14 CFR Appendix A to Part 121 - First Aid Kits and Emergency Medical Kits

Code of Federal Regulations, 2010 CFR

2010-01-01

..., 50cc 1 Epinephrine 1:1000, single dose ampule or equivalent) 2 Diphenhydramine HC1 injection, single dose ampule or equivalent 2 Nitroglycerin tablets 10 Basic instructions for use of the drugs in the kit 1 protective nonpermeable gloves or equivalent 1 pair 2. As of April 12, 2004, at least one approved...

14 CFR Appendix A to Part 121 - First Aid Kits and Emergency Medical Kits

Code of Federal Regulations, 2014 CFR

2014-01-01

..., 50cc 1 Epinephrine 1:1000, single dose ampule or equivalent) 2 Diphenhydramine HC1 injection, single dose ampule or equivalent 2 Nitroglycerin tablets 10 Basic instructions for use of the drugs in the kit 1 protective nonpermeable gloves or equivalent 1 pair 2. As of April 12, 2004, at least one approved...

14 CFR Appendix A to Part 121 - First Aid Kits and Emergency Medical Kits

Code of Federal Regulations, 2011 CFR

2011-01-01

..., 50cc 1 Epinephrine 1:1000, single dose ampule or equivalent) 2 Diphenhydramine HC1 injection, single dose ampule or equivalent 2 Nitroglycerin tablets 10 Basic instructions for use of the drugs in the kit 1 protective nonpermeable gloves or equivalent 1 pair 2. As of April 12, 2004, at least one approved...

14 CFR Appendix A to Part 121 - First Aid Kits and Emergency Medical Kits

Code of Federal Regulations, 2012 CFR

2012-01-01

..., 50cc 1 Epinephrine 1:1000, single dose ampule or equivalent) 2 Diphenhydramine HC1 injection, single dose ampule or equivalent 2 Nitroglycerin tablets 10 Basic instructions for use of the drugs in the kit 1 protective nonpermeable gloves or equivalent 1 pair 2. As of April 12, 2004, at least one approved...

Effect of influx on the free surface transport within a hollow ampule

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

Chen, S.C.; Vafai, K.

1994-07-01

A numerical investigation of free surface transport within a hollow glass ampule with feed-in boundary conditions is presented. The glass ampule is treated as a vertical film with a finite pressure difference across the film, with applied influx on the upper boundary, and with applied heat flux at the outer free surface. Two different sizes of glass ampules, along with different influx values are investigated. A finite element method with full consideration of surface tension and viscosity effects is used to solve the transient Navier-Stokes equations in cylindrical coordinates. Radiative and convective boundary conditions are incorporated when solving the energymore » equation. The movement of the inner and outer free surfaces with the specified feed-in velocity for different dimensions and temporal temperature distribution are analyzed. It is found that the feed-in mechanism rather than the pressure difference provides the more dominant driving forces. Also studied is the effect of using different feed-in velocities on the flow and temperature fields. The results presented in this work illustrate the basic effects of the feed-in mechanism of the free surface transport phenomenon.« less

Acidic Residues Control the Dimerization of the N-terminal Domain of Black Widow Spiders’ Major Ampullate Spidroin 1

NASA Astrophysics Data System (ADS)

Bauer, Joschka; Schaal, Daniel; Eisoldt, Lukas; Schweimer, Kristian; Schwarzinger, Stephan; Scheibel, Thomas

2016-09-01

Dragline silk is the most prominent amongst spider silks and comprises two types of major ampullate spidroins (MaSp) differing in their proline content. In the natural spinning process, the conversion of soluble MaSp into a tough fiber is, amongst other factors, triggered by dimerization and conformational switching of their helical amino-terminal domains (NRN). Both processes are induced by protonation of acidic residues upon acidification along the spinning duct. Here, the structure and monomer-dimer-equilibrium of the domain NRN1 of Latrodectus hesperus MaSp1 and variants thereof have been investigated, and the key residues for both could be identified. Changes in ionic composition and strength within the spinning duct enable electrostatic interactions between the acidic and basic pole of two monomers which prearrange into an antiparallel dimer. Upon naturally occurring acidification this dimer is stabilized by protonation of residue E114. A conformational change is independently triggered by protonation of clustered acidic residues (D39, E76, E81). Such step-by-step mechanism allows a controlled spidroin assembly in a pH- and salt sensitive manner, preventing premature aggregation of spider silk proteins in the gland and at the same time ensuring fast and efficient dimer formation and stabilization on demand in the spinning duct.

Diversified Structural Basis of a Conserved Molecular Mechanism for pH-Dependent Dimerization in Spider Silk N-Terminal Domains.

PubMed

Otikovs, Martins; Chen, Gefei; Nordling, Kerstin; Landreh, Michael; Meng, Qing; Jörnvall, Hans; Kronqvist, Nina; Rising, Anna; Johansson, Jan; Jaudzems, Kristaps

2015-08-17

Conversion of spider silk proteins from soluble dope to insoluble fibers involves pH-dependent dimerization of the N-terminal domain (NT). This conversion is tightly regulated to prevent premature precipitation and enable rapid silk formation at the end of the duct. Three glutamic acid residues that mediate this process in the NT from Euprosthenops australis major ampullate spidroin 1 are well conserved among spidroins. However, NTs of minor ampullate spidroins from several species, including Araneus ventricosus ((Av)MiSp NT), lack one of the glutamic acids. Here we investigate the pH-dependent structural changes of (Av)MiSp NT, revealing that it uses the same mechanism but involves a non-conserved glutamic acid residue instead. Homology modeling of the structures of other MiSp NTs suggests that these harbor different compensatory residues. This indicates that, despite sequence variations, the molecular mechanism underlying pH-dependent dimerization of NT is conserved among different silk types. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Protein composition correlates with the mechanical properties of spider ( Argiope trifasciata ) dragline silk.

PubMed

Marhabaie, Mohammad; Leeper, Thomas C; Blackledge, Todd A

2014-01-13

We investigated the natural variation in silk composition and mechanical performance of the orb-weaving spider Argiope trifasciata at multiple spatial and temporal scales in order to assess how protein composition contributes to the remarkable material properties of spider dragline silk. Major ampullate silk in orb-weaving spiders consists predominantly of two proteins (MaSp1 and MaSp2) with divergent amino acid compositions and functionally different microstructures. Adjusting the expression of these two proteins therefore provides spiders with a simple mechanism to alter the material properties of their silk. We first assessed the reliability and precision of the Waters AccQ-Tag amino acid composition analysis kit for determining the amino acid composition of small quantities of spider silk. We then tested how protein composition varied within single draglines, across draglines spun by the same spider on different days, and finally between spiders. Then, we correlated chemical composition with the material properties of dragline silk. Overall, we found that the chemical composition of major ampullate silk was in general homogeneous among individuals of the same population. Variation in chemical composition was not detectable within silk spun by a single spider on a single day. However, we found that variation within a single spider's silk across different days could, in rare instances, be greater than variation among individual spiders. Most of the variation in silk composition in our investigation resulted from a small number of outliers (three out of sixteen individuals) with a recent history of stress, suggesting stress affects silk production process in orb web spiders. Based on reported sequences for MaSp genes, we developed a gene expression model showing the covariation of the most abundant amino acids in major ampullate silk. Our gene expression model supports that dragline silk composition was mostly determined by the relative abundance of MaSp1 and MaSp2. Finally, we showed that silk composition (especially proline content) strongly correlated with some measures of mechanical performance, particularly how much fibers shrunk during supercontraction as well as their breaking strains. Our findings suggest that spiders are able to change the relative expression rates of different MaSp genes to produce silk fibers with different chemical compositions, and hence, different material properties.

Glass Particulate Contamination from Medications Aspirated from Glass Ampules: Comparison of Filtered Versus Non-Filtered Needles

DTIC Science & Technology

1994-09-01

with giant cells found in the spleen and lungs. A second experiment 3 (Brewer & Dunning, 1947) was conducted where 1,089 mice were injected...crystals, or starch. They conducted experiments where rabbits received I I.V. normal saline via the ear vein. Each rabbit received a different volume...conducted a similar experiment examining the incidence of drug contamination with particles from the external surface of glass ampules. Methylene blue

Supercritical hydrogen-free and catalyst-free hydrogenation: Possibilities of the method

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

Gubin, S.P.

1995-12-01

In this work, the authors generalize the results of preliminary investigations of a catalyst-free hydrogenation process, which roughly revealed the applicability limits of the method and its potentialities. Experiments were carried out in standard autoclaves of various volume and also in glass ampules placed into an autoclave, which contained the same solvent as the contents of the ampule. The transition into the supercritical state was accomplished by increasing the reactor temperature and, hence, the internal pressure.

MCNP simulations of material exposure experiments (u)

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

Temple, Brian A

2010-12-08

Simulations of proposed material exposure experiments were performed using MCNP6. The experiments will expose ampules containing different materials of interest with radiation to observe the chemical breakdown of the materials. Simulations were performed to map out dose in materials as a function of distance from the source, dose variation between materials, dose variation due to ampule orientation, and dose variation due to different source energy. This write up is an overview of the simulations and will provide guidance on how to use the data in the spreadsheet.

Postirradiation thermocyclic loading of ferritic-martensitic structural materials

NASA Astrophysics Data System (ADS)

Belyaeva, L.; Orychtchenko, A.; Petersen, C.; Rybin, V.

Thermonuclear fusion reactors of the Tokamak-type will be unique power engineering plants to operate in thermocyclic mode only. Ferritic-martensitic stainless steels are prime candidate structural materials for test blankets of the ITER fusion reactor. Beyond the radiation damage, thermomechanical cyclic loading is considered as the most detrimental lifetime limiting phenomenon for the above structure. With a Russian and a German facility for thermal fatigue testing of neutron irradiated materials a cooperation has been undertaken. Ampule devices to irradiate specimens for postirradiation thermal fatigue tests have been developed by the Russian partner. The irradiation of these ampule devices loaded with specimens of ferritic-martensitic steels, like the European MANET-II, the Russian 05K12N2M and the Japanese Low Activation Material F82H-mod, in a WWR-M-type reactor just started. A description of the irradiation facility, the qualification of the ampule device and the modification of the German thermal fatigue facility will be presented.

Ampule tests to simulate glass corrosion in ambient temperature lithium batteries. Volume 2

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

Douglas, S.C.; Bunker, B.C.; Crafts, C.C.

1984-06-01

Glass corrosion in battery headers has been found to limit the shelf life of ambient temperature lithium batteries. Glass corrosion can lead to loss of battery electrolytes or to shorts across the conductive corrosion product. Tests have been conducted which simulate the corrosive environment in a battery by sealing headers attached to lithium metal into Pyrex ampules containing battery electrolyte. Using the ampule test, glass corrosion kinetics have been determined at 70/sup 0/C for the Li/SO/sub 2/, Li/SOCl/sub 2/, and Li/SOCl/sub 2/ + BrCl battery systems. Test results indicate that corrosion of commercial glass compositions is extensive in all electrolytesmore » tested, resulting in predicted battery failures after several months. Sandia's TA-23 glass corrodes at a much slower rate, indicating a projected battery lifetime of over five years in the Li/SO/sub 2/ system. Test results reveal that corrosion kinetics are sensitive to header polarization, stress, and configuration as well as glass composition.« less

Comparison of PCE and TCE disappearance in heated volatile organic analysis vials and flame-sealed ampules.

PubMed

Costanza, Jed; Pennell, Kurt D

2008-02-01

The rates of hydrolysis reported for tetrachloroethylene (PCE) and trichloroethylene (TCE) at elevated temperatures range over two orders-of-magnitude, where some of the variability may be due to the presence of a gas phase. Recent studies suggest that volatile organic analysis (VOA) vials provide a low-cost and readily available zero headspace system for measuring aqueous-phase hydrolysis rates. This work involved measuring rates of PCE and TCE disappearance and the corresponding appearance of dechlorination products in water-filled VOA vials and flame-sealed ampules incubated at 21 and 55 degrees C for up to 95.5 days. While PCE and TCE concentrations readily decreased in the VOA vials to yield first-order half lives of 11.2 days for PCE and 21.1 days for TCE at 55 degrees C, concentrations of anticipated dechlorination products, including chloride, remained constant or were not detected. The rate of PCE disappearance was 34 times faster in VOA vials at 55 degrees C compared to values obtained with flame-sealed ampules containing PCE-contaminated water. In addition, the concentration of TCE increased slightly in flame-sealed ampules incubated at 55 degrees C, while a decrease in TCE levels was observed in the VOA vials. The observed losses of PCE and TCE in the VOA vials were attributed to diffusion and sorption in the septa, rather than to dechlorination. These findings demonstrate that VOA vials are not suitable for measuring rates of volatile organic compound hydrolysis at elevated temperatures.

Evaluation of high-temperature and short-time sterilization of injection ampules by microwave heating.

PubMed

Sasaki, K; Honda, W; Miyake, Y

1998-01-01

The high-temperature and short-time sterilization by microwave heating with a continuous microwave sterilizer (MWS) was evaluated. The evaluation were performed with respect to: [1] lethal effect against microorganisms corresponding to F-value, and [2] reliability of MWS sterilization process. Bacillus stearothermophilus ATCC 7953 spores were used as the biological indicator and the heat-resistance of spores was evaluated with conventional heating method (121-129 degrees C). In MWS sterilization (125-135 degrees C), the actual lethal effect against B. stearothermophilus spores was almost in agreement with the F-value and the survival curve against the F-value was quite consistent with that for the autoclave. These results suggest that the actual lethal effect could be estimated by the F-value with heat-resistance parameters of spores from lower than actual temperatures and that there was no nonthermal effect of the microwave on B. stearothermophilus spores. The reliability of sterilization with the MWS was confirmed using more than 25,000 test ampules containing biological indicators. All biological indicators were killed, thus the present study shows that the MWS was completely reliable for all ampules.

Long-term study of volatile organic compound recovery from ampulated, dry, fortified soils

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

Minnich, M.M.; Zimmerman, J.H.; Schumacher, B.A.

1997-01-01

Our objective was to evaluate the stability and extractability of volatile organic compounds (VOCs) when fortified on dry soils and stored in sealed ampules. Two desiccator-dried soils were fortified with benzene, toluene, ethylbenzene, o-xylene, 1,1,1-trichloroethane (TCA), trichloroethene (TCE), tetrachloroethene (PCE), and 1,1,2,2-tetrachloroethane (TTCA) at 800 ng each VOC/g soil. The fortified soil was portioned into ampules, sealed, and stored in the dark at 25{degrees}C for up to 56 wk. Replicate ampules were analyzed after 2 d and 2,4,8,13,34, and 56 wk by two extraction procedures modified from the US Environmental Protection Agency`s (USEPA`s) low- and high-level purge-and-trap procedures (SW-846 Methodsmore » 5030/8021). The modified procedure (1-h methanol extraction at 25{degree}C prior to purge-and-trap analysis) yielded significantly higher recoveries of all compounds on both soils as compared with the low-level procedure, with the exception of benzene on the Charleston soil. Moreover, when measured by the high-level procedure, concentrations of benzene, toluene, ethylbenzene, and o-xylene (BTEX) remained relatively unchanged during the 56-wk study. Results indicate that the 1-h, 25{degrees}C methanol extraction was sufficient for extraction of the BTEX compounds from these soils. For the chlorinated compounds, regression analysis demonstrated significant trends of changing concentrations over time. Recoveries of TCA decreased at a rate of 3 and 4 ng/g/week and recoveries of TTCA decreased at rates of 8 and 17 ng/g/week on the Hayesville and Charleston soils, respectively. PCE concentrations did not show any significant concentration changes, while TCE concentrations increased at 6 and 7 ng/g/week for the Hayesville and Charleston soils, respectively. 19 refs., 2 figs., 5 tabs.« less

Heroin and methadone prescriptions from a London drug clinic over the first 15 years of operation (1968-1983): old records examined.

PubMed

Strang, John; Sheridan, Janie

2006-01-01

We charted changes in the prescriptions issued to opiate addicts in treatment at a London clinic over the first 15 years of operation of one of the new National Health Service (NHS) drug clinics established in 1968. Having located the original handwritten ledger records of prescriptions issued by the drug addict treatment clinic, an SPSS data file was created of the prescriptions given to each of the clinic patients each month over the period 1968-1983 to permit examination of changes over this 15-year period in the drugs prescribed (e.g., heroin, methadone), the form (e.g., injectable or oral), the daily doses, and the extent of multiple items for single patients (e.g., both injectable ampule and oral forms). For each month, a list was available of all current patients detailing which drug(s) they had received during that month, in what form(s) and what dose(s). These items were the basic units of study. We report changes over the 15-year period for which the data were available. For the first 5 years, more than half of the prescriptions were for heroin (diamorphine hydrochloride), with the remainder of the prescriptions mostly comprising oral methadone. After 1973, methadone ampules for injection were increasingly commonly prescribed and thereafter remained at about a quarter of the prescriptions for the remaining 10 years for which data are available, whereas heroin prescriptions declined over the mid-1970s to only 20%. From 1973 onward, oral methadone was increasingly prescribed, rising from approximately one third of prescriptions in the early 1970s to more than two thirds by the early 1980s. Individual patients often received more than one drug or form of drug: From 1969 onward, oral methadone was commonly prescribed as a supplement to heroin prescriptions. This same practice was widespread with prescriptions for methadone ampules prescribed as a supplement to heroin prescriptions. Daily doses of heroin were at a mean of from 160 to 540 mg, in contrast with means of 20 to 40 mg and 25 to 50 mg daily for the injectable methadone ampules and the oral methadone solution, respectively. Major changes occurred in the prescribing practices of this London drug clinic over the first 15 years of operation of the new NHS clinics. However, these changes did not occur overnight and can be seen to have been gradual evolutions of practice with the preservation of heroin prescription through the first 5 years and the subsequent move to increased prescribing of injectable methadone, with both these practices being overtaken by the subsequent increased prominence of oral methadone syrup as the main drug prescribed. Reference to the original records reveals a more interesting picture than might be evident from the potentially selective recall of contemporary or historical commentators.

Corrosion resistance of 0Kh18N10T steel in gadolinium nitrate solutions in the liquid regulation of the reactivity of nuclear reactors

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

Ganzha, V.D.; Konoplev, K.A.; Mashchetov, V.P.

1986-03-01

This study was carried out in connection with the preparation of the design for the PIK research reactor. The corrosion resistance of 0Kh18N10T steel in gadolinium nitrate solutions was tested in laboratory, ampule, and loop corrosion tests. At all stages of the tests, the authors investigated the effect produced on the corrosion processes by factors related to the technology of preparation of the equipment (mechanical working of the surfaces, welding, sensitizing, annealing, stressed state of the material, cracks, etc.). Ampule tests were conducted in order to determine the effect produced by reactor radiation and shutdown regimes on the corrosion resistancemore » of the steel. Special ampules made of 0Kh18N10T steel were filled with gadolinium nitrate solutions of various concentrations, sealed, and irradiated for a long period in the core of the VVR-M reactor at a temperature of 20-50 degrees C. The results of the tests are shown. The investigations showed that the corrosion of 0Kh18N10T steel in solutions of gadolinium nitrate is uniform, regardless of the state of the surface, the concentration of gadolinium nitrate, the duration of the tests, the action of the reactor radiation under static and dynamic conditions, and the presence of mechanical stresses.« less

Radiolytic decomposition of ammonium halides

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

Orlov, S.L.; Gromov, V.V.; Saunin, E.I.

1988-11-01

Chromatographic analyses were made of the gaseous products of the radiolysis of polycrystalline NH/sub 4/F, NH/sub 4/Cl, NH/sub 4/Br, and NH/sub 4/I, of particle size 0.25-0.5 mm. The irradiation was performed with /sup 60/Co ..sigma..-quanta, at room temperature in previously evacuated and sealed glass ampules. Determination was made of the amount of gas liberated into the space of the ampule during the irradiation, and of the amount retained in the crystal matrix and evolved on dissolution of the resulting samples in deaerated water. At the same time quantitative determinations of halogen were made by the thiosulfate method. It was shownmore » that hydrogen and nitrogen were formed in the radiolysis of all the compounds investigated. The yields are listed.« less

New stable perfluoroallyl radical from perfluoro-2,4-dimethyl-3-ethylpentene-2 and its photoconversion reactions

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

Shvedova, M.K.; Allayarov, S.R.; Barkalov, I.M.

1988-05-01

The thermally and chemically stable perfluoroally radical is formed in the radiolysis of perfluoro-2, 4-dimethyl-3-ethylpentene-2. A phototransformation of this radical into other radicals takes place under the action of UV light (/lambda/ < 300 nm) which are thermally unstable. Samples containing up to 90% FMP and 10% of its isomers were placed into ampules made of quartz or SK-4B glass, which gave to EPR signal after irradiation; the ampules were evacuated to a pressure of 0.13 Pa, frozen to 77 K, and irradiated with /sup 60/Co /lambda/-quanta at 77 K with doses up to 200 kGy. Irradiation with UV lightmore » was performed at 77 K with light from a DRSh-1000 lamp.« less

Determination of the /sup 237/Np(n, 2n) reaction cross section in the core of the BN-350 reactor

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

Goncharov, R.K.; Zvonarev, A.V.; Ivanov, V.I.

1987-05-01

Analysis of irradiated fuel (regular fuel elements and special ampule samples) makes it possible to obtain data on the neutron-physical characteristics that do not lend themselves to measurement in experiments with a low neutron flux. The authors studied samples of spent fuel from regular fuel elements and samples of /sup 236/U and /sup 237/Np irradiated in special ampules. We give the results of measurements of the ratio (sigma/sub n,2n/ + sigma/sub ..gamma..,n/)sigma/sub c/ for /sup 237/Np in different zones of the BN-350 reactor and the results of calculations performed using the neptunium group constants calculated from the data of themore » files ENDFB IV and ENDFB V« less

29 CFR 1915.98 - First aid.

Code of Federal Regulations, 2011 CFR

2011-07-01

... items: Gauze roller bandages, 1 inch and 2 inch. Gauze compress bandages, 4 inch. Adhesive bandages, 1 inch. Triangular bandage, 40 inch. Ammonia inhalants and ampules. Antiseptic applicators or swabs. Burn...

44 CFR Appendix 1 to Part 323 - List of Essential Survival Items

Code of Federal Regulations, 2014 CFR

2014-10-01

.... Laboratory glassware. Microscope and slides. Water purification apparatus. Group B None. ii. food Group A 1...) in drums, cans, ampules. Iodine tablets. Liquid chlorine, including containers. Chlorine compounds...

Fluid injection device for high-pressure systems

NASA Technical Reports Server (NTRS)

Copeland, E. J.; Ward, J. B.

1970-01-01

Screw activated device, consisting of a compressor, shielded replaceable ampules, a multiple-element rubber gland, and a specially constructed fluid line fitting, injects measured amounts of fluids into a pressurized system. It is sturdy and easily manipulated.

Insecticidal activity of neem oil against Gyropsylla spegazziniana (Hemiptera: Psyllidae) nymphs on Paraguay tea seedlings.

PubMed

Formentini, M A; Alves, L F A; Schapovaloff, M E

2016-01-01

Gyropsylla spegazziniana (Paraguay tea ampul) is one of the most important pests of Paraguay tea plants, and prohibition of synthetic insecticide use for control of this pest has led to the search for alternative methods. This laboratory study aimed to compare different control strategies for G. spegazziniana, utilizing a commercial neem seed oil product. Paraguay tea seedlings were treated with neem oil solution both pre- and post-infestation with 5th instar nymphs. The systemic action of neem oil was also evaluated by treating plant soil with the neem oil solution, followed by transfer of the insects to plants 24 h post-treatment. Spray treatments were effective against the pest, especially post-infestation (80% mortality), demonstrating the potential of neem oil for control of the Paraguay tea ampul. No significant effects were observed with respect to systemic activity.

Autoclave performance and practitioner knowledge of autoclave use: a survey of selected UK practices.

PubMed

Burke, F J; Coulter, W A; Cheung, S W; Palenik, C J

1998-04-01

It is essential that the dental surgery autoclave be tested regularly to ensure that it is operating at a temperature and pressure that will kill all microorganisms. The aims of this study were to investigate the knowledge of general dental practitioners on aspects of autoclave use, to examine their autoclaving routines, and to test the effectiveness of the sterilization cycle of their practice's autoclave. A 35-question questionnaire was distributed to 840 dental practitioners in the United Kingdom. They were also sent three spore test ampules with details of their function and instructions on their use. The practitioners were asked to use the spore test ampules in their own practice's autoclave and to return these for testing. Four hundred one questionnaires and associated spore test ampules were returned for analysis, a 47.7% response rate. Eight practice autoclaves (2.0%) failed to sterilize the spores. These practices were offered a retest following counseling. A total of 77.8% of respondents had received formal training in infection control. Of the 71.3% of respondents who stated that they check the performance of their autoclave routinely, 31.5% use a chemical strip every cycle, 17.5% use it once per day, and 30.4% use it once per week. However, only five respondents (1.2%) use a spore test; two of these respondents use it every cycle, one once per day, and two once per week. Further education of practitioners may be necessary to enhance their awareness of the need for routine checking of autoclave effectiveness.

The mechanical design of spider silks: from fibroin sequence to mechanical function.

PubMed

Gosline, J M; Guerette, P A; Ortlepp, C S; Savage, K N

1999-12-01

Spiders produce a variety of silks, and the cloning of genes for silk fibroins reveals a clear link between protein sequence and structure-property relationships. The fibroins produced in the spider's major ampullate (MA) gland, which forms the dragline and web frame, contain multiple repeats of motifs that include an 8-10 residue long poly-alanine block and a 24-35 residue long glycine-rich block. When fibroins are spun into fibres, the poly-alanine blocks form (&bgr;)-sheet crystals that crosslink the fibroins into a polymer network with great stiffness, strength and toughness. As illustrated by a comparison of MA silks from Araneus diadematus and Nephila clavipes, variation in fibroin sequence and properties between spider species provides the opportunity to investigate the design of these remarkable biomaterials.

[Economic impact of strategies using ephedrine prefilled syringes].

PubMed

Crégut-Corbaton, J; Malbranche, C; Guignard, M-H; Fagnoni, P

2013-11-01

Ephedrine is an emergency drug available in ampules and syringes need to be prepared in advance according to one of two strategies in our establishment: strategy 1 (S1: 1 ampule per patient) and strategy 2 (S2: 1 ampule per operating room). There are also prefilled syringes. Because of their high cost and conflicting results in the literature, we assessed the economic interest of using prefilled syringes compared with strategies S1 and S2. This was a prospective observational study. The consumption of ephedrine was recorded over two periods of 14 days: P1 with syringes prepared in advance according to S1 or S2 and P2 with the on-demand use of prefilled syringes. The cost of a syringe of ephedrine prepared in advance (nurse time preparation included) was evaluated at €1.65 vs. €3.57 for a prefilled syringe. In operating rooms using S1, the use of prefilled syringes reduced overall the cost per patient about €1.22 and global annual costs by 72% (€2830), while the decrease was about €0.32 for the cost per patient and about 47% (€2760) for global annual costs for operating rooms using S2. The interest of our study is that we investigated different supply strategies for ephedrine within a large number of operating rooms. In our establishment, it was decided to use prefilled syringes in operating rooms that used S1. As well as the economic interest, prefilled syringes contributed to improved safety and saved nursing time. Copyright © 2013 Société française d’anesthésie et de réanimation (Sfar). Published by Elsevier SAS. All rights reserved.

Effects of women's body mass index on in vitro fertilization success: a retrospective cohort study.

PubMed

Haghighi, Zahra; Rezaei, Zahra; Es-Haghi Ashtiani, Somayyeh

2012-07-01

The purpose of this study is to evaluate the influence of body mass index (BMI) on the reproductive outcomes and clinical pregnancy rate after in vitro fertilization (IVF). This retrospective study was performed on 230 women undergoing first cycle of standard IVF between October 2008 and February 2010. The patients were classified into three groups according to their BMI (BMI < 20 kg/m², 20 kg/m² < BMI < 27.9 kg/m² and BMI > 28 kg/m²). Information regarding clinical pregnancy was compared within these three groups. There was no significant relation between BMI and age, the number of aspirated follicles, transferred embryos, mature oocytes, days of taking human menopausal gonadotropin (HMG) ampules and the total number of HMG ampules among three BMI studied groups. Statistically significant difference was detected between BMI and endometrial thickness. BMI has no effect on IVF outcomes and clinical pregnancy after IVF. However, losing weight in obese women seems reasonable to prevent possible obstetrics complications.

A simple device for efficient transfer and unit dose packaging of Xe-127: concise communication.

PubMed

Kowalsky, R J; Dalton, D R; Saylor, W L

1978-04-01

An inexpensive system has been devised for the efficient transfer of Xe-127 gas from the manufacturer's ampule into individual dose vials for patient use. By displacing the gas with an aqueous solution, the initial transfer is made from an ampule of known activity into an evacuated serum vial of predetermined volume with transfer efficiency greater than 99%. A similar principle is used to transfer Xe-127 from the stock serum vial into individual dose vials, with total xenon recovery exceeding 98%. Ability to deliver the desired activity to each vial is within 90-110% of that predicted by calculation. Reproducibility in delivering a given activity was excellent, with all vials falling between 95 and 105% of the mean activity. Stability studies showed that 94% of the Xe-127 activity can be removed from the vials with only 6% absorbed in the rubber stopper after 5 wk of storage. The device costs less than $25.00 and can be constructed easily from common laboratory materials.

Gravimetric method for the determination of diclofenac in pharmaceutical preparations.

PubMed

Tubino, Matthieu; De Souza, Rafael L

2005-01-01

A gravimetric method for the determination of diclofenac in pharmaceutical preparations was developed. Diclofenac is precipitated from aqueous solution with copper(II) acetate in pH 5.3 (acetic acid/acetate buffer). Sample aliquots had approximately the same quantity of the drug content in tablets (50 mg) or in ampules (75 mg). The observed standard deviation was about +/- 2 mg; therefore, the relative standard deviation (RSD) was approximately 4% for tablet and 3% for ampule preparations. The results were compared with those obtained with the liquid chromatography method recommended in the United States Pharmacopoeia using the statistical Student's t-test. Complete agreement was observed. It is possible to obtain more precise results using higher aliquots, for example 200 mg, in which case the RSD falls to 1%. This gravimetric method, contrary to what is expected for this kind of procedure, is relatively fast and simple to perform. The main advantage is the absolute character of the gravimetric analysis.

Preparation of organic and water hydrogen for stable isotope analysis. Effects due to reaction vessels and zinc reagent

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

Schimmelmann, A.; DeNiro, M.J.

1993-03-15

Combustion of organic matter in sealed Pyrex, Vycor, and quartz ampules at temperatures between 520 and 900[degrees]C yields less than stoichiometric amounts of water. The loss of hydrogen to hydration reactions between water vapor and glass/quartz interferes with the determination of C/H and N/H elemental ratios in organic matter. The effect increases from quartz to Vycor to Pyrex, but the incomplete yield does not significantly affect the precision and accuracy of the determination of stable hydrogen isotope ratios. Reactions between water and Pyrex do not affect the conversion of water to hydrogen with zinc in Pyrex ampules at 500[degrees]C, whichmore » is quantitative, but even preoutgassed zinc contains a deuterium-depleted hydrogen blank. D/H ratios in hydrogen from the Zn method require a nonlinear correction to achieve compatibility with [delta]D values from the uranium method. 19 refs., 4 tabs.« less

40 CFR 265.315 - Special requirements for containers.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 25 2010-07-01 2010-07-01 false Special requirements for containers..., STORAGE, AND DISPOSAL FACILITIES Landfills § 265.315 Special requirements for containers. Unless they are very small, such as an ampule, containers must be either: (a) At least 90 percent full when placed in...

40 CFR 264.315 - Special requirements for containers.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 25 2010-07-01 2010-07-01 false Special requirements for containers... FACILITIES Landfills § 264.315 Special requirements for containers. Unless they are very small, such as an ampule, containers must be either: (a) At least 90 percent full when placed in the landfill; or (b...

21 CFR 522.1850 - Polysulfated glycosaminoglycan.

Code of Federal Regulations, 2012 CFR

2012-04-01

... § 522.1850 Polysulfated glycosaminoglycan. (a) Specifications. (1) Each 1-milliliter (mL) ampule of solution contains 250 milligrams (mg) polysulfated glycosaminoglycan. (2) Each mL of solution packaged in 5... weekly for up to 4 weeks (maximum of 8 injections). [72 FR 56896, Oct. 5, 2007, as amended at 74 FR 67816...

Failure analysis of fuze power supply

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

Menke, J.T.

1996-10-01

Batteries in storage which were used in electronic fuzes were found to be leaking after 5 years. The leaking battery ampules were made of copper and contained mixture of fluoboric acid and methylene bromide. The corrosion mechanism is described along with the testing/analysis required to simulate the field failures.

9 CFR 98.19 - Arrival and inspection at the port of entry.

Code of Federal Regulations, 2011 CFR

2011-01-01

... IMPORTATION OF CERTAIN ANIMAL EMBRYOS AND ANIMAL SEMEN Ruminant and Swine Embryos From Regions Where... with the original health certificate and the original import permit for the embryos. (b) The shipping container and all straws or ampules containing embryos must be made available to an inspector at the port of...

9 CFR 98.19 - Arrival and inspection at the port of entry.

Code of Federal Regulations, 2010 CFR

2010-01-01

... IMPORTATION OF CERTAIN ANIMAL EMBRYOS AND ANIMAL SEMEN Ruminant and Swine Embryos From Regions Where... with the original health certificate and the original import permit for the embryos. (b) The shipping container and all straws or ampules containing embryos must be made available to an inspector at the port of...

9 CFR 98.19 - Arrival and inspection at the port of entry.

Code of Federal Regulations, 2012 CFR

2012-01-01

... IMPORTATION OF CERTAIN ANIMAL EMBRYOS AND ANIMAL SEMEN Ruminant and Swine Embryos From Regions Where... with the original health certificate and the original import permit for the embryos. (b) The shipping container and all straws or ampules containing embryos must be made available to an inspector at the port of...

9 CFR 98.19 - Arrival and inspection at the port of entry.

Code of Federal Regulations, 2014 CFR

2014-01-01

... IMPORTATION OF CERTAIN ANIMAL EMBRYOS AND ANIMAL SEMEN Ruminant and Swine Embryos From Regions Where... with the original health certificate and the original import permit for the embryos. (b) The shipping container and all straws or ampules containing embryos must be made available to an inspector at the port of...

9 CFR 98.19 - Arrival and inspection at the port of entry.

Code of Federal Regulations, 2013 CFR

2013-01-01

... IMPORTATION OF CERTAIN ANIMAL EMBRYOS AND ANIMAL SEMEN Ruminant and Swine Embryos From Regions Where... with the original health certificate and the original import permit for the embryos. (b) The shipping container and all straws or ampules containing embryos must be made available to an inspector at the port of...

[Microfloral study of bull seminal fluid stored at low temperatures].

PubMed

Korudzhiĭski, N

1979-01-01

Hundred twenty three samples of bull semen fluid frozen at 196 degrees C including 83 plastic ampules, 20 granules and 20 plastic straws obtained from the containers of the insemination stations of 10 farms from the Sofia district were investigated. Two hundred twelve strains were isolated and identified as: Escherichia coli--25 strains, Hafnia--16 strains, Citrobacter, Enterobacter and Proteus mirabilis--9 strains of each. The remaining Gram-negative genera and species were more rarely encountered. Gram positive bacteria: Micrococcus--19 strains, Staphylococcus aureus--17 strains, Staph. epidermidis--15 strains, Bacillus cereus--15 strains, B. subtilis--12 strains. Other representatives of Gram-positive bacteria were also found but in lower percentages. Least bacteria were observed in semen fluid frozen in plastic straws and most--in plastic ampules which were mainly used until recently for cow insemination. It was established that the same bacteria isolated by other authors from fresh sperm were encountered in semen fluid stored at minus temperatures. The conclusion is made that semen fluid stored at low temperature is contaminated with bacteria. It is only natural that these bacteria are introduced in cow genitals by insemination.

Performance testing accountability measurements

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

Oldham, R.D.; Mitchell, W.G.; Spaletto, M.I.

The New Brunswick Laboratory (NBL) provides assessment support to the DOE Operations Offices in the area of Material Control and Accountability (MC and A). During surveys of facilities, the Operations Offices have begun to request from NBL either assistance in providing materials for performance testing of accountability measurements or both materials and personnel to do performance testing. To meet these needs, NBL has developed measurement and measurement control performance test procedures and materials. The present NBL repertoire of performance tests include the following: (1) mass measurement performance testing procedures using calibrated and traceable test weights, (2) uranium elemental concentration (assay)more » measurement performance tests which use ampulated solutions of normal uranyl nitrate containing approximately 7 milligrams of uranium per gram of solution, and (3) uranium isotopic measurement performance tests which use ampulated uranyl nitrate solutions with enrichments ranging from 4% to 90% U-235. The preparation, characterization, and packaging of the uranium isotopic and assay performance test materials were done in cooperation with the NBL Safeguards Measurements Evaluation Program since these materials can be used for both purposes.« less

Reanalysis of tritium production in a sphere of /sup 6/LiD irradiated by 14-MeV neutrons

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

Fawcett, L.R. Jr.

1985-08-01

Tritium production and activation of radiochemical detector foils in a sphere of /sup 6/LiD irradiated by a central source of 14-MeV neutrons has been reanalyzed. The /sup 6/LiD sphere consisted of 10 solid hemispherical nested shells with ampules of /sup 6/LiH, /sup 7/LiH, and activation foils located 2.2, 5, 7.7, 12.6, 20, and 30 cm from the center. The Los Alamos Monte Carlo Neutron Photon Transport Code (MCNP) was used to calculate neutron transport through the /sup 6/LiD, tritium production in the ampules, and foil activation. The MCNP input model was three-dimensional and employed ENDF/B-V cross sections for transport, tritiummore » production, and (where available) foil activation. The reanalyzed experimentally observed-to-calculated values of tritium production were 1.053 +- 2.1% in /sup 6/LiH and 0.999 +- 2.1% in /sup 7/LiH. The recalculated foil activation observed-to-calculated ratios were not generally improved over those reported in the original analysis.« less

Addition of Sodium Bicarbonate to Irrigation Solution May Assist in Dissolution of Uric Acid Fragments During Ureteroscopy.

PubMed

Paonessa, Jessica E; Williams, James C; Lingeman, James E

2018-04-01

We hypothesized that adding sodium bicarbonate (bicarb) to normal saline (NS) irrigation during ureteroscopy in patients with uric acid (UA) nephrolithiasis may assist in dissolving small stone fragments produced during laser lithotripsy. In vitro testing was performed to determine whether dissolution of UA fragments could be accomplished within 1 hour. In total 100% UA renal calculi were fragmented, filtered, and separated by size. Fragment sizes were <0.5 mm and 0.5 to 1 mm. Similar amounts of stone material were agitated in solution at room temperature. Four solutions were tested (NS, NS +1 ampule bicarb/L, NS +2, NS +3). Both groups were filtered to remove solutions after fixed periods. Filtered specimens were dried and weighed. Fragment dissolution rates were calculated as percent removed per hour. Additional testing was performed to determine whether increasing the temperature of solution affected dissolution rates. For fragments <0.5 mm, adding 2 or 3 bicarb ampules/L NS produced a dissolution rate averaging 91% ± 29% per hour. This rate averaged 226% faster than NS alone. With fragments 0.5 to 1 mm, addition of 2 or 3 bicarb ampules/L NS yielded a dissolution rate averaging 22% ± 7% per hour, which was nearly five times higher than NS alone. There was a trend for an increase in mean dissolution rate with higher temperature but this increase was not significant (p = 0.30). The addition of bicarbonate to NS more than doubles the dissolution rate of UA stone fragments and fragments less than 0.5 mm can be completely dissolved within 1 hour. Addition of bicarb to NS irrigation is a simple and inexpensive approach that may assist in the dissolution of UA fragments produced during ureteroscopic laser lithotripsy. Further studies are needed to determine whether a clinical benefit exists.

Role of pharmacists in reducing occupational exposure to HIV.

PubMed

Morris, S N

1989-12-01

The role of pharmacists in reducing the occupational hazard of human immunodeficiency virus (HIV) transmission via needle-stick injuries is described. Some 40% of all pharmaceuticals used in hospitals are now administered by injection, and sales of large-volume injectable drug products continue to grow. Most needle-stick injuries in which health-care workers are exposed to HIV-contaminated blood occur during recapping of used needles, picking up and carrying the needle, or placing it in a receptacle. Pharmacists are responsible not only for the purchase, storage, dispensing, and use of drug products but also for providing information about their administration and safe disposal. Single-use vials, ampuls, and prefilled syringes must all be evaluated for availability, ease of use, and disposal. A major factor in drug-purchasing decisions must be the safety of nurses. Syringes that have been redesigned to eliminate the need for recapping offer a major safety advantage. Needle disposal units should be made more conveniently accessible. Pharmacists can help prevent the transmission of HIV to health-care workers by using their influence as educators and decision makers to reduce the risk of needle-stick injury.

Mathematical model for the Bridgman-Stockbarger crystal growing system

NASA Technical Reports Server (NTRS)

Roberts, G. O.

1986-01-01

In a major technical breakthrough, a computer model for Bridgman-Stockbarger crystal growth was developed. The model includes melt convection, solute effects, thermal conduction in the ampule, melt, and crystal, and the determination of the curved moving crystal-melt interface. The key to the numerical method is the use of a nonuniform computational mesh which moves with the interface, so that the interface is a mesh surface. In addition, implicit methods are used for advection and diffusion of heat, concentration, and vorticity, for interface movement, and for internal gracity waves. This allows large time-steps without loss of stability or accuracy. Numerical results are presented for the interface shape, temperature distribution, and concentration distribution, in steady-state crystl growth. Solutions are presented for two test cases using water, with two different salts in solution. The two diffusivities differ by a factor of ten, and the concentrations differ by a factor of twenty.

Dynamic behaviour of silks: Nature's precision nanocomposites

NASA Astrophysics Data System (ADS)

Drodge, D. R.; Mortimer, B.; Siviour, C. R.; Holland, C.

2012-08-01

Silk is often cited as a material worth imitating, due to its high strength and toughness. In order to produce a synthetic analogue, or enhanced natural version, the microstructural basis of these properties must be understood. Current understanding is that silk deforms through the detachment of nano-scale crystallites, in the manner of a damaged composite. This picture forms the basis for constitutive models, but validation data is limited to low strain-rates. Here we present a programme of research in which high-rate behaviour is studied through ballistic impact experiments. These have been applied to the silk of the Bombyx mori moth, as harvested from cocoons, and to the major ampullate thread of the golden orb weaver spider Nephila edulis. Longitudinal wave-speeds, and air drag coefficients, have been calculated for selected cases. Differences between the response of various silks and a similar synthetic fibre, nylon, are discussed, and future plans are presented.

Non-invasive determination of the complete elastic moduli of spider silks

NASA Astrophysics Data System (ADS)

Koski, Kristie J.; Akhenblit, Paul; McKiernan, Keri; Yarger, Jeffery L.

2013-03-01

Spider silks possess nature’s most exceptional mechanical properties, with unrivalled extensibility and high tensile strength. Unfortunately, our understanding of silks is limited because the complete elastic response has never been measured—leaving a stark lack of essential fundamental information. Using non-invasive, non-destructive Brillouin light scattering, we obtain the entire stiffness tensors (revealing negative Poisson’s ratios), refractive indices, and longitudinal and transverse sound velocities for major and minor ampullate spider silks: Argiope aurantia, Latrodectus hesperus, Nephila clavipes, Peucetia viridans. These results completely quantify the linear elastic response for all possible deformation modes, information unobtainable with traditional stress-strain tests. For completeness, we apply the principles of Brillouin imaging to spatially map the elastic stiffnesses on a spider web without deforming or disrupting the web in a non-invasive, non-contact measurement, finding variation among discrete fibres, junctions and glue spots. Finally, we provide the stiffness changes that occur with supercontraction.

Reception and study of lunar surface material in inert gas medium. [considering laboratory vacuum receiving chamber

NASA Technical Reports Server (NTRS)

Surkov, Y. A.; Rudnitskiy, Y. M.; Glotov, V. A.

1974-01-01

The reception and study of lunar material returned by the Luna 16 space station is described. The layout of a vacuum receiving chamber for working with material in a helium atmosphere is examined along with the main operations involved in extracting the material from the ampule and drill.

Preparation of sterile xenon-133 in saline for tissue perfusion studies

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

DiPiazza, H.J.; Harbert, J.C.

1983-11-01

A simple, inexpensive method of obtaining Xe-133 in sterile saline is presented. The method uses commercial xenon ampules supplied for pulmonary ventilation studies. As much as 10% of the gas activity can be recovered per aliquot by cooling the saline to 4/sup 0/C. The specific activities obtained are adequate for most tissue perfusion studies.

Fate of TCE in heated Fort Lewis soil.

PubMed

Costanza, Jed; Fletcher, Kelly E; Löffler, Frank E; Pennell, Kurt D

2009-02-01

This study explores the transformation of trichloroethene (TCE) caused by heating contaminated soil and groundwater samples obtained from the East Gate Disposal Yard (EGDY) located in Fort Lewis, WA. After field samples transferring into glass ampules and introducing 1.5 micromol of TCE, the sealed ampules were incubated at temperatures of 25, 50, and 95 degrees C for periods of up to 95.5 days. Although TCE was completely transformed into cis-1,2-dichloroethene (cis-DCE) after 42 days at 25 degrees C by microbial activity, this transformation was not observed at 50 or 95 degrees C. Chloride levels increased after 42 days at 25 degrees C corresponding to the mass of TCE transformed to cis-DCE, were constant at 50 degrees C, and increased at 95 degrees C yielding a TCE degradation half-life of 1.6-1.9 years. These findings indicate that indigenous microbes contribute to the partial dechlorination of TCE to cis-DCE at temperatures of less than 50 degrees C, whereas interphase mass transfer and physical recovery of TCE will predominate over in situ degradation processes at temperatures of greater than 50 degrees C during thermal treatment at the EGDY site.

Improved method for the determination of nonpurgeable suspended organic carbon in natural water by silver filter filtration, wet chemical oxidation, and infrared spectrometry

USGS Publications Warehouse

Burkhardt, Mark R.; Brenton, Ronald W.; Kammer, James A.; Jha, Virenda K.; O'Mara-Lopez, Peggy G.; Woodworth, Mark T.

1999-01-01

Precision and accuracy are reported for the first time for the analysis of nonpurgeable suspended organic carbon by silver membrane filtration followed by wet chemical oxidation. A water sample is pressure filtered through a 0.45‐μm‐pore‐size, 47‐mm‐diameter silver membrane filter. The silver membrane filter then is cut into ribbons and placed in a flame‐sealable glass ampule. The organic material trapped on the membrane filter strips is acidified, purged with oxygen to remove inorganic carbonates and volatile organic compounds, and oxidized to carbon dioxide (CO2) using phosphoric acid and potassium persulfate in the sealed glass ampule. The resulting CO2 is measured by a nondispersive infrared CO2 detector. The amount of CO2 is proportional to the concentration of chemically oxidizable nonpurgeable organic carbon in the environmental water sample. The quantitation and method detection limit for routine analysis is 0.2 mg/L. The average percent recovery in five representative matrices was 97 ± 11%. The errors associated with sampling and sample preparation of nonpurgeable suspended organic carbon are also described.

Monitor for Sterilization Procedures

DTIC Science & Technology

2001-10-25

were tested using ampules of Bacillus stearothermophilus spores commercially manufactured by Barnstead/Thermolyne for testing sterilization procedures...Monitor for Sterilization Procedures F. Cleary1,2, H.-Y. Mason2, C. Estes2, A. Duncan2, W. Ellis, Jr.2 and L. Powers2 1Moses Brown High School...accurate determination of the efficacy of sterilization procedures is demonstrated using a hand-held instrument based on the intrinsic fluorescence of

[Spectrophotometric determination of prodigiozan in ampule solutions].

PubMed

Shchedrina, L E; Brutko, L I; Rastunova, G A; Shcherbakova, E G

1984-06-01

Based on a study of the absorption properties of prodigiosan it has been shown that its UV absorption spectrum is characterized by an arm at 250-260 nm with an inflection point at 260 nm. The concentration ranges within which the optical density of prodigiosan solution obeyed the Bouguer-Lambert-Beer law were measured. This allowed the development of a quantitative spectrophotometric method for determination of prodigiosan in ampouled solutions.

Purification of sulfide-alkali effluent with the aid of ionizing radiation. [Gamma radiation

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

Petryaev, E.P.; Gerasimovich, O.A.; Kovalevskaya, A.M.

1984-03-01

The treatment of sulfide-alkali effluent under the effect of ionizing radiation was investigated. The source was an LMB-..gamma..-1M ..gamma..-apparatus with /sup 137/Cs source. The dose rate was 52 rad/s. Irradiation was done in glass ampules and in vessels allowing bubbling with air and irradiation to be carried out at the same time. 7 references, 1 figure, 1 table.

The feasibility of single-port laparoscopic appendectomy using a solo approach: a comparative study.

PubMed

Kim, Say-June; Choi, Byung-Jo; Jeong, Wonjun; Lee, Sang Chul

2016-03-01

To investigate the feasibility and safety of solo surgery with single-port laparoscopic appendectomy, which is termed herein solo-SPLA (solo-single-port laparoscopic appendectomy). This study prospectively collected and retrospectively analyzed data from patients who had undergone either non-solo-SPLA (n = 150) or solo-SPLA (n = 150). Several devices were utilized for complete, skin-to-skin solo-SPSA, including a Lone Star Retractor System and an adjustable mechanical camera holder. Operating times were not significantly different between solo- and non-solo-SPLA (45.0 ± 21.0 minutes vs. 46.7 ± 26.1 minutes, P = 0.646). Most postoperative variables were also comparable between groups, including the necessity for intravenous analgesics (0.7 ± 1.2 ampules [solo-SPLA] vs. 0.9 ± 1.5 ampules [non-solo-SPLA], P = 0.092), time interval to gas passing (1.3 ± 1.0 days vs. 1.4 ± 1.0 days, P = 0.182), and the incidence of postoperative complications (4.0% vs. 8.7%, P = 0.153). Moreover, solo-SPLA effectively lowered the operating cost by reducing surgical personnel expenses. Solo-SPLA economized staff numbers and thus lowered hospital costs without lengthening of operating time. Therefore, solo-SPLA could be considered a safe and feasible alternative to non-solo-SPLA.

Physical and biological regulation of neuron regenerative growth and network formation on recombinant dragline silks

DOE PAGES

An, Bo; Tang-Schomer, Min D.; Huang, Wenwen; ...

2015-02-11

In this paper, recombinant spider silks produced in transgenic goat milk were studied as cell culture matrices for neuronal growth. Major ampullate spidroin 1 (MaSp1) supported neuronal growth, axon extension and network connectivity, with cell morphology comparable to the gold standard poly-lysine. In addition, neurons growing on MaSp1 films had increased neural cell adhesion molecule (NCAM) expression at both mRNA and protein levels. The results indicate that MaSp1 films present useful surface charge and substrate stiffness to support the growth of primary rat cortical neurons. Moreover, a putative neuron-specific surface binding sequence GRGGL within MaSp1 may contribute to the biologicalmore » regulation of neuron growth. These findings indicate that MaSp1 could regulate neuron growth through its physical and biological features. Finally, this dual regulation mode of MaSp1 could provide an alternative strategy for generating functional silk materials for neural tissue engineering.« less

Physical and biological regulation of neuron regenerative growth and network formation on recombinant dragline silks

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

An, Bo; Tang-Schomer, Min D.; Huang, Wenwen

In this paper, recombinant spider silks produced in transgenic goat milk were studied as cell culture matrices for neuronal growth. Major ampullate spidroin 1 (MaSp1) supported neuronal growth, axon extension and network connectivity, with cell morphology comparable to the gold standard poly-lysine. In addition, neurons growing on MaSp1 films had increased neural cell adhesion molecule (NCAM) expression at both mRNA and protein levels. The results indicate that MaSp1 films present useful surface charge and substrate stiffness to support the growth of primary rat cortical neurons. Moreover, a putative neuron-specific surface binding sequence GRGGL within MaSp1 may contribute to the biologicalmore » regulation of neuron growth. These findings indicate that MaSp1 could regulate neuron growth through its physical and biological features. Finally, this dual regulation mode of MaSp1 could provide an alternative strategy for generating functional silk materials for neural tissue engineering.« less

Inducing β-Sheets Formation in Synthetic Spider Silk Fibers by Aqueous Post-Spin Stretching

PubMed Central

Hinman, Michael B.; Holland, Gregory P.; Yarger, Jeffery L.; Lewis, Randolph V.

2012-01-01

As a promising biomaterial with numerous potential applications, various types of synthetic spider silk fibers have been produced and studied in an effort to produce manmade fibers with mechanical and physical properties comparable to those of native spider silk. In this study, two recombinant proteins based on Nephila clavipes Major ampullate Spidroin 1 (MaSp1) consensus repeat sequence were expressed and spun into fibers. Mechanical test results showed that fiber spun from the higher molecular weight protein had better overall mechanical properties (70 KD versus 46 KD), whereas postspin stretch treatment in water helped increase fiber tensile strength significantly. Carbon-13 solid-state NMR studies of those fibers further revealed that the postspin stretch in water promoted protein molecule rearrangement and the formation of β-sheets in the polyalanine region of the silk. The rearrangement correlated with improved fiber mechanical properties and indicated that postspin stretch is key to helping the spider silk proteins in the fiber form correct secondary structures, leading to better quality fibers. PMID:21574576

Structure and function of the major ampullate spinning duct of the golden orb weaver, Nephila edulis.

PubMed

Davies, G J G; Knight, D P; Vollrath, F

2013-10-01

Silks are fibres produced by spiders, some insects and even a crustacean, and are formed from protein solution by a pulltrusion process that is not well understood. Here we describe three aspects of the functional anatomy of the spinning apparatus in a spider: (i) changes in the diameter of the duct of the silk gland along its length for individuals at different stages of development, (ii) the correlation between the morphology of the duct and size and (iii) changes in the thickness of the wall of the duct. We conclude that in the distal part of the duct both the lumen's geometry and change in diameter with distance remains remarkably constant as the duct increases in length from moult to moult as the spider grows. This suggests constancy in the region where the nascent silk filament is drawn down within the lumen of the duct, which is likely to be fundamental for forming strong and tough fibres. Copyright © 2013 Elsevier Ltd. All rights reserved.

Physical and biological regulation of neuron regenerative growth and network formation on recombinant dragline silks.

PubMed

An, Bo; Tang-Schomer, Min; Huang, Wenwen; He, Jiuyang; Jones, Justin; Lewis, Randolph V; Kaplan, David L

2015-04-01

Recombinant spider silks produced in transgenic goat milk were studied as cell culture matrices for neuronal growth. Major ampullate spidroin 1 (MaSp1) supported neuronal growth, axon extension and network connectivity, with cell morphology comparable to the gold standard poly-lysine. In addition, neurons growing on MaSp1 films had increased neural cell adhesion molecule (NCAM) expression at both mRNA and protein levels. The results indicate that MaSp1 films present useful surface charge and substrate stiffness to support the growth of primary rat cortical neurons. Moreover, a putative neuron-specific surface binding sequence GRGGL within MaSp1 may contribute to the biological regulation of neuron growth. These findings indicate that MaSp1 could regulate neuron growth through its physical and biological features. This dual regulation mode of MaSp1 could provide an alternative strategy for generating functional silk materials for neural tissue engineering. Copyright © 2015 Elsevier Ltd. All rights reserved.

Apparatus and method for downhole injection of radioactive tracer

DOEpatents

Potter, R.M.; Archuleta, J.; Fink, C.F.

The disclosure relates to downhole injection of radioactive /sup 82/Br and monitoring its progress through fractured structure to determine the nature thereof. An ampule containing granular /sup 82/Br is remotely crushed and water is repeatedly flushed through it to cleanse the instrument as well as inject the /sup 82/Br into surrounding fractured strata. A sensor in a remote horehole reads progress of the radioactive material through fractured structure.

Apparatus and method for downhole injection of radioactive tracer

DOEpatents

Potter, Robert M.; Archuleta, Jacobo R.; Fink, Conrad F.

1983-01-01

The disclosure relates to downhole injection of radioactive .sup.82 Br and monitoring its progress through fractured structure to determine the nature thereof. An ampule containing granular .sup.82 Br is remotely crushed and water is repeatedly flushed through it to cleanse the instrument as well as inject the .sup.82 Br into surrounding fractured strata. A sensor in a remote borehole reads progress of the radioactive material through fractured structure.

Optical diagnostics of mercuric iodide crystal growth

NASA Astrophysics Data System (ADS)

Burger, A.; Morgan, S. H.; Silberman, E.; Nason, D.

Two optical methods were recently developed for in situ monitoring of the growth process of mercuric iodide crystals. The first method uses resonance fluorescence spectroscopy (RFS) for the determination of iodine vapor present in the growth ampule, which is an important parameter in determining the stoichiometry, and therefore the quality of the crystals. The second method, Reflectance Spectroscopy Thermometry (RST) measures the crystal face temperature with a percent accuracy of plus or minus 1.5 C.

Optical diagnostics of mercuric iodide crystal growth

NASA Astrophysics Data System (ADS)

Burger, Arnold; Morgan, Steven H.; Silberman, Enrique; Nason, Donald

1991-12-01

Two optical methods were recently developed for in situ monitoring of the growth process of mercuric iodide crystals. The first method uses resonance fluorescence spectroscopy (RFS) for the determination of iodine vapor present in the growth ampule, which is an important parameter in determining the stoichiometry, and therefore the quality of the crystals. The second method, reflectance spectroscopy thermometry (RST) measures the crystal face temperature with a present accuracy of +/- 1.5 degree(s)C.

Rapid Diagnosis of Arbovirus and Arenavirus Infections by Immunofluorescence.

DTIC Science & Technology

1980-01-01

addition to Banzi virus in the blood of viremic mice, other viruses were tested with a view to correlate in an amplifying cell culture system the result of... Virus identification. Two viruses , F-41451 and Aus-CF 122, partially identified at the originating laboratories, were submitted to YARU for final...two ampules of the corresponding virus stocks and 6 x 0.5 ml of hyperimmune mouse serum were included In the shipment. The viruses and cells used and

The feasibility of single-port laparoscopic appendectomy using a solo approach: a comparative study

PubMed Central

Kim, Say-June; Choi, Byung-Jo; Jeong, Wonjun

2016-01-01

Purpose To investigate the feasibility and safety of solo surgery with single-port laparoscopic appendectomy, which is termed herein solo-SPLA (solo-single-port laparoscopic appendectomy). Methods This study prospectively collected and retrospectively analyzed data from patients who had undergone either non-solo-SPLA (n = 150) or solo-SPLA (n = 150). Several devices were utilized for complete, skin-to-skin solo-SPSA, including a Lone Star Retractor System and an adjustable mechanical camera holder. Results Operating times were not significantly different between solo- and non-solo-SPLA (45.0 ± 21.0 minutes vs. 46.7 ± 26.1 minutes, P = 0.646). Most postoperative variables were also comparable between groups, including the necessity for intravenous analgesics (0.7 ± 1.2 ampules [solo-SPLA] vs. 0.9 ± 1.5 ampules [non-solo-SPLA], P = 0.092), time interval to gas passing (1.3 ± 1.0 days vs. 1.4 ± 1.0 days, P = 0.182), and the incidence of postoperative complications (4.0% vs. 8.7%, P = 0.153). Moreover, solo-SPLA effectively lowered the operating cost by reducing surgical personnel expenses. Conclusion Solo-SPLA economized staff numbers and thus lowered hospital costs without lengthening of operating time. Therefore, solo-SPLA could be considered a safe and feasible alternative to non-solo-SPLA. PMID:26942160

Integrated Real Time Contamination Monitor IRTCM

NASA Technical Reports Server (NTRS)

Luttges, W. E.

1976-01-01

Engineering and design work was performed on a monitoring device for particulate and gas contamination to be used in the space shuttle cargo area during launch at altitudes up to 50 km and during return phases of the flight. The gas sampling device consists of ampules filled with specific absorber materials which are opened and/or sealed at preprogrammed intervals. The design eliminates the use of valves which, according to experiments, are never sealing properly at hard vacuum. Methods of analysis including in-flight measuring possibilities are discussed.

Trends and anomalies in gas evolution from coal samples

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

Vorres, K.S.

1993-09-01

As part of the stability studies on these sealed samples a number of the samples were given to the Analytical Chemistry Laboratory at ANL for periodic gas analysis. 1. Higher rank coals evolve methane, and lower rank coals evolve carbon dioxide with some evolution of both gases for the intermediate ranks. 2. The evolution proceeds over times of years for pulverized coals in sealed ampules. 3. Gas concentrations are higher above -20 mesh samples than above -100 mesh material. 4. Carbon monoxide is not evolved.

Calorimetry Studies of Ammonia, Nitric Acid, and Ammonium Nitrate

DTIC Science & Technology

1979-10-01

50 microns of Hg. Glass ampules containing NH4NO3were filled in the dry box and then flame-sealed under a nitrogen atmosphere. A Karl - Fischer titration...was standardized by potentiometric titration against standard 1 N HCI, For calorimetric measurements, samples were transferred by syringe into weighed... potentiometric titration against standard 1 N NaOH, was 99.6 + 0.2 wt% HNO3. As a measure of tte extent of reaction with the wall oTthe3* calorimeter, HNO3

Low-temperature, high yield synthesis, and convenient isolation of the high-electron-density cluster compound Ta6Br14.8H2O for use in biomacromolecular crystallographic phase determination.

PubMed

Hay, Daniel N T; Messerle, Louis

2002-09-01

Reduction of TaBr(5) with Ga in the presence of KBr in a sealed borosilicate ampule at 400 degrees, followed by aqueous Soxhlet extraction and addition of stannous bromide and hydrobromic acid to the extract, yielded Ta(6)Br(14).8H(2)O in 80-84% yield. The new procedure provides a convenient, low temperature, high yield route to the synthesis of the title compound from inexpensive precursors.

Spider Silk: Mother Nature's Bio-Superlens

NASA Astrophysics Data System (ADS)

Monks, James N.; Yan, Bing; Hawkins, Nicholas; Vollrath, Fritz; Wang, Zengbo

2016-09-01

This paper demonstrates a possible new microfiber bio near field lens that uses minor ampullate spider silk,spun from the Nephila edulis spider, to create a real time image of a surface using near field optical techniques. The microfiber bio lens is the world's first natural superlens created by exploring biological materials. The resolution of the surface image overcomes the diffraction limit, with the ability to resolve patterns at 100 nm under a standard white light source in reflection mode. This resolution offers further developments in superlens technology and paves the way for new bio optics.

Impact of oxygen dissolved at bottling and transmitted through closures on the composition and sensory properties of a Sauvignon Blanc wine during bottle storage.

PubMed

Lopes, Paulo; Silva, Maria A; Pons, Alexandre; Tominaga, Takatoshi; Lavigne, Valérie; Saucier, Cédric; Darriet, Philippe; Teissedre, Pierre-Louis; Dubourdieu, Denis

2009-11-11

This work outlines the results from an investigation to determine the effect of the oxygen dissolved at bottling and the specific oxygen barrier properties of commercially available closures on the composition, color and sensory properties of a Bordeaux Sauvignon Blanc wine during two years of storage. The importance of oxygen for wine development after bottling was also assessed using an airtight bottle ampule. Wines were assessed for the antioxidants (SO(2) and ascorbic acid), varietal thiols (4-mercapto-4-methylpentan-2-one, 3-mercaptohexan-1-ol), hydrogen sulfide and sotolon content, and color throughout 24 months of storage. In addition, the aroma and palate properties of wines were also assessed. The combination of oxygen dissolved at bottling and the oxygen transferred through closures has a significant effect on Sauvignon Blanc development after bottling. Wines highly exposed to oxygen at bottling and those sealed with a synthetic, Nomacorc classic closure, highly permeable to oxygen, were relatively oxidized in aroma, brown in color, and low in antioxidants and volatile compounds compared to wines sealed with other closures. Conversely, wines sealed under more airtight conditions, bottle ampule and screw cap Saran-tin, have the slowest rate of browning, and displayed the greatest contents of antioxidants and varietal thiols, but also high levels of H(2)S, which were responsible for the reduced dominating character found in these wines, while wines sealed with cork stoppers and screw cap Saranex presented negligible reduced and oxidized characters.

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

An, Bo; Jenkins, Janelle E; Sampath, Sujatha

Dragline silk from orb-weaving spiders is a copolymer of two large proteins, major ampullate spidroin 1 (MaSp1) and 2 (MaSp2). The ratio of these proteins is known to have a large variation across different species of orb-weaving spiders. NMR results from gland material of two different species of spiders, N. clavipes and A. aurantia, indicates that MaSp1 proteins are more easily formed into β-sheet nanostructures, while MaSp2 proteins form random coil and helical structures. To test if this behavior of natural silk proteins could be reproduced by recombinantly produced spider silk mimic protein, recombinant MaSp1/MaSp2 mixed fibers as well asmore » chimeric silk fibers from MaSp1 and MaSp2 sequences in a single protein were produced based on the variable ratio and conserved motifs of MaSp1 and MaSp2 in native silk fiber. Mechanical properties, solid-state NMR, and XRD results of tested synthetic fibers indicate the differing roles of MaSp1 and MaSp2 in the fiber and verify the importance of postspin stretching treatment in helping the fiber to form the proper spatial structure.« less

Crystal face temperature determination means

DOEpatents

Nason, D.O.; Burger, A.

1994-11-22

An optically transparent furnace having a detection apparatus with a pedestal enclosed in an evacuated ampule for growing a crystal thereon is disclosed. Temperature differential is provided by a source heater, a base heater and a cold finger such that material migrates from a polycrystalline source material to grow the crystal. A quartz halogen lamp projects a collimated beam onto the crystal and a reflected beam is analyzed by a double monochromator and photomultiplier detection spectrometer and the detected peak position in the reflected energy spectrum of the reflected beam is interpreted to determine surface temperature of the crystal. 3 figs.

Unsuspected Clenbuterol Toxicity in a Patient Using Intramuscular Testosterone

PubMed Central

Griswold, Matthew K.; Blohm, Eike; Cross, Roderick; Boyer, Edward W.; Carey, Jennifer L.

2017-01-01

Clenbuterol is a beta-agonist that has been abused by fitness-oriented individuals for muscle growth and weight loss. We report a case of a 46-year-old man who presented tachycardic, hypokalemic, and hyperglycemic after injecting testosterone obtained from Brazil. He developed refractory hypotension and was started on an esmolol infusion for suspected beta-agonist toxicity. Laboratory analysis showed a detectable clenbuterol serum concentration. Analysis of an unopened ampule contained boldenone undecylenate, clenbuterol, and vitamin E. This case illustrates a novel exposure that caused beta-agonist toxicity and was treated successfully with rapid-onset beta blocker. PMID:29849287

Using the Estimating Supplies Program to Develop Materiel Solutions for the U.S. Air Force Aeromedical Evacuation In-Flight Kit (FFQDM)

DTIC Science & Technology

2008-07-07

Ibuprofen 800-mg tablet. Because of several negative side effects, Chlorpromazine HCL INJ can be replaced with Haloperidol HCL INJ or Promethazine HCL...CART 10S EA 6505013548591 FLUMAZENIL INJ 0.1MG/ML 10ML VI 10S VI 6505002688530 HALOPERIDOL INJ 5MG/ML 1ML AMPUL 10S AM 6505001538480 HYDROGEN...DIAZEPAM TAB 5MG INDIVIDUALLY SEALED 100S TB 6505013548591 FLUMAZENIL INJ 0.1MG/ML 10ML VI 10S VI 6505002688530 HALOPERIDOL INJ 5MG/ML 1ML AMP 10S AM

In situ temperature measurement of. alpha. -mercuric iodide by reflection spectroscopy

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

Nason, D.; Burger, A.

1991-12-30

Crystal face temperatures of single crystals of {alpha}-HgI{sub 2} growing in transparent ampules by physical vapor transport have been measured, {ital in} {ital situ}, by a novel, noncontact method which may be called reflectance spectroscopy thermometry. The method is based on the temperature dependence of the energy of the free-exciton peak as detected with a low-energy reflected beam. As presently configured, the accuracy is {plus minus}1.5 {degree}C for a slowly varying surface temperature. The method has potential for noncontact temperature measurement in some systems for which pyrometry is unsatisfactory.

[Expression changes of major outer membrane protein antigens in Leptospira interrogans during infection and its mechanism].

PubMed

Zheng, Linli; Ge, Yumei; Hu, Weilin; Yan, Jie

2013-03-01

To determine expression changes of major outer membrane protein(OMP) antigens of Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai strain Lai during infection of human macrophages and its mechanism. OmpR encoding genes and OmpR-related histidine kinase (HK) encoding gene of L.interrogans strain Lai and their functional domains were predicted using bioinformatics technique. mRNA level changes of the leptospiral major OMP-encoding genes before and after infection of human THP-1 macrophages were detected by real-time fluorescence quantitative RT-PCR. Effects of the OmpR-encoding genes and HK-encoding gene on the expression of leptospiral OMPs during infection were determined by HK-peptide antiserum block assay and closantel inhibitive assays. The bioinformatics analysis indicated that LB015 and LB333 were referred to OmpR-encoding genes of the spirochete, while LB014 might act as a OmpR-related HK-encoding gene. After the spirochete infecting THP-1 cells, mRNA levels of leptospiral lipL21, lipL32 and lipL41 genes were rapidly and persistently down-regulated (P <0.01), whereas mRNA levels of leptospiral groEL, mce, loa22 and ligB genes were rapidly but transiently up-regulated (P<0.01). The treatment with closantel and HK-peptide antiserum partly reversed the infection-based down-regulated mRNA levels of lipL21 and lipL48 genes (P <0.01). Moreover, closantel caused a decrease of the infection-based up-regulated mRNA levels of groEL, mce, loa22 and ligB genes (P <0.01). Expression levels of L.interrogans strain Lai major OMP antigens present notable changes during infection of human macrophages. There is a group of OmpR-and HK-encoding genes which may play a major role in down-regulation of expression levels of partial OMP antigens during infection.

The effect of intraurethral dexpanthenol on healing and fibrosis in rats with experimentally induced urethral trauma.

PubMed

Yardimci, Ibrahim; Karakan, Tolga; Resorlu, Berkan; Doluoglu, Omer Gokhan; Ozcan, Serkan; Aydın, Arif; Demirbas, Arif; Unverdi, Hatice; Eroglu, Muzaffer

2015-01-01

To determine the efficacy of dexpanthenol applied early after urethral trauma for preventing inflammation and spongiofibrosis. Twenty-seven rats were randomized and divided into 3 groups, with 9 rats in each group. The urethras of all rats were traumatized with a pediatric urethrotome knife at 6-o' clock. For 14 days, group I was given 0.9% saline twice a day (control group), group II was given dexpanthenol 500 mg/kg ampules once a day and 0.9% saline once a day, and group III was given dexpanthenol 500 mg/kg ampules twice a day intraurethrally using a 22 ga catheter sheath. On day 15, the penises of the rats were degloved to perform penectomy. The mean fibrosis scores were 2.4, 2.2, and 1.4, and mean inflammation scar scores were 2, 1.4, and 1.3 in groups I, II, and III, respectively. There was a significant difference between groups I and II for inflammation (P = .011); however, the difference for fibrosis was not significant (P = .331). The differences between groups I and III were statistically significantly different both for inflammation and fibrosis (P = .004 and P = .003, respectively). Groups II and III were not different significantly for inflammation (P = .638); however, there was less fibrosis in group III, in which high-dose dexpanthenol was administered. We showed that dexpanthenol applied early after urethral trauma significantly decreased inflammation and spongiofibrosis. We hope that our study will help to decrease strictures after urethral trauma and contribute to pharmaceutical investigations aiming to improve the success of the surgery for urethral strictures. Copyright © 2015 Elsevier Inc. All rights reserved.

Arsenic ambient conditions preventing surface degradation of GaAs during capless annealing at high temperatures

NASA Technical Reports Server (NTRS)

Kang, C. H.; Kondo, K.; Lagowski, J.; Gatos, H. C.

1987-01-01

Changes in surface morphology and composition caused by capless annealing of GaAs were studied as a function of annealing temperature, T(GaAs), and the ambient arsenic pressure controlled by the temperature, T(As), of an arsenic source in the annealing ampul. It was established that any degradation of the GaAs surface morphology could be completely prevented, providing that T(As) was more than about 0.315T(GaAs) + 227 C. This empirical relationship is valid up to the melting point temperature of GaAs (1238 C), and it may be useful in some device-processing steps.

Thermoelectric properties of rare earth chalcogenides

NASA Technical Reports Server (NTRS)

Danielson, L. R.; Raag, V.; Wood, C.

1985-01-01

The rare earth chalcogenides are important thermoelectric materials due to their high melting points, self-doping capabilities, and low thermal conductivities. Lanthanum sulfides and lanthanum tellurides have been synthesized in quartz ampules, hot-pressed into samples, and measured. The n-type Seebeck coefficients, electrical resistivities, and power factors generally all increased as the temperature increased from 200 to 1000 C. The figure-of-merit for nonstoichiometric lanthanum telluride was 0.001/deg C at 1000 C, considerably higher than for silicon-germanium. Thermoelectric measurements were made for LaTe(2) and YbS(1.4), and p-type behavior was observed for these compounds from 300 to 1100 C.

