Biology subjects

Chen, C.

Publications and source records attributed to Chen, C..

At least 451 records · Page 25Linked to original sources

bioRxiv2022

Quantification of adulterated fox-derived components in meat Products by Drop Digital Polymerase Chain Reaction

There are still large research gaps in the testing standards for non-edible meat-derived components at present. Here we report a novel approach to quantification of adulterated fox-derived components in meat products by drop digital polymerase chain reaction(ddPCR). It was better to identify the adulteration that has been added either inadvertently or deliberately during the process by designing single primers on housekeeping genes. In this paper, the fox meat was used as the experimental materials and the relationship between sample quality and copy number was established by extracting DNA and using DNA concentration as an intermediary. The results of ddPCR showed that both the relationships between meat weight and DNA concentration and between DNA concentration and DNA copy number (C) were nearly linear within the dynamic range. The DNA concentration was utilized as an intermediate value to establish the formulae about the relationship between the original meat weight and DNA copy number: Mfox=0.05C+2.7. The methods feasibility was validated using artificial adulteration of different proportions The establishment of this method provides technical support for relevant regulatory authorities to monitor the adulteration of fox meat.

molecular biology↗

bioRxiv2022

Evaluating spatially variable gene detection methods for spatial transcriptomics data

The identification of genes that vary across spatial domains in tissues and cells is an essential step for spatial transcriptomics data analysis. Given the critical role it serves for downstream data interpretations, various methods for detecting spatially variable genes (SVGs) have been proposed. The availability of multiple methods for detecting SVGs bears questions such as whether different methods select a similar set of SVGs, how reliable is the reported statistical significance from each method, how accurate and robust is each method in terms of SVG detection, and how well the selected SVGs perform in downstream applications such as clustering of spatial domains. Besides these, practical considerations such as computational time and memory usage are also crucial for deciding which method to use. In this study, we address the above questions by systematically evaluating a panel of popular SVG detection methods on a large collection of spatial transcriptomics datasets, covering various tissue types, biotechnologies, and spatial resolutions. Our results shed light on the performance of each method from multiple aspects and highlight the discrepancy among different methods especially on calling statistically significant SVGs across datasets. Taken together, our work provides useful considerations for choosing methods for identifying SVGs and serves as a key reference for the future development of such methods.

bioinformatics↗

bioRxiv2022

Organization, genomic targeting and assembly of three distinct SWI/SNF chromatin remodeling complexes in Arabidopsis

Switch defective/sucrose non-fermentable (SWI/SNF) complexes are evolutionarily conserved multi-subunit machines that play vital roles in chromatin architecture regulation for modulating gene expression via sliding or ejection of nucleosomes in eukaryotes. In plants, perturbations of SWI/SNF subunits often result in severe developmental disorders. However, the subunit composition, pathways of assembly, and genomic targeting of the plant SWI/SNF complexes remain undefined. Here, we reveal the organization, genomic targeting and assembly of three distinct Arabidopsis SWI/SNF complexes: BRAHMA-Associated SWI/SNF complexes (BAS), SPLAYED-Associated SWI/SNF complexes (SAS) and MINUSCULE-Associated SWI/SNF complexes (MAS). We show that BAS complexes are equivalent to human ncBAF, whereas SAS and MAS complexes evolve in multiple subunits unique to plants, suggesting a plant-specific functional evolution of SWI/SNF complexes. We further demonstrate overlapping and specific genomic targeting of the three plant SWI/SNF complexes on chromatin and reveal that SAS complexes are necessary for the correct genomic localization of the BAS complexes. Finally, we define the role of core module subunit in the assembly of the plant SWI/SNF complexes and highlight that ATPase module subunit is required for global complex stability and the interaction of core module subunits in SAS and BAS complexes in Arabidopsis. Together, our work highlights the divergence of SWI/SNF chromatin remodelers during the eukaryote evolution and provides a comprehensive landscape for understanding the plant SWI/SNF complexes organization, assembly, genomic targeting, and function. One-sentence summaryComprehensively define the organization, genomic targeting and assembly of three distinct SWI/SNF chromatin remodeling complexes in Arabidopsis

plant biology↗

bioRxiv2022

Multi-omics analyses of single cell-derived colorectal cancer organoids reveal intratumor heterogeneity and immune response diversity

