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228 results on '"Hodgman, Charlie"'

14. Tackling Drought Stress: RECEPTOR-LIKE KINASES Present New Approaches

Author

Marshall, Alex, Aalen, Reidunn B., Audenaert, Dominique, Beeckman, Tom, Broadley, Martin R., Butenko, Melinka A., Caño-Delgado, Ana I., de Vries, Sacco, Dresselhaus, Thomas, Felix, Georg, Graham, Neil S., Foulkes, John, Granier, Christine, Greb, Thomas, Grossniklaus, Ueli, Hammond, John P., Heidstra, Renze, Hodgman, Charlie, Hothorn, Michael, Inzé, Dirk, Østergaard, Lars, Russinova, Eugenia, Simon, Rüdiger, Skirycz, Aleksandra, Stahl, Yvonne, Zipfel, Cyril, and De Smet, Ive

Published
2012

16. Unraveling the Evolution of Auxin Signaling

Author

De Smet, Ive, Voβ, Ute, Lau, Steffen, Wilson, Michael, Shao, Ning, Timme, Ruth E., Swarup, Ranjan, Kerr, Ian, Hodgman, Charlie, Bock, Ralph, Bennett, Malcolm, Jürgens, Gerd, and Beeckman, Tom

Published
2011

21. A genome-scale model of Clostridium autoethanogenum reveals optimal bioprocess conditions for high-value chemical production from carbon monoxide

Author

Norman, Rupert, Millat, Thomas, Schatschneider, Sarah, Henstra, Anne, Breitkopf, Ronja, Pander, Bart, Annan, Florence, Piatek, Pawel, Hartman, Hassan, Poolman, Mark, Fell, David, Winzer, Klaus, Minton, Nigel, and Hodgman, Charlie

Abstract

Clostridium autoethanogenum is an industrial microbe used for the commercial-scale production of ethanol from carbon monoxide. While significant progress has been made in the attempted diversification of this bioprocess, further improvements are desirable, particularly in the formation of the high-value platform chemicals, such as 2,3-butanediol. A new, experimentally parameterised genome scale model of C. autoethanogenum predicts dramatically increased 2,3-butanediol production under non-carbon-limited conditions when thermodynamic constraints on hydrogen production are considered.

Published
2019

23. Genome‐scale model of C. autoethanogenum reveals optimal bioprocess conditions for high‐value chemical production from carbon monoxide

Author

Norman, Rupert O.J., primary, Millat, Thomas, additional, Schatschneider, Sarah, additional, Henstra, Anne M., additional, Breitkopf, Ronja, additional, Pander, Bart, additional, Annan, Florence J., additional, Piatek, Pawel, additional, Hartman, Hassan B., additional, Poolman, Mark G., additional, Fell, David A., additional, Winzer, Klaus, additional, Minton, Nigel P., additional, and Hodgman, Charlie, additional

Published
2019
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25. Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis

Author

Hodgman Charlie, Taubert Jan, Hassani-Pak Keywan, Defoin-Platel Michael, Lysenko Artem, Rawlings Christopher J, and Saqi Mansoor

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Combining multiple evidence-types from different information sources has the potential to reveal new relationships in biological systems. The integrated information can be represented as a relationship network, and clustering the network can suggest possible functional modules. The value of such modules for gaining insight into the underlying biological processes depends on their functional coherence. The challenges that we wish to address are to define and quantify the functional coherence of modules in relationship networks, so that they can be used to infer function of as yet unannotated proteins, to discover previously unknown roles of proteins in diseases as well as for better understanding of the regulation and interrelationship between different elements of complex biological systems. Results We have defined the functional coherence of modules with respect to the Gene Ontology (GO) by considering two complementary aspects: (i) the fragmentation of the GO functional categories into the different modules and (ii) the most representative functions of the modules. We have proposed a set of metrics to evaluate these two aspects and demonstrated their utility in Arabidopsis thaliana. We selected 2355 proteins for which experimentally established protein-protein interaction (PPI) data were available. From these we have constructed five relationship networks, four based on single types of data: PPI, co-expression, co-occurrence of protein names in scientific literature abstracts and sequence similarity and a fifth one combining these four evidence types. The ability of these networks to suggest biologically meaningful grouping of proteins was explored by applying Markov clustering and then by measuring the functional coherence of the clusters. Conclusions Relationship networks integrating multiple evidence-types are biologically informative and allow more proteins to be assigned to a putative functional module. Using additional evidence types concentrates the functional annotations in a smaller number of modules without unduly compromising their consistency. These results indicate that integration of more data sources improves the ability to uncover functional association between proteins, both by allowing more proteins to be linked and producing a network where modular structure more closely reflects the hierarchy in the gene ontology.