Magnetic properties of mixed sulfides MUS/sub 3/ (M = V, Cr, Nb, Ta)

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

Nutsubidze, P.V.; Chechernikov, V.I.; Gracheva, N.V.

1985-08-01

The authors synthesized US/sub 2/ (Beta-US/sub 2/), VS, CrS, NbS, and TaS by the vacuum-thermal method in quartz ampules heated to 1170 degrees K. They homogenized and sintered these samples and remixed and sintered appropriate amounts to form MUS/sub 2/, which crystallizes in a rhombic structure. They studied the magnetic properties of MUS/sub 2/ on a vibration magnetometer in the range 75500 degrees K. The results of their analysis of the magnetic coefficients proved consistent with thermodynamic theory. They present their data in a series of four charts and two tables.

The role of porcine reproductive and respiratory syndrome (PRRS) virus structural and non-structural proteins in virus pathogenesis.

PubMed

Music, Nedzad; Gagnon, Carl A

2010-12-01

Porcine reproductive and respiratory syndrome (PRRS) is an economically devastating viral disease affecting the swine industry worldwide. The etiological agent, PRRS virus (PRRSV), possesses a RNA viral genome with nine open reading frames (ORFs). The ORF1a and ORF1b replicase-associated genes encode the polyproteins pp1a and pp1ab, respectively. The pp1a is processed in nine non-structural proteins (nsps): nsp1α, nsp1β, and nsp2 to nsp8. Proteolytic cleavage of pp1ab generates products nsp9 to nsp12. The proteolytic pp1a cleavage products process and cleave pp1a and pp1ab into nsp products. The nsp9 to nsp12 are involved in virus genome transcription and replication. The 3' end of the viral genome encodes four minor and three major structural proteins. The GP(2a), GP₃ and GP₄ (encoded by ORF2a, 3 and 4), are glycosylated membrane associated minor structural proteins. The fourth minor structural protein, the E protein (encoded by ORF2b), is an unglycosylated membrane associated protein. The viral envelope contains two major structural proteins: a glycosylated major envelope protein GP₅ (encoded by ORF5) and an unglycosylated membrane M protein (encoded by ORF6). The third major structural protein is the nucleocapsid N protein (encoded by ORF7). All PRRSV non-structural and structural proteins are essential for virus replication, and PRRSV infectivity is relatively intolerant to subtle changes within the structural proteins. PRRSV virulence is multigenic and resides in both the non-structural and structural viral proteins. This review discusses the molecular characteristics, biological and immunological functions of the PRRSV structural and nsps and their involvement in the virus pathogenesis.

The great billion-year war between ribosome- and capsid-encoding organisms (cells and viruses) as the major source of evolutionary novelties.

PubMed

Forterre, Patrick; Prangishvili, David

2009-10-01

Our conceptions on the origin, nature, and role of viruses have been shaken recently by several independent lines of research. There are many reasons to believe now that viruses are more ancient than modern cells and have always been more abundant and diverse than their cellular targets. Viruses can be defined as capsid-encoding organisms that transform their "host" cell into a viral factory. If capsid-encoding organisms (viruses) and ribosome-encoding organisms (cells) are the major types of living entities on our planet, it seems logical to conclude that their conflict has been a major engine of biological evolution (in the framework of natural selection). In particular, many novelties first selected in the viral world might have been transferred to cells as a consequence of the continuous flow of viral genes into cellular genomes. We discuss recent observations and hypotheses suggesting that viruses have played a major role at different stages of biological evolution, such as the RNA to DNA transition, the origin of the eukaryotic nucleus, or, alternatively, the origin of unique features in multicellular macrobes.

Phylogenetic affinities of Phobetinus to other pirate spider genera (Araneae: Mimetidae) as indicated by spinning field morphology.

PubMed

Townley, Mark A; Harms, Danilo; Benjamin, Suresh P

2013-09-01

Spinnerets from Phobetinus sagittifer and an undescribed Phobetinus species were examined by scanning electron microscopy to gain a better understanding of this genus' relationships to other genera in the family Mimetidae. Consistent with placement of Phobetinus in Mimetinae, females possessed two synapomorphies of this subfamily; enlarged cylindrical silk gland spigots with domed shafts and a single cylindrical spigot per posterior lateral spinneret (PLS). Spinning field features overall suggest Phobetinus is most closely related to Mimetus, followed by Australomimetus, then Ero. A possible synapomorphy of a clade including Mimetus and Phobetinus is a pair of modified piriform silk gland spigots on each anterior lateral spinneret of adult males located adjacent to the secondary major ampullate silk gland tartipore. These spigots were present in P. sagittifer; however, similarly positioned spigots in the undescribed species were not obviously modified (i.e., wider or with larger openings relative to the other piriform spigots). Close affinity to Mimetus was also indicated by tartipore-accommodated PLS aciniform silk glands in both Phobetinus species. These have been consistently observed in Mimetus, but not in Australomimetus or Ero. Somatic and genitalic drawings of P. sagittifer are provided to aid identification and similarities are noted between male pedipalps of Mimetus and Phobetinus. Copyright © 2013 Elsevier Ltd. All rights reserved.

Post-secretion processing influences spider silk performance

PubMed Central

Blamires, Sean J.; Wu, Chung-Lin; Blackledge, Todd A.; Tso, I-Min

2012-01-01

Phenotypic variation facilitates adaptations to novel environments. Silk is an example of a highly variable biomaterial. The two-spidroin (MaSp) model suggests that spider major ampullate (MA) silk is composed of two proteins—MaSp1 predominately contains alanine and glycine and forms strength enhancing β-sheet crystals, while MaSp2 contains proline and forms elastic spirals. Nonetheless, mechanical properties can vary in spider silks without congruent amino acid compositional changes. We predicted that post-secretion processing causes variation in the mechanical performance of wild MA silk independent of protein composition or spinning speed across 10 species of spider. We used supercontraction to remove post-secretion effects and compared the mechanics of silk in this ‘ground state’ with wild native silks. Native silk mechanics varied less among species compared with ‘ground state’ silks. Variability in the mechanics of ‘ground state’ silks was associated with proline composition. However, variability in native silks did not. We attribute interspecific similarities in the mechanical properties of native silks, regardless of amino acid compositions, to glandular processes altering molecular alignment of the proteins prior to extrusion. Such post-secretion processing may enable MA silk to maintain functionality across environments, facilitating its function as a component of an insect-catching web. PMID:22628213

Isotopic anomalies of H2 and C in the peat from the Tunguska meteorite impact area

NASA Astrophysics Data System (ADS)

Kolesnikov, E. M.

Core samples of peat collected at the site of the Tunguska meteorite impact were mixed with CuO and burned inside evacuated and sealed quartz ampules. As a result, the organic components of peat were transformed to H2O and CO2 which were then separated and analyzed using a mass spectrometer. Results show that layers located above the level dated by 1908 are characterized by lighter H2 isotopes and heavier C isotopes, compared with lower layers. These effects are ascribed to the conservation and gradual redistribution of cosmic matter (e.g., regular chondrites, achondrites, and C4-type carbon chondrites) in the upper peat layers.

Preparation of high purity plutonium oxide for radiochemistry instrument calibration standards and working standards

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

Wong, A.S.; Stalnaker, N.D.

1997-04-01

Due to the lack of suitable high level National Institute of Standards and Technology (NIST) traceable plutonium solution standards from the NIST or commercial vendors, the CST-8 Radiochemistry team at Los Alamos National Laboratory (LANL) has prepared instrument calibration standards and working standards from a well-characterized plutonium oxide. All the aliquoting steps were performed gravimetrically. When a {sup 241}Am standardized solution obtained from a commercial vendor was compared to these calibration solutions, the results agreed to within 0.04% for the total alpha activity. The aliquots of the plutonium standard solutions and dilutions were sealed in glass ampules for long termmore » storage.« less

Crystal face temperature determination means

DOEpatents

Nason, Donald O.; Burger, Arnold

1994-01-01

An optically transparent furnace (10) having a detection apparatus (29) with a pedestal (12) enclosed in an evacuated ampule (16) for growing a crystal (14) thereon. Temperature differential is provided by a source heater (20), a base heater (24) and a cold finger (26) such that material migrates from a polycrystalline source material (18) to grow the crystal (14). A quartz halogen lamp (32) projects a collimated beam (30) onto the crystal (14) and a reflected beam (34) is analyzed by a double monochromator and photomultiplier detection spectrometer (40) and the detected peak position (48) in the reflected energy spectrum (44) of the reflected beam (34) is interpreted to determine surface temperature of the crystal (14).

Impact of a Computer System and the Encoding Staff Organization on the Encoding Stays and on Health Institution Financial Production in France.

PubMed

Sarazin, Marianne; El Merini, Amine; Staccini, Pascal

2016-01-01

In France, medicalization of information systems program (PMSI) is an essential tool for the management planning and funding of health. The performance of encoding data inherent to hospital stays has become a major challenge for health institutions. Some studies have highlighted the impact of organizations set up on encoding quality and financial production. The aim of this study is to evaluate a computerized information system and new staff organization impact for treatment of the encoded information.

Thermal Stability of Jet Fuels: Kinetics of Forming Deposit Precursors

NASA Technical Reports Server (NTRS)

Naegeli, David W.

1997-01-01

The focus of this study was on the autoxidation kinetics of deposit precursor formation in jet fuels. The objectives were: (1) to demonstrate that laser-induced fluorescence is a viable kinetic tool for measuring rates of deposit precursor formation in jet fuels; (2) to determine global rate expressions for the formation of thermal deposit precursors in jet fuels; and (3) to better understand the chemical mechanism of thermal stability. The fuels were isothermally stressed in small glass ampules in the 120 to 180 C range. Concentrations of deposit precursor, hydroperoxide and oxygen consumption were measured over time in the thermally stressed fuels. Deposit precursors were measured using laser-induced fluorescence (LIF), hydroperoxides using a spectrophotometric technique, and oxygen consumption by the pressure loss in the ampule. The expressions, I.P. = 1.278 x 10(exp -11)exp(28,517.9/RT) and R(sub dp) = 2.382 x 10(exp 17)exp(-34,369.2/RT) for the induction period, I.P. and rate of deposit precursor formation R(sub dp), were determined for Jet A fuel. The results of the study support a new theory of deposit formation in jet fuels, which suggest that acid catalyzed ionic reactions compete with free radical reactions to form deposit precursors. The results indicate that deposit precursors form only when aromatics are present in the fuel. Traces of sulfur reduce the rate of autoxidation but increase the yield of deposit precursor. Free radical chemistry is responsible for hydroperoxide formation and the oxidation of sulfur compounds to sulfonic acids. Phenols are then formed by the acid catalyzed decomposition of benzylic hydroperoxides, and deposit precursors are produced by the reaction of phenols with aldehydes, which forms a polymer similar to Bakelite. Deposit precursors appear to have a phenolic resin-like structure because the LIF spectra of the deposit precursors were similar to that of phenolic resin dissolved in TAM.

Characterization of a family of cysteine rich proteins and development of a MaSp1 derived miniature fibroin

NASA Astrophysics Data System (ADS)

Chuang, Tyler Casey

Spider silk displays a unique balance of high tensile strength and extensibility, making it one of the toughest materials on the planet. Dragline silk, also known as the lifeline of the spider, represents one of the best studied fiber types and many labs are attempting to produce synthetic dragline silk fibers for commercial applications. In these studies, we develop a minifibroin for expression studies in bacteria. Using recombinant DNA methodology and protein expression studies, we develop a natural minifibroin that contains the highly conserved N- and C-terminal domains, along with several internal block repeats of MaSp1. We also characterize a family of small cysteine-rich proteins (CRPs) and demonstrate that these factors are present within the spinning dope of the major ampullate gland using MS analysis. Biochemical studies and characterization of one of the family members, CRP1, demonstrate that this factor can self-polymerize into higher molecular weight complexes under oxidizing conditions, but can be converted into a monomeric species under reducing conditions. Self-polymerization of CRP1 is also shown to be independent of pH and salt concentration, two important chemical cues that help fibroin aggregation. Overall, our data demonstrate that the polymerization state of CRP1 is dependent upon redox state, suggesting that the redox environment during fiber extrusion may help regulate the oligomerization of CRP molecules during dragline silk production.

Heat Capacity of Spider Silk-like Block Copolymers

PubMed Central

Huang, Wenwen; Krishnaji, Sreevidhya; Hu, Xiao; Kaplan, David; Cebe, Peggy

2012-01-01

We synthesized and characterized a new family of di-block copolymers based on the amino acid sequences of Nephila clavipes major ampulate dragline spider silk, having the form HABn and HBAn (n=1–3), comprising an alanine-rich hydrophobic block, A, a glycine-rich hydrophilic block, B, and a histidine tag, H. The reversing heat capacities, Cp(T), for temperatures below and above the glass transition, Tg, were measured by temperature modulated differential scanning calorimetry. For the solid state, we then calculated the heat capacities of our novel block copolymers based on the vibrational motions of the constituent poly(amino acid)s, whose heat capacities are known or can be estimated from the ATHAS Data Bank. For the liquid state, the heat capacity was estimated by using the rotational and translational motions in the polymer chain. Excellent agreement was found between the measured and calculated values of the heat capacity, showing that this method can serve as a standard by which to assess the Cp for other biologically inspired block copolymers. The fraction of beta sheet crystallinity of spider silk block copolymers was also determined by using the predicted Cp, and was verified by wide angle X-ray diffraction and Fourier transform infrared spectroscopy. The glass transition temperatures of spider silk block copolymer were fitted by Kwei’s equation and the results indicate that attractive interaction exists between the A-block and B-block. PMID:23869111

Economic feasibility and environmental impact of synthetic spider silk production from escherichia coli.

PubMed

Edlund, Alan M; Jones, Justin; Lewis, Randolph; Quinn, Jason C

2018-05-25

Major ampullate spider silk represents a promising protein-based biomaterial with diverse commercial potential ranging from textiles to medical devices due to its excellent physical and thermal properties. Recent advancements in synthetic biology have facilitated the development of recombinant spider silk proteins from Escherichia coli (E. coli). This study specifically investigates the economic feasibility and environmental impact of synthetic spider silk manufacturing. Pilot scale data was used to validate an engineering process model that includes all of the required sub-processing steps for synthetic fiber manufacture: production, harvesting, purification, drying, and spinning. Modeling was constructed modularly to support assessment of alternative downstream processing technologies. The techno-economic analysis indicates a minimum sale price from pioneer and optimized E. coli plants of $761 kg -1 and $23 kg -1 with greenhouse gas emissions of 572 kg CO 2-eq. kg -1 and 55 kg CO 2-eq. kg -1 , respectively. Elevated costs and emissions from the pioneer plant can be directly tied to the high material consumption and low protein yield. Decreased production costs associated with the optimized plant includes improved protein yield, process optimization, and an N th plant assumption. Discussion focuses on the commercial potential of spider silk, the production performance requirements for commercialization, and the impact of alternative technologies on the system. Copyright © 2018 Elsevier B.V. All rights reserved.

Development of a correction factor for Xe-133 vials for use with a dose calibrator

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

Gels, G.L.; Piltingsrud, H.V.

1982-04-01

Manufacturers of dose calibrators who give calibration settings for various radionuclies sometimes do not specify the type of radionuclide container the calibration is for. The container, moreover, may not be of the same type as those a user might purchase. When these factors are not considered, the activity administered to the patient may be significantly different from that intended. An experiment is described in which calibration factors are determined for measurement of Xe-133 activity in vials in a dose calibrator. This was accomplished by transferring the Xe-133 from the commercial vials to standard NBS calibration ampules. Based on ten suchmore » transfers, the resulting correction factor for the dose calibrator was 1.22.« less

Low-temperature radiation copolymerization of tetrafluoroethylene with perfluorovinyl ethers

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

Kim, I.P.; Pirozhnaya, L.N.; Loginova, N.N.

1986-12-01

The copolymerization of perfluorovinyl ethers with tetrafluoroethylene at low temperature was studied and compared with the process conducted with chemical initiation in bulk or aqueous medium. A calorimetric method was used for studying the kinetics of copolymerization, the phase state of the system, and the phase transition dynamics. Ampules containing the samples of monomers and mixtures were irradiated at 77/sup 0/K with /sup 60/Co ..gamma.. rays with a dose rate of 25 kGy/h. Radiolysis in the solid phase at 77/sup 0/K with a 130 kGy dose resulted in the formation of 0.5-1.0 wt.% of a polymer, and this polymer wasmore » soluble in the monomer.« less

Role of Viral miRNAs and Epigenetic Modifications in Epstein-Barr Virus-Associated Gastric Carcinogenesis.

PubMed

Giudice, Aldo; D'Arena, Giovanni; Crispo, Anna; Tecce, Mario Felice; Nocerino, Flavia; Grimaldi, Maria; Rotondo, Emanuela; D'Ursi, Anna Maria; Scrima, Mario; Galdiero, Massimiliano; Ciliberto, Gennaro; Capunzo, Mario; Franci, Gianluigi; Barbieri, Antonio; Bimonte, Sabrina; Montella, Maurizio

2016-01-01

MicroRNAs are short (21-23 nucleotides), noncoding RNAs that typically silence posttranscriptional gene expression through interaction with target messenger RNAs. Currently, miRNAs have been identified in almost all studied multicellular eukaryotes in the plant and animal kingdoms. Additionally, recent studies reported that miRNAs can also be encoded by certain single-cell eukaryotes and by viruses. The vast majority of viral miRNAs are encoded by the herpesviruses family. These DNA viruses including Epstein-Barr virus encode their own miRNAs and/or manipulate the expression of cellular miRNAs to facilitate respective infection cycles. Modulation of the control pathways of miRNAs expression is often involved in the promotion of tumorigenesis through a specific cascade of transduction signals. Notably, latent infection with Epstein-Barr virus is considered liable of causing several types of malignancies, including the majority of gastric carcinoma cases detected worldwide. In this review, we describe the role of the Epstein-Barr virus in gastric carcinogenesis, summarizing the functions of the Epstein-Barr virus-encoded viral proteins and related epigenetic alterations as well as the roles of Epstein-Barr virus-encoded and virally modulated cellular miRNAs.

Weak encoding of faces predicts socially influenced judgments of facial attractiveness.

PubMed

Schnuerch, Robert; Koppehele-Gossel, Judith; Gibbons, Henning

2015-01-01

Conforming to the majority can be seen as a heuristic type of judgment, as it allows the individual to easily choose the most accurate or most socially acceptable type of behavior. People who process the currently to-be-judged items in a superficial, heuristic way should tend to conform to group judgment more than people processing these items in a systematic and elaborate way. We investigated this hypothesis using electroencephalography (EEG), analyzing whether the strength of neural encoding of faces was related to the tendency to adopt a group's evaluative judgments regarding these faces. As expected, we found that the amplitude of the N170, a specific neural correlate of face encoding, was inversely related to conformity across participants: The weaker the faces were encoded, the more the majority response regarding the faces' attractiveness was adopted instead of relying on the actual qualities of the faces. Applying neurophysiological methodology, we thus provide support for previous claims, based on behavioral data and theorizing, that social conformity is a heuristic type of judgment. We propose that weak encoding of judgment-relevant information is a typical, possibly even necessary, precursor of socially adjusted judgments, irrespective of one's current motivational goal (i.e., to be accurate or accepted).

Removal of nanoaerosol during the bubbling of the salt melt of beryllium and lithium fluorides for the preparation of reactor radioisotopes

NASA Astrophysics Data System (ADS)

Zagnit'ko, A. V.; Chuvilin, D. Yu.

2010-06-01

The parameters of aerosol particles formed in the course of the spontaneous thermal condensation of vapors and bubbling a 66LiF-34BeF2 (mol %) eutectic salt mixture with helium have been studied. For this purpose, a vertical bubbling mode at T ≈ 900 K and an ampule device for obtaining reactor radioisotopes for medical applications were used. The rate of the bulk removal and the chemical composition of aerosols were measured. The size distribution of the aerosol particles was bimodal, and the mass concentration of the particles exceeded by far the maximum permissible concentration (MPC). The characteristics of regenerated nickel multilayer nanofilters for ultrahigh filtration of aerosols from the salt liquid melt were analyzed.

Technology for increased human productivity and safety on orbit

NASA Technical Reports Server (NTRS)

Ambrus, Judith; Gartrell, Charles F.

1991-01-01

Technologies are addressed that can facilitate the efficient performance of station operations on the Space Station Freedom (SSF) and thereby optimize the utilization of SSF for scientific research. The dedication of SSF capabilities to scientific study and to the payload-user community is a key goal of the program. Robotics applications are discussed in terms of automating the processing of experiment materials on-orbit by transferring ampules to a furnace system or by handling plant-tissue cultures. Noncontact temperature measurement and medical support technology are considered important technologies for maximizing time for scientific purposes. Detailed examinations are conducted of other technologies including advanced data systems and furnace designs. The addition of the listed technologies can provide an environment in which scientific research is more efficient and accurate.

Radiation-induced polymerization of cyclophosphazene trimers. Final report, 1 September 1985-30 September 1988

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

Stannett, V.T.

1989-01-04

Hexachlorophosphazene was irradiated in bulk and in solution after various methods of purification. When rigorously dried and purified, good yields of polymer were obtained. Poor reproducibility was found in the bulk but reasonably good results were obtained in decalin solution. The best yields and highest molecular weights were obtained after the addition of small amounts of the bulky electron acceptor pyromellitic dianhydride. Hexachlorocyclotriphosphazene was purified by recrystallization for various times from dried heptane. The trimer was then further purified by repeated sublimation steps under high vacuum. Finally the trimer was dried in the melt over rigorously baked out barium oxide.more » The monomer was then transferred to ampules or the NMR tubes for radiation and subsequent determination of the polymer content.« less

International Metadata Initiatives: Lessons in Bibliographic Control.

ERIC Educational Resources Information Center

Caplan, Priscilla

This paper looks at a subset of metadata schemes, including the Text Encoding Initiative (TEI) header, the Encoded Archival Description (EAD), the Dublin Core Metadata Element Set (DCMES), and the Visual Resources Association (VRA) Core Categories for visual resources. It examines why they developed as they did, major point of difference from…

Nanostructural and mechanical property changes to spider silk as a consequence of insecticide exposure.

PubMed

Benamú, Marco; Lacava, Mariángeles; García, Luis F; Santana, Martín; Fang, Jian; Wang, Xungai; Blamires, Sean J

2017-08-01

Neonicotinoids are one of the world's most extensively used insecticides, but their sub-lethal influences on non-target and beneficial organisms are not well known. Here we exposed the orb web spider Parawixia audax, which is found on arable lands in Uruguay, to a sub-lethal concentration of the broad spectrum insecticide Geonex (thiamethoxam + lambda-cyhalothrin) and monitored their web building. We collected their major ampullate silk and subjected it to tensile tests, wide-angle X-ray diffraction (WAXS) analysis, and amino acid composition analysis. Around half of the exposed spiders failed to build webs. Those that built webs produced irregular webs lacking spiral threads. The mechanical properties, nanostructures, and amino acid compositions of the silk were all significantly affected when the spiders were exposed to insecticides. We found that silk proline, glutamine, alanine and glycine compositions differed between treatments, indicating that insecticide exposure induced downregulation of the silk protein MaSp2. The spiders in the control group had stronger, tougher and more extensible silks than those in the insecticide exposed group. Our WAXS analyses showed the amorphous region nanostructures became misaligned in insecticide exposed silks, explaining their greater stiffness. While the insecticide dose we subjected P. audax to was evidently sub-lethal, the changes in silk physicochemical properties and the impairment to web building will indelibly affect their ability to catch prey. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nutrient-mediated architectural plasticity of a predatory trap.

PubMed

Blamires, Sean J; Tso, I-Min

2013-01-01

Nutrients such as protein may be actively sought by foraging animals. Many predators exhibit foraging plasticity, but how their foraging strategies are affected when faced with nutrient deprivation is largely unknown. In spiders, the assimilation of protein into silk may be in conflict with somatic processes so we predicted web building to be affected under protein depletion. To assess the influence of protein intake on foraging plasticity we fed the orb-web spiders Argiope aemula and Cyclosa mulmeinensis high, low or no protein solutions over 10 days and allowed them to build webs. We compared post-feeding web architectural components and major ampullate (MA) silk amino acid compositions. We found that the number of radii in webs increased in both species when fed high protein solutions. Mesh size increased in A. aemula when fed a high protein solution. MA silk proline and alanine compositions varied in each species with contrasting variations in alanine between the two species. Glycine compositions only varied in C. mulmeinensis silk. No spiders significantly lost or gained mass on any feeding treatment, so they did not sacrifice somatic maintenance for amino acid investment in silk. Our results show that the amount of protein taken in significantly affects the foraging decisions of trap-building predators, such as orb web spiders. Nevertheless, the subtle differences found between species in the association between protein intake, the amino acids invested in silk and web architectural plasticity show that the influence of protein deprivation on specific foraging strategies differs among different spiders.

Punctuated evolution of viscid silk in spider orb webs supported by mechanical behavior of wet cribellate silk

NASA Astrophysics Data System (ADS)

Piorkowski, Dakota; Blackledge, Todd A.

2017-08-01

The origin of viscid capture silk in orb webs, from cribellate silk-spinning ancestors, is a key innovation correlated with significant diversification of web-building spiders. Ancestral cribellate silk consists of dry nanofibrils surrounding a stiff, axial fiber that adheres to prey through van der Waals interactions, capillary forces, and physical entanglement. In contrast, viscid silk uses chemically adhesive aqueous glue coated onto a highly compliant and extensible flagelliform core silk. The extensibility of the flagelliform fiber accounts for half of the total work of adhesion for viscid silk and is enabled by water in the aqueous coating. Recent cDNA libraries revealed the expression of flagelliform silk proteins in cribellate orb-weaving spiders. We hypothesized that the presence of flagelliform proteins in cribellate silk could have allowed for a gradual shift in mechanical performance of cribellate axial silk, whose effect was masked by the dry nature of its adhesive. We measured supercontraction and mechanical performance of cribellate axial silk, in wet and dry states, for two species of cribellate orb web-weaving spiders to see if water enabled flagelliform silk-like performance. We found that compliance and extensibility of wet cribellate silk increased compared to dry state as expected. However, when compared to other silk types, the response to water was more similar to other web silks, like major and minor ampullate silk, than to viscid silk. These findings support the punctuated evolution of viscid silk mechanical performance.

Binding an Event to Its Source at Encoding Improves Children's Source Monitoring

ERIC Educational Resources Information Center

Roberts, Kim P.; Evans, Angela D.; Duncanson, Sara

2016-01-01

Children learn information from a variety of sources and often remember the content but forget the source. Whereas the majority of research has focused on retrieval mechanisms for such difficulties, the present investigation examines whether the way in which sources are "encoded" influences future source monitoring. In Study 1, 86…

Effect of impurities in polybutene on the quality of alkenylsuccinic anhydrides

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

Yarmolyuk, B.M.; Pustovit, V.E.; Bereza, L.I.

1984-03-01

Synthesis of alkenylsuccini anhydrides (ASAs) was carried out in thermostable ampules at 230/sup 0/C in the course of 12 hours at an MA:PB molar ratio of 1.3:1 in a medium of prepurified petroleum xylene (30%). Freshly distilled maleic anhydride and industrial specimens of polybutene were used in the experiments. It was established that the main impurities which are formed in the production of polybutene and in its processing are ions of sodium, peroxide compounds and products of decomposition of the polymerization catalyst. The concentration of sodium ion was determined by an atomic adsorption method on an A-3000 instrument, the concentrationmore » of peroxides was determined by iodometry (3), and the concentration of catalyst decomposition products was determined from the amount of mechanical impurities.« less

Bottlenecks of Motion Processing during a Visual Glance: The Leaky Flask Model

PubMed Central

Öğmen, Haluk; Ekiz, Onur; Huynh, Duong; Bedell, Harold E.; Tripathy, Srimant P.

2013-01-01

Where do the bottlenecks for information and attention lie when our visual system processes incoming stimuli? The human visual system encodes the incoming stimulus and transfers its contents into three major memory systems with increasing time scales, viz., sensory (or iconic) memory, visual short-term memory (VSTM), and long-term memory (LTM). It is commonly believed that the major bottleneck of information processing resides in VSTM. In contrast to this view, we show major bottlenecks for motion processing prior to VSTM. In the first experiment, we examined bottlenecks at the stimulus encoding stage through a partial-report technique by delivering the cue immediately at the end of the stimulus presentation. In the second experiment, we varied the cue delay to investigate sensory memory and VSTM. Performance decayed exponentially as a function of cue delay and we used the time-constant of the exponential-decay to demarcate sensory memory from VSTM. We then decomposed performance in terms of quality and quantity measures to analyze bottlenecks along these dimensions. In terms of the quality of information, two thirds to three quarters of the motion-processing bottleneck occurs in stimulus encoding rather than memory stages. In terms of the quantity of information, the motion-processing bottleneck is distributed, with the stimulus-encoding stage accounting for one third of the bottleneck. The bottleneck for the stimulus-encoding stage is dominated by the selection compared to the filtering function of attention. We also found that the filtering function of attention is operating mainly at the sensory memory stage in a specific manner, i.e., influencing only quantity and sparing quality. These results provide a novel and more complete understanding of information processing and storage bottlenecks for motion processing. PMID:24391806

Bottlenecks of motion processing during a visual glance: the leaky flask model.

PubMed

Öğmen, Haluk; Ekiz, Onur; Huynh, Duong; Bedell, Harold E; Tripathy, Srimant P

2013-01-01

Where do the bottlenecks for information and attention lie when our visual system processes incoming stimuli? The human visual system encodes the incoming stimulus and transfers its contents into three major memory systems with increasing time scales, viz., sensory (or iconic) memory, visual short-term memory (VSTM), and long-term memory (LTM). It is commonly believed that the major bottleneck of information processing resides in VSTM. In contrast to this view, we show major bottlenecks for motion processing prior to VSTM. In the first experiment, we examined bottlenecks at the stimulus encoding stage through a partial-report technique by delivering the cue immediately at the end of the stimulus presentation. In the second experiment, we varied the cue delay to investigate sensory memory and VSTM. Performance decayed exponentially as a function of cue delay and we used the time-constant of the exponential-decay to demarcate sensory memory from VSTM. We then decomposed performance in terms of quality and quantity measures to analyze bottlenecks along these dimensions. In terms of the quality of information, two thirds to three quarters of the motion-processing bottleneck occurs in stimulus encoding rather than memory stages. In terms of the quantity of information, the motion-processing bottleneck is distributed, with the stimulus-encoding stage accounting for one third of the bottleneck. The bottleneck for the stimulus-encoding stage is dominated by the selection compared to the filtering function of attention. We also found that the filtering function of attention is operating mainly at the sensory memory stage in a specific manner, i.e., influencing only quantity and sparing quality. These results provide a novel and more complete understanding of information processing and storage bottlenecks for motion processing.

Mutational analysis of the major soybean UreF paralogue involved in urease activation

USDA-ARS?s Scientific Manuscript database

In soybean, mutation at Eu2 or Eu3 eliminates the urease activities of both the embryo-specific and the tissue-ubiquitous (assimilatory) isozymes, encoded by Eu1 and Eu4, respectively. Eu3 encodes UreG, a GTP’ase necessary for proper emplacement of Ni and carbon dioxide in the urease active site. ...

An edge preserving differential image coding scheme

NASA Technical Reports Server (NTRS)

Rost, Martin C.; Sayood, Khalid

1992-01-01

Differential encoding techniques are fast and easy to implement. However, a major problem with the use of differential encoding for images is the rapid edge degradation encountered when using such systems. This makes differential encoding techniques of limited utility, especially when coding medical or scientific images, where edge preservation is of utmost importance. A simple, easy to implement differential image coding system with excellent edge preservation properties is presented. The coding system can be used over variable rate channels, which makes it especially attractive for use in the packet network environment.

Genome-Wide Architecture of Disease Resistance Genes in Lettuce

PubMed Central

Christopoulou, Marilena; Wo, Sebastian Reyes-Chin; Kozik, Alex; McHale, Leah K.; Truco, Maria-Jose; Wroblewski, Tadeusz; Michelmore, Richard W.

2015-01-01

Genome-wide motif searches identified 1134 genes in the lettuce reference genome of cv. Salinas that are potentially involved in pathogen recognition, of which 385 were predicted to encode nucleotide binding-leucine rich repeat receptor (NLR) proteins. Using a maximum-likelihood approach, we grouped the NLRs into 25 multigene families and 17 singletons. Forty-one percent of these NLR-encoding genes belong to three families, the largest being RGC16 with 62 genes in cv. Salinas. The majority of NLR-encoding genes are located in five major resistance clusters (MRCs) on chromosomes 1, 2, 3, 4, and 8 and cosegregate with multiple disease resistance phenotypes. Most MRCs contain primarily members of a single NLR gene family but a few are more complex. MRC2 spans 73 Mb and contains 61 NLRs of six different gene families that cosegregate with nine disease resistance phenotypes. MRC3, which is 25 Mb, contains 22 RGC21 genes and colocates with Dm13. A library of 33 transgenic RNA interference tester stocks was generated for functional analysis of NLR-encoding genes that cosegregated with disease resistance phenotypes in each of the MRCs. Members of four NLR-encoding families, RGC1, RGC2, RGC21, and RGC12 were shown to be required for 16 disease resistance phenotypes in lettuce. The general composition of MRCs is conserved across different genotypes; however, the specific repertoire of NLR-encoding genes varied particularly of the rapidly evolving Type I genes. These tester stocks are valuable resources for future analyses of additional resistance phenotypes. PMID:26449254

On the Relationships between Generative Encodings, Regularity, and Learning Abilities when Evolving Plastic Artificial Neural Networks

PubMed Central

Tonelli, Paul; Mouret, Jean-Baptiste

2013-01-01

A major goal of bio-inspired artificial intelligence is to design artificial neural networks with abilities that resemble those of animal nervous systems. It is commonly believed that two keys for evolving nature-like artificial neural networks are (1) the developmental process that links genes to nervous systems, which enables the evolution of large, regular neural networks, and (2) synaptic plasticity, which allows neural networks to change during their lifetime. So far, these two topics have been mainly studied separately. The present paper shows that they are actually deeply connected. Using a simple operant conditioning task and a classic evolutionary algorithm, we compare three ways to encode plastic neural networks: a direct encoding, a developmental encoding inspired by computational neuroscience models, and a developmental encoding inspired by morphogen gradients (similar to HyperNEAT). Our results suggest that using a developmental encoding could improve the learning abilities of evolved, plastic neural networks. Complementary experiments reveal that this result is likely the consequence of the bias of developmental encodings towards regular structures: (1) in our experimental setup, encodings that tend to produce more regular networks yield networks with better general learning abilities; (2) whatever the encoding is, networks that are the more regular are statistically those that have the best learning abilities. PMID:24236099

High bit rate convolutional channel encoder/decoder

NASA Technical Reports Server (NTRS)

1977-01-01

A detailed description of the design approach and tradeoffs encountered during the development of the 50 MBPS decoder system is presented. A functional analysis of each of the major logical functions is given, and the system's major components are listed.

Isolation and characterization of major histocompatibility complex class IIB genes from the nurse shark.

PubMed

Bartl, S; Weissman, I L

1994-01-04

The major histocompatibility complex (MHC) contains a set of linked genes which encode cell surface proteins involved in the binding of small peptide antigens for their subsequent recognition by T lymphocytes. MHC proteins share structural features and the presence and location of polymorphic residues which play a role in the binding of antigens. In order to compare the structure of these molecules and gain insights into their evolution, we have isolated two MHC class IIB genes from the nurse shark, Ginglymostoma cirratum. Two clones, most probably alleles, encode proteins which differ by 13 amino acids located in the putative antigen-binding cleft. The protein structure and the location of polymorphic residues are similar to their mammalian counterparts. Although these genes appear to encode a typical MHC protein, no T-cell-mediated responses have been demonstrated in cartilaginous fish. The nurse shark represents the most phylogenetically primitive organism in which both class IIA [Kasahara, M., Vazquez, M., Sato, K., McKinney, E.C. & Flajnik, M.F. (1992) Proc. Natl. Acad. Sci USA 89, 6688-6692] and class IIB genes, presumably encoding the alpha/beta heterodimer, have been isolated.

The Allosterically Unregulated Isoform of ADP-Glucose Pyrophosphorylase from Barley Endosperm Is the Most Likely Source of ADP-Glucose Incorporated into Endosperm Starch.

PubMed

Doan; Rudi; Olsen

1999-11-01

We present the results of studies of an unmodified version of the recombinant major barley (Hordeum vulgare) endosperm ADP-glucose pyrophoshorylase (AGPase) expressed in insect cells, which corroborate previous data that this isoform of the enzyme acts independently of the allosteric regulators 3-phosphoglycerate and inorganic phosphate. We also present a characterization of the individual subunits expressed separately in insect cells, showing that the SS AGPase is active in the presence of 3-phosphoglycerate and is inhibited by inorganic phosphate. As a step toward the elucidation of the role of the two AGPase isoforms in barley, the temporal and spatial expression profile of the four barley AGPase transcripts encoding these isoforms were studied. The results show that the steady-state level of beps and bepl, the transcripts encoding the major endosperm isoform, correlated positively with the rate of endosperm starch accumulation. In contrast, blps and blpl, the transcripts encoding the major leaf isoform, were constitutively expressed at a very low steady-state level throughout the barley plant. The implications of these findings for the evolution of plant AGPases are discussed.

The Allosterically Unregulated Isoform of ADP-Glucose Pyrophosphorylase from Barley Endosperm Is the Most Likely Source of ADP-Glucose Incorporated into Endosperm Starch1

PubMed Central

Doan, Danny N.P.; Rudi, Heidi; Olsen, Odd-Arne

1999-01-01

We present the results of studies of an unmodified version of the recombinant major barley (Hordeum vulgare) endosperm ADP-glucose pyrophoshorylase (AGPase) expressed in insect cells, which corroborate previous data that this isoform of the enzyme acts independently of the allosteric regulators 3-phosphoglycerate and inorganic phosphate. We also present a characterization of the individual subunits expressed separately in insect cells, showing that the SS AGPase is active in the presence of 3-phosphoglycerate and is inhibited by inorganic phosphate. As a step toward the elucidation of the role of the two AGPase isoforms in barley, the temporal and spatial expression profile of the four barley AGPase transcripts encoding these isoforms were studied. The results show that the steady-state level of beps and bepl, the transcripts encoding the major endosperm isoform, correlated positively with the rate of endosperm starch accumulation. In contrast, blps and blpl, the transcripts encoding the major leaf isoform, were constitutively expressed at a very low steady-state level throughout the barley plant. The implications of these findings for the evolution of plant AGPases are discussed. PMID:10557246

Signatures of Value Comparison in Ventral Striatum Neurons

PubMed Central

Strait, Caleb E.; Sleezer, Brianna J.; Hayden, Benjamin Y.

2015-01-01

The ventral striatum (VS), like its cortical afferents, is closely associated with processing of rewards, but the relative contributions of striatal and cortical reward systems remains unclear. Most theories posit distinct roles for these structures, despite their similarities. We compared responses of VS neurons to those of ventromedial prefrontal cortex (vmPFC) Area 14 neurons, recorded in a risky choice task. Five major response patterns observed in vmPFC were also observed in VS: (1) offer value encoding, (2) value difference encoding, (3) preferential encoding of chosen relative to unchosen value, (4) a correlation between residual variance in responses and choices, and (5) prominent encoding of outcomes. We did observe some differences as well; in particular, preferential encoding of the chosen option was stronger and started earlier in VS than in vmPFC. Nonetheless, the close match between vmPFC and VS suggests that cortex and its striatal targets make overlapping contributions to economic choice. PMID:26086735

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

Stols, L.; Donnelly, M.I.; Kulkarni, G.

The malic enzyme gene of Ascaris suum was cloned into the vector pTRC99a in two forms encoding alternative amino-termini. The resulting plasmids, pMEA1 and pMEA2, were introduced into Escherichia coli NZN111, a strain that is unable to grow fermentatively because of inactivation of the genes encoding pyruvate dissimilation. Induction of pMEA1, which encodes the native animoterminus, gave better overexpression of malic enzyme, approx 12-fold compared to uninduced cells. Under the appropriate culture conditions, expression of malic enzyme allowed the fermentative dissimilation of glucose by NZN111. The major fermentation product formed in induced cultures was succinic acid.

Three-dimensional analysis of flow and segregation in vertical Bridgman crystal growth under axial and transversal magnetic fields

NASA Astrophysics Data System (ADS)

Lan, C. W.; Lee, I. F.; Yeh, B. C.

2003-07-01

Three-dimensional simulation, both pseudo-steady and time-dependent states, is carried out to illustrate the effects of magnetic fields on the flow and segregation in a vertical Bridgman crystal growth. With an axial magnetic field in a perfectly vertical growth, the calculated results are in good agreement with those obtained by a two-dimensional axisymmetric model. The asymptotic scaling of flow damping is also consistent with the boundary layer approximation regardless to the magnetic orientation. Radial and axial segregations are further discussed concluding that radial segregation could be severe if the flow damping is not adequate. Moreover, there is a regime of enhanced global dopant mixing due to the flow stretching by the axial field. Accordingly, the transversal field is more effective in pushing the growth to the diffusion-controlled limit and suppressing the asymmetric global flow due to ampule tilting.

In-Situ Optical Determination of Thermomechanical Properties of ZnSe and ZnTe Crystals

NASA Technical Reports Server (NTRS)

Burger, A.; Ndap, J.-O.; Chattopadhyay, K.; Ma, X.; Silberman, E.; Feth, S.; Palosz, W.; Su, C.-H.

1999-01-01

At temperatures above 1/2 T(sub m), the generation and movement of dislocations may result due to the load created by the weight of the crystal itself The deformation may be expected to increase the line defect density and may result in generation of low angle grain boundaries, especially in the regions of the crystal attached to the ampule. It has often been suspected that elimination of this effect in space can improve crystallinity of crystals grown under microgravity conditions, however, a direct experimental proof of such relation is still missing. In this work we have designed and built a system of in-situ optical detection and measurement of the mechanical deformations of a crystal wafer under its own weight, and studied the deformation effects as a function of temperature. The results of the measurements for ZnSe and ZnTe crystal wafers will be presented.

Bureau of Mines method of calibrating a primary radon-measuring apparatus

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

Holub, R.R.; Stroud, W.P.

1990-01-01

One important requirement for accurate monitoring of radon in working environments, dwellings, and outdoors is to ensure that the measurement instrumentation is properly calibrated against a recognized standard. To achieve this goal, the U.S. Department of Interior Bureau of Mines (BoM) Radiation Laboratory has participated since 1983 in a program to establish international radon measurement standards. While the National Institute of Standards and Technology (NIST) radium solution ampules are acceptable to all participating laboratories as a primary standard, a method of transferring radon from the NIST source into each laboratory's primary counting apparatus is a critical problem. The Bureau's methodmore » transfers radon from the primary solution by bubbling 3 L of air through it into a steel cylinder. After homogenizing the radon concentrations in the cylinder, eight alpha-scintillation cells are filled consecutively and measured in a standard counting system. The resulting efficiency is 81.7 + or - 1.2%.« less

The section TiInSe/sub 2/-TiSbSe/sub 2/ of the system Ti-In-Sb-Se

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

Guseinov, G.D.; Chapanova, L.M.; Mal'sagov, A.U.

1985-09-01

The ternary compounds A /SUP I/ B /SUP III/ C/sub 2/ /SUP VI/ (A /SUP I/ is univalent Ti; B /SUP III/ is Ga or In; and C /SUP VI/ is S, Se or Te) form a class of semiconductors with a large number of different gap widths. The compounds crystallize in the chalcopyrite structure. Solid solutions based on these compounds, which permit varying smoothly the gap width and other physical parameters over wide limits, are of great interest. The authors synthesized the compounds TiInSe/sub 2/ and TiSbSe/sub 2/ from the starting materials Ti-000, In-000, Sb-000 and Se-OSCh-17-4 by directmore » fusion of the components, taken in a stoichiometric ratio, in quartz ampules evacuated to 1.3 X 10/sup -3/ Pa and sealed.« less

Growth of GaAs crystals from the melt in a partially confined configuration

NASA Technical Reports Server (NTRS)

Gatos, Harry C.; Lagowski, Jacek

1988-01-01

The experimental approach was directed along two main goals: (1) the implementation of an approach to melt growth in a partially confined configuration; and (2) the investigation of point defect interaction and electronic characteristics as related to thermal treatment following solidification and stoichiometry. Significant progress was made along both fronts. Crystal growth of GaAs in triangular ampuls was already carried out successfully and consistent with the model. In fact, pronounced surface tension phenomena which cannot be observed in ordinary confinement system were identified and should premit the assessment of Maragoni effects prior to space processing. Regarding thermal treatment, it was discovered that the rate of cooling from elevated temperatures is primarily responsible for a whole class of defect interactions affecting the electronic characteristics of GaAs and that stoichiometry plays a critical role in the quality of GaAs.

Nutrient-Mediated Architectural Plasticity of a Predatory Trap

PubMed Central

Blamires, Sean J.; Tso, I-Min

2013-01-01

Background Nutrients such as protein may be actively sought by foraging animals. Many predators exhibit foraging plasticity, but how their foraging strategies are affected when faced with nutrient deprivation is largely unknown. In spiders, the assimilation of protein into silk may be in conflict with somatic processes so we predicted web building to be affected under protein depletion. Methodology/Principal Findings To assess the influence of protein intake on foraging plasticity we fed the orb-web spiders Argiope aemula and Cyclosa mulmeinensis high, low or no protein solutions over 10 days and allowed them to build webs. We compared post-feeding web architectural components and major ampullate (MA) silk amino acid compositions. We found that the number of radii in webs increased in both species when fed high protein solutions. Mesh size increased in A. aemula when fed a high protein solution. MA silk proline and alanine compositions varied in each species with contrasting variations in alanine between the two species. Glycine compositions only varied in C. mulmeinensis silk. No spiders significantly lost or gained mass on any feeding treatment, so they did not sacrifice somatic maintenance for amino acid investment in silk. Conclusions/Significance Our results show that the amount of protein taken in significantly affects the foraging decisions of trap-building predators, such as orb web spiders. Nevertheless, the subtle differences found between species in the association between protein intake, the amino acids invested in silk and web architectural plasticity show that the influence of protein deprivation on specific foraging strategies differs among different spiders. PMID:23349928

Web building and silk properties functionally covary among species of wolf spider.

PubMed

Lacava, Mariángeles; Camargo, Arley; Garcia, Luis F; Benamú, Marco A; Santana, Martin; Fang, Jian; Wang, Xungai; Blamires, Sean J

2018-04-15

Although phylogenetic studies have shown covariation between the properties of spider major ampullate (MA) silk and web building, both spider webs and silks are highly plastic so we cannot be sure whether these traits functionally covary or just vary across environments that the spiders occupy. As MaSp2-like proteins provide MA silk with greater extensibility, their presence is considered necessary for spider webs to effectively capture prey. Wolf spiders (Lycosidae) are predominantly non-web building, but a select few species build webs. We accordingly collected MA silk from two web-building and six non-web-building species found in semirural ecosystems in Uruguay to test whether the presence of MaSp2-like proteins (indicated by amino acid composition, silk mechanical properties and silk nanostructures) was associated with web building across the group. The web-building and non-web-building species were from disparate subfamilies so we estimated a genetic phylogeny to perform appropriate comparisons. For all of the properties measured, we found differences between web-building and non-web-building species. A phylogenetic regression model confirmed that web building and not phylogenetic inertia influences silk properties. Our study definitively showed an ecological influence over spider silk properties. We expect that the presence of the MaSp2-like proteins and the subsequent nanostructures improves the mechanical performance of silks within the webs. Our study furthers our understanding of spider web and silk co-evolution and the ecological implications of spider silk properties. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Synthetic spider silk sustainability verification by techno-economic and life cycle analysis

NASA Astrophysics Data System (ADS)

Edlund, Alan

Major ampullate spider silk represents a promising biomaterial with diverse commercial potential ranging from textiles to medical devices due to the excellent physical and thermal properties from the protein structure. Recent advancements in synthetic biology have facilitated the development of recombinant spider silk proteins from Escherichia coli (E. coli), alfalfa, and goats. This study specifically investigates the economic feasibility and environmental impact of synthetic spider silk manufacturing. Pilot scale data was used to validate an engineering process model that includes all of the required sub-processing steps for synthetic fiber manufacture: production, harvesting, purification, drying, and spinning. Modeling was constructed modularly to support assessment of alternative protein production methods (alfalfa and goats) as well as alternative down-stream processing technologies. The techno-economic analysis indicates a minimum sale price from pioneer and optimized E. coli plants at 761 kg-1 and 23 kg-1 with greenhouse gas emissions of 572 kg CO2-eq. kg-1 and 55 kg CO2-eq. kg-1, respectively. Spider silk sale price estimates from goat pioneer and optimized results are 730 kg-1 and 54 kg-1, respectively, with pioneer and optimized alfalfa plants are 207 kg-1 and 9.22 kg-1 respectively. Elevated costs and emissions from the pioneer plant can be directly tied to the high material consumption and low protein yield. Decreased production costs associated with the optimized plants include improved protein yield, process optimization, and an Nth plant assumption. Discussion focuses on the commercial potential of spider silk, the production performance requirements for commercialization, and impact of alternative technologies on the sustainability of the system.

Multiscale mechanisms of nutritionally induced property variation in spider silks.

PubMed

Blamires, Sean J; Nobbs, Madeleine; Martens, Penny J; Tso, I-Min; Chuang, Wei-Tsung; Chang, Chung-Kai; Sheu, Hwo-Shuenn

2018-01-01

Variability in spider major ampullate (MA) silk properties at different scales has proven difficult to determine and remains an obstacle to the development of synthetic fibers mimicking MA silk performance. A multitude of techniques may be used to measure multiscale aspects of silk properties. Here we fed five species of Araneoid spider solutions that either contained protein or were protein deprived and performed silk tensile tests, small and wide-angle X-ray scattering (SAXS/WAXS), amino acid composition analyses, and silk gene expression analyses, to resolve persistent questions about how nutrient deprivation induces variations in MA silk mechanical properties across scales. Our analyses found that the properties of each spider's silk varied differently in response to variations in their protein intake. We found changes in the crystalline and non-crystalline nanostructures to play specific roles in inducing the property variations we found. Across treatment MaSp expression patterns differed in each of the five species. We found that in most species MaSp expression and amino acid composition variations did not conform with our predictions based on a traditional MaSp expression model. In general, changes to the silk's alanine and proline compositions influenced the alignment of the proteins within the silk's amorphous region, which influenced silk extensibility and toughness. Variations in structural alignment in the crystalline and non-crystalline regions influenced ultimate strength independent of genetic expression. Our study provides the deepest insights thus far into the mechanisms of how MA silk properties vary from gene expression to nanostructure formations to fiber mechanics. Such knowledge is imperative for promoting the production of synthetic silk fibers.

Detection of a Bacteriophage Gene Encoding a Mu-like Portal Protein in Haemophilus parasuis Reference Strains and Field Isolates by Nested Polymerase Chain Reaction

USDA-ARS?s Scientific Manuscript database

A nested PCR assay was developed to determine the presence of a gene encoding a bacteriophage Mu-like portal protein, gp29, in 15 reference strains and 31 field isolates of Haemophilus parasuis. Specific primers, based on the gene’s sequence, were utilized. A majority of the virulent reference strai...

Coat protein expression strategy of oat blue dwarf virus.

PubMed

Edwards, Michael C; Weiland, John J

2014-02-01

Oat blue dwarf virus (OBDV) is a member of the genus Marafivirus whose genome encodes a 227 kDa polyprotein (p227) ostensibly processed post-translationally into its functional components. Encoded near the 3' terminus and coterminal with the p227 ORF are ORFs specifying major and minor capsid proteins (CP). Since the CP expression strategy of marafiviruses has not been thoroughly investigated, we produced a series of point mutants in the OBDV CP encoding gene and examined expression in protoplasts. Results support a model in which the 21 kDa major CP is the product of direct translation of a sgRNA, while the 24 kDa minor CP is a cleavage product derived from both the polyprotein and a larger ~26 kDa precursor translated directly from the sgRNA. Cleavage occurs at an LXG[G/A] motif conserved in many viruses that use papain-like proteases for polyprotein processing and protection against degradation via the ubiquitin-proteasome system. Published by Elsevier Inc.

Diversity Analysis of Dairy and Nondairy Lactococcus lactis Isolates, Using a Novel Multilocus Sequence Analysis Scheme and (GTG)5-PCR Fingerprinting▿

PubMed Central

Rademaker, Jan L. W.; Herbet, Hélène; Starrenburg, Marjo J. C.; Naser, Sabri M.; Gevers, Dirk; Kelly, William J.; Hugenholtz, Jeroen; Swings, Jean; van Hylckama Vlieg, Johan E. T.

2007-01-01

The diversity of a collection of 102 lactococcus isolates including 91 Lactococcus lactis isolates of dairy and nondairy origin was explored using partial small subunit rRNA gene sequence analysis and limited phenotypic analyses. A subset of 89 strains of L. lactis subsp. cremoris and L. lactis subsp. lactis isolates was further analyzed by (GTG)5-PCR fingerprinting and a novel multilocus sequence analysis (MLSA) scheme. Two major genomic lineages within L. lactis were found. The L. lactis subsp. cremoris type-strain-like genotype lineage included both L. lactis subsp. cremoris and L. lactis subsp. lactis isolates. The other major lineage, with a L. lactis subsp. lactis type-strain-like genotype, comprised L. lactis subsp. lactis isolates only. A novel third genomic lineage represented two L. lactis subsp. lactis isolates of nondairy origin. The genomic lineages deviate from the subspecific classification of L. lactis that is based on a few phenotypic traits only. MLSA of six partial genes (atpA, encoding ATP synthase alpha subunit; pheS, encoding phenylalanine tRNA synthetase; rpoA, encoding RNA polymerase alpha chain; bcaT, encoding branched chain amino acid aminotransferase; pepN, encoding aminopeptidase N; and pepX, encoding X-prolyl dipeptidyl peptidase) revealed 363 polymorphic sites (total length, 1,970 bases) among 89 L. lactis subsp. cremoris and L. lactis subsp. lactis isolates with unique sequence types for most isolates. This allowed high-resolution cluster analysis in which dairy isolates form subclusters of limited diversity within the genomic lineages. The pheS DNA sequence analysis yielded two genetic groups dissimilar to the other genotyping analysis-based lineages, indicating a disparate acquisition route for this gene. PMID:17890345

Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting.

PubMed

Rademaker, Jan L W; Herbet, Hélène; Starrenburg, Marjo J C; Naser, Sabri M; Gevers, Dirk; Kelly, William J; Hugenholtz, Jeroen; Swings, Jean; van Hylckama Vlieg, Johan E T

2007-11-01

The diversity of a collection of 102 lactococcus isolates including 91 Lactococcus lactis isolates of dairy and nondairy origin was explored using partial small subunit rRNA gene sequence analysis and limited phenotypic analyses. A subset of 89 strains of L. lactis subsp. cremoris and L. lactis subsp. lactis isolates was further analyzed by (GTG)(5)-PCR fingerprinting and a novel multilocus sequence analysis (MLSA) scheme. Two major genomic lineages within L. lactis were found. The L. lactis subsp. cremoris type-strain-like genotype lineage included both L. lactis subsp. cremoris and L. lactis subsp. lactis isolates. The other major lineage, with a L. lactis subsp. lactis type-strain-like genotype, comprised L. lactis subsp. lactis isolates only. A novel third genomic lineage represented two L. lactis subsp. lactis isolates of nondairy origin. The genomic lineages deviate from the subspecific classification of L. lactis that is based on a few phenotypic traits only. MLSA of six partial genes (atpA, encoding ATP synthase alpha subunit; pheS, encoding phenylalanine tRNA synthetase; rpoA, encoding RNA polymerase alpha chain; bcaT, encoding branched chain amino acid aminotransferase; pepN, encoding aminopeptidase N; and pepX, encoding X-prolyl dipeptidyl peptidase) revealed 363 polymorphic sites (total length, 1,970 bases) among 89 L. lactis subsp. cremoris and L. lactis subsp. lactis isolates with unique sequence types for most isolates. This allowed high-resolution cluster analysis in which dairy isolates form subclusters of limited diversity within the genomic lineages. The pheS DNA sequence analysis yielded two genetic groups dissimilar to the other genotyping analysis-based lineages, indicating a disparate acquisition route for this gene.

Information analysis of posterior canal afferents in the turtle, Trachemys scripta elegans.

PubMed

Rowe, Michael H; Neiman, Alexander B

2012-01-24

We have used sinusoidal and band-limited Gaussian noise stimuli along with information measures to characterize the linear and non-linear responses of morpho-physiologically identified posterior canal (PC) afferents and to examine the relationship between mutual information rate and other physiological parameters. Our major findings are: 1) spike generation in most PC afferents is effectively a stochastic renewal process, and spontaneous discharges are fully characterized by their first order statistics; 2) a regular discharge, as measured by normalized coefficient of variation (cv*), reduces intrinsic noise in afferent discharges at frequencies below the mean firing rate; 3) coherence and mutual information rates, calculated from responses to band-limited Gaussian noise, are jointly determined by gain and intrinsic noise (discharge regularity), the two major determinants of signal to noise ratio in the afferent response; 4) measures of optimal non-linear encoding were only moderately greater than optimal linear encoding, indicating that linear stimulus encoding is limited primarily by internal noise rather than by non-linearities; and 5) a leaky integrate and fire model reproduces these results and supports the suggestion that the combination of high discharge regularity and high discharge rates serves to extend the linear encoding range of afferents to higher frequencies. These results provide a framework for future assessments of afferent encoding of signals generated during natural head movements and for comparison with coding strategies used by other sensory systems. This article is part of a Special Issue entitled: Neural Coding. Copyright © 2011 Elsevier B.V. All rights reserved.

Mutations in the Gene Encoding the Ancillary Pilin Subunit of the Streptococcus suis srtF Cluster Result in Pili Formed by the Major Subunit Only

PubMed Central

Fittipaldi, Nahuel; Takamatsu, Daisuke; Domínguez-Punaro, María de la Cruz; Lecours, Marie-Pier; Montpetit, Diane; Osaki, Makoto; Sekizaki, Tsutomu; Gottschalk, Marcelo

2010-01-01

Pili have been shown to contribute to the virulence of different Gram-positive pathogenic species. Among other critical steps of bacterial pathogenesis, these structures participate in adherence to host cells, colonization and systemic virulence. Recently, the presence of at least four discrete gene clusters encoding putative pili has been revealed in the major swine pathogen and emerging zoonotic agent Streptococcus suis. However, pili production by this species has not yet been demonstrated. In this study, we investigated the functionality of one of these pili clusters, known as the srtF pilus cluster, by the construction of mutant strains for each of the four genes of the cluster as well as by the generation of antibodies against the putative pilin subunits. Results revealed that the S. suis serotype 2 strain P1/7, as well as several other highly virulent invasive S. suis serotype 2 isolates express pili from this cluster. However, in most cases tested, and as a result of nonsense mutations at the 5′ end of the gene encoding the minor pilin subunit (a putative adhesin), pili were formed by the major pilin subunit only. We then evaluated the role these pili play in S. suis virulence. Abolishment of the expression of srtF cluster-encoded pili did not result in impaired interactions of S. suis with porcine brain microvascular endothelial cells. Furthermore, non-piliated mutants were as virulent as the wild type strain when evaluated in a murine model of S. suis sepsis. Our results show that srtF cluster-encoded, S. suis pili are atypical compared to other Gram-positive pili. In addition, since the highly virulent strains under investigation are unlikely to produce other pili, our results suggest that pili might be dispensable for critical steps of the S. suis pathogenesis of infection. PMID:20052283

Overproduction, purification, and biochemical characterization of the dual specificity H1 protein phosphatase encoded by variola major virus.

PubMed

Tropea, Joseph E; Phan, Jason; Waugh, David S

2006-11-01

Smallpox, a highly contagious infectious disease caused by the variola major virus, has an overall mortality rate of about 30%. Because there currently is no specific treatment for smallpox, and the only prevention is vaccination, there is an urgent need for the development of effective antiviral drugs. The dual specificity protein phosphatase encoded by the smallpox virus (H1) is essential for the production of infectious viral particles, making it a promising molecular target for antiviral therapeutics. Here, we report the molecular cloning, overproduction, purification, and initial biochemical characterization of H1 phosphatase, thereby paving the way for the discovery of small molecule inhibitors.

The cell biology of aging.

PubMed

Hayflick, L

1985-02-01

It is only within the past ten years that biogerontology has become attractive to a sufficient number of biologists so that the field can be regarded as a seriously studied discipline. Cytogerontology, or the study of aging at the cellular level, had its genesis about 20 years ago when the dogma that maintained that cultured normal cells could replicate forever was overturned. Normal human and animal cells have a finite capacity to replicate and function whether they are cultured in vitro or transplanted as grafts in vivo. This phenomenon has been interpreted to be aging at the cellular level. Only abnormal somatic cells are capable of immortality. In recent years it has been found that the number of population doublings of which cultured normal cells are capable is inversely proportional to donor age. There is also good evidence that the number of population doublings of cultured normal fibroblasts is directly proportional to the maximum lifespan of ten species that have been studied. Cultures prepared from patients with accelerated aging syndromes (progeria and Werner's syndrome) undergo far fewer doublings than do those of age-matched controls. The normal human fibroblast cell strain WI-38 was established in 1962 from fetal lung, and several hundred ampules of these cells were frozen in liquid nitrogen at that time. These ampules have been reconstituted periodically and shown to be capable of replication. This represents the longest period of time that a normal human cell has ever been frozen. Normal human fetal cell strains such as WI-38 have the capacity to double only about 50 times. If cultures are frozen at various population doublings, the number of doublings remaining after reconstitution is equal to 50 minus the number of doublings that occurred prior to freezing. The memory of the cells has been found to be accurate after 23 years of preservation in liquid nitrogen. Normal human cells incur many physiologic decrements that herald the approach of their failure to divide. Many of these functional decrements are identical to decrements found in humans as they age. Thus it is likely that these decrements are also the precursors of age changes in vivo. The finite replicative capacity of normal cells is never seen to occur in vivo because aging and death of the individual occurs well before the doubling limit is reached.

Dual genetically encoded phage-displayed ligands.

PubMed

Mohan, Kritika; Weiss, Gregory A

2014-05-15

M13 bacteriophage display presents polypeptides as fusions to phage coat proteins. Such phage-displayed ligands offer useful reagents for biosensors. Here, we report a modified phage propagation protocol for the consistent and robust display of two different genetically encoded ligands on the major coat protein, P8. The results demonstrate that the phage surface reaches a saturation point for maximum peptide display. Copyright © 2014 Elsevier Inc. All rights reserved.

Learning from Bacteriophages - Advantages and Limitations of Phage and Phage-Encoded Protein Applications

PubMed Central

Drulis-Kawa, Zuzanna; Majkowska-Skrobek, Grażyna; Maciejewska, Barbara; Delattre, Anne-Sophie; Lavigne, Rob

2012-01-01

The emergence of bacteria resistance to most of the currently available antibiotics has become a critical therapeutic problem. The bacteria causing both hospital and community-acquired infections are most often multidrug resistant. In view of the alarming level of antibiotic resistance between bacterial species and difficulties with treatment, alternative or supportive antibacterial cure has to be developed. The presented review focuses on the major characteristics of bacteriophages and phage-encoded proteins affecting their usefulness as antimicrobial agents. We discuss several issues such as mode of action, pharmacodynamics, pharmacokinetics, resistance and manufacturing aspects of bacteriophages and phage-encoded proteins application. PMID:23305359

Identification of the gene encoding the major NAD(P)H-flavin oxidoreductase of the bioluminescent bacterium Vibrio fischeri ATCC 7744.

PubMed Central

Zenno, S; Saigo, K; Kanoh, H; Inouye, S

1994-01-01

The gene encoding the major NAD(P)H-flavin oxidoreductase (flavin reductase) of the luminous bacterium Vibrio fischeri ATCC 7744 was isolated by using synthetic oligonucleotide probes corresponding to the N-terminal amino acid sequence of the enzyme. Nucleotide sequence analysis suggested that the major flavin reductase of V. fischeri consisted of 218 amino acids and had a calculated molecular weight of 24,562. Cloned flavin reductase expressed in Escherichia coli was purified virtually to homogeneity, and its basic biochemical properties were examined. As in the major flavin reductase in crude extracts of V. fischeri, cloned flavin reductase showed broad substrate specificity and served well as a catalyst to supply reduced flavin mononucleotide (FMNH2) to the bioluminescence reaction. The major flavin reductase of V. fischeri not only showed significant similarity in amino acid sequence to oxygen-insensitive NAD(P)H nitroreductases of Salmonella typhimurium, Enterobacter cloacae, and E. coli but also was associated with a low level of nitroreductase activity. The major flavin reductase of V. fischeri and the nitroreductases of members of the family Enterobacteriaceae would thus appear closely related in evolution and form a novel protein family. Images PMID:8206830

Extensive Microbial and Functional Diversity within the Chicken Cecal Microbiome

PubMed Central

Sergeant, Martin J.; Constantinidou, Chrystala; Cogan, Tristan A.; Bedford, Michael R.; Penn, Charles W.; Pallen, Mark J.

2014-01-01

Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, including the ceca. We have carried out deep microbial community profiling of the microbiota in twenty cecal samples via 16S rRNA gene sequences and an in-depth metagenomics analysis of a single cecal microbiota. We recovered 699 phylotypes, over half of which appear to represent previously unknown species. We obtained 648,251 environmental gene tags (EGTs), the majority of which represent new species. These were binned into over two-dozen draft genomes, which included Campylobacter jejuni and Helicobacter pullorum. We found numerous polysaccharide- and oligosaccharide-degrading enzymes encoding within the metagenome, some of which appeared to be part of polysaccharide utilization systems with genetic evidence for the co-ordination of polysaccharide degradation with sugar transport and utilization. The cecal metagenome encodes several fermentation pathways leading to the production of short-chain fatty acids, including some with novel features. We found a dozen uptake hydrogenases encoded in the metagenome and speculate that these provide major hydrogen sinks within this microbial community and might explain the high abundance of several genera within this microbiome, including Campylobacter, Helicobacter and Megamonas. PMID:24657972

Fast Kinetics of Calcium Signaling and Sensor Design

PubMed Central

Tang, Shen; Reddish, Florence; Zhuo, You; Yang, Jenny J.

2015-01-01

Fast calcium signaling is regulated by numerous calcium channels exhibiting high spatiotemporal profiles which are currently measured by fluorescent calcium sensors. There is still a strong need to improve the kinetics of genetically encoded calcium indicators (sensors) to capture calcium dynamics in the millisecond time frame. In this review, we summarize several major fast calcium signaling pathways and discuss the recent developments and application of genetically encoded calcium indicators to detect these pathways. A new class of genetically encoded calcium indicators designed with site-directed mutagenesis on the surface of beta-barrel fluorescent proteins to form a pentagonal bipyramidal-like calcium binding domain dramatically accelerates calcium binding kinetics. Furthermore, novel genetically encoded calcium indicators with significantly increased fluorescent lifetime change are advantageous in deep-field imaging with high light-scattering and notable morphology change. PMID:26151819

Molecular characterization and expression of the M6 gene of grass carp hemorrhage virus (GCHV), an aquareovirus.

PubMed

Qiu, T; Lu, R H; Zhang, J; Zhu, Z Y

2001-07-01

The complete nucleotide sequence of M6 gene of grass carp hemorrhage virus (GCHV) was determined. It is 2039 nucleotides in length and contains a single large open reading frame that could encode a protein of 648 amino acids with predicted molecular mass of 68.7 kDa. Amino acid sequence comparison revealed that the protein encoded by GCHV M6 is closely related to the protein mu1 of mammalian reovirus. The M6 gene, encoding the major outer-capsid protein, was expressed using the pET fusion protein vector in Escherichia coli and detected by Western blotting using chicken anti-GCHV immunoglobulin (IgY). The result indicates that the protein encoded by M6 may share a putative Asn-42-Pro-43 proteolytic cleavage site with mu1.

Self-initiated encoding facilitates object working memory in schizophrenia: implications for the etiology of working memory deficit.

PubMed

Kim, Jejoong; Park, Sohee; Shin, Yong-Wook; Jin Lee, Kyung; Kwon, Jun Soo

2006-02-15

Working memory (WM) deficit is present in a majority of patients with schizophrenia but it is unclear which components of WM are impaired. Past studies suggest that encoding may be compromised. One important determinant of encoding is the deployment of selective attention to the target stimulus. In addition, attention and encoding are modulated by motivational factors. In this study, we investigated the effects of self-initiated encoding (i.e., voluntary attention) on WM. 19 patients with schizophrenia and 19 matched control subjects participated in visual WM and control tasks. Encoding was manipulated by asking subjects to select from two face targets and memorize 1) one of the two identical faces (Non-preference condition), 2) one that is marked (Non-choice condition), and 3) one they prefer (Preference condition). WM accuracy for both location (spatial) and identity (object) was measured. Overall, patients with schizophrenia were less accurate and slower than the control subjects but the deficit was greater for object WM. However, patients were more accurate in object WM when they selected a preferred face as their target during encoding (preference condition) compared with the other two conditions. This effect was not significant for spatial WM. These results suggest that voluntary, self-initiated attention may facilitate object encoding especially if the selection of the target involves affective choice, and that attention may play different roles in encoding 'what' versus 'where' in WM. Since encoding affects all forms of memory, these results may have a more general implication for memory.

Draft Genome Sequence of Enterohemorrhagic Escherichia coli O157:H7 Strain MC2 Isolated from Cattle in France

PubMed Central

Auffret, Pauline; Segura, Audrey; Klopp, Christophe; Bouchez, Olivier; Kérourédan, Monique; Bibbal, Delphine; Brugère, Hubert; Forano, Evelyne

2017-01-01

ABSTRACT Enterohemorrhagic Escherichia coli (EHEC) with serotype O157:H7 is a major foodborne pathogen. Here, we report the draft genome sequence of EHEC O157:H7 strain MC2 isolated from cattle in France. The assembly contains 5,400,376 bp that encoded 5,914 predicted genes (5,805 protein-encoding genes and 109 RNA genes). PMID:28983004

Characterization of HKE2: an ancient antigen encoded in the major histocompatibility complex.

PubMed

Ostrov, D A; Barnes, C L; Smith, L E; Binns, S; Brusko, T M; Brown, A C; Quint, P S; Litherland, S A; Roopenian, D C; Iczkowski, K A

2007-02-01

Genes at the centromeric end of the human leukocyte antigen region influence adaptive autoimmune diseases and cancer. In this study, we characterized protein expression of HKE2, a gene located in the centromeric portion of the class II region of the major histocompatibility complex encoding subunit 6 of prefoldin. Immunohistochemical analysis using an anti-HKE2 antibody indicated that HKE2 protein expression is dramatically upregulated as a consequence of activation. In a tissue microarray and in several tumors, HKE2 was overexpressed in certain cancers compared with normal counterparts. The localization of the HKE2 gene to the class II region, its cytoplasmic expression and putative protein-binding domain suggest that HKE2 may function in adaptive immunity and cancer.

The Polyketide Components of Waxes and the Cer-cqu Gene Cluster Encoding a Novel Polyketide Synthase, the β-Diketone Synthase, DKS.

PubMed

von Wettstein-Knowles, Penny

2017-07-10

The primary function of the outermost, lipophilic layer of plant aerial surfaces, called the cuticle, is preventing non-stomatal water loss. Its exterior surface is often decorated with wax crystals, imparting a blue-grey color. Identification of the barley Cer-c , -q and -u genes forming the 101 kb Cer-cqu gene cluster encoding a novel polyketide synthase-the β-diketone synthase (DKS), a lipase/carboxyl transferase, and a P450 hydroxylase, respectively, establishes a new, major pathway for the synthesis of plant waxes. The major product is a β-diketone (14,16-hentriacontane) aliphatic that forms long, thin crystalline tubes. A pathway branch leads to the formation of esterified alkan-2-ols.

Genomic polymorphism, recombination, and linkage disequilibrium in human major histocompatibility complex-encoded antigen-processing genes.

PubMed Central

van Endert, P M; Lopez, M T; Patel, S D; Monaco, J J; McDevitt, H O

1992-01-01

Recently, two subunits of a large cytosolic protease and two putative peptide transporter proteins were found to be encoded by genes within the class II region of the major histocompatibility complex (MHC). These genes have been suggested to be involved in the processing of antigenic proteins for presentation by MHC class I molecules. Because of the high degree of polymorphism in MHC genes, and previous evidence for both functional and polypeptide sequence polymorphism in the proteins encoded by the antigen-processing genes, we tested DNA from 27 consanguineous human cell lines for genomic polymorphism by restriction fragment length polymorphism (RFLP) analysis. These studies demonstrate a strong linkage disequilibrium between TAP1 and LMP2 RFLPs. Moreover, RFLPs, as well as a polymorphic stop codon in the telomeric TAP2 gene, appear to be in linkage disequilibrium with HLA-DR alleles and RFLPs in the HLA-DO gene. A high rate of recombination, however, seems to occur in the center of the complex, between the TAP1 and TAP2 genes. Images PMID:1360671

Both flagella and F4 fimbriae from F4ac+ enterotoxigenic Escherichia coli contribute to attachment to IPEC-J2 cells in vitro.

