of the derivatized silicon wafer. Finally, the applicability of this technique for the longer-term studies of changes in molecular structure in the presence of electrical bias is discussed.

Molecular characterization, biological forms and sporozoite rate of Anopheles stephensi in southern Iran

PubMed Central

Chavshin, Ali Reza; Oshaghi, Mohammad Ali; Vatandoost, Hasan; Hanafi-Bojd, Ahmad Ali; Raeisi, Ahmad; Nikpoor, Fatemeh

2014-01-01

Objective To identify the biological forms, sporozoite rate and molecular characterization of the Anopheles stephensi (An. stephensi) in Hormozgan and Sistan-Baluchistan provinces, the most important malarious areas in Iran. Methods Wild live An. stephensi samples were collected from different malarious areas in southern Iran. The biological forms were identified based on number of egg-ridges. Molecular characterization of biological forms was verified by analysis of the mitochondrial cytochrome oxidase subunit I and II (mtDNA-COI/COII). The Plasmodium infection was examined in the wild female specimens by species-specific nested–PCR method. Results Results showed that all three biological forms including mysorensis, intermediate and type are present in the study areas. Molecular investigations revealed no genetic variation between mtDNA COI/COII sequences of the biological forms and no Plasmodium parasites was detected in the collected mosquito samples. Conclusions Presence of three biological forms with identical sequences showed that the known biological forms belong to a single taxon and the various vectorial capacities reported for these forms are more likely corresponded to other epidemiological factors than to the morphotype of the populations. Lack of malaria parasite infection in An. stephensi, the most important vector of malaria, may be partly due to the success and achievement of ongoing active malaria control program in the region. PMID:24144130

First molecular characterization of canine hepatozoonosis in Argentina: evaluation of asymptomatic Hepatozoon canis infection in dogs from Buenos Aires.

PubMed

Eiras, Diego Fernando; Basabe, Julia; Scodellaro, Carla F; Banach, Diana B; Matos, María L; Krimer, Alejandro; Baneth, Gad

2007-11-10

Canine hepatozoonosis is an expanding tick-borne disease in Argentina. Hepatozoonosis was studied during 1 year in six dogs from the same household in Buenos Aires. Blood parasitemia with Hepatozoon gamonts was found in five dogs and all six were positive by PCR for Hepatozoon sp. Although the levels of parasitemia fluctuated during the year, no clinical signs of disease were detected during the follow up period. Amplification and sequencing of a 650 bases fragment of the 18S rRNA gene from all six dogs yielded fragments that were 99% identical to H. canis. The results of the partial 18S rRNA genotyping with the sub-clinical course of infection and lack of severe hematological abnormalities are compatible with clinical and molecular descriptions of Hepatozoon canis infection from other areas of the world. This is the first molecular characterization of Hepatozoon from Argentina.

Trimetallic oxide nanocomposites of transition metals titanium and vanadium by sol-gel technique: synthesis, characterization and electronic properties

NASA Astrophysics Data System (ADS)

Kumar, Amit; Mishra, Neeraj Kumar; Sachan, Komal; Ali, Md Asif; Soaham Gupta, Sachchidanand; Singh, Rajeev

2018-04-01

Novel titanium and vanadium based trimetallic oxide nanocomposites (TMONCs) have been synthesized using metal salts of titanium-vanadium along with three others metals viz. tin, aluminium and zinc as precursors by the sol-gel method. Aqueous ammonia and hydrazine hydrate were used as the reducing agents. The preparations of nanocomposites were monitored by observing the visual changes during each step of synthesis. The synthesized TMONCs were characterized using UV–vis, SEM, EDX, TEM and DLS. Band gap of the synthesized TMONCs ranges from 3–4.5 eV determined using tauc plot. FTIR study revealed the molecular stretching and bending peaks of corresponding M–O/M–O–M bonds thus confirming their formation. Molecular composition and particle size were determined using EDX and DLS respectively. Molecular shape, size and surface morphology have been examined by SEM and TEM.

Near-monodisperse sodium polymethacrylates: characterization by linear salt gradient anion-exchange chromatography

PubMed

Freydank; Krasia; Tiddy; Patrickios

2000-05-01

A family of six near-monodisperse homopolymers of sodium methacrylate (Mn = 1100, 3200, 5500, 7200, 14100, and 21000) is characterized by linear salt gradient anion-exchange chromatography. Although the retention times depend on the initial and final salt concentrations of the gradient, they are almost independent of the molecular weight of poly(sodium methacrylate). This suggests that anion-exchange chromatography is incapable of resolving mixtures of a given polyelectrolyte to their components of various molecular weights, and it is therefore impossible to identify the polydispersity of such a sample using this method. The independence of the retention times from molecular weight is also predicted by a theory based on stoichiometric mass-action ion-exchange. Using this theory and our experimental retention times, the equilibrium anion-exchange constant and the corresponding Gibbs free energy of anion-exchange of the monomer repeat unit are calculated to be around 2.1 and -1.8 kJ/mol, respectively.

Microfluidic Exosome Analysis toward Liquid Biopsy for Cancer.

PubMed

He, Mei; Zeng, Yong

2016-08-01

Assessment of a tumor's molecular makeup using biofluid samples, known as liquid biopsy, is a prominent research topic in precision medicine for cancer, due to its noninvasive property allowing repeat sampling for monitoring molecular changes of tumors over time. Circulating exosomes recently have been recognized as promising tumor surrogates because they deliver enriched biomarkers, such as proteins, RNAs, and DNA. However, purification and characterization of these exosomes are technically challenging. Microfluidic lab-on-a-chip technology effectively addresses these challenges owing to its inherent advantages in integration and automation of multiple functional modules, enhancing sensing performance, and expediting analysis processes. In this article, we review the state-of-the-art development of microfluidic technologies for exosome isolation and molecular characterization with emphasis on their applications toward liquid biopsy-based analysis of cancer. Finally, we share our perspectives on current challenges and future directions of microfluidic exosome analysis. © 2016 Society for Laboratory Automation and Screening.

Anaplastic Thyroid Carcinoma: Current Treatments and Potential New Therapeutic Options with Emphasis on TfR1/CD71

PubMed Central

Salvatorelli, Lucia; Magro, Gaetano

2014-01-01

Anaplastic thyroid carcinoma (ATC) is one of the most aggressive human cancers. Actually, ATC is refractory to conventional therapies, including surgery, chemotherapy, radiotherapy, and radioiodine (131I) therapy. Accordingly, genetic and molecular characterizations of ATC have been frequently and periodically reviewed in order to identify potential biological markers exploitable for target therapy. This review briefly focuses on main molecular events that characterize ATC and provides an update about preclinical studies. In addition, the overexpression of transferrin receptor 1 (TfR1/CD71) by neoplastic cells of ATC is emphasized in that it could represent a potential therapeutic target. In this regard, new therapeutic approaches based on the use of monoclonal or recombinant antibodies, or transferrin-gallium-TfR1/CD71 molecular complexes, or lastly small interfering RNAs (siRNAs) are proposed. PMID:25097549

Positional cloning in maize (Zea mays subsp. mays, Poaceae)1

PubMed Central

Gallavotti, Andrea; Whipple, Clinton J.

2015-01-01

• Premise of the study: Positional (or map-based) cloning is a common approach to identify the molecular lesions causing mutant phenotypes. Despite its large and complex genome, positional cloning has been recently shown to be feasible in maize, opening up a diverse collection of mutants to molecular characterization. • Methods and Results: Here we outline a general protocol for positional cloning in maize. While the general strategy is similar to that used in other plant species, we focus on the unique resources and approaches that should be considered when applied to maize mutants. • Conclusions: Positional cloning approaches are appropriate for maize mutants and quantitative traits, opening up to molecular characterization the large array of genetic diversity in this agronomically important species. The cloning approach described should be broadly applicable to other species as more plant genomes become available. PMID:25606355

Targeting PSMA by radioligands in non-prostate disease-current status and future perspectives.

PubMed

Backhaus, Philipp; Noto, Benjamin; Avramovic, Nemanja; Grubert, Lena Sophie; Huss, Sebastian; Bögemann, Martin; Stegger, Lars; Weckesser, Matthias; Schäfers, Michael; Rahbar, Kambiz

2018-05-01

Prostate-specific membrane antigen (PSMA) is the up-and-coming target for molecular imaging of prostate cancer. Despite its name, non-prostate-related PSMA expression in physiologic tissue as well as in benign and malignant disease has been reported in various publications. Unlike in prostate cancer, PSMA expression is only rarely observed in non-prostate tumor cells. Instead, expression occurs in endothelial cells of tumor-associated neovasculature, although no endothelial expression is observed under physiologic conditions. The resulting potential for tumor staging in non-prostate malignant tumors has been demonstrated in first patient studies. This review summarizes the first clinical studies and deduces future perspectives in staging, molecular characterization, and PSMA-targeted radionuclide therapy based on histopathologic examinations of PSMA expression. The non-exclusivity of PSMA in prostate cancer opens a window to utilize the spectrum of available radioactive PSMA ligands for imaging and molecular characterization and maybe even therapy of non-prostate disease.

Neutron Reflectivity as a Tool for Physics-Based Studies of Model Bacterial Membranes.

PubMed

Barker, Robert D; McKinley, Laura E; Titmuss, Simon

2016-01-01

The principles of neutron reflectivity and its application as a tool to provide structural information at the (sub-) molecular unit length scale from models for bacterial membranes are described. The model membranes can take the form of a monolayer for a single leaflet spread at the air/water interface, or bilayers of increasing complexity at the solid/liquid interface. Solid-supported bilayers constrain the bilayer to 2D but can be used to characterize interactions with antimicrobial peptides and benchmark high throughput lab-based techniques. Floating bilayers allow for membrane fluctuations, making the phase behaviour more representative of native membranes. Bilayers of varying levels of compositional accuracy can now be constructed, facilitating studies with aims that range from characterizing the fundamental physical interactions, through to the characterization of accurate mimetics for the inner and outer membranes of Gram-negative bacteria. Studies of the interactions of antimicrobial peptides with monolayer and bilayer models for the inner and outer membranes have revealed information about the molecular control of the outer membrane permeability, and the mode of interaction of antimicrobials with both inner and outer membranes.

Biological intuition in alignment-free methods: response to Posada.

PubMed

Ragan, Mark A; Chan, Cheong Xin

2013-08-01

A recent editorial in Journal of Molecular Evolution highlights opportunities and challenges facing molecular evolution in the era of next-generation sequencing. Abundant sequence data should allow more-complex models to be fit at higher confidence, making phylogenetic inference more reliable and improving our understanding of evolution at the molecular level. However, concern that approaches based on multiple sequence alignment may be computationally infeasible for large datasets is driving the development of so-called alignment-free methods for sequence comparison and phylogenetic inference. The recent editorial characterized these approaches as model-free, not based on the concept of homology, and lacking in biological intuition. We argue here that alignment-free methods have not abandoned models or homology, and can be biologically intuitive.

Direction-dependent secondary bonds and their stepwise melting in a uracil-based molecular crystal studied by infrared spectroscopy and theoretical modeling

NASA Astrophysics Data System (ADS)

Szekrényes, Zsolt; Nagy, Péter R.; Tarczay, György; Maggini, Laura; Bonifazi, Davide; Kamarás, Katalin

2018-01-01

Three types of supramolecular interactions are identified in the three crystallographic directions in crystals of 1,4-bis[(1-hexylurac-6-yl) ethynyl]benzene, a uracil-based molecule with a linear backbone. These three interactions, characterized by their strongest component, are: intermolecular double H-bonds along the molecular axis, London dispersion interaction of hexyl chains connecting these linear assemblies, and π - π stacking of the aromatic rings perpendicular to the molecular planes. On heating, two transitions happen, disordering of hexyl chains at 473 K, followed by H-bond melting at 534 K. The nature of the bonds and transitions was established by matrix-isolation and temperature-dependent infrared spectroscopy and supported by theoretical computations.

Evolution of microbiological analytical methods for dairy industry needs

PubMed Central

Sohier, Danièle; Pavan, Sonia; Riou, Armelle; Combrisson, Jérôme; Postollec, Florence

2014-01-01

Traditionally, culture-based methods have been used to enumerate microbial populations in dairy products. Recent developments in molecular methods now enable faster and more sensitive analyses than classical microbiology procedures. These molecular tools allow a detailed characterization of cell physiological states and bacterial fitness and thus, offer new perspectives to integration of microbial physiology monitoring to improve industrial processes. This review summarizes the methods described to enumerate and characterize physiological states of technological microbiota in dairy products, and discusses the current deficiencies in relation to the industry’s needs. Recent studies show that Polymerase chain reaction-based methods can successfully be applied to quantify fermenting microbes and probiotics in dairy products. Flow cytometry and omics technologies also show interesting analytical potentialities. However, they still suffer from a lack of validation and standardization for quality control analyses, as reflected by the absence of performance studies and official international standards. PMID:24570675

Evolution of microbiological analytical methods for dairy industry needs.

PubMed

Sohier, Danièle; Pavan, Sonia; Riou, Armelle; Combrisson, Jérôme; Postollec, Florence

2014-01-01

Traditionally, culture-based methods have been used to enumerate microbial populations in dairy products. Recent developments in molecular methods now enable faster and more sensitive analyses than classical microbiology procedures. These molecular tools allow a detailed characterization of cell physiological states and bacterial fitness and thus, offer new perspectives to integration of microbial physiology monitoring to improve industrial processes. This review summarizes the methods described to enumerate and characterize physiological states of technological microbiota in dairy products, and discusses the current deficiencies in relation to the industry's needs. Recent studies show that Polymerase chain reaction-based methods can successfully be applied to quantify fermenting microbes and probiotics in dairy products. Flow cytometry and omics technologies also show interesting analytical potentialities. However, they still suffer from a lack of validation and standardization for quality control analyses, as reflected by the absence of performance studies and official international standards.

Toward Personalized Targeted Therapeutics: An Overview.

PubMed

Weathers, Shiao-Pei S; Gilbert, Mark R

2017-04-01

In neuro-oncology, there has been a movement towards personalized medicine, or tailoring treatment to the individual patient. Ideally, tumor and patient evaluations would lead to the selection of the best treatment (based on tumor characterization) and the right dosing schedule (based on patient characterization). The recent advances in the molecular analysis of glioblastoma have created optimism that personalized targeted therapy is within reach. Although our understanding of the molecular complexity of glioblastoma has increased over the years, the path to developing effective targeted therapeutic strategies is wrought with many challenges, as described in this review. These challenges include disease heterogeneity, clinical and genomic patient variability, limited number of effective treatments, clinical trial inefficiency, drug delivery, and clinical trial support and accrual. To confront these challenges, it will be imperative to devise innovative and adaptive clinical trials in order to accelerate our efforts in improving the outcomes for our patients who have been in desperate need.

Molecular bases of circadian rhythmicity in renal physiology and pathology

PubMed Central

Bonny, Olivier; Vinciguerra, Manlio; Gumz, Michelle L.; Mazzoccoli, Gianluigi

2013-01-01

The physiological processes that maintain body homeostasis oscillate during the day. Diurnal changes characterize kidney functions, comprising regulation of hydro-electrolytic and acid-base balance, reabsorption of small solutes and hormone production. Renal physiology is characterized by 24-h periodicity and contributes to circadian variability of blood pressure levels, related as well to nychthemeral changes of sodium sensitivity, physical activity, vascular tone, autonomic function and neurotransmitter release from sympathetic innervations. The circadian rhythmicity of body physiology is driven by central and peripheral biological clockworks and entrained by the geophysical light/dark cycle. Chronodisruption, defined as the mismatch between environmental–social cues and physiological–behavioral patterns, causes internal desynchronization of periodic functions, leading to pathophysiological mechanisms underlying degenerative, immune related, metabolic and neoplastic diseases. In this review we will address the genetic, molecular and anatomical elements that hardwire circadian rhythmicity in renal physiology and subtend disarray of time–dependent changes in renal pathology. PMID:23901050

Hybrid nanomembrane-based capacitors for the determination of the dielectric constant of semiconducting molecular ensembles.

PubMed

Petrini, Paula A; Silva, Ricardo M L; de Oliveira, Rafael F; Merces, Leandro; Bof Bufon, Carlos C

2018-06-29

Considerable advances in the field of molecular electronics have been achieved over the recent years. One persistent challenge, however, is the exploitation of the electronic properties of molecules fully integrated into devices. Typically, the molecular electronic properties are investigated using sophisticated techniques incompatible with a practical device technology, such as the scanning tunneling microscopy. The incorporation of molecular materials in devices is not a trivial task as the typical dimensions of electrical contacts are much larger than the molecular ones. To tackle this issue, we report on hybrid capacitors using mechanically-compliant nanomembranes to encapsulate ultrathin molecular ensembles for the investigation of molecular dielectric properties. As the prototype material, copper (II) phthalocyanine (CuPc) has been chosen as information on its dielectric constant (k CuPc ) at the molecular scale is missing. Here, hybrid nanomembrane-based capacitors containing metallic nanomembranes, insulating Al 2 O 3 layers, and the CuPc molecular ensembles have been fabricated and evaluated. The Al 2 O 3 is used to prevent short circuits through the capacitor plates as the molecular layer is considerably thin (<30 nm). From the electrical measurements of devices with molecular layers of different thicknesses, the CuPc dielectric constant has been reliably determined (k CuPc  = 4.5 ± 0.5). These values suggest a mild contribution of the molecular orientation on the CuPc dielectric properties. The reported nanomembrane-based capacitor is a viable strategy for the dielectric characterization of ultrathin molecular ensembles integrated into a practical, real device technology.

Hybrid nanomembrane-based capacitors for the determination of the dielectric constant of semiconducting molecular ensembles

NASA Astrophysics Data System (ADS)

Petrini, Paula A.; Silva, Ricardo M. L.; de Oliveira, Rafael F.; Merces, Leandro; Bof Bufon, Carlos C.

2018-06-01

Considerable advances in the field of molecular electronics have been achieved over the recent years. One persistent challenge, however, is the exploitation of the electronic properties of molecules fully integrated into devices. Typically, the molecular electronic properties are investigated using sophisticated techniques incompatible with a practical device technology, such as the scanning tunneling microscopy. The incorporation of molecular materials in devices is not a trivial task as the typical dimensions of electrical contacts are much larger than the molecular ones. To tackle this issue, we report on hybrid capacitors using mechanically-compliant nanomembranes to encapsulate ultrathin molecular ensembles for the investigation of molecular dielectric properties. As the prototype material, copper (II) phthalocyanine (CuPc) has been chosen as information on its dielectric constant (k CuPc) at the molecular scale is missing. Here, hybrid nanomembrane-based capacitors containing metallic nanomembranes, insulating Al2O3 layers, and the CuPc molecular ensembles have been fabricated and evaluated. The Al2O3 is used to prevent short circuits through the capacitor plates as the molecular layer is considerably thin (<30 nm). From the electrical measurements of devices with molecular layers of different thicknesses, the CuPc dielectric constant has been reliably determined (k CuPc = 4.5 ± 0.5). These values suggest a mild contribution of the molecular orientation on the CuPc dielectric properties. The reported nanomembrane-based capacitor is a viable strategy for the dielectric characterization of ultrathin molecular ensembles integrated into a practical, real device technology.

Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics.

PubMed

Hirsch, B; Endris, V; Lassmann, S; Weichert, W; Pfarr, N; Schirmacher, P; Kovaleva, V; Werner, M; Bonzheim, I; Fend, F; Sperveslage, J; Kaulich, K; Zacher, A; Reifenberger, G; Köhrer, K; Stepanow, S; Lerke, S; Mayr, T; Aust, D E; Baretton, G; Weidner, S; Jung, A; Kirchner, T; Hansmann, M L; Burbat, L; von der Wall, E; Dietel, M; Hummel, M

2018-04-01

The simultaneous detection of multiple somatic mutations in the context of molecular diagnostics of cancer is frequently performed by means of amplicon-based targeted next-generation sequencing (NGS). However, only few studies are available comparing multicenter testing of different NGS platforms and gene panels. Therefore, seven partner sites of the German Cancer Consortium (DKTK) performed a multicenter interlaboratory trial for targeted NGS using the same formalin-fixed, paraffin-embedded (FFPE) specimen of molecularly pre-characterized tumors (n = 15; each n = 5 cases of Breast, Lung, and Colon carcinoma) and a colorectal cancer cell line DNA dilution series. Detailed information regarding pre-characterized mutations was not disclosed to the partners. Commercially available and custom-designed cancer gene panels were used for library preparation and subsequent sequencing on several devices of two NGS different platforms. For every case, centrally extracted DNA and FFPE tissue sections for local processing were delivered to each partner site to be sequenced with the commercial gene panel and local bioinformatics. For cancer-specific panel-based sequencing, only centrally extracted DNA was analyzed at seven sequencing sites. Subsequently, local data were compiled and bioinformatics was performed centrally. We were able to demonstrate that all pre-characterized mutations were re-identified correctly, irrespective of NGS platform or gene panel used. However, locally processed FFPE tissue sections disclosed that the DNA extraction method can affect the detection of mutations with a trend in favor of magnetic bead-based DNA extraction methods. In conclusion, targeted NGS is a very robust method for simultaneous detection of various mutations in FFPE tissue specimens if certain pre-analytical conditions are carefully considered.

Novel method for the determination of average molecular weight of natural polymers based on 2D DOSY NMR and chemometrics: Example of heparin.

PubMed

Monakhova, Yulia B; Diehl, Bernd W K; Do, Tung X; Schulze, Margit; Witzleben, Steffen

2018-02-05

Apart from the characterization of impurities, the full characterization of heparin and low molecular weight heparin (LMWH) also requires the determination of average molecular weight, which is closely related to the pharmaceutical properties of anticoagulant drugs. To determine average molecular weight of these animal-derived polymer products, partial least squares regression (PLS) was utilized for modelling of diffused-ordered spectroscopy NMR data (DOSY) of a representative set of heparin (n=32) and LMWH (n=30) samples. The same sets of samples were measured by gel permeation chromatography (GPC) to obtain reference data. The application of PLS to the data led to calibration models with root mean square error of prediction of 498Da and 179Da for heparin and LMWH, respectively. The average coefficients of variation (CVs) did not exceed 2.1% excluding sample preparation (by successive measuring one solution, n=5) and 2.5% including sample preparation (by preparing and analyzing separate samples, n=5). An advantage of the method is that the sample after standard 1D NMR characterization can be used for the molecular weight determination without further manipulation. The accuracy of multivariate models is better than the previous results for other matrices employing internal standards. Therefore, DOSY experiment is recommended to be employed for the calculation of molecular weight of heparin products as a complementary measurement to standard 1D NMR quality control. The method can be easily transferred to other matrices as well. Copyright © 2017 Elsevier B.V. All rights reserved.

[Morphological and molecular characterization of isolates of Macrophomina phaseolina associated with sugarcane in Mexico].

PubMed

Leyva-Mir, Santos G; Velázquez-Martínez, Guadalupe C; Tlapal-Bolaños, Bertha; Tovar-Pedraza, Juan M; Rosas-Saito, Greta H; Alvarado-Gómez, Omar G

2015-01-01

Charcoal rot caused by Macrophomina phaseolina is an important disease of sugarcane in Mexico. This study was carried out to characterize isolates of M. phaseolina obtained from sugarcane by the combination of morphological and molecular analyses. The morphological characterization of 10 isolates was performed using scanning electron microscopy and light microscopy. To confirm the morphological identification, rDNA from two representative isolates was extracted, and the internal transcribed spacer (ITS) region was amplified by polymerase chain reaction and sequenced using specific primers MpKF1 and MpKR1. Based on their morphological characteristics, all isolates were identified as M. phaseolina. Moreover, the analysis of two ITS sequences showed 100% similarity with the M. phaseolina sequences deposited in the GenBank. To our knowledge, this is the first study in the world aimed at characterizing isolates of M. phaseolina obtained from sugarcane. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Molecular Markers and Targeted Therapeutics in Metastatic Tumors of the Spine: Changing the Treatment Paradigms.

PubMed

Goodwin, C Rory; Abu-Bonsrah, Nancy; Rhines, Laurence D; Verlaan, Jorrit-Jan; Bilsky, Mark H; Laufer, Ilya; Boriani, Stefano; Sciubba, Daniel M; Bettegowda, Chetan

2016-10-15

A review of the literature. The aim of this study was to discuss the evolution of molecular signatures and the history and development of targeted therapeutics in metastatic tumor types affecting the spinal column. Molecular characterization of metastatic spine tumors is expected to usher in a revolution in diagnostic and treatment paradigms. Molecular characterization will provide critical information that can be used for initial diagnosis, prognosticating the ideal treatment strategy, assessment of treatment efficacy, surveillance and monitoring recurrence, and predicting complications, clinical outcome, and overall survival in patients diagnosed with metastatic cancers to the spinal column. A review of the literature was performed focusing on illustrative examples of the role that molecular-based therapeutics have played in clinical outcomes for patients diagnosed with metastatic tumor types affecting the spinal column. The impact of molecular therapeutics including receptor tyrosine kinases and immune checkpoint inhibitors and the ability of molecular signatures to provide prognostic information are discussed in metastatic breast cancer, lung cancer, prostate cancer, melanoma, and renal cell cancer affecting the spinal column. For the providers who will ultimately counsel patients diagnosed with metastases to the spinal column, molecular advancements will radically alter the management/surgical paradigms utilized. Ultimately, the translation of these molecular advancements into routine clinical care will greatly improve the quality and quantity of life for patients diagnosed with spinal malignancies and provide better overall outcomes and counseling for treating physicians. N/A.

Application of supervised and unsupervised tools to direct effects-based monitoring efforts in the Great Lakes areas of concern: Maumee River, Ohio

EPA Science Inventory

Effects-based approaches that employ molecular and tissue level tools to detect and characterize biological responses to contaminants can be a useful complement to chemical monitoring approaches. When the source/type of contamination is known, a predetermined, or supervised, set...

Improved Prediction of Blood-Brain Barrier Permeability Through Machine Learning with Combined Use of Molecular Property-Based Descriptors and Fingerprints.

PubMed

Yuan, Yaxia; Zheng, Fang; Zhan, Chang-Guo

2018-03-21

Blood-brain barrier (BBB) permeability of a compound determines whether the compound can effectively enter the brain. It is an essential property which must be accounted for in drug discovery with a target in the brain. Several computational methods have been used to predict the BBB permeability. In particular, support vector machine (SVM), which is a kernel-based machine learning method, has been used popularly in this field. For SVM training and prediction, the compounds are characterized by molecular descriptors. Some SVM models were based on the use of molecular property-based descriptors (including 1D, 2D, and 3D descriptors) or fragment-based descriptors (known as the fingerprints of a molecule). The selection of descriptors is critical for the performance of a SVM model. In this study, we aimed to develop a generally applicable new SVM model by combining all of the features of the molecular property-based descriptors and fingerprints to improve the accuracy for the BBB permeability prediction. The results indicate that our SVM model has improved accuracy compared to the currently available models of the BBB permeability prediction.

Transcriptome-wide analysis of WRKY transcription factors in wheat and their leaf rust responsive expression profiling.

PubMed

Satapathy, Lopamudra; Singh, Dharmendra; Ranjan, Prashant; Kumar, Dhananjay; Kumar, Manish; Prabhu, Kumble Vinod; Mukhopadhyay, Kunal

2014-12-01

WRKY, a plant-specific transcription factor family, has important roles in pathogen defense, abiotic cues and phytohormone signaling, yet little is known about their roles and molecular mechanism of function in response to rust diseases in wheat. We identified 100 TaWRKY sequences using wheat Expressed Sequence Tag database of which 22 WRKY sequences were novel. Identified proteins were characterized based on their zinc finger motifs and phylogenetic analysis clustered them into six clades consisting of class IIc and class III WRKY proteins. Functional annotation revealed major functions in metabolic and cellular processes in control plants; whereas response to stimuli, signaling and defense in pathogen inoculated plants, their major molecular function being binding to DNA. Tag-based expression analysis of the identified genes revealed differential expression between mock and Puccinia triticina inoculated wheat near isogenic lines. Gene expression was also performed with six rust-related microarray experiments at Gene Expression Omnibus database. TaWRKY10, 15, 17 and 56 were common in both tag-based and microarray-based differential expression analysis and could be representing rust specific WRKY genes. The obtained results will bestow insight into the functional characterization of WRKY transcription factors responsive to leaf rust pathogenesis that can be used as candidate genes in molecular breeding programs to improve biotic stress tolerance in wheat.

Free Energy Computations by Minimization of Kullback-Leibler Divergence: An Efficient Adaptive Biasing Potential Method for Sparse Representations

DTIC Science & Technology

2011-10-14

landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells and...statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells and estimating the free energy...experimentally, to characterize global changes as well as investigate relative stabilities. In most applications, a brute- force computation based on

Molecular characterization of Fagaceae species using inter-primer binding site (iPBS) markers.

PubMed

Coutinho, João Paulo; Carvalho, Ana; Martín, Antonio; Lima-Brito, José

2018-04-01

Retrotransposons (RTNs) contribute for genome evolution, influencing its size and structure. We investigated the utility of the RTN-based markers inter-primer binding site (iPBS) for the molecular characterization of 25 Fagaceae species from genera Castanea, Fagus and Quercus. The assessment of genetic diversity, relationships and structure, as well as taxonomic classification of Fagaceae based on molecular data is important for definition of conservation, forestry management strategies and discrimination among natural hybrids and their parents since natural hybridization may increase with the climate changes. Here, iPBS primers designed by other authors were tested alone and combined. Some of them were discriminative, revealed polymorphism within and among taxa allowing the production of a total of 150 iPBS markers. In addition, several monomorphic iPBS markers were also amplified in each taxon. The UPGMA dendrogram based on the pooled iPBS data revealed 27% of genetic similarity among species. The individuals were clustered per genus and most of the oaks per infrageneric group corroborating the adopted taxonomy. Globally, the iPBS markers demonstrated suitability for DNA fingerprinting, determination of phylogenies and taxonomic discrimination in Fagaceae, and could constitute a useful and alternative tool for germplasm characterization, and for definition of conservation strategies and forestry management. Moreover, these markers would be useful for fingerprinting natural hybrids that share morphological similarities with their parents. Since iPBS markers could also enable insights about RTNs evolution, an eventual correlation among iPBS polymorphism, variability of RTN insertions and/or genome size in Fagaceae is discussed.

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids.

PubMed

Tan, Kemin; Chang, Changsoo; Cuff, Marianne; Osipiuk, Jerzy; Landorf, Elizabeth; Mack, Jamey C; Zerbs, Sarah; Joachimiak, Andrzej; Collart, Frank R

2013-10-01

Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins. Copyright © 2013 Wiley Periodicals, Inc.

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids

PubMed Central

Tan, Kemin; Chang, Changsoo; Cuff, Marianne; Osipiuk, Jerzy; Landorf, Elizabeth; Mack, Jamey C.; Zerbs, Sarah; Joachimiak, Andrzej; Collart, Frank R.

2013-01-01

Lignin comprises 15.25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP.binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute.binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins. PMID:23606130

Dynamic characterization of viscoelastic polymer solutions in a lubricated cylinder - Plate apparatus

NASA Technical Reports Server (NTRS)

Doremus, P.; Piau, J. M.; Altman, R. L.

1987-01-01

The characterization of several viscoelastic lubricants which are oil or water based has been studied in an apparatus consisting of a lubricated cylinder-plate contact. The friction loads were measured as a function of speed. The experimental results show the influence of the molecular weight and of the concentration of the polymeric additive as well as the influence of the viscosity of the oil-base on the load and friction coefficient. Also a test for mechanical degradation was performed on the polymer solutions. Several additives can favor a viscoelastic lubrication.

Detection and Characterization of Viral Species/Subspecies Using Isothermal Recombinase Polymerase Amplification (RPA) Assays.

PubMed

Glais, Laurent; Jacquot, Emmanuel

2015-01-01

Numerous molecular-based detection protocols include an amplification step of the targeted nucleic acids. This step is important to reach the expected sensitive detection of pathogens in diagnostic procedures. Amplifications of nucleic acid sequences are generally performed, in the presence of appropriate primers, using thermocyclers. However, the time requested to amplify molecular targets and the cost of the thermocycler machines could impair the use of these methods in routine diagnostics. Recombinase polymerase amplification (RPA) technique allows rapid (short-term incubation of sample and primers in an enzymatic mixture) and simple (isothermal) amplification of molecular targets. RPA protocol requires only basic molecular steps such as extraction procedures and agarose gel electrophoresis. Thus, RPA can be considered as an interesting alternative to standard molecular-based diagnostic tools. In this paper, the complete procedures to set up an RPA assay, applied to detection of RNA (Potato virus Y, Potyvirus) and DNA (Wheat dwarf virus, Mastrevirus) viruses, are described. The proposed procedure allows developing species- or subspecies-specific detection assay.

Structural and physicochemical characterization of pyridine derivative salts of anti-inflammatory drugs

NASA Astrophysics Data System (ADS)

Nechipadappu, Sunil Kumar; Trivedi, Darshak R.

2017-08-01

Salts of common anti-inflammatory drugs mefenamic acid (MFA), tolfenamic acid (TFA) and naproxen (NPX) with various pyridine derivatives (4-amino pyridine (4AP), 4-dimethylaminopyridine (DMAP) and 2-amino pyridine (2AP)) were synthesized by crystal engineering approach based on the pKa values of API's and the salt former. All the salts were characterized systematically by various spectroscopic methods including FT-IR and 1H NMR and the crystal structure was determined by single-crystal X-ray diffraction techniques (SCXRD). DMAP salt of NPX and 2AP salts of MFA and TFA were not obtained in the salt screening experiments. All the molecular salts exhibited 1:1 molecular stoichiometry in the asymmetric unit and except NPX-2AP salt, all the molecular salts included a water molecule in the crystal lattice. Physicochemical and structural properties between drug-drug molecular salts of MFA-4AP, TFA-4AP and NPX-4AP have been evaluated and it was found that these molecular salts were found to be stable for a time period of six months at ambient condition and further hydration of molecular salts were not observed even at accelerated humid conditions (∼75% RH). It was found that 4AP salts of MFA and TFA and DMAP salts of MFA and TFA are isostructural.

Recent Advances in Cardiac Computed Tomography: Dual Energy, Spectral and Molecular CT Imaging

PubMed Central

Danad, Ibrahim; Fayad, Zahi A.; Willemink, Martin J.; Min, James K.

2015-01-01

Computed tomography (CT) evolved into a powerful diagnostic tool and it is impossible to imagine current clinical practice without CT imaging. Due to its widespread availability, ease of clinical application, superb sensitivity for detection of CAD, and non-invasive nature, CT has become a valuable tool within the armamentarium of the cardiologist. In the last few years, numerous technological advances in CT have occurred—including dual energy CT (DECT), spectral CT and CT-based molecular imaging. By harnessing the advances in technology, cardiac CT has advanced beyond the mere evaluation of coronary stenosis to an imaging modality tool that permits accurate plaque characterization, assessment of myocardial perfusion and even probing of molecular processes that are involved in coronary atherosclerosis. Novel innovations in CT contrast agents and pre-clinical spectral CT devices have paved the way for CT-based molecular imaging. PMID:26068288

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

PubMed

Linehan, W Marston; Spellman, Paul T; Ricketts, Christopher J; Creighton, Chad J; Fei, Suzanne S; Davis, Caleb; Wheeler, David A; Murray, Bradley A; Schmidt, Laura; Vocke, Cathy D; Peto, Myron; Al Mamun, Abu Amar M; Shinbrot, Eve; Sethi, Anurag; Brooks, Samira; Rathmell, W Kimryn; Brooks, Angela N; Hoadley, Katherine A; Robertson, A Gordon; Brooks, Denise; Bowlby, Reanne; Sadeghi, Sara; Shen, Hui; Weisenberger, Daniel J; Bootwalla, Moiz; Baylin, Stephen B; Laird, Peter W; Cherniack, Andrew D; Saksena, Gordon; Haake, Scott; Li, Jun; Liang, Han; Lu, Yiling; Mills, Gordon B; Akbani, Rehan; Leiserson, Mark D M; Raphael, Benjamin J; Anur, Pavana; Bottaro, Donald; Albiges, Laurence; Barnabas, Nandita; Choueiri, Toni K; Czerniak, Bogdan; Godwin, Andrew K; Hakimi, A Ari; Ho, Thai H; Hsieh, James; Ittmann, Michael; Kim, William Y; Krishnan, Bhavani; Merino, Maria J; Mills Shaw, Kenna R; Reuter, Victor E; Reznik, Ed; Shelley, Carl S; Shuch, Brian; Signoretti, Sabina; Srinivasan, Ramaprasad; Tamboli, Pheroze; Thomas, George; Tickoo, Satish; Burnett, Kenneth; Crain, Daniel; Gardner, Johanna; Lau, Kevin; Mallery, David; Morris, Scott; Paulauskis, Joseph D; Penny, Robert J; Shelton, Candace; Shelton, W Troy; Sherman, Mark; Thompson, Eric; Yena, Peggy; Avedon, Melissa T; Bowen, Jay; Gastier-Foster, Julie M; Gerken, Mark; Leraas, Kristen M; Lichtenberg, Tara M; Ramirez, Nilsa C; Santos, Tracie; Wise, Lisa; Zmuda, Erik; Demchok, John A; Felau, Ina; Hutter, Carolyn M; Sheth, Margi; Sofia, Heidi J; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C; Zhang, Jiashan; Ayala, Brenda; Baboud, Julien; Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; Wan, Yunhu; Wu, Ye; Ally, Adrian; Balasundaram, Miruna; Balu, Saianand; Beroukhim, Rameen; Bodenheimer, Tom; Buhay, Christian; Butterfield, Yaron S N; Carlsen, Rebecca; Carter, Scott L; Chao, Hsu; Chuah, Eric; Clarke, Amanda; Covington, Kyle R; Dahdouli, Mahmoud; Dewal, Ninad; Dhalla, Noreen; Doddapaneni, Harsha V; Drummond, Jennifer A; Gabriel, Stacey B; Gibbs, Richard A; Guin, Ranabir; Hale, Walker; Hawes, Alicia; Hayes, D Neil; Holt, Robert A; Hoyle, Alan P; Jefferys, Stuart R; Jones, Steven J M; Jones, Corbin D; Kalra, Divya; Kovar, Christie; Lewis, Lora; Li, Jie; Ma, Yussanne; Marra, Marco A; Mayo, Michael; Meng, Shaowu; Meyerson, Matthew; Mieczkowski, Piotr A; Moore, Richard A; Morton, Donna; Mose, Lisle E; Mungall, Andrew J; Muzny, Donna; Parker, Joel S; Perou, Charles M; Roach, Jeffrey; Schein, Jacqueline E; Schumacher, Steven E; Shi, Yan; Simons, Janae V; Sipahimalani, Payal; Skelly, Tara; Soloway, Matthew G; Sougnez, Carrie; Tam, Angela; Tan, Donghui; Thiessen, Nina; Veluvolu, Umadevi; Wang, Min; Wilkerson, Matthew D; Wong, Tina; Wu, Junyuan; Xi, Liu; Zhou, Jane; Bedford, Jason; Chen, Fengju; Fu, Yao; Gerstein, Mark; Haussler, David; Kasaian, Katayoon; Lai, Phillip; Ling, Shiyun; Radenbaugh, Amie; Van Den Berg, David; Weinstein, John N; Zhu, Jingchun; Albert, Monique; Alexopoulou, Iakovina; Andersen, Jeremiah J; Auman, J Todd; Bartlett, John; Bastacky, Sheldon; Bergsten, Julie; Blute, Michael L; Boice, Lori; Bollag, Roni J; Boyd, Jeff; Castle, Erik; Chen, Ying-Bei; Cheville, John C; Curley, Erin; Davies, Benjamin; DeVolk, April; Dhir, Rajiv; Dike, Laura; Eckman, John; Engel, Jay; Harr, Jodi; Hrebinko, Ronald; Huang, Mei; Huelsenbeck-Dill, Lori; Iacocca, Mary; Jacobs, Bruce; Lobis, Michael; Maranchie, Jodi K; McMeekin, Scott; Myers, Jerome; Nelson, Joel; Parfitt, Jeremy; Parwani, Anil; Petrelli, Nicholas; Rabeno, Brenda; Roy, Somak; Salner, Andrew L; Slaton, Joel; Stanton, Melissa; Thompson, R Houston; Thorne, Leigh; Tucker, Kelinda; Weinberger, Paul M; Winemiller, Cynthia; Zach, Leigh Anne; Zuna, Rosemary

2016-01-14

Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist. We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis. Type 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH). Type 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).

Overproduction, purification and characterization of human interferon alpha2a-human serum albumin fusion protein produced in methilotropic yeast Pichia pastoris

NASA Astrophysics Data System (ADS)

Ningrum, R. A.; Santoso, A.; Herawati, N.

2017-05-01

Human interferon alpha2a (hIFNα2a) is a therapeutic protein that used in cancer and hepatitis B/C therapy. The main problem of using hIFNα-2a is its short elimination half life due to its low molecular weight. Development of higher molecular weight protein by albumin fusion technology is a rational strategy to solve the problem. In our previous research we constructed an open reading frame (ORF) encoding hIFNα2a-human serum albumin (HSA) fusion protein that expressed in Pichia pastoris (P. pastoris) protease deficient strain SMD1168. This research was performed to overproduce, purify and characterize the fusion protein. To overproduce the protein, cultivation was performed in buffered complex medium containing glyserol (BMGY) for 24 h and protein overproduction was applied in buffered complex medium containing methanol (BMMY) for 48 hours at 30°C. The fusion protein was purified by blue sepharose affinity chromatography. Molecular weight characterization by SDS PAGE corresponds with its theoretical size, 85 kDa. Western blot analysis demonstrated that the fusion protein was recognized by anti hIFNα2 and anti HSA monoclonal antibody as well. Amino acid sequence of the fusion protein was determined by LC MS/MS2 mass spectrometry with trypsin as proteolitic enzyme. There were three fragments that identified as hIFNα2a and seven fragments that identified as HSA. Total identified amino acids were 150 residues with 20% coverage from total residues. To conclude, hIFNα2a-HSA fusion protein was overproduced, purified and characterized. Characterization based on molecular weight, antibody recognition and amino acid sequence confirmed that the fusion protein has correct identity as theoretically thought.

A network of molecular switches controls the activation of the two-component response regulator NtrC

NASA Astrophysics Data System (ADS)

Vanatta, Dan K.; Shukla, Diwakar; Lawrenz, Morgan; Pande, Vijay S.

2015-06-01

Recent successes in simulating protein structure and folding dynamics have demonstrated the power of molecular dynamics to predict the long timescale behaviour of proteins. Here, we extend and improve these methods to predict molecular switches that characterize conformational change pathways between the active and inactive state of nitrogen regulatory protein C (NtrC). By employing unbiased Markov state model-based molecular dynamics simulations, we construct a dynamic picture of the activation pathways of this key bacterial signalling protein that is consistent with experimental observations and predicts new mutants that could be used for validation of the mechanism. Moreover, these results suggest a novel mechanistic paradigm for conformational switching.

Sequencing-based breast cancer diagnostics as an alternative to routine biomarkers.

PubMed

Rantalainen, Mattias; Klevebring, Daniel; Lindberg, Johan; Ivansson, Emma; Rosin, Gustaf; Kis, Lorand; Celebioglu, Fuat; Fredriksson, Irma; Czene, Kamila; Frisell, Jan; Hartman, Johan; Bergh, Jonas; Grönberg, Henrik

2016-11-30

Sequencing-based breast cancer diagnostics have the potential to replace routine biomarkers and provide molecular characterization that enable personalized precision medicine. Here we investigate the concordance between sequencing-based and routine diagnostic biomarkers and to what extent tumor sequencing contributes clinically actionable information. We applied DNA- and RNA-sequencing to characterize tumors from 307 breast cancer patients with replication in up to 739 patients. We developed models to predict status of routine biomarkers (ER, HER2,Ki-67, histological grade) from sequencing data. Non-routine biomarkers, including mutations in BRCA1, BRCA2 and ERBB2(HER2), and additional clinically actionable somatic alterations were also investigated. Concordance with routine diagnostic biomarkers was high for ER status (AUC = 0.95;AUC(replication) = 0.97) and HER2 status (AUC = 0.97;AUC(replication) = 0.92). The transcriptomic grade model enabled classification of histological grade 1 and histological grade 3 tumors with high accuracy (AUC = 0.98;AUC(replication) = 0.94). Clinically actionable mutations in BRCA1, BRCA2 and ERBB2(HER2) were detected in 5.5% of patients, while 53% had genomic alterations matching ongoing or concluded breast cancer studies. Sequencing-based molecular profiling can be applied as an alternative to histopathology to determine ER and HER2 status, in addition to providing improved tumor grading and clinically actionable mutations and molecular subtypes. Our results suggest that sequencing-based breast cancer diagnostics in a near future can replace routine biomarkers.

Nanogap structures for molecular nanoelectronics.

PubMed

Motto, Paolo; Dimonte, Alice; Rattalino, Ismael; Demarchi, Danilo; Piccinini, Gianluca; Civera, Pierluigi

2012-02-09

This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes.

Molecular Diagnostics in Pathology: Time for a Next-Generation Pathologist?

PubMed

Fassan, Matteo

2018-03-01

- Comprehensive molecular investigations of mainstream carcinogenic processes have led to the use of effective molecular targeted agents in most cases of solid tumors in clinical settings. - To update readers regarding the evolving role of the pathologist in the therapeutic decision-making process and the introduction of next-generation technologies into pathology practice. - Current literature on the topic, primarily sourced from the PubMed (National Center for Biotechnology Information, Bethesda, Maryland) database, were reviewed. - Adequate evaluation of cytologic-based and tissue-based predictive diagnostic biomarkers largely depends on both proper pathologic characterization and customized processing of biospecimens. Moreover, increased requests for molecular testing have paralleled the recent, sharp decrease in tumor material to be analyzed-material that currently comprises cytology specimens or, at minimum, small biopsies in most cases of metastatic/advanced disease. Traditional diagnostic pathology has been completely revolutionized by the introduction of next-generation technologies, which provide multigene, targeted mutational profiling, even in the most complex of clinical cases. Combining traditional and molecular knowledge, pathologists integrate the morphological, clinical, and molecular dimensions of a disease, leading to a proper diagnosis and, therefore, the most-appropriate tailored therapy.

Discovering interesting molecular substructures for molecular classification.

PubMed

Lam, Winnie W M; Chan, Keith C C

2010-06-01

Given a set of molecular structure data preclassified into a number of classes, the molecular classification problem is concerned with the discovering of interesting structural patterns in the data so that "unseen" molecules not originally in the dataset can be accurately classified. To tackle the problem, interesting molecular substructures have to be discovered and this is done typically by first representing molecular structures in molecular graphs, and then, using graph-mining algorithms to discover frequently occurring subgraphs in them. These subgraphs are then used to characterize different classes for molecular classification. While such an approach can be very effective, it should be noted that a substructure that occurs frequently in one class may also does occur in another. The discovering of frequent subgraphs for molecular classification may, therefore, not always be the most effective. In this paper, we propose a novel technique called mining interesting substructures in molecular data for classification (MISMOC) that can discover interesting frequent subgraphs not just for the characterization of a molecular class but also for the distinguishing of it from the others. Using a test statistic, MISMOC screens each frequent subgraph to determine if they are interesting. For those that are interesting, their degrees of interestingness are determined using an information-theoretic measure. When classifying an unseen molecule, its structure is then matched against the interesting subgraphs in each class and a total interestingness measure for the unseen molecule to be classified into a particular class is determined, which is based on the interestingness of each matched subgraphs. The performance of MISMOC is evaluated using both artificial and real datasets, and the results show that it can be an effective approach for molecular classification.

Synthesis of surface molecular imprinted polymers based on carboxyl-modified silica nanoparticles with the selective detection of dibutyl phthalate from tap water samples

NASA Astrophysics Data System (ADS)

Xu, Wanzhen; Zhang, Xiaoming; Huang, Weihong; Luan, Yu; Yang, Yanfei; Zhu, Maiyong; Yang, Wenming

2017-12-01

In this work, the molecular imprinted polymers were synthesized with the low monomer concentrations for dibutyl phthalate (DBP). The polymers were prepared over carboxyl-modified silica nanoparticle, which used methacrylic acid as the functional monomer, ethylene glycol dimethacrylate as the cross-linker agent and azoisobutyronitrile as the initiator in the process of preparation. Various measures were used to characterize the structure and morphology in order to get the optimal polymer. The characterization results show that the optimal polymer has suitable features for further adsorption process. And adsorption capacity experiments were evaluated to analyze its adsorption performance, through adsorption isotherms/kinetics, selectivity adsorption and desorption and regeneration experiments. These results showed that the molecular imprinted polymers had a short equilibrium time about 60 min and high stability with 88% after six cycles. Furthermore, the molecular imprinted polymers were successfully applied to remove dibutyl phthalate. The concentration range was 5.0-30.0 μmol L-1, and the limit of detection was 0.06 μmol L-1 in tap water samples.

Synthesis, characterization and biological application of four novel metal-Schiff base complexes derived from allylamine and their interactions with human serum albumin: Experimental, molecular docking and ONIOM computational study.

PubMed

Kazemi, Zahra; Rudbari, Hadi Amiri; Sahihi, Mehdi; Mirkhani, Valiollah; Moghadam, Majid; Tangestaninejad, Shahram; Mohammadpoor-Baltork, Iraj; Gharaghani, Sajjad

2016-09-01

Novel metal-based drug candidate including VOL2, NiL2, CuL2 and PdL2 have been synthesized from 2-hydroxy-1-allyliminomethyl-naphthalen ligand and have been characterized by means of elemental analysis (CHN), FT-IR and UV-vis spectroscopies. In addition, (1)H and (13)C NMR techniques were employed for characterization of the PdL2 complex. Single-crystal X-ray diffraction technique was utilized to characterise the structure of the complexes. The Cu(II), Ni(II) and Pd(II) complexes show a square planar trans-coordination geometry, while in the VOL2, the vanadium center has a distorted tetragonal pyramidal N2O3 coordination sphere. The HSA-binding was also determined, using fluorescence quenching, UV-vis spectroscopy, and circular dichroism (CD) titration method. The obtained results revealed that the HSA affinity for binding the synthesized compounds follows as PdL2>CuL2>VOL2>NiL2, indicating the effect of metal ion on binding constant. The distance between these compounds and HSA was obtained based on the Förster's theory of non-radiative energy transfer. Furthermore, computational methods including molecular docking and our Own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) were carried out to investigate the HSA-binding of the compounds. Molecular docking calculation indicated the existence of hydrogen bond between amino acid residues of HSA and all synthesized compounds. The formation of the hydrogen bond in the HSA-compound systems leads to their stabilization. The ONIOM method was utilized in order to investigate HSA binding of compounds more precisely in which molecular mechanics method (UFF) and semi empirical method (PM6) were selected for the low layer and the high layer, respectively. The results show that the structural parameters of the compounds changed along with binding to HSA, indicating the strong interaction between the compounds and HSA. The value of binding constant depends on the extent of the resultant changes. This should be mentioned that both theoretical methods calculated the Kb values in the same sequence and are in a good agreement with the experimental data. Copyright © 2016 Elsevier B.V. All rights reserved.

MOLECULAR CHARACTERIZATION OF VIBRIO CHOLERAE GENES FLGO AND FLGP

DTIC Science & Technology

2006-12-01

From - To) 25-01-2007 THESIS 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER MOLECULAR CHARACTERIZATION OF VIBRIO CHOLERAE GENES FLGO AND FLGP 5b. GRANT...CHARACTERIZATION OF VIBRIO CHOLERAE GENES FLGO AND FLGP by DAVID C. MORRIS, B.S. THESIS Presented to the Graduate Faculty of The University of Texas at San Antonio...U.S. Air Force for providing me the opportunity and means to complete the thesis. December 2006 v MOLECULAR CHARACTERIZATION OF VIBRIO CHOLERAE GENES

Surface, Water and Air Biocharacterization - A Comprehensive Characterization of Microorganisms and Allergens in Spacecraft Environment

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Ott, C. Mark; Cruz, Patricia; Buttner, Mark P.

2009-01-01

A Comprehensive Characterization of Microorganisms and Allergens in Spacecraft (SWAB) will use advanced molecular techniques to comprehensively evaluate microbes on board the space station, including pathogens (organisms that may cause disease). It also will track changes in the microbial community as spacecraft visit the station and new station modules are added. This study will allow an assessment of the risk of microbes to the crew and the spacecraft. Research Summary: Previous microbial analysis of spacecraft only identify microorganisms that will grow in culture, omitting greater than 90% of all microorganisms including pathogens such as Legionella (the bacterium which causes Legionnaires' disease) and Cryptosporidium (a parasite common in contaminated water) The incidence of potent allergens, such as dust mites, has never been systematically studied in spacecraft environments and microbial toxins have not been previously monitored. This study will use modern molecular techniques to identify microorganisms and allergens. Direct sampling of the ISS allows identification of the microbial communities present, and determination of whether these change or mutate over time. SWAB complements the nominal ISS environmental monitoring by providing a comparison of analyses from current media-based and advanced molecular-based technologies.

3D-liquid chromatography as a complex mixture characterization tool for knowledge-based downstream process development.

PubMed

Hanke, Alexander T; Tsintavi, Eleni; Ramirez Vazquez, Maria Del Pilar; van der Wielen, Luuk A M; Verhaert, Peter D E M; Eppink, Michel H M; van de Sandt, Emile J A X; Ottens, Marcel

2016-09-01

Knowledge-based development of chromatographic separation processes requires efficient techniques to determine the physicochemical properties of the product and the impurities to be removed. These characterization techniques are usually divided into approaches that determine molecular properties, such as charge, hydrophobicity and size, or molecular interactions with auxiliary materials, commonly in the form of adsorption isotherms. In this study we demonstrate the application of a three-dimensional liquid chromatography approach to a clarified cell homogenate containing a therapeutic enzyme. Each separation dimension determines a molecular property relevant to the chromatographic behavior of each component. Matching of the peaks across the different separation dimensions and against a high-resolution reference chromatogram allows to assign the determined parameters to pseudo-components, allowing to determine the most promising technique for the removal of each impurity. More detailed process design using mechanistic models requires isotherm parameters. For this purpose, the second dimension consists of multiple linear gradient separations on columns in a high-throughput screening compatible format, that allow regression of isotherm parameters with an average standard error of 8%. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1283-1291, 2016. © 2016 American Institute of Chemical Engineers.

