Rapid Concentration of Ga-68 and Proof-of-Concept Microscale Labeling of [68Ga]Ga-PSMA-11 in a Droplet Reactor.

The radiometal gallium-68 (Ga-68) has garnered significant interest due to its convenient production via compact and widely available generators and the high performance of 68Ga-labeled compounds for positron-emission tomography (PET) imaging for cancer diagnosis and management of patients undergoing targeted radionuclide therapy. Given the short half life of Ga-68 (68 min), microfluidic-based radiosynthesis is a promising avenue to establish very rapid, efficient, and routine radiolabeling with Ga-68; however, the typical elution volume of Ga-68 from a generator (4-10 mL) is incompatible with the microliter reaction volumes of microfluidic devices. To bridge this gap, we developed a microscale cartridge-based approach to concentrate Ga-68. By optimizing cartridge design, resin type, resin mass, and eluent composition, Ga-68 was reliably concentrated from ~6 mL to ~80 µL with high recovery efficiency (>97%, n = 14). Furthermore, this method is suitable for both single- and dual-generator setups. To demonstrate suitability of the concentrated radiometal for radiolabeling, we performed microdroplet synthesis of [68Ga]Ga-PSMA-11, achieving high radiochemical yield (83 ± 11%, n = 3), excellent radiochemical purity (>99%), and high apparent specific activity (255-320 MBq/µg). The entire process, including Ga-68 concentration, radiosynthesis, purification, and formulation, was completed in 12 min. Starting with activity of 0.81-0.84 GBq, 0.51-0.64 GBq of product was produced, sufficient for multiple patient doses. This work paves the way to clinical-scale production of other 68Ga-labeled compounds using droplet microreactor methods, or high-throughput labeling optimization or compound screening of 68Ga-labeled probes using droplet reaction arrays.

Identification of pathogen composition in a Chinese population with iatrogenic and native vertebral osteomyelitis by using mNGS.

BACKGROUND: Early antimicrobial therapy is crucial regarding the prognosis of vertebral osteomyelitis, but early pathogen diagnosis remains challenging. OBJECTIVE: In this study, we aimed to differentiate the types of pathogens in iatrogenic vertebral osteomyelitis (IVO) and native vertebral osteomyelitis (NVO) to guide early antibiotic treatment. METHODS: A total of 145 patients, who had confirmed spinal infection and underwent metagenomic next-generation sequencing (mNGS) testing, were included, with 114 in the NVO group and 31 in the IVO group. Using mNGS, we detected and classified 53 pathogens in the 31 patients in the IVO group and 169 pathogens in the 114 patients in the NVO group. To further distinguish IVO from NVO, we employed machine learning algorithms to select serum biomarkers and developed a nomogram model. RESULTS: The results revealed that the proportion of the Actinobacteria phylum in the NVO group was approximately 28.40%, which was significantly higher than the 15.09% in the IVO group. Conversely, the proportion of the Firmicutes phylum (39.62%) in the IVO group was markedly increased compared to the 21.30% in the NVO group. Further genus-level classification demonstrated that Staphylococcus was the most common pathogen in the IVO group, whereas Mycobacterium was predominant in the NVO group. Through LASSO regression and random forest algorithms, we identified 5 serum biomarkers including percentage of basophils (BASO%), percentage of monocytes (Mono%), platelet volume (PCT), globulin (G), activated partial thromboplastin time (APTT) for distinguishing IVO from NVO. Based on these biomarkers, we established a nomogram model capable of accurately discriminating between the two conditions. CONCLUSION: The results of this study hold promise in providing valuable guidance to clinical practitioners for the differential diagnosis and early antimicrobial treatment of vertebral osteomyelitis.

A Regulatory Mechanism on Pathways: Modulating Roles of MYC2 and BBX21 in the Flavonoid Network.

Genes of metabolic pathways are individually or collectively regulated, often via unclear mechanisms. The anthocyanin pathway, well known for its regulation by the MYB/bHLH/WDR (MBW) complex but less well understood in its connections to MYC2, BBX21, SPL9, PIF3, and HY5, is investigated here for its direct links to the regulators. We show that MYC2 can activate the structural genes of the anthocyanin pathway but also suppress them (except F3'H) in both Arabidopsis and Oryza when a local MBW complex is present. BBX21 or SPL9 can activate all or part of the structural genes, respectively, but the effects can be largely overwritten by the local MBW complex. HY5 primarily influences expressions of the early genes (CHS, CHI, and F3H). TF-TF relationships can be complex here: PIF3, BBX21, or SPL9 can mildly activate MYC2; MYC2 physically interacts with the bHLH (GL3) of the MBW complex and/or competes with strong actions of BBX21 to lessen a stimulus to the anthocyanin pathway. The dual role of MYC2 in regulating the anthocyanin pathway and a similar role of BBX21 in regulating BAN reveal a network-level mechanism, in which pathways are modulated locally and competing interactions between modulators may tone down strong environmental signals before they reach the network.