Colorectal cancer (CRC) organoids have similar genomic and functional characteristics to the original specimens. They have become a novel and promising tumor model. However, systematic research of heterogeneity and evolution based on tumor organoids and unbiased evaluation of CD4+ T cell-mediated tumor recognition is presently lacking. Here, we study the variability in genomic characterization and single-cell transcriptome between different tumor organoid clones derived from the same CRC patient. While clone-specific differences in driver gene mutations and cancer stem cell (CSC) subpopulations were observed, inter-clone heterogeneity was even more prevalent. Using single-cell RNA sequencing, we found that compared with bulk organoids, CRC organoid clones are mainly composed of cancer stem cells and transiently-amplifying cells (TACs), but no epithelial-mesenchymal transition (EMT)-like (S100A4+CDH1-) cells. In addition, we study the phenotypic characteristics and TCR properties of tumor-reactive CD4+ T cells by coupling the organoid-TILs co-culture model, single-cell profiling, and recognition testing of candidate TCRs. We found that the proliferating CD4+ T cells increased significantly from 7.1% to 35.4%, and the TCR clonotypes increased from 110 to 1043 after co-culture with organoids. Moreover, 4 of 10 (40%) candidate TCRs with a significant increase in clone abundance exhibited tumor recognition. These results provide evidence that the proliferating CD4+ T cells with clonal expansion after co-culture with tumor organoids are the potential tumor-reactive T cells. Collectively, we reconstructed intra-patient heterogeneity in single cell-derived organoid models and characterized the phenotypic characteristics and functional properties of tumor-reactive CD4+ T cells.

cancer biology↗

bioRxiv2022

MERISTEM-DEFECTIVE/DEFECTIVELY ORGANIZED TRIBUTARIES2 regulates the balance between stemness and differentiation in the root meristem through RNA splicing control.

Plants respond to environmental stresses through controlled stem cell maintenance and meristem activity. One level of transcriptional control is RNA alternative splicing. However the mechanistic link between stress, meristem function and RNA splicing is poorly understood. The MERISTEM-DEFECTIVE (MDF)/DEFECTIVELY ORGANIZED TRIBUTARIES (DOT2) gene of Arabidopsis encodes a SR-related family protein, required for meristem function and leaf vascularization, and is the likely orthologue of the human SART1 and yeast snu66 splicing factors. MDF is required for the correct splicing and expression of key transcripts associated with root meristem function. We identified RSZ33 and ACC1, both known to regulate cell patterning, as splicing targets required for MDF function in the meristem. MDF expression is modulated by osmotic and cold stress, associated with differential splicing and specific isoform accumulation and shuttling between nucleus and cytosol, and acts in part via a splicing target SR34. We propose a model in which MDF controls splicing in the root meristem to promote stemness and repress stress response and cell differentiation pathways. Summary statementThe protein MERISTEM-DEFECTIVE regulates Arabidopsis meristem function through its role as a splicing factor, mediated through splicing targets RSZ33, ACC1 and SR34.

plant biology↗

bioRxiv2022

Cholinergic-estrogen interaction underpins the effect of education on attenuating cognitive sex differences in a Thai healthy population

The development of human brain is shaped by both genetic and environmental factors. Sex differences in cognitive function have been found in humans as a result of sexual dimorphism in neural information transmission. Numerous studies have reported the positive effects of education on cognitive functions. However, little work has investigated the effect of education on attenuating cognitive sex differences and the neural mechanisms behind it based on healthy population. In this study, the Wisconsin Card Sorting Test (WCST) was employed to examine sex differences in cognitive function in 135 Thai healthy subjects, and label-free proteomic method and bioinformatic analysis were used to study sex-specific neurotransmission-related protein expression profiles. The results showed a sex difference in two WCST subscores: percentage of Total corrects and Total errors in the primary education group (Bayes factor>100) with males performed better, while such differences eliminated in secondary and tertiary education level. Moreover, 11 differentially expressed proteins (DEPs) between men and women (FDR<0.1) were presented in both education groups, with majority of them upregulated in females. Half of those DEPs interacted directly with nAChR3, whereas the other DEPs were indirectly connected to the cholinergic pathways through interaction with estrogen. These findings implied that Cholinergic-estrogen interaction underpins the effect of education on attenuating cognitive sex differences in a Thai healthy population.

neuroscience↗

bioRxiv2022

Epigenetic silencing by SMYD3 represses tumor intrinsic interferon response in HPV-negative squamous cell carcinoma of the head and neck.

