Soft Ultrathin Electronics Innervated Adaptive Fully Soft Robots.

PubMed

Wang, Chengjun; Sim, Kyoseung; Chen, Jin; Kim, Hojin; Rao, Zhoulyu; Li, Yuhang; Chen, Weiqiu; Song, Jizhou; Verduzco, Rafael; Yu, Cunjiang

2018-03-01

Soft robots outperform the conventional hard robots on significantly enhanced safety, adaptability, and complex motions. The development of fully soft robots, especially fully from smart soft materials to mimic soft animals, is still nascent. In addition, to date, existing soft robots cannot adapt themselves to the surrounding environment, i.e., sensing and adaptive motion or response, like animals. Here, compliant ultrathin sensing and actuating electronics innervated fully soft robots that can sense the environment and perform soft bodied crawling adaptively, mimicking an inchworm, are reported. The soft robots are constructed with actuators of open-mesh shaped ultrathin deformable heaters, sensors of single-crystal Si optoelectronic photodetectors, and thermally responsive artificial muscle of carbon-black-doped liquid-crystal elastomer (LCE-CB) nanocomposite. The results demonstrate that adaptive crawling locomotion can be realized through the conjugation of sensing and actuation, where the sensors sense the environment and actuators respond correspondingly to control the locomotion autonomously through regulating the deformation of LCE-CB bimorphs and the locomotion of the robots. The strategy of innervating soft sensing and actuating electronics with artificial muscles paves the way for the development of smart autonomous soft robots. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain.

PubMed

Koch, Miriam; Willi, Jessica; Pradère, Ugo; Hall, Jonathan; Polacek, Norbert

2017-06-20

The nascent peptide exit tunnel has recently been identified as a functional region of ribosomes contributing to translation regulation and co-translational protein folding. Inducible expression of the erm resistance genes depends on ribosome stalling at specific codons of an upstream open reading frame in the presence of an exit tunnel-bound macrolide antibiotic. The molecular basis for this translation arrest is still not fully understood. Here, we used a nucleotide analog interference approach to unravel important functional groups on 23S rRNA residues in the ribosomal exit tunnel for ribosome stalling on the ErmC leader peptide. By replacing single nucleobase functional groups or even single atoms we were able to demonstrate the importance of A2062, A2503 and U2586 for drug-dependent ribosome stalling. Our data show that the universally conserved A2062 and A2503 are capable of forming a non-Watson-Crick base pair that is critical for sensing and transmitting the stalling signal from the exit tunnel back to the peptidyl transferase center of the ribosome. The nucleobases of A2062, A2503 as well as U2586 do not contribute significantly to the overall mechanism of protein biosynthesis, yet their elaborate role for co-translational monitoring of nascent peptide chains inside the exit tunnel can explain their evolutionary conservation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Self-assembly of marine exudate particles and their impact on the CCN properties of nascent marine aerosol

NASA Astrophysics Data System (ADS)

Schill, S.; Zimmermann, K.; Ryder, O. S.; Campbell, N.; Collins, D. B.; Gianneschi, N.; Bertram, T. H.

2013-12-01

Spontaneous self-assembly of marine exudate particles has previously been observed in filtered seawater samples. The chemicophysical properties of these particles may alter the chemical composition and CCN properties of nascent marine aerosol, yet to date simultaneous measurement of seawater exudate particle formation rates and number distributions, with aerosol particle formation rates and CCN activity are lacking. Here, we use a novel Marine Aerosol Reference Tank (MART) system to experimentally mimic a phytoplankton bloom via sequential addition of biological surrogates, including sterol, galactose, lipopolysaccharide, BSA protein, and dipalmitoylphosphatidylcholine. Nascent sea-spray aerosol are generated in the MART system via a continuous plunging waterfall. Exudate particle assembly in the water is monitored via dynamic light scattering (DLS) and transmission electron microscopy (TEM) to obtain both the assembly kinetics of the particles as well as particle number distributions Simultaneous characterization of both particle production rates and super-saturated particle hygroscopicity are also discussed. This study permits analysis of the controlling role of the molecular composition of dissolved organic carbon in setting the production rates of colloidal material in the surface oceans.

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.

PubMed

Andersson, Leif; Archibald, Alan L; Bottema, Cynthia D; Brauning, Rudiger; Burgess, Shane C; Burt, Dave W; Casas, Eduardo; Cheng, Hans H; Clarke, Laura; Couldrey, Christine; Dalrymple, Brian P; Elsik, Christine G; Foissac, Sylvain; Giuffra, Elisabetta; Groenen, Martien A; Hayes, Ben J; Huang, LuSheng S; Khatib, Hassan; Kijas, James W; Kim, Heebal; Lunney, Joan K; McCarthy, Fiona M; McEwan, John C; Moore, Stephen; Nanduri, Bindu; Notredame, Cedric; Palti, Yniv; Plastow, Graham S; Reecy, James M; Rohrer, Gary A; Sarropoulou, Elena; Schmidt, Carl J; Silverstein, Jeffrey; Tellam, Ross L; Tixier-Boichard, Michele; Tosser-Klopp, Gwenola; Tuggle, Christopher K; Vilkki, Johanna; White, Stephen N; Zhao, Shuhong; Zhou, Huaijun

2015-03-25

We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.

Coordinated international action to accelerate genome-to-phenome with FAANG, The Functional Annotation of Animal Genomes project

USDA-ARS?s Scientific Manuscript database

We describe the organization of a nascent international effort - the "Functional Annotation of ANimal Genomes" project - whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species....

Three-dimensional organization of nascent rod outer segment disk membranes.

PubMed

Volland, Stefanie; Hughes, Louise C; Kong, Christina; Burgess, Barry L; Linberg, Kenneth A; Luna, Gabriel; Zhou, Z Hong; Fisher, Steven K; Williams, David S

2015-12-01

The vertebrate photoreceptor cell contains an elaborate cilium that includes a stack of phototransductive membrane disks. The disk membranes are continually renewed, but how new disks are formed remains poorly understood. Here we used electron microscope tomography to obtain 3D visualization of the nascent disks of rod photoreceptors in three mammalian species, to gain insight into the process of disk morphogenesis. We observed that nascent disks are invariably continuous with the ciliary plasma membrane, although, owing to partial enclosure, they can appear to be internal in 2D profiles. Tomographic analyses of the basal-most region of the outer segment show changes in shape of the ciliary plasma membrane indicating an invagination, which is likely a first step in disk formation. The invagination flattens to create the proximal surface of an evaginating lamella, as well as membrane protrusions that extend between adjacent lamellae, thereby initiating a disk rim. Immediately distal to this initiation site, lamellae of increasing diameter are evident, indicating growth outward from the cilium. In agreement with a previous model, our data indicate that mature disks are formed once lamellae reach full diameter, and the growth of a rim encloses the space between adjacent surfaces of two lamellae. This study provides 3D data of nascent and mature rod photoreceptor disk membranes at unprecedented z-axis depth and resolution, and provides a basis for addressing fundamental questions, ranging from protein sorting in the photoreceptor cilium to photoreceptor electrophysiology.

DYNAMICS OF NASCENT AND ACTIVE ZONE ULTRASTRUCTURE AS SYNAPSES ENLARGE DURING LTP IN MATURE HIPPOCAMPUS

PubMed Central

Bell, Maria Elizabeth; Bourne, Jennifer N.; Chirillo, Michael A.; Mendenhall, John M.; Kuwajima, Masaaki; Harris, Kristen M.

2014-01-01

Nascent zones and active zones are adjacent synaptic regions that share a postsynaptic density, but nascent zones lack the presynaptic vesicles found at active zones. Here dendritic spine synapses were reconstructed through serial section electron microscopy (3DEM) and EM tomography to investigate nascent zone dynamics during long-term potentiation (LTP) in mature rat hippocampus. LTP was induced with theta-burst stimulation and comparisons were made to control stimulation in the same hippocampal slices at 5 minutes, 30 minutes, and 2 hours post-induction and to perfusion-fixed hippocampus in vivo. Nascent zones were present at the edges of ~35% of synapses in perfusion-fixed hippocampus and as many as ~50% of synapses in some hippocampal slice conditions. By 5 minutes, small dense core vesicles known to transport active zone proteins moved into more presynaptic boutons. By 30 minutes, nascent zone area decreased without significant change in synapse area, suggesting that presynaptic vesicles were recruited to pre-existing nascent zones. By 2 hours, both nascent and active zones were enlarged. Immunogold labeling revealed that glutamate receptors can be found in nascent zones; however, average distances from nascent zones to docked presynaptic vesicles ranged from 170±5 nm in perfusion-fixed hippocampus to 251±4 nm at enlarged synapses by 2 hours during LTP. Prior stochastic modeling suggests that falloff in glutamate concentration reduces the probability of glutamate receptor activation from 0.4 at the center of release to 0.1 just 200 nm away. Thus, conversion of nascent zones to functional active zones likely requires the recruitment of presynaptic vesicles during LTP. PMID:25043676

EGFR and HER2 activate rigidity sensing only on rigid matrices

NASA Astrophysics Data System (ADS)

Saxena, Mayur; Liu, Shuaimin; Yang, Bo; Hajal, Cynthia; Changede, Rishita; Hu, Junqiang; Wolfenson, Haguy; Hone, James; Sheetz, Michael P.

2017-07-01

Epidermal growth factor receptor (EGFR) interacts with integrins during cell spreading and motility, but little is known about the role of EGFR in these mechanosensing processes. Here we show, using two different cell lines, that in serum- and EGF-free conditions, EGFR or HER2 activity increase spreading and rigidity-sensing contractions on rigid, but not soft, substrates. Contractions peak after 15-20 min, but diminish by tenfold after 4 h. Addition of EGF at that point increases spreading and contractions, but this can be blocked by myosin-II inhibition. We further show that EGFR and HER2 are activated through phosphorylation by Src family kinases (SFK). On soft surfaces, neither EGFR inhibition nor EGF stimulation have any effect on cell motility. Thus, EGFR or HER2 can catalyse rigidity sensing after associating with nascent adhesions under rigidity-dependent tension downstream of SFK activity. This has broad implications for the roles of EGFR and HER2 in the absence of EGF both for normal and cancerous growth.

EGFR and HER2 Activate Rigidity Sensing Only on Rigid Matrices

PubMed Central

Saxena, Mayur; Liu, Shuaimin; Yang, Bo; Hajal, Cynthia; Changede, Rishita; Hu, Junqiang

2017-01-01

Epidermal growth factor receptor (EGFR) interacts with integrins during cell spreading and motility, but little is known about the role of EGFR in these mechanosensing processes. Here we show, using two different cell lines, that in serum- and EGF-free conditions, EGFR or HER2 activity increase spreading and rigidity-sensing contractions on rigid, but not soft, substrates. Contractions peak after 15–20 min, but diminish by 10-fold after 4 hours. Addition of EGF at that point increases spreading and contractions, but this can be blocked by myosin-II inhibition. We further show that EGFR and HER2 are activated through phosphorylation by Src family kinases (SFK). On soft surfaces, neither EGFR inhibition nor EGF stimulation have any effect on cell motility. Thus, EGFR or HER2 can catalyse rigidity sensing after associating with nascent adhesions under rigidity-dependent tension downstream of SFK activity. This has broad implications for the roles of EGFR and HER2 in absence of EGF both for normal and cancerous growth. PMID:28459445

Strolling Toward New Concepts.

PubMed

Ito, Koreaki

2016-09-08

For more than four decades now, I have been studying how genetic information is transformed into protein-based cellular functions. This has included investigations into the mechanisms supporting cellular localization of proteins, disulfide bond formation, quality control of membranes, and translation. I tried to extract new principles and concepts that are universal among living organisms from our observations of Escherichia coli. While I wanted to distill complex phenomena into basic principles, I also tried not to overlook any serendipitous observations. In the first part of this article, I describe personal experiences during my studies of the Sec pathway, which have centered on the SecY translocon. In the second part, I summarize my views of the recent revival of translation studies, which has given rise to the concept that nonuniform polypeptide chain elongation is relevant for the subsequent fates of newly synthesized proteins. Our studies of a class of regulatory nascent polypeptides advance this concept by showing that the dynamic behaviors of the extraribosomal part of the nascent chain affect the ongoing translation process. Vibrant and regulated molecular interactions involving the ribosome, mRNA, and nascent polypeptidyl-tRNA are based, at least partly, on their autonomously interacting properties.

Subliminal (latent) processing of pain and its evolution to conscious awareness

PubMed Central

Borsook, David; Youssef, Andrew M.; Barakat, Nadia; Sieberg, Christine B.; Elman, Igor

2018-01-01

By unconscious or covert processing of pain we refer to nascent interactions that affect the eventual deliverance of pain awareness. Thus, internal processes (viz., repeated nociceptive events, inflammatory kindling, re-organization of brain networks, genetic) or external processes (viz., environment, socioeconomic levels, modulation of epigenetic status) contribute to enhancing or inhibiting the presentation of pain awareness. Here we put forward the notion that for many patients, ongoing sub-conscious changes in brain function are significant players in the eventual manifestation of chronic pain. In this review, we provide clinical examples of nascent or what we term pre-pain processes and the neurobiological mechanisms of how these changes may contribute to pain, but also potential opportunities to define the process for early therapeutic interventions. PMID:29476771

Molecular mechanism and structure of Trigger Factor bound to the translating ribosome

PubMed Central

Merz, Frieder; Boehringer, Daniel; Schaffitzel, Christiane; Preissler, Steffen; Hoffmann, Anja; Maier, Timm; Rutkowska, Anna; Lozza, Jasmin; Ban, Nenad; Bukau, Bernd; Deuerling, Elke

2008-01-01

Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions of Escherichia coli TF and nascent chains during translation. Furthermore, we provide the first full-length structure of TF associated with ribosome–nascent chain complexes by using cryo-electron microscopy. In its active state, TF arches over the ribosomal exit tunnel accepting nascent chains in a protective void. The growing nascent chain initially follows a predefined path through the entire interior of TF in an unfolded conformation, and even after folding into a domain it remains accommodated inside the protective cavity of ribosome-bound TF. The adaptability to accept nascent chains of different length and folding states may explain how TF is able to assist co-translational folding of all kinds of nascent polypeptides during ongoing synthesis. Moreover, we suggest a model of how TF's chaperoning function can be coordinated with the co-translational processing and membrane targeting of nascent polypeptides by other ribosome-associated factors. PMID:18497744

Experimental Investigation of Nascent Soot Physical Properties and The Influence on Particle Morphology and Growth

NASA Astrophysics Data System (ADS)

Lieb, Sydnie Marie

Soot released to the atmosphere is a dangerous pollutant for human health and the environment. Understanding the physical properties and surface properties of these particles is important to properly explaining the growth of soot particles in flames as well as their interactions with other particles and gases in the environment. Particles below 15 nm in diameter, nascent soot particles, dominate the early growth stages of soot formation; previously these particles were characterized as hard graphitic spheres. New evidence derived from the current dissertation work, to a large extent, challenges this prior characterization. This dissertation study begins by revisiting the use of atomic force microscope (AFM) as a tool to investigate the structural properties of nascent soot. The impact of tip artifacts, which are known to complicate measurements of features below 10 nm in diameter, are carefully considered so as to provide a concise interpretation of the morphology of nascent soot as seen by AFM. The results of the AFM morphology collaborate with earlier photo- and thermal-fragmentation particle mass spectrometry and Fourier transform infrared spectroscopy that nascent soot is not a graphitized carbon material and that they are not spherical. Furthermore, phase mode imaging is introduced as a method to investigate the physical properties of nascent soot particles in a greater detail and finer resolution. The helium ion microscope (HIM) has been identified as a useful technique for the imaging of nascent soot. Using this imaging method nascent soot particles were imaged with a high resolution that had not been obtained by prior techniques. The increased contrast provides a closer look at the nascent soot particles and further suggested that these particles are not as structurally homogeneous as previously thought. Geometric shape analysis was performed to characterize the particles in terms of sphericity, circularity, and fractal dimension. The geometric analysis showed that the particles deviate from spherical and that they are not characterized by a defined structure. This observation supports the theory that nascent soot is not homogenous in structure or composition, and challenges the classical assumption that spherical growth and aggregation are separate, size dependent processes. In light of the new evidence that suggests nascent soot particles are structurally inhomogenous, careful consideration must be given to mobility measurements of particle mass and size. The interpretation of particle volume of irregularly shaped nascent soot particles is considered in this dissertation work. Additionally, uncertainties in the mass density of nascent soot are reviewed and the error in mass calculation is quantified.

How Messenger RNA and Nascent Chain Sequences Regulate Translation Elongation.

PubMed

Choi, Junhong; Grosely, Rosslyn; Prabhakar, Arjun; Lapointe, Christopher P; Wang, Jinfan; Puglisi, Joseph D

2018-06-20

Translation elongation is a highly coordinated, multistep, multifactor process that ensures accurate and efficient addition of amino acids to a growing nascent-peptide chain encoded in the sequence of translated messenger RNA (mRNA). Although translation elongation is heavily regulated by external factors, there is clear evidence that mRNA and nascent-peptide sequences control elongation dynamics, determining both the sequence and structure of synthesized proteins. Advances in methods have driven experiments that revealed the basic mechanisms of elongation as well as the mechanisms of regulation by mRNA and nascent-peptide sequences. In this review, we highlight how mRNA and nascent-peptide elements manipulate the translation machinery to alter the dynamics and pathway of elongation.

Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication.

PubMed

Bj Rås, Karine Ø; Sousa, Mirta M L; Sharma, Animesh; Fonseca, Davi M; S Gaard, Caroline K; Bj Rås, Magnar; Otterlei, Marit

2017-08-21

Base lesions in DNA can stall the replication machinery or induce mutations if bypassed. Consequently, lesions must be repaired before replication or in a post-replicative process to maintain genomic stability. Base excision repair (BER) is the main pathway for repair of base lesions and is known to be associated with DNA replication, but how BER is organized during replication is unclear. Here we coupled the iPOND (isolation of proteins on nascent DNA) technique with targeted mass-spectrometry analysis, which enabled us to detect all proteins required for BER on nascent DNA and to monitor their spatiotemporal orchestration at replication forks. We demonstrate that XRCC1 and other BER/single-strand break repair (SSBR) proteins are enriched in replisomes in unstressed cells, supporting a cellular capacity of post-replicative BER/SSBR. Importantly, we identify for the first time the DNA glycosylases MYH, UNG2, MPG, NTH1, NEIL1, 2 and 3 on nascent DNA. Our findings suggest that a broad spectrum of DNA base lesions are recognized and repaired by BER in a post-replicative process. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Seipin is required for converting nascent to mature lipid droplets

PubMed Central

Wang, Huajin; Becuwe, Michel; Housden, Benjamin E; Chitraju, Chandramohan; Porras, Ashley J; Graham, Morven M; Liu, Xinran N; Thiam, Abdou Rachid; Savage, David B; Agarwal, Anil K; Garg, Abhimanyu; Olarte, Maria-Jesus; Lin, Qingqing; Fröhlich, Florian; Hannibal-Bach, Hans Kristian; Upadhyayula, Srigokul; Perrimon, Norbert; Kirchhausen, Tomas; Ejsing, Christer S; Walther, Tobias C; Farese, Robert V

2016-01-01

How proteins control the biogenesis of cellular lipid droplets (LDs) is poorly understood. Using Drosophila and human cells, we show here that seipin, an ER protein implicated in LD biology, mediates a discrete step in LD formation—the conversion of small, nascent LDs to larger, mature LDs. Seipin forms discrete and dynamic foci in the ER that interact with nascent LDs to enable their growth. In the absence of seipin, numerous small, nascent LDs accumulate near the ER and most often fail to grow. Those that do grow prematurely acquire lipid synthesis enzymes and undergo expansion, eventually leading to the giant LDs characteristic of seipin deficiency. Our studies identify a discrete step of LD formation, namely the conversion of nascent LDs to mature LDs, and define a molecular role for seipin in this process, most likely by acting at ER-LD contact sites to enable lipid transfer to nascent LDs. DOI: http://dx.doi.org/10.7554/eLife.16582.001 PMID:27564575

Actin cable dynamics and Rho/Rock orchestrate a polarized cytoskeletal architecture in the early steps of assembling a stratified epithelium.

PubMed

Vaezi, Alec; Bauer, Christoph; Vasioukhin, Valeri; Fuchs, Elaine

2002-09-01

To enable stratification and barrier function, the epidermis must permit self-renewal while maintaining adhesive connections. By generating K14-GFP-actin mice to monitor actin dynamics in cultured primary keratinocytes, we uncovered a role for the actin cytoskeleton in establishing cellular organization. During epidermal sheet formation, a polarized network of nascent intercellular junctions and radial actin cables assemble in the apical plane of the monolayer. These actin fibers anchor to a central actin-myosin network, creating a tension-based plane of cytoskeleton across the apical surface of the sheet. Movement of the sheet surface relative to its base expands the zone of intercellular overlap, catalyzing new sites for nascent intercellular junctions. This polarized cytoskeleton is dependent upon alpha-catenin, Rho, and Rock, and its regulation may be important for wound healing and/or stratification, where coordinated tissue movements are involved.

Self-organized Motion During Dictyostelium amoebae aggregation

NASA Astrophysics Data System (ADS)

Levine, Herbert

2004-03-01

After starvation, amoeba of the cellular slime mold Dictyostelium discoideum aggregate to form rudimentary multicellular organisms. The coordination of the individual motions of hundreds of thousands of individual cells is an important ingredient in the success of this process. This coordination is accomplished by chemical signaling during the early stages and by direct cell-cell interactions once the cells reach the nascent mound. This talk will review the basic nonequilibrium physics underlying the spatial patterns formed by these cooperative motions, including high-density incoming streams and spontaneously rotating mounds.

Interconnected Cavernous Structure of Bacterial Fruiting Bodies

DOE PAGES

Harvey, Cameron W.; Du, Huijing; Xu, Zhiliang; ...

2012-12-27

The formation of spore-filled fruiting bodies by myxobacteria is a fascinating case of multicelular self-organization by bacteria. The organization of Myxococcus xanthus into fruiting bodies has long been studied not only as an important example of collective motion of bacteria, but also as a simplified model for developmental morphogenesis. Sporulation within the nascent fruiting body requires signaling between moving cells in order that the rod-shaped self-propelled cells differentiate into spores at the appropriate time. Probing the three-dimensional structure of myxobacteria fruiting bodies has previously presented a challenge due to Imitations at different imaging methods. A new technique using Infrared Opticalmore » Coherence Tomography (OCT) revealed previously unknown details of the Internal structure of M. xanthus fruiting bodies consisting of interconnected pockets of relative nigh and low spore density regions. Here, to make sense of the experimentally observed structure, modeling and computer simulations were used to test a hypothesized mechanism that could produce high density pockets of spores. The mechanism consists of self-propelled cells aligning with each other and signaling by end-to-end contact to coordinate the process of differentiation resulting in a pattern of clusters observed in the experiment. The Integration of novel OCT experimental techniques with computational simulations can provide new insight Into the mechanisms that can give rise to the pattern formation seen In other biological systems such as dlctyostelids, social amoeba known to form multicellular aggregates observed as slugs under starvation conditions.« less

Interplay of signal recognition particle and trigger factor at L23 near the nascent chain exit site on the Escherichia coli ribosome

PubMed Central

Ullers, Ronald S.; Houben, Edith N.G.; Raine, Amanda; ten Hagen-Jongman, Corinne M.; Ehrenberg, Måns; Brunner, Joseph; Oudega, Bauke; Harms, Nellie; Luirink, Joen

2003-01-01

As newly synthesized polypeptides emerge from the ribosome, they interact with chaperones and targeting factors that assist in folding and targeting to the proper location in the cell. In Escherichia coli, the chaperone trigger factor (TF) binds to nascent polypeptides early in biosynthesis facilitated by its affinity for the ribosomal proteins L23 and L29 that are situated around the nascent chain exit site on the ribosome. The targeting factor signal recognition particle (SRP) interacts specifically with the signal anchor (SA) sequence in nascent inner membrane proteins (IMPs). Here, we have used photocross-linking to map interactions of the SA sequence in a short, in vitro–synthesized, nascent IMP. Both TF and SRP were found to interact with the SA with partially overlapping binding specificity. In addition, extensive contacts with L23 and L29 were detected. Both purified TF and SRP could be cross-linked to L23 on nontranslating ribosomes with a competitive advantage for SRP. The results suggest a role for L23 in the targeting of IMPs as an attachment site for TF and SRP that is close to the emerging nascent chain. PMID:12756233

The recruitment of the U5 snRNP to nascent transcripts requires internal loop 1 of U5 snRNA.

PubMed

Kim, Rebecca; Paschedag, Joshua; Novikova, Natalya; Bellini, Michel

2012-12-01

In this study, we take advantage of the high spatial resolution offered by the nucleus and lampbrush chromosomes of the amphibian oocyte to investigate the mechanisms that regulate the intranuclear trafficking of the U5 snRNP and its recruitment to nascent transcripts. We monitor the fate of newly assembled fluorescent U5 snRNP in Xenopus oocytes depleted of U4 and/or U6 snRNAs and demonstrate that the U4/U6.U5 tri-snRNP is not required for the association of U5 snRNP with Cajal bodies, splicing speckles, and nascent transcripts. In addition, using a mutational analysis, we show that a non-functional U5 snRNP can associate with nascent transcripts, and we further characterize internal loop structure 1 of U5 snRNA as a critical element for licensing U5 snRNP to target both nascent transcripts and splicing speckles. Collectively, our data support the model where the recruitment of snRNPs onto pre-mRNAs is independent of spliceosome assembly and suggest that U5 snRNP may promote the association of the U4/U6.U5 tri-snRNP with nascent transcripts.

Developmental and microbiological analysis of the inception of bioluminescent symbiosis in the marine fish Nuchequula nuchalis (Perciformes: Leiognathidae).

PubMed

Dunlap, Paul V; Davis, Kimberly M; Tomiyama, Shinichi; Fujino, Misato; Fukui, Atsushi

2008-12-01

Many marine fish harbor luminous bacteria as bioluminescent symbionts. Despite the diversity, abundance, and ecological importance of these fish and their apparent dependence on luminous bacteria for survival and reproduction, little is known about developmental and microbiological events surrounding the inception of their symbioses. To gain insight on these issues, we examined wild-caught larvae of the leiognathid fish Nuchequula nuchalis, a species that harbors Photobacterium leiognathi as its symbiont, for the presence, developmental state, and microbiological status of the fish's internal, supraesophageal light organ. Nascent light organs were evident in the smallest specimens obtained, flexion larvae of 6.0 to 6.5 mm in notochord length (NL), a developmental stage at which the stomach had not yet differentiated and the nascent gasbladder had not established an interface with the light organ. Light organs of certain of the specimens in this size range apparently lacked bacteria, whereas light organs of other specimens of 6.5 mm in NL and of all larger specimens harbored large populations of bacteria, representatives of which were identified as P. leiognathi. Bacteria identified as Vibrio harveyi were also present in the light organ of one larval specimen. Light organ populations were composed typically of two or three genetically distinct strain types of P. leiognathi, similar to the situation in adult fish, and the same strain type was only rarely found in light organs of different larval, juvenile, or adult specimens. Light organs of larvae carried a smaller proportion of strains merodiploid for the lux-rib operon, 79 of 249 strains, than those of adults (75 of 91 strains). These results indicate that light organs of N. nuchalis flexion and postflexion larvae of 6.0 to 6.7 mm in NL are at an early stage of development and that inception of the symbiosis apparently occurs in flexion larvae of 6.0 to 6.5 mm in NL. Ontogeny of the light organ therefore apparently precedes acquisition of the symbiotic bacteria. Furthermore, bacterial populations in larval light organs near inception of the symbiosis are genetically diverse, like those of adult fish.

Developmental and Microbiological Analysis of the Inception of Bioluminescent Symbiosis in the Marine Fish Nuchequula nuchalis (Perciformes: Leiognathidae)▿

PubMed Central

Dunlap, Paul V.; Davis, Kimberly M.; Tomiyama, Shinichi; Fujino, Misato; Fukui, Atsushi

2008-01-01

Many marine fish harbor luminous bacteria as bioluminescent symbionts. Despite the diversity, abundance, and ecological importance of these fish and their apparent dependence on luminous bacteria for survival and reproduction, little is known about developmental and microbiological events surrounding the inception of their symbioses. To gain insight on these issues, we examined wild-caught larvae of the leiognathid fish Nuchequula nuchalis, a species that harbors Photobacterium leiognathi as its symbiont, for the presence, developmental state, and microbiological status of the fish's internal, supraesophageal light organ. Nascent light organs were evident in the smallest specimens obtained, flexion larvae of 6.0 to 6.5 mm in notochord length (NL), a developmental stage at which the stomach had not yet differentiated and the nascent gasbladder had not established an interface with the light organ. Light organs of certain of the specimens in this size range apparently lacked bacteria, whereas light organs of other specimens of 6.5 mm in NL and of all larger specimens harbored large populations of bacteria, representatives of which were identified as P. leiognathi. Bacteria identified as Vibrio harveyi were also present in the light organ of one larval specimen. Light organ populations were composed typically of two or three genetically distinct strain types of P. leiognathi, similar to the situation in adult fish, and the same strain type was only rarely found in light organs of different larval, juvenile, or adult specimens. Light organs of larvae carried a smaller proportion of strains merodiploid for the lux-rib operon, 79 of 249 strains, than those of adults (75 of 91 strains). These results indicate that light organs of N. nuchalis flexion and postflexion larvae of 6.0 to 6.7 mm in NL are at an early stage of development and that inception of the symbiosis apparently occurs in flexion larvae of 6.0 to 6.5 mm in NL. Ontogeny of the light organ therefore apparently precedes acquisition of the symbiotic bacteria. Furthermore, bacterial populations in larval light organs near inception of the symbiosis are genetically diverse, like those of adult fish. PMID:18978090

Nascent RNA kinetics: Transient and steady state behavior of models of transcription

NASA Astrophysics Data System (ADS)

Choubey, Sandeep

2018-02-01

Regulation of transcription is a vital process in cells, but mechanistic details of this regulation still remain elusive. The dominant approach to unravel the dynamics of transcriptional regulation is to first develop mathematical models of transcription and then experimentally test the predictions these models make for the distribution of mRNA and protein molecules at the individual cell level. However, these measurements are affected by a multitude of downstream processes which make it difficult to interpret the measurements. Recent experimental advancements allow for counting the nascent mRNA number of a gene as a function of time at the single-inglr cell level. These measurements closely reflect the dynamics of transcription. In this paper, we consider a general mechanism of transcription with stochastic initiation and deterministic elongation and probe its impact on the temporal behavior of nascent RNA levels. Using techniques from queueing theory, we derive exact analytical expressions for the mean and variance of the nascent RNA distribution as functions of time. We apply these analytical results to obtain the mean and variance of nascent RNA distribution for specific models of transcription. These models of initiation exhibit qualitatively distinct transient behaviors for both the mean and variance which further allows us to discriminate between them. Stochastic simulations confirm these results. Overall the analytical results presented here provide the necessary tools to connect mechanisms of transcription initiation to single-cell measurements of nascent RNA.

Cotranslational structure acquisition of nascent polypeptides monitored by NMR spectroscopy.

PubMed

Eichmann, Cédric; Preissler, Steffen; Riek, Roland; Deuerling, Elke

2010-05-18

The folding of proteins in living cells may start during their synthesis when the polypeptides emerge gradually at the ribosomal exit tunnel. However, our current understanding of cotranslational folding processes at the atomic level is limited. We employed NMR spectroscopy to monitor the conformation of the SH3 domain from alpha-spectrin at sequential stages of elongation via in vivo ribosome-arrested (15)N,(13)C-labeled nascent polypeptides. These nascent chains exposed either the entire SH3 domain or C-terminally truncated segments thereof, thus providing snapshots of the translation process. We show that nascent SH3 polypeptides remain unstructured during elongation but fold into a compact, native-like beta-sheet assembly when the entire sequence information is available. Moreover, the ribosome neither imposes major conformational constraints nor significantly interacts with exposed unfolded nascent SH3 domain moieties. Our data provide evidence for a domainwise folding of the SH3 domain on ribosomes without significant population of folding intermediates. The domain follows a thermodynamically favorable pathway in which sequential folding units are stabilized, thus avoiding kinetic traps during the process of cotranslational folding.

Thermodynamics and kinetics of protein folding on the ribosome: Alteration in energy landscapes, denatured state, and transition state ensembles

NASA Astrophysics Data System (ADS)

O'Brien, Edward; Vendruscolo, Michele; Dobson, Christopher

2010-03-01

In vitro experiments examining cotranslational folding utilize ribosome-nascent chain complexes (RNCs) in which the nascent chain is stalled at different points of its biosynthesis on the ribosome. We investigate the thermodynamics, kinetics, and structural properties of RNCs containing five different globular and repeat proteins stalled at ten different nascent chain lengths using coarse grained replica exchange simulations. We find that when the proteins are stalled near the ribosome exit tunnel opening they exhibit altered folding coopserativity, quantified by the van't Hoff enthalpy criterion; a significantly altered denatured state ensemble, in terms of Rg and shape parameters (Rg tensor); and the appearance of partially folded intermediates during cotranslation, evidenced by the appearance of a third basin in the free energy profile. These trends are due in part to excluded volume (crowding) interactions between the ribosome and nascent chain. We perform in silico temperature-jump experiments on the RNCs and examine nascent chain folding kinetics and structural changes in the transition state ensemble at various stall lengths.

Synthetic Morphogenesis.

PubMed

Teague, Brian P; Guye, Patrick; Weiss, Ron

2016-09-01

Throughout biology, function is intimately linked with form. Across scales ranging from subcellular to multiorganismal, the identity and organization of a biological structure's subunits dictate its properties. The field of molecular morphogenesis has traditionally been concerned with describing these links, decoding the molecular mechanisms that give rise to the shape and structure of cells, tissues, organs, and organisms. Recent advances in synthetic biology promise unprecedented control over these molecular mechanisms; this opens the path to not just probing morphogenesis but directing it. This review explores several frontiers in the nascent field of synthetic morphogenesis, including programmable tissues and organs, synthetic biomaterials and programmable matter, and engineering complex morphogenic systems de novo. We will discuss each frontier's objectives, current approaches, constraints and challenges, and future potential. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

Systematic review of smartphone-based passive sensing for health and wellbeing.

PubMed

Cornet, Victor P; Holden, Richard J

2018-01-01

To review published empirical literature on the use of smartphone-based passive sensing for health and wellbeing. A systematic review of the English language literature was performed following PRISMA guidelines. Papers indexed in computing, technology, and medical databases were included if they were empirical, focused on health and/or wellbeing, involved the collection of data via smartphones, and described the utilized technology as passive or requiring minimal user interaction. Thirty-five papers were included in the review. Studies were performed around the world, with samples of up to 171 (median n = 15) representing individuals with bipolar disorder, schizophrenia, depression, older adults, and the general population. The majority of studies used the Android operating system and an array of smartphone sensors, most frequently capturing accelerometry, location, audio, and usage data. Captured data were usually sent to a remote server for processing but were shared with participants in only 40% of studies. Reported benefits of passive sensing included accurately detecting changes in status, behavior change through feedback, and increased accountability in participants. Studies reported facing technical, methodological, and privacy challenges. Studies in the nascent area of smartphone-based passive sensing for health and wellbeing demonstrate promise and invite continued research and investment. Existing studies suffer from weaknesses in research design, lack of feedback and clinical integration, and inadequate attention to privacy issues. Key recommendations relate to developing passive sensing strategies matching the problem at hand, using personalized interventions, and addressing methodological and privacy challenges. As evolving passive sensing technology presents new possibilities for health and wellbeing, additional research must address methodological, clinical integration, and privacy issues. Doing so depends on interdisciplinary collaboration between informatics and clinical experts. Copyright © 2017 Elsevier Inc. All rights reserved.

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

FLANAGAN,J.M.; BEWLEY,M.C.

It is generally accepted that the information necessary to specify the native, functional, three-dimensional structure of a protein is encoded entirely within its amino acid sequence; however, efficient reversible folding and unfolding is observed only with a subset of small single-domain proteins. Refolding experiments often lead to the formation of kinetically-trapped, misfolded species that aggregate, even in dilute solution. In the cellular environment, the barriers to efficient protein folding and maintenance of native structure are even larger due to the nature of this process. First, nascent polypeptides must fold in an extremely crowded environment where the concentration of macromolecules approachesmore » 300-400 mg/mL and on average, each ribosome is within its own diameter of another ribosome (1-3). These conditions of severe molecular crowding, coupled with high concentrations of nascent polypeptide chains, favor nonspecific aggregation over productive folding (3). Second, folding of newly-translated polypeptides occurs in the context of their vehtorial synthesis process. Amino acids are added to a growing nascent chain at the rate of -5 residues per set, which means that for a 300 residue protein its N-terminus will be exposed to the cytosol {approx}1 min before its C-terminus and be free to begin the folding process. However, because protein folding is highly cooperative, the nascent polypeptide cannot reach its native state until a complete folding domain (50-250 residues) has emerged from the ribosome. Thus, for a single-domain protein, the final steps in folding are only completed post-translationally since {approx}40 residues of a nascent chain are sequestered within the exit channel of the ribosome and are not available for folding (4). A direct consequence of this limitation in cellular folding is that during translation incomplete domains will exist in partially-folded states that tend to expose hydrophobic residues that are prone to aggregation and/or misfolding. Thus it is not surprising that, in cells, the protein folding process is error prone and organisms have evolved ''editing'' or quality control (QC) systems to assist in the folding, maintenance and, when necessary, selective removal of damaged proteins. In fact, there is growing evidence that failure of these QC-systems contributes to a number of disease states (5-8). This chapter describes our current understanding of the nature and mechanisms of the protein quality control systems in the cytosol of bacteria. Parallel systems are exploited in the cytosol and mitochondria of eukaryotes to prevent the accumulation of misfolded proteins.« less

Korean Military Advisory Group (KMAG): A Model for Success

DTIC Science & Technology

2010-05-15

43-45. 16 Alan Millett, The War in Korea, 1945-1950: A House Burning, ( Lawrence : University Press of Kansas, 2005), 172 17 Ibid., 75 18...A great step forward for the advisory effort came in the form of US Army Captain James H. Hausman . Captain Hausman came to Korea in 1946 as one of...group that Hausman joined in 1946 was an organization in crisis, run with limited resources. His mandate from the nascent advisory group’s commander

Nascent life cycles and the emergence of higher-level individuality.

PubMed

Ratcliff, William C; Herron, Matthew; Conlin, Peter L; Libby, Eric

2017-12-05

Evolutionary transitions in individuality (ETIs) occur when formerly autonomous organisms evolve to become parts of a new, 'higher-level' organism. One of the first major hurdles that must be overcome during an ETI is the emergence of Darwinian evolvability in the higher-level entity (e.g. a multicellular group), and the loss of Darwinian autonomy in the lower-level units (e.g. individual cells). Here, we examine how simple higher-level life cycles are a key innovation during an ETI, allowing this transfer of fitness to occur 'for free'. Specifically, we show how novel life cycles can arise and lead to the origin of higher-level individuals by (i) mitigating conflicts between levels of selection, (ii) engendering the expression of heritable higher-level traits and (iii) allowing selection to efficiently act on these emergent higher-level traits. Further, we compute how canonical early life cycles vary in their ability to fix beneficial mutations via mathematical modelling. Life cycles that lack a persistent lower-level stage and develop clonally are far more likely to fix 'ratcheting' mutations that limit evolutionary reversion to the pre-ETI state. By stabilizing the fragile first steps of an evolutionary transition in individuality, nascent higher-level life cycles may play a crucial role in the origin of complex life.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'. © 2017 The Author(s).

Prefoldin 6 is required for normal microtubule dynamics and organization in Arabidopsis

PubMed Central

Gu, Ying; Deng, Zhiping; Paredez, Alexander R.; DeBolt, Seth; Wang, Zhi-Yong; Somerville, Chris

2008-01-01

Newly translated tubulin molecules undergo a series of complex interactions with nascent chain-binding chaperones, including prefoldin (PFD) and chaperonin-containing TCP-1 (CCT). By screening for oryzalin hypersensitivity, we identified several mutants of Arabidopsis that have lesions in PFD subunits. The pfd6–1 mutant exhibits a range of microtubule defects, including hypersensitivity to oryzalin, defects in cell division, cortical array organization, and microtubule dynamicity. Consistent with phenotypic analysis, proteomic analysis indicates several isoforms of tubulins were reduced in pfd6–1. These results support the concept that the function of microtubules is critically dependent on the absolute amount of tubulins. PMID:19004800

CAT-tailing as a fail-safe mechanism for efficient degradation of stalled nascent polypeptides

PubMed Central

Kostova, Kamena K.; Hickey, Kelsey L.; Osuna, Beatriz A.; Hussmann, Jeffrey A.; Frost, Adam; Weinberg, David E.; Weissman, Jonathan S.

2017-01-01

Ribosome stalling leads to recruitment of the Ribosome Quality control Complex (RQC), which targets the partially synthesized polypeptide for proteasomal degradation through the action of the ubiquitin ligase Ltn1p. A second core RQC component, Rqc2p, modifies the nascent polypeptide by adding a Carboxy-terminal Alanine and Threonine (CAT) tail through a non-canonical elongation reaction. Here we explore the role of CATtailing in nascent-chain degradation in budding yeast. We show that Ltn1p can efficiently access only nascent chain lysines immediately proximal to the ribosome exit tunnel. For substrates without Ltn1p-accessible lysines, CAT-tailing enables degradation by exposing lysines sequestered in the ribosome exit tunnel. Thus, CAT-tails do not serve as a degron, but rather provide a fail-safe mechanism that expands the range of RQC-degradable substrates. PMID:28751611

Efficient Synthesis of Molecular Precursors for Para-Hydrogen-Induced Polarization of Ethyl Acetate-1-(13) C and Beyond.

PubMed

Shchepin, Roman V; Barskiy, Danila A; Coffey, Aaron M; Manzanera Esteve, Isaac V; Chekmenev, Eduard Y

2016-05-10

A scalable and versatile methodology for production of vinylated carboxylic compounds with (13) C isotopic label in C1 position is described. It allowed synthesis of vinyl acetate-1-(13) C, which is a precursor for preparation of (13) C hyperpolarized ethyl acetate-1-(13) C, which provides a convenient vehicle for potential in vivo delivery of hyperpolarized acetate to probe metabolism in living organisms. Kinetics of vinyl acetate molecular hydrogenation and polarization transfer from para-hydrogen to (13) C via magnetic field cycling were investigated. Nascent proton nuclear spin polarization (%PH ) of ca. 3.3 % and carbon-13 polarization (%P13C ) of ca. 1.8 % were achieved in ethyl acetate utilizing 50 % para-hydrogen corresponding to ca. 50 % polarization transfer efficiency. The use of nearly 100% para-hydrogen and the improvements of %PH of para-hydrogen-nascent protons may enable production of (13) C hyperpolarized contrast agents with %P13C of 20-50 % in seconds using this chemistry. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A strategy for co-translational folding studies of ribosome-bound nascent chain complexes using NMR spectroscopy.

PubMed

Cassaignau, Anaïs M E; Launay, Hélène M M; Karyadi, Maria-Evangelia; Wang, Xiaolin; Waudby, Christopher A; Deckert, Annika; Robertson, Amy L; Christodoulou, John; Cabrita, Lisa D

2016-08-01

During biosynthesis on the ribosome, an elongating nascent polypeptide chain can begin to fold, in a process that is central to all living systems. Detailed structural studies of co-translational protein folding are now beginning to emerge; such studies were previously limited, at least in part, by the inherently dynamic nature of emerging nascent chains, which precluded most structural techniques. NMR spectroscopy is able to provide atomic-resolution information for ribosome-nascent chain complexes (RNCs), but it requires large quantities (≥10 mg) of homogeneous, isotopically labeled RNCs. Further challenges include limited sample working concentration and stability of the RNC sample (which contribute to weak NMR signals) and resonance broadening caused by attachment to the large (2.4-MDa) ribosomal complex. Here, we present a strategy to generate isotopically labeled RNCs in Escherichia coli that are suitable for NMR studies. Uniform translational arrest of the nascent chains is achieved using a stalling motif, and isotopically labeled RNCs are produced at high yield using high-cell-density E. coli growth conditions. Homogeneous RNCs are isolated by combining metal affinity chromatography (to isolate ribosome-bound species) with sucrose density centrifugation (to recover intact 70S monosomes). Sensitivity-optimized NMR spectroscopy is then applied to the RNCs, combined with a suite of parallel NMR and biochemical analyses to cross-validate their integrity, including RNC-optimized NMR diffusion measurements to report on ribosome attachment in situ. Comparative NMR studies of RNCs with the analogous isolated proteins permit a high-resolution description of the structure and dynamics of a nascent chain during its progressive biosynthesis on the ribosome.

A study of the dynamics and photochemistry of vibrationally excited ozone in the middle atmosphere

NASA Astrophysics Data System (ADS)

Kaufmann, M.; Gil-Lopez, S.; Imk-Iaa Mipas/Envisat Team

The vibrational states of ozone depart from local thermodynamic equilibrium (LTE) due to radiative absorption, chemical pumping, spontaneous emission, and photochemical reaction. The recombination reaction of O+O_2 is the most important source of highly excited ozone, however the distribution of the energy disposal (nascent distribution) is poorly known. In addition, the collisional relaxation scheme is another significant source of uncertainty in the modeling of ozone infrared radiation. We have built a non-LTE model being part of the Generic RAdiative traNsfer AnD non-LTE population Algorithm (GRANADA) that represents the nascent distribution by means of a linear surprisal model. For the collisional relaxation we extrapolate measured rates of the fundamental bands to hot band transitions by using a Landau-Teller type scaling in combination with a relaxation-path dependent energy-gap model. In this talk we present model results in terms of ozone vibrational temperatures and atmospheric limb radiances in the 4-15 μm region. The modeled limb spectra will be compared with measurements from the MIPAS (Michelson Interferometer for Passive Atmosphere Sounding) instrument on board of the polar orbiter ENVISAT. The high spectral resolution of this instrument gives a unique opportunity to observe ozone non-LTE emissions down to the lower stratosphere where ozone densities are high enough to sense even highly excited vibrational states. These give valuable information for the validation of the non-LTE scheme, and therefore will improve the quality of upper mesospheric ozone retrievals.

A study on a nascent entomopathogenic association between caenorhabditis briggsae and serratia sp.SCBI

NASA Astrophysics Data System (ADS)

Abebe-Akele, Feseha

Life is inconceivable in the absence of interactions which could be cooperative, antagonistic or neutral. Interactions are in constant flux because on one hand it is often difficult to demarcate where one form of interaction ends and the other begins on the other hand what is cooperative at one point in time could evolve into antagonistic or neutral or vice versa. Thus, organisms, as a consequence of mutation, adaptation and natural selection would inevitably enter into natural associations from which they emerge as mutual partners, inveterate enemies or passive cohabitants. Entomopathogenic nematode (EPN) partnerships are tripartite interactions where a nematode-bacteria symbiont duo attacks a third organism -an insect or insect larva-for the mutual benefit of the attacking partners and the detriment of the insect they invade. All three participants in the interaction---the nematode worms with their symbiont bacteria and the target insect host-are among the most ancient, diverse and abundant species on earth, however, these EPN partnerships are not as common as circumstances would suggest. EPN associations, which are arguably at the peak of evolutionary co adaptations, where two primitive forms of life cooperate to take advantage of a larger species are not only fascinating but immensely important for humans. The biological and molecular mechanisms underlying entomopathogenesis have been studied in great detail for decades for their potential as biological control agents against invasive insects. In spite of intense research in The EPN field, the evolutionary history of EPN associations are largely unknown because there are no known intermediate forms. In this thesis, a nascent EPN partnership is described between Caenorhabditid nematodes and Serratia sp. SCBI. Comparative analysis of this association with other EPNs suggests that crucial aspect of EPN associations may be the ability of partners to co-exist without killing each other and that the end results of EPN associations- insect killing, cadaver bioconversion and re-colonization-could be achieved by dissimilar and/or overlapping, mechanisms in different symbiotic partners. This study also suggests that the urea metabolism pathway may play a pivotal role in EPN complex formation. This nascent EPN association will be an important resource in understanding EPN evolution.

Structural Insights into High Density Lipoprotein: Old Models and New Facts

PubMed Central

Gogonea, Valentin

2016-01-01

The physiological link between circulating high density lipoprotein (HDL) levels and cardiovascular disease is well-documented, albeit its intricacies are not well-understood. An improved appreciation of HDL function and overall role in vascular health and disease requires at its foundation a better understanding of the lipoprotein's molecular structure, its formation, and its process of maturation through interactions with various plasma enzymes and cell receptors that intervene along the pathway of reverse cholesterol transport. This review focuses on summarizing recent developments in the field of lipid free apoA-I and HDL structure, with emphasis on new insights revealed by newly published nascent and spherical HDL models constructed by combining low resolution structures obtained from small angle neutron scattering (SANS) with contrast variation and geometrical constraints derived from hydrogen–deuterium exchange (HDX), crosslinking mass spectrometry, electron microscopy, Förster resonance energy transfer, and electron spin resonance. Recently published low resolution structures of nascent and spherical HDL obtained from SANS with contrast variation and isotopic labeling of apolipoprotein A-I (apoA-I) will be critically reviewed and discussed in terms of how they accommodate existing biophysical structural data from alternative approaches. The new low resolution structures revealed and also provided some answers to long standing questions concerning lipid organization and particle maturation of lipoproteins. The review will discuss the merits of newly proposed SANS based all atom models for nascent and spherical HDL, and compare them with accepted models. Finally, naturally occurring and bioengineered mutations in apoA-I, and their impact on HDL phenotype, are reviewed and discuss together with new therapeutics employed for restoring HDL function. PMID:26793109

Entrepreneurial Identity and Role Expectations in Nascent Entrepreneurship

ERIC Educational Resources Information Center

Lundqvist, Mats; Middleton, Karen Williams; Nowell, Pamela

2015-01-01

Entrepreneurship has been defined as an individual?new value creation dialogic. To study how entrepreneurial identity evolves, this article, drawing on entrepreneurial learning theory, adds an entrepreneurial role expectations dialogic. Longitudinal evidence from nascent entrepreneurs working in venture teams on invention disclosures offers an…

CAT-tailing as a fail-safe mechanism for efficient degradation of stalled nascent polypeptides.

PubMed

Kostova, Kamena K; Hickey, Kelsey L; Osuna, Beatriz A; Hussmann, Jeffrey A; Frost, Adam; Weinberg, David E; Weissman, Jonathan S

2017-07-28

Ribosome stalling leads to recruitment of the ribosome quality control complex (RQC), which targets the partially synthesized polypeptide for proteasomal degradation through the action of the ubiquitin ligase Ltn1p. A second core RQC component, Rqc2p, modifies the nascent polypeptide by adding a carboxyl-terminal alanine and threonine (CAT) tail through a noncanonical elongation reaction. Here we examined the role of CAT-tailing in nascent-chain degradation in budding yeast. We found that Ltn1p efficiently accessed only nascent-chain lysines immediately proximal to the ribosome exit tunnel. For substrates without Ltn1p-accessible lysines, CAT-tailing enabled degradation by exposing lysines sequestered in the ribosome exit tunnel. Thus, CAT-tails do not serve as a degron, but rather provide a fail-safe mechanism that expands the range of RQC-degradable substrates. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Bioorthogonal Metabolic Labeling of Nascent RNA in Neurons Improves the Sensitivity of Transcriptome-Wide Profiling.

PubMed

Zajaczkowski, Esmi L; Zhao, Qiong-Yi; Zhang, Zong Hong; Li, Xiang; Wei, Wei; Marshall, Paul R; Leighton, Laura J; Nainar, Sarah; Feng, Chao; Spitale, Robert C; Bredy, Timothy W

2018-06-15

Transcriptome-wide expression profiling of neurons has provided important insights into the underlying molecular mechanisms and gene expression patterns that transpire during learning and memory formation. However, there is a paucity of tools for profiling stimulus-induced RNA within specific neuronal cell populations. A bioorthogonal method to chemically label nascent (i.e., newly transcribed) RNA in a cell-type-specific and temporally controlled manner, which is also amenable to bioconjugation via click chemistry, was recently developed and optimized within conventional immortalized cell lines. However, its value within a more fragile and complicated cellular system such as neurons, as well as for transcriptome-wide expression profiling, has yet to be demonstrated. Here, we report the visualization and sequencing of activity-dependent nascent RNA derived from neurons using this labeling method. This work has important implications for improving transcriptome-wide expression profiling and visualization of nascent RNA in neurons, which has the potential to provide valuable insights into the mechanisms underlying neural plasticity, learning, and memory.

Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

PubMed Central

Menet, Jerome S; Rodriguez, Joseph; Abruzzi, Katharine C; Rosbash, Michael

2012-01-01

A substantial fraction of the metazoan transcriptome undergoes circadian oscillations in many cells and tissues. Based on the transcription feedback loops important for circadian timekeeping, it is commonly assumed that this mRNA cycling reflects widespread transcriptional regulation. To address this issue, we directly measured the circadian dynamics of mouse liver transcription using Nascent-Seq (genome-wide sequencing of nascent RNA). Although many genes are rhythmically transcribed, many rhythmic mRNAs manifest poor transcriptional rhythms, indicating a prominent contribution of post-transcriptional regulation to circadian mRNA expression. This analysis of rhythmic transcription also showed that the rhythmic DNA binding profile of the transcription factors CLOCK and BMAL1 does not determine the transcriptional phase of most target genes. This likely reflects gene-specific collaborations of CLK:BMAL1 with other transcription factors. These insights from Nascent-Seq indicate that it should have broad applicability to many other gene expression regulatory issues. DOI: http://dx.doi.org/10.7554/eLife.00011.001 PMID:23150795

Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains

PubMed Central

Shen, Peter S.; Park, Joseph; Qin, Yidan; Li, Xueming; Parsawar, Krishna; Larson, Matthew H.; Cox, James; Cheng, Yifan; Lambowitz, Alan M.; Weissman, Jonathan S.; Brandman, Onn; Frost, Adam

2015-01-01

In Eukarya, stalled translation induces 40S dissociation and recruitment of the Ribosome Quality control Complex (RQC) to the 60S subunit, which mediates nascent chain degradation. Here, we report cryoEM structures revealing that the RQC components Rqc2p (YPL009C/Tae2) and Ltn1p (YMR247C/Rkr1) bind to the 60S at sites exposed after 40S dissociation, placing the Ltn1p RING domain near the exit channel and Rqc2p over the P-site tRNA. We further demonstrate that Rqc2p recruits alanine and threonine charged tRNA to the A-site and directs elongation of nascent chains independently of mRNA or 40S subunits. Our work uncovers an unexpected mechanism of protein synthesis in which a protein—not an mRNA—determines tRNA recruitment and the tagging of nascent chains with Carboxy-terminal Ala and Thr extensions (“CAT tails”). PMID:25554787

Nonenzymatic Role for WRN in Preserving Nascent DNA Strands after Replication Stress

DOE PAGES

Su, Fengtao; Mukherjee, Shibani; Yang, Yanyong; ...

2014-11-20

WRN, the protein defective in Werner syndrome (WS), is a multifunctional nuclease involved in DNA damage repair, replication, and genome stability maintenance. It was assumed that the nuclease activities of WRN were critical for these functions. Here, we report a nonenzymatic role for WRN in preserving nascent DNA strands following replication stress. We found that lack of WRN led to shortening of nascent DNA strands after replication stress. Furthermore, we discovered that the exonuclease activity of MRE11 was responsible for the shortening of newly replicated DNA in the absence of WRN. Mechanistically, the N-terminal FHA domain of NBS1 recruits WRNmore » to replication-associated DNA double-stranded breaks to stabilize Rad51 and to limit the nuclease activity of its C-terminal binding partner MRE11. Thus, this previously unrecognized nonenzymatic function of WRN in the stabilization of nascent DNA strands sheds light on the molecular reason for the origin of genome instability in WS individuals.« less

Gene cloning and biochemical characterization of a catalase from Gluconobacter oxydans.

PubMed

Yamaguchi, Haruhiko; Sugiyama, Keigo; Hosoya, Miho; Takahashi, Seiji; Nakayama, Toru

2011-05-01

Gluconobacter oxydans has a large number of membrane-bound dehydrogenases linked to the respiratory chain that catalyze incomplete oxidation of a wide range of organic compounds by oxidative fermentation. Because the respiratory chain is a primary site of reactive oxygen species (ROS) production, the bacterium is expected to have a high capacity to detoxify nascent ROS. In the present study, a gene that encodes a catalase of G. oxydans, which might act as a potential scavenger of H(2)O(2), was cloned, and the expression product (termed rGoxCat) was characterized biochemically. rGoxCat is a heme b-containing tetrameric protein (molecular mass, 320 kDa) consisting of identical subunits. The recombinant enzyme displayed a strong catalase activity with a k(cat) of 6.28×10(4) s(-1) and a K(m) for H(2)O(2) of 61 mM; however, rGoxCat exhibited no peroxidase activity. These results, along with the phylogenetic position of the enzyme, provide conclusive evidence that rGoxCat is a monofunctional, large-subunit catalase. The enzyme was most stable in the pH range of 4-9, and greater than 60% of the original activity was retained after treatment at pH 3.0 and 40°C for 1h. Moreover, the enzyme exhibited excellent thermostability for a catalase from a mesophilic organism, retaining full activity after incubation for 30 min at 70°C. The observed catalytic properties of rGoxCat, as well as its stability in a slightly acidic environment, are consistent with its role in the elimination of nascent H(2)O(2) in a bacterium that produces a large amount of organic acid via oxidative fermentation. Copyright © 2010. Published by Elsevier B.V.

Septal membrane localization by C-terminal amphipathic α-helices of MinD in Bacillus subtilis mutant cells lacking MinJ or DivIVA.

PubMed

Ishikawa, Kazuki; Matsuoka, Satoshi; Hara, Hiroshi; Matsumoto, Kouji

2017-10-18

The Min system, which inhibits assembly of the cytokinetic protein FtsZ, is largely responsible for positioning the division site in rod-shaped bacteria. It has been reported that MinJ, which bridges DivIVA and MinD, is targeted to the cell poles by an interaction with DivIVA, and that MinJ in turn recruits MinCD to the cell poles. MinC, however, is located primarily at active division sites at mid-cell when expressed from its native promoter. Surprisingly, we found that Bacillus subtilis MinD is located at nascent septal membranes and at an asymmetric site on lateral membranes between nascent septal membranes in filamentous cells lacking MinJ or DivIVA. Bacillus subtilis MinD has two amphipathic α-helices rich in basic amino acid residues at its C-terminus; one of these, named MTS1 here, is the counterpart of the membrane targeting sequence (MTS) in Escherichia coli MinD while the other, named MTS-like sequence (MTSL), is the nearest helix to MTS1. These amphipathic helices were located independently at nascent septal membranes in cells lacking MinJ or DivIVA, whereas elimination of the helices from the wild type protein reduced its localization considerably. MinD variants with altered MTS1 and MTSL, in which basic amino acid residues were replaced with proline or acidic residues, were not located at nascent septal membranes, indicating that the binding to the nascent septal membranes requires basic residues and a helical structure. The septal localization of MTSL, but not of MTS1, was dependent on host cell MinD. These results suggest that MinD is targeted to nascent septal membranes via its C-terminal amphipathic α-helices in B. subtilis cells lacking MinJ or DivIVA. Moreover, the diffuse distribution of MinD lacking both MTSs suggests that only a small fraction of MinD depends on MinJ for its localization to nascent septal membranes.

Accelerators as Authentic Training Experiences for Nascent Entrepreneurs

ERIC Educational Resources Information Center

Miles, Morgan P.; de Vries, Huibert; Harrison, Geoff; Bliemel, Martin; de Klerk, Saskia; Kasouf, Chick J.

2017-01-01

Purpose: The purpose of this paper is to address the role of accelerators as authentic learning-based entrepreneurial training programs. Accelerators facilitate the development and assessment of entrepreneurial competencies in nascent entrepreneurs through the process of creating a start-up venture. Design/methodology/approach: Survey data from…

Rad51 recombinase prevents Mre11 nuclease-dependent degradation and excessive PrimPol-mediated elongation of nascent DNA after UV irradiation

PubMed Central

Vallerga, María Belén; Mansilla, Sabrina F.; Federico, María Belén; Bertolin, Agustina P.; Gottifredi, Vanesa

2015-01-01

After UV irradiation, DNA polymerases specialized in translesion DNA synthesis (TLS) aid DNA replication. However, it is unclear whether other mechanisms also facilitate the elongation of UV-damaged DNA. We wondered if Rad51 recombinase (Rad51), a factor that escorts replication forks, aids replication across UV lesions. We found that depletion of Rad51 impairs S-phase progression and increases cell death after UV irradiation. Interestingly, Rad51 and the TLS polymerase polη modulate the elongation of nascent DNA in different ways, suggesting that DNA elongation after UV irradiation does not exclusively rely on TLS events. In particular, Rad51 protects the DNA synthesized immediately before UV irradiation from degradation and avoids excessive elongation of nascent DNA after UV irradiation. In Rad51-depleted samples, the degradation of DNA was limited to the first minutes after UV irradiation and required the exonuclease activity of the double strand break repair nuclease (Mre11). The persistent dysregulation of nascent DNA elongation after Rad51 knockdown required Mre11, but not its exonuclease activity, and PrimPol, a DNA polymerase with primase activity. By showing a crucial contribution of Rad51 to the synthesis of nascent DNA, our results reveal an unanticipated complexity in the regulation of DNA elongation across UV-damaged templates. PMID:26627254

Engineering radical polymer electrodes for electrochemical energy storage

NASA Astrophysics Data System (ADS)

Nevers, Douglas R.; Brushett, Fikile R.; Wheeler, Dean R.

2017-06-01

In principle a wide range of organic materials can store energy in the form of reversible redox conversions of stable radicals. Such chemistry holds great promise for energy storage applications due to high theoretical capacities, high rate capabilities, intrinsic structural tunability, and the possibility of low-cost "green" syntheses from renewable sources. There have been steady improvements in the design of organic radical polymers, in which radicals are incorporated into the backbone and/or as pendant groups. This review highlights opportunities for improved redox molecule and polymer design along with the key challenges (e.g., transport phenomena, solubility, and reaction mechanisms) to transitioning known organic radicals into high-performance electrodes. Ultimately, organic-based batteries are still a nascent field with many open questions. Further advances in molecular design, electrode engineering, and device architecture will be required for these systems to reach their full potential and meet the diverse and increasing demands for energy storage.

Self-organization of muscle cell structure and function.

PubMed

Grosberg, Anna; Kuo, Po-Ling; Guo, Chin-Lin; Geisse, Nicholas A; Bray, Mark-Anthony; Adams, William J; Sheehy, Sean P; Parker, Kevin Kit

2011-02-01

The organization of muscle is the product of functional adaptation over several length scales spanning from the sarcomere to the muscle bundle. One possible strategy for solving this multiscale coupling problem is to physically constrain the muscle cells in microenvironments that potentiate the organization of their intracellular space. We hypothesized that boundary conditions in the extracellular space potentiate the organization of cytoskeletal scaffolds for directed sarcomeregenesis. We developed a quantitative model of how the cytoskeleton of neonatal rat ventricular myocytes organizes with respect to geometric cues in the extracellular matrix. Numerical results and in vitro assays to control myocyte shape indicated that distinct cytoskeletal architectures arise from two temporally-ordered, organizational processes: the interaction between actin fibers, premyofibrils and focal adhesions, as well as cooperative alignment and parallel bundling of nascent myofibrils. Our results suggest that a hierarchy of mechanisms regulate the self-organization of the contractile cytoskeleton and that a positive feedback loop is responsible for initiating the break in symmetry, potentiated by extracellular boundary conditions, is required to polarize the contractile cytoskeleton.

