Monday, April 23, 2018

On the shore between industry and academia

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Eithne Browne
Eithne Browne, Research Masters student at NUI Galway

My interest in science, in particular plants and agriculture, began early. I grew up on a farm in rural County Donegal surrounded by meadows, wildflowers and crops. My parents fostered and supported my love of science by taking me to ‘Science Week’ events held by our local Institute of Technology. Hearing researchers passionately explain their work fascinated me. I would often follow my mother as she planted flower bulbs and trees, sharing her expert knowledge of growth patterns and species. My father, an agricultural consultant, took me along on farm visits, and I noted the skills and fierce pride of farmers and their care of the land. Growing up in rural Ireland taught me a lot about food crops and the importance of biodiversity and conservation on a working farm, and showed me the many opportunities to work in preserving Ireland’s unique habitats. For me, it was a natural progression to undertake a 4-year undergraduate degree in Science at NUI Galway, which encompassed my passions of conservation, sustainability and agriculture.

I began a bachelor’s degree in Undenominated Science at NUI Galway in 2012. Because of the course framework and flexibility, I was able to study many subjects including organic chemistry, zoology, physics, and botany and plant science. Being able to gain insight into such different fields allowed me to make an informed decision about which subject to specialise in. I found it very difficult to choose between Biochemistry and Botany and Plant Science — both subjects fascinated me, from the intricacies of protein function and genomics to aquaculture and seaweed biotechnology. However, through studying both I realised that there are many commonalities: for example, many experimental techniques are widely used in different discipline areas. In my third year I particularly enjoyed the plant and algal biotechnology module, and I was excited to choose Botany and Plant Science as my final year subject.

Strawberry fruits at various ripening stages
Strawberry fruits at various ripening stages

My final year research project, supervised by Dr. Zoë Popper, investigated the use of seaweed polysaccharides as potential anti-fungal agents. I thoroughly enjoyed each step of my first introduction into research: problem solving, scientific writing, literature review and scientific communication through oral presentations. It reignited the excitement and enthusiasm I had felt as a child at ‘Science Week’ events. The project encompassed polysaccharide (bio)chemistry, agricultural methods, biotechnology, microbiology and botany, and I was given the freedom to suggest methods and formulate experiments, fostering the creativity vital for research. Dr Popper was very supportive, and we shared the enthusiasm which I believe made the project exciting.

Chondrus crispus (Irish moss)
Chondrus crispus (Irish moss)

After finishing my thesis, my supervisor told me about an opportunity to apply for a Research Masters in partnership with industry — The Irish Research Council (IRC) Enterprise Partnership Scheme. I would be able to expand on the research I began in my undergraduate and get an insight into research and development in industry. I had done extensive market reviews on other eco-friendly agrochemicals for my undergraduate thesis, and so the possibility of working with industry and learning about the business side of research was highly appealing. My supervisor suggested CyberColloids Ltd as an Enterprise Partner, because of their extensive experience with seaweed and plant polysaccharides, and their applications in food-, cosmetic- and agricultural- industries. The director, Ross Campbell, expressed interest in the project, and we immediately began writing a funding application. After finishing my final year, CyberColloids offered me a position as a Research Assistant. I was delighted to gain insight into industry, and I worked on some fascinating (and confidential) projects, for which the knowledge and skills gained during my Botany and Plant Science degree were put into practice. While working at CyberColloids, I received the news that the funding application to IRC had been successful! I was elated. After working in industry for 6 months I felt prepared and excited to begin my Masters project. My project is supported by an academic supervisor, Dr. Popper, and an Enterprise Mentor, Dr. Sarah Hotchkiss, who is my link to the company. Dr. Hotchkiss’s extensive expertise of the seaweed industry has been vital to the project. Throughout the first year of my project she has always, and continues to be, a source of great help and friendly discussion, which has made my introduction into industry both enjoyable and comfortable.

I am currently one year into my 2-year research project. Throughout the past year I have expanded my research expertise and had some great experiences: from moving to another city for industry placement to presenting a poster at my first conference. I am thankful for the opportunity that has been given to me, and the supervisors and colleagues who make my life as an early-stage researcher so interesting and enjoyable. My advice to those thinking about pursing a degree in science is simple — work hard and do not be afraid to ask for help when you need it; everyone starts somewhere!