Consortium for Molecular Characterization of Screen-Detected Lesions Created: Eight Grants Awarded | Division of Cancer Prevention

Cancer.gov

The NCI has awarded eight grants to create the Consortium for Molecular Characterization of Screen-Detected Lesions. The consortium has seven molecular characterization laboratories (MCLs) and a coordinating center, and is supported by the Division of Cancer Prevention and the Division of Cancer Biology. | 7 laboratories and a coordinating center focused on identifying

A critique of the molecular target-based drug discovery paradigm based on principles of metabolic control: advantages of pathway-based discovery.

PubMed

Hellerstein, Marc K

2008-01-01

Contemporary drug discovery and development (DDD) is dominated by a molecular target-based paradigm. Molecular targets that are potentially important in disease are physically characterized; chemical entities that interact with these targets are identified by ex vivo high-throughput screening assays, and optimized lead compounds enter testing as drugs. Contrary to highly publicized claims, the ascendance of this approach has in fact resulted in the lowest rate of new drug approvals in a generation. The primary explanation for low rates of new drugs is attrition, or the failure of candidates identified by molecular target-based methods to advance successfully through the DDD process. In this essay, I advance the thesis that this failure was predictable, based on modern principles of metabolic control that have emerged and been applied most forcefully in the field of metabolic engineering. These principles, such as the robustness of flux distributions, address connectivity relationships in complex metabolic networks and make it unlikely a priori that modulating most molecular targets will have predictable, beneficial functional outcomes. These same principles also suggest, however, that unexpected therapeutic actions will be common for agents that have any effect (i.e., that complexity can be exploited therapeutically). A potential operational solution (pathway-based DDD), based on observability rather than predictability, is described, focusing on emergent properties of key metabolic pathways in vivo. Recent examples of pathway-based DDD are described. In summary, the molecular target-based DDD paradigm is built on a naïve and misleading model of biologic control and is not heuristically adequate for advancing the mission of modern therapeutics. New approaches that take account of and are built on principles described by metabolic engineers are needed for the next generation of DDD.

CAPILLARY CONDENSATION IN MMS AND PORE STRUCTURE CHARACTERIZATION. (R825959)

EPA Science Inventory

Phenomena of capillary condensation and desorption in siliceous mesoporous molecular sieves (MMS) with cylindrical channels are studied by means of the non-local density functional theory (NLDFT). The results are compared with macroscopic thermodynamic approaches based on Kelv...

Toxico-Cheminformatics and QSPR Modeling of the Carcinogenic Potency Database

EPA Science Inventory

Report on the development of a tiered, confirmatory scheme for prediction of chemical carcinogenicity based on QSAR studies of compounds with available mutagenic and carcinogenic data. For 693 such compounds from the Carcinogenic Potency Database characterized molecular topologic...

Geometrical eigen-subspace framework based molecular conformation representation for efficient structure recognition and comparison

NASA Astrophysics Data System (ADS)

Li, Xiao-Tian; Yang, Xiao-Bao; Zhao, Yu-Jun

2017-04-01

We have developed an extended distance matrix approach to study the molecular geometric configuration through spectral decomposition. It is shown that the positions of all atoms in the eigen-space can be specified precisely by their eigen-coordinates, while the refined atomic eigen-subspace projection array adopted in our approach is demonstrated to be a competent invariant in structure comparison. Furthermore, a visual eigen-subspace projection function (EPF) is derived to characterize the surrounding configuration of an atom naturally. A complete set of atomic EPFs constitute an intrinsic representation of molecular conformation, based on which the interatomic EPF distance and intermolecular EPF distance can be reasonably defined. Exemplified with a few cases, the intermolecular EPF distance shows exceptional rationality and efficiency in structure recognition and comparison.

Note: A short-pulse high-intensity molecular beam valve based on a piezoelectric stack actuator

NASA Astrophysics Data System (ADS)

Abeysekera, Chamara; Joalland, Baptiste; Shi, Yuanyuan; Kamasah, Alexander; Oldham, James M.; Suits, Arthur G.

2014-11-01

Solenoid and piezoelectric disk valves, which are widely used to generate molecular beam pulses, still suffer from significant restrictions, such as pulse durations typically >50 μs, low repetition rates, and limited gas flows and operational times. Much of this arises owing to the limited forces these actuators can achieve. To overcome these limitations, we have developed a new pulsed valve based on a high-force piezoelectric stack actuator. We show here that operation with pulse durations as low as 20 μs and repetition rates up to 100 Hz can be easily achieved by operating the valve in conjunction with a commercial fast high-voltage switch. We outline our design and demonstrate its performance with molecular beam characterization via velocity map ion imaging.

Note: a short-pulse high-intensity molecular beam valve based on a piezoelectric stack actuator.

PubMed

Abeysekera, Chamara; Joalland, Baptiste; Shi, Yuanyuan; Kamasah, Alexander; Oldham, James M; Suits, Arthur G

2014-11-01

Solenoid and piezoelectric disk valves, which are widely used to generate molecular beam pulses, still suffer from significant restrictions, such as pulse durations typically >50 μs, low repetition rates, and limited gas flows and operational times. Much of this arises owing to the limited forces these actuators can achieve. To overcome these limitations, we have developed a new pulsed valve based on a high-force piezoelectric stack actuator. We show here that operation with pulse durations as low as 20 μs and repetition rates up to 100 Hz can be easily achieved by operating the valve in conjunction with a commercial fast high-voltage switch. We outline our design and demonstrate its performance with molecular beam characterization via velocity map ion imaging.

New Image-Based Techniques for Prostate Biopsy and Treatment

DTIC Science & Technology

2012-04-01

C-arm fluoroscopy, MICCAI 2011, Toronto, Canada, 2011. 4) Poster Presentation: Prostate Cancer Probability Estimation Based on DCE- DTI Features...and P. Kozlowski, “Prostate Cancer Probability Estimation Based on DCE- DTI Features and Support Vector Machine Classification,” Annual Meeting of... DTI ), which characterize the de-phasing of the MR signal caused by molecular diffusion. Prostate cancer causes a pathological change in the tissue

Low Molecular Weight Norbornadiene Derivatives for Molecular Solar‐Thermal Energy Storage

PubMed Central

Quant, Maria; Lennartson, Anders; Dreos, Ambra; Kuisma, Mikael; Erhart, Paul; Börjesson, Karl

2016-01-01

Abstract Molecular solar‐thermal energy storage systems are based on molecular switches that reversibly convert solar energy into chemical energy. Herein, we report the synthesis, characterization, and computational evaluation of a series of low molecular weight (193–260 g mol−1) norbornadiene–quadricyclane systems. The molecules feature cyano acceptor and ethynyl‐substituted aromatic donor groups, leading to a good match with solar irradiation, quantitative photo‐thermal conversion between the norbornadiene and quadricyclane, as well as high energy storage densities (396–629 kJ kg−1). The spectroscopic properties and energy storage capability have been further evaluated through density functional theory calculations, which indicate that the ethynyl moiety plays a critical role in obtaining the high oscillator strengths seen for these molecules. PMID:27492997

Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase

PubMed Central

Lucas, James E; Siegel, Justin B

2015-01-01

Enzyme active site residues are often highly conserved, indicating a significant role in function. In this study we quantitate the functional contribution for all conserved molecular interactions occurring within a Michaelis complex for mannitol 2-dehydrogenase derived from Pseudomonas fluorescens (pfMDH). Through systematic mutagenesis of active site residues, we reveal that the molecular interactions in pfMDH mediated by highly conserved residues not directly involved in reaction chemistry can be as important to catalysis as those directly involved in the reaction chemistry. This quantitative analysis of the molecular interactions within the pfMDH active site provides direct insight into the functional role of each molecular interaction, several of which were unexpected based on canonical sequence conservation and structural analyses. PMID:25752240

Thermal Decomposition of Condensed-Phase Nitromethane from Molecular Dynamics from ReaxFF Reactive Dynamics

DTIC Science & Technology

2011-05-04

pubs.acs.org/JPCB Thermal Decomposition of Condensed-Phase Nitromethane from Molecular Dynamics from ReaxFF Reactive Dynamics Si-ping Han,†,‡ Adri C. T. van...ABSTRACT: We studied the thermal decomposition and subsequent reaction of the energetic material nitromethane (CH3NO2) using molec- ular dynamics...with ReaxFF, a first principles-based reactive force field. We characterize the chemistry of liquid and solid nitromethane at high temperatures (2000

Molecular and Morphological Characterizations of Echinococcus granulosus from Human and Animal Isolates in Kashan, Markazi Province, Iran

PubMed Central

ARBABI, Mohsen; PIRESTANI, Majid; DELAVARI, Mahdi; HOOSHYAR, Hossein; ABDOLI, Amir; SARVI, Shahab

2017-01-01

Background: One of the most important zoonotic helminths in the world is known as Echinococcus granulosus. Different strains of the E. granulosus have been described based on morphological and molecular characterizations, however, there is limited information regarding the characteristics of the phenotypes and genotypes of E. granulosus in Iran. Methods: The present study was prepared to evaluate the phenotypic and genotypic diversity of E. granulosus isolates collected from human, goat, sheep, and cattle based on 19 standard morphometric parameters and mitochondrial and nuclear genes (CO1, ND1, and ITS1) in Kashan, Markazi Province, Iran during 2013–2014. Results: The biometric analysis for the 19 characters revealed that the 19 morphometric values of cattle isolates were exceptionally higher than human, goat, and sheep isolates (P<0.05). Molecular analysis confirms the morphological findings. Phylogenic analysis of the CO1, NAD1 and ITS1 genes for all isolates, independent of the host, revealed that the common sheep strain (G1) is traveling among livestock in Kashan and the strains are highly adapted to goats, cattle, sheep, and humans. Conclusion: Both morphological and molecular results of this study indicated that the only genotype G1 of E. granulosus travels between humans and other intermediate hosts of this parasite in the area study. PMID:28761477

Toward Precision Medicine: A Cancer Molecular Subtyping Nano-Strategy for RNA Biomarkers in Tumor and Urine.

PubMed

Koo, Kevin M; Wee, Eugene J H; Mainwaring, Paul N; Wang, Yuling; Trau, Matt

2016-12-01

Cancer is a heterogeneous disease which manifests as different molecular subtypes due to the complex nature of tumor initiation, progression, and metastasis. The concept of precision medicine aims to exploit this cancer heterogeneity by incorporating diagnostic technology to characterize each cancer patient's molecular subtype for tailored treatments. To characterize cancer molecular subtypes accurately, a suite of multiplexed bioassays have currently been developed to detect multiple oncogenic biomarkers. Despite the reliability of current multiplexed detection techniques, novel strategies are still needed to resolve limitations such as long assay time, complex protocols, and difficulty in interpreting broad overlapping spectral peaks of conventional fluorescence readouts. Herein a rapid (80 min) multiplexed platform strategy for subtyping prostate cancer tumor and urine samples based on their RNA biomarker profiles is presented. This is achieved by combining rapid multiplexed isothermal reverse transcription-recombinase polymerase amplification (RT-RPA) of target RNA biomarkers with surface-enhanced Raman spectroscopy (SERS) nanotags for "one-pot" readout. This is the first translational application of a RT-RPA/SERS-based platform for multiplexed cancer biomarker detection to address a clinical need. With excellent sensitivity of 200 zmol (100 copies) and specificity, we believed that this platform methodology could be a useful tool for rapid multiplexed subtyping of cancers. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Production and characterization of films based on blends of chitosan from blue crab (Callinectes sapidus) waste and pectin from Orange (Citrus sinensis Osbeck) peel.

PubMed

Baron, Ricardo Duran; Pérez, Latife Lúquez; Salcedo, Jesús Mejía; Córdoba, Luis Pérez; Sobral, Paulo José do Amaral

2017-05-01

The objective of this study was to develop and characterize films based on blends of chitosan and pectin, produced in laboratory scale, from industrial wastes. The chitosan was obtained by termoalcaline deacetylation of chitin, extracted from blue crab (Callinectes sapidus) waste and characterized according to degree of deacetylation (DD) and viscosimetric molecular weight (Mw); and pectin was extracted by conventional heating, from orange (Citrus sinensis Osbeck) peel and characterized according to degree of esterification (DE) and molecular weight (Mw). The Ch:P based films were prepared by the casting method in different Ch:P ratios [0: 100, 25:75, 50:50, 75:25 and 100:0], and compared to two controls [0:100 and 100:0], of commercial pectin and chitosan. Glycerol was used as a plasticizer at concentrations of 0.2g/g macromolecules. The addition of high concentrations of pectin in the formulations resulted in films with high solubility and an increase in moisture. No significant difference (P>0.05) in the degree of swelling (DS) and water vapor permeability (WVP) of the films was observed. Ch:P blend films were less stiff and therefore more elastic and flexible than films based on only one biopolymer. The control films presented better results in terms of color, being brighter and less opaque than other film formulations. These data suggest that chitosan or pectin obtained from agro-industrial waste is a potential matrix to produce biodegradable films for future food applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Understanding aneuploidy in cancer through the lens of system inheritance, fuzzy inheritance and emergence of new genome systems.

PubMed

Ye, Christine J; Regan, Sarah; Liu, Guo; Alemara, Sarah; Heng, Henry H

2018-01-01

In the past 15 years, impressive progress has been made to understand the molecular mechanism behind aneuploidy, largely due to the effort of using various -omics approaches to study model systems (e.g. yeast and mouse models) and patient samples, as well as the new realization that chromosome alteration-mediated genome instability plays the key role in cancer. As the molecular characterization of the causes and effects of aneuploidy progresses, the search for the general mechanism of how aneuploidy contributes to cancer becomes increasingly challenging: since aneuploidy can be linked to diverse molecular pathways (in regards to both cause and effect), the chances of it being cancerous is highly context-dependent, making it more difficult to study than individual molecular mechanisms. When so many genomic and environmental factors can be linked to aneuploidy, and most of them not commonly shared among patients, the practical value of characterizing additional genetic/epigenetic factors contributing to aneuploidy decreases. Based on the fact that cancer typically represents a complex adaptive system, where there is no linear relationship between lower-level agents (such as each individual gene mutation) and emergent properties (such as cancer phenotypes), we call for a new strategy based on the evolutionary mechanism of aneuploidy in cancer, rather than continuous analysis of various individual molecular mechanisms. To illustrate our viewpoint, we have briefly reviewed both the progress and challenges in this field, suggesting the incorporation of an evolutionary-based mechanism to unify diverse molecular mechanisms. To further clarify this rationale, we will discuss some key concepts of the genome theory of cancer evolution, including system inheritance, fuzzy inheritance, and cancer as a newly emergent cellular system. Illustrating how aneuploidy impacts system inheritance, fuzzy inheritance and the emergence of new systems is of great importance. Such synthesis encourages efforts to apply the principles/approaches of complex adaptive systems to ultimately understand aneuploidy in cancer.

Characterization and Higher-Order Structure Assessment of an Interchain Cysteine-Based ADC: Impact of Drug Loading and Distribution on the Mechanism of Aggregation.

PubMed

Guo, Jianxin; Kumar, Sandeep; Chipley, Mark; Marcq, Olivier; Gupta, Devansh; Jin, Zhaowei; Tomar, Dheeraj S; Swabowski, Cecily; Smith, Jacquelynn; Starkey, Jason A; Singh, Satish K

2016-03-16

The impact of drug loading and distribution on higher order structure and physical stability of an interchain cysteine-based antibody drug conjugate (ADC) has been studied. An IgG1 mAb was conjugated with a cytotoxic auristatin payload following the reduction of interchain disulfides. The 2-D LC-MS analysis shows that there is a preference for certain isomers within the various drug to antibody ratios (DARs). The physical stability of the unconjugated monoclonal antibody, the ADC, and isolated conjugated species with specific DAR, were compared using calorimetric, thermal, chemical denaturation and molecular modeling techniques, as well as techniques to assess hydrophobicity. The DAR was determined to have a significant impact on the biophysical properties and stability of the ADC. The CH2 domain was significantly perturbed in the DAR6 species, which was attributable to quaternary structural changes as assessed by molecular modeling. At accelerated storage temperatures, the DAR6 rapidly forms higher molecular mass species, whereas the DAR2 and the unconjugated mAb were largely stable. Chemical denaturation study indicates that DAR6 may form multimers while DAR2 and DAR4 primarily exist in monomeric forms in solution at ambient conditions. The physical state differences were correlated with a dramatic increase in the hydrophobicity and a reduction in the surface tension of the DAR6 compared to lower DAR species. Molecular modeling of the various DAR species and their conformers demonstrates that the auristatin-based linker payload directly contributes to the hydrophobicity of the ADC molecule. Higher order structural characterization provides insight into the impact of conjugation on the conformational and colloidal factors that determine the physical stability of cysteine-based ADCs, with implications for process and formulation development.

Soft matter interactions at the molecular scale: interaction forces and energies between single hydrophobic model peptides.

PubMed

Stock, Philipp; Utzig, Thomas; Valtiner, Markus

2017-02-08

In all realms of soft matter research a fundamental understanding of the structure/property relationships based on molecular interactions is crucial for developing a framework for the targeted design of soft materials. However, a molecular picture is often difficult to ascertain and yet essential for understanding the many different competing interactions at play, including entropies and cooperativities, hydration effects, and the enormous design space of soft matter. Here, we characterized for the first time the interaction between single hydrophobic molecules quantitatively using atomic force microscopy, and demonstrated that single molecular hydrophobic interaction free energies are dominated by the area of the smallest interacting hydrophobe. The interaction free energy amounts to 3-4 kT per hydrophobic unit. Also, we find that the transition state of the hydrophobic interactions is located at 3 Å with respect to the ground state, based on Bell-Evans theory. Our results provide a new path for understanding the nature of hydrophobic interactions at the single molecular scale. Our approach enables us to systematically vary hydrophobic and any other interaction type by utilizing peptide chemistry providing a strategic advancement to unravel molecular surface and soft matter interactions at the single molecular scale.

Advances in the molecular genetics of gliomas - implications for classification and therapy.

PubMed

Reifenberger, Guido; Wirsching, Hans-Georg; Knobbe-Thomsen, Christiane B; Weller, Michael

2017-07-01

Genome-wide molecular-profiling studies have revealed the characteristic genetic alterations and epigenetic profiles associated with different types of gliomas. These molecular characteristics can be used to refine glioma classification, to improve prediction of patient outcomes, and to guide individualized treatment. Thus, the WHO Classification of Tumours of the Central Nervous System was revised in 2016 to incorporate molecular biomarkers - together with classic histological features - in an integrated diagnosis, in order to define distinct glioma entities as precisely as possible. This paradigm shift is markedly changing how glioma is diagnosed, and has important implications for future clinical trials and patient management in daily practice. Herein, we highlight the developments in our understanding of the molecular genetics of gliomas, and review the current landscape of clinically relevant molecular biomarkers for use in classification of the disease subtypes. Novel approaches to the genetic characterization of gliomas based on large-scale DNA-methylation profiling and next-generation sequencing are also discussed. In addition, we illustrate how advances in the molecular genetics of gliomas can promote the development and clinical translation of novel pathogenesis-based therapeutic approaches, thereby paving the way towards precision medicine in neuro-oncology.

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

PubMed Central

2013-01-01

Background Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. Results NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. Conclusions NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps. PMID:24099179

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.

PubMed

Kuperstein, Inna; Cohen, David P A; Pook, Stuart; Viara, Eric; Calzone, Laurence; Barillot, Emmanuel; Zinovyev, Andrei

2013-10-07

Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps.

Study design requirements for RNA sequencing-based breast cancer diagnostics.

PubMed

Mer, Arvind Singh; Klevebring, Daniel; Grönberg, Henrik; Rantalainen, Mattias

2016-02-01

Sequencing-based molecular characterization of tumors provides information required for individualized cancer treatment. There are well-defined molecular subtypes of breast cancer that provide improved prognostication compared to routine biomarkers. However, molecular subtyping is not yet implemented in routine breast cancer care. Clinical translation is dependent on subtype prediction models providing high sensitivity and specificity. In this study we evaluate sample size and RNA-sequencing read requirements for breast cancer subtyping to facilitate rational design of translational studies. We applied subsampling to ascertain the effect of training sample size and the number of RNA sequencing reads on classification accuracy of molecular subtype and routine biomarker prediction models (unsupervised and supervised). Subtype classification accuracy improved with increasing sample size up to N = 750 (accuracy = 0.93), although with a modest improvement beyond N = 350 (accuracy = 0.92). Prediction of routine biomarkers achieved accuracy of 0.94 (ER) and 0.92 (Her2) at N = 200. Subtype classification improved with RNA-sequencing library size up to 5 million reads. Development of molecular subtyping models for cancer diagnostics requires well-designed studies. Sample size and the number of RNA sequencing reads directly influence accuracy of molecular subtyping. Results in this study provide key information for rational design of translational studies aiming to bring sequencing-based diagnostics to the clinic.

Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip

PubMed Central

Hill, Theresa A.; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W.; Van Deynze, Allen

2013-01-01

The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among Capsicum annuum. PMID:23409153

Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip.

PubMed

Hill, Theresa A; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W; Van Deynze, Allen

2013-01-01

The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among Capsicum annuum.

Technique development for characterization of metalloorganics in acid-base-neutral fractions of heavy petroleum residues: Topical report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pearson, C.D.; Green, J.B.

1988-01-01

A novel approach for the characterization of metallorganic compounds in heavy petroleum residues has been developed. Wilmington 1000/sup 0/ F+ and Mayan 925/sup 0/ F+ residues and hydrotreated products were separated into acid-base-neutral (ABN) fractions by a unique nonaqueous ion-exchange technique developed at NIPER. The metal complexes in the feeds, hydrotreated products and ABN fractions were then characterized by determining the total vanadium and nickel and by measuring the vanadium and nickel porphyrin content of each fraction. Molecular weight distribution profiles of the vanadium and nickel compounds in the feed, 400/sup 0/C hydrotreated product and corresponding ABN fractions were obtainedmore » by size exclusion chromatography/inductively coupled plasma. The majority of the metal appeared to be in non-porphyrinic form. The vanadium and nickel complexes were distributed into all of the ABN fractions. In the feed and the whole hydrotreated products the porphyrin levels decreased as hydrotreating temperatures increased. In contrast to previously reported work, porphyrins do not always decrease when hydrotreated. The amount of porphyrins in certain ABN fractions increased after hydrotreating at moderate temperatures. The Mayan V and Ni complexes were more resistant to hydrotreating than the Wilmington metal complexes; in particular, the high molecular weight Mayan metal complexes were more resistant to hydrotreating than the high molecular weight Wilmington metal complexes. 15 refs., 11 figs., 10 tabs.« less

A novel PCR-RFLP assay for molecular characterization of Echinococcus granulosus sensu lato and closely related species in developing countries.

PubMed

Chaâbane-Banaoues, Raja; Oudni-M'rad, Myriam; M'rad, Selim; Amani, Hizem; Mezhoud, Habib; Babba, Hamouda

2016-10-01

Cystic echinococcosis, due to Echinococcus granulosus sensu lato (s. l.), currently affects three million people, especially in low-income countries and results in high livestock production loss. DNA-based methods demonstrated genetic variability of E. granulosus s. l., and five species were recognized to belong to the complex, including E. granulosus sensu stricto (s.s) (genotypes G1-G3), Echinococcus equinus (genotype G4), Echinococcus ortleppi (genotype G5), Echinococcus canadensis (genotypes G6-G10), and the lion strain Echinococcus felidis. The characterization of Echinococcus species responsible for human and animal echinococcosis is crucial to adapt the preventive measures against this parasitic disease. The sequencing approach is the gold standard for genotyping assays. Unfortunately, developing countries do not often have access to these techniques. Based on in silico RFLP tools, we described an accurate PCR-RFLP method for Echinococcus spp. characterization. The double digestion with the HaeIII and HinfI restriction enzymes of the PCR product from nad1 gene (1071 bp) led to a clear discrimination between E. granulosus s. l. and most closely related species (Echinococcus shiquicus and Echinococcus multilocularis).Molecular procedures and phylogenetic analysis confirmed the efficiency and the reproducibility of this simple and fast PCR-RFLP method. This technique is proved useful for fresh/unfixed and FF-PET tissues and enables large-scale molecular epidemiological screening in developing countries.

Molecular and excited state properties of isomeric scarlet disperse dyes

NASA Astrophysics Data System (ADS)

Lim, Jihye; Szymczyk, Malgorzata; Mehraban, Nahid; Ding, Yi; Parrillo-Chapman, Lisa; El-Shafei, Ahmed; Freeman, Harold S.

2018-06-01

This work was part of an investigation aimed at characterizing the molecular and excited state properties of currently available disperse dyes developed to provide stability to extensive sunlight exposures when adsorbed on poly(ethylene terephthalate) (PET) fibers. Having completed the characterization of yellow, magenta, and cyan disperse dyes for PET-based fabrics used outdoors, our attention turned to the colors designed to enhance the color gamut of a standard 4-member (cyan/yellow/magenta/black) color set. The present study pertained specifically to the characterization of commercially available scarlet dyes. In this regard, HPLC analysis showed that a scarlet product used for PET coloration was mainly a 70/30 mixture of dyes, and the use of HRMS and single crystal X-ray diffraction analyses indicated that these two dyes were azo compounds derived from isomeric pyridine-based couplers which differed in the location of the primary amino (sbnd NH2) and anilino (sbnd NHPh) groups attached to the pyridine ring. One dye structure has the sbnd NHPh group para to the azo group (Sc2), while the other has that group in the ortho position (Sc3). The presence of either ortho substituent provides photostabilization through intramolecular H-bonding with the azo moiety. Further, results from molecular modeling studies showed that the lower excited state oxidation potential of Sc3 relative to that of Sc2 allows Sc3 to function as an energy quencher for the excited state of Sc2 - through thermodynamically favorable electron transfer.

Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duncan, Katherine R.; Crüsemann, Max; Lechner, Anna

Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. In this paper, we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains, including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated themore » identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. Finally, these efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches.« less

Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

DOE PAGES

Duncan, Katherine R.; Crüsemann, Max; Lechner, Anna; ...

2015-04-09

Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. In this paper, we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains, including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated themore » identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. Finally, these efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches.« less

Watson-Crick Base Pair Radical Cation as a Model for Oxidative Damage in DNA.

PubMed

Feketeová, Linda; Chan, Bun; Khairallah, George N; Steinmetz, Vincent; Maitre, Philippe; Radom, Leo; O'Hair, Richard A J

2017-07-06

The deleterious cellular effects of ionizing radiation are well-known, but the mechanisms causing DNA damage are poorly understood. The accepted molecular events involve initial oxidation and deprotonation at guanine sites, triggering hydrogen atom abstraction reactions from the sugar moieties, causing DNA strand breaks. Probing the chemistry of the initially formed radical cation has been challenging. Here, we generate, spectroscopically characterize, and examine the reactivity of the Watson-Crick nucleobase pair radical cation in the gas phase. We observe rich chemistry, including proton transfer between the bases and propagation of the radical site in deoxyguanosine from the base to the sugar, thus rupturing the sugar. This first example of a gas-phase model system providing molecular-level details on the chemistry of an ionized DNA base pair paves the way toward a more complete understanding of molecular processes induced by radiation. It also highlights the role of radical propagation in chemistry, biology, and nanotechnology.

Silicon Phthalocyanines Axially Disubstituted with Erlotinib toward Small-Molecular-Target-Based Photodynamic Therapy.

PubMed

Chen, Juan-Juan; Huang, Yi-Zhen; Song, Mei-Ru; Zhang, Zhi-Hong; Xue, Jin-Ping

2017-09-21

Small-molecular-target-based photodynamic therapy-a promising targeted anticancer strategy-was developed by conjugating zinc(II) phthalocyanine with a small-molecular-target-based anticancer drug. To prevent self-aggregation and avoid problems of phthalocyanine isomerization, two silicon phthalocyanines di-substituted axially with erlotinib have been synthesized and fully characterized. These conjugates are present in monomeric form in various solvents as well as culture media. Cell-based experiments showed that these conjugates localize in lysosomes and mitochondria, while maintaining high photodynamic activities (IC 50 values as low as 8 nm under a light dose of 1.5 J cm -2 ). With erlotinib as the targeting moiety, two conjugates were found to exhibit high specificity for EGFR-overexpressing cancer cells. Various poly(ethylene glycol) (PEG) linker lengths were shown to have an effect on the photophysical/photochemical properties and on in vitro phototoxicity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mining the oral mycobiome: Methods, components, and meaning

PubMed Central

Diaz, Patricia I.; Hong, Bo-Young; Dupuy, Amanda K.; Strausbaugh, Linda D.

2017-01-01

ABSTRACT Research on oral fungi has centered on Candida. However, recent internal transcribed spacer (ITS)-based studies revealed a vast number of fungal taxa as potential oral residents. We review DNA-based studies of the oral mycobiome and contrast them with cultivation-based surveys, showing that most genera encountered by cultivation have also been detected molecularly. Some taxa such as Malassezia, however, appear in high prevalence and abundance in molecular studies but have not been cultivated. Important technical and bioinformatic challenges to ITS-based oral mycobiome studies are discussed. These include optimization of sample lysis, variability in length of ITS amplicons, high intra-species ITS sequence variability, high inter-species variability in ITS copy number and challenges in nomenclature and maintenance of curated reference databases. Molecular surveys are powerful first steps to characterize the oral mycobiome but further research is needed to unravel which fungi detected by DNA are true oral residents and what role they play in oral homeostasis. PMID:27791473

Molecular Networking and Pattern-Based Genome Mining Improves discovery of biosynthetic gene clusters and their products from Salinispora species

PubMed Central

Duncan, Katherine R.; Crüsemann, Max; Lechner, Anna; Sarkar, Anindita; Li, Jie; Ziemert, Nadine; Wang, Mingxun; Bandeira, Nuno; Moore, Bradley S.; Dorrestein, Pieter C.; Jensen, Paul R.

2015-01-01

Summary Genome sequencing has revealed that bacteria contain many more biosynthetic gene clusters than predicted based on the number of secondary metabolites discovered to date. While this biosynthetic reservoir has fostered interest in new tools for natural product discovery, there remains a gap between gene cluster detection and compound discovery. Here we apply molecular networking and the new concept of pattern-based genome mining to 35 Salinispora strains including 30 for which draft genome sequences were either available or obtained for this study. The results provide a method to simultaneously compare large numbers of complex microbial extracts, which facilitated the identification of media components, known compounds and their derivatives, and new compounds that could be prioritized for structure elucidation. These efforts revealed considerable metabolite diversity and led to several molecular family-gene cluster pairings, of which the quinomycin-type depsipeptide retimycin A was characterized and linked to gene cluster NRPS40 using pattern-based bioinformatic approaches. PMID:25865308

Molecular Characterization of Swine Manure Lagoon Microbial and Antibiotic Resistant Populations

USDA-ARS?s Scientific Manuscript database

Background: The differences in swine manure lagoon effluent based on differing management styles or approaches such as different stages of swine rearing determines the presence of variable antibiotic resistance determinants and functional microbial populations. These concerns determine the suitabil...

Prediction of the Chapman-Jouguet chemical equilibrium state in a detonation wave from first principles based reactive molecular dynamics.

PubMed

Guo, Dezhou; Zybin, Sergey V; An, Qi; Goddard, William A; Huang, Fenglei

2016-01-21

The combustion or detonation of reacting materials at high temperature and pressure can be characterized by the Chapman-Jouguet (CJ) state that describes the chemical equilibrium of the products at the end of the reaction zone of the detonation wave for sustained detonation. This provides the critical properties and product kinetics for input to macroscale continuum simulations of energetic materials. We propose the ReaxFF Reactive Dynamics to CJ point protocol (Rx2CJ) for predicting the CJ state parameters, providing the means to predict the performance of new materials prior to synthesis and characterization, allowing the simulation based design to be done in silico. Our Rx2CJ method is based on atomistic reactive molecular dynamics (RMD) using the QM-derived ReaxFF force field. We validate this method here by predicting the CJ point and detonation products for three typical energetic materials. We find good agreement between the predicted and experimental detonation velocities, indicating that this method can reliably predict the CJ state using modest levels of computation.

Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog

PubMed Central

Spring-Connell, Alexander M.; Evich, Marina G.; Debelak, Harald; Seela, Frank; Germann, Markus W.

2016-01-01

A truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many candidates either destabilize the duplex or do not base pair indiscriminatingly. The novel base 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin- 4-amine) N8-(2′deoxyribonucleoside), a deoxyadenosine analog (UB), pairs with each of the natural DNA bases with little sequence preference. We have utilized NMR complemented with molecular dynamic calculations to characterize the structure and dynamics of a UB incorporated into a DNA duplex. The UB participates in base stacking with little to no perturbation of the local structure yet forms an unusual base pair that samples multiple conformations. These local dynamics result in the complete disappearance of a single UB proton resonance under native conditions. Accommodation of the UB is additionally stabilized via heightened backbone conformational sampling. NMR combined with various computational techniques has allowed for a comprehensive characterization of both structural and dynamic effects of the UB in a DNA duplex and underlines that the UB as a strong candidate for universal base applications. PMID:27566150

Quantum mechanical calculations related to ionization and charge transfer in DNA

NASA Astrophysics Data System (ADS)

Cauët, E.; Valiev, M.; Weare, J. H.; Liévin, J.

2012-07-01

Ionization and charge migration in DNA play crucial roles in mechanisms of DNA damage caused by ionizing radiation, oxidizing agents and photo-irradiation. Therefore, an evaluation of the ionization properties of the DNA bases is central to the full interpretation and understanding of the elementary reactive processes that occur at the molecular level during the initial exposure and afterwards. Ab initio quantum mechanical (QM) methods have been successful in providing highly accurate evaluations of key parameters, such as ionization energies (IE) of DNA bases. Hence, in this study, we performed high-level QM calculations to characterize the molecular energy levels and potential energy surfaces, which shed light on ionization and charge migration between DNA bases. In particular, we examined the IEs of guanine, the most easily oxidized base, isolated and embedded in base clusters, and investigated the mechanism of charge migration over two and three stacked guanines. The IE of guanine in the human telomere sequence has also been evaluated. We report a simple molecular orbital analysis to explain how modifications in the base sequence are expected to change the efficiency of the sequence as a hole trap. Finally, the application of a hybrid approach combining quantum mechanics with molecular mechanics brings an interesting discussion as to how the native aqueous DNA environment affects the IE threshold of nucleobases.

Molecular threading: mechanical extraction, stretching and placement of DNA molecules from a liquid-air interface.

PubMed

Payne, Andrew C; Andregg, Michael; Kemmish, Kent; Hamalainen, Mark; Bowell, Charlotte; Bleloch, Andrew; Klejwa, Nathan; Lehrach, Wolfgang; Schatz, Ken; Stark, Heather; Marblestone, Adam; Church, George; Own, Christopher S; Andregg, William

2013-01-01

We present "molecular threading", a surface independent tip-based method for stretching and depositing single and double-stranded DNA molecules. DNA is stretched into air at a liquid-air interface, and can be subsequently deposited onto a dry substrate isolated from solution. The design of an apparatus used for molecular threading is presented, and fluorescence and electron microscopies are used to characterize the angular distribution, straightness, and reproducibility of stretched DNA deposited in arrays onto elastomeric surfaces and thin membranes. Molecular threading demonstrates high straightness and uniformity over length scales from nanometers to micrometers, and represents an alternative to existing DNA deposition and linearization methods. These results point towards scalable and high-throughput precision manipulation of single-molecule polymers.

Harnessing Reversible Electronic Energy Transfer: From Molecular Dyads to Molecular Machines.

PubMed

Denisov, Sergey A; Yu, Shinlin; Pozzo, Jean-Luc; Jonusauskas, Gediminas; McClenaghan, Nathan D

2016-06-17

Reversible electronic energy transfer (REET) may be instilled in bi-/multichromophoric molecule-based systems, following photoexcitation, upon judicious structural integration of matched chromophores. This leads to a new set of photophysical properties for the ensemble, which can be fully characterized by steady-state and time-resolved spectroscopic methods. Herein, we take a comprehensive look at progress in the development of this type of supermolecule in the last five years, which has seen systems evolve from covalently tethered dyads to synthetic molecular machines, exemplified by two different pseudorotaxanes. Indeed, REET holds promise in the control of movement in molecular machines, their assembly/disassembly, as well as in charge separation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Endometriosis: translation of molecular insights to management.

PubMed

Langan, K L; Farrell, M E; Keyser, E A; Salyer, B A; Burney, R O

2014-09-01

Endometriosis is a debilitating gynecologic disorder causing pelvic pain and infertility and characterized by the implantation of endometrial tissue to extrauterine locations. Though aspects of the condition remain enigmatic, the molecular pathophysiology of endometriosis appears to be clarifying. Estrogen dependence of the disease is a sentinel endocrine feature and reduction of estrogen bioavailability is the therapeutic principle upon which traditional treatment and prevention approaches have been based. Endometriosis is a chronic inflammatory condition associated with lesional neoangiogenesis and attenuated progesterone action at the level of the endometrium. The elucidation of the molecular pathways mediating these observations has revealed new targets for directed medical and surgical treatment. This paper will review current approaches to the management of endometriosis in the context of the molecular pathophysiology.

Molecular therapy for acute myeloid leukaemia

PubMed Central

Coombs, Catherine C.; Tallman, Martin S.; Levine, Ross L.

2017-01-01

Acute myeloid leukaemia (AML) is a heterogeneous disease that is, in general, associated with a very poor prognosis. Multiple cytogenetic and molecular abnormalities that characterize different forms of AML have been used to better prognosticate patients and inform treatment decisions. Indeed, risk status in patients with this disease has classically been based on cytogenetic findings; however, additional molecular characteristics have been shown to inform risk assessment, including FLT3, NPM1, KIT, and CEBPA mutation status. Advances in sequencing technology have led to the discovery of novel somatic mutations in tissue samples from patients with AML, providing deeper insight into the mutational landscape of the disease. The majority of patients with AML (>97%) are found to have a clonal somatic abnormality on mutational profiling. Nevertheless, our understanding of the utility of mutation profiling in clinical practice remains incomplete and is continually evolving, and evidence-based approaches to application of these data are needed. In this Review, we discuss the evidence-base for integrating mutational data into treatment decisions for patients with AML, and propose novel therapeutic algorithms in the era of molecular medicine. PMID:26620272

Lab Plays Central Role in Groundbreaking National Clinical Trial in Precision Medicine | Poster

Cancer.gov

The Molecular Characterization Laboratory lies at the heart of an ambitious new approach for testing cancer drugs that will use the newest tools of precision medicine to select the best treatment for individual patients based on the genetic makeup of their tumors. The protocol, called NCI-Molecular Analysis for Therapy Choice (NCI-MATCH), will start with tumor biopsies from as many as 3,000 patients to see if they have genetic defects for which a targeted cancer drug is available. Cancers will be treated based on their genetic profiles rather than by their location in the body, which is the conventional approach.

Helical self-organization and hierarchical self-assembly of an oligoheterocyclic pyridine-pyridazine strand into extended supramolecular fibers.

PubMed

Cuccia, Louis A; Ruiz, Eliseo; Lehn, Jean-Marie; Homo, Jean-Claude; Schmutz, Marc

2002-08-02

The synthesis and characterization of an alternating pyridine-pyridazine strand comprising thirteen heterocycles are described. Spontaneous folding into a helical secondary structure is based on a general molecular self-organization process enforced by the conformational information encoded within the primary structure of the molecular strand itself. Conformational control based on heterocyclic "helicity codons" illustrates a strategy for designing folding properties into synthetic oligomers (foldamers). Strong intermolecular interactions of the highly ordered lock-washer subunits of compound 3 results in hierarchical supramolecular self-assembly into protofibrils and fibrils. Compound 3 also forms mechanically stable two-dimensional Langmuir-Blodgett and cast thin films.

Mass-spectrometric analysis of hydroperoxy- and hydroxy-derivatives of cardiolipin and phosphatidylserine in cells and tissues induced by pro-apoptotic and pro-inflammatory stimuli

PubMed Central

Tyurin, Vladimir A.; Tyurina, Yulia Y.; Jung, Mi-Yeon; Tungekar, Muhammad A.; Wasserloos, Karla J.; Bayir, Hülya; Greenberger, Joel S.; Kochanek, Patrick M.; Shvedova, Anna A.; Pitt, Bruce; Kagan, Valerian E.

2009-01-01

Oxidation of two anionic phospholipids - cardiolipin (CL) in mitochondria and phosphatidylserine (PS) in extramitochondrial compartments - are important signaling events, particularly during the execution of programmed cell death and clearance of apoptotic cells. Quantitative analysis of CL and PS oxidation products is central to understanding their molecular mechanisms of action. We combined the identification of diverse phospholipid molecular species by ESI-MS with quantitative assessments of lipid hydroperoxides using a fluorescence HPLC-based protocol. We characterized CL and PS oxidation products formed in a model system (cyt c/H2O2), in apoptotic cells (neurons, pulmonary artery endothelial cells) and mouse lung under inflammatory/oxidative stress conditions (hyperoxia, inhalation of single walled carbon nanotubes). Our results demonstrate the usefulness of this approach for quantitative assessments, identification of individual molecular species and structural characterization of anionic phospholipids that are involved in oxidative modification in cells and tissues. PMID:19328050

Molecular Epidemiology of Influenza A/H3N2 Viruses Circulating in Mexico from 2003 to 2012

PubMed Central

Escalera-Zamudio, Marina; Nelson, Martha I.; Cobián Güemes, Ana Georgina; López-Martínez, Irma; Cruz-Ortiz, Natividad; Iguala-Vidales, Miguel; García, Elvia Rodríguez; Barrera-Badillo, Gisela; Díaz-Quiñonez, Jose Alberto; López, Susana; Arias, Carlos F.; Isa, Pavel

2014-01-01

In this work, nineteen influenza A/H3N2 viruses isolated in Mexico between 2003 and 2012 were studied. Our findings show that different human A/H3N2 viral lineages co-circulate within a same season and can also persist locally in between different influenza seasons, increasing the chance for genetic reassortment events. A novel minor cluster was also identified, named here as Korea, that circulated worldwide during 2003. Frequently, phylogenetic characterization did not correlate with the determined antigenic identity, supporting the need for the use of molecular evolutionary tools additionally to antigenic data for the surveillance and characterization of viral diversity during each flu season. This work represents the first long-term molecular epidemiology study of influenza A/H3N2 viruses in Mexico based on the complete genomic sequences and contributes to the monitoring of evolutionary trends of A/H3N2 influenza viruses within North and Central America. PMID:25075517

Selective Modulators of PPAR-γ Activity: Molecular Aspects Related to Obesity and Side-Effects

PubMed Central

Zhang, Fang; Lavan, Brian E.; Gregoire, Francine M.

2007-01-01

Peroxisome proliferator-activated receptor γ (PPAR-γ) is a key regulator of lipid metabolism and energy balance implicated in the development of insulin resistance and obesity. The identification of putative natural and synthetic ligands and activators of PPAR-γ has helped to unravel the molecular basis of its function, including molecular details regarding ligand binding, conformational changes of the receptor, and cofactor binding, leading to the emergence of the concept of selective PPAR-γ modulators (SPPARγMs). SPPARγMs bind in distinct manners to the ligand-binding pocket of PPAR-γ, leading to alternative receptor conformations, differential cofactor recruitment/displacement, differential gene expression, and ultimately differential biological responses. Based on this concept, new and improved antidiabetic agents for the treatment of diabetes are in development. This review summarizes the current knowledge on the mechanism of action and biological effects of recently characterized SPPARγMs, including metaglidasen/halofenate, PA-082, and the angiotensin receptor antagonists, recently characterized as a new class of SPPARγMs. PMID:17389769

Synthesis, characterization, crystal structure and HSA binding of two new N,O,O-donor Schiff-base ligands derived from dihydroxybenzaldehyde and tert-butylamine

NASA Astrophysics Data System (ADS)

Khosravi, Iman; Hosseini, Farnaz; Khorshidifard, Mahsa; Sahihi, Mehdi; Rudbari, Hadi Amiri

2016-09-01

Two new o-hydroxy Schiff-bases compounds, L1 and L2, were derived from the 1:1 M condensation of 2,3-dihydroxybenzaldehyde and 2,4-dihydroxybenzaldehyde with tert-butylamine and were characterized by elemental analysis, FT-IR, 1H and 13C NMR spectroscopies. The crystal structure of L2 was also determined by single crystal X-ray analysis. The crystal structure of L2 showed that the compound exists as a zwitterionic form in the solid state, with the H atom of the phenol group being transferred to the imine N atom. It adopts an E configuration about the central Cdbnd N double bond. Furthermore, binding of these Schiff base ligands to Human Serum Albumin (HSA) was investigated by fluorescence quenching, absorption spectroscopy, molecular docking and molecular dynamics (MD) simulation methods. The fluorescence emission of HSA was quenched by ligands. Also, suitable models were used to analyze the UV-vis absorption spectroscopy data for titration of HSA solution by various amounts of Schiff bases. The spectroscopic studies revealed that these Schiff bases formed 1:1 complex with HSA. Energy transfer mechanism of quenching was discussed and the values of 3.35 and 1.57 nm as the mean distances between the bound ligands and the HSA were calculated for L1 and L2, respectively. Molecular docking results indicated that the main active binding site for these Schiff bases ligands is in subdomain IB. Moreover, MD simulation results suggested that this Schiff base complex can interact with HSA, with a slight modification of its tertiary structure.

The emergence of top-down proteomics in clinical research

PubMed Central

2013-01-01

Proteomic technology has advanced steadily since the development of 'soft-ionization' techniques for mass-spectrometry-based molecular identification more than two decades ago. Now, the large-scale analysis of proteins (proteomics) is a mainstay of biological research and clinical translation, with researchers seeking molecular diagnostics, as well as protein-based markers for personalized medicine. Proteomic strategies using the protease trypsin (known as bottom-up proteomics) were the first to be developed and optimized and form the dominant approach at present. However, researchers are now beginning to understand the limitations of bottom-up techniques, namely the inability to characterize and quantify intact protein molecules from a complex mixture of digested peptides. To overcome these limitations, several laboratories are taking a whole-protein-based approach, in which intact protein molecules are the analytical targets for characterization and quantification. We discuss these top-down techniques and how they have been applied to clinical research and are likely to be applied in the near future. Given the recent improvements in mass-spectrometry-based proteomics and stronger cooperation between researchers, clinicians and statisticians, both peptide-based (bottom-up) strategies and whole-protein-based (top-down) strategies are set to complement each other and help researchers and clinicians better understand and detect complex disease phenotypes. PMID:23806018

Molecular quantum control landscapes in von Neumann time-frequency phase space

NASA Astrophysics Data System (ADS)

Ruetzel, Stefan; Stolzenberger, Christoph; Fechner, Susanne; Dimler, Frank; Brixner, Tobias; Tannor, David J.

2010-10-01

Recently we introduced the von Neumann representation as a joint time-frequency description for femtosecond laser pulses and suggested its use as a basis for pulse shaping experiments. Here we use the von Neumann basis to represent multidimensional molecular control landscapes, providing insight into the molecular dynamics. We present three kinds of time-frequency phase space scanning procedures based on the von Neumann formalism: variation of intensity, time-frequency phase space position, and/or the relative phase of single subpulses. The shaped pulses produced are characterized via Fourier-transform spectral interferometry. Quantum control is demonstrated on the laser dye IR140 elucidating a time-frequency pump-dump mechanism.

Molecular quantum control landscapes in von Neumann time-frequency phase space.

PubMed

Ruetzel, Stefan; Stolzenberger, Christoph; Fechner, Susanne; Dimler, Frank; Brixner, Tobias; Tannor, David J

2010-10-28

Recently we introduced the von Neumann representation as a joint time-frequency description for femtosecond laser pulses and suggested its use as a basis for pulse shaping experiments. Here we use the von Neumann basis to represent multidimensional molecular control landscapes, providing insight into the molecular dynamics. We present three kinds of time-frequency phase space scanning procedures based on the von Neumann formalism: variation of intensity, time-frequency phase space position, and/or the relative phase of single subpulses. The shaped pulses produced are characterized via Fourier-transform spectral interferometry. Quantum control is demonstrated on the laser dye IR140 elucidating a time-frequency pump-dump mechanism.

Surveyor assay to diagnose persistent Müllerian duct syndrome in Miniature Schnauzers.

PubMed

Kim, Young June; Kwon, Hyuk Jin; Byun, Hyuk Soo; Yeom, Donguk; Choi, Jea-Hong; Kim, Joong-Hyun; Shim, Hosup

2017-12-31

Persistent Müllerian duct syndrome (PMDS) is a pseudohermaphroditism in males characterized by the presence of Müllerian duct derivatives. As PMDS dogs often lack clinical symptoms, a molecular diagnosis is essential to identify the syndrome in these animals. In this study, a new molecular method using DNA mismatch-specific Surveyor nuclease was developed. The Surveyor nuclease assay identified the AMHR2 mutation that produced PMDS in a Miniature Schnauzer as accurately as that obtained by using the conventional method based on restriction digestion. As an alternative to the current molecular diagnostic method, the new method may result in increased accuracy when detecting PMDS.

Surveyor assay to diagnose persistent Müllerian duct syndrome in Miniature Schnauzers

PubMed Central

Kim, Young June; Kwon, Hyuk Jin; Byun, Hyuk Soo; Yeom, Donguk; Choi, Jea-Hong; Kim, Joong-Hyun

2017-01-01

Persistent Müllerian duct syndrome (PMDS) is a pseudohermaphroditism in males characterized by the presence of Müllerian duct derivatives. As PMDS dogs often lack clinical symptoms, a molecular diagnosis is essential to identify the syndrome in these animals. In this study, a new molecular method using DNA mismatch-specific Surveyor nuclease was developed. The Surveyor nuclease assay identified the AMHR2 mutation that produced PMDS in a Miniature Schnauzer as accurately as that obtained by using the conventional method based on restriction digestion. As an alternative to the current molecular diagnostic method, the new method may result in increased accuracy when detecting PMDS. PMID:27515263

Nanogap structures for molecular nanoelectronics

PubMed Central

2012-01-01

This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes. PMID:22321736

A platform for efficient genotyping in Musa using microsatellite markers

PubMed Central

Christelová, Pavla; Valárik, Miroslav; Hřibová, Eva; Van den houwe, Ines; Channelière, Stéphanie; Roux, Nicolas; Doležel, Jaroslav

2011-01-01

Background and aims Bananas and plantains (Musa spp.) are one of the major fruit crops worldwide with acknowledged importance as a staple food for millions of people. The rich genetic diversity of this crop is, however, endangered by diseases, adverse environmental conditions and changed farming practices, and the need for its characterization and preservation is urgent. With the aim of providing a simple and robust approach for molecular characterization of Musa species, we developed an optimized genotyping platform using 19 published simple sequence repeat markers. Methodology The genotyping system is based on 19 microsatellite loci, which are scored using fluorescently labelled primers and high-throughput capillary electrophoresis separation with high resolution. This genotyping platform was tested and optimized on a set of 70 diploid and 38 triploid banana accessions. Principal results The marker set used in this study provided enough polymorphism to discriminate between individual species, subspecies and subgroups of all accessions of Musa. Likewise, the capability of identifying duplicate samples was confirmed. Based on the results of a blind test, the genotyping system was confirmed to be suitable for characterization of unknown accessions. Conclusions Here we report on the first complex and standardized platform for molecular characterization of Musa germplasm that is ready to use for the wider Musa research and breeding community. We believe that this genotyping system offers a versatile tool that can accommodate all possible requirements for characterizing Musa diversity, and is economical for samples ranging from one to many accessions. PMID:22476494

A molecularly imprinted polymer (MIP)-coated microbeam MEMS sensor for chemical detection

NASA Astrophysics Data System (ADS)

Holthoff, Ellen L.; Li, Lily; Hiller, Tobias; Turner, Kimberly L.

2015-05-01

Recently, microcantilever-based technology has emerged as a viable sensing platform due to its many advantages such as small size, high sensitivity, and low cost. However, microcantilevers lack the inherent ability to selectively identify hazardous chemicals (e.g., explosives, chemical warfare agents). The key to overcoming this challenge is to functionalize the top surface of the microcantilever with a receptor material (e.g., a polymer coating) so that selective binding between the cantilever and analyte of interest takes place. Molecularly imprinted polymers (MIPs) can be utilized as artificial recognition elements for target chemical analytes of interest. Molecular imprinting involves arranging polymerizable functional monomers around a template molecule followed by polymerization and template removal. The selectivity for the target analyte is based on the spatial orientation of the binding site and covalent or noncovalent interactions between the functional monomer and the analyte. In this work, thin films of sol-gel-derived xerogels molecularly imprinted for TNT and dimethyl methylphosphonate (DMMP), a chemical warfare agent stimulant, have demonstrated selectivity and stability in combination with a fixed-fixed beam microelectromechanical systems (MEMS)-based gas sensor. The sensor was characterized by parametric bifurcation noise-based tracking.

Can we better predict the biologic behavior of incidental IPMN? A comprehensive analysis of molecular diagnostics and biomarkers in intraductal papillary mucinous neoplasms of the pancreas.

