Christopher Cullis - Academia.edu (original) (raw)

Papers by Christopher Cullis

Genetic Manipulation of Woody Plants, 1988

EDULEARN proceedings, Jul 1, 2019

The resources dedicated to undergraduate laboratory courses are not insignificant. However, the m... more The resources dedicated to undergraduate laboratory courses are not insignificant. However, the majority of the time these courses are designed around repeating a task with a known outcome. The exceptions to this scenario are the Course-based Undergraduate Research Experiences (CUREs). However, one area that could benefit from an injection of resources is the characterization of orphan crops, particularly those from Africa. These species have not received much attention, either scientifically, or through funded resources, since they do not readily lend themselves to rapid commercial exploitation. However, they do provide a rich source of enquiry for laboratory courses that generate novel data and require the students to interpret new data, not simply decide if they got the 'right' answer. One example of such a course and collaboration is between Case Western Reserve University (CWRU),

BMC Plant Biology, Nov 18, 2014

Background: Nodules play an important role in fixing atmospheric nitrogen for soybean growth. Pre... more Background: Nodules play an important role in fixing atmospheric nitrogen for soybean growth. Premature senescence of nodules can negatively impact on nitrogen availability for plant growth and, as such, we need a better understanding of nodule development and senescence. Cysteine proteases are known to play a role in nodule senescence, but knowledge is still fragmented regarding the function their inhibitors (cystatins) during the development and senescence of soybean nodules. This study provides the first data with regard to cystatin expression during nodule development combined with biochemical characterization of their inhibition strength. Results: Seventy nine non-redundant cysteine protease gene sequences with homology to papain, belonging to different subfamilies, and several legumain-like cysteine proteases (vacuole processing enzymes) were identified from the soybean genome assembly with eighteen of these cysteine proteases actively transcribed during nodule development and senescence. In addition, nineteen non-redundant cystatins similar to oryzacystatin-I and belonging to cystatin subgroups A and C were identified from the soybean genome assembly with seven actively transcribed in nodules. Most cystatins had preferential affinity to cathepsin L-like cysteine proteases. Transcription of cystatins Glyma05g28250, Glyma15g12211, Glyma15g36180 particularly increased during onset of senescence, possibly regulating proteolysis when nodules senesce and undergo programmed cell death. Both actively transcribed and non-actively transcribed nodule cystatins inhibited cathepsin-Land B-like activities in different age nodules and they also inhibited papain and cathepsin-L activity when expressed and purified from bacterial cells. Conclusions: Overlap in activities and specificities of actively and non-actively transcribed cystatins raises the question if non-transcribed cystatins provide a reservoir for response to particular environments. This data might be applicable to the development of strategies to extend the active life span of nodules or prevent environmentally induced senescence.

bioRxiv (Cold Spring Harbor Laboratory), Mar 29, 2023

doi: bioRxiv preprint Comparative Analysis of Tylosema esculentum Mitochondrial DNA Revealed Two ... more doi: bioRxiv preprint Comparative Analysis of Tylosema esculentum Mitochondrial DNA Revealed Two Distinct Genome Structures Highlight The analysis of marama mitogenomes revealed two germplasms and the structural variation affects certain gene copy numbers. Soil moisture levels may have played important roles in the mitogenome divergence.

bioRxiv (Cold Spring Harbor Laboratory), Mar 17, 2023

Tylosema esculentum (marama bean), an underutilized orphan legume, has long been considered to ha... more Tylosema esculentum (marama bean), an underutilized orphan legume, has long been considered to have the potential to be domesticated as a crop to improve local food security due to the nutrient-rich seeds. As a plant species that grows naturally in the deserts of southern Africa, marama also serves as a good model for studying plant adaptation to extreme environments. In this study, HMW leaf DNA samples were prepared to generate 21.6 Gb PacBio HiFi data, which was assembled into to a raw tetraploid genome assembly of 1.24 Gb using Canu and into a partially phased assembly of 564.8 Mb by Hifiasm. The N50 values were 1.28 Mb and 2.75 Mb, respectively, and the BUSCO completeness were all above 99%. Repeats were found to account for 27.35% of the genome. The k-mer analysis indicated that marama was likely to be an autotetraploid plant with an estimated haplotype genome size of only 277 Mb. The current assembly was aligned with the genome of Bauhinia variegata, the closest species to marama whose genome has been sequenced, with an overall alignment rate of only 20.36% indicating a significant divergence between the two. This is the first high-quality genome assembly of marama bean, albeit unphased and still fragmented. However, some of the long contigs, which can be close to half the chromosome length, can serve as good references for studying the genes underlying the traits of interest. This will greatly facilitate the molecular breeding of the bean.