A Physically Based Framework for Modelling the Organic Fractionation of Sea Spray Aerosol from Bubble Film Langmuir Equilibria

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

Burrows, Susannah M.; Ogunro, O.; Frossard, Amanda

2014-12-19

The presence of a large fraction of organic matter in primary sea spray aerosol (SSA) can strongly affect its cloud condensation nuclei activity and interactions with marine clouds. Global climate models require new parameterizations of the SSA composition in order to improve the representation of these processes. Existing proposals for such a parameterization use remotely-sensed chlorophyll-a concentrations as a proxy for the biogenic contribution to the aerosol. However, both observations and theoretical considerations suggest that existing relationships with chlorophyll-a, derived from observations at only a few locations, may not be representative for all ocean regions. We introduce a novel frameworkmore » for parameterizing the fractionation of marine organic matter into SSA based on a competitive Langmuir adsorption equilibrium at bubble surfaces. Marine organic matter is partitioned into classes with differing molecular weights, surface excesses, and Langmuir adsorption parameters. The classes include a lipid-like mixture associated with labile dissolved organic carbon (DOC), a polysaccharide-like mixture associated primarily with semi-labile DOC, a protein-like mixture with concentrations intermediate between lipids and polysaccharides, a processed mixture associated with recalcitrant surface DOC, and a deep abyssal humic-like mixture. Box model calculations have been performed for several cases of organic adsorption to illustrate the underlying concepts. We then apply the framework to output from a global marine biogeochemistry model, by partitioning total dissolved organic carbon into several classes of macromolecule. Each class is represented by model compounds with physical and chemical properties based on existing laboratory data. This allows us to globally map the predicted organic mass fraction of the nascent submicron sea spray aerosol. Predicted relationships between chlorophyll-\\textit{a} and organic fraction are similar to existing empirical parameterizations, but can vary between biologically productive and non-productive regions, and seasonally within a given region. Major uncertainties include the bubble film thickness at bursting and the variability of organic surfactant activity in the ocean, which is poorly constrained. In addition, marine colloids and cooperative adsorption of polysaccharides may make important contributions to the aerosol, but are not included here. This organic fractionation framework is an initial step towards a closer linking of ocean biogeochemistry and aerosol chemical composition in Earth system models. Future work should focus on improving constraints on model parameters through new laboratory experiments or through empirical fitting to observed relationships in the real ocean and atmosphere, as well as on atmospheric implications of the variable composition of organic matter in sea spray.« less

Plant gravity sensing

NASA Technical Reports Server (NTRS)

Sack, F. D.

1991-01-01

This review of plant gravity sensing examines sensing in organ gravitropism, sensing in single-cell gravitropism, and nongravitropic sensing. Topics related to sensing in organ gravitropism are (1) identification of the gravitropic susceptors, including intracellular asymmetry in equilibrium position and after reorientation, susceptor signal-to-noise ratio, signal integration over threshold stimulation periods, intracellular asymmetry and gravitropic competence, and starch deficiency and gravitropic competence; (2) possible root statocytes and receptors, including identification of presumptive statocytes, cytology, and possible receptors and models of sensing; and (3) negatively gravitropic organs, including identification and distribution of presumptive statocytes and cytology and possible receptors. Topics related to nongravitropic sensing include gravitaxis, reaction wood, gravimorphogenesis, other gravity-influenced organ movements, and cytoplasmic streaming.

The Complex Dynamics of Student Engagement in Novel Engineering Design Activities

NASA Astrophysics Data System (ADS)

McCormick, Mary

In engineering design, making sense of "messy," design situations is at the heart of the discipline (Schon, 1983); engineers in practice bring structure to design situations by organizing, negotiating, and coordinating multiple aspects (Bucciarelli, 1994; Stevens, Johri, & O'Connor, 2014). In classroom settings, however, students are more often given well-defined, content-focused engineering tasks (Jonassen, 2014). These tasks are based on the assumption that elementary students are unable to grapple with the complexity or open-endedness of engineering design (Crismond & Adams, 2012). The data I present in this dissertation suggest the opposite. I show that students are not only able to make sense of, or frame (Goffman, 1974), complex design situations, but that their framings dynamically involve their nascent abilities for engineering design. The context of this work is Novel Engineering, a larger research project that explores using children's literature as an access point for engineering design. Novel Engineering activities are inherently messy: there are characters with needs, settings with implicit constraints, and rich design situations. In a series of three studies, I show how students' framings of Novel Engineering design activities involve their reasoning and acting as beginning engineers. In the first study, I show two students whose caring for the story characters contributes to their stability in framing the task: they identify the needs of their fictional clients and iteratively design a solution to meet their clients' needs. In the second, I show how students' shifting and negotiating framings influence their engineering assumptions and evaluation criteria. In the third, I show how students' coordinating framings involve navigating a design process to meet clients' needs, classroom expectations, and technical requirements. Collectively, these studies contribute to literature by documenting students' productive beginnings in engineering design. The implications span research and practice, specifically targeting how we attend to and support students as they engage in engineering design.

Self-Organization and Forces in the Mitotic Spindle.

PubMed

Pavin, Nenad; Tolić, Iva M

2016-07-05

At the onset of division, the cell forms a spindle, a precise self-constructed micromachine composed of microtubules and the associated proteins, which divides the chromosomes between the two nascent daughter cells. The spindle arises from self-organization of microtubules and chromosomes, whose different types of motion help them explore the space and eventually approach and interact with each other. Once the interactions between the chromosomes and the microtubules have been established, the chromosomes are moved to the equatorial plane of the spindle and ultimately toward the opposite spindle poles. These transport processes rely on directed forces that are precisely regulated in space and time. In this review, we discuss how microtubule dynamics and their rotational movement drive spindle self-organization, as well as how the forces acting in the spindle are generated, balanced, and regulated.

Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013

PubMed Central

2014-01-01

A conference entitled ‘Human microbiome science: Vision for the future’ was organized in Bethesda, MD from July 24 to 26, 2013. The event brought together experts in the field of human microbiome research and aimed at providing a comprehensive overview of the state of microbiome research, but more importantly to identify and discuss gaps, challenges and opportunities in this nascent field. This report summarizes the presentations but also describes what is needed for human microbiome research to move forward and deliver medical translational applications.

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

Fredrickson, James K.

In synthetic ecology, a nascent offshoot of synthetic biology, scientists aim to design and construct microbial communities with desirable properties. Such mixed populations of microorganisms can simultaneously perform otherwise incompatible functions. Compared with individual organisms, they can also better resist losses in function as a result of environmental perturbation or invasion by other species. Synthetic ecology may thus be a promising approach for developing robust, stable biotechnological processes, such as the conversion of cellulosic biomass to biofuels. However, achieving this will require detailed knowledge of the principles that guide the structure and function of microbial communities.

Cloning of nascent monkey DNA synthesized early in the cell cycle.

PubMed

Kaufmann, G; Zannis-Hadjopoulos, M; Martin, R G

1985-04-01

To study the structure and complexity of animal cell replication origins, we have isolated and cloned nascent DNA from the onset of S phase as follows: African green monkey kidney cells arrested in G1 phase were serum stimulated in the presence of the DNA replication inhibitor aphidicolin. After 18 h, the drug was removed, and DNA synthesis was allowed to proceed in vivo for 1 min. Nuclei were then prepared, and DNA synthesis was briefly continued in the presence of Hg-dCTP. The mercury-labeled nascent DNA was purified in double-stranded form by extrusion (M. Zannis-Hadjopoulos, M. Perisco, and R. G. Martin, Cell 27:155-163, 1981) followed by sulfhydryl-agarose affinity chromatography. Purified nascent DNA (ca. 500 to 2,000 base pairs) was treated with mung bean nuclease to remove single-stranded ends and inserted into the NruI site of plasmid pBR322. The cloned fragments were examined for their time of replication by hybridization to cellular DNA fractions synthesized at various intervals of the S phase. Among five clones examined, four hybridized preferentially with early replicating fractions.

Pervasive Targeting of Nascent Transcripts by Hfq.

PubMed

Kambara, Tracy K; Ramsey, Kathryn M; Dove, Simon L

2018-05-01

Hfq is an RNA chaperone and an important post-transcriptional regulator in bacteria. Using chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq), we show that Hfq associates with hundreds of different regions of the Pseudomonas aeruginosa chromosome. These associations are abolished when transcription is inhibited, indicating that they reflect Hfq binding to transcripts during their synthesis. Analogous ChIP-seq analyses with the post-transcriptional regulator Crc reveal that it associates with many of the same nascent transcripts as Hfq, an activity we show is Hfq dependent. Our findings indicate that Hfq binds many transcripts co-transcriptionally in P. aeruginosa, often in concert with Crc, and uncover direct regulatory targets of these proteins. They also highlight a general approach for studying the interactions of RNA-binding proteins with nascent transcripts in bacteria. The binding of post-transcriptional regulators to nascent mRNAs may represent a prevalent means of controlling translation in bacteria where transcription and translation are coupled. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Binding of Signal Recognition Particle Gives Ribosome/Nascent Chain Complexes a Competitive Advantage in Endoplasmic Reticulum Membrane Interaction

PubMed Central

Neuhof, Andrea; Rolls, Melissa M.; Jungnickel, Berit; Kalies, Kai-Uwe; Rapoport, Tom A.

1998-01-01

Most secretory and membrane proteins are sorted by signal sequences to the endoplasmic reticulum (ER) membrane early during their synthesis. Targeting of the ribosome-nascent chain complex (RNC) involves the binding of the signal sequence to the signal recognition particle (SRP), followed by an interaction of ribosome-bound SRP with the SRP receptor. However, ribosomes can also independently bind to the ER translocation channel formed by the Sec61p complex. To explain the specificity of membrane targeting, it has therefore been proposed that nascent polypeptide-associated complex functions as a cytosolic inhibitor of signal sequence- and SRP-independent ribosome binding to the ER membrane. We report here that SRP-independent binding of RNCs to the ER membrane can occur in the presence of all cytosolic factors, including nascent polypeptide-associated complex. Nontranslating ribosomes competitively inhibit SRP-independent membrane binding of RNCs but have no effect when SRP is bound to the RNCs. The protective effect of SRP against ribosome competition depends on a functional signal sequence in the nascent chain and is also observed with reconstituted proteoliposomes containing only the Sec61p complex and the SRP receptor. We conclude that cytosolic factors do not prevent the membrane binding of ribosomes. Instead, specific ribosome targeting to the Sec61p complex is provided by the binding of SRP to RNCs, followed by an interaction with the SRP receptor, which gives RNC–SRP complexes a selective advantage in membrane targeting over nontranslating ribosomes. PMID:9436994

Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis.

PubMed

Fritch, Benjamin; Kosolapov, Andrey; Hudson, Phillip; Nissley, Daniel A; Woodcock, H Lee; Deutsch, Carol; O'Brien, Edward P

2018-04-18

Mechanical forces acting on the ribosome can alter the speed of protein synthesis, indicating that mechanochemistry can contribute to translation control of gene expression. The naturally occurring sources of these mechanical forces, the mechanism by which they are transmitted 10 nm to the ribosome's catalytic core, and how they influence peptide bond formation rates are largely unknown. Here, we identify a new source of mechanical force acting on the ribosome by using in situ experimental measurements of changes in nascent-chain extension in the exit tunnel in conjunction with all-atom and coarse-grained computer simulations. We demonstrate that when the number of residues composing a nascent chain increases, its unstructured segments outside the ribosome exit tunnel generate piconewtons of force that are fully transmitted to the ribosome's P-site. The route of force transmission is shown to be through the nascent polypetide's backbone, not through the wall of the ribosome's exit tunnel. Utilizing quantum mechanical calculations we find that a consequence of such a pulling force is to decrease the transition state free energy barrier to peptide bond formation, indicating that the elongation of a nascent chain can accelerate translation. Since nascent protein segments can start out as largely unfolded structural ensembles, these results suggest a pulling force is present during protein synthesis that can modulate translation speed. The mechanism of force transmission we have identified and its consequences for peptide bond formation should be relevant regardless of the source of the pulling force.

Live Cell Imaging of the Nascent Inactive X Chromosome during the Early Differentiation Process of Naive ES Cells towards Epiblast Stem Cells

PubMed Central

Guyochin, Aurélia; Maenner, Sylvain; Chu, Erin Tsi-Jia; Hentati, Asma; Attia, Mikael; Avner, Philip; Clerc, Philippe

2014-01-01

Random X-chromosome inactivation ensures dosage compensation in mammals through the transcriptional silencing of one of the two X chromosomes present in each female cell. Silencing is initiated in the differentiating epiblast of the mouse female embryos through coating of the nascent inactive X chromosome by the non-coding RNA Xist, which subsequently recruits the Polycomb Complex PRC2 leading to histone H3-K27 methylation. Here we examined in mouse ES cells the early steps of the transition from naive ES cells towards epiblast stem cells as a model for inducing X chromosome inactivation in vitro. We show that these conditions efficiently induce random XCI. Importantly, in a transient phase of this differentiation pathway, both X chromosomes are coated with Xist RNA in up to 15% of the XX cells. In an attempt to determine the dynamics of this process, we designed a strategy aimed at visualizing the nascent inactive X-chromosome in live cells. We generated transgenic female XX ES cells expressing the PRC2 component Ezh2 fused to the fluorescent protein Venus. The fluorescent fusion protein was expressed at sub-physiological levels and located in nuclei of ES cells. Upon differentiation of ES cell towards epiblast stem cell fate, Venus-fluorescent territories appearing in interphase nuclei were identified as nascent inactive X chromosomes by their association with Xist RNA. Imaging of Ezh2-Venus for up to 24 hours during the differentiation process showed survival of some cells with two fluorescent domains and a surprising dynamics of the fluorescent territories across cell division and in the course of the differentiation process. Our data reveal a strategy for visualizing the nascent inactive X chromosome and suggests the possibility for a large plasticity of the nascent inactive X chromosome. PMID:25546018

A novel compound inhibits rHDL assembly and blocks nascent HDL biogenesis downstream of apoAI binding to ABCA1 expressing cells

PubMed Central

Lyssenko, Nicholas N.; Brubaker, Gregory; Smith, Bradley D.; Smith, Jonathan D.

2011-01-01

Objective Nascent high-density lipoprotein (HDL) particles form from cellular lipids and extracellular lipid-free apolipoprotein AI (apoAI) in a process mediated by ATP-binding cassette transporter A1 (ABCA1). We have sought out compounds that inhibit nascent HDL biogenesis without affecting ABCA1 activity. Methods and Results Reconstituted HDL (rHDL) formation and cellular cholesterol efflux assays were used to show that two compounds that bond via hydrogen with phospholipids inhibit rHDL and nascent HDL production. In rHDL formation assays, the inhibitory effect of compound 1 (methyl 3α-acetoxy-7α,12α-di[(phenylaminocarbonyl)amino]-5β-cholan-24-oate), the more active of the two, depended on its ability to associate with phospholipids. In cell assays, compound 1 suppressed ABCA1-mediated cholesterol efflux to apoAI, the 18A peptide, and taurocholate with high specificity, without affecting ABCA1-independent cellular cholesterol efflux to HDL and endocytosis of acetylated low-density lipoprotein (AcLDL) and transferrin. Furthermore, compound 1 did not affect ABCA1 activity adversely, as ABCA1-mediated shedding of microparticles proceeded unabated and apoAI binding to ABCA1-expressing cells increased in its presence. Conclusions The inhibitory effects of compound 1 support a three-step model of nascent HDL biogenesis: plasma membrane remodeling by ABCA1, apoAI binding to ABCA1, and lipoprotein particle assembly. The compound inhibits the final step, causing accumulation of apoAI in ABCA1-expressing cells. PMID:21836073

Does Ethicality Wane with Adulthood? A Study of the Ethical Values of Entrepreneurship Students and Nascent Entrepreneurs

ERIC Educational Resources Information Center

Lourenço, Fernando; Sappleton, Natalie; Cheng, Ranis

2015-01-01

The authors examined the following questions: Does gender influence the ethicality of enterprise students to a greater extent than it does nascent entrepreneurs? If this is the case, then is it due to factors associated with adulthood such as age, work experience, marital status, and parental status? Sex-role socialization theory and moral…

A Primer on the Pathway to Scholarly Writing: Helping Nascent Writers to Unlearn Conditioned Habits

ERIC Educational Resources Information Center

McDougall, Dennis; Ornelles, Cecily; Rao, Kavita

2015-01-01

In this article, we identify eight common error patterns of nascent writers when they attempt to navigate the pathway to scholarly writing. We illustrate each error pattern via examples and counter-examples (corrections). We also describe how to identify such patterns, why those patterns might occur and persist, and why each pattern is…

Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila

PubMed Central

Hur, Junho K.; Luo, Yicheng; Moon, Sungjin; Ninova, Maria; Marinov, Georgi K.; Chung, Yun D.; Aravin, Alexei A.

2016-01-01

The conserved THO/TREX (transcription/export) complex is critical for pre-mRNA processing and mRNA nuclear export. In metazoa, TREX is loaded on nascent RNA transcribed by RNA polymerase II in a splicing-dependent fashion; however, how TREX functions is poorly understood. Here we show that Thoc5 and other TREX components are essential for the biogenesis of piRNA, a distinct class of small noncoding RNAs that control expression of transposable elements (TEs) in the Drosophila germline. Mutations in TREX lead to defects in piRNA biogenesis, resulting in derepression of multiple TE families, gametogenesis defects, and sterility. TREX components are enriched on piRNA precursors transcribed from dual-strand piRNA clusters and colocalize in distinct nuclear foci that overlap with sites of piRNA transcription. The localization of TREX in nuclear foci and its loading on piRNA precursor transcripts depend on Cutoff, a protein associated with chromatin of piRNA clusters. Finally, we show that TREX is required for accumulation of nascent piRNA precursors. Our study reveals a novel splicing-independent mechanism for TREX loading on nascent RNA and its importance in piRNA biogenesis. PMID:27036967

Elastic Coupling of Nascent apCAM Adhesions to Flowing Actin Networks

PubMed Central

Mejean, Cecile O.; Schaefer, Andrew W.; Buck, Kenneth B.; Kress, Holger; Shundrovsky, Alla; Merrill, Jason W.; Dufresne, Eric R.; Forscher, Paul

2013-01-01

Adhesions are multi-molecular complexes that transmit forces generated by a cell’s acto-myosin networks to external substrates. While the physical properties of some of the individual components of adhesions have been carefully characterized, the mechanics of the coupling between the cytoskeleton and the adhesion site as a whole are just beginning to be revealed. We characterized the mechanics of nascent adhesions mediated by the immunoglobulin-family cell adhesion molecule apCAM, which is known to interact with actin filaments. Using simultaneous visualization of actin flow and quantification of forces transmitted to apCAM-coated beads restrained with an optical trap, we found that adhesions are dynamic structures capable of transmitting a wide range of forces. For forces in the picoNewton scale, the nascent adhesions’ mechanical properties are dominated by an elastic structure which can be reversibly deformed by up to 1 µm. Large reversible deformations rule out an interface between substrate and cytoskeleton that is dominated by a number of stiff molecular springs in parallel, and favor a compliant cross-linked network. Such a compliant structure may increase the lifetime of a nascent adhesion, facilitating signaling and reinforcement. PMID:24039928

Programmable autonomous synthesis of single-stranded DNA

NASA Astrophysics Data System (ADS)

Kishi, Jocelyn Y.; Schaus, Thomas E.; Gopalkrishnan, Nikhil; Xuan, Feng; Yin, Peng

2018-02-01

DNA performs diverse functional roles in biology, nanotechnology and biotechnology, but current methods for autonomously synthesizing arbitrary single-stranded DNA are limited. Here, we introduce the concept of primer exchange reaction (PER) cascades, which grow nascent single-stranded DNA with user-specified sequences following prescribed reaction pathways. PER synthesis happens in a programmable, autonomous, in situ and environmentally responsive fashion, providing a platform for engineering molecular circuits and devices with a wide range of sensing, monitoring, recording, signal-processing and actuation capabilities. We experimentally demonstrate a nanodevice that transduces the detection of a trigger RNA into the production of a DNAzyme that degrades an independent RNA substrate, a signal amplifier that conditionally synthesizes long fluorescent strands only in the presence of a particular RNA signal, molecular computing circuits that evaluate logic (AND, OR, NOT) combinations of RNA inputs, and a temporal molecular event recorder that records in the PER transcript the order in which distinct RNA inputs are sequentially detected.

Programmable autonomous synthesis of single-stranded DNA.

PubMed

Kishi, Jocelyn Y; Schaus, Thomas E; Gopalkrishnan, Nikhil; Xuan, Feng; Yin, Peng

2018-02-01

DNA performs diverse functional roles in biology, nanotechnology and biotechnology, but current methods for autonomously synthesizing arbitrary single-stranded DNA are limited. Here, we introduce the concept of primer exchange reaction (PER) cascades, which grow nascent single-stranded DNA with user-specified sequences following prescribed reaction pathways. PER synthesis happens in a programmable, autonomous, in situ and environmentally responsive fashion, providing a platform for engineering molecular circuits and devices with a wide range of sensing, monitoring, recording, signal-processing and actuation capabilities. We experimentally demonstrate a nanodevice that transduces the detection of a trigger RNA into the production of a DNAzyme that degrades an independent RNA substrate, a signal amplifier that conditionally synthesizes long fluorescent strands only in the presence of a particular RNA signal, molecular computing circuits that evaluate logic (AND, OR, NOT) combinations of RNA inputs, and a temporal molecular event recorder that records in the PER transcript the order in which distinct RNA inputs are sequentially detected.

25th Anniversary Article: Ordered Polymer Structures for the Engineering of Photons and Phonons

PubMed Central

Lee, Jae-Hwang; Koh, Cheong Yang; Singer, Jonathan P; Jeon, Seog-Jin; Maldovan, Martin; Stein, Ori; Thomas, Edwin L

2014-01-01

The engineering of optical and acoustic material functionalities via construction of ordered local and global architectures on various length scales commensurate with and well below the characteristic length scales of photons and phonons in the material is an indispensable and powerful means to develop novel materials. In the current mature status of photonics, polymers hold a pivotal role in various application areas such as light-emission, sensing, energy, and displays, with exclusive advantages despite their relatively low dielectric constants. Moreover, in the nascent field of phononics, polymers are expected to be a superior material platform due to the ability for readily fabricated complex polymer structures possessing a wide range of mechanical behaviors, complete phononic bandgaps, and resonant architectures. In this review, polymer-centric photonic and phononic crystals and metamaterials are highlighted, and basic concepts, fabrication techniques, selected functional polymers, applications, and emerging ideas are introduced. PMID:24338738

Structural insights into the rhabdovirus transcription/replication complex.

PubMed

Ivanov, Ivan; Yabukarski, Filip; Ruigrok, Rob W H; Jamin, Marc

2011-12-01

The rhabdoviruses have a non-segmented single stranded negative-sense RNA genome. Their multiplication in a host cell requires three viral proteins in addition to the viral RNA genome. The nucleoprotein (N) tightly encapsidates the viral RNA, and the N-RNA complex serves as the template for both transcription and replication. The viral RNA-dependent RNA polymerase is a two subunit complex that consists of a large subunit, L, and a non-catalytic cofactor, the phosphoprotein, P. P also acts as a chaperone of nascent RNA-free N by forming a N(0)-P complex that prevents N from binding to cellular RNAs and from polymerizing in the absence of RNA. Here, we discuss the recent molecular and structural studies of individual components and multi-molecular complexes that are involved in the transcription/replication complex of these viruses with regard to their implication in viral transcription and replication. Copyright © 2011 Elsevier B.V. All rights reserved.

Global effects of the CSR-1 RNA interference pathway on the transcriptional landscape.

PubMed

Cecere, Germano; Hoersch, Sebastian; O'Keeffe, Sean; Sachidanandam, Ravi; Grishok, Alla

2014-04-01

Argonaute proteins and their small RNA cofactors short interfering RNAs are known to inhibit gene expression at the transcriptional and post-transcriptional levels. In Caenorhabditis elegans, the Argonaute CSR-1 binds thousands of endogenous siRNAs (endo-siRNAs) that are antisense to germline transcripts. However, its role in gene expression regulation remains controversial. Here we used genome-wide profiling of nascent RNA transcripts and found that the CSR-1 RNA interference pathway promoted sense-oriented RNA polymerase II transcription. Moreover, a loss of CSR-1 function resulted in global increase in antisense transcription and ectopic transcription of silent chromatin domains, which led to reduced chromatin incorporation of centromere-specific histone H3. On the basis of these findings, we propose that the CSR-1 pathway helps maintain the directionality of active transcription, thereby propagating the distinction between transcriptionally active and silent genomic regions.

Trends in communicative access solutions for children with cerebral palsy.

PubMed

Myrden, Andrew; Schudlo, Larissa; Weyand, Sabine; Zeyl, Timothy; Chau, Tom

2014-08-01

Access solutions may facilitate communication in children with limited functional speech and motor control. This study reviews current trends in access solution development for children with cerebral palsy, with particular emphasis on the access technology that harnesses a control signal from the user (eg, movement or physiological change) and the output device (eg, augmentative and alternative communication system) whose behavior is modulated by the user's control signal. Access technologies have advanced from simple mechanical switches to machine vision (eg, eye-gaze trackers), inertial sensing, and emerging physiological interfaces that require minimal physical effort. Similarly, output devices have evolved from bulky, dedicated hardware with limited configurability, to platform-agnostic, highly personalized mobile applications. Emerging case studies encourage the consideration of access technology for all nonverbal children with cerebral palsy with at least nascent contingency awareness. However, establishing robust evidence of the effectiveness of the aforementioned advances will require more expansive studies. © The Author(s) 2014.

The Battle of RNA Synthesis: Virus versus Host.

PubMed

Harwig, Alex; Landick, Robert; Berkhout, Ben

2017-10-21

Transcription control is the foundation of gene regulation. Whereas a cell is fully equipped for this task, viruses often depend on the host to supply tools for their transcription program. Over the course of evolution and adaptation, viruses have found diverse ways to optimally exploit cellular host processes such as transcription to their own benefit. Just as cells are increasingly understood to employ nascent RNAs in transcription regulation, recent discoveries are revealing how viruses use nascent RNAs to benefit their own gene expression. In this review, we first outline the two different transcription programs used by viruses, i.e., transcription (DNA-dependent) and RNA-dependent RNA synthesis. Subsequently, we use the distinct stages (initiation, elongation, termination) to describe the latest insights into nascent RNA-mediated regulation in the context of each relevant stage.

Structure of nascent replicative form DNA of coliphage M13

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

Dasgupta, S.; Mitra, S.

Nascent replicative form type II (RFII) DNA of coliphage M13 synthesized in an Escherichia coli mutant deficient in the 5' ..-->.. 3' exonuclease associated with DNA polymerase I contains ribonucleotides that are retained in the covalently closed RFI DNA sealed in vitro by the joint action of T5 phage DNA polymerase and T4 phage DNA ligase. These RFI molecules are labile to alkali and RNase H, unlike the RFI produced either in vivo or from RFII with E. coli DNA polymerase I and E. coli DNA ligase. The ribonucleotides are located at one site and predominantly in one strand ofmore » the nascent RF DNA. Furthermore, these molecules contain multiple small gaps, randomly located, and one large gap in the intracistronic region.« less

Roles of the International Council for Laboratory Animal Science (ICLAS) and International Association of Colleges of Laboratory Animal Medicine (IACLAM) in the Global Organization and Support of 3Rs Advances in Laboratory Animal Science

PubMed Central

Turner, Patricia V; Pekow, Cynthia; Clark, Judy MacArthur; Vergara, Patri; Bayne, Kathryn; White, William J; Kurosawa, Tsutomu Miki; Seok, Seung-Hyeok; Baneux, Philippe

2015-01-01

Practical implementation of the 3Rs at national and regional levels around the world requires long-term commitment, backing, and coordinated efforts by international associations for laboratory animal medicine and science, including the International Association of Colleges of Laboratory Animal Medicine (IACLAM) and the International Council for Laboratory Animal Science (ICLAS). Together these organizations support the efforts of regional organization and communities of laboratory animal science professionals as well as the development of local associations and professional colleges that promote the training and continuing education of research facility personnel and veterinary specialists. The recent formation of a World Organization for Animal Health (OIE) Collaborating Center for Laboratory Animal Science and Welfare emphasizes the need for research into initiatives promoting laboratory animal welfare, particularly in emerging economies and regions with nascent associations of laboratory animal science. PMID:25836964

Roles of the International Council for Laboratory Animal Science (ICLAS) and International Association of Colleges of Laboratory Animal Medicine (IACLAM) in the Global Organization and Support of 3Rs Advances in Laboratory Animal Science.

PubMed

Turner, Patricia V; Pekow, Cynthia; Clark, Judy MacArthur; Vergara, Patri; Bayne, Kathryn; White, William J; Kurosawa, Tsutomu Miki; Seok, Seung-Hyeok; Baneux, Philippe

2015-03-01

Practical implementation of the 3Rs at national and regional levels around the world requires long-term commitment, backing, and coordinated efforts by international associations for laboratory animal medicine and science, including the International Association of Colleges of Laboratory Animal Medicine (IACLAM) and the International Council for Laboratory Animal Science (ICLAS). Together these organizations support the efforts of regional organization and communities of laboratory animal science professionals as well as the development of local associations and professional colleges that promote the training and continuing education of research facility personnel and veterinary specialists. The recent formation of a World Organization for Animal Health (OIE) Collaborating Center for Laboratory Animal Science and Welfare emphasizes the need for research into initiatives promoting laboratory animal welfare, particularly in emerging economies and regions with nascent associations of laboratory animal science.

The Endoplasmic Reticulum-Associated Degradation Pathways of Budding Yeast

PubMed Central

Thibault, Guillaume; Ng, Davis T.W.

2012-01-01

Protein misfolding is a common cellular event that can produce intrinsically harmful products. To reduce the risk, quality control mechanisms are deployed to detect and eliminate misfolded, aggregated, and unassembled proteins. In the secretory pathway, it is mainly the endoplasmic reticulum-associated degradation (ERAD) pathways that perform this role. Here, specialized factors are organized to monitor and process the folded states of nascent polypeptides. Despite the complex structures, topologies, and posttranslational modifications of client molecules, the ER mechanisms are the best understood among all protein quality-control systems. This is the result of convergent and sometimes serendipitous discoveries by researchers from diverse fields. Although major advances in ER quality control and ERAD came from all model organisms, this review will focus on the discoveries culminating from the simple budding yeast. PMID:23209158

Nascent chain-monitored remodeling of the Sec machinery for salinity adaptation of marine bacteria

PubMed Central

Ishii, Eiji; Chiba, Shinobu; Hashimoto, Narimasa; Kojima, Seiji; Homma, Michio; Ito, Koreaki; Akiyama, Yoshinori; Mori, Hiroyuki

2015-01-01

SecDF interacts with the SecYEG translocon in bacteria and enhances protein export in a proton-motive-force-dependent manner. Vibrio alginolyticus, a marine-estuarine bacterium, contains two SecDF paralogs, V.SecDF1 and V.SecDF2. Here, we show that the export-enhancing function of V.SecDF1 requires Na+ instead of H+, whereas V.SecDF2 is Na+-independent, presumably requiring H+. In accord with the cation-preference difference, V.SecDF2 was only expressed under limited Na+ concentrations whereas V.SecDF1 was constitutive. However, it is not the decreased concentration of Na+ per se that the bacterium senses to up-regulate the V.SecDF2 expression, because marked up-regulation of the V.SecDF2 synthesis was observed irrespective of Na+ concentrations under certain genetic/physiological conditions: (i) when the secDF1VA gene was deleted and (ii) whenever the Sec export machinery was inhibited. VemP (Vibrio export monitoring polypeptide), a secretory polypeptide encoded by the upstream ORF of secDF2VA, plays the primary role in this regulation by undergoing regulated translational elongation arrest, which leads to unfolding of the Shine–Dalgarno sequence for translation of secDF2VA. Genetic analysis of V. alginolyticus established that the VemP-mediated regulation of SecDF2 is essential for the survival of this marine bacterium in low-salinity environments. These results reveal that a class of marine bacteria exploits nascent-chain ribosome interactions to optimize their protein export pathways to propagate efficiently under different ionic environments that they face in their life cycles. PMID:26392525

Role of DNA polymerase I-associated 5'-exonuclease in replication of coliphage M13 replicative-form DNA

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

Dasgupta, S.; Mitra, S.

The conversion of both parental- and progeny-nascent open circular M13 RF DNA into covalently closed RF I is drastically reduced in an E. coli mutant deficient in the 5' ..-->.. 3' exonuclease associated with DNA polymerase I. The nascent progeny RF DNA also contains a significant proportion of fragments of smaller than unit length.

Modulation of in vitro transformation and the early and late modes of DNA replication of uv-irradiation Syrian hamster cells by caffeine

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

Doniger, J.; DiPaolo, J.A.

1981-09-01

The effect of caffeine on post-uv DNA replication was studied to determine its relevance to carcinogenesis. The level of uv-induced transformed colonies of Syrian hamster embryo cells (HEC) was increased up to fivefold when caffeine was added to cells between 0 and 6 h post-uv. The greatest increase was observed when the interval between uv irradiation and caffeine addition was 4 h. Two modes of DNA replication occurred after uv irradiation. During the early mode (0 to 3 h post-uv) the size of nascent strands, as measured by alkaline sucrose sedimentation, was smaller than those in nonirradiated cells, whereas duringmore » the late mode they recovered to normal size. Caffeine inhibited the rate of elongation of nascent strands during the early mode. When caffeine was added immediately after uv irradiation, the conversion of the early mode to the late mode was inhibited. Studies on the effects of caffeine have now been extended to the late mode. While caffeine has little effect with the fd elements beginning from the 10th day after irradiation is connected with their proliferation but not with the migration out from lymphoid organs.« less

A Possible Role of the Full-Length Nascent Protein in Post-Translational Ribosome Recycling.

PubMed

Das, Debasis; Samanta, Dibyendu; Bhattacharya, Arpita; Basu, Arunima; Das, Anindita; Ghosh, Jaydip; Chakrabarti, Abhijit; Das Gupta, Chanchal

2017-01-01

Each cycle of translation initiation in bacterial cell requires free 50S and 30S ribosomal subunits originating from the post-translational dissociation of 70S ribosome from the previous cycle. Literature shows stable dissociation of 70S from model post-termination complexes by the concerted action of Ribosome Recycling Factor (RRF) and Elongation Factor G (EF-G) that interact with the rRNA bridge B2a/B2b joining 50S to 30S. In such experimental models, the role of full-length nascent protein was never considered seriously. We observed relatively slow release of full-length nascent protein from 50Sof post translation ribosome, and in that process, its toe prints on the rRNA in vivo and in in vitro translation with E.coli S30 extract. We reported earlier that a number of chemically unfolded proteins like bovine carbonic anhydrase (BCA), lactate dehydrogenase (LDH), malate dehydrogenase (MDH), lysozyme, ovalbumin etc., when added to free 70Sin lieu of the full length nascent proteins, also interact with identical RNA regions of the 23S rRNA. Interestingly the rRNA nucleotides that slow down release of the C-terminus of full-length unfolded protein were found in close proximity to the B2a/B2b bridge. It indicated a potentially important chemical reaction conserved throughout the evolution. Here we set out to probe that conserved role of unfolded protein conformation in splitting the free or post-termination 70S. How both the RRF-EFG dependent and the plausible nascent protein-EFG dependent ribosome recycling pathways might be relevant in bacteria is discussed here.

A Possible Role of the Full-Length Nascent Protein in Post-Translational Ribosome Recycling

PubMed Central

Das, Debasis; Samanta, Dibyendu; Bhattacharya, Arpita; Basu, Arunima; Das, Anindita; Ghosh, Jaydip; Chakrabarti, Abhijit; Das Gupta, Chanchal

2017-01-01

Each cycle of translation initiation in bacterial cell requires free 50S and 30S ribosomal subunits originating from the post-translational dissociation of 70S ribosome from the previous cycle. Literature shows stable dissociation of 70S from model post-termination complexes by the concerted action of Ribosome Recycling Factor (RRF) and Elongation Factor G (EF-G) that interact with the rRNA bridge B2a/B2b joining 50S to 30S. In such experimental models, the role of full-length nascent protein was never considered seriously. We observed relatively slow release of full-length nascent protein from 50Sof post translation ribosome, and in that process, its toe prints on the rRNA in vivo and in in vitro translation with E.coli S30 extract. We reported earlier that a number of chemically unfolded proteins like bovine carbonic anhydrase (BCA), lactate dehydrogenase (LDH), malate dehydrogenase (MDH), lysozyme, ovalbumin etc., when added to free 70Sin lieu of the full length nascent proteins, also interact with identical RNA regions of the 23S rRNA. Interestingly the rRNA nucleotides that slow down release of the C-terminus of full-length unfolded protein were found in close proximity to the B2a/B2b bridge. It indicated a potentially important chemical reaction conserved throughout the evolution. Here we set out to probe that conserved role of unfolded protein conformation in splitting the free or post-termination 70S. How both the RRF-EFG dependent and the plausible nascent protein–EFG dependent ribosome recycling pathways might be relevant in bacteria is discussed here. PMID:28099529

Long-read sequencing of nascent RNA reveals coupling among RNA processing events.

PubMed

Herzel, Lydia; Straube, Korinna; Neugebauer, Karla M

2018-06-14

Pre-mRNA splicing is accomplished by the spliceosome, a megadalton complex that assembles de novo on each intron. Because spliceosome assembly and catalysis occur cotranscriptionally, we hypothesized that introns are removed in the order of their transcription in genomes dominated by constitutive splicing. Remarkably little is known about splicing order and the regulatory potential of nascent transcript remodeling by splicing, due to the limitations of existing methods that focus on analysis of mature splicing products (mRNAs) rather than substrates and intermediates. Here, we overcome this obstacle through long-read RNA sequencing of nascent, multi-intron transcripts in the fission yeast Schizosaccharomyces pombe Most multi-intron transcripts were fully spliced, consistent with rapid cotranscriptional splicing. However, an unexpectedly high proportion of transcripts were either fully spliced or fully unspliced, suggesting that splicing of any given intron is dependent on the splicing status of other introns in the transcript. Supporting this, mild inhibition of splicing by a temperature-sensitive mutation in prp2 , the homolog of vertebrate U2AF65, increased the frequency of fully unspliced transcripts. Importantly, fully unspliced transcripts displayed transcriptional read-through at the polyA site and were degraded cotranscriptionally by the nuclear exosome. Finally, we show that cellular mRNA levels were reduced in genes with a high number of unspliced nascent transcripts during caffeine treatment, showing regulatory significance of cotranscriptional splicing. Therefore, overall splicing of individual nascent transcripts, 3' end formation, and mRNA half-life depend on the splicing status of neighboring introns, suggesting crosstalk among spliceosomes and the polyA cleavage machinery during transcription elongation. © 2018 Herzel et al.; Published by Cold Spring Harbor Laboratory Press.

Oligosaccharyltransferase directly binds to ribosome at a location near the translocon-binding site

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

Harada, Y.; Li, H.; Li, Hua

2009-04-28

Oligosaccharyltransferase (OT) transfers high mannose-type glycans to the nascent polypeptides that are translated by the membrane-bound ribosome and translocated into the lumen of the endoplasmic reticulum through the Sec61 translocon complex. In this article, we show that purified ribosomes and OT can form a binary complex with a stoichiometry of {approx}1 to 1 in the presence of detergent. We present evidence that OT may bind to the large ribosomal subunit near the site where nascent polypeptides exit. We further show that OT and the Sec61 complex can simultaneously bind to ribosomes in vitro. Based on existing data and our findings,more » we propose that cotranslational translocation and N-glycosylation of nascent polypeptides are mediated by a ternary supramolecular complex consisting of OT, the Sec61 complex, and ribosomes.« less

Oligosaccharyltransferase directly binds to ribosome at a location near the translocon-binding site

PubMed Central

Harada, Yoichiro; Li, Hua; Li, Huilin; Lennarz, William J.

2009-01-01

Oligosaccharyltransferase (OT) transfers high mannose-type glycans to the nascent polypeptides that are translated by the membrane-bound ribosome and translocated into the lumen of the endoplasmic reticulum through the Sec61 translocon complex. In this article, we show that purified ribosomes and OT can form a binary complex with a stoichiometry of ≈1 to 1 in the presence of detergent. We present evidence that OT may bind to the large ribosomal subunit near the site where nascent polypeptides exit. We further show that OT and the Sec61 complex can simultaneously bind to ribosomes in vitro. Based on existing data and our findings, we propose that cotranslational translocation and N-glycosylation of nascent polypeptides are mediated by a ternary supramolecular complex consisting of OT, the Sec61 complex, and ribosomes. PMID:19365066

Increasing protein production rates can decrease the rate at which functional protein is produced

NASA Astrophysics Data System (ADS)

Sharma, Ajeet; O'Brien, Edward

The rate at which soluble, functional protein is produced by the ribosome has recently been found to vary in complex and unexplained ways as various translation-associated rates are altered through synonymous codon substitutions. We combine a well-established ribosome-traffic model with a master-equation model of co-translational domain folding to explore the scenarios that are possible for the protein production rate, J, and the functional-nascent protein production rate, F, as the rates associated with translation are altered. We find that while J monotonically increases as the rates of translation-initiation, -elongation and -termination increase, F can either increase or decrease. F exhibits non-monotonic behavior because increasing these rates can cause a protein to be synthesized more rapidly but provide less time for nascent-protein domains to co-translationally fold thereby producing less functional nascent protein immediately after synthesis. We further demonstrate that these non-monotonic changes in Faffect the post-translational, steady-state levels of functional protein in a similar manner. Our results provide a possible explanation for recent experimental observations that the specific activity of enzymatic proteins can decrease with increased synthesis rates and can in principle be used to rationally-design transcripts to maximize the production of functional nascent protein.

Protein charge distribution in proteomes and its impact on translation

PubMed Central

Requião, Rodrigo D.; Fernandes, Luiza; de Souza, Henrique José Araujo; Rossetto, Silvana; Domitrovic, Tatiana

2017-01-01

As proteins are synthesized, the nascent polypeptide must pass through a negatively charged exit tunnel. During this stage, positively charged stretches can interact with the ribosome walls and slow the translation. Therefore, charged polypeptides may be important factors that affect protein expression. To determine the frequency and distribution of positively and negatively charged stretches in different proteomes, the net charge was calculated for every 30 consecutive amino acid residues, which corresponds to the length of the ribosome exit tunnel. The following annotated and reviewed proteins in the UniProt database (Swiss-Prot) were analyzed: 551,705 proteins from different organisms and a total of 180 million protein segments. We observed that there were more negative than positive stretches and that super-charged positive sequences (i.e., net charges ≥ 14) were underrepresented in the proteomes. Overall, the proteins were more positively charged at their N-termini and C-termini, and this feature was present in most organisms and subcellular localizations. To investigate whether the N-terminal charges affect the elongation rates, previously published ribosomal profiling data obtained from S. cerevisiae, without translation-interfering drugs, were analyzed. We observed a nonlinear effect of the charge on the ribosome occupancy in which values ≥ +5 and ≤ -6 showed increased and reduced ribosome densities, respectively. These groups also showed different distributions across 80S monosomes and polysomes. Basic polypeptides are more common within short proteins that are translated by monosomes, whereas negative stretches are more abundant in polysome-translated proteins. These findings suggest that the nascent peptide charge impacts translation and can be one of the factors that regulate translation efficiency and protein expression. PMID:28531225

Prefoldin–Nascent Chain Complexes in the Folding of Cytoskeletal Proteins

PubMed Central

Hansen, William J.; Cowan, Nicholas J.; Welch, William J.

1999-01-01

In vitro transcription/translation of actin cDNA and analysis of the translation products by native-PAGE was used to study the maturation pathway of actin. During the course of actin synthesis, several distinct actin-containing species were observed and the composition of each determined by immunological procedures. After synthesis of the first ∼145 amino acids, the nascent ribosome-associated actin chain binds to the recently identified heteromeric chaperone protein, prefoldin (PFD). PFD remains bound to the relatively unfolded actin polypeptide until its posttranslational delivery to cytosolic chaperonin (CCT). We show that α- and β-tubulin follow a similar maturation pathway, but to date find no evidence for an interaction between PFD and several noncytoskeletal proteins. We conclude that PFD functions by selectively targeting nascent actin and tubulin chains pending their transfer to CCT for final folding and/or assembly. PMID:10209023

Tail-extension following the termination codon is critical for release of the nascent chain from membrane-bound ribosomes in a reticulocyte lysate cell-free system.

PubMed

Takahara, Michiyo; Sakaue, Haruka; Onishi, Yukiko; Yamagishi, Marifu; Kida, Yuichiro; Sakaguchi, Masao

2013-01-11

Nascent chain release from membrane-bound ribosomes by the termination codon was investigated using a cell-free translation system from rabbit supplemented with rough microsomal membrane vesicles. Chain release was extremely slow when mRNA ended with only the termination codon. Tail extension after the termination codon enhanced the release of the nascent chain. Release reached plateau levels with tail extension of 10 bases. This requirement was observed with all termination codons: TAA, TGA and TAG. Rapid release was also achieved by puromycin even in the absence of the extension. Efficient translation termination cannot be achieved in the presence of only a termination codon on the mRNA. Tail extension might be required for correct positioning of the termination codon in the ribosome and/or efficient recognition by release factors. Copyright © 2012. Published by Elsevier Inc.

The Fate of Nascent APP in Hippocampal Neurons: A Live Cell Imaging Study.

PubMed

DelBove, Claire E; Deng, Xian-Zhen; Zhang, Qi

2018-06-21

Amyloid precursor protein (APP) is closely associated with Alzheimer's disease (AD) because its proteolytic products form amyloid plaques and its mutations are linked to familial AD patients. As a membrane protein, APP is involved in neuronal development and plasticity. However, it remains unclear how nascent APP is distributed and transported to designated membrane compartments to execute its diverse functions. Here, we employed a dual-tagged APP fusion protein in combination with a synaptic vesicle marker to study the surface trafficking and cleavage of APP in hippocampal neurons immediately after its synthesis. Using long-term time-lapse imaging, we found that a considerable amount of nascent APP was directly transported to the somatodendritic surface, from which it propagates to distal neurites. Some APP in the plasma membrane was endocytosed and some was cleaved by α-secretase. Hence, we conclude that surface transportation of APP is a major step preceding its proteolytic processing and neuritic distribution.

RNA polymerase pausing and nascent RNA structure formation are linked through clamp domain movement

PubMed Central

Hein, Pyae P.; Kolb, Kellie E.; Windgassen, Tricia; Bellecourt, Michael J.; Darst, Seth A.; Mooney, Rachel A.; Landick, Robert

2014-01-01

The rates of RNA synthesis and nascent RNA folding into biologically active structures are linked via pausing by RNA polymerase (RNAP). Structures that form within the RNA exit channel can increase pausing by interacting with bacterial RNAP or decrease pausing by preventing backtracking. Conversely, pausing is required for proper folding of some RNAs. Opening of the RNAP clamp domain is proposed to mediate some effects of nascent RNA structures. However, the connections among RNA structure formation, clamp movement, and catalytic activity remain uncertain. We assayed exit-channel structure formation in Escherichia coli RNAP together with disulfide crosslinks that favor closed or open clamp conformations and found that clamp position directly influences RNA structure formation and catalytic activity. We report that exit-channel RNA structures slow pause escape by favoring clamp opening and through interactions with the flap that slow translocation. PMID:25108353

A glimpse on biological activities of tellurium compounds.

PubMed

Cunha, Rodrigo L O R; Gouvea, Iuri E; Juliano, Luiz

2009-09-01

Tellurium is a rare element which has been regarded as a toxic, non-essential trace element and its biological role is not clearly established to date. Besides of that, the biological effects of elemental tellurium and some of its inorganic and organic derivatives have been studied, leading to a set of interesting and promising applications. As an example, it can be highlighted the uses of alkali-metal tellurites and tellurates in microbiology, the antioxidant effects of organotellurides and diorganoditellurides and the immunomodulatory effects of the non-toxic inorganic tellurane, named AS-101, and the plethora of its uses. Inasmuch, the nascent applications of organic telluranes (organotelluranes) as protease inhibitors and its applications in disease models are the most recent contribution to the scenario of the biological effects and applications of tellurium and its compounds discussed in this manuscript.

Affective Neuronal Selection: The Nature of the Primordial Emotion Systems

PubMed Central

Toronchuk, Judith A.; Ellis, George F. R.

2013-01-01

Based on studies in affective neuroscience and evolutionary psychiatry, a tentative new proposal is made here as to the nature and identification of primordial emotional systems. Our model stresses phylogenetic origins of emotional systems, which we believe is necessary for a full understanding of the functions of emotions and additionally suggests that emotional organizing systems play a role in sculpting the brain during ontogeny. Nascent emotional systems thus affect cognitive development. A second proposal concerns two additions to the affective systems identified by Panksepp. We suggest there is substantial evidence for a primary emotional organizing program dealing with power, rank, dominance, and subordination which instantiates competitive and territorial behavior and is an evolutionary contributor to self-esteem in humans. A program underlying disgust reactions which originally functioned in ancient vertebrates to protect against infection and toxins is also suggested. PMID:23316177

Hormones in the city: endocrine ecology of urban birds.

PubMed

Bonier, Frances

2012-05-01

Urbanization dramatically changes the landscape, presenting organisms with novel challenges and often leading to reduced species diversity. Urban ecologists have documented numerous biotic and abiotic consequences of urbanization, such as altered climate, species interactions, and community composition, but we lack an understanding of the mechanisms underlying organisms' responses to urbanization. Here, I review findings from the nascent field of study of the endocrine ecology of urban birds. Thus far, no clear or consistent patterns have been revealed, but we do have evidence that urban habitat can shape endocrine traits, and that those traits might contribute to adaptation to the urban environment. I suggest strong approaches for future work addressing exciting questions about the role of endocrine traits in mediating responses to urbanization within species across the globe. Copyright © 2012 Elsevier Inc. All rights reserved.

Mars primordial crust: unique sites for investigating proto-biologic properties.

PubMed

Perry, Randall S; Hartmann, William K

2006-12-01

The Martian meteorite collection suggests that intact outcrops or boulder-scale fragments of the 4.5 Ga Martian crust exist within tens of meters of the present day surface of Mars. Mars may be the only planet where such primordial crust samples, representing the first 100 Ma of a planet's environment, are available. The primordial crust has been destroyed on Earth by plate tectonics and other geological phenomena and is buried on the Moon under hundreds or thousands of meters of megaregoltih. Early Mars appears to have been remarkably similar to early Earth, and samples of rock from the first few Ma or first 100 Ma may reveal "missing link" proto-biological forms that could shed light on the transition from abiotic organic chemistry to living cells. Such organic snapshots of nascent life are unlikely to be found on Earth.

Ethical challenges for accountable care organizations: a structured review.

PubMed

DeCamp, Matthew; Farber, Neil J; Torke, Alexia M; George, Maura; Berger, Zackary; Keirns, Carla C; Kaldjian, Lauris C

2014-10-01

Accountable care organizations (ACOs) are proliferating as a solution to the cost crisis in American health care, and already involve as many as 31 million patients. ACOs hold clinicians, group practices, and in many circumstances hospitals financially accountable for reducing expenditures and improving their patients' health outcomes. The structure of health care affects the ethical issues arising in the practice of medicine; therefore, like all health care organizational structures, ACOs will experience ethical challenges. No framework exists to assist key ACO stakeholders in identifying or managing these challenges. We conducted a structured review of the medical ACO literature using qualitative content analysis to inform identification of ethical challenges for ACOs. Our analysis found infrequent discussion of ethics as an explicit concern for ACOs. Nonetheless, we identified nine critical ethical challenges, often described in other terms, for ACO stakeholders. Leaders could face challenges regarding fair resource allocation (e.g., about fairly using ACOs' shared savings), protection of professionals' ethical obligations (especially related to the design of financial incentives), and development of fair decision processes (e.g., ensuring that beneficiary representatives on the ACO board truly represent the ACO's patients). Clinicians could perceive threats to their professional autonomy (e.g., through cost control measures), a sense of dual or conflicted responsibility to their patients and the ACO, or competition with other clinicians. For patients, critical ethical challenges will include protecting their autonomy, ensuring privacy and confidentiality, and effectively engaging them with the ACO. ACOs are not inherently more or less "ethical" than other health care payment models, such as fee-for-service or pure capitation. ACOs' nascent development and flexibility in design, however, present a time-sensitive opportunity to ensure their ethical operation, promote their success, and refine their design and implementation by identifying, managing, and conducting research into the ethical issues they might face.

Applications of oligomers for nanostructured conducting polymers.

PubMed

Wang, Yue; Tran, Henry D; Kaner, Richard B

2011-01-03

This Feature Article provides an overview of the distinctive nanostructures that aniline oligomers form and the applications of these oligomers for shaping the nanoscale morphologies and chirality of conducting polymers. We focus on the synthetic methods for achieving such goals and highlight the underlying mechanisms. The clear advantages of each method and their possible drawbacks are discussed. Assembly and applications of these novel organic (semi)conducting nanomaterials are also outlined. We conclude this article with our perspective on the main challenges, new opportunities, and future directions for this nascent yet vibrant field of research. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integrated self-organization of transitional ER and early Golgi compartments.

PubMed

Glick, Benjamin S

2014-02-01

COPII coated vesicles bud from an ER domain termed the transitional ER (tER), but the mechanism that clusters COPII vesicles at tER sites is unknown. tER sites are closely associated with early Golgi or pre-Golgi structures, suggesting that the clustering of nascent COPII vesicles could be achieved by tethering to adjacent membranes. This model challenges the prevailing view that COPII vesicles are clustered by a scaffolding protein at the ER surface. Although Sec16 was proposed to serve as such a scaffolding protein, recent data suggest that rather than organizing COPII into higher-order structures, Sec16 acts at the level of individual COPII vesicles to regulate COPII turnover. A plausible synthesis is that tER sites are created by tethering to Golgi membranes and are regulated by Sec16. Meanwhile, the COPII vesicles that bud from tER sites are thought to nucleate new Golgi cisternae. Thus, an integrated self-organization process may generate tER-Golgi units. © 2014 WILEY Periodicals, Inc.

Crystallizing Classroom Chemists: From Isolated Disorder to Organized Interaction in the Teaching of Chemistry. A History of the Effort To Create a National Chemical Education Organization

NASA Astrophysics Data System (ADS)

Bohning, James J.

2003-06-01

Chemistry was an integral part of the culture of the earliest settlements in America, but for almost two centuries it languished as a nascent profession, plagued in part by a lack of suitable textbooks and a "dearth of competent teachers". A few individuals, such as Benjamin Silliman and Amos Eaton, acted as seed crystals in attracting and preparing some chemistry teachers, yet as late as the beginning of World War I, "the average isolated teacher had to work out his own salvation as best he could with the aid of an occasional book agent". Small regional organizations of teachers did exist at this time, but achieved little in connecting teachers on a national level. It was out of this amorphous mixture that the American Chemical Society‘s Division of Chemical Education (DIVCHED) solidified, uniting at last a dedicated group of teachers with common problems and a passionate dedication to their discipline and their students.

38 CFR 4.87a - Schedule of ratings-other sense organs.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ratings—other sense organs. Rating 6275Sense of smell, complete loss 10 6276Sense of taste, complete loss 10 Note: Evaluation will be assigned under diagnostic codes 6275 or 6276 only if there is an anatomical or pathological basis for the condition. (Authority: 38 U.S.C. 1155) [64 FR 25210, May 11, 1999...

NOGGIN IS REQUIRED FOR NORMAL LOBE PATTERNING AND DUCTAL BUDDING IN THE MOUSE PROSTATE

PubMed Central

Cook, Crist; Vezina, Chad M.; Hicks, Sarah M.; Shaw, Aubie; Yu, Min; Peterson, Richard E.; Bushman, Wade

2008-01-01

Mesenchymal expression of the BMP antagonist NOGGIN during prostate development plays a critical role in pre-natal ventral prostate development and opposes BMP4-mediated inhibition of cell proliferation during postnatal ductal development. Morphologic examination of newborn Noggin-/- male fetuses revealed genitourinary anomalies including cryptorchidism, incomplete separation of the hindgut from the urogenital sinus (UGS), absence of the ventral mesenchymal pad and a complete loss of ventral prostate (VP) budding. Examination of lobe-specific marker expression in the E14 Noggin-/- UGS rescued by transplantation under the renal capsule of a male nude mouse confirmed a complete loss of VP determination. More modest effects were observed in the other lobes, including decreased number of ductal buds in the dorsal and lateral prostates of newborn Noggin-/- males. BMP4 and BMP7 have been shown to inhibit ductal budding and outgrowth by negatively regulating epithelial cell proliferation. We show here that NOGGIN can neutralize budding inhibition by BMP4 and rescues branching morphogenesis of BMP4-exposed UGS in organ culture and show that the effects of BMP4 and NOGGIN activities converge on P63+ epithelial cells located at nascent duct tips. Together, these studies show that the BMP-NOGGIN axis regulates patterning of the ventral prostate, regulates ductal budding, and controls proliferation of P63+ epithelial cells in the nascent ducts of developing mouse prostate. PMID:18028901

Synthesis of refractory organic matter in the ionized gas phase of the solar nebula.

PubMed

Kuga, Maïa; Marty, Bernard; Marrocchi, Yves; Tissandier, Laurent

2015-06-09

In the nascent solar system, primitive organic matter was a major contributor of volatile elements to planetary bodies, and could have played a key role in the development of the biosphere. However, the origin of primitive organics is poorly understood. Most scenarios advocate cold synthesis in the interstellar medium or in the outer solar system. Here, we report the synthesis of solid organics under ionizing conditions in a plasma setup from gas mixtures (H2(O)-CO-N2-noble gases) reminiscent of the protosolar nebula composition. Ionization of the gas phase was achieved at temperatures up to 1,000 K. Synthesized solid compounds share chemical and structural features with chondritic organics, and noble gases trapped during the experiments reproduce the elemental and isotopic fractionations observed in primitive organics. These results strongly suggest that both the formation of chondritic refractory organics and the trapping of noble gases took place simultaneously in the ionized areas of the protoplanetary disk, via photon- and/or electron-driven reactions and processing. Thus, synthesis of primitive organics might not have required a cold environment and could have occurred anywhere the disk is ionized, including in its warm regions. This scenario also supports N2 photodissociation as the cause of the large nitrogen isotopic range in the solar system.

Synthesis of refractory organic matter in the ionized gas phase of the solar nebula

PubMed Central

Kuga, Maïa; Marty, Bernard; Marrocchi, Yves; Tissandier, Laurent

2015-01-01

In the nascent solar system, primitive organic matter was a major contributor of volatile elements to planetary bodies, and could have played a key role in the development of the biosphere. However, the origin of primitive organics is poorly understood. Most scenarios advocate cold synthesis in the interstellar medium or in the outer solar system. Here, we report the synthesis of solid organics under ionizing conditions in a plasma setup from gas mixtures (H2(O)−CO−N2−noble gases) reminiscent of the protosolar nebula composition. Ionization of the gas phase was achieved at temperatures up to 1,000 K. Synthesized solid compounds share chemical and structural features with chondritic organics, and noble gases trapped during the experiments reproduce the elemental and isotopic fractionations observed in primitive organics. These results strongly suggest that both the formation of chondritic refractory organics and the trapping of noble gases took place simultaneously in the ionized areas of the protoplanetary disk, via photon- and/or electron-driven reactions and processing. Thus, synthesis of primitive organics might not have required a cold environment and could have occurred anywhere the disk is ionized, including in its warm regions. This scenario also supports N2 photodissociation as the cause of the large nitrogen isotopic range in the solar system. PMID:26039983

Spatial organization and dynamics of RNase E and ribosomes in Caulobacter crescentus.

PubMed

Bayas, Camille A; Wang, Jiarui; Lee, Marissa K; Schrader, Jared M; Shapiro, Lucy; Moerner, W E

2018-04-17

We report the dynamic spatial organization of Caulobacter crescentus RNase E (RNA degradosome) and ribosomal protein L1 (ribosome) using 3D single-particle tracking and superresolution microscopy. RNase E formed clusters along the central axis of the cell, while weak clusters of ribosomal protein L1 were deployed throughout the cytoplasm. These results contrast with RNase E and ribosome distribution in Escherichia coli , where RNase E colocalizes with the cytoplasmic membrane and ribosomes accumulate in polar nucleoid-free zones. For both RNase E and ribosomes in Caulobacter , we observed a decrease in confinement and clustering upon transcription inhibition and subsequent depletion of nascent RNA, suggesting that RNA substrate availability for processing, degradation, and translation facilitates confinement and clustering. Importantly, RNase E cluster positions correlated with the subcellular location of chromosomal loci of two highly transcribed rRNA genes, suggesting that RNase E's function in rRNA processing occurs at the site of rRNA synthesis. Thus, components of the RNA degradosome and ribosome assembly are spatiotemporally organized in Caulobacter , with chromosomal readout serving as the template for this organization.

Theory of Force Regulation by Nascent Adhesion Sites

PubMed Central

Bruinsma, Robijn

2005-01-01

The mechanical coupling of a cell with the extracellular matrix relies on adhesion sites, clusters of membrane-associated proteins that communicate forces generated along the F-Actin filaments of the cytoskeleton to connecting tissue. Nascent adhesion sites have been shown to regulate these forces in response to tissue rigidity. Force-regulation by substrate rigidity of adhesion sites with fixed area is not possible for stationary adhesion sites, according to elasticity theory. A simple model is presented to describe force regulation by dynamical adhesion sites. PMID:15849245

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

Albert G. Baca; Edwin J. Heller; Gregory C. Frye-Mason

High sensitivity acoustic wave chemical microsensors are being developed on GaAs substrates. These devices take advantage of the piezoelectric properties of GaAs as well as its mature microelectronics fabrication technology and nascent micromachining technology. The design, fabrication, and response of GaAs SAW chemical microsensors are reported. Functional integrated GaAs SAW oscillators, suitable for chemical sensing, have been produced. The integrated oscillator requires 20 mA at 3 VK, operates at frequencies up to 500 MHz, and occupies approximately 2 mmz. Discrete GaAs sensor components, including IC amplifiers, SAW delay lines, and IC phase comparators have been fabricated and tested. A temperaturemore » compensation scheme has been developed that overcomes the large temperature dependence of GaAs acoustic wave devices. Packaging issues related to bonding miniature flow channels directly to the GaAs substrates have been resolved. Micromachining techniques for fabricating FPW and TSM microsensors on thin GaAs membranes are presented and GaAs FPW delay line performance is described. These devices have potentially higher sensitivity than existing GaAs and quartz SAW sensors.« less

Antigen Binding and Site-Directed Labeling of Biosilica-Immobilized Fusion Proteins Expressed in Diatoms

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

Ford, Nicole R.; Hecht, Karen A.; Hu, Dehong

2016-01-08

The diatom Thalassiosira pseudonana was genetically modified to express biosilica-targeted fusion proteins incorporating a tetracysteine tag for site-directed labeling with biarsenical affinity probes and either EGFP or single chain antibody to test colocalization of probes with the EGFP-tagged recombinant protein or binding of biosilica-immobilized antibodies to large and small molecule antigens, respectively. Site-directed labeling with the biarsenical probes demonstrated colocalization with EGFP-encoded proteins in nascent and mature biosilica, supporting their use in studying biosilica maturation. Isolated biosilica transformed with a single chain antibody against either the Bacillus anthracis surface layer protein EA1 or small molecule explosive trinitrotoluene (TNT) effectively boundmore » the respective antigens. A marked increase in fluorescence lifetime of the TNT surrogate Alexa Fluor 555-trinitrobenzene reflected the high binding specificity of the transformed isolated biosilica. These results demonstrated the potential use of biosilica-immobilized single chain antibodies as binders for large and small molecule antigens in sensing and therapeutics.« less

Global effects of the CSR-1 RNA interference pathway on transcriptional landscape

PubMed Central

Cecere, Germano; Hoersch, Sebastian; O’Keeffe, Sean; Sachidanandam, Ravi; Grishok, Alla

2014-01-01

Argonaute proteins and their small RNA co-factors short interfering RNAs (siRNAs) are known to inhibit gene expression at the transcriptional and post-transcriptional levels. In Caenorhabditis elegans, the Argonaute CSR-1 binds thousands of endogenous siRNAs (endo-siRNAs) antisense to germline transcripts and associates with chromatin in a siRNA-dependent manner. However, its role in gene expression regulation remains controversial. Here, we used a genome-wide profiling of nascent RNA transcripts to demonstrate that the CSR-1 RNAi pathway promotes sense-oriented Pol II transcription. Moreover, a loss of CSR-1 function resulted in global increase in antisense transcription and ectopic transcription of silent chromatin domains, which led to reduced chromatin incorporation of centromere-specific histone H3. Based on these findings, we propose that the CSR-1 pathway has a role in maintaining the directionality of active transcription thereby propagating the distinction between transcriptionally active and silent genomic regions. PMID:24681887

High-performance 3D compressive sensing MRI reconstruction.

