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Sample records for genetically encoded indicators

  1. Genetically Encoded Voltage Indicators in Circulation Research.

    Science.gov (United States)

    Kaestner, Lars; Tian, Qinghai; Kaiser, Elisabeth; Xian, Wenying; Müller, Andreas; Oberhofer, Martin; Ruppenthal, Sandra; Sinnecker, Daniel; Tsutsui, Hidekazu; Miyawaki, Atsushi; Moretti, Alessandra; Lipp, Peter

    2015-09-08

    Membrane potentials display the cellular status of non-excitable cells and mediate communication between excitable cells via action potentials. The use of genetically encoded biosensors employing fluorescent proteins allows a non-invasive biocompatible way to read out the membrane potential in cardiac myocytes and other cells of the circulation system. Although the approaches to design such biosensors date back to the time when the first fluorescent-protein based Förster Resonance Energy Transfer (FRET) sensors were constructed, it took 15 years before reliable sensors became readily available. Here, we review different developments of genetically encoded membrane potential sensors. Furthermore, it is shown how such sensors can be used in pharmacological screening applications as well as in circulation related basic biomedical research. Potentials and limitations will be discussed and perspectives of possible future developments will be provided.

  2. Genetically Encoded Voltage Indicators in Circulation Research

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    Lars Kaestner

    2015-09-01

    Full Text Available Membrane potentials display the cellular status of non-excitable cells and mediate communication between excitable cells via action potentials. The use of genetically encoded biosensors employing fluorescent proteins allows a non-invasive biocompatible way to read out the membrane potential in cardiac myocytes and other cells of the circulation system. Although the approaches to design such biosensors date back to the time when the first fluorescent-protein based Förster Resonance Energy Transfer (FRET sensors were constructed, it took 15 years before reliable sensors became readily available. Here, we review different developments of genetically encoded membrane potential sensors. Furthermore, it is shown how such sensors can be used in pharmacological screening applications as well as in circulation related basic biomedical research. Potentials and limitations will be discussed and perspectives of possible future developments will be provided.

  3. Monitoring activity in neural circuits with genetically encoded indicators

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    Gerard Joseph Broussard

    2014-12-01

    Full Text Available Recent developments in genetically encoded indicators of neural activity (GINAs have greatly advanced the field of systems neuroscience. As they are encoded by DNA, GINAs can be targeted to genetically defined cellular populations. Combined with fluorescence microscopy, most notably multi-photon imaging, GINAs allow chronic simultaneous optical recordings from large populations of neurons or glial cells in awake, behaving mammals, particularly rodents. This large-scale recording of neural activity at multiple temporal and spatial scales has greatly advanced our understanding of the dynamics of neural circuitry underlying behavior—a critical first step toward understanding the complexities of brain function, such as sensorimotor integration and learning.Here, we summarize the recent development and applications of the major classes of GINAs. In particular, we take an in-depth look at the design of available GINA families with a particular focus on genetically encoded calcium indicators, sensors probing synaptic activity, and genetically encoded voltage indicators. Using the family of the genetically encoded calcium indicator GCaMP as an example, we review established sensor optimization pipelines. We also discuss practical considerations for end users of GINAs about experimental methods including approaches for gene delivery, imaging system requirements, and data analysis techniques. With the growing toolbox of GINAs and with new microscopy techniques pushing beyond their current limits, the age of light can finally achieve the goal of broad and dense sampling of neuronal activity across time and brain structures to obtain a dynamic picture of brain function.

  4. Optogenetic Monitoring of Synaptic Activity with Genetically Encoded Voltage Indicators

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    Nakajima, Ryuichi; Jung, Arong; Yoon, Bong-June; Baker, Bradley J.

    2016-01-01

    The age of genetically encoded voltage indicators (GEVIs) has matured to the point that changes in membrane potential can now be observed optically in vivo. Improving the signal size and speed of these voltage sensors has been the primary driving forces during this maturation process. As a result, there is a wide range of probes using different voltage detecting mechanisms and fluorescent reporters. As the use of these probes transitions from optically reporting membrane potential in single, cultured cells to imaging populations of cells in slice and/or in vivo, a new challenge emerges—optically resolving the different types of neuronal activity. While improvements in speed and signal size are still needed, optimizing the voltage range and the subcellular expression (i.e., soma only) of the probe are becoming more important. In this review, we will examine the ability of recently developed probes to report synaptic activity in slice and in vivo. The voltage-sensing fluorescent protein (VSFP) family of voltage sensors, ArcLight, ASAP-1, and the rhodopsin family of probes are all good at reporting changes in membrane potential, but all have difficulty distinguishing subthreshold depolarizations from action potentials and detecting neuronal inhibition when imaging populations of cells. Finally, we will offer a few possible ways to improve the optical resolution of the various types of neuronal activities. PMID:27547183

  5. Chronic imaging of cortical sensory map dynamics using a genetically encoded calcium indicator

    OpenAIRE

    Minderer, M; Liu, W.; Sumanovski, L. T.; Kügler, S; Helmchen, F; Margolis, D. J.

    2012-01-01

    Abstract  In vivo optical imaging can reveal the dynamics of large-scale cortical activity, but methods for chronic recording are limited. Here we present a technique for long-term investigation of cortical map dynamics using wide-field ratiometric fluorescence imaging of the genetically encoded calcium indicator (GECI) Yellow Cameleon 3.60. We find that wide-field GECI signals report sensory-evoked activity in anaesthetized mouse somatosensory cortex with high sensitivity and spatiotemporal ...

  6. Chronic imaging of cortical sensory map dynamics using a genetically encoded calcium indicator.

    Science.gov (United States)

    Minderer, Matthias; Liu, Wenrui; Sumanovski, Lazar T; Kügler, Sebastian; Helmchen, Fritjof; Margolis, David J

    2012-01-01

    In vivo optical imaging can reveal the dynamics of large-scale cortical activity, but methods for chronic recording are limited. Here we present a technique for long-term investigation of cortical map dynamics using wide-field ratiometric fluorescence imaging of the genetically encoded calcium indicator (GECI) Yellow Cameleon 3.60. We find that wide-field GECI signals report sensory-evoked activity in anaesthetized mouse somatosensory cortex with high sensitivity and spatiotemporal precision, and furthermore, can be measured repeatedly in separate imaging sessions over multiple weeks. This method opens new possibilities for the longitudinal study of stability and plasticity of cortical sensory representations.

  7. Genetically encoded pH‐indicators reveal activity‐dependent cytosolic acidification of Drosophila motor nerve termini in vivo

    National Research Council Canada - National Science Library

    Rossano, Adam J; Chouhan, Amit K; Macleod, Gregory T

    2013-01-01

    .... •  At the fruit fly larval neuromuscular junction, fluorescent genetically encoded pH‐indicators (GEpHIs) revealed significant cytosolic acidification of presynaptic termini during nerve activity...

  8. Genetically encoded Ca2+ indicators; expanded affinity range, color hue and compatibility with optogenetics

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    Takeharu eNagai

    2014-11-01

    Full Text Available Fluorescent protein-based indicators are invaluable tools for functional imaging of living cells and organisms. Genetically encoded calcium indicators (GECIs such as derivatives of yellow cameleons (YCs and GCaMPs/pericams (Miyawaki et al., 1997; Nakai et al., 2001; Nagai et al., 2001 are a highly advanced class of indicators. Continued efforts for improvement of the performance of GECIs have resulted in brighter indicators with better photo-stability and expanded dynamic range, thus improving the sensitivity of detection. Fine-tuning of other properties, including Ca2+ affinity and Hill constant, have also contributed to increase the detectability of Ca2+ dynamics. Emerging optogenetic technology has forced the spectrally compatible GECI color variants. In this opinion, we highlight the recent development of GECIs including photo-switchable Ca2+ indicators and bioluminescence-based Ca2+ indicator, mainly invented in our group, focusing especially on the parameters determining their performance in order to provide a guideline for the selection of appropriate GECI for a given experiment.

  9. Imaging the response of the retina to electrical stimulation with genetically encoded calcium indicators.

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    Weitz, Andrew C; Behrend, Matthew R; Lee, Nan Sook; Klein, Ronald L; Chiodo, Vince A; Hauswirth, William W; Humayun, Mark S; Weiland, James D; Chow, Robert H

    2013-04-01

    Epiretinal implants for the blind are designed to stimulate surviving retinal neurons, thus bypassing the diseased photoreceptor layer. Single-unit or multielectrode recordings from isolated animal retina are commonly used to inform the design of these implants. However, such electrical recordings provide limited information about the spatial patterns of retinal activation. Calcium imaging overcomes this limitation, as imaging enables high spatial resolution mapping of retinal ganglion cell (RGC) activity as well as simultaneous recording from hundreds of RGCs. Prior experiments in amphibian retina have demonstrated proof of principle, yet experiments in mammalian retina have been hindered by the inability to load calcium indicators into mature mammalian RGCs. Here, we report a method for labeling the majority of ganglion cells in adult rat retina with genetically encoded calcium indicators, specifically GCaMP3 and GCaMP5G. Intravitreal injection of an adeno-associated viral vector targets ∼85% of ganglion cells with high specificity. Because of the large fluorescence signals provided by the GCaMP sensors, we can now for the first time visualize the response of the retina to electrical stimulation in real-time. Imaging transduced retinas mounted on multielectrode arrays reveals how stimulus pulse shape can dramatically affect the spatial extent of RGC activation, which has clear implications in prosthetic applications. Our method can be easily adapted to work with other fluorescent indicator proteins in both wild-type and transgenic mammals.

  10. Imaging the awake visual cortex with a genetically encoded voltage indicator.

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    Carandini, Matteo; Shimaoka, Daisuke; Rossi, L Federico; Sato, Tatsuo K; Benucci, Andrea; Knöpfel, Thomas

    2015-01-07

    Genetically encoded voltage indicators (GEVIs) promise to reveal the membrane potential of genetically targeted neuronal populations through noninvasive, chronic imaging of large portions of cortical space. Here we test a promising GEVI in mouse cortex during wakefulness, a challenging condition due to large hemodynamic activity, and we introduce a straightforward projection method to separate a signal dominated by membrane voltage from a signal dominated by hemodynamic activity. We expressed VSFP-Butterfly 1.2 plasmid in layer 2/3 pyramidal cells of visual cortex through electroporation in utero. We then used wide-field imaging with two cameras to measure both fluorophores of the indicator in response to visual stimuli. By taking weighted sums and differences of the two measurements, we obtained clear separation of hemodynamic and voltage signals. The hemodynamic signal showed strong heartbeat oscillations, superimposed on slow dynamics similar to blood oxygen level-dependent (BOLD) or "intrinsic" signals. The voltage signal had fast dynamics similar to neural responses measured electrically, and showed an orderly retinotopic mapping. We compared this voltage signal with calcium signals imaged in transgenic mice that express a calcium indicator (GCaMP3) throughout cortex. The voltage signal from VSFP had similar signal-to-noise ratios as the calcium signal, it was more immune to vascular artifacts, and it integrated over larger regions of visual space, which was consistent with its reporting mostly subthreshold activity rather than the spiking activity revealed by calcium signals. These results demonstrate that GEVIs provide a powerful tool to study the dynamics of neural populations at mesoscopic spatial scales in the awake cortex. Copyright © 2015 Carandini et al.

  11. Calcium Signaling throughout the Toxoplasma gondii Lytic Cycle: A STUDY USING GENETICALLY ENCODED CALCIUM INDICATORS.

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    Borges-Pereira, Lucas; Budu, Alexandre; McKnight, Ciara A; Moore, Christina A; Vella, Stephen A; Hortua Triana, Miryam A; Liu, Jing; Garcia, Celia R S; Pace, Douglas A; Moreno, Silvia N J

    2015-11-01

    Toxoplasma gondii is an obligate intracellular parasite that invades host cells, creating a parasitophorous vacuole where it communicates with the host cell cytosol through the parasitophorous vacuole membrane. The lytic cycle of the parasite starts with its exit from the host cell followed by gliding motility, conoid extrusion, attachment, and invasion of another host cell. Here, we report that Ca(2+) oscillations occur in the cytosol of the parasite during egress, gliding, and invasion, which are critical steps of the lytic cycle. Extracellular Ca(2+) enhances each one of these processes. We used tachyzoite clonal lines expressing genetically encoded calcium indicators combined with host cells expressing transiently expressed calcium indicators of different colors, and we measured Ca(2+) changes in both parasites and host simultaneously during egress. We demonstrated a link between cytosolic Ca(2+) oscillations in the host and in the parasite. Our approach also allowed us to measure two new features of motile parasites, which were enhanced by Ca(2+) influx. This is the first study showing, in real time, Ca(2+) signals preceding egress and their direct link with motility, an essential virulence trait.

  12. Imaging activity in astrocytes and neurons with genetically encoded calcium indicators following in utero electroporation

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    J. Michael eGee

    2015-04-01

    Full Text Available Complex interactions between networks of astrocytes and neurons are beginning to be appreciated, but remain poorly understood. Transgenic mice expressing fluorescent protein reporters of cellular activity, such as the GCaMP family of genetically encoded calcium indicators, have been used to explore network behavior. However, in some cases, it may be desirable to use long-established rat models that closely mimic particular aspects of human conditions such as Parkinson’s disease and the development of epilepsy following status epilepticus. Methods for expressing reporter proteins in the rat brain are relatively limited. Transgenic rat technologies exist but are fairly immature. Viral-mediated expression is robust but unstable, requires invasive injections, and only works well for fairly small genes (< 5 kb. In utero electroporation offers a valuable alternative. IUE is a proven method for transfecting populations of astrocytes and neurons in the rat brain without the strict limitations on transgene size. We built a toolset of IUE plasmids carrying GCaMP variants 3, 6s or 6f driven by CAG and targeted to the cytosol or the plasma membrane. Because low baseline fluorescence of GCaMP can hinder identification of transfected cells, we included the option of co-expressing a cytosolic tdTomato protein. A binary system consisting of a plasmid carrying a piggyBac inverted terminal repeat-flanked CAG-GCaMP-IRES-tdTomato cassette and a separate plasmid encoding for expression of piggyBac transposase was employed to stably express GCaMP and tdTomato. The plasmids were co-electroporated on embryonic days 13.5-14.5 and astrocytic and neuronal activity was subsequently imaged in acute or cultured brain slices prepared from the cortex or hippocampus. Large spontaneous transients were detected in slices obtained from rats of varying ages up to 127 days. In this report, we demonstrate the utility of this toolset for interrogating astrocytic and neuronal

  13. Exploration of genetically encoded voltage indicators based on a chimeric voltage sensing domain

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    Yukiko eMishina

    2014-09-01

    Full Text Available Deciphering how the brain generates cognitive function from patterns of electrical signals is one of the ultimate challenges in neuroscience. To this end, it would be highly desirable to monitor the activities of very large numbers of neurons while an animal engages in complex behaviours. Optical imaging of electrical activity using genetically encoded voltage indicators (GEVIs has the potential to meet this challenge. Currently prevalent GEVIs are based on the voltage-sensitive fluorescent protein (VSFP prototypical design or on the voltage dependent state transitions of microbial opsins.We recently introduced a new VSFP design in which the voltage-sensing domain (VSD is sandwiched between a FRET pair of fluorescent proteins (termed VSFP-Butterflies and also demonstrated a series of chimeric VSD in which portions of the VSD of Ciona intestinalis voltage-sensitive phosphatase (Ci-VSP are substituted by homologous portions of a voltage-gated potassium channel subunit. These chimeric VSD had faster sensing kinetics than that of the native Ci-VSD. Here, we describe a new set of VSFPs that combine chimeric VSD with the Butterfly structure. We show that these chimeric VSFP-Butterflies can report membrane voltage oscillations of up to 200 Hz in cultured cells and report sensory evoked cortical population responses in living mice. This class of GEVIs may be suitable for imaging of brain rhythms in behaving mammalians.

  14. Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics

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    Jasper eAkerboom

    2013-03-01

    Full Text Available Genetically encoded calcium indicators (GECIs are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, RCaMPs, engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca2+-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca2+] and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2 or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca2+ affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics.

  15. Genetically encoded green fluorescent Ca2+ indicators with improved detectability for neuronal Ca2+ signals.

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    Ohkura, Masamichi; Sasaki, Takuya; Sadakari, Junko; Gengyo-Ando, Keiko; Kagawa-Nagamura, Yuko; Kobayashi, Chiaki; Ikegaya, Yuji; Nakai, Junichi

    2012-01-01

    Imaging the activities of individual neurons with genetically encoded Ca(2+) indicators (GECIs) is a promising method for understanding neuronal network functions. Here, we report GECIs with improved neuronal Ca(2+) signal detectability, termed G-CaMP6 and G-CaMP8. Compared to a series of existing G-CaMPs, G-CaMP6 showed fairly high sensitivity and rapid kinetics, both of which are suitable properties for detecting subtle and fast neuronal activities. G-CaMP8 showed a greater signal (F(max)/F(min) = 38) than G-CaMP6 and demonstrated kinetics similar to those of G-CaMP6. Both GECIs could detect individual spikes from pyramidal neurons of cultured hippocampal slices or acute cortical slices with 100% detection rates, demonstrating their superior performance to existing GECIs. Because G-CaMP6 showed a higher sensitivity and brighter baseline fluorescence than G-CaMP8 in a cellular environment, we applied G-CaMP6 for Ca(2+) imaging of dendritic spines, the putative postsynaptic sites. By expressing a G-CaMP6-actin fusion protein for the spines in hippocampal CA3 pyramidal neurons and electrically stimulating the granule cells of the dentate gyrus, which innervate CA3 pyramidal neurons, we found that sub-threshold stimulation triggered small Ca(2+) responses in a limited number of spines with a low response rate in active spines, whereas supra-threshold stimulation triggered large fluorescence responses in virtually all of the spines with a 100% activity rate.

  16. Optimal microscopic systems for long-term imaging of intracellular calcium using a ratiometric genetically-encoded calcium indicator.

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    Miyamoto, Akitoshi; Bannai, Hiroko; Michikawa, Takayuki; Mikoshiba, Katsuhiko

    2013-05-03

    Monitoring the pattern of intracellular Ca(2+) signals that control many diverse cellular processes is essential for understanding regulatory mechanisms of cellular functions. Various genetically encoded Ca(2+) indicators (GECIs) are used for monitoring intracellular Ca(2+) changes under several types of microscope systems. However, it has not yet been explored which microscopic system is ideal for long-term imaging of the spatiotemporal patterns of Ca(2+) signals using GECIs. We here compared the Ca(2+) signals reported by a fluorescence resonance energy transfer (FRET)-based ratiometric GECI, yellow cameleon 3.60 (YC3.60), stably expressed in DT40 B lymphocytes, using three different imaging systems. These systems included a wide-field fluorescent microscope, a multipoint scanning confocal system, and a single-point scanning confocal system. The degree of photobleaching and the signal-to-noise ratio of YC3.60 in DT40 cells were highly dependent on the fluorescence excitation method, although the total illumination energy was maintained at a constant level within each of the imaging systems. More strikingly, the Ca(2+) responses evoked by B-cell antigen receptor stimulation in YC3.60-expressing DT40 cells were different among the imaging systems, and markedly affected by the illumination power used. Our results suggest that optimization of the imaging system, including illumination and acquisition conditions, is crucial for accurate visualization of intracellular Ca(2+) signals.

  17. Use of genetically-encoded calcium indicators for live cell calcium imaging and localization in virus-infected cells.

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    Perry, Jacob L; Ramachandran, Nina K; Utama, Budi; Hyser, Joseph M

    2015-11-15

    Calcium signaling is a ubiquitous and versatile process involved in nearly every cellular process, and exploitation of host calcium signals is a common strategy used by viruses to facilitate replication and cause disease. Small molecule fluorescent calcium dyes have been used by many to examine changes in host cell calcium signaling and calcium channel activation during virus infections, but disadvantages of these dyes, including poor loading and poor long-term retention, complicate analysis of calcium imaging in virus-infected cells due to changes in cell physiology and membrane integrity. The recent expansion of genetically-encoded calcium indicators (GECIs), including blue and red-shifted color variants and variants with calcium affinities appropriate for calcium storage organelles like the endoplasmic reticulum (ER), make the use of GECIs an attractive alternative for calcium imaging in the context of virus infections. Here we describe the development and testing of cell lines stably expressing both green cytoplasmic (GCaMP5G and GCaMP6s) and red ER-targeted (RCEPIAer) GECIs. Using three viruses (rotavirus, poliovirus and respiratory syncytial virus) previously shown to disrupt host calcium homeostasis, we show the GECI cell lines can be used to detect simultaneous cytoplasmic and ER calcium signals. Further, we demonstrate the GECI expression has sufficient stability to enable long-term confocal imaging of both cytoplasmic and ER calcium during the course of virus infections.

  18. Imaging intracellular Ca²⁺ signals in striatal astrocytes from adult mice using genetically-encoded calcium indicators.

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    Jiang, Ruotian; Haustein, Martin D; Sofroniew, Michael V; Khakh, Baljit S

    2014-11-19

    Astrocytes display spontaneous intracellular Ca(2+) concentration fluctuations ([Ca(2+)]i) and in several settings respond to neuronal excitation with enhanced [Ca(2+)]i signals. It has been proposed that astrocytes in turn regulate neurons and blood vessels through calcium-dependent mechanisms, such as the release of signaling molecules. However, [Ca(2+)]i imaging in entire astrocytes has only recently become feasible with genetically encoded calcium indicators (GECIs) such as the GCaMP series. The use of GECIs in astrocytes now provides opportunities to study astrocyte [Ca(2+)]i signals in detail within model microcircuits such as the striatum, which is the largest nucleus of the basal ganglia. In the present report, detailed surgical methods to express GECIs in astrocytes in vivo, and confocal imaging approaches to record [Ca(2+)]i signals in striatal astrocytes in situ, are described. We highlight precautions, necessary controls and tests to determine if GECI expression is selective for astrocytes and to evaluate signs of overt astrocyte reactivity. We also describe brain slice and imaging conditions in detail that permit reliable [Ca(2+)]i imaging in striatal astrocytes in situ. The use of these approaches revealed the entire territories of single striatal astrocytes and spontaneous [Ca(2+)]i signals within their somata, branches and branchlets. The further use and expansion of these approaches in the striatum will allow for the detailed study of astrocyte [Ca(2+)]i signals in the striatal microcircuitry.

  19. Genetically encoded pH-indicators reveal activity-dependent cytosolic acidification of Drosophila motor nerve termini in vivo.

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    Rossano, Adam J; Chouhan, Amit K; Macleod, Gregory T

    2013-04-01

    All biochemical processes, including those underlying synaptic function and plasticity, are pH sensitive. Cytosolic pH (pH(cyto)) shifts are known to accompany nerve activity in situ, but technological limitations have prevented characterization of such shifts in vivo. Genetically encoded pH-indicators (GEpHIs) allow for tissue-specific in vivo measurement of pH. We expressed three different GEpHIs in the cytosol of Drosophila larval motor neurons and observed substantial presynaptic acidification in nerve termini during nerve stimulation in situ. SuperEcliptic pHluorin was the most useful GEpHI for studying pH(cyto) shifts in this model system. We determined the resting pH of the nerve terminal cytosol to be 7.30 ± 0.02, and observed a decrease of 0.16 ± 0.01 pH units when the axon was stimulated at 40 Hz for 4 s. Realkalinization occurred upon cessation of stimulation with a time course of 20.54 ± 1.05 s (τ). The chemical pH-indicator 2,7-bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein corroborated these changes in pH(cyto). Bicarbonate-derived buffering did not contribute to buffering of acid loads from short (≤ 4 s) trains of action potentials but did buffer slow (~60 s) acid loads. The magnitude of cytosolic acid transients correlated with cytosolic Ca(2+) increase upon stimulation, and partial inhibition of the plasma membrane Ca(2+)-ATPase, a Ca(2+)/H(+) exchanger, attenuated pH(cyto) shifts. Repeated stimulus trains mimicking motor patterns generated greater cytosolic acidification (~0.30 pH units). Imaging through the cuticle of intact larvae revealed spontaneous pH(cyto) shifts in presynaptic termini in vivo, similar to those seen in situ during fictive locomotion, indicating that presynaptic pH(cyto) shifts cannot be dismissed as artifacts of ex vivo preparations.

  20. Genetically-encoded yellow fluorescent cAMP indicator with an expanded dynamic range for dual-color imaging.

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    Haruki Odaka

    Full Text Available Cyclic AMP is a ubiquitous second messenger, which mediates many cellular responses mainly initiated by activation of cell surface receptors. Various Förster resonance energy transfer-based ratiometric cAMP indicators have been created for monitoring the spatial and temporal dynamics of cAMP at the single-cell level. However, single fluorescent protein-based cAMP indicators have been poorly developed, with improvement required for dynamic range and brightness. Based on our previous yellow fluorescent protein-based cAMP indicator, Flamindo, we developed an improved yellow fluorescent cAMP indicator named Flamindo2. Flamindo2 has a 2-fold expanded dynamic range and 8-fold increased brightness compared with Flamindo by optimization of linker peptides in the vicinity of the chromophore. We found that fluorescence intensity of Flamindo2 was decreased to 25% in response to cAMP. Live-cell cAMP imaging of the cytosol and nucleus in COS7 cells using Flamindo2 and nlsFlamindo2, respectively, showed that forskolin elevated cAMP levels in each compartment with different kinetics. Furthermore, dual-color imaging of cAMP and Ca2+ with Flamindo2 and a red fluorescent Ca2+ indicator, R-GECO, showed that cAMP and Ca2+ elevation were induced by noradrenaline in single HeLa cells. Our study shows that Flamindo2, which is feasible for multi-color imaging with other intracellular signaling molecules, is useful and is an alternative tool for live-cell imaging of intracellular cAMP dynamics.

  1. Genetically-Encoded Yellow Fluorescent cAMP Indicator with an Expanded Dynamic Range for Dual-Color Imaging

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    Odaka, Haruki; Arai, Satoshi; Inoue, Takafumi; Kitaguchi, Tetsuya

    2014-01-01

    Cyclic AMP is a ubiquitous second messenger, which mediates many cellular responses mainly initiated by activation of cell surface receptors. Various Förster resonance energy transfer-based ratiometric cAMP indicators have been created for monitoring the spatial and temporal dynamics of cAMP at the single-cell level. However, single fluorescent protein-based cAMP indicators have been poorly developed, with improvement required for dynamic range and brightness. Based on our previous yellow fluorescent protein-based cAMP indicator, Flamindo, we developed an improved yellow fluorescent cAMP indicator named Flamindo2. Flamindo2 has a 2-fold expanded dynamic range and 8-fold increased brightness compared with Flamindo by optimization of linker peptides in the vicinity of the chromophore. We found that fluorescence intensity of Flamindo2 was decreased to 25% in response to cAMP. Live-cell cAMP imaging of the cytosol and nucleus in COS7 cells using Flamindo2 and nlsFlamindo2, respectively, showed that forskolin elevated cAMP levels in each compartment with different kinetics. Furthermore, dual-color imaging of cAMP and Ca2+ with Flamindo2 and a red fluorescent Ca2+ indicator, R-GECO, showed that cAMP and Ca2+ elevation were induced by noradrenaline in single HeLa cells. Our study shows that Flamindo2, which is feasible for multi-color imaging with other intracellular signaling molecules, is useful and is an alternative tool for live-cell imaging of intracellular cAMP dynamics. PMID:24959857

  2. Auto-luminescent genetically-encoded ratiometric indicator for real-time Ca2+ imaging at the single cell level.

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    Kenta Saito

    Full Text Available BACKGROUND: Efficient bioluminescence resonance energy transfer (BRET from a bioluminescent protein to a fluorescent protein with high fluorescent quantum yield has been utilized to enhance luminescence intensity, allowing single-cell imaging in near real time without external light illumination. METHODOLOGY/PRINCIPAL FINDINGS: We applied BRET to develop an autoluminescent Ca(2+ indicator, BRAC, which is composed of Ca(2+-binding protein, calmodulin, and its target peptide, M13, sandwiched between a yellow fluorescent protein variant, Venus, and an enhanced Renilla luciferase, RLuc8. Adjusting the relative dipole orientation of the luminescent protein's chromophores improved the dynamic range of BRET signal change in BRAC up to 60%, which is the largest dynamic range among BRET-based indicators reported so far. Using BRAC, we demonstrated successful visualization of Ca(2+ dynamics at the single-cell level with temporal resolution at 1 Hz. Moreover, BRAC signals were acquired by ratiometric imaging capable of canceling out Ca(2+-independent signal drifts due to change in cell shape, focus shift, etc. CONCLUSIONS/SIGNIFICANCE: The brightness and large dynamic range of BRAC should facilitate high-sensitive Ca(2+ imaging not only in single live cells but also in small living subjects.

  3. Optical recording of neuronal activity with a genetically-encoded calcium indicator in anesthetized and freely moving mice

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    Henry Lütcke

    2010-04-01

    Full Text Available Fluorescent calcium (Ca2+ indicator proteins (FCIPs are promising tools for functional imaging of cellular activity in living animals. However, they have still not reached their full potential for in vivo imaging of neuronal activity due to limitations in expression levels, dynamic range, and sensitivity for reporting action potentials. Here, we report that viral expression of the ratiometric Ca2+ sensor yellow cameleon 3.60 (YC3.60 in pyramidal neurons of mouse barrel cortex enables in vivo measurement of neuronal activity with high dynamic range and sensitivity across multiple spatial scales. By combining juxtacellular recordings and two-photon imaging in vitro and in vivo, we demonstrate that YC3.60 can resolve single action potential (AP-evoked Ca2+ transients and reliably reports bursts of APs with negligible saturation. Spontaneous and whisker-evoked Ca2+ transients were detected in individual apical dendrites and somata as well as in local neuronal populations. Moreover, bulk measurements using wide-field imaging or fiber-optics revealed sensory-evoked YC3.60 signals in large areas of the barrel field. Fiber-optic recordings in particular enabled measurements in awake, freely moving mice and revealed complex Ca2+ dynamics, possibly reflecting different behavior-related brain states. Viral expression of YC3.60 - in combination with various optical techniques - thus opens a multitude of opportunities for functional studies of the neural basis of animal behavior, from dendrites to the levels of local and large-scale neuronal populations.

  4. Genetically Encoded Sensors for Metabolites

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    Deuschle, Karen; Fehr, Marcus; Hilpert, Melanie; Lager, Ida; Lalonde, Sylvie; Looger, Loren L.; Okumoto, Sakiko; Persson, Jörgen; Schmidt, Anja; Frommer, Wolf B.

    2009-01-01

    Background Metabolomics, i.e., the multiparallel analysis of metabolite changes occurring in a cell or an organism, has become feasible with the development of highly efficient mass spectroscopic technologies. Functional genomics as a standard tool helped to identify the function of many of the genes that encode important transporters and metabolic enzymes over the past few years. Advanced expression systems and analysis technologies made it possible to study the biochemical properties of the corresponding proteins in great detail. We begin to understand the biological functions of the gene products by systematic analysis of mutants using systematic PTGS/RNAi, knockout and TILLING approaches. However, one crucial set of data especially relevant in the case of multicellular organisms is lacking: the knowledge of the spatial and temporal profiles of metabolite levels at cellular and subcellular levels. Methods We therefore developed genetically encoded nanosensors for several metabolites to provide a basic set of tools for the determination of cytosolic and subcellular metabolite levels in real time by using fluorescence microscopy. Results Prototypes of these sensors were successfully used in vitro and also in vivo, i.e., to measure sugar levels in fungal and animal cells. Conclusions One of the future goals will be to expand the set of sensors to a wider spectrum of substrates by using the natural spectrum of periplasmic binding proteins from bacteria and by computational design of proteins with altered binding pockets in conjunction with mutagenesis. This toolbox can then be applied for four-dimensional imaging of cells and tissues to elucidate the spatial and temporal distribution of metabolites as a discovery tool in functional genomics, as a tool for high-throughput, high-content screening for drugs, to test metabolic models, and to analyze the interplay of cells in a tissue or organ. PMID:15688353

  5. Dual optical recordings for action potentials and calcium handling in induced pluripotent stem cell models of cardiac arrhythmias using genetically encoded fluorescent indicators.

    Science.gov (United States)

    Song, LouJin; Awari, Daniel W; Han, Elizabeth Y; Uche-Anya, Eugenia; Park, Seon-Hye E; Yabe, Yoko A; Chung, Wendy K; Yazawa, Masayuki

    2015-05-01

    Reprogramming of human somatic cells to pluripotency has been used to investigate disease mechanisms and to identify potential therapeutics. However, the methods used for reprogramming, in vitro differentiation, and phenotyping are still complicated, expensive, and time-consuming. To address the limitations, we first optimized a protocol for reprogramming of human fibroblasts and keratinocytes into pluripotency using single lipofection and the episomal vectors in a 24-well plate format. This method allowed us to generate multiple lines of integration-free and feeder-free induced pluripotent stem cells (iPSCs) from seven patients with cardiac diseases and three controls. Second, we differentiated human iPSCs derived from patients with Timothy syndrome into cardiomyocytes using a monolayer differentiation method. We found that Timothy syndrome cardiomyocytes showed slower, irregular contractions and abnormal calcium handling compared with the controls. The results are consistent with previous reports using a retroviral method for reprogramming and an embryoid body-based method for cardiac differentiation. Third, we developed an efficient approach for recording the action potentials and calcium transients simultaneously in control and patient cardiomyocytes using genetically encoded fluorescent indicators, ArcLight and R-GECO1. The dual optical recordings enabled us to observe prolonged action potentials and abnormal calcium handling in Timothy syndrome cardiomyocytes. We confirmed that roscovitine rescued the phenotypes in Timothy syndrome cardiomyocytes and that these findings were consistent with previous studies using conventional electrophysiological recordings and calcium imaging with dyes. The approaches using our optimized methods and dual optical recordings will improve iPSC applicability for disease modeling to investigate mechanisms underlying cardiac arrhythmias and to test potential therapeutics.

  6. Toward Better Genetically Encoded Sensors of Membrane Potential.

    Science.gov (United States)

    Storace, Douglas; Sepehri Rad, Masoud; Kang, BokEum; Cohen, Lawrence B; Hughes, Thom; Baker, Bradley J

    2016-05-01

    Genetically encoded optical sensors of cell activity are powerful tools that can be targeted to specific cell types. This is especially important in neuroscience because individual brain regions can include a multitude of different cell types. Optical imaging allows for simultaneous recording from numerous neurons or brain regions. Optical signals of membrane potential are useful because membrane potential changes are a direct sign of both synaptic and action potentials. Here we describe recent improvements in the in vitro and in vivo signal size and kinetics of genetically encoded voltage indicators (GEVIs) and discuss their relationship to alternative sensors of neural activity.

  7. Mouse redox histology using genetically encoded probes.

    Science.gov (United States)

    Fujikawa, Yuuta; Roma, Leticia P; Sobotta, Mirko C; Rose, Adam J; Diaz, Mauricio Berriel; Locatelli, Giuseppe; Breckwoldt, Michael O; Misgeld, Thomas; Kerschensteiner, Martin; Herzig, Stephan; Müller-Decker, Karin; Dick, Tobias P

    2016-03-15

    Mapping the in vivo distribution of endogenous oxidants in animal tissues is of substantial biomedical interest. Numerous health-related factors, including diet, physical activity, infection, aging, toxins, or pharmacological intervention, may cause redox changes. Tools are needed to pinpoint redox state changes to particular organs, tissues, cell types, and subcellular organelles. We describe a procedure that preserves the in vivo redox state of genetically encoded redox biosensors within histological tissue sections, thus providing "redox maps" for any tissue and comparison of interest. We demonstrate the utility of the technique by visualizing endogenous redox differences and changes in the context of tumor growth, inflammation, embryonic development, and nutrient starvation. Copyright © 2016, American Association for the Advancement of Science.

  8. Data-driven encoding for quantitative genetic trait prediction.

    Science.gov (United States)

    He, Dan; Wang, Zhanyong; Parida, Laxmi

    2015-01-01

    Given a set of biallelic molecular markers, such as SNPs, with genotype values on a collection of plant, animal or human samples, the goal of quantitative genetic trait prediction is to predict the quantitative trait values by simultaneously modeling all marker effects. Quantitative genetic trait prediction is usually represented as linear regression models which require quantitative encodings for the genotypes: the three distinct genotype values, corresponding to one heterozygous and two homozygous alleles, are usually coded as integers, and manipulated algebraically in the model. Further, epistasis between multiple markers is modeled as multiplication between the markers: it is unclear that the regression model continues to be effective under this. In this work we investigate the effects of encodings to the quantitative genetic trait prediction problem. We first showed that different encodings lead to different prediction accuracies, in many test cases. We then proposed a data-driven encoding strategy, where we encode the genotypes according to their distribution in the phenotypes and we allow each marker to have different encodings. We show in our experiments that this encoding strategy is able to improve the performance of the genetic trait prediction method and it is more helpful for the oligogenic traits, whose values rely on a relatively small set of markers. To the best of our knowledge, this is the first paper that discusses the effects of encodings to the genetic trait prediction problem.

  9. Use of genetically encoded calcium indicators (GECIs combined with advanced motion tracking techniques to examine the behavior of neurons and glia in the enteric nervous system of the intact murine colon

    Directory of Open Access Journals (Sweden)

    Grant Willem Hennig

    2015-11-01

    Full Text Available Genetically encoded Ca2+ indicators (GECIs have been used extensively in many body systems to detect Ca2+ transients associated with neuronal activity. Their adoption in enteric neurobiology has been slower, although they offer many advantages in terms of selectivity, signal-to-noise and non-invasiveness. Our aims were to utilize a number of cell-specific promoters to express the Ca2+ indicator GCaMP3 in different classes of neurons and glia to determine their effectiveness in measuring activity in enteric neural networks during colonic motor behaviors. We developed several GCaMP3 mice: 1 Wnt1-GCaMP3, all enteric neurons and glia; 2 GFAP-GCaMP3, enteric glia; 3 nNOS-GaMP3, enteric nitrergic neurons, and 4 ChAT-GCaMP3, enteric cholinergic neurons. These mice allowed us to study the behavior of the enteric neurons in the intact colon maintained at a physiological temperature, especially during the colonic migrating motor complex (CMMC, using low power Ca2+ imaging. In this preliminary study, we observed neuronal and glial cell Ca2+ transients in specific cells in both the myenteric and submucous plexus in all of the transgenic mice variants. The number of cells that could be simultaneously imaged at low power (100-1000 active cells through the undissected gut required advanced motion tracking and analysis routines. The pattern of Ca2+ transients in myenteric neurons showed significant differences in response to spontaneous, oral or anal stimulation. Brief anal elongation or mucosal stimulation, which evokes a CMMC, were the most effective stimuli and elicited a powerful synchronized and prolonged burst of Ca2+ transients in many myenteric neurons, especially when compared with the same neurons during a spontaneous CMMC. In contrast, oral elongation, which normally inhibits CMMCs, appeared to suppress Ca2+ transients some of the neurons active during a spontaneous or an anally evoked CMMC. The activity in glial networks appeared to follow neural

  10. Genetically-encoded biosensors for monitoring cellular stress in bioprocessing.

    Science.gov (United States)

    Polizzi, Karen M; Kontoravdi, Cleo

    2015-02-01

    With the current wealth of transcriptomic data, it is possible to design genetically-encoded biosensors for the detection of stress responses and apply these to high-throughput bioprocess development and monitoring of cellular health. Such biosensors can sense extrinsic factors such as nutrient or oxygen deprivation and shear stress, as well as intrinsic stress factors like oxidative damage and unfolded protein accumulation. Alongside, there have been developments in biosensing hardware and software applicable to the field of genetically-encoded biosensors in the near future. This review discusses the current state-of-the-art in biosensors for monitoring cultures during biological manufacturing and the future challenges for the field. Connecting the individual achievements into a coherent whole will enable the application of genetically-encoded biosensors in industry.

  11. A genetically encoded, high-signal-to-noise maltose sensor

    Energy Technology Data Exchange (ETDEWEB)

    Marvin, Jonathan S.; Schreiter, Eric R.; Echevarría, Ileabett M.; Looger, Loren L. (Puerto Rico); (HHMI)

    2012-10-23

    We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes.

  12. Aerodynamic Shape Optimization Using A Real-Number-Encoded Genetic Algorithm

    Science.gov (United States)

    Holst, Terry L.; Pulliam, Thomas H.

    2001-01-01

    A new method for aerodynamic shape optimization using a genetic algorithm with real number encoding is presented. The algorithm is used to optimize three different problems, a simple hill climbing problem, a quasi-one-dimensional nozzle problem using an Euler equation solver and a three-dimensional transonic wing problem using a nonlinear potential solver. Results indicate that the genetic algorithm is easy to implement and extremely reliable, being relatively insensitive to design space noise.

  13. Photoacoustic imaging using genetically encoded reporters: a review

    Science.gov (United States)

    Brunker, Joanna; Yao, Junjie; Laufer, Jan; Bohndiek, Sarah E.

    2017-07-01

    Genetically encoded contrast in photoacoustic imaging (PAI) is complementary to the intrinsic contrast provided by endogenous absorbing chromophores such as hemoglobin. The use of reporter genes expressing absorbing proteins opens the possibility of visualizing dynamic cellular and molecular processes. This is an enticing prospect but brings with it challenges and limitations associated with generating and detecting different types of reporters. The purpose of this review is to compare existing PAI reporters and signal detection strategies, thereby offering a practical guide, particularly for the nonbiologist, to choosing the most appropriate reporter for maximum sensitivity in the biological and technological system of interest.

  14. Recent Advances in Development of Genetically Encoded Fluorescent Sensors.

    Science.gov (United States)

    Sanford, Lynn; Palmer, Amy

    2017-01-01

    Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, fluorescence-modulated single FP-based sensors, translocation sensors, complementation sensors, and dimerization-based sensors. We discuss elements of sensor design and engineering for each platform, including the incorporation of new types of FPs and sensor screening techniques. Finally, we summarize the wide range of sensors in the literature, exploring creative new sensor architectures suitable for different applications.

  15. Engineering Genetically-Encoded Mineralization and Magnetism via Directed Evolution.

    Science.gov (United States)

    Liu, Xueliang; Lopez, Paola A; Giessen, Tobias W; Giles, Michael; Way, Jeffrey C; Silver, Pamela A

    2016-11-29

    Genetically encoding the synthesis of functional nanomaterials such as magnetic nanoparticles enables sensitive and non-invasive biological sensing and control. Via directed evolution of the natural iron-sequestering ferritin protein, we discovered key mutations that lead to significantly enhanced cellular magnetism, resulting in increased physical attraction of ferritin-expressing cells to magnets and increased contrast for cellular magnetic resonance imaging (MRI). The magnetic mutants further demonstrate increased iron biomineralization measured by a novel fluorescent genetic sensor for intracellular free iron. In addition, we engineered Escherichia coli cells with multiple genomic knockouts to increase cellular accumulation of various metals. Lastly to explore further protein candidates for biomagnetism, we characterized members of the DUF892 family using the iron sensor and magnetic columns, confirming their intracellular iron sequestration that results in increased cellular magnetization.

  16. Genetically encoded optical sensors for monitoring of intracellular chloride and chloride-selective channel activity

    Directory of Open Access Journals (Sweden)

    Piotr Bregestovski

    2009-12-01

    Full Text Available This review briefly discusses the main approaches for monitoring chloride (Cl−, the most abundant physiological anion. Noninvasive monitoring of intracellular Cl− ([Cl−]i is a challenging task owing to two main difficulties: (i the low transmembrane ratio for Cl−, approximately 10:1; and (ii the small driving force for Cl−, as the Cl− reversal potential (ECl is usually close to the resting potential of the cells. Thus, for reliable monitoring of intracellular Cl−, one has to use highly sensitive probes. From several methods for intracellular Cl− analysis, genetically encoded chloride indicators represent the most promising tools. Recent achievements in the development of genetically encoded chloride probes are based on the fact that yellow fluorescent protein (YFP exhibits Cl−-sensitivity. YFP-based probes have been successfully used for quantitative analysis of Cl− transport in different cells and for high-throughput screening of modulators of Cl−-selective channels. Development of a ratiometric genetically encoded probe, Clomeleon, has provided a tool for noninvasive estimation of intracellular Cl− concentrations. While the sensitivity of this protein to Cl− is low (EC50 about 160 mM, it has been successfully used for monitoring intracellular Cl− in different cell types. Recently a CFP–YFP-based probe with a relatively high sensitivity to Cl− (EC50 about 30 mM has been developed. This construct, termed Cl-Sensor, allows ratiometric monitoring using the fluorescence excitation ratio. Of particular interest are genetically encoded probes for monitoring of ion channel distribution and activity. A new molecular probe has been constructed by introducing into the cytoplasmic domain of the Cl−-selective glycine receptor (GlyR channel the CFP–YFP-based Cl-Sensor. This construct, termed BioSensor-GlyR, has been successfully expressed in cell lines. The new genetically encoded chloride probes offer means of screening

  17. Fluorescent Proteins as Genetically Encoded FRET Biosensors in Life Sciences

    Science.gov (United States)

    Hochreiter, Bernhard; Pardo Garcia, Alan; Schmid, Johannes A.

    2015-01-01

    Fluorescence- or Förster resonance energy transfer (FRET) is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a) cleavage; (b) conformational-change; (c) mechanical force and (d) changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them. PMID:26501285

  18. Fluorescent Proteins as Genetically Encoded FRET Biosensors in Life Sciences

    Directory of Open Access Journals (Sweden)

    Bernhard Hochreiter

    2015-10-01

    Full Text Available Fluorescence- or Förster resonance energy transfer (FRET is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a cleavage; (b conformational-change; (c mechanical force and (d changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them.

  19. Fluorescent proteins as genetically encoded FRET biosensors in life sciences.

    Science.gov (United States)

    Hochreiter, Bernhard; Garcia, Alan Pardo; Schmid, Johannes A

    2015-10-16

    Fluorescence- or Förster resonance energy transfer (FRET) is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a) cleavage; (b) conformational-change; (c) mechanical force and (d) changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them.

  20. Investigating genetic loci that encode plant-derived paleoclimate proxies

    Science.gov (United States)

    Bender, A. L. D.; Suess, M.; Chitwood, D. H.; Bradley, A. S.

    2016-12-01

    Long chain (>C25) n-alkanes in sediments predominantly derive from terrestrial plant waxes. Hydrogen isotope ratios (δD) of leaf wax hydrocarbons correlate with δDH2O of precipitation and are commonly used as paleoclimate proxies. However, biological variability in the isotopic fractionations between water and plant materials also affects the n-alkane δD values. Correct interpretation of this paleoclimate proxy requires that we resolve genetic and environmental effects. Genetic variability underlying differences in leaf wax structure and isotopic composition can be quantitatively determined through the use of model organisms. Interfertile Solanum sect. Lycopersicon (tomato) species provide an ideal model species complex for this approach. We used a set of 76 precisely defined near-isogenic lines (introgression lines [ILs]) in which small genomic regions from the wild tomato relative Solanum pennellii have been introduced into the genome of the domestic tomato, S. lycopersicum. By characterizing quantitative traits of these ILs (leaf wax structure and isotopic composition), we can resolve the degree to which each trait is regulated by genetic versus environmental factors. We present data from two growth experiments conducted with all 76 ILs. In this study, we quantify leaf wax traits, including δD values, δ13C values, and structural metrics including the methylation index (a variable that describes the ratio of iso­- and anteiso- to n-alkanes). Among ILs, δD values vary by up to 35‰ and 60‰ for C31 and C33 n-alkanes, respectively. Many ILs have methylation indices that are discernably different from the parent domesticated tomato (p < 0.001), which suggests that methylation is a highly polygenic trait. This pattern is similar to the genetics that control leaf shape, another trait commonly used as a paleoclimate proxy. Based on our preliminary analysis, we propose candidate genes that control aspects of plant physiology that affect these quantitative

  1. Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction

    OpenAIRE

    Lang, Kathrin; Davis, Lloyd; Torres-Kolbus, Jessica; Chou, Chungjung; Deiters, Alexander; Chin, Jason W.

    2012-01-01

    The site-specific incorporation of bioorthogonal groups via genetic code expansion provides a powerful general strategy for site-specifically labelling proteins with any probe. However, the slow reactivity of the bioorthogonal functional groups that can be encoded genetically limits the utility of this strategy. We demonstrate the genetic encoding of a norbornene amino acid using the pyrrolysyl tRNA synthetase/tRNACUA pair in Escherichia coli and mammalian cells. We developed a series of tetr...

  2. Evaluating a genetically encoded optical sensor of neural activity using electrophysiology in intact adult fruit flies

    Directory of Open Access Journals (Sweden)

    Gilles Laurent

    2007-11-01

    Full Text Available Genetically encoded optical indicators hold the promise of enabling non-invasive monitoring of activity in identified neurons in behaving organisms. However, the interpretation of images of brain activity produced using such sensors is not straightforward. Several recent studies of sensory coding used G-CaMP 1.3-a calcium sensor-as an indicator of neural activity; some of these studies characterized the imaged neurons as having narrow tuning curves, a conclusion not always supported by parallel electrophysiological studies. To better understand the possible cause of these conflicting results, we performed simultaneous in vivo 2-photon imaging and electrophysiological recording of G-CaMP 1.3 expressing neurons in the antennal lobe (AL of intact fruitflies. We find that G-CaMP has a relatively high threshold, that its signal often fails to capture spiking response kinetics, and that it can miss even high instantaneous rates of activity if those are not sustained. While G-CaMP can be misleading, it is clearly useful for the identification of promising neural targets: when electrical activity is well above the sensor's detection threshold, its signal is fairly well correlated with mean firing rate and G-CaMP does not appear to alter significantly the responses of neurons that express it. The methods we present should enable any genetically encoded sensor, activator, or silencer to be evaluated in an intact neural circuit in vivo in Drosophila.

  3. Visualizing presynaptic calcium dynamics and vesicle fusion with a single genetically encoded reporter at individual synapses

    Directory of Open Access Journals (Sweden)

    Rachel E Jackson

    2016-07-01

    Full Text Available Synaptic transmission depends on the influx of calcium into the presynaptic compartment, which drives neurotransmitter release. Genetically encoded reporters are widely used tools to understand these processes, particularly pHluorin-based reporters that report vesicle exocytosis and endocytosis through pH dependent changes in fluorescence, and genetically encoded calcium indicators (GECIs that exhibit changes in fluorescence upon binding to calcium. The recent expansion of the color palette of available indicators has made it possible to image multiple probes simultaneously within a cell. We have constructed a single molecule reporter capable of concurrent imaging of both presynaptic calcium influx and exocytosis, by fusion of sypHy, the vesicle associated protein synaptophysin containing a GFP-based pHluorin sensor, with the red-shifted GECI R-GECO1. Due to the fixed stoichiometry of the two probes, the ratio of the two responses can also be measured, providing an all optical correlate of the calcium dependence of release. Here, we have characterized stimulus-evoked sypHy-RGECO responses of hippocampal synapses in vitro, exploring the effects of different stimulus strengths and frequencies as well as variations in external calcium concentrations. By combining live sypHy-RGECO imaging with post-hoc fixation and immunofluorescence, we have also investigated correlations between structural and functional properties of synapses.

  4. Nonlinear inversion of potential-field data using a hybrid-encoding genetic algorithm

    Science.gov (United States)

    Chen, C.; Xia, J.; Liu, J.; Feng, G.

    2006-01-01

    Using a genetic algorithm to solve an inverse problem of complex nonlinear geophysical equations is advantageous because it does not require computer gradients of models or "good" initial models. The multi-point search of a genetic algorithm makes it easier to find the globally optimal solution while avoiding falling into a local extremum. As is the case in other optimization approaches, the search efficiency for a genetic algorithm is vital in finding desired solutions successfully in a multi-dimensional model space. A binary-encoding genetic algorithm is hardly ever used to resolve an optimization problem such as a simple geophysical inversion with only three unknowns. The encoding mechanism, genetic operators, and population size of the genetic algorithm greatly affect search processes in the evolution. It is clear that improved operators and proper population size promote the convergence. Nevertheless, not all genetic operations perform perfectly while searching under either a uniform binary or a decimal encoding system. With the binary encoding mechanism, the crossover scheme may produce more new individuals than with the decimal encoding. On the other hand, the mutation scheme in a decimal encoding system will create new genes larger in scope than those in the binary encoding. This paper discusses approaches of exploiting the search potential of genetic operations in the two encoding systems and presents an approach with a hybrid-encoding mechanism, multi-point crossover, and dynamic population size for geophysical inversion. We present a method that is based on the routine in which the mutation operation is conducted in the decimal code and multi-point crossover operation in the binary code. The mix-encoding algorithm is called the hybrid-encoding genetic algorithm (HEGA). HEGA provides better genes with a higher probability by a mutation operator and improves genetic algorithms in resolving complicated geophysical inverse problems. Another significant

  5. Inter-population differences in otolith morphology are genetically encoded in the killifish Aphanius fasciatus (Cyprinodontiformes

    Directory of Open Access Journals (Sweden)

    Ali Annabi

    2013-06-01

    Full Text Available Inter-population differences in otolith shape, morphology and chemistry have been used effectively as indicators for stock assessment or for recognizing environmental adaptation in fishes. However, the precise parameters that affect otolith morphology remain incompletely understood. Here we provide the first direct support for the hypothesis that inter-population differences in otolith morphology are genetically encoded. The study is based on otolith morphology and two mitochondrial markers (D-loop, 16S rRNA of three natural populations of Aphanius fasciatus (Teleostei: Cyprinodontidae from Southeast Tunisia. Otolith and genetic data yielded congruent tree topologies. Divergence of populations likely results from isolation events in the course of the Pleistocene sea level drops. We propose that otolith morphology is a valuable tool for resolving genetic diversity also within other teleost species, which may be important for ecosystem management and conservation of genetic diversity. As reconstructions of ancient teleost fish faunas are often solely based on fossil otoliths, our discoveries may also lead to a new approach to research in palaeontology.

  6. Procedures for estimation of genetic persistency indices for milk ...

    African Journals Online (AJOL)

    Procedures for estimation of genetic persistency indices for milk production for the ... as included in the National Dairy Genetic Evaluations of South Africa, of the ... records to calculate 60-day and 280-day yields for each cow and lactation.

  7. Genetic encoding of the post-translational modification 2-hydroxyisobutyryl-lysine

    OpenAIRE

    Knight, William A.; Cropp, T.Ashton

    2015-01-01

    We report the synthesis and genetic encoding of a recently discovered posttranslational modification, 2-hydroxyisobutryl-lysine, to the genetic code of E. coli. The production of homogeneous proteins containing this amino acid will facilitate the study of modification in full-length proteins.

  8. Genetically encoded tools: bridging the gap between neuronal identity and function.

    Science.gov (United States)

    Cho, Yong Ku

    2015-01-21

    Genetically encoded tools are positioned to serve a unique and critical role in bridging the gap between the genetic identity of neurons and their functional properties. However, the use of these tools is limited by our current understanding of cell-type identity. As we make technological advances that focus on capturing functional aspects of neurons such as connectivity, activity, and metabolic states, our understanding of neuronal identity will deepen and may enable the use of genetically encoded tools for modulating disease-specific circuits for therapeutic purposes.

  9. A genetically encoded biosensor for visualising hypoxia responses in vivo

    Science.gov (United States)

    Misra, Tvisha; Baccino-Calace, Martin; Meyenhofer, Felix; Rodriguez-Crespo, David; Akarsu, Hatice; Armenta-Calderón, Ricardo; Gorr, Thomas A.; Frei, Christian; Cantera, Rafael; Egger, Boris

    2017-01-01

    ABSTRACT Cells experience different oxygen concentrations depending on location, organismal developmental stage, and physiological or pathological conditions. Responses to reduced oxygen levels (hypoxia) rely on the conserved hypoxia-inducible factor 1 (HIF-1). Understanding the developmental and tissue-specific responses to changing oxygen levels has been limited by the lack of adequate tools for monitoring HIF-1 in vivo. To visualise and analyse HIF-1 dynamics in Drosophila, we used a hypoxia biosensor consisting of GFP fused to the oxygen-dependent degradation domain (ODD) of the HIF-1 homologue Sima. GFP-ODD responds to changing oxygen levels and to genetic manipulations of the hypoxia pathway, reflecting oxygen-dependent regulation of HIF-1 at the single-cell level. Ratiometric imaging of GFP-ODD and a red-fluorescent reference protein reveals tissue-specific differences in the cellular hypoxic status at ambient normoxia. Strikingly, cells in the larval brain show distinct hypoxic states that correlate with the distribution and relative densities of respiratory tubes. We present a set of genetic and image analysis tools that enable new approaches to map hypoxic microenvironments, to probe effects of perturbations on hypoxic signalling, and to identify new regulators of the hypoxia response. PMID:28011628

  10. Controlling Macromolecular Topology with Genetically Encoded SpyTag-SpyCatcher Chemistry

    OpenAIRE

    Zhang, Wen-Bin; Sun, Fei; Tirrell, David A.; Arnold, Frances H.

    2013-01-01

    Control of molecular topology constitutes a fundamental challenge in macromolecular chemistry. Here we describe the synthesis and characterization of artificial elastin-like proteins (ELPs) with unconventional nonlinear topologies including circular, tadpole, star, and H-shaped proteins using genetically encoded SpyTag–SpyCatcher chemistry. SpyTag is a short polypeptide that binds its protein partner SpyCatcher and forms isopeptide bonds under physiological conditions. Sequences encoding SpyT...

  11. Characterization of the Single Stranded DNA Binding Protein SsbB Encoded in the Gonoccocal Genetic Island

    NARCIS (Netherlands)

    Jain, Samta; Zweig, Maria; Peeters, Eveline; Siewering, Katja; Hackett, Kathleen T.; Dillard, Joseph P.; van der Does, Chris

    2012-01-01

    Background: Most strains of Neisseria gonorrhoeae carry a Gonococcal Genetic Island which encodes a type IV secretion system involved in the secretion of ssDNA. We characterize the GGI-encoded ssDNA binding protein, SsbB. Close homologs of SsbB are located within a conserved genetic cluster found in

  12. Exploring dynamics of molybdate in living animal cells by a genetically encoded FRET nanosensor.

    Science.gov (United States)

    Nakanishi, Yoichi; Iida, Syuntaro; Ueoka-Nakanishi, Hanayo; Niimi, Tomoaki; Tomioka, Rie; Maeshima, Masayoshi

    2013-01-01

    Molybdenum (Mo) is an essential trace element for almost all living organisms including animals. Mo is used as a catalytic center of molybdo-enzymes for oxidation/reduction reactions of carbon, nitrogen, and sulfur metabolism. Whilst living cells are known to import inorganic molybdate oxyanion from the surrounding environment, the in vivo dynamics of cytosolic molybdate remain poorly understood as no appropriate indicator is available for this trace anion. We here describe a genetically encoded Förester-resonance-energy-transfer (FRET)-based nanosensor composed of CFP, YFP and the bacterial molybdate-sensor protein ModE. The nanosensor MolyProbe containing an optimized peptide-linker responded to nanomolar-range molybdate selectively, and increased YFP:CFP fluorescence intensity ratio by up to 109%. By introduction of the nanosensor, we have been able to successfully demonstrate the real-time dynamics of molybdate in living animal cells. Furthermore, time course analyses of the dynamics suggest that novel oxalate-sensitive- and sulfate-resistant- transporter(s) uptake molybdate in a model culture cell.

  13. Imaging Membrane Potential with Two Types of Genetically Encoded Fluorescent Voltage Sensors.

    Science.gov (United States)

    Lee, Sungmoo; Piao, Hong Hua; Sepheri-Rad, Masoud; Jung, Arong; Sung, Uhna; Song, Yoon-Kyu; Baker, Bradley J

    2016-02-04

    Genetically encoded voltage indicators (GEVIs) have improved to the point where they are beginning to be useful for in vivo recordings. While the ultimate goal is to image neuronal activity in vivo, one must be able to image activity of a single cell to ensure successful in vivo preparations. This procedure will describe how to image membrane potential in a single cell to provide a foundation to eventually image in vivo. Here we describe methods for imaging GEVIs consisting of a voltage-sensing domain fused to either a single fluorescent protein (FP) or two fluorescent proteins capable of Förster resonance energy transfer (FRET) in vitro. Using an image splitter enables the projection of images created by two different wavelengths onto the same charge-coupled device (CCD) camera simultaneously. The image splitter positions a second filter cube in the light path. This second filter cube consists of a dichroic and two emission filters to separate the donor and acceptor fluorescent wavelengths depending on the FPs of the GEVI. This setup enables the simultaneous recording of both the acceptor and donor fluorescent partners while the membrane potential is manipulated via whole cell patch clamp configuration. When using a GEVI consisting of a single FP, the second filter cube can be removed allowing the mirrors in the image splitter to project a single image onto the CCD camera.

  14. Common genetic variation in the human CTF1 locus, encoding cardiotrophin-1, determines insulin sensitivity.

    Directory of Open Access Journals (Sweden)

    Stefan Z Lutz

    Full Text Available AIMS/HYPOTHESIS: Recently, cardiotrophin-1, a member of the interleukin-6 family of cytokines was described to protect beta-cells from apoptosis, to improve glucose-stimulated insulin secretion and insulin resistance, and to prevent streptozotocin-induced diabetes in mice. Here, we studied whether common single nucleotide polymorphisms (SNPs in the CTF1 locus, encoding cardiotrophin-1, influence insulin secretion and insulin sensitivity in humans. METHODS: We genotyped 1,771 German subjects for three CTF1 tagging SNPs (rs1046276, rs1458201, and rs8046707. The subjects were metabolically characterized by an oral glucose tolerance test. Subgroups underwent magnetic resonance (MR imaging/spectroscopy and hyperinsulinaemic-euglycaemic clamps. RESULTS: After appropriate adjustment, the minor allele of CTF1 SNP rs8046707 was significantly associated with decreased in vivo measures of insulin sensitivity. The other tested SNPs were not associated with OGTT-derived sensitivity parameters, nor did the three tested SNPs show any association with OGTT-derived parameters of insulin release. In the MR subgroup, SNP rs8046707 was nominally associated with lower visceral adipose tissue. Furthermore, the SNP rs1458201 showed a nominal association with increased VLDL levels. CONCLUSIONS: In conclusion, this study, even though preliminary and awaiting further confirmation by independent replication, provides first evidence that common genetic variation in CTF1 could contribute to insulin sensitivity in humans. Our SNP data indicate an insulin-desensitizing effect of cardiotrophin-1 and underline that cardiotrophin-1 represents an interesting target to influence insulin sensitivity.

  15. Organoids and the genetically encoded self-assembly of embryonic stem cells.

    Science.gov (United States)

    Turner, David A; Baillie-Johnson, Peter; Martinez Arias, Alfonso

    2016-02-01

    Understanding the mechanisms of early embryonic patterning and the timely allocation of specific cells to embryonic regions and fates as well as their development into tissues and organs, is a fundamental problem in Developmental Biology. The classical explanation for this process had been built around the notion of positional information. Accordingly the programmed appearance of sources of Morphogens at localized positions within a field of cells directs their differentiation. Recently, the development of organs and tissues from unpatterned and initially identical stem cells (adult and embryonic) has challenged the need for positional information and even the integrity of the embryo, for pattern formation. Here we review the emerging area of organoid biology from the perspective of Developmental Biology. We argue that the events underlying the development of these systems are not purely linked to self-organization, as often suggested, but rather to a process of genetically encoded self-assembly where genetic programs encode and control the emergence of biological structures.

  16. Application of Hybrid Encoding Genetic Algorithm on Pickup and Delivery Traveling Salesman Problem with Traffic Conditions

    Directory of Open Access Journals (Sweden)

    S. Patvichaichod

    2011-01-01

    Full Text Available Problem statement: This study deals with the pickup and delivery traveling salesman problem with traffic conditions (PDTSPTW, an extension of the pickup and delivery traveling salesman problem (PDTSP where each customer to be served is associated with two quantities of product to be collected and delivered. Almost PDTSP problems uses distance between each point of customers as Euclidean Distance and are not concerned with other parameters to find minimal cost. Approach: The PDTSPTC concerns more parameters, such as street network and vehicle speed, which results it closer to the real world condition. The study also proposes the developed genetic algorithm called “Hybrid Encoding Genetic Algorithm (HEGA”. The concept is to combine binary encoding and integer encoding together, causing the in complexity of the algorithm structure and the ease of implementation. Results: the HEGA can save the travel cost about 26-57%. It is obviously seen that HEGA in the PDTSPTC test problems result the fast convergence that is about 12-43% and in all, the computational time is under 6 seconds. Conclusion: The HEGA performs quite well when testing a test problem. Computation times are small in all case. The PDTSPTC is closer to real-world conditions than PDTSP. This problem can be applied in logistics immediately if the distance of streets, traffic conditions (average vehicle speed in each street and vehicle conditions (fuel consumption rate and vehicle capacity are known.

  17. Drosophila domino Exhibits Genetic Interactions with a Wide Spectrum of Chromatin Protein-Encoding Loci.

    Science.gov (United States)

    Ellis, Kaitlyn; Friedman, Chloe; Yedvobnick, Barry

    2015-01-01

    The Drosophila domino gene encodes protein of the SWI2/SNF2 family that has widespread roles in transcription, replication, recombination and DNA repair. Here, the potential relationship of Domino protein to other chromatin-associated proteins has been investigated through a genetic interaction analysis. We scored for genetic modification of a domino wing margin phenotype through coexpression of RNAi directed against a set of previously characterized and more newly characterized chromatin-encoding loci. A set of other SWI2/SNF2 loci were also assayed for interaction with domino. Our results show that the majority of tested loci exhibit synergistic enhancement or suppression of the domino wing phenotype. Therefore, depression in domino function sensitizes the wing margin to alterations in the activity of numerous chromatin components. In several cases the genetic interactions are associated with changes in the level of cell death measured across the dorsal-ventral margin of the wing imaginal disc. These results highlight the broad realms of action of many chromatin proteins and suggest significant overlap with Domino function in fundamental cell processes, including cell proliferation, cell death and cell signaling.

  18. Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain.

    Directory of Open Access Journals (Sweden)

    Corey M Hudson

    Full Text Available Multidrug-resistant Enterobacteriaceae are emerging as a serious infectious disease challenge. These strains can accumulate many antibiotic resistance genes though horizontal transfer of genetic elements, those for β-lactamases being of particular concern. Some β-lactamases are active on a broad spectrum of β-lactams including the last-resort carbapenems. The gene for the broad-spectrum and carbapenem-active metallo-β-lactamase NDM-1 is rapidly spreading. We present the complete genome of Klebsiella pneumoniae ATCC BAA-2146, the first U.S. isolate found to encode NDM-1, and describe its repertoire of antibiotic-resistance genes and mutations, including genes for eight β-lactamases and 15 additional antibiotic-resistance enzymes. To elucidate the evolution of this rich repertoire, the mobile elements of the genome were characterized, including four plasmids with varying degrees of conservation and mosaicism and eleven chromosomal genomic islands. One island was identified by a novel phylogenomic approach, that further indicated the cps-lps polysaccharide synthesis locus, where operon translocation and fusion was noted. Unique plasmid segments and mosaic junctions were identified. Plasmid-borne blaCTX-M-15 was transposed recently to the chromosome by ISEcp1. None of the eleven full copies of IS26, the most frequent IS element in the genome, had the expected 8-bp direct repeat of the integration target sequence, suggesting that each copy underwent homologous recombination subsequent to its last transposition event. Comparative analysis likewise indicates IS26 as a frequent recombinational junction between plasmid ancestors, and also indicates a resolvase site. In one novel use of high-throughput sequencing, homologously recombinant subpopulations of the bacterial culture were detected. In a second novel use, circular transposition intermediates were detected for the novel insertion sequence ISKpn21 of the ISNCY family, suggesting that it uses

  19. Genetic encoding of caged cysteine and caged homocysteine in bacterial and mammalian cells.

    Science.gov (United States)

    Uprety, Rajendra; Luo, Ji; Liu, Jihe; Naro, Yuta; Samanta, Subhas; Deiters, Alexander

    2014-08-18

    We report the genetic incorporation of caged cysteine and caged homocysteine into proteins in bacterial and mammalian cells. The genetic code of these cells was expanded with an engineered pyrrolysine tRNA/tRNA synthetase pair that accepts both light-activatable amino acids as substrates. Incorporation was validated by reporter assays, western blots, and mass spectrometry, and differences in incorporation efficiency were explained by molecular modeling of synthetase-amino acid interactions. As a proof-of-principle application, the genetic replacement of an active-site cysteine residue with a caged cysteine residue in Renilla luciferase led to a complete loss of enzyme activity; however, upon brief exposure to UV light, a >150-fold increase in enzymatic activity was observed, thus showcasing the applicability of the caged cysteine in live human cells. A simultaneously conducted genetic replacement with homocysteine yielded an enzyme with greatly reduced activity, thereby demonstrating the precise probing of a protein active site. These discoveries provide a new tool for the optochemical control of protein function in mammalian cells and expand the set of genetically encoded unnatural amino acids.

  20. StrigoQuant: A genetically encoded biosensor for quantifying strigolactone activity and specificity

    KAUST Repository

    Samodelov, S. L.

    2016-11-05

    Strigolactones are key regulators of plant development and interaction with symbiotic fungi; however, quantitative tools for strigolactone signaling analysis are lacking. We introduce a genetically encoded hormone biosensor used to analyze strigolactone-mediated processes, including the study of the components involved in the hormone perception/signaling complex and the structural specificity and sensitivity of natural and synthetic strigolactones in Arabidopsis, providing quantitative insights into the stereoselectivity of strigolactone perception. Given the high specificity, sensitivity, dynamic range of activity, modular construction, ease of implementation, and wide applicability, the biosensor StrigoQuant will be useful in unraveling multiple levels of strigolactone metabolic and signaling networks.

  1. Rapid Cellular Phenotyping of Human Pluripotent Stem Cell-Derived Cardiomyocytes using a Genetically Encoded Fluorescent Voltage Sensor

    Directory of Open Access Journals (Sweden)

    Jordan S. Leyton-Mange

    2014-02-01

    Full Text Available In addition to their promise in regenerative medicine, pluripotent stem cells have proved to be faithful models of many human diseases. In particular, patient-specific stem cell-derived cardiomyocytes recapitulate key features of several life-threatening cardiac arrhythmia syndromes. For both modeling and regenerative approaches, phenotyping of stem cell-derived tissues is critical. Cellular phenotyping has largely relied upon expression of lineage markers rather than physiologic attributes. This is especially true for cardiomyocytes, in part because electrophysiological recordings are labor intensive. Likewise, most optical voltage indicators suffer from phototoxicity, which damages cells and degrades signal quality. Here we present the use of a genetically encoded fluorescent voltage indicator, ArcLight, which we demonstrate can faithfully report transmembrane potentials in human stem cell-derived cardiomyocytes. We demonstrate the application of this fluorescent sensor in high-throughput, serial phenotyping of differentiating cardiomyocyte populations and in screening for drug-induced cardiotoxicity.

  2. pHlash: A New Genetically Encoded and Ratiometric Luminescence Sensor of Intracellular pH

    Science.gov (United States)

    Robertson, J. Brian; Johnson, Carl Hirschie

    2012-01-01

    We report the development of a genetically encodable and ratiometic pH probe named “pHlash” that utilizes Bioluminescence Resonance Energy Transfer (BRET) rather than fluorescence excitation. The pHlash sensor–composed of a donor luciferase that is genetically fused to a Venus fluorophore–exhibits pH dependence of its spectral emission in vitro. When expressed in either yeast or mammalian cells, pHlash reports basal pH and cytosolic acidification in vivo. Its spectral ratio response is H+ specific; neither Ca++, Mg++, Na+, nor K+ changes the spectral form of its luminescence emission. Moreover, it can be used to image pH in single cells. This is the first BRET-based sensor of H+ ions, and it should allow the approximation of pH in cytosolic and organellar compartments in applications where current pH probes are inadequate. PMID:22905204

  3. pHlash: a new genetically encoded and ratiometric luminescence sensor of intracellular pH.

