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Jenkins lab

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Kaiserli Lab

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Research interests

Plants exhibit enormous plasticity, therefore they provide a great model for studying how cells and organisms respond and adapt to the constantly changing environment. Light is an environmental stimulus essential not only for energy production, but also for triggering a plethora of developmental and photoprotective responses.

‌‌The majority of light signalling components are constitutively localised or translocated into the nucleus and form subnuclear structures, also referred to as nuclear foci, photobodies or speckles to regulate gene expression, protein modification and DNA repair. Studies in animal systems indicate a direct correlation between the disruption of nuclear microdomains and the onset of heritable diseases, ageing and cancer. Any new findings in this area could have major applications in healthcare, agricultural sustainability and basic biosciences.

The focus of my research is to understand how environmental stimuli and genotoxic stress affect the organization of the plant nucleus, and how this translates into changes in cell elongation, division and differentiation. Identification and characterisation of novel components that bridge light signalling to protein stability, transcriptional regulation or DNA damage repair will provide better understanding of the role of photobody formation in plant growth, development and photoprotection.

‌

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Plants exhibit enormous plasticity, therefore they provide a great model for studying how cells and organisms respond and adapt to the constantly changing environment. Light is an environmental stimulus essential not only for energy production, but also for triggering a plethora of developmental and photoprotective responses.

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Carrer de la Vall Moronta, 08193 Cerdanyola del Vallès, Barcelona, España

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Universitat Autònoma de Barcelona (UAB), Dept. of Biochemistry and Molecular Biology

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Universitat Autònoma de Barcelona (UAB), Dept. of Biochemistry and Molecular Biology

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Jordi Moreno-Romero, PhD
Searching for the epigenetic mechanisms that regulate plant response to light with special interest on plant proximity.
Focused on histone code and particularly on Polycomb activity.

Former member of Jaume Martínez-García Lab at CRAG and IBMCP (CSIC-UPV).

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Research Link, Temasek Life Sciences Laboratory Limited, Singapore

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Research Link, Temasek Life Sciences Laboratory Limited, Singapore

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Research Link, Temasek Life Sciences Laboratory Limited, Singapore

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Radix - Wageningen campus, Droevendaalsesteeg, Wageningen

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The WUR Times (Timing of Environmental Signaling) lab

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Our world is dynamic! We live in a world that spins around its axis with a period close to 24 h. This has created rhytmic changes in the environment, such as the day-night cycle, or changes in temperature, humidity, UV light. This in turn has shaped the evolution of most organisms that live on earth, which have evolved an internal time-keeping mechanism to help them predict these changes: the circadian clock.

My current research interests. Plants have inherent plasticity. Their general body plan is genetically encoded, but plant architecture can be modified to adjust to the environment that surrounds it. In this sense, environmental signals have a profound effect on plant growth and development, ultimately affecting a plant's fitness, disease resistance and productivity. An important feature of this process is the "gating" of signals through the plant's internal clock, which results in the rhythmical inhibition of the activity of environmental inputs to ensure proper temporal coordination of regulatory processes. Besides its obvious relevance for crop improvement, research into time-of-day dependent modulation of plant plasticity will advance understanding of this fundamental property that underlies the extraordinary evolutionary success of plants.

Brief Bio I am a circadian biologist that has ventured into photobiology and bioinformatics, now combining all to answer fundamental biological questions in plant sciences. I have strong background expertise in the molecular biology and physiology of circadian rhythms, photobiology, next-generation sequencing and bioinformatics analysis. During my PhD, I helped establish the first circadian Caenorhabditis elegans lab of Argentina and build a South American network of worm labs. As part of a neuroscience team (Golombek lab, Argentina), I pioneered the discovery of many circadian behaviours in this organism. After this, for my first postdoc, I devoted my research to understanding how environmental cues and endogenous rhythms could regulate alternative splicing (AS) events in plants, hence affecting their physiology (Yanovsky lab, Fundacion Instituto Leloir, Argentina). For this, I switched models and quickly transitioned into working with Arabidopsis thaliana. There, I performed the first circadian mRNAseq time-series of these plants and developed a powerful bioinformatics analysis pipeline to analyse circadian gene expression and AS events. I later moved to Scotland for my second postdoc (Halliday Lab, University of Edinburgh, UK) to gain insights into how light affects leaf development in A. thaliana. Currently, my research is focused on understanding how plants optimise their growth and development in response to a changing environment.

I also have a personal interest on promoting an equal and diverse research culture (EDI committee, SBS, UoE), and am a strong advocate for open science and making research data FAIR (BioRDM team, ReproducibiliTEA, EORC - SBS, UoE). Additionally, I am an Executive ECR Member of Edinburgh Plant Science, where we focus on building bridges between different Edinburgh plant science research nodes to connect research to society.

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GPlantS unit - Genomics of Plant Stress

https://www.itqb.unl.pt/labs/gplants

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Monroe Lab: Plant Genomics and Climate Adaptation

monroelab.org

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Anne-Sophie Fiorucci (Sébastien Thomine's lab, I2BC)
--> Adjusting nitrate fluxes in plant growth responses to shade or temperature

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Page equipe Thomine - Institute for Integrative Biology of the Cell

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We use electrophysiology and expression in heterologous systems to investigate the properties of ion transport systems at the molecular level. To integrate this molecular knowledge in a cellular framework, we are developing biosensors and microfluidics coupled to fluorescence microscopy. Molecular genetics and genomics allow us to further integrate the function of ion transport systems at organism and environmental levels.

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Universidade de São Paulo - Butanta, São Paulo - SP

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Universidade de São Paulo - Butanta, São Paulo - SP

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Universidade de São Paulo - Butanta, São Paulo - SP

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Michigan State University, Michigan, USA

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Michigan State University, Michigan, USA

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Michigan State University, Michigan, USA

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Farre Lab

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Our goal is to understand how circadian clocks work and why they play such an important role in growth and stress responses in photosynthetic organisms. We use a wide range of molecular, computational and physiological approaches to study how plants and unicellular algae adapt to daily environmental cycles.

Genevieve successfully defended her dissertation on April 26th. Congratulations!

Listen to Eva Farre, Miles Roberts and Kevin Folta discuss about circadian clocks: http://www.talkingbiotechpodcast.com/249-circadian-clocks/ - July 2020

Congratulations Genevieve for being awarded a predoctoral AFRI NIFA Fellowship! - June 2020

May 2020:

Congratulations Amni for your graduation !!

Our grant to investigate the circadian clock in potato has started:

See the announcement in MSU Today

April 2020: Publication updates

Farre EM (2020) The brown clock: circadian rhythms in stramenopiles. Physiologia Plantarum (doi: 10.1111/ppl.13104). Online ahead of print

January 2020: Publication updates

Zienkiewicz A, Zienkiewicz K, Poliner E, Pulman JA, Du ZY, Stefano G, Tsai CH, Horn P, Feussner I, Farre EM, Childs KL, Brandizzi F, Benning C (2020) The Microalga Nannochloropsis during Transition from Quiescence to Autotrophy in Response to Nitrogen Availability. Plant Physiol. 182(2):819-839. doi: 10.1104/pp.19.00854 . [PubMed]

Poliner E, Clark E, Cummings C, Benning C, Farre EM (2020) A high-capacity gene stacking toolkit for the oleaginous microalga, Nannochloropsis oceanica CCMP1779. Algal Research, 45, doi.org/10.1016/j.algal.2019.101664 [link]

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Our goal is to understand how circadian clocks work and why they play such an important role in growth and stress responses in photosynthetic organisms. We use a wide range of molecular, computational and physiological approaches to study how plants and unicellular algae adapt to daily environmental cycles.

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Matt Jones lab

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Carrer Pedro Duque, 46022 València, Valencia, España

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Carrer Enginyer Fausto Elio, s/n València, Valencia, España

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Carrer Enginyer Fausto Elio, s/n València, Valencia, España

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Martinez-Garcia LAB @ IBMCP (CSIC-UPV)

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Kaiserli Lab

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Sensory and Physiological Ecology of Plants (SenPEP)
P.I.: Pedro J. Aphalo

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Sensory and Physiological Ecology of Plants

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Our Update article has been published in July's issue of Plant Physiology. It summarizes the current state of knowledge including the new understanding and insights brought to light by the research by our group in Helsinki, done with the help of several collaborators.

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975 N Warson Rd, St. Louis, MO 63132, USA

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Dmitri Nusinow, Donald Danforth Plant Science Center

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Dmitri Nusinow, Donald Danforth Plant Science Center

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http://danusinow.github.io/

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Earlham Institute (EI), Colney Lane, Norwich, UK

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Earlham Institute (EI), Colney Lane, Norwich, UK

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Earlham Institute (EI), Colney Lane, Norwich, UK

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Hall Lab, Circadian clock

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Earlham Institute | Decoding Living Systems

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We are a research institute tackling global challenges through life science research.

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Instituto de Biología Molecular y Celular de Rosario

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Instituto de Investigaciones Fisiológicas y Ecológicas vinculadas a la Agricultura (IFEVA) - UBA, Avenida San Martín, C1417DSE, Buenos Aires, Argentina

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Instituto de Investigaciones Fisiológicas y Ecológicas vinculadas a la Agricultura (IFEVA) - UBA, Avenida San Martín, C1417DSE, Buenos Aires, Argentina

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Instituto de Investigaciones Fisiológicas y Ecológicas vinculadas a la Agricultura (IFEVA) - UBA, Avenida San Martín, C1417DSE, Buenos Aires, Argentina

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Ballaré Lab

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We are interested in understanding how plants use the phytochromes to obtain information about the proximity of other plants. In many ecological scenarios, the success of the individual plant is defined by the behavioral decisions that it makes when confronted with the risks of competition with other plants and biomass losses to consumer organisms (such as pathogens and herbivorous insects).