PubMed

Kim, Daehyun; Trzasko, Joshua D; Smelyanskiy, Mikhail; Haider, Clifton R; Manduca, Armando; Dubey, Pradeep

2010-01-01

Compressive Sensing (CS) is a nascent sampling and reconstruction paradigm that describes how sparse or compressible signals can be accurately approximated using many fewer samples than traditionally believed. In magnetic resonance imaging (MRI), where scan duration is directly proportional to the number of acquired samples, CS has the potential to dramatically decrease scan time. However, the computationally expensive nature of CS reconstructions has so far precluded their use in routine clinical practice - instead, more-easily generated but lower-quality images continue to be used. We investigate the development and optimization of a proven inexact quasi-Newton CS reconstruction algorithm on several modern parallel architectures, including CPUs, GPUs, and Intel's Many Integrated Core (MIC) architecture. Our (optimized) baseline implementation on a quad-core Core i7 is able to reconstruct a 256 × 160×80 volume of the neurovasculature from an 8-channel, 10 × undersampled data set within 56 seconds, which is already a significant improvement over existing implementations. The latest six-core Core i7 reduces the reconstruction time further to 32 seconds. Moreover, we show that the CS algorithm benefits from modern throughput-oriented architectures. Specifically, our CUDA-base implementation on NVIDIA GTX480 reconstructs the same dataset in 16 seconds, while Intel's Knights Ferry (KNF) of the MIC architecture even reduces the time to 12 seconds. Such level of performance allows the neurovascular dataset to be reconstructed within a clinically viable time.

'2A-Like' Signal Sequences Mediating Translational Recoding: A Novel Form of Dual Protein Targeting.

PubMed

Roulston, Claire; Luke, Garry A; de Felipe, Pablo; Ruan, Lin; Cope, Jonathan; Nicholson, John; Sukhodub, Andriy; Tilsner, Jens; Ryan, Martin D

2016-08-01

We report the initial characterization of an N-terminal oligopeptide '2A-like' sequence that is able to function both as a signal sequence and as a translational recoding element. Owing to this translational recoding activity, two forms of nascent polypeptide are synthesized: (i) when 2A-mediated translational recoding has not occurred: the nascent polypeptide is fused to the 2A-like N-terminal signal sequence and the fusion translation product is targeted to the exocytic pathway, and, (ii) a translation product where 2A-mediated translational recoding has occurred: the 2A-like signal sequence is synthesized as a separate translation product and, therefore, the nascent (downstream) polypeptide lacks the 2A-like signal sequence and is localized to the cytoplasm. This type of dual-functional signal sequence results, therefore, in the partitioning of the translation products between the two sub-cellular sites and represents a newly described form of dual protein targeting. © 2016 The Authors. Traffic published by John Wiley & Sons Ltd.

An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq.

PubMed

Azofeifa, Joseph G; Allen, Mary A; Lladser, Manuel E; Dowell, Robin D

2017-01-01

We present a fast and simple algorithm to detect nascent RNA transcription in global nuclear run-on sequencing (GRO-seq). GRO-seq is a relatively new protocol that captures nascent transcripts from actively engaged polymerase, providing a direct read-out on bona fide transcription. Most traditional assays, such as RNA-seq, measure steady state RNA levels which are affected by transcription, post-transcriptional processing, and RNA stability. GRO-seq data, however, presents unique analysis challenges that are only beginning to be addressed. Here, we describe a new algorithm, Fast Read Stitcher (FStitch), that takes advantage of two popular machine-learning techniques, hidden Markov models and logistic regression, to classify which regions of the genome are transcribed. Given a small user-defined training set, our algorithm is accurate, robust to varying read depth, annotation agnostic, and fast. Analysis of GRO-seq data without a priori need for annotation uncovers surprising new insights into several aspects of the transcription process.

Role of the visual experience-dependent nascent proteome in neuronal plasticity

PubMed Central

Liu, Han-Hsuan; McClatchy, Daniel B; Schiapparelli, Lucio; Shen, Wanhua; Yates, John R

2018-01-01

Experience-dependent synaptic plasticity refines brain circuits during development. To identify novel protein synthesis-dependent mechanisms contributing to experience-dependent plasticity, we conducted a quantitative proteomic screen of the nascent proteome in response to visual experience in Xenopus optic tectum using bio-orthogonal metabolic labeling (BONCAT). We identified 83 differentially synthesized candidate plasticity proteins (CPPs). The CPPs form strongly interconnected networks and are annotated to a variety of biological functions, including RNA splicing, protein translation, and chromatin remodeling. Functional analysis of select CPPs revealed the requirement for eukaryotic initiation factor three subunit A (eIF3A), fused in sarcoma (FUS), and ribosomal protein s17 (RPS17) in experience-dependent structural plasticity in tectal neurons and behavioral plasticity in tadpoles. These results demonstrate that the nascent proteome is dynamic in response to visual experience and that de novo synthesis of machinery that regulates RNA splicing and protein translation is required for experience-dependent plasticity. PMID:29412139

A conceptual framework for the evolutionary origins of multicellularity

NASA Astrophysics Data System (ADS)

Libby, Eric; Rainey, Paul B.

2013-06-01

The evolution of multicellular organisms from unicellular counterparts involved a transition in Darwinian individuality from single cells to groups. A particular challenge is to understand the nature of the earliest groups, the causes of their evolution, and the opportunities for emergence of Darwinian properties. Here we outline a conceptual framework based on a logical set of possible pathways for evolution of the simplest self-replicating groups. Central to these pathways is the recognition of a finite number of routes by which genetic information can be transmitted between individual cells and groups. We describe the form and organization of each primordial group state and consider factors affecting persistence and evolution of the nascent multicellular forms. Implications arising from our conceptual framework become apparent when attempting to partition fitness effects at individual and group levels. These are discussed with reference to the evolutionary emergence of individuality and its manifestation in extant multicellular life—including those of marginal Darwinian status.

Microfluidic systems for investigating host-microbe relationship

NASA Astrophysics Data System (ADS)

Bhattacharjee, Arunima; Vincent, Lionel; Nawroth, Janna; Ruby, Ned; McFall-Ngai, Margaret; Kanso, Eva; Biodynamics Laboratory Collaboration; Pacific Biosciences Research Center Collaboration

2017-11-01

The symbiosis between the bioluminescent bacterium, Vibrio fisheri, and the Hawaiian bobtail squid, Euprymna scolopes, has been widely studied, and this association is used as a model system for studying bacterial colonization of ciliated host tissues. The recruitment of Vibrio fisheri to a specialized light organ in the nascent squid is facilitated by various chemosensing and mechanosensing events. To decipher the effects of such environmental and host-derived sensors on bacterial physiology, we use specifically designed microfluidic channels to engineer chemical and mechanical fields similar to those observed in the light organ of the squid. These in vitrostudies are aimed at complementing ongoing in vivo studies in the system squid-vibrio system. This approach enables us, for the first time, to isolate the effect of mechanical and chemical cues on bacterial motility in this symbiosis and to quantify the bacterial response to these cues. NSF Inspire.

Motifs, modules and games in bacteria.

PubMed

Wolf, Denise M; Arkin, Adam P

2003-04-01

Global explorations of regulatory network dynamics, organization and evolution have become tractable thanks to high-throughput sequencing and molecular measurement of bacterial physiology. From these, a nascent conceptual framework is developing, that views the principles of regulation in term of motifs, modules and games. Motifs are small, repeated, and conserved biological units ranging from molecular domains to small reaction networks. They are arranged into functional modules, genetically dissectible cellular functions such as the cell cycle, or different stress responses. The dynamical functioning of modules defines the organism's strategy to survive in a game, pitting cell against cell, and cell against environment. Placing pathway structure and dynamics into an evolutionary context begins to allow discrimination between those physical and molecular features that particularize a species to its surroundings, and those that provide core physiological function. This approach promises to generate a higher level understanding of cellular design, pathway evolution and cellular bioengineering.

Motifs, modules and games in bacteria

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

Wolf, Denise M.; Arkin, Adam P.

2003-04-01

Global explorations of regulatory network dynamics, organization and evolution have become tractable thanks to high-throughput sequencing and molecular measurement of bacterial physiology. From these, a nascent conceptual framework is developing, that views the principles of regulation in term of motifs, modules and games. Motifs are small, repeated, and conserved biological units ranging from molecular domains to small reaction networks. They are arranged into functional modules, genetically dissectible cellular functions such as the cell cycle, or different stress responses. The dynamical functioning of modules defines the organism's strategy to survive in a game, pitting cell against cell, and cell against environment.more » Placing pathway structure and dynamics into an evolutionary context begins to allow discrimination between those physical and molecular features that particularize a species to its surroundings, and those that provide core physiological function. This approach promises to generate a higher level understanding of cellular design, pathway evolution and cellular bioengineering.« less

Method and apparatus for detection of chemical vapors

DOEpatents

Mahurin, Shannon Mark [Knoxville, TN; Dai, Sheng [Knoxville, TN; Caja, Josip [Knoxville, TN

2007-05-15

The present invention is a gas detector and method for using the gas detector for detecting and identifying volatile organic and/or volatile inorganic substances present in unknown vapors in an environment. The gas detector comprises a sensing means and a detecting means for detecting electrical capacitance variance of the sensing means and for further identifying the volatile organic and volatile inorganic substances. The sensing means comprises at least one sensing unit and a sensing material allocated therein the sensing unit. The sensing material is an ionic liquid which is exposed to the environment and is capable of dissolving a quantity of said volatile substance upon exposure thereto. The sensing means constitutes an electrochemical capacitor and the detecting means is in electrical communication with the sensing means.

Remote sensing procurement package: Remote Sensing Industry Directory

NASA Technical Reports Server (NTRS)

1981-01-01

A directory of over 140 firms and organizations which contains detailed information in the types of products, services and equipment which they offer is presented. Also included for each firm or organization are addresses, phone numbers, contact person(s), and experience in the remote sensing field.

Earth view: A business guide to orbital remote sensing

NASA Technical Reports Server (NTRS)

Bishop, Peter C.

1990-01-01

The following subject areas are covered: Earth view - a guide to orbital remote sensing; current orbital remote sensing systems (LANDSAT, SPOT image, MOS-1, Soviet remote sensing systems); remote sensing satellite; and remote sensing organizations.

An international organization for remote sensing

NASA Technical Reports Server (NTRS)

Helm, Neil R.; Edelson, Burton I.

1991-01-01

A recommendation is presented for the formation of a new commercially oriented international organization to acquire or develop, coordinate or manage, the space and ground segments for a global operational satellite system to furnish the basic data for remote sensing and meteorological, land, and sea resource applications. The growing numbers of remote sensing programs are examined and possible ways of reducing redundant efforts and improving the coordination and distribution of these global efforts are discussed. This proposed remote sensing organization could play an important role in international cooperation and the distribution of scientific, commercial, and public good data.

A short history of nearly every sense - The evolutionary history of vertebrate sensory cell types.

PubMed

Schlosser, Gerhard

2018-05-08

Evolving from filter feeding chordate ancestors, vertebrates adopted a more active life style. These ecological and behavioral changes went along with an elaboration of the vertebrate head including novel complex paired sense organs such as the eyes, inner ears and olfactory epithelia. However, the photoreceptors, mechanoreceptors and chemoreceptors used in these sense organs have a long evolutionary history and homologous cell types can be recognized in many other bilaterians or even cnidarians. After briefly introducing some of the major sensory cell types found in vertebrates, this review summarizes the phylogenetic distribution of sensory cell types in metazoans and presents a scenario for the evolutionary history of various sensory cell types involving several cell type diversification and fusion events. It is proposed that the evolution of novel cranial sense organs in vertebrates involved the redeployment of evolutionarily ancient sensory cell types for building larger and more complex sense organs.

Genesis of the anti-plague system: the Tsarist period.

PubMed

Melikishvili, Alexander

2006-01-01

Although the anti-plague system of the former Soviet Union developed fully during the Soviet era, its foundations were laid long before the Bolshevik Revolution of 1917. This article traces the evolution of the anti-plague measures from imposition of temporary quarantine in affected areas to the creation of the standard response system and the establishment of permanent anti-plague organizations. The purpose of this article is to demonstrate that by the end of the nineteenth century and the beginning of the twentieth century, despite numerous setbacks, the Russian imperial authorities succeeded in creating a nascent system of disease surveillance dedicated to protecting the population from especially dangerous infectious diseases such as plague.

The use of centrifugation to study early Drosophila embryogenesis

NASA Technical Reports Server (NTRS)

Abbott, M. K.; Spooner, B. S. (Principal Investigator)

1993-01-01

By the end of 10th nuclear cycle, the somatic nuclei of the Drosophila embryo have migrated to the periphery of the egg. Centrifugation of embryos did not result in the displacement of these nuclei, since cytoskeletal elements anchor them to the cortex. But, mild centrifugal forces displace the centrally located, nascent yolk nuclei. If this increased sensitivity to hypergravity occurs before the beginning of nuclear differentiation during cycle 8, when the nascent yolk and somatic nuclei physically separate, then it would mark the earliest functional difference between these two lineages.

Cranial nerves in the Australian lungfish, Neoceratodus forsteri, and in fossil relatives (Osteichthyes: Dipnoi).

PubMed

Kemp, A

2017-02-01

Three systems, two sensory and one protective, are present in the skin of the living Australian lungfish, Neoceratodus forsteri, and in fossil lungfish, and the arrangement and innervation of the sense organs is peculiar to lungfish. Peripheral branches of nerves that innervate the sense organs are slender and unprotected, and form before any skeletal structures appear. When the olfactory capsule develops, it traps some of the anterior branches of cranial nerve V, which emerged from the chondrocranium from the lateral sphenotic foramen. Cranial nerve I innervates the olfactory organ enclosed within the olfactory capsule and cranial nerve II innervates the eye. Cranial nerve V innervates the sense organs of the snout and upper lip, and, in conjunction with nerve IX and X, the sense organs of the posterior and lateral head. Cranial nerve VII is primarily a motor nerve, and a single branch innervates sense organs in the mandible. There are no connections between nerves V and VII, although both emerge from the brain close to each other. The third associated system consists of lymphatic vessels covered by an extracellular matrix of collagen, mineralised as tubules in fossils. Innervation of the sensory organs is separate from the lymphatic system and from the tubule system of fossil lungfish. Copyright © 2016 Elsevier Ltd. All rights reserved.

Sensing of Substrate Vibrations in the Adult Cicada Okanagana rimosa (Hemiptera: Cicadidae).

PubMed

Alt, Joscha A; Lakes-Harlan, Reinhard

2018-05-01

Detection of substrate vibrations is an evolutionarily old sensory modality and is important for predator detection as well as for intraspecific communication. In insects, substrate vibrations are detected mainly by scolopidial (chordotonal) sense organs found at different sites in the legs. Among these sense organs, the tibial subgenual organ (SGO) is one of the most sensitive sensors. The neuroanatomy and physiology of vibratory sense organs of cicadas is not well known. Here, we investigated the leg nerve by neuronal tracing and summed nerve recordings. Tracing with Neurobiotin revealed that the cicada Okanagana rimosa (Say) (Hemiptera: Cicadidae) has a femoral chordotonal organ with about 20 sensory cells and a tibial SGO with two sensory cells. Recordings from the leg nerve show that the vibrational response is broadly tuned with a threshold of about 1 m/s2 and a minimum latency of about 6 ms. The vibratory sense of cicadas might be used in predator avoidance and intraspecific communication, although no tuning to the peak frequency of the calling song (9 kHz) could be found.

Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins

PubMed Central

Foulk, Michael S.; Urban, John M.; Casella, Cinzia; Gerbi, Susan A.

2015-01-01

Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (λ-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent strands intact. We used genomics and biochemical approaches to determine if λ-exo digests all parental DNA sequences equally. We report that λ-exo does not efficiently digest G-quadruplex (G4) structures in a plasmid. Moreover, λ-exo digestion of nonreplicating genomic DNA (LexoG0) enriches GC-rich DNA and G4 motifs genome-wide. We used LexoG0 data to control for nascent strand–independent λ-exo biases in NS-seq and validated this approach at the rDNA locus. The λ-exo–controlled NS-seq peaks are not GC-rich, and only 35.5% overlap with 6.8% of all G4s, suggesting that G4s are not general determinants for origin specification but may play a role for a subset. Interestingly, we observed a periodic spacing of G4 motifs and nucleosomes around the peak summits, suggesting that G4s may position nucleosomes at this subset of origins. Finally, we demonstrate that use of Na+ instead of K+ in the λ-exo digestion buffer reduced the effect of G4s on λ-exo digestion and discuss ways to increase both the sensitivity and specificity of NS-seq. PMID:25695952

Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins.

PubMed

Foulk, Michael S; Urban, John M; Casella, Cinzia; Gerbi, Susan A

2015-05-01

Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (λ-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent strands intact. We used genomics and biochemical approaches to determine if λ-exo digests all parental DNA sequences equally. We report that λ-exo does not efficiently digest G-quadruplex (G4) structures in a plasmid. Moreover, λ-exo digestion of nonreplicating genomic DNA (LexoG0) enriches GC-rich DNA and G4 motifs genome-wide. We used LexoG0 data to control for nascent strand-independent λ-exo biases in NS-seq and validated this approach at the rDNA locus. The λ-exo-controlled NS-seq peaks are not GC-rich, and only 35.5% overlap with 6.8% of all G4s, suggesting that G4s are not general determinants for origin specification but may play a role for a subset. Interestingly, we observed a periodic spacing of G4 motifs and nucleosomes around the peak summits, suggesting that G4s may position nucleosomes at this subset of origins. Finally, we demonstrate that use of Na(+) instead of K(+) in the λ-exo digestion buffer reduced the effect of G4s on λ-exo digestion and discuss ways to increase both the sensitivity and specificity of NS-seq. © 2015 Foulk et al.; Published by Cold Spring Harbor Laboratory Press.

Nascent Phosphorus Oxide

NASA Astrophysics Data System (ADS)

Sumida, David Shuji

PO(X('2)(PI)) is produced via the collision-free infrared multiple photon dissociation (IRMPD) of volatile organophosphorus molecules, and is detected by 2-frequency 2-photon ionization, using the B('2)(SIGMA)('+) state to provide a spectral signature from which X('2)(PI) populations are obtained. Sequential dissociations occur during the IR laser photolysis, in which nascent fragments continue to undergo IRMPD, and PO(X('2)(PI)) accrues from a series of bond fission reactions. Nascent vibrational, rotational, and translational excitations are in sensible accord with this mechanism, except for a few rotational states near J = 19.5. Unlike the nuclear degrees of freedom, the PO(X('2)(PI)) spin-orbit states are populated quite selectively. The ('2)(PI)(,3/2) state, lying only 224 cm('-1) above the ('2)(PI)(,1/2) ground state, contains only (TURN)11% of the population, compared to 34% for a 300K sample. This result is unambiguous; it persists with all precursors, laser fluences, etc., and is verified by comparisons to spectra obtained using a microwave discharge, a flame, and when thermalizing nascent excitations with an inert diluent. This result underscores the sanctity of the separate potential surfaces which correlate to the product spin -orbit states, and the small amount of ('2)(PI)(,3/2) population can be accounted for by non-adiabatic coupling during dissociation, and/or 'freezing' the amount of S(,1) character in an excited precursor in which S(,0) and S(,1) are coupled non-radiatively. We note that such electronic specificity should be dealt with in the analogous recombination reactions. (Copies available exclusively from Micrographics Department, Doheny Library, USC, Los Angeles, CA 90089.).

The Impact of Aerosol Particle Mixing State on the Hygroscopicity of Sea Spray Aerosol.

PubMed

Schill, Steven R; Collins, Douglas B; Lee, Christopher; Morris, Holly S; Novak, Gordon A; Prather, Kimberly A; Quinn, Patricia K; Sultana, Camille M; Tivanski, Alexei V; Zimmermann, Kathryn; Cappa, Christopher D; Bertram, Timothy H

2015-06-24

Aerosol particles influence global climate by determining cloud droplet number concentrations, brightness, and lifetime. Primary aerosol particles, such as those produced from breaking waves in the ocean, display large particle-particle variability in chemical composition, morphology, and physical phase state, all of which affect the ability of individual particles to accommodate water and grow into cloud droplets. Despite such diversity in molecular composition, there is a paucity of methods available to assess how particle-particle variability in chemistry translates to corresponding differences in aerosol hygroscopicity. Here, an approach has been developed that allows for characterization of the distribution of aerosol hygroscopicity within a chemically complex population of atmospheric particles. This methodology, when applied to the interpretation of nascent sea spray aerosol, provides a quantitative framework for connecting results obtained using molecular mimics generated in the laboratory with chemically complex ambient aerosol. We show that nascent sea spray aerosol, generated in situ in the Atlantic Ocean, displays a broad distribution of particle hygroscopicities, indicative of a correspondingly broad distribution of particle chemical compositions. Molecular mimics of sea spray aerosol organic material were used in the laboratory to assess the volume fractions and molecular functionality required to suppress sea spray aerosol hygroscopicity to the extent indicated by field observations. We show that proper accounting for the distribution and diversity in particle hygroscopicity and composition are important to the assessment of particle impacts on clouds and global climate.

A novel microbial fuel cell sensor with biocathode sensing element.

PubMed

Jiang, Yong; Liang, Peng; Liu, Panpan; Wang, Donglin; Miao, Bo; Huang, Xia

2017-08-15

The traditional microbial fuel cell (MFC) sensor with bioanode as sensing element delivers limited sensitivity to toxicity monitoring, restricted application to only anaerobic and organic rich water body, and increased potential fault warning to the combined shock of organic matter/toxicity. In this study, the biocathode for oxygen reduction reaction was employed for the first time as the sensing element in MFC sensor for toxicity monitoring. The results shown that the sensitivity of MFC sensor with biocathode sensing element (7.4±2.0 to 67.5±4.0mA% -1 cm -2 ) was much greater than that showed by bioanode sensing element (3.4±1.5 to 5.5±0.7mA% -1 cm -2 ). The biocathode sensing element achieved the lowest detection limit reported to date using MFC sensor for formaldehyde detection (0.0005%), while the bioanode was more applicable for higher concentration (>0.0025%). There was a quicker response of biocathode sensing element with the increase of conductivity and dissolved oxygen (DO). The biocathode sensing element made the MFC sensor directly applied to clean water body monitoring, e.g., drinking water and reclaimed water, without the amending of background organic matter, and it also decreased the warning failure when challenged by a combined shock of organic matter/toxicity. Copyright © 2017 Elsevier B.V. All rights reserved.

Highly hydrogenated graphene via active hydrogen reduction of graphene oxide in the aqueous phase at room temperature.

PubMed

Sofer, Zdeněk; Jankovský, Ondřej; Šimek, Petr; Soferová, Lýdie; Sedmidubský, David; Pumera, Martin

2014-02-21

Hydrogenated graphene and graphane are in the forefront of graphene research. Hydrogenated graphene is expected to exhibit ferromagnetism, tunable band gap, fluorescence, and high thermal and low electrical conductivity. Currently available techniques for fabrication of highly hydrogenated graphene use either a liquid ammonia (-33 °C) reduction pathway using alkali metals or plasma low pressure or ultra high pressure hydrogenation. These methods are either technically challenging or pose inherent risks. Here we wish to demonstrate that highly hydrogenated graphene can be prepared at room temperature in the aqueous phase by reduction of graphene oxide by nascent hydrogen generated by dissolution of metal in acid. Nascent hydrogen is known to be a strong reducing agent. We studied the influence of metal involved in nascent hydrogen generation and characterized the samples in detail. The resulting reduced graphenes and hydrogenated graphenes were characterized in detail. The resulting hydrogenated graphene had the chemical formula C1.16H1O0.66. Such simple hydrogenation of graphene is of high importance for large scale safe synthesis of hydrogenated graphene.

Basal body assembly in ciliates: the power of numbers

PubMed Central

Pearson, Chad G.; Winey, Mark

2009-01-01

Centrioles perform the dual functions of organizing both centrosomes and cilia. The biogenesis of nascent centrioles is an essential cellular event that is tightly coupled to the cell cycle so that each cell contains only two or four centrioles at any given point in the cell cycle. The assembly of centrioles and their analogs, basal bodies, is well characterized at the ultrastructural level whereby structural modules are built into a functional organelle. Genetic studies in model organisms combined with proteomic, bioinformatic, and identifying ciliary disease gene orthologs have revealed a wealth of molecules requiring further analysis to determine their roles in centriole duplication, assembly, and function. Nonetheless, at this stage our understanding of how molecular components interact to build new centrioles and basal bodies is limited. The ciliates, Tetrahymena and Paramecium, historically have been the subject of cytological and genetic study of basal bodies. Recent advances in the ciliate genetic and molecular toolkit have placed these model organisms in a favorable position to study the molecular mechanisms of centriole and basal body assembly. PMID:19192246

The Hygroscopicity Parameter of Marine Organics in Sea Spray Aerosols

NASA Astrophysics Data System (ADS)

Boyer, M.; Chang, R. Y. W.

2015-12-01

The effects of aerosols on climate are poorly understood, specifically with respect to their influence on cloud properties. Since oceans cover >70% of Earth's surface, sea spray aerosols (SSA), which act efficiently as cloud condensation nuclei (CCN), may have important implications on Earth's radiation budget. Surface active organic species readily accumulate in the sea surface microlayer (SML), located at the ocean-atmosphere interface, and transfer onto nascent SSA. While it is understood that SSA are commonly enriched with organics, the resulting effect of the organic content on CCN activation remains unresolved. The hygroscopicity parameter, kappa (k), allows for the cloud nucleating properties of individual components to be predicted in particles of mixed composition; however, most studies typically infer k from ambient measurements without assessing the contribution of the individual components to the overall k. In this study, a method for quantifying the cloud nucleating properties of the organic species in surface seawater using k-Kohler theory is proposed. Ambient SML and bulk water samples will be collected and atomized to generate particles such that the overall k can be inferred from CCN measurements. The inorganic and organic components will be quantified, and the organic component will be separated so that the hygroscopicity of only the organic constituents can be determined. By comparing the inferred k values for the samples before and after removal of the inorganic component, the hygroscopicity of the organic constituents alone can be calculated, providing insight on the effect of organic species on CCN activation in SSA.

Self-organizing sensing and actuation for automatic control

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

Cheng, George Shu-Xing

A Self-Organizing Process Control Architecture is introduced with a Sensing Layer, Control Layer, Actuation Layer, Process Layer, as well as Self-Organizing Sensors (SOS) and Self-Organizing Actuators (SOA). A Self-Organizing Sensor for a process variable with one or multiple input variables is disclosed. An artificial neural network (ANN) based dynamic modeling mechanism as part of the Self-Organizing Sensor is described. As a case example, a Self-Organizing Soft-Sensor for CFB Boiler Bed Height is presented. Also provided is a method to develop a Self-Organizing Sensor.

Device Engineered Organic Transistors for Flexible Sensing Applications.

PubMed

Zang, Yaping; Huang, Dazhen; Di, Chong-An; Zhu, Daoben

2016-06-01

Organic thin-film transistors (OFETs) represent a promising candidate for next-generation sensing applications because of the intrinsic advantages of organic semiconductors. The development of flexible sensing devices has received particular interest in the past few years. The recent efforts of developing OFETs for sensitive and specific flexible sensors are summarized from the standpoint of device engineering. The tuning of signal transduction and signal amplification are highlighted based on an overview of active-layer thickness modulation, functional receptor implantation and device geometry optimization. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mini Review: Biomaterials for Enhancing Neuronal Repair

NASA Astrophysics Data System (ADS)

Cangellaris, Olivia V.; Gillette, Martha U.

2018-04-01

As they differentiate from neuroblasts, nascent neurons become highly polarized and elongate. Neurons extend and elaborate fine and fragile cellular extensions that form circuits enabling long-distance communication and signal integration within the body. While other organ systems are developing, projections of differentiating neurons find paths to distant targets. Subsequent post-developmental neuronal damage is catastrophic because the cues for reinnervation are no longer active. Advances in biomaterials are enabling fabrication of micro-environments that encourage neuronal regrowth and restoration of function by recreating these developmental cues. This mini-review considers new materials that employ topographical, chemical, electrical, and/or mechanical cues for use in neuronal repair. Manipulating and integrating these elements in different combinations will generate new technologies to enhance neural repair.

Isolation of Chromoplasts and Suborganellar Compartments from Tomato and Bell Pepper Fruit.

PubMed

Barsan, Cristina; Kuntz, Marcel; Pech, Jean-Claude

2017-01-01

Tomato is a model for fruit development and ripening. The isolation of intact plastids from this organism is therefore important for metabolic and proteomic analyses. Pepper, a species from the same family, is also of interest since it allows isolation of intact chromoplasts in large amounts. Here, we provide a detailed protocol for the isolation of tomato plastids at three fruit developmental stages, namely, nascent chromoplasts from the mature green stage, chromoplasts from an intermediate stage, and fully differentiated red chromoplasts. The method relies on sucrose density gradient centrifugations. It yields high purity organelles suitable for proteome analyses. Enzymatic and microscopy assays are summarized to assess purity and intactness. A method is also described for subfractionation of pepper chromoplast lipoprotein structures.

Topographic control on the nascent Mediterranean outflow

NASA Astrophysics Data System (ADS)

Gasser, M.; Pelegrí, J. L.; Nash, J. D.; Peters, H.; García-Lafuente, J.

2011-12-01

Data collected during a 12-day cruise in July 2009 served to examine the structure of the nascent Mediterranean Outflow Water (MOW) immediately west of the Espartel Sill, the westernmost sill in the Strait of Gibraltar. The MOW is characterized by high salinities (>37.0 and reaching 38.3) and high velocities (exceeding 1 m s-1 at 100 m above the seafloor), and follows a submerged valley along a 30 km stretch, the natural western extension of the strait. It is approx. 150 m thick and 10 km wide, and experiences a substantial drop from 420 to 530 m over a distance of some 3 km between two relatively flat regions. Measurements indicate that the nascent MOW behaves as a gravity current with nearly maximal traveling speed; if this condition is maintained, then the maximum MOW velocity would decrease slowly with distance from the Espartel Sill, remaining significantly high until the gravity current excess density is only a small fraction of its original value. The sharp pycnocline between the Mediterranean and the overlying North Atlantic Central waters is dynamically unstable, particularly where the flow interacts with the 100 m decrease in bottom depth. Here, subcritical gradient Richardson numbers coincide with the development of large interfacial undulations and billows. The very energetic downslope flow is likely responsible for the development of a narrow V-shaped channel downstream of the seafloor drop along the axis of the submerged valley, this probably being the very first erosional scour produced by the nascent MOW. The coincidence of subcritical gradient Richardson numbers with relatively high turbidity values above the channel flanks suggests it may be undergoing upstream erosion.

Nascent PO(X 2Π) E,V,R,T excitations from collision-free IR laser photolysis: Specificity toward the PO(X 2Pi 1/2) spin-orbit statea)

NASA Astrophysics Data System (ADS)

Chou, Jim-Son; Sumida, David S.; Wittig, C.

1985-02-01

PO (X 2Π) is produced via the collision-free infrared multiple photon dissociation (IRMPD) of volatile organophosphorous molecules, and is detected by two-frequency two-photon ionization, using the B 2Σ+ state to provide a spectral signature from which X 2Π populations are obtained. Sequential dissociations occur during the IR laser photolysis, in which nascent fragments continue to undergo IRMPD, and PO (X 2Π) accrues from a series of bond fission reactions. Nascent vibrational, rotational, and translational excitations are in sensible accord with this mechanism, except for a few rotational states near J=19.5. Unlike the nuclear degrees of freedom, the PO (X 2Π) spin-orbit states are populated quite selectively. The 2Π3/2 state, lying only 224 cm-1 above the 2Π1/2 ground state, contains only ˜11% of the population, compared to 34% for a 300 K sample. This result is unambiguous; it persists with all precursors, laser fluences, etc., and is verified by comparisons to spectra obtained using a microwave discharge, a flame, and when thermalizing nascent excitations with an inert diluent. This result underscores the importance of the separate potential surfaces which correlate to the product spin-orbit states, and the small amount of 2Π3/2 population can be accounted for by nonadiabatic coupling during dissociation, and/or ``freezing'' the amount of S1 character in an excited precursor in which S0 and S1 are coupled nonradiatively. We note that such electronic specificity should be dealt with in the analogous recombination reactions.

Probing the Role of Nascent Helicity in p27 Function as a Cell Cycle Regulator

PubMed Central

Otieno, Steve; Kriwacki, Richard

2012-01-01

p27 regulates the activity of Cdk complexes which are the principal governors of phase transitions during cell division. Members of the p27 family of proteins, which also includes p21 and p57, are called the Cip/Kip cyclin-dependent kinase regulators (CKRs). Interestingly, the Cip/Kip CKRs play critical roles in cell cycle regulation by being intrinsically unstructured, a characteristic contrary to the classical structure-function paradigm. They exhibit nascent helicity which has been localized to a segment referred to as sub-domain LH. The nascent helicity of this sub-domain is conserved and we hypothesize that it is an important determinant of their functional properties. To test this hypothesis, we successfully designed and prepared p27 variants in which domain LH was either more or less helical with respect to the wild-type protein. Thermal denaturation experiments showed that the ternary complexes of the p27 variants bound to Cdk2/Cyclin A were less stable compared to the wild-type complex. Isothermal titration calorimetry experiments showed a decrease in the enthalpy of binding for all the mutants with respect to p27. The free energies of binding varied within a much narrower range. In vitro Cdk2 inhibition assays showed that the p27 variants exhibited disparate inhibitory potencies. Furthermore, when over-expressed in NIH 3T3 mouse fibroblast cells, the less helical p27 variants were less effective in causing cell cycle arrest relative to the wild-type p27. Our results indicate that the nascent helicity of sub-domain LH plays a key role mediating the biological function of p27. PMID:23071750

SWI/SNF Associates with Nascent Pre-mRNPs and Regulates Alternative Pre-mRNA Processing

PubMed Central

Tyagi, Anu; Ryme, Jessica; Brodin, David; Östlund Farrants, Ann Kristin; Visa, Neus

2009-01-01

The SWI/SNF chromatin remodeling complexes regulate the transcription of many genes by remodeling nucleosomes at promoter regions. In Drosophila, SWI/SNF plays an important role in ecdysone-dependent transcription regulation. Studies in human cells suggest that Brahma (Brm), the ATPase subunit of SWI/SNF, regulates alternative pre-mRNA splicing by modulating transcription elongation rates. We describe, here, experiments that study the association of Brm with transcribed genes in Chironomus tentans and Drosophila melanogaster, the purpose of which was to further elucidate the mechanisms by which Brm regulates pre-mRNA processing. We show that Brm becomes incorporated into nascent Balbiani ring pre-mRNPs co-transcriptionally and that the human Brm and Brg1 proteins are associated with RNPs. We have analyzed the expression profiles of D. melanogaster S2 cells in which the levels of individual SWI/SNF subunits have been reduced by RNA interference, and we show that depletion of SWI/SNF core subunits changes the relative abundance of alternative transcripts from a subset of genes. This observation, and the fact that a fraction of Brm is not associated with chromatin but with nascent pre-mRNPs, suggest that SWI/SNF affects pre-mRNA processing by acting at the RNA level. Ontology enrichment tests indicate that the genes that are regulated post-transcriptionally by SWI/SNF are mostly enzymes and transcription factors that regulate postembryonic developmental processes. In summary, the data suggest that SWI/SNF becomes incorporated into nascent pre-mRNPs and acts post-transcriptionally to regulate not only the amount of mRNA synthesized from a given promoter but also the type of alternative transcript produced. PMID:19424417

Pharyngeal sense organs drive robust sugar consumption in Drosophila

PubMed Central

LeDue, Emily E; Chen, Yu-Chieh; Jung, Aera Y; Dahanukar, Anupama; Gordon, Michael D

2015-01-01

The fly pharyngeal sense organs lie at the transition between external and internal nutrient sensing mechanisms. Here, we investigate the function of pharyngeal sweet gustatory receptor neurons (GRNs), demonstrating that they express a subset of the nine previously identified sweet receptors and respond to stimulation with a panel of sweet compounds. We show that pox-neuro (poxn) mutants lacking taste function in the legs and labial palps have intact pharyngeal sweet taste, which is both necessary and sufficient to drive preferred consumption of sweet compounds by prolonging ingestion. Moreover, flies putatively lacking all sweet taste show little preference for nutritive or non-nutritive sugars in a short-term feeding assay. Together, our data demonstrate that pharyngeal sense organs play an important role in directing sustained consumption of sweet compounds, and suggest that post-ingestive sugar sensing does not effectively drive food choice in a simple short-term feeding paradigm. PMID:25807033

Size matters: the interplay between sensing and size in aquatic environments

NASA Astrophysics Data System (ADS)

Wadhwa, Navish; Martens, Erik A.; Lindemann, Christian; Jacobsen, Nis S.; Andersen, Ken H.; Visser, Andre

2015-11-01

Sensing the presence or absence of other organisms in the surroundings is critical for the survival of any aquatic organism. This is achieved via the use of various sensory modes such as chemosensing, mechanosensing, vision, hearing, and echolocation. We ask how the size of an organism determines what sensory modes are available to it while others are not. We investigate this by examining the physical laws governing signal generation, transmission, and reception, together with the limits set by physiology. Hydrodynamics plays an important role in sensing; in particular chemosensing and mechanosensing are constrained by the physics of fluid motion at various scales. Through our analysis, we find a hierarchy of sensing modes determined by body size. We theoretically predict the body size limits for various sensory modes, which align well with size ranges found in the literature. Our analysis of all ocean life, from unicellular organisms to whales, demonstrates how body size determines available sensing modes, and thereby acts as a major structuring factor of aquatic life. The Centre for Ocean Life is a VKR center of excellence supported by the Villum Foundation.

The selective autophagy receptor p62 forms a flexible filamentous helical scaffold.

PubMed

Ciuffa, Rodolfo; Lamark, Trond; Tarafder, Abul K; Guesdon, Audrey; Rybina, Sofia; Hagen, Wim J H; Johansen, Terje; Sachse, Carsten

2015-05-05

The scaffold protein p62/SQSTM1 is involved in protein turnover and signaling and is commonly found in dense protein bodies in eukaryotic cells. In autophagy, p62 acts as a selective autophagy receptor that recognizes and shuttles ubiquitinated proteins to the autophagosome for degradation. The structural organization of p62 in cellular bodies and the interplay of these assemblies with ubiquitin and the autophagic marker LC3 remain to be elucidated. Here, we present a cryo-EM structural analysis of p62. Together with structures of assemblies from the PB1 domain, we show that p62 is organized in flexible polymers with the PB1 domain constituting a helical scaffold. Filamentous p62 is capable of binding LC3 and addition of long ubiquitin chains induces disassembly and shortening of filaments. These studies explain how p62 assemblies provide a large molecular scaffold for the nascent autophagosome and reveal how they can bind ubiquitinated cargo. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Nogo-B Receptor stabilizes Niemann-Pick Type C2 protein and regulates intracellular cholesterol trafficking

PubMed Central

Harrison, Kenneth D.; Miao, Robert Qing; Fernandez-Hernándo, Carlos; Suárez, Yajaira; Dávalos, Alberto; Sessa, William C.

2009-01-01

Summary The Nogo-B Receptor (NgBR) is a recently identified receptor for the N-terminus of Reticulon 4B/Nogo-B. Other than its role in binding Nogo-B, little is known about the biology of NgBR. To elucidate a basic cellular role for NgBR, we performed a yeast-2-hybrid screen for interacting proteins using the C-terminal domain as bait and identified Niemann-Pick Type C2 protein (NPC2) as an NgBR-interacting protein. NPC2 protein levels are increased in the presence of NgBR and NgBR enhances NPC2 protein stability. NgBR localizes primarily to the endoplasmic reticulum (ER), and regulates the stability of nascent NPC2. RNAi-mediated disruption of NgBR or genetic deficiency in NgBR leads to a decrease in NPC2 levels, increased intracellular cholesterol accumulation and a loss of sterol sensing, all hallmarks of an NPC2 mutation. These data identify NgBR as an NPC2-interacting protein and provide evidence of a role for NgBR in intracellular cholesterol trafficking. PMID:19723497

The Impact of Organic Surfactants and Coatings in Regulating Heterogeneous N2O5 Reaction Kinetics on Nascent Marine Aerosol

NASA Astrophysics Data System (ADS)

Ryder, O. S.; Campbell, N.; Schill, S.; Pöhlker, C.; Andreae, M. O.; Bertram, T. H.

2013-12-01

The heterogeneous reaction of N2O5 on aerosol particles impacts both the lifetime of nitrogen oxides, and the production rate of chlorine radicals following the activation of particulate chloride to nitryl chloride in both coastal and continental regions. The extent to which N2O5 reactivity impacts oxidant loadings depends on the heterogeneous reaction rate, which is directly influenced by aerosol chemical composition, morphology, and physical phase state. In the marine environment, the chemical composition of aerosol particles produced via wave induced bubble bursting mechanisms varies greatly and is influenced by the composition of the sea surface microlayer . Here, we present direct measurements of N2O5 reaction kinetics determined using model sea-spray particles generated in a novel Marine Aerosol Reference Tank (MART), capable of generating accurate mimics of ambient sea spray particles, in a lab environment. Here, a synthetic sea salt ocean was sequentially doped with organic molecules chosen to mimic organic species present in natural sea water over the course of a phytoplankton bloom in the open ocean. These included sterol, galactose, lippolysaccharide, BSA protein, and 1,2-dipalmitoyl-sn-glycero-3-phosphate (DPPA). These observations permit discussion of the role of marine organics in regulating heterogeneous reaction kinetics, as well a re-evaluation of potential organic lab proxies for marine organics.

Use of remote sensing for land use policy formulation

NASA Technical Reports Server (NTRS)

Boylan, M.; Vlasin, R. D.

1976-01-01

Uses of remote sensing imagery were investigated based on exploring and evaluating the capability and reliability of all kinds of imagery for improving decision making on issues of land use at all scales of governmental administration. Emphasis was placed on applications to solving immediate problems confronting public agencies and private organizations. Resulting applications of remote sensing use by public agencies, public organizations, and related private corporations are described.

Binding of transcription termination protein nun to nascent RNA and template DNA.

PubMed

Watnick, R S; Gottesman, M E

1999-12-17

The amino-terminal arginine-rich motif of coliphage HK022 Nun binds phage lambda nascent transcript, whereas the carboxyl-terminal domain interacts with RNA polymerase (RNAP) and blocks transcription elongation. RNA binding is inhibited by zinc (Zn2+) and stimulated by Escherichia coli NusA. To study these interactions, the Nun carboxyl terminus was extended by a cysteine residue conjugated to a photochemical cross-linker. The carboxyl terminus contacted NusA and made Zn2+-dependent intramolecular contacts. When Nun was added to a paused transcription elongation complex, it cross-linked to the DNA template. Nun may arrest transcription by anchoring RNAP to DNA.

Protecting the proteome: Eukaryotic cotranslational quality control pathways

PubMed Central

2014-01-01

The correct decoding of messenger RNAs (mRNAs) into proteins is an essential cellular task. The translational process is monitored by several quality control (QC) mechanisms that recognize defective translation complexes in which ribosomes are stalled on substrate mRNAs. Stalled translation complexes occur when defects in the mRNA template, the translation machinery, or the nascent polypeptide arrest the ribosome during translation elongation or termination. These QC events promote the disassembly of the stalled translation complex and the recycling and/or degradation of the individual mRNA, ribosomal, and/or nascent polypeptide components, thereby clearing the cell of improper translation products and defective components of the translation machinery. PMID:24535822

Selective ribosome profiling as a tool to study the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes

PubMed Central

Becker, Annemarie H.; Oh, Eugene; Weissman, Jonathan S.; Kramer, Günter; Bukau, Bernd

2014-01-01

A plethora of factors is involved in the maturation of newly synthesized proteins, including chaperones, membrane targeting factors, and enzymes. Many factors act cotranslationally through association with ribosome-nascent chain complexes (RNCs), but their target specificities and modes of action remain poorly understood. We developed selective ribosome profiling (SeRP) to identify substrate pools and points of RNC engagement of these factors. SeRP is based on sequencing mRNA fragments covered by translating ribosomes (general ribosome profiling, RP), combined with a procedure to selectively isolate RNCs whose nascent polypeptides are associated with the factor of interest. Factor–RNC interactions are stabilized by crosslinking, the resulting factor–RNC adducts are then nuclease-treated to generate monosomes, and affinity-purified. The ribosome-extracted mRNA footprints are converted to DNA libraries for deep sequencing. The protocol is specified for general RP and SeRP in bacteria. It was first applied to the chaperone trigger factor and is readily adaptable to other cotranslationally acting factors, including eukaryotic factors. Factor–RNC purification and sequencing library preparation takes 7–8 days, sequencing and data analysis can be completed in 5–6 days. PMID:24136347

Structural Basis for Recognition and Sequestration of UUUOH 3 ' Temini of Nascent RNA Polymerase III Transcripts by La, a Rheumatic Disease Autoantigen

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

Teplova,M.; Yuan, Y.; Phan, A.

2006-01-01

The nuclear phosphoprotein La was identified as an autoantigen in patients with systemic lupus erythematosus and Sjogren's syndrome. La binds to and protects the UUUOH 3' terminii of nascent RNA polymerase III transcripts from exonuclease digestion. We report the 1.85 Angstroms crystal structure of the N-terminal domain of human La, consisting of La and RRM1 motifs, bound to r(U1-G2-C3-U4-G5-U6-U7-U8-U9OH). The U7-U8-U9OH 3' end, in a splayed-apart orientation, is sequestered within a basic and aromatic amino acid-lined cleft between the La and RRM1 motifs. The specificity-determining U8 residue bridges both motifs, in part through unprecedented targeting of the {beta} sheet edge,more » rather than the anticipated face, of the RRM1 motif. Our structural observations, supported by mutation studies of both La and RNA components, illustrate the principles behind RNA sequestration by a rheumatic disease autoantigen, whereby the UUUOH 3' ends of nascent RNA transcripts are protected during downstream processing and maturation events.« less

The Exosome Associates Cotranscriptionally with the Nascent Pre-mRNP through Interactions with Heterogeneous Nuclear Ribonucleoproteins

PubMed Central

Hessle, Viktoria; Björk, Petra; Sokolowski, Marcus; de Valdivia, Ernesto González; Silverstein, Rebecca; Artemenko, Konstantin; Tyagi, Anu; Maddalo, Gianluca; Ilag, Leopold; Helbig, Roger; Zubarev, Roman A.

2009-01-01

Eukaryotic cells have evolved quality control mechanisms to degrade aberrant mRNA molecules and prevent the synthesis of defective proteins that could be deleterious for the cell. The exosome, a protein complex with ribonuclease activity, is a key player in quality control. An early quality checkpoint takes place cotranscriptionally but little is known about the molecular mechanisms by which the exosome is recruited to the transcribed genes. Here we study the core exosome subunit Rrp4 in two insect model systems, Chironomus and Drosophila. We show that a significant fraction of Rrp4 is associated with the nascent pre-mRNPs and that a specific mRNA-binding protein, Hrp59/hnRNP M, interacts in vivo with multiple exosome subunits. Depletion of Hrp59 by RNA interference reduces the levels of Rrp4 at transcription sites, which suggests that Hrp59 is needed for the exosome to stably interact with nascent pre-mRNPs. Our results lead to a revised mechanistic model for cotranscriptional quality control in which the exosome is constantly recruited to newly synthesized RNAs through direct interactions with specific hnRNP proteins. PMID:19494042

Focal Adhesion Induction at the Tip of a Functionalized Nanoelectrode

PubMed Central

Fuentes, Daniela E.; Bae, Chilman; Butler, Peter J.

2012-01-01

Cells dynamically interact with their physical micro-environment through the assembly of nascent focal contacts and focal adhesions. The dynamics and mechanics of these contact points are controlled by transmembrane integrins and an array of intracellular adaptor proteins. In order to study the mechanics and dynamics of focal adhesion assembly, we have developed a technique for the timed induction of a nascent focal adhesion. Bovine aortic endothelial cells were approached at the apical surface by a nanoelectrode whose position was controlled with a resolution of 10s of nanometers using changes in electrode current to monitor distance from the cell surface. Since this probe was functionalized with fibronectin, a focal contact formed at the contact location. Nascent focal adhesion assembly was confirmed using time-lapse confocal fluorescent images of red fluorescent protein (RFP) – tagged talin, an adapter protein that binds to activated integrins. Binding to the cell was verified by noting a lack of change of electrode current upon retraction of the electrode. This study demonstrates that functionalized nanoelectrodes can enable precisely-timed induction and 3-D mechanical manipulation of focal adhesions and the assay of the detailed molecular kinetics of their assembly. PMID:22247742

Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen.

PubMed

Teplova, Marianna; Yuan, Yu-Ren; Phan, Anh Tuân; Malinina, Lucy; Ilin, Serge; Teplov, Alexei; Patel, Dinshaw J

2006-01-06

The nuclear phosphoprotein La was identified as an autoantigen in patients with systemic lupus erythematosus and Sjogren's syndrome. La binds to and protects the UUU(OH) 3' terminii of nascent RNA polymerase III transcripts from exonuclease digestion. We report the 1.85 angstroms crystal structure of the N-terminal domain of human La, consisting of La and RRM1 motifs, bound to r(U1-G2-C3-U4-G5-U6-U7-U8-U9OH). The U7-U8-U9OH 3' end, in a splayed-apart orientation, is sequestered within a basic and aromatic amino acid-lined cleft between the La and RRM1 motifs. The specificity-determining U8 residue bridges both motifs, in part through unprecedented targeting of the beta sheet edge, rather than the anticipated face, of the RRM1 motif. Our structural observations, supported by mutation studies of both La and RNA components, illustrate the principles behind RNA sequestration by a rheumatic disease autoantigen, whereby the UUU(OH) 3' ends of nascent RNA transcripts are protected during downstream processing and maturation events.

Mechanical Modulation of Nascent Stem Cell Lineage Commitment in Tissue Engineering Scaffolds

PubMed Central

Song, Min Jae; Dean, David; Tate, Melissa L. Knothe

2013-01-01

Taking inspiration from tissue morphogenesis in utero, this study tests the concept of using tissue engineering scaffolds as delivery devices to modulate emergent structure-function relationships at early stages of tissue genesis. We report on the use of a combined computational fluid dynamics (CFD) modeling, advanced manufacturing methods, and experimental fluid mechanics (micro-piv and strain mapping) for the prospective design of tissue engineering scaffold geometries that deliver spatially resolved mechanical cues to cells seeded within. When subjected to a constant magnitude global flow regime, the local scaffold geometry dictates the magnitudes of mechanical stresses and strains experienced by a given cell, and in a spatially resolved fashion, similar to patterning during morphogenesis. In addition, early markers of mesenchymal stem cell lineage commitment relate significantly to the local mechanical environment of the cell. Finally, by plotting the range of stress-strain states for all data corresponding to nascent cell lineage commitment (95% CI), we begin to “map the mechanome”, defining stress-strain states most conducive to targeted cell fates. In sum, we provide a library of reference mechanical cues that can be delivered to cells seeded on tissue engineering scaffolds to guide target tissue phenotypes in a temporally and spatially resolved manner. Knowledge of these effects allows for prospective scaffold design optimization using virtual models prior to prototyping and clinical implementation. Finally, this approach enables the development of next generation scaffolds cum delivery devices for genesis of complex tissues with heterogenous properties, e.g., organs, joints or interface tissues such as growth plates. PMID:23660249

Mechanical modulation of nascent stem cell lineage commitment in tissue engineering scaffolds.

PubMed

Song, Min Jae; Dean, David; Knothe Tate, Melissa L

2013-07-01

Taking inspiration from tissue morphogenesis in utero, this study tests the concept of using tissue engineering scaffolds as delivery devices to modulate emergent structure-function relationships at early stages of tissue genesis. We report on the use of a combined computational fluid dynamics (CFD) modeling, advanced manufacturing methods, and experimental fluid mechanics (micro-piv and strain mapping) for the prospective design of tissue engineering scaffold geometries that deliver spatially resolved mechanical cues to stem cells seeded within. When subjected to a constant magnitude global flow regime, the local scaffold geometry dictates the magnitudes of mechanical stresses and strains experienced by a given cell, and in a spatially resolved fashion, similar to patterning during morphogenesis. In addition, early markers of mesenchymal stem cell lineage commitment relate significantly to the local mechanical environment of the cell. Finally, by plotting the range of stress-strain states for all data corresponding to nascent cell lineage commitment (95% CI), we begin to "map the mechanome", defining stress-strain states most conducive to targeted cell fates. In sum, we provide a library of reference mechanical cues that can be delivered to cells seeded on tissue engineering scaffolds to guide target tissue phenotypes in a temporally and spatially resolved manner. Knowledge of these effects allows for prospective scaffold design optimization using virtual models prior to prototyping and clinical implementation. Finally, this approach enables the development of next generation scaffolds cum delivery devices for genesis of complex tissues with heterogenous properties, e.g., organs, joints or interface tissues such as growth plates. Copyright © 2013 Elsevier Ltd. All rights reserved.

Secretion of prebeta HDL increases with the suppression of cholesteryl ester transfer protein in Hep G2 cells.

PubMed

Sawada, S; Sugano, M; Makino, N; Okamoto, H; Tsuchida, K

1999-10-01

Prebeta HDL are small, protein rich lipoproteins that are predominantly composed of apo A-I, without apo A-II. Prebeta HDL are secreted from the liver as nascent HDL and/or are produced in the incubated plasma by cholesteryl ester transfer protein (CETP). However, the role of CETP in the secretion of HDL from the liver has yet to be determined. In the present study, we examined the effect of the suppression of hepatic CETP by antisense oligodeoxynucleotides (ODNs) against CETP targeted to the liver on the secretion of apo A-I using a Hep G2 cell culture. The ODNs against CETP were coupled to asialoglycoprotein (ASOR) carrier molecules, which serve as an important method for the regulation of liver gene expression. Hep G2 cells were cultured in DMEM supplemented with 10 FBS. After 2 days, the medium was changed to DMEM with EGF and the cells were divided into three groups. The control group received saline, while the sense group was mixed with the sense ODNs complex and the antisense group was mixed with the antisense ODNs complex, respectively, for 2 days. Both the hepatic CETP mRNA and the CETP mass in the medium in the antisense group decreased significantly more than in the sense and the control groups (CETP mass: 1.697 + /- 0.410 ng/mg cell protein vs. 2.367 + /- 0.22 and 2.360 + /- 0.139, n = 3 in each determination). In contrast, both the hepatic apo A-I mRNA and the apo A-I mass in the medium in the antisense group were significantly higher than those in the sense and the control groups (apo A-I mass; 1.877 + /- 0.215 micro/mg cell protein vs. 1.213 + /- 0.282 and 1.097 + /- 0.144, n = 3 in each determination). The increase in apo A-I was mainly due to the increase in prebeta apo A-I. These findings may partly explain why HDL and apo A-I increase in patients with CETP deficiency, while also indicating the possibility that the original level of prebeta HDL is sufficient in such patients.

THE EPA REMOTE SENSING ARCHIVE

EPA Science Inventory

What would you do if you were faced with organizing 30 years of remote sensing projects that had been haphazardly stored at two separate locations for years then combined? The EPA Remote Sensing Archive, currently located in Las Vegas, Nevada. contains the remote sensing data and...

Liquid-Solid Dual-Gate Organic Transistors with Tunable Threshold Voltage for Cell Sensing.

PubMed

Zhang, Yu; Li, Jun; Li, Rui; Sbircea, Dan-Tiberiu; Giovannitti, Alexander; Xu, Junling; Xu, Huihua; Zhou, Guodong; Bian, Liming; McCulloch, Iain; Zhao, Ni

2017-11-08

Liquid electrolyte-gated organic field effect transistors and organic electrochemical transistors have recently emerged as powerful technology platforms for sensing and simulation of living cells and organisms. For such applications, the transistors are operated at a gate voltage around or below 0.3 V because prolonged application of a higher voltage bias can lead to membrane rupturing and cell death. This constraint often prevents the operation of the transistors at their maximum transconductance or most sensitive regime. Here, we exploit a solid-liquid dual-gate organic transistor structure, where the threshold voltage of the liquid-gated conduction channel is controlled by an additional gate that is separated from the channel by a metal-oxide gate dielectric. With this design, the threshold voltage of the "sensing channel" can be linearly tuned in a voltage window exceeding 0.4 V. We have demonstrated that the dual-gate structure enables a much better sensor response to the detachment of human mesenchymal stem cells. In general, the capability of tuning the optimal sensing bias will not only improve the device performance but also broaden the material selection for cell-based organic bioelectronics.

Volatile organic compound sensor system

DOEpatents

Schabron, John F [Laramie, WY; Rovani, Jr., Joseph F.; Bomstad, Theresa M [Laramie, WY; Sorini-Wong, Susan S [Laramie, WY

2009-02-10

Generally, this invention relates to the development of field monitoring methodology for new substances and sensing chemical warfare agents (CWAs) and terrorist substances. It also relates to a portable test kit which may be utilized to measure concentrations of halogenated volatile organic compounds (VOCs) in the field. Specifically it relates to systems for reliably field sensing the potential presence of such items while also distinguishing them from other elements potentially present. It also relates to overall systems and processes for sensing, reacting, and responding to an indicated presence of such substance, including modifications of existing halogenated sensors and arrayed sensing systems and methods.

Volatile organic compound sensor system

DOEpatents

Schabron, John F.; Rovani, Jr., Joseph F.; Bomstad, Theresa M.; Sorini-Wong, Susan S.; Wong, Gregory K.

2011-03-01

Generally, this invention relates to the development of field monitoring methodology for new substances and sensing chemical warfare agents (CWAs) and terrorist substances. It also relates to a portable test kit which may be utilized to measure concentrations of halogenated volatile organic compounds (VOCs) in the field. Specifically it relates to systems for reliably field sensing the potential presence of such items while also distinguishing them from other elements potentially present. It also relates to overall systems and processes for sensing, reacting, and responding to an indicated presence of such substance, including modifications of existing halogenated sensors and arrayed sensing systems and methods.

Sensing and capture of toxic and hazardous gases and vapors by metal-organic frameworks.

PubMed

Wang, Hao; Lustig, William P; Li, Jing

2018-03-13

Toxic and hazardous chemical species are ubiquitous, predominantly emitted by anthropogenic activities, and pose serious risks to human health and the environment. Thus, the sensing and subsequent capture of these chemicals, especially in the gas or vapor phase, are of extreme importance. To this end, metal-organic frameworks have attracted significant interest, as their high porosity and wide tunability make them ideal for both applications. These tailorable framework materials are particularly promising for the specific sensing and capture of targeted chemicals, as they can be designed to fit a diverse range of required conditions. This review will discuss the advantages of metal-organic frameworks in the sensing and capture of harmful gases and vapors, as well as principles and strategies guiding the design of these materials. Recent progress in the luminescent detection of aromatic and aliphatic volatile organic compounds, toxic gases, and chemical warfare agents will be summarized, and the adsorptive removal of fluorocarbons/chlorofluorocarbons, volatile radioactive species, toxic industrial gases and chemical warfare agents will be discussed.

COGNITRON THEORY,

DTIC Science & Technology

ARTIFICIAL INTELLIGENCE , THEORY), NERVE CELLS, SIMULATION, SENSE ORGANS, SENSES(PHYSIOLOGY), CONDITIONED RESPONSE, MATRICES(MATHEMATICS), MAPPING (TRANSFORMATIONS), MATHEMATICAL MODELS, FEEDBACK, BIONICS

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

PubMed Central

Fang, Bin; Everett, Logan J.; Jager, Jennifer; Briggs, Erika; Armour, Sean M.; Feng, Dan; Roy, Ankur; Gerhart-Hines, Zachary; Sun, Zheng; Lazar, Mitchell A.

2014-01-01

SUMMARY Mammalian transcriptomes display complex circadian rhythms with multiple phases of gene expression that cannot be accounted for by current models of the molecular clock. We have determined the underlying mechanisms by measuring nascent RNA transcription around the clock in mouse liver. Unbiased examination of eRNAs that cluster in specific circadian phases identified functional enhancers driven by distinct transcription factors (TFs). We further identify on a global scale the components of the TF cistromes that function to orchestrate circadian gene expression. Integrated genomic analyses also revealed novel mechanisms by which a single circadian factor controls opposing transcriptional phases. These findings shed new light on the diversity and specificity of TF function in the generation of multiple phases of circadian gene transcription in a mammalian organ. PMID:25416951

Circadian enhancers coordinate multiple phases of rhythmic gene transcription in vivo.

PubMed

Fang, Bin; Everett, Logan J; Jager, Jennifer; Briggs, Erika; Armour, Sean M; Feng, Dan; Roy, Ankur; Gerhart-Hines, Zachary; Sun, Zheng; Lazar, Mitchell A

2014-11-20

Mammalian transcriptomes display complex circadian rhythms with multiple phases of gene expression that cannot be accounted for by current models of the molecular clock. We have determined the underlying mechanisms by measuring nascent RNA transcription around the clock in mouse liver. Unbiased examination of enhancer RNAs (eRNAs) that cluster in specific circadian phases identified functional enhancers driven by distinct transcription factors (TFs). We further identify on a global scale the components of the TF cistromes that function to orchestrate circadian gene expression. Integrated genomic analyses also revealed mechanisms by which a single circadian factor controls opposing transcriptional phases. These findings shed light on the diversity and specificity of TF function in the generation of multiple phases of circadian gene transcription in a mammalian organ.

DNA nanotechnology for nanophotonic applications.

PubMed

Samanta, Anirban; Banerjee, Saswata; Liu, Yan

2015-02-14

DNA nanotechnology has touched the epitome of miniaturization by integrating various nanometer size particles with nanometer precision. This enticing bottom-up approach has employed small DNA tiles, large multi-dimensional polymeric structures or more recently DNA origami to organize nanoparticles of different inorganic materials, small organic molecules or macro-biomolecules like proteins, and RNAs into fascinating patterns that are difficult to achieve by other conventional methods. Here, we are especially interested in the self-assembly of nanomaterials that are potentially attractive elements in the burgeoning field of nanophotonics. These materials include plasmonic nanoparticles, quantum dots, fluorescent organic dyes, etc. DNA based self-assembly allows excellent control over distance, orientation and stoichiometry of these nano-elements that helps to engineer intelligent systems that can potentially pave the path for future technology. Many outstanding structures have been fabricated that are capable of fine tuning optical properties, such as fluorescence intensity and lifetime modulation, enhancement of Raman scattering and emergence of circular dichroism responses. Within the limited scope of this review we have tried to give a glimpse of the development of this still nascent but highly promising field to its current status as well as the existing challenges before us.

Nanoscale Metal Oxide Semiconductors for Gas Sensing

NASA Technical Reports Server (NTRS)

Hunter, Gary W.; Evans, Laura; Xu, Jennifer C.; VanderWal, Randy L.; Berger, Gordon M.; Kulis, Michael J.

