Efficacy of some colloidal silver preparations and silver salts against Proteus bacteria, one possible cause of rheumatoid arthritis.

PubMed

Disaanayake, D M B T; Faoagali, Joan; Laroo, Hans; Hancock, Gerald; Whitehouse, Michael

2014-04-01

There has been increased interest in the role of anti-Proteus antibodies in the aetiology of rheumatoid arthritis (RA) and whether chemotherapeutic agents active against Proteus species might reduce the risk and/or exacerbations of RA. We examined the in vitro antibacterial effects of ten different silver preparations which were either ionic silver [Ag(I)] solutions or nanoparticulate silver (NPS) (Ag(0)) suspensions against ATCC and two wild (clinical) strains of Proteus. The data establish the low minimum inhibitory concentration and minimum bactericidal concentration of all the silver formulations tested against these four Proteus strains. In a pilot study, a potent NPS preparation ex vivo showed long-lasting anti-Proteus activity in a normal human volunteer.

Proteus: Mythology to modern times

PubMed Central

Sellaturay, Senthy V.; Nair, Raj; Dickinson, Ian K.; Sriprasad, Seshadri

2012-01-01

Aims: It is common knowledge that proteus bacteria are associated with urinary tract infections and urinary stones. Far more interesting however, is the derivation of the word proteus. This study examines the origin of the word proteus, its mythological, historical and literary connections and evolution to present-day usage. Materials and Methods: A detailed search for primary and secondary sources was undertaken using the library and internet. Results: Greek mythology describes Proteus as an early sea-god, noted for being versatile and capable of assuming many different forms. In the 8th century BC, the ancient Greek poet, Homer, famous for his epic poems the Iliad and Odyssey, describes Proteus as a prophetic old sea-god, and herdsman of the seals of Poseidon, God of the Sea. Shakespeare re-introduced Proteus into English literature, in the 15th century AD, in the comedy The Two Gentleman of Verona, as one of his main characters who is inconstant with his affections. The ‘elephant man’ was afflicted by a severely disfiguring disease, described as ‘Proteus syndrome’. It is particularly difficult to distinguish from neurofibromatosis, due to its various forms in different individuals. The Oxford English Dictionary defines the word ‘protean’ as to mean changeable, variable, and existing in multiple forms. Proteus bacteria directly derive their name from the Sea God, due to their rapid swarming growth and motility on agar plates. They demonstrate versatility by secreting enzymes, which allow them to evade the host's defense systems. Conclusions: Thus proteus, true to its name, has had a myriad of connotations over the centuries. PMID:23450503

Impact of Morphological Changes on the Motility of Amoeba proteus

NASA Astrophysics Data System (ADS)

Shroff N, Sunitha

2016-11-01

Bio-mechanical properties of cell membrane, actin and cytoskeleton have influence on the cell locomotion. To explore, morphological changes were induced in Amoeba proteus by depriving nutrition, also either through ATP mediated or through KCl mediated membrane depolarization. We observed that, membrane depolarization leads to complete loss/reduction of pseudopodia in a dose dependent manner, gradually A. proteus becomes globular. We also report that with depravation of its nutrition (Chilomonas) A. proteus transforms them into tube/filament like structure and this transformation is reversible with the supply of Chilomonas. Results indicate that the structural and locomotion variation of A. proteus through nucleotides may not be just a membrane phenomenon, but may involve signaling mechanisms. Further, we carried out immunostaining of A. proteus with P2X2 and P2Y2 antibodies to analyze their localization and the extent of expression. The result indicated that in normal A. proteus receptors are dispersed uniformly, whereas in filament shaped A. proteus P2X2-receptor was found to be localized, unlike P2Y2 receptor. As nucleotides are known to cause structural changes in the organism, we report corresponding changes in their locomotion. Assistant Professor, Department of Biotechnology. Mount Carmel College, Bangalore 560 052.

Towards Clinical Molecular Diagnosis of Inherited Cardiac Conditions: A Comparison of Bench-Top Genome DNA Sequencers

PubMed Central

Wilkinson, Samuel L.; John, Shibu; Walsh, Roddy; Novotny, Tomas; Valaskova, Iveta; Gupta, Manu; Game, Laurence; Barton, Paul J R.; Cook, Stuart A.; Ware, James S.

2013-01-01

Background Molecular genetic testing is recommended for diagnosis of inherited cardiac disease, to guide prognosis and treatment, but access is often limited by cost and availability. Recently introduced high-throughput bench-top DNA sequencing platforms have the potential to overcome these limitations. Methodology/Principal Findings We evaluated two next-generation sequencing (NGS) platforms for molecular diagnostics. The protein-coding regions of six genes associated with inherited arrhythmia syndromes were amplified from 15 human samples using parallelised multiplex PCR (Access Array, Fluidigm), and sequenced on the MiSeq (Illumina) and Ion Torrent PGM (Life Technologies). Overall, 97.9% of the target was sequenced adequately for variant calling on the MiSeq, and 96.8% on the Ion Torrent PGM. Regions missed tended to be of high GC-content, and most were problematic for both platforms. Variant calling was assessed using 107 variants detected using Sanger sequencing: within adequately sequenced regions, variant calling on both platforms was highly accurate (Sensitivity: MiSeq 100%, PGM 99.1%. Positive predictive value: MiSeq 95.9%, PGM 95.5%). At the time of the study the Ion Torrent PGM had a lower capital cost and individual runs were cheaper and faster. The MiSeq had a higher capacity (requiring fewer runs), with reduced hands-on time and simpler laboratory workflows. Both provide significant cost and time savings over conventional methods, even allowing for adjunct Sanger sequencing to validate findings and sequence exons missed by NGS. Conclusions/Significance MiSeq and Ion Torrent PGM both provide accurate variant detection as part of a PCR-based molecular diagnostic workflow, and provide alternative platforms for molecular diagnosis of inherited cardiac conditions. Though there were performance differences at this throughput, platforms differed primarily in terms of cost, scalability, protocol stability and ease of use. Compared with current molecular genetic diagnostic tests for inherited cardiac arrhythmias, these NGS approaches are faster, less expensive, and yet more comprehensive. PMID:23861798

[RATIONAL ASPECTS OF BACTERIOPHAGES USE].

PubMed

Vakarina, A A; Kataeva, L V; Karpukhina, N F

2015-01-01

Analysis of existing aspects of bacteriophage use and study features of their lytic activity by using various techniques. Effect of monophages and associated bacteriophages (staphylococci, piopolyvalent and piocombined, intestiphage, pneumonia klebsiella and polyvalent klebsiella produced by "Microgen") was studied with 380 strains of Staphylococcus aureus and 279 cultures of Klebsiella pneumoniae in liquid and solid nutrient media. From patients with intestinal disorder, sensitivity was analyzed to 184 strains of Salmonella genus bacteria 18 serological variants to salmonella bacteriophages, 137 strains of Escherichia coli (lactose-negative, hemolytic), as well as some members of OKA groups (21 serovars) to coli-proteic and piopolyvalent bacteriophages. Lytic ability of the piobacteriophage against Klebsiella and Proteus genus bacteria was determined. Staphylococcus aureus was sensitive to staphylococcus bacteriophage in 71.6% of cases and to piobacteriophage--in 86.15% of cases. A 100% lytic ability of salmonella bacteriophage against Salmonella spp. was established. Sensitivity of E. coli of various serogroups to coli-proteic and piobacteriophage was 66 - 100%. Klebsiella, Proteus genus bacteria were sensitive to piobacteriophage in only 35% and 43.15% of cases, respectively. A more rational use of bacteriophages is necessary: development of a technique, evaluation of sensitivity of bacteria to bacteriophage, introduction of corrections into their production (expansion of bacteriophage spectra, determination and indication of their concentration in accompanying documents).

QCL-based standoff and proximal chemical detectors

NASA Astrophysics Data System (ADS)

Dupuis, Julia R.; Hensley, Joel; Cosofret, Bogdan R.; Konno, Daisei; Mulhall, Phillip; Schmit, Thomas; Chang, Shing; Allen, Mark; Marinelli, William J.

2016-05-01

The development of two longwave infrared quantum cascade laser (QCL) based surface contaminant detection platforms supporting government programs will be discussed. The detection platforms utilize reflectance spectroscopy with application to optically thick and thin materials including solid and liquid phase chemical warfare agents, toxic industrial chemicals and materials, and explosives. Operation at standoff (10s of m) and proximal (1 m) ranges will be reviewed with consideration given to the spectral signatures contained in the specular and diffusely reflected components of the signal. The platforms comprise two variants: Variant 1 employs a spectrally tunable QCL source with a broadband imaging detector, and Variant 2 employs an ensemble of broadband QCLs with a spectrally selective detector. Each variant employs a version of the Adaptive Cosine Estimator for detection and discrimination in high clutter environments. Detection limits of 5 μg/cm2 have been achieved through speckle reduction methods enabling detector noise limited performance. Design considerations for QCL-based standoff and proximal surface contaminant detectors are discussed with specific emphasis on speckle-mitigated and detector noise limited performance sufficient for accurate detection and discrimination regardless of the surface coverage morphology or underlying surface reflectivity. Prototype sensors and developmental test results will be reviewed for a range of application scenarios. Future development and transition plans for the QCL-based surface detector platforms are discussed.

Probing the kinetic stabilities of Friedreich's ataxia clinical variants using a solid phase GroEL chaperonin capture platform.

PubMed

Correia, Ana R; Naik, Subhashchandra; Fisher, Mark T; Gomes, Cláudio M

2014-10-20

Numerous human diseases are caused by protein folding defects where the protein may become more susceptible to degradation or aggregation. Aberrant protein folding can affect the kinetic stability of the proteins even if these proteins appear to be soluble in vivo. Experimental discrimination between functional properly folded and misfolded nonfunctional conformers is not always straightforward at near physiological conditions. The differences in the kinetic behavior of two initially folded frataxin clinical variants were examined using a high affinity chaperonin kinetic trap approach at 25 °C. The kinetically stable wild type frataxin (FXN) shows no visible partitioning onto the chaperonin. In contrast, the clinical variants FXN-p.Asp122Tyr and FXN-p.Ile154Phe kinetically populate partial folded forms that tightly bind the GroEL chaperonin platform. The initially soluble FXN-p.Ile154Phe variant partitions onto GroEL more rapidly and is more kinetically liable. These differences in kinetic stability were confirmed using differential scanning fluorimetry. The kinetic and aggregation stability differences of these variants may lead to the distinct functional impairments described in Friedreich's ataxia, the neurodegenerative disease associated to frataxin functional deficiency. This chaperonin platform approach may be useful for identifying small molecule stabilizers since stabilizing ligands to frataxin variants should lead to a concomitant decrease in chaperonin binding.

Immunochemical characterization of the O antigens of two Proteus strains, O8-related antigen of Proteus mirabilis 12 B-r and O2-related antigen of Proteus genomospecies 5/6 12 B-k, infecting a hospitalized patient in Poland.

PubMed

Drzewiecka, Dominika; Shashkov, Alexander S; Arbatsky, Nikolay P; Knirel, Yuriy A

2016-05-01

A hospitalized 73-year-old woman was infected with a Proteus mirabilis strain, 12 B-r, isolated from the place of injection of a blood catheter. Another strain, 12 B-k, recognized as Proteus genomospecies 5 or 6, was isolated from the patient's faeces, which was an example of a nosocomial infection rather than an auto-infection. Serological investigation using ELISA and Western blotting showed that strain 12 B-k from faeces belonged to the Proteus O2 serogroup. Strain 12 B-r from the wound displayed cross-reactions with several Proteus O serogroups due to common epitopes on the core or O-specific parts of the lipopolysaccharide. Studies of the isolated 12 B-r O-specific polysaccharide by NMR spectroscopy revealed its close structural similarity to that of Proteus O8. The only difference in 12 B-r was the presence of an additional GlcNAc-linked phosphoethanolamine residue, which creates a putative epitope responsible for the cross-reactivity with Pt. mirabilis O16. The new O-antigen form could appear as a result of adaptation of the bacterium to a changing environment. On the basis of the data obtained, we suggest division of the O8 serogroup into two subgroups: O8a for strains of various Proteus species that have been previously classified into the O8 serogroup, and O8a,b for Pt. mirabilis 12 B-r, where 'a' is a common epitope and 'b' is a phosphoethanolamine-associated epitope. These findings further confirm serological and structural heterogeneity of O antigens of Proteus strains isolated lately from patients in Poland.

HTR-PROTEUS pebble bed experimental program cores 9 & 10: columnar hexagonal point-on-point packing with a 1:1 moderator-to-fuel pebble ratio

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

Bess, John D.

2014-03-01

PROTEUS is a zero-power research reactor based on a cylindrical graphite annulus with a central cylindrical cavity. The graphite annulus remains basically the same for all experimental programs, but the contents of the central cavity are changed according to the type of reactor being investigated. Through most of its service history, PROTEUS has represented light-water reactors, but from 1992 to 1996 PROTEUS was configured as a pebble-bed reactor (PBR) critical facility and designated as HTR-PROTEUS. The nomenclature was used to indicate that this series consisted of High Temperature Reactor experiments performed in the PROTEUS assembly. During this period, seventeen criticalmore » configurations were assembled and various reactor physics experiments were conducted. These experiments included measurements of criticality, differential and integral control rod and safety rod worths, kinetics, reaction rates, water ingress effects, and small sample reactivity effects (Ref. 3). HTR-PROTEUS was constructed, and the experimental program was conducted, for the purpose of providing experimental benchmark data for assessment of reactor physics computer codes. Considerable effort was devoted to benchmark calculations as a part of the HTR-PROTEUS program. References 1 and 2 provide detailed data for use in constructing models for codes to be assessed. Reference 3 is a comprehensive summary of the HTR-PROTEUS experiments and the associated benchmark program. This document draws freely from these references. Only Cores 9 and 10 are evaluated in this benchmark report due to similarities in their construction. The other core configurations of the HTR-PROTEUS program are evaluated in their respective reports as outlined in Section 1.0. Cores 9 and 10 were evaluated and determined to be acceptable benchmark experiments.« less

HTR-PROTEUS PEBBLE BED EXPERIMENTAL PROGRAM CORES 5, 6, 7, & 8: COLUMNAR HEXAGONAL POINT-ON-POINT PACKING WITH A 1:2 MODERATOR-TO-FUEL PEBBLE RATIO

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

John D. Bess

2013-03-01

PROTEUS is a zero-power research reactor based on a cylindrical graphite annulus with a central cylindrical cavity. The graphite annulus remains basically the same for all experimental programs, but the contents of the central cavity are changed according to the type of reactor being investigated. Through most of its service history, PROTEUS has represented light-water reactors, but from 1992 to 1996 PROTEUS was configured as a pebble-bed reactor (PBR) critical facility and designated as HTR-PROTEUS. The nomenclature was used to indicate that this series consisted of High Temperature Reactor experiments performed in the PROTEUS assembly. During this period, seventeen criticalmore » configurations were assembled and various reactor physics experiments were conducted. These experiments included measurements of criticality, differential and integral control rod and safety rod worths, kinetics, reaction rates, water ingress effects, and small sample reactivity effects (Ref. 3). HTR-PROTEUS was constructed, and the experimental program was conducted, for the purpose of providing experimental benchmark data for assessment of reactor physics computer codes. Considerable effort was devoted to benchmark calculations as a part of the HTR-PROTEUS program. References 1 and 2 provide detailed data for use in constructing models for codes to be assessed. Reference 3 is a comprehensive summary of the HTR-PROTEUS experiments and the associated benchmark program. This document draws freely from these references. Only Cores 9 and 10 are evaluated in this benchmark report due to similarities in their construction. The other core configurations of the HTR-PROTEUS program are evaluated in their respective reports as outlined in Section 1.0. Cores 9 and 10 were evaluated and determined to be acceptable benchmark experiments.« less

HTR-PROTEUS PEBBLE BED EXPERIMENTAL PROGRAM CORES 9 & 10: COLUMNAR HEXAGONAL POINT-ON-POINT PACKING WITH A 1:1 MODERATOR-TO-FUEL PEBBLE RATIO

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

John D. Bess

2013-03-01

PROTEUS is a zero-power research reactor based on a cylindrical graphite annulus with a central cylindrical cavity. The graphite annulus remains basically the same for all experimental programs, but the contents of the central cavity are changed according to the type of reactor being investigated. Through most of its service history, PROTEUS has represented light-water reactors, but from 1992 to 1996 PROTEUS was configured as a pebble-bed reactor (PBR) critical facility and designated as HTR-PROTEUS. The nomenclature was used to indicate that this series consisted of High Temperature Reactor experiments performed in the PROTEUS assembly. During this period, seventeen criticalmore » configurations were assembled and various reactor physics experiments were conducted. These experiments included measurements of criticality, differential and integral control rod and safety rod worths, kinetics, reaction rates, water ingress effects, and small sample reactivity effects (Ref. 3). HTR-PROTEUS was constructed, and the experimental program was conducted, for the purpose of providing experimental benchmark data for assessment of reactor physics computer codes. Considerable effort was devoted to benchmark calculations as a part of the HTR-PROTEUS program. References 1 and 2 provide detailed data for use in constructing models for codes to be assessed. Reference 3 is a comprehensive summary of the HTR-PROTEUS experiments and the associated benchmark program. This document draws freely from these references. Only Cores 9 and 10 are evaluated in this benchmark report due to similarities in their construction. The other core configurations of the HTR-PROTEUS program are evaluated in their respective reports as outlined in Section 1.0. Cores 9 and 10 were evaluated and determined to be acceptable benchmark experiments.« less

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.

PubMed

Quail, Michael A; Smith, Miriam; Coupland, Paul; Otto, Thomas D; Harris, Simon R; Connor, Thomas R; Bertoni, Anna; Swerdlow, Harold P; Gu, Yong

2012-07-24

Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent's PGM, Pacific Biosciences' RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy. Sequence generated by Ion Torrent, MiSeq and Pacific Biosciences technologies displays near perfect coverage behaviour on GC-rich, neutral and moderately AT-rich genomes, but a profound bias was observed upon sequencing the extremely AT-rich genome of Plasmodium falciparum on the PGM, resulting in no coverage for approximately 30% of the genome. We analysed the ability to call variants from each platform and found that we could call slightly more variants from Ion Torrent data compared to MiSeq data, but at the expense of a higher false positive rate. Variant calling from Pacific Biosciences data was possible but higher coverage depth was required. Context specific errors were observed in both PGM and MiSeq data, but not in that from the Pacific Biosciences platform. All three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support.

Scaled Composites' Proteus aircraft and an F/A-18 Hornet from NASA's Dryden Flight Research Center d

NASA Technical Reports Server (NTRS)

2002-01-01

Scaled Composites' Proteus aircraft and an F/A-18 Hornet from NASA's Dryden Flight Research Center during a low-level flyby at Las Cruces Airport in New Mexico. The unique Proteus aircraft served as a test bed for NASA-sponsored flight tests designed to validate collision-avoidance technologies proposed for uninhabited aircraft. The tests, flown over southern New Mexico in March, 2002, used the Proteus as a surrogate uninhabited aerial vehicle (UAV) while three other aircraft flew toward the Proteus from various angles on simulated collision courses. Radio-based 'detect, see and avoid' equipment on the Proteus successfully detected the other aircraft and relayed that information to a remote pilot on the ground at Las Cruces Airport. The pilot then transmitted commands to the Proteus to maneuver it away from the potential collisions. The flight demonstration, sponsored by NASA Dryden Flight Research Center, New Mexico State University, Scaled Composites, the U.S. Navy and Modern Technology Solutions, Inc., were intended to demonstrate that UAVs can be flown safely and compatibly in the same skies as piloted aircraft.

Proteus in flight over Southern California

NASA Image and Video Library

2003-03-27

Scaled Composites' unique tandem-wing Proteus was the testbed for a series of UAV collision-avoidance flight demonstrations. An Amphitech 35GHz radar unit installed below Proteus' nose was the primary sensor for the Detect, See and Avoid tests.

Proteus front view in flight

NASA Image and Video Library

2003-03-27

Scaled Composites' unique tandem-wing Proteus was the testbed for a series of UAV collision-avoidance flight demonstrations. An Amphitech 35GHz radar unit installed below Proteus' nose was the primary sensor for the Detect, See and Avoid tests.

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

Bess, John D.; Sterbentz, James W.; Snoj, Luka

PROTEUS is a zero-power research reactor based on a cylindrical graphite annulus with a central cylindrical cavity. The graphite annulus remains basically the same for all experimental programs, but the contents of the central cavity are changed according to the type of reactor being investigated. Through most of its service history, PROTEUS has represented light-water reactors, but from 1992 to 1996 PROTEUS was configured as a pebble-bed reactor (PBR) critical facility and designated as HTR-PROTEUS. The nomenclature was used to indicate that this series consisted of High Temperature Reactor experiments performed in the PROTEUS assembly. During this period, seventeen criticalmore » configurations were assembled and various reactor physics experiments were conducted. These experiments included measurements of criticality, differential and integral control rod and safety rod worths, kinetics, reaction rates, water ingress effects, and small sample reactivity effects (Ref. 3). HTR-PROTEUS was constructed, and the experimental program was conducted, for the purpose of providing experimental benchmark data for assessment of reactor physics computer codes. Considerable effort was devoted to benchmark calculations as a part of the HTR-PROTEUS program. References 1 and 2 provide detailed data for use in constructing models for codes to be assessed. Reference 3 is a comprehensive summary of the HTR-PROTEUS experiments and the associated benchmark program. This document draws freely from these references. Only Cores 9 and 10 are evaluated in this benchmark report due to similarities in their construction. The other core configurations of the HTR-PROTEUS program are evaluated in their respective reports as outlined in Section 1.0. Cores 9 and 10 were evaluated and determined to be acceptable benchmark experiments.« less

Proteus in flight over Rosamond Dry lakebed

NASA Image and Video Library

2003-03-27

Scaled Composites' unique tandem-wing Proteus was the testbed for a series of UAV collision-avoidance flight demonstrations. An Amphitech 35GHz radar unit installed below Proteus' nose was the primary sensor for the Detect, See and Avoid tests.

Meeting the Challenge of Distributed Real-Time & Embedded (DRE) Systems

DTIC Science & Technology

2012-05-10

IP RTOS Middleware Middleware Services DRE Applications Operating Sys & Protocols Hardware & Networks Middleware Middleware Services DRE...Services COTS & standards-based middleware, language, OS , network, & hardware platforms • Real-time CORBA (TAO) middleware • ADAPTIVE Communication...SPLs) F-15 product variant A/V 8-B product variant F/A 18 product variant UCAV product variant Software Produce-Line Hardware (CPU, Memory, I/O) OS

PROTEUS-SN User Manual

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

Shemon, Emily R.; Smith, Micheal A.; Lee, Changho

2016-02-16

PROTEUS-SN is a three-dimensional, highly scalable, high-fidelity neutron transport code developed at Argonne National Laboratory. The code is applicable to all spectrum reactor transport calculations, particularly those in which a high degree of fidelity is needed either to represent spatial detail or to resolve solution gradients. PROTEUS-SN solves the second order formulation of the transport equation using the continuous Galerkin finite element method in space, the discrete ordinates approximation in angle, and the multigroup approximation in energy. PROTEUS-SN’s parallel methodology permits the efficient decomposition of the problem by both space and angle, permitting large problems to run efficiently on hundredsmore » of thousands of cores. PROTEUS-SN can also be used in serial or on smaller compute clusters (10’s to 100’s of cores) for smaller homogenized problems, although it is generally more computationally expensive than traditional homogenized methodology codes. PROTEUS-SN has been used to model partially homogenized systems, where regions of interest are represented explicitly and other regions are homogenized to reduce the problem size and required computational resources. PROTEUS-SN solves forward and adjoint eigenvalue problems and permits both neutron upscattering and downscattering. An adiabatic kinetics option has recently been included for performing simple time-dependent calculations in addition to standard steady state calculations. PROTEUS-SN handles void and reflective boundary conditions. Multigroup cross sections can be generated externally using the MC2-3 fast reactor multigroup cross section generation code or internally using the cross section application programming interface (API) which can treat the subgroup or resonance table libraries. PROTEUS-SN is written in Fortran 90 and also includes C preprocessor definitions. The code links against the PETSc, METIS, HDF5, and MPICH libraries. It optionally links against the MOAB library and is a part of the SHARP multi-physics suite for coupled multi-physics analysis of nuclear reactors. This user manual describes how to set up a neutron transport simulation with the PROTEUS-SN code. A companion methodology manual describes the theory and algorithms within PROTEUS-SN.« less

Molecular analysis, biochemical characterization, antimicrobial activity and immunological analysis of proteus mirabilis isolated from broilers

USDA-ARS?s Scientific Manuscript database

Proteus mirabilis, a peritrichously flagellated Gram-negative bacterium, is ubiquitous in the environment and is the normal microflora in the human gastrointestinal tract. However, this bacterium is an opportunistic pathogen for human, often causing urinary tract infection. Moreover, Proteus has b...

Proteus syndrome: association with gingival hyperplasia.

PubMed

Arendorf, T M; Hanslo, B

1995-09-01

A 9-year old Black boy with gigantism of the hands and feet, and recurrent gingival hyperplasia, diagnosed as Proteus syndrome is presented. The oral manifestations of this syndrome are described. To the best of our knowledge, this is the first reported case of gingival hyperplasia associated with Proteus syndrome.

Scaled Composites' Proteus aircraft with an F/A-18 Hornet and a Beechcraft KingAir from NASA's Dryden Flight Research Center during a low-level flyby at Mojave Airport in Southern California.

NASA Image and Video Library

2003-04-03

Scaled Composites' Proteus aircraft with an F/A-18 Hornet and a Beechcraft KingAir from NASA's Dryden Flight Research Center during a low-level flyby at Mojave Airport in Southern California. The unique tandem-wing Proteus was the testbed for a series of UAV collision-avoidance flight demonstrations. An Amphitech 35GHz radar unit installed below Proteus' nose was the primary sensor for the Detect, See and Avoid tests.

Scaled Composites' Proteus aircraft and an F/A-18 Hornet from NASA's Dryden Flight Research Center at Mojave Airport in Southern California.

NASA Image and Video Library

2003-04-03

Scaled Composites' Proteus aircraft and an F/A-18 Hornet from NASA's Dryden Flight Research Center at Mojave Airport in Southern California. The unique tandem-wing Proteus was the testbed for a series of UAV collision-avoidance flight demonstrations. An Amphitech 35GHz radar unit installed below Proteus' nose was the primary sensor for the Detect, See and Avoid tests. NASA Dryden's F/A-18 Hornet was one of many different aircraft used in the tests.

Professor Krystyna Kotełko and her contribution to the study of Proteus endotoxin.

PubMed

Różalski, Antoni W

2018-04-01

Professor Krystyna Kotełko was working as a microbiologist at the University of Łódź (Poland). Her main object of study was the LPS (endotoxin) of opportunistic urinary pathogens from the genus Proteus. She demonstrated, for the first time, the presence of uronic acids and amino acids, as well as two heptoses (L- glycero-D- manno-heptose and D- glycero-D- manno-heptose) and hexosamines in Proteus LPS, and developed a classification scheme of the Proteus LPS into chemotypes. Prof Kotełko also initiated studies on the chemical structure of Proteus O-specific polysaccharide and investigations on the serological specificity of this part of LPS, as well its core region. She also analysed the virulence factors of these bacteria, such as haemolysin and invasiveness.

Benchmark Evaluation of the HTR-PROTEUS Absorber Rod Worths (Core 4)

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

John D. Bess; Leland M. Montierth

2014-06-01

PROTEUS was a zero-power research reactor at the Paul Scherrer Institute (PSI) in Switzerland. The critical assembly was constructed from a large graphite annulus surrounding a central cylindrical cavity. Various experimental programs were investigated in PROTEUS; during the years 1992 through 1996, it was configured as a pebble-bed reactor and designated HTR-PROTEUS. Various critical configurations were assembled with each accompanied by an assortment of reactor physics experiments including differential and integral absorber rod measurements, kinetics, reaction rate distributions, water ingress effects, and small sample reactivity effects [1]. Four benchmark reports were previously prepared and included in the March 2013 editionmore » of the International Handbook of Evaluated Reactor Physics Benchmark Experiments (IRPhEP Handbook) [2] evaluating eleven critical configurations. A summary of that effort was previously provided [3] and an analysis of absorber rod worth measurements for Cores 9 and 10 have been performed prior to this analysis and included in PROTEUS-GCR-EXP-004 [4]. In the current benchmark effort, absorber rod worths measured for Core Configuration 4, which was the only core with a randomly-packed pebble loading, have been evaluated for inclusion as a revision to the HTR-PROTEUS benchmark report PROTEUS-GCR-EXP-002.« less

User Manual for the PROTEUS Mesh Tools

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

Smith, Micheal A.; Shemon, Emily R

2016-09-19

PROTEUS is built around a finite element representation of the geometry for visualization. In addition, the PROTEUS-SN solver was built to solve the even-parity transport equation on a finite element mesh provided as input. Similarly, PROTEUS-MOC and PROTEUS-NEMO were built to apply the method of characteristics on unstructured finite element meshes. Given the complexity of real world problems, experience has shown that using commercial mesh generator to create rather simple input geometries is overly complex and slow. As a consequence, significant effort has been put into place to create multiple codes that help assist in the mesh generation and manipulation.more » There are three input means to create a mesh in PROTEUS: UFMESH, GRID, and NEMESH. At present, the UFMESH is a simple way to generate two-dimensional Cartesian and hexagonal fuel assembly geometries. The UFmesh input allows for simple assembly mesh generation while the GRID input allows the generation of Cartesian, hexagonal, and regular triangular structured grid geometry options. The NEMESH is a way for the user to create their own mesh or convert another mesh file format into a PROTEUS input format. Given that one has an input mesh format acceptable for PROTEUS, we have constructed several tools which allow further mesh and geometry construction (i.e. mesh extrusion and merging). This report describes the various mesh tools that are provided with the PROTEUS code giving both descriptions of the input and output. In many cases the examples are provided with a regression test of the mesh tools. The most important mesh tools for any user to consider using are the MT_MeshToMesh.x and the MT_RadialLattice.x codes. The former allows the conversion between most mesh types handled by PROTEUS while the second allows the merging of multiple (assembly) meshes into a radial structured grid. Note that the mesh generation process is recursive in nature and that each input specific for a given mesh tool (such as .axial or .merge) can be used as “mesh” input for any of the mesh tools discussed in this manual.« less

Functional morphology of the inner ear and underwater audiograms of Proteus anguinus (Amphibia, Urodela).

PubMed

Bulog, B; Schlegel, P

2000-01-01

Octavolateral sensory organs (auditory and lateral line organs) of cave salamander Proteus anguinus are highly differentiated. In the saccular macula of the inner ear the complex pattern of hair cell orientation and the large otoconial mass enable particle displacement direction detection. Additionally, the same organ, through air cavities within the body, enables detection of underwater sound pressure changes thus acting as a hearing organ. The cavities in the lungs and mouth of Proteus are a resonators that transmit underwater sound pressure to the inner ear. Behaviourally determined audiograms indicate hearing sensitivity of 60 dB (rel. 1 microPa) at frequencies between 1 and 10 kHz. The hearing frequency range was between 10 Hz and 10 kHz. The hearing sensitivities of depigmented Proteus and black Proteus were compared. The highest sensitivities of the depigmented animals (N=4) were at frequencies 1.3-1.7 kHz and it was 2 kHz in black animals (N=1). Excellent underwater hearing abilities of Proteus are sensory adaptations to cave habitat.

Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes

PubMed Central

Shringarpure, Suyash S.; Carroll, Andrew; De La Vega, Francisco M.; Bustamante, Carlos D.

2015-01-01

Population scale sequencing of whole human genomes is becoming economically feasible; however, data management and analysis remains a formidable challenge for many research groups. Large sequencing studies, like the 1000 Genomes Project, have improved our understanding of human demography and the effect of rare genetic variation in disease. Variant calling on datasets of hundreds or thousands of genomes is time-consuming, expensive, and not easily reproducible given the myriad components of a variant calling pipeline. Here, we describe a cloud-based pipeline for joint variant calling in large samples using the Real Time Genomics population caller. We deployed the population caller on the Amazon cloud with the DNAnexus platform in order to achieve low-cost variant calling. Using our pipeline, we were able to identify 68.3 million variants in 2,535 samples from Phase 3 of the 1000 Genomes Project. By performing the variant calling in a parallel manner, the data was processed within 5 days at a compute cost of $7.33 per sample (a total cost of $18,590 for completed jobs and $21,805 for all jobs). Analysis of cost dependence and running time on the data size suggests that, given near linear scalability, cloud computing can be a cheap and efficient platform for analyzing even larger sequencing studies in the future. PMID:26110529

Evaluation of exome variants using the Ion Proton Platform to sequence error-prone regions.

PubMed

Seo, Heewon; Park, Yoomi; Min, Byung Joo; Seo, Myung Eui; Kim, Ju Han

2017-01-01

The Ion Proton sequencer from Thermo Fisher accurately determines sequence variants from target regions with a rapid turnaround time at a low cost. However, misleading variant-calling errors can occur. We performed a systematic evaluation and manual curation of read-level alignments for the 675 ultrarare variants reported by the Ion Proton sequencer from 27 whole-exome sequencing data but that are not present in either the 1000 Genomes Project and the Exome Aggregation Consortium. We classified positive variant calls into 393 highly likely false positives, 126 likely false positives, and 156 likely true positives, which comprised 58.2%, 18.7%, and 23.1% of the variants, respectively. We identified four distinct error patterns of variant calling that may be bioinformatically corrected when using different strategies: simplicity region, SNV cluster, peripheral sequence read, and base inversion. Local de novo assembly successfully corrected 201 (38.7%) of the 519 highly likely or likely false positives. We also demonstrate that the two sequencing kits from Thermo Fisher (the Ion PI Sequencing 200 kit V3 and the Ion PI Hi-Q kit) exhibit different error profiles across different error types. A refined calling algorithm with better polymerase may improve the performance of the Ion Proton sequencing platform.

[Joint action of aminoglycoside antibiotics and nitrofurans with bile on bacteria of the genus Proteus].

PubMed

Sytnik, I A; Puzakova, E V

1980-06-01

The combined effect of monomycin, kanamycin, neomycin and nitrofurans, such as furacillin, furagin, nitrofurantoin and furazolidone with bovine bile was studied on 36 strains of Proteus mirabilis and 14 strains of Proteus vulgaris. It was found that sub-bacteriostatic doses of the bile significantly increased the antiproteus activity of the aminoglycoside antibiotics and nitrofurans. The combinations of the bile with monomycin and kanamycin and the bile with furazolidone and nitrofurantoin proved to be most effective. Clinical trials of the drugs in treatment of inflammatory diseases of the biliferous system of the Proteus etiology are recommended.

Convergence acceleration of the Proteus computer code with multigrid methods

NASA Technical Reports Server (NTRS)

Demuren, A. O.; Ibraheem, S. O.

1992-01-01

Presented here is the first part of a study to implement convergence acceleration techniques based on the multigrid concept in the Proteus computer code. A review is given of previous studies on the implementation of multigrid methods in computer codes for compressible flow analysis. Also presented is a detailed stability analysis of upwind and central-difference based numerical schemes for solving the Euler and Navier-Stokes equations. Results are given of a convergence study of the Proteus code on computational grids of different sizes. The results presented here form the foundation for the implementation of multigrid methods in the Proteus code.

Proteus DSA control room in Mojave, CA

NASA Image and Video Library

2003-04-03

Proteus DSA control room in Mojave, CA (L to R) Jean-Pierre Soucy; Amphitech International Software engineer Craig Bomben; NASA Dryden Test Pilot Pete Siebold; (with headset, at computer controls) Scaled Composites pilot Bob Roehm; New Mexico State University (NMSU) UAV Technical Analysis Application Center (TAAC) Chuck Coleman; Scaled Composites Pilot Kari Sortland; NMSU TAAC Russell Wolfe; Modern Technology Solutions, Inc. Scaled Composites' unique tandem-wing Proteus was the testbed for a series of UAV collision-avoidance flight demonstrations. An Amphitech 35GHz radar unit installed below Proteus' nose was the primary sensor for the Detect, See and Avoid tests.

Defense function of pigment granules in the ciliate Blepharisma japonicum against two predatory protists, Amoeba proteus (Rhizopodea) and Climacostomum virens (Ciliata).

PubMed

Terazima, Masayo Noda; Harumoto, Terue

2004-08-01

The defense function of pigment granules in the red ciliate Blepharisma japonicum against two predatory protists, Amoeba proteus and Climacostomum virens, was investigated by (1) comparing normally-pigmented and albino mutant cells of B. japonicum as the prey of these predators and (2) comparing resistance of the predators to blepharismin, the toxic pigment contained in the pigment granules of B. japonicum. Normally pigmented cells which contained more blepharismin than albino cells were less vulnerable to A. proteus than albino cells, but not to C. virens. C. virens was more resistant than A. proteus to the lethal effect of blepharismin. The results indicate that pigment granules of B. japonicum function as defense organelles against A. proteus but not against C. virens and suggest that successful defense against a predator depends on the susceptibility of the predator to blepharismin.

FY17 Status Report on NEAMS Neutronics Activities

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

Lee, C. H.; Jung, Y. S.; Smith, M. A.

2017-09-30

Under the U.S. DOE NEAMS program, the high-fidelity neutronics code system has been developed to support the multiphysics modeling and simulation capability named SHARP. The neutronics code system includes the high-fidelity neutronics code PROTEUS, the cross section library and preprocessing tools, the multigroup cross section generation code MC2-3, the in-house meshing generation tool, the perturbation and sensitivity analysis code PERSENT, and post-processing tools. The main objectives of the NEAMS neutronics activities in FY17 are to continue development of an advanced nodal solver in PROTEUS for use in nuclear reactor design and analysis projects, implement a simplified sub-channel based thermal-hydraulic (T/H)more » capability into PROTEUS to efficiently compute the thermal feedback, improve the performance of PROTEUS-MOCEX using numerical acceleration and code optimization, improve the cross section generation tools including MC2-3, and continue to perform verification and validation tests for PROTEUS.« less

FY16 Status Report on NEAMS Neutronics Activities

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

Lee, C. H.; Shemon, E. R.; Smith, M. A.

2016-09-30

The goal of the NEAMS neutronics effort is to develop a neutronics toolkit for use on sodium-cooled fast reactors (SFRs) which can be extended to other reactor types. The neutronics toolkit includes the high-fidelity deterministic neutron transport code PROTEUS and many supporting tools such as a cross section generation code MC 2-3, a cross section library generation code, alternative cross section generation tools, mesh generation and conversion utilities, and an automated regression test tool. The FY16 effort for NEAMS neutronics focused on supporting the release of the SHARP toolkit and existing and new users, continuing to develop PROTEUS functions necessarymore » for performance improvement as well as the SHARP release, verifying PROTEUS against available existing benchmark problems, and developing new benchmark problems as needed. The FY16 research effort was focused on further updates of PROTEUS-SN and PROTEUS-MOCEX and cross section generation capabilities as needed.« less

The Proteus Cabinet, or "We Are Here but Not Here"

ERIC Educational Resources Information Center

Nield, Sophie

2008-01-01

In the early nineteenth century, there were three stage illusions in which a magician could cause a person to disappear. In one of these, the Proteus Cabinet, participants would enter a box, and simply vanish. As the designers of the Proteus Cabinet said of them, they were "Here, but not Here." My essay explores this concept in relation to…

Electron microscopy of the nuclear membrane of Amoeba proteus.

PubMed

FRAJOLA, W J; GREIDER, M H; KOSTIR, W J

1956-07-25

An electron microscope study of the nuclear membrane of Amoeba proteus by thin sectioning techniques has revealed an ultrastructure in the outer layer of the membrane that is homologous to the pores and annuli observed in the nuclear membranes of many other cell types studied by these techniques. An inner honeycombed layer apparently unique to Amoeba proteus is also described.

Evaluation of Proteus as a Tool for the Rapid Development of Models of Hydrologic Systems

NASA Astrophysics Data System (ADS)

Weigand, T. M.; Farthing, M. W.; Kees, C. E.; Miller, C. T.

2013-12-01

Models of modern hydrologic systems can be complex and involve a variety of operators with varying character. The goal is to implement approximations of such models that are both efficient for the developer and computationally efficient, which is a set of naturally competing objectives. Proteus is a Python-based toolbox that supports prototyping of model formulations as well as a wide variety of modern numerical methods and parallel computing. We used Proteus to develop numerical approximations for three models: Richards' equation, a brine flow model derived using the Thermodynamically Constrained Averaging Theory (TCAT), and a multiphase TCAT-based tumor growth model. For Richards' equation, we investigated discontinuous Galerkin solutions with higher order time integration based on the backward difference formulas. The TCAT brine flow model was implemented using Proteus and a variety of numerical methods were compared to hand coded solutions. Finally, an existing tumor growth model was implemented in Proteus to introduce more advanced numerics and allow the code to be run in parallel. From these three example models, Proteus was found to be an attractive open-source option for rapidly developing high quality code for solving existing and evolving computational science models.

Environmental DNA in subterranean biology: range extension and taxonomic implications for Proteus

NASA Astrophysics Data System (ADS)

Gorički, Špela; Stanković, David; Snoj, Aleš; Kuntner, Matjaž; Jeffery, William R.; Trontelj, Peter; Pavićević, Miloš; Grizelj, Zlatko; Năpăruş-Aljančič, Magdalena; Aljančič, Gregor

2017-03-01

Europe’s obligate cave-dwelling amphibian Proteus anguinus inhabits subterranean waters of the north-western Balkan Peninsula. Because only fragments of its habitat are accessible to humans, this endangered salamander’s exact distribution has been difficult to establish. Here we introduce a quantitative real time polymerase chain reaction-based environmental DNA (eDNA) approach to detect the presence of Proteus using water samples collected from karst springs, wells or caves. In a survey conducted along the southern limit of its known range, we established a likely presence of Proteus at seven new sites, extending its range to Montenegro. Next, using specific molecular probes to discriminate the rare black morph of Proteus from the closely related white morph, we detected its eDNA at five new sites, thus more than doubling the known number of sites. In one of these we found both black and white Proteus eDNA together. This finding suggests that the two morphs may live in contact with each other in the same body of groundwater and that they may be reproductively isolated species. Our results show that the eDNA approach is suitable and efficient in addressing questions in biogeography, evolution, taxonomy and conservation of the cryptic subterranean fauna.

Reducing false-positive incidental findings with ensemble genotyping and logistic regression based variant filtering methods.

PubMed

Hwang, Kyu-Baek; Lee, In-Hee; Park, Jin-Ho; Hambuch, Tina; Choe, Yongjoon; Kim, MinHyeok; Lee, Kyungjoon; Song, Taemin; Neu, Matthew B; Gupta, Neha; Kohane, Isaac S; Green, Robert C; Kong, Sek Won

2014-08-01

As whole genome sequencing (WGS) uncovers variants associated with rare and common diseases, an immediate challenge is to minimize false-positive findings due to sequencing and variant calling errors. False positives can be reduced by combining results from orthogonal sequencing methods, but costly. Here, we present variant filtering approaches using logistic regression (LR) and ensemble genotyping to minimize false positives without sacrificing sensitivity. We evaluated the methods using paired WGS datasets of an extended family prepared using two sequencing platforms and a validated set of variants in NA12878. Using LR or ensemble genotyping based filtering, false-negative rates were significantly reduced by 1.1- to 17.8-fold at the same levels of false discovery rates (5.4% for heterozygous and 4.5% for homozygous single nucleotide variants (SNVs); 30.0% for heterozygous and 18.7% for homozygous insertions; 25.2% for heterozygous and 16.6% for homozygous deletions) compared to the filtering based on genotype quality scores. Moreover, ensemble genotyping excluded > 98% (105,080 of 107,167) of false positives while retaining > 95% (897 of 937) of true positives in de novo mutation (DNM) discovery in NA12878, and performed better than a consensus method using two sequencing platforms. Our proposed methods were effective in prioritizing phenotype-associated variants, and an ensemble genotyping would be essential to minimize false-positive DNM candidates. © 2014 WILEY PERIODICALS, INC.

Crystal Structure of the Dithiol Oxidase DsbA Enzyme from Proteus Mirabilis Bound Non-covalently to an Active Site Peptide Ligand

PubMed Central

Kurth, Fabian; Duprez, Wilko; Premkumar, Lakshmanane; Schembri, Mark A.; Fairlie, David P.; Martin, Jennifer L.

2014-01-01

The disulfide bond forming DsbA enzymes and their DsbB interaction partners are attractive targets for development of antivirulence drugs because both are essential for virulence factor assembly in Gram-negative pathogens. Here we characterize PmDsbA from Proteus mirabilis, a bacterial pathogen increasingly associated with multidrug resistance. PmDsbA exhibits the characteristic properties of a DsbA, including an oxidizing potential, destabilizing disulfide, acidic active site cysteine, and dithiol oxidase catalytic activity. We evaluated a peptide, PWATCDS, derived from the partner protein DsbB and showed by thermal shift and isothermal titration calorimetry that it binds to PmDsbA. The crystal structures of PmDsbA, and the active site variant PmDsbAC30S were determined to high resolution. Analysis of these structures allows categorization of PmDsbA into the DsbA class exemplified by the archetypal Escherichia coli DsbA enzyme. We also present a crystal structure of PmDsbAC30S in complex with the peptide PWATCDS. The structure shows that the peptide binds non-covalently to the active site CXXC motif, the cis-Pro loop, and the hydrophobic groove adjacent to the active site of the enzyme. This high-resolution structural data provides a critical advance for future structure-based design of non-covalent peptidomimetic inhibitors. Such inhibitors would represent an entirely new antibacterial class that work by switching off the DSB virulence assembly machinery. PMID:24831013

[Etiological and molecular characteristics of diarrhea caused Proteus mirabilis].

PubMed

Shi, Xiaolu; Hu, Qinghua; Lin, Yiman; Qiu, Yaqun; Li, Yinghui; Jiang, Min; Chen, Qiongcheng

2014-06-01

To analyze the etiological characteristics, virulence genes and plasmids that carrying diarrhea-causing Proteus mirabilis and to assess their relationship with drug resistance and pathogenicity. Proteus mirabilis coming from six different sources (food poisoning, external environment and healthy people) were analyzed biochemically, on related susceptibility and pulsed-field gel electrophoresis (PFGE). Virulence genes were detected by PCR. Plasmids were extracted and sequenced after gel electrophoresis purification. The biochemical characteristics of Proteus mirabilis from different sources seemed basically the same, and each of them showed having common virulence genes, as ureC, rsmA, hpmA and zapA. However, the PFGE patterns and susceptibility of these strains were different, so as the plasmids that they carried. Plasmid that presented in the sequenced strain showed that the 2 683 bp length plasmid encodes qnrD gene was associated with the quinolone resistance. Etiological characteristics and molecular characteristics of Proteus mirabilis gathered from different sources, were analyzed. Results indicated that traditional biochemical analysis and common virulence gene identification might be able to distinguish the strains with different sources. However, PFGE and plasmids analysis could distinguish the sources of strains and to identify those plasmids that commonly carried by the drug-resistant strains. These findings also provided theoretical basis for further study on the nature of resistance and pathogenicity in Proteus mirabilis.

Proteus vulgaris and Proteus mirabilis Decrease Candida albicans Biofilm Formation by Suppressing Morphological Transition to Its Hyphal Form.

PubMed

Lee, Kyoung Ho; Park, Su Jung; Choi, Sun Ju; Park, Joo Young

2017-11-01

Candida albicans (C. albicans) and Proteus species are causative agents in a variety of opportunistic nosocomial infections, and their ability to form biofilms is known to be a virulence factor. In this study, the influence of co-cultivation with Proteus vulgaris (P. vulgaris) and Proteus mirabilis (P. mirabilis) on C. albicans biofilm formation and its underlying mechanisms were examined. XTT reduction assays were adopted to measure biofilm formation, and viable colony counts were performed to quantify yeast growth. Real-time reverse transcriptase polymerase chain reaction was used to evaluate the expression of yeast-specific genes (rhd1 and rbe1), filament formation inhibiting genes (tup1 and nrg1), and hyphae-related genes (als3, ece1, hwp1, and sap5). Candida biofilm formation was markedly inhibited by treatment with either living or heat-killed P. vulgaris and P. mirabilis. Proteus-cultured supernatant also inhibited Candida biofilm formation. Likewise, treatment with live P. vulgaris or P. mirabilis or with Proteus-cultured supernatant decreased expression of hyphae-related C. albicans genes, while the expression of yeast-specific genes and the filament formation inhibiting genes of C. albicans were increased. Heat-killed P. vulgaris and P. mirabilis treatment, however, did not affect the expression of C. albicans morphology-related genes. These results suggest that secretory products from P. vulgaris and P. mirabilis regulate the expression of genes related to morphologic changes in C. albicans such that transition from the yeast form to the hyphal form can be inhibited. © Copyright: Yonsei University College of Medicine 2017

Experimental Proteus mirabilis Burn Surface Infection

DTIC Science & Technology

1982-02-01

Reprinted from the Achie of Surgery ECTE February 1982, Volume 117 Copyright 19 2. American Medical Association MAY 2 8 1982 V0A Experimental Proteus ... mirabilis Burn Surface Infection Albert T. McManus, PhD; Charles G. McLeod, Jr, DVM; Arthur D. Mason, Jr, MD * We established a human burn Isolate of... Proteus mirabills as have examined human burn isolates from the genera an experimental pathogen. Infliction of a nonfatal scald injury Enterobacter

Support Between USAMRDC and USDA for Cooperative Research Under the Ration Sustainment Testing Program.

DTIC Science & Technology

1992-12-31

mirabilis ( proteus ). The tine tests were applied to the ventral forearm of each soldier in the morning, but after blood samples had been taken. After...streptococcus), Mycobacterium tuberculosis (tuberculin, old), Candida albicans (candida), Trichophyton mentagrophytes (trichophyton), and Proteus ...responses to test antigens diphtheria, at the end of the jungle phase, proteus , at the end of both the jungle and desert phases, and tuberculin, at the end of

Proteus - A Free and Open Source Sensor Observation Service (SOS) Client

NASA Astrophysics Data System (ADS)

Henriksson, J.; Satapathy, G.; Bermudez, L. E.

2013-12-01

The Earth's 'electronic skin' is becoming ever more sophisticated with a growing number of sensors measuring everything from seawater salinity levels to atmospheric pressure. To further the scientific application of this data collection effort, it is important to make the data easily available to anyone who wants to use it. Making Earth Science data readily available will allow the data to be used in new and potentially groundbreaking ways. The US National Science and Technology Council made this clear in its most recent National Strategy for Civil Earth Observations report, when it remarked that Earth observations 'are often found to be useful for additional purposes not foreseen during the development of the observation system'. On the road to this goal the Open Geospatial Consortium (OGC) is defining uniform data formats and service interfaces to facilitate the discovery and access of sensor data. This is being done through the Sensor Web Enablement (SWE) stack of standards, which include the Sensor Observation Service (SOS), Sensor Model Language (SensorML), Observations & Measurements (O&M) and Catalog Service for the Web (CSW). End-users do not have to use these standards directly, but can use smart tools that leverage and implement them. We have developed such a tool named Proteus. Proteus is an open-source sensor data discovery client. The goal of Proteus is to be a general-purpose client that can be used by anyone for discovering and accessing sensor data via OGC-based services. Proteus is a desktop client and supports a straightforward workflow for finding sensor data. The workflow takes the user through the process of selecting appropriate services, bounding boxes, observed properties, time periods and other search facets. NASA World Wind is used to display the matching sensor offerings on a map. Data from any sensor offering can be previewed in a time series. The user can download data from a single sensor offering, or download data in bulk from all matching sensor offerings. Proteus leverages NASA World Wind's WMS capabilities and allow overlaying sensor offerings on top of any map. Specific search criteria (i.e. user discoveries) can be saved and later restored. Proteus is supports two user types: 1) the researcher/scientist interested in discovering and downloading specific sensor data as input to research processes, and 2) the data manager responsible for maintaining sensor data services (e.g. SOSs) and wants to ensure proper data and metadata delivery, verify sensor data, and receive sensor data alerts. Proteus has a Web-based companion product named the Community Hub that is used to generate sensor data alerts. Alerts can be received via an RSS feed, viewed in a Web browser or displayed directly in Proteus via a Web-based API. To advance the vision of making Earth Science data easily discoverable and accessible to end-users, professional or laymen, Proteus is available as open-source on GitHub (https://github.com/intelligentautomation/proteus).

Validation and optimization of the Ion Torrent S5 XL sequencer and Oncomine workflow for BRCA1 and BRCA2 genetic testing.

PubMed

Shin, Saeam; Kim, Yoonjung; Chul Oh, Seoung; Yu, Nae; Lee, Seung-Tae; Rak Choi, Jong; Lee, Kyung-A

2017-05-23

In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA). All expected 681 single nucleotide variants, 15 small indels, and three copy number variants were correctly called, except one common variant adjacent to a rare variant on the primer-binding site. The sensitivity, specificity, false positive rate, and accuracy for detection of single nucleotide variant and small indels of S5 XL sequencing were 99.85%, 100%, 0%, and 99.99% for the Torrent Variant Caller and 99.85%, 99.99%, 0.14%, and 99.99% for NextGENe, respectively. The reproducibility of variant calling was 100%, and the precision of variant frequency also showed good performance with coefficients of variation between 0.32 and 5.29%. We obtained highly accurate data through uniform and sufficient coverage depth over all target regions and through optimization of the bioinformatics pipeline. We confirmed that our platform is accurate and practical for diagnostic BRCA1/2 testing in a clinical laboratory.

SXT/R391 integrative and conjugative elements in Proteus species reveal abundant genetic diversity and multidrug resistance

PubMed Central

Li, Xinyue; Du, Yu; Du, Pengcheng; Dai, Hang; Fang, Yujie; Li, Zhenpeng; Lv, Na; Zhu, Baoli; Kan, Biao; Wang, Duochun

2016-01-01

SXT/R391 integrative and conjugative elements (ICEs) are self-transmissible mobile genetic elements that are found in most members of Enterobacteriaceae. Here, we determined fifteen SXT/R391 ICEs carried by Proteus isolates from food (4.2%) and diarrhoea patients (17.3%). BLASTn searches against GenBank showed that the fifteen SXT/R391 ICEs were closely related to that from different Enterobacteriaceae species, including Proteus mirabilis. Using core gene phylogenetic analysis, the fifteen SXT/R391 ICEs were grouped into six distinct clusters, including a dominant cluster and three clusters that have not been previously reported in Proteus isolates. The SXT/R391 ICEs shared a common structure with a set of conserved genes, five hotspots and two variable regions, which contained more foreign genes, including drug-resistance genes. Notably, a class A β-lactamase gene was identified in nine SXT/R391 ICEs. Collectively, the ICE-carrying isolates carried resistance genes for 20 tested drugs. Six isolates were resistant to chloramphenicol, kanamycin, streptomycin, trimethoprim-sulfamethoxazole, sulfisoxazole and tetracycline, which are drug resistances commonly encoded by ICEs. Our results demonstrate abundant genetic diversity and multidrug resistance of the SXT/R391 ICEs carried by Proteus isolates, which may have significance for public health. It is therefore necessary to continuously monitor the antimicrobial resistance and related mobile elements among Proteus isolates. PMID:27892525

Reducing false positive incidental findings with ensemble genotyping and logistic regression-based variant filtering methods

PubMed Central

Hwang, Kyu-Baek; Lee, In-Hee; Park, Jin-Ho; Hambuch, Tina; Choi, Yongjoon; Kim, MinHyeok; Lee, Kyungjoon; Song, Taemin; Neu, Matthew B.; Gupta, Neha; Kohane, Isaac S.; Green, Robert C.; Kong, Sek Won

2014-01-01

As whole genome sequencing (WGS) uncovers variants associated with rare and common diseases, an immediate challenge is to minimize false positive findings due to sequencing and variant calling errors. False positives can be reduced by combining results from orthogonal sequencing methods, but costly. Here we present variant filtering approaches using logistic regression (LR) and ensemble genotyping to minimize false positives without sacrificing sensitivity. We evaluated the methods using paired WGS datasets of an extended family prepared using two sequencing platforms and a validated set of variants in NA12878. Using LR or ensemble genotyping based filtering, false negative rates were significantly reduced by 1.1- to 17.8-fold at the same levels of false discovery rates (5.4% for heterozygous and 4.5% for homozygous SNVs; 30.0% for heterozygous and 18.7% for homozygous insertions; 25.2% for heterozygous and 16.6% for homozygous deletions) compared to the filtering based on genotype quality scores. Moreover, ensemble genotyping excluded > 98% (105,080 of 107,167) of false positives while retaining > 95% (897 of 937) of true positives in de novo mutation (DNM) discovery, and performed better than a consensus method using two sequencing platforms. Our proposed methods were effective in prioritizing phenotype-associated variants, and ensemble genotyping would be essential to minimize false positive DNM candidates. PMID:24829188

Chaotic behavior in the locomotion of Amoeba proteus.

PubMed

Miyoshi, H; Kagawa, Y; Tsuchiya, Y

2001-01-01

The locomotion of Amoeba proteus has been investigated by algorithms evaluating correlation dimension and Lyapunov spectrum developed in the field of nonlinear science. It is presumed by these parameters whether the random behavior of the system is stochastic or deterministic. For the analysis of the nonlinear parameters, n-dimensional time-delayed vectors have been reconstructed from a time series of periphery and area of A. proteus images captured with a charge-coupled-device camera, which characterize its random motion. The correlation dimension analyzed has shown the random motion of A. proteus is subjected only to 3-4 macrovariables, though the system is a complex system composed of many degrees of freedom. Furthermore, the analysis of the Lyapunov spectrum has shown its largest exponent takes positive values. These results indicate the random behavior of A. proteus is chaotic and deterministic motion on an attractor with low dimension. It may be important for the elucidation of the cell locomotion to take account of nonlinear interactions among a small number of dynamics such as the sol-gel transformation, the cytoplasmic streaming, and the relating chemical reaction occurring in the cell.

Corot telescope (COROTEL)

NASA Astrophysics Data System (ADS)

Viard, Thierry; Mathieu, Jean-Claude; Fer, Yann; Bouzou, Nathalie; Spalinger, Etienne; Chataigner, Bruno; Bodin, Pierre; Magnan, Alain; Baglin, Annie

2017-11-01

COROTEL is the telescope of the COROT Satellite which aims at measuring stellar flux variations very accurately. To perform this mission, COROTEL has to be very well protected against straylight (from Sun and Earth) and must be very stable with time. Thanks to its high experience in this field, Alcatel Alenia Space has proposed, manufactured and tested an original telescope concept associated with a high baffling performance. Since its delivery to LAM (Laboratoire d'Astrophysique de Marseille, CNRS) the telescope has passed successfully the qualification tests at instrument level performed by CNES. Now, the instrument is mounted on a Proteus platform and should be launched end of 2006. The satellite should bring to scientific community for the first time precious data coming from stars and their possible companions.

The Proteus Navier-Stokes code

NASA Technical Reports Server (NTRS)

Towne, Charles E.; Bui, Trong T.; Cavicchi, Richard H.; Conley, Julianne M.; Molls, Frank B.; Schwab, John R.

1992-01-01

An effort is currently underway at NASA Lewis to develop two- and three-dimensional Navier-Stokes codes, called Proteus, for aerospace propulsion applications. The emphasis in the development of Proteus is not algorithm development or research on numerical methods, but rather the development of the code itself. The objective is to develop codes that are user-oriented, easily-modified, and well-documented. Well-proven, state-of-the-art solution algorithms are being used. Code readability, documentation (both internal and external), and validation are being emphasized. This paper is a status report on the Proteus development effort. The analysis and solution procedure are described briefly, and the various features in the code are summarized. The results from some of the validation cases that have been run are presented for both the two- and three-dimensional codes.

Automated Assessment in Massive Open Online Courses

ERIC Educational Resources Information Center

Ivaniushin, Dmitrii A.; Shtennikov, Dmitrii G.; Efimchick, Eugene A.; Lyamin, Andrey V.

2016-01-01

This paper describes an approach to use automated assessments in online courses. Open edX platform is used as the online courses platform. The new assessment type uses Scilab as learning and solution validation tool. This approach allows to use automated individual variant generation and automated solution checks without involving the course…

FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets

PubMed Central

2013-01-01

Background Characterising genetic diversity through the analysis of massively parallel sequencing (MPS) data offers enormous potential to significantly improve our understanding of the genetic basis for observed phenotypes, including predisposition to and progression of complex human disease. Great challenges remain in resolving genetic variants that are genuine from the millions of artefactual signals. Results FAVR is a suite of new methods designed to work with commonly used MPS analysis pipelines to assist in the resolution of some of the issues related to the analysis of the vast amount of resulting data, with a focus on relatively rare genetic variants. To the best of our knowledge, no equivalent method has previously been described. The most important and novel aspect of FAVR is the use of signatures in comparator sequence alignment files during variant filtering, and annotation of variants potentially shared between individuals. The FAVR methods use these signatures to facilitate filtering of (i) platform and/or mapping-specific artefacts, (ii) common genetic variants, and, where relevant, (iii) artefacts derived from imbalanced paired-end sequencing, as well as annotation of genetic variants based on evidence of co-occurrence in individuals. We applied conventional variant calling applied to whole-exome sequencing datasets, produced using both SOLiD and TruSeq chemistries, with or without downstream processing by FAVR methods. We demonstrate a 3-fold smaller rare single nucleotide variant shortlist with no detected reduction in sensitivity. This analysis included Sanger sequencing of rare variant signals not evident in dbSNP131, assessment of known variant signal preservation, and comparison of observed and expected rare variant numbers across a range of first cousin pairs. The principles described herein were applied in our recent publication identifying XRCC2 as a new breast cancer risk gene and have been made publically available as a suite of software tools. Conclusions FAVR is a platform-agnostic suite of methods that significantly enhances the analysis of large volumes of sequencing data for the study of rare genetic variants and their influence on phenotypes. PMID:23441864

21 CFR 866.3410 - Proteus spp. (Weil-Felix) serological reagents.

Code of Federal Regulations, 2011 CFR

2011-04-01

... fluorescent dye (immunofluorescent reagents), derived from the bacterium Proteus vulgaris used in... (virus-like bacteria) in serum. Test results aid in the diagnosis of diseases caused by bacteria...

21 CFR 866.3410 - Proteus spp. (Weil-Felix) serological reagents.

Code of Federal Regulations, 2010 CFR

2010-04-01

... fluorescent dye (immunofluorescent reagents), derived from the bacterium Proteus vulgaris used in... (virus-like bacteria) in serum. Test results aid in the diagnosis of diseases caused by bacteria...

GenomeVIP: a cloud platform for genomic variant discovery and interpretation

PubMed Central

Mashl, R. Jay; Scott, Adam D.; Huang, Kuan-lin; Wyczalkowski, Matthew A.; Yoon, Christopher J.; Niu, Beifang; DeNardo, Erin; Yellapantula, Venkata D.; Handsaker, Robert E.; Chen, Ken; Koboldt, Daniel C.; Ye, Kai; Fenyö, David; Raphael, Benjamin J.; Wendl, Michael C.; Ding, Li

2017-01-01

Identifying genomic variants is a fundamental first step toward the understanding of the role of inherited and acquired variation in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional “download and analyze” paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis. Here, we introduce the Genome Variant Investigation Platform (GenomeVIP), an open-source framework for performing genomics variant discovery and annotation using cloud- or local high-performance computing infrastructure. GenomeVIP orchestrates the analysis of whole-genome and exome sequence data using a set of robust and popular task-specific tools, including VarScan, GATK, Pindel, BreakDancer, Strelka, and Genome STRiP, through a web interface. GenomeVIP has been used for genomic analysis in large-data projects such as the TCGA PanCanAtlas and in other projects, such as the ICGC Pilots, CPTAC, ICGC-TCGA DREAM Challenges, and the 1000 Genomes SV Project. Here, we demonstrate GenomeVIP's ability to provide high-confidence annotated somatic, germline, and de novo variants of potential biological significance using publicly available data sets. PMID:28522612

Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data

NASA Astrophysics Data System (ADS)

Sandmann, Sarah; de Graaf, Aniek O.; Karimi, Mohsen; van der Reijden, Bert A.; Hellström-Lindberg, Eva; Jansen, Joop H.; Dugas, Martin

2017-02-01

Valid variant calling results are crucial for the use of next-generation sequencing in clinical routine. However, there are numerous variant calling tools that usually differ in algorithms, filtering strategies, recommendations and thus, also in the output. We evaluated eight open-source tools regarding their ability to call single nucleotide variants and short indels with allelic frequencies as low as 1% in non-matched next-generation sequencing data: GATK HaplotypeCaller, Platypus, VarScan, LoFreq, FreeBayes, SNVer, SAMtools and VarDict. We analysed two real datasets from patients with myelodysplastic syndrome, covering 54 Illumina HiSeq samples and 111 Illumina NextSeq samples. Mutations were validated by re-sequencing on the same platform, on a different platform and expert based review. In addition we considered two simulated datasets with varying coverage and error profiles, covering 50 samples each. In all cases an identical target region consisting of 19 genes (42,322 bp) was analysed. Altogether, no tool succeeded in calling all mutations. High sensitivity was always accompanied by low precision. Influence of varying coverages- and background noise on variant calling was generally low. Taking everything into account, VarDict performed best. However, our results indicate that there is a need to improve reproducibility of the results in the context of multithreading.

The Calipso Thermal Control Subsystem

NASA Technical Reports Server (NTRS)

Gasbarre, Joseph F.; Ousley, Wes; Valentini, Marc; Thomas, Jason; Dejoie, Joel

2007-01-01

The Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) is a joint NASA-CNES mission to study the Earth s cloud and aerosol layers. The satellite is composed of a primary payload (built by Ball Aerospace) and a spacecraft platform bus (PROTEUS, built by Alcatel Alenia Space). The thermal control subsystem (TCS) for the CALIPSO satellite is a passive design utilizing radiators, multi-layer insulation (MLI) blankets, and both operational and survival surface heaters. The most temperature sensitive component within the satellite is the laser system. During thermal vacuum testing of the integrated satellite, the laser system s operational heaters were found to be inadequate in maintaining the lasers required set point. In response, a solution utilizing the laser system s survival heaters to augment the operational heaters was developed with collaboration between NASA, CNES, Ball Aerospace, and Alcatel-Alenia. The CALIPSO satellite launched from Vandenberg Air Force Base in California on April 26th, 2006. Evaluation of both the platform and payload thermal control systems show they are performing as expected and maintaining the critical elements of the satellite within acceptable limits.

The CALIPSO Integrated Thermal Control Subsystem

NASA Technical Reports Server (NTRS)

Gasbarre, Joseph F.; Ousley, Wes; Valentini, Marc; Thomas, Jason; Dejoie, Joel

2007-01-01

The Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) is a joint NASA-CNES mission to study the Earth's cloud and aerosol layers. The satellite is composed of a primary payload (built by Ball Aerospace) and a spacecraft platform bus (PROTEUS, built by Alcatel Alenia Space). The thermal control subsystem (TCS) for the CALIPSO satellite is a passive design utilizing radiators, multi-layer insulation (MLI) blankets, and both operational and survival surface heaters. The most temperature sensitive component within the satellite is the laser system. During thermal vacuum testing of the integrated satellite, the laser system's operational heaters were found to be inadequate in maintaining the lasers required set point. In response, a solution utilizing the laser system's survival heaters to augment the operational heaters was developed with collaboration between NASA, CNES, Ball Aerospace, and Alcatel-Alenia. The CALIPSO satellite launched from Vandenberg Air Force Base in California on April 26th, 2006. Evaluation of both the platform and payload thermal control systems show they are performing as expected and maintaining the critical elements of the satellite within acceptable limits.

[Proteus mirabilis septic arthritis].

PubMed

Sbiti, Mohammed; Bouhamidi, Bahia; Louzi, Lhoussaine

2017-01-01

Acute septic arthritis is rare. It is associated with poor prognosis in terms of mortality and morbidity. We report the case of a 61-year old patient with spontaneous Proteus mirabilis septic arthritis. He suffered from complicated diabetes associated with positive blood cultures and synovial fluid cultures. Patient's evolution was favorable thanks to early diagnosis and initiation of adequate antibiotic therapy. Proteus mirabilis septic arthritis is rare. On that basis we conducted a literature review of cases of Proteus mirabilis pyogenic arthritis to highlight the risk factors, pathogenesis, treatment and evolution of these diseases. Diagnosis is commonly based on microbiological analysis, early articular puncture biopsy is performed before the initiation of antibiotic treatment, direct examination, culture and antibiogram which are useful as guidance for antibiotic therapy. Septic arthritis is a diagnostic and therapeutic emergency; early management of this disease allows total healing without after-effects.

The Location GNSS Modules for the Components of Proteus System

NASA Astrophysics Data System (ADS)

Brzostowski, K.; Darakchiev, R.; Foks-Ryznar, A.; Sitek, P.

2012-01-01

The Proteus system - the Integrated Mobile System for Counterterrorism and Rescue Operations is a complex innovative project. To assure the best possible localization of mobile components of the system, many different Global Navigation Satellite System (GNSS) modules were taken into account. In order to chose the best solution many types of tests were done. Full results and conclusions are presented in this paper. The idea of measurements was to test modules in GPS Standard Positioning Service (SPS) with EGNOS system specification according to certain algorithms. The tests had to answer the question: what type of GNSS modules should be used on different components with respect to specific usage of Proteus system. The second goal of tests was to check the solution quality of integrated GNSS/INS (Inertial Navigation System) and its possible usage in some Proteus system components.

Characterisation of the Rac/PAK pathway in Amoeba proteus.

PubMed

Kłopocka, W; Moraczewska, J; Redowicz, M J

2005-04-01

Molecular mechanisms underlying the unique locomotion of the highly motile Amoeba proteus still remain poorly understood. Recently, we have shown that blocking the endogenous amoebal Rac-like protein(s) leads to distinct and irreversible changes in the appearance of these large migrating cells as well as to a significant inhibition of their locomotion. To elucidate the mechanism of the Rac pathway in Amoeba proteus, we tested the effects of blocking the endogenous myosin I heavy chain kinase (MIHCK), one of the Rac effectors in Acanthamoeba castellanii and Dictyostelium discoideum, with anti-MIHCK antibodies in migrating amoebae, as well as the effect of inhibiting Rac and MIHCK on the actin polymerisation process. Antibodies against A. castellanii MIHCK detected an A. proteus protein with a molecular mass (ca. 95 kDa) similar to the A. castellanii kinase. The cellular distribution of MIHCK in A. proteus was very similar to those of Rac-like protein in amoebae and MIHCK in A. castellanii. Amoebae microinjected with anti-MIHCK antibodies moved slower and protruded fewer wide pseudopodia (5-6) than the control cells (9-10), resembling to some extent the phenotype of cells microinjected with anti-Rac antibodies. The in vitro studies indicate that the A. proteus Rac-like protein, but not the MIHCK isoform, is engaged in the regulation of the nucleation step of the actin polymerisation process. These observations suggest that MIHCK may be one of the effectors for Rac in these extremely large cells.

Crystal structure of the dithiol oxidase DsbA enzyme from proteus mirabilis bound non-covalently to an active site peptide ligand.

PubMed

Kurth, Fabian; Duprez, Wilko; Premkumar, Lakshmanane; Schembri, Mark A; Fairlie, David P; Martin, Jennifer L

2014-07-11

The disulfide bond forming DsbA enzymes and their DsbB interaction partners are attractive targets for development of antivirulence drugs because both are essential for virulence factor assembly in Gram-negative pathogens. Here we characterize PmDsbA from Proteus mirabilis, a bacterial pathogen increasingly associated with multidrug resistance. PmDsbA exhibits the characteristic properties of a DsbA, including an oxidizing potential, destabilizing disulfide, acidic active site cysteine, and dithiol oxidase catalytic activity. We evaluated a peptide, PWATCDS, derived from the partner protein DsbB and showed by thermal shift and isothermal titration calorimetry that it binds to PmDsbA. The crystal structures of PmDsbA, and the active site variant PmDsbAC30S were determined to high resolution. Analysis of these structures allows categorization of PmDsbA into the DsbA class exemplified by the archetypal Escherichia coli DsbA enzyme. We also present a crystal structure of PmDsbAC30S in complex with the peptide PWATCDS. The structure shows that the peptide binds non-covalently to the active site CXXC motif, the cis-Pro loop, and the hydrophobic groove adjacent to the active site of the enzyme. This high-resolution structural data provides a critical advance for future structure-based design of non-covalent peptidomimetic inhibitors. Such inhibitors would represent an entirely new antibacterial class that work by switching off the DSB virulence assembly machinery. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.