Published
2011
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26. Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate

Author

Giri, Jitender, Bhosale, Rahul, Huang, Guoqiang, Pandey, Bipin K., Parker, Hélène, Zappala, Susan, Yang, Jin, Diévart, Anne, Bureau, Charlotte, Ljung, Karin, Price, Adam H., Rose, Terry, Larrieu, Antoine, Mairhofer, Stefan, Sturrock, Craig, White, Philip, Dupuy, Lionel, Hawkesford, Malcolm, Périn, Christophe, Liang, Wanqi, Péret, Benjamin, Hodgman, Charlie T., Lynch, Jonathan P., Wissuwa, Mathieu, Zhang, Dabing, Pridmore, Tony P., Mooney, Sacha J., Guiderdoni, Emmanuel, Swarup, Ranjan, Bennett, Malcolm J., Giri, Jitender, Bhosale, Rahul, Huang, Guoqiang, Pandey, Bipin K., Parker, Hélène, Zappala, Susan, Yang, Jin, Diévart, Anne, Bureau, Charlotte, Ljung, Karin, Price, Adam H., Rose, Terry, Larrieu, Antoine, Mairhofer, Stefan, Sturrock, Craig, White, Philip, Dupuy, Lionel, Hawkesford, Malcolm, Périn, Christophe, Liang, Wanqi, Péret, Benjamin, Hodgman, Charlie T., Lynch, Jonathan P., Wissuwa, Mathieu, Zhang, Dabing, Pridmore, Tony P., Mooney, Sacha J., Guiderdoni, Emmanuel, Swarup, Ranjan, and Bennett, Malcolm J.

Abstract

Root traits such as root angle and hair length influence resource acquisition particularly for immobile nutrients like phosphorus (P). Here, we attempted to modify root angle in rice by disrupting the OsAUX1 auxin influx transporter gene in an effort to improve rice P acquisition efficiency. We show by X-ray microCT imaging that root angle is altered in the osaux1 mutant, causing preferential foraging in the top soil where P normally accumulates, yet surprisingly, P acquisition efficiency does not improve. Through closer investigation, we reveal that OsAUX1 also promotes root hair elongation in response to P limitation. Reporter studies reveal that auxin response increases in the root hair zone in low P environments. We demonstrate that OsAUX1 functions to mobilize auxin from the root apex to the differentiation zone where this signal promotes hair elongation when roots encounter low external P. We conclude that auxin and OsAUX1 play key roles in promoting root foraging for P in rice.

Published
2018

30. Author Correction: Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate

Author

Giri, Jitender, primary, Bhosale, Rahul, additional, Huang, Guoqiang, additional, Pandey, Bipin K., additional, Parker, Helen, additional, Zappala, Susan, additional, Yang, Jing, additional, Dievart, Anne, additional, Bureau, Charlotte, additional, Ljung, Karin, additional, Price, Adam, additional, Rose, Terry, additional, Larrieu, Antoine, additional, Mairhofer, Stefan, additional, Sturrock, Craig J., additional, White, Philip, additional, Dupuy, Lionel, additional, Hawkesford, Malcolm, additional, Perin, Christophe, additional, Liang, Wanqi, additional, Peret, Benjamin, additional, Hodgman, Charlie T., additional, Lynch, Jonathan, additional, Wissuwa, Matthias, additional, Zhang, Dabing, additional, Pridmore, Tony, additional, Mooney, Sacha J., additional, Guiderdoni, Emmanuel, additional, Swarup, Ranjan, additional, and Bennett, Malcolm J., additional

Published
2018
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32. Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate

