Dr Carlos Rodriguez Lopez
I lead a laboratory group (Environmental Epigenetics and Genetics Group (EEGG)) based in the Plant Research Building at the Waite Campus.
Awards and Achievements
| Date | Type | Title | Institution Name | Amount |
|---|---|---|---|---|
| 2017 | Invitation | Co-chair of the Environmental Epigenomics session at Combio 2017 | Combio | |
| 2017 | Invitation | Invited speaker Science in the Pub Adelaide | Science in the Pub Adelaide | Free Beer |
| 2017 | Invitation | Invited speaker Centre for Integrative Ecology | Deakin University | Travel and accommodation fully funded |
| 2017 | Invitation | Invited Speaker Adelaide RNA Special Interest Group & EpiCSA Monthly Seminar Series | ||
| 2015 | Research Award | Jerome P. Miksche Young Plant Investigator Grant Award | Plant and Animal Genome XXIV | USD1500 |
| 2015 | Research Award | Aquaculture Species Group Student and Postdoctoral Fellowship Bursaries | PAG XXIV | USD1000 |
Education
| Date | Institution name | Country | Title |
|---|---|---|---|
| Universidad de La Laguna | Spain | BSc |
Postgraduate Training
| Date | Title | Institution | Country |
|---|---|---|---|
| PhD in molecular biology | University of Reading, Reading | United Kingdom | |
| MSc Plant Biotechnology | University of Reading, Reading | United Kingdom |
Journals
| Year | Citation |
|---|---|
| 2017 | Fabres, P., Collins, C., Cavagnaro, T. & López, C. (2017). A concise review on multi-omics data integration for terroir analysis in vitis vinifera. Frontiers in Plant Science, 8, -. 10.3389/fpls.2017.01065 |
| 2017 | Rodriguez Lopez, C. M., konate, M. & thomson, V. (2017). MSAP In Tiger Snakes: Island Populations Are Epigenetically More Divergent. BioRxiv, -. 10.1101/118836 |
| 2017 | Xie, H., Konate, M., Sai, N., Gebremicael Tesfamicael, K., Cavagnaro, T., Gilliham, M. ... Rodriguez Lopez, C. M. (2017). Environmental Conditions And Agronomic Practices Induce Consistent Global Changes In DNA Methylation Patterns In Grapevine (Vitis vinifera cv Shiraz). BioRxiv, -. 10.1101/127977 |
| 2017 | Grigg, D., Methven, D., De Bei, R., Rodriguez Lopez, C. M., Dry, P. & Collins, C. (2017). Vine age effects on vine performance of Shiraz in the Barossa Valley, Australia. Australian Journal of Grape and Wine Research, -. |
| 2016 | Rodriguez Lopez, C. M. (2016). Protected areas of Spain preserve the neutral genetic diversity of Quercus ilex L. irrespective of glacial refugia. Tree Genetics & Genomes, -. |
| 2016 | Breen, J., Mur, L. A., Sivakumaran, A., Akinyemi, A., Wilkinson, M. & Rodriguez Lopez, C. M. (2016). Botrytis cinerea loss and restoration of virulence during in vitro culture follows flux in global DNA methylation. BioRXiv, OnlinePubl, 1-49. 10.1101/059477 |
| 2016 | Consuegra, S. & Rodríguez López, C. (2016). Epigenetic-induced alterations in sex-ratios in response to climate change: An epigenetic trap?. BioEssays, 38, 10, 950-958. 10.1002/bies.201600058 |
| 2016 | Bianco-Miotto, T., Mayne, B., Buckberry, S., Breen, J., Rodriguez Lopez, C. & Roberts, C. (2016). Recent progress towards understanding the role of DNA methylation in human placental development. Reproduction, 152, 1, 23-30. 10.1530/REP-16-0014 |