Scalable droplet-based radiosynthesis of [18F]fluorobenzyltriphenylphosphonium cation ([18F]FBnTP) via a "numbering up" approach.

The [18F]fluorobenzyltriphenylphosphonium cation ([18F]FBnTP) has emerged as a highly promising positron emission tomography (PET) tracer for myocardial perfusion imaging (MPI) due to its uniform distribution in the myocardium and favorable organ biodistribution demonstrated in preclinical studies. However, a complex and low-efficiency radiosynthesis procedure has significantly hindered its broader preclinical and clinical explorations. Recently, Zhang et al. developed a pinacolyl arylboronate precursor, enabling a one-step synthesis process that greatly streamlines the production of [18F]FBnTP. Building upon this progress, our group successfully adapted the approach to a microdroplet reaction format and demonstrated improved radiosynthesis performance in a preliminary optimization study. However, scaling up to clinical dose amounts was not explored. In this work, we demonstrate that scale-up can be performed in a straightforward manner using a "numbering up" strategy (i.e. performing multiple droplet reactions in parallel and pooling the crude products). The resulting radiochemical yield after purification and formulation was high, up to 66 ± 1% (n = 4) for a set of experiments involving pooling of 4 droplet reactions, accompanied by excellent radiochemical purity (>99%) and molar activity (339-710 GBq µmol-1). Notably, we efficiently achieved sufficient activity yield (0.76-1.84 GBq) for multiple clinical doses from 1.6 to 3.7 GBq of [18F]fluoride in just 37-47 min.

Linking New Alleles at the Oscillator Loci to Flowering and Expansion of Asian Rice.

The central oscillator is believed to be the key mechanism by which plants adapt to new environments. However, impacts from hybridization, the natural environment, and human selection have rarely been assessed on the oscillator of a crop. Here, from clearly identified alleles at oscillator loci (OsCCA1/LHY, OsPRR95, OsPRR37, OsPRR59, and OsPRR1) in ten diverse genomes of Oryza sativa, additional accessions, and functional analysis, we show that rice's oscillator was rebuilt primarily by new alleles from recombining parental sequences and subsequent 5' or/and coding mutations. New alleles may exhibit altered transcript levels from that of a parental allele and are transcribed variably among genetic backgrounds and natural environments in RIL lines. Plants carrying more expressed OsCCA1_a and less transcribed OsPRR1_e flower early in the paddy field. 5' mutations are instrumental in varied transcription, as shown by EMSA tests on one deletion at the 5' region of highly transcribed OsPRR1_a. Compared to relatively balanced mutations at oscillator loci of Arabidopsis thaliana, 5' mutations of OsPRR37 (and OsCCA1 to a less degree) were under negative selection while those of OsPRR1 alleles were under strong positive selection. Together, range expansion of Asian rice can be elucidated by human selection on OsPRR1 alleles via local flowering time-yield relationships.

Proof-of-concept optimization of a copper-mediated 18F-radiosynthesis of a novel MAGL PET tracer on a high-throughput microdroplet platform and its macroscale translation.

Copper-mediated radiofluorination has demonstrated remarkable potential in forming aromatic C-18F bonds of radioligands for positron emission tomography (PET). Achieving optimal results often requires optimization efforts, requiring a substantial amount of radiolabeling precursor and time, severely limiting the experimental throughput. Recently, we successfully showcased the feasibility of performing and optimizing Cu-mediated radiosynthesis on a high-throughput microdroplet platform using the well-known and clinically used radioligand [18F]FDOPA as an illustrative example. In our current work, we optimized the Cu-mediated synthesis of a novel monoacylglycerol lipase (MAGL) PET tracer ([18F]YH149), showing the versatility of droplet-based techniques for early stage tracer development. Across 5 days, we conducted a total of 117 experiments, studying 36 distinct conditions, while utilizing <15 mg of total organoboron precursor. Compared to the original report in which the radiochemical yield (RCY) was 4.4 ± 0.5% (n = 5), the optimized droplet condition provided a substantial improvement in RCY (52 ± 8%, n = 4) and showed excellent radiochemical purity (100%) and molar activity (77-854 GBq µmol-1), using a starting activity of 0.2-1.45 GBq. Furthermore, we showed for the first time a translation of the optimized microscale conditions to a vial-based method. With similar starting activity (0.2-1.44 GBq), the translated synthesis exhibited a comparable RCY of 50 ± 10% (n = 4) while maintaining excellent radiochemical purity (100%) and acceptable molar activity (20-46 GBq µmol-1). The successful translation to vial-based reactions ensures wider applicability of the optimized synthesis by leveraging widely available commercial vial-based synthesis modules.

