Biology subjects

Burgess, S. J.

Publications and source records attributed to Burgess, S. J..

14 recordsLinked to original sources

bioRxiv2025

Evaluating effects of elevated and accelerated NPQ relaxation on yield, physiology and transcription in soybean

Improving photosynthetic efficiency is proposed as a means of enhancing crop productivity under rising atmospheric CO2 concentrations ([CO2]). To assess whether additive gains can be realized from simultaneous improvements in light use-efficiency and carbon assimilation, we investigated the physiological and molecular responses to elevated CO2 (e[CO2]) of a transgenic soybean line (VPZ-34A) expressing the genes violaxanthin de-epoxidase (VDE), Photosystem II subunit S (PsbS) and zeaxanthin epoxidase (ZEP) from Arabidopsis thaliana (arabidopsis) (AtVPZ). Plants were grown at a free-air CO2 enrichment facility (SoyFACE) in 2021, with physiological and transcriptomic measurements collected during vegetative (V4-5) and reproductive stages (R5-6), then compared to final biomass and seed production parameters. VPZ-34A showed increased maximum quantum photosynthetic efficiency of photosynthesis ({varphi}PSIImax) under fluctuating light during vegetative stages, but no increase in maximum efficiency of carbon assimilation ({varphi}CO2, max), and no significant increase in seed or biomass related traits under ambient or e[CO2]. Transcriptome analysis showed the VPZ construct impacted a small number of genes, among them downregulation of a mitochondrial thioredoxin (Trx o1) and up-regulation of two AP2 transcription factors in VPZ lines may suggest alterations in redox balance and seed development. In conclusion, the improvements in {varphi}PSIImax and NPQ in VPZ-34A were unaffected by e[CO2] but didnt translate to stimulation of yield. Our data highlight the complexity of VPZ manipulation on plant performance and provide avenues for future research to optimize this strategy to improve crop yields.

plant biology↗

bioRxiv2024

The role of phosphorylation and dephosphorylation in the regulation of Rubisco activase

Rubisco activase is an ATP-dependent chaperone that facilitates dissociation of inhibitory sugar phosphates from the catalytic sites of ribulose-1,5-bisphosphate carboxylase/oxygenase during photosynthesis. In Arabidopsis, Rubisco activase is negatively regulated by dark-dependent phosphorylation of threonine 78. The prevalence of threonine 78 in Rubisco activase was investigated across sequences from 91 plant species, finding 29 ([~]32%) species shared a threonine in the same position. Analysis of seven C3 species with an antibody raised against a threonine 78 phospho-peptide demonstrated that this position is phosphorylated in multiple genera. However, light-dependent dephosphorylation of threonine 78 was observed only in Arabidopsis. Further, phosphorylation of threonine 78 could not be detected in any of the four C4 grass species examined. The results suggest that despite conservation of threonine 78 in Rubisco activase from a wide range of species, a regulatory role for phosphorylation at this site is more limited. This provides a case study for how variation in post-translational regulation can amplify functional divergence across the phylogeny of plants beyond what is explained by sequence variation in a metabolically important protein.

plant biology↗

bioRxiv2024

Variation in relaxation of non-photochemical quenching between the founder genotypes of the soybean (Glycine max) nested association mapping population

Improving the efficiency of crop photosynthesis has the potential to increase yields. Genetic manipulation showed photosynthesis can be improved by speeding up relaxation of photoprotective mechanisms during sun to shade transitions. However, it is unclear if natural variation in relaxation of non-photochemical quenching (NPQ) can be exploited in crop breeding programs. To address this issue, we measured six NPQ parameters in the 40 founder lines and common parent of a Soybean Nested Association Mapping (SoyNAM) panel over two field seasons in Illinois. NPQ parameters did not show consistently variable trends throughout development, and variation between sampling days suggests environmental impacts on NPQ which last more than 24 hours. 17 genotypes were found to show small but consistent differences in NPQ relaxation kinetics relative to a reference line providing a basis for future mapping studies. Finally, a soybean canopy model predicted available phenotypic variation could result in a 1.6% difference in carbon assimilation when comparing fastest and slowest relaxing NPQ values. Significance StatementEvidence suggests increasing the rate of relaxation of photoprotection can lead to improved biomass and yield. We compare photoprotection relaxation rates in 41 diverse soybean genotypes grown in the field, identifying lines with faster rates of relaxation, and predict a potential 1.6% difference in daily carbon assimilation which could contribute to improving soybean performance.