2011-01-01

A report describes the fabrication and testing of nanoscale metal oxide semiconductors (MOSs) for gas and chemical sensing. This document examines the relationship between processing approaches and resulting sensor behavior. This is a core question related to a range of applications of nanotechnology and a number of different synthesis methods are discussed: thermal evaporation- condensation (TEC), controlled oxidation, and electrospinning. Advantages and limitations of each technique are listed, providing a processing overview to developers of nanotechnology- based systems. The results of a significant amount of testing and comparison are also described. A comparison is made between SnO2, ZnO, and TiO2 single-crystal nanowires and SnO2 polycrystalline nanofibers for gas sensing. The TECsynthesized single-crystal nanowires offer uniform crystal surfaces, resistance to sintering, and their synthesis may be done apart from the substrate. The TECproduced nanowire response is very low, even at the operating temperature of 200 C. In contrast, the electrospun polycrystalline nanofiber response is high, suggesting that junction potentials are superior to a continuous surface depletion layer as a transduction mechanism for chemisorption. Using a catalyst deposited upon the surface in the form of nanoparticles yields dramatic gains in sensitivity for both nanostructured, one-dimensional forms. For the nanowire materials, the response magnitude and response rate uniformly increase with increasing operating temperature. Such changes are interpreted in terms of accelerated surface diffusional processes, yielding greater access to chemisorbed oxygen species and faster dissociative chemisorption, respectively. Regardless of operating temperature, sensitivity of the nanofibers is a factor of 10 to 100 greater than that of nanowires with the same catalyst for the same test condition. In summary, nanostructure appears critical to governing the reactivity, as measured by electrical resistance of these SnO2 nanomaterials towards reducing gases. With regard to the sensitivity of the different nascent nanostructures, the electrospun nanofibers appear preferable

Competition between Vibrio fischeri strains during initiation and maintenance of a light organ symbiosis.

PubMed

Lee, K H; Ruby, E G

1994-04-01

Colonization of the light-emitting organ of the Hawaiian squid Euprymna scolopes is initiated when the nascent organ of a newly hatched squid becomes inoculated with Vibrio fischeri cells present in the ambient seawater. Although they are induced for luminescence in the light organ, these symbiotic strains are characteristically non-visibly luminous (NVL) when grown in laboratory culture. The more typical visibly luminous (VL) type of V. fischeri co-occurs in Hawaiian seawater with these NVL strains; thus, two phenotypically distinct groups of this species potentially have access to the symbiotic niche, yet only the NVL ones are found there. In laboratory inoculation experiments, VL strains, when presented in pure culture, showed the same capability for colonizing the light organ as NVL strains. However, in experiments with mixed cultures composed of both VL and NVL strains, the VL ones were unable to compete with the NVL ones and did not persist within the light organ as the symbiosis became established. In addition, NVL strains entered light organs that had already been colonized by VL strains and displaced them. The mechanism underlying the symbiotic competitiveness exhibited by NVL strains remains unknown; however, it does not appear to be due to a higher potential for siderophore activity. While a difference in luminescence phenotype between VL and NVL strains in culture is not likely to be significant in the symbiosis, it has helped identify two distinct groups of V. fischeri that express different colonization capabilities in the squid light organ. This competitive difference provides a useful indication of important traits in light organ colonization.

Competition between Vibrio fischeri strains during initiation and maintenance of a light organ symbiosis.

PubMed Central

Lee, K H; Ruby, E G

1994-01-01

Colonization of the light-emitting organ of the Hawaiian squid Euprymna scolopes is initiated when the nascent organ of a newly hatched squid becomes inoculated with Vibrio fischeri cells present in the ambient seawater. Although they are induced for luminescence in the light organ, these symbiotic strains are characteristically non-visibly luminous (NVL) when grown in laboratory culture. The more typical visibly luminous (VL) type of V. fischeri co-occurs in Hawaiian seawater with these NVL strains; thus, two phenotypically distinct groups of this species potentially have access to the symbiotic niche, yet only the NVL ones are found there. In laboratory inoculation experiments, VL strains, when presented in pure culture, showed the same capability for colonizing the light organ as NVL strains. However, in experiments with mixed cultures composed of both VL and NVL strains, the VL ones were unable to compete with the NVL ones and did not persist within the light organ as the symbiosis became established. In addition, NVL strains entered light organs that had already been colonized by VL strains and displaced them. The mechanism underlying the symbiotic competitiveness exhibited by NVL strains remains unknown; however, it does not appear to be due to a higher potential for siderophore activity. While a difference in luminescence phenotype between VL and NVL strains in culture is not likely to be significant in the symbiosis, it has helped identify two distinct groups of V. fischeri that express different colonization capabilities in the squid light organ. This competitive difference provides a useful indication of important traits in light organ colonization. PMID:8144466

Hybrid organic semiconductor lasers for bio-molecular sensing.

PubMed

Haughey, Anne-Marie; Foucher, Caroline; Guilhabert, Benoit; Kanibolotsky, Alexander L; Skabara, Peter J; Burley, Glenn; Dawson, Martin D; Laurand, Nicolas

2014-01-01

Bio-functionalised luminescent organic semiconductors are attractive for biophotonics because they can act as efficient laser materials while simultaneously interacting with molecules. In this paper, we present and discuss a laser biosensor platform that utilises a gain layer made of such an organic semiconductor material. The simple structure of the sensor and its operation principle are described. Nanolayer detection is shown experimentally and analysed theoretically in order to assess the potential and the limits of the biosensor. The advantage conferred by the organic semiconductor is explained, and comparisons to laser sensors using alternative dye-doped materials are made. Specific biomolecular sensing is demonstrated, and routes to functionalisation with nucleic acid probes, and future developments opened up by this achievement, are highlighted. Finally, attractive formats for sensing applications are mentioned, as well as colloidal quantum dots, which in the future could be used in conjunction with organic semiconductors.

SOIL GAS SENSING FOR DETECTION AND MAPPING OF VOLATILE ORGANICS

EPA Science Inventory

The document is an attempt at compiling all pertinent information on the current state of the art of soil gas sensing as it relates to the detection of subsurface organic contaminants. It is hoped that such a document will better assist all those individuals who are faced with as...

Protein folding on the ribosome studied using NMR spectroscopy

PubMed Central

Waudby, Christopher A.; Launay, Hélène; Cabrita, Lisa D.; Christodoulou, John

2013-01-01

NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome–nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity. PMID:24083462

Smarcal1-Mediated Fork Reversal Triggers Mre11-Dependent Degradation of Nascent DNA in the Absence of Brca2 and Stable Rad51 Nucleofilaments.

PubMed

Kolinjivadi, Arun Mouli; Sannino, Vincenzo; De Antoni, Anna; Zadorozhny, Karina; Kilkenny, Mairi; Técher, Hervé; Baldi, Giorgio; Shen, Rong; Ciccia, Alberto; Pellegrini, Luca; Krejci, Lumir; Costanzo, Vincenzo

2017-09-07

Brca2 deficiency causes Mre11-dependent degradation of nascent DNA at stalled forks, leading to cell lethality. To understand the molecular mechanisms underlying this process, we isolated Xenopus laevis Brca2. We demonstrated that Brca2 protein prevents single-stranded DNA gap accumulation at replication fork junctions and behind them by promoting Rad51 binding to replicating DNA. Without Brca2, forks with persistent gaps are converted by Smarcal1 into reversed forks, triggering extensive Mre11-dependent nascent DNA degradation. Stable Rad51 nucleofilaments, but not RPA or Rad51 T131P mutant proteins, directly prevent Mre11-dependent DNA degradation. Mre11 inhibition instead promotes reversed fork accumulation in the absence of Brca2. Rad51 directly interacts with the Pol α N-terminal domain, promoting Pol α and δ binding to stalled replication forks. This interaction likely promotes replication fork restart and gap avoidance. These results indicate that Brca2 and Rad51 prevent formation of abnormal DNA replication intermediates, whose processing by Smarcal1 and Mre11 predisposes to genome instability. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Recent Developments in the Synthesis of Biomacromolecules and their Conjugates by Single Electron Transfer-Living Radical Polymerization.

PubMed

Lligadas, Gerard; Grama, Silvia; Percec, Virgil

2017-04-10

Single electron transfer-living radical polymerization (SET-LRP) represents a robust and versatile tool for the synthesis of vinyl polymers with well-defined topology and chain end functionality. The crucial step in SET-LRP is the disproportionation of the Cu(I)X generated by activation with Cu(0) wire, powder, or nascent Cu(0) generated in situ into nascent, extremely reactive Cu(0) atoms and nanoparticles and Cu(II)X 2 . Nascent Cu(0) activates the initiator and dormant chains via a homogeneous or heterogeneous outer-sphere single-electron transfer mechanism (SET-LRP). SET-LRP provides an ultrafast polymerization of a plethora of monomers (e.g., (meth)-acrylates, (meth)-acrylamides, styrene, and vinyl chloride) including hydrophobic and water insoluble to hydrophilic and water soluble. Some advantageous features of SET-LRP are (i) the use of Cu(0) wire or powder as readily available catalysts under mild reaction conditions, (ii) their excellent control over molecular weight evolution and distribution as well as polymer chain ends, (iii) their high functional group tolerance allowing the polymerization of commercial-grade monomers, and (iv) the limited purification required for the resulting polymers. In this Perspective, we highlight the recent advancements of SET-LRP in the synthesis of biomacromolecules and of their conjugates.

Light sensing in a photoresponsive, organic-based complementary inverter.

PubMed

Kim, Sungyoung; Lim, Taehoon; Sim, Kyoseung; Kim, Hyojoong; Choi, Youngill; Park, Keechan; Pyo, Seungmoon

2011-05-01

A photoresponsive organic complementary inverter was fabricated and its light sensing characteristics was studied. An organic circuit was fabricated by integrating p-channel pentacene and n-channel copper hexadecafluorophthalocyanine (F16CuPc) organic thin-film transistors (OTFTs) with a polymeric gate dielectric. The F16CuPc OTFT showed typical n-type characteristics and a strong photoresponse under illumination. Whereas under illumination, the pentacene OTFT showed a relatively weak photoresponse with typical p-type characteristics. The characteristics of the organic electro-optical circuit could be controlled by the incident light intensity, a gate bias, or both. The logic threshold (V(M), when V(IN) = V(OUT)) was reduced from 28.6 V without illumination to 19.9 V at 6.94 mW/cm². By using solely optical or a combination of optical and electrical pulse signals, light sensing was demonstrated in this type of organic circuit, suggesting that the circuit can be potentially used in various optoelectronic applications, including optical sensors, photodetectors and electro-optical transceivers.

The three faces of ecological fitness.

PubMed

Peacock, Kent A

2011-03-01

This paper argues that fitness is most usefully understood as those properties of organisms that are explanatory of survival in the broadest sense, not merely descriptive of reproductive success. Borrowing from Rosenberg and Bouchard (2009), fitness in this sense is ecological in that it is defined by the interactions between organisms and environments. There are three sorts of ecological fitness: the well-documented ability to compete, the ability to cooperate (as in mutualistic symbiosis), and a third sense of fitness that has received insufficient attention in evolutionary theory, the ability to construct. Following Lotka, it can be understood thermodynamically as the ability to maintain or enlarge the energy-circulating capacity of an ecosystem. An organism that does this could end with its gene frequency unchanged but its probability of survival enhanced since it would sustain or increase the total carrying capacity of its ecosystem. Photosynthesizers and other autotrophs are obvious candidates for organisms that are fit in the constructive sense, but any organisms, including heterotrophs, can exhibit constructive fitness if they have some mechanism for channeling external flows of free energy into their ecosystems. I will briefly examine the prospects for the human species in the light of these considerations. Copyright © 2010 Elsevier Ltd. All rights reserved.

Proximal sensing for soil carbon accounting

NASA Astrophysics Data System (ADS)

England, Jacqueline R.; Viscarra Rossel, Raphael A.

2018-05-01

Maintaining or increasing soil organic carbon (C) is vital for securing food production and for mitigating greenhouse gas (GHG) emissions, climate change, and land degradation. Some land management practices in cropping, grazing, horticultural, and mixed farming systems can be used to increase organic C in soil, but to assess their effectiveness, we need accurate and cost-efficient methods for measuring and monitoring the change. To determine the stock of organic C in soil, one requires measurements of soil organic C concentration, bulk density, and gravel content, but using conventional laboratory-based analytical methods is expensive. Our aim here is to review the current state of proximal sensing for the development of new soil C accounting methods for emissions reporting and in emissions reduction schemes. We evaluated sensing techniques in terms of their rapidity, cost, accuracy, safety, readiness, and their state of development. The most suitable method for measuring soil organic C concentrations appears to be visible-near-infrared (vis-NIR) spectroscopy and, for bulk density, active gamma-ray attenuation. Sensors for measuring gravel have not been developed, but an interim solution with rapid wet sieving and automated measurement appears useful. Field-deployable, multi-sensor systems are needed for cost-efficient soil C accounting. Proximal sensing can be used for soil organic C accounting, but the methods need to be standardized and procedural guidelines need to be developed to ensure proficient measurement and accurate reporting and verification. These are particularly important if the schemes use financial incentives for landholders to adopt management practices to sequester soil organic C. We list and discuss requirements for developing new soil C accounting methods based on proximal sensing, including requirements for recording, verification, and auditing.

Mechanistic, Mathematical Model to Predict the Dynamics of Tissue Genesis in Bone Defects via Mechanical Feedback and Mediation of Biochemical Factors

PubMed Central

Moore, Shannon R.; Saidel, Gerald M.; Knothe, Ulf; Knothe Tate, Melissa L.

2014-01-01

The link between mechanics and biology in the generation and the adaptation of bone has been well studied in context of skeletal development and fracture healing. Yet, the prediction of tissue genesis within - and the spatiotemporal healing of - postnatal defects, necessitates a quantitative evaluation of mechano-biological interactions using experimental and clinical parameters. To address this current gap in knowledge, this study aims to develop a mechanistic mathematical model of tissue genesis using bone morphogenetic protein (BMP) to represent of a class of factors that may coordinate bone healing. Specifically, we developed a mechanistic, mathematical model to predict the dynamics of tissue genesis by periosteal progenitor cells within a long bone defect surrounded by periosteum and stabilized via an intramedullary nail. The emergent material properties and mechanical environment associated with nascent tissue genesis influence the strain stimulus sensed by progenitor cells within the periosteum. Using a mechanical finite element model, periosteal surface strains are predicted as a function of emergent, nascent tissue properties. Strains are then input to a mechanistic mathematical model, where mechanical regulation of BMP-2 production mediates rates of cellular proliferation, differentiation and tissue production, to predict healing outcomes. A parametric approach enables the spatial and temporal prediction of endochondral tissue regeneration, assessed as areas of cartilage and mineralized bone, as functions of radial distance from the periosteum and time. Comparing model results to histological outcomes from two previous studies of periosteum-mediated bone regeneration in a common ovine model, it was shown that mechanistic models incorporating mechanical feedback successfully predict patterns (spatial) and trends (temporal) of bone tissue regeneration. The novel model framework presented here integrates a mechanistic feedback system based on the mechanosensitivity of periosteal progenitor cells, which allows for modeling and prediction of tissue regeneration on multiple length and time scales. Through combination of computational, physical and engineering science approaches, the model platform provides a means to test new hypotheses in silico and to elucidate conditions conducive to endogenous tissue genesis. Next generation models will serve to unravel intrinsic differences in bone genesis by endochondral and intramembranous mechanisms. PMID:24967742

Tumor-targeting Salmonella typhimurium A1-R Inhibits Osteosarcoma Angiogenesis in the In Vivo Gelfoam® Assay Visualized by Color-coded Imaging.

PubMed

Kiyuna, Tasuku; Tome, Yasunori; Uehara, Fuminari; Murakami, Takashi; Zhang, Yong; Zhao, Ming; Kanaya, Fuminori; Hoffman, Robert M

2018-01-01

We previously developed a color-coded imaging model that can quantify the length of nascent blood vessels using Gelfoam® implanted in nestin-driven green fluorescent protein (ND-GFP) nude mice. In this model, nascent blood vessels selectively express GFP. We also previously showed that osteosarcoma cells promote angiogenesis in this assay. We have also previously demonstrated the tumor-targeting bacteria Salmonella typhimurium A1-R (S. typhimurium A1-R) can inhibit or regress all tested tumor types in mouse models. The aim of the present study was to determine if S. typhimurium A1-R could inhibit osteosarcoma angiogenesis in the in vivo Gelfoam® color-coded imaging assay. Gelfoam® was implanted subcutaneously in ND-GFP nude mice. Skin flaps were made 7 days after implantation and 143B-RFP human osteosarcoma cells expressing red fluorescent protein (RFP) were injected into the implanted Gelfoam. After establishment of tumors in the Gelfoam®, control-group mice were treated with phosphate buffered saline via tail-vein injection (iv) and the experimental group was treated with S. typhimurium A1-R iv Skin flaps were made at day 7, 14, 21, and 28 after implantation of the Gelfoam® to allow imaging of vascularization in the Gelfoam® using a variable-magnification small-animal imaging system and confocal fluorescence microscopy. Nascent blood vessels expressing ND-GFP extended into the Gelfoam® over time in both groups. However, the extent of nascent blood-vessel growth was significantly inhibited by S. typhimurium A1-R treatment by day 28. The present results indicate S. typhimurium A1-R has potential for anti-angiogenic targeted therapy of osteosarcoma. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Mouse Mix gene is activated early during differentiation of ES and F9 stem cells and induces endoderm in frog embryos.

PubMed

Mohn, Deanna; Chen, Siming W; Dias, Dora Campos; Weinstein, Daniel C; Dyer, Michael A; Sahr, Kenneth; Ducker, Charles E; Zahradka, Elizabeth; Keller, Gordon; Zaret, Kenneth S; Gudas, Lorraine J; Baron, Margaret H

2003-03-01

In frog and zebrafish, the Mix/Bix family of paired type homeodomain proteins play key roles in specification and differentiation of mesendoderm. However, in mouse, only a single Mix gene (mMix) has been identified to date and its function is unknown. We have analyzed the expression of mouse Mix RNA and protein in embryos, embryoid bodies formed from embryonic stem cells and F9 teratocarcinoma cells, as well as several differentiated cell types. Expression in embryoid bodies in culture mirrors that in embryos, where Mix is transcribed transiently in primitive (visceral) endoderm (VE) and in nascent mesoderm. In F9 cells induced by retinoic acid to differentiate to VE, mMix is coordinately expressed with three other endodermal transcription factors, well before AFP, and its protein product is localized to the nucleus. In a subpopulation of nascent mesodermal cells from embryonic stem cell embryoid bodies, mMix is coexpressed with Brachyury. Intriguingly, mMix mRNA is detected in a population (T+Flk1+) of cells which may contain hemangioblasts, before the onset of hematopoiesis and activation of hematopoietic markers. In vitro and in vivo, mMix expression in nascent mesoderm is rapidly down-regulated and becomes undetectable in differentiated cell types. In the region of the developing gut, mMix expression is confined to the mesoderm of mid- and hindgut but is absent from definitive endoderm. Injection of mouse mMix RNA into early frog embryos results in axial truncation of developing tadpoles and, in animal cap assays, mMix alone is sufficient to activate expression of several endodermal (but not mesodermal) markers. Although these observations do not exclude a possible cell-autonomous function for mMix in mesendodermal progenitor cells, they do suggest an additional, non-cell autonomous role in nascent mesoderm in the formation and/or patterning of adjacent definitive endoderm. Copyright 2003 Wiley-Liss, Inc.

Structure, dynamics and folding of an immunoglobulin domain of the gelation factor (ABP-120) from Dictyostelium discoideum.

PubMed

Hsu, Shang-Te Danny; Cabrita, Lisa D; Fucini, Paola; Dobson, Christopher M; Christodoulou, John

2009-05-15

We have carried out a detailed structural and dynamical characterisation of the isolated fifth repeat of the gelation factor (ABP-120) from Dictyostelium discoideum (ddFLN5) by NMR spectroscopy to provide a basis for studies of co-translational folding on the ribosome of this immunoglobulin-like domain. The isolated ddFLN5 can fold autonomously in solution into a structure that resembles very closely the crystal structure of the domain in a construct in which the adjacent sixth repeat (ddFLN6) is covalently linked to its C-terminus in tandem but deviates locally from a second crystal structure in which ddFLN5 is flanked by ddFLN4 and ddFLN6 at both N- and C-termini. Conformational fluctuations were observed via (15)N relaxation methods and are primarily localised in the interstrand loops that encompass the C-terminal hemisphere. These fluctuations are distinct in location from the region where line broadening is observed in ddFLN5 when attached to the ribosome as part of a nascent chain. This observation supports the conclusion that the broadening is associated with interactions with the ribosome surface [Hsu, S. T. D., Fucini, P., Cabrita, L. D., Launay, H., Dobson, C. M. & Christodoulou, J. (2007). Structure and dynamics of a ribosome-bound nascent chain by NMR spectroscopy. Proc. Natl. Acad. Sci. USA, 104, 16516-16521]. The unfolding of ddFLN5 induced by high concentrations of urea shows a low population of a folding intermediate, as inferred from an intensity-based analysis, a finding that differs from that of ddFLN5 as a ribosome-bound nascent chain. These results suggest that interesting differences in detail may exist between the structure of the domain in isolation and when linked to the ribosome and between protein folding in vitro and the folding of a nascent chain as it emerges from the ribosome.

A combined crossed-beam and theoretical study of the reaction dynamics of O(3P) + C2H3 → C2H2 + OH: analysis of the nascent OH products with the preferential population of the Π(A') component.

PubMed

Park, Min-Jin; Jang, Su-Chan; Choi, Jong-Ho

2012-11-28

The gas-phase reaction dynamics of ground-state atomic oxygen [O((3)P) from the photo-dissociation of NO(2)] with vinyl radicals [C(2)H(3) from the supersonic flash pyrolysis of vinyl iodide, C(2)H(3)I] has been investigated using a combination of high-resolution laser-induced fluorescence spectroscopy in a crossed-beam configuration and ab initio calculations. Unlike the previous gas-phase bulk kinetic experiments by Baulch et al. [J. Phys. Chem. Ref. Data 34, 757 (2005)], a new exothermic channel of O((3)P) + C(2)H(3) → C(2)H(2) + OH (X (2)Π: υ" = 0) has been identified for the first time, and the population analysis shows bimodal nascent rotational distributions of OH products with low- and high-N" components with a ratio of 2.4:1. No spin-orbit propensities were observed, and the averaged ratios of Π(A('))∕Π(A") were determined to be 1.66 ± 0.27. On the basis of computations at the CBS-QB3 theory level and comparison with prior theory, the microscopic mechanisms responsible for the nascent populations can be understood in terms of two competing dynamical pathways: a direct abstraction process in the low-N" regime as the major pathway and an addition-complex forming process in the high-N" regime as the minor pathway. Particularly, during the bond cleavage process of the weakly bound van der Waals complex C(2)H(2)-OH, the characteristic pathway from the low dihedral-angle geometry was consistent with the observed preferential population of the Π(A') component in the nascent OH products. A molecular-level discussion of the reactivity, mechanism, and dynamical features of the title reaction are presented together with a comparison to gas-phase oxidation reactions of a series of prototypical hydrocarbon radicals.

Transgenic approaches to altering carbon and nitrogen partitioning in whole plants: assessing the potential to improve crop yields and nutritional quality

DOE PAGES

Yadav, Umesh P.; Ayre, Brian G.; Bush, Daniel R.

2015-04-22

The principal components of plant productivity and nutritional value, from the standpoint of modern agriculture, are the acquisition and partitioning of organic carbon (C) and nitrogen (N) compounds among the various organs of the plant. The flow of essential organic nutrients among the plant organ systems is mediated by its complex vascular system, and is driven by a series of transport steps including export from sites of primary assimilation, transport into and out of the phloem and xylem, and transport into the various import-dependent organs. Manipulating C and N partitioning to enhance yield of harvested organs is evident in themore » earliest crop domestication events and continues to be a goal for modern plant biology. Research on the biochemistry, molecular and cellular biology, and physiology of C and N partitioning has now matured to an extent that strategic manipulation of these transport systems through biotechnology are being attempted to improve movement from source to sink tissues in general, but also to target partitioning to specific organs. These nascent efforts are demonstrating the potential of applied biomass targeting but are also identifying interactions between essential nutrients that require further basic research. In this review, we summarize the key transport steps involved in C and N partitioning, and discuss various transgenic approaches for directly manipulating key C and N transporters involved. In addition, we propose several experiments that could enhance biomass accumulation in targeted organs while simultaneously testing current partitioning models.« less

Transgenic approaches to altering carbon and nitrogen partitioning in whole plants: assessing the potential to improve crop yields and nutritional quality

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

Yadav, Umesh P.; Ayre, Brian G.; Bush, Daniel R.

The principal components of plant productivity and nutritional value, from the standpoint of modern agriculture, are the acquisition and partitioning of organic carbon (C) and nitrogen (N) compounds among the various organs of the plant. The flow of essential organic nutrients among the plant organ systems is mediated by its complex vascular system, and is driven by a series of transport steps including export from sites of primary assimilation, transport into and out of the phloem and xylem, and transport into the various import-dependent organs. Manipulating C and N partitioning to enhance yield of harvested organs is evident in themore » earliest crop domestication events and continues to be a goal for modern plant biology. Research on the biochemistry, molecular and cellular biology, and physiology of C and N partitioning has now matured to an extent that strategic manipulation of these transport systems through biotechnology are being attempted to improve movement from source to sink tissues in general, but also to target partitioning to specific organs. These nascent efforts are demonstrating the potential of applied biomass targeting but are also identifying interactions between essential nutrients that require further basic research. In this review, we summarize the key transport steps involved in C and N partitioning, and discuss various transgenic approaches for directly manipulating key C and N transporters involved. In addition, we propose several experiments that could enhance biomass accumulation in targeted organs while simultaneously testing current partitioning models.« less

Vision in Plants via Plant-Specific Ocelli?

PubMed

Baluška, Frantisek; Mancuso, Stefano

2016-09-01

Although plants are sessile organisms, almost all of their organs move in space and thus require plant-specific senses to find their proper place with respect to their neighbours. Here we discuss recent studies suggesting that plants are able to sense shapes and colours via plant-specific ocelli. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Sense of Community: Collaboration in a Large Anthropology Class.

ERIC Educational Resources Information Center

Lancy, David F.; And Others

1994-01-01

A large introductory anthropology course at Utah State University was organized to promote collaboration among and between students and faculty. Students were divided into and worked in "clans" for the entire term. A study of the course suggests that learning and a sense of community resulted directly from this organization. (MSE)

A Qualitative Organic Analysis that Exploits the Senses of Smell, Touch, and Sound

ERIC Educational Resources Information Center

Bromfield-Lee, Deborah C.; Oliver-Hoyo, Maria T.

2007-01-01

This laboratory experiment utilizes the characteristic aromas of some functional groups to exploit the sense of smell as a discriminating tool in an organic qualitative analysis scheme. Students differentiate a variety of compounds by their aromas and based on their olfactory classification identify an unknown functional group. Students then…

Highly selective luminescent sensing of picric acid based on a water-stable europium metal-organic framework

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

Xia, Tifeng; Zhu, Fengliang; Cui, Yuanjing, E-mail: cuiyj@zju.edu.cn

A water-stable metal-organic framework (MOF) EuNDC has been synthesized for selective detection of the well-known contaminant and toxicant picric acid (PA) in aqueous solution. Due to the photo-induced electron transfer and self-absorption mechanism, EuNDC displayed rapid, selective and sensitive detection of PA with a detection limit of 37.6 ppb. Recyclability experiments revealed that EuNDC retains its initial luminescent intensity and same quenching efficiency in each cycle, suggesting high photostability and reusability for long-term sensing applications. The excellent detection performance of EuNDC makes it a promising PA sensing material for practical applications. - Graphical abstract: A water-stable europium-based metal-organic framework hasmore » been reported for highly selective sensing of picric acid (PA) with a detection limit of 37.6 ppb in aqueous solution. - Highlights: • A water-stable metal-organic framework (MOF) EuNDC was synthesized. • The highly selective detection of picric acid with a detection limit of 37.6 ppb was realized. • The detection mechanism were also presented and discussed.« less

Literature relevant to remote sensing of water quality

NASA Technical Reports Server (NTRS)

Middleton, E. M.; Marcell, R. F.

1983-01-01

References relevant to remote sensing of water quality were compiled, organized, and cross-referenced. The following general categories were included: (1) optical properties and measurement of water characteristics; (2) interpretation of water characteristics by remote sensing, including color, transparency, suspended or dissolved inorganic matter, biological materials, and temperature; (3) application of remote sensing for water quality monitoring; (4) application of remote sensing according to water body type; and (5) manipulation, processing and interpretation of remote sensing digital water data.

Sensory neuroanatomy of stick insects highlights the evolutionary diversity of the orthopteroid subgenual organ complex.

PubMed

Strauß, Johannes; Lakes-Harlan, Reinhard

2013-11-01

The subgenual organ is a scolopidial sense organ located in the tibia of many insects. In this study the neuroanatomy of the subgenual organ complex of stick insects is clarified for two species, Carausius morosus and Siyploidea sipylus. Neuronal tracing shows a subgenual organ complex that consists of a subgenual organ and a distal organ. There are no differences in neuroanatomy between the three thoracic leg pairs, and the sensory structures are highly similar in both species. A comparison of the neuroanatomy with other orthopteroid insects highlights two features unique in Phasmatodea. The subgenual organ contains a set of densely arranged sensory neurons in the anterior-ventral part of the organ, and a distal organ with 16-17 scolopidial sensilla in C. morosus and 20-22 scolopidial sensilla in S. sipylus. The somata of sensory neurons in the distal organ are organized in a linear array extending distally into the tibia, with only a few exceptions of closely associated neurons. The stick insect sense organs show a case of an elaborate scolopidial sense organ that evolved in addition to the subgenual organ. The neuroanatomy of stick insects is compared to that studied in other orthopteroid taxa (cockroaches, locusts, crickets, tettigoniids). The comparison of sensory structures indicates that elaborate scolopidial organs have evolved repeatedly among orthopteroids. The distal organ in stick insects has the highest number of sensory neurons known for distal organs so far. Copyright © 2013 Wiley Periodicals, Inc.

Apparatus for sensing volatile organic chemicals in fluids

DOEpatents

Hughes, Robert C.; Manginell, Ronald P.; Jenkins, Mark W.; Kottenstette, Richard; Patel, Sanjay V.

2005-06-07

A chemical-sensing apparatus is formed from the combination of a chemical preconcentrator which sorbs and concentrates particular volatile organic chemicals (VOCs) and one or more chemiresistors that sense the VOCs after the preconcentrator has been triggered to release them in concentrated form. Use of the preconcentrator and chemiresistor(s) in combination allows the VOCs to be detected at lower concentration than would be possible using the chemiresistor(s) alone and further allows measurements to be made in a variety of fluids, including liquids (e.g. groundwater). Additionally, the apparatus provides a new mode of operation for sensing VOCs based on the measurement of decay time constants, and a method for background correction to improve measurement precision.

Treasure Your Exceptions: An Interview with 2017 George Beadle Award Recipient Susan A. Gerbi.

PubMed

Gerbi, Susan A

2017-12-01

THE Genetics Society of America's (GSA) George W. Beadle Award honors individuals who have made outstanding contributions to the community of genetics researchers and who exemplify the qualities of its namesake. The 2017 recipient is Susan A. Gerbi, who has been a prominent leader and advocate for the scientific community. In the course of her research on DNA replication, Gerbi helped develop the method of Replication Initiation Point (RIP) mapping to map replication origins at the nucleotide level, improving resolution by two orders of magnitude. RIP mapping also provides the basis for the now popular use of λ-exonuclease to enrich nascent DNA to map replication origins genome-wide. Gerbi's second area of research on ribosomal RNA revealed a conserved core secondary structure, as well as conserved nucleotide elements (CNEs). Some CNEs are universally conserved, while other CNEs are conserved in all eukaryotes but not in archaea or bacteria, suggesting a eukaryotic function. Intriguingly, the majority of the eukaryotic-specific CNEs line the tunnel of the large ribosomal subunit through which the nascent polypeptide exits. Gerbi has promoted the fly Sciara coprophila as a model organism ever since she used its enormous polytene chromosomes to help develop the method of in situ hybridization during her Ph.D. research in Joe Gall's laboratory. The Gerbi laboratory maintains the Sciara International Stock Center and manages its future, actively spreading Sciara stocks to other laboratories. Gerbi has also served in many leadership roles, working on issues of science policy, women in science, scientific training, and career preparation. This is an abridged version of the interview. The full interview is available on the Genes to Genomes blog, at genestogenomes.org/gerbi. Copyright © 2017 by the Genetics Society of America.

Mammalian DNA enriched for replication origins is enriched for snap-back sequences.

PubMed

Zannis-Hadjopoulos, M; Kaufmann, G; Martin, R G

1984-11-15

Using the instability of replication loops as a method for the isolation of double-stranded nascent DNA, extruded DNA enriched for replication origins was obtained and denatured. Snap-back DNA, single-stranded DNA with inverted repeats (palindromic sequences), reassociates rapidly into stem-loop structures with zero-order kinetics when conditions are changed from denaturing to renaturing, and can be assayed by chromatography on hydroxyapatite. Origin-enriched nascent DNA strands from mouse, rat and monkey cells growing either synchronously or asynchronously were purified and assayed for the presence of snap-back sequences. The results show that origin-enriched DNA is also enriched for snap-back sequences, implying that some origins for mammalian DNA replication contain or lie near palindromic sequences.

Structurally Integrated Photoluminescent Chemical and Biological Sensors: An Organic Light-Emitting Diode-Based Platform

NASA Astrophysics Data System (ADS)

Shinar, J.; Shinar, R.

The chapter describes the development, advantages, challenges, and potential of an emerging, compact photoluminescence-based sensing platform for chemical and biological analytes, including multiple analytes. In this platform, the excitation source is an array of organic light-emitting device (OLED) pixels that is structurally integrated with the sensing component. Steps towards advanced integration with additionally a thin-film-based photodetector are also described. The performance of the OLED-based sensing platform is examined for gas-phase and dissolved oxygen, glucose, lactate, ethanol, hydrazine, and anthrax lethal factor.

ACOs Holding Commercial Contracts Are Larger And More Efficient Than Noncommercial ACOs

PubMed Central

Peiris, David; Phipps-Taylor, Madeleine C.; Stachowski, Courtney A.; Kao, Lee-Sien; Shortell, Stephen M.; Lewis, Valerie A.; Rosenthal, Meredith B.; Colla, Carrie H.

2016-01-01

Accountable care organizations (ACOs) have diverse contracting arrangements and have displayed wide variations in their performance. Using data from national surveys of 399 ACOs, we examined differences between the 228 commercial ACOs (those with commercial payer contracts) and the 171 noncommercial ACOs (those with only public contracts, such as with Medicare or Medicaid). Commercial ACOs were significantly larger and more integrated with hospitals, and had lower benchmark expenditures and higher quality scores, compared to noncommercial ACOs. Among all of the ACOs, there was low uptake of quality and efficiency activities. However, commercial ACOs reported more use of disease monitoring tools, patient satisfaction data, and quality improvement methods than did noncommercial ACOs. Few ACOs reported having high-level performance monitoring capabilities. About two-thirds of the ACOs had established processes for distributing any savings accrued, and these ACOs allocated approximately the same amount of savings to the ACOs themselves, participating member organizations, and physicians. Our findings demonstrate that ACO delivery systems remain at a nascent stage. Structural differences between commercial and noncommercial ACOs are important factors to consider as public policy efforts continue to evolve. PMID:27702959

Saccharomyces pastorianus: genomic insights inspiring innovation for industry.

PubMed

Gibson, Brian; Liti, Gianni

2015-01-01

A combination of biological and non-biological factors has led to the interspecific hybrid yeast species Saccharomyces pastorianus becoming one of the world's most important industrial organisms. This yeast is used in the production of lager-style beers, the fermentation of which requires very low temperatures compared to other industrial fermentation processes. This group of organisms has benefited from both the whole-genome duplication in its ancestral lineage and the subsequent hybridization event between S. cerevisiae and S. eubayanus, resulting in strong fermentative ability. The hybrid has key traits, such as cold tolerance and good maltose- and maltotriose-utilizing ability, inherited either from the parental species or originating from genetic interactions between the parent genomes. Instability in the nascent allopolyploid hybrid genome may have contributed to rapid evolution of the yeast to tolerate conditions prevalent in the brewing environment. The recent discovery of S. eubayanus has provided new insights into the evolutionary history of S. pastorianus and may offer new opportunities for generating novel industrially-beneficial lager yeast strains. Copyright © 2014 John Wiley & Sons, Ltd.

Development and regeneration of the electric organ.

PubMed

Zakon, H H; Unguez, G A

1999-05-01

The electric organ has evolved independently from muscle in at least six lineages of fish. How does a differentiated muscle cell change its fate to become an electrocyte? Is the process by which this occurs similar in different lineages? We have begun to answer these questions by studying the formation and maintenance of electrocytes in the genus Sternopygus, a weakly electric teleost. Electrocytes arise from the fusion of fully differentiated muscle fibers, mainly those expressing fast isoforms of myosin. Electrocytes briefly co-express sarcomeric proteins, such as myosin and tropomyosin, and keratin, a protein not found in mature muscle. The sarcomeric proteins are subsequently down-regulated, but keratin expression persists. We investigated whether the maintenance of the electrocyte phenotype depends on innervation. We found that, after spinal cord transection, which silences the electromotor neurons that innervate the electrocytes, or destruction of the spinal cord, which denervates the electrocytes, mature electrocytes re-express sarcomeric myosin and tropomyosin, although keratin expression persists. Ultrastructural examination of denervated electrocytes revealed nascent sarcomeres. Thus, the maintenance of the electrocyte phenotype depends on neural activity.

Microtubule nucleation and organization in dendrites

PubMed Central

Delandre, Caroline; Amikura, Reiko; Moore, Adrian W.

2016-01-01

ABSTRACT Dendrite branching is an essential process for building complex nervous systems. It determines the number, distribution and integration of inputs into a neuron, and is regulated to create the diverse dendrite arbor branching patterns characteristic of different neuron types. The microtubule cytoskeleton is critical to provide structure and exert force during dendrite branching. It also supports the functional requirements of dendrites, reflected by differential microtubule architectural organization between neuron types, illustrated here for sensory neurons. Both anterograde and retrograde microtubule polymerization occur within growing dendrites, and recent studies indicate that branching is enhanced by anterograde microtubule polymerization events in nascent branches. The polarities of microtubule polymerization events are regulated by the position and orientation of microtubule nucleation events in the dendrite arbor. Golgi outposts are a primary microtubule nucleation center in dendrites and share common nucleation machinery with the centrosome. In addition, pre-existing dendrite microtubules may act as nucleation sites. We discuss how balancing the activities of distinct nucleation machineries within the growing dendrite can alter microtubule polymerization polarity and dendrite branching, and how regulating this balance can generate neuron type-specific morphologies. PMID:27097122

Control of Smc Coiled Coil Architecture by the ATPase Heads Facilitates Targeting to Chromosomal ParB/parS and Release onto Flanking DNA

PubMed Central

Minnen, Anita; Bürmann, Frank; Wilhelm, Larissa; Anchimiuk, Anna; Diebold-Durand, Marie-Laure; Gruber, Stephan

2016-01-01

Summary Smc/ScpAB promotes chromosome segregation in prokaryotes, presumably by compacting and resolving nascent sister chromosomes. The underlying mechanisms, however, are poorly understood. Here, we investigate the role of the Smc ATPase activity in the recruitment of Smc/ScpAB to the Bacillus subtilis chromosome. We demonstrate that targeting of Smc/ScpAB to ParB/parS loading sites is strictly dependent on engagement of Smc head domains and relies on an open organization of the Smc coiled coils. We find that dimerization of the Smc hinge domain stabilizes closed Smc rods and hinders head engagement as well as chromosomal targeting. Conversely, the ScpAB sub-complex promotes head engagement and Smc rod opening and thereby facilitates recruitment of Smc to parS sites. Upon ATP hydrolysis, Smc/ScpAB is released from loading sites and relocates within the chromosome—presumably through translocation along DNA double helices. Our findings define an intermediate state in the process of chromosome organization by Smc. PMID:26904953

H2-rich fluids from serpentinization: Geochemical and biotic implications

PubMed Central

Sleep, N. H.; Meibom, A.; Fridriksson, Th.; Coleman, R. G.; Bird, D. K.

2004-01-01

Metamorphic hydration and oxidation of ultramafic rocks produces serpentinites, composed of serpentine group minerals and varying amounts of brucite, magnetite, and/or FeNi alloys. These minerals buffer metamorphic fluids to extremely reducing conditions that are capable of producing hydrogen gas. Awaruite, FeNi3, forms early in this process when the serpentinite minerals are Fe-rich. Olivine with the current mantle Fe/Mg ratio was oxidized during serpentinization after the Moon-forming impact. This process formed some of the ferric iron in the Earth's mantle. For the rest of Earth's history, serpentinites covered only a small fraction of the Earth's surface but were an important prebiotic and biotic environment. Extant methanogens react H2 with CO2 to form methane. This is a likely habitable environment on large silicate planets. The catalytic properties of FeNi3 allow complex organic compounds to form within serpentinite and, when mixed with atmospherically produced complex organic matter and waters that circulated through basalts, constitutes an attractive prebiotic substrate. Conversely, inorganic catalysis of methane by FeNi3 competes with nascent and extant life. PMID:15326313

Unfolding the chaperone story

PubMed Central

Hartl, F. Ulrich

2017-01-01

Protein folding in the cell was originally assumed to be a spontaneous process, based on Anfinsen’s discovery that purified proteins can fold on their own after removal from denaturant. Consequently cell biologists showed little interest in the protein folding process. This changed only in the mid and late 1980s, when the chaperone story began to unfold. As a result, we now know that in vivo, protein folding requires assistance by a complex machinery of molecular chaperones. To ensure efficient folding, members of different chaperone classes receive the nascent protein chain emerging from the ribosome and guide it along an ordered pathway toward the native state. I was fortunate to contribute to these developments early on. In this short essay, I will describe some of the critical steps leading to the current concept of protein folding as a highly organized cellular process. PMID:29084909

TRPV2 has a pivotal role in macrophage particle binding and phagocytosis.

PubMed

Link, Tiffany M; Park, Una; Vonakis, Becky M; Raben, Daniel M; Soloski, Mark J; Caterina, Michael J

2010-03-01

Macrophage phagocytosis is critical for defense against pathogens. Whereas many steps of phagocytosis involve ionic flux, the underlying ion channels remain ill defined. Here we show that zymosan-, immunoglobulin G (IgG)- and complement-mediated particle binding and phagocytosis were impaired in macrophages lacking the cation channel TRPV2. TRPV2 was recruited to the nascent phagosome and depolarized the plasma membrane. Depolarization increased the synthesis of phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P(2)), which triggered the partial actin depolymerization necessary for occupancy-elicited phagocytic receptor clustering. TRPV2-deficient macrophages were also defective in chemoattractant-elicited motility. Consequently, TRPV2-deficient mice showed accelerated mortality and greater organ bacterial load when challenged with Listeria monocytogenes. Our data demonstrate the participation of TRPV2 in early phagocytosis and its fundamental importance in innate immunity.

Sense-Making in a Temporary Organization: Implementing a New Curriculum in a Swedish Municipality

ERIC Educational Resources Information Center

Nordholm, Daniel Erik

2015-01-01

This article explores sense-making in a municipality-led temporary organization established in response to the introduction of a new curriculum and marking system in Sweden. Qualitative data were extracted from audio-recorded interviews (n = 18) and observations of central subject group meetings (n = 6). By applying core elements of sociological…

Community Organizations and Sense of Community: Further Development in Theory and Measurement

ERIC Educational Resources Information Center

Peterson, N. Andrew; Speer, Paul W.; Hughey, Joseph; Armstead, Theresa L.; Schneider, John E.; Sheffer, Megan A.

2008-01-01

The Community Organization Sense of Community Scale (COSOC) is a frequently used or cited measure of the construct in community psychology and other disciplines, despite a lack of confirmation of its underlying 4-factor framework. Two studies were conducted to test the hypothesized structure of the COSOC, the potential effects of method bias on…

Sensing, physiological effects and molecular response to elevated CO2 levels in eukaryotes

PubMed Central

Sharabi, Kfir; Lecuona, Emilia; Helenius, Iiro Taneli; Beitel, Greg J; Sznajder, Jacob Iasha; Gruenbaum, Yosef

2009-01-01

Carbon dioxide (CO2) is an important gaseous molecule that maintains biosphere homeostasis and is an important cellular signalling molecule in all organisms. The transport of CO2 through membranes has fundamental roles in most basic aspects of life in both plants and animals. There is a growing interest in understanding how CO2 is transported into cells, how it is sensed by neurons and other cell types and in understanding the physiological and molecular consequences of elevated CO2 levels (hypercapnia) at the cell and organism levels. Human pulmonary diseases and model organisms such as fungi, C. elegans, Drosophila and mice have been proven to be important in understanding of the mechanisms of CO2 sensing and response. PMID:19863692

Electrochemical sensing of heavy metal ions with inorganic, organic and bio-materials.

PubMed

Cui, Lin; Wu, Jie; Ju, Huangxian

2015-01-15

As heavy metal ions severely harm human health, it is important to develop simple, sensitive and accurate methods for their detection in environment and food. Electrochemical detection featured with short analytical time, low power cost, high sensitivity and easy adaptability for in-situ measurement is one of the most developed methods. This review introduces briefly the recent achievements in electrochemical sensing of heavy metal ions with inorganic, organic and bio-materials modified electrodes. In particular, the unique properties of inorganic nanomaterials, organic small molecules or their polymers, enzymes and nucleic acids for detection of heavy metal ions are highlighted. By employing some representative examples, the design and sensing mechanisms of these electrodes are discussed. Copyright © 2014 Elsevier B.V. All rights reserved.

Antigen Binding and Site-Directed Labeling of Biosilica-Immobilized Fusion Proteins Expressed in Diatoms.

PubMed

Ford, Nicole R; Hecht, Karen A; Hu, DeHong; Orr, Galya; Xiong, Yijia; Squier, Thomas C; Rorrer, Gregory L; Roesijadi, Guritno

2016-03-18

The diatom Thalassiosira pseudonana was genetically modified to express biosilica-targeted fusion proteins comprising either enhanced green fluorescent protein (EGFP) or single chain antibodies engineered with a tetracysteine tagging sequence. Of interest were the site-specific binding of (1) the fluorescent biarsenical probe AsCy3 and AsCy3e to the tetracysteine tagged fusion proteins and (2) high and low molecular mass antigens, the Bacillus anthracis surface layer protein EA1 or small molecule explosive trinitrotoluene (TNT), to biosilica-immobilized single chain antibodies. Analysis of biarsenical probe binding using fluorescence and structured illumination microscopy indicated differential colocalization with EGFP in nascent and mature biosilica, supporting the use of either EGFP or bound AsCy3 and AsCy3e in studying biosilica maturation. Large increases in the lifetime of a fluorescent analogue of TNT upon binding single chain antibodies provided a robust signal capable of discriminating binding to immobilized antibodies in the transformed frustule from nonspecific binding to the biosilica matrix. In conclusion, our results demonstrate an ability to engineer diatoms to create antibody-functionalized mesoporous silica able to selectively bind chemical and biological agents for the development of sensing platforms.

Recent rift formation and impact on the structural integrity of the Brunt Ice Shelf, East Antarctica

NASA Astrophysics Data System (ADS)

De Rydt, Jan; Hilmar Gudmundsson, G.; Nagler, Thomas; Wuite, Jan; King, Edward C.

2018-02-01

We report on the recent reactivation of a large rift in the Brunt Ice Shelf, East Antarctica, in December 2012 and the formation of a 50 km long new rift in October 2016. Observations from a suite of ground-based and remote sensing instruments between January 2000 and July 2017 were used to track progress of both rifts in unprecedented detail. Results reveal a steady accelerating trend in their width, in combination with alternating episodes of fast ( > 600 m day-1) and slow propagation of the rift tip, controlled by the heterogeneous structure of the ice shelf. A numerical ice flow model and a simple propagation algorithm based on the stress distribution in the ice shelf were successfully used to hindcast the observed trajectories and to simulate future rift progression under different assumptions. Results show a high likelihood of ice loss at the McDonald Ice Rumples, the only pinning point of the ice shelf. The nascent iceberg calving and associated reduction in pinning of the Brunt Ice Shelf may provide a uniquely monitored natural experiment of ice shelf variability and provoke a deeper understanding of similar processes elsewhere in Antarctica.

Navigating Ethics in the Digital Age: Introducing Connected and Open Research Ethics (CORE), a Tool for Researchers and Institutional Review Boards

PubMed Central

Torous, John

2017-01-01

Research studies that leverage emerging technologies, such as passive sensing devices and mobile apps, have demonstrated encouraging potential with respect to favorably influencing the human condition. As a result, the nascent fields of mHealth and digital medicine have gained traction over the past decade as demonstrated in the United States by increased federal funding for research that cuts across a broad spectrum of health conditions. The existence of mHealth and digital medicine also introduced new ethical and regulatory challenges that both institutional review boards (IRBs) and researchers are struggling to navigate. In response, the Connected and Open Research Ethics (CORE) initiative was launched. The CORE initiative has employed a participatory research approach, whereby researchers and IRB affiliates are involved in identifying the priorities and functionality of a shared resource. The overarching goal of CORE is to develop dynamic and relevant ethical practices to guide mHealth and digital medicine research. In this Viewpoint paper, we describe the CORE initiative and call for readers to join the CORE Network and contribute to the bigger conversation on ethics in the digital age. PMID:28179216

Silver lining: building a shared Sudanese identity through food.

PubMed

Crofts, A V

2010-01-01

The displaced of Sudan, due to both decades of civil war and natural disasters, are disproportionately female and many are responsible for dependents. For those settling in the capital, Khartoum, their livelihood depends on carving out ways to earn money in an urban area that is experiencing tremendous growth from the millions of recent arrivals. When confronted with the immediate need to provide for their families, women turn to a skill universally expected of them: cooking. Therefore, Khartoum is home to a thriving micro-economy of food vendors. By selling these dishes in the capital, they broaden the culinary horizons of the city while preserving their own food traditions. Their growing numbers provide an opportunity for regional foodways to gain wider introduction, adaptation, and, finally, adoption. These same vendors also facilitate a nascent sense of a shared Sudanese identity and nationalism. For established Khartoum urbanites, the definition of Sudanese food (and, by extension, what it means to be Sudanese) expands as street-vendor fare moves to restaurants and becomes more widely available throughout the city. As urban Sudanese overcome their preconceptions and discover a taste for regional cuisines, meals function as unofficial diplomacy during this turbulent time in Sudan's history.

The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs

PubMed Central

Garzia, Aitor; Jafarnejad, Seyed Mehdi; Meyer, Cindy; Chapat, Clément; Gogakos, Tasos; Morozov, Pavel; Amiri, Mehdi; Shapiro, Maayan; Molina, Henrik; Tuschl, Thomas; Sonenberg, Nahum

2017-01-01

Cryptic polyadenylation within coding sequences (CDS) triggers ribosome-associated quality control (RQC), followed by degradation of the aberrant mRNA and polypeptide, ribosome disassembly and recycling. Although ribosomal subunit dissociation and nascent peptide degradation are well-understood, the molecular sensors of aberrant mRNAs and their mechanism of action remain unknown. We studied the Zinc Finger Protein 598 (ZNF598) using PAR-CLIP and revealed that it cross-links to tRNAs, mRNAs and rRNAs, thereby placing the protein on translating ribosomes. Cross-linked reads originating from AAA-decoding tRNALys(UUU) were 10-fold enriched over its cellular abundance, and poly-lysine encoded by poly(AAA) induced RQC in a ZNF598-dependent manner. Encounter with translated polyA segments by ZNF598 triggered ubiquitination of several ribosomal proteins, requiring the E2 ubiquitin ligase UBE2D3 to initiate RQC. Considering that human CDS are devoid of >4 consecutive AAA codons, sensing of prematurely placed polyA tails by a specialized RNA-binding protein is a novel nucleic-acid-based surveillance mechanism of RQC. PMID:28685749

The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs.

PubMed

Garzia, Aitor; Jafarnejad, Seyed Mehdi; Meyer, Cindy; Chapat, Clément; Gogakos, Tasos; Morozov, Pavel; Amiri, Mehdi; Shapiro, Maayan; Molina, Henrik; Tuschl, Thomas; Sonenberg, Nahum

2017-07-07

Cryptic polyadenylation within coding sequences (CDS) triggers ribosome-associated quality control (RQC), followed by degradation of the aberrant mRNA and polypeptide, ribosome disassembly and recycling. Although ribosomal subunit dissociation and nascent peptide degradation are well-understood, the molecular sensors of aberrant mRNAs and their mechanism of action remain unknown. We studied the Zinc Finger Protein 598 (ZNF598) using PAR-CLIP and revealed that it cross-links to tRNAs, mRNAs and rRNAs, thereby placing the protein on translating ribosomes. Cross-linked reads originating from AAA-decoding tRNA Lys (UUU) were 10-fold enriched over its cellular abundance, and poly-lysine encoded by poly(AAA) induced RQC in a ZNF598-dependent manner. Encounter with translated polyA segments by ZNF598 triggered ubiquitination of several ribosomal proteins, requiring the E2 ubiquitin ligase UBE2D3 to initiate RQC. Considering that human CDS are devoid of >4 consecutive AAA codons, sensing of prematurely placed polyA tails by a specialized RNA-binding protein is a novel nucleic-acid-based surveillance mechanism of RQC.

Fabrication and performance of pressure-sensing device consisting of electret film and organic semiconductor

NASA Astrophysics Data System (ADS)

Kodzasa, Takehito; Nobeshima, Daiki; Kuribara, Kazunori; Uemura, Sei; Yoshida, Manabu

2017-04-01

We propose a new concept of a pressure-sensitive device that consists of an organic electret film and an organic semiconductor. This device exhibits high sensitivity and selectivity against various types of pressure. The sensing mechanism of this device originates from a modulation of the electric conductivity of the organic semiconductor film induced by the interaction between the semiconductor film and the charged electret film placed face to face. It is expected that a complicated sensor array will be fabricated by using a roll-to-roll manufacturing system, because this device can be prepared by an all-printing and simple lamination process without high-level positional adjustment for printing processes. This also shows that this device with a simple structure is suitable for application to a highly flexible device array sheet for an Internet of Things (IoT) or wearable sensing system.

Bibliography of Remote Sensing Techniques Used in Wetland Research.

DTIC Science & Technology

1993-01-01

remote sensing technology for detecting changes in wetland environments. This report documents a bibliographic search conducted as part of that work unit on applications of remote sensing techniques in wetland research. Results were used to guide research efforts on the use of remote sensing technology for wetland change detection and assessment. The citations are presented in three appendixes, organized by wetland type, sensor type, and author.... Change detection, Wetland assessment, Remote sensing ,

Where are you, my beloved? On absence, loss, and the enigma of telepathic dreams.

PubMed

Eshel, Ofra

2006-12-01

The subject of dream telepathy (especially patients' telepathic dreams) and related phenomena in the psychoanalytic context has been a controversial, disturbing 'foreign body' ever since it was introduced into psychoanalysis by Freud in 1921. Telepathy- suffering (or intense feeling) at a distance (Greek: pathos + tele)-is the transfer or communication of thoughts, impressions and information over distance between two people without the normal operation of the recognized sense organs. The author offers a comprehensive historical review of the psychoanalytic literature on this controversial issue, beginning with Freud's years-long struggles over the possibility of thoughttransference and dream telepathy. She then describes her own analytic encounter over the years with five patients' telepathic dreams-dreams involving precise details of the time, place, sensory impressions, and experiential states that the analyst was in at that time, which the patients could not have known through ordinary sensory perception and communication. The author's ensuing explanation combines contributory factors involving patient, archaic communication and analyst. Each of these patients, in early childhood, had a mother who was emotionally absent-within-absence, due to the absence of a significant figure in her own life. This primary traumatic loss was imprinted in their nascent selves and inchoate relating to others, with a fixation on a nonverbal, archaic mode of communication. The patient's telepathic dream is formed as a search engine when the analyst is suddenly emotionally absent, in order to find the analyst and thus halt the process of abandonment and prevent collapse into the despair of the early traumatization. Hence, the telepathic dream embodies an enigmatic 'impossible' extreme of patient-analyst deep-level interconnectedness and unconscious communication in the analytic process. This paper is part of the author's endeavour to grasp the true experiential scope and therapeutic significance of this dimension of fundamental patient-analyst interconnectedness.

Directional gravity sensing in gravitropism.

PubMed

Morita, Miyo Terao

2010-01-01

Plants can reorient their growth direction by sensing organ tilt relative to the direction of gravity. With respect to gravity sensing in gravitropism, the classic starch statolith hypothesis, i.e., that starch-accumulating amyloplast movement along the gravity vector within gravity-sensing cells (statocytes) is the probable trigger of subsequent intracellular signaling, is widely accepted. Several lines of experimental evidence have demonstrated that starch is important but not essential for gravity sensing and have suggested that it is reasonable to regard plastids (containers of starch) as statoliths. Although the word statolith means sedimented stone, actual amyloplasts are not static but instead possess dynamic movement. Recent studies combining genetic and cell biological approaches, using Arabidopsis thaliana, have demonstrated that amyloplast movement is an intricate process involving vacuolar membrane structures and the actin cytoskeleton. This review covers current knowledge regarding gravity sensing, particularly gravity susception, and the factors modulating the function of amyloplasts for sensing the directional change of gravity. Specific emphasis is made on the remarkable differences in the cytological properties, developmental origins, tissue locations, and response of statocytes between root and shoot systems. Such an approach reveals a common theme in directional gravity-sensing mechanisms in these two disparate organs.

A Supercomplex Spanning the Inner and Outer Membranes Mediates the Biogenesis of β-Barrel Outer Membrane Proteins in Bacteria.

PubMed

Wang, Yan; Wang, Rui; Jin, Feng; Liu, Yang; Yu, Jiayu; Fu, Xinmiao; Chang, Zengyi

2016-08-05

β-barrel outer membrane proteins (OMPs) are ubiquitously present in Gram-negative bacteria, mitochondria and chloroplasts, and function in a variety of biological processes. The mechanism by which the hydrophobic nascent β-barrel OMPs are transported through the hydrophilic periplasmic space in bacterial cells remains elusive. Here, mainly via unnatural amino acid-mediated in vivo photo-crosslinking studies, we revealed that the primary periplasmic chaperone SurA interacts with nascent β-barrel OMPs largely via its N-domain but with β-barrel assembly machine protein BamA mainly via its satellite P2 domain, and that the nascent β-barrel OMPs interact with SurA via their N- and C-terminal regions. Additionally, via dual in vivo photo-crosslinking, we demonstrated the formation of a ternary complex involving β-barrel OMP, SurA, and BamA in cells. More importantly, we found that a supercomplex spanning the inner and outer membranes and involving the BamA, BamB, SurA, PpiD, SecY, SecE, and SecA proteins appears to exist in living cells, as revealed by a combined analyses of sucrose-gradient ultra-centrifugation, Blue native PAGE and mass spectrometry. We propose that this supercomplex integrates the translocation, transportation, and membrane insertion events for β-barrel OMP biogenesis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Sall1 Maintains Nephron Progenitors and Nascent Nephrons by Acting as Both an Activator and a Repressor

PubMed Central

Kanda, Shoichiro; Tanigawa, Shunsuke; Ohmori, Tomoko; Taguchi, Atsuhiro; Kudo, Kuniko; Suzuki, Yutaka; Sato, Yuki; Hino, Shinjiro; Sander, Maike; Perantoni, Alan O.; Sugano, Sumio; Nakao, Mitsuyoshi

2014-01-01

The balanced self-renewal and differentiation of nephron progenitors are critical for kidney development and controlled, in part, by the transcription factor Six2, which antagonizes canonical Wnt signaling-mediated differentiation. A nuclear factor, Sall1, is expressed in Six2-positive progenitors as well as differentiating nascent nephrons, and it is essential for kidney formation. However, the molecular functions and targets of Sall1, especially the functions and targets in the nephron progenitors, remain unknown. Here, we report that Sall1 deletion in Six2-positive nephron progenitors results in severe progenitor depletion and apoptosis of the differentiating nephrons in mice. Analysis of mice with an inducible Sall1 deletion revealed that Sall1 activates genes expressed in progenitors while repressing genes expressed in differentiating nephrons. Sall1 and Six2 co-occupied many progenitor-related gene loci, and Sall1 bound to Six2 biochemically. In contrast, Sall1 did not bind to the Wnt4 locus suppressed by Six2. Sall1-mediated repression was also independent of its binding to DNA. Thus, Sall1 maintains nephron progenitors and their derivatives by a unique mechanism, which partly overlaps but is distinct from that of Six2: Sall1 activates progenitor-related genes in Six2-positive nephron progenitors and represses gene expression in Six2-negative differentiating nascent nephrons. PMID:24744442

A Supercomplex Spanning the Inner and Outer Membranes Mediates the Biogenesis of β-Barrel Outer Membrane Proteins in Bacteria*

PubMed Central

Wang, Yan; Wang, Rui; Jin, Feng; Liu, Yang; Yu, Jiayu; Fu, Xinmiao; Chang, Zengyi

2016-01-01

β-barrel outer membrane proteins (OMPs) are ubiquitously present in Gram-negative bacteria, mitochondria and chloroplasts, and function in a variety of biological processes. The mechanism by which the hydrophobic nascent β-barrel OMPs are transported through the hydrophilic periplasmic space in bacterial cells remains elusive. Here, mainly via unnatural amino acid-mediated in vivo photo-crosslinking studies, we revealed that the primary periplasmic chaperone SurA interacts with nascent β-barrel OMPs largely via its N-domain but with β-barrel assembly machine protein BamA mainly via its satellite P2 domain, and that the nascent β-barrel OMPs interact with SurA via their N- and C-terminal regions. Additionally, via dual in vivo photo-crosslinking, we demonstrated the formation of a ternary complex involving β-barrel OMP, SurA, and BamA in cells. More importantly, we found that a supercomplex spanning the inner and outer membranes and involving the BamA, BamB, SurA, PpiD, SecY, SecE, and SecA proteins appears to exist in living cells, as revealed by a combined analyses of sucrose-gradient ultra-centrifugation, Blue native PAGE and mass spectrometry. We propose that this supercomplex integrates the translocation, transportation, and membrane insertion events for β-barrel OMP biogenesis. PMID:27298319

Simultaneous observation of nascent plasma and bubble induced by laser ablation in water with various pulse durations

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

Tamura, Ayaka, E-mail: atamura@hiroshima-u.ac.jp; Matsumoto, Ayumu; Nishi, Naoya

2015-05-07

We investigate the effects of pulse duration on the dynamics of the nascent plasma and bubble induced by laser ablation in water. To examine the relationship between the nascent plasma and the bubble without disturbed by shot-to-shot fluctuation, we observe the images of the plasma and the bubble simultaneously by using two intensified charge coupled device detectors. We successfully observe the images of the plasma and bubble during the pulsed-irradiation, when the bubble size is as small as 20 μm. The light-emitting region of the plasma during the laser irradiation seems to exceed the bubble boundary in the case of themore » short-pulse (30-ns pulse) irradiation, while the size of the plasma is significantly smaller than that of the bubble in the case of the long-pulse (100-ns pulse) irradiation. The results suggest that the extent of the plasma quenching in the initial stage significantly depends on the pulse duration. Also, we investigate how the plasma-bubble relationship in the very early stage affects the shape of the atomic spectral lines observed at the later delay time of 600 ns. The present work gives important information to obtain high quality spectra in the application of underwater laser-induced breakdown spectroscopy, as well as to clarify the mechanism of liquid-phase laser ablation.« less

Eccentricity Evolution of Extrasolar Multiple Planetary Systems Due to the Depletion of Nascent Protostellar Disks

NASA Astrophysics Data System (ADS)

Nagasawa, M.; Lin, D. N. C.; Ida, S.

