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  1. Article: Transcriptional Regulation of Pine Male and Female Cone Initiation and Development: Key Players Identified Through Comparative Transcriptomics.

    Fritsche, Steffi / Rippel Salgado, Leonardo / Boron, Agnieszka K / Hanning, Kyrin R / Donaldson, Lloyd A / Thorlby, Glenn

    Frontiers in genetics

    2022  Volume 13, Page(s) 815093

    Abstract: With long reproductive timescales, large complex genomes, and a lack of reliable reference genomes, understanding gene function in conifers is extremely challenging. Consequently, our understanding of which genetic factors influence the development of ... ...

    Abstract With long reproductive timescales, large complex genomes, and a lack of reliable reference genomes, understanding gene function in conifers is extremely challenging. Consequently, our understanding of which genetic factors influence the development of reproductive structures (cones) in monoecious conifers remains limited. Genes with inferred roles in conifer reproduction have mostly been identified through homology and phylogenetic reconstruction with their angiosperm counterparts. We used RNA-sequencing to generate transcriptomes of the early morphological stages of cone development in the conifer species
    Language English
    Publishing date 2022-03-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2022.815093
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  2. Article ; Online: Deep mutational scanning for therapeutic antibody engineering.

    Hanning, Kyrin R / Minot, Mason / Warrender, Annmaree K / Kelton, William / Reddy, Sai T

    Trends in pharmacological sciences

    2021  Volume 43, Issue 2, Page(s) 123–135

    Abstract: The biophysical and functional properties of monoclonal antibody (mAb) drug candidates are often improved by protein engineering methods to increase the probability of clinical efficacy. One emerging method is deep mutational scanning (DMS) which ... ...

    Abstract The biophysical and functional properties of monoclonal antibody (mAb) drug candidates are often improved by protein engineering methods to increase the probability of clinical efficacy. One emerging method is deep mutational scanning (DMS) which combines the power of exhaustive protein mutagenesis and functional screening with deep sequencing and bioinformatics. The application of DMS has yielded significant improvements to the affinity, specificity, and stability of several preclinical antibodies alongside novel applications such as introducing multi-specific binding properties. DMS has also been applied directly on target antigens to precisely map antibody-binding epitopes and notably to profile the mutational escape potential of viral targets (e.g., SARS-CoV-2 variants). Finally, DMS combined with machine learning is enabling advances in the computational screening and engineering of therapeutic antibodies.
    MeSH term(s) Antibodies, Viral ; COVID-19 ; Humans ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
    Chemical Substances Antibodies, Viral ; Spike Glycoprotein, Coronavirus
    Language English
    Publishing date 2021-12-09
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 282846-7
    ISSN 1873-3735 ; 0165-6147
    ISSN (online) 1873-3735
    ISSN 0165-6147
    DOI 10.1016/j.tips.2021.11.010
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1513: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 6: Show issues

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  3. Article ; Online: Degradation and adsorption of synthetic DNA water tracers in environmental matrices.

    Pang, Liping / Heiligenthal, Laura / Premaratne, Aruni / Hanning, Kyrin R / Abraham, Phillip / Sutton, Richard / Hadfield, John / Billington, Craig

    The Science of the total environment

    2022  Volume 844, Page(s) 157146

    Abstract: Synthetic DNA tracers are gaining interest as tools for tracking contamination pathways and hydraulic connections in surface water and groundwater systems. However, few quantitative data exist that describe DNA tracer degradation and adsorption in ... ...