| 2016 | Adu-Gyamfi, R., Wetten, A. & Rodriguez Lopez, C. (2016). Effect of cryopreservation and post-cryopreservation somatic embryogenesis on the epigenetic fidelity of cocoa (Theobroma cacao L.). PLoS One, 11, 7, e0158857-1-e0158857-13. 10.1371/journal.pone.0158857 |
| 2015 | Kitimu, S., Taylor, J., March, T., Tairo, F., Wilkinson, M. & Rodriguez Lopez, C. (2015). Meristem micropropagation of cassava (Manihot esculenta) evokes genome-wide changes in DNA methylation. Frontiers in Plant Science, 6, Aug, 590-1-590-12. 10.3389/fpls.2015.00590 |
| 2015 | Rodriguez Lopez, C. & Wilkinson, M. (2015). Epi-fingerprinting and epi-interventions for improved crop production and food quality. Frontiers in Plant Science, 6, June, 397-1-397-14. 10.3389/fpls.2015.00397 |
| 2015 | Guzmán, B., Rodriguez Lopez, C., Forrest, A., Cano, E. & Vargas, P. (2015). Protected areas of Spain preserve the genetic diversity of Quercus ilex L. irrespective of glacial refugia. Tree Genetics and Genomes, 11, 124, -. 10.1007/s11295-015-0950-2 |
| 2015 | Ellison, A., Rodriguez Lopez, C., Moran, P., Breen, J., Swain, M., Megias, M. ... Consuegra, S. (2015). Epigenetic regulation of sex-ratios may explain natural variation in self-fertilization rates. Proceedings of the Royal Society of London. Series B, 282, 1819, 1-9. 10.1098/rspb.2015.1900 |
| 2013 | Tricker, P., Rodriguez Lopez, C., Hadley, P., Wagstaff, C. & Wilkinson, M. (2013). Pre-conditioning the epigenetic response to high vapor pressure deficit increases the drought tolerance of Arabidopsis thaliana. Plant Signaling & Behavior, 8, 10, e25974-1-e25974-3. 10.4161/psb.25974 |
| 2013 | Rois, A., Rodriguez Lopez, C., Cortinhas, A., Erben, M., Espirito-Santo, D., Wilkinson, M. & Caperta, A. (2013). Epigenetic rather than genetic factors may explain phenotypic divergence between coastal populations of diploid and tetraploid Limonium spp. (Plumbaginaceae) in Portugal. BMC Plant Biology, 13, 1, 1-16. 10.1186/1471-2229-13-205 |
| 2013 | Tricker, P., Rodriguez Lopez, C., Gibbings, J., Hadley, P. & Wilkinson, M. (2013). Transgenerational, dynamic methylation of stomata genes in response to low relative humidity. International Journal of Molecular Sciences, 14, 4, 6674-6689. 10.3390/ijms14046674 |
| 2012 | Rodriguez Lopez, C., Lloyd, A. J., Leonard, K. & Wilkinson, M. J. (2012). Differential effect of three base modifications on DNA thermostability revealed by high resolution melting. Analytical Chemistry, 84, 17, 7336-7342. 10.1021/ac301459x |
| 2012 | Amoah, S., Kurup, S., Rodriguez Lopez, C., Welham, S., Powers, S., Hopkins, C. ... King, G. (2012). A Hypomethylated population of Brassica rapa for forward and reverse Epi-genetics. BMC Plant Biology, 12, 193, 1-17. 10.1186/1471-2229-12-193 |
| 2012 | Rodríguez López, C. M., Morán, P., Lago, F., Espiñeira, M., Beckmann, M. & Consuegra, S. (2012). Detection and quantification of tissue of origin in salmon and veal products using methylation sensitive AFLPs. Food Chemistry, 131, 4, 1493-1498. 10.1016/j.foodchem.2011.09.120 |
| 2012 | Tricker, P., Gibbings, J., Rodriguez Lopez, C., Hadley, P. & Wilkinson, M. (2012). Low relative humidity triggers RNA-directed de novo DNA methylation and suppression of genes controlling stomatal development. Journal of Experimental Botany, 63, 10, 3799-3814. 10.1093/jxb/ers076 |