Journal of Visualized Experiments, Dec 19, 2014

Agrobacterium-mediated plant transformation via floral-dip is a widely used technique in the fiel... more Agrobacterium-mediated plant transformation via floral-dip is a widely used technique in the field of plant transformation and has been reported to be successful for many plant species. However, flax (Linum usitatissimum) transformation by floral-dip has not been reported. The goal of this protocol is to establish that Agrobacterium and the floral-dip method can be used to generate transgenic flax. We show that this technique is simple, inexpensive, efficient, and more importantly, gives a higher transformation rate than the current available methods of flax transformation. In summary, inflorescences of flax were dipped in a solution of Agrobacterium carrying a binary vector plasmid (T-DNA fragment plus the Linum Insertion Sequence, LIS-1) for 1-2 min. The plants were laid flat on their side for 24 hr. Then, plants were maintained under normal growth conditions until the next treatment. The process of dipping was repeated 2-3 times, with approximately 10-14 day intervals between dipping. The T1 seeds were collected and germinated on soil. After approximately two weeks, treated progenies were tested by direct PCR; 2-3 leaves were used per plant plus the appropriate T-DNA primers. Positive transformants were selected and grown to maturity. The transformation rate was unexpectedly high, with 50-60% of the seeds from treated plants being positive transformants. This is a higher transformation rate than those reported for Arabidopsis thaliana and other plant species, using floral-dip transformation. It is also the highest, which has been reported so far, for flax transformation using other methods for transformation.

Research and reports in biology, Feb 1, 2012

Flax undergoes heritable genomic changes in response to nutrient stress, including changes in tot... more Flax undergoes heritable genomic changes in response to nutrient stress, including changes in total DNA content, rDNA copy number variation, and the appearance of Linum Insertion Sequence 1 (LIS-1). The nature of the genomic changes suggests a very different mechanism, which is not yet understood, from that of other DNA changes in response to stress, such as the activation of transposable elements. To identify the genes that control genomic changes in response to stress in flax, reciprocal crosses were made between a responsive flax line, Stormont cirrus, and an unresponsive line, Bethune. The ability of the F2 generation (from selfed F1 plants) to respond to nutrient stress was assayed using the insertion of LIS-1 as the criteria for responsiveness. Twenty-nine out of 89 F2s responded at 5 weeks, suggesting that 3-4 dominant loci were all necessary for early LIS-1 insertion. Seventy out of 76 responded at 10 weeks, indicating two dominant loci independently capable of initiating LIS-1 insertion under prolonged nutrient stress. F1 plants and their progeny with either Pl or Bethune as the maternal parent were capable of responding with LIS-1 insertion, indicating that LIS-1 insertion is under nuclear genetic control and does not involve maternal factors. Thus, a small number of loci within the genome of Stormont cirrus appear to control the ability to respond to nutrient stress with LIS-1 insertion. A genetic map of the flax genome is currently under construction, and will be used to identify these loci within the genome.

Plant Cell and Environment, Aug 14, 2017

Bread wheat (Triticum aestivum L.) provides about 19% of global dietary energy. Environmental str... more Bread wheat (Triticum aestivum L.) provides about 19% of global dietary energy. Environmental stress, such as drought, affects wheat growth causing premature plant senescence and ultimately plant death. A plant response to drought is an increase in protease-mediated proteolysis with rapid degradation of proteins required for metabolic processes. Among the plant proteases that are increased in their activity following stress, cysteine proteases are the best characterized. Very little is known about particular wheat cysteine protease sequences, their expression and also localization. The current knowledge on wheat cysteine proteases belonging to the five clans (CA, CD, CE, CF and CP) is outlined, in particular their expression and possible function under drought. The first successes in establishing an annotated wheat genome database are further highlighted which has allowed more detailed mining of cysteine proteases. We also share our thoughts on future research directions considering the growing availability of genomic resources of this very important food crop. Finally, we also outline future application of developed knowledge in transgenic wheat plants for environmental stress protection and also as senescence markers to monitor wheat growth under environmental stress conditions.