Accelerating radiochemistry development: Automated robotic platform for performing up to 64 droplet radiochemical reactions in a morning.

The growing discovery and development of novel radiopharmaceuticals and radiolabeling methods requires an increasing capacity for radiochemistry experiments. However, such studies typically rely on radiosynthesizers designed for clinical batch production rather than research, greatly limiting throughput. Two general solutions are being pursued to address this: developing new synthesis optimization algorithms to minimize how many experiments are needed, and developing apparatus with enhanced experiment throughput. We describe here a novel high-throughput system based on performing arrays of droplet-based reactions at 10 µL volume scale in parallel. The automatic robotic platform can perform a set of 64 experiments in ~3 h (from isotope loading to crude product, plus sampling onto TLC plates), plus ~1 h for off-line radio-TLC analysis and radioactivity measurements, rather than the weeks or months that would be needed using a conventional system. We show the high repeatability and low crosstalk of the platform and demonstrate optimization studies for two 18F-labeled tracers. This novel automated platform greatly increases the practicality of performing arrays of droplet reactions by eliminating human error, vastly reducing tedium and fatigue, minimizing radiation exposure, and freeing up radiochemist time for other intellectually valuable pursuits.

Gene Genealogy-Based Mutation Analysis Reveals Emergence of Aus, Tropical japonica, and Aromatic of Oryza sativa during the Later Stage of Rice Domestication.

Asian rice (Oryza sativa L.) has become a model for understanding gene functions and domestication in recent decades; however, its own diversification is still controversial. Although the division of indica and japonica and five subgroups (aus, indica (sensu stricto), japonica (sensu stricto), tropical japonica, and aromatic) are broadly accepted, how they are phylogenetically related is not transparent. To clarify their relationships, a sample of 121 diverse genes was chosen here from 12 Oryza genomes (two parental and ten O. sativa (Os)) in parallel to allow gene genealogy-based mutation (GGM) analysis. From the sample, 361 Os mutations were shared by two or more subgroups (referred to here as trans mutations) from 549 mutations identified at 51 Os loci. The GGM analysis and related tests indicates that aus diverged from indica at a time significantly earlier than when tropical japonica split from japonica. The results also indicate that aromatic was selected from hybrid progeny of aus and tropical japonica and that all five subgroups share a significant number of the early mutations identified previously. The results suggest that aus, tropical japonica, and aromatic emerged sequentially within the most recent 4-5 millennia of rice domestication after the split of indica and japonica.

A rapid and systematic approach for the optimization of radio thin-layer chromatography resolution.

Radiopharmaceutical analysis is limited by conventional methods. Radio-HPLC may be inaccurate for some compounds (e.g., 18F-radiopharmaceuticals) due to radionuclide sequester. Radio-TLC is simpler, faster, and detects all species but has limited resolution. Imaging-based readout of TLC plates (e.g., using Cerenkov luminescence imaging) can improve readout resolution, but the underlying chromatographic separation efficiency may be insufficient to resolve chemically similar species such as product and precursor-derived impurities. This study applies a systematic mobile phase optimization method, PRISMA, to improve radio-TLC resolution. The PRISMA method optimizes the mobile phase by selecting the correct solvent, optimizing solvent polarity, and optimizing composition. Without prior knowledge of impurities and by simply observing the separation resolution between a radiopharmaceutical and its nearest radioactive or non-radioactive impurities (observed via UV imaging) for different mobile phases, the PRISMA method enabled the development of high-resolution separation conditions for a wide range of 18F-radiopharmaceuticals ( [18F]PBR-06, [18F]FEPPA, [18F]Fallypride, [18F]FPEB, and [18F]FDOPA). Each optimization required a single batch of crude radiopharmaceutical and a few hours. Interestingly, the optimized TLC method provided greater accuracy (compared to other published TLC methods) in determining the product abundance of one radiopharmaceutical studied in more depth ( [18F]Fallypride) and was capable of resolving a comparable number of species as isocratic radio-HPLC. We used the PRISMA-optimized mobile phase for [18F]FPEB in combination with multi-lane radio-TLC techniques to evaluate reaction performance during high-throughput synthesis optimization of [18F]FPEB. The PRISMA methodology, in combination with high-resolution radio-TLC readout, enables a rapid and systematic approach to achieving high-resolution and accurate analysis of radiopharmaceuticals without the need for radio-HPLC.