| 2011 | Geyer, K., Rodriguez Lopez, C., Chalmers, I., Munshi, S., Truscott, M., Heald, J. ... Hoffmann, K. (2011). Cytosine methylation regulates oviposition in the pathogenic blood fluke Schistosoma mansoni. Nature Communications, 2, article 424, 1-10. 10.1038/ncomms1433 |
| 2010 | Rodriguez Lopez, C., Asenjo, B., Lloyd, A. & Wilkinson, M. (2010). Direct Detection and Quantification of Methylation in Nucleic Acid Sequences using High-Resolution Melting Analysis. Analytical Chemistry, 82, 21, 9100-9108. 10.1021/ac1024057 |
| 2010 | rodriguez lopez, C., Bravo, H. S., Wetten, A. C. & Wilkinson, M. J. (2010). Detection of somaclonal variation during cocoa somatic embryogenesis characterised using cleaved amplified polymorphic sequence and the new freeware Artbio. Molecular Breeding, 25, 3, 501-516. 10.1007/s11032-009-9348-x |
| 2010 | Rodriguez Lopez, C., Wetten, A. & Wilkinson, M. (2010). Progressive erosion of genetic and epigenetic variation in callus-derived cocoa (Theobroma cacao) plants. New Phytologist, 186, 4, 856-868. 10.1111/j.1469-8137.2010.03242.x |
| 2009 | Wetten, A., Adu-Gyamfi, R., Fang, J. -. Y. & Rodriguez-Lopez, C. (2009). CRYOPRESERVATION OF COCOA (THEOBROMA CACAO L.) SOMATIC EMBRYOS - IS SOMACLONAL VARIATION AN ISSUE?. CRYOLETTERS, 30, 1, 84-85. |
| 2009 | Fang, J., Wetten, A., Adu-Gyamfi, R., Wilkinson, M. & Rodriguez Lopez, C. (2009). Use of secondary somatic embryos promotes genetic fidelity in cryopreservation of cocoa (Theobroma cacao L.). Agricultural and Food Science, 18, 2, 152-159. 10.2137/145960609789267579 |
| 2008 | Lopez, C. M. R., Croxford, A. E. & Wilkinson, M. J. (2008). High-resolution melt analysis for SNP discovery, linkage mapping and analysis of DNA methylation. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY, 150, 3, S49-S50. 10.1016/j.cbpa.2008.04.035 |
| 2007 | Fang, J. -. Y., Rodriguez Lopez, C. M. & Wetten, A. (2007). Screening for genetic fidelity of cocoa (theobroma cacao l.) somatic embryos following cryopreservation. Cryobiology, -. |
| 2004 | Rodríguez López, C., Wetten, A. & Wilkinson, M. (2004). Detection and quantification of in vitro-culture induced chimerism using simple sequence repeat (SSR) analysis in Theobroma cacao (L.). Theoretical and Applied Genetics, 110, 1, 157-166. 10.1007/s00122-004-1823-5 |
| 2002 | Rodriguez Lopez, C. M., Wetten, A. C. & Wilkinson, M. J. (2002). Assessment of somaclonal variation in somatic embryo-derived cocoa (Theobroma cacao). In Vitro Cellular and Developmental Biology: Animal, 38, Abstract, 126.A-. |
| 2001 | ALBANI, M., Rodriguez Lopez, C. M., Taylor, S., CEKIC, C., AL-SHEIKH, M., GREENLAND, A. ... Battey, N. (2001). Fragaria vesca.... One way to understand flowering in perennials. Flowering Newsletters, -. |
Book Chapters
| Year | Citation |
|---|---|
| 2012 | Escamilla, J. -. M., Rodriguez Lopez, C. M., Bäuerl, C., Pekkala, S. P., Navarro, S. & Barettino, D. (2012). Retinoic-Acid-induced downregulation of the expression of the 67 KDa Laminin Receptor correlates with reduced biological aggressiveness of human neuroblastoma cells. In H. Shimada (Ed.), Neuroblastoma- Present and Future (pp. 217-232). Intech. |
Conference Papers