Cancers often display immune escape, but the mechanisms and potential for reversibility are incompletely understood. Epigenetic dysregulation has been implicated in the immune escape of various cancer types. We have identified the epigenetic modifier SET and MYND-domain containing protein 3 (SMYD3) as a mediator of immune escape in human papilloma virus (HPV)- negative head and neck squamous cell carcinoma (HNSCC), an aggressive disease with poor prognosis and low response to immunotherapy with pembrolizumab, a programmed-death-1 (PD-1) targeting antibody. SMYD3 loss increased the sensitivity of HNSCC cancer cells to IFN-{beta}, resulting in upregulation of type I IFN response and antigen presentation machinery genes. We found that SMYD3 regulates the transcription of Ubiquitin-Like PHD And RING Finger Domain- Containing Protein 1 (UHRF1), a key epigenetic reader of trimethylated lysine 9 on histone H3 (H3K9me3), which binds to H3K9me3-enriched promoters of key immune-related genes and silences their expression. SMYD3 further maintains the repression of immune-related genes through the deposition of H4K20me3 within the gene body regions of these genes. In an anti-PD-1 immune checkpoint resistant syngeneic mouse model of HPV-negative HNSCC, Smyd3 depletion induced influx of CD8+ T-cells, upregulated PD-L1 and MHC class I molecules, and increased sensitivity to anti-PD-1 therapy. SMYD3 overexpression was associated with decreased CD8 T-cell infiltration in tumor samples from patients with HPV-negative HNSCC, and was associated with poor response to pembrolizumab. Overall, these data highlight a previously unreported function of SMYD3 as a master epigenetic regulator of anti-tumor immune response in HPV-negative HNSCC and provide a rationale for translational approaches combining SMYD3 depletion strategies with checkpoint blockade to overcome anti-PD-1 resistance in this devastating disease.

cancer biology↗

bioRxiv2022

Network Occlusion Sensitivity Analysis Identifies Regional Contributions to Brain Age Prediction

Deep learning frameworks utilizing convolutional neural networks (CNNs) have frequently been used for brain age prediction and have achieved outstanding performance. Nevertheless, deep learning remains a black box as it is hard to interpret which brain parts contribute significantly to the predictions. To tackle this challenge, we first trained a lightweight, fully CNN model for brain age estimation on a large sample data set (N = 3054, age range = [8,80 years]) and tested it on an independent data set (N = 555, mean absolute error (MAE) = 4.45 years, r = 0.96). We then developed an interpretable scheme combining network occlusion sensitivity analysis (NOSA) with a fine-grained human brain atlas to uncover the learned invariance of the model. Our findings show that the dorsolateral, dorsomedial frontal cortex, anterior cingulate cortex, and thalamus had the highest contributions to age prediction across the lifespan. More interestingly, we observed that different regions showed divergent patterns in their predictions for specific age groups and that the bilateral hemispheres contributed differently to the predictions. Regions in the frontal lobe were essential predictors in both the developmental and aging stages with the thalamus remaining relatively stable and saliently correlated with other regional changes throughout the lifespan. The lateral and medial temporal brain regions gradually became involved during the aging phase. At the network level, the frontoparietal and the default mode networks show an inverted U-shape contribution from the developmental to the aging stages. The framework could identify regional contributions to the brain age prediction model, which could help increase the model interpretability when serving as an aging biomarker.

neuroscience↗

bioRxiv2022

LRRK2 regulates dendritic spine dynamics through interaction with post-synaptic actin cytoskeleton