2003-04-01

Most extrasolar planets are observed to have eccentricities much larger than those in the solar system. Some of these planets have sibling planets, with comparable masses, orbiting around the same host stars. In these multiple planetary systems, eccentricity is modulated by the planets' mutual secular interaction as a consequence of angular momentum exchange between them. For mature planets, the eigenfrequencies of this modulation are determined by their mass and semimajor axis ratios. However, prior to the disk depletion, self-gravity of the planets' nascent disks dominates the precession eigenfrequencies. We examine here the initial evolution of young planets' eccentricity due to the apsidal libration or circulation induced by both the secular interaction between them and the self-gravity of their nascent disks. We show that as the latter effect declines adiabatically with disk depletion, the modulation amplitude of the planets' relative phase of periapsis is approximately invariant despite the time-asymmetrical exchange of angular momentum between planets. However, as the young planets' orbits pass through a state of secular resonance, their mean eccentricities undergo systematic quantitative changes. For applications, we analyze the eccentricity evolution of planets around υ Andromedae and HD 168443 during the epoch of protostellar disk depletion. We find that the disk depletion can change the planets' eccentricity ratio. However, the relatively large amplitude of the planets' eccentricity cannot be excited if all the planets had small initial eccentricities.

Nucleolin is a nuclear target of heparan sulfate derived from glypican-1

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

Cheng, Fang; Belting, Mattias; Fransson, Lars-Åke

The recycling, S-nitrosylated heparan sulfate (HS) proteoglycan glypican-1 releases anhydromannose (anMan)-containing HS chains by a nitrosothiol-catalyzed cleavage in endosomes that can be constitutive or induced by ascorbate. The HS-anMan chains are then transported to the nucleus. A specific nuclear target for HS-anMan has not been identified. We have monitored endosome-to-nucleus trafficking of HS-anMan by deconvolution and confocal immunofluorescence microscopy using an anMan-specific monoclonal antibody in non-growing, ascorbate-treated, and growing, untreated, wild-type mouse embryonic fibroblasts and hypoxia-exposed Alzheimer mouse Tg2576 fibroblasts and human U87 glioblastoma cells. In all cells, nuclear HS-anMan targeted a limited number of sites of variable size wheremore » it colocalized with DNA and nucleolin, an established marker for nucleoli. HS-anMan also colocalized with ethynyl uridine-tagged nascent RNA and two acetylated forms of histone H3. Acute hypoxia increased the formation of HS-anMan in both Tg2576 and U87 cells. A portion of HS-anMan colocalized with nucleolin at small discrete sites, while most of the nucleolin and nascent RNA was dispersed. In U87 cells, HS-anMan, nucleolin and nascent RNA reassembled after prolonged hypoxia. Nucleolar HS may modulate synthesis and/or release of rRNA.« less

Organizational identification and commitment: correlates of sense of belonging and affective commitment.

PubMed

Dávila, Ma Celeste; Jiménez García, Gemma

2012-03-01

The general purpose of this work is to analyze the overlap between organizational identification and commitment. Specifically, our study focuses on the analysis of the differences and similarities between sense of belonging (a dimension of organizational identification) and affective commitment (a dimension of organizational commitment). In order to do this, we analyzed their discriminant validity and raised their relationship with variables that previous research had showed like precedent and subsequent variables of them: value congruence, perceived support, organizational citizenship behavior, and intention to continue in the organization. A total of 292 people at one organization completed surveys measuring the variables previously described. The results showed that sense of belonging and affective commitment are different concepts and they have different relationships with relation to precedent and subsequent variables. Affective commitment seems to be more useful than sense of belonging to predict organizational citizenship behavior aimed at the organization and intention to continue. Some practical implications are described.

Cell-free synthetic biology for environmental sensing and remediation.

PubMed

Karig, David K

2017-06-01

The fields of biosensing and bioremediation leverage the phenomenal array of sensing and metabolic capabilities offered by natural microbes. Synthetic biology provides tools for transforming these fields through complex integration of natural and novel biological components to achieve sophisticated sensing, regulation, and metabolic function. However, the majority of synthetic biology efforts are conducted in living cells, and concerns over releasing genetically modified organisms constitute a key barrier to environmental applications. Cell-free protein expression systems offer a path towards leveraging synthetic biology, while preventing the spread of engineered organisms in nature. Recent efforts in the areas of cell-free approaches for sensing, regulation, and metabolic pathway implementation, as well as for preserving and deploying cell-free expression components, embody key steps towards realizing the potential of cell-free systems for environmental sensing and remediation. Copyright © 2017 The Author. Published by Elsevier Ltd.. All rights reserved.

[Acute toxicity analysis performance of CellSense biosensor with E. coli].

PubMed

Wang, Xue-Jiang; Wang, Hong; Zhao, Jian-Fu; Xia, Si-Qing; Zhao, Hong-Ning

2009-04-15

E. coli microbial electrodes for CellSense biosensor were prepared by polycarbonate membrane immobilization process, and their performance for heavy metals and toxic organic compounds acute toxicity determination were studied. The results showed that when E. coli was in logarithmic and stationary phase, the CellSense biosensor with E. coli showed good performance in heavy metal ions and organic pollutants acute toxicity analysis, when E. coli was in its decline phase, the stability and sensitivity of the CellSense biosensor was poor. The EC50 values of Hg2+, Cu2+, Zn2+, o-chlorophenol (2-CP) and p-nitrophenol (4-NP) detected by CellSense biosensor with E. coli were 0.6, 3.1, 5.8, 180 and 94 microg/mL, respectively. The immobilized E. coli electrodes could still suit for acute toxicity assessment after 2 months storage at 4 degrees C.

Counselling Remaining Employees in Redundancy Situations.

ERIC Educational Resources Information Center

Vinten, Gerald; Lane, David A.

2002-01-01

Interviews with 50 managers in organizations that had experienced downsizing or restructuring elicited three themes: sense of loss, sense of realism, and sense of support. The experience changed their concept of organizational mission and required an organizational response. It was recommended that management of restructuring and layoff include…

Estimating dissolved organic carbon concentration in turbid coastal waters using optical remote sensing observations

NASA Astrophysics Data System (ADS)

Cherukuru, Nagur; Ford, Phillip W.; Matear, Richard J.; Oubelkheir, Kadija; Clementson, Lesley A.; Suber, Ken; Steven, Andrew D. L.

2016-10-01

Dissolved Organic Carbon (DOC) is an important component in the global carbon cycle. It also plays an important role in influencing the coastal ocean biogeochemical (BGC) cycles and light environment. Studies focussing on DOC dynamics in coastal waters are data constrained due to the high costs associated with in situ water sampling campaigns. Satellite optical remote sensing has the potential to provide continuous, cost-effective DOC estimates. In this study we used a bio-optics dataset collected in turbid coastal waters of Moreton Bay (MB), Australia, during 2011 to develop a remote sensing algorithm to estimate DOC. This dataset includes data from flood and non-flood conditions. In MB, DOC concentration varied over a wide range (20-520 μM C) and had a good correlation (R2 = 0.78) with absorption due to coloured dissolved organic matter (CDOM) and remote sensing reflectance. Using this data set we developed an empirical algorithm to derive DOC concentrations from the ratio of Rrs(412)/Rrs(488) and tested it with independent datasets. In this study, we demonstrate the ability to estimate DOC using remotely sensed optical observations in turbid coastal waters.

From protest to productivity: the evolution of indigenous federations in Ecuador.

PubMed

Bebbington, A; Carrasco, H; Peralbo, L; Ramon, G; Torres, V H; Trujillo, J

1992-01-01

A broad grassroots movement of Native American organizations has banded together in Ecuador around the struggle for land, civil rights, and cultural identity. Examples of success include the titling of communal land claims, proliferation of bilingual education and literacy programs, reclamation of native musical and art forms, and a generally stronger determination of indigenous peoples to exercise their citizens' rights. Evidence of this latter achievement was most pronounced in June 1990, when the National Confederation of Indigenous Ecuadorians called for a nonviolent rural mobilization to publicize the government's failure to fulfill its commitments to Indian communities. The protest shut down major transportation arteries throughout the countryside and received broad media coverage. Even though few tangible results were immediately forthcoming, the action voiced loudly and clearly the disgruntlement and power of these peoples. Having tasted the potential for change and their own nascent power, members now want their organizations to go beyond efforts to revitalize culture and leverage better services from the state. They want help in earning and maintaining a secure family income in a time of national economic crisis, structural adjustment, and declining public sector support. These indigenous organizations are effectively being asked to become development organizations. The central question, however, is whether they can make the shift to generating income-producing projects. In an attempt to determine which economic roles these organizations are best suited to play, the authors review how existing federations have evolved.

Analysis of Organic Anionic Surfactants in Fine and Coarse Fractions of Freshly Emitted Sea Spray Aerosol

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

Cochran, Richard E.; Laskina, Olga; Jayarathne, Thilina

The inclusion of organic compounds in freshly emitted sea spray aerosol (SSA) has been shown to be size-dependent, with an increasing organic fraction in smaller particles. Defining the molecular composition of sea spray aerosol has proven challenging, due to the mix of continental and background particles even in remote marine environments. Here we have used electrospray ionization-high resolution mass spectrometry in negative ion mode to identify organic compounds in nascent sea spray collected throughout a 25-day mesocosm experiment. Over 280 organic compounds from ten major homologous series were identified. These compounds were operationally defined as molecules containing a hydrophobic alkylmore » chain with a hydrophilic head group making them surface active. The most abundant class of molecules detected were saturated (C8–C24) and unsaturated (C12–C22) fatty acids. Fatty acid derivatives (including saturated oxo-fatty acids (C5–C18) and saturated hydroxy-fatty acids (C5–C18) were also identified. Interestingly, anthropogenic influences on SSA from the seawater were observed in the form of sulfate (C2–C7, C12–C17) and sulfonate (C16–C22) species. During the mesocosm, the distributions of molecules within each homologous series were observed to respond to variations among the levels of phytoplankton and bacteria in the seawater, indicating an important role of biological processes in determining the composition of SSA.« less

Identifying Functional Neighborhoods within the Cell Nucleus: Proximity Analysis of Early S-Phase Replicating Chromatin Domains to Sites of Transcription, RNA Polymerase II, HP1γ, Matrin 3 and SAF-A

PubMed Central

Malyavantham, Kishore S; Bhattacharya, Sambit; Barbeitos, Marcos; Mukherjee, Lopamudra; Xu, Jinhui; Fackelmayer, Frank O; Berezney, Ronald

2009-01-01

Higher order chromatin organization in concert with epigenetic regulation is a key process that determines gene expression at the global level. The organization of dynamic chromatin domains and their associated protein factors is intertwined with nuclear function to create higher levels of functional zones within the cell nucleus. As a step towards elucidating the organization and dynamics of these functional zones, we have investigated the spatial proximities among a constellation of functionally related sites that are found within euchromatic regions of the cell nucleus including: HP1γ, nascent transcript sites (TS), active DNA replicating sites in early S phase (PCNA) and RNA polymerase II sites. We report close associations among these different sites with proximity values specific for each combination. Analysis of matrin 3 and SAF-A sites demonstrates that these nuclear matrix proteins are highly proximal with the functionally related sites as well as to each other and display closely aligned and overlapping regions following application of the minimal spanning tree (MST) algorithm to visualize higher order network-like patterns. Our findings suggest that multiple factors within the nuclear microenvironment collectively form higher order combinatorial arrays of function. We propose a model for the organization of these functional neighborhoods which takes into account the proximity values of the individual sites and their spatial organization within the nuclear architecture. PMID:18618731

Understanding global changes on the land - A potential focus for NASA earth sciences and land remote sensing

NASA Technical Reports Server (NTRS)

Erickson, J. D.; Tuyahov, A. J.; Hogg, H. C.

1983-01-01

Planned NASA contributions to the study of the interaction of living organisms with their physical and chemical environments are discussed. Five major land-related research objectives are stated and the role of remote sensing in achieving them is addressed. The importance of improved sensors and cooperation with domestic and international organizations is stressed.

Bimaterial Microcantilevers as a Hybrid Sensing Platform

DTIC Science & Technology

2008-01-01

cantilevers are immersed in dilute solution (milli molar) of desired organic molecule (e.g., alkanethiols) in aqueous or organic solvent (e.g., water... active layers, and some of the im- portant applications. Emphasizing the material design aspects, the review underscores the most important findings... active sensing materials in microelectromechanical systems (MEMS), soft matter-inclusive sensors bring a desir- able diversity in signal transduction

NASA Workshop on Animal Gravity-Sensing Systems

NASA Technical Reports Server (NTRS)

Corcoran, M. L. (Editor)

1986-01-01

The opportunity for space flight has brought about the need for well-planned research programs that recognize the significance of space flight as a scientific research tool for advancing knowledge of life on Earth, and that utilize each flight opportunity to its fullest. For the first time in history, gravity can be almost completely eliminated. Thus, studies can be undertaken that will help to elucidate the importance of gravity to the normal functioning of living organisms, and to determine the effects microgravity may have on an organism. This workshop was convened to organize a plan for space research on animal gravity-sensing systems and the role that gravity plays in the development and normal functioning of these systems. Scientists working in the field of animal gravity-sensing systems use a wide variety of organisms in their research. The workshop presentations dealt with topics which ranged from the indirect gravity receptor of the water flea, Daphnia (whose antennal setae apparently act as current-sensing receptors as the animal moves up and down in water), through specialized statocyst structures found in jellyfish and gastropods, to the more complex vestibular systems that are characteristic of amphibians, avians, and mammals.

Cotranslocational degradation: utilitarianism in the ER stress response.

PubMed

Pearse, Bradley R; Hebert, Daniel N

2006-09-15

Recently, a new layer of the unfolded protein response was discovered that supports the cotranslocational degradation of nascent chains stalled in endoplasmic reticulum translocons (Oyadomari et al., 2006).

Hydrophobicity as a driver of MHC class I antigen processing

PubMed Central

Huang, Lan; Kuhls, Matthew C; Eisenlohr, Laurence C

2011-01-01

The forces that drive conversion of nascent protein to major histocompatibility complex (MHC) class I-restricted peptides remain unknown. We explored the fundamental property of overt hydrophobicity as such a driver. Relocation of a membrane glycoprotein to the cytosol via signal sequence ablation resulted in rapid processing of nascent protein not because of the misfolded luminal domain but because of the unembedded transmembrane (TM) domain, which serves as a dose-dependent degradation motif. Dislocation of the TM domain during the natural process of endoplasmic reticulum-associated degradation (ERAD) similarly accelerated peptide production, but in the context of markedly prolonged processing that included nonnascent species. These insights into intracellular proteolytic pathways and their selective contributions to MHC class I-restricted peptide supply, may point to new approaches in rational vaccine design. PMID:21378750

Hydrophobicity as a driver of MHC class I antigen processing.

PubMed

Huang, Lan; Kuhls, Matthew C; Eisenlohr, Laurence C

2011-04-20

The forces that drive conversion of nascent protein to major histocompatibility complex (MHC) class I-restricted peptides remain unknown. We explored the fundamental property of overt hydrophobicity as such a driver. Relocation of a membrane glycoprotein to the cytosol via signal sequence ablation resulted in rapid processing of nascent protein not because of the misfolded luminal domain but because of the unembedded transmembrane (TM) domain, which serves as a dose-dependent degradation motif. Dislocation of the TM domain during the natural process of endoplasmic reticulum-associated degradation (ERAD) similarly accelerated peptide production, but in the context of markedly prolonged processing that included nonnascent species. These insights into intracellular proteolytic pathways and their selective contributions to MHC class I-restricted peptide supply, may point to new approaches in rational vaccine design.

A two-way street: regulatory interplay between RNA polymerase and nascent RNA structure

PubMed Central

Zhang, Jinwei; Landick, Robert

2016-01-01

The vectorial (5′-to-3′ at varying velocity) synthesis of RNA by cellular RNA polymerases creates a rugged kinetic landscape, demarcated by frequent, sometimes long-lived pauses. In addition to myriad gene-regulatory roles, these pauses temporally and spatially program the co-transcriptional, hierarchical folding of biologically active RNAs. Conversely, these RNA structures, which form inside or near the RNA exit channel, interact with the polymerase and adjacent protein factors to influence RNA synthesis by modulating pausing, termination, antitermination, and slippage. Here we review the evolutionary origin, mechanistic underpinnings, and regulatory consequences of this interplay between RNA polymerase and nascent RNA structure. We categorize and attempt to rationalize the extensive linkage between the transcriptional machinery and its product, and provide a framework for future studies. PMID:26822487

Multi-imaging analysis of nascent surface structures generated during femtosecond laser irradiation of silicon in high vacuum

NASA Astrophysics Data System (ADS)

Gesuele, F.; JJ Nivas, J.; Fittipaldi, R.; Altucci, C.; Bruzzese, R.; Maddalena, P.; Amoruso, S.

2018-02-01

We report a correlative imaging analysis of a crystalline silicon target after irradiation with a low number of 1055 nm, 850 fs laser pulses with several microscopy techniques (e.g., scanning electron microscopy, atomic force microscopy, Raman micro-imaging and confocal optical microscopy). The analysis is carried out on samples irradiated both in high vacuum and at atmospheric pressure conditions, evidencing interesting differences induced by the ambient environment. In high-vacuum conditions, the results evidence the formation of a halo, which is constituted by alternate stripes of amorphous and crystalline silicon, around the nascent ablation crater. In air, such an effect is drastically reduced, due to the significant back-deposition of nanoparticulate material induced by the larger ambient pressure.

Aerodynamic loads on a Darrieus rotor blade

NASA Astrophysics Data System (ADS)

Wilson, R. E.; McKie, W. R.; Lissaman, P. B. S.; James, M.

1983-03-01

A method is presented for the free vortex analysis of a Darrieus rotor blade in nonsteady motion, which employs the circle theorem to map the moving rotor airfoil into the circle plane and models the wake generated in terms of point vortices. Nascent vortex strength and position are taken from the Kutta condition, so that the nascent vortex has the same strength as a vortex sheet of uniform strength. Pressure integration over the plate and wake vortex impulse methods yields the same numerical results. The numerical results presented for a one-bladed Darrieus rotor at a tip/speed ratio of three, and two different chord sizes, indicate that the moment on the blade can be adequately approximated by quasi-steady relationships, although the accurate determination of local velocity and circulation are still required.

Emerging technologies for biotherapeutic bioanalysis from a high-throughput and multiplexing perspective: insights from an AAPS emerging technology action program committee.

PubMed

Purushothama, Shobha; Dysinger, Mark; Chen, Yao; Österlund, Karolina; Mora, Johanna; Chunyk, Allison Given; Peloquin, Russ

2018-02-01

This manuscript aims to provide insights and updates on emerging technologies from a throughput and multiplexing perspective and to update readers on changes in previously reported technologies. The technologies discussed range from nascent (ultrasensitive Cira, Intellicyt ® , Dynaxi and Captsure™) to the more established (Ella and SQIDlite™). For the nascent technologies, there was an emphasis on user interviews and reviews, where available, to help provide an unbiased view to our readers. For the Ella, a review of published user data as well as author and other user experiences are summarized. Due to their emergent nature, all the technologies described are applicable in the early drug development stage, may require an upfront investment of capital and may not perform as expected.

Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain

PubMed Central

Lintner, Nathanael G.; McClure, Kim F.; Petersen, Donna; Londregan, Allyn T.; Piotrowski, David W.; Wei, Liuqing; Xiao, Jun; Bolt, Michael; Loria, Paula M.; Maguire, Bruce; Geoghegan, Kieran F.; Huang, Austin; Rolph, Tim; Liras, Spiros; Doudna, Jennifer A.; Dullea, Robert G.

2017-01-01

Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a key role in regulating the levels of plasma low-density lipoprotein cholesterol (LDL-C). Here, we demonstrate that the compound PF-06446846 inhibits translation of PCSK9 by inducing the ribosome to stall around codon 34, mediated by the sequence of the nascent chain within the exit tunnel. We further show that PF-06446846 reduces plasma PCSK9 and total cholesterol levels in rats following oral dosing. Using ribosome profiling, we demonstrate that PF-06446846 is highly selective for the inhibition of PCSK9 translation. The mechanism of action employed by PF-06446846 reveals a previously unexpected tunability of the human ribosome that allows small molecules to specifically block translation of individual transcripts. PMID:28323820

Subliminal (latent) processing of pain and its evolution to conscious awareness.

PubMed

Borsook, David; Youssef, Andrew M; Barakat, Nadia; Sieberg, Christine B; Elman, Igor

2018-05-01

By unconscious or covert processing of pain we refer to nascent interactions that affect the eventual deliverance of pain awareness. Thus, internal processes (viz., repeated nociceptive events, inflammatory kindling, reorganization of brain networks, genetic) or external processes (viz., environment, socioeconomic levels, modulation of epigenetic status) contribute to enhancing or inhibiting the presentation of pain awareness. Here we put forward the notion that for many patients, ongoing sub-conscious changes in brain function are significant players in the eventual manifestation of chronic pain. In this review, we provide clinical examples of nascent or what we term pre-pain processes and the neurobiological mechanisms of how these changes may contribute to pain, but also potential opportunities to define the process for early therapeutic interventions. Copyright © 2018. Published by Elsevier Ltd.

Digital Inverter Amine Sensing via Synergistic Responses by n and p Organic Semiconductors.

PubMed

Tremblay, Noah J; Jung, Byung Jun; Breysse, Patrick; Katz, Howard E

2011-11-22

Chemiresistors and sensitive OFETs have been substantially developed as cheap, scalable, and versatile sensing platforms. While new materials are expanding OFET sensing capabilities, the device architectures have changed little. Here we report higher order logic circuits utilizing OFETs sensitive to amine vapors. The circuits depend on the synergistic responses of paired p- and n-channel organic semiconductors, including an unprecedented analyte-induced current increase by the n-channel semiconductor. This represents the first step towards 'intelligent sensors' that utilize analog signal changes in sensitive OFETs to produce direct digital readouts suitable for further logic operations.

Digital Inverter Amine Sensing via Synergistic Responses by n and p Organic Semiconductors

PubMed Central

Tremblay, Noah J.; Jung, Byung Jun; Breysse, Patrick; Katz, Howard E.

2013-01-01

Chemiresistors and sensitive OFETs have been substantially developed as cheap, scalable, and versatile sensing platforms. While new materials are expanding OFET sensing capabilities, the device architectures have changed little. Here we report higher order logic circuits utilizing OFETs sensitive to amine vapors. The circuits depend on the synergistic responses of paired p- and n-channel organic semiconductors, including an unprecedented analyte-induced current increase by the n-channel semiconductor. This represents the first step towards ‘intelligent sensors’ that utilize analog signal changes in sensitive OFETs to produce direct digital readouts suitable for further logic operations. PMID:23754969

Bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions.

PubMed

Römling, Ute; Galperin, Michael Y

2015-09-01

Recent studies of bacterial cellulose biosynthesis, including structural characterization of a functional cellulose synthase complex, provided the first mechanistic insight into this fascinating process. In most studied bacteria, just two subunits, BcsA and BcsB, are necessary and sufficient for the formation of the polysaccharide chain in vitro. Other subunits - which differ among various taxa - affect the enzymatic activity and product yield in vivo by modulating (i) the expression of the biosynthesis apparatus, (ii) the export of the nascent β-D-glucan polymer to the cell surface, and (iii) the organization of cellulose fibers into a higher-order structure. These auxiliary subunits play key roles in determining the quantity and structure of resulting biofilms, which is particularly important for the interactions of bacteria with higher organisms - leading to rhizosphere colonization and modulating the virulence of cellulose-producing bacterial pathogens inside and outside of host cells. We review the organization of four principal types of cellulose synthase operon found in various bacterial genomes, identify additional bcs genes that encode components of the cellulose biosynthesis and secretion machinery, and propose a unified nomenclature for these genes and subunits. We also discuss the role of cellulose as a key component of biofilms and in the choice between acute infection and persistence in the host. Copyright © 2015 Elsevier Ltd. All rights reserved.

Professional Certification

EPA Pesticide Factsheets

The WaterSense Professional Certification Program Labeling System specifies the requirements a professional certifying organization must meet to have the professional certification program labeled under one of the WaterSense program specifications.

Science & the Senses: Perceptions & Deceptions

ERIC Educational Resources Information Center

Stansfield, William D.

2012-01-01

Science requires the acquisition and analysis of empirical (sense-derived) data. Given the same physical objects or phenomena, the sense organs of all people do not respond equally to these stimuli, nor do their minds interpret sensory signals identically. Therefore, teachers should develop lectures on human sensory systems that include some…

Lanthanide-Functionalized Metal-Organic Framework Hybrid Systems To Create Multiple Luminescent Centers for Chemical Sensing.

PubMed

Yan, Bing

2017-11-21

Metal-organic frameworks (MOFs) possess an important advantage over other candidate classes for chemosensory materials because of their exceptional structural tunability and properties. Luminescent sensing using MOFs is a simple, intuitive, and convenient method to recognize species, but the method has limitations, such as insufficient chemical selectivity and signal loss. MOFs contain versatile building blocks (linkers or ligands) with special chemical reactivity, and postsynthetic modification (PSM) provides an opportunity to exploit and expand their unique properties. The linkers in most MOFs contain aromatic subunits that can readily display luminescence after ultraviolet or visible (typically blue) excitation, and this is the main luminescent nature of most MOFs. The introduction of photoactive lanthanide ions (Ln 3+ ) into the MOF hosts may produce new luminescent signals at different positions from that of the MOF linker, but this depends on the intramolecular energy transfer (antenna effect) from the MOF (linkers) to the Ln 3+ ions. Controlling the Ln 3+ content in MOF hybrids may create multiple luminescent centers. The nature of the unique luminescent centers may cause different responses to sensing species (i.e., ratiometric sensing), which may provide a new opportunity for luminescence research with applications to chemical sensing. In this Account, recent research progress on using lanthanide-functionalized MOF hybrid materials to create multiple luminescent centers for chemical sensing is described. Here we propose a general strategy to functionalize MOF hosts with lanthanide ions, compounds, or other luminescent species (organic dyes or carbon dots) and to assemble types of photofunctional hybrid systems based on lanthanide-functionalized MOFs. Five main methods were used to functionalize the MOFs and assemble the hybrid materials: in situ composition, ionic doping, ionic exchange, covalent PSM, and coordinated PSM. Through the lanthanide functionalization, multiple (double or triple) luminescent centers were created with different luminescent bands in the visible region. Because of the different luminescent natures of the lanthanide ions, MOF linkers, and other species (organic dyes or carbon dots), they display different responses to sensing species. Currently, using these strategies, we have utilized a dual-response luminescent probe to realize chemical sensing of different types of cations (Fe 3+ /Fe 2+ , Hg 2+ , and Cd 2+ ), anions (Cr 2 O 7 2- /CrO 4 - and CO 3 2- ), molecules (volatile organic compounds and O 2 ), special air pollutants (formaldehyde), and biomarkers of food spoilage as well as pH and temperature. Additionally, we have achieved triple-luminescence-response sensing of ions (Ag + , Hg 2+ , and S 2- ) in complicated aqueous environments, which was developed using a logic operation.

How cells jump: Ultrafast motions in the single-celled micro-organism Halteria grandinella

NASA Astrophysics Data System (ADS)

Krishnamurthy, Deepak; Cockenpot, Fabien; Prakash, Manu

Here we describe a novel behavior of ''jumping'' in micro-organisms, observed in the common freshwater ciliate Halteria grandinella. This organism's swimming motion is characterized by periods of forward swimming at around 10 body lengths/s punctuated by extremely rapid backward ''jumps'' where the organism reaches speeds of more than 150 body lengths/s. We show, using detailed measurements of the swimming motion through high-speed video microscopy, that the extreme swimming speeds are achieved by the motile cilia transitioning to a beating mode characterized by a significantly larger beat amplitude and an associated reversal in the direction of thrust production. We further show that H.grandinella cells can sense a fluid shear stress signal and ''jump'' in response: a possible predator avoidance mechanism. We investigate this mechanism of shear sensing and study the role of the long, slender structures known as ''cirri'' as microscale sensors of shear stress. The jumping of H.grandinella is at the limits of the metabolic rate of the organism and thus offers insights into the limiting factors governing energy storage and mechanical power release at the microscale. Concurrently their sensing apparatus allows an understanding of the physical limits of microscale mechanical sensing. This material is based on work supported by, or in part by, the US Army Research Laboratory and the US Army Research Office under contract/Grant Number W911NF-15-1-0358.

Organic Electronics for Point-of-Care Metabolite Monitoring.

PubMed

Pappa, Anna-Maria; Parlak, Onur; Scheiblin, Gaetan; Mailley, Pascal; Salleo, Alberto; Owens, Roisin M

2018-01-01

In this review we focus on demonstrating how organic electronic materials can solve key problems in biosensing thanks to their unique material properties and implementation in innovative device configurations. We highlight specific examples where these materials solve multiple issues related to complex sensing environments, and we benchmark these examples by comparing them to state-of-the-art commercially available sensing using alternative technologies. We have categorized our examples by sample type, focusing on sensing from body fluids in vitro and on wearable sensors, which have attracted significant interest owing to their integration with everyday life activities. We finish by describing a future trend for in vivo, implantable sensors, which aims to build on current progress from sensing in biological fluids ex vivo. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular Nitrogen Fluorescence Lidar for Remote Sensing of the Auroral Ionosphere

DTIC Science & Technology

1994-02-24

AD-A280 716 PL-TR-94-2044 MOLECULAR NITROGEN FLUORESCENCE LIDAR FOR REMOTE SENSING OF THE AURORAL IONOSPHERE Richard Garner Michael Burka...6. AUTHOR(S) Richard Garner Contract F19628-92-C-0160 Michael Burka 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION...by Richard Dickmuaz of the HIPAS observatory and by Ralph Wuerker of UCLA PPL. 29 le

Testing the Vibrational Theory of Olfaction: A Bio-Organic Chemistry Laboratory Experiment Using Hooke's Law and Chirality

ERIC Educational Resources Information Center

Muthyala, Rajeev S.; Butani, Deepali; Nelson, Michelle; Tran, Kiet

2017-01-01

Sense of smell is one of the important senses that enables us to interact with our environment. The molecular basis of olfactory signal transduction is a fascinating area for organic chemistry educators to explore in terms of developing undergraduate laboratory activities at the interface of chemistry and biology. In this paper, a guided-inquiry…

75 FR 63037 - General Pulaski Memorial Day, 2010

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-13

... resist subjugation. During his subsequent exile to France, he learned of our nascent struggle for... solemn obligations to each other's security and our shared values, including a deep and abiding...

Mechanisms of nascent fiber formation during avian skeletal muscle hypertrophy

NASA Technical Reports Server (NTRS)

McCormick, K. M.; Schultz, E.

1992-01-01

This study examined two putative mechanisms of new fiber formation in postnatal skeletal muscle, namely longitudinal fragmentation of existing fibers and de novo formation. The relative contributions of these two mechanisms to fiber formation in hypertrophying anterior latissimus dorsi (ALD) muscle were assessed by quantitative analysis of their nuclear populations. Muscle hypertrophy was induced by wing-weighting for 1 week. All nuclei formed during the weighting period were labeled by continuous infusion of 5-bromo-2'-deoxyuridine (BrdU), a thymidine analog, and embryonic-like fibers were identified using an antibody to ventricular-like embryonic (V-EMB) myosin. The number of BrdU-labeled and unlabeled nuclei in V-EMB-positive fibers were counted. Wing-weighting resulted in significant muscle enlargement and the appearance of many V-EMB+ fibers. The majority of V-EMB+ fibers were completely independent of mature fibers and had a nuclear density characteristics of developing fibers. Furthermore, nearly 100% of the nuclei in independent V-EMB+ fibers were labeled. These findings strongly suggest that most V-EMB+ fibers were nascent fibers formed de novo during the weighting period by satellite cell activation and fusion. Nascent fibers were found primarily in the space between fascicles where they formed a complex anastomosing network of fibers running at angles to one another. Although wing-weighting induced an increase in the number of branched fibers, there was no evidence that V-EMB+ fibers were formed by longitudinal fragmentation. The location of newly formed fibers in wing-weighted and regenerating ALD muscle was compared to determine whether satellite cells in the ALD muscle were unusual in that, if stimulated to divide, they would form fibers in the inter- and intrafascicular space. In contrast to wing-weighted muscle, nascent fibers were always found closely associated with necrotic fibers. These results suggest that wing-weighting is not simply another model of regeneration, but rather produces a unique environment which induces satellite cell migration and subsequent fiber formation in the interfascicular space. De novo fiber formation is apparently the principal mechanism for the hyperplasia reported to occur in the ALD muscle undergoing hypertrophy induced by wing-weighting.

A combined crossed-beam and theoretical study of the reaction dynamics of O(3P) + C2H3 → C2H2 + OH: Analysis of the nascent OH products with the preferential population of the Π(A') component

NASA Astrophysics Data System (ADS)

Park, Min-Jin; Jang, Su-Chan; Choi, Jong-Ho

2012-11-01

The gas-phase reaction dynamics of ground-state atomic oxygen [O(3P) from the photo-dissociation of NO2] with vinyl radicals [C2H3 from the supersonic flash pyrolysis of vinyl iodide, C2H3I] has been investigated using a combination of high-resolution laser-induced fluorescence spectroscopy in a crossed-beam configuration and ab initio calculations. Unlike the previous gas-phase bulk kinetic experiments by Baulch et al. [J. Phys. Chem. Ref. Data 34, 757 (2005)], 10.1063/1.1748524, a new exothermic channel of O(3P) + C2H3 → C2H2 + OH (X 2Π: υ″ = 0) has been identified for the first time, and the population analysis shows bimodal nascent rotational distributions of OH products with low- and high-N″ components with a ratio of 2.4:1. No spin-orbit propensities were observed, and the averaged ratios of Π(A')/Π(A″) were determined to be 1.66 ± 0.27. On the basis of computations at the CBS-QB3 theory level and comparison with prior theory, the microscopic mechanisms responsible for the nascent populations can be understood in terms of two competing dynamical pathways: a direct abstraction process in the low-N″ regime as the major pathway and an addition-complex forming process in the high-N″ regime as the minor pathway. Particularly, during the bond cleavage process of the weakly bound van der Waals complex C2H2—OH, the characteristic pathway from the low dihedral-angle geometry was consistent with the observed preferential population of the Π(A') component in the nascent OH products. A molecular-level discussion of the reactivity, mechanism, and dynamical features of the title reaction are presented together with a comparison to gas-phase oxidation reactions of a series of prototypical hydrocarbon radicals.

On the Use of Ocean Color Remote Sensing to Measure the Transport of Dissolved Organic Carbon by the Mississippi River Plume

NASA Technical Reports Server (NTRS)

DelCastillo, Carlos E.; Miller, Richard L.

2007-01-01

We investigated the use of ocean color remote sensing to measure transport of dissolved organic carbon (DOC) by the Mississippi River to the Gulf of Mexico. From 2000 to 2005 we recorded surface measurements of DOC, colored dissolved organic matter (CDOM), salinity, and water-leaving radiances during five cruises to the Mississippi River Plume. These measurements were used to develop empirical relationships to derive CDOM, DOC, and salinity from monthly composites of SeaWiFS imagery collected from 1998 through 2005. We used river flow data and a two-end-member mixing model to derive DOC concentrations in the river end-member, river flow, and DOC transport using remote sensing data. We compared our remote sensing estimates of river flow and DOC transport with data collected by the United States Geological Survey (USGS) from 1998 through 2005. Our remote sensing estimates of river flow and DOC transport correlated well (r2 0.70) with the USGS data. Our remote sensing estimates and USGS field data showed low variability in DOC concentrations in the river end-member (7-11%), and high seasonal variability in river flow (50%). Therefore, changes in river flow control the variability in DOC transport, indicating that the remote sensing estimate of river flow is the most critical element of our DOC transport measurement. We concluded that it is possible to use this method to estimate DOC transport by other large rivers if there are data on the relationship between CDOM, DOC, and salinity in the river plume.

Gravimetric chemical sensors based on silica-based mesoporous organic-inorganic hybrids.

PubMed

Xu, Jiaqiang; Zheng, Qi; Zhu, Yongheng; Lou, Huihui; Xiang, Qun; Cheng, Zhixuan

2014-09-01

Silica-based mesoporous organic-inorganic hybrid material modified quartz crystal microbalance (QCM) sensors have been examined for their ability to achieve highly sensitive and selective detection. Mesoporous silica SBA-15 serves as an inorganic host with large specific surface area, facilitating gas adsorption, and thus leads to highly sensitive response; while the presence of organic functional groups contributes to the greatly improved specific sensing property. In this work, we summarize our efforts in the rational design and synthesis of novel sensing materials for the detection of hazardous substances, including simulant nerve agent, organic vapor, and heavy metal ion, and develop high-performance QCM-based chemical sensors.

Contrasting seasonality in optical-biogeochemical properties of the Baltic Sea.

PubMed

Simis, Stefan G H; Ylöstalo, Pasi; Kallio, Kari Y; Spilling, Kristian; Kutser, Tiit

2017-01-01

Optical-biogeochemical relationships of particulate and dissolved organic matter are presented in support of remote sensing of the Baltic Sea pelagic. This system exhibits strong seasonality in phytoplankton community composition and wide gradients of chromophoric dissolved organic matter (CDOM), properties which are poorly handled by existing remote sensing algorithms. Absorption and scattering properties of particulate matter reflected the seasonality in biological (phytoplankton succession) and physical (thermal stratification) processes. Inherent optical properties showed much wider variability when normalized to the chlorophyll-a concentration compared to normalization to either total suspended matter dry weight or particulate organic carbon. The particle population had the largest optical variability in summer and was dominated by organic matter in both seasons. The geographic variability of CDOM and relationships with dissolved organic carbon (DOC) are also presented. CDOM dominated light absorption at blue wavelengths, contributing 81% (median) of the absorption by all water constituents at 400 nm and 63% at 442 nm. Consequentially, 90% of water-leaving radiance at 412 nm originated from a layer (z90) no deeper than approximately 1.0 m. With water increasingly attenuating light at longer wavelengths, a green peak in light penetration and reflectance is always present in these waters, with z90 up to 3.0-3.5 m depth, whereas z90 only exceeds 5 m at biomass < 5 mg Chla m-3. High absorption combined with a weakly scattering particle population (despite median phytoplankton biomass of 14.1 and 4.3 mg Chla m-3 in spring and summer samples, respectively), characterize this sea as a dark water body for which dedicated or exceptionally robust remote sensing techniques are required. Seasonal and regional optical-biogeochemical models, data distributions, and an extensive set of simulated remote-sensing reflectance spectra for testing of remote sensing algorithms are provided as supplementary data.

Useless hearing in male Emblemasoma auditrix (Diptera, Sarcophagidae)--a case of intralocus sexual conflict during evolution of a complex sense organ?

PubMed

Lakes-Harlan, Reinhard; Devries, Thomas; Stölting, Heiko; Stumpner, Andreas

2014-01-01

Sensory modalities typically are important for both sexes, although sex-specific functional adaptations may occur frequently. This is true for hearing as well. Consequently, distinct behavioural functions were identified for the different insect hearing systems. Here we describe a first case, where a trait of an evolutionary novelty and a highly specialized hearing organ is adaptive in only one sex. The main function of hearing of the parasitoid fly Emblemasoma auditrix is to locate the host, males of the cicada species Okanagana rimosa, by their calling song. This task is performed by female flies, which deposit larvae into the host. We show that male E. auditrix possess a hearing sense as well. The morphology of the tympanal organ of male E. auditrix is rather similar to the female ear, which is 8% broader than the male ear. In both sexes the physiological hearing threshold is tuned to 5 kHz. Behavioural tests show that males are able to orient towards the host calling song, although phonotaxis often is incomplete. However, despite extensive observations in the field and substantial knowledge of the biology of E. auditrix, no potentially adaptive function of the male auditory sense has been identified. This unique hearing system might represent an intralocus sexual conflict, as the complex sense organ and the behavioural relevant neuronal network is adaptive for only one sex. The correlated evolution of the sense organ in both sexes might impose substantial constraints on the sensory properties of the ear. Similar constraints, although hidden, might also apply to other sensory systems in which behavioural functions differ between sexes.

Visual Image Sensor Organ Replacement

NASA Technical Reports Server (NTRS)

Maluf, David A.

2014-01-01

This innovation is a system that augments human vision through a technique called "Sensing Super-position" using a Visual Instrument Sensory Organ Replacement (VISOR) device. The VISOR device translates visual and other sensors (i.e., thermal) into sounds to enable very difficult sensing tasks. Three-dimensional spatial brightness and multi-spectral maps of a sensed image are processed using real-time image processing techniques (e.g. histogram normalization) and transformed into a two-dimensional map of an audio signal as a function of frequency and time. Because the human hearing system is capable of learning to process and interpret extremely complicated and rapidly changing auditory patterns, the translation of images into sounds reduces the risk of accidentally filtering out important clues. The VISOR device was developed to augment the current state-of-the-art head-mounted (helmet) display systems. It provides the ability to sense beyond the human visible light range, to increase human sensing resolution, to use wider angle visual perception, and to improve the ability to sense distances. It also allows compensation for movement by the human or changes in the scene being viewed.

First principles of Hamiltonian medicine.

PubMed

Crespi, Bernard; Foster, Kevin; Úbeda, Francisco

2014-05-19

We introduce the field of Hamiltonian medicine, which centres on the roles of genetic relatedness in human health and disease. Hamiltonian medicine represents the application of basic social-evolution theory, for interactions involving kinship, to core issues in medicine such as pathogens, cancer, optimal growth and mental illness. It encompasses three domains, which involve conflict and cooperation between: (i) microbes or cancer cells, within humans, (ii) genes expressed in humans, (iii) human individuals. A set of six core principles, based on these domains and their interfaces, serves to conceptually organize the field, and contextualize illustrative examples. The primary usefulness of Hamiltonian medicine is that, like Darwinian medicine more generally, it provides novel insights into what data will be productive to collect, to address important clinical and public health problems. Our synthesis of this nascent field is intended predominantly for evolutionary and behavioural biologists who aspire to address questions directly relevant to human health and disease.

Centriole maturation requires regulated Plk1 activity during two consecutive cell cycles.

PubMed

Kong, Dong; Farmer, Veronica; Shukla, Anil; James, Jana; Gruskin, Richard; Kiriyama, Shigeo; Loncarek, Jadranka

2014-09-29

Newly formed centrioles in cycling cells undergo a maturation process that is almost two cell cycles long before they become competent to function as microtubule-organizing centers and basal bodies. As a result, each cell contains three generations of centrioles, only one of which is able to form cilia. It is not known how this long and complex process is regulated. We show that controlled Plk1 activity is required for gradual biochemical and structural maturation of the centrioles and timely appendage assembly. Inhibition of Plk1 impeded accumulation of appendage proteins and appendage formation. Unscheduled Plk1 activity, either in cycling or interphase-arrested cells, accelerated centriole maturation and appendage and cilia formation on the nascent centrioles, erasing the age difference between centrioles in one cell. These findings provide a new understanding of how the centriole cycle is regulated and how proper cilia and centrosome numbers are maintained in the cells.

Centriole maturation requires regulated Plk1 activity during two consecutive cell cycles

PubMed Central

Kong, Dong; Farmer, Veronica; Shukla, Anil; James, Jana; Gruskin, Richard; Kiriyama, Shigeo

2014-01-01

Newly formed centrioles in cycling cells undergo a maturation process that is almost two cell cycles long before they become competent to function as microtubule-organizing centers and basal bodies. As a result, each cell contains three generations of centrioles, only one of which is able to form cilia. It is not known how this long and complex process is regulated. We show that controlled Plk1 activity is required for gradual biochemical and structural maturation of the centrioles and timely appendage assembly. Inhibition of Plk1 impeded accumulation of appendage proteins and appendage formation. Unscheduled Plk1 activity, either in cycling or interphase-arrested cells, accelerated centriole maturation and appendage and cilia formation on the nascent centrioles, erasing the age difference between centrioles in one cell. These findings provide a new understanding of how the centriole cycle is regulated and how proper cilia and centrosome numbers are maintained in the cells. PMID:25246616

Biomimetic Delivery with Micro- and Nanoparticles

PubMed Central

Balmert, Stephen C.; Little, Steven R.

2013-01-01

The nascent field of biomimetic delivery with micro- and nanoparticles (MNP) has advanced considerably in recent years. Drawing inspiration from the ways that cells communicate in the body, several different modes of “delivery” (i.e. temporospatial presentation of biological signals) have been investigated in a number of therapeutic contexts. In particular, this review focuses on (1) controlled release formulations that deliver natural soluble factors with physiologically relevant temporal context, (2) presentation of surface-bound ligands to cells, with spatial organization of ligands ranging from isotropic to dynamically anisotropic, and (3) physical properties of particles, including size, shape and mechanical stiffness, which mimic those of natural cells. Importantly, the context provided by multimodal, or multifactor delivery represents a key element of most biomimetic MNP systems, a concept illustrated by an analogy to human interpersonal communication. Regulatory implications of increasingly sophisticated and “cell-like” biomimetic MNP systems are also discussed. PMID:22528985

Development of lamellar structures in natural waxes - an electron diffraction investigation

NASA Astrophysics Data System (ADS)

Dorset, Douglas L.

1999-06-01

When they are recrystallized from the melt, natural plant or insect waxes tend to form solid phases with a nematic-like structure (i.e. a parallel array of polymethylene chains with little or no aggregation of the molecules into distinct layers). An electron diffraction study of carnauba wax and two types of beeswax has shown that the degree of molecular organization into lamellar structures can be enhanced by annealing in the presence of benzoic acid, which also acts as an epitaxial substrate. Nevertheless, the resultant layer structure in the annealed solid is not the same as that found for paraffin wax fractions refined from petroleum. Probably because of a small but significant fraction of a very long chain ingredient, the lamellar separation is incomplete, incorporating a number of `bridging molecules' that span the nascent lamellar interface.The same phenomenon has been described recently for a low molecular weight polyethylene.

Emergence of an apical epithelial cell surface in vivo

PubMed Central

Sedzinski, Jakub; Hannezo, Edouard; Tu, Fan; Biro, Maté; Wallingford, John B.

2016-01-01

Epithelial sheets are crucial components of all metazoan animals, enclosing organs and protecting the animal from its environment. Epithelial homeostasis poses unique challenges, as addition of new cells and loss of old cells must be achieved without disrupting the fluid-tight barrier and apicobasal polarity of the epithelium. Several studies have identified cell biological mechanisms underlying extrusion of cells from epithelia, but far less is known of the converse mechanism by which new cells are added. Here, we combine molecular, pharmacological and laser-dissection experiments with theoretical modelling to characterize forces driving emergence of an apical surface as single nascent cells are added to a vertebrate epithelium in vivo. We find that this process involves the interplay between cell-autonomous actin-generated pushing forces in the emerging cell and mechanical properties of neighboring cells. Our findings define the forces driving this cell behavior, contributing to a more comprehensive understanding of epithelial homeostasis. PMID:26766441

The first international workshop on the epigenetics of osteoarthritis.

PubMed

Meulenbelt, Ingrid M; Bhutani, Nidhi; den Hollander, Wouter; Gay, Steffen; Oppermann, Udo; Reynard, Louise N; Skelton, Andrew J; Young, David A; Beier, Frank; Loughlin, John

2017-01-01

Osteoarthritis (OA) is a major clinical problem across the world, in part due to the lack of disease-modifying drugs resulting, to a significant degree, from our incomplete understanding of the underlying molecular mechanisms of the disease. Emerging evidence points to a role of epigenetics in the pathogenesis of OA, but research in this area is still in its early stages. In order to summarize current knowledge and to facilitate the potential coordination of future research activities, the first international workshop on the epigenetics of OA was held in Amsterdam in October 2015. Recent findings on DNA methylation and hydroxymethylation, histone modifications, noncoding RNAs, and other epigenetic mechanisms were presented and discussed. The workshop demonstrated the advantage of bringing together those working in this nascent field and highlights from the event are summarized in this report in the form of summaries from invited speakers and organizers.

Dietary Nutrients and Bioactive Substances Modulate Heat Shock Protein (HSP) Expression: A Review.

PubMed

Moura, Carolina Soares; Lollo, Pablo Christiano Barboza; Morato, Priscila Neder; Amaya-Farfan, Jaime

2018-05-28

Interest in the heat shock proteins (HSPs), as a natural physiological toolkit of living organisms, has ranged from their chaperone function in nascent proteins to the remedial role following cell stress. As part of the defence system, HSPs guarantee cell tolerance against a variety of stressors, including exercise, oxidative stress, hyper and hypothermia, hyper and hypoxia and improper diets. For the past couple of decades, research on functional foods has revealed a number of substances likely to trigger cell protection through mechanisms that involve the induction of HSP expression. This review will summarize the occurrence of the most easily inducible HSPs and describe the effects of dietary proteins, peptides, amino acids, probiotics, high-fat diets and other food-derived substances reported to induce HSP response in animals and humans studies. Future research may clarify the mechanisms and explore the usefulness of this natural alternative of defense and the modulating mechanism of each substance.

A Molecular Description of Cellulose Biosynthesis

PubMed Central

McNamara, Joshua T.; Morgan, Jacob L.W.; Zimmer, Jochen

2016-01-01

Cellulose is the most abundant biopolymer on Earth, and certain organisms from bacteria to plants and animals synthesize cellulose as an extracellular polymer for various biological functions. Humans have used cellulose for millennia as a material and an energy source, and the advent of a lignocellulosic fuel industry will elevate it to the primary carbon source for the burgeoning renewable energy sector. Despite the biological and societal importance of cellulose, the molecular mechanism by which it is synthesized is now only beginning to emerge. On the basis of recent advances in structural and molecular biology on bacterial cellulose synthases, we review emerging concepts of how the enzymes polymerize glucose molecules, how the nascent polymer is transported across the plasma membrane, and how bacterial cellulose biosynthesis is regulated during biofilm formation. Additionally, we review evolutionary commonalities and differences between cellulose synthases that modulate the nature of the cellulose product formed. PMID:26034894

Planar cell polarity genes control the connectivity of enteric neurons

PubMed Central

Sasselli, Valentina; Boesmans, Werend; Vanden Berghe, Pieter; Tissir, Fadel; Goffinet, André M.; Pachnis, Vassilis

2013-01-01

A highly complex network of intrinsic enteric neurons is required for the digestive and homeostatic functions of the gut. Nevertheless, the genetic and molecular mechanisms that regulate their assembly into functional neuronal circuits are currently unknown. Here we report that the planar cell polarity (PCP) genes Celsr3 and Fzd3 are required during murine embryogenesis to specifically control the guidance and growth of enteric neuronal projections relative to the longitudinal and radial gut axes. Ablation of these genes disrupts the normal organization of nascent neuronal projections, leading to subtle changes of axonal tract configuration in the mature enteric nervous system (ENS), but profound abnormalities in gastrointestinal motility. Our data argue that PCP-dependent modules of connectivity established at early stages of enteric neurogenesis control gastrointestinal function in adult animals and provide the first evidence that developmental deficits in ENS wiring may contribute to the pathogenesis of idiopathic bowel disorders. PMID:23478408

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes.

PubMed

Theis, Kevin R; Dheilly, Nolwenn M; Klassen, Jonathan L; Brucker, Robert M; Baines, John F; Bosch, Thomas C G; Cryan, John F; Gilbert, Scott F; Goodnight, Charles J; Lloyd, Elisabeth A; Sapp, Jan; Vandenkoornhuyse, Philippe; Zilber-Rosenberg, Ilana; Rosenberg, Eugene; Bordenstein, Seth R

2016-01-01

Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization-what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.

Shifts in the architecture of the Nationwide Health Information Network.

PubMed

Lenert, Leslie; Sundwall, David; Lenert, Michael Edward

2012-01-01

In the midst of a US $30 billion USD investment in the Nationwide Health Information Network (NwHIN) and electronic health records systems, a significant change in the architecture of the NwHIN is taking place. Prior to 2010, the focus of information exchange in the NwHIN was the Regional Health Information Organization (RHIO). Since 2010, the Office of the National Coordinator (ONC) has been sponsoring policies that promote an internet-like architecture that encourages point to-point information exchange and private health information exchange networks. The net effect of these activities is to undercut the limited business model for RHIOs, decreasing the likelihood of their success, while making the NwHIN dependent on nascent technologies for community level functions such as record locator services. These changes may impact the health of patients and communities. Independent, scientifically focused debate is needed on the wisdom of ONC's proposed changes in its strategy for the NwHIN.

Speciation driven by hybridization and chromosomal plasticity in a wild yeast.

PubMed

Leducq, Jean-Baptiste; Nielly-Thibault, Lou; Charron, Guillaume; Eberlein, Chris; Verta, Jukka-Pekka; Samani, Pedram; Sylvester, Kayla; Hittinger, Chris Todd; Bell, Graham; Landry, Christian R

2016-01-11

Hybridization is recognized as a powerful mechanism of speciation and a driving force in generating biodiversity. However, only few multicellular species, limited to a handful of plants and animals, have been shown to fulfil all the criteria of homoploid hybrid speciation. This lack of evidence could lead to the interpretation that speciation by hybridization has a limited role in eukaryotes, particularly in single-celled organisms. Laboratory experiments have revealed that fungi such as budding yeasts can rapidly develop reproductive isolation and novel phenotypes through hybridization, showing that in principle homoploid speciation could occur in nature. Here, we report a case of homoploid hybrid speciation in natural populations of the budding yeast Saccharomyces paradoxus inhabiting the North American forests. We show that the rapid evolution of chromosome architecture and an ecological context that led to secondary contact between nascent species drove the formation of an incipient hybrid species with a potentially unique ecological niche.

Rapid, sensitive, and selective fluorescent DNA detection using iron-based metal-organic framework nanorods: Synergies of the metal center and organic linker.

PubMed

Tian, Jingqi; Liu, Qian; Shi, Jinle; Hu, Jianming; Asiri, Abdullah M; Sun, Xuping; He, Yuquan

2015-09-15

Considerable recent attention has been paid to homogeneous fluorescent DNA detection with the use of nanostructures as a universal "quencher", but it still remains a great challenge to develop such nanosensor with the benefits of low cost, high speed, sensitivity, and selectivity. In this work, we report the use of iron-based metal-organic framework nanorods as a high-efficient sensing platform for fluorescent DNA detection. It only takes about 4 min to complete the whole "mix-and-detect" process with a low detection limit of 10 pM and a strong discrimination of single point mutation. Control experiments reveal the remarkable sensing behavior is a consequence of the synergies of the metal center and organic linker. This work elucidates how composition control of nanostructures can significantly impact their sensing properties, enabling new opportunities for the rational design of functional materials for analytical applications. Copyright © 2015 Elsevier B.V. All rights reserved.

Sensing of volatile organic compounds by copper phthalocyanine thin films

NASA Astrophysics Data System (ADS)

Ridhi, R.; Saini, G. S. S.; Tripathi, S. K.

2017-02-01

Thin films of copper phthalocyanine have been deposited by thermal evaporation technique. We have subsequently exposed these films to the vapours of methanol, ethanol and propanol. Optical absorption, infrared spectra and electrical conductivities of these films before and after exposure to chemical vapours have been recorded in order to study their sensing mechanisms towards organic vapours. These films exhibit maximum sensing response to methanol while low sensitivities of the films towards ethanol and propanol have been observed. The changes in sensitivities have been correlated with presence of carbon groups in the chemical vapours. The effect of different types of electrodes on response-recovery times of the thin film with organic vapours has been studied and compared. The electrodes gap distance affects the sensitivity as well as response-recovery time values of the thin films.

Highly selective luminescent sensing of picric acid based on a water-stable europium metal-organic framework

NASA Astrophysics Data System (ADS)

Xia, Tifeng; Zhu, Fengliang; Cui, Yuanjing; Yang, Yu; Wang, Zhiyu; Qian, Guodong

2017-01-01

A water-stable metal-organic framework (MOF) EuNDC has been synthesized for selective detection of the well-known contaminant and toxicant picric acid (PA) in aqueous solution. Due to the photo-induced electron transfer and self-absorption mechanism, EuNDC displayed rapid, selective and sensitive detection of PA with a detection limit of 37.6 ppb. Recyclability experiments revealed that EuNDC retains its initial luminescent intensity and same quenching efficiency in each cycle, suggesting high photostability and reusability for long-term sensing applications. The excellent detection performance of EuNDC makes it a promising PA sensing material for practical applications.

A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure.

PubMed

Zhang, Jinwei; Landick, Robert

2016-04-01

The vectorial (5'-to-3' at varying velocity) synthesis of RNA by cellular RNA polymerases (RNAPs) creates a rugged kinetic landscape, demarcated by frequent, sometimes long-lived, pauses. In addition to myriad gene-regulatory roles, these pauses temporally and spatially program the co-transcriptional, hierarchical folding of biologically active RNAs. Conversely, these RNA structures, which form inside or near the RNA exit channel, interact with the polymerase and adjacent protein factors to influence RNA synthesis by modulating pausing, termination, antitermination, and slippage. Here, we review the evolutionary origin, mechanistic underpinnings, and regulatory consequences of this interplay between RNAP and nascent RNA structure. We categorize and rationalize the extensive linkage between the transcriptional machinery and its product, and provide a framework for future studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Isolation of nucleoli from Ehrlich ascites tumor cells and dynamics of nascent RNA within isolated nucleoli.

PubMed

Thiry, Marc; Ploton, Dominique

2008-01-01

Here we describe a new, rapid method for isolating nucleoli from Ehrlich tumor cells that preserves their morphological integrity and high transcriptional activity. Until now, methods for isolation of nucleoli were generally assumed to empty one of their three main compartments, the fibrillar center, of its contents. This new method consists of sonicating cells in an isotonic medium containing MgSO(4), spermidine, and spermine, followed by separation of nucleoli through a Percoll density gradient. Using the nonisotopic approach of labelling with BrUTP, we have further investigated the dynamics of nascent ribosomal RNAs (rRNAs) within morphologically intact isolated nucleoli at the electron microscope level. We show that ribosomal transcripts are elongated in the cortex of the fibrillar center and then enter the surrounding dense fibrillar component.

Computational Sensing and in vitro Classification of GMOs and Biomolecular Events

DTIC Science & Technology

2008-12-01

COMPUTATIONAL SENSING AND IN VITRO CLASSIFICATION OF GMOs AND BIOMOLECULAR EVENTS Elebeoba May1∗, Miler T. Lee2†, Patricia Dolan1, Paul Crozier1...modified organisms ( GMOs ) in the pres- ence of non-lethal agents. Using an information and coding- theoretic framework we develop a de novo method for...high through- put screening, distinguishing genetically modified organisms ( GMOs ), molecular computing, differentiating biological mark- ers

Photoionization mass spectrometry for the investigation of combustion generated nascent nanoparticles and their relation to laser induced incandescence

NASA Astrophysics Data System (ADS)

Grotheer, H.-H.; Wolf, K.; Hoffmann, K.

2011-08-01

Premixed laminar flat ethylene flames were investigated for nascent nanoparticles through photoionization mass spectrometry (PIMS). Using an atmospheric McKenna burner and ethylene air flames coupled to an atmospheric sampling system, within a relatively narrow C/O range two modes of these particles were found, which can be clearly distinguished with regard to their temperature dependence, their reactivity, and their ionization behaviour. Behind a diesel engine the same particles were observed. These results were corroborated using a low pressure ethylene-O2 flame coupled to a high resolution mass spectrometer. In this case, due to a special inlet system, it was possible to operate the flame in a fairly wide C/O range without clogging of the inlet nozzles. This allowed pursuing the development of particle size distribution functions (PSDF) well into the regime of mature soot. In addition, on the low mass side of the particle spectra measurements with unity resolution were possible and this allowed gaining information concerning their growth mechanism and structure. Finally, in an attempt to mimic Laser Induced Incandescence (LII) experiments the soot-laden molecular beam was exposed to IR irradiation. This resulted in a near complete destruction of nascent particles under LII typical fluences. Small C clusters between 3 and 17 C atoms were found. In addition and with much higher intensities, clusters comprising several hundreds of C atoms were also detected, the latter even at very low fluences when small clusters were totally absent.

GABA Signaling Promotes Synapse Elimination and Axon Pruning in Developing Cortical Inhibitory Interneurons

PubMed Central

Wu, Xiaoyun; Fu, Yu; Knott, Graham; Lu, Jiangteng; Di Cristo, Graziella

2012-01-01

Accumulating evidence indicates that GABA acts beyond inhibitory synaptic transmission and regulates the development of inhibitory synapses in the vertebrate brain, but the underlying cellular mechanism is not well understood. We have combined live imaging of cortical GABAergic axons across time scales from minutes to days with single-cell genetic manipulation of GABA release to examine its role in distinct steps of inhibitory synapse formation in the mouse neocortex. We have shown previously, by genetic knockdown of GABA synthesis in developing interneurons, that GABA signaling promotes the maturation of inhibitory synapses and axons. Here we found that a complete blockade of GABA release in basket interneurons resulted in an opposite effect, a cell-autonomous increase in axon and bouton density with apparently normal synapse structures. These results not only demonstrate that GABA is unnecessary for synapse formation per se but also uncover a novel facet of GABA in regulating synapse elimination and axon pruning. Live imaging revealed that developing GABAergic axons form a large number of transient boutons, but only a subset was stabilized. Release blockade led to significantly increased bouton stability and filopodia density, increased axon branch extension, and decreased branch retraction. Our results suggest that a major component of GABA function in synapse development is transmission-mediated elimination of subsets of nascent contacts. Therefore, GABA may regulate activity-dependent inhibitory synapse formation by coordinately eliminating certain nascent contacts while promoting the maturation of other nascent synapses. PMID:22219294

Origin and heterogeneity of HDL subspecies

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

Nichols, A.V.; Gong, E.L.; Blanche, P.J.

1987-09-01

A major determinant of mature HDL particle size and apolar core content, in the absence of remodeling factors, is most likely the size and apolipoprotein content of the precursor particle. Depending on the number of apoA-I molecules per analog particle, the LCAT-induced transformation follows either a fusion pathway (for precursors with 2 apoA-I per particle) or a pathway (for precursors with more than 2 apoA-I per particle) that conserves the apolipoprotein number. According to our analog results, small nascent HDL probably serve as precursors to the major (apoA-I without apoA-II)-subpopulation in the size interval. Our studies with the large discoidalmore » analog suggest that HDL/sub 2/ (apoA-I without apoA-II)-subpopulations probably originate from the large discoidal nascent HDL that contain a higher number of apolipoprotein molecules per particle than the small nascent HDL. Intermediate transformation products of the large discoidal analog, described in the present study, resemble deformable species found in human lymph and are characterized by a relatively high surface-to-core lipid ratio. Whether large discoidal precursors containing apoE transform in comparable manner but with eventual interchange of apoA-I for apoE (10,15) is under investigation in our laboratory. Likewise, detailed delineation of pathways whereby the (apoA-I with apoA-II)-HDL subpopulations are formed is yet to be accomplished. 23 refs., 6 figs., 2 tabs.« less

Quantum-state resolved reactive scattering at the gas-liquid interface: F+squalane (C30H62) dynamics via high-resolution infrared absorption of nascent HF(v,J).

PubMed

Zolot, Alexander M; Dagdigian, Paul J; Nesbitt, David J

2008-11-21

Exothermic chemical reaction dynamics at the gas-liquid interface have been investigated by colliding a supersonic beam of F atoms [E(com)=0.7(3) kcalmol] with a continuously refreshed liquid hydrocarbon (squalane) surface under high vacuum conditions. Absolute HF(v,J) product densities are determined by infrared laser absorption spectroscopy, with velocity distributions along the probe axis derived from high resolution Dopplerimetry. Nascent HF(v

Quantum-state resolved reactive scattering at the gas-liquid interface: F +squalane (C30H62) dynamics via high-resolution infrared absorption of nascent HF(v,J)

NASA Astrophysics Data System (ADS)

Zolot, Alexander M.; Dagdigian, Paul J.; Nesbitt, David J.