| Year | Citation |
|---|---|
| 2015 | Bianco-Miotto, T., Lopez, C. R., Leemaqz, S., Buckberry, S., McCullough, D., Zhuang, Z. ... Roberts, C. (2015). DNA METHYLATION BIOMARKERS FOR PREDICTING PREGNANCY COMPLICATIONS. 10.1016/j.placenta.2015.07.302 |
| 2015 | Rodriguez Lopez, C. M., Breen, J. M., De Bei, R., Searle, I., Davis, R. & Collins, C. (2015). We Prefer Them Old: Epigenetic Control of Wine Quality in Response to Grapevine Age. Plant and Animal Genome XXIII. San Diego, USA. |
| 2015 | Rodriguez Lopez, C., Ellison, A., Moran, P., Swain, M., Megias, M., Hegarty, M. ... Consuegra, S. (2015). Can Epigenetic Regulation of Sex-Ratios Explain Natural Variation in Self-Fertilization Rates?. Plant and Animal Genome XXIII. San Diego, USA. |
Conference Items
| Year | Citation |
|---|---|
| 2017 | Rodriguez Lopez, C. M. (2017). Multi-omics data integration approaches for genome by environment interactions analysis in Vitis Vinifera. International Plant & Animal Genome XXV. San Diego, USA. |
| 2017 | Rodriguez Lopez, C. M., Konate, M., Sanders, K. & Thomson, V. A. (2017). Epigenetic divergence contributes to tiger snake adaptation to island environments. ComBio 2017. Adelaide, SA. |
| 2017 | Rodriguez Lopez, C. M. (2017). Botrytis cinerea loss and restoration of virulence during in vitro culture follows flux in global DNA methylation. International Plant & Animal Genome XXV. San Diego, USA. |
| 2016 | Konate, M., Wilkinson, M. J., Scott, E., Mayne, B., Berger, B. & Rodriguez Lopez, C. M. (2016). Tissue specificity of salinity stress induced DNA methylation markers in barley (Hordeum vulgare). ComBio 2016. Brisbane. |
| 2016 | Rodriguez Lopez, C. M. (2016). Next generation sequencing (NGS) for the study of DNA methylation. Australian Genome Research Facility ltd-Special Interest Groups. Adelaide, SA, Australia. |
| 2015 | Bianco-Miotto, , Rodriguez Lopez, , Leemaqz, , Zhuang, Z., McCullough, , Dekker, ... Roberts, C. (2015). Predicting Pregnancy Complications from Maternal Buffy Coat DNA at 15 Weeks Gestation. Endocrine Society of Australia (ESA) and Society for Reproductive Biology (SRB) Annual Scientific Meeting. Adelaide, Australia. |
| 2015 | Rodriguez Lopez, C. M. (2015). GBS for methylome fingerprinting and epiallele discovery: A forward genetics and a diagnostic tool. SNPseq workshop. Adelaide. |
| 2014 | Zhuang, , Rodriguez Lopez, , Chiam, K., Harryanto, H., Ryan, N. K., Jindal, S. ... Bianco-Miotto, (2014). A high fat diet early in life and prostate cancer risk. The Australian Health and Medical Research Congress. Melbourne, Australia. |
| 2010 | Tricker, P. J., Gibbings, J. G., Rodriguez Lopez, C. M., Hadley, P. & Wilkinson, M. J. (2010). An Inherited Epigenetic Response to Environmental Stress in Arabidopsis. Symposium on Biological Complexity: EMERGING CONCEPTS and TRENDS. |
| 2010 | Rodriguez Lopez, C. M., Brukhin, V., Croxford, A., Meade, A., Hadley, P. & Wilkinson, M. J. (2010). From Arabidopsis to Theobroma: Transferring Epigenetic Information from Model Organisms to Non-model Crops?. Symposium on Biological Complexity: EMERGING CONCEPTS and TRENDS. Salk Institute, La Jolla, California, USA. |