Author

Giri, Jitender, primary, Bhosale, Rahul, additional, Huang, Guoqiang, additional, Pandey, Bipin K., additional, Parker, Helen, additional, Zappala, Susan, additional, Yang, Jing, additional, Dievart, Anne, additional, Bureau, Charlotte, additional, Ljung, Karin, additional, Price, Adam, additional, Rose, Terry, additional, Larrieu, Antoine, additional, Mairhofer, Stefan, additional, Sturrock, Craig J., additional, White, Philip, additional, Dupuy, Lionel, additional, Hawkesford, Malcolm, additional, Perin, Christophe, additional, Liang, Wanqi, additional, Peret, Benjamin, additional, Hodgman, Charlie T., additional, Lynch, Jonathan, additional, Wissuwa, Matthias, additional, Zhang, Dabing, additional, Pridmore, Tony, additional, Mooney, Sacha J., additional, Guiderdoni, Emmanuel, additional, Swarup, Ranjan, additional, and Bennett, Malcolm J., additional

Published
2018
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34. Occurrence of a quadruplex motif in a unique insert within exon C of the bovine estrogen receptor [alpha] gene (ESR1)

Author

Derecka, Kamila, Balkwill, Graham D., Garner, Thomas P., Hodgman, Charlie, Flint, Anthony P.F., and Searle, Mark S.

Subjects
Exon (Molecular genetics) -- Analysis, G proteins -- Structure, G proteins -- Chemical properties, Single nucleotide polymorphisms -- Analysis, Estrogen -- Receptors, Estrogen -- Research, Biological sciences, Chemistry
Abstract

Biophysical studies have shown that the 22 base insert has led to the formation of a family of stable G-quadruplex structures that are unaffected by the single nucleotide (G/A) polymorphism. Mutations that destabilize the quadruplex have led to a 15-fold enhancement of translational efficiency, which has shown that a biological role of the insert in exon C of the bovine estrogen receptor [alpha] gene (bov-ESR1) is to regulate translation of the exon.

Published
2010

36. Mitochondrial phosphoenolpyruvate carboxykinase (PEPCK-M) and serine biosynthetic pathway genes are co-ordinately increased during anabolic agent-induced skeletal muscle growth

Author

Brown, D.M., Williams, H., Ryan, K.J.P., Wilson, T.L., Daniel, Zoe, Mareko, M.H.D., Emes, Richard D., Harris, D.W., Jones, Sarah, Wattis, Jonathan A.D., Dryden, Ian L., Hodgman, Charlie, Brameld, John M., and Parr, Tim

Abstract

We aimed to identify novel molecular mechanisms for muscle growth during administration of anabolic agents. Growing pigs (Duroc/(Landrace/Large-White)) were administered Ractopamine (a beta-adrenergic agonist; BA; 20 ppm in feed) or Reporcin (recombinant growth hormone; GH; 10 mg/48 hours injected) and compared to a control cohort (feed only; no injections) over a 27-day time course (1, 3, 7, 13 or 27-days). Longissimus Dorsi muscle gene expression was analyzed using Agilent porcine transcriptome microarrays and clusters of genes displaying similar expression profiles were identified using a modified maSigPro clustering algorithm. Anabolic agents increased carcass (p = 0.002) and muscle weights (Vastus Lateralis: p < 0.001; Semitendinosus: p = 0.075). Skeletal muscle mRNA expression of serine/one-carbon/glycine biosynthesis pathway genes (Phgdh, Psat1 and Psph) and the gluconeogenic enzyme, phosphoenolpyruvate carboxykinase-M (Pck2/PEPCK-M), increased during treatment with BA, and to a lesser extent GH (p < 0.001, treatment x time interaction). Treatment with BA, but not GH, caused a 2-fold increase in phosphoglycerate dehydrogenase (PHGDH) protein expression at days 3 (p < 0.05) and 7 (p < 0.01), and a 2-fold increase in PEPCK-M protein expression at day 7 (p < 0.01). BA treated pigs exhibit a profound increase in expression of PHGDH and PEPCK-M in skeletal muscle, implicating a role for biosynthetic metabolic pathways in muscle growth.