PubMed

Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

2016-01-01

Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available. We have therefore developed a new pipeline called MutAid to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. It performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid is freely available at https://sourceforge.net/projects/mutaid.

MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics

PubMed Central

Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

2016-01-01

Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available. We have therefore developed a new pipeline called MutAid to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. It performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid is freely available at https://sourceforge.net/projects/mutaid. PMID:26840129

CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.

PubMed

Gai, Xiaowu; Perin, Juan C; Murphy, Kevin; O'Hara, Ryan; D'arcy, Monica; Wenocur, Adam; Xie, Hongbo M; Rappaport, Eric F; Shaikh, Tamim H; White, Peter S

2010-02-04

Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist. We developed a suite of software tools and resources (CNV Workshop) for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV. To our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and is an ideal platform for coordinating multiple associated projects. Available on the web at: http://sourceforge.net/projects/cnv.

New workflow for classification of genetic variants' pathogenicity applied to hereditary recurrent fevers by the International Study Group for Systemic Autoinflammatory Diseases (INSAID).

PubMed

Van Gijn, Marielle E; Ceccherini, Isabella; Shinar, Yael; Carbo, Ellen C; Slofstra, Mariska; Arostegui, Juan I; Sarrabay, Guillaume; Rowczenio, Dorota; Omoyımnı, Ebun; Balci-Peynircioglu, Banu; Hoffman, Hal M; Milhavet, Florian; Swertz, Morris A; Touitou, Isabelle

2018-03-29

Hereditary recurrent fevers (HRFs) are rare inflammatory diseases sharing similar clinical symptoms and effectively treated with anti-inflammatory biological drugs. Accurate diagnosis of HRF relies heavily on genetic testing. This study aimed to obtain an experts' consensus on the clinical significance of gene variants in four well-known HRF genes: MEFV , TNFRSF1A , NLRP3 and MVK . We configured a MOLGENIS web platform to share and analyse pathogenicity classifications of the variants and to manage a consensus-based classification process. Four experts in HRF genetics submitted independent classifications of 858 variants. Classifications were driven to consensus by recruiting four more expert opinions and by targeting discordant classifications in five iterative rounds. Consensus classification was reached for 804/858 variants (94%). None of the unsolved variants (6%) remained with opposite classifications (eg, pathogenic vs benign). New mutational hotspots were found in all genes. We noted a lower pathogenic variant load and a higher fraction of variants with unknown or unsolved clinical significance in the MEFV gene. Applying a consensus-driven process on the pathogenicity assessment of experts yielded rapid classification of almost all variants of four HRF genes. The high-throughput database will profoundly assist clinicians and geneticists in the diagnosis of HRFs. The configured MOLGENIS platform and consensus evolution protocol are usable for assembly of other variant pathogenicity databases. The MOLGENIS software is available for reuse at http://github.com/molgenis/molgenis; the specific HRF configuration is available at http://molgenis.org/said/. The HRF pathogenicity classifications will be published on the INFEVERS database at https://fmf.igh.cnrs.fr/ISSAID/infevers/. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Taxonomic characterisation of Proteus terrae sp. nov., a N2O-producing, nitrate-ammonifying soil bacterium.

PubMed

Behrendt, Undine; Augustin, Jürgen; Spröer, Cathrin; Gelbrecht, Jörg; Schumann, Peter; Ulrich, Andreas

2015-12-01

In the context of studying the influence of N-fertilization on N2 and N2O flux rates in relation to the soil bacterial community composition in fen peat grassland, a group of bacterial strains was isolated that performed dissimilatory nitrate reduction to ammonium and concomitantly produced N2O. The amount of nitrous oxide produced was influenced by the C/N ratio of the medium. The potential to generate nitrous oxide was increased by higher availability of nitrate-N. Phylogenetic analysis based on the 16S rRNA and the rpoB gene sequences demonstrated that the investigated isolates belong to the genus Proteus, showing high similarity with the respective type strains of Proteus vulgaris and Proteus penneri. DNA-DNA hybridization studies revealed differences at the species level. These differences were substantiated by MALDI-TOF MS analysis and several distinct physiological characteristics. On the basis of these results, it was concluded that the soil isolates represent a novel species for which the name Proteus terrae sp. nov. (type strain N5/687(T) =DSM 29910(T) =LMG 28659(T)) is proposed.

Viper Plague Project

DTIC Science & Technology

2009-07-01

labeled with the conjugated Proteus antibody, 40x………………………………………………………………………………………………………………………………………….……18 Figure 10i, 10j. Staphylococcus aureus ...Figure 10i, 10j. Staphylococcus aureus and Streptococcus pyogenes, (gram positive), labeled with the conjugated Proteus antibody, 40x...15 10. Proteus OX19 Aptamer

Antimicrobial activity Study of triclosan-loaded WBPU on Proteus mirabilis in vitro.

PubMed

Tian, Ye; Jian, Zhongyu; Wang, Jianzhong; He, Wei; Liu, Qinyu; Wang, Kunjie; Li, Hong; Tan, Hong

2017-04-01

To evaluate the antimicrobial activity study of triclosan-loaded waterborne polyurethanes (WBPU) on Proteus mirabilis in vitro. Inhibition zone assays on petri plates with triclosan-loaded WBPU samples were used to test its antimicrobial activity on Proteus mirabilis. Models of the catheterized bladder supplied with artificial urine infected with Proteus mirabilis were employed to confirm the antimicrobial activity of triclosan-loaded WBPU. Bacteria colony counting, pH of the residual urine at each time point and catheter blockage time were recorded. Confocal laser scanning microscopy, scanning electron microscopy and encrustation deposits dry weighing were used for evaluating the biofilm formation. Inhibition zones formed in the triclosan-loaded WBPU groups in a dose-response manner (the radius for samples with 1, 0.1 and 0.01 mg triclosan were 9.93 ± 1.08, 6.07 ± 0.54 and 2.47 ± 0.25 mm, P < 0.001). The bacterial growth in the triclosan group was markedly inhibited, which was almost undetectable after 12 h of bladder running. Residual urine pH in the control group increased significantly in comparison with the triclosan group (9.50 ± 0.04 vs. 6.17 ± 0.01 at 24 h, P < 0.001). The presence of triclosan-loaded WBPU decreased catheter encrustations and markedly postponed the catheter blockage time, as well as suppressed the Proteus mirabilis biofilm formation (33.9 ± 13.9 mg vs. 1.4 ± 1.5 mg, P = 0.016). Triclosan-loaded WBPU significantly inhibited Proteus mirabilis' growth and biofilm formation, indicating the promising antibacterial effects on Proteus mirabilis in vitro. Further efforts are under way that involves coating the material onto the urinary catheters and in vivo studies.

Chemometric analysis of attenuated total reflectance infrared spectra of Proteus mirabilis strains with defined structures of LPS.

PubMed

Zarnowiec, Paulina; Mizera, Andrzej; Chrapek, Magdalena; Urbaniak, Mariusz; Kaca, Wieslaw

2016-07-01

Proteus spp. strains are some of the most important pathogens associated with complicated urinary tract infections and bacteremia affecting patients with immunodeficiency and long-term urinary catheterization. For epidemiological purposes, various molecular typing methods have been developed for this pathogen. However, these methods are labor intensive and time consuming. We evaluated a new method of differentiation between strains. A collection of Proteus spp. strains was analyzed by attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy in the mid-infrared region. ATR FT-IR spectroscopy used in conjunction with a diamond ATR accessory directly produced the biochemical profile of the surface chemistry of bacteria. We conclude that a combination of ATR FT-IR spectroscopy and mathematical modeling provides a fast and reliable alternative for discrimination between Proteus isolates, contributing to epidemiological research. © The Author(s) 2016.

Effects of ceftazidime and ciprofloxacin on biofilm formation in Proteus mirabilis rods.

PubMed

Kwiecińska-Piróg, Joanna; Bogiel, Tomasz; Gospodarek, Eugenia

2013-10-01

Proteus mirabilis rods are one of the most commonly isolated species of the Proteus genus from human infections, mainly those from the urinary tract and wounds. They are often related to biofilm structure formation. The bacterial cells of the biofilm are less susceptible to routinely used antimicrobials, making the treatment more difficult. The aim of this study was to evaluate quantitatively the influence of ceftazidime and ciprofloxacin on biofilm formation on the polyvinyl chloride surface by 42 P. mirabilis strains isolated from urine, purulence, wound swab and bedsore samples. It has been shown that ceftazidime and ciprofloxacin at concentrations equal to 1/4, 1/2 and 1 times their MIC values for particular Proteus spp. strains decrease their ability to form biofilms. Moreover, ciprofloxacin at concentrations equal to 1/4, 1/2 and 1 times their MIC values for particular P. mirabilis strains reduces biofilm formation more efficiently than ceftazidime at the corresponding concentration values.

[Sensitivity of clinical Proteus strains to antibiotics and their combinations].

PubMed

Sheina, E P; Arutcheva, A A

1978-05-01

In 1976 isolation of Proteus from wounds of patients with various purulent processes amounted to 14.5 per cent. Serotypes 0-10, 0-3 and H-3 predominated among the isolates. Sensitivity of 35 clinical strains of Proteus to 10 antibiotics, furagin and nevigramone was studied by the method of serial dilutions in liquid media. All the isolates were highly resistant to the antibiotics except gentamicin, furagin and nevigramone, the MIC of which for most of the strains was 3.12, 1.6-3.12 and 6.25-12.5 gamma/ml, respectively. The effect of 14 combinations of chemotherapeutics was also studied. The combinations of gentamicin with carbenicillin, gentamicin with ampicillin and monomycin with ampicillin proved to be most effective against the Proteus strains tested. The following combinations may be of practical value: monomycin + carbenicillin, kanamycin + ampicillin, kanamycin + carbenicillin, ampicillin + furagin, gentamicin + nevigramone. The combinations of carbenicillin with furagin and gentamicin with furagin were also rational.

Proteus mirabilis inhibits cancer growth and pulmonary metastasis in a mouse breast cancer model

PubMed Central

Zhang, Hong; Diao, Hongxiu; Jia, Lixin; Yuan, Yujing; Thamm, Douglas H.; Wang, Huanan; Jin, Yipeng; Pei, Shimin; Zhou, Bin; Yu, Fang; Zhao, Linna; Cheng, Nan; Du, Hongchao; Huang, Ying; Lin, Degui

2017-01-01

A variety of bacteria have been used as agents and vectors for antineoplastic therapy. A series of mechanisms, including native bacterial toxicity, sensitization of the immune system and competition for nutrients, may contribute to antitumor effects. However, the antitumor effects of Proteus species have been minimally studied, and it is not clear if bacteria can alter tumor hypoxia as a component of their antineoplastic effect. In the present study, Proteus mirabilis bacteria were evaluated for the ability to proliferate and accumulate in murine tumors after intravenous injection. To further investigate the efficacy and safety of bacterial injection, mice bearing 4T1 tumors were treated with an intravenous dose of 5×107 CFU Proteus mirabilis bacteria via the tail vein weekly for three treatments. Histopathology, immunohistochemistry (IHC) and western analysis were then performed on excised tumors. The results suggested Proteus mirabilis localized preferentially to tumor tissues and remarkably suppressed the growth of primary breast cancer and pulmonary metastasis in murine 4T1 models. Results showed that the expression of NKp46 and CD11c was significantly increased after bacteria treatment. Furthermore, tumor expression of carbonic anhydrase IX (CA IX) and hypoxia inducible factor-1a (HIF-1a), surrogates for hypoxia, was significantly lower in the treated group than the control group mice as assessed by IHC and western analysis. These findings demonstrated that Proteus mirabilis may a promising bacterial strain for used against primary tumor growth and pulmonary metastasis, and the immune system and reduction of tumor hypoxia may contribute to the antineoplastic and antimetastatic effects observed. PMID:29206859

Proteus mirabilis inhibits cancer growth and pulmonary metastasis in a mouse breast cancer model.

PubMed

Zhang, Hong; Diao, Hongxiu; Jia, Lixin; Yuan, Yujing; Thamm, Douglas H; Wang, Huanan; Jin, Yipeng; Pei, Shimin; Zhou, Bin; Yu, Fang; Zhao, Linna; Cheng, Nan; Du, Hongchao; Huang, Ying; Zhang, Di; Lin, Degui

2017-01-01

A variety of bacteria have been used as agents and vectors for antineoplastic therapy. A series of mechanisms, including native bacterial toxicity, sensitization of the immune system and competition for nutrients, may contribute to antitumor effects. However, the antitumor effects of Proteus species have been minimally studied, and it is not clear if bacteria can alter tumor hypoxia as a component of their antineoplastic effect. In the present study, Proteus mirabilis bacteria were evaluated for the ability to proliferate and accumulate in murine tumors after intravenous injection. To further investigate the efficacy and safety of bacterial injection, mice bearing 4T1 tumors were treated with an intravenous dose of 5×107 CFU Proteus mirabilis bacteria via the tail vein weekly for three treatments. Histopathology, immunohistochemistry (IHC) and western analysis were then performed on excised tumors. The results suggested Proteus mirabilis localized preferentially to tumor tissues and remarkably suppressed the growth of primary breast cancer and pulmonary metastasis in murine 4T1 models. Results showed that the expression of NKp46 and CD11c was significantly increased after bacteria treatment. Furthermore, tumor expression of carbonic anhydrase IX (CA IX) and hypoxia inducible factor-1a (HIF-1a), surrogates for hypoxia, was significantly lower in the treated group than the control group mice as assessed by IHC and western analysis. These findings demonstrated that Proteus mirabilis may a promising bacterial strain for used against primary tumor growth and pulmonary metastasis, and the immune system and reduction of tumor hypoxia may contribute to the antineoplastic and antimetastatic effects observed.

ERAST Program Proteus Aircraft in Flight

NASA Image and Video Library

1999-07-26

The unusual design of the Proteus high-altitude aircraft, incorporating a gull-wing shape for its main wing and a long, slender forward canard, is clearly visible in this view of the aircraft in flight over the Mojave Desert in California.

Systematic comparison of variant calling pipelines using gold standard personal exome variants

PubMed Central

Hwang, Sohyun; Kim, Eiru; Lee, Insuk; Marcotte, Edward M.

2015-01-01

The success of clinical genomics using next generation sequencing (NGS) requires the accurate and consistent identification of personal genome variants. Assorted variant calling methods have been developed, which show low concordance between their calls. Hence, a systematic comparison of the variant callers could give important guidance to NGS-based clinical genomics. Recently, a set of high-confident variant calls for one individual (NA12878) has been published by the Genome in a Bottle (GIAB) consortium, enabling performance benchmarking of different variant calling pipelines. Based on the gold standard reference variant calls from GIAB, we compared the performance of thirteen variant calling pipelines, testing combinations of three read aligners—BWA-MEM, Bowtie2, and Novoalign—and four variant callers—Genome Analysis Tool Kit HaplotypeCaller (GATK-HC), Samtools mpileup, Freebayes and Ion Proton Variant Caller (TVC), for twelve data sets for the NA12878 genome sequenced by different platforms including Illumina2000, Illumina2500, and Ion Proton, with various exome capture systems and exome coverage. We observed different biases toward specific types of SNP genotyping errors by the different variant callers. The results of our study provide useful guidelines for reliable variant identification from deep sequencing of personal genomes. PMID:26639839

β-lactamases produced by amoxicillin-clavulanate-resistant enterobacteria isolated in Buenos Aires, Argentina: a new blaTEM gene.

PubMed

Di Conza, José A; Badaracco, Alejandra; Ayala, Juan; Rodríguez, Cynthia; Famiglietti, Angela; Gutkind, Gabriel O

2014-01-01

Resistance to β-lactam/β-lactamase inhibitors in enterobacteria is a growing problem that has not been intensively studied in Argentina. In the present work, 54/843 enterobacteria collected in a teaching hospital of Buenos Aires city were ampicillin-sulbactam-resistant isolates remaining susceptible to second- and third-generation cephalosporins. The enzymatic mechanisms present in the isolates, which were also amoxicillin-clavulanic acid (AMC)-resistant (18/54) were herein analyzed. Sequencing revealed two different variants of blaTEM-1, being blaTEM-1b the most frequently detected allelle (10 Escherichia coli, 3 Klebsiella pneumoniae, 2 Proteus mirabilis and 1 Raoultella terrigena) followed by blaTEM-1a (1 K. pneumoniae). Amoxicillin-clavulanate resistance seems to be mainly associated with TEM-1 overproduction (mostly in E. coli) or co-expressed with OXA-2-like and/or SHV β-lactamases (K. pneumoniae and P. mirabilis). A new blaTEM variant (TEM-163) was described in an E. coli strain having an AMC MIC value of 16/8μg/ml. TEM-163 contains Arg275Gln and His289Leu amino acid substitutions. On the basis of the high specific activity and low IC50 for clavulanic acid observed, the resistance pattern seems to be due to overproduction of the new variant of broad spectrum β-lactamase rather than to an inhibitor-resistant TEM (IRT)-like behavior. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España. All rights reserved.

XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets.

PubMed

Yu, Yao; Hu, Hao; Bohlender, Ryan J; Hu, Fulan; Chen, Jiun-Sheng; Holt, Carson; Fowler, Jerry; Guthery, Stephen L; Scheet, Paul; Hildebrandt, Michelle A T; Yandell, Mark; Huff, Chad D

2018-04-06

High-throughput sequencing data are increasingly being made available to the research community for secondary analyses, providing new opportunities for large-scale association studies. However, heterogeneity in target capture and sequencing technologies often introduce strong technological stratification biases that overwhelm subtle signals of association in studies of complex traits. Here, we introduce the Cross-Platform Association Toolkit, XPAT, which provides a suite of tools designed to support and conduct large-scale association studies with heterogeneous sequencing datasets. XPAT includes tools to support cross-platform aware variant calling, quality control filtering, gene-based association testing and rare variant effect size estimation. To evaluate the performance of XPAT, we conducted case-control association studies for three diseases, including 783 breast cancer cases, 272 ovarian cancer cases, 205 Crohn disease cases and 3507 shared controls (including 1722 females) using sequencing data from multiple sources. XPAT greatly reduced Type I error inflation in the case-control analyses, while replicating many previously identified disease-gene associations. We also show that association tests conducted with XPAT using cross-platform data have comparable performance to tests using matched platform data. XPAT enables new association studies that combine existing sequencing datasets to identify genetic loci associated with common diseases and other complex traits.

The Finnish disease heritage database (FinDis) update-a database for the genes mutated in the Finnish disease heritage brought to the next-generation sequencing era.

PubMed

Polvi, Anne; Linturi, Henna; Varilo, Teppo; Anttonen, Anna-Kaisa; Byrne, Myles; Fokkema, Ivo F A C; Almusa, Henrikki; Metzidis, Anthony; Avela, Kristiina; Aula, Pertti; Kestilä, Marjo; Muilu, Juha

2013-11-01

The Finnish Disease Heritage Database (FinDis) (http://findis.org) was originally published in 2004 as a centralized information resource for rare monogenic diseases enriched in the Finnish population. The FinDis database originally contained 405 causative variants for 30 diseases. At the time, the FinDis database was a comprehensive collection of data, but since 1994, a large amount of new information has emerged, making the necessity to update the database evident. We collected information and updated the database to contain genes and causative variants for 35 diseases, including six more genes and more than 1,400 additional disease-causing variants. Information for causative variants for each gene is collected under the LOVD 3.0 platform, enabling easy updating. The FinDis portal provides a centralized resource and user interface to link information on each disease and gene with variant data in the LOVD 3.0 platform. The software written to achieve this has been open-sourced and made available on GitHub (http://github.com/findis-db), allowing biomedical institutions in other countries to present their national data in a similar way, and to both contribute to, and benefit from, standardized variation data. The updated FinDis portal provides a unique resource to assist patient diagnosis, research, and the development of new cures. © 2013 WILEY PERIODICALS, INC.

Proteus syndrome*

PubMed Central

Rocha, Ritha de Cássia Capelato; Estrella, Mariani Paulino Soriano; do Amaral, Danielle Mechereffe; Barbosa, Angela Marques; de Abreu, Marilda Aparecida Milanez Morgado

2017-01-01

Proteus syndrome is a rare syndrome characterized by disproportionate overgrowth of limbs, multiple hamartomas, and vascular malformations. The cerebriform connective tissue nevi, also called cerebriform plantar hyperplasia, are present in most patients, and is the main characteristic of the syndrome. If present, even alone, they can be considered as a pathognomonic sign. This article reports a classic case of Proteus syndrome in a 2-year-old male patient who began to show a discrete asymmetry of the right hemibody in relation to the left one after birth, which increased over the months. He also showed cerebriform plantar hyperplasia and Port-wine stains, among other alterations. PMID:29166516

The antigens contributing to the serological cross-reactions of Proteus antisera with Klebsiella representatives.

PubMed

Palusiak, Agata

2015-03-01

Proteus sp. and Klebsiella sp. mainly cause infections of the urinary and respiratory tracts or wounds in humans. The representatives of both genera produce virulence factors like lipopolysaccharide (LPS) or outer membrane proteins (OMPs) having much in common in the structures and/or functions. To check how far this similarity is revealed in the serological cross-reactivity, the bacterial masses of 24 tested Klebsiella sp. strains were tested in ELISA with polyclonal rabbit antisera specific to the representatives of 79 Proteus O serogroups. The strongest reacting systems were selected to Western blot, where the majority of Klebsiella masses reacted in a way characteristic for electrophoretic patterns of proteins. The strongest reactions were obtained for proteins of near 67 and 40 kDa and 12.5 kDa. Mass spectrometry analysis of the proteins samples of one Proteus sp. and one Klebsiella sp. strain showed the GroEL like protein of a sequence GI number 2980926 to be similar for both strains. In Western blot some Klebsiella sp. masses reacted similarly to the homologous Proteus LPSs. The LPS contribution in the observed reactions of the high molecular-mass LPS species was confirmed for Klebsiella oxytoca 0.062. Copyright © 2014 Elsevier Ltd. All rights reserved.

Histopathological features of Proteus syndrome.

PubMed

Hoey, S E H; Eastwood, D; Monsell, F; Kangesu, L; Harper, J I; Sebire, N J

2008-05-01

Proteus syndrome is a rare, sporadic overgrowth disorder for which the underlying genetic defect remains unknown. Although the clinical course is well-described there is no systematic histopathological description of the lesional pathology. To describe the histopathological features encountered in a series of patients with Proteus syndrome from a single centre. Patients with Proteus syndrome who had undergone therapeutic surgical resection or biopsy were identified from a database and the histopathological findings were reviewed, with particular regard to descriptive features of the underlying tissue abnormality. There were 18 surgical specimens from nine patients, median age 4 years (range 1-9), classified into four main categories: soft-tissue swellings (lipomatous lesions), vascular anomalies (vascular malformation and haemangioma), macrodactyly (hamartomatous overgrowth) and others (sebaceous naevus and nonspecific features). In all cases, the clinical features of overgrowth were due to increased amounts of disorganized tissue, indicating a hamartomatous-type defect in which normal tissue constituents were present, but with an abnormal distribution and architecture. Vascular malformations represented a prominent category of lesions, accounting for 50% of the specimens, predominantly comprising lymphatic and lymphovascular malformations. No malignancy or cytological atypia was identified in any case. The histopathological features of lesions resected from children with Proteus syndrome predominantly include hamartomatous mixed connective tissue lesions, benign neoplasms such as lipomata, and lymphatic-rich vascular malformations.

Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies.

PubMed

Damiati, E; Borsani, G; Giacopuzzi, Edoardo

2016-05-01

The Ion Proton platform allows to perform whole exome sequencing (WES) at low cost, providing rapid turnaround time and great flexibility. Products for WES on Ion Proton system include the AmpliSeq Exome kit and the recently introduced HiQ sequencing chemistry. Here, we used gold standard variants from GIAB consortium to assess the performances in variants identification, characterize the erroneous calls and develop a filtering strategy to reduce false positives. The AmpliSeq Exome kit captures a large fraction of bases (>94 %) in human CDS, ClinVar genes and ACMG genes, but with 2,041 (7 %), 449 (13 %) and 11 (19 %) genes not fully represented, respectively. Overall, 515 protein coding genes contain hard-to-sequence regions, including 90 genes from ClinVar. Performance in variants detection was maximum at mean coverage >120×, while at 90× and 70× we measured a loss of variants of 3.2 and 4.5 %, respectively. WES using HiQ chemistry showed ~71/97.5 % sensitivity, ~37/2 % FDR and ~0.66/0.98 F1 score for indels and SNPs, respectively. The proposed low, medium or high-stringency filters reduced the amount of false positives by 10.2, 21.2 and 40.4 % for indels and 21.2, 41.9 and 68.2 % for SNP, respectively. Amplicon-based WES on Ion Proton platform using HiQ chemistry emerged as a competitive approach, with improved accuracy in variants identification. False-positive variants remain an issue for the Ion Torrent technology, but our filtering strategy can be applied to reduce erroneous variants.

Concept Study on a Flexible Standard Bus for Small Scientific Satellites

NASA Astrophysics Data System (ADS)

Fukuda, Seisuke; Sawai, Shujiro; Sakai, Shin-Ichiro; Saito, Hirobumi; Tohma, Takayuki; Takahashi, Junko; Toriumi, Tsuyoshi; Kitade, Kenji

In this paper, a new standard bus system for a series of small scientific satellites in the Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (ISAS/JAXA) is described. Since each mission proposed for the series has a wide variety of requirements, a lot of efforts are needed to enhance flexibility of the standard bus. Some concepts from different viewpoints are proposed. First, standardization layers concerning satellite configuration, instruments, interfaces, and design methods are defined respectively. Methods of product platform engineering, which classify specifications of the bus system into a core platform, alternative variants, and selectable variants, are also investigated in order to realize a semi-custom-made bus. Furthermore, a tradeoff between integration and modularization architecture is fully considered.

DMET-Miner: Efficient discovery of association rules from pharmacogenomic data.

PubMed

Agapito, Giuseppe; Guzzi, Pietro H; Cannataro, Mario

2015-08-01

Microarray platforms enable the investigation of allelic variants that may be correlated to phenotypes. Among those, the Affymetrix DMET (Drug Metabolism Enzymes and Transporters) platform enables the simultaneous investigation of all the genes that are related to drug absorption, distribution, metabolism and excretion (ADME). Although recent studies demonstrated the effectiveness of the use of DMET data for studying drug response or toxicity in clinical studies, there is a lack of tools for the automatic analysis of DMET data. In a previous work we developed DMET-Analyzer, a methodology and a supporting platform able to automatize the statistical study of allelic variants, that has been validated in several clinical studies. Although DMET-Analyzer is able to correlate a single variant for each probe (related to a portion of a gene) through the use of the Fisher test, it is unable to discover multiple associations among allelic variants, due to its underlying statistic analysis strategy that focuses on a single variant for each time. To overcome those limitations, here we propose a new analysis methodology for DMET data based on Association Rules mining, and an efficient implementation of this methodology, named DMET-Miner. DMET-Miner extends the DMET-Analyzer tool with data mining capabilities and correlates the presence of a set of allelic variants with the conditions of patient's samples by exploiting association rules. To face the high number of frequent itemsets generated when considering large clinical studies based on DMET data, DMET-Miner uses an efficient data structure and implements an optimized search strategy that reduces the search space and the execution time. Preliminary experiments on synthetic DMET datasets, show how DMET-Miner outperforms off-the-shelf data mining suites such as the FP-Growth algorithms available in Weka and RapidMiner. To demonstrate the biological relevance of the extracted association rules and the effectiveness of the proposed approach from a medical point of view, some preliminary studies on a real clinical dataset are currently under medical investigation. Copyright © 2015 Elsevier Inc. All rights reserved.

Cooperative Collision Avoidance Step 1 - Technology Demonstration Flight Test Report. Revision 1

NASA Technical Reports Server (NTRS)

Trongale, Nicholas A.

2006-01-01

The National Aeronautics and Space Administration (NASA) Access 5 Project Office sponsored a cooperative collision avoidance flight demonstration program for unmanned aircraft systems (UAS). This flight test was accomplished between September 21st and September 27th 2005 from the Mojave Airport, Mojave, California. The objective of these flights was to collect data for the Access 5 Cooperative Collision Avoidance (CCA) Work Package simulation effort, i.e., to gather data under select conditions to allow validation of the CCA simulation. Subsequent simulation to be verified were: Demonstrate the ability to detect cooperative traffic and provide situational awareness to the ROA pilot; Demonstrate the ability to track the detected cooperative traffic and provide position information to the ROA pilot; Demonstrate the ability to determine collision potential with detected cooperative traffic and provide notification to the ROA pilot; Demonstrate that the CCA subsystem provides information in sufficient time for the ROA pilot to initiate an evasive maneuver to avoid collision; Demonstrate an evasive maneuver that avoids collision with the threat aircraft; and lastly, Demonstrate the ability to assess the adequacy of the maneuver and determine that the collision potential has been avoided. The Scaled Composites, LLC Proteus Optionally Piloted Vehicle (OPV) was chosen as the test platform. Proteus was manned by two on-board pilots but was also capable of being controlled from an Air Vehicle Control Station (AVCS) located on the ground. For this demonstration, Proteus was equipped with cooperative collision sensors and the required hardware and software to place the data on the downlink. Prior to the flight phase, a detailed set of flight test scenarios were developed to address the flight test objectives. Two cooperative collision avoidance sensors were utilized for detecting aircraft in the evaluation: Traffic Alert and Collision Avoidance System-II (TCAS-II) and Automatic Dependent Surveillance Broadcast (ADS-B). A single intruder aircraft was used during all the flight testing, a NASA Gulfstream III (G-III). During the course of the testing, six geometrically different near-collision scenarios were evaluated. These six scenarios were each tested using various combinations of sensors and collision avoidance software. Of the 54 planned test points 49 were accomplished successfully. Proteus flew a total of 21.5 hours during the testing and the G-III flew 19.8 hours. The testing fully achieved all flight test objectives. The Flight IPT performed an analysis to determine the accuracy of the simulation model used to predict the location of the host aircraft downstream during an avoidance maneuver. The data collected by this flight program was delivered to the Access 5 Cooperative Collision Avoidance (CCA) Work Package Team who was responsible for reporting on their analysis of this flight data.

Host Defense against Opportunist Microorganisms Following Trauma

DTIC Science & Technology

1991-09-30

Proteus mirabills. No evidence was obtained supporting involvement of lipoxygenase metabolites L. the bactericidal defect of neutrophils or the...burn wound sepsis with P. aeruginosa and Proteus mirabills were investigated [16]. The bacteria were spread over the surface of the burn wound to

Characterization of Proteus mirabilis isolates from broilers

USDA-ARS?s Scientific Manuscript database

Background: Proteus mirabilis is ubiquitous in the environment and is regarded as a part of the normal flora in human gastrointestinal tract. However, this bacterium is also an opportunistic human pathogen that causes urinary tract infections. Recently, this microorganism has been isolated from m...

21 CFR 520.90d - Ampicillin trihydrate for oral suspension.

Code of Federal Regulations, 2011 CFR

2011-04-01

...., Staphylococcus spp., and Streptococcus spp., urinary tract infections (cystitis) due to E. coli, Staphylococcus spp., Streptococcus spp., and Proteus spp.; bacterial gastroenteritis due to E. coli; generalized... (bacterial pneumonia) due to Staphylococcus spp., Streptococcus spp., E. coli, and Proteus spp.; urinary...

21 CFR 520.90d - Ampicillin trihydrate for oral suspension.

Code of Federal Regulations, 2010 CFR

2010-04-01

...., Staphylococcus spp., and Streptococcus spp., urinary tract infections (cystitis) due to E. coli, Staphylococcus spp., Streptococcus spp., and Proteus spp.; bacterial gastroenteritis due to E. coli; generalized... (bacterial pneumonia) due to Staphylococcus spp., Streptococcus spp., E. coli, and Proteus spp.; urinary...

pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data.

PubMed

Beyens, Matthias; Boeckx, Nele; Van Camp, Guy; Op de Beeck, Ken; Vandeweyer, Geert

2017-12-14

Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. However, involved wet-lab procedures may introduce false positives that need to be considered in subsequent data-analysis. No variant filtering rationale addressing amplicon enrichment related systematic errors, in the form of an all-in-one package, exists to our knowledge. We present pyAmpli, a platform independent parallelized Python package that implements an amplicon-based germline and somatic variant filtering strategy for Haloplex data. pyAmpli can filter variants for systematic errors by user pre-defined criteria. We show that pyAmpli significantly increases specificity, without reducing sensitivity, essential for reporting true positive clinical relevant mutations in gene panel data. pyAmpli is an easy-to-use software tool which increases the true positive variant call rate in targeted resequencing data. It specifically reduces errors related to PCR-based enrichment of targeted regions.

Thesaurus of DDC Descriptors

DTIC Science & Technology

1966-06-01

BIRDS BLASTOMYCES BLATTIDAE BOVINES CANDIDA CANNABIS CARNIVORA CATS CEPHALOPODA CEREALS CETACEA CHICKENS CHILDREN CHIMPANZEES CHLORELLA...POLIOMYELITIS VIRUS POX VIRUSES PROTEUS PROTEUS VULGAR1S PROTOZOA PSEUOOMONADACEAE PSEUUOMONADALES PSEUDOMONAS PSEUDOMONAS AEROGINOSA RABIES VIRUS...ISLANUS MARYLAND MASSACHUSETTS MASSACHUSETTS BAY MEDITERRANEAN SEA MEDITERRANEAN SEA ISLANDS MELANESIA MEXICO MEXICO GULF MICHIGAN MICRONESIA

ERAST Program Proteus Aircraft in Flight over the Mojave Desert in California

NASA Image and Video Library

1999-07-26

The unusual design of the Proteus high-altitude aircraft, incorporating a gull-wing shape for its main wing and a long, slender forward canard, is clearly visible in this view of the aircraft in flight over the Mojave Desert in California.

Proteus mirabilis interkingdom swarming signals attract blow flies

USDA-ARS?s Scientific Manuscript database

Flies transport specific bacteria with their larvae which provides a wider range of nutrients for those bacteria. Our hypothesis was that this symbiotic interaction may depend on interkingdom signaling. We obtained Proteus mirabilis from the salivary glands of the blow fly Lucilia sericat. This s...

Isolation, characterization and immunological reaction of proteus mirabilis isolates from broilers

USDA-ARS?s Scientific Manuscript database

Introduction: Proteus mirabilis, which is ubiquitous in the environment, is an opportunistic human pathogen that causes urinary tract infections. Recently, this bacterium has been isolated from many food producing animals, including poultry and its products. Moreover, reports have shown P. mirabi...

Ureases as a target for the treatment of gastric and urinary infections.

PubMed

Follmer, C

2010-05-01

Urease is known to be a major contributor to pathologies induced by Helicobacter pylori and Proteus species. In H pylori, urease allows the bacteria to survive in an acidic gastric environment during colonisation, playing an important role in the pathogenesis of gastric and peptic ulcers. Ureolytic activity also results in the production of ammonia in close proximity to the gastric epithelium, causing cell damage and inflammation. In the case of Proteus species (notably Proteus mirabilis) infection, stones are formed due to the presence of ammonia and carbon dioxide released by urease action. In addition, the ammonia released is able to damage the glycosaminoglycan layer, which protects the urothelial surface against bacterial infection. In this context, the administration of urease inhibitors may be an effective therapy for urease-dependent pathogenic bacteria. This is a review of the role of ureases in H pylori and Proteus species infections, focussing on the biochemical and clinical aspects of the most promising and/or potent urease inhibitors for the treatment of gastric and urinary tract infections.

The surfaces of Larissa and Proteus

NASA Astrophysics Data System (ADS)

Stooke, Philip J.

1994-01-01

Topographic models of Neptune's small inner satellites Larissa and Proteus were derived from the shapes of limbs and terminators in Voyager images, modified locally to accomodate large craters and ridges. The models are presented here in tabular and graphic form, including the first map of Larissa and the first detailed relief map of Proteus. The shape of Larissa is approximated by a triaxial ellipsoid with axes of 208, 192 and 178 km, but is only weakly constrained by the single available view. The volume is estimated to be 3.5 +/- 1.0 x 106cu km. The surface is heavily cratered and may be crossed by one or two poorly seen linear ridges. Proteus is approximated by a triaxial ellipsoid with axes of 424, 390 and 396 km (the latter being the rotation axis dimension). The volume is estimated to be 3.4 +/- 0.4 x 107 cu km. Its surface appears to be very heavily cratered and extensive evidence for linear fractures is observed despite very low image quality.

Proteus syndrome: a case report.

PubMed

Pangkanon, S; Limpongsanurak, W; Sangtawesin, V

2001-05-01

Proteus syndrome is a rare genetic disorder, characterized by partial gigantism of the hands and/or feet, asymmetry of the limbs, plantar hyperplasia, multiple hamartomatous subcutaneous tumors, hyperostoses, and long bone overgrowth. A one day old Thai male infant is reported with macrosomia, hemihypertrophy of the left side of the face and left leg, large feet, macrodactyly of toes, plantar hyperplasia, large subcutaneous mass with a violet-red surface over the left side of the chest wall and a large port-wine stain involving the lateral aspect of the right chest wall. The clinical findings, diagnostic criteria, differential diagnosis, and management of the Proteus syndrome are reviewed.

Infective organisms in the cytoplasm of Amoeba proteus.

PubMed

ROTH, L E; DANIELS, E W

1961-02-01

Evidence from electron and phase microscopy is given which shows that infective organisms are present in the cytoplasm of Amoeba proteus. Vesicles containing living organisms have been observed after repeated washing and starvation of the amebae for a period of 2 weeks. Exposure to gamma-radiation in conjunction with starvation, repeated washing, isolation of single amebae, refeeding with contaminant-free Tetrahymena, and clone selection has produced clones with reduced cytoplasmic infection. These findings are discussed in regard to the autoradiographic studies of other investigators on Amoeba proteus. The controversies over whether DNA and RNA are synthesized in the cytoplasm may be resolved by the finding of cytoplasmic infection.

INFECTIVE ORGANISMS IN THE CYTOPLASM OF AMOEBA PROTEUS

PubMed Central

Roth, L. E.; Daniels, E. W.

1961-01-01

Evidence from electron and phase microscopy is given which shows that infective organisms are present in the cytoplasm of Amoeba proteus. Vesicles containing living organisms have been observed after repeated washing and starvation of the amebae for a period of 2 weeks. Exposure to γ-radiation in conjunction with starvation, repeated washing, isolation of single amebae, refeeding with contaminant-free Tetrahymena, and clone selection has produced clones with reduced cytoplasmic infection. These findings are discussed in regard to the autoradiographic studies of other investigators on Amoeba proteus. The controversies over whether DNA and RNA are synthesized in the cytoplasm may be resolved by the finding of cytoplasmic infection. PMID:13743844

Empowered genome community: leveraging a bioinformatics platform as a citizen-scientist collaboration tool.

PubMed

Wendelsdorf, Katherine; Shah, Sohela

2015-09-01

There is on-going effort in the biomedical research community to leverage Next Generation Sequencing (NGS) technology to identify genetic variants that affect our health. The main challenge facing researchers is getting enough samples from individuals either sick or healthy - to be able to reliably identify the few variants that are causal for a phenotype among all other variants typically seen among individuals. At the same time, more and more individuals are having their genome sequenced either out of curiosity or to identify the cause of an illness. These individuals may benefit from of a way to view and understand their data. QIAGEN's Ingenuity Variant Analysis is an online application that allows users with and without extensive bioinformatics training to incorporate information from published experiments, genetic databases, and a variety of statistical models to identify variants, from a long list of candidates, that are most likely causal for a phenotype as well as annotate variants with what is already known about them in the literature and databases. Ingenuity Variant Analysis is also an information sharing platform where users may exchange samples and analyses. The Empowered Genome Community (EGC) is a new program in which QIAGEN is making this on-line tool freely available to any individual who wishes to analyze their own genetic sequence. EGC members are then able to make their data available to other Ingenuity Variant Analysis users to be used in research. Here we present and describe the Empowered Genome Community in detail. We also present a preliminary, proof-of-concept study that utilizes the 200 genomes currently available through the EGC. The goal of this program is to allow individuals to access and understand their own data as well as facilitate citizen-scientist collaborations that can drive research forward and spur quality scientific dialogue in the general public.

Rare-Variant Association Analysis: Study Designs and Statistical Tests

PubMed Central

Lee, Seunggeung; Abecasis, Gonçalo R.; Boehnke, Michael; Lin, Xihong

2014-01-01

Despite the extensive discovery of trait- and disease-associated common variants, much of the genetic contribution to complex traits remains unexplained. Rare variants can explain additional disease risk or trait variability. An increasing number of studies are underway to identify trait- and disease-associated rare variants. In this review, we provide an overview of statistical issues in rare-variant association studies with a focus on study designs and statistical tests. We present the design and analysis pipeline of rare-variant studies and review cost-effective sequencing designs and genotyping platforms. We compare various gene- or region-based association tests, including burden tests, variance-component tests, and combined omnibus tests, in terms of their assumptions and performance. Also discussed are the related topics of meta-analysis, population-stratification adjustment, genotype imputation, follow-up studies, and heritability due to rare variants. We provide guidelines for analysis and discuss some of the challenges inherent in these studies and future research directions. PMID:24995866

Synthetic extreme environments: overlooked sources of potential biotechnologically relevant microorganisms.

PubMed

Sibanda, Timothy; Selvarajan, Ramganesh; Tekere, Memory

2017-05-01

Synthetic extreme environments like carwash effluent tanks and drains are potential sources of biotechnologically important microorganisms and molecules which have, however, remained unexplored. Using culture- and molecular-based methods, a total of 17 bacterial isolates belonging to the genera Shewanella, Proteus, Paenibacillus, Enterobacter and Citrobacter, Aeromonas, Pseudomonas and Pantoea were identified. Hydrocarbon utilization and enzyme production screening assays showed that Aeromonas sp. CAC11, Paenibacillus sp. CAC12 and Paenibacillus sp. CAC13 and Citrobacter sp. PCW7 were able to degrade benzanthracene, naphthalene and diesel oil, Paenibacillus sp. CAC12 and Paenibacillus sp. CAC13 could produce cellulase enzyme, while Proteus sp. BPS2, Pseudomonas sp. SAS8 and Proteus sp. CAL3 could produce lipase. GC-MS analysis of bacterial secondary metabolites resulted in identification of 107 different compounds produced by Proteus sp. BPS2, Paenibacillus sp. CAC12, Pseudomonas sp. SAS8, Proteus sp. CAL3 and Paenibacillus sp. CAC13. Most of the compounds identified by both GC-MS and LC-MS have previously been determined to have antibacterial, antifungal and/or anticancer properties. Further, microbial metabolites which have previously been known to be produced only by plants or microorganisms found in natural extreme environments were also identified in this study. This research has revealed the immense bioresource potential of microorganisms inhabiting synthetic extreme environments. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Molecular dissection of the interactions of an antitumor interleukin-2-derived mutein on a phage display-based platform.

PubMed

Rojas, Gertrudis; Carmenate, Tania; Leon, Kalet

2015-04-01

A mutein with stronger antitumor activity and lower toxicity than wild-type human interleukin-2 (IL-2) has been recently described. The rationale behind its design was to reinforce the immunostimulatory potential through the introduction of four mutations that would selectively disrupt the interaction with the IL-2 receptor alpha chain (thought to be critical for both IL-2-driven expansion of T regulatory cells and IL-2-mediated toxic effects). Despite the successful results of the mutein in several tumor models, characterization of its interactions was still to be performed. The current work, based on phage display of IL-2-derived variants, showed the individual contribution of each mutation to the impairment of alpha chain binding. A more sensitive assay, based on the ability of phage-displayed IL-2 variants to induce proliferation of the IL-2-dependent CTLL-2 cell line, revealed differences between the mutated variants. The results validated the mutein design, highlighting the importance of the combined effects of the four mutations. The developed phage display-based platform is robust and sensitive, allows a fast comparative evaluation of multiple variants, and could be broadly used to engineer IL-2 and related cytokines, accelerating the development of cytokine-derived therapeutics. Copyright © 2015 John Wiley & Sons, Ltd.

Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism.

PubMed

Archer, John; Weber, Jan; Henry, Kenneth; Winner, Dane; Gibson, Richard; Lee, Lawrence; Paxinos, Ellen; Arts, Eric J; Robertson, David L; Mimms, Larry; Quiñones-Mateu, Miguel E

2012-01-01

HIV-1 coreceptor tropism assays are required to rule out the presence of CXCR4-tropic (non-R5) viruses prior treatment with CCR5 antagonists. Phenotypic (e.g., Trofile™, Monogram Biosciences) and genotypic (e.g., population sequencing linked to bioinformatic algorithms) assays are the most widely used. Although several next-generation sequencing (NGS) platforms are available, to date all published deep sequencing HIV-1 tropism studies have used the 454™ Life Sciences/Roche platform. In this study, HIV-1 co-receptor usage was predicted for twelve patients scheduled to start a maraviroc-based antiretroviral regimen. The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences), Illumina®, and Ion Torrent™ (Life Technologies). Cross-platform variation was evaluated, including number of reads, read length and error rates. HIV-1 tropism was inferred using Geno2Pheno, Web PSSM, and the 11/24/25 rule and compared with Trofile™ and virologic response to antiretroviral therapy. Error rates related to insertions/deletions (indels) and nucleotide substitutions introduced by the four NGS platforms were low compared to the actual HIV-1 sequence variation. Each platform detected all major virus variants within the HIV-1 population with similar frequencies. Identification of non-R5 viruses was comparable among the four platforms, with minor differences attributable to the algorithms used to infer HIV-1 tropism. All NGS platforms showed similar concordance with virologic response to the maraviroc-based regimen (75% to 80% range depending on the algorithm used), compared to Trofile (80%) and population sequencing (70%). In conclusion, all four NGS platforms were able to detect minority non-R5 variants at comparable levels suggesting that any NGS-based method can be used to predict HIV-1 coreceptor usage.

21 CFR 866.3410 - Proteus spp. (Weil-Felix) serological reagents.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Proteus spp. (Weil-Felix) serological reagents. 866.3410 Section 866.3410 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3410...

21 CFR 866.3410 - Proteus spp. (Weil-Felix) serological reagents.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Proteus spp. (Weil-Felix) serological reagents. 866.3410 Section 866.3410 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3410...

21 CFR 866.3410 - Proteus spp. (Weil-Felix) serological reagents.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Proteus spp. (Weil-Felix) serological reagents. 866.3410 Section 866.3410 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3410...

Isolation and partial characterization of two plasmid deoxyribonucleic acids from endosymbiotic bacteria of Amoeba proteus.

PubMed Central

Han, J H; Jeon, K W

1980-01-01

Obligatory endosymbiotic bacteria in a strain of Amoeba proteus were found to harbor two distinct species of plasmid, pHJ11 and pHJ12. Their molecular weights were 39 x 10(6) and 14 x 10(6), respectively. Images PMID:7364732

First Earth-based observations of Neptune's satellite Proteus

NASA Astrophysics Data System (ADS)

Colas, F.; Buil, C.

1992-08-01

Proteus (Neptune III) was discovered from Voyager Spacecraft images in 1989 (Smith, 1989). It was never observed from ground-based observatories because of its magnitude (m = 20.3) and closeness to Neptune (maximum elongation = 6 arcsec). In October 1991, we used the 2.2 m telescope at the European Southern Observatory (La Silla, Chile) to look for it. The observation success is mainly due to the use of an anti blooming CCD and to good seeing conditions (less than 1 arcsec). We give the differential positions of Proteus referred to Neptune and we compare with theoretical positions issued from Voyager's data (Owen et al., 1991). We found that the rms orbital residual was about 0.1 arcsec.

An automated microfluidic DNA microarray platform for genetic variant detection in inherited arrhythmic diseases.

PubMed

Huang, Shu-Hong; Chang, Yu-Shin; Juang, Jyh-Ming Jimmy; Chang, Kai-Wei; Tsai, Mong-Hsun; Lu, Tzu-Pin; Lai, Liang-Chuan; Chuang, Eric Y; Huang, Nien-Tsu

2018-03-12

In this study, we developed an automated microfluidic DNA microarray (AMDM) platform for point mutation detection of genetic variants in inherited arrhythmic diseases. The platform allows for automated and programmable reagent sequencing under precise conditions of hybridization flow and temperature control. It is composed of a commercial microfluidic control system, a microfluidic microarray device, and a temperature control unit. The automated and rapid hybridization process can be performed in the AMDM platform using Cy3 labeled oligonucleotide exons of SCN5A genetic DNA, which produces proteins associated with sodium channels abundant in the heart (cardiac) muscle cells. We then introduce a graphene oxide (GO)-assisted DNA microarray hybridization protocol to enable point mutation detection. In this protocol, a GO solution is added after the staining step to quench dyes bound to single-stranded DNA or non-perfectly matched DNA, which can improve point mutation specificity. As proof-of-concept we extracted the wild-type and mutant of exon 12 and exon 17 of SCN5A genetic DNA from patients with long QT syndrome or Brugada syndrome by touchdown PCR and performed a successful point mutation discrimination in the AMDM platform. Overall, the AMDM platform can greatly reduce laborious and time-consuming hybridization steps and prevent potential contamination. Furthermore, by introducing the reciprocating flow into the microchannel during the hybridization process, the total assay time can be reduced to 3 hours, which is 6 times faster than the conventional DNA microarray. Given the automatic assay operation, shorter assay time, and high point mutation discrimination, we believe that the AMDM platform has potential for low-cost, rapid and sensitive genetic testing in a simple and user-friendly manner, which may benefit gene screening in medical practice.

Genome sequence of a Proteus mirabilis strain isolated from the salivary glands of larval Lucilia sericata

USDA-ARS?s Scientific Manuscript database

We announced a draft genome sequence of a Proteus mirabilis strain derived from Lucilia sericata salivary glands. This strain is demonstrated to attract and induce oviposition by L. sericata, a common blow fly important to medicine, agriculture, and forensics. The genome will help to dissect inter...

Adapt Design: A Methodology for Enabling Modular Design for Mission Specific SUAS

DTIC Science & Technology

2016-08-24

ADAPT DESIGN: A METHODOLOGY FOR ENABLING MODULAR DESIGN FOR MISSION SPECIFIC SUAS Zachary C. Fisher David Locascio K. Daniel Cooksey...vehicle’s small scale. This paper considers a different approach to SUAS design aimed at addressing this issue. In this approach, a hybrid modular and...Two types of platforms have been identified: scalable platforms where variants are produced by varying scalable design variables, and modular

OTG-snpcaller: An Optimized Pipeline Based on TMAP and GATK for SNP Calling from Ion Torrent Data

PubMed Central

Huang, Wenpan; Xi, Feng; Lin, Lin; Zhi, Qihuan; Zhang, Wenwei; Tang, Y. Tom; Geng, Chunyu; Lu, Zhiyuan; Xu, Xun

2014-01-01

Because the new Proton platform from Life Technologies produced markedly different data from those of the Illumina platform, the conventional Illumina data analysis pipeline could not be used directly. We developed an optimized SNP calling method using TMAP and GATK (OTG-snpcaller). This method combined our own optimized processes, Remove Duplicates According to AS Tag (RDAST) and Alignment Optimize Structure (AOS), together with TMAP and GATK, to call SNPs from Proton data. We sequenced four sets of exomes captured by Agilent SureSelect and NimbleGen SeqCap EZ Kit, using Life Technology’s Ion Proton sequencer. Then we applied OTG-snpcaller and compared our results with the results from Torrent Variants Caller. The results indicated that OTG-snpcaller can reduce both false positive and false negative rates. Moreover, we compared our results with Illumina results generated by GATK best practices, and we found that the results of these two platforms were comparable. The good performance in variant calling using GATK best practices can be primarily attributed to the high quality of the Illumina sequences. PMID:24824529

OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data.

PubMed

Zhu, Pengyuan; He, Lingyu; Li, Yaqiao; Huang, Wenpan; Xi, Feng; Lin, Lin; Zhi, Qihuan; Zhang, Wenwei; Tang, Y Tom; Geng, Chunyu; Lu, Zhiyuan; Xu, Xun

2014-01-01

Because the new Proton platform from Life Technologies produced markedly different data from those of the Illumina platform, the conventional Illumina data analysis pipeline could not be used directly. We developed an optimized SNP calling method using TMAP and GATK (OTG-snpcaller). This method combined our own optimized processes, Remove Duplicates According to AS Tag (RDAST) and Alignment Optimize Structure (AOS), together with TMAP and GATK, to call SNPs from Proton data. We sequenced four sets of exomes captured by Agilent SureSelect and NimbleGen SeqCap EZ Kit, using Life Technology's Ion Proton sequencer. Then we applied OTG-snpcaller and compared our results with the results from Torrent Variants Caller. The results indicated that OTG-snpcaller can reduce both false positive and false negative rates. Moreover, we compared our results with Illumina results generated by GATK best practices, and we found that the results of these two platforms were comparable. The good performance in variant calling using GATK best practices can be primarily attributed to the high quality of the Illumina sequences.

Warthog: Coupling Status Update

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

Hart, Shane W. D.; Reardon, Bradley T.

The Warthog code was developed to couple codes that are developed in both the Multi-Physics Object-Oriented Simulation Environment (MOOSE) from Idaho National Laboratory (INL) and SHARP from Argonne National Laboratory (ANL). The initial phase of this work, focused on coupling the neutronics code PROTEUS with the fuel performance code BISON. The main technical challenge involves mapping the power density solution determined by PROTEUS to the fuel in BISON. This presents a challenge since PROTEUS uses the MOAB mesh format, but BISON, like all other MOOSE codes, uses the libMesh format. When coupling the different codes, one must consider that Warthogmore » is a light-weight MOOSE-based program that uses the Data Transfer Kit (DTK) to transfer data between the various mesh types. Users set up inputs for the codes they want to run, and then Warthog transfers the data between them. Currently Warthog supports XSProc from SCALE or the Sub-Group Application Programming Interface (SGAPI) in PROTEUS for generating cross sections. It supports arbitrary geometries using PROTEUS and BISON. DTK will transfer power densities and temperatures between the codes where the domains overlap. In the past fiscal year (FY), much work has gone into demonstrating two-way coupling for simple pin cells of various materials. XSProc was used to calculate the cross sections, which were then passed to PROTEUS in an external file. PROTEUS calculates the fission/power density, and Warthog uses DTK to pass this information to BISON, where it is used as the heat source. BISON then calculates the temperature profile of the pin cell and sends it back to XSProc to obtain the temperature corrected cross sections. This process is repeated until the convergence criteria (tolerance on BISON solve, or number of time steps) is reached. Models have been constructed and run for both uranium oxide and uranium silicide fuels. These models demonstrate a clear difference in power shape that is not accounted for in a stand-alone BISON run. Future work involves improving the user interface (UI), likely through integration with the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench. Furthermore, automating the input creation would ease the user experience. The next priority is to continue coupling the work with other codes in the SHARP package. Efforts on other projects include work to couple the Nek5000 thermo-hydraulics code to MOOSE, but this is in the preliminary stages.« less

Early Strains of Multidrug-Resistant Salmonella enterica Serovar Kentucky Sequence Type 198 from Southeast Asia Harbor Salmonella Genomic Island 1-J Variants with a Novel Insertion Sequence

PubMed Central

Le Hello, Simon; Weill, François-Xavier; Guibert, Véronique; Praud, Karine; Cloeckaert, Axel

2012-01-01

Salmonella genomic island 1 (SGI1) is a 43-kb integrative mobilizable element that harbors a great diversity of multidrug resistance gene clusters described in numerous Salmonella enterica serovars and also in Proteus mirabilis. The majority of SGI1 variants contain an In104-derivative complex class 1 integron inserted between resolvase gene res and open reading frame (ORF) S044 in SGI1. Recently, the international spread of ciprofloxacin-resistant S. enterica serovar Kentucky sequence type 198 (ST198) containing SGI1-K variants has been reported. A retrospective study was undertaken to characterize ST198 S. Kentucky strains isolated before the spread of the epidemic ST198-SGI1-K population in Africa and the Middle East. Here, we characterized 12 ST198 S. Kentucky strains isolated between 1969 and 1999, mainly from humans returning from Southeast Asia (n = 10 strains) or Israel (n = 1 strain) or from meat in Egypt (n = 1 strain). All these ST198 S. Kentucky strains did not belong to the XbaI pulsotype X1 associated with the African epidemic clone but to pulsotype X2. SGI1-J subgroup variants containing different complex integrons with a partial transposition module and inserted within ORF S023 of SGI1 were detected in six strains. The SGI1-J4 variant containing a partially deleted class 1 integron and thus showing a narrow resistance phenotype to sulfonamides was identified in two epidemiologically unrelated strains from Indonesia. The four remaining strains harbored a novel SGI1-J variant, named SGI1-J6, which contained aadA2, floR2, tetR(G)-tetA(G), and sul1 resistance genes within its complex integron. Moreover, in all these S. Kentucky isolates, a novel insertion sequence related to the IS630 family and named ISSen5 was found inserted upstream of the SGI1 complex integron in ORF S023. Thus, two subpopulations of S. Kentucky ST198 independently and exclusively acquired the SGI1 during the 1980s and 1990s. Unlike the ST198-X1 African epidemic subpopulation, the ST198-X2 subpopulation mainly from Asia harbors variants of the SGI1-J subgroup that are encountered mainly in the Far East, as previously described for S. enterica serovars Emek and Virchow. PMID:22802251

Early strains of multidrug-resistant Salmonella enterica serovar Kentucky sequence type 198 from Southeast Asia harbor Salmonella genomic island 1-J variants with a novel insertion sequence.

PubMed

Le Hello, Simon; Weill, François-Xavier; Guibert, Véronique; Praud, Karine; Cloeckaert, Axel; Doublet, Benoît

2012-10-01

Salmonella genomic island 1 (SGI1) is a 43-kb integrative mobilizable element that harbors a great diversity of multidrug resistance gene clusters described in numerous Salmonella enterica serovars and also in Proteus mirabilis. The majority of SGI1 variants contain an In104-derivative complex class 1 integron inserted between resolvase gene res and open reading frame (ORF) S044 in SGI1. Recently, the international spread of ciprofloxacin-resistant S. enterica serovar Kentucky sequence type 198 (ST198) containing SGI1-K variants has been reported. A retrospective study was undertaken to characterize ST198 S. Kentucky strains isolated before the spread of the epidemic ST198-SGI1-K population in Africa and the Middle East. Here, we characterized 12 ST198 S. Kentucky strains isolated between 1969 and 1999, mainly from humans returning from Southeast Asia (n = 10 strains) or Israel (n = 1 strain) or from meat in Egypt (n = 1 strain). All these ST198 S. Kentucky strains did not belong to the XbaI pulsotype X1 associated with the African epidemic clone but to pulsotype X2. SGI1-J subgroup variants containing different complex integrons with a partial transposition module and inserted within ORF S023 of SGI1 were detected in six strains. The SGI1-J4 variant containing a partially deleted class 1 integron and thus showing a narrow resistance phenotype to sulfonamides was identified in two epidemiologically unrelated strains from Indonesia. The four remaining strains harbored a novel SGI1-J variant, named SGI1-J6, which contained aadA2, floR2, tetR(G)-tetA(G), and sul1 resistance genes within its complex integron. Moreover, in all these S. Kentucky isolates, a novel insertion sequence related to the IS630 family and named ISSen5 was found inserted upstream of the SGI1 complex integron in ORF S023. Thus, two subpopulations of S. Kentucky ST198 independently and exclusively acquired the SGI1 during the 1980s and 1990s. Unlike the ST198-X1 African epidemic subpopulation, the ST198-X2 subpopulation mainly from Asia harbors variants of the SGI1-J subgroup that are encountered mainly in the Far East, as previously described for S. enterica serovars Emek and Virchow.

Synonymous ABCA3 Variants Do Not Increase Risk for Neonatal Respiratory Distress Syndrome

PubMed Central

Wambach, Jennifer A.; Wegner, Daniel J.; Heins, Hillary B.; Druley, Todd E.; Mitra, Robi D.; Hamvas, Aaron; Cole, F. Sessions

2014-01-01

Objective To determine whether synonymous variants in the adenosine triphosphate-binding cassette A3 transporter (ABCA3) gene increase the risk for neonatal respiratory distress syndrome (RDS) in term and late preterm infants of European and African descent. Study design Using next-generation pooled sequencing of race-stratified DNA samples from infants of European and African descent at $34 weeks gestation with and without RDS (n = 503), we scanned all exons of ABCA3, validated each synonymous variant with an independent genotyping platform, and evaluated race-stratified disease risk associated with common synonymous variants and collapsed frequencies of rare synonymous variants. Results The synonymous ABCA3 variant frequency spectrum differs between infants of European descent and those of African descent. Using in silico prediction programs and statistical strategies, we found no potentially disruptive synonymous ABCA3 variants or evidence of selection pressure. Individual common synonymous variants and collapsed frequencies of rare synonymous variants did not increase disease risk in term and late-preterm infants of European or African descent. Conclusion In contrast to rare, nonsynonymous ABCA3 mutations, synonymous ABCA3 variants do not increase the risk for neonatal RDS among term and late-preterm infants of European or African descent. PMID:24657120

THE CONTENT AND RELATIVE BASE RATIOS OF RIBONUCLEIC ACID IN AMOEBA

PubMed Central

Iverson, Ray M.

1964-01-01

The amount and relative base ratios of ribonucleic acid (RNA) in the nucleus and cytoplasm of Amoeba proteus and A. dubia, and of homospecies cells obtained by nuclear transfer with A. proteus, have been determined by microelectrophoresis. In A. proteus the average amounts of RNA in the nucleus and the cytoplasm were 134. micromicrograms and 2520. micromicrograms; in A. dubia the averages for the nucleus and cytoplasm were 67. micromicrograms and 1427. micromicrograms. The relative base ratio of RNA of the nucleus is similar to that of the RNA of the cytoplasm within a species, but the two species differed in this respect. Homospecies nuclear transfer did not affect the relative base ratio or amount of RNA. PMID:14105213

A hybrid computational strategy to address WGS variant analysis in >5000 samples.

PubMed

Huang, Zhuoyi; Rustagi, Navin; Veeraraghavan, Narayanan; Carroll, Andrew; Gibbs, Richard; Boerwinkle, Eric; Venkata, Manjunath Gorentla; Yu, Fuli

2016-09-10

The decreasing costs of sequencing are driving the need for cost effective and real time variant calling of whole genome sequencing data. The scale of these projects are far beyond the capacity of typical computing resources available with most research labs. Other infrastructures like the cloud AWS environment and supercomputers also have limitations due to which large scale joint variant calling becomes infeasible, and infrastructure specific variant calling strategies either fail to scale up to large datasets or abandon joint calling strategies. We present a high throughput framework including multiple variant callers for single nucleotide variant (SNV) calling, which leverages hybrid computing infrastructure consisting of cloud AWS, supercomputers and local high performance computing infrastructures. We present a novel binning approach for large scale joint variant calling and imputation which can scale up to over 10,000 samples while producing SNV callsets with high sensitivity and specificity. As a proof of principle, we present results of analysis on Cohorts for Heart And Aging Research in Genomic Epidemiology (CHARGE) WGS freeze 3 dataset in which joint calling, imputation and phasing of over 5300 whole genome samples was produced in under 6 weeks using four state-of-the-art callers. The callers used were SNPTools, GATK-HaplotypeCaller, GATK-UnifiedGenotyper and GotCloud. We used Amazon AWS, a 4000-core in-house cluster at Baylor College of Medicine, IBM power PC Blue BioU at Rice and Rhea at Oak Ridge National Laboratory (ORNL) for the computation. AWS was used for joint calling of 180 TB of BAM files, and ORNL and Rice supercomputers were used for the imputation and phasing step. All other steps were carried out on the local compute cluster. The entire operation used 5.2 million core hours and only transferred a total of 6 TB of data across the platforms. Even with increasing sizes of whole genome datasets, ensemble joint calling of SNVs for low coverage data can be accomplished in a scalable, cost effective and fast manner by using heterogeneous computing platforms without compromising on the quality of variants.

A Sensor To Detect the Early Stages in the Development of Crystalline Proteus mirabilis Biofilm on Indwelling Bladder Catheters

PubMed Central

Stickler, D. J.; Jones, S. M.; Adusei, G. O.; Waters, M. G.

2006-01-01

A simple sensor has been developed to detect the early stages of urinary catheter encrustation and avoid the clinical crises induced by catheter blockage. In laboratory models of colonization by Proteus mirabilis, the sensor signaled encrustation at an average time of 43 h before catheters were blocked with crystalline biofilm. PMID:16597888

[Possibility of fortifying milk nutrient mixtures for children with lactoglobulin against E. coli and Proteus].

PubMed

Zlatnik, E Iu

1986-01-01

Sweet milk nutrient mixtures, biologically active additives (BAA) and lactic acid ferments, intended for child nutrition, were enriched with the immune preparation lactoglobulin against E. coli and Proteus. Serological and immunochemical investigations of hemagglutinating activity and other characteristics of lactoglobulin in the enriched milk mixtures and BAA evidenced that the preparation retained its full value during the technological process and in the period of storage. No signs of lactoglobulin degradation during the production of a test batch of the milk mixture and BAA were detected, and a high hemagglutinating activity with respect to enteropathogenic E. coli and Proteus was recorded. This permitted the author to recommend the lactoglobulin-enriched sweet mixtures for prevention of acute intestinal infections and dysbacteriosis in young children. The in vitro study of the lactoglobulin interaction with pure cultures of lactobacillus and bifidobacteria showed its inertness to eubacteria. Four strains studied retained their growth and acid-forming properties after combined incubation with lactoglobulin and did not inhibit its activity. A conclusion has been made on the possibility of enrichment of lactic acid products, intended for child nutrition, with lactoglobulin against E. coli and Proteus.

Development of a Phage Cocktail to Control Proteus mirabilis Catheter-associated Urinary Tract Infections

PubMed Central

Melo, Luís D. R.; Veiga, Patrícia; Cerca, Nuno; Kropinski, Andrew M.; Almeida, Carina; Azeredo, Joana; Sillankorva, Sanna

2016-01-01

Proteus mirabilis is an enterobacterium that causes catheter-associated urinary tract infections (CAUTIs) due to its ability to colonize and form crystalline biofilms on the catheters surface. CAUTIs are very difficult to treat, since biofilm structures are highly tolerant to antibiotics. Phages have been used widely to control a diversity of bacterial species, however, a limited number of phages for P. mirabilis have been isolated and studied. Here we report the isolation of two novel virulent phages, the podovirus vB_PmiP_5460 and the myovirus vB_PmiM_5461, which are able to target, respectively, 16 of the 26 and all the Proteus strains tested in this study. Both phages have been characterized thoroughly and sequencing data revealed no traces of genes associated with lysogeny. To further evaluate the phages’ ability to prevent catheter’s colonization by Proteus, the phages adherence to silicone surfaces was assessed. Further tests in phage-coated catheters using a dynamic biofilm model simulating CAUTIs, have shown a significant reduction of P. mirabilis biofilm formation up to 168 h of catheterization. These results highlight the potential usefulness of the two isolated phages for the prevention of surface colonization by this bacterium. PMID:27446059

Oriented thick and thin filaments in amoeba proteus

PubMed Central

Rinaldi, RA; Hrebenda, B

1975-01-01

Actin and myosin filaments as a foundation of contractile systems are well established from ameba to man (3). Wolpert et al. (19) isolated by differential centrifugation from Amoeba proteus a motile fraction composed of filaments which moved upon the addition of ATP. Actin filaments are found in amebas (1, 12, 13) which react with vertebrate heavy meromyosin (HMM), forming arrowhead complexes as vertebrate actin (3, 9), and are prominent within the ectoplasmic tube where some of them are attached to the plasmalemma (1, 12). Thick and thin filaments possessing the morphological characteristics of myosin and actin have been obtained from isolated ameba cytoplasm (18, 19). In addition, there are filaments exhibiting ATPase activity in amebas which react with actin (12, 16, 17). However, giant ameba (Chaos-proteus) shapes are difficult to preserve, and the excellent contributions referred to above are limited by visible distortions occurring in the amebas (rounding up, pseudopods disappearing, and cellular organelles swelling) upon fixation. Achievement of normal ameboid shape in recent glycerination work (15) led us to attempt other electron microscope fixation techniques, resulting in a surprising preservation of A. proteus with a unique orientation of thick and thin filaments in the ectoplasmic region. PMID:1141376

Oriented thick and thin filaments in Amoeba proteus.

PubMed

Rinaldi, R A; Hrebenda, B

1975-07-01

Actin and myosin filaments as a foundation of contractile systems are well established from ameba to man (3). Wolpert et al. (19) isolated by differential centrifugation from Amoeba proteus a motile fraction composed of filaments which moved upon the addition of ATP. Actin filaments are found in amebas (1, 12, 13) which react with vertebrate heavy meromyosin (HMM), forming arrowhead complexes as vertebrate actin (3, 9), and are prominent within the ectoplasmic tube where some of them are attached to the plasmalemma (1, 12). Thick and thin filaments possessing the morphological characteristics of myosin and actin have been obtained from isolated ameba cytoplasm (18, 19). In addition, there are filaments exhibiting ATPase activity in amebas which react with actin (12, 16, 17). However, giant ameba (Chaos-proteus) shapes are difficult to preserve, and the excellent contributions referred to above are limited by visible distortions occurring in the amebas (rounding up, pseudopods disappearing, and cellular organelles swelling) upon fixation. Achievement of normal ameboid shape in recent glycerination work (15) led us to attempt other electron microscope fixation techniques, resulting in a surprising preservation of A. proteus with a unique orientation of thick and thin filaments in the ectoplasmic region.

Neonatal Meningoventriculitis Due to Proteus Mirabilis – A Case Report

PubMed Central

Juyal, Deepak; Rathaur, Vyas Kumar; Sharma, Neelam

2013-01-01

A five day old full term born baby was admitted to our Neonatal Intensive Care Unit with seizures, opisthotonous posture and was icteric upto thigh. Baby had a three day history of poor feeding, lethargy and abnormal body movements. Mother was a 29 years old primigravida and had a normal vaginal delivery at home. Sepsis profile of the patient was requested, lumbar puncture and ventricular tap was performed. Patient was put on third generation cephalosporins, aminoglycosides and phenobarbitone. Culture and sensitivity report of blood, Cerebro spinal fluid and ventricular fluid showed Proteus mirabilis. Computerized Tomography scan showed a large parenchymal lesion in the right frontal lobe and diffuse ependymal enhancement along both the lateral ventricles suggestive of meningoventriculitis. We hereby present a fatal case of neonatal meningoventriculitis due to Proteus mirabilis. PMID:23543669

User Manual for the PROTEUS Mesh Tools

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

Smith, Micheal A.; Shemon, Emily R.