| 2005 | Rodriguez Lopez, C. M., Pekkala, S. P., Bauerle, C. & Barettino, D. (2005). Retinoic-Acid reduces the expression of the 67 KDa Laminin Receptor in human neuroblastoma cells.. XXVIII Congress of the Spanish Society of Biochemistry and Molecular Biology. Zaragoza, Spain. |
Patents
| Year | Citation |
|---|---|
| 2015 | Wilkinson, M. & Rodriguez Lopez, C.; (2015); Methods for Selecting Methylation Markers; |
| 2011 | Tricker, P. J., Rodriguez Lopez, C. M., Wilkinson, M. J. & Hadley, P.; (2011); Method for producing a stress tolerant plant or precursor thereof; |
| 2008 | Rodriguez Lopez, C. M. & Wilkinson, M. J.; (2008); Detection of Methylation in Nucleic Acid Sequences; |
Datasets
| Year | Citation |
|---|---|
| 2017 | Breen, J. & Rodriguez Lopez, C. M.; (2017); Virulent/avirulent Botrytis cinerea whole genome/methylome sequence; |
| 2017 | Xie, H., DeBei, R., Metcalfe, A., Cavaganaro, T., Collins, C., Gilliham, M. ... Rodriguez Lopez, C. M.; (2017); msGBS Barossa Shiraz dataset 1; |
| 2014 | Guzman, B., Rodriguez Lopez, C. M., Forrest, A., Cano, E. & Vargas, P.; (2014); Protected areas of Spain preserve the genetic diversity of Quercus ilex L. irrespective of glacial refugia; |
Software
| Year | Citation |
|---|---|
| 2017 | Sai, N., Rodriguez Lopez, C. M., Bogias, K., Pederson, S., Burgess, A., Breen, J. ... David, R.; (2017); Bioinformatic pipeline to detect di-cistronic RNA transcripts from RNA-sequencing data; |
| 2016 | Mayne, B., Leemaqz, S., Buckberry, S., rodriguez lopez, C. M., roberts, C., bianco-miotto, T. & Breen, J.; (2016); msgbsR: an R package for analysing methylation sensitive genotyping by sequencing data; |
| 2004 | Rodriguez Lopez, C. M. & SICILIA BRAVO, H.; (2004); ArtBio; |
1. ARC, Training Centre for Innovative Wine Production, IC170100008, 2017-2022, $4.5M, CI, led by Prof Vladimir Jiranek
2. Genomics of Barossa Shiraz Terroir, June 2017. ($25K), CI, led by A. Prof. Cassandra Collins. Australian Grape and Wine Authority/Australian Genomics Research Facility/School of Agriculture Food and Wine $15k/$5k/$5k.
3. Epi-breeding-Using the epigenetic memory of stress to prime Australian grapevines for a changing environment. Australian Grape and Wine Authority (AGWA). July 2016–June 2018. ($195k). CI.
4. Ecogenomics of Terroir. Australian Genome Research Facility ltd Pilot program in Genomics application ($50k). Co-CI with Collins.
5. Use of Epigenetic markers for early diagnosis of cancer. Foresight Health Pty Ltd. 2015. ($15k). Co-CI with Bianco-Miotto.
6. Epigenetics Research Platform. Waite Research Institute Research Capacity Development Funding 2015 ($74k). CI.
7. Breeding drought and heat tolerant grapevines using epigenetic tools. Australian Grape and Wine Authority (AGWA) Incubator Project call 2014. ($9,358). Co-CI with De Bei.
8. Epigenetic control of wine quality in response to grapevine age. Waite Research Institute grant 2013/14 ($15k)). Co-CI with Collins.
9. Demonstrating the potential of mobile RNAs for grafted epibreeding-a paradigm shift for plant and animal breeding. University of Adelaide Interdisciplinary Research Fund (IRF) 2013/14 grant ($32500). Searle (CI).
10. Diagnosing the response of Calendula officinalis to saline water irrigation. Jurlique Limited funded grant 2013/14 ($27k). PI Led by Prof Mike Wilkinson.