Journal of Nucleic Acids Investigation, Jun 5, 2012

Linum usitatissimum (Flax) is an important agronomic crop grown for its fiber (linen) and oil (li... more Linum usitatissimum (Flax) is an important agronomic crop grown for its fiber (linen) and oil (linseed oil). In spite of thousands of years of breeding some fiber varieties have been shown to rapidly respond to environmental stress with heritable changes to its genome. Many microRNAs (miRNAs) appear to be induced by abiotic or biotic conditions experienced through the plant life cycle. Here a bioinformatics approach is used to screen for miRNAs previously identified in other plant species, as well as to predict putative miRNAs unique to a particular species which may not have been identified as they are less abundant or dependent upon a specific set of environmental conditions. Twelve miRNA genes were identified in flax on the basis of unique pre-miRNA positions with structural homology to plant pre-miRNAs and complete sequence homology to published plant miRNAs. These miRNAs were found to belong to seven miRNA families, with an additional two matches corresponding to as yet unnamed poplar miRNAs and a parologous miRNA with partial sequence homology to mtr-miR4414b. An additional 649 novel and distinct flax miRNA genes were identified to form from canonical hairpin structures and to have putative targets among the ~30,000 flax Unigenes.

Technology transfer and entrepreneurship, Oct 23, 2017

Springer eBooks, 1991

The advances in DNA technology over the past few decades have significantly altered the range of ... more The advances in DNA technology over the past few decades have significantly altered the range of investigations with all organisms. Genetic engineering is clearly still in its developmental stages, but a number of the new technologies can be incorporated into existing strategies for identifying important and desirable new material. In the case of higher plants, both the traditional breeding and the biotechnological approaches are directed towards the same goals. These are: 1. To increase the knowledge about the way in which genes determine the observed phenotype 2. To use the knowledge to identify and manipulate plants to meet particular needs.

Springer eBooks, May 4, 2007

Journal of Experimental Botany, Jan 31, 2017

Tylosema esculentum (marama bean) is being developed as a possible crop for resource-poor farmers... more Tylosema esculentum (marama bean) is being developed as a possible crop for resource-poor farmers in arid regions of Southern Africa. As part of the molecular characterization of this species, the chloroplast genome has been assembled from next-generation sequencing using both Illumina and Pac-Bio data. The genome is of typical organization with a large single-copy region and a small single-copy region separated by a pair of inverted repeats and covers 161 537 bp. It contains a unique inversion not present in any other legumes, even in the closest relatives for which the complete chloroplast genome is available, and two complete copies of the ycf1 gene. These data extend the range of variability of legume chloroplast genomes. The sequencing of multiple individuals has identified two different chloroplast genomes which were geographically separated. The current sampling is limited so that the extent of the intraspecific variation is still to be determined, leaving open the question of legume chloroplast genomes adapted to particular arid environments.

Plant breeding and biotechnology, 1991

Food and Energy Security, Sep 14, 2022

Recent focus on indigenous knowledge of plant species that have long been consumed by mankind, bu... more Recent focus on indigenous knowledge of plant species that have long been consumed by mankind, but not having a prominent place in organized agriculture, has raised the profile of what steps are needed to bring such potentially useful plant species into formal agriculture practice. Many of these orphan plants have been cultivated, albeit usually without much improvement. Tylosema esculentum (marama bean) is unusual; in that, it has not been grown as a crop but only collected from wild stands. The nutritious seeds have been consumed, and other potentially useful products from the marama seeds and tubers have been identified. The marama bean grows under inhospitable environments, particularly hot arid conditions, and, if domesticated, could be grown in environments where there are no high‐yielding alternatives. The perspective of this article is to view the current status of the marama bean domestication and the possible pathways to bring this plant into wider agricultural use. The scientific basis for an improved crop yield needs to be coupled with the identification of possible added value characteristics for growers. These include acceptability as a food, possible industrial use, the development and distribution of improved seed, and the recruitment of growers to plant marama as a crop. The authors' international collaboration has already made advances in some of these areas. We discuss the current ongoing developments and existing gaps in moving this plant into formal agriculture, along with a plan for the future developments necessary for marama to provide food security under climate change, particularly in Africa. Even as the process of domestication of marama bean is proceeding, its unusual and potentially useful characteristics will greatly benefit the improvement of other legume crops needed to provide adequate nutrition to about 35% of the world population living in semi‐arid to arid regions of the developing world.