Native species respond differently to nitrogen addition and disturbance

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Nitrogen deposition and fire regime suppression are key drivers of vegetation change in urbanising grasslands. In the natural grasslands that surround Melbourne, Australia, some native species have become rarer (decreaser species) across the landscape, while others have become more widespread (increaser species).

Wild flowers

In this study, Zeeman and Morgan examine experimentally the response of increaser and decreaser native plant species to nitrogen addition/depletion, and the presence/absence of annual disturbance to the vegetation. Their results provide evidence that by affecting plant growth, nitrogen deposition and declines in disturbance frequency could be key drivers of biotic homogenisation in urban grasslands.

Reference

Zeeman, B. J., & Morgan, J. W. (2018). Increasing and declining native species in urban remnant grasslands respond differently to nitrogen addition and disturbance. Annals of Botany, 121(4), 691–697. https://doi.org/10.1093/aob/mcx200

Advancing plant science through functional-structural plant (FSP) modelling

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The need to integrate the expanding body of knowledge in the plant sciences has led to the development of sophisticated modelling approaches, such as functional-structural plant (FSP) modelling, which are the result of cross-fertilization between the domains of plant science, computer science and mathematics. FSP models simulate growth and morphology of individual plants and interactions with the environment, from which complex plant community properties emerge.

conceptual art

Evers et al., in the preface to this 2018 Annals of Botany Special Issue, present the latest developments in FSP modelling, including simulation of novel plant ecophysiological concepts and new model applications. FSP modelling is now an established approach that has matured over the years, offering opportunities for computational botany to address questions in complex plant systems that cannot be fully explained by empirical approaches alone.

This paper is part of the Annals of Botany Special Issue on Functional-Structural Plant Growth Modelling. It will be free access until June 2018, then available only to subscribers until April 2019 when it will be free access again.

Reference

Evers, J. B., Letort, V., Renton, M., & Kang, M. (2018). Computational botany: advancing plant science through functional–structural plant modelling. Annals of Botany, 121(5), 767–772. https://doi.org/10.1093/aob/mcy050

Tree seedling growth capacity under climate change

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The Boston Area Climate Experiment (BACE) field site in Waltham, MA. Photo credit: J.S. Dukes.

Predicting the effects of climate change on tree species and communities is critical for understanding the future state of our forested ecosystems. In a recent study published in AoB PLANTS, Rodgers et al. used a fully factorial precipitation by warming experiment in an old-field ecosystem in the northeastern United States to study the climatic sensitivity of seedlings of six native tree species. Warm and dry conditions suppressed seedling growth, but affected species differently by increasing mortality, enhancing rates of herbivory, or decreasing foliar carbon uptake. Their results indicate that, in the northeastern US, dry years in a future warmer environment could have damaging effects on the growth capacity of early secondary successional forests, through species-specific effects on leaf production, herbivory, and mortality.

Reference

Rodgers, V. L., Smith, N. G., Hoeppner, S. S., & Dukes, J. S. (2018). Warming increases the sensitivity of seedling growth capacity to rainfall in six temperate deciduous tree species. AoB PLANTS, 10(1). http://dx.doi.org/10.1093/aobpla/ply003

New insights into the biology of high-latitude Mesozoic trees

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The biology of extinct trees that grew in high-latitude forests during warmer geological periods is of major interest to understand past and future ecosystem dynamics. Decombeix et al. describe a detailed anatomical study of new fossil gymnosperms from the Triassic (ca. 240 my) of Antarctica.

Disrupted growth in the wood of a Triassic trunk
Disrupted growth in the wood of a Triassic (ca. 240 my) trunk from the Central Transantarctic Mountains. These new Antarctic fossils document the first co-occurrence of traumatic growth zones and epicormic shoots in an extinct plant, and provide new information on the biology of trees that grew in high-latitude forests under past greenhouse climates.

The Triassic trees formed epicormic shoots and had traumatic growth zones in their wood indicating that they were subjected to environmental stresses not seen previously from this region. This study provides new insights into aspects of tree growth and response to disturbance in these warm high-latitude forests that have no equivalent today.