    Directory of Open Access Journals (Sweden)

    Yunfei Zhang

    Full Text Available We report the development of a genetically encodable and ratiometic pH probe named "pHlash" that utilizes Bioluminescence Resonance Energy Transfer (BRET rather than fluorescence excitation. The pHlash sensor-composed of a donor luciferase that is genetically fused to a Venus fluorophore-exhibits pH dependence of its spectral emission in vitro. When expressed in either yeast or mammalian cells, pHlash reports basal pH and cytosolic acidification in vivo. Its spectral ratio response is H(+ specific; neither Ca(++, Mg(++, Na(+, nor K(+ changes the spectral form of its luminescence emission. Moreover, it can be used to image pH in single cells. This is the first BRET-based sensor of H(+ ions, and it should allow the approximation of pH in cytosolic and organellar compartments in applications where current pH probes are inadequate.

  4. Genetic control of encoding strategy in a food-sensing neural circuit

    Science.gov (United States)

    Diana, Giovanni; Patel, Dhaval S; Entchev, Eugeni V; Zhan, Mei; Lu, Hang; Ch'ng, QueeLim

    2017-01-01

    Neuroendocrine circuits encode environmental information via changes in gene expression and other biochemical activities to regulate physiological responses. Previously, we showed that daf-7 TGFβ and tph-1 tryptophan hydroxylase expression in specific neurons encode food abundance to modulate lifespan in Caenorhabditis elegans, and uncovered cross- and self-regulation among these genes (Entchev et al., 2015). Here, we now extend these findings by showing that these interactions between daf-7 and tph-1 regulate redundancy and synergy among neurons in food encoding through coordinated control of circuit-level signal and noise properties. Our analysis further shows that daf-7 and tph-1 contribute to most of the food-responsiveness in the modulation of lifespan. We applied a computational model to capture the general coding features of this system. This model agrees with our previous genetic analysis and highlights the consequences of redundancy and synergy during information transmission, suggesting a rationale for the regulation of these information processing features. DOI: http://dx.doi.org/10.7554/eLife.24040.001 PMID:28166866

  5. FRET-based genetically-encoded sensors for quantitative monitoring of metabolites.

    Science.gov (United States)

    Mohsin, Mohd; Ahmad, Altaf; Iqbal, Muhammad

    2015-10-01

    Neighboring cells in the same tissue can exist in different states of dynamic activities. After genomics, proteomics and metabolomics, fluxomics is now equally important for generating accurate quantitative information on the cellular and sub-cellular dynamics of ions and metabolite, which is critical for functional understanding of organisms. Various spectrometry techniques are used for monitoring ions and metabolites, although their temporal and spatial resolutions are limited. Discovery of the fluorescent proteins and their variants has revolutionized cell biology. Therefore, novel tools and methods targeting sub-cellular compartments need to be deployed in specific cells and targeted to sub-cellular compartments in order to quantify the target-molecule dynamics directly. We require tools that can measure cellular activities and protein dynamics with sub-cellular resolution. Biosensors based on fluorescence resonance energy transfer (FRET) are genetically encoded and hence can specifically target sub-cellular organelles by fusion to proteins or targetted sequences. Since last decade, FRET-based genetically encoded sensors for molecules involved in energy production, reactive oxygen species and secondary messengers have helped to unravel key aspects of cellular physiology. This review, describing the design and principles of sensors, presents a database of sensors for different analytes/processes, and illustrate examples of application in quantitative live cell imaging.

  6. Genetic analysis of processed in-line mastitis indicator data

    DEFF Research Database (Denmark)

    Sørensen, Lars Peter; Løvendahl, Peter

    2013-01-01

    on exponential smoothing of the SCC values followed by factor analysis for estimation of the latent variable EMR was used. Finally, EMR was expressed as a continuum on the interval [0;1] using sigmoid transformation. Thus, an EMR value close to zero indicates low risk of mastitis and a value close to one...... indicates high risk of mastitis. The EMR values were summarized for each cow using the log-transformed median EMR. A second trait was defined as the median of the log-transformed SCC values from 5 to 305 d in milk. A bivariate animal model was used for estimation of co-variance components for the 2 traits....... The fixed part of the model included herd and parity. Estimates of heritability were 0.08 (SE = 0.04) and 0.14 (SE = 0.05) for EMR and SCC, respectively. The genetic correlation between the 2 traits was 0.97 (SE = 0.08). The high genetic correlation indicates that the 2 traits are influenced by common genes...

  7. Genetic characterization of psp encoding the DING protein in Pseudomonas fluorescens SBW25

    Directory of Open Access Journals (Sweden)

    Zhang Xue-Xian

    2007-12-01

    Full Text Available Abstract Background DING proteins constitute a conserved and broadly distributed set of proteins found in bacteria, fungi, plants and animals (including humans. Characterization of DING proteins from animal and plant tissues indicated ligand-binding ability suggesting a role for DING proteins in cell signaling and biomineralization. Surprisingly, the genes encoding DING proteins in eukaryotes have not been identified in the eukaryotic genome or EST databases. Recent discovery of a DING homologue (named Psp here in the genome of Pseudomonas fluorescens SBW25 provided a unique opportunity to investigate the physiological roles of DING proteins. P. fluorescens SBW25 is a model bacterium that can efficiently colonize plant surfaces and enhance plant health. In this report we genetically characterize Psp with a focus on conditions under which psp is expressed and the protein exported. Results Psp is closely related to the periplasmic Pi binding component of the ABC-type phosphate transporter system (Pst. psp is flanked by a gene cluster predicted to function as a type II protein secretion system (Hxc. Deletion analysis combined with chromosomally integrated 'lacZ fusions showed that both psp and pstC are induced by Pi limitation and that pstC is required for competitive growth of the bacterium in Pi limited medium. hxcR is not regulated by Pi limitation. Psp was detected (using anti-DING serum in the supernatant of wild-type culture but was greatly reduced in the supernatant of an isogenic strain carrying an hxcR mutation (ΔhxcR. A promoter fusion between hxcR and a promoterless copy of a gene ('dapB essential for growth in the plant environment showed that expression of hxcR is elevated during colonization of sugar beet seedlings. A similar analysis of psp showed that it is not induced in the plant environment. Conclusion Psp gene is expressed under conditions of Pi limitation. It is an exoprotein secreted mainly via the Hxc type II secretion

  8. Calibration and functional analysis of three genetically encoded Cl−/pH sensors

    Directory of Open Access Journals (Sweden)

    Marat eMukhtarov

    2013-04-01

    Full Text Available Monitoring of the intracellular concentrations of Cl− and H+ requires sensitive probes that allow reliable quantitative measurements without perturbation of cell functioning. For these purposes the most promising are genetically encoded fluorescent biosensors, which have become powerful tools for non-invasive intracellular monitoring of ions, molecules and enzymatic activity. A ratiometric CFP/YFP-based construct with a relatively good sensitivity to Cl− has been developed (Markova et al., 2008; Waseem et al., 2010. Recently, a combined Cl−/pH sensor (ClopHensor opened the way for simultaneous ratiometric measurement of these two ions (Arosio et al., 2010. ClopHensor was obtained by fusion of a red-fluorescent protein (DsRed-monomer to the E2GFP variant that contains a specific Cl−-binding site. This construct possesses pKa = 6.8 for H+ and Kd in the 40-50 mM range for Cl− at physiological pH (~7.3 As in the majority of cell types the intracellular Cl− concentration ([Cl−]i is about 10 mM, the development of sensors with higher sensitivity is highly desirable. Here we report the intracellular calibration and functional characterization of ClopHensor and its two derivatives: the membrane targeting PalmPalm-ClopHensor and the H148G/V224L mutant with improved Cl− affinity, reduced pH dependence and pKa shifted to more alkaline values. For functional analysis, constructs were expressed in CHO cells and [Cl−]i was changed by using pipettes with different Cl− concentrations during whole-cell recordings. Kd values for Cl− measured at 33°C and pH ~ 7.3 were, respectively, 39 mM, 47 mM and 21 mM for ClopHensor, PalmPalm-ClopHensor and the H148G/V224L mutant. PalmPalm-ClopHensor resolved responses to activation of Cl−-selective glycine receptor channels better than did ClopHensor. Our observations indicate that these different ClopHensor constructs are promising tools for non-invasive measurement of [Cl−]i in various living

  9. Illumination of the Spatial Order of Intracellular pH by Genetically Encoded pH-Sensitive Sensors

    Directory of Open Access Journals (Sweden)

    Mojca Benčina

    2013-12-01

    Full Text Available Fluorescent proteins have been extensively used for engineering genetically encoded sensors that can monitor levels of ions, enzyme activities, redox potential, and metabolites. Certain fluorescent proteins possess specific pH-dependent spectroscopic features, and thus can be used as indicators of intracellular pH. Moreover, concatenated pH-sensitive proteins with target proteins pin the pH sensors to a definite location within the cell, compartment, or tissue. This study provides an overview of the continually expanding family of pH-sensitive fluorescent proteins that have become essential tools for studies of pH homeostasis and cell physiology. We describe and discuss the design of intensity-based and ratiometric pH sensors, their spectral properties and pH-dependency, as well as their performance. Finally, we illustrate some examples of the applications of pH sensors targeted at different subcellular compartments.

  10. Shining light on signaling and metabolic networks by genetically encoded biosensors

    Science.gov (United States)

    Lalonde, Sylvie; Ehrhardt, David W; Frommer, Wolf B

    2009-01-01

    Fluorescent labels have revolutionized cell biology. Signaling intermediates and metabolites can be measured in real time with subcellular spatial resolution. Most of these sensors are based on fluorescent proteins, and many report fluorescence resonance energy transfer. Because the biosensors are genetically encoded, a toolbox for addressing cell biological questions at the systems level is now available. Fluorescent biosensors are able to determine the localization of proteins and their dynamics, to reveal the cellular and subcellular localization of the respective interactions and activities, and to provide complementary data on the steady state levels of ions, metabolites, and signaling intermediates with high temporal and spatial resolution. They represent the basis for cell-based high-throughput assays that are necessary for a systems perspective on plant cell function. PMID:16188489

  11. Probing the Catalytic Charge-Relay System in Alanine Racemase with Genetically Encoded Histidine Mimetics.

    Science.gov (United States)

    Sharma, Vangmayee; Wang, Yane-Shih; Liu, Wenshe R

    2016-12-16

    Histidine is a unique amino acid with an imidazole side chain in which both of the nitrogen atoms are capable of serving as a proton donor and proton acceptor in hydrogen bonding interactions. In order to probe the functional role of histidine involved in hydrogen bonding networks, fine-tuning the hydrogen bonding potential of the imidazole side chain is required but not feasible through traditional mutagenesis methods. Here, we show that two close mimetics of histidine, 3-methyl-histidine and thiazole alanine, can be genetically encoded using engineered pyrrolysine incorporation machinery. Replacement of the three histidine residues predicted to be involved in an extended charge-relay system in alanine racemase with 3-methyl-histidine or thiazole alanine shows a dramatic loss in the enzyme's catalytic efficiency, implying the role of this extended charge-relay system in activating the active site residue Y265, a general acid/base catalyst in the enzyme.

  12. Statistical sulcal shape comparisons: application to the detection of genetic encoding of the central sulcus shape

    DEFF Research Database (Denmark)

    Le Goualher, G; Argenti, A.M.; Duyme, M

    2000-01-01

    Principal Component Analysis allows a quantitative description of shape variability with a restricted number of parameters (or modes) which can be used to quantify the difference between two shapes through the computation of a modal distance. A statistical test can then be applied to this set...... encoding. When applied to real data, this study highlighted genetic constraints on the shape of the central sulcus. We found from 10 pairs of monozygotic twins that the intrapair modal distance of the central sulcus was significantly smaller than the interpair modal distance, for both the left central...... sulcus (Z = -2.66; P definition of the central sulcus shape were confirmed by applying the same experiment to 10 pairs of normal young individuals (Z = -1.39; Z = -0.63, i.e., values not significant at the P

  13. A fully genetically encoded protein architecture for optical control of peptide ligand concentration

    Science.gov (United States)

    Schmidt, Daniel; Tillberg, Paul W.; Chen, Fei; Boyden, Edward S.

    2014-01-01

    Ion channels are among the most important proteins in biology, regulating the activity of excitable cells and changing in diseases. Ideally it would be possible to actuate endogenous ion channels, in a temporally precise and reversible manner, and without requiring chemical cofactors. Here we present a modular protein architecture for fully genetically encoded, light-modulated control of ligands that modulate ion channels of a targeted cell. Our reagent, which we call a lumitoxin, combines a photoswitch and an ion channel-blocking peptide toxin. Illumination causes the photoswitch to unfold, lowering the toxin's local concentration near the cell surface, and enabling the ion channel to function. We explore lumitoxin modularity by showing operation with peptide toxins that target different voltage-dependent K+ channels. The lumitoxin architecture may represent a new kind of modular protein-engineering strategy for designing light-activated proteins, and thus may enable development of novel tools for modulating cellular physiology.

  14. Node ordinal encoded genetic algorithm for the optimal allocation of water resources

    Institute of Scientific and Technical Information of China (English)

    YANG Xiaohua; YANG Zhifeng; SHEN Zhenyao; LI Jianqiang

    2005-01-01

    A new method, node ordinal encoded genetic algorithm (NOEGA), is proposed for solving water resources optimal allocation problems, in which the capacity of water resources is split into a number of smaller parts so that successive operations can be overlapped. Our objective is to maximize the whole benefit function. To overcome the "dimensionality and algorithm complexity curse" while searching for solutions and looking for an optimal solution, the operations of one-point crossover operator, gene exchange operator, gene random operator, gene shift operator and node ordinal strings are established. It is proved to be an effective optimal method in searching for global solutions. The NOEGA does not need a diversity of initial population, and it does not have the problem of immature convergence. The results of two cases show that using NOEGA to solve the optimal allocation model is very efficient and robust. In addition, the algorithm complexity of NOEGA is discussed.

  15. Development and properties of genetically encoded pH sensors in plants.

    Directory of Open Access Journals (Sweden)

    Alexandre eMartinière

    2013-12-01

    Full Text Available Fluorescent proteins (FPs have given access to a large choice of live imaging techniques and has thereby profoundly modified our view of plant cells. Together with technological improvement of imaging, they have opened the possibility to monitor physico-chemical changes within cells. For this purpose, a new generation of fluorescent proteins has been engineered. For instance, pHluorin, a point mutated version of GFP, allows to get local pH estimates. In this paper, we will describe how genetically encoded sensors can be used to measure pH in the microenvironment of living tissues and subsequently discuss the role of pH in (i exocytosis, (ii ion uptake by plant roots, (iii cell growth and (iv protein trafficking.

  16. Lentivectors encoding immunosuppressive proteins genetically engineer pancreatic beta-cells to correct diabetes in allogeneic mice.

    Science.gov (United States)

    Kojaoghlanian, T; Joseph, A; Follenzi, A; Zheng, J H; Leiser, M; Fleischer, N; Horwitz, M S; DiLorenzo, T P; Goldstein, H

    2009-03-01

    The effectiveness of genetic engineering with lentivectors to protect transplanted cells from allogeneic rejection was examined using, as a model, type 1 diabetes treatment with beta-cell transplantation, whose widespread use has been limited by the requirement for sustained immunosuppressive treatment to prevent graft rejection. We examined whether lentivectors expressing select immunosuppressive proteins encoded by the adenoviral genome early region 3 (AdE3) would protect transplanted beta-cells from an alloimmune attack. The insulin-producing beta-cell line beta TC-tet (C3HeB/FeJ-derived) was transduced with lentiviruses encoding the AdE3 proteins gp19K and RID alpha/beta. The efficiency of lentiviral transduction of beta TC-tet cells exceeded 85%. Lentivector expression of gp19K decreased surface class I major histocompatibility complex expression by over 90%, whereas RID alpha/beta expression inhibited cytokine-induced Fas upregulation by over 75%. beta TC-tet cells transduced with gp19K and RID alpha/beta lentivectors, but not with a control lentivector, provided prolonged correction of hyperglycemia after transplantation into diabetic BALB/c severe combined immunodeficient mice reconstituted with allogeneic immune effector cells or into diabetic allogeneic BALB/c mice. Thus, genetic engineering of beta-cells using gp19K- and RID alpha/beta-expressing lentiviral vectors may provide an alternative that has the potential to eliminate or reduce treatment with the potent immunosuppressive agents necessary at present for prolonged engraftment with transplanted islets.

  17. Reversibly switchable photoacoustic tomography using a genetically encoded near-infrared phytochrome

    Science.gov (United States)

    Yao, Junjie; Kaberniuk, Andrii A.; Li, Lei; Shcherbakova, Daria M.; Zhang, Ruiying; Wang, Lidai; Li, Guo; Verkhusha, Vladislav V.; Wang, Lihong V.

    2016-03-01

    Optical imaging of genetically encoded probes has revolutionized biomedical studies by providing valuable information about targeted biological processes. Here, we report a novel imaging technique, termed reversibly switchable photoacoustic tomography (RS-PAT), which exhibits large penetration depth, high detection sensitivity, and super-resolution. RS-PAT combines advanced photoacoustic imaging techniques with, for the first time, a nonfluorescent photoswitchable bacterial phytochrome. This bacterial phytochrome is the most near-infrared shifted genetically encoded probe reported so far. Moreover, this bacterial phytochrome is reversibly photoconvertible between its far-red and near-infrared light absorption states. Taking maximum advantage of the powerful imaging capability of PAT and the unique photochemical properties of the phytochrome, RS-PAT has broken through both the optical diffusion limit for deep-tissue imaging and the optical diffraction limit for super-resolution photoacoustic microscopy. Specifically, with RS-PAT we have achieved an unprecedented detection sensitivity of ~2 μM, or as few as ~20 tumor cells, at a centimeter depth. Such high sensitivity is fully demonstrated in our study by monitoring tumor growth and metastasis at whole-body level with ~100 μm resolution. Moreover, our microscopic implementation of RS-PAT is capable of imaging mammalian cells with a sub-diffraction lateral resolution of ~140 nm and axial resolution of ~400 nm, which are respectively ~2-fold and ~75-fold finer than those of our conventional photoacoustic microscopy. Overall, RS-PAT is a new and promising imaging technology for studying biological processes at different length scales.

  18. Controlling enzyme inhibition using an expanded set of genetically encoded amino acids.

    Science.gov (United States)

    Zheng, Shun; Kwon, Inchan

    2013-09-01

    Enzyme inhibition plays an important role in drug development, metabolic pathway regulation, and biocatalysis with product inhibition. When an inhibitor has high structural similarities to the substrate of an enzyme, controlling inhibitor binding without affecting enzyme substrate binding is often challenging and requires fine-tuning of the active site. We hypothesize that an extended set of genetically encoded amino acids can be used to design an enzyme active site that reduces enzyme inhibitor binding without compromising substrate binding. As a model case, we chose murine dihydrofolate reductase (mDHFR), substrate dihydrofolate, and inhibitor methotrexate. Structural models of mDHFR variants containing non-natural amino acids complexed with each ligand were constructed to identify a key residue for inhibitor binding and non-natural amino acids to replace the key residue. Then, we discovered that replacing the key phenylalanine residue with two phenylalanine analogs (p-bromophenylalanine (pBrF) and L-2-naphthylalanine (2Nal)) enhances binding affinity toward the substrate dihydrofolate over the inhibitor by 4.0 and 5.8-fold, respectively. Such an enhanced selectivity is mainly due to a reduced inhibitor binding affinity by 2.1 and 4.3-fold, respectively. The catalytic efficiency of the mDHFR variant containing pBrF is comparable to that of wild-type mDHFR, whereas the mDHFR variant containing 2Nal exhibits a moderate decrease in the catalytic efficiency. The work described here clearly demonstrates the feasibility of selectively controlling enzyme inhibition using an expanded set of genetically encoded amino acids.

  19. A Discussion on Possible Indicators Related to Genetic Structure Changes in Plant Germplasm Conservation

    Institute of Scientific and Technical Information of China (English)

    GAI Jun-yi

    2004-01-01

    The purpose of the present paper is to study and develop indicators and procedures for the evaluation of genetic structure changes in germplasm conservation due to social and natural environment reasons.Some basic concepts in germplasm study were introduced at first. Then, six kinds of indicators for genetic diversity as a measure of genetic potential of a germplasm collection were presented, i.e.,numbers of different entities at certain level, evenness of the entity distribution, genetic similarityand genetic distance, genetic variance and genetic coefficient of variation, multivariate genetic variation indices, and coefficient of parentage. It was pointed out that genetic dispersion did not provide a complete concept of genetic diversity if without any information from genetic richness. Based on the above, the indicators for genetic erosion as the genetic structure changes of germplasm conservation due to social reasons, the indicators of genetic vulnerability as the genetic structure changes of germplasm conservation due to environmental stresses, the measurement of genetic drift and genetic shift as the genetic structure changes of germplasm collection during reproduction or seed increase were reviewed and developed. Furthermore, the estimation procedures of the indicators by using molecular markers were suggested. Finally, the case studies on suitable conservation sample size of self-pollinated and open-pollinated populations were given for reference.

  20. Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways.

    Science.gov (United States)

    Michener, Joshua K; Thodey, Kate; Liang, Joe C; Smolke, Christina D

    2012-05-01

    Cells are filled with biosensors, molecular systems that measure the state of the cell and respond by regulating host processes. In much the same way that an engineer would monitor a chemical reactor, the cell uses these sensors to monitor changing intracellular environments and produce consistent behavior despite the variable environment. While natural systems derive a clear benefit from pathway regulation, past research efforts in engineering cellular metabolism have focused on introducing new pathways and removing existing pathway regulation. Synthetic biology is a rapidly growing field that focuses on the development of new tools that support the design, construction, and optimization of biological systems. Recent advances have been made in the design of genetically-encoded biosensors and the application of this class of molecular tools for optimizing and regulating heterologous pathways. Biosensors to cellular metabolites can be taken directly from natural systems, engineered from natural sensors, or constructed entirely in vitro. When linked to reporters, such as antibiotic resistance markers, these metabolite sensors can be used to report on pathway productivity, allowing high-throughput screening for pathway optimization. Future directions will focus on the application of biosensors to introduce feedback control into metabolic pathways, providing dynamic control strategies to increase the efficient use of cellular resources and pathway reliability.

  1. Engineering genetically encoded nanosensors for real-time in vivo measurements of citrate concentrations.

    Directory of Open Access Journals (Sweden)

    Jennifer C Ewald

    Full Text Available Citrate is an intermediate in catabolic as well as biosynthetic pathways and is an important regulatory molecule in the control of glycolysis and lipid metabolism. Mass spectrometric and NMR based metabolomics allow measuring citrate concentrations, but only with limited spatial and temporal resolution. Methods are so far lacking to monitor citrate levels in real-time in-vivo. Here, we present a series of genetically encoded citrate sensors based on Förster resonance energy transfer (FRET. We screened databases for citrate-binding proteins and tested three candidates in vitro. The citrate binding domain of the Klebsiella pneumoniae histidine sensor kinase CitA, inserted between the FRET pair Venus/CFP, yielded a sensor highly specific for citrate. We optimized the peptide linkers to achieve maximal FRET change upon citrate binding. By modifying residues in the citrate binding pocket, we were able to construct seven sensors with different affinities spanning a concentration range of three orders of magnitude without losing specificity. In a first in vivo application we show that E. coli maintains the capacity to take up glucose or acetate within seconds even after long-term starvation.

  2. Flow Cytometry Enables Multiplexed Measurements of Genetically Encoded Intramolecular FRET Sensors Suitable for Screening.

    Science.gov (United States)

    Doucette, Jaimee; Zhao, Ziyan; Geyer, Rory J; Barra, Melanie M; Balunas, Marcy J; Zweifach, Adam

    2016-07-01

    Genetically encoded sensors based on intramolecular FRET between CFP and YFP are used extensively in cell biology research. Flow cytometry has been shown to offer a means to measure CFP-YFP FRET; we suspected it would provide a unique way to conduct multiplexed measurements from cells expressing different FRET sensors, which is difficult to do with microscopy, and that this could be used for screening. We confirmed that flow cytometry accurately measures FRET signals using cells transiently transfected with an ERK activity reporter, comparing responses measured with imaging and cytometry. We created polyclonal long-term transfectant lines, each expressing a different intramolecular FRET sensor, and devised a way to bar-code four distinct populations of cells. We demonstrated the feasibility of multiplexed measurements and determined that robust multiplexed measurements can be conducted in plate format. To validate the suitability of the method for screening, we measured responses from a plate of bacterial extracts that in unrelated experiments we had determined contained the protein kinase C (PKC)-activating compound teleocidin A-1. The multiplexed assay correctly identifying the teleocidin A-1-containing well. We propose that multiplexed cytometric FRET measurements will be useful for analyzing cellular function and for screening compound collections.

  3. EPR Distance Measurements in Native Proteins with Genetically Encoded Spin Labels.

    Science.gov (United States)

    Schmidt, Moritz J; Fedoseev, Artem; Bücker, Dennis; Borbas, Julia; Peter, Christine; Drescher, Malte; Summerer, Daniel

    2015-12-18

    The genetic encoding of nitroxide amino acids in combination with electron paramagnetic resonance (EPR) distance measurements enables precise structural studies of native proteins, i.e. without the need for mutations to create unique reactive sites for chemical labeling and thus with minimal structural perturbation. We here report on in vitro DEER measurements in native E. coli thioredoxin (TRX) that establish the nitroxide amino acid SLK-1 as a spectroscopic probe that reports distances and conformational flexibilities in the enzyme with nonmutated catalytic centers that are not accessible by the use of the traditional methanethiosulfonate spin label (MTSSL). We generated a rotamer library for SLK-1 that in combination with molecular dynamics (MD) simulation enables predictions of distance distributions between two SLK-1 labels incorporated into a target protein. Toward a routine use of SLK-1 for EPR distance measurements in proteins and the advancement of the approach to intracellular environments, we study the stability of SLK-1 in E. coli cultures and lysates and establish guidelines for protein expression and purification that offer maximal nitroxide stability. These advancements and insights provide new perspectives for facile structural studies of native, endogenous proteins by EPR distance measurements.

  4. Live cell monitoring of glycine betaine by FRET-based genetically encoded nanosensor.

    Science.gov (United States)

    Ahmad, Mohammad; Ameen, Seema; Siddiqi, Tariq Omar; Khan, Parvez; Ahmad, Altaf

    2016-12-15

    Glycine betaine (GB) is one of the key compatible solutes that accumulate in the cell at exceedingly high level under the conditions of high salinity. It plays a crucial role in the maintenance of osmolarity of the cell without affecting the physiological processes. Analysis of stress-induced physiological conditions in living cells, therefore, requires real-time monitoring of cellular GB level. Glycine Betaine Optical Sensor (GBOS), a genetically-encoded FRET-based nanosensor developed in this study, allows the real-time monitoring of GB levels inside living cells. This nanosensor has been developed by sandwiching GB binding protein (ProX) between the Förster resonance energy transfer (FRET) pair, the cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP). Conformational change in ProX, which was used as sensory domain, reported the change in the level of this compatible solute in in vitro and in vivo conditions. Binding of the GB to the sensory domain fetches close to both the fluorescent moieties that result in the form of increased FRET ratio. So, any change in the concentration of GB is correlated with change in FRET ratio. This sensor also reported the GB cellular dynamics in real-time in Escherichia coli cells after the addition of its precursor, choline. The GBOS was also expressed in yeast and mammalian cells to monitor the intracellular GB. Therefore, the GBOS represents a unique FRET-based nanosensor which allows the non-invasive ratiometric analysis of the GB in living cells.

  5. Probing Protein-Protein Interactions with Genetically Encoded Photoactivatable Cross-Linkers.

    Science.gov (United States)

    Cooley, Richard B; Sondermann, Holger

    2017-01-01

    Fundamental to all living organisms is the ability of proteins to interact with other biological molecules at the right time and location, with the proper affinity, and to do so reversibly. One well-established technique to study protein interactions is chemical cross-linking, a process in which proteins in close spatial proximity are covalently tethered together. An emerging technology that overcomes many limitations of traditional cross-linking methods is one in which photoactivatable cross-linking noncanonical amino acids are genetically encoded into a protein of interest using the cell's native translational machinery. These proteins can then be used to trap interacting biomolecules upon UV illumination. Here, we describe a method for the site-specific incorporation of photoactivatable cross-linking amino acids into fluorescently tagged proteins of interest in E. coli. Photo-cross-linking and analysis by SDS-PAGE using in-gel fluorescence detection, which provides rapid, highly sensitive, and specific detection of cross-linked adducts even in impure systems, are also described. An example expression and cross-linking experiment involving transmembrane signaling of a bacterial second messenger receptor system that controls biofilm formation is shown. All reagents needed to carry out these experiments are commercially available, and do not require special or unique technology to perform, making this method tractable to a broad community studying protein structure and function.

  6. A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms.

    Directory of Open Access Journals (Sweden)

    Xiaokun Shu

    2011-04-01

    Full Text Available Electron microscopy (EM achieves the highest spatial resolution in protein localization, but specific protein EM labeling has lacked generally applicable genetically encoded tags for in situ visualization in cells and tissues. Here we introduce "miniSOG" (for mini Singlet Oxygen Generator, a fluorescent flavoprotein engineered from Arabidopsis phototropin 2. MiniSOG contains 106 amino acids, less than half the size of Green Fluorescent Protein. Illumination of miniSOG generates sufficient singlet oxygen to locally catalyze the polymerization of diaminobenzidine into an osmiophilic reaction product resolvable by EM. MiniSOG fusions to many well-characterized proteins localize correctly in mammalian cells, intact nematodes, and rodents, enabling correlated fluorescence and EM from large volumes of tissue after strong aldehyde fixation, without the need for exogenous ligands, probes, or destructive permeabilizing detergents. MiniSOG permits high quality ultrastructural preservation and 3-dimensional protein localization via electron tomography or serial section block face scanning electron microscopy. EM shows that miniSOG-tagged SynCAM1 is presynaptic in cultured cortical neurons, whereas miniSOG-tagged SynCAM2 is postsynaptic in culture and in intact mice. Thus SynCAM1 and SynCAM2 could be heterophilic partners. MiniSOG may do for EM what Green Fluorescent Protein did for fluorescence microscopy.

  7. Characterizing ligand-gated ion channel receptors with genetically encoded Ca2++ sensors.

    Directory of Open Access Journals (Sweden)

    John G Yamauchi

    Full Text Available We present a cell based system and experimental approach to characterize agonist and antagonist selectivity for ligand-gated ion channels (LGIC by developing sensor cells stably expressing a Ca(2+ permeable LGIC and a genetically encoded Förster (or fluorescence resonance energy transfer (FRET-based calcium sensor. In particular, we describe separate lines with human α7 and human α4β2 nicotinic acetylcholine receptors, mouse 5-HT(3A serotonin receptors and a chimera of human α7/mouse 5-HT(3A receptors. Complete concentration-response curves for agonists and Schild plots of antagonists were generated from these sensors and the results validate known pharmacology of the receptors tested. Concentration-response relations can be generated from either the initial rate or maximal amplitudes of FRET-signal. Although assaying at a medium throughput level, this pharmacological fluorescence detection technique employs a clonal line for stability and has versatility for screening laboratory generated congeners as agonists or antagonists on multiple subtypes of ligand-gated ion channels. The clonal sensor lines are also compatible with in vivo usage to measure indirectly receptor activation by endogenous neurotransmitters.

  8. Peripheral genetic structure of Helicoverpa zea indicates asymmetrical panmixia

    Science.gov (United States)

    Seasonal climatic shifts create peripheral habitats that alternate between habitable and uninhabitable for migratory species. Such dynamic peripheral habitats are potential sites where migratory species could evolve high genetic diversity resulting from convergence of immigrants from multiple region...

  9. Genetic variability of Chlamydophila abortus strains assessed by PCR-RFLP analysis of polymorphic membrane protein-encoding genes.

    Science.gov (United States)

    Sait, Michelle; Clark, Ewan M; Wheelhouse, Nicholas; Spalding, Lucy; Livingstone, Morag; Sachse, Konrad; Markey, Bryan K; Magnino, Simone; Siarkou, Victoria I; Vretou, Evangelia; Caro, María R; Yaga, Raja; Lainson, F Alex; Smith, David G E; Wright, Frank; Longbottom, David

    2011-08-05

    This study used PCR-RFLP to investigate the genetic variability of pmp-encoding genes from fifty-two Chlamydophila abortus (C. abortus) strains originating from abortion cases from various geographical regions and host species. Six primer pairs were used to PCR-amplify DNA fragments encoding eighteen pmps. PCR products were digested using four restriction endonucleases and Bayesian methodologies were used to compare RFLP profiles and assign strains to a RFLP genotype. Strains could be assigned to 2 genotypes in the region encoding pmp18D, 3 genotypes in the regions encoding pmp1A-pmp2B, pmp3E-pmp6H and pmp11G-pmp15G, 4 genotypes in the region encoding pmp7G-pmp10G and 5 genotypes in the region encoding pmp16G-pmp17G. In all regions, the majority of strains (88.4-96.1%) had the same genotype as the reference strain S26/3. No correlation could be made between genotype, host species or geographical origin except for the two variant Greek strains, LLG and POS, which formed a discrete genotype in all pmp-encoding regions except pmp18D. Relative rates of evolution calculated for each pmp-encoding gene locus suggest that differing selective pressures and functional constraints may exist on C. abortus polymorphic membrane proteins. These findings suggest that although intraspecies heterogeneity of pmp-encoding genes in C. abortus is low, the sequence heterogeneity should be an important consideration when using pmps as the basis for novel diagnostics or vaccine development.

  10. Molecular and genetic analysis of the gene encoding the Saccharomyces cerevisiae strand exchange protein Sep1.

    Science.gov (United States)

    Tishkoff, D X; Johnson, A W; Kolodner, R D

    1991-05-01

    Vegetatively grown Saccharomyces cerevisiae cells contain an activity that promotes a number of homologous pairing reactions. A major portion of this activity is due to strand exchange protein 1 (Sep1), which was originally purified as a 132,000-Mr species (R. Kolodner, D. H. Evans, and P. T. Morrison, Proc. Natl. Acad. Sci. USA 84:5560-5564, 1987). The gene encoding Sep1 was cloned, and analysis of the cloned gene revealed a 4,587-bp open reading frame capable of encoding a 175,000-Mr protein. The protein encoded by this open reading frame was overproduced and purified and had a relative molecular weight of approximately 160,000. The 160,000-Mr protein was at least as active in promoting homologous pairing as the original 132,000-Mr species, which has been shown to be a fragment of the intact 160,000-Mr Sep1 protein. The SEP1 gene mapped to chromosome VII within 20 kbp of RAD54. Three Tn10LUK insertion mutations in the SEP1 gene were characterized. sep1 mutants grew more slowly than wild-type cells, showed a two- to fivefold decrease in the rate of spontaneous mitotic recombination between his4 heteroalleles, and were delayed in their ability to return to growth after UV or gamma irradiation. Sporulation of sep1/sep1 diploids was defective, as indicated by both a 10- to 40-fold reduction in spore formation and reduced spore viability of approximately 50%. The majority of sep1/sep1 diploid cells arrested in meiosis after commitment to recombination but prior to the meiosis I cell division. Return-to-growth experiments showed that sep1/sep1 his4X/his4B diploids exhibited a five- to sixfold greater meiotic induction of His+ recombinants than did isogenic SEP1/SEP1 strains. sep1/sep1 mutants also showed an increased frequency of exchange between HIS4, LEU2, and MAT and a lack of positive interference between these markers compared with wild-type controls. The interaction between sep1, rad50, and spo13 mutations suggested that SEP1 acts in meiosis in a pathway that is

  11. Macrocephaly as a clinical indicator of genetic subtypes in autism.

    Science.gov (United States)

    Klein, Steven; Sharifi-Hannauer, Pantea; Martinez-Agosto, Julian A

    2013-02-01

    An association between autism and macrocephaly has been previously described. A subset of cases with extreme macrocephaly (>3 standard deviation [SD], 99.7th percentile) have been correlated to mutations in the gene phosphatase and tensin homolog (PTEN). However, the phenotypic and genetic characterization of the remaining cases remains unclear. We report the phenotypic classification and genetic testing evaluation of a cohort of 33 patients with autism and macrocephaly. Within our cohort, we confirm the association of PTEN mutations and extreme macrocephaly (>3 SD, 99.7th percentile) and identify mutations in 22% of cases, including three novel PTEN mutations. In addition, we define three phenotypic subgroups: (a) those cases associated with somatic overgrowth, (b) those with disproportionate macrocephaly, and (c) those with relative macrocephaly. We have devised a novel way to segregate patients into these subgroups that will aide in the stratification of autism macrocephaly cases. Within these subgroups, we further expand the genetic etiologies for autism cases with macrocephaly by describing two novel suspected pathogenic copy number variants located at 6q23.2 and 10q24.32. These findings demonstrate the phenotypic heterogeneity of autism cases associated with macrocephaly and their genetic etiologies. The clinical yield from PTEN mutation analysis is 22% and 9% from chromosomal microarray (CMA) testing within this cohort. The identification of three distinct phenotypic subgroups within macrocephaly autism patients may allow for the identification of their respective distinct genetic etiologies that to date have remained elusive.

  12. Characterization of the single stranded DNA binding protein SsbB encoded in the Gonoccocal Genetic Island.

    Directory of Open Access Journals (Sweden)

    Samta Jain

    Full Text Available BACKGROUND: Most strains of Neisseria gonorrhoeae carry a Gonococcal Genetic Island which encodes a type IV secretion system involved in the secretion of ssDNA. We characterize the GGI-encoded ssDNA binding protein, SsbB. Close homologs of SsbB are located within a conserved genetic cluster found in genetic islands of different proteobacteria. This cluster encodes DNA-processing enzymes such as the ParA and ParB partitioning proteins, the TopB topoisomerase, and four conserved hypothetical proteins. The SsbB homologs found in these clusters form a family separated from other ssDNA binding proteins. METHODOLOGY/PRINCIPAL FINDINGS: In contrast to most other SSBs, SsbB did not complement the Escherichia coli ssb deletion mutant. Purified SsbB forms a stable tetramer. Electrophoretic mobility shift assays and fluorescence titration assays, as well as atomic force microscopy demonstrate that SsbB binds ssDNA specifically with high affinity. SsbB binds single-stranded DNA with minimal binding frames for one or two SsbB tetramers of 15 and 70 nucleotides. The binding mode was independent of increasing Mg(2+ or NaCl concentrations. No role of SsbB in ssDNA secretion or DNA uptake could be identified, but SsbB strongly stimulated Topoisomerase I activity. CONCLUSIONS/SIGNIFICANCE: We propose that these novel SsbBs play an unknown role in the maintenance of genetic islands.

  13. Genetically-encoded tools for cAMP probing and modulation in living systems.

    Directory of Open Access Journals (Sweden)

    Valeriy M Paramonov

    2015-09-01

    Full Text Available Intracellular 3'-5'-cyclic adenosine monophosphate (cAMP is one of the principal second messengers downstream of a manifold of signal transduction pathways, including the ones triggered by G protein-coupled receptors. Not surprisingly, biochemical assays for cAMP have been instrumental for basic research and drug discovery for decades, providing insights into cellular physiology and guiding pharmaceutical industry. However, despite impressive track record, the majority of conventional biochemical tools for cAMP probing share the same fundamental shortcoming - all the measurements require sample disruption for cAMP liberation. This common bottleneck, together with inherently low spatial resolution of measurements (as cAMP is typically analyzed in lysates of thousands of cells, underpin the ensuing limitations of the conventional cAMP assays: 1 genuine kinetic measurements of cAMP levels over time in a single given sample are unfeasible; 2 inability to obtain precise information on cAMP spatial distribution and transfer at subcellular levels, let alone the attempts to pinpoint dynamic interactions of cAMP and its effectors. At the same time, tremendous progress in synthetic biology over the recent years culminated in drastic refinement of our toolbox, allowing us not only to bypass the limitations of conventional assays, but to put intracellular cAMP life-span under tight control – something, that seemed scarcely attainable before. In this review article we discuss the main classes of modern genetically-encoded tools tailored for cAMP probing and modulation in living systems. We examine the capabilities and weaknesses of these different tools in the context of their operational characteristics and applicability to various experimental set-ups involving living cells, providing the guidance for rational selection of the best tools for particular needs.

  14. Visualization of glutamine transporter activities in living cells using genetically encoded glutamine sensors.

    Directory of Open Access Journals (Sweden)

    Katrin Gruenwald

    Full Text Available Glutamine plays a central role in the metabolism of critical biological molecules such as amino acids, proteins, neurotransmitters, and glutathione. Since glutamine metabolism is regulated through multiple enzymes and transporters, the cellular glutamine concentration is expected to be temporally dynamic. Moreover, differentiation in glutamine metabolism between cell types in the same tissue (e.g. neuronal and glial cells is often crucial for the proper function of the tissue as a whole, yet assessing cell-type specific activities of transporters and enzymes in such heterogenic tissue by physical fractionation is extremely challenging. Therefore, a method of reporting glutamine dynamics at the cellular level is highly desirable. Genetically encoded sensors can be targeted to a specific cell type, hence addressing this knowledge gap. Here we report the development of Föster Resonance Energy Transfer (FRET glutamine sensors based on improved cyan and yellow fluorescent proteins, monomeric Teal Fluorescent Protein (mTFP1 and venus. These sensors were found to be specific to glutamine, and stable to pH-changes within a physiological range. Using cos7 cells expressing the human glutamine transporter ASCT2 as a model, we demonstrate that the properties of the glutamine transporter can easily be analyzed with these sensors. The range of glutamine concentration change in a given cell can also be estimated using sensors with different affinities. Moreover, the mTFP1-venus FRET pair can be duplexed with another FRET pair, mAmetrine and tdTomato, opening up the possibility for real-time imaging of another molecule. These novel glutamine sensors will be useful tools to analyze specificities of glutamine metabolism at the single-cell level.

  15. Studies of twins indicate that genetics influence dietary intake

    DEFF Research Database (Denmark)

    Hasselbalch, Ann Louise; Heitmann, Berit L; Kyvik, Kirsten O

    2008-01-01

    Habitual dietary intake is a complex behavior that may have both biological and nonbiological bases. We estimated the contribution of genetic and environmental influences on dietary intake in a large population-based sample of healthy twins. Data originated from a cross-sectional study of 600 mal...

  16. Engineering of a Genetically Encodable Fluorescent Voltage Sensor Exploiting Fast Ci-VSP Voltage-Sensing Movements

    OpenAIRE

    Alicia Lundby; Hiroki Mutoh; Dimitar Dimitrov; Walther Akemann; Thomas Knöpfel

    2008-01-01

    Ci-VSP contains a voltage-sensing domain (VSD) homologous to that of voltage-gated potassium channels. Using charge displacement ('gating' current) measurements we show that voltage-sensing movements of this VSD can occur within 1 ms in mammalian membranes. Our analysis lead to development of a genetically encodable fluorescent protein voltage sensor (VSFP) in which the fast, voltage-dependent conformational changes of the Ci-VSP voltage sensor are transduced to similarly fast fluorescence re...

  17. Inhibition of Exotoxin Production by Mobile Genetic Element SCCmec-Encoded psm-mec RNA Is Conserved in Staphylococcal Species

    OpenAIRE

    Mariko Ikuo; Gentaro Nagano; Yuki Saito; Han Mao; Kazuhisa Sekimizu; Chikara Kaito

    2014-01-01

    Staphylococcal species acquire antibiotic resistance by incorporating the mobile-genetic element SCCmec. We previously found that SCCmec-encoded psm-mec RNA suppresses exotoxin production as a regulatory RNA, and the psm-mec translation product increases biofilm formation in Staphylococcus aureus. Here, we examined whether the regulatory role of psm-mec on host bacterial virulence properties is conserved among other staphylococcal species, S. epidermidis and S. haemolyticus, both of which are...

  18. Satellite range scheduling with the priority constraint: An improved genetic algorithm using a station ID encoding method

    Directory of Open Access Journals (Sweden)

    Li Yuqing

    2015-06-01

    Full Text Available Satellite range scheduling with the priority constraint is one of the most important problems in the field of satellite operation. This paper proposes a station coding based genetic algorithm to solve this problem, which adopts a new chromosome encoding method that arranges tasks according to the ground station ID. The new encoding method contributes to reducing the complexity in conflict checking and resolving, and helps to improve the ability to find optimal resolutions. Three different selection operators are designed to match the new encoding strategy, namely random selection, greedy selection, and roulette selection. To demonstrate the benefits of the improved genetic algorithm, a basic genetic algorithm is designed in which two cross operators are presented, a single-point crossover and a multi-point crossover. For the purpose of algorithm test and analysis, a problem-generating program is designed, which can simulate problems by modeling features encountered in real-world problems. Based on the problem generator, computational results and analysis are made and illustrated for the scheduling of multiple ground stations.

  19. Development of an automated fluorescence microscopy system for photomanipulation of genetically encoded photoactivatable proteins (optogenetics) in live cells.

    Science.gov (United States)

    Araki, Nobukazu; Ikeda, Yuka; Kato, Takuma; Kawai, Katsuhisa; Egami, Youhei; Miyake, Katsuya; Tsurumaki, Nobuhide; Yamaguchi, Mitsunari

    2014-06-01

    Photomanipulation of genetically encoded light-sensitive protein activity, also known as optogenetics, is one of the most innovative recent microscopy techniques in the fields of cell biology and neurobiology. Although photomanipulation is usually performed by diverting the photobleaching mode of a confocal laser microscope, photobleaching by the laser scanning unit is not always suitable for photoactivation. We have developed a simple automated wide-field fluorescence microscopy system for the photomanipulation of genetically encoded photoactivatable proteins in live cells. An electrically automated fluorescence microscope can be controlled through MetaMorph imaging software, making it possible to acquire time-lapse, multiwavelength images of live cells. Using the journal (macro recording) function of MetaMorph, we wrote a macro program to change the excitation filter for photoactivation and illumination area during the intervals of image acquisition. When this program was run on the wide-field fluorescence microscope, cells expressing genetically encoded photoactivatable Rac1, which is activated under blue light, showed morphological changes such as lamellipodial extension and cell surface ruffling in the illuminated region. Using software-based development, we successfully constructed a fully automated photoactivation microscopy system for a mercury lamp-based fluorescence microscope.

  20. Genetic analysis of earliness indicators in upland cotton

    Directory of Open Access Journals (Sweden)

    Amir Shakeel

    2013-05-01

    Full Text Available Genetic bases of earliness in upland cotton were investigated by recording and analyzing data on different phenological and morphological traits related to earliness. All traits inclusive of days to squaring, days to flowering, vertical flowering interval, horizontal flowering interval, days to first boll opening, boll maturity period, node number for the first fruiting branch and height for first fruiting showed significant variation. Additive components D was significant for all the traits studied and more than the values of dominance components H1 and H2 thus confirming the presence of additive gene action. Estimates of narrow sense heritability were low for days to squaring, moderate in the boll maturity period and high for all other traits. Degree of dominance was less than unity hence partial dominance is found in almost all the traits. The predominance of additive genetic effects along with reasonable estimates of heritability suggested early generation selection and pedigree method of selection may be followed for almost all the traits.

  1. Genetic analysis of field and physiological indicators of drought ...

    African Journals Online (AJOL)

    Jane

    2011-10-10

    Oct 10, 2011 ... In order to study the inheritance of field, physiological and metabolite indicators of drought tolerance in wheat .... and the quantum yield was recorded after dark adaptation using a ..... The theory and analysis of diallel crosses.

  2. Genetic analysis of processed in-line mastitis indicator data

    DEFF Research Database (Denmark)

    Sørensen, Lars Peter; Løvendahl, Peter

    2013-01-01

    on exponential smoothing of the SCC values followed by factor analysis for estimation of the latent variable EMR was used. Finally, EMR was expressed as a continuum on the interval [0;1] using sigmoid transformation. Thus, an EMR value close to zero indicates low risk of mastitis and a value close to one...... indicates high risk of mastitis. The EMR values were summarized for each cow using the log-transformed median EMR. A second trait was defined as the median of the log-transformed SCC values from 5 to 305 d in milk. A bivariate animal model was used for estimation of co-variance components for the 2 traits...

  3. A Fuzzy Genetic Algorithm Based on Binary Encoding for Solving Multidimensional Knapsack Problems

    Directory of Open Access Journals (Sweden)

    M. Jalali Varnamkhasti

    2012-01-01

    Full Text Available The fundamental problem in genetic algorithms is premature convergence, and it is strongly related to the loss of genetic diversity of the population. This study aims at proposing some techniques to tackle the premature convergence by controlling the population diversity. Firstly, a sexual selection mechanism which utilizes the mate chromosome during selection is used. The second technique focuses on controlling the genetic parameters by applying the fuzzy logic controller. Computational experiments are conducted on the proposed techniques and the results are compared with other genetic operators, heuristics, and local search algorithms commonly used for solving multidimensional 0/1 knapsack problems published in the literature.

  4. A strategy for genetic modification of the spike-encoding segment of human reovirus T3D for reovirus targeting.

    Science.gov (United States)

    van den Wollenberg, D J M; van den Hengel, S K; Dautzenberg, I J C; Cramer, S J; Kranenburg, O; Hoeben, R C

    2008-12-01

    Human Orthoreovirus Type 3 Dearing is not pathogenic to humans and has been evaluated clinically as an oncolytic agent. Its transduction efficiency and the tumor cell selectivity may be enhanced by incorporating ligands for alternative receptors. However, the genetic modification of reoviruses has been difficult, and genetic targeting of reoviruses has not been reported so far. Here we describe a technique for generating genetically targeted reoviruses. The propagation of wild-type reoviruses on cells expressing a modified sigma 1-encoding segment embedded in a conventional RNA polymerase II transcript leads to substitution of the wild-type genome segment by the modified version. This technique was used for generating reoviruses that are genetically targeted to an artificial receptor expressed on U118MG cells. These cells lack the junction adhesion molecule-1 and therefore resist infection by wild-type reoviruses. The targeted reoviruses were engineered to carry the ligand for this receptor at the C terminus of the sigma 1 spike protein. This demonstrates that the C terminus of the sigma 1 protein is a suitable locale for the insertion of oligopeptide ligands and that targeting of reoviruses is feasible. The genetically targeted viruses can be propagated using the modified U118MG cells as helper cells. This technique may be applicable for the improvement of human reoviruses as oncolytic agents.

  5. Interleukin-Encoding Adenoviral Vectors as Genetic Adjuvant for Vaccination against Retroviral Infection

    Science.gov (United States)

    Ohs, Inga; Windmann, Sonja; Wildner, Oliver; Dittmer, Ulf; Bayer, Wibke

    2013-01-01

    Interleukins (IL) are cytokines with stimulatory and modulatory functions in the immune system. In this study, we have chosen interleukins which are involved in the enhancement of TH2 responses and B cell functions to analyze their potential to improve a prophylactic adenovirus-based anti-retroviral vaccine with regard to antibody and virus-specific CD4+ T cell responses. Mice were vaccinated with an adenoviral vector which encodes and displays the Friend Virus (FV) surface envelope protein gp70 (Ad.pIXgp70) in combination with adenoviral vectors encoding the interleukins IL4, IL5, IL6, IL7 or IL23. Co-application of Ad.pIXgp70 with Ad.IL5, Ad.IL6 or Ad.IL23 resulted in improved protection with high control over FV-induced splenomegaly and reduced viral loads. Mice co-immunized with adenoviral vectors encoding IL5 or IL23 showed increased neutralizing antibody responses while mice co-immunized with Ad.IL6 or Ad.IL23 showed improved FV-specific CD4+ T cell responses compared to mice immunized with Ad.pIXgp70 alone. We show that the co-application of adenoviral vectors encoding specific interleukins is suitable to improve the vaccination efficacy of an anti-retroviral vaccine. Improved protection correlated with improved CD4+ T cell responses and especially with higher neutralizing antibody titers. The co-application of selected interleukin-encoding adenoviral vectors is a valuable tool for vaccination with regard to enhancement of antibody mediated immunity. PMID:24349306

  6. Interleukin-encoding adenoviral vectors as genetic adjuvant for vaccination against retroviral infection.

    Directory of Open Access Journals (Sweden)

    Inga Ohs

    Full Text Available Interleukins (IL are cytokines with stimulatory and modulatory functions in the immune system. In this study, we have chosen interleukins which are involved in the enhancement of TH2 responses and B cell functions to analyze their potential to improve a prophylactic adenovirus-based anti-retroviral vaccine with regard to antibody and virus-specific CD4(+ T cell responses. Mice were vaccinated with an adenoviral vector which encodes and displays the Friend Virus (FV surface envelope protein gp70 (Ad.pIXgp70 in combination with adenoviral vectors encoding the interleukins IL4, IL5, IL6, IL7 or IL23. Co-application of Ad.pIXgp70 with Ad.IL5, Ad.IL6 or Ad.IL23 resulted in improved protection with high control over FV-induced splenomegaly and reduced viral loads. Mice co-immunized with adenoviral vectors encoding IL5 or IL23 showed increased neutralizing antibody responses while mice co-immunized with Ad.IL6 or Ad.IL23 showed improved FV-specific CD4(+ T cell responses compared to mice immunized with Ad.pIXgp70 alone. We show that the co-application of adenoviral vectors encoding specific interleukins is suitable to improve the vaccination efficacy of an anti-retroviral vaccine. Improved protection correlated with improved CD4(+ T cell responses and especially with higher neutralizing antibody titers. The co-application of selected interleukin-encoding adenoviral vectors is a valuable tool for vaccination with regard to enhancement of antibody mediated immunity.

  7. Interleukin-encoding adenoviral vectors as genetic adjuvant for vaccination against retroviral infection.

    Science.gov (United States)

    Ohs, Inga; Windmann, Sonja; Wildner, Oliver; Dittmer, Ulf; Bayer, Wibke

    2013-01-01

    Interleukins (IL) are cytokines with stimulatory and modulatory functions in the immune system. In this study, we have chosen interleukins which are involved in the enhancement of TH2 responses and B cell functions to analyze their potential to improve a prophylactic adenovirus-based anti-retroviral vaccine with regard to antibody and virus-specific CD4(+) T cell responses. Mice were vaccinated with an adenoviral vector which encodes and displays the Friend Virus (FV) surface envelope protein gp70 (Ad.pIXgp70) in combination with adenoviral vectors encoding the interleukins IL4, IL5, IL6, IL7 or IL23. Co-application of Ad.pIXgp70 with Ad.IL5, Ad.IL6 or Ad.IL23 resulted in improved protection with high control over FV-induced splenomegaly and reduced viral loads. Mice co-immunized with adenoviral vectors encoding IL5 or IL23 showed increased neutralizing antibody responses while mice co-immunized with Ad.IL6 or Ad.IL23 showed improved FV-specific CD4(+) T cell responses compared to mice immunized with Ad.pIXgp70 alone. We show that the co-application of adenoviral vectors encoding specific interleukins is suitable to improve the vaccination efficacy of an anti-retroviral vaccine. Improved protection correlated with improved CD4(+) T cell responses and especially with higher neutralizing antibody titers. The co-application of selected interleukin-encoding adenoviral vectors is a valuable tool for vaccination with regard to enhancement of antibody mediated immunity.

  8. Engineering of a genetically encodable fluorescent voltage sensor exploiting fast Ci-VSP voltage-sensing movements

    DEFF Research Database (Denmark)

    Lundby, Alicia; Mutoh, Hiroki; Dimitrov, Dimitar

    2008-01-01

    Ci-VSP contains a voltage-sensing domain (VSD) homologous to that of voltage-gated potassium channels. Using charge displacement ('gating' current) measurements we show that voltage-sensing movements of this VSD can occur within 1 ms in mammalian membranes. Our analysis lead to development of a g...... of a genetically encodable fluorescent protein voltage sensor (VSFP) in which the fast, voltage-dependent conformational changes of the Ci-VSP voltage sensor are transduced to similarly fast fluorescence read-outs....

  9. Expression cloning of different bacterial phosphatase-encoding genes by histochemical screening of genomic libraries onto an indicator medium containing phenolphthalein diphosphate and methyl green.

    Science.gov (United States)

    Riccio, M L; Rossolini, G M; Lombardi, G; Chiesurin, A; Satta, G

    1997-02-01

    A system for expression cloning of bacterial phosphatase-encoding genes has been developed, and its potential has been investigated. The system is based on histochemical screening of bacterial genomic libraries, constructed in an Escherichia coli multicopy plasmid vector, for phosphatase-producing clones using an indicator medium (named TPMG) made of Tryptose-Phosphate agar supplemented with the phosphatase substrate phenolphthalein diphosphate and the stain methyl green. To test the performance of this system, three genomic libraries were constructed from bacterial strains of different species which showed different patterns of phosphatase activity, and were screened using the TPMG medium. Following a partial screening, three different phosphatase-encoding genes (respectively encoding a class A non-specific acid phosphatase, an acid-hexose phosphatase and a non-specific alkaline phosphatase) were shotgun-cloned from the above libraries, indicating that the TPMG-based expression cloning system can be useful for rapid isolation of different bacterial phosphatase-encoding genes.

  10. Plant genetics. A Y-chromosome-encoded small RNA acts as a sex determinant in persimmons.

    Science.gov (United States)

    Akagi, Takashi; Henry, Isabelle M; Tao, Ryutaro; Comai, Luca

    2014-10-31

    In plants, multiple lineages have evolved sex chromosomes independently, providing a powerful comparative framework, but few specific determinants controlling the expression of a specific sex have been identified. We investigated sex determinants in the Caucasian persimmon, Diospyros lotus, a dioecious plant with heterogametic males (XY). Male-specific short nucleotide sequences were used to define a male-determining region. A combination of transcriptomics and evolutionary approaches detected a Y-specific sex-determinant candidate, OGI, that displays male-specific conservation among Diospyros species. OGI encodes a small RNA targeting the autosomal MeGI gene, a homeodomain transcription factor regulating anther fertility in a dosage-dependent fashion. This identification of a feminizing gene suppressed by a Y-chromosome-encoded small RNA contributes to our understanding of the evolution of sex chromosome systems in higher plants. Copyright © 2014, American Association for the Advancement of Science.

  11. Multi-Features Encoding and Selecting Based on Genetic Algorithm for Human Action Recognition from Video

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    Chenglong Yu

    2013-05-01

    Full Text Available In this study, we proposed multiple local features encoded for recognizing the human actions. The multiple local features were obtained from the simple feature description of human actions in video. The simple features are two kinds of important features, optical flow and edge, to represent the human perception for the video behavior. As the video information descriptors, optical flow and edge, which their computing speeds are very fast and their requirement of memory consumption is very low, can represent respectively the motion information and shape information. Furthermore, key local multi-features are extracted and encoded by GA in order to reduce the computational complexity of the algorithm. After then, the Multi-SVM classifier is applied to discriminate the human actions.

  12. A comparative genomics study of genetic products potentially encoding ladderane lipid biosynthesis

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    Jetten Mike SM

    2009-02-01

    Full Text Available Abstract Background The fatty acids of anaerobic ammonium oxidizing (anammox bacteria contain linearly concatenated cyclobutane moieties, so far unique to biology. These moieties are under high ring strain and are synthesised by a presently unknown biosynthetic pathway. Results Gene clusters encoding enzymes of fatty acid biosynthesis in the anammox bacterium Kuenenia stuttgartiensis and 137 other organisms were analysed and compared in silico to gain further insight into the pathway of (ladderane fatty acid biosynthesis. In K. stuttgartiensis four large gene clusters encode fatty acid biosynthesis. Next to the regular enzyme complex needed for fatty acid biosynthesis (FASII, the presence of four putative S-adenosyl-methionine (SAM radical enzymes, two enzymes similar to phytoene desaturases and many divergent paralogues of β-ketoacyl-ACP synthase (fabF were unusual. Surprisingly, extensive synteny was observed with FASII gene clusters in the deltaproteobacterium Desulfotalea psychrophila. No ladderane lipids were detected in lipid extracts of this organism but we did find unusual polyunsaturated hydrocarbons (PUHC, not detected in K. stuttgartiensis. Conclusion We suggest that the unusual gene clusters of K. stuttgartiensis and D. psychrophila encode a novel pathway for anaerobic PUFA biosynthesis and that K. stuttgartiensis further processes PUFA into ladderane lipids, in similar fashion to the previously proposed route of ladderane lipid biosynthesis. However, the presence of divergent paralogues of fabF with radically different active site topologies may suggest an alternative pathway where ladderane moieties are synthesised externally and are recruited into the pathway of fatty acid biosynthesis. Reviewers This article was reviewed by Dr Michael Galperin (nominated by Prof E. Koonin, Dr Andrei Osterman and Dr Jeremy Selengut.

  13. Genetic analysis of a novel plasmid encoded durancin locus in Enterococcus durans 41D

    Science.gov (United States)

    Enterococcus durans is commonly found in the intestinal tract in humans and animals and several strains are known to produce bacteriocins. Durancin GL, a novel bacteriocin of Enterococcus durans 41D with antilisterial activity was isolated from artisanal cheese samples and its genetic determinants ...

  14. Genetic diversity and population structure of genes encoding vaccine candidate antigens of Plasmodium vivax

    Directory of Open Access Journals (Sweden)

    Chenet Stella M

    2012-03-01

    Full Text Available Abstract Background A major concern in malaria vaccine development is genetic polymorphisms typically observed among Plasmodium isolates in different geographical areas across the world. Highly polymorphic regions have been observed in Plasmodium falciparum and Plasmodium vivax antigenic surface proteins such as Circumsporozoite protein (CSP, Duffy-binding protein (DBP, Merozoite surface protein-1 (MSP-1, Apical membrane antigen-1 (AMA-1 and Thrombospondin related anonymous protein (TRAP. Methods Genetic variability was assessed in important polymorphic regions of various vaccine candidate antigens in P. vivax among 106 isolates from the Amazon Region of Loreto, Peru. In addition, genetic diversity determined in Peruvian isolates was compared to population studies from various geographical locations worldwide. Results The structured diversity found in P. vivax populations did not show a geographic pattern and haplotypes from all gene candidates were distributed worldwide. In addition, evidence of balancing selection was found in polymorphic regions of the trap, dbp and ama-1 genes. Conclusions It is important to have a good representation of the haplotypes circulating worldwide when implementing a vaccine, regardless of the geographic region of deployment since selective pressure plays an important role in structuring antigen diversity.

  15. Real encoded genetic algorithm and response surface methodology to optimize production of an indolizidine alkaloid, swainsonine, from Metarhizium anisopliae.

    Science.gov (United States)

    Singh, Digar; Kaur, Gurvinder

    2013-09-01

    Response surface methodology (RSM) and artificial neural network-real encoded genetic algorithm (ANN-REGA) were employed to develop a process for fermentative swainsonine production from Metarhizium anisopliae (ARSEF 1724). The effect of finally screened process variables viz. inoculum size, oatmeal extract, glucose, and CaCl2 were investigated through central composite design and were further utilized for training sets in ANN with training and test R values of 0.99 and 0.94, respectively. ANN-REGA was finally employed to simulate the predictive swainsonine production with best evolved media composition. ANN-REGA predicted a more precise fermentation model with 103 % (shake flask) increase in alkaloid production compared to 75.62 % (shake flask) obtained with RSM model upon validation.

  16. Genetically Encoded Spy Peptide Fusion System to Detect Plasma Membrane-Localized Proteins In Vivo.

    Science.gov (United States)

    Bedbrook, Claire N; Kato, Mihoko; Ravindra Kumar, Sripriya; Lakshmanan, Anupama; Nath, Ravi D; Sun, Fei; Sternberg, Paul W; Arnold, Frances H; Gradinaru, Viviana

    2015-08-20

    Membrane proteins are the main gatekeepers of cellular state, especially in neurons, serving either to maintain homeostasis or instruct response to synaptic input or other external signals. Visualization of membrane protein localization and trafficking in live cells facilitates understanding the molecular basis of cellular dynamics. We describe here a method for specifically labeling the plasma membrane-localized fraction of heterologous membrane protein expression using channelrhodopsins as a case study. We show that the genetically encoded, covalent binding SpyTag and SpyCatcher pair from the Streptococcus pyogenes fibronectin-binding protein FbaB can selectively label membrane-localized proteins in living cells in culture and in vivo in Caenorhabditis elegans. The SpyTag/SpyCatcher covalent labeling method is highly specific, modular, and stable in living cells. We have used the binding pair to develop a channelrhodopsin membrane localization assay that is amenable to high-throughput screening for opsin discovery and engineering.

  17. Genuine genetic redundancy in maleylacetate-reductase-encoding genes involved in degradation of haloaromatic compounds by Cupriavidus necator JMP134.

    Science.gov (United States)

    Pérez-Pantoja, Danilo; Donoso, Raúl A; Sánchez, Miguel A; González, Bernardo

    2009-11-01

    Maleylacetate reductases (MAR) are required for biodegradation of several substituted aromatic compounds. To date, the functionality of two MAR-encoding genes (tfdF(I) and tfdF(II)) has been reported in Cupriavidus necator JMP134(pJP4), a known degrader of aromatic compounds. These two genes are located in tfd gene clusters involved in the turnover of 2,4-dichlorophenoxyacetate (2,4-D) and 3-chlorobenzoate (3-CB). The C. necator JMP134 genome comprises at least three other genes that putatively encode MAR (tcpD, hqoD and hxqD), but confirmation of their functionality and their role in the catabolism of haloaromatic compounds has not been assessed. RT-PCR expression analyses of C. necator JMP134 cells exposed to 2,4-D, 3-CB, 2,4,6-trichlorophenol (2,4,6-TCP) or 4-fluorobenzoate (4-FB) showed that tfdF(I) and tfdF(II) are induced by haloaromatics channelled to halocatechols as intermediates. In contrast, 2,4,6-TCP only induces tcpD, and any haloaromatic compounds tested did not induce hxqD and hqoD. However, the tcpD, hxqD and hqoD gene products showed MAR activity in cell extracts and provided the MAR function for 2,4-D catabolism when heterologously expressed in MAR-lacking strains. Growth tests for mutants of the five MAR-encoding genes in strain JMP134 showed that none of these genes is essential for degradation of the tested compounds. However, the role of tfdF(I)/tfdF(II) and tcpD genes in the expression of MAR activity during catabolism of 2,4-D and 2,4,6-TCP, respectively, was confirmed by enzyme activity tests in mutants. These results reveal a striking example of genetic redundancy in the degradation of aromatic compounds.

  18. Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion.

    Science.gov (United States)

    Hoban, Sean; Arntzen, Jan A; Bruford, Michael W; Godoy, José A; Rus Hoelzel, A; Segelbacher, Gernot; Vilà, Carles; Bertorelle, Giorgio

    2014-11-01

    Genetic biodiversity contributes to individual fitness, species' evolutionary potential, and ecosystem stability. Temporal monitoring of the genetic status and trends of wild populations' genetic diversity can provide vital data to inform policy decisions and management actions. However, there is a lack of knowledge regarding which genetic metrics, temporal sampling protocols, and genetic markers are sufficiently sensitive and robust, on conservation-relevant timescales. Here, we tested six genetic metrics and various sampling protocols (number and arrangement of temporal samples) for monitoring genetic erosion following demographic decline. To do so, we utilized individual-based simulations featuring an array of different initial population sizes, types and severity of demographic decline, and DNA markers [single nucleotide polymorphisms (SNPs) and microsatellites] as well as decline followed by recovery. Number of alleles markedly outperformed other indicators across all situations. The type and severity of demographic decline strongly affected power, while the number and arrangement of temporal samples had small effect. Sampling 50 individuals at as few as two time points with 20 microsatellites performed well (good power), and could detect genetic erosion while 80-90% of diversity remained. This sampling and genotyping effort should often be affordable. Power increased substantially with more samples or markers, and we observe that power of 2500 SNPs was nearly equivalent to 250 microsatellites, a result of theoretical and practical interest. Our results suggest high potential for using historic collections in monitoring programs, and demonstrate the need to monitor genetic as well as other levels of biodiversity.

  19. Microsatellite-encoded domain in rodent Sry functions as a genetic capacitor to enable the rapid evolution of biological novelty.

    Science.gov (United States)

    Chen, Yen-Shan; Racca, Joseph D; Sequeira, Paul W; Phillips, Nelson B; Weiss, Michael A

    2013-08-13

    The male program of therian mammals is determined by Sry, a transcription factor encoded by the Y chromosome. Specific DNA binding is mediated by a high mobility group (HMG) box. Expression of Sry in the gonadal ridge activates a Sox9-dependent gene regulatory network leading to testis formation. A subset of Sry alleles in superfamily Muroidea (order Rodentia) is remarkable for insertion of an unstable DNA microsatellite, most commonly encoding (as in mice) a CAG repeat-associated glutamine-rich domain. We provide evidence, based on an embryonic pre-Sertoli cell line, that this domain functions at a threshold length as a genetic capacitor to facilitate accumulation of variation elsewhere in the protein, including the HMG box. The glutamine-rich domain compensates for otherwise deleterious substitutions in the box and absence of nonbox phosphorylation sites to ensure occupancy of DNA target sites. Such compensation enables activation of a male transcriptional program despite perturbations to the box. Whereas human SRY requires nucleocytoplasmic shuttling and coupled phosphorylation, mouse Sry contains a defective nuclear export signal analogous to a variant human SRY associated with inherited sex reversal. We propose that the rodent glutamine-rich domain has (i) fostered accumulation of cryptic intragenic variation and (ii) enabled unmasking of such variation due to DNA replicative slippage. This model highlights genomic contingency as a source of protein novelty at the edge of developmental ambiguity and may underlie emergence of non-Sry-dependent sex determination in the radiation of Muroidea.

  20. Genetic Structure Associated with blaOXA-18, Encoding a Clavulanic Acid-Inhibited Extended-Spectrum Oxacillinase▿

    Science.gov (United States)

    Naas, Thierry; Namdari, Fatemeh; Bogaerts, Pierre; Huang, Te-Din; Glupczynski, Youri; Nordmann, Patrice

    2008-01-01

    The genetic environment of the blaOXA-18 gene encoding a peculiar clavulanic acid-inhibitable Ambler class D extended-spectrum β-lactamase was determined from the prototype OXA-18-producing Pseudomonas aeruginosa MUS clinical isolate. An 8.2-kb genomic DNA fragment containing blaOXA-18 was cloned from P. aeruginosa MUS. Although most oxacillinases are located in integrons, blaOXA-18 lacked gene cassette-specific features. It was bracketed by two duplicated sequences containing ISCR19, a novel insertion sequence of the ISCR family of mobile elements; ΔintI1, a truncated integrase gene; and a truncated Δaac6′-Ib gene cassette. It is likely that ISCR19 was at the origin of the blaOXA-18 gene mobilization by a rolling-circle transposition event followed by homologous recombination. Furthermore, analysis of the cloned genomic DNA fragment revealed the presence of the integron-containing blaOXA-20 gene. Concomitantly, three P. aeruginosa clinical isolates, displaying a synergy image as determined by double-disk diffusion tests on cloxacillin-containing plates, were isolated from three patients hospitalized in different wards over a 9-month period at the Saint-Luc University hospital (Brussels, Belgium). These isolates were positive by PCR for blaOXA-18 and blaOXA-20 genes, genetically related to P. aeruginosa MUS as determined by pulsed-field gel electrophoresis, and carried the same blaOXA-18/blaOXA-20-associated genetic structures. This report characterized the genetic elements likely at the origin of blaOXA-18 gene mobilization in P. aeruginosa and suggests the spread of oxacillin-type extended-spectrum β-lactamases in P. aeruginosa at the Saint-Luc University hospital of Brussels, Belgium. PMID:18663027

  1. Establishing the outcome indicators for the essential nursing competencies and curricula guidelines for genetics and genomics.