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Mike Behrenfeld's lab at Oregon State University

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Physiological-ecology of marine algae, biogeochemcial cycles, remote sensing of the biosphere, novel optical approaches to understanding algal ecology/physiology, biochemistry and biophysics of photosynthesis, physiological responses of plants to environmental stresses, and regional and global ecological modeling, climate change and carbon cycling.

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Copenhagen Plant Science Center
Stephan Wenkel

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Stephan Wenkel

Associate Professor

Section for Plant Biochemistry

Thorvaldsensvej 40, 1871 Frederiksberg C

In my research group, we are interested in how plants adjust their development to environmental signals. Currently we work on two main topics:

1/ Regulation of protein activity by microProteins
Many proteins achieve their function by acting as part of multi-protein complexes. The formation of these complexes is highly regulated and mediated through domains of protein-protein interaction. Disruption of a complex or of the ability of the proteins to form homodimers, heterodimers or multimers can have severe consequences for cellular function. In this context, the formation of dimers and multimers can be perturbed by proteins we refer to as 'microProteins'. These disruptive protein species contain the protein-interaction domains of bona fide interaction partners, but lack the functional domains required for the activation of, for example, transcription or DNA binding. MicroProteins thus behave as post-translational regulators by forming homotypic dimers with their targets, and act through the dominant-negative suppression of protein complex function. We study microProtein function in model in crop plants.

2/ Environmental control of morphogenesis in plants
Plants are sessile organisms and have thus to cope with the environment they are exposed to. In order to optimize reproductive success, plants have evolved refined mechanisms to respond to environmental cues by adjusting developmental processes. Small changes in the red to far-red light ratio, for example, can be detected by the plant phytochrome system and translated into growth responses. My laboratory is interested in understanding how the environment influences the basic patterning machinery and how basic patterning modules are used to steer developmental processes required for adaptive growth responses.

ID: 122852975

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department of plant and environmental sciences

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Stephan Wenkel Associate Professor Thorvaldsensvej 40, 1871 Frederiksberg C In my research group, we are interested in how plants adjust their development to environmental signals. Currently we work on two main topics: 1/ Regulation of protein activity by microProteinsMany proteins achieve their function by acting as part of multi-protein complexes.

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Av. Patricias Argentinas 435, C1405BWE CABA, Argentina

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Av. Patricias Argentinas 435, C1405BWE CABA, Argentina

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Av. Patricias Argentinas 435, C1405BWE CABA, Argentina

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Comparative Genomics of Plant Development

Marcelo J. Yanovsky - Fundación Instituto Leloir

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Our laboratory studies the genetic basis that mediate the adjustment of growth and development of plants to their environment. Mainly, studying post-transcriptional mechanisms that regulates the circadian rhythms of the model plant Arabidopsis thaliana. For this high throughput analysis and molecular and physiological approaches are combined.

Sanchez, et. al. Elife (2013) .
Perez-Santángelo, et al. Brief Funct Genomics (2013).
Mancini, E., Sanchez, S. E., Romanowski, A., Schlaen, R. G., Sanchez‐Lamas, M., Cerdán, P. D., & Yanovsky, M. J.Acute Effects of Light on Alternative Splicing in Light‐Grown Plants. Photochemistry and photobiology (2016) 92(1), 126-133. PubMed

Schlaen RG, Mancini E, Sanchez SE, Perez-Santángelo S, Rugnone ML, Simpson CG, Brown JW, Zhang X, Chernomoretz A, Yanovsky MJ. The spliceosome assembly factor GEMIN2 attenuates the effects of temperature on alternative splicing and circadian rhythms. Proc Natl Acad Sci USA (2015) V 112 p.9382-9387.

Romanowski A, Yanovsky MJ. Circadian rhythms and post-transcriptional regulation in higher plants. Frontiers in Plant Science (2015). Vol 6 p.437.

Hernando, Carlos E; Sanchez, Sabrina E; Mancini, Estefanía; Yanovsky, Marcelo J. Genome wide comparative analysis of the effects of PRMT5 and PRMT4/CARM1 arginine methyltransferases on the Arabidopsis thaliana transcriptome. BMC genomics (2015). Vol 16 p. 192.

Perez-Santángelo S, Mancini E, Francey LJ, Schlaen RG, Chernomoretz A, Hogenesch JB, Yanovsky MJ (2014). Role for LSM genes in the regulation of circadian rhythms. Proc Natl Acad Sci U S A;111(42):15166-71.

Beckwith EJ, Yanovsky MJ. Circadian regulation of gene expression: at the crossroads of transcriptional and post-transcriptional regulatory networks. Curr Opin Genet Dev. (2014). 27:35-42.

Perez-Santángelo S, Schlaen RG, Yanovsky MJ. Genomic analysis reveals novel connections between alternative splicing and circadian regulatory networks. Brief Funct Genomics . (2013). Review.

Rugnone ML, Faigón Soverna A, Sanchez SE, Schlaen RG, Hernando CE, Seymour DK, Mancini E, Chernomoretz A, Weigel D, Más P, Yanovsky MJ (2013). LNK genes integrate light and clock signaling networks at the core of the Arabidopsis oscillator. Proc Natl Acad Sci USA (2013). 110(29):12120-5.

Sanchez SE, Petrillo E, Kornblihtt AR, Yanovsky MJ. Alternative splicing at the right time. . (2011). 8(6):954-9. Review. PubMed

Sánchez SE, Petrillo E, Beckwith EJ, Zhang Xu, Rugnone ML, Hernando CE, Cuevas J, Godoy Herz MA, Depetris-Chauvin A, Simpson CG, Brown JWS, Cerdán PD, Borevitz JO, Mas P, Ceriani MF, Kornblihtt AR & Yanovsky MJ. A methyl transferase links the circadian clock to the regulation of alternative splicing. Nature (2010). 468, 112-116.

Más P, Yanovsky MJ. Time for circadian rhythms: plants get synchronized. Curr Opin Plant Biol . (2009). (5):574-9. Review. PubMed

Faigón-Soverna A, Harmon FG, Storani L, Karayekov E, Staneloni RJ, Gassmann W, Más P, Casal JJ, Kay SA, Yanovsky MJ. A constitutive shade-avoidance mutant implicates TIR-NBS-LRR proteins in Arabidopsis photomorphogenic development. Plant Cell (2006). (11):2919-2928.

Yanovsky, M.J., Kay, S.A. Molecular basis of seasonal time measurement in Arabidopsis. Nature. 419:308-312 (2002).

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Comparative Genomics of Plant Development | Marcelo J. Yanovsky

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Our laboratory studies the genetic basis that mediate the adjustment of growth and development of plants to their environment. Mainly, studying post-transcriptional mechanisms that regulates the circadian rhythms of the model plant Arabidopsis thaliana. For this high throughput analysis and molecular and physiological approaches are combined. Sanchez, et. al.

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Via Augusta, 390, 08017 Barcelona, España

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Institut Químic de Sarrià - Universitat Ramon Llull

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Institut Químic de Sarrià - Universitat Ramon Llull

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Pablo Leivar Lab
Microalgae Synthetic Biology and Biotechnology Unit
Biochemistry Lab
https://www.iqs.edu/en/dr-pablo-leivar-rico

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Devlin lab

https://pure.royalholloway.ac.uk/portal/en/persons/paul-devlin(35c26f46-d131-45f9-b937-213a1b7d4cc6).html

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509-335-3625
adhingra@wsu.edu
www.genomics.wsu.edu
Professor, Department of Horticulture. Ph.D. 2000, University of Delhi South Campus, India, and Rutgers, The State University of New Jersey.

Research

Horticultural crops have unique biology and are thus an intriguing study system Investigations in my research program are focused on understanding important biological phenomenon in horticultural crops. We integrate transcriptomics, molecular biology, plant physiology, functional and translational genomics approaches to identify gene(s) participating in a biological process. In collaboration with the in-house bioinformatics expertise in Rosaceae, the ultimate goal is to develop resources that will support the establishment of time saving and cost effective methodologies for effective horticultural crop improvement.

I have had a long standing interest in chloroplast genomics, plastid transformation and gene expression. The recently described ASAP methodology (Dhingra and Folta, 2005), which facilitates the rapid and economical sequencing of chloroplast genomes is being employed to resolve phylogenetic issues in plant Orders and Families. A bioinformatics resource for organelle genomics is being developed based on this method. Plastid transformation offers several benefits compared to nuclear integration of transgenes. Maternal inheritance of plastid genome in majority of crops mitigates concerns of transgene outcross. We are interested in extending this technology to tree fruit crops as an additional research resource and a novel product for the market.

An additional interest includes photobiology and photosynthesis engineering. We have recently described the effect of green light, considered to be a benign part of the light spectrum, on the plastid transcriptome. I am interested in the identification of green light response elements in the chloroplast genome. Photosynthetic efficiency can have a bearing on the biomass production in plants. We are interested in modifying Rubisco to tamper with its affinity for oxygen and efficiency of carbon dioxide capture for eventually improving biomass.