    Abstract Synthetic DNA tracers are gaining interest as tools for tracking contamination pathways and hydraulic connections in surface water and groundwater systems. However, few quantitative data exist that describe DNA tracer degradation and adsorption in environmental matrices. We undertook laboratory experiments to quantify the degradation of multiple double-stranded DNA tracers in stream water, groundwater, and domestic and dairy-shed effluent, and adsorption to stream sediments, soils, coastal sand aquifer media and alluvial sandy gravel aquifer media. Faster DNA tracer degradation seemed to be associated with high bacterial concentrations in the liquid phase. Overall, the degradation of the 352 base pair (bp) DNA tracers in the aqueous phase was significantly (P = 0.018) slower than that of the 302 bp DNA tracers. Although the tracers' internal amplicon lengths were similar, the longer non-amplified flanking regions of the 352 bp tracers may better protect them from environmental degradation. Thermodynamic analysis suggests that longer flanking regions contribute to greater tracer stability. This finding may explain our previous field observations that 352 bp tracer mass reductions were often lower than 302 bp tracer mass reductions. The 2 sets of DNA tracers did not differ significantly regarding their adsorption to stream sediment-stream water or aquifer media-groundwater mixtures (P > 0.067), but the 352 bp tracers showed significantly less adsorption to soil-effluent mixtures than the 302 bp tracers (P = 0.005). The DNA tracers' adsorption to soil-effluent mixtures was comparatively less than their adsorption to the aquifer media-groundwater and stream sediment-stream water mixtures, suggesting that DNA tracers may compete with like-charged organic matter for adsorption sites. These findings provide insights into the fate of DNA tracers in the environment. The DNA tracers' degradation rate constants determined in this study for a range of environmental conditions could assist the design of future field investigations.
    MeSH term(s) Adsorption ; DNA ; Environmental Monitoring ; Groundwater ; Soil ; Water/analysis ; Water Pollutants, Chemical/analysis
    Chemical Substances Soil ; Water Pollutants, Chemical ; Water (059QF0KO0R) ; DNA (9007-49-2)
    Language English
    Publishing date 2022-07-04
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2022.157146
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 949: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article: Degradation and adsorption of synthetic DNA water tracers in environmental matrices

    Pang, Liping / Heiligenthal, Laura / Premaratne, Aruni / Hanning, Kyrin R. / Abraham, Phillip / Sutton, Richard / Hadfield, John / Billington, Craig

    Science of the total environment. 2022 Oct. 20, v. 844

    2022  

    Abstract: Synthetic DNA tracers are gaining interest as tools for tracking contamination pathways and hydraulic connections in surface water and groundwater systems. However, few quantitative data exist that describe DNA tracer degradation and adsorption in ... ...

    Abstract Synthetic DNA tracers are gaining interest as tools for tracking contamination pathways and hydraulic connections in surface water and groundwater systems. However, few quantitative data exist that describe DNA tracer degradation and adsorption in environmental matrices. We undertook laboratory experiments to quantify the degradation of multiple double-stranded DNA tracers in stream water, groundwater, and domestic and dairy-shed effluent, and adsorption to stream sediments, soils, coastal sand aquifer media and alluvial sandy gravel aquifer media. Faster DNA tracer degradation seemed to be associated with high bacterial concentrations in the liquid phase. Overall, the degradation of the 352 base pair (bp) DNA tracers in the aqueous phase was significantly (P = 0.018) slower than that of the 302 bp DNA tracers. Although the tracers' internal amplicon lengths were similar, the longer non-amplified flanking regions of the 352 bp tracers may better protect them from environmental degradation. Thermodynamic analysis suggests that longer flanking regions contribute to greater tracer stability. This finding may explain our previous field observations that 352 bp tracer mass reductions were often lower than 302 bp tracer mass reductions. The 2 sets of DNA tracers did not differ significantly regarding their adsorption to stream sediment-stream water or aquifer media-groundwater mixtures (P > 0.067), but the 352 bp tracers showed significantly less adsorption to soil-effluent mixtures than the 302 bp tracers (P = 0.005). The DNA tracers' adsorption to soil-effluent mixtures was comparatively less than their adsorption to the aquifer media-groundwater and stream sediment-stream water mixtures, suggesting that DNA tracers may compete with like-charged organic matter for adsorption sites. These findings provide insights into the fate of DNA tracers in the environment. The DNA tracers' degradation rate constants determined in this study for a range of environmental conditions could assist the design of future field investigations.
    Keywords DNA ; adsorption ; aquifers ; environmental degradation ; gravel ; groundwater ; liquids ; organic matter ; sand ; streams ; surface water ; thermodynamics
    Language English
    Dates of publication 2022-1020
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 121506-1
    ISSN 1879-1026 ; 0048-9697
    ISSN (online) 1879-1026
    ISSN 0048-9697
    DOI 10.1016/j.scitotenv.2022.157146
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    In stock of ZB MED Bonn / Germany