    Science.gov (United States)

    Calzone, Kathleen A; Jenkins, Jean; Prows, Cynthia A; Masny, Agnes

    2011-01-01

    The translation of genetics/genomics to clinical care has implications for nurses. The Essential Nursing Competencies and Curricula Guidelines for Genetics and Genomics, established by consensus, apply to all registered nurses. Learning outcomes and clinical practice indicators have been developed to provide additional guidance. The Essentials Advisory Group (EAG) established a team to establish the Outcome Indicators. A draft was developed based on published peer-reviewed documents and syllabi. The draft underwent three layers of review: (a) critique by the EAG; (b) review by representatives at a Genetics/Genomics Toolkit for Faculty meeting; and (c) review by workshop attendees of the American Association of Colleges of Nursing's baccalaureate and master's education conferences, followed by EAG's final approval. Outcome Indicators clarify specific knowledge areas and suggest clinical performance indicators for each competency. They provide the foundation to establish a competency-based education repository with outcome indicator mapping matrixes for genetic/genomic education resources. A gap analysis of education resources identified resource deficits, and online unfolding case studies were developed. Outcome Indicators assist the academic and continuing education nurse community to prepare the nursing workforce in genetics/genomics and provide a platform from which to build tools needed to achieve this goal.

  2. Abundant genetic overlap between blood lipids and immune-mediated diseases indicates shared molecular genetic mechanisms.

    Directory of Open Access Journals (Sweden)

    Ole A Andreassen

    Full Text Available Epidemiological studies suggest a relationship between blood lipids and immune-mediated diseases, but the nature of these associations is not well understood. We used genome-wide association studies (GWAS to investigate shared single nucleotide polymorphisms (SNPs between blood lipids and immune-mediated diseases. We analyzed data from GWAS (n~200,000 individuals, applying new False Discovery Rate (FDR methods, to investigate genetic overlap between blood lipid levels [triglycerides (TG, low density lipoproteins (LDL, high density lipoproteins (HDL] and a selection of archetypal immune-mediated diseases (Crohn's disease, ulcerative colitis, rheumatoid arthritis, type 1 diabetes, celiac disease, psoriasis and sarcoidosis. We found significant polygenic pleiotropy between the blood lipids and all the investigated immune-mediated diseases. We discovered several shared risk loci between the immune-mediated diseases and TG (n = 88, LDL (n = 87 and HDL (n = 52. Three-way analyses differentiated the pattern of pleiotropy among the immune-mediated diseases. The new pleiotropic loci increased the number of functional gene network nodes representing blood lipid loci by 40%. Pathway analyses implicated several novel shared mechanisms for immune pathogenesis and lipid biology, including glycosphingolipid synthesis (e.g. FUT2 and intestinal host-microbe interactions (e.g. ATG16L1. We demonstrate a shared genetic basis for blood lipids and immune-mediated diseases independent of environmental factors. Our findings provide novel mechanistic insights into dyslipidemia and immune-mediated diseases and may have implications for therapeutic trials involving lipid-lowering and anti-inflammatory agents.

  3. Assessing T lymphocyte function and differentiation by genetically encoded reporter systems.

    Science.gov (United States)

    Hoekstra, Mirjam E; Dijkgraaf, Feline E; Schumacher, Ton N; Rohr, Jan C

    2015-07-01

    Upon infection, antigen-specific T lymphocytes become activated, proliferate, differentiate, and acquire various effector functions. Much of our understanding of the molecular mechanisms underlying these processes derives from studies leveraging gene deletion, RNAi, and overexpression approaches. However, these perturbations do not inform on the regulation of gene activity under physiological conditions. Genetic reporter systems that couple biological events to detectable output signals are capable of providing this information. Here, we review the reporter approaches being currently used to investigate various aspects of T cell behavior, and discuss advantages and disadvantages inherent to different designs. We outline emerging applications based on recent advances in other fields, and highlight the potential of synthetic biology and genome engineering to address open questions in the field.

  4. Global to local genetic diversity indicators of evolutionary potential in tree species within and outside forests

    DEFF Research Database (Denmark)

    Graudal, Lars; Aravanopoulos, Filippos; Bennadji, Zohra

    2014-01-01

    There is a general trend of biodiversity loss at global, regional, national and local levels. To monitor this trend, international policy processes have created a wealth of indicators over the last two decades. However, genetic diversity indicators are regrettably absent from comprehensive bio-mo...

  5. Global to local genetic diversity indicators of evolutionary potential in tree species within and outside forests

    DEFF Research Database (Denmark)

    Graudal, Lars; Aravanopoulos, Filippos; Bennadji, Zohra

    2014-01-01

    diversity. Revealing benefits of genetic diversity related to ecosystem services is complex, but current trends in plantation performance offer the possibility of an indicator of benefit. Response indicators are generally much easier to define, because recognition and even quantification of, e.g., research...

  6. Genetic variation in genes encoding airway epithelial potassium channels is associated with chronic rhinosinusitis in a pediatric population.

    Directory of Open Access Journals (Sweden)

    Michael T Purkey

    Full Text Available BACKGROUND: Apical potassium channels regulate ion transport in airway epithelial cells and influence air surface liquid (ASL hydration and mucociliary clearance (MCC. We sought to identify whether genetic variation within genes encoding airway potassium channels is associated with chronic rhinosinusitis (CRS. METHODS: Single nucleotide polymorphism (SNP genotypes for selected potassium channels were derived from data generated on the Illumnia HumanHap550 BeadChip or Illumina Human610-Quad BeadChip for 828 unrelated individuals diagnosed with CRS and 5,083 unrelated healthy controls from the Children's Hospital of Philadelphia (CHOP. Statistical analysis was performed with set-based tests using PLINK, and corrected for multiple testing. RESULTS: Set-based case control analysis revealed the gene KCNMA1 was associated with CRS in our Caucasian subset of the cohort (598 CRS cases and 3,489 controls; p = 0.022, based on 10,000 permutations. In addition there was borderline evidence that the gene KCNQ5 (p = 0.0704 was associated with the trait in our African American subset of the cohort (230 CRS cases and 1,594 controls. In addition to the top significant SNPs rs2917454 and rs6907229, imputation analysis uncovered additional genetic variants in KCNMA1 and in KCNQ5 that were associated with CRS. CONCLUSIONS: We have implicated two airway epithelial potassium channels as novel susceptibility loci in contributing to the pathogenesis of CRS.

  7. Generation of a genetically encoded marker of rod photoreceptor outer segment growth and renewal

    Directory of Open Access Journals (Sweden)

    John J. Willoughby

    2011-10-01

    Vertebrate photoreceptors are specialized light sensing neurons. The photoreceptor outer segment is a highly modified cilium where photons of light are transduced into a chemical and electrical signal. The outer segment has the typical cilary axoneme but, in addition, it has a large number of densely packed, stacked, intramembranous discs. The molecular and cellular mechanisms that contribute to vertebrate photoreceptor outer segment morphogenesis are still largely unknown. Unlike typical cilia, the outer segment is continuously regenerated or renewed throughout the life of the animal through the combined process of distal outer segment shedding and proximal outer segment growth. The process of outer segment renewal was discovered over forty years ago, but we still lack an understanding of how photoreceptors renew their outer segments and few, if any, molecular mechanisms that regulate outer segment growth or shedding have been described. Our lack of progress in understanding how photoreceptors renew their outer segments has been hampered by the difficulty in measuring rates of renewal. We have created a new method that uses heat-shock induction of a fluorescent protein that can be used to rapidly measure outer segment growth rates. We describe this method, the stable transgenic line we created, and the growth rates observed in larval and adult rod photoreceptors using this new method. This new method will allow us to begin to define the genetic and molecular mechanisms that regulate rod outer segment renewal, a crucial aspect of photoreceptor function and, possibly, viability.

  8. Optimization of a whole-cell biocatalyst by employing genetically encoded product sensors inside nanolitre reactors

    Science.gov (United States)

    Meyer, Andreas; Pellaux, René; Potot, Sébastien; Becker, Katja; Hohmann, Hans-Peter; Panke, Sven; Held, Martin

    2015-08-01

    Microcompartmentalization offers a high-throughput method for screening large numbers of biocatalysts generated from genetic libraries. Here we present a microcompartmentalization protocol for benchmarking the performance of whole-cell biocatalysts. Gel capsules served as nanolitre reactors (nLRs) for the cultivation and analysis of a library of Bacillus subtilis biocatalysts. The B. subtilis cells, which were co-confined with E. coli sensor cells inside the nLRs, converted the starting material cellobiose into the industrial product vitamin B2. Product formation triggered a sequence of reactions in the sensor cells: (1) conversion of B2 into flavin mononucleotide (FMN), (2) binding of FMN by a RNA riboswitch and (3) self-cleavage of RNA, which resulted in (4) the synthesis of a green fluorescent protein (GFP). The intensity of GFP fluorescence was then used to isolate B. subtilis variants that convert cellobiose into vitamin B2 with elevated efficiency. The underlying design principles of the assay are general and enable the development of similar protocols, which ultimately will speed up the optimization of whole-cell biocatalysts.

  9. PEP1 of Arabis alpina is encoded by two overlapping genes that contribute to natural genetic variation in perennial flowering.

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    Maria C Albani

    Full Text Available Higher plants exhibit a variety of different life histories. Annual plants live for less than a year and after flowering produce seeds and senesce. By contrast perennials live for many years, dividing their life cycle into episodes of vegetative growth and flowering. Environmental cues control key check points in both life histories. Genes controlling responses to these cues exhibit natural genetic variation that has been studied most in short-lived annuals. We characterize natural genetic variation conferring differences in the perennial life cycle of Arabis alpina. Previously the accession Pajares was shown to flower after prolonged exposure to cold (vernalization and only for a limited period before returning to vegetative growth. We describe five accessions of A. alpina that do not require vernalization to flower and flower continuously. Genetic complementation showed that these accessions carry mutant alleles at PERPETUAL FLOWERING 1 (PEP1, which encodes a MADS box transcription factor orthologous to FLOWERING LOCUS C in the annual Arabidopsis thaliana. Each accession carries a different mutation at PEP1, suggesting that such variation has arisen independently many times. Characterization of these alleles demonstrated that in most accessions, including Pajares, the PEP1 locus contains a tandem arrangement of a full length and a partial PEP1 copy, which give rise to two full-length transcripts that are differentially expressed. This complexity contrasts with the single gene present in A. thaliana and might contribute to the more complex expression pattern of PEP1 that is associated with the perennial life-cycle. Our work demonstrates that natural accessions of A. alpina exhibit distinct life histories conferred by differences in PEP1 activity, and that continuous flowering forms have arisen multiple times by inactivation of the floral repressor PEP1. Similar phenotypic variation is found in other herbaceous perennial species, and our results

  10. Commensal E. coli as an Important Reservoir of Resistance Encoding Genetic Elements

    Directory of Open Access Journals (Sweden)

    Azam Mahmoudi-Aznaveh

    2013-11-01

    Full Text Available Background: Diarrheagenic E. coli is the most important cause of diarrhea in children and is a public health concern in developing countries. A major public problem is acquisition and transmission of antimicrobial resistance via mobile genetic elements including plasmids, conjugative transposons, and integrons which may occur through horizontal gene transfer. Objectives: The aim of this study was to investigate the distribution of class 1 and 2 integrons among commensal and enteropathogenic E. coli isolates and assess the role of commensal E. coli population as a reservoir in the acquisition and transmission of antimicrobial resistance. Materials and Methods: Swabs were collected directly from stool samples of the children with diarrhea admitted to three hospitals in Tehran, Iran during July 2012 through October 2012. Antimicrobial susceptibility testing and PCR analysis were performed for analysis of the resistance pattern and integron content of isolates. Results: A total of 20 enteropathogenic E.coli (identified as eae+stx1-stx2- and 20 commensal E.coli were selected for analysis. The resistance pattern in commensal and pathogenic E.coli was very similar. In both groups a high rate of resistance was seen to tetracycline, streptomycin, cotrimoxazole, nalidixic acid, and minocycline. Of 20 EPEC strains, 3 strains (15 % and 1 strain (5% had positive results for int and hep genes, respectively. Among 20 commensal, 65% (13 strains and 10% (2 strains had positive results for int and hep genes, respectively. Conclusions: The higher rate of class 1 integron occurrence among commensal population proposes the commensal intestinal organisms as a potential reservoir of mobile resistance gene elements which could transfer the resistance gene cassettes to other pathogenic and/or nonpathogenic organisms in the intestinal lumen at different occasions.

  11. Genetically encoded fluorescent probe to visualize intracellular phosphatidylinositol 3,5-bisphosphate localization and dynamics.

    Science.gov (United States)

    Li, Xinran; Wang, Xiang; Zhang, Xiaoli; Zhao, Mingkun; Tsang, Wai Lok; Zhang, Yanling; Yau, Richard Gar Wai; Weisman, Lois S; Xu, Haoxing

    2013-12-24

    Phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2] is a low-abundance phosphoinositide presumed to be localized to endosomes and lysosomes, where it recruits cytoplasmic peripheral proteins and regulates endolysosome-localized membrane channel activity. Cells lacking PI(3,5)P2 exhibit lysosomal trafficking defects, and human mutations in the PI(3,5)P2-metabolizing enzymes cause lysosome-related diseases. The spatial and temporal dynamics of PI(3,5)P2, however, remain unclear due to the lack of a reliable detection method. Of the seven known phosphoinositides, only PI(3,5)P2 binds, in the low nanomolar range, to a cytoplasmic phosphoinositide-interacting domain (ML1N) to activate late endosome and lysosome (LEL)-localized transient receptor potential Mucolipin 1 (TRPML1) channels. Here, we report the generation and characterization of a PI(3,5)P2-specific probe, generated by the fusion of fluorescence tags to the tandem repeats of ML1N. The probe was mainly localized to the membranes of Lamp1-positive compartments, and the localization pattern was dynamically altered by either mutations in the probe, or by genetically or pharmacologically manipulating the cellular levels of PI(3,5)P2. Through the use of time-lapse live-cell imaging, we found that the localization of the PI(3,5)P2 probe was regulated by serum withdrawal/addition, undergoing rapid changes immediately before membrane fusion of two LELs. Our development of a PI(3,5)P2-specific probe may facilitate studies of both intracellular signal transduction and membrane trafficking in the endosomes and lysosomes.

  12. Analysis of Current DNA Encoded Library Screening Data Indicates Higher False Negative Rates for Numerically Larger Libraries.

    Science.gov (United States)

    Satz, Alexander L; Hochstrasser, Remo; Petersen, Ann C

    2017-04-10

    To optimize future DNA-encoded library design, we have attempted to quantify the library size at which the signal becomes undetectable. To accomplish this we (i) have calculated that percent yields of individual library members following a screen range from 0.002 to 1%, (ii) extrapolated that ∼1 million copies per library member are required at the outset of a screen, and (iii) from this extrapolation predict that false negative rates will begin to outweigh the benefit of increased diversity at library sizes >10(8). The above analysis is based upon a large internal data set comprising multiple screens, targets, and libraries; we also augmented our internal data with all currently available literature data. In theory, high false negative rates may be overcome by employing larger amounts of library; however, we argue that using more than currently reported amounts of library (≫10 nmoles) is impractical. The above conclusions may be generally applicable to other DNA encoded library platforms, particularly those platforms that do not allow for library amplification.

  13. A genetically encoded FRET lactate sensor and its use to detect the Warburg effect in single cancer cells.

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    Alejandro San Martín

    Full Text Available Lactate is shuttled between and inside cells, playing metabolic and signaling roles in healthy tissues. Lactate is also a harbinger of altered metabolism and participates in the pathogenesis of inflammation, hypoxia/ischemia, neurodegeneration and cancer. Many tumor cells show high rates of lactate production in the presence of oxygen, a phenomenon known as the Warburg effect, which has diagnostic and possibly therapeutic implications. In this article we introduce Laconic, a genetically-encoded Forster Resonance Energy Transfer (FRET-based lactate sensor designed on the bacterial transcription factor LldR. Laconic quantified lactate from 1 µM to 10 mM and was not affected by glucose, pyruvate, acetate, betahydroxybutyrate, glutamate, citrate, α-ketoglutarate, succinate, malate or oxalacetate at concentrations found in mammalian cytosol. Expressed in astrocytes, HEK cells and T98G glioma cells, the sensor allowed dynamic estimation of lactate levels in single cells. Used in combination with a blocker of the monocarboxylate transporter MCT, the sensor was capable of discriminating whether a cell is a net lactate producer or a net lactate consumer. Application of the MCT-block protocol showed that the basal rate of lactate production is 3-5 fold higher in T98G glioma cells than in normal astrocytes. In contrast, the rate of lactate accumulation in response to mitochondrial inhibition with sodium azide was 10 times lower in glioma than in astrocytes, consistent with defective tumor metabolism. A ratio between the rate of lactate production and the rate of azide-induced lactate accumulation, which can be estimated reversibly and in single cells, was identified as a highly sensitive parameter of the Warburg effect, with values of 4.1 ± 0.5 for T98G glioma cells and 0.07 ± 0.007 for astrocytes. In summary, this article describes a genetically-encoded sensor for lactate and its use to measure lactate concentration, lactate flux, and the Warburg

  14. The physiological effects of deleting the mouse SLC30A8 gene encoding zinc transporter-8 are influenced by gender and genetic background.

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    Lynley D Pound

    Full Text Available The SLC30A8 gene encodes the islet-specific transporter ZnT-8, which is hypothesized to provide zinc for insulin-crystal formation. A polymorphic variant in SLC30A8 is associated with altered susceptibility to type 2 diabetes. Several groups have examined the effect of global Slc30a8 gene deletion but the results have been highly variable, perhaps due to the mixed 129SvEv/C57BL/6J genetic background of the mice studied. We therefore sought to remove the conflicting effect of 129SvEv-specific modifier genes.The impact of Slc30a8 deletion was examined in the context of the pure C57BL/6J genetic background.Male C57BL/6J Slc30a8 knockout (KO mice had normal fasting insulin levels and no change in glucose-stimulated insulin secretion (GSIS from isolated islets in marked contrast to the ∼50% and ∼35% decrease, respectively, in both parameters observed in male mixed genetic background Slc30a8 KO mice. This observation suggests that 129SvEv-specific modifier genes modulate the impact of Slc30a8 deletion. In contrast, female C57BL/6J Slc30a8 KO mice had reduced (∼20% fasting insulin levels, though this was not associated with a change in fasting blood glucose (FBG, or GSIS from isolated islets. This observation indicates that gender also modulates the impact of Slc30a8 deletion, though the physiological explanation as to why impaired insulin secretion is not accompanied by elevated FBG is unclear. Neither male nor female C57BL/6J Slc30a8 KO mice showed impaired glucose tolerance.Our data suggest that, despite a marked reduction in islet zinc content, the absence of ZnT-8 does not have a substantial impact on mouse physiology.

  15. Global connectivity of hub residues in Oncoprotein structures encodes genetic factors dictating personalized drug response to targeted Cancer therapy

    Science.gov (United States)

    Soundararajan, Venky; Aravamudan, Murali

    2014-12-01

    The efficacy and mechanisms of therapeutic action are largely described by atomic bonds and interactions local to drug binding sites. Here we introduce global connectivity analysis as a high-throughput computational assay of therapeutic action - inspired by the Google page rank algorithm that unearths most ``globally connected'' websites from the information-dense world wide web (WWW). We execute short timescale (30 ps) molecular dynamics simulations with high sampling frequency (0.01 ps), to identify amino acid residue hubs whose global connectivity dynamics are characteristic of the ligand or mutation associated with the target protein. We find that unexpected allosteric hubs - up to 20Å from the ATP binding site, but within 5Å of the phosphorylation site - encode the Gibbs free energy of inhibition (ΔGinhibition) for select protein kinase-targeted cancer therapeutics. We further find that clinically relevant somatic cancer mutations implicated in both drug resistance and personalized drug sensitivity can be predicted in a high-throughput fashion. Our results establish global connectivity analysis as a potent assay of protein functional modulation. This sets the stage for unearthing disease-causal exome mutations and motivates forecast of clinical drug response on a patient-by-patient basis. We suggest incorporation of structure-guided genetic inference assays into pharmaceutical and healthcare Oncology workflows.

  16. Inhibition of exotoxin production by mobile genetic element SCCmec-encoded psm-mec RNA is conserved in staphylococcal species.

    Science.gov (United States)

    Ikuo, Mariko; Nagano, Gentaro; Saito, Yuki; Mao, Han; Sekimizu, Kazuhisa; Kaito, Chikara

    2014-01-01

    Staphylococcal species acquire antibiotic resistance by incorporating the mobile-genetic element SCCmec. We previously found that SCCmec-encoded psm-mec RNA suppresses exotoxin production as a regulatory RNA, and the psm-mec translation product increases biofilm formation in Staphylococcus aureus. Here, we examined whether the regulatory role of psm-mec on host bacterial virulence properties is conserved among other staphylococcal species, S. epidermidis and S. haemolyticus, both of which are important causes of nosocomial infections. In S. epidermidis, introduction of psm-mec decreased the production of cytolytic toxins called phenol-soluble modulins (PSMs) and increased biofilm formation. Introduction of psm-mec with a stop-codon mutation that did not express PSM-mec protein but did express psm-mec RNA also decreased PSM production, but did not increase biofilm formation. Thus, the psm-mec RNA inhibits PSM production, whereas the PSM-mec protein increases biofilm formation in S. epidermidis. In S. haemolyticus, introduction of psm-mec decreased PSM production, but did not affect biofilm formation. The mutated psm-mec with a stop-codon also caused the same effect. Thus, the psm-mec RNA also inhibits PSM production in S. haemolyticus. These findings suggest that the inhibitory role of psm-mec RNA on exotoxin production is conserved among staphylococcal species, although the stimulating effect of the psm-mec gene on biofilm formation is not conserved.

  17. Redesign of genetically encoded biosensors for monitoring mitochondrial redox status in a broad range of model eukaryotes.

    Science.gov (United States)

    Albrecht, Simone C; Sobotta, Mirko C; Bausewein, Daniela; Aller, Isabel; Hell, Rüdiger; Dick, Tobias P; Meyer, Andreas J

    2014-03-01

    The development of genetically encoded redox biosensors has paved the way toward chemically specific, quantitative, dynamic, and compartment-specific redox measurements in cells and organisms. In particular, redox-sensitive green fluorescent proteins (roGFPs) have attracted major interest as tools to monitor biological redox changes in real time and in vivo. Most recently, the engineering of a redox relay that combines glutaredoxin (Grx) with roGFP2 as a translational fusion (Grx1-roGFP2) led to a biosensor for the glutathione redox potential (EGSH ). The expression of this probe in mitochondria is of particular interest as mitochondria are the major source of oxidants, and their redox status is closely connected to cell fate decisions. While Grx1-roGFP2 can be expressed in mammalian mitochondria, it fails to enter mitochondria in various nonmammalian model organisms. Here we report that inversion of domain order from Grx1-roGFP2 to roGFP2-Grx1 yields a biosensor with perfect mitochondrial targeting while fully maintaining its biosensor capabilities. The redesigned probe thus allows extending in vivo observations of mitochondrial redox homeostasis to important nonmammalian model organisms, particularly plants and insects.

  18. A genetic algorithm encoded with the structural information of amino acids and dipeptides for efficient conformational searches of oligopeptides.

    Science.gov (United States)

    Ru, Xiao; Song, Ce; Lin, Zijing

    2016-05-15

    The genetic algorithm (GA) is an intelligent approach for finding minima in a highly dimensional parametric space. However, the success of GA searches for low energy conformations of biomolecules is rather limited so far. Herein an improved GA scheme is proposed for the conformational search of oligopeptides. A systematic analysis of the backbone dihedral angles of conformations of amino acids (AAs) and dipeptides is performed. The structural information is used to design a new encoding scheme to improve the efficiency of GA search. Local geometry optimizations based on the energy calculations by the density functional theory are employed to safeguard the quality and reliability of the GA structures. The GA scheme is applied to the conformational searches of Lys, Arg, Met-Gly, Lys-Gly, and Phe-Gly-Gly representative of AAs, dipeptides, and tripeptides with complicated side chains. Comparison with the best literature results shows that the new GA method is both highly efficient and reliable by providing the most complete set of the low energy conformations. Moreover, the computational cost of the GA method increases only moderately with the complexity of the molecule. The GA scheme is valuable for the study of the conformations and properties of oligopeptides. © 2016 Wiley Periodicals, Inc.

  19. Genetically Encoded FRET-Sensor Based on Terbium Chelate and Red Fluorescent Protein for Detection of Caspase-3 Activity

    Directory of Open Access Journals (Sweden)

    Alexander S. Goryashchenko

    2015-07-01

    Full Text Available This article describes the genetically encoded caspase-3 FRET-sensor based on the terbium-binding peptide, cleavable linker with caspase-3 recognition site, and red fluorescent protein TagRFP. The engineered construction performs two induction-resonance energy transfer processes: from tryptophan of the terbium-binding peptide to Tb3+ and from sensitized Tb3+ to acceptor—the chromophore of TagRFP. Long-lived terbium-sensitized emission (microseconds, pulse excitation source, and time-resolved detection were utilized to eliminate directly excited TagRFP fluorescence and background cellular autofluorescence, which lasts a fraction of nanosecond, and thus to improve sensitivity of analyses. Furthermore the technique facilitates selective detection of fluorescence, induced by uncleaved acceptor emission. For the first time it was shown that fluorescence resonance energy transfer between sensitized terbium and TagRFP in the engineered construction can be studied via detection of microsecond TagRFP fluorescence intensities. The lifetime and distance distribution between donor and acceptor were calculated using molecular dynamics simulation. Using this data, quantum yield of terbium ions with binding peptide was estimated.

  20. A genetically encoded reporter for real-time imaging of cofilin-actin rods in living neurons.

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    Jianjie Mi

    Full Text Available Filament bundles (rods of cofilin and actin (1:1 form in neurites of stressed neurons where they inhibit synaptic function. Live-cell imaging of rod formation is hampered by the fact that overexpression of a chimera of wild type cofilin with a fluorescent protein causes formation of spontaneous and persistent rods, which is exacerbated by the photostress of imaging. The study of rod induction in living cells calls for a rod reporter that does not cause spontaneous rods. From a study in which single cofilin surface residues were mutated, we identified a mutant, cofilinR21Q, which when fused with monomeric Red Fluorescent Protein (mRFP and expressed several fold above endogenous cofilin, does not induce spontaneous rods even during the photostress of imaging. CofilinR21Q-mRFP only incorporates into rods when they form from endogenous proteins in stressed cells. In neurons, cofilinR21Q-mRFP reports on rods formed from endogenous cofilin and induced by all modes tested thus far. Rods have a half-life of 30-60 min upon removal of the inducer. Vesicle transport in neurites is arrested upon treatments that form rods and recovers as rods disappear. CofilinR21Q-mRFP is a genetically encoded rod reporter that is useful in live cell imaging studies of induced rod formation, including rod dynamics, and kinetics of rod elimination.

  1. Real-time determination of intracellular oxygen in bacteria using a genetically encoded FRET-based biosensor

    Directory of Open Access Journals (Sweden)

    Potzkei Janko

    2012-03-01

    Full Text Available Abstract Background Molecular oxygen (O2 is one of the key metabolites of all obligate and facultative aerobic pro- and eukaryotes. It plays a fundamental role in energy homeostasis whereas oxygen deprivation, in turn, broadly affects various physiological and pathophysiological processes. Therefore, real-time monitoring of cellular oxygen levels is basically a prerequisite for the analysis of hypoxia-induced processes in living cells and tissues. Results We developed a genetically encoded Förster resonance energy transfer (FRET-based biosensor allowing the observation of changing molecular oxygen concentrations inside living cells. This biosensor named FluBO (fluorescent protein-based biosensor for oxygen consists of the yellow fluorescent protein (YFP that is sensitive towards oxygen depletion and the hypoxia-tolerant flavin-binding fluorescent protein (FbFP. Since O2 is essential for the formation of the YFP chromophore, efficient FRET from the FbFP donor domain to the YFP acceptor domain only occurs in the presence but not in the absence of oxygen. The oxygen biosensor was used for continuous real-time monitoring of temporal changes of O2 levels in the cytoplasm of Escherichia coli cells during batch cultivation. Conclusions FluBO represents a unique FRET-based oxygen biosensor which allows the non-invasive ratiometric readout of cellular oxygen. Thus, FluBO can serve as a novel and powerful probe for investigating the occurrence of hypoxia and its effects on a variety of (pathophysiological processes in living cells.

  2. Mobile genetic element SCCmec-encoded psm-mec RNA suppresses translation of agrA and attenuates MRSA virulence.

    Science.gov (United States)

    Kaito, Chikara; Saito, Yuki; Ikuo, Mariko; Omae, Yosuke; Mao, Han; Nagano, Gentaro; Fujiyuki, Tomoko; Numata, Shunsuke; Han, Xiao; Obata, Kazuaki; Hasegawa, Setsuo; Yamaguchi, Hiroki; Inokuchi, Koiti; Ito, Teruyo; Hiramatsu, Keiichi; Sekimizu, Kazuhisa

    2013-01-01

    Community acquired-methicillin resistant Staphylococcus aureus (CA-MRSA) is a socially problematic pathogen that infects healthy individuals, causing severe disease. CA-MRSA is more virulent than hospital associated-MRSA (HA-MRSA). The underlying mechanism for the high virulence of CA-MRSA is not known. The transcription product of the psm-mec gene, located in the mobile genetic element SCCmec of HA-MRSA, but not CA-MRSA, suppresses the expression of phenol-soluble modulin α (PSMα), a cytolytic toxin of S. aureus. Here we report that psm-mec RNA inhibits translation of the agrA gene encoding a positive transcription factor for the PSMα gene via specific binding to agrA mRNA. Furthermore, 25% of 325 clinical MRSA isolates had a mutation in the psm-mec promoter that attenuated transcription, and 9% of the strains had no psm-mec. In most of these psm-mec-mutated or psm-mec-deleted HA-MRSAs, PSMα expression was increased compared with strains carrying intact psm-mec, and some mutated strains produced high amounts of PSMα comparable with that of CA-MRSA. Deletion of psm-mec from HA-MRSA strains carrying intact psm-mec increased the expression of AgrA protein and PSMα, and virulence in mice. Thus, psm-mec RNA suppresses MRSA virulence via inhibition of agrA translation and the absence of psm-mec function in CA-MRSA causes its high virulence property.

  3. Association of genetic variations of genes encoding thrombospondin, type 1, domain-containing 4 and 7A with low bone mineral density in Japanese women with osteoporosis.

    Science.gov (United States)

    Mori, Seijiro; Kou, Ikuyo; Sato, Hidenori; Emi, Mitsuru; Ito, Hideki; Hosoi, Takayuki; Ikegawa, Shiro

    2008-01-01

    Twins and family studies have shown that genetic factors are important determinants of bone mass. Important aspects of bone mineral density (BMD) regulation are endocrine systems, notably hormonal regulation of adrenal corticoids, as indicated by clinical knowledge of glucocorticoid-induced osteoporosis. Glucocorticoid is known to negatively regulate bone mass in vivo, and glucocorticoid increases thrombospondin messenger ribonucleic acid (mRNA) levels. We studied single nucleotide polymorphisms (SNPs) in genes encoding thrombospondin, type 1, domain-containing 4 and 7A (THSD4 and THSD7A) for possible association with lumbar and femoral BMD among 337 Japanese women with osteoporosis who participated in the BioBank Japan project. Genetic variations of THSD4 and THSD7A loci displayed significant association with lumbar and femoral BMD. Most significant correlation was observed for THSD7A SNP rs12673692 with lumbar BMD (P = 0.00017). Homozygous carriers of the major (G) allele had the highest BMD [0.886 +/- 0.011 g/cm2, mean +/- standard deviation (SD)], whereas heterozygous carriers were intermediate (0.872 +/- 0.013 g/cm2) and homozygous A-allele carriers had the lowest (0.753 +/- 0.023 g/cm2). THSD4 SNP rs10851839 also displayed strong association with lumbar BMD (P = 0.0092). In addition, both THSD7A and THSD4 displayed significant association with femoral BMD in a recessive model (P = 0.036 and P = 0.0046, respectively). Results suggest that variations of THSD7A and THSD4 loci may be important determinants of osteoporosis in Japanese women.

  4. Indicators of genetic erosion in an endangered population: the Alentejana cattle breed in Portugal.

    Science.gov (United States)

    Carolino, N; Gama, L T

    2008-01-01

    A study was conducted to characterize genetic diversity in the Alentejana breed of cattle based on its demographic trends and to investigate the major factors affecting genetic erosion in this breed. Herdbook information collected between 1940 and 2004, including pedigree records on 100,562 animals in 155 herds, was used to estimate demographic parameters. The mean generation intervals were 6.0 +/- 2.4 yr and 6.8 +/- 3.2 yr for sires and dams of calves, respectively. Average inbreeding increased steadily over the period analyzed, with an annual rate of inbreeding of 0.33 +/- 0.004% (P < 0.01) and an effective population size of 23.3. In the reference population (28,531 calves born between 2000 and 2003) the average inbreeding was 8.35 +/- 9.02% and nearly 80% of the calves were inbred, whereas the average relationship among all animals was 0.026 +/- 0.040. Nevertheless, the mean relationship was 0.328 +/- 0.264 and 0.022 +/- 0.026 for animals born in the same and in different herds, respectively. The computed genetic contributions to the reference population resulted in estimates for the effective number of founders, ancestors, founding herds, and herds supplying sires of 121.6, 55.0, 17.1, and 26.9, respectively, the 2 most influential herds and ancestors contributing 24.2 and 15.1%, respectively, of the current genetic pool. Of the 671 founding sires, only 24 Y-chromosomes are currently represented, but 1 sire alone contributes nearly 60% of this representation, such that the effective number of Y-chromosomes is only 2.73. The observed inbreeding per herd was, on average, 0.053 +/- 0.071 lower than expected from the relationship among the generation of parents of calves in the reference population, indicating that producers have followed breeding strategies that have kept inbreeding at lower levels than anticipated with random selection and mating. When compared with other cattle breeds, Alentejana has some of the highest levels of mean inbreeding and annual rate

  5. Genetic Sensitivity to Phenylthiocarbamide – Effect on Body Mass Indices and DNA damage

    Directory of Open Access Journals (Sweden)

    Gursatej Gandhi

    2012-06-01

    Full Text Available As sensitivity to bitter taste (phenylthiocarbamide [PTC] perception has been maintained at high frequency worldwide, its use as a potential genetic marker for food preferences and dietary choices and its influence on body weight/adiposity which in turn maybe a contributor to various co-morbidities including malignancy needs to be explored in the Punjabi context where there is higher per capita income, an adapted ‘western’ dietary pattern with traditional culinary habits and reduced physical activity. Since studies linking PTC tasting status, indices of obesity and DNA damage have not come to attention, the present study, using the alkaline Single Cell Gel Electrophoresis assay was carried out to assess genomic damage in peripheral blood leukocytes (PBL of 144 individuals, both obese (n=96, as determined by body mass index [BMI] and waist-hip ratio [WHR] and normal weight healthy (n=46 subjects. Their PTC status revealed 73 tasters and 69 non-tasters. The odds ratio revealed a 2.51 times increased risk in non-tasters (OR=2.51; 95%CI 1.20-5.25 for having BMI≥ 25.0 kg/m2 in comparison to risk in tasters while the risk ratio revealed a 1.32 times increased probability of non-tasters for having BMI≥ 25.0 kg/m2 in comparison to tasters (RR=1.32; 95%CI 1.05-1.66. The genetic damage in the obese group (characterized on the bases of their gender and PTC tasting ability was very highly significant (p<0.001 compared to the values in the matched control group (healthy, normal weight subjects. In both the taster and non-taster groups, BMI and WC (waist circumference significantly correlated to genetic damage indices though PTC tasting ability did not appear to influence BMI, WHR and WC.

  6. Case studies on genetically modified organisms (GMOs): Potential risk scenarios and associated health indicators.

    Science.gov (United States)

    De Santis, Barbara; Stockhofe, Norbert; Wal, Jean-Michel; Weesendorp, Eefke; Lallès, Jean-Paul; van Dijk, Jeroen; Kok, Esther; De Giacomo, Marzia; Einspanier, Ralf; Onori, Roberta; Brera, Carlo; Bikker, Paul; van der Meulen, Jan; Gijs, Kleter

    2017-08-30

    Within the frame of the EU-funded MARLON project, background data were reviewed to explore the possibility of measuring health indicators during post-market monitoring for potential effects of feeds, particularly genetically modified (GM) feeds, on livestock animal health, if applicable. Four case studies (CSs) of potential health effects on livestock were framed and the current knowledge of a possible effect of GM feed was reviewed. Concerning allergenicity (CS-1), there are no case-reports of allergic reactions or immunotoxic effects resulting from GM feed consumption as compared with non-GM feed. The likelihood of horizontal gene transfer (HGT; CS-2) of GMO-related DNA to different species is not different from that for other DNA and is unlikely to raise health concerns. Concerning mycotoxins (CS-3), insect-resistant GM maize may reduce fumonisins contamination as a health benefit, yet other Fusarium toxins and aflatoxins show inconclusive results. For nutritionally altered crops (CS-4), the genetic modifications applied lead to compositional changes which require special considerations of their nutritional impacts. No health indicators were thus identified except for possible beneficial impacts of reduced mycotoxins and nutritional enhancement. More generally, veterinary health data should ideally be linked with animal exposure information so as to be able to establish cause-effect relationships. Copyright © 2017. Published by Elsevier Ltd.

  7. Molecular Characterization of Trypanosoma cruzi Tc8.2 Gene Indicates Two Differential Locations for the Encoded Protein in Epimastigote and Trypomastigote Forms.

    Science.gov (United States)

    Kian, Danielle; Lancheros, César Armando Contreras; Damiani, Igor Alexandre Campos; Fernandes, Tamiris Zanforlin Olmos; Pinge-Filho, Phileno; Santos, Márcia Regina Machado dos; Silveira, José Franco da; Nakamura, Celso Vataru; Silva, João Santana da; Yamada-Ogatta, Sueli Fumie; Yamauchi, Lucy Megumi

    2015-08-01

    This report describes the molecular characterization of the Tc8.2 gene of Trypanosoma cruzi. Both the Tc8.2 gene and its encoded protein were analyzed by bioinformatics, while Northern blot and RT-PCR were used for the transcripts. Besides, immunolocalization of recombinant protein was done by immunofluorescence and electron microscopy. Analysis indicated the presence of a single copy of Tc8.2 in the T. cruzi genome and 2-different sized transcripts in epimastigotes/amastigotes and trypomastigotes. Immunoblotting showed 70 and 80 kDa polypeptides in epimastigotes and trypomastigotes, respectively, and a differential pattern of immunolocalization. Overall, the results suggest that Tc8.2 is differentially expressed during the T. cruzi life cycle.

  8. Genetically encoded photocrosslinkers locate the high-affinity binding site of antidepressant drugs in the human serotonin transporter

    DEFF Research Database (Denmark)

    Rannversson, Hafsteinn; Andersen, Jacob; Hall, Lena Sørensen;

    2016-01-01

    Despite the well-established role of the human serotonin transporter (hSERT) in the treatment of depression, the molecular details of antidepressant drug binding are still not fully understood. Here we utilize amber codon suppression in a membrane-bound transporter protein to encode photocrosslin......Despite the well-established role of the human serotonin transporter (hSERT) in the treatment of depression, the molecular details of antidepressant drug binding are still not fully understood. Here we utilize amber codon suppression in a membrane-bound transporter protein to encode...

  9. Organic and genetically modified soybean diets: consequences in growth and in hematological indicators of aged rats.

    Science.gov (United States)

    Daleprane, Julio Beltrame; Feijó, Tatiana Silveira; Boaventura, Gilson Teles

    2009-03-01

    The aim of this study was to evaluate the protein quality of organic and genetically modified soy by feeding specific diets to rats. Three groups of Wistar rats (n=10) were used, and each group was named according to the food that they ate. There was an organic soy group (OG), a genetically modified soy group (GG), and a control group (CG). All animals received water and diet ad libitum for 455 days. At the end of this period, the weight of the GG group was the same as that of the OG, and both were higher than CG. Protein intake was similar for the OG and GG, which were significantly lower (p<0.0005) than the CG. The growth rate (GR) of the rats, albumin levels, and total levels of serum protein were comparable for all groups. Hematocrit (p<0.04) and hemoglobin (p<0.03) for the OG and GG were less than the CG. Although the OG and GG demonstrated reduced hematocrit and hemoglobin, both types of soy were utilized in a way similar to casein. This result suggests that the protein quality of soy is parallel to the standard protein casein in terms of growth promotion but not hematological indicators.

  10. A novel homologous dominant selection marker for genetic transformation of Penicillium chrysogenum: overexpression of squalene epoxidase-encoding ergA.

    Science.gov (United States)

    Sigl, Claudia; Handler, Monika; Sprenger, Georg; Kürnsteiner, Hubert; Zadra, Ivo

    2010-11-01

    Genetic engineering requires genetic selection markers. For generation of biosafe strains in industrial applications, homologous dominant selection markers allowing "self-cloning" are best suited but scarce. Here we describe a novel homologous dominant genetic selection system for the filamentous fungus Penicillium chrysogenum based on overexpression of the P. chrysogenum squalene epoxidase-encoding ergA gene, which confers resistance against terbinafine. Terbinafine (TRB) is a potent antifungal drug used in therapy of fungal infections. Overexpression of ergA was driven by the P. chrysogenum endoxylanase xylP promoter that is highly inducible by xylose. The suitability of the novel selection marker cassette for genetic manipulation was proven by its use for targeted deletion of the transcription factor nosA in P. chrysogenum. NosA-deficiency did not affect growth rates on solid or in liquid media, conidiation in light or darkness, and resistance to hydrogen peroxide. However, NosA-deficiency significantly decreased penicillin productivity. As TRB inhibits the growth of a variety of fungal species, this novel selection marker is expected to be suitable for genetic engineering of diverse fungal species.

  11. Identification of TENP as the Gene Encoding Chicken Egg White Ovoglobulin G2 and Demonstration of Its High Genetic Variability in Chickens.

    Science.gov (United States)

    Kinoshita, Keiji; Shimogiri, Takeshi; Ibrahim, Hisham R; Tsudzuki, Masaoki; Maeda, Yoshizane; Matsuda, Yoichi

    2016-01-01

    Ovoglobulin G2 (G2) has long been known as a major protein constituent of chicken egg white. However, little is known about the biochemical properties and biological functions of G2 because the gene encoding G2 has not been identified. Therefore, the identification of the gene encoding G2 and an analysis of its genetic variability is an important step toward the goal of understanding the biological functions of the G2 protein and its utility in poultry production. To identify and characterize the gene encoding G2, we separated G2 from egg white using electrophoresis on a non-denaturing polyacrylamide gel. Two polymorphic forms of G2 protein (G2A and G2B), with different mobilities (fast and slow respectively), were detected by staining. The protein band corresponding to G2B was electro-eluted from the native gel, re-electrophoresed under denaturing conditions and its N-terminal sequence was determined by Edman degradation following transfer onto a membrane. Sequencing of the 47 kDa G2B band revealed it to be identical to TENP (transiently expressed in neural precursors), also known as BPI fold-containing family B, member 2 (BPIFB2), a protein with strong homology to a bacterial permeability-increasing protein family (BPI) in mammals. Full-length chicken TENP cDNA sequences were determined for 78 individuals across 29 chicken breeds, lines, and populations, and consequently eleven non-synonymous substitutions were detected in the coding region. Of the eleven non-synonymous substitutions, A329G leading to Arg110Gln was completely associated with the noted differential electrophoretic mobility of G2. Specifically G2B, with a slower mobility is encoded by A329 (Arg110), whereas G2A, with a faster mobility, is encoded by G329 (Gln110). The sequence data, derived from the coding region, also revealed that the gene encoding G2 demonstrates significant genetic variability across different chicken breeds/lines/populations. These variants, and how they correlate with egg

  12. [Edwards syndrome--most frequent indications for genetic amniocentesis. Analysis of the last 5 years].

    Science.gov (United States)

    Chuchracki, Marek; Janiak, Justyna; Ziółkowska, Katarzyna; Sedziak, Anna; Opala, Tomasz

    2012-01-01

    Edwards syndrome (trisomy 18) occurs in 1: 8000 live births and is closely related to the mother's age. Most of the embryos and fetuses with trisomy of 18 chromosome pair undergo natural abortion. Change in number and structure of chromosomes usually takes place spontaneously. However, the incidence of chromosome mutations increases with the presence of mutagenic factors. One of the chemical mutagenic factors is benzopyrene - present in cigarette smoke. Prenatal cytogenetic diagnostic is used for detecting diseases and clinical syndromes conditioned by chromosome aberrations. To this date the "golden standard" of this diagnostic is the assessment of the fetus karyotype by means of analysis of chromosome banding pattern from amniotic fluid-derived cells. The aim of the study was the analysis of indications for genetic amniocenteses carried out in the last 5 years and in case of which trisomy of chromosome 18 (Edwards syndrome) was diagnosed. The analysis covered 1593 results of fetus karyotypes obtained from Cytogenetic Laboratory of the Central Gynecological-Obstetric Clinical Hospital in Poznań over the last 5 years. The study procedure consisted in producing cell culture from amniotic fluid, appliance of appropriate color techniques and thorough microscopic analysis of chromosome banding pattern. As a result of the analysis it was discovered that in 1538 cases the karyotype was normal, and in 55 cases trisomy 18 was diagnosed, which constituted 3% of all cytogenetic tests. The highest number of trisomy 18 cases was noted in 2009 - 19 cases, which constitutes 5% of all tests. In 2010 and 2011 the results included respectively 2% and 3% of diagnosed trisomy 18 (Edwards syndrome). In the last 5 years normal results for karyotypes constituted 87%, in 10% cases other aberrations were diagnosed through cystogenetic tests, whereas 3% of the results have shown trisomy 18 (Edwards syndrome The most frequent indications for performing genetic amniocentesis, as a result of

  13. Genetic dissection of methylcrotonyl CoA carboxylase indicates a complex role for mitochondrial leucine catabolism during seed development and germination.

    Science.gov (United States)

    Ding, Geng; Che, Ping; Ilarslan, Hilal; Wurtele, Eve S; Nikolau, Basil J

    2012-05-01

    3-methylcrotonyl CoA carboxylase (MCCase) is a nuclear-encoded, mitochondrial-localized biotin-containing enzyme. The reaction catalyzed by this enzyme is required for leucine (Leu) catabolism, and it may also play a role in the catabolism of isoprenoids and the mevalonate shunt. In Arabidopsis, two MCCase subunits (the biotinylated MCCA subunit and the non-biotinylated MCCB subunit) are each encoded by single genes (At1g03090 and At4g34030, respectively). A reverse genetic approach was used to assess the physiological role of MCCase in plants. We recovered and characterized T-DNA and transposon-tagged knockout alleles of the MCCA and MCCB genes. Metabolite profiling studies indicate that mutations in either MCCA or MCCB block mitochondrial Leu catabolism, as inferred from the increased accumulation of Leu. Under light deprivation conditions, the hyper-accumulation of Leu, 3-methylcrotonyl CoA and isovaleryl CoA indicates that mitochondrial and peroxisomal Leu catabolism pathways are independently regulated. This biochemical block in mitochondrial Leu catabolism is associated with an impaired reproductive growth phenotype, which includes aberrant flower and silique development and decreased seed germination. The decreased seed germination phenotype is only observed for homozygous mutant seeds collected from a parent plant that is itself homozygous, but not from a parent plant that is heterozygous. These characterizations may shed light on the role of catabolic processes in growth and development, an area of plant biology that is poorly understood.

  14. Genetics and Molecular Biology of Epstein-Barr Virus-Encoded BART MicroRNA: A Paradigm for Viral Modulation of Host Immune Response Genes and Genome Stability

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    David H. Dreyfus

    2017-01-01

    Full Text Available Epstein-Barr virus, a ubiquitous human herpesvirus, is associated through epidemiologic evidence with common autoimmune syndromes and cancers. However, specific genetic mechanisms of pathogenesis have been difficult to identify. In this review, the author summarizes evidence that recently discovered noncoding RNAs termed microRNA encoded by Epstein-Barr virus BARF (BamHI A right frame termed BART (BamHI A right transcripts are modulators of human immune response genes and genome stability in infected and bystander cells. BART expression is apparently regulated by complex feedback loops with the host immune response regulatory NF-κB transcription factors. EBV-encoded BZLF-1 (ZEBRA protein could also regulate BART since ZEBRA contains a terminal region similar to ankyrin proteins such as IκBα that regulate host NF-κB. BALF-2 (BamHI A left frame transcript, a viral homologue of the immunoglobulin and T cell receptor gene recombinase RAG-1 (recombination-activating gene-1, may also be coregulated with BART since BALF-2 regulatory sequences are located near the BART locus. Viral-encoded microRNA and viral mRNA transferred to bystander cells through vesicles, defective viral particles, or other mechanisms suggest a new paradigm in which bystander or hit-and-run mechanisms enable the virus to transiently or chronically alter human immune response genes as well as the stability of the human genome.

  15. Towards PDT with Genetically Encoded Photosensitizer KillerRed: A Comparison of Continuous and Pulsed Laser Regimens in an Animal Tumor Model.

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    Marina Shirmanova

    Full Text Available The strong phototoxicity of the red fluorescent protein KillerRed allows it to be considered as a potential genetically encoded photosensitizer for the photodynamic therapy (PDT of cancer. The advantages of KillerRed over chemical photosensitizers are its expression in tumor cells transduced with the appropriate gene and direct killing of cells through precise damage to any desired cell compartment. The ability of KillerRed to affect cell division and to induce cell death has already been demonstrated in cancer cell lines in vitro and HeLa tumor xenografts in vivo. However, the further development of this approach for PDT requires optimization of the method of treatment. In this study we tested the continuous wave (593 nm and pulsed laser (584 nm, 10 Hz, 18 ns modes to achieve an antitumor effect. The research was implemented on CT26 subcutaneous mouse tumors expressing KillerRed in fusion with histone H2B. The results showed that the pulsed mode provided a higher rate of photobleaching of KillerRed without any temperature increase on the tumor surface. PDT with the continuous wave laser was ineffective against CT26 tumors in mice, whereas the pulsed laser induced pronounced histopathological changes and inhibition of tumor growth. Therefore, we selected an effective regimen for PDT when using the genetically encoded photosensitizer KillerRed and pulsed laser irradiation.

  16. Prediction of genetic gain from selection indices for disease resistance in papaya hybrids

    Directory of Open Access Journals (Sweden)

    Marcelo Vivas

    2012-12-01

    Full Text Available In order to select superior hybrids for the concentration of favorable alleles for resistance to papaya black spot, powdery mildew and phoma spot, 67 hybrids were evaluated in two seasons, in 2007, in a randomized block design with two replications. Genetic gains were estimated from the selection indices of Smith & Hazel, Pesek & Baker, Williams, Mulamba & Mock, with selection intensity of 22.39%, corresponding to 15 hybrids. The index of Mulamba & Mock showed gains more suitable for the five traits assessed when it was used the criterion of economic weight tentatively assigned. Together, severity of black spot on leaves and on fruits, characteristics considered most relevant to the selection of resistant materials, expressed percentage gain of -44.15%. In addition, there were gains for other characteristics, with negative predicted selective percentage gain. The results showed that the index of Mulamba & Mock is the most efficient procedure for simultaneous selection of papaya hybrid resistant to black spot, powdery mildew and phoma spot.

  17. Research Regarding the New Biodiversity Indicators in Genetic Diversity of the Region -Country Hateg

    Directory of Open Access Journals (Sweden)

    Iudith Ipate

    2010-05-01

    Full Text Available The present research started in June 2009 by identification of the species and breeds in the livestock of the 11 villages and 1 town existing in the Hatseg Land area. We use the modern genotyping tool for the study of zootechnical biodiversity- molecular biology tests- based on identification, amplification and characterization of nucleic acid, revolutionized the conservation of indigene animal genetic resources, gene assisted selection, pathology diagnostic and food traceability. The original Tipy Fix methods – internatinal patented by Prof.Brem - that were used in Romania (using for the first time in Romania by the researchers of CSCBA to reveal DNA polymorphism are described as their applicability in species identification and meat traceability. Vulnerability of farm animal breeds is caused by the lack of interest apart breeders for one breed. In Hateg land area the main mean of reducing biodiversity in farm animals is the crossbreeding. It was analysis the prion protein for scrapie resistance genotyping as codonamino acid at codon 136, 154, 171 from 5 known haplotypes resulting PrP Genotype .In results of analysis in Hateg country 41 the probes present the arginine (R at codon 171 of the prion protein who confers resistance to the structural change of prion scrapie.We presented biodiversity indicator for domestic animal in Hateg country.

  18. Calcium Green FlAsH as a genetically targeted small-molecule calcium indicator.

    Science.gov (United States)

    Tour, Oded; Adams, Stephen R; Kerr, Rex A; Meijer, Rene M; Sejnowski, Terrence J; Tsien, Richard W; Tsien, Roger Y

    2007-07-01

    Intracellular Ca(2+) regulates numerous proteins and cellular functions and can vary substantially over submicron and submillisecond scales, so precisely localized fast detection is desirable. We have created a approximately 1-kDa biarsenical Ca(2+) indicator, called Calcium Green FlAsH (CaGF, 1), to probe [Ca(2+)] surrounding genetically targeted proteins. CaGF attached to a tetracysteine motif becomes ten-fold more fluorescent upon binding Ca(2+), with a K(d) of approximately 100 microM, <1-ms kinetics and good Mg(2+) rejection. In HeLa cells expressing tetracysteine-tagged connexin 43, CaGF labels gap junctions and reports Ca(2+) waves after injury. Total internal reflection microscopy of tetracysteine-tagged, CaGF-labeled alpha(1C) L-type calcium channels shows fast-rising depolarization-evoked Ca(2+) transients, whose lateral nonuniformity suggests that the probability of channel opening varies greatly over micron dimensions. With moderate Ca(2+) buffering, these transients decay surprisingly slowly, probably because most of the CaGF signal comes from closed channels feeling Ca(2+) from a tiny minority of clustered open channels. With high Ca(2+) buffering, CaGF signals decay as rapidly as the calcium currents, as expected for submicron Ca(2+) domains immediately surrounding active channels. Thus CaGF can report highly localized, rapid [Ca(2+)] dynamics.

  19. Genetic programming based quantitative structure-retention relationships for the prediction of Kovats retention indices.

    Science.gov (United States)

    Goel, Purva; Bapat, Sanket; Vyas, Renu; Tambe, Amruta; Tambe, Sanjeev S

    2015-11-13

    The development of quantitative structure-retention relationships (QSRR) aims at constructing an appropriate linear/nonlinear model for the prediction of the retention behavior (such as Kovats retention index) of a solute on a chromatographic column. Commonly, multi-linear regression and artificial neural networks are used in the QSRR development in the gas chromatography (GC). In this study, an artificial intelligence based data-driven modeling formalism, namely genetic programming (GP), has been introduced for the development of quantitative structure based models predicting Kovats retention indices (KRI). The novelty of the GP formalism is that given an example dataset, it searches and optimizes both the form (structure) and the parameters of an appropriate linear/nonlinear data-fitting model. Thus, it is not necessary to pre-specify the form of the data-fitting model in the GP-based modeling. These models are also less complex, simple to understand, and easy to deploy. The effectiveness of GP in constructing QSRRs has been demonstrated by developing models predicting KRIs of light hydrocarbons (case study-I) and adamantane derivatives (case study-II). In each case study, two-, three- and four-descriptor models have been developed using the KRI data available in the literature. The results of these studies clearly indicate that the GP-based models possess an excellent KRI prediction accuracy and generalization capability. Specifically, the best performing four-descriptor models in both the case studies have yielded high (>0.9) values of the coefficient of determination (R(2)) and low values of root mean squared error (RMSE) and mean absolute percent error (MAPE) for training, test and validation set data. The characteristic feature of this study is that it introduces a practical and an effective GP-based method for developing QSRRs in gas chromatography that can be gainfully utilized for developing other types of data-driven models in chromatography science.

  20. The role of genetic factors and pre- and perinatal influences in the etiology of autism spectrum disorders – indications for genetic referral

    Directory of Open Access Journals (Sweden)

    Filip Rybakowski

    2016-06-01

    Full Text Available Autism spectrum disorders (ASD are caused by disruptions in early stages of central nervous system development and are usually diagnosed in first years of life. Despite common features such as impairment of socio-communicative development and stereotypical behaviours, ASD are characterised by heterogeneous course and clinical picture. The most important aetiological factors comprise genetic and environmental influences acting at prenatal, perinatal and neonatal period. The role of rare variants with large effect i.e. copy number variants in genes regulating synapse formation and intrasynaptic connections is emphasised. Common variants with small effect may also be involved, i.e. polymorphisms in genes encoding prosocial peptides system – oxytocin and vasopressin. The environmental factors may include harmful effects acting during pregnancy and labour, however their specificity until now is not confirmed, and in some of them a primary genetic origin cannot be excluded. In several instances, especially with comorbid disorders – intellectual disability, epilepsy and dysmorphias – a detailed molecular diagnostics is warranted, which currently may elucidate the genetic background of disorder in about 20% of cases.

  1. Real-time and high-throughput analysis of mitochondrial metabolic states in living cells using genetically encoded NAD(+)/NADH sensors.

    Science.gov (United States)

    Zhao, Yuzheng; Yang, Yi

    2016-11-01

    Mitochondria are central organelles that regulate cellular bioenergetics, biosynthesis, and signaling processes. NADH, a key player in cell metabolism, is often considered as a marker of mitochondrial function. However, traditional methods for NADH measurements are either destructive or unable to distinguish between NADH and NADPH. In contrast to traditional methods, genetically encoded NADH sensors can be used for the real-time tracking and quantitative measurement of subcellular NADH levels in living cells. Therefore, these sensors provide innovative tools and address the limitations of current techniques. We herein summarize the properties of different types of recently developed NADH biosensors, discuss their advantages and disadvantages, and focus on the high-throughput analysis of mitochondrial function by using highly responsive NAD(+)/NADH sensors.

  2. Landscape genetics informs mesohabitat preference and conservation priorities for a surrogate indicator species in a highly fragmented river system.

    Science.gov (United States)

    Lean, J; Hammer, M P; Unmack, P J; Adams, M; Beheregaray, L B

    2017-04-01

    Poor dispersal species represent conservative benchmarks for biodiversity management because they provide insights into ecological processes influenced by habitat fragmentation that are less evident in more dispersive organisms. Here we used the poorly dispersive and threatened river blackfish (Gadopsis marmoratus) as a surrogate indicator system for assessing the effects of fragmentation in highly modified river basins and for prioritizing basin-wide management strategies. We combined individual, population and landscape-based approaches to analyze genetic variation in samples spanning the distribution of the species in Australia's Murray-Darling Basin, one of the world's most degraded freshwater systems. Our results indicate that G. marmoratus displays the hallmark of severe habitat fragmentation with notably scattered, small and demographically isolated populations with very low genetic diversity-a pattern found not only between regions and catchments but also between streams within catchments. By using hierarchically nested population sampling and assessing relationships between genetic uniqueness and genetic diversity across populations, we developed a spatial management framework that includes the selection of populations in need of genetic rescue. Landscape genetics provided an environmental criterion to identify associations between landscape features and ecological processes. Our results further our understanding of the impact that habitat quality and quantity has on habitat specialists with similarly low dispersal. They should also have practical applications for prioritizing both large- and small-scale conservation management actions for organisms inhabiting highly fragmented ecosystems.

  3. Co-administration of a plasmid DNA encoding IL-15 improves long-term protection of a genetic vaccine against Trypanosoma cruzi.

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    Christopher S Eickhoff

    Full Text Available BACKGROUND: Immunization of mice with the Trypanosoma cruzi trans-sialidase (TS gene using plasmid DNA, adenoviral vector, and CpG-adjuvanted protein delivery has proven highly immunogenic and provides protection against acute lethal challenge. However, long-term protection induced by TS DNA vaccines has not been reported. The goal of the present work was to test whether the co-administration of a plasmid encoding IL-15 (pIL-15 could improve the duration of protection achieved through genetic vaccination with plasmid encoding TS (pTS alone. METHODOLOGY: We immunized BALB/c mice with pTS in the presence or absence of pIL-15 and studied immune responses [with TS-specific IFN-γ ELISPOT, serum IgG ELISAs, intracellular cytokine staining (IFN-γ, TNF-α, and IL-2, tetramer staining, and CFSE dilution assays] and protection against lethal systemic challenge at 1 to 6 months post vaccination. Mice receiving pTS alone developed robust TS-specific IFN-γ responses and survived a lethal challenge given within the first 3 months following immunization. The addition of pIL-15 to pTS vaccination did not significantly alter T cell responses or protection during this early post-vaccination period. However, mice vaccinated with both pTS and pIL-15 challenged 6 months post-vaccination were significantly more protected against lethal T. cruzi challenges than mice vaccinated with pTS alone (P6 months post immunization. Also, these TS-specific T cells were better able to expand after in vitro re-stimulation. CONCLUSION: Addition of pIL-15 during genetic vaccination greatly improved long-term T cell survival, memory T cell expansion, and long-term protection against the important human parasite, T. cruzi.

  4. Giardia intestinalis: conservation of the variant-specific surface protein VSP417-1 (TSA417) and identification of a divergent homologue encoded at a duplicated locus in genetic group II isolates.

    Science.gov (United States)

    Ey, P L; Darby, J M

    1998-11-01

    The stability of the gene encoding TSA417, a 72-kDa variant-specific surface protein (VSP) produced by trophozoites of Giardia intestinalis isolate WB-C6, was investigated in isolates of similar (Assemblage A / Group I) or distinct (Assemblage A / Group II) genotype. Using primers specific for the WB-C6 tsa417 gene, DNA amplified in polymerase chain reactions from genomic DNA indicated the presence, in every isolate, of an intact coding sequence possessing conserved restriction sites diagnostic for this locus (herein designated vsp417-1). Sequence analysis of the DNA amplified from the genomes of genetic Group I ("A-I") isolates revealed complete identity with the published WB-C6 tsa417 (vsp417-1(A-I)) sequence. Equivalent products, amplified from the genomes of genetic Group II ("A-II") isolates, similarly yielded an invariant and apparently allelic 2142-bp coding sequence (designated vsp417-1(A-II)) possessing 79% nucleotide identity with vsp417-1(A-I) and polymorphisms unique to Group II organisms. The encoded polypeptides (VSP417-1(A-I) and VSP417-1(A-II)) are identical at 75% of amino acid positions. Substitutions are concentrated within the N-terminal portions of the proteins, but the overall structure of VSP417-1 has changed little during the evolution of the Group I and Group II genotypes from their common clonal ancestor. An additional 0.7-kb DNA, representing a separate locus (vsp417-5) encoding a 22.3-kDa VSP, was amplified from genetic Group II genomes exclusively but only using particular primer combinations. The vsp417-5(A-II) gene exhibits >85% sequence identity with the 5' and 3' segments of vsp417-1(A-I) and vsp417-1(A-II) but it lacks a 1482-bp segment that comprises the central portion of the vsp417-1 locus. Excision of this segment seems to have occurred by intragenic recombination, possibly initiated by a stem loop formed between palindromic sequences which border the 1482-bp segment within vsp417-1 but which are contiguous in vsp417-5(A

  5. Combination encoding genetic algorithm for dynamic transmission network planning%动态输电网络规划的组合编码遗传算法

    Institute of Scientific and Technical Information of China (English)

    高元海; 王淳

    2013-01-01

    A combination encoding is proposed for handling the time decision variable in a dynamic transmission network planning (DTNP). The time decision variable is implied in the combination encoding, which converts the DTNP problem into a static programming problem. The encoding satisfies 1 to 1 mapping between the phenotype and genotype, and meets the consistency of phenotypic space distance and genotypic space distance, which ensure the search efficiency of genetic algorithm. Moreover, according to the characteristics of DTNP problem, some improvement measures are given for crossover operators, mutation mode, fitness function, penalty coefficient so as to enhance the performance of the genetic algorithm to solve DTNP problem. The proposed method is validated using a 19-node system, and results show that the optimal solution can be obtained within reasonable evolutionary generation.%  针对动态输电网络规划过程中需要考虑时间决策量的问题,提出了组合编码方式。组合编码方式将多阶段输电网络规划中的时间决策量隐含在编码中,从而使得多阶段的动态输电网络规划问题能够转换成静态规划问题进行求解。该编码方式满足表现型和基因型的1对1映射,及表现型空间与基因型空间距离上的一致性,从而保证了遗传算法的搜索效率。此外,针对动态输电网络规划的特点,对遗传算法的交叉算子、变异方式、适应度函数、惩罚系数等方面进行了改进,进一步改善了遗传算法求解多阶段输电网络规划问题的性能。以19节点系统为例对算法进行了验证,结果表明能够在较短的进化代数内得到问题的最优解。

  6. Applicability of universal Bacteroidales genetic marker for microbial monitoring of drinking water sources in comparison to conventional indicators.

    Science.gov (United States)

    Shahryari, A; Nikaeen, M; Khiadani Hajian, M; Nabavi, F; Hatamzadeh, M; Hassanzadeh, A

    2014-11-01

    Water quality monitoring is essential for the provision of safe drinking water. In this study, we compared a selection of fecal indicators with universal Bacteroidales genetic marker to identify fecal pollution of a variety of drinking water sources. A total of 60 samples were collected from water sources. The microbiological parameters included total coliforms, fecal coliforms, Escherichia coli and fecal streptococci as the fecal indicator bacteria (FIB), Clostridium perfringens and H2S bacteria as alternative indicators, universal Bacteroidales genetic marker as a promising alternative fecal indicator, and Salmonella spp., Shigella spp., and E. coli O157 as pathogenic bacteria. From 60 samples analyzed, Bacteroidales was the most frequently detected indicator followed by total coliforms. However, the Bacteroidales assay failed to detect the marker in nine samples positive for FIB and other alternative indicators. The results of our study showed that the absence of Bacteroidales is not necessarily an evidence of fecal and pathogenic bacteria absence and may be unable to ensure the safety of the water. Further research, however, is required for a better understanding of the use of a Bacteroidales genetic marker as an indicator in water quality monitoring programs.

  7. In vivo characterization of genetic expression of virus-transduced calcium indicators in retinal ganglion cells using a low-cost funduscope.

    Science.gov (United States)

    Chang, Yao-Chuan; Walston, Steven T; Chow, Robert H; Weiland, James D

    2016-08-01

    Virus-transduced calcium indicators are effective reporters of neural activity, offering the advantage of cell-specific labeling. To track the level of in vivo expression of genetically encoded calcium indicators (GECIs) in rodent retina, we developed a noninvasive imaging approach based on a custom-modified low-cost and simple fundus system that enabled us to monitor and characterize in vivo bright-field and fluorescence retinal image. The system clearly resolves individual retinal ganglion cells (RGCs) and axons. RGC fluorescence intensity and number of observable fluorescent cells show a consistent rising trend from week 1 to week 3 after viral injection, indicating a uniform increase of GCaMP6f expression. At defined time points, we prepared wholemount retina mounted on a transparent multielectrode array (MEA) and used calcium imaging to identify the optimal time for studying the responsiveness of RGCs to external electrical stimulation. The results show that the fluorescence-endoscopy fundus system is a powerful and widely accessible tool for evaluating in vivo fluorescence reporter expression.

  8. Sharp genetic breaks among populations of Haptosquilla pulchella (Stomatopoda) indicate limits to larval transport: patterns, causes, and consequences.

    Science.gov (United States)

    Barber, P H; Palumbi, S R; Erdmann, M V; Moosa, M K

    2002-04-01

    To help stem the precipitous decline of coral reef ecosystems world-wide, conservation efforts are focused on establishing interconnected reserve networks to protect threatened populations. Because many coral reef organisms have a planktonic or pelagic larval dispersal phase, it is critical to understand the patterns of ecological connectivity between reserve populations that result from larval dispersal. We used genetics to infer dispersal patterns among 24 Indo-West Pacific populations of the mantis shrimp, Haptosquilla pulchella. Contrary to predictions of high dispersal facilitated by the strong currents of the Indonesian throughflow, mitochondrial DNA sequences from 393 individuals displayed striking patterns of regional genetic differentiation concordant with ocean basins isolated during periods of lowered sea level. Patterns of genetic structuring indicate that although dispersal within geographical regions with semicontiguous coastlines spanning thousands of kilometres may be common, ecologically meaningful connections can be rare among populations separated by as little as 300 km of open ocean. Strong genetic mosaics in a species with high dispersal potential highlight the utility of genetics for identifying regional patterns of genetic connectivity between marine populations and show that the assumption that ocean currents will provide ecological connectivity among marine populations must be empirically tested in the design of marine reserve networks.

  9. Partitioning of genetic variation between regulatory and coding gene segments: the predominance of software variation in genes encoding introvert proteins.

    Science.gov (United States)

    Mitchison, A

    1997-01-01

    In considering genetic variation in eukaryotes, a fundamental distinction can be made between variation in regulatory (software) and coding (hardware) gene segments. For quantitative traits the bulk of variation, particularly that near the population mean, appears to reside in regulatory segments. The main exceptions to this rule concern proteins which handle extrinsic substances, here termed extrovert proteins. The immune system includes an unusually large proportion of this exceptional category, but even so its chief source of variation may well be polymorphism in regulatory gene segments. The main evidence for this view emerges from genome scanning for quantitative trait loci (QTL), which in the case of the immune system points to a major contribution of pro-inflammatory cytokine genes. Further support comes from sequencing of major histocompatibility complex (Mhc) class II promoters, where a high level of polymorphism has been detected. These Mhc promoters appear to act, in part at least, by gating the back-signal from T cells into antigen-presenting cells. Both these forms of polymorphism are likely to be sustained by the need for flexibility in the immune response. Future work on promoter polymorphism is likely to benefit from the input from genome informatics.

  10. EFFECT OF DIETARY LYSINE AND GENETICS ON INDICES OF ENERGY AND PROTEIN METABOLISM IN RAINBOW TROUT

    Science.gov (United States)

    Since feed cost represents about 70% of production cost, inexpensive protein alternatives are desirable replacements for fish meal. One drawback to the replacement of fish meal with soybean meal is that the latter protein source is first limiting in lysine. To investigate if different genetic line...

  11. Predicting the effect of naltrexone and acamprosate in alcohol-dependent patients using genetic indicators

    NARCIS (Netherlands)

    Ooteman, W.; Naassila, M.; Koeter, M.W.J.; Verheul, R.; Schippers, G.M.; Houchi, H.; Daoust, M.; van den Brink, W.

    2009-01-01

    Acamprosate and naltrexone are effective medications in the treatment of alcoholism. However. effect sizes are modest. Pharmacogenomics may improve patient-treatment-matching and effect sizes. It is hypothesized that naltrexone exerts its effect through genetic characteristics associated with the do

  12. Fluorescence-based characterization of genetically encoded peptides that fold in live cells: progress toward a generic hairpin scaffold

    Science.gov (United States)

    Cheng, Zihao; Campbell, Robert E.