Early Domestication History of Asian Rice Revealed by Mutations and Genome-Wide Analysis of Gene Genealogies.

BACKGROUND: Asian rice (Oryza sativa L.) has been a model plant but its cultivation history is inadequately understood, and its origin still under debate. Several enigmas remain, including how this annual crop shifted its growth habit from its perennial ancestor, O. rufipogon, why genetic divergence between indica and japonica appears older than the history of human domestication, and why some domestication genes do not show signals of introgression between subgroups. Addressing these issues may benefit both basic research and rice breeding. RESULTS: Gene genealogy-based mutation (GGM) analysis shows that history of Asian rice is divided into two phases (Phase I and II) of about equal lengths. Mutations occurred earlier than the partition of indica and japonica to Os genome mark Phase-I period. We diagnosed 91 such mutations among 101 genes sampled across 12 chromosomes of Asian rice and its wild relatives. Positive selection, detected more at 5' regions than at coding regions of some of the genes, involved 22 loci (e.g., An-1, SH4, Rc, Hd3a, GL3.2, OsMYB3, OsDFR, and OsMYB15), which affected traits from easy harvesting, grain color, flowering time, productivity, to likely taste and tolerance. Phase-I mutations of OsMYB3, OsHd3a and OsDFR were experimentally tested and all caused enhanced functions of the genes in vivo. Phase-II period features separate cultivations, lineage-specific selection, and expanded domestication to more genes. Further genomic analysis, along with phenotypic comparisons, indicates that O. sativa is hybrid progeny of O. rufipogon and O. nivara, inherited slightly more genes of O. rufipogon. Congruently, modern alleles of the sampled genes are approximately 6% ancient, 38% uni-specific, 40% bi-specific (mixed), and 15% new after accumulating significant mutations. Results of sequencing surveys across modern cultivars/landraces indicate locus-specific usages of various alleles while confirming the associated mutations. CONCLUSIONS: Asian rice was initially domesticated as one crop and later separate selection mediated by human resulted in its major subgroups. This history and the hybrid origin well explain previous puzzles. Positive selection, particularly in 5' regions, was the major force underlying trait domestication. Locus-specific domestication can be characterized and the result may facilitate breeders in developing better rice varieties in future.

Economical droplet-based microfluidic production of [18F]FET and [18F]Florbetaben suitable for human use.

Current equipment and methods for preparation of radiopharmaceuticals for positron emission tomography (PET) are expensive and best suited for large-scale multi-doses batches. Microfluidic radiosynthesizers have been shown to provide an economic approach to synthesize these compounds in smaller quantities, but can also be scaled to clinically-relevant levels. Batch microfluidic approaches, in particular, offer significant reduction in system size and reagent consumption. Here we show a simple and rapid technique to concentrate the radioisotope, prior to synthesis in a droplet-based radiosynthesizer, enabling production of clinically-relevant batches of [18F]FET and [18F]FBB. The synthesis was carried out with an automated synthesizer platform based on a disposable Teflon-silicon surface-tension trap chip. Up to 0.1 mL (4 GBq) of radioactivity was used per synthesis by drying cyclotron-produced aqueous [18F]fluoride in small increments directly inside the reaction site. Precursor solution (10 µL) was added to the dried [18F]fluoride, the reaction chip was heated for 5 min to perform radiofluorination, and then a deprotection step was performed with addition of acid solution and heating. The product was recovered in 80 µL volume and transferred to analytical HPLC for purification. Purified product was formulated via evaporation and resuspension or a micro-SPE formulation system. Quality control testing was performed on 3 sequential batches of each tracer. The method afforded production of up to 0.8 GBq of [18F]FET and [18F]FBB. Each production was completed within an hour. All batches passed quality control testing, confirming suitability for human use. In summary, we present a simple and efficient synthesis of clinically-relevant batches of [18F]FET and [18F]FBB using a microfluidic radiosynthesizer. This work demonstrates that the droplet-based micro-radiosynthesizer has a potential for batch-on-demand synthesis of 18F-labeled radiopharmaceuticals for human use.