Published
2016

37. Repression of translation of human estrogen receptor [alpha] by G-quadruplex formation

Author

Balkwill, Graham D., Derecka, Kamila, Garner, Thomas P., Hodgman, Charlie, Flint, Anthony P. F., and Searle, Mark S.

Subjects
Circular dichroism -- Usage, Nuclear magnetic resonance spectroscopy -- Usage, Genetic transcription -- Analysis, Nucleotide sequence -- Analysis, DNA -- Structure, DNA -- Chemical properties, Biological sciences, Chemistry
Abstract

Combination of circular dichroism, UV, and NMR spectroscopic studies are carried out to demonstrate a stable DNA G-quadruplex motif formed within the exon C gene sequence. The exon C G-quadruplex motif which is present in the 5'-untranslated region (5'-UTR) of the mRNA transcript are found to modulate the efficiency of translation.

Published
2009

41. A DEMETER-like DNA demethylase protein governs tomato fruit ripening

Author

Liu, Rui E., How-Kit, Alexandre, Stammitti, Linda, Teyssier, Emeline, Rolin, Dominique, Bertrand, Anne, Halle, Stefanie, Liu, Mingchun, Kong, Junhua, Wu, Chaoqun, Degraeve-Guibault, Charlotte, Chapman, Natalie, Maucourt, Mickael, Hodgman, Charlie, Tost, Jörg, Bouzayen, Mondher, Hong, Yiguo, Seymour, Graham B., Giovannoni, James, and Gallusci, Philippe

Subjects
fungi, food and beverages
Abstract

In plants, genomic DNA methylation which contributes to development and stress responses can be actively removed by DEMETER-like DNA demethylases (DML). Indeed, in Arabidopsis DMLs are important for maternal imprinting and endosperm demethylation, but only few studies demonstrate the developmental roles of active DNA demethylation conclusively in this plant. Here we show a direct cause and effect relationship between active DNA demethylation mainly mediated by the tomato DML, SlDML2, and fruit ripening; an important developmental process unique to plants. RNAi SlDML2 knock-down results in ripening inhibition via hypermethylation and repression of the expression of genes encoding ripening transcription factors and rate-limiting enzymes of key biochemical processes such as carotenoid synthesis. Our data demonstrate that active DNA demethylation is central to the control of ripening in tomato

Published
2015

42. Additional file 4: of Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

Author

Humphreys, Christopher, McLean, Samantha, Schatschneider, Sarah, Millat, Thomas, Henstra, Anne, Annan, Florence, Breitkopf, Ronja, Pander, Bart, Piatek, Pawel, Rowe, Peter, Wichlacz, Alexander, Woods, Craig, Norman, Rupert, Blom, Jochen, Goesman, Alexander, Hodgman, Charlie, Barrett, David, Thomas, Neil, Winzer, Klaus, and Minton, Nigel

Abstract

Illumina mapping summary report. (DOCX 84 kb)

Published
2015
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43. Additional file 5: of Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

Author

Humphreys, Christopher, McLean, Samantha, Schatschneider, Sarah, Millat, Thomas, Henstra, Anne, Annan, Florence, Breitkopf, Ronja, Pander, Bart, Piatek, Pawel, Rowe, Peter, Wichlacz, Alexander, Woods, Craig, Norman, Rupert, Blom, Jochen, Goesman, Alexander, Hodgman, Charlie, Barrett, David, Thomas, Neil, Winzer, Klaus, and Minton, Nigel

Abstract

List of primers used in this study. A list of a forward and reverse primers used in this study for verification of whole genome sequencing. (DOCX 17 kb)

Published
2015
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44. Additional file 1: of Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

Author

Humphreys, Christopher, McLean, Samantha, Schatschneider, Sarah, Millat, Thomas, Henstra, Anne, Annan, Florence, Breitkopf, Ronja, Pander, Bart, Piatek, Pawel, Rowe, Peter, Wichlacz, Alexander, Woods, Craig, Norman, Rupert, Blom, Jochen, Goesman, Alexander, Hodgman, Charlie, Barrett, David, Thomas, Neil, Winzer, Klaus, and Minton, Nigel