    2007-02-01

    Binding proteins suitable for expression and high affinity molecular recognition in the cytoplasm or nucleus of live cells have numerous applications in the biological sciences. In an effort to add a new minimal motif to the growing repertoire of validated non-immunoglobulin binding proteins, we have undertaken the development of a generic protein scaffold based on a single β-hairpin that can fold efficiently in the cytoplasm. We have developed a method, based on the measurement of fluorescence resonance energy transfer (FRET) between a genetically fused cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP), that allows the structural stability of recombinant β-hairpin peptides to be rapidly assessed both in vitro and in vivo. We have previously reported the validation of this method when applied to a 16mer tryptophan zipper β-hairpin. We now describe the use of this method to evaluate the potential of a designed 20mer β-hairpin peptide with a 3rd Trp/Trp cross-strand pair to function as a generic protein scaffold. Quantitative analysis of the FRET efficiency, resistance to proteolysis (assayed by loss of FRET), and circular dichroism spectra revealed that the 20mer peptide is significantly more tolerant of destabilizing mutations than the 16mer peptide. Furthermore, we experimentally demonstrate that the in vitro determined β-hairpin stabilities are well correlated with in vivo β-hairpin stabilities as determined by FRET measurements of colonies of live bacteria expressing the recombinant peptides flanked by CFP and YFP. Finally, we report on our progress to develop highly folded 24mer and 28mer β-hairpin peptides through the use of fluorescence-based library screening.

  13. Karyotype analysis with amniotic fluid in 12365 pregnant women with indications for genetic amniocentesis and strategies of prenatal diagnosis.

    Science.gov (United States)

    Xiao, H; Yang, Y L; Zhang, C Y; Liao, E J; Zhao, H R; Liao, S X

    2016-01-01

    We explored the strategies of prenatal diagnosis by foetal karyotype analysis in pregnant women with indications for genetic amniocentesis. Karyotype analysis of amniotic fluid was performed on 12365 pregnant women with indications for genetic amniocentesis. The detection rates and distributions of abnormal karyotypes were observed in a variety of indications for genetic amniocentesis. The detection rates of abnormal karyotype were 57.4% in either a mother or father with chromosomal abnormality, 8.5% in the pregnant women with pathological ultrasound finding (PUF), 2.79% in the pregnant women with advanced age (35 years and over) and 2.23% in the women with abnormal maternal serum screening (MSS) tests. Foetal abnormal karyotype was found in 86 pregnant women with PUF; of the 86 pregnant women, 42 had trisomy 13, 18 or 21. Of the 12365 pregnant women, foetal abnormal karyotype was found in 428 (3.46%); of the 428 foetuses, only 154 had trisomy 13, 18 or 21. In the pregnant women with abnormal MSS, 111 foetuses had abnormal karyotype, but only 36 foetuses had trisomy 13, 18 or 21. We conclude that (1) ultrasound is an important approach to prevent the birth of foetuses with chromosomal disease. (2) Non-invasive prenatal DNA detection cannot completely replace invasive prenatal diagnosis and MSS. (3) The strategies of prenatal diagnosis: Genetic amniocentesis is strongly recommended for the pregnant women with indications for genetic amniocentesis. For pregnant women who refuse invasive prenatal diagnosis, non-invasive prenatal DNA detection is first performed. If the results of non-invasive prenatal DNA detection are negative, the pregnant women are followed up by ultrasound; if the results of non-invasive prenatal DNA detection are positive, the pregnant women should undergo invasive prenatal diagnosis.

  14. Calcium imaging in the Drosophila olfactory system with a genetic indicator.

    Science.gov (United States)

    Root, Cory M; Wong, Allan M; Flores, Jorge; Wang, Jing W

    2013-11-01

    Insects show sophisticated odor-mediated behaviors controlled by an olfactory system that is genetically and anatomically simpler than that of vertebrates, providing an attractive system to investigate the mechanistic link between behavior and odor perception. Advances in neuroscience have been facilitated by modern optical imaging technologies--both in instrumentation and in probe design--that permit the visualization of functional neural circuits. Imaging calcium activity in genetically defined populations of neurons provides an important tool for investigating the function of neural circuits. This article describes a two-photon imaging system for monitoring neural activity in the Drosophila antennal lobe. Odor-evoked calcium activity is followed by measuring the specific expression of the calcium-sensitive green fluorescent protein G-CaMP in Drosophila antennae-brain preparations.

  15. Genetic structure of Florida green turtle rookeries as indicated by mitochondrial DNA control region sequences

    Science.gov (United States)

    Shamblin, Brian M.; Bagley, Dean A.; Ehrhart, Llewellyn M.; Desjardin, Nicole A.; Martin, R. Erik; Hart, Kristen M.; Naro-Maciel, Eugenia; Rusenko, Kirt; Stiner, John C.; Sobel, Debra; Johnson, Chris; Wilmers, Thomas; Wright, Laura J.; Nairn, Campbell J.

    2014-01-01

    Green turtle (Chelonia mydas) nesting has increased dramatically in Florida over the past two decades, ranking the Florida nesting aggregation among the largest in the Greater Caribbean region. Individual beaches that comprise several hundred kilometers of Florida’s east coast and Keys support tens to thousands of nests annually. These beaches encompass natural to highly developed habitats, and the degree of demographic partitioning among rookeries was previously unresolved. We characterized the genetic structure of ten Florida rookeries from Cape Canaveral to the Dry Tortugas through analysis of 817 base pair mitochondrial DNA (mtDNA) control region sequences from 485 nesting turtles. Two common haplotypes, CM-A1.1 and CM-A3.1, accounted for 87 % of samples, and the haplotype frequencies were strongly partitioned by latitude along Florida’s Atlantic coast. Most genetic structure occurred between rookeries on either side of an apparent genetic break in the vicinity of the St. Lucie Inlet that separates Hutchinson Island and Jupiter Island, representing the finest scale at which mtDNA structure has been documented in marine turtle rookeries. Florida and Caribbean scale analyses of population structure support recognition of at least two management units: central eastern Florida and southern Florida. More thorough sampling and deeper sequencing are necessary to better characterize connectivity among Florida green turtle rookeries as well as between the Florida nesting aggregation and others in the Greater Caribbean region.

  16. Genetics of Fertility Indicators Based on Behaviour and Progesterone in Milk

    DEFF Research Database (Denmark)

    Løvendahl, P; Chagunda, M; O'Connell, J;

    2009-01-01

    Genetic selection for female is diffecult because current records based on AI information are biased from farmer's decisions and have low heritablity (h2 = 0.03). Automated on-farm progesterone based heat detection methods are becoming commercially available, as has eqipment based on behaviour...... monitoring using activity meters already been for some time. Data from a research herd show that the heritablility of days to first oestrus is between 0.21 and 0.27 using these types of equipments. Collection of data from both types of automated equipment would offer unbiased informationon days to first...

  17. Distribution and regulation of the mobile genetic element-encoded phenol-soluble modulin PSM-mec in methicillin-resistant Staphylococcus aureus.

    Science.gov (United States)

    Chatterjee, Som S; Chen, Liang; Joo, Hwang-Soo; Cheung, Gordon Y C; Kreiswirth, Barry N; Otto, Michael

    2011-01-01

    The phenol-soluble modulin PSM-mec is the only known staphylococcal toxin that is encoded on a mobile antibiotic resistance determinant, namely the staphylococcal cassette chromosome (SCC) element mec encoding resistance to methicillin. Here we show that the psm-mec gene is found frequently among methicillin-resistant Staphylococcus aureus (MRSA) strains of SCCmec types II, III, and VIII, and is a conserved part of the class A mec gene complex. Controlled expression of AgrA versus RNAIII in agr mutants of all 3 psm-mec-positive SCCmec types demonstrated that expression of psm-mec, which is highly variable, is controlled by AgrA in an RNAIII-independent manner. Furthermore, psm-mec isogenic deletion mutants showed only minor changes in PSMα peptide production and unchanged (or, as previously described, diminished) virulence compared to the corresponding wild-type strains in a mouse model of skin infection. This indicates that the recently reported regulatory impact of the psm-mec locus on MRSA virulence, which is opposite to that of the PSM-mec peptide and likely mediated by a regulatory RNA, is minor when analyzed in the original strain background. Our study gives new insight in the distribution, regulation, and role in virulence of the PSM-mec peptide and the psm-mec gene locus.

  18. Multi-trait BLUP model indicates sorghum hybrids with genetic potential for agronomic and nutritional traits.

    Science.gov (United States)

    Almeida Filho, J E; Tardin, F D; Guimarães, J F R; Resende, M D V; Silva, F F; Simeone, M L; Menezes, C B; Queiroz, V A V

    2016-02-26

    The breeding of sorghum, Sorghum bicolor (L.) Moench, aimed at improving its nutritional quality, is of great interest, since it can be used as a highly nutritive alternative food source and can possibly be cultivated in regions with low rainfall. The objective of the present study was to evaluate the potential and genetic diversity of grain-sorghum hybrids for traits of agronomic and nutritional interest. To this end, the traits grain yield and flowering, and concentrations of protein, potassium, calcium, magnesium, sulfur, iron, manganese, and zinc in the grain were evaluated in 25 grain-sorghum hybrids, comprising 18 experimental hybrids of Embrapa Milho e Sorgo and seven commercial hybrids. The genetic potential was analyzed by a multi-trait best linear unbiased prediction (BLUP) model, and cluster analysis was accomplished by squared Mahalanobis distance using the predicted genotypic values. Hybrids 0306037 and 0306034 stood out in the agronomic evaluation. The hybrids with agronomic prominence, however, did not stand out for the traits related to the nutritional quality of the grain. Three clusters were formed from the dendrogram obtained with the unweighted pair group method with arithmetic mean method. From the results of the genotypic BLUP and the analysis of the dendrogram, hybrids 0577337, 0441347, 0307651, and 0306037 were identified as having the potential to establish a population that can aggregate alleles for all the evaluated traits of interest.

  19. REE Geochemical Characteristics of Tungsten Minerals as a Discriminant Indicator of Genetic Types of Ore Deposits

    Institute of Scientific and Technical Information of China (English)

    张玉学; 刘文茂; 等

    1990-01-01

    Tungsten minerals (scheelite and wolframite)from two genetic types of granitoids show significant dif-ferences in REE distribution,probably due to different material sources and origins.Tungsten miner-als in granite porphyry of the crust-mantle source are relatively high in ∑REE(1884ppm on average).∑ Ce is rich relative to ∑Y and ∑Ce/∑Y is relatively high(>1).The chondrite-normalized REE distribution patterns are characterized by a group of rightward-inclined curves.Tungsten minerals in quartz veins intruding the granites of crust origin have lower ∑REE (335 ppm on average).∑Y is rich relative to ∑Ce and ∑Ce/∑Y is relatively low(<1).The chondrite-normalized REE distribution patterns are characterized by a group of leftward-inclined curves.So the REE distribution patterns can be used to discriminate the sources of rock-and ore-forming materials and the genetic types of W deposits so as to provide clues to ore prospecting.

  20. Genetic variability of Yersinia pestis isolates as predicted by PCR-based IS100 genotyping and analysis of structural genes encoding glycerol-3-phosphate dehydrogenase (glpD).

    Science.gov (United States)

    Motin, Vladimir L; Georgescu, Anca M; Elliott, Jeffrey M; Hu, Ping; Worsham, Patricia L; Ott, Linda L; Slezak, Tomas R; Sokhansanj, Bahrad A; Regala, Warren M; Brubaker, Robert R; Garcia, Emilio

    2002-02-01

    A PCR-based genotyping system that detects divergence of IS100 locations within the Yersinia pestis genome was used to characterize a large collection of isolates of different biovars and geographical origins. Using sequences derived from the glycerol-negative biovar orientalis strain CO92, a set of 27 locus-specific primers was designed to amplify fragments between the end of IS100 and its neighboring gene. Geographically diverse members of the orientalis biovar formed a homogeneous group with identical genotype with the exception of strains isolated in Indochina. In contrast, strains belonging to the glycerol-positive biovar antiqua showed a variety of fingerprinting profiles. Moreover, strains of the biovar medievalis (also glycerol positive) clustered together with the antiqua isolates originated from Southeast Asia, suggesting their close phylogenetic relationships. Interestingly, a Manchurian biovar antiqua strain Nicholisk 51 displayed a genotyping pattern typical of biovar orientalis isolates. Analysis of the glycerol pathway in Y. pestis suggested that a 93-bp deletion within the glpD gene encoding aerobic glycerol-3-phosphate dehydrogenase might account for the glycerol-negative phenotype of the orientalis biovar. The glpD gene of strain Nicholisk 51 did not possess this deletion, although it contained two nucleotide substitutions characteristic of the glpD version found exclusively in biovar orientalis strains. To account for this close relationship between biovar orientalis strains and the antiqua Nicholisk 51 isolate, we postulate that the latter represents a variant of this biovar with restored ability to ferment glycerol. The fact that such a genetic lesion might be repaired as part of the natural evolutionary process suggests the existence of genetic exchange between different Yersinia strains in nature. The relevance of this observation on the emergence of epidemic Y. pestis strains is discussed.

  1. Decay of Bacteroidales genetic markers in relation to traditional fecal indicators for water quality modeling of drinking water sources.

    Science.gov (United States)

    Sokolova, Ekaterina; Aström, Johan; Pettersson, Thomas J R; Bergstedt, Olof; Hermansson, Malte

    2012-01-17

    The implementation of microbial fecal source tracking (MST) methods in drinking water management is limited by the lack of knowledge on the transport and decay of host-specific genetic markers in water sources. To address these limitations, the decay and transport of human (BacH) and ruminant (BacR) fecal Bacteroidales 16S rRNA genetic markers in a drinking water source (Lake Rådasjön in Sweden) were simulated using a microbiological model coupled to a three-dimensional hydrodynamic model. The microbiological model was calibrated using data from outdoor microcosm trials performed in March, August, and November 2010 to determine the decay of BacH and BacR markers in relation to traditional fecal indicators. The microcosm trials indicated that the persistence of BacH and BacR in the microcosms was not significantly different from the persistence of traditional fecal indicators. The modeling of BacH and BacR transport within the lake illustrated that the highest levels of genetic markers at the raw water intakes were associated with human fecal sources (on-site sewers and emergency sewer overflow). This novel modeling approach improves the interpretation of MST data, especially when fecal pollution from the same host group is released into the water source from different sites in the catchment.

  2. Engineering a genetically encoded competitive inhibitor of the KEAP1-NRF2 interaction via structure-based design and phage display.

    Science.gov (United States)

    Guntas, Gurkan; Lewis, Steven M; Mulvaney, Kathleen M; Cloer, Erica W; Tripathy, Ashutosh; Lane, Thomas R; Major, Michael B; Kuhlman, Brian

    2016-01-01

    In its basal state, KEAP1 binds the transcription factor NRF2 (Kd = 5 nM) and promotes its degradation by ubiquitylation. Changes in the redox environment lead to modification of key cysteines within KEAP1, resulting in NRF2 protein accumulation and the transcription of genes important for restoring the cellular redox state. Using phage display and a computational loop grafting protocol, we engineered a monobody (R1) that is a potent competitive inhibitor of the KEAP1-NRF2 interaction. R1 bound to KEAP1 with a Kd of 300 pM and in human cells freed NRF2 from KEAP1 resulting in activation of the NRF2 promoter. Unlike cysteine-reactive small molecules that lack protein specificity, R1 is a genetically encoded, reversible inhibitor designed specifically for KEAP1. R1 should prove useful for studying the role of the KEAP1-NRF2 interaction in several disease states. The structure-based phage display strategy employed here is a general approach for engineering high-affinity binders that compete with naturally occurring interactions.

  3. Combinatorial mutagenesis of the voltage-sensing domain enables the optical resolution of action potentials firing at 60 Hz by a genetically encoded fluorescent sensor of membrane potential.

    Science.gov (United States)

    Piao, Hong Hua; Rajakumar, Dhanarajan; Kang, Bok Eum; Kim, Eun Ha; Baker, Bradley J

    2015-01-07

    ArcLight is a genetically encoded fluorescent voltage sensor using the voltage-sensing domain of the voltage-sensing phosphatase from Ciona intestinalis that gives a large but slow-responding optical signal in response to changes in membrane potential (Jin et al., 2012). Fluorescent voltage sensors using the voltage-sensing domain from other species give faster yet weaker optical signals (Baker et al., 2012; Han et al., 2013). Sequence alignment of voltage-sensing phosphatases from different species revealed conserved polar and charged residues at 7 aa intervals in the S1-S3 transmembrane segments of the voltage-sensing domain, suggesting potential coil-coil interactions. The contribution of these residues to the voltage-induced optical signal was tested using a cassette mutagenesis screen by flanking each transmembrane segment with unique restriction sites to allow for the testing of individual mutations in each transmembrane segment, as well as combinations in all four transmembrane segments. Addition of a counter charge in S2 improved the kinetics of the optical response. A double mutation in the S4 domain dramatically reduced the slow component of the optical signal seen in ArcLight. Combining that double S4 mutant with the mutation in the S2 domain yielded a probe with kinetics voltage-sensing domain could potentially lead to fluorescent sensors capable of optically resolving neuronal inhibition and subthreshold synaptic activity.

  4. Genetics studies indicate that neural induction and early neuronal maturation are disturbed in autism.

    Directory of Open Access Journals (Sweden)

    Emily L. Casanova

    2014-11-01

    Full Text Available Postmortem neuropathological studies of autism consistently reveal distinctive types of malformations, including cortical dysplasias, heterotopias, and various neuronomorphometric abnormalities. In keeping with these observations, we review here that 88% of high-risk genes for autism influence neural induction and early maturation of the neuroblast. In addition, 80% of these same genes influence later stages of differentiation, including neurite and synapse development, suggesting that these gene products exhibit long-lasting developmental effects on cell development as well as extensive functional redundancy in processes of neural proliferation, growth, and maturation. We also address the putative genetic overlap of autism with conditions like epilepsy and schizophrenia, with implications to shared and divergent etiologies. This review imports the necessity of a frameshift in our understanding of the neurodevelopmental basis of autism to include all stages of neuronal maturation, ranging from neural induction to synaptogenesis.

  5. Obesity-related genetic polymorphisms and adiposity indices in a young Italian population.

    Science.gov (United States)

    Bordoni, Laura; Marchegiani, Francesca; Piangerelli, Marco; Napolioni, Valerio; Gabbianelli, Rosita

    2017-02-01

    Pediatric obesity develops when a complex biological predisposition collides with an obesogenic environment. To further elucidate the role of genetics in obesity onset, we performed a candidate-gene association study in a young and sportive Italian population by testing the association of functional polymorphisms in ACE (rs4646994), FTO (rs9939609), MC4R (rs17782313) and PPARG (rs1801282) genes with body mass index (BMI) and waist-to-height ratio (WHtR). We also tested the combinations of identified risk genotypes and epistatic interactions among them to determine the existence of cumulative effects in predicting the predisposition to gain weight. Our results confirm a significant direct influence of MC4R rs17782313 and PPARG rs1801282 on body composition, that is, minor allele homozygotes showed significantly higher BMI (rs17782313, β = 1.258, P = 0.031; rs1801282, β = 6.689, P = 1.2 × 10(-4) ) and WHtR (rs17782313, β = 0.021, P = 0.005; rs1801282, β = 0.069, P = 0.003) values. Moreover, by leveraging multifactor dimensionality reduction and general linear model (GLM) approaches we identified an epistatic interaction between ACE and MC4R, where heterozygosity at ACE rs4646994 seems to protect from the unfavorable predisposition to gain weight given by C/C genotype at MC4R rs17782313 (GLM, P = 0.004). In conclusion, to clarify the role of genetics in multifactorial diseases remains a difficult goal, even for the most investigated polymorphisms and in controlled populations. Further studies on epistasis and gene-gene interaction will help to elucidate this complex scenario. © 2017 IUBMB Life, 69(2):98-105, 2017. © 2017 International Union of Biochemistry and Molecular Biology.

  6. Genetic variation within native populations of endemic silkmoth Antheraea assamensis (Helfer from Northeast India indicates need for in situ conservation.

    Directory of Open Access Journals (Sweden)

    Y Tunginba Singh

    Full Text Available A. assamensis is a phytophagous Lepidoptera from Northeast India reared on host trees of Lauraceae family for its characteristic cocoon silk. Source of these cocoons are domesticated farm stocks that crash frequently and/or wild insect populations that provide new cultures. The need to reduce dependence on wild populations for cocoons necessitates assessment of genetic diversity in cultivated and wild populations. Molecular markers based on PCR of Inter-simple sequence repeats (ISSR and simple sequence repeats (SSR were used with four populations of wild insects and eleven populations of cultivated insects. Wild populations had high genetic diversity estimates (H(i = 0.25; H(S = 0.28; H(E = 0.42 and at least one population contained private alleles. Both marker systems indicated that genetic variability within populations examined was significantly high. Among cultivated populations, insects of the Upper Assam region (H(i = 0.19; H(S = 0.18; H(E = 0 were genetically distinct (F(ST = 0.38 with both marker systems from insects of Lower Assam (H(i =0.24; H(S =0.25; H(E = 0.3. Sequencing of polymorphic amplicons suggested transposition as a mechanism for maintaining genomic diversity. Implications for conservation of native populations in the wild and preserving in-farm diversity are discussed.

  7. Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (Solanum sect. Lycopersicon; Solanaceae).

    Science.gov (United States)

    Muir, Christopher D; Pease, James B; Moyle, Leonie C

    2014-12-01

    Adaptive evolution requires both raw genetic material and an accessible path of high fitness from one fitness peak to another. In this study, we used an introgression line (IL) population to map quantitative trait loci (QTL) for leaf traits thought to be associated with adaptation to precipitation in wild tomatoes (Solanum sect. Lycopersicon; Solanaceae). A QTL sign test showed that several traits likely evolved under directional natural selection. Leaf traits correlated across species do not share a common genetic basis, consistent with a scenario in which selection maintains trait covariation unconstrained by pleiotropy or linkage disequilibrium. Two large effect QTL for stomatal distribution colocalized with key genes in the stomatal development pathway, suggesting promising candidates for the molecular bases of adaptation in these species. Furthermore, macroevolutionary transitions between vastly different stomatal distributions may not be constrained when such large-effect mutations are available. Finally, genetic correlations between stomatal traits measured in this study and data on carbon isotope discrimination from the same ILs support a functional hypothesis that the distribution of stomata affects the resistance to CO2 diffusion inside the leaf, a trait implicated in climatic adaptation in wild tomatoes. Along with evidence from previous comparative and experimental studies, this analysis indicates that leaf traits are an important component of climatic niche adaptation in wild tomatoes and demonstrates that some trait transitions between species could have involved few, large-effect genetic changes, allowing rapid responses to new environmental conditions.

  8. Tracing fecal pollution sources in karst groundwater by Bacteroidales genetic biomarkers, bacterial indicators, and environmental variables.

    Science.gov (United States)

    Zhang, Ya; Kelly, Walton R; Panno, Samuel V; Liu, Wen-Tso

    2014-08-15

    Fecal contamination in Midwestern karst regions was evaluated by simultaneously measuring traditional bacterial indicators (coliforms and Escherichia coli), Bacteroidales-based biomarkers, and environmental variables. Water samples from springs and wells were collected from karst regions in Illinois (IL), Wisconsin (WI), Kentucky (KY), and Missouri (MO). Quantitative PCR (Q-PCR) with seven primer sets targeting different members of Bacteroidales was used to determine the origin of fecal contamination (i.e., from human waste, livestock waste, or both). Most samples were contaminated by both human and animal waste, with a few samples showing pollution solely by one or the other. Spring water tended to have higher levels of contamination than well water, and higher concentrations of fecal biomarkers were detected in urban springs compared to rural spring systems. However, there were discrepancies on contamination profile determined by Bacteroidales-based biomarkers and by traditional bacterial indicators. Among all the environmental parameters examined, E. coli, sulfate, total dissolved solids (TDS), and silicon were significantly correlated (pgroundwater systems in Midwestern regions, and the inclusion of traditional bacterial indicators, environmental variables, and Bacteroidales-based MST is an effective approach for identifying fecal contamination in karst regions. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Genetic diversity of EBV-encoded LMP1 in the Swiss HIV Cohort Study and implication for NF-Κb activation.

    Directory of Open Access Journals (Sweden)

    Emilie Zuercher

    Full Text Available Epstein-Barr virus (EBV is associated with several types of cancers including Hodgkin's lymphoma (HL and nasopharyngeal carcinoma (NPC. EBV-encoded latent membrane protein 1 (LMP1, a multifunctional oncoprotein, is a powerful activator of the transcription factor NF-κB, a property that is essential for EBV-transformed lymphoblastoid cell survival. Previous studies reported LMP1 sequence variations and induction of higher NF-κB activation levels compared to the prototype B95-8 LMP1 by some variants. Here we used biopsies of EBV-associated cancers and blood of individuals included in the Swiss HIV Cohort Study (SHCS to analyze LMP1 genetic diversity and impact of sequence variations on LMP1-mediated NF-κB activation potential. We found that a number of variants mediate higher NF-κB activation levels when compared to B95-8 LMP1 and mapped three single polymorphisms responsible for this phenotype: F106Y, I124V and F144I. F106Y was present in all LMP1 isolated in this study and its effect was variant dependent, suggesting that it was modulated by other polymorphisms. The two polymorphisms I124V and F144I were present in distinct phylogenetic groups and were linked with other specific polymorphisms nearby, I152L and D150A/L151I, respectively. The two sets of polymorphisms, I124V/I152L and F144I/D150A/L151I, which were markers of increased NF-κB activation in vitro, were not associated with EBV-associated HL in the SHCS. Taken together these results highlighted the importance of single polymorphisms for the modulation of LMP1 signaling activity and demonstrated that several groups of LMP1 variants, through distinct mutational paths, mediated enhanced NF-κB activation levels compared to B95-8 LMP1.

  10. Biosynthesis of the 22nd Genetically Encoded Amino Acid Pyrrolysine: Structure and Reaction Mechanism of PylC at 1.5Å Resolution

    KAUST Repository

    Quitterer, Felix

    2012-12-01

    The second step in the biosynthesis of the 22nd genetically encoded amino acid pyrrolysine (Pyl) is catalyzed by PylC that forms the pseudopeptide l-lysine-Nε-3R-methyl-d-ornithine. Here, we present six crystal structures of the monomeric active ligase in complex with substrates, reaction intermediates, and products including ATP, the non-hydrolyzable ATP analogue 5′-adenylyl-β-γ-imidodiphosphate, ADP, d-ornithine (d-Orn), l-lysine (Lys), phosphorylated d-Orn, l-lysine-Nε-d-ornithine, inorganic phosphate, carbonate, and Mg2 +. The overall structure of PylC reveals similarities to the superfamily of ATP-grasp enzymes; however, there exist unique structural and functional features for a topological control of successive substrate entry and product release. Furthermore, the presented high-resolution structures provide detailed insights into the reaction mechanism of isopeptide bond formation starting with phosphorylation of d-Orn by transfer of a phosphate moiety from activated ATP. The binding of Lys to the enzyme complex is then followed by an SN2 reaction resulting in l-lysine-Nε-d-ornithine and inorganic phosphate. Surprisingly, PylC harbors two adenine nucleotides bound at the active site, what has not been observed in any ATP-grasp protein analyzed to date. Whereas one ATP molecule is involved in catalysis, the second adenine nucleotide functions as a selective anchor for the C- and N-terminus of the Lys substrate and is responsible for protein stability as shown by mutagenesis. © 2012 Elsevier Ltd.

  11. Application of a genetically encoded biosensor for live cell imaging of L-valine production in pyruvate dehydrogenase complex-deficient Corynebacterium glutamicum strains.

    Science.gov (United States)

    Mustafi, Nurije; Grünberger, Alexander; Mahr, Regina; Helfrich, Stefan; Nöh, Katharina; Blombach, Bastian; Kohlheyer, Dietrich; Frunzke, Julia

    2014-01-01

    The majority of biotechnologically relevant metabolites do not impart a conspicuous phenotype to the producing cell. Consequently, the analysis of microbial metabolite production is still dominated by bulk techniques, which may obscure significant variation at the single-cell level. In this study, we have applied the recently developed Lrp-biosensor for monitoring of amino acid production in single cells of gradually engineered L-valine producing Corynebacterium glutamicum strains based on the pyruvate dehydrogenase complex-deficient (PDHC) strain C. glutamicum ΔaceE. Online monitoring of the sensor output (eYFP fluorescence) during batch cultivation proved the sensor's suitability for visualizing different production levels. In the following, we conducted live cell imaging studies on C. glutamicum sensor strains using microfluidic chip devices. As expected, the sensor output was higher in microcolonies of high-yield producers in comparison to the basic strain C. glutamicum ΔaceE. Microfluidic cultivation in minimal medium revealed a typical Gaussian distribution of single cell fluorescence during the production phase. Remarkably, low amounts of complex nutrients completely changed the observed phenotypic pattern of all strains, resulting in a phenotypic split of the population. Whereas some cells stopped growing and initiated L-valine production, others continued to grow or showed a delayed transition to production. Depending on the cultivation conditions, a considerable fraction of non-fluorescent cells was observed, suggesting a loss of metabolic activity. These studies demonstrate that genetically encoded biosensors are a valuable tool for monitoring single cell productivity and to study the phenotypic pattern of microbial production strains.

  12. Mapping the subcellular distribution of α-synuclein in neurons using genetically encoded probes for correlated light and electron microscopy: implications for Parkinson's disease pathogenesis.

    Science.gov (United States)

    Boassa, Daniela; Berlanga, Monica L; Yang, Mary Ann; Terada, Masako; Hu, Junru; Bushong, Eric A; Hwang, Minju; Masliah, Eliezer; George, Julia M; Ellisman, Mark H

    2013-02-06

    Modifications to the gene encoding human α-synuclein have been linked to the development of Parkinson's disease. The highly conserved structure of α-synuclein suggests a functional interaction with membranes, and several lines of evidence point to a role in vesicle-related processes within nerve terminals. Using recombinant fusions of human α-synuclein, including new genetic tags developed for correlated light microscopy and electron microscopy (the tetracysteine-biarsenical labeling system or the new fluorescent protein for electron microscopy, MiniSOG), we determined the distribution of α-synuclein when overexpressed in primary neurons at supramolecular and cellular scales in three dimensions (3D). We observed specific association of α-synuclein with a large and otherwise poorly characterized membranous organelle system of the presynaptic terminal, as well as with smaller vesicular structures within these boutons. Furthermore, α-synuclein was localized to multiple elements of the protein degradation pathway, including multivesicular bodies in the axons and lysosomes within neuronal cell bodies. Examination of synapses in brains of transgenic mice overexpressing human α-synuclein revealed alterations of the presynaptic endomembrane systems similar to our findings in cell culture. Three-dimensional electron tomographic analysis of enlarged presynaptic terminals in several brain areas revealed that these terminals were filled with membrane-bounded organelles, including tubulovesicular structures similar to what we observed in vitro. We propose that α-synuclein overexpression is associated with hypertrophy of membrane systems of the presynaptic terminal previously shown to have a role in vesicle recycling. Our data support the conclusion that α-synuclein is involved in processes associated with the sorting, channeling, packaging, and transport of synaptic material destined for degradation.

  13. Mapping the subcellular distribution of alpha-synuclein in neurons using genetically encoded probes for correlated light and electron microscopy: Implications for Parkinson’s disease pathogenesis

    Science.gov (United States)

    Boassa, D.; Berlanga, M.L.; Yang, M.-L.; Terada, M.; Hu, J.; Bushong, E.A.; Hwang, M.; Masliah, E.; George, J.M.; Ellisman, M.H.

    2013-01-01

    Modifications to the gene encoding human alpha-synuclein have been linked to development of Parkinson’s disease. The highly conserved structure of alpha-synuclein suggests a functional interaction with membranes, and several lines of evidence point to a role in vesicle-related processes within nerve terminals. Using recombinant fusions of human alpha-synuclein including new genetic tags developed for correlated LM and EM (the tetracysteine-biarsenical labeling system or the new fluorescent protein for EM, MiniSOG), we determined the distribution of alpha-synuclein when over-expressed in primary neurons at supramolecular and cellular scales, in three dimensions (3D). We observed specific association of alpha-synuclein with a large and otherwise poorly characterized membranous organelle system of the presynaptic terminal, as well as with smaller vesicular structures within these boutons. Furthermore, alpha-synuclein was localized to multiple elements of the protein degradation pathway, including multivesicular bodies in the axons and lysosomes within neuronal cell bodies. Examination of synapses in brains of transgenic mice over-expressing human alpha-synuclein revealed alterations of the presynaptic endomembrane systems similar to our findings in cell culture. 3D electron tomographic analysis of enlarged presynaptic terminals in several brain areas revealed that these terminals were filled with membrane-bounded organelles, including tubulo-vesicular structures similar to what observed in vitro. We propose that alpha-synuclein over-expression is associated with hypertrophy of membrane systems of the presynaptic terminal previously shown to have a role in vesicle recycling. Our data support the conclusion that alpha- synuclein is involved in processes associated with the sorting, channeling, packaging and transport of synaptic material destined for degradation. PMID:23392688

  14. Structural analysis of the PSD-95 cluster by electron tomography and CEMOVIS: a proposal for the application of the genetically encoded metallothionein tag.

    Science.gov (United States)

    Hirabayashi, Ai; Fukunaga, Yuko; Miyazawa, Atsuo

    2014-06-01

    Postsynaptic density-95 (PSD-95) accumulates at excitatory postsynapses and plays important roles in the clustering and anchoring of numerous proteins at the PSD. However, a detailed ultrastructural analysis of clusters exclusively consisting of PSD-95 has never been performed. Here, we employed a genetically encoded tag, three tandem repeats of metallothionein (3MT), to study the structure of PSD-95 clusters in cells by electron tomography and cryo-electron microscopy of vitreous sections. We also performed conventional transmission electron microscopy (TEM). Cultured hippocampal neurons expressing a fusion protein of PSD-95 coupled to 3MT (PDS-95-3MT) were incubated with CdCl2 to result in the formation of Cd-bound PSD-95-3MT. Two types of electron-dense deposits composed of Cd-bound PSD-95-3MT were observed in these cells by TEM, as reported previously. Electron tomography revealed the presence of membrane-shaped structures representing PSD-95 clusters at the PSD and an ellipsoidal structure located in the non-synaptic cytoplasm. By TEM, the PSD-95 clusters appeared to be composed of a number of dense cores. In frozen hydrated sections, these dense cores were also found beneath the postsynaptic membrane. Taken together, our findings suggest that dense cores of PSD-95 aggregate to form the larger clusters present in the PSD and the non-synaptic cytoplasm. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  16. Distribution of FcγR gene polymorphisms among two sympatric populations in Mali: differing allele frequencies, associations with malariometric indices and implications for genetic susceptibility to malaria.

    Science.gov (United States)

    Cherif, Mariama; Amoako-Sakyi, Daniel; Dolo, Amagana; Pearson, Jan-Olov; Gyan, Ben; Obiri-Yeboah, Dorcas; Nebie, Issa; Sirima, Sodiomon B; Doumbo, Ogobara; Troye-Blomberg, Marita; Bakary, Maiga

    2016-01-19

    Genetic polymorphisms in the complex gene cluster encoding human Fc-gamma receptors (FcγRs) may influence malaria susceptibility and pathogenesis. Studying genetic susceptibility to malaria is ideal among sympatric populations because the distribution of polymorphic genes among such populations can help in the identification malaria candidate genes. This study determined the distribution of three FcyRs single nucleotide polymorphisms (SNPs) (FcγRIIB-rs1050519, FcγRIIC-rs3933769 and FcγRIIIA-rs396991) among sympatric Fulani and Dogon children with uncomplicated malaria. The association of these SNPs with clinical, malariometric and immunological indices was also tested. This study involved 242 Fulani and Dogon volunteers from Mali age under 15 years. All SNPs were genotyped with predesigned TaqMan(®) SNP Genotyping Assays. Genotypic and allelic distribution of SNPs was compared across ethnic groups using the Fisher exact test. Variations in clinical, malariometric and immunologic indices between groups were tested with Kruskal-Wallis H, Mann-Whitney U test and Fisher exact test where appropriate. The study confirmed known malariometric and immunologic differences between sympatric Fulani and non-Fulani tribes. Parasite density was lower in the Fulani than the Dogon (p Dogon (p Dogon (p = 0.0043). The difference in the mutant allele frequency of FcγRIIB (rs1050519) between the two ethnic groups was however not statistically significant (p = 0.064). The mutant allele of rs396991 was associated with high malaria-specific IgG1 and IgG3 in the entire study population and Dogon tribe, p = 0.023 and 0.015, respectively. Parasite burden was lower in carriers of the FcγRIIC (rs3933769) mutant allele than non-carriers in the entire study population (p Dogon indirectly suggest that these SNPs may influence malaria susceptibility and pathogenesis in the study population. The high frequency of the FcγRIIC (rs3933769) mutant allele in the Fulani and its

  17. Partial Correction of Psoriasis upon Genetic Knock-Down of Human TNF-α by Lentivirus-Encoded shRNAs in a Xenograft Mouse Model

    DEFF Research Database (Denmark)

    Jakobsen, Maria; Stenderup, Karin; Rosada, Cecilia

    with lentiviral vectors encoding an irrelevant shRNA. In conclusion, our results demonstrate that lentiviral vector-encoded TNF- shRNAs have the potential to down-regulate TNF- production both in vitro and in vivo. Phenotypic changes in shRNA-treated psoriatic skin suggest that TNF- -encoding RNA is a valid......The proinflammatory cytokine Tumor Necrosis Factor alpha (TNF- ) is upregulated in inflammatory psoriatic skin. The increased level of TNF- protein is thought to cause keratinocyte hyperproliferation, leukocyte infiltration as well as growth and dilation of superficial blood vessels, which are all...... characteristics of human psoriasis skin. Blockade of TNF- function with specific inhibitors at the protein level has resulted in a rapid clinical improvement in psoriasis patients, demonstrating that TNF- inhibition offers a promising therapy of psoriasis. Whether TNF- -encoding RNA is a valid therapeutic target...

  18. An ecologically-based method for selecting ecological indicators for assessing risks to biological diversity from genetically-engineered plants

    DEFF Research Database (Denmark)

    Andow, D. A.; Lövei, Gabor L; Arpaia, Salvatore

    2013-01-01

    into ecological functional groups and selecting those that deliver the identified environmental values. (3) All of the species or ecosystem processes related to the selected functional groups are identified and (4) multi-criteria decision analysis (MCDA) is used to rank the indicator endpoint entities, which may......-driven, ecologically-based decision-making and provides formal methods for completing a screening level-ERA that can focus ERA on the most significant concerns. The process requires substantial human input but the human capital is available in most countries and regions of the world.......The environmental risks associated with genetically-engineered (GE) organisms have been controversial, and so have the models for the assessment of these risks. We propose an ecologically-based environmental risk assessment (ERA) model that follows the 1998 USEPA guidelines, focusing on potential...

  19. Novel Variants of Streptococcus thermophilus Bacteriophages Are Indicative of Genetic Recombination among Phages from Different Bacterial Species

    Science.gov (United States)

    Szymczak, Paula; Neves, Ana Rute; Kot, Witold; Hansen, Lars H.; Lametsch, René; Neve, Horst; Franz, Charles M. A. P.

    2016-01-01

    ABSTRACT Bacteriophages are the main cause of fermentation failures in dairy plants. The majority of Streptococcus thermophilus phages can be divided into either cos- or pac-type phages and are additionally characterized by examining the V2 region of their antireceptors. We screened a large number of S. thermophilus phages from the Chr. Hansen A/S collection, using PCR specific for the cos- or pac-type phages, as well as for the V2 antireceptor region. Three phages did not produce positive results with the assays. Analysis of phage morphologies indicated that two of these phages, CHPC577 and CHPC926, had shorter tails than the traditional S. thermophilus phages. The third phage, CHPC1151, had a tail size similar to those of the cos- or pac-type phages, but it displayed a different baseplate structure. Sequencing analysis revealed the genetic similarity of CHPC577 and CHPC926 with a subgroup of Lactococcus lactis P335 phages. Phage CHPC1151 was closely related to the atypical S. thermophilus phage 5093, homologous with a nondairy streptococcal prophage. By testing adsorption of the related streptococcal and lactococcal phages to the surface of S. thermophilus and L. lactis strains, we revealed the possibility of cross-interactions. Our data indicated that the use of S. thermophilus together with L. lactis, extensively applied for dairy fermentations, triggered the recombination between phages infecting different bacterial species. A notable diversity among S. thermophilus phage populations requires that a new classification of the group be proposed. IMPORTANCE Streptococcus thermophilus is a component of thermophilic starter cultures commonly used for cheese and yogurt production. Characterizing streptococcal phages, understanding their genetic relationships, and studying their interactions with various hosts are the necessary steps for preventing and controlling phage attacks that occur during dairy fermentations. PMID:28039135

  20. [Indications for genetic amniocentesis investigated at the Department of Gynecology, Obstetrics, and Oncologic Gynecology, Nicolaus Copernicus University, Collegium Medicum, Bydgoszcz].

    Science.gov (United States)

    Sadłecki, Paweł; Walentowicz-Sadłecka, Małgorzata; Pasińska, Magdalena; Adamczak, Rafał; Grabiec, Marek

    2014-06-01

    Genetic amniocentesis (GA) is the most common prenatal diagnostic test. One of the main indications for GA is maternal age of > or = 35 years. In many countries, the age indication has been replaced by an assessment of individual risk for chromosomal abnormalities, calculated on the basis of maternal age, pregnancy duration, as well as a combination of biochemical and ultrasound markers. The aim of the study was to investigate indications for and results of GA performed between 2010-2012 at the Department of Gynecology Obstetrics, and Oncologic Gynecology Nicolaus Copernicus University Collegium Medicum, Bydgoszcz. A total of 632 GA tests were performed at the Department of Gynecology Obstetrics, and Oncologic Gynecology Nicolaus Copernicus University Collegium Medicum, Bydgoszcz. Average maternal age was 34 (between 17 and 47 years), with patients or = 35 constituting 52.1% (N = 329) of the investigated group. Indications for GA as well as test results were analyzed in relation to maternal age. The result of earlier non-invasive tests were also analyzed. Abnormal ultrasound findings, combined with abnormal first-trimester screening results, were the most common indication (46.53%) for GA in patients or = 35 years. Mean time of GA was 16 gestational weeks in both groups. Abnormal karyotype was detected in 74 (11.7%) cases. 13 or any other abnormal karyotypes occurrence were observed in both age groups. GA-related complications (miscarriage/intrauterine fetal death) occurred in 9 (1.42%) cases. If performed properly GA between 15 and 20 weeks of pregnancy is a harmless procedure both, for the mother and the fetus, associated with an acceptable complication rate. Prenatal screening for the most common malformations and chromosomal aberrations should be offered to all pregnant women in Poland, regardless of their age.

  1. Sensing Cardiac Electrical Activity With a Cardiac Myocyte--Targeted Optogenetic Voltage Indicator

    NARCIS (Netherlands)

    Chang Liao, Mei-Ling; de Boer, Teun P; Mutoh, Hiroki; Raad, Nour; Richter, Claudia; Wagner, Eva; Downie, Bryan R; Unsöld, Bernhard; Arooj, Iqra; Streckfuss-Bömeke, Katrin; Döker, Stephan; Luther, Stefan; Guan, Kaomei; Wagner, Stefan; Lehnart, Stephan E; Maier, Lars S; Stühmer, Walter; Wettwer, Erich; van Veen, Toon; Morlock, Michael M; Knöpfel, Thomas; Zimmermann, Wolfram-Hubertus

    2015-01-01

    RATIONALE: Monitoring and controlling cardiac myocyte activity with optogenetic tools offer exciting possibilities for fundamental and translational cardiovascular research. Genetically encoded voltage indicators may be particularly attractive for minimal invasive and repeated assessments of cardiac

  2. Genetic and biochemical analyses of chromosome and plasmid gene homologues encoding ICL and ArCP domains in Vibrio anguillarum strain 775.

    Science.gov (United States)

    Di Lorenzo, Manuela; Stork, Michiel; Crosa, Jorge H

    2011-08-01

    Anguibactin, the siderophore produced by Vibrio anguillarum 775 is synthesized from 2,3-dihydroxybenzoic acid (DHBA), cysteine and hydroxyhistamine via a nonribosomal peptide synthetase (NRPS) mechanism. Most of the genes encoding anguibactin biosynthetic proteins are harbored by the pJM1 plasmid. In this work we report the identification of a homologue of the plasmid-encoded angB on the chromosome of strain 775. The product of both genes harbor an isochorismate lyase (ICL) domain that converts isochorismic acid to 2,3-dihydro-2,3-dihydroxybenzoic acid, one of the steps of DHBA synthesis. We show in this work that both ICL domains are functional in the production of DHBA in V. anguillarum as well as in E. coli. Substitution by alanine of the aspartic acid residue in the active site of both ICL domains completely abolishes their isochorismate lyase activity in vivo. The two proteins also carry an aryl carrier protein (ArCP) domain. In contrast with the ICL domains only the plasmid encoded ArCP can participate in anguibactin production as determined by complementation analyses and site-directed mutagenesis in the active site of the plasmid encoded protein, S248A. The site-directed mutants, D37A in the ICL domain and S248A in the ArCP domain of the plasmid encoded AngB were also tested in vitro and clearly show the importance of each residue for the domain function and that each domain operates independently.

  3. Monitoring cytosolic and ER Zn2+ in stimulated breast cancer cells using genetically encoded FRET sensors† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5mt00257e Click here for additional data file.

    Science.gov (United States)

    Hessels, Anne M.; Taylor, Kathryn M.

    2016-01-01

    The Zn2+-specific ion channel ZIP7 has been implicated to play an important role in releasing Zn2+ from the ER. External stimulation of breast cancer cells has been proposed to induce phosphorylation of ZIP7 by CK2α, resulting in ZIP7-mediated Zn2+ release from the ER into the cytosol. Here, we examined whether changes in cytosolic and ER Zn2+ concentrations can be detected upon such external stimuli. Two previously developed FRET sensors for Zn2+, eZinCh-2 (K d = 1 nM at pH 7.1) and eCALWY-4 (K d = 0.63 nM at pH 7.1), were expressed in both the cytosol and the ER of wild-type MCF-7 and TamR cells. Treatment of MCF-7 and TamR cells with external Zn2+ and pyrithione, one of the previously used triggers, resulted in an immediate increase in free Zn2+ in both cytosol and ER, suggesting that Zn2+ was directly transferred across the cellular membranes by pyrithione. Cells treated with a second trigger, EGF/ionomycin, showed no changes in intracellular Zn2+ levels, neither in multicolor imaging experiments that allowed simultaneous imaging of cytosolic and ER Zn2+, nor in experiments in which cytosolic and ER Zn2+ were monitored separately. In contrast to previous work using small-molecule fluorescent dyes, these results indicate that EGF–ionomycin treatment does not result in significant changes in cytosolic Zn2+ levels as a result from Zn2+ release from the ER. These results underline the importance of using genetically encoded fluorescent sensors to complement and verify intracellular imaging experiments with synthetic fluorescent Zn2+ dyes. PMID:26739447

  4. Genetically encoded synthesis of protein-based polymers with precisely specified molecular weight and sequence by recursive directional ligation: examples from the elastin-like polypeptide system.

    Science.gov (United States)

    Meyer, Dan E; Chilkoti, Ashutosh

    2002-01-01

    We report a new strategy for the synthesis of genes encoding repetitive, protein-based polymers of specified sequence, chain length, and architecture. In this stepwise approach, which we term "recursive directional ligation" (RDL), short gene segments are seamlessly combined in tandem using recombinant DNA techniques. The resulting larger genes can then be recursively combined until a gene of a desired length is obtained. This approach is modular and can be used to combine genes encoding different polypeptide sequences. We used this method to synthesize three different libraries of elastin-like polypeptides (ELPs); each library encodes a unique ELP sequence with systematically varied molecular weights. We also combined two of these sequences to produce a block copolymer. Because the thermal properties of ELPs depend on their sequence and chain length, the synthesis of these polypeptides provides an example of the importance of precise control over these parameters that is afforded by RDL.

  5. Genetic architecture of a reinforced, postmating, reproductive isolation barrier between Neurospora species indicates evolution via natural selection.

    Directory of Open Access Journals (Sweden)

    Elizabeth Turner

    2011-08-01

    Full Text Available A role for natural selection in reinforcing premating barriers is recognized, but selection for reinforcement of postmating barriers remains controversial. Organisms lacking evolvable premating barriers can theoretically reinforce postmating isolation, but only under restrictive conditions: parental investment in hybrid progeny must inhibit subsequent reproduction, and selected postmating barriers must restore parents' capacity to reproduce successfully. We show that reinforced postmating isolation markedly increases maternal fitness in the fungus Neurospora crassa, and we detect the evolutionary genetic signature of natural selection by quantitative trait locus (QTL analysis of the reinforced barrier. Hybrid progeny of N. crassa and N. intermedia are highly inviable. Fertilization by local N. intermedia results in early abortion of hybrid fruitbodies, and we show that abortion is adaptive because only aborted maternal colonies remain fully receptive to future reproduction. In the first QTL analysis of postmating reinforcement in microbial eukaryotes, we identify 11 loci for abortive hybrid fruitbody development, including three major QTLs that together explain 30% of trait variance. One of the major QTLs and six QTLs of lesser effect are found on the mating-type determining chromosome of Neurospora. Several reinforcement QTLs are flanked by genetic markers showing either segregation distortion or non-random associations with alleles at other loci in a cross between N. crassa of different clades, suggesting that the loci also are associated with local effects on same-species reproduction. Statistical analysis of the allelic effects distribution for abortive hybrid fruitbody development indicates its evolution occurred under positive selection. Our results strongly support a role for natural selection in the evolution of reinforced postmating isolation in N. crassa.

  6. Partial Correction of Psoriasis upon Genetic Knock-Down of Human TNF-α by Lentivirus-Encoded shRNAs in a Xenograft Mouse Model

    DEFF Research Database (Denmark)

    Jakobsen, Maria; Stenderup, Karin; Rosada, Cecilia

    reduced the amount of released TNF- more than 50% upon viral transduction, was selected for in vivo studies. In vivo studies were carried out in a xenograft mouse model in which human psoriatic plaques keratome skin biopsies were transplanted onto SCID mice. Initial studies using eGFP-encoding lentiviral...... vectors demonstrated efficient transduction of human psoriatic skin. Grafted psoriatic skin was exposed to viral vector-encoded TNF- shRNAs by a single intradermal injection of purified VSV-G-pseudotyped lentiviral vectors (150 l containing 46.4 ng p24/ l was injected at a single site). Biopsies were...

  7. Genetic and biochemical analyses of chromosome and plasmid gene homologues encoding ICL and ArCP domains in Vibrioanguillarum strain 775

    NARCIS (Netherlands)

    Di Lorenzo, M.; Stork, M.; Crosa, J.H.

    2011-01-01

    Anguibactin, the siderophore produced by Vibrio anguillarum 775 is synthesized from 2,3-dihydroxybenzoic acid (DHBA), cysteine and hydroxyhistamine via a nonribosomal peptide synthetase (NRPS) mechanism. Most of the genes encoding anguibactin biosynthetic proteins are harbored by the pJM1 plasmid. I

  8. Generation of Interleukin-2 Receptor Gamma Gene Knockout Pigs from Somatic Cells Genetically Modified by Zinc Finger Nuclease-Encoding mRNA

    Science.gov (United States)

    Watanabe, Masahito; Nakano, Kazuaki; Matsunari, Hitomi; Matsuda, Taisuke; Maehara, Miki; Kanai, Takahiro; Kobayashi, Mirina; Matsumura, Yukina; Sakai, Rieko; Kuramoto, Momoko; Hayashida, Gota; Asano, Yoshinori; Takayanagi, Shuko; Arai, Yoshikazu; Umeyama, Kazuhiro; Nagaya, Masaki; Hanazono, Yutaka; Nagashima, Hiroshi

    2013-01-01

    Zinc finger nuclease (ZFN) is a powerful tool for genome editing. ZFN-encoding plasmid DNA expression systems have been recently employed for the generation of gene knockout (KO) pigs, although one major limitation of this technology is the use of potentially harmful genome-integrating plasmid DNAs. Here we describe a simple, non-integrating strategy for generating KO pigs using ZFN-encoding mRNA. The interleukin-2 receptor gamma (IL2RG) gene was knocked out in porcine fetal fibroblasts using ZFN-encoding mRNAs, and IL2RG KO pigs were subsequently generated using these KO cells through somatic cell nuclear transfer (SCNT). The resulting IL2RG KO pigs completely lacked a thymus and were deficient in T and NK cells, similar to human X-linked SCID patients. Our findings demonstrate that the combination of ZFN-encoding mRNAs and SCNT provides a simple robust method for producing KO pigs without genomic integration. PMID:24130776

  9. Computational Intelligence and Its Encoding Mechanism

    Institute of Scientific and Technical Information of China (English)

    LIU Man-dan

    2004-01-01

    The origin and characteristics of computational intelligence, and several typical computational intelligence algorithms such as genetic algorithm and DNA computing are described, and the influence of evolution strategies and convergence properties on the encoding mechanism is discussed. A novel genetic algorithm based on degressive carry number encoding is then proposed. This algorithm uses degressive carry number encoding in the evolutionary process instead of commonly used fixed carry number. Finally a novel encoding mechanism and a new algorithm are proposed, which combine modern computational intelligence with the traditional Chinese methodology.

  10. Computational Intelligence and Its Encoding Mechanism

    Institute of Scientific and Technical Information of China (English)

    LIUMan-dan

    2004-01-01

    The origin and characteristics of computational intelligence, and several typical computational intelligence algorithms such as genetic algorithm and DNA computing are described, and the influence of evolution strategies and convergence properties on the encoding mechanism is discussed. A novel genetic algorithm based on degressive carry number encoding is then proposed. This algorithm uses degressive carry number encoding in the evolutionary process instead of commonly used fixed carry number. Finally a novel encoding mechanism and a new algorithm are proposed, which combine modem computational intelligence with the traditional Chinese methodology.

  11. Population genetic analysis of Bromus tectorum (Poaceae) indicates recent range expansion may be facilitated by specialist genotypes

    Science.gov (United States)

    Keith R. Merrill; Susan E. Meyer; Craig E. Coleman

    2012-01-01

    The mechanisms for range expansion in invasive species depend on how genetic variation is structured in the introduced range. This study examined neutral genetic variation in the invasive annual grass Bromus tectorum in the Intermountain Western United States. Patterns of microsatellite (SSR) genotype distribution in this highly inbreeding species were used to make...

  12. Distribution, Functional Expression, and Genetic Organization of Cif, a Phage-Encoded Type III-Secreted Effector from Enteropathogenic and Enterohemorrhagic Escherichia coli▿

    Science.gov (United States)

    Loukiadis, Estelle; Nobe, Rika; Herold, Sylvia; Tramuta, Clara; Ogura, Yoshitoshi; Ooka, Tadasuke; Morabito, Stefano; Kérourédan, Monique; Brugère, Hubert; Schmidt, Herbert; Hayashi, Tetsuya; Oswald, Eric

    2008-01-01

    Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) inject effector proteins into host cells via a type III secretion system encoded by the locus of enterocyte effacement (LEE). One of these effectors is Cif, encoded outside the LEE by a lambdoid prophage. In this study, we demonstrated that the Cif-encoding prophage of EPEC strain E22 is inducible and produces infectious phage particles. We investigated the distribution and functional expression of Cif in 5,049 E. coli strains of human, animal, and environmental origins. A total of 115 E. coli isolates from diverse origins and geographic locations carried cif. The presence of cif was tightly associated with the LEE, since all the cif-positive isolates were positive for the LEE. These results suggested that the Cif-encoding prophages have been widely disseminated within the natural population of E. coli but positively selected within the population of LEE-positive strains. Nonetheless, 66% of cif-positive E. coli strains did not induce a typical Cif-related phenotype in eukaryotic cells due to frameshift mutations or insertion of an IS element in the cif gene. The passenger region of the prophages carrying cif was highly variable and showed various combinations of IS elements and genes coding for other effectors such as nleB, nleC, nleH, nleG, espJ, and nleA/espI (some of which were also truncated). This diversity and the presence of nonfunctional effectors should be taken into account to assess EPEC and EHEC pathogenicity and tropism. PMID:17873042

  13. Distribution, functional expression, and genetic organization of Cif, a phage-encoded type III-secreted effector from enteropathogenic and enterohemorrhagic Escherichia coli.

    Science.gov (United States)

    Loukiadis, Estelle; Nobe, Rika; Herold, Sylvia; Tramuta, Clara; Ogura, Yoshitoshi; Ooka, Tadasuke; Morabito, Stefano; Kérourédan, Monique; Brugère, Hubert; Schmidt, Herbert; Hayashi, Tetsuya; Oswald, Eric

    2008-01-01

    Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) inject effector proteins into host cells via a type III secretion system encoded by the locus of enterocyte effacement (LEE). One of these effectors is Cif, encoded outside the LEE by a lambdoid prophage. In this study, we demonstrated that the Cif-encoding prophage of EPEC strain E22 is inducible and produces infectious phage particles. We investigated the distribution and functional expression of Cif in 5,049 E. coli strains of human, animal, and environmental origins. A total of 115 E. coli isolates from diverse origins and geographic locations carried cif. The presence of cif was tightly associated with the LEE, since all the cif-positive isolates were positive for the LEE. These results suggested that the Cif-encoding prophages have been widely disseminated within the natural population of E. coli but positively selected within the population of LEE-positive strains. Nonetheless, 66% of cif-positive E. coli strains did not induce a typical Cif-related phenotype in eukaryotic cells due to frameshift mutations or insertion of an IS element in the cif gene. The passenger region of the prophages carrying cif was highly variable and showed various combinations of IS elements and genes coding for other effectors such as nleB, nleC, nleH, nleG, espJ, and nleA/espI (some of which were also truncated). This diversity and the presence of nonfunctional effectors should be taken into account to assess EPEC and EHEC pathogenicity and tropism.

  14. Heat transfer analysis of unsteady graphene oxide nanofluid flow using a fuzzy identifier evolved by genetically encoded mutable smart bee algorithm

    Directory of Open Access Journals (Sweden)

    Mohammadreza Azimi

    2015-03-01

    Full Text Available In the current research, the unsteady two dimensional Graphene Oxide water based nanofluid heat transfer between two moving parallel plates is analyzed using an intelligent black-box identifier. The developed intelligent tool is known as evolvable evolutionary fuzzy inference system (EE-FIS which is based on the integration of low-level fuzzy programming and hyper-level evolutionary computing concepts. Here, the authors propose the use of a modified evolutionary algorithm (EA which is called hybrid genetic mutable smart bee algorithm (HGMSBA. The proposed HGMSBA is used to evolve both antecedent and consequent parts of fuzzy rule base. Besides, it tries to prune the rule base of fuzzy inference system (FIS to decrease its computational complexity and increase its interpretability. By considering the prediction error of the fuzzy identifier as the objective function of HGMSBA, an automatic soft interpolation machine is developed which can intuitively increase the robustness and accuracy of the final model. Here, HGMSBA-FIS is used to provide a nonlinear map between inputs, i.e. nanoparticles solid volume fraction (ϕ, Eckert number (Ec and a moving parameter which describes the movements of plates (S, and output, i.e. Nusselt number (Nu. Prior to proceeding with the modeling process, a comprehensive numerical comparative study is performed to investigate the potentials of the proposed model for nonlinear system identification. After demonstrating the efficacy of HGMSBA for training the FIS, the system is applied to the considered problem. Based on the obtained results, it can be inferred that the developed HGMSBA-FIS black-box identifier can be used as a very authentic tool with respect to accuracy and robustness. Besides, as the proposed black-box is not a physics-based identifier, it frees experts from the cumbersome mathematical formulations, and can be used for advanced real-time applications such as model-based control. The simulations

  15. Reduced hippocampal activation during episodic encoding in middle-aged individuals at genetic risk of Alzheimer's Disease: a cross-sectional study

    Directory of Open Access Journals (Sweden)

    Torgerson Britta M

    2006-01-01

    Full Text Available Abstract Background The presence of the apolipoprotein E (APOE ε4 allele is a major risk factor for the development of Alzheimer's disease (AD, and has been associated with metabolic brain changes several years before the onset of typical AD symptoms. Functional MRI (fMRI is a brain imaging technique that has been used to demonstrate hippocampal activation during measurement of episodic encoding, but the effect of the ε4 allele on hippocampal activation has not been firmly established. Methods The present study examined the effects of APOE genotype on brain activation patterns in the medial temporal lobe (MTL during an episodic encoding task using a well-characterized novel item versus familiar item contrast in cognitively normal, middle-aged (mean = 54 years individuals who had at least one parent with AD. Results We found that ε3/4 heterozygotes displayed reduced activation in the hippocampus and MTL compared to ε3/3 homozygotes. There were no significant differences between the groups in age, education or neuropsychological functioning, suggesting that the altered brain activation seen in ε3/4 heterozygotes was not associated with impaired cognitive function. We also found that participants' ability to encode information on a neuropsychological measure of learning was associated with greater activation in the anterior MTL in the ε3/3 homozygotes, but not in the ε3/4 heterozygotes. Conclusion Together with previous studies reporting reduced glucose metabolism and AD-related neuropathology, this study provides convergent validity for the idea that the MTL exhibits functional decline associated with the APOE ε4 allele. Importantly, these changes were detected in the absence of meaningful neuropsychological differences between the groups. A focus of ongoing work in this laboratory is to determine if these findings are predictive of subsequent cognitive decline.

  16. The Association between Genetic Variations of CHI3L1, Levels of the Encoded Glycoprotein YKL-40 and the Lipid Profile in a Danish Population

    DEFF Research Database (Denmark)

    Thomsen, Stine Brinkløv; Rathcke, Camilla Noelle; Skaaby, Tea

    2012-01-01

    The inflammatory biomarker YKL-40 seems to play a role in atherosclerosis and is elevated in patients with obesity, cardiovascular disease and type 2 diabetes. Single nucleotide polymorphisms (SNPs) of the YKL-40 encoding gene, CHI3L1, are associated with inter-individual YKL-40 levels. One study...... of the differentiated lipid profile in a Danish general population....... has described an association between a promoter polymorphism of CHI3L1 and levels of low density lipoprotein. The objective of this study was to evaluate the influence of YKL-40 on lipid parameters by determining the association between polymorphisms of CHI3L1, serum YKL-40 and levels...

  17. Molecular analysis of the bacteriocin-encoding plasmid pDGL1 from Enterococcus durans and genetic characterization of the durancin locus

    Science.gov (United States)

    Enterococci constitute a significant component of lactic acid bacteria normally present in the intestinal microflora and include strains that produce bacteriocins. The genetic determinants for durancin GL in Enterococcus durans 41D were identified on the 8,347 bp plasmid pDGL1 by plasmid curing exp...

  18. Genetic and morphological analyses indicate that the Australian endemic scorpion Urodacus yaschenkoi (Scorpiones: Urodacidae) is a species complex

    Science.gov (United States)

    Luna-Ramirez, Karen; Miller, Adam D.

    2017-01-01

    Background Australian scorpions have received far less attention from researchers than their overseas counterparts. Here we provide the first insight into the molecular variation and evolutionary history of the endemic Australian scorpion Urodacus yaschenkoi. Also known as the inland robust scorpion, it is widely distributed throughout arid zones of the continent and is emerging as a model organism in biomedical research due to the chemical nature of its venom. Methods We employed Bayesian Inference (BI) methods for the phylogenetic reconstructions and divergence dating among lineages, using unique haplotype sequences from two mitochondrial loci (COXI, 16S) and one nuclear locus (28S). We also implemented two DNA taxonomy approaches (GMYC and PTP/dPTP) to evaluate the presence of cryptic species. Linear Discriminant Analysis was used to test whether the linear combination of 21 variables (ratios of morphological measurements) can predict individual’s membership to a putative species. Results Genetic and morphological data suggest that U. yaschenkoi is a species complex. High statistical support for the monophyly of several divergent lineages was found both at the mitochondrial loci and at a nuclear locus. The extent of mitochondrial divergence between these lineages exceeds estimates of interspecific divergence reported for other scorpion groups. The GMYC model and the PTP/bPTP approach identified major lineages and several sub-lineages as putative species. Ratios of several traits that approximate body shape had a strong predictive power (83–100%) in discriminating two major molecular lineages. A time-calibrated phylogeny dates the early divergence at the onset of continental-wide aridification in late Miocene and Pliocene, with finer-scale phylogeographic patterns emerging during the Pleistocene. This structuring dynamics is congruent with the diversification history of other fauna of the Australian arid zones. Discussion Our results indicate that the

  19. From phenotyping towards breeding strategies: using in vivo indicator traits and genetic markers to improve meat quality in an endangered pig breed.

    Science.gov (United States)

    Biermann, A D M; Yin, T; König von Borstel, U U; Rübesam, K; Kuhn, B; König, S

    2015-06-01

    In endangered and local pig breeds of small population sizes, production has to focus on alternative niche markets with an emphasis on specific product and meat quality traits to achieve economic competiveness. For designing breeding strategies on meat quality, an adequate performance testing scheme focussing on phenotyped selection candidates is required. For the endangered German pig breed 'Bunte Bentheimer' (BB), no breeding program has been designed until now, and no performance testing scheme has been implemented. For local breeds, mainly reared in small-scale production systems, a performance test based on in vivo indicator traits might be a promising alternative in order to increase genetic gain for meat quality traits. Hence, the main objective of this study was to design and evaluate breeding strategies for the improvement of meat quality within the BB breed using in vivo indicator traits and genetic markers. The in vivo indicator trait was backfat thickness measured by ultrasound (BFiv), and genetic markers were allele variants at the ryanodine receptor 1 (RYR1) locus. In total, 1116 records of production and meat quality traits were collected, including 613 in vivo ultrasound measurements and 713 carcass and meat quality records. Additionally, 700 pigs were genotyped at the RYR1 locus. Data were used (1) to estimate genetic (co)variance components for production and meat quality traits, (2) to estimate allele substitution effects at the RYR1 locus using a selective genotyping approach and (3) to evaluate breeding strategies on meat quality by combining results from quantitative-genetic and molecular-genetic approaches. Heritability for the production trait BFiv was 0.27, and 0.48 for backfat thickness measured on carcass. Estimated heritabilities for meat quality traits ranged from 0.14 for meat brightness to 0.78 for the intramuscular fat content (IMF). Genetic correlations between BFiv and IMF were higher than estimates based on carcass backfat

  20. Indicators of theory of mind in narrative production : a comparison between individuals with genetic syndromes and typically developing children

    NARCIS (Netherlands)

    Lorusso, M. L.; Galli, R.; Libera, L.; Gagliardi, C.; Borgatti, R.; Hollebrandse, B.

    2007-01-01

    It is a matter of debate whether the development of theory of mind (ToM) depends on linguistic development or is, rather, an expression of cognitive development. The study of genetic syndromes, which are characterized by intellectual impairment as well as by different linguistic profiles, may provid

  1. Indicators of theory of mind in narrative production : a comparison between individuals with genetic syndromes and typically developing children

    NARCIS (Netherlands)

    Lorusso, M. L.; Galli, R.; Libera, L.; Gagliardi, C.; Borgatti, R.; Hollebrandse, B.

    2007-01-01

    It is a matter of debate whether the development of theory of mind (ToM) depends on linguistic development or is, rather, an expression of cognitive development. The study of genetic syndromes, which are characterized by intellectual impairment as well as by different linguistic profiles, may provid

  2. Genetic analysis of metabolites in apple fruits indicates an mQTL hotspot for phenolic compounds on linkage group 16

    NARCIS (Netherlands)

    Khan, S.A.; Chibon, P.Y.F.R.P.; Vos, de R.C.H.; Schipper, B.A.; Walraven, A.E.J.; Beekwilder, M.J.; Dijk, van T.; Finkers, H.J.; Visser, R.G.F.; Weg, van de W.E.; Bovy, A.G.; Cestaro, A.; Velasco, R.; Jacobsen, E.; Schouten, H.J.

    2012-01-01

    Apple (Malus×domestica Borkh) is among the main sources of phenolic compounds in the human diet. The genetic basis of the quantitative variations of these potentially beneficial phenolic compounds was investigated. A segregating F(1) population was used to map metabolite quantitative trait loci (mQT

  3. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  4. Genetic Analysis Reveals a Hierarchy of Interactions between Polycystin-Encoding Genes and Genes Controlling Cilia Function during Left-Right Determination.

    Directory of Open Access Journals (Sweden)

    Daniel T Grimes

    2016-06-01

    Full Text Available During mammalian development, left-right (L-R asymmetry is established by a cilia-driven leftward fluid flow within a midline embryonic cavity called the node. This 'nodal flow' is detected by peripherally-located crown cells that each assemble a primary cilium which contain the putative Ca2+ channel PKD2. The interaction of flow and crown cell cilia promotes left side-specific expression of Nodal in the lateral plate mesoderm (LPM. Whilst the PKD2-interacting protein PKD1L1 has also been implicated in L-R patterning, the underlying mechanism by which flow is detected and the genetic relationship between Polycystin function and asymmetric gene expression remains unknown. Here, we characterize a Pkd1l1 mutant line in which Nodal is activated bilaterally, suggesting that PKD1L1 is not required for LPM Nodal pathway activation per se, but rather to restrict Nodal to the left side downstream of nodal flow. Epistasis analysis shows that Pkd1l1 acts as an upstream genetic repressor of Pkd2. This study therefore provides a genetic pathway for the early stages of L-R determination. Moreover, using a system in which cultured cells are supplied artificial flow, we demonstrate that PKD1L1 is sufficient to mediate a Ca2+ signaling response after flow stimulation. Finally, we show that an extracellular PKD domain within PKD1L1 is crucial for PKD1L1 function; as such, destabilizing the domain causes L-R defects in the mouse. Our demonstration that PKD1L1 protein can mediate a response to flow coheres with a mechanosensation model of flow sensation in which the force of fluid flow drives asymmetric gene expression in the embryo.

  5. Genetic Analysis Reveals a Hierarchy of Interactions between Polycystin-Encoding Genes and Genes Controlling Cilia Function during Left-Right Determination.

    Science.gov (United States)

    Grimes, Daniel T; Keynton, Jennifer L; Buenavista, Maria T; Jin, Xingjian; Patel, Saloni H; Kyosuke, Shinohara; Vibert, Jennifer; Williams, Debbie J; Hamada, Hiroshi; Hussain, Rohanah; Nauli, Surya M; Norris, Dominic P

    2016-06-01

    During mammalian development, left-right (L-R) asymmetry is established by a cilia-driven leftward fluid flow within a midline embryonic cavity called the node. This 'nodal flow' is detected by peripherally-located crown cells that each assemble a primary cilium which contain the putative Ca2+ channel PKD2. The interaction of flow and crown cell cilia promotes left side-specific expression of Nodal in the lateral plate mesoderm (LPM). Whilst the PKD2-interacting protein PKD1L1 has also been implicated in L-R patterning, the underlying mechanism by which flow is detected and the genetic relationship between Polycystin function and asymmetric gene expression remains unknown. Here, we characterize a Pkd1l1 mutant line in which Nodal is activated bilaterally, suggesting that PKD1L1 is not required for LPM Nodal pathway activation per se, but rather to restrict Nodal to the left side downstream of nodal flow. Epistasis analysis shows that Pkd1l1 acts as an upstream genetic repressor of Pkd2. This study therefore provides a genetic pathway for the early stages of L-R determination. Moreover, using a system in which cultured cells are supplied artificial flow, we demonstrate that PKD1L1 is sufficient to mediate a Ca2+ signaling response after flow stimulation. Finally, we show that an extracellular PKD domain within PKD1L1 is crucial for PKD1L1 function; as such, destabilizing the domain causes L-R defects in the mouse. Our demonstration that PKD1L1 protein can mediate a response to flow coheres with a mechanosensation model of flow sensation in which the force of fluid flow drives asymmetric gene expression in the embryo.