Parkinsons disease (PD) is a multisystemic disorder that manifests through motor and non-motor symptoms. Motor dysfunction is the most debilitating and it is caused by the degeneration of dopamine-producing neurons in the substantia nigra pars compacta (SNpc). Increasing evidence suggests that synapse dysfunction precedes neuronal loss by years. Still, early synaptic alterations in PD remain poorly understood. Here we integrate literature meta-analysis, proteomics and phosphoproteomics with biochemical, imaging and electrophysiological measurements in neurons and brains from knockout and knockin Lrrk2 mouse models, as well as human iPSC-derived neurons lacking LRRK2. We demonstrate that phosphorylation of LRRK2 at Ser935 and of RAB proteins is induced by brain-derived neurotrophic factor (BDNF) stimulation in differentiated SH-SY5Y cells and primary mouse neurons. Affinity-purification coupled with mass spectrometry (AP-MS/MS) revealed a significant remodelling of the LRRK2 interactome following BDNF treatment, with enhanced association of LRRK2 to a network of actin cytoskeleton-related proteins. Gene-ontology analyses of both literature-curated LRRK2 interactors and phospho-proteome from striatal tissues with elevated LRRK2 activity (G2019S knockin mice) highlight synapse-actin remodelling as major affected pathways. We further observed that loss of LRRK2 impairs BDNF signaling and alters postsynaptic density architecture. One month-old Lrrk2 knockout mice display structural alterations in dendritic protrusions, a phenotype that normalizes with age. In human iPSC-derived neurons, BDNF enhances the frequency of miniature excitatory post-synaptic currents (mEPSC) in wild-type cells, an effect that is abolished in the absence of LRRK2. Taken together, our study discloses a critical role of LRRK2 in BDNF-dependent synaptic modulation and identifies the synaptic actin cytoskeleton as a convergent site of LRRK2-associated pathophysiological processes in PD.

neuroscience↗

bioRxiv2022

Morphoelastic modeling of pattern development in the petal epidermal cell cuticle

We use the model system Hibiscus trionum as a vehicle to study the origin and propagation of surface nano-ridges in plant petal epidermal cells by tracking the development of the cell shape and the cuticle. In this system, the cuticle develops two distinct subdomains, (i) an uppermost layer which increases in thickness and in-plane extension and (ii) a substrate. We quantify the pattern formation and geometrical changes and then postulate a mechanical model assuming that the cuticle behaves as a growing bi-layer. The model is a quasi-static morpho-elastic system and it is numerically investigated in two and three dimensional settings, using different laws of film and substrate expansion and boundary conditions. We recreate several features of the observed developmental trajectories in petals. We establish the respective roles of the layers stiffness mismatch, the underlying cell-wall curvature, the cell in-plane expansion and the thickness growth rates of the layers in determining the observed pattern features, such as the variance observed in amplitude and wavelength. Our observations provide evidence which justify the growing bi-layer description, and provide valuable insights into why some systems develop surface patterns and others do not.

plant biology↗

bioRxiv2022

The C-terminal domain of RNase H and the C-terminus amino acid residue regulate virus release and autoprocessing of a defective HIV-1 possessing M50I and V151I changes in integrase

Previously, we reported that an HIV-1 variant containing Met-to-Ile change at codon 50 and Val-to-Ile mutation at codon 151 of integrase (IN), HIV(IN:M50I/V151I), was an impaired virus. Despite the mutations being in IN, the virus release was significantly suppressed (p < 0.0001) and the initiation of autoprocessing was inhibited; the mechanism of the defect remains unknown. In the current study, we attempted to identify the critical domains or amino acid (aa) residue(s) that promote defects in HIV(IN:M50I/V151I), using a series of variants, including truncated or aa-substituted RNase H (RH) or IN. The results demonstrated that virus release and the initiation of autoprocessing were regulated by the C-terminal domains (CTDs) of RH and IN. Further studies illustrated that Asp at codon 109 of RH CTD and Asp at the C terminus of IN induces the defect. This result indicated that the CTD of RH and IN in GagPol and particular aa positions in RH and IN regulated the virus release and the initiation of autoprocessing, and these sites could be potential targets for the developing new therapies.

microbiology↗

bioRxiv2022

A meta-analysis of genome-wide association studies identifies new genetic loci associated with all-cause and vascular dementia

Dementia is multifactorial with Alzheimer (AD) and vascular (VaD) pathologies making the largest contributions. Genome-wide association studies (GWAS) have identified over 70 genetic risk loci for AD but the genomic determinants of other dementias, including VaD remain understudied. We hypothesize that common forms of dementia will share genetic risk factors and conducted the largest GWAS to date of "all-cause dementia" (ACD) and examined the genetic overlap with VaD. Our dataset includes 809,299 individuals from European, African, Asian, and Hispanic ancestries with 46,902 and 8,702 cases of ACD and VaD, respectively. We replicated known AD loci at genome-wide significance for both ACD and VaD and conducted bioinformatic analyses to prioritize genes that are likely functionally relevant, and shared with closely related traits and risk factors. For ACD, novel loci identified were associated with energy transport (SEMA4D), neuronal excitability (ANO3), amyloid deposition in the brain (RBFOX1), and MRI markers of small vessel disease (HBEGF). Novel VaD loci were associated with hypertension, diabetes, and neuron maintenance (SPRY2, FOXA2, AJAP1, and PSMA3). Our study identified genetic risks underlying all-cause dementia, demonstrating overlap with neurodegenerative processes, vascular risk factors (Type-II diabetes, blood pressure, lipid) and cerebral small vessel disease. These novel insights could lead to new prevention and treatment strategies for all dementias.