Self-Assembly of Copolymer Micelles: Higher-Level Assembly for Constructing Hierarchical Structure.

In recent years, the self-assembly of copolymer micelles has become an appealing frontier of supramolecular chemistry as a strategy to construct superstructures with multiple levels of complexity. The assembly of copolymer micelles is a form of higher-level self-assembly occurring at the nanoscale level where the building blocks are preassembled micelles. Compared to one-step hierarchical self-assembly, this assembly strategy is superior for manipulating multilevel architectures because the structures of the building blocks and higher-order hierarchies can be regulated separately in the first and higher-level assembly, respectively. However, despite the substantial advances in the self-assembly of copolymer micelles in recent years, universal laws have not been comprehensively summarized. This review article aims to provide an overview of the current progress and developing prospects of the self-assembly of copolymer micelles. In particular, the significant role of theoretical simulations in revealing the mechanism of copolymer micelle self-assembly is discussed.

HPLC-free in situ18F-fluoromethylation of bioactive molecules by azidation and MTBD scavenging.

Sequential usage of azide and MTBD, which generates pure [18F]fluoromethyl tosylate and scavenges unreacted desmethyl precursors, provided an efficient HPLC-free strategy for the radiosynthesis of 18F-fluoromethylated compounds with high radiochemical yields and purity. This in situ18F-fluoromethylation can serve as a facile and efficient tool for the development of radiopharmaceuticals.

Supramolecular "Step Polymerization" of Preassembled Micelles: A Study of "Polymerization" Kinetics.

In nature, sophisticated functional materials are created through hierarchical self-assembly of nanoscale motifs, which has inspired the fabrication of man-made materials with complex architectures for a variety of applications. Herein, a kinetic study on the self-assembly of spindle-like micelles preassembled from polypeptide graft copolymers is reported. The addition of dimethylformamide and, subsequently, a selective solvent (water) can generate a "reactive point" at both ends of the spindles as a result of the existence of structural defects, which induces the "polymerization" of the spindles into nanowires. Experimental results combined with dissipative particle dynamics simulations show that the polymerization of the micellar subunits follows a step-growth polymerization mechanism with a second-order reaction characteristic. The assembly rate of the micelles is dependent on the subunit concentration and on the activity of the reactive points. The present work reveals a law governing the self-assembly kinetics of micelles with structural defects and opens the door for the construction of hierarchical structures with a controllable size through supramolecular step polymerization.

Polypeptide self-assemblies: nanostructures and bioapplications.

Polypeptide copolymers can self-assemble into diverse aggregates. The morphology and structure of aggregates can be varied by changing molecular architectures, self-assembling conditions, and introducing secondary components such as polymers and nanoparticles. Polypeptide self-assemblies have gained significant attention because of their potential applications as delivery vehicles for therapeutic payloads and as additives in the biomimetic mineralization of inorganics. This review article provides an overview of recent advances in nanostructures and bioapplications related to polypeptide self-assemblies. We highlight recent contributions to developing strategies for the construction of polypeptide assemblies with increasing complexity and novel functionality that are suitable for bioapplications. The relationship between the structure and properties of the polypeptide aggregates is emphasized. Finally, we briefly outline our perspectives and discuss the challenges in the field.

Formation of CaCO3 fibres directed by polypeptide vesicles.

Mineralization behaviour of CaCO3 in the presence of polypeptide vesicles self-assembled from poly(l-glutamic acid)-block-poly(propylene oxide)-block-poly(l-glutamic acid) (PLGA-b-PPO-b-PLGA) triblock copolymers was studied. Under the mediation of PLGA-b-PPO-b-PLGA vesicles, CaCO3 fibre clusters were obtained. The structure of fibres could be regulated by the mineralization temperature, copolymer composition, copolymer concentration, and Ca2+ concentration. The investigation of the fibre growth process suggested a solution-precursor-solid mechanism via transient amorphous precursors. Since the polypeptide vesicles could serve as both the modifier and template for the formation of amorphous precursors, the properties of amorphous precursors were affected by the vesicular structure. The variation in the fibre structure was ascribed to the different aggregation and transformation behaviours of amorphous particles. These findings can provide useful information for the design of novel inorganic materials with fibrous structures and enrich our existing knowledge of the crystallization process from the amorphous phase.

Characterization of the cis elements in the proximal promoter regions of the anthocyanin pathway genes reveals a common regulatory logic that governs pathway regulation.