Reference

Decombeix, A.-L., Serbet, R., & Taylor, E. L. (2018). Under pressure? Epicormic shoots and traumatic growth zones in high-latitude Triassic trees from East Antarctica. Annals of Botany, 121(4), 681–689. https://doi.org/10.1093/aob/mcx199

Seaweeds for a “broken heart”

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Seaweeds or macroalgae are a large and diverse group of marine organisms with more than 10,000 different species described to date. Seaweeds have been traditionally used in the food industry as additives (food stabilizers) and as flavouring materials in many Asian countries. Did you know that seaweed is served in approximately 21% of the meals in Japan?

Recently, scientists have turned their attention to new applications of marine ingredients in food, as some proteins and peptides from marine origin have shown heart-protective activities, being especially active in fighting hypertension.

Seaweed in a Valentine heart shape
Protect your heart with seaweed.

Hypertension or high blood pressure is one of the main, yet controllable, risk factors in cardiovascular diseases. Synthetic drugs against hypertension can come with negative side effects like skin or respiratory problems. There is increased interest in discovering natural products that could be cheaper and easier to include in the lifestyle of the general population through food, and without the negative side effects of the currently used drugs.

This new use of seaweed proteins and peptides against hypertension presents multiple scientific challenges: (1) how to produce proteins and peptides with anti-hypertensive activities and (2) how to incorporate these new ingredients in the food products (food formulation).

(1) Production of anti-hypertensive peptides.

Bioactive peptides are sequences of between 2-30 amino acids in length, which can be generated from various protein sources, including seaweed. These bioactive peptides are inert within their parent protein. This means that the protein source first needs to undergo certain treatments in order to release the peptide. This might happen through enzyme hydrolysis, fermentation, pasteurization and other food processing procedures, or indeed following gastrointestinal digestion. Once released, the peptides may display different beneficial biological activities.

Bioactive peptides have been described as mimic hormones with drug-like activities, and they may alter physiological functions when consumed. Seaweed-derived bioactive peptides identified to date include potent inhibitors of enzymes involved in hypertension, such as renin and angiotensin-I-converting enzyme (ACE-I). Seasonal variations in protein or amino acid profiles in seaweed may also influence the generation of anti-hypertensive peptides. The ACE-I-inhibitory activity of a peptide is influenced by the content of different amino acids (such as tyrosine, phenylalanine, tryptophan, proline, lysine) and the sequence or position of these amino acids in the peptides.

(2) Incorporation of seaweed proteins in food products

The food industry is interested in incorporating bioactive proteins and peptides into various food products such as bread or pasta. This will need to be guided by several factors: the nutritional composition of the peptides, the biological activity of the compounds, and the behaviour of the ingredients in a food matrix, such as the ability of the proteins to create stable structures (i.e. foams).

Recently, protein extracted from the seaweed Himanthalia elongata (Linnaeus) S. F. Gray or seaweed spaghetti showed high levels of essential amino acids, i.e. lysine and methionine. These amino acids cannot be synthesized by the human body and have to be absorbed from the diet. Furthermore, these proteins could be used to create strong foams, following agitation, and stable emulsions when mixed with various vegetable oils. These foaming and emulsifying properties are really appreciated in the food industry, as it allows the new ingredients to be used in a wide variety of food products including bread and pastries, but also sausages and salad dressings.

Clearly, incorporating bioactive peptides into our food is more challenging than simply sprinkling dried seaweed over a salad. However, the discovery, generation and formulation of food products containing bioactive peptides derived from seaweed could be an additional strategy to fight heart attacks using our day-by-day food.