    Z 74/341: Show issues

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  5. Article ; Online: Comparison of D1´- and D1-containing PS II reaction centre complexes under different environmental conditions in Synechocystis sp. PCC 6803.

    Crawford, Tim S / Hanning, Kyrin R / Chua, Jocelyn P S / Eaton-Rye, Julian J / Summerfield, Tina C

    Plant, cell & environment

    2016  Volume 39, Issue 8, Page(s) 1715–1726

    Abstract: In oxygenic photosynthesis, the D1 protein of Photosystem II is the primary target of photodamage and environmental stress can accelerate this process. The cyanobacterial response to stress includes transcriptional regulation of genes encoding D1, ... ...

    Abstract In oxygenic photosynthesis, the D1 protein of Photosystem II is the primary target of photodamage and environmental stress can accelerate this process. The cyanobacterial response to stress includes transcriptional regulation of genes encoding D1, including low-oxygen-induction of psbA1 encoding the D1´ protein in Synechocystis sp. PCC 6803. The psbA1 gene is also transiently up-regulated in high light, and its deletion has been reported to increase ammonium-induced photoinhibition. Therefore we investigated the role of D1´-containing PS II centres under different environmental conditions. A strain containing only D1´-PS II centres under aerobic conditions exhibited increased sensitivity to ammonium chloride and high light compared to a D1-containing strain. Additionally a D1´-PS II strain was outperformed by a D1-PS II strain under normal conditions; however, a strain containing low-oxygen-induced D1´-PS II centres was more resilient under high light than an equivalent D1 strain. These D1´-containing centres had chlorophyll a fluorescence characteristics indicative of altered forward electron transport and back charge recombination with the donor side of PS II. Our results indicate D1´-PS II centres are important in the reconfiguration of thylakoid electron transport in response to high light and low oxygen.
    Language English
    Publishing date 2016-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 391893-2
    ISSN 1365-3040 ; 0140-7791
    ISSN (online) 1365-3040
    ISSN 0140-7791
    DOI 10.1111/pce.12738
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  6. Article: Comparison of D1´‐ and D1‐containing PS II reaction centre complexes under different environmental conditions in Synechocystis sp. PCC 6803

    Crawford, Tim S / Jocelyn P.S. Chua / Julian J. Eaton‐Rye / Kyrin R. Hanning / Tina C. Summerfield

    Plant, cell and environment. 2016 Aug., v. 39, no. 8

    2016  

    Abstract: In oxygenic photosynthesis, the D1 protein of Photosystem II is the primary target of photodamage and environmental stress can accelerate this process. The cyanobacterial response to stress includes transcriptional regulation of genes encoding D1, ... ...