  6. A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2.

    Science.gov (United States)

    Hambly, E; Tétart, F; Desplats, C; Wilson, W H; Krisch, H M; Mann, N H

    2001-09-25

    Sequence analysis of a 10-kb region of the genome of the marine cyanomyovirus S-PM2 reveals a homology to coliphage T4 that extends as a contiguous block from gene (g)18 to g23. The order of the S-PM2 genes in this region is similar to that of T4, but there are insertions and deletions of small ORFs of unknown function. In T4, g18 codes for the tail sheath, g19, the tail tube, g20, the head portal protein, g21, the prohead core protein, g22, a scaffolding protein, and g23, the major capsid protein. Thus, the entire module that determines the structural components of the phage head and contractile tail is conserved between T4 and this cyanophage. The significant differences in the morphology of these phages must reflect the considerable divergence of the amino acid sequence of their homologous virion proteins, which uniformly exceeds 50%. We suggest that their enormous diversity in the sea could be a result of genetic shuffling between disparate phages mediated by such commonly shared modules. These conserved sequences could facilitate genetic exchange by providing partially homologous substrates for recombination between otherwise divergent phage genomes. Such a mechanism would thus expand the pool of phage genes accessible by recombination to all those phages that share common modules.

  7. Genetic and environmental influences on the continuous scales of the Myers-Briggs Type Indicator: an analysis based on twins reared apart.

    Science.gov (United States)

    Bouchard, T J; Hur, Y M

    1998-04-01

    The Myers-Briggs Type Indicator was administered to a sample of 61 monozygotic twins reared apart (MZA), 49 dizygotic twins reared apart (DZA), and 92 spouses, who participated in the Minnesota Study of Twins Reared Apart (MISTRA) from 1979 to 1995. Twins' scores on the continuous scales were subjected to behavior genetic model-fitting procedures. Extraversion-Introversion and Thinking-Feeling yielded heritabilities of about .60, consisting largely of nonadditive genetic variance. Sensing-Intuition and Judgment-Perception yielded heritabilities of about .40, consisting largely of additive genetic variance. Spouse correlations for three of the four scales were near zero and not statistically significant; one spouse correlation (Sensing-Intuition) was modestly positive and statistically significant.

  8. Two-photon scanning microscopy of in vivo sensory responses of cortical neurons genetically encoded with a fluorescent voltage sensor in rat

    Directory of Open Access Journals (Sweden)

    Kurt F Ahrens

    2012-03-01

    Full Text Available A fluorescent voltage sensor protein Flare was created from a Kv1.4 potassium channel with YFP situated to report voltage-induced conformational changes in vivo. The RNA virus Sindbis introduced Flare into neurons in the binocular visual crescent in rat. Injection sites were selected based on intrinsic optical imaging. Expression of Flare occurred in the cell bodies and dendritic processes. Neurons imaged in vivo using two-photon scanning microscopy typically revealed the soma best, discernable against the background labeling of the neuropil. Somatic fluorescence changes were correlated with flashed visual stimuli; however, averaging was essential to observe these changes. This study demonstrates that the genetic modification of single neurons to express a fluorescent voltage sensor can be used to assess neuronal activity in vivo.

  9. Two-photon scanning microscopy of in vivo sensory responses of cortical neurons genetically encoded with a fluorescent voltage sensor in rat

    Science.gov (United States)

    Ahrens, Kurt F.; Heider, Barbara; Lee, Hanson; Isacoff, Ehud Y.; Siegel, Ralph M.

    2012-01-01

    A fluorescent voltage sensor protein “Flare” was created from a Kv1.4 potassium channel with YFP situated to report voltage-induced conformational changes in vivo. The RNA virus Sindbis introduced Flare into neurons in the binocular region of visual cortex in rat. Injection sites were selected based on intrinsic optical imaging. Expression of Flare occurred in the cell bodies and dendritic processes. Neurons imaged in vivo using two-photon scanning microscopy typically revealed the soma best, discernable against the background labeling of the neuropil. Somatic fluorescence changes were correlated with flashed visual stimuli; however, averaging was essential to observe these changes. This study demonstrates that the genetic modification of single neurons to express a fluorescent voltage sensor can be used to assess neuronal activity in vivo. PMID:22461770

  10. A Preliminary Study of DBH (Encoding Dopamine Beta-Hydroxylase) Genetic Variation and Neural Correlates of Emotional and Motivational Processing in Individuals With and Without Pathological Gambling.

    Science.gov (United States)

    Yang, Bao-Zhu; Balodis, Iris M; Lacadie, Cheryl M; Xu, Jiansong; Potenza, Marc N

    2016-06-01

    Background and aims Corticostriatal-limbic neurocircuitry, emotional and motivational processing, dopaminergic and noradrenergic systems and genetic factors have all been implicated in pathological gambling (PG). However, allelic variants of genes influencing dopaminergic and noradrenergic neurotransmitters have not been investigated with respect to the neural correlates of emotional and motivational states in PG. Dopamine beta-hydroxylase (DBH) converts dopamine to norepinephrine; the T allele of a functional single-nucleotide polymorphism rs1611115 (C-1021T) in the DBH gene is associated with less DBH activity and has been linked to emotional processes and addiction. Here, we investigate the influence of rs1611115 on the neural correlates of emotional and motivational processing in PG and healthy comparison (HC) participants. Methods While undergoing functional magnetic resonance imaging, 18 PG and 25 HC participants, all European Americans, viewed gambling-, sad-, and cocaine-related videotapes. Analyses focused on brain activation differences related to DBH genotype (CC/T-carrier [i.e., CT and TT]) and condition (sad/gambling/cocaine). Results CC participants demonstrated greater recruitment of corticostriatal-limbic regions, relative to T-carriers. DBH variants were also associated with altered corticostriatal-limbic activations across the different videotape conditions, and this association appeared to be driven by greater activation in CC participants relative to T-carriers during the sad condition. CC relative to T-carrier subjects also reported greater subjective sadness to the sad videotapes. Conclusions Individual differences in genetic composition linked to aminergic function contribute significantly to emotional regulation across diagnostic groups and warrant further investigation in PG.

  11. Nucleotide sequence and molecular genetic analysis of the vaccinia virus HindIII N/M region encoding the genes responsible for resistance to alpha-amanitin.

    Science.gov (United States)

    Tamin, A; Villarreal, E C; Weinrich, S L; Hruby, D E

    1988-07-01

    The genomic location of the gene(s) which provides vaccinia virus (VV) alpha-amanitin-resistant mutants with a drug-resistant phenotype have been mapped to the HindIII N/M region of the genome by the use of marker rescue techniques [E. C. Villarreal and D. E. Hruby (1986) J. Virol. 57, 65-70]. Nucleotide sequencing of a 2356-bp HindIII-Sau3A fragment of the vaccinia virus genome encompassing this region reveals the presence of two complete leftward-reading open reading frames (ORFs, N2 and M1) and two incomplete ORFs (N1 and M2). By computer analysis the N2 and M1 ORFs would be predicted to encode soluble VV polypeptides with molecular weights of approximately 20 and 48 kDa, respectively. The N2 and M1 ORFs have extremely A-T-rich 5'-proximal sequences, consistent with previous data regarding the location and A-T-richness of viral early promoters. Likewise, the consensus signal believed to be involved in terminating VV early gene transcription, TTTTTNT, was evident at the 3'-boundary of both the N2 and M1 ORFs suggesting that these genes may be VV early genes. The in vivo transcriptional activity, orientation, and limits of these putative transcriptional units were investigated by Northern blot, nuclease S1, and primer extension analysis. Both N2- and M1-specific transcripts were detected in the cytoplasm of VV-infected cells, suggesting that these loci are bonafide viral genes. Time-course nuclease S1 experiments revealed that the N2 gene was transcribed exclusively prior to VV DNA replication. In contrast, the M1 gene was transcribed throughout infection, although different start sites were used at early versus late times postinfection. These results are discussed in relation to the drug-resistant phenotype and future experiments to identify the viral gene product responsible.

  12. Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR loci

    Directory of Open Access Journals (Sweden)

    Babiker Hiba MA

    2011-05-01

    Full Text Available Abstract Background There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region. Result We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia. Conclusion We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.

  13. HLA similarities indicate shared genetic risk in 21-hydroxylase autoantibody positive South African and United States Addison's disease.

    Science.gov (United States)

    Ross, I L; Babu, S; Armstrong, T; Zhang, L; Schatz, D; Pugliese, A; Eisenbarth, G; Baker Ii, P

    2014-10-01

    Genetic similarities between patients from the United States and South African (SA) Addison's Disease (AD) strengthen evidence for genetic association. SA-AD (n = 73), SA healthy controls (N = 78), and US-AD patients (N = 83) were genotyped for DQA1, DQB1, DRB1, and HLA-B alleles. Serum was tested for the quantity of 21OH-AA and IFNα-AA at the Barbara Davis Center. Although not as profound as in US-AD, in SA-AD 21OH-AA + subjects the predominantly associated risk haplotypes were DRB1*0301-DQB1*0201 (DR3), DRB1*04xx-DQB1*0302 (DR4), and the combined DR3/4 genotype. DQB1*0302 associated DRB1*04xx haplotypes conferred higher risk than those DRB1*04xx haplotypes associated with other DQB1 alleles. We found negative association in 21OH-AA + SA-AD for DQA1*0201-DQB1*0202 and DQA1*0101-DQB1*0501 vs SA controls, and positive association for DQA1*0401-DQB1*0402 vs US-AD. Apart from the class II DR3 haplotype, HLA-B8 did not have an independent effect; however together DR3 and HLA-B8 conferred the highest risk vs 21OH-AA negative SA-AD and SA-controls. HLA-B7 (often with DR4) conferred novel risk in 21OH-AA + SA-AD vs controls. This study represents the first comparison between South African and United States AD populations utilizing genotyping and serology performed at the same center. SA-AD and US-AD 21OH-AA + patients share common HLA risk haplotypes including DR4 (with HLA-B7) and DR3 (with HLA-B8), strengthening previously described HLA associations and implicating similar genetic etiology. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  14. Gardner's syndrome: Genetic testing and colonoscopy are indicated in adolescents and young adults with cranial osteomas: A case report

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    We present a case of a 25-year-old female with diagnosed familial adenomatous polyposis and elevated carcinoembryonic antigen with negative family history.The suspicion of Gardner's syndrome was raised because extirpation of an osteoma of the left temporo-occipital region was made 10 years ago. Restorative proctocolectomy and ileal pouch anal anastomosis was made but histology delineated adenocarcinoma of the rectum (Dukes C stage). We conclude that cranial osteomas often precede gastrointestinal manifestations of familial adenomatous polyposis or Gardner's syndrome and such patients should be evaluated with genetic testing followed by colonoscopy if results are positive to prevent the development of colorectal carcinoma. If the diagnosis is positive all family members should be evaluated for familial adenomatous polyposis.

  15. An ecologically-based method for selecting ecological indicators for assessing risks to biological diversity from genetically-engineered plants

    DEFF Research Database (Denmark)

    Andow, D. A.; Lövei, Gabor L; Arpaia, Salvatore

    2013-01-01

    -driven, ecologically-based decision-making and provides formal methods for completing a screening level-ERA that can focus ERA on the most significant concerns. The process requires substantial human input but the human capital is available in most countries and regions of the world.......The environmental risks associated with genetically-engineered (GE) organisms have been controversial, and so have the models for the assessment of these risks. We propose an ecologically-based environmental risk assessment (ERA) model that follows the 1998 USEPA guidelines, focusing on potential....... Knowledge about the specific transgene and its possible environmental effects in other countries can be used to assist development of risk hypotheses. (6) The risk hypotheses are ranked using MCDA with criteria related to the severity of the potential risk. The model emphasizes transparent, expert...

  16. A New Comparative-Genomics Approach for Defining Phenotype-Specific Indicators Reveals Specific Genetic Markers in Predatory Bacteria.

    Science.gov (United States)

    Pasternak, Zohar; Ben Sasson, Tom; Cohen, Yossi; Segev, Elad; Jurkevitch, Edouard

    2015-01-01

    Predatory bacteria seek and consume other live bacteria. Although belonging to taxonomically diverse groups, relatively few bacterial predator species are known. Consequently, it is difficult to assess the impact of predation within the bacterial realm. As no genetic signatures distinguishing them from non-predatory bacteria are known, genomic resources cannot be exploited to uncover novel predators. In order to identify genes specific to predatory bacteria, we developed a bioinformatic tool called DiffGene. This tool automatically identifies marker genes that are specific to phenotypic or taxonomic groups, by mapping the complete gene content of all available fully-sequenced genomes for the presence/absence of each gene in each genome. A putative 'predator region' of ~60 amino acids in the tryptophan 2,3-dioxygenase (TDO) protein was found to probably be a predator-specific marker. This region is found in all known obligate predator and a few facultative predator genomes, and is absent from most facultative predators and all non-predatory bacteria. We designed PCR primers that uniquely amplify a ~180bp-long sequence within the predators' TDO gene, and validated them in monocultures as well as in metagenetic analysis of environmental wastewater samples. This marker, in addition to its usage in predator identification and phylogenetics, may finally permit reliable enumeration and cataloguing of predatory bacteria from environmental samples, as well as uncovering novel predators.

  17. Ecological and genetic data indicate recovery of the endangered coral Acropora palmata in Los Roques, Southern Caribbean

    Science.gov (United States)

    Zubillaga, A. L.; Márquez, L. M.; Cróquer, A.; Bastidas, C.

    2008-03-01

    The rapid decline of Acropora cervicornis and Acropora palmata has often been linked with coral reef deterioration in the Caribbean; yet, it remains controversial whether these species are currently recovering or still declining. In this study, the status of ten populations of A. palmata in Los Roques National Park (LRNP), Venezuela is presented. Six of these populations showed signs of recovery. Ten 80 m2 belt-transects were surveyed at each of the ten reef sites. Within belt-transects, each colony was measured (maximum diameter and height) and its status (healthy, diseased or injured) was recorded. Populations in recovery were defined by a dominance of small to medium-sized colonies in densities >1 colony per 10 m2, together with 75% undamaged colonies, a low prevalence of diseases (<10%), and a low density of predators (0.25 snails per colony). Based on allozyme analysis of seven polymorphic loci in four populations ( N = 30), a moderate to high-genetic connectivity among these populations ( F ST = 0.048) was found with a predominance of sexual over asexual reproduction ( N* : N = 1; N go : N = 0.93-1). Both ecological and molecular data support a good prognosis for the recovery of this species in Los Roques.

  18. Age-Related Shifts in the Density and Distribution of Genetic Marker Water Quality Indicators in Cow and Calf Feces

    Science.gov (United States)

    Recent studies have shown that different adult bovine animal feeding practices dramatically influence fecal indicator bacteria shedding, however very little is known about juvenile milk-fed calves. Calves (≤ 6 months of age) make up about 16% of the current bovine population in ...

  19. Information-theoretic indices and an approximate significance test for testing the molecular clock hypothesis with genetic distances.

    Science.gov (United States)

    Xia, Xuhua

    2009-09-01

    Distance-based phylogenetic methods are widely used in biomedical research. However, distance-based dating of speciation events and the test of the molecular clock hypothesis are relatively underdeveloped. Here I develop an approximate test of the molecular clock hypothesis for distance-based trees, as well as information-theoretic indices that have been used frequently in model selection, for use with distance matrices. The results are in good agreement with the conventional sequence-based likelihood ratio test. Among the information-theoretic indices, AICu is the most consistent with the sequence-based likelihood ratio test. The confidence in model selection by the indices can be evaluated by bootstrapping. I illustrate the usage of the indices and the approximate significance test with both empirical and simulated sequences. The tests show that distance matrices from protein gel electrophoresis and from genome rearrangement events do not violate the molecular clock hypothesis, and that the evolution of the third codon position conforms to the molecular clock hypothesis better than the second codon position in vertebrate mitochondrial genes. I outlined evolutionary distances that are appropriate for phylogenetic reconstruction and dating.

  20. Combining Diffusion Models and Macroeconomic Indicators with a Modified Genetic Programming Method: Implementation in Forecasting the Number of Mobile Telecommunications Subscribers in OECD Countries

    Directory of Open Access Journals (Sweden)

    Konstantinos Salpasaranis

    2014-01-01

    Full Text Available This paper proposes a modified Genetic Programming method for forecasting the mobile telecommunications subscribers’ population. The method constitutes an expansion of the hybrid Genetic Programming (hGP method improved by the introduction of diffusion models for technological forecasting purposes in the initial population, such as the Logistic, Gompertz, and Bass, as well as the Bi-Logistic and LogInLog. In addition, the aforementioned functions and models expand the function set of hGP. The application of the method in combination with macroeconomic indicators such as Gross Domestic Product per Capita (GDPpC and Consumer Prices Index (CPI leads to the creation of forecasting models and scenarios for medium- and long-term level of predictability. The forecasting module of the program has also been improved with the multi-levelled use of the statistical indices as fitness functions and model selection indices. The implementation of the modified-hGP in the datasets of mobile subscribers in the Organisation for Economic Cooperation and Development (OECD countries shows very satisfactory forecasting performance.

  1. Investigation of RBC Indices and HbA2 Levels in Parents of Beta-Thalassemia Patients: Impacts on Premarital Genetic Counseling

    Directory of Open Access Journals (Sweden)

    Mina Izadyar

    2007-06-01

    Full Text Available Objective: This study was designed to investigate RBC indices and HbA2 levels in parents of major beta-thalassemia patients to detect possible silent beta- thalassemia carriers and examine its potential impact on the premarital genetic counseling.Materials and Methods: This cross sectional study was performed at Children Medical Center from 2004 to 2006. After genetic counseling and getting informed consent, peripheral blood sampling was carried out on 185 carrier parents of regularly blood transfused thalassemia children. Then RBC indices and HbA2 concentration were measured. Samples with MCV and MCH higher than and/or HbA2 lower than cut off values were rechecked. Results: In one case, MCV and MCH indices were within the limits defined for non beta- thalassemia carriers. Furthermore, four other cases were found to have decreased values of MCV and MCH but normal HbA2 levels.Conclusion: About 3% of beta-thalassemia carriers in our country may potentially be missed using current screening methods. Further studies are required to assess the need for presenting a new threshold for thalassemia carrier screening. Defining the causative mutations using molecular methods would pave the way for establishing a protocol for a premarital screening program in conditions when one of couples is a confirmed carrier.

  2. Genetic transformation of cotton with a harpin-encoding gene hpaXoo confers an enhanced defense response against different pathogens through a priming mechanism

    Directory of Open Access Journals (Sweden)

    Song Congfeng

    2010-04-01

    Full Text Available Abstract Background The soil-borne fungal pathogen Verticillium dahliae Kleb causes Verticillium wilt in a wide range of crops including cotton (Gossypium hirsutum. To date, most upland cotton varieties are susceptible to V. dahliae and the breeding for cotton varieties with the resistance to Verticillium wilt has not been successful. Results Hpa1Xoo is a harpin protein from Xanthomonas oryzae pv. oryzae which induces the hypersensitive cell death in plants. When hpa1Xoo was transformed into the susceptible cotton line Z35 through Agrobacterium-mediated transformation, the transgenic cotton line (T-34 with an improved resistance to Verticillium dahliae was obtained. Cells of the transgenic T-34, when mixed with the conidia suspension of V. dahliae, had a higher tolerance to V. dahliae compared to cells of untransformed Z35. Cells of T-34 were more viable 12 h after mixing with V. dahliae conidia suspension. Immunocytological analysis showed that Hpa1Xoo, expressed in T-34, accumulated as clustered particles along the cell walls of T-34. In response to the infection caused by V. dahliae, the microscopic cell death and the generation of reactive oxygen intermediates were observed in leaves of T-34 and these responses were absent in leaves of Z35 inoculated with V. dahliae. Quantitative RT-PCR analysis indicated that five defense-related genes, ghAOX1, hin1, npr1, ghdhg-OMT, and hsr203J, were up-regulated in T-34 inoculated with V. dahliae. The up-regulations of these defense-relate genes were not observed or in a less extent in leaves of Z-35 after the inoculation. Conclusions Hpa1Xoo accumulates along the cell walls of the transgenic T-34, where it triggers the generation of H2O2 as an endogenous elicitor. T-34 is thus in a primed state, ready to protect the host from the pathogen. The results of this study suggest that the transformation of cotton with hpa1Xoo could be an effective approach for the development of cotton varieties with the

  3. Genotyping-by-sequencing approach indicates geographic distance as the main factor affecting genetic structure and gene flow in Brazilian populations of Grapholita molesta (Lepidoptera, Tortricidae).

    Science.gov (United States)

    Silva-Brandão, Karina Lucas; Silva, Oscar Arnaldo Batista Neto E; Brandão, Marcelo Mendes; Omoto, Celso; Sperling, Felix A H

    2015-06-01

    The oriental fruit moth Grapholita molesta is one of the major pests of stone and pome fruit species in Brazil. Here, we applied 1226 SNPs obtained by genotyping-by-sequencing to test whether host species associations or other factors such as geographic distance structured populations of this pest. Populations from the main areas of occurrence of G. molesta were sampled principally from peach and apple orchards. Three main clusters were recovered by neighbor-joining analysis, all defined by geographic proximity between sampling localities. Overall genetic structure inferred by a nonhierarchical amova resulted in a significant ΦST value = 0.19109. Here, we demonstrate for the first time that SNPs gathered by genotyping-by-sequencing can be used to infer genetic structure of a pest insect in Brazil; moreover, our results indicate that those markers are very informative even over a restricted geographic scale. We also demonstrate that host plant association has little effect on genetic structure among Brazilian populations of G. molesta; on the other hand, reduced gene flow promoted by geographic isolation has a stronger impact on population differentiation.

  4. Analysis of genetic diversity of Brassica rapa var. chinensis using ISSR markers and development of SCAR marker specific for Fragrant Bok Choy, a product of geographic indication.

    Science.gov (United States)

    Shen, X L; Zhang, Y M; Xue, J Y; Li, M M; Lin, Y B; Sun, X Q; Hang, Y Y

    2016-04-25

    Non-heading Chinese cabbage [Brassica rapa var. chinensis (Linnaeus) Kitamura] is a popular vegetable and is also used as a medicinal plant in traditional Chinese medicine. Fragrant Bok Choy is a unique accession of non-heading Chinese cabbage and a product of geographic indication certified by the Ministry of Agriculture of China, which is noted for its rich aromatic flavor. However, transitional and overlapping morphological traits can make it difficult to distinguish this accession from other non-heading Chinese cabbages. This study aimed to develop a molecular method for efficient identification of Fragrant Bok Choy. Genetic diversity analysis, based on inter-simple sequence repeat molecular markers, was conducted for 11 non-heading Chinese cabbage accessions grown in the Yangtze River Delta region. Genetic similarity coefficients between the 11 accessions ranged from 0.5455 to 0.8961, and the genetic distance ranged from 0.0755 to 0.4475. Cluster analysis divided the 11 accessions into two major groups. The primer ISSR-840 amplified a fragment specific for Fragrant Bok Choy. A pair of specific sequence-characterized amplified region (SCAR) primers based on this fragment amplified a target band in Fragrant Bok Choy individuals, but no band was detected in individuals of other accessions. In conclusion, this study has developed an efficient strategy for authentication of Fragrant Bok Choy. The SCAR marker described here will facilitate the conservation and utilization of this unique non-heading Chinese cabbage germplasm resource.

  5. Multilocus analysis indicates that Trypanosoma cruzi I genetic substructure associated with sylvatic and domestic cycles is not an attribute conserved throughout Colombia.

    Science.gov (United States)

    Gómez-Palacio, Andrés; Lopera, Juan; Rojas, Winston; Bedoya, Gabriel; Cantillo-Barraza, Omar; Marín-Suarez, Johana; Triana-Chávez, Omar; Mejía-Jaramillo, Ana

    2016-03-01

    Trypanosoma cruzi, the causative agent of Chagas disease, has been classified into six discrete typing units (DTUs) named TcI to TcVI. Furthermore, subcontinental scale studies based on analysis of the splice leader intergenic region (SL-IR) of the mini-exon gene have subdivided TcI in five genetic groups (Ia-Ie) related to the domestic and non-domestic cycles. However, a current review of this marker among all the sequences deposited in the GenBank demonstrates no correlation between the genetic structure and the eco-epidemiological features of parasite transmission. In this study, we performed a multilocus analysis of TcI isolates from a diverse array of hosts and vectors in a wide eco-geographical area of Colombia. Sequences from SL-IR and mitochondrial cyt b genes as well as PCR-RFLP profiles for four nuclear genes were analyzed. Multilocus analysis indicates that genetic structuration associated with sylvatic and domestic cycles in Colombia is not an attribute conserved across the entire eco-geography where TcI can be found.

  6. Spatial Genetic Structure of Coffee-Associated Xylella fastidiosa Populations Indicates that Cross Infection Does Not Occur with Sympatric Citrus Orchards.

    Science.gov (United States)

    Francisco, Carolina S; Ceresini, Paulo C; Almeida, Rodrigo P P; Coletta-Filho, Helvécio D

    2017-04-01

    Xylella fastidiosa, an economically important plant-pathogenic bacterium, infects both coffee and citrus trees in Brazil. Although X. fastidiosa in citrus is well studied, knowledge about the population structure of this bacterium infecting coffee remains unknown. Here, we studied the population structure of X. fastidiosa infecting coffee trees in São Paulo State, Brazil, in four regions where citrus is also widely cultivated. Genotyping of over 500 isolates from coffee plants using 14 genomic microsatellite markers indicated that populations were largely geographically isolated, as previously found with populations of X. fastidiosa infecting citrus. These results were supported by a clustering analysis, which indicated three major genetic groups among the four sampled regions. Overall, approximately 38% of isolates showed significant membership coefficients not related to their original geographical populations (i.e., migrants), characterizing a significant degree of genotype flow among populations. To determine whether admixture occurred between isolates infecting citrus and coffee plants, one site with citrus and coffee orchards adjacent to each other was selected; over 100 isolates were typed from each host plant. No signal of natural admixture between citrus- and coffee-infecting isolates was found; artificial cross-infection assays with representative isolates also yielded no successful cross infection. A comparison determined that X. fastidiosa populations from coffee have higher genetic diversity and allelic richness compared with citrus. The results showed that coffee and citrus X. fastidiosa populations are effectively isolated from each other and, although coffee populations are spatially structured, migration has an important role in shaping diversity.

  7. Genetically encoded fluorescent coumarin amino acids

    Science.gov (United States)

    Wang, Jiangyun; Xie, Jianming; Schultz, Peter G.

    2010-10-05

    The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetases that can incorporate the coumarin unnatural amino acid L-(7-hydroxycoumarin-4-yl) ethylglycine into proteins produced in eubacterial host cells such as E. coli. The invention provides, for example but not limited to, novel orthogonal synthetases, methods for identifying and making the novel synthetases, methods for producing proteins containing the unnatural amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine and related translation systems.

  8. Genetically encoded fluorescent coumarin amino acids

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jiangyun [San Diego, CA; Xie, Jianming [San Diego, CA; Schultz, Peter G [La Jolla, CA

    2012-06-05

    The invention relates to orthogonal pairs of tRNAs and aminoacyl-tRNA synthetases that can incorporate the coumarin unnatural amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine into proteins produced in eubacterial host cells such as E. coli. The invention provides, for example but not limited to, novel orthogonal synthetases, methods for identifying and making the novel synthetases, methods for producing proteins containing the unnatural amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine and related translation systems.

  9. Enhanced anti-tumor effect of a gene gun-delivered DNA vaccine encoding the human papillomavirus type 16 oncoproteins genetically fused to the herpes simplex virus glycoprotein D

    Directory of Open Access Journals (Sweden)

    M.O. Diniz

    2011-05-01

    Full Text Available Anti-cancer DNA vaccines have attracted growing interest as a simple and non-invasive method for both the treatment and prevention of tumors induced by human papillomaviruses. Nonetheless, the low immunogenicity of parenterally administered vaccines, particularly regarding the activation of cytotoxic CD8+ T cell responses, suggests that further improvements in both vaccine composition and administration routes are still required. In the present study, we report the immune responses and anti-tumor effects of a DNA vaccine (pgD-E7E6E5 expressing three proteins (E7, E6, and E5 of the human papillomavirus type 16 genetically fused to the glycoprotein D of the human herpes simplex virus type 1, which was administered to mice by the intradermal (id route using a gene gun. A single id dose of pgD-E7E6E5 (2 µg/dose induced a strong activation of E7-specific interferon-γ (INF-γ-producing CD8+ T cells and full prophylactic anti-tumor effects in the vaccinated mice. Three vaccine doses inhibited tumor growth in 70% of the mice with established tumors. In addition, a single vaccine dose consisting of the co-administration of pgD-E7E6E5 and the vector encoding interleukin-12 or granulocyte-macrophage colony-stimulating factor further enhanced the therapeutic anti-tumor effects and conferred protection to 60 and 50% of the vaccinated mice, respectively. In conclusion, id administration of pgD-E7E6E5 significantly enhanced the immunogenicity and anti-tumor effects of the DNA vaccine, representing a promising administration route for future clinical trials.

  10. Synaptic encoding of temporal contiguity

    Directory of Open Access Journals (Sweden)

    Srdjan eOstojic

    2013-04-01

    Full Text Available Often we need to perform tasks in an environment that changes stochastically. In these situations it is important to learn the statistics of sequences of events in order to predict the future and the outcome of our actions. The statistical description of many of these sequences can be reduced to the set of probabilities that a particular event follows another event (temporal contiguity. Under these conditions, it is important to encode and store in our memory these transition probabilities. Here we show that for a large class of synaptic plasticity models, the distribution of synaptic strengths encodes transitions probabilities. Specifically, when the synaptic dynamics depend on pairs of contiguous events and the synapses can remember multiple instances of the transitions, then the average synaptic weights are a monotonic function of the transition probabilities. The synaptic weights converge to the distribution encoding the probabilities also when the correlations between consecutive synaptic modifications are considered. We studied how this distribution depends on the number of synaptic states for a specific model of a multi-state synapse with hard bounds. In the case of bistable synapses, the average synaptic weights are a smooth function of the transition probabilities and the accuracy of the encoding depends on the learning rate. As the number of synaptic states increases, the average synaptic weights become a step function of the transition probabilities. We finally show that the information stored in the synaptic weights can be read out by a simple rate-based neural network. Our study shows that synapses encode transition probabilities under general assumptions and this indicates that temporal contiguity is likely to be encoded and harnessed in almost every neural circuit in the brain.

  11. Determining resistance to mastitis in a bovine subject involves detecting presence or absence of genetic marker associated with trait indicative of mastitis resistance of the bovine subject and/or off-spring from it

    DEFF Research Database (Denmark)

    2010-01-01

    -spring from it, where the genetic marker is located on the bovine chromosome BTA11 in the region flanked by and including the zeta-chain associated protein 70kD (ZAP70) and CD8B genes, where the presence or absence of the genetic marker is indicative of mastitis resistance. USE - For determining resistance...

  12. Isozyme markers associated with O(3) tolerance indicate shift in genetic structure of ponderosa and Jeffrey pine in Sequoia National Park, California.

    Science.gov (United States)

    Staszak, J; Grulke, N E; Marrett, M J; Prus-Glowacki, W

    2007-10-01

    Effects of canopy ozone (O(3)) exposure and signatures of genetic structure using isozyme markers associated with O(3) tolerance were analyzed in approximately 20-, approximately 80-, and >200-yr-old ponderosa (Pinus ponderosa Dougl. ex Laws.) and Jeffrey pine (Pinus jeffreyi Grev. & Balf.) in Sequoia National Park, California. For both species, the number of alleles and genotypes per loci was higher in parental trees relative to saplings. In ponderosa pine, the heterozygosity value increased, and the fixation index indicated reduction of homozygosity with increasing tree age class. The opposite tendencies were observed for Jeffrey pine. Utilizing canopy attributes known to be responsive to O(3) exposure, ponderosa pine was more symptomatic than Jeffrey pine, and saplings were more symptomatic than old growth trees. We suggest that these trends are related to differing sensitivity of the two species to O(3) exposure, and to higher O(3) exposures and drought stress that younger trees may have experienced during germination and establishment.

  13. Genetic analysis of the Arabidopsis protein kinases MAP3Kε1 and MAP3Kε2 indicates roles in cell expansion and embryo development.

    Science.gov (United States)

    Chaiwongsar, Suraphon; Strohm, Allison K; Su, Shih-Heng; Krysan, Patrick J

    2012-01-01

    MAP3Kε1 and MAP3Kε2 are a pair of Arabidopsis thaliana genes that encode protein kinases related to cdc7p from Saccharomyces cerevisiae. We have previously shown that the map3kε1;map3kε2 double-mutant combination causes pollen lethality. In this study, we have used an ethanol-inducible promoter construct to rescue this lethal phenotype and create map3kε1(-/-);map3kε2(-/-) double-mutant plants in order to examine the function of these genes in the sporophyte. These rescued double-mutant plants carry a yellow fluorescent protein (YFP)-MAP3Kε1 transgene under the control of the alcohol-inducible AlcA promoter from Aspergillus nidulans. The double-mutant plants were significantly smaller and had shorter roots than wild-type when grown in the absence of ethanol treatment. Microscopic analysis indicated that cell elongation was reduced in the roots of the double-mutant plants and cell expansion was reduced in rosette leaves. Treatment with ethanol to induce expression of YFP-MAP3Kε1 largely rescued the leaf phenotypes. The double-mutant combination also caused embryos to arrest in the early stages of development. Through the use of YFP reporter constructs we determined that MAP3Kε1 and MAP3Kε2 are expressed during embryo development, and also in root tissue. Our results indicate that MAP3Kε1 and MAP3Kε2 have roles outside of pollen development and that these genes affect several aspects of sporophyte development.

  14. The Role of Oxidative Stress in Diabetic Neuropathy: Generation of Free Radical Species in the Glycation Reaction and Gene Polymorphisms Encoding Antioxidant Enzymes to Genetic Susceptibility to Diabetic Neuropathy in Population of Type I Diabetic Patients.

    Science.gov (United States)

    Babizhayev, Mark A; Strokov, Igor A; Nosikov, Valery V; Savel'yeva, Ekaterina L; Sitnikov, Vladimir F; Yegorov, Yegor E; Lankin, Vadim Z

    2015-04-01

    pathway are detoxified by the glyoxalase system with reduced glutathione as co-factor. The concentration of reduced glutathione may be decreased by oxidative stress and by decreased in situ glutathione reductase activity in diabetes mellitus. Genetic variations within the antioxidant genes therefore could be implicated in the pathogenesis of DN. In this work, the supporting data about the association between the -262T > C polymorphism of the catalase (CAT) gene and DN were shown. The -262TT genotype of the CAT gene was significantly associated with higher erythrocyte catalase activity in blood of DN patients compared to the -262CC genotype (17.8 ± 2.7 × 10(4) IU/g Hb vs. 13.5 ± 3.2 × 10(4) IU/g Hb, P = 0.0022). The role of these factors in the development of diabetic complications and the prospective prevention of DN by supplementation in formulations of transglycating imidazole-containing peptide-based antioxidants (non-hydrolyzed carnosine, carcinine, n-acetylcarcinine) scavenging ROS in the glycation reaction, modifying the activity of enzymic and non-enzymic antioxidant defenses that participate in metabolic processes with ability of controlling at transcriptional levels the differential expression of several genes encoding antioxidant enzymes inherent to DN in Type I Diabetic patients, now deserve investigation.

  15. The pattern of genetic variability in apomictic clones of Taraxacum officinale indicates the alternation of asexual and sexual histories of apomicts.

    Directory of Open Access Journals (Sweden)

    Luboš Majeský

    Full Text Available Dandelions (genus Taraxacum comprise a group of sexual diploids and apomictic polyploids with a complicated reticular evolution. Apomixis (clonal reproduction through seeds in this genus is considered to be obligate, and therefore represent a good model for studying the role of asexual reproduction in microevolutionary processes of apomictic genera. In our study, a total of 187 apomictic individuals composing a set of nine microspecies (sampled across wide geographic area in Europe were genotyped for six microsatellite loci and for 162 amplified fragment length polymorphism (AFLP markers. Our results indicated that significant genetic similarity existed within accessions with low numbers of genotypes. Genotypic variability was high among accessions but low within accessions. Clustering methods discriminated individuals into nine groups corresponding to their phenotypes. Furthermore, two groups of apomictic genotypes were observed, which suggests that they had different asexual histories. A matrix compatibility test suggests that most of the variability within accession groups was mutational in origin. However, the presence of recombination was also detected. The accumulation of mutations in asexual clones leads to the establishment of a network of clone mates. However, this study suggests that the clones primarily originated from the hybridisation between sexual and apomicts.

  16. The pattern of genetic variability in apomictic clones of Taraxacum officinale indicates the alternation of asexual and sexual histories of apomicts.

    Science.gov (United States)

    Majeský, Luboš; Vašut, Radim J; Kitner, Miloslav; Trávníček, Bohumil

    2012-01-01

    Dandelions (genus Taraxacum) comprise a group of sexual diploids and apomictic polyploids with a complicated reticular evolution. Apomixis (clonal reproduction through seeds) in this genus is considered to be obligate, and therefore represent a good model for studying the role of asexual reproduction in microevolutionary processes of apomictic genera. In our study, a total of 187 apomictic individuals composing a set of nine microspecies (sampled across wide geographic area in Europe) were genotyped for six microsatellite loci and for 162 amplified fragment length polymorphism (AFLP) markers. Our results indicated that significant genetic similarity existed within accessions with low numbers of genotypes. Genotypic variability was high among accessions but low within accessions. Clustering methods discriminated individuals into nine groups corresponding to their phenotypes. Furthermore, two groups of apomictic genotypes were observed, which suggests that they had different asexual histories. A matrix compatibility test suggests that most of the variability within accession groups was mutational in origin. However, the presence of recombination was also detected. The accumulation of mutations in asexual clones leads to the establishment of a network of clone mates. However, this study suggests that the clones primarily originated from the hybridisation between sexual and apomicts.

  17. Phylogenetic analysis of human influenza A/H3N2 viruses isolated in 2015 in Germany indicates significant genetic divergence from vaccine strains.

    Science.gov (United States)

    Mostafa, Ahmed; Abdelwhab, El-Sayed M; Slanina, Heiko; Hussein, Mohamed A; Kuznetsova, Irina; Schüttler, Christian G; Ziebuhr, John; Pleschka, Stephan

    2016-06-01

    Infections by H3N2-type influenza A viruses (IAV) resulted in significant numbers of hospitalization in several countries in 2014-2015, causing disease also in vaccinated individuals and, in some cases, fatal outcomes. In this study, sequence analysis of H3N2 viruses isolated in Germany from 1998 to 2015, including eleven H3N2 isolates collected early in 2015, was performed. Compared to the vaccine strain A/Texas/50/2012 (H3N2), the 2015 strains from Germany showed up to 4.5 % sequence diversity in their HA1 protein, indicating substantial genetic drift. The data further suggest that two distinct phylogroups, 3C.2 and 3C.3, with 1.6-2.3 % and 0.3-2.4 % HA1 nucleotide and amino acid sequence diversity, respectively, co-circulated in Germany in the 2014/2015 season. Distinct glycosylation patterns and amino acid substitutions in the hemagglutinin and neuraminidase proteins were identified, possibly contributing to the unusually high number of H3N2 infections in this season and providing important information for developing vaccines that are effective against both genotypes.

  18. The Golden Ratio Encoder

    CERN Document Server

    Daubechies, I; Wang, Y; Yilmaz, Ö

    2008-01-01

    This paper proposes a novel Nyquist-rate analog-to-digital (A/D) conversion algorithm which achieves exponential accuracy in the bit-rate despite using imperfect components. The proposed algorithm is based on a robust implementation of a beta-encoder where the value of the base beta is equal to golden mean. It was previously shown that beta-encoders can be implemented in such a way that their exponential accuracy is robust against threshold offsets in the quantizer element. This paper extends this result by allowing for imperfect analog multipliers with imprecise gain values as well. A formal computational model for algorithmic encoders and a general test bed for evaluating their robustness is also proposed.

  19. Dopamine receptor genetic polymorphisms and body composition in undernourished pastoralists: An exploration of nutrition indices among nomadic and recently settled Ariaal men of northern Kenya

    Directory of Open Access Journals (Sweden)

    Gray Peter B

    2008-06-01

    Full Text Available Abstract Background Minor alleles of the human dopamine receptor polymorphisms, DRD2/TaqI A and DRD4/48 bp, are related to decreased functioning and/or numbers of their respective receptors and have been shown to be correlated with body mass, height and food craving. In addition, the 7R minor allele of the DRD4 gene is at a higher frequency in nomadic compared to sedentary populations. Here we examine polymorphisms in the DRD2 and DRD4 genes with respect to body mass index (BMI and height among men in two populations of Ariaal pastoralists, one recently settled (n = 87 and the other still nomadic (n = 65. The Ariaal live in northern Kenya, are chronically undernourished and are divided socially among age-sets. Results Frequencies of the DRD4/7R and DRD2/A1 alleles were 19.4% and 28.2%, respectively and did not differ between the nomadic and settled populations. BMI was higher in those with one or two DRD4/7R alleles in the nomadic population, but lower among the settled. Post-hoc analysis suggests that the DRD4 differences in BMI were due primarily to differences in fat free body mass. Height was unrelated to either DRD2/TaqI A or DRD4/48 bp genotypes. Conclusion Our results indicate that the DRD4/7R allele may be more advantageous among nomadic than settled Ariaal men. This result suggests that a selective advantage mediated through behaviour may be responsible for the higher frequency of the 7R alleles in nomadic relative to sedentary populations around the world. In contrast to previous work, we did not find an association between DRD2 genotypes and height. Our results support the idea that human phenotypic expression of genotypes should be rigorously evaluated in diverse environments and genetic backgrounds.

  20. Genetic characterization of oropharyngeal trichomonad isolates from wild birds indicates that genotype is associated with host species, diet and presence of pathognomonic lesions.

    Science.gov (United States)

    Martínez-Herrero, M C; Sansano-Maestre, J; López Márquez, I; Obón, E; Ponce, C; González, J; Garijo-Toledo, M M; Gómez-Muñoz, M T

    2014-01-01

    Oropharyngeal trichomonad isolates of wild birds from Spain were studied. A total of 1688 samples (1214 of predator birds and 474 of prey species) from wildlife recovery centres and scientific bird-ringing campaigns were analysed from 2011 to 2013. The overall infection prevalence was 20.3% (11.4% in predator birds and 43.3% in prey species). Pathognomonic lesions were present in 26% of the infected birds (57.3% in predator birds and 4.9% in prey species). The most commonly parasitized species were the goshawk (Accipiter gentilis, 74.5%) and the rock pigeon (Columba livia, 79.4%). Host species in which the parasite has not been previously analysed by polymerase chain reaction and sequencing in Spain are also reported: Columba palumbus, Streptopelia turtur, Pica pica, A. gentilis, Accipiter nisus, Asio otus, Bubo bubo, Buteo buteo, Circus aeruginosus, Circus cyaneus, Falco naumanni, Falco peregrinus, Neophron percnopterus, Otus scops, Pernis apivorus and Strix aluco. Sequence analysis of the ITS1/5.8S/ITS2 region revealed five different genotypes and also some mixed infections. A relationship between genotype and host species was observed, but only two genotypes (ITS-OBT-Tg-1and ITS-OBT-Tg-2) were widely distributed. Genotype ITS-OBT-Tg-1 was most frequently found in predator birds and statistically associated with pathognomonic lesions. Non-strict ornithophagous species were at higher risk to develop disease than ornithophagous ones. Genotypes ITS-OBT-Tcl-1 and ITS-OBT-Tcl-2 are new reports, and ITS-OBT-Tvl-5 is reported for the first time in Spain. They showed higher genetic homology to Trichomonas canistomae and Trichomonas vaginalis than to Trichomonas gallinae, indicating the possibility of new species within this genus.

  1. Negative Beta Encoder

    CERN Document Server

    Kohda, Tohru; Aihara, Kazuyuki

    2008-01-01

    A new class of analog-digital (A/D), digital-analog (D/A) converters as an alternative to conventional ones, called $\\beta$-encoder, has been shown to have exponential accuracy in the bit rates while possessing self-correction property for fluctuations of amplifier factor $\\beta$ and quantizer threshold $\

  2. DNA sequences encoding erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, F.K.

    1987-10-27

    A purified and isolated DNA sequence is described consisting essentially of a DNA sequence encoding a polypeptide having an amino acid sequence sufficiently duplicative of that of erythropoietin to allow possession of the biological property of causing bone marrow cells to increase production of reticulocytes and red blood cells, and to increase hemoglobin synthesis or iron uptake.

  3. Time-Encoded Imagers.

    Energy Technology Data Exchange (ETDEWEB)

    Marleau, Peter; Brubaker, Erik

    2014-11-01

    This report provides a short overview of the DNN R&D funded project, Time-Encoded Imagers. The project began in FY11 and concluded in FY14. The Project Description below provides the overall motivation and objectives for the project as well as a summary of programmatic direction. It is followed by a short description of each task and the resulting deliverables.

  4. Applications of Genetic Programming

    DEFF Research Database (Denmark)

    Gaunholt, Hans; Toma, Laura

    1996-01-01

    In this report a study of genetic programming (GP) has been performed with respect to a number of applications such as Symbolic function regression, Solving Symbolic Differential Equations, Image encoding, the ant problem etc.......In this report a study of genetic programming (GP) has been performed with respect to a number of applications such as Symbolic function regression, Solving Symbolic Differential Equations, Image encoding, the ant problem etc....

  5. Applications of Genetic Programming

    DEFF Research Database (Denmark)

    Gaunholt, Hans; Toma, Laura

    1996-01-01

    In this report a study of genetic programming (GP) has been performed with respect to a number of applications such as Symbolic function regression, Solving Symbolic Differential Equations, Image encoding, the ant problem etc.......In this report a study of genetic programming (GP) has been performed with respect to a number of applications such as Symbolic function regression, Solving Symbolic Differential Equations, Image encoding, the ant problem etc....

  6. On Derivations Of Genetic Algebras

    Science.gov (United States)

    Mukhamedov, Farrukh; Qaralleh, Izzat

    2014-11-01

    A genetic algebra is a (possibly non-associative) algebra used to model inheritance in genetics. In application of genetics this algebra often has a basis corresponding to genetically different gametes, and the structure constant of the algebra encode the probabilities of producing offspring of various types. In this paper, we find the connection between the genetic algebras and evolution algebras. Moreover, we prove the existence of nontrivial derivations of genetic algebras in dimension two.

  7. Determining resistance to mastitis in a bovine subject involves detecting presence or absence of genetic marker associated with trait indicative of mastitis resistance of the bovine subject and/or off-spring from it

    DEFF Research Database (Denmark)

    2010-01-01

    subject. The bovine subject is a member of Finnish Ayrshire, Swedish Red and White, or Danish Red cattle breed (claimed). ADVANTAGE - The method efficiently selects bovine subjects with increased resistance to mastitis and thereby avoiding economic losses in connection with animals suffering from mastitis......NOVELTY - Determining (m1) resistance to mastitis in a bovine subject, involves detecting in a sample from the bovine subject the presence or absence of at least one genetic marker that is associated with at least one trait indicative of mastitis resistance of the bovine subject and/or off......-spring from it, where the genetic marker is located on the bovine chromosome BTA11 in the region flanked by and including the zeta-chain associated protein 70kD (ZAP70) and CD8B genes, where the presence or absence of the genetic marker is indicative of mastitis resistance. USE - For determining resistance...

  8. Determining resistance to mastitis in a bovine subject comprises detecting the presence or absence of a genetic marker that is linked to a trait indicative of mastitis resistance

    DEFF Research Database (Denmark)

    2007-01-01

    The invention relates to a method for determining mastitis resistance in bovine subjects, wherein mastitis resistance comprise resistance to both sub-clinical and clinical mastitis. In particular, the method of the invention involves identification of genetic markers and/or Quantitative Trait Locus...... (QTL) for the determination of mastitis resistance in a bovine subject. The determination of mastitis resistance involves resolution of the specific microsatellite status. Furthermore, the invention relates to a diagnostic kit for detection of genetic marker(s) associated with mastitis resistance....... The method and kit of the present invention can be applied for selection of bovine subjects for breeding purposes. Thus, the invention provides a method of genetically selecting bovine subjects with mastitis resistance, thereby yielding cows less prone to mastitis...

  9. Genetics of alcoholism.

    Science.gov (United States)

    Edenberg, Howard J; Foroud, Tatiana

    2014-01-01

    Multiple lines of evidence strongly indicate that genetic factors contribute to the risk for alcohol use disorders (AUD). There is substantial heterogeneity in AUD, which complicates studies seeking to identify specific genetic factors. To identify these genetic effects, several different alcohol-related phenotypes have been analyzed, including diagnosis and quantitative measures related to AUDs. Study designs have used candidate gene analyses, genetic linkage studies, genomewide association studies (GWAS), and analyses of rare variants. Two genes that encode enzymes of alcohol metabolism have the strongest effect on AUD: aldehyde dehydrogenase 2 and alcohol dehydrogenase 1B each has strongly protective variants that reduce risk, with odds ratios approximately 0.2-0.4. A number of other genes important in AUD have been identified and replicated, including GABRA2 and alcohol dehydrogenases 1B and 4. GWAS have identified additional candidates. Rare variants are likely also to play a role; studies of these are just beginning. A multifaceted approach to gene identification, targeting both rare and common variations and assembling much larger datasets for meta-analyses, is critical for identifying the key genes and pathways important in AUD.

  10. Virus-Encoded microRNAs: Future Therapeutic Targets?

    Institute of Scientific and Technical Information of China (English)

    Peng Qi; Jinxiang Han; Yanqin Lu; Chuanxi Wang; Fanfeng Bu

    2006-01-01

    The discovery of microRNAs (miRNAs) is a remarkable breakthrough in the field of molecular genetics, as miRNAs are key actors which regulate gene expression in diverse cellular processes from unicellular yeast to human. The recent discovery of virus-encoded miRNAs indicates that viruses also use this fundamental mode of gene regulation. Research into viral miRNAs function demonstrates that some miRNAs play an important role in regulating both the viral life cycle and the interaction between viruses and their hosts. The first in vivo "antagomir" study provides an exciting first step towards miRNA therapy, and the potential for ultimately designing molecular medicines based on the modulation of miRNAs seems good.

  11. Optimization of unit commitment based on genetic algorithms

    Institute of Scientific and Technical Information of China (English)

    蔡兴国; 初壮

    2002-01-01

    How to solve unit commitment and load dispatch of power system by genetic algorithms is discussed in this paper. A combination encoding scheme of binary encoding and floating number encoding and corresponding genetic operators are developed. Meanwhile a contract mapping genetic algorithm is used to enhance traditional GA' s convergence. The result of a practical example shows that this algorithm is effective.

  12. Determining resistance to mastitis in a bovine subject comprises detecting the presence or absence of a genetic marker that is linked to a trait indicative of mastitis resistance

    DEFF Research Database (Denmark)

    2007-01-01

    The invention relates to a method for determining mastitis resistance in bovine subjects, wherein mastitis resistance comprise resistance to both sub-clinical and clinical mastitis. In particular, the method of the invention involves identification of genetic markers and/or Quantitative Trait Loc...

  13. Genetic screening for von Hippel-Lindau gene mutations in non-syndromic pheochromocytoma: low prevalence and false-positives or misdiagnosis indicate a need for caution.

    NARCIS (Netherlands)

    Eisenhofer, G.; Vocke, C.D.; Elkahloun, A.; Huynh, T.T.; Prodanov, T.; Lenders, J.W.M.; Timmers, H.J.L.M.; Benhammou, J.N.; Linehan, W.M.; Pacak, K.

    2012-01-01

    Genetic testing of tumor susceptibility genes is now recommended in most patients with pheochromocytoma or paraganglioma (PPGL), even in the absence of a syndromic presentation. Once a mutation is diagnosed there is rarely follow-up validation to assess the possibility of misdiagnosis. This study

  14. Spectrally encoded confocal microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tearney, G.J.; Webb, R.H.; Bouma, B.E. [Wellman Laboratories of Photomedicine, Massachusetts General Hospital, 50 Blossom Street, BAR 703, Boston, Massachusetts 02114 (United States)

    1998-08-01

    An endoscope-compatible, submicrometer-resolution scanning confocal microscopy imaging system is presented. This approach, spectrally encoded confocal microscopy (SECM), uses a quasi-monochromatic light source and a transmission diffraction grating to detect the reflectivity simultaneously at multiple points along a transverse line within the sample. Since this method does not require fast spatial scanning within the probe, the equipment can be miniaturized and incorporated into a catheter or endoscope. Confocal images of an electron microscope grid were acquired with SECM to demonstrate the feasibility of this technique. {copyright} {ital 1998} {ital Optical Society of America}

  15. Analysis of the optimality of the standard genetic code.

    Science.gov (United States)

    Kumar, Balaji; Saini, Supreet

    2016-07-19

    Many theories have been proposed attempting to explain the origin of the genetic code. While strong reasons remain to believe that the genetic code evolved as a frozen accident, at least for the first few amino acids, other theories remain viable. In this work, we test the optimality of the standard genetic code against approximately 17 million genetic codes, and locate 29 which outperform the standard genetic code at the following three criteria: (a) robustness to point mutation; (b) robustness to frameshift mutation; and (c) ability to encode additional information in the coding region. We use a genetic algorithm to generate and score codes from different parts of the associated landscape, which are, as a result, presumably more representative of the entire landscape. Our results show that while the genetic code is sub-optimal for robustness to frameshift mutation and the ability to encode additional information in the coding region, it is very strongly selected for robustness to point mutation. This coupled with the observation that the different performance indicator scores for a particular genetic code are negatively correlated makes the standard genetic code nearly optimal for the three criteria tested in this work.

  16. Multichannel compressive sensing MRI using noiselet encoding.

    Directory of Open Access Journals (Sweden)

    Kamlesh Pawar

    Full Text Available The incoherence between measurement and sparsifying transform matrices and the restricted isometry property (RIP of measurement matrix are two of the key factors in determining the performance of compressive sensing (CS. In CS-MRI, the randomly under-sampled Fourier matrix is used as the measurement matrix and the wavelet transform is usually used as sparsifying transform matrix. However, the incoherence between the randomly under-sampled Fourier matrix and the wavelet matrix is not optimal, which can deteriorate the performance of CS-MRI. Using the mathematical result that noiselets are maximally incoherent with wavelets, this paper introduces the noiselet unitary bases as the measurement matrix to improve the incoherence and RIP in CS-MRI. Based on an empirical RIP analysis that compares the multichannel noiselet and multichannel Fourier measurement matrices in CS-MRI, we propose a multichannel compressive sensing (MCS framework to take the advantage of multichannel data acquisition used in MRI scanners. Simulations are presented in the MCS framework to compare the performance of noiselet encoding reconstructions and Fourier encoding reconstructions at different acceleration factors. The comparisons indicate that multichannel noiselet measurement matrix has better RIP than that of its Fourier counterpart, and that noiselet encoded MCS-MRI outperforms Fourier encoded MCS-MRI in preserving image resolution and can achieve higher acceleration factors. To demonstrate the feasibility of the proposed noiselet encoding scheme, a pulse sequences with tailored spatially selective RF excitation pulses was designed and implemented on a 3T scanner to acquire the data in the noiselet domain from a phantom and a human brain. The results indicate that noislet encoding preserves image resolution better than Fouirer encoding.

  17. Multichannel compressive sensing MRI using noiselet encoding.

    Science.gov (United States)

    Pawar, Kamlesh; Egan, Gary; Zhang, Jingxin

    2015-01-01

    The incoherence between measurement and sparsifying transform matrices and the restricted isometry property (RIP) of measurement matrix are two of the key factors in determining the performance of compressive sensing (CS). In CS-MRI, the randomly under-sampled Fourier matrix is used as the measurement matrix and the wavelet transform is usually used as sparsifying transform matrix. However, the incoherence between the randomly under-sampled Fourier matrix and the wavelet matrix is not optimal, which can deteriorate the performance of CS-MRI. Using the mathematical result that noiselets are maximally incoherent with wavelets, this paper introduces the noiselet unitary bases as the measurement matrix to improve the incoherence and RIP in CS-MRI. Based on an empirical RIP analysis that compares the multichannel noiselet and multichannel Fourier measurement matrices in CS-MRI, we propose a multichannel compressive sensing (MCS) framework to take the advantage of multichannel data acquisition used in MRI scanners. Simulations are presented in the MCS framework to compare the performance of noiselet encoding reconstructions and Fourier encoding reconstructions at different acceleration factors. The comparisons indicate that multichannel noiselet measurement matrix has better RIP than that of its Fourier counterpart, and that noiselet encoded MCS-MRI outperforms Fourier encoded MCS-MRI in preserving image resolution and can achieve higher acceleration factors. To demonstrate the feasibility of the proposed noiselet encoding scheme, a pulse sequences with tailored spatially selective RF excitation pulses was designed and implemented on a 3T scanner to acquire the data in the noiselet domain from a phantom and a human brain. The results indicate that noislet encoding preserves image resolution better than Fouirer encoding.

  18. Natural Crossbreeding between Sympatric Species of the Phyllosoma Complex (Insecta: Hemiptera: Reduviidae) Indicate the Existence of Only One Species with Morphologic and Genetic Variations

    Science.gov (United States)

    Martínez-Hernandez, Fernando; Martínez-Ibarra, Jose A.; Catalá, Silvia; Villalobos, Guiehdani; de la Torre, Patricia; Laclette, Juan P.; Alejandre-Aguilar, Ricardo; Espinoza, Bertha

    2010-01-01

    The nucleotide sequences of the cytochrome B gene and the antennal phenotypes were analyzed for the following triatomine species: Triatoma longipennis, Triatoma pallidipennis, and Triatoma picturata, which belong to the Phyllosoma complex. These species inhabit sympatric areas from Talpa de Allende, Autlan de Navarro, and Teocuitatlan de Corona in Jalisco, Mexico. Molecular marker analysis showed that the sympatric individuals are the natural crossbred descendents of different individuals living in close proximity in these natural areas that resulted in mixed populations. The antennal phenotype results are coincident with these genetic findings, which point to the high similitude between all Phyllosoma complex populations analyzed. These data support the hypothesis that these species are morphotypes with chromatic and genetic varieties, which preserves the possibility of natural breeding with fertile descent. In conclusion, our results strongly support the hypothesis that T. pallidipennis, T. longipennis, and T. picturata are subspecies of the Phyllosoma complex. PMID:20064999

  19. Genetic parameters for androstenone and skatole as indicators of boar taint and their relationship to production and litter size traits in Danish Landrace

    DEFF Research Database (Denmark)

    Strathe, Anders Bjerring; Velander, I. H.; Mark, Thomas

    2013-01-01

    to production and litter size traits. Concentrations of skatole and androstenone in the back fat were available for approximately 6,000 and 1,000 Landrace boars, respectively. The concentrations were log-transformed to align phenotypic measures to a normal distribution. Heritability estimates for Log....... The relationship between litter size traits (measured on sows related to boars) and boar taint compounds was low and not significantly different from zero. In conclusion, skatole and androstenone can be reduced through selection without affecting important economical production and litter size traits. Thus, animal......Boar taint is an offensive odor, which affects the smell and taste of cooked pork, resulting mainly from the accumulation of skatole and androstenone in the back fat of intact males. The aim of the study was to estimate genetic parameters for skatole and androstenone and their genetic relationship...

  20. Single-kernel ionomic profiles are highly heritable indicators of genetic and environmental influences on elemental accumulation in maize grain (Zea mays.

    Directory of Open Access Journals (Sweden)

    Ivan R Baxter

    Full Text Available The ionome, or elemental profile, of a maize kernel can be viewed in at least two distinct ways. First, the collection of elements within the kernel are food and feed for people and animals. Second, the ionome of the kernel represents a developmental end point that can summarize the life history of a plant, combining genetic programs and environmental interactions. We assert that single-kernel-based phenotyping of the ionome is an effective method of analysis, as it represents a reasonable compromise between precision, efficiency, and power. Here, we evaluate potential pitfalls of this sampling strategy using several field-grown maize sample sets. We demonstrate that there is enough genetically determined diversity in accumulation of many of the elements assayed to overcome potential artifacts. Further, we demonstrate that environmental signals are detectable through their influence on the kernel ionome. We conclude that using single kernels as the sampling unit is a valid approach for understanding genetic and environmental effects on the maize kernel ionome.

  1. Determining fertility in a bovine subject comprises detecting in a sample from the bovine subject the presence or absence of genetic marker alleles associated with a trait indicative of fertility of the bovine subject and/or off-spring

    DEFF Research Database (Denmark)

    2009-01-01

    for determining fertility in a bovine subject; and selecting bovine subjects for breeding purposes (all claimed). DETAILED DESCRIPTION - Determining fertility in a bovine subject comprises detecting in a sample from the bovine subject the presence or absence of two or more genetic marker alleles......NOVELTY - Determining fertility in a bovine subject comprises detecting in a sample from the bovine subject the presence or absence of two or more genetic marker alleles that are associated with a trait indicative of fertility of the bovine subject and/or off-spring. USE - The methods are useful...... purposes; and (2) a diagnostic kit for detecting the presence or absence in a bovine subject of two or more genetic marker alleles comprising a detection member....

  2. Recent genetic discoveries in osteoporosis, sarcopenia and obesity.

    Science.gov (United States)

    Urano, Tomohiko; Inoue, Satoshi

    2015-01-01

    Osteoporosis is a skeletal disorder characterized by low bone mineral density (BMD) and an increased susceptibility to fractures. Evidence from genetic studies indicates that BMD, a complex quantitative trait with a normal distribution, is genetically controlled. Genome-wide association studies (GWAS) as well as studies using candidate gene approaches have identified single-nucleotide polymorphisms (SNPs) that are associated with BMD, osteoporosis and osteoporotic fractures. These SNPs have been mapped close to or within genes including those encoding WNT/β-catenin signaling proteins. Understanding the genetics of osteoporosis will help to identify novel candidates for diagnostic and therapeutic targets. Genetic factors are also important for the development of sarcopenia, which is characterized by a loss of lean body mass, and obesity, which is characterized by high fat mass. Hence, in this review, we discuss the genetic factors, identified by genetic studies, which regulate the body components related to osteoporosis, sarcopenia, and obesity.

  3. Dynamical encoding of cursive handwriting.

    Science.gov (United States)

    Singer, Y; Tishby, N

    1994-01-01

    A model-based approach to on-line cursive handwriting analysis and recognition is presented and evaluated. In this model, on-line handwriting is considered as a modulation of a simple cycloidal pen motion, described by two coupled oscillations with a constant linear drift along the line of the writing. By slow modulations of the amplitudes and phase lags of the two oscillators, a general pen trajectory can be efficiently encoded. These parameters are then quantized into a small number of values without altering the writing intelligibility. A general procedure for the estimation and quantization of these cycloidal motion parameters for arbitrary handwriting is presented. The result is a discrete motor control representation of the continuous pen motion, via the quantized levels of the model parameters. This motor control representation enables successful word spotting and matching of cursive scripts. Our experiments clearly indicate the potential of this dynamic representation for complete cursive handwriting recognition.

  4. 47 CFR 11.32 - EAS Encoder.

    Science.gov (United States)

    2010-10-01

    ... codes shall be retained even with the power removed. (7) Indicator. An aural or visible means that it... levels of the mark or space frequencies. (9) Attention Signal generator. The encoder must provide an attention signal that complies with the following: (i) Tone Frequencies. The audio tones shall have...

  5. Genetic variants of TNFα, IL10, IL1β, CTLA4 and TGFβ1 modulate the indices of alcohol-induced liver injury in East Indian population.

    Science.gov (United States)

    Roy, Neelanjana; Mukhopadhyay, Indranil; Das, Kausik; Pandit, Pratap; Majumder, Partha P; Santra, Amal; Datta, Simanti; Banerjee, Soma; Chowdhury, Abhijit

    2012-11-01

    Alcohol induced liver disease or alcoholic liver disease (ALD), a complex trait, encompasses a gamut of pathophysiological alterations in the liver due to continuous exposure to a toxic amount of alcohol (more than 80 g per day). Of all chronic heavy drinkers, only 15-20% develops hepatitis or cirrhosis concomitantly or in succession. Several studies revealed that inter-individual as well as inter-ethnic genetic variation is one of the major factors that predispose to ALD. The role of genetic factors in ALD has long been sought for in ethnically distinct population groups. ALD is fast emerging as an important cause of chronic liver disease in India; even in populations such as "Bengalis" who were "culturally immune" earlier. While the genetic involvement in the pathogenesis of ALD is being sought for in different races, the complex pathophysiology of ALD as well as the knowledge of population level diversity of the relevant alcohol metabolizing and inflammatory pathways mandates the need for well designed studies of genetic factors in ethnically distinct population groups. An array of cytokines plays a critical role as mediators of injury, inflammation, fibrosis and cirrhosis in ALD. We, therefore, studied the association of polymorphisms in five relevant cytokine genes with "clinically significant" ALD in an ethnic "Bengali" population in Eastern India. Compared with "alcoholic" controls without liver disease (n=110), TNFα -238AA genotype, IL1β -511CC genotype, TGFβ1 -509CC genotype and IL10 -592AA genotype were significantly overrepresented in ALD patients (n=181; OR=2.4 and 95% CI 1.2-5.5, P(genotype)=0.042, P(allelic)=0.008; OR=2.7 and 95% CI 1.2-5.9, P(genotype)=0.018, P(allelic)=0.023; OR=4.7 and 95% CI 1.7-13.1, P(genotype)=0.003, P(allelic)=0.014; and OR=2.2 and 95% CI 1.1-4.8, P(genotype)=0.04, P(allelic)=0.039 respectively). Moreover a cumulative genetic risk analysis revealed a significant trend for developing ALD with an increase in the number of

  6. Symmetrical and Thermodynamic Properties of Phenotypic Graphs of Amino Acids Encoded by the Primeval RNY Code

    Science.gov (United States)

    José, Marco V.; Zamudio, Gabriel S.; Palacios-Pérez, Miryam; Bobadilla, Juan R.; de Farías, Sávio Torres

    2015-06-01

    The 12 different types of graphs of the 8 amino acids encoded by the presumably primeval RNY code are derived. The symmetry groups of these graphs are analyzed and coincide with the corresponding values of polar requirement for each amino acid. The symmetry groups at the codon level are partially carried over as a group or subgroup at the amino acid level. Measures of centrality of the 12 graphs indicate that all amino acids were equally relevant irrespective of its chronological order of its appearance. The elimination of any amino acid would be strongly selected against and therefore the genetic code at this stage was already frozen.

  7. Genetics of stroke

    OpenAIRE

    Guo, Jin-Min; Liu, Ai-Jun; Su, Ding-Feng

    2010-01-01

    Stroke is the second most common cause of death and the most common cause of disability in developed countries. Stroke is a multi-factorial disease caused by a combination of environmental and genetic factors. Numerous epidemiologic studies have documented a significant genetic component in the occurrence of strokes. Genes encoding products involved in lipid metabolism, thrombosis, and inflammation are believed to be potential genetic factors for stroke. Although a large group of candidate ge...

  8. Early age of alcohol initiation is not the cause of alcohol use disorders in adulthood, but is a major indicator of genetic risk. A population-based twin study.

    Science.gov (United States)

    Ystrom, Eivind; Kendler, Kenneth S; Reichborn-Kjennerud, Ted

    2014-11-01

    An early age of alcohol initiation (AAI) is associated with and has been hypothesized to be a cause of alcohol use disorders (AUD) in adulthood. Results from twin studies, however, indicate that AAI is an indicator of risk for AUD. We aimed to test a causal hypothesis versus a risk indicator hypothesis for the relationship between early AAI and AUD. A population-based twin study using biometric twin modelling. Norway. A population-based sample of 1336 Norwegian twins. Life-time DSM-IV AUDs were assessed by structured clinical interview and AAI by questionnaire. The risk indicator model in which the association between AAI and AUD was explained by common vulnerability was the best fitted to the data. The heritability was 37% [95% confidence interval (CI) = 21%, 53%] for AAI and 62% (95% CI = 51%, 73%) for AUD. Genetic risk for AAI accounted for 44% (95% CI = 17%, 71%) of the total genetic risk for AUD and the correlation between genetic factors for AAI and AUD was -0.66 (95%CI -0.87, -0.46). Individual-specific environmental risk for AAI explained only 1% (95% CI = 0%, 3%) of the risk for AUD. Shared environmental factors did not influence AUD, but accounted for 25% (95% CI = 7%, 35%) of the variance in AAI. The association between early age of alcohol initiation and alcohol use disorders in later life does not reflect a causal relationship, but is due almost entirely to common genetic risk factors. © 2014 Society for the Study of Addiction.

  9. A genetic structure of novel population of Fascioloides magna from Poland, Podkarpackie Province, indicates an expanding second European natural focus of fascioloidosis.

    Science.gov (United States)

    Juhásová, Ľudmila; Bazsalovicsová, Eva; Králová-Hromadová, Ivica; Karamon, Jacek

    2016-12-01

    The veterinary important parasite of ruminants, giant liver fluke Fascioloides magna(Trematoda: Fasciolidae), isolated from liver of farmed fallow deer (Dama dama) from Podkarpackie Province (southeastern Poland) was genotypized by mitochondrial cytochrome c oxidase (cox1) and nicotinamide dehydrogenase (nad1) markers. The data on this newly emerged population were compared with mitochondrial haplotypes of recently detected Polish population of F. magna from Lower Silesian Wilderness (southwestern Poland) and with European populations of the parasite from all three natural foci; northern Italy, Czech Republic and the Danube floodplain forests. The flukes from Podkarpackie Province were found to be genetically identical with flukes from Czech Republic and Lower Silesian Wilderness in Poland. It is evident that central and southwestern Czech Republic, recognized as one of the endemic area of F. magna in Europe, has been enlarging and parasite has been invading several novel localities in Poland.

  10. Detection and organization of atrazine-degrading genetic potential of seventeen bacterial isolates belonging to divergent taxa indicate a recent common origin of their catabolic functions

    DEFF Research Database (Denmark)

    El Azhari, Najoi

    2007-01-01

    A collection of 17 atrazine-degrading bacteria isolated from soils was studied to determine the composition of the atrazine-degrading genetic potential (i.e. trzN, trzD and atz) and the presence of IS1071. The characterization of seven new atrazine-degrading bacteria revealed for the first time...... the trzN-atzBC gene composition in Gram-negative bacteria such as Sinorhizobium sp. or Polaromonas sp. Three main atrazine-degrading gene combinations (i) trzN–atzBC, (ii) atzABC–trzD and (iii) atzABCDEF were observed. The atz and trz genes were often located on plasmids, suggesting that plasmid...... the atrazine-degrading genes....