PubMed

Zhou, Mingxu; Duan, Qiangde; Zhu, Xiaofang; Guo, Zhiyan; Li, Yinchau; Hardwidge, Philip R; Zhu, Guoqiang

2013-05-13

The role of flagella in the pathogenesis of F4ac+ Enterotoxigenic Escherichia coli (ETEC) mediated neonatal and post-weaning diarrhea (PWD) is not currently understood. We targeted the reference C83902 ETEC strain (O8:H19:F4ac+ LT+ STa+ STb+), to construct isogenic mutants in the fliC (encoding the major flagellin protein), motA (encoding the flagella motor), and faeG (encoding the major subunit of F4 fimbriae) genes. Both the ΔfliC and ΔfaeG mutants had a reduced ability to adhere to porcine intestinal epithelial IPEC-J2 cells. F4 fimbriae expression was significantly down-regulated after deleting fliC, which revealed that co-regulation exists between flagella and F4 fimbriae. However, there was no difference in adhesion between the ΔmotA mutant and its parent strain. These data demonstrate that both flagella and F4 fimbriae are required for efficient F4ac+ ETEC adhesion in vitro.

Structure, Expression, Chromosomal Location and Product of the Gene Encoding Adh2 in Petunia

PubMed Central

Gregerson, R. G.; Cameron, L.; McLean, M.; Dennis, P.; Strommer, J.

1993-01-01

In most higher plants the genes encoding alcohol dehydrogenase comprise a small gene family, usually with two members. The Adh1 gene of Petunia has been cloned and analyzed, but a second identifiable gene was not recovered from any of three genomic libraries. We have therefore employed the polymerase chain reaction to obtain the major portion of a second Adh gene. From sequence, mapping and northern data we conclude this gene encodes ADH2, the major anaerobically inducible Adh gene of Petunia. The availability of both Adh1 and Adh2 from Petunia has permitted us to compare their structures and patterns of expression to those of the well-studied Adh genes of maize, of which one is highly expressed developmentally, while both are induced in response to hypoxia. Despite their evolutionary distance, evidenced by deduced amino acid sequence as well as taxonomic classification, the pairs of genes are regulated in strikingly similar ways in maize and Petunia. Our findings suggest a significant biological basis for the regulatory strategy employed by these distant species for differential expression of multiple Adh genes. PMID:8096485

Encoding-related brain activity dissociates between the recollective processes underlying successful recall and recognition: a subsequent-memory study.

PubMed

Sadeh, Talya; Maril, Anat; Goshen-Gottstein, Yonatan

2012-07-01

The subsequent-memory (SM) paradigm uncovers brain mechanisms that are associated with mnemonic activity during encoding by measuring participants' neural activity during encoding and classifying the encoding trials according to performance in the subsequent retrieval phase. The majority of these studies have converged on the notion that the mechanism supporting recognition is mediated by familiarity and recollection. The process of recollection is often assumed to be a recall-like process, implying that the active search for the memory trace is similar, if not identical, for recall and recognition. Here we challenge this assumption and hypothesize - based on previous findings obtained in our lab - that the recollective processes underlying recall and recognition might show dissociative patterns of encoding-related brain activity. To this end, our design controlled for familiarity, thereby focusing on contextual, recollective processes. We found evidence for dissociative neurocognitive encoding mechanisms supporting subsequent-recall and subsequent-recognition. Specifically, the contrast of subsequent-recognition versus subsequent-recall revealed activation in the Parahippocampal cortex (PHc) and the posterior hippocampus--regions associated with contextual processing. Implications of our findings and their relation to current cognitive models of recollection are discussed. Copyright © 2012 Elsevier Ltd. All rights reserved.

Genome-Wide Identification and Mapping of NBS-Encoding Resistance Genes in Solanum tuberosum Group Phureja

PubMed Central

Lozano, Roberto; Ponce, Olga; Ramirez, Manuel; Mostajo, Nelly; Orjeda, Gisella

2012-01-01

The majority of disease resistance (R) genes identified to date in plants encode a nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain containing protein. Additional domains such as coiled-coil (CC) and TOLL/interleukin-1 receptor (TIR) domains can also be present. In the recently sequenced Solanum tuberosum group phureja genome we used HMM models and manual curation to annotate 435 NBS-encoding R gene homologs and 142 NBS-derived genes that lack the NBS domain. Highly similar homologs for most previously documented Solanaceae R genes were identified. A surprising ∼41% (179) of the 435 NBS-encoding genes are pseudogenes primarily caused by premature stop codons or frameshift mutations. Alignment of 81.80% of the 577 homologs to S. tuberosum group phureja pseudomolecules revealed non-random distribution of the R-genes; 362 of 470 genes were found in high density clusters on 11 chromosomes. PMID:22493716

Optimized Reaction Conditions for Amide Bond Formation in DNA-Encoded Combinatorial Libraries.

PubMed

Li, Yizhou; Gabriele, Elena; Samain, Florent; Favalli, Nicholas; Sladojevich, Filippo; Scheuermann, Jörg; Neri, Dario

2016-08-08

DNA-encoded combinatorial libraries are increasingly being used as tools for the discovery of small organic binding molecules to proteins of biological or pharmaceutical interest. In the majority of cases, synthetic procedures for the formation of DNA-encoded combinatorial libraries incorporate at least one step of amide bond formation between amino-modified DNA and a carboxylic acid. We investigated reaction conditions and established a methodology by using 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide, 1-hydroxy-7-azabenzotriazole and N,N'-diisopropylethylamine (EDC/HOAt/DIPEA) in combination, which provided conversions greater than 75% for 423/543 (78%) of the carboxylic acids tested. These reaction conditions were efficient with a variety of primary and secondary amines, as well as with various types of amino-modified oligonucleotides. The reaction conditions, which also worked efficiently over a broad range of DNA concentrations and reaction scales, should facilitate the synthesis of novel DNA-encoded combinatorial libraries.

A novel method for intelligent fault diagnosis of rolling bearings using ensemble deep auto-encoders

NASA Astrophysics Data System (ADS)

Shao, Haidong; Jiang, Hongkai; Lin, Ying; Li, Xingqiu

2018-03-01

Automatic and accurate identification of rolling bearings fault categories, especially for the fault severities and fault orientations, is still a major challenge in rotating machinery fault diagnosis. In this paper, a novel method called ensemble deep auto-encoders (EDAEs) is proposed for intelligent fault diagnosis of rolling bearings. Firstly, different activation functions are employed as the hidden functions to design a series of auto-encoders (AEs) with different characteristics. Secondly, EDAEs are constructed with various auto-encoders for unsupervised feature learning from the measured vibration signals. Finally, a combination strategy is designed to ensure accurate and stable diagnosis results. The proposed method is applied to analyze the experimental bearing vibration signals. The results confirm that the proposed method can get rid of the dependence on manual feature extraction and overcome the limitations of individual deep learning models, which is more effective than the existing intelligent diagnosis methods.

Systematic Analysis and Comparison of Nucleotide-Binding Site Disease Resistance Genes in a Diploid Cotton Gossypium raimondii

PubMed Central

Wei, Hengling; Li, Wei; Sun, Xiwei; Zhu, Shuijin; Zhu, Jun

2013-01-01

Plant disease resistance genes are a key component of defending plants from a range of pathogens. The majority of these resistance genes belong to the super-family that harbors a Nucleotide-binding site (NBS). A number of studies have focused on NBS-encoding genes in disease resistant breeding programs for diverse plants. However, little information has been reported with an emphasis on systematic analysis and comparison of NBS-encoding genes in cotton. To fill this gap of knowledge, in this study, we identified and investigated the NBS-encoding resistance genes in cotton using the whole genome sequence information of Gossypium raimondii. Totally, 355 NBS-encoding resistance genes were identified. Analyses of the conserved motifs and structural diversity showed that the most two distinct features for these genes are the high proportion of non-regular NBS genes and the high diversity of N-termini domains. Analyses of the physical locations and duplications of NBS-encoding genes showed that gene duplication of disease resistance genes could play an important role in cotton by leading to an increase in the functional diversity of the cotton NBS-encoding genes. Analyses of phylogenetic comparisons indicated that, in cotton, the NBS-encoding genes with TIR domain not only have their own evolution pattern different from those of genes without TIR domain, but also have their own species-specific pattern that differs from those of TIR genes in other plants. Analyses of the correlation between disease resistance QTL and NBS-encoding resistance genes showed that there could be more than half of the disease resistance QTL associated to the NBS-encoding genes in cotton, which agrees with previous studies establishing that more than half of plant resistance genes are NBS-encoding genes. PMID:23936305

Dual Thermosensitive Hydrogels Assembled from the Conserved C-Terminal Domain of Spider Dragline Silk.

PubMed

Qian, Zhi-Gang; Zhou, Ming-Liang; Song, Wen-Wen; Xia, Xiao-Xia

2015-11-09

Stimuli-responsive hydrogels have great potentials in biomedical and biotechnological applications. Due to the advantages of precise control over molecular weight and being biodegradable, protein-based hydrogels and their applications have been extensively studied. However, protein hydrogels with dual thermosensitive properties are rarely reported. Here we present the first report of dual thermosensitive hydrogels assembled from the conserved C-terminal domain of spider dragline silk. First, we found that recombinant C-terminal domain of major ampullate spidroin 1 (MaSp1) of the spider Nephila clavipes formed hydrogels when cooled to approximately 2 °C or heated to 65 °C. The conformational changes and self-assembly of the recombinant protein were studied to understand the mechanism of the gelation processes using multiple methods. It was proposed that the gelation in the low-temperature regime was dominated by hydrogen bonding and hydrophobic interaction between folded protein molecules, whereas the gelation in the high-temperature regime was due to cross-linking of the exposed hydrophobic patches resulting from partial unfolding of the protein upon heating. More interestingly, genetic fusion of the C-terminal domain to a short repetitive region of N. clavipes MaSp1 resulted in a chimeric protein that formed a hydrogel with significantly improved mechanical properties at low temperatures between 2 and 10 °C. Furthermore, the formation of similar hydrogels was observed for the recombinant C-terminal domains of dragline silk of different spider species, thus demonstrating the conserved ability to form dual thermosensitive hydrogels. These findings may be useful in the design and construction of novel protein hydrogels with tunable multiple thermosensitivity for applications in the future.

Understanding the Mechanical Properties and Structure Transition of Antheraea pernyi Silk Fiber Induced by Its Contraction.

PubMed

Wang, Yu; Wen, Jianchuan; Peng, Bo; Hu, Bingwen; Chen, Xin; Shao, Zhengzhong

2018-02-23

Like most major ampullate silks of spider, the length of Antheraea pernyi silkworm silk can shrink to a certain degree when the fiber is in contact with water. However, what happens in terms of molecule chain level and how it correlates to the mechanical properties of the silk during its contraction is not yet fully understood. Here, we investigate the water-induced mechanical property changes as well as the structure transition of two kinds of A. pernyi silk fiber, which are forcibly reeled from two different individuals (silkworm a and silkworm b; the silk fiber from either one represents the lower and upper limit of the distribution of mechanical properties, respectively). The tensile test results present that most of the mechanical parameters except the post-yield modulus and breaking strain for both silk fibers have the same variation trend before and after their water contraction. Synchrotron FTIR and Raman spectra show that the native filament from silkworm a contains more α-helix structures than that in silkworm b filament, and these α-helices are partially converted to β-sheet structures after the contraction of the fibers, while the order of both β-sheet and α-helix slightly increase. On the other side, the content and orientation of both secondary structural components in silkworm b fiber keep unchanged, no matter if it is native or contracted. 13 C CP/MAS NMR results further indicate that the α-helix/random coil to β-sheet conformational transition that occurred in the silk of silkworm a corresponds the Ala residues. Based upon these results, the detailed structure transition models of both as-reeled A. pernyi silk fibers during water contraction are proposed finally to interpret their properties transformation.

Multiscale mechanisms of nutritionally induced property variation in spider silks

PubMed Central

Nobbs, Madeleine; Martens, Penny J.; Tso, I-Min; Chuang, Wei-Tsung; Chang, Chung-Kai; Sheu, Hwo-Shuenn

2018-01-01

Variability in spider major ampullate (MA) silk properties at different scales has proven difficult to determine and remains an obstacle to the development of synthetic fibers mimicking MA silk performance. A multitude of techniques may be used to measure multiscale aspects of silk properties. Here we fed five species of Araneoid spider solutions that either contained protein or were protein deprived and performed silk tensile tests, small and wide-angle X-ray scattering (SAXS/WAXS), amino acid composition analyses, and silk gene expression analyses, to resolve persistent questions about how nutrient deprivation induces variations in MA silk mechanical properties across scales. Our analyses found that the properties of each spider’s silk varied differently in response to variations in their protein intake. We found changes in the crystalline and non-crystalline nanostructures to play specific roles in inducing the property variations we found. Across treatment MaSp expression patterns differed in each of the five species. We found that in most species MaSp expression and amino acid composition variations did not conform with our predictions based on a traditional MaSp expression model. In general, changes to the silk’s alanine and proline compositions influenced the alignment of the proteins within the silk’s amorphous region, which influenced silk extensibility and toughness. Variations in structural alignment in the crystalline and non-crystalline regions influenced ultimate strength independent of genetic expression. Our study provides the deepest insights thus far into the mechanisms of how MA silk properties vary from gene expression to nanostructure formations to fiber mechanics. Such knowledge is imperative for promoting the production of synthetic silk fibers. PMID:29390013

International consensus on (ICON) anaphylaxis

PubMed Central

2014-01-01

ICON: Anaphylaxis provides a unique perspective on the principal evidence-based anaphylaxis guidelines developed and published independently from 2010 through 2014 by four allergy/immunology organizations. These guidelines concur with regard to the clinical features that indicate a likely diagnosis of anaphylaxis -- a life-threatening generalized or systemic allergic or hypersensitivity reaction. They also concur about prompt initial treatment with intramuscular injection of epinephrine (adrenaline) in the mid-outer thigh, positioning the patient supine (semi-reclining if dyspneic or vomiting), calling for help, and when indicated, providing supplemental oxygen, intravenous fluid resuscitation and cardiopulmonary resuscitation, along with concomitant monitoring of vital signs and oxygenation. Additionally, they concur that H1-antihistamines, H2-antihistamines, and glucocorticoids are not initial medications of choice. For self-management of patients at risk of anaphylaxis in community settings, they recommend carrying epinephrine auto-injectors and personalized emergency action plans, as well as follow-up with a physician (ideally an allergy/immunology specialist) to help prevent anaphylaxis recurrences. ICON: Anaphylaxis describes unmet needs in anaphylaxis, noting that although epinephrine in 1 mg/mL ampules is available worldwide, other essentials, including supplemental oxygen, intravenous fluid resuscitation, and epinephrine auto-injectors are not universally available. ICON: Anaphylaxis proposes a comprehensive international research agenda that calls for additional prospective studies of anaphylaxis epidemiology, patient risk factors and co-factors, triggers, clinical criteria for diagnosis, randomized controlled trials of therapeutic interventions, and measures to prevent anaphylaxis recurrences. It also calls for facilitation of global collaborations in anaphylaxis research. In addition to confirming the alignment of major anaphylaxis guidelines, ICON: Anaphylaxis adds value by including summary tables and citing 130 key references. It is published as an information resource about anaphylaxis for worldwide use by healthcare professionals, academics, policy-makers, patients, caregivers, and the public. PMID:24920969

Membrane and envelope virus proteins co-expressed as lysosome associated membrane protein (LAMP) fused antigens: a potential tool to develop DNA vaccines against flaviviruses.

PubMed

Dhalia, Rafael; Maciel, Milton; Cruz, Fábia S P; Viana, Isabelle F T; Palma, Mariana L; August, Thomas; Marques, Ernesto T A

2009-12-01

Vaccination is the most practical and cost-effective strategy to prevent the majority of the flavivirus infection to which there is an available vaccine. However, vaccines based on attenuated virus can potentially promote collateral side effects and even rare fatal reactions. Given this scenario, the development of alternative vaccination strategies such as DNA-based vaccines encoding specific flavivirus sequences are being considered. Endogenous cytoplasmic antigens, characteristically plasmid DNA-vaccine encoded, are mainly presented to the immune system through Major Histocompatibility Complex class I - MHC I molecules. The MHC I presentation via is mostly associated with a cellular cytotoxic response and often do not elicit a satisfactory humoral response. One of the main strategies to target DNA-encoded antigens to the MHC II compartment is expressing the antigen within the Lysosome-Associated Membrane Protein (LAMP). The flavivirus envelope protein is recognized as the major virus surface protein and the main target for neutralizing antibodies. Different groups have demonstrated that co-expression of flavivirus membrane and envelope proteins in mammalian cells, fused with the carboxyl-terminal of LAMP, is able to induce satisfactory levels of neutralizing antibodies. Here we reviewed the use of the envelope flavivirus protein co-expression strategy as LAMP chimeras with the aim of developing DNA vaccines for dengue, West Nile and yellow fever viruses.

[Genetic instability of probiotic characteristics in the Bifidobacterium longum subsp. longum B379M strain during cultivation and maintenance].

PubMed

Averina, O V; Nezametdinova, V Z; Alekseeva, M G; Danilenko, V N

2012-11-01

The stability of inheriting several genes in the Russian commercial strain Bifidobacterium longum subsp. longum B379M during cultivation and maintenance under laboratory conditions has been studied. The examined genes code for probiotic characteristics, such as utilization of several sugars (lacA2 gene, encoding beta-galactosidase; ara gene, encoding arabinosidase; and galA gene, encoding arabinogalactan endo-beta-galactosidase); synthesis of bacteriocins (lans gene, encoding lanthionine synthetase); and mobile gene tet(W), conferring resistance to the antibiotic tetracycline. The other gene families studied include the genes responsible for signal transduction and adaptation to stress conditions in the majority of bacteria (serine/threonine protein kinases and the toxin-antitoxin systems of MazEF and RelBE types) and transcription regulators (genes encoding WhiB family proteins). Genomic DNA was analyzed by PCR using specially selected primers. A loss of the genes galA and tet(W) has been shown. It is proposed to expand the requirements on probiotic strains, namely, to control retention of the key probiotic genes using molecular biological methods.

Identification of candidate transmission-blocking antigen genes in Theileria annulata and related vector-borne apicomplexan parasites.

PubMed

Lempereur, Laetitia; Larcombe, Stephen D; Durrani, Zeeshan; Karagenc, Tulin; Bilgic, Huseyin Bilgin; Bakirci, Serkan; Hacilarlioglu, Selin; Kinnaird, Jane; Thompson, Joanne; Weir, William; Shiels, Brian

2017-06-05

Vector-borne apicomplexan parasites are a major cause of mortality and morbidity to humans and livestock globally. The most important disease syndromes caused by these parasites are malaria, babesiosis and theileriosis. Strategies for control often target parasite stages in the mammalian host that cause disease, but this can result in reservoir infections that promote pathogen transmission and generate economic loss. Optimal control strategies should protect against clinical disease, block transmission and be applicable across related genera of parasites. We have used bioinformatics and transcriptomics to screen for transmission-blocking candidate antigens in the tick-borne apicomplexan parasite, Theileria annulata. A number of candidate antigen genes were identified which encoded amino acid domains that are conserved across vector-borne Apicomplexa (Babesia, Plasmodium and Theileria), including the Pfs48/45 6-cys domain and a novel cysteine-rich domain. Expression profiling confirmed that selected candidate genes are expressed by life cycle stages within infected ticks. Additionally, putative B cell epitopes were identified in the T. annulata gene sequences encoding the 6-cys and cysteine rich domains, in a gene encoding a putative papain-family cysteine peptidase, with similarity to the Plasmodium SERA family, and the gene encoding the T. annulata major merozoite/piroplasm surface antigen, Tams1. Candidate genes were identified that encode proteins with similarity to known transmission blocking candidates in related parasites, while one is a novel candidate conserved across vector-borne apicomplexans and has a potential role in the sexual phase of the life cycle. The results indicate that a 'One Health' approach could be utilised to develop a transmission-blocking strategy effective against vector-borne apicomplexan parasites of animals and humans.

The Polyketide Components of Waxes and the Cer-cqu Gene Cluster Encoding a Novel Polyketide Synthase, the β-Diketone Synthase, DKS

PubMed Central

von Wettstein-Knowles, Penny

2017-01-01

The primary function of the outermost, lipophilic layer of plant aerial surfaces, called the cuticle, is preventing non-stomatal water loss. Its exterior surface is often decorated with wax crystals, imparting a blue–grey color. Identification of the barley Cer-c, -q and -u genes forming the 101 kb Cer-cqu gene cluster encoding a novel polyketide synthase—the β-diketone synthase (DKS), a lipase/carboxyl transferase, and a P450 hydroxylase, respectively, establishes a new, major pathway for the synthesis of plant waxes. The major product is a β-diketone (14,16-hentriacontane) aliphatic that forms long, thin crystalline tubes. A pathway branch leads to the formation of esterified alkan-2-ols. PMID:28698520

Cloning and Expression of Genes for Dengue Virus Type-2 Encoded-Antigens for Rapid Diagnosis and Vaccine Development

DTIC Science & Technology

1988-10-31

00 0 Cloning and Expression of Genes for Dengue Virus (Type-2 Encoded-Antigens for Rapid ODiagnosis and Vaccine DevelopmentN| ANNUAL PROGRESS REPORT...11. TITLE (include Security Classification) Cloning and Expression of Genes f or Dengue Virus Type 2 Fncoded Antigens for Rapid Diagnosis and Vaccine ...epidemics in Central and South Americas and the Caribbean is a cause of major concern. An effective vaccine is not available to protect individuals

Combinations of glycerol percent, glycerol equilibration time, and thawing rate upon freezability of bull spermatozoa in plastic straws.

PubMed

Wiggin, H B; Almquist, J O

1975-03-01

Twelve ejaculates were used in a central composite experiment to test 15 combinations of glycerol (7, 9, 11, 13, or 15%), glycerol equilibration times (1, 2, 4, 8, or 16 h) and thawing rates (water at 35 C for 15 s, 50 C for 13 s, 65 C for 11 s, 80 C for 9 s, or 95 C for 7 s). Semen was diluted in heated skim milk-glycerol, packaged in .3-ml. Continental U.S. straws and frozen in liquid nitrogen vapor. Based on post-thaw progressive sperm motility after storage at -196 C for 9 to 11 days, estimated optima from multiple regression were 10.7% for glycerol, 2.0 h for glycerol equilibration time, and 76 C for thawing bath temperature. Only the linear effect for each variable was significant. Much faster thawing rates and shorter glycerol equilibration times than those for freezing bull spermatozoa in glass ampules should be used for maximum post-thaw sperm motility in straws.

Glasses of the As/sub 2/S/sub 3/-T1/sub 2/S system

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

Gutenev, M.S.

1986-08-01

A dielcometric study of (AsS /SUB 1.5/ ) /SUB 1-x/ (TiS /SUB 0.5/ ) /SUB x/ (0 is less than or equal to x is less than or equal to 0.61) glasses was carried out. Glassforming alloys were prepared in thin-walled quartz ampules by rapid cooling from 700 C in air. The methods of determination of permittivity, refractive index, and density, the values of which are shown here, have been previously discussed. The molar infrared polarizability is calculated from the experimental data previously gathered, and the concentration dependence is shown. In this paper, the presence of chemical atomic order inmore » T1AsS/sub 2/ glass described by TISAsS /SUB 2/2/ structural units was experimentally proved. An assumption was made of strong mutual influence of T1AsS/sub 2/ and AsS /SUB 1.5/ complexes caused by coordination of thallium with bridging sulfur atoms.« less

Solidification and crystal growth of solid solution semiconducting alloys

NASA Technical Reports Server (NTRS)

Lehoczky, S. L.; Szofran, F. R.

1984-01-01

Problems associated with the solidification and crytal growth of solid-solution semiconducting alloy crystals in a terrestrial environment are described. A detailed description is given of the results for the growth of mercury cadmium telluride (HgCdTe) alloy crystals by directional solidification, because of their considerable technological importance. A series of HgCdTe alloy crystals are grown from pseudobinary melts by a vertical Bridgman method using a wide range of growth rates and thermal conditions. Precision measurements are performed to establish compositional profiles for the crystals. The compositional variations are related to compositional variations in the melts that can result from two-dimensional diffusion or density gradient driven flow effects ahead of the growth interface. These effects are discussed in terms of the alloy phase equilibrium properties, the recent high temperature thermophysical data for the alloys and the highly unusual heat transfer characteristics of the alloy/ampule/furnace system that may readily lead to double diffusive convective flows in a gravitational environment.

Growth of In/sub 2/S/sub 3/ and CdIn/sub 2/S/sub 4/ single crystals from a solution in a melt

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

Buzhor, V.P.; Lyalikova, R. Yu.; Radautsan, S.I.

1986-08-01

The authors studied the reaction of In/sub 2/S/sub 3/ and CdIn/sub 2/S/sub 4/ with melts based on cadmium chloride. As the initial materials, they used polycrystalline In/sub 2/S/sub 3/ and CdIn/sub 2/S/sub 4/, cadmium chloride, and cadmium sulfide. The studies were carried out by the method of thermal analysis in sealed quartz ampules on an MOM derivatotograph. The solubility curve of In/sub 2/S/sub 3/ in a cadmium chloride melt is given. Nucleation occurs both within the liquid pahse and on the walls of the reaction container. At cooling rates of 4-5 K/h, with a charge of 100 g in amore » reaction container of diameter 20 mm the authors obtained In/sub 2/S/sub 3/ and CdIn/sub 2/S/sub 4/ crystals measuring 10-12 mm in size.« less

Reactivity of amine antioxidants relative to OH and anti e

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

Minkhadzhidinova, D.R.; Nikiforov, G.A.; Khrapova, N.G.

1986-06-20

An ESR study was carried out on the reactivity of various types of amines relative to OH/sup ./ and anti e. The selection of these compounds having anti-oxidant properties was also based on the circumstance that amine molecules contain a set of functional groups which may be potential sites for the attack of both OH and anti e radicals. A sample of 6 M H/sub 3/PO/sub 4/ was used for the matrix solutions and forms a glass upon rapid insertion into liquid nitrogen. The phosphoric acid solutions of these compounds taken in concentrations from 0.025 to 0.05 M were flushedmore » with argon to remove oxygen. Ampules containing the solutions were inserted into liquid nitrogen and irradiated from a cobalt source. The ESR spectra of the irradiated solutions clearly show the components of the atomic hydrogen doublet with a = 50 mT and of H/sub 2/PO/sub 4//sup ./ radicals in the central region of the spectrum.« less

The neural representation of social networks.

PubMed

Weaverdyck, Miriam E; Parkinson, Carolyn

2018-05-24

The computational demands associated with navigating large, complexly bonded social groups are thought to have significantly shaped human brain evolution. Yet, research on social network representation and cognitive neuroscience have progressed largely independently. Thus, little is known about how the human brain encodes the structure of the social networks in which it is embedded. This review highlights recent work seeking to bridge this gap in understanding. While the majority of research linking social network analysis and neuroimaging has focused on relating neuroanatomy to social network size, researchers have begun to define the neural architecture that encodes social network structure, cognitive and behavioral consequences of encoding this information, and individual differences in how people represent the structure of their social world. Copyright © 2018 Elsevier Ltd. All rights reserved.

Complementary DNA sequences encoding the multimammate rat MHC class II DQ alpha and beta chains and cross-species sequence comparison in rodents.

PubMed

de Bellocq, J Goüy; Leirs, H

2009-09-01

Sequences of the complete open reading frame (ORF) for rodents major histocompatibility complex (MHC) class II genes are rare. Multimammate rat (Mastomys natalensis) complementary DNA (cDNA) encoding the alpha and beta chains of MHC class II DQ gene was cloned from a rapid amplifications of cDNA Emds (RACE) cDNA library. The ORFs consist of 801 and 771 bp encoding 266 and 256 amino acid residues for DQB and DQA, respectively. The genomic structure of Mana-DQ genes is globally analogous to that described for other rodents except for the insertion of a serine residue in the signal peptide of Mana-DQB, which is unique among known rodents.

Investigations of interpolation errors of angle encoders for high precision angle metrology

NASA Astrophysics Data System (ADS)

Yandayan, Tanfer; Geckeler, Ralf D.; Just, Andreas; Krause, Michael; Asli Akgoz, S.; Aksulu, Murat; Grubert, Bernd; Watanabe, Tsukasa

2018-06-01

Interpolation errors at small angular scales are caused by the subdivision of the angular interval between adjacent grating lines into smaller intervals when radial gratings are used in angle encoders. They are often a major error source in precision angle metrology and better approaches for determining them at low levels of uncertainty are needed. Extensive investigations of interpolation errors of different angle encoders with various interpolators and interpolation schemes were carried out by adapting the shearing method to the calibration of autocollimators with angle encoders. The results of the laboratories with advanced angle metrology capabilities are presented which were acquired by the use of four different high precision angle encoders/interpolators/rotary tables. State of the art uncertainties down to 1 milliarcsec (5 nrad) were achieved for the determination of the interpolation errors using the shearing method which provides simultaneous access to the angle deviations of the autocollimator and of the angle encoder. Compared to the calibration and measurement capabilities (CMC) of the participants for autocollimators, the use of the shearing technique represents a substantial improvement in the uncertainty by a factor of up to 5 in addition to the precise determination of interpolation errors or their residuals (when compensated). A discussion of the results is carried out in conjunction with the equipment used.

Effect of phase-encoding direction on group analysis of resting-state functional magnetic resonance imaging.

PubMed

Mori, Yasuo; Miyata, Jun; Isobe, Masanori; Son, Shuraku; Yoshihara, Yujiro; Aso, Toshihiko; Kouchiyama, Takanori; Murai, Toshiya; Takahashi, Hidehiko

2018-05-17

Echo-planar imaging is a common technique used in functional magnetic resonance imaging (fMRI), however it suffers from image distortion and signal loss because of large susceptibility effects that are related to the phase-encoding direction of the scan. Despite this relationship, the majority of neuroimaging studies have not considered the influence of phase-encoding direction. Here, we aimed to clarify how phase-encoding direction can affect the outcome of an fMRI connectivity study of schizophrenia. Resting-state fMRI using anterior to posterior (A-P) and posterior to anterior (P-A) directions was used to examine 25 patients with schizophrenia (SC) and 37 matched healthy controls (HC). We conducted a functional connectivity analysis using independent component analysis and performed three group comparisons: A-P vs. P-A (all participants), SC vs. HC for the A-P and P-A datasets, and the interaction between phase-encoding direction and participant group. The estimated functional connectivity differed between the two phase-encoding directions in areas that were more extensive than those where signal loss has been reported. Although functional connectivity in the SC group was lower than that in the HC group for both directions, the A-P and P-A conditions did not exhibit the same specific pattern of differences. Further, we observed an interaction between participant group and the phase-encoding direction in the left temporo-parietal junction and left fusiform gyrus. Phase-encoding direction can influence the results of functional connectivity studies. Thus, appropriate selection and documentation of phase-encoding direction will be important in future resting-state fMRI studies. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Determining the Neural Substrate for Encoding a Memory of Human Pain and the Influence of Anxiety

PubMed Central

Kong, Yazhuo; Tracey, Irene

2017-01-01

To convert a painful stimulus into a briefly maintainable construct when the painful stimulus is no longer accessible is essential to guide human behavior and avoid dangerous situations. Because of the aversive nature of pain, this encoding process might be influenced by emotional aspects and could thus vary across individuals, but we have yet to understand both the basic underlying neural mechanisms as well as potential interindividual differences. Using fMRI in combination with a delayed-discrimination task in healthy volunteers of both sexes, we discovered that brain regions involved in this working memory encoding process were dissociable according to whether the to-be-remembered stimulus was painful or not, with the medial thalamus and the rostral anterior cingulate cortex encoding painful and the primary somatosensory cortex encoding nonpainful stimuli. Encoding of painful stimuli furthermore significantly enhanced functional connectivity between the thalamus and medial prefrontal cortex (mPFC). With regards to emotional aspects influencing encoding processes, we observed that more anxious participants showed significant performance advantages when encoding painful stimuli. Importantly, only during the encoding of pain, the interindividual differences in anxiety were associated with the strength of coupling between medial thalamus and mPFC, which was furthermore related to activity in the amygdala. These results indicate not only that there is a distinct signature for the encoding of a painful experience in humans, but also that this encoding process involves a strong affective component. SIGNIFICANCE STATEMENT To convert the sensation of pain into a briefly maintainable construct is essential to guide human behavior and avoid dangerous situations. Although this working memory encoding process is implicitly contained in the majority of studies, the underlying neural mechanisms remain unclear. Using fMRI in a delayed-discrimination task, we found that the encoding of pain engaged the activation of the medial thalamus and the functional connectivity between the thalamus and medial prefrontal cortex. These fMRI data were directly and indirectly related to participants' self-reported trait and state anxiety. Our findings indicate that the mechanisms responsible for the encoding of noxious stimuli differ from those for the encoding of innocuous stimuli, and that these mechanisms are shaped by an individual's anxiety levels. PMID:29097595

Determining the Neural Substrate for Encoding a Memory of Human Pain and the Influence of Anxiety.

PubMed

Tseng, Ming-Tsung; Kong, Yazhuo; Eippert, Falk; Tracey, Irene

2017-12-06

To convert a painful stimulus into a briefly maintainable construct when the painful stimulus is no longer accessible is essential to guide human behavior and avoid dangerous situations. Because of the aversive nature of pain, this encoding process might be influenced by emotional aspects and could thus vary across individuals, but we have yet to understand both the basic underlying neural mechanisms as well as potential interindividual differences. Using fMRI in combination with a delayed-discrimination task in healthy volunteers of both sexes, we discovered that brain regions involved in this working memory encoding process were dissociable according to whether the to-be-remembered stimulus was painful or not, with the medial thalamus and the rostral anterior cingulate cortex encoding painful and the primary somatosensory cortex encoding nonpainful stimuli. Encoding of painful stimuli furthermore significantly enhanced functional connectivity between the thalamus and medial prefrontal cortex (mPFC). With regards to emotional aspects influencing encoding processes, we observed that more anxious participants showed significant performance advantages when encoding painful stimuli. Importantly, only during the encoding of pain, the interindividual differences in anxiety were associated with the strength of coupling between medial thalamus and mPFC, which was furthermore related to activity in the amygdala. These results indicate not only that there is a distinct signature for the encoding of a painful experience in humans, but also that this encoding process involves a strong affective component. SIGNIFICANCE STATEMENT To convert the sensation of pain into a briefly maintainable construct is essential to guide human behavior and avoid dangerous situations. Although this working memory encoding process is implicitly contained in the majority of studies, the underlying neural mechanisms remain unclear. Using fMRI in a delayed-discrimination task, we found that the encoding of pain engaged the activation of the medial thalamus and the functional connectivity between the thalamus and medial prefrontal cortex. These fMRI data were directly and indirectly related to participants' self-reported trait and state anxiety. Our findings indicate that the mechanisms responsible for the encoding of noxious stimuli differ from those for the encoding of innocuous stimuli, and that these mechanisms are shaped by an individual's anxiety levels. Copyright © 2017 Tseng et al.

Discerning regulation of cis- and trans-presentation of CD8+ T-cell epitopes by EBV-encoded oncogene LMP-1 through self-aggregation.

PubMed

Smith, Corey; Wakisaka, Naohiro; Crough, Tania; Peet, Jesse; Yoshizaki, Tomokazu; Beagley, Leone; Khanna, Rajiv

2009-06-11

Activation of the nuclear factor-kappaB pathway by Epstein-Barr virus-encoded latent membrane protein-1 (LMP-1) leads to an up-regulation of the major histocompatibility complex class I antigen-processing pathway. Paradoxically, LMP-1 itself induces a subdominant CD8+ T-cell response and appears to have evolved to avoid immune recognition. Here we show that, although expression of LMP-1 in human cells dramatically enhanced the trans-presentation of CD8+ T-cell epitopes, cis-presentation of LMP-1-derived epitopes was severely impaired. Testing of a series of LMP-1 mutants revealed that deletion of the first transmembrane domain of LMP-1, which prevented self-aggregation, significantly enhanced cis-presentation of T-cell epitopes from this protein, whereas it lost its ability to up-regulate trans-presentation. Interestingly, we also found that cis-presentation of LMP-1 epitopes was rescued by blocking the proteasome function. Taken together, these results delineate a novel mechanism of immune evasion, which renders a virally encoded oncogene inaccessible to the conventional major histocompatibility complex class I pathway limiting its cis-presentation to effector cells.

Cloning and sequencing of a gene encoding the 69-kDa extracellular chitinase of Janthinobacterium lividum.

PubMed

Gleave, A P; Taylor, R K; Morris, B A; Greenwood, D R

1995-09-15

Janthinobacterium lividum secretes a major 56-kDa chitinase and a minor 69-kDa chitinase. A chitinase gene was defined on a 3-kb fragment of clone pRKT10, by virtue of fluorescent colonies in the presence of 4-methylumbelliferyl-beta-D-N,N',N"-chitotrioside. Nucleotide sequencing revealed an 1998-bp open reading frame with the potential to encode a 69,716-Da protein with amino acid sequences similar to those in other chitinases, suggesting it encodes the minor chitinase (Chi69). Chitinase activity of Escherichia coli (pRKT10) lysates was detected mainly in the periplasmic fraction and immunoblotting detected a 70-kDa protein in this fraction. Chi69 has an N-terminal secretory leader peptide preceding two probable chitin-binding domains and a catalytic domain. These functional domains are separated by linker regions of proline-threonine repeats. Amino acid sequencing of cyanogen bromide cleavage-derived peptides from the major 56-kDa chitinase suggested that Chi69 may be a precursor of Chi56. In addition, an N-terminally truncated version of Chi69 retained chitinase activity as expected if in vivo processing of Chi69 generates Chi56.

A Complex Distribution of Elongation Family GTPases EF1A and EFL in Basal Alveolate Lineages

PubMed Central

Mikhailov, Kirill V.; Janouškovec, Jan; Tikhonenkov, Denis V.; Mirzaeva, Gulnara S.; Diakin, Andrei Yu.; Simdyanov, Timur G.; Mylnikov, Alexander P.; Keeling, Patrick J.; Aleoshin, Vladimir V.

2014-01-01

Translation elongation factor-1 alpha (EF1A) and the related GTPase EF-like (EFL) are two proteins with a complex mutually exclusive distribution across the tree of eukaryotes. Recent surveys revealed that the distribution of the two GTPases in even closely related taxa is frequently at odds with their phylogenetic relationships. Here, we investigate the distribution of EF1A and EFL in the alveolate supergroup. Alveolates comprise three major lineages: ciliates and apicomplexans encode EF1A, whereas dinoflagellates encode EFL. We searched transcriptome databases for seven early-diverging alveolate taxa that do not belong to any of these groups: colpodellids, chromerids, and colponemids. Current data suggest all seven are expected to encode EF1A, but we find three genera encode EFL: Colpodella, Voromonas, and the photosynthetic Chromera. Comparing this distribution with the phylogeny of alveolates suggests that EF1A and EFL evolution in alveolates cannot be explained by a simple horizontal gene transfer event or lineage sorting. PMID:25179686

Correlation of rare coding variants in the gene encoding human glucokinase regulatory protein with phenotypic, cellular, and kinetic outcomes.

PubMed

Rees, Matthew G; Ng, David; Ruppert, Sarah; Turner, Clesson; Beer, Nicola L; Swift, Amy J; Morken, Mario A; Below, Jennifer E; Blech, Ilana; Mullikin, James C; McCarthy, Mark I; Biesecker, Leslie G; Gloyn, Anna L; Collins, Francis S

2012-01-01

Defining the genetic contribution of rare variants to common diseases is a major basic and clinical science challenge that could offer new insights into disease etiology and provide potential for directed gene- and pathway-based prevention and treatment. Common and rare nonsynonymous variants in the GCKR gene are associated with alterations in metabolic traits, most notably serum triglyceride levels. GCKR encodes glucokinase regulatory protein (GKRP), a predominantly nuclear protein that inhibits hepatic glucokinase (GCK) and plays a critical role in glucose homeostasis. The mode of action of rare GCKR variants remains unexplored. We identified 19 nonsynonymous GCKR variants among 800 individuals from the ClinSeq medical sequencing project. Excluding the previously described common missense variant p.Pro446Leu, all variants were rare in the cohort. Accordingly, we functionally characterized all variants to evaluate their potential phenotypic effects. Defects were observed for the majority of the rare variants after assessment of cellular localization, ability to interact with GCK, and kinetic activity of the encoded proteins. Comparing the individuals with functional rare variants to those without such variants showed associations with lipid phenotypes. Our findings suggest that, while nonsynonymous GCKR variants, excluding p.Pro446Leu, are rare in individuals of mixed European descent, the majority do affect protein function. In sum, this study utilizes computational, cell biological, and biochemical methods to present a model for interpreting the clinical significance of rare genetic variants in common disease.

[The ENCODE project and functional genomics studies].

PubMed

Ding, Nan; Qu, Hongzhu; Fang, Xiangdong

2014-03-01

Upon the completion of the Human Genome Project, scientists have been trying to interpret the underlying genomic code for human biology. Since 2003, National Human Genome Research Institute (NHGRI) has invested nearly $0.3 billion and gathered over 440 scientists from more than 32 institutions in the United States, China, United Kingdom, Japan, Spain and Singapore to initiate the Encyclopedia of DNA Elements (ENCODE) project, aiming to identify and analyze all regulatory elements in the human genome. Taking advantage of the development of next-generation sequencing technologies and continuous improvement of experimental methods, ENCODE had made remarkable achievements: identified methylation and histone modification of DNA sequences and their regulatory effects on gene expression through altering chromatin structures, categorized binding sites of various transcription factors and constructed their regulatory networks, further revised and updated database for pseudogenes and non-coding RNA, and identified SNPs in regulatory sequences associated with diseases. These findings help to comprehensively understand information embedded in gene and genome sequences, the function of regulatory elements as well as the molecular mechanism underlying the transcriptional regulation by noncoding regions, and provide extensive data resource for life sciences, particularly for translational medicine. We re-viewed the contributions of high-throughput sequencing platform development and bioinformatical technology improve-ment to the ENCODE project, the association between epigenetics studies and the ENCODE project, and the major achievement of the ENCODE project. We also provided our prospective on the role of the ENCODE project in promoting the development of basic and clinical medicine.

Relative cue encoding in the context of sophisticated models of categorization: Separating information from categorization.

PubMed

Apfelbaum, Keith S; McMurray, Bob

2015-08-01

Traditional studies of human categorization often treat the processes of encoding features and cues as peripheral to the question of how stimuli are categorized. However, in domains where the features and cues are less transparent, how information is encoded prior to categorization may constrain our understanding of the architecture of categorization. This is particularly true in speech perception, where acoustic cues to phonological categories are ambiguous and influenced by multiple factors. Here, it is crucial to consider the joint contributions of the information in the input and the categorization architecture. We contrasted accounts that argue for raw acoustic information encoding with accounts that posit that cues are encoded relative to expectations, and investigated how two categorization architectures-exemplar models and back-propagation parallel distributed processing models-deal with each kind of information. Relative encoding, akin to predictive coding, is a form of noise reduction, so it can be expected to improve model accuracy; however, like predictive coding, the use of relative encoding in speech perception by humans is controversial, so results are compared to patterns of human performance, rather than on the basis of overall accuracy. We found that, for both classes of models, in the vast majority of parameter settings, relative cues greatly helped the models approximate human performance. This suggests that expectation-relative processing is a crucial precursor step in phoneme categorization, and that understanding the information content is essential to understanding categorization processes.

Relative cue encoding in the context of sophisticated models of categorization: Separating information from categorization

PubMed Central

McMurray, Bob

2014-01-01

Traditional studies of human categorization often treat the processes of encoding features and cues as peripheral to the question of how stimuli are categorized. However, in domains where the features and cues are less transparent, how information is encoded prior to categorization may constrain our understanding of the architecture of categorization. This is particularly true in speech perception, where acoustic cues to phonological categories are ambiguous and influenced by multiple factors. Here, it is crucial to consider the joint contributions of the information in the input and the categorization architecture. We contrasted accounts that argue for raw acoustic information encoding with accounts that posit that cues are encoded relative to expectations, and investigated how two categorization architectures—exemplar models and back-propagation parallel distributed processing models—deal with each kind of information. Relative encoding, akin to predictive coding, is a form of noise reduction, so it can be expected to improve model accuracy; however, like predictive coding, the use of relative encoding in speech perception by humans is controversial, so results are compared to patterns of human performance, rather than on the basis of overall accuracy. We found that, for both classes of models, in the vast majority of parameter settings, relative cues greatly helped the models approximate human performance. This suggests that expectation-relative processing is a crucial precursor step in phoneme categorization, and that understanding the information content is essential to understanding categorization processes. PMID:25475048

PCR cloning and characterization of multiple ADP-glucose pyrophosphorylase cDNAs from tomato

NASA Technical Reports Server (NTRS)

Chen, B. Y.; Janes, H. W.; Gianfagna, T.

1998-01-01

Four ADP-glucose pyrophosphorylase (AGP) cDNAs were cloned from tomato fruit and leaves by the PCR techniques. Three of them (agp S1, agp S2, and agp S3) encode the large subunit of AGP, the fourth one (agp B) encodes the small subunit. The deduced amino acid sequences of the cDNAs show very high identities (96-98%) to the corresponding potato AGP isoforms, although there are major differences in tissue expression profiles. All four tomato AGP transcripts were detected in fruit and leaves; the predominant ones in fruit are agp B and agp S1, whereas in leaves they are agp B and agp S3. Genomic southern analysis suggests that the four AGP transcripts are encoded by distinct genes.

Simultaneous multiplexing and encoding of multiple images based on a double random phase encryption system

NASA Astrophysics Data System (ADS)

Alfalou, Ayman; Mansour, Ali

2009-09-01

Nowadays, protecting information is a major issue in any transmission system, as showed by an increasing number of research papers related to this topic. Optical encoding methods, such as a Double Random Phase encryption system i.e. DRP, are widely used and cited in the literature. DRP systems have very simple principle and they are easily applicable to most images (B&W, gray levels or color). Moreover, some applications require an enhanced encoding level based on multiencryption scheme and including biometric keys (as digital fingerprints). The enhancement should be done without increasing transmitted or stored information. In order to achieve that goal, a new approach for simultaneous multiplexing & encoding of several target images is developed in this manuscript. By introducing two additional security levels, our approach enhances the security level of a classic "DRP" system. Our first security level consists in using several independent image-keys (randomly and structurally) along with a new multiplexing algorithm. At this level, several target images (multiencryption) are used. This part can reduce needed information (encoding information). At the second level a standard DRP system is included. Finally, our approach can detect if any vandalism attempt has been done on transmitted encrypted images.

DNA-encoded libraries - an efficient small molecule discovery technology for the biomedical sciences.

PubMed

Kunig, Verena; Potowski, Marco; Gohla, Anne; Brunschweiger, Andreas

2018-06-27

DNA-encoded compound libraries are a highly attractive technology for the discovery of small molecule protein ligands. These compound collections consist of small molecules covalently connected to individual DNA sequences carrying readable information about the compound structure. DNA-tagging allows for efficient synthesis, handling and interrogation of vast numbers of chemically synthesized, drug-like compounds. They are screened on proteins by an efficient, generic assay based on Darwinian principles of selection. To date, selection of DNA-encoded libraries allowed for the identification of numerous bioactive compounds. Some of these compounds uncovered hitherto unknown allosteric binding sites on target proteins; several compounds proved their value as chemical biology probes unraveling complex biology; and the first examples of clinical candidates that trace their ancestry to a DNA-encoded library were reported. Thus, DNA-encoded libraries proved their value for the biomedical sciences as a generic technology for the identification of bioactive drug-like molecules numerous times. However, large scale experiments showed that even the selection of billions of compounds failed to deliver bioactive compounds for the majority of proteins in an unbiased panel of target proteins. This raises the question of compound library design.

Effortful semantic decision-making boosts memory performance in older adults.

PubMed

Fu, Li; Maes, Joseph H R; Varma, Samarth; Kessels, Roy P C; Daselaar, Sander M

2017-04-01

A major concern in age-related cognitive decline is episodic memory (EM). Previous studies indicate that both resource and binding deficits contribute to EM decline. Environmental support by task manipulations encouraging stronger cognitive effort and deeper levels of processing may facilitate compensation for these two deficits. To clarify factors that can counteract age-related EM decline, we assessed effects of cognitive effort (four levels) and level of processing (LoP, shallow/deep) during encoding on subsequent retrieval. Young (YAs, N = 23) and older (OAs, N = 23) adults performed two incidental encoding tasks, deep/semantic and shallow/perceptual. Cognitive effort was manipulated by varying decision-making demands. EM performance, indexed by d-prime, was later tested using a recognition task. Results showed that regardless of LoP, increased cognitive effort caused higher d-primes in both age groups. Compared to YAs, OAs showed a lower d-prime after shallow encoding across all cognitive effort levels, and after deep encoding with low cognitive effort. Deep encoding with higher levels of cognitive effort completely eliminated these age differences. Our findings support an environmental-compensatory account of cognitive ageing and can have important therapeutic implications.

Distinct cagA EPIYA motifs are associated with ethnic diversity in Malaysia and Singapore.

PubMed

Schmidt, Heather-Marie A; Goh, Khean-Lee; Fock, Kwong Ming; Hilmi, Ida; Dhamodaran, Subbiah; Forman, David; Mitchell, Hazel

2009-08-01

In vitro studies have shown that the biologic activity of CagA is influenced by the number and class of EPIYA motifs present in its variable region as these motifs correspond to the CagA phosphorylation sites. It has been hypothesized that strains possessing specific combinations of these motifs may be responsible for gastric cancer development. This study investigated the prevalence of cagA and the EPIYA motifs with regard to number, class, and patterns in strains from the three major ethnic groups within the Malaysian and Singaporean populations in relation to disease development. Helicobacter pylori isolates from 49 Chinese, 43 Indian, and 14 Malay patients with functional dyspepsia (FD) and 21 gastric cancer (GC) cases were analyzed using polymerase chain reaction for the presence of cagA and the number, type, and pattern of EPIYA motifs. Additionally, the EPIYA motifs of 47 isolates were sequenced. All 126 isolates possessed cagA, with the majority encoding EPIYA-A (97.6%) and all encoding EPIYA-B. However, while the cagA of 93.0% of Indian FD isolates encoded EPIYA-C as the third motif, 91.8% of Chinese FD isolates and 81.7% of Chinese GC isolates encoded EPIYA-D (p < .001). Of Malay FD isolates, 61.5% and 38.5% possessed EPIYA-C and EPIYA-D, respectively. The majority of isolates possessed three EPIYA motifs; however, Indian isolates were significantly more likely to have four or more (p < .05). Although, H. pylori strains with distinct cagA-types are circulating within the primary ethnic groups resident in Malaysia and Singapore, these genotypes appear unassociated with the development of GC in the ethnic Chinese population. The phenomenon of distinct strains circulating within different ethnic groups, in combination with host and certain environmental factors, may help to explain the rates of GC development in Malaysia.

White matter pathway supporting phonological encoding in speech production: a multi-modal imaging study of brain damage patients.

PubMed

Han, Zaizhu; Ma, Yujun; Gong, Gaolang; Huang, Ruiwang; Song, Luping; Bi, Yanchao

2016-01-01

In speech production, an important step before motor programming is the retrieval and encoding of the phonological elements of target words. It has been proposed that phonological encoding is supported by multiple regions in the left frontal, temporal and parietal regions and their underlying white matter, especially the left arcuate fasciculus (AF) or superior longitudinal fasciculus (SLF). It is unclear, however, whether the effects of AF/SLF are indeed related to phonological encoding for output and whether there are other white matter tracts that also contribute to this process. We comprehensively investigated the anatomical connectivity supporting phonological encoding in production by studying the relationship between the integrity of all major white matter tracts across the entire brain and phonological encoding deficits in a group of 69 patients with brain damage. The integrity of each white matter tract was measured both by the percentage of damaged voxels (structural imaging) and the mean fractional anisotropy value (diffusion tensor imaging). The phonological encoding deficits were assessed by various measures in two oral production tasks that involve phonological encoding: the percentage of nonword (phonological) errors in oral picture naming and the accuracy of word reading aloud with word comprehension ability regressed out. We found that the integrity of the left SLF in both the structural and diffusion tensor imaging measures consistently predicted the severity of phonological encoding impairment in the two phonological production tasks. Such effects of the left SLF on phonological production remained significant when a range of potential confounding factors were considered through partial correlation, including total lesion volume, demographic factors, lesions on phonological-relevant grey matter regions, or effects originating from the phonological perception or semantic processes. Our results therefore conclusively demonstrate the central role of the left SLF in phonological encoding in speech production.

Facilitation of memory encoding in primate hippocampus by a neuroprosthesis that promotes task-specific neural firing

NASA Astrophysics Data System (ADS)

Hampson, Robert E.; Song, Dong; Opris, Ioan; Santos, Lucas M.; Shin, Dae C.; Gerhardt, Greg A.; Marmarelis, Vasilis Z.; Berger, Theodore W.; Deadwyler, Sam A.

2013-12-01

Objective. Memory accuracy is a major problem in human disease and is the primary factor that defines Alzheimer’s, ageing and dementia resulting from impaired hippocampal function in the medial temporal lobe. Development of a hippocampal memory neuroprosthesis that facilitates normal memory encoding in nonhuman primates (NHPs) could provide the basis for improving memory in human disease states. Approach. NHPs trained to perform a short-term delayed match-to-sample (DMS) memory task were examined with multi-neuron recordings from synaptically connected hippocampal cell fields, CA1 and CA3. Recordings were analyzed utilizing a previously developed nonlinear multi-input multi-output (MIMO) neuroprosthetic model, capable of extracting CA3-to-CA1 spatiotemporal firing patterns during DMS performance. Main results. The MIMO model verified that specific CA3-to-CA1 firing patterns were critical for the successful encoding of sample phase information on more difficult DMS trials. This was validated by the delivery of successful MIMO-derived encoding patterns via electrical stimulation to the same CA1 recording locations during the sample phase which facilitated task performance in the subsequent, delayed match phase, on difficult trials that required more precise encoding of sample information. Significance. These findings provide the first successful application of a neuroprosthesis designed to enhance and/or repair memory encoding in primate brain.

Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex.

PubMed

Osada, Naoki; Akashi, Hiroshi

2012-01-01

Accelerated rates of mitochondrial protein evolution have been proposed to reflect Darwinian coadaptation for efficient energy production for mammalian flight and brain activity. However, several features of mammalian mtDNA (absence of recombination, small effective population size, and high mutation rate) promote genome degradation through the accumulation of weakly deleterious mutations. Here, we present evidence for "compensatory" adaptive substitutions in nuclear DNA- (nDNA) encoded mitochondrial proteins to prevent fitness decline in primate mitochondrial protein complexes. We show that high mutation rate and small effective population size, key features of primate mitochondrial genomes, can accelerate compensatory adaptive evolution in nDNA-encoded genes. We combine phylogenetic information and the 3D structure of the cytochrome c oxidase (COX) complex to test for accelerated compensatory changes among interacting sites. Physical interactions among mtDNA- and nDNA-encoded components are critical in COX evolution; amino acids in close physical proximity in the 3D structure show a strong tendency for correlated evolution among lineages. Only nuclear-encoded components of COX show evidence for positive selection and adaptive nDNA-encoded changes tend to follow mtDNA-encoded amino acid changes at nearby sites in the 3D structure. This bias in the temporal order of substitutions supports compensatory weak selection as a major factor in accelerated primate COX evolution.

Facilitation of Memory Encoding in Primate Hippocampus by a Neuroprosthesis that Promotes Task Specific Neural Firing

PubMed Central

Hampson, Robert E.; Song, Dong; Opris, Ioan; Santos, Lucas M.; Shin, Dae C.; Gerhardt, Greg A.; Marmarelis, Vasilis Z.; Berger, Theodore W.; Deadwyler, Sam A.

2014-01-01

Objective Memory accuracy is a major problem in human disease and is the primary factor that defines Alzheimer’s’, aging and dementia resulting from impaired hippocampal function in medial temporal lobe. Development of a hippocampal memory neuroprosthesis that facilitates normal memory encoding in nonhuman primates (NHPs) could provide the basis for improving memory in human disease states. Approach NHPs trained to perform a short-term delayed match to sample (DMS) memory task were examined with multi-neuron recordings from synaptically connected hippocampal cell fields, CA1 and CA3. Recordings were analyzed utilizing a previously developed nonlinear multi-input multi-output (MIMO) neuroprosthetic model, capable of extracting CA3-to-CA1 spatiotemporal firing patterns during DMS performance. Main Results The MIMO model verified that specific CA3-to-CA1 firing patterns were critical for successful encoding of Sample phase information on more difficult DMS trials. This was validated by delivery of successful MIMO-derived encoding patterns via electrical stimulation to the same CA1 recording locations during the Sample phase which facilitated task performance in the subsequent delayed Match phase on difficult trials that required more precise encoding of Sample information. Significance These findings provide the first successful application of a neuroprosthesis designed to enhance and/or repair memory encoding in primate brain. PMID:24216292

Suppression of the lethal effect of acidic-phospholipid deficiency by defective formation of the major outer membrane lipoprotein in Escherichia coli.

PubMed Central

Asai, Y; Katayose, Y; Hikita, C; Ohta, A; Shibuya, I

1989-01-01

The Escherichia coli pgsA3 allele encoding a defective phosphatidylglycerophosphate synthase is lethal for all but certain strains. Genetic analysis of such strains has revealed that the lethal effect is fully suppressed by the lack of the major outer membrane lipoprotein that consumes phosphatidylglycerol for its maturation. Images PMID:2556377

TU-AB-BRA-09: A Novel Method of Generating Ultrafast Volumetric Cine MRI (VC-MRI) Using Prior 4D-MRI and On-Board Phase-Skipped Encoding Acquisition for Radiotherapy Target Localization

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

Wang, C; Yin, F; Harris, W

Purpose: To develop a technique generating ultrafast on-board VC-MRI using prior 4D-MRI and on-board phase-skipped encoding k-space acquisition for real-time 3D target tracking of liver and lung radiotherapy. Methods: The end-of-expiration (EOE) volume in 4D-MRI acquired during the simulation was selected as the prior volume. 3 major respiratory deformation patterns were extracted through the principal component analysis of the deformation field maps (DFMs) generated between EOE and all other phases. The on-board VC-MRI at each instant was considered as a deformation of the prior volume, and the deformation was modeled as a linear combination of the extracted 3 major deformationmore » patterns. To solve the weighting coefficients of the 3 major patterns, a 2D slice was extracted from VC-MRI volume to match with the 2D on-board sampling data, which was generated by 8-fold phase skipped-encoding k-space acquisition (i.e., sample 1 phase-encoding line out of every 8 lines) to achieve an ultrafast 16–24 volumes/s frame rate. The method was evaluated using XCAT digital phantom to simulate lung cancer patients. The 3D volume of end-ofinhalation (EOI) phase at the treatment day was used as ground-truth onboard VC-MRI with simulated changes in 1) breathing amplitude and 2) breathing amplitude/phase change from the simulation day. A liver cancer patient case was evaluated for in-vivo feasibility demonstration. Results: The comparison between ground truth and estimated on-board VC-MRI shows good agreements. In XCAT study with changed breathing amplitude, the volume-percent-difference(VPD) between ground-truth and estimated tumor volumes at EOI was 6.28% and the Center-of-Mass-Shift(COMS) was 0.82mm; with changed breathing amplitude and phase, the VPD was 8.50% and the COMS was 0.54mm. The study of liver patient case also demonstrated a promising in vivo feasibility of the proposed method Conclusion: Preliminary results suggest the feasibility to estimate ultrafast VC-MRI for on-board target localization with phase skipped-encoding k-space acquisition. Research grant from NIH R01-184173.« less

Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association.

PubMed

Torres-Cortés, Gloria; Ghignone, Stefano; Bonfante, Paola; Schüßler, Arthur

2015-06-23

For more than 450 million years, arbuscular mycorrhizal fungi (AMF) have formed intimate, mutualistic symbioses with the vast majority of land plants and are major drivers in almost all terrestrial ecosystems. The obligate plant-symbiotic AMF host additional symbionts, so-called Mollicutes-related endobacteria (MRE). To uncover putative functional roles of these widespread but yet enigmatic MRE, we sequenced the genome of DhMRE living in the AMF Dentiscutata heterogama. Multilocus phylogenetic analyses showed that MRE form a previously unidentified lineage sister to the hominis group of Mycoplasma species. DhMRE possesses a strongly reduced metabolic capacity with 55% of the proteins having unknown function, which reflects unique adaptations to an intracellular lifestyle. We found evidence for transkingdom gene transfer between MRE and their AMF host. At least 27 annotated DhMRE proteins show similarities to nuclear-encoded proteins of the AMF Rhizophagus irregularis, which itself lacks MRE. Nuclear-encoded homologs could moreover be identified for another AMF, Gigaspora margarita, and surprisingly, also the non-AMF Mortierella verticillata. Our data indicate a possible origin of the MRE-fungus association in ancestors of the Glomeromycota and Mucoromycotina. The DhMRE genome encodes an arsenal of putative regulatory proteins with eukaryotic-like domains, some of them encoded in putative genomic islands. MRE are highly interesting candidates to study the evolution and interactions between an ancient, obligate endosymbiotic prokaryote with its obligate plant-symbiotic fungal host. Our data moreover may be used for further targeted searches for ancient effector-like proteins that may be key components in the regulation of the arbuscular mycorrhiza symbiosis.

Metagenomic Insights into the Fibrolytic Microbiome in Yak Rumen

PubMed Central

Song, Lei; Liu, Di; Liu, Li; Chen, Furong; Wang, Min; Li, Jiabao; Zeng, Xiaowei; Dong, Zhiyang; Hu, Songnian; Li, Lingyan; Xu, Jian; Huang, Li; Dong, Xiuzhu

2012-01-01

The rumen hosts one of the most efficient microbial systems for degrading plant cell walls, yet the predominant cellulolytic proteins and fibrolytic mechanism(s) remain elusive. Here we investigated the cellulolytic microbiome of the yak rumen by using a combination of metagenome-based and bacterial artificial chromosome (BAC)-based functional screening approaches. Totally 223 fibrolytic BAC clones were pyrosequenced and 10,070 ORFs were identified. Among them 150 were annotated as the glycoside hydrolase (GH) genes for fibrolytic proteins, and the majority (69%) of them were clustered or linked with genes encoding related functions. Among the 35 fibrolytic contigs of >10 Kb in length, 25 were derived from Bacteroidetes and four from Firmicutes. Coverage analysis indicated that the fibrolytic genes on most Bacteroidetes-contigs were abundantly represented in the metagenomic sequences, and they were frequently linked with genes encoding SusC/SusD-type outer-membrane proteins. GH5, GH9, and GH10 cellulase/hemicellulase genes were predominant, but no GH48 exocellulase gene was found. Most (85%) of the cellulase and hemicellulase proteins possessed a signal peptide; only a few carried carbohydrate-binding modules, and no cellulosomal domains were detected. These findings suggest that the SucC/SucD-involving mechanism, instead of one based on cellulosomes or the free-enzyme system, serves a major role in lignocellulose degradation in yak rumen. Genes encoding an endoglucanase of a novel GH5 subfamily occurred frequently in the metagenome, and the recombinant proteins encoded by the genes displayed moderate Avicelase in addition to endoglucanase activities, suggesting their important contribution to lignocellulose degradation in the exocellulase-scarce rumen. PMID:22808161

Genome-Wide Identification and Expression Analysis of Homeodomain Leucine Zipper Subfamily IV (HDZ IV) Gene Family from Musa accuminata

PubMed Central

Pandey, Ashutosh; Misra, Prashant; Alok, Anshu; Kaur, Navneet; Sharma, Shivani; Lakhwani, Deepika; Asif, Mehar H.; Tiwari, Siddharth; Trivedi, Prabodh K.

2016-01-01

The homeodomain zipper family (HD-ZIP) of transcription factors is present only in plants and plays important role in the regulation of plant-specific processes. The subfamily IV of HDZ transcription factors (HD-ZIP IV) has primarily been implicated in the regulation of epidermal structure development. Though this gene family is present in all lineages of land plants, members of this gene family have not been identified in banana, which is one of the major staple fruit crops. In the present work, we identified 21 HDZIV encoding genes in banana by the computational analysis of banana genome resource. Our analysis suggested that these genes putatively encode proteins having all the characteristic domains of HDZIV transcription factors. The phylogenetic analysis of the banana HDZIV family genes further confirmed that after separation from a common ancestor, the banana, and poales lineages might have followed distinct evolutionary paths. Further, we conclude that segmental duplication played a major role in the evolution of banana HDZIV encoding genes. All the identified banana HDZIV genes expresses in different banana tissue, however at varying levels. The transcript levels of some of the banana HDZIV genes were also detected in banana fruit pulp, suggesting their putative role in fruit attributes. A large number of genes of this family showed modulated expression under drought and salinity stress. Taken together, the present work lays a foundation for elucidation of functional aspects of the banana HDZIV encoding genes and for their possible use in the banana improvement programs. PMID:26870050

Regulatory Shifts in Plastid Transcription Play a Key Role in Morphological Conversions of Plastids during Plant Development.

PubMed

Liebers, Monique; Grübler, Björn; Chevalier, Fabien; Lerbs-Mache, Silva; Merendino, Livia; Blanvillain, Robert; Pfannschmidt, Thomas

2017-01-01

Plastids display a high morphological and functional diversity. Starting from an undifferentiated small proplastid, these plant cell organelles can develop into four major forms: etioplasts in the dark, chloroplasts in green tissues, chromoplasts in colored flowers and fruits and amyloplasts in roots. The various forms are interconvertible into each other depending on tissue context and respective environmental condition. Research of the last two decades uncovered that each plastid type contains its own specific proteome that can be highly different from that of the other types. Composition of these proteomes largely defines the enzymatic functionality of the respective plastid. The vast majority of plastid proteins is encoded in the nucleus and must be imported from the cytosol. However, a subset of proteins of the photosynthetic and gene expression machineries are encoded on the plastid genome and are transcribed by a complex transcriptional apparatus consisting of phage-type nuclear-encoded RNA polymerases and a bacterial-type plastid-encoded RNA polymerase. Both types recognize specific sets of promoters and transcribe partly over-lapping as well as specific sets of genes. Here we summarize the current knowledge about the sequential activity of these plastid RNA polymerases and their relative activities in different types of plastids. Based on published plastid gene expression profiles we hypothesize that each conversion from one plastid type into another is either accompanied or even preceded by significant changes in plastid transcription suggesting that these changes represent important determinants of plastid morphology and protein composition and, hence, the plastid type.

Regulatory Shifts in Plastid Transcription Play a Key Role in Morphological Conversions of Plastids during Plant Development

PubMed Central

Liebers, Monique; Grübler, Björn; Chevalier, Fabien; Lerbs-Mache, Silva; Merendino, Livia; Blanvillain, Robert; Pfannschmidt, Thomas

2017-01-01

Plastids display a high morphological and functional diversity. Starting from an undifferentiated small proplastid, these plant cell organelles can develop into four major forms: etioplasts in the dark, chloroplasts in green tissues, chromoplasts in colored flowers and fruits and amyloplasts in roots. The various forms are interconvertible into each other depending on tissue context and respective environmental condition. Research of the last two decades uncovered that each plastid type contains its own specific proteome that can be highly different from that of the other types. Composition of these proteomes largely defines the enzymatic functionality of the respective plastid. The vast majority of plastid proteins is encoded in the nucleus and must be imported from the cytosol. However, a subset of proteins of the photosynthetic and gene expression machineries are encoded on the plastid genome and are transcribed by a complex transcriptional apparatus consisting of phage-type nuclear-encoded RNA polymerases and a bacterial-type plastid-encoded RNA polymerase. Both types recognize specific sets of promoters and transcribe partly over-lapping as well as specific sets of genes. Here we summarize the current knowledge about the sequential activity of these plastid RNA polymerases and their relative activities in different types of plastids. Based on published plastid gene expression profiles we hypothesize that each conversion from one plastid type into another is either accompanied or even preceded by significant changes in plastid transcription suggesting that these changes represent important determinants of plastid morphology and protein composition and, hence, the plastid type. PMID:28154576

Characterisation of major histocompatibility complex class I transcripts in an Australian dragon lizard.

PubMed

Hacking, Jessica; Bertozzi, Terry; Moussalli, Adnan; Bradford, Tessa; Gardner, Michael

2018-07-01

Characterisation of squamate major histocompatibility complex (MHC) genes has lagged behind other taxonomic groups. MHC genes encode cell-surface glycoproteins that present self- and pathogen-derived peptides to T cells and play a critical role in pathogen recognition. Here we characterise MHC class I transcripts for an agamid lizard (Ctenophorus decresii) and investigate the evolution of MHC class I in Iguanian lizards. An iterative assembly strategy was used to identify six full-length C. decresii MHC class I transcripts, which were validated as likely to encode classical class I MHC molecules. Evidence for exon shuffling recombination was uncovered for C. decresii transcripts and Bayesian phylogenetic analysis of Iguanian MHC class I sequences revealed a pattern expected under a birth-and-death mode of evolution. This work provides a stepping stone towards further research on the agamid MHC class I region. Copyright © 2018 Elsevier Ltd. All rights reserved.

Diverse expression levels of two codon-optimized genes that encode human papilloma virus type 16 major protein L1 in Hansenula polymorpha.

PubMed

Liu, Cunbao; Yang, Xu; Yao, Yufeng; Huang, Weiwei; Sun, Wenjia; Ma, Yanbing

2014-05-01

Two versions of an optimized gene that encodes human papilloma virus type 16 major protein L1 were designed according to the codon usage frequency of Pichia pastoris. Y16 was highly expressed in both P. pastoris and Hansenula polymorpha. M16 expression was as efficient as that of Y16 in P. pastoris, but merely detectable in H. polymorpha even though transcription levels of M16 and Y16 were similar. H. polymorpha had a unique codon usage frequency that contains many more rare codons than Saccharomyces cerevisiae or P. pastoris. These findings indicate that even codon-optimized genes that are expressed well in S. cerevisiae and P. pastoris may be inefficiently expressed in H. polymorpha; thus rare codons must be avoided when universal optimized gene versions are designed to facilitate expression in a variety of yeast expression systems, especially H. polymorpha is involved.

Flagellin and F4 fimbriae have opposite effects on biofilm formation and quorum sensing in F4ac+ enterotoxigenic Escherichia coli.

PubMed

Zhou, Mingxu; Guo, Zhiyan; Yang, Yang; Duan, Qiangde; Zhang, Qi; Yao, Fenghua; Zhu, Jun; Zhang, Xinjun; Hardwidge, Philip R; Zhu, Guoqiang

2014-01-10

Bacteria that form biofilms are often highly resistant to antibiotics and are capable of evading the host immune system. To evaluate the role of flagellin and F4 fimbriae on biofilm formation by enterotoxigenic Escherichia coli (ETEC), we deleted the fliC (encoding the major flagellin protein) and/or the faeG (encoding the major subunit of F4 fimbriae) genes from ETEC C83902. Biofilm formation was reduced in the fliC mutant but increased in the faeG mutant, as compared with the wild-type strain. The expression of AI-2 quorum sensing associated genes was regulated in the fliC and faeG mutants, consistent with the biofilm formation of these strains. But, deleting fliC and/or faeG also inhibited AI-2 quorum sensing activity. Copyright © 2013 Elsevier B.V. All rights reserved.

Four rice seed cDNA clones belonging to the alpha-amylase/trypsin inhibitor gene family encode potential rice allergens.

PubMed

Alvarez, A M; Fukuhara, E; Nakase, M; Adachi, T; Aoki, N; Nakamura, R; Matsuda, T

1995-07-01

Four rice seed proteins encoded by cDNAs belonging to the alpha-amylase/trypsin inhibitor gene family were overexpressed as TrpE-fusion proteins in E. coli. The expressed rice proteins were detected by SDS-PAGE as major proteins in bacterial cell lysates. Western blot analyses showed that all the recombinant proteins were immunologically reactive to rabbit polyclonal antibodies and to a mouse monoclonal antibody (25B9) specific for a previously isolated rice allergen of 16 kDa. Some truncated proteins from deletion mutants of the cDNAs retained their reactivity to the specific antibodies. These results suggest that the cDNAs encode potential rice allergens and that some epitopes of the recombinant proteins are still immunoreactive when they are expressed as their fragments.

Impact of Oxidative Stress on Ascorbate Biosynthesis in Chlamydomonas via Regulation of the VTC2 Gene Encoding a GDP-l-galactose Phosphorylase*

PubMed Central

Urzica, Eugen I.; Adler, Lital N.; Page, M. Dudley; Linster, Carole L.; Arbing, Mark A.; Casero, David; Pellegrini, Matteo; Merchant, Sabeeha S.; Clarke, Steven G.

2012-01-01

The l-galactose (Smirnoff-Wheeler) pathway represents the major route to l-ascorbic acid (vitamin C) biosynthesis in higher plants. Arabidopsis thaliana VTC2 and its paralogue VTC5 function as GDP-l-galactose phosphorylases converting GDP-l-galactose to l-galactose-1-P, thus catalyzing the first committed step in the biosynthesis of l-ascorbate. Here we report that the l-galactose pathway of ascorbate biosynthesis described in higher plants is conserved in green algae. The Chlamydomonas reinhardtii genome encodes all the enzymes required for vitamin C biosynthesis via the l-galactose pathway. We have characterized recombinant C. reinhardtii VTC2 as an active GDP-l-galactose phosphorylase. C. reinhardtii cells exposed to oxidative stress show increased VTC2 mRNA and l-ascorbate levels. Genes encoding enzymatic components of the ascorbate-glutathione system (e.g. ascorbate peroxidase, manganese superoxide dismutase, and dehydroascorbate reductase) are also up-regulated in response to increased oxidative stress. These results indicate that C. reinhardtii VTC2, like its plant homologs, is a highly regulated enzyme in ascorbate biosynthesis in green algae and that, together with the ascorbate recycling system, the l-galactose pathway represents the major route for providing protective levels of ascorbate in oxidatively stressed algal cells. PMID:22393048

Prime time news: the influence of primed positive and negative emotion on susceptibility to false memories.