genetics↗

bioRxiv2022

The metabolite alpha-ketobutyrate increases health and life spans by activating AMPK

Aging is a complex process that is directly related to human health and disease. The extraordinary finding that aging is malleable, as shown in model organisms whose life and health spans are extended by specific gene mutations or dietary or pharmacological perturbations 1-3, has offered enormous hope for our understanding and treatment of aging and related diseases. Although many molecules have been identified that can extend the lifespan of model organisms, few have been shown to alleviate age-related symptoms or illness in mammals 4. Here we show that supplementation with the endogenous metabolite -ketobutyrate (-KB) increases the lifespan of adult C. elegans. Using Gelfree DARTS-PROTOMAP, we identified microtubule-actin cross-linking factor (MACF1) that was protected against proteolysis in the presence of -KB. MACF1 belongs to the spectraplakin family of giant, evolutionarily conserved proteins with versatile functions 5, but their link to longevity regulation has not been explored. -KBs longevity effect in C. elegans is abrogated by loss-of-function mutation in vab-10, encoding the worm ortholog of mammalian MACF1 6. Like -KB treatment, vab-10 knockdown activates AMP-activated protein kinase (AMPK), and AMPK is required for -KB effects on longevity. The findings suggest a model in which -KB increases longevity by activating AMPK via VAB-10/MACF1 modulation. -KB also delays aging in mammals, increasing the lifespan of aged male mice and the healthspan of both male and female animals. Targeting of broadly expressed scaffolding proteins in connection to cellular energy homeostasis seems to be a clever way that nature has devised for metabolite signals to impinge upon multiple organ and tissue systems, which may have utility for controlling aging and related diseases.

physiology↗

bioRxiv2022

Electrophysiological population dynamics reveal context dependencies during decision making in human frontal cortex

During economic choice, evidence from monkeys and humans suggest that activity in the orbitofrontal cortex (OFC) encodes the subjective values of options under consideration. Monkey data further suggests that value representations in the OFC are context dependent, representing subjective value in a way influenced by the decision makers recent experience. Using stereo electroencephalography (sEEG) in human subjects, we investigated the neural representations of both past and present subjective values in the OFC, insula, cingulate and parietal cortices, amygdala, hippocampus and striatum. Patients with epilepsy (n=20) reported their willingness to pay--a measure of subjective value--for snack food items in a Becker-DeGroot-Marschack (BDM) auction task. We found that the high frequency power (gamma and high-gamma bands) in the OFC positively correlated with the current subjective value but negatively correlated with the subjective value of the good offered on the last trial - a kind of temporal context dependency not yet observed in humans. These representations were observed at both the group level (across electrode contacts and subjects) and at the level of individual contacts. Noticeably, the majority of significant contacts represented either the present or past subjective value, but not both. A dynamic dimensionality-reduction analysis of OFC population trajectories suggested that the past trial begin to influence activity early in the current trial after the current offer was revealed, and that these two properties--current and past subjective values--dominate the electrophysiological signals. Together, these findings indicate that information about the value of the past and present rewards are simultaneously represented in the human OFC, and offer insights into the algorithmic structure of context-dependent computation during human economic choice.

neuroscience↗

bioRxiv2022

Coding of unsupervised predictable sound-context associations in the auditory midbrain