  11. FEEDING OF GENETICALLY MODIFIED CROPS AND THEIR EFFECT ON THE FATTENING, CARCASS AND QUALITATIVE INDICATORS OF PIGS SKRMOVANIE GENETICKY MODIFIKOVANCH PLODN A ICH VPLYV NA VKRMOV, JATOCN A KVALITATVNE PARAMETRE OPANCH

    Directory of Open Access Journals (Sweden)

    JURAJ MLYNEK

    2013-03-01

    Full Text Available In the experiment we judged the influence of genetically modified plants on the fattening-, carcass-, and pig quality parameters. We have recorded better fattening parameters in the group fed with the GM crops. We recorded statistically provable differences in the number of the test fattening days (30 100 kg, in the lifelong average daily gains, in the test fodder consumption (30 100 kg. We have recorded better carcass indicators in the group fed without the GM plants, which was statistically confirmed in the valuable meaty parts as well as thigh portions. There were no statistically provable differences found out in the meat quality indicators between the groups.

  12. Genetic variation in WDR1 is associated with gout risk and gout-related metabolic indices in the Han Chinese population.

    Science.gov (United States)

    Liu, L J; Zhang, X Y; He, N; Liu, K; Shi, X G; Feng, T; Geng, T T; Yuan, D Y; Kang, L L; Jin, T B

    2016-04-28

    Gout is the most common form of inflammatory arthritis affecting men, and current evidence suggests that genetic factors contribute to its progression. As a previous study identified that WD40 repeat protein 1 (WDR1) is associated with gout in populations of European descent, we sought to investigate its relationship with this disease in the Han Chinese population. We genotyped six WDR1 single nucleotide polymorphisms in 143 gout cases and 310 controls using Sequenom MassARRAY technology. The SPSS 16.0 software was used to perform statistical analyses. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by unconditional logistic regression, with adjustments for age and gender. In an analysis using an allelic model, we identified that the minor alleles of rs3756230 (OR = 0.64, 95%CI = 0.450-0.911, P = 0.013) and rs12498927 (OR = 1.377, 95%CI = 1.037-1.831, P = 0.027) were associated with gout risk. In addition, we found that the "A/A" genotype of rs12498927 was associated with increased risk of gout under codominant (OR = 2.22, 95%CI = 1.12- 4.40, P = 0.042) and recessive models (OR = 2.24, 95%CI = 1.20-4.17, P = 0.012). We also determined the "A/G" genotype of rs12498927 to be significantly associated with higher urea levels in gout patients (P = 0.017). Our data shed new light on the association between genetic variations in the WDR1 gene and gout susceptibility in the Han Chinese population.

  13. Selecting Operations for Assembler Encoding

    Directory of Open Access Journals (Sweden)

    Tomasz Praczyk

    2010-04-01

    Full Text Available Assembler Encoding is a neuro-evolutionary method in which a neural network is represented in the form of a simple program called Assembler Encoding Program. The task of the program is to create the so-called Network Definition Matrix which maintains all the information necessary to construct the network. To generate Assembler Encoding Programs and the subsequent neural networks evolutionary techniques are used.
    The performance of Assembler Encoding strongly depends on operations used in Assembler Encoding Programs. To select the most effective operations, experiments in the optimization and the predator-prey problem were carried out. In the experiments, Assembler Encoding Programs equipped with different types of operations were tested. The results of the tests are presented at the end of the paper.

  14. Biotic interactions and sunlight affect persistence of fecal indicator bacteria and microbial source tracking genetic markers in the Upper Mississippi River

    Science.gov (United States)

    Sanitary quality of recreational waters is assessed by enumerating fecal indicator bacteria (FIB) (Escherichia coli and enterococci); organisms present in the gastrointestinal tract of humans and many other animals, hence providing no information about the pollution source. Micro...

  15. Mouse Y-Encoded Transcription Factor Zfy2 Is Essential for Sperm Head Remodelling and Sperm Tail Development.

    Directory of Open Access Journals (Sweden)

    Nadege Vernet

    Full Text Available A previous study indicated that genetic information encoded on the mouse Y chromosome short arm (Yp is required for efficient completion of the second meiotic division (that generates haploid round spermatids, restructuring of the sperm head, and development of the sperm tail. Using mouse models lacking a Y chromosome but with varying Yp gene complements provided by Yp chromosomal derivatives or transgenes, we recently identified the Y-encoded zinc finger transcription factors Zfy1 and Zfy2 as the Yp genes promoting the second meiotic division. Using the same mouse models we here show that Zfy2 (but not Zfy1 contributes to the restructuring of the sperm head and is required for the development of the sperm tail. The preferential involvement of Zfy2 is consistent with the presence of an additional strong spermatid-specific promotor that has been acquired by this gene. This is further supported by the fact that promotion of sperm morphogenesis is also seen in one of the two markedly Yp gene deficient models in which a Yp deletion has created a Zfy2/1 fusion gene that is driven by the strong Zfy2 spermatid-specific promotor, but encodes a protein almost identical to that encoded by Zfy1. Our results point to there being further genetic information on Yp that also has a role in restructuring the sperm head.

  16. Improved humoral and cellular immune responses against the gp120 V3 loop of HIV-1 following genetic immunization with a chimeric DNA vaccine encoding the V3 inserted into the hepatitis B surface antigen

    DEFF Research Database (Denmark)

    Fomsgaard, A; Nielsen, H V; Bryder, K

    1998-01-01

    with the HIV MN gp160 envelope plasmid induced a slow and low titred anti-MN V3 antibody response at 12 weeks post-inoculation (p.i.) and a late appearing (7 weeks), weak and variable CTL response. In contrast, DNA vaccination with the HBsAg-encoding plasmid induced a rapid and high titred anti-HBsAg antibody...... response and a uniform strong anti-HBs CTL response already 1 week p.i. in all mice. DNA vaccination with the chimeric MN V3/HBsAg plasmid elicited humoral responses against both viruses within 3-6 weeks which peaked at 6-12 weeks and remained stable for at least 25 weeks. In addition, specific CTL......-2d-restricted cytotoxic T lymphocyte (CTL) epitope. In an attempt to improve the immunogenicity of V3 in DNA vaccines, a plasmid expressing MN V3 as a fusion protein with the highly immunogenic middle (pre-S2 + S) surface antigen of hepatitis B virus (HBsAg) was constructed. Epidermal inoculation...

  17. Improved humoral and cellular immune response against the gp120 V3 loop of HIV-1 following genetic immunization with a chimeric DNA vaccine encoding the V3 inserted into the hepatites B surface antigen

    DEFF Research Database (Denmark)

    Fomsgaard, A.; Nielsen, H.V.; Bryder, K.

    1998-01-01

    MN gp160 envelope plasmid induced a slow and low titred anti-MN V3 antibody response at 12 weeks post-inoculation (p.i.) and a late appearing (7 weeks), weak and variable CTL response. In contrast, DNA vaccination with the HBsAg-encoding plasmid induced a rapid and high titred anti-HBsAg antibody...... response and a uniform strong anti-HBs CTL response already 1 week p.i. in all mice. DNA vaccination with the chimeric MN V2/HBsAg plasmid elicited humoral responses against both viruses within 3-6 weeks which peaked at 6-12 weeks and remained stable for at least 25 weeks. In addition, specific CTL......-2d-restricted cytotoxic T lymphocyte (CTL) epitope. In an attempt to improve the immunogenicity of V3 in DNA vaccines, a plasmid expressing MN V3 as a fusion protein with the highly immunogenic middle (pre-S2+S) surface antigen of hepatitis B virus (HBsAg) was constructed. Epidermal inoculation...

  18. Cache directory lookup reader set encoding for partial cache line speculation support

    Science.gov (United States)

    Gara, Alan; Ohmacht, Martin

    2014-10-21

    In a multiprocessor system, with conflict checking implemented in a directory lookup of a shared cache memory, a reader set encoding permits dynamic recordation of read accesses. The reader set encoding includes an indication of a portion of a line read, for instance by indicating boundaries of read accesses. Different encodings may apply to different types of speculative execution.

  19. Genetic evidence for host specificity in the adhesin-encoding genes hxaA of Helicobacter acinonyx, hnaA of H. nemestrinae and hpaA of H. pylori.

    Science.gov (United States)

    Evans, D G; Lampert, H C; Nakano, H; Eaton, K A; Burnens, A P; Bronsdon, M A; Evans, D J

    1995-09-22

    Gastric and non-gastric species of Helicobacter were examined for the presence of the adhesin-encoding gene, hpaA, from the human-associated gastric Helicobacter H. pylori (Hp), and for adhesin subunit protein HpaA. Amplification of a 375-bp internal DNA fragment of hpaA by PCR demonstrated the presence of the gene in Hp and in two closely related gastric Helicobacters, H. nemestrinae (Hn) and H. acinonyx (Hx), but not in the more distantly related H. felis (Hf) and H. mustelae (Hm). The non-gastric Helicobacters, H. canis (Hc), H. muridarum (Hr), H. fennelliae (He) and H. cinaedi (Hi), were all negative for hpaA. An immunoblot assay of water extracts with adhesin-specific antibody confirmed these results. The deduced amino acid (aa) sequences of Hp HpaA and Hn adhesin A (hereafter termed HnaA) are very similar, having identical receptor-binding motifs (rbm); also, the hemagglutination (HA) properties of Hn and Hp cells were indistinguishable. In contrast, the rbm of Hx adhesin A (hereafter termed HxaA), compared to that of Hp, contained a non-conservative aa substitution (Ile to Thr); also, there was variance in five consecutive aa from 10 to 14 residues upstream from the rbm. We conclude that these aa substitutions in HxaA are probably responsible for the difference in receptor recognition of this adhesin, as evidenced by the resistance of Hx HA to inhibition with N-acetylneuraminyl-alpha(2,3)-lactose. These results are consistent with the biological similarity between the natural host(s) of Hp and Hn; i.e., human and non-human primates, and the dissimilarity between these hosts and the feline host, the cheetah.

  20. Effects of genetically modified Bt maize on growth performance and organ indices in growing Wuzhishan pigs%转Bt玉米对生长期五指山猪生长性能及器官指数的影响

    Institute of Scientific and Technical Information of China (English)

    孙哲; 刘圈炜; 谭树义; 杨晓光; 张宏福

    2013-01-01

    为研究转Bt玉米对五指山猪生长性能及器官指数的影响,评价其饲用安全性,选取2月龄遗传背景相近、初始体重(9.80± 0.41)kg、健康断奶五指山猪72头,随机分为2处理组,每个处理6个重复,每个重复6头.分别饲喂含转Bt玉米(试验组)和非转基因玉米(对照组)的日粮.试验为期68 d,于68 d屠宰取样.结果表明:①试验组的末重、平均日增重、平均日采食量及料重比均与对照组间差异不显著(P>0.05);②两组的器官指数间也未达到显著差异的水平(P>0.05).结果提示,转Bt玉米对生长期五指山猪的生长性能和器官指数未产生不良影响.%In order to investigate the influences of genetically modified Bt maize on growth performance and organ indices of growing Wuzhishan pigs and to evaluate the safety, seventy-two 2-month-old healthy weaning pigs with average initial weight of (9.80±0.41) kg and the similar genetic backgrounds were randomly divided into two treatments, 6 replicates of 6 pigs each. Pigs were fed with diets containing genetically modified Bt maize (experimental group) or non-genetically modified maize (control one) during the period of 68 days, respectively. Pigs were slaughtered on 68 d for sampling. The results showed that: ①final weight, average daily gain, average daily feed intake and feed/gain ratio of experimental group were not significantly different from those of control one (P>0.05); ②there were no significant differences in organ indices between the two groups (P>0.05). In conclusion, there were no adverse effects of genetically modified Bt maize on growth performance and organ indices of growing Wuzhishan pigs.

  1. Genetic association and gene-smoking interaction study of carotid intima-media thickness at five GWAS-indicated genes: the Bogalusa Heart Study.

    Science.gov (United States)

    Li, Changwei; Chen, Wei; Jiang, Fan; Simino, Jeannette; Srinivasan, Sathanur R; Berenson, Gerald S; Mei, Hao

    2015-05-15

    To examine the associations of five GWAS-identified genes with carotid intima-media thickness (IMT) in a biracial sample from the Bogalusa Heart Study, and evaluate their participation in gene-smoking interactions. Far wall IMTs of common carotid arteries were measured using high-resolution B-mode ultrasound. Both the gene-smoking interactions and single-marker associations were evaluated by linear models of carotid IMT levels, while the gene-based analyses were assessed through the truncated product method. A Bonferroni multiple testing correction was applied. Marker rs7840785 (PINX1) was significantly associated with right carotid IMT (p=0.0003) using all participants; mean levels for the CC, TC, and TT genotypes were 0.74 (0.73 to 0.75), 0.76 (0.75 to 0.78), and 0.78 (0.75, 0.81), respectively. Similar trends were observed in blacks (p=0.0031) and whites (p=0.0118). Marker rs7844465 (ZHX2) was significantly associated with left carotid IMT in whites (p=0.0005); mean IMT levels for the GG, TG, and TT genotypes were 0.73 (0.71 to 0.74), 0.75 (0.74 to 0.77) and 0.78 (0.75 to 0.81), respectively. Marker rs6841473 (EDNRA) modified the association between smoking and left carotid IMT in blacks (p=2.79×10(-5)). In addition, gene-based analysis demonstrated that EDNRA and ZHX2 were associated with left carotid IMT in the white and overall participants, respectively, while PINX1 was associated with right carotid IMT in both blacks and whites. We identified two novel markers that were associated with IMT in both blacks and whites. One gene-smoking interaction was identified in blacks only. Three genes showed gene-based associations with IMT levels. However, genetic markers with small effects may have been missed due to the limited number of black participants. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Genetic determination of fast plasma glucose concentration and correlation with anthropometric indices%空腹血糖的遗传率及其与人体测量学指标的遗传相关分析

    Institute of Scientific and Technical Information of China (English)

    简蔚霞; 苏青; 罗敏

    2009-01-01

    Objective To study the genetic determination of fast plasma glucose (FPG) and correlation with its potential correlated traits, anthropometric measures and blood pressure. Methods Two hundred and eighteen Type 2 diabetes mellitus(T2DM) pedigrees composed of 1383 Chinese Han individuals residing in the East and South-East China were analyzed. Univariate variance decomposition analyses were used to estimate the narrow-sense heritability (h2) of FPG, anthropometric indices and blood pressure, and bivariate quantitative genetic analyses were used to estimate the genetic and environmental correlations between FPG and anthropometric measures or blood pressure. Results We found that FPG, blood pressure and all anthropometric indices except for waist to hip ratio were under significant genetic determination, and the h2 was from 0.28 to 0.43. We did not find significant genetic and environmental correlation between FPG and anthropometric indices and blood pressure. Conclusion The present study demonstrated that T2DM, obesity and hypertension were controlled by some genetic factors, and FPG shares little common genetic and environmental factors with obesity-related anthropometric indices and blood pressure in our Chinese sample population.%目的 研究空腹血糖的遗传率及其与肥胖相关人体测量学指标和血压的遗传相关.方法 分析由1383个个体组成的218个2型糖尿病家系,采用单变量方差分解分析估计空腹血糖,人体测量学指标和血压的狭义遗传率(h2),双变量数量性状遗传分析估计空腹血糖和人体测量学指标及血压间的遗传及环境相关.结果 空腹血糖,血压和除腰臀比之外的人体测量学指标都受显著的遗传决定作用,h的范围为0.28~0.43.空腹血糖与肥胖相关人体测量学指标等数量性状之间的遗传或环境相关分析未发现显著结果.结论 本研究结果表明2型糖尿病,高血压和肥胖为一定的遗传因素所控制,而空腹血糖与

  3. Genetics of Hereditary Angioedema Revisited.

    Science.gov (United States)

    Germenis, Anastasios E; Speletas, Matthaios

    2016-10-01

    Contemporary genetic research has provided evidences that angioedema represents a diverse family of disorders related to kinin metabolism, with a much greater genetic complexity than was initially considered. Convincing data have also recently been published indicating that the clinical heterogeneity of hereditary angioedema due to C1 inhibitor deficiency (classified as C1-INH-HAE) could be attributed at least in part, either to the type of SERPING1 mutations or to mutations in genes encoding for enzymes involved in the metabolism and function of bradykinin. Alterations detected in at least one more gene (F12) are nowadays considered responsible for 25 % of cases of hereditary angioedema with normal C1-INH (type III hereditary angioedema (HAE), nlC1-INH-HAE). Interesting data derived from genetic approaches of non-hereditary angioedemas indicate that other immune pathways might be implicated in the pathogenesis of HAE. More than 125 years after the recognition of the hereditary nature of HAE by Osler, the heterogeneity of clinical expressions, the genetics of this disorder, and the genotype-phenotype relationships, still presents a challenge that will be discussed in this review. Large scale, in-depth genetic studies are expected not only to answer these emerging questions but also to further elucidate many of the unmet aspects of angioedema pathogenesis. Uncovering genetic biomarkers affecting the severity of the disease and/or the effectiveness of the various treatment modalities might lead to the prevention of attacks and the optimization of C1-INH-HAE management that is expected to provide a valuable benefit to the sufferers of angioedema.

  4. Genetic algorithms as global random search methods

    Science.gov (United States)

    Peck, Charles C.; Dhawan, Atam P.

    1995-01-01

    Genetic algorithm behavior is described in terms of the construction and evolution of the sampling distributions over the space of candidate solutions. This novel perspective is motivated by analysis indicating that the schema theory is inadequate for completely and properly explaining genetic algorithm behavior. Based on the proposed theory, it is argued that the similarities of candidate solutions should be exploited directly, rather than encoding candidate solutions and then exploiting their similarities. Proportional selection is characterized as a global search operator, and recombination is characterized as the search process that exploits similarities. Sequential algorithms and many deletion methods are also analyzed. It is shown that by properly constraining the search breadth of recombination operators, convergence of genetic algorithms to a global optimum can be ensured.

  5. PNA-encoded chemical libraries.

    Science.gov (United States)

    Zambaldo, Claudio; Barluenga, Sofia; Winssinger, Nicolas

    2015-06-01

    Peptide nucleic acid (PNA)-encoded chemical libraries along with DNA-encoded libraries have provided a powerful new paradigm for library synthesis and ligand discovery. PNA-encoding stands out for its compatibility with standard solid phase synthesis and the technology has been used to prepare libraries of peptides, heterocycles and glycoconjugates. Different screening formats have now been reported including selection-based and microarray-based methods that have yielded specific ligands against diverse target classes including membrane receptors, lectins and challenging targets such as Hsp70.

  6. Genetic Diversity of the fliC Genes Encoding the Flagellar Antigen H19 of Escherichia coli and Application to the Specific Identification of Enterohemorrhagic E. coli O121:H19.

    Science.gov (United States)

    Beutin, Lothar; Delannoy, Sabine; Fach, Patrick

    2015-06-15

    Enterohemorrhagic Escherichia coli (EHEC) O121:H19 belong to a specific clonal type distinct from other classical EHEC and major enteropathogenic E. coli groups and is regarded as one of the major EHEC serogroups involved in severe infections in humans. Sequencing of the fliC genes associated with the flagellar antigen H19 (fliCH19) revealed the genetic diversity of the fliCH19 gene sequences in E. coli. A cluster analysis of 12 fliCH19 sequences, 4 from O121 and 8 from non-O121 E. coli strains, revealed five different genotypes. All O121:H19 strains fell into one cluster, whereas a second cluster was formed by five non-O121:H19 strains. Cluster 1 and cluster 2 strains differ by 27 single nucleotide exchanges in their fliCH19 genes (98.5% homology). Based on allele discrimination of the fliCH19 genes, a real-time PCR test was designed for specific identification of EHEC O121:H19. The O121 fliCH19 PCR tested negative in 73 E. coli H19 strains that belonged to serogroups other than O121, including 28 different O groups, O-nontypeable H19, and O-rough:H19 strains. The O121 fliCH19 PCR reacted with all 16 tested O121:H19 strains and 1 O-rough:H19 strain which was positive for the O121 wzx gene. A cross-reaction was observed only with E. coli H32 strains which share sequence similarities in the target region of the O121 fliCH19 PCR. The combined use of O-antigen genotyping (O121 wzx) and the detection of O121 fliCH19 allele type contributes to improving the identification and molecular serotyping of EHEC O121:H19 motile and nonmotile strains and variants of these strains lacking stx genes.

  7. Genetically-Encoded Photocrosslinkers Determine the Biological Binding Site of Exendin-4 in the N-Terminal Domain of the Intact Human Glucagon-Like Peptide-1 Receptor (GLP-1R).

    Science.gov (United States)

    Koole, Cassandra; Reynolds, Christopher A; Mobarec, Juan C; Hick, Caroline; Sexton, Patrick M; Sakmar, Thomas P

    2017-03-10

    The glucagon-like peptide-1 receptor (GLP-1R) is a key therapeutic target in the management of type II diabetes mellitus, with actions including regulation of insulin biosynthesis and secretion, promotion of satiety and preservation of β-cell mass. Like most class B G protein-coupled receptors (GPCRs), there is limited knowledge linking biological activity of the GLP-1R with the molecular structure of an intact, full-length, functional receptor-ligand complex. In this study, we have utilized genetic code expansion to site-specifically incorporate the photoactive amino acid p-azido-L-phenylalanine (azF) into N-terminal residues of a full-length, functional human GLP-1R in mammalian cells. UV-mediated photolysis of azF was then carried out to induce targeted photocrosslinking to determine the proximity of the azido group in the mutant receptor with the peptide exendin-4. Crosslinking data were compared directly to the crystal structure of the isolated N-terminal extracellular domain (ECD) of the GLP-1R in complex with exendin(9-39), revealing both similarities as well as distinct differences in the mode of interaction. Generation of a molecular model to accommodate the photocrosslinking constraints highlights the potential influence of environmental conditions on the conformation of the receptor-peptide complex, including folding dynamics of the peptide and formation of dimeric and higher order oligomeric receptor multimers. These data demonstrate that crystal structures of isolated receptor regions may not give a complete reflection of peptide-receptor interactions, and should be combined with additional experimental constraints to reveal peptide-receptor interactions occurring in the dynamic, native, full-length receptor state.

  8. Compressed Encoding for Rank Modulation

    CERN Document Server

    Gad, Eyal En; Jiang,; Bruck, Jehoshua

    2011-01-01

    Rank modulation has been recently proposed as a scheme for storing information in flash memories. While rank modulation has advantages in improving write speed and endurance, the current encoding approach is based on the "push to the top" operation that is not efficient in the general case. We propose a new encoding procedure where a cell level is raised to be higher than the minimal necessary subset - instead of all - of the other cell levels. This new procedure leads to a significantly more compressed (lower charge levels) encoding. We derive an upper bound for a family of codes that utilize the proposed encoding procedure, and consider code constructions that achieve that bound for several special cases.

  9. Cell encoding recombinant human erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Beck, A.K.; Withy, R.M.; Zabrecky, J.R.; Masiello, N.C.

    1990-09-04

    This patent describes a C127 cell transformed with a recombinant DNA vector. It comprises: a DNA sequence encoding human erythropoietin, the transformed cell being capable of producing N-linked and O-linked glycosylated human erythropoietin.

  10. Self-Organising Stochastic Encoders

    CERN Document Server

    Luttrell, Stephen

    2010-01-01

    The processing of mega-dimensional data, such as images, scales linearly with image size only if fixed size processing windows are used. It would be very useful to be able to automate the process of sizing and interconnecting the processing windows. A stochastic encoder that is an extension of the standard Linde-Buzo-Gray vector quantiser, called a stochastic vector quantiser (SVQ), includes this required behaviour amongst its emergent properties, because it automatically splits the input space into statistically independent subspaces, which it then separately encodes. Various optimal SVQs have been obtained, both analytically and numerically. Analytic solutions which demonstrate how the input space is split into independent subspaces may be obtained when an SVQ is used to encode data that lives on a 2-torus (e.g. the superposition of a pair of uncorrelated sinusoids). Many numerical solutions have also been obtained, using both SVQs and chains of linked SVQs: (1) images of multiple independent targets (encod...

  11. Genetic Diversity of the fliC Genes Encoding the Flagellar Antigen H19 of Escherichia coli and Application to the Specific Identification of Enterohemorrhagic E. coli O121:H19

    Science.gov (United States)

    Beutin, Lothar; Delannoy, Sabine

    2015-01-01

    Enterohemorrhagic Escherichia coli (EHEC) O121:H19 belong to a specific clonal type distinct from other classical EHEC and major enteropathogenic E. coli groups and is regarded as one of the major EHEC serogroups involved in severe infections in humans. Sequencing of the fliC genes associated with the flagellar antigen H19 (fliCH19) revealed the genetic diversity of the fliCH19 gene sequences in E. coli. A cluster analysis of 12 fliCH19 sequences, 4 from O121 and 8 from non-O121 E. coli strains, revealed five different genotypes. All O121:H19 strains fell into one cluster, whereas a second cluster was formed by five non-O121:H19 strains. Cluster 1 and cluster 2 strains differ by 27 single nucleotide exchanges in their fliCH19 genes (98.5% homology). Based on allele discrimination of the fliCH19 genes, a real-time PCR test was designed for specific identification of EHEC O121:H19. The O121 fliCH19 PCR tested negative in 73 E. coli H19 strains that belonged to serogroups other than O121, including 28 different O groups, O-nontypeable H19, and O-rough:H19 strains. The O121 fliCH19 PCR reacted with all 16 tested O121:H19 strains and 1 O-rough:H19 strain which was positive for the O121 wzx gene. A cross-reaction was observed only with E. coli H32 strains which share sequence similarities in the target region of the O121 fliCH19 PCR. The combined use of O-antigen genotyping (O121 wzx) and the detection of O121 fliCH19 allele type contributes to improving the identification and molecular serotyping of EHEC O121:H19 motile and nonmotile strains and variants of these strains lacking stx genes. PMID:25862232

  12. Surfactant Protein-D-Encoding Gene Variant Polymorphisms Are Linked to Respiratory Outcome in Premature Infants

    DEFF Research Database (Denmark)

    Sorensen, Grith Lykke; Dahl, Marianne; Tan, Qihua

    2014-01-01

    OBJECTIVE: Associations between the genetic variation within or downstream of the surfactant protein-D-encoding gene (SFTPD), which encodes the collectin surfactant protein-D (SP-D) and may lead to respiratory distress syndrome or bronchopulmonary dysplasia, recently were reported. Our aim was to...

  13. Incidental and intentional encoding in young and elderly adults.

    Science.gov (United States)

    Téllez-Alanís, Bernarda; Cansino, Selene

    2004-08-06

    Event-related potentials (ERPs) were recorded in young and elderly adults during the performance of an incidental encoding task (subjects were unexpectedly given a recognition test) followed by an intentional task (subjects expected the recognition test). Both tasks consisted of an encoding stage in which subjects classified words (natural/artificial) and a recognition stage in which they indicated whether the words were old (presented during the encoding stage) or new. In both groups and tasks, the ERPs, during encoding, differed as a function of subsequent recognition: the old words correctly recognized generated greater amplitude potentials than the incorrect ones. The memory processes expressed by these ERPs are preserved in elderly adults, independently of whether the information is incidentally or intentionally encoded.

  14. Bacillus caldolyticus prs gene encoding phosphoribosyldiphosphate synthase

    DEFF Research Database (Denmark)

    Krath, Britta N.; Hove-Jensen, Bjarne

    1996-01-01

    The prs gene, encoding phosphoribosyl-diphosphate (PRPP) synthase, as well as the flanking DNA sequences were cloned and sequenced from the Gram-positive thermophile, Bacillus caldolyticus. Comparison with the homologous sequences from the mesophile, Bacillus subtilis, revealed a gene (gca......D) encoding N-acetylglucosamine-l-phosphate uridyltransferase upstream of prs, and a gene homologous to ctc downstream of prs. cDNA synthesis with a B. caldolyticus gcaD-prs-ctc-specified mRNA as template, followed by amplification utilising the polymerase chain reaction indicated that the three genes are co......-transcribed. Comparison of amino acid sequences revealed a high similarity among PRPP synthases across a wide phylogenetic range. An E. coli strain harbouring the B. caldolyticus prs gene in a multicopy plasmid produced PRPP synthase activity 33-fold over the activity of a haploid B. caldolyticus strain. B. caldolyticus...

  15. Research on a novel orientation algorithm of single-ring absolute photoelectric shaft encoder

    Institute of Scientific and Technical Information of China (English)

    CHEN Yun

    2007-01-01

    A novel single-ring absolute optical shaft encoder is designed by studying the encoding principle of traditional absolute optical shaft encoder in this paper. The description of the orientation algorithm of the encoder is specified,and an example for explaining the orientation arithmetic is given,which indicates that the theory of the encoder works. The visual interface to acquire signals of CCD is shown with VB,which provides reliable foundation to process data. The effective factors of measurement precision of the encoder are analyzed.

  16. Dissociative effects of true and false recall as a function of different encoding strategies.

    Science.gov (United States)

    Goodwin, Kerri A

    2007-01-01

    Goodwin, Meissner, and Ericsson (2001) proposed a path model in which elaborative encoding predicted the likelihood of verbalisation of critical, nonpresented words at encoding, which in turn predicted the likelihood of false recall. The present study tested this model of false recall experimentally with a manipulation of encoding strategy and the implementation of the process-tracing technique of protocol analysis. Findings indicated that elaborative encoding led to more verbalisations of critical items during encoding than rote rehearsal of list items, but false recall rates were reduced under elaboration conditions (Experiment 2). Interestingly, false recall was more likely to occur when items were verbalised during encoding than not verbalised (Experiment 1), and participants tended to reinstate their encoding strategies during recall, particularly after elaborative encoding (Experiment 1). Theoretical implications for the interplay of encoding and retrieval processes of false recall are discussed.

  17. Complementation of a phycocyanin-bilin lyase from Synechocystis sp. PCC 6803 with a nucleomorph-encoded open reading frame from the cryptophyte Guillardia theta

    Directory of Open Access Journals (Sweden)

    Nyalwidhe Julius

    2008-05-01

    Full Text Available Abstract Background Cryptophytes are highly compartmentalized organisms, expressing a secondary minimized eukaryotic genome in the nucleomorph and its surrounding remnant cytoplasm, in addition to the cell nucleus, the mitochondrion and the plastid. Because the members of the nucleomorph-encoded proteome may contribute to essential cellular pathways, elucidating nucleomorph-encoded functions is of utmost interest. Unfortunately, cryptophytes are inaccessible for genetic transformations thus far. Therefore the functions of nucleomorph-encoded proteins must be elucidated indirectly by application of methods in genetically accessible organisms. Results Orf222, one of the uncharacterized nucleomorph-specific open reading frames of the cryptophyte Guillardia theta, shows homology to slr1649 of Synechocystis sp. PCC 6803. Recently a further homolog from Synechococcus sp. PCC 7002 was characterized to encode a phycocyanin-β155-bilin lyase. Here we show by insertion mutagenesis that the Synechocystis sp. PCC 6803 slr1649-encoded protein also acts as a bilin lyase, and additionally contributes to linker attachment and/or stability of phycobilisomes. Finally, our results indicate that the phycocyanin-β155-bilin lyase of Synechocystis sp. PCC 6803 can be complemented in vivo by the nucleomorph-encoded open reading frame orf222. Conclusion Our data show that the loss of phycocyanin-lyase function causes pleiotropic effects in Synechocystis sp. PCC 6803 and indicate that after separating from a common ancestor protein, the phycoerythrin lyase from Guillardia theta has retained its capacity to couple a bilin group to other phycobiliproteins. This is a further, unexpected example of the universality of phycobiliprotein lyases.

  18. CARB-9, a Carbenicillinase Encoded in the VCR Region of Vibrio cholerae Non-O1, Non-O139 Belongs to a Family of Cassette-Encoded β-Lactamases†

    OpenAIRE

    Petroni, Alejandro; Melano, Roberto G.; Saka, Héctor A.; Garutti, Alicia; Mange, Laura; Pasterán, Fernando; Rapoport, Melina; Miranda, Mariana; Faccone, Diego; Rossi, Alicia; Hoffman, Paul S.; Galas, Marcelo F.

    2004-01-01

    The gene blaCARB-9 was located in the Vibrio cholerae super-integron, but in a different location relative to blaCARB-7. CARB-9 (pI 5.2) conferred β-lactam MICs four to eight times lower than those conferred by CARB-7, differing at Ambler's positions V97I, L124F, and T228K. Comparison of the genetic environments of all reported blaCARB genes indicated that the CARB enzymes constitute a family of cassette-encoded β-lactamases.

  19. CARB-9, a Carbenicillinase Encoded in the VCR Region of Vibrio cholerae Non-O1, Non-O139 Belongs to a Family of Cassette-Encoded β-Lactamases†

    Science.gov (United States)

    Petroni, Alejandro; Melano, Roberto G.; Saka, Héctor A.; Garutti, Alicia; Mange, Laura; Pasterán, Fernando; Rapoport, Melina; Miranda, Mariana; Faccone, Diego; Rossi, Alicia; Hoffman, Paul S.; Galas, Marcelo F.

    2004-01-01

    The gene blaCARB-9 was located in the Vibrio cholerae super-integron, but in a different location relative to blaCARB-7. CARB-9 (pI 5.2) conferred β-lactam MICs four to eight times lower than those conferred by CARB-7, differing at Ambler's positions V97I, L124F, and T228K. Comparison of the genetic environments of all reported blaCARB genes indicated that the CARB enzymes constitute a family of cassette-encoded β-lactamases. PMID:15388476

  20. Multidimensionally encoded magnetic resonance imaging.

    Science.gov (United States)

    Lin, Fa-Hsuan

    2013-07-01

    Magnetic resonance imaging (MRI) typically achieves spatial encoding by measuring the projection of a q-dimensional object over q-dimensional spatial bases created by linear spatial encoding magnetic fields (SEMs). Recently, imaging strategies using nonlinear SEMs have demonstrated potential advantages for reconstructing images with higher spatiotemporal resolution and reducing peripheral nerve stimulation. In practice, nonlinear SEMs and linear SEMs can be used jointly to further improve the image reconstruction performance. Here, we propose the multidimensionally encoded (MDE) MRI to map a q-dimensional object onto a p-dimensional encoding space where p > q. MDE MRI is a theoretical framework linking imaging strategies using linear and nonlinear SEMs. Using a system of eight surface SEM coils with an eight-channel radiofrequency coil array, we demonstrate the five-dimensional MDE MRI for a two-dimensional object as a further generalization of PatLoc imaging and O-space imaging. We also present a method of optimizing spatial bases in MDE MRI. Results show that MDE MRI with a higher dimensional encoding space can reconstruct images more efficiently and with a smaller reconstruction error when the k-space sampling distribution and the number of samples are controlled.

  1. Waste indicators

    Energy Technology Data Exchange (ETDEWEB)

    Dall, O.; Lassen, C.; Hansen, E. [Cowi A/S, Lyngby (Denmark)

    2003-07-01

    The Waste Indicator Project focuses on methods to evaluate the efficiency of waste management. The project proposes the use of three indicators for resource consumption, primary energy and landfill requirements, based on the life-cycle principles applied in the EDIP Project. Trial runs are made With the indicators on paper, glass packaging and aluminium, and two models are identified for mapping the Danish waste management, of which the least extensive focuses on real and potential savings. (au)

  2. Quality indicators

    DEFF Research Database (Denmark)

    Hjorth-Andersen, Christian

    1991-01-01

    In recent literature it has been suggested that consumers need have no knowledge of product quality as a number of quality indicators (or signals) may be used as substitutes. Very little attention has been paid to the empirical verification of these studies. The present paper is devoted...... to the issue of how well these indicators perform, using market data provided by consumer magazines from 3 countries. The results strongly indicate that price is a poor quality indicator. The paper also presents some evidence which suggests that seller reputation and easily observable characteristics are also...

  3. Genetic basis of chronic pancreatitis

    NARCIS (Netherlands)

    Jansen, JBMJ; Morsche, RT; van Goor, Harry; Drenth, JPH

    2002-01-01

    Background: Pancreatitis has a proven genetic basis in a minority of patients. Methods: Review of the literature on genetics of pancreatitis. Results: Ever since the discovery that in most patients with hereditary pancreatitis a mutation in the gene encoding for cationic trypsinogen (R122H) was

  4. Genetic basis of chronic pancreatitis

    NARCIS (Netherlands)

    Jansen, JBMJ; Morsche, RT; van Goor, Harry; Drenth, JPH

    2002-01-01

    Background: Pancreatitis has a proven genetic basis in a minority of patients. Methods: Review of the literature on genetics of pancreatitis. Results: Ever since the discovery that in most patients with hereditary pancreatitis a mutation in the gene encoding for cationic trypsinogen (R122H) was foun

  5. Constraints on the Genetic and Antigenic Variability of Measles Virus.

    Science.gov (United States)

    Beaty, Shannon M; Lee, Benhur

    2016-04-21

    Antigenic drift and genetic variation are significantly constrained in measles virus (MeV). Genetic stability of MeV is exceptionally high, both in the lab and in the field, and few regions of the genome allow for rapid genetic change. The regions of the genome that are more tolerant of mutations (i.e., the untranslated regions and certain domains within the N, C, V, P, and M proteins) indicate genetic plasticity or structural flexibility in the encoded proteins. Our analysis reveals that strong constraints in the envelope proteins (F and H) allow for a single serotype despite known antigenic differences among its 24 genotypes. This review describes some of the many variables that limit the evolutionary rate of MeV. The high genomic stability of MeV appears to be a shared property of the Paramyxovirinae, suggesting a common mechanism that biologically restricts the rate of mutation.

  6. Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins

    Directory of Open Access Journals (Sweden)

    Cai Hong

    2010-06-01

    Full Text Available Abstract Background Species of the family Vibrionaceae are ubiquitous in marine environments. Several of these species are important pathogens of humans and marine species. Evidence indicates that genetic exchange plays an important role in the emergence of new pathogenic strains within this family. Data from the sequenced genomes of strains in this family could show how the genes encoded by all these strains, known as the pangenome, are distributed. Information about the core, accessory and panproteome of this family can show how, for example, genes encoding virulence-associated proteins are distributed and help us understand how virulence emerges. Results We deduced the complete set of orthologs for eleven strains from this family. The core proteome consists of 1,882 orthologous groups, which is 28% of the 6,629 orthologous groups in this family. There were 4,411 accessory orthologous groups (i.e., proteins that occurred in from 2 to 10 proteomes and 5,584 unique proteins (encoded once on only one of the eleven genomes. Proteins that have been associated with virulence in V. cholerae were widely distributed across the eleven genomes, but the majority was found only on the genomes of the two V. cholerae strains examined. Conclusions The proteomes are reflective of the differing evolutionary trajectories followed by different strains to similar phenotypes. The composition of the proteomes supports the notion that genetic exchange among species of the Vibrionaceae is widespread and that this exchange aids these species in adapting to their environments.

  7. Virally encoded 7TM receptors

    DEFF Research Database (Denmark)

    Rosenkilde, M M; Waldhoer, M; Lüttichau, H R

    2001-01-01

    A number of herpes- and poxviruses encode 7TM G-protein coupled receptors most of which clearly are derived from their host chemokine system as well as induce high expression of certain 7TM receptors in the infected cells. The receptors appear to be exploited by the virus for either immune evasion...... in various parts of the viral life cyclus. Most of the receptors encoded by human pathogenic virus are still orphan receptors, i.e. the endogenous ligand is unknown. In the few cases where it has been possible to characterize these receptors pharmacologically, they have been found to bind a broad spectrum...... expression of this single gene in certain lymphocyte cell lineages leads to the development of lesions which are remarkably similar to Kaposi's sarcoma, a human herpesvirus 8 associated disease. Thus, this and other virally encoded 7TM receptors appear to be attractive future drug targets....

  8. An expansive human regulatory lexicon encoded in transcription factor footprints.

    Science.gov (United States)

    Neph, Shane; Vierstra, Jeff; Stergachis, Andrew B; Reynolds, Alex P; Haugen, Eric; Vernot, Benjamin; Thurman, Robert E; John, Sam; Sandstrom, Richard; Johnson, Audra K; Maurano, Matthew T; Humbert, Richard; Rynes, Eric; Wang, Hao; Vong, Shinny; Lee, Kristen; Bates, Daniel; Diegel, Morgan; Roach, Vaughn; Dunn, Douglas; Neri, Jun; Schafer, Anthony; Hansen, R Scott; Kutyavin, Tanya; Giste, Erika; Weaver, Molly; Canfield, Theresa; Sabo, Peter; Zhang, Miaohua; Balasundaram, Gayathri; Byron, Rachel; MacCoss, Michael J; Akey, Joshua M; Bender, M A; Groudine, Mark; Kaul, Rajinder; Stamatoyannopoulos, John A

    2012-09-06

    Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency.

  9. Imaging the nanomolar range of nitric oxide with an amplifier-coupled fluorescent indicator in living cells

    Science.gov (United States)

    Sato, Moritoshi; Hida, Naoki; Umezawa, Yoshio

    2005-10-01

    Nitric oxide (NO) is a small uncharged free radical that is involved in diverse physiological and pathophysiological mechanisms. NO is generated by three isoforms of NO synthase, endothelial, neuronal, and inducible ones. When generated in vascular endothelial cells, NO plays a key role in vascular tone regulation, in particular. Here, we describe an amplifier-coupled fluorescent indicator for NO to visualize physiological nanomolar dynamics of NO in living cells (detection limit of 0.1 nM). This genetically encoded high-sensitive indicator revealed that 1 nM of NO, which is enough to relax blood vessels, is generated in vascular endothelial cells even in the absence of shear stress. The nanomolar range of basal endothelial NO thus revealed appears to be fundamental to vascular homeostasis. fluorescence resonance energy transfer | genetic encoding

  10. Next-generation genomic shotgun sequencing indicates greater genetic variability in the mitochondria of Hypophthalmichthys molitrix relative to H. nobilis from the Mississippi River, USA and provides tools for research and detection

    Science.gov (United States)

    Miller, John J; Eackles, Michael S.; Stauffer, Jay R; King, Timothy L.

    2015-01-01

    We characterized variation within the mitochondrial genomes of the invasive silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis) from the Mississippi River drainage by mapping our Next-Generation sequences to their publicly available genomes. Variant detection resulted in 338 single-nucleotide polymorphisms for H. molitrix and 39 for H. nobilis. The much greater genetic variation in H. molitrix mitochondria relative to H. nobilis may be indicative of a greater North American female effective population size of the former. When variation was quantified by gene, many tRNA loci appear to have little or no variability based on our results whereas protein-coding regions were more frequently polymorphic. These results provide biologists with additional regions of DNA to be used as markers to study the invasion dynamics of these species.

  11. Genetic elements of plant viruses as tools for genetic engineering.

    OpenAIRE

    Mushegian, A R; Shepherd, R J

    1995-01-01

    Viruses have developed successful strategies for propagation at the expense of their host cells. Efficient gene expression, genome multiplication, and invasion of the host are enabled by virus-encoded genetic elements, many of which are well characterized. Sequences derived from plant DNA and RNA viruses can be used to control expression of other genes in vivo. The main groups of plant virus genetic elements useful in genetic engineering are reviewed, including the signals for DNA-dependent a...

  12. Genetically Engineered Cyanobacteria

    Science.gov (United States)

    Zhou, Ruanbao (Inventor); Gibbons, William (Inventor)

    2015-01-01

    The disclosed embodiments provide cyanobacteria spp. that have been genetically engineered to have increased production of carbon-based products of interest. These genetically engineered hosts efficiently convert carbon dioxide and light into carbon-based products of interest such as long chained hydrocarbons. Several constructs containing polynucleotides encoding enzymes active in the metabolic pathways of cyanobacteria are disclosed. In many instances, the cyanobacteria strains have been further genetically modified to optimize production of the carbon-based products of interest. The optimization includes both up-regulation and down-regulation of particular genes.

  13. Solar Indices

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Collection includes a variety of indices related to solar activity contributed by a number of national and private solar observatories located worldwide. This...

  14. PKCα is genetically linked to memory capacity in healthy subjects and to risk for posttraumatic stress disorder in genocide survivors.

    Science.gov (United States)

    de Quervain, Dominique J-F; Kolassa, Iris-Tatjana; Ackermann, Sandra; Aerni, Amanda; Boesiger, Peter; Demougin, Philippe; Elbert, Thomas; Ertl, Verena; Gschwind, Leo; Hadziselimovic, Nils; Hanser, Edveena; Heck, Angela; Hieber, Petra; Huynh, Kim-Dung; Klarhöfer, Markus; Luechinger, Roger; Rasch, Björn; Scheffler, Klaus; Spalek, Klara; Stippich, Christoph; Vogler, Christian; Vukojevic, Vanja; Stetak, Attila; Papassotiropoulos, Andreas

    2012-05-29

    Strong memory of a traumatic event is thought to contribute to the development and symptoms of posttraumatic stress disorder (PTSD). Therefore, a genetic predisposition to build strong memories could lead to increased risk for PTSD after a traumatic event. Here we show that genetic variability of the gene encoding PKCα (PRKCA) was associated with memory capacity--including aversive memory--in nontraumatized subjects of European descent. This finding was replicated in an independent sample of nontraumatized subjects, who additionally underwent functional magnetic resonance imaging (fMRI). fMRI analysis revealed PRKCA genotype-dependent brain activation differences during successful encoding of aversive information. Further, the identified genetic variant was also related to traumatic memory and to the risk for PTSD in heavily traumatized survivors of the Rwandan genocide. Our results indicate a role for PKCα in memory and suggest a genetic link between memory and the risk for PTSD.

  15. Genetically encoded biosensors based on engineered fluorescent proteins.

    Science.gov (United States)

    Frommer, Wolf B; Davidson, Michael W; Campbell, Robert E

    2009-10-01

    Fluorescent proteins have revolutionized cell biology by allowing researchers to non-invasively peer into the inner workings of cells and organisms. While the most common applications of fluorescent proteins are to image expression, localization, and dynamics of protein chimeras, there is a growing interest in using fluorescent proteins to create biosensors for minimally invasive imaging of concentrations of ions and small molecules, the activity of enzymes, and changes in the conformation of proteins in living cells. This tutorial review provides an overview of the progress made in the development of fluorescent protein-based biosensors to date.

  16. A genetically encoded fluorescent probe in mammalian cells.

    Science.gov (United States)

    Chatterjee, Abhishek; Guo, Jiantao; Lee, Hyun Soo; Schultz, Peter G

    2013-08-28

    Fluorescent reporters are useful in vitro and in vivo probes of protein structure, function, and localization. Here we report that the fluorescent amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), can be site-specifically incorporated into proteins in mammalian cells in response to the TAG codon with high efficiency using an orthogonal amber suppressor tRNA/aminoacyl-tRNA synthetase (aaRS) pair. We further demonstrate that Anap can be used to image the subcellular localization of proteins in live mammalian cells. The small size of Anap, its environment-sensitive fluorescence, and the ability to introduce Anap at specific sites in the proteome by simple mutagenesis make it a unique and valuable tool in eukaryotic cell biology.

  17. Genetic heterogeneity of hepatocellular carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Unsal, H.; Isselbacher, K.J. (Massachusetts General Hospital Cancer Center, Charlestown, MA (United States)); Yakicier, C.; Marcais, C.; Ozturk, M. (Institut National de la Sante et de la Recherche Medicale, Lyon (France)); Kew, M. (Univ. of Witwatersrand, Johannesburg (South Africa)); Volkmann, M. (Univ. of Heidelberg (Germany)); Zentgraf, H. (Deutsches Krebsforschungszentrum, Heidelberg (Germany))

    1994-01-18

    The authors studied 80 hepatocellular carcinomas from three continents for p53 gene (TP53) mutations and hepatitis B virus (HBV) sequences. p53 mutations were frequent in tumors from Mozambique but not in tumors from South Africa, China, and Germany. Independent of geographic origin, most tumors were positive for HBV sequences. X gene coding sequences of HBV were detected in 78% of tumors, whereas viral sequences in the surface antigen- and core antigen-encoding regions were present in less than 35% of tumors. These observations indicate that hepatocellular carcinomas are genetically heterogeneous. Mozambican-types of hepatocellular carcinomas are characterized by a high incidence of p53 mutations related to aflatoxins. In other tumors, the rarity of p53 mutations combined with the frequent presence of viral X gene coding sequences suggests a possible interference of HBV with the wild-type p53 function.

  18. Arabidopsis TRANSCURVATA1 encodes NUP58, a component of the nucleopore central channel.

    Directory of Open Access Journals (Sweden)

    Almudena Ferrández-Ayela

    Full Text Available The selective trafficking of proteins and RNAs through the nuclear envelope regulates nuclear-cytoplasmic segregation of macromolecules and is mediated by nucleopore complexes (NPCs, which consist of about 400 nucleoporins (Nups of about 30 types. Extensive studies of nucleoporin function in yeast and vertebrates showed that Nups function in nucleocytoplasmic trafficking and other processes. However, limited studies of plant Nups have identified only a few mutations, which cause pleiotropic phenotypes including reduced growth and early flowering. Here, we describe loss-of-function alleles of Arabidopsis TRANSCURVATA1 (TCU1; these mutations cause increased hypocotyl and petiole length, reticulate and asymmetrically epinastic leaf laminae of reduced size, and early flowering. TCU1 is transcribed in all of the organs and tissues examined, and encodes the putative ortholog of yeast and vertebrate Nup58, a nucleoporin of the Nup62 subcomplex. Nup58 forms the central channel of the NPC and acts directly in translocation of proteins through the nuclear envelope in yeast and vertebrates. Yeast two-hybrid (Y2H assays identified physical interactions between TCU1/NUP58 and 34 proteins, including nucleoporins, SCF (Skp1/Cul1/F-box ubiquitin ligase complex components and other nucleoplasm proteins. Genetic interactions were also found between TCU1 and genes encoding nucleoporins, soluble nuclear transport receptors and components of the ubiquitin-proteasome and auxin signaling pathways. These genetic and physical interactions indicate that TCU1/NUP58 is a member of the Nup62 subcomplex of the Arabidopsis NPC. Our findings also suggest regulatory roles for TCU1/NUP58 beyond its function in nucleocytoplasmic trafficking, a hypothesis that is supported by the Y2H and genetic interactions that we observed.

  19. Arabidopsis TRANSCURVATA1 Encodes NUP58, a Component of the Nucleopore Central Channel

    Science.gov (United States)

    Ferrández-Ayela, Almudena; Alonso-Peral, María Magdalena; Pérez-Pérez, José Manuel; Micol, José Luis; Ponce, María Rosa

    2013-01-01

    The selective trafficking of proteins and RNAs through the nuclear envelope regulates nuclear-cytoplasmic segregation of macromolecules and is mediated by nucleopore complexes (NPCs), which consist of about 400 nucleoporins (Nups) of about 30 types. Extensive studies of nucleoporin function in yeast and vertebrates showed that Nups function in nucleocytoplasmic trafficking and other processes. However, limited studies of plant Nups have identified only a few mutations, which cause pleiotropic phenotypes including reduced growth and early flowering. Here, we describe loss-of-function alleles of Arabidopsis TRANSCURVATA1 (TCU1); these mutations cause increased hypocotyl and petiole length, reticulate and asymmetrically epinastic leaf laminae of reduced size, and early flowering. TCU1 is transcribed in all of the organs and tissues examined, and encodes the putative ortholog of yeast and vertebrate Nup58, a nucleoporin of the Nup62 subcomplex. Nup58 forms the central channel of the NPC and acts directly in translocation of proteins through the nuclear envelope in yeast and vertebrates. Yeast two-hybrid (Y2H) assays identified physical interactions between TCU1/NUP58 and 34 proteins, including nucleoporins, SCF (Skp1/Cul1/F-box) ubiquitin ligase complex components and other nucleoplasm proteins. Genetic interactions were also found between TCU1 and genes encoding nucleoporins, soluble nuclear transport receptors and components of the ubiquitin-proteasome and auxin signaling pathways. These genetic and physical interactions indicate that TCU1/NUP58 is a member of the Nup62 subcomplex of the Arabidopsis NPC. Our findings also suggest regulatory roles for TCU1/NUP58 beyond its function in nucleocytoplasmic trafficking, a hypothesis that is supported by the Y2H and genetic interactions that we observed. PMID:23840761

  20. Encoding information into precipitation structures

    Science.gov (United States)

    Martens, Kirsten; Bena, Ioana; Droz, Michel; Rácz, Zoltan

    2008-12-01

    Material design at submicron scales would be profoundly affected if the formation of precipitation patterns could be easily controlled. It would allow the direct building of bulk structures, in contrast to traditional techniques which consist of removing material in order to create patterns. Here, we discuss an extension of our recent proposal of using electrical currents to control precipitation bands which emerge in the wake of reaction fronts in A+ + B- → C reaction-diffusion processes. Our main result, based on simulating the reaction-diffusion-precipitation equations, is that the dynamics of the charged agents can be guided by an appropriately designed time-dependent electric current so that, in addition to the control of the band spacing, the width of the precipitation bands can also be tuned. This makes straightforward the encoding of information into precipitation patterns and, as an amusing example, we demonstrate the feasibility by showing how to encode a musical rhythm.

  1. Genetic analysis of nifF and nifA and site-directed mutagenesis of nifE in Azotobacter vinelandii

    OpenAIRE

    Bennett, Lisa Tracy

    1989-01-01

    Nitrogenase-catalyzed nitrogen fixation is a biochemically and genetically complex process requiring the participation of a number of different nif (nitrogen fixation) gene products. The nifF (electron transport), nifA (nif gene regulation) and nifE (FeMo-cofactor biosynthesis) genes from Azotobacter vinelandii were genetically analyzed. The nucleotide sequence of the nifF gene, which encodes a flavodoxin, was determined. Specific mutation strains indicated that in A vineland...

  2. Geometric Hyperplanes: Desargues Encodes Doily

    CERN Document Server

    Saniga, Metod

    2011-01-01

    It is shown that the structure of the generalized quadrangle of order two is fully encoded in the properties of the Desargues configuration. A point of the quadrangle is represented by a geometric hyperplane of the Desargues configuration and its line by a set of three hyperplanes such that one of them is the complement of the symmetric difference of the remaining two and they all share a pair of non-collinear points.

  3. Vector Encoding in Biochemical Networks

    Science.gov (United States)

    Potter, Garrett; Sun, Bo

    Encoding of environmental cues via biochemical signaling pathways is of vital importance in the transmission of information for cells in a network. The current literature assumes a single cell state is used to encode information, however, recent research suggests the optimal strategy utilizes a vector of cell states sampled at various time points. To elucidate the optimal sampling strategy for vector encoding, we take an information theoretic approach and determine the mutual information of the calcium signaling dynamics obtained from fibroblast cells perturbed with different concentrations of ATP. Specifically, we analyze the sampling strategies under the cases of fixed and non-fixed vector dimension as well as the efficiency of these strategies. Our results show that sampling with greater frequency is optimal in the case of non-fixed vector dimension but that, in general, a lower sampling frequency is best from both a fixed vector dimension and efficiency standpoint. Further, we find the use of a simple modified Ornstein-Uhlenbeck process as a model qualitatively captures many of our experimental results suggesting that sampling in biochemical networks is based on a few basic components.

  4. Genetic Discrimination

    Science.gov (United States)

    ... in Genetics Archive Regulation of Genetic Tests Genetic Discrimination Overview Many Americans fear that participating in research ... I) and employment (Title II). Read more Genetic Discrimination and Other Laws Genetic Discrimination and Other Laws ...

  5. Social indicators.

    Science.gov (United States)

    Sheldon, E B; Parke, R

    1975-05-16

    The notions of social indicators and social accounting, expressed by analogy with the national economic accounts, generated excitement in the 1960's, and the interest continues to grow if we may judge from governmental activity and the publication of programmatic and research papers. But the concepts which focused much of the early enthusiasm gave exaggerated promise of policy applications and provided an unproductive basis for research. The essential theoretical prerequisites for developing a system of social accounts-defining the variables and the interrelationships among them-are missing. It is now realized that evaluation research, particularly experimentation, must be relied on for evaluation of government programs. Through the development and analysis of descriptive time series and the modeling of social processes, we will be able to describe the state of the society and its dynamics and thus improve immensely our ability to state problems in a productive fashion, obtain clues as to promising lines of endeavor, and ask good questions. But these activities cannot measure program effectiveness. Finally, we must be skeptical about definitions of the social indicators enterprise which confine it to social engineering efforts. The issue is not whether social indicators are useful for policy but, rather, how this usefulness comes about. The interest in social indicators has stimulated a revival of interest in quantitative, comparative, social analysis (60), in the analysis of social change, in conceptual and measurement work on such topics as prejudice, crime, and learning, and in the development of models of social processes. The fruit of these efforts will be more directly a contribution to the policy-maker's cognition than to his decisions. Decision emerges from a mosaic of inputs, including valuational and political, as well as technical components. The work we have described deals with only one type of input; it is a contribution to the intellectual mapping

  6. Hall effect encoding of brushless dc motors

    Science.gov (United States)

    Berard, C. A.; Furia, T. J.; Goldberg, E. A.; Greene, R. C.

    1970-01-01

    Encoding mechanism integral to the motor and using the permanent magnets embedded in the rotor eliminates the need for external devices to encode information relating the position and velocity of the rotating member.

  7. Genetic Control of Potassium Channels.

    Science.gov (United States)

    Amin, Ahmad S; Wilde, Arthur A M

    2016-06-01

    Approximately 80 genes in the human genome code for pore-forming subunits of potassium (K(+)) channels. Rare variants (mutations) in K(+) channel-encoding genes may cause heritable arrhythmia syndromes. Not all rare variants in K(+) channel-encoding genes are necessarily disease-causing mutations. Common variants in K(+) channel-encoding genes are increasingly recognized as modifiers of phenotype in heritable arrhythmia syndromes and in the general population. Although difficult, distinguishing pathogenic variants from benign variants is of utmost importance to avoid false designations of genetic variants as disease-causing mutations.

  8. Indicators of coal metamorphism

    Energy Technology Data Exchange (ETDEWEB)

    Proskuryakov, A.E.

    1982-06-01

    Important in determining metamorphism of coal is the reliability of indicators of coalification. Both the reflection of vitrinite and emission of volatile matter have been used for this purpose. To determine which indicator more accurately characterizes metamorphism of coal, their conformity to the following demands was established: 1. uniformity in direction of change of parameters with degree of metamorphism; 2. independence of the indicator of the genetic characteristics of coal (petrographic composition, reduction and oxidation of coal); 3. sensitivity of indicator. Both indicators conform to the first requirement. Emission of volatile substance decreases and reflective capacity of vitrinite increases uniformly with degree of metamorphism. However, the reflectivity of vitrinite is not influenced by petrographic composition of coals and is less dependent on the oxidation and reduction of coal than emission of volatile matter. It is also a more sensitive indicator distinguishing more degrees of metamorphism than emission of volatile matter. Reflectivity of vitrinite is a more reliable indicator of metamorphism than emission of volatile matter. However, in many laboratories this indicator is not measured with sufficient accuracy. To correct this, measuring equipment must be standardized.

  9. Occurrence of human-associated Bacteroidetes genetic source tracking markers in raw and treated wastewater of municipal and domestic origin and comparison to standard and alternative indicators of faecal pollution.

    Science.gov (United States)

    Mayer, R E; Bofill-Mas, S; Egle, L; Reischer, G H; Schade, M; Fernandez-Cassi, X; Fuchs, W; Mach, R L; Lindner, G; Kirschner, A; Gaisbauer, M; Piringer, H; Blaschke, A P; Girones, R; Zessner, M; Sommer, R; Farnleitner, A H

    2016-03-01

    This was a detailed investigation of the seasonal occurrence, dynamics, removal and resistance of human-associated genetic Bacteroidetes faecal markers (GeBaM) compared with ISO-based standard faecal indicator bacteria (SFIB), human-specific viral faecal markers and one human-associated Bacteroidetes phage in raw and treated wastewater of municipal and domestic origin. Characteristics of the selected activated sludge wastewater treatment plants (WWTPs) from Austria and Germany were studied in detail (WWTPs, n = 13, connected populations from 3 to 49000 individuals), supported by volume-proportional automated 24-h sampling and chemical water quality analysis. GeBaM were consistently detected in high concentrations in raw (median log10 8.6 marker equivalents (ME) 100 ml(-1)) and biologically treated wastewater samples (median log10 6.2-6.5 ME 100 ml(-1)), irrespective of plant size, type and time of the season (n = 53-65). GeBaM, Escherichia coli, and enterococci concentrations revealed the same range of statistical variability for raw (multiplicative standard deviations s* = 2.3-3.0) and treated wastewater (s* = 3.7-4.5), with increased variability after treatment. Clostridium perfringens spores revealed the lowest variability for raw wastewater (s* = 1.5). In raw wastewater correlations among microbiological parameters were only detectable between GeBaM, C. perfringens and JC polyomaviruses. Statistical associations amongst microbial parameters increased during wastewater treatment. Two plants with advanced treatment were also investigated, revealing a minimum log10 5.0 (10th percentile) reduction of GeBaM in the activated sludge membrane bioreactor, but no reduction of the genetic markers during UV irradiation (254 nm). This study highlights the potential of human-associated GeBaM to complement wastewater impact monitoring based on the determination of SFIB. In addition, human-specific JC polyomaviruses and adenoviruses seem to be a valuable support

  10. Amplifying genetic logic gates.

    Science.gov (United States)

    Bonnet, Jerome; Yin, Peter; Ortiz, Monica E; Subsoontorn, Pakpoom; Endy, Drew

    2013-05-03

    Organisms must process information encoded via developmental and environmental signals to survive and reproduce. Researchers have also engineered synthetic genetic logic to realize simpler, independent control of biological processes. We developed a three-terminal device architecture, termed the transcriptor, that uses bacteriophage serine integrases to control the flow of RNA polymerase along DNA. Integrase-mediated inversion or deletion of DNA encoding transcription terminators or a promoter modulates transcription rates. We realized permanent amplifying AND, NAND, OR, XOR, NOR, and XNOR gates actuated across common control signal ranges and sequential logic supporting autonomous cell-cell communication of DNA encoding distinct logic-gate states. The single-layer digital logic architecture developed here enables engineering of amplifying logic gates to control transcription rates within and across diverse organisms.

  11. [Neurons that encode sound direction].

    Science.gov (United States)

    Peña, J L

    In the auditory system, the inner ear breaks down complex signals into their spectral components, and encodes the amplitude and phase of each. In order to infer sound direction in space, a computation on each frequency component of the sound must be performed. Space specific neurons in the owl s inferior colliculus respond only to sounds coming from a particular direction and represent the results of this computation. The interaural time difference (ITD) and interaural level difference (ILD define the auditory space for the owl and are processed in separate neural pathways. The parallel pathways that process these cues merge in the external nucleus of the inferior colliculus where the space specific neurons are selective to combinations of ITD and ILD. How do inputs from the two sources interact to produce combination selectivity to ITD ILD pairs? A multiplication of postsynaptic potentials tuned to ITD and ILD can account for the subthreshold responses of these neurons to ITD ILD pairs. Examples of multiplication by neurons or neural circuits are scarce, but many computational models assume the existence of this basic operation. The owl s auditory system uses such operation to create a 2 dimensional map of auditory space. The map of space in the owl s auditory system shows important similarities with representations of space in the cerebral cortex and other sensory systems. In encoding space or other stimulus features, individual neurons appear to possess analogous functional properties related to the synthesis of high order receptive fields.

  12. Brain activity underlying encoding and retrieval of source memory.

    Science.gov (United States)

    Cansino, Selene; Maquet, Pierre; Dolan, Raymond J; Rugg, Michael D

    2002-10-01

    Neural activity elicited during the encoding and retrieval of source information was investigated with event-related functional magnetic resonance imaging (efMRI). During encoding, 17 subjects performed a natural/artificial judgement on pictures of common objects which were presented randomly in one of the four quadrants of the display. At retrieval, old pictures were mixed with new ones and subjects judged whether each picture was new or old and, if old, indicated in which quadrant it was presented at encoding. During encoding, study items that were later recognized and assigned a correct source judgement elicited greater activity than recognized items given incorrect judgements in a variety of regions, including right lateral occipital and left prefrontal cortex. At retrieval, regions showing greater activity for recognized items given correct versus incorrect source judgements included the right hippocampal formation and the left prefrontal cortex. These findings indicate a role for these regions in the encoding and retrieval of episodic information beyond that required for simple item recognition.

  13. Successful Scene Encoding in Presymptomatic Early-Onset Alzheimer's Disease.

    Science.gov (United States)

    Quiroz, Yakeel T; Willment, Kim Celone; Castrillon, Gabriel; Muniz, Martha; Lopera, Francisco; Budson, Andrew; Stern, Chantal E

    2015-01-01

    Brain regions critical to episodic memory are altered during the preclinical stages of Alzheimer's disease (AD). However, reliable means of identifying cognitively-normal individuals at higher risk to develop AD have not been established. To examine whether functional MRI can detect early functional changes associated with scene encoding in a group of presymptomatic presenilin-1 (PSEN1) E280A mutation carriers. Participants were 39 young, cognitively-normal individuals from an autosomal dominant early-onset AD kindred, located in Antioquia, Colombia. Participants performed a functional MRI scene encoding task and a post-scan subsequent memory test. PSEN1 mutation carriers exhibited hyperactivation within medial temporal lobe regions (hippocampus,parahippocampal formation) during successful scene encoding compared to age-matched non-carriers. Hyperactivation in medial temporal lobe regions during scene encoding is seen in individuals genetically-determined to develop AD years before their clinical onset. Our findings will guide future research with the ultimate goal of using functional neuroimaging in the early detection of preclinical AD.

  14. Reducing the genetic code induces massive rearrangement of the proteome.

    Science.gov (United States)

    O'Donoghue, Patrick; Prat, Laure; Kucklick, Martin; Schäfer, Johannes G; Riedel, Katharina; Rinehart, Jesse; Söll, Dieter; Heinemann, Ilka U

    2014-12-02

    Expanding the genetic code is an important aim of synthetic biology, but some organisms developed naturally expanded genetic codes long ago over the course of evolution. Less than 1% of all sequenced genomes encode an operon that reassigns the stop codon UAG to pyrrolysine (Pyl), a genetic code variant that results from the biosynthesis of Pyl-tRNA(Pyl). To understand the selective advantage of genetically encoding more than 20 amino acids, we constructed a markerless tRNA(Pyl) deletion strain of Methanosarcina acetivorans (ΔpylT) that cannot decode UAG as Pyl or grow on trimethylamine. Phenotypic defects in the ΔpylT strain were evident in minimal medium containing methanol. Proteomic analyses of wild type (WT) M. acetivorans and ΔpylT cells identified 841 proteins from >7,000 significant peptides detected by MS/MS. Protein production from UAG-containing mRNAs was verified for 19 proteins. Translation of UAG codons was verified by MS/MS for eight proteins, including identification of a Pyl residue in PylB, which catalyzes the first step of Pyl biosynthesis. Deletion of tRNA(Pyl) globally altered the proteome, leading to >300 differentially abundant proteins. Reduction of the genetic code from 21 to 20 amino acids led to significant down-regulation in translation initiation factors, amino acid metabolism, and methanogenesis from methanol, which was offset by a compensatory (100-fold) up-regulation in dimethyl sulfide metabolic enzymes. The data show how a natural proteome adapts to genetic code reduction and indicate that the selective value of an expanded genetic code is related to carbon source range and metabolic efficiency.

  15. The lethal toxin from Australian funnel-web spiders is encoded by an intronless gene.

    Science.gov (United States)

    Pineda, Sandy Steffany; Wilson, David; Mattick, John S; King, Glenn F

    2012-01-01

    Australian funnel-web spiders are generally considered the most dangerous spiders in the world, with envenomations from the Sydney funnel-web spider Atrax robustus resulting in at least 14 human fatalities prior to the introduction of an effective anti-venom in 1980. The clinical envenomation syndrome resulting from bites by Australian funnel-web spiders is due to a single 42-residue peptide known as δ-hexatoxin. This peptide delays the inactivation of voltage-gated sodium channels, which results in spontaneous repetitive firing and prolongation of action potentials, thereby causing massive neurotransmitter release from both somatic and autonomic nerve endings. Here we show that δ-hexatoxin from the Australian funnel-web spider Hadronyche versuta is produced from an intronless gene that encodes a prepropeptide that is post-translationally processed to yield the mature toxin. A limited sampling of genes encoding unrelated venom peptides from this spider indicated that they are all intronless. Thus, in distinct contrast to cone snails and scorpions, whose toxin genes contain introns, spiders may have developed a quite different genetic strategy for evolving their venom peptidome.

  16. The lethal toxin from Australian funnel-web spiders is encoded by an intronless gene.

    Directory of Open Access Journals (Sweden)

    Sandy Steffany Pineda

    Full Text Available Australian funnel-web spiders are generally considered the most dangerous spiders in the world, with envenomations from the Sydney funnel-web spider Atrax robustus resulting in at least 14 human fatalities prior to the introduction of an effective anti-venom in 1980. The clinical envenomation syndrome resulting from bites by Australian funnel-web spiders is due to a single 42-residue peptide known as δ-hexatoxin. This peptide delays the inactivation of voltage-gated sodium channels, which results in spontaneous repetitive firing and prolongation of action potentials, thereby causing massive neurotransmitter release from both somatic and autonomic nerve endings. Here we show that δ-hexatoxin from the Australian funnel-web spider Hadronyche versuta is produced from an intronless gene that encodes a prepropeptide that is post-translationally processed to yield the mature toxin. A limited sampling of genes encoding unrelated venom peptides from this spider indicated that they are all intronless. Thus, in distinct contrast to cone snails and scorpions, whose toxin genes contain introns, spiders may have developed a quite different genetic strategy for evolving their venom peptidome.

  17. A Prophage-Encoded Small RNA Controls Metabolism and Cell Division in Escherichia coli.

    Science.gov (United States)

    Balasubramanian, Divya; Ragunathan, Preethi T; Fei, Jingyi; Vanderpool, Carin K

    2016-01-01

    Hundreds of small RNAs (sRNAs) have been identified in diverse bacterial species, and while the functions of most remain unknown, some regulate key processes, particularly stress responses. The sRNA DicF was identified over 25 years ago as an inhibitor of cell division but since then has remained uncharacterized. DicF consists of 53 nucleotides and is encoded by a gene carried on a prophage (Qin) in the genomes of many Escherichia coli strains. We demonstrated that DicF inhibits cell division via direct base pairing with ftsZ mRNA to repress translation and prevent new synthesis of the bacterial tubulin homolog FtsZ. Systems analysis using computational and experimental methods identified additional mRNA targets of DicF: xylR and pykA mRNAs, encoding the xylose uptake and catabolism regulator and pyruvate kinase, respectively. Genetic analyses showed that DicF directly base pairs with and represses translation of these targets. Phenotypes of cells expressing DicF variants demonstrated that DicF-associated growth inhibition is not solely due to repression of ftsZ, indicating that the physiological consequences of DicF-mediated regulation extend beyond effects on cell division caused by reduced FtsZ synthesis. IMPORTANCE sRNAs are ubiquitous and versatile regulators of bacterial gene expression. A number of well-characterized examples in E. coli are highly conserved and present in the E. coli core genome. In contrast, the sRNA DicF (identified over 20 years ago but remaining poorly characterized) is encoded by a gene carried on a defective prophage element in many E. coli genomes. Here, we characterize DicF in order to better understand how horizontally acquired sRNA regulators impact bacterial gene expression and physiology. Our data confirm the long-hypothesized DicF-mediated regulation of ftsZ, encoding the bacterial tubulin homolog required for cell division. We further uncover DicF-mediated posttranscriptional control of metabolic gene expression. Ectopic

  18. Off-fault tip splay networks: a genetic and generic property of faults indicative of their long-term propagation, and a major component of off-fault damage

    Science.gov (United States)

    Perrin, C.; Manighetti, I.; Gaudemer, Y.