PubMed

Tulla, Kiara A; Maker, Ajay V

2018-03-01

Predicting the biologic behavior of intraductal papillary mucinous neoplasm (IPMN) remains challenging. Current guidelines utilize patient symptoms and imaging characteristics to determine appropriate surgical candidates. However, the majority of resected cysts remain low-risk lesions, many of which may be feasible to have under surveillance. We herein characterize the most promising and up-to-date molecular diagnostics in order to identify optimal components of a molecular signature to distinguish levels of IPMN dysplasia. A comprehensive systematic review of pertinent literature, including our own experience, was conducted based on the PRISMA guidelines. Molecular diagnostics in IPMN patient tissue, duodenal secretions, cyst fluid, saliva, and serum were evaluated and organized into the following categories: oncogenes, tumor suppressor genes, glycoproteins, markers of the immune response, proteomics, DNA/RNA mutations, and next-generation sequencing/microRNA. Specific targets in each of these categories, and in aggregate, were identified by their ability to both characterize a cyst as an IPMN and determine the level of cyst dysplasia. Combining molecular signatures with clinical and imaging features in this era of next-generation sequencing and advanced computational analysis will enable enhanced sensitivity and specificity of current models to predict the biologic behavior of IPMN.

Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations.

PubMed

Druliner, Brooke R; Wang, Panwen; Bae, Taejeong; Baheti, Saurabh; Slettedahl, Seth; Mahoney, Douglas; Vasmatzis, Nikolaos; Xu, Hang; Kim, Minsoo; Bockol, Matthew; O'Brien, Daniel; Grill, Diane; Warner, Nathaniel; Munoz-Gomez, Miguel; Kossick, Kimberlee; Johnson, Ruth; Mouchli, Mohamad; Felmlee-Devine, Donna; Washechek-Aletto, Jill; Smyrk, Thomas; Oberg, Ann; Wang, Junwen; Chia, Nicholas; Abyzov, Alexej; Ahlquist, David; Boardman, Lisa A

2018-02-16

The majority of colorectal cancer (CRC) arises from precursor lesions known as polyps. The molecular determinants that distinguish benign from malignant polyps remain unclear. To molecularly characterize polyps, we utilized Cancer Adjacent Polyp (CAP) and Cancer Free Polyp (CFP) patients. CAPs had tissues from the residual polyp of origin and contiguous cancer; CFPs had polyp tissues matched to CAPs based on polyp size, histology and dysplasia. To determine whether molecular features distinguish CAPs and CFPs, we conducted Whole Genome Sequencing, RNA-seq, and RRBS on over 90 tissues from 31 patients. CAPs had significantly more mutations, altered expression and hypermethylation compared to CFPs. APC was significantly mutated in both polyp groups, but mutations in TP53, FBXW7, PIK3CA, KIAA1804 and SMAD2 were exclusive to CAPs. We found significant expression changes between CAPs and CFPs in GREM1, IGF2, CTGF, and PLAU, and both expression and methylation alterations in FES and HES1. Integrative analyses revealed 124 genes with alterations in at least two platforms, and ERBB3 and E2F8 showed aberrations specific to CAPs across all platforms. These findings provide a resource of molecular distinctions between polyps with and without cancer, which have the potential to enhance the diagnosis, risk assessment and management of polyps.

Characterizing early molecular biomarkers of zinc-induced adaptive and adverseoxidative stress responses in human bronchial epithelial cells

EPA Science Inventory

Determining mechanism-based biomarkers that distinguish adaptive and adverse cellular processes is critical to understanding the health effects of environmental exposures. Here, we examined cellular responses of the tracheobronchial airway to zinc (Zn) exposure. A pharmacokinetic...

How may targeted proteomics complement genomic data in breast cancer?

PubMed

Guerin, Mathilde; Gonçalves, Anthony; Toiron, Yves; Baudelet, Emilie; Audebert, Stéphane; Boyer, Jean-Baptiste; Borg, Jean-Paul; Camoin, Luc

2017-01-01

Breast cancer (BC) is the most common female cancer in the world and was recently deconstructed in different molecular entities. Although most of the recent assays to characterize tumors at the molecular level are genomic-based, proteins are the actual executors of cellular functions and represent the vast majority of targets for anticancer drugs. Accumulated data has demonstrated an important level of quantitative and qualitative discrepancies between genomic/transcriptomic alterations and their protein counterparts, mostly related to the large number of post-translational modifications. Areas covered: This review will present novel proteomics technologies such as Reverse Phase Protein Array (RPPA) or mass-spectrometry (MS) based approaches that have emerged and that could progressively replace old-fashioned methods (e.g. immunohistochemistry, ELISA, etc.) to validate proteins as diagnostic, prognostic or predictive biomarkers, and eventually monitor them in the routine practice. Expert commentary: These different targeted proteomic approaches, able to complement genomic data in BC and characterize tumors more precisely, will permit to go through a more personalized treatment for each patient and tumor.

Low Molecular Weight Norbornadiene Derivatives for Molecular Solar-Thermal Energy Storage.

PubMed

Quant, Maria; Lennartson, Anders; Dreos, Ambra; Kuisma, Mikael; Erhart, Paul; Börjesson, Karl; Moth-Poulsen, Kasper

2016-09-05

Molecular solar-thermal energy storage systems are based on molecular switches that reversibly convert solar energy into chemical energy. Herein, we report the synthesis, characterization, and computational evaluation of a series of low molecular weight (193-260 g mol(-1) ) norbornadiene-quadricyclane systems. The molecules feature cyano acceptor and ethynyl-substituted aromatic donor groups, leading to a good match with solar irradiation, quantitative photo-thermal conversion between the norbornadiene and quadricyclane, as well as high energy storage densities (396-629 kJ kg(-1) ). The spectroscopic properties and energy storage capability have been further evaluated through density functional theory calculations, which indicate that the ethynyl moiety plays a critical role in obtaining the high oscillator strengths seen for these molecules. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Carbonic anhydrase inhibition of Schiff base derivative of imino-methyl-naphthalen-2-ol: Synthesis, structure elucidation, molecular docking, dynamic simulation and density functional theory calculations

NASA Astrophysics Data System (ADS)

Abbas, Saghir; Nasir, Hafiza Huma; Zaib, Sumera; Ali, Saqib; Mahmood, Tariq; Ayub, Khurshid; Tahir, Muhammad Nawaz; Iqbal, Jamshed

2018-03-01

In the present study, we have designed and synthesized a Schiff base derivative 3 and characterized by FT-IR, 1H and 13C NMR spectroscopy. Single crystal X-ray diffraction and NMR studies were also performed. The synthetic compound was screened for its inhibitory potential against carbonic anhydrase II. The experimental results were validated by molecular docking and dynamic simulations of compound 3 in the active pocket of enzyme. Important binding interactions with the key residues in the active site of the carbonic anhydrase enzyme were revealed. Moreover, supramolecular assembly of the title compound was analyzed by density functional theory (DFT) calculations. These studies rendered a more clear understanding for the demonstration of novel molecular mechanism involved in CA II inhibition by the synthesized compound.

Note: A short-pulse high-intensity molecular beam valve based on a piezoelectric stack actuator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abeysekera, Chamara; Joalland, Baptiste; Shi, Yuanyuan

2014-11-15

Solenoid and piezoelectric disk valves, which are widely used to generate molecular beam pulses, still suffer from significant restrictions, such as pulse durations typically >50 μs, low repetition rates, and limited gas flows and operational times. Much of this arises owing to the limited forces these actuators can achieve. To overcome these limitations, we have developed a new pulsed valve based on a high-force piezoelectric stack actuator. We show here that operation with pulse durations as low as 20 μs and repetition rates up to 100 Hz can be easily achieved by operating the valve in conjunction with a commercialmore » fast high-voltage switch. We outline our design and demonstrate its performance with molecular beam characterization via velocity map ion imaging.« less

An artificial muscle model unit based on inorganic nanosheet sliding by photochemical reaction.

PubMed

Nabetani, Yu; Takamura, Hazuki; Hayasaka, Yuika; Sasamoto, Shin; Tanamura, Yoshihiko; Shimada, Tetsuya; Masui, Dai; Takagi, Shinsuke; Tachibana, Hiroshi; Tong, Zhiwei; Inoue, Haruo

2013-04-21

From the viewpoint of developing photoresponsive supramolecular systems in microenvironments to exhibit more sophisticated photo-functions even at the macroscopic level, inorganic/organic hybrid compounds based on clay or niobate nanosheets as the microenvironments were prepared, characterized, and examined for their photoreactions. We show here a novel type of artificial muscle model unit having much similarity with that in natural muscle fibrils. Upon photoirradiation, the organic/inorganic hybrid nanosheets reversibly slide horizontally on a giant scale, and the interlayer spaces in the layered hybrid structure shrink and expand vertically. In particular, our layered hybrid molecular system exhibits a macroscopic morphological change on a giant scale (~1500 nm) compared with the molecular size of ~1 nm, based on a reversible sliding mechanism.

Molecular Characterization of H.pylori Strains and Biomarkers in Gastric Cancer

DTIC Science & Technology

2017-07-01

AWARD NUMBER: W81XWH-16-1-0274 TITLE: Molecular Characterization of H.pylori Strains and Biomarkers in Gastric Cancer PRINCIPAL INVESTIGATOR...SUBTITLE Molecular Characterization of H.pylori Strains and Biomarkers in Gastric Cancer 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-16-1-0274 5c...different individuals develop different gastroduodenal diseases. Our objectives are (1) to determine genetic features present in Hp GC isolates not

How enhanced molecular ions in Cold EI improve compound identification by the NIST library.

PubMed

Alon, Tal; Amirav, Aviv

2015-12-15

Library-based compound identification with electron ionization (EI) mass spectrometry (MS) is a well-established identification method which provides the names and structures of sample compounds up to the isomer level. The library (such as NIST) search algorithm compares different EI mass spectra in the library's database with the measured EI mass spectrum, assigning each of them a similarity score called 'Match' and an overall identification probability. Cold EI, electron ionization of vibrationally cold molecules in supersonic molecular beams, provides mass spectra with all the standard EI fragment ions combined with enhanced Molecular Ions and high-mass fragments. As a result, Cold EI mass spectra differ from those provided by standard EI and tend to yield lower matching scores. However, in most cases, library identification actually improves with Cold EI, as library identification probabilities for the correct library mass spectra increase, despite the lower matching factors. This research examined the way that enhanced molecular ion abundances affect library identification probability and the way that Cold EI mass spectra, which include enhanced molecular ions and high-mass fragment ions, typically improve library identification results. It involved several computer simulations, which incrementally modified the relative abundances of the various ions and analyzed the resulting mass spectra. The simulation results support previous measurements, showing that while enhanced molecular ion and high-mass fragment ions lower the matching factor of the correct library compound, the matching factors of the incorrect library candidates are lowered even more, resulting in a rise in the identification probability for the correct compound. This behavior which was previously observed by analyzing Cold EI mass spectra can be explained by the fact that high-mass ions, and especially the molecular ion, characterize a compound more than low-mass ions and therefore carries more weight in library search identification algorithms. These ions are uniquely abundant in Cold EI, which therefore enables enhanced compound characterization along with improved NIST library based identification. Copyright © 2015 John Wiley & Sons, Ltd.

Structural and molecular docking studies of biologically active mercaptopyrimidine Schiff bases

NASA Astrophysics Data System (ADS)

Kirubavathy, S. Jone; Velmurugan, R.; Karvembu, R.; Bhuvanesh, N. S. P.; Enoch, Israel V. M. V.; Selvakumar, P. Mosae; Premnath, D.; Chitra, S.

2017-01-01

Novel Schiff bases derived from the treatment of mercapto-diamino pyrimidine with two different aldehydes are characterized using elemental analysis, single crystal X-ray diffraction and 1H NMR spectroscopy. The pharmacological action of the synthesized compounds viz., antimicrobial, anticancer and antitubercular activities is studied. The Schiff bases show a very good activity against various test pathogens. DNA and β-CD binding interactions of the compounds are studied using UV-Visible absorption and fluorescence spectral measurements. The binding constants of the compounds towards β-CD are in the order of 103 to 104. Molecular docking is done using MOE program on the 3D structure of the enzymes, viz., human thymidylate synthase complexed with dump and raltitrex, candida albicans N-myristoyltransferasepeptidic inhibitor, catalytic domain of protein kinase pKnb from mycobacterium tuberculosis in complex with mitoxantrone, pare, topoisomerase atpase inhibitor, E. coli and lactobacillus casdihydrofolatereductase. The MIC/IC50 values of the Schiff bases are compared with the glide scores from the molecular docking studies. The number of hydrogen bonding interactions between the Schiff bases and amino acid residues are also reported.

Using graph-based assessments within socratic tutorials to reveal and refine students' analytical thinking about molecular networks.

PubMed

Trujillo, Caleb; Cooper, Melanie M; Klymkowsky, Michael W

2012-01-01

Biological systems, from the molecular to the ecological, involve dynamic interaction networks. To examine student thinking about networks we used graphical responses, since they are easier to evaluate for implied, but unarticulated assumptions. Senior college level molecular biology students were presented with simple molecular level scenarios; surprisingly, most students failed to articulate the basic assumptions needed to generate reasonable graphical representations; their graphs often contradicted their explicit assumptions. We then developed a tiered Socratic tutorial based on leading questions designed to provoke metacognitive reflection. The activity is characterized by leading questions (prompts) designed to provoke meta-cognitive reflection. When applied in a group or individual setting, there was clear improvement in targeted areas. Our results highlight the promise of using graphical responses and Socratic prompts in a tutorial context as both a formative assessment for students and an informative feedback system for instructors, in part because graphical responses are relatively easy to evaluate for implied, but unarticulated assumptions. Copyright © 2011 Wiley Periodicals, Inc.

A machine learning approach to computer-aided molecular design

NASA Astrophysics Data System (ADS)

Bolis, Giorgio; Di Pace, Luigi; Fabrocini, Filippo

1991-12-01

Preliminary results of a machine learning application concerning computer-aided molecular design applied to drug discovery are presented. The artificial intelligence techniques of machine learning use a sample of active and inactive compounds, which is viewed as a set of positive and negative examples, to allow the induction of a molecular model characterizing the interaction between the compounds and a target molecule. The algorithm is based on a twofold phase. In the first one — the specialization step — the program identifies a number of active/inactive pairs of compounds which appear to be the most useful in order to make the learning process as effective as possible and generates a dictionary of molecular fragments, deemed to be responsible for the activity of the compounds. In the second phase — the generalization step — the fragments thus generated are combined and generalized in order to select the most plausible hypothesis with respect to the sample of compounds. A knowledge base concerning physical and chemical properties is utilized during the inductive process.

In vitro DNA binding, pBR322 plasmid cleavage and molecular modeling study of chiral benzothiazole Schiff-base-valine Cu(II) and Zn(II) complexes to evaluate their enantiomeric biological disposition for molecular target DNA

NASA Astrophysics Data System (ADS)

Alizadeh, Rahman; Afzal, Mohd; Arjmand, Farukh

2014-10-01

Bicyclic heterocyclic compounds viz. benzothiazoles are key components of deoxyribonucleic acid (DNA) molecules and participate directly in the encoding of genetic information. Benzothiazoles, therefore, represent a potent and selective class of antitumor compounds. The design and synthesis of chiral antitumor chemotherapeutic agents of Cu(II) and Zn(II), L- and -D benzothiazole Schiff base-valine complexes 1a &b and 2a &b, respectively were carried out and thoroughly characterized by spectroscopic and analytical techniques. Interaction of 1a and b and 2a and b with CT DNA by employing UV-vis, florescence, circular dichroic methods and cleavage studies of 1a with pBR322 plasmid, molecular docking were done in order to demonstrate their enantiomeric disposition toward the molecular drug target DNA. Interestingly, these studies unambiguously demonstrated the greater potency of L-enantiomer in comparison to D-enantiomer.

Pure spin current and phonon thermoelectric transport in a triangulene-based molecular junction.

PubMed

Wang, Qiang; Li, Jianwei; Nie, Yihang; Xu, Fuming; Yu, Yunjin; Wang, Bin

2018-06-13

The experimental synthesis and characterization of enigmatic triangulene were reported for the first time recently. Based on this enigmatic molecule, we proposed a triangulene-based molecular junction and presented first principles calculations to investigate the electron and phonon thermoelectric transport properties. Numerical results show that the spin polarized electric transport properties of the triangulene-based molecular junction can be adjusted effectively by bias voltage and gate voltage. Through varying the gate voltage applied on the triangulene molecule, the system can exhibit a perfect spin filter effect. When a temperature gradient is applied between the two leads, spin up current and spin down current flow along opposite directions in the system simultaneously. Thus pure spin current can be obtained on a large scale by changing the temperature, temperature gradient, and gate voltage. When the phonon vibration effect is considered in thermal transport, the figure of merit is suppressed distinctively especially when the temperature is within the 10 K < T < 100 K range. More importantly, a large spin figure of merit can be achieved accompanied by a small charge figure of merit by adjusting the temperature, gate voltage and chemical potential in a wide range, which indicates a favorable application prospect of the triangulene-based molecular junction as a spin calorigenic device.

Molecular weight distribution of phosphorus fraction of aquatic dissolved organic matter.

PubMed

Ged, Evan C; Boyer, Treavor H

2013-05-01

This study characterized dissolved organic phosphorus (DOP) that is discharged from the Everglades Agricultural Area as part of the larger pool of aquatic dissolved organic matter (DOM). Whole water samples collected at the Everglades stormwater treat area 1 West (STA-1 W) were fractionated using a batch ultrafiltration method to separate organic compounds based on apparent molecular weight (AMW). Each AMW fraction of DOM was characterized for phosphorus, carbon, nitrogen, UV absorbance, and fluorescence. The DOP content of the Everglades water matrix was characteristically variable constituting 4-56% of total phosphorus (TP) and demonstrated no correlation with dissolved organic carbon (DOC). Measured values for DOP exceeded 14μgL(-1) in four out of five sampling dates making phosphorus load reductions problematic for the stormwater treatment areas (STAs), which target inorganic phosphorus and have a goal of 10μgL(-1) as TP. The molecular weight distributions revealed 40% of DOP is high molecular weight, aromatic-rich DOM. The results of this research are expected to be of interest to environmental chemists, environmental engineers, and water resources managers because DOP presents a major obstacle to achieving TP levels <10μgL(-1). Copyright © 2013 Elsevier Ltd. All rights reserved.

Integrative molecular and microanalytical studies of syntrophic partnerships linking C, S, and N cycles in anoxic environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orphan, Victoria

2016-07-15

Syntrophy and other forms of symbiotic associations between microorganisms are central to carbon and nutrient cycling in the environment. However, the inherent interdependence of these interactions, dynamic behavior, and frequent existence at thermodynamic limits has hindered our ability to both recognize syntrophic partnerships in nature and effectively study their behavior in the laboratory. To characterize and understand the underlying factors influencing syntrophic associations within complex communities requires a suite of tools that extend beyond basic molecular identification and cultivation. This specifically includes methods that preserve the natural spatial relationships between metabolically interdependent microorganisms while allowing downstream geochemical and/or molecular analysis.more » With support from this award, we have developed and applied new combinations of molecular, microscopy, and stable isotope-based methodologies that enable the characterization of fundamental links between phylogenetically-identified microorganisms and their specific metabolic activities and interactions in the environment. Through the coupling of fluorescence in situ hybridization (FISH) with cell capture and targeted metagenomics (Magneto-FISH), and FISH + secondary ion mass spectrometry (i.e. FISH-SIMS or FISH-nanoSIMS), we have defined new microbial interactions and the ecophysiology of anaerobic microorganisms involved in environmental methane cycling.« less

Molecular and agro-morphological characterization of ancient wheat landraces of turkey.

PubMed

Gurcan, Kahraman; Demirel, Fatih; Tekin, Mehmet; Demirel, Serap; Akar, Taner

2017-11-14

Turkey is one of the important gene centers for many crop species. In this research, some ancient wheats such as tetraploid and diploid hulled wheats together with hexaploid tir wheats (Triticum aestivum ssp. leucospermum Korn.) landraces mainly adapted to harsh winter conditions of Eastern Anatolian region of Turkey were characterized at agro-morphological and molecular level. Totally 50 hulled wheat population from Kastamonu, Konya and Kayseri provinces and 15 tir wheats from Kars provinces of Turkey were in-situ collected for characterization in 2013. Some quantitative and qualitative traits of each population were determined. Twenty three hulled wheat population collected from Kastamonu province were distinguished into nine emmer and 14 einkorn wheats at morphological level. Additionally, Konya, Kayseri and Kars population were characterized as einkorn, emmer and tir wheat, respectively. Among the evaluated traits, protein ratios of hulled wheats were strikingly higher than registered cultivars. All the populations were also examined by molecular level by using fluorescently labelled 11 polymorphic SSRs primers. The primers exhibited 104 bands, ranging from 6 to 16 with a mean value 9.45 per loci. The clustering analysis separated the germplasm into two clusters which were also divided into two subclusters based on genetic similarity coefficient. Sixty-five population and five checks were analyzed to estimate mean number of alleles (N), expected and observed heterozygoties (He and Ho), polymorphism information content (PIC), Wright fix index (F), genetic deviation from Hardy-Weinberg expectation (Fit-Fis) and genetic variation (Fst) were determined as 9.45, 0.71, 0.07, 0.67, 0.90, 0.39, 0.87 and 0.39, respectively. A clear genetic deviation from Hardy - Weinberg expectation was observed among population in particular. These results showed considerable genetic variation among landraces rather than within population. These molecular information has revealed genetically diverse einkorn, emmer wheat and tir wheat population could be used as parents for further breeding studies in both Turkey and abroad. Furthermore, the molecular analysis has also generally discriminated the germplasm into ploidy level.

Energy-Based Tissue Fusion for Sutureless Closure: Applications, Mechanisms, and Potential for Functional Recovery.

PubMed

Kramer, Eric A; Rentschler, Mark E

2018-06-04

As minimally invasive surgical techniques progress, the demand for efficient, reliable methods for vascular ligation and tissue closure becomes pronounced. The surgical advantages of energy-based vessel sealing exceed those of traditional, compression-based ligatures in procedures sensitive to duration, foreign bodies, and recovery time alike. Although the use of energy-based devices to seal or transect vasculature and connective tissue bundles is widespread, the breadth of heating strategies and energy dosimetry used across devices underscores an uncertainty as to the molecular nature of the sealing mechanism and induced tissue effect. Furthermore, energy-based techniques exhibit promise for the closure and functional repair of soft and connective tissues in the nervous, enteral, and dermal tissue domains. A constitutive theory of molecular bonding forces that arise in response to supraphysiological temperatures is required in order to optimize and progress the use of energy-based tissue fusion. While rapid tissue bonding has been suggested to arise from dehydration, dipole interactions, molecular cross-links, or the coagulation of cellular proteins, long-term functional tissue repair across fusion boundaries requires that the reaction to thermal damage be tailored to catalyze the onset of biological healing and remodeling. In this review, we compile and contrast findings from published thermal fusion research in an effort to encourage a molecular approach to characterization of the prevalent and promising energy-based tissue bond.

Fluorescent techniques for discovery and characterization of phosphopantetheinyl transferase inhibitors

PubMed Central

Kosa, Nicolas M.; Foley, Timothy L.; Burkart, Michael D.

2016-01-01

Phosphopantetheinyl transferase (E.C. 2.7.8.-) activates biosynthetic pathways that synthesize both primary and secondary metabolites in bacteria. Inhibitors of these enzymes have the potential to serve as antibiotic compounds that function through a unique mode of action and possess clinical utility. Here we report a direct and continuous assay for this enzyme class based upon monitoring polarization of a fluorescent phosphopantetheine analog as it is transferred from a low molecular weight coenzyme A substrate to higher molecular weight protein acceptor. We demonstrate the utility of this method for the biochemical characterization of phosphopantetheinyl transferase Sfp, a canonical representative from this class. We also establish the portability of this technique to other homologs by adapting the assay to function with the human phosphopantetheinyl transferase, a target for which a microplate detection method does not currently exist. Comparison of these targets provides a basis to predict therapeutic index of inhibitor candidates and offers a valuable characterization of enzyme activity. PMID:24192555

Core Canonical Pathways Involved in Developing Human Glioblastoma Multiforme (GBM).

PubMed

Ghosh, Somiranjan; Dutta, Sisir; Thorne, Gabriel; Boston, Ava; Barfield, Alexis; Banerjee, Narendra; Walker, Rayshawn; Banerjee, Hirendra Nath

2017-02-01

Glioblastoma multiforme (GBM) is the most common and aggressive type of the primary brain tumors with pathologic hallmarks of necrosis and vascular proliferation. The diagnosis of GBM is currently mostly based on histological examination of brain tumor tissues, after radiological characterization and surgical biopsy. The ability to characterize tumors comprehensively at the molecular level raises the possibility that diagnosis can be made based on molecular profiling with or without histological examination, rather than solely on histological phenotype. The development of novel genomic and proteomic techniques will foster in the identification of such diagnostic and prognostic molecular markers. We analyzed the global differential gene expression of a GBM cell line HTB15 in comparison to normal human Astrocytes, and established a few canonical pathways that are important in determining the molecular mechanisms of cancer using global gene expression microarray, coupled with the Ingenuity Pathway Analysis ( IPA ®). Overall, we revealed a discrete gene expression profile in the experimental model that resembled progression of GBM cancer. The canonical pathway analysis showed the involvement of genes that differentially expressed in such a disease condition that included Inositol pathway, Polo like kinases, nNOS signaling , and Tetrapyrrole biosynthesis . Our findings established that the gene expression pattern of this dreaded brain cancer will probably help the cancer research community by finding out newer therapeutic strategies to combat this dreaded cancer type that leads to the identification of high-risk population in this category, with almost hundred percent mortality rate.

Construction of the Free Energy Landscape of Peptide Aggregation from Molecular Dynamics Simulations.

PubMed

Riccardi, Laura; Nguyen, Phuong H; Stock, Gerhard

2012-04-10

To describe the structure and dynamics of oligomers during peptide aggregation, a method is proposed that considers both the intramolecular and intermolecular structures of the multimolecule system and correctly accounts for its degeneracy. The approach is based on the "by-parts" strategy, which partitions a complex molecular system into parts, determines the metastable conformational states of each part, and describes the overall conformational state of the system in terms of a product basis of the states of the parts. Starting from a molecular dynamics simulation of n molecules, the method consists of three steps: (i) characterization of the intramolecular structure, that is, of the conformational states of a single molecule in the presence of the other molecules (e.g., β-strand or random coil); (ii) characterization of the intermolecular structure through the identification of all occurring aggregate states of the peptides (dimers, trimers, etc.); and (iii) construction of the overall conformational states of the system in terms of a product basis of the n "single-molecule" states and the aggregate states. Considering the Alzheimer β-amyloid peptide fragment Aβ16-22 as a first application, about 700 overall conformational states of the trimer (Aβ16-22)3 were constructed from all-atom molecular dynamics simulation in explicit water. Based on these states, a transition network reflecting the free energy landscape of the aggregation process can be constructed that facilitates the identification of the aggregation pathways.

Systems Biology Methods for Alzheimer's Disease Research Toward Molecular Signatures, Subtypes, and Stages and Precision Medicine: Application in Cohort Studies and Trials.

PubMed

Castrillo, Juan I; Lista, Simone; Hampel, Harald; Ritchie, Craig W

2018-01-01

Alzheimer's disease (AD) is a complex multifactorial disease, involving a combination of genomic, interactome, and environmental factors, with essential participation of (a) intrinsic genomic susceptibility and (b) a constant dynamic interplay between impaired pathways and central homeostatic networks of nerve cells. The proper investigation of the complexity of AD requires new holistic systems-level approaches, at both the experimental and computational level. Systems biology methods offer the potential to unveil new fundamental insights, basic mechanisms, and networks and their interplay. These may lead to the characterization of mechanism-based molecular signatures, and AD hallmarks at the earliest molecular and cellular levels (and beyond), for characterization of AD subtypes and stages, toward targeted interventions according to the evolving precision medicine paradigm. In this work, an update on advanced systems biology methods and strategies for holistic studies of multifactorial diseases-particularly AD-is presented. This includes next-generation genomics, neuroimaging and multi-omics methods, experimental and computational approaches, relevant disease models, and latest genome editing and single-cell technologies. Their progressive incorporation into basic research, cohort studies, and trials is beginning to provide novel insights into AD essential mechanisms, molecular signatures, and markers toward mechanism-based classification and staging, and tailored interventions. Selected methods which can be applied in cohort studies and trials, with the European Prevention of Alzheimer's Dementia (EPAD) project as a reference example, are presented and discussed.

Structural and spectral comparisons between isomeric benzisothiazole and benzothiazole based aromatic heterocyclic dyes

NASA Astrophysics Data System (ADS)

Wang, Yin-Ge; Wang, Yue-Hua; Tao, Tao; Qian, Hui-Fen; Huang, Wei

2015-09-01

A pair of isomeric heterocyclic compounds, namely 3-amino-5-nitro-[2,1]-benzisothiazole and 2-amino-6-nitrobenzothiazole, are used as the diazonium components to couple with two N-substituted 4-aminobenzene derivatives. As a result, two pairs of isomeric aromatic heterocyclic azo dyes have been produced and they are structurally and spectrally characterized and compared including single-crystal structures, electronic spectra, solvatochromism and reversible acid-base discoloration, thermal stability and theoretically calculations. It is concluded that both benzisothiazole and benzothiazole based dyes show planar molecular structures and offset π-π stacking interactions, solvatochromism and reversible acid-base discoloration. Furthermore, benzisothiazole based aromatic heterocyclic dyes exhibit higher thermal stability, larger solvatochromic effects and maximum absorption wavelengths than corresponding benzothiazole based ones, which can be explained successfully by the differences of their calculated isomerization energy, dipole moment and molecular band gaps.

Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

PubMed

Guttikonda, Satish K; Marri, Pradeep; Mammadov, Jafar; Ye, Liang; Soe, Khaing; Richey, Kimberly; Cruse, James; Zhuang, Meibao; Gao, Zhifang; Evans, Clive; Rounsley, Steve; Kumpatla, Siva P

2016-01-01

Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions.

Characterization of a pepper collection (Capsicum frutescens L.) from Brazil.

PubMed

Lima, M F; Carvalho, S I C; Ragassi, C F; Bianchetti, L B; Faleiro, F G; Reifschneider, F J B

2017-08-31

Germplasm banks are essential as sources of genetic variability for plant breeding programs. To characterize a Brazilian Capsicum frutescens collection, 21 malagueta and 5 Tabasco hot pepper accessions were evaluated under field and greenhouse conditions regarding morphological and molecular traits, as well as resistance to viruses. Morphological characterization was performed using 53 IPGRI (International Plant Genetic Resources Institute) descriptors, 15 vegetative, 13 inflorescence, 22 fruit, and 3 seed. Molecular characterization was carried out with 60 polymorphic markers from 29 RAPD primers. The incidence of major viruses infecting Capsicum spp, Tomato spotted wilt virus (TSWV), Groundnut ringspot virus (GRSV), Potato virus Y (PVY), Pepper yellow mosaic virus (PepYMV), Pepper mild mottle virus (PMMoV), and Cucumber mosaic virus (CMV) was evaluated by ELISA. Based on the average genetic distance among genotypes, six groups were defined for the 53 IPGRI descriptors. When considering only 11 quantitative traits (five vegetative and six fruit), six groups were also determined, and the traits plant canopy width (56.05%) and days to fruiting (25.07%) most explained the genetic diversity among genotypes. Molecular analysis defined five groups of accessions with partial correspondence to the morphological characterization data. The incidence of viruses in field-grown plants varied among genotypes and according to virus species, from 5.6% (GRSV; CNPH 3286) to 100% (PMMoV; CNPH2871), and indicated some accessions as potential sources of virus resistance. These results demonstrate the genetic variability within the group of 26 hot pepper accessions, as well as virus-resistant genotypes that can be used in breeding programs.

Examining the Self-Assembly of Rod-Coil Block Copolymers via Physics Based Polymer Models and Polarized X-Ray Scattering

NASA Astrophysics Data System (ADS)

Hannon, Adam; Sunday, Daniel; Windover, Donald; Liman, Christopher; Bowen, Alec; Khaira, Gurdaman; de Pablo, Juan; Delongchamp, Dean; Kline, R. Joseph

Photovoltaics, flexible electronics, and stimuli-responsive materials all require enhanced methodology to examine their nanoscale molecular orientation. The mechanical, electronic, optical, and transport properties of devices made from these materials are all a function of this orientation. The polymer chains in these materials are best modeled as semi-flexible to rigid rods. Characterizing the rigidity and molecular orientation of these polymers non-invasively is currently being pursued by using polarized resonant soft X-ray scattering (P-RSoXS). In this presentation, we show recent work on implementing such a characterization process using a rod-coil block copolymer system in the rigid-rod limit. We first demonstrate how we have used physics based models such as self-consistent field theory (SCFT) in non-polarized RSoXS work to fit scattering profiles for thin film coil-coil PS- b-PMMA block copolymer systems. We then show by using a wormlike chain partition function in the SCFT formulism to model the rigid-rod block, the methodology can be used there as well to extract the molecular orientation of the rod block from a simulated P-RSoXS experiment. The results from the work show the potential of the technique to extract thermodynamic and morphological sample information.

A novel integrated framework and improved methodology of computer-aided drug design.

PubMed

Chen, Calvin Yu-Chian

2013-01-01

Computer-aided drug design (CADD) is a critical initiating step of drug development, but a single model capable of covering all designing aspects remains to be elucidated. Hence, we developed a drug design modeling framework that integrates multiple approaches, including machine learning based quantitative structure-activity relationship (QSAR) analysis, 3D-QSAR, Bayesian network, pharmacophore modeling, and structure-based docking algorithm. Restrictions for each model were defined for improved individual and overall accuracy. An integration method was applied to join the results from each model to minimize bias and errors. In addition, the integrated model adopts both static and dynamic analysis to validate the intermolecular stabilities of the receptor-ligand conformation. The proposed protocol was applied to identifying HER2 inhibitors from traditional Chinese medicine (TCM) as an example for validating our new protocol. Eight potent leads were identified from six TCM sources. A joint validation system comprised of comparative molecular field analysis, comparative molecular similarity indices analysis, and molecular dynamics simulation further characterized the candidates into three potential binding conformations and validated the binding stability of each protein-ligand complex. The ligand pathway was also performed to predict the ligand "in" and "exit" from the binding site. In summary, we propose a novel systematic CADD methodology for the identification, analysis, and characterization of drug-like candidates.

The effect of poly(vinyl alcohol) type and radiation treatment on the properties of starch-poly(vinyl alcohol) films

NASA Astrophysics Data System (ADS)

Cieśla, Krystyna; Abramowska, Anna; Boguski, Jacek; Drewnik, Joanna

2017-12-01

Our present study concerns the effect of application of various PVA substrates and the influence of ionising radiation on the properties of films based on starch and PVA. Four PVAs revealing various molecular masses (in the range of 11-145 kDa) were selected for this purpose. The films characterized by starch: PVA ratios of 40:60 were prepared by solution casting and irradiated with 60Co gamma rays (under nitrogen) and with fast electrons (under air) applying the absorbed dose of 25 kGy. Mechanical properties of the films (tensile strength, elongation at break and Young Modulus) were examined, as well as the contact angle to water and swelling in water, in regard for evaluation of the hydrophilic/hydrophobic properties. Gel content in the samples was also determined. Physicochemical properties of the films and their sensitivity to irradiation strongly depend on the applied PVA substrate. This can be related to differences in the capability of particular PVAs for forming the crosslinked starch-PVA network during the films' synthesis and future treatment. In particular, the usage of the PVA characterized by the high molecular mass has appeared more rewarding as compared to those based on the low molecular mass PVAs. Additionally, properties of these films were not affected or improved after irradiation.

Syntheses, spectroscopic characterization, thermal study, molecular modeling, and biological evaluation of novel Schiff's base benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) with Ni(II), and Cu(II) metal complexes

NASA Astrophysics Data System (ADS)

Chandra, Sulekh; Gautam, Seema; Rajor, Hament Kumar; Bhatia, Rohit

2015-02-01

Novel Schiff's base ligand, benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) was synthesized by the condensation of benzil and 5-amino-1,3,4-thiadiazole-2-thiol in 1:2 ratio. The structure of ligand was determined on the basis of elemental analyses, IR, 1H NMR, mass, and molecular modeling studies. Synthesized ligand behaved as tetradentate and coordinated to metal ion through sulfur atoms of thiol ring and nitrogen atoms of imine group. Ni(II), and Cu(II) complexes were synthesized with this nitrogen-sulfur donor (N2S2) ligand. Metal complexes were characterized by elemental analyses, molar conductance, magnetic susceptibility measurements, IR, electronic spectra, EPR, thermal, and molecular modeling studies. All the complexes showed molar conductance corresponding to non-electrolytic nature, expect [Ni(L)](NO3)2 complex, which was 1:2 electrolyte in nature. [Cu(L)(SO4)] complex may possessed square pyramidal geometry, [Ni(L)](NO3)2 complex tetrahedral and rest of the complexes six coordinated octahedral/tetragonal geometry. Newly synthesized ligand and its metal complexes were examined against the opportunistic pathogens. Results suggested that metal complexes were more biological sensitive than free ligand.

Structural systems pharmacology: a new frontier in discovering novel drug targets.

PubMed

Tan, Hepan; Ge, Xiaoxia; Xie, Lei

2013-08-01

The modern target-based drug discovery process, characterized by the one-drug-one-gene paradigm, has been of limited success. In contrast, phenotype-based screening produces thousands of active compounds but gives no hint as to what their molecular targets are or which ones merit further research. This presents a question: What is a suitable target for an efficient and safe drug? In this paper, we argue that target selection should take into account the proteome-wide energetic and kinetic landscape of drug-target interactions, as well as their cellular and organismal consequences. We propose a new paradigm of structural systems pharmacology to deconvolute the molecular targets of successful drugs as well as to identify druggable targets and their drug-like binders. Here we face two major challenges in structural systems pharmacology: How do we characterize and analyze the structural and energetic origins of drug-target interactions on a proteome scale? How do we correlate the dynamic molecular interactions to their in vivo activity? We will review recent advances in developing new computational tools for biophysics, bioinformatics, chemoinformatics, and systems biology related to the identification of genome-wide target profiles. We believe that the integration of these tools will realize structural systems pharmacology, enabling us to both efficiently develop effective therapeutics for complex diseases and combat drug resistance.

NEXAFS and XPS characterization of molecular oxygen adsorbed on Ni(100) at 80 K

NASA Astrophysics Data System (ADS)

Kim, C. M.; Jeong, H. S.; Kim, E. H.

2000-07-01

X-ray photoelectron spectroscopy (XPS), thermal desorption spectroscopy (TDS) and near edge extended X-ray absorption fine structure (NEXAFS) have been combined to investigate the adsorption of oxygen on Ni(100) at 80 K. Three O(1s) XPS features were observed at 530.0, 531.1 and 534.7 eV when the Ni(100) surface was exposed to 600 L of oxygen at 80 K. They are assigned as O 2-, O 1- and molecular oxygen species, respectively. The presence of molecular oxygen has been confirmed by TDS and NEXAFS. Molecular O 2 on Ni(100) is oriented perpendicular to the surface, and the OO bond length is estimated to be 1.24 Å, based on the NEXAFS σ ∗ resonance energy.

Computer-aided design of polymers and composites

NASA Technical Reports Server (NTRS)

Kaelble, D. H.

1985-01-01

This book on computer-aided design of polymers and composites introduces and discusses the subject from the viewpoint of atomic and molecular models. Thus, the origins of stiffness, strength, extensibility, and fracture toughness in composite materials can be analyzed directly in terms of chemical composition and molecular structure. Aspects of polymer composite reliability are considered along with characterization techniques for composite reliability, relations between atomic and molecular properties, computer aided design and manufacture, polymer CAD/CAM models, and composite CAD/CAM models. Attention is given to multiphase structural adhesives, fibrous composite reliability, metal joint reliability, polymer physical states and transitions, chemical quality assurance, processability testing, cure monitoring and management, nondestructive evaluation (NDE), surface NDE, elementary properties, ionic-covalent bonding, molecular analysis, acid-base interactions, the manufacturing science, and peel mechanics.

Ultrasonic promoted synthesis of novel s-triazine-Schiff base derivatives; molecular structure, spectroscopic studies and their preliminary anti-proliferative activities

NASA Astrophysics Data System (ADS)

El-Faham, Ayman; Soliman, Saied M.; Ghabbour, Hazem A.; Elnakady, Yasser A.; Mohaya, Talal A.; Siddiqui, Mohammed R. H.; Albericio, Fernando

2016-12-01

Novel series of s-triazine-Schiff base derivatives were synthesized employing ultrasonic irradiation and characterized by NMR (1H and 13C), FT-IR, and elemental analysis. The use of ultrasonic irradiation has allowed the preparation of the target products with better yields in shorter reaction time and excellent purities compared to the conventional heating. X-ray single crystal diffraction experiments verified the molecular structure of four from the new prepared s-triaizne-Schiff base derivatives. The molecular structures of the studied compounds are computerized using DFT/B3LYP method. The effects of substituent at the triazine and phenyl ring on the electronic and spectroscopic properties of the studied compounds were also investigated. The natural atomic charges showed that pipridino-s-triazine derivatives are richer in electrons than those having morpholino derivatives. The anti-proliferative effects for the prepared compounds were tested against three different cancer cell lines.

Identification of molecular markers associated with fruit traits in olive and assessment of olive core collection with AFLP markers and fruit traits.

PubMed

Ipek, M; Seker, M; Ipek, A; Gul, M K

2015-03-31

The purpose of this study was to characterize olive core collection with amplified fragment length polymorphism (AFLP) markers and fruit traits and to determine AFLP markers significantly associated with these fruit characters in olive. A total of 168 polymorphic AFLP markers generated by five primer combinations and nine fruit traits were used to characterize relationships between 18 olive cultivars. Although all olive cultivars were discriminated from each other by either AFLP markers (<0.75 similarity level) or fruit traits, clustering based on the AFLP markers and fruit traits was not significantly correlated (r = 0.13). Partial clustering of olive cultivars by AFLP markers according to their geographical origin was observed. Associations of AFLP markers with fruits were determined using a multiple-regression analysis with stepwise addition of AFLP markers. Significant associations between eight AFLP markers and fruit traits were identified. While five AFLP markers demonstrated significant negative correlation with fruit and stone weight, width and length and total polyphenols (P < 0.05), three AFLP markers displayed significant positive correlation with α-tocopherol and γ-tocopherol (P < 0.01). This is the first report on the association of molecular markers with fruit traits in olive. Molecular markers associated with morphological and agronomic traits could be utilized for the breeding of olive cultivars. However, the association power of these markers needs to be confirmed in larger populations, and highly correlated markers should then be converted to PCR-based DNA markers such as sequence-characterized amplified region markers for better utilization.

A general analytical strategy for the characterization of phenolic compounds in fruit juices by high-performance liquid chromatography with diode array detection coupled to electrospray ionization and triple quadrupole mass spectrometry.

PubMed

Abad-García, Beatriz; Berrueta, Luis A; Garmón-Lobato, Sergio; Gallo, Blanca; Vicente, Francisca

2009-07-10

In the present study, a methodology based on liquid chromatography with diode array detection (HPLC/DAD) coupled to an electrospray ionization (ESI) interface and a triple quadrupole mass spectrometer for the simultaneous identification of phenolic compounds in fruit juices has been developed. 72 available phenolic compound standards from diverse families present in fruits have been studied in order to analyze their fragmentation pattern. As a result, a general strategy for the characterization of unknown phenolic compounds in fruit juices was designed: (i) taking into account its UV-visible spectrum and elution order, assign the unknown polyphenol to a polyphenol class, (ii) identify the quasi-molecular ion using positive and negative MS spectra, being supported by adducts generated with solvent or sodium and molecular complexes, (iii) determinate the pattern of glycosylation in positive mode using ESI(+)-CID MS/MS product ion scan experiments, selecting the quasi-molecular ion as precursor ion, and finally, (iv) study the identity of the aglycone through ESI(+)-CID MS/MS product ion spectra from the protonated aglycone, [Y(0)](+). This strategy was successfully employed for the characterization of known and unknown phenolic compounds in juices from 17 different fruits.

Advanced solvent based methods for molecular characterization of soil organic matter by high-resolution mass spectrometry.

PubMed

Tfaily, Malak M; Chu, Rosalie K; Tolić, Nikola; Roscioli, Kristyn M; Anderton, Christopher R; Paša-Tolić, Ljiljana; Robinson, Errol W; Hess, Nancy J

2015-01-01

Soil organic matter (SOM), a complex, heterogeneous mixture of above and belowground plant litter and animal and microbial residues at various degrees of decomposition, is a key reservoir for carbon (C) and nutrient biogeochemical cycling in soil based ecosystems. A limited understanding of the molecular composition of SOM limits the ability to routinely decipher chemical processes within soil and accurately predict how terrestrial carbon fluxes will respond to changing climatic conditions and land use. To elucidate the molecular-level structure of SOM, we selectively extracted a broad range of intact SOM compounds by a combination of different organic solvents from soils with a wide range of C content. Our use of electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and a suite of solvents with varying polarity significantly expands the inventory of the types of organic molecules present in soils. Specifically, we found that hexane is selective for lipid-like compounds with very low O/C ratios (<0.1); water (H2O) was selective for carbohydrates with high O/C ratios; acetonitrile (ACN) preferentially extracts lignin, condensed structures, and tannin polyphenolic compounds with O/C > 0.5; methanol (MeOH) has higher selectivity toward compounds characterized with low O/C < 0.5; and hexane, MeOH, ACN, and H2O solvents increase the number and types of organic molecules extracted from soil for a broader range of chemically diverse soil types. Our study of SOM molecules by ESI FTICR MS revealed new insight into the molecular-level complexity of organics contained in soils. We present the first comparative study of the molecular composition of SOM from different ecosystems using ultra high-resolution mass spectrometry.

Characterization of secondary organic aerosol from photo-oxidation of gasoline exhaust and specific sources of major components.

PubMed

Ma, Pengkun; Zhang, Peng; Shu, Jinian; Yang, Bo; Zhang, Haixu

2018-01-01

To further explore the composition and distribution of secondary organic aerosol (SOA) components from the photo-oxidation of light aromatic precursors (toluene, m-xylene, and 1,3,5-trimethylbenzene (1,3,5-TMB)) and idling gasoline exhaust, a vacuum ultraviolet photoionization mass spectrometer (VUV-PIMS) was employed. Peaks of the molecular ions of the SOA components with minimum molecular fragmentation were clearly observed from the mass spectra of SOA, through the application of soft ionization methods in VUV-PIMS. The experiments comparing the exhaust-SOA and light aromatic mixture-SOA showed that the observed distributions of almost all the predominant cluster ions in the exhaust-SOA were similar to that of the mixture-SOA. Based on the characterization experiments of SOA formed from individual light aromatic precursors, the SOA components with molecular weights of 98 and 110 amu observed in the exhaust-SOA resulted from the photo-oxidation of toluene and m-xylene; the components with a molecular weight of 124 amu were derived mainly from m-xylene; and the components with molecular weights of 100, 112, 128, 138, and 156 amu were mainly derived from 1,3,5-TMB. These results suggest that C 7 -C 9 light aromatic hydrocarbons are significant SOA precursors and that major SOA components originate from gasoline exhaust. Additionally, some new light aromatic hydrocarbon-SOA components were observed for the first time using VUV-PIMS. The corresponding reaction mechanisms were also proposed in this study to enrich the knowledge base of the formation mechanisms of light aromatic hydrocarbon-SOA compounds. Copyright © 2017 Elsevier Ltd. All rights reserved.

IDENTIFICATION OF CRYPTOSPORIDIUM SPECIES AND SOURCES IN RAW WASTEWATER USING A SMALL SUBUNIT RRNA-BASED PCR-RFLP TOOL

EPA Science Inventory

The species composition and source of Cryptosporidium oocysts in wastewater have never been determined, even though it is widely assumed that these oocysts are from human sewage. Recent molecular characterizations of Cryptosporidium parasites make it possible to differentiate hum...

IDENTIFICATION OF CRYPTOSPORIDIUM SPECIES AND THE SOURCES IN RAW WASTEWATER USING A SMALL SUBUNIT RRNA-BASED PCR-RFLP TOOL

EPA Science Inventory

The species composition and source of Cryptosporidium oocysts in wastewater have never been determined, even though it is widely assumed that these oocysts are from human sewage. Recent molecular characterizations of Cryptosporidium parasites make it possible to differentiate hum...

Molecular marker based characterization and genetic diversity of wheat genotypes in relation to boron efficiency

USDA-ARS?s Scientific Manuscript database

Boron deficient soils pose a critical problem to wheat production in many areas of the world including Bangladesh and causes significant yield reduction. Therefore, in the present study, 21 diverse wheat (Triticum aestivum L.) genotypes collected from three different countries (Bangladesh, India, a...

Kim Magrini | NREL

Science.gov Websites

Developing char-based soil amendments Soil carbon and char analysis via molecular beam mass spectrometry depth profiling, Fourier transform infrared [FTIR]) Rapid soil carbon analysis using analytical DRIFTS, 13C NMR, and py-MBMS to Characterize the Effects of Soil Science Oxidation Assays on Soil Organic

Molecular Characterization and Genetic Structure in Avocado (Persea americana Mill.) Using Simple Sequence Repeat (SSR) Markers

USDA-ARS?s Scientific Manuscript database

Avocado (Persea americana Mill.) is an economically important tropical fruit native to Mesoamerica. It belongs to the Lauraceae family and is subdivided in three horticultural races (Guatemalan, Mexican, and West Indian) based primarily on ecological adaptation, botanical and physiological traits. T...

Synthesis, Photophysical Characterization, and Gelation Studies of a Stilbene-Cholesterol Derivative

ERIC Educational Resources Information Center

Geiger, H. Christina; Geiger, David K.; Baldwin, Christine

2006-01-01

Organogels are low molar mass organic compounds with the ability to immobilize an incredible quantity of solvent and fibrous aggregation of these compounds formed by noncovalent interaction usually involves hydrogen bonding. For stilbene-cholesterol based gelators, the driving force for molecular aggregation are weak van der Waal interactions…

Metal-organic frameworks with dynamic interlocked components

NASA Astrophysics Data System (ADS)

Vukotic, V. Nicholas; Harris, Kristopher J.; Zhu, Kelong; Schurko, Robert W.; Loeb, Stephen J.

2012-06-01

The dynamics of mechanically interlocked molecules such as rotaxanes and catenanes have been studied in solution as examples of rudimentary molecular switches and machines, but in this medium, the molecules are randomly dispersed and their motion incoherent. As a strategy for achieving a higher level of molecular organization, we have constructed a metal-organic framework material using a [2]rotaxane as the organic linker and binuclear Cu(II) units as the nodes. Activation of the as-synthesized material creates a void space inside the rigid framework that allows the soft macrocyclic ring of the [2]rotaxane to rotate rapidly, unimpeded by neighbouring molecular components. Variable-temperature 13C and 2H solid-state NMR experiments are used to characterize the nature and rate of the dynamic processes occurring inside this unique material. These results provide a blueprint for the future creation of solid-state molecular switches and molecular machines based on mechanically interlocked molecules.

Chirped Laser Dispersion Spectroscopy for Remote Open-Path Trace-Gas Sensing

PubMed Central

Nikodem, Michal; Wysocki, Gerard

2012-01-01

In this paper we present a prototype instrument for remote open-path detection of nitrous oxide. The sensor is based on a 4.53 μm quantum cascade laser and uses the chirped laser dispersion spectroscopy (CLaDS) technique for molecular concentration measurements. To the best of our knowledge this is the first demonstration of open-path laser-based trace-gas detection using a molecular dispersion measurement. The prototype sensor achieves a detection limit down to the single-ppbv level and exhibits excellent stability and robustness. The instrument characterization, field deployment performance, and the advantages of applying dispersion sensing to sensitive trace-gas detection in a remote open-path configuration are presented. PMID:23443389

Chirped laser dispersion spectroscopy for remote open-path trace-gas sensing.

PubMed

Nikodem, Michal; Wysocki, Gerard

2012-11-28

In this paper we present a prototype instrument for remote open-path detection of nitrous oxide. The sensor is based on a 4.53 μm quantum cascade laser and uses the chirped laser dispersion spectroscopy (CLaDS) technique for molecular concentration measurements. To the best of our knowledge this is the first demonstration of open-path laser-based trace-gas detection using a molecular dispersion measurement. The prototype sensor achieves a detection limit down to the single-ppbv level and exhibits excellent stability and robustness. The instrument characterization, field deployment performance, and the advantages of applying dispersion sensing to sensitive trace-gas detection in a remote open-path configuration are presented.

Characterization of hydrotreated Mayan and Wilmington vacuum tower bottoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pearson, C.D.; Green, J.B.; Bhan, O.K.

1989-04-01

Mayan and Wilmington vacuum tower bottoms were hydrotreated at various severity levels in a batch autoclave with and without catalyst. Each of the feeds and the hydrotreated products was separated into acid-base (ABN) fraction using a unique non-aqueous ion exchange technique. The feeds, hydrotreated whole products, and the ABN fractions were characterized by determining their elemental and metal content. Selected samples were analyzed by size exclusion chromatography/inductively coupled plasma technique to determine molecular size distribution of various species.

Novel high contrast electrochromic polymer materials based on 3,4-propylenedioxythiophene

NASA Astrophysics Data System (ADS)

Sahoo, Rabindra; Mishra, Sarada P.; Kumar, Anil; Sindhu, S.; Narasimha Rao, K.; Gopal, E. S. R.

2007-09-01

Mono and di allyl and napthyl substituted 3,4-propylenedioxythiophenes were synthesized and polymerized electrochemically. All the monomers were characterized for their molecular structures, and the polymers were characterized for their electrochemical properties. The disubstituted derivatives showed higher contrast than the corresponding mono substituted derivatives. The allyl substituted polymers showed higher contrast and faster switching time than corresponding napthyl substituted derivatives. The presence of the allyl group as the pendant can be used for further functionalization of the polymer.

Comprehensive structure-selective characterization of dissolved organic matter by reducing molecular complexity and increasing analytical dimensions.