2008-11-01

Exothermic chemical reaction dynamics at the gas-liquid interface have been investigated by colliding a supersonic beam of F atoms [Ecom=0.7(3)kcal/mol] with a continuously refreshed liquid hydrocarbon (squalane) surface under high vacuum conditions. Absolute HF(v,J) product densities are determined by infrared laser absorption spectroscopy, with velocity distributions along the probe axis derived from high resolution Dopplerimetry. Nascent HF(v ⩽3) products are formed in a highly nonequilibrium (inverted) vibrational distribution [⟨Evib⟩=13.2(2)kcal/mol], reflecting insufficient time for complete thermal accommodation with the surface prior to desorption. Colder, but still non-Boltzmann, rotational state populations [⟨Erot⟩=1.0(1)kcal/mol] indicate that some fraction of molecules directly scatter into the gas phase without rotationally equilibrating with the surface. Nascent HF also recoils from the liquid surface with excess translational energy, resulting in Doppler broadened linewidths that increase systematically with internal HF excitation. The data are consistent with microscopic branching in HF-surface dynamics following the reactive event, with (i) a direct reactive scattering fraction of newly formed product molecules leaving the surface promptly and (ii) a trapping desorption fraction that accommodates rotationally (though still not vibrationally) with the bulk liquid. Comparison with analogous gas phase F +hydrocarbon processes reveals that the liquid acts as a partial "heat sink" for vibrational energy flow on the time scale of the chemical reaction event.

Remote sensing utility in a disaster struck urban environment

NASA Technical Reports Server (NTRS)

Rush, M.; Holguin, A.; Vernon, S.

1974-01-01

A project to determine the ways in which remote sensing can contribute to solutions of urban public health problems in time of natural disaster is discussed. The objectives of the project are to determine and describe remote sensing standard operating procedures for public health assistance during disaster relief operations which will aid the agencies and organizations involved in disaster intervention. Proposed tests to determine the validity of the remote sensing system are reported.

Bibliography of Remote Sensing Techniques Used in Wetland Research

DTIC Science & Technology

1993-01-01

8217 is investigating the application of remote sensing technology for detecting changes in wetland environments. This report documents a bibliographic...search conducted as part of that work unit on applications of remote sensing techniques in wetland research. Results were used to guide research...efforts on the use of remote sensing technology for wetland change detection and assessment. The citations are presented in three appendixes, organized by wetland type, sensor type, and author.

Flexible and self-powered temperature-pressure dual-parameter sensors using microstructure-frame-supported organic thermoelectric materials.

PubMed

Zhang, Fengjiao; Zang, Yaping; Huang, Dazhen; Di, Chong-an; Zhu, Daoben

2015-09-21

Skin-like temperature- and pressure-sensing capabilities are essential features for the next generation of artificial intelligent products. Previous studies of e-skin and smart elements have focused on flexible pressure sensors, whereas the simultaneous and sensitive detection of temperature and pressure with a single device remains a challenge. Here we report developing flexible dual-parameter temperature-pressure sensors based on microstructure-frame-supported organic thermoelectric (MFSOTE) materials. The effective transduction of temperature and pressure stimuli into two independent electrical signals permits the instantaneous sensing of temperature and pressure with an accurate temperature resolution of <0.1 K and a high-pressure-sensing sensitivity of up to 28.9 kPa(-1). More importantly, these dual-parameter sensors can be self-powered with outstanding sensing performance. The excellent sensing properties of MFSOTE-based devices, together with their unique advantages of low cost and large-area fabrication, make MFSOTE materials possess promising applications in e-skin and health-monitoring elements.

Sensing abilities of functionalized calix[4]arene coated QCM sensors towards volatile organic compounds in aqueous media

NASA Astrophysics Data System (ADS)

Temel, Farabi; Ozcelik, Egemen; Ture, Ayse Gul; Tabakci, Mustafa

2017-08-01

This study presents the sensing studies of QCM sensors which coated with calix[4]arene derivatives bearing different functional groups towards some selected Volatile Organic Compounds (VOCs). Initial experiments revealed that QCM sensor coated with calix-3 bearing bromopropyl functionalities was relatively more effective sensor for methylene chloride (MC) emissions than the other calix[4]arene coated QCM sensors, in aqueous media. In further experiments, this effective calix-3 coated QCM sensor were used in detailed sensing studies of selected VOCs. However, the results demonstrated that calix-3 coated QCM sensor was most useful sensor for toluene (TOL) emissions among all. Moreover, the sensing of TOLs with calix-3 coated QCM sensor was also evaluated in terms of sorption phenomena. Consequently, calix-3 coated QCM sensor was good sensor for TOL emissions, and thus it demonstrated that the coating of QCM sensor surface with calixarenes was good approach for sensing of the VOCs.

Flexible and self-powered temperature-pressure dual-parameter sensors using microstructure-frame-supported organic thermoelectric materials

NASA Astrophysics Data System (ADS)

Zhang, Fengjiao; Zang, Yaping; Huang, Dazhen; di, Chong-An; Zhu, Daoben

2015-09-01

Skin-like temperature- and pressure-sensing capabilities are essential features for the next generation of artificial intelligent products. Previous studies of e-skin and smart elements have focused on flexible pressure sensors, whereas the simultaneous and sensitive detection of temperature and pressure with a single device remains a challenge. Here we report developing flexible dual-parameter temperature-pressure sensors based on microstructure-frame-supported organic thermoelectric (MFSOTE) materials. The effective transduction of temperature and pressure stimuli into two independent electrical signals permits the instantaneous sensing of temperature and pressure with an accurate temperature resolution of <0.1 K and a high-pressure-sensing sensitivity of up to 28.9 kPa-1. More importantly, these dual-parameter sensors can be self-powered with outstanding sensing performance. The excellent sensing properties of MFSOTE-based devices, together with their unique advantages of low cost and large-area fabrication, make MFSOTE materials possess promising applications in e-skin and health-monitoring elements.

Contemporary Remotely Sensed Data Products Refine Invasive Plants Risk Mapping in Data Poor Regions.

PubMed

Truong, Tuyet T A; Hardy, Giles E St J; Andrew, Margaret E

2017-01-01

Invasive weeds are a serious problem worldwide, threatening biodiversity and damaging economies. Modeling potential distributions of invasive weeds can prioritize locations for monitoring and control efforts, increasing management efficiency. Forecasts of invasion risk at regional to continental scales are enabled by readily available downscaled climate surfaces together with an increasing number of digitized and georeferenced species occurrence records and species distribution modeling techniques. However, predictions at a finer scale and in landscapes with less topographic variation may require predictors that capture biotic processes and local abiotic conditions. Contemporary remote sensing (RS) data can enhance predictions by providing a range of spatial environmental data products at fine scale beyond climatic variables only. In this study, we used the Global Biodiversity Information Facility (GBIF) and empirical maximum entropy (MaxEnt) models to model the potential distributions of 14 invasive plant species across Southeast Asia (SEA), selected from regional and Vietnam's lists of priority weeds. Spatial environmental variables used to map invasion risk included bioclimatic layers and recent representations of global land cover, vegetation productivity (GPP), and soil properties developed from Earth observation data. Results showed that combining climate and RS data reduced predicted areas of suitable habitat compared with models using climate or RS data only, with no loss in model accuracy. However, contributions of RS variables were relatively limited, in part due to uncertainties in the land cover data. We strongly encourage greater adoption of quantitative remotely sensed estimates of ecosystem structure and function for habitat suitability modeling. Through comprehensive maps of overall predicted area and diversity of invasive species, we found that among lifeforms (herb, shrub, and vine), shrub species have higher potential invasion risk in SEA. Native invasive species, which are often overlooked in weed risk assessment, may be as serious a problem as non-native invasive species. Awareness of invasive weeds and their environmental impacts is still nascent in SEA and information is scarce. Freely available global spatial datasets, not least those provided by Earth observation programs, and the results of studies such as this one provide critical information that enables strategic management of environmental threats such as invasive species.

Contemporary Remotely Sensed Data Products Refine Invasive Plants Risk Mapping in Data Poor Regions

PubMed Central

Truong, Tuyet T. A.; Hardy, Giles E. St. J.; Andrew, Margaret E.

2017-01-01

Invasive weeds are a serious problem worldwide, threatening biodiversity and damaging economies. Modeling potential distributions of invasive weeds can prioritize locations for monitoring and control efforts, increasing management efficiency. Forecasts of invasion risk at regional to continental scales are enabled by readily available downscaled climate surfaces together with an increasing number of digitized and georeferenced species occurrence records and species distribution modeling techniques. However, predictions at a finer scale and in landscapes with less topographic variation may require predictors that capture biotic processes and local abiotic conditions. Contemporary remote sensing (RS) data can enhance predictions by providing a range of spatial environmental data products at fine scale beyond climatic variables only. In this study, we used the Global Biodiversity Information Facility (GBIF) and empirical maximum entropy (MaxEnt) models to model the potential distributions of 14 invasive plant species across Southeast Asia (SEA), selected from regional and Vietnam’s lists of priority weeds. Spatial environmental variables used to map invasion risk included bioclimatic layers and recent representations of global land cover, vegetation productivity (GPP), and soil properties developed from Earth observation data. Results showed that combining climate and RS data reduced predicted areas of suitable habitat compared with models using climate or RS data only, with no loss in model accuracy. However, contributions of RS variables were relatively limited, in part due to uncertainties in the land cover data. We strongly encourage greater adoption of quantitative remotely sensed estimates of ecosystem structure and function for habitat suitability modeling. Through comprehensive maps of overall predicted area and diversity of invasive species, we found that among lifeforms (herb, shrub, and vine), shrub species have higher potential invasion risk in SEA. Native invasive species, which are often overlooked in weed risk assessment, may be as serious a problem as non-native invasive species. Awareness of invasive weeds and their environmental impacts is still nascent in SEA and information is scarce. Freely available global spatial datasets, not least those provided by Earth observation programs, and the results of studies such as this one provide critical information that enables strategic management of environmental threats such as invasive species. PMID:28555147

45 CFR 2104.103 - Definition.

Code of Federal Regulations, 2013 CFR

2013-10-01

... following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive; genitourinary; hemic and lymphatic; skin; and endocrine...

47 CFR 1.1803 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-10-01

... or more of the following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive; genitourinary; hemic and...

22 CFR 1600.103 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive; genitourinary; hemic and lymphatic; skin; and endocrine...

45 CFR 1181.103 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-10-01

... following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive; genitourinary; hemic and lymphatic; skin; and endocrine...

22 CFR 219.103 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive; genitourinary; hemic and lymphatic; skin; and endocrine...

Remote sensing - A new view for public health

NASA Technical Reports Server (NTRS)

Morrison, D. R.; Barnes, C. M.; Fuller, C. E.

1973-01-01

It is shown that the technology of remote sensing can be of great importance to the field of public health. This possibility is based on the deepened understanding of the biologies and ecologies of the vector/organism/host interelationships of arthropod-, soil-, and water-borne diseases to result from the information that remote sensing can provide.

Self-Organized Air Tasking: Examining a Non-Hierarchical Model for Joint Air Operations

DTIC Science & Technology

2004-06-01

refers to systems with this dynamic incoherence as “strong sense of agency ” systems, and uses “weak sense of agency ” to refer to more predictable...agent-based systems, such as robotics or state-determined automata. Increasing the level of dynamic incoherency indicates a stronger sense of agency . This

GRADIENT: Graph Analytic Approach for Discovering Irregular Events, Nascent and Temporal

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

Hogan, Emilie

2015-03-31

Finding a time-ordered signature within large graphs is a computationally complex problem due to the combinatorial explosion of potential patterns. GRADIENT is designed to search and understand that problem space.

GRADIENT: Graph Analytic Approach for Discovering Irregular Events, Nascent and Temporal

ScienceCinema

Hogan, Emilie

2018-01-16

Finding a time-ordered signature within large graphs is a computationally complex problem due to the combinatorial explosion of potential patterns. GRADIENT is designed to search and understand that problem space.

38 CFR 15.103 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... one or more of the following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive; genitourinary; hemic and...

45 CFR 1803.3 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-10-01

... one or more of the following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive; genitourinary; hemic and...

5 CFR 1850.103 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... one or more of the following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive; genitourinary; hemic and...

22 CFR 1510.103 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... one or more of the following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive; genitourinary; hemic and...

5 CFR 1636.103 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... one or more of the following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive; genitourinary; hemic and...

45 CFR 1214.103 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-10-01

... more of the following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive; genitourinary; hemic and lymphatic; skin...

29 CFR 33.3 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... one or more of the following body systems: neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive; genitourinary; hemic and...

Hierarchies in light sensing and dynamic interactions between ocular and extraocular sensory networks in a flatworm

PubMed Central

Shettigar, Nishan; Joshi, Asawari; Dalmeida, Rimple; Gopalkrishna, Rohini; Chakravarthy, Anirudh; Patnaik, Siddharth; Mathew, Manoj; Palakodeti, Dasaradhi; Gulyani, Akash

2017-01-01

Light sensing has independently evolved multiple times under diverse selective pressures but has been examined only in a handful among the millions of light-responsive organisms. Unsurprisingly, mechanistic insights into how differential light processing can cause distinct behavioral outputs are limited. We show how an organism can achieve complex light processing with a simple “eye” while also having independent but mutually interacting light sensing networks. Although planarian flatworms lack wavelength-specific eye photoreceptors, a 25 nm change in light wavelength is sufficient to completely switch their phototactic behavior. Quantitative photoassays, eye-brain confocal imaging, and RNA interference/knockdown studies reveal that flatworms are able to compare small differences in the amounts of light absorbed at the eyes through a single eye opsin and convert them into binary behavioral outputs. Because planarians can fully regenerate, eye-brain injury-regeneration studies showed that this acute light intensity sensing and processing are layered on simple light detection. Unlike intact worms, partially regenerated animals with eyes can sense light but cannot sense finer gradients. Planarians also show a “reflex-like,” eye-independent (extraocular/whole-body) response to low ultraviolet A light, apart from the “processive” eye-brain–mediated (ocular) response. Competition experiments between ocular and extraocular sensory systems reveal dynamic interchanging hierarchies. In intact worms, cerebral ocular response can override the reflex-like extraocular response. However, injury-regeneration again offers a time window wherein both responses coexist, but the dominance of the ocular response is reversed. Overall, we demonstrate acute light intensity–based behavioral switching and two evolutionarily distinct but interacting light sensing networks in a regenerating organism. PMID:28782018

Ultra-sensitive Trace-Water Optical Sensor with In situ- synthesized Metal-Organic Framework in Glass Paper.

PubMed

Ohira, Shin-Ichi; Nakamura, Nao; Endo, Masaaki; Miki, Yusuke; Hirose, Yasuo; Toda, Kei

2018-01-01

Monitoring of trace water in industrial gases is strongly recommended because contaminants cause serious problems during use, especially in the semiconductor industry. An ultra-sensitive trace-water sensor was developed with an in situ-synthesized metal-organic framework as the sensing material. The sample gas is passed through the sensing membrane and efficiently and rapidly collected by the sensing material in the newly designed gas collection/detection cell. The sensing membrane, glass paper impregnated with copper 1,3,5-benzenetricarboxylate (Cu-BTC), is also newly developed. The amount and density of the sensing material in the sensing membrane must be well balanced to achieve rapid and sensitive responses. In the present study, Cu-BTC was synthesized in situ in glass paper. The developed system gave high sensing performances with a limit of detection (signal/noise ratio = 3) of 9 parts per billion by volume (ppbv) H 2 O and a 90% response time of 86 s for 200 ppbv H 2 O. The reproducibility of the responses within and between lots had relative standard deviations for 500 ppbv H 2 O of 0.8% (n = 10) and 1.5% (n = 3), respectively. The long-term (2 weeks) stability was 7.3% for 400 ppbv H 2 O and one-year continuous monitoring test showed the sensitivity change of <∼3% before and after the study. Furthermore, the system response was in good agreement with the response achieved in cavity ring-down spectroscopy. These performances are sufficient for monitoring trace water in industrial gases. The integrated system with light and gas transparent structure for gas collection/absorbance detection can also be used for other target gases, using specific metal-organic frameworks.

Irregular chiasm-C-roughest, a member of the immunoglobulin superfamily, affects sense organ spacing on the Drosophila antenna by influencing the positioning of founder cells on the disc ectoderm.

PubMed

Venugopala Reddy, G; Reiter, C; Shanbhag, S; Fischbach, K F; Rodrigues, V

1999-10-01

We describe a role for Irregular chiasmC-roughest (IrreC-rst), an immunoglobulin (Ig) superfamily member, in patterning sense organs on the Drosophila antenna. IrreC-rst protein is initially expressed homogeneously on apical profiles of ectodermal cells in regions of the antennal disc. During specification of founder cells (FCs), the intracellular protein distribution changes and becomes concentrated in regions where specific intercellular contacts presumably occur. Loss of function mutations as well as misexpression of irreC-rst results in an altered arrangement of FCs within the disc compared to wildtype. Sense organ development occurs normally, although spacing is affected. Unlike its role in interommatidial spacing, irreC-rst does not affect apoptosis during antennal development. We propose that IrreC-rst affects the spatial relationship between sensory and ectodermal cells during FC delamination.

Pi sensing and signalling: from prokaryotic to eukaryotic cells.

PubMed

Qi, Wanjun; Baldwin, Stephen A; Muench, Stephen P; Baker, Alison

2016-06-15

Phosphorus is one of the most important macronutrients and is indispensable for all organisms as a critical structural component as well as participating in intracellular signalling and energy metabolism. Sensing and signalling of phosphate (Pi) has been extensively studied and is well understood in single-cellular organisms like bacteria (Escherichia coli) and Saccharomyces cerevisiae In comparison, the mechanism of Pi regulation in plants is less well understood despite recent advances in this area. In most soils the available Pi limits crop yield, therefore a clearer understanding of the molecular basis underlying Pi sensing and signalling is of great importance for the development of plants with improved Pi use efficiency. This mini-review compares some of the main Pi regulation pathways in prokaryotic and eukaryotic cells and identifies similarities and differences among different organisms, as well as providing some insight into future research. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Luminescent metal-organic frameworks for chemical sensing and explosive detection.

PubMed

Hu, Zhichao; Deibert, Benjamin J; Li, Jing

2014-08-21

Metal-organic frameworks (MOFs) are a unique class of crystalline solids comprised of metal cations (or metal clusters) and organic ligands that have shown promise for a wide variety of applications. Over the past 15 years, research and development of these materials have become one of the most intensely and extensively pursued areas. A very interesting and well-investigated topic is their optical emission properties and related applications. Several reviews have provided a comprehensive overview covering many aspects of the subject up to 2011. This review intends to provide an update of work published since then and focuses on the photoluminescence (PL) properties of MOFs and their possible utility in chemical and biological sensing and detection. The spectrum of this review includes the origin of luminescence in MOFs, the advantages of luminescent MOF (LMOF) based sensors, general strategies in designing sensory materials, and examples of various applications in sensing and detection.

Is aberrant mammary tissue a marker for chronic alcoholism or kidney-urinary tract malformations?

PubMed

Camacho, F M; Moreno-Giménez, J C; García-Hernández, M J

1998-01-01

Numerous publications describe the relationship between aberrant mammary tissue (AMT) and kidney-urinary tract malformations, individual/ familial alcoholism and sense organ disorders. We investigated these possible associations and reviewed 72 cases observed in our Department during the past 3 years: 30 men and 42 women, 17 of them with bilateral AMT (7 men and 10 women) and 25 patients from 9 families. Diagnosis was made according to Kajawa's classification. A detailed family history was performed asking for individual or familial alcoholism, especially in the mother, in addition to blood tests and ultrasonographic examination of the abdomen and the kidneys. We only found 1 family history of alcoholism in 3 families, but in the father, never in the mother or the affected subject. No congenital/ hereditary nephrourinary defects or sense organ disorders were found. We believe that in our population AMT is not a marker for alcoholism, kidney-urinary malformations nor sense organ disorders.

Comparative VOCs sensing performance for conducting polymer and porphyrin functionalized carbon nanotubes based sensors

NASA Astrophysics Data System (ADS)

Datta, Kunal; Rushi, Arti; Ghosh, Prasanta; Shirsat, Mahendra

2018-05-01

We report sensors for detection of ethyl alcohol, a prominent volatile organic compound (VOC). Single walled carbon nanotubes were selected as main sensing backbone. As efficiency of sensor is dependent upon the choice of sensing materials, the performances of conducting polymer and porphyrin based sensors were compared. Chemiresistive sensing modality was adopted to observe the performance of sensors. It has been found that porphyrin based sensor shows higher affinity towards ethyl alcohol.

The Data Science Landscape

NASA Astrophysics Data System (ADS)

Mentzel, C.

2017-12-01

Modern scientific data continue to increase in volume, variety, and velocity, and though the hype of big data has subsided, its usefulness for scientific discovery has only just begun. Harnessing these data for new insights, more efficient decision making, and other mission critical uses requires a combination of skills and expertise, often labeled data science. Data science can be thought of as a combination of statistics, computation and the domain from which the data relate, and so is a true interdisciplinary pursuit. Though it has reaped large benefits in companies able to afford the high cost of the severely limited talent pool, it suffers from lack of support in mission driven organizations. Not purely in any one historical field, data science is proving difficult to find a home in traditional university academic departments and other research organizations. The landscape of data science efforts, from academia, industry and government, can be characterized as nascent, enthusiastic, uneven, and highly competitive. Part of the challenge in documenting these trends is the lack of agreement about what data science is, and who is a data scientist. Defining these terms too closely and too early runs the risk of cutting off a tremendous amount of productive creativity, but waiting too long leaves many people without a sustainable career, and many organizations without the necessary skills to gain value from their data. This talk will explore the landscape of data science efforts in the US, including how organizations are building and sustaining data science teams.

Growth and flagellation of Vibrio fischeri during initiation of the sepiolid squid light organ symbiosis.

PubMed

Ruby, E G; Asato, L M

1993-01-01

A pure culture of the luminous bacterium Vibrio fischeri is maintained in the light-emitting organ of the sepiolid squid Euprymna scolopes. When the juvenile squid emerges from its egg it is symbiont-free and, because bioluminescence is part of an anti-predatory behavior, therefore must obtain a bacterial inoculum from the surrounding environment. We document here the kinetics of the process by which newly hatched juvenile squids become infected by symbiosis-competent V. fischeri. When placed in seawater containing as few as 240 colony-forming-units (CFU) per ml, the juvenile became detectably bioluminescent within a few hours. Colonization of the nascent light organ was initiated with as few as 1 to 10 bacteria, which rapidly began to grow at an exponential rate until they reached a population size of approximately 10(5) cells by 12 h after the initial infection. Subsequently, the number of bacteria in the established symbiosis was maintained essentially constant by a combination of both a > 20-fold reduction in bacterial growth rate, and an expulsion of excess bacteria into the surrounding seawater. While V. fischeri cells are normally flagellated and motile, these bacteria did not elaborate these appendages once the symbiosis was established; however, they quickly began to synthesize flagella when they were removed from the light organ environment. Thus, two important biological characteristics, growth rate and flagellation, were modulated during establishment of the association, perhaps as part of a coordinated series of symbiotic responses.

A systems concept of the vestibular organs

NASA Technical Reports Server (NTRS)

Mayne, R.

1974-01-01

A comprehensive model of vestibular organ function is presented. The model is based on an analogy with the inertial guidance systems used in navigation. Three distinct operations are investigated: angular motion sensing, linear motion sensing, and computation. These operations correspond to the semicircular canals, the otoliths, and central processing respectively. It is especially important for both an inertial guidance system and the vestibular organs to distinguish between attitude with respect to the vertical on the one hand, and linear velocity and displacement on the other. The model is applied to various experimental situations and found to be corroborated by them.

H2-rich fluids from serpentinization: geochemical and biotic implications.

PubMed

Sleep, N H; Meibom, A; Fridriksson, Th; Coleman, R G; Bird, D K

2004-08-31

Metamorphic hydration and oxidation of ultramafic rocks produces serpentinites, composed of serpentine group minerals and varying amounts of brucite, magnetite, and/or FeNi alloys. These minerals buffer metamorphic fluids to extremely reducing conditions that are capable of producing hydrogen gas. Awaruite, FeNi3, forms early in this process when the serpentinite minerals are Fe-rich. Olivine with the current mantle Fe/Mg ratio was oxidized during serpentinization after the Moon-forming impact. This process formed some of the ferric iron in the Earth's mantle. For the rest of Earth's history, serpentinites covered only a small fraction of the Earth's surface but were an important prebiotic and biotic environment. Extant methanogens react H2 with CO2 to form methane. This is a likely habitable environment on large silicate planets. The catalytic properties of FeNi3 allow complex organic compounds to form within serpentinite and, when mixed with atmospherically produced complex organic matter and waters that circulated through basalts, constitutes an attractive prebiotic substrate. Conversely, inorganic catalysis of methane by FeNi3 competes with nascent and extant life. Copyright 2004 The National Academy of Sciencs of the USA

Lateral assembly of the immunoglobulin protein SynCAM 1 controls its adhesive function and instructs synapse formation.

PubMed

Fogel, Adam I; Stagi, Massimiliano; Perez de Arce, Karen; Biederer, Thomas

2011-09-16

Synapses are specialized adhesion sites between neurons that are connected by protein complexes spanning the synaptic cleft. These trans-synaptic interactions can organize synapse formation, but their macromolecular properties and effects on synaptic morphology remain incompletely understood. Here, we demonstrate that the synaptic cell adhesion molecule SynCAM 1 self-assembles laterally via its extracellular, membrane-proximal immunoglobulin (Ig) domains 2 and 3. This cis oligomerization generates SynCAM oligomers with increased adhesive capacity and instructs the interactions of this molecule across the nascent and mature synaptic cleft. In immature neurons, cis assembly promotes the adhesive clustering of SynCAM 1 at new axo-dendritic contacts. Interfering with the lateral self-assembly of SynCAM 1 in differentiating neurons strongly impairs its synaptogenic activity. At later stages, the lateral oligomerization of SynCAM 1 restricts synaptic size, indicating that this adhesion molecule contributes to the structural organization of synapses. These results support that lateral interactions assemble SynCAM complexes within the synaptic cleft to promote synapse induction and modulate their structure. These findings provide novel insights into synapse development and the adhesive mechanisms of Ig superfamily members.

A branching morphogenesis program governs embryonic growth of the thyroid gland

PubMed Central

Liang, Shawn; Johansson, Ellen; Barila, Guillermo; Altschuler, Daniel L.; Fagman, Henrik

2018-01-01

ABSTRACT The developmental program that regulates thyroid progenitor cell proliferation is largely unknown. Here, we show that branching-like morphogenesis is a driving force to attain final size of the embryonic thyroid gland in mice. Sox9, a key factor in branching organ development, distinguishes Nkx2-1+ cells in the thyroid bud from the progenitors that originally form the thyroid placode in anterior endoderm. As lobes develop the thyroid primordial tissue branches several generations. Sox9 and Fgfr2b are co-expressed distally in the branching epithelium prior to folliculogenesis. The thyroid in Fgf10 null mutants has a normal shape but is severely hypoplastic. Absence of Fgf10 leads to defective branching and disorganized angiofollicular units although Sox9/Fgfr2b expression and the ability of cells to differentiate and form nascent follicles are not impaired. These findings demonstrate a novel mechanism of thyroid development reminiscent of the Fgf10-Sox9 program that characterizes organogenesis in classical branching organs, and provide clues to aid understanding of how the endocrine thyroid gland once evolved from an exocrine ancestor present in the invertebrate endostyle. PMID:29361553

A branching morphogenesis program governs embryonic growth of the thyroid gland.

PubMed

Liang, Shawn; Johansson, Ellen; Barila, Guillermo; Altschuler, Daniel L; Fagman, Henrik; Nilsson, Mikael

2018-01-25

The developmental program that regulates thyroid progenitor cell proliferation is largely unknown. Here, we show that branching-like morphogenesis is a driving force to attain final size of the embryonic thyroid gland in mice. Sox9, a key factor in branching organ development, distinguishes Nkx2-1 + cells in the thyroid bud from the progenitors that originally form the thyroid placode in anterior endoderm. As lobes develop the thyroid primordial tissue branches several generations. Sox9 and Fgfr2b are co-expressed distally in the branching epithelium prior to folliculogenesis. The thyroid in Fgf10 null mutants has a normal shape but is severely hypoplastic. Absence of Fgf10 leads to defective branching and disorganized angiofollicular units although Sox9/Fgfr2b expression and the ability of cells to differentiate and form nascent follicles are not impaired. These findings demonstrate a novel mechanism of thyroid development reminiscent of the Fgf10-Sox9 program that characterizes organogenesis in classical branching organs, and provide clues to aid understanding of how the endocrine thyroid gland once evolved from an exocrine ancestor present in the invertebrate endostyle. © 2018. Published by The Company of Biologists Ltd.

The LGI1–ADAM22 protein complex directs synapse maturation through regulation of PSD-95 function

PubMed Central

Lovero, Kathryn L.; Fukata, Yuko; Granger, Adam J.; Fukata, Masaki; Nicoll, Roger A.

2015-01-01

Synapse development is coordinated by a number of transmembrane and secreted proteins that come together to form synaptic organizing complexes. Whereas a variety of synaptogenic proteins have been characterized, much less is understood about the molecular networks that support the maintenance and functional maturation of nascent synapses. Here, we demonstrate that leucine-rich, glioma-inactivated protein 1 (LGI1), a secreted protein previously shown to modulate synaptic AMPA receptors, is a paracrine signal released from pre- and postsynaptic neurons that acts specifically through a disintegrin and metalloproteinase protein 22 (ADAM22) to set postsynaptic strength. We go on to describe a novel role for ADAM22 in maintaining excitatory synapses through PSD-95/Dlg1/zo-1 (PDZ) domain interactions. Finally, we show that in the absence of LGI1, the mature synapse scaffolding protein PSD-95, but not the immature synapse scaffolding protein SAP102, is unable to modulate synaptic transmission. These results indicate that LGI1 and ADAM22 form an essential synaptic organizing complex that coordinates the maturation of excitatory synapses by regulating the functional incorporation of PSD-95. PMID:26178195

Transplant Ethics: Let's Begin the Conversation Anew : A Critical Look at One Institute's Experience with Transplant Related Ethical Issues.

PubMed

Shafran, David; Smith, Martin L; Daly, Barbara J; Goldfarb, David

2016-06-01

Standardizing consultation processes is increasingly important as clinical ethics consultation (CEC) becomes more utilized in and vital to medical practice. Solid organ transplant represents a relatively nascent field replete with complex ethical issues that, while explored, have not been systematically classified. In this paper, we offer a proposed taxonomy that divides issues of resource allocation from viable solutions to the issue of organ shortage in transplant and then further distinguishes between policy and bedside level issues. We then identify all transplant related ethics consults performed at the Cleveland Clinic (CC) between 2008 and 2013 in order to identify how consultants conceptually framed their consultations by the domains they ascribe to the case. We code the CC domains to those in the Core Competencies for Healthcare Consultation Ethics in order to initiate a broader conversation regarding best practices in these highly complex cases. A discussion of the ethical issues underlying living donor and recipient related consults ensues. Finally, we suggest that the ethical domains prescribed in the Core Competencies provide a strong starting ground for a common intra-disciplinary language in the realm of formal CEC.

ACOs Holding Commercial Contracts Are Larger And More Efficient Than Noncommercial ACOs.

PubMed

Peiris, David; Phipps-Taylor, Madeleine C; Stachowski, Courtney A; Kao, Lee-Sien; Shortell, Stephen M; Lewis, Valerie A; Rosenthal, Meredith B; Colla, Carrie H

2016-10-01

Accountable care organizations (ACOs) have diverse contracting arrangements and have displayed wide variation in their performance. Using data from national surveys of 399 ACOs, we examined differences between the 228 commercial ACOs (those with commercial payer contracts) and the 171 noncommercial ACOs (those with only public contracts, such as with Medicare or Medicaid). Commercial ACOs were significantly larger and more integrated with hospitals, and had lower benchmark expenditures and higher quality scores, compared to noncommercial ACOs. Among all of the ACOs, there was low uptake of quality and efficiency activities. However, commercial ACOs reported more use of disease monitoring tools, patient satisfaction data, and quality improvement methods than did noncommercial ACOs. Few ACOs reported having high-level performance monitoring capabilities. About two-thirds of the ACOs had established processes for distributing any savings accrued, and these ACOs allocated approximately the same amount of savings to the ACOs themselves, participating member organizations, and physicians. Our findings demonstrate that ACO delivery systems remain at a nascent stage. Structural differences between commercial and noncommercial ACOs are important factors to consider as public policy efforts continue to evolve. Project HOPE—The People-to-People Health Foundation, Inc.

The conserved transmembrane proteoglycan Perdido/Kon-tiki is essential for myofibrillogenesis and sarcomeric structure in Drosophila

PubMed Central

Pérez-Moreno, Juan J.; Bischoff, Marcus; Martín-Bermudo, Maria D.; Estrada, Beatriz

2014-01-01

ABSTRACT Muscle differentiation requires the assembly of high-order structures called myofibrils, composed of sarcomeres. Even though the molecular organization of sarcomeres is well known, the mechanisms underlying myofibrillogenesis are poorly understood. It has been proposed that integrin-dependent adhesion nucleates myofibrils at the periphery of the muscle cell to sustain sarcomere assembly. Here, we report a role for the gene perdido (perd, also known as kon-tiki, a transmembrane chondroitin proteoglycan) in myofibrillogenesis. Expression of perd RNAi in muscles, prior to adult myogenesis, can induce misorientation and detachment of Drosophila adult abdominal muscles. In comparison to controls, perd-depleted muscles contain fewer myofibrils, which are localized at the cell periphery. These myofibrils are detached from each other and display a defective sarcomeric structure. Our results demonstrate that the extracellular matrix receptor Perd has a specific role in the assembly of myofibrils and in sarcomeric organization. We suggest that Perd acts downstream or in parallel to integrins to enable the connection of nascent myofibrils to the Z-bands. Our work identifies the Drosophila adult abdominal muscles as a model to investigate in vivo the mechanisms behind myofibrillogenesis. PMID:24794494

Proteostasis: bad news and good news from the endoplasmic reticulum.

PubMed

Noack, Julia; Brambilla Pisoni, Giorgia; Molinari, Maurizio

2014-01-01

The endoplasmic reticulum (ER) is an intracellular compartment dedicated to the synthesis and maturation of secretory and membrane proteins, totalling about 30% of the total eukaryotic cells proteome. The capacity to produce correctly folded polypeptides and to transport them to their correct intra- or extracellular destinations relies on proteostasis networks that regulate and balance the activity of protein folding, quality control, transport and degradation machineries. Nutrient and environmental changes, pathogen infection aging and, more relevant for the topics discussed in this review, mutations that impair attainment of the correct 3D structure of nascent polypeptide chains may compromise the activity of the proteostasis networks with devastating consequences on cells, organs and organisms' homeostasis. Here we present a review of mechanisms regulating folding and quality control of proteins expressed in the ER, and we describe the protein degradation and the ER stress pathways activated by the expression of misfolded proteins in the ER lumen. Finally, we highlight select examples of proteopathies (also known as conformational disorders or protein misfolding diseases) caused by protein misfolding in the ER and/or affecting cellular proteostasis and therapeutic interventions that might alleviate or cure the disease symptoms.

Embryo mechanics: balancing force production with elastic resistance during morphogenesis.

PubMed

Davidson, Lance A

2011-01-01

Morphogenesis requires the spatial and temporal control of embryo mechanics, including force production and mechanical resistance to those forces, to coordinate tissue deformation and large-scale movements. Thus, biomechanical processes play a key role in directly shaping the embryo. Additional roles for embryo mechanics during development may include the patterning of positional information and to provide feedback to ensure the success of morphogenetic movements in shaping the larval body and organs. To understand the multiple roles of mechanics during development requires familiarity with engineering principles of the mechanics of structures, the viscoelastic properties of biomaterials, and the integration of force and stress within embryonic structures as morphogenesis progresses. In this chapter, we review the basic engineering principles of biomechanics as they relate to morphogenesis, introduce methods for quantifying embryo mechanics and the limitations of these methods, and outline a formalism for investigating the role of embryo mechanics in birth defects. We encourage the nascent field of embryo mechanics to adopt standard engineering terms and test methods so that studies of diverse organisms can be compared and universal biomechanical principles can be revealed. Copyright © 2011 Elsevier Inc. All rights reserved.

Metal-Organic Frameworks-Derived Hierarchical Co3O4 Structures as Efficient Sensing Materials for Acetone Detection.

PubMed

Zhang, Rui; Zhou, Tingting; Wang, Lili; Zhang, Tong

2018-03-21

Highly sensitive and stable gas sensors have attracted much attention because they are the key to innovations in the fields of environment, health, energy savings and security, etc. Sensing materials, which influence the practical sensing performance, are the crucial parts for gas sensors. Metal-organic frameworks (MOFs) are considered as alluring sensing materials for gas sensors because of the possession of high specific surface area, unique morphology, abundant metal sites, and functional linkers. Herein, four kinds of porous hierarchical Co 3 O 4 structures have been selectively controlled by optimizing the thermal decomposition (temperature, rate, and atmosphere) using ZIF-67 as precursor that was obtained from coprecipitation method with the co-assistance of cobalt salt and 2-methylimidazole in the solution of methanol. These hierarchical Co 3 O 4 structures, with controllable cross-linked channels, meso-/micropores, and adjustable surface area, are efficient catalytic materials for gas sensing. Benefits from structural advantages, core-shell, and porous core-shell Co 3 O 4 exhibit enhanced sensing performance compared to those of porous popcorn and nanoparticle Co 3 O 4 to acetone gas. These novel MOF-templated Co 3 O 4 hierarchical structures are so fantastic that they can be expected to be efficient sensing materials for development of low-temperature operating gas sensors.

12 CFR 794.103 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., or anatomical loss affecting one or more of the following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive...

12 CFR 606.603 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... affecting one or more of the following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive; genitourinary; hemic and...

45 CFR 707.3 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-10-01

..., or anatomical loss affecting one or more of the following body systems: Neurological, musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive...

22 CFR 711.103 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

..., or anatomical loss affecting one or more of the following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive...

22 CFR 1005.103 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

..., or anatomical loss affecting one or more of the following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive...

Remote sensing procurement package: A management report for state and local governments

NASA Technical Reports Server (NTRS)

1981-01-01

An overview of the remote sensing procurement process is presented for chief executives, senior administrators, and other local and state officials responsible for purchasing remote sensing products, services, or equipment. Guidelines are provided for planning, organizing, staffing, and implementing such a procurement project. Other sections of the four-volume package are described and their benefits examined.

Highly Sensitive and Selective Sensing of Free Bilirubin Using Metal-Organic Frameworks-Based Energy Transfer Process.

PubMed

Du, Yaran; Li, Xiqian; Lv, Xueju; Jia, Qiong

2017-09-13

Free bilirubin, a key biomarker for jaundice, was detected with a newly designed fluorescent postsynthetically modified metal organic framework (MOF) (UIO-66-PSM) sensor. UiO-66-PSM was prepared based on the aldimine condensation reaction of UiO-66-NH 2 with 2,3,4-trihydroxybenzaldehyde. The fluorescence of UIO-66-PSM could be effectively quenched by free bilirubin via a fluorescent resonant energy transfer process, thus achieving its recognition of free bilirubin. It was the first attempt to design a MOF-based fluorescent probe for sensing free bilirubin. The probe exhibited fast response time, low detection limit, wide linear range, and high selectivity toward free bilirubin. The sensing system enabled the monitor of free bilirubin in real human serum. Hence, the reported free bilirubin sensing platform has potential applications for clinical diagnosis of jaundice.

Carbon dioxide-sensing in organisms and its implications for human disease

PubMed Central

Cummins, Eoin P.; Selfridge, Andrew C.; Sporn, Peter H.; Sznajder, Jacob I.; Taylor, Cormac T.

2013-01-01

The capacity of organisms to sense changes in the levels of internal and external gases and to respond accordingly is central to a range of physiologic and pathophysiologic processes. Carbon dioxide, a primary product of oxidative metabolism is one such gas that can be sensed by both prokaryotic and eukaryotic cells and in response to altered levels, elicit the activation of multiple adaptive pathways. The outcomes of activating CO2-sensitive pathways in various species include increased virulence of fungal and bacterial pathogens, prey-seeking behavior in insects as well as taste perception, lung function, and the control of immunity in mammals. In this review, we discuss what is known about the mechanisms underpinning CO2 sensing across a range of species and consider the implications of this for physiology, disease progression, and the possibility of developing new therapeutics for inflammatory and infectious disease. PMID:24045706

Hydrogen sensing properties of nanocomposite graphene oxide/Co-based metal organic frameworks (Co-MOFs@GO)

NASA Astrophysics Data System (ADS)

Fardindoost, Somayeh; Hatamie, Shadie; Iraji Zad, Azam; Razi Astaraei, Fatemeh

2018-01-01

This paper reports on hydrogen sensing based graphene oxide hybrid with Co-based metal organic frameworks (Co-MOFs@GO) prepared by the hydrothermal process. The texture and morphology of the hybrid were characterized by powder x-ray diffraction, scanning electron microscopy and Brunauer-Emmett-Teller analysis. Porous flower like structures assembled from Co-MOFs and GO flakes with sufficient specific surface area are obtained, which are ideal for gas molecules diffusion and interactions. Sensing performance of Co-MOFs@GO were tested and also improved by sputtering platinum (Pt) as a catalyst. The Pt-sputtered Co-MOFs@GO show outstanding hydrogen resistive-sensing with response and recovery times below 12 s at 15 °C. Also, they show stable, repeatable and selective responses to the target gas which make it suitable for the development of a high performance hydrogen sensor.

Evolution of photoperiod sensing in plants and algae.

PubMed

Serrano-Bueno, Gloria; Romero-Campero, Francisco J; Lucas-Reina, Eva; Romero, Jose M; Valverde, Federico

2017-06-01

Measuring day length confers a strong fitness improvement to photosynthetic organisms as it allows them to anticipate light phases and take the best decisions preceding diurnal transitions. In close association with signals from the circadian clock and the photoreceptors, photoperiodic sensing constitutes also a precise way to determine the passing of the seasons and to take annual decisions such as the best time to flower or the beginning of dormancy. Photoperiodic sensing in photosynthetic organisms is ancient and two major stages in its evolution could be identified, the cyanobacterial time sensing and the evolutionary tool kit that arose in green algae and developed into the photoperiodic system of modern plants. The most recent discoveries about the evolution of the perception of light, measurement of day length and relationship with the circadian clock along the evolution of the eukaryotic green lineage will be discussed in this review. Copyright © 2017 Elsevier Ltd. All rights reserved.

41 CFR 51-10.103 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., or anatomical loss affecting one or more of the following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive...

41 CFR 51-10.103 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

..., or anatomical loss affecting one or more of the following body systems: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular; reproductive; digestive...

Curriculum evaluation and revision in a nascent field: the utility of the retrospective pretest--posttest model in a homeland security program of study.

PubMed

Pelfrey, William V; Pelfrey, William V

2009-02-01

Although most academic disciplines evolve at a measured pace, the emerging field of homeland security must, for reasons of safety and security, evolve rapidly. The Department of Homeland Security sponsored the establishment of a graduate educational program for key officials holding homeland security roles. Because homeland security is a nascent field, the establishment of a program curriculum was forced to draw from a variety of disciplines. Curriculum evaluation was complicated by the rapid changes occurring in the emerging discipline, producing response shift bias, and interfering with the pre-post assessments. To compensate for the validity threat associated with response shift bias, a retrospective pretest-posttest evaluative methodology was used. Data indicate the program has evolved in a significant and orderly fashion and these data support the use of this innovative evaluation approach in the development of any discipline.

The structure of Escherichia coli signal recognition particle revealed by scanning transmission electron microscopy.

PubMed

Mainprize, Iain L; Beniac, Daniel R; Falkovskaia, Elena; Cleverley, Robert M; Gierasch, Lila M; Ottensmeyer, F Peter; Andrews, David W

2006-12-01

Structural studies on various domains of the ribonucleoprotein signal recognition particle (SRP) have not converged on a single complete structure of bacterial SRP consistent with the biochemistry of the particle. We obtained a three-dimensional structure for Escherichia coli SRP by cryoscanning transmission electron microscopy and mapped the internal RNA by electron spectroscopic imaging. Crystallographic data were fit into the SRP reconstruction, and although the resulting model differed from previous models, they could be rationalized by movement through an interdomain linker of Ffh, the protein component of SRP. Fluorescence resonance energy transfer experiments determined interdomain distances that were consistent with our model of SRP. Docking our model onto the bacterial ribosome suggests a mechanism for signal recognition involving interdomain movement of Ffh into and out of the nascent chain exit site and suggests how SRP could interact and/or compete with the ribosome-bound chaperone, trigger factor, for a nascent chain during translation.

Substantial Goodness and Nascent Human Life.

PubMed

Floyd, Shawn

2015-09-01

Many believe that moral value is--at least to some extent--dependent on the developmental states necessary for supporting rational activity. My paper rejects this view, but does not aim simply to register objections to it. Rather, my essay aims to answer the following question: if a human being's developmental state and occurrent capacities do not bequeath moral standing, what does? The question is intended to prompt careful consideration of what makes human beings objects of moral value, dignity, or (to employ my preferred term) goodness. Not only do I think we can answer this question, I think we can show that nascent human life possesses goodness of precisely this sort. I appeal to Aquinas's metaethics to establish the conclusion that the goodness of a human being--even if that being is an embryo or fetus--resides at the substratum of her existence. If she possesses goodness, it is because human existence is good.

Prion-Associated Toxicity is Rescued by Elimination of Cotranslational Chaperones

PubMed Central

Keefer, Kathryn M.; True, Heather L.

2016-01-01

The nascent polypeptide-associated complex (NAC) is a highly conserved but poorly characterized triad of proteins that bind near the ribosome exit tunnel. The NAC is the first cotranslational factor to bind to polypeptides and assist with their proper folding. Surprisingly, we found that deletion of NAC subunits in Saccharomyces cerevisiae rescues toxicity associated with the strong [PSI+] prion. This counterintuitive finding can be explained by changes in chaperone balance and distribution whereby the folding of the prion protein is improved and the prion is rendered nontoxic. In particular, the ribosome-associated Hsp70 Ssb is redistributed away from Sup35 prion aggregates to the nascent chains, leading to an array of aggregation phenotypes that can mimic both overexpression and deletion of Ssb. This toxicity rescue demonstrates that chaperone modification can block key steps of the prion life cycle and has exciting implications for potential treatment of many human protein conformational disorders. PMID:27828954

Transmembrane Segments Form Tertiary Hairpins in the Folding Vestibule of the Ribosome.

PubMed Central

Tu, LiWei; Khanna, Pooja; Deutsch, Carol

2013-01-01

Folding of membrane proteins begins in the ribosome as the peptide is elongated. During this process, the nascent peptide navigates along 100 Å of tunnel from the peptidyltransferase center to the exit port. Proximal to the exit port is a ‘folding vestibule’ that permits the nascent peptide to compact and explore conformational space for potential tertiary folding partners. The latter occurs for cytosolic subdomains, but has not yet been shown for transmembrane segments. We now demonstrate, using an accessibility assay and an improved, intramolecular crosslinking assay, that the helical transmembrane S3b-S4 hairpin (‘paddle’) of a voltage-gated potassium (Kv) channel, a critical region of the Kv voltage sensor, forms in the vestibule. S3-S4 hairpin interactions are detected at an early stage of Kv biogenesis. Moreover, this vestibule hairpin is consistent with a closed-state conformation of the Kv channel in the plasma membrane. PMID:24055377

A Proteomic Characterization of Factors Enriched at Nascent DNA Molecules

PubMed Central

Lopez-Contreras, Andres J.; Ruppen, Isabel; Nieto-Soler, Maria; Murga, Matilde; Rodriguez-Acebes, Sara; Remeseiro, Silvia; Rodrigo-Perez, Sara; Rojas, Ana M.; Mendez, Juan; Muñoz, Javier; Fernandez-Capetillo, Oscar

2013-01-01

SUMMARY DNA replication is facilitated by multiple factors that concentrate in the vicinity of replication forks. Here, we developed an approach that combines the isolation of proteins on nascent DNA chains with mass spectrometry (iPOND-MS), allowing a comprehensive proteomic characterization of the human replisome and replisome-associated factors. In addition to known replisome components, we provide a broad list of proteins that reside in the vicinity of the replisome, some of which were not previously associated with replication. For instance, our data support a link between DNA replication and the Williams-Beuren syndrome and identify ZNF24 as a replication factor. In addition, we reveal that SUMOylation is wide-spread for factors that concentrate near replisomes, which contrasts with lower UQylation levels at these sites. This resource provides a panoramic view of the proteins that concentrate in the surroundings of the replisome, which should facilitate future investigations on DNA replication and genome maintenance. PMID:23545495

Fluorescence lifetime imaging of microviscosity changes during ER autophagy in live cells

NASA Astrophysics Data System (ADS)

He, Ying; Samanta, Soham; Gong, Wanjun; Liu, Wufan; Pan, Wenhui; Yang, Zhigang; Qu, Junle

2018-02-01

Unfolded or misfolded protein accumulation inside Endoplasmic Reticulum (ER) will cause ER stress and subsequently will activate cellular autophagy to release ER stress, which would ultimately result in microviscosity changes. However, even though, it is highly significant to gain a quantitative assessment of microviscosity changes during ER autophagy to study ER stress and autophagy behaviors related diseases, it has rarely been reported yet. In this work, we have reported a BODIPY based fluorescent molecular rotor that can covalently bind with vicinal dithiols containing nascent proteins in ER and hence can result in ER stress through the inhibition of the folding of nascent proteins. The change in local viscosity, caused by the release of the stress in cells through autophagy, was quantified by the probe using fluorescence lifetime imaging. This work basically demonstrates the possibility of introducing synthetic chemical probe as a promising tool to diagnose ER-viscosity-related diseases.

Do chromatin changes around a nascent double strand DNA break spread spherically into linearly non-adjacent chromatin?

PubMed

Savic, Velibor

2013-01-01

In the last decade, a lot has been done in elucidating the sequence of events that occur at the nascent double strand DNA break. Nevertheless, the overall structure formed by the DNA damage response (DDR) factors around the break site, the repair focus, remains poorly understood. Although most of the data presented so far only address events that occur in chromatin in cis around the break, there are strong indications that in mammalian systems it may also occur in trans, analogous to the recent findings showing this if budding yeast. There have been attempts to address the issue but the final proof is still missing due to lack of a proper experimental system. If found to be true, the spatial distribution of DDR factors would have a major impact on the neighboring chromatin both in cis and in trans, significantly affecting local chromatin function; gene transcription and potentially other functions.

Method for the production of fabricated hollow microspheroids

DOEpatents

Wickramanayake, Shan; Luebke, David R.

2015-06-09

The method relates to the fabrication of a polymer microspheres comprised of an asymmetric layer surrounding a hollow interior. The fabricated hollow microsphere is generated from a nascent hollow microsphere comprised of an inner core of core fluid surrounded by a dope layer of polymer dope, where the thickness of the dope layer is at least 10% and less than 50% of the diameter of the inner core. The nascent hollow microsphere is exposed to a gaseous environment, generating a vitrified hollow microsphere, which is subsequently immersed in a coagulation bath. Solvent exchange produces a fabricated hollow microsphere comprised of a densified outer skin surrounding a macroporous inner layer, which surrounds a hollow interior. In an embodiment, the polymer is a polyimide or a polyamide-imide, and the non-solvent in the core fluid and the coagulation bath is water. The fabricated hollow microspheres are particularly suited as solvent supports for gas separation processes.

Evaluating Suspension Formulations of Theophylline Cocrystals With Artificial Sweeteners.

PubMed

Aitipamula, Srinivasulu; Wong, Annie B H; Kanaujia, Parijat

2018-02-01

Pharmaceutical cocrystals have garnered significant interest as potential solids to address issues associated with formulation development of drug substances. However, studies concerning the understanding of formulation behavior of cocrystals are still at the nascent stage. We present results of our attempts to evaluate suspension formulations of cocrystals of an antiasthmatic drug, theophylline, with 2 artificial sweeteners. Stability, solubility, drug release, and taste of the suspension formulations were evaluated. Suspension that contained cocrystal with acesulfame showed higher drug release rate, while a cocrystal with saccharin showed a significant reduction in drug release rate. The cocrystal with saccharin was found stable in suspension for over 9 weeks at accelerated test condition; in contrast, the cocrystal with acesulfame was found unstable. Taste analysis using an electronic taste-sensing system revealed improved sweetness of the suspension formulations with cocrystals. Theophylline has a narrow therapeutic index with a short half-life which necessitates frequent dosing. This adversely impacts patient compliance and enhances risk of gastrointestinal and cardiovascular adverse effects. The greater thermodynamic stability, sweetness, and sustained drug release of the suspension formulation of theophylline-saccharin could offer an alternative solution to the short half-life of theophylline and make it a promising formulation for treating asthmatic pediatric and geriatric patients. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Navigating Ethics in the Digital Age: Introducing Connected and Open Research Ethics (CORE), a Tool for Researchers and Institutional Review Boards.

PubMed

Torous, John; Nebeker, Camille

2017-02-08

Research studies that leverage emerging technologies, such as passive sensing devices and mobile apps, have demonstrated encouraging potential with respect to favorably influencing the human condition. As a result, the nascent fields of mHealth and digital medicine have gained traction over the past decade as demonstrated in the United States by increased federal funding for research that cuts across a broad spectrum of health conditions. The existence of mHealth and digital medicine also introduced new ethical and regulatory challenges that both institutional review boards (IRBs) and researchers are struggling to navigate. In response, the Connected and Open Research Ethics (CORE) initiative was launched. The CORE initiative has employed a participatory research approach, whereby researchers and IRB affiliates are involved in identifying the priorities and functionality of a shared resource. The overarching goal of CORE is to develop dynamic and relevant ethical practices to guide mHealth and digital medicine research. In this Viewpoint paper, we describe the CORE initiative and call for readers to join the CORE Network and contribute to the bigger conversation on ethics in the digital age. ©John Torous, Camille Nebeker. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 08.02.2017.

The comet-like composition of a protoplanetary disk as revealed by complex cyanides.

PubMed

Öberg, Karin I; Guzmán, Viviana V; Furuya, Kenji; Qi, Chunhua; Aikawa, Yuri; Andrews, Sean M; Loomis, Ryan; Wilner, David J

2015-04-09

Observations of comets and asteroids show that the solar nebula that spawned our planetary system was rich in water and organic molecules. Bombardment brought these organics to the young Earth's surface. Unlike asteroids, comets preserve a nearly pristine record of the solar nebula composition. The presence of cyanides in comets, including 0.01 per cent of methyl cyanide (CH3CN) with respect to water, is of special interest because of the importance of C-N bonds for abiotic amino acid synthesis. Comet-like compositions of simple and complex volatiles are found in protostars, and can readily be explained by a combination of gas-phase chemistry (to form, for example, HCN) and an active ice-phase chemistry on grain surfaces that advances complexity. Simple volatiles, including water and HCN, have been detected previously in solar nebula analogues, indicating that they survive disk formation or are re-formed in situ. It has hitherto been unclear whether the same holds for more complex organic molecules outside the solar nebula, given that recent observations show a marked change in the chemistry at the boundary between nascent envelopes and young disks due to accretion shocks. Here we report the detection of the complex cyanides CH3CN and HC3N (and HCN) in the protoplanetary disk around the young star MWC 480. We find that the abundance ratios of these nitrogen-bearing organics in the gas phase are similar to those in comets, which suggests an even higher relative abundance of complex cyanides in the disk ice. This implies that complex organics accompany simpler volatiles in protoplanetary disks, and that the rich organic chemistry of our solar nebula was not unique.

The comet-like composition of a protoplanetary disk as revealed by complex cyanides

NASA Astrophysics Data System (ADS)

Öberg, Karin I.; Guzmán, Viviana V.; Furuya, Kenji; Qi, Chunhua; Aikawa, Yuri; Andrews, Sean M.; Loomis, Ryan; Wilner, David J.

2015-04-01

Observations of comets and asteroids show that the solar nebula that spawned our planetary system was rich in water and organic molecules. Bombardment brought these organics to the young Earth's surface. Unlike asteroids, comets preserve a nearly pristine record of the solar nebula composition. The presence of cyanides in comets, including 0.01 per cent of methyl cyanide (CH3CN) with respect to water, is of special interest because of the importance of C-N bonds for abiotic amino acid synthesis. Comet-like compositions of simple and complex volatiles are found in protostars, and can readily be explained by a combination of gas-phase chemistry (to form, for example, HCN) and an active ice-phase chemistry on grain surfaces that advances complexity. Simple volatiles, including water and HCN, have been detected previously in solar nebula analogues, indicating that they survive disk formation or are re-formed in situ. It has hitherto been unclear whether the same holds for more complex organic molecules outside the solar nebula, given that recent observations show a marked change in the chemistry at the boundary between nascent envelopes and young disks due to accretion shocks. Here we report the detection of the complex cyanides CH3CN and HC3N (and HCN) in the protoplanetary disk around the young star MWC 480. We find that the abundance ratios of these nitrogen-bearing organics in the gas phase are similar to those in comets, which suggests an even higher relative abundance of complex cyanides in the disk ice. This implies that complex organics accompany simpler volatiles in protoplanetary disks, and that the rich organic chemistry of our solar nebula was not unique.

Remote sensing program

NASA Technical Reports Server (NTRS)

Philipson, W. R. (Principal Investigator)

1983-01-01

Built on Cornell's thirty years of experience in aerial photographic studies, the NASA-sponsored remote sensing program strengthened instruction and research in remote sensing, established communication links within and beyond the university community, and conducted research projects for or with town, county, state, federal, and private organizations in New York State. The 43 completed applied research projects are listed as well as 13 spinoff grants/contracts. The curriculum offered, consultations provided, and data processing facilities available are described. Publications engendered are listed including the thesis of graduates in the remote sensing program.

Active and Passive Remote Sensing of Ice

DTIC Science & Technology

1993-01-26

92 4. TITLE AND SUBTITLE S. FUNDING NUMBERS Active and Passive Remote Sensing of Ice NO0014-89-J-l 107 6. AUTHOR(S) 425f023-08 Prof. J.A. Kong 7... REMOTE SENSING OF ICE Sponsored by: Department of the Navy Office of Naval Research Contract number: N00014-89-J-1107 Research Organization: Center for...J. A. Kong Period covered: October 1, 1988 - November 30, 1992 St ACTIVE AND PASSIVE REMOTE SENSING OF ICE FINAL REPORT This annual report covers

Paranoia as an Antecedent and Consequence of Getting Ahead in Organizations: Time-Lagged Effects Between Paranoid Cognitions, Self-Monitoring, and Changes in Span of Control

PubMed Central

Van Quaquebeke, Niels

2016-01-01

A 6-month, time-lagged online survey among 441 employees in diverse industries was conducted to investigate the role paranoia plays as an antecedent and as a consequence of advancement in organizations. The background of the study is the argument that it requires active social sense-making and behavioral adaptability to advance in organizations. The present paper thus explores the extent to which employees’ paranoid cognitions—representative of a heightened albeit suspicious sense-making and behavioral adaptability—link with their advancement in organizations (operationalized as changes in afforded span of control), both as an antecedent and an outcome. Following the strategy to illuminate the process by interaction analysis, both conditions (antecedent and outcome) are examined in interaction with employees’ self-monitoring, which is considered representative of a heightened but healthy sense-making and behavioral adaptability. Results support the expected interference interaction between paranoid cognitions and self-monitoring in that each can to some degree compensate for the other in explaining employees’ organizational advancement. Reversely, changes in span of control also affected paranoid cognitions. In particular, low self-monitors, i.e., those low in adaptive sense-making, reacted with heightened paranoid cognitions when demoted. In effect, the present study is thus the first to empirically support that paranoid cognitions can be a consequence but also a prerequisite for getting ahead in organizations. Practical advice should, however, be suspended until it is better understood whether and under what circumstances paranoia may relate not only to personally getting ahead but also to an increased effectiveness for the benefit of the organization. PMID:27713724

Use of remote sensing in agriculture

NASA Technical Reports Server (NTRS)

Pettry, D. E.; Powell, N. L.; Newhouse, M. E.

1974-01-01

Remote sensing studies in Virginia and Chesapeake Bay areas to investigate soil and plant conditions via remote sensing technology are reported ant the results given. Remote sensing techniques and interactions are also discussed. Specific studies on the effects of soil moisture and organic matter on energy reflection of extensively occurring Sassafras soils are discussed. Greenhouse and field studies investigating the effects of chlorophyll content of Irish potatoes on infrared reflection are presented. Selected ground truth and environmental monitoring data are shown in summary form. Practical demonstrations of remote sensing technology in agriculture are depicted and future use areas are delineated.

Making sense of polarities in health organizations for policy and leadership.

PubMed

Martin, Carmel M

2010-10-01

Making sense of complex adaptive clinical practice and health systems is a pressing challenge as health services continue to struggle to adapt to changing internal and external constraints. In this Forum, we begin with Dervin's Sense-Making theories and research in communications. This provides a conceptual and theoretical context for this editions research on comparative complexity of family medicine consultations in the USA, models for adaptive leadership in clinical care and social networking to make sense of health promotion challenges for young people. Finally, a Sense-Making schema is proposed. © 2010 Blackwell Publishing Ltd.

Bacterial cellulose biosynthesis: diversity of operons, subunits, products and functions

PubMed Central

Römling, Ute; Galperin, Michael Y.

2015-01-01

Summary Recent studies of bacterial cellulose biosynthesis, including structural characterization of a functional cellulose synthase complex, provided the first mechanistic insight into this fascinating process. In most studied bacteria, just two subunits, BcsA and BcsB, are necessary and sufficient for the formation of the polysaccharide chain in vitro. Other subunits – which differ among various taxa – affect the enzymatic activity and product yield in vivo by modulating expression of biosynthesis apparatus, export of the nascent β-D-glucan polymer to the cell surface, and the organization of cellulose fibers into a higher-order structure. These auxiliary subunits play key roles in determining the quantity and structure of the resulting biofilm, which is particularly important for interactions of bacteria with higher organisms that lead to rhizosphere colonization and modulate virulence of cellulose-producing bacterial pathogens inside and outside of host cells. Here we review the organization of four principal types of cellulose synthase operons found in various bacterial genomes, identify additional bcs genes that encode likely components of the cellulose biosynthesis and secretion machinery, and propose a unified nomenclature for these genes and subunits. We also discuss the role of cellulose as a key component of biofilms formed by a variety of free-living and pathogenic bacteria and, for the latter, in the choice between acute infection and persistence in the host. PMID:26077867

The mouse homeobox gene Noto regulates node morphogenesis, notochordal ciliogenesis, and left–right patterning

PubMed Central

Beckers, Anja; Alten, Leonie; Viebahn, Christoph; Andre, Philipp; Gossler, Achim

2007-01-01

The mouse homeobox gene Noto represents the homologue of zebrafish floating head (flh) and is expressed in the organizer node and in the nascent notochord. Previous analyses suggested that Noto is required exclusively for the formation of the caudal part of the notochord. Here, we show that Noto is also essential for node morphogenesis, controlling ciliogenesis in the posterior notochord, and the establishment of laterality, whereas organizer functions in anterior–posterior patterning are apparently not compromised. In mutant embryos, left–right asymmetry of internal organs and expression of laterality markers was randomized. Mutant posterior notochord regions were variable in size and shape, cilia were shortened with highly irregular axonemal microtubuli, and basal bodies were, in part, located abnormally deep in the cytoplasm. The transcription factor Foxj1, which regulates the dynein gene Dnahc11 and is required for the correct anchoring of basal bodies in lung epithelial cells, was down-regulated in mutant nodes. Likewise, the transcription factor Rfx3, which regulates cilia growth, was not expressed in Noto mutants, and various other genes important for cilia function or assembly such as Dnahc5 and Nphp3 were down-regulated. Our results establish Noto as an essential regulator of node morphogenesis and ciliogenesis in the posterior notochord, and suggest Noto acts upstream of Foxj1 and Rfx3. PMID:17884984

Proxies for soil organic carbon derived from remote sensing

NASA Astrophysics Data System (ADS)

Rasel, S. M. M.; Groen, T. A.; Hussin, Y. A.; Diti, I. J.