2015-06-01

This report describes the various mesh tools that are provided with the PROTEUS code giving both descriptions of the input and output. In many cases the examples are provided with a regression test of the mesh tools. The most important mesh tools for any user to consider using are the MT_MeshToMesh.x and the MT_RadialLattice.x codes. The former allows the conversion between most mesh types handled by PROTEUS while the second allows the merging of multiple (assembly) meshes into a radial structured grid. Note that the mesh generation process is recursive in nature and that each input specific for a givenmore » mesh tool (such as .axial or .merge) can be used as “mesh” input for any of the mesh tools discussed in this manual.« less

Novel polymer membrane process for pre-combustion CO{sub 2} capture from coal-fired syngas

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

Merkel, Tim

2011-09-14

This final report describes work conducted for the Department of Energy (DOE NETL) on development of a novel polymer membrane process for pre-combustion CO{sub 2} capture from coalfired syngas (award number DE-FE0001124). The work was conducted by Membrane Technology and Research, Inc. (MTR) from September 15, 2009, through December 14, 2011. Tetramer Technologies, LLC (Tetramer) was our subcontract partner on this project. The National Carbon Capture Center (NCCC) at Wilsonville, AL, provided access to syngas gasifier test facilities. The main objective of this project was to develop a cost-effective membrane process that could be used in the relatively near-term tomore » capture CO{sub 2} from shifted syngas generated by a coal-fired Integrated Gasification Combined Cycle (IGCC) power plant. In this project, novel polymeric membranes (designated as Proteus™ membranes) with separation properties superior to conventional polymeric membranes were developed. Hydrogen permeance of up to 800 gpu and H{sub 2}/CO{sub 2} selectivity of >12 was achieved using a simulated syngas mixture at 150°C and 50 psig, which exceeds the original project targets of 200 gpu for hydrogen permeance and 10 for H{sub 2}/CO{sub 2} selectivity. Lab-scale Proteus membrane modules (with a membrane area of 0.13 m{sup 2}) were also developed using scaled-up Proteus membranes and high temperature stable module components identified during this project. A mixed-gas hydrogen permeance of about 160 gpu and H{sub 2}/CO{sub 2} selectivity of >12 was achieved using a simulated syngas mixture at 150°C and 100 psig. We believe that a significant improvement in the membrane and module performance is likely with additional development work. Both Proteus membranes and lab-scale Proteus membrane modules were further evaluated using coal-derived syngas streams at the National Carbon Capture Center (NCCC). The results indicate that all module components, including the Proteus membrane, were stable under the field conditions (feed pressures: 150-175 psig and feed temperatures: 120-135°C) for over 600 hours. The field performance of both Proteus membrane stamps and Proteus membrane modules is consistent with the results obtained in the lab, suggesting that the presence of sulfur-containing compounds (up to 780 ppm hydrogen sulfide), saturated water vapor, carbon monoxide and heavy hydrocarbons in the syngas feed stream has no adverse effect on the Proteus membrane or module performance. We also performed an economic analysis for a number of membrane process designs developed in this project (using hydrogen-selective membranes, alone or in the combination with CO{sub 2}- selective membranes). The current field performance for Proteus membranes was used in the design analysis. The study showed the current best design has the potential to reduce the increase in Levelized Cost of Electricity (LCOE) caused by 90% CO{sub 2} capture to about 15% if co-sequestration of H{sub 2}S is viable. This value is still higher than the DOE target for increase in LCOE (10%); however, compared to the base-case Selexol process that gives a 30% increase in LCOE at 90% CO2 capture, the membrane-based process appears promising. We believe future improvements in membrane performance have the potential to reach the DOE target.« less

Mutation Update of ARSA and PSAP Genes Causing Metachromatic Leukodystrophy.

PubMed

Cesani, Martina; Lorioli, Laura; Grossi, Serena; Amico, Giulia; Fumagalli, Francesca; Spiga, Ivana; Filocamo, Mirella; Biffi, Alessandra

2016-01-01

Metachromatic leukodystrophy is a neurodegenerative disorder characterized by progressive demyelination. The disease is caused by variants in the ARSA gene, which codes for the lysosomal enzyme arylsulfatase A, or, more rarely, in the PSAP gene, which codes for the activator protein saposin B. In this Mutation Update, an extensive review of all the ARSA- and PSAP-causative variants published in the literature to date, accounting for a total of 200 ARSA and 10 PSAP allele types, is presented. The detailed ARSA and PSAP variant lists are freely available on the Leiden Online Variation Database (LOVD) platform at http://www.LOVD.nl/ARSA and http://www.LOVD.nl/PSAP, respectively. © 2015 WILEY PERIODICALS, INC.

Host Defense against Opportunist Microorganisms Following Trauma.

DTIC Science & Technology

1988-06-30

aeruginosa and Proteus mirabilis . Drugs (10-20 ag/kg) or placebo were administered intramuscularly to thermally injured guinea pigs at 3 hr postburn and...and Proteus mirabilis were also investigated. Since certain NSAIDs have discrete inhibitory effects on PMNs that occur independently of the classic...25 in thermally injured animals treated with NSAIDs or placebo. Figure 7. Mortality from burn wound infection with P. mirabilis 26 in thermally

Detection of KPC-2 in a Clinical Isolate of Proteus mirabilis and First Reported Description of Carbapenemase Resistance Caused by a KPC Beta-Lactamase in P. mirabilis

USDA-ARS?s Scientific Manuscript database

An isolate of Proteus mirabilis recovered from bacterial cultures was shown to be resistant to imipenem, meropenem, and ertapenem by disk diffusion susceptibility testing. Amplification of whole cell and/or plasmid DNA recovered from the isolate using primers specific for the blaKPC carbapenemase g...

From days to hours: reporting clinically actionable variants from whole genome sequencing.

PubMed

Middha, Sumit; Baheti, Saurabh; Hart, Steven N; Kocher, Jean-Pierre A

2014-01-01

As the cost of whole genome sequencing (WGS) decreases, clinical laboratories will be looking at broadly adopting this technology to screen for variants of clinical significance. To fully leverage this technology in a clinical setting, results need to be reported quickly, as the turnaround rate could potentially impact patient care. The latest sequencers can sequence a whole human genome in about 24 hours. However, depending on the computing infrastructure available, the processing of data can take several days, with the majority of computing time devoted to aligning reads to genomics regions that are to date not clinically interpretable. In an attempt to accelerate the reporting of clinically actionable variants, we have investigated the utility of a multi-step alignment algorithm focused on aligning reads and calling variants in genomic regions of clinical relevance prior to processing the remaining reads on the whole genome. This iterative workflow significantly accelerates the reporting of clinically actionable variants with no loss of accuracy when compared to genotypes obtained with the OMNI SNP platform or to variants detected with a standard workflow that combines Novoalign and GATK.

VARiD: a variation detection framework for color-space and letter-space platforms.

PubMed

Dalca, Adrian V; Rumble, Stephen M; Levy, Samuel; Brudno, Michael

2010-06-15

High-throughput sequencing (HTS) technologies are transforming the study of genomic variation. The various HTS technologies have different sequencing biases and error rates, and while most HTS technologies sequence the residues of the genome directly, generating base calls for each position, the Applied Biosystem's SOLiD platform generates dibase-coded (color space) sequences. While combining data from the various platforms should increase the accuracy of variation detection, to date there are only a few tools that can identify variants from color space data, and none that can analyze color space and regular (letter space) data together. We present VARiD--a probabilistic method for variation detection from both letter- and color-space reads simultaneously. VARiD is based on a hidden Markov model and uses the forward-backward algorithm to accurately identify heterozygous, homozygous and tri-allelic SNPs, as well as micro-indels. Our analysis shows that VARiD performs better than the AB SOLiD toolset at detecting variants from color-space data alone, and improves the calls dramatically when letter- and color-space reads are combined. The toolset is freely available at http://compbio.cs.utoronto.ca/varid.

Robustness of Massively Parallel Sequencing Platforms

PubMed Central

Kavak, Pınar; Yüksel, Bayram; Aksu, Soner; Kulekci, M. Oguzhan; Güngör, Tunga; Hach, Faraz; Şahinalp, S. Cenk; Alkan, Can; Sağıroğlu, Mahmut Şamil

2015-01-01

The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications. PMID:26382624

A comprehensive SNP and indel imputability database.

PubMed

Duan, Qing; Liu, Eric Yi; Croteau-Chonka, Damien C; Mohlke, Karen L; Li, Yun

2013-02-15

Genotype imputation has become an indispensible step in genome-wide association studies (GWAS). Imputation accuracy, directly influencing downstream analysis, has shown to be improved using re-sequencing-based reference panels; however, this comes at the cost of high computational burden due to the huge number of potentially imputable markers (tens of millions) discovered through sequencing a large number of individuals. Therefore, there is an increasing need for access to imputation quality information without actually conducting imputation. To facilitate this process, we have established a publicly available SNP and indel imputability database, aiming to provide direct access to imputation accuracy information for markers identified by the 1000 Genomes Project across four major populations and covering multiple GWAS genotyping platforms. SNP and indel imputability information can be retrieved through a user-friendly interface by providing the ID(s) of the desired variant(s) or by specifying the desired genomic region. The query results can be refined by selecting relevant GWAS genotyping platform(s). This is the first database providing variant imputability information specific to each continental group and to each genotyping platform. In Filipino individuals from the Cebu Longitudinal Health and Nutrition Survey, our database can achieve an area under the receiver-operating characteristic curve of 0.97, 0.91, 0.88 and 0.79 for markers with minor allele frequency >5%, 3-5%, 1-3% and 0.5-1%, respectively. Specifically, by filtering out 48.6% of markers (corresponding to a reduction of up to 48.6% in computational costs for actual imputation) based on the imputability information in our database, we can remove 77%, 58%, 51% and 42% of the poorly imputed markers at the cost of only 0.3%, 0.8%, 1.5% and 4.6% of the well-imputed markers with minor allele frequency >5%, 3-5%, 1-3% and 0.5-1%, respectively. http://www.unc.edu/∼yunmli/imputability.html

GARFIELD-NGS: Genomic vARiants FIltering by dEep Learning moDels in NGS.

PubMed

Ravasio, Viola; Ritelli, Marco; Legati, Andrea; Giacopuzzi, Edoardo

2018-04-14

Exome sequencing approach is extensively used in research and diagnostic laboratories to discover pathological variants and study genetic architecture of human diseases. However, a significant proportion of identified genetic variants are actually false positive calls, and this pose serious challenges for variants interpretation. Here, we propose a new tool named GARFIELD-NGS (Genomic vARiants FIltering by dEep Learning moDels in NGS), which rely on deep learning models to dissect false and true variants in exome sequencing experiments performed with Illumina or ION platforms. GARFIELD-NGS showed strong performances for both SNP and INDEL variants (AUC 0.71 - 0.98) and outperformed established hard filters. The method is robust also at low coverage down to 30X and can be applied on data generated with the recent Illumina two-colour chemistry. GARFIELD-NGS processes standard VCF file and produces a regular VCF output. Thus, it can be easily integrated in existing analysis pipeline, allowing application of different thresholds based on desired level of sensitivity and specificity. GARFIELD-NGS available at https://github.com/gedoardo83/GARFIELD-NGS. edoardo.giacopuzzi@unibs.it. Supplementary data are available at Bioinformatics online.

A novel functional class 2 integron in clinical Proteus mirabilis isolates.

PubMed

Wei, Quhao; Hu, Qingfeng; Li, Shanshan; Lu, Huoyang; Chen, Guoqiang; Shen, Beiqiong; Zhang, Ping; Zhou, Yonglie

2014-04-01

To describe a novel functional class 2 integron that was found in clinical Proteus mirabilis isolates. Class 1 and 2 integrons were screened by PCR in 153 clinical Proteus isolates. The variable regions of class 1 and 2 integrons were determined by restriction analysis and sequencing. The mutations of internal stop codons in class 2 integrons and their common promoters were also determined by sequencing. Enterobacterial repetitive intergenic consensus (ERIC)-PCR was used to analyse the phylogenetic relations of class 2 integron-positive P. mirabilis isolates. Class 1 integrons were detected in 96 (63%) of 153 Proteus isolates: eight different gene cassette arrays were detected, including dfrA32-ereA1-aadA2, which was detected for the first time in P. mirabilis. Class 2 integrons were detected in 101 (66%) of 153 Proteus isolates: four different gene cassette arrays were detected, including dfrA1-catB2-sat2-aadA1, which was detected for the first time in a class 2 integron. A novel functional class 2 integron was detected in 38 P. mirabilis isolates with a common promoter (-35 TTTAAT|16 bp|-10 TAAAGT). The variable region of this functional class 2 integron contained dfrA14 and three novel open reading frames with unknown functions. Very similar ERIC-PCR fingerprinting patterns were detected in these 38 P. mirabilis isolates and were different from other class 2 integron-positive isolates. A novel functional class 2 integron was found for the first time in P. mirabilis. These functional class 2 integron-harbouring P. mirabilis isolates were likely to be clonally spread in our hospital.

Experimental critical loadings and control rod worths in LWR-PROTEUS configurations compared with MCNPX results

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

Plaschy, M.; Murphy, M.; Jatuff, F.

2006-07-01

The PROTEUS research reactor at the Paul Scherrer Inst. (PSI) has been operating since the sixties and has already permitted, due to its high flexibility, investigation of a large range of very different nuclear systems. Currently, the ongoing experimental programme is called LWR-PROTEUS. This programme was started in 1997 and concerns large-scale investigations of advanced light water reactors (LWR) fuels. Until now, the different LWR-PROTEUS phases have permitted to study more than fifteen different configurations, each of them having to be demonstrated to be operationally safe, in particular, for the Swiss safety authorities. In this context, recent developments of themore » PSI computer capabilities have made possible the use of full-scale SD-heterogeneous MCNPX models to calculate accurately different safety related parameters (e.g. the critical driver loading and the shutdown rod worth). The current paper presents the MCNPX predictions of these operational characteristics for seven different LWR-PROTEUS configurations using a large number of nuclear data libraries. More specifically, this significant benchmarking exercise is based on the ENDF/B6v2, ENDF/B6v8, JEF2.2, JEFF3.0, JENDL3.2, and JENDL3.3 libraries. The results highlight certain library specific trends in the prediction of the multiplication factor k{sub eff} (e.g. the systematically larger reactivity calculated with JEF2.2 and the smaller reactivity associated with JEFF3.0). They also confirm the satisfactory determination of reactivity variations by all calculational schemes, for instance, due to the introduction of a safety rod pair, these calculations having been compared with experiments. (authors)« less

The multi-state energy landscape of the SAM-I riboswitch: A single-molecule Förster resonance energy transfer spectroscopy study

NASA Astrophysics Data System (ADS)

Manz, Christoph; Kobitski, Andrei Yu.; Samanta, Ayan; Jäschke, Andres; Nienhaus, G. Ulrich

2018-03-01

RNA (ribonucleic acid) molecules are highly flexible biopolymers fluctuating at physiological temperatures among many different conformations that are represented by minima in a hierarchical conformational free energy landscape. Here we have employed single-molecule FRET (smFRET) to explore the energy landscape of the B. subtilis yitJ SAM-I riboswitch (RS). In this small RNA molecule, specific binding of an S-adenosyl-L-methionine (SAM) ligand in the aptamer domain regulates gene expression by inducing structural changes in another domain, the expression platform, causing transcription termination by the RNA polymerase. We have measured smFRET histograms over wide ranges of Mg2+ concentration for three RS variants that were specifically labeled with fluorescent dyes on different sites. In the analysis, different conformations are associated with discrete Gaussian model distributions, which are typically fairly broad on the FRET efficiency scale and thus can be extremely challenging to unravel due to their mutual overlap. Our earlier work on two SAM-I RS variants revealed four major conformations. By introducing a global fitting procedure which models both the Mg2+ concentration dependencies of the fractional populations and the average FRET efficiencies of the individual FRET distributions according to Mg2+ binding isotherms, we were able to consistently describe the histogram data of both variants at all studied Mg2+ concentrations. With the third FRET-labeled variant, however, we found significant deviations when applying the four-state model to the data. This can arise because the different FRET labeling of the new variant allows two states to be distinguished that were previously not separable due to overlap. Indeed, the resulting five-state model presented here consistently describes the smFRET histograms of all three variants as well as their variations with Mg2+ concentration. We also performed a triangulation of the donor position for two of the constructs to explore how the expression platform is oriented with respect to the aptamer.

[Current resistence situation in a surgical and urological department].

PubMed

Wacha, H; Stix, H

1976-04-15

Spectrum and sensitivity of bacteria were studied at the Surgical (534 positive wound smears) and the Urological Clinics (7879 urine specimens). Krankenhaus Nordwest, Frankfurt/M., during the period of 1969-1971 and in 1973. The most common organisms identified in wound smears were E. coli, followed by Staph. areus, Aerobacter and Proteus species. E. coli were also predominant in urine, but followed by Enterococci, Proteus and Pseudomonas. E. coli, Proteus species and especially Pseudomonas increased in number whereas Enterococci decreased. There was no pronounced increase in resistance to 9 current antibiotics as well as to chemotherapeutics during the observation period which was particularly striking in the case of Ampicillin used on a large scale. The results of our study support the presently employed therapeutic method using bactericidal antibiotics of the penicillin group in strict indications.

Peptides as modifiers of Na+-induced pinocytosis in starved Amoeba proteus.

PubMed

Josefsson, J O; Johansson, P

1985-01-01

Low concentrations of six peptide hormones; glucagon, vasoactive intestinal peptide, substance P, angiotensin II, lysine-vasopressin, arginine-vasopressin, and the chemotactic peptide fMet-Leu-Phe, activated the capacity for pinocytosis in starved Amoeba proteus. Competitive inhibitors of the chemotactic peptide in leucocytes inhibited activation by fMet-Leu-Phe, suggesting that its action in the amoeba is mediated by specific receptors. The opioid peptides, beta-endorphin, dynorphin (1-13) and leu-enkephalin abolished through a naloxone-sensitive mechanism activation by hormones and several other activating agents. Also, low concentrations of beef and pork insulin inhibited activation by peptide hormones. An insulin analogue of low potency in mammalian cells was inactive in the amoeba. These results support the hypothesis that besides opioid receptors, there may be insulin receptors and possibly receptors for several other peptide hormones in Amoeba proteus.

DaMold: A data-mining platform for variant annotation and visualization in molecular diagnostics research.

PubMed

Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

2017-07-01

Next-generation sequencing (NGS) has become a powerful and efficient tool for routine mutation screening in clinical research. As each NGS test yields hundreds of variants, the current challenge is to meaningfully interpret the data and select potential candidates. Analyzing each variant while manually investigating several relevant databases to collect specific information is a cumbersome and time-consuming process, and it requires expertise and familiarity with these databases. Thus, a tool that can seamlessly annotate variants with clinically relevant databases under one common interface would be of great help for variant annotation, cross-referencing, and visualization. This tool would allow variants to be processed in an automated and high-throughput manner and facilitate the investigation of variants in several genome browsers. Several analysis tools are available for raw sequencing-read processing and variant identification, but an automated variant filtering, annotation, cross-referencing, and visualization tool is still lacking. To fulfill these requirements, we developed DaMold, a Web-based, user-friendly tool that can filter and annotate variants and can access and compile information from 37 resources. It is easy to use, provides flexible input options, and accepts variants from NGS and Sanger sequencing as well as hotspots in VCF and BED formats. DaMold is available as an online application at http://damold.platomics.com/index.html, and as a Docker container and virtual machine at https://sourceforge.net/projects/damold/. © 2017 Wiley Periodicals, Inc.

Scaled Composites' Doug Shane examines the screen of his ground control station during tests in New Mexico. Shane used this configuration as the ground control station to remotely pilot the Proteus aircraft during a NASA sponsored series of tests.

NASA Image and Video Library

2002-03-13

Scaled Composites' Doug Shane examines the screen of his ground control station during tests in New Mexico. Shane used this configuration as the ground control station to remotely pilot the Proteus aircraft during a NASA sponsored series of tests.

Fourier Transform Infrared Spectroscopy as a Tool in Analysis of Proteus mirabilis Endotoxins.

PubMed

Żarnowiec, Paulina; Czerwonka, Grzegorz; Kaca, Wiesław

2017-01-01

Fourier transform infrared spectroscopy (FT-IR) was used to scan whole bacterial cells as well as lipopolysaccharides (LPSs, endotoxins) isolated from them. Proteus mirabilis cells, with chemically defined LPSs, served as a model for the ATR FT-IR method. The paper focuses on three steps of infrared spectroscopy: (1) sample preparation, (2) IR scanning, and (3) multivariate analysis of IR data (principal component analysis, PCA).

Arthrite septique à Proteus mirabilis

PubMed Central

Sbiti, Mohammed; Bouhamidi, Bahia; Louzi, Lhoussaine

2017-01-01

L'arthrite septique aigue est une pathologie peu fréquente mais grevée d'un pronostic lourd en termes de mortalité et morbidité. Nous rapportons un cas d'arthrite septique à Proteus mirabilis survenue de façon spontanée chez un patient de 61 ansprésentant un diabète compliqué,associée à des hémoculturespositives et des cultures positives du liquide articulaire. L'évolution était favorable grâce au diagnostic précoce et à l'institution d'une antibiothérapie adéquate. L'arthrite septique à Proteus Mirabilis est rare, ce qui nous a incité à revoir dans la littérature des séries d'arthrites à pyogènes incluant Proteus mirabilis portant sur les facteurs de risque, la pathogénie, le traitement et l'évolution de ces pathologies. Le diagnostic est avant tout microbiologique, la ponction articulaire précoce est réalisée avant toute antibiothérapie, l'examen direct, la culture et l'antibiogramme qui va guider le choix d'une antibiothérapie. L'arthrite septique est une urgence diagnostique et thérapeutique, la prise en charge précoce de cette pathologie permet une guérison sans séquelles. PMID:28674590

Pathogenetic insights from quantification of the cerebriform connective tissue nevus in Proteus syndrome.

PubMed

Nathan, Neera R; Patel, Rachna; Crenshaw, Molly M; Lindhurst, Marjorie J; Olsen, Cara; Biesecker, Leslie G; Keppler-Noreuil, Kim M; Darling, Thomas N

2018-04-01

The plantar cerebriform connective tissue nevus (CCTN) is the most common and problematic cutaneous manifestation of Proteus syndrome. To gain insights into CCTN pathogenesis and natural history. The size and location of plantar CCTN was measured on 152 images from 22 individuals with Proteus syndrome by 2 independent, blinded reviewers. Average measures of plantar CCTN were transformed into a linear mixed model to estimate proportionate change in size with age. Median patient age was 6.9 years at study onset. The intraclass correlation coefficient between 2 blinded reviewers was 0.946 for CCTN single measures. The CCTN relative area increased with age in children (n = 18, P < .0001) by 5.6% per year. Confluent papules and nodules extending beyond the boundaries of CCTNs were gradually replaced by typical CCTN over time. The location of CCTN in different individuals overlapped near the ball of the foot. A positive relationship between CCTN growth rate and AKT1 mutant allele frequency was observed (0.62, P = .10, n = 8). This was a retrospective review using photographs. CCTN growth is affected by age and extent of the CCTN precursor lesion. Monitoring of CCTN size might prove useful for evaluating drug response in the treatment of Proteus syndrome. Published by Elsevier Inc.

The nuclear membrane-associated honeycomb structure of the unicellular organism Amoeba proteus: on the search for homologies with the nuclear lamina of metazoa.

PubMed

Schmidt, M; Grossmann, U; Krohne, G

1995-07-01

In the protozoon Amoeba proteus, a complex and highly organized structure with the morphology of a honeycomb is associated with the nucleoplasmic surface of the nuclear membrane. We have tested whether this structure exhibits similarity to the nuclear lamina of metazoic organisms. First, we have shown that the honeycomb layer is composed of 3 to 5 nm thick protein fibrils resistant to treatment with detergent, high salt, and digestion with nucleases, thus possessing properties typical for karyoskeletal elements. However, in contrast to the meshwork of lamin filaments in somatic cells of metazoic organisms, the honeycomb layer is not tightly anchored to the nucleoplasmic side of pore complexes, or to the inner nuclear membrane. Second, in microinjection experiments we investigated whether fluorescently labeled lamins of Xenopus laevis (lamins A and LI) and Drosophila melanogaster (lamin Dmo) were able to associate in vivo with the Amoeba proteus honeycomb structure. In microinjected amoeba these three lamins were efficiently transported into the nucleus, but did not associate with the nuclear envelope. Our results suggest that the Amoeba proteus nuclear envelope, including the honeycomb layer, does not contain proteins exhibiting high homologies to lamins of metazoan species thus preventing the localized assembly of microinjected lamins along the nuclear periphery.

Presence of aquaporin and V-ATPase on the contractile vacuole of Amoeba proteus.

PubMed

Nishihara, Eri; Yokota, Etsuo; Tazaki, Akira; Orii, Hidefumi; Katsuhara, Maki; Kataoka, Kensuke; Igarashi, Hisako; Moriyama, Yoshinori; Shimmen, Teruo; Sonobe, Seiji

2008-03-01

The results of water permeability measurements suggest the presence of an AQP (aquaporin) in the membrane of the CV (contractile vacuole) in Amoeba proteus [Nishihara, Shimmen and Sonobe (2004) Cell Struct. Funct. 29, 85-90]. In the present study, we cloned an AQP gene from A. proteus [ApAQP (A. proteus AQP)] that encodes a 295-amino-acid protein. The protein has six putative TMs (transmembrane domains) and two NPA (Asn-Pro-Ala) motifs, which are conserved among various AQPs and are thought to be involved in the formation of water channels that span the lipid bilayer. Using Xenopus oocytes, we have demonstrated that the ApAQP protein product can function as a water channel. Immunofluorescence microscopy with anti-ApAQP antibody revealed that ApAQP is detected on the CV membrane and on the vesicles around the CV. The presence of V-ATPase (vacuolar H+-ATPase) on the vesicle membrane around the CV was also detected. Our data on ApAQP allow us to provide the first informed explanation of the high water permeability of the CV membrane in amoeba. Moreover, the results suggest that vesicles possessing V-ATPase are involved in generating an osmotic gradient. Based on our findings, we propose a new hypothesis for the mechanism of CV function.

Review of Software Platforms for Agent Based Models

DTIC Science & Technology

2008-04-01

EINSTein 4.3.2 Battlefield Python (optional, for batch runs) MANA 4.3.3 Battlefield N/A MASON 4.3.4 General Java NetLogo 4.3.5 General Logo-variant...through the use of relatively simple Python scripts. It also has built-in functions for parameter sweeps, and can plot the resulting fitness landscape ac...Nonetheless its ease of use, and support for automatic drawing of agents in 2D or 3D2 makes this a suitable platform for beginner programmers. 2Only in the

Assessment of the Accuracy of Certain Reduced Order Models used in the Prediction of Occupant Injury during Under-Body Blast Events

DTIC Science & Technology

2014-04-15

the floor on which the platform is dropped upon. Alternatively, a base excitation can be provided to the sliding platform in the upward vertical...7ms clips of chest resultant acceleration, (7) 7ms clip of pelvic vertical acceleration, (8,9) Peak and 30ms clips of lumbar spine compression, and...10) Pelvic vertical Dynamic Response Index (DRI)[12]. The sample size for each of the three seating variants consisted of 230 MADYMO

Detection of SGI1/PGI1 Elements and Resistance to Extended-Spectrum Cephalosporins in Proteae of Animal Origin in France

PubMed Central

Schultz, Eliette; Cloeckaert, Axel; Doublet, Benoît; Madec, Jean-Yves; Haenni, Marisa

2017-01-01

Proteae, and especially Proteus mirabilis, are often the cause of urinary tract infections (UTIs) in humans. They were reported as carriers of extended-spectrum β-lactamase (ESBL) genes, and recently of carbapenemases, mostly carried by the Salmonella genomic island 1 (SGI1) and Proteus genomic island 1 (PGI1). Proteae have also lately become an increasing cause of UTIs in companion animals, but antimicrobial susceptibility data in animals are still scarce. Here, we report the characterization of 468 clinical epidemiologically unrelated Proteae strains from animals collected between 2013 and 2015 in France. Seventeen P. mirabilis strains (3.6%) were positive for SGI1/PGI1 and 18 Proteae (3.8%) were resistant to extended-spectrum cephalosporins (ESC). The 28 isolates carrying SGI1/PGI1 and/or ESC-resistance genes were isolated from cats, dogs, and horses. ESBL genes were detected in six genetically related P. mirabilis harboring blaV EB-6 on the SGI1-V variant, but also independently of the SGI1-V, in 3 P. mirabilis strains (blaVEB-6 and blaCTX-M-15) and 1 Providencia rettgeri strain (blaCTX-M-1). The AmpC resistance genes blaCMY -2 and/or blaDHA-16 were detected in 9 P. mirabilis strains. One strain presented both an ESBL and AmpC gene. Interestingly, the majority of the ESBL/AmpC resistance genes were located on the chromosome. In conclusion, multiple ESC-resistance genetic determinants are circulating in French animals, even though SGI1-V-carrying P. mirabilis seems to be mainly responsible for the spread of the ESBL gene blaVEB-6 in dogs and horses. These results are of public health relevance and show that companion animals in close contact with humans should be regarded as a potential reservoir of ESC-resistant bacteria as well as a reservoir of ESC-resistance genes that could further disseminate to human pathogens. PMID:28154560

Characterization of CTX-M-140, a Variant of CTX-M-14 Extended-Spectrum β-Lactamase with Decreased Cephalosporin Hydrolytic Activity, from Cephalosporin-Resistant Proteus mirabilis.

PubMed

Tian, Guo-Bao; Jiang, Yi-Qi; Huang, Ying-Min; Qin, Yun; Feng, Lian-Qiang; Zhang, Xue-Fei; Li, Hong-Yu; Zhong, Lan-Lan; Zeng, Kun-Jiao; Patil, Sandip; Xing, Yong; Huang, Xi

2016-10-01

CTX-M-140, a novel CTX-M-type extended-spectrum β-lactamase (ESBL), was identified in cephalosporin-resistant clinical isolates of Proteus mirabilis CTX-M-140 contained an alanine-to-threonine substitution at position 109 compared to its putative progenitor, CTX-M-14. When it was expressed in an Escherichia coli isogenic background, CTX-M-140 conferred 4- to 32-fold lower MICs of cephalosporins than those with CTX-M-14, indicating that the phenotype was attributable to this single substitution. For four mutants of CTX-M-14 that were constructed by site-directed mutagenesis (A109E, A109D, A109K, and A109R mutants), MICs of cephalosporins were similar to those for the E. coli host strain, which suggested that the alanine at position 109 was essential for cephalosporin hydrolysis. The kinetic properties of native CTX-M-14 and CTX-M-140 were consistent with the MICs for the E. coli clones. Compared with that of CTX-M-14, a lower hydrolytic activity against cephalosporins was observed for CTX-M-140. blaCTX-M-140 is located on the chromosome as determined by I-CeuI pulsed-field gel electrophoresis (I-CeuI-PFGE) and Southern hybridization. The genetic environment surrounding blaCTX-M-140 is identical to the sequence found in different plasmids with blaCTX-M-9-group genes among the Enterobacteriaceae Genome sequencing and analysis showed that P. mirabilis strains with blaCTX-M-140 have a genome size of ∼4 Mbp, with a GC content of 38.7% and 23 putative antibiotic resistance genes. Our results indicate that alanine at position 109 is critical for the hydrolytic activity of CTX-M-14 against oxyimino-cephalosporins. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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

Wu, Hong; Zeng, Hong; Lam, Robert

Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson–Crick base pairs in the genome. Pathogenic mutations in theMLH1gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. Lastly, the structure shares a high degree of similarity with previously determined prokaryoticMLH1homologs; however, this structure affords a more accurate platform for the classification ofMLH1variants.

SMART on FHIR Genomics: facilitating standardized clinico-genomic apps.

PubMed

Alterovitz, Gil; Warner, Jeremy; Zhang, Peijin; Chen, Yishen; Ullman-Cullere, Mollie; Kreda, David; Kohane, Isaac S

2015-11-01

Supporting clinical decision support for personalized medicine will require linking genome and phenome variants to a patient's electronic health record (EHR), at times on a vast scale. Clinico-genomic data standards will be needed to unify how genomic variant data are accessed from different sequencing systems. A specification for the basis of a clinic-genomic standard, building upon the current Health Level Seven International Fast Healthcare Interoperability Resources (FHIR®) standard, was developed. An FHIR application protocol interface (API) layer was attached to proprietary sequencing platforms and EHRs in order to expose gene variant data for presentation to the end-user. Three representative apps based on the SMART platform were built to test end-to-end feasibility, including integration of genomic and clinical data. Successful design, deployment, and use of the API was demonstrated and adopted by HL7 Clinical Genomics Workgroup. Feasibility was shown through development of three apps by various types of users with background levels and locations. This prototyping work suggests that an entirely data (and web) standards-based approach could prove both effective and efficient for advancing personalized medicine. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Proteus Survey: Technical Manual and Codebook

DTIC Science & Technology

1992-06-01

Reserve Officer Training Corp, 20% from Officer Candidate School and Direct Commission) and by gender . Female officers were supposed to be oversampled...stratified by source of commission (40% USMA, 40% ROTC, 20% OCS and DC) and by gender , as in previous years. A total of approximately 7,000 surveys were...for the 1987 Proteus Survey and the population percentages from the OLRDB for each of the key strata ( gender and source of commission) reportedly used

Proteus mirabilis fimbriae- and urease-dependent clusters assemble in an extracellular niche to initiate bladder stone formation.

PubMed

Schaffer, Jessica N; Norsworthy, Allison N; Sun, Tung-Tien; Pearson, Melanie M

2016-04-19

The catheter-associated uropathogenProteus mirabilisfrequently causes urinary stones, but little has been known about the initial stages of bladder colonization and stone formation. We found thatP. mirabilisrapidly invades the bladder urothelium, but generally fails to establish an intracellular niche. Instead, it forms extracellular clusters in the bladder lumen, which form foci of mineral deposition consistent with development of urinary stones. These clusters elicit a robust neutrophil response, and we present evidence of neutrophil extracellular trap generation during experimental urinary tract infection. We identified two virulence factors required for cluster development: urease, which is required for urolithiasis, and mannose-resistantProteus-like fimbriae. The extracellular cluster formation byP. mirabilisstands in direct contrast to uropathogenicEscherichia coli, which readily formed intracellular bacterial communities but not luminal clusters or urinary stones. We propose that extracellular clusters are a key mechanism ofP. mirabilissurvival and virulence in the bladder.

Linear Cowden nevus: a new distinct epidermal nevus.

PubMed

Happle, Rudolf

2007-01-01

Within the group of epidermal nevi, a so far nameless disorder is described under the term "linear Cowden nevus". This non-organoid epidermal nevus is caused by loss of heterozygosity, occurring at an early developmental stage in an embryo with a germline PTEN mutation, giving rise to Cowden disease. Hence, linear Cowden nevus can be categorized as a characteristic feature of type 2 segmental Cowden disease. Until now, several authors had mistaken this epidermal nevus as a manifestation of Proteus syndrome. The concept of linear Cowden nevus implies that Proteus syndrome is by no means caused by PTEN mutations. As a clinical difference, linear Cowden nevus is markedly papillomatous and thick, whereas linear Proteus nevus tends to be rather flat. Moreover, the spectrum of possibly associated cutaneous or extracutaneous anomalies differs in the two types of nevi. In conclusion, linear Cowden nevus, that may also be called "linear PTEN nevus", represents a distinct clinicogenetic entity.

Intracellular pressure is a motive force for cell motion in Amoeba proteus.

PubMed

Yanai, M; Kenyon, C M; Butler, J P; Macklem, P T; Kelly, S M

1996-01-01

The cortical filament layer of free-living amoebae contains concentrated actomyosin, suggesting that it can contract and produce an internal hydrostatic pressure. We report here on direct and dynamic intracellular pressure (P(ic)) measurements in Amoeba proteus made using the servo-null technique. In resting apolar A. proteus, P(ic) increased while the cells remained immobile and at apparently constant volume. P(ic) then decreased approximately coincident with pseudopod formation. There was a positive correlation between P(ic) at the onset of movement and the rate of pseudopod formation. These results are the first direct evidence that hydrostatic pressure may be a motive force for cell motion. We postulate that contractile elements in the amoeba's cortical layer contract and increase P(ic) and that this P(ic) is utilized to overcome the viscous flow resistance of the intracellular contents during pseudopod formation.

CYTOPLASMIC DNA SYNTHESIS IN AMOEBA PROTEUS

PubMed Central

Rabinovitch, M.; Plaut, W.

1962-01-01

The incorporation of tritiated thymidine in Amoeba proteus was reinvestigated in order to see if it could be associated with microscopically detectable structures. Staining experiments with basic dyes, including the fluorochrome acridine orange, revealed the presence of large numbers of 0.3 to 0.5 µ particles in the cytoplasm of all cells studied. The effect of nuclease digestion on the dye affinity of the particles suggests that they contain DNA as well as RNA. Centrifugation of living cells at 10,000 g leads to the sedimentation of the particles in the centrifugal third of the ameba near the nucleus. Analysis of centrifuged cells which had been incubated with H3-thymidine showed a very high degree of correlation between the location of the nucleic acid-containing granules and that of acid-insoluble, deoxyribonuclease-sensitive labeled molecules and leads to the conclusion that cytoplasmic DNA synthesis in Amoeba proteus occurs in association with these particles. PMID:13972870

Elemental maps of Amoeba proteus by a scanning proton microprobe

NASA Astrophysics Data System (ADS)

Li, Minqian; Zhu, Jingde; Zhu, Jieqing; Zhou, Zheng; Huang, Zeqi; Zhou, Weiying; Cholewa, M.; Legge, G. J. F.

1991-03-01

Elemental maps for P, S, Cl, K, Ca and Zn of individual Amoeba proteus were obtained with the Melbourne scanning proton microprobe. The emphasis was put on the relationship of both distribution and concentration of Zn within the cell and the growth inhibitory effect of higher Zn concentrations in the culture medium. At a concentration of 0.04 mmol ZnCl 2, Amoeba growth was inhibited. But at a concentration of 0.0016 mmol, the Amoeba grew as well as a control grown without addition of Zn. We found that in the former (0.04 mmol) Zn concentrated three times more than in the latter (0.0016 mmol), and also that Zn was enriched much more in the nucleus and endoplasm (five to six times) than in other parts of the cell (two times). Future work along these lines may provide insight into the mechanism by which Zn affects the growth of Amoeba proteus and other cells.

Status Report on NEAMS PROTEUS/ORIGEN Integration

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

Wieselquist, William A

2016-02-18

The US Department of Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) Program has contributed significantly to the development of the PROTEUS neutron transport code at Argonne National Laboratory and to the Oak Ridge Isotope Generation and Depletion Code (ORIGEN) depletion/decay code at Oak Ridge National Laboratory. PROTEUS’s key capability is the efficient and scalable (up to hundreds of thousands of cores) neutron transport solver on general, unstructured, three-dimensional finite-element-type meshes. The scalability and mesh generality enable the transfer of neutron and power distributions to other codes in the NEAMS toolkit for advanced multiphysics analysis. Recently, ORIGEN has received considerablemore » modernization to provide the high-performance depletion/decay capability within the NEAMS toolkit. This work presents a description of the initial integration of ORIGEN in PROTEUS, mainly performed during FY 2015, with minor updates in FY 2016.« less

[Regulation of cortical cytoskeleton dynamics during migration of free-living amoebae].

PubMed

Kłopocka, Wanda; Redowicz, Maria Jolanta; Wasik, Anna

2009-01-01

Amoeba proteus and smaller by an order of magnitude (and evolutionary younger) Acanthamoeba castellanii have been for many years model cells for studies of amoeboidal (crawling) type of movement, characteristic also for some of metazoan cells such as fibroblasts, granulocytes and macrophages. Amoeboidal migration is indispensable of organization and dynamics of actin-based cytoskeleton. While there is a number of data on molecular mechanisms of motility of A. castellanii, there is very little known about bases of migration of A. proteus. Noteworthy, a large A. proteus (length approximately 600 microm) have been from over a century an object for studies on biology and physiology of cellular migration. This review describes the current knowledge on molecular aspects of force generation required for migration of these two amoebae and attempts to compare the functioning and regulation of actin cytoskeleton in these free-living unicellular species.

Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics

PubMed Central

Radonić, Aleksandar; Kocak Tufan, Zeliha; Domingo, Cristina

2017-01-01

Background We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. Methodology An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients. Principal findings The multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1–10 genome equivalents) and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours. Conclusions Virus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring. PMID:29155823

Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics.

PubMed

Brinkmann, Annika; Ergünay, Koray; Radonić, Aleksandar; Kocak Tufan, Zeliha; Domingo, Cristina; Nitsche, Andreas

2017-11-01

We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients. The multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1-10 genome equivalents) and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours. Virus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring.

Characterization of free thiol variants of an IgG1 by reversed phase ultra high pressure liquid chromatography coupled with mass spectrometry.

PubMed

Liu, Hongbin; Jeong, Justin; Kao, Yung-Hsiang; Zhang, Yonghua Taylor

2015-05-10

RP-HPLC has been demonstrated as a powerful tool to study antibody free thiol and disulfide variants. Recently, the introduction of UHPLC columns with wide pore size (300Å) and small particle size (1.7μm) offered the opportunity to further improve the separation of such variants. This paper describes a systematic evaluation of stationary phases, operating parameters, and mobile phases for a UHPLC based method to separate free thiol variants of a recombinant monoclonal antibody (referred as mAb A), targeting high resolution, high throughput and improved recovery. Among the four different stationary phases evaluated, UHPLC diphenyl columns were found to provide the best separation. Using an optimized UHPLC method, free thiol variants of mAb A were separated in 5min. Importantly, the UHPLC method revealed minor variants that had coeluted in an HPLC based method, and the UHPLC method is also applicable as a platform method for characterization of other mAbs as well. Furthermore, an on-line UHPLC-MS method was developed to characterize the separated variants, and this method can streamline the characterization of fully assembled monoclonal and bispecific therapeutic antibodies. Copyright © 2015 Elsevier B.V. All rights reserved.

Clinical Interpretation and Implications of Whole-Genome Sequencing

PubMed Central

Dewey, Frederick E.; Grove, Megan E.; Pan, Cuiping; Goldstein, Benjamin A.; Bernstein, Jonathan A.; Chaib, Hassan; Merker, Jason D.; Goldfeder, Rachel L.; Enns, Gregory M.; David, Sean P.; Pakdaman, Neda; Ormond, Kelly E.; Caleshu, Colleen; Kingham, Kerry; Klein, Teri E.; Whirl-Carrillo, Michelle; Sakamoto, Kenneth; Wheeler, Matthew T.; Butte, Atul J.; Ford, James M.; Boxer, Linda; Ioannidis, John P. A.; Yeung, Alan C.; Altman, Russ B.; Assimes, Themistocles L.; Snyder, Michael; Ashley, Euan A.; Quertermous, Thomas

2014-01-01

IMPORTANCE Whole-genome sequencing (WGS) is increasingly applied in clinical medicine and is expected to uncover clinically significant findings regardless of sequencing indication. OBJECTIVES To examine coverage and concordance of clinically relevant genetic variation provided by WGS technologies; to quantitate inherited disease risk and pharmacogenomic findings in WGS data and resources required for their discovery and interpretation; and to evaluate clinical action prompted by WGS findings. DESIGN, SETTING, AND PARTICIPANTS An exploratory study of 12 adult participants recruited at Stanford University Medical Center who underwent WGS between November 2011 and March 2012. A multidisciplinary team reviewed all potentially reportable genetic findings. Five physicians proposed initial clinical follow-up based on the genetic findings. MAIN OUTCOMES AND MEASURES Genome coverage and sequencing platform concordance in different categories of genetic disease risk, person-hours spent curating candidate disease-risk variants, interpretation agreement between trained curators and disease genetics databases, burden of inherited disease risk and pharmacogenomic findings, and burden and interrater agreement of proposed clinical follow-up. RESULTS Depending on sequencing platform, 10% to 19% of inherited disease genes were not covered to accepted standards for single nucleotide variant discovery. Genotype concordance was high for previously described single nucleotide genetic variants (99%-100%) but low for small insertion/deletion variants (53%-59%). Curation of 90 to 127 genetic variants in each participant required a median of 54 minutes (range, 5-223 minutes) per genetic variant, resulted in moderate classification agreement between professionals (Gross κ, 0.52; 95%CI, 0.40-0.64), and reclassified 69%of genetic variants cataloged as disease causing in mutation databases to variants of uncertain or lesser significance. Two to 6 personal disease-risk findings were discovered in each participant, including 1 frameshift deletion in the BRCA1 gene implicated in hereditary breast and ovarian cancer. Physician review of sequencing findings prompted consideration of a median of 1 to 3 initial diagnostic tests and referrals per participant, with fair interrater agreement about the suitability of WGS findings for clinical follow-up (Fleiss κ, 0.24; P < 001). CONCLUSIONS AND RELEVANCE In this exploratory study of 12 volunteer adults, the use of WGS was associated with incomplete coverage of inherited disease genes, low reproducibility of detection of genetic variation with the highest potential clinical effects, and uncertainty about clinically reportable findings. In certain cases, WGS will identify clinically actionable genetic variants warranting early medical intervention. These issues should be considered when determining the role of WGS in clinical medicine. PMID:24618965

Multi-Antenna Radar Systems for Doppler Rain Measurements

NASA Technical Reports Server (NTRS)

Durden, Stephen; Tanelli, Simone; Siqueira, Paul

2007-01-01

Use of multiple-antenna radar systems aboard moving high-altitude platforms has been proposed for measuring rainfall. The basic principle of the proposed systems is a variant of that of along-track interferometric synthetic-aperture radar systems used previously to measure ocean waves and currents.

Best practices for evaluating single nucleotide variant calling methods for microbial genomics

PubMed Central

Olson, Nathan D.; Lund, Steven P.; Colman, Rebecca E.; Foster, Jeffrey T.; Sahl, Jason W.; Schupp, James M.; Keim, Paul; Morrow, Jayne B.; Salit, Marc L.; Zook, Justin M.

2015-01-01

Innovations in sequencing technologies have allowed biologists to make incredible advances in understanding biological systems. As experience grows, researchers increasingly recognize that analyzing the wealth of data provided by these new sequencing platforms requires careful attention to detail for robust results. Thus far, much of the scientific Communit’s focus for use in bacterial genomics has been on evaluating genome assembly algorithms and rigorously validating assembly program performance. Missing, however, is a focus on critical evaluation of variant callers for these genomes. Variant calling is essential for comparative genomics as it yields insights into nucleotide-level organismal differences. Variant calling is a multistep process with a host of potential error sources that may lead to incorrect variant calls. Identifying and resolving these incorrect calls is critical for bacterial genomics to advance. The goal of this review is to provide guidance on validating algorithms and pipelines used in variant calling for bacterial genomics. First, we will provide an overview of the variant calling procedures and the potential sources of error associated with the methods. We will then identify appropriate datasets for use in evaluating algorithms and describe statistical methods for evaluating algorithm performance. As variant calling moves from basic research to the applied setting, standardized methods for performance evaluation and reporting are required; it is our hope that this review provides the groundwork for the development of these standards. PMID:26217378

Variability extraction and modeling for product variants.

PubMed

Linsbauer, Lukas; Lopez-Herrejon, Roberto Erick; Egyed, Alexander

2017-01-01

Fast-changing hardware and software technologies in addition to larger and more specialized customer bases demand software tailored to meet very diverse requirements. Software development approaches that aim at capturing this diversity on a single consolidated platform often require large upfront investments, e.g., time or budget. Alternatively, companies resort to developing one variant of a software product at a time by reusing as much as possible from already-existing product variants. However, identifying and extracting the parts to reuse is an error-prone and inefficient task compounded by the typically large number of product variants. Hence, more disciplined and systematic approaches are needed to cope with the complexity of developing and maintaining sets of product variants. Such approaches require detailed information about the product variants, the features they provide and their relations. In this paper, we present an approach to extract such variability information from product variants. It identifies traces from features and feature interactions to their implementation artifacts, and computes their dependencies. This work can be useful in many scenarios ranging from ad hoc development approaches such as clone-and-own to systematic reuse approaches such as software product lines. We applied our variability extraction approach to six case studies and provide a detailed evaluation. The results show that the extracted variability information is consistent with the variability in our six case study systems given by their variability models and available product variants.

An exploration of the accuracy of an invasive method for measuring the volume of specimens of Amoeba proteus.

PubMed

Whalen, T A; Demarco, A J

1999-10-01

A method is described for measuring the volume of individual specimens of Amoeba proteus which utilizes an easily constructed compressor to flatten the specimen to a known thickness. The microscopic image of the flattened specimen is captured on tape, digitized and analysed with the NIH Image software. The results from one specimen are given to illustrate the sources and magnitude of errors affecting these volume measurements.

Proteus Syndrome With a Cranial Intraosseous Lipoma.

PubMed

Wolfswinkel, Erik M; Imahiyerobo, Thomas A; McComb, J Gordon; Sanchez-Lara, Pedro A; Urata, Mark M

2017-11-01

Intraosseous lipomas are almost exclusively seen in the long bones. Presence in the craniofacial skeleton is extremely rare. A 7-year-old male is presented with a marked craniofacial deformation from a bony tumor containing an intraosseous lipoma. This finding established a clinical diagnosis of Proteus syndrome. Given the size of the tumor, producing an extensive deformity, three-dimensional modeling was used to generate a three-dimensional printed implant. The process to achieve a successful outcome is herein described.

[CHROMATIN ORGANIZATION IN CELL CYCLE OF AMOEBA PROTEUS ACCORDING TO OPTICAL TOMOGRAPHY DATA].

PubMed

Demin, S Yu; Berdieva, M A; Podlipaeva, Yu I; Yudin, A L; Goodkov, A V

2015-01-01

For the first time the nuclear cycle of large freshwater amoeba Amoeba proteus was studied by the method of optical tomography. The nuclei were fixed in situ in the cells of synchronized culture, stained by DAPI and examined by confocal laser scanning microscope. 3D-images of intranuclear chromatin were studied in details at different stages of nuclear cycle. The obtained data, together with literary ones allow represent the dynamics of structural organization of the nucleus in Amoeba proteus cell cycle in a new fashion. It was concluded that in this species the two-stage interphase takes place, as well as mitosis of peculiar type which does not correspond to any known type of mitosis according to classification existing now. It is presumed that in the course of nuclear cycle the chromosomes and/or their fragments are amplified, this presumption being in a good correspondence with the data about nuclear DNA hyperreplication in the cell cycle of A. proteus. As a result of chromosomes amplification their number may vary at different stages of cell cycle, and it allows to explain the contradictory data concerning the exact number of chromosomes in this species. The elimination of extra-DNA occurs mainly at the stage between prophase and prometaphase. We presume the majority of chromosomes, or may be even all of them to be referred to cholocentric type according to their behaviour during the mitosis.

A simple and low-cost platform technology for producing pexiganan antimicrobial peptide in E. coli.

PubMed

Zhao, Chun-Xia; Dwyer, Mirjana Dimitrijev; Yu, Alice Lei; Wu, Yang; Fang, Sheng; Middelberg, Anton P J

2015-05-01

Antimicrobial peptides, as a new class of antibiotics, have generated tremendous interest as potential alternatives to classical antibiotics. However, the large-scale production of antimicrobial peptides remains a significant challenge. This paper reports a simple and low-cost chromatography-free platform technology for producing antimicrobial peptides in Escherichia coli (E. coli). A fusion protein comprising a variant of the helical biosurfactant protein DAMP4 and the known antimicrobial peptide pexiganan is designed by joining the two polypeptides, at the DNA level, via an acid-sensitive cleavage site. The resulting DAMP4(var)-pexiganan fusion protein expresses at high level and solubility in recombinant E. coli, and a simple heat-purification method was applied to disrupt cells and deliver high-purity DAMP4(var)-pexiganan protein. Simple acid cleavage successfully separated the DAMP4 variant protein and the antimicrobial peptide. Antimicrobial activity tests confirmed that the bio-produced antimicrobial peptide has the same antimicrobial activity as the equivalent product made by conventional chemical peptide synthesis. This simple and low-cost platform technology can be easily adapted to produce other valuable peptide products, and opens a new manufacturing approach for producing antimicrobial peptides at large scale using the tools and approaches of biochemical engineering. © 2014 Wiley Periodicals, Inc.

Molecular Background of Colorectal Tumors From Patients with Lynch Syndrome Associated With Germline Variants in PMS2.

PubMed

Ten Broeke, S W; van Bavel, T C; Jansen, A M L; Gómez-García, E; Hes, F J; van Hest, L P; Letteboer, T G W; Olderode-Berends, M J W; Ruano, D; Spruijt, L; Suerink, M; Tops, C M; van Eijk, R; Morreau, H; van Wezel, T; Nielsen, M

2018-05-11

Germline variants in the mismatch repair genes MLH1, MSH2 (EPCAM), MSH6, or PMS2 cause Lynch syndrome. Patients with these variants have an increased risk of developing colorectal cancers (CRCs) that differ from sporadic CRCs in genetic and histologic features. It has been a challenge to study CRCs associated with PMS2 variants (PMS2-associated CRCs) because these develop less frequently and in patients of older ages than colorectal tumors with variants in the other mismatch repair genes. We analyzed 20 CRCs associated with germline variants in PMS2, 22 sporadic CRCs, 18 CRCs with germline variants in MSH2, and 24 CRCs from patients with germline variants in MLH1. Tumor tissue blocks were collected from Dutch pathology departments in 2017. After extraction of tumor DNA, we used a platform designed to detect approximately 3000 somatic hotspot variants in 55 genes (including KRAS, APC, CTNNB1, and TP53). Somatic variant frequencies were compared using the Fisher's exact test. None of the PMS2-associated CRCs contained any somatic variants in the catenin beta 1 gene (CTNNB1), which encodes β-catenin, whereas 14/24 MLH1-associated CRCs (58%) contained variants in CTNNB1. Half of PMS2-associated CRCs contained KRAS variants, but only 20% of these were in hotspots that encoded G12D or G13D. These hotspot variants occurred more frequently in CRCs associated with variants in MLH1 (37.5%, P=.44) and MSH2 (and 71.4%, P=.035) than with variants in PMS2. In a genetic analysis of 84 colorectal tumors, we found tumors from patients with PMS2-associated Lynch syndrome to be distinct from colorectal tumors associated with defects in other mismatch repair genes. This might account for differences in development and less frequent occurrence. Copyright © 2018 AGA Institute. Published by Elsevier Inc. All rights reserved.

Verification of the proteus two-dimensional Navier-Stokes code for flat plate and pipe flows

NASA Technical Reports Server (NTRS)

Conley, Julianne M.; Zeman, Patrick L.

1991-01-01

The Proteus Navier-Stokes Code is evaluated for 2-D/axisymmetric, viscous, incompressible, internal, and external flows. The particular cases to be discussed are laminar and turbulent flows over a flat plate, laminar and turbulent developing pipe flows, and turbulent pipe flow with swirl. Results are compared with exact solutions, empirical correlations, and experimental data. A detailed description of the code set-up, including boundary conditions, initial conditions, grid size, and grid packing is given for each case.

The development of an intelligent interface to a computational fluid dynamics flow-solver code

NASA Technical Reports Server (NTRS)

Williams, Anthony D.

1988-01-01

Researchers at NASA Lewis are currently developing an 'intelligent' interface to aid in the development and use of large, computational fluid dynamics flow-solver codes for studying the internal fluid behavior of aerospace propulsion systems. This paper discusses the requirements, design, and implementation of an intelligent interface to Proteus, a general purpose, 3-D, Navier-Stokes flow solver. The interface is called PROTAIS to denote its introduction of artificial intelligence (AI) concepts to the Proteus code.

The development of an intelligent interface to a computational fluid dynamics flow-solver code

NASA Technical Reports Server (NTRS)

Williams, Anthony D.

1988-01-01

Researchers at NASA Lewis are currently developing an 'intelligent' interface to aid in the development and use of large, computational fluid dynamics flow-solver codes for studying the internal fluid behavior of aerospace propulsion systems. This paper discusses the requirements, design, and implementation of an intelligent interface to Proteus, a general purpose, three-dimensional, Navier-Stokes flow solver. The interface is called PROTAIS to denote its introduction of artificial intelligence (AI) concepts to the Proteus code.

Water quality bioassay using selected protozoa. I. [Paramecium candatum; Amoeba proteus; Euglena gracilis

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

Mills, W.L.

1976-01-01

The suitability of certain species of protozoa as indicators of water quality has been determined. Experiments were conducted under laboratory conditions to standardize a bioassay procedure for water quality using either Paramecium caudatum, Amoeba proteus, or Euglena gracilis as the indicator organism. The bioassay, which consists of exposing the organisms to a known concentration of pollutant under laboratory conditions, followed by microscopic observation to establish the time of death, affords a reliable, convenient and inexpensive way to monitor for water quality.

IMP-27, a Unique Metallo-β-Lactamase Identified in Geographically Distinct Isolates of Proteus mirabilis.

PubMed

Dixon, Nyssa; Fowler, Randal C; Yoshizumi, A; Horiyama, Tsukasa; Ishii, Y; Harrison, Lucas; Geyer, Chelsie N; Moland, Ellen Smith; Thomson, Kenneth; Hanson, Nancy D

2016-10-01

A novel metallo-β-lactamase gene, blaIMP-27, was identified in unrelated Proteus mirabilis isolates from two geographically distinct locations in the United States. Both isolates harbor blaIMP-27 as part of the first gene cassette in a class 2 integron. Antimicrobial susceptibility testing indicated susceptibility to aztreonam, piperacillin-tazobactam, and ceftazidime but resistance to ertapenem. However, hydrolysis assays indicated that ceftazidime was a substrate for IMP-27. Copyright © 2016 Dixon et al.

Toward a Mathematical Theory of Counterterrorism (Proteus USA, Volume 1, Issue 2, December 2007)

DTIC Science & Technology

2007-12-01

Toward a MaTheMaTical Theory of counTerTerrorisM The Proteus Monograph Series Volume 1, Issue 2 December 2007 Report Documentation Page Form...COVERED 00-00-2007 to 00-00-2007 4. TITLE AND SUBTITLE Toward a Mathematical Theory of Counterterrorism 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c...Army War College,Center for Strategic Leadership ,650 Wright Avenue,Carlisle,PA,17013-5049 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING

Analyzing Future Complex National Security Challenges within the Joint, Interagency, Intergovernmental, and Multinational Environment. Proteus Futures Academic Workshop Held in Carlisle Barracks, Pennsylvania on 22-24 August 2006

DTIC Science & Technology

2006-08-01

AVAILABILITY STATEMENT Approved for public release; distribution unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT 15. SUBJECT TERMS 16. SECURITY...threats, or financial insecurities. Yankee Going Home: The world of 2020 looks like a confused mess! Little is clear except that the world has... statements from Proteus: Insights from 2020 are highly releant when thinking about the current strategic picture in the context of Power: “When Power

Genetic high throughput screening in Retinitis Pigmentosa based on high resolution melting (HRM) analysis.

PubMed

Anasagasti, Ander; Barandika, Olatz; Irigoyen, Cristina; Benitez, Bruno A; Cooper, Breanna; Cruchaga, Carlos; López de Munain, Adolfo; Ruiz-Ederra, Javier

2013-11-01

Retinitis Pigmentosa (RP) involves a group of genetically determined retinal diseases caused by a large number of mutations that result in rod photoreceptor cell death followed by gradual death of cone cells. Most cases of RP are monogenic, with more than 80 associated genes identified so far. The high number of genes and variants involved in RP, among other factors, is making the molecular characterization of RP a real challenge for many patients. Although HRM has been used for the analysis of isolated variants or single RP genes, as far as we are concerned, this is the first study that uses HRM analysis for a high-throughput screening of several RP genes. Our main goal was to test the suitability of HRM analysis as a genetic screening technique in RP, and to compare its performance with two of the most widely used NGS platforms, Illumina and PGM-Ion Torrent technologies. RP patients (n = 96) were clinically diagnosed at the Ophthalmology Department of Donostia University Hospital, Spain. We analyzed a total of 16 RP genes that meet the following inclusion criteria: 1) size: genes with transcripts of less than 4 kb; 2) number of exons: genes with up to 22 exons; and 3) prevalence: genes reported to account for, at least, 0.4% of total RP cases worldwide. For comparison purposes, RHO gene was also sequenced with Illumina (GAII; Illumina), Ion semiconductor technologies (PGM; Life Technologies) and Sanger sequencing (ABI 3130xl platform; Applied Biosystems). Detected variants were confirmed in all cases by Sanger sequencing and tested for co-segregation in the family of affected probands. We identified a total of 65 genetic variants, 15 of which (23%) were novel, in 49 out of 96 patients. Among them, 14 (4 novel) are probable disease-causing genetic variants in 7 RP genes, affecting 15 patients. Our HRM analysis-based study, proved to be a cost-effective and rapid method that provides an accurate identification of genetic RP variants. This approach is effective for medium sized (<4 kb transcript) RP genes, which constitute over 80% of the total of known RP genes.

Genetic highthroughput screening in retinitis pigmentosa based on high resolution melting (HRM) analysis.

PubMed

Anasagasti, Ander; Barandika, Olatz; Irigoyen, Cristina; Benitez, Bruno A; Cooper, Breanna; Cruchaga, Carlos; López de Munain, Adolfo; Ruiz-Ederra, Javier

2013-10-24

Retinitis Pigmentosa (RP) involves a group of genetically determined retinal diseases caused by a large number of mutations that result in rod photoreceptor cell death followed by gradual death of cone cells. Most cases of RP are monogenic, with more than 80 associated genes identified so far. The high number of genes and variants involved in RP, among other factors, is making the molecular characterization of RP a real challenge for many patients. Although HRM has been used for the analysis of isolated variants or single RP genes, as far as we are concerned, this is the first study that uses HRM analysis for a high-throughput screening of several RP genes. Our main goal was to test the suitability of HRM analysis as a genetic screening technique in RP, and to compare its performance with two of the most widely used NGS platforms, Illumina and PGM-Ion Torrent technologies. RP patients (n=96) were clinically diagnosed at the Ophthalmology Department of Donostia University Hospital, Spain. We analyzed a total of 16 RP genes that meet the following inclusion criteria: 1) size: genes with transcripts of less than 4 kb; 2) number of exons: genes with up to 22 exons; and 3) prevalence: genes reported to account for, at least, 0.4 % of total RP cases worldwide. For comparison purposes, RHO gene was also sequenced with Illumina (GAII; Illumina), Ion semiconductor technologies (PGM; Life Technologies) and Sanger sequencing (ABI 3130xl platform; Applied Biosystems). Detected variants were confirmed in all cases by Sanger sequencing and tested for co-segregation in the family of affected probands. We identified a total of 65 genetic variants, 15 of which (23%) were novel, in 49 out of 96 patients. Among them, 14 (4 novel) are probable disease-causing genetic variants in 7 RP genes, affecting 15 patients. Our HRM analysis-based study, proved to be a cost-effective and rapid method that provides an accurate identification of genetic RP variants. This approach is effective for medium sized (<4 kb transcript) RP genes, which constitute over 80% of the total of known RP genes. © 2013 Published by Elsevier Ltd.

Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic Variants.

PubMed

Kim, Kyung; Seong, Moon-Woo; Chung, Won-Hyong; Park, Sung Sup; Leem, Sangseob; Park, Won; Kim, Jihyun; Lee, KiYoung; Park, Rae Woong; Kim, Namshin

2015-06-01

Sequencing depth, which is directly related to the cost and time required for the generation, processing, and maintenance of next-generation sequencing data, is an important factor in the practical utilization of such data in clinical fields. Unfortunately, identifying an exome sequencing depth adequate for clinical use is a challenge that has not been addressed extensively. Here, we investigate the effect of exome sequencing depth on the discovery of sequence variants for clinical use. Toward this, we sequenced ten germ-line blood samples from breast cancer patients on the Illumina platform GAII(x) at a high depth of ~200×. We observed that most function-related diverse variants in the human exonic regions could be detected at a sequencing depth of 120×. Furthermore, investigation using a diagnostic gene set showed that the number of clinical variants identified using exome sequencing reached a plateau at an average sequencing depth of about 120×. Moreover, the phenomena were consistent across the breast cancer samples.

Multi-locus mixed model analysis of stem rust resistance in a worldwide collection of winter wheat

USDA-ARS?s Scientific Manuscript database

Genome-wide association mapping is a powerful tool for dissecting the relationship between phenotypes and genetic variants in diverse populations. With improved cost efficiency of high-throughput genotyping platforms, association mapping is a desirable method to mine populations for favorable allele...

Proteus mirabilis fimbriae- and urease-dependent clusters assemble in an extracellular niche to initiate bladder stone formation

PubMed Central

Schaffer, Jessica N.; Norsworthy, Allison N.; Sun, Tung-Tien

2016-01-01

The catheter-associated uropathogen Proteus mirabilis frequently causes urinary stones, but little has been known about the initial stages of bladder colonization and stone formation. We found that P. mirabilis rapidly invades the bladder urothelium, but generally fails to establish an intracellular niche. Instead, it forms extracellular clusters in the bladder lumen, which form foci of mineral deposition consistent with development of urinary stones. These clusters elicit a robust neutrophil response, and we present evidence of neutrophil extracellular trap generation during experimental urinary tract infection. We identified two virulence factors required for cluster development: urease, which is required for urolithiasis, and mannose-resistant Proteus-like fimbriae. The extracellular cluster formation by P. mirabilis stands in direct contrast to uropathogenic Escherichia coli, which readily formed intracellular bacterial communities but not luminal clusters or urinary stones. We propose that extracellular clusters are a key mechanism of P. mirabilis survival and virulence in the bladder. PMID:27044107

In Vitro Studies of Semisynthetic α- (Substituted-Ureido) Penicillins

PubMed Central

Bodey, Gerald P.; Stewart, Dorothy

1971-01-01

The activity of three α-(substituted-ureido) penicillins was evaluated in vitro against 599 clinical isolates of gram-negative bacilli, by use of the broth-dilution technique. At a concentration of 12.5 μg or less/ml, BL-P1597 inhibited 90% of isolates of Pseudomonas sp., 56% of Enterobacter sp., 67% of indole-positive Proteus spp., 72% of Escherichia coli, and 85% of Proteus mirabilis. BL-P1654 had similar activity, whereas BL-P1532 was much less active. At a concentration of 25 μg or less/ml, BL-P1597 also inhibited nearly 60% of isolates of Klebsiella sp. and nearly 40% of Serratia sp. BL-P1597 and BL-P1654 were as active as ampicillin and carbenicillin against E. coli and P. mirabilis. They were less active than carbenicillin against indole-positive Proteus spp. Both drugs were substantially more active than carbenicillin against Pseudomonas sp. A strain of Pseudomonas sp. which developed resistance to carbenicillin also developed resistance to the α-(substituted-ureido) penicillins simultaneously. PMID:4930281

Cytoplasmic DNA synthesis in Amoeba proteus. I. On the particulate nature of the DNA-containing elements.

PubMed

RABINOVITCH, M; PLAUT, W

1962-12-01

The incorporation of tritiated thymidine in Amoeba proteus was reinvestigated in order to see if it could be associated with microscopically detectable structures. Staining experiments with basic dyes, including the fluorochrome acridine orange, revealed the presence of large numbers of 0.3 to 0.5 micro particles in the cytoplasm of all cells studied. The effect of nuclease digestion on the dye affinity of the particles suggests that they contain DNA as well as RNA. Centrifugation of living cells at 10,000 g leads to the sedimentation of the particles in the centrifugal third of the ameba near the nucleus. Analysis of centrifuged cells which had been incubated with H(3)-thymidine showed a very high degree of correlation between the location of the nucleic acid-containing granules and that of acid-insoluble, deoxyribonuclease-sensitive labeled molecules and leads to the conclusion that cytoplasmic DNA synthesis in Amoeba proteus occurs in association with these particles.

Handling Different Spatial Resolutions in Image Fusion by Multivariate Curve Resolution-Alternating Least Squares for Incomplete Image Multisets.

PubMed

Piqueras, Sara; Bedia, Carmen; Beleites, Claudia; Krafft, Christoph; Popp, Jürgen; Maeder, Marcel; Tauler, Romà; de Juan, Anna

2018-06-05

Data fusion of different imaging techniques allows a comprehensive description of chemical and biological systems. Yet, joining images acquired with different spectroscopic platforms is complex because of the different sample orientation and image spatial resolution. Whereas matching sample orientation is often solved by performing suitable affine transformations of rotation, translation, and scaling among images, the main difficulty in image fusion is preserving the spatial detail of the highest spatial resolution image during multitechnique image analysis. In this work, a special variant of the unmixing algorithm Multivariate Curve Resolution Alternating Least Squares (MCR-ALS) for incomplete multisets is proposed to provide a solution for this kind of problem. This algorithm allows analyzing simultaneously images collected with different spectroscopic platforms without losing spatial resolution and ensuring spatial coherence among the images treated. The incomplete multiset structure concatenates images of the two platforms at the lowest spatial resolution with the image acquired with the highest spatial resolution. As a result, the constituents of the sample analyzed are defined by a single set of distribution maps, common to all platforms used and with the highest spatial resolution, and their related extended spectral signatures, covering the signals provided by each of the fused techniques. We demonstrate the potential of the new variant of MCR-ALS for multitechnique analysis on three case studies: (i) a model example of MIR and Raman images of pharmaceutical mixture, (ii) FT-IR and Raman images of palatine tonsil tissue, and (iii) mass spectrometry and Raman images of bean tissue.

Detection of human antibodies binding with smooth and rough LPSs from Proteus mirabilis O3 strains S1959, R110, R45.

PubMed

Gleńska-Olender, J; Durlik, K; Konieczna, I; Kowalska, P; Gawęda, J; Kaca, W

2017-11-01

Bacteria of the genus Proteus of the family Enterobacteriaceae are facultative human pathogens responsible mainly for urinary tract and wound infections, bacteremia and the development of rheumatoid arthritis (RA). We have analyzed and compared by ELISA the titer of antibodies in plasmas of healthy individuals and in sera of rheumatoid arthritis patients recognizing a potential host cross-reactive epitope (lysine-galacturonic acid epitopes) present in Proteus lipopolysaccharide (LPS). In our experiments LPSs isolated from two mutants of smooth Proteus mirabilis 1959 (O3), i.e. strains R110 and R45, were used. R110 (Ra type mutant) is lacking the O-specific polysaccharide, but possesses a complete core oligosaccharide, while R45 (Re type) has a reduced core oligosaccharide and contains two 3-deoxy-D-manno-oct-2-ulosonic acid residues and one of 4-amino-4-deoxy-L-arabinopyranose residues. Titer of P. mirabilis S1959 LPS-specific-antibodies increased with the age of blood donors. RA and blood donors' sera contained antibodies against S and Ra and Re type of P. mirabilis O3 LPSs. Antibodies recognizing lysine-galacturonic acid epitopes of O3 LPS were detected by ELISA in some plasmas of healthy individuals and sera of rheumatoid arthritis patients. RA patients antibodies reacting with P. mirabilis S1959 S and R LPSs may indicate a potential role of anti-LPS antibodies in molecular mimicry in RA diseases.

Preliminary Analysis of the Transient Reactor Test Facility (TREAT) with PROTEUS

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

Connaway, H. M.; Lee, C. H.

The neutron transport code PROTEUS has been used to perform preliminary simulations of the Transient Reactor Test Facility (TREAT). TREAT is an experimental reactor designed for the testing of nuclear fuels and other materials under transient conditions. It operated from 1959 to 1994, when it was placed on non-operational standby. The restart of TREAT to support the U.S. Department of Energy’s resumption of transient testing is currently underway. Both single assembly and assembly-homogenized full core models have been evaluated. Simulations were performed using a historic set of WIMS-ANL-generated cross-sections as well as a new set of Serpent-generated cross-sections. To supportmore » this work, further analyses were also performed using additional codes in order to investigate particular aspects of TREAT modeling. DIF3D and the Monte-Carlo codes MCNP and Serpent were utilized in these studies. MCNP and Serpent were used to evaluate the effect of geometry homogenization on the simulation results and to support code-to-code comparisons. New meshes for the PROTEUS simulations were created using the CUBIT toolkit, with additional meshes generated via conversion of selected DIF3D models to support code-to-code verifications. All current analyses have focused on code-to-code verifications, with additional verification and validation studies planned. The analysis of TREAT with PROTEUS-SN is an ongoing project. This report documents the studies that have been performed thus far, and highlights key challenges to address in future work.« less

Cytotoxicity of polyamines to Amoeba proteus: role of polyamine oxidase.