11. Detection of nucleotide modifications in nucleic acid sequence. Welsh Academic Expertise for Business Grant 2009/10 (HE 11 POC 1008 A4B) (£48k/$98k). Co-CI with Wilkinson.
12. The exploitation Of Variably Methylated Epigenetic Markers 'Sentinels' In Drug Discovery. BBSRC Pathfinder Grant 2010/11 (BB/FOF/PF/17/10) (£15k/$30k). Co-CI with Wilkinson.
Student scholarships: Since 2015 I have helped drafting 14 successful student scholarship/awards applications as principal or co-supervisor .
- PhD student Mr Pastor Jullian Fabres: 1) Adelaide Graduate Research Scholarship (Full international tuition fees plus a living allowance of AUD$26,682- Dec 2015), 2) Wine Australia PhD Scholarship ($41,136-Feb 2016), 3) WRI travel award ($300-Jun 2016), 4) Winter School in Mathematical and Computational Biology 2017 travel award ($300-Jun 2016).
- PhD student Miss Jia Zhou: 1) Adelaide Graduate Research Scholarship (Full international tuition fees plus a living allowance of AUD$26,682-Dec 2016), 2) WRI travel award ($300-Jun 2016) (As Master Student).
- Master Student Huahan Xie: WRI travel award ($300-Jun 2016).
- Honours student Mr Konstantinos Bogias: 1) AFW summer student scholarship (Dec 2016) ($1500), 2) AFW Honours Scholarship ($3000), 3) Winter School in Mathematical and Computational Biology 2017 travel award ($300), 4) Institute Molecular Bioscience (UQ) postgraduate student grant ($200) and 5) AR Riddle Grant scholarship ($600).
- Summer student Miss Na Sai(Dec 2016): 1) ARC Centre of Excellence for Plant Energy Biology summer student Scholarship ($3000). 2) WRI travel award ($300) (As Master Student (Jun 2016)).
My teaching time is dedicated to coordinating in the Master in Plant Biotechnology courses “Extended Research Project” and “Regulatory Approval of GM Plants”. I have also taught in the Bachelor of Applied Biology course “Research Skills for Applied Biology II”.
Student scholarships: Since 2015 I have helped drafting 14 successful student scholarship/awards applications as principal or co-supervisor .
- PhD student Mr Pastor Jullian Fabres: 1) Adelaide Graduate Research Scholarship (Full international tuition fees plus a living allowance of AUD$26,682- Dec 2015), 2) Wine Australia PhD Scholarship ($41,136-Feb 2016), 3) WRI travel award ($300-Jun 2016), 4) Winter School in Mathematical and Computational Biology 2017 travel award ($300-Jun 2016).
- PhD student Miss Jia Zhou: 1) Adelaide Graduate Research Scholarship (Full international tuition fees plus a living allowance of AUD$26,682-Dec 2016), 2) WRI travel award ($300-Jun 2016) (As Master Student).
- Master Student Huahan Xie: WRI travel award ($300-Jun 2016).
- Honours student Mr Konstantinos Bogias: 1) AFW summer student scholarship (Dec 2016) ($1500), 2) AFW Honours Scholarship ($3000), 3) Winter School in Mathematical and Computational Biology 2017 travel award ($300), 4) Institute Molecular Bioscience (UQ) postgraduate student grant ($200) and 5) AR Riddle Grant scholarship ($600).
- Summer student Miss Na Sai(Dec 2016): 1) ARC Centre of Excellence for Plant Energy Biology summer student Scholarship ($3000). 2) WRI travel award ($300) (As Master Student (Jun 2016)).
Committee Memberships
| Date | Role | Committee | Institution | Country |
|---|---|---|---|---|
| 2015 - ongoing | Co-Chair | Epigenetics Consortium of South Australia (EpiCSA) Inc | Australia |
Position
PDRA
Phone
83130779
Campus
Waite
Building
Plant Research Centre
Room Number
1 83
Org Unit
School of Agriculture, Food and Wine