PubMed

Li, Yan; Harir, Mourad; Lucio, Marianna; Gonsior, Michael; Koch, Boris P; Schmitt-Kopplin, Philippe; Hertkorn, Norbert

2016-12-01

Deciphering the molecular codes of dissolved organic matter (DOM) improves our understanding of its role in the global element cycles and its active involvement in ecosystem services. This study demonstrates comprehensive characterization of DOM by an initial polarity-based stepwise solid phase extraction (SPE) with single methanol elution of the cartridges, but separate collection of equal aliquots of eluate. The reduction of molecular complexity in the individual DOM fractions attenuates intermolecular interactions and substantially increases the disposable resolution of any structure selective characterization. Suwannee River DOM (SR DOM) was used to collect five distinct SPE fractions with overall 91% DOC recovery. Optical spectroscopy (UV and fluorescence spectroscopy), high-field Fourier transform ion cyclotron mass spectrometry (FTICR MS) and nuclear magnetic resonance (NMR) spectroscopy showed analogous hierarchical clustering among the five eluates corroborating the robustness of this approach. Two abundant moderately hydrophobic fractions contained most of the SR DOM compounds, with substantial proportions of aliphatics, carboxylic-rich alicyclic molecules, carbohydrates and aromatics. A minor early eluting hydrophilic fraction was highly aliphatic and presented a large diversity of alicyclic carboxylic acids, whereas the two late eluting, minor hydrophobic fractions appeared as a largely defunctionalized mixture of aliphatic molecules. Comparative mass analysis showed that fractionation of SR DOM was governed by multiple molecular interactions depending on O/C ratio, molecular weight and aromaticity. The traditional optical indices SUVA 254 and fluorescence index (FI) indicated the relative aromaticity in agreement with FTICR mass and NMR spectra; the classical fluorescent peaks A and C were observed in all four latter eluates. This versatile approach can be easily expanded to preparative scale under field conditions, and transferred to different DOM sources and SPE conditions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Prediction and redesign of protein–protein interactions

PubMed Central

Lua, Rhonald C.; Marciano, David C.; Katsonis, Panagiotis; Adikesavan, Anbu K.; Wilkins, Angela D.; Lichtarge, Olivier

2014-01-01

Understanding the molecular basis of protein function remains a central goal of biology, with the hope to elucidate the role of human genes in health and in disease, and to rationally design therapies through targeted molecular perturbations. We review here some of the computational techniques and resources available for characterizing a critical aspect of protein function – those mediated by protein–protein interactions (PPI). We describe several applications and recent successes of the Evolutionary Trace (ET) in identifying molecular events and shapes that underlie protein function and specificity in both eukaryotes and prokaryotes. ET is a part of analytical approaches based on the successes and failures of evolution that enable the rational control of PPI. PMID:24878423

Fungal burden exposure assessment in podiatry clinics from Ireland.

PubMed

Viegas, Carla; Coggins, Ann Marie; Faria, Tiago; Caetano, Liliana Aranha; Gomes, Anita Quintal; Sabino, Raquel; Verissimo, Cristina; Roberts, Nigel; Watterson, David; MacGilchrist, Claire; Fleming, Gerard T A

2018-03-26

Fungi are amongst the bioaerosols of most importance, as indicated by the growing interest in this field of research. The aim was to characterize the exposure to fungal burden in podiatry clinics using culture-based and molecular methods. Airborne fungi were collected using an impaction air sampler and surface samples were also performed. Fourteen air samples were collected for direct detection of fungal DNA from filamentous fungi and dermatophytes. Overall, 63.6 % of the evening samples and 46 % of the morning samples surpassed the threshold values (150 CFU/m 3 ). Molecular detection, by real time PCR, of the target fungal species/strains (Aspergillus and Stachybotrys species) was negative for all samples collected. Trichophyton rubrum was detected by PCR analysis in one DNA sample collected on day six. Results suggest the use of both culture-based and molecular methodologies are desirable for a complete evaluation of fungal burden in this particular health care setting.

Chemical fabrication of heterometallic nanogaps for molecular transport junctions.

PubMed

Chen, Xiaodong; Yeganeh, Sina; Qin, Lidong; Li, Shuzhou; Xue, Can; Braunschweig, Adam B; Schatz, George C; Ratner, Mark A; Mirkin, Chad A

2009-12-01

We report a simple and reproducible method for fabricating heterometallic nanogaps, which are made of two different metal nanorods separated by a nanometer-sized gap. The method is based upon on-wire lithography, which is a chemically enabled technique used to synthesize a wide variety of nanowire-based structures (e.g., nanogaps and disk arrays). This method can be used to fabricate pairs of metallic electrodes, which exhibit distinct work functions and are separated by gaps as small as 2 nm. Furthermore, we demonstrate that a symmetric thiol-terminated molecule can be assembled into such heterometallic nanogaps to form molecular transport junctions (MTJs) that exhibit molecular diode behavior. Theoretical calculations demonstrate that the coupling strength between gold and sulfur (Au-S) is 2.5 times stronger than that of Pt-S. In addition, the structures form Raman hot spots in the gap, allowing the spectroscopic characterization of the molecules that make up the MTJs.

Synthesis and Characterization of Gelatin-Based Crosslinkers for the Fabrication of Superabsorbent Hydrogels

PubMed Central

Amonpattaratkit, Penphitcha; Khunmanee, Sureerat; Kim, Dong Hyun; Park, Hansoo

2017-01-01

In this work, crosslinkers were prepared by conjugating high- and low-molecular-weight gelatin with different mole ratios of itaconic acid (IA) with double bonds. Then, the gelatin-itaconic acid (gelatin-IA) crosslinkers were compared with the gelatin-methacrylate (gelatin-MA) crosslinkers. The molecular weights and structures of gelatin-MA and gelatin-IA were confirmed using gel permeation chromatography (GPC) and nuclear magnetic resonance (NMR). Additionally, the swelling ratio and biodegradation properties of the hydrogels using IA as starting monomers and gelatin-IA and gelatin-MA as crosslinkers were investigated. Both hydrogels prepared with high and low molecular weights of gelatin-IA showed higher swelling ratios than those prepared with the gelatin-MA. The results also showed that absorbent hydrogels with different biodegradabilities and swelling ratios could be prepared by changing the ratio of the gelatin-based crosslinkers. PMID:28773186

Surface properties of poly(acrylonitrile) (PAN) precipitation polymerized in supercritical CO2 and the influence of the molecular weight.

PubMed

Shen, Qing; Gu, Qing-Feng; Hu, Jian-Feng; Teng, Xin-Rong; Zhu, Yun-Feng

2003-11-15

In this paper, the surface properties, e.g., the total surface free energy and the related Lifshitz-van der Waals and Lewis acid-base components, of polyacrylonitrile (PAN) precipitation polymerized in supercritical CO(2) have been characterized. Moreover, the influence of molecular weight varying has been also investigated. Results show that the surface properties of PAN resulting from supercritical CO(2) are different from those obtained by the conventional method. Of these data, one important finding is that the supercritical CO(2) PAN seems to decrease the surface free energy with the increased molecular weight. Based on previous recorded NMR spectra of this PAN and especially compared to commercial PAN, such phenomena are discussed and ascribed to an increase of the H-bonds and a reduction of the isotacticity in the supercritical CO(2) condition for PAN.

Effect of substituents on prediction of TLC retention of tetra-dentate Schiff bases and their Copper(II) and Nickel(II) complexes.

PubMed

Stevanović, Nikola R; Perušković, Danica S; Gašić, Uroš M; Antunović, Vesna R; Lolić, Aleksandar Đ; Baošić, Rada M

2017-03-01

The objectives of this study were to gain insights into structure-retention relationships and to propose the model to estimating their retention. Chromatographic investigation of series of 36 Schiff bases and their copper(II) and nickel(II) complexes was performed under both normal- and reverse-phase conditions. Chemical structures of the compounds were characterized by molecular descriptors which are calculated from the structure and related to the chromatographic retention parameters by multiple linear regression analysis. Effects of chelation on retention parameters of investigated compounds, under normal- and reverse-phase chromatographic conditions, were analyzed by principal component analysis, quantitative structure-retention relationship and quantitative structure-activity relationship models were developed on the basis of theoretical molecular descriptors, calculated exclusively from molecular structure, and parameters of retention and lipophilicity. Copyright © 2016 John Wiley & Sons, Ltd.

Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies.

PubMed

Soler, Miguel A; de Marco, Ario; Fortuna, Sara

2016-10-10

Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and whole-molecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules.

Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies

NASA Astrophysics Data System (ADS)

Soler, Miguel A.; De Marco, Ario; Fortuna, Sara

2016-10-01

Nanobodies (VHHs) have proved to be valuable substitutes of conventional antibodies for molecular recognition. Their small size represents a precious advantage for rational mutagenesis based on modelling. Here we address the problem of predicting how Camelidae nanobody sequences can tolerate mutations by developing a simulation protocol based on all-atom molecular dynamics and whole-molecule docking. The method was tested on two sets of nanobodies characterized experimentally for their biophysical features. One set contained point mutations introduced to humanize a wild type sequence, in the second the CDRs were swapped between single-domain frameworks with Camelidae and human hallmarks. The method resulted in accurate scoring approaches to predict experimental yields and enabled to identify the structural modifications induced by mutations. This work is a promising tool for the in silico development of single-domain antibodies and opens the opportunity to customize single functional domains of larger macromolecules.

CAST: a new program package for the accurate characterization of large and flexible molecular systems.

PubMed

Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

2014-09-15

The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

Materials-by-design: computation, synthesis, and characterization from atoms to structures

NASA Astrophysics Data System (ADS)

Yeo, Jingjie; Jung, Gang Seob; Martín-Martínez, Francisco J.; Ling, Shengjie; Gu, Grace X.; Qin, Zhao; Buehler, Markus J.

2018-05-01

In the 50 years that succeeded Richard Feynman’s exposition of the idea that there is ‘plenty of room at the bottom’ for manipulating individual atoms for the synthesis and manufacturing processing of materials, the materials-by-design paradigm is being developed gradually through synergistic integration of experimental material synthesis and characterization with predictive computational modeling and optimization. This paper reviews how this paradigm creates the possibility to develop materials according to specific, rational designs from the molecular to the macroscopic scale. We discuss promising techniques in experimental small-scale material synthesis and large-scale fabrication methods to manipulate atomistic or macroscale structures, which can be designed by computational modeling. These include recombinant protein technology to produce peptides and proteins with tailored sequences encoded by recombinant DNA, self-assembly processes induced by conformational transition of proteins, additive manufacturing for designing complex structures, and qualitative and quantitative characterization of materials at different length scales. We describe important material characterization techniques using numerous methods of spectroscopy and microscopy. We detail numerous multi-scale computational modeling techniques that complements these experimental techniques: DFT at the atomistic scale; fully atomistic and coarse-grain molecular dynamics at the molecular to mesoscale; continuum modeling at the macroscale. Additionally, we present case studies that utilize experimental and computational approaches in an integrated manner to broaden our understanding of the properties of two-dimensional materials and materials based on silk and silk-elastin-like proteins.

Rheological Properties of Gels from Pyrene Based Low Molecular Weight Gelators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leivo, Kimmo T.; Hahma, Arno P.

2008-07-07

Gels of pyrene derived low molecular weight organogelators (LMOGs) in primary alcohols have been characterized by rheometry and scanning electron microscopy. Total gelator concentration was 1-2.7 % w/w depending on the solvent and the gelator, including equimolar amounts of the gelator and 2,4,7-trinitrofluorenone (TNF), which is necessary for gelation. Thermoreversible and strongly shear thinning gels were achieved as the two components interact non-covalently to form a gel network. A qualitative correlation between the rheological properties and the nanoscale gel structure were found.

Rheological Properties of Gels from Pyrene Based Low Molecular Weight Gelators

NASA Astrophysics Data System (ADS)

Leivo, Kimmo T.; Hahma, Arno P.

2008-07-01

Gels of pyrene derived low molecular weight organogelators (LMOGs) in primary alcohols have been characterized by rheometry and scanning electron microscopy. Total gelator concentration was 1-2.7 % w/w depending on the solvent and the gelator, including equimolar amounts of the gelator and 2,4,7-trinitrofluorenone (TNF), which is necessary for gelation. Thermoreversible and strongly shear thinning gels were achieved as the two components interact non-covalently to form a gel network. A qualitative correlation between the rheological properties and the nanoscale gel structure were found.

Recent Developments in Hydrogen Evolving Molecular Cobalt(II)-Polypyridyl Catalysts

PubMed Central

Queyriaux, N.; Jane, R. T.; Massin, J.; Artero, V.; Chavarot-Kerlidou, M.

2015-01-01

The search for efficient noble metal-free hydrogen-evolving catalysts is the subject of intense research activity. A new family of molecular cobalt(II)-polypyridyl catalysts has recently emerged. These catalysts prove more robust under reductive conditions than other cobalt-based systems and display high activities under fully aqueous conditions. This review discusses the design, characterization, and evaluation of these catalysts for electrocatalytic and light-driven hydrogen production. Mechanistic considerations are addressed and structure-catalytic activity relationships identified in order to guide the future design of more efficient catalytic systems. PMID:26688590

Molecular Analysis of Date Palm Genetic Diversity Using Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeats (ISSRs).

PubMed

El Sharabasy, Sherif F; Soliman, Khaled A

2017-01-01

The date palm is an ancient domesticated plant with great diversity and has been cultivated in the Middle East and North Africa for at last 5000 years. Date palm cultivars are classified based on the fruit moisture content, as dry, semidry, and soft dates. There are a number of biochemical and molecular techniques available for characterization of the date palm variation. This chapter focuses on the DNA-based markers random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) techniques, in addition to biochemical markers based on isozyme analysis. These techniques coupled with appropriate statistical tools proved useful for determining phylogenetic relationships among date palm cultivars and provide information resources for date palm gene banks.

Structure-based Design, Synthesis, Biochemical and Pharmacological Characterization of Novel Salvinorin A Analogues as Active State Probes of the κ-Opioid Receptor

PubMed Central

Yan, Feng; Bikbulatov, Ruslan V.; Mocanu, Viorel; Dicheva, Nedyalka; Parker, Carol E.; Wetsel, William C.; Mosier, Philip D.; Westkaemper, Richard B.; Allen, John A.; Zjawiony, Jordan K.; Roth, Bryan L.

2009-01-01

Salvinorin A, the most potent naturally occurring hallucinogen, has gained increasing attention since the κ-opioid receptor (KOR) was identified as its principal molecular target by us (Roth et al, PNAS, 2002). Here we report the design, synthesis and biochemical characterization of novel, irreversible, salvinorin A-derived ligands suitable as active state probes of the KOR. Based on prior substituted cysteine accessibility and molecular modeling studies, C3157.38 was chosen as a potential anchoring point for covalent labeling of salvinorin A-derived ligands. Automated docking of a series of potential covalently-bound ligands suggested that either a haloacetate moiety or other similar electrophilic groups could irreversibly bind with C3157.38. 22-thiocyanatosalvinorin A (RB-64) and 22-chlorosalvinorin A (RB-48) were both found to be extraordinarily potent and selective KOR agonists in vitro and in vivo. As predicted based on molecular modeling studies, RB-64 induced wash-resistant inhibition of binding with a strict requirement for a free cysteine in or near the binding pocket. Mass spectrometry (MS) studies utilizing synthetic KOR peptides and RB-64 supported the hypothesis that the anchoring residue was C3157.38 and suggested one biochemical mechanism for covalent binding. These studies provide direct evidence for the presence of a free cysteine in the agonist-bound state of KOR and provide novel insights into the mechanism by which salvinorin A binds to and activates KOR. PMID:19555087

Morphological and molecular characterization of Fusarium. solani and F. oxysporum associated with crown disease of oil palm.

PubMed

Hafizi, R; Salleh, B; Latiffah, Z

2013-01-01

Crown disease (CD) is infecting oil palm in the early stages of the crop development. Previous studies showed that Fusarium species were commonly associated with CD. However, the identity of the species has not been resolved. This study was carried out to identify and characterize through morphological approaches and to determine the genetic diversity of the Fusarium species. 51 isolates (39%) of Fusarium solani and 40 isolates (31%) of Fusarium oxysporum were recovered from oil palm with typical CD symptoms collected from nine states in Malaysia, together with samples from Padang and Medan, Indonesia. Based on morphological characteristics, isolates in both Fusarium species were classified into two distinct morphotypes; Morphotypes I and II. Molecular characterization based on IGS-RFLP analysis produced 27 haplotypes among the F. solani isolates and 33 haplotypes for F. oxysporum isolates, which indicated high levels of intraspecific variations. From UPGMA cluster analysis, the isolates in both Fusarium species were divided into two main clusters with the percentage of similarity from 87% to 100% for F. solani, and 89% to 100% for F. oxysporum isolates, which was in accordance with the Morphotypes I and II. The results of the present study indicated that F. solani and F. oxysporum associated with CD of oil palm in Malaysia and Indonesia were highly variable.

Small acid soluble proteins for rapid spore identification.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Branda, Steven S.; Lane, Todd W.; VanderNoot, Victoria A.

2006-12-01

This one year LDRD addressed the problem of rapid characterization of bacterial spores such as those from the genus Bacillus, the group that contains pathogenic spores such as B. anthracis. In this effort we addressed the feasibility of using a proteomics based approach to spore characterization using a subset of conserved spore proteins known as the small acid soluble proteins or SASPs. We proposed developing techniques that built on our previous expertise in microseparations to rapidly characterize or identify spores. An alternative SASP extraction method was developed that was amenable to both the subsequent fluorescent labeling required for laser-induced fluorescencemore » detection and the low ionic strength requirements for isoelectric focusing. For the microseparations, both capillary isoelectric focusing and chip gel electrophoresis were employed. A variety of methods were evaluated to improve the molecular weight resolution for the SASPs, which are in a molecular weight range that is not well resolved by the current methods. Isoelectric focusing was optimized and employed to resolve the SASPs using UV absorbance detection. Proteomic signatures of native wild type Bacillus spores and clones genetically engineered to produce altered SASP patterns were assessed by slab gel electrophoresis, capillary isoelectric focusing with absorbance detection as well as microchip based gel electrophoresis employing sensitive laser-induced fluorescence detection.« less

Recombinant allergy vaccines based on allergen-derived B cell epitopes.

PubMed

Valenta, Rudolf; Campana, Raffaela; Niederberger, Verena

2017-09-01

Immunoglobulin E (IgE)-associated allergy is the most common immunologically-mediated hypersensitivity disease. It affects more than 25% of the population. In IgE-sensitized subjects, allergen encounter can causes a variety of symptoms ranging from hayfever (allergic rhinoconjunctivitis) to asthma, skin inflammation, food allergy and severe life-threatening anaphylactic shock. Allergen-specific immunotherapy (AIT) is based on vaccination with the disease-causing allergens. AIT is an extremely effective, causative and disease-modifying treatment. However, administration of natural allergens can cause severe side effects and the quality of natural allergen extracts limits its application. Research in the field of molecular allergen characterization has allowed deciphering the molecular structures of the disease-causing allergens and it has become possible to engineer novel molecular allergy vaccines which precisely target the mechanisms of the allergic immune response and even appear suitable for prophylactic allergy vaccination. Here we discuss recombinant allergy vaccines which are based on allergen-derived B cell epitopes regarding their molecular and immunological properties and review the results obtained in clinical studies with this new type of allergy vaccines. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments.

PubMed

Chaudhary, Prem Prashant; Brablcová, Lenka; Buriánková, Iva; Rulík, Martin

2013-09-01

Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.

Molecular phylogeny, pathogenicity and toxigenicity of Fusarium oxysporum f. sp. lycopersici

PubMed Central

Nirmaladevi, D.; Venkataramana, M.; Srivastava, Rakesh K.; Uppalapati, S. R.; Gupta, Vijai Kumar; Yli-Mattila, T.; Clement Tsui, K. M.; Srinivas, C.; Niranjana, S. R.; Chandra, Nayaka S.

2016-01-01

The present study aimed at the molecular characterization of pathogenic and non pathogenic F. oxysporum f. sp. lycopersici strains isolated from tomato. The causal agent isolated from symptomatic plants and soil samples was identified based on morphological and molecular analyses. Pathogenicity testing of 69 strains on five susceptible tomato varieties showed 45% of the strains were highly virulent and 30% were moderately virulent. Molecular analysis based on the fingerprints obtained through ISSR indicated the presence of wide genetic diversity among the strains. Phylogenetic analysis based on ITS sequences showed the presence of at least four evolutionary lineages of the pathogen. The clustering of F. oxysporum with non pathogenic isolates and with the members of other formae speciales indicated polyphyletic origin of F. oxysporum f. sp. lycopersici. Further analysis revealed intraspecies variability and nucleotide insertions or deletions in the ITS region among the strains in the study and the observed variations were found to be clade specific. The high genetic diversity in the pathogen population demands for development of effective resistance breeding programs in tomato. Among the pathogenic strains tested, toxigenic strains harbored the Fum1 gene clearly indicating that the strains infecting tomato crops have the potential to produce Fumonisin. PMID:26883288

Identifying Recent HIV Infections: From Serological Assays to Genomics.

PubMed

Moyo, Sikhulile; Wilkinson, Eduan; Novitsky, Vladimir; Vandormael, Alain; Gaseitsiwe, Simani; Essex, Max; Engelbrecht, Susan; de Oliveira, Tulio

2015-10-23

In this paper, we review serological and molecular based methods to identify HIV infection recency. The accurate identification of recent HIV infection continues to be an important research area and has implications for HIV prevention and treatment interventions. Longitudinal cohorts that follow HIV negative individuals over time are the current gold standard approach, but they are logistically challenging, time consuming and an expensive enterprise. Methods that utilize cross-sectional testing and biomarker information have become an affordable alternative to the longitudinal approach. These methods use well-characterized biological makers to differentiate between recent and established HIV infections. However, recent results have identified a number of limitations in serological based assays that are sensitive to the variability in immune responses modulated by HIV subtypes, viral load and antiretroviral therapy. Molecular methods that explore the dynamics between the timing of infection and viral evolution are now emerging as a promising approach. The combination of serological and molecular methods may provide a good solution to identify recent HIV infection in cross-sectional data. As part of this review, we present the advantages and limitations of serological and molecular based methods and their potential complementary role for the identification of HIV infection recency.

Functional markers based molecular characterization and cloning of resistance gene analogs encoding NBS-LRR disease resistance proteins in finger millet (Eleusine coracana).

PubMed

Panwar, Preety; Jha, Anand Kumar; Pandey, P K; Gupta, Arun K; Kumar, Anil

2011-06-01

Magnaporthe grisea, the blast fungus is one of the main pathological threats to finger millet crop worldwide. A systematic search for the blast resistance gene analogs was carried out, using functional molecular markers. Three-fourths of the recognition-dependent disease resistance genes (R-genes) identified in plants encodes nucleotide binding site (NBS) leucine-rich repeat (LRR) proteins. NBS-LRR homologs have only been isolated on a limited scale from Eleusine coracana. Genomic DNA sequences sharing homology with NBS region of resistance gene analogs were isolated and characterized from resistant genotypes of finger millet using PCR based approach with primers designed from conserved regions of NBS domain. Attempts were made to identify molecular markers linked to the resistance gene and to differentiate the resistant bulk from the susceptible bulk. A total of 9 NBS-LRR and 11 EST-SSR markers generated 75.6 and 73.5% polymorphism respectively amongst 73 finger millet genotypes. NBS-5, NBS-9, NBS-3 and EST-SSR-04 markers showed a clear polymorphism which differentiated resistant genotypes from susceptible genotypes. By comparing the banding pattern of different resistant and susceptible genotypes, five DNA amplifications of NBS and EST-SSR primers (NBS-05(504,) NBS-09(711), NBS-07(688), NBS-03(509) and EST-SSR-04(241)) were identified as markers for the blast resistance in resistant genotypes. Principal coordinate plot and UPGMA analysis formed similar groups of the genotypes and placed most of the resistant genotypes together showing a high level of genetic relatedness and the susceptible genotypes were placed in different groups on the basis of differential disease score. Our results provided a clue for the cloning of finger millet blast resistance gene analogs which not only facilitate the process of plant breeding but also molecular characterization of blast resistance gene analogs from Eleusine coracana.

DNA-based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi.

PubMed

Krüger, Manuela; Stockinger, Herbert; Krüger, Claudia; Schüssler, Arthur

2009-01-01

* At present, molecular ecological studies of arbuscular mycorrhizal fungi (AMF) are only possible above species level when targeting entire communities. To improve molecular species characterization and to allow species level community analyses in the field, a set of newly designed AMF specific PCR primers was successfully tested. * Nuclear rDNA fragments from diverse phylogenetic AMF lineages were sequenced and analysed to design four primer mixtures, each targeting one binding site in the small subunit (SSU) or large subunit (LSU) rDNA. To allow species resolution, they span a fragment covering the partial SSU, whole internal transcribed spacer (ITS) rDNA region and partial LSU. * The new primers are suitable for specifically amplifying AMF rDNA from material that may be contaminated by other organisms (e.g., samples from pot cultures or the field), characterizing the diversity of AMF species from field samples, and amplifying a SSU-ITS-LSU fragment that allows phylogenetic analyses with species level resolution. * The PCR primers can be used to monitor entire AMF field communities, based on a single rDNA marker region. Their application will improve the base for deep sequencing approaches; moreover, they can be efficiently used as DNA barcoding primers.

Experimental and modeling study on charge storage/transfer mechanism of graphene-based supercapacitors

NASA Astrophysics Data System (ADS)

Ban, Shuai; Jing, Xie; Zhou, Hongjun; Zhang, Lei; Zhang, Jiujun

2014-12-01

A symmetrical graphene-based supercapacitor is constructed for studying the charge-transfer mechanism within the graphene-based electrodes using both experiment measurements and molecular simulation. The in-house synthesized graphene is characterized by XRD, SEM and BET measurements for morphology and surface area. It is observed that the electric capacity of graphene electrode can be reduced by both high internal resistance and limited mass transfer. Computer modeling is conducted at the molecular level to characterize the diffusion behavior of electrolyte ions to the interior of electrode with emphasis on the unique 2D confinement imposed by graphene layers. Although graphene powder poses a moderate internal surface of 400 m2 g-1, the capacitance performance of graphene electrode can be as good as that of commercial activated carbon which has an overwhelming surface area of 1700 m2 g-1. An explanation to this abnormal correlation is that graphene material has an intrinsic capability of adaptively reorganizing its microporous structure in response to intercalation of ions and immergence of electrolyte solvent. The accessible surface of graphene is believed to be dramatically enlarged for ion adsorption during the charging process of capacitor.

Microbiological investigation of an industrial ultra pure supply water plant using cultivation-based and cultivation-independent methods.

PubMed

Bohus, Veronika; Tóth, Erika M; Székely, Anna J; Makk, Judit; Baranyi, Krisztián; Patek, Gábor; Schunk, János; Márialigeti, Károly

2010-12-01

Ultra pure waters (UPW), characterized by extremely low salt and nutrient concentrations, can suffer from microbial contamination which causes biofouling and biocorrosion, possibly leading to reduced lifetime and increased operational costs. Samples were taken from an ultra pure supply water producing plant of a power plant. Scanning electron microscopic examination was carried out on the biofilms formed in the system. Biofilm, ion exchange resin, and water samples were characterized by culture-based methods and molecular fingerprinting (terminal restriction fragment length polymorphism [T-RFLP] analysis and molecular cloning). Identification of bacteria was based on 16S rDNA sequence comparison. A complex microbial community structure was revealed. Nearly 46% of the clones were related to as yet uncultured bacteria. The community profiles of the water samples were the most diverse and most of bacteria were recruited from bacterial communities of tube surface and ion exchange resin biofilms. Microbiota of different layers of the mixed bed ion exchange resin showed the highest similarity. Most of the identified taxa (dominated by β-Proteobacteria) could take part in microbially influenced corrosion. Copyright © 2010 Elsevier Ltd. All rights reserved.

Top-down approach for the direct characterization of low molecular weight heparins using LC-FT-MS.

PubMed

Li, Lingyun; Zhang, Fuming; Zaia, Joseph; Linhardt, Robert J

2012-10-16

Low molecular heparins (LMWHs) are structurally complex, heterogeneous, polydisperse, and highly negatively charged mixtures of polysaccharides. The direct characterization of LMWH is a major challenge for currently available analytical technologies. Electrospray ionization (ESI) liquid chromatography-mass spectrometry (LC-MS) is a powerful tool for the characterization complex biological samples in the fields of proteomics, metabolomics, and glycomics. LC-MS has been applied to the analysis of heparin oligosaccharides, separated by size exclusion, reversed phase ion-pairing chromatography, and chip-based amide hydrophilic interaction chromatography (HILIC). However, there have been limited applications of ESI-LC-MS for the direct characterization of intact LMWHs (top-down analysis) due to their structural complexity, low ionization efficiency, and sulfate loss. Here we present a simple and reliable HILIC-Fourier transform (FT)-ESI-MS platform to characterize and compare two currently marketed LMWH products using the top-down approach requiring no special sample preparation steps. This HILIC system relies on cross-linked diol rather than amide chemistry, affording highly resolved chromatographic separations using a relatively high percentage of acetonitrile in the mobile phase, resulting in stable and high efficiency ionization. Bioinformatics software (GlycReSoft 1.0) was used to automatically assign structures within 5-ppm mass accuracy.

Molecular-Scale Electronics: From Concept to Function.

PubMed

Xiang, Dong; Wang, Xiaolong; Jia, Chuancheng; Lee, Takhee; Guo, Xuefeng

2016-04-13

Creating functional electrical circuits using individual or ensemble molecules, often termed as "molecular-scale electronics", not only meets the increasing technical demands of the miniaturization of traditional Si-based electronic devices, but also provides an ideal window of exploring the intrinsic properties of materials at the molecular level. This Review covers the major advances with the most general applicability and emphasizes new insights into the development of efficient platform methodologies for building reliable molecular electronic devices with desired functionalities through the combination of programmed bottom-up self-assembly and sophisticated top-down device fabrication. First, we summarize a number of different approaches of forming molecular-scale junctions and discuss various experimental techniques for examining these nanoscale circuits in details. We then give a full introduction of characterization techniques and theoretical simulations for molecular electronics. Third, we highlight the major contributions and new concepts of integrating molecular functionalities into electrical circuits. Finally, we provide a critical discussion of limitations and main challenges that still exist for the development of molecular electronics. These analyses should be valuable for deeply understanding charge transport through molecular junctions, the device fabrication process, and the roadmap for future practical molecular electronics.

Interface-Engineered Charge-Transport Properties in Benzenedithiol Molecular Electronic Junctions via Chemically p-Doped Graphene Electrodes.

PubMed

Jang, Yeonsik; Kwon, Sung-Joo; Shin, Jaeho; Jeong, Hyunhak; Hwang, Wang-Taek; Kim, Junwoo; Koo, Jeongmin; Ko, Taeg Yeoung; Ryu, Sunmin; Wang, Gunuk; Lee, Tae-Woo; Lee, Takhee

2017-12-06

In this study, we fabricated and characterized vertical molecular junctions consisting of self-assembled monolayers of benzenedithiol (BDT) with a p-doped multilayer graphene electrode. The p-type doping of a graphene film was performed by treating pristine graphene (work function of ∼4.40 eV) with trifluoromethanesulfonic (TFMS) acid, producing a significantly increased work function (∼5.23 eV). The p-doped graphene-electrode molecular junctions statistically showed an order of magnitude higher current density and a lower charge injection barrier height than those of the pristine graphene-electrode molecular junctions, as a result of interface engineering. This enhancement is due to the increased work function of the TFMS-treated p-doped graphene electrode in the highest occupied molecular orbital-mediated tunneling molecular junctions. The validity of these results was proven by a theoretical analysis based on a coherent transport model that considers asymmetric couplings at the electrode-molecule interfaces.

Morphological and molecular characterization of novel species of Henneguya found in the gills of farm-raised channel catfish, Ictalurus punctatus

USDA-ARS?s Scientific Manuscript database

Channel catfish Ictalurus punctatus is host to at least eight different species of myxozoan parasites in the genus Henneguya. Four of these species have been molecularly characterized; however, the life cycles of only two have been experimentally and molecularly confirmed. Some of these species can...

Advances and unresolved challenges in the structural characterization of isomeric lipids.

PubMed

Hancock, Sarah E; Poad, Berwyck L J; Batarseh, Amani; Abbott, Sarah K; Mitchell, Todd W

2017-05-01

As the field of lipidomics grows and its application becomes wide and varied it is important that we don't forget its foundation, i.e. the identification and measurement of molecular lipids. Advances in liquid chromatography and the emergence of ion mobility as a useful tool in lipid analysis are allowing greater separation of lipid isomers than ever before. At the same time, novel ion activation techniques, such as ozone-induced dissociation, are pushing lipid structural characterization by mass spectrometry to new levels. Nevertheless, the quantitative capacity of these techniques is yet to be proven and further refinements are required to unravel the high level of lipid complexity found in biological samples. At present there is no one technique capable of providing full structural characterization of lipids from a biological sample. There are however, numerous techniques now available (as discussed in this review) that could be deployed in a targeted approach. Moving forward, the combination of advanced separation and ion activation techniques is likely to provide mass spectrometry-based lipidomics with its best opportunity to achieve complete molecular-level lipid characterization and measurement from complex mixtures. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

Evaluation of FTA paper and phenol for storage, extraction and molecular characterization of infectious bursal disease virus.

PubMed

Purvis, Linda B; Villegas, Pedro; Perozo, Francisco

2006-12-01

Infectious bursal disease virus (IBDV) is an important poultry pathogen and is distributed world wide that can cause immune suppression and lesions of the bursa of Fabricius. The main component of the virus, VP2, is not only responsible for the bird's immune response, but is important for the molecular identification of this virus as well. The nucleic acid of the virus must be adequately preserved to be analyzed by reverse-transcriptase PCR (RT-PCR) and sequenced for the molecular characterization of the field strain. Phenol inactivation has been the standard for IBDV tissue collection and international shipment; however, there have been some reports of interference with molecular detection capabilities when using phenol. Phenol is also a hazardous chemical and must be handled and shipped carefully. The ability to use the Flinders Technology Associates filter paper (FTA card) for inactivation of several avian pathogens has been proven previously, however no work has been published on its use in IBDV nucleic acid detection. Bursas from experimentally infected birds was imprinted on FTA cards, and then placed in phenol. Samples were evaluated and compared based on molecular detection capabilities between the two inactivation methods. The nucleic acid of the virus was detected in 85% of the FTA card inactivated samples compared to 71% in the phenol inactivated samples. Sequence analysis was performed on samples inactivated by both methods and no differences were found. When comparing the RNA stability at different temperatures, euthanized IBDV infected birds were held at two different temperatures before sampling. No differences were detected for FTA sampling; however, for tissues in phenol the nucleic acid was only detectable up to 2 h post-mortem in the tissues held at 4 degrees C prior to sampling. These findings indicate that the FTA card is an efficient and reliable alternative collection method for molecular detection and characterization of IBDV.

Synthesis of Long-Chain-Branched (LCB) Polysulfones for Multifunctional Transport Membranes

DTIC Science & Technology

2010-09-01

R.; Dutta, N. K. Interfacial Interactions in Aprotic Ionic Liquid Based Protonic Membrane and Its Correlation with High Temperature Conductivity...rigidity. The series of novel polymers was characterized for chemical structure, thermal transitions, and molecular weight. Ionic conductivity was tested...Although much progress exists based on perfluorosulfonated platforms ( Nafion , σ ≈ 10-1 – 10-2 S/cm) new and more complicated parameters arise as

Impacts of Sampling and Handling Procedures on DNA- and RNA-based Microbial Characterization and Quantification of Groundwater and Saturated Soil

DTIC Science & Technology

2012-07-01

use of molecular biological techniques (MBTs) has allowed microbial ecologists and environmental engineers to determine microbial community...metabolic genes). The most common approaches used in bioremediation research are those based on the polymerase chain reaction (PCR) amplification of... bioremediation . Because of its sensitivity compared to direct hybridization/probing, PCR is increasingly used to analyze groundwater samples and soil samples

Test-beds for molecular electronics: metal-molecules-metal junctions based on Hg electrodes.

PubMed

Simeone, Felice Carlo; Rampi, Maria Anita

2010-01-01

Junctions based on mesoscopic Hg electrodes are used to characterize the electrical properties of the organic molecules organized in self-assembled monolayers (SAMs). The junctions M-SAM//SAM-Hg are formed by one electrode based on metals (M) such as Hg, Ag, Au, covered by a SAM, and by a second electrode always formed by a Hg drop carrying also a SAM. The electrodes, brought together by using a micromanipulator, sandwich SAMs of different nature at the contact area (approximately = 0.7 microm2). The high versatility of the system allows a series of both electrical and electrochemical junctions to be assembled and characterized: (i) The compliant nature of the Hg electrodes allows incorporation into the junction and measurement of the electrical behavior of a large number of molecular systems and correlation of their electronic structure to the electrical behavior; (ii) by functionalizing both electrodes with SAMs exposing different functional groups, X and Y, it is possible to compare the rate of electron transfer through different X...Y molecular interactions; (iii) when the junction incorporates one of the electrode formed by a semitransparent film of Au, it allows electrical measurements under irradiation of the sandwiched SAMs. In this case the junction behaves as a photoswitch; iv) incorporation of redox centres with low lying, easily reachable energy levels, provides electron stations as indicated by the hopping mechanism dominating the current flow; (v) electrochemical junctions incorporating redox centres by both covalent and electrostatic interactions permit control of the potential of the electrodes with respect to that of the redox state by means of an external reference electrode. Both these junctions show an electrical behavior similar to that of conventional diodes, even though the mechanism generating the current flow is different. These systems, demonstrating high mechanical stability and reproducibility, easy assembly, and a wide variety of produced results, are convenient test-beds for molecular electronics and represent a useful complement to physics-based experimental methods.

Solid-State NMR Study of the Cicada Wing.

PubMed

Gullion, John D; Gullion, Terry

2017-08-17

Wings of flying insects are part of the cuticle which forms the exoskeleton. The primary molecular components of cuticle are protein, chitin, and lipid. How these components interact with one another to form the exoskeleton is not completely understood. The difficulty in characterizing the cuticle arises because it is insoluble and noncrystalline. These properties severely limit the experimental tools that can be used for molecular characterization. Solid-state nuclear magnetic resonance experiments have been used in the past to characterize the exoskeleton of beetles and have found that chitin and protein make comparable contributions to the molecular matrix. However, little work has been done to characterize the components of the wing, which includes vein and membrane. In this work, solid-state NMR was used to characterize the wing of the 17-year cycle cicada (Magicicada cassini) that appeared in northern West Virginia during the summer of 2016. The NMR results show noticeable differences between the molecular components of the vein and membrane.

First Molecular Characterization of Feline Immunodeficiency Virus in Domestic Cats from Mainland China.

PubMed

Zhang, Jilei; Wang, Liang; Li, Jing; Kelly, Patrick; Price, Stuart; Wang, Chengming

2017-01-01

The feline immunodeficiency virus (FIV) is a retrovirus of the Lentivirus genus that was initially isolated from a colony of domestic cats in California in 1986 and has now been recognized as a common feline pathogen worldwide. To date, there is only one recent serology-based report on FIV in mainland China which was published in 2016. We designed this study to investigate the molecular prevalence and diversity of feline immunodeficiency virus (FIV) in domestic cats from mainland China. We studied the prevalence of FIV in whole blood samples of 615 domestic cats in five cities (Beijing, Guangzhou, Nanjing, Shanghai and Yangzhou) of mainland China and examined them using FRET-PCR (Fluorescence Resonance Energy Transfer-Polymerase Chain Reaction) and regular PCRs for the gag and env genes. Overall, 1.3% (8/615) of the cats were positive for provirus DNA with nucleotide analysis using PCRs for the gag and env sequences showing the cats were infected with FIV subtype A. This is the first molecular characterization of FIV in mainland China and the first description of subtype A in continental Asia.

Molecular characterization and phylogenetic analysis of the causative agent of hemoplasma infection in small Indian Mongoose (Herpestes Javanicus).

PubMed

Sharifiyazdi, Hassan; Nazifi, Saeed; Shirzad Aski, Hesamaddin; Shayegh, Hossein

2014-09-01

Hemoplasmas are the trivial name for a group of erythrocyte-parasitizing bacteria of the genus Mycoplasma. This study is the first report of hemoplasma infection in Small Indian Mongoose (Herpestes Javanicus) based on molecular analysis of 16S rDNA. Whole blood samples were collected by sterile methods, from 14 live captured mongooses, in the south of Iran. Candidatus Mycoplasma turicensis (CMt)-like hemoplasma was detected in blood samples from one animal tested. BLAST search and phylogenetic analysis of partial 16S rDNA sequence (933bp) of the hemoplasma from Small Indian mongoose (KJ530704) revealed only 96-97% identity to the previously described CMt followed by 95% and 91% similarity with Mycoplasma coccoides and Mycoplasma haemomuris, respectively. Accordingly, the Iranian mongoose CMt isolate showed a high intra-specific genetic variation compared to all previously reported CMt strains in GenBank. Further molecular studies using multiple phylogenetic markers are required to characterize the exact species of Mongoose-derived hemoplasma. Copyright © 2014 Elsevier Ltd. All rights reserved.

Integrating molecular and morphological approaches for characterizing parasite cryptic species: implications for parasitology.

PubMed

Nadler, Steven A; DE León, Gerardo Pérez-Ponce

2011-11-01

Herein we review theoretical and methodological considerations important for finding and delimiting cryptic species of parasites (species that are difficult to recognize using traditional systematic methods). Applications of molecular data in empirical investigations of cryptic species are discussed from an historical perspective, and we evaluate advantages and disadvantages of approaches that have been used to date. Developments concerning the theory and practice of species delimitation are emphasized because theory is critical to interpretation of data. The advantages and disadvantages of different molecular methodologies, including the number and kind of loci, are discussed relative to tree-based approaches for detecting and delimiting cryptic species. We conclude by discussing some implications that cryptic species have for research programmes in parasitology, emphasizing that careful attention to the theory and operational practices involved in finding, delimiting, and describing new species (including cryptic species) is essential, not only for fully characterizing parasite biodiversity and broader aspects of comparative biology such as systematics, evolution, ecology and biogeography, but to applied research efforts that strive to improve development and understanding of epidemiology, diagnostics, control and potential eradication of parasitic diseases.

Molecular markers in disease detection and follow-up of patients with non-muscle invasive bladder cancer.

PubMed

Maas, Moritz; Walz, Simon; Stühler, Viktoria; Aufderklamm, Stefan; Rausch, Steffen; Bedke, Jens; Stenzl, Arnulf; Todenhöfer, Tilman

2018-05-01

Diagnosis and surveillance of non-muscle invasive bladder cancer (NMIBC) is mainly based on endoscopic bladder evaluation and urine cytology. Several assays for determining additional molecular markers (urine-, tissue- or blood-based) have been developed in recent years but have not been included in clinical guidelines so far. Areas covered: This review gives an update on different molecular markers in the urine and evaluates their role in patients with NMIBC in disease detection and surveillance. Moreover, the potential of recent approaches such as DNA methylation assays, multi-panel RNA gene expression assays and cell-free DNA analysis is assessed. Expert commentary: Most studies on various molecular urine markers have mainly focused on a potential replacement of cystoscopy. New developments in high throughput technologies and urine markers may offer further advantages as they may represent a non-invasive approach for molecular characterization of the disease. This opens new options for individualized surveillance strategies and may help to choose the best therapeutic option. The implementation of these technologies in well-designed clinical trials is essential to further promote the use of urine diagnostics in the management of patients with NMIBC.

Preparation of ellagic acid molecularly imprinted polymeric microspheres based on distillation-precipitation polymerization for the efficient purification of a crude extract.

PubMed

Zhang, Hua; Zhao, Shangge; Zhang, Lu; Han, Bo; Yao, Xincheng; Chen, Wen; Hu, Yanli

2016-08-01

Molecularly imprinted polymeric microspheres with a high recognition ability toward the template molecule, ellagic acid, were synthesized based on distillation-precipitation polymerization. The as-obtained polymers were characterized by scanning electron microscopy, infrared spectroscopy, and thermogravimetric analysis. Static, dynamic, and selective binding tests were adopted to study the binding properties and the molecular recognition ability of the prepared polymers for ellagic acid. The results indicated that the maximum static adsorption capacity of the prepared polymers toward ellagic acid was 37.07 mg/g and the adsorption equilibrium time was about 100 min when the concentration of ellagic acid was 40 mg/mL. Molecularly imprinted polymeric microspheres were also highly selective toward ellagic acid compared with its analogue quercetin. It was found that the content of ellagic acid in the pomegranate peel extract was enhanced from 23 to 86% after such molecularly imprinted solid-phase extraction process. This work provides an efficient way for effective separation and enrichment of ellagic acid from complex matrix, which is especially valuable in industrial production. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ultrafast and nonlinear spectroscopy of brilliant green-based nanoGUMBOS with enhanced near-infrared emission

NASA Astrophysics Data System (ADS)

Karam, Tony E.; Siraj, Noureen; Zhang, Zhenyu; Ezzir, Abdulrahman F.; Warner, Isiah M.; Haber, Louis H.

2017-10-01

The synthesis, characterization, ultrafast dynamics, and nonlinear spectroscopy of 30 nm nanospheres of brilliant green-bis(pentafluoroethylsulfonyl)imide ([BG][BETI]) in water are reported. These thermally stable nanoparticles are derived from a group of uniform materials based on organic salts (nanoGUMBOS) that exhibit enhanced near-infrared emission compared with the molecular dye in water. The examination of ultrafast transient absorption spectroscopy results reveals that the overall excited-state relaxation lifetimes of [BG][BETI] nanoGUMBOS are longer than the brilliant green molecular dye in water due to steric hindrance of the torsional degrees of freedom of the phenyl rings around the central carbon. Furthermore, the second harmonic generation signal of [BG][BETI] nanoGUMBOS is enhanced by approximately 7 times and 23 times as compared with colloidal gold nanoparticles of the same size and the brilliant green molecular dye in water, respectively. A very clear third harmonic generation signal is observed from the [BG][BETI] nanoGUMBOS but not from either the molecular dye or the gold nanoparticles. Overall, these results show that [BG][BETI] nanoGUMBOS exhibit altered ultrafast and nonlinear spectroscopy that is beneficial for various applications including nonlinear imaging probes, biomedical imaging, and molecular sensing.

Facile characterization of aptamer kinetic and equilibrium binding properties using surface plasmon resonance

PubMed Central

Chang, Andrew L.; McKeague, Maureen; Smolke, Christina D.

2015-01-01

Nucleic acid aptamers find widespread use as targeting and sensing agents in nature and biotechnology. Their ability to bind an extensive range of molecular targets, including small molecules, proteins, and ions, with high affinity and specificity enables their use in diverse diagnostic, therapeutic, imaging, and gene-regulatory applications. Here, we describe methods for characterizing aptamer kinetic and equilibrium binding properties using a surface plasmon resonance-based platform. This aptamer characterization platform is broadly useful for studying aptamer–ligand interactions, comparing aptamer properties, screening functional aptamers during in vitro selection processes, and prototyping aptamers for integration into nucleic acid devices. PMID:25432760

Characterization of glycoprotein biopharmaceutical products by Caliper LC90 CE-SDS gel technology.

PubMed

Chen, Grace; Ha, Sha; Rustandi, Richard R

2013-01-01

Over the last decade, science has greatly improved in the area of protein sizing and characterization. Efficient high-throughput methods are now available to substitute for the traditional labor-intensive SDS-PAGE methods, which alternatively take days to analyze a very limited number of samples. Currently, PerkinElmer(®) (Caliper) has designed an automated chip-based fluorescence detection method capable of analyzing proteins in minutes with sensitivity similar to standard SDS-PAGE. Here, we describe the use and implementation of this technology to characterize and screen a large number of formulations of target glycoproteins in the 14-200 kDa molecular weight range.

Clinical and molecular characterization of Chilean patients with Léri-Weill dyschondrosteosis.

PubMed

Rodríguez, Fernando Adrián; Unanue, Nancy; Hernandez, María Isabel; Basaure, Javiera; Heath, Karen Elise; Cassorla, Fernando

2013-01-01

Léri-Weill dyschondrosteosis (LWD) is a mesomelic dysplasia with disproportionate short stature associated with short stature homeobox-containing gene (SHOX) haploinsufficiency. The objective of this study was to improve the diagnosis of patients with suspected LWD through molecular analysis. Twelve patients from 11 families with a clinical diagnosis of LWD were analyzed with multiplex ligation-dependent probe amplification to detect deletions and duplications of SHOX and its enhancer regions. High resolution melting and sequencing was employed to screen for mutations in SHOX coding exons. The molecular-based screening strategy applied in these patients allowed detection of five SHOX deletions and two previously unreported SHOX missense mutations. Molecular studies confirmed the clinical diagnosis of LWD in seven out of 12 patients, which provided support for therapeutic decisions and improved genetic counseling in their families.

Molecular characterization of Fasciola gigantica from Mauritania based on mitochondrial and nuclear ribosomal DNA sequences.

PubMed

Amor, Nabil; Farjallah, Sarra; Salem, Mohamed; Lamine, Dia Mamadou; Merella, Paolo; Said, Khaled; Ben Slimane, Badreddine

2011-10-01

Fasciolosis caused by Fasciola hepatica and Fasciola gigantica (Platyhelminthes: Trematoda: Digenea) is considered the most important helminth infection of ruminants in tropical countries, causing considerable socioeconomic problems. From Africa, F. gigantica has been previously characterized from Burkina Faso, Senegal, Kenya, Zambia and Mali, while F. hepatica has been reported from Morocco and Tunisia, and both species have been observed from Ethiopia and Egypt on the basis of morphometric differences, while the use of molecular markers is necessary to distinguish exactly between species. Samples identified morphologically as F. gigantica (n=60) from sheep and cattle from different geographical localities of Mauritania were genetically characterized by sequences of the first (ITS-1), the 5.8S, and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA) genes and the mitochondrial Cytochrome c Oxidase I (COI) gene. Comparison of the sequences of the Mauritanian samples with sequences of Fasciola spp. from GenBank confirmed that all samples belong to the species F. gigantica. The nucleotide sequencing of ITS rDNA of F. gigantica showed no nucleotide variation in the ITS-1, 5.8S, and ITS-2 rDNA sequences among all samples examined and those from Burkina Faso, Kenya, Egypt and Iran. The phylogenetic trees based on the ITS-1 and ITS-2 sequences showed a close relationship of the Mauritanian samples with isolates of F. gigantica from different localities of Africa and Asia. The COI genotypes of the Mauritanian specimens of F. gigantica had a high level of diversity, and they belonged to the F. gigantica phylogenically distinguishable clade. The present study is the first molecular characterization of F. gigantica in sheep and cattle from Mauritania, allowing a reliable approach for the genetic differentiation of Fasciola spp. and providing basis for further studies on liver flukes in the African countries. Copyright © 2011 Elsevier Inc. All rights reserved.

Molecular cloning and characterization of G alpha proteins from the western tarnished plant bug, Lygus hesperus

USDA-ARS?s Scientific Manuscript database

The G-alpha subunits of heterotrimeric G proteins play critical roles in the activation of diverse signal transduction cascades. However, the role of these genes in chemosensation remains to be fully elucidated. To initiate a comprehensive survey of signal transduction genes, we used homology-base...

Sequence-characterized amplified polymorphism markers for selecting rind stripe pattern in watermelon (Citrullus lanatus var. lanatus)

USDA-ARS?s Scientific Manuscript database

The inheritance of foreground stripe pattern in rind of watermelon fruits [Citrullus lanatus (Thunb.) Matsum. & Nakai] was evaluated and the molecular markers for selecting the JT stripe pattern were developed based on bulked segregant analysis (BSA). Divergence in rind pattern among F2 progeny deri...

Screening and rapid identification of Campylobacter spp. DNA by FlaA PCR based method on chicken and human fecal samples in Egypt

USDA-ARS?s Scientific Manuscript database

Campylobacter is a foodborne pathogen which has a potential public health concern worldwide. Due to discriminatory problems encountered by conventional isolation of Campylobacter spp. and its genetic similarities, rapid molecular techniques for its genetic characterization are useful. In this study,...

Molecular genetic characterization of lasquerella new industrial crop using DArTseq markers

USDA-ARS?s Scientific Manuscript database

DArTseq, a new SNP-based marker platform, was developed and used to analyze the genetic diversity of the US germplasm collection of lesquerella. Lesquerella is a new oilseed crop in the Brassica family found native in the American Southwest. The potential of the species as a domestic source of indu...