PubMed

Schenkel, E; Dubois, J G; Helson-Cambier, M; Hanocq, M

1996-02-01

It has been shown that oxidation of polyamines by polyamine oxidases can produce toxic compounds (H2O2, aldehydes, ammonia) and that the polyamine oxidase-polyamine system is implicated, in vitro, in the death of several parasites. Using Amoeba proteus as an in vitro model, we studied the cytotoxicity to these cells of spermine, spermidine, their acetyl derivatives, and their hypothetical precursors. Spermine and N1-acetylspermine were more toxic than emetine, an amoebicidal reference drug. Spermine presented a short-term toxicity, but a 48-h contact time was necessary for the high toxicity of spermidine. The uptake by Amoeba cells of the different polyamines tested was demonstrated. On the other hand, a high polyamine oxidase activity was identified in Amoeba proteus crude extract. Spermine (theoretical 100%) and N1-acetylspermine (64%) were the best substrates at pH 9.5, while spermidine, its acetyl derivatives, and putrescine were very poorly oxidized by this enzyme (3-20%). Spermine oxidase activity was inhibited by phenylhydrazine (nil) and isoniazid (approximately 50%). Mepacrine did not inhibit the enzyme activity at pH 8. Neither monoamine nor diamine oxidase activity (approximately 10%) was found. It must be emphasized that spermine, the best enzyme substrate, is the most toxic polyamine. This finding suggests that knowledge of polyamine oxidase specificity can be used to modulate the cytotoxicity of polyamine derivatives. Amoeba proteus was revealed as a simple model for investigation of the connection between cytotoxicity and enzyme activity.

Pinocytosis and locomotion of amoebae. XV. Visualization of Ca++-dynamics by chlorotetracycline (CTC) fluorescence during induced pinocytosis in living Amoeba proteus.

PubMed

Gawlitta, W; Stockem, W; Wehland, J; Weber, K

1980-01-01

The dynamics of Ca++ during induced pinocytosis were studied in Amoeba proteus using chlorotetracycline (CTC). The fluorescence of the Ca++ - CTC-complex was monitored by an image intensification system, which has certain advantages over standard equipment: (1) Living cells are not subjected to the damaging influence of intensive microscopic illumination, (2) fluorescent probes are not bleached during observation, and (3) the rapid dynamics of the Ca++ -fluxes can be recorded using short exposure times. The results demonstrate the existence of Ca++ bound to intracellular and extracellular sites of the cell membrane complex in normal locomoting and pinocytotic Amoeba proteus. The application of cations inducing pinocytosis causes a rapid decrease in the external CTC-fluorescence probably due to a release of Ca++ from the mucous layer. The degree of fluorescence intensity is correlated with the capacity of pinocytotic channel formation, i.e., the fluorescence decreases as the number of channels increases. During the phase of vesiculation a distinct fluorescence mainly restricted to the basal region of the channels is observed. Intracellular Ca++ was detected in close vicinity to the plasma membrane after both microinjection and external application of CTC. The internal CTC-fluorescence is slightly decreased during the induction phase of pinocytosis. The observations are in good agreement with previous results on the localization of Ca++ -binding sites at the plasma membrane of Amoeba proteus and demonstrate the important role of Ca++ -fluxes for the process of pinocytosis.

Regularized rare variant enrichment analysis for case-control exome sequencing data.

PubMed

Larson, Nicholas B; Schaid, Daniel J

2014-02-01

Rare variants have recently garnered an immense amount of attention in genetic association analysis. However, unlike methods traditionally used for single marker analysis in GWAS, rare variant analysis often requires some method of aggregation, since single marker approaches are poorly powered for typical sequencing study sample sizes. Advancements in sequencing technologies have rendered next-generation sequencing platforms a realistic alternative to traditional genotyping arrays. Exome sequencing in particular not only provides base-level resolution of genetic coding regions, but also a natural paradigm for aggregation via genes and exons. Here, we propose the use of penalized regression in combination with variant aggregation measures to identify rare variant enrichment in exome sequencing data. In contrast to marginal gene-level testing, we simultaneously evaluate the effects of rare variants in multiple genes, focusing on gene-based least absolute shrinkage and selection operator (LASSO) and exon-based sparse group LASSO models. By using gene membership as a grouping variable, the sparse group LASSO can be used as a gene-centric analysis of rare variants while also providing a penalized approach toward identifying specific regions of interest. We apply extensive simulations to evaluate the performance of these approaches with respect to specificity and sensitivity, comparing these results to multiple competing marginal testing methods. Finally, we discuss our findings and outline future research. © 2013 WILEY PERIODICALS, INC.

GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR.

PubMed

Gubelmann, Carine; Gattiker, Alexandre; Massouras, Andreas; Hens, Korneel; David, Fabrice; Decouttere, Frederik; Rougemont, Jacques; Deplancke, Bart

2011-01-01

The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and patterns of these variants with high sensitivity. High-throughput quantitative real-time polymerase chain reaction (qPCR) is an ideal technique to accurately quantify nucleic acid sequences including splice variants. However, currently available primer design programs do not distinguish between splice variants and also differ substantially in overall quality, functionality or throughput mode. Here, we present GETPrime, a primer database supported by a novel platform that uniquely combines and automates several features critical for optimal qPCR primer design. These include the consideration of all gene splice variants to enable either gene-specific (covering the majority of splice variants) or transcript-specific (covering one splice variant) expression profiling, primer specificity validation, automated best primer pair selection according to strict criteria and graphical visualization of the latter primer pairs within their genomic context. GETPrime primers have been extensively validated experimentally, demonstrating high transcript specificity in complex samples. Thus, the free-access, user-friendly GETPrime database allows fast primer retrieval and visualization for genes or groups of genes of most common model organisms, and is available at http://updepla1srv1.epfl.ch/getprime/. Database URL: http://deplanckelab.epfl.ch.

GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR

PubMed Central

Gubelmann, Carine; Gattiker, Alexandre; Massouras, Andreas; Hens, Korneel; David, Fabrice; Decouttere, Frederik; Rougemont, Jacques; Deplancke, Bart

2011-01-01

The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and patterns of these variants with high sensitivity. High-throughput quantitative real-time polymerase chain reaction (qPCR) is an ideal technique to accurately quantify nucleic acid sequences including splice variants. However, currently available primer design programs do not distinguish between splice variants and also differ substantially in overall quality, functionality or throughput mode. Here, we present GETPrime, a primer database supported by a novel platform that uniquely combines and automates several features critical for optimal qPCR primer design. These include the consideration of all gene splice variants to enable either gene-specific (covering the majority of splice variants) or transcript-specific (covering one splice variant) expression profiling, primer specificity validation, automated best primer pair selection according to strict criteria and graphical visualization of the latter primer pairs within their genomic context. GETPrime primers have been extensively validated experimentally, demonstrating high transcript specificity in complex samples. Thus, the free-access, user-friendly GETPrime database allows fast primer retrieval and visualization for genes or groups of genes of most common model organisms, and is available at http://updepla1srv1.epfl.ch/getprime/. Database URL: http://deplanckelab.epfl.ch. PMID:21917859

Changes in global gene expression profiles induced by HPV 16 E6 oncoprotein variants in cervical carcinoma C33-A cells

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

Zacapala-Gómez, Ana Elvira, E-mail: zak_ana@yahoo.com.mx; Del Moral-Hernández, Oscar, E-mail: odelmoralh@gmail.com; Villegas-Sepúlveda, Nicolás, E-mail: nvillega@cinvestav.mx

We analyzed the effects of the expression of HPV 16 E6 oncoprotein variants (AA-a, AA-c, E-A176/G350, E-C188/G350, E-G350), and the E-Prototype in global gene expression profiles in an in vitro model. E6 gene was cloned into an expression vector fused to GFP and was transfected in C33-A cells. Affymetrix GeneChip Human Transcriptome Array 2.0 platform was used to analyze the expression of over 245,000 coding transcripts. We found that HPV16 E6 variants altered the expression of 387 different genes in comparison with E-Prototype. The altered genes are involved in cellular processes related to the development of cervical carcinoma, such asmore » adhesion, angiogenesis, apoptosis, differentiation, cell cycle, proliferation, transcription and protein translation. Our results show that polymorphic changes in HPV16 E6 natural variants are sufficient to alter the overall gene expression profile in C33-A cells, explaining in part the observed differences in oncogenic potential of HPV16 variants. - Highlights: • Amino acid changes in HPV16 E6 variants modulate the transciption of specific genes. • This is the first comparison of global gene expression profile of HPV 16 E6 variants. • Each HPV 16 E6 variant appears to have its own molecular signature.« less

Investigation of Experimental Factors That Underlie BRCA1/2 mRNA Isoform Expression Variation: Recommendations for Utilizing Targeted RNA Sequencing to Evaluate Potential Spliceogenic Variants

PubMed Central

Lattimore, Vanessa L.; Pearson, John F.; Currie, Margaret J.; Spurdle, Amanda B.; Robinson, Bridget A.; Walker, Logan C.

2018-01-01

PCR-based RNA splicing assays are commonly used in diagnostic and research settings to assess the potential effects of variants of uncertain clinical significance in BRCA1 and BRCA2. The Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium completed a multicentre investigation to evaluate differences in assay design and the integrity of published data, raising a number of methodological questions associated with cell culture conditions and PCR-based protocols. We utilized targeted RNA-seq to re-assess BRCA1 and BRCA2 mRNA isoform expression patterns in lymphoblastoid cell lines (LCLs) previously used in the multicentre ENIGMA study. Capture of the targeted cDNA sequences was carried out using 34 BRCA1 and 28 BRCA2 oligonucleotides from the Illumina Truseq Targeted RNA Expression platform. Our results show that targeted RNA-seq analysis of LCLs overcomes many of the methodology limitations associated with PCR-based assays leading us to make the following observations and recommendations: (1) technical replicates (n > 2) of variant carriers to capture methodology induced variability associated with RNA-seq assays, (2) LCLs can undergo multiple freeze/thaw cycles and can be cultured up to 2 weeks without noticeably influencing isoform expression levels, (3) nonsense-mediated decay inhibitors are essential prior to splicing assays for comprehensive mRNA isoform detection, (4) quantitative assessment of exon:exon junction levels across BRCA1 and BRCA2 can help distinguish between normal and aberrant isoform expression patterns. Experimentally derived recommendations from this study will facilitate the application of targeted RNA-seq platforms for the quantitation of BRCA1 and BRCA2 mRNA aberrations associated with sequence variants of uncertain clinical significance. PMID:29774201

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

Hornung, Richard D.; Hones, Holger E.

The RAJA Performance Suite is designed to evaluate performance of the RAJA performance portability library on a wide variety of important high performance computing (HPC) algorithmic lulmels. These kernels assess compiler optimizations and various parallel programming model backends accessible through RAJA, such as OpenMP, CUDA, etc. The Initial version of the suite contains 25 computational kernels, each of which appears in 6 variants: Baseline SequcntiaJ, RAJA SequentiaJ, Baseline OpenMP, RAJA OpenMP, Baseline CUDA, RAJA CUDA. All variants of each kernel perform essentially the same mathematical operations and the loop body code for each kernel is identical across all variants. Theremore » are a few kernels, such as those that contain reduction operations, that require CUDA-specific coding for their CUDA variants. ActuaJ computer instructions executed and how they run in parallel differs depending on the parallel programming model backend used and which optimizations are perfonned by the compiler used to build the Perfonnance Suite executable. The Suite will be used primarily by RAJA developers to perform regular assessments of RAJA performance across a range of hardware platforms and compilers as RAJA features are being developed. It will also be used by LLNL hardware and software vendor panners for new defining requirements for future computing platform procurements and acceptance testing. In particular, the RAJA Performance Suite will be used for compiler acceptance testing of the upcoming CORAUSierra machine {initial LLNL delivery expected in late-2017/early 2018) and the CORAL-2 procurement. The Suite will aJso be used to generate concise source code reproducers of compiler and runtime issues we uncover so that we may provide them to relevant vendors to be fixed.« less

Investigation of Experimental Factors That Underlie BRCA1/2 mRNA Isoform Expression Variation: Recommendations for Utilizing Targeted RNA Sequencing to Evaluate Potential Spliceogenic Variants.

PubMed

Lattimore, Vanessa L; Pearson, John F; Currie, Margaret J; Spurdle, Amanda B; Robinson, Bridget A; Walker, Logan C

2018-01-01

PCR-based RNA splicing assays are commonly used in diagnostic and research settings to assess the potential effects of variants of uncertain clinical significance in BRCA1 and BRCA2 . The Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium completed a multicentre investigation to evaluate differences in assay design and the integrity of published data, raising a number of methodological questions associated with cell culture conditions and PCR-based protocols. We utilized targeted RNA-seq to re-assess BRCA1 and BRCA2 mRNA isoform expression patterns in lymphoblastoid cell lines (LCLs) previously used in the multicentre ENIGMA study. Capture of the targeted cDNA sequences was carried out using 34 BRCA1 and 28 BRCA2 oligonucleotides from the Illumina Truseq Targeted RNA Expression platform. Our results show that targeted RNA-seq analysis of LCLs overcomes many of the methodology limitations associated with PCR-based assays leading us to make the following observations and recommendations: (1) technical replicates ( n  > 2) of variant carriers to capture methodology induced variability associated with RNA-seq assays, (2) LCLs can undergo multiple freeze/thaw cycles and can be cultured up to 2 weeks without noticeably influencing isoform expression levels, (3) nonsense-mediated decay inhibitors are essential prior to splicing assays for comprehensive mRNA isoform detection, (4) quantitative assessment of exon:exon junction levels across BRCA1 and BRCA2 can help distinguish between normal and aberrant isoform expression patterns. Experimentally derived recommendations from this study will facilitate the application of targeted RNA-seq platforms for the quantitation of BRCA1 and BRCA2 mRNA aberrations associated with sequence variants of uncertain clinical significance.

Cerebriform connective tissue nevus of lumbar.

PubMed

Chen, Jinbo; Chen, Liuqing; Duan, Yiqun; Li, Dongsheng; Dong, Bilin

2015-02-01

Connective tissue nevi represents a kind of hamartoma, and coalescence of the lesions in a cerebriform mode in the lumbar region without Proteus syndrome is rarely seen. Here, we report a 26-year-old woman presenting with nodules and plaques in her left lumbar region of 26 years in duration. Histopathological examination and Masson-trichrome stain showed increased dermal collagen bundles in a haphazard array. The diagnosis of connective tissue nevi was made. This is the first case report on cerebriform connective tissue nevi without Proteus syndrome in the lumbar region. © 2014 Japanese Dermatological Association.

Proteus syndrome: A rare cause of gigantic limb.

PubMed

Chakrabarti, Nandini; Chattopadhyay, Chandan; Bhuban, Majhi; Pal, Salil Kumar

2014-04-01

A congenital disorder with variable manifestations, including partial gigantism of the hands and feet with hypertrophy of soles, nevi, hemihypertrophy, gynecomastia, macrocephaly and other skull abnormalities, and abdominal lipomatosis. The cause is unknown, although a genetic origin, generally of autosomal-dominant transmission, has been conjectured. Symptoms can be treated, but there is no known cure. We present the case of a young male with grotesque overgrowth of the right lower limb, splenomegaly and multiple nevi. Angiography revealed venous malformation within the limb. The findings are in conformity to the criteria for the Proteus syndrome.

Collective motion in Proteus mirabilis swarms

NASA Astrophysics Data System (ADS)

Haoran, Xu

Proteus mirabilisis a Gram-negative, rod-shaped bacterium. It is widely distributed in soil and water, and it is well known for exhibiting swarming motility on nutrient agar surfaces. In our study, we focused on the collective motility of P. mirabilis and uncovered a range of interesting phenomena. Here we will present our efforts to understand these phenomena through experiments and simulation. Mailing address: Room 306 Science Centre North Block, The Chinese University of Hong Kong, Shatin, N.T. Hong Kong SAR. Phone: +852-3943-6354. Fax: +852-2603-5204. E-mail:xhrphx@gmail.com.

Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome

DOE PAGES

Wu, Hong; Zeng, Hong; Lam, Robert; ...

2015-08-01

Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson–Crick base pairs in the genome. Pathogenic mutations in theMLH1gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. Lastly, the structure shares a high degree of similarity with previously determined prokaryoticMLH1homologs; however, this structure affords a more accurate platform for the classification ofMLH1variants.

HTR-PROTEUS PEBBLE BED EXPERIMENTAL PROGRAM CORE 4: RANDOM PACKING WITH A 1:1 MODERATOR-TO-FUEL PEBBLE RATIO

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

John D. Bess; Leland M. Montierth

2013-03-01

In its deployment as a pebble bed reactor (PBR) critical facility from 1992 to 1996, the PROTEUS facility was designated as HTR-PROTEUS. This experimental program was performed as part of an International Atomic Energy Agency (IAEA) Coordinated Research Project (CRP) on the Validation of Safety Related Physics Calculations for Low Enriched HTGRs. Within this project, critical experiments were conducted for graphite moderated LEU systems to determine core reactivity, flux and power profiles, reaction-rate ratios, the worth of control rods, both in-core and reflector based, the worth of burnable poisons, kinetic parameters, and the effects of moisture ingress on these parameters.more » One benchmark experiment was evaluated in this report: Core 4. Core 4 represents the only configuration with random pebble packing in the HTR-PROTEUS series of experiments, and has a moderator-to-fuel pebble ratio of 1:1. Three random configurations were performed. The initial configuration, Core 4.1, was rejected because the method for pebble loading, separate delivery tubes for the moderator and fuel pebbles, may not have been completely random; this core loading was rejected by the experimenters. Cores 4.2 and 4.3 were loaded using a single delivery tube, eliminating the possibility for systematic ordering effects. The second and third cores differed slightly in the quantity of pebbles loaded (40 each of moderator and fuel pebbles), stacked height of the pebbles in the core cavity (0.02 m), withdrawn distance of the stainless steel control rods (20 mm), and withdrawn distance of the autorod (30 mm). The 34 coolant channels in the upper axial reflector and the 33 coolant channels in the lower axial reflector were open. Additionally, the axial graphite fillers used in all other HTR-PROTEUS configurations to create a 12-sided core cavity were not used in the randomly packed cores. Instead, graphite fillers were placed on the cavity floor, creating a funnel-like base, to discourage ordering effects during pebble loading. Core 4 was determined to be acceptable benchmark experiment.« less

HTR-proteus pebble bed experimental program core 4: random packing with a 1:1 moderator-to-fuel pebble ratio

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

Bess, John D.; Montierth, Leland M.; Sterbentz, James W.

2014-03-01

In its deployment as a pebble bed reactor (PBR) critical facility from 1992 to 1996, the PROTEUS facility was designated as HTR-PROTEUS. This experimental program was performed as part of an International Atomic Energy Agency (IAEA) Coordinated Research Project (CRP) on the Validation of Safety Related Physics Calculations for Low Enriched HTGRs. Within this project, critical experiments were conducted for graphite moderated LEU systems to determine core reactivity, flux and power profiles, reaction-rate ratios, the worth of control rods, both in-core and reflector based, the worth of burnable poisons, kinetic parameters, and the effects of moisture ingress on these parameters.more » One benchmark experiment was evaluated in this report: Core 4. Core 4 represents the only configuration with random pebble packing in the HTR-PROTEUS series of experiments, and has a moderator-to-fuel pebble ratio of 1:1. Three random configurations were performed. The initial configuration, Core 4.1, was rejected because the method for pebble loading, separate delivery tubes for the moderator and fuel pebbles, may not have been completely random; this core loading was rejected by the experimenters. Cores 4.2 and 4.3 were loaded using a single delivery tube, eliminating the possibility for systematic ordering effects. The second and third cores differed slightly in the quantity of pebbles loaded (40 each of moderator and fuel pebbles), stacked height of the pebbles in the core cavity (0.02 m), withdrawn distance of the stainless steel control rods (20 mm), and withdrawn distance of the autorod (30 mm). The 34 coolant channels in the upper axial reflector and the 33 coolant channels in the lower axial reflector were open. Additionally, the axial graphite fillers used in all other HTR-PROTEUS configurations to create a 12-sided core cavity were not used in the randomly packed cores. Instead, graphite fillers were placed on the cavity floor, creating a funnel-like base, to discourage ordering effects during pebble loading. Core 4 was determined to be acceptable benchmark experiment.« less

Initial Comparison of Direct and Legacy Modeling Approaches for Radial Core Expansion Analysis

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

Shemon, Emily R.

2016-10-10

Radial core expansion in sodium-cooled fast reactors provides an important reactivity feedback effect. As the reactor power increases due to normal start up conditions or accident scenarios, the core and surrounding materials heat up, causing both grid plate expansion and bowing of the assembly ducts. When the core restraint system is designed correctly, the resulting structural deformations introduce negative reactivity which decreases the reactor power. Historically, an indirect procedure has been used to estimate the reactivity feedback due to structural deformation which relies upon perturbation theory and coupling legacy physics codes with limited geometry capabilities. With advancements in modeling andmore » simulation, radial core expansion phenomena can now be modeled directly, providing an assessment of the accuracy of the reactivity feedback coefficients generated by indirect legacy methods. Recently a new capability was added to the PROTEUS-SN unstructured geometry neutron transport solver to analyze deformed meshes quickly and directly. By supplying the deformed mesh in addition to the base configuration input files, PROTEUS-SN automatically processes material adjustments including calculation of region densities to conserve mass, calculation of isotopic densities according to material models (for example, sodium density as a function of temperature), and subsequent re-homogenization of materials. To verify the new capability of directly simulating deformed meshes, PROTEUS-SN was used to compute reactivity feedback for a series of contrived yet representative deformed configurations for the Advanced Burner Test Reactor design. The indirect legacy procedure was also performed to generate reactivity feedback coefficients for the same deformed configurations. Interestingly, the legacy procedure consistently overestimated reactivity feedbacks by 35% compared to direct simulations by PROTEUS-SN. This overestimation indicates that the legacy procedures are in fact not conservative and could be overestimating reactivity feedback effects that are closely tied to reactor safety. We conclude that there is indeed value in performing direct simulation of deformed meshes despite the increased computational expense. PROTEUS-SN is already part of the SHARP multi-physics toolkit where both thermal hydraulics and structural mechanical feedback modeling can be applied but this is the first comparison of direct simulation to legacy techniques for radial core expansion.« less

Mechanics and control of the cytoskeleton in Amoeba proteus.

PubMed Central

Dembo, M

1989-01-01

Many models of the cytoskeletal motility of Amoeba proteus can be formulated in terms of the theory of reactive interpenetrating flow (Dembo and Harlow, 1986). We have devised numerical methodology for testing such models against the phenomenon of steady axisymmetric fountain flow. The simplest workable scheme revealed by such tests (the minimal model) is the main preoccupation of this study. All parameters of the minimal model are determined from available data. Using these parameters the model quantitatively accounts for the self assembly of the cytoskeleton of A. proteus: for the formation and detailed morphology of the endoplasmic channel, the ectoplasmic tube, the uropod, the plasma gel sheet, and the hyaline cap. The model accounts for the kinematics of the cytoskeleton: the detailed velocity field of the forward flow of the endoplasm, the contraction of the ectoplasmic tube, and the inversion of the flow in the fountain zone. The model also gives a satisfactory account of measurements of pressure gradients, measurements of heat dissipation, and measurements of the output of useful work by amoeba. Finally, the model suggests a very promising (but still hypothetical) continuum formulation of the free boundary problem of amoeboid motion. by balancing normal forces on the plasma membrane as closely as possible, the minimal model is able to predict the turgor pressure and surface tension of A. proteus. Several dynamical factors are crucial to the success of the minimal model and are likely to be general features of cytoskeletal mechanics and control in amoeboid cells. These are: a constitutive law for the viscosity of the contractile network that includes an automatic process of gelation as the network density gets large; a very vigorous cycle of network polymerization and depolymerization (in the case of A. proteus, the time constant for this reaction is approximately 12 s); control of network contractility by a diffusible factor (probably calcium ion); and control of the adhesive interaction between the cytoskeleton and the inner surface of the plasma membrane. Images FIGURE 1 FIGURE 2 FIGURE 7 PMID:2765645

Analysis of plasmid-mediated quinolone resistance genes in clinical isolates of the tribe Proteeae from Argentina: First report of qnrD in the Americas.

PubMed

Albornoz, Ezequiel; Lucero, Celeste; Romero, Genara; Rapoport, Melina; Guerriero, Leonor; Andres, Patricia; Galas, Marcelo; Corso, Alejandra; Petroni, Alejandro

2014-12-01

To analyse the occurrence and prevalence of plasmid-mediated quinolone resistance (PMQR) genes in the tribe Proteeae, 81 isolates (65 Proteus spp., 12 Morganella morganii and 4 Providencia stuartii) consecutively collected in 66 hospitals belonging to the WHONET-Argentina Resistance Surveillance Network were studied. Of the 81 isolates, 50 (62%) were susceptible to quinolones [43/65 (66%) Proteus spp. and 7/12 (58%) M. morganii). The remaining 31 isolates (22 Proteus spp., 5 M. morganii and all P. stuartii) showed high-level resistance to nalidixic acid (NAL) and decreased susceptibility or resistance to ciprofloxacin. All NAL-resistant isolates harboured mutations associated with quinolone resistance (MAQRs) in both gyrA (S83I/R) and parC (S80I/R), and some also had MAQRs in gyrB (S464Y/F). The unique PMQR gene detected was qnrD, which was found in 2/81 isolates (Proteus mirabilis Q1084 and Proteus vulgaris Q5169), giving a prevalence of 2.5% in Proteeae. These two isolates were from different geographical regions and both harboured MAQRs in gyrA and parC. The qnrD genes were located on the related plasmids pEAD1-1 (2683bp) and pEAD1-2 (2669bp). Plasmid pEAD1-1 was 100% identical to pCGH15 and differed in only three nucleotides from pDIJ09-518a, which were previously found in clinical isolates of P. mirabilis (China) and Providencia rettgeri (France), respectively, whilst pEAD1-2 was not previously described. The extended-spectrum β-lactamase CTX-M-2 was found in 27% (22/81) of the isolates and was significantly associated with quinolone resistance but not with qnrD (only P. mirabilis Q1084 expressed CTX-M-2). This is the first report of qnrD in the Americas. Copyright © 2014 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

MC-GenomeKey: a multicloud system for the detection and annotation of genomic variants.

PubMed

Elshazly, Hatem; Souilmi, Yassine; Tonellato, Peter J; Wall, Dennis P; Abouelhoda, Mohamed

2017-01-20

Next Generation Genome sequencing techniques became affordable for massive sequencing efforts devoted to clinical characterization of human diseases. However, the cost of providing cloud-based data analysis of the mounting datasets remains a concerning bottleneck for providing cost-effective clinical services. To address this computational problem, it is important to optimize the variant analysis workflow and the used analysis tools to reduce the overall computational processing time, and concomitantly reduce the processing cost. Furthermore, it is important to capitalize on the use of the recent development in the cloud computing market, which have witnessed more providers competing in terms of products and prices. In this paper, we present a new package called MC-GenomeKey (Multi-Cloud GenomeKey) that efficiently executes the variant analysis workflow for detecting and annotating mutations using cloud resources from different commercial cloud providers. Our package supports Amazon, Google, and Azure clouds, as well as, any other cloud platform based on OpenStack. Our package allows different scenarios of execution with different levels of sophistication, up to the one where a workflow can be executed using a cluster whose nodes come from different clouds. MC-GenomeKey also supports scenarios to exploit the spot instance model of Amazon in combination with the use of other cloud platforms to provide significant cost reduction. To the best of our knowledge, this is the first solution that optimizes the execution of the workflow using computational resources from different cloud providers. MC-GenomeKey provides an efficient multicloud based solution to detect and annotate mutations. The package can run in different commercial cloud platforms, which enables the user to seize the best offers. The package also provides a reliable means to make use of the low-cost spot instance model of Amazon, as it provides an efficient solution to the sudden termination of spot machines as a result of a sudden price increase. The package has a web-interface and it is available for free for academic use.

Persistence of antibiotic-resistant and -sensitive Proteus mirabilis strains in the digestive tract of the housefly (Musca domestica) and green bottle flies (Calliphoridae).

PubMed

Wei, Ting; Miyanaga, Kazuhiko; Tanji, Yasunori

2014-10-01

Synanthropic flies have been implicated in the rapid dissemination of antibiotic-resistant bacteria and resistance determinants in the biosphere. These flies stably harbor a considerable number of bacteria that exhibit resistance to various antibiotics, but the mechanisms underlying this phenomenon remain unclear. In this study, we investigated the persistence of antibiotic-resistant bacteria in the digestive tract of houseflies and green bottle flies, using Proteus mirabilis as a model microorganism. One resistant strain carried the blaTEM and aphA1 genes, and another carried a plasmid containing qnrD gene. Quantitative PCR and 454 pyrosequencing were used to monitor the relative abundance of the Proteus strains, as well as potential changes in the overall structure of the whole bacterial community incurred by the artificial induction of Proteus cultures. Both antibiotic-resistant and -sensitive P. mirabilis strains persisted in the fly digestive tract for at least 3 days, and there was no significant difference in the relative abundance of resistant and sensitive strains despite the lower growth rate of resistant strains when cultured in vitro. Therefore, conditions in the fly digestive tract may allow resistant strains to survive the competition with sensitive strains in the absence of antibiotic selective pressure. The composition of the fly-associated bacterial community changed over time, but the contribution of the artificially introduced P. mirabilis strains to these changes was not clear. In order to explain these changes, it will be necessary to obtain more information about bacterial interspecies antagonism in the fly digestive tract.

Phenotypic and molecular characterization of antimicrobial resistance in Proteus mirabilis isolates from dogs.

PubMed

Harada, Kazuki; Niina, Ayaka; Shimizu, Takae; Mukai, Yujiro; Kuwajima, Ken; Miyamoto, Tadashi; Kataoka, Yasushi

2014-11-01

Large-scale monitoring of resistance to 14 antimicrobial agents was performed using 103 Proteus mirabilis strains isolated from dogs in Japan. Resistant strains were analysed to identify their resistance mechanisms. Rates of resistance to chloramphenicol, streptomycin, enrofloxacin, trimethoprim/sulfamethoxazole, kanamycin, ampicillin, ciprofloxacin, cephalothin, gentamicin, cefoxitin and cefotaxime were 20.4, 15.5, 12.6, 10.7, 9.7, 8.7, 5.8, 2.9, 2.9, 1.9 and 1.9%, respectively. No resistance to ceftazidime, aztreonam or imipenem was found. Class 1 and 2 integrases were detected in 2.9 and 11.7% of isolates, respectively. Class 1 integrons contained aadB or aadB-catB-like-blaOXA10-aadA1, whereas those of class 2 contained sat-aadA1, dhfr1-sat-aadA1 or none of the anticipated resistance genes. Of five distinct plasmid-mediated quinolone-resistance (PMQR) genes, only qnrD gene was detected in 1.9% of isolates. Quinolone-resistance determining regions (QRDRs) of gyrA and parC from 13 enrofloxacin-intermediate and -resistant isolates were sequenced. Seven strains had double mutations and three had single mutations. Three of nine ampicillin-resistant isolates harboured AmpC-type β-lactamases (i.e. blaCMY-2, blaCMY-4 and blaDHA-1). These results suggest that canine Proteus mirabilis deserves continued surveillance as an important reservoir of antimicrobial resistance determinants. This is the first report, to our knowledge, describing integrons, PMQRs and QRDR mutations in Proteus mirabilis isolates from companion animals. © 2014 The Authors.

A novel molecular diagnostics platform for somatic and germline precision oncology.

PubMed

Cabanillas, Rubén; Diñeiro, Marta; Castillo, David; Pruneda, Patricia C; Penas, Cristina; Cifuentes, Guadalupe A; de Vicente, Álvaro; Durán, Noelia S; Álvarez, Rebeca; Ordóñez, Gonzalo R; Cadiñanos, Juan

2017-07-01

Next-generation sequencing (NGS) opens new options in clinical oncology, from therapy selection to genetic counseling. However, realization of this potential not only requires succeeding in the bioinformatics and interpretation of the results, but also in their integration into the clinical practice. We have developed a novel NGS diagnostic platform aimed at detecting (1) somatic genomic alterations associated with the response to approved targeted cancer therapies and (2) germline mutations predisposing to hereditary malignancies. Next-generation sequencing libraries enriched in the exons of 215 cancer genes (97 for therapy selection and 148 for predisposition, with 30 informative for both applications), as well as selected introns from 17 genes involved in drug-related rearrangements, were prepared from 39 tumors (paraffin-embedded tissues/cytologies), 36 germline samples (blood) and 10 cell lines using hybrid capture. Analysis of NGS results was performed with specifically developed bioinformatics pipelines. The platform detects single-nucleotide variants (SNVs) and insertions/deletions (indels) with sensitivity and specificity >99.5% (allelic frequency ≥0.1), as well as copy-number variants (CNVs) and rearrangements. Somatic testing identified tailored approved targeted drugs in 35/39 tumors (89.74%), showing a diagnostic yield comparable to that of leading commercial platforms. A somatic EGFR p.E746_S752delinsA mutation in a mediastinal metastasis from a breast cancer prompted its anatomopathologic reassessment, its definite reclassification as a lung cancer and its treatment with gefitinib (partial response sustained for 15 months). Testing of 36 germline samples identified two pathogenic mutations (in CDKN2A and BRCA2 ). We propose a strategy for interpretation and reporting of results adaptable to the aim of the request, the availability of tumor and/or normal samples and the scope of the informed consent. With an adequate methodology, it is possible to translate to the clinical practice the latest advances in precision oncology, integrating under the same platform the identification of somatic and germline genomic alterations.

Monogenic diabetes syndromes: Locus‐specific databases for Alström, Wolfram, and Thiamine‐responsive megaloblastic anemia

PubMed Central

Astuti, Dewi; Sabir, Ataf; Fulton, Piers; Zatyka, Malgorzata; Williams, Denise; Hardy, Carol; Milan, Gabriella; Favaretto, Francesca; Yu‐Wai‐Man, Patrick; Rohayem, Julia; López de Heredia, Miguel; Hershey, Tamara; Tranebjaerg, Lisbeth; Chen, Jian‐Hua; Chaussenot, Annabel; Nunes, Virginia; Marshall, Bess; McAfferty, Susan; Tillmann, Vallo; Maffei, Pietro; Paquis‐Flucklinger, Veronique; Geberhiwot, Tarekign; Mlynarski, Wojciech; Parkinson, Kay; Picard, Virginie; Bueno, Gema Esteban; Dias, Renuka; Arnold, Amy; Richens, Caitlin; Paisey, Richard; Urano, Fumihiko; Semple, Robert; Sinnott, Richard

2017-01-01

Abstract We developed a variant database for diabetes syndrome genes, using the Leiden Open Variation Database platform, containing observed phenotypes matched to the genetic variations. We populated it with 628 published disease‐associated variants (December 2016) for: WFS1 (n = 309), CISD2 (n = 3), ALMS1 (n = 268), and SLC19A2 (n = 48) for Wolfram type 1, Wolfram type 2, Alström, and Thiamine‐responsive megaloblastic anemia syndromes, respectively; and included 23 previously unpublished novel germline variants in WFS1 and 17 variants in ALMS1. We then investigated genotype–phenotype relations for the WFS1 gene. The presence of biallelic loss‐of‐function variants predicted Wolfram syndrome defined by insulin‐dependent diabetes and optic atrophy, with a sensitivity of 79% (95% CI 75%–83%) and specificity of 92% (83%–97%). The presence of minor loss‐of‐function variants in WFS1 predicted isolated diabetes, isolated deafness, or isolated congenital cataracts without development of the full syndrome (sensitivity 100% [93%–100%]; specificity 78% [73%–82%]). The ability to provide a prognostic prediction based on genotype will lead to improvements in patient care and counseling. The development of the database as a repository for monogenic diabetes gene variants will allow prognostic predictions for other diabetes syndromes as next‐generation sequencing expands the repertoire of genotypes and phenotypes. The database is publicly available online at https://lovd.euro-wabb.org. PMID:28432734

Proteus mirabilis uroepithelial cell adhesin (UCA) fimbria plays a role in the colonization of the urinary tract.

PubMed

Pellegrino, Rafael; Scavone, Paola; Umpiérrez, Ana; Maskell, Duncan J; Zunino, Pablo

2013-03-01

Urinary tract infections (UTIs) are among the most common bacterial infections in humans. Proteus mirabilis is an opportunistic pathogen, capable of causing severe UTIs, with serious kidney damage that may even lead to death. Several virulence factors are involved in the pathogenicity of this bacterium. Among these, adherence to the uroepithelium mediated by fimbriae appears to be a significant bacterial attribute related to urovirulence. Proteus mirabilis expresses several types of fimbriae that could be involved in the pathogenesis of UTI, including uroepithelial cell adhesin (UCA). In this report, we used an uropathogenic P. mirabilis wild-type strain and an isogenic ucaA mutant unable to express UCA to study the pathogenic role of this fimbria in UTI. Ability of the mutant to adhere to desquamated uroepithelial cells and to infect mice using different experimental UTI models was significantly impaired. These results allow us to conclude that P. mirabilis UCA plays an important role in the colonization of the urinary tract. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Mass mortality in ornamental fish, Cyprinus carpio koi caused by a bacterial pathogen, Proteus hauseri.

PubMed

Kumar, Raj; Swaminathan, T Raja; Kumar, Rahul G; Dharmaratnam, Arathi; Basheer, V S; Jena, J K

2015-09-01

Moribund koi carp, Cyprinus carpio koi, from a farm with 50% cumulative mortality were sampled with the aim of isolating and detecting the causative agent. Three bacterial species viz., Citrobacter freundii (NSCF-1), Klebsiella pneumoniae (NSKP-1) and Proteus hauseri [genomospecies 3 of Proteus vulgaris Bio group 3] (NSPH-1) were isolated, identified and characterized on the basis of biochemical tests and sequencing of the 16S rDNA gene using universal bacterial primers. Challenge experiments with these isolates using healthy koi carp showed that P. hauseri induced identical clinical and pathological states within 3 d of intramuscular injection. The results suggest P. hauseri (NSPH-1) was the causative agent. In phylogenetic analysis, strain NSPH-1 formed a distinct cluster with other P. hauseri reference strains with ≥99% sequence similarity. P. hauseri isolates were found sensitive to Ampicillin, Cefalexin, Ciprofloxacin and Cefixime and resistant to Gentamycin, Oxytetracycline, Chloramphenicol, and Kanamycin. The affected fish recovered from the infection after ciprofloxacin treatment. Copyright © 2015 Elsevier B.V. All rights reserved.

Characteristics of trajectory in the migration of Amoeba proteus.

PubMed

Miyoshi, Hiromi; Masaki, Noritaka; Tsuchiya, Yoshimi

2003-01-01

We investigated the behavior of migration of Amoeba proteus in an isotropic environment. We found that the trajectory in the migration of A. proteus is smooth in the observation time of 500-1000 s, but its migration every second (the cell velocity) on the trajectory randomly changes. Stochastic analysis of the cell velocity and the turn angle of the trajectory has shown that the histograms of the both variables well fit to Gaussian curves. Supposing a simple model equation for the cell motion, we have estimated the motive force of the migrating cell, which is of the order of piconewton. Furthermore, we have found that the cell velocity and the turn angle have a negative cross-correlation coefficient, which suggests that the amoeba explores better environment by changing frequently its migrating direction at a low speed and it moves rectilinearly to the best environment at a high speed. On the other hand, the model equation has simulated the negative correlation between the cell velocity and the turn angle. This indicates that the apparently rational behavior comes from intrinsic characteristics in the dynamical system where the motive force is not torquelike.

Calcium and initial surface binding phase of pinocytosis in Amoeba proteus.

PubMed

Prusch, R D

1986-08-01

The uptake of membrane-bound solute and external medium by bulk-phase pinocytosis in Amoeba proteus is influenced by the level of Ca2+ in the external medium. Increasing external Ca2+ to approximately 10(-4) M increases pinocytotic intensity, while increases in Ca2+ above this level decrease the intensity of pinocytosis. The initial interaction of pinocytotic inducers and Ca2+ at the surface of Amoeba proteus was therefore examined. Alcian blue and Na+, both inducers of pinocytosis, differ in the manner with which they associate with the amoeba surface, suggesting the possibility of different pinocytosis-inducing sites on the amoeba surface. Low levels of external Ca2+ in the range of 3 X 10(-5) to 1.5 X 10(-4) M increase the amount of cationic inducer associated with the cell surface while, at the same time, decreasing anion association with the cell surface. It is suggested that Ca2+ influences ion association with the cell surface by controlling the availability of negative surface sites, which in turn influences pinocytotic intensity.

Genovar: a detection and visualization tool for genomic variants.

PubMed

Jung, Kwang Su; Moon, Sanghoon; Kim, Young Jin; Kim, Bong-Jo; Park, Kiejung

2012-05-08

Along with single nucleotide polymorphisms (SNPs), copy number variation (CNV) is considered an important source of genetic variation associated with disease susceptibility. Despite the importance of CNV, the tools currently available for its analysis often produce false positive results due to limitations such as low resolution of array platforms, platform specificity, and the type of CNV. To resolve this problem, spurious signals must be separated from true signals by visual inspection. None of the previously reported CNV analysis tools support this function and the simultaneous visualization of comparative genomic hybridization arrays (aCGH) and sequence alignment. The purpose of the present study was to develop a useful program for the efficient detection and visualization of CNV regions that enables the manual exclusion of erroneous signals. A JAVA-based stand-alone program called Genovar was developed. To ascertain whether a detected CNV region is a novel variant, Genovar compares the detected CNV regions with previously reported CNV regions using the Database of Genomic Variants (DGV, http://projects.tcag.ca/variation) and the Single Nucleotide Polymorphism Database (dbSNP). The current version of Genovar is capable of visualizing genomic data from sources such as the aCGH data file and sequence alignment format files. Genovar is freely accessible and provides a user-friendly graphic user interface (GUI) to facilitate the detection of CNV regions. The program also provides comprehensive information to help in the elimination of spurious signals by visual inspection, making Genovar a valuable tool for reducing false positive CNV results. http://genovar.sourceforge.net/.

svviz: a read viewer for validating structural variants.

PubMed

Spies, Noah; Zook, Justin M; Salit, Marc; Sidow, Arend

2015-12-15

Visualizing read alignments is the most effective way to validate candidate structural variants (SVs) with existing data. We present svviz, a sequencing read visualizer for SVs that sorts and displays only reads relevant to a candidate SV. svviz works by searching input bam(s) for potentially relevant reads, realigning them against the inferred sequence of the putative variant allele as well as the reference allele and identifying reads that match one allele better than the other. Separate views of the two alleles are then displayed in a scrollable web browser view, enabling a more intuitive visualization of each allele, compared with the single reference genome-based view common to most current read browsers. The browser view facilitates examining the evidence for or against a putative variant, estimating zygosity, visualizing affected genomic annotations and manual refinement of breakpoints. svviz supports data from most modern sequencing platforms. svviz is implemented in python and freely available from http://svviz.github.io/. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions

PubMed Central

Brezovský, Jan

2016-01-01

An important message taken from human genome sequencing projects is that the human population exhibits approximately 99.9% genetic similarity. Variations in the remaining parts of the genome determine our identity, trace our history and reveal our heritage. The precise delineation of phenotypically causal variants plays a key role in providing accurate personalized diagnosis, prognosis, and treatment of inherited diseases. Several computational methods for achieving such delineation have been reported recently. However, their ability to pinpoint potentially deleterious variants is limited by the fact that their mechanisms of prediction do not account for the existence of different categories of variants. Consequently, their output is biased towards the variant categories that are most strongly represented in the variant databases. Moreover, most such methods provide numeric scores but not binary predictions of the deleteriousness of variants or confidence scores that would be more easily understood by users. We have constructed three datasets covering different types of disease-related variants, which were divided across five categories: (i) regulatory, (ii) splicing, (iii) missense, (iv) synonymous, and (v) nonsense variants. These datasets were used to develop category-optimal decision thresholds and to evaluate six tools for variant prioritization: CADD, DANN, FATHMM, FitCons, FunSeq2 and GWAVA. This evaluation revealed some important advantages of the category-based approach. The results obtained with the five best-performing tools were then combined into a consensus score. Additional comparative analyses showed that in the case of missense variations, protein-based predictors perform better than DNA sequence-based predictors. A user-friendly web interface was developed that provides easy access to the five tools’ predictions, and their consensus scores, in a user-understandable format tailored to the specific features of different categories of variations. To enable comprehensive evaluation of variants, the predictions are complemented with annotations from eight databases. The web server is freely available to the community at http://loschmidt.chemi.muni.cz/predictsnp2. PMID:27224906

PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.

PubMed

Bendl, Jaroslav; Musil, Miloš; Štourač, Jan; Zendulka, Jaroslav; Damborský, Jiří; Brezovský, Jan

2016-05-01

An important message taken from human genome sequencing projects is that the human population exhibits approximately 99.9% genetic similarity. Variations in the remaining parts of the genome determine our identity, trace our history and reveal our heritage. The precise delineation of phenotypically causal variants plays a key role in providing accurate personalized diagnosis, prognosis, and treatment of inherited diseases. Several computational methods for achieving such delineation have been reported recently. However, their ability to pinpoint potentially deleterious variants is limited by the fact that their mechanisms of prediction do not account for the existence of different categories of variants. Consequently, their output is biased towards the variant categories that are most strongly represented in the variant databases. Moreover, most such methods provide numeric scores but not binary predictions of the deleteriousness of variants or confidence scores that would be more easily understood by users. We have constructed three datasets covering different types of disease-related variants, which were divided across five categories: (i) regulatory, (ii) splicing, (iii) missense, (iv) synonymous, and (v) nonsense variants. These datasets were used to develop category-optimal decision thresholds and to evaluate six tools for variant prioritization: CADD, DANN, FATHMM, FitCons, FunSeq2 and GWAVA. This evaluation revealed some important advantages of the category-based approach. The results obtained with the five best-performing tools were then combined into a consensus score. Additional comparative analyses showed that in the case of missense variations, protein-based predictors perform better than DNA sequence-based predictors. A user-friendly web interface was developed that provides easy access to the five tools' predictions, and their consensus scores, in a user-understandable format tailored to the specific features of different categories of variations. To enable comprehensive evaluation of variants, the predictions are complemented with annotations from eight databases. The web server is freely available to the community at http://loschmidt.chemi.muni.cz/predictsnp2.

TEM-72, a New Extended-Spectrum β-Lactamase Detected in Proteus mirabilis and Morganella morganii in Italy

PubMed Central

Perilli, Mariagrazia; Segatore, Bernardetta; Rosaria De Massis, Maria; Riccio, Maria Letizia; Bianchi, Ciro; Zollo, Alessandro; Rossolini, Gian Maria; Amicosante, Gianfranco

2000-01-01

A new natural TEM-2 derivative, named TEM-72, was identified in a Proteus mirabilis strain and in a Morganella morganii strain isolated in Italy in 1999. Compared to TEM-1, TEM-72 contains the following amino acid substitutions: Q39K, M182T, G238S, and E240K. Kinetic analysis showed that TEM-72 exhibits an extended-spectrum activity, including activity against oxyimino-cephalosporins and aztreonam. Expression of blaTEM-72 in Escherichia coli was capable of decreasing the host susceptibility to the above drugs. PMID:10952610

Analysis of changes in intestinal microflora of irradiated mice. [Gamma radiation

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

Mal'tsev, V.N.; Pinegin, B.V.; Korshunov, V.M.

1977-01-01

In experiments on 3 groups of CBA mice exposed to doses of 900, 600 and 300 R ..gamma..-rays, it was demonstrated that the integral severity of post-radiation microflora in the intestine can be determined by means of information index h, which takes into consideration all changes occurring in different representatives of the intestinal microflora. Differential analysis of the mechanisms of radioinduced changes in microflora indicates that it is based on a decrease in lactobacilli and increase in enterococcus, proteus, colibacillus and yeast in the small intestine, with increase in colibacillus, clostridia, proteus and enterococcus in the large intestine.

Doppler flow imaging of cytoplasmic streaming using spectral domain phase microscopy

NASA Astrophysics Data System (ADS)

Choma, Michael A.; Ellerbee, Audrey K.; Yazdanfar, Siavash; Izatt, Joseph A.

2006-03-01

Spectral domain phase microscopy (SDPM) is a function extension of spectral domain optical coherence tomography. SDPM achieves exquisite levels of phase stability by employing common-path interferometry. We discuss the theory and limitations of Doppler flow imaging using SDPM, demonstrate monitoring the thermal contraction of a glass sample with nanometer per second velocity sensitivity, and apply this technique to measurement of cytoplasmic streaming in an Amoeba proteus pseudopod. We observe reversal of cytoplasmic flow induced by extracellular CaCl2, and report results that suggest parabolic flow of cytoplasm in the A. proteus pseudopod.

Proteus-MOC: A 3D deterministic solver incorporating 2D method of characteristics

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

Marin-Lafleche, A.; Smith, M. A.; Lee, C.

2013-07-01

A new transport solution methodology was developed by combining the two-dimensional method of characteristics with the discontinuous Galerkin method for the treatment of the axial variable. The method, which can be applied to arbitrary extruded geometries, was implemented in PROTEUS-MOC and includes parallelization in group, angle, plane, and space using a top level GMRES linear algebra solver. Verification tests were performed to show accuracy and stability of the method with the increased number of angular directions and mesh elements. Good scalability with parallelism in angle and axial planes is displayed. (authors)

[Polyamines and cell growth: specific aspects in Amoeba proteus and in certain cancer cell lines].

PubMed

Dubois, J; Schenkel, E; Hanocq, M

1995-01-01

The differences between the metabolic schemes of polyamines can be the starting point to investigate the discovery of new antiparasitic or anticancer drugs which would be cell type specific. The studies, which were undertaken with the P388 cancer cells and Amoeba proteus, have shown that the pool of polyamine was very different in both cell types. Moreover, the cytotoxicity of putrescine, spermidine, spermine and 1-3 diaminopropane was found to be dependent of the activity of cell enzymes which could play a role to control cell proliferation by producing toxic metabolites.

Automated platform for designing multiple robot work cells

NASA Astrophysics Data System (ADS)

Osman, N. S.; Rahman, M. A. A.; Rahman, A. A. Abdul; Kamsani, S. H.; Bali Mohamad, B. M.; Mohamad, E.; Zaini, Z. A.; Rahman, M. F. Ab; Mohamad Hatta, M. N. H.

2017-06-01

Designing the multiple robot work cells is very knowledge-intensive, intricate, and time-consuming process. This paper elaborates the development process of a computer-aided design program for generating the multiple robot work cells which offer a user-friendly interface. The primary purpose of this work is to provide a fast and easy platform for less cost and human involvement with minimum trial and errors adjustments. The automated platform is constructed based on the variant-shaped configuration concept with its mathematical model. A robot work cell layout, system components, and construction procedure of the automated platform are discussed in this paper where integration of these items will be able to automatically provide the optimum robot work cell design according to the information set by the user. This system is implemented on top of CATIA V5 software and utilises its Part Design, Assembly Design, and Macro tool. The current outcomes of this work provide a basis for future investigation in developing a flexible configuration system for the multiple robot work cells.

Company profile: Complete Genomics Inc.

PubMed

Reid, Clifford

2011-02-01

Complete Genomics Inc. is a life sciences company that focuses on complete human genome sequencing. It is taking a completely different approach to DNA sequencing than other companies in the industry. Rather than building a general-purpose platform for sequencing all organisms and all applications, it has focused on a single application - complete human genome sequencing. The company's Complete Genomics Analysis Platform (CGA™ Platform) comprises an integrated package of biochemistry, instrumentation and software that sequences human genomes at the highest quality, lowest cost and largest scale available. Complete Genomics offers a turnkey service that enables customers to outsource their human genome sequencing to the company's genome sequencing center in Mountain View, CA, USA. Customers send in their DNA samples, the company does all the library preparation, DNA sequencing, assembly and variant analysis, and customers receive research-ready data that they can use for biological discovery.

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

PubMed Central

2012-01-01

Background High-density genotyping arrays that measure hybridization of genomic DNA fragments to allele-specific oligonucleotide probes are widely used to genotype single nucleotide polymorphisms (SNPs) in genetic studies, including human genome-wide association studies. Hybridization intensities are converted to genotype calls by clustering algorithms that assign each sample to a genotype class at each SNP. Data for SNP probes that do not conform to the expected pattern of clustering are often discarded, contributing to ascertainment bias and resulting in lost information - as much as 50% in a recent genome-wide association study in dogs. Results We identified atypical patterns of hybridization intensities that were highly reproducible and demonstrated that these patterns represent genetic variants that were not accounted for in the design of the array platform. We characterized variable intensity oligonucleotide (VINO) probes that display such patterns and are found in all hybridization-based genotyping platforms, including those developed for human, dog, cattle, and mouse. When recognized and properly interpreted, VINOs recovered a substantial fraction of discarded probes and counteracted SNP ascertainment bias. We developed software (MouseDivGeno) that identifies VINOs and improves the accuracy of genotype calling. MouseDivGeno produced highly concordant genotype calls when compared with other methods but it uniquely identified more than 786000 VINOs in 351 mouse samples. We used whole-genome sequence from 14 mouse strains to confirm the presence of novel variants explaining 28000 VINOs in those strains. We also identified VINOs in human HapMap 3 samples, many of which were specific to an African population. Incorporating VINOs in phylogenetic analyses substantially improved the accuracy of a Mus species tree and local haplotype assignment in laboratory mouse strains. Conclusion The problems of ascertainment bias and missing information due to genotyping errors are widely recognized as limiting factors in genetic studies. We have conducted the first formal analysis of the effect of novel variants on genotyping arrays, and we have shown that these variants account for a large portion of miscalled and uncalled genotypes. Genetic studies will benefit from substantial improvements in the accuracy of their results by incorporating VINOs in their analyses. PMID:22260749

Informatic search strategies to discover analogues and variants of natural product archetypes.

PubMed

Johnston, Chad W; Connaty, Alex D; Skinnider, Michael A; Li, Yong; Grunwald, Alyssa; Wyatt, Morgan A; Kerr, Russell G; Magarvey, Nathan A

2016-03-01

Natural products are a crucial source of antimicrobial agents, but reliance on low-resolution bioactivity-guided approaches has led to diminishing interest in discovery programmes. Here, we demonstrate that two in-house automated informatic platforms can be used to target classes of biologically active natural products, specifically, peptaibols. We demonstrate that mass spectrometry-based informatic approaches can be used to detect natural products with high sensitivity, identifying desired agents present in complex microbial extracts. Using our specialised software packages, we could elaborate specific branches of chemical space, uncovering new variants of trichopolyn and demonstrating a way forward in mining natural products as a valuable source of potential pharmaceutical agents.

Genetic and Computational Approaches for Studying Plant Development and Abiotic Stress Responses Using Image-Based Phenotyping

NASA Astrophysics Data System (ADS)

Campbell, M. T.; Walia, H.; Grondin, A.; Knecht, A.

2017-12-01

The development of abiotic stress tolerant crops (i.e. drought, salinity, or heat stress) requires the discovery of DNA sequence variants associated with stress tolerance-related traits. However, many traits underlying adaptation to abiotic stress involve a suite of physiological pathways that may be induced at different times throughout the duration of stress. Conventional single-point phenotyping approaches fail to fully capture these temporal responses, and thus downstream genetic analysis may only identify a subset of the genetic variants that are important for adaptation to sub-optimal environments. Although genomic resources for crops have advanced tremendously, the collection of phenotypic data for morphological and physiological traits is laborious and remains a significant bottleneck in bridging the phenotype-genotype gap. In recent years, the availability of automated, image-based phenotyping platforms has provided researchers with an opportunity to collect morphological and physiological traits non-destructively in a highly controlled environment. Moreover, these platforms allow abiotic stress responses to be recorded throughout the duration of the experiment, and have facilitated the use of function-valued traits for genetic analyses in major crops. We will present our approaches for addressing abiotic stress tolerance in cereals. This talk will focus on novel open-source software to process and extract biological meaningful data from images generated from these phenomics platforms. In addition, we will discuss the statistical approaches to model longitudinal phenotypes and dissect the genetic basis of dynamic responses to these abiotic stresses throughout development.

Specific Infectious Organisms Associated With Poor Outcomes in Treatment for Hip Periprosthetic Infection.

PubMed

Cunningham, Daniel J; Kavolus, Joseph J; Bolognesi, Michael P; Wellman, Samuel S; Seyler, Thorsten M

2017-06-01

Periprosthetic hip infection treatment remains a significant challenge for orthopedics. Some studies have suggested that methicillin resistance and gram-negative organism type are associated with increased treatment failure. The aim of this research is to determine if specific organisms were associated with poor outcomes in treatment for hip periprosthetic infection. Records were reviewed of all patients between 2005 and 2015 who underwent treatment for infected partial or total hip arthroplasty. Characteristics of each patient's treatment course were determined including baseline characteristics, infecting organism(s), infection status at final follow-up, surgeries for infection, and time in hospital. Baseline characteristics and organisms that were associated with clinical outcomes in univariate analysis were incorporated into multivariable outcomes models. When compared with patients infected with other organism(s), patients infected with the following organisms had significantly decreased infection-free rates: Pseudomonas, methicillin-resistant Staphylococcus aureus (MRSA), and Proteus. Infection with certain organisms was associated with 1.13-2.58 additional surgeries: methicillin-sensitive S aureus, coagulase-negative Staphylococcus, MRSA, Pseudomonas, Peptostreptococcus, Klebsiella, Candida, diphtheroids, Propionibacterium acnes, and Proteus species. Specific organisms were associated with 8.56-24.54 additional days in hospital for infection: methicillin-sensitive S aureus, coagulase-negative Staphylococcus, Proteus, MRSA, Enterococcus, Pseudomonas, Klebsiella, beta-hemolytic Streptococcus, and diphtheroids. Higher comorbidity score was also associated with greater length of hospitalization. MRSA, Pseudomonas, and Proteus were associated with all 3 outcomes of lower infection-free rate, more surgery, and more time in hospital in treatment for hip periprosthetic infection. Organism-specific outcome information may help individualize patient-physician discussions about the expected course of treatment for hip periprosthetic infection. Copyright © 2017 Elsevier Inc. All rights reserved.

Proteus mirabilis and its role in dacryocystitis.

PubMed

Borgman, Christopher J

2014-09-01

Dacryocystitis is a common inflammation of the lacrimal sac, usually from an underlying bacterial infection. Most cases can be attributed to common ocular flora such as Staphylococcus aureus or Streptococcus pneumoniae; however, uncommon bacterial causes such as Proteus mirabilis can still occur. P. mirabilis is a gram-negative bacillus that is found abundantly in people who have undergone long-term catheterization and is uncommonly found in or around the eyes except in people who have undergone long-term catheterization. Proteus species can cause conjunctivitis, canaliculitis, and dacryocystitis and have the ability to manifest into preseptal cellulitis; therefore, timely recognition and treatment are important to prevent potential further complications. An 84-year-old white man had several recurrences of acute dacryocystitis that had marginal improvement with empiric antibiotic treatment. Resultant culture of the ocular discharge revealed an uncommon bacterium, P. mirabilis. Successful dosing of oral antibiotics resolved the infection but ultimately the patient required an external dacryocystorhinostomy (DCR) procedure to maintain patency of the nasolacrimal lacrimal system and prevent recurrence. At 3 months after external DCR, the patient was symptom free with no recurrences. Dacryocystitis has a distinctive clinical presentation and is usually easily treated when appropriate oral antibiotics are directed at the underlying pathogen. In nonresponsive cases, culturing of the ocular discharge should be performed to identify the underlying pathogen. Cases of dacryocystitis caused by Proteus species are usually responsive to several standard antibiotics used orally in eye care; however, culturing and susceptibility testing can streamline the diagnostic and management sequence considerably in unclear or unresponsive cases. Typically, patients with dacryocystitis return to normal after appropriate treatment, but chronic recurrences and epiphora are potential sequelae. Patients should be educated that a DCR surgical procedure may be needed to prevent future recurrences in some cases.

Innovation Online Teaching Module Plus Digital Engineering Kit with Proteus Software through Hybrid Learning Method to Improve Student Skills

NASA Astrophysics Data System (ADS)

Kholis, Nur; Syariffuddien Zuhrie, Muhamad; Rahmadian, Reza

2018-04-01

Demands the competence (competence) needs of the industry today is a competent workforce to the field of work. However, during this lecture material Digital Engineering (Especially Digital Electronics Basics and Digital Circuit Basics) is limited to the delivery of verbal form of lectures (classical method) is dominated by the Lecturer (Teacher Centered). Though the subject of Digital Engineering requires learning tools and is required understanding of electronic circuits, digital electronics and high logic circuits so that learners can apply in the world of work. One effort to make it happen is by creating an online teaching module and educational aids (Kit) with the help of Proteus software that can improve the skills of learners. This study aims to innovate online teaching modules plus kits in Proteus-assisted digital engineering courses through hybrid learning approaches to improve the skills of learners. The process of innovation is done by considering the skills and mastery of the technology of students (students) Department of Electrical Engineering - Faculty of Engineering – Universitas Negeri Surabaya to produce quality graduates Use of online module plus Proteus software assisted kit through hybrid learning approach. In general, aims to obtain adequate results with affordable cost of investment, user friendly, attractive and interactive (easily adapted to the development of Information and Communication Technology). With the right design, implementation and operation, both in the form of software both in the form of Online Teaching Module, offline teaching module, Kit (Educational Viewer), and e-learning learning content (both online and off line), the use of the three tools of the expenditure will be able to adjust the standard needs of Information and Communication Technology world, both nationally and internationally.

Cooperative Collision Avoidance Technology Demonstration Data Analysis Report

NASA Technical Reports Server (NTRS)

2007-01-01

This report details the National Aeronautics and Space Administration (NASA) Access 5 Project Office Cooperative Collision Avoidance (CCA) Technology Demonstration for unmanned aircraft systems (UAS) conducted from 21 to 28 September 2005. The test platform chosen for the demonstration was the Proteus Optionally Piloted Vehicle operated by Scaled Composites, LLC, flown out of the Mojave Airport, Mojave, CA. A single intruder aircraft, a NASA Gulf stream III, was used during the demonstration to execute a series of near-collision encounter scenarios. Both aircraft were equipped with Traffic Alert and Collision Avoidance System-II (TCAS-II) and Automatic Dependent Surveillance Broadcast (ADS-B) systems. The objective of this demonstration was to collect flight data to support validation efforts for the Access 5 CCA Work Package Performance Simulation and Systems Integration Laboratory (SIL). Correlation of the flight data with results obtained from the performance simulation serves as the basis for the simulation validation. A similar effort uses the flight data to validate the SIL architecture that contains the same sensor hardware that was used during the flight demonstration.

Loss-of-function DNA sequence variant in the CLCNKA chloride channel implicates the cardio-renal axis in interindividual heart failure risk variation.

PubMed

Cappola, Thomas P; Matkovich, Scot J; Wang, Wei; van Booven, Derek; Li, Mingyao; Wang, Xuexia; Qu, Liming; Sweitzer, Nancy K; Fang, James C; Reilly, Muredach P; Hakonarson, Hakon; Nerbonne, Jeanne M; Dorn, Gerald W

2011-02-08

Common heart failure has a strong undefined heritable component. Two recent independent cardiovascular SNP array studies identified a common SNP at 1p36 in intron 2 of the HSPB7 gene as being associated with heart failure. HSPB7 resequencing identified other risk alleles but no functional gene variants. Here, we further show no effect of the HSPB7 SNP on cardiac HSPB7 mRNA levels or splicing, suggesting that the SNP marks the position of a functional variant in another gene. Accordingly, we used massively parallel platforms to resequence all coding exons of the adjacent CLCNKA gene, which encodes the K(a) renal chloride channel (ClC-K(a)). Of 51 exonic CLCNKA variants identified, one SNP (rs10927887, encoding Arg83Gly) was common, in linkage disequilibrium with the heart failure risk SNP in HSPB7, and associated with heart failure in two independent Caucasian referral populations (n = 2,606 and 1,168; combined P = 2.25 × 10(-6)). Individual genotyping of rs10927887 in the two study populations and a third independent heart failure cohort (combined n = 5,489) revealed an additive allele effect on heart failure risk that is independent of age, sex, and prior hypertension (odds ratio = 1.27 per allele copy; P = 8.3 × 10(-7)). Functional characterization of recombinant wild-type Arg83 and variant Gly83 ClC-K(a) chloride channel currents revealed ≈ 50% loss-of-function of the variant channel. These findings identify a common, functionally significant genetic risk factor for Caucasian heart failure. The variant CLCNKA risk allele, telegraphed by linked variants in the adjacent HSPB7 gene, uncovers a previously overlooked genetic mechanism affecting the cardio-renal axis.

Houston Methodist Variant Viewer: An Application to Support Clinical Laboratory Interpretation of Next-generation Sequencing Data for Cancer

PubMed Central

Christensen, Paul A.; Ni, Yunyun; Bao, Feifei; Hendrickson, Heather L.; Greenwood, Michael; Thomas, Jessica S.; Long, S. Wesley; Olsen, Randall J.

2017-01-01

Introduction: Next-generation-sequencing (NGS) is increasingly used in clinical and research protocols for patients with cancer. NGS assays are routinely used in clinical laboratories to detect mutations bearing on cancer diagnosis, prognosis and personalized therapy. A typical assay may interrogate 50 or more gene targets that encompass many thousands of possible gene variants. Analysis of NGS data in cancer is a labor-intensive process that can become overwhelming to the molecular pathologist or research scientist. Although commercial tools for NGS data analysis and interpretation are available, they are often costly, lack key functionality or cannot be customized by the end user. Methods: To facilitate NGS data analysis in our clinical molecular diagnostics laboratory, we created a custom bioinformatics tool termed Houston Methodist Variant Viewer (HMVV). HMVV is a Java-based solution that integrates sequencing instrument output, bioinformatics analysis, storage resources and end user interface. Results: Compared to the predicate method used in our clinical laboratory, HMVV markedly simplifies the bioinformatics workflow for the molecular technologist and facilitates the variant review by the molecular pathologist. Importantly, HMVV reduces time spent researching the biological significance of the variants detected, standardizes the online resources used to perform the variant investigation and assists generation of the annotated report for the electronic medical record. HMVV also maintains a searchable variant database, including the variant annotations generated by the pathologist, which is useful for downstream quality improvement and research projects. Conclusions: HMVV is a clinical grade, low-cost, feature-rich, highly customizable platform that we have made available for continued development by the pathology informatics community. PMID:29226007

Impact of Human Immunodeficiency Virus Type 1 Minority Variants on the Virus Response to a Rilpivirine-Based First-line Regimen.

PubMed

Raymond, Stéphanie; Nicot, Florence; Pallier, Coralie; Bellecave, Pantxika; Maillard, Anne; Trabaud, Mary Anne; Morand-Joubert, Laurence; Rodallec, Audrey; Amiel, Corinne; Mourez, Thomas; Bocket, Laurence; Beby-Defaux, Agnès; Bouvier-Alias, Magali; Lambert-Niclot, Sidonie; Charpentier, Charlotte; Malve, Brice; Mirand, Audrey; Dina, Julia; Le Guillou-Guillemette, Hélène; Marque-Juillet, Stéphanie; Signori-Schmuck, Anne; Barin, Francis; Si-Mohamed, Ali; Avettand Fenoel, Véronique; Roussel, Catherine; Calvez, Vincent; Saune, Karine; Marcelin, Anne Geneviève; Rodriguez, Christophe; Descamps, Diane; Izopet, Jacques

2018-05-02

Minority resistant variants of human immunodeficiency virus type 1 (HIV-1) could influence the virological response to treatment based on nonnucleoside reverse transcriptase inhibitors (NNRTIs). Data on minority rilpivirine-resistant variants are scarce. This study used next-generation sequencing (NGS) to identify patients harboring minority resistant variants to nucleos(t)ide reverse transcriptase inhibitors and NNRTIs and to assess their influence on the virological response (VR). All the subjects, 541 HIV-1-infected patients started a first-line regimen containing rilpivirine. VR was defined as a HIV-1 RNA load <50 copies/mL at month 6 with continued suppression at month 12. NGS was performed at baseline (retrospectively) on the 454 GS-FLX platform (Roche). NGS revealed resistance-associated mutations accounting for 1% to <5% of variants in 17.2% of samples, for 5%-20% in 5.7% of samples, and for >20% in 29% of samples. We identified 43 (8.8%) and 36 (7.4%) patients who harbored rilpivirine-resistant variants with a 1% sensitivity threshold according to the French National Agency for Research on AIDS and Viral Hepatitis and Stanford algorithms, respectively. The VR was 96.9% at month 12. Detection of minority rilpivirine resistant variants was not associated with virological failure (VF). Multivariate analysis indicated that VF at month 12 was associated with a CD4 count <250 cells/µL at baseline, a slower decrease in viral load at month 3, and rilpivirine resistance at baseline using the Stanford algorithm with a 20% threshold. Minority resistant variants had no impact on the VR of treatment-naive patients to a rilpivirine-based regimen.

Mutation update of transcription factor genes FOXE3, HSF4, MAF, and PITX3 causing cataracts and other developmental ocular defects.

PubMed

Anand, Deepti; Agrawal, Smriti A; Slavotinek, Anne; Lachke, Salil A

2018-04-01

Mutations in the transcription factor genes FOXE3, HSF4, MAF, and PITX3 cause congenital lens defects including cataracts that may be accompanied by defects in other components of the eye or in nonocular tissues. We comprehensively describe here all the variants in FOXE3, HSF4, MAF, and PITX3 genes linked to human developmental defects. A total of 52 variants for FOXE3, 18 variants for HSF4, 20 variants for MAF, and 19 variants for PITX3 identified so far in isolated cases or within families are documented. This effort reveals FOXE3, HSF4, MAF, and PITX3 to have 33, 16, 18, and 7 unique causal mutations, respectively. Loss-of-function mutant animals for these genes have served to model the pathobiology of the associated human defects, and we discuss the currently known molecular function of these genes, particularly with emphasis on their role in ocular development. Finally, we make the detailed FOXE3, HSF4, MAF, and PITX3 variant information available in the Leiden Online Variation Database (LOVD) platform at https://www.LOVD.nl/FOXE3, https://www.LOVD.nl/HSF4, https://www.LOVD.nl/MAF, and https://www.LOVD.nl/PITX3. Thus, this article informs on key variants in transcription factor genes linked to cataract, aphakia, corneal opacity, glaucoma, microcornea, microphthalmia, anterior segment mesenchymal dysgenesis, and Ayme-Gripp syndrome, and facilitates their access through Web-based databases. © 2018 Wiley Periodicals, Inc.

Utility of NIST Whole-Genome Reference Materials for the Technical Validation of a Multigene Next-Generation Sequencing Test.

PubMed

Shum, Bennett O V; Henner, Ilya; Belluoccio, Daniele; Hinchcliffe, Marcus J

2017-07-01

The sensitivity and specificity of next-generation sequencing laboratory developed tests (LDTs) are typically determined by an analyte-specific approach. Analyte-specific validations use disease-specific controls to assess an LDT's ability to detect known pathogenic variants. Alternatively, a methods-based approach can be used for LDT technical validations. Methods-focused validations do not use disease-specific controls but use benchmark reference DNA that contains known variants (benign, variants of unknown significance, and pathogenic) to assess variant calling accuracy of a next-generation sequencing workflow. Recently, four whole-genome reference materials (RMs) from the National Institute of Standards and Technology (NIST) were released to standardize methods-based validations of next-generation sequencing panels across laboratories. We provide a practical method for using NIST RMs to validate multigene panels. We analyzed the utility of RMs in validating a novel newborn screening test that targets 70 genes, called NEO1. Despite the NIST RM variant truth set originating from multiple sequencing platforms, replicates, and library types, we discovered a 5.2% false-negative variant detection rate in the RM truth set genes that were assessed in our validation. We developed a strategy using complementary non-RM controls to demonstrate 99.6% sensitivity of the NEO1 test in detecting variants. Our findings have implications for laboratories or proficiency testing organizations using whole-genome NIST RMs for testing. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Analysis of single nucleotide polymorphisms in case-control studies.