Selected Publications

Schaeffer SM, Christian R, Castro-Velasquez N, Hyden B, Lynch-Holm V, Dhingra A (2017) Comparative ultrastructure of fruit plastids in three genetically diverse genotypes of apple ( Malus × domestica Borkh.) during development. Plant Cell Reports. doi:10.1007/s00299-017-2179-z

Ikiz D, Gallardo RK, Dhingra A, Hewitt S. (2017) Assessing consumers' preferences and willingness to pay for novel sliced packed fresh pears: A latent class approach. Agribusiness. doi: 10.1002/agr.21532.

Hewitt, S., Kilian, B., Hari, R., Koepke, T., Sharpe, R., & Dhingra, A. (2017). Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry ( Prunus avium L.). Computational and Structural Biotechnology Journal. doi:http://dx.doi.org/10.1016/j.csbj.2017.03.00 2

Lawrence NC, Hauvermale AL, Dhingra A, Burke IC (2017) Population structure and genetic diversity of Bromus tectorum within the small grain production region of the Pacific Northwest. Ecology and Evolution. doi: 10.1002/ece3.3386

Yin C, Schlatter D, Schroeder K, Mueth N, Prescott A, Dhingra A, Hulbert S, Paulitz TC (2017) Bacterial communities on wheat grown under long-term conventional tillage and no-till in the Pacific Northwest of the US. Phytobiomes. doi:10.1094/PBIOMES-09-16-0008-R

Zúñiga, C. E., Jarolmasjed, S., Sinha, R., Zhang, C., Kalcsits, L., Dhingra, A., & Sankaran, S. (2017). Spectrometric techniques for elemental profile analysis associated with bitter pit in apples. Postharvest Biology and Technology, 128, 121-129. doi:http://dx.doi.org/10.1016/j.postharvbio.2017.02.009 Zunigaetal_2017

Davis, G., Kanazawa, A, Schottler, M., Kohzuma, K., Froehlich, JE, Rutherford, W., Satoh-Cruz, M., Minhas, D., Dhingra, A. & Kramer, DM (2016). Limitations to Photosynthesis by Proton Motive Force-Induced Photosystem II Photodamage. eLife 5: e16921.

Schaeffer S, Hendrickson C, Fox R, Dhingra A (2016) Identification of Differentially Expressed Genes between 'Honeycrisp' and 'Golden Delicious' Apple Fruit Tissues Reveal Candidates for Crop Improvement. Horticulturae 2016, 2(3), 11; doi: 10.3390/horticulturae2030011

Sharpe RM, Koepke T, Harper A, Grimes J, Galli M, Satoh-Cruz M, Kalyanaraman A, Evans K, Kramer D, Dhingra A (2016) CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites. PLoS One 11: e0152404

Strand, SD., Livingston, A., Satoh-Cruz, M., Koepke, T., Enlow, HM*., Fisher, N., Froehlich, JE., Cruz, JA., Minhas, D., Hixson, KK., Kohzuma, K., Lipton, M., Dhingra, A. and Kramer, D (2016). Defects in Expression of Chloroplast Proteins Leads to H2O2 Accumulation and Activation of Cyclic Electron Flow around Photosystem I. Frontiers in Plant Science 7 doi:10.3389/fpls.2016.02073.

Wang, J., Zhai, Y., Liu, W., Dhingra, A., Pappu, H. R., & Liu, Q. (2016). Structure and Genome Organization of Cherry Virus A (Capillovirus, Betaflexiviridae) from China Using Small RNA Sequencing. Genome announcements, 4(3). doi:10.1128/genomeA.00364-16

Bodah E, Porter L, Cordova B and Dhingra A (2015) Phenotypic Evaluation and Classification of Pea (Pisum sativum L.) Accessions and Commercial Cultivars for Fusarium Root Rot Resistance. Euphytica 208: 63-72.

Mandadi N., Hendrickson C., Savithri H.S., Thippeswamy R., Pai N.R., Javeed S., Verghese A., Rai A., Pappu A., Nagaraje G. and Dhingra A (2015) Genome sequences of Photorhabdus luminescens strains isolated from entomopathogenic nematodes from southern India. Genomics Data 6: 46-47.

Syamaladevi R, Adhikari A, Lupien SL, Dugan F, Bhunia K, Dhingra A & Sablani SS (2015) Ultraviolet-C light inactivation of Penicillium expansum on fruit surfaces, Food Control, 50: 297-303

Syamaladevi RM, Lupien SL, Bhuniaa K, Sablania SS, Dugan F, Rasco B, Killinger K, Dhingra A, Ross C (2014) UV-C light inactivation kinetics of Penicillium expansum on pearsurfaces: Influence on physicochemical and sensory quality during storage. Postharvest Biology and Technology 87:27-32

Koepke T, Schaeffer S, Harper A, Dicenta F, Edwards M, Henry RJ, Moller BL, Meisel L, Oraguzie N, Silva H, Sanchez-Perez R, Dhingra A (2013) Comparative genomics analysis in Prunoideae to identify biologically relevant polymorphisms. Plant Biotechnol J. doi:10.1111/pbi.12081

Koepke T, Dhingra A (2013) Rootstock scion somatogenetic interactions in perennial composite plants. Plant Cell Rep 32 (9):1321-1337. doi:10.1007/s00299-013-1471-9

Jiwan D, Roalson EH, Main D, Dhingra A (2013) Antisense expression of peach mildew resistance locus O (PpMlo1) gene confers cross-species resistance to powdery mildew in Fragaria x ananassa. Transgenic Res. doi:10.1007/s11248-013-9715-6

Garczynski SF, Coates BS, Unruh TR, Schaeffer S, Jiwan D, Koepke T, Dhingra A (2013) Application of Cydia pomonella expressed sequence tags: Identification and expression of three general odorant binding proteins in codling moth. Insect Sci 20 (5):559-574. doi:10.1111/j.1744-7917.2012.01560.x

KL Nicholson, N Tarlyn, T Armour, M Swanson and A Dhingra 2012. Effect of phyllotactic position and cultural treatments toward successful direct shoot organogenesis in dwarf 'Pixie' grapevine ( Vitis vinifera L.). Plant Cell, Tissue and Organ Culture DOI: 10.1007/s11240-012-0173-2

Syamaladevi RM, Lu X, Sablani SS, Insan SK, Adhikari A, Killinger K, Rasco B, Dhingra A, Bandyopadhyay A, Annapure U (2012) Inactivation of Escherichia coli Population on Fruit Surfaces Using Ultraviolet-C Light: Influence of Fruit Surface Characteristics. Food and Bioprocess Technology DOI 10.1007/s11947-012-0989-0

A Fernandez I Marti, B Athanson, T Koepke, C Font I Forcada, A Dhingra, N Oraguzie. 2012 Genetic diversity and relatedness of sweet cherry (Prunus avium L.) cultivars based on single nucleotide polymorphic markers. Frontiers in Plant Science 3: 116.

K Kohzuma, CD Bosco, A Kanazawa, A Dhingra, W Nitschke, J Meurer and DM Kramer. 2012 Thioredoxin-insensitive plastid ATP synthase that performs moonlighting functions. Proceedings of the National Academy of Sciences USA DOI: 10.1073/pnas.1115728109

T Koepke, S Schaeffer, V Krishnan, D Jiwan, A Harper, M Whiting, N Oraguzie and A Dhingra. 2012 Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3′UTR sequencing. BMC Genomics 13: 18.

R Ahmad, DE Parfitt, J Fass, E Ogundiwin, A Dhingra, TM Gradziel, D Lin, NA Joshi, P Martinez-Garcia and CH Crisosto. 2011 Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection. BMC Genomics. 12:569.

J Rosnow, S Offermann, J Park, T Okita, N Tarlyn, A Dhingra and G Edwards. 2011 In vitro cultures and regeneration of Bienertia sinuspersici (Chenopodiaceae) under increasing concentrations of sodium chloride and carbon dioxide. Plant Cell Reports 30:1541-53.

M Moore, N Hassan, M Gitzendanner, R Bruenn, M Croley, A Vandeventer, J Horn, A Dhingra, S Brockington, M Latvis, J Ramdial, R Alexandre, A Piedrahita, Z Xi, C Davis, P Soltis & D Soltis. 2011 Phylogenetic analysis of the plastid inverted repeat for 244 species: insights into deeper-level angiosperm relationships from a long, slowly evolving sequence region. International Journal of Plant Sciences 172: 541-558.

R Velasco, A Zharkikh, J Affourtit, A Dhingra, A Cestaro, A Kalyanaraman et al. 2010 The genome of the domesticated apple (Malus x domestica Borkh.). Nature Genetics 42: 833-839.

K Folta, MA Clancy, S Chamala, AM Brunings, A Dhingra, L Gomide, RJ Kulathinal, N Peres, TM Davis & WB Barbazuk. 2010 A transcript accounting from diverse tissues of a cultivated strawberry. The Plant Genome 3: 1-16.

