Biology subjects

Jiao, Y.

Publications and source records attributed to Jiao, Y..

7 recordsLinked to original sources

bioRxiv2018

System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

BackgroundLiving organisms need to allocate their limited resources in a manner that optimizes their overall fitness by simultaneously achieving several different biological objectives. Examination of these biological trade-offs can provide invaluable information regarding the biophysical and biochemical bases behind observed cellular phenotypes. A quantitative knowledge of a cell systems critical objectives is also needed for engineering of cellular metabolism, where there is interest in mitigating the fitness costs that may result from human manipulation.\n\nResultsTo study metabolism in photoheterotrophs, we developed and validated a genome-scale model of metabolism in Rhodopseudomonas palustris, a metabolically versatile gram-negative purple non-sulfur bacterium capable of growing phototrophically on various carbons sources, including inorganic carbon and aromatic compounds. To quantitatively assess trade-offs among a set of important biological objectives during different metabolic growth modes, we used our new model to conduct an 8-dimensional multi-objective flux analysis of metabolism in R. palustris. Our results revealed that phototrophic metabolism in R. palustris is a light-limited growth mode under anaerobic conditions, regardless of the available carbon source. Under photoheterotrophic conditions, R. Palustris prioritizes the optimization of carbon efficiency, followed by ATP production and biomass production rate, in a Pareto-optimal manner. To achieve maximum carbon fixation, cells appear to divert limited energy resources away from growth and toward CO2 fixation, even in presence of excess reduced carbon. We also found that to achieve the theoretical maximum rate of biomass production, anaerobic metabolism requires import of additional compounds (such as protons) to serve as electron acceptors. Finally, we found that production of hydrogen gas, of potential interest as a candidate biofuel, lowers the cellular growth rates under all circumstances.\n\nConclusionsPhotoheterotrophic metabolism of R. palustris is primarily regulated by the amount of light it can absorb and not the availability of carbon. However, despite carbons secondary role as a regulating factor, R. palustris metabolism strives for maximum carbon efficiency, even when this increased efficiency leads to slightly lower growth rates.

systems biology↗

bioRxiv2018

Duplications and functional specialization force distinct evolution of isoflavonoid biosynthetic genes in legumes

Isoflavonoids are specialized plant metabolites, almost exclusive to legumes, and synthesized by the phenylpropanoid pathway. Leguminous plants produce 5-deoxyflavonoids and 5-deoxyisoflavonoids that act in symbiosis with nitrogen-fixing bacteria and involved in plant pathogen and stress response. However, little is known about evolutional origin of legume-specific isoflavonoid biosynthesis pathway. Here, we explored the genome-wide analysis of key genes: chalcone synthase (CHS), chalcone reductase (CHR), isoflavone synthase (IFS) and isoflavone reductase (IFR), encoding enzymes involved in the biosynthesis of (iso) flavonoids in legumes and nonlegumes. Among them, CHS, CHR and IFR comprise multigene families, underling the significant role of gene duplication in the evolutionary. Most duplications of CHS were highly the conventional leguminous type, whereas some were grouped with nonleguminous CHS genes. We also found that CHR homologs in soybean and Sesbania rostrata previously reported were ambiguous and should be re-identified. Phylogenetic analysis and protein sequences alignment indicated that IFSs in legumes are highly conserved. Intriguingly, unlike other IFRs in legumes, IFR-like homologs in Sophora flavescens and Lupinus angustifolius shared high sequence similarity and protein structures with homologs in nonlegumes. Overall, these results offer reasonable gene annotations and comparative analysis and also provided a glimpse into evolutional route of legume-specific isoflavonoid biosynthesis.\n\nHighlightIsoflavonoids are specialized plant metabolites, almost exclusive to legumes. We firstly provide evidence that evolutional origin of legume-specific isoflavonoid biosynthesis may be driven by gene duplications and functional specialization.

genomics↗

bioRxiv2018

Uniform distribution of 35S promoter-driven mDII auxin control sensor in leaf primordia