PubMed

Li, Yonghong; Shiffman, Dov; Oberbauer, Rainer

2011-01-01

Single nucleotide polymorphisms (SNPs) are the most common type of genetic variants in the human genome. SNPs are known to modify susceptibility to complex diseases. We describe and discuss methods used to identify SNPs associated with disease in case-control studies. An outline on study population selection, sample collection and genotyping platforms is presented, complemented by SNP selection, data preprocessing and analysis.

Performance Comparison of Bench-Top Next Generation Sequencers Using Microdroplet PCR-Based Enrichment for Targeted Sequencing in Patients with Autism Spectrum Disorder

PubMed Central

Okamoto, Nobuhiko; Nakashima, Mitsuko; Tsurusaki, Yoshinori; Miyake, Noriko; Saitsu, Hirotomo; Matsumoto, Naomichi

2013-01-01

Next-generation sequencing (NGS) combined with enrichment of target genes enables highly efficient and low-cost sequencing of multiple genes for genetic diseases. The aim of this study was to validate the accuracy and sensitivity of our method for comprehensive mutation detection in autism spectrum disorder (ASD). We assessed the performance of the bench-top Ion Torrent PGM and Illumina MiSeq platforms as optimized solutions for mutation detection, using microdroplet PCR-based enrichment of 62 ASD associated genes. Ten patients with known mutations were sequenced using NGS to validate the sensitivity of our method. The overall read quality was better with MiSeq, largely because of the increased indel-related error associated with PGM. The sensitivity of SNV detection was similar between the two platforms, suggesting they are both suitable for SNV detection in the human genome. Next, we used these methods to analyze 28 patients with ASD, and identified 22 novel variants in genes associated with ASD, with one mutation detected by MiSeq only. Thus, our results support the combination of target gene enrichment and NGS as a valuable molecular method for investigating rare variants in ASD. PMID:24066114

The suitability of matrix assisted laser desorption/ionization time of flight mass spectrometry in a laboratory developed test using cystic fibrosis carrier screening as a model.

PubMed

Farkas, Daniel H; Miltgen, Nicholas E; Stoerker, Jay; van den Boom, Dirk; Highsmith, W Edward; Cagasan, Lesley; McCullough, Ron; Mueller, Reinhold; Tang, Lin; Tynan, John; Tate, Courtney; Bombard, Allan

2010-09-01

We designed a laboratory developed test (LDT) by using an open platform for mutation/polymorphism detection. Using a 108-member (mutation plus variant) cystic fibrosis carrier screening panel as a model, we completed the last phase of LDT validation by using matrix-assisted laser desorption/ionization time of flight mass spectrometry. Panel customization was accomplished via specific amplification primer and extension probe design. Amplified genomic DNA was subjected to allele specific, single base extension endpoint analysis by mass spectrometry for inspection of the cystic fibrosis transmembrane regulator gene (NM_000492.3). The panel of mutations and variants was tested against 386 blinded samples supplied by "authority" laboratories highly experienced in cystic fibrosis transmembrane regulator genotyping; >98% concordance was observed. All discrepant and discordant results were resolved satisfactorily. Taken together, these results describe the concluding portion of the LDT validation process and the use of mass spectrometry to detect a large number of complex reactions within a single run as well as its suitability as a platform appropriate for interrogation of scores to hundreds of targets.

Morphological Diversity of the Colony Produced by Bacteria Proteus mirabilis

NASA Astrophysics Data System (ADS)

Nakahara, Akio; Shimada, Yuji; Wakita, Jun-ichi; Matsushita, Mitsugu; Matsuyama, Tohey

1996-08-01

Morphological changes of colonies have been investigatedfor a bacterial strain of Proteus mirabilis, which is a famous speciesfor producing concentric-ring-like colonies. It was found that colony patterns can be classified into three types,i.e., cyclic spreading, diffusion-limited growth (DLA-like)and three-dimensional growth (inside the agar medium) patterns. Cyclic spreading patterns can further be classifiedinto three subgroups, i.e., concentric-ring, homogeneous and spatiotemporal patterns. These subgroups were classified by examining the development of colony structure after colonies spread all over petri-dishes. Comparison of the results with thoseof another bacterial species Bacillus subtilis is also discussed.

Computational study concerning the effect of some pesticides on the Proteus Mirabilis catalase activity

NASA Astrophysics Data System (ADS)

Isvoran, Adriana

2016-03-01

Assessment of the effects of the herbicides nicosulfuron and chlorsulfuron and the fungicides difenoconazole and drazoxlone upon catalase produced by soil microorganism Proteus mirabilis is performed using the molecular docking technique. The interactions of pesticides with the enzymes are predicted using SwissDock and PatchDock docking tools. There are correlations for predicted binding energy values for enzyme-pesticide complexes obtained using the two docking tools, all the considered pesticides revealing favorable binding to the enzyme, but only the herbicides bind to the catalytic site. These results suggest the inhibitory potential of chlorsulfuron and nicosulfuron on the catalase activity in soil.

TEM-187, a new extended-spectrum β-lactamase with weak activity in a Proteus mirabilis clinical strain.

PubMed

Corvec, Stéphane; Beyrouthy, Racha; Crémet, Lise; Aubin, Guillaume Ghislain; Robin, Frédéric; Bonnet, Richard; Reynaud, Alain

2013-05-01

A Proteus mirabilis clinical strain (7001324) was isolated from urine sample of a patient hospitalized in a long-term-care facility. PCR and cloning experiments performed with this strain identified a novel TEM-type β-lactamase (TEM-187) differing by four amino acid substitutions (Leu21Phe, Arg164His, Ala184Val, and Thr265Met) from TEM-1. This characterization provides further evidence for the diversity of extended-spectrum β-lactamases (ESBL) produced by P. mirabilis and for their potential spread to other Enterobacteriaceae due to a lack of sensitive detection methods used in daily practice.

Mathematical Modeling the Geometric Regularity in Proteus Mirabilis Colonies

NASA Astrophysics Data System (ADS)

Zhang, Bin; Jiang, Yi; Minsu Kim Collaboration

Proteus Mirabilis colony exhibits striking spatiotemporal regularity, with concentric ring patterns with alternative high and low bacteria density in space, and periodicity for repetition process of growth and swarm in time. We present a simple mathematical model to explain the spatiotemporal regularity of P. Mirabilis colonies. We study a one-dimensional system. Using a reaction-diffusion model with thresholds in cell density and nutrient concentration, we recreated periodic growth and spread patterns, suggesting that the nutrient constraint and cell density regulation might be sufficient to explain the spatiotemporal periodicity in P. Mirabilis colonies. We further verify this result using a cell based model.

A new species of Neocarus Chamberlin & Mulaik, 1942 (Opilioacarida, Opilioacaridae) from Brazil, with remarks on its postlarval development

PubMed Central

Bernardi, Leopoldo Ferreira de Oliveira; Klompen, Hans; Zacarias, Mauricio Sergio; Ferreira, Rodrigo Lopes

2013-01-01

Abstract Neocarus proteus sp. n., is described from caves and the surrounding epigean environment of ferruginous outcrops (Cangas) in Minas Gerais, Brazil. In addition, some notes about development in this species are presented. Neocarus proteus is the only species in the genus that has smooth or barbed genital setae and that carries coronidia on the basitarsi, tibiae and genua of legs II–III. Females carry additional setae with rounded tips on the subcapitulum, and are, on average, larger than males. This distinct sexual dimorphism appears in the tritonymphal instar and is maintained in the adults. PMID:24363585

A Modified Mixing Length Turbulence Model for Zero and Adverse Pressure Gradients. M.S. Thesis - Akron Univ., 1993

NASA Technical Reports Server (NTRS)

Conley, Julianne M.; Leonard, B. P.

1994-01-01

The modified mixing length (MML) turbulence model was installed in the Proteus Navier-Stokes code, then modified to make it applicable to a wider range of flows typical of aerospace propulsion applications. The modifications are based on experimental data for three flat-plate flows having zero, mild adverse, and strong adverse pressure gradients. Three transonic diffuser test cases were run with the new version of the model in order to evaluate its performance. All results are compared with experimental data and show improvements over calculations made using the Baldwin-Lomax turbulence model, the standard algebraic model in Proteus.

ELECTRON MICROSCOPIC OBSERVATIONS OF AMOEBA PROTEUS IN GROWTH AND INANITION

PubMed Central

Cohen, Adolph I.

1957-01-01

Electron microscopic observations have been made on growing and dividing specimens of Amoeba proteus and also on starving animals. Structures presumably corresponding to the mitochondria, alpha particles, vacuoles, and Golgi material are described. A new entity, designated as a foamy particle, is noted. Descriptions are given of the cytoplasmic and nuclear membranes. During division the inner, thick nuclear membrane component is seen to vanish and the outer membrane persist. Measurements suggest a gradual reappearance of the inner component with growth. Starving animals show a loss of cytoplasmic granularity and an increase in the electron density of mitochondria, presumably due to lipide accumulation. PMID:13481020

Electron microscopic observations of amoeba proteus in growth and inanition.

PubMed

COHEN, A I

1957-11-25

Electron microscopic observations have been made on growing and dividing specimens of Amoeba proteus and also on starving animals. Structures presumably corresponding to the mitochondria, alpha particles, vacuoles, and Golgi material are described. A new entity, designated as a foamy particle, is noted. Descriptions are given of the cytoplasmic and nuclear membranes. During division the inner, thick nuclear membrane component is seen to vanish and the outer membrane persist. Measurements suggest a gradual reappearance of the inner component with growth. Starving animals show a loss of cytoplasmic granularity and an increase in the electron density of mitochondria, presumably due to lipide accumulation.

Information extraction for enhanced access to disease outbreak reports.

PubMed

Grishman, Ralph; Huttunen, Silja; Yangarber, Roman

2002-08-01

Document search is generally based on individual terms in the document. However, for collections within limited domains it is possible to provide more powerful access tools. This paper describes a system designed for collections of reports of infectious disease outbreaks. The system, Proteus-BIO, automatically creates a table of outbreaks, with each table entry linked to the document describing that outbreak; this makes it possible to use database operations such as selection and sorting to find relevant documents. Proteus-BIO consists of a Web crawler which gathers relevant documents; an information extraction engine which converts the individual outbreak events to a tabular database; and a database browser which provides access to the events and, through them, to the documents. The information extraction engine uses sets of patterns and word classes to extract the information about each event. Preparing these patterns and word classes has been a time-consuming manual operation in the past, but automated discovery tools now make this task significantly easier. A small study comparing the effectiveness of the tabular index with conventional Web search tools demonstrated that users can find substantially more documents in a given time period with Proteus-BIO.

Tuberculous Otitis with Proteus mirabilis Co-Infection: An Unsuspected Presentation Encountered in Clinical Practice.

PubMed

Rajesh Gandham, Nageswari; Sardar, Moumita; Jadhav, Savita Vivek; Vyawahare, Chanda; Misra, Rabindranath

2014-05-01

Tuberculosis, a contagious bacterial disease which is caused by Mycobacterium tuberculosis, primarily involves the lungs.Though Pulmonary tuberculosis (PTB) is the commonest clinical presentation, there is a need for alertness towards uncommon presentations which involve other organs. Tuberculous otitis media (TOM) is one such rare presentation seen in paediatric practice. It is characterized by painless otorrhoea which fails to respond to the routine antibacterial treatment. TOM usually occurs secondary to PTB. Here is a case of tuberculous otitis media with Proteus mirabilis co-infection, with no evidence of PTB. In the sample of ear discharge obtained from the patient, acid fast bacilli were demonstrated on direct microscopy after Ziehl-Neelsen staining. Culture done on Lowenstein-Jensen medium demonstrated slow-growing Mycobacterium. Bacteriological culture and identification helped in isolating Proteus mirabilis. PCR, followed by Line- Probe Assay for early identification and susceptibility testing to primary drugs, was done. Further, patient tested negative for the Mantoux test. Patient was enrolled in National Tuberculosis programme- RNTCP. This case emphasizes on one of the less common presentations of a common disease. A high clinical suspicion and laboratory confirmation are required for appropriate patient management.

Tuberculous Otitis with Proteus mirabilis Co-Infection: An Unsuspected Presentation Encountered in Clinical Practice

PubMed Central

Sardar, Moumita; Jadhav, Savita Vivek; Vyawahare, Chanda; Misra, Rabindranath

2014-01-01

Tuberculosis, a contagious bacterial disease which is caused by Mycobacterium tuberculosis, primarily involves the lungs.Though Pulmonary tuberculosis (PTB) is the commonest clinical presentation, there is a need for alertness towards uncommon presentations which involve other organs. Tuberculous otitis media (TOM) is one such rare presentation seen in paediatric practice. It is characterized by painless otorrhoea which fails to respond to the routine antibacterial treatment. TOM usually occurs secondary to PTB. Here is a case of tuberculous otitis media with Proteus mirabilis co-infection, with no evidence of PTB. In the sample of ear discharge obtained from the patient, acid fast bacilli were demonstrated on direct microscopy after Ziehl-Neelsen staining. Culture done on Lowenstein-Jensen medium demonstrated slow-growing Mycobacterium. Bacteriological culture and identification helped in isolating Proteus mirabilis. PCR, followed by Line- Probe Assay for early identification and susceptibility testing to primary drugs, was done. Further, patient tested negative for the Mantoux test. Patient was enrolled in National Tuberculosis programme- RNTCP. This case emphasizes on one of the less common presentations of a common disease. A high clinical suspicion and laboratory confirmation are required for appropriate patient management. PMID:24995225

Nucleus-associated actin in Amoeba proteus.

PubMed

Berdieva, Mariia; Bogolyubov, Dmitry; Podlipaeva, Yuliya; Goodkov, Andrew

2016-10-01

The presence, spatial distribution and forms of intranuclear and nucleus-associated cytoplasmic actin were studied in Amoeba proteus with immunocytochemical approaches. Labeling with different anti-actin antibodies and staining with TRITC-phalloidin and fluorescent deoxyribonuclease I were used. We showed that actin is abundant within the nucleus as well as in the cytoplasm of A. proteus cells. According to DNase I experiments, the predominant form of intranuclear actin is G-actin which is associated with chromatin strands. Besides, unpolymerized actin was shown to participate in organization of a prominent actin layer adjacent to the outer surface of nuclear envelope. No significant amount of F-actin was found in the nucleus. At the same time, the amoeba nucleus is enclosed in a basket-like structure formed by circumnuclear actin filaments and bundles connected with global cytoplasmic actin cytoskeleton. A supposed architectural function of actin filaments was studied by treatment with actin-depolymerizing agent latrunculin A. It disassembled the circumnuclear actin system, but did not affect the intranuclear chromatin structure. The results obtained for amoeba cells support the modern concept that actin is involved in fundamental nuclear processes that have evolved in the cells of multicellular organisms. Copyright © 2016 Elsevier GmbH. All rights reserved.

A possible signal-coupling role for cyclic AMP during endocytosis in Amoeba proteus.

PubMed

Prusch, R D; Roscoe, J C

1993-01-01

Cytoplasmic levels of cAMP in Amoeba proteus were measured utilizing radioimmunoassays under control conditions and when stimulated by inducers of either pinocytosis or phagocytosis. In control cells, cytoplasmic cAMP levels were approximately 0.39 pM/mg cells. When exposed to either chemotactic peptide or mannose which stimulate phagocytosis in the amoeba, there is a rapid doubling of the cAMP level within 45 sec of stimulation which then returns to the control level within 3-5 min. Theophylline prolongs the elevation of cytoplasmic cAMP in stimulated cells and is also capable of eliciting food vacuole formation in the amoeba. In addition isoproterenol also causes food vacuole formation in the amoeba as well as a large and prolonged increase in cytoplasmic cAMP levels. Inducers of pinocytosis (BSA and Na Cl) also elicit changes in cytoplasmic cAMP in the amoeba, but the response appears to differ from that elicited by inducers of phagocytosis in that the peak cAMP levels are broader and biphasic. It is concluded that cAMP plays a signal-coupling role during the early phases of both forms of endocytosis in Amoeba proteus.

Ongoing Dynamics and Evolution of Neptune's Ring-Moon System

NASA Astrophysics Data System (ADS)

Showalter, Mark R.; de Pater, Imke; Lissauer, Jack J.; French, Robert S.

2017-06-01

We report results derived from observations of the Neptune system using the Hubble Space Telescope (HST) during August 2016. These observations entail repeated, extremely long exposures through the broadest available filter on the WFC3/UVIS instrument to reveal details of Neptune's faint rings and small, inner moons. The work complements similar observations performed by HST in 2004-2005 and 2009. A principal goal was the recovery of the small moon S/2004 N 1 (henceforth N14), which was first reported in 2009. New images show the moon clearly and make it possible to obtain accurate orbital elements for the first time. A complete analysis of all data 2004-2016 reveals that the mean motion n = 378.90616 +/- 0.00003 degrees per day, corresponding to a semimajor axis a = 105,283 km. Eccentricity and inclination are quite small, with e < 0.001 and i < 0.1 degrees. (This result accounts for the local Laplace Plane tilt of ~ 0.4 degrees). N14 has a physical radius R = 13-15 km, assuming its albedo is 0.09 +/- 0.01, which is the range of Neptune's other inner moons. It orbits interior to the much larger moon Proteus (a = 117,647 km; R = 210 km). Tides are believed to have caused Proteus to spiral outward significantly since its origin, and we find that N14 orbits within the radial zone likely crossed by Proteus. We suggest that N14 may have originated as debris ejected from an impact into Proteus; Proteus subsequently continued to evolve outward but the debris accreted into N14 and remains at its original point of origin. Naiad, the innermost of Neptune's moons, is now orbiting ~ 120 degrees ahead of its published orbital elements. This represents only a 1-sigma correction from its mean motion as derived from Voyager data, but it indicates that later, purported detections of Naiad with the Keck telescope were almost certainly misidentifications. The arcs in the Adams ring show that trends reported previously have continued: the two leading arcs are no longer visible, but the trailing two persist and have been relatively stable. Their mean motion is 820.1119 +/- 0.0003 degrees/day. This value has sufficient precision to rule out any of the previously proposed resonant confinement mechanisms.

Warthog: A MOOSE-Based Application for the Direct Code Coupling of BISON and PROTEUS

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

McCaskey, Alexander J.; Slattery, Stuart; Billings, Jay Jay

The Nuclear Energy Advanced Modeling and Simulation (NEAMS) program from the Department of Energy's Office of Nuclear Energy provides a robust toolkit for the modeling and simulation of current and future advanced nuclear reactor designs. This toolkit provides these technologies organized across product lines: two divisions targeted at fuels and end-to-end reactor modeling, and a third for integration, coupling, and high-level workflow management. The Fuels Product Line and the Reactor Product line provide advanced computational technologies that serve each respective field well, however, their current lack of integration presents a major impediment to future improvements of simulation solution fidelity. Theremore » is a desire for the capability to mix and match tools across Product Lines in an effort to utilize the best from both to improve NEAMS modeling and simulation technologies. This report details a new effort to provide this Product Line interoperability through the development of a new application called Warthog. This application couples the BISON Fuel Performance application from the Fuels Product Line and the PROTEUS Core Neutronics application from the Reactors Product Line in an effort to utilize the best from all parts of the NEAMS toolkit and improve overall solution fidelity of nuclear fuel simulations. To achieve this, Warthog leverages as much prior work from the NEAMS program as possible, and in doing so, enables interoperability between the disparate MOOSE and SHARP frameworks, and the libMesh and MOAB mesh data formats. This report describes this work in full. We begin with a detailed look at the individual NEAMS framework technologies used and developed in the various Product Lines, and the current status of their interoperability. We then introduce the Warthog application: its overall architecture and the ways it leverages the best existing tools from across the NEAMS toolkit to enable BISON-PROTEUS integration. Furthermore, we show how Warthog leverages a tool known as DataTransferKit to seamlessly enable the transfer for solution data between disparate frameworks and mesh formats. To end, we demonstrate tests for the direct software coupling of BISON and PROTEUS using Warthog, and discuss current impediments and solutions to the construction of physically realistic input models for this coupled BISON-PROTEUS system.« less

Customisation of the exome data analysis pipeline using a combinatorial approach.

PubMed

Pattnaik, Swetansu; Vaidyanathan, Srividya; Pooja, Durgad G; Deepak, Sa; Panda, Binay

2012-01-01

The advent of next generation sequencing (NGS) technologies have revolutionised the way biologists produce, analyse and interpret data. Although NGS platforms provide a cost-effective way to discover genome-wide variants from a single experiment, variants discovered by NGS need follow up validation due to the high error rates associated with various sequencing chemistries. Recently, whole exome sequencing has been proposed as an affordable option compared to whole genome runs but it still requires follow up validation of all the novel exomic variants. Customarily, a consensus approach is used to overcome the systematic errors inherent to the sequencing technology, alignment and post alignment variant detection algorithms. However, the aforementioned approach warrants the use of multiple sequencing chemistry, multiple alignment tools, multiple variant callers which may not be viable in terms of time and money for individual investigators with limited informatics know-how. Biologists often lack the requisite training to deal with the huge amount of data produced by NGS runs and face difficulty in choosing from the list of freely available analytical tools for NGS data analysis. Hence, there is a need to customise the NGS data analysis pipeline to preferentially retain true variants by minimising the incidence of false positives and make the choice of right analytical tools easier. To this end, we have sampled different freely available tools used at the alignment and post alignment stage suggesting the use of the most suitable combination determined by a simple framework of pre-existing metrics to create significant datasets.

Combining Protein and Strain Engineering for the Production of Glyco-Engineered Horseradish Peroxidase C1A in Pichia pastoris

PubMed Central

Capone, Simona; Ćorajević, Lejla; Bonifert, Günther; Murth, Patrick; Maresch, Daniel; Altmann, Friedrich; Herwig, Christoph; Spadiut, Oliver

2015-01-01

Horseradish peroxidase (HRP), conjugated to antibodies and lectins, is widely used in medical diagnostics. Since recombinant production of the enzyme is difficult, HRP isolated from plant is used for these applications. Production in the yeast Pichia pastoris (P. pastoris), the most promising recombinant production platform to date, causes hyperglycosylation of HRP, which in turn complicates conjugation to antibodies and lectins. In this study we combined protein and strain engineering to obtain an active and stable HRP variant with reduced surface glycosylation. We combined four mutations, each being beneficial for either catalytic activity or thermal stability, and expressed this enzyme variant as well as the unmutated wildtype enzyme in both a P. pastoris benchmark strain and a strain where the native α-1,6-mannosyltransferase (OCH1) was knocked out. Considering productivity in the bioreactor as well as enzyme activity and thermal stability, the mutated HRP variant produced in the P. pastoris benchmark strain turned out to be interesting for medical diagnostics. This variant shows considerable catalytic activity and thermal stability and is less glycosylated, which might allow more controlled and efficient conjugation to antibodies and lectins. PMID:26404235

Detection of influenza antigenic variants directly from clinical samples using polyclonal antibody based proximity ligation assays

PubMed Central

Martin, Brigitte E.; Jia, Kun; Sun, Hailiang; Ye, Jianqiang; Hall, Crystal; Ware, Daphne; Wan, Xiu-Feng

2016-01-01

Identification of antigenic variants is the key to a successful influenza vaccination program. The empirical serological methods to determine influenza antigenic properties require viral propagation. Here a novel quantitative PCR-based antigenic characterization method using polyclonal antibody and proximity ligation assays, or so-called polyPLA, was developed and validated. This method can detect a viral titer that is less than 1000 TCID50/mL. Not only can this method differentiate between different HA subtypes of influenza viruses but also effectively identify antigenic drift events within the same HA subtype of influenza viruses. Applications in H3N2 seasonal influenza data showed that the results from this novel method are consistent with those from the conventional serological assays. This method is not limited to the detection of antigenic variants in influenza but also other pathogens. It has the potential to be applied through a large-scale platform in disease surveillance requiring minimal biosafety and directly using clinical samples. PMID:25546251

Three-dimensional structure of a variant `Termamyl-like' Geobacillus stearothermophilus α-amylase at 1.9 Å resolution.

PubMed

Offen, Wendy A; Viksoe-Nielsen, Anders; Borchert, Torben V; Wilson, Keith S; Davies, Gideon J

2015-01-01

The enzyme-catalysed degradation of starch is central to many industrial processes, including sugar manufacture and first-generation biofuels. Classical biotechnological platforms involve steam explosion of starch followed by the action of endo-acting glycoside hydrolases termed α-amylases and then exo-acting α-glucosidases (glucoamylases) to yield glucose, which is subsequently processed. A key enzymatic player in this pipeline is the `Termamyl' class of bacterial α-amylases and designed/evolved variants thereof. Here, the three-dimensional structure of one such Termamyl α-amylase variant based upon the parent Geobacillus stearothermophilus α-amylase is presented. The structure has been solved at 1.9 Å resolution, revealing the classical three-domain fold stabilized by Ca2+ and a Ca2+-Na+-Ca2+ triad. As expected, the structure is similar to the G. stearothermophilus α-amylase but with main-chain deviations of up to 3 Å in some regions, reflecting both the mutations and differing crystal-packing environments.

Exome Sequencing Analysis Reveals Variants in Primary Immunodeficiency Genes in Patients With Very Early Onset Inflammatory Bowel Disease

PubMed Central

Kelsen, Judith R.; Dawany, Noor; Moran, Christopher J.; Petersen, Britt-Sabina; Sarmady, Mahdi; Sasson, Ariella; Pauly-Hubbard, Helen; Martinez, Alejandro; Maurer, Kelly; Soong, Joanne; Rappaport, Eric; Franke, Andre; Keller, Andreas; Winter, Harland S.; Mamula, Petar; Piccoli, David; Artis, David; Sonnenberg, Gregory F.; Daly, Mark; Sullivan, Kathleen E.; Baldassano, Robert N.; Devoto, Marcella

2016-01-01

Background & Aims Very early onset inflammatory bowel disease (VEO-IBD), IBD diagnosed ≤5 y of age, frequently presents with a different and more severe phenotype than older-onset IBD. We investigated whether patients with VEO-IBD carry rare or novel variants in genes associated with immunodeficiencies that might contribute to disease development. Methods Patients with VEO-IBD and parents (when available) were recruited from the Children's Hospital of Philadelphia from March 2013 through July 2014. We analyzed DNA from 125 patients with VEO-IBD (ages 3 weeks to 4 y) and 19 parents, 4 of whom also had IBD. Exome capture was performed by Agilent SureSelect V4, and sequencing was performed using the Illumina HiSeq platform. Alignment to human genome GRCh37 was achieved followed by post-processing and variant calling. Following functional annotation, candidate variants were analyzed for change in protein function, minor allele frequency <0.1%, and scaled combined annotation dependent depletion scores ≤10. We focused on genes associated with primary immunodeficiencies and related pathways. An additional 210 exome samples from patients with pediatric IBD (n=45) or adult-onset Crohn's disease (n=20) and healthy individuals (controls, n=145) were obtained from the University of Kiel, Germany and used as control groups. Results Four-hundred genes and regions associated with primary immunodeficiency, covering approximately 6500 coding exons totaling > 1 Mbp of coding sequence, were selected from the whole exome data. Our analysis revealed novel and rare variants within these genes that could contribute to the development of VEO-IBD, including rare heterozygous missense variants in IL10RA and previously unidentified variants in MSH5 and CD19. Conclusions In an exome sequence analysis of patients with VEO-IBD and their parents, we identified variants in genes that regulate B- and T-cell functions and could contribute to pathogenesis. Our analysis could lead to the identification of previously unidentified IBD-associated variants. PMID:26193622

Exome-chip association analysis reveals an Asian-specific missense variant in PAX4 associated with type 2 diabetes in Chinese individuals.

PubMed

Cheung, Chloe Y Y; Tang, Clara S; Xu, Aimin; Lee, Chi-Ho; Au, Ka-Wing; Xu, Lin; Fong, Carol H Y; Kwok, Kelvin H M; Chow, Wing-Sun; Woo, Yu-Cho; Yuen, Michele M A; Hai, JoJo S H; Jin, Ya-Li; Cheung, Bernard M Y; Tan, Kathryn C B; Cherny, Stacey S; Zhu, Feng; Zhu, Tong; Thomas, G Neil; Cheng, Kar-Keung; Jiang, Chao-Qiang; Lam, Tai-Hing; Tse, Hung-Fat; Sham, Pak-Chung; Lam, Karen S L

2017-01-01

Genome-wide association studies (GWASs) have identified many common type 2 diabetes-associated variants, mostly at the intronic or intergenic regions. Recent advancements of exome-array genotyping platforms have opened up a novel means for detecting the associations of low-frequency or rare coding variants with type 2 diabetes. We conducted an exomechip association analysis to identify additional type 2 diabetes susceptibility variants in the Chinese population. An exome-chip association study was conducted by genotyping 5640 Chinese individuals from Hong Kong, using a custom designed exome array, the Asian Exomechip. Single variant association analysis was conducted on 77,468 single nucleotide polymorphisms (SNPs). Fifteen SNPs were subsequently genotyped for replication analysis in an independent Chinese cohort comprising 12,362 individuals from Guangzhou. A combined analysis involving 7189 cases and 10,813 controls was performed. In the discovery stage, an Asian-specific coding variant rs2233580 (p.Arg192His) in PAX4, and two variants at the known loci, CDKN2B-AS1 and KCNQ1, were significantly associated with type 2 diabetes with exome-wide significance (p discovery  < 6.45 × 10 -7 ). The risk allele (T) of PAX4 rs2233580 was associated with a younger age at diabetes diagnosis. This variant was replicated in an independent cohort and demonstrated a stronger association that reached genome-wide significance (p meta-analysis [p meta ] = 3.74 × 10 -15 ) in the combined analysis. We identified the association of a PAX4 Asian-specific missense variant rs2233580 with type 2 diabetes in an exome-chip association analysis, supporting the involvement of PAX4 in the pathogenesis of type 2 diabetes. Our findings suggest PAX4 is a possible effector gene of the 7q32 locus, previously identified from GWAS in Asians.

Variant discovery in the sheep milk transcriptome using RNA sequencing.

PubMed

Suárez-Vega, Aroa; Gutiérrez-Gil, Beatriz; Klopp, Christophe; Tosser-Klopp, Gwenola; Arranz, Juan José

2017-02-15

The identification of genetic variation underlying desired phenotypes is one of the main challenges of current livestock genetic research. High-throughput transcriptome sequencing (RNA-Seq) offers new opportunities for the detection of transcriptome variants (SNPs and short indels) in different tissues and species. In this study, we used RNA-Seq on Milk Sheep Somatic Cells (MSCs) with the goal of characterizing the genetic variation within the coding regions of the milk transcriptome in Churra and Assaf sheep, two common dairy sheep breeds farmed in Spain. A total of 216,637 variants were detected in the MSCs transcriptome of the eight ewes analyzed. Among them, a total of 57,795 variants were detected in the regions harboring Quantitative Trait Loci (QTL) for milk yield, protein percentage and fat percentage, of which 21.44% were novel variants. Among the total variants detected, 561 (2.52%) and 1,649 (7.42%) were predicted to produce high or moderate impact changes in the corresponding transcriptional unit, respectively. In the functional enrichment analysis of the genes positioned within selected QTL regions harboring novel relevant functional variants (high and moderate impact), the KEGG pathway with the highest enrichment was "protein processing in endoplasmic reticulum". Additionally, a total of 504 and 1,063 variants were identified in the genes encoding principal milk proteins and molecules involved in the lipid metabolism, respectively. Of these variants, 20 mutations were found to have putative relevant effects on the encoded proteins. We present herein the first transcriptomic approach aimed at identifying genetic variants of the genes expressed in the lactating mammary gland of sheep. Through the transcriptome analysis of variability within regions harboring QTL for milk yield, protein percentage and fat percentage, we have found several pathways and genes that harbor mutations that could affect dairy production traits. Moreover, remarkable variants were also found in candidate genes coding for major milk proteins and proteins related to milk fat metabolism. Several of the SNPs found in this study could be included as suitable markers in genotyping platforms or custom SNP arrays to perform association analyses in commercial populations and apply genomic selection protocols in the dairy production industry.

Seshat: A Web service for accurate annotation, validation, and analysis of TP53 variants generated by conventional and next-generation sequencing.

PubMed

Tikkanen, Tuomas; Leroy, Bernard; Fournier, Jean Louis; Risques, Rosa Ana; Malcikova, Jitka; Soussi, Thierry

2018-07-01

Accurate annotation of genomic variants in human diseases is essential to allow personalized medicine. Assessment of somatic and germline TP53 alterations has now reached the clinic and is required in several circumstances such as the identification of the most effective cancer therapy for patients with chronic lymphocytic leukemia (CLL). Here, we present Seshat, a Web service for annotating TP53 information derived from sequencing data. A flexible framework allows the use of standard file formats such as Mutation Annotation Format (MAF) or Variant Call Format (VCF), as well as common TXT files. Seshat performs accurate variant annotations using the Human Genome Variation Society (HGVS) nomenclature and the stable TP53 genomic reference provided by the Locus Reference Genomic (LRG). In addition, using the 2017 release of the UMD_TP53 database, Seshat provides multiple statistical information for each TP53 variant including database frequency, functional activity, or pathogenicity. The information is delivered in standardized output tables that minimize errors and facilitate comparison of mutational data across studies. Seshat is a beneficial tool to interpret the ever-growing TP53 sequencing data generated by multiple sequencing platforms and it is freely available via the TP53 Website, http://p53.fr or directly at http://vps338341.ovh.net/. © 2018 Wiley Periodicals, Inc.

Kinematic, kinetic and EMG analysis of four front crawl flip turn techniques.

PubMed

Pereira, Suzana Matheus; Ruschel, Caroline; Hubert, Marcel; Machado, Leandro; Roesler, Helio; Fernandes, Ricardo Jorge; Vilas-Boas, João Paulo

2015-01-01

This study aimed to analyse the kinematic, kinetic and electromyographic characteristics of four front crawl flip turn technique variants. The variants distinguished from each other by differences in body position (i.e., dorsal, lateral, ventral) during rolling, wall support, pushing and gliding phases. Seventeen highly trained swimmers (17.9 ± 3.2 years old) participated in interventional sessions and performed three trials of each variant, being monitored with a 3-D video system, a force platform and an electromyography (EMG) system. Studied variables: rolling time and distance, wall support time, push-off time, peak force and horizontal impulse at wall support and push-off, centre of mass horizontal velocity at the end of the push-off, gliding time, centre of mass depth, distance, average and final velocity during gliding, total turn time and electrical activity of Gastrocnemius Medialis, Tibialis Anterior, Biceps Femoris and Vastus Lateralis muscles. Depending on the variant, total turn time ranged from 2.37 ± 0.32 to 2.43 ± 0.33 s, push-off force from 1.86 ± 0.33 to 1.92 ± 0.26 BW and centre of mass velocity during gliding from 1.78 ± 0.21 to 1.94 ± 0.22 m · s(-1). The variants were not distinguishable in terms of kinematical, kinetic and EMG parameters during the rolling, wall support, pushing and gliding phases.

Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

PubMed Central

Lasitschka, Bärbel; Jones, David; Northcott, Paul; Hutter, Barbara; Jäger, Natalie; Kool, Marcel; Taylor, Michael; Lichter, Peter; Pfister, Stefan; Wolf, Stephan; Brors, Benedikt; Eils, Roland

2013-01-01

The emergence of high-throughput, next-generation sequencing technologies has dramatically altered the way we assess genomes in population genetics and in cancer genomics. Currently, there are four commonly used whole-genome sequencing platforms on the market: Illumina’s HiSeq2000, Life Technologies’ SOLiD 4 and its completely redesigned 5500xl SOLiD, and Complete Genomics’ technology. A number of earlier studies have compared a subset of those sequencing platforms or compared those platforms with Sanger sequencing, which is prohibitively expensive for whole genome studies. Here we present a detailed comparison of the performance of all currently available whole genome sequencing platforms, especially regarding their ability to call SNVs and to evenly cover the genome and specific genomic regions. Unlike earlier studies, we base our comparison on four different samples, allowing us to assess the between-sample variation of the platforms. We find a pronounced GC bias in GC-rich regions for Life Technologies’ platforms, with Complete Genomics performing best here, while we see the least bias in GC-poor regions for HiSeq2000 and 5500xl. HiSeq2000 gives the most uniform coverage and displays the least sample-to-sample variation. In contrast, Complete Genomics exhibits by far the smallest fraction of bases not covered, while the SOLiD platforms reveal remarkable shortcomings, especially in covering CpG islands. When comparing the performance of the four platforms for calling SNPs, HiSeq2000 and Complete Genomics achieve the highest sensitivity, while the SOLiD platforms show the lowest false positive rate. Finally, we find that integrating sequencing data from different platforms offers the potential to combine the strengths of different technologies. In summary, our results detail the strengths and weaknesses of all four whole-genome sequencing platforms. It indicates application areas that call for a specific sequencing platform and disallow other platforms. This helps to identify the proper sequencing platform for whole genome studies with different application scopes. PMID:23776689

[Homozygous ectonucleotide pyrophosphatase/phosphodiesterase 1 variants in a girl with hypophosphatemic rickets and literature review].

PubMed

Liu, Z Q; Chen, X B; Song, F Y; Gao, K; Qiu, M F; Qian, Y; Du, M

2017-11-02

Objective: To investigate the clinical features and genetic characteristics of patients with ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) gene variants. Method: The clinical data of a patient with ENPP1 homozygous variants from Capital Institute of Pediatrics was collected, the related literature was searched from China National Knowledge Infrastructure, Wanfang Data Knowledge Service Platform, National Center from Biotechnology Information and PubMed by using search term "ENPP1" , "hypophosphatemic rickets" . The literature retrieval was confined from 1980 to February 2017. The clinical manifestations, bone metabolism examinations, X-RAY and genotypes were reviewed. Result: Our patient was an 11 years old girl, with 7 years history of lower limb malformation. She showed significant valgus deformity of the knee (genu valgum). Metabolic examination revealed reduced level of plasma phosphate (0.86 mmol/L), a normal level of plasma calcium (2.30 mmol/L) and an elevated alkaline phosphatase level of 688 IU/L. The calcium-phosphorus product was 25.9. A homozygous nonsense variants of ENPP1 gene, c.783C>G (p.Tyr261X) in exon 7 was identified in the patient. Both parents were heterozygous carriers. Literature review identified 3 Chinese patients from one publication and 17 cases from twenty one publications around the world. None of the patients was found PHEX variants which is the most common variants among hypophosphatemic rickets patients. The disease onset age was 11 months to 10 years. Eight patients had short stature, five patients had the history of generalized arterial calcification of infancy. Four suffered from deafness, three showed localized calcifications of arteries, three patients manifested pseudoxanthoma elasticum and two suffered from ossification of posterior longitudinal ligament. Nine missense variants, six splicing variants and 4 nonsense variants were reported among these twenty patients. c.783C>G was found in two Chinese patients. Conclusion: ENPP1 gene mutation was a cause of patient with hypophosphatemic rickets. Comorbid features included generalized arterial calcification of infancy, early onset hearing loss, pseudoxanthoma and ossification of posterior longitudinal ligament. ENPP1 gene testing should be performed on hypophosphatemic rickets patients without PHEX gene variants. Long-term follow up is recommended. The most common types of ENPP1 gene variants were nonsense/splicing variants. The gene c.783C>G was the most common variants in Chinese patients.

VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering.

PubMed

Verbist, Bie M P; Thys, Kim; Reumers, Joke; Wetzels, Yves; Van der Borght, Koen; Talloen, Willem; Aerssens, Jeroen; Clement, Lieven; Thas, Olivier

2015-01-01

In virology, massively parallel sequencing (MPS) opens many opportunities for studying viral quasi-species, e.g. in HIV-1- and HCV-infected patients. This is essential for understanding pathways to resistance, which can substantially improve treatment. Although MPS platforms allow in-depth characterization of sequence variation, their measurements still involve substantial technical noise. For Illumina sequencing, single base substitutions are the main error source and impede powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores (Qs) that are useful for differentiating errors from the real low-frequency mutations. A variant calling tool, Q-cpileup, is proposed, which exploits the Qs of nucleotides in a filtering strategy to increase specificity. The tool is imbedded in an open-source pipeline, VirVarSeq, which allows variant calling starting from fastq files. Using both plasmid mixtures and clinical samples, we show that Q-cpileup is able to reduce the number of false-positive findings. The filtering strategy is adaptive and provides an optimized threshold for individual samples in each sequencing run. Additionally, linkage information is kept between single-nucleotide polymorphisms as variants are called at the codon level. This enables virologists to have an immediate biological interpretation of the reported variants with respect to their antiviral drug responses. A comparison with existing SNP caller tools reveals that calling variants at the codon level with Q-cpileup results in an outstanding sensitivity while maintaining a good specificity for variants with frequencies down to 0.5%. The VirVarSeq is available, together with a user's guide and test data, at sourceforge: http://sourceforge.net/projects/virtools/?source=directory. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Analysis of selected genes associated with cardiomyopathy by next-generation sequencing.

PubMed

Szabadosova, Viktoria; Boronova, Iveta; Ferenc, Peter; Tothova, Iveta; Bernasovska, Jarmila; Zigova, Michaela; Kmec, Jan; Bernasovsky, Ivan

2018-02-01

As the leading cause of congestive heart failure, cardiomyopathy represents a heterogenous group of heart muscle disorders. Despite considerable progress being made in the genetic diagnosis of cardiomyopathy by detection of the mutations in the most prevalent cardiomyopathy genes, the cause remains unsolved in many patients. High-throughput mutation screening in the disease genes for cardiomyopathy is now possible because of using target enrichment followed by next-generation sequencing. The aim of the study was to analyze a panel of genes associated with dilated or hypertrophic cardiomyopathy based on previously published results in order to identify the subjects at risk. The method of next-generation sequencing by IlluminaHiSeq 2500 platform was used to detect sequence variants in 16 individuals diagnosed with dilated or hypertrophic cardiomyopathy. Detected variants were filtered and the functional impact of amino acid changes was predicted by computational programs. DNA samples of the 16 patients were analyzed by whole exome sequencing. We identified six nonsynonymous variants that were shown to be pathogenic in all used prediction softwares: rs3744998 (EPG5), rs11551768 (MGME1), rs148374985 (MURC), rs78461695 (PLEC), rs17158558 (RET) and rs2295190 (SYNE1). Two of the analyzed sequence variants had minor allele frequency (MAF)<0.01: rs148374985 (MURC), rs34580776 (MYBPC3). Our data support the potential role of the detected variants in pathogenesis of dilated or hypertrophic cardiomyopathy; however, the possibility that these variants might not be true disease-causing variants but are susceptibility alleles that require additional mutations or injury to cause the clinical phenotype of disease must be considered. © 2017 Wiley Periodicals, Inc.

Comparative transcriptome analysis of three color variants of the sea cucumber Apostichopus japonicus.

PubMed

Jo, Jihoon; Park, Jongsun; Lee, Hyun-Gwan; Kern, Elizabeth M A; Cheon, Seongmin; Jin, Soyeong; Park, Joong-Ki; Cho, Sung-Jin; Park, Chungoo

2016-08-01

The sea cucumber Apostichopus japonicus Selenka 1867 represents an important resource in biomedical research, traditional medicine, and the seafood industry. Much of the commercial value of A. japonicus is determined by dorsal/ventral color variation (red, green, and black), yet the taxonomic relationships between these color variants are not clearly understood. We performed the first comparative analysis of de novo assembled transcriptome data from three color variants of A. japonicus. Using the Illumina platform, we sequenced nearly 177,596,774 clean reads representing a total of 18.2Gbp of sea cucumber transcriptome. A comparison of over 0.3 million transcript scaffolds against the Uniprot/Swiss-Prot database yielded 8513, 8602, and 8588 positive matches for green, red, and black body color transcriptomes, respectively. Using the Panther gene classification system, we assessed an extensive and diverse set of expressed genes in three color variants and found that (1) among the three color variants of A. japonicus, genes associated with RNA binding protein, oxidoreductase, nucleic acid binding, transferase, and KRAB box transcription factor were most commonly expressed; and (2) the main protein functional classes are differently regulated in all three color variants (extracellular matrix protein and phosphatase for green color, transporter and potassium channel for red color, and G-protein modulator and enzyme modulator for black color). This work will assist in the discovery and annotation of novel genes that play significant morphological and physiological roles in color variants of A. japonicus, and these sequence data will provide a useful set of resources for the rapidly growing sea cucumber aquaculture industry. Copyright © 2016 Elsevier B.V. All rights reserved.

A statistical method for the detection of variants from next-generation resequencing of DNA pools.

PubMed

Bansal, Vikas

2010-06-15

Next-generation sequencing technologies have enabled the sequencing of several human genomes in their entirety. However, the routine resequencing of complete genomes remains infeasible. The massive capacity of next-generation sequencers can be harnessed for sequencing specific genomic regions in hundreds to thousands of individuals. Sequencing-based association studies are currently limited by the low level of multiplexing offered by sequencing platforms. Pooled sequencing represents a cost-effective approach for studying rare variants in large populations. To utilize the power of DNA pooling, it is important to accurately identify sequence variants from pooled sequencing data. Detection of rare variants from pooled sequencing represents a different challenge than detection of variants from individual sequencing. We describe a novel statistical approach, CRISP [Comprehensive Read analysis for Identification of Single Nucleotide Polymorphisms (SNPs) from Pooled sequencing] that is able to identify both rare and common variants by using two approaches: (i) comparing the distribution of allele counts across multiple pools using contingency tables and (ii) evaluating the probability of observing multiple non-reference base calls due to sequencing errors alone. Information about the distribution of reads between the forward and reverse strands and the size of the pools is also incorporated within this framework to filter out false variants. Validation of CRISP on two separate pooled sequencing datasets generated using the Illumina Genome Analyzer demonstrates that it can detect 80-85% of SNPs identified using individual sequencing while achieving a low false discovery rate (3-5%). Comparison with previous methods for pooled SNP detection demonstrates the significantly lower false positive and false negative rates for CRISP. Implementation of this method is available at http://polymorphism.scripps.edu/~vbansal/software/CRISP/.

High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic.

PubMed

Sealfon, Rachel; Gire, Stephen; Ellis, Crystal; Calderwood, Stephen; Qadri, Firdausi; Hensley, Lisa; Kellis, Manolis; Ryan, Edward T; LaRocque, Regina C; Harris, Jason B; Sabeti, Pardis C

2012-09-11

Whole-genome sequencing is an important tool for understanding microbial evolution and identifying the emergence of functionally important variants over the course of epidemics. In October 2010, a severe cholera epidemic began in Haiti, with additional cases identified in the neighboring Dominican Republic. We used whole-genome approaches to sequence four Vibrio cholerae isolates from Haiti and the Dominican Republic and three additional V. cholerae isolates to a high depth of coverage (>2000x); four of the seven isolates were previously sequenced. Using these sequence data, we examined the effect of depth of coverage and sequencing platform on genome assembly and identification of sequence variants. We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads. Phylogenetic analysis between the newly sequenced and thirty-three previously sequenced V. cholerae isolates indicates that the Haitian and Dominican Republic isolates are closest to strains from South Asia. The Haitian and Dominican Republic isolates form a tight cluster, with only four variants unique to individual isolates. These variants are located in the CTX region, the SXT region, and the core genome. Of the 126 mutations identified that separate the Haiti-Dominican Republic cluster from the V. cholerae reference strain (N16961), 73 are non-synonymous changes, and a number of these changes cluster in specific genes and pathways. Sequence variant analyses of V. cholerae isolates, including multiple isolates from the Haitian outbreak, identify coverage-specific and technology-specific effects on variant detection, and provide insight into genomic change and functional evolution during an epidemic.

CYTOPLASMIC DNA SYNTHESIS IN AMOEBA PROTEUS

PubMed Central

Rabinovitch, M.; Plaut, W.

1962-01-01

Nucleic acid-containing particles in the cytoplasm of Amoeba proteus (cf. reference 1) were counted after acridine orange staining. The number of particles per ameba was found to be correlated with cell age and size. Fresh daughters had a mean particle number of 5400, whereas predivision amebae contained around 11,000 particles. Amebae from two other strains contained similar particles. The particles were found to be clustered in fasted cells and redispersed after feeding. A marked increase in the particle population was noted in anucleate fragments. These results, together with those previously presented, suggest that the particles multiply intracellularly. Their nature and their relationship to previous work on nucleic acid labeling in Amoeba are discussed. PMID:13972869

Prostaglandins may play a signal-coupling role during phagocytosis in Amoeba proteus.

PubMed

Prusch, R D; Goette, S M; Haberman, P

1989-03-01

Phagocytosis in Amoeba proteus can be induced with prostaglandins (PG). In addition, arachidonic acid (the fatty acid precursor to the PG-2 series) also induces phagocytosis. The induction of phagocytosis with arachidonic acid can be partially inhibited by the cyclooxygenase inhibitor indomethacin. Phagocytosis in the amoeba can also be induced with the chemotactic peptide N-formylmethionyl-leucylphenylalanine (NFMLP). The peptide presumably induces phagocytosis by interacting with receptors on the amoeba surface, which may initiate the release of arachidonic acid from membrane lipids. NFMLP-induced phagocytosis can also be partially inhibited by indomethacin. It is suggested that PG's or biochemically related substances may play a signal-coupling role during phagocytosis in the amoeba.

Calcium and initial surface binding phase of pinocytosis in Amoeba proteus

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

Prusch, R.D.

1986-08-01

The uptake of membrane-bound solute and external medium by bulk-phase pinocytosis in Amoeba proteus is influenced by the level of Ca/sup 2 +/ in the external medium. Increasing external Ca/sup 2 +/ to approx.10/sup -4/ M increases pinocytotic intensity, while increases in Ca/sup 2 +/ above this level decrease the intensity of pinocytosis. The initial interaction of pinocytotic inducers and Ca/sup +2/ at the surface of A moeba proteus was therefore examined. Alcain blue and Na/sup +/, both inducers of pinocytosis, differ in the manner with which they associate with the amoeba surface, suggesting the possibility of different pinocytosis-inducing sitesmore » on the amoeba surface. Low levels of external Ca/sup 2 +/ in the range of 3 x 10/sup -5/ to 4.5 x 10/sup -4/ M increase the amount of cationic inducer associated with the cell surface while, at the same time, decreasing anion association with the cell surface. It is suggested that Ca/sup 2 +/ influences ion association with the cell surface by controlling the availability of negative surface sites, which in turn influences pinocytotic intensity. Surface binding of Na/sup +/, Ca/sup 2 +/ and Cl/sup -/ was determined by adding /sup 22/Na, /sup 45/Ca or /sup 36/Cl.« less

The Ciprofloxacin Impact on Biofilm Formation by Proteus Mirabilis and P. Vulgaris Strains

PubMed Central

Kwiecinska-Pirog, Joanna; Skowron, Krzysztof; Bartczak, Wojciech; Gospodarek-Komkowska, Eugenia

2016-01-01

Background Proteus spp. bacilli belong to opportunistic human pathogens, which are primarily responsible for urinary tract and wound infections. An important virulence factor is their ability to form biofilms that greatly reduce the effectiveness of antibiotics in the site of infection. Objectives The aim of this study was to determine the value of the minimum concentration of ciprofloxacin that eradicates a biofilm of Proteus spp. strains. Materials and Methods A biofilm formation of 20 strains of P. mirabilis and 20 strains of P. vulgaris were evaluated by a spectrophotometric method using 0.1% 2, 3, 5-Triphenyl-tetrazolium chloride solution (TTC, AVANTORTM). On the basis of the results of the absorbance of the formazan, a degree of reduction of biofilm and minimum biofilm eradication (MBE) values of MBE50 and MBE90 were determined. Results All tested strains formed a biofilm. A value of 1.0 μg/mL ciprofloxacin is MBE50 for the strains of both tested species. An MBE90 value of ciprofloxacin for isolates of P. vulgaris was 2 μg/mL and for P. mirabilis was 512 μg/mL. Conclusions Minimum biofilm eradication values of ciprofloxacin obtained in the study are close to the values of the minimal inhibition concentration (MIC). PMID:27303616

Anaerobic choline metabolism in microcompartments promotes growth and swarming of Proteus mirabilis.

PubMed

Jameson, Eleanor; Fu, Tiantian; Brown, Ian R; Paszkiewicz, Konrad; Purdy, Kevin J; Frank, Stefanie; Chen, Yin

2016-09-01

Gammaproteobacteria are important gut microbes but only persist at low levels in the healthy gut. The ecology of Gammaproteobacteria in the gut environment is poorly understood. Here, we demonstrate that choline is an important growth substrate for representatives of Gammaproteobacteria. Using Proteus mirabilis as a model, we investigate the role of choline metabolism and demonstrate that the cutC gene, encoding a choline-trimethylamine lyase, is essential for choline degradation to trimethylamine by targeted mutagenesis of cutC and subsequent complementation experiments. Proteus mirabilis can rapidly utilize choline to enhance growth rate and cell yield in broth culture. Importantly, choline also enhances swarming-associated colony expansion of P. mirabilis under anaerobic conditions on a solid surface. Comparative transcriptomics demonstrated that choline not only induces choline-trimethylamine lyase but also genes encoding shell proteins for the formation of bacterial microcompartments. Subsequent analyses by transmission electron microscopy confirmed the presence of such novel microcompartments in cells cultivated in liquid broth and hyper-flagellated swarmer cells from solid medium. Together, our study reveals choline metabolism as an adaptation strategy for P. mirabilis and contributes to better understand the ecology of this bacterium in health and disease. © 2015 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

The Assessment of Proteus mirabilis Susceptibility to Ceftazidime and Ciprofloxacin and the Impact of These Antibiotics at Subinhibitory Concentrations on Proteus mirabilis Biofilms

PubMed Central

Kwiecińska-Piróg, Joanna; Zniszczol, Katarzyna; Gospodarek, Eugenia

2013-01-01

Rods of the Proteus genus are commonly isolated from patients, especially from the urinary tracts of the catheterised patients. The infections associated with biomaterials are crucial therapeutic obstacles, due to the bactericidal resistance of the biofilm. The aim of this study was to assess the susceptibility of P. mirabilis planktonic forms to ciprofloxacin and ceftazidime, the ability to form biofilm, and the impact of chosen sub-MIC concentrations of these antibiotics on biofilm at different stages of its formation. The research included 50 P. mirabilis strains isolated from wounds and the urinary tracts from patients of the University Hospital No. 1 in Bydgoszcz. The assessment of susceptibility to ciprofloxacin and ceftazidime was conducted using micromethods. The impact of sub-MIC concentrations of the chosen antibiotics on the biofilm was measured using the TTC method. The resistance to ciprofloxacin was confirmed for 20 strains (40.0%) while to ceftazidime for 32 (64.0%) of the tested P. mirabilis strains. All of the tested strains formed biofilm: 24.0% weakly, 26.0% moderately, and 50.0% strongly. It was determined that ciprofloxacin and ceftazidime caused eradication of the biofilm. Moreover, the connection between origin of the strains, biofilm maturity level, and resistance to antibiotics was proved. PMID:24151628

Application of two different kinds of sera against the Proteus penneri lipopolysaccharide core region in search of epitopes determining cross-reactions with antibodies.

PubMed

Palusiak, Agata; Dzieciatkowska, Monika; Sidorczyk, Zygmunt

2008-01-01

Proteus penneri lipopolysaccharide (LPS) core regions are characterized by a greater structural variability than that observed in other Enterobacteriaceae. This fact and the small amount of published data concerning the serological activity of this part of P. penneri LPS prompted an examination of which fragment might determine cross-reactions with antibodies. To date, such epitopes have been found in the LPS core regions of P. mirabilis and P. vulgaris strains. Proteus sp. LPSs were tested with unabsorbed rabbit antisera by enzyme-linked immunosorbent assay (ELISA), sodium dodecyl sulfate polyacrylamide gel electrophoresis and Western blot, and once again by ELISA or passive immunohemolysis after the absorption of these antisera with selected LPSs. The serological studies of P. penneri 8 LPS demonstrated antibodies in the tested antisera recognizing a common epitope located in the core regions of six of the LPSs, i.e. P. penneri 8, 34, 133, 7, 14, and 15. Additionally, another type of antibody directed against some fragment of P. penneri 13 and the core regions of other LPSs investigated was observed in one antiserum. A distal, trisaccharide fragment of the P. penneri 8 LPS core region is suggested to determine the cross-reactions of the tested antisera with the six P. penneri LPSs.

Actin dynamics in Amoeba proteus motility.

PubMed

Pomorski, P; Krzemiński, P; Wasik, A; Wierzbicka, K; Barańska, J; Kłopocka, W

2007-01-01

We studied the distribution of the endogenous Arp2/3 complex in Amoeba proteus and visualised the ratio of filamentous (F-actin) to total actin in living cells. The presented results show that in the highly motile Amoeba proteus, Arp2/3 complex-dependent actin polymerisation is involved in the formation of the branching network of the contractile layer, adhesive structures, and perinuclear cytoskeleton. The aggregation of the Arp2/3 complex in the cortical network, with the exception of the uroid and advancing fronts, and the spatial orientation of microfilaments at the leading edge suggest that actin polymerisation in this area is not sufficient to provide the driving force for membrane displacement. The examined proteins were enriched in the pinocytotic pseudopodia and the perinuclear cytoskeleton in pinocytotic amoebae. In migrating amoebae, the course of changes in F-actin concentration corresponded with the distribution of tension in the cell cortex. The maximum level of F-actin in migrating amoebae was observed in the middle-posterior region and in the front of retracting pseudopodia. Arp2/3 complex-dependent actin polymerisation did not seem to influence F-actin concentration. The strongly condensed state of the microfilament system could be attributed to strong isometric contraction of the cortical layer accompanied by its retraction from distal cell regions. Isotonic contraction was limited to the uroid.

The assessment of Proteus mirabilis susceptibility to ceftazidime and ciprofloxacin and the impact of these antibiotics at subinhibitory concentrations on Proteus mirabilis biofilms.

PubMed

Kwiecińska-Piróg, Joanna; Skowron, Krzysztof; Zniszczol, Katarzyna; Gospodarek, Eugenia

2013-01-01

Rods of the Proteus genus are commonly isolated from patients, especially from the urinary tracts of the catheterised patients. The infections associated with biomaterials are crucial therapeutic obstacles, due to the bactericidal resistance of the biofilm. The aim of this study was to assess the susceptibility of P. mirabilis planktonic forms to ciprofloxacin and ceftazidime, the ability to form biofilm, and the impact of chosen sub-MIC concentrations of these antibiotics on biofilm at different stages of its formation. The research included 50 P. mirabilis strains isolated from wounds and the urinary tracts from patients of the University Hospital No. 1 in Bydgoszcz. The assessment of susceptibility to ciprofloxacin and ceftazidime was conducted using micromethods. The impact of sub-MIC concentrations of the chosen antibiotics on the biofilm was measured using the TTC method. The resistance to ciprofloxacin was confirmed for 20 strains (40.0%) while to ceftazidime for 32 (64.0%) of the tested P. mirabilis strains. All of the tested strains formed biofilm: 24.0% weakly, 26.0% moderately, and 50.0% strongly. It was determined that ciprofloxacin and ceftazidime caused eradication of the biofilm. Moreover, the connection between origin of the strains, biofilm maturity level, and resistance to antibiotics was proved.

High-throughput sequencing of mGluR signaling pathway genes reveals enrichment of rare variants in autism.

PubMed

Kelleher, Raymond J; Geigenmüller, Ute; Hovhannisyan, Hayk; Trautman, Edwin; Pinard, Robert; Rathmell, Barbara; Carpenter, Randall; Margulies, David

2012-01-01

Identification of common molecular pathways affected by genetic variation in autism is important for understanding disease pathogenesis and devising effective therapies. Here, we test the hypothesis that rare genetic variation in the metabotropic glutamate-receptor (mGluR) signaling pathway contributes to autism susceptibility. Single-nucleotide variants in genes encoding components of the mGluR signaling pathway were identified by high-throughput multiplex sequencing of pooled samples from 290 non-syndromic autism cases and 300 ethnically matched controls on two independent next-generation platforms. This analysis revealed significant enrichment of rare functional variants in the mGluR pathway in autism cases. Higher burdens of rare, potentially deleterious variants were identified in autism cases for three pathway genes previously implicated in syndromic autism spectrum disorder, TSC1, TSC2, and SHANK3, suggesting that genetic variation in these genes also contributes to risk for non-syndromic autism. In addition, our analysis identified HOMER1, which encodes a postsynaptic density-localized scaffolding protein that interacts with Shank3 to regulate mGluR activity, as a novel autism-risk gene. Rare, potentially deleterious HOMER1 variants identified uniquely in the autism population affected functionally important protein regions or regulatory sequences and co-segregated closely with autism among children of affected families. We also identified rare ASD-associated coding variants predicted to have damaging effects on components of the Ras/MAPK cascade. Collectively, these findings suggest that altered signaling downstream of mGluRs contributes to the pathogenesis of non-syndromic autism.

High-Throughput Sequencing of mGluR Signaling Pathway Genes Reveals Enrichment of Rare Variants in Autism

PubMed Central

Hovhannisyan, Hayk; Trautman, Edwin; Pinard, Robert; Rathmell, Barbara; Carpenter, Randall; Margulies, David

2012-01-01

Identification of common molecular pathways affected by genetic variation in autism is important for understanding disease pathogenesis and devising effective therapies. Here, we test the hypothesis that rare genetic variation in the metabotropic glutamate-receptor (mGluR) signaling pathway contributes to autism susceptibility. Single-nucleotide variants in genes encoding components of the mGluR signaling pathway were identified by high-throughput multiplex sequencing of pooled samples from 290 non-syndromic autism cases and 300 ethnically matched controls on two independent next-generation platforms. This analysis revealed significant enrichment of rare functional variants in the mGluR pathway in autism cases. Higher burdens of rare, potentially deleterious variants were identified in autism cases for three pathway genes previously implicated in syndromic autism spectrum disorder, TSC1, TSC2, and SHANK3, suggesting that genetic variation in these genes also contributes to risk for non-syndromic autism. In addition, our analysis identified HOMER1, which encodes a postsynaptic density-localized scaffolding protein that interacts with Shank3 to regulate mGluR activity, as a novel autism-risk gene. Rare, potentially deleterious HOMER1 variants identified uniquely in the autism population affected functionally important protein regions or regulatory sequences and co-segregated closely with autism among children of affected families. We also identified rare ASD-associated coding variants predicted to have damaging effects on components of the Ras/MAPK cascade. Collectively, these findings suggest that altered signaling downstream of mGluRs contributes to the pathogenesis of non-syndromic autism. PMID:22558107

Reduction of Urease Activity by Interaction with the Flap Covering the Active Site

PubMed Central

Macomber, Lee; Minkara, Mona S.; Hausinger, Robert P.; Merz, Kenneth M.

2015-01-01

With the increasing appreciation for the human microbiome coupled with the global rise of antibiotic resistant organisms, it is imperative that new methods be developed to specifically target pathogens. To that end, a novel computational approach was devised to identify compounds that reduce the activity of urease, a medically important enzyme of Helicobacter pylori, Proteus mirabilis, and many other microorganisms. Urease contains a flexible loop that covers its active site; Glide was used to identify small molecules predicted to lock this loop in an open conformation. These compounds were screened against the model urease from Klebsiella aerogenes and the natural products epigallocatechin and quercetin were shown to inhibit at low and high micromolar concentrations, respectively. These molecules exhibit a strong time-dependent inactivation of urease that was not due to their oxygen sensitivity. Rather, these compounds appear to inactivate urease by reacting with a specific Cys residue located on the flexible loop. Substitution of this cysteine by alanine in the C319A variant increased the urease resistance to both epigallocatechin and quercetin, as predicted by the computational studies. Protein dynamics are integral to the function of many enzymes; thus, identification of compounds that lock an enzyme into a single conformation presents a useful approach to define potential inhibitors. PMID:25594724

Greek rheumatoid arthritis patients have elevated levels of antibodies against antigens from Proteus mirabilis.

PubMed

Christopoulos, Georgios; Christopoulou, V; Routsias, J G; Babionitakis, A; Antoniadis, C; Vaiopoulos, G

2017-03-01

Patients with rheumatoid arthritis (RA) from different ethnic groups present elevated levels of antibodies against Proteus mirabilis. This finding implicates P. mirabilis in the development of RA. The aim of this study was to investigate the importance of P. mirabilis in the etiopathogenesis of RA in Greek RA patients. In this study, 63 patients with RA and 38 healthy controls were included. Class-specific antibodies IgM, IgG, and IgA against three human cross-reactive and non-cross-reactive synthetic peptides from P. mirabilis-hemolysin (HpmB), urease C (UreC), and urease F (UreF)-were performed in all subjects, using the ELISA method. RA patients had elevated levels of IgM, IgG, and IgA antibodies against HpmB and UreC Proteus peptide which are significantly different compared to healthy controls: p = 0.005, p < 0.001, and p = 0.003 and p = 0.007, p = 0.002, and p < 0.001, correspondingly. Also, elevated levels of IgM, IgG, and IgA antibodies against the UreF Proteus peptide-which are non-cross-reactive with human tissue antigens-were observed and their significant difference compared to healthy controls (p = 0.007, p < 0.001, p < 0.001). Anti-peptide antibodies in RA patients showed a significant correlation with rheumatoid factors (Rf), erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP), especially when patients were divided into subgroups according to the receiving treatment. Greek RA patients present elevated levels of antibodies against P. mirabilis antigenic epitopes, such as in North European populations, albeit Greek RA patients presenting the cross-reaction antigen in a low percentage. These results indicate that P. mirabilis through the molecular mimicry mechanism leads to inflammation and damage of the joints in RA.

Proteus genomic island 1 (PGI1), a new resistance genomic island from two Proteus mirabilis French clinical isolates.

PubMed

Siebor, Eliane; Neuwirth, Catherine

2014-12-01

To analyse the genetic environment of the antibiotic resistance genes in two clinical Proteus mirabilis isolates resistant to multiple antibiotics. PCR, gene walking and whole-genome sequencing were used to determine the sequence of the resistance regions, the surrounding genetic structure and the flanking chromosomal regions. A genomic island of 81.1 kb named Proteus genomic island 1 (PGI1) located at the 3'-end of trmE (formerly known as thdF) was characterized. The large MDR region of PGI1 (55.4 kb) included a class 1 integron (aadB and aadA2) and regions deriving from several transposons: Tn2 (blaTEM-135), Tn21, Tn6020-like transposon (aphA1b), a hybrid Tn502/Tn5053 transposon, Tn501, a hybrid Tn1696/Tn1721 transposon [tetA(A)] carrying a class 1 integron (aadA1) and Tn5393 (strA and strB). Several ISs were also present (IS4321, IS1R and IS26). The PGI1 backbone (25.7 kb) was identical to that identified in Salmonella Heidelberg SL476 and shared some identity with the Salmonella genomic island 1 (SGI1) backbone. An IS26-mediated recombination event caused the division of the MDR region into two parts separated by a large chromosomal DNA fragment of 197 kb, the right end of PGI1 and this chromosomal sequence being in inverse orientation. PGI1 is a new resistance genomic island from P. mirabilis belonging to the same island family as SGI1. The role of PGI1 in the spread of antimicrobial resistance genes among Enterobacteriaceae of medical importance needs to be evaluated. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The PROTEUS Experiment: Active Source Seismic Imaging of the Crustal Magma Plumbing Structure of the Santorini Arc Volcano

NASA Astrophysics Data System (ADS)

Hooft, E. E. E.; Morgan, J. V.; Nomikou, P.; Toomey, D. R.; Papazachos, C. V.; Warner, M.; Heath, B.; Christopoulou, M. E.; Lampridou, D.; Kementzetzidou, D.

2016-12-01

The goal of the PROTEUS seismic experiment (Plumbing Reservoirs Of The Earth Under Santorini) is to examine the entire crustal magma plumbing system beneath a continental arc volcano and determine the magma geometry and connections throughout the crust. These physical parameters control magma migration, storage, and eruption and inform the question of how physical and chemical processing of magma at arc volcanoes forms the andesitic rock compositions that dominate the lower continental crust. These physical parameters are also important to understand volcanic-tectonic interactions and geohazards. Santorini is ideal for these goals because the continental crust has been thinned by extension and so the deep magmatic system is more accessible, also it is geologically well studied. Since the volcano is a semi-submerged, it was possible to collect a unique 3D marine-land active source seismic dataset. During the PROTEUS experiment in November-December of 2015, we recorded 14,300 marine sound sources from the US R/V Langseth on 89 OBSIP short period ocean bottom seismometers and 60 German and 5 Greek land seismometers. The experiment was designed for high-density spatial sampling of the seismic wavefield to allow us to apply two state-of-the-art 3D inversion methods: travel time tomography and full waveform inversion. A preliminary travel time tomography model of the upper crustal seismic velocity structure of the volcano and surrounding region is presented in an accompanying poster. We also made marine geophysical maps of the seafloor using multi-beam bathymetry and of the gravity and magnetic fields. The new seafloor map reveals the detailed structure of the major fault system between Santorini and Amorgos, of associated landslides, and of newly discovered volcanic features. The PROTEUS project will provide new insights into the structure of the whole crustal magmatic system of a continental arc volcano and its evolution within the surrounding tectonic setting.

HTR-PROTEUS Pebble Bed Experimental Program Cores 1, 1A, 2, and 3: Hexagonal Close Packing with a 1:2 Moderator-to-Fuel Pebble Ratio

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

John D. Bess; Barbara H. Dolphin; James W. Sterbentz

2013-03-01

In its deployment as a pebble bed reactor (PBR) critical facility from 1992 to 1996, the PROTEUS facility was designated as HTR-PROTEUS. This experimental program was performed as part of an International Atomic Energy Agency (IAEA) Coordinated Research Project (CRP) on the Validation of Safety Related Physics Calculations for Low Enriched HTGRs. Within this project, critical experiments were conducted for graphite moderated LEU systems to determine core reactivity, flux and power profiles, reaction-rate ratios, the worth of control rods, both in-core and reflector based, the worth of burnable poisons, kinetic parameters, and the effects of moisture ingress on these parameters.more » Four benchmark experiments were evaluated in this report: Cores 1, 1A, 2, and 3. These core configurations represent the hexagonal close packing (HCP) configurations of the HTR-PROTEUS experiment with a moderator-to-fuel pebble ratio of 1:2. Core 1 represents the only configuration utilizing ZEBRA control rods. Cores 1A, 2, and 3 use withdrawable, hollow, stainless steel control rods. Cores 1 and 1A are similar except for the use of different control rods; Core 1A also has one less layer of pebbles (21 layers instead of 22). Core 2 retains the first 16 layers of pebbles from Cores 1 and 1A and has 16 layers of moderator pebbles stacked above the fueled layers. Core 3 retains the first 17 layers of pebbles but has polyethylene rods inserted between pebbles to simulate water ingress. The additional partial pebble layer (layer 18) for Core 3 was not included as it was used for core operations and not the reported critical configuration. Cores 1, 1A, 2, and 3 were determined to be acceptable benchmark experiments.« less

HTR-PROTEUS Pebble Bed Experimental Program Cores 1, 1A, 2, and 3: Hexagonal Close Packing with a 1:2 Moderator-to-Fuel Pebble Ratio

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

John D. Bess; Barbara H. Dolphin; James W. Sterbentz

2012-03-01

In its deployment as a pebble bed reactor (PBR) critical facility from 1992 to 1996, the PROTEUS facility was designated as HTR-PROTEUS. This experimental program was performed as part of an International Atomic Energy Agency (IAEA) Coordinated Research Project (CRP) on the Validation of Safety Related Physics Calculations for Low Enriched HTGRs. Within this project, critical experiments were conducted for graphite moderated LEU systems to determine core reactivity, flux and power profiles, reaction-rate ratios, the worth of control rods, both in-core and reflector based, the worth of burnable poisons, kinetic parameters, and the effects of moisture ingress on these parameters.more » Four benchmark experiments were evaluated in this report: Cores 1, 1A, 2, and 3. These core configurations represent the hexagonal close packing (HCP) configurations of the HTR-PROTEUS experiment with a moderator-to-fuel pebble ratio of 1:2. Core 1 represents the only configuration utilizing ZEBRA control rods. Cores 1A, 2, and 3 use withdrawable, hollow, stainless steel control rods. Cores 1 and 1A are similar except for the use of different control rods; Core 1A also has one less layer of pebbles (21 layers instead of 22). Core 2 retains the first 16 layers of pebbles from Cores 1 and 1A and has 16 layers of moderator pebbles stacked above the fueled layers. Core 3 retains the first 17 layers of pebbles but has polyethylene rods inserted between pebbles to simulate water ingress. The additional partial pebble layer (layer 18) for Core 3 was not included as it was used for core operations and not the reported critical configuration. Cores 1, 1A, 2, and 3 were determined to be acceptable benchmark experiments.« less

The preliminary assessment of anti-microbial activity of HPLC separated components of Kirkia wilmsii.