2017-07-01

The possibility of carbon storage in soils is of interest because compared to vegetation it contains more carbon. Estimation of soil carbon through remote sensing based techniques can be a cost effective approach, but is limited by available methods. This study aims to develop a model based on remotely sensed variables (elevation, forest type and above ground biomass) to estimate soil carbon stocks. Field observations on soil organic carbon, species composition, and above ground biomass were recorded in the subtropical forest of Chitwan, Nepal. These variables were also estimated using LiDAR data and a WorldView 2 image. Above ground biomass was estimated from the LiDAR image using a novel approach where the image was segmented to identify individual trees, and for these trees estimates of DBH and Height were made. Based on AIC (Akaike Information Criterion) a regression model with above ground biomass derived from LiDAR data, and forest type derived from WorldView 2 imagery was selected to estimate soil organic carbon (SOC) stocks. The selected model had a coefficient of determination (R2) of 0.69. This shows the scope of estimating SOC with remote sensing derived variables in sub-tropical forests.

77 FR 4056 - Agency Information Collection Activities: Submitted for Office of Management and Budget (OMB...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-26

... university and State organizations in a ready to use form; and to expand the science of remote sensing... requirements for the National Land Remote Sensing Education, Outreach and Research Activity (NLRSEORA) and...

All-organic optoelectronic sensor for pulse oximetry

NASA Astrophysics Data System (ADS)

Lochner, Claire M.; Khan, Yasser; Pierre, Adrien; Arias, Ana C.

2014-12-01

Pulse oximetry is a ubiquitous non-invasive medical sensing method for measuring pulse rate and arterial blood oxygenation. Conventional pulse oximeters use expensive optoelectronic components that restrict sensing locations to finger tips or ear lobes due to their rigid form and area-scaling complexity. In this work, we report a pulse oximeter sensor based on organic materials, which are compatible with flexible substrates. Green (532 nm) and red (626 nm) organic light-emitting diodes (OLEDs) are used with an organic photodiode (OPD) sensitive at the aforementioned wavelengths. The sensor’s active layers are deposited from solution-processed materials via spin-coating and printing techniques. The all-organic optoelectronic oximeter sensor is interfaced with conventional electronics at 1 kHz and the acquired pulse rate and oxygenation are calibrated and compared with a commercially available oximeter. The organic sensor accurately measures pulse rate and oxygenation with errors of 1% and 2%, respectively.

Photosystem II Component Lifetimes in the Cyanobacterium Synechocystis sp. Strain PCC 6803

PubMed Central

Yao, Danny C. I.; Brune, Daniel C.; Vavilin, Dmitri; Vermaas, Wim F. J.

2012-01-01

To gain insight in the lifetimes of photosystem II (PSII) chlorophyll and proteins, a combined stable isotope labeling (15N)/mass spectrometry method was used to follow both old and new pigments and proteins. Photosystem I-less Synechocystis cells were grown to exponential or post-exponential phase and then diluted in BG-11 medium with [15N]ammonium and [15N]nitrate. PSII was isolated, and the masses of PSII protein fragments and chlorophyll were determined. Lifetimes of PSII components ranged from 1.5 to 40 h, implying that at least some of the proteins and chlorophyll turned over independently from each other. Also, a significant amount of nascent PSII components accumulated in thylakoids when cells were in post-exponential growth phase. In a mutant lacking small Cab-like proteins (SCPs), most PSII protein lifetimes were unaffected, but the lifetime of chlorophyll and the amount of nascent PSII components that accumulated were decreased. In the absence of SCPs, one of the PSII biosynthesis intermediates, the monomeric PSII complex without CP43, was missing. Therefore, SCPs may stabilize nascent PSII protein complexes. Moreover, upon SCP deletion, the rate of chlorophyll synthesis and the accumulation of early tetrapyrrole precursors were drastically reduced. When [14N]aminolevulinic acid (ALA) was supplemented to 15N-BG-11 cultures, the mutant lacking SCPs incorporated much more exogenous ALA into chlorophyll than the control demonstrating that ALA biosynthesis was impaired in the absence of SCPs. This illustrates the major effects that nonstoichiometric PSII components such as SCPs have on intermediates and assembly but not on the lifetime of PSII proteins. PMID:22090028

Comparative Dynamics of Retrograde Actin Flow and Focal Adhesions: Formation of Nascent Adhesions Triggers Transition from Fast to Slow Flow

PubMed Central

Alexandrova, Antonina Y.; Arnold, Katya; Schaub, Sébastien; Vasiliev, Jury M.; Meister, Jean-Jacques; Bershadsky, Alexander D.; Verkhovsky, Alexander B.

2008-01-01

Dynamic actin network at the leading edge of the cell is linked to the extracellular matrix through focal adhesions (FAs), and at the same time it undergoes retrograde flow with different dynamics in two distinct zones: the lamellipodium (peripheral zone of fast flow), and the lamellum (zone of slow flow located between the lamellipodium and the cell body). Cell migration involves expansion of both the lamellipodium and the lamellum, as well as formation of new FAs, but it is largely unknown how the position of the boundary between the two flow zones is defined, and how FAs and actin flow mutually influence each other. We investigated dynamic relationship between focal adhesions and the boundary between the two flow zones in spreading cells. Nascent FAs first appeared in the lamellipodium. Within seconds after the formation of new FAs, the rate of actin flow decreased locally, and the lamellipodium/lamellum boundary advanced towards the new FAs. Blocking fast actin flow with cytochalasin D resulted in rapid dissolution of nascent FAs. In the absence of FAs (spreading on poly-L-lysine-coated surfaces) retrograde flow was uniform and the velocity transition was not observed. We conclude that formation of FAs depends on actin dynamics, and in its turn, affects the dynamics of actin flow by triggering transition from fast to slow flow. Extension of the cell edge thus proceeds through a cycle of lamellipodium protrusion, formation of new FAs, advance of the lamellum, and protrusion of the lamellipodium from the new base. PMID:18800171

Strand-Specific Analysis of DNA Synthesis and Proteins Association with DNA Replication Forks in Budding Yeast.

PubMed

Yu, Chuanhe; Gan, Haiyun; Zhang, Zhiguo

2018-01-01

DNA replication initiates at DNA replication origins after unwinding of double-strand DNA(dsDNA) by replicative helicase to generate single-stranded DNA (ssDNA) templates for the continuous synthesis of leading-strand and the discontinuous synthesis of lagging-strand. Therefore, methods capable of detecting strand-specific information will likely yield insight into the association of proteins at leading and lagging strand of DNA replication forks and the regulation of leading and lagging strand synthesis during DNA replication. The enrichment and Sequencing of Protein-Associated Nascent DNA (eSPAN), which measure the relative amounts of proteins at nascent leading and lagging strands of DNA replication forks, is a step-wise procedure involving the chromatin immunoprecipitation (ChIP) of a protein of interest followed by the enrichment of protein-associated nascent DNA through BrdU immunoprecipitation. The isolated ssDNA is then subjected to strand-specific sequencing. This method can detect whether a protein is enriched at leading or lagging strand of DNA replication forks. In addition to eSPAN, two other strand-specific methods, (ChIP-ssSeq), which detects potential protein-ssDNA binding and BrdU-IP-ssSeq, which can measure synthesis of both leading and lagging strand, were developed along the way. These methods can provide strand-specific and complementary information about the association of the target protein with DNA replication forks as well as synthesis of leading and lagging strands genome wide. Below, we describe the detailed eSPAN, ChIP-ssSeq, and BrdU-IP-ssSeq protocols.

5S Ribosomal RNA Is an Essential Component of a Nascent Ribosomal Precursor Complex that Regulates the Hdm2-p53 Checkpoint

PubMed Central

Donati, Giulio; Peddigari, Suresh; Mercer, Carol A.; Thomas, George

2013-01-01

SUMMARY Recently, we demonstrated that RPL5 and RPL11 act in a mutually dependent manner to inhibit Hdm2 and stabilize p53 following impaired ribosome biogenesis. Given that RPL5 and RPL11 form a preribosomal complex with noncoding 5S ribosomal RNA (rRNA) and the three have been implicated in the p53 response, we reasoned they may be part of an Hdm2-inhibitory complex. Here, we show that small interfering RNAs directed against 5S rRNA have no effect on total or nascent levels of the noncoding rRNA, though they prevent the reported Hdm4 inhibition of p53. To achieve efficient inhibition of 5S rRNA synthesis, we targeted TFIIIA, a specific RNA polymerase III cofactor, which, like depletion of either RPL5 or RPL11, did not induce p53. Instead, 5S rRNA acts in a dependent manner with RPL5 and RPL11 to inhibit Hdm2 and stabilize p53. Moreover, depletion of any one of the three components abolished the binding of the other two to Hdm2, explaining their common dependence. Finally, we demonstrate that the RPL5/RPL11/5S rRNA preribosomal complex is redirected from assembly into nascent 60S ribosomes to Hdm2 inhibition as a consequence of impaired ribosome biogenesis. Thus, the activation of the Hdm2-inhibitory complex is not a passive but a regulated event, whose potential role in tumor suppression has been recently noted. PMID:23831031

Trace Gas Measurements in Nascent, Aged and Cloud-processed Smoke from Africa Savanna Fires by Airborne Fourier Transform Infrared Spectroscopy (AFTIR)

NASA Technical Reports Server (NTRS)

Yokelson, Robert J.; Bertschi, Isaac T.; Christian, Ted J.; Hobbs, Peter V.; Ward, Darold E.; Hao, Wei Min

2003-01-01

We measured stable and reactive trace gases with an airborne Fourier transform infrared spectrometer (AFTIR) on the University of Washington Convair-580 research aircraft in August/September 2000 during the SAFARI 2000 dry season campaign in Southern Africa. The measurements included vertical profiles of C02, CO, H20, and CH4 up to 5.5 km on six occasions above instrumented ground sites and below the TERRA satellite and ER-2 high-flying research aircraft. We also measured the trace gas emissions from 10 African savanna fires. Five of these fires featured extensive ground-based fuel characterization, and two were in the humid savanna ecosystem that accounts for most African biomass burning. The major constituents we detected in nascent CH3OOH, HCHO, CH30H, HCN, NH3, HCOOH, and C2H2. These are the first quantitative measurements of the initial emissions of oxygenated volatile organic compounds (OVOC), NH3, and HCN from African savanna fires. On average, we measured 5.3 g/kg of OVOC and 3.6 g/kg of hydrocarbons (including CH4) in the initial emissions from the fires. Thus, the OVOC will have profound, largely unexplored effects on tropical tropospheric chemistry. The HCN emission factor was only weakly dependent on fire type; the average value (0.53 g/kg) is about 20 times that of a previous recommendation. HCN may be useful as a tracer for savanna fires. Delta O3/Delta CO and Delta CH3COO/Delta CO increased to as much as 9% in <1 h of photochemical processing downwind of fires. Direct measurements showed that cloud processing of smoke greatly reduced CH30H, NH3, CH3COOH, SO2, and NO2 levels, but significantly increased HCHO and NO.

Macrophage activation and muscle remodeling at myotendinous junctions after modifications in muscle loading.

PubMed Central

St Pierre, B. A.; Tidball, J. G.

1994-01-01

Modifications in muscle loading have been reported previously to result in increased numbers of mononucleated cells and changes in myofibril organization at myotendinous junctions (MTJs). The goals of this study were to determine the identity of those mononucleated cells and to examine the relationships between changes in their structure, location, and number with structural aspects of remodeling at MTJs experiencing modified loading. Soleus muscles from rats subjected to 10 days of hindlimb suspension were analyzed 0, 2, 4, and 7 days after return to weight bearing. Immunohistochemistry showed that ED1+, ED2+ and Ia+ macrophages were present at the MTJ and microtendon of control muscle. After reloading, ED2+ macrophages increased in number and size at MTJs and microtendons, indicating their activation. ED1+ cells showed no change in size or number whereas Ia+ cells were increased in size at day 7 of reloading. Electron microscopic observations showed that mononucleated cells near MTJs of control or suspended muscle were not highly active in protein synthesis or secretion. However, in reloaded muscle, mononucleated cells were found to be in close proximity to MTJs and to contain a high concentration of organelles associated with protein secretion. During these stages of reloading, extensive remodeling of myofibril-membrane associations occurred and nascent sarcomeres appeared in the MTJ regions of muscle fibers. Immunohistochemistry showed that during these stages of nascent sarcomere formation, there was renewed expression of developmental myosin heavy chain at MTJs, with this heavy chain appearing most prominently at the MTJ at day 7 of reloading. The activation and increased numbers of macrophages at MTJs and the close apposition of secretory cells to the MTJ membrane during remodeling lead us to propose that macrophage-derived factors may influence remodeling of MTJs in muscles experiencing modified loading. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 PMID:7992849

Perturbation of Chromatin Structure Globally Affects Localization and Recruitment of Splicing Factors

PubMed Central

Risso, Guillermo J.; Pawellek, Andrea; Ule, Jernej; Lamond, Angus I.; Kornblihtt, Alberto R.

2012-01-01

Chromatin structure is an important factor in the functional coupling between transcription and mRNA processing, not only by regulating alternative splicing events, but also by contributing to exon recognition during constitutive splicing. We observed that depolarization of neuroblastoma cell membrane potential, which triggers general histone acetylation and regulates alternative splicing, causes a concentration of SR proteins in nuclear speckles. This prompted us to analyze the effect of chromatin structure on splicing factor distribution and dynamics. Here, we show that induction of histone hyper-acetylation results in the accumulation in speckles of multiple splicing factors in different cell types. In addition, a similar effect is observed after depletion of the heterochromatic protein HP1α, associated with repressive chromatin. We used advanced imaging approaches to analyze in detail both the structural organization of the speckle compartment and nuclear distribution of splicing factors, as well as studying direct interactions between splicing factors and their association with chromatin in vivo. The results support a model where perturbation of normal chromatin structure decreases the recruitment efficiency of splicing factors to nascent RNAs, thus causing their accumulation in speckles, which buffer the amount of free molecules in the nucleoplasm. To test this, we analyzed the recruitment of the general splicing factor U2AF65 to nascent RNAs by iCLIP technique, as a way to monitor early spliceosome assembly. We demonstrate that indeed histone hyper-acetylation decreases recruitment of U2AF65 to bulk 3′ splice sites, coincident with the change in its localization. In addition, prior to the maximum accumulation in speckles, ∼20% of genes already show a tendency to decreased binding, while U2AF65 seems to increase its binding to the speckle-located ncRNA MALAT1. All together, the combined imaging and biochemical approaches support a model where chromatin structure is essential for efficient co-transcriptional recruitment of general and regulatory splicing factors to pre-mRNA. PMID:23152763

Photoluminescent Metal–Organic Frameworks for Gas Sensing

PubMed Central

Lin, Rui‐Biao; Liu, Si‐Yang; Ye, Jia‐Wen; Li, Xu‐Yu

2016-01-01

Luminescence of porous coordination polymers (PCPs) or metal–organic frameworks (MOFs) is sensitive to the type and concentration of chemical species in the surrounding environment, because these materials combine the advantages of the highly regular porous structures and various luminescence mechanisms, as well as diversified host‐guest interactions. In the past few years, luminescent MOFs have attracted more and more attention for chemical sensing of gas‐phase analytes, including common gases and vapors of solids/liquids. While liquid‐phase and gas‐phase luminescence sensing by MOFs share similar mechanisms such as host‐guest electron and/or energy transfer, exiplex formation, and guest‐perturbing of excited‐state energy level and radiation pathways, via various types of host‐guest interactions, gas‐phase sensing has its unique advantages and challenges, such as easy utilization of encapsulated guest luminophores and difficulty for accurate measurement of the intensity change. This review summarizes recent progresses by using luminescent MOFs as reusable sensing materials for detection of gases and vapors of solids/liquids especially for O2, highlighting various strategies for improving the sensitivity, selectivity, stability, and accuracy, reducing the materials cost, and developing related devices. PMID:27818903

Poly(3-Methylthiophene) Thin Films Deposited Electrochemically on QCMs for the Sensing of Volatile Organic Compounds

PubMed Central

Öztürk, Sadullah; Kösemen, Arif; Şen, Zafer; Kılınç, Necmettin; Harbeck, Mika

2016-01-01

Poly(3-methylthiophene) (PMeT) thin films were electrochemically deposited on quartz crystal microbalance QCM transducers to investigate their volatile organic compound (VOC) sensing properties depending on ambient conditions. Twelve different VOCs including alcohols, ketones, chlorinated compounds, amines, and the organosphosphate dimethyl methylphosphonate (DMMP) were used as analytes. The responses of the chemical sensors against DMMP were the highest among the tested analytes; thus, fabricated chemical sensors based on PMeT can be evaluated as potential candidates for selectively detecting DMMP. Generally, detection limits in the low ppm range could be achieved. The gas sensing measurements were recorded at various humid air conditions to investigate the effects of the humidity on the gas sensing properties. The sensing performance of the chemical sensors was slightly reduced in the presence of humidity in ambient conditions. While a decrease in sensitivity was observed for humidity levels up to 50% r.h., the sensitivity was nearly unaffected for higher humidity levels and a reliable detection of the VOCs and DMMP was possible with detection limits in the low ppm range. PMID:27023539

Contrasting seasonality in optical-biogeochemical properties of the Baltic Sea

PubMed Central

Ylöstalo, Pasi; Kallio, Kari Y.; Spilling, Kristian; Kutser, Tiit

2017-01-01

Optical-biogeochemical relationships of particulate and dissolved organic matter are presented in support of remote sensing of the Baltic Sea pelagic. This system exhibits strong seasonality in phytoplankton community composition and wide gradients of chromophoric dissolved organic matter (CDOM), properties which are poorly handled by existing remote sensing algorithms. Absorption and scattering properties of particulate matter reflected the seasonality in biological (phytoplankton succession) and physical (thermal stratification) processes. Inherent optical properties showed much wider variability when normalized to the chlorophyll-a concentration compared to normalization to either total suspended matter dry weight or particulate organic carbon. The particle population had the largest optical variability in summer and was dominated by organic matter in both seasons. The geographic variability of CDOM and relationships with dissolved organic carbon (DOC) are also presented. CDOM dominated light absorption at blue wavelengths, contributing 81% (median) of the absorption by all water constituents at 400 nm and 63% at 442 nm. Consequentially, 90% of water-leaving radiance at 412 nm originated from a layer (z90) no deeper than approximately 1.0 m. With water increasingly attenuating light at longer wavelengths, a green peak in light penetration and reflectance is always present in these waters, with z90 up to 3.0–3.5 m depth, whereas z90 only exceeds 5 m at biomass < 5 mg Chla m-3. High absorption combined with a weakly scattering particle population (despite median phytoplankton biomass of 14.1 and 4.3 mg Chla m-3 in spring and summer samples, respectively), characterize this sea as a dark water body for which dedicated or exceptionally robust remote sensing techniques are required. Seasonal and regional optical-biogeochemical models, data distributions, and an extensive set of simulated remote-sensing reflectance spectra for testing of remote sensing algorithms are provided as supplementary data. PMID:28384157

Quorum signaling and sensing by nontypeable Haemophilus influenzae.

PubMed

Swords, W Edward

2012-01-01

Quorum signals are diffusible factors produced by bacteria that coordinate communal responses. For nontypeable Haemophilus influenzae (NTHi), a series of recent papers indicate that production and sensing of quorum signals are determinants of biofilm formation/maturation and persistence in vivo. In this mini-review I will summarize the current knowledge about quorum signaling/sensing by this organism, and identify specific topics for additional study.

Quorum signaling and sensing by nontypeable Haemophilus influenzae

PubMed Central

Swords, W. Edward

2012-01-01

Quorum signals are diffusible factors produced by bacteria that coordinate communal responses. For nontypeable Haemophilus influenzae (NTHi), a series of recent papers indicate that production and sensing of quorum signals are determinants of biofilm formation/maturation and persistence in vivo. In this mini-review I will summarize the current knowledge about quorum signaling/sensing by this organism, and identify specific topics for additional study. PMID:22919689

R-loops in bacterial transcription: their causes and consequences.

PubMed

Gowrishankar, J; Leela, J Krishna; Anupama, K

2013-01-01

Nascent untranslated transcripts in bacteria are prone to generating RNA-DNA hybrids (R-loops); Rho-dependent transcription termination acts to reduce their prevalence. Here we discuss the mechanisms of R-loop formation and growth inhibition in bacteria.

Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD3CN treated with a parallel multi-state EVB model

NASA Astrophysics Data System (ADS)

Glowacki, David R.; Orr-Ewing, Andrew J.; Harvey, Jeremy N.

2015-07-01

We describe a parallelized linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM and TINKER. Forces are obtained using the Hellmann-Feynman relationship, giving continuous gradients, and good energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to explicitly correlated coupled cluster theory, we built a 64-state MS-EVB model designed to study the F + CD3CN → DF + CD2CN reaction in CD3CN solvent (recently reported in Dunning et al. [Science 347(6221), 530 (2015)]). This approach allows us to build a reactive potential energy surface whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We ran molecular dynamics simulations to examine a range of observables which follow in the wake of the reactive event: energy deposition in the nascent reaction products, vibrational relaxation rates of excited DF in CD3CN solvent, equilibrium power spectra of DF in CD3CN, and time dependent spectral shifts associated with relaxation of the nascent DF. Many of our results are in good agreement with time-resolved experimental observations, providing evidence for the accuracy of our MS-EVB framework in treating both the solute and solute/solvent interactions. The simulations provide additional insight into the dynamics at sub-picosecond time scales that are difficult to resolve experimentally. In particular, the simulations show that (immediately following deuterium abstraction) the nascent DF finds itself in a non-equilibrium regime in two different respects: (1) it is highly vibrationally excited, with ˜23 kcal mol-1 localized in the stretch and (2) its post-reaction solvation environment, in which it is not yet hydrogen-bonded to CD3CN solvent molecules, is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational relaxation of the nascent DF results in a spectral blue shift, while relaxation of the post-reaction solvation environment results in a red shift. These two competing effects mean that the post-reaction relaxation profile is distinct from what is observed when Franck-Condon vibrational excitation of DF occurs within a microsolvation environment initially at equilibrium. Our conclusions, along with the theoretical and parallel software framework presented in this paper, should be more broadly applicable to a range of complex reactive systems.

The role of the style as a sense-organ in relation to wilting of the flower.

PubMed

Gilissen, L J

1976-01-01

Pollen tube growth in the style (Petunia ♀xNicotiana ♂) accelerated wilting. Pollination and germination on the stigmatic surface (Petunia ♀xAtropa ♂) did not change the stage of flowering in comparison with unpollinated flowers. Wilting of the corolla was accelerated by cutting off the stigma or cutting the style half-way down. Removal of the entire style also brought about an acceleration, however, to a lesser extent. The role of the style as a sense-organ with regard to the transmission of information from stigma and style to other flower organs is discussed.

The World Hypotheses: Implications for Intercultural Communication Research.

ERIC Educational Resources Information Center

Ting-Toomey, Stella

The "sense making" process structures humans' categorization, perceptual, and expressive processes. These "sense making" references are ultimately derived from four distinct "root metaphors": mechanism or mechanistic thinking (machine), formism or formistic thinking (similarity), organicism or organistic thinking (organic process), and…

Investigation of fugitive emissions from petrochemical transport barges using optical remote sensing

EPA Science Inventory

Recent airborne remote sensing survey data acquired with passive gas imaging equipment (PGIE), in this case infrared cameras, have shown potentially significant fugitive volatile organic carbon (VOC) emissions from petrochemical transport barges. The experiment found remote sens...

Devices and methods to detect and quantify trace gases

DOEpatents

Allendorf, Mark D.; Robinson, Alex

2016-05-03

Sensing devices based on a surface acoustic wave ("SAW") device coated with an absorbent crystalline or amorphous layer for detecting at least one chemical analyte in a gaseous carrier. Methods for detecting the presence of a chemical analyte in a gaseous carrier using such devices are also disclosed. The sensing devices and methods for their use may be configured for sensing chemical analytes selected from the group consisting of water vapor, carbon dioxide, methanol, ethanol, carbon monoxide, nitric oxide, nitrous oxide, organic amines, organic compounds containing NO.sub.2 groups, halogenated hydrocarbons, acetone, hexane, toluene, isopropanol, alcohols, alkanes, alkenes, benzene, functionalized aromatics, ammonia (NH.sub.3), phosgene (COCl.sub.2), sulfur mustard, nerve agents, sulfur dioxide, tetrahydrofuran (THF) and methyltertbutyl ether (MTBE) and combinations thereof.

Using aligned poly(3-hexylthiophene)/poly(methyl methacrylate) blend fibers to detect volatile organic compounds

NASA Astrophysics Data System (ADS)

Chan, Shun-Hsiang; Lin, Tz-Feng; Wu, Ming-Chung; Chen, Shih-Hsuan; Su, Wei-Fang; Lai, Chao-Sung

2018-04-01

In this study, we developed a novel sensing material fabricated using a poly(3-hexylthiophene) (P3HT)/poly(methyl methacrylate) (PMMA) blend fiber on a glass substrate. The sensing materials can easily be used for sensing toluene vapor detected from extinction spectral changes. The extinction spectra variation is noted from the absorption of volatile organic compounds in a highly specific surface area of fibrous coating. An electrospinning technique is applied to generate a nonwoven structure and uniaxial orientation by fibrous coating. The response of the uniaxially orientated fibrous film is even improved at several toluene vapor concentrations. The best detection limit of this well-aligned fibrous film is up to 200 ppm for toluene vapor.

Sense of place among New England organic farmers and commercial fishermen: How social context shapes identity and environmentally responsible behavior

NASA Astrophysics Data System (ADS)

Mueller, Anneliese Marie

Given the prominence of sense of place in new environmental education curricula, this study aims to strengthen the conceptual and empirical foundations of sense of place, and to determine how sense of place may be linked to environmentally responsible behavior. For this study, five commercial fishermen and five organic farmers from the New England Seacoast region participated in a series of in-depth phenomenological interviews and observations. The data was systematically coded in order to allow themes and categories to emerge. The results indicate that aspects of the existing conceptual framework of sense of place, such as place attachment, ecological knowledge, and public involvement, do in fact describe the relationship between people and place. However, the results also indicate that two conceptual elements---attention to social context and awareness of moral theory---are missing from the current conceptual framework in EE theory. These results suggest that the current framework should be expanded to emphasize the role of human and non-human communities: the development of a sense of place and the learning of environmentally responsible behavior must be situated within a social context. This study lends support to the view that for sense of place to move people to ethical action, it is crucial for them to recognize, and to participate in, a community of support and care.

A phenomenological approach to the ethics of transplantation medicine: sociality and sharing when living-with and dying-with others.

PubMed

Zeiler, Kristin

2014-10-01

Recent years have seen a rise in the number of sociological, anthropological, and ethnological works on the gift metaphor in organ donation contexts, as well as in the number of philosophical and theological analyses of giving and generosity, which has been mirrored in the ethical debate on organ donation. In order to capture the breadth of this field, four frameworks for thinking about bodily exchanges in medicine have been distinguished: property rights, heroic gift-giving, sacrifice, and gift-giving as aporia. Unfortunately, they all run into difficulties in terms of both making sense of the relational dimensions of postmortem and live organ donations and being normatively adequate in the sense of shedding light and providing guidance on ethical concerns when body parts are donated. For this reason, this article presents a phenomenological framework of giving-through-sharing, based on Maurice Merleau-Ponty's philosophy. This framework makes sense of relational dimensions of postmortem and live organ donation. It also sheds light on three highly debated concerns in organ donation ethics: indebtedness on the part of recipients, the fact that some live donors do not experience donation as a matter of choice, and the potentially painful experience of donors' relatives, who need to make decisions about postmortem organ donation at a time of bereavement. It can indirectly support what may be called a normalization of bodily exchanges in medicine.

Organizing for Instruction: A Comparative Study of Public, Charter, and Catholic Schools

ERIC Educational Resources Information Center

Dorner, Lisa M.; Spillane, James P.; Pustejovsky, James

2011-01-01

Guided by theories of institutions, organizations, and sense-making, this manuscript examines how public, charter, and Catholic school staff in a large urban area organize for instruction and respond to educational change. To build theory about institutional processes of "organizing" from participants' perspectives, data included a…

A High Sensitivity and Wide Dynamic Range Fiber-Optic Sensor for Low-Concentration VOC Gas Detection

PubMed Central

Khan, Md. Rajibur Rahaman; Kang, Shin-Won

2014-01-01

In this paper, we propose a volatile organic compound (VOC) gas sensing system with high sensitivity and a wide dynamic range that is based on the principle of the heterodyne frequency modulation method. According to this method, the time period of the sensing signal shift when Nile Red containing a VOC-sensitive membrane of a fiber-optic sensing element comes into contact with a VOC. This sensing membrane produces strong, fast and reversible signals when exposed to VOC gases. The response and recovery times of the proposed sensing system were less than 35 s, and good reproducibility and accuracy were obtained. PMID:25490592

Environmental Sense Box: A Strategy for Helping Elementary School Students Understand Abstract Environments through Concrete Learning Activities.

ERIC Educational Resources Information Center

Sesow, F. Wm.

This paper suggests a technique for the development, collection, and organization of materials that will aid learning through the use of the senses by building an environmental sense box. England is used as an example of a place that provides many sensory experiences which can be duplicated in such a box. The box can be made from a cardboard…

Disseminating technological information on remote sensing to potential users

NASA Technical Reports Server (NTRS)

Russell, J. D.; Lindenlaub, J. C.

1977-01-01

The Laboratory for Applications of Remote Sensing developed materials and programs which range from short tutorial brochures to post-doctoral research programs which may span several years. To organize both the content and the instructional techniques, a matrix of instructional materials was conceptualized. Each row in the matrix represents a subject area in remote sensing and each column in the matrix represents a different type media or instructional strategy.

Metal-organic frameworks as biosensors for luminescence-based detection and imaging

PubMed Central

Miller, Sophie E.; Teplensky, Michelle H.; Moghadam, Peyman Z.; Fairen-Jimenez, David

2016-01-01

Metal-organic frameworks (MOFs), formed by the self-assembly of metal centres or clusters and organic linkers, possess many key structural and chemical features that have enabled them to be used in sensing platforms for a variety of environmentally, chemically and biomedically relevant compounds. In particular, their high porosity, large surface area, tuneable chemical composition, high degree of crystallinity, and potential for post-synthetic modification for molecular recognition make MOFs promising candidates for biosensing applications. In this review, we separate our discussion of MOF biosensors into two categories: quantitative sensing, focusing specifically on luminescence-based sensors for the direct measurement of a specific analyte, and qualitative sensing, where we describe MOFs used for fluorescence microscopy and as magnetic resonance imaging contrast agents. We highlight several key publications in each of these areas, concluding that MOFs present an exciting, versatile new platform for biosensing applications and imaging, and we expect to see their usage grow as the field progresses. PMID:27499847

Assembly of ZIF-67 Metal-Organic Framework over Tin Oxide Nanoparticles for Synergistic Chemiresistive CO2 Gas Sensing.

PubMed

DMello, Marilyn Esclance; Sundaram, Nalini G; Kalidindi, Suresh Babu

2018-05-03

Metal-organic frameworks (MOFs) are widely known for their record storage capacities of small gas molecules (H 2 , CO 2 , and CH 4 ). Assembly of such porous materials onto well-known chemiresistive gas sensing elements such as SnO 2 could be an attractive prospect to achieve novel sensing properties as this affects the surface chemistry of SnO 2 . Cobalt-imidazole based ZIF-67 MOF was grown onto preformed SnO 2 nanoparticles to realize core-shell like architecture and explored for greenhouse gas CO 2 sensing. CO 2 sensing over SnO 2 is a challenge because its interaction with SnO 2 surface is minimal. The ZIF-67 coating over SnO 2 improved the response of SnO 2 up to 12-fold (for 50 % CO 2 ). The SnO 2 @ZIF-67 also showed a response of 16.5±2.1 % for 5000 ppm CO 2 (threshold limit value (TLV)) at 205 °C, one of the best values reported for a SnO 2 -based sensor. The observed novel CO 2 sensing characteristics are assigned to electronic structure changes at the interface of ZIF-67 and SnO 2 . © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recalibrating sleep: is recalibration and readjustment of sense organs and brain-body connections the core function of sleep?

PubMed

Smetacek, Victor

2010-10-01

Sleep is an enigma because we all know what it means and does to us, yet a scientific explanation for why animals including humans need to sleep is still lacking. However, the enigma can be resolved if the animal body is regarded as a purposeful machine whose moving parts are coordinated with spatial information provided by a disparate array of sense organs. The performance of all complex machines deteriorates with time due to inevitable instrument drift of the individual sensors combined with wear and tear of the moving parts which result in declining precision and coordination. Peak performance is restored by servicing the machine, which involves calibrating the sensors against baselines and standards, then with one another, and finally readjusting the connections between instruments and moving parts. It follows that the animal body and its sensors will also require regular calibration of sense organs and readjustment of brain-body connections which will need to be carried out while the animal is not in functional but in calibration mode. I suggest that this is the core function of sleep. This recalibration hypothesis of sleep can be tested subjectively. We all know from personal experience that sleep is needed to recover from tiredness that sets in towards the end of a long day. This tiredness, which is quite distinct from mental or muscular exhaustion caused by strenuous exertion, manifests itself in deteriorating general performance: the sense organs lose precision, movements become clumsy and the mind struggles to maintain focus. We can all agree that sleep sharpens the sense organs and restores agility to mind and body. I now propose that the sense of freshness and buoyancy after a good night's sleep is the feeling of recalibrated sensory and motor systems. The hypothesis can be tested rigorously by examining available data on sleep cycles and stages against this background. For instance, REM and deep sleep cycles can be interpreted as successive, separate calibration runs of the vestibulo-ocular reflex and the sensory-motor systems, respectively, amongst other functions running in parallel, such as dreaming. Because the split-second connections between sensory information and emotional responses will also require calibration, some aspects of dreaming could be interpreted in this light. Much of the baffling behaviour and patterns of brain activity of sleeping animals and humans make sense in the framework of this technological paradigm since different animal lineages will have evolved different techniques to achieve calibration. Copyright 2010 Elsevier Ltd. All rights reserved.

A Self-Sustained Wireless Multi-Sensor Platform Integrated with Printable Organic Sensors for Indoor Environmental Monitoring

PubMed Central

Wu, Chun-Chang; Chuang, Wen-Yu; Wu, Ching-Da; Su, Yu-Cheng; Huang, Yung-Yang; Huang, Yang-Jing; Peng, Sheng-Yu; Yu, Shih-An; Lin, Chih-Ting; Lu, Shey-Shi

2017-01-01

A self-sustained multi-sensor platform for indoor environmental monitoring is proposed in this paper. To reduce the cost and power consumption of the sensing platform, in the developed platform, organic materials of PEDOT:PSS and PEDOT:PSS/EB-PANI are used as the sensing films for humidity and CO2 detection, respectively. Different from traditional gas sensors, these organic sensing films can operate at room temperature without heating processes or infrared transceivers so that the power consumption of the developed humidity and the CO2 sensors can be as low as 10 μW and 5 μW, respectively. To cooperate with these low-power sensors, a Complementary Metal-Oxide-Semiconductor (CMOS) system-on-chip (SoC) is designed to amplify and to read out multiple sensor signals with low power consumption. The developed SoC includes an analog-front-end interface circuit (AFE), an analog-to-digital convertor (ADC), a digital controller and a power management unit (PMU). Scheduled by the digital controller, the sensing circuits are power gated with a small duty-cycle to reduce the average power consumption to 3.2 μW. The designed PMU converts the power scavenged from a dye sensitized solar cell (DSSC) module into required supply voltages for SoC circuits operation under typical indoor illuminance conditions. To our knowledge, this is the first multiple environmental parameters (Temperature/CO2/Humidity) sensing platform that demonstrates a true self-powering functionality for long-term operations. PMID:28353680

Effect of certain natural products and organic solvents on quorum sensing in Chromobacterium violaceum.

PubMed

Chaudhari, Vimla; Gosai, Haren; Raval, Shreya; Kothari, Vijay

2014-09-01

To investigate the effect of seed extracts of Pongamia pinnata, Pyrus pyrifolia, and Manilkara hexandra, bacterial pigment prodigiosin, and three organic solvents (ethanol, methanol, and dimethylsulfoxide), on quorum sensing (QS) in Chromobacterium violaceum (C. violaceum). C. violaceum was challenged with plant extracts prepared by microwave assisted extraction method, prodigiosin, and organic solvents. Effect of these test substances on C. violaceum growth, and quorum sensing regulated pigment (violacein) production was studied by broth dilution assay. High performance liquid chromatography was also applied to generate chromatographic fingerprint of the active extracts. Effect of sub-minimum inhibitory concentration level of the antibiotic streptomycin on quorum sensing regulated pigment production was also studied. Pongamia pinnata seed extracts and prodigiosin were found to possess anti-QS, and Manilkara hexandra and Pyrus pyrifolia seed extracts to possess QS-enhancing effect in C. violaceum. Dimethylsulfoxide was found to enhance violacein production, whereas ethanol and methanol reduced violacein production in C. violaceum. Streptomycin at sub-minimum inhibitory concentration level was able to significantly arrest QS-regulated pigment production in C. violaceum and Serratia marcescens. Prodigiosin and the seed extracts used in this study could affect quorum sensing in C. violaceum to a notable extent. Results of this study also emphasize the importance of inclusion of appropriate solvent controls (negative controls) in bioassays designed for screening of antimicrobial and/or anti-QS compounds. Antipathogenic potential of low concentrations of streptomycin was also demonstrated. Copyright © 2014 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

A Self-Sustained Wireless Multi-Sensor Platform Integrated with Printable Organic Sensors for Indoor Environmental Monitoring.

PubMed

Wu, Chun-Chang; Chuang, Wen-Yu; Wu, Ching-Da; Su, Yu-Cheng; Huang, Yung-Yang; Huang, Yang-Jing; Peng, Sheng-Yu; Yu, Shih-An; Lin, Chih-Ting; Lu, Shey-Shi

2017-03-29

A self-sustained multi-sensor platform for indoor environmental monitoring is proposed in this paper. To reduce the cost and power consumption of the sensing platform, in the developed platform, organic materials of PEDOT:PSS and PEDOT:PSS/EB-PANI are used as the sensing films for humidity and CO₂ detection, respectively. Different from traditional gas sensors, these organic sensing films can operate at room temperature without heating processes or infrared transceivers so that the power consumption of the developed humidity and the CO₂ sensors can be as low as 10 μW and 5 μW, respectively. To cooperate with these low-power sensors, a Complementary Metal-Oxide-Semiconductor (CMOS) system-on-chip (SoC) is designed to amplify and to read out multiple sensor signals with low power consumption. The developed SoC includes an analog-front-end interface circuit (AFE), an analog-to-digital convertor (ADC), a digital controller and a power management unit (PMU). Scheduled by the digital controller, the sensing circuits are power gated with a small duty-cycle to reduce the average power consumption to 3.2 μW. The designed PMU converts the power scavenged from a dye sensitized solar cell (DSSC) module into required supply voltages for SoC circuits operation under typical indoor illuminance conditions. To our knowledge, this is the first multiple environmental parameters (Temperature/CO₂/Humidity) sensing platform that demonstrates a true self-powering functionality for long-term operations.

A consumer's guide to superorganisms.

PubMed

Ghiselin, Michael T

2011-01-01

The organism, like the molecule, the cell, and the species, is one of the fundamental levels in our hierarchical classification of life and its components. The units ranked at these levels, being concrete, particular things, are individuals in the broadest philosophical sense. But in a much narrower and more familiar sense, individual means an individual organism. Like species, the term individual is hard to define, but in most biological discourse it has meant the unit of philosophical autonomy. Some authors have attempted to revise this terminology, restricting individual to organisms, and redefining organism to include families and other units. Such semantic surgery is unnecessary if the goal is merely to justify selection at more than one level. Analogies between levels may be interesting, but many of them do not deserve to be taken seriously.

Dataset on the mean, standard deviation, broad-sense heritability and stability of wheat quality bred in three different ways and grown under organic and low-input conventional systems.

PubMed

Rakszegi, Marianna; Löschenberger, Franziska; Hiltbrunner, Jürg; Vida, Gyula; Mikó, Péter

2016-06-01

An assessment was previously made of the effects of organic and low-input field management systems on the physical, grain compositional and processing quality of wheat and on the performance of varieties developed using different breeding methods ("Comparison of quality parameters of wheat varieties with different breeding origin under organic and low-input conventional conditions" [1]). Here, accompanying data are provided on the performance and stability analysis of the genotypes using the coefficient of variation and the 'ranking' and 'which-won-where' plots of GGE biplot analysis for the most important quality traits. Broad-sense heritability was also evaluated and is given for the most important physical and quality properties of the seed in organic and low-input management systems, while mean values and standard deviation of the studied properties are presented separately for organic and low-input fields.

Metal organic frameworks enhanced graphene oxide electrode for humidity sensor

NASA Astrophysics Data System (ADS)

Zhang, Wen; Meng, Siyu; Wang, Hui; He, Yongning

2018-03-01

Copper benzene-1,3,5-tricarboxylate (Cu-BTC), a typical metal organic framework, is deposited on the graphene oxide (GO) film to prepare a resistance humidity sensor (Cu- BTC/GO) for improving humidity sensing. The characteristics of Cu-BTC, GO and Cu- BTC/GO were measured by scanning electron microscopy (SEM), X-ray diffraction (XRD), nitrogen isotherm adsorption and electrochemical impedance spectroscopy (EIS). The humidity sensing properties of the Cu-BTC/GO were investigated in detail. The obtained Cu-BTC/GO demonstrates good sensitivity and repeatability over 11%-85% relative humidity (RH) measurements. The Cu-BTC/GO coated device shows high normalized response (S) value (6200%), which is much higher than that of pure GO coated device. Sensing mechanism of Cu- BTC/GO is discussed based on different RH and the results indicate that moderate amounts of Cu-BTC deposition can enhance sensing abilities of GO. High specific surface area and interfacial conductivity are crucial factors to fabricate humidity sensors with high performance.

Neuronal Calcium Signaling in Metabolic Regulation and Adaptation to Nutrient Stress.

PubMed

Jayakumar, Siddharth; Hasan, Gaiti

2018-01-01

All organisms can respond physiologically and behaviorally to environmental fluxes in nutrient levels. Different nutrient sensing pathways exist for specific metabolites, and their inputs ultimately define appropriate nutrient uptake and metabolic homeostasis. Nutrient sensing mechanisms at the cellular level require pathways such as insulin and target of rapamycin (TOR) signaling that integrates information from different organ systems like the fat body and the gut. Such integration is essential for coordinating growth with development. Here we review the role of a newly identified set of integrative interneurons and the role of intracellular calcium signaling within these neurons, in regulating nutrient sensing under conditions of nutrient stress. A comparison of the identified Drosophila circuit and cellular mechanisms employed in this circuit, with vertebrate systems, suggests that the identified cell signaling mechanisms may be conserved for neural circuit function related to nutrient sensing by central neurons. The ideas proposed are potentially relevant for understanding the molecular basis of metabolic disorders, because these are frequently linked to nutritional stress.

Symbiosis initiation in the bacterially luminous sea urchin cardinalfish Siphamia versicolor.

PubMed

Dunlap, P V; Gould, A L; Wittenrich, M L; Nakamura, M

2012-09-01

To determine how each new generation of the sea urchin cardinalfish Siphamia versicolor acquires the symbiotic luminous bacterium Photobacterium mandapamensis, and when in its development the S. versicolor initiates the symbiosis, procedures were established for rearing S. versicolor larvae in an aposymbiotic state. Under the conditions provided, larvae survived and developed for 28 days after their release from the mouths of males. Notochord flexion began at 8 days post release (dpr). By 28 dpr, squamation was evident and the caudal complex was complete. The light organ remained free of bacteria but increased in size and complexity during development of the larvae. Thus, aposymbiotic larvae of the fish can survive and develop for extended periods, major components of the luminescence system develop in the absence of the bacteria and the bacteria are not acquired directly from a parent, via the egg or during mouth brooding. Presentation of the symbiotic bacteria to aposymbiotic larvae at 8-10 dpr, but not earlier, led to initiation of the symbiosis. Upon colonization of the light organ, the bacterial population increased rapidly and cells forming the light-organ chambers exhibited a differentiated appearance. Therefore, the light organ apparently first becomes receptive to colonization after 1 week post-release development, the symbiosis is initiated by bacteria acquired from the environment and bacterial colonization induces morphological changes in the nascent light organ. The abilities to culture larvae of S. versicolor for extended periods and to initiate the symbiosis in aposymbiotic larvae are key steps in establishing the experimental tractability of this highly specific vertebrate and microbe mutualism. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Organic nanofibrils based on linear carbazole trimer for explosive sensing.

PubMed

Zhang, Chengyi; Che, Yanke; Yang, Xiaomei; Bunes, Benjamin R; Zang, Ling

2010-08-14

Organic fluorescent nanofibrils were fabricated from a linear carbazole trimer and employed for expedient detection of nitroaromatic explosives (DNT and TNT) and highly volatile nitroaliphatic explosives (nitromethane).

Characterization of the endolysin from the Enterococcus faecalis bacteriophage VD13

USDA-ARS?s Scientific Manuscript database

Bacteriophage infecting bacteria produce endolysins (peptidoglycan hydrolases) to lyse the host cell from within and release nascent bacteriophage particles. Recombinant endolysins can also lyse Gram-positive bacteria when added exogenously. As a potential alternative to antibiotics, we cloned and...

Catalysis-reduction strategy for sensing inorganic and organic mercury based on gold nanoparticles.

PubMed

Li, Xiaokun; Zhang, Youlin; Chang, Yulei; Xue, Bin; Kong, Xianggui; Chen, Wei

2017-06-15

In view of the high biotoxicity and trace concentration of mercury (Hg) in environmental water, developing simple, ultra-sensitive and highly selective method capable of simultaneous determination of various Hg species has attracted wide attention. Here, we present a novel catalysis-reduction strategy for sensing inorganic and organic mercury in aqueous solution through the cooperative effect of AuNP-catalyzed properties and the formation of gold amalgam. For the first time, a new AuNP-catalyzed-organic reaction has been discovered and directly used for sensing Hg 2+ , Hg 2 2+ and CH 3 Hg + according to the change of the amount of the catalytic product induced by the deposition of Hg atoms on the surface of AuNPs. The detection limit of Hg species is 5.0pM (1 ppt), which is 3 orders of magnitude lower than the U.S. Environmental Protection Agency (EPA) limit value of Hg for drinking water (2 ppb). The high selectivity can be exceptionally achieved by the specific formation of gold amalgam. Moreover, the application for detecting tap water samples further demonstrates that this AuNP-based assay can be an excellent method used for sensing mercury at very low content in the environment. Copyright © 2016 Elsevier B.V. All rights reserved.

Ultrafast water sensing and thermal imaging by a metal-organic framework with switchable luminescence

NASA Astrophysics Data System (ADS)

Chen, Ling; Ye, Jia-Wen; Wang, Hai-Ping; Pan, Mei; Yin, Shao-Yun; Wei, Zhang-Wen; Zhang, Lu-Yin; Wu, Kai; Fan, Ya-Nan; Su, Cheng-Yong

2017-06-01

A convenient, fast and selective water analysis method is highly desirable in industrial and detection processes. Here a robust microporous Zn-MOF (metal-organic framework, Zn(hpi2cf)(DMF)(H2O)) is assembled from a dual-emissive H2hpi2cf (5-(2-(5-fluoro-2-hydroxyphenyl)-4,5-bis(4-fluorophenyl)-1H-imidazol-1-yl)isophthalic acid) ligand that exhibits characteristic excited state intramolecular proton transfer (ESIPT). This Zn-MOF contains amphipathic micropores (<3 Å) and undergoes extremely facile single-crystal-to-single-crystal transformation driven by reversible removal/uptake of coordinating water molecules simply stimulated by dry gas blowing or gentle heating at 70 °C, manifesting an excellent example of dynamic reversible coordination behaviour. The interconversion between the hydrated and dehydrated phases can turn the ligand ESIPT process on or off, resulting in sensitive two-colour photoluminescence switching over cycles. Therefore, this Zn-MOF represents an excellent PL water-sensing material, showing a fast (on the order of seconds) and highly selective response to water on a molecular level. Furthermore, paper or in situ grown ZnO-based sensing films have been fabricated and applied in humidity sensing (RH<1%), detection of traces of water (<0.05% v/v) in various organic solvents, thermal imaging and as a thermometer.

Exploring the mammalian sensory space: co-operations and trade-offs among senses.

PubMed

Nummela, Sirpa; Pihlström, Henry; Puolamäki, Kai; Fortelius, Mikael; Hemilä, Simo; Reuter, Tom

2013-12-01

The evolution of a particular sensory organ is often discussed with no consideration of the roles played by other senses. Here, we treat mammalian vision, olfaction and hearing as an interconnected whole, a three-dimensional sensory space, evolving in response to ecological challenges. Until now, there has been no quantitative method for estimating how much a particular animal invests in its different senses. We propose an anatomical measure based on sensory organ sizes. Dimensions of functional importance are defined and measured, and normalized in relation to animal mass. For 119 taxonomically and ecologically diverse species, we can define the position of the species in a three-dimensional sensory space. Thus, we can ask questions related to possible trade-off vs. co-operation among senses. More generally, our method allows morphologists to identify sensory organ combinations that are characteristic of particular ecological niches. After normalization for animal size, we note that arboreal mammals tend to have larger eyes and smaller noses than terrestrial mammals. On the other hand, we observe a strong correlation between eyes and ears, indicating that co-operation between vision and hearing is a general mammalian feature. For some groups of mammals we note a correlation, and possible co-operation between olfaction and whiskers.

Plasmonic nanopatch array with integrated metal–organic framework for enhanced infrared absorption gas sensing

DOE PAGES

Chong, Xinyuan; Kim, Ki-joong; Zhang, Yujing; ...

2017-06-06

In this letter, we present a nanophotonic device consisting of plasmonic nanopatch array (NPA) with integrated metal–organic framework (MOF) for enhanced infrared absorption gas sensing. By designing a gold NPA on a sapphire substrate, we are able to achieve enhanced optical field that spatially overlaps with the MOF layer, which can adsorb carbon dioxide (CO 2) with high capacity. Additionally, experimental results show that this hybrid plasmonic–MOF device can effectively increase the infrared absorption path of on-chip gas sensors by more than 1100-fold. Lastly, the demonstration of infrared absorption spectroscopy of CO 2 using the hybrid plasmonic–MOF device proves amore » promising strategy for future on-chip gas sensing with ultra-compact size.« less

Nanostructured Gas Sensors for Health Care: An Overview

PubMed Central

Kaushik, Ajeet; Kumar, Rajesh; Jayant, Rahul Dev; Nair, Madhavan

2015-01-01

Nanostructured platforms have been utilized for fabrication of small, sensitive and reliable gas sensing devices owing to high functionality, enhanced charge transport and electro-catalytic property. As a result of globalization, rapid, sensitive and selective detection of gases in environment is essential for health care and security. Nonmaterial such as metal, metal oxides, organic polymers, and organic-inorganic hybrid nanocomposites exhibit interesting optical, electrical, magnetic and molecular properties, and hence are found potential gas sensing materials. Morphological, electrical, and optical properties of such nanostructures can be tailored via controlling the precursor concentration and synthesis conditions resulting to achieve desired sensing. This review presents applications of nano-enabling gas sensors to detect gases for environment monitoring. The recent update, challenges, and future vision for commercial applications of such sensor are also described here. PMID:26491544

Plasmonic nanopatch array with integrated metal–organic framework for enhanced infrared absorption gas sensing

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

Chong, Xinyuan; Kim, Ki-joong; Zhang, Yujing

In this letter, we present a nanophotonic device consisting of plasmonic nanopatch array (NPA) with integrated metal–organic framework (MOF) for enhanced infrared absorption gas sensing. By designing a gold NPA on a sapphire substrate, we are able to achieve enhanced optical field that spatially overlaps with the MOF layer, which can adsorb carbon dioxide (CO 2) with high capacity. Additionally, experimental results show that this hybrid plasmonic–MOF device can effectively increase the infrared absorption path of on-chip gas sensors by more than 1100-fold. Lastly, the demonstration of infrared absorption spectroscopy of CO 2 using the hybrid plasmonic–MOF device proves amore » promising strategy for future on-chip gas sensing with ultra-compact size.« less

Remote Sensing of Ecology, Biodiversity and Conservation: A Review from the Perspective of Remote Sensing Specialists

PubMed Central

Wang, Kai; Franklin, Steven E.; Guo, Xulin; Cattet, Marc

2010-01-01

Remote sensing, the science of obtaining information via noncontact recording, has swept the fields of ecology, biodiversity and conservation (EBC). Several quality review papers have contributed to this field. However, these papers often discuss the issues from the standpoint of an ecologist or a biodiversity specialist. This review focuses on the spaceborne remote sensing of EBC from the perspective of remote sensing specialists, i.e., it is organized in the context of state-of-the-art remote sensing technology, including instruments and techniques. Herein, the instruments to be discussed consist of high spatial resolution, hyperspectral, thermal infrared, small-satellite constellation, and LIDAR sensors; and the techniques refer to image classification, vegetation index (VI), inversion algorithm, data fusion, and the integration of remote sensing (RS) and geographic information system (GIS). PMID:22163432

Remote sensing of ecology, biodiversity and conservation: a review from the perspective of remote sensing specialists.

PubMed

Wang, Kai; Franklin, Steven E; Guo, Xulin; Cattet, Marc

2010-01-01

Remote sensing, the science of obtaining information via noncontact recording, has swept the fields of ecology, biodiversity and conservation (EBC). Several quality review papers have contributed to this field. However, these papers often discuss the issues from the standpoint of an ecologist or a biodiversity specialist. This review focuses on the spaceborne remote sensing of EBC from the perspective of remote sensing specialists, i.e., it is organized in the context of state-of-the-art remote sensing technology, including instruments and techniques. Herein, the instruments to be discussed consist of high spatial resolution, hyperspectral, thermal infrared, small-satellite constellation, and LIDAR sensors; and the techniques refer to image classification, vegetation index (VI), inversion algorithm, data fusion, and the integration of remote sensing (RS) and geographic information system (GIS).

A new centrifuge microscope reveals that mobile plastids trigger gravity sensing in Arabidopsis inflorescence stems

NASA Astrophysics Data System (ADS)

Toyota, Masatsugu; Tasaka, Masao; Morita, Miyo T.; Gilroy, Simon

2012-07-01

The starch-statolith hypothesis is the most widely accepted model for plant gravity sensing and proposes that the sedimentation of high-density starch-filled plastids (amyloplasts) in shoot endodermal cells and root columella cells is important for gravity sensing of each organ. However, starch-deficient phosphoglucomutase (pgm-1) mutants sense gravity and show gravitropism in inflorescence stems, even though most starchless amyloplasts in this mutant fail to sediment toward the gravity vector. These results raise the questions about the role of starch in gravity sensing and the features of statolith/statocyte essential for shoot gravity sensing. To address these questions, we developed a new centrifuge microscope and analyzed two gravitropic mutants, i.e., pgm-1 and endodermal-amyloplast less 1 (eal1). All optical devices (e.g., objective lens, light source and CCD camera) and specimens were rotated on a direct-drive motor, and acquired images were wirelessly transmitted during centrifugation. Live-cell imaging during centrifugation revealed that the starchless amyloplasts sedimented to the hypergravity vector (10 and 30 g) in endodermal cells of pgm-1 stems, indicating that the density of the starchless amyloplasts is higher than that of cytoplasm. Electron micrographs of shoot endodermal cells in pgm-1 mutants suggested that the starchless amyloplast contains an organized thylakoid membrane but not starch granules, which morphologically resembles chloroplasts in the adjacent cortical cells. Therefore, the shoot amyloplasts without starch are possibly as dense as chloroplasts. We examined eal1 mutants, an allele of shoot gravitropism (sgr) 7/short-root (shr), which also have starchless amyloplasts due to abnormal differentiation of amyloplasts and show no gravitropic response at 1 g. Hypergravity up to 30 g induced little gravitropism in eal1 stems and the starchless amyloplasts failed to sediment under 30 g conditions. However, the eal1 mutants treated with latrunculin B, an actin disrupting drug, showed gravitropism under 30 g conditions, during which amyloplasts were artificially sedimented by hypergravity. These results suggest that shoot amyloplasts are intrinsically dense enough to trigger gravity sensing without starch and, rather, intracellular environments that render amyloplasts sedimentable/mobile, such as actin organization, are essential for gravity sensing in Arabidopsis inflorescence stems.

Influence of oxidized purine processing on strand directionality of mismatch repair.

PubMed

Repmann, Simone; Olivera-Harris, Maite; Jiricny, Josef

2015-04-17

Replicative DNA polymerases are high fidelity enzymes that misincorporate nucleotides into nascent DNA with a frequency lower than [1/10(5)], and this precision is improved to about [1/10(7)] by their proofreading activity. Because this fidelity is insufficient to replicate most genomes without error, nature evolved postreplicative mismatch repair (MMR), which improves the fidelity of DNA replication by up to 3 orders of magnitude through correcting biosynthetic errors that escaped proofreading. MMR must be able to recognize non-Watson-Crick base pairs and excise the misincorporated nucleotides from the nascent DNA strand, which carries by definition the erroneous genetic information. In eukaryotes, MMR is believed to be directed to the nascent strand by preexisting discontinuities such as gaps between Okazaki fragments in the lagging strand or breaks in the leading strand generated by the mismatch-activated endonuclease of the MutL homologs PMS1 in yeast and PMS2 in vertebrates. We recently demonstrated that the eukaryotic MMR machinery can make use also of strand breaks arising during excision of uracils or ribonucleotides from DNA. We now show that intermediates of MutY homolog-dependent excision of adenines mispaired with 8-oxoguanine (G(O)) also act as MMR initiation sites in extracts of human cells or Xenopus laevis eggs. Unexpectedly, G(O)/C pairs were not processed in these extracts and failed to affect MMR directionality, but extracts supplemented with exogenous 8-oxoguanine DNA glycosylase (OGG1) did so. Because OGG1-mediated excision of G(O) might misdirect MMR to the template strand, our findings suggest that OGG1 activity might be inhibited during MMR. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

5S ribosomal RNA is an essential component of a nascent ribosomal precursor complex that regulates the Hdm2-p53 checkpoint.

PubMed

Donati, Giulio; Peddigari, Suresh; Mercer, Carol A; Thomas, George

2013-07-11

Recently, we demonstrated that RPL5 and RPL11 act in a mutually dependent manner to inhibit Hdm2 and stabilize p53 following impaired ribosome biogenesis. Given that RPL5 and RPL11 form a preribosomal complex with noncoding 5S ribosomal RNA (rRNA) and the three have been implicated in the p53 response, we reasoned they may be part of an Hdm2-inhibitory complex. Here, we show that small interfering RNAs directed against 5S rRNA have no effect on total or nascent levels of the noncoding rRNA, though they prevent the reported Hdm4 inhibition of p53. To achieve efficient inhibition of 5S rRNA synthesis, we targeted TFIIIA, a specific RNA polymerase III cofactor, which, like depletion of either RPL5 or RPL11, did not induce p53. Instead, 5S rRNA acts in a dependent manner with RPL5 and RPL11 to inhibit Hdm2 and stabilize p53. Moreover, depletion of any one of the three components abolished the binding of the other two to Hdm2, explaining their common dependence. Finally, we demonstrate that the RPL5/RPL11/5S rRNA preribosomal complex is redirected from assembly into nascent 60S ribosomes to Hdm2 inhibition as a consequence of impaired ribosome biogenesis. Thus, the activation of the Hdm2-inhibitory complex is not a passive but a regulated event, whose potential role in tumor suppression has been recently noted. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Broadband pH-Sensing Organic Transistors with Polymeric Sensing Layers Featuring Liquid Crystal Microdomains Encapsulated by Di-Block Copolymer Chains.

PubMed

Seo, Jooyeok; Song, Myeonghun; Jeong, Jaehoon; Nam, Sungho; Heo, Inseok; Park, Soo-Young; Kang, Inn-Kyu; Lee, Joon-Hyung; Kim, Hwajeong; Kim, Youngkyoo

2016-09-14

We report broadband pH-sensing organic field-effect transistors (OFETs) with the polymer-dispersed liquid crystal (PDLC) sensing layers. The PDLC layers are prepared by spin-coating using ethanol solutions containing 4-cyano-4'-pentyl-biphenyl (5CB) and a diblock copolymer (PAA-b-PCBOA) that consists of LC-philic block [poly(4-cyano-biphenyl-4-oxyundecyl acrylate) (PCBOA)] and acrylic acid block [poly(acrylic acid) (PAA)]. The spin-coated sensing layers feature of 5CB microdomains (<5 μm) encapsulated by the PAA-b-PCBOA polymer chains. The resulting LC-integrated-OFETs (PDLC-i-OFETs) can detect precisely and reproducibly a wide range of pH with only small amounts (10-40 μL) of analyte solutions in both static and dynamic perfusion modes. The positive drain current change is measured for acidic solutions (pH < 7), whereas basic solutions (pH > 7) result in the negative change of drain current. The drain current trend in the present PDLC-i-OFET devices is explained by the shrinking-expanding mechanism of the PAA chains in the diblock copolymer layers.

Transcriptional and Cell Cycle Alterations Mark Aging of Primary Human Adipose-Derived Stem Cells.

PubMed

Shan, Xiaoyin; Roberts, Cleresa; Kim, Eun Ji; Brenner, Ariana; Grant, Gregory; Percec, Ivona

2017-05-01

Adult stem cells play a critical role in the maintenance of tissue homeostasis and prevention of aging. While the regenerative potential of stem cells with low cellular turnover, such as adipose-derived stem cells (ASCs), is increasingly recognized, the study of chronological aging in ASCs is technically difficult and remains poorly understood. Here, we use our model of chronological aging in primary human ASCs to examine genome-wide transcriptional networks. We demonstrate first that the transcriptome of aging ASCs is distinctly more stable than that of age-matched fibroblasts, and further, that age-dependent modifications in cell cycle progression and translation initiation specifically characterize aging ASCs in conjunction with increased nascent protein synthesis and a distinctly shortened G1 phase. Our results reveal novel chronological aging mechanisms in ASCs that are inherently different from differentiated cells and that may reflect an organismal attempt to meet the increased demands of tissue and organ homeostasis during aging. Stem Cells 2017;35:1392-1401. © 2017 AlphaMed Press.

Innovation in Hospital Revenues: Developing Retail Sales Channels.

PubMed

Wright, Edward W; Marvel, Jon; Wright, Matthew K

Hospitals are facing increasing cost pressures due to cutbacks by Medicare, Medicaid, and managed-care organizations. There are also rising concerns that public policy may exacerbate the problem. In lieu of these concerns, nascent innovative ways of generating increased revenues are beginning to appear. In particular, a few hospitals have adopted retail sales practices to generate significant nonmedical services revenues. The hospital retail sales opportunity has been compared with that of the airport industry where nearly 50% of revenues are generated by sales of retail products as opposed to aeronautical-related transactions. This initial investigation included a qualitative interview of a health care retail sales expert and a pilot survey of 100 hospital senior executives to gauge the current state of this phenomenon. The industry expert suggested that only 2% of US hospitals have pursued this initiative in a meaningful way. Of the 44 survey responses, only 9 institutions were engaged in e-commerce or retail sales activities. Questions remain as to why this opportunity remains unrealized, and additional research is proposed.

Chaperonin polymers in archaea: The cytoskeleton of prokaryotes?

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

Trent, J.D.; Kagawa, H.K.; Zaluzec, N.J.

Chaperonins are protein complexes that play a critical role in folding nascent polypeptides under normal conditions and refolding damaged proteins under stress conditions. In all organisms these complexes are composed of evolutionarily conserved 60-kDa proteins arranged in double-ring structures with between 7 and 9 protein subunits per ring. These double ring structures are assumed to be the functional units in vivo, although they have never been observed inside cells. Here the authors show that the purified chaperonin from the hyperthermophilic archaeon Sulfolobus shibatae, which is closely related to chaperonins in eukaryotes, has a double ring structure at low concentrations (0.1more » mg/ml), but at more physiological concentrations, the rings stack end to end to form polymers. The polymers are stable at physiological temperatures (75 C) and closely resemble structures observed inside unfixed S. shibatae cells. The authors suggest that in vivo chaperonin activity may be regulated by polymerization and that chaperonin polymers may act as a cytoskeleton-like structure in archaea and bacteria.« less

The Role of the Pulmonary Embolism Response Team: How to Build One, Who to Include, Scenarios, Organization, and Algorithms.