PubMed

Porter, Stephen; ten Brinke, Leanne; Riley, Sean N; Baker, Alysha

2014-01-01

We examined the relation between emotion and susceptibility to misinformation using a novel paradigm, the ambiguous stimuli affective priming (ASAP) paradigm. Participants (N = 88) viewed ambiguous neutral images primed either at encoding or retrieval to be interpreted as either highly positive or negative (or neutral/not primed). After viewing the images, they either were asked misleading or non-leading questions. Following a delay, memory accuracy for the original images was assessed. Results indicated that any emotional priming at encoding led to a higher susceptibility to misinformation relative to priming at recall. In particular, inducing a negative interpretation of the image at encoding led to an increased susceptibility of false memories for major misinformation (an entire object not actually present in the scene). In contrast, this pattern was reversed when priming was used at recall; a negative reinterpretation of the image decreased memory distortion relative to unprimed images. These findings suggest that, with precise experimental control, the experience of emotion at event encoding, in particular, is implicated in false memory susceptibility.

Step-by-step magic state encoding for efficient fault-tolerant quantum computation

PubMed Central

Goto, Hayato

2014-01-01

Quantum error correction allows one to make quantum computers fault-tolerant against unavoidable errors due to decoherence and imperfect physical gate operations. However, the fault-tolerant quantum computation requires impractically large computational resources for useful applications. This is a current major obstacle to the realization of a quantum computer. In particular, magic state distillation, which is a standard approach to universality, consumes the most resources in fault-tolerant quantum computation. For the resource problem, here we propose step-by-step magic state encoding for concatenated quantum codes, where magic states are encoded step by step from the physical level to the logical one. To manage errors during the encoding, we carefully use error detection. Since the sizes of intermediate codes are small, it is expected that the resource overheads will become lower than previous approaches based on the distillation at the logical level. Our simulation results suggest that the resource requirements for a logical magic state will become comparable to those for a single logical controlled-NOT gate. Thus, the present method opens a new possibility for efficient fault-tolerant quantum computation. PMID:25511387

Step-by-step magic state encoding for efficient fault-tolerant quantum computation.

PubMed

Goto, Hayato

2014-12-16

Quantum error correction allows one to make quantum computers fault-tolerant against unavoidable errors due to decoherence and imperfect physical gate operations. However, the fault-tolerant quantum computation requires impractically large computational resources for useful applications. This is a current major obstacle to the realization of a quantum computer. In particular, magic state distillation, which is a standard approach to universality, consumes the most resources in fault-tolerant quantum computation. For the resource problem, here we propose step-by-step magic state encoding for concatenated quantum codes, where magic states are encoded step by step from the physical level to the logical one. To manage errors during the encoding, we carefully use error detection. Since the sizes of intermediate codes are small, it is expected that the resource overheads will become lower than previous approaches based on the distillation at the logical level. Our simulation results suggest that the resource requirements for a logical magic state will become comparable to those for a single logical controlled-NOT gate. Thus, the present method opens a new possibility for efficient fault-tolerant quantum computation.

Imaging dynamic redox processes with genetically encoded probes.

PubMed

Ezeriņa, Daria; Morgan, Bruce; Dick, Tobias P

2014-08-01

Redox signalling plays an important role in many aspects of physiology, including that of the cardiovascular system. Perturbed redox regulation has been associated with numerous pathological conditions; nevertheless, the causal relationships between redox changes and pathology often remain unclear. Redox signalling involves the production of specific redox species at specific times in specific locations. However, until recently, the study of these processes has been impeded by a lack of appropriate tools and methodologies that afford the necessary redox species specificity and spatiotemporal resolution. Recently developed genetically encoded fluorescent redox probes now allow dynamic real-time measurements, of defined redox species, with subcellular compartment resolution, in intact living cells. Here we discuss the available genetically encoded redox probes in terms of their sensitivity and specificity and highlight where uncertainties or controversies currently exist. Furthermore, we outline major goals for future probe development and describe how progress in imaging methodologies will improve our ability to employ genetically encoded redox probes in a wide range of situations. This article is part of a special issue entitled "Redox Signalling in the Cardiovascular System." Copyright © 2014 Elsevier Ltd. All rights reserved.

Characteristics of a ugp-encoded and phoB-dependent glycerophosphoryl diester phosphodiesterase which is physically dependent on the ugp transport system of Escherichia coli.

PubMed

Brzoska, P; Boos, W

1988-09-01

The ugp-encoded transport system of Escherichia coli accumulates sn-glycerol-3-phosphate with high affinity; it is binding protein mediated and part of the pho regulon. Here, we report that glycerophosphoryl diesters (deacylated phospholipids) are also high-affinity substrates for the ugp-encoded system. The diesters are not taken up in an unaltered form but are hydrolyzed during transport to sn-glycerol-3-phosphate plus the corresponding alcohols. The enzyme responsible for this reaction is not essential for the translocation of sn-glycerol-3-phosphate or for the glycerophosphoryl diesters but can only hydrolyze diesters that are in the process of being transported. Diesters in the periplasm or in the cytoplasm were not recognized, and no enzymatic activity could be detected in cellular extracts. The enzyme is encoded by the last gene in the ugp operon, termed ugpQ. The product of the ugpQ gene, expressed in minicells, has an apparent molecular weight of 17,500. We present evidence that only one major phoB-dependent promoter controls all ugp genes.

Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids

PubMed Central

Wald, Naama; Alroy, Maya; Botzman, Maya; Margalit, Hanah

2012-01-01

Synonymous codons are unevenly distributed among genes, a phenomenon termed codon usage bias. Understanding the patterns of codon bias and the forces shaping them is a major step towards elucidating the adaptive advantage codon choice can confer at the level of individual genes and organisms. Here, we perform a large-scale analysis to assess codon usage bias pattern of pyrimidine-ending codons in highly expressed genes in prokaryotes. We find a bias pattern linked to the degeneracy of the encoded amino acid. Specifically, we show that codon-pairs that encode two- and three-fold degenerate amino acids are biased towards the C-ending codon while codons encoding four-fold degenerate amino acids are biased towards the U-ending codon. This codon usage pattern is widespread in prokaryotes, and its strength is correlated with translational selection both within and between organisms. We show that this bias is associated with an improved correspondence with the tRNA pool, avoidance of mis-incorporation errors during translation and moderate stability of codon–anticodon interaction, all consistent with more efficient translation. PMID:22581775

Antigen I/II encoded by integrative and conjugative elements of Streptococcus agalactiae and role in biofilm formation.

PubMed

Chuzeville, Sarah; Dramsi, Shaynoor; Madec, Jean-Yves; Haenni, Marisa; Payot, Sophie

2015-11-01

Streptococcus agalactiae (i.e. Group B streptococcus, GBS) is a major human and animal pathogen. Genes encoding putative surface proteins and in particular an antigen I/II have been identified on Integrative and Conjugative Elements (ICEs) found in GBS. Antigens I/II are multimodal adhesins promoting colonization of the oral cavity by streptococci such as Streptococcus gordonii and Streptococcus mutans. The prevalence and diversity of antigens I/II in GBS were studied by a bioinformatic analysis. It revealed that antigens I/II, which are acquired by horizontal transfer via ICEs, exhibit diversity and are widespread in GBS, in particular in the serotype Ia/ST23 invasive strains. This study aimed at characterizing the impact on GBS biology of proteins encoded by a previously characterized ICE of S. agalactiae (ICE_515_tRNA(Lys)). The production and surface exposition of the antigen I/II encoded by this ICE was examined using RT-PCR and immunoblotting experiments. Surface proteins of ICE_515_tRNA(Lys) were found to contribute to GBS biofilm formation and to fibrinogen binding. Contribution of antigen I/II encoded by SAL_2056 to biofilm formation was also demonstrated. These results highlight the potential for ICEs to spread microbial adhesins between species. Copyright © 2015 Elsevier Ltd. All rights reserved.

Closing the Loop for Memory Prostheses: Detecting the Role of Hippocampal Neural Ensembles Using Nonlinear Models

PubMed Central

Hampson, Robert E.; Song, Dong; Chan, Rosa H.M.; Sweatt, Andrew J.; Riley, Mitchell R.; Goonawardena, Anushka V.; Marmarelis, Vasilis Z.; Gerhardt, Greg A.; Berger, Theodore W.; Deadwyler, Sam A.

2012-01-01

A major factor involved in providing closed loop feedback for control of neural function is to understand how neural ensembles encode online information critical to the final behavioral endpoint. This issue was directly assessed in rats performing a short-term delay memory task in which successful encoding of task information is dependent upon specific spatiotemporal firing patterns recorded from ensembles of CA3 and CA1 hippocampal neurons. Such patterns, extracted by a specially designed nonlinear multi-input multi-output (MIMO) nonlinear mathematical model, were used to predict successful performance online via a closed loop paradigm which regulated trial difficulty (time of retention) as a function of the “strength” of stimulus encoding. The significance of the MIMO model as a neural prosthesis has been demonstrated by substituting trains of electrical stimulation pulses to mimic these same ensemble firing patterns. This feature was used repeatedly to vary “normal” encoding as a means of understanding how neural ensembles can be “tuned” to mimic the inherent process of selecting codes of different strength and functional specificity. The capacity to enhance and tune hippocampal encoding via MIMO model detection and insertion of critical ensemble firing patterns shown here provides the basis for possible extension to other disrupted brain circuitry. PMID:22498704

CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription

PubMed Central

Carlson, Jonathan; Yan, Jiyu; Akinsiku, Olusimidele T.; Schaefer, Malinda; Sabbaj, Steffanie; Bet, Anne; Levy, David N.; Heath, Sonya; Tang, Jianming; Kaslow, Richard A.; Walker, Bruce D.; Ndung’u, Thumbi; Goulder, Philip J.; Heckerman, David; Hunter, Eric; Goepfert, Paul A.

2010-01-01

Retroviruses pack multiple genes into relatively small genomes by encoding several genes in the same genomic region with overlapping reading frames. Both sense and antisense HIV-1 transcripts contain open reading frames for known functional proteins as well as numerous alternative reading frames (ARFs). At least some ARFs have the potential to encode proteins of unknown function, and their antigenic properties can be considered as cryptic epitopes (CEs). To examine the extent of active immune response to virally encoded CEs, we analyzed human leukocyte antigen class I–associated polymorphisms in HIV-1 gag, pol, and nef genes from a large cohort of South Africans with chronic infection. In all, 391 CEs and 168 conventional epitopes were predicted, with the majority (307; 79%) of CEs derived from antisense transcripts. In further evaluation of CD8 T cell responses to a subset of the predicted CEs in patients with primary or chronic infection, both sense- and antisense-encoded CEs were immunogenic at both stages of infection. In addition, CEs often mutated during the first year of infection, which was consistent with immune selection for escape variants. These findings indicate that the HIV-1 genome might encode and deploy a large potential repertoire of unconventional epitopes to enhance vaccine-induced antiviral immunity. PMID:20065064

Multiple Regions of a Cortical Network Commonly Encode the Meaning of Words in Multiple Grammatical Positions of Read Sentences.

PubMed

Anderson, Andrew James; Lalor, Edmund C; Lin, Feng; Binder, Jeffrey R; Fernandino, Leonardo; Humphries, Colin J; Conant, Lisa L; Raizada, Rajeev D S; Grimm, Scott; Wang, Xixi

2018-05-16

Deciphering how sentence meaning is represented in the brain remains a major challenge to science. Semantically related neural activity has recently been shown to arise concurrently in distributed brain regions as successive words in a sentence are read. However, what semantic content is represented by different regions, what is common across them, and how this relates to words in different grammatical positions of sentences is weakly understood. To address these questions, we apply a semantic model of word meaning to interpret brain activation patterns elicited in sentence reading. The model is based on human ratings of 65 sensory/motor/emotional and cognitive features of experience with words (and their referents). Through a process of mapping functional Magnetic Resonance Imaging activation back into model space we test: which brain regions semantically encode content words in different grammatical positions (e.g., subject/verb/object); and what semantic features are encoded by different regions. In left temporal, inferior parietal, and inferior/superior frontal regions we detect the semantic encoding of words in all grammatical positions tested and reveal multiple common components of semantic representation. This suggests that sentence comprehension involves a common core representation of multiple words' meaning being encoded in a network of regions distributed across the brain.

Bureau of Mines method of calibrating a primary radon measuring apparatus

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

Holub, R.F.; Stroud, W.P.

1991-04-01

This paper reports on the Bureau of Mines method of calibrating a primary radon measuring apparatus. One requirement for accurate monitoring of radon in working environments, dwellings, and outdoors is to ensure that the measurement instrumentation is properly calibrated against a recognized standard. To achieve this goal, the U.S. Bureau of Mines Radiation Laboratory has participated since 1988 in a program to establish international radon measurement standards. Originally sponsored by the Organization for Economic Cooperation and Development (OECD), the program is also sponsored by the International Atomic Energy Agency. While the National Institute of Standards and Technology (NIST) radium solutionmore » ampules are acceptable to all participating laboratories as a primary standard, a method of transferring radon from the NIST source into The Bureau's method transfers radon from the primary solution by bubbling 3 L of air through it into a steel cylinder. After homogenizing the radon concentrations in the cylinder, eight alpha-scintillation cells are filled consecutively and measured in a standard counting system. The resulting efficiency is 81.7 {plus minus} 1.2 pct.« less

Phase relations in the system Cu-Ho-O and stability of Cu{sub 2}Ho{sub 2}O{sub 5}

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

Matthews, T.; Jacob, K.T.

1994-01-01

The phase relations in the system Cu-Ho-O have been determined at 1300 K using X-ray diffraction, optical microscopy, and electron microprobe analysis of samples equilibrated in evacuated quartz ampules and in pure oxygen. Only one ternary compound, Cu{sub 2}Ho{sub 2}O{sub 5}, was found to be stable. The Gibbs free energy of formation of this compound has been measured. Since the formation is endothermic, Cu{sub 2}Ho{sub 2}O{sub 5} becomes thermodynamically unstable with respect to CuO and Ho{sub 2}O{sub 3} below 810 K. When the oxygen partial pressure over Cu{sub 2}Ho{sub 2}O{sub 5} is lowered, it decomposes. The decomposition temperature at anmore » oxygen partial pressure of 1.52 X 10{sup 4} Pa was measured using a combined DTA-TGA apparatus. Based on these results, an oxygen potential diagram for the system Cu-Ho-O at 1300 K is presented.« less

The neural fate of neutral information in emotion-enhanced memory.

PubMed

Watts, Sarah; Buratto, Luciano G; Brotherhood, Emilie V; Barnacle, Gemma E; Schaefer, Alexandre

2014-07-01

In this study, we report evidence that neural activity reflecting the encoding of emotionally neutral information in memory is reduced when neutral and emotional stimuli are intermixed during encoding. Specifically, participants studied emotional and neutral pictures organized in mixed lists (in which emotional and neutral pictures were intermixed) or in pure lists (only-neutral or only-emotional pictures) and performed a recall test. To estimate encoding efficiency, we used the Dm effect, measured with event-related potentials. Recall for neutral items was lower in mixed compared to pure lists and posterior Dm activity for neutral items was reduced in mixed lists, whereas it remained robust in pure lists. These findings might be caused by an asymmetrical competition for attentional and working memory resources between emotional and neutral information, which could be a major determinant of emotional memory effects. Copyright © 2014 Society for Psychophysiological Research.

Identification of the gene for fly non-muscle myosin heavy chain: Drosophila myosin heavy chains are encoded by a gene family.

PubMed Central

Kiehart, D P; Lutz, M S; Chan, D; Ketchum, A S; Laymon, R A; Nguyen, B; Goldstein, L S

1989-01-01

In contrast to vertebrate species Drosophila has a single myosin heavy chain gene that apparently encodes all sarcomeric heavy chain polypeptides. Flies also contain a cytoplasmic myosin heavy chain polypeptide that by immunological and peptide mapping criteria is clearly different from the major thoracic muscle isoform. Here, we identify the gene that encodes this cytoplasmic isoform and demonstrate that it is distinct from the muscle myosin heavy chain gene. Thus, fly myosin heavy chains are the products of a gene family. Our data suggest that the contractile function required to power myosin based movement in non-muscle cells requires myosin diversity beyond that available in a single heavy chain gene. In addition, we show, that accumulation of cytoplasmic myosin transcripts is regulated in a developmental stage specific fashion, consistent with a key role for this protein in the movements of early embryogenesis. Images PMID:2498088

Neural encoding of competitive effort in the anterior cingulate cortex.

PubMed

Hillman, Kristin L; Bilkey, David K

2012-09-01

In social environments, animals often compete to obtain limited resources. Strategically electing to work against another animal represents a cost-benefit decision. Is the resource worth an investment of competitive effort? The anterior cingulate cortex (ACC) has been implicated in cost-benefit decision-making, but its role in competitive effort has not been examined. We recorded ACC neurons in freely moving rats as they performed a competitive foraging choice task. When at least one of the two choice options demanded competitive effort, the majority of ACC neurons exhibited heightened and differential firing between the goal trajectories. Inter- and intrasession manipulations revealed that differential firing was not attributable to effort or reward in isolation; instead ACC encoding patterns appeared to indicate net utility assessments of available choice options. Our findings suggest that the ACC is important for encoding competitive effort, a cost-benefit domain that has received little neural-level investigation despite its predominance in nature.

Genes encoding giant danio and golden shiner ependymin.

PubMed

Adams, D S; Kiyokawa, M; Getman, M E; Shashoua, V E

1996-03-01

Ependymin (EPN) is a brain glycoprotein that functions as a neurotrophic factor in optic nerve regeneration and long-term memory consolidation in goldfish. To date, true epn genes have been characterized in one order of teleost fish, Cypriniformes. In the study presented here, polymerase chain reactions were used to analyze the complete epn genes, gd (1480 bp), and sh (2071 bp), from Cypriniformes giant danio and shiner, respectively. Southern hybridizations demonstrated the existence of one copy of each gene per corresponding haploid genome. Each gene was found to contain six exons and five introns. Gene gd encodes a predicted 218-amino acid (aa) protein GD 93 percent conserved to goldfish EPN, while sh encodes a predicted 214-aa protein SH 91 percent homologous to goldfish. Evidence is presented classifying proteins previously termed "EPNs" into two major categories: true EPNs and non-EPN cerebrospinal fluid glycoproteins. Proteins GD and SH contain all the hallmark, features of true EPNs.

Active touch and self-motion encoding by Merkel cell-associated afferents

PubMed Central

Severson, Kyle S.; Xu, Duo; Van de Loo, Margaret; Bai, Ling; Ginty, David D.; O’Connor, Daniel H.

2017-01-01

Summary Touch perception depends on integrating signals from multiple types of peripheral mechanoreceptors. Merkel-cell associated afferents are thought to play a major role in form perception by encoding surface features of touched objects. However, activity of Merkel afferents during active touch has not been directly measured. Here, we show that Merkel and unidentified slowly adapting afferents in the whisker system of behaving mice respond to both self-motion and active touch. Touch responses were dominated by sensitivity to bending moment (torque) at the base of the whisker and its rate of change, and largely explained by a simple mechanical model. Self-motion responses encoded whisker position within a whisk cycle (phase), not absolute whisker angle, and arose from stresses reflecting whisker inertia and activity of specific muscles. Thus, Merkel afferents send to the brain multiplexed information about whisker position and surface features, suggesting that proprioception and touch converge at the earliest neural level. PMID:28434802

The Astrocentric Hypothesis: proposed role of astrocytes in consciousness and memory formation.

PubMed

Robertson, James M

2002-01-01

Consciousness is self-awareness. This process is closely associated with attention and working memory, a special form of short-term memory, which is vital when solving explicit task. Edelman has equated consciousness as the "remembered present" to highlight the importance of this form of memory (G.M. Edelman, Bright Air, Brilliant Fire, Basic Books, New York, 1992). The majority of other memories are recollections of past events that are encoded, stored, and brought back into consciousness if appropriate for solving new problems. Encoding prior experiences into memories is based on the salience of each event (A.R. Damasio, Descartes' Error, G.P. Putnam's Sons, New York, 1994; G.M. Edelman, Bright Air, Brilliant Fire, Basic Books, New York, 1992). It is proposed that protoplasmic astrocytes bind attended sensory information into consciousness and store encoded memories. This conclusion is supported by research conducted by gliobiologist over the past 15 years. Copyright 2002 Elsevier Science Ltd.

GlycomeDB – integration of open-access carbohydrate structure databases

PubMed Central

Ranzinger, René; Herget, Stephan; Wetter, Thomas; von der Lieth, Claus-Wilhelm

2008-01-01

Background Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. Results We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. Conclusion GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource. PMID:18803830

Novel plasmids and resistance phenotypes in Yersinia pestis: unique plasmid inventory of strain Java 9 mediates high levels of arsenic resistance.

PubMed

Eppinger, Mark; Radnedge, Lyndsay; Andersen, Gary; Vietri, Nicholas; Severson, Grant; Mou, Sherry; Ravel, Jacques; Worsham, Patricia L

2012-01-01

Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium.

Novel Plasmids and Resistance Phenotypes in Yersinia pestis: Unique Plasmid Inventory of Strain Java 9 Mediates High Levels of Arsenic Resistance

PubMed Central

Eppinger, Mark; Radnedge, Lyndsay; Andersen, Gary; Vietri, Nicholas; Severson, Grant; Mou, Sherry; Ravel, Jacques; Worsham, Patricia L.

2012-01-01

Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium. PMID:22479347

Characterization of the Genes Encoding the Cytosolic and Plastidial Forms of ADP-Glucose Pyrophosphorylase in Wheat Endosperm1

PubMed Central

Burton, Rachel A.; Johnson, Philip E.; Beckles, Diane M.; Fincher, Geoffrey B.; Jenner, Helen L.; Naldrett, Mike J.; Denyer, Kay

2002-01-01

In most species, the synthesis of ADP-glucose (Glc) by the enzyme ADP-Glc pyrophosphorylase (AGPase) occurs entirely within the plastids in all tissues so far examined. However, in the endosperm of many, if not all grasses, a second form of AGPase synthesizes ADP-Glc outside the plastid, presumably in the cytosol. In this paper, we show that in the endosperm of wheat (Triticum aestivum), the cytosolic form accounts for most of the AGPase activity. Using a combination of molecular and biochemical approaches to identify the cytosolic and plastidial protein components of wheat endosperm AGPase we show that the large and small subunits of the cytosolic enzyme are encoded by genes previously thought to encode plastidial subunits, and that a gene, Ta.AGP.S.1, which encodes the small subunit of the cytosolic form of AGPase, also gives rise to a second transcript by the use of an alternate first exon. This second transcript encodes an AGPase small subunit with a transit peptide. However, we could not find a plastidial small subunit protein corresponding to this transcript. The protein sequence of the purified plastidial small subunit does not match precisely to that encoded by Ta.AGP.S.1 or to the predicted sequences of any other known gene from wheat or barley (Hordeum vulgare). Instead, the protein sequence is most similar to those of the plastidial small subunits from chickpea (Cicer arietinum) and maize (Zea mays) and rice (Oryza sativa) seeds. These data suggest that the gene encoding the major plastidial small subunit of AGPase in wheat endosperm has yet to be identified. PMID:12428011

Genomic structure and chromosomal mapping of the human CD22 gene

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

Wilson, G.L.; Kozlow, E.; Kehrl, J.H.

1993-06-01

The human CD22 gene is expressed specifically in B lymphocytes and likely has an important function in cell-cell interactions. A nearly full length human CD22 cDNA clone was used to isolate genomic clones that span the CD22 gene. The CD22 gene is spread over 22 kb of DNA and is composed of 15 exons. The first exon contains the major transcriptional start sites. The translation initiation codon is located in exon 3, which also encodes a portion of the signal peptide. Exons 4 to 10 encode the seven Ig domains of CD22, exon 11 encodes the transmembrane domain, exons 12more » to 15 encode the intracytoplasmic domain of CD22, and exon 15 also contains the 3' untranslated region. A minor form of CD22 mRNA likely results from splicing of exon 5 to exon 8, skipping exons 6 and 7. A 4.6-kb Xbal fragment of the CD22 gene was used to map the chromosomal location of CD22 by fluorescence in situ hybridization. The hybridization locus was identified by combining fluorescent images of the probe with the chromosomal banding pattern generated by an Alu probe. The results demonstrate the CD22 is located within the band region q13.1 of chromosome 19. Two closely clustered major transcription start sites and several minor start sites were mapped by primer extension. Similarly to many other lymphoid-specific genes, the CD22 promoter lacks an obvious TATA box. Approximately 4 kb of DNA 5' of the transcription start sites were sequenced and found to contain multiple Alu elements. Potential binding sites for the transcriptional factors NF-kB, AP-1, and Oct-2 are located within 300 bp 5' of the major transcription start sites. A 400-bp fragment (bp -339 through +71) of the CD22 promoter region was subcloned into a pGEM-chloramphenicol acetyltransferase vector and after transfection into B and T cells was found to be active in both B and T cells. 45 refs., 7 figs., 2 tabs.« less

Inhibition of CD1 antigen presentation by human cytomegalovirus.

PubMed

Raftery, Martin J; Hitzler, Manuel; Winau, Florian; Giese, Thomas; Plachter, Bodo; Kaufmann, Stefan H E; Schönrich, Günther

2008-05-01

The betaherpesvirus human cytomegalovirus (HCMV) encodes several molecules that block antigen presentation by the major histocompatibility complex (MHC) proteins. Humans also possess one other family of antigen-presenting molecules, the CD1 family; however, the effect of HCMV on CD1 expression is unknown. The majority of CD1 molecules are classified on the basis of homology as group 1 CD1 and are present almost exclusively on professional antigen-presenting cells such as dendritic cells, which are a major target for HCMV infection and latency. We have determined that HCMV encodes multiple blocking strategies targeting group 1 CD1 molecules. CD1 transcription is strongly inhibited by the HCMV interleukin-10 homologue cmvIL-10. HCMV also blocks CD1 antigen presentation posttranscriptionally by the inhibition of CD1 localization to the cell surface. This function is not performed by a known HCMV MHC class I-blocking molecule and is substantially stronger than the blockage induced by herpes simplex virus type 1. Antigen presentation by CD1 is important for the development of the antiviral immune response and the generation of mature antigen-presenting cells. HCMV present in antigen-presenting cells thus blunts the immune response by the blockage of CD1 molecules.

JPEG 2000 Encoding with Perceptual Distortion Control

NASA Technical Reports Server (NTRS)

Watson, Andrew B.; Liu, Zhen; Karam, Lina J.

2008-01-01

An alternative approach has been devised for encoding image data in compliance with JPEG 2000, the most recent still-image data-compression standard of the Joint Photographic Experts Group. Heretofore, JPEG 2000 encoding has been implemented by several related schemes classified as rate-based distortion-minimization encoding. In each of these schemes, the end user specifies a desired bit rate and the encoding algorithm strives to attain that rate while minimizing a mean squared error (MSE). While rate-based distortion minimization is appropriate for transmitting data over a limited-bandwidth channel, it is not the best approach for applications in which the perceptual quality of reconstructed images is a major consideration. A better approach for such applications is the present alternative one, denoted perceptual distortion control, in which the encoding algorithm strives to compress data to the lowest bit rate that yields at least a specified level of perceptual image quality. Some additional background information on JPEG 2000 is prerequisite to a meaningful summary of JPEG encoding with perceptual distortion control. The JPEG 2000 encoding process includes two subprocesses known as tier-1 and tier-2 coding. In order to minimize the MSE for the desired bit rate, a rate-distortion- optimization subprocess is introduced between the tier-1 and tier-2 subprocesses. In tier-1 coding, each coding block is independently bit-plane coded from the most-significant-bit (MSB) plane to the least-significant-bit (LSB) plane, using three coding passes (except for the MSB plane, which is coded using only one "clean up" coding pass). For M bit planes, this subprocess involves a total number of (3M - 2) coding passes. An embedded bit stream is then generated for each coding block. Information on the reduction in distortion and the increase in the bit rate associated with each coding pass is collected. This information is then used in a rate-control procedure to determine the contribution of each coding block to the output compressed bit stream.

The Complete Set of Genes Encoding Major Intrinsic Proteins in Arabidopsis Provides a Framework for a New Nomenclature for Major Intrinsic Proteins in Plants1

PubMed Central

Johanson, Urban; Karlsson, Maria; Johansson, Ingela; Gustavsson, Sofia; Sjövall, Sara; Fraysse, Laure; Weig, Alfons R.; Kjellbom, Per

2001-01-01

Major intrinsic proteins (MIPs) facilitate the passive transport of small polar molecules across membranes. MIPs constitute a very old family of proteins and different forms have been found in all kinds of living organisms, including bacteria, fungi, animals, and plants. In the genomic sequence of Arabidopsis, we have identified 35 different MIP-encoding genes. Based on sequence similarity, these 35 proteins are divided into four different subfamilies: plasma membrane intrinsic proteins, tonoplast intrinsic proteins, NOD26-like intrinsic proteins also called NOD26-like MIPs, and the recently discovered small basic intrinsic proteins. In Arabidopsis, there are 13 plasma membrane intrinsic proteins, 10 tonoplast intrinsic proteins, nine NOD26-like intrinsic proteins, and three small basic intrinsic proteins. The gene structure in general is conserved within each subfamily, although there is a tendency to lose introns. Based on phylogenetic comparisons of maize (Zea mays) and Arabidopsis MIPs (AtMIPs), it is argued that the general intron patterns in the subfamilies were formed before the split of monocotyledons and dicotyledons. Although the gene structure is unique for each subfamily, there is a common pattern in how transmembrane helices are encoded on the exons in three of the subfamilies. The nomenclature for plant MIPs varies widely between different species but also between subfamilies in the same species. Based on the phylogeny of all AtMIPs, a new and more consistent nomenclature is proposed. The complete set of AtMIPs, together with the new nomenclature, will facilitate the isolation, classification, and labeling of plant MIPs from other species. PMID:11500536

The European Eel NCCβ Gene Encodes a Thiazide-resistant Na-Cl Cotransporter*

PubMed Central

Moreno, Erika; Plata, Consuelo; Rodríguez-Gama, Alejandro; Argaiz, Eduardo R.; Vázquez, Norma; Leyva-Ríos, Karla; Islas, León; Cutler, Christopher; Pacheco-Alvarez, Diana; Mercado, Adriana; Cariño-Cortés, Raquel; Castañeda-Bueno, María; Gamba, Gerardo

2016-01-01

The thiazide-sensitive Na-Cl cotransporter (NCC) is the major pathway for salt reabsorption in the mammalian distal convoluted tubule. NCC plays a key role in the regulation of blood pressure. Its inhibition with thiazides constitutes the primary baseline therapy for arterial hypertension. However, the thiazide-binding site in NCC is unknown. Mammals have only one gene encoding for NCC. The eel, however, contains a duplicate gene. NCCα is an ortholog of mammalian NCC and is expressed in the kidney. NCCβ is present in the apical membrane of the rectum. Here we cloned and functionally characterized NCCβ from the European eel. The cRNA encodes a 1043-amino acid membrane protein that, when expressed in Xenopus oocytes, functions as an Na-Cl cotransporter with two major characteristics, making it different from other known NCCs. First, eel NCCβ is resistant to thiazides. Single-point mutagenesis supports that the absence of thiazide inhibition is, at least in part, due to the substitution of a conserved serine for a cysteine at position 379. Second, NCCβ is not activated by low-chloride hypotonic stress, although the unique Ste20-related proline alanine-rich kinase (SPAK) binding site in the amino-terminal domain is conserved. Thus, NCCβ exhibits significant functional differences from NCCs that could be helpful in defining several aspects of the structure-function relationship of this important cotransporter. PMID:27587391

Metabolic engineering and adaptive evolution for efficient production of D-lactic acid in Saccharomyces cerevisiae.

PubMed

Baek, Seung-Ho; Kwon, Eunice Y; Kim, Yong Hwan; Hahn, Ji-Sook

2016-03-01

There is an increasing demand for microbial production of lactic acid (LA) as a monomer of biodegradable poly lactic acid (PLA). Both optical isomers, D-LA and L-LA, are required to produce stereocomplex PLA with improved properties. In this study, we developed Saccharomyces cerevisiae strains for efficient production of D-LA. D-LA production was achieved by expressing highly stereospecific D-lactate dehydrogenase gene (ldhA, LEUM_1756) from Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 in S. cerevisiae lacking natural LA production activity. D-LA consumption after glucose depletion was inhibited by deleting DLD1 encoding D-lactate dehydrogenase and JEN1 encoding monocarboxylate transporter. In addition, ethanol production was reduced by deleting PDC1 and ADH1 genes encoding major pyruvate decarboxylase and alcohol dehydrogenase, respectively, and glycerol production was eliminated by deleting GPD1 and GPD2 genes encoding glycerol-3-phosphate dehydrogenase. LA tolerance of the engineered D-LA-producing strain was enhanced by adaptive evolution and overexpression of HAA1 encoding a transcriptional activator involved in weak acid stress response, resulting in effective D-LA production up to 48.9 g/L without neutralization. In a flask fed-batch fermentation under neutralizing condition, our evolved strain produced 112.0 g/L D-LA with a yield of 0.80 g/g glucose and a productivity of 2.2 g/(L · h).

Instructional Design and Directed Cognitive Processing.

ERIC Educational Resources Information Center

Bovy, Ruth Colvin

This paper argues that the information processing model provides a promising basis on which to build a comprehensive theory of instruction. Characteristics of the major information processing constructs are outlined including attention, encoding and rehearsal, working memory, long term memory, retrieval, and metacognitive processes, and a unifying…

Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome

PubMed Central

Dorrell, Richard G; Gile, Gillian; McCallum, Giselle; Méheust, Raphaël; Bapteste, Eric P; Klinger, Christen M; Brillet-Guéguen, Loraine; Freeman, Katalina D; Richter, Daniel J; Bowler, Chris

2017-01-01

Plastids are supported by a wide range of proteins encoded within the nucleus and imported from the cytoplasm. These plastid-targeted proteins may originate from the endosymbiont, the host, or other sources entirely. Here, we identify and characterise 770 plastid-targeted proteins that are conserved across the ochrophytes, a major group of algae including diatoms, pelagophytes and kelps, that possess plastids derived from red algae. We show that the ancestral ochrophyte plastid proteome was an evolutionary chimera, with 25% of its phylogenetically tractable nucleus-encoded proteins deriving from green algae. We additionally show that functional mixing of host and plastid proteomes, such as through dual-targeting, is an ancestral feature of plastid evolution. Finally, we detect a clear phylogenetic signal from one ochrophyte subgroup, the lineage containing pelagophytes and dictyochophytes, in plastid-targeted proteins from another major algal lineage, the haptophytes. This may represent a possible serial endosymbiosis event deep in eukaryotic evolutionary history. DOI: http://dx.doi.org/10.7554/eLife.23717.001 PMID:28498102

Animal Rights as a Mainstream Phenomenon.

PubMed

Rollin, Bernard E

2011-01-19

Businesses and professions must stay in accord with social ethics, or risk losing their autonomy.A major social ethical issue that has emerged in the past four decades is the treatment of animals in various areas of human use. Society's moral concern has outgrown the traditional ethic of animal cruelty that began in biblical times and is encoded in the laws of all civilized societies. There are five major reasons for this new social concern, most importantly, the replacement of husbandry-based agriculture with industrial agriculture. This loss of husbandry to industry has threatened the traditional fair contract between humans and animals, and resulted in significant amounts of animal suffering arising on four different fronts. Because such suffering is not occasioned by cruelty, a new ethic for animals was required to express social concerns. Since ethics proceed from preexisting ethics rather than ex nihilo, society has looked to its ethic for humans, appropriately modified, to find moral categories applicable to animals. This concept of legally encoded rights for animals has emerged as a plausible vehicle for reform.

In vivo immunologic selection of class I major histocompatibility complex gene deletion variants from the B16-BL6 melanoma.

PubMed

Talmadge, J E; Talmadge, C B; Zbar, B; McEwen, R; Meeker, A K; Tribble, H

1987-06-01

The mechanism by which tumor allografts escape host immunologic attack was investigated. B16-BL6 cells (the bladder 6 subline of the B16 melanoma) (H-2b) were transfected with a gene (Dd) encoding an allogeneic class I major histocompatibility complex antigen. Clones that expressed Dd antigen were injected into the footpads of nonimmune syngeneic mice, syngeneic immune mice, and nude mice. Under conditions of immunologic selection a clone that contained multiple copies of the transfected gene formed variants that lacked the transfected gene. Primary tumors and pulmonary metastases of immunized mice and pulmonary metastases of nonimmunized mice had lost the Dd gene and, in most cases, all of the associated plasmid. In contrast, in immunodeficient nude mice, primary tumors and pulmonary metastases retained the Dd gene and the associated plasmid. Deletion of genes encoding cell surface antigens may be one of the mechanisms by which allogeneic tumors escape immunologic attack.

Visualization and characterization of individual type III protein secretion machines in live bacteria

PubMed Central

Lara-Tejero, María; Bewersdorf, Jörg; Galán, Jorge E.

2017-01-01

Type III protein secretion machines have evolved to deliver bacterially encoded effector proteins into eukaryotic cells. Although electron microscopy has provided a detailed view of these machines in isolation or fixed samples, little is known about their organization in live bacteria. Here we report the visualization and characterization of the Salmonella type III secretion machine in live bacteria by 2D and 3D single-molecule switching superresolution microscopy. This approach provided access to transient components of this machine, which previously could not be analyzed. We determined the subcellular distribution of individual machines, the stoichiometry of the different components of this machine in situ, and the spatial distribution of the substrates of this machine before secretion. Furthermore, by visualizing this machine in Salmonella mutants we obtained major insights into the machine’s assembly. This study bridges a major resolution gap in the visualization of this nanomachine and may serve as a paradigm for the examination of other bacterially encoded molecular machines. PMID:28533372

Drosophila variable nurse cells encodes Arrest defective 1 (ARD1), the catalytic subunit of the major N-terminal acetyltransferase complex

PubMed Central

Wang, Ying; Mijares, Michelle; Gall, Megan D.; Turan, Tolga; Javier, Anna; Bornemann, Douglas J; Manage, Kevin; Warrior, Rahul

2010-01-01

Mutations in the Drosophila variable nurse cells (vnc) gene result in female sterility and oogenesis defects, including egg chambers with too many or too few nurse cells. We show that vnc corresponds to Arrest Defective1 (Ard1) and encodes the catalytic subunit of NatA, the major N-terminal acetyl-transferase complex. While N-terminal acetylation is one of the most prevalent covalent protein modifications in eukaryotes, analysis of its role in development has been challenging since mutants that compromise NatA activity have not been described in any multicellular animal. Our data show that reduced ARD1 levels result in pleiotropic oogenesis defects including abnormal cyst encapsulation, desynchronized cystocyte division, disrupted nurse cell chromosome dispersion and abnormal chorion patterning, consistent with the wide range of predicted NatA substrates. Further we find that loss of Ard1 affects cell survival/proliferation and is lethal for the animal, providing the first demonstration that this modification is essential in higher eukaryotes. PMID:20882681

Genome complexity in the coelacanth is reflected in its adaptive immune system

USGS Publications Warehouse

Saha, Nil Ratan; Ota, Tatsuya; Litman, Gary W.; Hansen, John; Parra, Zuly; Hsu, Ellen; Buonocore, Francesco; Canapa, Adriana; Cheng, Jan-Fang; Amemiya, Chris T.

2014-01-01

We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several different experimental strategies. Four distinct sets of genes encoding Ig light chains were identified. This includes a variant sigma-type Ig light chain previously identified only in cartilaginous fishes and which is now provisionally denoted sigma-2. Genes encoding α/β and γ/δ T-cell receptors, and CD3, CD4, and CD8 co-receptors also were characterized. Ig heavy chain variable region genes and TCR components are interspersed within the TCR α/δ locus; this organization previously was reported only in tetrapods and raises questions regarding evolution and functional cooption of genes encoding variable regions. The composition, organization and syntenic conservation of the major histocompatibility complex locus have been characterized. We also identified large numbers of genes encoding cytokines and their receptors, and other genes associated with adaptive immunity. In terms of sequence identity and organization, the adaptive immune genes of the coelacanth more closely resemble orthologous genes in tetrapods than those in teleost fishes, consistent with current phylogenomic interpretations. Overall, the work reported described herein highlights the complexity inherent in the coelacanth genome and provides a rich catalog of immune genes for future investigations.

Variation in Protein Intake Induces Variation in Spider Silk Expression

PubMed Central

Blamires, Sean J.; Wu, Chun-Lin; Tso, I-Min

2012-01-01

Background It is energetically expensive to synthesize certain amino acids. The proteins (spidroins) of spider major ampullate (MA) silk, MaSp1 and MaSp2, differ in amino acid composition. Glutamine and proline are prevalent in MaSp2 and are expensive to synthesize. Since most orb web spiders express high proline silk they might preferentially attain the amino acids needed for silk from food and shift toward expressing more MaSp1 in their MA silk when starved. Methodology/Principal Findings We fed three spiders; Argiope aetherea, Cyrtophora moluccensis and Leucauge blanda, high protein, low protein or no protein solutions. A. aetherea and L. blanda MA silks are high in proline, while C. moluccesnsis MA silks are low in proline. After 10 days of feeding we determined the amino acid compositions and mechanical properties of each species' MA silk and compared them between species and treatments with pre-treatment samples, accounting for ancestry. We found that the proline and glutamine of A. aetherea and L. blanda silks were affected by protein intake; significantly decreasing under the low and no protein intake treatments. Glutmaine composition in C. moluccensis silk was likewise affected by protein intake. However, the composition of proline in their MA silk was not significantly affected by protein intake. Conclusions Our results suggest that protein limitation induces a shift toward different silk proteins with lower glutamine and/or proline content. Contradictions to the MaSp model lie in the findings that C. moluccensis MA silks did not experience a significant reduction in proline and A. aetherea did not experience a significant reduction in serine on low/no protein. The mechanical properties of the silks could not be explained by a MaSp1 expressional shift. Factors other than MaSp expression, such as the expression of spidroin-like orthologues, may impact on silk amino acid composition and spinning and glandular processes may impact mechanics. PMID:22363691

A novel frame-level constant-distortion bit allocation for smooth H.264/AVC video quality

NASA Astrophysics Data System (ADS)

Liu, Li; Zhuang, Xinhua

2009-01-01

It is known that quality fluctuation has a major negative effect on visual perception. In previous work, we introduced a constant-distortion bit allocation method [1] for H.263+ encoder. However, the method in [1] can not be adapted to the newest H.264/AVC encoder directly as the well-known chicken-egg dilemma resulted from the rate-distortion optimization (RDO) decision process. To solve this problem, we propose a new two stage constant-distortion bit allocation (CDBA) algorithm with enhanced rate control for H.264/AVC encoder. In stage-1, the algorithm performs RD optimization process with a constant quantization QP. Based on prediction residual signals from stage-1 and target distortion for smooth video quality purpose, the frame-level bit target is allocated by using a close-form approximations of ratedistortion relationship similar to [1], and a fast stage-2 encoding process is performed with enhanced basic unit rate control. Experimental results show that, compared with original rate control algorithm provided by H.264/AVC reference software JM12.1, the proposed constant-distortion frame-level bit allocation scheme reduces quality fluctuation and delivers much smoother PSNR on all testing sequences.

New scene change control scheme based on pseudoskipped picture

NASA Astrophysics Data System (ADS)

Lee, Youngsun; Lee, Jinwhan; Chang, Hyunsik; Nam, Jae Y.

1997-01-01

A new scene change control scheme which improves the video coding performance for sequences that have many scene changed pictures is proposed in this paper. The scene changed pictures except intra-coded picture usually need more bits than normal pictures in order to maintain constant picture quality. The major idea of this paper is how to obtain extra bits which are needed to encode scene changed pictures. We encode a B picture which is located before a scene changed picture like a skipped picture. We call such a B picture as a pseudo-skipped picture. By generating the pseudo-skipped picture like a skipped picture. We call such a B picture as a pseudo-skipped picture. By generating the pseudo-skipped picture, we can save some bits and they are added to the originally allocated target bits to encode the scene changed picture. The simulation results show that the proposed algorithm improves encoding performance about 0.5 to approximately 2.0 dB of PSNR compared to MPEG-2 TM5 rate controls scheme. In addition, the suggested algorithm is compatible with MPEG-2 video syntax and the picture repetition is not recognizable.

Cloning and characterization of cDNAs encoding human gastrin-releasing peptide.

PubMed Central

Spindel, E R; Chin, W W; Price, J; Rees, L H; Besser, G M; Habener, J F

1984-01-01

We have prepared and cloned cDNAs derived from poly(A)+ RNA from a human pulmonary carcinoid tumor rich in immunoreactivity to gastrin-releasing peptide, a peptide closely related in structure to amphibian bombesin. Mixtures of synthetic oligodeoxyribonucleotides corresponding to amphibian bombesin were used as hybridization probes to screen a cDNA library prepared from the tumor RNA. Sequencing of the recombinant plasmids shows that human gastrin-releasing peptide (hGRP) mRNA encodes a precursor of 148 amino acids containing a typical signal sequence, hGRP consisting of 27 or 28 amino acids, and a carboxyl-terminal extension peptide. hGRP is flanked at its carboxyl terminus by two basic amino acids, following a glycine used for amidation of the carboxyl-terminal methionine. RNA blot analyses of tumor RNA show a major mRNA of 900 bases and a minor mRNA of 850 bases. Blot hybridization analyses using human genomic DNA are consistent with a single hGRP-encoding gene. The presence of two mRNAs encoding the hGRP precursor protein in the face of a single hGRP gene raises the possibility of alternative processing of the single RNA transcript. Images PMID:6207529

Brief Note Low diversity of the major histocompatibility complex class II DRA gene in domestic goats (Capra hircus) in Southern China.

PubMed

Chen, L P; E, G X; Zhao, Y J; Na, R S; Zhao, Z Q; Zhang, J H; Ma, Y H; Sun, Y W; Zhong, T; Zhang, H P; Huang, Y F

2015-06-18

DRA encodes the alpha chain of the DR heterodimer, is closely linked to DRB and is considered almost monomorphic in major histocompatibility complex region. In this study, we identified the exon 2 of DRA to evaluate the immunogenetic diversity of Chinese south indigenous goat. Two single nucleotide polymorphisms in an untranslated region and one synonymous substitution in coding region were identified. These data suggest that high immunodiversity in native Chinese population.

Using "Pseudomonas Putida xylE" Gene to Teach Molecular Cloning Techniques for Undergraduates

ERIC Educational Resources Information Center

Dong, Xu; Xin, Yi; Ye, Li; Ma, Yufang

2009-01-01

We have developed and implemented a serial experiment in molecular cloning laboratory course for undergraduate students majored in biotechnology. "Pseudomonas putida xylE" gene, encoding catechol 2, 3-dioxygenase, was manipulated to learn molecular biology techniques. The integration of cloning, expression, and enzyme assay gave students…

Glutathione Modulates Recominant Rat Arsenic (+3 Oxidation State) Methyltransferase-Catalyzed Formation of Trimethylarsine Oxide and Trimethylarsine

EPA Science Inventory

Humans and other species enzymatically convert inorganic arsenic (iAs) into methylated metabolites. Although the major metabolites are mono- and dimethylated arsenicals, trimethylated arsenicals have been detected in urine following exposure to iAs. The AS3MT gene encodes an ars...

Levels of Processing: A Reply to Eysenck

ERIC Educational Resources Information Center

Lockhart, Robert S.; Craik, Fergus I. M.

1978-01-01

These comments take up the major issues raised in Eyseck's (1978) critique (AA 528 584) of Craik & Lockhart (1972): the problem of circularity in the definition of "depth", the distinction between qualitative and quantitative differences in encoding, and the relationships between the concepts of depth, strength and elaboration. (Editor/RK)

Uncovering co-expression gene network regulating fruit acidity in diverse apples

USDA-ARS?s Scientific Manuscript database

Acidity is a major contributor to fruit quality. Several organic acids are present in apple fruit, but malic acid is predominant and determines fruit acidity. The trait is largely controlled by the Malic acid (Ma) locus, underpinning which Ma1 that encodes an Aluminum-activated Malate Transporter1 (...

The beet R locus encodes a new cytochrome P450 required for red betalain production

USDA-ARS?s Scientific Manuscript database

The anthocyanins are the major red and violet pigments that color flowers, fruits, and epidermal tissues in virtually all flowering plants. A single order, the Caryophyllales, contains families where the anthocyanins are supplanted in all biological contexts by the unrelated betalain pigments. The b...

Nitrate transporter genes in apple and the effect of water deficit on their expression

USDA-ARS?s Scientific Manuscript database

Nitrogen transporters are members of a large superfamily, the Major Facilitator Superfamily (MFS). This family is ubiquitous and diverse, and includes proteins that facilitate the transport of a wide range of substrates across the cytoplasmic or intracellular membranes. Among the proteins encoded ...

Import of a major mitochondrial enzyme depends on synergy between two distinct helices of its presequence

USDA-ARS?s Scientific Manuscript database

The human mitochondrial glutamate dehydrogenase isozymes (hGDH1 and 2) are abundant matrix-localized proteins encoded by nuclear genes. The proteins are synthesized in the cytoplasm, with an atypically long N-terminal mitochondrial targeting sequence (MTS). The results of secondary structure predi...

Deltabaculoviruses encode a functional type I budded virus envelope fusion protein

USDA-ARS?s Scientific Manuscript database

Envelope fusion proteins (F proteins) are major constituents of budded viruses (BVs) of alpha- and betabaculoviruses (Baculoviridae) and are essential for the systemic infection of insect larvae and insect cells in culture. An F protein homolog gene was absent in gammabaculoviruses. Here we show tha...

Structural Heterogeneity and Functional Domains of Murine Immunoglobulin G Fc Receptors

NASA Astrophysics Data System (ADS)

Ravetch, Jeffrey V.; Luster, Andrew D.; Weinshank, Richard; Kochan, Jarema; Pavlovec, Amalia; Portnoy, Daniel A.; Hulmes, Jeffrey; Pan, Yu-Ching E.; Unkeless, Jay C.

1986-11-01

Binding of antibodies to effector cells by way of receptors to their constant regions (Fc receptors) is central to the pathway that leads to clearance of antigens by the immune system. The structure and function of this important class of receptors on immune cells is addressed through the molecular characterization of Fc receptors (FcR) specific for the murine immunoglobulin G isotype. Structural diversity is encoded by two genes that by alternative splicing result in expression of molecules with highly conserved extracellular domains and different transmembrane and intracytoplasmic domains. The proteins encoded by these genes are members of the immunoglobulin supergene family, most homologous to the major histocompatibility complex molecule Eβ. Functional reconstitution of ligand binding by transfection of individual FcR genes demonstrates that the requirements for ligand binding are encoded in a single gene. These studies demonstrate the molecular basis for the functional heterogeneity of FcR's, accounting for the possible transduction of different signals in response to a single ligand.

Characterization of 17 chaperone-usher fimbriae encoded by Proteus mirabilis reveals strong conservation

PubMed Central

Kuan, Lisa; Schaffer, Jessica N.; Zouzias, Christos D.

2014-01-01

Proteus mirabilis is a Gram-negative enteric bacterium that causes complicated urinary tract infections, particularly in patients with indwelling catheters. Sequencing of clinical isolate P. mirabilis HI4320 revealed the presence of 17 predicted chaperone-usher fimbrial operons. We classified these fimbriae into three groups by their genetic relationship to other chaperone-usher fimbriae. Sixteen of these fimbriae are encoded by all seven currently sequenced P. mirabilis genomes. The predicted protein sequence of the major structural subunit for 14 of these fimbriae was highly conserved (≥95 % identity), whereas three other structural subunits (Fim3A, UcaA and Fim6A) were variable. Further examination of 58 clinical isolates showed that 14 of the 17 predicted major structural subunit genes of the fimbriae were present in most strains (>85 %). Transcription of the predicted major structural subunit genes for all 17 fimbriae was measured under different culture conditions designed to mimic conditions in the urinary tract. The majority of the fimbrial genes were induced during stationary phase, static culture or colony growth when compared to exponential-phase aerated culture. Major structural subunit proteins for six of these fimbriae were detected using MS of proteins sheared from the surface of broth-cultured P. mirabilis, demonstrating that this organism may produce multiple fimbriae within a single culture. The high degree of conservation of P. mirabilis fimbriae stands in contrast to uropathogenic Escherichia coli and Salmonella enterica, which exhibit greater variability in their fimbrial repertoires. These findings suggest there may be evolutionary pressure for P. mirabilis to maintain a large fimbrial arsenal. PMID:24809384

Systematic network coding for two-hop lossy transmissions

NASA Astrophysics Data System (ADS)

Li, Ye; Blostein, Steven; Chan, Wai-Yip

2015-12-01

In this paper, we consider network transmissions over a single or multiple parallel two-hop lossy paths. These scenarios occur in applications such as sensor networks or WiFi offloading. Random linear network coding (RLNC), where previously received packets are re-encoded at intermediate nodes and forwarded, is known to be a capacity-achieving approach for these networks. However, a major drawback of RLNC is its high encoding and decoding complexity. In this work, a systematic network coding method is proposed. We show through both analysis and simulation that the proposed method achieves higher end-to-end rate as well as lower computational cost than RLNC for finite field sizes and finite-sized packet transmissions.

In Silico Identification of Epitopes in Mycobacterium avium subsp. paratuberculosis Proteins That Were Upregulated under Stress Conditions

PubMed Central

Gurung, Ratna B.; Purdie, Auriol C.; Begg, Douglas J.

2012-01-01

Johne's disease in ruminants is caused by Mycobacterium avium subsp. paratuberculosis. Diagnosis of M. avium subsp. paratuberculosis infection is difficult, especially in the early stages. To date, ideal antigen candidates are not available for efficient immunization or immunodiagnosis. This study reports the in silico selection and subsequent analysis of epitopes of M. avium subsp. paratuberculosis proteins that were found to be upregulated under stress conditions as a means to identify immunogenic candidate proteins. Previous studies have reported differential regulation of proteins when M. avium subsp. paratuberculosis is exposed to stressors which induce a response similar to dormancy. Dormancy may be involved in evading host defense mechanisms, and the host may also mount an immune response against these proteins. Twenty-five M. avium subsp. paratuberculosis proteins that were previously identified as being upregulated under in vitro stress conditions were analyzed for B and T cell epitopes by use of the prediction tools at the Immune Epitope Database and Analysis Resource. Major histocompatibility complex class I T cell epitopes were predicted using an artificial neural network method, and class II T cell epitopes were predicted using the consensus method. Conformational B cell epitopes were predicted from the relevant three-dimensional structure template for each protein. Based on the greatest number of predicted epitopes, eight proteins (MAP2698c [encoded by desA2], MAP2312c [encoded by fadE19], MAP3651c [encoded by fadE3_2], MAP2872c [encoded by fabG5_2], MAP3523c [encoded by oxcA], MAP0187c [encoded by sodA], and the hypothetical proteins MAP3567 and MAP1168c) were identified as potential candidates for study of antibody- and cell-mediated immune responses within infected hosts. PMID:22496492

Yeast PAH1-encoded phosphatidate phosphatase controls the expression of CHO1-encoded phosphatidylserine synthase for membrane phospholipid synthesis.

PubMed

Han, Gil-Soo; Carman, George M

2017-08-11

The PAH1 -encoded phosphatidate phosphatase (PAP), which catalyzes the committed step for the synthesis of triacylglycerol in Saccharomyces cerevisiae , exerts a negative regulatory effect on the level of phosphatidate used for the de novo synthesis of membrane phospholipids. This raises the question whether PAP thereby affects the expression and activity of enzymes involved in phospholipid synthesis. Here, we examined the PAP-mediated regulation of CHO1 -encoded phosphatidylserine synthase (PSS), which catalyzes the committed step for the synthesis of major phospholipids via the CDP-diacylglycerol pathway. The lack of PAP in the pah1 Δ mutant highly elevated PSS activity, exhibiting a growth-dependent up-regulation from the exponential to the stationary phase of growth. Immunoblot analysis showed that the elevation of PSS activity results from an increase in the level of the enzyme encoded by CHO1 Truncation analysis and site-directed mutagenesis of the CHO1 promoter indicated that Cho1 expression in the pah1 Δ mutant is induced through the inositol-sensitive upstream activation sequence (UAS INO ), a cis -acting element for the phosphatidate-controlled Henry (Ino2-Ino4/Opi1) regulatory circuit. The abrogation of Cho1 induction and PSS activity by a CHO1 UAS INO mutation suppressed pah1 Δ effects on lipid synthesis, nuclear/endoplasmic reticulum membrane morphology, and lipid droplet formation, but not on growth at elevated temperature. Loss of the DGK1 -encoded diacylglycerol kinase, which converts diacylglycerol to phosphatidate, partially suppressed the pah1 Δ-mediated induction of Cho1 and PSS activity. Collectively, these data showed that PAP activity controls the expression of PSS for membrane phospholipid synthesis. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Wireless live streaming video of laparoscopic surgery: a bandwidth analysis for handheld computers.

PubMed

Gandsas, Alex; McIntire, Katherine; George, Ivan M; Witzke, Wayne; Hoskins, James D; Park, Adrian

2002-01-01

Over the last six years, streaming media has emerged as a powerful tool for delivering multimedia content over networks. Concurrently, wireless technology has evolved, freeing users from desktop boundaries and wired infrastructures. At the University of Kentucky Medical Center, we have integrated these technologies to develop a system that can wirelessly transmit live surgery from the operating room to a handheld computer. This study establishes the feasibility of using our system to view surgeries and describes the effect of bandwidth on image quality. A live laparoscopic ventral hernia repair was transmitted to a single handheld computer using five encoding speeds at a constant frame rate, and the quality of the resulting streaming images was evaluated. No video images were rendered when video data were encoded at 28.8 kilobytes per second (Kbps), the slowest encoding bitrate studied. The highest quality images were rendered at encoding speeds greater than or equal to 150 Kbps. Of note, a 15 second transmission delay was experienced using all four encoding schemes that rendered video images. We believe that the wireless transmission of streaming video to handheld computers has tremendous potential to enhance surgical education. For medical students and residents, the ability to view live surgeries, lectures, courses and seminars on handheld computers means a larger number of learning opportunities. In addition, we envision that wireless enabled devices may be used to telemonitor surgical procedures. However, bandwidth availability and streaming delay are major issues that must be addressed before wireless telementoring becomes a reality.

Chromobacterium pathogenicity island 1 type III secretion system is a major virulence determinant for Chromobacterium violaceum-induced cell death in hepatocytes.

PubMed

Miki, Tsuyoshi; Iguchi, Mirei; Akiba, Kinari; Hosono, Masato; Sobue, Tomoyoshi; Danbara, Hirofumi; Okada, Nobuhiko

2010-08-01

Chromobacterium violaceum is a Gram-negative bacterium that causes fatal septicaemia in humans and animals. C. violaceum ATCC 12472 possesses genes associated with two distinct type III secretion systems (T3SSs). One of these systems is encoded by Chromobacterium pathogenicity islands 1 and 1a (Cpi-1/-1a), another is encoded by Chromobacterium pathogenicity island 2 (Cpi-2). Here we show that C. violaceum causes fulminant hepatitis in a mouse infection model, and Cpi-1/-1a-encoded T3SS is required for its virulence. In addition, using C. violaceum strains with defined mutations in the genes that encode the Cpi-1/-1a or Cpi-2 locus in combination with cultured mammalian cell lines, we found that C. violaceum is able to induce cytotoxicity in a Cpi-1/-1a-dependent manner. Characterization of Chromobacterium-induced cytotoxicity revealed that cell lysis by C. violaceum infection involves the formation of pore structures on the host cell membrane, as demonstrated by protection by cytotoxicity in the presence of osmoprotectants. Finally, we demonstrated that CipB, a Cpi-1/-1a effector, is implicated in translocator-mediated pore formation and the ability of CipB to form a pore is essential for Chromobacterium-induced cytotoxicity. These results strongly suggest that Cpi-1/-1a-encoded T3SS is a virulence determinant that causes fatal infection by the induction of cell death in hepatocytes. © 2010 Blackwell Publishing Ltd.

Methylotrophic Bacillus methanolicus Encodes Two Chromosomal and One Plasmid Born NAD+ Dependent Methanol Dehydrogenase Paralogs with Different Catalytic and Biochemical Properties

PubMed Central

Müller, Jonas E. N.; Kupper, Christiane E.; Schneider, Olha; Vorholt, Julia A.; Ellingsen, Trond E.; Brautaset, Trygve

2013-01-01

Bacillus methanolicus can utilize methanol as the sole carbon source for growth and it encodes an NAD+-dependent methanol dehydrogenase (Mdh), catalyzing the oxidation of methanol to formaldehyde. Recently, the genomes of the B. methanolicus strains MGA3 (ATCC53907) and PB1 (NCIMB13113) were sequenced and found to harbor three different putative Mdh encoding genes, each belonging to the type III Fe-NAD+-dependent alcohol dehydrogenases. In each strain, two of these genes are encoded on the chromosome and one on a plasmid; only one chromosomal act gene encoding the previously described activator protein ACT was found. The six Mdhs and the ACT proteins were produced recombinantly in Escherichia coli, purified, and characterized. All Mdhs required NAD+ as cosubstrate, were catalytically stimulated by ACT, exhibited a broad and different substrate specificity range and displayed both dehydrogenase and reductase activities. All Mdhs catalyzed the oxidation of methanol; however the catalytic activity for methanol was considerably lower than for most other alcohols tested, suggesting that these enzymes represent a novel class of alcohol dehydrogenases. The kinetic constants for the Mdhs were comparable when acting as pure enzymes, but together with ACT the differences were more pronounced. Quantitative PCR experiments revealed major differences with respect to transcriptional regulation of the paralogous genes. Taken together our data indicate that the repertoire of methanol oxidizing enzymes in thermotolerant bacilli is larger than expected with complex mechanisms involved in their regulation. PMID:23527128

Methylotrophic Bacillus methanolicus encodes two chromosomal and one plasmid born NAD+ dependent methanol dehydrogenase paralogs with different catalytic and biochemical properties.

PubMed

Krog, Anne; Heggeset, Tonje M B; Müller, Jonas E N; Kupper, Christiane E; Schneider, Olha; Vorholt, Julia A; Ellingsen, Trond E; Brautaset, Trygve

2013-01-01

Bacillus methanolicus can utilize methanol as the sole carbon source for growth and it encodes an NAD(+)-dependent methanol dehydrogenase (Mdh), catalyzing the oxidation of methanol to formaldehyde. Recently, the genomes of the B. methanolicus strains MGA3 (ATCC53907) and PB1 (NCIMB13113) were sequenced and found to harbor three different putative Mdh encoding genes, each belonging to the type III Fe-NAD(+)-dependent alcohol dehydrogenases. In each strain, two of these genes are encoded on the chromosome and one on a plasmid; only one chromosomal act gene encoding the previously described activator protein ACT was found. The six Mdhs and the ACT proteins were produced recombinantly in Escherichia coli, purified, and characterized. All Mdhs required NAD(+) as cosubstrate, were catalytically stimulated by ACT, exhibited a broad and different substrate specificity range and displayed both dehydrogenase and reductase activities. All Mdhs catalyzed the oxidation of methanol; however the catalytic activity for methanol was considerably lower than for most other alcohols tested, suggesting that these enzymes represent a novel class of alcohol dehydrogenases. The kinetic constants for the Mdhs were comparable when acting as pure enzymes, but together with ACT the differences were more pronounced. Quantitative PCR experiments revealed major differences with respect to transcriptional regulation of the paralogous genes. Taken together our data indicate that the repertoire of methanol oxidizing enzymes in thermotolerant bacilli is larger than expected with complex mechanisms involved in their regulation.

PCR amplification and sequence analysis of the major capsid protein gene of megalocytiviruses isolated in Taiwan.

PubMed

Wang, C S; Chao, S Y; Ku, C C; Wen, C M; Shih, H H

2009-06-01

Viruses belonging to the genus Megalocytivirus in the family Iridoviridae are one of the major agents causing mass mortalities in marine and freshwater fish in Asian countries. Outbreaks of iridovirus disease have been reported among various fish species in Taiwan. However, the genotypes of these iridoviruses have not yet been determined. In this study, seven megalocytivirus isolates from four fish species: king grouper, Epinephelus lanceolatus (Bloch), barramundi perch, Lates calcarifer (Bloch), silver sea bream, Rhabdosargus sarba (Forsskal), and common ponyfish, Leiognathus equulus (Forsskal), cultured in three different regions of Taiwan were collected. The full open reading frame encoding the viral major capsid protein gene was amplified using PCR. The PCR products of approximately 1581 bp were cloned and the nucleotide sequences were phylogenetically analysed. Results showed that all seven PCR products contained a unique open reading frame with 1362 nucleotides and encoded a structural protein with 453 amino acids. Even though the nucleotide sequences were not identical, these seven megalocytiviruses were classified into one cluster and showed very high homology with red sea bream iridovirus (RSIV) with more than 97% identity. Thus, the seven iridovirus strains isolated from cultured marine fish in Taiwan were closer to the RSIV genotype than the infectious spleen and kidney necrosis virus genotype.

The candidate histocompatibility locus of a Basal chordate encodes two highly polymorphic proteins.

PubMed

Nydam, Marie L; Netuschil, Nikolai; Sanders, Erin; Langenbacher, Adam; Lewis, Daniel D; Taketa, Daryl A; Marimuthu, Arumugapradeep; Gracey, Andrew Y; De Tomaso, Anthony W

2013-01-01

The basal chordate Botryllus schlosseri undergoes a natural transplantation reaction governed by a single, highly polymorphic locus called the fuhc. Our initial characterization of this locus suggested it encoded a single gene alternatively spliced into two transcripts: a 555 amino acid-secreted form containing the first half of the gene, and a full-length, 1008 amino acid transmembrane form, with polymorphisms throughout the ectodomain determining outcome. We have now found that the locus encodes two highly polymorphic genes which are separated by a 227 bp intergenic region: first, the secreted form as previously described, and a second gene encoding a 531 amino acid membrane-bound gene containing three extracellular immunoglobulin domains. While northern blotting revealed only these two mRNAs, both PCR and mRNA-seq detect a single capped and polyadenylated transcript that encodes processed forms of both genes linked by the intergenic region, as well as other transcripts in which exons of the two genes are spliced together. These results might suggest that the two genes are expressed as an operon, during which both genes are co-transcribed and then trans-spliced into two separate messages. This type of transcriptional regulation has been described in tunicates previously; however, the membrane-bound gene does not encode a typical Splice Leader (SL) sequence at the 5' terminus that usually accompanies trans-splicing. Thus, the presence of stable transcripts encoding both genes may suggest a novel mechanism of regulation, or conversely may be rare but stable transcripts in which the two mRNAs are linked due to a small amount of read-through by RNA polymerase. Both genes are highly polymorphic and co-expressed on tissues involved in histocompatibility. In addition, polymorphisms on both genes correlate with outcome, although we have found a case in which it appears that the secreted form may be major allorecognition determinant.

Hippocampal place cell encoding of sloping terrain.

PubMed

Porter, Blake S; Schmidt, Robert; Bilkey, David K

2018-05-21

Effective navigation relies on knowledge of one's environment. A challenge to effective navigation is accounting for the time and energy costs of routes. Irregular terrain in ecological environments poses a difficult navigational problem as organisms ought to avoid effortful slopes to minimize travel costs. Route planning and navigation have previously been shown to involve hippocampal place cells and their ability to encode and store information about an organism's environment. However, little is known about how place cells may encode the slope of space and associated energy costs as experiments are traditionally carried out in flat, horizontal environments. We set out to investigate how dorsal-CA1 place cells in rats encode systematic changes to the slope of an environment by tilting a shuttle box from flat to 15° and 25° while minimizing external cue change. Overall, place cell encoding of tilted space was as robust as their encoding of flat ground as measured by traditional place cell metrics such as firing rates, spatial information, coherence, and field size. A large majority of place cells did, however, respond to slope by undergoing partial, complex remapping when the environment was shifted from one tilt angle to another. The propensity for place cells to remap did not, however, depend on the vertical distance the field shifted. Changes in slope also altered the temporal coding of information as measured by the rate of theta phase precession of place cell spikes, which decreased with increasing tilt angles. Together these observations indicate that place cells are sensitive to relatively small changes in terrain slope and that terrain slope may be an important source of information for organizing place cell ensembles. The terrain slope information encoded by place cells could be utilized by efferent regions to determine energetically advantageous routes to goal locations. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

Comparative genomics analysis of Lactobacillus species associated with weight gain or weight protection.

PubMed

Drissi, F; Merhej, V; Angelakis, E; El Kaoutari, A; Carrière, F; Henrissat, B; Raoult, D

2014-02-24

Some Lactobacillus species are associated with obesity and weight gain while others are associated with weight loss. Lactobacillus spp. and bifidobacteria represent a major bacterial population of the small intestine where lipids and simple carbohydrates are absorbed, particularly in the duodenum and jejunum. The objective of this study was to identify Lactobacillus spp. proteins involved in carbohydrate and lipid metabolism associated with weight modifications. We examined a total of 13 complete genomes belonging to seven different Lactobacillus spp. previously associated with weight gain or weight protection. We combined the data obtained from the Rapid Annotation using Subsystem Technology, Batch CD-Search and Gene Ontology to classify gene function in each genome. We observed major differences between the two groups of genomes. Weight gain-associated Lactobacillus spp. appear to lack enzymes involved in the catabolism of fructose, defense against oxidative stress and the synthesis of dextrin, L-rhamnose and acetate. Weight protection-associated Lactobacillus spp. encoded a significant gene amount of glucose permease. Regarding lipid metabolism, thiolases were only encoded in the genome of weight gain-associated Lactobacillus spp. In addition, we identified 18 different types of bacteriocins in the studied genomes, and weight gain-associated Lactobacillus spp. encoded more bacteriocins than weight protection-associated Lactobacillus spp. The results of this study revealed that weight protection-associated Lactobacillus spp. have developed defense mechanisms for enhanced glycolysis and defense against oxidative stress. Weight gain-associated Lactobacillus spp. possess a limited ability to breakdown fructose or glucose and might reduce ileal brake effects.

Characterization of a major late herpes simplex virus type 1 mRNA.

PubMed

Costa, R H; Devi, B G; Anderson, K P; Gaylord, B H; Wagner, E K

1981-05-01

A major, late 6-kilobase (6-kb) mRNa mapping in the large unique region of herpes simplex virus type 1 (HSV-1) was characterized by using two recombinant DNA clones, one containing EcoRI fragment G (0.190 to 0.30 map units) in lambda. WES.B (L. Enquist, M. Madden, P. Schiop-Stansly, and G. Vandl Woude, Science 203:541-544, 1979) and one containing HindIII fragment J (0.181 to 0.259 map units) in pBR322. This 6-kb mRNA had its 3' end to the left of 0.231 on the prototypical arrangement of the HSV-1 genome and was transcribed from right to left. It was bounded on both sides by regions containing a large number of distinct mRNA species, and its 3' end was partially colinear with a 1.5-kb mRNA which encoded a 35,000-dalton polypeptide. The 6-kb mRNA encoded a 155,000-dalton polypeptide which was shown to be the only one of this size detectable by hybrid-arrested translation encoded by late polyadenylated polyribosomal RNA. The S1 nuclease mapping experiments indicated that there were no introns in the coding sequence for this mRNA and that its 3' end mapped approximately 800 nucleotides to the left of the BglII site at 0.231, whereas its 5' end extended very close to the BamHI site at 0.266.

A genome-wide supported variant in CACNA1C influences hippocampal activation during episodic memory encoding and retrieval.

PubMed

Krug, Axel; Witt, Stephanie H; Backes, Heidelore; Dietsche, Bruno; Nieratschker, Vanessa; Shah, N Jon; Nöthen, Markus M; Rietschel, Marcella; Kircher, Tilo

2014-03-01

The alpha 1C subunit of the L-type voltage-gated calcium channel (CACNA1C) gene is one of the best replicated susceptibility loci for bipolar disorder, schizophrenia and major depression. It is involved in learning, memory and brain plasticity. Genetic studies using functional magnetic resonance imaging (fMRI) reported evidence of association with the CACNA1C single nucleotide polymorphism rs1006737 with functional correlates of episodic memory encoding and retrieval, especially activations in the hippocampus. These results, however, are inconsistent with regard to the magnitude and directionality of effect. In the present study, brain activation was measured with fMRI during an episodic memory encoding and retrieval task using neutral faces in two independent samples of 94 and 111 healthy subjects, respectively. Within whole brain analyses, a main effect of genotype emerged mainly in the right hippocampus during encoding as well as retrieval within the first sample: Carriers of the minor allele (A) exhibited lower activations compared to G/G allele carriers. This effect could be replicated within the second sample, however, only for the retrieval condition. The results strengthen findings that rs1006737 is associated with neural systems related to memory processes in hippocampal regions which are detectable in healthy subjects.