PubMed

Chigayo, K; Mojapelo, P E L; Bessong, P; Gumbo, J R

2014-01-01

Most communities in developing countries rely on traditional medicines for the treatment of diseases. In South Africa, the Limpopo province, within the Lebowakgomo district, uses tuberous roots of Kirkia wilmsii, after infusion in water for the treatment of a wide range of diseases by Sotho communities. The main objective of the study was to assess the anti-microbial activity of separated aqueous components of the Kirkia wilmsii tuberous roots. The clear aqueous extracts that were obtained after a 0.45 µm membrane filtration (Millipore Millex-HV Hydrophillic PVDF filter), were then injected into a preparative high performance liquid chromatography instrument in which pure components, as shown by peaks, were collected and evaluated for anti-microbial activity against a range of microorganisms. The eight separated components were obtained, out of which four components showed anti-microbial activity (AMA). The freeze dried components were re-dissolved in deionised water and then evaluated for AMA against Vibrio cholerae, Shigella dysenteriae, Aeromonas hydrophilia, Salmonella typhi Proteus mirabilis, Escherichia coli, Staphylococcus aureus, Candida albicans and Enterobacter aerogenes. Component one exhibited antimicrobial activity against Shigella dysenteriae, Aeromonas hydrophilia, Salmonella typhi, Proteus mirabilis, Escherichia coli and Staphylococcus aureus with a minimum inhibitory concentration (MIC), of 3.445 mg/ml. Component five was only active against Proteus mirabilis with a MIC of 0.08 mg/ml. Component 7, was active against Shigella dysenteriae, Staphylococcus aureus and Escherichia coli with a MIC of 0.365 mg/ml against both Shigella dysenteriae and Staphylococcus aureus and 0.091 mg/ml against Escherichia coli. Component 8, was active against Shigella, Aeromonas hydrophilia, Salmonella, Proteus mirabilis, Escherichia coli with a MIC of 155 mg/ml. Only four out of eight aqueous extracts showed AMA against both gram negative and positive bacteria and showed no AMA against Candida albicans, Enterobacter aerogenes and Vibrio cholerae. Therefore the Kirkia wilmsii plant root may be used as a broad spectrum antibiotic.

Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases

PubMed Central

Das, Sayoni; Dawson, Natalie L.; Dobrijevic, Dragana; Orengo, Christine

2016-01-01

Beta-lactamases represent the main bacterial mechanism of resistance to beta-lactam antibiotics and are a significant challenge to modern medicine. We have developed an automated classification and analysis protocol that exploits structure- and sequence-based approaches and which allows us to propose a grouping of serine beta-lactamases that more consistently captures and rationalizes the existing three classification schemes: Classes, (A, C and D, which vary in their implementation of the mechanism of action); Types (that largely reflect evolutionary distance measured by sequence similarity); and Variant groups (which largely correspond with the Bush-Jacoby clinical groups). Our analysis platform exploits a suite of in-house and public tools to identify Functional Determinants (FDs), i.e. residue sites, responsible for conferring different phenotypes between different classes, different types and different variants. We focused on Class A beta-lactamases, the most highly populated and clinically relevant class, to identify FDs implicated in the distinct phenotypes associated with different Class A Types and Variants. We show that our FunFHMMer method can separate the known beta-lactamase classes and identify those positions likely to be responsible for the different implementations of the mechanism of action in these enzymes. Two novel algorithms, ASSP and SSPA, allow detection of FD sites likely to contribute to the broadening of the substrate profiles. Using our approaches, we recognise 151 Class A types in UniProt. Finally, we used our beta-lactamase FunFams and ASSP profiles to detect 4 novel Class A types in microbiome samples. Our platforms have been validated by literature studies, in silico analysis and some targeted experimental verification. Although developed for the serine beta-lactamases they could be used to classify and analyse any diverse protein superfamily where sub-families have diverged over both long and short evolutionary timescales. PMID:27332861

Proteus: a direct forcing method in the simulations of particulate flows

NASA Astrophysics Data System (ADS)

Feng, Zhi-Gang; Michaelides, Efstathios E.

2005-01-01

A new and efficient direct numerical method for the simulation of particulate flows is introduced. The method combines desired elements of the immersed boundary method, the direct forcing method and the lattice Boltzmann method. Adding a forcing term in the momentum equation enforces the no-slip condition on the boundary of a moving particle. By applying the direct forcing scheme, Proteus eliminates the need for the determination of free parameters, such as the stiffness coefficient in the penalty scheme or the two relaxation parameters in the adaptive-forcing scheme. The method presents a significant improvement over the previously introduced immersed-boundary-lattice-Boltzmann method (IB-LBM) where the forcing term was computed using a penalty method and a user-defined parameter. The method allows the enforcement of the rigid body motion of a particle in a more efficient way. Compared to the "bounce-back" scheme used in the conventional LBM, the direct-forcing method provides a smoother computational boundary for particles and is capable of achieving results at higher Reynolds number flows. By using a set of Lagrangian points to track the boundary of a particle, Proteus eliminates any need for the determination of the boundary nodes that are prescribed by the "bounce-back" scheme at every time step. It also makes computations for particles of irregular shapes simpler and more efficient. Proteus has been developed in two- as well as three-dimensions. This new method has been validated by comparing its results with those from experimental measurements for a single sphere settling in an enclosure under gravity. As a demonstration of the efficiency and capabilities of the present method, the settling of a large number (1232) of spherical particles is simulated in a narrow box under two different boundary conditions. It is found that when the no-slip boundary condition is imposed at the front and rear sides of the box the particles motion is significantly hindered. Under the periodic boundary conditions, the particles move faster. The simulations show that the sedimentation characteristics in a box with periodic boundary conditions at the two sides are very close to those found in the sedimentation of two-dimensional circular particles. In the Greek mythology Proteus is a hero, the son of Poseidon. In addition to his ability to change shapes and take different forms at will, Zeus granted him the power to make correct predictions for the future. One cannot expect better attributes from a numerical code.

ClusterCAD: a computational platform for type I modular polyketide synthase design

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

Eng, Clara H.; Backman, Tyler W H; Bailey, Constance B.

Here, we present ClusterCAD, a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKSmore » chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify the process of designing experiments to test strategies for engineering PKS variants. ClusterCAD provides chemical structures with stereochemistry for the intermediates generated by each PKS module, as well as sequence- and structure-based search tools that allow users to identify modules based either on amino acid sequence or on the chemical structure of the cognate polyketide intermediate. ClusterCAD can be accessed at https://clustercad.jbei.org and at http://clustercad.igb.uci.edu.« less

Diversity of the TLR4 Immunity Receptor in Czech Native Cattle Breeds Revealed Using the Pacific Biosciences Sequencing Platform.

PubMed

Novák, Karel; Pikousová, Jitka; Czerneková, Vladimíra; Mátlová, Věra

2017-07-03

The allelic variants of immunity genes in historical breeds likely reflect local infection pressure and therefore represent a reservoir for breeding. Screening to determine the diversity of the Toll-like receptor gene TLR4 was conducted in two conserved cattle breeds: Czech Red and Czech Red Pied. High-throughput sequencing of pooled PCR amplicons using the PacBio platform revealed polymorphisms, which were subsequently confirmed via genotyping techniques. Eight SNPs found in coding and adjacent regions were grouped into 18 haplotypes, representing a significant portion of the known diversity in the global breed panel and presumably exceeding diversity in production populations. Notably, the ancient Czech Red breed appeared to possess greater haplotype diversity than the Czech Red Pied breed, a Simmental variant, although the haplotype frequencies might have been distorted by significant crossbreeding and bottlenecks in the history of Czech Red cattle. The differences in haplotype frequencies validated the phenotypic distinctness of the local breeds. Due to the availability of Czech Red Pied production herds, the effect of intensive breeding on TLR diversity can be evaluated in this model. The advantages of the Pacific Biosciences technology for the resequencing of long PCR fragments with subsequent direct phasing were independently validated.

ClusterCAD: a computational platform for type I modular polyketide synthase design

DOE PAGES

Eng, Clara H.; Backman, Tyler W H; Bailey, Constance B.; ...

2017-10-11

Here, we present ClusterCAD, a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKSmore » chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify the process of designing experiments to test strategies for engineering PKS variants. ClusterCAD provides chemical structures with stereochemistry for the intermediates generated by each PKS module, as well as sequence- and structure-based search tools that allow users to identify modules based either on amino acid sequence or on the chemical structure of the cognate polyketide intermediate. ClusterCAD can be accessed at https://clustercad.jbei.org and at http://clustercad.igb.uci.edu.« less

Demonstrating Bacterial Flagella.

ERIC Educational Resources Information Center

Porter, John R.; And Others

1992-01-01

Describes an effective laboratory method for demonstrating bacterial flagella that utilizes the Proteus mirabilis organism and a special harvesting technique. Includes safety considerations for the laboratory exercise. (MDH)

Adaptive infrared-reflecting systems inspired by cephalopods

NASA Astrophysics Data System (ADS)

Xu, Chengyi; Stiubianu, George T.; Gorodetsky, Alon A.

2018-03-01

Materials and systems that statically reflect radiation in the infrared region of the electromagnetic spectrum underpin the performance of many entrenched technologies, including building insulation, energy-conserving windows, spacecraft components, electronics shielding, container packaging, protective clothing, and camouflage platforms. The development of their adaptive variants, in which the infrared-reflecting properties dynamically change in response to external stimuli, has emerged as an important unmet scientific challenge. By drawing inspiration from cephalopod skin, we developed adaptive infrared-reflecting platforms that feature a simple actuation mechanism, low working temperature, tunable spectral range, weak angular dependence, fast response, stability to repeated cycling, amenability to patterning and multiplexing, autonomous operation, robust mechanical properties, and straightforward manufacturability. Our findings may open opportunities for infrared camouflage and other technologies that regulate infrared radiation.

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

Wu, Hong; Zeng, Hong; Lam, Robert

The crystal structure of the human MLH1 N-terminus is reported at 2.30 Å resolution. The overall structure is described along with an analysis of two clinically important mutations. Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson–Crick base pairs in the genome. Pathogenic mutations in the MLH1 gene are associated with a predisposition to Lynch and Turcot’s syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. The structure shares a high degree ofmore » similarity with previously determined prokaryotic MLH1 homologs; however, this structure affords a more accurate platform for the classification of MLH1 variants.« less

Merging mythology and morphology: the multifaceted lifestyle of Proteus mirabilis.

PubMed

Armbruster, Chelsie E; Mobley, Harry L T

2012-11-01

Proteus mirabilis, named for the Greek god who changed shape to avoid capture, has fascinated microbiologists for more than a century with its unique swarming differentiation, Dienes line formation and potent urease activity. Transcriptome profiling during both host infection and swarming motility, coupled with the availability of the complete genome sequence for P. mirabilis, has revealed the occurrence of interbacterial competition and killing through a type VI secretion system, and the reciprocal regulation of adhesion and motility, as well as the intimate connections between metabolism, swarming and virulence. This Review addresses some of the unique and recently described aspects of P. mirabilis biology and pathogenesis, and emphasizes the potential role of this bacterium in single-species and polymicrobial urinary tract infections.

Merging mythology and morphology: the multifaceted lifestyle of Proteus mirabilis

PubMed Central

Armbruster, Chelsie E.; Mobley, Harry L. T.

2013-01-01

Proteus mirabilis, named for the Greek god who changed shape to avoid capture, has fascinated microbiologists for more than a century with its unique swarming differentiation, Dienes line formation and potent urease activity. Transcriptome profiling during both host infection and swarming motility, coupled with the availability of the complete genome sequence for P. mirabilis, has revealed the occurrence of interbacterial competition and killing through a type VI secretion system, and the reciprocal regulation of adhesion and motility, as well as the intimate connections between metabolism, swarming and virulence. This Review addresses some of the unique and recently described aspects of P. mirabilis biology and pathogenesis, and emphasizes the potential role of this bacterium in single- species and polymicrobial urinary tract infections. PMID:23042564

DE-NE0008277_PROTEUS final technical report 2018

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

Enqvist, Andreas

This project details re-evaluations of experiments of gas-cooled fast reactor (GCFR) core designs performed in the 1970s at the PROTEUS reactor and create a series of International Reactor Physics Experiment Evaluation Project (IRPhEP) benchmarks. Currently there are no gas-cooled fast reactor (GCFR) experiments available in the International Handbook of Evaluated Reactor Physics Benchmark Experiments (IRPhEP Handbook). These experiments are excellent candidates for reanalysis and development of multiple benchmarks because these experiments provide high-quality integral nuclear data relevant to the validation and refinement of thorium, neptunium, uranium, plutonium, iron, and graphite cross sections. It would be cost prohibitive to reproduce suchmore » a comprehensive suite of experimental data to support any future GCFR endeavors.« less

Design, synthesis, molecular docking, anti-Proteus mirabilis and urease inhibition of new fluoroquinolone carboxylic acid derivatives.

PubMed

Abdullah, Mohammed A A; Abuo-Rahma, Gamal El-Din A A; Abdelhafez, El-Shimaa M N; Hassan, Heba A; Abd El-Baky, Rehab M

2017-02-01

New hydroxamic acid, hydrazide and amide derivatives of ciprofloxacin in addition to their analogues of levofloxacin were prepared and identified by different spectroscopic techniques. Some of the prepared compounds revealed good activity against the urease splitting bacteria, Proteus mirabilis. The urease inhibitory activity was investigated using indophenol method. Most of the tested compounds showed better activity than the reference acetohydroxamic acid (AHA). The ciprofloxacin hydrazide derivative 3a and levofloxacin hydroxamic acid 7 experienced the highest activity (IC 50 =1.22μM and 2.20μM, respectively). Molecular docking study revealed high spontaneous binding ability of the tested compounds to the active site of urease. Copyright © 2016 Elsevier Inc. All rights reserved.

From Catheter to Kidney Stone: The Uropathogenic Lifestyle of Proteus mirabilis

PubMed Central

Norsworthy, Allison N.; Pearson, Melanie M.

2017-01-01

Proteus mirabilis is a model organism for urease-producing uropathogens. These diverse bacteria cause infection stones in the urinary tract and form crystalline biofilms on indwelling urinary catheters, frequently leading to poly-microbial infection. Recent work has elucidated how P. mirabilis causes all of these disease states. Particularly exciting is the discovery that this bacterium forms large clusters in the bladder lumen that are sites for stone formation. These clusters, and other steps of infection, require two virulence factors in particular: urease and MR/P fimbriae. Highlighting the importance of MR/P fimbriae is the cotranscribed regulator, MrpJ, which globally controls virulence. Overall, P. mirabilis exhibits an extraordinary lifestyle, and further probing will answer exciting basic microbiological and clinically relevant questions. PMID:28017513

CYTOPLASMIC DNA SYNTHESIS IN AMOEBA PROTEUS

PubMed Central

Wolstenholme, D. R.; Plaut, W.

1964-01-01

The application of electron microscope autoradiography to Amoeba proteus cells labeled with tritiated thymidine has permitted the identification of morphologically distinct particles in the cytoplasm as the sites of incorporated DNA precursor. The particles correspond to those previously described from light microscope studies, with respect to both H3Tdr incorporation and distribution in centrifugally stratified amoebae. Ingested bacteria differ from the particles, in morphology as well as in the absence of associated label. Attempts to introduce a normal particle labeling pattern by incubating amoebae with labeled sediment derived from used amoeba medium failed. The resultant conclusion, that the particles are maintained in the amoeba by self-duplication, is supported by the presence of particles in configurations suggestive of division. PMID:14208356

Lysolecithin as a modifier of induced pinocytosis in Amoeba proteus.

PubMed

Arvidson, G; Josefsson, J O

1982-08-01

Lysolecithin was found to modify cation-induced pinocytosis in Amoeba proteus. It is shown here that lysolecithin (LPC) in the concentration range of 10(-15) to 10(-10) g/ml has the same effect on Na+ -induced pinocytosis as cAMP and a pinocytosis regulating factor (PRF) which is secreted by the amoeba. Thus, LPC activated Na+-induced pinocytosis in starved amoebae and decreased the sensitivity to the inducer in normal cells. Pinocytosis depressed by treatment with EGTA or dibucaine became normal upon addition of LPC to the inducer. These effects were also obtained with lysolecithin isolated from the amoeba. It is suggested that PRF and amoeba LPC may be closely related and that phospholipase activity of the amoeba may regulate its capacity for pinocytosis.

Cytoplasmic DNA synthesis in Amoeba proteus. II. On the behavior and possible nature of the DNA-containing elements.

PubMed

RABINOVITCH, M; PLAUT, W

1962-12-01

Nucleic acid-containing particles in the cytoplasm of Amoeba proteus (cf. reference 1) were counted after acridine orange staining. The number of particles per ameba was found to be correlated with cell age and size. Fresh daughters had a mean particle number of 5400, whereas predivision amebae contained around 11,000 particles. Amebae from two other strains contained similar particles. The particles were found to be clustered in fasted cells and redispersed after feeding. A marked increase in the particle population was noted in anucleate fragments. These results, together with those previously presented, suggest that the particles multiply intracellularly. Their nature and their relationship to previous work on nucleic acid labeling in Amoeba are discussed.

Duplex Identification of Staphylococcus aureus by Aptamer and Gold Nanoparticles.

PubMed

Chang, Tianjun; Wang, Libo; Zhao, Kexu; Ge, Yu; He, Meng; Li, Gang

2016-06-01

Staphylococcus aureus is the top common pathogen causing infections and food poisoning. Identification of S. aureus is crucial for the disease diagnosis and regulation of food hygiene. Herein, we report an aptamer-AuNPs based method for duplex identification of S. aureus. Using AuNPs as an indicator, SA23, an aptamer against S. aureus, can well identify its target from Escherichia coli, Listeria monocytogenes and Pseudomonas aeruginosa. Furthermore, we find citrate-coated AuNPs can strongly bind to S. aureus, but not bind to Salmonella enterica and Proteus mirabilis, which leads to different color changes in salt solution. This colorimetric response is capable of distinguishing S. aureus from S. enteritidis and P. mirabilis. Thus, using the aptasensor and AuNPs together, S. aureus can be accurately identified from the common pathogens. This duplex identification system is a promising platform for simple visual identification of S. aureus. Additionally, in the aptasensing process, bacteria are incubated with aptamers and then be removed before the aptamers adding to AuNPs, which may avoid the interactions between bacteria and AuNPs. This strategy can be potentially applied in principle to detect other cells by AuNPs-based aptasensors.

IgG Fc variant cross-reactivity between human and rhesus macaque FcγRs

PubMed Central

Boesch, Austin W.; Miles, Adam R.; Chan, Ying N.; Osei-Owusu, Nana Y.; Ackerman, Margaret E.

2017-01-01

ABSTRACT Non-human primate (NHP) studies are often an essential component of antibody development efforts before human trials. Because the efficacy or toxicity of candidate antibodies may depend on their interactions with Fcγ receptors (FcγR) and their resulting ability to induce FcγR-mediated effector functions such as antibody-dependent cell-meditated cytotoxicity and phagocytosis (ADCP), the evaluation of human IgG variants with modulated affinity toward human FcγR is becoming more prevalent in both infectious disease and oncology studies in NHP. Reliable translation of these results necessitates analysis of the cross-reactivity of these human Fc variants with NHP FcγR. We report evaluation of the binding affinities of a panel of human IgG subclasses, Fc amino acid point mutants and Fc glycosylation variants against the common allotypes of human and rhesus macaque FcγR by applying a high-throughput array-based surface plasmon resonance platform. The resulting data indicate that amino acid variation present in rhesus FcγRs can result in disrupted, matched, or even increased affinity of IgG Fc variants compared with human FcγR orthologs. These observations emphasize the importance of evaluating species cross-reactivity and developing an understanding of the potential limitations or suitability of representative in vitro and in vivo models before human clinical studies when either efficacy or toxicity may be associated with FcγR engagement. PMID:28055295

Single-Exome sequencing identified a novel RP2 mutation in a child with X-linked retinitis pigmentosa.

PubMed

Lim, Hassol; Park, Young-Mi; Lee, Jong-Keuk; Taek Lim, Hyun

2016-10-01

To present an efficient and successful application of a single-exome sequencing study in a family clinically diagnosed with X-linked retinitis pigmentosa. Exome sequencing study based on clinical examination data. An 8-year-old proband and his family. The proband and his family members underwent comprehensive ophthalmologic examinations. Exome sequencing was undertaken in the proband using Agilent SureSelect Human All Exon Kit and Illumina HiSeq 2000 platform. Bioinformatic analysis used Illumina pipeline with Burrows-Wheeler Aligner-Genome Analysis Toolkit (BWA-GATK), followed by ANNOVAR to perform variant functional annotation. All variants passing filter criteria were validated by Sanger sequencing to confirm familial segregation. Analysis of exome sequence data identified a novel frameshift mutation in RP2 gene resulting in a premature stop codon (c.665delC, p.Pro222fsTer237). Sanger sequencing revealed this mutation co-segregated with the disease phenotype in the child's family. We identified a novel causative mutation in RP2 from a single proband's exome sequence data analysis. This study highlights the effectiveness of the whole-exome sequencing in the genetic diagnosis of X-linked retinitis pigmentosa, over the conventional sequencing methods. Even using a single exome, exome sequencing technology would be able to pinpoint pathogenic variant(s) for X-linked retinitis pigmentosa, when properly applied with aid of adequate variant filtering strategy. Copyright © 2016 Canadian Ophthalmological Society. Published by Elsevier Inc. All rights reserved.

Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity.

PubMed

Terekhov, Stanislav S; Smirnov, Ivan V; Stepanova, Anastasiya V; Bobik, Tatyana V; Mokrushina, Yuliana A; Ponomarenko, Natalia A; Belogurov, Alexey A; Rubtsova, Maria P; Kartseva, Olga V; Gomzikova, Marina O; Moskovtsev, Alexey A; Bukatin, Anton S; Dubina, Michael V; Kostryukova, Elena S; Babenko, Vladislav V; Vakhitova, Maria T; Manolov, Alexander I; Malakhova, Maja V; Kornienko, Maria A; Tyakht, Alexander V; Vanyushkina, Anna A; Ilina, Elena N; Masson, Patrick; Gabibov, Alexander G; Altman, Sidney

2017-03-07

Ultrahigh-throughput screening (uHTS) techniques can identify unique functionality from millions of variants. To mimic the natural selection mechanisms that occur by compartmentalization in vivo, we developed a technique based on single-cell encapsulation in droplets of a monodisperse microfluidic double water-in-oil-in-water emulsion (MDE). Biocompatible MDE enables in-droplet cultivation of different living species. The combination of droplet-generating machinery with FACS followed by next-generation sequencing and liquid chromatography-mass spectrometry analysis of the secretomes of encapsulated organisms yielded detailed genotype/phenotype descriptions. This platform was probed with uHTS for biocatalysts anchored to yeast with enrichment close to the theoretically calculated limit and cell-to-cell interactions. MDE-FACS allowed the identification of human butyrylcholinesterase mutants that undergo self-reactivation after inhibition by the organophosphorus agent paraoxon. The versatility of the platform allowed the identification of bacteria, including slow-growing oral microbiota species that suppress the growth of a common pathogen, Staphylococcus aureus , and predicted which genera were associated with inhibitory activity.

A platform for rapid exploration of aging and diseases in a naturally short-lived vertebrate

PubMed Central

Harel, Itamar; Benayoun, Bérénice A.; Machado, Ben; Singh, Param Priya; Hu, Chi-Kuo; Pech, Matthew F.; Valenzano, Dario R.; Zhang, Elisa; Sharp, Sabrina C.; Artandi, Steven E.; Brunet, Anne

2015-01-01

Summary Aging is a complex process that affects multiple organs. Modeling aging and age-related diseases in the lab is challenging because classical vertebrate models have relatively long lifespans. Here we develop the first platform for rapid exploration of age-dependent traits and diseases in vertebrates, using the naturally short-lived African turquoise killifish. We provide an integrative genomic and genome-editing toolkit in this organism using our de novo-assembled genome and the CRISPR/Cas9 technology. We mutate many genes encompassing the hallmarks of aging, and for a subset, we produce stable lines within 2–3 months. As a proof-of-principle, we show that fish deficient for the protein subunit of telomerase exhibit the fastest onset of telomere-related pathologies among vertebrates. We further demonstrate the feasibility of creating specific genetic variants. This genome-to-phenotype platform represents a unique resource for studying vertebrate aging and disease in a high throughput manner and for investigating candidates arising from human genome-wide studies. PMID:25684364

Designing scalable product families by the radial basis function-high-dimensional model representation metamodelling technique

NASA Astrophysics Data System (ADS)

Pirmoradi, Zhila; Haji Hajikolaei, Kambiz; Wang, G. Gary

2015-10-01

Product family design is cost-efficient for achieving the best trade-off between commonalization and diversification. However, for computationally intensive design functions which are viewed as black boxes, the family design would be challenging. A two-stage platform configuration method with generalized commonality is proposed for a scale-based family with unknown platform configuration. Unconventional sensitivity analysis and information on variation in the individual variants' optimal design are used for platform configuration design. Metamodelling is employed to provide the sensitivity and variable correlation information, leading to significant savings in function calls. A family of universal electric motors is designed for product performance and the efficiency of this method is studied. The impact of the employed parameters is also analysed. Then, the proposed method is modified for obtaining higher commonality. The proposed method is shown to yield design solutions with better objective function values, allowable performance loss and higher commonality than the previously developed methods in the literature.

Current state-of-art of STR sequencing in forensic genetics.

PubMed

Alonso, Antonio; Barrio, Pedro A; Müller, Petra; Köcher, Steffi; Berger, Burkhard; Martin, Pablo; Bodner, Martin; Willuweit, Sascha; Parson, Walther; Roewer, Lutz; Budowle, Bruce

2018-05-11

The current state of validation and implementation strategies of MPS technology for the analysis of STR markers for forensic genetics use is described, covering the topics of the current catalogue of commercial MPS-STR panels, leading MPS-platforms, and MPS-STR data analysis tools. In addition, the developmental and internal validation studies carried out to date to evaluate reliability, sensitivity, mixture analysis, concordance, and the ability to analyze challenged samples are summarized. The results of various MPS-STR population studies that showed a large number of new STR sequence variants that increase the power of discrimination in several forensically-relevant loci are also presented. Finally, various initiatives developed by several international projects and standardization (or guidelines) groups to facilitate application of MPS technology for STR marker analyses are discussed in regard to promoting a standard STR sequence nomenclature, performing population studies to detect sequence variants, and developing a universal system to translate sequence variants into a simple STR nomenclature (numbers and letters) compatible with national STR databases. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Reference genotype and exome data from an Australian Aboriginal population for health-based research

PubMed Central

Tang, Dave; Anderson, Denise; Francis, Richard W.; Syn, Genevieve; Jamieson, Sarra E.; Lassmann, Timo; Blackwell, Jenefer M.

2016-01-01

Genetic analyses, including genome-wide association studies and whole exome sequencing (WES), provide powerful tools for the analysis of complex and rare genetic diseases. To date there are no reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of variants called after sequencing the exomes of 72 Aboriginal individuals to a depth of 20X coverage in ∼80% of the sequenced nucleotides. We determined 320,976 single nucleotide variants (SNVs) and 47,313 insertions/deletions using the Genome Analysis Toolkit. We had previously genotyped a subset of the Aboriginal individuals (70/72) using the Illumina Omni2.5 BeadChip platform and found ~99% concordance at overlapping sites, which suggests high quality genotyping. Finally, we compared our SNVs to six publicly available variant databases, such as dbSNP and the Exome Sequencing Project, and 70,115 of our SNVs did not overlap any of the single nucleotide polymorphic sites in all the databases. Our data set provides a useful reference point for genomic studies on Aboriginal Australians. PMID:27070114

Reference genotype and exome data from an Australian Aboriginal population for health-based research.

PubMed

Tang, Dave; Anderson, Denise; Francis, Richard W; Syn, Genevieve; Jamieson, Sarra E; Lassmann, Timo; Blackwell, Jenefer M

2016-04-12

Genetic analyses, including genome-wide association studies and whole exome sequencing (WES), provide powerful tools for the analysis of complex and rare genetic diseases. To date there are no reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of variants called after sequencing the exomes of 72 Aboriginal individuals to a depth of 20X coverage in ∼80% of the sequenced nucleotides. We determined 320,976 single nucleotide variants (SNVs) and 47,313 insertions/deletions using the Genome Analysis Toolkit. We had previously genotyped a subset of the Aboriginal individuals (70/72) using the Illumina Omni2.5 BeadChip platform and found ~99% concordance at overlapping sites, which suggests high quality genotyping. Finally, we compared our SNVs to six publicly available variant databases, such as dbSNP and the Exome Sequencing Project, and 70,115 of our SNVs did not overlap any of the single nucleotide polymorphic sites in all the databases. Our data set provides a useful reference point for genomic studies on Aboriginal Australians.

Numerical analysis of seawater circulation in carbonate platforms: II. The dynamic interaction between geothermal and brine reflux circulation

USGS Publications Warehouse

Jones, G.D.; Whitaker, F.F.; Smart, P.L.; Sanford, W.E.

2004-01-01

Density-driven seawater circulation may occur in carbonate platforms due to geothermal heating and / or reflux of water of elevated salinity. In geothermal circulation lateral contrasts in temperature between seawater and platform groundwaters warmed by the geothermal heat flux result in upward convective flow, with colder seawater drawn into the platform at depth. With reflux circulation, platform-top waters concentrated by evaporation flow downward, displacing less dense underlying groundwaters. We have used a variable density groundwater flow model to examine the pattern, magnitude and interaction of these two different circulation mechanisms, for mesosaline platform-top waters (50???) and brines concentrated up to saturation with respect to gypsum (150???) and halite (246???). Geothermal circulation, most active around the platform margin, becomes restricted and eventually shut-off by reflux of brines from the platform interior towards the margin. The persistence of geothermal circulation is dependent on the rate of brine reflux, which is proportional to the concentration of platform-top brines and also critically dependent on the magnitude and distribution of permeability. Low permeability evaporites can severely restrict reflux whereas high permeability units in hydraulic continuity enhance brine transport. Reduction in permeability with depth and anisotropy of permeability (kv < < kh) focuses flow laterally in the shallow subsurface (<1 km), resulting in a horizontally elongated brine plume. Aquifer porosity and dispersivity are relatively minor controls on reflux. Platform brines can entrain surficial seawater when brine generating conditions cease but the platform-top remains submerged, a variant of reflux we term "latent reflux". Brines concentrated up to gypsum saturation have relatively long residence times of at least 100 times the duration of the reflux event. They thus represent a long-term control on post-reflux groundwater circulation, and consequently on the rates and spatial patterns of shallow burial diagenesis, such as dolomitization.

Exome sequencing analysis reveals variants in primary immunodeficiency genes in patients with very early onset inflammatory bowel disease.

PubMed

Kelsen, Judith R; Dawany, Noor; Moran, Christopher J; Petersen, Britt-Sabina; Sarmady, Mahdi; Sasson, Ariella; Pauly-Hubbard, Helen; Martinez, Alejandro; Maurer, Kelly; Soong, Joanne; Rappaport, Eric; Franke, Andre; Keller, Andreas; Winter, Harland S; Mamula, Petar; Piccoli, David; Artis, David; Sonnenberg, Gregory F; Daly, Mark; Sullivan, Kathleen E; Baldassano, Robert N; Devoto, Marcella

2015-11-01

Very early onset inflammatory bowel disease (VEO-IBD), IBD diagnosed at 5 years of age or younger, frequently presents with a different and more severe phenotype than older-onset IBD. We investigated whether patients with VEO-IBD carry rare or novel variants in genes associated with immunodeficiencies that might contribute to disease development. Patients with VEO-IBD and parents (when available) were recruited from the Children's Hospital of Philadelphia from March 2013 through July 2014. We analyzed DNA from 125 patients with VEO-IBD (age, 3 wk to 4 y) and 19 parents, 4 of whom also had IBD. Exome capture was performed by Agilent SureSelect V4, and sequencing was performed using the Illumina HiSeq platform. Alignment to human genome GRCh37 was achieved followed by postprocessing and variant calling. After functional annotation, candidate variants were analyzed for change in protein function, minor allele frequency less than 0.1%, and scaled combined annotation-dependent depletion scores of 10 or less. We focused on genes associated with primary immunodeficiencies and related pathways. An additional 210 exome samples from patients with pediatric IBD (n = 45) or adult-onset Crohn's disease (n = 20) and healthy individuals (controls, n = 145) were obtained from the University of Kiel, Germany, and used as control groups. Four hundred genes and regions associated with primary immunodeficiency, covering approximately 6500 coding exons totaling more than 1 Mbp of coding sequence, were selected from the whole-exome data. Our analysis showed novel and rare variants within these genes that could contribute to the development of VEO-IBD, including rare heterozygous missense variants in IL10RA and previously unidentified variants in MSH5 and CD19. In an exome sequence analysis of patients with VEO-IBD and their parents, we identified variants in genes that regulate B- and T-cell functions and could contribute to pathogenesis. Our analysis could lead to the identification of previously unidentified IBD-associated variants. Copyright © 2015 AGA Institute. Published by Elsevier Inc. All rights reserved.

Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients.

PubMed

Lim, Eileen C P; Brett, Maggie; Lai, Angeline H M; Lee, Siew-Peng; Tan, Ee-Shien; Jamuar, Saumya S; Ng, Ivy S L; Tan, Ene-Choo

2015-12-14

Next-generation sequencing (NGS) has revolutionized genetic research and offers enormous potential for clinical application. Sequencing the exome has the advantage of casting the net wide for all known coding regions while targeted gene panel sequencing provides enhanced sequencing depths and can be designed to avoid incidental findings in adult-onset conditions. A HaloPlex panel consisting of 180 genes within commonly altered chromosomal regions is available for use on both the Ion Personal Genome Machine (PGM) and MiSeq platforms to screen for causative mutations in these genes. We used this Haloplex ICCG panel for targeted sequencing of 15 patients with clinical presentations indicative of an abnormality in one of the 180 genes. Sequencing runs were done using the Ion 318 Chips on the Ion Torrent PGM. Variants were filtered for known polymorphisms and analysis was done to identify possible disease-causing variants before validation by Sanger sequencing. When possible, segregation of variants with phenotype in family members was performed to ascertain the pathogenicity of the variant. More than 97% of the target bases were covered at >20×. There was an average of 9.6 novel variants per patient. Pathogenic mutations were identified in five genes for six patients, with two novel variants. There were another five likely pathogenic variants, some of which were unreported novel variants. In a cohort of 15 patients, we were able to identify a likely genetic etiology in six patients (40%). Another five patients had candidate variants for which further evaluation and segregation analysis are ongoing. Our results indicate that the HaloPlex ICCG panel is useful as a rapid, high-throughput and cost-effective screening tool for 170 of the 180 genes. There is low coverage for some regions in several genes which might have to be supplemented by Sanger sequencing. However, comparing the cost, ease of analysis, and shorter turnaround time, it is a good alternative to exome sequencing for patients whose features are suggestive of a genetic etiology involving one of the genes in the panel.

SeqReporter: automating next-generation sequencing result interpretation and reporting workflow in a clinical laboratory.

PubMed

Roy, Somak; Durso, Mary Beth; Wald, Abigail; Nikiforov, Yuri E; Nikiforova, Marina N

2014-01-01

A wide repertoire of bioinformatics applications exist for next-generation sequencing data analysis; however, certain requirements of the clinical molecular laboratory limit their use: i) comprehensive report generation, ii) compatibility with existing laboratory information systems and computer operating system, iii) knowledgebase development, iv) quality management, and v) data security. SeqReporter is a web-based application developed using ASP.NET framework version 4.0. The client-side was designed using HTML5, CSS3, and Javascript. The server-side processing (VB.NET) relied on interaction with a customized SQL server 2008 R2 database. Overall, 104 cases (1062 variant calls) were analyzed by SeqReporter. Each variant call was classified into one of five report levels: i) known clinical significance, ii) uncertain clinical significance, iii) pending pathologists' review, iv) synonymous and deep intronic, and v) platform and panel-specific sequence errors. SeqReporter correctly annotated and classified 99.9% (859 of 860) of sequence variants, including 68.7% synonymous single-nucleotide variants, 28.3% nonsynonymous single-nucleotide variants, 1.7% insertions, and 1.3% deletions. One variant of potential clinical significance was re-classified after pathologist review. Laboratory information system-compatible clinical reports were generated automatically. SeqReporter also facilitated quality management activities. SeqReporter is an example of a customized and well-designed informatics solution to optimize and automate the downstream analysis of clinical next-generation sequencing data. We propose it as a model that may envisage the development of a comprehensive clinical informatics solution. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Incidental germline variants in 1000 advanced cancers on a prospective somatic genomic profiling protocol.

PubMed

Meric-Bernstam, F; Brusco, L; Daniels, M; Wathoo, C; Bailey, A M; Strong, L; Shaw, K; Lu, K; Qi, Y; Zhao, H; Lara-Guerra, H; Litton, J; Arun, B; Eterovic, A K; Aytac, U; Routbort, M; Subbiah, V; Janku, F; Davies, M A; Kopetz, S; Mendelsohn, J; Mills, G B; Chen, K

2016-05-01

Next-generation sequencing in cancer research may reveal germline variants of clinical significance. We report patient preferences for return of results and the prevalence of incidental pathogenic germline variants (PGVs). Targeted exome sequencing of 202 genes was carried out in 1000 advanced cancers using tumor and normal DNA in a research laboratory. Pathogenic variants in 18 genes, recommended for return by The American College of Medical Genetics and Genomics, as well as PALB2, were considered actionable. Patient preferences of return of incidental germline results were collected. Return of results was initiated with genetic counseling and repeat CLIA testing. Of the 1000 patients who underwent sequencing, 43 had likely PGVs: APC (1), BRCA1 (11), BRCA2 (10), TP53 (10), MSH2 (1), MSH6 (4), PALB2 (2), PTEN (2), TSC2 (1), and RB1 (1). Twenty (47%) of 43 variants were previously known based on clinical genetic testing. Of the 1167 patients who consented for a germline testing protocol, 1157 (99%) desired to be informed of incidental results. Twenty-three previously unrecognized mutations identified in the research environment were confirmed with an orthogonal CLIA platform. All patients approached decided to proceed with formal genetic counseling; in all cases where formal genetic testing was carried out, the germline variant of concern validated with clinical genetic testing. In this series, 2.3% patients had previously unrecognized pathogenic germline mutations in 19 cancer-related genes. Thus, genomic sequencing must be accompanied by a plan for return of germline results, in partnership with genetic counseling. © The Author 2016. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

PubMed Central

Olson, Nathan D.; Lund, Steven P.; Zook, Justin M.; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S.; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B.

2015-01-01

This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies. PMID:27077030

A multidimensional platform for the purification of non-coding RNA species

PubMed Central

Chionh, Yok Hian; Ho, Chia-Hua; Pruksakorn, Dumnoensun; Ramesh Babu, I.; Ng, Chee Sheng; Hia, Fabian; McBee, Megan E.; Su, Dan; Pang, Yan Ling Joy; Gu, Chen; Dong, Hongping; Prestwich, Erin G.; Shi, Pei-Yong; Preiser, Peter Rainer; Alonso, Sylvie; Dedon, Peter C.

2013-01-01

A renewed interest in non-coding RNA (ncRNA) has led to the discovery of novel RNA species and post-transcriptional ribonucleoside modifications, and an emerging appreciation for the role of ncRNA in RNA epigenetics. Although much can be learned by amplification-based analysis of ncRNA sequence and quantity, there is a significant need for direct analysis of RNA, which has led to numerous methods for purification of specific ncRNA molecules. However, no single method allows purification of the full range of cellular ncRNA species. To this end, we developed a multidimensional chromatographic platform to resolve, isolate and quantify all canonical ncRNAs in a single sample of cells or tissue, as well as novel ncRNA species. The applicability of the platform is demonstrated in analyses of ncRNA from bacteria, human cells and plasmodium-infected reticulocytes, as well as a viral RNA genome. Among the many potential applications of this platform are a system-level analysis of the dozens of modified ribonucleosides in ncRNA, characterization of novel long ncRNA species, enhanced detection of rare transcript variants and analysis of viral genomes. PMID:23907385

Convergence acceleration of the Proteus computer code with multigrid methods

NASA Technical Reports Server (NTRS)

Demuren, A. O.; Ibraheem, S. O.

1995-01-01

This report presents the results of a study to implement convergence acceleration techniques based on the multigrid concept in the two-dimensional and three-dimensional versions of the Proteus computer code. The first section presents a review of the relevant literature on the implementation of the multigrid methods in computer codes for compressible flow analysis. The next two sections present detailed stability analysis of numerical schemes for solving the Euler and Navier-Stokes equations, based on conventional von Neumann analysis and the bi-grid analysis, respectively. The next section presents details of the computational method used in the Proteus computer code. Finally, the multigrid implementation and applications to several two-dimensional and three-dimensional test problems are presented. The results of the present study show that the multigrid method always leads to a reduction in the number of iterations (or time steps) required for convergence. However, there is an overhead associated with the use of multigrid acceleration. The overhead is higher in 2-D problems than in 3-D problems, thus overall multigrid savings in CPU time are in general better in the latter. Savings of about 40-50 percent are typical in 3-D problems, but they are about 20-30 percent in large 2-D problems. The present multigrid method is applicable to steady-state problems and is therefore ineffective in problems with inherently unstable solutions.

Phylogenetic characterization of Legionella-like endosymbiotic X-bacteria in Amoeba proteus: a proposal for 'Candidatus Legionella jeonii' sp. nov.

PubMed

Park, Miey; Yun, Seong Tae; Kim, Mu Soo; Chun, Jongsik; Ahn, Tae In

2004-12-01

The X-bacteria which initiated organismic association with the D strain of Amoeba proteus in 1966 as parasites have changed to obligate endosymbionts on which the host depends for survival. Owing to the difficulty in cultivating the bacteria in vitro, the identity of X-bacteria has not been determined. As the life cycle of X-bacteria is similar to that of Legionella spp. in soil amoebae, we applied the polymerase chain reaction method with specific primers aimed at Legionella spp. for the detection and cloning of 16S rRNA gene. The identity and intracellular localization of the endosymbiont were confirmed by the application of a specific fluorescently labelled 16S rRNA-targeted probe. In addition we cloned RNA polymerase beta-subunit gene (rpoB) of X-bacteria by genomic library tagging. A phylogenetic analysis of the 16S rRNA gene placed the bacterium within a unique monophyletic group containing all other members of the genus Legionella. Phylogeny from rpoB and mip genes further confirmed the taxonomic context of X-bacteria to be a Legionella sp. In all three phylogenic analyses, X-bacterium was placed apart from Legionella-like amoebal pathogens present in soil amoebae. Thus, we propose the name 'Candidatus Legionella jeonii' sp. nov. for the endosymbiotic X-bacteria in Amoeba proteus.

Reanalysis of the gas-cooled fast reactor experiments at the zero power facility proteus - Spectral indices

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

Perret, G.; Pattupara, R. M.; Girardin, G.

2012-07-01

The gas-cooled fast reactor (GCFR) concept was investigated experimentally in the PROTEUS zero power facility at the Paul Scherrer Inst. during the 1970's. The experimental program was aimed at neutronics studies specific to the GCFR and at the validation of nuclear data in fast spectra. A significant part of the program used thorium oxide and thorium metal fuel either distributed quasi-homogeneously in the reference PuO{sub 2}/UO{sub 2} lattice or introduced in the form of radial and axial blanket zones. Experimental results obtained at the time are still of high relevance in view of the current consideration of the Gas-cooled Fastmore » Reactor (GFR) as a Generation-IV nuclear system, as also of the renewed interest in the thorium cycle. In this context, some of the experiments have been modeled with modern Monte Carlo codes to better account for the complex PROTEUS whole-reactor geometry and to allow validating recent continuous neutron cross-section libraries. As a first step, the MCNPX model was used to test the JEFF-3.1, JEFF-3.1.1, ENDF/B-VII.0 and JENDL-3.3 libraries against spectral indices, notably involving fission and capture of {sup 232}Th and {sup 237}Np, measured in GFR-like lattices. (authors)« less

Characterization of a cDNA of peroxiredoxin II responding to hydrogen peroxide and phagocytosis in Amoeba proteus.

PubMed

Park, Miey; Shin, Hae J; Lee, Soo Y; Ahn, Tae I

2005-01-01

Phagocytic cells have defense systems against reactive oxygen species generated as the first non-specific defense mechanism against invading pathogens or microorganisms. We cloned a cDNA encoding a 21.69-kDa protein in Amoeba proteus homologous to 2-Cys peroxiredoxin (Prx-Ap). In the disk inhibition assay using H2O2 as an oxidizing agent, Escherichia coli overproducing Prx-Ap showed better viability than did E. coli transformed with pBluescript II SK for control. Monoclonal antibodies (mAb) produced against Prx-Ap reacted with a 22.5-kDa protein and several minor proteins. In Western blot analysis, levels of the 22.5-kDa protein in amoebae treated with 2-mM H2O2 for 1 h increased about 2-fold over those in control cells. Immunofluorescence scattered throughout the cytoplasm also increased after H2O2 treatment. In Northern blot analysis using the cDNA as a probe, the level of transcripts also changed with H2O2 treatment. When amoebae were fed with Tetrahymena, the intensity of immunofluorescence increased from 15 min and persisted until 2 h after phagocytosis. These results suggest that the 22.5-kDa protein of A. proteus is a Prx protein and that it has an antioxidant property responding to phagocytosis.

Hyperspectral Observations of Land Surfaces Using Ground-based, Airborne, and Satellite Sensors

NASA Astrophysics Data System (ADS)

Knuteson, R. O.; Best, F. A.; Revercomb, H. E.; Tobin, D. C.

2006-12-01

The University of Wisconsin-Madison Space Science and Engineering Center (UW-SSEC) has helped pioneer the use of high spectral resolution infrared spectrometers for application to atmospheric and surface remote sensing. This paper is focused on observations of land surface infrared emission from high spectral resolution measurements collected over the past 15 years using airborne, ground-based, and satellite platforms. The earliest data was collected by the High-resolution Interferometer Sounder (HIS), an instrument designed in the 1980s for operation on the NASA ER-2 high altitude aircraft. The HIS was replaced in the late 1990s by the Scanning-HIS instrument which has flown on the NASA ER-2, WB-57, DC-8, and Scaled Composites Proteus aircraft and continues to support field campaigns, such as those for EOS Terra, Aqua, and Aura validation. Since 1995 the UW-SSEC has fielded a ground-based Atmospheric Emitted Radiance Interferometer (AERI) in a research vehicle (the AERIBAGO) which has allowed for direct field measurements of land surface emission from a height of about 16 ft above the ground. Several ground-based and aircraft campaigns were conducted to survey the region surrounding the ARM Southern Great Plains site in north central Oklahoma. The ground- based AERIBAGO has also participated in surface emissivity campaigns in the Western U.S.. Since 2002, the NASA Atmospheric InfraRed Sounder (AIRS) has provided similar measurements from the Aqua platform in an afternoon sun-synchronous polar orbit. Ground-based and airborne observations are being used to validate the land surface products derived from the AIRS observations. These cal/val activities are in preparation for similar measurements anticipated from the operational Cross-track InfraRed Sounder (CrIS) on the NPOESS Preparatory Platform (NPP), expected to be launched in 2008. Moreover, high spectral infrared observations will soon be made by the Infrared Atmospheric Sounder Interferometer (IASI) on the European MetOp platform as well as a planned series of Chinese polar orbiting satellites. The detailed understanding of the land surface infrared emission is a crucial step in the effective utilization of these advanced sounder instruments for the extraction of atmospheric composition information (esp. water vapor vertical profile) over land, which is a key goal for numerical weather prediction data assimilation.

Antimicrobial activity of Gymnema sylvestre leaf extract.

PubMed

Satdive, R K; Abhilash, P; Fulzele, Devanand P

2003-12-01

The ethanolic extract of Gymnema sylvestre leaves demonstrated antimicrobial activity against Bacillus pumilis, B. subtilis, Pseudomonas aeruginosa and Staphylococcus aureus and inactivity against Proteus vulgaris and Escherichia coli.

21 CFR 520.88f - Amoxicillin trihydrate tablets.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., Streptococcus spp., Staphylococcus spp., and Escherichia coli; and soft tissue infections (abscesses, wounds, lacerations) due to S. aureus, Streptococcus spp., E. coli, Proteus mirabilis, and Staphylococcus spp. (iii...

21 CFR 520.88f - Amoxicillin trihydrate tablets.

Code of Federal Regulations, 2011 CFR

2011-04-01

..., Streptococcus spp., Staphylococcus spp., and Escherichia coli; and soft tissue infections (abscesses, wounds, lacerations) due to S. aureus, Streptococcus spp., E. coli, Proteus mirabilis, and Staphylococcus spp. (iii...

From Catheter to Kidney Stone: The Uropathogenic Lifestyle of Proteus mirabilis.

PubMed

Norsworthy, Allison N; Pearson, Melanie M

2017-04-01

Proteus mirabilis is a model organism for urease-producing uropathogens. These diverse bacteria cause infection stones in the urinary tract and form crystalline biofilms on indwelling urinary catheters, frequently leading to polymicrobial infection. Recent work has elucidated how P. mirabilis causes all of these disease states. Particularly exciting is the discovery that this bacterium forms large clusters in the bladder lumen that are sites for stone formation. These clusters, and other steps of infection, require two virulence factors in particular: urease and MR/P fimbriae. Highlighting the importance of MR/P fimbriae is the cotranscribed regulator, MrpJ, which globally controls virulence. Overall, P. mirabilis exhibits an extraordinary lifestyle, and further probing will answer exciting basic microbiological and clinically relevant questions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Observation of multicellular spinning behavior of Proteus mirabilis by atomic force microscopy and multifunctional microscopy.

PubMed

Liu, Yanxia; Deng, Yuanxin; Luo, Shuxiu; Deng, Yu; Guo, Linming; Xu, Weiwei; Liu, Lei; Liu, Junkang

2014-01-01

This study aimed to observe the multicellular spinning behavior of Proteus mirabilis by atomic force microscopy (AFM) and multifunctional microscopy in order to understand the mechanism underlying this spinning movement and its biological significance. Multifunctional microscopy with charge-coupled device (CCD) and real-time AFM showed changes in cell structure and shape of P. mirabilis during multicellular spinning movement. Specifically, the morphological characteristics of P. mirabilis, multicellular spinning dynamics, and unique movement were observed. Our findings indicate that the multicellular spinning behavior of P. mirabilis may be used to collect nutrients, perform colonization, and squeeze out competitors. The movement characteristics of P. mirabilis are vital to the organism's biological adaptability to the surrounding environment. Copyright © 2013 Elsevier Ltd. All rights reserved.

Necrotizing suppurative nephritis in a Japanese black feedlot steer due to Proteus mirabilis infection.

PubMed

Abe, Tadatsugu; Iizuka, Ayako; Kojima, Hirokazu; Kimura, Kumiko; Shibahara, Tomoyuki; Haritani, Makoto

2017-04-05

A Japanese black feedlot steer suddenly died after exhibiting astasia and cramping of the extremities. Necropsy of the animal revealed that the right kidney was enlarged and pale with severe nephrolithiasis. The urinary bladder displayed mucosal hemorrhage. Upon bacteriological investigation, Proteus mirabilis was isolated from the liver, spleen, right kidney, lungs and urine. Histopathological examination revealed necrotizing suppurative nephritis with the presence of numerous gram-negative bacilli and fibrinous suppurative cystitis with no bacilli. Immunohistochemical analysis revealed that the bacteria and cytoplasm of the macrophages stained positively with P. mirabilis antiserum. Electron microscopy revealed the presence of numerous bacteria in the renal tubules. To our knowledge, this is the first report describing the histopathological aspects of nephritis caused by P. mirabilis in cattle.

[Joint action of nitrofuran preparations and bile acids on bacteria of the genus Proteus].

PubMed

Sytnik, I A; Puzakova, E V

1975-01-01

Sensitivity of 25 fresh isolates of Proteus to some nitrofuran drugs most widely used in the clinical practice, such as furacillin, furagin, furazolidone and nitrofurantoin was studied. When the drugs were used in combination with some bile acids, i.e. desoxycholic, dehydrocholic, cholic and glycocholic acids, significant in vitro potentiation of the antibacterial activity of the nitrofurans against the isolates was observed. The combinations of the drugs with desoxycholic acid proved to be most effective. In the presence of this acid the bacteriostatic dose of the drugs decreased several thousand times. Combination of the nitrofurans with the other acids resulted in an increase in the antimicrobial activity amounting to several hundred times. The combinations of the drugs with the bile acids had not only bacteriostatic but also bactericidal effect.

Expression and regulation of the penicillin G acylase gene from Proteus rettgeri cloned in Escherichia coli.

PubMed

Daumy, G O; Williams, J A; McColl, A S; Zuzel, T J; Danley, D

1986-10-01

The penicillin G acylase genes from the Proteus rettgeri wild type and from a hyperproducing mutant which is resistant to succinate repression were cloned in Escherichia coli K-12. Expression of both wild-type and mutant P. rettgeri acylase genes in E. coli K-12 was independent of orientation in the cloning vehicle and apparently resulted from recognition in E. coli of the P. rettgeri promoter sequences. The P. rettgeri acylase was secreted into the E. coli periplasmic space and was composed of subunits electrophoretically identical to those made in P. rettgeri. Expression of these genes in E. coli K-12 was not repressed by succinate as it is in P. rettgeri. Instead, expression of the enzymes was regulated by glucose catabolite repression.

[Experience in the use of anti-colibacillus and Proteus lactoglobulin as a supplement to milk products in diet therapy at a specialized childrens' collective].

PubMed

Soboleva, S V; Zlatnik, E Ia; Mineeva, L D; Kaplin, M M; Shamanova, G P

1989-01-01

A new biologically active supplement (BAS) for infant food was tested at an Infant's Home. BAS-IG contains lactoglobulin, an immune preparation against colibacillus and Proteus. During the primary examination of the infants in the Infant's Home intestinal dysbacteriosis was revealed in 100% of the infants, clinical signs of dysbacteriosis were detected in 88.4% of the infants. Two successive courses of feeding the infants with products enriched with the new supplement resulted in a significant improvement of the microflora composition in them and in normalizing their clinical condition. At the same time positive changes in a number of immunological factors were recorded. The authors have recommended using BAS-IG for correction of dysbacteriosis in children at Infant's Homes.

Development of Cross Section Library and Application Programming Interface (API)

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

Lee, C. H.; Marin-Lafleche, A.; Smith, M. A.

2014-04-09

The goal of NEAMS neutronics is to develop a high-fidelity deterministic neutron transport code termed PROTEUS for use on all reactor types of interest, but focused primarily on sodium-cooled fast reactors. While PROTEUS-SN has demonstrated good accuracy for homogeneous fast reactor problems and partially heterogeneous fast reactor problems, the simulation results were not satisfactory when applied on fully heterogeneous thermal problems like the Advanced Test Reactor (ATR). This is mainly attributed to the quality of cross section data for heterogeneous geometries since the conventional cross section generation approach does not work accurately for such irregular and complex geometries. Therefore, onemore » of the NEAMS neutronics tasks since FY12 has been the development of a procedure to generate appropriate cross sections for a heterogeneous geometry core.« less

CYTOPLASMIC DNA SYNTHESIS IN AMOEBA PROTEUS. 3. FURTHER STUDIES ON THE NATURE OF THE DNA--CONTAINING ELEMENTS.

PubMed

WOLSTENHOLME, D R; PLAUT, W

1964-09-01

The application of electron microscope autoradiography to Amoeba proteus cells labeled with tritiated thymidine has permitted the identification of morphologically distinct particles in the cytoplasm as the sites of incorporated DNA precursor. The particles correspond to those previously described from light microscope studies, with respect to both H(3)Tdr incorporation and distribution in centrifugally stratified amoebae. Ingested bacteria differ from the particles, in morphology as well as in the absence of associated label. Attempts to introduce a normal particle labeling pattern by incubating amoebae with labeled sediment derived from used amoeba medium failed. The resultant conclusion, that the particles are maintained in the amoeba by self-duplication, is supported by the presence of particles in configurations suggestive of division.

Canary: an atomic pipeline for clinical amplicon assays.

PubMed

Doig, Kenneth D; Ellul, Jason; Fellowes, Andrew; Thompson, Ella R; Ryland, Georgina; Blombery, Piers; Papenfuss, Anthony T; Fox, Stephen B

2017-12-15

High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number of shortcomings: they lack robustness and have many components written in multiple languages, each with a variety of resource requirements. Pipeline components must be linked together with a workflow system to achieve the processing of FASTQ files through to a VCF file of variants. Crafting these pipelines requires considerable bioinformatics and IT skills beyond the reach of many clinical laboratories. Here we present Canary, a single program that can be run on a laptop, which takes FASTQ files from amplicon assays through to an annotated VCF file ready for clinical analysis. Canary can be installed and run with a single command using Docker containerization or run as a single JAR file on a wide range of platforms. Although it is a single utility, Canary performs all the functions present in more complex and unwieldy pipelines. All variants identified by Canary are 3' shifted and represented in their most parsimonious form to provide a consistent nomenclature, irrespective of sequencing variation. Further, proximate in-phase variants are represented as a single HGVS 'delins' variant. This allows for correct nomenclature and consequences to be ascribed to complex multi-nucleotide polymorphisms (MNPs), which are otherwise difficult to represent and interpret. Variants can also be annotated with hundreds of attributes sourced from MyVariant.info to give up to date details on pathogenicity, population statistics and in-silico predictors. Canary has been used at the Peter MacCallum Cancer Centre in Melbourne for the last 2 years for the processing of clinical sequencing data. By encapsulating clinical features in a single, easily installed executable, Canary makes sequencing more accessible to all pathology laboratories. Canary is available for download as source or a Docker image at https://github.com/PapenfussLab/Canary under a GPL-3.0 License.

Integrated microfluidic platforms for investigating neuronal networks

NASA Astrophysics Data System (ADS)

Kim, Hyung Joon

This dissertation describes the development and application of integrated microfluidics-based assay platforms to study neuronal activities in the nervous system in-vitro. The assay platforms were fabricated using soft lithography and micro/nano fabrication including microfluidics, surface patterning, and nanomaterial synthesis. The use of integrated microfluidics-based assay platform allows culturing and manipulating many types of neuronal tissues in precisely controlled microenvironment. Furthermore, they provide organized multi-cellular in-vitro model, long-term monitoring with live cell imaging, and compatibility with molecular biology techniques and electrophysiology experiment. In this dissertation, the integrated microfluidics-based assay platforms are developed for investigation of neuronal activities such as local protein synthesis, impairment of axonal transport by chemical/physical variants, growth cone path finding under chemical/physical cues, and synaptic transmission in neuronal circuit. Chapter 1 describes the motivation, objectives, and scope for developing in-vitro platform to study various neuronal activities. Chapter 2 introduces microfluidic culture platform for biochemical assay with large-scale neuronal tissues that are utilized as model system in neuroscience research. Chapter 3 focuses on the investigation of impaired axonal transport by beta-Amyloid and oxidative stress. The platform allows to control neuronal processes and to quantify mitochondrial movement in various regions of axons away from applied drugs. Chapter 4 demonstrates the development of microfluidics-based growth cone turning assay to elucidate the mechanism underlying axon guidance under soluble factors and shear flow. Using this platform, the behaviors of growth cone of mammalian neurons are verified under the gradient of inhibitory molecules and also shear flow in well-controlled manner. In Chapter 5, I combine in-vitro multicellular model with microfabricated MEA (multielectrode array) or nanowire electrode array to study electrophysiology in neuronal network. Also, "diode-like" microgrooves to control the number of neuronal processes is embedded in this platform. Chapter 6 concludes with a possible future direction of this work. Interfacing micro/nanotechnology with primary neuron culture would open many doors in fundamental neuroscience research and also biomedical innovation.

Real-Time Vertical Temperature, and Velocity Profiles from a Wave Glider

DTIC Science & Technology

2012-09-30

Ocean in September 2010 during the ITOP experiment. ADOS platforms are also deployed by the NOAA funded Global Drifter Program in the north Atlantic...class of instrument is termed ADOS (Autonomous Drifting Ocean Station) and several variants exist. The ADOS-A, which measures temperature and...during the hurricane season to measure the thermal structure of the ocean ahead of storms and in their wakes. Both the ADOS-A and the M- ADOS-A are

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction

PubMed Central

Laehnemann, David; Borkhardt, Arndt

2016-01-01

Characterizing the errors generated by common high-throughput sequencing platforms and telling true genetic variation from technical artefacts are two interdependent steps, essential to many analyses such as single nucleotide variant calling, haplotype inference, sequence assembly and evolutionary studies. Both random and systematic errors can show a specific occurrence profile for each of the six prominent sequencing platforms surveyed here: 454 pyrosequencing, Complete Genomics DNA nanoball sequencing, Illumina sequencing by synthesis, Ion Torrent semiconductor sequencing, Pacific Biosciences single-molecule real-time sequencing and Oxford Nanopore sequencing. There is a large variety of programs available for error removal in sequencing read data, which differ in the error models and statistical techniques they use, the features of the data they analyse, the parameters they determine from them and the data structures and algorithms they use. We highlight the assumptions they make and for which data types these hold, providing guidance which tools to consider for benchmarking with regard to the data properties. While no benchmarking results are included here, such specific benchmarks would greatly inform tool choices and future software development. The development of stand-alone error correctors, as well as single nucleotide variant and haplotype callers, could also benefit from using more of the knowledge about error profiles and from (re)combining ideas from the existing approaches presented here. PMID:26026159

HemOnc.org: A Collaborative Online Knowledge Platform for Oncology Professionals

PubMed Central

Warner, Jeremy L.; Cowan, Andrew J.; Hall, Aric C.; Yang, Peter C.

2015-01-01

Purpose: Cancer care involves extensive knowledge about numerous chemotherapy drugs and chemotherapy regimens. This information is constantly evolving, and there has been no freely available, comprehensive, centralized repository of chemotherapy information to date. Methods: We created an online, freely accessible, ad-free, collaborative wiki of chemotherapy information entitled HemOnc.org to address the unmet need for a central repository of this information. This Web site was developed with wiki development software and is hosted on a cloud platform. Chemotherapy drug and regimen information (including regimen variants), as well as other information of interest to hematology/oncology professionals, is housed on the site in a fully referenced and standardized format. Accredited users are allowed to freely contribute information to the site. Results: From its inception in November 2011, HemOnc.org has grown rapidly and most recently has detailed information on 383 drugs and 1,298 distinct chemotherapy regimens (not counting variants) in 92 disease subtypes. There are regularly more than 2,000 visitors per week from the United States and international locations. A user evaluation demonstrated that users find the site useful, usable, and recommendable. Conclusion: HemOnc.org is now the largest free source of chemotherapy drug and regimen information and is widely used. Future enhancements, including more metadata about drugs and increasingly detailed efficacy and toxicity information, will continue to improve the value of the resource. PMID:25736385

Mid-Atlantic multichannel seismic-reflection profiles 14, 15, 16, and 17

USGS Publications Warehouse

Schlee, John Stevens

1980-01-01

The U. S. Geological Survey (USGS) is making available four multi­channel profiles collected by Teledyne Exploration in 1977 by means of a 48-channel streamer (3600 m long) and four airguns (2160 in). Profiles 15 and 16 were processed by.Teledyne Exploration and profiles 14 and 17 were processed on the Phoenix "I"* computer·by the USGS. The processing included standard demultiplexing, deconvolution before and aftfer stack, Common Depth Point (CDP) gathers, velocity analyses every 3 km, move-out correction, stacking, time-variant, filtering, and time-variant scaling.The released lines are over the outer edge of the Continental Shelf in the northern part of the Baltimore Canyon trough (Line 14: 140 km long and Line 15: 157 km long), over the Long Island platform. (Line 16: 313 km long), and over the Carolina platform (Line 17: 186 km long). These profiles were collected as a part of a regional grid over offshore Atlantic sedimentary basins in a continuing program to assess the resource potential by means of nonproprietary data.These profiles, plus the velocity scans and shotpoint maps, may be viewed at U. S. Geological Survey, Quissett Campus, Woods Hole, MA. 02543, and U. S. Geological Survey, Bldg. 25, Denver Federal Center, Denver, CO. Copies of maps, scans, and profiles can be purchased only from the National Geophysical Solar-Terrestrial Data Center, Environmental Data Service (NOM), Code D 621, Boulder, CO 80302.

HemOnc.org: A Collaborative Online Knowledge Platform for Oncology Professionals.

PubMed

Warner, Jeremy L; Cowan, Andrew J; Hall, Aric C; Yang, Peter C

2015-05-01

Cancer care involves extensive knowledge about numerous chemotherapy drugs and chemotherapy regimens. This information is constantly evolving, and there has been no freely available, comprehensive, centralized repository of chemotherapy information to date. We created an online, freely accessible, ad-free, collaborative wiki of chemotherapy information entitled HemOnc.org to address the unmet need for a central repository of this information. This Web site was developed with wiki development software and is hosted on a cloud platform. Chemotherapy drug and regimen information (including regimen variants), as well as other information of interest to hematology/oncology professionals, is housed on the site in a fully referenced and standardized format. Accredited users are allowed to freely contribute information to the site. From its inception in November 2011, HemOnc.org has grown rapidly and most recently has detailed information on 383 drugs and 1,298 distinct chemotherapy regimens (not counting variants) in 92 disease subtypes. There are regularly more than 2,000 visitors per week from the United States and international locations. A user evaluation demonstrated that users find the site useful, usable, and recommendable. HemOnc.org is now the largest free source of chemotherapy drug and regimen information and is widely used. Future enhancements, including more metadata about drugs and increasingly detailed efficacy and toxicity information, will continue to improve the value of the resource. Copyright © 2015 by American Society of Clinical Oncology.

21 CFR 522.90c - Ampicillin sodium.

Code of Federal Regulations, 2011 CFR

2011-04-01

.... (including S. equi), Escherichia coli, and Proteus mirabilis, and skin and soft tissue infections (abscesses and wounds) due to Staphylococcus spp., Streptococcus spp., E. coli, and P. mirabilis, when caused by...

21 CFR 522.90c - Ampicillin sodium.

Code of Federal Regulations, 2010 CFR

2010-04-01

.... (including S. equi), Escherichia coli, and Proteus mirabilis, and skin and soft tissue infections (abscesses and wounds) due to Staphylococcus spp., Streptococcus spp., E. coli, and P. mirabilis, when caused by...

Proteus Syndrome Foundation

MedlinePlus

... Syndrome Diagnostic Criteria & FAQs Medical Research Glossary Donate Cash Donation Life Insurance Gift Matching Gift Stock Gift ... data It’s easy to join There is no cost to you: the costs are supported by the ...

APOL1–Mediated Cell Injury Involves Disruption of Conserved Trafficking Processes

PubMed Central

Kruzel-Davila, Etty; Shemer, Revital; Ofir, Ayala; Bavli-Kertselli, Ira; Darlyuk-Saadon, Ilona; Oren-Giladi, Pazit; Wasser, Walter G.; Magen, Daniella; Zaknoun, Eid; Schuldiner, Maya; Salzberg, Adi; Kornitzer, Daniel; Marelja, Zvonimir; Simons, Matias

2017-01-01

APOL1 harbors C–terminal sequence variants (G1 and G2), which account for much of the increased risk for kidney disease in sub–Saharan African ancestry populations. Expression of the risk variants has also been shown to cause injury to podocytes and other cell types, but the underlying mechanisms are not understood. We used Drosophila melanogaster and Saccharomyces cerevisiae to help clarify these mechanisms. Ubiquitous expression of the human APOL1 G1 and G2 disease risk alleles caused near-complete lethality in D. melanogaster, with no effect of the G0 nonrisk APOL1 allele, corresponding to the pattern of human disease risk. We also observed a congruent pattern of cellular damage with tissue-specific expression of APOL1. In particular, expression of APOL1 risk variants in D. melanogaster nephrocytes caused cell-autonomous accumulation of the endocytic tracer atrial natriuretic factor-red fluorescent protein at early stages and nephrocyte loss at later stages. We also observed differential toxicity of the APOL1 risk variants compared with the APOL1 nonrisk variants in S. cerevisiae, including impairment of vacuole acidification. Yeast strains defective in endosomal trafficking or organelle acidification but not those defective in autophagy displayed augmented APOL1 toxicity with all isoforms. This pattern of differential injury by the APOL1 risk alleles compared with the nonrisk alleles across evolutionarily divergent species is consistent with an impairment of conserved core intracellular endosomal trafficking processes. This finding should facilitate the identification of cell injury pathways and corresponding therapeutic targets of interest in these amenable experimental platforms. PMID:27864431

High throughput microscopy identifies bisphenol AP, a bisphenol A analog, as a novel AR down-regulator.

PubMed

Stossi, Fabio; Dandekar, Radhika D; Bolt, Michael J; Newberg, Justin Y; Mancini, Maureen G; Kaushik, Akash K; Putluri, Vasanta; Sreekumar, Arun; Mancini, Michael A

2016-03-29

Prostate cancer remains a deadly disease especially when patients become resistant to drugs that target the Androgen Receptor (AR) ligand binding domain. At this stage, patients develop recurring castrate-resistant prostate cancers (CRPCs). Interestingly, CRPC tumors maintain dependency on AR for growth; moreover, in CRPCs, constitutively active AR splice variants (e.g., AR-V7) begin to be expressed at higher levels. These splice variants lack the ligand binding domain and are rendered insensitive to current endocrine therapies. Thus, it is of paramount importance to understand what regulates the expression of AR and its splice variants to identify new therapeutic strategies in CRPCs. Here, we used high throughput microscopy and quantitative image analysis to evaluate effects of selected endocrine disruptors on AR levels in multiple breast and prostate cancer cell lines. Bisphenol AP (BPAP), which is used in chemical and medical industries, was identified as a down-regulator of both full length AR and the AR-V7 splice variant. We validated its activity by performing time-course, dose-response, Western blot and qPCR analyses. BPAP also reduced the percent of cells in S phase, which was accompanied by a ~60% loss in cell numbers and colony formation in anchorage-independent growth assays. Moreover, it affected mitochondria size and cell metabolism. In conclusion, our high content analysis-based screening platform was used to classify the effect of compounds on endogenous ARs, and identified BPAP as being capable of causing AR (both full-length and variants) down-regulation, cell cycle arrest and metabolic alterations in CRPC cell lines.

Use of MicroMaps for Satellite Validation and Potential UAV Applications

NASA Astrophysics Data System (ADS)

Connors, V. S.; Sachse, G. W.; Hopkins, P. E.; Morrow, W.; McMillan, W. W.