The DII sensor has been an invaluable tool to map spatiotemporal auxin response and distribution in the model plant Arabidopsis thaliana. The DII sensor and mDII control sensor are driven by the widely used constitutive 35S promoter. However, the reliability of DII sensor has recently been questioned (Bhatia and Heisler, 2018). Here we provide additional evidence to show that the mDII control sensor is indeed uniformly distributed in early leaf primordia, which echoes the original reports (Vernoux et al., 2011; Brunoud et al., 2012). We also use DII/mDII and the PRS5A promoter-driven R2D2 sensors to confirm asymmetric auxin signaling in early leaf primordia. On the other hand, we provide evidence that light penetration may lead to artifacts during whole-mount imaging.

plant biology↗

bioRxiv2017

Kernel multitask regression for toxicogenetics

The development of high-throughput in vitro assays to study quantitatively the toxicity of chemical compounds on genetically characterized human-derived cell lines paves the way to predictive toxicogenetics, where one would be able to predict the toxicity of any particular compound on any particular individual. In this paper we present a machine learning-based approach for that purpose, kernel multitask regression (KMR), which combines chemical characterizations of molecular compounds with genetic and transcriptomic characterizations of cell lines to predict the toxicity of a given compound on a given cell line. We demonstrate the relevance of the method on the recent DREAM8 Toxicogenetics challenge, where it ranked among the best state-of-the-art models, and discuss the importance of choosing good descriptors for cell lines and chemicals.

bioinformatics↗

bioRxiv2017

Signaling Pathway Activities Improve Prognosis for Breast Cancer

With the advent of high-throughput technologies for genome-wide expression profiling, a large number of methods have been proposed to discover gene-based signatures as biomarkers to guide cancer prognosis. However, it is often difficult to interpret the list of genes in a prognostic signature regarding the underlying biological processes responsible for disease progression or therapeutic response. A particularly interesting alternative to gene-based biomarkers is mechanistic biomarkers, derived from signaling pathway activities, which are known to play a key role in cancer progression and thus provide more informative insights into cellular functions involved in cancer mechanism. In this study, we demonstrate that pathway-level features, such as the activity of signaling circuits, outperform conventional gene-level features in prediction performance in breast cancer prognosis. We also show that the proposed classification scheme can even suggest, in addition to relevant signaling circuits related to disease outcome, a list of genes that do not code for signaling proteins whose contribution to cancer prognosis potentially supplements the mechanisms detected by pathway analysis.

bioinformatics↗

bioRxiv2017

Complex interactions in legume/cereal intercropping system : role of root exudates in root-to-root communication

Dear Editor,\n\nLegume/cereal intercropping systems have been regarded as the practical application of basic ecological principles such as diversity, competition and facilitation. In a recent PNAS paper, Li et al. (1) describe the novel finding that maize exudates promote faba bean nodulation and nitrogen fixation by upregulating genes involved in (iso)flavonoids synthesis (chalcone-flavanone isomerase) within faba bean, resulting in production of more genistein, a legume-to-rhizobia signal during establishment of the faba bean N2-fixing symbiosis. Although we salute the authors methodological efforts, there is another mechanism that could be responsible for the effect of corn root exudates on faba been nitrogen fixation observed in this article (1). The authors may misunderstand their data and the signalling role of maize exudates, thus got a defective model for the root interactions between faba bean and maize.

plant biology↗

bioRxiv2016

The complex sequence landscape of maize revealed by single molecule technologies

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate elucidation of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here, we report the assembly and annotation of maize, a genetic and agricultural model species, using Single Molecule Real-Time (SMRT) sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and significant improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed over 130,000 intact transposable elements (TEs), allowing us to identify TE lineage expansions unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by SMRT sequencing. In addition, comparative optical mapping of two other inbreds revealed a prevalence of deletions in the low gene density region and maize lineage-specific genes.

genomics↗