Interactive searching of facial image databases

NASA Astrophysics Data System (ADS)

Nicholls, Robert A.; Shepherd, John W.; Shepherd, Jean

1995-09-01

A set of psychological facial descriptors has been devised to enable computerized searching of criminal photograph albums. The descriptors have been used to encode image databased of up to twelve thousand images. Using a system called FACES, the databases are searched by translating a witness' verbal description into corresponding facial descriptors. Trials of FACES have shown that this coding scheme is more productive and efficient than searching traditional photograph albums. An alternative method of searching the encoded database using a genetic algorithm is currenly being tested. The genetic search method does not require the witness to verbalize a description of the target but merely to indicate a degree of similarity between the target and a limited selection of images from the database. The major drawback of FACES is that is requires a manual encoding of images. Research is being undertaken to automate the process, however, it will require an algorithm which can predict human descriptive values. Alternatives to human derived coding schemes exist using statistical classifications of images. Since databases encoded using statistical classifiers do not have an obvious direct mapping to human derived descriptors, a search method which does not require the entry of human descriptors is required. A genetic search algorithm is being tested for such a purpose.

LAMP-1-chimeric DNA vaccines enhance the antibody response in Japanese flounder, Paralichthys olivaceus.

PubMed

Rondón-Barragán, Iang; Nozaki, Reiko; Hirono, Ikuo; Kondo, Hidehiro

2017-08-01

DNA vaccination is one method to protect farmed fish from viral and bacterial diseases. Chimeric antigens encoded by DNA vaccines have been shown to increase the resistance to viral diseases. Here, we sequenced the gene encoding lysosome-associated membrane protein-1 from Japanese flounder, Paralichthys olivaceus, (JfLAMP-1) and assessed its use in a chimeric DNA vaccine fused with the major capsule protein (MCP) from red seabream iridovirus (RSIV). JfLAMP-1 cDNA has a length of 1248 bp encoding 415 aa, which contains transmembrane and cytoplasmic domains. JfLAMP-1 is constitutively expressed in several tissues and its expression in spleen was upregulated following injection of formalin-killed cells (FKC) of Edwardsiella tarda. Immunofluorescence analysis showed that JfLAMP-1 is distributed in the small and large granules in the cytoplasm and groups close to the nucleus. The DNA encoding the luminal domain of JfLAMP-1 was replaced with the gene for the RSIV MCP, and the construct was cloned in an expression vector (pCIneo). Fish vaccinated with pCLAMP-MCP had significantly higher antibody levels than fish vaccinated with pCIneo vector harboring the MCP gene (p < 0.05) at day 30 post-vaccination. Copyright © 2017 Elsevier Ltd. All rights reserved.

ACC Neuro-over-Connectivity Is Associated with Mathematically Modeled Additional Encoding Operations of Schizophrenia Stroop-Task Performance

PubMed Central

Taylor, Reggie; Théberge, Jean; Williamson, Peter C.; Densmore, Maria; Neufeld, Richard W. J.

2016-01-01

Functional magnetic resonance imaging at 7.0 Tesla was undertaken among Schizophrenia participants (Sz), and clinical (major mood disorder; MDD) and healthy controls (HC), during performance of the Stoop task. Stroop conditions included congruent and incongruent word color items, color-only items, and word-only items. Previous modeling results extended to this most widely used selective-attention task. All groups executed item-encoding operations (subprocesses of the item encoding process) at the same rate (performance accuracy being similarly high throughout), thus displaying like processing capacity; Sz participants, however, employed more subprocesses for item completions than did the MDD participants, who in turn used more subprocesses than the HC group. The reduced efficiency in deploying cognitive-workload capacity among the Sz participants was paralleled by more diffuse neuroconnectivity (Blood-Oxygen-Level-Dependent co-activation) with the anterior cingulate cortex (ACC) (Broadman Area 32), spreading away from this encoding-intensive region; and by less evidence of network dissociation across Stroop conditions. Estimates of cognitive work done to accomplish item completion were greater for the Sz participants, as were estimates of entropy in both the modeled trial-latency distribution, and its associated neuro-circuitry. Findings are held to be symptom and assessment significant, and to have potential implications for clinical intervention. PMID:27695425

Identifying Facilitators and Barriers for Patient Safety in a Medicine Label Design System Using Patient Simulation and Interviews.

PubMed

Dieckmann, Peter; Clemmensen, Marianne Hald; Sørensen, Trine Kart; Kunstek, Pina; Hellebek, Annemarie

2016-12-01

Medicine label design plays an important role in improving patient safety. This study aimed at identifying facilitators and barriers in a medicine label system to prevent medication errors in clinical use by health care professionals. The study design is qualitative and exploratory, with a convenience sample of 10 nurses and 10 physicians from different acute care specialties working in hospitals in the Capital Region of Denmark. In 2 patient simulation scenarios and a sorting task, the participants selected the medicines from a range of ampules, vials, and infusion bags. After each scenario and in the end of the study, the participants were interviewed. Notes were validated with the participants, and content was analyzed. The label design benefited from the standardized construction of the labels, the clear layout and font, and some warning signs. The complexity of the system and some inconsistencies (different meaning of colors) posed challenges, when considered with the actual application context, in which there is little time to get familiar with the design features. For optimizing medicine labels and obtaining the full benefit of label design features on patient safety, it is necessary to consider the context in which they are used.

Magnetism and 155Gd Mössbauer spectroscopy of GdAuMg

NASA Astrophysics Data System (ADS)

Łątka, Kazimierz; Kmieć, Roman; Pacyna, Andrzej W.; Fickenscher, Thomas; Hoffmann, Rolf-Dieter; Pöttgen, Rainer

2004-03-01

GdAuMg was synthesized by reaction of the elements in a sealed tantalum ampule in a high-frequency furnace. The structure was investigated by X-ray diffraction on both powders and single crystals: ZrNiAl type, P 6¯2m , a=756.3(1), c=412.71(7) pm, wR2=0.0285 for 308 F2 values, 14 variables. Geometrical motifs of the GdAuMg structure are gold centered tricapped trigonal prisms [Au1Mg 3Gd 6] and [Au2Mg 6Gd 3]. Together the gold and magnesium atoms form a three-dimensional [AuMg] network in which the gadolinium atoms fill distorted hexagonal channels. Bulk magnetic properties have been investigated by means of AC and DC magnetic susceptibility measurements and 155Gd Mössbauer spectroscopy was used to monitor the local electronic and magnetic structure. Two magnetic phase transitions were found. One transition, at T1= TN=81.1(1) K, is from a paramagnetic to an antiferromagnetic state of collinear character and the other at T2=19.0(1) from the antiferromagnetic to a kind of canted magnetic ordering characterized by a very narrow hysteresis loop.

Determination of stable carbon and hydrogen isotopes of light hydrocarbons

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

Dumke, I.; Faber, E.; Poggenburg, J.

1989-10-01

A combined system for the measurement of {sup 13}C/{sup 12}C and D/H ratios on light hydrocarbons (C{sub 1}-C{sub 3}) and CO{sub 2} is described. The system is designed for natural gas and sediment gas analyses. It comprises gas chromatographic separation with online combustion of hydrocarbons to CO{sub 2} and H{sub 2}O, reduction of H{sub 2}O to H{sub 2} on zinc in closed ampules, and mass spectrometric determination of isotope ratios ({delta}{sup 13}C, {delta}D) using a mass spectrometer inlet system especially designed for low hydrogen gas quantities. Isotope analyses can be carried out in the range of 3-10,000 {mu}L of CO{submore » 2} and 100-10,000 {mu}L of H{sub 2} (gas quantities converted from sample compounds during preparation, STP). Including all preparation steps, reproducibility of isotope values for large sample quantities (>100 {mu}L of produced CO{sub 2} and >1,000 {mu}L of produced H{sub 2}). is {plus minus}0.2{per thousand} for {delta}{sup 13}C and {plus minus}3{per thousand} for {delta}D.« less

Impotence evaluated by the use of prostaglandin E1

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

Hwang, T.I.; Yang, C.R.; Wang, S.J.

1989-06-01

We screened 80 patients at our hospital for the differential diagnosis of impotence using intracavernous injection of prostaglandin E1 (20 micrograms). The rate of positive response was 78.8 per cent (63 patients). Neither systemic reactions nor priapism occurred. However, a considerable incidence (23.8 per cent, 19 of 80 patients) of tolerable injection pain was encountered. The 133-xenon penile washout study was conducted routinely in impotent men for hemodynamic evaluation of penile vascularity. In 80 patients a positive correlation between the response of intracavernous prostaglandin E1 injection and the result of the washout study was found (r equals 0.381, p lessmore » than 0.0002). We selected 14 subjects randomly to receive additional intravenous infusions of prostaglandin E1 (6 ampules, 120 micrograms total) for 3 days, after which another 133-xenon washout study was done. The washout studies before and after intravenous prostaglandin E1 infusion were compared, and 10 patients (71.4 per cent) appeared to obtain improvement in half-time clearance and penile blood flow. However, only 3 patients noticed improvement subjectively. We suggest that prostaglandin E1 could be a desirable alternative for the diagnosis and treatment of impotence.« less

Vapor containment tests of the rapid response system glovebox. Final report, December 1995-April 1996

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

Arca, V.J.; Blewett, W.K.; Kinne, W.E.

1996-10-01

The Rapid Response System (RRS) is a trailer-mounted facility for demilitarizing Chemical Agent Identification Sets (CAIS), obsolete training kits containing ampules and/or bottles of chemical warfare agents (mustard and lewisite), or other industrial chemical compounds. The main component of the RRS is a glovebox divided into three areas - an airlock station, unpack station, and neutralization station, and the CAIS items are processed through each station by use of 11 glove ports. The glovebox is maintained at negative pressure differential by a gas-particulate filter-blower unit. To measure the performance of the glovebox in containing chemical vapors/gases, a series of testsmore » was conducted on 811 April 1996 at Tooele Army Depot, UT, with methyl salicylate, a simulant for mustard. This testing addressed performance in steady state operation, airlock cycling, waste barrel changeout, and glove changeout. Two trials were also conducted in a simulated power-failure condition to determine the rate of leakage if system airflow is interrupted. The glovebox and its engineering controls provided a very high level of protection. Some procedural changes were recommended to increase the protection factor in glove and barrel changeout operations.« less

Conjugative type IVb pilus recognizes lipopolysaccharide of recipient cells to initiate PAPI-1 pathogenicity island transfer in Pseudomonas aeruginosa

USDA-ARS?s Scientific Manuscript database

Pseudomonas aeruginosa pathogenicity island 1 (PAPI-1) is one of the largest genomic islands of this important opportunistic human pathogen. Previous studies have shown that PAPI-1 encodes several putative virulence factors, a major regulator of biofilm formation, and antibiotic-resistance traits, a...

Congenital Disorders of Glycosylation and Intellectual Disability

ERIC Educational Resources Information Center

Wolfe, Lynne A.; Krasnewich, Donna

2013-01-01

The congenital disorders of glycosylation (CDG) are a rapidly growing group of inborn errors of metabolism that result from defects in the synthesis of glycans. Glycosylation is a major post-translational protein modification and an estimated 2% of the human genome encodes proteins for glycosylation. The molecular bases for the current 60…

Expression of an Arabidopsis sodium/proton antiporter gene (AtNHX1)in peanut to improve salt tolerance

USDA-ARS?s Scientific Manuscript database

Salinity is a major environmental stress that affects agricultural productivity worldwide. One approach to improving salt tolerance in crops is through high expression of the Arabidopsis gene AtNHX1, which encodes a vacuolar sodium/proton antiporter that sequesters excess sodium ion into the large i...

Design Strategy of Multi-electron Transfer Catalysts Based on a Bioinformatic Analysis of Oxygen Evolution and Reduction Enzymes.

PubMed

Ooka, Hideshi; Hashimoto, Kazuhito; Nakamura, Ryuhei

2018-05-14

Understanding the design strategy of photosynthetic and respiratory enzymes is important to develop efficient artificial catalysts for oxygen evolution and reduction reactions. Here, based on a bioinformatic analysis of cyanobacterial oxygen evolution and reduction enzymes (photosystem II: PS II and cytochrome c oxidase: COX, respectively), the gene encoding the catalytic D1 subunit of PS II was found to be expressed individually across 38 phylogenetically diverse strains, which is in contrast to the operon structure of the genes encoding major COX subunits. Selective synthesis of the D1 subunit minimizes the repair cost of PS II, which allows compensation for its instability by lowering the turnover number required to generate a net positive energy yield. The different bioenergetics observed between PS II and COX suggest that in addition to the catalytic activity rationalized by the Sabatier principle, stability factors have also provided a major influence on the design strategy of biological multi-electron transfer enzymes. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Food commensal microbes as a potentially important avenue in transmitting antibiotic resistance genes.

PubMed

Wang, Hua H; Manuzon, Michele; Lehman, Mark; Wan, Kai; Luo, Hongliang; Wittum, Thomas E; Yousef, Ahmed; Bakaletz, Lauren O

2006-01-01

The rapid emergence of antibiotic-resistant (ART) pathogens is a major threat to public health. While the surfacing of ART food-borne pathogens is alarming, the magnitude of the antibiotic resistance (AR) gene pool in food-borne commensal microbes is yet to be revealed. Incidence of ART commensals in selected retail food products was examined in this study. The presence of 10(2)-10(7) CFU of ART bacteria per gram of foods in many samples, particularly in ready-to-eat, 'healthy' food items, indicates that the ART bacteria are abundant in the food chain. AR-encoding genes were detected in ART isolates, and Streptococcus thermophilus was found to be a major host for AR genes in cheese microbiota. Lactococcus lactis and Leuconostoc sp. isolates were also found carrying AR genes. The data indicate that food could be an important avenue for ART bacterial evolution and dissemination. AR-encoding plasmids from several food-borne commensals were transmitted to Streptococcus mutans via natural gene transformation under laboratory conditions, suggesting the possible transfer of AR genes from food commensals to human residential bacteria via horizontal gene transfer.

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA.

PubMed

Kapranov, Philipp; St Laurent, Georges; Raz, Tal; Ozsolak, Fatih; Reynolds, C Patrick; Sorensen, Poul H B; Reaman, Gregory; Milos, Patrice; Arceci, Robert J; Thompson, John F; Triche, Timothy J

2010-12-21

Discovery that the transcriptional output of the human genome is far more complex than predicted by the current set of protein-coding annotations and that most RNAs produced do not appear to encode proteins has transformed our understanding of genome complexity and suggests new paradigms of genome regulation. However, the fraction of all cellular RNA whose function we do not understand and the fraction of the genome that is utilized to produce that RNA remain controversial. This is not simply a bookkeeping issue because the degree to which this un-annotated transcription is present has important implications with respect to its biologic function and to the general architecture of genome regulation. For example, efforts to elucidate how non-coding RNAs (ncRNAs) regulate genome function will be compromised if that class of RNAs is dismissed as simply 'transcriptional noise'. We show that the relative mass of RNA whose function and/or structure we do not understand (the so called 'dark matter' RNAs), as a proportion of all non-ribosomal, non-mitochondrial human RNA (mt-RNA), can be greater than that of protein-encoding transcripts. This observation is obscured in studies that focus only on polyA-selected RNA, a method that enriches for protein coding RNAs and at the same time discards the vast majority of RNA prior to analysis. We further show the presence of a large number of very long, abundantly-transcribed regions (100's of kb) in intergenic space and further show that expression of these regions is associated with neoplastic transformation. These overlap some regions found previously in normal human embryonic tissues and raises an interesting hypothesis as to the function of these ncRNAs in both early development and neoplastic transformation. We conclude that 'dark matter' RNA can constitute the majority of non-ribosomal, non-mitochondrial-RNA and a significant fraction arises from numerous very long, intergenic transcribed regions that could be involved in neoplastic transformation.

Social problem-solving and mild intellectual disabilities: relations with externalizing behavior and therapeutic context.

PubMed

van Nieuwenhuijzen, Maroesjka; de Castro, Bram Orobio; Wijnroks, Lex; Vermeer, Adri; Matthys, Walter

2009-01-01

Relations among externalizing behavior, therapeutic context (community care vs. residential care), and social problem-solving by children with mild intellectual disabilities or borderline intelligence were examined. Participants were 186 children (12 to 14 years of age) who responded to a video-based social problem-solving task. Of these, 130 received residential care and the majority suffered from severe externalizing behavior problems. The results indicated that externalizing behavior was related to encoding, generation of aggressive responses, and negative evaluation of assertive responses. Therapeutic context was related to encoding, positive evaluation of assertive responses, and negative evaluation of aggressive responses. Results indicate a discrepancy between appropriate problem-solving skills and behavior in daily life. Implications for interventions are discussed.

Multi-functional acetyl-CoA carboxylase from Brassica napus is encoded by a multi-gene family: indication for plastidic localization of at least one isoform.

PubMed

Schulte, W; Töpfer, R; Stracke, R; Schell, J; Martini, N

1997-04-01

Three genes coding for different multifunctional acetyl-CoA carboxylase (ACCase; EC 6.4.1.2) isoenzymes from Brassica napus were isolated and divided into two major classes according to structural features in their 5' regions: class I comprises two genes with an additional coding exon of approximately 300 bp at the 5' end, and class II is represented by one gene carrying an intron of 586 bp in its 5' untranslated region. Fusion of the peptide sequence encoded by the additional first exon of a class I ACCase gene to the jellyfish Aequorea victoria green fluorescent protein (GFP) and transient expression in tobacco protoplasts targeted GFP to the chloroplasts. In contrast to the deduced primary structure of the biotin carboxylase domain encoded by the class I gene, the corresponding amino acid sequence of the class II ACCase shows higher identity with that of the Arabidopsis ACCase, both lacking a transit peptide. The Arabidopsis ACCase has been proposed to be a cytosolic isoenzyme. These observations indicate that the two classes of ACCase genes encode plastidic and cytosolic isoforms of multi-functional, eukaryotic type, respectively, and that B. napus contains at least one multi-functional ACCase besides the multi-subunit, prokaryotic type located in plastids. Southern blot analysis of genomic DNA from B. napus, Brassica rapa, and Brassica oleracea, the ancestors of amphidiploid rapeseed, using a fragment of a multi-functional ACCase gene as a probe revealed that ACCase is encoded by a multi-gene family of at least five members.

The ribosomal protein genes and Minute loci of Drosophila melanogaster

PubMed Central

Marygold, Steven J; Roote, John; Reuter, Gunter; Lambertsson, Andrew; Ashburner, Michael; Millburn, Gillian H; Harrison, Paul M; Yu, Zhan; Kenmochi, Naoya; Kaufman, Thomas C; Leevers, Sally J; Cook, Kevin R

2007-01-01

Background Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster, disruption of RP genes can result in the 'Minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged development, short and thin bristles, and poor fertility and viability. While more than 50 Minute loci have been defined genetically, only 15 have so far been characterized molecularly and shown to correspond to RP genes. Results We combined bioinformatic and genetic approaches to conduct a systematic analysis of the relationship between RP genes and Minute loci. First, we identified 88 genes encoding 79 different cytoplasmic RPs (CRPs) and 75 genes encoding distinct mitochondrial RPs (MRPs). Interestingly, nine CRP genes are present as duplicates and, while all appear to be functional, one member of each gene pair has relatively limited expression. Next, we defined 65 discrete Minute loci by genetic criteria. Of these, 64 correspond to, or very likely correspond to, CRP genes; the single non-CRP-encoding Minute gene encodes a translation initiation factor subunit. Significantly, MRP genes and more than 20 CRP genes do not correspond to Minute loci. Conclusion This work answers a longstanding question about the molecular nature of Minute loci and suggests that Minute phenotypes arise from suboptimal protein synthesis resulting from reduced levels of cytoribosomes. Furthermore, by identifying the majority of haplolethal and haplosterile loci at the molecular level, our data will directly benefit efforts to attain complete deletion coverage of the D. melanogaster genome. PMID:17927810

Dynamic coding of vertical facilitated vergence by premotor saccadic burst neurons.

PubMed

Van Horn, Marion R; Cullen, Kathleen E

2008-10-01

To redirect our gaze in three-dimensional space we frequently combine saccades and vergence. These eye movements, known as disconjugate saccades, are characterized by eyes rotating by different amounts, with markedly different dynamics, and occur whenever gaze is shifted between near and far objects. How the brain ensures the precise control of binocular positioning remains controversial. It has been proposed that the traditionally assumed "conjugate" saccadic premotor pathway does not encode conjugate commands but rather encodes monocular commands for the right or left eye during saccades. Here, we directly test this proposal by recording from the premotor neurons of the horizontal saccade generator during a dissociation task that required a vergence but no horizontal conjugate saccadic command. Specifically, saccadic burst neurons (SBNs) in the paramedian pontine reticular formation were recorded while rhesus monkeys made vertical saccades made between near and far targets. During this task, we first show that peak vergence velocities were enhanced to saccade-like speeds (e.g., >150 vs. <100 degrees/s during saccade-free movements for comparable changes in vergence angle). We then quantified the discharge dynamics of SBNs during these movements and found that the majority of the neurons preferentially encode the velocity of the ipsilateral eye. Notably, a given neuron typically encoded the movement of the same eye during horizontal saccades that were made in depth. Taken together, our findings demonstrate that the brain stem saccadic burst generator encodes integrated conjugate and vergence commands, thus providing strong evidence for the proposal that the classic saccadic premotor pathway controls gaze in three-dimensional space.

Mechanisms of Memory Dysfunction during High Altitude Hypoxia Training in Military Aircrew.

PubMed

Nation, Daniel A; Bondi, Mark W; Gayles, Ellis; Delis, Dean C

2017-01-01

Cognitive dysfunction from high altitude exposure is a major cause of civilian and military air disasters. Pilot training improves recognition of the early symptoms of altitude exposure so that countermeasures may be taken before loss of consciousness. Little is known regarding the nature of cognitive impairments manifesting within this critical window when life-saving measures may still be taken. Prior studies evaluating cognition during high altitude simulation have predominantly focused on measures of reaction time and other basic attention or motor processes. Memory encoding, retention, and retrieval represent critical cognitive functions that may be vulnerable to acute hypoxic/ischemic events and could play a major role in survival of air emergencies, yet these processes have not been studied in the context of high altitude simulation training. In a series of experiments, military aircrew underwent neuropsychological testing before, during, and after brief (15 min) exposure to high altitude simulation (20,000 ft) in a pressure-controlled chamber. Acute exposure to high altitude simulation caused rapid impairment in learning and memory with relative preservation of basic visual and auditory attention. Memory dysfunction was predominantly characterized by deficiencies in memory encoding, as memory for information learned during high altitude exposure did not improve after washout at sea level. Retrieval and retention of memories learned shortly before altitude exposure were also impaired, suggesting further impairment in memory retention. Deficits in memory encoding and retention are rapidly induced upon exposure to high altitude, an effect that could impact life-saving situational awareness and response. (JINS, 2017, 23, 1-10).

Cysteine degradation gene yhaM, encoding cysteine desulfidase, serves as a genetic engineering target to improve cysteine production in Escherichia coli.

PubMed

Nonaka, Gen; Takumi, Kazuhiro

2017-12-01

Cysteine is an important amino acid for various industries; however, there is no efficient microbial fermentation-based production method available. Owing to its cytotoxicity, bacterial intracellular levels of cysteine are stringently controlled via several modes of regulation, including cysteine degradation by cysteine desulfhydrases and cysteine desulfidases. In Escherichia coli, several metabolic enzymes are known to exhibit cysteine degradative activities, however, their specificity and physiological significance for cysteine detoxification via degradation are unclear. Relaxing the strict regulation of cysteine is crucial for its overproduction; therefore, identifying and modulating the major degradative activity could facilitate the genetic engineering of a cysteine-producing strain. In the present study, we used genetic screening to identify genes that confer cysteine resistance in E. coli and we identified yhaM, which encodes cysteine desulfidase and decomposes cysteine into hydrogen sulfide, pyruvate, and ammonium. Phenotypic characterization of a yhaM mutant via growth under toxic concentrations of cysteine followed by transcriptional analysis of its response to cysteine showed that yhaM is cysteine-inducible, and its physiological role is associated with resisting the deleterious effects of cysteine in E. coli. In addition, we confirmed the effects of this gene on the fermentative production of cysteine using E. coli-based cysteine-producing strains. We propose that yhaM encodes the major cysteine-degrading enzyme and it has the most significant role in cysteine detoxification among the numerous enzymes reported in E. coli, thereby providing a core target for genetic engineering to improve cysteine production in this bacterium.

Suppression of 9-cis-epoxycarotenoid dioxygenase, which encodes a key enzyme in abscisic acid biosynthesis, alters fruit texture in transgenic tomato.

PubMed

Sun, Liang; Sun, Yufei; Zhang, Mei; Wang, Ling; Ren, Jie; Cui, Mengmeng; Wang, Yanping; Ji, Kai; Li, Ping; Li, Qian; Chen, Pei; Dai, Shengjie; Duan, Chaorui; Wu, Yan; Leng, Ping

2012-01-01

Cell wall catabolism during fruit ripening is under complex control and is key for fruit quality and shelf life. To examine the role of abscisic acid (ABA) in tomato (Solanum lycopersicum) fruit ripening, we suppressed SlNCED1, which encodes 9-cis-epoxycarotenoid dioxygenase (NCED), a key enzyme in the biosynthesis of ABA. To suppress SlNCED1 specifically in tomato fruits, and thus avoid the pleiotropic phenotypes associated with ABA deficiency, we used an RNA interference construct driven by the fruit-specific E8 promoter. ABA accumulation and SlNCED1 transcript levels in the transgenic fruit were down-regulated to between 20% and 50% of the levels measured in the control fruit. This significant reduction in NCED activity led to a down-regulation in the transcription of genes encoding major cell wall catabolic enzymes, specifically polygalacturonase (SlPG), pectin methyl esterase (SlPME), β-galactosidase precursor mRNA (SlTBG), xyloglucan endotransglycosylase (SlXET), endo-1,4-β-cellulose (SlCels), and expansin (SlExp). This resulted in an increased accumulation of pectin during ripening. In turn, this led to a significant extension of the shelf life to 15 to 29 d compared with a shelf life of only 7 d for the control fruit and an enhancement of fruit firmness at the mature stage by 30% to 45%. In conclusion, ABA affects cell wall catabolism during tomato fruit ripening via down-regulation of the expression of major catabolic genes (SlPG, SlPME, SlTBG, SlXET, SlCels, and SlExp).

Comparative genomics analysis of Lactobacillus species associated with weight gain or weight protection

PubMed Central

Drissi, F; Merhej, V; Angelakis, E; El Kaoutari, A; Carrière, F; Henrissat, B; Raoult, D

2014-01-01

BACKGROUND: Some Lactobacillus species are associated with obesity and weight gain while others are associated with weight loss. Lactobacillus spp. and bifidobacteria represent a major bacterial population of the small intestine where lipids and simple carbohydrates are absorbed, particularly in the duodenum and jejunum. The objective of this study was to identify Lactobacillus spp. proteins involved in carbohydrate and lipid metabolism associated with weight modifications. METHODS: We examined a total of 13 complete genomes belonging to seven different Lactobacillus spp. previously associated with weight gain or weight protection. We combined the data obtained from the Rapid Annotation using Subsystem Technology, Batch CD-Search and Gene Ontology to classify gene function in each genome. RESULTS: We observed major differences between the two groups of genomes. Weight gain-associated Lactobacillus spp. appear to lack enzymes involved in the catabolism of fructose, defense against oxidative stress and the synthesis of dextrin, L-rhamnose and acetate. Weight protection-associated Lactobacillus spp. encoded a significant gene amount of glucose permease. Regarding lipid metabolism, thiolases were only encoded in the genome of weight gain-associated Lactobacillus spp. In addition, we identified 18 different types of bacteriocins in the studied genomes, and weight gain-associated Lactobacillus spp. encoded more bacteriocins than weight protection-associated Lactobacillus spp. CONCLUSIONS: The results of this study revealed that weight protection-associated Lactobacillus spp. have developed defense mechanisms for enhanced glycolysis and defense against oxidative stress. Weight gain-associated Lactobacillus spp. possess a limited ability to breakdown fructose or glucose and might reduce ileal brake effects. PMID:24567124

In Vivo Evolution of Bacterial Resistance in Two Cases of Enterobacter aerogenes Infections during Treatment with Imipenem

PubMed Central

Santini, Sébastien; Pinet, Elizabeth; Claverie, Jean-Michel; Davin-Régli, Anne-Véronique; Pagès, Jean-Marie; Masi, Muriel

2015-01-01

Infections caused by multidrug resistant (MDR) bacteria are a major concern worldwide. Changes in membrane permeability, including decreased influx and/or increased efflux of antibiotics, are known as key contributors of bacterial MDR. Therefore, it is of critical importance to understand molecular mechanisms that link membrane permeability to MDR in order to design new antimicrobial strategies. In this work, we describe genotype-phenotype correlations in Enterobacter aerogenes, a clinically problematic and antibiotic resistant bacterium. To do this, series of clinical isolates have been periodically collected from two patients during chemotherapy with imipenem. The isolates exhibited different levels of resistance towards multiple classes of antibiotics, consistently with the presence or the absence of porins and efflux pumps. Transport assays were used to characterize membrane permeability defects. Simultaneous genome-wide analysis allowed the identification of putative mutations responsible for MDR. The genome of the imipenem-susceptible isolate G7 was sequenced to closure and used as a reference for comparative genomics. This approach uncovered several loci that were specifically mutated in MDR isolates and whose products are known to control membrane permeability. These were omp35 and omp36, encoding the two major porins; rob, encoding a global AraC-type transcriptional activator; cpxA, phoQ and pmrB, encoding sensor kinases of the CpxRA, PhoPQ and PmrAB two-component regulatory systems, respectively. This report provides a comprehensive analysis of membrane alterations relative to mutational steps in the evolution of MDR of a recognized nosocomial pathogen. PMID:26398358

Korean, Japanese, and Chinese populations featured similar genes encoding drug-metabolizing enzymes and transporters: a DMET Plus microarray assessment.

PubMed

Yi, SoJeong; An, Hyungmi; Lee, Howard; Lee, Sangin; Ieiri, Ichiro; Lee, Youngjo; Cho, Joo-Youn; Hirota, Takeshi; Fukae, Masato; Yoshida, Kenji; Nagatsuka, Shinichiro; Kimura, Miyuki; Irie, Shin; Sugiyama, Yuichi; Shin, Dong Wan; Lim, Kyoung Soo; Chung, Jae-Yong; Yu, Kyung-Sang; Jang, In-Jin

2014-10-01

Interethnic differences in genetic polymorphism in genes encoding drug-metabolizing enzymes and transporters are one of the major factors that cause ethnic differences in drug response. This study aimed to investigate genetic polymorphisms in genes involved in drug metabolism, transport, and excretion among Korean, Japanese, and Chinese populations, the three major East Asian ethnic groups. The frequencies of 1936 variants representing 225 genes encoding drug-metabolizing enzymes and transporters were determined from 786 healthy participants (448 Korean, 208 Japanese, and 130 Chinese) using the Affymetrix Drug-Metabolizing Enzymes and Transporters Plus microarray. To compare allele or genotype frequencies in the high-dimensional data among the three East Asian ethnic groups, multiple testing, principal component analysis (PCA), and regularized multinomial logit model through least absolute shrinkage and selection operator were used. On microarray analysis, 1071 of 1936 variants (>50% of markers) were found to be monomorphic. In a large number of genetic variants, the fixation index and Pearson's correlation coefficient of minor allele frequencies were less than 0.034 and greater than 0.95, respectively, among the three ethnic groups. PCA identified 47 genetic variants with multiple testing, but was unable to discriminate ethnic groups by the first three components. Multinomial least absolute shrinkage and selection operator analysis identified 269 genetic variants that showed different frequencies among the three ethnic groups. However, none of those variants distinguished between the three ethnic groups during subsequent PCA. Korean, Japanese, and Chinese populations are not pharmacogenetically distant from one another, at least with regard to drug disposition, metabolism, and elimination.

Lymphomas in Ile-Ife, Nigeria: Immunohistochemical Characterization and Detection of Epstein-Barr virus Encoded RNA.

PubMed

Onwubuya, Ifeyinwa M; Adelusola, Kayode A; Durosinmi, Muheez A; Sabageh, Donatus; Ezike, Kevin N

2015-06-01

The proper histopathological characterization of malignant lymphomas requires the use of immunohistochemistry along with other molecular pathology techniques. Malignant lymphomas histologically diagnosed in our hospital were reclassified according to the WHO scheme using immunohistochemistry while in-situ hybridization was performed for the detection of Epstein-Barr virus encoded RNA. There were 83 cases of lymphoma. The male to female ratio was 1.9:1 while the overall mean age was 41.7 years. Non-Hodgkin lymphomas (NHL) constituted about 79.5% of cases. The majority of cases (98.8%) were B-cell lymphomas. Nine subtypes of lymphomas were identified with diffuse large B-cell lymphomas (56.4% of which were of the germinal centre type) constituting the largest group (47.0%). Intermediate and high grade subtypes were more common. The majority of cases (72.3%) were nodal lymphomas with cervical lymph node being the commonest site (48.2%). Only classical Hodgkin lymphoma (HL) (20.5%) was seen of which the mixed cellularity subtype was the most common. Epstein Barr virus (EBV) encoded ribonucleic acid was detected in 7 cases (8.4%) including 4 cases of HL, 2 cases of Burkitt lymphoma and the only case of plasmablastic lymphoma. About five cases were reclassified as non-lymphoid malignant lesions. Immunohistochemistry is vital to the proper classification of lymphomas even in a resource poor environment. Although nine subtypes of lymphomas were identified, diffuse large B-cell lymphomas formed the largest single group. Epstein-Barr virus probably plays an important role in lymphomatogenesis in this environment. A larger multicentre study is required to prove this.

In Vivo Evolution of Bacterial Resistance in Two Cases of Enterobacter aerogenes Infections during Treatment with Imipenem.

PubMed

Philippe, Nadège; Maigre, Laure; Santini, Sébastien; Pinet, Elizabeth; Claverie, Jean-Michel; Davin-Régli, Anne-Véronique; Pagès, Jean-Marie; Masi, Muriel

2015-01-01

Infections caused by multidrug resistant (MDR) bacteria are a major concern worldwide. Changes in membrane permeability, including decreased influx and/or increased efflux of antibiotics, are known as key contributors of bacterial MDR. Therefore, it is of critical importance to understand molecular mechanisms that link membrane permeability to MDR in order to design new antimicrobial strategies. In this work, we describe genotype-phenotype correlations in Enterobacter aerogenes, a clinically problematic and antibiotic resistant bacterium. To do this, series of clinical isolates have been periodically collected from two patients during chemotherapy with imipenem. The isolates exhibited different levels of resistance towards multiple classes of antibiotics, consistently with the presence or the absence of porins and efflux pumps. Transport assays were used to characterize membrane permeability defects. Simultaneous genome-wide analysis allowed the identification of putative mutations responsible for MDR. The genome of the imipenem-susceptible isolate G7 was sequenced to closure and used as a reference for comparative genomics. This approach uncovered several loci that were specifically mutated in MDR isolates and whose products are known to control membrane permeability. These were omp35 and omp36, encoding the two major porins; rob, encoding a global AraC-type transcriptional activator; cpxA, phoQ and pmrB, encoding sensor kinases of the CpxRA, PhoPQ and PmrAB two-component regulatory systems, respectively. This report provides a comprehensive analysis of membrane alterations relative to mutational steps in the evolution of MDR of a recognized nosocomial pathogen.

Mobilization of a plant transposon by expression of the transposon-encoded anti-silencing factor.

PubMed

Fu, Yu; Kawabe, Akira; Etcheverry, Mathilde; Ito, Tasuku; Toyoda, Atsushi; Fujiyama, Asao; Colot, Vincent; Tarutani, Yoshiaki; Kakutani, Tetsuji

2013-08-28

Transposable elements (TEs) have a major impact on genome evolution, but they are potentially deleterious, and most of them are silenced by epigenetic mechanisms, such as DNA methylation. Here, we report the characterization of a TE encoding an activity to counteract epigenetic silencing by the host. In Arabidopsis thaliana, we identified a mobile copy of the Mutator-like element (MULE) with degenerated terminal inverted repeats (TIRs). This TE, named Hiun (Hi), is silent in wild-type plants, but it transposes when DNA methylation is abolished. When a Hi transgene was introduced into the wild-type background, it induced excision of the endogenous Hi copy, suggesting that Hi is the autonomously mobile copy. In addition, the transgene induced loss of DNA methylation and transcriptional activation of the endogenous Hi. Most importantly, the trans-activation of Hi depends on a Hi-encoded protein different from the conserved transposase. Proteins related to this anti-silencing factor, which we named VANC, are widespread in the non-TIR MULEs and may have contributed to the recent success of these TEs in natural Arabidopsis populations.

On the possible roles of microsaccades and drifts in visual perception.

PubMed

Ahissar, Ehud; Arieli, Amos; Fried, Moshe; Bonneh, Yoram

2016-01-01

During natural viewing large saccades shift the visual gaze from one target to another every few hundreds of milliseconds. The role of microsaccades (MSs), small saccades that show up during long fixations, is still debated. A major debate is whether MSs are used to redirect the visual gaze to a new location or to encode visual information through their movement. We argue that these two functions cannot be optimized simultaneously and present several pieces of evidence suggesting that MSs redirect the visual gaze and that the visual details are sampled and encoded by ocular drifts. We show that drift movements are indeed suitable for visual encoding. Yet, it is not clear to what extent drift movements are controlled by the visual system, and to what extent they interact with saccadic movements. We analyze several possible control schemes for saccadic and drift movements and propose experiments that can discriminate between them. We present the results of preliminary analyses of existing data as a sanity check to the testability of our predictions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparative genomics of defense systems in archaea and bacteria

PubMed Central

Makarova, Kira S.; Wolf, Yuri I.; Koonin, Eugene V.

2013-01-01

Our knowledge of prokaryotic defense systems has vastly expanded as the result of comparative genomic analysis, followed by experimental validation. This expansion is both quantitative, including the discovery of diverse new examples of known types of defense systems, such as restriction-modification or toxin-antitoxin systems, and qualitative, including the discovery of fundamentally new defense mechanisms, such as the CRISPR-Cas immunity system. Large-scale statistical analysis reveals that the distribution of different defense systems in bacterial and archaeal taxa is non-uniform, with four groups of organisms distinguishable with respect to the overall abundance and the balance between specific types of defense systems. The genes encoding defense system components in bacterial and archaea typically cluster in defense islands. In addition to genes encoding known defense systems, these islands contain numerous uncharacterized genes, which are candidates for new types of defense systems. The tight association of the genes encoding immunity systems and dormancy- or cell death-inducing defense systems in prokaryotic genomes suggests that these two major types of defense are functionally coupled, providing for effective protection at the population level. PMID:23470997

HEx: A heterologous expression platform for the discovery of fungal natural products

PubMed Central

Schlecht, Ulrich; Horecka, Joe; Lin, Hsiao-Ching; Naughton, Brian; Miranda, Molly; Li, Yong Fuga; Hennessy, James R.; Vandova, Gergana A.; Steinmetz, Lars M.; Sattely, Elizabeth; Khosla, Chaitan; Hillenmeyer, Maureen E.

2018-01-01

For decades, fungi have been a source of U.S. Food and Drug Administration–approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth, with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molecules are difficult or impossible to access because the organisms are uncultivable or the genes are transcriptionally silent. To overcome this bottleneck in natural product discovery, we developed the HEx (Heterologous EXpression) synthetic biology platform for rapid, scalable expression of fungal biosynthetic genes and their encoded metabolites in Saccharomyces cerevisiae. We applied this platform to 41 fungal biosynthetic gene clusters from diverse fungal species from around the world, 22 of which produced detectable compounds. These included novel compounds with unexpected biosynthetic origins, particularly from poorly studied species. This result establishes the HEx platform for rapid discovery of natural products from any fungal species, even those that are uncultivable, and opens the door to discovery of the next generation of natural products. PMID:29651464

Gene family encoding the major toxins of lethal Amanita mushrooms

PubMed Central

Hallen, Heather E.; Luo, Hong; Scott-Craig, John S.; Walton, Jonathan D.

2007-01-01

Amatoxins, the lethal constituents of poisonous mushrooms in the genus Amanita, are bicyclic octapeptides. Two genes in A. bisporigera, AMA1 and PHA1, directly encode α-amanitin, an amatoxin, and the related bicyclic heptapeptide phallacidin, a phallotoxin, indicating that these compounds are synthesized on ribosomes and not by nonribosomal peptide synthetases. α-Amanitin and phallacidin are synthesized as proproteins of 35 and 34 amino acids, respectively, from which they are predicted to be cleaved by a prolyl oligopeptidase. AMA1 and PHA1 are present in other toxic species of Amanita section Phalloidae but are absent from nontoxic species in other sections. The genomes of A. bisporigera and A. phalloides contain multiple sequences related to AMA1 and PHA1. The predicted protein products of this family of genes are characterized by a hypervariable “toxin” region capable of encoding a wide variety of peptides of 7–10 amino acids flanked by conserved sequences. Our results suggest that these fungi have a broad capacity to synthesize cyclic peptides on ribosomes. PMID:18025465

Impaired Visuospatial Short-Term Memory in Children with ADHD.

PubMed

Narimoto, Tadamasa; Matsuura, Naomi; Hiratani, Michio

2018-01-01

Previous studies provide clear evidence that visuospatial memory performance in children with attention-deficit/hyperactivity disorder (ADHD) is significantly lower than in typically developing children. In the present study, we investigated a major cause of their low performance using a spatial span test. Possibly, inattention resulting from lack of motivation or interest causes their low performance so that they do not correctly encode targets to be remembered. On the other hand, a deficit in temporary maintenance per se may cause their low performance; that is, their inefficient use of rehearsal during a retention interval may lead to memory traces' fast decay. Results in this study indicated that children with ADHD could sustain attention during the encoding phase. Furthermore, their performance at delayed recall was significantly lower than immediate recall, but delayed recall did not affect typically developing children's performance. These results provide evidence for the likelihood that a factor causing children with ADHD difficulty in temporarily maintaining visuospatial information is fast decay of memory traces as a result of inefficient use of rehearsal, not inattention in the encoding phase.

Expression of the tachykinin receptor mRNAs in healthy human colon.

PubMed

Jaafari, Nadia; Hua, Guoqiang; Adélaïde, José; Julé, Yvon; Imbert, Jean

2008-12-03

Tachykinins are a family of neuropeptides, involved in a variety of physiological and pathological processes occurring in the gastrointestinal tract. They act via three distinct types of receptors, tachykinin NK(1), NK(2), and NK(3) receptors, which belong to the family of G protein-coupled receptors. The aim of the present study was to characterize, for the first time in the healthy human colon, the TACR(1), TACR(2) and TACR(3) mRNAs encoding the three different tachykinin receptors and to measure their relative expression by quantitative reverse transcription-PCR assay. Our results confirm the broad distribution of the tachykinin receptors but evidenced significant differences in the expression level of their respective mRNAs. A higher expression level of the TACR2 mRNA alpha isoform, the gene encoding the functional tachykinin NK(2) receptor, was observed in comparison to TACR1 and TACR3 mRNAs genes encoding for NK(1) and NK(3) receptors respectively. The prevalence of the TACR2 mRNA alpha isoform strongly suggests a major involvement of tachykinin NK(2) receptor in the regulation of human colonic functions.

What the Toadfish Ear Tells the Toadfish Brain About Sound.

PubMed

Edds-Walton, Peggy L

2016-01-01

Of the three, paired otolithic endorgans in the ear of teleost fishes, the saccule is the one most often demonstrated to have a major role in encoding frequencies of biologically relevant sounds. The toadfish saccule also encodes sound level and sound source direction in the phase-locked activity conveyed via auditory afferents to nuclei of the ipsilateral octaval column in the medulla. Although paired auditory receptors are present in teleost fishes, binaural processes were believed to be unimportant due to the speed of sound in water and the acoustic transparency of the tissues in water. In contrast, there are behavioral and anatomical data that support binaural processing in fishes. Studies in the toadfish combined anatomical tract-tracing and physiological recordings from identified sites along the ascending auditory pathway to document response characteristics at each level. Binaural computations in the medulla and midbrain sharpen the directional information provided by the saccule. Furthermore, physiological studies in the central nervous system indicated that encoding frequency, sound level, temporal pattern, and sound source direction are important components of what the toadfish ear tells the toadfish brain about sound.

Between-language repetition priming in antonym generation: evidence that translation-equivalent adjectives have shared conceptual representations across languages.

PubMed

Taylor, Randolph S; Francis, Wendy S

2017-03-01

Previous literature has demonstrated conceptual repetition priming across languages in bilinguals. This between-language priming effect is taken as evidence that translation equivalents have shared conceptual representations across languages. However, the vast majority of this research has been conducted using only concrete nouns as stimuli. The present experiment examined conceptual repetition priming within and between languages in adjectives, a part of speech not previously investigated in studies of bilingual conceptual representation. The participants were 100 Spanish-English bilinguals who had regular exposure to both languages. At encoding, participants performed a shallow processing task and a deep-processing task on English and Spanish adjectives. At test, they performed an antonym-generation task in English, in which the target responses were either adjectives presented at encoding or control adjectives not previously presented. The measure of priming was the response time advantage for producing repeated adjectives relative to control adjectives. Significant repetition priming was observed both within and between languages under deep, but not shallow, encoding conditions. The results indicate that the conceptual representations of adjective translation equivalents are shared across languages.

Functional characterization of the triple gene block 1 (TGB1) gene of Pepino mosaic virus in tomato

USDA-ARS?s Scientific Manuscript database

Pepino mosaic virus (PepMV) has caused serious economic losses to many greenhouse tomato productions around the world. This potexvirus genome contains five major open reading frames (ORFs) encoding for a 164-kDa RNA-dependent RNA polymerase (RdRp), three triple gene block (TGB) proteins of 26, 14 an...

Untangling a Cholinergic Pathway from Wakefulness to Memory.

PubMed

Gais, Steffen; Schönauer, Monika

2017-05-17

Acetylcholine is a major modulator of learning and memory, and its availability varies across the sleep-wake cycle. In this issue of Neuron, Papouin et al. (2017) describe a D-serine-dependent pathway involving astroglia by which the transmitter tunes the hippocampus toward memory encoding during wakefulness. Copyright © 2017. Published by Elsevier Inc.

Teaching the Toolkit: A Laboratory Series to Demonstrate the Evolutionary Conservation of Metazoan Cell Signaling Pathways

ERIC Educational Resources Information Center

LeClair, Elizabeth E.

2008-01-01

A major finding of comparative genomics and developmental genetics is that metazoans share certain conserved, embryonically deployed signaling pathways that instruct cells as to their ultimate fate. Because the DNA encoding these pathways predates the evolutionary split of most animal groups, it should in principle be possible to clone…

A Cross-cultural Study of the Communication of Emotion by Facial and Gestural Cues

ERIC Educational Resources Information Center

Graham, Jean Ann; And Others

1975-01-01

Discusses a study dealing with English, Northern Italian and Southern Italian encoders role-playing specific emotions and degrees of two dimensions of emotion, and presents evidence suggesting that for neither the English nor the Italians, do hand gestures and other bodily cues function as a major communication channel for emotion. Available from:…

Aluminum-activated citrate and malate transporters from the MATE and ALMT families function independently to confer Arabidopsis aluminum tolerance

USDA-ARS?s Scientific Manuscript database

Aluminum (Al) activated root malate and citrate exudation play an important role in Al tolerance in many plant species. AtALMT1, an Al-activated malate transporter, is a major contributor to Arabidopsis Al tolerance. Here, we demonstrate that a second, unrelated gene, AtMATE, encodes an Arabidopsi...

What Is So Difficult about Telicity Marking in L2 Russian?

ERIC Educational Resources Information Center

Slabakova, Roumyana

2005-01-01

Two major mechanisms of encoding telicity across languages are either marking the object as exhaustively countable or measurable, or utilizing a specific prefix on the verbal form. English predominantly uses the first mechanism, while Russian mostly utilizes the second. The learning task of an English speaker acquiring Russian, then, is two-fold:…

Evidence of intralocus recombination at the Glu-3 loci in bread wheat (Triticum aestivum L.)

USDA-ARS?s Scientific Manuscript database

The low-molecular weight glutenin subunits (LMW-GSs) are one of the major components of wheat seed storage proteins and play a critical role in the determination of wheat flour bread-making quality. The genes encoding for this class of proteins are mainly located at the orthologous Glu-3 loci (Glu-A...

Genome sequence of the thermotolerant foodborne pathogen Salmonella enterica serovar Senftenberg ATCC 43845 and phylogenetic analysis of Loci encoding increased protein quality control mechanisms

USDA-ARS?s Scientific Manuscript database

Salmonella enterica subsp. enterica bacteria are important foodborne pathogens with major economic impact. Some isolates exhibit increased heat tolerance, a concern for food safety. Analysis of a finished-quality genome sequence of an isolate commonly used in heat resistance studies, S. enterica sub...

Development of haplotype-specific molecular markers for the low-molecular-weight glutenin subunits

USDA-ARS?s Scientific Manuscript database

Low-molecular-weight glutenin subunits (LMW-GSs) are one of the major components of gluten and their allelic variation has been widely associated with numerous wheat end-use quality parameters. These proteins are encoded by multigene families located at the orthologous Glu-3 loci (Glu-A3, Glu-B3 and...

LMOf2365_0442 encoding for a fructose specific PTS permease IIA may Be required for virulence in L. monocytogenes Strain F2365

USDA-ARS?s Scientific Manuscript database

Listeria monocytogenes is a foodborne pathogen that causes listeriosis, which is a major public health concern due to the high fatality rate. The Phosphotransferase Transport System (PTS) is responsible for sugar transport. In previous studies, in-frame deletion mutants of a putative fructose-spec...

Construction and expression of immunogenic hybrid enterotoxigenic Escherichia coli CFA/I and CS2 colonization fimbriae for use in vaccines.

PubMed

Tobias, Joshua; Svennerholm, Ann-Mari; Holmgren, Jan; Lebens, Michael

2010-07-01

Enterotoxigenic Escherichia coli (ETEC) are an important cause of diarrheal morbidity in developing countries, especially in children and also of traveler's diarrhea. Colonization factors (CFs) of ETEC, like CFA/I and CS2 which are genetically and structurally related, play a substantial role in pathogenicity, and since intestinal-mucosal immune responses against CFs appear to be protective, much effort has focused on the development of a CF-based ETEC vaccine. We have constructed hybrid operons in which the major CS2 subunit-encoding cotA gene was inserted into the CFA/I operon, either replacing (hybrid I) or being added to the major CFA/I subunit-encoding cfaB gene (hybrid II). Using specific monoclonal antibodies against the major subunits of CFA/I and CS2, high levels of surface expression of both fimbrial subunits were shown in E. coli carrying the hybrid II operon. Oral immunization of mice with formalin-killed bacteria expressing hybrid II fimbriae induced strong CFA/I- and CS2-specific serum IgG + IgM and fecal IgA antibody responses, which were higher than those achieved by similar immunization with the reference strains. Bacteria expressing hybrid fimbriae are potential candidate strains in an oral-killed CF-ETEC vaccine, and the approach represents an attractive and novel means of producing a broad-spectrum ETEC vaccine.

Light-Regulated Transcription of Genes Encoding Peridinin Chlorophyll a Proteins and the Major Intrinsic Light-Harvesting Complex Proteins in the Dinoflagellate Amphidinium carterae Hulburt (Dinophycae)1

PubMed Central

ten Lohuis, Michael R.; Miller, David J.

1998-01-01

In the dinoflagellate Amphidinium carterae, photoadaptation involves changes in the transcription of genes encoding both of the major classes of light-harvesting proteins, the peridinin chlorophyll a proteins (PCPs) and the major a/c-containing intrinsic light-harvesting proteins (LHCs). PCP and LHC transcript levels were increased up to 86- and 6-fold higher, respectively, under low-light conditions relative to cells grown at high illumination. These increases in transcript abundance were accompanied by decreases in the extent of methylation of CpG and CpNpG motifs within or near PCP- and LHC-coding regions. Cytosine methylation levels in A. carterae are therefore nonstatic and may vary with environmental conditions in a manner suggestive of involvement in the regulation of gene expression. However, chemically induced undermethylation was insufficient in activating transcription, because treatment with two methylation inhibitors had no effect on PCP mRNA or protein levels. Regulation of gene activity through changes in DNA methylation has traditionally been assumed to be restricted to higher eukaryotes (deuterostomes and green plants); however, the atypically large genomes of dinoflagellates may have generated the requirement for systems of this type in a relatively “primitive” organism. Dinoflagellates may therefore provide a unique perspective on the evolution of eukaryotic DNA-methylation systems. PMID:9576788

Adaptation of Escherichia coli Traversing From the Faecal Environment to the Urinary Tract

PubMed Central

Nielsen, Karen L.; Stegger, Marc; Godfrey, Paul A.; Feldgarden, Michael; Andersen, Paal S.; Frimodt-Møller, Niels

2016-01-01

The majority of extraintestinal pathogenic Escherichia coli (ExPEC) causing urinary tract infections (UTI) are found in the patient's own gut flora, but only limited knowledge is available on the potential adaptation that may occur in the bacteria for them to traverse the perineum and successfully infect the urinary tract. Here, matching faecal and UTI isolates from 42 patients were compared pairwise using in-depth whole-genome sequencing to investigate whether genetic changes were evident for successful colonization in these two different environments. The identified non-synonymous mutations (0-12 substitutions in each pair) were primarily associated to genes encoding virulence factors and nutrient metabolism; and indications of parallel evolution were observed in genes encoding the major phase-variable protein antigen 43, a toxin/antitoxin locus and haemolysin B. No differences in virulence potential were observed in a mouse UTI model for five matching faecal and UTI isolates with or without mutations in antigen 43 and haemolysin B. Variations in plasmid content were observed in only four of the 42 pairs. Although, we observed mutations in known UTI virulence genes for a few pairs, the majority showed no detectable differences in mutations or mobilome changes when compared to their faecal counterpart. The results show that UPECs are successful in colonizing both the bladder and gut without adaptation. PMID:27825516

Adaptation of Escherichia coli traversing from the faecal environment to the urinary tract.

PubMed

Nielsen, Karen L; Stegger, Marc; Godfrey, Paul A; Feldgarden, Michael; Andersen, Paal S; Frimodt-Møller, Niels

2016-12-01

The majority of extraintestinal pathogenic Escherichia coli (ExPEC) causing urinary tract infections (UTI) are found in the patient's own gut flora, but only limited knowledge is available on the potential adaptation that may occur in the bacteria in order to traverse the perineum and successfully infect the urinary tract. Here, matching pairs of faecal and UTI isolates from 42 patients were compared pairwise using in-depth whole-genome sequencing to investigate whether genetic changes were evident for successful colonization in these two different environments. The identified non-synonymous mutations (0-12 substitutions in each pair) were primarily associated to genes encoding virulence factors and nutrient metabolism; and indications of parallel evolution were observed in genes encoding the major phase-variable protein antigen 43, a toxin/antitoxin locus and haemolysin B. No differences in virulence potential were observed in a mouse UTI model for five matching faecal and UTI isolates with or without mutations in antigen 43 and haemolysin B. Variations in plasmid content were observed in only four of the 42 pairs. Although, we observed mutations in known UTI virulence genes for a few pairs, the majority showed no detectable differences with respect to mutations or mobilome when compared to their faecal counterpart. The results show that UPECs are successful in colonizing both the bladder and gut without adaptation. Copyright © 2016 Elsevier GmbH. All rights reserved.

Molecular and genomic basis of volatile-mediated indirect defense against insects in rice.

PubMed

Yuan, Joshua S; Köllner, Tobias G; Wiggins, Greg; Grant, Jerome; Degenhardt, Jörg; Chen, Feng

2008-08-01

Rice plants fed on by fall armyworm (Spodoptera frugiperda, FAW) caterpillars emit a blend of volatiles dominated by terpenoids. These volatiles were highly attractive to females of the parasitoid Cotesia marginiventris. Microarray analysis identified 196 rice genes whose expression was significantly upregulated by FAW feeding, 18 of which encode metabolic enzymes potentially involved in volatile biosynthesis. Significant induction of expression of seven of the 11 terpene synthase (TPS) genes identified through the microarray experiments was confirmd using real-time RT-PCR. Enzymes encoded by three TPS genes, Os02g02930, Os08g07100 and Os08g04500, were biochemically characterized. Os02g02930 was found to encode a monoterpene synthase producing the single product S-linalool, which is the most abundant volatile emitted from FAW-damaged rice plants. Both Os08g07100 and Os08g04500 were found to encode sesquiterpene synthases, each producing multiple products. These three enzymes are responsible for production of the majority of the terpenes released from FAW-damaged rice plants. In addition to TPS genes, several key genes in the upstream terpenoid pathways were also found to be upregulated by FAW feeding. This paper provides a comprehensive analysis of FAW-induced volatiles and the corresponding volatile biosynthetic genes potentially involved in indirect defense in rice. Evolution of the genetic basis governing volatile terpenoid biosynthesis for indirect defense is discussed.

Subjective evaluation of HEVC in mobile devices

NASA Astrophysics Data System (ADS)

Garcia, Ray; Kalva, Hari

2013-03-01

Mobile compute environments provide a unique set of user needs and expectations that designers must consider. With increased multimedia use in mobile environments, video encoding methods within the smart phone market segment are key factors that contribute to positive user experience. Currently available display resolutions and expected cellular bandwidth are major factors the designer must consider when determining which encoding methods should be supported. The desired goal is to maximize the consumer experience, reduce cost, and reduce time to market. This paper presents a comparative evaluation of the quality of user experience when HEVC and AVC/H.264 video coding standards were used. The goal of the study was to evaluate any improvements in user experience when using HEVC. Subjective comparisons were made between H.264/AVC and HEVC encoding standards in accordance with Doublestimulus impairment scale (DSIS) as defined by ITU-R BT.500-13. Test environments are based on smart phone LCD resolutions and expected cellular bit rates, such as 200kbps and 400kbps. Subjective feedback shows both encoding methods are adequate at 400kbps constant bit rate. However, a noticeable consumer experience gap was observed for 200 kbps. Significantly less H.264 subjective quality is noticed with video sequences that have multiple objects moving and no single point of visual attraction. Video sequences with single points of visual attraction or few moving objects tended to have higher H.264 subjective quality.

The 2p21 deletion syndrome: characterization of the transcription content.

PubMed

Parvari, Ruti; Gonen, Yael; Alshafee, Ismael; Buriakovsky, Sophia; Regev, Kfir; Hershkovitz, Eli

2005-08-01

The vast majority of small-deletion syndromes are caused by haploinsufficiency of one or several genes and are transmitted as dominant traits. We have previously identified a homozygous deletion of 179,311 bp on chromosome 2p21 as the cause of a unique syndrome, inherited in a recessive mode, consisting of cystinuria, neonatal seizures, hypotonia, severe somatic and developmental delay, facial dysmorphism, and reduced activity of all the respiratory chain enzymatic complexes that are encoded in the mitochondria. We now present the transcription content of this region: Multiple splicing variants of the genes protein phosphatase 1B (formerly 2C) magnesium-dependent, beta isoform (PPM1B), SLC3A1, and KIAA0436 (approved gene symbol PREPL) were identified and their patterns of expression analyzed. The spliced variants are predicted to have additional functions compared to the known variants and their patterns of expression fit the tissues affected by the syndrome. The first exon of an additional gene (C2orf34) is encoded in the deleted region and the gene is not expressed in the patients. In addition several transcripts with very short open reading frames are also encoded in the deletion. The identification of all transcripts encoded in the region deleted in the patients is the first step in the study of the genotype-phenotype correlation of the 2p21 patients.

Virus-encoded microRNAs

PubMed Central

Grundhoff, Adam; Sullivan, Christopher S.

2011-01-01

microRNAs (miRNAs) are the subject of enormous interest. They are small non-coding RNAs that play a regulatory role in numerous and diverse cellular processes such as immune function, apoptosis and tumorigenesis. Several virus families have been shown to encode miRNAs, and an appreciation for their roles in the viral infectious cycle continues to grow. Despite the identification of numerous (>225) viral miRNAs, an in depth functional understanding of most virus-encoded miRNAs is lacking. Here we focus on a few viral miRNAs with well-defined functions. We use these examples to extrapolate general themes of viral miRNA activities including autoregulation of gene expression, avoidance of host defenses, and a likely important role in maintaining latent and persistent infections. We hypothesize that although the molecular mechanisms and machinery are similar, the majority of viral miRNAs may utilize a target strategy that differs from host miRNAs. That is, many viral miRNAs may have evolved to regulate viral-encoded transcripts or networks of host genes that are unique to viral miRNAs. Included in this latter category are a likely abundant class of viral miRNAs that may regulate only one or a few principal host genes. Key steps forward for the field are discussed, including the need for additional functional studies that utilize surgical viral miRNA mutants combined with relevant models of infection. PMID:21277611

Emerging depression is associated with face memory deficits in adolescent girls.

PubMed

Guyer, Amanda E; Choate, Victoria R; Grimm, Kevin J; Pine, Daniel S; Keenan, Kate

2011-02-01

To examine the association between memory for previously encoded emotional faces and depression symptoms assessed over 4 years in adolescent girls. Investigating the interface between memory deficits and depression in adolescent girls may provide clues about depression pathophysiology. Participants were 213 girls recruited from a longitudinal, community-based study; the majority were African American. Scores on depressive screening measures at age 8 were used to increase the base rate of depression. Depression symptoms and diagnoses were assessed annually for 4 years. In year 4, when the girls were 12 to 13 years old, a face emotion encoding task was administered during which ratings were generated in response to sad, fearful, angry, and happy faces. A surprise memory task followed whereby participants identified which of two faces, displaying neutral expressions, they had seen previously. Girls with higher depression symptom levels from ages 9 to 12 years evidenced lower accuracy in identifying previously encoded emotional faces. Controlling for IQ, higher depression symptom level was associated with a memory deficit specific to previously encoded sad and happy faces. These effects were not moderated by race. Individual differences in face memory deficits relate to individual differences in emerging, early adolescent depression, and may be vulnerability markers for depression. Copyright © 2011 American Academy of Child and Adolescent Psychiatry. Published by Elsevier Inc. All rights reserved.

Encoding of Tactile Stimuli by Mechanoreceptors and Interneurons of the Medicinal Leech

PubMed Central

Kretzberg, Jutta; Pirschel, Friederice; Fathiazar, Elham; Hilgen, Gerrit

2016-01-01

For many animals processing of tactile information is a crucial task in behavioral contexts like exploration, foraging, and stimulus avoidance. The leech, having infrequent access to food, developed an energy efficient reaction to tactile stimuli, avoiding unnecessary muscle movements: The local bend behavior moves only a small part of the body wall away from an object touching the skin, while the rest of the animal remains stationary. Amazingly, the precision of this localized behavioral response is similar to the spatial discrimination threshold of the human fingertip, although the leech skin is innervated by an order of magnitude fewer mechanoreceptors and each midbody ganglion contains only 400 individually identified neurons in total. Prior studies suggested that this behavior is controlled by a three-layered feed-forward network, consisting of four mechanoreceptors (P cells), approximately 20 interneurons and 10 individually characterized motor neurons, all of which encode tactile stimulus location by overlapping, symmetrical tuning curves. Additionally, encoding of mechanical force was attributed to three types of mechanoreceptors reacting to distinct intensity ranges: T cells for touch, P cells for pressure, and N cells for strong, noxious skin stimulation. In this study, we provide evidences that tactile stimulus encoding in the leech is more complex than previously thought. Combined electrophysiological, anatomical, and voltage sensitive dye approaches indicate that P and T cells both play a major role in tactile information processing resulting in local bending. Our results indicate that tactile encoding neither relies on distinct force intensity ranges of different cell types, nor location encoding is restricted to spike count tuning. Instead, we propose that P and T cells form a mixed type population, which simultaneously employs temporal response features and spike counts for multiplexed encoding of touch location and force intensity. This hypothesis is supported by our finding that previously identified local bend interneurons receive input from both P and T cells. Some of these interneurons seem to integrate mechanoreceptor inputs, while others appear to use temporal response cues, presumably acting as coincidence detectors. Further voltage sensitive dye studies can test these hypotheses how a tiny nervous system performs highly precise stimulus processing. PMID:27840612

Anxiety Evokes Hypofrontality and Disrupts Rule-Relevant Encoding by Dorsomedial Prefrontal Cortex Neurons.

PubMed

Park, Junchol; Wood, Jesse; Bondi, Corina; Del Arco, Alberto; Moghaddam, Bita

2016-03-16

Anxiety is a debilitating symptom of most psychiatric disorders, including major depression, post-traumatic stress disorder, schizophrenia, and addiction. A detrimental aspect of anxiety is disruption of prefrontal cortex (PFC)-mediated executive functions, such as flexible decision making. Here we sought to understand how anxiety modulates PFC neuronal encoding of flexible shifting between behavioral strategies. We used a clinically substantiated anxiogenic treatment to induce sustained anxiety in rats and recorded from dorsomedial PFC (dmPFC) and orbitofrontal cortex (OFC) neurons while they were freely moving in a home cage and while they performed a PFC-dependent task that required flexible switches between rules in two distinct perceptual dimensions. Anxiety elicited a sustained background "hypofrontality" in dmPFC and OFC by reducing the firing rate of spontaneously active neuronal subpopulations. During task performance, the impact of anxiety was subtle, but, consistent with human data, behavior was selectively impaired when previously correct conditions were presented as conflicting choices. This impairment was associated with reduced recruitment of dmPFC neurons that selectively represented task rules at the time of action. OFC rule representation was not affected by anxiety. These data indicate that a neural substrate of the decision-making deficits in anxiety is diminished dmPFC neuronal encoding of task rules during conflict-related actions. Given the translational relevance of the model used here, the data provide a neuronal encoding mechanism for how anxiety biases decision making when the choice involves overcoming a conflict. They also demonstrate that PFC encoding of actions, as opposed to cues or outcome, is especially vulnerable to anxiety. A debilitating aspect of anxiety is its impact on decision making and flexible control of behavior. These cognitive constructs depend on proper functioning of the prefrontal cortex (PFC). Understanding how anxiety affects PFC encoding of cognitive events is of great clinical and evolutionary significance. Using a clinically valid experimental model, we find that, under anxiety, decision making may be skewed by salient and conflicting environmental stimuli at the expense of flexible top-down guided choices. We also find that anxiety suppresses spontaneous activity of PFC neurons, and weakens encoding of task rules by dorsomedial PFC neurons. These data provide a neuronal encoding scheme for how anxiety disengages PFC during decision making. Copyright © 2016 the authors 0270-6474/16/363322-14$15.00/0.

Transcriptome analysis of Neisseria meningitidis in human whole blood and mutagenesis studies identify virulence factors involved in blood survival.

PubMed

Echenique-Rivera, Hebert; Muzzi, Alessandro; Del Tordello, Elena; Seib, Kate L; Francois, Patrice; Rappuoli, Rino; Pizza, Mariagrazia; Serruto, Davide

2011-05-01

During infection Neisseria meningitidis (Nm) encounters multiple environments within the host, which makes rapid adaptation a crucial factor for meningococcal survival. Despite the importance of invasion into the bloodstream in the meningococcal disease process, little is known about how Nm adapts to permit survival and growth in blood. To address this, we performed a time-course transcriptome analysis using an ex vivo model of human whole blood infection. We observed that Nm alters the expression of ≈30% of ORFs of the genome and major dynamic changes were observed in the expression of transcriptional regulators, transport and binding proteins, energy metabolism, and surface-exposed virulence factors. In particular, we found that the gene encoding the regulator Fur, as well as all genes encoding iron uptake systems, were significantly up-regulated. Analysis of regulated genes encoding for surface-exposed proteins involved in Nm pathogenesis allowed us to better understand mechanisms used to circumvent host defenses. During blood infection, Nm activates genes encoding for the factor H binding proteins, fHbp and NspA, genes encoding for detoxifying enzymes such as SodC, Kat and AniA, as well as several less characterized surface-exposed proteins that might have a role in blood survival. Through mutagenesis studies of a subset of up-regulated genes we were able to identify new proteins important for survival in human blood and also to identify additional roles of previously known virulence factors in aiding survival in blood. Nm mutant strains lacking the genes encoding the hypothetical protein NMB1483 and the surface-exposed proteins NalP, Mip and NspA, the Fur regulator, the transferrin binding protein TbpB, and the L-lactate permease LctP were sensitive to killing by human blood. This increased knowledge of how Nm responds to adaptation in blood could also be helpful to develop diagnostic and therapeutic strategies to control the devastating disease cause by this microorganism.

Transcriptome Analysis of Neisseria meningitidis in Human Whole Blood and Mutagenesis Studies Identify Virulence Factors Involved in Blood Survival

PubMed Central

Del Tordello, Elena; Seib, Kate L.; Francois, Patrice; Rappuoli, Rino; Pizza, Mariagrazia; Serruto, Davide

2011-01-01

During infection Neisseria meningitidis (Nm) encounters multiple environments within the host, which makes rapid adaptation a crucial factor for meningococcal survival. Despite the importance of invasion into the bloodstream in the meningococcal disease process, little is known about how Nm adapts to permit survival and growth in blood. To address this, we performed a time-course transcriptome analysis using an ex vivo model of human whole blood infection. We observed that Nm alters the expression of ≈30% of ORFs of the genome and major dynamic changes were observed in the expression of transcriptional regulators, transport and binding proteins, energy metabolism, and surface-exposed virulence factors. In particular, we found that the gene encoding the regulator Fur, as well as all genes encoding iron uptake systems, were significantly up-regulated. Analysis of regulated genes encoding for surface-exposed proteins involved in Nm pathogenesis allowed us to better understand mechanisms used to circumvent host defenses. During blood infection, Nm activates genes encoding for the factor H binding proteins, fHbp and NspA, genes encoding for detoxifying enzymes such as SodC, Kat and AniA, as well as several less characterized surface-exposed proteins that might have a role in blood survival. Through mutagenesis studies of a subset of up-regulated genes we were able to identify new proteins important for survival in human blood and also to identify additional roles of previously known virulence factors in aiding survival in blood. Nm mutant strains lacking the genes encoding the hypothetical protein NMB1483 and the surface-exposed proteins NalP, Mip and NspA, the Fur regulator, the transferrin binding protein TbpB, and the L-lactate permease LctP were sensitive to killing by human blood. This increased knowledge of how Nm responds to adaptation in blood could also be helpful to develop diagnostic and therapeutic strategies to control the devastating disease cause by this microorganism. PMID:21589640

Molecular cloning and developmental expression of the catalytic and 65-kDa regulatory subunits of protein phosphatase 2A in Drosophila.

PubMed Central

Mayer-Jaekel, R E; Baumgartner, S; Bilbe, G; Ohkura, H; Glover, D M; Hemmings, B A

1992-01-01

cDNA clones encoding the catalytic subunit and the 65-kDa regulatory subunit of protein phosphatase 2A (PR65) from Drosophila melanogaster have been isolated by homology screening with the corresponding human cDNAs. The Drosophila clones were used to analyze the spatial and temporal expression of the transcripts encoding these two proteins. The Drosophila PR65 cDNA clones contained an open reading frame of 1773 nucleotides encoding a protein of 65.5 kDa. The predicted amino acid sequence showed 75 and 71% identity to the human PR65 alpha and beta isoforms, respectively. As previously reported for the mammalian PR65 isoforms, Drosophila PR65 is composed of 15 imperfect repeating units of approximately 39 amino acids. The residues contributing to this repeat structure show also the highest sequence conservation between species, indicating a functional importance for these repeats. The gene encoding Drosophila PR65 was located at 29B1,2 on the second chromosome. A major transcript of 2.8 kilobase (kb) encoding the PR65 subunit and two transcripts of 1.6 and 2.5 kb encoding the catalytic subunit could be detected throughout Drosophila development. All of these mRNAs were most abundant during early embryogenesis and were expressed at lower levels in larvae and adult flies. In situ hybridization of different developmental stages showed a colocalization of the PR65 and catalytic subunit transcripts. The mRNA expression is high in the nurse cells and oocytes, consistent with a high equally distributed expression in early embryos. In later embryonal development, the expression remains high in the nervous system and the gonads but the overall transcript levels decrease. In third instar larvae, high levels of mRNA could be observed in brain, imaginal discs, and in salivary glands. These results indicate that protein phosphatase 2A transcript levels change during development in a tissue and in a time-specific manner. Images PMID:1320961

Anion channels: master switches of stress responses.

PubMed

Roelfsema, M Rob G; Hedrich, Rainer; Geiger, Dietmar

2012-04-01

During stress, plant cells activate anion channels and trigger the release of anions across the plasma membrane. Recently, two new gene families have been identified that encode major groups of anion channels. The SLAC/SLAH channels are characterized by slow voltage-dependent activation (S-type), whereas ALMT genes encode rapid-activating channels (R-type). Both S- and R-type channels are stimulated in guard cells by the stress hormone ABA, which leads to stomatal closure. Besides their role in ABA-dependent stomatal movement, anion channels are also activated by biotic stress factors such as microbe-associated molecular patterns (MAMPs). Given that anion channels occur throughout the plant kingdom, they are likely to serve a general function as master switches of stress responses. Copyright © 2012 Elsevier Ltd. All rights reserved.

Molecular characterization of ESBL-producing Escherichia coli isolates from hospital- and community-acquired infections in NW Mexico.