2005-12-01

The MicroMAPS instrument is a nadir-viewing, gas filter-correlated radiometer which operates in the 4.67 micrometer fundamental band of carbon monoxide. Originally designed and built for a space mission, this CO remote sensor is being flown in support of satellite validation and science instrument demonstrations for potential UAV applications. The MicroMAPS CO instrument was flown for the first time during the Summer-Fall 2004 on-board the Proteus aircraft, which is owned and operated by Scaled Composites, in Mojave, CA. The insturment system, flown on Proteus, was designed by a student team as a senior design project in the Aerospace Engineering Department, Virginia Tech, in Blacksburg, VA. This proposed design was reviewed and revised by Systems Engineers at NASA Langley; the final instrument system was integrated and tested at NASA LaRC in partnership with Scaled Composites and Virginia Space Grant Consortium, which supervised the fabrication of the nacelle which housed the instrument system on the right rear tail boom of Proteus. Full system integration and flight testing was performed at Scaled Composites, in Mojave, in June 2004. Its successful performance enabled participation in three international science missions: INTEX -NA over eastern North America in July 2004, ADRIEX over the Mediterranean region and EAQUATE over the United Kingdom region in September 2004, piggy-backing with the IPO-sponsored payload flown on Proteus. These flights resulted in nearly 100 hours of science measurements and in-flight calibrations. In parallel with the engineering devlopments, theoretical radiative transfer models were developed specifically for the MicroMAPS instrument system at the University of Virginia, Aerospace and Mechanical Engineering Department by a combined undergraduate and graduate student team. With techical support from Resonance Ltd. In June 2005, in Barrie, Canada, the MicroMAPS instrument was calibrated for the conditions underwhich the Summer-Fall 2004 flights occurred. The analyses of the calibration data, combined with the theoretical radiative transfer models, will provide the first data reduction for the science flights. These early results and comparisons with profile data from the NASA DC-8 and the coincident AIRS CO retrievals will be presented.

Proteus: a random forest classifier to predict disorder-to-order transitioning binding regions in intrinsically disordered proteins

NASA Astrophysics Data System (ADS)

Basu, Sankar; Söderquist, Fredrik; Wallner, Björn

2017-05-01

The focus of the computational structural biology community has taken a dramatic shift over the past one-and-a-half decades from the classical protein structure prediction problem to the possible understanding of intrinsically disordered proteins (IDP) or proteins containing regions of disorder (IDPR). The current interest lies in the unraveling of a disorder-to-order transitioning code embedded in the amino acid sequences of IDPs/IDPRs. Disordered proteins are characterized by an enormous amount of structural plasticity which makes them promiscuous in binding to different partners, multi-functional in cellular activity and atypical in folding energy landscapes resembling partially folded molten globules. Also, their involvement in several deadly human diseases (e.g. cancer, cardiovascular and neurodegenerative diseases) makes them attractive drug targets, and important for a biochemical understanding of the disease(s). The study of the structural ensemble of IDPs is rather difficult, in particular for transient interactions. When bound to a structured partner, an IDPR adapts an ordered conformation in the complex. The residues that undergo this disorder-to-order transition are called protean residues, generally found in short contiguous stretches and the first step in understanding the modus operandi of an IDP/IDPR would be to predict these residues. There are a few available methods which predict these protean segments from their amino acid sequences; however, their performance reported in the literature leaves clear room for improvement. With this background, the current study presents `Proteus', a random forest classifier that predicts the likelihood of a residue undergoing a disorder-to-order transition upon binding to a potential partner protein. The prediction is based on features that can be calculated using the amino acid sequence alone. Proteus compares favorably with existing methods predicting twice as many true positives as the second best method (55 vs. 27%) with a much higher precision on an independent data set. The current study also sheds some light on a possible `disorder-to-order' transitioning consensus, untangled, yet embedded in the amino acid sequence of IDPs. Some guidelines have also been suggested for proceeding with a real-life structural modeling involving an IDPR using Proteus.

The fate and origin of the nuclear envelope during and after mitosis in Amoeba proteus. I. Synthesis and behavior of phospholipids of the nuclear envelope during the cell life cycle

PubMed Central

1975-01-01

The synthesis and behavior of Amoeba proteus nuclear envelope (NE) phospholipids were studied. Most NE phospholipid synthesis occurs during G2 and little during mitosis or S. (A. proteus has no G1 phase). Autoradiographic observations after implantation of [3-H] choline nuclei into unlabeled cells reveal little turnover of NE phospholipid during interphase but during mitosis all the label is dispersed through the cytoplasm. Beginning at telophase all the label is dispersed through the cytoplasm. Beginning at telophase all the NE phospholipid label returns to the daughter NEs. This observation, along with the finding that no NE phospholipid synthesis occurs during mitosis or S, indicates that no de novo NE phospholipid production is required for newly forming NEs. Similarlyemetine, at concentrations that inhibit 97 percent of protein synthesis, does not prevent the post mitotic formation of NEs, suggesting that previously manufactured proteins are used in making new NEs. If a nucleus containing labeled NE phospholipids is transplanted into an unlabeled nucleate cell and the cell is allowed to grow and divide, the resultant four nuclei are equally labeled. This finding supports, but does not prove (see next paragraph), the conclusion that there probably is no continuity of the A. proteus NE during mitosis. When a phospholipid-labeled nucleus is implanted into a cell in mitosis, the grafted nucleus is not induced to enter mitosis. There is, however, a marked increase in the turnover of that nucleus's NE phospholipids with no apparent breakdown of the NE; this indicated that the mitotic cytoplasm possesses a factor that stimulates NE phospholipid exchange with the cytoplasm. That enhanced turnover is not accompanied by visible structural alteration makes less certain the earlier conclusion that no NE continuity exists during mitosis. Perhaps the most important finding in this study is that there are present, at restricted times in the cell cycle, factors capable of inducing accelerated exchange of structural components without microscopically detectable disruptions of structure. PMID:805790

Use of whole exome sequencing for the identification of Ito-based arrhythmia mechanism and therapy.

PubMed

Sturm, Amy C; Kline, Crystal F; Glynn, Patric; Johnson, Benjamin L; Curran, Jerry; Kilic, Ahmet; Higgins, Robert S D; Binkley, Philip F; Janssen, Paul M L; Weiss, Raul; Raman, Subha V; Fowler, Steven J; Priori, Silvia G; Hund, Thomas J; Carnes, Cynthia A; Mohler, Peter J

2015-05-26

Identified genetic variants are insufficient to explain all cases of inherited arrhythmia. We tested whether the integration of whole exome sequencing with well-established clinical, translational, and basic science platforms could provide rapid and novel insight into human arrhythmia pathophysiology and disease treatment. We report a proband with recurrent ventricular fibrillation, resistant to standard therapeutic interventions. Using whole-exome sequencing, we identified a variant in a previously unidentified exon of the dipeptidyl aminopeptidase-like protein-6 (DPP6) gene. This variant is the first identified coding mutation in DPP6 and augments cardiac repolarizing current (Ito) causing pathological changes in Ito and action potential morphology. We designed a therapeutic regimen incorporating dalfampridine to target Ito. Dalfampridine, approved for multiple sclerosis, normalized the ECG and reduced arrhythmia burden in the proband by >90-fold. This was combined with cilostazol to accelerate the heart rate to minimize the reverse-rate dependence of augmented Ito. We describe a novel arrhythmia mechanism and therapeutic approach to ameliorate the disease. Specifically, we identify the first coding variant of DPP6 in human ventricular fibrillation. These findings illustrate the power of genetic approaches for the elucidation and treatment of disease when carefully integrated with clinical and basic/translational research teams. © 2015 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Clinical testing of BRCA1 and BRCA2: a worldwide snapshot of technological practices.

PubMed

Toland, Amanda Ewart; Forman, Andrea; Couch, Fergus J; Culver, Julie O; Eccles, Diana M; Foulkes, William D; Hogervorst, Frans B L; Houdayer, Claude; Levy-Lahad, Ephrat; Monteiro, Alvaro N; Neuhausen, Susan L; Plon, Sharon E; Sharan, Shyam K; Spurdle, Amanda B; Szabo, Csilla; Brody, Lawrence C

2018-01-01

Clinical testing of BRCA1 and BRCA2 began over 20 years ago. With the expiration and overturning of the BRCA patents, limitations on which laboratories could offer commercial testing were lifted. These legal changes occurred approximately the same time as the widespread adoption of massively parallel sequencing (MPS) technologies. Little is known about how these changes impacted laboratory practices for detecting genetic alterations in hereditary breast and ovarian cancer genes. Therefore, we sought to examine current laboratory genetic testing practices for BRCA1 / BRCA2 . We employed an online survey of 65 questions covering four areas: laboratory characteristics, details on technological methods, variant classification, and client-support information. Eight United States (US) laboratories and 78 non-US laboratories completed the survey. Most laboratories (93%; 80/86) used MPS platforms to identify variants. Laboratories differed widely on: (1) technologies used for large rearrangement detection; (2) criteria for minimum read depths; (3) non-coding regions sequenced; (4) variant classification criteria and approaches; (5) testing volume ranging from 2 to 2.5 × 10 5 tests annually; and (6) deposition of variants into public databases. These data may be useful for national and international agencies to set recommendations for quality standards for BRCA1/BRCA2 clinical testing. These standards could also be applied to testing of other disease genes.

21 CFR 522.56 - Amikacin sulfate injection.

Code of Federal Regulations, 2010 CFR

2010-04-01

...) caused by susceptible strains of Escherichia coli and Proteus spp. and skin and soft tissue infections caused by susceptible strains of Pseudomonas spp. and E. coli. (3) Limitations. The drug is administered...

[Microbial colonization of the caviar of the sturgeon fishes].

PubMed

Boĭko, A V; Pogorelova, N P; Zhuravlëva, L A; Lartseva, L V

1993-11-01

Samples of black caviar in 47.7% of cases are contaminated by opportunistic bacteria Aeromonas, Proteus, Vibrio, V. parahaemolyticus. Standardization of these micro-organisms content in black caviar is recommended.

21 CFR 520.1618 - Orbifloxacin suspension.

Code of Federal Regulations, 2014 CFR

2014-04-01

... infections (wounds and abscesses) in dogs caused by susceptible strains of Staphylococcus pseudintermedius, Staphylococcus aureus, coagulase-positive staphylococci, Pasteurella multocida, Proteus mirabilis, Pseudomonas... urinary tract infections (cystitis) in dogs caused by susceptible strains of Staphylococcus...

21 CFR 520.1618 - Orbifloxacin suspension.

Code of Federal Regulations, 2012 CFR

2012-04-01

... infections (wounds and abscesses) in dogs caused by susceptible strains of Staphylococcus pseudintermedius, Staphylococcus aureus, coagulase-positive staphylococci, Pasteurella multocida, Proteus mirabilis, Pseudomonas... urinary tract infections (cystitis) in dogs caused by susceptible strains of Staphylococcus...

21 CFR 520.1618 - Orbifloxacin suspension.

Code of Federal Regulations, 2013 CFR

2013-04-01

... infections (wounds and abscesses) in dogs caused by susceptible strains of Staphylococcus pseudintermedius, Staphylococcus aureus, coagulase-positive staphylococci, Pasteurella multocida, Proteus mirabilis, Pseudomonas... urinary tract infections (cystitis) in dogs caused by susceptible strains of Staphylococcus...

Antibacterial Activity of Anthraquinone from Aloe on Spiced Pig Head

NASA Astrophysics Data System (ADS)

Xu, Lingyi; Li, Xiao; Cui, Yuqian; Pang, Meixia; Wang, Fang; Qi, Jinghua

2017-12-01

[Objective] To optimize the extraction of anthraquinone from Aloe by ultrasonic extraction and its antibacterialactivity. [Method]The influences of different extraction time and ethanol concentration, on anthraquinone contentwere evaluated by asingle factor experiment. And anthraquinone content was determined by ultraviolet spectrophotometry. The bacteriostasis of anthraquinone on spiced pig head’s common putrefying bacteria: Staphylococcus, Serratieae, Bacillus, Proteus and the minimal inhibitory concentration (MIC) were studied by oxford plate assay system. [Result]The best extraction time was 30 minutes and the best ethanol concentration was 80%. The antibacterial activity of the Aloe anthraquinone on Staphylococcus Aureus, Bacillus Proteus is obviously, the minimum inhibitory concentrations were 0.0625 g/mL, 0.05 g/mL, 0.125 g/mL respectively and no inhibitory effect on Serratieae. [Conclusions] The anthraquinones from Aloe can inhibit a part Of spoilage bacteria inspiced pig heads.

Report: Studies on antibacterial activity of some traditional medicinal plants used in folk medicine.

PubMed

Israr, Fozia; Hassan, Fouzia; Naqvi, Baqir Shyum; Azhar, Iqbal; Jabeen, Sabahat; Hasan, S M Farid

2012-07-01

Ethanolic extracts of eight medicinal plants commonly used in folk medicine were tested for their antibacterial activity against four Gram positive strains (Bacillus subtilis, Staphylococcus aureus, Staphylococcus epidermidis and, Streptococcus pneumoniae) and six Gram negative strains (Escherichia coli, Proteus vulgaris, Proteus mirabilis. Salmonella typhi para A, Salmonella typhi para B and Shigella dysenteriae) that were obtained from different pathological laboratories located in Karachi, Pakistan. Disc diffusion method was used to analyze antibacterial activity. Out of eight, five medicinal plants showed antibacterial activity against two or more than two microbial species. The most effective antimicrobial plant found to be Punica granatum followed by Curcuma zedoaria Rosc, Grewia asiatica L and Carissa carandas L, Curcuma caesia Roxb respectively. From these results, it is evident that medicinal plants could be used as a potential source of new antibacterial agents.

A comparison of certain extracting agents for extraction of adenosine triphosphate (ATP) from microorganisms for use in the firefly luciferase ATP assay

NASA Technical Reports Server (NTRS)

Knust, E. A.; Chappelle, E. W.; Picciolo, G. L.

1975-01-01

Firefly luciferase ATP assay is used in clinical and industrial applications, such as determination of urinary infection levels, microbial susceptibility testing, and monitoring of yeast levels in beverages. Three categories of extractants were investigated for their extracting efficiency. They were ionizing organic solvents, nonionizing organic solvents, and inorganic acids. Dimethylsulfoxide and formamide represented the ionizing organic solvents, while n-butanol, chloroform, ethanol, acetone, and methylene chloride were used for the nonionizing organic solvents. Nitric acid and perchloric acid were chosen for the inorganic acids category. Pathogens were tested with each solvent. They included: Saccharomyces carlsbergensis, E. coli, Staphylococcus aureus, Klebsiella pneumoniae, Enterobacter species, Proteus mirabilis, Proteus vulgaris, Staphylococcus epidermidis, Streptococcus faecalis, Pseudomonas aeruginosa, and Candida albicans. These results are shown in graphic representations.

Transcriptome of Proteus mirabilis in the Murine Urinary Tract: Virulence and Nitrogen Assimilation Gene Expression▿†

PubMed Central

Pearson, Melanie M.; Yep, Alejandra; Smith, Sara N.; Mobley, Harry L. T.

2011-01-01

The enteric bacterium Proteus mirabilis is a common cause of complicated urinary tract infections. In this study, microarrays were used to analyze P. mirabilis gene expression in vivo from experimentally infected mice. Urine was collected at 1, 3, and 7 days postinfection, and RNA was isolated from bacteria in the urine for transcriptional analysis. Across nine microarrays, 471 genes were upregulated and 82 were downregulated in vivo compared to in vitro broth culture. Genes upregulated in vivo encoded mannose-resistant Proteus-like (MR/P) fimbriae, urease, iron uptake systems, amino acid and peptide transporters, pyruvate metabolism enzymes, and a portion of the tricarboxylic acid (TCA) cycle enzymes. Flagella were downregulated. Ammonia assimilation gene glnA (glutamine synthetase) was repressed in vivo, while gdhA (glutamate dehydrogenase) was upregulated in vivo. Contrary to our expectations, ammonia availability due to urease activity in P. mirabilis did not drive this gene expression. A gdhA mutant was growth deficient in minimal medium with citrate as the sole carbon source, and loss of gdhA resulted in a significant fitness defect in the mouse model of urinary tract infection. Unlike Escherichia coli, which represses gdhA and upregulates glnA in vivo and cannot utilize citrate, the data suggest that P. mirabilis uses glutamate dehydrogenase to monitor carbon-nitrogen balance, and this ability contributes to the pathogenic potential of P. mirabilis in the urinary tract. PMID:21505083

Epidemiology of extended-spectrum β-lactamase, AmpC, and carbapenemase production in Proteus mirabilis.

PubMed

Datta, Priya; Gupta, Varsha; Arora, Shilpa; Garg, Shivani; Chander, Jagdish

2014-01-01

Proteus mirabilis strains that produce extended-spectrum β-lactamase (ESBL), AmpC β-lactamase, and carbapenemase pose potential threats to patient care because most clinical diagnostic laboratories may not attempt to detect these three major groups of enzymes. Therefore, the objective of this study was to ascertain if P. mirabilis isolates collected from our heathcare facility possess various mechanisms of resistance to β-lactams (i.e., ESBL, AmpC, and carbapenemases) and to additionally arrive at conclusions regarding concurrent testing for these three mechanism of drug resistance in order to reduce cost and time in routine diagnostic testing. Between January 2011 and June 2011, 60 consecutive non-repeated strains of P. mirabilis were evaluated for production of ESBLs, AmpC β-lactamases, and carbapenemases. Of these, 36 isolates were found to be ESBL producers, and 7 (12%) were positive for production of AmpC β-lactamases and ESBLs. Therefore, 19.4% of ESBL-producing Proteus strains coproduced AmpC enzymes. The modified Hodge test confirmed carbapenemase production in only 1 isolate (1.7%), which was also ESBL- and AmpC-positive. The clinical impact of additional AmpC expression in ESBL-producing P. mirabilis results in a newly acquired resistance to β-lactamase inhibitors. In addition, to save time and costs, we recommend the use of cefepime/cefepime-clavulanate or boronic acid for the ESBL detection but in only those strains that were positive for ESBL by screening and negative by confirmatory tests.

Babes in the wood – a unique window into sea scorpion ontogeny

PubMed Central

2013-01-01

Background Few studies on eurypterids have taken into account morphological changes that occur throughout postembryonic development. Here two species of eurypterid are described from the Pragian Beartooth Butte Formation of Cottonwood Canyon in Wyoming and included in a phylogenetic analysis. Both species comprise individuals from a number of instars, and this allows for changes that occur throughout their ontogeny to be documented, and how ontogenetically variable characters can influence phylogenetic analysis to be tested. Results The two species of eurypterid are described as Jaekelopterus howelli (Kjellesvig-Waering and Størmer, 1952) and Strobilopterus proteus sp. nov. Phylogenetic analysis places them within the Pterygotidae and Strobilopteridae respectively, both families within the Eurypterina. Jaekelopterus howelli shows positive allometry of the cheliceral denticles throughout ontogeny, while a number of characteristics including prosomal appendage length, carapace shape, lateral eye position, and relative breadth all vary during the growth of Strobilopterus proteus. Conclusions The ontogeny of Strobilopterus proteus shares much in common with that of modern xiphosurans, however certain characteristics including apparent true direct development suggest a closer affinity to arachnids. The ontogenetic development of the genital appendage also supports the hypothesis that the structure is homologous to the endopods of the trunk limbs of other arthropods. Including earlier instars in the phylogenetic analysis is shown to destabilise the retrieved topology. Therefore, coding juveniles as individual taxa in an analysis is shown to be actively detrimental and alternative ways of coding ontogenetic data into phylogenetic analyses should be explored. PMID:23663507

[Tartrate-sensitive and tartrate-resistant acid phosphatases in Amoeba proteus].

PubMed

Sopina, V A; Beliaeva, T N

2000-01-01

In free-living Amoeba proteus (strain B), acid phosphatase (AcP) was examined by disc-electrophoresis in polyacrylamide gel. The tartrate-sensitive amebian AcP was greatly inhibited by dithiothreitol and Cu2+, and only partly inhibited by sodium orthovanadate, ammonium molybdate, EDTA, disodium salt and Mg2+, Ca2+, Zn2+ and Mn2+. On the contrary, it appeared to be resistant to sulfhydryl reagents--4(hydroxymercury) benzoic acid, sodium salt and N-ethylmaleimide. Unlike the tartrate-sensitive enzyme, the tartrate-resistant AcP was greatly inhibited by EDTA and partly inhibited by dithiothreitol, Mg2+ and Cu2+ (Mn2+ > Cu2+), being activated by orthovanadate, molybdate, sulfhydryl reagents, Mg2+, Ca2+ and Zn2+. Both tartrate-sensitive and tartrate-resistant AcPs lack apparently free SH-groups necessary for their catalytic activities. Using 2-naphthyl phosphate as a substrate at pH 4.5, six AcP electromorphs were revealed in cytosol and sediment, four of these being most frequently localized in the former, and two in the latter. Two other AcP electromorphs were confined to the sediment only. Depending on the quantity of sedimented amoebae making a homogenate (0.5 or 2.0 cm3), that was added to Percoll solution, the lysosomal AcP fraction in polyacrylamide gel was represented by one or two tartrate-sensitive electromorphs. Therefore, tartrate-resistant AcP in A. proteus may be a lysosomal enzyme, while tartrate-resistant AcP may correspond to serine/threonine protein phosphatase.

Continuously tunable nucleic acid hybridization probes.

PubMed

Wu, Lucia R; Wang, Juexiao Sherry; Fang, John Z; Evans, Emily R; Pinto, Alessandro; Pekker, Irena; Boykin, Richard; Ngouenet, Celine; Webster, Philippa J; Beechem, Joseph; Zhang, David Yu

2015-12-01

In silico-designed nucleic acid probes and primers often do not achieve favorable specificity and sensitivity tradeoffs on the first try, and iterative empirical sequence-based optimization is needed, particularly in multiplexed assays. We present a novel, on-the-fly method of tuning probe affinity and selectivity by adjusting the stoichiometry of auxiliary species, which allows for independent and decoupled adjustment of the hybridization yield for different probes in multiplexed assays. Using this method, we achieved near-continuous tuning of probe effective free energy. To demonstrate our approach, we enforced uniform capture efficiency of 31 DNA molecules (GC content, 0-100%), maximized the signal difference for 11 pairs of single-nucleotide variants and performed tunable hybrid capture of mRNA from total RNA. Using the Nanostring nCounter platform, we applied stoichiometric tuning to simultaneously adjust yields for a 24-plex assay, and we show multiplexed quantitation of RNA sequences and variants from formalin-fixed, paraffin-embedded samples.

Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma.

PubMed

Wrzeszczynski, Kazimierz O; Frank, Mayu O; Koyama, Takahiko; Rhrissorrakrai, Kahn; Robine, Nicolas; Utro, Filippo; Emde, Anne-Katrin; Chen, Bo-Juen; Arora, Kanika; Shah, Minita; Vacic, Vladimir; Norel, Raquel; Bilal, Erhan; Bergmann, Ewa A; Moore Vogel, Julia L; Bruce, Jeffrey N; Lassman, Andrew B; Canoll, Peter; Grommes, Christian; Harvey, Steve; Parida, Laxmi; Michelini, Vanessa V; Zody, Michael C; Jobanputra, Vaidehi; Royyuru, Ajay K; Darnell, Robert B

2017-08-01

To analyze a glioblastoma tumor specimen with 3 different platforms and compare potentially actionable calls from each. Tumor DNA was analyzed by a commercial targeted panel. In addition, tumor-normal DNA was analyzed by whole-genome sequencing (WGS) and tumor RNA was analyzed by RNA sequencing (RNA-seq). The WGS and RNA-seq data were analyzed by a team of bioinformaticians and cancer oncologists, and separately by IBM Watson Genomic Analytics (WGA), an automated system for prioritizing somatic variants and identifying drugs. More variants were identified by WGS/RNA analysis than by targeted panels. WGA completed a comparable analysis in a fraction of the time required by the human analysts. The development of an effective human-machine interface in the analysis of deep cancer genomic datasets may provide potentially clinically actionable calls for individual patients in a more timely and efficient manner than currently possible. NCT02725684.

Epidermal growth factor receptor and variant III targeted immunotherapy

PubMed Central

Congdon, Kendra L.; Gedeon, Patrick C.; Suryadevara, Carter M.; Caruso, Hillary G.; Cooper, Laurence J.N.; Heimberger, Amy B.; Sampson, John H.

2014-01-01

Immunotherapeutic approaches to cancer have shown remarkable promise. A critical barrier to successfully executing such immune-mediated interventions is the selection of safe yet immunogenic targets. As patient deaths have occurred when tumor-associated antigens shared by normal tissue have been targeted by strong cellular immunotherapeutic platforms, route of delivery, target selection and the immune-mediated approach undertaken must work together to maximize efficacy with safety. Selected tumor-specific targets can spare potential toxicity to normal tissue; however, they are far less common than tumor-associated antigens and may not be present on all patients. In the context of immunotherapy for high-grade glioma, 2 of the most prominently studied antigens are the tumor-associated epidermal growth factor receptor and its tumor-specific genetic deletion variant III. In this review, we will summarize the immune-mediated strategies employed against these targets as well as the caveats particular to these approaches. PMID:25342601

The Piancatelli reaction and its variants: recent applications to high added-value chemicals and biomass valorization.

PubMed

Verrier, Charlie; Moebs-Sanchez, Sylvie; Queneau, Yves; Popowycz, Florence

2018-01-31

The Piancatelli reaction, also called the Piancatelli rearrangement, consists in the direct conversion of furfuryl alcohols to cyclopentenone derivatives through a furan ring opening-electrocyclization process. Discovered in the late 70's, this reaction has been scarcely used for more than 40 years but recently has been the focus of particular interest from the scientific community and an increasing number of publications on the topic have emerged in the last few years. The first part of this review provides an overview of the recent achievements in classical Piancatelli reactions, discussing reaction conditions and catalytic systems, whereas the second part focuses on the variants recently developed, including the use of new nucleophiles in the process. Finally, the third part of this review deals with the recent application of this transformation to the production of commodity chemicals from renewable carbon feedstocks based on sugar-derived furanic platforms.

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

Abercrombie, Robert Knox; Richardson, Gregory David; Scudiere, Matthew Bligh

A pad is disclosed for use in a weighing system for weighing a load. The pad includes a weighing platform, load cells, and foot members. Improvements to the pad reduce or substantially eliminate rotation of one or more of the corner foot members. A flexible foot strap disposed between the corner foot members reduces rotation of the respective foot members about vertical axes through the corner foot members and couples the corner foot members such that rotation of one corner foot member results in substantially the same amount of rotation of the other corner foot member. In a strapless variantmore » one or more fasteners prevents substantially all rotation of a foot member. In a diagonal variant, a foot strap extends between a corner foot member and the weighing platform to reduce rotation of the foot member about a vertical axis through the corner foot member.« less

Combining microfluidics, optogenetics and calcium imaging to study neuronal communication in vitro.

PubMed

Renault, Renaud; Sukenik, Nirit; Descroix, Stéphanie; Malaquin, Laurent; Viovy, Jean-Louis; Peyrin, Jean-Michel; Bottani, Samuel; Monceau, Pascal; Moses, Elisha; Vignes, Maéva

2015-01-01

In this paper we report the combination of microfluidics, optogenetics and calcium imaging as a cheap and convenient platform to study synaptic communication between neuronal populations in vitro. We first show that Calcium Orange indicator is compatible in vitro with a commonly used Channelrhodopsine-2 (ChR2) variant, as standard calcium imaging conditions did not alter significantly the activity of transduced cultures of rodent primary neurons. A fast, robust and scalable process for micro-chip fabrication was developed in parallel to build micro-compartmented cultures. Coupling optical fibers to each micro-compartment allowed for the independent control of ChR2 activation in the different populations without crosstalk. By analyzing the post-stimuli activity across the different populations, we finally show how this platform can be used to evaluate quantitatively the effective connectivity between connected neuronal populations.

Open systems storage platforms

NASA Technical Reports Server (NTRS)

Collins, Kirby

1992-01-01

The building blocks for an open storage system includes a system platform, a selection of storage devices and interfaces, system software, and storage applications CONVEX storage systems are based on the DS Series Data Server systems. These systems are a variant of the C3200 supercomputer with expanded I/O capabilities. These systems support a variety of medium and high speed interfaces to networks and peripherals. System software is provided in the form of ConvexOS, a POSIX compliant derivative of 4.3BSD UNIX. Storage applications include products such as UNITREE and EMASS. With the DS Series of storage systems, Convex has developed a set of products which provide open system solutions for storage management applications. The systems are highly modular, assembled from off the shelf components with industry standard interfaces. The C Series system architecture provides a stable base, with the performance and reliability of a general purpose platform. This combination of a proven system architecture with a variety of choices in peripherals and application software allows wide flexibility in configurations, and delivers the benefits of open systems to the mass storage world.

A Neuron-Based Screening Platform for Optimizing Genetically-Encoded Calcium Indicators

PubMed Central

Schreiter, Eric R.; Hasseman, Jeremy P.; Tsegaye, Getahun; Fosque, Benjamin F.; Behnam, Reza; Shields, Brenda C.; Ramirez, Melissa; Kimmel, Bruce E.; Kerr, Rex A.; Jayaraman, Vivek; Looger, Loren L.; Svoboda, Karel; Kim, Douglas S.

2013-01-01

Fluorescent protein-based sensors for detecting neuronal activity have been developed largely based on non-neuronal screening systems. However, the dynamics of neuronal state variables (e.g., voltage, calcium, etc.) are typically very rapid compared to those of non-excitable cells. We developed an electrical stimulation and fluorescence imaging platform based on dissociated rat primary neuronal cultures. We describe its use in testing genetically-encoded calcium indicators (GECIs). Efficient neuronal GECI expression was achieved using lentiviruses containing a neuronal-selective gene promoter. Action potentials (APs) and thus neuronal calcium levels were quantitatively controlled by electrical field stimulation, and fluorescence images were recorded. Images were segmented to extract fluorescence signals corresponding to individual GECI-expressing neurons, which improved sensitivity over full-field measurements. We demonstrate the superiority of screening GECIs in neurons compared with solution measurements. Neuronal screening was useful for efficient identification of variants with both improved response kinetics and high signal amplitudes. This platform can be used to screen many types of sensors with cellular resolution under realistic conditions where neuronal state variables are in relevant ranges with respect to timing and amplitude. PMID:24155972

Porting the Starlink Software Collection to GNU Autotools

NASA Astrophysics Data System (ADS)

Gray, N.; Jenness, T.; Allan, A.; Berry, D. S.; Currie, M. J.; Draper, P. W.; Taylor, M. B.; Cavanagh, B.

2005-12-01

The Starlink software collection currently runs on three different Unix platforms and contains around 100 separate software items, totaling 2.5 million lines of code, in a mixture of languages. We have changed the build system from a hand-maintained collection of makefiles with hard-wired OS variants to a scheme involving feature-discovery via GNU Autoconf. As a result of this work, we have already ported the collection to Mac OS X and Cygwin. This had some unexpected benefits and costs, and valuable lessons.

Passive vibration isolation of reaction wheel disturbances using a low frequency flexible space platform

NASA Astrophysics Data System (ADS)

Kamesh, D.; Pandiyan, R.; Ghosal, Ashitava

2012-03-01

Reaction wheel assemblies (RWAs) are momentum exchange devices used in fine pointing control of spacecrafts. Even though the spinning rotor of the reaction wheel is precisely balanced to minimize emitted vibration due to static and dynamic imbalances, precision instrument payloads placed in the neighborhood can always be severely impacted by residual vibration forces emitted by reaction wheel assemblies. The reduction of the vibration level at sensitive payloads can be achieved by placing the RWA on appropriate mountings. A low frequency flexible space platform consisting of folded continuous beams has been designed to serve as a mount for isolating a disturbance source in precision payloads equipped spacecrafts. Analytical and experimental investigations have been carried out to test the usefulness of the low frequency flexible platform as a vibration isolator for RWAs. Measurements and tests have been conducted at varying wheel speeds, to quantify and characterize the amount of isolation obtained from the reaction wheel generated vibration. These tests are further extended to other variants of similar design in order to bring out the best isolation for given disturbance loads. Both time and frequency domain analysis of test data show that the flexible beam platform as a mount for reaction wheels is quite effective and can be used in spacecrafts for passive vibration control.

2D and 3D virtual interactive laboratories of physics on Unity platform

NASA Astrophysics Data System (ADS)

González, J. D.; Escobar, J. H.; Sánchez, H.; De la Hoz, J.; Beltrán, J. R.

2017-12-01

Using the cross-platform game engine Unity, we develop virtual laboratories for PC, consoles, mobile devices and website as an innovative tool to study physics. There is extensive uptake of ICT in the teaching of science and its impact on the learning, and considering the limited availability of laboratories for physics teaching and the difficulties this causes in the learning of school students, we design the virtual laboratories to enhance studentâĂŹs knowledge of concepts in physics. To achieve this goal, we use Unity due to provide support bump mapping, reflection mapping, parallax mapping, dynamics shadows using shadows maps, full-screen post-processing effects and render-to-texture. Unity can use the best variant for the current video hardware and, if none are compatible, to use an alternative shader that may sacrifice features for performance. The control over delivery to mobile devices, web browsers, consoles and desktops is the main reason Unity is the best option among the same kind cross-platform. Supported platforms include Android, Apple TV, Linux, iOS, Nintendo 3DS line, macOS, PlayStation 4, Windows Phone 8, Wii but also an asset server and Nvidia’s PhysX physics engine which is the most relevant tool on Unity for our PhysLab.

Genetic Modifiers of Neurofibromatosis Type 1-Associated Café-au-Lait Macule Count Identified Using Multi-platform Analysis

PubMed Central

Pemov, Alexander; Sung, Heejong; Hyland, Paula L.; Sloan, Jennifer L.; Ruppert, Sarah L.; Baldwin, Andrea M.; Boland, Joseph F.; Bass, Sara E.; Lee, Hyo Jung; Jones, Kristine M.; Zhang, Xijun; Mullikin, James C.; Widemann, Brigitte C.; Wilson, Alexander F.; Stewart, Douglas R.

2014-01-01

Neurofibromatosis type 1 (NF1) is an autosomal dominant, monogenic disorder of dysregulated neurocutaneous tissue growth. Pleiotropy, variable expressivity and few NF1 genotype-phenotype correlates limit clinical prognostication in NF1. Phenotype complexity in NF1 is hypothesized to derive in part from genetic modifiers unlinked to the NF1 locus. In this study, we hypothesized that normal variation in germline gene expression confers risk for certain phenotypes in NF1. In a set of 79 individuals with NF1, we examined the association between gene expression in lymphoblastoid cell lines with NF1-associated phenotypes and sequenced select genes with significant phenotype/expression correlations. In a discovery cohort of 89 self-reported European-Americans with NF1 we examined the association between germline sequence variants of these genes with café-au-lait macule (CALM) count, a tractable, tumor-like phenotype in NF1. Two correlated, common SNPs (rs4660761 and rs7161) between DPH2 and ATP6V0B were significantly associated with the CALM count. Analysis with tiled regression also identified SNP rs4660761 as significantly associated with CALM count. SNP rs1800934 and 12 rare variants in the mismatch repair gene MSH6 were also associated with CALM count. Both SNPs rs7161 and rs4660761 (DPH2 and ATP6V0B) were highly significant in a mega-analysis in a combined cohort of 180 self-reported European-Americans; SNP rs1800934 (MSH6) was near-significant in a meta-analysis assuming dominant effect of the minor allele. SNP rs4660761 is predicted to regulate ATP6V0B, a gene associated with melanosome biology. Individuals with homozygous mutations in MSH6 can develop an NF1-like phenotype, including multiple CALMs. Through a multi-platform approach, we identified variants that influence NF1 CALM count. PMID:25329635

Proteus at Play with the Past: Historical Versus Mythical Thinking

ERIC Educational Resources Information Center

Stephens, Lester D.

1975-01-01

The use of primary materials, interpretations, pictorial materials, and statistical information are recommended to break the hold of the mythical image of the past and replace it with a historical past. (Author/DE)

Proteus in Another Guise: The Changing Shape of Art Education

ERIC Educational Resources Information Center

MacGregor, Ronald N.

1973-01-01

This article attempts to outline five major areas of components, selected by virtue of the attention paid them in recent writings, which could provide the content for various combinations of art activities. (Author)

GSTM1, GSTP1, and GSTT1 genetic variability in Turkish and worldwide populations.

PubMed

Karaca, Sefayet; Karaca, Mehmet; Cesuroglu, Tomris; Erge, Sema; Polimanti, Renato

2015-01-01

Glutathione S-transferase (GST) variants have been widely investigated to better understand their role in several pathologic conditions. To our knowledge, no data about these genetic polymorphisms within the Turkish population are currently available. The aim of this study was to analyze GSTM1 positive/null, GSTT1 positive/null, GSTP1*I105V (rs1695), and GSTP1*A114V (rs1138272) variants in the general Turkish population, to provide information about its genetic diversity, and predisposition to GST-related diseases. Genotyping was performed in 500 Turkish individuals using the Sequenom MassARRAY platform. A comparative analysis was executed using the data from the HapMap and Human Genome Diversity Projects (HGDP). Sequence variation was deeply explored using the Phase 1 data of the 1,000 Genomes Project. The variability of GSTM1, GSTT1, and GSTP1 polymorphisms in the Turkish population was similar to that observed in Central Asian, European, and Middle Eastern populations. The high linkage disequilibrium between GSTP1*I105V and GSTP1*A114V in these populations may have a confounding effect on GSTP1 genetic association studies. In analyzing GSTM1, GSTT1, and GSTP1 sequence variation, we observed other common functional variants that may be candidates for associated studies of diseases related to GST genes (e.g., cancer, cardiovascular disease, and allergy). This study provides novel data about GSTM1 positive/null, GSTT1 positive/null, GSTP1*I105V, and GSTP1*A114V variants in the Turkish population, and other functional variants that may affect GSTM1, GSTT1, and GSTP1 functions among worldwide populations. This information can assist in the design of future genetic association studies investigating oxidative stress-related diseases. © 2014 Wiley Periodicals, Inc.

Evaluation of a next generation direct whole blood enzymatic assay for hemoglobin A1c on the ARCHITECT c8000 chemistry system.

PubMed

Teodoro-Morrison, Tracy; Janssen, Marcel J W; Mols, Jasper; Hendrickx, Ben H E; Velmans, Mathieu H; Lotz, Johannes; Lackner, Karl; Lennartz, Lieselotte; Armbruster, David; Maine, Gregory; Yip, Paul M

2015-01-01

The utility of HbA1c for the diagnosis of type 2 diabetes requires an accurate, precise and robust test measurement system. Currently, immunoassay and HPLC are the most popular methods for HbA1c quantification, noting however the limitations associated with some platforms, such as imprecision or interference from common hemoglobin variants. Abbott Diagnostics has introduced a fully automated direct enzymatic method for the quantification of HbA1c from whole blood on the ARCHITECT chemistry system. Here we completed a method evaluation of the ARCHITECT HbA1c enzymatic assay for imprecision, accuracy, method comparison, interference from hemoglobin variants and specimen stability. This was completed at three independent clinical laboratories in North America and Europe. The total imprecision ranged from 0.5% to 2.2% CV with low and high level control materials. Around the diagnostic cut-off of 48 mmol/mol, the total imprecision was 0.6% CV. Mean bias using reference samples from IFCC and CAP ranged from -1.1 to 1.0 mmol/mol. The enzymatic assay also showed excellent agreement with HPLC methods, with slopes of 1.01 and correlation coefficients ranging from 0.984 to 0.996 compared to Menarini Adams HA-8160, Bio-Rad Variant II and Variant II Turbo instruments. Finally, no significant effect was observed for erythrocyte sedimentation or interference from common hemoglobin variants in patient samples containing heterozygous HbS, HbC, HbD, HbE, and up to 10% HbF. The ARCHITECT enzymatic assay for HbA1c is a robust and fully automated method that meets the performance requirements to support the diagnosis of type 2 diabetes.

A deep sequencing reveals significant diversity among dominant variants and evolutionary dynamics of avian leukosis viruses in two infectious ecosystems.

PubMed

Meng, Fanfeng; Dong, Xuan; Hu, Tao; Chang, Shuang; Fan, Jianhua; Zhao, Peng; Cui, Zhizhong

2016-12-19

As a typical retrovirus, the evolution of Avian leukosis virus subgroup J (ALV-J) in different infectious ecosystems is not characterized, what we know is there are a cloud of diverse variants, namely quasispecies with considerable genetic diversity. This study is to explore the selection of infectious ecosystems on dominant variants and their evolutionary dynamics of ALV-J between DF1 cells and specific-pathogen-free (SPF) chickens. High-throughput sequencing platforms provide an approach for detecting quasispecies diversity more fully. An average of about 20,000 valid reads were obtained from two variable regions of gp85 gene and LTR-U3 region from each sample in different infectious ecosystems. The top 10 dominant variants among ALV-J from chicken plasmas, DF1 cells and liver tumor were completely different from each other. Also there was a difference of shannon entropy and global selection pressure values (ω) in different infectious ecosystems. In the plasmas of two chickens, a large portion of quasispecies contained a 3-peptides "LSD" repeat insertion that was only less than 0.01% in DF1 cell culture supernatants. In parallel studies, the LTR-U3 region of ALV-J from the chicken plasmas demonstrated more variants with mutations in their transcription regulatory elements than those from DF1 cells. Our data taken together suggest that the molecular epidemiology based on isolated ALV-J in cell culture may not represent the true evolution of virus in chicken flocks in the field. The biological significance of the "LSD" insert and mutations in LTR-U3 needs to be further studied.

One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies

PubMed Central

Yuan, Shuai; Johnston, H. Richard; Zhang, Guosheng; Li, Yun; Hu, Yi-Juan; Qin, Zhaohui S.

2015-01-01

With rapid decline of the sequencing cost, researchers today rush to embrace whole genome sequencing (WGS), or whole exome sequencing (WES) approach as the next powerful tool for relating genetic variants to human diseases and phenotypes. A fundamental step in analyzing WGS and WES data is mapping short sequencing reads back to the reference genome. This is an important issue because incorrectly mapped reads affect the downstream variant discovery, genotype calling and association analysis. Although many read mapping algorithms have been developed, the majority of them uses the universal reference genome and do not take sequence variants into consideration. Given that genetic variants are ubiquitous, it is highly desirable if they can be factored into the read mapping procedure. In this work, we developed a novel strategy that utilizes genotypes obtained a priori to customize the universal haploid reference genome into a personalized diploid reference genome. The new strategy is implemented in a program named RefEditor. When applying RefEditor to real data, we achieved encouraging improvements in read mapping, variant discovery and genotype calling. Compared to standard approaches, RefEditor can significantly increase genotype calling consistency (from 43% to 61% at 4X coverage; from 82% to 92% at 20X coverage) and reduce Mendelian inconsistency across various sequencing depths. Because many WGS and WES studies are conducted on cohorts that have been genotyped using array-based genotyping platforms previously or concurrently, we believe the proposed strategy will be of high value in practice, which can also be applied to the scenario where multiple NGS experiments are conducted on the same cohort. The RefEditor sources are available at https://github.com/superyuan/refeditor. PMID:26267278

Evaluation of three read-depth based CNV detection tools using whole-exome sequencing data.

PubMed

Yao, Ruen; Zhang, Cheng; Yu, Tingting; Li, Niu; Hu, Xuyun; Wang, Xiumin; Wang, Jian; Shen, Yiping

2017-01-01

Whole exome sequencing (WES) has been widely accepted as a robust and cost-effective approach for clinical genetic testing of small sequence variants. Detection of copy number variants (CNV) within WES data have become possible through the development of various algorithms and software programs that utilize read-depth as the main information. The aim of this study was to evaluate three commonly used, WES read-depth based CNV detection programs using high-resolution chromosomal microarray analysis (CMA) as a standard. Paired CMA and WES data were acquired for 45 samples. A total of 219 CNVs (size ranged from 2.3 kb - 35 mb) identified on three CMA platforms (Affymetrix, Agilent and Illumina) were used as standards. CNVs were called from WES data using XHMM, CoNIFER, and CNVnator with modified settings. All three software packages detected an elevated proportion of small variants (< 20 kb) compared to CMA. XHMM and CoNIFER had poor detection sensitivity (22.2 and 14.6%), which correlated with the number of capturing probes involved. CNVnator detected most variants and had better sensitivity (87.7%); however, suffered from an overwhelming detection of small CNVs below 20 kb, which required further confirmation. Size estimation of variants was exaggerated by CNVnator and understated by XHMM and CoNIFER. Low concordances of CNV, detected by three different read-depth based programs, indicate the immature status of WES-based CNV detection. Low sensitivity and uncertain specificity of WES-based CNV detection in comparison with CMA based CNV detection suggests that CMA will continue to play an important role in detecting clinical grade CNV in the NGS era, which is largely based on WES.

CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences.

PubMed

Chou, A; Burke, J

1999-05-01

DNA sequence clustering has become a valuable method in support of gene discovery and gene expression analysis. Our interest lies in leveraging the sequence diversity within clusters of expressed sequence tags (ESTs) to model gene structure for the study of gene variants that arise from, among other things, alternative mRNA splicing, polymorphism, and divergence after gene duplication, fusion, and translocation events. In previous work, CRAW was developed to discover gene variants from assembled clusters of ESTs. Most importantly, novel gene features (the differing units between gene variants, for example alternative exons, polymorphisms, transposable elements, etc.) that are specialized to tissue, disease, population, or developmental states can be identified when these tools collate DNA source information with gene variant discrimination. While the goal is complete automation of novel feature and gene variant detection, current methods are far from perfect and hence the development of effective tools for visualization and exploratory data analysis are of paramount importance in the process of sifting through candidate genes and validating targets. We present CRAWview, a Java based visualization extension to CRAW. Features that vary between gene forms are displayed using an automatically generated color coded index. The reporting format of CRAWview gives a brief, high level summary report to display overlap and divergence within clusters of sequences as well as the ability to 'drill down' and see detailed information concerning regions of interest. Additionally, the alignment viewing and editing capabilities of CRAWview make it possible to interactively correct frame-shifts and otherwise edit cluster assemblies. We have implemented CRAWview as a Java application across windows NT/95 and UNIX platforms. A beta version of CRAWview will be freely available to academic users from Pangea Systems (http://www.pangeasystems.com). Contact :

Comparison of performance of three commercial platforms for warfarin sensitivity genotyping.

PubMed

Babic, Nikolina; Haverfield, Eden V; Burrus, Julie A; Lozada, Anthony; Das, Soma; Yeo, Kiang-Teck J

2009-08-01

We performed a 3-way comparison on the Osmetech eSensor, AutoGenomics INFINITI, and a real-time PCR method (Paragonx reagents/Stratagene RT-PCR platform) for their FDA-cleared warfarin panels, and additional polymorphisms (CYP2C9*5, *6, and 11 and extended VKORC1 panels) where available. One hundred de-identified DNA samples were used in this IRB-approved study. Accuracy was determined by comparison of genotyping results across three platforms. Any discrepancy was resolved by bi-directional sequencing. The CYP4F2 on Osmetech was validated by bi-directional sequencing. Accuracies for CYP2C9*2 and *3 were 100% for all 3 platforms. VKORC1 3673 genotyping accuracies were 100% on eSensor and 97% on Infiniti. CYP2C9*5, *6 and *11 showed 100% concordance between eSensor and Infiniti. VKORC1 6484 and 9041 variants compared between ParagonDx and Infiniti analyzer were 100% (6484) and 99% (9041) concordant. CYP4F2 was 100% concordant with sequencing results. The time required to generate the results from automated DNA extraction-to-result was approximately 8h on Infiniti, and 4h on eSensor and ParagonDx, respectively. Overall, we observed excellent CYP2C9*2 and *3 genotyping accuracy for all three platforms. For VKORC1 3673 genotyping, eSensor demonstrated a slightly higher accuracy than the Infiniti, and CYP4F2 on Osmetech was 100% accurate.

Disease Variant Landscape of a Large Multiethnic Population of Moyamoya Patients by Exome Sequencing

PubMed Central

Shoemaker, Lorelei D.; Clark, Michael J.; Patwardhan, Anil; Chandratillake, Gemma; Garcia, Sarah; Chen, Rong; Morgan, Alexander A.; Leng, Nan; Kirk, Scott; Chen, Richard; Cook, Douglas J.; Snyder, Michael; Steinberg, Gary K.

2015-01-01

Moyamoya disease (MMD) is a rare disorder characterized by cerebrovascular occlusion and development of hemorrhage-prone collateral vessels. Approximately 10–12% of cases are familial, with a presumed low penetrance autosomal dominant pattern of inheritance. Diagnosis commonly occurs only after clinical presentation. The recent identification of the RNF213 founder mutation (p.R4810K) in the Asian population has made a significant contribution, but the etiology of this disease remains unclear. To further develop the variant landscape of MMD, we performed high-depth whole exome sequencing of 125 unrelated, predominantly nonfamilial, ethnically diverse MMD patients in parallel with 125 internally sequenced, matched controls using the same exome and analysis platform. Three subpopulations were established: Asian, Caucasian, and non-RNF213 founder mutation cases. We provided additional support for the previously observed RNF213 founder mutation (p.R4810K) in Asian cases (P = 6.01×10−5) that was enriched among East Asians compared to Southeast Asian and Pacific Islander cases (P = 9.52×10−4) and was absent in all Caucasian cases. The most enriched variant in Caucasian (P = 7.93×10−4) and non-RNF213 founder mutation (P = 1.51×10−3) cases was ZXDC (p.P562L), a gene involved in MHC Class II activation. Collapsing variant methodology ranked OBSCN, a gene involved in myofibrillogenesis, as most enriched in Caucasian (P = 1.07×10−4) and non-RNF213 founder mutation cases (P = 5.31×10−5). These findings further support the East Asian origins of the RNF213 (p.R4810K) variant and more fully describe the genetic landscape of multiethnic MMD, revealing novel, alternative candidate variants and genes that may be important in MMD etiology and diagnosis. PMID:26530418

21 CFR 522.88 - Amoxicillin.

Code of Federal Regulations, 2014 CFR

2014-04-01

..., tracheobronchitis) due to Staphylococcus aureus, Streptococcus spp., Escherichia coli, and Proteus mirabilis...: Upper respiratory infections due to S. aureus, Staphylococcus spp., Streptococcus spp., Haemophilus spp..., lacerations, and wounds) due to S. aureus, Staphylococcus spp., Streptococcus spp., E. coli, and Pasteurella...

Antibacterial activity of anthraquinone from cassia seed on spiced pig head

NASA Astrophysics Data System (ADS)

Xu, L. Y.; Li, X.; Cui, Y. Q.; Pang, M. X.; Wang, F.; Qi, J. H.

2018-01-01

[Objective] To optimize the extraction of anthraquinone from cassia seed by ultrasonic extraction and its antibacterial activity. [Method] The influences of different extraction time and ethanol concentration, on anthraquinone content were evaluated by a single factor experiment. And anthraquinone content was determined by ultraviolet spectrophotometry. The bacteriostasis of anthraquinone on spiced pig head’s common putrefying bacteria: Staphylococcus, Serratieae, Bacillus, Proteus and the minimal inhibitory concentration (MIC) were studied by oxford plate assay system. [Result] The best extraction time was 30 minutes and the best ethanol concentration was 80%. The antibacterial activity of the cassia seed anthraquinone on Staphylococcus Aureus, Bacillus Proteus is obviously, the minimum inhibitory concentrations were 0.125 g/mL, 0.125 g/mL, 1 g/mL respectively and no inhibitory effect on Serratieae. [Conclusions] The anthraquinones from Cassia seed can inhibit a part of spoilage bacteria in spiced pig heads.

Isolation and Purification of Complex II from Proteus Mirabilis Strain ATCC 29245

PubMed Central

Shabbiri, Khadija; Ahmad, Waqar; Syed, Quratulain; Adnan, Ahmad

2010-01-01

A respiratory complex was isolated from plasma membrane of pathogenic Proteus mirabilis strain ATCC 29245. It was identified as complex II consisting of succinate:quinone oxidoreductase (EC 1.3.5.1) containing single heme b. The complex II was purified by ion-exchange chromatography and gel filtration. The molecular weight of purified complex was 116.5 kDa and it was composed of three subunits with molecular weights of 19 kDa, 29 kDa and 68.5 kDa. The complex II contained 9.5 nmoles of cytochrome b per mg protein. Heme staining indicated that the 19 kDa subunit was cytochrome b. Its reduced form showed absorptions peaks at 557.0, 524.8 and 424.4 nm. The α-band was shifted from 557.0 nm to 556.8 nm in pyridine ferrohemochrome spectrum. The succinate: quinone oxidoreductase activity was found to be high in this microorganism. PMID:24031557

Mimicking a New 2-Phenylethanol Production Pathway from Proteus mirabilis JN458 in Escherichia coli.

PubMed

Liu, Jinbin; Jiang, Jing; Bai, Yajun; Fan, Tai-Ping; Zhao, Ye; Zheng, Xiaohui; Cai, Yujie

2018-04-04

Bacteria rarely produce natural 2-phenylethanol. We verified a new pathway from Proteus mirabilis JN458 to produce 2-phenylethanol using Escherichia coli to coexpress l-amino acid deaminase, α-keto acid decarboxylase, and alcohol dehydrogenase from P. mirabilis. Based on this pathway, a glucose dehydrogenase coenzyme regeneration system was constructed. The optimal conditions of biotransformation by the recombinant strain E-pAEAKaG were at 40 °C and pH 7.0. Finally, the recombinant strain E-pAEAKaG produced 3.21 ± 0.10 g/L 2-phenylethanol in M9 medium containing 10 g/L l-phenylalanine after a 16 h transformation. Furthermore, when the concentration of l-phenylalanine was 4 g/L (24 mM), the production of 2-phenylethanol reached 2.88 ± 0.18 g/L and displayed a higher conversion rate of 97.38 mol %.

Comparative Screening of Digestion Tract Toxic Genes in Proteus mirabilis

PubMed Central

Shi, Xiaolu; Lin, Yiman; Qiu, Yaqun; Li, Yinghui; Jiang, Min; Chen, Qiongcheng; Jiang, Yixiang; Yuan, Jianhui; Cao, Hong; Hu, Qinghua; Huang, Shenghe

2016-01-01

Proteus mirabilis is a common urinary tract pathogen, and may induce various inflammation symptoms. Its notorious ability to resist multiple antibiotics and to form urinary tract stones makes its treatment a long and painful process, which is further challenged by the frequent horizontal gene transferring events in P. mirabilis genomes. Three strains of P. mirabilis C02011/C04010/C04013 were isolated from a local outbreak of a food poisoning event in Shenzhen, China. Our hypothesis is that new genes may have been acquired horizontally to exert the digestion tract infection and toxicity. The functional characterization of these three genomes shows that each of them independently acquired dozens of virulent genes horizontally from the other microbial genomes. The representative strain C02011 induces the symptoms of both vomit and diarrhea, and has recently acquired a complete type IV secretion system and digestion tract toxic genes from the other bacteria. PMID:27010388

Comparative Screening of Digestion Tract Toxic Genes in Proteus mirabilis.

PubMed

Shi, Xiaolu; Lin, Yiman; Qiu, Yaqun; Li, Yinghui; Jiang, Min; Chen, Qiongcheng; Jiang, Yixiang; Yuan, Jianhui; Cao, Hong; Hu, Qinghua; Huang, Shenghe

2016-01-01

Proteus mirabilis is a common urinary tract pathogen, and may induce various inflammation symptoms. Its notorious ability to resist multiple antibiotics and to form urinary tract stones makes its treatment a long and painful process, which is further challenged by the frequent horizontal gene transferring events in P. mirabilis genomes. Three strains of P. mirabilis C02011/C04010/C04013 were isolated from a local outbreak of a food poisoning event in Shenzhen, China. Our hypothesis is that new genes may have been acquired horizontally to exert the digestion tract infection and toxicity. The functional characterization of these three genomes shows that each of them independently acquired dozens of virulent genes horizontally from the other microbial genomes. The representative strain C02011 induces the symptoms of both vomit and diarrhea, and has recently acquired a complete type IV secretion system and digestion tract toxic genes from the other bacteria.

In Vitro Activity of Cephalothin and Three Penicillins Against Escherichia coli and Proteus Species

PubMed Central

Barry, Arthur L.; Hoeprich, Paul D.

1973-01-01

The susceptibility of clinical isolates of Escherichia coli (67) and Proteus species (58) to cephalothin, ampicillin, benzyl penicillin, and phenoxymethyl penicillin was determined in vitro by using broth dilution and disk diffusion tests. The data were correlated by using a four-category scheme for interpreting minimal inhibitory concentrations (groups 1 to 4) as recommended by a subcommittee of an international collaborative study of susceptibility testing. With cephalothin and ampicillin, groups 1 (susceptible) and 2 (moderately susceptible) were susceptible by the disk test, and with benzyl penicillin, similar results were observed when the interpretive zone standards were changed. Strains categorized as group 4 (very resistant) were resistant by the disk method, but group 3 (moderately resistant) strains were not adequately distinguished by disk testing. Group 3 susceptibility to benzyl and phenoxymethyl penicillins can be predicted by extrapolating results from tests with ampicillin disks. PMID:4202343

l-Asparaginase from Proteus vulgaris1

PubMed Central

Tosa, Tetsuya; Sano, Ryujiro; Yamamoto, Kozo; Nakamura, Masatoshi; Ando, Katsuko; Chibata, Ichiro

1971-01-01

To produce an immunologically and enzymologically new type of l-asparaginase, 108 strains of bacteria were screened for enzyme production. As a result, 13 bacteria belonging to the genera Alcaligenes, Bacterium, and Proteus were found to produce l-asparaginases in high levels. Among these l-asparaginases, partially purified l-asparaginases from B. cadaveris and P. vulgaris showed antitumor activity. A partially purified l-asparaginase preparation of P. vulgaris did not react with the antibody of Escherichia colil-asparaginase on the Ouchterlony agar plate. Culture conditions for the production of l-asparaginase by P. vulgaris were investigated in detail. The enzyme was produced in high yields when cells were grown aerobically in a medium containing sodium fumarate and corn steep liquor. The addition of glucose or ammonium ion to the medium, however, resulted in depressed production of l-asparaginase. Under the optimum conditions, 3,700 international units of l-asparaginase was obtained from 1 liter of culture medium. Images PMID:5000866

Digestion of cellulose and xylan by symbiotic bacteria in the intestine of the Indian flying fox (Pteropus giganteus).

PubMed

Prem Anand, A Alwin; Sripathi, K

2004-09-01

Bats (Order Chiroptera) are a widely distributed group of mammals. Pteropus giganteus belongs to the Suborder Megachiroptera. This bat consumes fruits and leaves as their major food. Cellulose and xylan are the major composition of leaves. As they consume leaves in their diet, their digestive tract must contain cellulolytic and xylanolytic bacteria which help in the digestion of cellulose and xylan. The cellulolytic and xylanolytic bacteria were isolated and screened on Berg's agar containing cellulose and xylan. The bacteria isolated were characterized biochemically and found to be Proteus vulgaris, Proteus mirabilis, Citrobacter freundii, Serratia liquefaciens and Klebsiella oxytoca. These bacteria help in digestion of cellulose and xylan in the diet of the bat, P. giganteus. Here we show that leaves are also used as a carbohydrate source by these bats. An insectivorous bat, Hipposideros fulvus, was used as a control and does not possess cellulolytic and xylanolytic bacteria.

Rapid Parameterization Schemes for Aircraft Shape Optimization

NASA Technical Reports Server (NTRS)

Li, Wu

2012-01-01

A rapid shape parameterization tool called PROTEUS is developed for aircraft shape optimization. This tool can be applied directly to any aircraft geometry that has been defined in PLOT3D format, with the restriction that each aircraft component must be defined by only one data block. PROTEUS has eight types of parameterization schemes: planform, wing surface, twist, body surface, body scaling, body camber line, shifting/scaling, and linear morphing. These parametric schemes can be applied to two types of components: wing-type surfaces (e.g., wing, canard, horizontal tail, vertical tail, and pylon) and body-type surfaces (e.g., fuselage, pod, and nacelle). These schemes permit the easy setup of commonly used shape modification methods, and each customized parametric scheme can be applied to the same type of component for any configuration. This paper explains the mathematics for these parametric schemes and uses two supersonic configurations to demonstrate the application of these schemes.

The s29x gene of symbiotic bacteria in Amoeba proteus with a novel promoter.

PubMed

Pak, J W; Jeon, K W

1996-05-24

Gram-symbiotic bacteria (called X-bacteria), present in the xD strain of Amoeba proteus as required cell components, synthesize and export a large amount of a 29-kDa protein, S29x. S29x is exported into the host's cytoplasm across the bacterial membranes and the symbiosome membrane. The complete nucleotide (nt) sequence of the s29x gene of X-bacteria has been determined, and the promoter sequence and tsp have also been identified. The gene has a nonconventional promoter with putative nt sequences different from the known consensus sequences. When Escherichia coli cells are transformed with s29x, the gene is expressed and the product is secreted into the culture medium. Functions of S29x are not fully known, but it is suspected that S29x plays an important role in the symbiotic relationship between amoebae and X-bacteria.

Differences in the motility of Amoeba proteus isolated fragments are determined by F-actin arrangement and cell nucleus presence.

PubMed

Grebecka, L; Pomorski, P; Lopatowska, A

1995-10-01

Isolated fragments produced by bisection of Amoeba proteus differ by their position in the original cell and by the presence or absence of the cell nucleus. Immediately after the operation, both types of anterior fragments preserve the former motory polarity, and do not interrupt locomotion. In the same time, all posterior fragments stop, round up and fail to react stimuli. In the second phase of experiment, these anterior fragments, which had no nucleus ceased to move, whereas the nucleated posterior ones resumed locomotion. It was demonstrated, that the behaviour of a fragment is primarily determined by the peripheral F-actin distribution, which is different depending on the origin of the fragment either from the anterior or from the posterior cell region. Later, the "inherited" F-actin distribution may be stabilized or reorganized in the presence of the nucleus, or desorganized in its absence.

Involvement of myosin VI immunoanalog in pinocytosis and phagocytosis in Amoeba proteus.

PubMed

Sobczak, Magdalena; Wasik, Anna; Kłopocka, Wanda; Redowicz, Maria Jolanta

2008-12-01

Recently, we found a 130-kDa myosin VI immunoanalog in amoeba, which bound to actin in an ATP-sensitive manner and in migrating amoebae colocalized to filamentous actin and dynamin II-containing vesicular structures. To further characterize this protein, we assessed its involvement in amoeba pinocytosis and phagocytosis. Confocal immunofluorescence microscopy and electron microscopy of immunogold-stained cells revealed that, in pinocytotic and phagocytotic amoebae, the myosin VI immunoanalog was visible throughout the cells, including pinocytotic channels and pinocytotic vesicles as well as phagosomes and emerging phagocytic cups. Blocking endogenous protein with anti-porcine myosin VI antibody (introduced into cells by means of microinjection) caused severe defects in pinocytosis and phagocytosis. In comparison with control cells, the treated amoebae formed ~75% less pinocytotic channels and phagocytosed ~65% less Tetrahymena cells. These data indicate that the myosin VI immunoanalog has an important role in pinocytosis and phagocytosis in Amoeba proteus (Pal.).

Contractility of glycerinated Amoeba proteus and Chaos-chaos.

PubMed

Rinaldi, R; Opas, M; Hrebenda, B

1975-05-01

Immediate contact with large volumes of cold 50% (v/v) buffered glycerol preserved typical ameboid shape of Chaos chaos and Amoeba proteus with no visible distortions. These technics allowed determination of the contraction sites in these glycerinated models upon applications of ATP-Ca-Mg-solutions. The ectoplasmic tube was the main site of contraction. Preliminary EM investigations revealed thick and thin filaments, associated with the ectoplasmic tube near the plasma-lemma, which appeared to be the basis for the contractility of the ectoplasmic tube. There was no predominant contraction of the pseudopodial tips or the endoplasm in these models. The changes of volume were as much as 50%, and in some cases were not accompanied by any change in the length of the ameba; however, lengthwise contractions of the ectoplasmic tube in some amebae occurred to as much as 25%. The data substantiate a basic requirement of the ectoplasmic tube contraction theory of ameboid locomotion.

[Phosphatase activity in Amoeba proteus at pH 9.0].

PubMed

Sopina, V A

2007-01-01

In the free-living amoeba Amoeba proteus (strain B), after PAAG disk-electrophoresis of the homogenate supernatant, at using 1-naphthyl phosphate as a substrate and pH 9.0, three forms of phosphatase activity were revealed; they were arbitrarily called "fast", "intermediate", and "slow" phosphatases. The fast phosphatase has been established to be a fraction of lysosomal acid phosphatase that preserves some low activity at alkaline pH. The question as to which particular class the intermediate phosphatase belongs to has remained unanswered: it can be both acid phosphatase and protein tyrosine phosphatase (PTP). Based on data of inhibitor analysis, large substrate specificity, results of experiments with reactivation by Zn ions after inactivation with EDTA, other than in the fast and intermediate phosphatases localization in the amoeba cell, it is concluded that only slow phosphatase can be classified as alkaline phosphatase (EC 3.1.3.1).

Identifying Likely Transmission Pathways within a 10-Year Community Outbreak of Tuberculosis by High-Depth Whole Genome Sequencing

PubMed Central

Sadsad, Rosemarie; Martinez, Elena; Jelfs, Peter; Hill-Cawthorne, Grant A.; Gilbert, Gwendolyn L.; Marais, Ben J.; Sintchenko, Vitali

2016-01-01

Background Improved tuberculosis control and the need to contain the spread of drug-resistant strains provide a strong rationale for exploring tuberculosis transmission dynamics at the population level. Whole-genome sequencing provides optimal strain resolution, facilitating detailed mapping of potential transmission pathways. Methods We sequenced 22 isolates from a Mycobacterium tuberculosis cluster in New South Wales, Australia, identified during routine 24-locus mycobacterial interspersed repetitive unit typing. Following high-depth paired-end sequencing using the Illumina HiSeq 2000 platform, two independent pipelines were employed for analysis, both employing read mapping onto reference genomes as well as de novo assembly, to control biases in variant detection. In addition to single-nucleotide polymorphisms, the analyses also sought to identify insertions, deletions and structural variants. Results Isolates were highly similar, with a distance of 13 variants between the most distant members of the cluster. The most sensitive analysis classified the 22 isolates into 18 groups. Four of the isolates did not appear to share a recent common ancestor with the largest clade; another four isolates had an uncertain ancestral relationship with the largest clade. Conclusion Whole genome sequencing, with analysis of single-nucleotide polymorphisms, insertions, deletions, structural variants and subpopulations, enabled the highest possible level of discrimination between cluster members, clarifying likely transmission pathways and exposing the complexity of strain origin. The analysis provides a basis for targeted public health intervention and enhanced classification of future isolates linked to the cluster. PMID:26938641

Photoacoustic spectroscopy for trace vapor detection and standoff detection of explosives

NASA Astrophysics Data System (ADS)

Holthoff, Ellen L.; Marcus, Logan S.; Pellegrino, Paul M.

2016-05-01

The Army is investigating several spectroscopic techniques (e.g., infrared spectroscopy) that could allow for an adaptable sensor platform. Current sensor technologies, although reasonably sized, are geared to more classical chemical threats, and the ability to expand their capabilities to a broader range of emerging threats is uncertain. Recently, photoacoustic spectroscopy (PAS), employed in a sensor format, has shown enormous potential to address these ever-changing threats. PAS is one of the more flexible IR spectroscopy variants, and that flexibility allows for the construction of sensors that are designed for specific tasks. PAS is well suited for trace detection of gaseous and condensed media. Recent research has employed quantum cascade lasers (QCLs) in combination with MEMS-scale photoacoustic cell designs. The continuous tuning capability of QCLs over a broad wavelength range in the mid-infrared spectral region greatly expands the number of compounds that can be identified. We will discuss our continuing evaluation of QCL technology as it matures in relation to our ultimate goal of a universal compact chemical sensor platform. Finally, expanding on our previously reported photoacoustic detection of condensed phase samples, we are investigating standoff photoacoustic chemical detection of these materials. We will discuss the evaluation of a PAS sensor that has been designed around increasing operator safety during detection and identification of explosive materials by performing sensing operations at a standoff distance. We investigate a standoff variant of PAS based upon an interferometric sensor by examining the characteristic absorption spectra of explosive hazards collected at 1 m.

SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data from 200 samples of a healthy aging cohort.

PubMed

Rueda, Manuel; Torkamani, Ali

2017-08-18

Whole genome and exome sequencing usually include reads containing mitochondrial DNA (mtDNA). Yet, state-of-the-art pipelines and services for human nuclear genome variant calling and annotation do not handle mitochondrial genome data appropriately. As a consequence, any researcher desiring to add mtDNA variant analysis to their investigations is forced to explore the literature for mtDNA pipelines, evaluate them, and implement their own instance of the desired tool. This task is far from trivial, and can be prohibitive for non-bioinformaticians. We have developed SG-ADVISER mtDNA, a web server to facilitate the analysis and interpretation of mtDNA genomic data coming from next generation sequencing (NGS) experiments. The server was built in the context of our SG-ADVISER framework and on top of the MtoolBox platform (Calabrese et al., Bioinformatics 30(21):3115-3117, 2014), and includes most of its functionalities (i.e., assembly of mitochondrial genomes, heteroplasmic fractions, haplogroup assignment, functional and prioritization analysis of mitochondrial variants) as well as a back-end and a front-end interface. The server has been tested with unpublished data from 200 individuals of a healthy aging cohort (Erikson et al., Cell 165(4):1002-1011, 2016) and their data is made publicly available here along with a preliminary analysis of the variants. We observed that individuals over ~90 years old carried low levels of heteroplasmic variants in their genomes. SG-ADVISER mtDNA is a fast and functional tool that allows for variant calling and annotation of human mtDNA data coming from NGS experiments. The server was built with simplicity in mind, and builds on our own experience in interpreting mtDNA variants in the context of sudden death and rare diseases. Our objective is to provide an interface for non-bioinformaticians aiming to acquire (or contrast) mtDNA annotations via MToolBox. SG-ADVISER web server is freely available to all users at https://genomics.scripps.edu/mtdna .

Chromosomal Amplification of the blaOXA-58 Carbapenemase Gene in a Proteus mirabilis Clinical Isolate.

PubMed

Girlich, Delphine; Bonnin, Rémy A; Bogaerts, Pierre; De Laveleye, Morgane; Huang, Daniel T; Dortet, Laurent; Glaser, Philippe; Glupczynski, Youri; Naas, Thierry

2017-02-01

Horizontal gene transfer may occur between distantly related bacteria, thus leading to genetic plasticity and in some cases to acquisition of novel resistance traits. Proteus mirabilis is an enterobacterial species responsible for human infections that may express various acquired β-lactam resistance genes, including different classes of carbapenemase genes. Here we report a Proteus mirabilis clinical isolate (strain 1091) displaying resistance to penicillin, including temocillin, together with reduced susceptibility to carbapenems and susceptibility to expanded-spectrum cephalosporins. Using biochemical tests, significant carbapenem hydrolysis was detected in P. mirabilis 1091. Since PCR failed to detect acquired carbapenemase genes commonly found in Enterobacteriaceae, we used a whole-genome sequencing approach that revealed the presence of bla OXA-58 class D carbapenemase gene, so far identified only in Acinetobacter species. This gene was located on a 3.1-kb element coharboring a bla AmpC -like gene. Remarkably, these two genes were bracketed by putative XerC-XerD binding sites and inserted at a XerC-XerD site located between the terminase-like small- and large-subunit genes of a bacteriophage. Increased expression of the two bla genes resulted from a 6-time tandem amplification of the element as revealed by Southern blotting. This is the first isolation of a clinical P. mirabilis strain producing OXA-58, a class D carbapenemase, and the first description of a XerC-XerD-dependent insertion of antibiotic resistance genes within a bacteriophage. This study revealed a new role for the XerC-XerD recombinase in bacteriophage biology. Copyright © 2017 American Society for Microbiology.