References

Garcia-Vaquero, M., & Hayes, M. (2015). Red and green macroalgae for fish and animal feed and human functional food development. Food Reviews International, 32(1), 15–45. https://doi.org/10.1080/87559129.2015.1041184

Garcia-Vaquero, M., Lopez-Alonso, M., & Hayes, M. (2017). Assessment of the functional properties of protein extracted from the brown seaweed Himanthalia elongata (Linnaeus) S. F. Gray. Food Research International, 99, 971–978. https://doi.org/10.1016/j.foodres.2016.06.023

Fitzgerald, C., Gallagher, E., Tasdemir, D., & Hayes, M. (2011). Heart Health Peptides from Macroalgae and Their Potential Use in Functional Foods. Journal of Agricultural and Food Chemistry, 59(13), 6829–6836. https://doi.org/10.1021/jf201114d

Harnedy, P. A., & FitzGerald, R. J. (2011). BIOACTIVE PROTEINS, PEPTIDES, AND AMINO ACIDS FROM MACROALGAE1. Journal of Phycology, 47(2), 218–232. https://doi.org/10.1111/j.1529-8817.2011.00969.x

Cardoso, S., Pereira, O., Seca, A., Pinto, D., & Silva, A. (2015). Seaweeds as Preventive Agents for Cardiovascular Diseases: From Nutrients to Functional Foods. Marine Drugs, 13(11), 6838–6865. https://doi.org/10.3390/md13116838

Chinese aspen with a dynamic Quaternary evolutionary history

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Populus adenopoda (Salicaceae), the Chinese aspen, occurs in the subtropical China region. Fen et al. report a genetic survey to reveal that it survived in multiple glacial refugia during the Last Glacial Maximum (ca. 21 to 18 thousand years ago).

Map of the presumed geographic distribution of P. adenopoda
Map of the presumed geographic distribution of P. adenopoda and the sampling locations of 39 populations addressed in this study (black circles).

Populations in its southern range contain high chloroplast DNA diversity but had little contribution to the post-glacial recolonization of its northern and eastern range. Demographic inferences suggest that P. adenopoda may have experienced multiple rounds of range contraction during the glacial periods and range expansion during interglacial periods. This emphasizes the importance to combine multiple lines of evidences when reconstructing Quaternary population evolutionary history.

Reference

Strong population bottleneck and repeated demographic expansions of Populus adenopoda (Salicaceae) in subtropical China. (2018). Annals of Botany, 121(4), 665–679. https://doi.org/10.1093/aob/mcx198

Mammoth news: Bees help plants

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What! That’s news?? Surely everybody knows that many plants are pollinated by bees? Hopefully, yes, but this item is not about that well-known plant-insect association. OK, but does it feature mammoths? No, but it does have an elephantine dimension.

Three elephants
Three African Bush Elephants in Serengeti. Photo: Ikiwaner / Wikipedia

Having laboured long and hard to plant and grow crops – to feed the family, and maybe have some surplus to sell to, or trade with, others – the last thing you need is for those plants to be trampled by … elephants. Yet, that is a major concern in parts of Africa (where the African elephant is an ever-present ‘threat’ to other life forms). A biocontrol method to ward off the elephants that’s having success in southern Africa is the humble bee.

Despite its apparent toughness and thickness, the elephant’s skin is rather sensitive to bee stings, and there is the real danger that a bee sting within the trunk could potentially lead to suffocation. So, elephants not only avoid bees (sensible animals that they are), but also the places where the bees buzz. Can this behaviour be exploited as a crop-damage-mitigation approach? Yes.

Experiments testing effectiveness of bees versus wire netting to deter elephant damage to marula trees (Sclerocarya birrea in an area near the Kruger National Park in South Africa concluded that the honeybee approach was a qualified success.* Which is arguably a triple bonus; if bees’ nests are located close to crops, elephants are kept away from them, there is the potential for a honey harvest for the farmer and his family (which might also be sold…), and pollination of those crops that the bees visit when they’re not engaged in pachyderm-bothering duties.** A sort of ‘wing’- win situation: Thank you, bees!

*Some of you may be thinking: Rather than use bees – which could sting humans – why not use mice, given that mice are creatures which elephants are, anecdotally, afraid of? Well, whilst mice might get rid of the elephants, they are primarily herbivores, and therefore would be likely to feast on the crops. Thereby replacing one pesky mammal with another… At least the bees only take a bit of pollen – and do something useful with it! Although it is argued that honeybees aren’t necessarily the right sort of bees to be encouraging for a more environmentally-considerate strategy…

**AND, keeping these African honeybees (Apis mellifera ssp. scutellata) in Africa on elephant patrol will also reduce the chances of them getting out of Africa and inter-breeding with other bee species and ‘Africanising’ them into aggressive aerial attackers of humans.