Our environment is made of a myriad of stimuli present in combinations often patterned in predictable ways. For example, there is a strong association between where we are and the sounds we hear. Like so many environmental patterns, sound-context associations are learned implicitly, in an unsupervised manner, and are highly informative and predictive of normality. Yet, we know little about where and how unsupervised sound-context associations are coded in the brain. Here we measured plasticity in the auditory midbrain of mice living over days in a naturalistic environment designed to present sound-context associations with different degrees of predictability. Plasticity in the auditory midbrain, a hub of auditory input and multimodal feedback, developed over days and reflected learning of contextual information in a manner that depended on the predictability of the sound-context association and not on reinforcement. Plasticity took the form of broad frequency shifts in tuning in auditory midbrain neurons. These shifts were paralleled by an increase in response gain and correlated with an increase in neuronal frequency discrimination. Thus, the auditory midbrain codes for unsupervised predictable sound-context associations, revealing a subcortical engagement in the detection of contextual sounds. This detection might facilitate the processing of behaviorally relevant foreground information described to occur in cortical auditory structures.

neuroscience↗

bioRxiv2022

Neutralization of SARS-CoV-2 Omicron BA.4/BA.5 subvariant by a booster dose of bivalent adjuvanted subunit vaccine containing Omicron BA.4/BA.5 and BA.1 subvariants

The dominance of SARS-CoV-2 variants of concern (VoC), such as the Omicron subvariants, is a threat to the current vaccination scheme due to increased resistance to immune neutralization and greater transmissibility. To develop the next generation of prefusion SARS-CoV-2 spike protein (S-2P) subunit vaccine adjuvanted with CpG1018 and aluminum hydroxide, mice immunized with two doses of the adjuvanted ancestral Wuhan strain (W) followed by the third dose of the W or Omicron variants (BA.1 or BA.4/BA.5) S-2P, or a combination of the above bivalent S-2Ps. Antisera from mice were tested against pseudovirus neutralization assay of ancestral SARS-CoV-2 (WT) and Omicron BA.4/BA.5 subvariant. Boosting with bivalent mixture of Omicron BA.4/BA.5 and W S-2P achieved the highest neutralizing antibody titers against BA.4/BA.5 subvariant pseudovirus compared to other types of S-2P as boosters.

immunology↗

bioRxiv2022

Inflammation drives age-induced loss of tissue resident macrophages

Low-grade chronic systemic inflammation, or inflammageing, is a hallmark of ageing and a risk factor for both morbidity and mortality in elderly people. Resident macrophages are tissue homeostasis sentinels that are embedded in their tissue of residence since embryonic development, thus been exposed to cumulative tissue insults throughout life. Therefore, resident macrophages, among other immune cells, emerge as potential key contributors to age-associated tissue dysfunction. Contrary to what is currently postulated, we demonstrate here that the pool of embryo-derived resident macrophages exhibits an age-dependent depletion in liver, and other solid organs and that they are not replaced by Hematopoietic Stem Cell (HSCs)-derived monocytes throughout life. Further, we demonstrate that gradual, cumulative inflammation during ageing induces this specific loss of tissue resident macrophages. Preserving a "youthful" density of resident macrophages attenuates classical hallmarks of liver age-associated dysfunction. SummaryThe pool of embryo-derived resident macrophages dwindles with age in most tissues, without compensation from Hematopoietic Stem Cell (HSC)-derived cells. This loss is not due to impaired self-renewal in old tissues but rather to increased cell death, which is driven by sustained inflammation. Attenuating inflammation sensing during ageing prevents age-induce macrophage loss and improves hallmarks of liver ageing.

immunology↗

bioRxiv2022

Curation of the Deep Green list of unannotated green lineage proteins to enable structural and functional characterization

An explosion of sequenced genomes and predicted proteomes enabled by low cost deep sequencing has revolutionized biology. Unfortunately, protein functional annotation is more complex, and has not kept pace with the sequencing revolution. We identified unannotated proteins in three model organisms representing distinct parts of the green lineage (Viridiplantae); Arabidopsis thaliana (dicot), Setaria viridis (monocot), and Chlamydomonas reinhardtii (Chlorophyte alga). Using similarity searching we found the subset of unannotated proteins that were conserved between these species and defined them as Deep Green proteins. Informatic, genomic, and structural predictions were leveraged to begin inferring functional information about Deep Green genes and proteins. The Deep Green set was enriched for proteins with predicted chloroplast targeting signals that are predictive of photosynthetic or plastid functions. Strikingly, structural predictions using AlphaFold and comparisons to known structures show that a significant proportion of Deep Green proteins may possess novel protein tertiary structures. The Deep Green genes and proteins provide a starting resource of high value targets for further investigation of potentially new protein structures and functions that are conserved in the green lineage.

plant biology↗