PubMed

Miranda-Romero, Ana Laura; Silva-Sanchez, Jesus; Garza-Ramos, Ulises; Barrios, Humberto; Sánchez-Pérez, Alejandro; Reyna-Flores, Fernando

2017-01-01

We investigated the molecular characteristics of ESBL-producing E. coli (ESBL-PEc) isolates from two hospitals and community settings in Ciudad Obregon, Sonora, Mexico. Between 2011 and 2014, thirty-seven ESBL-PEc isolates were collected. The major encoded ESBL was the bla CTX-M-15 gene (97%); followed by 13.5% of the bla SHV-12 gene, and 5.5% encoded the bla TLA-1 gene. The PMQR gene aac(6´)-Ib-cr was detected in 97% of the isolates and the qnrB gene, in one isolate. The ESBL-PEc isolates corresponded to phylogenetic group B2, ST131. Our results highlight the dissemination of ESBL-PEc isolates in northwest Mexico (Ciudad Obregon, Sonora). Copyright © 2016 Elsevier Inc. All rights reserved.

The synaptic plasticity and memory hypothesis: encoding, storage and persistence

PubMed Central

Takeuchi, Tomonori; Duszkiewicz, Adrian J.; Morris, Richard G. M.

2014-01-01

The synaptic plasticity and memory hypothesis asserts that activity-dependent synaptic plasticity is induced at appropriate synapses during memory formation and is both necessary and sufficient for the encoding and trace storage of the type of memory mediated by the brain area in which it is observed. Criteria for establishing the necessity and sufficiency of such plasticity in mediating trace storage have been identified and are here reviewed in relation to new work using some of the diverse techniques of contemporary neuroscience. Evidence derived using optical imaging, molecular-genetic and optogenetic techniques in conjunction with appropriate behavioural analyses continues to offer support for the idea that changing the strength of connections between neurons is one of the major mechanisms by which engrams are stored in the brain. PMID:24298167

Prioritized LT Codes

NASA Technical Reports Server (NTRS)

Woo, Simon S.; Cheng, Michael K.

2011-01-01

The original Luby Transform (LT) coding scheme is extended to account for data transmissions where some information symbols in a message block are more important than others. Prioritized LT codes provide unequal error protection (UEP) of data on an erasure channel by modifying the original LT encoder. The prioritized algorithm improves high-priority data protection without penalizing low-priority data recovery. Moreover, low-latency decoding is also obtained for high-priority data due to fast encoding. Prioritized LT codes only require a slight change in the original encoding algorithm, and no changes at all at the decoder. Hence, with a small complexity increase in the LT encoder, an improved UEP and low-decoding latency performance for high-priority data can be achieved. LT encoding partitions a data stream into fixed-sized message blocks each with a constant number of information symbols. To generate a code symbol from the information symbols in a message, the Robust-Soliton probability distribution is first applied in order to determine the number of information symbols to be used to compute the code symbol. Then, the specific information symbols are chosen uniform randomly from the message block. Finally, the selected information symbols are XORed to form the code symbol. The Prioritized LT code construction includes an additional restriction that code symbols formed by a relatively small number of XORed information symbols select some of these information symbols from the pool of high-priority data. Once high-priority data are fully covered, encoding continues with the conventional LT approach where code symbols are generated by selecting information symbols from the entire message block including all different priorities. Therefore, if code symbols derived from high-priority data experience an unusual high number of erasures, Prioritized LT codes can still reliably recover both high- and low-priority data. This hybrid approach decides not only "how to encode" but also "what to encode" to achieve UEP. Another advantage of the priority encoding process is that the majority of high-priority data can be decoded sooner since only a small number of code symbols are required to reconstruct high-priority data. This approach increases the likelihood that high-priority data is decoded first over low-priority data. The Prioritized LT code scheme achieves an improvement in high-priority data decoding performance as well as overall information recovery without penalizing the decoding of low-priority data, assuming high-priority data is no more than half of a message block. The cost is in the additional complexity required in the encoder. If extra computation resource is available at the transmitter, image, voice, and video transmission quality in terrestrial and space communications can benefit from accurate use of redundancy in protecting data with varying priorities.

Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti by the Trans-Encoded Small RNA MmgR

PubMed Central

Lagares, Antonio; Borella, Germán Ceizel; Linne, Uwe; Becker, Anke

2017-01-01

ABSTRACT Riboregulation has a major role in the fine-tuning of multiple bacterial processes. Among the RNA players, trans-encoded untranslated small RNAs (sRNAs) regulate complex metabolic networks by tuning expression from multiple target genes in response to numerous signals. In Sinorhizobium meliloti, over 400 sRNAs are expressed under different stimuli. The sRNA MmgR (standing for Makes more granules Regulator) has been of particular interest to us since its sequence and structure are highly conserved among the alphaproteobacteria and its expression is regulated by the amount and quality of the bacterium's available nitrogen source. In this work, we explored the biological role of MmgR in S. meliloti 2011 by characterizing the effect of a deletion of the internal conserved core of mmgR (mmgRΔ33–51). This mutation resulted in larger amounts of polyhydroxybutyrate (PHB) distributed into more intracellular granules than are found in the wild-type strain. This phenotype was expressed upon cessation of balanced growth owing to nitrogen depletion in the presence of surplus carbon (i.e., at a carbon/nitrogen molar ratio greater than 10). The normal PHB accumulation was complemented with a wild-type mmgR copy but not with unrelated sRNA genes. Furthermore, the expression of mmgR limited PHB accumulation in the wild type, regardless of the magnitude of the C surplus. Quantitative proteomic profiling and quantitative reverse transcription-PCR (qRT-PCR) revealed that the absence of MmgR results in a posttranscriptional overexpression of both PHB phasin proteins (PhaP1 and PhaP2). Together, our results indicate that the widely conserved alphaproteobacterial MmgR sRNA fine-tunes the regulation of PHB storage in S. meliloti. IMPORTANCE High-throughput RNA sequencing has recently uncovered an overwhelming number of trans-encoded small RNAs (sRNAs) in diverse prokaryotes. In the nitrogen-fixing alphaproteobacterial symbiont of alfalfa root nodules Sinorhizobium meliloti, only four out of hundreds of identified sRNA genes have been functionally characterized. Thus, uncovering the biological role of sRNAs currently represents a major issue and one that is particularly challenging because of the usually subtle quantitative regulation contributed by most characterized sRNAs. Here, we have characterized the function of the broadly conserved alphaproteobacterial sRNA gene mmgR in S. meliloti. Our results strongly suggest that mmgR encodes a negative regulator of the accumulation of polyhydroxybutyrate, the major carbon and reducing power storage polymer in S. meliloti cells growing under conditions of C/N overbalance. PMID:28167519

The cDNA sequence of a neutral horseradish peroxidase.

PubMed

Bartonek-Roxå, E; Eriksson, H; Mattiasson, B

1991-02-16

A cDNA clone encoding a horseradish (Armoracia rusticana) peroxidase has been isolated and characterized. The cDNA contains 1378 nucleotides excluding the poly(A) tail and the deduced protein contains 327 amino acids which includes a 28 amino acid leader sequence. The predicted amino acid sequence is nine amino acids shorter than the major isoenzyme belonging to the horseradish peroxidase C group (HRP-C) and the sequence shows 53.7% identity with this isoenzyme. The described clone encodes nine cysteines of which eight correspond well with the cysteines found in HRP-C. Five potential N-glycosylation sites with the general sequence Asn-X-Thr/Ser are present in the deduced sequence. Compared to the earlier described HRP-C this is three glycosylation sites less. The shorter sequence and fewer N-glycosylation sites give the native isoenzyme a molecular weight of several thousands less than the horseradish peroxidase C isoenzymes. Comparison with the net charge value of HRP-C indicates that the described cDNA clone encodes a peroxidase which has either the same or a slightly less basic pI value, depending on whether the encoded protein is N-terminally blocked or not. This excludes the possibility that HRP-n could belong to either the HRP-A, -D or -E groups. The low sequence identity (53.7%) with HRP-C indicates that the described clone does not belong to the HRP-C isoenzyme group and comparison of the total amino acid composition with the HRP-B group does not place the described clone within this isoenzyme group. Our conclusion is that the described cDNA clone encodes a neutral horseradish peroxidase which belongs to a new, not earlier described, horseradish peroxidase group.

Neuronal representation of individual heroin choices in the orbitofrontal cortex.

PubMed

Guillem, Karine; Brenot, Viridiana; Durand, Audrey; Ahmed, Serge H

2018-05-01

Drug addiction is a harmful preference for drug use over and at the expense of other non-drug-related activities. We previously identified in the rat orbitofrontal cortex (OFC) a mechanism that influences individual preferences between cocaine use and an alternative action rewarded by a non-drug reward (i.e. sweet water). Here, we sought to test the generality of this mechanism to a different addictive drug, heroin. OFC neuronal activity was recorded while rats responded for heroin or the alternative non-drug reward separately or while they chose between the two. First, we found that heroin-rewarded and sweet water-rewarded actions were encoded by two non-overlapping OFC neuronal populations and that the relative size of the heroin population represented individual drug choices. Second, OFC neurons encoding the preferred action-which was the non-drug action in the large majority of individuals-progressively fired more than non-preferred action-coding neurons 1 second after the onset of choice trials and around 1 second before the preferred action was actually chosen, suggesting a pre-choice neuronal competition for action selection. Together with a previous study on cocaine choice, the present study on heroin choice reveals important commonalities in how OFC neurons encode individual drug choices and preferences across different classes of drugs. It also reveals some drug-specific differences in OFC encoding activity. Notably, the proportion of neurons that non-selectively encode both the drug and the non-drug reward was higher when the drug was heroin (present study) than when it was cocaine (previous study). We will discuss the potential functional significance of these commonalities and differences in OFC neuronal activity across different drugs for understanding drug choice. © 2017 Society for the Study of Addiction.

Breaking the news on mobile TV: user requirements of a popular mobile content

NASA Astrophysics Data System (ADS)

Knoche, Hendrik O.; Sasse, M. Angela

2006-02-01

This paper presents the results from three lab-based studies that investigated different ways of delivering Mobile TV News by measuring user responses to different encoding bitrates, image resolutions and text quality. All studies were carried out with participants watching News content on mobile devices, with a total of 216 participants rating the acceptability of the viewing experience. Study 1 compared the acceptability of a 15-second video clip at different video and audio encoding bit rates on a 3G phone at a resolution of 176x144 and an iPAQ PDA (240x180). Study 2 measured the acceptability of video quality of full feature news clips of 2.5 minutes which were recorded from broadcast TV, encoded at resolutions ranging from 120x90 to 240x180, and combined with different encoding bit rates and audio qualities presented on an iPAQ. Study 3 improved the legibility of the text included in the video simulating a separate text delivery. The acceptability of News' video quality was greatly reduced at a resolution of 120x90. The legibility of text was a decisive factor in the participants' assessment of the video quality. Resolutions of 168x126 and higher were substantially more acceptable when they were accompanied by optimized high quality text compared to proportionally scaled inline text. When accompanied by high quality text TV news clips were acceptable to the vast majority of participants at resolutions as small as 168x126 for video encoding bitrates of 160kbps and higher. Service designers and operators can apply this knowledge to design a cost-effective mobile TV experience.

Staphylococcus aureus innate immune evasion is lineage-specific: a bioinfomatics study.

PubMed

McCarthy, Alex J; Lindsay, Jodi A

2013-10-01

Staphylococcus aureus is a major human pathogen, and is targeted by the host innate immune system. In response, S. aureus genomes encode dozens of secreted proteins that inhibit complement, chemotaxis and neutrophil activation resulting in successful evasion of innate immune responses. These proteins include immune evasion cluster proteins (IEC; Chp, Sak, Scn), staphylococcal superantigen-like proteins (SSLs), phenol soluble modulins (PSMs) and several leukocidins. Biochemical studies have indicated that genetic variants of these proteins can have unique functions. To ascertain the scale of genetic variation in secreted immune evasion proteins, whole genome sequences of 88 S. aureus isolates, representing 25 clonal complex (CC) lineages, in the public domain were analysed across 43 genes encoding 38 secreted innate immune evasion protein complexes. Twenty-three genes were variable, with between 2 and 15 variants, and the variants had lineage-specific distributions. They include genes encoding Eap, Ecb, Efb, Flipr/Flipr-like, Hla, Hld, Hlg, Sbi, Scin-B/C and 13 SSLs. Most of these protein complexes inhibit complement, chemotaxis and neutrophil activation suggesting that isolates from each S. aureus lineage respond to the innate immune system differently. In contrast, protein complexes that lyse neutrophils (LukSF-PVL, LukMF, LukED and PSMs) were highly conserved, but can be carried on mobile genetic elements (MGEs). MGEs also encode proteins with narrow host-specificities arguing that their acquisition has important roles in host/environmental adaptation. In conclusion, this data suggests that each lineage of S. aureus evades host immune responses differently, and that isolates can adapt to new host environments by acquiring MGEs and the immune evasion protein complexes that they encode. Cocktail therapeutics that targets multiple variant proteins may be the most appropriate strategy for controlling S. aureus infections. Copyright © 2013 Elsevier B.V. All rights reserved.

Epistatic interaction of genetic depression risk variants in the human subgenual cingulate cortex during memory encoding

PubMed Central

Schott, B H; Assmann, A; Schmierer, P; Soch, J; Erk, S; Garbusow, M; Mohnke, S; Pöhland, L; Romanczuk-Seiferth, N; Barman, A; Wüstenberg, T; Haddad, L; Grimm, O; Witt, S; Richter, S; Klein, M; Schütze, H; Mühleisen, T W; Cichon, S; Rietschel, M; Noethen, M M; Tost, H; Gundelfinger, E D; Düzel, E; Heinz, A; Meyer-Lindenberg, A; Seidenbecher, C I; Walter, H

2014-01-01

Recent genome-wide association studies have pointed to single-nucleotide polymorphisms (SNPs) in genes encoding the neuronal calcium channel CaV1.2 (CACNA1C; rs1006737) and the presynaptic active zone protein Piccolo (PCLO; rs2522833) as risk factors for affective disorders, particularly major depression. Previous neuroimaging studies of depression-related endophenotypes have highlighted the role of the subgenual cingulate cortex (CG25) in negative mood and depressive psychopathology. Here, we aimed to assess how recently associated PCLO and CACNA1C depression risk alleles jointly affect memory-related CG25 activity as an intermediate phenotype in clinically healthy humans. To investigate the combined effects of rs1006737 and rs2522833 on the CG25 response, we conducted three functional magnetic resonance imaging studies of episodic memory formation in three independent cohorts (N=79, 300, 113). An epistatic interaction of PCLO and CACNA1C risk alleles in CG25 during memory encoding was observed in all groups, with carriers of no risk allele and of both risk alleles showing higher CG25 activation during encoding when compared with carriers of only one risk allele. Moreover, PCLO risk allele carriers showed lower memory performance and reduced encoding-related hippocampal activation. In summary, our results point to region-specific epistatic effects of PCLO and CACNA1C risk variants in CG25, potentially related to episodic memory. Our data further suggest that genetic risk factors on the SNP level do not necessarily have additive effects but may show complex interactions. Such epistatic interactions might contribute to the ‘missing heritability' of complex phenotypes. PMID:24643163

Reconstructing the phylogeny of Scolytinae and close allies: Major obstacles and prospects for a solution

Treesearch

Bjarte H. Jordal

2007-01-01

To enable the resolution of deep phylogenetic divergence in Scolytinae and closely related weevils, several new molecular markers were screened for their phylogenetic potential. The nuclear protein encoding genes, CAD and Arginine Kinase, were particularly promising and will be added to future phylogenetic studies in combination with 28S, COI, and Elongation Factor 1...

Evaluation of the ruminal bacterial diversity of cattle fed diets containing citrus pulp pellets (CPP) using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

USDA-ARS?s Scientific Manuscript database

The rumen microbial ecosystem has been extensively studied, but remains a mystery from a quantitative perspective. Dietary components and changes cause shifts in the ruminal microflora that can affect animal health and productivity, but the majority of these changes remain unknown. The objective of ...

Integrated source and channel encoded digital communication system design study

NASA Technical Reports Server (NTRS)

Huth, G. K.; Trumpis, B. D.; Udalov, S.

1975-01-01

Various aspects of space shuttle communication systems were studied. The following major areas were investigated: burst error correction for shuttle command channels; performance optimization and design considerations for Costas receivers with and without bandpass limiting; experimental techniques for measuring low level spectral components of microwave signals; and potential modulation and coding techniques for the Ku-band return link. Results are presented.

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

Fu, Yuanhui; College of Life Sciences and Bioengineering, Beijing Jiaotong University, 3 Shangyuan Residence, Haidian District, Beijing, 100044; He, Jinsheng, E-mail: jshhe@bjtu.edu.cn

Human respiratory syncytial virus (RSV) is a serious pediatric pathogen of the lower respiratory tract worldwide. There is currently no clinically approved vaccine against RSV infection. Recently, it has been shown that a replication-deficient first generation adenoviral vector (FGAd), which encodes modified RSV attachment glycoprotein (G), elicits long-term protective immunity against RSV infection in mice. The major problem in developing such a vaccine is that G protein lacks MHC-I-restricted epitopes. However, RSV fusion glycoprotein (F) is a major cytotoxic T-lymphocyte epitope in humans and mice, therefore, an FGAd-encoding F (FGAd-F) was constructed and evaluated for its potential as an RSVmore » vaccine in a murine model. Intranasal (i.n.) immunization with FGAd-F generated serum IgG, bronchoalveolar lavage secretory IgA, and RSV-specific CD8+ T-cell responses in BALB/c mice, with characteristic balanced or mixed Th1/Th2 CD4+ T-cell responses. Serum IgG was significantly elevated after boosting with i.n. FGAd-F. Upon challenge, i.n. immunization with FGAd-F displayed an effective protective role against RSV infection. These results demonstrate FGAd-F is able to induce effective protective immunity and is a promising vaccine regimen against RSV infection.« less

Crenothrix are major methane consumers in stratified lakes

PubMed Central

Oswald, Kirsten; Graf, Jon S; Littmann, Sten; Tienken, Daniela; Brand, Andreas; Wehrli, Bernhard; Albertsen, Mads; Daims, Holger; Wagner, Michael; Kuypers, Marcel MM; Schubert, Carsten J; Milucka, Jana

2017-01-01

Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth’s natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous bacteria have been known as contaminants of drinking water supplies since 1870, but their role in the environmental methane removal has remained unclear. While oxidizing methane, these organisms were assigned an ‘unusual’ methane monooxygenase (MMO), which was only distantly related to ‘classical’ MMO of gamma-proteobacterial methanotrophs. We now correct this assignment and show that Crenothrix encode a typical gamma-proteobacterial PmoA. Stable isotope labeling in combination swith single-cell imaging mass spectrometry revealed methane-dependent growth of the lacustrine Crenothrix with oxygen as well as under oxygen-deficient conditions. Crenothrix genomes encoded pathways for the respiration of oxygen as well as for the reduction of nitrate to N2O. The observed abundance and planktonic growth of Crenothrix suggest that these methanotrophs can act as a relevant biological sink for methane in stratified lakes and should be considered in the context of environmental removal of methane. PMID:28585934

Crenothrix are major methane consumers in stratified lakes.

PubMed

Oswald, Kirsten; Graf, Jon S; Littmann, Sten; Tienken, Daniela; Brand, Andreas; Wehrli, Bernhard; Albertsen, Mads; Daims, Holger; Wagner, Michael; Kuypers, Marcel Mm; Schubert, Carsten J; Milucka, Jana

2017-09-01

Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth's natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous bacteria have been known as contaminants of drinking water supplies since 1870, but their role in the environmental methane removal has remained unclear. While oxidizing methane, these organisms were assigned an 'unusual' methane monooxygenase (MMO), which was only distantly related to 'classical' MMO of gamma-proteobacterial methanotrophs. We now correct this assignment and show that Crenothrix encode a typical gamma-proteobacterial PmoA. Stable isotope labeling in combination swith single-cell imaging mass spectrometry revealed methane-dependent growth of the lacustrine Crenothrix with oxygen as well as under oxygen-deficient conditions. Crenothrix genomes encoded pathways for the respiration of oxygen as well as for the reduction of nitrate to N 2 O. The observed abundance and planktonic growth of Crenothrix suggest that these methanotrophs can act as a relevant biological sink for methane in stratified lakes and should be considered in the context of environmental removal of methane.

Biofilm density and detection of biofilm-producing genes in methicillin-resistant Staphylococcus aureus strains.

PubMed

Szczuka, Ewa; Urbańska, Katarzyna; Pietryka, Marta; Kaznowski, Adam

2013-01-01

Many serious diseases caused by Staphylococcus aureus appear to be associated with biofilms. Therefore, we investigated the biofilm-forming ability of the methicillin-resistant S. aureus (MRSA) isolates collected from hospitalized patients. As many as 96 % strains had the ability to form biofilm in vitro. The majority of S. aureus strains formed biofilm in ica-dependent mechanism. However, 23 % of MRSA isolates formed biofilm in ica-independent mechanism. Half of these strains carried fnbB genes encoding surface proteins fibronectin-binding protein B involved in intercellular accumulation and biofilm development in S. aureus strains. The biofilm structures were examined via confocal laser scanning microscopy (CLSM) and three-dimensional structures were reconstructed. The images obtained in CLSM revealed that the biofilm created by ica-positive strains was different from biofilm formed by ica-negative strains. The MRSA population showed a large genetic diversity and we did not find a single clone that occurred preferentially in hospital environment. Our results demonstrated the variation in genes encoding adhesins for the host matrix proteins (elastin, laminin, collagen, fibronectin, and fibrinogen) and in the gene involved in biofilm formation (icaA) within the majority of S. aureus clones.

The major facilitator superfamily transporter Knq1p modulates boron homeostasis in Kluyveromyces lactis.

PubMed

Svrbicka, Alexandra; Toth Hervay, Nora; Gbelska, Yvetta

2016-03-01

Boron is an essential micronutrient for living cells, yet its excess causes toxicity. To date, the mechanisms of boron toxicity are poorly understood. Recently, the ScATR1 gene has been identified encoding the main boron efflux pump in Saccharomyces cerevisiae. In this study, we analyzed the ScATR1 ortholog in Kluyveromyces lactis--the KNQ1 gene, to understand whether it participates in boron stress tolerance. We found that the KNQ1 gene, encoding a permease belonging to the major facilitator superfamily, is required for K. lactis boron tolerance. Deletion of the KNQ1 gene led to boron sensitivity and its overexpression increased K. lactis boron tolerance. The KNQ1 expression was induced by boron and the intracellular boron concentration was controlled by Knq1p. The KNQ1 promoter contains two putative binding motifs for the AP-1-like transcription factor KlYap1p playing a central role in oxidative stress defense. Our results indicate that the induction of the KNQ1 expression requires the presence of KlYap1p and that Knq1p like its ortholog ScAtr1p in S. cerevisiae functions as a boron efflux pump providing boron resistance in K. lactis.

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

PubMed Central

Charneski, Catherine A.; Hurst, Laurence D.

2013-01-01

Both for understanding mechanisms of disease and for the design of transgenes, it is important to understand the determinants of ribosome velocity, as changes in the rate of translation are important for protein folding, error attenuation, and localization. While there is great variation in ribosomal occupancy along even a single transcript, what determines a ribosome's occupancy is unclear. We examine this issue using data from a ribosomal footprinting assay in yeast. While codon usage is classically considered a major determinant, we find no evidence for this. By contrast, we find that positively charged amino acids greatly retard ribosomes downstream from where they are encoded, consistent with the suggestion that positively charged residues interact with the negatively charged ribosomal exit tunnel. Such slowing is independent of and greater than the average effect owing to mRNA folding. The effect of charged amino acids is additive, with ribosomal occupancy well-predicted by a linear fit to the density of positively charged residues. We thus expect that a translated poly-A tail, encoding for positively charged lysines regardless of the reading frame, would act as a sandtrap for the ribosome, consistent with experimental data. PMID:23554576

Genomic comparison of Escherichia coli K1 strains isolated from the cerebrospinal fluid of patients with meningitis.

PubMed

Yao, Yufeng; Xie, Yi; Kim, Kwang Sik

2006-04-01

Escherichia coli is a major cause of enteric/diarrheal diseases, urinary tract infections, and sepsis. E. coli K1 is the leading gram-negative organism causing neonatal meningitis, but the microbial basis of E. coli K1 meningitis is incompletely understood. Here we employed comparative genomic hybridization to investigate 11 strains of E. coli K1 isolated from the cerebrospinal fluid (CSF) of patients with meningitis. These 11 strains cover the majority of common O serotypes in E. coli K1 isolates from CSF. Our data demonstrated that these 11 strains of E. coli K1 can be categorized into two groups based on their profile for putative virulence factors, lipoproteins, proteases, and outer membrane proteins. Of interest, we showed that some open reading frames (ORFs) encoding the type III secretion system apparatus were found in group 2 strains but not in group 1 strains, while ORFs encoding the general secretory pathway are predominant in group 1 strains. These findings suggest that E. coli K1 strains isolated from CSF can be divided into two groups and these two groups of E. coli K1 may utilize different mechanisms to induce meningitis.

Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation.

PubMed

Zhang, Bo; Tieman, Denise M; Jiao, Chen; Xu, Yimin; Chen, Kunsong; Fei, Zhangjun; Giovannoni, James J; Klee, Harry J

2016-11-01

Commercial tomatoes are widely perceived by consumers as lacking flavor. A major part of that problem is a postharvest handling system that chills fruit. Low-temperature storage is widely used to slow ripening and reduce decay. However, chilling results in loss of flavor. Flavor-associated volatiles are sensitive to temperatures below 12 °C, and their loss greatly reduces flavor quality. Here, we provide a comprehensive view of the effects of chilling on flavor and volatiles associated with consumer liking. Reduced levels of specific volatiles are associated with significant reductions in transcripts encoding key volatile synthesis enzymes. Although expression of some genes critical to volatile synthesis recovers after a return to 20 °C, some genes do not. RNAs encoding transcription factors essential for ripening, including RIPENING INHIBITOR (RIN), NONRIPENING, and COLORLESS NONRIPENING are reduced in response to chilling and may be responsible for reduced transcript levels in many downstream genes during chilling. Those reductions are accompanied by major changes in the methylation status of promoters, including RIN Methylation changes are transient and may contribute to the fidelity of gene expression required to provide maximal beneficial environmental response with minimal tangential influence on broader fruit developmental biology.

A proteomics study of barley powdery mildew haustoria.

PubMed

Godfrey, Dale; Zhang, Ziguo; Saalbach, Gerhard; Thordal-Christensen, Hans

2009-06-01

A number of fungal and oomycete plant pathogens of major economic importance feed on their hosts by means of haustoria, which they place inside living plant cells. The underlying mechanisms are poorly understood, partly due to difficulty in preparing haustoria. We have therefore developed a procedure for isolating haustoria from the barley powdery mildew fungus (Blumeria graminis f.sp. hordei, Bgh). We subsequently aimed to understand the molecular mechanisms of haustoria through a study of their proteome. Extracted proteins were digested using trypsin, separated by LC, and analysed by MS/MS. Searches of a custom Bgh EST sequence database and the NCBI-NR fungal protein database, using the MS/MS data, identified 204 haustoria proteins. The majority of the proteins appear to have roles in protein metabolic pathways and biological energy production. Surprisingly, pyruvate decarboxylase (PDC), involved in alcoholic fermentation and commonly abundant in fungi and plants, was absent in our Bgh proteome data set. A sequence encoding this enzyme was also absent in our EST sequence database. Significantly, BLAST searches of the recently available Bgh genome sequence data also failed to identify a sequence encoding this enzyme, strongly indicating that Bgh does not have a gene for PDC.

Enhanced Transgene Expression in Sugarcane by Co-Expression of Virus-Encoded RNA Silencing Suppressors

PubMed Central

Park, Jong-Won; Beyene, Getu; Buenrostro-Nava, Marco T.; Molina, Joe; Wang, Xiaofeng; Ciomperlik, Jessica J.; Manabayeva, Shuga A.; Alvarado, Veria Y.; Rathore, Keerti S.; Scholthof, Herman B.; Mirkov, T. Erik

2013-01-01

Post-transcriptional gene silencing is commonly observed in polyploid species and often poses a major limitation to plant improvement via biotechnology. Five plant viral suppressors of RNA silencing were evaluated for their ability to counteract gene silencing and enhance the expression of the Enhanced Yellow Fluorescent Protein (EYFP) or the β-glucuronidase (GUS) reporter gene in sugarcane, a major sugar and biomass producing polyploid. Functionality of these suppressors was first verified in Nicotiana benthamiana and onion epidermal cells, and later tested by transient expression in sugarcane young leaf segments and protoplasts. In young leaf segments co-expressing a suppressor, EYFP reached its maximum expression at 48–96 h post-DNA introduction and maintained its peak expression for a longer time compared with that in the absence of a suppressor. Among the five suppressors, Tomato bushy stunt virus-encoded P19 and Barley stripe mosaic virus-encoded γb were the most efficient. Co-expression with P19 and γb enhanced EYFP expression 4.6-fold and 3.6-fold in young leaf segments, and GUS activity 2.3-fold and 2.4-fold in protoplasts compared with those in the absence of a suppressor, respectively. In transgenic sugarcane, co-expression of GUS and P19 suppressor showed the highest accumulation of GUS levels with an average of 2.7-fold more than when GUS was expressed alone, with no detrimental phenotypic effects. The two established transient expression assays, based on young leaf segments and protoplasts, and confirmed by stable transgene expression, offer a rapid versatile system to verify the efficiency of RNA silencing suppressors that proved to be valuable in enhancing and stabilizing transgene expression in sugarcane. PMID:23799071

Identification of potential platelet alloantigens in the Equidae family by comparison of gene sequences encoding major platelet membrane glycoproteins.

PubMed

Boudreaux, Mary K; Humphries, Drew M

2013-12-01

Platelet alloantigens in horses may play an important role in the development of neonatal alloimmune thrombocytopenia (NAIT). The objective of this study was to evaluate genes encoding major platelet glycoproteins within the Equidae family in an effort to identify potential alloantigens. DNA was isolated from blood samples obtained from Equidae family members, including a Holsteiner-Oldenburg cross, a Quarter horse, a donkey, and a Plains zebra (Equus burchelli). Gene sequences encoding equine platelet membrane glycoproteins IIb, IIIa (integrin subunits αIIb and β3), Ia (integrin subunit α2), and Ibα were determined using PCR. Gene sequences were compared to the equine genome available on GenBank. Polymorphisms that would be predicted to result in amino acid changes on platelet surfaces were documented and compared with known alloantigenic sites documented on human platelets. Amino acid differences were predicted based on nucleotide sequences for all 4 genes. Nine differences were documented for αIIb, 5 differences were documented for β3, 7 differences were documented for α2, and 16 differences were documented for Ibα outside the macroglycopeptide region. This study represents the first effort at identifying potential platelet alloantigens in members of the Equidae Family based on evaluation of gene sequences. The data obtained form the groundwork for identifying potential platelet alloantigens involved in transfusion reactions and neonatal alloimmune thrombocytopenia (NAIT). More work is required to determine whether the predicted amino acid differences documented in this study play a role in alloimmunity, and whether other polymorphisms not detected in this study are present that may result in alloimmunity. © 2013 American Society for Veterinary Clinical Pathology.

Suppression of 9-cis-Epoxycarotenoid Dioxygenase, Which Encodes a Key Enzyme in Abscisic Acid Biosynthesis, Alters Fruit Texture in Transgenic Tomato1[W][OA

PubMed Central

Sun, Liang; Sun, Yufei; Zhang, Mei; Wang, Ling; Ren, Jie; Cui, Mengmeng; Wang, Yanping; Ji, Kai; Li, Ping; Li, Qian; Chen, Pei; Dai, Shengjie; Duan, Chaorui; Wu, Yan; Leng, Ping

2012-01-01

Cell wall catabolism during fruit ripening is under complex control and is key for fruit quality and shelf life. To examine the role of abscisic acid (ABA) in tomato (Solanum lycopersicum) fruit ripening, we suppressed SlNCED1, which encodes 9-cis-epoxycarotenoid dioxygenase (NCED), a key enzyme in the biosynthesis of ABA. To suppress SlNCED1 specifically in tomato fruits, and thus avoid the pleiotropic phenotypes associated with ABA deficiency, we used an RNA interference construct driven by the fruit-specific E8 promoter. ABA accumulation and SlNCED1 transcript levels in the transgenic fruit were down-regulated to between 20% and 50% of the levels measured in the control fruit. This significant reduction in NCED activity led to a down-regulation in the transcription of genes encoding major cell wall catabolic enzymes, specifically polygalacturonase (SlPG), pectin methyl esterase (SlPME), β-galactosidase precursor mRNA (SlTBG), xyloglucan endotransglycosylase (SlXET), endo-1,4-β-cellulose (SlCels), and expansin (SlExp). This resulted in an increased accumulation of pectin during ripening. In turn, this led to a significant extension of the shelf life to 15 to 29 d compared with a shelf life of only 7 d for the control fruit and an enhancement of fruit firmness at the mature stage by 30% to 45%. In conclusion, ABA affects cell wall catabolism during tomato fruit ripening via down-regulation of the expression of major catabolic genes (SlPG, SlPME, SlTBG, SlXET, SlCels, and SlExp). PMID:22108525

Lymphomas in Ile-Ife, Nigeria: Immunohistochemical Characterization and Detection of Epstein-Barr virus Encoded RNA

PubMed Central

Onwubuya, Ifeyinwa M.; Adelusola, Kayode A.; Durosinmi, Muheez A.; Ezike, Kevin N.

2015-01-01

Background The proper histopathological characterization of malignant lymphomas requires the use of immunohistochemistry along with other molecular pathology techniques. Materials and Methods Malignant lymphomas histologically diagnosed in our hospital were reclassified according to the WHO scheme using immunohistochemistry while in-situ hybridization was performed for the detection of Epstein-Barr virus encoded RNA. Results There were 83 cases of lymphoma. The male to female ratio was 1.9:1 while the overall mean age was 41.7 years. Non-Hodgkin lymphomas (NHL) constituted about 79.5% of cases. The majority of cases (98.8%) were B-cell lymphomas. Nine subtypes of lymphomas were identified with diffuse large B-cell lymphomas (56.4% of which were of the germinal centre type) constituting the largest group (47.0%). Intermediate and high grade subtypes were more common. The majority of cases (72.3%) were nodal lymphomas with cervical lymph node being the commonest site (48.2%). Only classical Hodgkin lymphoma (HL) (20.5%) was seen of which the mixed cellularity subtype was the most common. Epstein Barr virus (EBV) encoded ribonucleic acid was detected in 7 cases (8.4%) including 4 cases of HL, 2 cases of Burkitt lymphoma and the only case of plasmablastic lymphoma. About five cases were reclassified as non-lymphoid malignant lesions. Conclusion Immunohistochemistry is vital to the proper classification of lymphomas even in a resource poor environment. Although nine subtypes of lymphomas were identified, diffuse large B-cell lymphomas formed the largest single group. Epstein-Barr virus probably plays an important role in lymphomatogenesis in this environment. A larger multicentre study is required to prove this. PMID:26266128

Multidrug resistance in fungi: regulation of transporter-encoding gene expression

PubMed Central

Paul, Sanjoy; Moye-Rowley, W. Scott

2014-01-01

A critical risk to the continued success of antifungal chemotherapy is the acquisition of resistance; a risk exacerbated by the few classes of effective antifungal drugs. Predictably, as the use of these drugs increases in the clinic, more resistant organisms can be isolated from patients. A particularly problematic form of drug resistance that routinely emerges in the major fungal pathogens is known as multidrug resistance. Multidrug resistance refers to the simultaneous acquisition of tolerance to a range of drugs via a limited or even single genetic change. This review will focus on recent progress in understanding pathways of multidrug resistance in fungi including those of most medical relevance. Analyses of multidrug resistance in Saccharomyces cerevisiae have provided the most detailed outline of multidrug resistance in a eukaryotic microorganism. Multidrug resistant isolates of S. cerevisiae typically result from changes in the activity of a pair of related transcription factors that in turn elicit overproduction of several target genes. Chief among these is the ATP-binding cassette (ABC)-encoding gene PDR5. Interestingly, in the medically important Candida species, very similar pathways are involved in acquisition of multidrug resistance. In both C. albicans and C. glabrata, changes in the activity of transcriptional activator proteins elicits overproduction of a protein closely related to S. cerevisiae Pdr5 called Cdr1. The major filamentous fungal pathogen, Aspergillus fumigatus, was previously thought to acquire resistance to azole compounds (the principal antifungal drug class) via alterations in the azole drug target-encoding gene cyp51A. More recent data indicate that pathways in addition to changes in the cyp51A gene are important determinants in A. fumigatus azole resistance. We will discuss findings that suggest azole resistance in A. fumigatus and Candida species may share more mechanistic similarities than previously thought. PMID:24795641

The methylotrophic Bacillus methanolicus MGA3 possesses two distinct fructose 1,6-bisphosphate aldolases.

PubMed

Stolzenberger, Jessica; Lindner, Steffen N; Wendisch, Volker F

2013-08-01

The thermotolerant Gram-positive methylotroph Bacillus methanolicus is able to grow with methanol, glucose or mannitol as a sole carbon and energy source. Fructose 1,6-bisphosphate aldolase (FBA), a key enzyme of glycolysis and gluconeogenesis, is encoded in the genome of B. methanolicus by two putative fba genes, the chromosomally located fba(C) and fba(P) on the naturally occurring plasmid pBM19. Their amino acid sequences share 75 % identity and suggest a classification as class II aldolases. Both enzymes were purified from recombinant Escherichia coli and were found to be active as homotetramers. Both enzymes were activated by either manganese or cobalt ions, and inhibited by ADP, ATP and EDTA. The kinetic parameters allowed us to distinguish the chromosomally encoded FBA(C) from the plasmid encoded FBA(P), since FBA(C) showed higher affinity towards fructose 1,6-bisphosphate (Km of 0.16±0.01 mM as compared to 2±0.08 mM) as well as higher glycolytic catalytic efficiency (31.3 as compared to 0.8 s(-1) mM(-1)) than FBA(P). However, FBA(P) exhibited a higher catalytic efficiency in gluconeogenesis (50.4 as compared to 1.4 s(-1) mM(-1) with dihydroxyacetone phosphate and 4 as compared to 0.4 s(-1) mM(-1) with glyceraldehyde 3-phosphate as limiting substrate). The aldolase-negative Corynebacterium glutamicum mutant Δfda could be complemented with both FBA genes from B. methanolicus. Based on the kinetic data, we propose that FBA(C) acts as major aldolase in glycolysis, whereas FBA(P) acts as major aldolase in gluconeogenesis in B. methanolicus.

Prospective, randomized, comparative study of Misgav Ladach versus traditional cesarean section at Nazareth Hospital, Kenya.

PubMed

Ansaloni, L; Brundisini, R; Morino, G; Kiura, A

2001-09-01

Cesarean section (CS) is the commonest major operation carried out in many low income countries. A new technique for CS, called the Misgav Ladach procedure, was evaluated in a randomized trial in Nazareth Hospital (Kiambu District, Kenya). A total of 160 patients were assigned to the Misgav Ladach procedure (n = 80) or to the traditional CS as performed in most rural hospitals in low income countries (n = 80). The two groups were analyzed by operating time, presence of infection and febrile morbidity, grade of postoperative pain, starting of fluid and solid alimentation, and development of incisional hernia and hypertrophic scar. The operating time of the Misgav Ladach procedure was significantly shorter. 20.4 (SD 6.1) minutes versus 30.4 (SD 6.1) minutes (p < 0.001). A total of 5 wound infections (6.2%) were seen with the Misgav Ladach procedure versus 16 (20.0%) in the control group (p = 0.01). The number of analgesic doses required during the postoperative period were significantly less in the Misgav Ladach group: 1.3 (SD 0.6) versus 1.9 (SD 0.7) ampuls of pethidine (p < 0.001) and 15.1 (SD 2.0) versus 16.4 (SD 1.8) tablets of ibuprofen (p < 0.001). Incisional pain was significantly less in the Misgav Ladach group: Visual Analogue Scale score 3.0 (SD 1.5) versus 4.9 (SD 2.0), p < 0.01. The patients in the Misgav Ladach group began drinking fluids voluntarily [19.1 (SD 4.5) hours versus 20.6 (SD 4.0) hours; p = 0.01] and eating solid food [41.2 (SD 9.3) hours versus 46.1 (SD 9.0) hours; p < 0.01] significantly before than those in the control group. At the 6-week follow-up, the presence of hypertrophic scar was significantly associated with the traditional procedure (2.1% vs. 48.8%; p < 0.001). We conclude that the Misgav Ladach operation should become the standard method for performing CS in low income countries, particularly in rural hospitals.

Synthesis and Luminescence Properties of Novel Ce(3+)- and Eu(2+)-Doped Lanthanum Bromothiosilicate La3Br(SiS4)2 Phosphors for White LEDs.

PubMed

Lee, Szu-Ping; Liu, Shuang-De; Chan, Ting-Shan; Chen, Teng-Ming

2016-04-13

Novel Ce(3+)- and Eu(2+)-doped lanthanum bromothiosilicate La3Br(SiS4)2:Ce(3+)and La3Br(SiS4)2:Eu(2+) phosphors were prepared by solid-state reaction in an evacuated and sealed quartz glass ampule. The La3Br(SiS4)2:Ce(3+) phosphor generates a cyan emission upon excitation at 375 nm, whereas the La3Br(SiS4)2:Eu(2+) phosphor could be excited with extremely broad range from UV to blue region (300 to 600 nm) and generates a reddish-orange broadband emission centered at 640 nm. In addition, thermal luminescence properties of La3Br(SiS4)2:Ce(3+)and La3Br(SiS4)2:Eu(2+) phosphors from 20 to 200 °C were investigated. The combination of a 450 nm blue InGaN-based LED chip with the red-emitting La3Br(SiS4)2:Eu(2+) phosphor, and green-emitting BOSE:Eu(2+) commercial phosphor produced a warm-white light with the CRI value of ∼95 and the CCT of 5,120 K. Overall, these results show that the prepared phosphors may have potential applications in pc-WLED.

[The vestibular apparatus of quail embryos in an experiment on the Kosmos-1129 biosatellite].

PubMed

Lychakov, D V; Il'inskaia, E V; Dadasheva, O A; Gur'eva, T S

1993-01-01

The light microscope was used to study serial sections of labyrinths of quail embryos incubated and reared during 12 d orbiting of Cosmos 1129. On recovery the embryos were aged 9, 11.5 and 12 days. No significant deviations in the development of the vestibular apparatus in flight species were noted as compared to the controls. Given this and our experimental data about in-space development of fish and amphibians we may deduce that hypo-g does not exert a noticeable altering effect on the vestibular embryogenesis. Nevertheless, it should be pointed out that in all otolith organs and semicircular channel ampules of the flight embryos cup-form neural endings innervating type I sensory cells were markedly swollen in contrast to the control. Earlier swollen cup-form nerve endings have been found in one adult rat after 7 days of space flight aboard Cosmos 1667. However, exposure in space does not bring about a substantial swelling of bud-like nerve endings which contact type II sensory cells. Thus, a conclusion may be drawn that spaceflight factors are liable to produce shifts in the type I sensory cell--cup-form nerve ending unit but they do not affect type II sensory cell--bud-like nerve ending unit to the extent when effects can be identified by light microscopy.

Rhenium solubility in borosilicate nuclear waste glass: implications for the processing and immobilization of technetium-99.

PubMed

McCloy, John S; Riley, Brian J; Goel, Ashutosh; Liezers, Martin; Schweiger, Michael J; Rodriguez, Carmen P; Hrma, Pavel; Kim, Dong-Sang; Lukens, Wayne W; Kruger, Albert A

2012-11-20

The immobilization of technetium-99 ((99)Tc) in a suitable host matrix has proven to be a challenging task for researchers in the nuclear waste community around the world. In this context, the present work reports on the solubility and retention of rhenium, a nonradioactive surrogate for (99)Tc, in a sodium borosilicate glass. Glasses containing target Re concentrations from 0 to 10,000 ppm [by mass, added as KReO(4) (Re(7+))] were synthesized in vacuum-sealed quartz ampules to minimize the loss of Re from volatilization during melting at 1000 °C. The rhenium was found as Re(7+) in all of the glasses as observed by X-ray absorption near-edge structure. The solubility of Re in borosilicate glasses was determined to be ~3000 ppm (by mass) using inductively coupled plasma optical emission spectroscopy. At higher rhenium concentrations, additional rhenium was retained in the glasses as crystalline inclusions of alkali perrhenates detected with X-ray diffraction. Since (99)Tc concentrations in a glass waste form are predicted to be <10 ppm (by mass), these Re results implied that the solubility should not be a limiting factor in processing radioactive wastes, assuming Tc as Tc(7+) and similarities between Re(7+) and Tc(7+) behavior in this glass system.

Molecular phylogeny and evolutionary timescale for the family of mammalian herpesviruses.

PubMed

McGeoch, D J; Cook, S; Dolan, A; Jamieson, F E; Telford, E A

1995-03-31

A detailed phylogenetic analysis for mammalian members of the family Herpesviridae, based on molecular sequences is reported. Sets of encoded amino acid sequences were collected for eight well conserved genes that are common to mammalian herpesviruses. Phylogenetic trees were inferred from alignments of these sequence sets using both maximum parsimony and distance methods, and evaluated by bootstrap analysis. In all cases the three recognised subfamilies (Alpha-, Beta- and Gammaherpesvirinae), and major sublineages in each subfamily, were clearly distinguished, but within sublineages some finer details of branching were incompletely resolved. Multiple-gene sets were assembled to give a broadly based tree. The root position of the tree was estimated by assuming a constant molecular clock and also by analysis of one herpesviral gene set (that encoding uracil-DNA glycosylase) using cellular homologues as outgroups. Both procedures placed the root between the Alphaherpesvirinae and the other two subfamilies. Substitution rates were calculated for the combined gene sets based on a previous estimate for alphaherpesviral UL27 genes, where the time base had been obtained according to the hypothesis of cospeciation of virus and host lineages. Assuming a constant molecular clock, it was then estimated that the three subfamilies arose approximately 180 to 220 million years ago, that major sublineages within subfamilies were probably generated before the mammalian radiation of 80 to 60 million years ago, and that speciations within sublineages took place in the last 80 million years, probably with a major component of cospeciation with host lineages.

Leishmania major survival in selective Phlebotomus papatasi sand fly vector requires a specific SCG-encoded lipophosphoglycan galactosylation pattern.

PubMed

Dobson, Deborah E; Kamhawi, Shaden; Lawyer, Phillip; Turco, Salvatore J; Beverley, Stephen M; Sacks, David L

2010-11-11

Phlebotomine sand flies that transmit the protozoan parasite Leishmania differ greatly in their ability to support different parasite species or strains in the laboratory: while some show considerable selectivity, others are more permissive. In "selective" sand flies, Leishmania binding and survival in the fly midgut typically depends upon the abundant promastigote surface adhesin lipophosphoglycan (LPG), which exhibits species- and strain-specific modifications of the dominant phosphoglycan (PG) repeat units. For the "selective" fly Phlebotomus papatasi PpapJ, side chain galactosyl-modifications (scGal) of PG repeats play key roles in parasite binding. We probed the specificity and properties of this scGal-LPG PAMP (Pathogen Associated Molecular Pattern) through studies of natural isolates exhibiting a wide range of galactosylation patterns, and of a panel of isogenic L. major engineered to express similar scGal-LPG diversity by transfection of SCG-encoded β1,3-galactosyltransferases with different activities. Surprisingly, both 'poly-scGal' and 'null-scGal' lines survived poorly relative to PpapJ-sympatric L. major FV1 and other 'mono-scGal' lines. However, survival of all lines was equivalent in P. duboscqi, which naturally transmit L. major strains bearing 'null-scGal'-LPG PAMPs. We then asked whether scGal-LPG-mediated interactions were sufficient for PpapJ midgut survival by engineering Leishmania donovani, which normally express unsubstituted LPG, to express a 'PpapJ-optimal' scGal-LPG PAMP. Unexpectedly, these "L. major FV1-cloaked" L. donovani-SCG lines remained unable to survive within PpapJ flies. These studies establish that midgut survival of L. major in PpapJ flies is exquisitely sensitive to the scGal-LPG PAMP, requiring a specific 'mono-scGal' pattern. However, failure of 'mono-scGal' L. donovani-SCG lines to survive in selective PpapJ flies suggests a requirement for an additional, as yet unidentified L. major-specific parasite factor(s). The interplay of the LPG PAMP and additional factor(s) with sand fly midgut receptors may determine whether a given sand fly host is "selective" or "permissive", with important consequences to both disease transmission and the natural co-evolution of sand flies and Leishmania.

Mechanisms of Surface Antigenic Variation in the Human Pathogenic Fungus Pneumocystis jirovecii.

PubMed

Schmid-Siegert, Emanuel; Richard, Sophie; Luraschi, Amanda; Mühlethaler, Konrad; Pagni, Marco; Hauser, Philippe M

2017-11-07

Microbial pathogens commonly escape the human immune system by varying surface proteins. We investigated the mechanisms used for that purpose by Pneumocystis jirovecii This uncultivable fungus is an obligate pulmonary pathogen that in immunocompromised individuals causes pneumonia, a major life-threatening infection. Long-read PacBio sequencing was used to assemble a core of subtelomeres of a single P. jirovecii strain from a bronchoalveolar lavage fluid specimen from a single patient. A total of 113 genes encoding surface proteins were identified, including 28 pseudogenes. These genes formed a subtelomeric gene superfamily, which included five families encoding adhesive glycosylphosphatidylinositol (GPI)-anchored glycoproteins and one family encoding excreted glycoproteins. Numerical analyses suggested that diversification of the glycoproteins relies on mosaic genes created by ectopic recombination and occurs only within each family. DNA motifs suggested that all genes are expressed independently, except those of the family encoding the most abundant surface glycoproteins, which are subject to mutually exclusive expression. PCR analyses showed that exchange of the expressed gene of the latter family occurs frequently, possibly favored by the location of the genes proximal to the telomere because this allows concomitant telomere exchange. Our observations suggest that (i) the P. jirovecii cell surface is made of a complex mixture of different surface proteins, with a majority of a single isoform of the most abundant glycoprotein, (ii) genetic mosaicism within each family ensures variation of the glycoproteins, and (iii) the strategy of the fungus consists of the continuous production of new subpopulations composed of cells that are antigenically different. IMPORTANCE Pneumocystis jirovecii is a fungus causing severe pneumonia in immunocompromised individuals. It is the second most frequent life-threatening invasive fungal infection. We have studied the mechanisms of antigenic variation used by this pathogen to escape the human immune system, a strategy commonly used by pathogenic microorganisms. Using a new DNA sequencing technology generating long reads, we could characterize the highly repetitive gene families encoding the proteins that are present on the cellular surface of this pest. These gene families are localized in the regions close to the ends of all chromosomes, the subtelomeres. Such chromosomal localization was found to favor genetic recombinations between members of each gene family and to allow diversification of these proteins continuously over time. This pathogen seems to use a strategy of antigenic variation consisting of the continuous production of new subpopulations composed of cells that are antigenically different. Such a strategy is unique among human pathogens. Copyright © 2017 Schmid-Siegert et al.

Unbiased View of Synaptic and Neuronal Gene Complement in Ctenophores: Are There Pan-neuronal and Pan-synaptic Genes across Metazoa?

PubMed Central

Moroz, Leonid L.; Kohn, Andrea B.

2015-01-01

Hypotheses of origins and evolution of neurons and synapses are controversial, mostly due to limited comparative data. Here, we investigated the genome-wide distribution of the bilaterian “synaptic” and “neuronal” protein-coding genes in non-bilaterian basal metazoans (Ctenophora, Porifera, Placozoa, and Cnidaria). First, there are no recognized genes uniquely expressed in neurons across all metazoan lineages. None of the so-called pan-neuronal genes such as embryonic lethal abnormal vision (ELAV), Musashi, or Neuroglobin are expressed exclusively in neurons of the ctenophore Pleurobrachia. Second, our comparative analysis of about 200 genes encoding canonical presynaptic and postsynaptic proteins in bilaterians suggests that there are no true “pan-synaptic” genes or genes uniquely and specifically attributed to all classes of synapses. The majority of these genes encode receptive and secretory complexes in a broad spectrum of eukaryotes. Trichoplax (Placozoa) an organism without neurons and synapses has more orthologs of bilaterian synapse-related/neuron-related genes than do ctenophores—the group with well-developed neuronal and synaptic organization. Third, the majority of genes encoding ion channels and ionotropic receptors are broadly expressed in unicellular eukaryotes and non-neuronal tissues in metazoans. Therefore, they cannot be viewed as neuronal markers. Nevertheless, the co-expression of multiple types of ion channels and receptors does correlate with the presence of neural and synaptic organization. As an illustrative example, the ctenophore genomes encode a greater diversity of ion channels and ionotropic receptors compared with the genomes of the placozoan Trichoplax and the demosponge Amphimedon. Surprisingly, both placozoans and sponges have a similar number of orthologs of “synaptic” proteins as we identified in the genomes of two ctenophores. Ctenophores have a distinct synaptic organization compared with other animals. Our analysis of transcriptomes from 10 different ctenophores did not detect recognized orthologs of synthetic enzymes encoding several classical, low-molecular-weight (neuro)transmitters; glutamate signaling machinery is one of the few exceptions. Novel peptidergic signaling molecules were predicted for ctenophores, together with the diversity of putative receptors including SCNN1/amiloride-sensitive sodium channel-like channels, many of which could be examples of a lineage-specific expansion within this group. In summary, our analysis supports the hypothesis of independent evolution of neurons and, as corollary, a parallel evolution of synapses. We suggest that the formation of synaptic machinery might occur more than once over 600 million years of animal evolution. PMID:26454853

Investigation of the Fusarium virguliforme Transcriptomes Induced during Infection of Soybean Roots Suggests that Enzymes with Hydrolytic Activities Could Play a Major Role in Root Necrosis

PubMed Central

Sahu, Binod B.; Baumbach, Jordan L.; Singh, Prashant; Srivastava, Subodh K.; Yi, Xiaoping

2017-01-01

Sudden death syndrome (SDS) is caused by the fungal pathogen, Fusarium virguliforme, and is a major threat to soybean production in North America. There are two major components of this disease: (i) root necrosis and (ii) foliar SDS. Root symptoms consist of root necrosis with vascular discoloration. Foliar SDS is characterized by interveinal chlorosis and leaf necrosis, and in severe cases by flower and pod abscission. A major toxin involved in initiating foliar SDS has been identified. Nothing is known about how root necrosis develops. In order to unravel the mechanisms used by the pathogen to cause root necrosis, the transcriptome of the pathogen in infected soybean root tissues of a susceptible cultivar, ‘Essex’, was investigated. The transcriptomes of the germinating conidia and mycelia were also examined. Of the 14,845 predicted F. virguliforme genes, we observed that 12,017 (81%) were expressed in germinating conidia and 12,208 (82%) in mycelia and 10,626 (72%) in infected soybean roots. Of the 10,626 genes induced in infected roots, 224 were transcribed only following infection. Expression of several infection-induced genes encoding enzymes with oxidation-reduction properties suggests that degradation of antimicrobial compounds such as the phytoalexin, glyceollin, could be important in early stages of the root tissue infection. Enzymes with hydrolytic and catalytic activities could play an important role in establishing the necrotrophic phase. The expression of a large number of genes encoding enzymes with catalytic and hydrolytic activities during the late infection stages suggests that cell wall degradation could be involved in root necrosis and the establishment of the necrotrophic phase in this pathogen. PMID:28095498

Genome-wide QTL and bulked transcriptomic analysis reveals new candidate genes for the control of tuber carotenoid content in potato (Solanum tuberosum L.).

PubMed

Campbell, Raymond; Pont, Simon D A; Morris, Jenny A; McKenzie, Gaynor; Sharma, Sanjeev Kumar; Hedley, Pete E; Ramsay, Gavin; Bryan, Glenn J; Taylor, Mark A

2014-09-01

Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9. The carotenoid content of edible plant storage organs is a key nutritional and quality trait. Although the structural genes that encode the biosynthetic enzymes are well characterised, much less is known about the factors that determine overall storage organ content. In this study, genome-wide QTL mapping, in concert with an efficient 'genetical genomics' analysis using bulked samples, has been employed to investigate the genetic architecture of potato tuber carotenoid content. Two diploid populations of Solanum tuberosum Group Phureja were genotyped (AFLP, SSR and DArT markers) and analysed for their tuber carotenoid content over two growing seasons. Common to both populations were QTL that explained relatively small proportions of the variation in constituent carotenoids and a major QTL on chromosome 3 explaining up to 71 % of the variation in carotenoid content. In one of the populations (01H15), a second major carotenoid QTL was identified on chromosome 9, explaining up to 20 % of the phenotypic variation. Whereas the major chromosome 3 QTL was likely to be due to an allele of a gene encoding β-carotene hydroxylase, no known carotenoid biosynthetic genes are located in the vicinity of the chromosome 9 QTL. A unique expression profiling strategy using phenotypically distinct bulks comprised individuals with similar carotenoid content provided further support for the QTL mapping to chromosome 9. This study shows the potential of using the potato genome sequence to link genetic maps to data arising from eQTL approaches to enhance the discovery of candidate genes underlying QTLs.

Investigation of the Fusarium virguliforme Transcriptomes Induced during Infection of Soybean Roots Suggests that Enzymes with Hydrolytic Activities Could Play a Major Role in Root Necrosis.

PubMed

Sahu, Binod B; Baumbach, Jordan L; Singh, Prashant; Srivastava, Subodh K; Yi, Xiaoping; Bhattacharyya, Madan K

2017-01-01

Sudden death syndrome (SDS) is caused by the fungal pathogen, Fusarium virguliforme, and is a major threat to soybean production in North America. There are two major components of this disease: (i) root necrosis and (ii) foliar SDS. Root symptoms consist of root necrosis with vascular discoloration. Foliar SDS is characterized by interveinal chlorosis and leaf necrosis, and in severe cases by flower and pod abscission. A major toxin involved in initiating foliar SDS has been identified. Nothing is known about how root necrosis develops. In order to unravel the mechanisms used by the pathogen to cause root necrosis, the transcriptome of the pathogen in infected soybean root tissues of a susceptible cultivar, 'Essex', was investigated. The transcriptomes of the germinating conidia and mycelia were also examined. Of the 14,845 predicted F. virguliforme genes, we observed that 12,017 (81%) were expressed in germinating conidia and 12,208 (82%) in mycelia and 10,626 (72%) in infected soybean roots. Of the 10,626 genes induced in infected roots, 224 were transcribed only following infection. Expression of several infection-induced genes encoding enzymes with oxidation-reduction properties suggests that degradation of antimicrobial compounds such as the phytoalexin, glyceollin, could be important in early stages of the root tissue infection. Enzymes with hydrolytic and catalytic activities could play an important role in establishing the necrotrophic phase. The expression of a large number of genes encoding enzymes with catalytic and hydrolytic activities during the late infection stages suggests that cell wall degradation could be involved in root necrosis and the establishment of the necrotrophic phase in this pathogen.

Vicilin and convicilin are potential major allergens from pea.

PubMed

Sanchez-Monge, R; Lopez-Torrejón, G; Pascual, C Y; Varela, J; Martin-Esteban, M; Salcedo, G

2004-11-01

Allergic reactions to pea (Pisum sativum) ingestion are frequently associated with lentil allergy in the Spanish population. Vicilin have been described as a major lentil allergen. To identify the main IgE binding components from pea seeds and to study their potential cross-reactivity with lentil vicilin. A serum pool or individual sera from 18 patients with pea allergy were used to detect IgE binding proteins from pea seeds by immunodetection and immunoblot inhibition assays. Protein preparations enriched in pea vicilin were obtained by gel filtration chromatography followed by reverse-phase high-performance liquid chromatography (HPLC). IgE binding components were identified by means of N-terminal amino acid sequencing. Complete cDNAs encoding pea vicilin were isolated by PCR, using primers based on the amino acid sequence of the reactive proteins. IgE immunodetection of crude pea extracts revealed that convicilin (63 kDa), as well as vicilin (44 kDa) and one of its proteolytic fragments (32 kDa), reacted with more than 50% of the individual sera tested. Additional proteolytic subunits of vicilin (36, 16 and 13 kDa) bound IgE from approximately 20% of the sera. The lentil vicilin allergen Len c 1 strongly inhibited the IgE binding to all components mentioned above. The characterization of cDNA clones encoding pea vicilin has allowed the deduction of its complete amino acid sequence (90% of sequence identity to Len c 1), as well as those of its reactive proteolytic processed subunits. Vicilin and convicilin are potential major allergens from pea seeds. Furthermore, proteolytic fragments from vicilin are also relevant IgE binding pea components. All these proteins cross-react with the major lentil allergen Len c 1.

Relationship between cardiac vagal activity and mood congruent memory bias in major depression.

PubMed

Garcia, Ronald G; Valenza, Gaetano; Tomaz, Carlos A; Barbieri, Riccardo

2016-01-15

Previous studies suggest that autonomic reactivity during encoding of emotional information could modulate the neural processes mediating mood-congruent memory. In this study, we use a point-process model to determine dynamic autonomic tone in response to negative emotions and its influence on long-term memory of major depressed subjects. Forty-eight patients with major depression and 48 healthy controls were randomly assigned to either neutral or emotionally arousing audiovisual stimuli. An adaptive point-process algorithm was applied to compute instantaneous estimates of the spectral components of heart rate variability [Low frequency (LF), 0.04-0.15 Hz; High frequency (HF), 0.15-0.4 Hz]. Three days later subjects were submitted to a recall test. A significant increase in HF power was observed in depressed subjects in response to the emotionally arousing stimulus (p=0.03). The results of a multivariate analysis revealed that the HF power during the emotional segment of the stimulus was independently associated with the score of the recall test in depressed subjects, after adjusting for age, gender and educational level (Coef. 0.003, 95%CI, 0.0009-0.005, p=0.008). These results could only be interpreted as responses to elicitation of specific negative emotions, the relationship between HF changes and encoding/recall of positive stimuli should be further examined. Alterations on parasympathetic response to emotion are involved in the mood-congruent cognitive bias observed in major depression. These findings are clinically relevant because it could constitute the mechanism by which depressed patients maintain maladaptive patterns of negative information processing that trigger and sustain depressed mood. Copyright © 2015 Elsevier B.V. All rights reserved.

Cyclotides Associate with Leaf Vasculature and Are the Products of a Novel Precursor in Petunia (Solanaceae)*

PubMed Central

Poth, Aaron G.; Mylne, Joshua S.; Grassl, Julia; Lyons, Russell E.; Millar, A. Harvey; Colgrave, Michelle L.; Craik, David J.

2012-01-01

Cyclotides are a large family of plant peptides that are structurally defined by their cyclic backbone and a trifecta of disulfide bonds, collectively known as the cyclic cystine knot (CCK) motif. Structurally similar cyclotides have been isolated from plants within the Rubiaceae, Violaceae, and Fabaceae families and share the CCK motif with trypsin-inhibitory knottins from a plant in the Cucurbitaceae family. Cyclotides have previously been reported to be encoded by dedicated genes or as a domain within a knottin-encoding PA1-albumin-like gene. Here we report the discovery of cyclotides and related non-cyclic peptides we called “acyclotides” from petunia of the agronomically important Solanaceae plant family. Transcripts for petunia cyclotides and acyclotides encode the shortest known cyclotide precursors. Despite having a different precursor structure, their sequences suggest that petunia cyclotides mature via the same biosynthetic route as other cyclotides. We assessed the spatial distribution of cyclotides within a petunia leaf section by MALDI imaging and observed that the major cyclotide component Phyb A was non-uniformly distributed. Dissected leaf midvein extracts contained significantly higher concentrations of this cyclotide compared with the lamina and outer margins of leaves. This is the third distinct type of cyclotide precursor, and Solanaceae is the fourth phylogenetically disparate plant family to produce these structurally conserved cyclopeptides, suggesting either convergent evolution upon the CCK structure or movement of cyclotide-encoding sequences within the plant kingdom. PMID:22700981

Identification of protein features encoded by alternative exons using Exon Ontology.

PubMed

Tranchevent, Léon-Charles; Aubé, Fabien; Dulaurier, Louis; Benoit-Pilven, Clara; Rey, Amandine; Poret, Arnaud; Chautard, Emilie; Mortada, Hussein; Desmet, François-Olivier; Chakrama, Fatima Zahra; Moreno-Garcia, Maira Alejandra; Goillot, Evelyne; Janczarski, Stéphane; Mortreux, Franck; Bourgeois, Cyril F; Auboeuf, Didier

2017-06-01

Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward this end, we developed a computational approach, named "Exon Ontology," based on terms corresponding to well-characterized protein features organized in an ontology tree. Exon Ontology is conceptually similar to Gene Ontology-based approaches but focuses on exon-encoded protein features instead of gene level functional annotations. Exon Ontology describes the protein features encoded by a selected list of exons and looks for potential Exon Ontology term enrichment. By applying this strategy to exons that are differentially spliced between epithelial and mesenchymal cells and after extensive experimental validation, we demonstrate that Exon Ontology provides support to discover specific protein features regulated by alternative splicing. We also show that Exon Ontology helps to unravel biological processes that depend on suites of coregulated alternative exons, as we uncovered a role of epithelial cell-enriched splicing factors in the AKT signaling pathway and of mesenchymal cell-enriched splicing factors in driving splicing events impacting on autophagy. Freely available on the web, Exon Ontology is the first computational resource that allows getting a quick insight into the protein features encoded by alternative exons and investigating whether coregulated exons contain the same biological information. © 2017 Tranchevent et al.; Published by Cold Spring Harbor Laboratory Press.

Sensitivity-encoded (SENSE) proton echo-planar spectroscopic imaging (PEPSI) in the human brain.

PubMed

Lin, Fa-Hsuan; Tsai, Shang-Yueh; Otazo, Ricardo; Caprihan, Arvind; Wald, Lawrence L; Belliveau, John W; Posse, Stefan

2007-02-01

Magnetic resonance spectroscopic imaging (MRSI) provides spatially resolved metabolite information that is invaluable for both neuroscience studies and clinical applications. However, lengthy data acquisition times, which are a result of time-consuming phase encoding, represent a major challenge for MRSI. Fast MRSI pulse sequences that use echo-planar readout gradients, such as proton echo-planar spectroscopic imaging (PEPSI), are capable of fast spectral-spatial encoding and thus enable acceleration of image acquisition times. Combining PEPSI with recent advances in parallel MRI utilizing RF coil arrays can further accelerate MRSI data acquisition. Here we investigate the feasibility of ultrafast spectroscopic imaging at high field (3T and 4T) by combining PEPSI with sensitivity-encoded (SENSE) MRI using eight-channel head coil arrays. We show that the acquisition of single-average SENSE-PEPSI data at a short TE (15 ms) can be accelerated to 32 s or less, depending on the field strength, to obtain metabolic images of choline (Cho), creatine (Cre), N-acetyl-aspartate (NAA), and J-coupled metabolites (e.g., glutamate (Glu) and inositol (Ino)) with acceptable spectral quality and localization. The experimentally measured reductions in signal-to-noise ratio (SNR) and Cramer-Rao lower bounds (CRLBs) of metabolite resonances were well explained by both the g-factor and reduced measurement times. Thus, this technology is a promising means of reducing the scan times of 3D acquisitions and time-resolved 2D measurements. Copyright (c) 2007 Wiley-Liss, Inc.

UV light selectively coinduces supply pathways from primary metabolism and flavonoid secondary product formation in parsley

PubMed Central

Logemann, Elke; Tavernaro, Annette; Schulz, Wolfgang; Somssich, Imre E.; Hahlbrock, Klaus

2000-01-01

The UV light-induced synthesis of UV-protective flavonoids diverts substantial amounts of substrates from primary metabolism into secondary product formation and thus causes major perturbations of the cellular homeostasis. Results from this study show that the mRNAs encoding representative enzymes from various supply pathways are coinduced in UV-irradiated parsley cells (Petroselinum crispum) with two mRNAs of flavonoid glycoside biosynthesis, encoding phenylalanine ammonia-lyase and chalcone synthase. Strong induction was observed for mRNAs encoding glucose 6-phosphate dehydrogenase (carbohydrate metabolism, providing substrates for the shikimate pathway), 3-deoxyarabinoheptulosonate 7-phosphate synthase (shikimate pathway, yielding phenylalanine), and acyl-CoA oxidase (fatty acid degradation, yielding acetyl-CoA), and moderate induction for an mRNA encoding S-adenosyl-homocysteine hydrolase (activated methyl cycle, yielding S-adenosyl-methionine for B-ring methylation). Ten arbitrarily selected mRNAs representing various unrelated metabolic activities remained unaffected. Comparative analysis of acyl-CoA oxidase and chalcone synthase with respect to mRNA expression modes and gene promoter structure and function revealed close similarities. These results indicate a fine-tuned regulatory network integrating those functionally related pathways of primary and secondary metabolism that are specifically required for protective adaptation to UV irradiation. Although the response of parsley cells to UV light is considerably broader than previously assumed, it contrasts greatly with the extensive metabolic reprogramming observed previously in elicitor-treated or fungus-infected cells. PMID:10677554

Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus

PubMed Central

2013-01-01

Background Agaricus bisporus is commercially grown on compost, in which the available carbon sources consist mainly of plant-derived polysaccharides that are built out of various different constituent monosaccharides. The major constituent monosaccharides of these polysaccharides are glucose, xylose, and arabinose, while smaller amounts of galactose, glucuronic acid, rhamnose and mannose are also present. Results In this study, genes encoding putative enzymes from carbon metabolism were identified and their expression was studied in different growth stages of A. bisporus. We correlated the expression of genes encoding plant and fungal polysaccharide modifying enzymes identified in the A. bisporus genome to the soluble carbohydrates and the composition of mycelium grown compost, casing layer and fruiting bodies. Conclusions The compost grown vegetative mycelium of A. bisporus consumes a wide variety of monosaccharides. However, in fruiting bodies only hexose catabolism occurs, and no accumulation of other sugars was observed. This suggests that only hexoses or their conversion products are transported from the vegetative mycelium to the fruiting body, while the other sugars likely provide energy for growth and maintenance of the vegetative mycelium. Clear correlations were found between expression of the genes and composition of carbohydrates. Genes encoding plant cell wall polysaccharide degrading enzymes were mainly expressed in compost-grown mycelium, and largely absent in fruiting bodies. In contrast, genes encoding fungal cell wall polysaccharide modifying enzymes were expressed in both fruiting bodies and vegetative mycelium, but different gene sets were expressed in these samples. PMID:24074284

Cerebellar granule cells encode the expectation of reward

PubMed Central

Wagner, Mark J; Kim, Tony Hyun; Savall, Joan; Schnitzer, Mark J; Luo, Liqun

2017-01-01

The human brain contains ~60 billion cerebellar granule cells1, which outnumber all other neurons combined. Classical theories posit that a large, diverse population of granule cells allows for highly detailed representations of sensorimotor context, enabling downstream Purkinje cells to sense fine contextual changes2–6. Although evidence suggests a role for cerebellum in cognition7–10, granule cells are known to encode only sensory11–13 and motor14 context. Using two-photon calcium imaging in behaving mice, here we show that granule cells convey information about the expectation of reward. Mice initiated voluntary forelimb movements for delayed water reward. Some granule cells responded preferentially to reward or reward omission, whereas others selectively encoded reward anticipation. Reward responses were not restricted to forelimb movement, as a Pavlovian task evoked similar responses. Compared to predictable rewards, unexpected rewards elicited markedly different granule cell activity despite identical stimuli and licking responses. In both tasks, reward signals were widespread throughout multiple cerebellar lobules. Tracking the same granule cells over several days of learning revealed that cells with reward-anticipating responses emerged from those that responded at the start of learning to reward delivery, whereas reward omission responses grew stronger as learning progressed. The discovery of predictive, non-sensorimotor encoding in granule cells is a major departure from current understanding of these neurons and dramatically enriches contextual information available to postsynaptic Purkinje cells, with important implications for cognitive processing in the cerebellum. PMID:28321129

A putative regulatory genetic locus modulates virulence in the pathogen Leptospira interrogans.

PubMed

Eshghi, Azad; Becam, Jérôme; Lambert, Ambroise; Sismeiro, Odile; Dillies, Marie-Agnès; Jagla, Bernd; Wunder, Elsio A; Ko, Albert I; Coppee, Jean-Yves; Goarant, Cyrille; Picardeau, Mathieu

2014-06-01

Limited research has been conducted on the role of transcriptional regulators in relation to virulence in Leptospira interrogans, the etiological agent of leptospirosis. Here, we identify an L. interrogans locus that encodes a sensor protein, an anti-sigma factor antagonist, and two genes encoding proteins of unknown function. Transposon insertion into the gene encoding the sensor protein led to dampened transcription of the other 3 genes in this locus. This lb139 insertion mutant (the lb139(-) mutant) displayed attenuated virulence in the hamster model of infection and reduced motility in vitro. Whole-transcriptome analyses using RNA sequencing revealed the downregulation of 115 genes and the upregulation of 28 genes, with an overrepresentation of gene products functioning in motility and signal transduction and numerous gene products with unknown functions, predicted to be localized to the extracellular space. Another significant finding encompassed suppressed expression of the majority of the genes previously demonstrated to be upregulated at physiological osmolarity, including the sphingomyelinase C precursor Sph2 and LigB. We provide insight into a possible requirement for transcriptional regulation as it relates to leptospiral virulence and suggest various biological processes that are affected due to the loss of native expression of this genetic locus.