Biochemistry and Molecular Biology Techniques for Person Characterization

ERIC Educational Resources Information Center

Herrero, Salvador; Ivorra, Jose Luis; Garcia-Sogo, Magdalena; Martinez-Cortina, Carmen

2008-01-01

Using the traditional serological tests and the most novel techniques for DNA fingerprinting, forensic scientists scan different traits that vary from person to person and use the data to include or exclude suspects based on matching with the evidence obtained in a criminal case. Although the forensic application of these methods is well known,…

Advanced solvent based methods for molecular characterization of soil organic matter by high-resolution mass spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tfaily, Malak M.; Chu, Rosalie K.; Tolic, Nikola

2015-05-19

Soil organic matter (SOM) a complex, heterogeneous mixture of above and belowground plant litter and animal and microbial residues at various degrees of decomposition, is a key reservoir for carbon (C) and nutrient biogeochemical cycling in soil based ecosystems. A limited understanding of the molecular composition of SOM limits the ability to routinely decipher chemical processes within soil and predict accurately how terrestrial carbon fluxes will response to changing climatic conditions and land use. To elucidate the molecular-level structure of SOM, we selectively extracted a broad range of intact SOM compounds by a combination of different organic solvents from soilsmore » with a wide range of C content. Our use of Electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and a suite of solvents with varying polarity significantly expands the inventory of the types of organic molecules present in soils. Specifically, we found that hexane is selective for lipid-like compounds with very low O:C ratios; water was selective for carbohydrates with high O:C ratios; acetonitrile preferentially extracts lignin, condensed structures, and tannin poly phenolic compounds with O:C > 0.5; methanol has higher selectivity towards compounds characterized with low O:C < 0.5; and hexane, MeOH, ACN and water solvents increase the number and types of organic molecules extracted from soil for a broader range of chemically diverse soil types. Our study of SOM molecules by ESI-FTICR MS revealed new insight into the molecular-level complexity of organics contained in soils.« less

Spectroscopic and molecular docking studies on the interaction of human serum albumin with copper(II) complexes

NASA Astrophysics Data System (ADS)

Guhathakurta, Bhargab; Pradhan, Ankur Bikash; Das, Suman; Bandyopadhyay, Nirmalya; Lu, Liping; Zhu, Miaoli; Naskar, Jnan Prakash

2017-02-01

Two osazone based ligands, butane-2,3-dione bis(2‧-pyridylhydrazone) (BDBPH) and hexane-3,4-dione bis(2‧-pyridylhydrazone) (HDBPH), were synthesized out of the 2:1 M Schiff base condensation of 2-hydrazino pyridine respectively with 2,3-butanedione and 3,4-hexanedione. The X-ray crystal structures of both the ligands have been determined. The copper(II) complex of HDBPH has also been synthesized and structurally characterized. HDBPH and its copper(II) complex have thoroughly been characterized through various spectroscopic and analytical techniques. The X-ray crystal structure of the copper complex of HDBPH shows that it is a monomeric Cu(II) complex having 'N4O2' co-ordination chromophore. Interaction of human serum albumin (HSA) with these ligands and their monomeric copper(II) complexes have been studied by various spectroscopic means. The experimental findings show that the ligands as well as their copper complexes are good HSA binders. Molecular docking investigations have also been done to unravel the mode of binding of the species with HSA.

Triazolopyridinyl-acrylonitrile derivatives as antimicrotubule agents: Synthesis, in vitro and in silico characterization of antiproliferative activity, inhibition of tubulin polymerization and binding thermodynamics.

PubMed

Briguglio, Irene; Laurini, Erik; Pirisi, Maria Antonietta; Piras, Sandra; Corona, Paola; Fermeglia, Maurizio; Pricl, Sabrina; Carta, Antonio

2017-12-01

In this paper we report the synthesis, in vitro anticancer activity, and the experimental/computational characterization of mechanism of action of a new series of E isomers of triazolo[4,5-b/c]pyridin-acrylonitrile derivatives (6c-g, 7d-e, 8d-e, 9c-f, 10d-e, 11d-e). All new compounds are endowed with moderate to interesting antiproliferative activity against 9 different cancer cell lines derived from solid and hematological human tumors. Fluorescence-based assays prove that these molecules interfere with tubulin polymerization. Furthermore, isothermal titration calorimetry (ITC) provides full tubulin/compound binding thermodynamics, thereby ultimately qualifying and quantifying the interactions of these molecular series with the target protein. Lastly, the analysis based on the tight coupling of in vitro and in silico modeling of the interactions between tubulin and the title compounds allows to propose a molecular rationale for their biological activity. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Characterization of micro-flocs of NOM coagulated by PACl, alum and polysilicate-iron in terms of molecular weight and floc size.

PubMed

Fusheng, Li; Akira, Yuasa; Yuka, Ando

2008-01-01

Micro-flocs of NOM coagulated by polyaluminium chloride (PACl), alum and polysilicate-iron (PSI) were characterized by flocs size, HPSEC-based molecular weight and the captured content of coagulants-based aluminium and iron. Changes in floc composition with respect to the mass ratios of captured NOM to Al and Fe were examined. Lowering water pH to optimum levels was found to be capable of removing small NOM constituents that are generally difficult to be precipitated at neutral pH levels. For PACl and PSI, the distribution of micro flocs (0.1-5.0 microm) reached steady stage after rapid mixing for 30 seconds, with NOM being found existent within the non-coagulated fraction (d<0.1 microm) and the coagulated fraction with floc sizes above 5.0 microm (d >5.0 microm). For alum, however, the existence of NOM inside intermediate floc fractions of d = 0.1-1.0 microm, 1.0-3.0microm and 3.0-5.0 microm was confirmed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Na; Zhang, Peng; Kang, Wei

Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters aremore » systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately.« less

Characterization of dipeptidylcarboxypeptidase of Leishmania donovani: a molecular model for structure based design of antileishmanials

NASA Astrophysics Data System (ADS)

Baig, Mirza Saqib; Kumar, Ashutosh; Siddiqi, Mohammad Imran; Goyal, Neena

2010-01-01

Leishmania donovani dipeptidylcarboxypeptidsae (LdDCP), an angiotensin converting enzyme (ACE) related metallopeptidase has been identified and characterized as a putative drug target for antileishmanial chemotherapy. The kinetic parameters for LdDCP with substrate, Hip-His-Leu were determined as, Km, 4 mM and Vmax, 1.173 μmole/ml/min. Inhibition studies revealed that known ACE inhibitors (captopril and bradykinin potentiating peptide; BPP1) were weak inhibitors for LdDCP as compared to human testicular ACE (htACE) with Ki values of 35.8 nM and 3.9 μM, respectively. Three dimensional model of LdDCP was generated based on crystal structure of Escherichia coli DCP (EcDCP) by means of comparative modeling and assessed using PROSAII, PROCHECK and WHATIF. Captopril docking with htACE, LdDCP and EcDCP and analysis of molecular electrostatic potentials (MEP) suggested that the active site domain of three enzymes has several minor but potentially important structural differences. These differences could be exploited for designing selective inhibitor of LdDCP thereby antileishmanial compounds either by denovo drug design or virtual screening of small molecule databases.

Adenosquamous carcinoma of the pancreas: Molecular characterization of 23 patients along with a literature review.

PubMed

Borazanci, Erkut; Millis, Sherri Z; Korn, Ron; Han, Haiyong; Whatcott, Clifford J; Gatalica, Zoran; Barrett, Michael T; Cridebring, Derek; Von Hoff, Daniel D

2015-09-15

Adenosquamous carcinoma of the pancreas (ASCP) is a rare entity. Like adenocarcinoma of the pancreas, overall survival is poor. Characteristics of ASCP include central tumor necrosis, along with osteoclasts and hypercalcemia. Various theories exist as to why this histological subtype exists, as normal pancreas tissue has no benign squamous epithelium. Due to the rarity of this disease, limited molecular analysis has been performed, and those reports indicate unique molecular features of ASCP. In this paper, we characterize 23 patients diagnosed with ASCP through molecular profiling using immunohistochemistry staining, fluorescent in situ hybridization, chromogenic in situ hybridization, and gene sequencing, Additionally, we provide a comprehensive literature review of what is known to date of ASCP. Molecular characterization revealed overexpression in MRP1 (80%), MGMT (79%), TOP2A (75), RRM1 (42%), TOPO1 (42%), PTEN (45%), CMET (40%), and C-KIT (10%) among others. One hundred percent of samples tested were positive for KRAS mutations. This analysis shows heretofore unsuspected leads to be considered for treatments of this rare type of exocrine pancreas cancer. Molecular profiling may be appropriate to provide maximum information regarding the patient's tumor. Further work should be pursued to better characterize this disease.

Next-generation sequencing-based molecular diagnosis of a Chinese patient cohort with autosomal recessive retinitis pigmentosa.

PubMed

Fu, Qing; Wang, Feng; Wang, Hui; Xu, Fei; Zaneveld, Jacques E; Ren, Huanan; Keser, Vafa; Lopez, Irma; Tuan, Han-Fang; Salvo, Jason S; Wang, Xia; Zhao, Li; Wang, Keqing; Li, Yumei; Koenekoop, Robert K; Chen, Rui; Sui, Ruifang

2013-06-14

Retinitis pigmentosa (RP) is a highly heterogeneous genetic disease; therefore, an accurate molecular diagnosis is essential for appropriate disease treatment and family planning. The prevalence of RP in China had been reported at 1 in 3800, resulting in an estimated total of 340,000 Chinese RP patients. However, genetic studies of Chinese RP patients have been very limited. To date, no comprehensive molecular diagnosis has been done for Chinese RP patients. With the emergence of next-generation sequencing (NGS), comprehensive molecular diagnosis of RP is now within reach. The purpose of this study was to perform the first NGS-based comprehensive molecular diagnosis for Chinese RP patients. Thirty-one well-characterized autosomal recessive RP (arRP) families were recruited. For each family, the DNA sample from one affected member was sequenced using our custom capture panel, which includes 163 retinal disease genes. Variants were called, filtered, and annotated by our in-house automatic pipeline. Twelve arRP families were successfully molecular diagnosed, achieving a diagnostic rate of approximately 40%. Interestingly, approximately 63% of the pathogenic mutations we identified are novel, which is higher than that observed in a similar study on European descent (45%). Moreover, the clinical diagnoses of two families were refined based on the pathogenic mutations identified in the patients. We conclude that comprehensive molecular diagnosis can be vital for an accurate clinical diagnosis of RP. Applying this tool on patients from different ethnic groups is essential for enhancing our knowledge of the global spectrum of RP disease-causing mutations.

Spectral Characterization and 3D Molecular Modeling Studies of Metal Complexes Involving the O, N-Donor Environment of Quinazoline-4(3H)-one Schiff Base and Their Biological Studies

PubMed Central

Siddappa, Kuruba; Mane, Sunilkumar B.

2014-01-01

A simple condensation of 3-amino-2-methylquinazoline-4-one with 2-hydroxy-1-naphthaldehyde produced new tridentate ONO donor Schiff base ligand with efficient yield. The structural characterization of ligand and its Cu(II), Ni(II), Co(II), Mn(II), Zn(II), and Cd(II) complexes were achieved by the aid of elemental analysis, spectral characterization such as (UV-visible, IR, NMR, mass, and ESR), and magnetic data. The analytical and spectroscopic studies suggest the octahedral geometries of Cu(II), Co(II), Ni(II) and Mn(II) complexes and tetrahedral geometry of Zn(II) and Cd(II) complexes with the tridentate ONO Schiff base ligand. Furthermore, the conclusions drawn from these studies afford further support to the mode of bonding discussed on the basis of their 3D molecular modeling studies by considering different bond lengths, bond angles, and bond distance. The ligand and its metal complexes evaluated for their antimicrobial activity against Staphylococcus aureus (MTCC number 7443), Bacillus subtilis (MTCC number 9878), Escherichia coli (MTCC number 1698), Aspergillus niger (MTCC number 281), and Aspergillus flavus (MTCC number 277). The MIC of these compounds was found to be most active at 10 μg/mL concentration in inhibiting the growth of the tested organisms. The DNA cleavage activity of all the complexes was studied by gel electrophoresis method. PMID:24678278

Synthesis and characterization of star-shaped oligo(ethylene glycol) with tyrosine derived moieties under variation of their molecular weight.

PubMed

Julich-Gruner, Konstanze K; Roch, Toralf; Ma, Nan; Neffe, Axel T; Lendlein, Andreas

2015-01-01

Desamino tyrosine (DAT) and desamino tyrosyl tyrosine (DATT) can be used to functionalize the end groups of water soluble polymers. The phenolic groups may enable physical interactions by π- π interaction and hydrogen bonds, which might lead to the formation of a hydrogel by physical crosslinking. However, using star-shaped oligo(ethylene glycols) (sOEG) with a molecular weight of 5 kDa for functionalization with DAT or DATT resulted in the formation of surfactants and not in hydrogels.As the molecular weight of the sOEG polymer chain can have an influence on forming physical cross links, DAT(T)-fuctionalization of sOEGs with higher molecular weight was investigated, the polymers were structurally characterized and for their mechanical properties were evaluated by rheological measurements.Aqueous solutions of DAT(T)-sOEGs with 10 and 20 kDa showed lower storage and loss moduli compared to unfunctionalized sOEGs indicating also the formation of surfactants. Cell-based assays showed that all sOEG solutions did not impair cell viability and were free of endotoxins, which could otherwise induce uncontrolled immune responses.Conclusively, our data suggested that the sOEG solutions have surface active properties without inducing unwanted cellular responses, which is required e.g. in pharmaceutical applications to solubilize hydophobic substances.

Peltier cooling in molecular junctions

NASA Astrophysics Data System (ADS)

Cui, Longji; Miao, Ruijiao; Wang, Kun; Thompson, Dakotah; Zotti, Linda Angela; Cuevas, Juan Carlos; Meyhofer, Edgar; Reddy, Pramod

2018-02-01

The study of thermoelectricity in molecular junctions is of fundamental interest for the development of various technologies including cooling (refrigeration) and heat-to-electricity conversion1-4. Recent experimental progress in probing the thermopower (Seebeck effect) of molecular junctions5-9 has enabled studies of the relationship between thermoelectricity and molecular structure10,11. However, observations of Peltier cooling in molecular junctions—a critical step for establishing molecular-based refrigeration—have remained inaccessible. Here, we report direct experimental observations of Peltier cooling in molecular junctions. By integrating conducting-probe atomic force microscopy12,13 with custom-fabricated picowatt-resolution calorimetric microdevices, we created an experimental platform that enables the unified characterization of electrical, thermoelectric and energy dissipation characteristics of molecular junctions. Using this platform, we studied gold junctions with prototypical molecules (Au-biphenyl-4,4'-dithiol-Au, Au-terphenyl-4,4''-dithiol-Au and Au-4,4'-bipyridine-Au) and revealed the relationship between heating or cooling and charge transmission characteristics. Our experimental conclusions are supported by self-energy-corrected density functional theory calculations. We expect these advances to stimulate studies of both thermal and thermoelectric transport in molecular junctions where the possibility of extraordinarily efficient energy conversion has been theoretically predicted2-4,14.

Molecular Characterization of Polio from Environmental Samples: ISSP, The Israeli Sewage Surveillance Protocol.

PubMed

Shulman, Lester M; Manor, Yossi; Hindiyeh, Musa; Sofer, Danit; Mendelson, Ella

2016-01-01

Polioviruses are enteric viruses that cause paralytic poliomyelitis in less than 0.5 % of infections and are asymptomatic in >90 % infections of naïve hosts. Environmental surveillance monitors polio in populations rather than in individuals. When this very low morbidity to infection ratio, drops drastically in highly vaccinated populations, environmental surveillance employing manual or automatic sampling coupled with molecular analysis carried out in well-equipped central laboratories becomes the surveillance method of choice since polioviruses are excreted by infected individuals regardless of whether or not the infection is symptomatic. This chapter describes a high throughput rapid turn-around time method for molecular characterization of polioviruses from sewage. It is presented in five modules: (1) Sewage collection and concentration of the viruses in the sewage; (2) Cell cultures for identification of virus in the concentrated sewage; (3) Nucleic acid extractions directly from sewage and from tissue cultures infected with aliquots of concentrated sewage; (4) Nucleic Acid Amplification for poliovirus serotype identification and intratypic differentiation (discriminating wild and vaccine derived polioviruses form vaccine strains); and (5) Molecular characterization of viral RNA by qRT-PCR, TR-PCR, and Sequence analysis. Monitoring silent or symptomatic transmission of vaccine-derived polioviruses or wild polioviruses is critical for the endgame of poliovirus eradication. We present methods for adapting standard kits and validating the changes for this purpose based on experience gained during the recent introduction and sustained transmission of a wild type 1 poliovirus in Israel in 2013 in a population with an initial IPV vaccine coverage >90 %.

An improved correlation to predict molecular weight between crosslinks based on equilibrium degree of swelling of hydrogel networks.

PubMed

Jimenez-Vergara, Andrea C; Lewis, John; Hahn, Mariah S; Munoz-Pinto, Dany J

2018-04-01

Accurate characterization of hydrogel diffusional properties is of substantial importance for a range of biotechnological applications. The diffusional capacity of hydrogels has commonly been estimated using the average molecular weight between crosslinks (M c ), which is calculated based on the equilibrium degree of swelling. However, the existing correlation linking M c and equilibrium swelling fails to accurately reflect the diffusional properties of highly crosslinked hydrogel networks. Also, as demonstrated herein, the current model fails to accurately predict the diffusional properties of hydrogels when polymer concentration and molecular weight are varied simultaneously. To address these limitations, we evaluated the diffusional properties of 48 distinct hydrogel formulations using two different photoinitiator systems, employing molecular size exclusion as an alternative methodology to calculate average hydrogel mesh size. The resulting data were then utilized to develop a revised correlation between M c and hydrogel equilibrium swelling that substantially reduces the limitations associated with the current correlation. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 1339-1348, 2018. © 2017 Wiley Periodicals, Inc.

In vitro DNA binding, pBR322 plasmid cleavage and molecular modeling study of chiral benzothiazole Schiff-base-valine Cu(II) and Zn(II) complexes to evaluate their enantiomeric biological disposition for molecular target DNA.

PubMed

Alizadeh, Rahman; Afzal, Mohd; Arjmand, Farukh

2014-10-15

Bicyclic heterocyclic compounds viz. benzothiazoles are key components of deoxyribonucleic acid (DNA) molecules and participate directly in the encoding of genetic information. Benzothiazoles, therefore, represent a potent and selective class of antitumor compounds. The design and synthesis of chiral antitumor chemotherapeutic agents of Cu(II) and Zn(II), L- and -D benzothiazole Schiff base-valine complexes 1a &b and 2a &b, respectively were carried out and thoroughly characterized by spectroscopic and analytical techniques. Interaction of 1a and b and 2a and b with CT DNA by employing UV-vis, florescence, circular dichroic methods and cleavage studies of 1a with pBR322 plasmid, molecular docking were done in order to demonstrate their enantiomeric disposition toward the molecular drug target DNA. Interestingly, these studies unambiguously demonstrated the greater potency of L-enantiomer in comparison to D-enantiomer. Copyright © 2014 Elsevier B.V. All rights reserved.

Molecular motors and their functions in plants

NASA Technical Reports Server (NTRS)

Reddy, A. S.

2001-01-01

Molecular motors that hydrolyze ATP and use the derived energy to generate force are involved in a variety of diverse cellular functions. Genetic, biochemical, and cellular localization data have implicated motors in a variety of functions such as vesicle and organelle transport, cytoskeleton dynamics, morphogenesis, polarized growth, cell movements, spindle formation, chromosome movement, nuclear fusion, and signal transduction. In non-plant systems three families of molecular motors (kinesins, dyneins, and myosins) have been well characterized. These motors use microtubules (in the case of kinesines and dyneins) or actin filaments (in the case of myosins) as tracks to transport cargo materials intracellularly. During the last decade tremendous progress has been made in understanding the structure and function of various motors in animals. These studies are yielding interesting insights into the functions of molecular motors and the origin of different families of motors. Furthermore, the paradigm that motors bind cargo and move along cytoskeletal tracks does not explain the functions of some of the motors. Relatively little is known about the molecular motors and their roles in plants. In recent years, by using biochemical, cell biological, molecular, and genetic approaches a few molecular motors have been isolated and characterized from plants. These studies indicate that some of the motors in plants have novel features and regulatory mechanisms. The role of molecular motors in plant cell division, cell expansion, cytoplasmic streaming, cell-to-cell communication, membrane trafficking, and morphogenesis is beginning to be understood. Analyses of the Arabidopsis genome sequence database (51% of genome) with conserved motor domains of kinesin and myosin families indicates the presence of a large number (about 40) of molecular motors and the functions of many of these motors remain to be discovered. It is likely that many more motors with novel regulatory mechanisms that perform plant-specific functions are yet to be discovered. Although the identification of motors in plants, especially in Arabidopsis, is progressing at a rapid pace because of the ongoing plant genome sequencing projects, only a few plant motors have been characterized in any detail. Elucidation of function and regulation of this multitude of motors in a given species is going to be a challenging and exciting area of research in plant cell biology. Structural features of some plant motors suggest calcium, through calmodulin, is likely to play a key role in regulating the function of both microtubule- and actin-based motors in plants.

Theory of attosecond delays in molecular photoionization.

PubMed

Baykusheva, Denitsa; Wörner, Hans Jakob

2017-03-28

We present a theoretical formalism for the calculation of attosecond delays in molecular photoionization. It is shown how delays relevant to one-photon-ionization, also known as Eisenbud-Wigner-Smith delays, can be obtained from the complex dipole matrix elements provided by molecular quantum scattering theory. These results are used to derive formulae for the delays measured by two-photon attosecond interferometry based on an attosecond pulse train and a dressing femtosecond infrared pulse. These effective delays are first expressed in the molecular frame where maximal information about the molecular photoionization dynamics is available. The effects of averaging over the emission direction of the electron and the molecular orientation are introduced analytically. We illustrate this general formalism for the case of two polyatomic molecules. N 2 O serves as an example of a polar linear molecule characterized by complex photoionization dynamics resulting from the presence of molecular shape resonances. H 2 O illustrates the case of a non-linear molecule with comparably simple photoionization dynamics resulting from a flat continuum. Our theory establishes the foundation for interpreting measurements of the photoionization dynamics of all molecules by attosecond metrology.

Controlling the rectification properties of molecular junctions through molecule–electrode coupling

DOE PAGES

Koepf, Matthieu; Koenigsmann, Christopher; Ding, Wendu; ...

2016-08-17

The development of molecular components functioning as switches, rectifiers or amplifiers is a great challenge in molecular electronics. A desirable property of such components is functional robustness, meaning that the intrinsic functionality of components must be preserved regardless of the strategy used to integrate them into the final assemblies. Here, this issue is investigated for molecular diodes based on N-phenylbenzamide (NPBA) backbones. The transport properties of molecular junctions derived from NPBA are characterized while varying the nature of the functional groups interfacing the backbone and the gold electrodes required for break-junction measurements. Furthermore, combining experimental and theoretical methods, it ismore » shown that at low bias (<0.85 V) transport is determined by the same frontier molecular orbital originating from the NPBA core, regardless of the anchoring group employed. The magnitude of rectification, however, is strongly dependent on the strength of the electronic coupling at the gold–NPBA interface and on the spatial distribution of the local density of states of the dominant transport channel of the molecular junction.« less

Controlling the rectification properties of molecular junctions through molecule–electrode coupling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koepf, Matthieu; Koenigsmann, Christopher; Ding, Wendu

The development of molecular components functioning as switches, rectifiers or amplifiers is a great challenge in molecular electronics. A desirable property of such components is functional robustness, meaning that the intrinsic functionality of components must be preserved regardless of the strategy used to integrate them into the final assemblies. Here, this issue is investigated for molecular diodes based on N-phenylbenzamide (NPBA) backbones. The transport properties of molecular junctions derived from NPBA are characterized while varying the nature of the functional groups interfacing the backbone and the gold electrodes required for break-junction measurements. Furthermore, combining experimental and theoretical methods, it ismore » shown that at low bias (<0.85 V) transport is determined by the same frontier molecular orbital originating from the NPBA core, regardless of the anchoring group employed. The magnitude of rectification, however, is strongly dependent on the strength of the electronic coupling at the gold–NPBA interface and on the spatial distribution of the local density of states of the dominant transport channel of the molecular junction.« less

DNA nanotechnology from the test tube to the cell.

PubMed

Chen, Yuan-Jyue; Groves, Benjamin; Muscat, Richard A; Seelig, Georg

2015-09-01

The programmability of Watson-Crick base pairing, combined with a decrease in the cost of synthesis, has made DNA a widely used material for the assembly of molecular structures and dynamic molecular devices. Working in cell-free settings, researchers in DNA nanotechnology have been able to scale up system complexity and quantitatively characterize reaction mechanisms to an extent that is infeasible for engineered gene circuits or other cell-based technologies. However, the most intriguing applications of DNA nanotechnology - applications that best take advantage of the small size, biocompatibility and programmability of DNA-based systems - lie at the interface with biology. Here, we review recent progress in the transition of DNA nanotechnology from the test tube to the cell. We highlight key successes in the development of DNA-based imaging probes, prototypes of smart therapeutics and drug delivery systems, and explore the future challenges and opportunities for cellular DNA nanotechnology.

Biocompatible fluorinated polyglycerols for droplet microfluidics as an alternative to PEG-based copolymer surfactants.

PubMed

Wagner, Olaf; Thiele, Julian; Weinhart, Marie; Mazutis, Linas; Weitz, David A; Huck, Wilhelm T S; Haag, Rainer

2016-01-07

In droplet-based microfluidics, non-ionic, high-molecular weight surfactants are required to stabilize droplet interfaces. One of the most common structures that imparts stability as well as biocompatibility to water-in-oil droplets is a triblock copolymer surfactant composed of perfluoropolyether (PFPE) and polyethylene glycol (PEG) blocks. However, the fast growing applications of microdroplets in biology would benefit from a larger choice of specialized surfactants. PEG as a hydrophilic moiety, however, is a very limited tool in surfactant modification as one can only vary the molecular weight and chain-end functionalization. In contrast, linear polyglycerol offers further side-chain functionalization to create custom-tailored, biocompatible droplet interfaces. Herein, we describe the synthesis and characterization of polyglycerol-based triblock surfactants with tailored side-chain composition, and exemplify their application in cell encapsulation and in vitro gene expression studies in droplet-based microfluidics.

SVM Based Descriptor Selection and Classification of Neurodegenerative Disease Drugs for Pharmacological Modeling.

PubMed

Shahid, Mohammad; Shahzad Cheema, Muhammad; Klenner, Alexander; Younesi, Erfan; Hofmann-Apitius, Martin

2013-03-01

Systems pharmacological modeling of drug mode of action for the next generation of multitarget drugs may open new routes for drug design and discovery. Computational methods are widely used in this context amongst which support vector machines (SVM) have proven successful in addressing the challenge of classifying drugs with similar features. We have applied a variety of such SVM-based approaches, namely SVM-based recursive feature elimination (SVM-RFE). We use the approach to predict the pharmacological properties of drugs widely used against complex neurodegenerative disorders (NDD) and to build an in-silico computational model for the binary classification of NDD drugs from other drugs. Application of an SVM-RFE model to a set of drugs successfully classified NDD drugs from non-NDD drugs and resulted in overall accuracy of ∼80 % with 10 fold cross validation using 40 top ranked molecular descriptors selected out of total 314 descriptors. Moreover, SVM-RFE method outperformed linear discriminant analysis (LDA) based feature selection and classification. The model reduced the multidimensional descriptors space of drugs dramatically and predicted NDD drugs with high accuracy, while avoiding over fitting. Based on these results, NDD-specific focused libraries of drug-like compounds can be designed and existing NDD-specific drugs can be characterized by a well-characterized set of molecular descriptors. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular testing for clinical diagnosis and epidemiological investigations of intestinal parasitic infections.

PubMed

Verweij, Jaco J; Stensvold, C Rune

2014-04-01

Over the past few decades, nucleic acid-based methods have been developed for the diagnosis of intestinal parasitic infections. Advantages of nucleic acid-based methods are numerous; typically, these include increased sensitivity and specificity and simpler standardization of diagnostic procedures. DNA samples can also be stored and used for genetic characterization and molecular typing, providing a valuable tool for surveys and surveillance studies. A variety of technologies have been applied, and some specific and general pitfalls and limitations have been identified. This review provides an overview of the multitude of methods that have been reported for the detection of intestinal parasites and offers some guidance in applying these methods in the clinical laboratory and in epidemiological studies.

Molecular Testing for Clinical Diagnosis and Epidemiological Investigations of Intestinal Parasitic Infections

PubMed Central

Stensvold, C. Rune

2014-01-01

SUMMARY Over the past few decades, nucleic acid-based methods have been developed for the diagnosis of intestinal parasitic infections. Advantages of nucleic acid-based methods are numerous; typically, these include increased sensitivity and specificity and simpler standardization of diagnostic procedures. DNA samples can also be stored and used for genetic characterization and molecular typing, providing a valuable tool for surveys and surveillance studies. A variety of technologies have been applied, and some specific and general pitfalls and limitations have been identified. This review provides an overview of the multitude of methods that have been reported for the detection of intestinal parasites and offers some guidance in applying these methods in the clinical laboratory and in epidemiological studies. PMID:24696439

Syntheses, spectroscopic characterization, thermal study, molecular modeling, and biological evaluation of novel Schiff's base benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) with Ni(II), and Cu(II) metal complexes.

PubMed

Chandra, Sulekh; Gautam, Seema; Rajor, Hament Kumar; Bhatia, Rohit

2015-02-25

Novel Schiff's base ligand, benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) was synthesized by the condensation of benzil and 5-amino-1,3,4-thiadiazole-2-thiol in 1:2 ratio. The structure of ligand was determined on the basis of elemental analyses, IR, (1)H NMR, mass, and molecular modeling studies. Synthesized ligand behaved as tetradentate and coordinated to metal ion through sulfur atoms of thiol ring and nitrogen atoms of imine group. Ni(II), and Cu(II) complexes were synthesized with this nitrogen-sulfur donor (N2S2) ligand. Metal complexes were characterized by elemental analyses, molar conductance, magnetic susceptibility measurements, IR, electronic spectra, EPR, thermal, and molecular modeling studies. All the complexes showed molar conductance corresponding to non-electrolytic nature, expect [Ni(L)](NO3)2 complex, which was 1:2 electrolyte in nature. [Cu(L)(SO4)] complex may possessed square pyramidal geometry, [Ni(L)](NO3)2 complex tetrahedral and rest of the complexes six coordinated octahedral/tetragonal geometry. Newly synthesized ligand and its metal complexes were examined against the opportunistic pathogens. Results suggested that metal complexes were more biological sensitive than free ligand. Copyright © 2014 Elsevier B.V. All rights reserved.

In vitro characterization of Leishmania (Viannia) braziliensis isolates from patients with different responses to Glucantime(®) treatment from Northwest Paraná, Brazil.

PubMed

Fernandes, Andrea Claudia Bekner Silva; Pedroso, Raíssa Bocchi; de Mello, Tatiane França Perles; Donatti, Lucélia; Venazzi, Eneide Aparecida Sabaini; Demarchi, Izabel Galhardo; Aristides, Sandra Mara Alessi; Lonardoni, Maria Valdrinez Campana; Silveira, Thaís Gomes Verzignassi

2016-08-01

Leishmaniasis is a group of diseases that presents various clinical manifestations. Many studies have shown that the parasite plays an important role in the clinical manifestations and prognosis of this disease. The cutaneous and mucosal forms of American tegumentary leishmaniasis (ATL) are associated with Leishmania (Viannia) braziliensis, which exhibits intraspecific genetic polymorphisms and various clinical manifestations. The present study focused on four different L. braziliensis strains that were isolated from patients with distinct Glucantime(®) treatment responses. The isolates were described based on their molecular, biological, and infective characteristics. Growth patterns in culture medium and different grow phases were analyzed, MID-Logarithimic (Mid-LOG), Logarithimic (LOG) and Stationary (STAT) phases. Complement resistance was evaluated using guinea pig serum. Infection to murine peritoneal macrophages, cytokine and nitric oxide were analyzed. Ultrastructural features were determined by transmission electron microscopy, and molecular characteristics were determined based on random amplified polymorphic DNA (RAPD). All of the L. braziliensis isolates showed typical growth and similar complement sensitivity patterns. Markedly lower infectivity indexes were observed for all strains in the LOG phase, with different cytokine profiles. The ultrastructure analysis revealed distinct differences between the MID-LOG, LOG, and STAT phases. The RAPD results showed a divergence between the isolates of the L. braziliensis. The in vitro characterization of L. braziliensis isolates from humans with different treatment responses using various parameters enabled us to observe differences among the isolates. Molecular and in vivo characterizations are currently under study to improve understanding of the parasite-host interaction that can imply in the clinical manifestation differences. Copyright © 2016 Elsevier Inc. All rights reserved.

A strategy for comprehensive identification of sequential constituents using ultra-high-performance liquid chromatography coupled with linear ion trap-Orbitrap mass spectrometer, application study on chlorogenic acids in Flos Lonicerae Japonicae.

PubMed

Zhang, Jia-yu; Wang, Zi-jian; Li, Yun; Liu, Ying; Cai, Wei; Li, Chen; Lu, Jian-qiu; Qiao, Yan-jiang

2016-01-15

The analytical methodologies for evaluation of multi-component system in traditional Chinese medicines (TCMs) have been inadequate or unacceptable. As a result, the unclarity of multi-component hinders the sufficient interpretation of their bioactivities. In this paper, an ultra-high-performance liquid chromatography coupled with linear ion trap-Orbitrap (UPLC-LTQ-Orbitrap)-based strategy focused on the comprehensive identification of TCM sequential constituents was developed. The strategy was characterized by molecular design, multiple ion monitoring (MIM), targeted database hits and mass spectral trees similarity filter (MTSF), and even more isomerism discrimination. It was successfully applied in the HRMS data-acquisition and processing of chlorogenic acids (CGAs) in Flos Lonicerae Japonicae (FLJ), and a total of 115 chromatographic peaks attributed to 18 categories were characterized, allowing a comprehensive revelation of CGAs in FLJ for the first time. This demonstrated that MIM based on molecular design could improve the efficiency to trigger MS/MS fragmentation reactions. Targeted database hits and MTSF searching greatly facilitated the processing of extremely large information data. Besides, the introduction of diagnostic product ions (DPIs) discrimination, ClogP analysis, and molecular simulation, raised the efficiency and accuracy to characterize sequential constituents especially position and geometric isomers. In conclusion, the results expanded our understanding on CGAs in FLJ, and the strategy could be exemplary for future research on the comprehensive identification of sequential constituents in TCMs. Meanwhile, it may propose a novel idea for analyzing sequential constituents, and is promising for quality control and evaluation of TCMs. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular prevalence and characterization of Hepatozoon ursi infection in Indian sloth bears (Melursus ursinus).

PubMed

Pawar, Rahul Mohanchandra; Poornachandar, Anantula; Arun, Attur Shanmugam; Manikandan, Santhanam; Shivaji, Sisinthy

2011-12-15

Hepatozoon species are parasites that infect a wide variety of domestic and wild animals. The objective of the study was to detect the occurrence of Hepatozoon ursi in Indian sloth bears and to characterize the parasite based on phylogenetic analysis of the partial 18S rRNA gene sequence. Hepatozoon infection could be detected in 38 (70%) out of fifty-four blood samples of Indian sloth bears (captive and wild), suggestive of high prevalence of Hepatozoon infection in Indian sloth bears. Sequencing of partial 18S rRNA gene of the positive samples and BLAST analysis indicated that the nearest phylogenetic neighbour was H. ursi with which they exhibited 99-100% similarity. Additionally, Hepatozoon sp. isolated from wild sloth bears of India were identical to those in captive sloth bears and phylogenetically related to H. ursi reported from Japanese black bears from Japan. To our knowledge, this is the first report on the molecular characterization of H. ursi infection in Indian sloth bears. Copyright © 2011 Elsevier B.V. All rights reserved.

On the characterization of inhomogeneity of the density distribution in supercritical fluids via molecular dynamics simulation and data mining analysis.

PubMed

Idrissi, Abdenacer; Vyalov, Ivan; Georgi, Nikolaj; Kiselev, Michael

2013-10-10

We combined molecular dynamics simulation and DBSCAN algorithm (Density Based Spatial Clustering of Application with Noise) in order to characterize the local density inhomogeneity distribution in supercritical fluids. The DBSCAN is an algorithm that is capable of finding arbitrarily shaped density domains, where domains are defined as dense regions separated by low-density regions. The inhomogeneity of density domain distributions of Ar system in sub- and supercritical conditions along the 50 bar isobar is associated with the occurrence of a maximum in the fluctuation of number of particles of the density domains. This maximum coincides with the temperature, Tα, at which the thermal expansion occurs. Furthermore, using Voronoi polyhedral analysis, we characterized the structure of the density domains. The results show that with increasing temperature below Tα, the increase of the inhomogeneity is mainly associated with the density fluctuation of the border particles of the density domains, while with increasing temperature above Tα, the decrease of the inhomogeneity is associated with the core particles.

A molecular scheme for improved characterization of human embryonic stem cell lines

PubMed Central

Josephson, Richard; Sykes, Gregory; Liu, Ying; Ording, Carol; Xu, Weining; Zeng, Xianmin; Shin, Soojung; Loring, Jeanne; Maitra, Anirban; Rao, Mahendra S; Auerbach, Jonathan M

2006-01-01

Background Human embryonic stem cells (hESC) offer a renewable source of a wide range of cell types for use in research and cell-based therapies to treat disease. Inspection of protein markers provides important information about the current state of the cells and data for subsequent manipulations. However, hESC must be routinely analyzed at the genomic level to guard against deleterious changes during extensive propagation, expansion, and manipulation in vitro. Results We found that short tandem repeat (STR) analysis, human leukocyte antigen (HLA) typing, single nucleotide polymorphism (SNP) genomic analysis, mitochondrial DNA sequencing, and gene expression analysis by microarray can be used to fully describe any hESC culture in terms of its identity, stability, and undifferentiated state. Conclusion Here we describe, using molecular biology alone, a comprehensive characterization of 17 different hESC lines. The use of amplified nucleic acids means that for the first time full characterization of hESC lines can be performed with little time investment and a minimum of material. The information thus gained will facilitate comparison of lines and replication of results between laboratories. PMID:16919167

Quantitative characterization of solid epoxy resins using comprehensive two dimensional liquid chromatography coupled with electrospray ionization-time of flight mass spectrometry.

PubMed

Julka, Samir; Cortes, Hernan; Harfmann, Robert; Bell, Bruce; Schweizer-Theobaldt, Andreas; Pursch, Matthias; Mondello, Luigi; Maynard, Shawn; West, David

2009-06-01

A comprehensive multidimensional liquid chromatography system coupled to Electrospray Ionization-Mass Spectrometry (LCxLC-ESI-MS) was developed for detailed characterization and quantitation of solid epoxy resin components. The two orthogonal modes of separation selected were size exclusion chromatography (SEC) in the first dimension and liquid chromatography at critical conditions (LCCC) in the second dimension. Different components present in the solid epoxy resins were separated and quantitated for the first time based on the functional groups and molecular weight heterogeneity. Coupling LCxLC separations with mass spectrometry enabled the identification of components resolved in the two-dimensional space. Several different functional group families of compounds were separated and identified, including epoxy-epoxy and epoxy-alpha-glycol functional oligomers, and their individual molecular weight ranges were determined. Repeatability obtained ranged from 0.5% for the main product to 21% for oligomers at the 0.4% concentration level.

Fluorescence-Raman Dual Modal Endoscopic System for Multiplexed Molecular Diagnostics

NASA Astrophysics Data System (ADS)

Jeong, Sinyoung; Kim, Yong-Il; Kang, Homan; Kim, Gunsung; Cha, Myeong Geun; Chang, Hyejin; Jung, Kyung Oh; Kim, Young-Hwa; Jun, Bong-Hyun; Hwang, Do Won; Lee, Yun-Sang; Youn, Hyewon; Lee, Yoon-Sik; Kang, Keon Wook; Lee, Dong Soo; Jeong, Dae Hong

2015-03-01

Optical endoscopic imaging, which was recently equipped with bioluminescence, fluorescence, and Raman scattering, allows minimally invasive real-time detection of pathologies on the surface of hollow organs. To characterize pathologic lesions in a multiplexed way, we developed a dual modal fluorescence-Raman endomicroscopic system (FRES), which used fluorescence and surface-enhanced Raman scattering nanoprobes (F-SERS dots). Real-time, in vivo, and multiple target detection of a specific cancer was successful, based on the fast imaging capability of fluorescence signals and the multiplex capability of simultaneously detected SERS signals using an optical fiber bundle for intraoperative endoscopic system. Human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR) on the breast cancer xenografts in a mouse orthotopic model were successfully detected in a multiplexed way, illustrating the potential of FRES as a molecular diagnostic instrument that enables real-time tumor characterization of receptors during routine endoscopic procedures.

In situ sum-frequency generation spectroscopy of ethylene-glycol and poly-N-isopropylacrylamide films

NASA Astrophysics Data System (ADS)

Kurz, Volker; Koelsch, Patrick

2009-03-01

Ethylene-glycol(EG)-based self-assembled monolayers (SAMs) are often used as a model systems for thin liquid films. Temperature series in heavy water were measured using a unique sample cell developed for in situ sum-frequency generation (SFG) spectroscopy experiments. Results obtained from model EG-SAMs with different lengths and terminating groups in various ionic solutions showed temperature-dependent changes in the molecular order. Films of poly-N-isopropylacrylamide(pNIPAM) were also characterized by in situ SFG spectroscopy in the CH, OH, OD and amide spectral regions under different polarization combinations. These systems have many applications as thermo-responsive polymers due to their ability to change solubility in water at the biologically relevant temperature of 32 C. This so-called lower critical solution temperature (LCST) phase transition was characterized in depth, allowing for the identification of the molecular groups involved in this process.

Investigating molecular changes in organic matter composition in two Holocene lake-sediment records from central Sweden using pyrolysis-GC/MS

NASA Astrophysics Data System (ADS)

Ninnes, Sofia; Tolu, Julie; Meyer-Jacob, Carsten; Mighall, Tim M.; Bindler, Richard

2017-06-01

Organic matter (OM) is a key component of lake sediments, affecting carbon, nutrient, and trace metal cycling at local and global scales. Yet little is known about long-term (millennial) changes in OM composition due to the inherent chemical complexity arising from multiple OM sources and from secondary transformations. In this study we explore how the molecular composition of OM changes throughout the Holocene in two adjacent boreal lakes in central Sweden and compare molecular-level information with conventional OM variables, including total carbon, total nitrogen, C:N ratios, δ13C, and δ15N. To characterize the molecular OM composition, we employed a new method based on pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), which yields semiquantitative data on >100 organic compounds of different origin and degradation status. We identify large changes in OM composition after deglaciation (circa 8500 ± 500 B.C.), associated with early landscape development, and during the most recent 40-50 years, driven by degradation processes. With molecular-level information we can also distinguish between natural landscape development and human catchment disturbance during the last 1700 years. Our study demonstrates that characterization of the molecular OM composition by the high-throughput Py-GC/MS method is an efficient complement to conventional OM variables for identification and understanding of past OM dynamics in lake-sediment records. Holocene changes observed for pyrolytic compounds and compound classes known for having different reactivity indicate the need for further paleo-reconstruction of the molecular OM composition to better understand both past and future OM dynamics and associated environmental changes.

Two-dimensional NMR spectroscopy links structural moieties of soil organic matter to the temperature sensitivity of its decomposition

NASA Astrophysics Data System (ADS)

Soucemarianadin, Laure; Erhagen, Björn; Öquist, Mats; Nilsson, Mats; Schleucher, Jürgen

2015-04-01

Soil organic matter (SOM) represents a huge carbon pool, specifically in boreal ecosystems. Warming-induced release of large amounts of CO2 from the soil carbon pool might become a significant exacerbating feedback to global warming, if decomposition rates of boreal soils were more sensitive to increased temperatures. Despite a large number of studies dedicated to the topic, it has proven difficult to elucidate how the organo-chemical composition of SOM influences its decomposition, or its quality as a substrate for microbial metabolism. A great part of this challenge results from our inability to achieve a detailed characterization of the complex composition of SOM on the level of molecular structural moieties. 13C nuclear magnetic resonance (NMR) spectroscopy is a common tool to characterize SOM. However, SOM is a very complex mixture and the chemical shift regions distinguished in the 13C NMR spectra often represent many different molecular fragments. For example, in the carbohydrates region, signals of all monosaccharides present in many different polymers overlap. This overlap thwarts attempts to identify molecular moieties, resulting in insufficient information to characterize SOM composition. We applied two-dimensional (2D) NMR to characterize SOM with highly increased resolution. We directly dissolved finely ground litters and forest floors'fibric and humic horizons'of both coniferous and deciduous boreal forests in dimethyl sulfoxide and analyzed the resulting solution with a 2D 1H-13C NMR experiment. In the 2D planes of these spectra, signals of CH groups can be resolved based on their 13C and 1H chemical shifts, hence the resolving power and information content of these NMR spectra is hugely increased. The 2D spectra indeed resolved overlaps observed in 1D 13C spectra, so that hundreds of distinct CH groups could be observed and many molecular fragments could be identified. For instance, in the aromatics region, signals from individual lignin units could be recognized. It was hence possible to follow the fate of specific structural moieties in soils. We observed differences between litter and soil samples, and were able to relate them to the decomposition of identifiable moieties. Using multivariate data analysis, we aimed at linking the detailed chemical fingerprints of SOM to turnover rates in a soil incubation experiment. With the multivariate models, we were able to relate signal patterns in the 2D spectra and intensities of identifiable molecular moieties to variability in the temperature response of organic matter decomposition, as assessed by Q10. In conclusion, the characterization of SOM composition at the molecular level by solution-state 2D NMR spectroscopy is highly promising; it offers unprecedented possibilities to link SOM molecular composition to ecosystem processes, and their responses to environmental changes.

Electron Transport through Porphyrin Molecular Junctions

NASA Astrophysics Data System (ADS)

Zhou, Qi

The goal of this work is to study the properties that would affect the electron transport through a porphyrin molecular junction. This work contributes to the field of electron transport in molecular junctions in the following 3 aspects. First of all, by carrying out experiments comparing the conductance of the iron (III) porphyrin (protected) and the free base porphyrin (protected), it is confirmed that the molecular energy level broadening and shifting occurs for porphyrin molecules when coupled with the metal electrodes, and this level broadening and shifting plays an important role in the electron transport through molecular junctions. Secondly, by carrying out an in-situ deprotection of the acetyl-protected free base porphyrin molecules, it is found out that the presence of acetyl groups reduces the conductance. Thirdly, by incorporating the Matrix-assisted laser desorption/ionization (MALDI) spectrum and the in-situ deprotection prior to formation of molecular junctions, it allows a more precise understanding of the molecules involved in the formation of molecular junctions, and therefore allows an accurate analysis of the conductance histogram. The molecules are prepared by self-assembly and the junctions are formed using a Scanning Tunneling Microscopy (STM) molecular break junction technique. The porphyrin molecules are characterized by MALDI in solution before self-assembly to a gold/mica substrate. The self-assembled monolayers (SAMs) of porphyrins on gold are characterized by Ultraviolet-visible (UV-Vis) reflection spectroscopy to confirm that the molecules are attached to the substrate. The SAMs are then characterized by Angle-Resolved X-ray photoelectron spectroscopy (ARXPS) to determine the thickness and the average molecular orientation of the molecular layer. The electron transport is measured by conductance-displacement (G-S) experiments under a given bias (-0.4V). The conductance value of a single molecule is identified by a statistical analysis over a large set of measurements. In this thesis, I focus on two factors that would affect the electron transport through the porphyrin molecules, namely, the metal ion center, and the deprotection of the end groups. The effect of metal ion center is studied by comparing the conductance of an iron (III) porphyrin (protected) to that of a free base porphyrin (protected). The in-situ deprotection of the molecules before forming the junctions is completed to study the effect of the molecular-electrode interaction. The first factor studied, that is, the metal ion center in the porphyrin molecule, show that the conductance for iron (III) porphyrin (protected) is 3.74 x10-5 G0, and the conductance for the free base porphyrin (protected) is 4.73x10-5 G0 , where G0 = e2 / pih = (25.8kO)-1 is the quantized unit of electrical conductance. Through our collaborative efforts, first principles calculations carried out by our collaborators for the molecular levels of an isolated molecule (without electrodes) show that the energy levels of an iron (III) porphyrin molecule are slightly shifted compared to that of the free base porphyrin. For the free base porphyrin, the highest occupied molecular orbital (HOMO) level (-4.952 eV) lies between the chemical potentials of the substrate (-4.7 eV) and the STM tip (-5.1 eV). This level serves as a channel for electron transport. For the iron (III) porphyrin, the HOMO is at -5.306 eV, which is not in between the chemical potentials of the substrate. Therefore, a significantly smaller conductance is expected for the iron (III) porphyrin compared to the conductance of a free base porphyrin, because of the lack of the electron transport channel. However, the conductance measured from G-S experiments is comparable, i.e. 3.74 x10-5 G0 for iron (III) porphyrin and 4.73x10-5 G0 for free base porphyrin. This suggests that the molecular energy level broadening and shifting occurs for porphyrin molecules when coupled with the metal electrodes, and this level broadening and shifting may significantly affect the electron transport through molecular junctions. The second factor studied, that is, the deprotection of the porphyrin end groups (acetylthio, -SCOCH3), was completed in-situ for the free base porphyrin through the reaction of the acetylthio with sulfuric acid at 35° Celsius for 3 hours. MALDI spectroscopy confirms that two additional deprotected porphyrin species are formed by deprotection, with protonated (MH+) molecular masses of 721 and 679, corresponding to a partially deprotected porphyrin (i.e. only one of the two end groups deprotected), and a fully deprotected porphyrin molecule. Along with the un-reacted acetyl protected porphyrin, a total of 3 porphyrin species are in the solution. This solution is used for self-assembly on a gold/mica surface. The thickness of the in-situ deprotected SAM is determined to be ˜1.7 nm, confirming a relatively upright molecular orientation (54.0°-63.5° between the substrate surface and the molecule), compared to a thickness of ˜1.5 nm for the protected SAM that has a more flat-lying molecular orientation (˜45.6° between the substrate surface and the molecule). From G-S measurements on SAMs prepared by in-situ deprotection, junctions with lower conductance steps at mid 10-5 G0 and junctions with higher conductance steps around 10-4 G 0 are observed. Supported by computational modeling from our collaborating research group, we associate the lower conductance steps to junctions based on the protected form of thiols at the tip-molecule interface, and the higher conductance steps to the deprotected form of the thiol contacts. We suggest that the reduced conductance in the protected porphyrin originates from the presence of the acetyl end groups (-COCH3), rather than from the elongation of the sulfur-gold (S-Au) bonds at the tip-molecule interface. By studying these two factors, I expect this work to provide insights into electron transport through molecules or metal-molecule-metal junctions, and in applications related to integrating molecules as functional units in electronic devices. Future work related to this thesis may include the molecular conductance based on reduction-oxidation (redox) properties of iron ligated porphyrins for the application of molecular switches and molecular memory elements.

The establishment and characterization of the first canine hepatocellular carcinoma cell line, which resembles human oncogenic expression patterns

PubMed Central

Boomkens, Sacha Y; Spee, Bart; IJzer, Jooske; Kisjes, Ronald; Egberink, Herman F; van den Ingh, Ted SGAM; Rothuizen, Jan; Penning, Louis C

2004-01-01

Background Hepatocellular carcinoma (HCC) is one of the most worldwide frequent primary carcinomas resulting in the death of many cirrhotic patients. Unfortunately, the molecular mechanisms of this cancer are not well understood; therefore, we need a good model system to study HCC. The dog is recognized as a promising model for human medical research, namely compared with rodents. The objective of this study was to establish and characterize a spontaneous canine tumor cell line as a potential model for studies on HCC. Results Histomorphological, biochemical, molecular biological and quantitative assays were performed to characterize the canine HCC cell line that originated from a dog with a spontaneous liver tumor. Morphological investigations provided strong evidence for the hepatocytic and neoplastic nature of the cell line, while biochemical assays showed that they produced liver-specific enzymes. PCR analysis confirmed expression of ceruloplasmin, alpha-fetoprotein and serum albumin. Quantitative RT-PCR showed that the canine HCC cell line resembles human HCC based on the measurements of expression profiles of genes involved in cell proliferation and apoptosis. Conclusions We have developed a novel, spontaneous tumor liver cell line of canine origin that has many characteristics of human HCC. Therefore, the canine HCC cell line might be an excellent model for comparative studies on the molecular pathogenesis of HCC. PMID:15566568

Molecular characterization of feline calicivirus variants from multicat household and public animal shelter in Rio de Janeiro, Brazil.

PubMed

Pereira, Joylson de Jesus; Baumworcel, Natasha; Fioretti, Júlia Monassa; Domingues, Cinthya Fonseca; Moraes, Laís Fernandes de; Marinho, Robson Dos Santos Souza; Vieira, Maria Clara Rodrigues; Pinto, Ana Maria Viana; de Castro, Tatiana Xavier

2018-02-28

The aim of this study was to perform the molecular characterization of conserved and variable regions of feline calicivirus capsid genome in order to investigate the molecular diversity of variants in Brazilian cat population. Twenty-six conjunctival samples from cats living in five public short-term animal shelters and three multicat life-long households were analyzed. Fifteen cats had conjunctivitis, three had oral ulceration, eight had respiratory signs (cough, sneeze and nasal discharge) and nine were asymptomatic. Feline calicivirus were isolated in CRFK cells and characterized by reverse transcription PCR target to both conserved and variable regions of open reading frame 2. The amplicons obtained were sequenced. A phylogenetic analysis along with most of the prototypes available in GenBank database and an amino acid analysis were performed. Phylogenetic analysis based on both conserved and variable region revealed two clusters with an aLTR value of 1.00 and 0.98 respectively and the variants from this study belong to feline calicivirus genogroup I. No association between geographical distribution and/or clinical signs and clustering in phylogenetic tree was observed. The variants circulating in public short-term animal shelter demonstrated a high variability because of the relatively rapid turnover of carrier cats constantly introduced of multiple viruses into this location over time. Copyright © 2018 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Development of a Novel NMR-based Rheb GTPase Assay and Molecular Characterization of TSC2 GAP Activity

DTIC Science & Technology

2010-05-01

GTPase) that belongs to the Ras superfamily and has homologs in yeast, fungi , slime mold, fruit fly, zebra fish, and mammals (1–3). Ge- netic and...characterization of TSC2 disease mutations affecting its GAP activity (months 9-12) While the final aspects of this task are yet to be completed, we have...domain mutants of TSC2 that we examined affected its enzymatic activ- ity. This method can now be applied to study the function and regulation of other

Characterizing gene responses to drought stress in fourwing saltbush [Atriplex canescens (Pursh.) Nutt.)

Treesearch

Linda S. Adair; David L. Andrews; John Cairney; Edward A. Funkhouser; Ronald J. Newton; Earl F. Aldon

1992-01-01

New techniques in molecular biology can be used to characterize genes whose expression is induced by drought stress. These techniques can be used to understand responses of range plants to environmental stresses at the biochemical and molecular level. For example, they can be used to characterize genes that respond to drought stress conditions in the native shrub

Charge transfer complex between 2,3-diaminopyridine with chloranilic acid. Synthesis, characterization and DFT, TD-DFT computational studies

NASA Astrophysics Data System (ADS)

Al-Ahmary, Khairia M.; Habeeb, Moustafa M.; Al-Obidan, Areej H.