Technology transfer and entrepreneurship, Nov 1, 2018

He organized several international and national meetings and symposia (IBRO meeting, Glia confere... more He organized several international and national meetings and symposia (IBRO meeting, Glia conferences etc.). His projects were funded by the EU, DFG, DAAD,national foundations and several industrial companies. He received several awards among them the MerckleForschungspreis 2001, the price of the Society of Steroid Biochemistry in 2002, and the RWTH Teaching Award in 2007. He is a member of the Editorial board of several peer-review journals such as the Annals of Anatomy and Current Neuropharmacology, and published several special issues in the Journal of Biochemistry and Molecular Biology. To this day, he published more than 190 peer reviewed articles with more than 3500 citations.

Frontiers research topics, 2016

Epigenetics is a new field that explains gene expression at the chromatin structure and organizat... more Epigenetics is a new field that explains gene expression at the chromatin structure and organization level. Three principal epigenetic mechanisms are known and hundreds of combinations among them can develop different phenotypic characteristics. DNA methylation, histone modifications and small RNAs have been identified, and their functions are being studied in order to understand the mechanisms of interaction and regulation among the different biological processes in plants. Although, fundamental epigenetic mechanisms in crop plants are beginning to be elucidated, the comprehension of the different epigenetic mechanisms, by which plant gene regulation and phenotype are modified, is a major topic to develop in the near future in order to increase crop productivity. Thus, the importance of epigenetics in improving crop productivity is undoubtedly growing. Current research on epigenetics suggest that DNA methylation, histone modifications and small RNAs are involved in almost every aspect of plant life including agronomically important traits such as flowering time, fruit development, responses to environmental factors, defense response and plant growth. The aim of this Research Topic is to explore the recent advances concerning the role of epigenetics in crop biotechnology, as well as to enhance and promote interactions among high quality researchers from different disciplines such as genetics, cell biology, pathology, microbiology, and evolutionary biology in order to join forces and decipher the epigenetic mechanisms in crop productivity

Plant genetics and genomics: crops and models, 2019

Flax has been a model system, while also being an important agronomic resource, for the identific... more Flax has been a model system, while also being an important agronomic resource, for the identification and characterization of disease resistances. The development of the gene-for-gene hypothesis of the interaction between a specific gene in the plant and its partner in the pathogen arose from the work on the interaction between flax and its pathogenic rust fungus, Melampsora lini. The genes involved were initially isolated through transposon tagging, but the subsequent availability of the complete assembled genome sequence of flax and its rust has helped elucidate the modes of action of the interaction between the two partners, with the demonstration of the direct interaction between the cognate genes from the plant and pathogen. The extensive collection of varieties and exotic germplasm, and the continuing molecular examination of the disease reactions to a series of fungal pathogens, has provided new insights into the genes and possible modes of action of resistance to diseases.

Current plant science and biotechnology in agriculture, 1999

Production of plants via in vitro micropropagation has developed into a multibillion market. This... more Production of plants via in vitro micropropagation has developed into a multibillion market. This market is, however, mainly covered by small to medium-sized companies producing from thousand to several million plants and only a small number of companies are producing up to 20 to 30 million commodity-type plants mainly in the ornamental sector. Since non-automated plant micropropagation is very labor-intensive, there has recently been a significant shift for low cost production to developing countries. With their lower wage scales, companies in developing countries have mostly buy-back arrangements with companies from developed countries, which might include both technology and equipment transfer.