A Livingston, JA Cruz, K Kohzuma, A Dhingra and DM Kramer. 2010 An Arabidopsis mutant with high cyclic electron flow around photosystem I ( hcef) involving the NDH complex. Plant Cell 22: 221 - 233

S Brockington, R Alexandre, J Ramdial, M Moore, S Crawley, A Dhingra, K Hilu, D Soltis and P Soltis. 2009 Phylogeny of the Caryophyllales sensu lato: revising hypothesis on pollination biology and perianth differentiation in the core Caryophyllales. International Journal of Plant Sciences 170: 627-643

Md M Haque, A Kalyanaraman, A Dhingra, N Abu-Lail and K Graybeal. 2009 DNA Jig: A new approach for building DNA nanostructures. IEEE International Conference on Bioinformatics & Biomedicine. Nov 1-4, Washington DC

B Sosinski, V Shulaev, A Dhingra, A Kalyanaraman, R Bumgarner, D Rokhsar, I Verde, R Velasco, A Abbot. 2009 Rosaceous Genome Sequencing: Perspectives and Progress. In: Folta KM and Gardner SE (eds) Genetics and Genomics of Rosaceae. Plant Genetics and Genomics: Crops and Models vol 6 pp 601 - 605

MD Logacheva, TH Samigullin, A Dhingra, AA Penin. 2008 Chloroplast genomics and phylogenetic analysis of Fagopyrum esculentum ssp ancestralis - a wild ancestor or cultivated buckwheat. BMC Plant Biology 8: 59

S Jian, P Soltis, M Gitzendanner, M Moore, R Li, T Hendry, Y Qiu, A Dhingra, C Bell, D Soltis. 2008. Resolving an ancient, rapid radiation in Saxifragales. Systematic Biology 57: 28-57

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Dr. Amit Dhingra | Molecular Plant Science Site | Washington State University

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Amit Dhingra 509-335-3625 adhingra@wsu.edu www.genomics.wsu.edu Professor, Department of Horticulture. Ph.D. 2000, University of Delhi South Campus, India, and Rutgers, The State University of New Jersey. Research Horticultural crops have unique biology and are thus an intriguing study system Investigations in my research program are focused on understanding important biological phenomenon in horticultural crops.

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Wachter Lab

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Eukaryotic organisms make extensive use of posttranscriptional mechanisms to regulate gene expression in the course of development and in response to diverse stresses. In particular alternative precursor mRNA splicing (AS) is a widespread mechanism that increases transcriptome diversity and contributes to critical developmental processes in higher eukaryotes (see graphical depiction below). However, our current understanding of the regulatory processes driving these alterations in gene expression as well as their functional implications is still very limited.

The research group Wachter addresses these open questions by examining the role of AS and regulated mRNA turnover in plant development and stress responses. Using a combination of genetics, biochemistry, cell biology, and plant physiology, we identify novel regulatory components and characterize the molecular principles underlying specific control of AS and mRNA turnover. While most of our current research is focused on the model plant Arabidopsis thaliana, future research will also test the evolutionary conservation and potential agricultural relevance of our findings in other plant species. Our aim is to gain a better understanding of RNA-mediated gene control mechanisms, which are increasingly being recognized to have important implications in both basic and applied research.

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Eukaryotic organisms make extensive use of posttranscriptional mechanisms to regulate gene expression in the course of development and in response to diverse stresses. In particular alternative precursor mRNA splicing (AS) is a widespread mechanism that increases transcriptome diversity and contributes to critical developmental processes in higher eukaryotes (see graphical depiction below).

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Unison, Centro, Hermosillo, Sonora, México

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Unison, Centro, Hermosillo, Sonora, México

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Unison, Centro, Hermosillo, Sonora, México

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K. Esquivel

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Universidad de Sonora welcomes you most cordially to our website with the purpose of publicizing the scientific production of our researchers. In addition, this portal serves as a mechanism to enhance opportunities for collaboration with academics and social sectors, the products for the government in the search for an effective link, the needs of these sectors to fulfill the institutional mission of generate, apply and transfer knowledge and technology in all fields of knowledge. You can edit your profile: For more information of the university go to the University Website

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Universidad de Sonora welcomes you most cordially to our website with the purpose of publicizing the scientific production of our researchers. In addition, this portal serves as a mechanism to enhance opportunities for collaboration with academics and social sectors, the products for the government in the search for an effective link, the needs of these sectors to fulfill the institutional mission of generate, apply and transfer knowledge and technology in all fields of knowledge.

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Enea Trisaia Research Center
http://www.trisaia.enea.it
omics.enea.trisaia@gmail.com
giorgio.perrella@enea.it paolo.facella@enea.it elio.fantini@enea.it

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PT Thomas Building, Aberystwyth SY23 3EB, UK

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National Plant Phenomics Centre, Aberystwyth SY23 3EB, UK

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National Plant Phenomics Centre, Aberystwyth SY23 3EB, UK

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www.plant-phenomics.ac.uk The NPPC is a National Capability funded by the BBSRC and available to researchers from academia and industry. The Centre employs a multidisciplinary approach,  bringing together engineers, computer scientists, and mathematicians to work with biologists to address how genetics and environment interact to give rise to the characteristics (or phenotype) of the individual organism.

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University of Delhi, Benito Juarez Marg, South Campus, South Moti Bagh, New Delhi, Delhi, India

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Prof. Jitendra P. Khurana lab, University of Delhi South Campus, New Delhi, Delhi, India

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Prof. Jitendra P. Khurana lab, University of Delhi South Campus, New Delhi, Delhi, India

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Jitendra P. Khurana

Professor, Department of Plant Molecular Biology & Director, University of Delhi South Campus

Telephone No.: 091 11 24115126 (work), 091 11 24119090 (home) Fax: 091 11 24111208, 24115270; E-mail: khuranaj@genomeindia.org

Specialization

Photoperception and Signal Transduction Mechanisms in plants; Plant Hormone Action Mechanisms; Structural and Functional Genomics in Plants

Research Interests

Our group has contributed extensively to the area of light perception and signal transduction mechanisms in plants. Some of the initial works on Arabidopsis mutants lead to the identification of the blue light receptor, phototropin1, which in fact remained elusive for over a century. During a screen for phototropism mutants, we also identified constitutively photomorphogenic mutants that display de-repression of gene expression in dark and flower precociously. Some other novel mutants characterized include bls1, cnr1 and prl2, which are defective in light, hormone and sugar signaling. The genes encoding blue light receptors, CRY1 and CRY2, have been isolated and sequenced from Brassica napus and CRY2 coding gene from rice and functionally validated in transgenics for their role in regulating agronomically important traits like plant height and flowering time. Based on the microarray analysis of transgenics, it has become obvious that CRY1 regulates plant height largely by modulating the expression of genes involved in GA biosynthesis, auxin signalling and cell wall modification enzymes. In addition, the genes for red/far-red sensing phytochromes (PHYAand PHYC) have been characterized from hexaploid wheat and their evolutionary relationship examined. More recently, we have chracterized rice bZIP protein coding genes, ortologous to HY5 of Arabdopsis. One of these rice orthologs, OsbZIP48, could functionally complement hy5 mutant of Arabidopsis, as also caused semi-dwarfism when over-exoressed in rice; strikingly, its T-DNA insertion line in rice was seedling lethal. In contrast to AtHY5, OsbZIP48 protein was found to be stable in dark. Thus, it appears that OsbZIP48 has undergone neofunctionalization during the course of evolutionin monocot systems like rice.

In the past over ten years, the focus in my lab has gradually shifted towards structural and functional genomics in plants. Our group at South Campus has actively participated in sequencing rice and tomato genomes as part of the International Consortia. Using genome sequence resources, we have phylogenetically analyzed and characterized several rice gene families, including auxin-inducible AUX/IAA, SAUR and GH3 gene families, and a sub-group of cytokinin-inducible Response Regulator (RR) genes. We have identified an interacting partner of one of these AUX/IAA proteins and demonstrated its role in stres signalling. In addition, an extensive bioinformatic analysis has also been carried out for two very important classes of transcription factor genes in rice encoding F-box proteins (involved in 26S proteasome-mediated protein degradation) and the basic leucine zipper (bZIP) proteins, known to be involved in light and hormone signalling. How the expression of these genes is altered during various stages of panicle and seed development and under various abiotic stress conditions has been analyzed for prioritization of genes for functional analysis in transgenics adopting RNAi approach. We have elucidated the role of one of these genes, OsFBK1, a component of E3 ligase, in lignin biosynthesis by regulating turnover of cinnamoyl-CoA reductase during anther and root development in rice.

We also have interest in genes involved in chromatin modulations, which are turning out to be of great significance in regulation of gene expression in living organisms. The genes encoding polycomb group/SET domain proteins have also been annotated and classified from rice. One such gene that preferentially expresses in the reproductive tissue has been characterized functionally. When over-expressed, it could restore telomere silencing in a yeast mutant, indicating functional conservation of gene repression mechanisms in eukaryotic chromatin. In addition, genes encoding topoisomerase 6 (TOP6A1, A2, A3 and TOP6B), a subclass of topoisomerase II, have been characterized from rice. When rice TOP6A1, TOP6A3 and TOP6B genes were over-expressed in Arabidopsis (as a model system), all the genes independently conferred tolerance to abiotic stress, suggesting their use in transgenic manipulation for stress tolerance in crop plants like rice.
Out of nearly 150 papers published, a select list of 15 is provided.

1. Borah, P. and Khurana, J.P. 2018. The OsFBK1 E3 ligase subunit affects anther and root secondary cell wall thickenings by mediating turn-over of a cinnamoyl-CoA reductase. Plant Physiology 176: 2148-2165.