    Abstract In oxygenic photosynthesis, the D1 protein of Photosystem II is the primary target of photodamage and environmental stress can accelerate this process. The cyanobacterial response to stress includes transcriptional regulation of genes encoding D1, including low‐oxygen‐induction of psbA1 encoding the D1´ protein in Synechocystis sp. PCC 6803. The psbA1 gene is also transiently up‐regulated in high light, and its deletion has been reported to increase ammonium‐induced photoinhibition. Therefore we investigated the role of D1´‐containing PS II centres under different environmental conditions. A strain containing only D1´‐PS II centres under aerobic conditions exhibited increased sensitivity to ammonium chloride and high light compared to a D1‐containing strain. Additionally a D1´‐PS II strain was outperformed by a D1‐PS II strain under normal conditions; however, a strain containing low‐oxygen‐induced D1´‐PS II centres was more resilient under high light than an equivalent D1 strain. These D1´‐containing centres had chlorophyll a fluorescence characteristics indicative of altered forward electron transport and back charge recombination with the donor side of PS II. Our results indicate D1´‐PS II centres are important in the reconfiguration of thylakoid electron transport in response to high light and low oxygen.
    Keywords aerobic conditions ; ammonium chloride ; chlorophyll ; D1 protein ; electron transfer ; fluorescence ; gene expression regulation ; genes ; oxygen ; photoinhibition ; photosystem II ; stress response ; Synechocystis ; thylakoids ; transcription (genetics)
    Language English
    Dates of publication 2016-08
    Size p. 1715-1726.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 391893-2
    ISSN 1365-3040 ; 0140-7791
    ISSN (online) 1365-3040
    ISSN 0140-7791
    DOI 10.1111/pce.12738
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  7. Article ; Online: Water tracking in surface water, groundwater and soils using free and alginate-chitosan encapsulated synthetic DNA tracers.

    Pang, Liping / Abeysekera, Gayan / Hanning, Kyrin / Premaratne, Aruni / Robson, Beth / Abraham, Phillip / Sutton, Richard / Hanson, Carl / Hadfield, John / Heiligenthal, Laura / Stone, Dana / McBeth, Kurt / Billington, Craig

    Water research

    2020  Volume 184, Page(s) 116192

    Abstract: Investigating contamination pathways and hydraulic connections in complex hydrological systems will benefit greatly from multi-tracer approaches. The use of non-toxic synthetic DNA tracers is promising, because unlimited numbers of tracers, each with a ... ...

    Abstract Investigating contamination pathways and hydraulic connections in complex hydrological systems will benefit greatly from multi-tracer approaches. The use of non-toxic synthetic DNA tracers is promising, because unlimited numbers of tracers, each with a unique DNA identifier, could be used concurrently and detected at extremely low concentrations. This study aimed to develop multiple synthetic DNA tracers as free molecules and encapsulated within microparticles of biocompatible and biodegradable alginate and chitosan, and to validate their field utility in different systems. Experiments encompassing a wide range of conditions and flow rates (19 cm/day-39 km/day) were conducted in a stream, an alluvial gravel aquifer, a fine coastal sand aquifer, and in lysimeters containing undisturbed silt loam over gravels. The DNA tracers were identifiable in all field conditions investigated, and they were directly detectable in the stream at a distance of at least 1 km. The DNA tracers showed promise at tracking fast-flowing water in the stream, gravel aquifer and permeable soils, but were unsatisfactory at tracking slow-moving groundwater in the fine sand aquifer. In the surface water experiments, the microencapsulated DNA tracers' concentrations and mass recoveries were 1-3 orders of magnitude greater than those of the free DNA tracers, because encapsulation protected them from environmental stressors and they were more negatively charged. The opposite was observed in the gravel aquifer, probably due to microparticle filtration by the aquifer media. Although these new DNA tracers showed promise in proof-of-concept field validations, further work is needed before they can be used for large-scale investigations.
    MeSH term(s) Alginates ; Chitosan ; DNA ; Environmental Monitoring ; Groundwater ; Soil ; Water ; Water Pollutants, Chemical/analysis
    Chemical Substances Alginates ; Soil ; Water Pollutants, Chemical ; Water (059QF0KO0R) ; DNA (9007-49-2) ; Chitosan (9012-76-4)
    Language English
    Publishing date 2020-07-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 202613-2
    ISSN 1879-2448 ; 0043-1354
    ISSN (online) 1879-2448
    ISSN 0043-1354
    DOI 10.1016/j.watres.2020.116192
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