[Ed. – Encouragingly, this honeybee approach also seems to work against Indian elephants – in Thailand at least. For those who appreciate a reminder of the differences between African and Indian elephants, a handy guide can be found at Major Differences.]

References

Pollination services in the UK: How important are honeybees? (2011). Agriculture, Ecosystems & Environment, 142(3-4), 137–143. https://doi.org/10.1016/j.agee.2011.03.020

Cook, R. M., Parrini, F., King, L. E., Witkowski, E. T. F., & Henley, M. D. (2018). African honeybees as a mitigation method for elephant impact on trees. Biological Conservation, 217, 329–336. https://doi.org/10.1016/j.biocon.2017.11.024

Genetic diversity and dispersal of manioc in Amazonia

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Amazonia is a major world centre of plant domestication, and manioc or cassava (Manihot esculenta, Euphorbiaceae) is currently the most important staple food crop that originated in this region. However, little is known about the dispersal of its two major cultivated groups (bitter and sweet manioc).

Manioc (Manihot esculenta Crantz) swidden overlooking the Negro River
Manioc (Manihot esculenta Crantz) swidden overlooking the Negro River, in the surroundings of Manaus, Amazonas, Brazil. In Brazilian Amazonia, smallholder farmers who live in small communities cultivate manioc in the floodplains and uplands along the Amazonian Rivers.

Alves-Pereira et al. evaluate the genetic diversity and structure of manioc along major Amazonian rivers using chloroplast and nuclear molecular markers. Bitter and sweet manioc have distinctive patterns of genetic structure across rivers, suggesting that they had distinct dispersal histories. Knowledge about how Amazonian people manage their crops is valuable for the maintenance and conservation of the impressive diversity of their native Amazonian genetic resources.

Reference

Alves-Pereira, A., Clement, C. R., Picanço-Rodrigues, D., Veasey, E. A., Dequigiovanni, G., Ramos, S. L. F., … Zucchi, M. I. (2018). Patterns of nuclear and chloroplast genetic diversity and structure of manioc along major Brazilian Amazonian rivers. Annals of Botany, 121(4), 625–639. https://doi.org/10.1093/aob/mcx190

Cell cycle arrest in plants

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Recently, Velappan et al. reviewed cell cycle arrest in plants, focussing on three types; meristem quiescence, dormancy and terminal differentiation. What is it that causes quiesence?

G1 – It’s just a phase

Mitosis is a fundamental process that governs the duplication of chromosomes, followed by the division of a single cell to form two genetically identical daughter cells. The mitotic cell cycle is essential in all multicellular organisms for development, growth and cell replacement.

Diagram showing the common stages of the cell cycle.
Diagram showing the common stages of the cell cycle. The mitotic phase usually takes up about 10% of the time. M = mitosis, C = cytokinesis, G1 = gap phase 1, S = synthesis phase, G2 = gap phase 2. Image: George Weller / Wikipedia

The plant cell cycle, like all eukaryotic cells, contains a sequence of regulated phases, including DNA synthesis (S), mitosis (M) and two gap phases, namely G1 and G2.

The S phase and gap phases are stages in which the cell is not dividing, collectively known as interphase. This period is longest phase of the cell cycle and allows the cell to grow and prepare for division in mitosis.

The main function of the G1 stage is to prepare nuclei for DNA synthesis in the S phase. In G1, the cell accomplishes the majority of its growth, along with the synthesis of mRNA and proteins required in subsequent steps.

The G1 phase also acts as a crucial checkpoint, allowing cells to decide whether they can truly commit to mitotic division. Cells can become arrested in G1, essentially exiting the cell cycle. In plants, these cells are described as quiescent. Control between cell quiescence and proliferation allows them to respond to factors, such as nutritional availability and abiotic/biotic stress.