    2015-12-01

    Faults grow over the long-term by accumulating displacement and lengthening, i.e., propagating laterally. We use fault maps and fault propagation evidences available in literature to examine geometrical relations between parent faults and off-fault splays. The population includes 47 worldwide crustal faults with lengths from millimeters to thousands of kilometers and of different slip modes. We show that fault splays form adjacent to any propagating fault tip, whereas they are absent at non-propagating fault ends. Independent of parent fault length, slip mode, context, etc, tip splay networks have a similar fan shape widening in direction of long-term propagation, a similar relative length and width (~30 and ~10 % of parent fault length, respectively), and a similar range of mean angles to parent fault (10-20°). Tip splays more commonly develop on one side only of the parent fault. We infer that tip splay networks are a genetic and a generic property of faults indicative of their long-term propagation. We suggest that they represent the most recent damage off-the parent fault, formed during the most recent phase of fault lengthening. The scaling relation between parent fault length and width of tip splay network implies that damage zones enlarge as parent fault length increases. Elastic properties of host rocks might thus be modified at large distances away from a fault, up to 10% of its length. During an earthquake, a significant fraction of coseismic slip and stress is dissipated into the permanent damage zone that surrounds the causative fault. We infer that coseismic dissipation might occur away from a rupture zone as far as a distance of 10% of the length of its causative fault. Coseismic deformations and stress transfers might thus be significant in broad regions about principal rupture traces. This work has been published in Comptes Rendus Geoscience under doi:10.1016/j.crte.2015.05.002 (http://www.sciencedirect.com/science/article/pii/S1631071315000528).

  19. New Genetics

    Science.gov (United States)

    ... Home > Science Education > The New Genetics The New Genetics Living Laboratories Classroom Poster Order a Free Copy ... Piece to a Century-Old Evolutionary Puzzle Computing Genetics Model Organisms RNA Interference The New Genetics is ...

  20. Genes, genetics, and Class III malocclusion.

    Science.gov (United States)

    Xue, F; Wong, R W K; Rabie, A B M

    2010-05-01

    To present current views that are pertinent to the investigation of the genetic etiology of Class III malocclusion. Class III malocclusion is thought to be a polygenic disorder that results from an interaction between susceptibility genes and environmental factors. However, research on family pedigrees has indicated that Class III malocclusion might also be a monogenic dominant phenotype. Recent studies have reported that genes that encode specific growth factors or other signaling molecules are involved in condylar growth under mechanical strain. These genes, which include Indian hedgehog homolog (IHH), parathyroid-hormone like hormone (PTHLH), insulin-like growth factor-1 (IGF-1), and vascular endothelial growth factor (VEGF), and variations in their levels of expression play an important role in the etiology of Class III malocclusion. In addition, genome-wide scans have revealed chromosomal loci that are associated with Class III malocclusion. It is likely that chromosomal loci 1p36, 12q23, and 12q13 harbor genes that confer susceptibility to Class III malocclusion. In a case-control association study, we identified erythrocyte membrane protein band 4.1 (EPB41) to be a new positional candidate gene that might be involved in susceptibility to mandibular prognathism. Most of the earlier studies on the genetic etiology of Class III malocclusion have focused on the patterns of inheritance of this phenotype. Recent investigations have focused on understanding the genetic variables that affect Class III malocclusion and might provide new approaches to uncovering the genetic etiology of this phenotype.

  1. Molecular mechanisms for protein-encoded inheritance.

    Science.gov (United States)

    Wiltzius, Jed J W; Landau, Meytal; Nelson, Rebecca; Sawaya, Michael R; Apostol, Marcin I; Goldschmidt, Lukasz; Soriaga, Angela B; Cascio, Duilio; Rajashankar, Kanagalaghatta; Eisenberg, David

    2009-09-01

    In prion inheritance and transmission, strains are phenotypic variants encoded by protein 'conformations'. However, it is unclear how a protein conformation can be stable enough to endure transmission between cells or organisms. Here we describe new polymorphic crystal structures of segments of prion and other amyloid proteins, which offer two structural mechanisms for the encoding of prion strains. In packing polymorphism, prion strains are encoded by alternative packing arrangements (polymorphs) of beta-sheets formed by the same segment of a protein; in segmental polymorphism, prion strains are encoded by distinct beta-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring conformations capable of encoding strains. These molecular mechanisms for transfer of protein-encoded information into prion strains share features with the familiar mechanism for transfer of nucleic acid-encoded information into microbial strains, including sequence specificity and recognition by noncovalent bonds.

  2. Molecular mechanisms for protein-encoded inheritance

    Energy Technology Data Exchange (ETDEWEB)

    Wiltzius, Jed J.W.; Landau, Meytal; Nelson, Rebecca; Sawaya, Michael R.; Apostol, Marcin I.; Goldschmidt, Lukasz; Soriaga, Angela B.; Cascio, Duilio; Rajashankar, Kanagalaghatta; Eisenberg, David; (Cornell); (HHMI)

    2009-12-01

    In prion inheritance and transmission, strains are phenotypic variants encoded by protein 'conformations'. However, it is unclear how a protein conformation can be stable enough to endure transmission between cells or organisms. Here we describe new polymorphic crystal structures of segments of prion and other amyloid proteins, which offer two structural mechanisms for the encoding of prion strains. In packing polymorphism, prion strains are encoded by alternative packing arrangements (polymorphs) of {beta}-sheets formed by the same segment of a protein; in segmental polymorphism, prion strains are encoded by distinct {beta}-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring conformations capable of encoding strains. These molecular mechanisms for transfer of protein-encoded information into prion strains share features with the familiar mechanism for transfer of nucleic acid-encoded information into microbial strains, including sequence specificity and recognition by noncovalent bonds.

  3. Characterization of genes encoding poly(A polymerases in plants: evidence for duplication and functional specialization.

    Directory of Open Access Journals (Sweden)

    Lisa R Meeks

    Full Text Available BACKGROUND: Poly(A polymerase is a key enzyme in the machinery that mediates mRNA 3' end formation in eukaryotes. In plants, poly(A polymerases are encoded by modest gene families. To better understand this multiplicity of genes, poly(A polymerase-encoding genes from several other plants, as well as from Selaginella, Physcomitrella, and Chlamydomonas, were studied. METHODOLOGY/PRINCIPAL FINDINGS: Using bioinformatics tools, poly(A polymerase-encoding genes were identified in the genomes of eight species in the plant lineage. Whereas Chlamydomonas reinhardtii was found to possess a single poly(A polymerase gene, other species possessed between two and six possible poly(A polymerase genes. With the exception of four intron-lacking genes, all of the plant poly(A polymerase genes (but not the C. reinhardtii gene possessed almost identical intron positions within the poly(A polymerase coding sequences, suggesting that all plant poly(A polymerase genes derive from a single ancestral gene. The four Arabidopsis poly(A polymerase genes were found to be essential, based on genetic analysis of T-DNA insertion mutants. GFP fusion proteins containing three of the four Arabidopsis poly(A polymerases localized to the nucleus, while one such fusion protein was localized in the cytoplasm. The fact that this latter protein is largely pollen-specific suggests that it has important roles in male gametogenesis. CONCLUSIONS/SIGNIFICANCE: Our results indicate that poly(A polymerase genes have expanded from a single ancestral gene by a series of duplication events during the evolution of higher plants, and that individual members have undergone sorts of functional specialization so as to render them essential for plant growth and development. Perhaps the most interesting of the plant poly(A polymerases is a novel cytoplasmic poly(A polymerase that is expressed in pollen in Arabidopsis; this is reminiscent of spermatocyte-specific cytoplasmic poly(A polymerases in

  4. Oceanographic Currents and Local Ecological Knowledge Indicate, and Genetics Does Not Refute, a Contemporary Pattern of Larval Dispersal for The Ornate Spiny Lobster, Panulirus ornatus in the South-East Asian Archipelago.

    Science.gov (United States)

    Dao, Hoc Tan; Smith-Keune, Carolyn; Wolanski, Eric; Jones, Clive M; Jerry, Dean R

    2015-01-01

    Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798) in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences ΦST = -0.008; microsatellite loci FST = 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock.

  5. Oceanographic Currents and Local Ecological Knowledge Indicate, and Genetics Does Not Refute, a Contemporary Pattern of Larval Dispersal for The Ornate Spiny Lobster, Panulirus ornatus in the South-East Asian Archipelago.

    Directory of Open Access Journals (Sweden)

    Hoc Tan Dao

    Full Text Available Here we utilize a combination of genetic data, oceanographic data, and local ecological knowledge to assess connectivity patterns of the ornate spiny lobster Panulirus ornatus (Fabricius, 1798 in the South-East Asian archipelago from Vietnam to Australia. Partial mitochondrial DNA control region and 10 polymorphic microsatellites did not detect genetic structure of 216 wild P. ornatus samples from Australia, Indonesia and Vietnam. Analyses show no evidence for genetic differentiation among populations (mtDNA control region sequences ΦST = -0.008; microsatellite loci FST = 0.003. A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow in P. ornatus throughout the South-East Asian Archipelago. This lack of genetic structure may be due to the oceanography-driven connectivity of the pelagic lobster larvae between spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. The connectivity cycle necessitates three generations. The lack of genetic structure of P. ornatus population in the South-East Asian archipelago has important implications for the sustainable management of this lobster in that the species within the region needs to be managed as one genetic stock.

  6. Conjugative botulinum neurotoxin-encoding plasmids in Clostridium botulinum.

    Directory of Open Access Journals (Sweden)

    Kristin M Marshall

    Full Text Available BACKGROUND: Clostridium botulinum produces seven distinct serotypes of botulinum neurotoxins (BoNTs. The genes encoding different subtype neurotoxins of serotypes A, B, F and several dual neurotoxin-producing strains have been shown to reside on plasmids, suggesting that intra- and interspecies transfer of BoNT-encoding plasmids may occur. The objective of the present study was to determine whether these C. botulinum BoNT-encoding plasmids are conjugative. METHODOLOGY/PRINCIPAL FINDINGS: C. botulinum BoNT-encoding plasmids pBotCDC-A3 (strain CDC-A3, pCLJ (strain 657Ba and pCLL (strain Eklund 17B were tagged with the erythromycin resistance marker (Erm using the ClosTron mutagenesis system by inserting a group II intron into the neurotoxin genes carried on these plasmids. Transfer of the tagged plasmids from the donor strains CDC-A3, 657Ba and Eklund 17B to tetracycline-resistant recipient C. botulinum strains was evaluated in mating experiments. Erythromycin and tetracycline resistant transconjugants were isolated from donor:recipient mating pairs tested. Transfer of the plasmids to the transconjugants was confirmed by pulsed-field gel electrophoresis (PFGE and Southern hybridizations. Transfer required cell-to-cell contact and was DNase resistant. This indicates that transfer of these plasmids occurs via a conjugation mechanism. CONCLUSIONS/SIGNIFICANCE: This is the first evidence supporting conjugal transfer of native botulinum neurotoxin-encoding plasmids in C. botulinum, and provides a probable mechanism for the lateral distribution of BoNT-encoding plasmids to other C. botulinum strains. The potential transfer of C. botulinum BoNT-encoding plasmids to other bacterial hosts in the environment or within the human intestine is of great concern for human pathogenicity and necessitates further characterization of these plasmids.

  7. Comunidade bacteriana como indicadora do efeito de feijoeiro geneticamente modificado sobre organismos não alvo Bacterial community as an indicator of genetically modified common bean effect on nontarget organisms

    Directory of Open Access Journals (Sweden)

    Adriano Moreira Knupp

    2009-12-01

    subgroup of the Proteobacteria phylum were obtained from uncultured cells and used for amplification. Using the Jaccard coefficient and UPGMA (Unweighted pair-group method with arithmetic mean, dendrograms comparing the conventional Olathe Pinto and the elite event Olathe M1-4 transgenic varieties were obtained. The clusters obtained from the 16S rDNA PCR-DGGE profiles indicate changes in the rhizosphere bacterial community in genetically modified plants, being more notable in the profiles obtained for alphaproteobacteria. Sample origin and plant development stages affect bacterial community profiles.

  8. Atmospheric effects on Quaternary polarization encoding for free space communication

    Science.gov (United States)

    Soorat, Ram; Vudayagiri, Ashok

    2016-10-01

    We have simulated atmospheric effects such as fog and smoke in laboratory environment to simulate depolarisation due to atmospheric effects during a free space optical communi- cation. This has been used to study noise in two components of quaternary encoding for polarization shift keying. Individual components of a Quaternary encoding, such as vertical and horizontal as well as 45$^\\circ$ and 135$^\\circ$ , are tested separately and indicates that the depo- larization effects are different for these two situation. However, due to a differential method used to extract information bits, the protocol shows extremely low bit error rates. The information obtained is useful during deployment of a fully functional Quaternary encoded PolSK scheme in free space.

  9. Identification and characterization of a gene encoding a putative lysophosphatidyl acyltransferase from Arachis hypogaea

    Indian Academy of Sciences (India)

    Si-Long Chen; Jia-Quan Huang; Lei Yong; Yue-Ting Zhang; Xiao-Ping Ren; Yu-Ning Chen; Hui-Fang Jiang; Li-Ying Yan; Yu-Rong Li; Bo-Shou Liao

    2012-12-01

    Lysophosphatidyl acyltransferase (LPAT) is the important enzyme responsible for the acylation of lysophosphatidic acid (LPA), leading to the generation of phosphatidic acid (PA) in plant. Its encoding gene is an essential candidate for oil crops to improve oil composition and increase seed oil content through genetic engineering. In this study, a full-length AhLPAT4 gene was isolated via cDNA library screening and rapid amplification of cDNA ends (RACE); our data demonstrated that AhLPAT4 had 1631 nucleotides, encoding a putative 43.8 kDa protein with 383 amino acid residues. The deduced protein included a conserved acyltransferase domain and four motifs (I–IV) with putative LPA and acyl-CoA catalytic and binding sites. Bioinformatic analysis indicated that AhLPAT4 contained four transmembrane domains (TMDs), localized to the endoplasmic reticulum (ER) membrane; detailed analysis indicated that motif I and motifs II–III in AhLPAT4 were separated by the third TMD, which located on cytosolic and ER luminal side respectively, and hydrophobic residues on the surface of AhLPAT4 protein fold to form a hydrophobic tunnel to accommodate the acyl chain. Subcellular localization analysis confirmed that AhLPAT4 was a cytoplasm protein. Phylogenetic analysis revealed that AhLPAT4 had a high homology (63.7–78.3%) with putative LPAT4 proteins from Glycine max, Arabidopsis thaliana and Ricinus communis. AhLPAT4 was ubiquitously expressed in diverse tissues except in flower, which is almost undetectable. The expression analysis in different developmental stages in peanut seeds indicated that AhLPAT4 did not coincide with oil accumulation.

  10. Antifungal activity of a virally encoded gene in transgenic wheat.

    Science.gov (United States)

    Clausen, M; Kräuter, R; Schachermayr, G; Potrykus, I; Sautter, C

    2000-04-01

    The cDNA encoding the antifungal protein KP4 from Ustilago maydis-infecting virus was inserted behind the ubiquitin promoter of maize and genetically transferred to wheat varieties particularly susceptible to stinking smut (Tilletia tritici) disease. The transgene was integrated and inherited over several generations. Of seven transgenic lines, three showed antifungal activity against U. maydis. The antifungal activity correlated with the presence of the KP4 transgene. KP4-transgenic, soil-grown wheat plants exhibit increased endogenous resistance against stinking smut.

  11. [Mutations in the gene encoding filaggrin cause ichthyosis vulgaris].

    Science.gov (United States)

    Prasad, Sumangali Chandra; Rasmussen, Kirsten; Bygum, Anette

    2011-02-14

    Ichthyosis vulgaris is a common genetic skin disorder with an estimated prevalence of 1:250 caused by mutations in the gene encoding filaggrin. This disorder manifests itself within the first year of life and is clinically characterized by dry, scaly skin, keratosis pilaris, palmar hyperlinearity and atopic manifestations. Patients with a severe phenotype are homozygous or compound heterozygous for the mutations, whereas heterozygous patients show mild disease, suggesting semidominant inheritance with incomplete penetrance. We present a patient with classic severe ichthyosis vulgaris, atopic eczema and two loss-of-function mutations.

  12. NMDA receptors and memory encoding.

    Science.gov (United States)

    Morris, Richard G M

    2013-11-01

    It is humbling to think that 30 years have passed since the paper by Collingridge, Kehl and McLennan showing that one of Jeff Watkins most interesting compounds, R-2-amino-5-phosphonopentanoate (d-AP5), blocked the induction of long-term potentiation in vitro at synapses from area CA3 of the hippocampus to CA1 without apparent effect on baseline synaptic transmission (Collingridge et al., 1983). This dissociation was one of the key triggers for an explosion of interest in glutamate receptors, and much has been discovered since that collectively contributes to our contemporary understanding of glutamatergic synapses - their biophysics and subunit composition, of the agonists and antagonists acting on them, and their diverse functions in different networks of the brain and spinal cord. It can be fairly said that Collingridge et al.'s (1983) observation was the stimulus that has led, on the one hand, to structural biological work at the atomic scale describing the key features of NMDA receptors that enables their coincidence function to happen; and, on the other, to work with whole animals investigating the contributions that calcium signalling via this receptor can have on rhythmical activities controlled by spinal circuits, memory encoding in the hippocampus (the topic of this article), visual cortical plasticity, sensitization in pain, and other functions. In this article, I lay out how my then interest in long-term potentiation (LTP) as a model of memory enabled me to recognise the importance of Collingridge et al.'s discovery - and how I and my colleagues endeavoured to take things forward in the area of learning and memory. This is in some respects a personal story, and I tell it as such. The idea that NMDA receptor activation is essential for memory encoding, though not for storage, took time to develop and to be accepted. Along the way, there have been confusions, challenges, and surprises surrounding the idea that activation of NMDA receptors can

  13. A new genetic representation for quadratic assignment problem

    Directory of Open Access Journals (Sweden)

    Kratica Jozef

    2011-01-01

    Full Text Available In this paper, we propose a new genetic encoding for well known Quadratic Assignment Problem (QAP. The new encoding schemes are implemented with appropriate objective function and modified genetic operators. The numerical experiments were carried out on the standard QAPLIB data sets known from the literature. The presented results show that in all cases proposed genetic algorithm reached known optimal solutions in reasonable time.

  14. Genetic biomarkers in hypertrophic cardiomyopathy.

    Science.gov (United States)

    Coats, Caroline J; Elliott, Perry M

    2013-08-01

    Hypertrophic cardiomyopathy is a common inherited heart muscle disorder associated with sudden cardiac death, arrhythmias and heart failure. Genetic mutations can be identified in approximately 60% of patients; these are commonest in genes that encode proteins of the cardiac sarcomere. Similar to other Mendelian diseases these mutations are characterized by incomplete penetrance and variable clinical expression. Our knowledge of this genetic diversity is rapidly evolving as high-throughput DNA sequencing technology is now used to characterize an individual patient's disease. In addition, the genomic basis of several multisystem diseases associated with a hypertrophic cardiomyopathy phenotype has been elucidated. Genetic biomarkers can be helpful in making an accurate diagnosis and in identifying relatives at risk of developing the condition. In the clinical setting, genetic testing and genetic screening should be used pragmatically with appropriate counseling. Here we review the current role of genetic biomarkers in hypertrophic cardiomyopathy, highlight recent progress in the field and discuss future challenges.

  15. Expanding the eukaryotic genetic code

    Energy Technology Data Exchange (ETDEWEB)

    Chin, Jason W.; Cropp, T. Ashton; Anderson, J. Christopher; Schultz, Peter G.

    2017-02-28

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  16. Molecular Genetics of Mitochondrial Disorders

    Science.gov (United States)

    Wong, Lee-Jun C.

    2010-01-01

    Mitochondrial respiratory chain (RC) disorders (RCDs) are a group of genetically and clinically heterogeneous diseases because of the fact that protein components of the RC are encoded by both mitochondrial and nuclear genomes and are essential in all cells. In addition, the biogenesis, structure, and function of mitochondria, including DNA…

  17. Expanding the eukaryotic genetic code

    Science.gov (United States)

    Chin, Jason W.; Cropp, T. Ashton; Anderson, J. Christopher; Schultz, Peter G.

    2013-01-22

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  18. Learning Intelligent Genetic Algorithms Using Japanese Nonograms

    Science.gov (United States)

    Tsai, Jinn-Tsong; Chou, Ping-Yi; Fang, Jia-Cen

    2012-01-01

    An intelligent genetic algorithm (IGA) is proposed to solve Japanese nonograms and is used as a method in a university course to learn evolutionary algorithms. The IGA combines the global exploration capabilities of a canonical genetic algorithm (CGA) with effective condensed encoding, improved fitness function, and modified crossover and…

  19. Learning Intelligent Genetic Algorithms Using Japanese Nonograms

    Science.gov (United States)

    Tsai, Jinn-Tsong; Chou, Ping-Yi; Fang, Jia-Cen

    2012-01-01

    An intelligent genetic algorithm (IGA) is proposed to solve Japanese nonograms and is used as a method in a university course to learn evolutionary algorithms. The IGA combines the global exploration capabilities of a canonical genetic algorithm (CGA) with effective condensed encoding, improved fitness function, and modified crossover and…

  20. Novelty's effect on memory encoding.

    Science.gov (United States)

    Rangel-Gomez, Mauricio; Janenaite, Sigita; Meeter, Martijn

    2015-07-01

    It is often thought that novelty benefits memory formation. However, support for this idea mostly comes from paradigms that are open to alternative explanations. In the present study we manipulated novelty in a word-learning task through task-irrelevant background images. These background images were either standard (presented repeatedly), or novel (presented only once). Two types of background images were used: Landscape pictures and fractals. EEG was also recorded during encoding. Contrary to the idea that novelty aids memory formation, memory performance was not affected by the novelty of the background. In the evoked response potentials, we found evidence of distracting effects of novelty: both the N1 and P3b components were smaller to words studied with novel backgrounds, and the amplitude of the N2b component correlated negatively with subsequent retrieval. We conclude that although evidence from other studies does suggest benefits on a longer time scale, novelty has no instantaneous benefits for learning. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. [Immunoglobulin genes encoding antibodies directed to oncodevelopmental carbohydrate antigens].

    Science.gov (United States)

    Zenita, K; Yago, K; Fujimoto, E; Kannagi, R

    1990-07-01

    We investigated the immunoglobulin genes which encode the variable region of the monoclonal antibodies directed to the onco-developmental carbohydrate antigens such SSEA-1, fucosyl SSEA-1, SSEA-3 and SSEA-4. The VH region of these antibodies was preferentially encoded by the gene members of the X24, VH7183 and Q52 families, the families which are known to be located at the 3'-end region of the murine germ line VH gene. This result is interesting particularly when considering that the members of the 3'-end VH families are known to be preferentially expressed in embryonic B lymphocytes by an intrinsic genetic program. The comparative study of the nucleic acid sequences of mRNAs encoding these antibodies and the sequences of the corresponding germ line VH genes disclosed that the sequences encoding the antibodies contain no mutation from the germ line VH genes, or contain only a few somatic mutations, which are thought to be insignificant for the reactivity of the antibodies to the nominal antigens. These results imply that some of the embryonic B lymphocytes that express the unmutated germ line VH genes of the 3'-end families can be reactive with embryonic carbohydrate antigens, albeit rearranged with appropriate D-JH gene segments, and coupled with proper light chains. The VH region of the syngenic monoclonal anti-idiotypic antibodies directed to these anti-carbohydrate antibodies were also encoded preferentially by the members of the 3'-end VH families. We propose here that a part of the virgin embryonic B lymphocytes, which express the antibody encoded by the gene members of the 3'-end VH families at the cell surface, will be stimulated by the embryonic carbohydrate antigens which are abundantly present in the internal milieu of the embryo. The clonally expanded B lymphocytes, in turn, will facilitate the proliferation of other populations of embryonic B lymphocytes expressing the corresponding anti-idiotypic antibodies, which are also encoded by the gene members

  2. [Genetics of migraine].

    Science.gov (United States)

    Ducros, A

    2013-05-01

    The aim of genetic studies in migraine is to identify key proteins in order to better understand the molecular mechanisms of this frequent but still incompletely understood condition. This review describes the current knowledge in the field of migraine genetics. Migraine genes have been, and still are, difficult to identify. The more common varieties of migraine are characterized by a high prevalence in the general population, and a high phenotypic variability. In the absence of any objective diagnosis marker, the status for genetic studies is established only clinically. The first breakthrough was permitted by the study of familial hemiplegic migraine, a variety of migraine with motor aura. This rare condition has a monogenic, autosomal dominant mode of inheritance, thus enabling genetic studies. The three first genes, identified from 1996 to 2005, all encode ion-channel transporters: a neuronal calcium channel (CACNA1A, FHM1), a glial sodium/potassium pump (ATP1A2, FHM2) and a neuronal sodium channel (SCN1A, FHM3). Study of cellular and animal models have shown that mutations in CACNA1A and ATP1A2 facilitated the initiation of cortical spreading depression waves, the mechanism underlying the migraine aura, and most likely increased neuronal excitability with an excess of glutamatergic neurotransmission. In 2012, PRRT2 has been identified as the fourth FHM gene, and encodes an axonal protein associated to the exocytosis complex. In the 1990s, family and twin studies showed that the more common varieties of migraine (migraine without aura and migraine with typical aura) were polygenic, with an overall heritability nearing 50 %. These genetic factors interact with environmental factors. The initial attempts to identify migraine genes by candidate gene approaches or by linkage studies were deceiving. Since 2010, three large genome-wide association studies (GWAS) have identified six genetic variants associated with migraine. Each variant has only a modest

  3. Encoder designed to work in harsh environments

    Energy Technology Data Exchange (ETDEWEB)

    Toop, L.

    2007-05-15

    Dynapar has developed the Acuro AX71 absolute encoder for use on offshore or land-based oil rig operations. It provides feedback on the operation of automated systems such as draw works, racking systems, rotary tables and top drives. By ensuring that automated systems function properly, this encoder responds to a need by the oil and gas industry to keep workers safe and improve efficiency, particularly for operations in rugged situations. The encoder provides feedback from motor systems to controllers, giving information about position and speed of downhole drill bits. This newly developed encoder is better than commonly used incremental encoders which are not precise in strong electrical noise environments. Rather, the absolute encoder uses a different method of reporting to the controller. A digital signal is transmitted constantly as the device operates. It is less susceptible to noise issues. It is highly accurate, tolerant of noise and is not affected by power outages. However, the absolute encoder is generally more delicate in drilling applications with high ambient temperatures and shock levels. Dynapar addressed this issue by developing compact stainless steel housing that is useful for corrosion resistance in marine applications. The AX71 absolute encoder can withstand up to 100 G of mechanical shock and ambient temperatures of up to 60 degrees C. The encoder is ATEX certified without barriers, and offers the high resolution feedback of 4,000 counts of multiturn rotation and 16,000 counts of position. 1 fig.

  4. Encoding of High Frequencies Improves with Maturation of Action Potential Generation in Cultured Neocortical Neurons

    Science.gov (United States)

    Nikitin, Evgeny S.; Bal, Natalia V.; Malyshev, Aleksey; Ierusalimsky, Victor N.; Spivak, Yulia; Balaban, Pavel M.; Volgushev, Maxim

    2017-01-01

    The ability of neocortical neurons to detect and encode rapid changes at their inputs is crucial for basic neuronal computations, such as coincidence detection, precise synchronization of activity and spike-timing dependent plasticity. Indeed, populations of cortical neurons can respond to subtle changes of the input very fast, on a millisecond time scale. Theoretical studies and model simulations linked the encoding abilities of neuronal populations to the fast onset dynamics of action potentials (APs). Experimental results support this idea, however mechanisms of fast onset of APs in cortical neurons remain elusive. Studies in neuronal cultures, that are allowing for accurate control over conditions of growth and microenvironment during the development of neurons and provide better access to the spike initiation zone, may help to shed light on mechanisms of AP generation and encoding. Here we characterize properties of AP encoding in neocortical neurons grown for 11–25 days in culture. We show that encoding of high frequencies improves upon culture maturation, which is accompanied by the development of passive electrophysiological properties and AP generation. The onset of APs becomes faster with culture maturation. Statistical analysis using correlations and linear model approaches identified the onset dynamics of APs as a major predictor of age-dependent changes of encoding. Encoding of high frequencies strongly correlated also with the input resistance of neurons. Finally, we show that maturation of encoding properties of neurons in cultures is similar to the maturation of encoding in neurons studied in slices. These results show that maturation of AP generators and encoding is, to a large extent, determined genetically and takes place even without normal micro-environment and activity of the whole brain in vivo. This establishes neuronal cultures as a valid experimental model for studying mechanisms of AP generation and encoding, and their maturation. PMID

  5. Virus-encoded microRNA contributes to the molecular profile of EBV-positive Burkitt lymphomas.

    Science.gov (United States)

    Piccaluga, Pier Paolo; Navari, Mohsen; De Falco, Giulia; Ambrosio, Maria Raffaella; Lazzi, Stefano; Fuligni, Fabio; Bellan, Cristiana; Rossi, Maura; Sapienza, Maria Rosaria; Laginestra, Maria Antonella; Etebari, Maryam; Rogena, Emily A; Tumwine, Lynnette; Tripodo, Claudio; Gibellini, Davide; Consiglio, Jessica; Croce, Carlo M; Pileri, Stefano A; Leoncini, Lorenzo

    2016-01-05

    Burkitt lymphoma (BL) is an aggressive neoplasm characterized by consistent morphology and phenotype, typical clinical behavior and distinctive molecular profile. The latter is mostly driven by the MYC over-expression associated with the characteristic translocation (8;14) (q24; q32) or with variant lesions. Additional genetic events can contribute to Burkitt Lymphoma pathobiology and retain clinical significance. A pathogenetic role for Epstein-Barr virus infection in Burkitt lymphomagenesis has been suggested; however, the exact function of the virus is largely unknown.In this study, we investigated the molecular profiles (genes and microRNAs) of Epstein-Barr virus-positive and -negative BL, to identify specific patterns relying on the differential expression and role of Epstein-Barr virus-encoded microRNAs.First, we found significant differences in the expression of viral microRNAs and in selected target genes. Among others, we identified LIN28B, CGNL1, GCET2, MRAS, PLCD4, SEL1L, SXX1, and the tyrosine kinases encoding STK10/STK33, all provided with potential pathogenetic significance. GCET2, also validated by immunohistochemistry, appeared to be a useful marker for distinguishing EBV-positive and EBV-negative cases. Further, we provided solid evidences that the EBV-encoded microRNAs (e.g. BART6) significantly mold the transcriptional landscape of Burkitt Lymphoma clones.In conclusion, our data indicated significant differences in the transcriptional profiles of EBV-positive and EBV-negative BL and highlight the role of virus encoded miRNA.

  6. Genetic algorithms

    Science.gov (United States)

    Wang, Lui; Bayer, Steven E.

    1991-01-01

    Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

  7. Genetic Mapping

    Science.gov (United States)

    ... Fact Sheets Fact Sheets En Español: Mapeo Genético Genetic Mapping What is genetic mapping? How do researchers create ... genetic map? What are genetic markers? What is genetic mapping? Among the main goals of the Human Genome ...

  8. Information quality measurement of medical encoding support based on usability.

    Science.gov (United States)

    Puentes, John; Montagner, Julien; Lecornu, Laurent; Cauvin, Jean-Michel

    2013-12-01

    Medical encoding support systems for diagnoses and medical procedures are an emerging technology that begins to play a key role in billing, reimbursement, and health policies decisions. A significant problem to exploit these systems is how to measure the appropriateness of any automatically generated list of codes, in terms of fitness for use, i.e. their quality. Until now, only information retrieval performance measurements have been applied to estimate the accuracy of codes lists as quality indicator. Such measurements do not give the value of codes lists for practical medical encoding, and cannot be used to globally compare the quality of multiple codes lists. This paper defines and validates a new encoding information quality measure that addresses the problem of measuring medical codes lists quality. It is based on a usability study of how expert coders and physicians apply computer-assisted medical encoding. The proposed measure, named ADN, evaluates codes Accuracy, Dispersion and Noise, and is adapted to the variable length and content of generated codes lists, coping with limitations of previous measures. According to the ADN measure, the information quality of a codes list is fully represented by a single point, within a suitably constrained feature space. Using one scheme, our approach is reliable to measure and compare the information quality of hundreds of codes lists, showing their practical value for medical encoding. Its pertinence is demonstrated by simulation and application to real data corresponding to 502 inpatient stays in four clinic departments. Results are compared to the consensus of three expert coders who also coded this anonymized database of discharge summaries, and to five information retrieval measures. Information quality assessment applying the ADN measure showed the degree of encoding-support system variability from one clinic department to another, providing a global evaluation of quality measurement trends.

  9. Operation-based Encoding and Neighborhood Search Genetic Algorithm for Job Shop Scheduling Optimization%基于工序编码和邻域搜索策略的遗传算法优化作业车间调度

    Institute of Scientific and Technical Information of China (English)

    赵诗奎; 方水良

    2013-01-01

    For the job shop scheduling optimization problem,population initialization method and neighborhood search mechanism of its solution genetic algorithm are studied.To improve the quality of the initial population,heuristic initialization method that combining active scheduling,non-delay scheduling with heuristic rules is adopted.Neighborhood structure is constructed based on the critical path.Neighborhood search moving of the key operations is carried out based on operation-based encoding to avoid infeasible solutions and chromosome testing-repair work.Different neighborhood moving for the first,inside and last operations of the operation block is defined respectively.Based on the active decoded gantt chart,to standardize the chromosome by the operation start time,and get the chromosome that the operation's position order is in accordance with the actual processing order on machines.For the expansion of the range of operation neighborhood search,the right moving is operated on the gantt chart,and to standardize the chromosome reversely by the operation completion time.Neighborhood search is implemented on the two standardized chromosome individuals obtained by forward and reverse standardization.Benchmark problems are applied to test the proposed algorithm,and effectiveress is verified.%针对作业车间调度优化问题,研究对其进行求解的遗传算法的种群初始方法和邻域搜索机制.为提高初始种群的质量,采用主动调度、无延迟调度与启发式规则相结合的启发式方法初始群体;基于关键路径构造邻域结构,将关键工序的邻域搜索移动与基于工序的编码方式相结合,避免不可行解的产生以及染色体的检测修复等工作;对工序块的块首、块内和块尾工序分别定义了不同的邻域移动操作.基于主动解码得到的甘特图,根据工序的开工时间,正向标准化染色体,使染色体中的工序位置顺序与机器上的工序实际加工顺序一致.为扩

  10. 结核分枝杆菌102株临床分离株的磷脂酶C编码基因多态性%Genetic diversity of phospholipase C-encoding genes among 102 clinical isolates of Mycobacterium tuberculosis

    Institute of Scientific and Technical Information of China (English)

    王兆芬; Michael R.Barer

    2011-01-01

    Objective To explore and analyze genetic mutations of phospholipase C (PLC)-encoding genes plcABCD among clinical isolates of Mycobacterium tuberculosis and to provide scientific basis for understanding virulence and pathogenesis of Mycobacterium tuberculosis. Methods A total of 102 isolates from patients with active tuberculosis were identified. Bacterial DNA was extracted. All plcABCD genes were amplified by polymerase chain reaction (PCR) and checked for deletions or mutations by agarose gel electrophoresis. Results According to presence or absence of plcABCD genes, 102 isolates were divided into 13 genotypes. Thirty-one (30.39%) isolates were plc wild genotype with all plcABCD genes; 71(69. 61%) isolates were plc mutant type with different plc gene deletions. Of 71 plc mutant isolates, 48 missed only one of four plc genes, 14 had deletions of 2 plc genes, 8 were triple mutants and 1 was quadruple mutant. There were 61 (59. 80%) isolates with plcD gene mutation, while the mutation rates of plcA, plcB and plcC genes were lower, which were 15. 69%(16/102), 9. 80%(10/102) and 16. 67%(17/ 102), respectively. Conclusion This study shows great diversity in plcABCD genes among clinical isolates of Mycobacterium tuberculosis, with the most common of plcD.%目的 分析临床分离的结核分枝杆菌中磷脂酶C(PLC)编码基因plcABCD的突变情况,以进一步了解结核分枝杆菌的致病力.方法 102株菌株均分离于结核病患者并准确鉴定.增菌后提取DNA,并对plcABCD 4个基因同时扩增,扩增产物经电泳后分析基因的突变或缺失.结果 根据plcABCD 4个基因的存在或缺失情况,102株菌可以分为13个基因型,其中31株含有完整的plcABCD所有基因.为plc野生株,占30.39%;71株菌有不同plc基因的缺失,为plc突变株,突变率为69.61%.71株突变型菌株中,只缺失任意1个plc基因的有48株,发生任意2个plc基因缺失或突变的共有14株,发生任意3个plc基因缺失或突变的共有8株

  11. RMI1/NCE4, a suppressor of genome instability, encodes a member of the RecQ helicase/Topo III complex

    NARCIS (Netherlands)

    Chang, M; Bellaoui, M; Zhang, CY; Desai, R; Morozov, P; Delgado-Cruzata, L; Rothstein, R; Freyer, GA; Boone, C; Brown, GW

    2005-01-01

    SGS1 encodes a DNA helicase whose homologues in human cells include the BLM, WRN, and RECQ4 genes, mutations in which lead to cancer-predisposition syndromes. Clustering of synthetic genetic interactions identified by large-scale genetic network analysis revealed that the genetic interaction profile

  12. Genetic Counseling

    Science.gov (United States)

    Genetic counseling provides information and support to people who have, or may be at risk for, genetic disorders. A ... meets with you to discuss genetic risks. The counseling may be for yourself or a family member. ...

  13. DNA-encoded chemical libraries: advancing beyond conventional small-molecule libraries.

    Science.gov (United States)

    Franzini, Raphael M; Neri, Dario; Scheuermann, Jörg

    2014-04-15

    DNA-encoded chemical libraries (DECLs) represent a promising tool in drug discovery. DECL technology allows the synthesis and screening of chemical libraries of unprecedented size at moderate costs. In analogy to phage-display technology, where large antibody libraries are displayed on the surface of filamentous phage and are genetically encoded in the phage genome, DECLs feature the display of individual small organic chemical moieties on DNA fragments serving as amplifiable identification barcodes. The DNA-tag facilitates the synthesis and allows the simultaneous screening of very large sets of compounds (up to billions of molecules), because the hit compounds can easily be identified and quantified by PCR-amplification of the DNA-barcode followed by high-throughput DNA sequencing. Several approaches have been used to generate DECLs, differing both in the methods used for library encoding and for the combinatorial assembly of chemical moieties. For example, DECLs can be used for fragment-based drug discovery, displaying a single molecule on DNA or two chemical moieties at the extremities of complementary DNA strands. DECLs can vary substantially in the chemical structures and the library size. While ultralarge libraries containing billions of compounds have been reported containing four or more sets of building blocks, also smaller libraries have been shown to be efficient for ligand discovery. In general, it has been found that the overall library size is a poor predictor for library performance and that the number and diversity of the building blocks are rather important indicators. Smaller libraries consisting of two to three sets of building blocks better fulfill the criteria of drug-likeness and often have higher quality. In this Account, we present advances in the DECL field from proof-of-principle studies to practical applications for drug discovery, both in industry and in academia. DECL technology can yield specific binders to a variety of target

  14. Improved Quantum Genetic Algorithm in Application of Scheduling Engineering Personnel

    Directory of Open Access Journals (Sweden)

    Huaixiao Wang

    2014-01-01

    Full Text Available To verify the availability of the improved quantum genetic algorithm in solving the scheduling engineering personnel problem, the following work has been carried out: the characteristics of the scheduling engineering personnel problem are analyzed, the quantum encoding method is proposed, and an improved quantum genetic algorithm is applied to address the issue. Taking the low efficiency and the bad performance of the conventional quantum genetic algorithm into account, a universal improved quantum genetic algorithm is introduced to solve the scheduling engineering personnel problem. Finally, the examples are applied to verify the effectiveness and superiority of the improved quantum genetic algorithm and the rationality of the encoding method.

  15. Cellular encoding for interactive evolutionary robotics

    NARCIS (Netherlands)

    Gruau, F.C.; Quatramaran, K.

    1996-01-01

    This work reports experiments in interactive evolutionary robotics. The goal is to evolve an Artificial Neural Network (ANN) to control the locomotion of an 8-legged robot. The ANNs are encoded using a cellular developmental process called cellular encoding. In a previous work similar experiments ha

  16. A METHOD OF SHAPE ENCODING AND RETRIEVAL

    Institute of Scientific and Technical Information of China (English)

    Huang Xianglin; Song Lei; Shen Lansun

    2002-01-01

    A method of shape encoding and retrieval is proposed in this letter, which uses centripetal code to encode shape and extracts shape's convex for retrieval. For the rotation invariance and translation invariance of the centripetal code and the normalization of convex,the proposed retrieval method is similarity transform resistant, Experimental results confirm this capability.

  17. Encoding asymmetry of the N-glycosylation motif facilitates glycoprotein evolution.

    Directory of Open Access Journals (Sweden)

    Ryan Williams

    Full Text Available Protein N-glycosylation is found in all domains of life and has a conserved role in glycoprotein folding and stability. In animals, glycoproteins transit through the Golgi where the N-glycans are trimmed and rebuilt with sequences that bind lectins, an innovation that greatly increases structural diversity and redundancy of glycoprotein-lectin interaction at the cell surface. Here we ask whether the natural tension between increasing diversity (glycan-protein interactions and site multiplicity (backup and status quo might be revealed by a phylogenic examination of glycoproteins and NXS/T(X ≠ P N-glycosylation sites. Site loss is more likely by mutation at Asn encoded by two adenosine (A-rich codons, while site gain is more probable by generating Ser or Thr downstream of an existing Asn. Thus mutations produce sites at novel positions more frequently than the reversal of recently lost sites, and therefore more paths though sequence space are made available to natural selection. An intra-species comparison of secretory and cytosolic proteins revealed a departure from equilibrium in sequences one-mutation-away from NXS/T and in (A content, indicating strong selective pressures and exploration of N-glycosylation positions during vertebrate evolution. Furthermore, secretory proteins have evolved at rates proportional to N-glycosylation site number, indicating adaptive interactions between the N-glycans and underlying protein. Given the topology of the genetic code, mutation of (A is more often nonsynonomous, and Lys, another target of many PTMs, is also encoded by two (A-rich codons. An examination of acetyl-Lys sites in proteins indicated similar evolutionary dynamics, consistent with asymmetry of the target and recognition portions of modified sites. Our results suggest that encoding asymmetry is an ancient mechanism of evolvability that increases diversity and experimentation with PTM site positions. Strong selective pressures on PTMs may have

  18. Nucleases Encoded by Integraded Elements CJIE2 and CJIE4 Inhibit Natural Transformation of Campylobacter Jejuni

    NARCIS (Netherlands)

    Gaasbeek, E.J.; Wagenaar, J.A.; Guilhabert, M.R.; Putten, van J.P.; Parker, C.T.; Wal, van der F.J.

    2010-01-01

    The species Campylobacter jejuni is naturally competent for DNA uptake; nevertheless, nonnaturally transformable strains do exist. For a subset of strains we previously showed that a periplasmic DNase, encoded by dns, inhibits natural transformation in C. jejuni. In the present study, genetic factor

  19. The Arabic Diatessaron Project: Digitalizing, Encoding, Lemmatization

    Directory of Open Access Journals (Sweden)

    Giuliano Lancioni

    2016-04-01

    Full Text Available The Arabic Diatessaron Project (henceforth ADP is an international research project in Digital Humanities that aims to collect, digitalise and encode all known manuscripts of the Arabic Diatessaron (henceforth AD, a text that has been relatively neglected in scholarly research. ADP’s final goal is to provide a number of tools that can enable scholars to effectively query, compare and investigate all known variants of the text that will be encoded as far as possible in compliance with the Text Encoding Initiative (TEI guidelines. The paper addresses a number of issues involved in the process of digitalising manuscripts included in the two existing editions (Ciasca 1888 and Marmardji 1935, adding variants in unedited manuscripts, encoding and lemmatising the text. Issues involved in the design of the ADP include presentation of variants, choice of the standard text, applicability of TEI guidelines, automatic translation between different encodings, cross-edition concordances and principles of lemmatisation.

  20. The Drosophila Medea gene is required downstream of dpp and encodes a functional homolog of human Smad4.

    Science.gov (United States)

    Hudson, J B; Podos, S D; Keith, K; Simpson, S L; Ferguson, E L

    1998-04-01

    The Transforming Growth Factor-beta superfamily member decapentaplegic (dpp) acts as an extracellular morphogen to pattern the embryonic ectoderm of the Drosophila embryo. To identify components of the dpp signaling pathway, we screened for mutations that act as dominant maternal enhancers of a weak allele of the dpp target gene zerknŁllt. In this screen, we recovered new alleles of the Mothers against dpp (Mad) and Medea genes. Phenotypic analysis of the new Medea mutations indicates that Medea, like Mad, is required for both embryonic and imaginal disc patterning. Genetic analysis suggests that Medea may have two independently mutable functions in patterning the embryonic ectoderm. Complete elimination of maternal and zygotic Medea activity in the early embryo results in a ventralized phenotype identical to that of null dpp mutants, indicating that Medea is required for all dpp-dependent signaling in embryonic dorsal-ventral patterning. Injection of mRNAs encoding DPP or a constitutively activated form of the DPP receptor, Thick veins, into embryos lacking all Medea activity failed to induce formation of any dorsal cell fates, demonstrating that Medea acts downstream of the thick veins receptor. We cloned Medea and found that it encodes a protein with striking sequence similarity to human SMAD4. Moreover, injection of human SMAD4 mRNA into embryos lacking all Medea activity conferred phenotypic rescue of the dorsal-ventral pattern, demonstrating conservation of function between the two gene products.

  1. A model for visual memory encoding.

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    Rodolphe Nenert

    Full Text Available Memory encoding engages multiple concurrent and sequential processes. While the individual processes involved in successful encoding have been examined in many studies, a sequence of events and the importance of modules associated with memory encoding has not been established. For this reason, we sought to perform a comprehensive examination of the network for memory encoding using data driven methods and to determine the directionality of the information flow in order to build a viable model of visual memory encoding. Forty healthy controls ages 19-59 performed a visual scene encoding task. FMRI data were preprocessed using SPM8 and then processed using independent component analysis (ICA with the reliability of the identified components confirmed using ICASSO as implemented in GIFT. The directionality of the information flow was examined using Granger causality analyses (GCA. All participants performed the fMRI task well above the chance level (>90% correct on both active and control conditions and the post-fMRI testing recall revealed correct memory encoding at 86.33 ± 5.83%. ICA identified involvement of components of five different networks in the process of memory encoding, and the GCA allowed for the directionality of the information flow to be assessed, from visual cortex via ventral stream to the attention network and then to the default mode network (DMN. Two additional networks involved in this process were the cerebellar and the auditory-insular network. This study provides evidence that successful visual memory encoding is dependent on multiple modules that are part of other networks that are only indirectly related to the main process. This model may help to identify the node(s of the network that are affected by a specific disease processes and explain the presence of memory encoding difficulties in patients in whom focal or global network dysfunction exists.

  2. A model for visual memory encoding.

    Science.gov (United States)

    Nenert, Rodolphe; Allendorfer, Jane B; Szaflarski, Jerzy P

    2014-01-01

    Memory encoding engages multiple concurrent and sequential processes. While the individual processes involved in successful encoding have been examined in many studies, a sequence of events and the importance of modules associated with memory encoding has not been established. For this reason, we sought to perform a comprehensive examination of the network for memory encoding using data driven methods and to determine the directionality of the information flow in order to build a viable model of visual memory encoding. Forty healthy controls ages 19-59 performed a visual scene encoding task. FMRI data were preprocessed using SPM8 and then processed using independent component analysis (ICA) with the reliability of the identified components confirmed using ICASSO as implemented in GIFT. The directionality of the information flow was examined using Granger causality analyses (GCA). All participants performed the fMRI task well above the chance level (>90% correct on both active and control conditions) and the post-fMRI testing recall revealed correct memory encoding at 86.33 ± 5.83%. ICA identified involvement of components of five different networks in the process of memory encoding, and the GCA allowed for the directionality of the information flow to be assessed, from visual cortex via ventral stream to the attention network and then to the default mode network (DMN). Two additional networks involved in this process were the cerebellar and the auditory-insular network. This study provides evidence that successful visual memory encoding is dependent on multiple modules that are part of other networks that are only indirectly related to the main process. This model may help to identify the node(s) of the network that are affected by a specific disease processes and explain the presence of memory encoding difficulties in patients in whom focal or global network dysfunction exists.

  3. Accelerated radial Fourier-velocity encoding using compressed sensing

    Energy Technology Data Exchange (ETDEWEB)

    Hilbert, Fabian; Han, Dietbert [Wuerzburg Univ. (Germany). Inst. of Radiology; Wech, Tobias; Koestler, Herbert [Wuerzburg Univ. (Germany). Inst. of Radiology; Wuerzburg Univ. (Germany). Comprehensive Heart Failure Center (CHFC)

    2014-10-01

    Purpose:Phase Contrast Magnetic Resonance Imaging (MRI) is a tool for non-invasive determination of flow velocities inside blood vessels. Because Phase Contrast MRI only measures a single mean velocity per voxel, it is only applicable to vessels significantly larger than the voxel size. In contrast, Fourier Velocity Encoding measures the entire velocity distribution inside a voxel, but requires a much longer acquisition time. For accurate diagnosis of stenosis in vessels on the scale of spatial resolution, it is important to know the velocity distribution of a voxel. Our aim was to determine velocity distributions with accelerated Fourier Velocity Encoding in an acquisition time required for a conventional Phase Contrast image. Materials and Methods:We imaged the femoral artery of healthy volunteers with ECG - triggered, radial CINE acquisition. Data acquisition was accelerated by undersampling, while missing data were reconstructed by Compressed Sensing. Velocity spectra of the vessel were evaluated by high resolution Phase Contrast images and compared to spectra from fully sampled and undersampled Fourier Velocity Encoding. By means of undersampling, it was possible to reduce the scan time for Fourier Velocity Encoding to the duration required for a conventional Phase Contrast image. Results:Acquisition time for a fully sampled data set with 12 different Velocity Encodings was 40 min. By applying a 12.6 - fold retrospective undersampling, a data set was generated equal to 3:10 min acquisition time, which is similar to a conventional Phase Contrast measurement. Velocity spectra from fully sampled and undersampled Fourier Velocity Encoded images are in good agreement and show the same maximum velocities as compared to velocity maps from Phase Contrast measurements. Conclusion: Compressed Sensing proved to reliably reconstruct Fourier Velocity Encoded data. Our results indicate that Fourier Velocity Encoding allows an accurate determination of the velocity

  4. An Encoding Technique for Multiobjective Evolutionary Algorithms Applied to Power Distribution System Reconfiguration

    Directory of Open Access Journals (Sweden)

    J. L. Guardado

    2014-01-01

    Full Text Available Network reconfiguration is an alternative to reduce power losses and optimize the operation of power distribution systems. In this paper, an encoding scheme for evolutionary algorithms is proposed in order to search efficiently for the Pareto-optimal solutions during the reconfiguration of power distribution systems considering multiobjective optimization. The encoding scheme is based on the edge window decoder (EWD technique, which was embedded in the Strength Pareto Evolutionary Algorithm 2 (SPEA2 and the Nondominated Sorting Genetic Algorithm II (NSGA-II. The effectiveness of the encoding scheme was proved by solving a test problem for which the true Pareto-optimal solutions are known in advance. In order to prove the practicability of the encoding scheme, a real distribution system was used to find the near Pareto-optimal solutions for different objective functions to optimize.

  5. An encoding technique for multiobjective evolutionary algorithms applied to power distribution system reconfiguration.

    Science.gov (United States)

    Guardado, J L; Rivas-Davalos, F; Torres, J; Maximov, S; Melgoza, E

    2014-01-01

    Network reconfiguration is an alternative to reduce power losses and optimize the operation of power distribution systems. In this paper, an encoding scheme for evolutionary algorithms is proposed in order to search efficiently for the Pareto-optimal solutions during the reconfiguration of power distribution systems considering multiobjective optimization. The encoding scheme is based on the edge window decoder (EWD) technique, which was embedded in the Strength Pareto Evolutionary Algorithm 2 (SPEA2) and the Nondominated Sorting Genetic Algorithm II (NSGA-II). The effectiveness of the encoding scheme was proved by solving a test problem for which the true Pareto-optimal solutions are known in advance. In order to prove the practicability of the encoding scheme, a real distribution system was used to find the near Pareto-optimal solutions for different objective functions to optimize.

  6. Functional fluorescent Ca2+ indicator proteins in transgenic mice under TET control.

    Directory of Open Access Journals (Sweden)

    Mazahir T Hasan

    2004-06-01

    Full Text Available Genetically encoded fluorescent calcium indicator proteins (FCIPs are promising tools to study calcium dynamics in many activity-dependent molecular and cellular processes. Great hopes-for the measurement of population activity, in particular-have therefore been placed on calcium indicators derived from the green fluorescent protein and their expression in (selected neuronal populations. Calcium transients can rise within milliseconds, making them suitable as reporters of fast neuronal activity. We here report the production of stable transgenic mouse lines with two different functional calcium indicators, inverse pericam and camgaroo-2, under the control of the tetracycline-inducible promoter. Using a variety of in vitro and in vivo assays, we find that stimuli known to increase intracellular calcium concentration (somatically triggered action potentials (APs and synaptic and sensory stimulation can cause substantial and rapid changes in FCIP fluorescence of inverse pericam and camgaroo-2.

  7. Rv0989c encodes a novel (E)-geranyl diphosphate synthase facilitating decaprenyl diphosphate biosynthesis in Mycobacterium tuberculosis.

    Science.gov (United States)

    Mann, Francis M; Thomas, Jill A; Peters, Reuben J

    2011-02-04

    Mycobacterium tuberculosis (Mtb) has a highly complex cell wall, which is required for both bacterial survival and infection. Cell wall biosynthesis is dependent on decaprenyl diphosphate as a glyco-carrier, which is hence an essential metabolite in this pathogen. Previous biochemical studies indicated (E)-geranyl diphosphate (GPP) is required for the synthesis of decaprenyl diphosphate. Here we demonstrate that Rv0989c encodes the "missing" GPP synthase, representing the first such enzyme to be characterized from bacteria, and which presumably is involved in decaprenyl diphosphate biosynthesis in Mtb. Our investigation also has revealed previously unrecognized substrate plasticity of the farnesyl diphosphate synthases from Mtb, resolving previous discrepancies between biochemical and genetic studies of cell wall biosynthesis.

  8. The you gene encodes an EGF-CUB protein essential for Hedgehog signaling in zebrafish.

    Directory of Open Access Journals (Sweden)

    Ian G Woods

    2005-03-01

    Full Text Available Hedgehog signaling is required for many aspects of development in vertebrates and invertebrates. Misregulation of the Hedgehog pathway causes developmental abnormalities and has been implicated in certain types of cancer. Large-scale genetic screens in zebrafish have identified a group of mutations, termed you-class mutations, that share common defects in somite shape and in most cases disrupt Hedgehog signaling. These mutant embryos exhibit U-shaped somites characteristic of defects in slow muscle development. In addition, Hedgehog pathway mutations disrupt spinal cord patterning. We report the positional cloning of you, one of the original you-class mutations, and show that it is required for Hedgehog signaling in the development of slow muscle and in the specification of ventral fates in the spinal cord. The you gene encodes a novel protein with conserved EGF and CUB domains and a secretory pathway signal sequence. Epistasis experiments support an extracellular role for You upstream of the Hedgehog response mechanism. Analysis of chimeras indicates that you mutant cells can appropriately respond to Hedgehog signaling in a wild-type environment. Additional chimera analysis indicates that wild-type you gene function is not required in axial Hedgehog-producing cells, suggesting that You is essential for transport or stability of Hedgehog signals in the extracellular environment. Our positional cloning and functional studies demonstrate that You is a novel extracellular component of the Hedgehog pathway in vertebrates.

  9. Sudden infant death syndrome and the genetics of inflammation

    Directory of Open Access Journals (Sweden)

    Linda eFerrante

    2015-02-01

    Full Text Available Several studies report signs of slight infection prior to death in cases of sudden infant death syndrome (SIDS. Based on this, a hypothesis of an altered immunological homeostasis has been postulated. The cytokines are important cellular mediators that are crucial for infant health by regulating cell activity during the inflammatory process. The pro-inflammatory cytokines favor inflammation; the most important of these are IL-1α, IL-1β, IL-6, IL-8, IL-12, IL-18, TNF-α and IFN-γ. These cytokines are controlled by the anti-inflammatory cytokines. This is accomplished by reducing the pro-inflammatory cytokine production, and thus counteracts their biological effect. The major anti-inflammatory cytokines are interleukin 1 receptor antagonist (IL-1ra, IL-4, IL-10, IL-11, and IL-13. The last decade there has been focus on genetic studies within genes that are important for the immune system, for SIDS with a special interest of the genes encoding the cytokines. This is because the cytokine genes are considered to be the genes most likely to explain the vulnerability to infection, and several studies have investigated these genes in an attempt to uncover associations between SIDS and different genetic variants. So far the genes encoding IL-1, IL-6, IL-10 and TNF-α are the most investigated within SIDS research, and several studies indicates associations between specific variants of these genes and SIDS. Taken together this may indicate that in at least a subset of SIDS predisposing genetic variants of the immune genes are involved. However, the immune system and the cytokine network are complex, and more studies are needed in order to better understand the interplay between different genetic variations and how this may contribute to an unfavorable immunological response.

  10. Cellobiohydrolase variants and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Wogulis, Mark

    2017-04-04

    The present invention relates to variants of a parent cellobiohydrolase II. The present invention also relates to polynucleotides encoding the variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the variants.

  11. Chemical Space of DNA-Encoded Libraries.

    Science.gov (United States)

    Franzini, Raphael M; Randolph, Cassie

    2016-07-28

    In recent years, DNA-encoded chemical libraries (DECLs) have attracted considerable attention as a potential discovery tool in drug development. Screening encoded libraries may offer advantages over conventional hit discovery approaches and has the potential to complement such methods in pharmaceutical research. As a result of the increased application of encoded libraries in drug discovery, a growing number of hit compounds are emerging in scientific literature. In this review we evaluate reported encoded library-derived structures and identify general trends of these compounds in relation to library design parameters. We in particular emphasize the combinatorial nature of these libraries. Generally, the reported molecules demonstrate the ability of this technology to afford hits suitable for further lead development, and on the basis of them, we derive guidelines for DECL design.

  12. [Genetic amniocentesis].

    Science.gov (United States)

    Violante Díaz, M; Carrillo Hinojosa, M; García Necoechea, M P; Escobedo Aguirre, F; Lowenberg Favela, E; Ahued Ahued, J R

    1989-04-01

    179 patients were studied by genetic amniocentesis (GA) in sessions of 3 punctures each. This was done in order to follow a prenatal diagnosis (PD) program and study amniotic fluid at the Hospital Regional 20 de Novembre (ISSSTE) between May 1983 and December 1987. The parameters taken were: age, indications, number of sessions, number punctures, echosonographic studies for gestational age, placental insertion, punction site, amniotic fluid volume, blood contamination, failures and handling of the patient. A low incidence of abortion is reported. We don't have cases of dripping of amniotic fluid or transvaginal haemorrhage. Multiple insertion of the needle and placental or vessel lesions of the cord, as causes of a fetal death are still argued if we have in mind avoiding chances; we didn't have those complications in our cases. The percent is low if there are not previous spontaneous abortions. 79% of the amniotic fluid samples were sent between the 15th and 17th weeks of pregnancy. For alpha fetus protein determination 12 and for biochemical studies 1, specially for beta-galactosidase level. This was done at the Biomedical Investigation Institute of the National Autonomous University of Mexico (in parents with generalized gangliosidosis GM1). Even though results were good, the technique has still risks and complications. An ultrasonic study of the procedures made by physicians with trustable experience is needed. Our country has the need to create more Prenatal Genetic Diagnosis Centers.

  13. Indicators for livestock and crop biodiversity

    NARCIS (Netherlands)

    Eaton, D.J.F.; Windig, J.J.; Hiemstra, S.J.; Veller, van M.G.P.; Trach, N.X.; Hao, P.X.; Doan, D.H.; Hu, R.

    2006-01-01

    The focus of this study is on indicators for genetic resources, relevant for food and agriculture, for future food security and other functions of genetic resources or agro-biodiversity. The is one small area in the range of levels and sectors. It is recognized that there are many interrelationships

  14. Clustering of polarization-encoded images.

    Science.gov (United States)

    Zallat, Jihad; Collet, Christophe; Takakura, Yoshitate

    2004-01-10

    Polarization-encoded imaging consists of the distributed measurements of polarization parameters for each pixel of an image. We address clustering of multidimensional polarization-encoded images. The spatial coherence of polarization information is considered. Two methods of analysis are proposed: polarization contrast enhancement and a more-sophisticated image-processing algorithm based on a Markovian model. The proposed algorithms are applied and validated with two different Mueller images acquired by a fully polarimetric imaging system.

  15. Using XML to encode TMA DES metadata

    Directory of Open Access Journals (Sweden)

    Oliver Lyttleton

    2011-01-01

    Full Text Available Background: The Tissue Microarray Data Exchange Specification (TMA DES is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. Materials and Methods: We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. Results: We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. Conclusions: All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs.

  16. Using XML to encode TMA DES metadata.

    Science.gov (United States)

    Lyttleton, Oliver; Wright, Alexander; Treanor, Darren; Lewis, Paul

    2011-01-01

    The Tissue Microarray Data Exchange Specification (TMA DES) is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs.

  17. Neurally Encoding Time for Olfactory Navigation.

    Directory of Open Access Journals (Sweden)

    In Jun Park

    2016-01-01

    Full Text Available Accurately encoding time is one of the fundamental challenges faced by the nervous system in mediating behavior. We recently reported that some animals have a specialized population of rhythmically active neurons in their olfactory organs with the potential to peripherally encode temporal information about odor encounters. If these neurons do indeed encode the timing of odor arrivals, it should be possible to demonstrate that this capacity has some functional significance. Here we show how this sensory input can profoundly influence an animal's ability to locate the source of odor cues in realistic turbulent environments-a common task faced by species that rely on olfactory cues for navigation. Using detailed data from a turbulent plume created in the laboratory, we reconstruct the spatiotemporal behavior of a real odor field. We use recurrence theory to show that information about position relative to the source of the odor plume is embedded in the timing between odor pulses. Then, using a parameterized computational model, we show how an animal can use populations of rhythmically active neurons to capture and encode this temporal information in real time, and use it to efficiently navigate to an odor source. Our results demonstrate that the capacity to accurately encode temporal information about sensory cues may be crucial for efficient olfactory navigation. More generally, our results suggest a mechanism for extracting and encoding temporal information from the sensory environment that could have broad utility for neural information processing.

  18. Current View on Phytoplasma Genomes and Encoded Metabolism

    Directory of Open Access Journals (Sweden)

    Michael Kube

    2012-01-01

    Full Text Available Phytoplasmas are specialised bacteria that are obligate parasites of plant phloem tissue and insects. These bacteria have resisted all attempts of cell-free cultivation. Genome research is of particular importance to analyse the genetic endowment of such bacteria. Here we review the gene content of the four completely sequenced ‘Candidatus Phytoplasma’ genomes that include those of ‘Ca. P. asteris’ strains OY-M and AY-WB, ‘Ca. P. australiense,’ and ‘Ca. P. mali’. These genomes are characterized by chromosome condensation resulting in sizes below 900 kb and a G + C content of less than 28%. Evolutionary adaption of the phytoplasmas to nutrient-rich environments resulted in losses of genetic modules and increased host dependency highlighted by the transport systems and limited metabolic repertoire. On the other hand, duplication and integration events enlarged the chromosomes and contribute to genome instability. Present differences in the content of membrane and secreted proteins reflect the host adaptation in the phytoplasma strains. General differences are obvious between different phylogenetic subgroups. ‘Ca. P. mali’ is separated from the other strains by its deviating chromosome organization, the genetic repertoire for recombination and excision repair of nucleotides or the loss of the complete energy-yielding part of the glycolysis. Apart from these differences, comparative analysis exemplified that all four phytoplasmas are likely to encode an alternative pathway to generate pyruvate and ATP.

  19. The expanded genetic alphabet.

    Science.gov (United States)

    Malyshev, Denis A; Romesberg, Floyd E

    2015-10-05

    All biological information, since the last common ancestor of all life on Earth, has been encoded by a genetic alphabet consisting of only four nucleotides that form two base pairs. Long-standing efforts to develop two synthetic nucleotides that form a third, unnatural base pair (UBP) have recently yielded three promising candidates, one based on alternative hydrogen bonding, and two based on hydrophobic and packing forces. All three of these UBPs are replicated and transcribed with remarkable efficiency and fidelity, and the latter two thus demonstrate that hydrogen bonding is not unique in its ability to underlie the storage and retrieval of genetic information. This Review highlights these recent developments as well as the applications enabled by the UBPs, including the expansion of the evolution process to include new functionality and the creation of semi-synthetic life that stores increased information.

  20. Neurophysiology of successful encoding and retrieval of source memory.

    Science.gov (United States)

    Cansino, Selene; Trejo-Morales, Patricia

    2008-03-01

    Event-related potentials were recorded during encoding, to identify whether brain activity predicts subsequent retrieval of spatial source information, and during retrieval, to investigate the neural correlates of successful and unsuccessful spatial context recollection. The amplitude registered during encoding for study items that were later recognized and assigned a correct source judgment was more positive than the amplitude for recognized items given incorrect source judgments; this difference started 480 msec poststimulus, predominantly at central and anterior sites. During retrieval, the waveform was more positive from 250 to 1,600 msec poststimulus when the brain had retrieved episodic information successfully than when it had failed. These findings indicate that brain electrical activity recorded during the first presentation of an item within its context predicts the subsequent retrieval of the specific spatial context. During retrieval, brain activity differed quantitatively at anterior sites and qualitatively at posterior sites according to the accuracy of source memory.

  1. Transduction and encoding sensory information by skin mechanoreceptors.

    Science.gov (United States)

    Hao, Jizhe; Bonnet, Caroline; Amsalem, Muriel; Ruel, Jérôme; Delmas, Patrick

    2015-01-01

    Physical contact with the external world occurs through specialized neural structures called mechanoreceptors. Cutaneous mechanoreceptors provide information to the central nervous system (CNS) about touch, pressure, vibration, and skin stretch. The physiological function of these mechanoreceptors is to convert physical forces into neuronal signals. Key questions concern the molecular identity of the mechanoelectric transducer channels and the mechanisms by which the physical parameters of the mechanical stimulus are encoded into patterns of action potentials (APs). Compelling data indicate that the biophysical traits of mechanosensitive channels combined with the collection of voltage-gated channels are essential to describe the nature of the stimulus. Recent research also points to a critical role of the auxiliary cell-nerve ending communication in encoding stimulus properties. This review describes the characteristics of ion channels responsible for translating mechanical stimuli into the neural codes that underlie touch perception and pain.

  2. Bacillus caldolyticus prs gene encoding phosphoribosyl-diphosphate synthase

    DEFF Research Database (Denmark)

    Krath, Britta N.; Hove-Jensen, Bjarne

    1996-01-01

    The prs gene, encoding phosphoribosyl-diphosphate (PRPP) synthase, as well as the flanking DNA sequences were cloned and sequenced from the Gram-positive thermophile, Bacillus caldolyticus. Comparison with the homologous sequences from the mesophile, Bacillus subtilis, revealed a gene (gca......D) encoding N-acetylglucosamine-1-phosphate uridyltransferase upstream of prs, and a gene homologous to ctc downstream of prs. cDNA synthesis with a B. caldolyticus gcaD-prs-ctc-specified mRNA as template, followed by amplification utilising the polymerase chain reaction indicated that the three genes are co......-transcribed. Comparison of amino acid sequences revealed a high similarity among PRPP synthases across a wide phylogenetic range. An E. coli strain harbouring the B. caldolyticus prs gene in a multicopy plasmid produced PRPP synthase activity 33-fold over the activity of a haploid B. caldolyticus strain. B. caldolyticus...

  3. Visually Improved Image Compression by Combining EZW Encoding with Texture Modeling using Huffman Encoder

    Directory of Open Access Journals (Sweden)

    Vinay U. Kale

    2010-05-01

    Full Text Available This paper proposes a technique for image compression which uses the Wavelet-based Image/Texture Coding Hybrid (WITCH scheme [1] in combination with Huffman encoder. It implements a hybrid coding approach, while nevertheless preserving the features of progressive and lossless coding. The hybrid scheme was designed to encode the structural image information by Embedded Zerotree Wavelet (EZW encoding algorithm [2] and the stochastic texture in a model-based manner and this encoded data is then compressed using Huffman encoder. The scheme proposed here achieves superior subjective quality while increasing the compression ratio by more than a factor of three or even four. With this technique, it is possible to achieve compression ratios as high as 10 to 12 but with some minor distortions in the encoded image.

  4. A new encoding scheme-based hybrid algorithm for minimising two-machine flow-shop group scheduling problem

    Science.gov (United States)

    Liou, Cheng-Dar; Hsieh, Yi-Chih; Chen, Yin-Yann

    2013-01-01

    This article investigates the two-machine flow-shop group scheduling problem (GSP) with sequence-dependent setup and removal times, and job transportation times between machines. The objective is to minimise the total completion time. As known, this problem is an NP-hard problem and generalises the typical two-machine GSPs. In this article, a new encoding scheme based on permutation representation is proposed to transform a random job permutation to a feasible permutation for GSPs. The proposed encoding scheme simultaneously determines both the sequence of jobs in each group and the sequence of groups. By reasonably combining particle swarm optimisation (PSO) and genetic algorithm (GA), we develop a fast and easily implemented hybrid algorithm (HA) for solving the considered problems. The effectiveness and efficiency of the proposed HA are demonstrated and compared with those of standard PSO and GA by numerical results of various tested instances with group numbers up to 20. In addition, three different lower bounds are developed to evaluate the solution quality of the HA. Limited numerical results indicate that the proposed HA is a viable and effective approach for the studied two-machine flow-shop group scheduling problem.

  5. DNA-encoded chemical libraries: foundations and applications in lead discovery.

    Science.gov (United States)

    Zimmermann, Gunther; Neri, Dario

    2016-11-01

    DNA-encoded chemical libraries have emerged as a powerful tool for hit identification in the pharmaceutical industry and in academia. Similar to biological display techniques (such as phage display technology), DNA-encoded chemical libraries contain a link between the displayed chemical building block and an amplifiable genetic barcode on DNA. Using routine procedures, libraries containing millions to billions of compounds can be easily produced within a few weeks. The resulting compound libraries are screened in a single test tube against proteins of pharmaceutical interest and hits can be identified by PCR amplification of DNA barcodes and subsequent high-throughput sequencing.