2. Burman, N., Bhatnagar, A. and Khurana, J.P. 2018. OsbZIP48, orthologous to AtHY5, exerts pleiotropic effects in light-regulated plant development. Plant Physiology 176: 1262-1285 (In Focus Issue "Energy: Light and Oxygen").

3. Jain, N., Vergish, S. and Khurana, J.P. 2018. Evaluation of house-keeping genes for normalization of gene expression data for diurnal/circadian studies in rice using RT-qPCR. Scientific Reports 8:3203; doi:10.1038/s41598-018-21374-1.

4. Borah, P., Sharma, E., Kaur, A., Chandel, G., Mohapatra, T., Kapoor, S. and Khurana, J.P. 2017. Analysis of the drought-signalling network in two contrasting varieties of rice by employing microarray-based transcriptomics approach. Scientific Reports 7: 42131. doi: 10.1038/srep42131.

5. Mishra, S. and Khurana, J.P. 2017. Emerging roles and new paradigms in signalling mechanisms of plant cryptochromes. Crit. Rev. Plant Sci. 36: 89-115.

6. The International Wheat Genome Sequencing Consortium (IWGSC) 2014. A chromosome-based draft sequence of the hexaploid bread wheat ( Triticum aestivum) genome. Science 345: 1251788-1 to 1251788-11.

7. Sharma, P., Chatterjee, M., Burman, N. and Khurana, J.P. 2014. Cryptochrome 1 regulates growth and development in Brassica through alteration in the expression of genes involved in light, phytohormone and stress signaling. Plant Cell Environ. 37: 961-977.

8. The Tomato Genome Sequencing Consortium 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641. (Authored as one of the Principal Investigators).

9. Jain, M. and Khurana, J.P. 2009. An expression compendium of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS J. 276: 3148-3162.

10. Nijhawan, A., Jain, M., Tyagi, A.K. and Khurana, J.P. 2008. A genomic survey and gene expression analysis of basic leucine zipper (bZIP) transcription factor family in rice. Plant Physiology 146: 333-350.

11. Jain, M., Nijhawan, A., Arora, R., Agarwal, P., Ray, S., Sharma, P., Kapoor, S., Tyagi, A.K. and Khurana, J.P. 2007. F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiology 143: 1467-1483.

12. Jain, M., Tyagi, A.K. and Khurana, J.P. 2006. The over-expression of putative topoisomerase 6 genes from rice confers stress tolerance in transgenic Arabidopsis plants. FEBS Journal 273: 5245-5260.

13. Chatterjee, M., Sharma, P. and Khurana, J.P. 2006. CRYPTOCHROME 1 from Brassica napus is upregulated by blue light and controls hypocotyl/stem growth and anthocyanin accumulation. Plant Physiology 141: 61-74.

14. International Rice Genome Sequencing Program 2005. The map-based sequence of the rice genome. Nature 436: 793-800.

15. Khurana, J.P. and Poff, K.L. 1989. Mutants of Arabidopsis thaliana with altered phototropism. Planta 178: 400-406.

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Department of Plant Molecular Biology - Jitendra P. Khurana

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Professor, Department of Plant Molecular Biology & Director, University of Delhi South Campus Telephone No.: 091 11 24115126 (work), 091 11 24119090 (home) Fax: 091 11 24111208, 24115270; E-mail: khuranaj@genomeindia.org Specialization Photoperception and Signal Transduction Mechanisms in plants; Plant Hormone Action Mechanisms; Structural and Functional Genomics in Plants Research Interests Our group has contributed extensively to the area of light perception and signal transduction mechanisms in plants.

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Johansson lab,  Genetics of Light Signaling Networks, Angewandte Genetik, Freie Universität Berlin
http://www.dcps.fu-berlin.de/research/Departments-members/applied_genetics/johansson/index.html

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Plant Health and Protection Lab

https://www.biw.kuleuven.be/biosyst/plantenbiotechniek/plant-health-and-protection-laboratory

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Van de Poel Lab

https://bramvandepoel.wixsite.com/vandepoel-lab

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The Australian National University, Canberra ACT, Australia

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Farquhar Lab - The Australian National University

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Farquhar Lab - The Australian National University

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#PlantPhysiology
Coordination of CO2 fixation and transpiration in plants

Integration of photosynthesis and growth with nitrogen and water use of plants

Stomatal physiology

Isotopic composition of plants

Global change science

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Group research topics include:

Integration of photosynthesis and growth with nitrogen and water use of plants

Stomatal physiology

Isotopic composition of plants

Global change science.

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Farquhar Group - Coordination of CO2 fixation and transpiration in plants

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Group research topics include: Integration of photosynthesis and growth with nitrogen and water use of plants Stomatal physiology Isotopic composition of plants Global change science.

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Facultad de Ciencias Exactas y Naturales - UBA, Avenida Intendente Cantilo, Buenos Aires, Argentina

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Facultad de Ciencias Exactas y Naturales - UBA, Avenida Intendente Cantilo, Buenos Aires, Argentina

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Facultad de Ciencias Exactas y Naturales - UBA, Avenida Intendente Cantilo, Buenos Aires, Argentina

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Department of Physiology, Molecular and Cell Biology.
Plant Environmental Memory Lab

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IISER Mohali, Sector 81, Sahibzada Ajit Singh Nagar, Punjab, India

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IISER Mohali, Sector 81, Sahibzada Ajit Singh Nagar, Punjab, India

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IISER Mohali, Sector 81, Sahibzada Ajit Singh Nagar, Punjab, India

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Dr Ram Yadav, Plant Development Biology Lab

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Selected Publications

Yadav, R.K., Perales M., Girke, T., & Reddy, G.V., (2011) WUSCHEL protein movement mediates stem cell homeostasis. Genes & Development 25, 2025-2030

Liu, M., Chakraborty, A., Yadav, R. K., Meenakshisundaram, G., Reddy, G. V. & Roy-Chowdhury, A. (2011). Adaptive cell segmentation and tracking for volumetric confocal microscopy images of a developing plant meristem. Molecular Plant 4, 922-931

Prasad, K., Grigg, S.P., Barkoulas, M., Yadav, R.K., Sanchez-Perez, G.F., Pinon, V.,Blilou, I., Hofhuis, H., Dhonukshe. P., Galinha, C., Mahonen, A.P., Muller, W.H., Raman, S., Verkleij. A.J., Snel, B., Reddy, G.V., Tsiantis, M., Scheres, B. (2011). Arabidopsis PLETHORA transcription factors control phyllotaxis. Current Biology 21, 1123-1128.

Yadav, R.K. Tavakkoli, M. & Reddy, G.V. (2010). WUSCHEL mediates stem-cell homeostasis by regulating stem-cell number and patterns of cell division and differentiation of stem-cell progenitors. Development 137, 3581-3589.

Yadav, R.K., Girke, T., Pasala, S., Xie, M. & Reddy, G.V. (2009). Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. Proc Natl Acad Sci U S A 106, 4941-4946.

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Selected Publications Yadav, R.K., Perales M., Girke, T., & Reddy, G.V., (2011) WUSCHEL protein movement mediates stem cell homeostasis. Genes & Development 25, 2025-2030 Liu, M., Chakraborty, A., Yadav, R. K., Meenakshisundaram, G., Reddy, G. V. & Roy-Chowdhury, A. (2011). Adaptive cell segmentation and tracking for volumetric confocal microscopy images of a developing plant meristem.

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Charlotte Gommers lab, working on chloroplast retrograde signalling, abiotic stress and photomorphogenesis
www.charlottegommers.nl

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Calle Américo Vespucio, 49, 41092 Sevilla, Spain

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Institute for Plant Biochemistry and Photosynthesis

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Institute for Plant Biochemistry and Photosynthesis

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Plant Development Unit - Research Group on Gene Regulatory Networks in Microalgae and Plants

https://www.ibvf.us-csic.es/

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Imaizumi lab
Circadian clock, Photoperiodism

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*** A postdoc wanted : we are seeking a postdoc who will work with us under NIH-funded research regarding the molecular mechanisms of seasonal sensing. Contact Takato Imaizumi, if you are interested in. (Nov, 2019)***
We are interested in understanding how organisms use their timing mechanisms, the circaden clocks, to optimize their development and physiology.

Below are the projects that we are currently interested in:
1) Understand the seasonal flowering mechanisms in nature at molecular levels.
Based on our recent work, we successfully optimized our lab growth conditions (i.e. adjusting red/far-red light ratio to 1 and adding duirnal temperature oscillation) to more precisely mimic seasonal flowering time regulation in natural long-day conditions. Now we are studying the molecular mechanisms of flowering in our optimized growth conditions. With this experimental modidications, whatever we find is most likely also happening in the natural environments.

2) Investigate the influence of circadian clocks on plant-polliator interactions.

We are interested in learning the influecnce of the internal timing mechanisms, circadian clocks, on interspecies interactions, since these interactions often occur at specific time of the day. Is it benefitical for them to have circadian clocks, which could coordinate timing of interactions? Which traits are regulated by the circadian clocks, and how do these traits affect the interactions? We currently use the plant-pollinator system to address this question.

We are also interested in other aspects influenced by the circadian clock. If you are interested in studying these topics, please come and visit our lab.

(Last updated: Oct, 2019)

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A postdoc wanted : we are seeking a postdoc who will work with us under NIH-funded research regarding the molecular mechanisms of seasonal sensing. Contact Takato Imaizumi, if you are interested in. (Nov, 2019)*** We are interested in understanding how organisms use their timing mechanisms, the circaden clocks, to optimize their development and physiology.