2018-05-01

New charge transfer complex (CTC) between the electron donor 2,3-diaminopyridine (DAP) with the electron acceptor chloranilic (CLA) acid has been synthesized and characterized experimentally and theoretically using a variety of physicochemical techniques. The experimental work included the use of elemental analysis, UV-vis, IR and 1H NMR studies to characterize the complex. Electronic spectra have been carried out in different hydrogen bonded solvents, methanol (MeOH), acetonitrile (AN) and 1:1 mixture from AN-MeOH. The molecular composition of the complex was identified to be 1:1 from Jobs and molar ratio methods. The stability constant was determined using minimum-maximum absorbances method where it recorded high values confirming the high stability of the formed complex. The solid complex was prepared and characterized by elemental analysis that confirmed its formation in 1:1 stoichiometric ratio. Both IR and NMR studies asserted the existence of proton and charge transfers in the formed complex. For supporting the experimental results, DFT computations were carried out using B3LYP/6-31G(d,p) method to compute the optimized structures of the reactants and complex, their geometrical parameters, reactivity parameters, molecular electrostatic potential map and frontier molecular orbitals. The analysis of DFT results strongly confirmed the high stability of the formed complex based on existing charge transfer beside proton transfer hydrogen bonding concordant with experimental results. The origin of electronic spectra was analyzed using TD-DFT method where the observed λmax are strongly consisted with the computed ones. TD-DFT showed the contributed states for various electronic transitions.

Isolation and molecular characterization of Leptospira borgpetersenii serovar Hardjo strain Hardjobovis in the urine of naturally infected cattle in Brazil.

PubMed

Chideroli, R T; Pereira, U P; Gonçalves, D D; Nakamura, A Y; Alfieri, A A; Alfieri, A F; Freitas, J C

2016-02-19

Most epidemiologic studies on bovine leptospirosis are based on serological tests that use antibodies against several serotypes, including the serovar Hardjo, which is widespread and considered to be the most adapted to bovine hosts. However, using only serological studies is not sufficient to identify and distinguish species of leptospires. The aim of this study was report the first isolation in Brazil of two strains serovar Hardjo obtained in urine samples from naturally infected cows in a small Brazilian dairy herd and find the genetic species and consequently the type strain Hardjobovis by molecular characterization. Fifteen dairy cows with a history of reproductive failure, such as abortion and infertility, were selected. Urine samples obtained from each animal were immediately seeded in tubes containing Ellinghausen-McCullough-Johnson-Harris culture medium. The identification of the isolates was performed by Multilocus variable-number tandem-repeat analysis (MLVA) technique and phylogenetic analysis of partial sequence of gene sec Y. From the 15 urine samples evaluated, two Leptospira were found and identified as the Londrina 49 and Londrina 54 strains. The MLVA profiles and sequencing of gene sec Y characterized the isolates as L. borgpetersenii serovar Hardjo strain Hadjobovis because it has different genetic pattern of Leptospira interrogans serovar Hardjo strain Hardjoprajitno. Therefore, more studies are needed including isolation and molecular characterization from regional strains to obtain a better knowledge about epidemiology of serovar Hardjo in bovine which may assist in future strategies of prevention and control of bovine leptospirosis.

Distinguishing molecular environments in supported Pt catalysts and their influences on activity and selectivity

NASA Astrophysics Data System (ADS)

Jones, Louis Chin

This thesis entails the synthesis, automated catalytic testing, and in situ molecular characterization of supported Pt and Pt-alloy nanoparticle (NP) catalysts, with emphasis on how to assess the molecular distributions of Pt environments that are affecting overall catalytic activity and selectivity. We have taken the approach of (a) manipulating nucleation and growth of NPs using oxide supports, surfactants, and inorganic complexes to create Pt NPs with uniform size, shape, and composition, (b) automating batch and continuous flow catalytic reaction tests, and (c) characterizing the molecular environments of Pt surfaces using in situ infrared (IR) spectroscopy and solid-state 195Pt NMR. The following will highlight the synthesis and characterization of Ag-doped Pt NPs and their influence on C 2H2 hydrogenation selectivity, and the implementation of advanced solid-state 195Pt NMR techniques to distinguish how distributions of molecular Pt environments vary with nanoparticle size, support, and surface composition.

Classification of solid dispersions: correlation to (i) stability and solubility (ii) preparation and characterization techniques.

PubMed

Meng, Fan; Gala, Urvi; Chauhan, Harsh

2015-01-01

Solid dispersion has been a topic of interest in recent years for its potential in improving oral bioavailability, especially for poorly water soluble drugs where dissolution could be the rate-limiting step of oral absorption. Understanding the physical state of the drug and polymers in solid dispersions is essential as it influences both the stability and solubility of these systems. This review emphasizes on the classification of solid dispersions based on the physical states of drug and polymer. Based on this classification, stability aspects such as crystallization tendency, glass transition temperature (Tg), drug polymer miscibility, molecular mobility, etc. and solubility aspects have been discussed. In addition, preparation and characterization methods for binary solid dispersions based on the classification have also been discussed.

Intraductal papillary-mucinous neoplasia of the pancreas: Histopathology and molecular biology.

PubMed

Verbeke, Caroline S

2010-10-27

Intraductal papillary-mucinous neoplasm (IPMN) of the pancreas is a clinically and morphologically distinctive precursor lesion of pancreatic cancer, characterized by gradual progression through a sequence of neoplastic changes. Based on the nature of the constituting neoplastic epithelium, degree of dysplasia and location within the pancreatic duct system, IPMNs are divided in several types which differ in their biological properties and clinical outcome. Molecular analysis and recent animal studies suggest that IPMNs develop in the context of a field-defect and reveal their possible relationship with other neoplastic precursor lesions of pancreatic cancer.

Preparation, characterization, and activity of α-Ti(HPO4)2 supported metallocene catalysts

NASA Astrophysics Data System (ADS)

Shi, Yasai; Yuan, Yuan; Xu, Qinghong; Yi, Jianjun

2016-10-01

A series of heterogeneous catalysts by loading metallocenes on surface of α-Ti(HPO4)2, a kind of solid acid, has been synthesized. Polymerization of alkenes, including ethylene and propylene, based on participation of the heterogeneous catalysts were studied and the results were compared to metallocenes supported on silica gel, α-Zr(HPO4)2 and clay. Higher catalytic activity, larger polymer molecular weight and narrow distribution of polymer molecular weight were obtained. Acidic strength of the support and its influence to metallocenes were studied to discover intrinsic factors in the polymerizations.

Continuous tooth replacement: the possible involvement of epithelial stem cells.

PubMed

Huysseune, Ann; Thesleff, Irma

2004-06-01

Epithelial stem cells have been identified in integumental structures such as hairs and continuously growing teeth of various rodents, and in the gut. Here we propose the involvement of epithelial stem cells in the continuous tooth replacement that characterizes non-mammalian vertebrates, as exemplified by the zebrafish. Arguments are based on morphological observations of tooth renewal in the zebrafish and on the similarities between molecular control of hair and tooth formation. Dissection of the molecular cascades underlying the regulation of the epithelial stem cell niche might open perspectives for new regenerative treatment strategies in clinical dentistry. Copyright 2004 Wiley Periodicals, Inc.

Molecular characterization of Trichuris serrata.

PubMed

Ketzis, Jennifer K; Verma, Ashutosh; Burgess, Graham

2015-05-01

Trichuris serrata, a whipworm of cats, can cause inflammation in the cecum and upper portion of the large intestine. It is unknown if the virulence and pathology of T. serrata differ from Trichuris campanula, the other species in cats. Distinguishing the species based on egg size is challenging. In addition, Trichuris eggs can be difficult to distinguish from Capillaria spp. This paper presents the first molecular description of T. serrata. The 18S ribosomal RNA (rRNA) gene was sequenced from male adult worms sourced from two unrelated cats on St. Kitts. Based on the analysis of 651 base pairs, T. serrata was found to be different than any other Trichuris species for which published sequencing of the 18S rRNA gene is available. A dendrogram was developed using Molecular Evolutionary Genetics Analysis version 6.0, and evolutionary history was inferred using the minimum evolution method. T. serrata was found to be most closely related to Trichuris vulpis, the Trichuris of dogs. Further development of the methodology could enable distinguishing T. serrata, T. campanula, and Capillaria spp. infections in cats and aid in diagnosis.

Characterization of aqueous two phase systems by combining lab-on-a-chip technology with robotic liquid handling stations.

PubMed

Amrhein, Sven; Schwab, Marie-Luise; Hoffmann, Marc; Hubbuch, Jürgen

2014-11-07

Over the last decade, the use of design of experiment approaches in combination with fully automated high throughput (HTP) compatible screenings supported by robotic liquid handling stations (LHS), adequate fast analytics and data processing has been developed in the biopharmaceutical industry into a strategy of high throughput process development (HTPD) resulting in lower experimental effort, sample reduction and an overall higher degree of process optimization. Apart from HTP technologies, lab-on-a-chip technology has experienced an enormous growth in the last years and allows further reduction of sample consumption. A combination of LHS and lab-on-a-chip technology is highly desirable and realized in the present work to characterize aqueous two phase systems with respect to tie lines. In particular, a new high throughput compatible approach for the characterization of aqueous two phase systems regarding tie lines by exploiting differences in phase densities is presented. Densities were measured by a standalone micro fluidic liquid density sensor, which was integrated into a liquid handling station by means of a developed generic Tip2World interface. This combination of liquid handling stations and lab-on-a-chip technology enables fast, fully automated, and highly accurate density measurements. The presented approach was used to determine the phase diagram of ATPSs composed of potassium phosphate (pH 7) and polyethylene glycol (PEG) with a molecular weight of 300, 400, 600 and 1000 Da respectively in the presence and in the absence of 3% (w/w) sodium chloride. Considering the whole ATPS characterization process, two complete ATPSs could be characterized within 24h, including four runs per ATPS for binodal curve determination (less than 45 min/run), and tie line determination (less than 45 min/run for ATPS preparation and 8h for density determination), which can be performed fully automated over night without requiring man power. The presented methodology provides a cost, time and material effective approach for characterization of ATPS phase diagram on base on highly accurate and comprehensive data. By this means the derived data opens the door for a more detailed description of ATPS towards generating mechanistic based models, since molecular approaches such as MD simulations or molecular descriptions along the line of QSAR heavily rely on accurate and comprehensive data. Copyright © 2014 Elsevier B.V. All rights reserved.

Design and characterization of molecular nonlinear optical switches.

PubMed

Castet, Frédéric; Rodriguez, Vincent; Pozzo, Jean-Luc; Ducasse, Laurent; Plaquet, Aurélie; Champagne, Benoît

2013-11-19

Nanoscale structures, including molecules, supramolecules, polymers, functionalized surfaces, and crystalline/amorphous solids, can commute between two or more forms, displaying contrasts in their nonlinear optical (NLO) properties. Because of this property, they have high potential for applications in data storage, signal processing, and sensing. As potential candidates for integration into responsive materials, scientists have been intensely studying organic and organometallic molecules with switchable first hyperpolarizability over the past two decades. As a result of this, researchers have been able to synthesize and characterize several families of molecular NLO switches that differ by the stimulus used to trigger the commutation. These stimuli can include light irradiation, pH variation, redox reaction, and ion recognition, among others. The design of multistate (including several switchable units) and multifunctional (triggered with different stimuli) systems has also motivated a large amount of work, aiming at the improvement of the storage capacity of optical memories or the diversification of the addressability of the devices. In complement to the synthesis of the compounds and the characterization of their NLO responses by means of hyper-Rayleigh scattering, quantum chemical calculations play a key role in the design of molecular switches with high first hyperpolarizability contrasts. Through the latter, we can gain a fundamental understanding of the various factors governing the efficiency of the switches. These are not easily accessible experimentally, and include donor/acceptor contributions, frequency dispersion, and solvent effects. In this Account, we illustrate the similarities of the experimental and theoretical tools to design and characterize highly efficient NLO switches but also the difficulties in comparing them. After providing a critical overview of the different theoretical approaches used for evaluating the first hyperpolarizabilities, we report two case studies in which theoretical simulations have provided guidelines to design NLO switches with improved efficiencies. The first example presents the joint theoretical/experimental characterization of a new family of multi-addressable NLO switches based on benzazolo-oxazolidine derivatives. The second focuses on the photoinduced commutation in merocyanine-spiropyran systems, where the significant NLO contrast could be exploited for metal cation identification in a new generation of multiusage sensing devices. Finally, we illustrate the impact of environment on the NLO switching properties, with examples based on the keto-enol equilibrium in anil derivatives. Through these representative examples, we demonstrate that the rational design of molecular NLO switches, which combines experimental and theoretical approaches, has reached maturity. Future challenges consist in extending the investigated objects to supramolecular architectures involving several NLO-responsive units, in order to exploit their cooperative effects for enhancing the NLO responses and contrasts.

Clinical and molecular characterization of females affected by X-linked retinoschisis.

PubMed

Staffieri, Sandra E; Rose, Loreto; Chang, Andrew; De Roach, John N; McLaren, Terri L; Mackey, David A; Hewitt, Alex W; Lamey, Tina M

2015-01-01

X-linked retinoschisis (XLRS) is a leading cause of juvenile macular degeneration associated with mutations in the RS1 gene. XLRS has a variable expressivity in males and shows no clinical phenotype in carrier females. Clinical and molecular characterization of male and female individuals affected with XLRS in a consanguineous family. Consanguineous Eastern European-Australian family Four clinically affected and nine unaffected family members were genetically and clinically characterized. Deoxyribonucleic acid (DNA) analysis was conducted by the Australian Inherited Retinal Disease Register and DNA Bank. Clinical and molecular characterization of the causative mutation in a consanguineous family with XLRS. By direct sequencing of the RS1 gene, one pathogenic variant, NM_000330.3: c.304C > T, p. R102W, was identified in all clinically diagnosed individuals analysed. The two females were homozygous for the variant, and the males were hemizygous. Clinical and genetic characterization of affected homozygous females in XLRS affords the rare opportunity to explore the molecular mechanisms of XLRS and the manifestation of these mutations as disease in humans. © 2015 Royal Australian and New Zealand College of Ophthalmologists.

Synthesis and characterization of antifouling poly(N-acryloylaminoethoxyethanol) with ultralow protein adsorption and cell attachment.

PubMed

Chen, Hong; Zhang, Mingzhen; Yang, Jintao; Zhao, Chao; Hu, Rundong; Chen, Qiang; Chang, Yung; Zheng, Jie

2014-09-02

Rational design of effective antifouling polymers is challenging but important for many fundamental and applied applications. Herein we synthesize and characterize an N-acryloylaminoethoxyethanol (AAEE) monomer, which integrates three hydrophilic groups of hydroxyl, amide, and ethylene glycol in the same material. AAEE monomers were further grafted and polymerized on gold substrates to form polyAAEE brushes with well-controlled thickness via surface-initiated atomic transfer radical polymerization (SI-ATRP), with particular attention to a better understanding of the molecular structure-antifouling property relationship of hydroxyl-acrylic-based polymers. The surface hydrophilicity and antifouling properties of polyAAEE brushes as a function of film thickness are studied by combined experimental and computational methods including surface plasmon resonance (SPR) sensors, atomic force microscopy (AFM), cell adhesion assay, and molecular dynamics (MD) simulations. With the optimal polymer film thicknesses (∼10-40 nm), polyAAEE-grafted surfaces can effectively resist protein adsorption from single-protein solutions and undiluted human blood plasma and serum to a nonfouling level (i.e., <0.3 ng/cm(2)). The polyAAEE brushes also highly resist mammalian cell attachment up to 3 days. MD simulations confirm that the integration of three hydrophilic groups induce a stronger and closer hydration layer around polyAAEE, revealing a positive relationship between surface hydration and antifouling properties. The molecular structure-antifouling properties relationship of a series of hydroxyl-acrylic-based polymers is also discussed. This work hopefully provides a promising structural motif for the design of new effective antifouling materials beyond traditional ethylene glycol-based antifouling materials.

Carbon Nanotube Based Molecular Electronics and Motors: A View from Classical and Quantum Dynamics Simulations

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Saini, Subhash (Technical Monitor)

1998-01-01

The tubular forms of fullerenes popularly known as carbon nanotubes are experimentally produced as single-, multiwall, and rope configurations. The nanotubes and nanoropes have shown to exhibit unusual mechanical and electronic properties. The single wall nanotubes exhibit both semiconducting and metallic behavior. In short undefected lengths they are the known strongest fibers which are unbreakable even when bent in half. Grown in ropes their tensile strength is approximately 100 times greater than steel at only one sixth the weight. Employing large scale classical and quantum molecular dynamics simulations we will explore the use of carbon nanotubes and carbon nanotube junctions in 2-, 3-, and 4-point molecular electronic device components, dynamic strength characterization for compressive, bending and torsional strains, and chemical functionalization for possible use in a nanoscale molecular motor. The above is an unclassified material produced for non-competitive basic research in the nanotechnology area.

Geminiviruses and Plant Hosts: A Closer Examination of the Molecular Arms Race.

PubMed

Ramesh, Shunmugiah V; Sahu, Pranav P; Prasad, Manoj; Praveen, Shelly; Pappu, Hanu R

2017-09-15

Geminiviruses are plant-infecting viruses characterized by a single-stranded DNA (ssDNA) genome. Geminivirus-derived proteins are multifunctional and effective regulators in modulating the host cellular processes resulting in successful infection. Virus-host interactions result in changes in host gene expression patterns, reprogram plant signaling controls, disrupt central cellular metabolic pathways, impair plant's defense system, and effectively evade RNA silencing response leading to host susceptibility. This review summarizes what is known about the cellular processes in the continuing tug of war between geminiviruses and their plant hosts at the molecular level. In addition, implications for engineered resistance to geminivirus infection in the context of a greater understanding of the molecular processes are also discussed. Finally, the prospect of employing geminivirus-based vectors in plant genome engineering and the emergence of powerful genome editing tools to confer geminivirus resistance are highlighted to complete the perspective on geminivirus-plant molecular interactions.

Geminiviruses and Plant Hosts: A Closer Examination of the Molecular Arms Race

PubMed Central

Ramesh, Shunmugiah V.; Sahu, Pranav P.; Prasad, Manoj; Praveen, Shelly; Pappu, Hanu R.

2017-01-01

Geminiviruses are plant-infecting viruses characterized by a single-stranded DNA (ssDNA) genome. Geminivirus-derived proteins are multifunctional and effective regulators in modulating the host cellular processes resulting in successful infection. Virus-host interactions result in changes in host gene expression patterns, reprogram plant signaling controls, disrupt central cellular metabolic pathways, impair plant’s defense system, and effectively evade RNA silencing response leading to host susceptibility. This review summarizes what is known about the cellular processes in the continuing tug of war between geminiviruses and their plant hosts at the molecular level. In addition, implications for engineered resistance to geminivirus infection in the context of a greater understanding of the molecular processes are also discussed. Finally, the prospect of employing geminivirus-based vectors in plant genome engineering and the emergence of powerful genome editing tools to confer geminivirus resistance are highlighted to complete the perspective on geminivirus-plant molecular interactions. PMID:28914771

Molecular typing of Sarcocystis neurona: current status and future trends.

PubMed

Elsheikha, Hany M; Mansfield, Linda S

2007-10-21

Sarcocystis neurona is an important protozoal pathogen because it causes the serious neurological disease equine protozoal myeloencephalitis (EPM). The capacity of this organism to cause a wide spectrum of neurological signs in horses and the broad geographic distribution of observed cases in the Americas drive the need for sensitive, reliable and rapid typing methods to characterize strains. Various molecular methods have been developed and used to diagnose EPM due to S. neurona, to identify S. neurona isolates and to determine the heterogeneity and evolutionary relatedness within this species and related Sarcocystis spp. These methods included sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), immuno-fluorescent assay (IFA), slide agglutination test (SAT), SnSAG-specific ELISA, random amplified polymorphic DNA (RAPD), PCR-based restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP) fingerprinting, and sequence analysis of surface protein genes, ribosomal genes, microsatellite alleles and other molecular markers. Here, the utility of these molecular methods is reviewed and evaluated with respect to the need for molecular approaches that utilize well-characterized polymorphic, simple, independent, and stable genetic markers. These tools have the potential to add to knowledge of the genetic population structure of S. neurona and to provide new insights into the pathogenesis of EPM and S. neurona epidemiology. In particular, these methods provide new tools to address the hypothesis that particular genetic variants are associated with adverse clinical outcomes (severe pathotypes). The ultimate goal is to utilize them in future studies to improve treatment and prevention strategies.

Evaluation of breast cancer using intravoxel incoherent motion (IVIM) histogram analysis: comparison with malignant status, histological subtype, and molecular prognostic factors.

PubMed

Cho, Gene Young; Moy, Linda; Kim, Sungheon G; Baete, Steven H; Moccaldi, Melanie; Babb, James S; Sodickson, Daniel K; Sigmund, Eric E

2016-08-01

To examine heterogeneous breast cancer through intravoxel incoherent motion (IVIM) histogram analysis. This HIPAA-compliant, IRB-approved retrospective study included 62 patients (age 48.44 ± 11.14 years, 50 malignant lesions and 12 benign) who underwent contrast-enhanced 3 T breast MRI and diffusion-weighted imaging. Apparent diffusion coefficient (ADC) and IVIM biomarkers of tissue diffusivity (Dt), perfusion fraction (fp), and pseudo-diffusivity (Dp) were calculated using voxel-based analysis for the whole lesion volume. Histogram analysis was performed to quantify tumour heterogeneity. Comparisons were made using Mann-Whitney tests between benign/malignant status, histological subtype, and molecular prognostic factor status while Spearman's rank correlation was used to characterize the association between imaging biomarkers and prognostic factor expression. The average values of the ADC and IVIM biomarkers, Dt and fp, showed significant differences between benign and malignant lesions. Additional significant differences were found in the histogram parameters among tumour subtypes and molecular prognostic factor status. IVIM histogram metrics, particularly fp and Dp, showed significant correlation with hormonal factor expression. Advanced diffusion imaging biomarkers show relationships with molecular prognostic factors and breast cancer malignancy. This analysis reveals novel diagnostic metrics that may explain some of the observed variability in treatment response among breast cancer patients. • Novel IVIM biomarkers characterize heterogeneous breast cancer. • Histogram analysis enables quantification of tumour heterogeneity. • IVIM biomarkers show relationships with breast cancer malignancy and molecular prognostic factors.

Molecular modification of native coffee polysaccharide using subcritical water treatment: Structural characterization, antioxidant, and DNA protecting activities.

PubMed

Getachew, Adane Tilahun; Chun, Byung Soo

2017-06-01

Polysaccharides are an abundant resource in coffee beans and have proved to show numerous bioactivities. Despite their abundance, their activities are not always satisfactory mostly due to their structure and large molecular size. Molecular modifications of native polysaccharides can overcome this problem. In this study, we used a novel and green method to modify native coffee polysaccharides using subcritical water (SCW) treatment. The SCW treatment was used at the temperature of 180°C-220°C and pressure of 30-60bar. The molecular and structural modification of the polysaccharides was confirmed using several techniques such as FT-IR, UV spectroscopy, XRD, and TGA. The antioxidant activity of the modified polysaccharides was evaluated using several chemical and Saccharomyces cerevisiae-based high throughput assays. The modified polysaccharides showed high antioxidant activities in all tested assays. Moreover, the polysaccharides showed high DNA protection activities. Therefore, SCW could be employed as a green solvent for molecular modification of polysaccharides. Copyright © 2017 Elsevier B.V. All rights reserved.

Breast Cancer Treatment in the Era of Molecular Imaging

PubMed Central

Edelhauser, Gundula; Funovics, Martin

2008-01-01

Summary Molecular imaging employs molecularly targeted probes to visualize and often quantify distinct disease-specific markers and pathways. Modalities like intravital confocal or multiphoton microscopy, near-infrared fluorescence combined with endoscopy, surface reflectance imaging, or fluorescence-mediated tomography, and radionuclide imaging with positron emission tomography (PET) and single-photon emission computed tomography (SPECT) are increasingly used for small animal high-throughput screening, drug development and testing, and monitoring gene therapy experiments. In the clinical treatment of breast cancer, PET and SPECT as well as magnetic resonance-based molecular imaging are already established for the staging of distant disease and intrathoracic nodal status, for patient selection regarding receptor-directed treatments, and to gain early information about treatment efficacy. In the near future, reporter gene imaging during gene therapy and further spatial and qualitative characterization of the disease can become clinically possible with radionuclide and optical methods. Ultimately, it may be expected that every level of breast cancer treatment will be affected by molecular imaging, including screening. PMID:21048912

Integrative Analysis of Salmonellosis Outbreaks in Israel 1999-2012 Revealed an Invasive S. enterica Serovar 9,12:l,v:- and Endemic S. Typhimurium DT104 strain

USDA-ARS?s Scientific Manuscript database

Salmonella enterica is the leading etiologic agent of bacterial foodborne outbreaks worldwide. Methods. Laboratory-based statistical surveillance, molecular and genomics analyses were applied to characterize Salmonella outbreaks pattern in Israel. 65,087 Salmonella isolates reported to the National ...

Toward topology-based characterization of small-scale mixing in compressible turbulence

NASA Astrophysics Data System (ADS)

Suman, Sawan; Girimaji, Sharath

2011-11-01

Turbulent mixing rate at small scales of motion (molecular mixing) is governed by the steepness of the scalar-gradient field which in turn is dependent upon the prevailing velocity gradients. Thus motivated, we propose a velocity-gradient topology-based approach for characterizing small-scale mixing in compressible turbulence. We define a mixing efficiency metric that is dependent upon the topology of the solenoidal and dilatational deformation rates of a fluid element. The mixing characteristics of solenoidal and dilatational velocity fluctuations are clearly delineated. We validate this new approach by employing mixing data from direct numerical simulations (DNS) of compressible decaying turbulence with passive scalar. For each velocity-gradient topology, we compare the mixing efficiency predicted by the topology-based model with the corresponding conditional scalar variance obtained from DNS. The new mixing metric accurately distinguishes good and poor mixing topologies and indeed reasonably captures the numerical values. The results clearly demonstrate the viability of the proposed approach for characterizing and predicting mixing in compressible flows.

Establishing the Bases for Introducing the Unexplored Portuguese Common Bean Germplasm into the Breeding World.

PubMed

Leitão, Susana T; Dinis, Marco; Veloso, Maria M; Šatović, Zlatko; Vaz Patto, Maria C

2017-01-01

Common bean ( Phaseolus vulgaris L.) is among the most important grain legumes for human consumption worldwide. Portugal has a potentially promising common bean germplasm, resulting from more than five centuries of natural adaptation and farmers' selection. Nevertheless, limited characterization of this resource hampers its exploitation by breeding programs. To support a more efficient conservation of the national bean germplasm and promote its use in crop improvement, we performed, for the first time, a simultaneous molecular marker (21 microsatellites and a DNA marker for phaseolin-type diversity analysis) and seed and plant morphological characterization (14 traits) of 175 accessions from Portuguese mainland and islands traditional bean-growing regions. A total of 188 different alleles were identified and an average pairwise Cavalli-Sforza and Edwards' chord genetic distance of 0.193 was estimated among accessions. To relate the Portuguese germplasm with the global common bean diversity, 17 wild relatives and representative accessions from the Andean and Mesoamerican gene pools were evaluated at the molecular level. No correlation was detected between the variability found and the geographic origin of accessions. Structure analysis divided the collection into three main clusters. Most of the Portuguese accessions grouped with the race representatives and wild relatives from the Andean region. One third of the national germplasm had admixed genetic origin and might represent putative hybrids among gene pools from the two original centers of domestication in the Andes and Mesoamerica. The molecular marker-based classification was largely congruent with the three most frequent phaseolin haplotype patterns observed in the accessions analyzed. Seed and plant morphological characterization of 150 Portuguese common bean accessions revealed a clear separation among genetic structure and phaseolin haplotype groups of accessions, with seed size and shape and the number of locules per pod the most discriminant traits. Additionally, we used molecular and morphological data to develop a series of smaller core collections that, by maximizing the genetic and morphological diversity of the original collection, represents the Portuguese common bean germplasm with minimum repetitiveness. A core collection with 37 accessions contained 100% of the genetic variation found in the entire collection. This core collection is appropriate for a more detailed characterization and should be explored, as a priority, in national and international common bean breeding efforts. Furthermore, the identified intermediate accessions (with admixed genetic origin) may have novel genetic combinations useful in future bean breeding.

Molecular survey and genetic characterization of Anaplasma centrale, A. marginale and A. bovis in cattle from Algeria.

PubMed

Rjeibi, M R; Ayadi, O; Rekik, M; Gharbi, M

2018-04-01

Bovine anaplasmosis could be caused by several Anaplasma species. The causative agents are transmitted by ticks and haematophagous arthropods with a high impact on both human and animal health. This study was conducted to estimate the infection rate and to characterize Anaplasma spp. in cattle from Algeria. A molecular survey was performed in Setif district (Northeast Algeria) where a total number of 180 cattle blood samples were collected and tested for the presence of Anaplasma spp. by PCR. Positive samples were genetically characterized based on the 16S rRNA and msp4 genes. PCRs revealed that the infection rates of Anaplasma spp., Anaplasma centrale, Anaplasma marginale and Anaplasma bovis were 42.2%; 39.4%; 11.1% and 4.4%, respectively. All tested animals were negative for A. phagocytophilum. Co-infection occurred in 10% (18/180) of the tested animals, and the most common co-infection pattern was an association between A. centrale and A. marginale (5.5%). Five cattle (2.7%) were co-infected by the three Anaplasma species. Holstein animals (58.1%) were more infected by A. centrale than the other breeds (p = .01). The molecular prevalence of A. centrale was significantly higher in males (54.2%) than in females (34.1%) (p = .001). A. marginale msp4 genetic analysis indicated a high sequence diversity of Algerian strains, suggesting the importation of live cattle from different origins. Phylogenetic analysis of the 16S rRNA gene of A. bovis and A. centrale revealed a low degree of genetic diversity. Our study suggests that different species of Anaplasma are simultaneously present in the Algerian cattle. To the best of our knowledge, this is the first molecular study and genetic characterization of Anaplasma spp. in Algerian cattle. © 2017 Blackwell Verlag GmbH.

Fast surface-based travel depth estimation algorithm for macromolecule surface shape description.

PubMed

Giard, Joachim; Alface, Patrice Rondao; Gala, Jean-Luc; Macq, Benoît

2011-01-01

Travel Depth, introduced by Coleman and Sharp in 2006, is a physical interpretation of molecular depth, a term frequently used to describe the shape of a molecular active site or binding site. Travel Depth can be seen as the physical distance a solvent molecule would have to travel from a point of the surface, i.e., the Solvent-Excluded Surface (SES), to its convex hull. Existing algorithms providing an estimation of the Travel Depth are based on a regular sampling of the molecule volume and the use of the Dijkstra's shortest path algorithm. Since Travel Depth is only defined on the molecular surface, this volume-based approach is characterized by a large computational complexity due to the processing of unnecessary samples lying inside or outside the molecule. In this paper, we propose a surface-based approach that restricts the processing to data defined on the SES. This algorithm significantly reduces the complexity of Travel Depth estimation and makes possible the analysis of large macromolecule surface shape description with high resolution. Experimental results show that compared to existing methods, the proposed algorithm achieves accurate estimations with considerably reduced processing times.

Trichocyanines: a Red-Hair-Inspired Modular Platform for Dye-Based One-Time-Pad Molecular Cryptography.

PubMed

Leone, Loredana; Pezzella, Alessandro; Crescenzi, Orlando; Napolitano, Alessandra; Barone, Vincenzo; d'Ischia, Marco

2015-06-01

Current molecular cryptography (MoCryp) systems are almost exclusively based on DNA chemistry and reports of cryptography technologies based on other less complex chemical systems are lacking. We describe herein, as proof of concept, the prototype of the first asymmetric MoCryp system, based on an 8-compound set of a novel bioinspired class of cyanine-type dyes called trichocyanines. These novel acidichromic cyanine-type dyes inspired by red hair pigments were synthesized and characterized with the aid of density functional theory (DFT) calculations. Trichocyanines consist of a modular scaffold easily accessible via an expedient condensation of 3-phenyl- or 3-methyl-2H-1,4-benzothiazines with N-dimethyl- or o-methoxyhydroxy-substituted benzaldehyde or cinnamaldehyde derivatives. The eight representative members synthesized herein can be classified as belonging to two three-state systems tunable through four different control points. This versatile dye platform can generate an expandable palette of colors and appears to be specifically suited to implement an unprecedented single-use asymmetric molecular cryptography system. With this system, we intend to pioneer the translation of digital public-key cryptography into a chemical-coding one-time-pad-like system.

Trichocyanines: a Red-Hair-Inspired Modular Platform for Dye-Based One-Time-Pad Molecular Cryptography

PubMed Central

Leone, Loredana; Pezzella, Alessandro; Crescenzi, Orlando; Napolitano, Alessandra; Barone, Vincenzo; d’Ischia, Marco

2015-01-01

Current molecular cryptography (MoCryp) systems are almost exclusively based on DNA chemistry and reports of cryptography technologies based on other less complex chemical systems are lacking. We describe herein, as proof of concept, the prototype of the first asymmetric MoCryp system, based on an 8-compound set of a novel bioinspired class of cyanine-type dyes called trichocyanines. These novel acidichromic cyanine-type dyes inspired by red hair pigments were synthesized and characterized with the aid of density functional theory (DFT) calculations. Trichocyanines consist of a modular scaffold easily accessible via an expedient condensation of 3-phenyl- or 3-methyl-2H-1,4-benzothiazines with N-dimethyl- or o-methoxyhydroxy-substituted benzaldehyde or cinnamaldehyde derivatives. The eight representative members synthesized herein can be classified as belonging to two three-state systems tunable through four different control points. This versatile dye platform can generate an expandable palette of colors and appears to be specifically suited to implement an unprecedented single-use asymmetric molecular cryptography system. With this system, we intend to pioneer the translation of digital public-key cryptography into a chemical-coding one-time-pad-like system. PMID:26246999

Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection.

PubMed

Taylor, Angela J; Lappi, Victoria; Wolfgang, William J; Lapierre, Pascal; Palumbo, Michael J; Medus, Carlota; Boxrud, David

2015-10-01

Salmonella enterica serovar Enteritidis is a significant cause of gastrointestinal illness in the United States; however, current molecular subtyping methods lack resolution for this highly clonal serovar. Advances in next-generation sequencing technologies have made it possible to examine whole-genome sequencing (WGS) as a potential molecular subtyping tool for outbreak detection and source trace back. Here, we conducted a retrospective analysis of S. Enteritidis isolates from seven epidemiologically confirmed foodborne outbreaks and sporadic isolates (not epidemiologically linked) to determine the utility of WGS to identify outbreaks. A collection of 55 epidemiologically characterized clinical and environmental S. Enteritidis isolates were sequenced. Single nucleotide polymorphism (SNP)-based cluster analysis of the S. Enteritidis genomes revealed well supported clades, with less than four-SNP pairwise diversity, that were concordant with epidemiologically defined outbreaks. Sporadic isolates were an average of 42.5 SNPs distant from the outbreak clusters. Isolates collected from the same patient over several weeks differed by only two SNPs. Our findings show that WGS provided greater resolution between outbreak, sporadic, and suspect isolates than the current gold standard subtyping method, pulsed-field gel electrophoresis (PFGE). Furthermore, results could be obtained in a time frame suitable for surveillance activities, supporting the use of WGS as an outbreak detection and characterization method for S. Enteritidis. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Prevalence study on bovine tuberculosis and molecular characterization of its causative agents in cattle slaughtered at Addis Ababa municipal abattoir, Central Ethiopia.

PubMed

Mekibeb, Abraham; Fulasa, Tadele Tolosa; Firdessa, Rebuma; Hailu, Elena

2013-03-01

A cross-sectional study was conducted on 500 cattle slaughtered at Addis Ababa abattoir to determine the prevalence of bovine tuberculosis (BTB) and characterize its causative agents. Postmortem examination, mycobacteriological culturing, region of difference-4 (RD4)-based PCR and spoligotyping were applied. The prevalence of BTB was 5 % on the basis of postmortem inspection alone but 1.2 % based on molecular confirmation. Factors including age, sex, and breed showed statistically significant association with BTB (p < 0.05). Gross lesions were observed most frequently (68 %) in the lungs and lung-associated lymph nodes compared to other organs and lymph nodes. Of the 25 grossly suspicious TB lesions processed and cultured, only six (24 %) were culture-positive, yielding Mycobacterium bovis confirmed by RD4 deletion typing. Further characterization of the six M. bovis isolates at the strain level by using spoligotyping revealed that one did not belong to any previously known type, while the others belonged to types SB1176 (two), SB1477 (two), and SB0133 (one). The new strain was submitted to the international M. Bovis.org database for international code designation. The study confirms the considerable prevalence of bovine tuberculosis in cattle slaughtered at Addis Ababa abattoir and highlights the need for control of bovine tuberculosis in the country.

Synthesis, Characterization, and Handling of Eu(II)-Containing Complexes for Molecular Imaging Applications

NASA Astrophysics Data System (ADS)

Basal, Lina A.; Allen, Matthew J.

2018-03-01

Considerable research effort has focused on the in vivo use of responsive imaging probes that change imaging properties upon reacting with oxygen because hypoxia is relevant to diagnosing, treating, and monitoring diseases. One promising class of compounds for oxygen-responsive imaging is Eu(II)-containing complexes because the Eu(II/III) redox couple enables imaging with multiple modalities including magnetic resonance and photoacoustic imaging. The use of Eu(II) requires care in handling to avoid unintended oxidation during synthesis and characterization. This review describes recent advances in the field of imaging agents based on discrete Eu(II)-containing complexes with specific focus on the synthesis, characterization, and handling of aqueous Eu(II)-containing complexes.

A unified model for the molecular basis of Xeroderma pigmentosum-Cockayne Syndrome

PubMed Central

Moriel-Carretero, María; Herrera-Moyano, Emilia; Aguilera, Andrés

2015-01-01

Nucleotide Excision Repair (NER) is a pathway that removes lesions distorting the DNA helix. The molecular basis of the rare diseases Xeroderma pigmentosum (XP) and Cockayne Syndrome (CS) are explained based on the defects happening in 2 NER branches: Global-Genome Repair and Transcription-Coupled Repair, respectively. Nevertheless, both afflictions sporadically occur together, giving rise to XP/CS; however, the molecular basis of XP/CS is not understood very well. Many efforts have been made to clarify why mutations in only 4 NER genes, namely XPB, XPD, XPF and XPG, are the basis of this disease. Effort has also been made to unravel why mutations within these genes lead to XP, XP/CS, or other pathologies. We have recently contributed to the disclosure of this puzzle by characterizing Rad3/XPD mutations in Saccharomyces cerevisiae and human cells. Based on our, and others', observations, we propose a model compatible with all XP/CS cases and the current bibliography. PMID:26460500

Evaluation of bending modulus of lipid bilayers using undulation and orientation analysis

NASA Astrophysics Data System (ADS)

Chaurasia, Adarsh K.; Rukangu, Andrew M.; Philen, Michael K.; Seidel, Gary D.; Freeman, Eric C.

2018-03-01

In the current paper, phospholipid bilayers are modeled using coarse-grained molecular dynamics simulations with the MARTINI force field. The extracted molecular trajectories are analyzed using Fourier analysis of the undulations and orientation vectors to establish the differences between the two approaches for evaluating the bending modulus. The current work evaluates and extends the implementation of the Fourier analysis for molecular trajectories using a weighted horizon-based averaging approach. The effect of numerical parameters in the analysis of these trajectories is explored by conducting parametric studies. Computational modeling results are validated against experimentally characterized bending modulus of lipid membranes using a shape fluctuation analysis. The computational framework is then used to estimate the bending moduli for different types of lipids (phosphocholine, phosphoethanolamine, and phosphoglycerol). This work provides greater insight into the numerical aspects of evaluating the bilayer bending modulus, provides validation for the orientation analysis technique, and explores differences in bending moduli based on differences in the lipid nanostructures.

Field determination and QSPR prediction of equilibrium-status soil/vegetation partition coefficient of PCDD/Fs.

PubMed

Li, Li; Wang, Qiang; Qiu, Xinghua; Dong, Yian; Jia, Shenglan; Hu, Jianxin

2014-07-15

Characterizing pseudo equilibrium-status soil/vegetation partition coefficient KSV, the quotient of respective concentrations in soil and vegetation of a certain substance at remote background areas, is essential in ecological risk assessment, however few previous attempts have been made for field determination and developing validated and reproducible structure-based estimates. In this study, KSV was calculated based on measurements of seventeen 2,3,7,8-substituted PCDD/F congeners in soil and moss (Dicranum angustum), and rouzi grass (Thylacospermum caespitosum) of two background sites, Ny-Ålesund of the Arctic and Zhangmu-Nyalam region of the Tibet Plateau, respectively. By both fugacity modeling and stepwise regression of field data, the air-water partition coefficient (KAW) and aqueous solubility (SW) were identified as the influential physicochemical properties. Furthermore, validated quantitative structure-property relationship (QSPR) model was developed to extrapolate the KSV prediction to all 210 PCDD/F congeners. Molecular polarizability, molecular size and molecular energy demonstrated leading effects on KSV. Copyright © 2014 Elsevier B.V. All rights reserved.

Molecular epidemiology and evolution of avian infectious bronchitis virus in Spain over a fourteen-year period.

PubMed

Dolz, Roser; Pujols, Joan; Ordóñez, German; Porta, Ramon; Majó, Natàlia

2008-04-25

An in-depth molecular study of infectious bronchitis viruses (IBV) with particular interest in evolutionary aspects of IBV in Spain was carried out in the present study based on the S1 gene molecular characterization of twenty-six Spanish strains isolated over a fourteen-year period. Four genotypes were identified based on S1 gene sequence analyses and phylogenetic studies. A drastic virus population shift was demonstrated along time and the novel Italy 02 serotype was shown to have displaced the previous predominant serotype 4/91 in the field. Detailed analyses of synonymous to non-synonymous ratio of the S1 gene sequences of this new serotype Italy 02 suggested positive selection pressures might have contributed to the successful establishment of Italy 02 serotype in our country. In addition, differences on the fitness abilities of new emergent genotypes were indicated. Furthermore, intergenic sequences (IGs)-like motifs within S1 gene sequences of IBV isolates were suggested to enhance the recombination abilities of certain serotypes.

A metabolomics-based approach identifies changes in the small molecular weight compound composition of the peanut as a result of dry-roasting.

PubMed

Klevorn, Claire M; Dean, Lisa L

2018-02-01

Raw peanuts in the USA are subjected to thermal processing, such as dry-roasting, prior to consumption. A multi-instrument metabolomics-based platform along with targeted analyses was used to determine changes in the low-molecular-weight compound composition of peanuts due to dry-roasting. Runner and virginia-type peanut seeds were characterized using several analytical platforms including (RP)/UPLC-MS/MS (positive and negative ion mode ESI) and HILIC/UPLC-MS/MS with negative ion mode ESI. Of the 383 compounds identified, 16 compounds were unique to the roasted peanuts. Using pathway analysis, compounds associated with arginine and proline metabolism were found to be the most changed. Products of chemical degradation and compounds contained within the vesicular bodies of the peanut increased after roasting. Dry-roasting had a significant impact on the levels and types of low-molecular-weight compounds present. These findings provide useful information about composition changes due to roasting. Published by Elsevier Ltd.

Horror Autoinflammaticus: The Molecular Pathophysiology of Autoinflammatory Disease*

PubMed Central

Masters, Seth L.; Simon, Anna; Aksentijevich, Ivona; Kastner, Daniel L.

2010-01-01

The autoinflammatory diseases are characterized by seemingly unprovoked episodes of inflammation, without high-titer autoantibodies or antigen-specific T cells. The concept was proposed ten years ago with the identification of the genes underlying hereditary periodic fever syndromes. This nosology has taken root because of the dramatic advances in our knowledge of the genetic basis of both mendelian and complex autoinflammatory diseases, and with the recognition that these illnesses derive from genetic variants of the innate immune system. Herein we propose an updated classification scheme based on the molecular insights garnered over the past decade, supplanting a clinical classification that has served well but is opaque to the genetic, immunologic, and therapeutic interrelationships now before us. We define six categories of autoinflammatory disease: IL-1β activation disorders (inflammasomopathies), NF-κB activation syndromes, protein misfolding disorders, complement regulatory diseases, disturbances in cytokine signaling, and macrophage activation syndromes. A system based on molecular pathophysiology will bring greater clarity to our discourse while catalyzing new hypotheses both at the bench and at the bedside. PMID:19302049

Synthesis and characterization of Cu(II)-based anticancer chemotherapeutic agent targeting topoisomerase Iα: in vitro DNA binding, pBR322 cleavage, molecular docking studies and cytotoxicity against human cancer cell lines.

PubMed

Tabassum, Sartaj; Zaki, Mehvash; Afzal, Mohd; Arjmand, Farukh

2014-03-03

New metal-based anticancer chemotherapeutic drug candidates [Cu(phen)L](NO₃)₂ (1) and [Zn(phen)L](NO₃)₂ (2) were synthesized from ligand L (derived from pharmacophore scaffold barbituric acid and pyrazole). In vitro DNA binding studies of the L, 1 and 2 were carried out by various biophysical techniques revealing electrostatic mode. Complex 1 cleaves pBR322 DNA via oxidative pathway and recognizes major groove of DNA double helix. The molecular docking study was carried out to ascertain the mode of action towards the molecular target DNA and enzymes. The complex 1 exhibited remarkably good anticancer activity on a panel of human cancer cell lines (GI₅₀ values < 10 μg/ml), and to elucidate the mechanism of cancer inhibition, Topo-I enzymatic activity was carried out. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Systematic Biological Filter Design with a Desired I/O Filtering Response Based on Promoter-RBS Libraries.

PubMed

Hsu, Chih-Yuan; Pan, Zhen-Ming; Hu, Rei-Hsing; Chang, Chih-Chun; Cheng, Hsiao-Chun; Lin, Che; Chen, Bor-Sen

2015-01-01

In this study, robust biological filters with an external control to match a desired input/output (I/O) filtering response are engineered based on the well-characterized promoter-RBS libraries and a cascade gene circuit topology. In the field of synthetic biology, the biological filter system serves as a powerful detector or sensor to sense different molecular signals and produces a specific output response only if the concentration of the input molecular signal is higher or lower than a specified threshold. The proposed systematic design method of robust biological filters is summarized into three steps. Firstly, several well-characterized promoter-RBS libraries are established for biological filter design by identifying and collecting the quantitative and qualitative characteristics of their promoter-RBS components via nonlinear parameter estimation method. Then, the topology of synthetic biological filter is decomposed into three cascade gene regulatory modules, and an appropriate promoter-RBS library is selected for each module to achieve the desired I/O specification of a biological filter. Finally, based on the proposed systematic method, a robust externally tunable biological filter is engineered by searching the promoter-RBS component libraries and a control inducer concentration library to achieve the optimal reference match for the specified I/O filtering response.

Linear Schiff-base fluorescence probe with aggregation-induced emission characteristics for Al3+ detection and its application in live cell imaging.

PubMed

Wen, Xiaoye; Fan, Zhefeng

2016-11-16

A simple Schiff-base derivative with salicylaldehyde moieties as fluorescent probe 1 was reported by aggregation-induced emission (AIE) characterization for the detection of metal ions. Spectral analysis revealed that probe 1 was highly selective and sensitive to Al 3+ . The probe 1 was also subject to minimal interference from other common competitive metal ions. The detection limit of Al 3+ was 0.4 μM, which is considerably lower than the World Health Organization standard (7.41 μM), and the acceptable level of Al 3+ (1.85 μM) in drinking water. The Job's plot and the results of 1 H-NMR and FT-IR analyses indicated that the binding stoichiometry ratio of probe 1 to Al 3+ was 1:2. Probe 1 demonstrated a fluorescence-enhanced response upon binding with Al 3+ based on AIE characterization. This response was due to the restricted molecular rotation and increased rigidity of the molecular assembly. Probe 1 exhibited good biocompatibility, and Al 3+ was detected in live cells. Therefore, probe 1 is a promising fluorescence probe for Al 3+ detection in the environment. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular characterization of the vitamin D receptor (VDR) gene in Holstein cows.

PubMed

Ali, Mayar O; El-Adl, Mohamed A; Ibrahim, Hussam M M; Elseedy, Youssef Y; Rizk, Mohamed A; El-Khodery, Sabry A

2018-06-01

Vitamin D plays a vital role in calcium homeostasis, growth, and immunoregulation. Because little is known about the vitamin D receptor (VDR) gene in cattle, the aim of the present investigation was to present the molecular characterization of exons 5 and 6 of the VDR gene in Holstein cows. DNA extraction, genomic sequencing, phylogenetic analysis, synteny mapping and single nucleotide gene polymorphism analysis of the VDR gene were performed to assess blood samples collected from 50 clinically healthy Holstein cows. The results revealed the presence of a 450-base pair (bp) nucleotide sequence that resembled exons 5 and 6 with intron 5 enclosed between these exons. Sequence alignment and phylogenetic analysis revealed a close relationship between the sequenced VDR region and that found in Hereford cattle. A close association between this region and the corresponding region in small ruminants was also documented. Moreover, a single nucleotide polymorphism (SNP) that caused the replacement of a glutamate with an arginine in the deduced amino acid sequence was detected at position 7 of exon 5. In conclusion, Holstein and Hereford cattle differ with respect to exon 5 of the VDR gene. Phylogenetic analysis of the VDR gene based on nucleotide sequence produced different results from prior analyses based on amino acid sequence. Copyright © 2018 Elsevier Ltd. All rights reserved.

Nuclear quantum fluctuations in ice I(h).

PubMed

Moreira, Pedro Augusto Franco Pinheiro; de Koning, Maurice

2015-10-14

We discuss the role of nuclear quantum fluctuations in ice Ih, focusing on the hydrogen-bond (HB) structure and the molecular dipole-moment distribution. For this purpose we carry out DFT-based first-principles molecular dynamics and path-integral molecular dynamics simulations at T = 100 K. We analyze the HB structure in terms of a set of parameters previously employed to characterize molecular structures in the liquid phase and compute the molecular dipole moments using the maximally-localized Wannier functions. The results show that the protons experience very large digressions driven by quantum fluctuations, accompanied by major rearrangements in the electronic density. As a result of these protonic quantum fluctuations the molecular dipole-moment distribution is substantially broadened as well as shifted to a larger mean value when compared to the results obtained when such fluctuations are neglected. In terms of dielectric constants, the reconciliation between the greater mean dipole moment and experimental indications that the dielectric constant of H2O ice is lower than that of D2O ice would indicate that the topology of the HB network is sensitive to protonic quantum fluctuations.

Molecular profiling of cancer--the future of personalized cancer medicine: a primer on cancer biology and the tools necessary to bring molecular testing to the clinic.

PubMed

Stricker, Thomas; Catenacci, Daniel V T; Seiwert, Tanguy Y

2011-04-01

Cancers arise as a result of an accumulation of genetic aberrations that are either acquired or inborn. Virtually every cancer has its unique set of molecular changes. Technologies have been developed to study cancers and derive molecular characteristics that increasingly have implications for clinical care. Indeed, the identification of key genetic aberrations (molecular drivers) may ultimately translate into dramatic benefit for patients through the development of highly targeted therapies. With the increasing availability of newer, more powerful, and cheaper technologies such as multiplex mutational screening, next generation sequencing, array-based approaches that can determine gene copy numbers, methylation, expression, and others, as well as more sophisticated interpretation of high-throughput molecular information using bioinformatics tools like signatures and predictive algorithms, cancers will routinely be characterized in the near future. This review examines the background information and technologies that clinicians and physician-scientists will need to interpret in order to develop better, personalized treatment strategies. Copyright © 2011 Elsevier Inc. All rights reserved.

Molecular characterization and identification of members of the Anopheles subpictus complex in Sri Lanka.

PubMed

Surendran, Sinnathamby N; Sarma, Devojit K; Jude, Pavilupillai J; Kemppainen, Petri; Kanthakumaran, Nadarajah; Gajapathy, Kanapathy; Peiris, Lalanthika B S; Ramasamy, Ranjan; Walton, Catherine

2013-08-30

Anopheles subpictus sensu lato is a major malaria vector in South and Southeast Asia. Based initially on polytene chromosome inversion polymorphism, and subsequently on morphological characterization, four sibling species A-D were reported from India. The present study uses molecular methods to further characterize and identify sibling species in Sri Lanka. Mosquitoes from Sri Lanka were morphologically identified to species and sequenced for the ribosomal internal transcribed spacer-2 (ITS2) and the mitochondrial cytochrome c oxidase subunit-I (COI) genes. These sequences, together with others from GenBank, were used to construct phylogenetic trees and parsimony haplotype networks and to test for genetic population structure. Both ITS2 and COI sequences revealed two divergent clades indicating that the Subpictus complex in Sri Lanka is composed of two genetically distinct species that correspond to species A and species B from India. Phylogenetic analysis showed that species A and species B do not form a monophyletic clade but instead share genetic similarity with Anopheles vagus and Anopheles sundaicus s.l., respectively. An allele specific identification method based on ITS2 variation was developed for the reliable identification of species A and B in Sri Lanka. Further multidisciplinary studies are needed to establish the species status of all chromosomal forms in the Subpictus complex. This study emphasizes the difficulties in using morphological characters for species identification in An. subpictus s.l. in Sri Lanka and demonstrates the utility of an allele specific identification method that can be used to characterize the differential bio-ecological traits of species A and B in Sri Lanka.

Revised systematics of Holospora-like bacteria and characterization of "Candidatus Gortzia infectiva", a novel macronuclear symbiont of Paramecium jenningsi.