Distribution of Suicin Gene Clusters in Streptococcus suis Serotype 2 Belonging to Sequence Types 25 and 28.

PubMed

Athey, Taryn B T; Vaillancourt, Katy; Frenette, Michel; Fittipaldi, Nahuel; Gottschalk, Marcelo; Grenier, Daniel

2016-01-01

Recently, we reported the purification and characterization of three distinct lantibiotics (named suicin 90-1330, suicin 3908, and suicin 65) produced by Streptococcus suis . In this study, we investigated the distribution of the three suicin lantibiotic gene clusters among serotype 2 S. suis strains belonging to sequence type (ST) 25 and ST28, the two dominant STs identified in North America. The genomes of 102 strains were interrogated for the presence of suicin gene clusters encoding suicins 90-1330, 3908, and 65. The gene cluster encoding suicin 65 was the most prevalent and mainly found among ST25 strains. In contrast, none of the genes related to suicin 90-1330 production were identified in 51 ST25 strains nor in 35/51 ST28 strains. However, the complete suicin 90-1330 gene cluster was found in ten ST28 strains, although some genes in the cluster were truncated in three of these isolates. The vast majority (101/102) of S. suis strains did not possess any of the genes encoding suicin 3908. In conclusion, this study indicates heterogeneous distribution of suicin genes in S. suis .

Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance.

PubMed

Davies, Mark R; Holden, Matthew T; Coupland, Paul; Chen, Jonathan H K; Venturini, Carola; Barnett, Timothy C; Zakour, Nouri L Ben; Tse, Herman; Dougan, Gordon; Yuen, Kwok-Yung; Walker, Mark J

2015-01-01

A scarlet fever outbreak began in mainland China and Hong Kong in 2011 (refs. 1-6). Macrolide- and tetracycline-resistant Streptococcus pyogenes emm12 isolates represent the majority of clinical cases. Recently, we identified two mobile genetic elements that were closely associated with emm12 outbreak isolates: the integrative and conjugative element ICE-emm12, encoding genes for tetracycline and macrolide resistance, and prophage ΦHKU.vir, encoding the superantigens SSA and SpeC, as well as the DNase Spd1 (ref. 4). Here we sequenced the genomes of 141 emm12 isolates, including 132 isolated in Hong Kong between 2005 and 2011. We found that the introduction of several ICE-emm12 variants, ΦHKU.vir and a new prophage, ΦHKU.ssa, occurred in three distinct emm12 lineages late in the twentieth century. Acquisition of ssa and transposable elements encoding multidrug resistance genes triggered the expansion of scarlet fever-associated emm12 lineages in Hong Kong. The occurrence of multidrug-resistant ssa-harboring scarlet fever strains should prompt heightened surveillance within China and abroad for the dissemination of these mobile genetic elements.

CatB is Critical for Total Catalase Activity and Reduces Bactericidal Effects of Phenazine-1-Carboxylic Acid on Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola.

PubMed

Pan, Xiayan; Wu, Jian; Xu, Shu; Duan, Yabing; Zhou, Mingguo

2017-02-01

Rice bacterial leaf blight, caused by Xanthomonas oryzae pv. oryzae, and rice bacterial leaf streak, caused by X. oryzae pv. oryzicola, are major diseases of rice. Phenazine-1-carboxylic acid (PCA) is a natural product that is isolated from Pseudomonas spp. and is used to control many important rice diseases in China. We previously reported that PCA disturbs the redox balance, which results in the accumulation of reactive oxygen species in X. oryzae pv. oryzae. In this study, we found that PCA significantly upregulated the transcript levels of catB and katE, which encode catalases, and that PCA sensitivity was reduced when X. oryzae pvs. oryzae and oryzicola were cultured with exogenous catalase. Furthermore, catB deletion mutants of X. oryzae pvs. oryzae and oryzicola showed dramatically decreased total catalase activity, increased sensitivity to PCA, and reduced virulence in rice. In contrast, deletion mutants of srpA and katG, which also encode catalases, exhibited little change in PCA sensitivity. The results indicate that catB in both X. oryzae pvs. oryzae and oryzicola encodes a catalase that helps protect the bacteria against PCA-induced stress.

The mapping of the human 52-kD Ro/SSA autoantigen gene to human chromosome II, and its polymorphisms

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

Frank, M.B.; Itoh, Kazuko; Fujisaku, Atsushi

1993-01-01

Autoantibodies to the ribonucleoprotein Ro/SSA occur in nearly half of the patients with systemic lupus erythematosus and are associated with lymphopenia, photosensitive dermatitis, and pulmonary and renal disease, which suggests that they have an immunopathologic role. The majority of Ro/SSA precipitin-positive patients produce serum antibodies that bind to the 60-kD and 52-kD Ro/SSA proteins. The authors previously isolated and determined the nucleotide sequence of a cDNA clone that encodes the 52-kD form of the human Ro/SSA protein. In the present study, they have determined the chromosomal location of the gene by in situ hybridization to the end of the shortmore » arm of chromosome 11. Hybridization of portions of the cDNA probe to restriction enzyme-digested DNA indicated the gene is composed of at least three exons. The exon encoding the putative zinc fingers of this protein was found to be distinct from that which encodes the leucine zipper. An RFLP of this gene was identified and is associated with the presence of lupus, primarily in black Americans. 60 refs., 3 figs., 3 tabs.« less

Characterization of cDNA encoding molt-inhibiting hormone of the crab, Cancer pagurus; expression of MIH in non-X-organ tissues.

PubMed

Lu, W; Wainwright, G; Olohan, L A; Webster, S G; Rees, H H; Turner, P C

2001-10-31

Synthesis of ecdysteroids (molting hormones) by crustacean Y-organs is regulated by a neuropeptide, molt-inhibiting hormone (MIH), produced in eyestalk neural ganglia. We report here the molecular cloning of a cDNA encoding MIH of the edible crab, Cancer pagurus. Full-length MIH cDNA was obtained by using reverse transcription-polymerase chain reaction (RT-PCR) with degenerate oligonucleotides based upon the amino acid sequence of MIH, in conjunction with 5'- and 3'-RACE. Full-length clones of MIH cDNA were obtained that encoded a 35 amino acid putative signal peptide and the mature 78 amino acid peptide. Of various tissues examined by Northern blot analysis, the X-organ was the sole major site of expression of the MIH gene. However, a nested-PCR approach using non-degenerate MIH-specific primers indicated the presence of MIH transcripts in other tissues. Southern blot analysis indicated a simple gene arrangement with at least two copies of the MIH gene in the genome of C. pagurus. Additional Southern blotting experiments detected MIH-hybridizing bands in another Cancer species, Cancer antennarius and another crab species, Carcinus maenas.

Histoplasma capsulatum encodes a dipeptidyl peptidase active against the mammalian immunoregulatory peptide, substance P.

PubMed

Cooper, Kendal G; Zarnowski, Robert; Woods, Jon P

2009-01-01

The pathogenic fungus Histoplasma capsulatum secretes dipeptidyl peptidase (Dpp) IV enzyme activity and has two putative DPPIV homologs (HcDPPIVA and HcDPPIVB). We previously showed that HcDPPIVB is the gene responsible for the majority of secreted DppIV activity in H. capsulatum culture supernatant, while we could not detect any functional contribution from HcDPPIVA. In order to determine whether HcDPPIVA encodes a functional DppIV enzyme, we expressed HcDPPIVA in Pichia pastoris and purified the recombinant protein. The recombinant enzyme cleaved synthetic DppIV substrates and had similar biochemical properties to other described DppIV enzymes, with temperature and pH optima of 42 degrees C and 8, respectively. Recombinant HcDppIVA cleaved the host immunoregulatory peptide substance P, indicating the enzyme has the potential to affect the immune response during infection. Expression of HcDPPIVA under heterologous regulatory sequences in H. capsulatum resulted in increased secreted DppIV activity, indicating that the encoded protein can be expressed and secreted by its native organism. However, HcDPPIVA was not required for virulence in a murine model of histoplasmosis. This work reports a fungal enzyme that can function to cleave the immunomodulatory host peptide substance P.

Tanscriptomic Study of the Soybean-Fusarium virguliforme Interaction Revealed a Novel Ankyrin-Repeat Containing Defense Gene, Expression of Whose during Infection Led to Enhanced Resistance to the Fungal Pathogen in Transgenic Soybean Plants

PubMed Central

Ngaki, Micheline N.; Wang, Bing; Sahu, Binod B.; Srivastava, Subodh K.; Farooqi, Mohammad S.; Kambakam, Sekhar; Swaminathan, Sivakumar

2016-01-01

Fusarium virguliforme causes the serious disease sudden death syndrome (SDS) in soybean. Host resistance to this pathogen is partial and is encoded by a large number of quantitative trait loci, each conditioning small effects. Breeding SDS resistance is therefore challenging and identification of single-gene encoded novel resistance mechanisms is becoming a priority to fight this devastating this fungal pathogen. In this transcriptomic study we identified a few putative soybean defense genes, expression of which is suppressed during F. virguliforme infection. The F. virguliforme infection-suppressed genes were broadly classified into four major classes. The steady state transcript levels of many of these genes were suppressed to undetectable levels immediately following F. virguliforme infection. One of these classes contains two novel genes encoding ankyrin repeat-containing proteins. Expression of one of these genes, GmARP1, during F. virguliforme infection enhances SDS resistance among the transgenic soybean plants. Our data suggest that GmARP1 is a novel defense gene and the pathogen presumably suppress its expression to establish compatible interaction. PMID:27760122

Bone Dysplasia Sclerosteosis Results from Loss of the SOST Gene Product, a Novel Cystine Knot–Containing Protein

PubMed Central

Brunkow, Mary E.; Gardner, Jessica C.; Van Ness, Jeff; Paeper, Bryan W.; Kovacevich, Brian R.; Proll, Sean; Skonier, John E.; Zhao, L.; Sabo, P. J.; Fu, Ying-Hui; Alisch, Reid S.; Gillett, Lucille; Colbert, Trenton; Tacconi, Paolo; Galas, David; Hamersma, Herman; Beighton, Peter; Mulligan, John T.

2001-01-01

Sclerosteosis is an autosomal recessive sclerosing bone dysplasia characterized by progressive skeletal overgrowth. The majority of affected individuals have been reported in the Afrikaner population of South Africa, where a high incidence of the disorder occurs as a result of a founder effect. Homozygosity mapping in Afrikaner families along with analysis of historical recombinants localized sclerosteosis to an interval of ∼2 cM between the loci D17S1787 and D17S930 on chromosome 17q12-q21. Here we report two independent mutations in a novel gene, termed “SOST.” Affected Afrikaners carry a nonsense mutation near the amino terminus of the encoded protein, whereas an unrelated affected person of Senegalese origin carries a splicing mutation within the single intron of the gene. The SOST gene encodes a protein that shares similarity with a class of cystine knot–containing factors including dan, cerberus, gremlin, prdc, and caronte. The specific and progressive effect on bone formation observed in individuals affected with sclerosteosis, along with the data presented in this study, together suggest that the SOST gene encodes an important new regulator of bone homeostasis. PMID:11179006

Bone dysplasia sclerosteosis results from loss of the SOST gene product, a novel cystine knot-containing protein.

PubMed

Brunkow, M E; Gardner, J C; Van Ness, J; Paeper, B W; Kovacevich, B R; Proll, S; Skonier, J E; Zhao, L; Sabo, P J; Fu, Y; Alisch, R S; Gillett, L; Colbert, T; Tacconi, P; Galas, D; Hamersma, H; Beighton, P; Mulligan, J

2001-03-01

Sclerosteosis is an autosomal recessive sclerosing bone dysplasia characterized by progressive skeletal overgrowth. The majority of affected individuals have been reported in the Afrikaner population of South Africa, where a high incidence of the disorder occurs as a result of a founder effect. Homozygosity mapping in Afrikaner families along with analysis of historical recombinants localized sclerosteosis to an interval of approximately 2 cM between the loci D17S1787 and D17S930 on chromosome 17q12-q21. Here we report two independent mutations in a novel gene, termed "SOST." Affected Afrikaners carry a nonsense mutation near the amino terminus of the encoded protein, whereas an unrelated affected person of Senegalese origin carries a splicing mutation within the single intron of the gene. The SOST gene encodes a protein that shares similarity with a class of cystine knot-containing factors including dan, cerberus, gremlin, prdc, and caronte. The specific and progressive effect on bone formation observed in individuals affected with sclerosteosis, along with the data presented in this study, together suggest that the SOST gene encodes an important new regulator of bone homeostasis.

Sequence-encoded colloidal origami and microbot assemblies from patchy magnetic cubes

PubMed Central

Han, Koohee; Shields, C. Wyatt; Diwakar, Nidhi M.; Bharti, Bhuvnesh; López, Gabriel P.; Velev, Orlin D.

2017-01-01

Colloidal-scale assemblies that reconfigure on demand may serve as the next generation of soft “microbots,” artificial muscles, and other biomimetic devices. This requires the precise arrangement of particles into structures that are preprogrammed to reversibly change shape when actuated by external fields. The design and making of colloidal-scale assemblies with encoded directional particle-particle interactions remain a major challenge. We show how assemblies of metallodielectric patchy microcubes can be engineered to store energy through magnetic polarization and release it on demand by microscale reconfiguration. The dynamic pattern of folding and reconfiguration of the chain-like assemblies can be encoded in the sequence of the cube orientation. The residual polarization of the metallic facets on the microcubes leads to local interactions between the neighboring particles, which is directed by the conformational restrictions of their shape after harvesting energy from external magnetic fields. These structures can also be directionally moved, steered, and maneuvered by global forces from external magnetic fields. We illustrate these capabilities by examples of assemblies of specific sequences that can be actuated, reoriented, and spatially maneuvered to perform microscale operations such as capturing and transporting live cells, acting as prototypes of microbots, micromixers, and other active microstructures. PMID:28798960

Genomic and functional characterisation of IncX3 plasmids encoding blaSHV-12 in Escherichia coli from human and animal origin.

PubMed

Liakopoulos, Apostolos; van der Goot, Jeanet; Bossers, Alex; Betts, Jonathan; Brouwer, Michael S M; Kant, Arie; Smith, Hilde; Ceccarelli, Daniela; Mevius, Dik

2018-05-16

The bla SHV-12 β-lactamase gene is one of the most prevalent genes conferring resistance to extended-spectrum β-lactams in Enterobacteriaceae disseminating within and between reservoirs, mostly via plasmid-mediated horizontal gene transfer. Yet, studies regarding the biology of plasmids encoding bla SHV-12 are very limited. In this study, we revealed the emergence of IncX3 plasmids alongside IncI1α/γ in bla SHV-12 in animal-related Escherichia coli isolates. Four representative bla SHV-12 -encoding IncX3 plasmids were selected for genome sequencing and further genetic and functional characterization. We report here the first complete sequences of IncX3 plasmids of animal origin and show that IncX3 plasmids exhibit remarkable synteny in their backbone, while the major differences lie in their bla SHV-12 -flanking region. Our findings indicate that plasmids of this subgroup are conjugative and highly stable, while they exert no fitness cost on their bacterial host. These favourable features might have contributed to the emergence of IncX3 amongst SHV-12-producing E. coli in the Netherlands, highlighting the epidemic potential of these plasmids.

The maize (Zea mays ssp. mays var. B73) genome encodes 33 members of the purple acid phosphatase family

PubMed Central

González-Muñoz, Eliécer; Avendaño-Vázquez, Aida-Odette; Montes, Ricardo A. Chávez; de Folter, Stefan; Andrés-Hernández, Liliana; Abreu-Goodger, Cei; Sawers, Ruairidh J. H.

2015-01-01

Purple acid phosphatases (PAPs) play an important role in plant phosphorus nutrition, both by liberating phosphorus from organic sources in the soil and by modulating distribution within the plant throughout growth and development. Furthermore, members of the PAP protein family have been implicated in a broader role in plant mineral homeostasis, stress responses and development. We have identified 33 candidate PAP encoding gene models in the maize (Zea mays ssp. mays var. B73) reference genome. The maize Pap family includes a clear single-copy ortholog of the Arabidopsis gene AtPAP26, shown previously to encode both major intracellular and secreted acid phosphatase activities. Certain groups of PAPs present in Arabidopsis, however, are absent in maize, while the maize family contains a number of expansions, including a distinct radiation not present in Arabidopsis. Analysis of RNA-sequencing based transcriptome data revealed accumulation of maize Pap transcripts in multiple plant tissues at multiple stages of development, and increased accumulation of specific transcripts under low phosphorus availability. These data suggest the maize PAP family as a whole to have broad significance throughout the plant life cycle, while highlighting potential functional specialization of individual family members. PMID:26042133

In silico analysis of subtilisin from Glaciozyma antarctica PI12

NASA Astrophysics Data System (ADS)

Mustafha, Siti Mardhiah; Murad, Abdul Munir Abdul; Mahadi, Nor Muhammad; Kamaruddin, Shazilah; Bakar, Farah Diba Abu

2015-09-01

Subtilisin constitute as a major player in industrial enzymes that has a wide range of application especially in the detergent industry. In this study, a cDNA encoding for subtilisin (GaSUBT) was extracted from the psychrophilic yeast, Glaciozyma antarctica PI12, PCR amplified and sequenced. Various bioinformatics tools were used to characterize the GaSUBT. GaSUBT contains 1587 bp nucleotides encoding for 529 amino acids. The predicted molecular weight of the deduced protein is 55.34 kDa with an isoelectric point of 6.25. GaSUBT was predicted to possess a signal peptide and pro-peptide consisting of a peptidase inhibitor I9 sequence. From the sequence alignment analysis of deduced amino acids with other subtilisins in the NCBI database showed that the sequences surrounding the catalytic triad that forms the catalytic domain are well conserved.

Expression of Duplicate msa Genes in the Salmonid Pathogen Renibacterium salmoninarum

PubMed Central

Rhodes, Linda D.; Coady, Alison M.; Strom, Mark S.

2002-01-01

Renibacterium salmoninarum is a gram-positive bacterium responsible for bacterial kidney disease of salmon and trout. R. salmoninarum has two identical copies of the gene encoding major soluble antigen (MSA), an immunodominant, extracellular protein. To determine whether one or both copies of msa are expressed, reporter plasmids encoding a fusion of MSA and green fluorescent protein controlled by 0.6 kb of promoter region from msa1 or msa2 were constructed and introduced into R. salmoninarum. Single copies of the reporter plasmids integrated into the chromosome by homologous recombination. Expression of mRNA and protein from the integrated plasmids was detected, and transformed cells were fluorescent, demonstrating that both msa1 and msa2 are expressed under in vitro conditions. This is the first report of successful transformation and homologous recombination in R. salmoninarum. PMID:12406741

The Differential Expression of Adhesion Molecule and Extracellular Matrix Genes in Mesenchymal Stromal Cells after Interaction with Cord Blood Hematopoietic Progenitors.

PubMed

Buravkova, L B; Andreeva, E R; Lobanova, M V; Cotnezova, E V; Grigoriev, A I

2018-03-01

The dynamics of the expression of genes encoding adhesion molecules, molecules of the connective tissue matrix, and its remodeling enzymes was studied in multipotent mesenchymal stromal cells (MSCs) from human adipose tissue after interaction with cord blood hematopoietic progenitors (HSPCs). An upregulation of ICAM1 and VCAM1, directly proportional to the coculture time (24-72 h), was found. After 72 h of culturing, a downregulation of the genes encoding the majority of matrix molecules (SPP1; COL6A2,7A1; MMP1,3; TIMP1,3; and HAS1) and cell-matrix adhesion molecules (ITGs) was revealed. The detected changes may ensure the realization of the stromal MSC function due to improvement of adhesion and transmigration of HSPCs into the subcellular space.

Disruption of non-anchored cell wall protein NCW-1 promotes cellulase production by increasing cellobiose uptake in Neurospora crassa.

PubMed

Lin, Liangcai; Chen, Yong; Li, Jingen; Wang, Shanshan; Sun, Wenliang; Tian, Chaoguang

2017-04-01

To elucidate the mechanism of cellulase signal transduction in filamentous fungi including the components of the cellulase induction pathway. Neurospora crassa ncw-1 encodes a non-anchored cell wall protein. The absence of ncw-1 increased cellulase gene expression and this is not due to relieving carbon catabolite repression mediated by the cre-1 pathway. A mutant lacking genes encoding both three major β-glucosidase enzymes and NCW-1 (Δ3βGΔncw-1) was constructed. Transcriptome analysis of the quadruple mutant demonstrated enhanced expression of cellodextrin transporters after ncw-1 deletion, indicating that ncw-1 affects cellulase expression and production by inhibiting the uptake of the cellodextrin. NCW-1 is a novel component that plays a critical role in the cellulase induction signaling pathway.

A Reduction in Age-Enhanced Gluconeogenesis Extends Lifespan

PubMed Central

Hachinohe, Mayumi; Yamane, Midori; Akazawa, Daiki; Ohsawa, Kazuhiro; Ohno, Mayumi; Terashita, Yuzu; Masumoto, Hiroshi

2013-01-01

The regulation of energy metabolism, such as calorie restriction (CR), is a major determinant of cellular longevity. Although augmented gluconeogenesis is known to occur in aged yeast cells, the role of enhanced gluconeogenesis in aged cells remains undefined. Here, we show that age-enhanced gluconeogenesis is suppressed by the deletion of the tdh2 gene, which encodes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a protein that is involved in both glycolysis and gluconeogenesis in yeast cells. The deletion of TDH2 restores the chronological lifespan of cells with deletions of both the HST3 and HST4 genes, which encode yeast sirtuins, and represses the activation of gluconeogenesis. Furthermore, the tdh2 gene deletion can extend the replicative lifespan in a CR pathway-dependent manner. These findings demonstrate that the repression of enhanced gluconeogenesis effectively extends the cellular lifespan. PMID:23342062

A reduction in age-enhanced gluconeogenesis extends lifespan.

PubMed

Hachinohe, Mayumi; Yamane, Midori; Akazawa, Daiki; Ohsawa, Kazuhiro; Ohno, Mayumi; Terashita, Yuzu; Masumoto, Hiroshi

2013-01-01

The regulation of energy metabolism, such as calorie restriction (CR), is a major determinant of cellular longevity. Although augmented gluconeogenesis is known to occur in aged yeast cells, the role of enhanced gluconeogenesis in aged cells remains undefined. Here, we show that age-enhanced gluconeogenesis is suppressed by the deletion of the tdh2 gene, which encodes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a protein that is involved in both glycolysis and gluconeogenesis in yeast cells. The deletion of TDH2 restores the chronological lifespan of cells with deletions of both the HST3 and HST4 genes, which encode yeast sirtuins, and represses the activation of gluconeogenesis. Furthermore, the tdh2 gene deletion can extend the replicative lifespan in a CR pathway-dependent manner. These findings demonstrate that the repression of enhanced gluconeogenesis effectively extends the cellular lifespan.

The C. elegans che-1 gene encodes a zinc finger transcription factor required for specification of the ASE chemosensory neurons.

PubMed

Uchida, Okiko; Nakano, Hiroyuki; Koga, Makoto; Ohshima, Yasumi

2003-04-01

Chemotaxis to water-soluble chemicals such as NaCl is an important behavior of C. elegans when seeking food. ASE chemosensory neurons have a major role in this behavior. We show that che-1, defined by chemotaxis defects, encodes a zinc-finger protein similar to the GLASS transcription factor required for photoreceptor cell differentiation in Drosophila, and that che-1 is essential for specification and function of ASE neurons. Expression of a che-1::gfp fusion construct was predominant in ASE. In che-1 mutants, expression of genes characterizing ASE such as seven-transmembrane receptors, guanylate cyclases and a cyclic-nucleotide gated channel is lost. Ectopic expression of che-1 cDNA induced expression of ASE-specific marker genes, a dye-filling defect in neurons other than ASE and dauer formation.

Aberrant alternative splicing is another hallmark of cancer.

PubMed

Ladomery, Michael

2013-01-01

The vast majority of human genes are alternatively spliced. Not surprisingly, aberrant alternative splicing is increasingly linked to cancer. Splice isoforms often encode proteins that have distinct and even antagonistic properties. The abnormal expression of splice factors and splice factor kinases in cancer changes the alternative splicing of critically important pre-mRNAs. Aberrant alternative splicing should be added to the growing list of cancer hallmarks.

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

USDA-ARS?s Scientific Manuscript database

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

Definition of the low molecular weight glutenin subunit gene family members in a set of standard bread wheat (Triticum aestivum L.) varieties

USDA-ARS?s Scientific Manuscript database

Low-molecular-weight glutenin subunits (LMW-GS) are a class of seed storage proteins that play a major role in the determination of the viscoelastic properties of wheat dough. Most of the LMW-GSs are encoded by a multi-gene family located on the short arms of the homoeologous group 1 chromosomes, at...

The major-effect quantitative trait locus CsARN6.1 encodes an AAA ATPase domain-containing protein that is associated with waterlogging stress tolerance by promoting adventitious root formation

USDA-ARS?s Scientific Manuscript database

In plants, the formation of hypocotyl-derived adventitious roots (AR) is an important morphological acclimation to waterlogging stress, but its genetic basis is largely unknown. In the present study, with combined use of bulked segregant analysis-based high throughput next-gen whole genome sequencin...

Special Area Coding Community College District Boundaries on the Los Angeles County DIME File.

ERIC Educational Resources Information Center

Kinney, Paul W.; And Others

This report documents the development of three major products: (1) a Los Angeles County Dual Independent Map Encoding (DIME) File to which community college district boundaries have been special area coded; (2) a book-like listing of all house number ranges and street names and the college district and census tract they are found in; and (3) a…

rigor mortis encodes a novel nuclear receptor interacting protein required for ecdysone signaling during Drosophila larval development.

PubMed

Gates, Julie; Lam, Geanette; Ortiz, José A; Losson, Régine; Thummel, Carl S

2004-01-01

Pulses of the steroid hormone ecdysone trigger the major developmental transitions in Drosophila, including molting and puparium formation. The ecdysone signal is transduced by the EcR/USP nuclear receptor heterodimer that binds to specific response elements in the genome and directly regulates target gene transcription. We describe a novel nuclear receptor interacting protein encoded by rigor mortis (rig) that is required for ecdysone responses during larval development. rig mutants display defects in molting, delayed larval development, larval lethality, duplicated mouth parts, and defects in puparium formation--phenotypes that resemble those seen in EcR, usp, E75A and betaFTZ-F1 mutants. Although the expression of these nuclear receptor genes is essentially normal in rig mutant larvae, the ecdysone-triggered switch in E74 isoform expression is defective. rig encodes a protein with multiple WD-40 repeats and an LXXLL motif, sequences that act as specific protein-protein interaction domains. Consistent with the presence of these elements and the lethal phenotypes of rig mutants, Rig protein interacts with several Drosophila nuclear receptors in GST pull-down experiments, including EcR, USP, DHR3, SVP and betaFTZ-F1. The ligand binding domain of betaFTZ-F1 is sufficient for this interaction, which can occur in an AF-2-independent manner. Antibody stains reveal that Rig protein is present in the brain and imaginal discs of second and third instar larvae, where it is restricted to the cytoplasm. In larval salivary gland and midgut cells, however, Rig shuttles between the cytoplasm and nucleus in a spatially and temporally regulated manner, at times that correlate with the major lethal phase of rig mutants and major switches in ecdysone-regulated gene expression. Taken together, these data indicate that rig exerts essential functions during larval development through gene-specific effects on ecdysone-regulated transcription, most likely as a cofactor for one or more nuclear receptors. Furthermore, the dynamic intracellular redistribution of Rig protein suggests that it may act to refine spatial and temporal responses to ecdysone during development.

Rice Ribosomal Protein Large Subunit Genes and Their Spatio-temporal and Stress Regulation

PubMed Central

Moin, Mazahar; Bakshi, Achala; Saha, Anusree; Dutta, Mouboni; Madhav, Sheshu M.; Kirti, P. B.

2016-01-01

Ribosomal proteins (RPs) are well-known for their role in mediating protein synthesis and maintaining the stability of the ribosomal complex, which includes small and large subunits. In the present investigation, in a genome-wide survey, we predicted that the large subunit of rice ribosomes is encoded by at least 123 genes including individual gene copies, distributed throughout the 12 chromosomes. We selected 34 candidate genes, each having 2–3 identical copies, for a detailed characterization of their gene structures, protein properties, cis-regulatory elements and comprehensive expression analysis. RPL proteins appear to be involved in interactions with other RP and non-RP proteins and their encoded RNAs have a higher content of alpha-helices in their predicted secondary structures. The majority of RPs have binding sites for metal and non-metal ligands. Native expression profiling of 34 ribosomal protein large (RPL) subunit genes in tissues covering the major stages of rice growth shows that they are predominantly expressed in vegetative tissues and seedlings followed by meiotically active tissues like flowers. The putative promoter regions of these genes also carry cis-elements that respond specifically to stress and signaling molecules. All the 34 genes responded differentially to the abiotic stress treatments. Phytohormone and cold treatments induced significant up-regulation of several RPL genes, while heat and H2O2 treatments down-regulated a majority of them. Furthermore, infection with a bacterial pathogen, Xanthomonas oryzae, which causes leaf blight also induced the expression of 80% of the RPL genes in leaves. Although the expression of RPL genes was detected in all the tissues studied, they are highly responsive to stress and signaling molecules indicating that their encoded proteins appear to have roles in stress amelioration besides house-keeping. This shows that the RPL gene family is a valuable resource for manipulation of stress tolerance in rice and other crops, which may be achieved by overexpressing and raising independent transgenic plants carrying the genes that became up-regulated significantly and instantaneously. PMID:27605933

Role of RNase Y in Clostridium perfringens mRNA Decay and Processing.

PubMed

Obana, Nozomu; Nakamura, Kouji; Nomura, Nobuhiko

2017-01-15

RNase Y is a major endoribonuclease that plays a crucial role in mRNA degradation and processing. We study the role of RNase Y in the Gram-positive anaerobic pathogen Clostridium perfringens, which until now has not been well understood. Our study implies an important role for RNase Y-mediated RNA degradation and processing in virulence gene expression and the physiological development of the organism. We began by constructing an RNase Y conditional knockdown strain in order to observe the importance of RNase Y on growth and virulence. Our resulting transcriptome analysis shows that RNase Y affects the expression of many genes, including toxin-producing genes. We provide data to show that RNase Y depletion repressed several toxin genes in C. perfringens and involved the virR-virS two-component system. We also observe evidence that RNase Y is indispensable for processing and stabilizing the transcripts of colA (encoding a major toxin collagenase) and pilA2 (encoding a major pilin component of the type IV pili). Posttranscriptional regulation of colA is known to be mediated by cleavage in the 5' untranslated region (5'UTR), and we observe that RNase Y depletion diminishes colA 5'UTR processing. We show that RNase Y is also involved in the posttranscriptional stabilization of pilA2 mRNA, which is thought to be important for host cell adherence and biofilm formation. RNases have important roles in RNA degradation and turnover in all organisms. C. perfringens is a Gram-positive anaerobic spore-forming bacterial pathogen that produces numerous extracellular enzymes and toxins, and it is linked to digestive disorders and disease. A highly conserved endoribonuclease, RNase Y, affects the expression of hundreds of genes, including toxin genes, and studying these effects is useful for understanding C. perfringens specifically and RNases generally. Moreover, RNase Y is involved in processing specific transcripts, and we observed that this processing in C. perfringens results in the stabilization of mRNAs encoding a toxin and bacterial extracellular apparatus pili. Our study shows that RNase activity is associated with gene expression, helping to determine the growth, proliferation, and virulence of C. perfringens. Copyright © 2016 American Society for Microbiology.

The vacuolar ATPase from Entamoeba histolytica: molecular cloning of the gene encoding for the B subunit and subcellular localization of the protein.

PubMed

Meléndez-Hernández, Mayra Gisela; Barrios, María Luisa Labra; Orozco, Esther; Luna-Arias, Juan Pedro

2008-12-23

Entamoeba histolytica is a professional phagocytic cell where the vacuolar ATPase plays a key role. This enzyme is a multisubunit complex that regulates pH in many subcellular compartments, even in those that are not measurably acidic. It participates in a wide variety of cellular processes such as endocytosis, intracellular transport and membrane fusion. The presence of a vacuolar type H+-ATPase in E. histolytica trophozoites has been inferred previously from inhibition assays of its activity, the isolation of the Ehvma1 and Ehvma3 genes, and by proteomic analysis of purified phagosomes. We report the isolation and characterization of the Ehvma2 gene, which encodes for the subunit B of the vacuolar ATPase. This polypeptide is a 55.3 kDa highly conserved protein with 34 to 80% identity to orthologous proteins from other species. Particularly, in silico studies showed that EhV-ATPase subunit B displays 78% identity and 90% similarity to its Dictyostelium ortholog. A 462 bp DNA fragment of the Ehvma2 gene was expressed in bacteria and recombinant polypeptide was used to raise mouse polyclonal antibodies. EhV-ATPase subunit B antibodies detected a 55 kDa band in whole cell extracts and in an enriched fraction of DNA-containing organelles named EhkOs. The V-ATPase subunit B was located by immunofluorescence and confocal microscopy in many vesicles, in phagosomes, plasma membrane and in EhkOs. We also identified the genes encoding for the majority of the V-ATPase subunits in the E. histolytica genome, and proposed a putative model for this proton pump. We have isolated the Ehvma2 gene which encodes for the V-ATPase subunit B from the E. histolytica clone A. This gene has a 154 bp intron and encodes for a highly conserved polypeptide. Specific antibodies localized EhV-ATPase subunit B in many vesicles, phagosomes, plasma membrane and in EhkOs. Most of the orthologous genes encoding for the EhV-ATPase subunits were found in the E. histolytica genome, indicating the conserved nature of V-ATPase in this parasite.

Molecular Characterization of the S-Layer Gene, sbpA, of Bacillus sphaericus CCM 2177 and Production of a Functional S-Layer Fusion Protein with the Ability To Recrystallize in a Defined Orientation while Presenting the Fused Allergen

PubMed Central

Ilk, Nicola; Völlenkle, Christine; Egelseer, Eva M.; Breitwieser, Andreas; Sleytr, Uwe B.; Sára, Margit

2002-01-01

The nucleotide sequence encoding the crystalline bacterial cell surface (S-layer) protein SbpA of Bacillus sphaericus CCM 2177 was determined by a PCR-based technique using four overlapping fragments. The entire sbpA sequence indicated one open reading frame of 3,804 bp encoding a protein of 1,268 amino acids with a theoretical molecular mass of 132,062 Da and a calculated isoelectric point of 4.69. The N-terminal part of SbpA, which is involved in anchoring the S-layer subunits via a distinct type of secondary cell wall polymer to the rigid cell wall layer, comprises three S-layer-homologous motifs. For screening of amino acid positions located on the outer surface of the square S-layer lattice, the sequence encoding Strep-tag I, showing affinity to streptavidin, was linked to the 5′ end of the sequence encoding the recombinant S-layer protein (rSbpA) or a C-terminally truncated form (rSbpA31-1068). The deletion of 200 C-terminal amino acids did not interfere with the self-assembly properties of the S-layer protein but significantly increased the accessibility of Strep-tag I. Thus, the sequence encoding the major birch pollen allergen (Bet v1) was fused via a short linker to the sequence encoding the C-terminally truncated form rSpbA31-1068. Labeling of the square S-layer lattice formed by recrystallization of rSbpA31-1068/Bet v1 on peptidoglycan-containing sacculi with a Bet v1-specific monoclonal mouse antibody demonstrated the functionality of the fused protein sequence and its location on the outer surface of the S-layer lattice. The specific interactions between the N-terminal part of SbpA and the secondary cell wall polymer will be exploited for an oriented binding of the S-layer fusion protein on solid supports to generate regularly structured functional protein lattices. PMID:12089001

The Calyptogena magnifica chemoautotrophic symbiont genome

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

Newton, I.L.; Woyke, T.; Auchtung, T.A.

2007-03-01

Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities. The genome encodes major chemoautotrophic pathways as well as pathways for biosynthesis of vitamins, cofactors, and all 20 amino acids required by the clam.

Alteration of a single amino acid in the basic domain of Marek's disease virus Meq oncoprotein plays an important role in T-cell transformation

USDA-ARS?s Scientific Manuscript database

Marek’s disease virus encoded oncoprotein, Meq, has been shown to play a major role in transformation of T-lymphocytes. We have earlier shown that replacement of the meq gene in the very virulent strain Md5 with that of vaccine strain CVI988/Rispens resulted in virus attenuation in chickens. To dete...

Pseudomonas syringae pv. tomato DC3000 CmaL (PSPTO4723), a DUF1330 family member, is needed to produce L-allo-isoleucine, a precursor for the phytotoxin coronatine

USDA-ARS?s Scientific Manuscript database

Pseudomonas syringae pathovar tomato DC3000 produces the phytotoxin coronatine, a major determinant of the leaf chlorosis associated with DC3000 pathogenesis. The DC3000 PSPTO4723 (cmaL) gene is located in a genomic region encoding type III effectors, however it promotes chlorosis in the model plant...

‘Mom—I don’t want to hear it’: Brain response to maternal praise and criticism in adolescents with major depressive disorder

PubMed Central

Lee, Kyung Hwa; Elliott, Rosalind D.; Hooley, Jill M.; Dahl, Ronald E.; Barber, Anita; Siegle, Greg J.

2017-01-01

Abstract Recent research has implicated altered neural response to interpersonal feedback as an important factor in adolescent depression, with existing studies focusing on responses to feedback from virtual peers. We investigated whether depressed adolescents differed from healthy youth in neural response to social evaluative feedback from mothers. During neuroimaging, twenty adolescents in a current episode of major depressive disorder (MDD) and 28 healthy controls listened to previously recorded audio clips of their own mothers’ praise, criticism and neutral comments. Whole-brain voxelwise analyses revealed that MDD youth, unlike controls, exhibited increased neural response to critical relative to neutral clips in the parahippocampal gyrus, an area involved in episodic memory encoding and retrieval. Depressed adolescents also showed a blunted response to maternal praise clips relative to neutral clips in the parahippocampal gyrus, as well as areas involved in reward and self-referential processing (i.e. ventromedial prefrontal cortex, precuneus, and thalamus/caudate). Findings suggest that maternal criticism may be more strongly encoded or more strongly activated during memory retrieval related to previous autobiographical instances of negative feedback from mothers in depressed youth compared to healthy youth. Furthermore, depressed adolescents may fail to process the reward value and self-relevance of maternal praise. PMID:28338795

Haploinsufficiency of a Spliceosomal GTPase Encoded by EFTUD2 Causes Mandibulofacial Dysostosis with Microcephaly

PubMed Central

Lines, Matthew A.; Huang, Lijia; Schwartzentruber, Jeremy; Douglas, Stuart L.; Lynch, Danielle C.; Beaulieu, Chandree; Guion-Almeida, Maria Leine; Zechi-Ceide, Roseli Maria; Gener, Blanca; Gillessen-Kaesbach, Gabriele; Nava, Caroline; Baujat, Geneviève; Horn, Denise; Kini, Usha; Caliebe, Almuth; Alanay, Yasemin; Utine, Gulen Eda; Lev, Dorit; Kohlhase, Jürgen; Grix, Arthur W.; Lohmann, Dietmar R.; Hehr, Ute; Böhm, Detlef; Majewski, Jacek; Bulman, Dennis E.; Wieczorek, Dagmar; Boycott, Kym M.

2012-01-01

Mandibulofacial dysostosis with microcephaly (MFDM) is a rare sporadic syndrome comprising craniofacial malformations, microcephaly, developmental delay, and a recognizable dysmorphic appearance. Major sequelae, including choanal atresia, sensorineural hearing loss, and cleft palate, each occur in a significant proportion of affected individuals. We present detailed clinical findings in 12 unrelated individuals with MFDM; these 12 individuals compose the largest reported cohort to date. To define the etiology of MFDM, we employed whole-exome sequencing of four unrelated affected individuals and identified heterozygous mutations or deletions of EFTUD2 in all four. Validation studies of eight additional individuals with MFDM demonstrated causative EFTUD2 mutations in all affected individuals tested. A range of EFTUD2-mutation types, including null alleles and frameshifts, is seen in MFDM, consistent with haploinsufficiency; segregation is de novo in all cases assessed to date. U5-116kD, the protein encoded by EFTUD2, is a highly conserved spliceosomal GTPase with a central regulatory role in catalytic splicing and post-splicing-complex disassembly. MFDM is the first multiple-malformation syndrome attributed to a defect of the major spliceosome. Our findings significantly extend the range of reported spliceosomal phenotypes in humans and pave the way for further investigation in related conditions such as Treacher Collins syndrome. PMID:22305528

Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation

PubMed Central

Zhang, Bo; Tieman, Denise M.; Jiao, Chen; Xu, Yimin; Chen, Kunsong; Fei, Zhangjun; Giovannoni, James J.; Klee, Harry J.

2016-01-01

Commercial tomatoes are widely perceived by consumers as lacking flavor. A major part of that problem is a postharvest handling system that chills fruit. Low-temperature storage is widely used to slow ripening and reduce decay. However, chilling results in loss of flavor. Flavor-associated volatiles are sensitive to temperatures below 12 °C, and their loss greatly reduces flavor quality. Here, we provide a comprehensive view of the effects of chilling on flavor and volatiles associated with consumer liking. Reduced levels of specific volatiles are associated with significant reductions in transcripts encoding key volatile synthesis enzymes. Although expression of some genes critical to volatile synthesis recovers after a return to 20 °C, some genes do not. RNAs encoding transcription factors essential for ripening, including RIPENING INHIBITOR (RIN), NONRIPENING, and COLORLESS NONRIPENING are reduced in response to chilling and may be responsible for reduced transcript levels in many downstream genes during chilling. Those reductions are accompanied by major changes in the methylation status of promoters, including RIN. Methylation changes are transient and may contribute to the fidelity of gene expression required to provide maximal beneficial environmental response with minimal tangential influence on broader fruit developmental biology. PMID:27791156

A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes.

PubMed

Bazak, Lily; Haviv, Ami; Barak, Michal; Jacob-Hirsch, Jasmine; Deng, Patricia; Zhang, Rui; Isaacs, Farren J; Rechavi, Gideon; Li, Jin Billy; Eisenberg, Eli; Levanon, Erez Y

2014-03-01

RNA molecules transmit the information encoded in the genome and generally reflect its content. Adenosine-to-inosine (A-to-I) RNA editing by ADAR proteins converts a genomically encoded adenosine into inosine. It is known that most RNA editing in human takes place in the primate-specific Alu sequences, but the extent of this phenomenon and its effect on transcriptome diversity are not yet clear. Here, we analyzed large-scale RNA-seq data and detected ∼1.6 million editing sites. As detection sensitivity increases with sequencing coverage, we performed ultradeep sequencing of selected Alu sequences and showed that the scope of editing is much larger than anticipated. We found that virtually all adenosines within Alu repeats that form double-stranded RNA undergo A-to-I editing, although most sites exhibit editing at only low levels (<1%). Moreover, using high coverage sequencing, we observed editing of transcripts resulting from residual antisense expression, doubling the number of edited sites in the human genome. Based on bioinformatic analyses and deep targeted sequencing, we estimate that there are over 100 million human Alu RNA editing sites, located in the majority of human genes. These findings set the stage for exploring how this primate-specific massive diversification of the transcriptome is utilized.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

PubMed

Birney, Ewan; Stamatoyannopoulos, John A; Dutta, Anindya; Guigó, Roderic; Gingeras, Thomas R; Margulies, Elliott H; Weng, Zhiping; Snyder, Michael; Dermitzakis, Emmanouil T; Thurman, Robert E; Kuehn, Michael S; Taylor, Christopher M; Neph, Shane; Koch, Christoph M; Asthana, Saurabh; Malhotra, Ankit; Adzhubei, Ivan; Greenbaum, Jason A; Andrews, Robert M; Flicek, Paul; Boyle, Patrick J; Cao, Hua; Carter, Nigel P; Clelland, Gayle K; Davis, Sean; Day, Nathan; Dhami, Pawandeep; Dillon, Shane C; Dorschner, Michael O; Fiegler, Heike; Giresi, Paul G; Goldy, Jeff; Hawrylycz, Michael; Haydock, Andrew; Humbert, Richard; James, Keith D; Johnson, Brett E; Johnson, Ericka M; Frum, Tristan T; Rosenzweig, Elizabeth R; Karnani, Neerja; Lee, Kirsten; Lefebvre, Gregory C; Navas, Patrick A; Neri, Fidencio; Parker, Stephen C J; Sabo, Peter J; Sandstrom, Richard; Shafer, Anthony; Vetrie, David; Weaver, Molly; Wilcox, Sarah; Yu, Man; Collins, Francis S; Dekker, Job; Lieb, Jason D; Tullius, Thomas D; Crawford, Gregory E; Sunyaev, Shamil; Noble, William S; Dunham, Ian; Denoeud, France; Reymond, Alexandre; Kapranov, Philipp; Rozowsky, Joel; Zheng, Deyou; Castelo, Robert; Frankish, Adam; Harrow, Jennifer; Ghosh, Srinka; Sandelin, Albin; Hofacker, Ivo L; Baertsch, Robert; Keefe, Damian; Dike, Sujit; Cheng, Jill; Hirsch, Heather A; Sekinger, Edward A; Lagarde, Julien; Abril, Josep F; Shahab, Atif; Flamm, Christoph; Fried, Claudia; Hackermüller, Jörg; Hertel, Jana; Lindemeyer, Manja; Missal, Kristin; Tanzer, Andrea; Washietl, Stefan; Korbel, Jan; Emanuelsson, Olof; Pedersen, Jakob S; Holroyd, Nancy; Taylor, Ruth; Swarbreck, David; Matthews, Nicholas; Dickson, Mark C; Thomas, Daryl J; Weirauch, Matthew T; Gilbert, James; Drenkow, Jorg; Bell, Ian; Zhao, XiaoDong; Srinivasan, K G; Sung, Wing-Kin; Ooi, Hong Sain; Chiu, Kuo Ping; Foissac, Sylvain; Alioto, Tyler; Brent, Michael; Pachter, Lior; Tress, Michael L; Valencia, Alfonso; Choo, Siew Woh; Choo, Chiou Yu; Ucla, Catherine; Manzano, Caroline; Wyss, Carine; Cheung, Evelyn; Clark, Taane G; Brown, James B; Ganesh, Madhavan; Patel, Sandeep; Tammana, Hari; Chrast, Jacqueline; Henrichsen, Charlotte N; Kai, Chikatoshi; Kawai, Jun; Nagalakshmi, Ugrappa; Wu, Jiaqian; Lian, Zheng; Lian, Jin; Newburger, Peter; Zhang, Xueqing; Bickel, Peter; Mattick, John S; Carninci, Piero; Hayashizaki, Yoshihide; Weissman, Sherman; Hubbard, Tim; Myers, Richard M; Rogers, Jane; Stadler, Peter F; Lowe, Todd M; Wei, Chia-Lin; Ruan, Yijun; Struhl, Kevin; Gerstein, Mark; Antonarakis, Stylianos E; Fu, Yutao; Green, Eric D; Karaöz, Ulaş; Siepel, Adam; Taylor, James; Liefer, Laura A; Wetterstrand, Kris A; Good, Peter J; Feingold, Elise A; Guyer, Mark S; Cooper, Gregory M; Asimenos, George; Dewey, Colin N; Hou, Minmei; Nikolaev, Sergey; Montoya-Burgos, Juan I; Löytynoja, Ari; Whelan, Simon; Pardi, Fabio; Massingham, Tim; Huang, Haiyan; Zhang, Nancy R; Holmes, Ian; Mullikin, James C; Ureta-Vidal, Abel; Paten, Benedict; Seringhaus, Michael; Church, Deanna; Rosenbloom, Kate; Kent, W James; Stone, Eric A; Batzoglou, Serafim; Goldman, Nick; Hardison, Ross C; Haussler, David; Miller, Webb; Sidow, Arend; Trinklein, Nathan D; Zhang, Zhengdong D; Barrera, Leah; Stuart, Rhona; King, David C; Ameur, Adam; Enroth, Stefan; Bieda, Mark C; Kim, Jonghwan; Bhinge, Akshay A; Jiang, Nan; Liu, Jun; Yao, Fei; Vega, Vinsensius B; Lee, Charlie W H; Ng, Patrick; Shahab, Atif; Yang, Annie; Moqtaderi, Zarmik; Zhu, Zhou; Xu, Xiaoqin; Squazzo, Sharon; Oberley, Matthew J; Inman, David; Singer, Michael A; Richmond, Todd A; Munn, Kyle J; Rada-Iglesias, Alvaro; Wallerman, Ola; Komorowski, Jan; Fowler, Joanna C; Couttet, Phillippe; Bruce, Alexander W; Dovey, Oliver M; Ellis, Peter D; Langford, Cordelia F; Nix, David A; Euskirchen, Ghia; Hartman, Stephen; Urban, Alexander E; Kraus, Peter; Van Calcar, Sara; Heintzman, Nate; Kim, Tae Hoon; Wang, Kun; Qu, Chunxu; Hon, Gary; Luna, Rosa; Glass, Christopher K; Rosenfeld, M Geoff; Aldred, Shelley Force; Cooper, Sara J; Halees, Anason; Lin, Jane M; Shulha, Hennady P; Zhang, Xiaoling; Xu, Mousheng; Haidar, Jaafar N S; Yu, Yong; Ruan, Yijun; Iyer, Vishwanath R; Green, Roland D; Wadelius, Claes; Farnham, Peggy J; Ren, Bing; Harte, Rachel A; Hinrichs, Angie S; Trumbower, Heather; Clawson, Hiram; Hillman-Jackson, Jennifer; Zweig, Ann S; Smith, Kayla; Thakkapallayil, Archana; Barber, Galt; Kuhn, Robert M; Karolchik, Donna; Armengol, Lluis; Bird, Christine P; de Bakker, Paul I W; Kern, Andrew D; Lopez-Bigas, Nuria; Martin, Joel D; Stranger, Barbara E; Woodroffe, Abigail; Davydov, Eugene; Dimas, Antigone; Eyras, Eduardo; Hallgrímsdóttir, Ingileif B; Huppert, Julian; Zody, Michael C; Abecasis, Gonçalo R; Estivill, Xavier; Bouffard, Gerard G; Guan, Xiaobin; Hansen, Nancy F; Idol, Jacquelyn R; Maduro, Valerie V B; Maskeri, Baishali; McDowell, Jennifer C; Park, Morgan; Thomas, Pamela J; Young, Alice C; Blakesley, Robert W; Muzny, Donna M; Sodergren, Erica; Wheeler, David A; Worley, Kim C; Jiang, Huaiyang; Weinstock, George M; Gibbs, Richard A; Graves, Tina; Fulton, Robert; Mardis, Elaine R; Wilson, Richard K; Clamp, Michele; Cuff, James; Gnerre, Sante; Jaffe, David B; Chang, Jean L; Lindblad-Toh, Kerstin; Lander, Eric S; Koriabine, Maxim; Nefedov, Mikhail; Osoegawa, Kazutoyo; Yoshinaga, Yuko; Zhu, Baoli; de Jong, Pieter J

2007-06-14

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Bacillus subtilis Mutants with Knockouts of the Genes Encoding Ribonucleases RNase Y and RNase J1 Are Viable, with Major Defects in Cell Morphology, Sporulation, and Competence

PubMed Central

Figaro, Sabine; Durand, Sylvain; Gilet, Laetitia; Cayet, Nadège; Sachse, Martin

2013-01-01

The genes encoding the ribonucleases RNase J1 and RNase Y have long been considered essential for Bacillus subtilis cell viability, even before there was concrete knowledge of their function as two of the most important enzymes for RNA turnover in this organism. Here we show that this characterization is incorrect and that ΔrnjA and Δrny mutants are both viable. As expected, both strains grow relatively slowly, with doubling times in the hour range in rich medium. Knockout mutants have major defects in their sporulation and competence development programs. Both mutants are hypersensitive to a wide range of antibiotics and have dramatic alterations to their cell morphologies, suggestive of cell envelope defects. Indeed, RNase Y mutants are significantly smaller in diameter than wild-type strains and have a very disordered peptidoglycan layer. Strains lacking RNase J1 form long filaments in tight spirals, reminiscent of mutants of the actin-like proteins (Mre) involved in cell shape determination. Finally, we combined the rnjA and rny mutations with mutations in other components of the degradation machinery and show that many of these strains are also viable. The implications for the two known RNA degradation pathways of B. subtilis are discussed. PMID:23504012

QTLs Regulating the Contents of Antioxidants, Phenolics, and Flavonoids in Soybean Seeds Share a Common Genomic Region.

PubMed

Li, Man-Wah; Muñoz, Nacira B; Wong, Chi-Fai; Wong, Fuk-Ling; Wong, Kwong-Sen; Wong, Johanna Wing-Hang; Qi, Xinpeng; Li, Kwan-Pok; Ng, Ming-Sin; Lam, Hon-Ming

2016-01-01

Soybean seeds are a rich source of phenolic compounds, especially isoflavonoids, which are important nutraceuticals. Our study using 14 wild- and 16 cultivated-soybean accessions shows that seeds from cultivated soybeans generally contain lower total antioxidants compared to their wild counterparts, likely an unintended consequence of domestication or human selection. Using a recombinant inbred population resulting from a wild and a cultivated soybean parent and a bin map approach, we have identified an overlapping genomic region containing major quantitative trait loci (QTLs) that regulate the seed contents of total antioxidants, phenolics, and flavonoids. The QTL for seed antioxidant content contains 14 annotated genes based on the Williams 82 reference genome (Gmax1.01). None of these genes encodes functions that are related to the phenylpropanoid pathway of soybean. However, we found three putative Multidrug And Toxic Compound Extrusion (MATE) transporter genes within this QTL and one adjacent to it (GmMATE1-4). Moreover, we have identified non-synonymous changes between GmMATE1 and GmMATE2, and that GmMATE3 encodes an antisense transcript that expresses in pods. Whether the polymorphisms in GmMATE proteins are major determinants of the antioxidant contents, or whether the antisense transcripts of GmMATE3 play important regulatory roles, awaits further functional investigations.

'Mom-I don't want to hear it': Brain response to maternal praise and criticism in adolescents with major depressive disorder.

PubMed

Silk, Jennifer S; Lee, Kyung Hwa; Elliott, Rosalind D; Hooley, Jill M; Dahl, Ronald E; Barber, Anita; Siegle, Greg J

2017-05-01

Recent research has implicated altered neural response to interpersonal feedback as an important factor in adolescent depression, with existing studies focusing on responses to feedback from virtual peers. We investigated whether depressed adolescents differed from healthy youth in neural response to social evaluative feedback from mothers. During neuroimaging, twenty adolescents in a current episode of major depressive disorder (MDD) and 28 healthy controls listened to previously recorded audio clips of their own mothers' praise, criticism and neutral comments. Whole-brain voxelwise analyses revealed that MDD youth, unlike controls, exhibited increased neural response to critical relative to neutral clips in the parahippocampal gyrus, an area involved in episodic memory encoding and retrieval. Depressed adolescents also showed a blunted response to maternal praise clips relative to neutral clips in the parahippocampal gyrus, as well as areas involved in reward and self-referential processing (i.e. ventromedial prefrontal cortex, precuneus, and thalamus/caudate). Findings suggest that maternal criticism may be more strongly encoded or more strongly activated during memory retrieval related to previous autobiographical instances of negative feedback from mothers in depressed youth compared to healthy youth. Furthermore, depressed adolescents may fail to process the reward value and self-relevance of maternal praise. © The Author (2017). Published by Oxford University Press.

Purification and cDNA cloning of SAPKK3, the major activator of RK/p38 in stress- and cytokine-stimulated monocytes and epithelial cells.

PubMed Central

Cuenda, A; Alonso, G; Morrice, N; Jones, M; Meier, R; Cohen, P; Nebreda, A R

1996-01-01

Two chromatographically distinct stress-activated protein kinase kinases (SAPKKs) have been identified in several mammalian cells, termed SAPKK2 and SAPKK3, which activate the MAP kinase family member RK/p38 but not JNK/SAPK in vitro. Here we demonstrate that SAPKK2 is identical or very closely related to the MAP kinase kinase family member MKK3. However, under our assay conditions, SAPKK3 was the major activator of RK/p38 detected in extracts prepared from stress- or interleukin-1-stimulated epithelial (KB) cells, from bacterial lipopolysaccharide and tumour necrosis factor alpha-stimulated THP1 monocytes or from rabbit skeletal muscle. The activated form of SAPKK3 was purified from muscle to near homogeneity, and tryptic peptide sequences were used to clone human and murine cDNAs encoding this enzyme. Human SAPKK3 comprised 334 amino acids and was 78% identical to MKK3. The murine and human SAPKK3 were 97% identical in their amino acid sequences. We also cloned a different murine cDNA that appears to encode a SAPKK3 protein truncated at the N-terminus. SAPKK3 is identical to the recently cloned MKK6. Images PMID:8861944

Genes of the class II and class III major histocompatibility complex are associated with typhoid fever in Vietnam.

PubMed

Dunstan, S J; Stephens, H A; Blackwell, J M; Duc, C M; Lanh, M N; Dudbridge, F; Phuong, C X; Luxemburger, C; Wain, J; Ho, V A; Hien, T T; Farrar, J; Dougan, G

2001-01-15

The influence of genes of the major histocompatibility complex (MHC) class II and class III loci on typhoid fever susceptibility was investigated. Individuals with blood culture-confirmed typhoid fever and control subjects from 2 distinct geographic locations in southern Vietnam were genotyped for HLA-DRB1 and HLA-DQB1 alleles, the gene that encodes tumor necrosis factor (TNF)-alpha (TNFA [-238] and TNFA [-308]), the gene that encodes lymphotoxin-alpha, and alleles of the TNF-alpha microsatellite. HLA-DRB1*0301/6/8, HLA-DQB1*0201-3, and TNFA*2 (-308) were associated with susceptibility to typhoid fever, whereas HLA-DRB1*04, HLA-DQB1*0401/2, and TNFA*1 (-308) were associated with disease resistance. The frequency of all possible haplotypes of the 3 individually associated loci were estimated and were found to be significantly different in typhoid case patients and control subjects (chi2=55.56, 32 df; P=.006). Haplotypes that were either protective (TNFA*1 [-308].DRB1*04) or predisposed individuals to typhoid fever (TNFA*2 [-308].DRB1*0301) were determined. This report identifies a genetic association in humans between typhoid fever and MHC class II and III genes.

The SOS and RpoS Regulons Contribute to Bacterial Cell Robustness to Genotoxic Stress by Synergistically Regulating DNA Polymerase Pol II.

PubMed

Dapa, Tanja; Fleurier, Sébastien; Bredeche, Marie-Florence; Matic, Ivan

2017-07-01

Mitomycin C (MMC) is a genotoxic agent that induces DNA cross-links, DNA alkylation, and the production of reactive oxygen species (ROS). MMC induces the SOS response and RpoS regulons in Escherichia coli SOS-encoded functions are required for DNA repair, whereas the RpoS regulon is typically induced by metabolic stresses that slow growth. Thus, induction of the RpoS regulon by MMC may be coincidental, because DNA damage slows growth; alternatively, the RpoS regulon may be an adaptive response contributing to cell survival. In this study, we show that the RpoS regulon is primarily induced by MMC-induced ROS production. We also show that RpoS regulon induction is required for the survival of MMC-treated growing cells. The major contributor to RpoS-dependent resistance to MMC treatment is DNA polymerase Pol II, which is encoded by the polB gene belonging to the SOS regulon. The observation that polB gene expression is controlled by the two major stress response regulons that are required to maximize survival and fitness further emphasizes the key role of this DNA polymerase as an important factor in genome stability. Copyright © 2017 by the Genetics Society of America.

Identification of the gene encoding the major capsid protein of fish lymphocystis disease virus.

PubMed

Schnitzler, P; Darai, G

1993-10-01

The gene encoding the major capsid protein (MCP) of fish lymphocystis disease virus (flounder isolate; FLCDV-f) has been identified by PCR using oligonucleotide primers corresponding to different regions of the MCP of Tipula iridescent virus (TIV), iridescent virus 22 (IV22) and Chilo iridescent virus (CIV). DNA fragments of 0.4 kbp, 0.5 kbp and 0.27 kbp in size were amplified using oligonucleotide primers corresponding to amino acids (aa) 146 to 153 (primer 1) and 274 to 268 (primer 6), or aa 146 to 153 (primer 1) and 313 to 304 (primer 8), or aa 304 to 312 (primer 7) and 385 to 381 (primer 9) of the MCP of TIV, respectively. The PCR products were used as hybridization probes for screening the gene library of FLCDV-f. The MCP gene of FLCDV-f(1377 bp; 459 aa; 51.4K) was identified within the DNA sequence of the EcoRI FLCDV-f DNA fragment C (11.2 kbp; 0.611 to 0.718 map units). A high degree of aa sequence identity/similarity was detected between the MCP of FLCDV-f and TIV (50.3%/33.8%), IV22 (49.1%/34.2%). CIV (53%/29.5%) and African swine fever virus (16%/38.1%).

Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti by the Trans-Encoded Small RNA MmgR.

PubMed

Lagares, Antonio; Ceizel Borella, Germán; Linne, Uwe; Becker, Anke; Valverde, Claudio

2017-04-15

Riboregulation has a major role in the fine-tuning of multiple bacterial processes. Among the RNA players, trans -encoded untranslated small RNAs (sRNAs) regulate complex metabolic networks by tuning expression from multiple target genes in response to numerous signals. In Sinorhizobium meliloti , over 400 sRNAs are expressed under different stimuli. The sRNA MmgR (standing for M akes m ore g ranules R egulator) has been of particular interest to us since its sequence and structure are highly conserved among the alphaproteobacteria and its expression is regulated by the amount and quality of the bacterium's available nitrogen source. In this work, we explored the biological role of MmgR in S. meliloti 2011 by characterizing the effect of a deletion of the internal conserved core of mmgR ( mmgR Δ33-51 ). This mutation resulted in larger amounts of polyhydroxybutyrate (PHB) distributed into more intracellular granules than are found in the wild-type strain. This phenotype was expressed upon cessation of balanced growth owing to nitrogen depletion in the presence of surplus carbon (i.e., at a carbon/nitrogen molar ratio greater than 10). The normal PHB accumulation was complemented with a wild-type mmgR copy but not with unrelated sRNA genes. Furthermore, the expression of mmgR limited PHB accumulation in the wild type, regardless of the magnitude of the C surplus. Quantitative proteomic profiling and quantitative reverse transcription-PCR (qRT-PCR) revealed that the absence of MmgR results in a posttranscriptional overexpression of both PHB phasin proteins (PhaP1 and PhaP2). Together, our results indicate that the widely conserved alphaproteobacterial MmgR sRNA fine-tunes the regulation of PHB storage in S. meliloti IMPORTANCE High-throughput RNA sequencing has recently uncovered an overwhelming number of trans -encoded small RNAs (sRNAs) in diverse prokaryotes. In the nitrogen-fixing alphaproteobacterial symbiont of alfalfa root nodules Sinorhizobium meliloti , only four out of hundreds of identified sRNA genes have been functionally characterized. Thus, uncovering the biological role of sRNAs currently represents a major issue and one that is particularly challenging because of the usually subtle quantitative regulation contributed by most characterized sRNAs. Here, we have characterized the function of the broadly conserved alphaproteobacterial sRNA gene mmgR in S. meliloti Our results strongly suggest that mmgR encodes a negative regulator of the accumulation of polyhydroxybutyrate, the major carbon and reducing power storage polymer in S. meliloti cells growing under conditions of C/N overbalance. Copyright © 2017 American Society for Microbiology.

Molecular cloning and immunoglobulin E reactivity of a natural rubber latex lecithinase homologue, the major allergenic component of Hev b 4.

PubMed

Sunderasan, E; Bahari, A; Arif, S A M; Zainal, Z; Hamilton, R G; Yeang, H Y

2005-11-01

Hev b 4 is an allergenic natural rubber latex (NRL) protein complex that is reactive in skin prick tests and in vitro immunoassays. On SDS-polyacrylamide gel electrophoresis (SDS-PAGE), Hev b 4 is discerned predominantly at 53-55 kDa together with a 57 kDa minor component previously identified as a cyanogenic glucosidase. Of the 13 NRL allergens recognized by the International Union of Immunological Societies, the 53-55 kDa Hev b 4 major protein is the only candidate that lacks complete cDNA and protein sequence information. We sought to clone the transcript encoding the Hev b 4 major protein, and characterize the native protein and its recombinant form in relation to IgE binding. The 5'/3' rapid amplification of cDNA ends method was employed to obtain the complete cDNA of the Hev b 4 major protein. A recombinant form of the protein was over-expressed in Escherichia coli. The native Hev b 4 major protein was deglycosylated by trifluoromethane sulphonic acid. Western immunoblots of the native, deglycosylated and recombinant proteins were performed using both polyclonal antibodies and sera from latex-allergic patients. The cDNA encoding the Hev b 4 major protein was cloned. Its open reading frame matched lecithinases in the conserved domain database and contained 10 predicted glycosylation sites. Detection of glycans on the Hev b 4 lecithinase homologue confirmed it to be a glycoprotein. The deglycosylated lecithinase homologue was discerned at 40 kDa on SDS-PAGE, this being comparable to the 38.53 kDa mass predicted by its cDNA. Deglycosylation of the lecithinase homologue resulted in the loss of IgE recognition, although reactivity to polyclonal rabbit anti-Hev b 4 was retained. IgE from latex-allergic patients also failed to recognize the non-glycosylated E. coli recombinant lecithinase homologue. The IgE epitopes of the Hev b 4 lecithinase homologue reside mainly in its carbohydrate moiety, which also account for the discrepancy between the observed molecular weight of the protein and the value calculated from its cDNA.

Regulative recovery in the sea urchin embryo and the stabilizing role of fail-safe gene network wiring

PubMed Central

Smith, Joel; Davidson, Eric H.

2009-01-01

Design features that ensure reproducible and invariant embryonic processes are major characteristics of current gene regulatory network models. New cis-regulatory studies on a gene regulatory network subcircuit activated early in the development of the sea urchin embryo reveal a sequence of encoded “fail-safe” regulatory devices. These ensure the maintenance of fate separation between skeletogenic and nonskeletogenic mesoderm lineages. An unexpected consequence of the network design revealed in the course of these experiments is that it enables the embryo to “recover” from regulatory interference that has catastrophic effects if this feature is disarmed. A reengineered regulatory system inserted into the embryo was used to prove how this system operates in vivo. Genomically encoded backup control circuitry thus provides the mechanism underlying a specific example of the regulative development for which the sea urchin embryo has long been famous. PMID:19822764

An Integrated Encyclopedia of DNA Elements in the Human Genome

PubMed Central

2012-01-01

Summary The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure, and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall the project provides new insights into the organization and regulation of our genes and genome, and an expansive resource of functional annotations for biomedical research. PMID:22955616

Characterization and Identification of Cryptic Biopeptides in Carya illinoinensis (Wangenh K. Koch) Storage Proteins.

PubMed

Mares-Mares, Everardo; Gutiérrez-Vargas, Santiago; Pérez-Moreno, Luis; Ordoñez-Acevedo, Leandro G; Barboza-Corona, José E; León-Galván, Ma Fabiola

2017-01-01

The objective of this research was to identify and characterize the encoded peptides present in nut storage proteins of Carya illinoinensis . It was found, through in silico prediction, proteomic analysis, and MS spectrometry, that bioactive peptides were mainly found in albumin and glutelin fractions. Glutelin was the major fraction with ~53% of the nut storage proteins containing at least 21 peptides with different putative biological activities, including antihypertensives, antioxidants, immunomodulators, protease inhibitors, and inhibitors of cell cycle progression in cancer cells. Data showed that using 50  μ g/mL tryptic digests of enriched peptides obtained from nut glutelins is able to induce up to 19% of apoptosis in both HeLa and CasKi cervical cancer cells. To our knowledge, this is the first report that shows the potential value of the nut-encoded peptides to be considered as adjuvants in cancer therapies.

Complementary DNA characterization and chromosomal localization of a human gene related to the poliovirus receptor-encoding gene.

PubMed

Lopez, M; Eberlé, F; Mattei, M G; Gabert, J; Birg, F; Bardin, F; Maroc, C; Dubreuil, P

1995-04-03

The human poliovirus (PV) receptor (PVR) is a member of the immunoglobulin (Ig) superfamily with unknown cellular function. We have isolated a human PVR-related (PRR) cDNA. The deduced amino acid (aa) sequence of PRR showed, in the extracellular region, 51.7 and 54.3% similarity with human PVR and with the murine PVR homolog, respectively. The cDNA coding sequence is 1.6-kb long and encodes a deduced 57-kDa protein; this protein has a structural organization analogous to that of PVR, that is, one V- and two C-set Ig domains, with a conserved number of aa. Northern blot analysis indicated that a major 5.9-kb transcript is present in all normal human tissues tested. In situ hybridization showed that the PRR gene is located at bands q23-q24 of human chromosome 11.

Chaski, a novel Drosophila lactate/pyruvate transporter required in glia cells for survival under nutritional stress.

PubMed

Delgado, María Graciela; Oliva, Carlos; López, Estefanía; Ibacache, Andrés; Galaz, Alex; Delgado, Ricardo; Barros, L Felipe; Sierralta, Jimena

2018-01-19

The intercellular transport of lactate is crucial for the astrocyte-to-neuron lactate shuttle (ANLS), a model of brain energetics according to which neurons are fueled by astrocytic lactate. In this study we show that the Drosophila chaski gene encodes a monocarboxylate transporter protein (MCT/SLC16A) which functions as a lactate/pyruvate transporter, as demonstrated by heterologous expression in mammalian cell culture using a genetically encoded FRET nanosensor. chaski expression is prominent in the Drosophila central nervous system and it is particularly enriched in glia over neurons. chaski mutants exhibit defects in a high energy demanding process such as synaptic transmission, as well as in locomotion and survival under nutritional stress. Remarkably, locomotion and survival under nutritional stress defects are restored by chaski expression in glia cells. Our findings are consistent with a major role for intercellular lactate shuttling in the brain metabolism of Drosophila.

Malondialdehyde Suppresses Cerebral Function by Breaking Homeostasis between Excitation and Inhibition in Turtle Trachemys scripta

PubMed Central

Li, Fangxu; Yang, Zhilai; Lu, Yang; Wei, Yan; Wang, Jinhui; Yin, Dazhong; He, Rongqiao

2010-01-01

The levels of malondialdehyde (MDA) are high in the brain during carbonyl stress, such as following daily activities and sleep deprivation. To examine our hypothesis that MDA is one of the major substances in the brain leading to fatigue, the influences of MDA on brain functions and neuronal encodings in red-eared turtle (Trachemys scripta) were studied. The intrathecal injections of MDA brought about sleep-like EEG and fatigue-like behaviors in a dose-dependent manner. These changes were found associated with the deterioration of encoding action potentials in cortical neurons. In addition, MDA increased the ratio of γ-aminobutyric acid to glutamate in turtle's brain, as well as the sensitivity of GABAergic neurons to inputs compared to excitatory neurons. Therefore, MDA, as a metabolic product in the brain, may weaken cerebral function during carbonyl stress through breaking the homeostasis between excitatory and inhibitory neurons. PMID:21203547

Monitoring thioredoxin redox with a genetically encoded red fluorescent biosensor.

PubMed

Fan, Yichong; Makar, Merna; Wang, Michael X; Ai, Hui-Wang

2017-09-01

Thioredoxin (Trx) is one of the two major thiol antioxidants, playing essential roles in redox homeostasis and signaling. Despite its importance, there is a lack of methods for monitoring Trx redox dynamics in live cells, hindering a better understanding of physiological and pathological roles of the Trx redox system. In this work, we developed the first genetically encoded fluorescent biosensor for Trx redox by engineering a redox relay between the active-site cysteines of human Trx1 and rxRFP1, a redox-sensitive red fluorescent protein. We used the resultant biosensor-TrxRFP1-to selectively monitor perturbations of Trx redox in various mammalian cell lines. We subcellularly localized TrxRFP1 to image compartmentalized Trx redox changes. We further combined TrxRFP1 with a green fluorescent Grx1-roGFP2 biosensor to simultaneously monitor Trx and glutathione redox dynamics in live cells in response to chemical and physiologically relevant stimuli.

CYTOMEGALOVIRUS VECTORS VIOLATE CD8+ T CELL EPITOPE RECOGNITION PARADIGMS

PubMed Central

Hansen, Scott G.; Sacha, Jonah B.; Hughes, Colette M.; Ford, Julia C.; Burwitz, Benjamin J.; Scholz, Isabel; Gilbride, Roxanne M.; Lewis, Matthew S.; Gilliam, Awbrey N.; Ventura, Abigail B.; Malouli, Daniel; Xu, Guangwu; Richards, Rebecca; Whizin, Nathan; Reed, Jason S.; Hammond, Katherine B.; Fischer, Miranda; Turner, John M.; Legasse, Alfred W.; Axthelm, Michael K.; Edlefsen, Paul T.; Nelson, Jay A.; Lifson, Jeffrey D.; Früh, Klaus; Picker, Louis J.