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Carnegie Institution for Science - Department of Plant Biology, Panama Street, Stanford, CA, USA

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Carnegie Institution for Science - Department of Plant Biology, Panama Street, Stanford, CA, USA

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Carnegie Institution for Science - Department of Plant Biology, Panama Street, Stanford, CA, USA

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Moi Exposito-Alonso Lab
moisesexpositoalonso.org

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Our lab works at the interface of evolutionary genetics, plant molecular biology and eco-informatics. We develop new computational methods and analyze genomic, experimental, and climate data to understand the dynamics of adaptation of populations and the mutations driving them. We then use this knowledge to forecast species evolutionary outcomes under global change and figure out how to genetically engineer adaptation rates in the future to avoid species extinctions. We are also very interested in understanding how a changing biosphere, in turn, affects human health.

An important current project of the lab, co-coordinated with François Vasseur (CNRS) and Niek Scheepens (U. Tübingen), is a distributed global evolution experiment, GrENE-net.org, which aims to test the evolvability of the plant Arabidopsis thaliana in many climates around the world.

The lab is located at the Department of Plant Biology of the Carnegie Institution for Science, based in Stanford University, where we are also co-affiliated to Stanford's Department of Biology

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Our lab works at the interface of evolutionary genetics, plant molecular biology and eco-informatics. We develop new computational methods and analyze genomic, experimental, and climate data to understand the dynamics of adaptation of populations and the mutations driving them.

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Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, NY, USA

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Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, NY, USA

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Cold Spring Harbor Laboratory, Bungtown Road, Cold Spring Harbor, NY, USA

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Ullas Pedmale
https://www.uplab.site/

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Senckenbergstraße 3, 35390 Gießen, Deutschland

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Institute for Plant Physiology
Zeidler lab

https://www.uni-giessen.de/fbz/fb08/Inst/pflphys/ag/ag-zeidler/

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UV-B Perception and Signaling in Plants
https://www.ulm-lab.ch/

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Toledo-Ortiz Lab
Lancaster Environment Centre
https://www.lancaster.ac.uk/lec/about-us/people/gabriela-toledo-ortiz

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Plant Photobiology, Prof. Ronald Pierik
https://plantphotobiology.wordpress.com/

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Kerry Franklin Lab
Plant light and temperature responses

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Summary

My group's research investigates the molecular mechanisms through which plants integrate light and temperature signals to regulate growth and development.

Shade Avoidance

Light signals, perceived by the red/ far-red (R/FR) light- absorbing phytochrome family of plant photoreceptors are amongst the most important environmental cues regulating plant development. A particularly important role of the phytochromes involves detection of the presence of neighbouring vegetation by sensing changes in the quality of reflected/transmitted light. The interaction of daylight with living vegetation leads to a relative depletion in red (R) wavelengths and a relative enrichment in far-red light (FR) wavelengths. These changes in light quality (reduced R:FR ratio) are detected by the phytochromes and, in many plant species, lead to dramatic elongation growth of stems and alterations in leaf morphology. Such responses (termed the shade avoidance syndrome) serve to elevate leaves towards unfiltered daylight and provide an essential survival strategy in rapidly growing populations. We are currently investigating how shade avoidance responses are inhibited by UV-B and applications of this inhibition response for glasshouse horticulture.

Light and Temperature Signal Integration

A primary research interest of the group is the interaction between light quality and temperature signalling pathways in the regulation of plant architecture. We have shown that some shade avoidance responses of the model species, Arabidopsis thaliana, are modulated by ambient growth temperature and have identified a number of genes which are regulated by phytochrome in a temperature-dependent manner. These include the CBF regulon of genes involved in cold acclimation and freezing tolerance. We have also established that the phytochrome-interacting factor PIF4 functions as a key regulator of plant architectural responses to elevated temperature, thereby operating as a central hub of light and temperature signal integration. We are currently investigating how high temperature is sensed and how UV-B signals interact with temperature signals to control plant growth and development.

Biography

2018- Present: Professor, University of Bristol.

2015-2018: Reader, University of Bristol.

2012-2015: Senior lecturer, University of Bristol.

2010-2012: Lecturer, University of Bristol.

2006- 2014: Royal Society University Research Fellow.

2006- 2010: Lecturer, University of Leicester.

2003: HFSP Fellow, Plant Gene Expression Centre, Albany, CA, USA.

2002-2006: Postdoctoral Research Associate, University of Leicester.

1998-2001: Ph.D. University of Southampton.

1997-1998: M.Res. Advanced Plant Science, University of Wales.

1994-1997: B.Sc. (Hons) Biology, University of Bristol.

My research career started in the field of plant photobiology with a PhD at the University of Southampton, UK (supervised by Matthew Terry). Here, my work focussed on the biochemistry of plant light perception. This was followed by a postdoctoral position in the lab of Professor Garry Whitelam (University of Leicester, UK) and a short HFSP fellowship in the lab of Professor Peter Quail (Plant Gene Expression Centre and U.C Berkely, USA). This work focussed on the roles of phytochrome photoreceptors and plant shade avoidance responses. In 2006, I was simultaneously awarded a Royal Society Research Fellowship and lectureship at the University of Leicester. In 2010, I moved to the University of Bristol and was awarded both The Society of Experimental Biology (SEB) President's Medal in Plant Science and the Federation of European Societies of Plant Biology (FESPB) Award.

Teaching

I coordinate and teach on the level 2 courses 'Cell and Developmental Biology' and 'Green Planet' and the level 3 course 'Plant Environmnetal Adaptation'. I additionally supervise 3rd year library and research projects.

Keywords

Methodologies

Plant Physiology

Gene expression

Protein expression

Recent publications

Sharma, A, Sharma, B, Hayes, S, Kerner, K, Hoecker, U, Jenkins, GI & Franklin, KA, 2019, 'UVR8 disrupts stabilisation of PIF5 by COP1 to inhibit plant stem elongation in sunlight'. Nature Communications, vol 10.

Isner, JC, Olteanu, VA, Hetherington, AJ, Coupel-Ledru, A, Sun, P, Pridgeon, AJ, Jones, GS, Oates, M, Williams, TA, Maathuis, FJ, Kift, R, Webb, AR, Gough, J, Franklin, KA & Hetherington, AM, 2019, 'Short- and Long-Term Effects of UVA on Arabidopsis Are Mediated by a Novel cGMP Phosphodiesterase'. Current Biology, vol 29., pp. 2580-2585.e4

Belbin, FE, Noordally, ZB, Wetherill, SJ, Atkins, KA, Franklin, KA & Dodd, AN, 2017, 'Integration of light and circadian signals that regulate chloroplast transcription by a nuclear-encoded sigma factor'. New Phytologist, vol 213., pp. 727?738

Fraser, DP, Sharma, A, Fletcher, T, Budge, S, Moncrieff, C, Dodd, AN & Franklin, KA, 2017, 'UV-B antagonises shade avoidance and increases levels of the flavonoid quercetin in coriander (Coriandrum sativum)'. Scientific Reports, vol 7.

Hayes, S, Sharma, A, Fraser, D, Trevisan, M, Cragg-Barber, CWK, Tavridou, E, Fankhauser, C, Jenkins, G & Franklin, K, 2017, 'UV-B perceived by the UVR8 photoreceptor inhibits plant thermomorphogenesis'. Current Biology, vol 27., pp. 120-127

Franklin, KA, 2016, 'Photomorphogenesis: Plants Feel Blue in the Shade'. Current Biology, vol 26., pp. R1275-R1276

Quint, M, Delker, C, Franklin, KA, Wigge, P, Halliday, K & van Zanten, M, 2016, 'Molecular and genetic control of plant thermomorphogenesis'. Nature Plants, vol 2.

Fraser, DP, Hayes, S & Franklin, KA, 2016, 'Photoreceptor crosstalk in shade avoidance'. Current Opinion in Plant Biology, vol 33., pp. 1-7

Hayes, S, Velanis, C, Jenkins, G & Franklin, KA, 2014, 'UV-B detected by the UVR8 photoreceptor antagonizes auxin signaling and plant shade avoidance'. Proceedings of the National Academy of Sciences of the United States of America, vol 111., pp. 11894-11899

Franklin, KA, Toledo-Ortiz, G, Pyott, D & Halliday, K, 2014, 'Interaction of light and temperature signalling'. Journal of Experimental Botany, vol 65., pp. 2859-2871

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university of bristol - person profile - school of biological sciences - professor keara franklin -  plant physiology

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My group's research investigates the molecular mechanisms through which plants integrate light and temperature signals to regulate growth and development. Shade Avoidance Light signals, perceived by the red/ far-red (R/FR) light- absorbing phytochrome family of plant photoreceptors are amongst the most important environmental cues regulating plant development.

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Salomé Prat Lab:
Light and temperature signalling in Arabidopsis
Day length control of potato tuberisation

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Institut de Biologie de l'Ecole Normale Superieure IBENS, Rue d'Ulm, Paris, France

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Epigenome adaptations to light signals https://www.ibens.ens.fr/spip.php?article152

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Indian Institute of Science Education and Research, Bhopal Bypass Rd, Bhauri, Madhya Pradesh, India

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Plant Cell and Developmental Biology Lab, IISER-Bhopal, Madhya Pradesh, India.

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Plant Cell and Developmental Biology Lab, IISER-Bhopal, Madhya Pradesh, India.