  6. An encyclopedia of mouse DNA elements (Mouse ENCODE).

    Science.gov (United States)

    Stamatoyannopoulos, John A; Snyder, Michael; Hardison, Ross; Ren, Bing; Gingeras, Thomas; Gilbert, David M; Groudine, Mark; Bender, Michael; Kaul, Rajinder; Canfield, Theresa; Giste, Erica; Johnson, Audra; Zhang, Mia; Balasundaram, Gayathri; Byron, Rachel; Roach, Vaughan; Sabo, Peter J; Sandstrom, Richard; Stehling, A Sandra; Thurman, Robert E; Weissman, Sherman M; Cayting, Philip; Hariharan, Manoj; Lian, Jin; Cheng, Yong; Landt, Stephen G; Ma, Zhihai; Wold, Barbara J; Dekker, Job; Crawford, Gregory E; Keller, Cheryl A; Wu, Weisheng; Morrissey, Christopher; Kumar, Swathi A; Mishra, Tejaswini; Jain, Deepti; Byrska-Bishop, Marta; Blankenberg, Daniel; Lajoie, Bryan R; Jain, Gaurav; Sanyal, Amartya; Chen, Kaun-Bei; Denas, Olgert; Taylor, James; Blobel, Gerd A; Weiss, Mitchell J; Pimkin, Max; Deng, Wulan; Marinov, Georgi K; Williams, Brian A; Fisher-Aylor, Katherine I; Desalvo, Gilberto; Kiralusha, Anthony; Trout, Diane; Amrhein, Henry; Mortazavi, Ali; Edsall, Lee; McCleary, David; Kuan, Samantha; Shen, Yin; Yue, Feng; Ye, Zhen; Davis, Carrie A; Zaleski, Chris; Jha, Sonali; Xue, Chenghai; Dobin, Alex; Lin, Wei; Fastuca, Meagan; Wang, Huaien; Guigo, Roderic; Djebali, Sarah; Lagarde, Julien; Ryba, Tyrone; Sasaki, Takayo; Malladi, Venkat S; Cline, Melissa S; Kirkup, Vanessa M; Learned, Katrina; Rosenbloom, Kate R; Kent, W James; Feingold, Elise A; Good, Peter J; Pazin, Michael; Lowdon, Rebecca F; Adams, Leslie B

    2012-08-13

    To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.

  7. Physical exercise during encoding improves vocabulary learning in young female adults: a neuroendocrinological study.

    Directory of Open Access Journals (Sweden)

    Maren Schmidt-Kassow

    Full Text Available Acute physical activity has been repeatedly shown to improve various cognitive functions. However, there have been no investigations comparing the effects of exercise during verbal encoding versus exercise prior to encoding on long-term memory performance. In this current psychoneuroendocrinological study we aim to test whether light to moderate ergometric bicycling during vocabulary encoding enhances subsequent recall compared to encoding during physical rest and encoding after being physically active. Furthermore, we examined the kinetics of brain-derived neurotrophic factor (BDNF in serum which has been previously shown to correlate with learning performance. We also controlled for the BDNF val66met polymorphism. We found better vocabulary test performance for subjects that were physically active during the encoding phase compared to sedentary subjects. Post-hoc tests revealed that this effect was particularly present in initially low performers. BDNF in serum and BDNF genotype failed to account for the current result. Our data indicates that light to moderate simultaneous physical activity during encoding, but not prior to encoding, is beneficial for subsequent recall of new items.

  8. Identification of a genetic cluster influencing memory performance and hippocampal activity in humans.

    Science.gov (United States)

    de Quervain, Dominique J-F; Papassotiropoulos, Andreas

    2006-03-14

    Experimental work in animals has shown that memory formation depends on a cascade of molecular events. Here we show that variability of human memory performance is related to variability in genes encoding proteins of this signaling cascade, including the NMDA and metabotrobic glutamate receptors, adenylyl cyclase, CAMKII, PKA, and PKC. The individual profile of genetic variability in these signaling molecules correlated significantly with episodic memory performance (P < 0.00001). Moreover, functional MRI during memory formation revealed that this genetic profile correlated with activations in memory-related brain regions, including the hippocampus and parahippocampal gyrus. The present study indicates that genetic variability in the human homologues of memory-related signaling molecules contributes to interindividual differences in human memory performance and memory-related brain activations.

  9. Genetic Disorders

    Science.gov (United States)

    ... This can cause a medical condition called a genetic disorder. You can inherit a gene mutation from ... during your lifetime. There are three types of genetic disorders: Single-gene disorders, where a mutation affects ...

  10. Genetic modification and genetic determinism.

    Science.gov (United States)

    Resnik, David B; Vorhaus, Daniel B

    2006-06-26

    In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions.

  11. Genetic variation in KCNA5

    DEFF Research Database (Denmark)

    Christophersen, Ingrid E; Olesen, Morten S; Liang, Bo

    2012-01-01

    (Kur). Three studies have identified loss-of-function mutations in KCNA5 in patients with idiopathic AF. We hypothesized that early-onset lone AF is associated with high prevalence of genetic variants in KCNA5 and KCNAB2.Methods and resultsThe coding sequences of KCNA5 and KCNAB2 were sequenced in 307 patients......AimsGenetic factors may be important in the development of atrial fibrillation (AF) in the young. KCNA5 encodes the potassium channel a-subunit K(V)1.5, which underlies the voltage-gated atrial-specific potassium current I(Kur). KCNAB2 encodes K(V)ß2, a ß-subunit of K(V)1.5, which increases I...

  12. Imaging Genetics

    Science.gov (United States)

    Munoz, Karen E.; Hyde, Luke W.; Hariri, Ahmad R.

    2009-01-01

    Imaging genetics is an experimental strategy that integrates molecular genetics and neuroimaging technology to examine biological mechanisms that mediate differences in behavior and the risks for psychiatric disorder. The basic principles in imaging genetics and the development of the field are discussed.

  13. Genetic principles.

    Science.gov (United States)

    Abuelo, D

    1987-01-01

    The author discusses the basic principles of genetics, including the classification of genetic disorders and a consideration of the rules and mechanisms of inheritance. The most common pitfalls in clinical genetic diagnosis are described, with emphasis on the problem of the negative or misleading family history.

  14. Imaging Genetics

    Science.gov (United States)

    Munoz, Karen E.; Hyde, Luke W.; Hariri, Ahmad R.

    2009-01-01

    Imaging genetics is an experimental strategy that integrates molecular genetics and neuroimaging technology to examine biological mechanisms that mediate differences in behavior and the risks for psychiatric disorder. The basic principles in imaging genetics and the development of the field are discussed.

  15. Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome

    Directory of Open Access Journals (Sweden)

    Marchesi Julian R

    2010-01-01

    Full Text Available Abstract Background Little is known regarding the pool of mobile genetic elements associated with the human gut microbiome. In this study we employed the culture independent TRACA system to isolate novel plasmids from the human gut microbiota, and a comparative metagenomic analysis to investigate the distribution and relative abundance of functions encoded by these plasmids in the human gut microbiome. Results Novel plasmids were acquired from the human gut microbiome, and homologous nucleotide sequences with high identity (>90% to two plasmids (pTRACA10 and pTRACA22 were identified in the multiple human gut microbiomes analysed here. However, no homologous nucleotide sequences to these plasmids were identified in the murine gut or environmental metagenomes. Functions encoded by the plasmids pTRACA10 and pTRACA22 were found to be more prevalent in the human gut microbiome when compared to microbial communities from other environments. Among the most prevalent functions identified was a putative RelBE toxin-antitoxin (TA addiction module, and subsequent analysis revealed that this was most closely related to putative TA modules from gut associated bacteria belonging to the Firmicutes. A broad phylogenetic distribution of RelE toxin genes was observed in gut associated bacterial species (Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria, but no RelE homologues were identified in gut associated archaeal species. We also provide indirect evidence for the horizontal transfer of these genes between bacterial species belonging to disparate phylogenetic divisions, namely Gram negative Proteobacteria and Gram positive species from the Firmicutes division. Conclusions The application of a culture independent system to capture novel plasmids from the human gut mobile metagenome, coupled with subsequent comparative metagenomic analysis, highlighted the unexpected prevalence of plasmid encoded functions in the gut microbial ecosystem. In

  16. Expression of genes encoding extracellular matrix proteins: a macroarray study.

    Science.gov (United States)

    Futyma, Konrad; Miotła, Paweł; Różyńska, Krystyna; Zdunek, Małgorzata; Semczuk, Andrzej; Rechberger, Tomasz; Wojcierowski, Jacek

    2014-12-01

    Endometrial cancer (EC) is one of the most common gynecological malignancies in Poland, with well-established risk factors. Genetic instability and molecular alterations responsible for endometrial carcinogenesis have been systematically investigated. The aim of the present study was to investigate, by means of cDNA macroarrays, the expression profiles of genes encoding extracellular matrix (ECM) proteins in ECs. Tissue specimens were collected during surgical procedures from 40 patients with EC, and control tissue was collected from 9 patients with uterine leiomyomas. RNA was isolated and RT-PCR with radioisotope-labeled cDNA was performed. The levels of ECM protein gene expression in normal endometrial tissues were compared to the expression of these genes in EC specimens. Statistically significant differences in gene expression, stratified by clinical stage of the ECs, were detected for aggrecan, vitronectin, tenascin R, nidogen and two collagen proteins: type VIII chain α1 and type XI chain α2. All of these proteins were overexpressed in stage III endometrial carcinomas compared to levels in stage I and II uterine neoplasms. In conclusion, increased expression of genes encoding ECM proteins may play an important role in facilitating accelerated disease progression of human ECs.

  17. On the edge of language acquisition: inherent constraints on encoding multisyllabic sequences in the neonate brain.

    Science.gov (United States)

    Ferry, Alissa L; Fló, Ana; Brusini, Perrine; Cattarossi, Luigi; Macagno, Francesco; Nespor, Marina; Mehler, Jacques

    2016-05-01

    To understand language, humans must encode information from rapid, sequential streams of syllables - tracking their order and organizing them into words, phrases, and sentences. We used Near-Infrared Spectroscopy (NIRS) to determine whether human neonates are born with the capacity to track the positions of syllables in multisyllabic sequences. After familiarization with a six-syllable sequence, the neonate brain responded to the change (as shown by an increase in oxy-hemoglobin) when the two edge syllables switched positions but not when two middle syllables switched positions (Experiment 1), indicating that they encoded the syllables at the edges of sequences better than those in the middle. Moreover, when a 25 ms pause was inserted between the middle syllables as a segmentation cue, neonates' brains were sensitive to the change (Experiment 2), indicating that subtle cues in speech can signal a boundary, with enhanced encoding of the syllables located at the edges of that boundary. These findings suggest that neonates' brains can encode information from multisyllabic sequences and that this encoding is constrained. Moreover, subtle segmentation cues in a sequence of syllables provide a mechanism with which to accurately encode positional information from longer sequences. Tracking the order of syllables is necessary to understand language and our results suggest that the foundations for this encoding are present at birth. © 2015 John Wiley & Sons Ltd.

  18. The yrpAB operon of Yersinia ruckeri encoding two putative U32 peptidases is involved in virulence and induced under microaerobic conditions.

    Science.gov (United States)

    Navais, Roberto; Méndez, Jessica; Pérez-Pascual, David; Cascales, Desirée; Guijarro, José A

    2014-07-01

    In an attempt to dissect the virulence mechanisms of Yersinia ruckeri two adjacent genes, yrpA and yrpB, encoding putative peptidases belonging to the U32 family, were analyzed. Similar genes, with the same genetic organization were identified in genomic analysis of human-pathogenic yersiniae. RT-PCR studies indicated that these genes form an operon in Y. ruckeri. Transcriptional studies using an yrpB::lacZY fusion showed high levels of expression of these genes in the presence of peptone in the culture medium, as well as under oxygen-limited conditions. These two factors had a synergic effect on gene induction when both were present simultaneously during bacterial incubation, which indicates the important role that environmental conditions in the fish gut can play in the regulation of specific genes. LD 50 experiments using an yrpA insertional mutant strain demonstrated the participation of this gene in the virulence of Y. ruckeri.

  19. Reader set encoding for directory of shared cache memory in multiprocessor system

    Science.gov (United States)

    Ahn, Dnaiel; Ceze, Luis H.; Gara, Alan; Ohmacht, Martin; Xiaotong, Zhuang

    2014-06-10

    In a parallel processing system with speculative execution, conflict checking occurs in a directory lookup of a cache memory that is shared by all processors. In each case, the same physical memory address will map to the same set of that cache, no matter which processor originated that access. The directory includes a dynamic reader set encoding, indicating what speculative threads have read a particular line. This reader set encoding is used in conflict checking. A bitset encoding is used to specify particular threads that have read the line.

  20. Nonlinear Inversion of Potential-Field Data Using an Improved Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    Feng Gangding; Chen Chao

    2004-01-01

    The genetic algorithm is useful for solving an inversion of complex nonlinear geophysical equations. The multi-point search of the genetic algorithm makes it easier to find a globally optimal solution and avoid falling into a local extremum. The search efficiency of the genetic algorithm is a key to producing successful solutions in a huge multi-parameter model space. The encoding mechanism of the genetic algorithm affects the searching processes in the evolution. Not all genetic operations perform perfectly in a search under either a binary or decimal encoding system. As such, a standard genetic algorithm (SGA) is sometimes unable to resolve an optimization problem such as a simple geophysical inversion. With the binary encoding system the operation of the crossover may produce more new individuals. The decimal encoding system, on the other hand, makes the mutation generate more new genes. This paper discusses approaches of exploiting the search potentials of genetic operations with different encoding systems and presents a hybrid-encoding mechanism for the genetic algorithm. This is referred to as the hybrid-encoding genetic algorithm (HEGA). The method is based on the routine in which the mutation operation is executed in decimal code and other operations in binary code. HEGA guarantees the birth of better genes by mutation processing with a high probability, so that it is beneficial for resolving the inversions of complicated problems. Synthetic and real-world examples demonstrate the advantages of using HEGA in the inversion of potential-field data.

  1. RNA chaperones encoded by RNA viruses

    Institute of Scientific and Technical Information of China (English)

    Jie Yang; Hongjie Xia; Qi Qian; Xi Zhou

    2015-01-01

    RNAs are functionally diverse macromolecules whose proper functions rely strictly upon their correct tertiary structures. However, because of their high structural flexibility, correct folding of RNAs is challenging and slow. Therefore, cells and viruses encode a variety of RNA remodeling proteins, including helicases and RNA chaperones. In RNA viruses, these proteins are believed to play pivotal roles in all the processes involving viral RNAs during the life cycle. RNA helicases have been studied extensively for decades, whereas RNA chaperones, particularly virus-encoded RNA chaperones, are often overlooked. This review describes the activities of RNA chaperones encoded by RNA viruses, particularly the ones identified and characterized in recent years, and the functions of these proteins in different steps of viral life cycles, and presents an overview of this unique group of proteins.

  2. Challenges in Decomposing Encodings of Verification Problems

    Directory of Open Access Journals (Sweden)

    Peter Schrammel

    2016-07-01

    Full Text Available Modern program verifiers use logic-based encodings of the verification problem that are discharged by a back end reasoning engine. However, instances of such encodings for large programs can quickly overwhelm these back end solvers. Hence, we need techniques to make the solving process scale to large systems, such as partitioning (divide-and-conquer and abstraction. In recent work, we showed how decomposing the formula encoding of a termination analysis can significantly increase efficiency. The analysis generates a sequence of logical formulas with existentially quantified predicates that are solved by a synthesis-based program analysis engine. However, decomposition introduces abstractions in addition to those required for finding the unknown predicates in the formula, and can hence deteriorate precision. We discuss the challenges associated with such decompositions and their interdependencies with the solving process.

  3. An information theoretic characterisation of auditory encoding.

    Directory of Open Access Journals (Sweden)

    Tobias Overath

    2007-10-01

    Full Text Available The entropy metric derived from information theory provides a means to quantify the amount of information transmitted in acoustic streams like speech or music. By systematically varying the entropy of pitch sequences, we sought brain areas where neural activity and energetic demands increase as a function of entropy. Such a relationship is predicted to occur in an efficient encoding mechanism that uses less computational resource when less information is present in the signal: we specifically tested the hypothesis that such a relationship is present in the planum temporale (PT. In two convergent functional MRI studies, we demonstrated this relationship in PT for encoding, while furthermore showing that a distributed fronto-parietal network for retrieval of acoustic information is independent of entropy. The results establish PT as an efficient neural engine that demands less computational resource to encode redundant signals than those with high information content.

  4. Cluster parallel rendering based on encoded mesh

    Institute of Scientific and Technical Information of China (English)

    QIN Ai-hong; XIONG Hua; PENG Hao-yu; LIU Zhen; SHI Jiao-ying

    2006-01-01

    Use of compressed mesh in parallel rendering architecture is still an unexplored area, the main challenge of which is to partition and sort the encoded mesh in compression-domain. This paper presents a mesh compression scheme PRMC (Parallel Rendering based Mesh Compression) supplying encoded meshes that can be partitioned and sorted in parallel rendering system even in encoded-domain. First, we segment the mesh into submeshes and clip the submeshes' boundary into Runs, and then piecewise compress the submeshes and Runs respectively. With the help of several auxiliary index tables, compressed submeshes and Runs can serve as rendering primitives in parallel rendering system. Based on PRMC, we design and implement a parallel rendering architecture. Compared with uncompressed representation, experimental results showed that PRMC meshes applied in cluster parallel rendering system can dramatically reduce the communication requirement.

  5. Genetic modification and genetic determinism

    OpenAIRE

    Vorhaus Daniel B; Resnik David B

    2006-01-01

    Abstract In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound....

  6. Eukaryotic penelope-like retroelements encode hammerhead ribozyme motifs.

    Science.gov (United States)

    Cervera, Amelia; De la Peña, Marcos

    2014-11-01

    Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life. In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns. Our bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes. The architecture of these ribozymes indicates that they may work as dimers, although their low self-cleavage activity in vitro suggests the requirement of other factors in vivo. In plants, however, PLEs show canonical HHRs, whereas fungi and protist PLEs encode ribozyme variants with a stable active conformation as monomers. Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  7. Copyright Protection of Color Imaging Using Robust-Encoded Watermarking

    Directory of Open Access Journals (Sweden)

    M. Cedillo-Hernandez

    2015-04-01

    Full Text Available In this paper we present a robust-encoded watermarking method applied to color images for copyright protection, which presents robustness against several geometric and signal processing distortions. Trade-off between payload, robustness and imperceptibility is a very important aspect which has to be considered when a watermark algorithm is designed. In our proposed scheme, previously to be embedded into the image, the watermark signal is encoded using a convolutional encoder, which can perform forward error correction achieving better robustness performance. Then, the embedding process is carried out through the discrete cosine transform domain (DCT of an image using the image normalization technique to accomplish robustness against geometric and signal processing distortions. The embedded watermark coded bits are extracted and decoded using the Viterbi algorithm. In order to determine the presence or absence of the watermark into the image we compute the bit error rate (BER between the recovered and the original watermark data sequence. The quality of the watermarked image is measured using the well-known indices: Peak Signal to Noise Ratio (PSNR, Visual Information Fidelity (VIF and Structural Similarity Index (SSIM. The color difference between the watermarked and original images is obtained by using the Normalized Color Difference (NCD measure. The experimental results show that the proposed method provides good performance in terms of imperceptibility and robustness. The comparison among the proposed and previously reported methods based on different techniques is also provided.

  8. RSV-encoded NS2 promotes epithelial cell shedding and distal airway obstruction

    Science.gov (United States)

    Liesman, Rachael M.; Buchholz, Ursula J.; Luongo, Cindy L.; Yang, Lijuan; Proia, Alan D.; DeVincenzo, John P.; Collins, Peter L.; Pickles, Raymond J.

    2014-01-01

    Respiratory syncytial virus (RSV) infection is the major cause of bronchiolitis in young children. The factors that contribute to the increased propensity of RSV-induced distal airway disease compared with other commonly encountered respiratory viruses remain unclear. Here, we identified the RSV-encoded nonstructural 2 (NS2) protein as a viral genetic determinant for initiating RSV-induced distal airway obstruction. Infection of human cartilaginous airway epithelium (HAE) and a hamster model of disease with recombinant respiratory viruses revealed that NS2 promotes shedding of infected epithelial cells, resulting in two consequences of virus infection. First, epithelial cell shedding accelerated the reduction of virus titers, presumably by clearing virus-infected cells from airway mucosa. Second, epithelial cells shedding into the narrow-diameter bronchiolar airway lumens resulted in rapid accumulation of detached, pleomorphic epithelial cells, leading to acute distal airway obstruction. Together, these data indicate that RSV infection of the airway epithelium, via the action of NS2, promotes epithelial cell shedding, which not only accelerates viral clearance but also contributes to acute obstruction of the distal airways. Our results identify RSV NS2 as a contributing factor for the enhanced propensity of RSV to cause severe airway disease in young children and suggest NS2 as a potential therapeutic target for reducing the severity of distal airway disease. PMID:24713657

  9. The Pun1 gene for pungency in pepper encodes a putative acyltransferase.

    Science.gov (United States)

    Stewart, Charles; Kang, Byoung-Cheorl; Liu, Kede; Mazourek, Michael; Moore, Shanna L; Yoo, Eun Young; Kim, Byung-Dong; Paran, Ilan; Jahn, Molly M

    2005-06-01

    Pungency in Capsicum fruits is due to the accumulation of the alkaloid capsaicin and its analogs. The biosynthesis of capsaicin is restricted to the genus Capsicum and results from the acylation of an aromatic moiety, vanillylamine, by a branched-chain fatty acid. Many of the enzymes involved in capsaicin biosynthesis are not well characterized and the regulation of the pathway is not fully understood. Based on the current pathway model, candidate genes were identified in public databases and the literature, and genetically mapped. A published EST co-localized with the Pun1 locus which is required for the presence of capsaicinoids. This gene, AT3, has been isolated and its nucleotide sequence has been determined in an array of genotypes within the genus. AT3 showed significant similarity to acyltransferases in the BAHD superfamily. The recessive allele at this locus contains a deletion spanning the promoter and first exon of the predicted coding region in every non-pungent accession tested. Transcript and protein expression of AT3 was tissue-specific and developmentally regulated. Virus-induced gene silencing of AT3 resulted in a decrease in the accumulation of capsaicinoids, a phenotype consistent with pun1. In conclusion, gene mapping, allele sequence data, expression profile and silencing analysis collectively indicate that the Pun1 locus in pepper encodes a putative acyltransferase, and the pun1 allele, used in pepper breeding for nearly 50 000 years, results from a large deletion at this locus.

  10. Characterization of the legumains encoded by the genome of Theobroma cacao L.

    Science.gov (United States)

    Santana, Juliano Oliveira; Freire, Laís; de Sousa, Aurizangela Oliveira; Fontes Soares, Virgínia Lúcia; Gramacho, Karina Peres; Pirovani, Carlos Priminho

    2016-01-01

    Legumains are cysteine proteases related to plant development, protein degradation, programmed cell death, and defense against pathogens. In this study, we have identified and characterized three legumains encoded by Theobroma cacao genome through in silico analyses, three-dimensional modeling, genetic expression pattern in different tissues and as a response to the inoculation of Moniliophthora perniciosa fungus. The three proteins were named TcLEG3, TcLEG6, and TcLEG9. Histidine and cysteine residue which are part of the catalytic site were conserved among the proteins, and they remained parallel in the loop region in the 3D modeling. Three-dimensional modeling showed that the propeptide, which is located in the terminal C region of legumains blocks the catalytic cleft. Comparing dendrogram data with the relative expression analysis, indicated that TcLEG3 is related to the seed legumain group, TcLEG6 is related with the group of embryogenesis activities, and protein TcLEG9, with processes regarding the vegetative group. Furthermore, the expression analyses proposes a significant role for the three legumains during the development of Theobroma cacao and in its interaction with M. perniciosa. Copyright © 2015 Universidade Estadual de Santa Cruz, CNPJ: 40738999/0001-95. Published by Elsevier Masson SAS.. All rights reserved.

  11. RABBIT EARS, encoding a SUPERMAN-like zinc finger protein, regulates petal development in Arabidopsis thaliana.

    Science.gov (United States)

    Takeda, Seiji; Matsumoto, Noritaka; Okada, Kiyotaka

    2004-01-01

    Floral organs usually initiate at fixed positions in concentric whorls within a flower. Although it is understood that floral homeotic genes determine the identity of floral organs, the mechanisms of position determination and the development of each organ have not been clearly explained. We isolated a novel mutant, rabbit ears (rbe), with defects in petal development. In rbe, under-developed petals are formed at the correct position in a flower, and the initiation of petal primordia is altered. The rbe mutation affects the second whorl organ shapes independently of the organ identity. RBE encodes a SUPERMAN-like protein and is located in the nucleus, and thus may be a transcription factor. RBE transcripts are expressed in petal primordia and their precursor cells, and disappeared at later stages. When cells that express RBE are ablated genetically, no petal primordia arise. RBE is not expressed in ap1-1 and ptl-1 mutants, indicating that RBE acts downstream of AP1 and PTL genes. These characteristics suggest that RBE is required for the early development of the organ primordia of the second whorl.

  12. Enhanced double patterning decomposition using lines encoding

    Directory of Open Access Journals (Sweden)

    Khaled M. Soradi

    2016-09-01

    Full Text Available Double patterning photolithography (DPL is considered one of the best solutions used for enabling 32 nm/22 nm technology. In this paper, we propose a new technique for double patterning post decomposition conflict resolution. The algorithm is based on lines positions encoding followed by code pattern matching. Experimental results show that the usage of encoded patterns decreases the time needed for pattern matching and increases the matching accuracy. The overall manual problem solution time is reduced to about 1%.

  13. Fidelity enhancement by logical qubit encoding.

    Science.gov (United States)

    Henry, Michael K; Ramanathan, Chandrasekhar; Hodges, Jonathan S; Ryan, Colm A; Ditty, Michael J; Laflamme, Raymond; Cory, David G

    2007-11-30

    We demonstrate coherent control of two logical qubits encoded in a decoherence free subspace (DFS) of four dipolar-coupled protons in an NMR quantum information processor. A pseudopure fiducial state is created in the DFS, and a unitary logical qubit entangling operator evolves the system to a logical Bell state. The four-spin molecule is partially aligned by a liquid crystal solvent, which introduces strong dipolar couplings among the spins. Although the system Hamiltonian is never fully specified, we demonstrate high fidelity control over the logical degrees of freedom. In fact, the DFS encoding leads to higher fidelity control than is available in the full four-spin Hilbert space.

  14. Complex chloroplast RNA metabolism: just debugging the genetic programme?

    Directory of Open Access Journals (Sweden)

    Schmitz-Linneweber Christian

    2008-08-01

    Full Text Available Abstract Background The gene expression system of chloroplasts is far more complex than that of their cyanobacterial progenitor. This gain in complexity affects in particular RNA metabolism, specifically the transcription and maturation of RNA. Mature chloroplast RNA is generated by a plethora of nuclear-encoded proteins acquired or recruited during plant evolution, comprising additional RNA polymerases and sigma factors, and sequence-specific RNA maturation factors promoting RNA splicing, editing, end formation and translatability. Despite years of intensive research, we still lack a comprehensive explanation for this complexity. Results We inspected the available literature and genome databases for information on components of RNA metabolism in land plant chloroplasts. In particular, new inventions of chloroplast-specific mechanisms and the expansion of some gene/protein families detected in land plants lead us to suggest that the primary function of the additional nuclear-encoded components found in chloroplasts is the transgenomic suppression of point mutations, fixation of which occurred due to an enhanced genetic drift exhibited by chloroplast genomes. We further speculate that a fast evolution of transgenomic suppressors occurred after the water-to-land transition of plants. Conclusion Our inspections indicate that several chloroplast-specific mechanisms evolved in land plants to remedy point mutations that occurred after the water-to-land transition. Thus, the complexity of chloroplast gene expression evolved to guarantee the functionality of chloroplast genetic information and may not, with some exceptions, be involved in regulatory functions.

  15. Quo Vadis, Medical Genetics?

    Science.gov (United States)

    Czeizel, Andrew E.

    The beginning of human genetics and its medical part: medical genetics was promising in the early decades of this century. Many genetic diseases and defects with Mendelian origin were identified and it helped families with significant genetic burden to limit their child number. Unfortunately this good start was shadowed by two tragic events. On the one hand, in the 1930s and early 1940s the German fascism brought about the dominance of an unscientific eugenics to mask vile political crimes. People with genetic diseases-defects were forced to sterilisation and several of them were killed. On the other hand, in the 1950s lysenkoism inhibitied the evolution of genetics in the Soviet Union and their satelite countries. Lysenko's doctrine declared genetics as a product of imperialism and a guilty science, therefore leading geneticists were ousted form their posts and some of them were executed or put in prison. Past decades genetics has resulted fantastic new results and achieved a leading position within the natural sciences. To my mind, however, the expected wider use of new eugenics indicates a new tragedy and this Cassandra's prediction is the topic of this presentation.

  16. Attitudes towards genetic testing: analysis of contradictions

    DEFF Research Database (Denmark)

    Jallinoja, P; Hakonen, A; Aro, A R

    1998-01-01

    A survey study was conducted among 1169 people to evaluate attitudes towards genetic testing in Finland. Here we present an analysis of the contradictions detected in people's attitudes towards genetic testing. This analysis focuses on the approval of genetic testing as an individual choice...... and on the confidence in control of the process of genetic testing and its implications. Our analysis indicated that some of the respondents have contradictory attitudes towards genetic testing. It is proposed that contradictory attitudes towards genetic testing should be given greater significance both in scientific...... studies on attitudes towards genetic testing as well as in the health care context, e.g. in genetic counselling....

  17. Glucocorticoid-related genetic susceptibility for Alzheimer's disease.

    Science.gov (United States)

    de Quervain, Dominique J-F; Poirier, Raphael; Wollmer, M Axel; Grimaldi, Luigi M E; Tsolaki, Magdalini; Streffer, Johannes R; Hock, Christoph; Nitsch, Roger M; Mohajeri, M Hasan; Papassotiropoulos, Andreas

    2004-01-01

    Because glucocorticoid excess increases neuronal vulnerability, genetic variations in the glucocorticoid system may be related to the risk for Alzheimer's disease (AD). We analyzed single-nucleotide polymorphisms in 10 glucocorticoid-related genes in a population of 814 AD patients and unrelated control subjects. Set-association analysis revealed that a rare haplotype in the 5' regulatory region of the gene encoding 11beta-hydroxysteroid dehydrogenase type 1 (HSD11B1) was associated with a 6-fold increased risk for sporadic AD. Results of a reporter-gene assay indicated that the rare risk-associated haplotype altered HSD11B1 transcription. HSD11B1 controls tissue levels of biologically active glucocorticoids and thereby influences neuronal vulnerability. Our results indicate that a functional variation in the glucocorticoid system increases the risk for AD, which may have important implications for the diagnosis and treatment of this disease.

  18. Genetic and molecular aspects of spinocerebellar ataxias

    OpenAIRE

    Honti, Viktor; Vécsei, László

    2005-01-01

    The group of spinocerebellar ataxias (SCAs) includes more than 20 subgroups based only on genetic research. The “ataxia genes” are autosomal; the “disease-alleles” are dominant, and many of them, but not all, encode a protein with an abnormally long polyglutamine domain. In DNA, this domain can be detected as an elongated CAG repeat region, which is the basis of genetic diagnostics. The polyglutamine tails often tend to aggregate and form inclusions. In some cases, protein–protein interaction...

  19. Clinical Genetic Testing in Gastroenterology

    Science.gov (United States)

    Goodman, Russell P; Chung, Daniel C

    2016-01-01

    Rapid advances in genetics have led to an increased understanding of the genetic determinants of human disease, including many gastrointestinal (GI) disorders. Coupled with a proliferation of genetic testing services, this has resulted in a clinical landscape where commercially available genetic tests for GI disorders are now widely available. In this review, we discuss the current status of clinical genetic testing for GI illnesses, review the available testing options, and briefly discuss indications for and practical aspects of such testing. Our goal is to familiarize the practicing gastroenterologist with this rapidly changing and important aspect of clinical care. PMID:27124700

  20. Indication of Genetic Linkage Map for Sunflower by SSR Markers%SSR分子标记丰富向日葵(Helianthus annuus L.)遗传图谱的研究

    Institute of Scientific and Technical Information of China (English)

    黄先群; Genzbitelle L.; Fabre F.; Saraffi A.

    2012-01-01

    为了提高向日葵遗传图谱的密度和实用性,以125个来源于PAC-2和RHA-266杂交的F(8)代重组自交系(RIIs)群体为材料,利用筒单序列重复(Simple sequence repeat,SSR)标记,采用MAPMARKER软件对向日英遗传图谱进行标注,并从300对SSR引物中筛选出51对多态性引物对群体进行标记.结果表明:①51对多态性引物中有19对引物无多态性或条带不清晰,32对引物表现多态性;②共检测到35个多态性位点,分布在图谱的15条连锁群上.③标记后的图谱总长度为2914.5 Cm,比原来的图谱增长7.5 Cm.④标记间平均距离由9.0 Cm缩短为8.1 Cm.%This study aimed to improve density and practicality of the genetic map of sunflower baaed on a 125 Fs RILa population derived from a cross between PAC-2 and RHA-266 by adding some SSR markers. A total of 300 pairs of SSR primers were used to screen polymorphic markers between the parents and some of their RILs, of which 51 pain of the primers showed polymorphism. The results of screening the RILs population revealed that 19 SSR primer without polymorphism or non-reading, 32 SSR pairs showed polymorphism with 35 alleles added into the map. They were distributed in the 15 linkage groups of the maps. The new map covered a total length of 2914.5 cM, 7.5 cM longer than the original map. The average distance between adjacent markers was 8.1 cM instead of original 9.0 cM.

  1. Encoded Archival Description as a Halfway Technology

    Science.gov (United States)

    Dow, Elizabeth H.

    2009-01-01

    In the mid 1990s, Encoded Archival Description (EAD) appeared as a revolutionary technology for publishing archival finding aids on the Web. The author explores whether or not, given the advent of Web 2.0, the archival community should abandon EAD and look for something to replace it. (Contains 18 notes.)

  2. Encoding and Decoding Procedures for Arrangements

    Directory of Open Access Journals (Sweden)

    Alexander A. Babaev

    2012-05-01

    Full Text Available This article discusses an algorithm based on the encoding procedure for representing a set of arrangement elements as a single number. Also the author provides the procedure for the inverse transformation of the code into arrangement elements. In addition the Article includes recommendations on the use of the above procedures in combinatorial algorithms of optimization.

  3. Design Primer for Reed-Solomon Encoders

    Science.gov (United States)

    Perlman, M.; Lee, J. J.

    1985-01-01

    Design and operation of Reed-Solomon (RS) encoders discussed in document prepared as instruction manual for computer designers and others in dataprocessing field. Conventional and Berlekamp architectures compared. Engineers who equip computer memory chips with burst-error and dropout detection and correction find report especially useful.

  4. Indication of Genetic Linkage Map for Sunflower (Helianthus annuus L.) by SSR Markers%转Bt基因水稻与非转基因水稻在虫压下的适合度差异

    Institute of Scientific and Technical Information of China (English)

    张富丽; 雷绍荣; 刘勇; 郭灵安; 尹全; 宋君; 王东; 常丽娟; 刘文娟; 周西全

    2012-01-01

    以转胁抗虫水稻Bt63、R1、R2和非转基因常规水稻Ⅱ优838为试材,采用高、低两个不同虫害胁迫水平和转基因与非转基凶水稻相间种植方式,通过观察水稻植株营养生长、结实以及对螟虫危害的抗性表现等差异,研究比较晚外源基因插入后对水稻植株适合度的影响,以解转基因水稻的基因扩散效率和潜在生态风险。结果表明:在低虫害胁迫条件下,转胁基因水稻在植株分蘖数、生物量鲜重等营养生长指标方面与非转基因对照品系间无明显差异,但株高、穗长、穗重等指标不及对照,且R2和Bt63与对照间差异显著;在高虫害胁迫条件下,3个转胁基凶水稻品系的分蘖数、穗长、穗重等指标明显高于对照。而不同转基因品系株高适合度效应不同,这可能与受体品系本身的特性相关。3种转基因水稻的单株结实粒数、千粒重与对照在两种虫害胁迫条件下均无显著性差异,Bt基因对受体植株的结实影响不明显。在高虫害胁迫条件下,3种转&基因水稻的抗虫能力均显著优于非转基因水稻,表明髓基因对受体植株的抗虫性影响显著。本研究结果还表明转Bt基因水稻的适合度代价较小,预示了抗虫转基因水稻外源胁基因在一定环境条件下具有逃逸的可能,但这种风险比较小。%[Objective] This study aimed to improve density and practicality of the ge- netic map of sunflower (Helianthus annuus L.) by adding some SSR markers. [Method] A total of 123 F8 RILs populations derived from a cross between PAC-2 and RHA-266 were selected as the materials, and a total of 300 pairs of SSR primers were used to screen polymorphic markers between the parents and some of their RILs, and finally 51 pairs of the primers producing polymorphic patterns were selected to construct the genetic map of the RILs populations. [Result] Nineteen pairs of SSR primers did not generate

  5. How Attention Modulates Encoding of Dynamic Stimuli

    Science.gov (United States)

    Oren, Noga; Shapira-Lichter, Irit; Lerner, Yulia; Tarrasch, Ricardo; Hendler, Talma; Giladi, Nir; Ash, Elissa L.

    2016-01-01

    When encoding a real-life, continuous stimulus, the same neural circuits support processing and integration of prior as well as new incoming information. This ongoing interplay is modulated by attention, and is evident in regions such as the prefrontal cortex section of the task positive network (TPN), and in the posterior cingulate cortex (PCC), a hub of the default mode network (DMN). Yet the exact nature of such modulation is still unclear. To investigate this issue, we utilized an fMRI task that employed movies as the encoded stimuli and manipulated attentional load via an easy or hard secondary task that was performed simultaneously with encoding. Results showed increased intersubject correlation (inter-SC) levels when encoding movies in a condition of high, as compared to low attentional load. This was evident in bilateral ventrolateral and dorsomedial prefrontal cortices and the dorsal PCC (dPCC). These regions became more attuned to the combination of the movie and the secondary task as the attentional demand of the latter increased. Activation analyses revealed that at higher load the prefrontal TPN regions were more activated, whereas the dPCC was more deactivated. Attentional load also influenced connectivity within and between the networks. At high load the dPCC was anti-correlated to the prefrontal regions, which were more functionally coherent amongst themselves. Finally and critically, greater inter-SC in the dPCC at high load during encoding predicted lower memory strength when that information was retrieved. This association between inter-SC levels and memory strength suggest that as attentional demands increased, the dPCC was more attuned to the secondary task at the expense of the encoded stimulus, thus weakening memory for the encoded stimulus. Together, our findings show that attentional load modulated the function of core TPN and DMN regions. Furthermore, the observed relationship between memory strength and the modulation of the dPCC points

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

    Science.gov (United States)

    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 pah1Δ 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 pah1Δ mutant is induced through the inositol-sensitive upstream activation sequence (UASINO), 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 UASINO mutation suppressed pah1Δ 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 pah1Δ-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.

  7. Amygdala neurons differentially encode motivation and reinforcement.

    Science.gov (United States)

    Tye, Kay M; Janak, Patricia H

    2007-04-11

    Lesion studies demonstrate that the basolateral amygdala complex (BLA) is important for assigning motivational significance to sensory stimuli, but little is known about how this information is encoded. We used in vivo electrophysiology procedures to investigate how the amygdala encodes motivating and reinforcing properties of cues that induce reinstatement of reward-seeking behavior. Two groups of rats were trained to respond to a sucrose reward. The "paired" group was trained with a reward-predictive cue, whereas the "unpaired" group was trained with a randomly presented cue. Both groups underwent identical extinction and reinstatement procedures during which the reward was withheld. The proportion of neurons that were phasically cue responsive during reinstatement was significantly higher in the paired group (46 of 100) than in the unpaired group (8 of 112). Cues that induce reward-seeking behavior can do so by acting as incentives or reinforcers. Distinct populations of neurons responded to the cue in trials in which the cue acted as an incentive, triggering a motivated reward-seeking state, or as a reinforcer, supporting continued instrumental responding. The incentive motivation-encoding population of neurons (34 of 46 cue-responsive neurons; 74%) extinguished in temporal agreement with a decrease in the rate of instrumental responding. The conditioned reinforcement-encoding population of neurons (12 of 46 cue-responsive neurons; 26%) maintained their response for the duration of cue-reinforced instrumental responding. These data demonstrate that separate populations of cue-responsive neurons in the BLA encode the motivating or reinforcing properties of a cue previously associated with a reward.

  8. Silencing of the major family of NBS-LRR-encoding genes in lettuce results in the loss of multiple resistance specificities.

    Science.gov (United States)

    Wroblewski, Tadeusz; Piskurewicz, Urszula; Tomczak, Anna; Ochoa, Oswaldo; Michelmore, Richard W

    2007-09-01

    The RGC2 gene cluster in lettuce (Lactuca sativa) is one of the largest known families of genes encoding nucleotide binding site-leucine-rich repeat (NBS-LRR) proteins. One of its members, RGC2B, encodes Dm3 which determines resistance to downy mildew caused by the oomycete Bremia lactucae carrying the cognate avirulence gene, Avr3. We developed an efficient strategy for analysis of this large family of low expressed genes using post-transcriptional gene silencing (PTGS). We transformed lettuce cv. Diana (carrying Dm3) using chimeric gene constructs designed to simultaneously silence RGC2B and the GUS reporter gene via the production of interfering hairpin RNA (ihpRNA). Transient assays of GUS expression in leaves accurately predicted silencing of both genes and were subsequently used to assay silencing in transgenic T(1) plants and their offspring. Levels of mRNA were reduced not only for RGC2B but also for all seven diverse RGC2 family members tested. We then used the same strategy to show that the resistance specificity encoded by the genetically defined Dm18 locus in lettuce cv. Mariska is the result of two resistance specificities, only one of which was silenced by ihpRNA derived from RGC2B. Analysis of progeny from crosses between transgenic, silenced tester stocks and lettuce accessions carrying other resistance genes previously mapped to the RGC2 locus indicated that two additional resistance specificities to B. lactucae, Dm14 and Dm16, as well as resistance to lettuce root aphid (Pemphigus bursarius L.), Ra, are encoded by RGC2 family members.

  9. Protein levels of genes encoded on chromosome 21 in fetal Down Syndrome brain (Part V): overexpression of phosphatidyl-inositol-glycan class P protein (DSCR5).

    Science.gov (United States)

    Ferrando-Miguel, R; Cheon, M S; Lubec, G

    2004-06-01

    Down Syndrome (DS, trisomy 21) is the most common genetic cause of mental retardation. The completed sequencing of genes encoded on chromosome 21 provides excellent basic information, however the molecular mechanisms leading to the phenotype of DS remain to be elucidated. Although overexpression of chromosome 21 encoded genes has been documented information at the protein expression level is mandatory as it is the proteins that carry out function. We therefore decided to evaluated expression level of seven proteins whose genes are encoded on chromosome 21: DSCR4, DSCR5, DSCR6; KIR4.2, GIRK2, KCNE1 and KCNE2 in fetal cortex brain of DS and controls at the early second trimester of pregnancy by Western blotting. beta-actin and neuron specific enolase (NSE) were used to normalise cell loss and neuronal loss. DSCR5 (PIG-P), a component of glycosylphosphatidylinositol- N-acetylglucosaminyltransferase (GPI-GnT), was overexpressed about twofold, even when levels were normalised with NSE. DSCR6 was overexpressed in addition but when normalised versus NSE, levels were comparable to controls. DSCR4 was not detectable in fetal brain. Potassium channels KIR4.2 and GIRK2 were comparable between DS and controls, whereas KCNE1 and KCNE2 were not detectable. Quantification of these proteins encoded on chromosome 21 revealed that not all gene products of the DS critical region are overexpressed in DS brain early in life, indicating that the DS phenotype cannot be simply explained by the gene dosage effect hypothesis. Overexpression of PIG-P (DSCR5) may lead to or represent impaired glycosylphosphatidylinositol- N-acetylglucosaminyltransferase mediated posttranslational modifications and subsequent anchoring of proteins to the plasma membrane.

  10. Analogue Encoding of Physicochemical Properties of Proteins in their Cognate Messenger RNAs

    OpenAIRE

    Polyansky, Anton A; Hlevnjak, Mario; Zagrovic, Bojan

    2013-01-01

    Being related by the genetic code, mRNAs and their cognate proteins exhibit mutually interdependent compositions, which implies the possibility of a direct connection between their general physicochemical properties. Here we probe the general potential of the cell to encode information about proteins in the average characteristics of their cognate mRNAs and decode it in a ribosome-independent manner. We show that average protein hydrophobicity, calculated from either sequences or 3D structure...

  11. On the Role of PDZ Domain-Encoding Genes in Drosophila Border Cell Migration

    OpenAIRE

    Aranjuez, George; Kudlaty, Elizabeth; Longworth, Michelle S; McDonald, Jocelyn A.

    2012-01-01

    Cells often move as collective groups during normal embryonic development and wound healing, although the mechanisms governing this type of migration are poorly understood. The Drosophila melanogaster border cells migrate as a cluster during late oogenesis and serve as a powerful in vivo genetic model for collective cell migration. To discover new genes that participate in border cell migration, 64 out of 66 genes that encode PDZ domain-containing proteins were systematically targeted by in v...

  12. Genetic barcodes

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Heinz -Ulrich G

    2015-08-04

    Herein are described multicolor FISH probe sets termed "genetic barcodes" targeting several cancer or disease-related loci to assess gene rearrangements and copy number changes in tumor cells. Two, three or more different fluorophores are used to detect the genetic barcode sections thus permitting unique labeling and multilocus analysis in individual cell nuclei. Gene specific barcodes can be generated and combined to provide both numerical and structural genetic information for these and other pertinent disease associated genes.

  13. An Encoder/Decoder Scheme of OCDMA Based on Waveguide

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A new encoder/decoder scheme of OCDMA based on waveguide isproposed in this paper. The principle as well as the structure of waveguide encoder/decoder is given. It can be seen that all-optical OCDMA encoder/decoder can be realized by the proposed scheme of the waveguide encoder/decoder. It can also make the OCDMA encoder/decoder integrated easily and the access controlled easily. The system based on this scheme can work under the entirely asynchronous condition.

  14. Random codon re-encoding induces stable reduction of replicative fitness of Chikungunya virus in primate and mosquito cells.

    Directory of Open Access Journals (Sweden)

    Antoine Nougairede

    2013-02-01

    Full Text Available Large-scale codon re-encoding represents a powerful method of attenuating viruses to generate safe and cost-effective vaccines. In contrast to specific approaches of codon re-encoding which modify genome-scale properties, we evaluated the effects of random codon re-encoding on the re-emerging human pathogen Chikungunya virus (CHIKV, and assessed the stability of the resultant viruses during serial in cellulo passage. Using different combinations of three 1.4 kb randomly re-encoded regions located throughout the CHIKV genome six codon re-encoded viruses were obtained. Introducing a large number of slightly deleterious synonymous mutations reduced the replicative fitness of CHIKV in both primate and arthropod cells, demonstrating the impact of synonymous mutations on fitness. Decrease of replicative fitness correlated with the extent of re-encoding, an observation that may assist in the modulation of viral attenuation. The wild-type and two re-encoded viruses were passaged 50 times either in primate or insect cells, or in each cell line alternately. These viruses were analyzed using detailed fitness assays, complete genome sequences and the analysis of intra-population genetic diversity. The response to codon re-encoding and adaptation to culture conditions occurred simultaneously, resulting in significant replicative fitness increases for both re-encoded and wild type viruses. Importantly, however, the most re-encoded virus failed to recover its replicative fitness. Evolution of these viruses in response to codon re-encoding was largely characterized by the emergence of both synonymous and non-synonymous mutations, sometimes located in genomic regions other than those involving re-encoding, and multiple convergent and compensatory mutations. However, there was a striking absence of codon reversion (<0.4%. Finally, multiple mutations were rapidly fixed in primate cells, whereas mosquito cells acted as a brake on evolution. In conclusion, random

  15. Genetics of osteoporosis

    Energy Technology Data Exchange (ETDEWEB)

    Urano, Tomohiko [Department of Geriatric Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655 (Japan); Inoue, Satoshi, E-mail: INOUE-GER@h.u-tokyo.ac.jp [Department of Geriatric Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655 (Japan); Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655 (Japan); Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama (Japan)

    2014-09-19

    Highlights: • Single-nucleotide polymorphisms (SNPs) associated with osteoporosis were identified. • SNPs mapped close to or within VDR and ESR1 are associated with bone mineral density. • WNT signaling pathway plays a pivotal role in regulating bone mineral density. • Genetic studies will be useful for identification of new therapeutic targets. - Abstract: Osteoporosis is a skeletal disease characterized by low bone mineral density (BMD) and microarchitectural deterioration of bone tissue, which increases susceptibility to fractures. BMD is a complex quantitative trait with normal distribution and seems to be genetically controlled (in 50–90% of the cases), according to studies on twins and families. Over the last 20 years, candidate gene approach and genome-wide association studies (GWAS) have identified single-nucleotide polymorphisms (SNPs) that are associated with low BMD, osteoporosis, and osteoporotic fractures. These SNPs have been mapped close to or within genes including those encoding nuclear receptors and WNT-β-catenin signaling proteins. Understanding the genetics of osteoporosis will help identify novel candidates for diagnostic and therapeutic targets.

  16. Genetics of Congenital Cataract.

    Science.gov (United States)

    Pichi, Francesco; Lembo, Andrea; Serafino, Massimiliano; Nucci, Paolo

    2016-01-01

    Congenital cataract is a type of cataract that presents at birth or during early childhood, and it is one of the most easily treatable causes of visual impairment and blindness during infancy, with an estimated prevalence of 1-6 cases per 10,000 live births. Approximately 50% of all congenital cataract cases may have a genetic cause, and such cases are quite heterogeneous. Although congenital nuclear cataract can be caused by multiple factors, genetic mutation remains the most common cause. All three types of Mendelian inheritance have been reported for cataract; however, autosomal dominant transmission seems to be the most frequent. The transparency and high refractive index of the lens are achieved by the precise architecture of fiber cells and homeostasis of the lens proteins in terms of their concentrations, stabilities, and supramolecular organization. Research on hereditary congenital cataract has led to the identification of several classes of candidate genes that encode proteins such crystallins, lens-specific connexins, aquaporin, cytoskeletal structural proteins, and developmental regulators. In this review, we highlight the identified genetic mutations that account for congenital nuclear cataract.

  17. Unnatural reactive amino acid genetic code additions

    Science.gov (United States)

    Deiters, Alexander; Cropp, Ashton T; Chin, Jason W; Anderson, Christopher J; Schultz, Peter G

    2013-05-21

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  18. Genetic engineering of sulfur-degrading Sulfolobus

    Energy Technology Data Exchange (ETDEWEB)

    Ho, N.W.Y.

    1991-01-01

    The objectives of the proposed research is to first establish a plasmid-mediated genetic transformation system for the sulfur degrading Sulfolobus, and then to clone and overexpress the genes encoding the organic-sulfur-degrading enzymes from Sulfolobus- as well as from other microorganisms, to develop a Sulfolobus-based microbial process for the removal of both organic and inorganic sulfur from coal.

  19. Unnatural reactive amino acid genetic code additions

    Science.gov (United States)

    Deiters, Alexander; Cropp, T. Ashton; Chin, Jason W.; Anderson, J. Christopher; Schultz, Peter G.

    2014-08-26

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  20. Stego-audio Using Genetic Algorithm Approach

    Directory of Open Access Journals (Sweden)

    V. Santhi

    2014-06-01

    Full Text Available With the rapid development of digital multimedia applications, the secure data transmission becomes the main issue in data communication system. So the multimedia data hiding techniques have been developed to ensure the secured data transfer. Steganography is an art of hiding a secret message within an image/audio/video file in such a way that the secret message cannot be perceived by hacker/intruder. In this study, we use RSA encryption algorithm to encrypt the message and Genetic Algorithm (GA to encode the message in the audio file. This study presents a method to access the negative audio bytes and includes the negative audio bytes in the message encoding and position embedding process. This increases the capacity of encoding message in the audio file. The use of GA operators in Genetic Algorithm reduces the noise distortions.

  1. Brassica napus DS-3, encoding a DELLA protein, negatively regulates stem elongation through gibberellin signaling pathway.

    Science.gov (United States)

    Zhao, Bo; Li, Haitao; Li, Juanjuan; Wang, Bo; Dai, Cheng; Wang, Jing; Liu, Kede

    2017-04-01

    Identification and characterization of a semi-dwarfing gene ds-3 encoding a mutant DELLA protein regulating plant height through gibberellin signaling pathway. Lodging is one of the most important factors causing severe yield loss in oilseed rape. Utilization of semi-dwarf varieties has been proved the most effective way to increase lodging resistance and yield in many crops. To develop semi-dwarf germplasm in oilseed rape, we identified a semi-dwarf mutant ds-3 which showed a reduced response to phytohormones gibberellins (GAs). Genetic analysis indicated the dwarfism was controlled by a single semi-dominant gene, ds-3. The DS-3 gene was mapped to a genomic region on chromosome C07, which is syntenic to the region of a previously identified semi-dwarf gene ds-1 (BnaA06.RGA). In this region, DS-3 (BnaC07.RGA) gene was identified to encode a DELLA protein that functions as a repressor in GA signaling pathway. A substitution of proline to leucine was identified in ds-3 in the conserved VHYNP motif, which is essential for GA-dependent interaction between gibberellin receptor GID1 and DELLA proteins. Segregation analysis in the F2 population derived from the cross between ds-1 and ds-3 demonstrated that BnaA06.RGA displayed a stronger effect on plant height than BnaC07.RGA, indicating that different RGA genes may play different roles in stem elongation. In addition to BnaA06.RGA and BnaC07.RGA, two more RGA genes (BnaA09.RGA and BnaC09.RGA) were identified in the Brassica napus (B. napus) genome. Reverse-transcription polymerase chain reaction (RT-PCR) and yeast two-hybrid (Y2H) assays suggest that both BnaA09.RGA and BnaC09.RGA are transcribed in leaves and stems and can mediate GA signaling in vivo. These genes represent potential targets for screening ideal semi-dwarfing alleles for oilseed rape breeding.

  2. Identification and characterization of the genes encoding a unique surface (S-) layer of Tannerella forsythia.

    Science.gov (United States)

    Lee, Seok-Woo; Sabet, Mojgan; Um, Heung-Sik; Yang, Jun; Kim, Hyeong C; Zhu, Weidong

    2006-04-12

    A newly emerged periodontopathic pathogen Tannerella forsythia (formerly Bacteroides forsythus), a Gram-negative, filament-shaped, strict anaerobic, non-pigmented oral bacterium, possesses a surface (S-) layer. In our previous studies, the S-layer has been isolated, and shown to mediate hemagglutination, adhesion/invasion of epithelial cell, and murine subcutaneous abscess formation. In the present study, biochemical and molecular genetic characterization of the S-layer are reported. Amino acid sequencing and mass spectrometry indicated that the S-layer is composed of two different proteins, termed 200 and 210 kDa proteins. It was also shown that these proteins are glycosylated. The genes encoding the core proteins of these glycoproteins, designated as tfsA and tfsB, have been identified in silico, cloned, and their sequences have been determined. The tfsA (3.5 kb) and tfsB (4.1 kb) genes are located in tandem, and encode for 135 and 152 kDa proteins, respectively. An apparent discrepancy in molecular weights, 135 vs. 200 kDa and 152 vs. 210 kDa, is accounted for carbohydrate residues attached to the core proteins. Amino acid sequence comparison exhibited a 24% similarity between the 200 and 210 kDa proteins. Further sequence analyses showed that TfsA and TfsB possess putative signal peptide sequences with cleavage sites at alanine residues, and transmembrane domains on the C-terminal region. Northern blot and RT-PCR analyses confirmed an operon structure of tfsAB, suggesting co-regulation of these genes in producing the S-layer. Putative promoter sequences and transcription termination sequences for this operon have also been identified. Comparison with database indicates that the S-layer of T. forsythia has a unique structure exhibiting no homology to other known S-layers of prokaryotic organisms. The present study shows that the T. forsythia S-layer is very unique, since it appears to be composed of two large glycoproteins, and it does not reveal any homology to

  3. Genetic modification and genetic determinism

    Directory of Open Access Journals (Sweden)

    Vorhaus Daniel B

    2006-06-01

    Full Text Available Abstract In this article we examine four objections to the genetic modification of human beings: the freedom argument, the giftedness argument, the authenticity argument, and the uniqueness argument. We then demonstrate that each of these arguments against genetic modification assumes a strong version of genetic determinism. Since these strong deterministic assumptions are false, the arguments against genetic modification, which assume and depend upon these assumptions, are therefore unsound. Serious discussion of the morality of genetic modification, and the development of sound science policy, should be driven by arguments that address the actual consequences of genetic modification for individuals and society, not by ones propped up by false or misleading biological assumptions.

  4. Pareto-optimal multi-objective dimensionality reduction deep auto-encoder for mammography classification.

    Science.gov (United States)

    Taghanaki, Saeid Asgari; Kawahara, Jeremy; Miles, Brandon; Hamarneh, Ghassan

    2017-07-01

    Feature reduction is an essential stage in computer aided breast cancer diagnosis systems. Multilayer neural networks can be trained to extract relevant features by encoding high-dimensional data into low-dimensional codes. Optimizing traditional auto-encoders works well only if the initial weights are close to a proper solution. They are also trained to only reduce the mean squared reconstruction error (MRE) between the encoder inputs and the decoder outputs, but do not address the classification error. The goal of the current work is to test the hypothesis that extending traditional auto-encoders (which only minimize reconstruction error) to multi-objective optimization for finding Pareto-optimal solutions provides more discriminative features that will improve classification performance when compared to single-objective and other multi-objective approaches (i.e. scalarized and sequential). In this paper, we introduce a novel multi-objective optimization of deep auto-encoder networks, in which the auto-encoder optimizes two objectives: MRE and mean classification error (MCE) for Pareto-optimal solutions, rather than just MRE. These two objectives are optimized simultaneously by a non-dominated sorting genetic algorithm. We tested our method on 949 X-ray mammograms categorized into 12 classes. The results show that the features identified by the proposed algorithm allow a classification accuracy of up to 98.45%, demonstrating favourable accuracy over the results of state-of-the-art methods reported in the literature. We conclude that adding the classification objective to the traditional auto-encoder objective and optimizing for finding Pareto-optimal solutions, using evolutionary multi-objective optimization, results in producing more discriminative features. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Short communication: Heat-resistant Escherichia coli as potential persistent reservoir of extended-spectrum β-lactamases and Shiga toxin-encoding phages in dairy.

    Science.gov (United States)

    Marti, Roger; Muniesa, Maite; Schmid, Michael; Ahrens, Christian H; Naskova, Javorka; Hummerjohann, Jörg

    2016-11-01

    Here we report the isolation of heat-resistant Escherichia coli from raw milk cheeses. Detection of the heat-resistance markers clpK and orfI by PCR was followed by phenotypical confirmation of increased heat-resistance. These strains were Shiga toxin-negative and, although several were found to be multidrug resistant, no plasmids encoding extended-spectrum β-lactamases (ESBL) were found in any of the isolates. The aim of this study was to assess the potential of these strains to acquire ESBL plasmids and a modified Shiga toxin-encoding phage. Only 4 ESBL-encoding, heat-sensitive E. coli strains were isolated from 1,251 dairy samples (2/455 raw milk and 2/796 raw milk cheese samples). One incompatibility group FII plasmid (CTX-M-14, 79.0 kb) and 3 incompatibility group I1 plasmids (CTX-M-15, 95.2, 96.1, and 97.8 kb) were fully sequenced and de novo assembled. All 4 plasmids are readily transferred to heat-resistant E. coli isolates in plate matings (9.7×10(-5) to 3.7×10(-1) exconjugants per recipient) and, to a lesser extent, in milk (up to 7.4×10(-5) exconjugants per recipient). Importantly, the plasmids are stably maintained during passaging in liquid media without antimicrobial pressure. The heat-resistant isolate FAM21805 was also shown to be capable of acting as donor of all 4 ESBL plasmids. In addition, 3 of 11 tested ESBL exconjugants of heat-resistant strains were lysogenized by the modified Shiga toxin-encoding phage 933W ∆stx::gfp::cat. The higher fraction of heat-resistant E. coli (93 of 256 isolates) compared with the estimated 2% previously predicted based on genomic prevalence of heat resistance genes seems to indicate a selection advantage in the raw milk cheese production environment. The combination of 2 factors may lead to said advantage: increased survival during thermization of raw milk (heating to subpasteurization temperatures) and increased survival rates during cheese ripening. Should these strains acquire ESBL-encoding plasmids, Shiga

  6. Genetic obesity syndromes.

    Science.gov (United States)

    Goldstone, Anthony P; Beales, Philip L

    2008-01-01

    There are numerous reports of multi-system genetic disorders with obesity. Many have a characteristic presentation and several, an overlapping phenotype indicating the likelihood of a shared common underlying mechanism or pathway. By understanding the genetic causes and functional perturbations of such syndromes we stand to gain tremendous insight into obesogenic pathways. In this review we focus particularly on Bardet-Biedl syndrome, whose molecular genetics and cell biology has been elucidated recently, and Prader-Willi syndrome, the commonest obesity syndrome due to loss of imprinted genes on 15q11-13. We also discuss highlights of other genetic obesity syndromes including Alstrom syndrome, Cohen syndrome, Albright's hereditary osteodystrophy (pseudohypoparathyroidism), Carpenter syndrome, MOMO syndrome, Rubinstein-Taybi syndrome, cases with deletions of 6q16, 1p36, 2q37 and 9q34, maternal uniparental disomy of chromosome 14, fragile X syndrome and Börjeson-Forssman-Lehman syndrome.

  7. Object recognition memory: neurobiological mechanisms of encoding, consolidation and retrieval.

    Science.gov (United States)

    Winters, Boyer D; Saksida, Lisa M; Bussey, Timothy J

    2008-07-01

    Tests of object recognition memory, or the judgment of the prior occurrence of an object, have made substantial contributions to our understanding of the nature and neurobiological underpinnings of mammalian memory. Only in recent years, however, have researchers begun to elucidate the specific brain areas and neural processes involved in object recognition memory. The present review considers some of this recent research, with an emphasis on studies addressing the neural bases of perirhinal cortex-dependent object recognition memory processes. We first briefly discuss operational definitions of object recognition and the common behavioural tests used to measure it in non-human primates and rodents. We then consider research from the non-human primate and rat literature examining the anatomical basis of object recognition memory in the delayed nonmatching-to-sample (DNMS) and spontaneous object recognition (SOR) tasks, respectively. The results of these studies overwhelmingly favor the view that perirhinal cortex (PRh) is a critical region for object recognition memory. We then discuss the involvement of PRh in the different stages--encoding, consolidation, and retrieval--of object recognition memory. Specifically, recent work in rats has indicated that neural activity in PRh contributes to object memory encoding, consolidation, and retrieval processes. Finally, we consider the pharmacological, cellular, and molecular factors that might play a part in PRh-mediated object recognition memory. Recent studies in rodents have begun to indicate the remarkable complexity of the neural substrates underlying this seemingly simple aspect of declarative memory.

  8. Genetic Engineering

    Science.gov (United States)

    Phillips, John

    1973-01-01

    Presents a review of genetic engineering, in which the genotypes of plants and animals (including human genotypes) may be manipulated for the benefit of the human species. Discusses associated problems and solutions and provides an extensive bibliography of literature relating to genetic engineering. (JR)

  9. Genetic Counseling

    Science.gov (United States)

    ... for certain types of genetic conditions (such as Down syndrome) in the baby if mother-to-be is 35 years of age or more, or is concerned at any age about her chances of having a child with a genetic condition To learn about the ...

  10. Shape-Reprogrammable Polymers: Encoding, Erasing, and Re-Encoding (Postprint)

    Science.gov (United States)

    2014-11-01

    4. TITLE AND SUBTITLE SHAPE-REPROGRAMMABLE POLYMERS: ENCODING, ERASING, AND RE-ENCODING (POSTPRINT) 5a. CONTRACT NUMBER In- House 5b. GRANT...heating, which leads to the formation of dome structures that resemble the profi le of a 3D Gaussian shape (Supporting Information, Figure S2a–c...S14). By changing the fi lm stretch ratios, various dome shapes can be created (Figure 2 e). In all cases, the buckling direction is towards the

  11. International Directory of Genetic Services. Second Edition.

    Science.gov (United States)

    Lynch, Henry T., Comp.

    The directory lists medical genetic units in the United States and elsewhere in the world. The director and address of each unit are specified; types of genetic services available are indicated by code. (JD)

  12. Model comparisons and genetic and environmental parameter ...

    African Journals Online (AJOL)

    arc

    South African Journal of Animal Science 2005, 35 (1) ... Genetic and environmental parameters were estimated for pre- and post-weaning average daily gain ..... and BWT (and medium maternal genetic correlations) indicates that these traits ...

  13. Chitosan-plasmid DNA nanoparticles encoding small hairpin RNA targeting MMP-3 and -13 to inhibit the expression of dedifferentiation related genes in expanded chondrocytes.

    Science.gov (United States)

    Zhao, Jingxin; Fan, Xiangli; Zhang, Qiang; Sun, Fangfei; Li, Xiaojian; Xiong, Chuan; Zhang, Chunli; Fan, Hongbin

    2014-02-01

    Overexpression of matrix metalloproteinase (MMP)-3 and -13 can lead to the dedifferentiation of expanded chondrocytes. After implanting dedifferentiated cells for cartilage defect repair, graft failure may occur. Short hairpin RNA (shRNA) is a powerful genetic tool to reduce the expression of target genes. This study investigated the effects of chitosan-plasmid DNA (pDNA) nanoparticles encoding shRNA targeting MMP-3 and -13 on the dedifferentiation of expanded chondrocytes. The objective was to optimize the parameters of chitosan-pDNA formulation for achieving higher efficiency of pDNA delivery and gene silencing. The chitosan-pDNA nanoparticles were prepared using a complex coacervation process. Then the characteristics including size, shape, stability, and transfection efficiency were compared in different groups. The results indicated that chitosan of 800 kDa at N/P ratio of 4 and pH 7.0 was optimal to prepare chitosan-pDNA nanoparticles. These nanoparticles showed high DNA loading efficiency (95.8 ± 1.5%) and high gene transfection efficiency (24.5 ± 1.6%). After the expanded chondrocytes were transfected by chitosan-pDNA nanoparticles, MMP-3-610 and MMP-13-2024 groups showed greater suppression in mRNA and protein levels. The results indicated that chitosan-pDNA nanoparticles encoding shRNA targeting MMP-3 and -13 had great potential in silencing the dedifferentiation-related genes for regenerating prolonged and endurable cartilage.

  14. Nucleic acid compositions and the encoding proteins

    Science.gov (United States)

    Preston, III, James F.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

    2014-09-02

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  15. Parameter Estimation of Turbo Code Encoder

    Directory of Open Access Journals (Sweden)

    Mehdi Teimouri

    2014-01-01

    Full Text Available The problem of reconstruction of a channel code consists of finding out its design parameters solely based on its output. This paper investigates the problem of reconstruction of parallel turbo codes. Reconstruction of a turbo code has been addressed in the literature assuming that some of the parameters of the turbo encoder, such as the number of input and output bits of the constituent encoders and puncturing pattern, are known. However in practical noncooperative situations, these parameters are unknown and should be estimated before applying reconstruction process. Considering such practical situations, this paper proposes a novel method to estimate the above-mentioned code parameters. The proposed algorithm increases the efficiency of the reconstruction process significantly by judiciously reducing the size of search space based on an analysis of the observed channel code output. Moreover, simulation results show that the proposed algorithm is highly robust against channel errors when it is fed with noisy observations.

  16. Robust macroscopic entanglement without complex encodings

    CERN Document Server

    Chaves, Rafael; Acín, Antonio

    2011-01-01

    One of the main challenges for the experimental manipulation and storage of macroscopic entanglement is its fragility under noise. We present a simple recipe for the systematic enhancement of the resistance of multipartite entanglement against any local noise with a privileged direction in the Bloch sphere. For the case of exact local dephasing along any given basis, and for all noise strengths, our prescription grants full robustness: even states whose entanglement decays exponentially with the number of parts are mapped to states whose entanglement is constant. In contrast to previous techniques resorting to complex logical-qubit encodings, such enhancement is attained simply by performing local unitary rotations before the noise acts. The scheme is therefore highly experimentally-friendly, as it brings no overhead of extra physical qubits to encode logical ones. In addition, we show that, apart from entanglement, the resilience of the states as resources for useful practical tasks such as metrology and non...

  17. Asymmetric synthesis using chiral-encoded metal

    Science.gov (United States)

    Yutthalekha, Thittaya; Wattanakit, Chularat; Lapeyre, Veronique; Nokbin, Somkiat; Warakulwit, Chompunuch; Limtrakul, Jumras; Kuhn, Alexander

    2016-08-01

    The synthesis of chiral compounds is of crucial importance in many areas of society and science, including medicine, biology, chemistry, biotechnology and agriculture. Thus, there is a fundamental interest in developing new approaches for the selective production of enantiomers. Here we report the use of mesoporous metal structures with encoded geometric chiral information for inducing asymmetry in the electrochemical synthesis of mandelic acid as a model molecule. The chiral-encoded mesoporous metal, obtained by the electrochemical reduction of platinum salts in the presence of a liquid crystal phase and the chiral template molecule, perfectly retains the chiral information after removal of the template. Starting from a prochiral compound we demonstrate enantiomeric excess of the (R)-enantiomer when using (R)-imprinted electrodes and vice versa for the (S)-imprinted ones. Moreover, changing the amount of chiral cavities in the material allows tuning the enantioselectivity.

  18. Multichannel Compressive Sensing MRI Using Noiselet Encoding

    CERN Document Server

    Pawar, Kamlesh; Zhang, Jingxin

    2014-01-01

    The incoherence between measurement and sparsifying transform matrices and the restricted isometry property (RIP) of measurement matrix are two of the key factors in determining the performance of compressive sensing (CS). In CS-MRI, the randomly under-sampled Fourier matrix is used as the measurement matrix and the wavelet transform is usually used as sparsifying transform matrix. However, the incoherence between the randomly under-sampled Fourier matrix and the wavelet matrix is not optimal, which can deteriorate the performance of CS-MRI. Using the mathematical result that noiselets are maximally incoherent with wavelets, this paper introduces the noiselet unitary bases as the measurement matrix to improve the incoherence and RIP in CS-MRI, and presents a method to design the pulse sequence for the noiselet encoding. This novel encoding scheme is combined with the multichannel compressive sensing (MCS) framework to take the advantage of multichannel data acquisition used in MRI scanners. An empirical RIP a...

  19. Compositional encoding for bounded model checking

    Institute of Scientific and Technical Information of China (English)

    Jun SUN; Yang LIU; Jin Song DONG; Jing SUN

    2008-01-01

    Verification techniques like SAT-based bounded model checking have been successfully applied to a variety of system models. Applying bounded model checking to compositional process algebras is, however, a highly non-trivial task. One challenge is that the number of system states for process algebra models is not statically known, whereas exploring the full state space is computa-tionally expensive. This paper presents a compositional encoding of hierarchical processes as SAT problems and then applies state-of-the-art SAT solvers for bounded model checking. The encoding avoids exploring the full state space for complex systems so as to deal with state space explosion. We developed an automated analyzer which combines complementing model checking tech-niques (I.e., bounded model checking and explicit on-the-fly model checking) to validate system models against event-based temporal properties. The experiment results show the analyzer handles large systems.

  20. DNA-Encoded Dynamic Combinatorial Chemical Libraries.

    Science.gov (United States)

    Reddavide, Francesco V; Lin, Weilin; Lehnert, Sarah; Zhang, Yixin

    2015-06-26

    Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA-encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal-to-noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA-encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high-affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA-templated chemical reactions.