2013-01-01

CD8+ T cell responses focus on a small fraction of pathogen- or vaccine-encoded peptides, and for some pathogens, these restricted recognition hierarchies limit the effectiveness of anti-pathogen immunity. We found that simian immunodeficiency virus (SIV) protein-expressing Rhesus Cytomegalovirus (RhCMV) vectors elicit SIV-specific CD8+ T cells that recognize unusual, diverse and highly promiscuous epitopes, including dominant responses to epitopes restricted by class II major histocompatibility complex (MHC) molecules. Induction of canonical SIV epitope-specific CD8+ T cell responses is suppressed by the RhCMV-encoded Rh189 (US11) gene, and the promiscuous MHC class I- and class II-restricted CD8+ T cell responses only occur in the absence of the Rh157.4-.6 (UL128-131) genes. Thus, CMV vectors can be genetically programmed to achieve distinct patterns of CD8+ T cell epitope recognition. PMID:23704576

Motif enrichment tool.

PubMed

Blatti, Charles; Sinha, Saurabh

2014-07-01

The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Phonological priming in young children who stutter: holistic versus incremental processing.

PubMed

Byrd, Courtney T; Conture, Edward G; Ohde, Ralph N

2007-02-01

To investigate the holistic versus incremental phonological encoding processes of young children who stutter (CWS; N = 26) and age- and gender-matched children who do not stutter (CWNS; N = 26) via a picture-naming auditory priming paradigm. Children named pictures during 3 auditory priming conditions: neutral, holistic, and incremental. Speech reaction time (SRT) was measured from the onset of picture presentation to the onset of participant response. CWNS shifted from being significantly faster in the holistic priming condition to being significantly faster in the incremental priming condition from 3 to 5 years of age. In contrast, the majority of 3- and 5-year-old CWS continued to exhibit faster SRT in the holistic than the incremental condition. CWS are delayed in making the developmental shift in phonological encoding from holistic to incremental processing, a delay that may contribute to their difficulties establishing fluent speech.

Entrainment, transport and concentration of meteorites in polar ice sheets

NASA Technical Reports Server (NTRS)

Drewry, D. J.

1986-01-01

Glaciers and ice sheets act as slow-moving conveyancing systems for material added to both their upper and lower surfaces. Because the transit time for most materials is extremely long the ice acts as a major global storage facility. The effects of horizontal and vertical motions on the flow patterns of Antarctic ice sheets are summarized. The determination of the source areas of meteorites and their transport paths is a problem of central importance since it relates not only directly to concentration mechanisms but also to the wider issues in glaciology and meteorites. The ice and snow into which a meteorite falls, and which moves with it to the concentration area, encodes information about the infall area. The principle environmental conditions being former elevation, temperature (also related to elevation), and age of the ice. This encoded information could be used to identify the infall area.

U.S. Geological Survey DLG-3 and Bureau of the Census TIGER data. Development and GIS applications

USGS Publications Warehouse

Batten, Lawrence G.

1990-01-01

The U.S. Geological Survey has been actively developing digital cartographic and geographic data and standards since the early 1970's. One product is Digital Line Graph data, which offer a consistently accurate source of base category geographic information. The Bureau of the Census has combined their Dual Independent Map Encoding data with the Geological Survey's 1:100,000-scale Digital Line Graph data to prepare for the 1990 decennial census. The resulting Topologically Integrated Geographic Encoding and Referencing data offer a wealth of information. A major area of research using these data is in transportation analysis. The attributes associated with Digital Line Graphs can be used to determine the average travel times along each segment. Geographic information system functions can then be used to optimize routes through the network and to generate street name lists. Additional aspects of the subject are discussed.

Characterization and Identification of Cryptic Biopeptides in Carya illinoinensis (Wangenh K. Koch) Storage Proteins

PubMed Central

Gutiérrez-Vargas, Santiago; Pérez-Moreno, Luis; Ordoñez-Acevedo, Leandro G.

2017-01-01

The objective of this research was to identify and characterize the encoded peptides present in nut storage proteins of Carya illinoinensis. It was found, through in silico prediction, proteomic analysis, and MS spectrometry, that bioactive peptides were mainly found in albumin and glutelin fractions. Glutelin was the major fraction with ~53% of the nut storage proteins containing at least 21 peptides with different putative biological activities, including antihypertensives, antioxidants, immunomodulators, protease inhibitors, and inhibitors of cell cycle progression in cancer cells. Data showed that using 50 μg/mL tryptic digests of enriched peptides obtained from nut glutelins is able to induce up to 19% of apoptosis in both HeLa and CasKi cervical cancer cells. To our knowledge, this is the first report that shows the potential value of the nut-encoded peptides to be considered as adjuvants in cancer therapies. PMID:29279842

Virocell Metabolism: Metabolic Innovations During Host-Virus Interactions in the Ocean.

PubMed

Rosenwasser, Shilo; Ziv, Carmit; Creveld, Shiri Graff van; Vardi, Assaf

2016-10-01

Marine viruses are considered to be major ecological, evolutionary, and biogeochemical drivers of the marine environment, responsible for nutrient recycling and determining species composition. Viruses can re-shape their host's metabolic network during infection, generating the virocell-a unique metabolic state that supports their specific requirement. Here we discuss the concept of 'virocell metabolism' and its formation by rewiring of host-encoded metabolic networks, or by introducing virus-encoded auxiliary metabolic genes which provide the virocell with novel metabolic capabilities. The ecological role of marine viruses is commonly assessed by their relative abundance and phylogenetic diversity, lacking the ability to assess the dynamics of active viral infection. The new ability to define a unique metabolic state of the virocell will expand the current virion-centric approaches in order to quantify the impact of marine viruses on microbial food webs. Copyright © 2016. Published by Elsevier Ltd.

Reassigning stop codons via translation termination: How a few eukaryotes broke the dogma.

PubMed

Alkalaeva, Elena; Mikhailova, Tatiana

2017-03-01

The genetic code determines how amino acids are encoded within mRNA. It is universal among the vast majority of organisms, although several exceptions are known. Variant genetic codes are found in ciliates, mitochondria, and numerous other organisms. All revealed genetic codes (standard and variant) have at least one codon encoding a translation stop signal. However, recently two new genetic codes with a reassignment of all three stop codons were revealed in studies examining the protozoa transcriptomes. Here, we discuss this finding and the recent studies of variant genetic codes in eukaryotes. We consider the possible molecular mechanisms allowing the use of certain codons as sense and stop signals simultaneously. The results obtained by studying these amazing organisms represent a new and exciting insight into the mechanism of stop codon decoding in eukaryotes. Also see the video abstract here. © 2017 WILEY Periodicals, Inc.

Constitutional Epi/Genetic Conditions: Genetic, Epigenetic, and Environmental Factors

PubMed Central

Schenkel, Laila C.; Rodenhiser, David; Siu, Victoria; McCready, Elizabeth; Ainsworth, Peter; Sadikovic, Bekim

2016-01-01

There are more than 4,000 phenotypes for which the molecular basis is at least partly known. Though defects in primary DNA structure constitute a major cause of these disorders, epigenetic disruption is emerging as an important alternative mechanism in the etiology of a broad range of congenital and developmental conditions. These include epigenetic defects caused by either localized (in cis) genetic alterations or more distant (in trans) genetic events but can also include environmental effects. Emerging evidence suggests interplay between genetic and environmental factors in the epigenetic etiology of several constitutional “epi/genetic” conditions. This review summarizes our broadening understanding of how epigenetics contributes to pediatric disease by exploring different classes of epigenomic disorders. It further challenges the simplistic dogma of “DNA encodes RNA encodes protein” to best understand the spectrum of factors that can influence genetic traits in a pediatric population. PMID:28180025

Putative recombination events and evolutionary history of five economically important viruses of fruit trees based on coat protein-encoding gene sequence analysis.

PubMed

Boulila, Moncef

2010-06-01

To enhance the knowledge of recombination as an evolutionary process, 267 accessions retrieved from GenBank were investigated, all belonging to five economically important viruses infecting fruit crops (Plum pox, Apple chlorotic leaf spot, Apple mosaic, Prune dwarf, and Prunus necrotic ringspot viruses). Putative recombinational events were detected in the coat protein (CP)-encoding gene using RECCO and RDP version 3.31beta algorithms. Based on RECCO results, all five viruses were shown to contain potential recombination signals in the CP gene. Reconstructed trees with modified topologies were proposed. Furthermore, RECCO performed better than the RDP package in detecting recombination events and exhibiting their evolution rate along the sequences of the five viruses. RDP, however, provided the possible major and minor parents of the recombinants. Thus, the two methods should be considered complementary.

Planning-free cerebral blood flow territory mapping in patients with intracranial arterial stenosis

PubMed Central

Arteaga, Daniel F; Strother, Megan K; Davis, L Taylor; Fusco, Matthew R; Faraco, Carlos C; Roach, Brent A; Scott, Allison O

2016-01-01

A noninvasive method for quantifying cerebral blood flow and simultaneously visualizing cerebral blood flow territories is vessel-encoded pseudocontinuous arterial spin labeling MRI. However, obstacles to acquiring such information include limited access to the methodology in clinical centers and limited work on how clinically acquired vessel-encoded pseudocontinuous arterial spin labeling data correlate with gold-standard methods. The purpose of this work is to develop and validate a semiautomated pipeline for the online quantification of cerebral blood flow maps and cerebral blood flow territories from planning-free vessel-encoded pseudocontinuous arterial spin labeling MRI with gold-standard digital subtraction angiography. Healthy controls (n = 10) and intracranial atherosclerotic disease patients (n = 34) underwent 3.0 T MRI imaging including vascular (MR angiography) and hemodynamic (cerebral blood flow-weighted arterial spin labeling) MRI. Patients additionally underwent catheter and/or CT angiography. Variations in cross-territorial filling were grouped according to diameters of circle of Willis vessels in controls. In patients, Cohen’s k-statistics were computed to quantify agreement in perfusion patterns between vessel-encoded pseudocontinuous arterial spin labeling and angiography. Cross-territorial filling patterns were consistent with circle of Willis anatomy. The intraobserver Cohen's k-statistics for cerebral blood flow territory and digital subtraction angiography perfusion agreement were 0.730 (95% CI = 0.593–0.867; reader one) and 0.708 (95% CI = 0.561–0.855; reader two). These results support the feasibility of a semiautomated pipeline for evaluating major neurovascular cerebral blood flow territories in patients with intracranial atherosclerotic disease. PMID:27389177

Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida

PubMed Central

2012-01-01

Background Spot 42 was discovered in Escherichia coli nearly 40 years ago as an abundant, small and unstable RNA. Its biological role has remained obscure until recently, and is today implicated in having broader roles in the central and secondary metabolism. Spot 42 is encoded by the spf gene. The gene is ubiquitous in the Vibrionaceae family of gamma-proteobacteria. One member of this family, Aliivibrio salmonicida, causes cold-water vibriosis in farmed Atlantic salmon. Its genome encodes Spot 42 with 84% identity to E. coli Spot 42. Results We generated a A. salmonicida spf deletion mutant. We then used microarray and Northern blot analyses to monitor global effects on the transcriptome in order to provide insights into the biological roles of Spot 42 in this bacterium. In the presence of glucose, we found a surprisingly large number of ≥ 2X differentially expressed genes, and several major cellular processes were affected. A gene encoding a pirin-like protein showed an on/off expression pattern in the presence/absence of Spot 42, which suggests that Spot 42 plays a key regulatory role in the central metabolism by regulating the switch between fermentation and respiration. Interestingly, we discovered an sRNA named VSsrna24, which is encoded immediately downstream of spf. This new sRNA has an expression pattern opposite to that of Spot 42, and its expression is repressed by glucose. Conclusions We hypothesize that Spot 42 plays a key role in the central metabolism, in part by regulating the pyruvat dehydrogenase enzyme complex via pirin. PMID:22272603

Isolation and characterization of a cDNA encoding a heat shock protein 70 from a sterile mutant of Ulva pertusa (Ulvales, Chlorophyta).

PubMed

Tominaga, Hiroshi; Coury, Daniel Adam; Amano, Hideomi; Kakinuma, Makoto

2010-03-01

Synthesis and accumulation of molecular chaperones are universal responses found in all cellular organisms when exposed to a variety of unfavorable conditions. Heat shock protein 70 (Hsp70), which is one of the major classes of molecular chaperones, plays a particularly important role in cellular stress responses, and the Hsp70 system is the most intensely studied in higher plants and algae. Therefore, we isolated and characterized a cDNA clone encoding Hsp70 from a sterile strain of Ulva pertusa (Ulvales, Chlorophyta). The sterile U. pertusa Hsp70 (UpHsp70) cDNA consisted of 2,272 nucleotides and had an open reading frame encoding a polypeptide of 663 amino acid (AA) residues with a molecular mass of 71.7 kDa. Amino acid alignment and phylogenetic analysis of Hsp70s from other organisms showed that UpHsp70 was more similar to cytoplasmic Hsp70s from green algae and higher plants (> or =75%) than to those from other algae and microorganisms. Southern blot analysis indicated that the sterile U. pertusa genome had at least four cytoplasmic Hsp70-encoding genes. UpHsp70 mRNA levels were significantly affected by diurnal changes, rapidly increased by high-temperature stress, and gradually increased by exposure to copper, cadmium, and lead. These results suggest that UpHsp70 plays particularly important roles in adaptation to high-temperature conditions and diurnal changes, and is potentially involved in tolerance to heavy metal toxicity.

Changes in Purkinje cell simple spike encoding of reach kinematics during adaption to a mechanical perturbation.

PubMed

Hewitt, Angela L; Popa, Laurentiu S; Ebner, Timothy J

2015-01-21

The cerebellum is essential in motor learning. At the cellular level, changes occur in both the simple spike and complex spike firing of Purkinje cells. Because simple spike discharge reflects the main output of the cerebellar cortex, changes in simple spike firing likely reflect the contribution of the cerebellum to the adapted behavior. Therefore, we investigated in Rhesus monkeys how the representation of arm kinematics in Purkinje cell simple spike discharge changed during adaptation to mechanical perturbations of reach movements. Monkeys rapidly adapted to a novel assistive or resistive perturbation along the direction of the reach. Adaptation consisted of matching the amplitude and timing of the perturbation to minimize its effect on the reach. In a majority of Purkinje cells, simple spike firing recorded before and during adaptation demonstrated significant changes in position, velocity, and acceleration sensitivity. The timing of the simple spike representations change within individual cells, including shifts in predictive versus feedback signals. At the population level, feedback-based encoding of position increases early in learning and velocity decreases. Both timing changes reverse later in learning. The complex spike discharge was only weakly modulated by the perturbations, demonstrating that the changes in simple spike firing can be independent of climbing fiber input. In summary, we observed extensive alterations in individual Purkinje cell encoding of reach kinematics, although the movements were nearly identical in the baseline and adapted states. Therefore, adaption to mechanical perturbation of a reaching movement is accompanied by widespread modifications in the simple spike encoding. Copyright © 2015 the authors 0270-6474/15/351106-19$15.00/0.

Changes in Purkinje Cell Simple Spike Encoding of Reach Kinematics during Adaption to a Mechanical Perturbation

PubMed Central

Hewitt, Angela L.; Popa, Laurentiu S.

2015-01-01

The cerebellum is essential in motor learning. At the cellular level, changes occur in both the simple spike and complex spike firing of Purkinje cells. Because simple spike discharge reflects the main output of the cerebellar cortex, changes in simple spike firing likely reflect the contribution of the cerebellum to the adapted behavior. Therefore, we investigated in Rhesus monkeys how the representation of arm kinematics in Purkinje cell simple spike discharge changed during adaptation to mechanical perturbations of reach movements. Monkeys rapidly adapted to a novel assistive or resistive perturbation along the direction of the reach. Adaptation consisted of matching the amplitude and timing of the perturbation to minimize its effect on the reach. In a majority of Purkinje cells, simple spike firing recorded before and during adaptation demonstrated significant changes in position, velocity, and acceleration sensitivity. The timing of the simple spike representations change within individual cells, including shifts in predictive versus feedback signals. At the population level, feedback-based encoding of position increases early in learning and velocity decreases. Both timing changes reverse later in learning. The complex spike discharge was only weakly modulated by the perturbations, demonstrating that the changes in simple spike firing can be independent of climbing fiber input. In summary, we observed extensive alterations in individual Purkinje cell encoding of reach kinematics, although the movements were nearly identical in the baseline and adapted states. Therefore, adaption to mechanical perturbation of a reaching movement is accompanied by widespread modifications in the simple spike encoding. PMID:25609626

Role and Regulation of the Flp/Tad Pilus in the Virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193

PubMed Central

Nykyri, Johanna; Mattinen, Laura; Niemi, Outi; Adhikari, Satish; Kõiv, Viia; Somervuo, Panu; Fang, Xin; Auvinen, Petri; Mäe, Andres; Palva, E. Tapio; Pirhonen, Minna

2013-01-01

In this study, we characterized a putative Flp/Tad pilus-encoding gene cluster, and we examined its regulation at the transcriptional level and its role in the virulence of potato pathogenic enterobacteria of the genus Pectobacterium. The Flp/Tad pilus-encoding gene clusters in Pectobacterium atrosepticum, Pectobacterium wasabiae and Pectobacterium aroidearum were compared to previously characterized flp/tad gene clusters, including that of the well-studied Flp/Tad pilus model organism Aggregatibacter actinomycetemcomitans, in which this pilus is a major virulence determinant. Comparative analyses revealed substantial protein sequence similarity and open reading frame synteny between the previously characterized flp/tad gene clusters and the cluster in Pectobacterium, suggesting that the predicted flp/tad gene cluster in Pectobacterium encodes a Flp/Tad pilus-like structure. We detected genes for a novel two-component system adjacent to the flp/tad gene cluster in Pectobacterium, and mutant analysis demonstrated that this system has a positive effect on the transcription of selected Flp/Tad pilus biogenesis genes, suggesting that this response regulator regulate the flp/tad gene cluster. Mutagenesis of either the predicted regulator gene or selected Flp/Tad pilus biogenesis genes had a significant impact on the maceration ability of the bacterial strains in potato tubers, indicating that the Flp/Tad pilus-encoding gene cluster represents a novel virulence determinant in Pectobacterium. Soft-rot enterobacteria in the genera Pectobacterium and Dickeya are of great agricultural importance, and an investigation of the virulence of these pathogens could facilitate improvements in agricultural practices, thus benefiting farmers, the potato industry and consumers. PMID:24040039

Role and regulation of the Flp/Tad pilus in the virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193.

PubMed

Nykyri, Johanna; Mattinen, Laura; Niemi, Outi; Adhikari, Satish; Kõiv, Viia; Somervuo, Panu; Fang, Xin; Auvinen, Petri; Mäe, Andres; Palva, E Tapio; Pirhonen, Minna

2013-01-01

In this study, we characterized a putative Flp/Tad pilus-encoding gene cluster, and we examined its regulation at the transcriptional level and its role in the virulence of potato pathogenic enterobacteria of the genus Pectobacterium. The Flp/Tad pilus-encoding gene clusters in Pectobacterium atrosepticum, Pectobacterium wasabiae and Pectobacterium aroidearum were compared to previously characterized flp/tad gene clusters, including that of the well-studied Flp/Tad pilus model organism Aggregatibacter actinomycetemcomitans, in which this pilus is a major virulence determinant. Comparative analyses revealed substantial protein sequence similarity and open reading frame synteny between the previously characterized flp/tad gene clusters and the cluster in Pectobacterium, suggesting that the predicted flp/tad gene cluster in Pectobacterium encodes a Flp/Tad pilus-like structure. We detected genes for a novel two-component system adjacent to the flp/tad gene cluster in Pectobacterium, and mutant analysis demonstrated that this system has a positive effect on the transcription of selected Flp/Tad pilus biogenesis genes, suggesting that this response regulator regulate the flp/tad gene cluster. Mutagenesis of either the predicted regulator gene or selected Flp/Tad pilus biogenesis genes had a significant impact on the maceration ability of the bacterial strains in potato tubers, indicating that the Flp/Tad pilus-encoding gene cluster represents a novel virulence determinant in Pectobacterium. Soft-rot enterobacteria in the genera Pectobacterium and Dickeya are of great agricultural importance, and an investigation of the virulence of these pathogens could facilitate improvements in agricultural practices, thus benefiting farmers, the potato industry and consumers.

Identification of a second PAD1 in Brettanomyces bruxellensis LAMAP2480.

PubMed

González, Camila; Godoy, Liliana; Ganga, Ma Angélica

2017-02-01

Volatile phenols are aromatic compounds produced by some yeasts of the genus Brettanomyces as defense against the toxicity of hydroxycinnamic acids (p-coumaric acid, ferulic acid and caffeic acid). The origin of these compounds in winemaking involves the sequential action of two enzymes: coumarate decarboxylase and vinylphenol reductase. The first one converts hydroxycinnamic acids into hydroxystyrenes, which are then reduced to ethyl derivatives by vinylphenol reductase. Volatile phenols derived from p-coumaric acid (4-vinylphenol and 4-ethylphenol) have been described as the major contributors to self-defeating aromas associated with stable, gouache, wet mouse, etc., which generates large economic losses in the wine industry. The gene responsible for the production of 4-vinylphenol from p-coumaric acid has been identified as PAD1, which encodes a phenylacrylic acid decarboxylase. PAD1 has been described for many species, among them Candida albicans, Candida dubliniensis, Debaryomyces hansenii and Pichia anomala. In Brettanomyces bruxellensis LAMAP2480, a 666 bp reading frame (DbPAD) encodes a coumarate decarboxylase. Recent studies have reported the existence of a new reading frame belonging to DbPAD called DbPAD2 of 531 bp, which could encode a protein with similar enzymatic activity to PAD1. The present study confirmed that the transformation of Saccharomyces cerevisiae strain BY4722 with reading frame DbPAD2 under the control of the B. bruxellensis ACT1 promoter, encodes an enzyme with coumarate decarboxylase activity. This work has provided deeper insight into the origin of aroma defects in wine due to contamination by Brettanomyces spp.

Genes encoding major light-harvesting polypeptides are clustered on the genome of the cyanobacterium Fremyella diplosiphon.

PubMed Central

Conley, P B; Lemaux, P G; Lomax, T L; Grossman, A R

1986-01-01

The polypeptide composition of the phycobilisome, the major light-harvesting complex of prokaryotic cyanobacteria and certain eukaryotic algae, can be modulated by different light qualities in cyanobacteria exhibiting chromatic adaptation. We have identified genomic fragments encoding a cluster of phycobilisome polypeptides (phycobiliproteins) from the chromatically adapting cyanobacterium Fremyella diplosiphon using previously characterized DNA fragments of phycobiliprotein genes from the eukaryotic alga Cyanophora paradoxa and from F. diplosiphon. Characterization of two lambda-EMBL3 clones containing overlapping genomic fragments indicates that three sets of phycobiliprotein genes--the alpha- and beta-allophycocyanin genes plus two sets of alpha- and beta-phycocyanin genes--are clustered within 13 kilobases on the cyanobacterial genome and transcribed off the same strand. The gene order (alpha-allophycocyanin followed by beta-allophycocyanin and beta-phycocyanin followed by alpha-phycocyanin) appears to be a conserved arrangement found previously in a eukaryotic alga and another cyanobacterium. We have reported that one set of phycocyanin genes is transcribed as two abundant red light-induced mRNAs (1600 and 3800 bases). We now present data showing that the allophycocyanin genes and a second set of phycocyanin genes are transcribed into major mRNAs of 1400 and 1600 bases, respectively. These transcripts are present in RNA isolated from cultures grown in red and green light, although lower levels of the 1600-base phycocyanin transcript are present in cells grown in green light. Furthermore, a larger transcript of 1750 bases hybridizes to the allophycocyanin genes and may be a precursor to the 1400-base species. Images PMID:3086870

Screening of Metagenomic and Genomic Libraries Reveals Three Classes of Bacterial Enzymes That Overcome the Toxicity of Acrylate

PubMed Central

Curson, Andrew R. J.; Burns, Oliver J.; Voget, Sonja; Daniel, Rolf; Todd, Jonathan D.; McInnis, Kathryn; Wexler, Margaret; Johnston, Andrew W. B.

2014-01-01

Acrylate is produced in significant quantities through the microbial cleavage of the highly abundant marine osmoprotectant dimethylsulfoniopropionate, an important process in the marine sulfur cycle. Acrylate can inhibit bacterial growth, likely through its conversion to the highly toxic molecule acrylyl-CoA. Previous work identified an acrylyl-CoA reductase, encoded by the gene acuI, as being important for conferring on bacteria the ability to grow in the presence of acrylate. However, some bacteria lack acuI, and, conversely, many bacteria that may not encounter acrylate in their regular environments do contain this gene. We therefore sought to identify new genes that might confer tolerance to acrylate. To do this, we used functional screening of metagenomic and genomic libraries to identify novel genes that corrected an E. coli mutant that was defective in acuI, and was therefore hyper-sensitive to acrylate. The metagenomic libraries yielded two types of genes that overcame this toxicity. The majority encoded enzymes resembling AcuI, but with significant sequence divergence among each other and previously ratified AcuI enzymes. One other metagenomic gene, arkA, had very close relatives in Bacillus and related bacteria, and is predicted to encode an enoyl-acyl carrier protein reductase, in the same family as FabK, which catalyses the final step in fatty-acid biosynthesis in some pathogenic Firmicute bacteria. A genomic library of Novosphingobium, a metabolically versatile alphaproteobacterium that lacks both acuI and arkA, yielded vutD and vutE, two genes that, together, conferred acrylate resistance. These encode sequential steps in the oxidative catabolism of valine in a pathway in which, significantly, methacrylyl-CoA is a toxic intermediate. These findings expand the range of bacteria for which the acuI gene encodes a functional acrylyl-CoA reductase, and also identify novel enzymes that can similarly function in conferring acrylate resistance, likely, again, through the removal of the toxic product acrylyl-CoA. PMID:24848004

[Virulence determinant of Chromobacterium violaceum].

PubMed

Miki, Tsuyoshi

2014-01-01

Chromobacterium violaceum is a Gram-negative bacterium that infects humans and animals with fatal sepsis. The infection with C. violaceum is rare in case of those who are healthy, but once established, C. violaceum causes sever disease accompanied by abscess formation in the lungs, liver and spleen. Furthermore, C. violaceum is resistant to a broad range of antibiotics, which in some cases renders the antimicrobial therapy for this infection difficult. Thus, the infection with C. violaceum displays high mortality rates unless initial proper antimicrobial therapy. In contrast, the infection mechanism had completely remained unknown. To this end, we have tried to identify virulence factors-associated with C. violaceum infection. Two distinct type III secretion systems (TTSSs) were thought to be one of the most important virulence factors, which are encoded by Chromobacterium pathogenicity island 1/1a and 2 (Cpi-1/-1a and -2) respectively. Our results have shown that Cpi-1/-1a-encoded TTSS, but not Cpi-2, is indispensable for the virulence in a mouse infection model. C. violaceum caused fulminant hepatitis in a Cpi-1/-1a-encoded TTSS-dependent manner. We next have identified 16 novel effectors secreted from Cpi-1/-1a-encoded TTS machinery. From these effectors, we found that CopE (Chromobacterium outer protein E) has similarities to a guanine nucleotide exchange factor (GEF) for Rho GTPases. CopE acts as GEF for Rac1 and Cdc42, leading to induction of actin cytoskeletal rearrangement. Interestingly, C. violaceum invades cultured human epithelial cells in a CopE-dependent manner. Finally, an inactivation of CopE by disruption of copE gene or amino acid point mutation leading to loss of GEF activity attenuates significantly the mouse virulence of C. violaceum. These results suggest that Cpi-1/-1a-encoded TTSS is a major virulence determinant for C. violaceum infection, and that CopE contributes to the virulence in part of this pathogen.

"Triplet" polycistronic vectors encoding Gata4, Mef2c, and Tbx5 enhances postinfarct ventricular functional improvement compared with singlet vectors.

PubMed

Mathison, Megumi; Singh, Vivek P; Gersch, Robert P; Ramirez, Maricela O; Cooney, Austin; Kaminsky, Stephen M; Chiuchiolo, Maria J; Nasser, Ahmed; Yang, Jianchang; Crystal, Ronald G; Rosengart, Todd K

2014-10-01

The in situ reprogramming of cardiac fibroblasts into induced cardiomyocytes by the administration of gene transfer vectors encoding Gata4 (G), Mef2c (M), and Tbx5 (T) has been shown to improve ventricular function in myocardial infarction models. The efficacy of this strategy could, however, be limited by the need for fibroblast targets to be infected 3 times--once by each of the 3 transgene vectors. We hypothesized that a polycistronic "triplet" vector encoding all 3 transgenes would enhance postinfarct ventricular function compared with use of "singlet" vectors. After validation of the polycistronic vector expression in vitro, adult male Fischer 344 rats (n=6) underwent coronary ligation with or without intramyocardial administration of an adenovirus encoding all 3 major vascular endothelial growth factor (VEGF) isoforms (AdVEGF-All6A positive), followed 3 weeks later by the administration to AdVEGF-All6A-positive treated rats of singlet lentivirus encoding G, M, or T (1×10(5) transducing units each) or the same total dose of a GMT "triplet" lentivirus vector. Western blots demonstrated that triplet and singlet vectors yielded equivalent GMT transgene expression, and fluorescence activated cell sorting demonstrated that triplet vectors were nearly twice as potent as singlet vectors in generating induced cardiomyocytes from cardiac fibroblasts. Echocardiography demonstrated that GMT triplet vectors were more effective than the 3 combined singlet vectors in enhancing ventricular function from postinfarct baselines (triplet, 37%±10%; singlet, 13%±7%; negative control, 9%±5%; P<.05). These data have confirmed that the in situ administration of G, M, and T induces postinfarct ventricular functional improvement and that GMT polycistronic vectors enhance the efficacy of this strategy. Copyright © 2014 The American Association for Thoracic Surgery. Published by Elsevier Inc. All rights reserved.

Weak reward source memory in depression reflects blunted activation of VTA/SN and parahippocampus

PubMed Central

Dobbins, Ian G.; Pizzagalli, Diego A.

2014-01-01

Reward responses in the medial temporal lobes and dopaminergic midbrain boost episodic memory formation in healthy adults, and weak memory for emotionally positive material in depression suggests this mechanism may be dysfunctional in major depressive disorder (MDD). To test this hypothesis, we performed a study in which unmedicated adults with MDD and healthy controls encoded drawings paired with reward or zero tokens during functional magnetic resonance imaging. In a recognition test, participants judged whether drawings were previously associated with the reward token (‘reward source’) or the zero token (‘zero source’). Unlike controls, depressed participants failed to show better memory for drawings from the reward source vs the zero source. Consistent with predictions, controls also showed a stronger encoding response to reward tokens vs zero tokens in the right parahippocampus and dopaminergic midbrain, whereas the MDD group showed the opposite pattern—stronger responses to zero vs reward tokens—in these regions. Differential activation of the dopaminergic midbrain by reward vs zero tokens was positively correlated with the reward source memory advantage in controls, but not depressed participants. These data suggest that weaker memory for positive material in depression reflects blunted encoding responses in the dopaminergic midbrain and medial temporal lobes. PMID:24078019

Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion

PubMed Central

Brüssow, Harald; Canchaya, Carlos; Hardt, Wolf-Dietrich

2004-01-01

Comparative genomics demonstrated that the chromosomes from bacteria and their viruses (bacteriophages) are coevolving. This process is most evident for bacterial pathogens where the majority contain prophages or phage remnants integrated into the bacterial DNA. Many prophages from bacterial pathogens encode virulence factors. Two situations can be distinguished: Vibrio cholerae, Shiga toxin-producing Escherichia coli, Corynebacterium diphtheriae, and Clostridium botulinum depend on a specific prophage-encoded toxin for causing a specific disease, whereas Staphylococcus aureus, Streptococcus pyogenes, and Salmonella enterica serovar Typhimurium harbor a multitude of prophages and each phage-encoded virulence or fitness factor makes an incremental contribution to the fitness of the lysogen. These prophages behave like “swarms” of related prophages. Prophage diversification seems to be fueled by the frequent transfer of phage material by recombination with superinfecting phages, resident prophages, or occasional acquisition of other mobile DNA elements or bacterial chromosomal genes. Prophages also contribute to the diversification of the bacterial genome architecture. In many cases, they actually represent a large fraction of the strain-specific DNA sequences. In addition, they can serve as anchoring points for genome inversions. The current review presents the available genomics and biological data on prophages from bacterial pathogens in an evolutionary framework. PMID:15353570

Mutations in GLDN, Encoding Gliomedin, a Critical Component of the Nodes of Ranvier, Are Responsible for Lethal Arthrogryposis.

PubMed

Maluenda, Jérôme; Manso, Constance; Quevarec, Loic; Vivanti, Alexandre; Marguet, Florent; Gonzales, Marie; Guimiot, Fabien; Petit, Florence; Toutain, Annick; Whalen, Sandra; Grigorescu, Romulus; Coeslier, Anne Dieux; Gut, Marta; Gut, Ivo; Laquerrière, Annie; Devaux, Jérôme; Melki, Judith

2016-10-06

Arthrogryposis multiplex congenita (AMC) is a developmental condition characterized by multiple joint contractures resulting from reduced or absent fetal movements. Through linkage analysis, homozygosity mapping, and exome sequencing in four unrelated families affected by lethal AMC, we identified biallelic mutations in GLDN in the affected individuals. GLDN encodes gliomedin, a secreted cell adhesion molecule involved in the formation of the nodes of Ranvier. Transmission electron microscopy of the sciatic nerve from one of the affected individuals showed a marked lengthening defect of the nodes. The GLDN mutations found in the affected individuals abolish the cell surface localization of gliomedin and its interaction with its axonal partner, neurofascin-186 (NF186), in a cell-based assay. The axoglial contact between gliomedin and NF186 is essential for the initial clustering of Na + channels at developing nodes. These results indicate a major role of gliomedin in node formation and the development of the peripheral nervous system in humans. These data indicate that mutations of GLDN or CNTNAP1 (MIM: 616286), encoding essential components of the nodes of Ranvier and paranodes, respectively, lead to inherited nodopathies, a distinct disease entity among peripheral neuropathies. Copyright © 2016 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Capturing novel mouse genes encoding chromosomal and other nuclear proteins.

PubMed

Tate, P; Lee, M; Tweedie, S; Skarnes, W C; Bickmore, W A

1998-09-01

The burgeoning wealth of gene sequences contrasts with our ignorance of gene function. One route to assigning function is by determining the sub-cellular location of proteins. We describe the identification of mouse genes encoding proteins that are confined to nuclear compartments by splicing endogeneous gene sequences to a promoterless betageo reporter, using a gene trap approach. Mouse ES (embryonic stem) cell lines were identified that express betageo fusions located within sub-nuclear compartments, including chromosomes, the nucleolus and foci containing splicing factors. The sequences of 11 trapped genes were ascertained, and characterisation of endogenous protein distribution in two cases confirmed the validity of the approach. Three novel proteins concentrated within distinct chromosomal domains were identified, one of which appears to be a serine/threonine kinase. The sequence of a gene whose product co-localises with splicesome components suggests that this protein may be an E3 ubiquitin-protein ligase. The majority of the other genes isolated represent novel genes. This approach is shown to be a powerful tool for identifying genes encoding novel proteins with specific sub-nuclear localisations and exposes our ignorance of the protein composition of the nucleus. Motifs in two of the isolated genes suggest new links between cellular regulatory mechanisms (ubiquitination and phosphorylation) and mRNA splicing and chromosome structure/function.

Osteocyte calcium signals encode strain magnitude and loading frequency in vivo.

PubMed

Lewis, Karl J; Frikha-Benayed, Dorra; Louie, Joyce; Stephen, Samuel; Spray, David C; Thi, Mia M; Seref-Ferlengez, Zeynep; Majeska, Robert J; Weinbaum, Sheldon; Schaffler, Mitchell B

2017-10-31

Osteocytes are considered to be the major mechanosensory cells of bone, but how osteocytes in vivo process, perceive, and respond to mechanical loading remains poorly understood. Intracellular calcium (Ca 2+ ) signaling resulting from mechanical stimulation has been widely studied in osteocytes in vitro and in bone explants, but has yet to be examined in vivo. This is achieved herein by using a three-point bending device which is capable of delivering well-defined mechanical loads to metatarsal bones of living mice while simultaneously monitoring the intracellular Ca 2+ responses of individual osteocytes by using a genetically encoded fluorescent Ca 2+ indicator. Osteocyte responses are imaged by using multiphoton fluorescence microscopy. We investigated the in vivo responses of osteocytes to strains ranging from 250 to 3,000 [Formula: see text] and frequencies from 0.5 to 2 Hz, which are characteristic of physiological conditions reported for bone. At all loading frequencies examined, the number of responding osteocytes increased strongly with applied strain magnitude. However, Ca 2+ intensity within responding osteocytes did not change significantly with physiological loading magnitudes. Our studies offer a glimpse into how these critical bone cells respond to mechanical load in vivo, as well as provide a technique to determine how the cells encode magnitude and frequency of loading. Published under the PNAS license.

Histoplasma capsulatum Encodes a Dipeptidyl Peptidase Active against the Mammalian Immunoregulatory Peptide, Substance P

PubMed Central

Cooper, Kendal G.; Zarnowski, Robert; Woods, Jon P.

2009-01-01

The pathogenic fungus Histoplasma capsulatum secretes dipeptidyl peptidase (Dpp) IV enzyme activity and has two putative DPPIV homologs (HcDPPIVA and HcDPPIVB). We previously showed that HcDPPIVB is the gene responsible for the majority of secreted DppIV activity in H. capsulatum culture supernatant, while we could not detect any functional contribution from HcDPPIVA. In order to determine whether HcDPPIVA encodes a functional DppIV enzyme, we expressed HcDPPIVA in Pichia pastoris and purified the recombinant protein. The recombinant enzyme cleaved synthetic DppIV substrates and had similar biochemical properties to other described DppIV enzymes, with temperature and pH optima of 42°C and 8, respectively. Recombinant HcDppIVA cleaved the host immunoregulatory peptide substance P, indicating the enzyme has the potential to affect the immune response during infection. Expression of HcDPPIVA under heterologous regulatory sequences in H. capsulatum resulted in increased secreted DppIV activity, indicating that the encoded protein can be expressed and secreted by its native organism. However, HcDPPIVA was not required for virulence in a murine model of histoplasmosis. This work reports a fungal enzyme that can function to cleave the immunomodulatory host peptide substance P. PMID:19384411

The C. elegans ceh-36 gene encodes a putative homemodomain transcription factor involved in chemosensory functions of ASE and AWC neurons.

PubMed

Koga, Makoto; Ohshima, Yasumi

2004-02-20

Chemotaxis to water-soluble chemicals such as sodium ion is an important behavior of Caenorhabditis elegans for seeking food, and ASE chemosensory neurons have a major role in this behavior. We isolated mutants defective in chemotaxis to sodium acetate. We show here that among them ks86 had a mutation in the ceh-36 gene. ceh-36 :: gfp reporter constructs were expressed in ASE and AWC neurons. In a mutant of the che-1 gene, which encodes another transcription factor and is required for specification of ASE neurons, expression of the ceh-36 :: gfp reporter in ASE is lost. This indicates that the ceh-36 gene functions downstream of the che-1 gene in ASE. In the ceh-36(ks86) mutant, expression of the tax-2 gene encoding a cyclic nucleotide-gated channel was reduced in ASE and AWC. This affords an explanation for defects of the ceh-36 mutant in the chemotaxis mediated by ASE and AWC. When a ceh-36 cDNA was expressed in an adult ceh-36 mutant by a heat shock promoter, chemotaxis to sodium acetate was recovered. These results suggest that ceh-36 is required for functions, and not for development, of ASE.

Only One of the Five Ralstonia solanacearum Long-Chain 3-Ketoacyl-Acyl Carrier Protein Synthase Homologues Functions in Fatty Acid Synthesis

PubMed Central

Cheng, Juanli; Ma, Jincheng; Lin, Jinshui; Fan, Zhen-Chuan; Cronan, John E.

2012-01-01

Ralstonia solanacearum, a major phytopathogenic bacterium, causes a bacterial wilt disease in diverse plants. Although fatty acid analyses of total membranes of R. solanacearum showed that they contain primarily palmitic (C16:0), palmitoleic (C16:1) and cis-vaccenic (C18:1) acids, little is known regarding R. solanacearum fatty acid synthesis. The R. solanacearum GMI1000 genome is unusual in that it contains four genes (fabF1, fabF2, fabF3, and fabF4) annotated as encoding 3-ketoacyl-acyl carrier protein synthase II homologues and one gene (fabB) annotated as encoding 3-ketoacyl-acyl carrier protein synthase I. We have analyzed this puzzling apparent redundancy and found that only one of these genes, fabF1, encoded a long-chain 3-ketoacyl-acyl carrier protein synthase, whereas the other homologues did not play roles in R. solanacearum fatty acid synthesis. Mutant strains lacking fabF1 are nonviable, and thus, FabF1 is essential for R. solanacearum fatty acid biosynthesis. Moreover, R. solanacearum FabF1 has the activities of both 3-ketoacyl-acyl carrier protein synthase II and 3-ketoacyl-acyl carrier protein synthase I. PMID:22194290

Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data.

PubMed

Li, Ruichao; Xie, Miaomiao; Dong, Ning; Lin, Dachuan; Yang, Xuemei; Wong, Marcus Ho Yin; Chan, Edward Wai-Chi; Chen, Sheng

2018-03-01

Multidrug resistance (MDR)-encoding plasmids are considered major molecular vehicles responsible for transmission of antibiotic resistance genes among bacteria of the same or different species. Delineating the complete sequences of such plasmids could provide valuable insight into the evolution and transmission mechanisms underlying bacterial antibiotic resistance development. However, due to the presence of multiple repeats of mobile elements, complete sequencing of MDR plasmids remains technically complicated, expensive, and time-consuming. Here, we demonstrate a rapid and efficient approach to obtaining multiple MDR plasmid sequences through the use of the MinION nanopore sequencing platform, which is incorporated in a portable device. By assembling the long sequencing reads generated by a single MinION run according to a rapid barcoding sequencing protocol, we obtained the complete sequences of 20 plasmids harbored by multiple bacterial strains. Importantly, single long reads covering a plasmid end-to-end were recorded, indicating that de novo assembly may be unnecessary if the single reads exhibit high accuracy. This workflow represents a convenient and cost-effective approach for systematic assessment of MDR plasmids responsible for treatment failure of bacterial infections, offering the opportunity to perform detailed molecular epidemiological studies to probe the evolutionary and transmission mechanisms of MDR-encoding elements.

QR-decomposition based SENSE reconstruction using parallel architecture.

PubMed

Ullah, Irfan; Nisar, Habab; Raza, Haseeb; Qasim, Malik; Inam, Omair; Omer, Hammad

2018-04-01

Magnetic Resonance Imaging (MRI) is a powerful medical imaging technique that provides essential clinical information about the human body. One major limitation of MRI is its long scan time. Implementation of advance MRI algorithms on a parallel architecture (to exploit inherent parallelism) has a great potential to reduce the scan time. Sensitivity Encoding (SENSE) is a Parallel Magnetic Resonance Imaging (pMRI) algorithm that utilizes receiver coil sensitivities to reconstruct MR images from the acquired under-sampled k-space data. At the heart of SENSE lies inversion of a rectangular encoding matrix. This work presents a novel implementation of GPU based SENSE algorithm, which employs QR decomposition for the inversion of the rectangular encoding matrix. For a fair comparison, the performance of the proposed GPU based SENSE reconstruction is evaluated against single and multicore CPU using openMP. Several experiments against various acceleration factors (AFs) are performed using multichannel (8, 12 and 30) phantom and in-vivo human head and cardiac datasets. Experimental results show that GPU significantly reduces the computation time of SENSE reconstruction as compared to multi-core CPU (approximately 12x speedup) and single-core CPU (approximately 53x speedup) without any degradation in the quality of the reconstructed images. Copyright © 2018 Elsevier Ltd. All rights reserved.

Wavelet-based Encoding Scheme for Controlling Size of Compressed ECG Segments in Telecardiology Systems.

PubMed

Al-Busaidi, Asiya M; Khriji, Lazhar; Touati, Farid; Rasid, Mohd Fadlee; Mnaouer, Adel Ben

2017-09-12

One of the major issues in time-critical medical applications using wireless technology is the size of the payload packet, which is generally designed to be very small to improve the transmission process. Using small packets to transmit continuous ECG data is still costly. Thus, data compression is commonly used to reduce the huge amount of ECG data transmitted through telecardiology devices. In this paper, a new ECG compression scheme is introduced to ensure that the compressed ECG segments fit into the available limited payload packets, while maintaining a fixed CR to preserve the diagnostic information. The scheme automatically divides the ECG block into segments, while maintaining other compression parameters fixed. This scheme adopts discrete wavelet transform (DWT) method to decompose the ECG data, bit-field preserving (BFP) method to preserve the quality of the DWT coefficients, and a modified running-length encoding (RLE) scheme to encode the coefficients. The proposed dynamic compression scheme showed promising results with a percentage packet reduction (PR) of about 85.39% at low percentage root-mean square difference (PRD) values, less than 1%. ECG records from MIT-BIH Arrhythmia Database were used to test the proposed method. The simulation results showed promising performance that satisfies the needs of portable telecardiology systems, like the limited payload size and low power consumption.

Antimicrobial properties of cultivable bacteria associated with seaweeds in the Gulf of Mannar on the southeast coast of India.

PubMed

Thilakan, B; Chakraborty, K; Chakraborty, R D

2016-08-01

In this study, 234 bacterial strains were isolated from 7 seaweed species in the Gulf of Mannar on the southeast coast of India. The strains having consistent antimicrobial activity were chosen for further studies, and this constituted about 9.8% of the active strains isolated. Phylogenetic analysis using 16S rDNA sequencing with the help of classical biochemical identification indicated the existence of 2 major phyla, Firmicutes and Proteobacteria. Antimicrobial activity analysis combined with the results of amplifying genes encoding for polyketide synthetase and nonribosomal peptide synthetase showed that seaweed-associated bacteria had broad-spectrum antimicrobial activity. These epibionts might be beneficial to seaweeds by limiting or preventing the development of competing or fouling bacteria. Phylogenetic analysis of ketosynthase (KS) regions with respect to the diverse range of KS domains showed that the KS domains from the candidate isolates were of Type I. The bacterial cultures retained their antimicrobial activities after plasmid curing, which further suggested that the antimicrobial activity of these isolates was not encoded by plasmid, and the genes encoding the antimicrobial product might be present within the genome. Seaweed-associated bacteria with potential antimicrobial activity suggested that the seaweed species are an ideal ecological niche harboring specific bacterial diversity representing a largely underexplored source of antimicrobial secondary metabolites.

Characterization and expression of genes encoding three small heat shock proteins in Sesamia inferens (Lepidoptera: Noctuidae).

PubMed

Sun, Meng; Lu, Ming-Xing; Tang, Xiao-Tian; Du, Yu-Zhou

2014-12-12

The pink stem borer, Sesamia inferens (Walker), is a major pest of rice and is endemic in China and other parts of Asia. Small heat shock proteins (sHSPs) encompass a diverse, widespread class of stress proteins that have not been characterized in S. inferens. In the present study, we isolated and characterized three S. inferens genes that encode members of the α-crystallin/sHSP family, namely, Sihsp21.4, Sihsp20.6, and Sihsp19.6. The three cDNAs encoded proteins of 187, 183 and 174 amino acids with calculated molecular weights of 21.4, 20.6 and 19.6 kDa, respectively. The deduced amino acid sequences of the three genes showed strong similarity to sHSPs identified in other lepidopteran insects. Sihsp21.4 contained an intron, but Sihsp20.6 and Sihsp19.6 lacked introns. Real-time quantitative PCR analyses revealed that Sihsp21.4 was most strongly expressed in S. inferens heads; Whereas expression of Sihsp20.6 and Sihsp19.6 was highest in eggs. The three S. inferens sHSP genes were up-regulated during low temperature stress. In summary, our results show that S. inferens sHSP genes have distinct regulatory roles in the physiology of S. inferens.

Characterization and Expression of Genes Encoding Three Small Heat Shock Proteins in Sesamia inferens (Lepidoptera: Noctuidae)

PubMed Central

Sun, Meng; Lu, Ming-Xing; Tang, Xiao-Tian; Du, Yu-Zhou

2014-01-01

The pink stem borer, Sesamia inferens (Walker), is a major pest of rice and is endemic in China and other parts of Asia. Small heat shock proteins (sHSPs) encompass a diverse, widespread class of stress proteins that have not been characterized in S. inferens. In the present study, we isolated and characterized three S. inferens genes that encode members of the α-crystallin/sHSP family, namely, Sihsp21.4, Sihsp20.6, and Sihsp19.6. The three cDNAs encoded proteins of 187, 183 and 174 amino acids with calculated molecular weights of 21.4, 20.6 and 19.6 kDa, respectively. The deduced amino acid sequences of the three genes showed strong similarity to sHSPs identified in other lepidopteran insects. Sihsp21.4 contained an intron, but Sihsp20.6 and Sihsp19.6 lacked introns. Real-time quantitative PCR analyses revealed that Sihsp21.4 was most strongly expressed in S. inferens heads; Whereas expression of Sihsp20.6 and Sihsp19.6 was highest in eggs. The three S. inferens sHSP genes were up-regulated during low temperature stress. In summary, our results show that S. inferens sHSP genes have distinct regulatory roles in the physiology of S. inferens. PMID:25514417

A Single IGF1 Allele Is a Major Determinant of Small Size in Dogs

PubMed Central

Sutter, Nathan B.; Bustamante, Carlos D.; Chase, Kevin; Gray, Melissa M.; Zhao, Keyan; Zhu, Lan; Padhukasahasram, Badri; Karlins, Eric; Davis, Sean; Jones, Paul G.; Quignon, Pascale; Johnson, Gary S.; Parker, Heidi G.; Fretwell, Neale; Mosher, Dana S.; Lawler, Dennis F.; Satyaraj, Ebenezer; Nordborg, Magnus; Lark, K. Gordon; Wayne, Robert K.; Ostrander, Elaine A.

2009-01-01

The domestic dog exhibits greater diversity in body size than any other terrestrial vertebrate. We used a strategy that exploits the breed structure of dogs to investigate the genetic basis of size. First, through a genome-wide scan, we identified a major quantitative trait locus (QTL) on chromosome 15 influencing size variation within a single breed. Second, we examined genetic variation in the 15-megabase interval surrounding the QTL in small and giant breeds and found marked evidence for a selective sweep spanning a single gene (IGF1), encoding insulin-like growth factor 1. A single IGF1 single-nucleotide polymorphism haplotype is common to all small breeds and nearly absent from giant breeds, suggesting that the same causal sequence variant is a major contributor to body size in all small dogs. PMID:17412960

A single IGF1 allele is a major determinant of small size in dogs.

PubMed

Sutter, Nathan B; Bustamante, Carlos D; Chase, Kevin; Gray, Melissa M; Zhao, Keyan; Zhu, Lan; Padhukasahasram, Badri; Karlins, Eric; Davis, Sean; Jones, Paul G; Quignon, Pascale; Johnson, Gary S; Parker, Heidi G; Fretwell, Neale; Mosher, Dana S; Lawler, Dennis F; Satyaraj, Ebenezer; Nordborg, Magnus; Lark, K Gordon; Wayne, Robert K; Ostrander, Elaine A

2007-04-06

The domestic dog exhibits greater diversity in body size than any other terrestrial vertebrate. We used a strategy that exploits the breed structure of dogs to investigate the genetic basis of size. First, through a genome-wide scan, we identified a major quantitative trait locus (QTL) on chromosome 15 influencing size variation within a single breed. Second, we examined genetic variation in the 15-megabase interval surrounding the QTL in small and giant breeds and found marked evidence for a selective sweep spanning a single gene (IGF1), encoding insulin-like growth factor 1. A single IGF1 single-nucleotide polymorphism haplotype is common to all small breeds and nearly absent from giant breeds, suggesting that the same causal sequence variant is a major contributor to body size in all small dogs.

Two-Component System RgfA/C Activates the fbsB Gene Encoding Major Fibrinogen-Binding Protein in Highly Virulent CC17 Clone Group B Streptococcus

PubMed Central

Safadi, Rim Al; Mereghetti, Laurent; Salloum, Mazen; Lartigue, Marie-Frédérique; Virlogeux-Payant, Isabelle; Quentin, Roland; Rosenau, Agnès

2011-01-01

Group B streptococcus (GBS) strains with the highest ability to bind to human fibrinogen belong to the highly invasive clonal complex (CC) 17. To investigate the fibrinogen-binding mechanisms of CC17 strains, we determined the prevalence of fibrinogen-binding genes (fbsA and fbsB), and fbs regulator genes (rogB encoding an fbsA activator, rovS encoding an fbsA repressor and rgf encoding a two-component system [TCS] whose role on fbs genes was not determined yet) in a collection of 134 strains representing the major CCs of the species. We showed that specific gene combinations were related to particular CCs; only CC17 strains contained the fbsA, fbsB, and rgf genes combination. Non polar rgfAC deletion mutants of three CC17 serotype III strains were constructed. They showed a 3.2- to 5.1-fold increase of fbsA transcripts, a 4.8- to 6.7-fold decrease of fbsB transcripts, and a 52% to 68% decreased fibrinogen-binding ability, demonstrating that the RgfA/RgfC TCS inhibits the fbsA gene and activates the fbsB gene. The relative contribution of the two fbs genes in fibrinogen-binding ability was determined by constructing isogenic fbsA, fbsB, deletion mutants of the three CC17 strains. The ability to bind to fibrinogen was reduced by 49% to 57% in ΔfbsA mutants, and by 78% to 80% in ΔfbsB mutants, suggesting that FbsB protein plays a greater role in the fibrinogen-binding ability of CC17 strains. Moreover, the relative transcription level of fbsB gene was 9.2- to 12.7-fold higher than that of fbsA gene for the three wild type strains. Fibrinogen-binding ability could be restored by plasmid-mediated expression of rgfAC, fbsA, and fbsB genes in the corresponding deletion mutants. Thus, our results demonstrate that a specific combination of fbs genes and fbs regulator genes account for the high fibrinogen-binding ability of CC17 strains that may participate to their enhanced invasiveness for neonates as compared to strains of other CCs. PMID:21326613

Unbiased View of Synaptic and Neuronal Gene Complement in Ctenophores: Are There Pan-neuronal and Pan-synaptic Genes across Metazoa?

PubMed

Moroz, Leonid L; Kohn, Andrea B

2015-12-01

Hypotheses of origins and evolution of neurons and synapses are controversial, mostly due to limited comparative data. Here, we investigated the genome-wide distribution of the bilaterian "synaptic" and "neuronal" protein-coding genes in non-bilaterian basal metazoans (Ctenophora, Porifera, Placozoa, and Cnidaria). First, there are no recognized genes uniquely expressed in neurons across all metazoan lineages. None of the so-called pan-neuronal genes such as embryonic lethal abnormal vision (ELAV), Musashi, or Neuroglobin are expressed exclusively in neurons of the ctenophore Pleurobrachia. Second, our comparative analysis of about 200 genes encoding canonical presynaptic and postsynaptic proteins in bilaterians suggests that there are no true "pan-synaptic" genes or genes uniquely and specifically attributed to all classes of synapses. The majority of these genes encode receptive and secretory complexes in a broad spectrum of eukaryotes. Trichoplax (Placozoa) an organism without neurons and synapses has more orthologs of bilaterian synapse-related/neuron-related genes than do ctenophores-the group with well-developed neuronal and synaptic organization. Third, the majority of genes encoding ion channels and ionotropic receptors are broadly expressed in unicellular eukaryotes and non-neuronal tissues in metazoans. Therefore, they cannot be viewed as neuronal markers. Nevertheless, the co-expression of multiple types of ion channels and receptors does correlate with the presence of neural and synaptic organization. As an illustrative example, the ctenophore genomes encode a greater diversity of ion channels and ionotropic receptors compared with the genomes of the placozoan Trichoplax and the demosponge Amphimedon. Surprisingly, both placozoans and sponges have a similar number of orthologs of "synaptic" proteins as we identified in the genomes of two ctenophores. Ctenophores have a distinct synaptic organization compared with other animals. Our analysis of transcriptomes from 10 different ctenophores did not detect recognized orthologs of synthetic enzymes encoding several classical, low-molecular-weight (neuro)transmitters; glutamate signaling machinery is one of the few exceptions. Novel peptidergic signaling molecules were predicted for ctenophores, together with the diversity of putative receptors including SCNN1/amiloride-sensitive sodium channel-like channels, many of which could be examples of a lineage-specific expansion within this group. In summary, our analysis supports the hypothesis of independent evolution of neurons and, as corollary, a parallel evolution of synapses. We suggest that the formation of synaptic machinery might occur more than once over 600 million years of animal evolution. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Self-registering spread-spectrum barcode method

DOEpatents

Cummings, Eric B.; Even Jr., William R.

2004-11-09

A novel spread spectrum barcode methodology is disclosed that allows a barcode to be read in its entirety even when a significant fraction or majority of the barcode is obscured. The barcode methodology makes use of registration or clocking information that is distributed along with the encoded user data across the barcode image. This registration information allows for the barcode image to be corrected for imaging distortion such as zoom, rotation, tilt, curvature, and perspective.

Is slack an intrinsic seizure terminator?

PubMed

Igelström, Kajsa M

2013-06-01

Understanding how epileptic seizures are initiated and propagated across large brain networks is difficult, but an even greater mystery is what makes them stop. Failure of spontaneous seizure termination leads to status epilepticus-a state of uninterrupted seizure activity that can cause death or permanent brain damage. Global factors, like changes in neuromodulators and ion concentrations, are likely to play major roles in spontaneous seizure cessation, but individual neurons also have intrinsic active ion currents that may contribute. The recently discovered gene Slack encodes a sodium-activated potassium channel that mediates a major proportion of the outward current in many neurons. Although given little attention, the current flowing through this channel may have properties consistent with a role in seizure termination.

Countermeasure development for Rift Valley fever: deletion, modification or targeting of major virulence factor NSs.

PubMed

Lihoradova, Olga; Ikegami, Tetsuro

2014-01-01

Rift Valley fever (RVF) is a mosquito-borne zoonotic disease characterized by a high rate of abortion in ruminants, and febrile illness, hemorrhagic fever, retinitis and encephalitis in humans. RVF is caused by the RVF virus (RVFV), belonging to the genus Phlebovirus of the family Bunyaviridae . RVFV encodes a major virulence factor, NSs , which is dispensable for viral replication, yet required for evasion of host innate immune responses. RVFV NSs inhibits host gene upregulation at the transcriptional level, while promoting viral translation in the cytoplasm. In this article, we summarize the virology and pathology of RVF, and countermeasure development for RVF, with emphasis on NSs function and applications.

Countermeasure development for Rift Valley fever: deletion, modification or targeting of major virulence factor NSs

PubMed Central

Lihoradova, Olga; Ikegami, Tetsuro

2014-01-01

Rift Valley fever (RVF) is a mosquito-borne zoonotic disease characterized by a high rate of abortion in ruminants, and febrile illness, hemorrhagic fever, retinitis and encephalitis in humans. RVF is caused by the RVF virus (RVFV), belonging to the genus Phlebovirus of the family Bunyaviridae. RVFV encodes a major virulence factor, NSs, which is dispensable for viral replication, yet required for evasion of host innate immune responses. RVFV NSs inhibits host gene upregulation at the transcriptional level, while promoting viral translation in the cytoplasm. In this article, we summarize the virology and pathology of RVF, and countermeasure development for RVF, with emphasis on NSs function and applications. PMID:24910709

NMDA Receptors Regulate Genes Responsible for Major Immune Functions of Mononuclears in Human Peripheral Blood.

PubMed

Kuzmina, U Sh; Zainullina, L F; Sadovnikov, S V; Vakhitov, V A; Vakhitova, Yu V

2018-06-19

To determine the role of NMDA receptors in the functional regulation of immunocompetent cells, comparative assay was carried out for genes expressed in the mononuclears in peripheral blood of healthy persons under normal conditions and after blockade of these receptors. The genes, whose expression changed in response to blockade of NMDA receptors in mononuclears, encode the products involved in regulation of the major functions of immune cells, such as proliferation (IL4, VCAM1, and CDKN2A), apoptosis (BAX, MYC, CDKN2A, HSPB1, and CADD45A), activation (IL4R, IL4, VCAM1, and CDKN2A), and differentiation (IL4, VCAM1, and BAX).

Clostridium difficile infection: New insights into therapeutic options.

PubMed

Kachrimanidou, Melina; Sarmourli, Theopisti; Skoura, Lemonia; Metallidis, Symeon; Malisiovas, Nikolaos

2016-09-01

Clostridium difficile infection (CDI) is an important cause of mortality and morbidity in healthcare settings and represents a major social and economic burden. The major virulence determinants are large clostridial toxins, toxin A (TcdA) and toxin B (TcdB), encoded within the pathogenicity locus. Traditional therapies, such as metronidazole and vancomycin, frequently lead to a vicious circle of recurrences due to their action against normal human microbiome. New disease management strategies together with the development of novel therapeutic and containment approaches are needed in order to better control outbreaks and treat patients. This article provides an overview of currently available CDI treatment options and discusses the most promising therapies under development.

Simultaneous encoding of carotid sinus pressure and dP/dt by NTS target neurons of myelinated baroreceptors.

PubMed

Rogers, R F; Rose, W C; Schwaber, J S

1996-10-01

1. We seek to understand the baroreceptor signal processing that occurs centrally, beginning with the transformation of the signal at the first stage of processing. Because quantitative descriptions of the encoding of mean arterial pressure and its derivative with respect to time by baroreceptive second-order neurons have been unavailable, we characterized the responses of nucleus tractus solitarius (NTS) neurons that receive direct myelinated baroreceptor inputs to combinations of these two stimulus variables. 2. In anesthetized, paralyzed, artificially ventilated rabbits, the carotid sinus was vascularly isolated and the carotid sinus nerve was dissected free from surrounding tissue. Single-unit extracellular recordings were made from NTS neurons that received direct (with the use of physiological criteria) synaptic inputs from carotid sinus baroreceptors with myelinated axons. The vast majority of these neurons did not receive ipsilateral aortic nerve convergent inputs. With the use of a computer-controlled linear motor, a piecewise linear pressure waveform containing 32 combinations of pressure and its rate of change with respect to time (dP/dt) was delivered to the ipsilateral carotid sinus. 3. The average NTS firing frequency during the different stimulus combinations of pressure and dP/dt was a nonlinear and interdependent function of both variables. Most notable was the "extinctive" encoding of carotid sinus pressure by these neurons. This was characterized by an increase in firing frequency going from low to medium mean pressures (analyzed at certain positive dP/dt values) followed by a decrease in activity during high-pressure stimuli. All second-order neurons analyzed had their maximal firing rates when dP/dt was positive. 4. All neurons had their maximal firing frequency locations ("receptive field centers") at just 3 of 32 possible pressure-dP/dt coordinates. The responses of a small population of neurons were used to generate a composite description of the encoding of pressure and dP/dt. When combined as a composite of individually normalized values, the encoding of carotid sinus pressure and dP/dt may be approximated with the use of two-dimensional Gaussian functions. 5. We conclude that the population of NTS neurons recorded most faithfully encodes the rate and direction of (mean) pressure change, as opposed to providing the CNS with an unambiguous encoding of absolute pressure. Instead, the activity of these neurons, individually or as a population, serves as an estimate for the first derivative of the myelinated baroreceptor signal's encoding of mean pressure. We therefore speculate that the output of these individual neurons is useful in dynamic, rather than static, arterial pressure control.

Leishmania major Survival in Selective Phlebotomus papatasi Sand Fly Vector Requires a Specific SCG-Encoded Lipophosphoglycan Galactosylation Pattern

PubMed Central

Dobson, Deborah E.; Kamhawi, Shaden; Lawyer, Phillip; Turco, Salvatore J.; Beverley, Stephen M.; Sacks, David L.

2010-01-01

Phlebotomine sand flies that transmit the protozoan parasite Leishmania differ greatly in their ability to support different parasite species or strains in the laboratory: while some show considerable selectivity, others are more permissive. In “selective” sand flies, Leishmania binding and survival in the fly midgut typically depends upon the abundant promastigote surface adhesin lipophosphoglycan (LPG), which exhibits species- and strain-specific modifications of the dominant phosphoglycan (PG) repeat units. For the “selective” fly Phlebotomus papatasi PpapJ, side chain galactosyl-modifications (scGal) of PG repeats play key roles in parasite binding. We probed the specificity and properties of this scGal-LPG PAMP (Pathogen Associated Molecular Pattern) through studies of natural isolates exhibiting a wide range of galactosylation patterns, and of a panel of isogenic L. major engineered to express similar scGal-LPG diversity by transfection of SCG-encoded β1,3-galactosyltransferases with different activities. Surprisingly, both ‘poly-scGal’ and ‘null-scGal’ lines survived poorly relative to PpapJ-sympatric L. major FV1 and other ‘mono-scGal’ lines. However, survival of all lines was equivalent in P. duboscqi, which naturally transmit L. major strains bearing ‘null-scGal’-LPG PAMPs. We then asked whether scGal-LPG-mediated interactions were sufficient for PpapJ midgut survival by engineering Leishmania donovani, which normally express unsubstituted LPG, to express a ‘PpapJ-optimal’ scGal-LPG PAMP. Unexpectedly, these “L. major FV1-cloaked” L. donovani-SCG lines remained unable to survive within PpapJ flies. These studies establish that midgut survival of L. major in PpapJ flies is exquisitely sensitive to the scGal-LPG PAMP, requiring a specific ‘mono-scGal’ pattern. However, failure of ‘mono-scGal’ L. donovani-SCG lines to survive in selective PpapJ flies suggests a requirement for an additional, as yet unidentified L. major-specific parasite factor(s). The interplay of the LPG PAMP and additional factor(s) with sand fly midgut receptors may determine whether a given sand fly host is “selective” or “permissive”, with important consequences to both disease transmission and the natural co-evolution of sand flies and Leishmania. PMID:21085609

Relief of Injection Pain During Delivery of Local Anesthesia by Computer-Controlled Anesthetic Delivery System for Periodontal Surgery: Randomized Clinical Controlled Trial.

PubMed

Chang, Hyeyoon; Noh, Jiyoung; Lee, Jungwon; Kim, Sungtae; Koo, Ki-Tae; Kim, Tae-Il; Seol, Yang-Jo; Lee, Yong-Moo; Ku, Young; Rhyu, In-Chul

2016-07-01

Pain from local anesthetic injection makes patients anxious when visiting a dental clinic. This study aims to determine differences in pain according to types of local anesthetizing methods and to identify the possible contributing factors (e.g., dental anxiety, stress, and sex). Thirty-one patients who underwent open-flap debridement in maxillary premolar and molar areas during treatment for chronic periodontitis were evaluated for this study. A randomized, split-mouth, single-masked clinical trial was implemented. The dental anxiety scale (DAS) and perceived stress scale (PSS) were administered before surgery. Two lidocaine ampules for each patient were used for local infiltration anesthesia (supraperiosteal injection). Injection pain was measured immediately after local infiltration anesthesia using the visual analog pain scale (VAS) questionnaire. Results from the questionnaire were used to assess degree of pain patients feel when a conventional local anesthetic technique (CNV) is used compared with a computer-controlled anesthetic delivery system (CNR). DAS and PSS did not correlate to injection pain. VAS scores were lower for CNR than for CNV regardless of the order in which anesthetic procedures were applied. VAS score did not differ significantly with sex. Pearson coefficient for correlation between VAS scores for the two procedures was 0.80, also indicating a strong correlation. Within the limitations of the present study, relief from injection pain is observed using CNR.

Field determination of PCB in transformer oil. Volume 2. Clor-N-Oil PCB screening test. Final report

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

Fisher, D.J.; Rouse, T.O.; Lynn, T.

1984-10-01

The requirements for handling and disposing of transformer minerals oils containing more than 50 ppM PCB are, by federal regulation, different from those for oils containing lower concentrations. A rapid and simple test to distinguish between samples containing more than or less than this concentration would simplify proper control of transformer oils. This report describes the development of a small disposable test kit that can be used on-site to screen the chlorine content of transformer oils. The kit consists of two soft plastic tubes in which thin walled glass ampules containing premeasured amounts of reagents are broken. The reaction sequencemore » in the kits converts the chlorine in PCB to chloride ion. The color of the liquid in the kit after the last step is blue to purple if the chloride content due to the initial chlorine concentration of the oil is less than 20 ppM. If the chlorine content of the oil is below 20 ppM, the PCB content must be below 50 ppM. The liquid is colorless if the chlorine content is greater than 20 ppM. In this latter case, it is necessary to determine by gas chromatography whether the PCB content is actually greater than 50 ppM or if there is some other source of chlorine in the oil.« less

Heat capacity and thermodynamic functions of some rare-earth arsenates in the range 298.15-673 K

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

Kasenov, B.K.; Mustafin, E.S.; Oralova, A.T.

1994-12-01

Rare earth arsenates are promising as semiconducting and ferroelectric materials. However, no experimental data on the thermodynamic properties of these material can be found in the literature to date. In this work, we report heat capacity measurements for La,Nd,Gd, and Er arsenates. We synthesized LaAsO{sub 4}, NdAsO{sub 4}, GdAsO{sub 4}, and ErAsO{sub 4} by solid-state reactions between stoichiometric amounts of As{sup 2}O{sub 5} and extra-pure-grade La{sub 2}O{sub 3}, Nd{sub 2}O{sub 3}, Gd{sub 2}O{sub 3}, or Er{sub 2}O{sub 3} in evacuated (0.13 Pa) quartz ampules. The heat capacity at constant pressure was measured within the temperature range 298.15-673 K with 25-Kmore » steps using a commercial ITS-400 calorimeter. The experimental data were used to calculate coefficients of the equations for heat capacity vs. temperature. The experimental and calculated values of C{sup o}{sub p}(298.15 K) are in agreement. For example, C{sup o}{sub p}(LaAsO{sub 4}, 298.15K)=112.5 J/(molK), as calculated by the Landiya method, which agrees with the corresponding experimental value within {approximately}4.0%« less

Mature forms of the major seed storage albumins in sunflower: A mass spectrometric approach.

PubMed

Franke, Bastian; Colgrave, Michelle L; Mylne, Joshua S; Rosengren, K Johan

2016-09-16

Seed storage albumins are abundant, water-soluble proteins that are degraded to provide critical nutrients for the germinating seedling. It has been established that the sunflower albumins encoded by SEED STORAGE ALBUMIN 2 (SESA2), SESA20 and SESA3 are the major components of the albumin-rich fraction of the common sunflower Helianthus annuus. To determine the structure of sunflowers most important albumins we performed a detailed chromatographic and mass spectrometric characterization to assess what post-translational processing they receive prior to deposition in the protein storage vacuole. We found that SESA2 and SESA20 each encode two albumins. The first of the two SESA2 albumins (SESA2-1) exists as a monomer of 116 or 117 residues, differing by a threonine at the C-terminus. The second of the two SESA2 albumins (SESA2-2) is a monomer of 128 residues. SESA20 encodes the albumin SESA20-2, which is a 127-residue monomer, whereas SESA20-1 was not abundant enough to be structurally described. SESA3, which has been partly characterized previously, was found in several forms with methylation of its asparagine residues. In contrast to other dicot albumins, which are generally matured into a heterodimer, all the dominant mature sunflower albumins SESA2, SESA20-2, SESA3 and its post-translationally modified analogue SESA3-a are monomeric. Sunflower plants have been bred to thrive in various climate zones making them favored crops to meet the growing worldwide demand by humans for protein. The abundance of seed storage proteins makes them an important source of protein for animal and human nutrition. This study explores the structures of the dominant sunflower napin-type seed storage albumins to understand what structures evolution has favored in the most abundant proteins in sunflower seed. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

N-Acetyltransferase-2 Genotypes Among Patients with Rheumatoid Arthritis Attending Jordan University Hospital

PubMed Central

Oqal, Muna K.; Mustafa, Khader N.

2012-01-01

Aim: To determine the frequency of major N-acetyltransferase (NAT2) alleles and genotypes among Jordanian patients with rheumatoid arthritis (RA). Methods: The study was approved by the IRB of the Jordan University Hospital. An informed consent was signed by every patient. DNA samples from 150 healthy volunteers and 108 patients with RA were analyzed by polymerase chain reaction followed by a restriction fragment length polymorphism assay (PCR-RFLP) to determine the frequency of four major alleles: NAT2*4, NAT2*5, NAT2*6, and NAT2*7. Results: The most prevalent genotypes are those that encode the slow acetylation phenotype. About 59.3% of the patients with RA carried the slow, 33.3% the intermediate, and 7.4% the fast-encoding genotypes. The frequency of NAT2 alleles was 0.241 (95% confidence interval [CI] 0.184–0.298) for NAT2*4, 0.449 (95% CI 0.383–0.515) for NAT2*5, 0.273 (95% CI 0.214–0.332) for NAT2*6, and 0.037 (95% CI 0.012–0.062) for NAT2*7 allele. The overall frequency of the slow acetylation genotype in patients with RA is similar to that in healthy Jordanian volunteers. However, the NAT2*5/7 genotype was found in seven patients (6.5%) with RA and was absent in Jordanian volunteers, and the z test revealed that the difference was statistically significant. This genotype constituted 10.9% of the genotypes encoding slow acetylation. Conclusion: The overall acetylator genotype in RA is similar to that in healthy volunteers. The overall slow acetylator genotypes do not seem to be a genetic risk factor for RA among Jordanians. However, the NAT2*5/7 genotype seems to be related to RA. The nature of this relationship needs further clarification. PMID:22731637