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Dr. Sourav Datta
https://home.iiserb.ac.in/~sdatta

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Liu Lab

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Hongtao Liu, Ph.D.

Professor National Key Laboratory of Plant Molecular Genetics

Institute of Plant Physiol& Ecology, Chinese Academy of Sciences

300 Fenglin Road, 200032 Shanghai, China

PROFESSIONAL EXPERIENCE

2011-   Professor, National Key Laboratory of Plant Molecular Genetics,Institute of

Plant Physiol& Ecology, Chinese Academy of Sciences

2010-2011 Staff Research Associate, MCDB, University of California, Los Angeles,

2005-2010 Postdoctoral Research Fellow, Department of Molecular, Cell and

Developmental Biology, University of California, Los Angeles

2002-2005 Graduate Research Assistant, Institute of Molecular Cellular Biology,

Hebei Normal University, Hebei, China

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National Institute of Science Education and Research, Tehsildar Office, Near, Jatni, Odisha, India

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National Institute of Science Education and Research,  Bhubaneswar, Khurda, Odisha, India

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National Institute of Science Education and Research,  Bhubaneswar, Khurda, Odisha, India

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kishlab , panigrahi@niser.ac.in

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*** NISER NEWS ERASMUS +KA107 - Funded Programme Advertisement- Call for Application for staff mobility | Call for Application for student mobility ****** International Conference "imoss 2020" plan to be hosted by Plant Biology Group NISER, Bhubanewsar ****International collaboration with the Max Planck institute under framework of DAAD sponsored sandwich Module PhD programme in force *** Awarded Erasmus Mudus Scholarship for bileteral tie-up with university of ZADAR, Croatia

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NISER NEWS ERASMUS +KA107 - Funded Programme Advertisement- Call for Application for staff mobility | Call for Application for student mobility ****** International Conference "imoss 2020" plan to be hosted by Plant Biology Group NISER, Bhubanewsar ****International collaboration with the Max Planck institute under framework of DAAD sponsored sandwich Module PhD programme in force *** Awarded Erasmus Mudus Scholarship for bileteral tie-up with university of ZADAR, Croatia

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대한민국 대전광역시 유성구 온천2동 대학로 291

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Department of Biological Sciences, KAIST, Daejeon 34141, Korea
https://sites.google.com/a/kaist.edu/phytochrome/home

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Ute Hoecker lab, University of Cologne
Light signaling in Arabidopsis and Physcomitrella
https://www.ag-hoecker.botanik.uni-koeln.de/1.html

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Christie Lab

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Universitätsstraße 69, 40225 Düsseldorf, Germany

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Universitätsstraße 1, 40225 Düsseldorf, Germany

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Universitätsstraße 1, 40225 Düsseldorf, Germany

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Zurbriggen lab optogenetics

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Die Heinrich-Heine-Universität Düsseldorf ist eine der jüngeren Hochschulen des Landes NRW - gegründet 1965. Seit 1988 trägt die Universität den Namen des großen Sohnes der Stadt

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Petroutsos Lab.
"Sensing and Signalling in Microalgae".
Plant and Cell Physiology Lab, CNRS, CEA Grenoble, University of Grenoble Alpes. http://www.lpcv.fr/en/signal

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Universitaet Freiburg Botanical Garden, Schänzlestraße 1, 79104 Freiburg im Breisgau, Germany

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Universitaet Freiburg Botanical Garden, Schänzlestraße 1, 79104 Freiburg im Breisgau, Germany

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Universitaet Freiburg Botanical Garden, Schänzlestraße 1, 79104 Freiburg im Breisgau, Germany

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Hiltbrunner Lab

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Christian Fankhauser's lab

https://www.unil.ch/cig/en/home/menuinst/research/prof-fankhauser.html

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Av. Patricias Argentinas 435, C1405BWE CABA, Argentina

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Av. Patricias Argentinas 435, C1405BWE CABA, Argentina

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Av. Patricias Argentinas 435, C1405BWE CABA, Argentina

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Cerdan Lab

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Just as we have photoreceptors in the eyes that we have to see, plants have several families of photoreceptors that give them the sensation and intensity of the light that reaches them, a measure of the presence of neighboring plants, as well as the length of the Days, which allows them to anticipate the arrival of winter and spring. Also, the plants can perceive the temperature. In our laboratory, we try to understand how plants perceive environmental variables such as light and temperature and how they act accordingly, modulating their development. Consider that our studies are important both to develop strategies to improve crops, and to advance in the understanding of the most basic mechanisms that are usually common to the organisms that inhabit the earth.

Question that you try to answer What are the molecular mechanisms that allow plants to regulate flowering in response to ambient light and temperature? Methodology used Our study model is a small plant called Arabidopsis thaliana. It is an ideal plant for genetic experiments for several reasons: it is easy to grow a very large number of plants on small surfaces, its life cycle is short and it is self-governing. Arabidopsis is a plant with long days and blooms in the spring, when the photoperiod lengthens. Some genotypes of Arabidopsis require prolonged exposure to cold, which "ensure" winter to pass before flowering in the spring. How do plants stop "measuring" the light that reaches them and the temperature at which they are exposed? How do they modify their development program based on the information obtained? To try to understand the process, we use genetic and biochemical approaches. As for the genetic approaches, we look for mutants affected in the induction of flowering, with the idea of ​​finding which are the genes involved in the process. When we find these genes, the biochemical approaches allow us to study which are the mechanisms that underlie their function. We try to understand if its operation is altered by light or temperature and which are the components that act "downstream". The biochemical approaches also allow us to identify which other proteins act in the same process and, little by little, to build a kind of map where we try to locate each component with its specific role. Achievements Regarding the response to temperature, we show that there are at least two genetically separable pathways that regulate flowering in response to moderately low temperatures. Regarding the responses to light, we produce plants without phytochromes, which are the photoreceptors of red and distant red light. These plants can not continue their development in red light, which indicates that the source of information provided by the light is strictly necessary for the development of the plants.

Christian Lorenzo, Pedro Gagliardi, Mariana Antonietti, Maximiliano Sánchez-Lamas, Estefania Mancini, Carlos Dezar, Martin Vazquez, Gerónimo Watson, Marcelo Yanovsky, Pablo Cerdán. Improvement of alfalfa forage quality and management through the downregulation of MsFTa1. Plant Biotechnology Journal. (2019)

Christian D. Lorenzo, Javier Alonso Iserte, Maximiliano Sanchez-Lamas, Mariana Sofia Antonietti, Pedro Garcia Gagliardi, Carlos E. Hernando, Carlos Alberto A. Dezar, Martin Vazquez, Jorge J. Casal, Marcelo J. Yanovsky, Pablo D. Cerdán. Shade delays flowering in Medicago sativa. Plant Journal, 2019.

Aime Jaskolowski, Sabrina Iñigo, Sofía M. Arellano, Leonardo A. Arias, Diego F. Fiol, Ana R. Sede, María B. Oldra, Hernán Lorenzi, Jorge P. Muschietti, Gabriela C. Pagnussat, Pablo D. Cerdán. The MED30 subunit of mediator complex is essential for early plant development and promotes flowering in Arabidopsis thaliana. Development, 2019.

Juan Cagnola, Pablo Cerdan, Manuel Pacín, Andrea Andrade, Verónica Rodriguez, Matías Zurbriggen, Martina Legris, Sabrina Buchovsky, Néstor Carrillo, Joanne Chory, Miguel Blázquez, Davil Alabadi y Jorge Casal. Long-day photoperiod enhances jasmonic acid-related plant defense. Plant Physiology. 2018 vol. 178 p. 163 - 173

Laura Luccioni, Martín Krzymuski, Maximiliano Sánchez-Lamas, Elizabeth Karayekov, Pablo Cerdán y Jorge Casal. Constans delays Arabidopsis flowering under short days. Plant Journal. 2018

Maximiliano Sánchez-Lamas, Christian Lorenzo y Pablo Cerdán. Bottom-up Assembly of the Phytochrome Network. Plos Genetics. 2016 vol. 12

Francisco Iglesias y Pablo Cerdán. Maintaining Epigenetic Inheritance During DNA Replication in Plants. Frontiers in plant science. Año: 2016 vol. 7 p. 1 - 8

Christian Lorenzo, Maximiliano Sanchez-Lamas, Mariana Antonietti y Pablo Cerdán. Emerging Hubs in Plant Light and Temperature Signaling. Photochemistry and Photobiology. Año: 2016 vol. 92 p. 3 - 13

Estefania Mancini, Sabrina Sanchez, Andrés Romanowski, R. Gustavo Schlaen, Maximiliano Sanchez-Lamas, Pablo Cerdan y Marcelo Yanovsky. Acute Effects of Light on Alternative Splicing in Light-Grown Plants. Photochemistry and Photobiology. Año: 2016 vol. 92 p. 126 - 133

Francisco Iglesias, Natalia Bruera, Sebastián Dergan-Dylon, Cristina Marino-Buslje, Hernán Lorenzi, Julieta Mateos, Franziska Turck, George Coupland y Pablo Cerdán. The Arabidopsis DNA Polymerase δ Has a Role in the Deposition of Transcriptionally Active Epigenetic Marks, Development and Flowering. Plos Genetics. Año: 2015 vol. 11 p. 1 - 25

Verónica Arana, Maximiliano Sánchez Lamas, Bárbara Strasser, Silvia Ibarra, Pablo Cerd´na, Javier Botto y Rodolfo Sánchez. Functional diversity of phytochrome family in the control of light and gibberellin-mediated germination in Arabidopsis. Journal of Experimental Botany. Año: 2014 vol. 37 p. 2014 - 2023

Martín Krzymuski, Pablo Cerdan; Ling,Zhu, Amanda Vinh, Joanne Chory, Enamul Huq y Jorge Casal. Phytochrome A antagonises PHYTOCHROME INTERACTING FACTOR 1 to prevent over-activation of photomorphogenesis. Molecular Plant. Año: 2014 vol. 7 p. 1415 - 1428.