Abstract

Discrepancies occurring between the current and Brown et al. finished genome sequence of C. autoethanogenum. This table shows all of the discrepancies that occur when our finished genome sequence (CLAU) is mapped against the Brown et al. finished genome sequence (BRO). Mutation column describes the mutation occurring in the CLAU genome compared to the BRO genome. Gene / region gives the gene name where the discrepancy occurs, â / â or similar denotes that the discrepancy occurred in a non-coding region between the named genes. Homopolymer length indicates the number of the same base occurring consecutively at the site of the discrepancy. Amino acid length gives the annotated protein length of the gene in which the discrepancy occurs, *indicates protein codes for multiple stop codons and ^indicates that no stop codon was found in the annotation. The sequence identity is relative to the CLAU C. autoethanogenum genome sequence when protein BLAST searched on the NCBI database. CLAU, C. autoethanogenum finished genome sequence in present study; CLJU, C. ljungdahlii DSM 13528 finished genome sequence (GCA_000143685.1); BRO, Brown et al. C. autoethanogenum finished genome sequence (GCA_000484505.1); CAUT, Bruno-Barcena et al. C. autoethanogenum draft genome sequence (GCA_000427255.1); NF, not found. (DOCX 73 kb)

Published
2015
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45. Additional file 2: of Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

Author

Humphreys, Christopher, McLean, Samantha, Schatschneider, Sarah, Millat, Thomas, Henstra, Anne, Annan, Florence, Breitkopf, Ronja, Pander, Bart, Piatek, Pawel, Rowe, Peter, Wichlacz, Alexander, Woods, Craig, Norman, Rupert, Blom, Jochen, Goesman, Alexander, Hodgman, Charlie, Barrett, David, Thomas, Neil, Winzer, Klaus, and Minton, Nigel

Subjects
genetic processes, information science, natural sciences, eye diseases
Abstract

Sanger sequencing of selected discrepancies between the current and Brown et al. sequences. Table showing the region around the discrepancies between our finished genome sequence, confirmed by Sanger sequencing, and the Brown et al. finished genome sequence. (DOCX 23 kb)

Published
2015
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47. Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

Author

Humphreys, Christopher M., primary, McLean, Samantha, additional, Schatschneider, Sarah, additional, Millat, Thomas, additional, Henstra, Anne M., additional, Annan, Florence J., additional, Breitkopf, Ronja, additional, Pander, Bart, additional, Piatek, Pawel, additional, Rowe, Peter, additional, Wichlacz, Alexander T., additional, Woods, Craig, additional, Norman, Rupert, additional, Blom, Jochen, additional, Goesman, Alexander, additional, Hodgman, Charlie, additional, Barrett, David, additional, Thomas, Neil R., additional, Winzer, Klaus, additional, and Minton, Nigel P., additional

Published
2015
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48. Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate.

Author

Bhosale, Rahul, Parker, Helen, Zappala, Susan, Larrieu, Antoine, Sturrock, Craig J., Peret, Benjamin, Hodgman, Charlie T., Mooney, Sacha J., Swarup, Ranjan, Bennett, Malcolm J., Lynch, Jonathan, Giri, Jitender, Pandey, Bipin K., Guoqiang Huang, Jing Yang, Wanqi Liang, Mairhofer, Stefan, Pridmore, Tony, White, Philip, and Dupuy, Lionel

Subjects
RICE, AUXIN, PHOSPHATES, PHOSPHORUS, X-ray microscopy
Abstract

Root traits such as root angle and hair length influence resource acquisition particularly for immobile nutrients like phosphorus (P). Here, we attempted to modify root angle in rice by disrupting the OsAUX1 auxin influx transporter gene in an effort to improve rice P acquisition efficiency. We show by X-ray microCT imaging that root angle is altered in the osaux1 mutant, causing preferential foraging in the top soil where P normally accumulates, yet surprisingly, P acquisition efficiency does not improve. Through closer investigation, we reveal that OsAUX1 also promotes root hair elongation in response to P limitation. Reporter studies reveal that auxin response increases in the root hair zone in low P environments. We demonstrate that OsAUX1 functions to mobilize auxin from the root apex to the differentiation zone where this signal promotes hair elongation when roots encounter low external P. We conclude that auxin and OsAUX1 play key roles in promoting root foraging for P in rice. [ABSTRACT FROM AUTHOR]

Published
2018
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