Chromosomal Amplification of the blaOXA-58 Carbapenemase Gene in a Proteus mirabilis Clinical Isolate

PubMed Central

Girlich, Delphine; Bogaerts, Pierre; De Laveleye, Morgane; Huang, Daniel T.; Glupczynski, Youri

2016-01-01

ABSTRACT Horizontal gene transfer may occur between distantly related bacteria, thus leading to genetic plasticity and in some cases to acquisition of novel resistance traits. Proteus mirabilis is an enterobacterial species responsible for human infections that may express various acquired β-lactam resistance genes, including different classes of carbapenemase genes. Here we report a Proteus mirabilis clinical isolate (strain 1091) displaying resistance to penicillin, including temocillin, together with reduced susceptibility to carbapenems and susceptibility to expanded-spectrum cephalosporins. Using biochemical tests, significant carbapenem hydrolysis was detected in P. mirabilis 1091. Since PCR failed to detect acquired carbapenemase genes commonly found in Enterobacteriaceae, we used a whole-genome sequencing approach that revealed the presence of blaOXA-58 class D carbapenemase gene, so far identified only in Acinetobacter species. This gene was located on a 3.1-kb element coharboring a blaAmpC-like gene. Remarkably, these two genes were bracketed by putative XerC-XerD binding sites and inserted at a XerC-XerD site located between the terminase-like small- and large-subunit genes of a bacteriophage. Increased expression of the two bla genes resulted from a 6-time tandem amplification of the element as revealed by Southern blotting. This is the first isolation of a clinical P. mirabilis strain producing OXA-58, a class D carbapenemase, and the first description of a XerC-XerD-dependent insertion of antibiotic resistance genes within a bacteriophage. This study revealed a new role for the XerC-XerD recombinase in bacteriophage biology. PMID:27855079

Prevalence of quinolone resistance determinant qnrA6 among broad- and extended-spectrum beta-lactam-resistant Proteus mirabilis and Morganella morganii clinical isolates with sul1-type class 1 integron association in a Tunisian Hospital.

PubMed

Mahrouki, Sihem; Perilli, Mariagrazia; Bourouis, Amel; Chihi, Hela; Ferjani, Mustapha; Ben Moussa, Mohamed; Amicosante, Gianfranco; Belhadj, Omrane

2013-08-01

The aim of this study was to investigate the prevalence and the emergence of plasmid-mediated quinolone resistance among broad-spectrum beta-lactam-resistant Proteus mirabilis and Morganella morganii clinical isolates recovered in the Military Hospital in Tunisia. Of 200 strains examined, 50 exhibited resistance to quinolones. Quinolone resistance determinants (qnr and aac(6')-Ib-cr) were characterized by multiplex PCR and sequencing. Chromosomal quinolone resistance mutations in the quinolone resistance-determining region (QRDR) and class 1 integron characterization were analysed by PCR and sequencing. The clonal relationship between the isolates was studied by pulsed-field gel electrophoresis (PFGE). Fourteen isolates harboured qnrA6 and among them 8 (57%) were extended-spectrum beta-lactamase (ESBL) producers, whilst 12 (85%) isolates harboured blaDHA-1. Mutations in the QRDR were detected in gyrA (Ser83Ile, Glu87Lys), gyrB (Ser464Phe), and parC (Ser80Ile). qnrA6 and blaDHA-1 genes were found embedded in complex sul1-type class 1 integrons. A gene cassette carrying aac(6')-Ib-cr was found located in the class 1 integron upstream of the qacEΔ1 gene. According to the PFGE analysis, the isolates were clonally unrelated. This is the first description in North Africa of class 1 integrons carrying blaDHA-1, qnrA6 gene, and aac(6')-Ib-cr determinants in clinical strains of Proteus mirabilis and Morganella morganii.

Role of DAF-21protein in Caenorhabditis elegans immunity against Proteus mirabilis infection.

PubMed

JebaMercy, Gnanasekaran; Durai, Sellegounder; Prithika, Udayakumar; Marudhupandiyan, Shanmugam; Dasauni, Pushpanjali; Kundu, Suman; Balamurugan, Krishnaswamy

2016-08-11

Caenorhabditis elegans is emerging as one of the handy model for proteome related studies due to its simplest system biology. The present study, deals with changes in protein expression in C. elegans infected with Proteus mirabilis. Proteins were separated using two-dimensional differential gel electrophoresis (2D-DIGE) and identified using MALDI-TOF. Twelve distinctly regulated proteins identified in the infected worms, included heat shock proteins involved stress pathway (HSP-1 and HSP-6), proteins involved in immune response pathway (DAF-21), enzymes involved in normal cellular process (Eukaryotic translation Elongation Factor, actin family member, S-adenosyl homocysteine hydrolase ortholog, glutamate dehydrogenase and Vacuolar H ATPase family member) and few least characterized proteins (H28O16.1 and H08J11.2). The regulation of selected players at the transcriptional level during Proteus mirabilis infection was analyzed using qPCR. Physiological experiments revealed the ability of P. mirabilis to kill daf-21 mutant C. elegans significantly compared with the wild type. This is the first report studying proteome changes in C. elegans and exploring the involvement of MAP Kinase pathway during P. mirabilis infection. This is the first report studying proteome changes in C. elegans during P. mirabilis infection. The present study explores the role and contribution of MAP Kinase pathway and its regulator protein DAF-21 involvement in the immunity against opportunistic pathogen P. mirabilis infection. Manipulation of this DAF-21 protein in host, may pave the way for new drug development or disease control strategy during opportunistic pathogen infections. Copyright © 2016 Elsevier B.V. All rights reserved.

Trichomoniasis and associated co-infections of the genital tract among pregnant women presenting at two hospitals in Ghana.

PubMed

Asmah, Richard H; Blankson, Harriet N A; Seanefu, Kekeli A; Obeng-Nkrumah, Noah; Awuah-Mensah, Georgina; Cham, Momodou; Ayeh-Kumi, Patrick F

2017-12-13

Trichomonas vaginalis (TV) infection is the most prevalent non-viral sexually transmitted pathogen worldwide. Among pregnant women, the infection may cause adverse birth outcomes such as premature rupture of membranes and premature labour. In view of the paucity of information relating to TV among Ghanaian pregnant women, this study investigated its prevalence and associated co-infections among pregnant women. High vaginal swabs were obtained from 99 pregnant women using sterile cotton swab sticks. Wet preparation, Grams staining, culturing, coagulase and sensitivity testing were carried out to determine the presence of TV and associated microorganisms. The prevalence of TV among the pregnant women was found to be 20.2% (n = 20). Concurring with Trichomoniasis, 75% (n = 15) of participants had other infections such as Candida with prevalence of 53% (n = 8), Proteus infection - 20% (n = 3), Streptococcus infection - 13% (n = 2) and other GNRs and Gonococci having 7% each (n = 1). Moreover, there was 86.9% (n = 86) prevalence of Staphylococcus spp. among study participants. There was statistically significant correlation between TV and Gonococci infection at a correlation co-efficient of 0.107 (P < 0.05) as well as significant correlation between TV and Proteus spp. at a correlation co-efficient of 0.189 (P < 0.05). TV infection was high (60%) among the most sexually active age group (19 to 29 yrs). There was 20.2% prevalence of TV among the pregnant women presenting at the hospitals, with Gonococci and Proteus infections being statistically significant associated infections.

Enzyme-Assisted Extraction Optimization, Characterization and Antioxidant Activity of Polysaccharides from Sea Cucumber Phyllophorus proteus.

PubMed

Qin, Yujing; Yuan, Qingxia; Zhang, Yuexing; Li, Jialu; Zhu, Xinjiao; Zhao, Lingling; Wen, Jing; Liu, Jikai; Zhao, Longyan; Zhao, Jinhua

2018-03-06

Enzyme-assisted extraction optimization, characterization and in vitro antioxidant activity of polysaccharides from sea cucumber Phyllophorus proteus (PPP) were investigated in the present study. The optimal extraction conditions with a yield of 6.44 ± 0.06% for PPP were determined as follows: Extraction time of 2.89 h, ratio of extraction solvent to raw material of 16.26 mL/g, extraction pH of 6.83, exraction temperature of 50 °C and papain concentration of 0.15%. Three purified fractions, PPP-1a, PPP-1b and PPP-2 with molecular weights of 369.60, 41.73 and 57.76 kDa, respectively, were obtained from PPP by chromatography of FPA98Cl and Sepharose CL-6B columns. Analysis of monosaccharide compositions showed that PPP-1a consisted of N -acetyl-galactosamine (GalNAc), galactose (Gal) and fucose (Fuc), PPP-1b of Fuc as the only monosaccharide and PPP-2 of glucuronic acid, GalNAc and Fuc. Sulfate contents of PPP, PPP-1a, PPP-1b and PPP-2 were determined to be 21.9%, 20.6%, 25.2% and 28.0% ( w / w ), respectively. PPP and PPP-1a had higher molecular weight and intrinsic viscosity than those of the PPP-1b and PPP-2. PPP, PPP-1a, PPP-1b and PPP-2 exhibited obvious activities of scavenging 1,1-diphenyl-2-picrylhydrazyl radical, hydroxyl radical, superoxide radical and ABTS radical in different extent, which suggested that the polysaccharides from Phyllophorus proteus may be novel agents having potential value for antioxidation.

[Swarming phenomenon of an aeromonas spec (author's transl)].

PubMed

Müller, H E; Lenz, W

1975-05-01

A genuine swarming phenomenon, such as has previously been known to occur in Proteus, Bacillus and Clostridium species only, was observed in an Aeromonas species. Fig. 1 shows the terraced swarming zones of the Aeromonas species on nutrient agar. The swarming rate, expressed as the growth of the swarming zone per time unit, was measured to be 70-120 mum/min on blood agar at 30 degrees C. The swarming could be inhibited by incubation at 37 degrees C (Table 2), by low saline concentrations (Table 3) as well as by addition of 4-nitro-phenylglycerol to the medium (Table 4). A DIENES-phenomenon between the swarming zones of Proteus strains and that of the Aeromonas species could not be observed (Fig. 2). The manner of swarming as seen in phase contrast microscopy was the same kind as that of Proteus. Furthermore, it could be shown by means of light- and electronmicroscopical investigations that the swarming phenomenon is connected with changes in the cell morphology and the form of flagellation (Figs. 4 and 5). Whereas in broth cultures (Fig. 3) as well as in the centre of colonies on solid media (Fig. 5a) the cells appeared as cocoid rods with polar flagellation, they developed elongated forms at the edge of the swarming zone, which - either in addition to or devoid of the polar flagella - were peritrichously populated with thin, flagella-like filaments (Figs. tb, 6, 7 and 8). The discussion deals with the various forms of bacterial surface translocation and investigates into the role of peritrichous flagella or fimbriae in the swarming phenomenon.

Nuclear Synthesis of Cytoplasmic Ribonucleic Acid in Amoeba proteus

PubMed Central

Prescott, David M.

1959-01-01

The enucleation technique has been applied to Amoeba proteus by several laboratories in attempts to determine whether the cytoplasm is capable of nucleus-independent ribonucleic acid synthesis. This cell is very convenient for micrurgy, but its use requires a thorough starvation period to eliminate the possibility of metabolic influence by food vacuoles and frequent washings and medium renewal to maintain asepsis. In the experiments described here, amoebae were starved for periods of 24 to 96 hours, cut into nucleated and enucleated halves, and exposed to either C-14 uracil, C-14 adenine, C-14 orotic acid, or a mixture of all three. When the starvation period was short (less than 72 hours), organisms (especially yeast cells) contained within amoeba food vacuoles frequently showed RNA synthesis in both nucleated and enucleated amoebae. When the preperiod of starvation was longer than 72 hours, food vacuole influence was apparently negligible, and a more meaningful comparison between enucleated and nucleated amoebae was possible. Nucleated cells incorporated all three precursors into RNA; enucleated cells were incapable of such incorporation. The experiments indicate a complete dependence on the nucleus for RNA synthesis. The conflict with the experimental results of others on this problem could possibly stem from differences in culture conditions, starvation treatment, or experimental conditions. For an unequivocal answer in experiments of this design, ideally the cells should be capable of growth on an entirely synthetic medium under aseptic conditions. The use of a synthetic medium (experiments with A. proteus are done under starvation conditions) would permit, moreover, a more realistic comparison of metabolic capacities of nucleated and enucleated cells. PMID:14434750

Characterization of sams genes of Amoeba proteus and the endosymbiotic X-bacteria.

PubMed

Jeon, Taeck J; Jeon, Kwang W

2003-01-01

As a result of harboring obligatory bacterial endosymbionts, the xD strain of Amoeba proteus no longer produces its own S-adenosylmethionine synthetase (SAMS). When symbiont-free D amoebae are infected with symbionts (X-bacteria), the amount of amoeba SAMS decreases to a negligible level within four weeks, but about 47% of the SAMS activity, which apparently comes from another source, is still detected. Complete nucleotide sequences of sams genes of D and xD amoebae are presented and show that there are no differences between the two. Long-established xD amoebae contain an intact sams gene and thus the loss of xD amoeba's SAMS is not due to the loss of the gene itself. The open reading frame of the amoeba's sams gene has 1,281 nucleotides, encoding SAMS of 426 amino acids with a mass of 48 kDa and pI of 6.5. The amino acid sequence of amoeba SAMS is longer than the SAMS of other organisms by having an extra internal stretch of 28 amino acids. The 5'-flanking region of amoeba sams contains consensus-binding sites for several transcription factors that are related to the regulation of sams genes in E. coli and yeast. The complete nucleotide sequence of the symbiont's sams gene is also presented. The open reading frame of X-bacteria sams is 1,146 nucleotides long, encoding SAMS of 381 amino acids with a mass of 41 kDa and pI of 6.0. The X-bacteria SAMS has 45% sequence identity with that of A. proteus.

Nuclear synthesis of cytoplasmic ribonucleic acid in Amoeba proteus.

PubMed

PRESCOTT, D M

1959-10-01

The enucleation technique has been applied to Amoeba proteus by several laboratories in attempts to determine whether the cytoplasm is capable of nucleus-independent ribonucleic acid synthesis. This cell is very convenient for micrurgy, but its use requires a thorough starvation period to eliminate the possibility of metabolic influence by food vacuoles and frequent washings and medium renewal to maintain asepsis. In the experiments described here, amoebae were starved for periods of 24 to 96 hours, cut into nucleated and enucleated halves, and exposed to either C-14 uracil, C-14 adenine, C-14 orotic acid, or a mixture of all three. When the starvation period was short (less than 72 hours), organisms (especially yeast cells) contained within amoeba food vacuoles frequently showed RNA synthesis in both nucleated and enucleated amoebae. When the preperiod of starvation was longer than 72 hours, food vacuole influence was apparently negligible, and a more meaningful comparison between enucleated and nucleated amoebae was possible. Nucleated cells incorporated all three precursors into RNA; enucleated cells were incapable of such incorporation. The experiments indicate a complete dependence on the nucleus for RNA synthesis. The conflict with the experimental results of others on this problem could possibly stem from differences in culture conditions, starvation treatment, or experimental conditions. For an unequivocal answer in experiments of this design, ideally the cells should be capable of growth on an entirely synthetic medium under aseptic conditions. The use of a synthetic medium (experiments with A. proteus are done under starvation conditions) would permit, moreover, a more realistic comparison of metabolic capacities of nucleated and enucleated cells.

Characterization of Amoeba proteus myosin VI immunoanalog.

PubMed

Dominik, Magdalena; Kłopocka, Wanda; Pomorski, Paweł; Kocik, Elzbieta; Redowicz, Maria Jolanta

2005-07-01

Amoeba proteus, the highly motile free-living unicellular organism, has been widely used as a model to study cell motility. However, molecular mechanisms underlying its unique locomotion and intracellular actin-based-only trafficking remain poorly understood. A search for myosin motors responsible for vesicular transport in these giant cells resulted in detection of 130-kDa protein interacting with several polyclonal antibodies against different tail regions of human and chicken myosin VI. This protein was binding to actin in the ATP-dependent manner, and immunoprecipitated with anti-myosin VI antibodies. In order to characterize its possible functions in vivo, its cellular distribution and colocalization with actin filaments and dynamin II during migration and pinocytosis were examined. In migrating amoebae, myosin VI immunoanalog localized to vesicular structures, particularly within the perinuclear and sub-plasma membrane areas, and colocalized with dynamin II immunoanalog and actin filaments. The colocalization was even more evident in pinocytotic cells as proteins concentrated within pinocytotic pseudopodia. Moreover, dynamin II and myosin VI immunoanalogs cosedimented with actin filaments, and were found on the same isolated vesicles. Blocking endogenous myosin VI immunoanalog with anti-myosin VI antibodies inhibited the rate of pseudopodia protrusion (about 19% decrease) and uroidal retraction (about 28% decrease) but did not affect cell morphology and the manner of cell migration. Treatment with anti-human dynamin II antibodies led to changes in directionality of amebae migration and affected the rate of only uroidal translocation (about 30% inhibition). These results indicate that myosin VI immunoanalog is expressed in protist Amoeba proteus and may be involved in vesicle translocation and cell locomotion.

21 CFR 520.90b - Ampicillin trihydrate tablets.

Code of Federal Regulations, 2011 CFR

2011-04-01

...., Staphylococcus spp., E., coli, P. mirabilis, and Enterococcus spp.; gastrointestinal infections due to Staphylococcus spp., Streptococcus spp., Enterococcus spp., and E. coli. ; infections associated with abscesses..., tonsillitis, and bronchitis due to Streptococcus spp., Staphylococcus spp., Escherichia coli, Proteus...

21 CFR 520.90b - Ampicillin trihydrate tablets.

Code of Federal Regulations, 2010 CFR

2010-04-01

...., Staphylococcus spp., E., coli, P. mirabilis, and Enterococcus spp.; gastrointestinal infections due to Staphylococcus spp., Streptococcus spp., Enterococcus spp., and E. coli. ; infections associated with abscesses..., tonsillitis, and bronchitis due to Streptococcus spp., Staphylococcus spp., Escherichia coli, Proteus...

Genetics Home Reference: Proteus syndrome

MedlinePlus

... genetic mutation is known as mosaicism . The AKT1 gene helps regulate cell growth and division (proliferation) and cell death. A mutation in this gene disrupts a cell's ability to regulate its own growth, allowing it to grow and divide abnormally. Increased ...

Distinct Residues Contribute to Motility Repression and Autoregulation in the Proteus mirabilis Fimbria-Associated Transcriptional Regulator AtfJ.

PubMed

Bode, Nadine J; Chan, Kun-Wei; Kong, Xiang-Peng; Pearson, Melanie M

2016-08-01

Proteus mirabilis contributes to a significant number of catheter-associated urinary tract infections, where coordinated regulation of adherence and motility is critical for ascending disease progression. Previously, the mannose-resistant Proteus-like (MR/P) fimbria-associated transcriptional regulator MrpJ has been shown to both repress motility and directly induce the transcription of its own operon; in addition, it affects the expression of a wide range of cellular processes. Interestingly, 14 additional mrpJ paralogs are included in the P. mirabilis genome. Looking at a selection of MrpJ paralogs, we discovered that these proteins, which consistently repress motility, also have nonidentical functions that include cross-regulation of fimbrial operons. A subset of paralogs, including AtfJ (encoded by the ambient temperature fimbrial operon), Fim8J, and MrpJ, are capable of autoinduction. We identified an element of the atf promoter extending from 487 to 655 nucleotides upstream of the transcriptional start site that is responsive to AtfJ, and we found that AtfJ directly binds this fragment. Mutational analysis of AtfJ revealed that its two identified functions, autoregulation and motility repression, are not invariably linked. Residues within the DNA-binding helix-turn-helix domain are required for motility repression but not necessarily autoregulation. Likewise, the C-terminal domain is dispensable for motility repression but is essential for autoregulation. Supported by a three-dimensional (3D) structural model, we hypothesize that the C-terminal domain confers unique regulatory capacities on the AtfJ family of regulators. Balancing adherence with motility is essential for uropathogens to successfully establish a foothold in their host. Proteus mirabilis uses a fimbria-associated transcriptional regulator to switch between these antagonistic processes by increasing fimbrial adherence while simultaneously downregulating flagella. The discovery of multiple related proteins, many of which also function as motility repressors, encoded in the P. mirabilis genome has raised considerable interest as to their functionality and potential redundancy in this organism. This study provides an important advance in this field by elucidating the nonidentical effects of these paralogs on a molecular level. Our mechanistic studies of one member of this group, AtfJ, shed light on how these differing functions may be conferred despite the limited sequence variety exhibited by the paralogous proteins. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

PROTEUS MIRABILIS VIABILITY AFTER LITHOTRIPSY OF STRUVITE CALCULI. (R825503)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

21 CFR 522.1044 - Gentamicin.

Code of Federal Regulations, 2011 CFR

2011-04-01

... old for treatment of porcine colibacillosis caused by strains of E. coli sensitive to gentamicin. (iii... early mortality caused by Escherichia coli. Salmonella typhimurium, and Pseudomonas aeruginosa that are... in the treatment of urinary tract infections (cystitis) caused by Proteus mirabilis, Escherichia coli...

21 CFR 522.1044 - Gentamicin.

Code of Federal Regulations, 2010 CFR

2010-04-01

... old for treatment of porcine colibacillosis caused by strains of E. coli sensitive to gentamicin. (iii... early mortality caused by Escherichia coli. Salmonella typhimurium, and Pseudomonas aeruginosa that are... in the treatment of urinary tract infections (cystitis) caused by Proteus mirabilis, Escherichia coli...

21 CFR 520.90d - Ampicillin trihydrate for oral suspension.

Code of Federal Regulations, 2012 CFR

2012-04-01

... infections (tracheobronchitis and tonsillitis) due to Escherichia coli, Pseudomonas spp., Proteus spp., Staphylococcus spp., and Streptococcus spp., urinary tract infections (cystitis) due to E. coli, Staphylococcus... infections (septicemia) associated with abscesses, lacerations, and wounds, due to Staphylococcus spp. and...

21 CFR 520.88a - Amoxicillin trihydrate film-coated tablets.

Code of Federal Regulations, 2013 CFR

2013-04-01

... tissues (abscesses, lacerations, wounds), caused by susceptible strains of Staphylococcus aureus, Streptococcus spp., Escherichia coli, Proteus mirabilis, and bacterial dermatitis caused by S. aureus... infections caused by susceptible organisms as follows: upper respiratory tract due to S. aureus...

21 CFR 520.314 - Cefadroxil.

Code of Federal Regulations, 2013 CFR

2013-04-01

... Staphylococcus aureus. For the treatment of genitourinary tract infections (cystitis) due to susceptible strains of Escherichia coli, Proteus mirabilis, and S. aureus. (ii) Cats. For the treatment of skin and soft... strains of Pasteurella multocida, S. aureus, Staphylococcus epidermidis, and Streptococcus spp. (3...

21 CFR 520.314 - Cefadroxil.

Code of Federal Regulations, 2010 CFR

2010-04-01

... Staphylococcus aureus. For the treatment of genitourinary tract infections (cystitis) due to susceptible strains of Escherichia coli, Proteus mirabilis, and S. aureus. (ii) Cats. For the treatment of skin and soft... strains of Pasteurella multocida, S. aureus, Staphylococcus epidermidis, and Streptococcus spp. (3...

21 CFR 520.314 - Cefadroxil.

Code of Federal Regulations, 2014 CFR

2014-04-01

... Staphylococcus aureus. For the treatment of genitourinary tract infections (cystitis) due to susceptible strains of Escherichia coli, Proteus mirabilis, and S. aureus. (ii) Cats. For the treatment of skin and soft... strains of Pasteurella multocida, S. aureus, Staphylococcus epidermidis, and Streptococcus spp. (3...

21 CFR 520.314 - Cefadroxil.

Code of Federal Regulations, 2012 CFR

2012-04-01

... Staphylococcus aureus. For the treatment of genitourinary tract infections (cystitis) due to susceptible strains of Escherichia coli, Proteus mirabilis, and S. aureus. (ii) Cats. For the treatment of skin and soft... strains of Pasteurella multocida, S. aureus, Staphylococcus epidermidis, and Streptococcus spp. (3...

21 CFR 520.314 - Cefadroxil.

Code of Federal Regulations, 2011 CFR

2011-04-01

... Staphylococcus aureus. For the treatment of genitourinary tract infections (cystitis) due to susceptible strains of Escherichia coli, Proteus mirabilis, and S. aureus. (ii) Cats. For the treatment of skin and soft... strains of Pasteurella multocida, S. aureus, Staphylococcus epidermidis, and Streptococcus spp. (3...

21 CFR 520.88f - Amoxicillin trihydrate tablets.

Code of Federal Regulations, 2013 CFR

2013-04-01

... day. (ii) Indications for use. Treatment of bacterial dermatitis due to Staphylococcus aureus, Streptococcus spp., Staphylococcus spp., and Escherichia coli; and soft tissue infections (abscesses, wounds, lacerations) due to S. aureus, Streptococcus spp., E. coli, Proteus mirabilis, and Staphylococcus spp. (iii...

21 CFR 520.88f - Amoxicillin trihydrate tablets.

Code of Federal Regulations, 2012 CFR

2012-04-01

... day. (ii) Indications for use. Treatment of bacterial dermatitis due to Staphylococcus aureus, Streptococcus spp., Staphylococcus spp., and Escherichia coli; and soft tissue infections (abscesses, wounds, lacerations) due to S. aureus, Streptococcus spp., E. coli, Proteus mirabilis, and Staphylococcus spp. (iii...

21 CFR 520.88f - Amoxicillin trihydrate tablets.

Code of Federal Regulations, 2014 CFR

2014-04-01

... day. (ii) Indications for use. Treatment of bacterial dermatitis due to Staphylococcus aureus, Streptococcus spp., Staphylococcus spp., and Escherichia coli; and soft tissue infections (abscesses, wounds, lacerations) due to S. aureus, Streptococcus spp., E. coli, Proteus mirabilis, and Staphylococcus spp. (iii...

21 CFR 520.88a - Amoxicillin trihydrate film-coated tablets.

Code of Federal Regulations, 2014 CFR

2014-04-01

... tissues (abscesses, lacerations, wounds), caused by susceptible strains of Staphylococcus aureus, Streptococcus spp., Escherichia coli, Proteus mirabilis, and bacterial dermatitis caused by S. aureus... infections caused by susceptible organisms as follows: upper respiratory tract due to S. aureus...

21 CFR 520.88a - Amoxicillin trihydrate film-coated tablets.

Code of Federal Regulations, 2012 CFR

2012-04-01

... tissues (abscesses, lacerations, wounds), caused by susceptible strains of Staphylococcus aureus, Streptococcus spp., Escherichia coli, Proteus mirabilis, and bacterial dermatitis caused by S. aureus... infections caused by susceptible organisms as follows: upper respiratory tract due to S. aureus...

Integrated microdroplet-based system for enzyme synthesis and sampling

NASA Astrophysics Data System (ADS)

Lapierre, Florian; Best, Michel; Stewart, Robert; Oakeshott, John; Peat, Thomas; Zhu, Yonggang

2013-12-01

Microdroplet-based microfluidic devices are emerging as powerful tools for a wide range of biochemical screenings and analyses. Monodispersed aqueous microdroplets from picoliters to nanoliters in volume are generated inside microfluidic channels within an immiscible oil phase. This results in the formation of emulsions which can contain various reagents for chemical reactions and can be considered as discrete bioreactors. In this paper an integrated microfluidic platform for the synthesis, screening and sorting of libraries of an organophosphate degrading enzyme is presented. The variants of the selected enzyme are synthesized from a DNA source using in-vitro transcription and translation method. The synthesis occurs inside water-in-oil emulsion droplets, acting as bioreactors. Through a fluorescence based detection system, only the most efficient enzymes are selected. All the necessary steps from the enzyme synthesis to selection of the best genes (producing the highest enzyme activity) are thus integrated inside a single and unique device. In the second part of the paper, an innovative design of the microfluidic platform is presented, integrating an electronic prototyping board for ensuring the communication between the various components of the platform (camera, syringe pumps and high voltage power supply), resulting in a future handheld, user-friendly, fully automated device for enzyme synthesis, screening and selection. An overview on the capabilities as well as future perspectives of this new microfluidic platform is provided.

The humankind genome: from genetic diversity to the origin of human diseases.

PubMed

Belizário, Jose E

2013-12-01

Genome-wide association studies have failed to establish common variant risk for the majority of common human diseases. The underlying reasons for this failure are explained by recent studies of resequencing and comparison of over 1200 human genomes and 10 000 exomes, together with the delineation of DNA methylation patterns (epigenome) and full characterization of coding and noncoding RNAs (transcriptome) being transcribed. These studies have provided the most comprehensive catalogues of functional elements and genetic variants that are now available for global integrative analysis and experimental validation in prospective cohort studies. With these datasets, researchers will have unparalleled opportunities for the alignment, mining, and testing of hypotheses for the roles of specific genetic variants, including copy number variations, single nucleotide polymorphisms, and indels as the cause of specific phenotypes and diseases. Through the use of next-generation sequencing technologies for genotyping and standardized ontological annotation to systematically analyze the effects of genomic variation on humans and model organism phenotypes, we will be able to find candidate genes and new clues for disease's etiology and treatment. This article describes essential concepts in genetics and genomic technologies as well as the emerging computational framework to comprehensively search websites and platforms available for the analysis and interpretation of genomic data.

Copy Number Variants in Obesity-Related Syndromes: Review and Perspectives on Novel Molecular Approaches

PubMed Central

Koiffmann, Celia Priszkulnik

2012-01-01

In recent decades, obesity has reached epidemic proportions worldwide and became a major concern in public health. Despite heritability estimates of 40 to 70% and the long-recognized genetic basis of obesity in a number of rare cases, the list of common obesity susceptibility variants by the currently published genome-wide association studies (GWASs) only explain a small proportion of the individual variation in risk of obesity. It was not until very recently that GWASs of copy number variants (CNVs) in individuals with extreme phenotypes reported a number of large and rare CNVs conferring high risk to obesity, and specifically deletions on chromosome 16p11.2. In this paper, we comment on the recent advances in the field of genetics of obesity with an emphasis on the genes and genomic regions implicated in highly penetrant forms of obesity associated with developmental disorders. Array genomic hybridization in this patient population has afforded discovery opportunities for CNVs that have not previously been detectable. This information can be used to generate new diagnostic arrays and sequencing platforms, which will likely enhance detection of known genetic conditions with the potential to elucidate new disease genes and ultimately help in developing a next-generation sequencing protocol relevant to clinical practice. PMID:23316347

In silico study of breast cancer associated gene 3 using LION Target Engine and other tools.

PubMed

León, Darryl A; Cànaves, Jaume M

2003-12-01

Sequence analysis of individual targets is an important step in annotation and validation. As a test case, we investigated human breast cancer associated gene 3 (BCA3) with LION Target Engine and with other bioinformatics tools. LION Target Engine confirmed that the BCA3 gene is located on 11p15.4 and that the two most likely splice variants (lacking exon 3 and exons 3 and 5, respectively) exist. Based on our manual curation of sequence data, it is proposed that an additional variant (missing only exon 5) published in a public sequence repository, is a prediction artifact. A significant number of new orthologs were also identified, and these were the basis for a high-quality protein secondary structure prediction. Moreover, our research confirmed several distinct functional domains as described in earlier reports. Sequence conservation from multiple sequence alignments, splice variant identification, secondary structure predictions, and predicted phosphorylation sites suggest that the removal of interaction sites through alternative splicing might play a modulatory role in BCA3. This in silico approach shows the depth and relevance of an analysis that can be accomplished by including a variety of publicly available tools with an integrated and customizable life science informatics platform.

Optimizing Irregular Applications for Energy and Performance on the Tilera Many-core Architecture

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

Chavarría-Miranda, Daniel; Panyala, Ajay R.; Halappanavar, Mahantesh

Optimizing applications simultaneously for energy and performance is a complex problem. High performance, parallel, irregular applications are notoriously hard to optimize due to their data-dependent memory accesses, lack of structured locality and complex data structures and code patterns. Irregular kernels are growing in importance in applications such as machine learning, graph analytics and combinatorial scientific computing. Performance- and energy-efficient implementation of these kernels on modern, energy efficient, multicore and many-core platforms is therefore an important and challenging problem. We present results from optimizing two irregular applications { the Louvain method for community detection (Grappolo), and high-performance conjugate gradient (HPCCG) {more » on the Tilera many-core system. We have significantly extended MIT's OpenTuner auto-tuning framework to conduct a detailed study of platform-independent and platform-specific optimizations to improve performance as well as reduce total energy consumption. We explore the optimization design space along three dimensions: memory layout schemes, compiler-based code transformations, and optimization of parallel loop schedules. Using auto-tuning, we demonstrate whole node energy savings of up to 41% relative to a baseline instantiation, and up to 31% relative to manually optimized variants.« less

I-SCAD® standoff chemical agent detector overview

NASA Astrophysics Data System (ADS)

Popa, Mirela O.; Griffin, Matthew T.

2012-06-01

This paper presents a system-level description of the I-SCAD® Standoff Chemical Agent Detector, a passive Fourier Transform InfraRed (FTIR) based remote sensing system, for detecting chemical vapor threats. The passive infrared detection system automatically searches the 7 to 14 micron region of the surrounding atmosphere for agent vapor clouds. It is capable of operating while on the move to accomplish reconnaissance, surveillance, and contamination avoidance missions. Additionally, the system is designed to meet the needs for application on air and sea as well as ground mobile and fixed site platforms. The lightweight, passive, and fully automatic detection system scans the surrounding atmosphere for chemical warfare agent vapors. It provides on-the-move, 360-deg coverage from a variety of tactical and reconnaissance platforms at distances up to 5 km. The core of the system is a rugged Michelson interferometer with a flexure spring bearing mechanism and bi-directional data acquisition capability. The modular system design facilitates interfacing to many platforms. A Reduced Field of View (RFOV) variant includes novel modifications to the scanner subcomponent assembly optical design that gives extended performance in detection range and detection probability without sacrificing existing radiometric sensitivity performance. This paper will deliver an overview of system.

21 CFR 522.90a - Ampicillin trihydrate sterile suspension.

Code of Federal Regulations, 2010 CFR

2010-04-01

... tract infections due to E. coli, Pseudomonas spp., Proteus spp., Staphylococcus spp., and Streptococcus spp.; tonsillitis due to E. coli, Pseudomonas spp., Streptococcus spp., and Staphylococcus spp.... Treatment of bacterial enteritis (colibacillosis) caused by E. coli and bacterial pneumonia caused by...

21 CFR 522.90a - Ampicillin trihydrate sterile suspension.

Code of Federal Regulations, 2011 CFR

2011-04-01

... tract infections due to E. coli, Pseudomonas spp., Proteus spp., Staphylococcus spp., and Streptococcus spp.; tonsillitis due to E. coli, Pseudomonas spp., Streptococcus spp., and Staphylococcus spp.... Treatment of bacterial enteritis (colibacillosis) caused by E. coli and bacterial pneumonia caused by...

21 CFR 520.1618 - Orbifloxacin suspension.

Code of Federal Regulations, 2011 CFR

2011-04-01

... spp., Klebsiella pneumoniae, E. coli, Enterobacter spp., Citrobacter spp., E. faecalis, β-hemolytic...) in cats caused by susceptible strains of S. aureus, E. coli, and P. multocida. [75 FR 26646, May 12... pseudintermedius, Proteus mirabilis, Escherichia coli, and Enterococcus faecalis and skin and soft tissue...

21 CFR 522.56 - Amikacin.

Code of Federal Regulations, 2014 CFR

2014-04-01

... FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS IMPLANTATION OR INJECTABLE DOSAGE FORM NEW ANIMAL DRUGS § 522.56 Amikacin. (a... Escherichia coli and Proteus spp. and skin and soft tissue infections caused by susceptible strains of...

21 CFR 522.56 - Amikacin.

Code of Federal Regulations, 2012 CFR

2012-04-01

... FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS IMPLANTATION OR INJECTABLE DOSAGE FORM NEW ANIMAL DRUGS § 522.56 Amikacin. (a... of Escherichia coli and Proteus spp. and skin and soft tissue infections caused by susceptible...

21 CFR 522.56 - Amikacin.

Code of Federal Regulations, 2013 CFR

2013-04-01

... FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS IMPLANTATION OR INJECTABLE DOSAGE FORM NEW ANIMAL DRUGS § 522.56 Amikacin. (a... of Escherichia coli and Proteus spp. and skin and soft tissue infections caused by susceptible...

21 CFR 520.88b - Amoxicillin trihydrate for oral suspension.

Code of Federal Regulations, 2012 CFR

2012-04-01

... as follows: respiratory tract (tonsillitis, tracheobronchitis) caused by Staphylococcus aureus, Streptococcus spp., Escherichia coli, and Proteus mirabilis; genitourinary tract (cystitis) caused by S. aureus...., Staphylococcus spp., and E. coli, and soft tissue infections (abscesses, wounds, lacerations) due to S. aureus...

21 CFR 520.88b - Amoxicillin trihydrate for oral suspension.

Code of Federal Regulations, 2013 CFR

2013-04-01

... as follows: respiratory tract (tonsillitis, tracheobronchitis) caused by Staphylococcus aureus, Streptococcus spp., Escherichia coli, and Proteus mirabilis; genitourinary tract (cystitis) caused by S. aureus...., Staphylococcus spp., and E. coli, and soft tissue infections (abscesses, wounds, lacerations) due to S. aureus...

21 CFR 520.88b - Amoxicillin trihydrate for oral suspension.

Code of Federal Regulations, 2014 CFR

2014-04-01

... as follows: respiratory tract (tonsillitis, tracheobronchitis) caused by Staphylococcus aureus, Streptococcus spp., Escherichia coli, and Proteus mirabilis; genitourinary tract (cystitis) caused by S. aureus...., Staphylococcus spp., and E. coli, and soft tissue infections (abscesses, wounds, lacerations) due to S. aureus...

Evolution of synthetic signaling scaffolds by recombination of modular protein domains.

PubMed

Lai, Andicus; Sato, Paloma M; Peisajovich, Sergio G

2015-06-19

Signaling scaffolds are proteins that interact via modular domains with multiple partners, regulating signaling networks in space and time and providing an ideal platform from which to alter signaling functions. However, to better exploit scaffolds for signaling engineering, it is necessary to understand the full extent of their modularity. We used a directed evolution approach to identify, from a large library of randomly shuffled protein interaction domains, variants capable of rescuing the signaling defect of a yeast strain in which Ste5, the scaffold in the mating pathway, had been deleted. After a single round of selection, we identified multiple synthetic scaffold variants with diverse domain architectures, able to mediate mating pathway activation in a pheromone-dependent manner. The facility with which this signaling network accommodates changes in scaffold architecture suggests that the mating signaling complex does not possess a single, precisely defined geometry into which the scaffold has to fit. These relaxed geometric constraints may facilitate the evolution of signaling networks, as well as their engineering for applications in synthetic biology.

Characterization of the ePix100 prototype: a front-end ASIC for second-generation LCLS integrating hybrid pixel detectors

NASA Astrophysics Data System (ADS)

Caragiulo, P.; Dragone, A.; Markovic, B.; Herbst, R.; Nishimura, K.; Reese, B.; Herrmann, S.; Hart, P.; Blaj, G.; Segal, J.; Tomada, A.; Hasi, J.; Carini, G.; Kenney, C.; Haller, G.

2014-09-01

ePix100 is the first variant of a novel class of integrating pixel ASICs architectures optimized for the processing of signals in second generation LINAC Coherent Light Source (LCLS) X-Ray cameras. ePix100 is optimized for ultra-low noise application requiring high spatial resolution. ePix ASICs are based on a common platform composed of a random access analog matrix of pixel with global shutter, fast parallel column readout, and dedicated sigma-delta analog to digital converters per column. The ePix100 variant has 50μmx50μm pixels arranged in a 352x384 matrix, a resolution of 50e- r.m.s. and a signal range of 35fC (100 photons at 8keV). In its final version it will be able to sustain a frame rate of 1kHz. A first prototype has been fabricated and characterized and the measurement results are reported here.

Continuously Tunable Nucleic Acid Hybridization Probes

PubMed Central

Wu, Lucia R.; Wang, J. Sherry; Fang, John Z.; Reiser, Emily; Pinto, Alessandro; Pekker, Irena; Boykin, Richard; Ngouenet, Celine; Webster, Philippa J.; Beechem, Joseph; Zhang, David Yu

2015-01-01

In silico designed nucleic acid probes and primers often fail to achieve favorable specificity and sensitivity tradeoffs on the first try, and iterative empirical sequence-based optimization is needed, particularly in multiplexed assays. Here, we present a novel, on-the-fly method of tuning probe affinity and selectivity via the stoichiometry of auxiliary species, allowing independent and decoupled adjustment of hybridization yield for different probes in multiplexed assays. Using this method, we achieve near-continuous tuning of probe effective free energy (0.03 kcal·mol−1 granularity). As applications, we enforced uniform capture efficiency of 31 DNA molecules (GC content 0% – 100%), maximized signal difference for 11 pairs of single nucleotide variants, and performed tunable hybrid-capture of mRNA from total RNA. Using the Nanostring nCounter platform, we applied stoichiometric tuning to simultaneously adjust yields for a 24-plex assay, and we show multiplexed quantitation of RNA sequences and variants from formalin-fixed, paraffin-embedded samples (FFPE). PMID:26480474

Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma

PubMed Central

Wrzeszczynski, Kazimierz O.; Frank, Mayu O.; Koyama, Takahiko; Rhrissorrakrai, Kahn; Robine, Nicolas; Utro, Filippo; Emde, Anne-Katrin; Chen, Bo-Juen; Arora, Kanika; Shah, Minita; Vacic, Vladimir; Norel, Raquel; Bilal, Erhan; Bergmann, Ewa A.; Moore Vogel, Julia L.; Bruce, Jeffrey N.; Lassman, Andrew B.; Canoll, Peter; Grommes, Christian; Harvey, Steve; Parida, Laxmi; Michelini, Vanessa V.; Zody, Michael C.; Jobanputra, Vaidehi; Royyuru, Ajay K.

2017-01-01

Objective: To analyze a glioblastoma tumor specimen with 3 different platforms and compare potentially actionable calls from each. Methods: Tumor DNA was analyzed by a commercial targeted panel. In addition, tumor-normal DNA was analyzed by whole-genome sequencing (WGS) and tumor RNA was analyzed by RNA sequencing (RNA-seq). The WGS and RNA-seq data were analyzed by a team of bioinformaticians and cancer oncologists, and separately by IBM Watson Genomic Analytics (WGA), an automated system for prioritizing somatic variants and identifying drugs. Results: More variants were identified by WGS/RNA analysis than by targeted panels. WGA completed a comparable analysis in a fraction of the time required by the human analysts. Conclusions: The development of an effective human-machine interface in the analysis of deep cancer genomic datasets may provide potentially clinically actionable calls for individual patients in a more timely and efficient manner than currently possible. ClinicalTrials.gov identifier: NCT02725684. PMID:28740869

PCR-free Quantification of Multiple Splice Variants in Cancer Gene by Surface Enhanced Raman Spectroscopy

PubMed Central

Sun, Lan; Irudayaraj, Joseph

2009-01-01

We demonstrate a surface enhanced Raman spectroscopy (SERS) based array platform to monitor gene expression in cancer cells in a multiplex and quantitative format without amplification steps. A strategy comprising of DNA/RNA hybridization, S1 nuclease digestion, and alkaline hydrolysis was adopted to obtain DNA targets specific to two splice junction variants Δ(9, 10) and Δ(5) of the breast cancer susceptibility gene 1 (BRCA1) from MCF-7 and MDA-MB-231 breast cancer cell lines. These two targets were identified simultaneously and their absolute quantities were estimated by a SERS strategy utilizing the inherent plasmon-phonon Raman mode of gold nanoparticle probes as a self-referencing standard to correct for variability in surface enhancement. Results were then validated by reverse transcription PCR (RT-PCR). Our proposed methodology could be expanded to a higher level of multiplexing for quantitative gene expression analysis of any gene without any amplification steps. PMID:19780515

Application of Nexus copy number software for CNV detection and analysis.

PubMed

Darvishi, Katayoon

2010-04-01

Among human structural genomic variation, copy number variants (CNVs) are the most frequently known component, comprised of gains/losses of DNA segments that are generally 1 kb in length or longer. Array-based comparative genomic hybridization (aCGH) has emerged as a powerful tool for detecting genomic copy number variants (CNVs). With the rapid increase in the density of array technology and with the adaptation of new high-throughput technology, a reliable and computationally scalable method for accurate mapping of recurring DNA copy number aberrations has become a main focus in research. Here we introduce Nexus Copy Number software, a platform-independent tool, to analyze the output files of all types of commercial and custom-made comparative genomic hybridization (CGH) and single-nucleotide polymorphism (SNP) arrays, such as those manufactured by Affymetrix, Agilent Technologies, Illumina, and Roche NimbleGen. It also supports data generated by various array image-analysis software tools such as GenePix, ImaGene, and BlueFuse. (c) 2010 by John Wiley & Sons, Inc.

Nomenclature for alleles of the thiopurine methyltransferase gene

PubMed Central

Appell, Malin L.; Berg, Jonathan; Duley, John; Evans, William E.; Kennedy, Martin A.; Lennard, Lynne; Marinaki, Tony; McLeod, Howard L.; Relling, Mary V.; Schaeffeler, Elke; Schwab, Matthias; Weinshilboum, Richard; Yeoh, Allen E.J.; McDonagh, Ellen M.; Hebert, Joan M.; Klein, Teri E.; Coulthard, Sally A.

2013-01-01

The drug-metabolizing enzyme thiopurine methyltransferase (TPMT) has become one of the best examples of pharmacogenomics to be translated into routine clinical practice. TPMT metabolizes the thiopurines 6-mercaptopurine, 6-thioguanine, and azathioprine, drugs that are widely used for treatment of acute leukemias, inflammatory bowel diseases, and other disorders of immune regulation. Since the discovery of genetic polymorphisms in the TPMT gene, many sequence variants that cause a decreased enzyme activity have been identified and characterized. Increasingly, to optimize dose, pretreatment determination of TPMT status before commencing thiopurine therapy is now routine in many countries. Novel TPMT sequence variants are currently numbered sequentially using PubMed as a source of information; however, this has caused some problems as exemplified by two instances in which authors’ articles appeared on PubMed at the same time, resulting in the same allele numbers given to different polymorphisms. Hence, there is an urgent need to establish an order and consensus to the numbering of known and novel TPMT sequence variants. To address this problem, a TPMT nomenclature committee was formed in 2010, to define the nomenclature and numbering of novel variants for the TPMT gene. A website (http://www.imh.liu.se/tpmtalleles) serves as a platform for this work. Researchers are encouraged to submit novel TPMT alleles to the committee for designation and reservation of unique allele numbers. The committee has decided to renumber two alleles: nucleotide position 106 (G > A) from TPMT*24 to TPMT*30 and position 611 (T > C, rs79901429) from TPMT*28 to TPMT*31. Nomenclature for all other known alleles remains unchanged. PMID:23407052

A map of human genome variation from population-scale sequencing.

PubMed

Abecasis, Gonçalo R; Altshuler, David; Auton, Adam; Brooks, Lisa D; Durbin, Richard M; Gibbs, Richard A; Hurles, Matt E; McVean, Gil A

2010-10-28

The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10(-8) per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research.

Construction of armored RNA containing long-size chimeric RNA by increasing the number and affinity of the pac site in exogenous rna and sequence coding coat protein of the MS2 bacteriophage.

PubMed

Wei, Baojun; Wei, Yuxiang; Zhang, Kuo; Yang, Changmei; Wang, Jing; Xu, Ruihuan; Zhan, Sien; Lin, Guigao; Wang, Wei; Liu, Min; Wang, Lunan; Zhang, Rui; Li, Jinming

2008-01-01

To construct a one-plasmid expression system of the armored RNA containing long chimeric RNA by increasing the number and affinity of the pac site. The plasmid pET-MS2-pac was constructed with one C-variant pac site, and then the plasmid pM-CR-2C containing 1,891-bp chimeric sequences and two C-variant pac sites was produced. Meanwhile, three plasmids (pM-CR-C, pM-CR-2W and pM-CR-W) were obtained as parallel controls with a different number and affinity of the pac site. Finally, the armored RNA was expressed and purified. The armored RNA with 1,891 bases target RNA was expressed successfully by the one-plasmid expression system with two C-variant pac sites, while for one pac site, no matter whether the affinity was changed or not, only the 1,200 bases target RNA was packaged. It was also found that the C-variant pac site could increase the expression efficiency of the armored RNA. The armored RNA with 1,891-bp exogenous RNA in our study showed the characterization of ribonuclease resistance and stability at different time points and temperature conditions. The armored RNA with 1,891 bases exogenous RNA was constructed and the expression system can be used as a platform for preparation of the armored RNA containing long RNA sequences. Copyright 2008 S. Karger AG, Basel.

High-Density Genetic Mapping Identifies New Susceptibility Variants in Sarcoidosis Phenotypes and Shows Genomic-driven Phenotypic Differences

PubMed Central

Ronninger, Marcus; Shchetynsky, Klementy; Franke, Andre; Nöthen, Markus M.; Müller-Quernheim, Joachim; Schreiber, Stefan; Adrianto, Indra; Karakaya, Bekir; van Moorsel, Coline H. M.; Navratilova, Zdenka; Kolek, Vitezslav; Rybicki, Benjamin A.; Iannuzzi, Michael C.; Petrek, Martin; Grutters, Jan C.; Montgomery, Courtney; Fischer, Annegret; Eklund, Anders; Padyukov, Leonid; Grunewald, Johan

2016-01-01

Rationale: Sarcoidosis is a multisystem disease of unknown cause. Löfgren’s syndrome (LS) is a characteristic subgroup of sarcoidosis that is associated with a good prognosis in sarcoidosis. However, little is known about its genetic architecture or its broader phenotype, non-LS sarcoidosis. Objectives: To address the genetic architecture of sarcoidosis phenotypes, LS and non-LS. Methods: An association study in a white Swedish cohort of 384 LS, 664 non-LS, and 2,086 control subjects, totaling 3,134 subjects using a fine-mapping genotyping platform was conducted. Replication was performed in four independent cohorts, three of white European descent (Germany, n = 4,975; the Netherlands, n = 613; and Czech Republic, n = 521), and one of black African descent (United States, n = 1,657), totaling 7,766 subjects. Measurements and Main Results: A total of 727 LS-associated variants expanding throughout the extended major histocompatibility complex (MHC) region and 68 non-LS–associated variants located in the MHC class II region were identified and confirmed. A shared overlap between LS and non-LS defined by 17 variants located in the MHC class II region was found. Outside the MHC region, two LS-associated loci, in ADCY3 and between CSMD1 and MCPH1, were observed and replicated. Conclusions: Comprehensive and integrative analyses of genetics, transcription, and pathway modeling on LS and non-LS indicates that these sarcoidosis phenotypes have different genetic susceptibility, genomic distributions, and cellular activities, suggesting distinct molecular mechanisms in pathways related to immune response with a common region. PMID:26651848

Antimicrobial activity of silver and gold in toothpastes: A comparative analysis.

PubMed

Junevičius, Jonas; Žilinskas, Juozas; Česaitis, Kęstutis; Česaitienė, Gabrielė; Gleiznys, Darius; Maželienė, Žaneta

2015-01-01

In this study, we compared the antimicrobial activity of identical toothpastes differing only in silver or gold nanoparticles against the activity of one of the common toothpastes containing a chemical active ingredient. We also compared the active concentrations of the toothpastes. For this study, we selected "Royal Denta" toothpastes containing silver and gold particles, and the "Blend-A-Med Complete" toothpaste containing zinc citrate as the active ingredient. We used 8 standard microorganism cultures on the basis of their individual mechanisms of protection. The antimicrobial activity of each studied preparation was evaluated at 9 concentrations. Most effective against gram-positive bacteria (Staphylococcus aureus and Enterococcus faecalis) was the "Silver Technology" – MIC was 0.004-0.0015 g/mL. Neither "Silver Technology" nor "Orange and Gold Technology" had any effect on Escherichia coli or Proteus mirabilis. Antimicrobial activity against the motile bacterium Proteus mirabilis was observed in "Silver Technology", "Orange and Gold Technology", and "Blend-A-Med Complete" – the MIC was 0.015 g/mL or lower. No antimicrobial activity against Candida albicans fungus at the studied concentrations was observed in the "Orange and Gold Technology". The toothpaste "Blend-A-Med" demonstrated the most effective antimicrobial activity - the MIC of 0.0015 g/mL and 0.015 g/mL inhibited Staphylococcus aureus and Enterococcus faecalis, respectively, and the MIC of 0.15 g/mL inhibited the growth of the bacteria Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, and fungus Candida albicans. Silver in toothpaste has a greater antimicrobial effect than gold, but its effect is still inferior to that of a chemical antimicrobial agent.

Involvement of polyphosphate kinase in virulence and stress tolerance of uropathogenic Proteus mirabilis.

PubMed

Peng, Liang; Jiang, Qiao; Pan, Jia-Yun; Deng, Cong; Yu, Jing-Yi; Wu, Xiao-Man; Huang, Sheng-He; Deng, Xiao-Yan

2016-04-01

Proteus mirabilis (P. mirabilis), a gram-negative enteric bacterium, frequently causes urinary tract infections. Many virulence factors of uropathogenic P. mirabilis have been identified, including urease, flagella, hemolysin and fimbriae. However, the functions of polyphosphate kinase (PPK), which are related to the pathogenicity of many bacteria, remain entirely unknown in P. mirabilis. In this study, a ppk gene encoding the PPK insertional mutant in P. mirabilis strain HI4320 was constructed, and its biological functions were examined. The results of survival studies demonstrated that the ppk mutant was deficient in resistance to oxidative, hyperosmotic and heat stress. The swarming and biofilm formation abilities of P. mirabilis were also attenuated after the ppk interruption. In vitro and in vivo experiments suggested that ppk was required for P. mirabilis to invade the bladder. The negative phenotypes of the ppk mutant could be restored by ppk gene complementation. Furthermore, two-dimensional gel electrophoresis and liquid chromatography-mass spectrometry were used to analyze the proteomes of the wild-type strain and the ppk mutant. Compared with the wild-type strain, seven proteins including TonB-dependent receptor, universal stress protein G, major mannose-resistant/Proteus-like fimbrial protein (MR/P fimbriae), heat shock protein, flagellar capping protein, putative membrane protein and multidrug efflux protein were down-regulated, and four proteins including exported peptidase, repressor protein for FtsI, FKBP-type peptidyl-prolyl cis-trans isomerase and phosphotransferase were up-regulated in the ppk mutant. As a whole, these results indicate that PPK is an important regulator and plays a crucial role in stress tolerance and virulence in uropathogenic P. mirabilis.

Comparison of phenotypic and virulence genes characteristics in human and chicken isolates of Proteus mirabilis.

PubMed

Barbour, Elie K; Hajj, Zahi G; Hamadeh, Shadi; Shaib, Houssam A; Farran, Mohamad T; Araj, George; Faroon, Obaid; Barbour, Kamil E; Jirjis, Faris; Azhar, Esam; Kumosani, Taha; Harakeh, Steve

2012-10-01

The objective of this work is to compare the phenotypic and virulence genes characteristics in human and chicken isolates of Proteus mirabilis. The bacterial examination of 50 livers of individual broilers, marketed by four major outlets, revealed a high recovery of P. mirabilis (66%), and a low recovery frequency of Salmonella spp. (4%), Serratia odorifera (2%), Citrobacter brakii (2%), and Providencia stuartii (2%). The phenotypic biochemical characterization of the recovered 33 chicken isolates of P. mirabilis were compared to 30 human isolates (23 urinary and six respiratory isolates). The comparison revealed significant differences in the presence of gelatinase enzyme (100% presence in chicken isolates versus 91.3 and 83.3% presence in human urinary and respiratory isolates, respectively, P,0.05). The H(2)S production occurred in 100% of chicken isolates versus 95.6 and 66.7% presence in human urinary and respiratory isolates, respectively, P,0.05). The other 17 biochemical characteristics did not differ significantly among the three groups of isolates (P.0.05). Two virulence genes, the mrpA and FliL, were having a typical 100% presence in randomly selected isolates of P. mirabilis recovered from chicken livers (N510) versus isolates recovered from urinary (N55) and respiratory specimens of humans (N55) (P.0.05). The average percentage similarity of mrpA gene nucleotide sequence of poultry isolates to human urinary and respiratory isolates was 93.2 and 97.5-%, respectively. The high similarity in phenotypic characteristics, associated with typical frequency of presence of two virulence genes, and high similarity in sequences of mrpA gene among poultry versus human P. mirabilis isolates justifies future investigations targeting the evaluation of adaptable pathogenicity of avian Proteus mirabilis isolates to mammalian hosts.

Molecular detection of HpmA and HlyA hemolysin of uropathogenic Proteus mirabilis.

PubMed

Cestari, Silvia Emanoele; Ludovico, Marilucia Santos; Martins, Fernando Henrique; da Rocha, Sérgio Paulo Dejato; Elias, Waldir Pereira; Pelayo, Jacinta Sanchez

2013-12-01

Urinary tract infection (UTI) is one of the bacterial infections frequently documented in humans. Proteus mirabilis is associated with UTI mainly in individuals with urinary tract abnormality or related with vesicular catheterism and it can be difficult to treat because of the formation of stones in the bladder and kidneys. These stones are formed due to the presence of urease synthesized by the bacteria. Another important factor is that P. mirabilis produces hemolysin HpmA, used by the bacteria to damage the kidney tissues. Proteus spp. samples can also express HlyA hemolysin, similar to that found in Escherichia coli. A total of 211 uropathogenic P. mirabilis isolates were analyzed to detect the presence of the hpmA and hpmB genes by the techniques of polymerase chain reaction (PCR) and dot blot and hlyA by PCR. The hpmA and hpmB genes were expressed by the RT-PCR technique and two P. mirabilis isolates were sequenced for the hpmA and hpmB genes. The presence of the hpmA and hpmB genes was confirmed by PCR in 205 (97.15 %) of the 211 isolates. The dot blot confirmed the presence of the hpmA and hpmB genes in the isolates that did not amplify in the PCR. None of the isolates studied presented the hlyA gene. The hpmA and hpmB genes that were sequenced presented 98 % identity with the same genes of the HI4320 P. mirabilis sample. This study showed that the PCR technique has good sensitivity for detecting the hpmA and hpmB genes of P. mirabilis.

Zinc uptake contributes to motility and provides a competitive advantage to Proteus mirabilis during experimental urinary tract infection.

PubMed

Nielubowicz, Greta R; Smith, Sara N; Mobley, Harry L T

2010-06-01

Proteus mirabilis, a Gram-negative bacterium, represents a common cause of complicated urinary tract infections in catheterized patients or those with functional or anatomical abnormalities of the urinary tract. ZnuB, the membrane component of the high-affinity zinc (Zn(2+)) transport system ZnuACB, was previously shown to be recognized by sera from infected mice. Since this system has been shown to contribute to virulence in other pathogens, its role in Proteus mirabilis was investigated by constructing a strain with an insertionally interrupted copy of znuC. The znuC::Kan mutant was more sensitive to zinc limitation than the wild type, was outcompeted by the wild type in minimal medium, displayed reduced swimming and swarming motility, and produced less flaA transcript and flagellin protein. The production of flagellin and swarming motility were restored by complementation with znuCB in trans. Swarming motility was also restored by the addition of Zn(2+) to the agar prior to inoculation; the addition of Fe(2+) to the agar also partially restored the swarming motility of the znuC::Kan strain, but the addition of Co(2+), Cu(2+), or Ni(2+) did not. ZnuC contributes to but is not required for virulence in the urinary tract; the znuC::Kan strain was outcompeted by the wild type during a cochallenge experiment but was able to colonize mice to levels similar to the wild-type level during independent challenge. Since we demonstrated a role for ZnuC in zinc transport, we hypothesize that there is limited zinc present in the urinary tract and P. mirabilis must scavenge this ion to colonize and persist in the host.

Assessment of Nasal Carriage of Staphylococcus Aureus and Axillar Flora in Patients With Acromegaly.

PubMed

Gen, Ramazan; Horasan, Elif Şahin; Çinkir, Ümit; Sezer, Kerem; Akbay, Esen

2017-05-01

Recent study showed that patients with acromegaly have typical skin findings including increased sebum secretion, decreased transepidermal water loss, more alkaline, and colder skin surface correlated with serum growth hormone and insulin-like growth factor 1 levels. Different anatomic localizations and texture of the skin differ in bacterial concentrations.Nasal carriage of Staphylococcus aureus and axillar flora in patients with acromegaly was compared with normal population with regard to duration of acromegaly as well as the growth hormone and insulin-like growth factor 1 levels. This patient-control prospective study was conducted in university hospitals in Mersin, Turkey. The study consisted of 30 active acromegalic patients and 60 healthy adults who had no previously diagnosed chronic illness as a control group. A total of 90 volunteers were enrolled in this study; nasal and axillar cultures were obtained. Axillar and nasal specimens from anterior nares of the individuals were taken using sterile swabs. Nasal colonization of Staphylococcus aureus was 13.3% in acromegalic patients, but 43.4% in control group. This difference was statistically significant (P = 0.004). Patients and control group compared according to axillar cultures, the authors determined proteus colonization 16.7% in patients with acromegaly but no proteus colonization in control group. This result was statistically significant (P = 0.001). Proteus colonization was negatively correlated only with disease duration in acromegalic patients (P = 0.017). The authors demonstrated that compared with healthy subjects, acromegalic patients had low percentage of nasal carriage of Staphylococcus aureus and more gram-negative basili in the axillar flora. These nasal and axillar flora changes should be considered for prophylactic antibiotics use before surgery and ampiric antibiotics use after surgery.

Molecular Analysis, Biochemical Characterization, Antimicrobial Activity, and Immunological Analysis of Proteus mirabilis Isolated from Broilers.

PubMed

Yeh, Hung-Yueh; Line, John E; Hinton, Arthur

2018-03-01

Proteus mirabilis, a Gram-negative bacterium, is ubiquitous in the environment and is considered as the normal microflora in the human gastrointestinal tract. However, this bacterium is an opportunistic pathogen in humans, often causing urinary tract infections. Moreover, Proteus has been frequently isolated from food animals, including poultry. Whether this bacterium contributes to the foodborne illness in humans is unclear. In this report, P. mirabilis isolates recovered from broilers during housing in the units were characterized, their antimicrobial activity was assayed, and broiler immune response to the soluble proteins was determined. Cecal contents and fecal droppings were treated according to the standard protocol for isolation. Speciation based on biochemical reactions and the antimicrobial activity of the isolates were carried out using commercial kits. Immunoblot was assayed to determine immune status of broilers against P. mirabilis. A total of 10 isolates of P. mirabilis were selected for further characterization. These isolates could grow in pH 6.0 and 1% NaCl conditions. They were resistant to sodium lactate, troleandomycin, rifamycin SV, vancomycin, but sensitive to nalidixic acid, cefotaxime and novobiocin. Moreover, the CTX, ACC, CMY-1, BIC, NDM, VEB, qnrB and qnrD genes were detected by PCR amplification in all isolates. Sera from broilers harboring this bacterium reacted to the P. mirabilis soluble proteins, but not from litter- and age-matched P. mirabilis negative and SPF chickens, indicating that this bacterium infected chickens that could have humoral immune response against P. mirabilis. This study provides a rationale for further monitoring P. mirabilis during poultry production to determine whether this bacterium poses potential threats to public health. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

Community-acquired urinary tract infection: age and gender-dependent etiology.

PubMed

Lo, Denise Swei; Shieh, Huei Hsin; Ragazzi, Selma Lopes Betta; Koch, Vera Hermina Kalika; Martinez, Marina Baquerizo; Gilio, Alfredo Elias

2013-01-01

Choosing the antimicrobial agent for initial therapy of urinary tract infection (UTI) is usually empirical and should consider the prevalence of uropathogens in different age groups and gender. To establish prevalence rates of uropathogens in community-acquired UTI in relation to age and gender. Cross-sectional study conducted in the emergency department (ED) of a general hospital, from January to December, 2010, in patients younger than 15 years old who had clinical suspicion of UTI and collected quantitative urine culture. UTI was defined as urine culture with growth of a single agent > 100.000 colony forming units (cfu)/mL in a midstream collection or ≥ 50.000 cfu/mL in urethral catheterization. There were 63.464 visits to ED. 2577 urine cultures were obtained, of whom 291 were positive for UTI (prevalence = 11.3% of clinical suspicion and 0.46% of visits), 212 cases (72.8%) in females, median age = 2.6 years. The predominant uropathogen was E. coli (76.6%), followed by Proteus mirabilis (10.3%) and Staphylococcus saprophyticus (4.1%). Among infants < 3 months, prevalence rates of E. coli were significantly lower (50% vs 78.4%; OR = 0.276; p = 0.006). Higher prevalences of Staphylococcus saprophyticus occurred among patients > 10 years (24.4% vs 0.4%; OR = 79.265; p < 0.0001). Proteus mirabilis was significantly more prevalent in boys than girls (24.0% vs 5.2%; OR = 5.786; p < 0.001). E. coli was the most prevalent community-acquired uropathogen. Nevertheless, initial empiric antimicrobial treatment of UTI should consider the significant prevalence of other agents different from E. coli in infants < 3 months, the high prevalence of Staphylococcus saprophyticus in patients > 10 years and Proteus mirabilis in males.

Secondary metabolites produced by marine streptomyces as antibiofilm and quorum-sensing inhibitor of uropathogen Proteus mirabilis.

PubMed

Younis, Khansa Mohammed; Usup, Gires; Ahmad, Asmat

2016-03-01

Quorum-sensing regulates bacterial biofilm formation and virulence factors, thereby making it an interesting target for attenuating pathogens. In this study, we investigated anti-biofilm and anti-quorum-sensing compounds from secondary metabolites of halophiles marine streptomyces against urinary catheter biofilm forming Proteus mirabilis without effect on growth viability. A total of 40 actinomycetes were isolated from samples collected from different places in Iraq including marine sediments and soil samples. Fifteen isolates identified as streptomyces and their supernatant screened as anti-quorum-sensing by inhibiting quorum-sensing regulated prodigiosin biosynthesis of Serratia marcescens strain Smj-11 as a reporter strain. Isolate Sediment Lake Iraq (sdLi) showed potential anti-quorum-sensing activity. Out of 35 clinical isolates obtained from Urinary catheter used by patient at the Universiti Kebangsaan Malaysia Medical Center, 22 isolates were characterized and identified as Proteus mirabilis. Isolate Urinary Catheter B4 (UCB4) showed the highest biofilm formation with highest resistance to used antibiotic and was chosen for further studies. Ethyl acetate secondary metabolites extract was produced from sdLi isolate. First, we determined the Minimum Inhibitory Concentration (MIC) of sdLi crude extract against UCB4 isolate, and all further experiments used concentrations below the MIC. Tests of subinhibitory concentrations of sdLi crude extract showed good inhibition against UCB4 isolate biofilm formation on urinary catheter and cover glass using Scanning electron microscopy and light microscopy respectively. The influence of sub-MIC of sdLi crude extract was also found to attenuate the quorum sensing (QS)-dependent factors such as hemolysin activity, urease activity, pH value, and motility of UCB4 isolate. Evidence is presented that these nontoxic secondary metabolites may act as antagonists of bacterial quorum sensing by competing with quorum-sensing signals for receptor binding.

Inhibition of Urease Enzyme Production and some Other Virulence Factors Expression in Proteus mirabilis by N-Acetyl Cysteine and Dipropyl Disulphide.

PubMed

Abdel-Baky, Rehab Mahmoud; Ali, Mohamed Abdullah; Abuo-Rahma, Gamal El-Din Ali A; AbdelAziz, Neveen

2017-01-01

Proteus mirabilis is one of the important pathogens that colonize the urinary tract and catheters resulting in various complications, such as blockage of the catheters and the formation of infective stones. In this study we evaluated the effect of N-acetyl cysteine (NAC) and dipropyl disulphide on some virulence factors expressed by a Proteus mirabilis strain isolated from a catheterized patient. Antibacterial activity of both compounds was determined by broth microdilution method. Their effect on different types of motility was determined by LB medium with variable agar content and sub-MIC of each drug. Their effect on adherence and mature biofilms was tested by tissue culture plate assay. Inhibitory effect on urease production was determined and supported by molecular docking studies. The minimum inhibitory concentration (MIC) of NAC and dipropyl disulphide was 25 mM and 100 mM, respectively. Both compounds decreased the swarming ability and biofilm formation of the tested isolate in a dose-dependent manner. NAC had higher urease inhibitory activity (IC50 249 ±0.05 mM) than that shown by dipropyl disulphide (IC 50 10±0.2 mM). Results were supported by molecular docking studies which showed that NAC and dipropyl disulphide interacted with urease enzyme with binding free energy of -4.8 and -8.528 kcal/mol, respectively. Docking studies showed that both compounds interacted with Ni ion and several amino acids (His-138, Gly-279, Cysteine-321, Met-366 and His-322) which are essential for the enzyme activity. NAC and dipropyl disulphide could be used in the control of P. mirabilis urinary tract infections.

Design of a proteus lattice representative of a burnt and fresh fuel interface at power conditions in light water reactors

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

Hursin, M.; Perret, G.

The research program LIFE (Large-scale Irradiated Fuel Experiment) between PSI and Swissnuclear has been started in 2006 to study the interaction between large sets of burnt and fresh fuel pins in conditions representative of power light water reactors. Reactor physics parameters such as flux ratios and reaction rate distributions ({sup 235}U and {sup 238}U fissions and {sup 238}U capture) are calculated to estimate an appropriate arrangement of burnt and fresh fuel pins within the central element of the test zone of the zero-power research reactor PROTEUS. The arrangement should minimize the number of burnt fuel pins to ease fuel handlingmore » and reduce costs, whilst guaranteeing that the neutron spectrum in both burnt and fresh fuel regions and at their interface is representative of a large uniform array of burnt and fresh pins in the same moderation conditions. First results are encouraging, showing that the burnt/fresh fuel interface is well represented with a 6 x 6 bundle of burnt pins. The second part of the project involves the use of TSUNAMI, CASMO-4E and DAKOTA to perform parametric and optimization studies on the PROTEUS lattice by varying its pitch (P) and fraction of D{sub 2}O in moderator (F{sub D2O}) to be as representative as possible of a power light water reactor core at hot full power conditions at beginning of cycle (BOC). The parameters P and F{sub D2O} that best represent a PWR at BOC are 1.36 cm and 5% respectively. (authors)« less

Calcium distribution in Amoeba proteus

PubMed Central

1979-01-01

A preliminary investigation of the distribution of cellular calcium in Amoeba proteus was undertaken. Total cellular calcium under control conditions was found to be 4.59 mmol/kg of cells. When the external Ca++ concentration is increased from the control level of 0.03 to 20 mM, a net Ca++ influx results with a new steady-state cellular calcium level being achieved in integral of 3 h. At steady state the amount of calcium per unit weight of cells is higher than the amount of calcium per unit weight of external solution when the external concentration of Ca++ is below 10 mM. At external Ca++ concentrations above this level, total cellular calcium approaches the medium level of Ca++. Steady- state calcium exchange in Amoeba proteus was determined with 45Ca. There is an immediate and rapid exchange of integral of 0.84 mmol/kg of cells or 18% of the total cellular calcium with the labelled Ca++. Following this initial exchange, there was very little if any further exchange observed. Most of this exchanged calcium could be eliminated from the cell with 1 mM La+++, suggesting that the exchanged calcium is associated with the surface of the cell. Increase in either the external Ca++ concentration of pH raise the amount of exchangeable calcium associated with the cell. Calcium may be associated with the cell surface as a co-ion in the diffuse double layer or bound to fixed negative sites on the surface of the cell. If Ca++-binding sites do exist on the cell surface, there may be more than one type and they may have different dissociation constants. The cytoplasmic Ca++ ion activity is probably maintained at very low levels. PMID:512628