plant biology↗

bioRxiv2024

Enhancing lipid production in plant cells through high-throughput genome editing and phenotyping via a scalable automated pipeline

Plant bioengineering is a time-consuming and labor-intensive process, with no guarantee of achieving the desired trait. Here we report a fast, automated, scalable, high-throughput pipeline for plant bioengineering (FAST-PB). FAST-PB achieves gene cloning, genome editing, and product characterization by integrating automated biofoundry engineering of callus and protoplast cells with single cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We first demonstrate that FAST-PB can streamline the Golden Gate cloning process, with the capacity to construct 96 vectors in parallel. To prove the concept, using FAST-PB, we first found that PEG2050 significantly increases transfection efficiency by over 45%. To validate the pipeline, we established a reporter-gene-free method for CRISPR editing via mutation of HCF136, affecting cellular chlorophyll fluorescence. Next, we applied this pipeline for lipid production and found that diverse lipids were significantly enhanced up to sixfold through introducing multi-gene cassettes via CRISPR activation, and regenerated plant using this platform. Lastly, we harnessed FAST-PB to achieve high-throughput single-cell lipid profiling through the integration of MALDI-MS with the biofoundry, and differentiated engineered and unengineered cells using the single-cell lipidomics. These innovations massively increase the throughput of synthetic biology, genome editing, and metabolic engineering, and change what is possibly using single-cell metabolomics in plants.

synthetic biology↗

bioRxiv2023

Insights from a survey of mentorship experiences by graduate and postdoctoral researchers

Mentorship is vital for early career researchers in training positions, allowing them to navigate the challenges of work and life in research environments. However, the quality of mentorship received by trainees can vary by investigator and by institution. One challenge faced by those hoping to improve trainee mentorship is that the extent to which mentorship is offered to and experienced by research trainees is not well characterized. To address this knowledge gap, we conducted a survey to examine the quality of mentorship received by trainees in research environments, to identify characteristics of positive and negative mentorship, and to highlight best practices to improve trainee mentorship. We received 2,114 responses from researchers at graduate and postdoctoral career stages worldwide. Quantitative analysis showed that at least [~]25-45% of respondents were dissatisfied with some aspects of their mentorship. Qualitative responses revealed that common issues in mentorship include unclear expectations in research and mentoring interactions, lack of guidance, and inadequate support of trainee independence and career goals. Our findings also identified key mentorship elements desired by trainee mentees. Based on trainee suggestions, we describe strategies for individual mentors, departments, and institutions to improve the training experience for graduate and postdoctoral researchers.

scientific communication and education↗

bioRxiv2022

The faculty-to-faculty mentorship experience: a survey on challenges and recommendations for improvements

Faculty at research institutions play a central role in advancing knowledge and careers, as well as promoting the well-being of students and colleagues in research environments. Faculty members must balance a host of activities - such as performing research, teaching, sourcing funds, administrative and service duties - with their roles as educators and mentors. Mentorship from experienced peers has been touted as critical for enabling these myriad roles to allow faculty development, career progression, and satisfaction. However, there is little information available on who supports faculty and best ways to structure a faculty mentorship program for early- and mid-career academics. Furthermore, the extent to which mentorship and mentoring programs have been offered to faculty members has not been widely characterized. It is also unclear what challenges faculty receiving mentorship may face and which aspects could be further improved. In the interest of advocating for increased and enhanced faculty mentoring and mentoring programs, we surveyed faculty (i.e., group leaders) around the world to gather data on whether and how they receive mentoring from peers, senior researchers, informal mentoring programs, or formal mentoring programs at their institutions. We received responses from 457 early- and mid-career faculty and found that a substantial portion of respondents either reported having no mentor or a lack of a formal mentoring scheme. Qualitative responses on the quality of mentorship revealed that the most common complaints regarding mentorship included lack of mentor availability, unsatisfactory commitment to mentorship, and non-specific or non-actionable advice. Our findings further identified key mentorship elements desired by faculty mentees. Based on these suggestions, we identify a need for training for faculty mentors as well as strategies for individual mentors, departments, and institutions for funding and design of more intentional and supportive mentorship programs for early- and mid-career faculty.