PubMed

Galmer, Andrew; Weinberg, Ido; Giri, Jay; Jaff, Michael; Weinberg, Mitchell

2017-09-01

Pulmonary embolism response teams (PERTs) are multidisciplinary response teams aimed at delivering a range of diagnostic and therapeutic modalities to patients with pulmonary embolism. These teams have gained traction on a national scale. However, despite sharing a common goal, individual PERT programs are quite individualized-varying in their methods of operation, team structures, and practice patterns. The tendency of such response teams is to become intensely structured, algorithmic, and inflexible. However, in their current form, PERT programs are quite the opposite. They are being creatively customized to meet the needs of the individual institution based on available resources, skills, personnel, and institutional goals. After a review of the essential core elements needed to create and operate a PERT team in any form, this article will discuss the more flexible feature development of the nascent PERT team. These include team planning, member composition, operational structure, benchmarking, market analysis, and rudimentary financial operations. Copyright © 2017 Elsevier Inc. All rights reserved.

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

PubMed Central

König, Julian; Zarnack, Kathi; Rot, Gregor; Curk, Tomaž; Kayikci, Melis; Zupan, Blaž; Turner, Daniel J.; Luscombe, Nicholas M.; Ule, Jernej

2010-01-01

In the nucleus of eukaryotic cells, nascent transcripts are associated with heterogeneous nuclear ribonucleoprotein (hnRNP) particles that are nucleated by hnRNP C. Despite their abundance however, it remained unclear whether these particles control pre-mRNA processing. Here, we developed individual-nucleotide resolution UV-cross-linking and immunoprecipitation (iCLIP) to study the role of hnRNP C in splicing regulation. iCLIP data demonstrate that hnRNP C recognizes uridine tracts with a defined long-range spacing consistent with hnRNP particle organization. hnRNP particles assemble on both introns and exons, but remain generally excluded from splice sites. Integration of transcriptome-wide iCLIP data and alternative splicing profiles into an ‘RNA map’ indicates how the positioning of hnRNP particles determines their effect on inclusion of alternative exons. The ability of high-resolution iCLIP data to provide insights into the mechanism of this regulation holds promise for studies of other higher-order ribonucleoprotein complexes. PMID:20601959

The Evolution of Public Health Emergency Management as a Field of Practice.

PubMed

Rose, Dale A; Murthy, Shivani; Brooks, Jennifer; Bryant, Jeffrey

2017-09-01

The health impacts of recent global infectious disease outbreaks and other disasters have demonstrated the importance of strengthening public health systems to better protect communities from naturally occurring and human-caused threats. Public health emergency management (PHEM) is an emergent field of practice that draws on specific sets of knowledge, techniques, and organizing principles necessary for the effective management of complex health events. We highlight how the nascent field of PHEM has evolved in recent years. We explore this development by first examining multiple sites of intersection between the fields of public health and emergency management. We then analyze 2 of the principal pillars on which PHEM was built: organizational and programmatic (i.e., industry) standards and the incident management system. This is followed by a sketch of the key domains, or functional areas, of PHEM and their application to the emergency management cycle. We conclude with some observations about PHEM in a global context and discuss how the field might continue to evolve.

The Psychology of Superorganisms: Collective Decision Making by Insect Societies.

PubMed

Sasaki, Takao; Pratt, Stephen C

2018-01-07

Under the superorganism concept, insect societies are so tightly integrated that they possess features analogous to those of single organisms, including collective cognition. If so, colony function might fruitfully be studied using methods developed to understand individual animals. Here, we review research that uses psychological approaches to understand decision making by colonies. The application of neural models to collective choice shows fundamental similarities between how brains and colonies balance speed/accuracy trade-offs in decision making. Experimental analyses have explored collective rationality, cognitive capacity, and perceptual discrimination at both individual and colony levels. A major theme is the emergence of improved colony-level function from interactions among relatively less capable individuals. However, colonies also encounter performance costs due to their reliance on positive feedback, which generates consensus but can also amplify errors. Collective learning is a nascent field for the further application of psychological methods to colonies. The research strategy reviewed here shows how the superorganism concept can serve as more than an illustrative analogy.

Recombination Proteins Mediate Meiotic Spatial Chromosome Organization and Pairing

PubMed Central

Storlazzi, Aurora; Gargano, Silvana; Ruprich-Robert, Gwenael; Falque, Matthieu; David, Michelle; Kleckner, Nancy; Zickler, Denise

2010-01-01

SUMMARY Meiotic chromosome pairing involves not only recognition of homology but also juxtaposition of entire chromosomes in a topologically regular way. Analysis of filamentous fungus Sordaria macrospora reveals that recombination proteins Mer3, Msh4 and Mlh1 play direct roles in all of these aspects, in advance of their known roles in recombination. Absence of Mer3 helicase results in interwoven chromosomes, thereby revealing the existence of features that specifically ensure “entanglement avoidance”. Entanglements that remain at zygotene, i.e. “interlockings”, require Mlh1 for resolution, likely to eliminate constraining recombinational connections. Patterns of Mer3 and Msh4 foci along aligned chromosomes show that the double-strand breaks mediating homologous alignment have spatially separated ends, one localized to each partner axis, and that pairing involves interference among developing interhomolog interactions. We propose that Mer3, Msh4 and Mlh1 execute all of these roles during pairing by modulating the state of nascent double-strand break/partner DNA contacts within axis-associated recombination complexes. PMID:20371348

The Evolution of Public Health Emergency Management as a Field of Practice

PubMed Central

Murthy, Shivani; Brooks, Jennifer; Bryant, Jeffrey

2017-01-01

The health impacts of recent global infectious disease outbreaks and other disasters have demonstrated the importance of strengthening public health systems to better protect communities from naturally occurring and human-caused threats. Public health emergency management (PHEM) is an emergent field of practice that draws on specific sets of knowledge, techniques, and organizing principles necessary for the effective management of complex health events. We highlight how the nascent field of PHEM has evolved in recent years. We explore this development by first examining multiple sites of intersection between the fields of public health and emergency management. We then analyze 2 of the principal pillars on which PHEM was built: organizational and programmatic (i.e., industry) standards and the incident management system. This is followed by a sketch of the key domains, or functional areas, of PHEM and their application to the emergency management cycle. We conclude with some observations about PHEM in a global context and discuss how the field might continue to evolve. PMID:28892444

Chaperonin Polymers in Archaea: The Cytoskeleton of Prokaryotes?

DOE R&D Accomplishments Database

Trent, J. D.; Kagawa, H. K.; Zaluzec, N. J.

1997-07-01

Chaperonins are protein complexes that play a critical role in folding nascent polypeptides under normal conditions and refolding damaged proteins under stress conditions. In all organisms these complexes are composed of evolutionarily conserved 60-kDa proteins arranged in double-ring structures with between 7 and 9 protein subunits per ring. These double ring structures are assumed to be the functional units in vivo, although they have never been observed inside cells. Here the authors show that the purified chaperonin from the hyperthermophilic archaeon Sulfolobus shibatae, which is closely related to chaperonins in eukaryotes, has a double ring structure at low concentrations (0.1 mg/ml), but at more physiological concentrations, the rings stack end to end to form polymers. The polymers are stable at physiological temperatures (75 C) and closely resemble structures observed inside unfixed S. shibatae cells. The authors suggest that in vivo chaperonin activity may be regulated by polymerization and that chaperonin polymers may act as a cytoskeleton-like structure in archaea and bacteria.

Polysemy in Sentence Comprehension: Effects of Meaning Dominance

ERIC Educational Resources Information Center

Foraker, Stephani; Murphy, Gregory L.

2012-01-01

Words like "church" are polysemous, having two related senses (a building and an organization). Three experiments investigated how polysemous senses are represented and processed during sentence comprehension. On one view, readers retrieve an underspecified, core meaning, which is later specified more fully with contextual information. On another…

The Five Senses of Christmas Chemistry

ERIC Educational Resources Information Center

Jackson, Derek A.; Dicks, Andrew P.

2012-01-01

This article describes the organic chemistry of five compounds that are directly associated with the Christmas season. These substances and related materials are presented within the framework of the five senses: silver fulminate (sound), alpha-pinene (sight), sodium acetate (touch), tryptophan (taste), and gingerol (smell). Connections with the…

High Performance Asynchronous Limited Sensing Algorithms for CSMA and CSMA-CD Channels.

DTIC Science & Technology

1985-03-01

for CSM and CSMA-CD Channels" M. Geargiopoulos L. Merakos P. Papantoni-Kazakos- Technical Report UCT/ DEECS /TR-85-2 Mrh1985 iDISTRIBUTION STAEmEN 2j C...Perforance Asynchronous Limited Sensing Algoit~5 forCSMAandCSMA-CD Channels" M1. Georgiop0 ul 0 5 L. Merakos P. PaPantoni-.Kazakos Technical Report UCT/ DEECS ...SCHEDULE unlimited. 4 PERFORMING ORGANiZATION REPORT NUMBERIS) 5. MONITORING ORGANIZATION REPORT NUMBERIS" UCT/ DEECS /TR-85-2 SR-TR. 85-0 398 6& NAME OF

Microbial detection method based on sensing molecular hydrogen

NASA Technical Reports Server (NTRS)

Wilkins, J. R.; Stoner, G. E.; Boykin, E. H.

1974-01-01

An approach involving the measurement of hydrogen evolution by test organisms was used to detect and enumerate various members of the Enterobacteriaceae group. The experimental setup for measuring hydrogen evolution consisted of a test tube containing two electrodes plus broth and organisms. The test tube was kept in a water bath at a temperature of 35 C. It is pointed out that the hydrogen-sensing method, coupled with the pressure transducer technique reported by Wilkins (1974) could be used in various experiments in which gas production by microorganisms is being measured.

46 CFR 507.103 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

...: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular..., such diseases and conditions as orthopedic, visual, speech, and hearing impairments, cerebral palsy, epilepsy, muscular dystrophy, multiple sclerosis, cancer, heart disease, diabetes, mental retardation...

45 CFR 1706.103 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

...: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular..., such diseases and conditions as orthopedic, visual, speech, and hearing impairments, cerebral palsy, epilepsy, muscular dystrophy, multiple sclerosis, cancer, heart disease, diabetes, mental retardation...

50 CFR 550.103 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

...: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular..., such diseases and conditions as orthopedic, visual, speech, and hearing impairments, cerebral palsy, epilepsy, muscular dystrophy, multiple sclerosis, cancer, heart disease, diabetes, mental retardation...

45 CFR 2490.103 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

...: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular..., such diseases and conditions as orthopedic, visual, speech, and hearing impairments, cerebral palsy, epilepsy, muscular dystrophy, multiple sclerosis, cancer, heart disease, diabetes, mental retardation...

28 CFR 39.103 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

...: Neurological; musculoskeletal; special sense organs; respiratory, including speech organs; cardiovascular..., such diseases and conditions as orthopedic, visual, speech, and hearing impairments, cerebral palsy, epilepsy, muscular dystrophy, multiple sclerosis, cancer, heart disease, diabetes, mental retardation...

Efficient responses to host and bacterial signals during Vibrio cholerae colonization

PubMed Central

Rothenbacher, Francesca P; Zhu, Jun

2014-01-01

Vibrio cholerae, the microorganism responsible for the diarrheal disease cholera, is able to sense and respond to a variety of changing stimuli in both its aquatic and human gastrointestinal environments. Here we present a review of research efforts aimed toward understanding the signals this organism senses in the human host. V. cholerae’s ability to sense and respond to temperature and pH, bile, osmolarity, oxygen and catabolite levels, nitric oxide, and mucus, as well as the quorum sensing signals produced in response to these factors will be discussed. We also review the known quorum sensing regulatory pathways and discuss their importance with regard to the regulation of virulence and colonization during infection. PMID:24256715

Indicators of international remote sensing activities

NASA Technical Reports Server (NTRS)

Spann, G. W.

1977-01-01

The extent of worldwide remote sensing activities, including the use of satellite and high/medium altitude aircraft data was studied. Data were obtained from numerous individuals and organizations with international remote sensing responsibilities. Indicators were selected to evaluate the nature and scope of remote sensing activities in each country. These indicators ranged from attendance at remote sensing workshops and training courses to the establishment of earth resources satellite ground stations and plans for the launch of earth resources satellites. Results indicate that this technology constitutes a rapidly increasing component of environmental, land use, and natural resources investigations in many countries, and most of these countries rely on the LANDSAT satellites for a major portion of their data.

Mapping Surface Soil Organic Carbon for Crop Fields with Remote Sensing

NASA Technical Reports Server (NTRS)

Chen, Feng; Kissel, David E.; West, Larry T.; Rickman, Doug; Luvall, J. C.; Adkins, Wayne

2004-01-01

The organic C concentration of surface soil can be used in agricultural fields to vary crop production inputs. Organic C is often highly spatially variable, so that maps of soil organic C can be used to vary crop production inputs using precision farming technology. The objective of this research was to demonstrate the feasibility of mapping soil organic C on three fields, using remotely sensed images of the fields with a bare surface. Enough soil samples covering the range in soil organic C must be taken from each field to develop a satisfactory relationship between soil organic C content and image reflectance values. The number of soil samples analyzed in the three fields varied from 22 to 26. The regression equations differed between fields, but gave highly significant relationships with R2 values of 0.93, 0.95, and 0.89 for the three fields. A comparison of predicted and measured values of soil organic C for an independent set of 2 soil samples taken on one of the fields gave highly satisfactory results, with a comparison equation of % organic C measured + 1.02% organic C predicted, with r2 = 0.87.

Alices in a nuclear Wonderland

NASA Astrophysics Data System (ADS)

Brown, Kate

2014-02-01

Denise Kiernan's The Girls of Atomic City tells the story of a dozen women who left rural America in the early 1940s and tumbled suddenly, like Alice down the rabbit hole, into the nascent US military-industrial complex, with all its regulations, factory discipline, dangers and surveillance.

Origin and domestication of papaya Yh chromosome

USDA-ARS?s Scientific Manuscript database

Sex in papaya is controlled by a pair of nascent sex chromosomes. Females are XX, and two slightly different Y chromosomes distinguish males (XY) and hermaphrodites (XYh). The hermaphrodite-specific region of the Yh chromosome (HSY) and its X chromosome counterpart were sequenced and analyzed previo...

CDK1 promotes nascent DNA synthesis and induces resistance of cancer cells to DNA-damaging therapeutic agents

PubMed Central

Liao, Hongwei; Ji, Fang; Geng, Xinwei; Xing, Meichun; Li, Wen; Chen, Zhihua; Shen, Huahao; Ying, Songmin

2017-01-01

Cyclin dependent kinase 1 (CDK1) is essential for cell viability and plays a vital role in many biological events including cell cycle control, DNA damage repair, and checkpoint activation. Here, we identify an unanticipated role for CDK1 in promoting nascent DNA synthesis during S-phase. We report that a short duration of CDK1 inhibition, which does not perturb cell cycle progression, triggers a replication-associated DNA damage response (DDR). This DDR is associated with a disruption of replication fork progression and leads to genome instability. Moreover, we show that compromised CDK1 activity dramatically increases the efficacy of chemotherapeutic agents that kill cancer cells through perturbing DNA replication, including Olaparib, an FDA approved PARP inhibitor. Our study has revealed an important role for CDK1 in the DNA replication program, and suggests that the therapeutic targeting CDK1 may be a novel approach for combination chemotherapy. PMID:29207595

Time-resolved diode laser infrared absorption spectroscopy of the nascent HCl in the infrared laser chemistry of 1,2-dichloro-1,1-difluoroethane

NASA Astrophysics Data System (ADS)

Dietrich, Peter; Quack, Martin; Seyfang, George

1990-04-01

The IR multiphoton excitation and the frequency, fluence and intensity dependence of the IR-laser chemical yields of CF 2ClCH 2Cl have been studied in the fluence range of 1 to 10 J cm -2 yielding a steady-state constant k(st)/ I=0.74×10 6 s -1 MW -1 cm 2 which is approximately independent of intensity. Time-resolved IR absorption spectroscopy with diode laser sources has been used to observe the nascent HCl during the first few 100 ns indicating a population inversion between the levels ν=1, J=4 and ν=2, J=5. At low reactant pressures ( p⩽10 Pa) the time-resolved measurement gives a steady-state rate constant consistent with the theoretical result adjusted to the static yield measurements. The capability of state-selective and time-resolved IR spectroscopy is thus demonstrated, giving real-time determinations of rate constants.

Translational Science by Public Biotechnology Companies in the IPO“Class of 2000”: The Impact of Technological Maturity

PubMed Central

McNamee, Laura; Ledley, Fred

2013-01-01

The biotechnology industry plays a central role in the translation of nascent biomedical science into both products that offer material health benefits and creating capital growth. This study examines the relationship between the maturity of technologies in a characteristic life cycle and value creation by biotechnology companies. We examined the core technology, product development pipelines, and capitalization for a cohort of biotechnology companies that completed an IPO in 2000. Each of these companies was well financed and had core technologies on the leading edge of biological science. We found that companies with the least mature technologies had significantly higher valuations at IPO, but failed to develop products based on these technologies over the ensuing decade, and created less capital growth than companies with more mature technologies at IPO. The observation that this cohort of recently public biotechnology companies was not effective in creating value from nascent science suggests the need for new, evidence-based business strategies for translational science. PMID:24358154

NT3-chitosan elicits robust endogenous neurogenesis to enable functional recovery after spinal cord injury

PubMed Central

Yang, Zhaoyang; Zhang, Aifeng; Duan, Hongmei; Zhang, Sa; Hao, Peng; Ye, Keqiang; Sun, Yi E.; Li, Xiaoguang

2015-01-01

Neural stem cells (NSCs) in the adult mammalian central nervous system (CNS) hold the key to neural regeneration through proper activation, differentiation, and maturation, to establish nascent neural networks, which can be integrated into damaged neural circuits to repair function. However, the CNS injury microenvironment is often inhibitory and inflammatory, limiting the ability of activated NSCs to differentiate into neurons and form nascent circuits. Here we report that neurotrophin-3 (NT3)-coupled chitosan biomaterial, when inserted into a 5-mm gap of completely transected and excised rat thoracic spinal cord, elicited robust activation of endogenous NSCs in the injured spinal cord. Through slow release of NT3, the biomaterial attracted NSCs to migrate into the lesion area, differentiate into neurons, and form functional neural networks, which interconnected severed ascending and descending axons, resulting in sensory and motor behavioral recovery. Our study suggests that enhancing endogenous neurogenesis could be a novel strategy for treatment of spinal cord injury. PMID:26460015

Plant-specific multisubunit RNA polymerase in gene silencing.

PubMed

Lahmy, Sylvie; Bies-Etheve, Natacha; Lagrange, Thierry

2010-01-01

In recent years, a major breakthrough in the study of epigenetic silencing in eukaryotes came with the discovery that the RNA-interference pathway (RNAi) is generally implicated in heterochromatin assembly and gene silencing. An important and paradoxical feature of the RNAi-mediated heterochromatin pathways is their requirement for some form of transcription. In fission yeast, Schizosaccharomyces pombe, centromeric siRNAs have been shown to derive from chromatin-bound nascent transcripts produced by RNA polymerase II (PolII) at the site of heterochromatin formation. Likewise, chromatin-bound nascent transcripts generated by a PolII-related DNA-dependent RNA polymerase, known as PolIVb/PolV, have recently been implicated in RNA-directed DNA methylation (RdDM), the prominent RNAi-mediated chromatin pathway in plants. In this review we discuss recent work on the plant-specific PolII variant enzymes and discuss the mechanistic convergences that have been observed in the role of these enzymes in their respective siRNA-mediated heterochromatin formation pathways.

The phosphoproteome of toll-like receptor-activated macrophages

PubMed Central

Weintz, Gabriele; Olsen, Jesper V; Frühauf, Katja; Niedzielska, Magdalena; Amit, Ido; Jantsch, Jonathan; Mages, Jörg; Frech, Cornelie; Dölken, Lars; Mann, Matthias; Lang, Roland

2010-01-01

Recognition of microbial danger signals by toll-like receptors (TLR) causes re-programming of macrophages. To investigate kinase cascades triggered by the TLR4 ligand lipopolysaccharide (LPS) on systems level, we performed a global, quantitative and kinetic analysis of the phosphoproteome of primary macrophages using stable isotope labelling with amino acids in cell culture, phosphopeptide enrichment and high-resolution mass spectrometry. In parallel, nascent RNA was profiled to link transcription factor (TF) phosphorylation to TLR4-induced transcriptional activation. We reproducibly identified 1850 phosphoproteins with 6956 phosphorylation sites, two thirds of which were not reported earlier. LPS caused major dynamic changes in the phosphoproteome (24% up-regulation and 9% down-regulation). Functional bioinformatic analyses confirmed canonical players of the TLR pathway and highlighted other signalling modules (e.g. mTOR, ATM/ATR kinases) and the cytoskeleton as hotspots of LPS-regulated phosphorylation. Finally, weaving together phosphoproteome and nascent transcriptome data by in silico promoter analysis, we implicated several phosphorylated TFs in primary LPS-controlled gene expression. PMID:20531401

Both DNA Polymerases δ and ε Contact Active and Stalled Replication Forks Differently

PubMed Central

Yu, Chuanhe; Gan, Haiyun

2017-01-01

ABSTRACT Three DNA polymerases, polymerases α, δ, and ε (Pol α, Pol δ, and Pol ε), are responsible for eukaryotic genome duplication. When DNA replication stress is encountered, DNA synthesis stalls until the stress is ameliorated. However, it is not known whether there is a difference in the association of each polymerase with active and stalled replication forks. Here, we show that each DNA polymerase has a distinct pattern of association with active and stalled replication forks. Pol α is enriched at extending Okazaki fragments of active and stalled forks. In contrast, although Pol δ contacts the nascent lagging strands of active and stalled forks, it binds to only the matured (and not elongating) Okazaki fragments of stalled forks. Pol ε has greater contact with the nascent single-stranded DNA (ssDNA) of the leading strand on active forks than on stalled forks. We propose that the configuration of DNA polymerases at stalled forks facilitates the resumption of DNA synthesis after stress removal. PMID:28784720

Asymmetric cell division requires specific mechanisms for adjusting global transcription.

PubMed

Mena, Adriana; Medina, Daniel A; García-Martínez, José; Begley, Victoria; Singh, Abhyudai; Chávez, Sebastián; Muñoz-Centeno, Mari C; Pérez-Ortín, José E

2017-12-01

Most cells divide symmetrically into two approximately identical cells. There are many examples, however, of asymmetric cell division that can generate sibling cell size differences. Whereas physical asymmetric division mechanisms and cell fate consequences have been investigated, the specific problem caused by asymmetric division at the transcription level has not yet been addressed. In symmetrically dividing cells the nascent transcription rate increases in parallel to cell volume to compensate it by keeping the actual mRNA synthesis rate constant. This cannot apply to the yeast Saccharomyces cerevisiae, where this mechanism would provoke a never-ending increasing mRNA synthesis rate in smaller daughter cells. We show here that, contrarily to other eukaryotes with symmetric division, budding yeast keeps the nascent transcription rates of its RNA polymerases constant and increases mRNA stability. This control on RNA pol II-dependent transcription rate is obtained by controlling the cellular concentration of this enzyme. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Regulators of Lysosome Function and Dynamics in Caenorhabditis elegans

PubMed Central

Gee, Kevin; Zamora, Danniel; Horm, Teresa; George, Laeth; Upchurch, Cameron; Randall, Justin; Weaver, Colby; Sanford, Caitlin; Miller, Austin; Hernandez, Sebastian; Dang, Hope; Fares, Hanna

2017-01-01

Lysosomes, the major membrane-bound degradative organelles, have a multitude of functions in eukaryotic cells. Lysosomes are the terminal compartments in the endocytic pathway, though they display highly dynamic behaviors, fusing with each other and with late endosomes in the endocytic pathway, and with the plasma membrane during regulated exocytosis and for wound repair. After fusing with late endosomes, lysosomes are reformed from the resulting hybrid organelles through a process that involves budding of a nascent lysosome, extension of the nascent lysosome from the hybrid organelle, while remaining connected by a membrane bridge, and scission of the membrane bridge to release the newly formed lysosome. The newly formed lysosomes undergo cycles of homotypic fusion and fission reactions to form mature lysosomes. In this study, we used a forward genetic screen in Caenorhabditis elegans to identify six regulators of lysosome biology. We show that these proteins function in different steps of lysosome biology, regulating lysosome formation, lysosome fusion, and lysosome degradation. PMID:28122949

Do chromatin changes around a nascent double strand DNA break spread spherically into linearly non-adjacent chromatin?

PubMed Central

Savic, Velibor

2013-01-01

In the last decade, a lot has been done in elucidating the sequence of events that occur at the nascent double strand DNA break. Nevertheless, the overall structure formed by the DNA damage response (DDR) factors around the break site, the repair focus, remains poorly understood. Although most of the data presented so far only address events that occur in chromatin in cis around the break, there are strong indications that in mammalian systems it may also occur in trans, analogous to the recent findings showing this if budding yeast. There have been attempts to address the issue but the final proof is still missing due to lack of a proper experimental system. If found to be true, the spatial distribution of DDR factors would have a major impact on the neighboring chromatin both in cis and in trans, significantly affecting local chromatin function; gene transcription and potentially other functions. PMID:23882282

Translational science by public biotechnology companies in the IPO "class of 2000": the impact of technological maturity.

PubMed

McNamee, Laura; Ledley, Fred

2013-01-01

The biotechnology industry plays a central role in the translation of nascent biomedical science into both products that offer material health benefits and creating capital growth. This study examines the relationship between the maturity of technologies in a characteristic life cycle and value creation by biotechnology companies. We examined the core technology, product development pipelines, and capitalization for a cohort of biotechnology companies that completed an IPO in 2000. Each of these companies was well financed and had core technologies on the leading edge of biological science. We found that companies with the least mature technologies had significantly higher valuations at IPO, but failed to develop products based on these technologies over the ensuing decade, and created less capital growth than companies with more mature technologies at IPO. The observation that this cohort of recently public biotechnology companies was not effective in creating value from nascent science suggests the need for new, evidence-based business strategies for translational science.

Cdc45-induced loading of human RPA onto single-stranded DNA

PubMed Central

Tessmer, Ingrid; Prus, Piotr; Schlott, Bernhard; Pospiech, Helmut

2017-01-01

Abstract Cell division cycle protein 45 (Cdc45) is an essential component of the eukaryotic replicative DNA helicase. We found that human Cdc45 forms a complex with the single-stranded DNA (ssDNA) binding protein RPA. Moreover, it actively loads RPA onto nascent ssDNA. Pull-down assays and surface plasmon resonance studies revealed that Cdc45-bound RPA complexed with ssDNA in the 8–10 nucleotide binding mode, but dissociated when RPA covered a 30-mer. Real-time analysis of RPA-ssDNA binding demonstrated that Cdc45 catalytically loaded RPA onto ssDNA. This placement reaction required physical contacts of Cdc45 with the RPA70A subdomain. Our results imply that Cdc45 controlled stabilization of the 8-nt RPA binding mode, the subsequent RPA transition into 30-mer mode and facilitated an ordered binding to ssDNA. We propose that a Cdc45-mediated loading guarantees a seamless deposition of RPA on newly emerging ssDNA at the nascent replication fork. PMID:28100698

A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest

NASA Astrophysics Data System (ADS)

Arenz, Stefan; Bock, Lars V.; Graf, Michael; Innis, C. Axel; Beckmann, Roland; Grubmüller, Helmut; Vaiana, Andrea C.; Wilson, Daniel N.

2016-07-01

Nascent polypeptides can induce ribosome stalling, regulating downstream genes. Stalling of ErmBL peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in Streptococcus sanguis. To reveal this stalling mechanism we obtained 3.6-Å-resolution cryo-EM structures of ErmBL-stalled ribosomes with erythromycin. The nascent peptide adopts an unusual conformation with the C-terminal Asp10 side chain in a previously unseen rotated position. Together with molecular dynamics simulations, the structures indicate that peptide-bond formation is inhibited by displacement of the peptidyl-tRNA A76 ribose from its canonical position, and by non-productive interactions of the A-tRNA Lys11 side chain with the A-site crevice. These two effects combine to perturb peptide-bond formation by increasing the distance between the attacking Lys11 amine and the Asp10 carbonyl carbon. The interplay between drug, peptide and ribosome uncovered here also provides insight into the fundamental mechanism of peptide-bond formation.

Duncan Tanner Essay Prize 2016: Historical Pageants, Citizenship, and the Performance of Women's History before Second-Wave Feminism.

PubMed

Thomas, Zoë

2017-09-01

This article argues that the early twentieth-century craze for historical pageants provided an opportunity for women's groups to bring a nascent, accessible form of women's history into the lives of local communities across Britain. Mainstream historical pageants were organized across the country, depicting selected episodes from the past usually relating to the local area. However, more than 200 inter-war pageants staged by women's organizations, church groups, and a number of university colleges have not yet been studied. In these pageants, women imaginatively portrayed professional, religious, political, noble, and 'ordinary' women from across history. Prior to second-wave feminism, when scholars advanced the study of women within the academy, thousands of people had been invested in re-enacting women's history since the inter-war years. Emphasizing the bravery and public duties of women in the past, historical pageants provided a non-controversial format through which women's groups could effectively project their beliefs about the role they felt women should play as newly enfranchised citizens. These popular performances capture the dispersed, yet committed, dedication to encouraging women's social citizenship in the inter-war years, and a more pluralistic understanding of women's engagement with 'feminist' ideas in everyday life across Britain. © The Author [2017]. Published by Oxford University Press.

Understanding Medicaid Managed Care Investments in Members' Social Determinants of Health.

PubMed

Gottlieb, Laura; Ackerman, Sara; Wing, Holly; Manchanda, Rishi

2017-08-01

Despite widespread interest in addressing social determinants of health (SDH) as a means to improve health and to reduce health care spending, little information is available about how to develop, sustain, and scale nonmedical interventions in diverse payer environments, including Medicaid Managed Care. This study aimed to explore how Medicaid Managed Care Organization (MMCO) leaders interpret their roles and responsibilities around SDH, how they garner resources to develop and sustain interventions to address SDH, and how they perceive the influences of external organizations on related activities. Semistructured qualitative key informant interviews were conducted with a purposive sample of 26 Medicaid Managed Care corporate executives. Data were analyzed with an iterative coding, thematic development and interpretation process. MMCO leaders' interests and activities around interventions to address SDH are described, as well as their perceptions of existing and potential incentives and barriers to expanding these interventions. Despite significant experimentation and programmatic diversity of interventions addressing social determinants, MMCO leaders struggle with clinical integration, financing, and evaluation efforts that could promote sustainability. Though their efforts are nascent, MMCO leaders are investing in tackling social determinants to improve health and to decrease health care spending in managed care settings that serve low-income populations. Results highlight both opportunities and concerns about sustaining and scaling clinical interventions addressing SDH.

Dynamics and Function of Nuclear Bodies during Embryogenesis.

PubMed

Arias Escayola, Dahyana; Neugebauer, Karla M

2018-05-01

Nuclear bodies are RNA-rich membraneless organelles in the cell nucleus that concentrate specific sets of nuclear proteins and RNA-protein complexes. Nuclear bodies such as the nucleolus, Cajal body (CB), and the histone locus body (HLB) concentrate factors required for nuclear steps of RNA processing. Formation of these nuclear bodies occurs on genomic loci and is frequently associated with active sites of transcription. Whether nuclear body formation is dependent on a particular gene element, an active process such as transcription, or the nascent RNA present at gene loci is a topic of debate. Recently, this question has been addressed through studies in model organisms and their embryos. The switch from maternally provided RNA and protein to zygotic gene products in early embryos has been well characterized in a variety of organisms. This process, termed maternal-to-zygotic transition, provides an excellent model for studying formation of nuclear bodies before, during, and after the transcriptional activation of the zygotic genome. Here, we review findings in embryos that reveal key principles in the study of the formation and function of nucleoli, CBs, and HLBs. We propose that while particular gene elements may contribute to formation of these nuclear bodies, active transcription promotes maturation of nuclear bodies and efficient RNA processing within them.

Subpolar addition of new cell wall is directed by DivIVA in mycobacteria

PubMed Central

Meniche, Xavier; Otten, Renee; Siegrist, M. Sloan; Baer, Christina E.; Murphy, Kenan C.; Bertozzi, Carolyn R.; Sassetti, Christopher M.

2014-01-01

Mycobacteria are surrounded by a complex multilayered envelope and elongate at the poles. The principles that organize the coordinated addition of chemically diverse cell wall layers during polar extension remain unclear. We show that enzymes mediating the terminal cytosolic steps of peptidoglycan, arabinogalactan, and mycolic acid synthesis colocalize at sites of cell growth or division. The tropomyosin-like protein, DivIVA, is targeted to the negative curvature of the pole, is enriched at the growing end, and determines cell shape from this site. In contrast, cell wall synthetic complexes are concentrated at a distinct subpolar location. When viewed at subdiffraction resolution, new peptidoglycan is deposited at this subpolar site, and inert cell wall covers the DivIVA-marked tip. The differentiation between polar tip and cell wall synthetic complexes is also apparent at the biochemical level. Enzymes that generate mycolate precursors interact with DivIVA, but the final condensation of mycolic acids occurs in a distinct protein complex at the site of nascent cell wall addition. We propose an ultrastructural model of mycobacterial polar growth where new cell wall is added in an annular zone below the cell tip. This model may be broadly applicable to other bacterial and fungal organisms that grow via polar extension. PMID:25049412

A Discovery Approach to Movement.

ERIC Educational Resources Information Center

O'Hagin, Isabel B.

1998-01-01

Investigates the effects of the discovery approach to movement-based instruction on children's level of musicality. Finds that the students with the highest musicality were girls, demonstrated reflective movements and a personal sense of style while moving, and made sense of the music by organizing, categorizing, and developing movement ideas.…

Investigation of the Influence of Leaf Thickness on Canopy Reflectance and Physiological Traits in Upland and Pima Cotton Populations

PubMed Central

Pauli, Duke; White, Jeffrey W.; Andrade-Sanchez, Pedro; Conley, Matthew M.; Heun, John; Thorp, Kelly R.; French, Andrew N.; Hunsaker, Douglas J.; Carmo-Silva, Elizabete; Wang, Guangyao; Gore, Michael A.

2017-01-01

Many systems for field-based, high-throughput phenotyping (FB-HTP) quantify and characterize the reflected radiation from the crop canopy to derive phenotypes, as well as infer plant function and health status. However, given the technology's nascent status, it remains unknown how biophysical and physiological properties of the plant canopy impact downstream interpretation and application of canopy reflectance data. In that light, we assessed relationships between leaf thickness and several canopy-associated traits, including normalized difference vegetation index (NDVI), which was collected via active reflectance sensors carried on a mobile FB-HTP system, carbon isotope discrimination (CID), and chlorophyll content. To investigate the relationships among traits, two distinct cotton populations, an upland (Gossypium hirsutum L.) recombinant inbred line (RIL) population of 95 lines and a Pima (G. barbadense L.) population composed of 25 diverse cultivars, were evaluated under contrasting irrigation regimes, water-limited (WL) and well-watered (WW) conditions, across 3 years. We detected four quantitative trait loci (QTL) and significant variation in both populations for leaf thickness among genotypes as well as high estimates of broad-sense heritability (on average, above 0.7 for both populations), indicating a strong genetic basis for leaf thickness. Strong phenotypic correlations (maximum r = −0.73) were observed between leaf thickness and NDVI in the Pima population, but not the RIL population. Additionally, estimated genotypic correlations within the RIL population for leaf thickness with CID, chlorophyll content, and nitrogen discrimination (r^gij = −0.32, 0.48, and 0.40, respectively) were all significant under WW but not WL conditions. Economically important fiber quality traits did not exhibit significant phenotypic or genotypic correlations with canopy traits. Overall, our results support considering variation in leaf thickness as a potential contributing factor to variation in NDVI or other canopy traits measured via proximal sensing, and as a trait that impacts fundamental physiological responses of plants. PMID:28868055

Person-Organization Fit and Research on Instruction

ERIC Educational Resources Information Center

Youngs, Peter; Pogodzinski, Ben; Grogan, Erin; Perrone, Frank

2015-01-01

Research from industrial and organizational (I-O) psychology indicates that outside of K-12 education, employees' sense of fit with their organizations is often associated with job satisfaction, performance, commitment, and retention. Person-organization (P-O) fit has been conceptualized as the degree of congruence between an…

Amino-Functionalized Luminescent Metal-Organic Framework Test Paper for Rapid and Selective Sensing of SO2 Gas and Its Derivatives by Luminescence Turn-On Effect.

PubMed

Wang, Meng; Guo, Lin; Cao, Dapeng

2018-03-06

Rapid and selective sensing of sulfur dioxide (SO 2 ) gas has attracted more and more attention because SO 2 not only causes environmental pollution but also severely affects the health of human beings. Here we report an amino-functionalized luminescent metal-organic framework (MOF) material (i.e., MOF-5-NH 2 ) and further investigate its sensing property for SO 2 gas and its derivatives as a luminescent probe. The results indicate that the MOF-5-NH 2 probe can selectively and sensitively sense SO 2 derivatives (i.e., SO 3 2- ) in real time by a luminescence turn-on effect with a lower detection limit of 0.168 ppm and a response time of less than 15 s. Importantly, the luminescence turn-on phenomenon can be observed by the naked eye. We also assembled MOF-5-NH 2 into a test paper to achieve the aim of portable detection, and the lower-limit concentration of the test paper for sensing SO 2 in real time was found to be about 0.05 ppm. Moreover, MOF-5-NH 2 also shows good anti-interference ability, strong luminescence stability, and reusability, which means that this material is an excellent sensing candidate. The amino functionalization may also provide a modification strategy to design luminescent sensors for other atmospheric pollutants.

Interpretations of integration in early accountable care organizations.

PubMed

Kreindler, Sara A; Larson, Bridget K; Wu, Frances M; Carluzzo, Kathleen L; Gbemudu, Josette N; Struthers, Ashley; VAN Citters, Aricca D; Shortell, Stephen M; Nelson, Eugene C; Fisher, Elliott S

2012-09-01

It is widely hoped that accountable care organizations (ACOs) will improve health care quality and reduce costs by fostering integration among diverse provider groups. But how do implementers actually envision integration, and what will integration mean in terms of managing the many social identities that ACOs bring together? Using the lens of the social identity approach, this qualitative study examined how four nascent ACOs engaged with the concept of integration. During multiday site visits, we conducted interviews (114 managers and physicians), observations, and document reviews. In no case was the ACO interpreted as a new, overarching entity uniting disparate groups; rather, each site offered a unique interpretation that flowed from its existing strategies for social-identity management: An independent practice association preserved members' cherished value of autonomy by emphasizing coordination, not "integration"; a medical group promoted integration within its employed core, but not with affiliates; a hospital, engaging community physicians who mistrusted integrated systems, reimagined integration as an equal partnership; an integrated delivery system advanced its careful journey towards intergroup consensus by presenting the ACO as a cultural, not structural, change. The ACO appears to be a model flexible enough to work in synchrony with whatever social strategies are most context appropriate, with the potential to promote alignment and functional integration without demanding common identification with a superordinate group. "Soft integration" may be a promising alternative to the vertically integrated model that, though widely assumed to be ideal, has remained unattainable for most organizations. © 2012 Milbank Memorial Fund.

Interpretations of Integration in Early Accountable Care Organizations

PubMed Central

Kreindler, Sara A; Larson, Bridget K; Wu, Frances M; Carluzzo, Kathleen L; Gbemudu, Josette N; Struthers, Ashley; Van Citters, Aricca D; Shortell, Stephen M; Nelson, Eugene C; Fisher, Elliott S

2012-01-01

Context It is widely hoped that accountable care organizations (ACOs) will improve health care quality and reduce costs by fostering integration among diverse provider groups. But how do implementers actually envision integration, and what will integration mean in terms of managing the many social identities that ACOs bring together? Methods Using the lens of the social identity approach, this qualitative study examined how four nascent ACOs engaged with the concept of integration. During multiday site visits, we conducted interviews (114 managers and physicians), observations, and document reviews. Findings In no case was the ACO interpreted as a new, overarching entity uniting disparate groups; rather, each site offered a unique interpretation that flowed from its existing strategies for social-identity management: An independent practice association preserved members’ cherished value of autonomy by emphasizing coordination, not “integration”; a medical group promoted integration within its employed core, but not with affiliates; a hospital, engaging community physicians who mistrusted integrated systems, reimagined integration as an equal partnership; an integrated delivery system advanced its careful journey towards intergroup consensus by presenting the ACO as a cultural, not structural, change. Conclusions The ACO appears to be a model flexible enough to work in synchrony with whatever social strategies are most context appropriate, with the potential to promote alignment and functional integration without demanding common identification with a superordinate group. “Soft integration” may be a promising alternative to the vertically integrated model that, though widely assumed to be ideal, has remained unattainable for most organizations. PMID:22985278

Reliability, validity, and significance of assessment of sense of contribution in the workplace.

PubMed

Takaki, Jiro; Taniguchi, Toshiyo; Fujii, Yasuhito

2014-01-29

The purpose of this study was to assess the validity and reliability of the Sense of Contribution Scale (SCS), a newly developed, 7-item questionnaire used to measure sense of contribution in the workplace. Workers at 272 organizations answered questionnaires that included the SCS. Because of non-participation or missing data, the number of subjects included in the analyses for internal consistency and validity varied from 1,675 to 2,462 (response rates 54.6%-80.2%). Fifty-four workers were included in the analysis of test-retest reliability (response rate, 77.1%). The SCS showed high internal consistency (Cronbach's α coefficients in men and women were 0.85 and 0.86, respectively) and test-retest reliability (intraclass correlation coefficient = 0.91). Significant (p < 0.001), positive, moderate correlations were found between the SCS score and scores for organization-based self-esteem and work engagement in both genders, which support the SCS's convergent and discriminant validity. The criterion validity of the SCS was supported by the finding that in both genders, the SCS scores were significantly (p < 0.05) and inversely associated with psychological distress and sleep disturbance in crude and in multivariable analyses that adjusted for demographics, organization-based self-esteem, work engagement, effort-reward ratio, workplace bullying, and procedural and interactional justice. The SCS is a psychometrically satisfactory measure of sense of contribution in the workplace. The SCS provides a new and useful instrument to measure sense of contribution, which is independently associated with mental health in workers, for studies in organizational science, occupational health psychology and occupational medicine.

Fabrication of a P3HT-ZnO Nanowires Gas Sensor Detecting Ammonia Gas

PubMed Central

Kuo, Chin-Guo; Chen, Jung-Hsuan; Chao, Yi-Chieh; Chen, Po-Lin

2017-01-01

In this study, an organic-inorganic semiconductor gas sensor was fabricated to detect ammonia gas. An inorganic semiconductor was a zinc oxide (ZnO) nanowire array produced by atomic layer deposition (ALD) while an organic material was a p-type semiconductor, poly(3-hexylthiophene) (P3HT). P3HT was suitable for the gas sensing application due to its high hole mobility, good stability, and good electrical conductivity. In this work, P3HT was coated on the zinc oxide nanowires by the spin coating to form an organic-inorganic heterogeneous interface of the gas sensor for detecting ammonia gas. The thicknesses of the P3HT were around 462 nm, 397 nm, and 277 nm when the speeds of the spin coating were 4000 rpm, 5000 rpm, and 6000 rpm, respectively. The electrical properties and sensing characteristics of the gas sensing device at room temperature were evaluated by Hall effect measurement and the sensitivity of detecting ammonia gas. The results of Hall effect measurement for the P3HT-ZnO nanowires semiconductor with 462 nm P3HT film showed that the carrier concentration and the mobility were 2.7 × 1019 cm−3 and 24.7 cm2∙V−1∙s−1 respectively. The gas sensing device prepared by the P3HT-ZnO nanowires semiconductor had better sensitivity than the device composed of the ZnO film and P3HT film. Additionally, this gas sensing device could reach a maximum sensitivity around 11.58 per ppm. PMID:29295573

Fabrication of a P3HT-ZnO Nanowires Gas Sensor Detecting Ammonia Gas.

PubMed

Kuo, Chin-Guo; Chen, Jung-Hsuan; Chao, Yi-Chieh; Chen, Po-Lin

2017-12-25

In this study, an organic-inorganic semiconductor gas sensor was fabricated to detect ammonia gas. An inorganic semiconductor was a zinc oxide (ZnO) nanowire array produced by atomic layer deposition (ALD) while an organic material was a p-type semiconductor, poly(3-hexylthiophene) (P3HT). P3HT was suitable for the gas sensing application due to its high hole mobility, good stability, and good electrical conductivity. In this work, P3HT was coated on the zinc oxide nanowires by the spin coating to form an organic-inorganic heterogeneous interface of the gas sensor for detecting ammonia gas. The thicknesses of the P3HT were around 462 nm, 397 nm, and 277 nm when the speeds of the spin coating were 4000 rpm, 5000 rpm, and 6000 rpm, respectively. The electrical properties and sensing characteristics of the gas sensing device at room temperature were evaluated by Hall effect measurement and the sensitivity of detecting ammonia gas. The results of Hall effect measurement for the P3HT-ZnO nanowires semiconductor with 462 nm P3HT film showed that the carrier concentration and the mobility were 2.7 × 10 19 cm -3 and 24.7 cm²∙V -1 ∙s -1 respectively. The gas sensing device prepared by the P3HT-ZnO nanowires semiconductor had better sensitivity than the device composed of the ZnO film and P3HT film. Additionally, this gas sensing device could reach a maximum sensitivity around 11.58 per ppm.

Reliability, Validity, and Significance of Assessment of Sense of Contribution in the Workplace

PubMed Central

Takaki, Jiro; Taniguchi, Toshiyo; Fujii, Yasuhito

2014-01-01

The purpose of this study was to assess the validity and reliability of the Sense of Contribution Scale (SCS), a newly developed, 7-item questionnaire used to measure sense of contribution in the workplace. Workers at 272 organizations answered questionnaires that included the SCS. Because of non-participation or missing data, the number of subjects included in the analyses for internal consistency and validity varied from 1,675 to 2,462 (response rates 54.6%–80.2%). Fifty-four workers were included in the analysis of test–retest reliability (response rate, 77.1%). The SCS showed high internal consistency (Cronbach’s α coefficients in men and women were 0.85 and 0.86, respectively) and test–retest reliability (intraclass correlation coefficient = 0.91). Significant (p < 0.001), positive, moderate correlations were found between the SCS score and scores for organization-based self-esteem and work engagement in both genders, which support the SCS’s convergent and discriminant validity. The criterion validity of the SCS was supported by the finding that in both genders, the SCS scores were significantly (p < 0.05) and inversely associated with psychological distress and sleep disturbance in crude and in multivariable analyses that adjusted for demographics, organization-based self-esteem, work engagement, effort–reward ratio, workplace bullying, and procedural and interactional justice. The SCS is a psychometrically satisfactory measure of sense of contribution in the workplace. The SCS provides a new and useful instrument to measure sense of contribution, which is independently associated with mental health in workers, for studies in organizational science, occupational health psychology and occupational medicine. PMID:24481035

[Outsourcing of nursing human resources from ethical to management: a survey in a Lazio Region Hospital].

PubMed

d'Amore, Maurizia; Peroni, Antonia

2008-01-01

In 2006, 279 nurses of a Lazio Region Hospital were assessed to verify whether certain Human Resources decisions, such as outsourcing, can negatively influence their working motivation and sense of belonging to a health organization and whether any dissatisfaction can be attributed to poor ethical information within the health service. The research method had a descriptive basis and for data collection a questionnaire with 35 questions was issued. Results showed that nurses felt strongly involved in the study and interesting aspects for management of human resources emerged, depicting an organization lacking in motivation : this confirmed one of the aspects of the study : poor levels of motivation and sense of belonging can be correlated to insufficient ethical information in local health organizations. The main working needs that emerged among the nurses of this hospital regarded economical retribution (90%), security and success (88%) , belonging (86%) and self-satisfaction (77%): the need for power was relatively low (40%). The strong points of the study were : the strong involvement of nurses, the value of the information gathered regarding working motivation, sense of belong to a nursing organization , working needs , ethical information in health environments, organization according to targets. The limits of the study were: limited number of nurses in outsourcing at the time of the study (12%), impossibility of comparing the results with data prior to the outsourcing choices made by the hospital in question.

The case for values as a basis for organizational culture.

PubMed

Brinkley, Ruth W

2013-01-01

At a time when almost every aspect of healthcare is rapidly and dramatically changing, it is important for healthcare leaders to maintain a moral compass--a clear sense of the morals or virtues that guide their decisions. A firmly rooted moral compass inspires, leads, guides, and provides a solid foundation--and some sense of security--for organizations navigating massive or significant transformational changes, such as those required by the Affordable Care Act. In addition, "smaller" changes, such as consolidation, rationalization, and relocation of services, have a strong chance of succeeding in organizations that operate within a moral framework from which the organization can shape its future strategies and make important decisions. Finally, an organization's moral compass guides actions, reactions, and behaviors when unexpected or devastating events occur in the lives of consumers, employees, physicians, business partners, patients, families, and members of the community. The direction toward which its moral compass is pointing determines the types and quality of relationships it has with those key stakeholders, and those individuals and groups come to depend on what they have observed and know to be true about how the organization behaves in certain circumstances. While no organization can predict the future and all of the implications of change, key stakeholder groups need and want to know how they will be treated in the face of such change-whether expected or unexpected. In this sense, every organization must establish ways to evaluate the validity of its moral compass and develop--and adhere to--guidelines that determine how its members will behave, whether in ordinary circumstances; in the face of extraordinary, high-impact situations; or in times of massive transformational change. Above all, executive leaders must always be mindful that their own personal moral compass becomes their organization's moral compass.

Polysemy in Sentence Comprehension: Effects of Meaning Dominance

PubMed Central

Foraker, Stephani; Murphy, Gregory L.

2012-01-01

Words like church are polysemous, having two related senses (a building and an organization). Three experiments investigated how polysemous senses are represented and processed during sentence comprehension. On one view, readers retrieve an underspecified, core meaning, which is later specified more fully with contextual information. On another view, readers retrieve one or more specific senses. In a reading task, context that was neutral or biased towards a particular sense preceded a polysemous word. Disambiguating material consistent with only one sense followed, in a second sentence (Experiment 1) or the same sentence (Experiments 2 & 3). Reading the disambiguating material was faster when it was consistent with that context, and dominant senses were committed to more strongly than subordinate senses. Critically, following neutral context, the continuation was read more quickly when it selected the dominant sense, and the degree of sense dominance partially explained the reading time advantage. Similarity of the senses also affected reading times. Across experiments, we found that sense selection may not be completed immediately following a polysemous word but is completed at a sentence boundary. Overall, the results suggest that readers select an individual sense when reading a polysemous word, rather than a core meaning. PMID:23185103

Review of Remote Sensing Needs and Applications in Africa

NASA Technical Reports Server (NTRS)

Brown, Molly E.

2007-01-01

Remote sensing data has had an important role in identifying and responding to inter-annual variations in the African environment during the past three decades. As a largely agricultural region with diverse but generally limited government capacity to acquire and distribute ground observations of rainfall, temperature and other parameters, remote sensing is sometimes the only reliable measure of crop growing conditions in Africa. Thus, developing and maintaining the technical and scientific capacity to analyze and utilize satellite remote sensing data in Africa is critical to augmenting the continent's local weather/climate observation networks as well as its agricultural and natural resource development and management. The report Review of Remote Sensing Needs and Applications in Africa' has as its central goal to recommend to the US Agency for International Development an appropriate approach to support sustainable remote sensing applications at African regional remote sensing centers. The report focuses on "RS applications" to refer to the acquisition, maintenance and archiving, dissemination, distribution, analysis, and interpretation of remote sensing data, as well as the integration of interpreted data with other spatial data products. The report focuses on three primary remote sensing centers: (1) The AGRHYMET Regional Center in Niamey, Niger, created in 1974, is a specialized institute of the Permanent Interstate Committee for Drought Control in the Sahel (CILSS), with particular specialization in science and techniques applied to agricultural development, rural development, and natural resource management. (2) The Regional Centre for Maiming of Resources for Development (RCMRD) in Nairobi, Kenya, established in 1975 under the auspices of the United Nations Economic Commission for Africa and the Organization of African Unity (now the African Union), is an intergovernmental organization, with 15 member states from eastern and southern Africa. (3) The Regional Remote Sensing Unit (RRSU) in Gaborone, Botswana, began work in June 1988 and operates under the Agriculture Information Management System (AIMS), as part of the Food, Agriculture and Natural Resources (FANR) Directorate, based at the Southern Africa Development Community (SADC) Secretariat.

NASA Fluid Lensing & MiDAR: Next-Generation Remote Sensing Technologies for Aquatic Remote Sensing

NASA Technical Reports Server (NTRS)

Chirayath, Ved

2018-01-01

We present two recent instrument technology developments at NASA, Fluid Lensing and MiDAR, and their application to remote sensing of Earth's aquatic systems. Fluid Lensing is the first remote sensing technology capable of imaging through ocean waves in 3D at sub-cm resolutions. MiDAR is a next-generation active hyperspectral remote sensing and optical communications instrument capable of active fluid lensing. Fluid Lensing has been used to provide 3D multispectral imagery of shallow marine systems from unmanned aerial vehicles (UAVs, or drones), including coral reefs in American Samoa and stromatolite reefs in Hamelin Pool, Western Australia. MiDAR is being deployed on aircraft and underwater remotely operated vehicles (ROVs) to enable a new method for remote sensing of living and nonliving structures in extreme environments. MiDAR images targets with high-intensity narrowband structured optical radiation to measure an objectâ€"TM"s non-linear spectral reflectance, image through fluid interfaces such as ocean waves with active fluid lensing, and simultaneously transmit high-bandwidth data. As an active instrument, MiDAR is capable of remotely sensing reflectance at the centimeter (cm) spatial scale with a signal-to-noise ratio (SNR) multiple orders of magnitude higher than passive airborne and spaceborne remote sensing systems with significantly reduced integration time. This allows for rapid video-frame-rate hyperspectral sensing into the far ultraviolet and VNIR wavelengths. Previously, MiDAR was developed into a TRL 2 laboratory instrument capable of imaging in thirty-two narrowband channels across the VNIR spectrum (400-950nm). Recently, MiDAR UV was raised to TRL4 and expanded to include five ultraviolet bands from 280-400nm, permitting UV remote sensing capabilities in UV A, B, and C bands and enabling mineral identification and stimulated fluorescence measurements of organic proteins and compounds, such as green fluorescent proteins in terrestrial and aquatic organics.

Proposal and Implementation of a Robust Sensing Method for DVB-T Signal

NASA Astrophysics Data System (ADS)

Song, Chunyi; Rahman, Mohammad Azizur; Harada, Hiroshi

This paper proposes a sensing method for TV signals of DVB-T standard to realize effective TV White Space (TVWS) Communication. In the TVWS technology trial organized by the Infocomm Development Authority (iDA) of Singapore, with regard to the sensing level and sensing time, detecting DVB-T signal at the level of -120dBm over an 8MHz channel with a sensing time below 1 second is required. To fulfill such a strict sensing requirement, we propose a smart sensing method which combines feature detection and energy detection (CFED), and is also characterized by using dynamic threshold selection (DTS) based on a threshold table to improve sensing robustness to noise uncertainty. The DTS based CFED (DTS-CFED) is evaluated by computer simulations and is also implemented into a hardware sensing prototype. The results show that the DTS-CFED achieves a detection probability above 0.9 for a target false alarm probability of 0.1 for DVB-T signals at the level of -120dBm over an 8MHz channel with the sensing time equals to 0.1 second.

Luminescent microporous metal–organic framework with functional Lewis basic sites on the pore surface: Quantifiable evaluation of luminescent sensing mechanisms towards Fe{sup 3+}

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

Jin, Jun-Cheng; Technology Promotion Center of Nano Composite Material of Biomimetic Sensor and Detecting Technology, Preparation and Application, Anhui Provincial Laboratory West Anhui University, Anhui 237012; Guo, Rui-Li

2016-11-15

A systematic study has been conducted on a novel luminescent metal-organic framework, ([Zn(bpyp)(L-OH)]·DMF·2H{sub 2}O){sub n} (1), to explore its sensing mechanisms to Fe{sup 3+}. Structure analyses show that compound 1 exist pyridine N atoms and -OH groups on the pore surface for specific sensing of metal ions via Lewis acid-base interactions. On this consideration, the quenching mechanisms are studied and the processes are controlled by multiple mechanisms in which dynamic and static mechanisms are calculated, achieving the quantification evaluation of the quenching process. This work not only achieves the quantitative evaluation of the luminescence quenching but also provides certain insightsmore » into the quenching process, and the possible mechanisms explored in this work may inspire future research and design of target luminescent metal-organic frameworks (LMOFs) with specific functions. - Graphical abstract: A systematic study has been conducted on a novel luminescent metal-organic framework to explore its sensing mechanisms to Fe{sup 3+}. The quenching mechanisms are studied and the processes are controlled by multiple mechanisms in which dynamic and static mechanisms are calculated, achieving the quantification evaluation of the quenching process. - Highlights: • A novel porous luminescent MOF containing uncoordinated groups in interlayer channels was successfully synthesized. • The compound 1 can exhibit significant luminescent sensitivity to Fe{sup 3+}, which make its good candidate as luminescent sensor. • The corresponding dynamic and static quenching constants are calculated, achieving the quantification evaluation of the quenching process.« less

A multifunctional chemical sensor based on a three-dimensional lanthanide metal-organic framework

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

Du, Pei-Yao; Liao, Sheng-Yun; Gu, Wen, E-mail: guwen68@nankai.edu.cn

2016-12-15

A 3D lanthanide MOF with formula [Sm{sub 2}(abtc){sub 1.5}(H{sub 2}O){sub 3}(DMA)]·H{sub 2}O·DMA (1) has been successfully synthesized via solvothermal method. Luminescence studies reveal that 1 exhibits dual functional detection benzyl alcohol and benzaldehyde among different aromatic molecules. In addition, 1 displays a turn-on luminescence sensing with respect to ethanol among different alcohol molecules, which suggests that 1 is also a promising luminescent probe for high selective sensing of ethanol. - Highlights: • A three-dimensional lanthanide metal-organic framework has been synthesized. • Complex 1 exhibits dual functional detection benzyl alcohol and benzaldehyde among different aromatic molecules. • Complex 1 displays amore » turn-on luminescence sensing with respect to ethanol among different alcohol molecules.« less

An overview of remote sensing technology transfer in Canada and the United States

NASA Technical Reports Server (NTRS)

Strome, W. M.; Lauer, D. T.

1977-01-01

To realize the maximum potential benefits of remote sensing, the technology must be applied by personnel responsible for the management of natural resources and the environment. In Canada and the United States, these managers are often in local offices and are not those responsible for the development of systems to acquire, preprocess, and disseminate remotely sensed data, nor those leading the research and development of techniques for analysis of the data. However, the latter organizations have recognized that the technology they develop must be transferred to the management agencies if the technology is to be useful to society. Problems of motivation and communication associated with the technology transfer process, and some of the methods employed by Federal, State, Provincial, and local agencies, academic institutions, and private organizations to overcome these problems are explored.

Embedded Touch Sensing Circuit Using Mutual Capacitance for Active-Matrix Organic Light-Emitting Diode Display

NASA Astrophysics Data System (ADS)

Park, Young-Ju; Seok, Su-Jeong; Park, Sang-Ho; Kim, Ohyun

2011-03-01

We propose and simulate an embedded touch sensing circuit for active-matrix organic light-emitting diode (AMOLED) displays. The circuit consists of three thin-film transistors (TFTs), one fixed capacitor, and one variable capacitor. AMOLED displays do not have a variable capacitance characteristic, so we realized a variable capacitor to detect touches in the sensing pixel by exploiting the change in the mutual capacitance between two electrodes that is caused by touch. When a dielectric substance approaches two electrodes, the electric field is shunted so that the mutual capacitance decreases. We use the existing TFT process to form the variable capacitor, so no additional process is needed. We use advanced solid-phase-crystallization TFTs because of their stability and uniformity. The proposed circuit detects multi-touch points by a scanning process.

Sensing response of copper phthalocyanine salt dispersed glass with organic vapours

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

Ridhi, R.; Sachdeva, Sheenam; Saini, G. S. S.

2016-05-06

Copper Phthalocyanine and other Metal Phthalocyanines are very flexible and tuned easily to modify their structural, spectroscopic, optical and electrical properties by either functionalizing them with various substituent groups or by replacing or adding a ligand to the central metal atom in the phthalocyanine ring and accordingly can be made sensitive and selective to various organic species or gaseous vapours. In the present work, we have dispersed Copper Phthalocyanine Salt (CuPcS) in sol-gel glass form using chemical route sol-gel method and studied its sensing mechanism with organic vapours like methanol and benzene and found that current increases onto their exposuremore » with vapours. A variation in the activation energies was also observed with exposure of vapours.« less

Sensing response of copper phthalocyanine salt dispersed glass with organic vapours

NASA Astrophysics Data System (ADS)

Ridhi, R.; Sachdeva, Sheenam; Saini, G. S. S.; Tripathi, S. K.

2016-05-01

Copper Phthalocyanine and other Metal Phthalocyanines are very flexible and tuned easily to modify their structural, spectroscopic, optical and electrical properties by either functionalizing them with various substituent groups or by replacing or adding a ligand to the central metal atom in the phthalocyanine ring and accordingly can be made sensitive and selective to various organic species or gaseous vapours. In the present work, we have dispersed Copper Phthalocyanine Salt (CuPcS) in sol-gel glass form using chemical route sol-gel method and studied its sensing mechanism with organic vapours like methanol and benzene and found that current increases onto their exposure with vapours. A variation in the activation energies was also observed with exposure of vapours.

Chemiresistive Sensor Arrays from Conductive 2D Metal–Organic Frameworks

DOE PAGES

Campbell, Michael G.; Liu, Sophie F.; Swager, Timothy M.; ...

2015-10-11

Applications of porous metal–organic frameworks (MOFs) in electronic devices are rare, owing in large part to a lack of MOFs that display electrical conductivity. Here, we describe the use of conductive two-dimensional (2D) MOFs as a new class of materials for chemiresistive sensing of volatile organic compounds (VOCs). We demonstrate that a family of structurally analogous 2D MOFs can be used to construct a cross-reactive sensor array that allows for clear discrimination between different categories of VOCs. Lastly, experimental data show that multiple sensing mechanisms are operative with high degrees of orthogonality, establishing that the 2D MOFs used here aremore » mechanistically unique and offer advantages relative to other known chemiresistor materials.« less

When time matters.

PubMed

Theadore, Jason C

2011-01-01

The most important organizational resource is energy. The most important resource in time management is energy. Managing energy, not time, can help create encouraging time management skills and appropriate work life balance. Once a leader understands that time should be spent on things that are important instead of everything that is urgent, you can begin to develop a balance that will support your values, your family, and your organization. When leaders find meaningful ways to add a sense of purpose to their work they can personally improve themselves and their organizations. If your personal values do not align with the values of your organization you will never work with a true sense of purpose. Make the time to manage your energy. You will be surprised how much free time you find.

Tetratopic phenyl compounds, related metal-organic framework materials and post-assembly elaboration

DOEpatents

Farha, Omar K.; Hupp, Joseph T.

2012-09-11

Disclosed are tetratopic carboxylic acid phenyl for use in metal-organic framework compounds. These compounds are useful in catalysis, gas storage, sensing, biological imaging, drug delivery and gas adsorption separation.

Tetratopic phenyl compounds, related metal-organic framework materials and post-assembly elaboration

DOEpatents

Farha, Omar K; Hupp, Joseph T

2013-06-25

Disclosed are tetratopic carboxylic acid phenyl for use in metal-organic framework compounds. These compounds are useful in catalysis, gas storage, sensing, biological imaging, drug delivery and gas adsorption separation.