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Plant Molecular Biology | Pablo D. Cerdán

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Just as we have photoreceptors in the eyes that we have to see, plants have several families of photoreceptors that give them the sensation and intensity of the light that reaches them, a measure of the presence of neighboring plants, as well as the length of the Days, which allows them to anticipate the arrival of winter and spring.

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Fundacion Instituto Leloir, Avenida Patricias Argentinas, BWE, Buenos Aires, Argentina

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Fundacion Instituto Leloir, Avenida Patricias Argentinas, C1405BWE, Buenos Aires, Argentina

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Fundacion Instituto Leloir, Avenida Patricias Argentinas, C1405BWE, Buenos Aires, Argentina

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Casal Lab

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Molecular Plant Physiology

Plants are able to perceive the signals provided by the light environment. These signals affect key aspects of plant physiology and plant yield. The aim of our group is to know and functionally understand the signalling networks linking photo-receptors to the points of control of plant body shape and function. Our idea is that the complexity of the signalling networks is justified by the complexity of the light environment that plants have to face. We use techniques of molecular biology, analysis of the transcriptome, genetics and cell biology in combination with light treatments that simulate selected aspects of the environment experienced by plants.

Sellaro, R., Smith, R.W., Legris, M., Fleck, C., Casal, J. J. 2018 Phytochrome B dynamics departs from photoequilibrium in the field. Plant, Cell & Environment (en prensa)

Achkar, N. P., Cho, S. K., Poulsen, C., Arce, A. L., Re, D. A., GiudicattI, A. J., Karayekov E, Ryu, M. Y., Choi, S. W., Harholt, J., Casal, J. J., Yang, S. W., Manavella, P. A. 2018. A Quick HYL1-Dependent Reactivation of MicroRNA Production Is Required for a Proper Developmental Response after Extended Periods of Light Deprivation. Developmental cell 46 (2), 236-247. e6

Cagnola, J. I., Cerdan, P., Pacin, M., Andrade, A., Rodriguez, M. V., Zurbriggen, M., Legris, M., Buchovsky, S., Carrillo, N., Chory, J, Blazquez, M. A., Alabadi, D., Casal, J. J. (2018) Long-day photoperiod enhances jasmonic acid-related plant defense. Plant physiology, pp. 00443.2018

Pucciariello, O., Legris, M., Costigliolo Rojas, C., Iglesias, M.J., Hernando, C.E., Dezar, C., Vazquez, M., Yanovsky, M.J., Finlayson, S.A., Prat, S., Casal, J.J. 2018. Rewiring of auxin signaling under persistent shade. Proceedings of the National Academy of Sciences. 115:5612-5617.

Moriconi, V., Binkert, M., Costigliolo, C., Sellaro, R., Ulm, R., Casal, J.J. 2018. Perception of plant canopy gaps by the UV-B photoreceptor UVR8. Plant Physiology (en prensa).

Cagnola, J.I., Dumont Chassart, G.J., Ibarra, S.E., Chimenti, C., Ricardi, M.M., Delzer, B., Ghiglione, H., Zhu, T., Otegui, M.A., Estevez, J.M., Casal, J.J. 2018. Reduced expression of selected FASCICLIN‐LIKE ARABINOGALACTAN PROTEIN genes associates with the abortion of kernels in field crops of Zea mays (maize) and of Arabidopsis seeds. Plant, Cell and Environment 41, 661-674

Casal, J. J., Qüesta, J. I. 2018. Light and temperature cues: Multitasking receptors and transcriptional integrators. New Phytologist 217, 1029-1034.

Iglesias, M. J. Sellaro, R., Zurbriggen, M. Casal, J.J. 2018. Multiple links between shade avoidance and auxin networks. Journal of Experimental Botany, 69, 213-228

López Pereira, M.,Sadras, V.O., Batista, W.,Casal, J.J., Hall, A.J. 2017. Light-mediated self-organization of sunflower stands increases oil yield in the field. Proceedings of the National Academy of Sciences of the United States of America, 114, 7975-7980.

Sellaro, R., Pacín, M., Casal, J.J. 2017. Meta-Analysis of the transcriptome reveals a core set of shade-avoidance genes in Arabidopsis. Photochemistry and Photobiology 93, 692-702

Legris, M., Nieto, C., Sellaro, R., Prat, S., Casal, J.J. 2017. Perception and signalling of light and temperature cues in plants. The Plant Journal 90, 683-697

Goyal, A., Karayekov, E., Costa Galvão, V., Casal, J.J., Fankhauser, C. 2016. Shade promotes phototropism through phytochrome B-controlled auxin production. Current Biology 26, 3280-3287.

Legris, M., Klose, C., Burgie, E.S., Costigliolo, C., Neme, M., Hiltbrunner, A., Wigge, P.A., Schäfer, E., Vierstra, R.D., Casal, J.J. 2016. Phytochrome B integrates light and temperature signals in Arabidopsis. Science 354, 897-900.

Lake, L., Li, Y., Casal, J.J., Sadras, V.O. 2016. Negative association between chickpea response to competition and crop yield: Phenotypic and genetic analysis. Field Crops Research 196, 409-41.

Pacín, M., Semmoloni, M., Legris, M., Finlayson, S.A., Casal, J.J. 2016. Convergence of CONSTITUTIVE PHOTOMORPHOGENESIS 1 and PHYTOCHROME INTERACTING FACTOR signalling during shade avoidance. New Phytologist 211, 967-979.

Casal, J.J. 2016. Seedling signalling: Ubiquitin ligases acting in tandem. Nature Plants 2, 16001

Crepy, M.A., Casal, J.J. 2016. Kin recognition by self‐referent phenotype matching in plants. New Phytologist 209, 15-16.

Krzymuski, M., Andrés, F., Cagnola, J. I., Jang, S., Yanovsky, M.J., Coupland, G., Casal, J.J. 2015. The dynamics of FLOWERING LOCUS T expression encodes long‐day information. Plant Journal 83, 952-961.

Crepy, M.A., Casal, J.J. 2015. Photoreceptor-mediated kin recognition in plants. New Phytologist 205, 329-338.

Storani, L., Hernando, C.E., Staneloni, R.J., Ploschuk, E., Rugnone, M.L., Striker, G.G., Casal, J.J., Chernomoretz, A., Yanovsky. M.J. 2015. AtCBF1 overexpression confers tolerance to high light conditions at warm temperatures in potato plants. American Journal of Potato Research 92, 619-635

Trupkin, S.A., Legris, M., Buchovsky, A.S., Tolvara Rivero, M.B., Casal, J.J. 2014. Phytochrome B nuclear bodies respond to the low red/far-red ratio and to the reduced irradiance of canopy shade in Arabidopsis. Plant physiology 165, 1698-1708.

Krzymuski, M., Cerdán, P.D., Zhu, L., Vinh, A., Chory, J., Huq, E., Casal, J.J. 2014. Phytochrome A antagonises PHYTOCHROME INTERACTING FACTOR 1 to prevent over-activation of photomorphogenesis. Molecular plant 7, 1415-1428.

Reddy, S.K., Holalu, S.V., Casal, J.J., Finlayson, S.A. (2014). The timing of low R: FR exposure profoundly affects Arabidopsis branching responses. Plant signaling & behavior 9 (3), e28668

Pacín, M., Legris, M., Casal, J.J. 2014. Rapid decline in nuclear CONSTITUTIVE PHOTOMORPHOGENESIS1 abundance anticipates the stabilisation of its target ELONGATED HYPOCOTYL5 in the light. Plant physiology 164, 1134-1138

Striker, G.G., Casal, C., Manzur, M.E., Ploschuk, R.A., Casal, J.J. 2014. Phenomic networks reveal largely independent root and shoot adjustment in waterlogged plants of Lotus japonicus. Plant, Cell & Environment 37, 2278-2293.

Mazzella, M.A., Casal, J.J., Muschietti, J-P., Fox, A.R. 2014. Hormonal networks involved in apical hook development in darkness and their response to light. Frontiers in Plant Science, doi: 10.3389

Casal, J.J., Candia, A.N., Sellaro, R. 2014. Light perception and signalling by phytochrome A. Journal of experimental botany 65, 2835-2845.

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Plant Molecular Physiology | Jorge Casal

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Plants are able to perceive the signals provided by the light environment. These signals affect key aspects of plant physiology and plant yield. The aim of our group is to know and functionally understand the signalling networks linking photo-receptors to the points of control of plant body shape and function.

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Daniel Rutherford Building, Kings Buildings, Mayfield Road, Edinburgh EH9, UK

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Daniel Rutherford Building, Kings Buildings, Mayfield Road, Edinburgh EH9, UK

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Daniel Rutherford Building, Kings Buildings, Mayfield Road, Edinburgh EH9, UK

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Halliday Lab
http://hallidaylab.bio.ed.ac.uk