scientific communication and education↗

bioRxiv2020

Creating Clear and Informative Image-based Figures for Scientific Publications

Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in three fields; plant sciences, cell biology and physiology (n=580 papers). Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16%, cell biology 12%, plant sciences 2%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing.

bioinformatics↗

bioRxiv2020

Variation in relaxation of non-photochemical quenching in a soybean nested association mapping panel as a potential source for breeding improved photosynthesis

Improving the efficiency of crop photosynthesis has the potential to increase yields. Genetic manipulation showed photosynthesis can be improved in Tobacco by speeding up relaxation of photoprotective mechanisms, known as non-photochemical quenching (NPQ), during high to low light transitions. However, it is unclear if natural variation in NPQ relaxation can be exploited in crop breeding programs. To address this issue, we measured NPQ relaxation in the 41 parents of a soybean NAM population in field experiments in Illinois during 2018 and 2019. There was significant variation in amount and rate of fast, energy dependent quenching (qE) between genotypes. However, strong environmental effects led to a lack of correlation between values measured over the two growing season, and low broad-sense heritability estimates (< 0.3). These data suggest that either improvements in screening techniques, or transgenic manipulation, will be required to unlock the potential for improving the efficiency of NPQ relaxation in soybean. Table of Abbreviations O_TBL View this table: org.highwire.dtl.DTLVardef@124cbaborg.highwire.dtl.DTLVardef@b7808eorg.highwire.dtl.DTLVardef@1591822org.highwire.dtl.DTLVardef@3f9d64org.highwire.dtl.DTLVardef@764eef_HPS_FORMAT_FIGEXP M_TBL C_TBL

plant biology↗

bioRxiv2019

Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature

BackgroundPreprint usage is growing rapidly in the life sciences; however, questions remain on the relative quality of preprints when compared to published articles. An objective dimension of quality that is readily measurable is completeness of reporting, as transparency can improve the readers ability to independently interpret data and reproduce findings. MethodsIn this observational study, we initially compared independent samples of articles published in bioRxiv and in PubMed-indexed journals in 2016 using a quality of reporting questionnaire. After that, we performed paired comparisons between preprints from bioRxiv to their own peer-reviewed versions in journals. ResultsPeer-reviewed articles had, on average, higher quality of reporting than preprints, although the difference was small, with absolute differences of 5.0% [95% CI 1.4, 8.6] and 4.7% [95% CI 2.4, 7.0] of reported items in the independent samples and paired sample comparison, respectively. There were larger differences favoring peer-reviewed articles in subjective ratings of how clearly titles and abstracts presented the main findings and how easy it was to locate relevant reporting information. Changes in reporting from preprints to peer-reviewed versions did not correlate with the impact factor of the publication venue or with the time lag from bioRxiv to journal publication. ConclusionsOur results suggest that, on average, publication in a peer-reviewed journal is associated with improvement in quality of reporting. They also show that quality of reporting in preprints in the life sciences is within a similar range as that of peer-reviewed articles, albeit slightly lower on average, supporting the idea that preprints should be considered valid scientific contributions.

scientific communication and education↗

bioRxiv2018

A single cis-element that controls cell-type specific expression in Arabidopsis

C4 photosynthesis evolved repeatedly from the ancestral C3 state, improving photosynthetic efficiency by ∼50%. In most C4 lineages photosynthesis is compartmented between mesophyll and bundle sheath cells but how gene expression is restricted to these cell types is poorly understood. Using the C3 model Arabidopsis thaliana we identified cis-elements and transcription factors driving expression in bundle sheath strands. Upstream of the bundle sheath preferentially expressed MYB76 gene we identified a region necessary and sufficient for expression containing two cis-elements associated with the MYC and MYB families of transcription factors. MYB76 expression is reduced in mutant alleles for each. Moreover, down-regulated genes shared by both mutants are preferentially expressed in the bundle sheath. Our findings are broadly relevant for understanding the spatial patterning of gene expression, provide specific insights into mechanisms associated with evolution of C4 photosynthesis and identify a short tuneable sequence for manipulating gene expression in the bundle sheath.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2017