PubMed

Boscaro, Vittorio; Fokin, Sergei I; Schrallhammer, Martina; Schweikert, Michael; Petroni, Giulio

2013-01-01

The genus Holospora (Rickettsiales) includes highly infectious nuclear symbionts of the ciliate Paramecium with unique morphology and life cycle. To date, nine species have been described, but a molecular characterization is lacking for most of them. In this study, we have characterized a novel Holospora-like bacterium (HLB) living in the macronuclei of a Paramecium jenningsi population. This bacterium was morphologically and ultrastructurally investigated in detail, and its life cycle and infection capabilities were described. We also obtained its 16S rRNA gene sequence and developed a specific probe for fluorescence in situ hybridization experiments. A new taxon, "Candidatus Gortzia infectiva", was established for this HLB according to its unique characteristics and the relatively low DNA sequence similarities shared with other bacteria. The phylogeny of the order Rickettsiales based on 16S rRNA gene sequences has been inferred, adding to the available data the sequence of the novel bacterium and those of two Holospora species (Holospora obtusa and Holospora undulata) characterized for the purpose. Our phylogenetic analysis provided molecular support for the monophyly of HLBs and showed a possible pattern of evolution for some of their features. We suggested to classify inside the family Holosporaceae only HLBs, excluding other more distantly related and phenotypically different Paramecium endosymbionts.

A bioinformatics approach for identifying transgene insertion sites using whole genome sequencing data.

PubMed

Park, Doori; Park, Su-Hyun; Ban, Yong Wook; Kim, Youn Shic; Park, Kyoung-Cheul; Kim, Nam-Soo; Kim, Ju-Kon; Choi, Ik-Young

2017-08-15

Genetically modified crops (GM crops) have been developed to improve the agricultural traits of modern crop cultivars. Safety assessments of GM crops are of paramount importance in research at developmental stages and before releasing transgenic plants into the marketplace. Sequencing technology is developing rapidly, with higher output and labor efficiencies, and will eventually replace existing methods for the molecular characterization of genetically modified organisms. To detect the transgenic insertion locations in the three GM rice gnomes, Illumina sequencing reads are mapped and classified to the rice genome and plasmid sequence. The both mapped reads are classified to characterize the junction site between plant and transgene sequence by sequence alignment. Herein, we present a next generation sequencing (NGS)-based molecular characterization method, using transgenic rice plants SNU-Bt9-5, SNU-Bt9-30, and SNU-Bt9-109. Specifically, using bioinformatics tools, we detected the precise insertion locations and copy numbers of transfer DNA, genetic rearrangements, and the absence of backbone sequences, which were equivalent to results obtained from Southern blot analyses. NGS methods have been suggested as an effective means of characterizing and detecting transgenic insertion locations in genomes. Our results demonstrate the use of a combination of NGS technology and bioinformatics approaches that offers cost- and time-effective methods for assessing the safety of transgenic plants.

Cytological and molecular characterization of three gametoclones of citrus clementina

USDA-ARS?s Scientific Manuscript database

Three gametoclonal plants of Citrus clementina Hort. ex Tan., cv. Nules, designated ESP, FRA, and ITA (derived from three labs in Spain, France, and Italy, respectively), were selected for cytological and molecular characterization in order to elucidate genomic rearrangements provoked by haploidizat...

Colorimetric test-systems for creatinine detection based on composite molecularly imprinted polymer membranes.

PubMed

Sergeyeva, T A; Gorbach, L A; Piletska, E V; Piletsky, S A; Brovko, O O; Honcharova, L A; Lutsyk, O D; Sergeeva, L M; Zinchenko, O A; El'skaya, A V

2013-04-03

An easy-to-use colorimetric test-system for the efficient detection of creatinine in aqueous samples was developed. The test-system is based on composite molecularly imprinted polymer (MIP) membranes with artificial receptor sites capable of creatinine recognition. A thin MIP layer was created on the surface of microfiltration polyvinylidene fluoride (PVDF) membranes using method of photo-initiated grafting polymerization. The MIP layer was obtained by co-polymerization of a functional monomer (e.g. 2-acrylamido-2-methyl-1-propanesulfonic acid, itaconic acid or methacrylic acid) with N, N'-methylenebisacrylamide as a cross-linker. The choice of the functional monomer was based on the results of computational modeling. The creatinine-selective composite MIP membranes were used for measuring creatinine in aqueous samples. Creatinine molecules were selectively adsorbed by the MIP membranes and quantified using color reaction with picrates. The intensity of MIP membranes staining was proportional to creatinine concentration in an analyzed sample. The colorimetric test-system based on the composite MIP membranes was characterized with 0.25 mM detection limit and 0.25-2.5mM linear dynamic range. Storage stability of the MIP membranes was estimated as at least 1 year at room temperature. As compared to the traditional methods of creatinine detection the developed test-system is characterized by simplicity of operation, small size and low cost. Copyright © 2013 Elsevier B.V. All rights reserved.

Temperature gating and competing temperature-dependent effects in DNA molecular wires

NASA Astrophysics Data System (ADS)

Wibowo, Denni; Narenji, Alaleh; Kassegne, Sam

2017-02-01

While recent research in electron-transport mechanism on a double strands DNA seems to converge into a consensus, experiments in direct electrical measurements on a long DNA molecules still lead to a conflicting result This study is the continuation of our previous research in electrical characterization of DNA molecular wires, where we furtherly investigate the effects of temperature on the electrical conductivity of DNA molecular wires by measuring its impedance response. We found that at higher temperatures, the expected increase in charge hopping mechanism may account for the decrease in impedance (and hence increase in conductivity) supporting the 'charge hopping mechanism' theory. UV light exposure, on the other hand, causes damage to GC base pairs reducing the path available for hopping mechanism and hence resulting in increased impedance - this again supporting the 'charge hopping mechanism' theory. We also report that λ-DNA molecular wires have differing impedance responses at two temperature regimes: impedance increases between 4 °C - 40 °C and then decreases between 40 °C - melting point (˜110 °C), after which λ-DNA denatures resulting in no current transduction. We submit that the low impedance of λ-DNA molecular wires observed at moderate to high frequencies may have significant implications to the field of DNA-based bionanoelectronics.

Tunable Affinity and Molecular Architecture Lead to Diverse Self-Assembled Supramolecular Structures in Thin Films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hsu, Chih-Hao; Dong, Xue-Hui; Lin, Zhiwei

2015-12-03

The self-assembly behaviors of specifically designed giant surfactants are systematically studied in thin films using grazing incident X-ray and transmission electron microscopy (TEM), focusing on the effects of head surface functionalities and molecular architectures on nanostructure formation. Two molecular nanoparticles (MNPs) with different affinities, i.e., hydrophilic carboxylic acid functionalized [60]fullerene (AC60) and omniphobic fluorinated polyhedral oligomeric silsesquioxane (FPOSS), are utilized as heads of the giant surfactants. By covalently tethering these functional MNPs onto the chain end or the junction point of polystyrene-block-poly(ethylene oxide) (PS-b-PEO) diblock copolymer, linear and star-like giant surfactants possess distinct molecular architectures are constructed. With fixed lengthmore » of the PEO block, the molecular weight change of the PS block originates the phase formation and transition. Due to the distinct affinity, the AC60-based giant surfactants form two-component morphologies, while three-component morphologies are found in the FPOSS-based ones. A PS block stretching parameter is introduced to characterize the PS chain conformation in different morphologies. The highly diverse self-assembly behaviors and the tunable dimensions in thin films suggest the giant surfactants could be a promising and robust platform for nanolithography applications.« less

Molecular epidemiology of Usher syndrome in Italy.

PubMed

Vozzi, Diego; Aaspõllu, Anu; Athanasakis, Emmanouil; Berto, Anna; Fabretto, Antonella; Licastro, Danilo; Külm, Maigi; Testa, Francesco; Trevisi, Patrizia; Vahter, Marju; Ziviello, Carmela; Martini, Alessandro; Simonelli, Francesca; Banfi, Sandro; Gasparini, Paolo

2011-01-01

Usher syndrome is an autosomal recessive disorder characterized by hearing and vision loss. Usher syndrome is divided into three clinical subclasses (type 1, type 2, and type 3), which differ in terms of the severity and progression of hearing loss and the presence or absence of vestibular symptoms. Usher syndrome is defined by significant genetic heterogeneity, with at least 12 distinct loci described and 9 genes identified. This study aims to provide a molecular epidemiology report of Usher syndrome in Italy. Molecular data have been obtained on 75 unrelated Italian patients using the most up-to date technology available for the screening of Usher syndrome gene mutations, i.e., the genotyping microarray developed by Asper Biotech (Tartu, Estonia), which simultaneously investigates 612 different marker positions using the well established arrayed primer extension methodology (APEX). Using this method, we found that 12% of cases (9 out of 75) harbored homozygous or compound heterozygous mutations in the gene positions analyzed, whereas 20% (15 out of 75) of the patients were characterized by the presence of only one mutated allele based on the positions analyzed. One patient was found to be compound heterozygous for mutations in two different genes and this represents an example of possible digenic inheritance in Usher syndrome. A total of 66.6% of cases (50 out of 75) were found to be completely negative for the presence of Usher syndrome gene mutations in the detected positions. Mutations detected by the array were confirmed by direct sequencing. These findings highlight the efficacy of the APEX-based genotyping approach in the molecular assessment of Usher patients, suggesting the presence of alleles not yet identified and/or the involvement of additional putative genes that may account for the pathogenesis of Usher syndrome.

Molecular epidemiology of Usher syndrome in Italy

PubMed Central

Vozzi, Diego; Aaspõllu, Anu; Athanasakis, Emmanouil; Berto, Anna; Fabretto, Antonella; Licastro, Danilo; Külm, Maigi; Testa, Francesco; Trevisi, Patrizia; Vahter, Marju; Ziviello, Carmela; Martini, Alessandro; Simonelli, Francesca; Banfi, Sandro

2011-01-01

Purpose Usher syndrome is an autosomal recessive disorder characterized by hearing and vision loss. Usher syndrome is divided into three clinical subclasses (type 1, type 2, and type 3), which differ in terms of the severity and progression of hearing loss and the presence or absence of vestibular symptoms. Usher syndrome is defined by significant genetic heterogeneity, with at least 12 distinct loci described and 9 genes identified. This study aims to provide a molecular epidemiology report of Usher syndrome in Italy. Methods Molecular data have been obtained on 75 unrelated Italian patients using the most up-to date technology available for the screening of Usher syndrome gene mutations, i.e., the genotyping microarray developed by Asper Biotech (Tartu, Estonia), which simultaneously investigates 612 different marker positions using the well established arrayed primer extension methodology (APEX). Results Using this method, we found that 12% of cases (9 out of 75) harbored homozygous or compound heterozygous mutations in the gene positions analyzed, whereas 20% (15 out of 75) of the patients were characterized by the presence of only one mutated allele based on the positions analyzed. One patient was found to be compound heterozygous for mutations in two different genes and this represents an example of possible digenic inheritance in Usher syndrome. A total of 66.6% of cases (50 out of 75) were found to be completely negative for the presence of Usher syndrome gene mutations in the detected positions. Mutations detected by the array were confirmed by direct sequencing. Conclusions These findings highlight the efficacy of the APEX-based genotyping approach in the molecular assessment of Usher patients, suggesting the presence of alleles not yet identified and/or the involvement of additional putative genes that may account for the pathogenesis of Usher syndrome. PMID:21738395

Unveiling an ancient biological invasion: molecular analysis of an old European alien, the crested porcupine (Hystrix cristata).

PubMed

Trucchi, Emiliano; Sbordoni, Valerio

2009-05-18

Biological invasions can be considered one of the main threats to biodiversity, and the recognition of common ecological and evolutionary features among invaders can help developing a predictive framework to control further invasions. In particular, the analysis of successful invasive species and of their autochthonous source populations by means of genetic, phylogeographic and demographic tools can provide novel insights into the study of biological invasion patterns. Today, long-term dynamics of biological invasions are still poorly understood and need further investigations. Moreover, distribution and molecular data on native populations could contribute to the recognition of common evolutionary features of successful aliens. We analyzed 2,195 mitochondrial base pairs, including Cytochrome b, Control Region and rRNA 12S, in 161 Italian and 27 African specimens and assessed the ancient invasive origin of Italian crested porcupine (Hystrix cristata) populations from Tunisia. Molecular coalescent-based Bayesian analyses proposed the Roman Age as a putative timeframe of introduction and suggested a retention of genetic diversity during the early phases of colonization. The characterization of the native African genetic background revealed the existence of two differentiated clades: a Mediterranean group and a Sub-Saharan one. Both standard population genetic and advanced molecular demography tools (Bayesian Skyline Plot) did not evidence a clear genetic signature of the expected increase in population size after introduction. Along with the genetic diversity retention during the bottlenecked steps of introduction, this finding could be better described by hypothesizing a multi-invasion event. Evidences of the ancient anthropogenic invasive origin of the Italian Hystrix cristata populations were clearly shown and the native African genetic background was preliminary described. A more complex pattern than a simple demographic exponential growth from a single propagule seems to have characterized this long-term invasion.

Molecular characterization of dissolved organic matter in contrasted freshwater environments by electrospray ionization mass spectrometry and EEM-PARAFAC

NASA Astrophysics Data System (ADS)

Parot, Jérémie; Parlanti, Edith; Guéguen, Céline

2015-04-01

Dissolved organic matter (DOM) is a key parameter in the fate, transport and mobility of inorganic and organic pollutants in natural waters. Excitation emission matrix (EEM) spectra coupled to parallel factor analysis (PARAFAC) provide insights on the main fluorescent DOM constituents. However, the molecular structures associated with PARAFAC DOM remain poorly understood. In this study, DOM from rivers, marshes and algal culture was characterized by EEM-PARAFAC and electrospray ionization Fourier transform mass spectrometry (ESI-FT-MS, Orbitrap Q Exactive). The high resolution of the Orbitrap (i.e. 140,000) allowed us to separate unique molecular species from the complex DOM mixtures. The majority of chemical species were found within the mass to charge ratio (m/z) 200 to 400. Weighted averages of neutral mass were 271.254, 236.480, 213.992Da for river, marsh and algal-derived DOM, respectively, congruent with previous studies. The assigned formula were dominated by CHO in humic-rich river waters whereas N- and S-containing compounds were predominant in marsh and algal samples. Marsh consisted of N and S-containing compounds, which were presumed to be linear alkylbenzene sulfonates. And the double bond equivalent (DBE) was higher in the marsh and in comparison was lower in the algal culture. Kendrick masses, used to identify homologous compounds differing only by a number of base units in high resolution mass spectra, and Van Krevelen diagrams, plot of molar ratio of hydrogen to carbon (H/C) versus oxygen to carbon (O/C), will be discussed in relation to PARAFAC components to further discriminate freshwater systems based on the origin and maturity of DOM. Together, these results showed that ESI-FT-MS has a great potential to distinguish freshwater DOM at the molecular level without any fractionation.

The diverse and expanding role of mass spectrometry in structural and molecular biology.

PubMed

Lössl, Philip; van de Waterbeemd, Michiel; Heck, Albert Jr

2016-12-15

The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

NaviCom: a web application to create interactive molecular network portraits using multi-level omics data.

PubMed

Dorel, Mathurin; Viara, Eric; Barillot, Emmanuel; Zinovyev, Andrei; Kuperstein, Inna

2017-01-01

Human diseases such as cancer are routinely characterized by high-throughput molecular technologies, and multi-level omics data are accumulated in public databases at increasing rate. Retrieval and visualization of these data in the context of molecular network maps can provide insights into the pattern of regulation of molecular functions reflected by an omics profile. In order to make this task easy, we developed NaviCom, a Python package and web platform for visualization of multi-level omics data on top of biological network maps. NaviCom is bridging the gap between cBioPortal, the most used resource of large-scale cancer omics data and NaviCell, a data visualization web service that contains several molecular network map collections. NaviCom proposes several standardized modes of data display on top of molecular network maps, allowing addressing specific biological questions. We illustrate how users can easily create interactive network-based cancer molecular portraits via NaviCom web interface using the maps of Atlas of Cancer Signalling Network (ACSN) and other maps. Analysis of these molecular portraits can help in formulating a scientific hypothesis on the molecular mechanisms deregulated in the studied disease. NaviCom is available at https://navicom.curie.fr. © The Author(s) 2017. Published by Oxford University Press.

Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus

PubMed Central

Singh, Swati; Gupta, Sanchita; Mani, Ashutosh; Chaturvedi, Anoop

2012-01-01

Humulus lupulus is commonly known as hops, a member of the family moraceae. Currently many projects are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. The genetically characterized domains in these databases are limited due to non-availability of reliable molecular markers. The large data of EST sequences are available in hops. The simple sequence repeat markers extracted from EST data are used as molecular markers for genetic characterization, in the present study. 25,495 EST sequences were examined and assembled to get full-length sequences. Maximum frequency distribution was shown by mononucleotide SSR motifs i.e. 60.44% in contig and 62.16% in singleton where as minimum frequency are observed for hexanucleotide SSR in contig (0.09%) and pentanucleotide SSR in singletons (0.12%). Maximum trinucleotide motifs code for Glutamic acid (GAA) while AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking primer pairs were designed in-silico for the SSR containing sequences. Functional categorization of SSRs containing sequences was done through gene ontology terms like biological process, cellular component and molecular function. PMID:22368382

Isolation of rare circulating tumor cells in cancer patients: technical aspects and clinical implications.

PubMed

Danova, Marco; Torchio, Martina; Mazzini, Giuliano

2011-06-01

Circulating tumor cells (CTCs) may be detected in the blood of patients with epithelial tumors using different analytical approaches. The relative number of CTCs is low and they include a heterogeneous population of cells with diverse biological and molecular characteristics, often different from those of the respective primary tumor. Until recently, they have been difficult to detect and, even though discordant results have been reported when different methods of detection were used, they may provide prognostic and predictive information. Several antibody- or molecular-based CTC detection methods have been developed, offering hope for individualized risk assessment by utilizing CTCs as biomarkers of disease progression and drug response. Pilot studies have also shown that by utilizing methods that permit, besides enumeration, a molecular characterization of CTCs, one could better identify high-risk patients, predict response to targeted therapies, analyze gene expression profiles (in order to identify new potential drug targets) and increase our knowledge of the metastatic process. In this article we review the techniques currently utilized for isolation and characterization of CTCs and we discuss their potential utility in clinical oncology focusing on the future perspectives in this field.

Efficacy of rifaximin vaginal tablets in treatment of bacterial vaginosis: a molecular characterization of the vaginal microbiota.

PubMed

Cruciani, Federica; Brigidi, Patrizia; Calanni, Fiorella; Lauro, Vittoria; Tacchi, Raffaella; Donders, Gilbert; Peters, Klaus; Guaschino, Secondo; Vitali, Beatrice

2012-08-01

Bacterial vaginosis (BV) is a common vaginal disorder characterized by an alteration of the vaginal bacterial morphotypes, associated with sexually transmitted infections and adverse pregnancy outcomes. The purpose of the present study was to evaluate the impact of different doses of rifaximin vaginal tablets (100 mg/day for 5 days, 25 mg/day for 5 days, and 100 mg/day for 2 days) on the vaginal microbiota of 102 European patients with BV enrolled in a multicenter, double-blind, randomized, placebo-controlled study. An integrated molecular approach based on quantitative PCR (qPCR) and PCR-denaturing gradient gel electrophoresis (PCR-DGGE) was used to investigate the effects of vaginal tablets containing the antibiotic. An increase in members of the genus Lactobacillus and a decrease in the BV-related bacterial groups after the antibiotic treatment were demonstrated by qPCR. PCR-DGGE profiles confirmed the capability of rifaximin to modulate the composition of the vaginal microbial communities and to reduce their complexity. This molecular analysis supported the clinical observation that rifaximin at 25 mg/day for 5 days represents an effective treatment to be used in future pivotal studies for the treatment of BV.

Efficacy of Rifaximin Vaginal Tablets in Treatment of Bacterial Vaginosis: a Molecular Characterization of the Vaginal Microbiota

PubMed Central

Cruciani, Federica; Brigidi, Patrizia; Calanni, Fiorella; Lauro, Vittoria; Tacchi, Raffaella; Donders, Gilbert; Peters, Klaus; Guaschino, Secondo

2012-01-01

Bacterial vaginosis (BV) is a common vaginal disorder characterized by an alteration of the vaginal bacterial morphotypes, associated with sexually transmitted infections and adverse pregnancy outcomes. The purpose of the present study was to evaluate the impact of different doses of rifaximin vaginal tablets (100 mg/day for 5 days, 25 mg/day for 5 days, and 100 mg/day for 2 days) on the vaginal microbiota of 102 European patients with BV enrolled in a multicenter, double-blind, randomized, placebo-controlled study. An integrated molecular approach based on quantitative PCR (qPCR) and PCR-denaturing gradient gel electrophoresis (PCR-DGGE) was used to investigate the effects of vaginal tablets containing the antibiotic. An increase in members of the genus Lactobacillus and a decrease in the BV-related bacterial groups after the antibiotic treatment were demonstrated by qPCR. PCR-DGGE profiles confirmed the capability of rifaximin to modulate the composition of the vaginal microbial communities and to reduce their complexity. This molecular analysis supported the clinical observation that rifaximin at 25 mg/day for 5 days represents an effective treatment to be used in future pivotal studies for the treatment of BV. PMID:22585228

De novo assembly and transcriptome characterization of the freshwater prawn Palaemonetes argentinus: Implications for a detoxification response.

PubMed

García, C Fernando; Pedrini, Nicolas; Sánchez-Paz, Arturo; Reyna-Blanco, Carlos S; Lavarias, Sabrina; Muhlia-Almazán, Adriana; Fernández-Giménez, Analía; Laino, Aldana; de-la-Re-Vega, Enrique; Lukaszewicz, German; López-Zavala, Alonso A; Brieba, Luis G; Criscitello, Michael F; Carrasco-Miranda, Jesús S; García-Orozco, Karina D; Ochoa-Leyva, Adrian; Rudiño-Piñera, Enrique; Sanchez-Flores, Alejandro; Sotelo-Mundo, Rogerio R

2018-02-01

Palaemonetes argentinus, an abundant freshwater prawn species in the northern and central region of Argentina, has been used as a bioindicator of environmental pollutants as it displays a very high sensitivity to pollutants exposure. Despite their extraordinary ecological relevance, a lack of genomic information has hindered a more thorough understanding of the molecular mechanisms potentially involved in detoxification processes of this species. Thus, transcriptomic profiling studies represent a promising approach to overcome the limitations imposed by the lack of extensive genomic resources for P. argentinus, and may improve the understanding of its physiological and molecular response triggered by pollutants. This work represents the first comprehensive transcriptome-based characterization of the non-model species P. argentinus to generate functional genomic annotations and provides valuable resources for future genetic studies. Trinity de novo assembly consisted of 24,738 transcripts with high representation of detoxification (phase I and II), anti-oxidation, osmoregulation pathways and DNA replication and bioenergetics. This crustacean transcriptome provides valuable molecular information about detoxification and biochemical processes that could be applied as biomarkers in further ecotoxicology studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Field Effect Sensors for Nucleic Acid Detection: Recent Advances and Future Perspectives

PubMed Central

Veigas, Bruno; Fortunato, Elvira; Baptista, Pedro V.

2015-01-01

In the last decade the use of field-effect-based devices has become a basic structural element in a new generation of biosensors that allow label-free DNA analysis. In particular, ion sensitive field effect transistors (FET) are the basis for the development of radical new approaches for the specific detection and characterization of DNA due to FETs’ greater signal-to-noise ratio, fast measurement capabilities, and possibility to be included in portable instrumentation. Reliable molecular characterization of DNA and/or RNA is vital for disease diagnostics and to follow up alterations in gene expression profiles. FET biosensors may become a relevant tool for molecular diagnostics and at point-of-care. The development of these devices and strategies should be carefully designed, as biomolecular recognition and detection events must occur within the Debye length. This limitation is sometimes considered to be fundamental for FET devices and considerable efforts have been made to develop better architectures. Herein we review the use of field effect sensors for nucleic acid detection strategies—from production and functionalization to integration in molecular diagnostics platforms, with special focus on those that have made their way into the diagnostics lab. PMID:25946631

Genomic and transcriptomic characterization of skull base chordoma

PubMed Central

Sa, Jason K.; Lee, In-Hee; Hong, Sang Duk; Kong, Doo-Sik; Nam, Do-Hyun

2017-01-01

Skull base chordoma is a primary rare malignant bone-origin tumor showing relatively slow growth pattern and locally destructive lesions, which can only be characterized by histologic components. There is no available prognostic or therapeutic biomarker to predict clinical outcome or treatment response and the molecular mechanisms underlying chordoma development still remain unexplored. Therefore, we sought out to identify novel somatic variations that are associated with chordoma progression and potentially employed as therapeutic targets. Thirteen skull base chordomas were subjected for whole-exome and/or whole-transcriptome sequencing. In process, we have identified chromosomal aberration in 1p, 7, 10, 13 and 17q, high frequency of functional germline SNP of the T gene, rs2305089 (P = 0.0038) and several recurrent alterations including MUC4, NBPF1, NPIPB15 mutations and novel gene fusion of SAMD5-SASH1 for the first time in skull base chordoma. PMID:27901492

Genomic and transcriptomic characterization of skull base chordoma.

PubMed

Sa, Jason K; Lee, In-Hee; Hong, Sang Duk; Kong, Doo-Sik; Nam, Do-Hyun

2017-01-03

Skull base chordoma is a primary rare malignant bone-origin tumor showing relatively slow growth pattern and locally destructive lesions, which can only be characterized by histologic components. There is no available prognostic or therapeutic biomarker to predict clinical outcome or treatment response and the molecular mechanisms underlying chordoma development still remain unexplored. Therefore, we sought out to identify novel somatic variations that are associated with chordoma progression and potentially employed as therapeutic targets. Thirteen skull base chordomas were subjected for whole-exome and/or whole-transcriptome sequencing. In process, we have identified chromosomal aberration in 1p, 7, 10, 13 and 17q, high frequency of functional germline SNP of the T gene, rs2305089 (P = 0.0038) and several recurrent alterations including MUC4, NBPF1, NPIPB15 mutations and novel gene fusion of SAMD5-SASH1 for the first time in skull base chordoma.

SPRUCE Advanced Molecular Techniques Provide a Rigorous Method for Characterizing Organic Matter Quality in Complex Systems: Supporting Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, Rachel M; Tfaily, Malak M

These data are provided in support of the Commentary, Advanced molecular techniques provide a rigorous method for characterizing organic matter quality in complex systems, Wilson and Tfaily (2018). Measurement results demonstrate that optical characterization of peatland dissolved organic matter (DOM) may not fully capture classically identified chemical characteristics and may, therefore, not be the best measure of organic matter quality.

Single-particle characterization of biomass burning organic aerosol (BBOA): evidence for non-uniform mixing of high molecular weight organics and potassium

NASA Astrophysics Data System (ADS)

Lee, Alex K. Y.; Willis, Megan D.; Healy, Robert M.; Wang, Jon M.; Jeong, Cheol-Heon; Wenger, John C.; Evans, Greg J.; Abbatt, Jonathan P. D.

2016-05-01

Biomass burning organic aerosol (BBOA) can be emitted from natural forest fires and human activities such as agricultural burning and domestic energy generation. BBOA is strongly associated with atmospheric brown carbon (BrC) that absorbs near-ultraviolet and visible light, resulting in significant impacts on regional visibility degradation and radiative forcing. The mixing state of BBOA can play a critical role in the prediction of aerosol optical properties. In this work, single-particle measurements from a Soot-Particle Aerosol Mass Spectrometer coupled with a light scattering module (LS-SP-AMS) were performed to examine the mixing state of BBOA, refractory black carbon (rBC), and potassium (K, a tracer for biomass burning aerosol) in an air mass influenced by wildfire emissions transported from northern Québec to Toronto, representing aged biomass burning plumes. Cluster analysis of single-particle measurements identified five BBOA-related particle types. rBC accounted for 3-14 wt % of these particle types on average. Only one particle type exhibited a strong ion signal for K+, with mass spectra characterized by low molecular weight organic species. The remaining four particle types were classified based on the apparent molecular weight of the BBOA constituents. Two particle types were associated with low potassium content and significant amounts of high molecular weight (HMW) organic compounds. Our observations indicate non-uniform mixing of particles within a biomass burning plume in terms of molecular weight and illustrate that HMW BBOA can be a key contributor to low-volatility BrC observed in BBOA particles. The average mass absorption efficiency of low-volatility BBOA is about 0.8-1.1 m2 g-1 based on a theoretical closure calculation. Our estimates indicate that low-volatility BBOA contributes ˜ 33-44 % of thermo-processed particle absorption at 405 nm; and almost all of the BBOA absorption was associated with low-volatility organics.

Adiabatic quantum computing with spin qubits hosted by molecules.

PubMed

Yamamoto, Satoru; Nakazawa, Shigeaki; Sugisaki, Kenji; Sato, Kazunobu; Toyota, Kazuo; Shiomi, Daisuke; Takui, Takeji

2015-01-28

A molecular spin quantum computer (MSQC) requires electron spin qubits, which pulse-based electron spin/magnetic resonance (ESR/MR) techniques can afford to manipulate for implementing quantum gate operations in open shell molecular entities. Importantly, nuclear spins, which are topologically connected, particularly in organic molecular spin systems, are client qubits, while electron spins play a role of bus qubits. Here, we introduce the implementation for an adiabatic quantum algorithm, suggesting the possible utilization of molecular spins with optimized spin structures for MSQCs. We exemplify the utilization of an adiabatic factorization problem of 21, compared with the corresponding nuclear magnetic resonance (NMR) case. Two molecular spins are selected: one is a molecular spin composed of three exchange-coupled electrons as electron-only qubits and the other an electron-bus qubit with two client nuclear spin qubits. Their electronic spin structures are well characterized in terms of the quantum mechanical behaviour in the spin Hamiltonian. The implementation of adiabatic quantum computing/computation (AQC) has, for the first time, been achieved by establishing ESR/MR pulse sequences for effective spin Hamiltonians in a fully controlled manner of spin manipulation. The conquered pulse sequences have been compared with the NMR experiments and shown much faster CPU times corresponding to the interaction strength between the spins. Significant differences are shown in rotational operations and pulse intervals for ESR/MR operations. As a result, we suggest the advantages and possible utilization of the time-evolution based AQC approach for molecular spin quantum computers and molecular spin quantum simulators underlain by sophisticated ESR/MR pulsed spin technology.

Activity-Based Protein Profiling of Microbes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sadler, Natalie C.; Wright, Aaron T.

Activity-Based Protein Profiling (ABPP) in conjunction with multimodal characterization techniques has yielded impactful findings in microbiology, particularly in pathogen, bioenergy, drug discovery, and environmental research. Using small molecule chemical probes that react irreversibly with specific proteins or protein families in complex systems has provided insights in enzyme functions in central metabolic pathways, drug-protein interactions, and regulatory protein redox, for systems ranging from photoautotrophic cyanobacteria to mycobacteria, and combining live cell or cell extract ABPP with proteomics, molecular biology, modeling, and other techniques has greatly expanded our understanding of these systems. New opportunities for application of ABPP to microbial systems include:more » enhancing protein annotation, characterizing protein activities in myriad environments, and reveal signal transduction and regulatory mechanisms in microbial systems.« less

[Entification of the Rubella virus genotype 1H in Western Siberia].

PubMed

Seregin, S V; Babkin, I V; Petrova, I D; Iashina, L N; Malkova, E M; Petrov, V S

2011-01-01

Molecular epidemiological study of novel strain of Rubella virus isolated during the outbreak in Western Siberia in 2004 was described. Detailed phylogenetic analysis performed based upon entire SP-region, which encodes all three Rubella structural proteins (C, E2, and E1), was implemented. This analysis provides characterization of this strain and classifies it as 1H genotype, thereby correcting previous classification of this strain based upon shorter nucleotide sequence, only encoding E1 protein. Therefore, this study identified the genotype of the Rubella virus not previously detected in Western Siberia (and even entire Russian Federation), which highlights the importance of more extensive characterization of genetic variability of the Rubella virus, especially with regard to potential influence of vaccination on the Rubella virus mutagenesis.

Recent Advances in the Molecular Characterization of Sweetpotato Begomoviruses

USDA-ARS?s Scientific Manuscript database

Although sweetpotato leaf curl disease has been observed on sweetpotato in Japan and Taiwan since 1985, molecular characterization of sweetpotato begomoviruses has only been conducted in recent years. In the U.S., two begomoviruses, Sweet potato leaf curl virus (SPLCV) and Sweet potato leaf curl Ge...

Preparation, Characterization, and UV Irradiation of Mars Soil Analogues Under Simulated Martian Conditions to Support Detection of Molecular Biomarkers

NASA Astrophysics Data System (ADS)

Fornaro, T.; Brucato, J. R.; ten Kate, I. L.; Siljeström, S.; Steele, A.; Cody, G. D.; Hazen, R. M.

2018-04-01

We present laboratory activities of preparation, characterization, and UV irradiation processing of Mars soil analogues, which are key to support both in situ exploration and sample return missions devoted to detection of molecular biomarkers on Mars.

Genetic-molecular characterization of backcross generations for sexual conversion in papaya (Carica papaya L.).

PubMed

Ramos, H C C; Pereira, M G; Pereira, T N S; Barros, G B A; Ferreguetti, G A

2014-12-04

The low number of improved cultivars limits the expansion of the papaya crop, particularly because of the time required for the development of new varieties using classical procedures. Molecular techniques associated with conventional procedures accelerate this process and allow targeted improvements. Thus, we used microsatellite markers to perform genetic-molecular characterization of papaya genotypes obtained from 3 backcross generations to monitor the inbreeding level and parental genome proportion in the evaluated genotypes. Based on the analysis of 20 microsatellite loci, 77 genotypes were evaluated, 25 of each generation of the backcross program as well as the parental genotypes. The markers analyzed were identified in 11 of the 12 linkage groups established for papaya, ranging from 1 to 4 per linkage group. The average values for the inbreeding coefficient were 0.88 (BC1S4), 0.47 (BC2S3), and 0.63 (BC3S2). Genomic analysis revealed average values of the recurrent parent genome of 82.7% in BC3S2, 64.4% in BC1S4, and 63.9% in BC2S3. Neither the inbreeding level nor the genomic proportions completely followed the expected average values. This demonstrates the significance of molecular analysis when examining different genotype values, given the importance of such information for selection processes in breeding programs.

First Molecular Characterization of Theileria ornithorhynchi Mackerras, 1959: yet Another Challenge to the Systematics of the Piroplasms.

PubMed

Paparini, Andrea; Macgregor, James; Ryan, Una M; Irwin, Peter J

2015-12-01

Piroplasms, tick-transmitted Apicomplexa of the genera Theileria, Babesia and Cytauxzoon, are blood-borne parasites of clinical and veterinary importance. The order Piroplasmida shows a puzzling systematics characterized by multiple clades, soft polytomies and paraphyletic/polyphyletic genera. In the present study, screening of platypuses (Ornithorhynchus anatinus), was performed to infer the parasite molecular phylogeny. DNA was extracted from blood, ectoparasites and tick eggs and the 18S rRNA- hsp70-genes were used for the phylogenetic reconstructions. Microscopic analyses detected pleomorphic intra-erythrocytic organisms and tetrads consistent with previous descriptions of Theileria ornithorhynchi Mackerras, 1959, but observation of possible schizonts could not be confirmed. DNA sequences obtained from blood and ticks allowed resolving the systematics of the first piroplasm infecting a monotreme host. Molecularly, T. ornithorhynchi formed a novel monophyletic group, basal to most known piroplasms' clades. The ancestral position of this clade, isolated from an ancient lineage of mammalian host appears particularly fascinating. The present paper discusses the inadequacies of the current molecular systematics for the Piroplasmida and the consequences of incomplete sampling, morphology-based classification and ambiguous microscopic identifications. Likely when the current sampling bias is rectified and more sequence data is made available, the phylogenetic position of T. ornithorhynchi will be further contextualized without ambiguity. Copyright © 2015 Elsevier GmbH. All rights reserved.

Identification of 1H-indene-(1,3,5,6)-tetrol derivatives as potent pancreatic lipase inhibitors using molecular docking and molecular dynamics approach.

PubMed

Kalathiya, Umesh; Padariya, M; Baginski, M

2016-11-01

Pancreatic lipase is a potential therapeutic target to treat diet-induced obesity in humans, as obesity-related diseases continue to be a global problem. Despite intensive research on finding potential inhibitors, very few compounds have been introduced to clinical studies. In this work, new chemical scaffold 1H-indene-(1,3,5,6)-tetrol was proposed using knowledge-based approach, and 36 inhibitors were derived by modifying its functional groups at different positions in scaffold. To explore binding affinity and interactions of ligands with protein, CDOCKER and AutoDock programs were used for molecular docking studies. Analyzing results of rigid and flexible docking algorithms, inhibitors C_12, C_24, and C_36 were selected based on different properties and high predicted binding affinities for further analysis. These three inhibitors have different moieties placed at different functional groups in scaffold, and to characterize structural rationales for inhibitory activities of compounds, molecular dynamics simulations were performed (500 nSec). It has been shown through simulations that two structural fragments (indene and indole) in inhibitor can be treated as isosteric structures and their position at binding cleft can be replaced by each other. Taking into account these information, two lines of inhibitors can further be developed, each line based on a different core scaffold, that is, indene/indole. © 2015 International Union of Biochemistry and Molecular Biology, Inc.

DSSR-enhanced visualization of nucleic acid structures in Jmol

PubMed Central

Hanson, Robert M.

2017-01-01

Abstract Sophisticated and interactive visualizations are essential for making sense of the intricate 3D structures of macromolecules. For proteins, secondary structural components are routinely featured in molecular graphics visualizations. However, the field of RNA structural bioinformatics is still lagging behind; for example, current molecular graphics tools lack built-in support even for base pairs, double helices, or hairpin loops. DSSR (Dissecting the Spatial Structure of RNA) is an integrated and automated command-line tool for the analysis and annotation of RNA tertiary structures. It calculates a comprehensive and unique set of features for characterizing RNA, as well as DNA structures. Jmol is a widely used, open-source Java viewer for 3D structures, with a powerful scripting language. JSmol, its reincarnation based on native JavaScript, has a predominant position in the post Java-applet era for web-based visualization of molecular structures. The DSSR-Jmol integration presented here makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or JSmol session and returns DSSR-derived structural features in JSON format. This seamless combination of DSSR and Jmol/JSmol brings the molecular graphics of 3D RNA structures to a similar level as that for proteins, and enables a much deeper analysis of structural characteristics. It fills a gap in RNA structural bioinformatics, and is freely accessible (via the Jmol application or the JSmol-based website http://jmol.x3dna.org). PMID:28472503

Methicillin-Resistant Staphylococcus aureus Ocular Infection in Taiwan

PubMed Central

Kang, Yu-Chuan; Hsiao, Ching-Hsi; Yeh, Lung-Kun; Ma, David H.K.; Chen, Phil Y.F.; Lin, Hsin-Chiung; Tan, Hsin-Yuan; Chen, Hung-Chi; Chen, Shin-Yi; Huang, Yhu-Chering

2015-01-01

Abstract Methicillin-resistant Staphylococcus aureus (MRSA) infection is an important public health issue. This observational study aimed to characterize clinical features, antibiotic susceptibility, and genotypes of ocular infections caused by MRSA based on the clinical and molecular definitions of community-associated (CA) and healthcare-associated (HA) strains. Fifty-nine patients with culture-proven S aureus ocular infection were enrolled from January 1, 2010 to December 31, 2011 at Chang Gung Memorial Hospital, Taiwan. Antibiotic susceptibility was verified using disk diffusion/E test. For characterization, staphylococcal cassette chromosome mec (SCCmec), pulsed-field gel electrophoresis (PFGE), multilocus sequence type (MLST), and Panton–Valentine leukocidin (PVL) gene, were performed. MRSA isolates from the patients with HA factors were classified as clinically defined HA-MRSA, and those carrying SCCmec type I to III as molecularly defined HA-MRSA. Thirty-four patients with MRSA ocular infection were identified. The most common clone of CA-MRSA and HA-MRSA isolates was ST59/PFGE type D/SCCmec IV,VT/PVL (+) (n = 12) and CC 239/PFGE type A/SCCmec III, IIIA/PVL(−) (n = 10), respectively. All the 11 patients with molecularly defined HA-MRSA infections and 50% of the 22 patients with molecularly defined CA-MRSA infections were found to have HA factors (P = .005). CA-MRSA tended to cause lid infections, whereas HA-MRSA tended to cause corneal infections. Contrary to HA-MRSA isolates, nearly all the CA-MRSA isolates were susceptible to trimethoprim/sulfamethoxazole and fluoroquinolones under either clinical or molecular classifications. In Taiwan, CA-MRSA isolates exhibited considerably higher susceptibility to fluoroquinolones when compared with HA-MRSA isolates. A strong correlation was observed between the HA factors and molecularly defined HA-MRSA isolates. PMID:26496268

Characterizing rare-event property distributions via replicate molecular dynamics simulations of proteins.

PubMed

Krishnan, Ranjani; Walton, Emily B; Van Vliet, Krystyn J

2009-11-01

As computational resources increase, molecular dynamics simulations of biomolecules are becoming an increasingly informative complement to experimental studies. In particular, it has now become feasible to use multiple initial molecular configurations to generate an ensemble of replicate production-run simulations that allows for more complete characterization of rare events such as ligand-receptor unbinding. However, there are currently no explicit guidelines for selecting an ensemble of initial configurations for replicate simulations. Here, we use clustering analysis and steered molecular dynamics simulations to demonstrate that the configurational changes accessible in molecular dynamics simulations of biomolecules do not necessarily correlate with observed rare-event properties. This informs selection of a representative set of initial configurations. We also employ statistical analysis to identify the minimum number of replicate simulations required to sufficiently sample a given biomolecular property distribution. Together, these results suggest a general procedure for generating an ensemble of replicate simulations that will maximize accurate characterization of rare-event property distributions in biomolecules.

Molecular Characterization and Analysis of Antimicrobial Activity of Endophytic Fungi From Medicinal Plants in Saudi Arabia

PubMed Central

Gashgari, Rukaia; Gherbawy, Youssuf; Ameen, Fuad; Alsharari, Salam

2016-01-01

Background: Endophytic fungi, which have been reported in numerous plant species, are important components of the forest community and contribute significantly to the diversity of natural ecosystems. Objectives: The current study aimed to evaluate and characterize, at the molecular level, the diversity and antimicrobial activities of endophytic fungi from medicinal plants in Saudi Arabia. Materials and Methods: Fungi growing on plant segments were isolated and identified based on morphological and molecular characteristics. The isolates were grouped into 35 distinct operational taxonomic units, based on the sequence of the internal transcribed spacer regions in the rRNA gene. The colonization frequency and the dominant fungi percentage of these endophytic fungi were calculated. A dual culture technique was adopted to investigate the antifungal activity of these endophytes. Results: Tamarix nilotica showed the highest endophytic diversity with a relative frequency of 27.27%, followed by Cressa cretica with a relative frequency of 19.27%. The most frequently isolated species was Penicillium chrysogenum with an overall colonization rate of 98.57%. Seven out of 35 endophytic fungi exhibited strong antifungal activity to all plant fungal pathogens tested. P. chrysogenum, Fusarium oxysporum, and F. nygamai exhibited the highest inhibition against the human pathogenic bacteria Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Aspergillus sydowii, P. chrysogenum, and Eupenicillium crustaceum showed strong antimicrobial activity against Enterococcus faecalis. Conclusions: The antimicrobial activity of these endophytic microorganisms could be exploited in biotechnology, medicine, and agriculture. PMID:27099679

Searching for protein binding sites from Molecular Dynamics simulations and paramagnetic fragment-based NMR studies.

PubMed

Bernini, Andrea; Henrici De Angelis, Lucia; Morandi, Edoardo; Spiga, Ottavia; Santucci, Annalisa; Assfalg, Michael; Molinari, Henriette; Pillozzi, Serena; Arcangeli, Annarosa; Niccolai, Neri

2014-03-01

Hotspot delineation on protein surfaces represents a fundamental step for targeting protein-protein interfaces. Disruptors of protein-protein interactions can be designed provided that the sterical features of binding pockets, including the transient ones, can be defined. Molecular Dynamics, MD, simulations have been used as a reliable framework for identifying transient pocket openings on the protein surface. Accessible surface area and intramolecular H-bond involvement of protein backbone amides are proposed as descriptors for characterizing binding pocket occurrence and evolution along MD trajectories. TEMPOL induced paramagnetic perturbations on (1)H-(15)N HSQC signals of protein backbone amides have been analyzed as a fragment-based search for surface hotspots, in order to validate MD predicted pockets. This procedure has been applied to CXCL12, a small chemokine responsible for tumor progression and proliferation. From combined analysis of MD data and paramagnetic profiles, two CXCL12 sites suitable for the binding of small molecules were identified. One of these sites is the already well characterized CXCL12 region involved in the binding to CXCR4 receptor. The other one is a transient pocket predicted by Molecular Dynamics simulations, which could not be observed from static analysis of CXCL12 PDB structures. The present results indicate how TEMPOL, instrumental in identifying this transient pocket, can be a powerful tool to delineate minor conformations which can be highly relevant in dynamic discovery of antitumoral drugs. Copyright © 2013 Elsevier B.V. All rights reserved.

Development and characterization of an electrochemical sensor for furosemide detection based on electropolymerized molecularly imprinted polymer.

PubMed

Kor, Kamalodin; Zarei, Kobra

2016-01-01

A novel electrochemical sensor based on a molecularly imprinted polymer, poly(o-phenylenediamine) (PoPD), has been developed for selective and sensitive detection of furosemide. The sensor was prepared by incorporating of furosemide as template molecules during the electropolymerization of o-phenylenediamine on a gold electrode. To develop the molecularly imprinted polymer (MIP), the template molecules were removed from the modified electrode's surface by washing it with 0.25 mol L(-1) NaOH solution. The imprinted layer was characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and atomic force microscopy (AFM). The sensor's preparation conditions including furosemide concentration, the number of CV cycles in the electropolymerization process, extraction solution of the template from the imprinted film, the incubation time and the pH level were optimized. The incubation of the MIP-modified electrode, with respect to furosemide concentration, resulted in a suppression of the K4[Fe(CN)6] oxidation process. Under the optimal experimental conditions, the response of the imprinted sensor was linear in the range of 1.0×10(-7)-7.0×10(-6) mol L(-1) of furosemide. The detection limit was obtained as 7.0×10(-8) mol L(-1) for furosemide by using this sensor. The sensor was successfully used to determine the furosemide amount in the tablet and in human urine samples with satisfactory results. Copyright © 2015 Elsevier B.V. All rights reserved.

Degradation of chitosan by gamma ray with presence of hydrogen peroxide

NASA Astrophysics Data System (ADS)

Mahmud, Maznah; Naziri, Muhammad Ihsan; Yacob, Norzita; Talip, Norhashidah; Abdullah, Zahid

2014-02-01

The radiation degraded chitosan samples were prepared by swelling the chitosan powder in water and exposed for gamma irradiation. The ratio chitosan to water was 1:6 with the presence of hydrogen peroxide (H2O2), 1%-5%. These chitosan-water mixtures were irradiated at 6kGy, which is the lowest irradiation dose that facility can offered. All samples were purified and proceed with characterization. The molecular weight (MW) study was monitored by size exclusion chromatography-multi angle laser light scattering (SEC-MALLS). Results showed that MW of chitosan reduced as the dose increased. Application of H2O2 enhanced the degradation rate of chitosan even at very low irradiation dose. Homogenous degradation also occurred during treatment with H2O2based on the polydispersity index (PDI) derived from the calculation of weight average molecular weight over number average molecular weight (Mw/Mn). Mechanism of chitosan radiation degradation with and without hydrogen peroxide was also discussed in this paper. Structure of degraded products was characterized with Fourier-transform infrared spectra. The degree of deacetylation (DDA) values of the samples was determined by acid-base titration. Solubility test results showed that, chitosan powder even at low Mw was insoluble in water even at low pH water. Chitosan as well as irradiated chitosan powder are soluble in strong and weak acid solution. Further discussion on behaviours of radiation degraded chitosan will be elaborated more in this paper.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mahmud, Maznah; Yacob, Norzita; Talip, Norhashidah

The radiation degraded chitosan samples were prepared by swelling the chitosan powder in water and exposed for gamma irradiation. The ratio chitosan to water was 1:6 with the presence of hydrogen peroxide (H{sub 2}O{sub 2}), 1%–5%. These chitosan-water mixtures were irradiated at 6kGy, which is the lowest irradiation dose that facility can offered. All samples were purified and proceed with characterization. The molecular weight (MW) study was monitored by size exclusion chromatography-multi angle laser light scattering (SEC-MALLS). Results showed that MW of chitosan reduced as the dose increased. Application of H{sub 2}O{sub 2} enhanced the degradation rate of chitosan evenmore » at very low irradiation dose. Homogenous degradation also occurred during treatment with H{sub 2}O{sub 2}based on the polydispersity index (PDI) derived from the calculation of weight average molecular weight over number average molecular weight (Mw/Mn). Mechanism of chitosan radiation degradation with and without hydrogen peroxide was also discussed in this paper. Structure of degraded products was characterized with Fourier-transform infrared spectra. The degree of deacetylation (DDA) values of the samples was determined by acid-base titration. Solubility test results showed that, chitosan powder even at low Mw was insoluble in water even at low pH water. Chitosan as well as irradiated chitosan powder are soluble in strong and weak acid solution. Further discussion on behaviours of radiation degraded chitosan will be elaborated more in this paper.« less

Electron-density descriptors as predictors in quantitative structure--activity/property relationships and drug design.

PubMed

Matta, Chérif F; Arabi, Alya A

2011-06-01

The use of electron density-based molecular descriptors in drug research, particularly in quantitative structure--activity relationships/quantitative structure--property relationships studies, is reviewed. The exposition starts by a discussion of molecular similarity and transferability in terms of the underlying electron density, which leads to a qualitative introduction to the quantum theory of atoms in molecules (QTAIM). The starting point of QTAIM is the topological analysis of the molecular electron-density distributions to extract atomic and bond properties that characterize every atom and bond in the molecule. These atomic and bond properties have considerable potential as bases for the construction of robust quantitative structure--activity/property relationships models as shown by selected examples in this review. QTAIM is applicable to the electron density calculated from quantum-chemical calculations and/or that obtained from ultra-high resolution x-ray diffraction experiments followed by nonspherical refinement. Atomic and bond properties are introduced followed by examples of application of each of these two families of descriptors. The review ends with a study whereby the molecular electrostatic potential, uniquely determined by the density, is used in conjunction with atomic properties to elucidate the reasons for the biological similarity of bioisosteres.

Mannich bases of 1,2,4-triazole-3-thione containing adamantane moiety: Synthesis, preliminary anticancer evaluation, and molecular modeling studies.

PubMed

Milošev, Milorad Z; Jakovljević, Katarina; Joksović, Milan D; Stanojković, Tatjana; Matić, Ivana Z; Perović, Milka; Tešić, Vesna; Kanazir, Selma; Mladenović, Milan; Rodić, Marko V; Leovac, Vukadin M; Trifunović, Snežana; Marković, Violeta

2017-06-01

A series of 18 novel N-Mannich bases derived from 5-adamantyl-1,2,4-triazole-3-thione was synthesized and characterized using NMR spectroscopy and X-ray diffraction technique. All derivatives were evaluated for their anticancer potential against four human cancer cell lines. Several tested compounds exerted good cytotoxic activities on K562 and HL-60 cell lines, along with pronounced selectivity, showing lower cytotoxicity against normal fibroblasts MRC-5 compared to cancer cells. The effects of compounds 5b, 5e, and 5j on the cell cycle were investigated by flow cytometric analysis. It was found that these compounds cause the accumulation of cells in the subG1 and G1 phases of the cell cycle and induce caspase-dependent apoptosis, while the anti-angiogenic effects of 5b, 5e, and 5j have been confirmed in EA.hy926 cells using a tube formation assay. Further, the interaction of Bax protein with compound 5b was investigated by means of molecular modeling, applying the combined molecular docking/molecular dynamics approach. © 2016 John Wiley & Sons A/S.

Systematic understanding the mechanisms of vitiligo pathogenesis and its treatment by Qubaibabuqi formula.

PubMed

Pei, Tianli; Zheng, Chunli; Huang, Chao; Chen, Xuetong; Guo, Zihu; Fu, Yingxue; Liu, Jianling; Wang, Yonghua

2016-08-22

Vitiligo is a depigmentation disorder, which results in substantial cosmetic disfigurement and poses a detriment to patients' physical as well as mental. Now the molecular pathogenesis of vitiligo still remains unclear, which leads to a daunting challenge for vitiligo therapy in modern medicine. Herbal medicines, characterized by multi-compound and multi-target, have long been shown effective in treating vitiligo, but their molecular mechanisms of action also remain ambiguous. Here we proposed a systems pharmacology approach using a clinically effective herb formula as a tool to detect the molecular pathogenesis of vitiligo. This study provided an integrative analysis of active chemicals, drug targets and interacting pathways of the Uygur medicine Qubaibabuqi formula for curing Vitiligo. The results show that 56 active ingredients of Qubaibabuqi interacting with 83 therapeutic proteins were identified. And Qubaibabuqi probably participate in immunomodulation, neuromodulation and keratinocytes apoptosis inhibition in treatment of vitiligo by a synergistic/cooperative way. The drug-target network-based analysis and pathway-based analysis can provide a new approach for understanding the pathogenesis of vitiligo and uncovering the molecular mechanisms of Qubaibabuqi, which will also facilitate the application of traditional Chinese herbs in modern medicine. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Synthesis and characterization of sugar based low molecular weight gelators and the preparation of chiral sulfinamides

NASA Astrophysics Data System (ADS)

Mangunuru, Hari Prasad Reddy

Low molecular weight gelators (LMWGs) have received considerable attention in the field of chemistry from last few decades. These compounds form self-assembled fibrous networks like micelles, cylindrical, sheets, fibers, layers and so on. The fibrous network entraps the solvent and forms gel, because of the self-assembly phenomenon and their demonstrated potential uses in a variety of areas, ranging from environmental to medicinal applications. Sugars are good starting materials to synthesize the new class of LMWG's, because these are different from some expensive materials, these are natural products. We have synthesized and characterized the LMGS's based on D-glucose and D-glucosamine. D-glucosamine is the versatile starting material to make different peptoids and triazoles. Several series of compounds were synthesized using compounds 1-3 as starting material and studied the gelation behavior all the compounds. We have studied the self-assembling properties of a new class of tripeptoids, synthesized by one-pot Ugi reaction from simple starting materials. Among the focused library of tripeptoids synthesized, we found that several efficient low molecular weight organogelators were obtained for aqueous DMSO and ethanol mixtures. We have also synthesized and characterized a series of monosaccharide triazole derivatives. These compounds were synthesized from N-acetyl glucosamine and D-glucose via a Cu(I) catalyzed azide/alkyne cycloaddition reaction (CuAAc). The compounds have been screened for their gelation properties and several efficient low molecular weight organo/hydro gelators were obtained, among these compounds, five per-acetyl glucosamine derivatives and one peracetyl glucose derivative were able to form gels in water. These new molecules are expected to be useful in drug delivery and tissue engineering.*. Asymmetric synthesis of chiral amines is a challenging in synthetic organic chemistry. The development of new catalysts for asymmetric organic transformations is a very important research goal in modern synthetic organic chemistry. We have synthesized a new class of chiral oxathiozinone from chiral amino phenol. From this synthesized chiral sulfinamides, ketimines followed by reducing the ketimines synthesized the highly hindered chiral amines. *Please refer to dissertation for diagrams.

Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.)

USDA-ARS?s Scientific Manuscript database

Cultivated peanut (Arachis hypogaea L.) is an important crop worldwide, valued for its edible oil and digestible protein. It has a very narrow genetic base that may well derive from a relatively recent single polyploidization event. Accordingly molecular markers have low levels of polymorphism and t...

Semi-Interpenetrating polymer network hydrogels based on aspen hemicellulose and chitosan: Effect of crosslinking sequence on hydrogel properties

Treesearch

Muzaffer Ahmet Karaaslan; Mandla A. Tshabalala; Gisela Buschle-Diller

2012-01-01

Semi-interpenetrating network hydrogel films were prepared using hemicellulose and chemically crosslinked chitosan. Hemicellulose was extracted from aspen by using a novel alkaline treatment and characterized by HPSEC, and consisted of a mixture of high and low molecular weight polymeric fractions. HPLC analysis of the acid hydrolysate of the hemicellulose showed that...

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines* | Office of Cancer Genomics

Cancer.gov

We report the results of a DREAM challenge designed to predict relative genetic essentialities based on a novel dataset testing 98,000 shRNAs against 149 molecularly characterized cancer cell lines. We analyzed the results of over 3,000 submissions over a period of 4 months.

Occurrence of Meloidogyne fallax in North America, and molecular characterization of M. fallax and M. minor from U.S. golf course greens

USDA-ARS?s Scientific Manuscript database

Several species of root-knot nematodes (Meloidogyne spp.) are known to have significant presence on turf grass in golf course greens, particularly in the western United States. Nematodes isolated from a golf course in King Co., Washington were identified as Meloidogyne minor based on analysis of the...

Isobutylene Dimerization: A Discovery-Based Exploration of Mechanism and Regioselectivity by NMR Spectroscopy and Molecular Modeling

ERIC Educational Resources Information Center

Schuster, Mariah L.; Peterson, Karl P.; Stoffregen, Stacey A.

2018-01-01

This two-period undergraduate laboratory experiment involves the synthesis of a mixture of isomeric unknowns, isolation of the mixture by means of distillation, and characterization of the two products primarily by NMR spectroscopy (1D and 2D) supported with IR spectroscopy and GC-MS techniques. Subsequent calculation and examination of the…

Recent Development in Spectroscopic and Chemical Characterization of Cellulose

DTIC Science & Technology

2005-01-01

specific to the reducing end groups of the polysaccharides , confirmed the parallel alignment of molecular chains within the microfibrils in native...they include primary, secondary, and tertiary structures. And indeed, crystallographic studies of the monosaccharides and of related structures...Two approaches were adopted for this purpose. The first was based on examining the Raman spectra of polysaccharide polymers and oligomers that

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. | Office of Cancer Genomics

Cancer.gov

We report the results of a DREAM challenge designed to predict relative genetic essentialities based on a novel dataset testing 98,000 shRNAs against 149 molecularly characterized cancer cell lines. We analyzed the results of over 3,000 submissions over a period of 4 months.

Old and new challenges in Parkinson's disease therapeutics.

PubMed

Pires, Ana O; Teixeira, F G; Mendes-Pinheiro, B; Serra, Sofia C; Sousa, Nuno; Salgado, António J

2017-09-01

Parkinson's disease (PD) is a neurodegenerative disorder characterized by the degeneration of dopaminergic neurons and/or loss od neuronal projections, in several dopaminergic networks. Current treatments for idiopathic PD rely mainly on the use of pharmacologic agents to improve motor symptomatology of PD patients. Nevertheless, so far PD remains an incurable disease. Therefore, it is of utmost importance to establish new therapeutic strategies for PD treatment. Over the last 20 years, several molecular, gene and cell/stem-cell therapeutic approaches have been developed with the aim of counteracting or retarding PD progression. The scope of this review is to provide an overview of PD related therapies and major breakthroughs achieved within this field. In order to do so, this review will start by focusing on PD characterization and current treatment options covering thereafter molecular, gene and cell/stem cell-based therapies that are currently being studied in animal models of PD or have recently been tested in clinical trials. Among stem cell-based therapies, those using MSCs as possible disease modifying agents for PD therapy and, specifically, the MSCs secretome contribution to meet the clinical challenge of counteracting or retarding PD progression, will be more deeply explored. Copyright © 2017 Elsevier Ltd. All rights reserved.

2D-HB-Network at the air-water interface: A structural and dynamical characterization by means of ab initio and classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Pezzotti, Simone; Serva, Alessandra; Gaigeot, Marie-Pierre

2018-05-01

Following our previous work where the existence of a special 2-Dimensional H-Bond (2D-HB)-Network was revealed at the air-water interface [S. Pezzotti et al., J. Phys. Chem. Lett. 8, 3133 (2017)], we provide here a full structural and dynamical characterization of this specific arrangement by means of both Density Functional Theory based and Force Field based molecular dynamics simulations. We show in particular that water at the interface with air reconstructs to maximize H-Bonds formed between interfacial molecules, which leads to the formation of an extended and non-interrupted 2-Dimensional H-Bond structure involving on average ˜90% of water molecules at the interface. We also show that the existence of such an extended structure, composed of H-Bonds all oriented parallel to the surface, constrains the reorientional dynamics of water that is hence slower at the interface than in the bulk. The structure and dynamics of the 2D-HB-Network provide new elements to possibly rationalize several specific properties of the air-water interface, such as water surface tension, anisotropic reorientation of interfacial water under an external field, and proton hopping.

Parameterizing the Morse Potential for Coarse-Grained Modeling of Blood Plasma

PubMed Central

Zhang, Na; Zhang, Peng; Kang, Wei; Bluestein, Danny; Deng, Yuefan

2014-01-01

Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters are systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately. PMID:24910470

Molecular characterization of Calocedrus rupestris Aver., H.T. Nguyen & L.K. Phan, 2008 (Cupressaceae) based on ITS1 partial sequence.

PubMed

Long, P K; Trang, N T P; Averyanov, L V; Loc, P K

2011-11-21

Calocedrus rupestris Aver., H.T. Nguyen & L.K. Phan was described in 2008 based on some morphological characters that were not sufficiently significant to discriminate it as a species distinct from C. macrolepis Kurz. We applied a new approach to resolve these conflicting views by using sequence data from DNA (ITS) to elucidate phylogenetic relationships between the two species. Analyses of a partial ITS1 sequence in 5 individuals of 2 subpopulations of C. macrolepis and 18 individuals of 8 subpopulations of C. rupestris collected in Vietnam were done. Molecular characterization of the two species showed its low divergence with the lack of autapomorphic characters. In addition, the ITS1 partial sequences of some C. rupestris individuals were identical with C. macrolepis. Due to the less distinctive morphology between C. rupestris and C. macrolepis, the divergence between them does not exceed the interspecific levels, and therefore, C. rupestris could not be regarded as an independent species in relation to C. macrolepis but only as one of its varieties, C. macrolepis var. rupestris (Aver., H.T. Nguyen & L.K. Phan) L.K. Phan, Long K. Phan & Aver.

MOLECULAR METHODS USED TO ASSESS THE RISKS OF TRANSGENE FLOW; BENEFITS AND LIMITATIONS

EPA Science Inventory

The US EPA WED has initiated a gene flow project to characterize ecological risks of gene flow from GM plants to native species. Development of molecular assays for risk characterization down to gene expression level is of high interest to the EPA. Phylogenetic analyses of ampl...

Molecular magnetic resonance imaging of atherosclerotic vessel wall disease.

PubMed

Nörenberg, Dominik; Ebersberger, Hans U; Diederichs, Gerd; Hamm, Bernd; Botnar, René M; Makowski, Marcus R

2016-03-01

Molecular imaging aims to improve the identification and characterization of pathological processes in vivo by visualizing the underlying biological mechanisms. Molecular imaging techniques are increasingly used to assess vascular inflammation, remodeling, cell migration, angioneogenesis and apoptosis. In cardiovascular diseases, molecular magnetic resonance imaging (MRI) offers new insights into the in vivo biology of pathological vessel wall processes of the coronary and carotid arteries and the aorta. This includes detection of early vascular changes preceding plaque development, visualization of unstable plaques and assessment of response to therapy. The current review focuses on recent developments in the field of molecular MRI to characterise different stages of atherosclerotic vessel wall disease. A variety of molecular MR-probes have been developed to improve the non-invasive detection and characterization of atherosclerotic plaques. Specifically targeted molecular probes allow for the visualization of key biological steps in the cascade leading to the development of arterial vessel wall lesions. Early detection of processes which lead to the development of atherosclerosis and the identification of vulnerable atherosclerotic plaques may enable the early assessment of response to therapy, improve therapy planning, foster the prevention of cardiovascular events and may open the door for the development of patient-specific treatment strategies. Targeted MR-probes allow the characterization of atherosclerosis on a molecular level. Molecular MRI can identify in vivo markers for the differentiation of stable and unstable plaques. Visualization of early molecular changes has the potential to improve patient-individualized risk-assessment.

Conductance based characterization of structure and hopping site density in 2D molecule-nanoparticle arrays

NASA Astrophysics Data System (ADS)

McCold, Cliff E.; Fu, Qiang; Howe, Jane Y.; Hihath, Joshua

2015-09-01

Composite molecule-nanoparticle hybrid systems have recently emerged as important materials for applications ranging from chemical sensing to nanoscale electronics. However, creating reproducible and repeatable composite materials with precise properties has remained one of the primary challenges to the implementation of these technologies. Understanding the sources of variation that dominate the assembly and transport behavior is essential for the advancement of nanoparticle-array based devices. In this work, we use a combination of charge-transport measurements, electron microscopy, and optical characterization techniques to determine the role of morphology and structure on the charge transport properties of 2-dimensional monolayer arrays of molecularly-interlinked Au nanoparticles. Using these techniques we are able to determine the role of both assembly-dependent and particle-dependent defects on the conductivities of the films. These results demonstrate that assembly processes dominate the dispersion of conductance values, while nanoparticle and ligand features dictate the mean value of the conductance. By performing a systematic study of the conductance of these arrays as a function of nanoparticle size we are able to extract the carrier mobility for specific molecular ligands. We show that nanoparticle polydispersity correlates with the void density in the array, and that because of this correlation it is possible to accurately determine the void density within the array directly from conductance measurements. These results demonstrate that conductance-based measurements can be used to accurately and non-destructively determine the morphological and structural properties of these hybrid arrays, and thus provide a characterization platform that helps move 2-dimensional nanoparticle arrays toward robust and reproducible electronic systems.Composite molecule-nanoparticle hybrid systems have recently emerged as important materials for applications ranging from chemical sensing to nanoscale electronics. However, creating reproducible and repeatable composite materials with precise properties has remained one of the primary challenges to the implementation of these technologies. Understanding the sources of variation that dominate the assembly and transport behavior is essential for the advancement of nanoparticle-array based devices. In this work, we use a combination of charge-transport measurements, electron microscopy, and optical characterization techniques to determine the role of morphology and structure on the charge transport properties of 2-dimensional monolayer arrays of molecularly-interlinked Au nanoparticles. Using these techniques we are able to determine the role of both assembly-dependent and particle-dependent defects on the conductivities of the films. These results demonstrate that assembly processes dominate the dispersion of conductance values, while nanoparticle and ligand features dictate the mean value of the conductance. By performing a systematic study of the conductance of these arrays as a function of nanoparticle size we are able to extract the carrier mobility for specific molecular ligands. We show that nanoparticle polydispersity correlates with the void density in the array, and that because of this correlation it is possible to accurately determine the void density within the array directly from conductance measurements. These results demonstrate that conductance-based measurements can be used to accurately and non-destructively determine the morphological and structural properties of these hybrid arrays, and thus provide a characterization platform that helps move 2-dimensional nanoparticle arrays toward robust and reproducible electronic systems. Electronic supplementary information (ESI) available: Temperature dependent measurements, activation energies, particle size distributions, void density-polydispersity relation, and DLS data. See DOI: 10.1039/c5nr04460j

Spectroscopic characteristic (FT-IR, 1H, 13C NMR and UV-Vis) and theoretical calculations (MEP, DOS, HOMO-LUMO, PES, NBO analysis and keto-enol tautomerism) of new tetradentate N,N‧-bis(4-hydroxysalicylidene)-1,4-phenylenediamine ligand as chelating agent for the synthesis of dinuclear Co(II), Ni(II), Cu(II) and Zn(II) complexes

NASA Astrophysics Data System (ADS)

Rajaei, Iman; Mirsattari, Seyed Nezamoddin

2018-07-01

The synthesis and characterization of a novel symmetrical Schiff base ligand N,Nʹ-bis(4-hydroxysalicylidene)-1,4-phenylenediamine (BHSP) was presented in this study and characterized by FT-IR, NMR (1H and 13C) and UV-Vis spectroscopy experimentally and theoretically. Also a series of binuclear Co(II), Ni(II), Cu(II) and Zn(II) complexes of BHSP ligand have been synthesized by conventional sequential route in 1:1 equivalent of L:M ratio and characterized by routine physicochemical characterizations. The molecular geometry and vibrational frequencies of the BHSP in the ground state were calculated by using density functional theory (DFT) B3LYP method invoking 6-31G(d,p) and 6-31++G(d,p) basis sets. To study different conformations of the molecule, potential energy surface (PES) scan investigations were performed. The energetic behavior of the ligand compound (BHSP) in solvent media has been examined using B3LYP method with the 6-31G(d,p) and 6-31++G(d,p) basis sets by applying the polarized continuum model (PCM). In addition, DFT calculations of the BHSP ligand, molecular electrostatic potential (MEP), contour map, natural bond orbital (NBO) analysis, frontier molecular orbitals (FMO) analysis, NMR analysis and TD-DFT calculations were conducted. The calculated properties are in agreement with the available experimental data and closely related molecule BSP. The calculated results show that the optimized geometry can well reproduce the crystal structural parameters.

Communication: Relationship between solute localization and diffusion in a dynamically constrained polymer system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saylor, David M.; Jawahery, Sudi; Silverstein, Joshua S.

2016-07-21

We investigate the link between dynamic localization, characterized by the Debye–Waller factor, 〈u{sup 2}〉, and solute self-diffusivity, D, in a polymer system using atomistic molecular dynamics simulations and vapor sorption experiments. We find a linear relationship between lnD and 1/〈u{sup 2}〉 over more than four decades of D, encompassing most of the glass formation regime. The observed linearity is consistent with the Langevin dynamics in a periodically varying potential field and may offer a means to rapidly assess diffusion based on the characterization of dynamic localization.

Extraction of hyaluronic acid (HA) from rooster comb and characterization using flow field-flow fractionation (FlFFF) coupled with multiangle light scattering (MALS).

PubMed

Kang, Dong Young; Kim, Won-Suk; Heo, In Sook; Park, Young Hun; Lee, Seungho

2010-11-01

Hyaluronic acid (HA) was extracted in a relatively large scale from rooster comb using a method similar to that reported previously. The extraction method was modified to simplify and to reduce time and cost in order to accommodate a large-scale extraction. Five hundred grams of frozen rooster combs yielded about 500 mg of dried HA. Extracted HA was characterized using asymmetrical flow field-flow fractionation (AsFlFFF) coupled online to a multiangle light scattering detector and a refractive index detector to determine the molecular size, molecular weight (MW) distribution, and molecular conformation of HA. For characterization of HA, AsFlFFF was operated by a simplified two-step procedure, instead of the conventional three-step procedure, where the first two steps (sample loading and focusing) were combined into one to avoid the adsorption of viscous HA onto the channel membrane. The simplified two-step AsFlFFF yielded reasonably good separations of HA molecules based on their MWs. The weight average MW (M(w) ) and the average root-mean-square (RMS) radius of HA extracted from rooster comb were 1.20×10(6) and 94.7 nm, respectively. When the sample solution was filtered through a 0.45 μm disposable syringe filter, they were reduced down to 3.8×10(5) and 50.1 nm, respectively. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transcriptome of the plant virus vector Graminella nigrifrons, and the molecular interactions of maize fine streak rhabdovirus transmission.

PubMed

Chen, Yuting; Cassone, Bryan J; Bai, Xiaodong; Redinbaugh, Margaret G; Michel, Andrew P

2012-01-01

Leafhoppers (HEmiptera: Cicadellidae) are plant-phloem feeders that are known for their ability to vector plant pathogens. The black-faced leafhopper (Graminella nigrifrons) has been identified as the only known vector for the Maize fine streak virus (MFSV), an emerging plant pathogen in the Rhabdoviridae. Within G. nigrifrons populations, individuals can be experimentally separated into three classes based on their capacity for viral transmission: transmitters, acquirers and non-acquirers. Understanding the molecular interactions between vector and virus can reveal important insights in virus immune defense and vector transmission. RNA sequencing (RNA-Seq) was performed to characterize the transcriptome of G. nigrifrons. A total of 38,240 ESTs of a minimum 100 bp were generated from two separate cDNA libraries consisting of virus transmitters and acquirers. More than 60% of known D. melanogaster, A. gambiae, T. castaneum immune response genes mapped to our G. nigrifrons EST database. Real time quantitative PCR (RT-qPCR) showed significant down-regulation of three genes for peptidoglycan recognition proteins (PGRP - SB1, SD, and LC) in G. nigrifrons transmitters versus control leafhoppers. Our study is the first to characterize the transcriptome of a leafhopper vector species. Significant sequence similarity in immune defense genes existed between G. nigrifrons and other well characterized insects. The down-regulation of PGRPs in MFSV transmitters suggested a possible role in rhabdovirus transmission. The results provide a framework for future studies aimed at elucidating the molecular mechanisms of plant virus vector competence.

Medium-Chain Acyl-CoA Deficiency: Outlines from Newborn Screening, In Silico Predictions, and Molecular Studies

PubMed Central

Catarzi, Serena; Caciotti, Anna; Thusberg, Janita; Tonin, Rodolfo; Malvagia, Sabrina; la Marca, Giancarlo; Pasquini, Elisabetta; Cavicchi, Catia; Ferri, Lorenzo; Donati, Maria A.; Baronio, Federico; Guerrini, Renzo; Mooney, Sean D.; Morrone, Amelia

2013-01-01

Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is a disorder of fatty acid oxidation characterized by hypoglycemic crisis under fasting or during stress conditions, leading to lethargy, seizures, brain damage, or even death. Biochemical acylcarnitines data obtained through newborn screening by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were confirmed by molecular analysis of the medium-chain acyl-CoA dehydrogenase (ACADM) gene. Out of 324.000 newborns screened, we identified 14 MCADD patients, in whom, by molecular analysis, we found a new nonsense c.823G>T (p.Gly275∗) and two new missense mutations: c.253G>C (p.Gly85Arg) and c.356T>A (p.Val119Asp). Bioinformatics predictions based on both phylogenetic conservation and functional/structural software were used to characterize the new identified variants. Our findings confirm the rising incidence of MCADD whose existence is increasingly recognized due to the efficacy of an expanded newborn screening panel by LC-MS/MS making possible early specific therapies that can prevent possible crises in at-risk infants. We noticed that the “common” p.Lys329Glu mutation only accounted for 32% of the defective alleles, while, in clinically diagnosed patients, this mutation accounted for 90% of defective alleles. Unclassified variants (UVs or VUSs) are especially critical when considering screening programs. The functional and pathogenic characterization of genetic variants presented here is required to predict their medical consequences in newborns. PMID:24294134

[Prediction of the molecular response to pertubations from single cell measurements].

PubMed

Remacle, Françoise; Levine, Raphael D

2014-12-01

The response of protein signalization networks to perturbations is analysed from single cell measurements. This experimental approach allows characterizing the fluctuations in protein expression levels from cell to cell. The analysis is based on an information theoretic approach grounded in thermodynamics leading to a quantitative version of Le Chatelier principle which allows to predict the molecular response. Two systems are investigated: human macrophages subjected to lipopolysaccharide challenge, analogous to the immune response against Gram-negative bacteria and the response of the proteins involved in the mTOR signalizing network of GBM cancer cells to changes in partial oxygen pressure. © 2014 médecine/sciences – Inserm.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herfort, Lydie; Peterson, Tawnya D.; McCue, Lee Ann

The Columbia River estuary is traditionally considered a detritus-based ecosystem fueled in summer by organic matter (OM) from expired freshwater diatoms. Since Estuarine Turbidity Maxima (ETM) are sites of accumulation and transformation of this phytoplankton-derived OM, to further characterize the ETM protist assemblage, we collected in August 2007 bottom waters throughout an ETM event, as well as surface water during the peak of bottom turbidity, and performed biogeochemical, microscopic and molecular (18S rRNA gene clone libraries) analyses. These data confirmed that the majority of the particulate OM in ETMs is derived from chlorophyll a-poor particulate organic carbon tagged by DNAmore » too damaged to be detected by molecular analysis.« less

Electronic and mechanical characteristics of stacked dimer molecular junctions.

PubMed

Magyarkuti, András; Adak, Olgun; Halbritter, Andras; Venkataraman, Latha

2018-02-15

Break-junction measurements are typically aimed at characterizing electronic properties of single molecules bound between two metal electrodes. Although these measurements have provided structure-function relationships for such devices, there is little work that studies the impact of molecule-molecule interactions on junction characteristics. Here, we use a scanning tunneling microscope based break-junction technique to study pi-stacked dimer junctions formed with two amine-terminated conjugated molecules. We show that the conductance, force and flicker noise of such dimers differ dramatically when compared with the corresponding monomer junctions and discuss the implications of these results on intra- and inter-molecular charge transport.

The molecular basis of ethylene signalling in Arabidopsis

NASA Technical Reports Server (NTRS)

Woeste, K.; Kieber, J. J.; Evans, M. L. (Principal Investigator)

1998-01-01

The simple gas ethylene profoundly influences plants at nearly every stage of growth and development. In the past ten years, the use of a genetic approach, based on the triple response phenotype, has been a powerful tool for investigating the molecular events that underlie these effects. Several fundamental elements of the pathway have been described: a receptor with homology to bacterial two-component histidine kinases (ETR1), elements of a MAP kinase cascade (CTR1) and a putative transcription factor (EIN3). Taken together, these elements can be assembled into a simple, linear model for ethylene signalling that accounts for most of the well-characterized ethylene mediated responses.

A combined molecular dynamics/micromechanics/finite element approach for multiscale constitutive modeling of nanocomposites with interface effects

NASA Astrophysics Data System (ADS)

Yang, B. J.; Shin, H.; Lee, H. K.; Kim, H.

2013-12-01

We introduce a multiscale framework based on molecular dynamic (MD) simulation, micromechanics, and finite element method (FEM). A micromechanical model, which considers influences of the interface properties, nanoparticle (NP) size, and microcracks, is developed. Then, we perform MD simulations to characterize the mechanical properties of the nanocomposite system (silica/nylon 6) with varying volume fraction and size of NPs. By comparing the MD with micromechanics results, intrinsic physical properties at interfacial region are derived. Finally, we implement the developed model in the FEM code with the derived interfacial parameters, and predict the mechanical behavior of the nanocomposite at the macroscopic scale.

Endocannabinoid signalling and the deteriorating brain

PubMed Central

Di Marzo, Vincenzo; Stella, Nephi; Zimmer, Andreas

2015-01-01

Ageing is characterized by the progressive impairment of physiological functions and increased risk of developing debilitating disorders, including chronic inflammation and neurodegenerative diseases. These disorders have common molecular mechanisms that can be targeted therapeutically. In the wake of the approval of the first cannabinoid-based drug for the symptomatic treatment of multiple sclerosis, we examine how endocannabinoid (eCB) signalling controls — and is affected by — normal ageing and neuroinflammatory and neurodegenerative disorders. We propose a conceptual framework linking eCB signalling to the control of the cellular and molecular hallmarks of these processes, and categorize the key components of endocannabinoid signalling that may serve as targets for novel therapeutics. PMID:25524120

Organization of Amphiphilic Molecular Disks with Branched Hydrophilic Tails and Hexa-peri-hexabenzocoronene Core

NASA Astrophysics Data System (ADS)

Lee, Myongsoo; Kim, Jung-Woo; Yoo, Yong-Sik; Peleshanko, Sergey; Larson, Kirsten; Vaknin, David; Markutsya, Sergei; Tsukruk, Vladimir V.

2002-03-01

Amphiphilic branched discotics consisting of the aromatic core and oligoethers as the branched peripheral chains have been characterized in bulk and monolayer states. The discotics based on di-branched oligoether side chains have been observed to self-organize into an ordered hexagonal columnar structure within liquid crystalline (LC) phases. The tetrabranched molecule showed only an isotropic liquid. The LC molecules with di-branched tails have been observed to form stable monolayers on the water surface in contrast to the tetra-branched tails. We suggest a crab-like molecular conformation and cluster-segregated monolayers with six-fold symmetry of face-on packing on a solid surface.

Studies of the structure-activity relationships of peptides and proteins involved in growth and development based on their three-dimensional structures.

PubMed

Nagata, Koji

2010-01-01

Peptides and proteins with similar amino acid sequences can have different biological functions. Knowledge of their three-dimensional molecular structures is critically important in identifying their functional determinants. In this review, I describe the results of our and other groups' structure-based functional characterization of insect insulin-like peptides, a crustacean hyperglycemic hormone-family peptide, a mammalian epidermal growth factor-family protein, and an intracellular signaling domain that recognizes proline-rich sequence.

Conformational analysis of a covalently cross-linked Watson-Crick base pair model.

PubMed

Jensen, Erik A; Allen, Benjamin D; Kishi, Yoshito; O'Leary, Daniel J

2008-11-15

Low-temperature NMR experiments and molecular modeling have been used to characterize the conformational behavior of a covalently cross-linked DNA base pair model. The data suggest that Watson-Crick or reverse Watson-Crick hydrogen bonding geometries have similar energies and can interconvert at low temperatures. This low-temperature process involves rotation about the crosslink CH(2)C(5') (psi) carbon-carbon bond, which is energetically preferred over the alternate CH(2)N(3) (phi) carbon-nitrogen bond rotation.

Development and Characterization of New Donor-Acceptor Conjugated Polymers and Fullerene Nanoparticles for High Performance Bulk Heterojunction Solar Cells

DTIC Science & Technology

2011-01-14

thieno[3,4-c] pyrrole -4,6-dione (TPD)–based donor–acceptor polymer, PBTTPD, that exhibits high crystallinity and a low-lying highest occupied molecular...release; distribution unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Bithiophene/thieno[3,4-c] pyrrole -4,6-dione (TPD)?based donor?acceptor polymer...nearby fullerene acceptors. The electron-deficient thieno[3,4-c] pyrrole -4,6-dione (TPD) moiety exhibits a symmetric, rigidly fused, coplanar

Molecular Confirmation of the Specific Status of Anopheles halophylus (Diptera: Culicidae) and Evidence of a New Cryptic Species within An. triannulatus in Central Brazil

DTIC Science & Technology

2006-01-01

unbiased genetic dis- tances and characterized using the unweighted pair group method with arithmetic means ( UPGMA ). Re- Table 1. Gene frequencies for...0.428, and between An. halophylus and the morpho- logical variant was 0.145, supporting the observations seen with allozymes. A UPGMA dendrogram based...and R. C. Wilkerson. 2005. Anopheles tri- annulatus (Neiva and Pinto): a new Anopheles record Fig. 2. UPGMA dendrogram constructed based on RAPD

Rapid screening of phytoremediation effluents by off-line tetramethylammonium hydroxide assisted thermochemolysis.

PubMed

Poerschmann, Juergen; Schultze-Nobre, Luciana

2015-06-15

Tetramethylammonium hydroxide-assisted thermochemolysis performed in an off-line mode proved a useful tool in determining organic compounds in the effluent from laboratory-scale phytoremediation systems. Studies were performed with artificial wastewaters contaminated with xylenols and densely rooted Juncus effuses plants. Analytes in these molecular-level based studies included xylenol substrates, an array of stable intermediates such as low molecular weight carboxylic acids and oxidative coupling products (tetramethyl biphenyldiols, tetramethyl diphenylether monools), diagnostic fatty acid biomarkers, as well as lignin-, carbohydrate-, and protein-based phenols and carboxylic acids. Lignin-based breakdown products belonged to p-hydroxyphenyl- and guaiacyl-units, with lower abundance of syringyl units and the dominance of acids over phenols. Monomeric lignin-, protein- and carbohydrate-based breakdown products could not be detected in the non-treated lyophilized effluent. The formation of diketopiperazines pointed to soluble peptides and proteins. The procedure described herein can easily be applied in every modern laboratory to characterize underlying processes in phytoremediation. Copyright © 2015 Elsevier B.V. All rights reserved.

Experimental and theoretical studies of Schiff bases as corrosion inhibitors.

PubMed

Jamil, Dalia M; Al-Okbi, Ahmed K; Al-Baghdadi, Shaimaa B; Al-Amiery, Ahmed A; Kadhim, Abdulhadi; Gaaz, Tayser Sumer; Kadhum, Abdul Amir H; Mohamad, Abu Bakar

2018-02-05

Relatively inexpensive, stable Schiff bases, namely 3-((4-hydroxybenzylidene)amino)-2-methylquinazolin-4(3H)-one (BZ3) and 3-((4-(dimethylamino)benzylidene)amino)-2-methylquinazolin-4(3H)-one (BZ4), were employed as highly efficient inhibitors of mild steel corrosion by corrosive acid. The inhibition efficiencies were estimated based on weight loss method. Moreover, scanning electron microscopy was used to investigate the inhibition mechanism. The synthesized Schiff bases were characterized by Fourier transform infrared spectroscopy, nuclear magnetic resonance spectroscopy and micro-elemental analysis. The inhibition efficiency depends on three factors: the amount of nitrogen in the inhibitor, the inhibitor concentration and the inhibitor molecular weight. Inhibition efficiencies of 96 and 92% were achieved with BZ4 and BZ3, respectively, at the maximum tested concentration. Density functional theory calculations of BZ3 and BZ4 were performed to compare the effects of hydroxyl and N,N-dimethylamino substituents on the inhibition efficiency, providing insight for designing new molecular structures that exhibit enhanced inhibition efficiencies.

Light, Molecules, Action: Using Ultrafast Uv-Visible and X-Ray Spectroscopy to Probe Excited State Dynamics in Photoactive Molecules

NASA Astrophysics Data System (ADS)

Sension, R. J.

2017-06-01

Light provides a versatile energy source capable of precise manipulation of material systems on size scales ranging from molecular to macroscopic. Photochemistry provides the means for transforming light energy from photon to process via movement of charge, a change in shape, a change in size, or the cleavage of a bond. Photochemistry produces action. In the work to be presented here ultrafast UV-Visible pump-probe, and pump-repump-probe methods have been used to probe the excited state dynamics of stilbene-based molecular motors, cyclohexadiene-based switches, and polyene-based photoacids. Both ultrafast UV-Visible and X-ray absorption spectroscopies have been applied to the study of cobalamin (vitamin B_{12}) based compounds. Optical measurements provide precise characterization of spectroscopic signatures of the intermediate species on the S_{1} surface, while time-resolved XANES spectra at the Co K-edge probe the structural changes that accompany these transformations.

Synthesis, spectroscopic characterization, DFT studies and antifungal activity of (E)-4-amino-5-[N'-(2-nitro-benzylidene)-hydrazino]-2,4-dihydro-[1,2,4]triazole-3-thione

NASA Astrophysics Data System (ADS)

Joshi, Rachana; Pandey, Nidhi; Yadav, Swatantra Kumar; Tilak, Ragini; Mishra, Hirdyesh; Pokharia, Sandeep

2018-07-01

The hydrazino Schiff base (E)-4-amino-5-[N'-(2-nitro-benzylidene)-hydrazino]-2,4-dihydro-[1,2,4]triazole-3-thione was synthesized and structurally characterized by elemental analysis, FT-IR, Raman, 1H and 13C-NMR and UV-Vis studies. A density functional theory (DFT) based electronic structure calculations were accomplished at B3LYP/6-311++G(d,p) level of theory. A comparative analysis of calculated vibrational frequencies with experimental vibrational frequencies was carried out and significant bands were assigned. The results indicate a good correlation (R2 = 0.9974) between experimental and theoretical IR frequencies. The experimental 1H and 13C-NMR resonance signals were also compared to the calculated values. The theoretical UV-Vis spectral studies were carried out using time dependent-DFT method in gas phase and IEFPCM model in solvent field calculation. The geometrical parameters were calculated in the gas phase. Atomic charges at selected atoms were calculated by Mulliken population analysis (MPA), Hirshfeld population analysis (HPA) and Natural population analysis (NPA) schemes. The molecular electrostatic potential (MEP) map was calculated to assign reactive site on the surface of the molecule. The conceptual-DFT based global and local reactivity descriptors were calculated to obtain an insight into the reactivity behaviour. The frontier molecular orbital analysis was carried out to study the charge transfer within the molecule. The detailed natural bond orbital (NBO) analysis was performed to obtain an insight into the intramolecular conjugative electronic interactions. The titled compound was screened for in vitro antifungal activity against four fungal strains and the results obtained are explained through in silico molecular docking studies.

Synthesis, characterization, crystal structure, DNA- and HSA-binding studies of a dinuclear Schiff base Zn(II) complex derived from 2-hydroxynaphtaldehyde and 2-picolylamine

NASA Astrophysics Data System (ADS)

Kazemi, Zahra; Rudbari, Hadi Amiri; Mirkhani, Valiollah; Sahihi, Mehdi; Moghadam, Majid; Tangestaninejad, Sharam; Mohammadpoor-Baltork, Iraj

2015-09-01

A tridentate Schiff base ligand NNO donor (HL: 1-((E)-((pyridin-2-yl)methylimino)methyl)naphthalen-2-ol was synthesized from condensation of 2-hydroxynaphtaldehyde and 2-picolylamine. Zinc complex, Zn2L2(NO3)2, was prepared from reaction of Zn(NO3)2 and HL at ambient temperature. The ligand and complex were characterized by FT-IR, 1H NMR, 13C NMR and elemental analysis (CHN). Furthermore, the structure of dinuclear Zn(II) complex was determined by single crystal X-ray analysis. The complex, Zn2L2(NO3)2, is centrosymmetric dimer in which deprotonated phenolates bridge the two Zn(II) atoms and link the two halves of the dimer. In the structure, Zinc(II) ions have a highly distorted six-coordinate structure bonded to two oxygen atoms from a bidentate nitrate group, the pyridine nitrogen, an amine nitrogen and phenolate oxygens. The interaction of dinuclear Zn(II) complex with fish sperm DNA (FS-DNA) and HSA was investigated under physiological conditions using fluorescence quenching, UV-Vis spectroscopy, molecular dynamics simulation and molecular docking methods. The estimated binding constants for the DNA-complex and HSA-complex were (3.60 ± 0.18) × 104 M-1 and (1.35 ± 0.24) × 104 M-1, respectively. The distance between dinuclear Zn(II) complex and HSA was obtained based on the Förster's theory of non-radiative energy transfer. Molecular docking studies revealed the binding of dinuclear Zn(II) complex to the major groove of FS-DNA and IIA site of protein by formation of hydrogen bond, π-cation and hydrophobic interactions.

Biophysical and computational characterization of vandetanib-lysozyme interaction

NASA Astrophysics Data System (ADS)

Kabir, Md. Zahirul; Hamzah, Nur Aziean Binti; Ghani, Hamidah; Mohamad, Saharuddin B.; Alias, Zazali; Tayyab, Saad

2018-01-01

Interaction of an anticancer drug, vandetanib (VDB) with a ligand transporter, lysozyme (LYZ) was explored using multispectroscopic techniques, such as fluorescence, absorption and circular dichroism along with computational analysis. Fluorescence data and absorption results confirmed VDB-LYZ complexation. VDB-induced quenching was characterized as static quenching based on inverse correlation of KSV with temperature as well as kq values. The complex was characterized by the weak binding constant (Ka = 4.96-3.14 × 103 M-1). Thermodynamic data (ΔS = + 12.82 J mol-1 K-1; ΔH = - 16.73 kJ mol-1) of VDB-LYZ interaction revealed participation of hydrophobic and van der Waals forces along with hydrogen bonds in VDB-LYZ complexation. Microenvironmental perturbations around tryptophan and tyrosine residues as well as secondary and tertiary structural alterations in LYZ upon addition of VDB were evident from the 3-D fluorescence, far- and near-UV CD spectral analyses, respectively. Interestingly, addition of VDB to LYZ significantly increased protein's thermostability. Molecular docking results suggested the location of VDB binding site near the LYZ active site while molecular dynamics simulation results suggested stability of VDB-LYZ complex. Presence of Mg2+, Ba2+ and Zn2+ was found to interfere with VDB-LYZ interaction.

In vivo interstitial glucose characterization and monitoring in the skin by ATR-FTIR spectroscopy

NASA Astrophysics Data System (ADS)

Skrebova Eikje, Natalja

2011-03-01

Successful development of real-time non-invasive glucose monitoring would represent a major advancement not only in the treatment and management of patients with diabetes mellitus and carbohydrate metabolism disorders, but also for understanding in those biochemical, metabolic and (patho-)physiological processes of glucose at the molecular level in vivo. Here, ATR-FTIR spectroscopy technique has been challenged not only for in vivo measurement of interstitial glucose levels, but also for their non-invasive molecular qualitative and quantitative comparative characterization in the skin tissue. The results, based on calculated mean values of determined 5 glucose-specific peaks in the glucose-related 1000-1160 cm-1 region, showed intra- and inter-subject differences in interstitial glucose activity levels with their changes at different times and doses of OGTT, while raising questions about the relationships between interstitial and blood glucose levels. In conclusion, the introduction of ATR-FTIR spectroscopy technique has opened up an access to the interstitial fluid space in the skin tissue for interstitial glucose characterization and monitoring in vivo. Though interstitial versus blood glucose monitoring has different characteristics, it can be argued that accurate and precise measurements of interstitial glucose levels may be more important clinically.

Photophysical characterization of low-molecular weight organogels for energy transfer and light harvesting

NASA Astrophysics Data System (ADS)

Atsbeha, T.; Bussotti, L.; Cicchi, S.; Foggi, P.; Ghini, G.; Lascialfari, L.; Marcelli, A.

2011-05-01

The choice of a donor and an acceptor with suitable optical and self-assembly properties is essential in the design of organogel-based light harvesting systems. Organogels can provide supramolecular structures capable of enhancing energy transfer processes. In this work, we present the characterization of N-(naphthalene-1-carboxyamide)-(3 S,4 S)-pyrrolidin-(3,4)-bisdodecyl-carbamoyldiester ( 1) and N-(4-nitrobenzofurazan-7-amino)-(3 S,4 S)-pyrrolidin-(3,4)-bisdodecyl-carbamoyldiester ( 2) which are used as donor and acceptor moieties, respectively. The donor molecule is hardly capable to form a gelon its own but it can be assembled at reasonable concentrations with the acceptor gelator to form a two-component donor-acceptor organogels in cyclohexane. Stable organogels are formed from cyclohexane for gelator concentrations as low as ≈10 -3 M. UV-vis and steady-state fluorescence spectroscopies were used to provide a characterization of their molecular interactions. The optical changes observed during the cooling of two-component solutions of these systems are indicative of typical sol-gel transitions. The occurrence of excitation energy transfer processes in the gels is confirmed by comparison of their excitation and absorption spectra.

Supercharging Reagent for Enhanced Liquid Chromatographic Separation and Charging of Sialylated and High-Molecular-Weight Glycopeptides for NanoHPLC-ESI-MS/MS Analysis.

PubMed

Lin, Chia-Wei; Haeuptle, Micha A; Aebi, Markus

2016-09-06

Recent developments in proteomic techniques have led to the development of mass spectrometry (MS)-based methods to characterize site-specific glycosylation of proteins. However, appropriate analytical tools to characterize acidic and high-molecular-weight (hMW) glycopeptides are still lacking. In this study, we demonstrate that the addition of supercharging reagent, m-nitrobenzyl alcohol (m-NBA), into mobile phases greatly facilitates the analysis of acidic and hMW glycopeptides. Using commercial glycoproteins, we demonstrated that in the presence of m-NBA the charge state of sialylated glycopeptides increased and the chromatographic separation of neutral and acidic glycopeptides revealed a remarkable improvement. Next, we applied this system to the characterization of a glycoconjugate vaccine candidate consisting of a genetically detoxified exotoxin A of Pseudomonas aeruginosa covalently linked to Shigella flexneri type 2a O-antigen (Sf2E) produced by engineered Escherichia coli. The addition of m-NBA, allowed us to identify peptides with glycan chains of unprecedented size, up to 20 repeat units (98 monosaccharides). Our results indicated that incorporation of m-NBA into reversed-phase liquid chromatography (LC) solvents improves sensitivity, charging, and chromatographic resolution for acidic and hMW glycopeptides.

A novel framework for molecular characterization of atmospherically relevant organic compounds based on collision cross section and mass-to-charge ratio

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xuan; Krechmer, Jordan E.; Groessl, Michael

Here, a new metric is introduced for representing the molecular signature of atmospherically relevant organic compounds, the collision cross section (Ω), a quantity that is related to the structure and geometry of molecules and is derived from ion mobility measurements. By combination with the mass-to-charge ratio ( m/z), a two-dimensional Ω – m/z space is developed to facilitate the comprehensive investigation of the complex organic mixtures. A unique distribution pattern of chemical classes, characterized by functional groups including amine, alcohol, carbonyl, carboxylic acid, ester, and organic sulfate, is developed on the 2-D Ω – m/z space. Species of the samemore » chemical class, despite variations in the molecular structures, tend to situate as a narrow band on the space and follow a trend line. Reactions involving changes in functionalization and fragmentation can be represented by the directionalities along or across these trend lines, thus allowing for the interpretation of atmospheric transformation mechanisms of organic species. The characteristics of trend lines for a variety of functionalities that are commonly present in the atmosphere can be predicted by the core model simulations, which provide a useful tool to identify the chemical class to which an unknown species belongs on the Ω – m/z space. Within the band produced by each chemical class on the space, molecular structural assignment can be achieved by utilizing collision-induced dissociation as well as by comparing the measured collision cross sections in the context of those obtained via molecular dynamics simulations.« less

A novel framework for molecular characterization of atmospherically relevant organic compounds based on collision cross section and mass-to-charge ratio

DOE PAGES

Zhang, Xuan; Krechmer, Jordan E.; Groessl, Michael; ...

2016-10-19

Here, a new metric is introduced for representing the molecular signature of atmospherically relevant organic compounds, the collision cross section (Ω), a quantity that is related to the structure and geometry of molecules and is derived from ion mobility measurements. By combination with the mass-to-charge ratio ( m/z), a two-dimensional Ω – m/z space is developed to facilitate the comprehensive investigation of the complex organic mixtures. A unique distribution pattern of chemical classes, characterized by functional groups including amine, alcohol, carbonyl, carboxylic acid, ester, and organic sulfate, is developed on the 2-D Ω – m/z space. Species of the samemore » chemical class, despite variations in the molecular structures, tend to situate as a narrow band on the space and follow a trend line. Reactions involving changes in functionalization and fragmentation can be represented by the directionalities along or across these trend lines, thus allowing for the interpretation of atmospheric transformation mechanisms of organic species. The characteristics of trend lines for a variety of functionalities that are commonly present in the atmosphere can be predicted by the core model simulations, which provide a useful tool to identify the chemical class to which an unknown species belongs on the Ω – m/z space. Within the band produced by each chemical class on the space, molecular structural assignment can be achieved by utilizing collision-induced dissociation as well as by comparing the measured collision cross sections in the context of those obtained via molecular dynamics simulations.« less

Translational research of optical molecular imaging for personalized medicine.

PubMed

Qin, C; Ma, X; Tian, J

2013-12-01

In the medical imaging field, molecular imaging is a rapidly developing discipline and forms many imaging modalities, providing us effective tools to visualize, characterize, and measure molecular and cellular mechanisms in complex biological processes of living organisms, which can deepen our understanding of biology and accelerate preclinical research including cancer study and medicine discovery. Among many molecular imaging modalities, although the penetration depth of optical imaging and the approved optical probes used for clinics are limited, it has evolved considerably and has seen spectacular advances in basic biomedical research and new drug development. With the completion of human genome sequencing and the emergence of personalized medicine, the specific drug should be matched to not only the right disease but also to the right person, and optical molecular imaging should serve as a strong adjunct to develop personalized medicine by finding the optimal drug based on an individual's proteome and genome. In this process, the computational methodology and imaging system as well as the biomedical application regarding optical molecular imaging will play a crucial role. This review will focus on recent typical translational studies of optical molecular imaging for personalized medicine followed by a concise introduction. Finally, the current challenges and the future development of optical molecular imaging are given according to the understanding of the authors, and the review is then concluded.

Tracing molecular dephasing in biological tissue

NASA Astrophysics Data System (ADS)

Mokim, M.; Carruba, C.; Ganikhanov, F.

2017-10-01

We demonstrate the quantitative spectroscopic characterization and imaging of biological tissue using coherent time-domain microscopy with a femtosecond resolution. We identify tissue constituents and perform dephasing time (T2) measurements of characteristic Raman active vibrations. This was shown in subcutaneous mouse fat embedded within collagen rich areas of the dermis and the muscle connective tissue. The demonstrated equivalent spectral resolution (<0.3 cm-1) is an order of magnitude better compared to commonly used frequency-domain methods for characterization of biological media. This provides with the important dimensions and parameters in biological media characterization and can become an effective tool in detecting minute changes in the bio-molecular composition and environment that is critical for molecular level diagnosis.

Diagnosis and therapy with CRISPR advanced CRISPR based tools for point of care diagnostics and early therapies.

PubMed

Uppada, Vanita; Gokara, Mahesh; Rasineni, Girish Kumar

2018-05-20

Molecular diagnostics is of critical importance to public health worldwide. It facilitates not only detection and characterization of diseases, but also monitors drug responses, assists in the identification of genetic modifiers and disease susceptibility. Based upon DNA variation, a wide range of molecular-based tests are available to assess/diagnose diseases. The CRISPR-Cas9 system has recently emerged as a versatile tool for biological and medical research. In this system, a single guide RNA (sgRNA) directs the endonuclease Cas9 to a targeted DNA sequence for site-specific manipulation. As designing CRISPR-guided nucleases can be done easily and relatively fast, the CRISPR/Cas9 system has evolved as widely used DNA editing tool. This technique led to a large number of gene editing studies in variety of organisms. CRISPR/Cas9-mediated diagnosis and therapy has picked up pace due to specificity and accuracy of CRISPR. The aim is not only to identify specific pathogens, especially virus but also to repair disease-causing alleles by changing the DNA sequence at the exact location on the chromosome. At present, PCR-based molecular diagnostic testing predominates; however, alternative technologies aimed at reducing genome complexity without PCR are anticipated to gain momentum in the coming years. Furthermore, development of integrated chip devices should allow point-of-care testing and facilitate genetic readouts from single cells and molecules. Together with molecular based therapy CRISPR based diagnostic testing will be a revolution in modern health care settings. In this review, we emphasize on current developing diagnostic techniques based upon CRISPR Cas approach along with short insights on its therapeutic usage. Copyright © 2018 Elsevier B.V. All rights reserved.

Design Principles of Nanoparticles as Contrast Agents for Magnetic Resonance Imaging

NASA Astrophysics Data System (ADS)

Shan, Liang; Gu, Xinbin; Wang, Paul

2013-09-01

Molecular imaging is an emerging field that introduces molecular agents into traditional imaging techniques, enabling visualization, characterization and measurement of biological processes at the molecular and cellular levels in humans and other living systems. The promise of molecular imaging lies in its potential for selective potency by targeting biomarkers or molecular targets and the imaging agents serve as reporters for the selectivity of targeting. Development of an efficient molecular imaging agent depends on well-controlled high-quality experiment design involving target selection, agent synthesis, in vitro characterization, and in vivo animal characterization before it is applied in humans. According to the analysis from the Molecular Imaging and Contrast Agent Database (MICAD, ), more than 6000 molecular imaging agents with sufficient preclinical evaluation have been reported to date in the literature and this number increases by 250-300 novel agents each year. The majority of these agents are radionuclides, which are developed for positron emission tomography (PET) and single photon emission computed tomography (SPECT). Contrast agents for magnetic resonance imaging (MRI) account for only a small part. This is largely due to the fact that MRI is currently not a fully quantitative imaging technique and is less sensitive than PET and SPECT. However, because of the superior ability to simultaneously extract molecular and anatomic information, molecular MRI is attracting significant interest and various targeted nanoparticle contrast agents have been synthesized for MRI. The first and one of the most critical steps in developing a targeted nanoparticle contrast agent is target selection, which plays the central role and forms the basis for success of molecular imaging. This chapter discusses the design principles of targeted contrast agents in the emerging frontiers of molecular MRI.

Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Drenscko, Mihaela

Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of small membranes using all atomistic and coarse-grained methods. The molecular interaction between common polymer chains used in biomedical applications and the cell membrane is unknown. This interaction may affect the biocompatibility of the polymer chains. Molecular dynamics simulations offer an emerging tool to characterize the interaction between common degradable polymer chains used in biomedical applications, such as polycaprolactone, and model cell membranes. We systematically characterize with long-time all-atomistic molecular dynamics simulations the interaction between single polycaprolactone chains of varying chain lengths with a model phospholipid membrane. We find that the length of polymer chain greatly affects the nature of interaction with the membrane, as well as the membrane properties. Furthermore, we next utilize advanced sampling techniques in molecular dynamics to characterize the two-dimensional free energy surface for the interaction of varying polymer chain lengths (short, intermediate, and long) with model cell membranes. We find that the free energy minimum shifts from the membrane-water interface to the hydrophobic core of the phospholipid membrane as a function of chain length. These results can be used to design polymer chain lengths and chemistries to optimize their interaction with cell membranes at the molecular level.

Molecular Characterization of Methicillin-Resistant Staphylococcus aureus Causing Fatal Purulent Pericarditis.

PubMed

Kumar, Vasudevan Anil; Nair, Nisha; Thachathodiyl, Rajesh; Nandakumar, Aswathy; Dinesh, Kavitha R; Thatcher, Eileen; Karim, Shamsul; Biswas, Raja

2013-07-01

Though pericardial disease is common in patients with renal disease, purulent pericarditis is very rare. We report a fatal case of purulent pericarditis and sepsis due to methicillin-resistant Staphylococcus aureus in a 78-year-old male with systemic hypertension and renal disease along with the molecular characterization of its resistant mechanism.

Biological and molecular characterization of a US isolate of Hosta virus X

USDA-ARS?s Scientific Manuscript database

Hosta virus X (HVX) is rapidly becoming a serious pathogen of commercially important hosta plants worldwide. We report here a biological and molecular characterization of a US isolate of HVX, HVX-37. HVX-37 infectivity was tested in 21 hosta cultivars over three growth seasons, and three types of re...

Molecular characterization of Salmonella Paratyphi B dT+ and Salmonella Heidelberg from poultry and retail chicken meat in Colombia by pulsed-field gel electrophoresis

USDA-ARS?s Scientific Manuscript database

Salmonella Paratyphi B dT+ variant (also termed Salmonella Java) and Salmonella Heidelberg are human pathogens frequently isolated from poultry. As a step towards implementing the Colombian Integrated Program for Antimicrobial Resistant Surveillance (COIPARS), this study characterized molecular patt...

Characterization of molecular identity and pathogenicity of rice blast fungus in Hunan province of China

USDA-ARS?s Scientific Manuscript database

Characterization of molecular identity and pathogenicity of the rice blast fungus benefits the deployment of effective blast resistance (R) genes. In order to identify blast resistance genes in rice producing areas where most of the hybrid rice is grown in Hunan province, 182 M. oryzae strains were ...

Molecular characterization and phylogenetic analysis of Citrus viroid VI variants from citrus in China

USDA-ARS?s Scientific Manuscript database

Citrus viroid VI (CVd-VI) was originally found from citrus and persimmon in Japan. We report here the identification and molecular characterization of CVd-VI from four production regions of China. A total of 90 cDNA clones from nine infected citrus cultivars were sequenced. The sequence homologies o...

Integrating concepts of landscape ecology with the molecular biology of forest pathogens

Treesearch

John E. Lundquist; Ned B. Klopfenstein

2001-01-01

Increasingly more research has focused on characterizing diversity within forest pathogen populations using molecular markers but few studies have characterized features of the landscape that help create or maintain this diversity. Forest diseases commonly occur in patchy distributions across natural landscapes which can be reflected in the genetic composition of the...