Major distinguishing regulators defining the decision of a dividing cell to quiesce, differentiate or enter dormancy.
Major distinguishing regulators defining the decision of a dividing cell to quiesce, differentiate or enter dormancy. Regulated proteolysis of transcription factors and other unknown targets by APC/C E3 ligase, activated by CCS52A2, operates in partnership with an oxidized cellular state (ROS), abscisic acid (ABA) signalling and cyclin-dependent kinase inhibitors (KRP) to define meristematic quiescence. In a similar way, regulated proteolysis by the APC/C, activated by CCS52A1, regulates the commitment to differentiation in partnership with the regulated balance of H2O2 and O2•− and cytokinin signalling. By contrast, dormancy is regulated at the level of chromatin accessibility, by the action of PcG-type histone modifications. Source: Velappan et al. 2017

Velappan et al. review three types of cell cycle arrest in plants, which have clear differences in physiology. However, they are all commonly referred to as cells under ‘G1 arrest’. Despite being largely characterised by G1 arrest, meristematic quiescence, dormancy and terminal differentiation are all regulated distinctly.

Meristematic Quiescence – Replenishing the Undifferentiated

Meristematic quiescence is the repression of division in undifferentiated cells of a plant’s meristem.

A plant’s meristem is it’s own personal resource of pluripotent stem cells. These cells are undifferentiated and can divide to become several different cell types. The apical meristem tissue consists of actively dividing cells, found at the tips of roots and stems. The root and shoot apical meristem (RAM, SAM), have an organising centre (OC) and quiescent centre (QC), respectively. These centres are reservoirs of quiescent cells, essential for the maintenance and replenishment of pluripotent stem cells.

Plants regulate meristematic quiescence in a number of ways. One method of regulation relies on redox and oxygen-dependent reactions. Reactive Oxygen Species (ROS) and redox signalling can determine the extent of quiescence and proliferation in the RAM and SAM. For example, the oxidation of antioxidants, ascorbate and glutathione, is highly linked to G1 arrest in the QC cells of RAM.

There is also evidence that meristem quiescence is linked to abscisic acid, a stress-related signalling molecule and mitotic inhibitor.

Dormancy – Sleeping through the Bad Weather

In plant physiology, dormancy evolved as a survival strategy. Dormancy can be switched on in different plant organs, such as seeds and buds, and is regulated by both genetic and environmental factors.

In response to unfavourable conditions, such as freezing temperatures, cells can become arrested in the G1 phase to inhibit cell growth and development. By halting cell division, the plant can conserve energy when conditions are unsuitable for growth.

Regulation dormancy in plant cells relates to the level of chromatin accessibility, which is regulated by histone modifications of dormancy genes.

The Polycomb group (PcG) and Trithorax group (TrxG) are two complexes that determine chromatin state during quiescence and proliferation of cells. The PcG complex inhibits gene activity by inducing a heterochromatin state associated with nuclear quiescence. The TrxG complex induces a more euchromatic state in the cell, which is ideal for active transcription. These two complexes regulate dormancy in plant cells through their modification of dormancy genes.

Terminal Differentiation – Saying Goodbye to the Cell Cycle

Terminal differentiation, also known as cell cycle exit, is a process in which pluripotent stem cells become differentiated into particular cell types. These different cell types have specific functions within the organism.

Proliferation arrest is linked to cells with distinct cell fates, formed through asymmetrical division in undifferentiated cells. G1 arrest is important in the process of terminal differentiation, since G1 is the phase in which commitment to differentiation is induced.

Regulation of terminal differentiation shares similarities with the control of meristematic quiescence. For example, research has determined that ROS levels also play a role in cell fate and commitment to differentiation. In most root cells, proliferation and elongation is controlled by O2·- and H2O2, respectively. This appears to be essential to a cell’s commitment to differentiate. Despite similarities, terminal differentiation has different activators to meristematic quiescence and a higher dependence on cytokinin signalling.

 

The three types of cellular quiescence are achieved through different molecular pathways, but all lead to G1 arrest. There are other cells locked in G1 too, such as those in senescence and stress-induced quiescence.

As research continues and evidence arises, we can hope to get a better picture of how and why these cells are locked up in a G1 prison. This will undoubtedly deepen our understanding of plant developmental and stress biology, whilst also contributing to other aspects of agriculture and ecology, such as darkness and nutrient limitation.

 

Reference

Velappan, Y., Signorelli, S., & Considine, M. J. (2017). Cell cycle arrest in plants: what distinguishes quiescence, dormancy and differentiated G1? Annals of Botany, 120(4), 495–509. https://doi.org/10.1093/aob/mcx082

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