Droplet-based microfluidic analysis and screening of single plant cells

Droplet-based microfluidics has been used to facilitate high throughput analysis of individual prokaryote and mammalian cells. However, there is a scarcity of similar workflows applicable to rapid phenotyping of plant systems. We report on-chip encapsulation and analysis of protoplasts isolated from the emergent plant model Marchantia polymorpha at processing rates of >100,000 protoplasts per hour. We use our microfluidic system to quantify the stochastic properties of a heat-inducible promoter across a population of transgenic protoplasts to demonstrate that it has the potential to assess gene expression activity in response to environmental conditions. We further demonstrate on-chip sorting of droplets containing YFP-expressing protoplasts from wild type cells using dielectrophoresis force. This work opens the door to droplet-based microfluidic analysis of plant cells for applications ranging from high-throughput characterisation of DNA parts to single-cell genomics.

synthetic biology↗

bioRxiv2017

A transcription factor binding atlas for photosynthesis in cereals identifies a key role for coding sequence in the regulation of gene expression

The majority of plants use C3 photosynthesis, but over sixty independent lineages of angiosperms have evolved the C4 pathway. In most C4 species, photosynthesis gene expression is compartmented between mesophyll and bundle sheath cells. We performed DNaseI-SEQ to identify genome-wide profiles of transcription factor binding in leaves of the C4 grasses Zea mays, Sorghum bicolor and Setaria italica as well as C3 Brachypodium distachyon. In C4 species, while bundle sheath strands and whole leaves shared similarity in the broad regions of DNA accessible to transcription factors, the short sequences bound varied. Transcription factor binding was prevalent in gene bodies as well as promoters, and many of these sites could represent duons that impact gene regulation in addition to amino acid sequence. Although globally there was little correlation between any individual DNaseI footprint and cell-specific gene expression, within individual species transcription factor binding to the same motifs in multiple genes provided evidence for shared mechanisms governing C4 photosynthesis gene expression. Furthermore, interspecific comparisons identified a small number of highly conserved transcription factor binding sites associated with leaves from species that diverged around 60 million years ago. These data therefore provide insight into the architecture associated with C4 photosynthesis gene expression in particular and characteristics of transcription factor binding in cereal crops in general.\n\nOne sentence summaryGenome-wide patterns of transcription factor binding in vivo defined by DNaseI for leaves of C3 and C4 grasses

plant biology↗

bioRxiv2016

Ancient coding sequences underpin the spatial patterning of gene expression in C4 leaves

Photosynthesis is compromised in most plants because an enzymatic side-reaction fixes O2 instead of CO2. The energetic cost of oxygenation led to the evolution of C4 photosynthesis. In almost all C4 leaves compartmentation of photosynthesis between cells reduces oxygenation and so increases photosynthetic efficiency. Here we report that spatial expression of most C4 genes is controlled by intragenic cis-elements rather than promoter sequence. Two DNA motifs that cooperatively specify the patterning of genes required for C4 photosynthesis are identified. They are conserved in plants and algae that use the ancestral C3 pathway. As these motifs are located in exons they represent duons determining both gene expression and amino acid sequence. Our findings provide functional evidence for the importance of transcription factors recognising coding sequence as previously defined by genome-wide binding studies. Furthermore, they indicate that C4 evolution is based on ancient DNA motifs found in exonic sequence.

plant biology↗

bioRxiv2016

Shared characteristics underpinning C4 leaf maturation derived from analysis of multiple C3 and C4 species of Flaveria

Most terrestrial plants use C3 photosynthesis to fix carbon. In multiple plant lineages a modified system known as C4 photosynthesis has evolved. To better understand the molecular patterns associated with induction of C4 photosynthesis the genus Flaveria that contains C3 and C4 species was used. A base to tip maturation gradient of leaf anatomy was defined, and RNA sequencing was undertaken along this gradient for two C3 and two C4 Flaveria species. Key C4 traits including vein density, mesophyll and bundle sheath cross-sectional area, chloroplast ultrastructure, and abundance of transcripts encoding proteins of C4 photosynthesis were quantified. Candidate genes underlying each of these C4 characteristics were identified. Principal Components Analysis indicated that leaf maturation and then photosynthetic pathway were responsible for the greatest amount of variation in transcript abundance. Photosynthesis genes were over-represented for a prolonged period in the C4 species. Through comparison with publically available datasets we identify a small number of transcriptional regulators that have been up-regulated in diverse C4 species. The analysis identifies similar patterns of expression in independent C4 lineages and so indicates that the complex C4 pathway is associated with parallel as well as convergent evolution.\n\nHighlightWe identify transcription factors that show conserved patterns of expression in multiple 29 C4 species, both within the Flaveria genus, but also in more distantly related C4 plants.

plant biology↗