Cellular activities such as compound synthesis often require the transcriptional activation of an entire pathway; however, the molecular mechanisms underlying pathway activation have rarely been explained. Here, the cis regulatory architecture of the anthocyanin pathway genes targeted by the transcription factor (TF) complex including MYB, bHLH, and WDR was systematically analysed in one species and the findings extended to others. In Ipomoea purpurea, the IpMYB1-IpbHLH2-IpWDR1 (IpMBW) complex was found to be orthologous to the PAP1-GL3-TTG1 (AtPGT) complex of Arabidopsis thaliana, and interacted with a 7-bp MYB-recognizing element (MRE) and a 6-bp bHLH-recognizing element (BRE) at the proximal promoter region of the pathway genes. There was little transcription of the gene in the absence of the MRE or BRE. The cis elements identified experimentally converged on two syntaxes, ANCNNCC for MREs and CACN(A/C/T)(G/T) for BREs, and our bioinformatic analysis showed that these were present within anthocyanin gene promoters in at least 35 species, including both gymnosperms and angiosperms. For the anthocyanin pathway, IpMBW and AtPGT recognized the interspecific promoters of both early and later genes. In A. thaliana, the seed-specific TF complex (TT2, TT8, and TTG1) may regulate all the anthocyanin pathway genes, in addition to the proanthocyanidin-specific BAN. When multiple TF complexes in the anthocyanin pathway were compared, the cis architecture played a role larger than the TF complex in determining the variation in promoter activity. Collectively, a cis logic common to the pathway gene promoters was found, and this logic is essential for the trans factors to regulate the pathway.

Transformation of the education of health professionals in China: progress and challenges.

In this Review we examine the progress and challenges of China's ambitious 1998 reform of the world's largest health professional educational system. The reforms merged training institutions into universities and greatly expanded enrolment of health professionals. Positive achievements include an increase in the number of graduates to address human resources shortages, acceleration of production of diploma nurses to correct skill-mix imbalance, and priority for general practitioner training, especially of rural primary care workers. These developments have been accompanied by concerns: rapid expansion of the number of students without commensurate faculty strengthening, worries about dilution effect on quality, outdated curricular content, and ethical professionalism challenged by narrow technical training and growing admissions of students who did not express medicine as their first career choice. In this Review we underscore the importance of rebalance of the roles of health sciences institutions and government in educational policies and implementation. The imperative for reform is shown by a looming crisis of violence against health workers hypothesised as a result of many factors including deficient educational preparation and harmful profit-driven clinical practices.

Dissecting organ-specific transcriptomes through RNA-sequencing.

BACKGROUND: Organ-specific gene expression contains rich information about in vivo biological processes. This kind of information, previously gathered through microarray profiling, has been proven fruitful to the understanding of specific mutants, regulatory events, signaling, and development. With the advent of the next-generation sequencing (NGS) of RNAs, more quantitative and detailed information of gene expressions than previously available can now be collected for each organ or organ developmental stages. The combination of an object-oriented experimental design and an efficient treatment of the high volume information generated through a NGS platform may offer a powerful tool for inferring previously intractable developmental processes. RESULTS: We collected transcriptomic data over a Solexa/Illumina platform on samples of Ipomoea leaf, sepal, and petals (at three developmental stages), and presented a method for analyzing transcriptomic variations within and between organs. We demonstrated that in vivo signals of transcriptomes can be retrieved de novo through the NGS techniques, proper data handling, bioinformatic tools, and the current understanding of molecular networks. We found that numbers of transcribed genes from both nuclear and chloroplast genomes decreased by the same order of leaf → sepal →petal. Petal resembled leaf in cell division patterns and abundance level of commonly expressed organelle genes. Its chloroplast transcripts constituted a subset of those in leaf. Moreover, reconstructions of multiple metabolic networks for each organ enabled inferences of substance flow, providing transcript evidence for the path of sucrose in leaf to anthocyanin synthesis in petal. CONCLUSION: Our results attest that developmental transcriptomes are highly informative for exploring connections between morphological traits and the associated molecular networks. Significant hypotheses have been developed, including that the petal is a derived organ of leaf and that its color can be modified by fluctuations of substance flow within the associated metabolic networks among organs.

A valid strategy for precise identifications of transcription factor binding sites in combinatorial regulation using bioinformatic and experimental approaches.

BACKGROUND: Transcription factor (TF) binding sites (cis element) play a central role in gene regulation, and eukaryotic organisms frequently adapt a combinatorial regulation to render sophisticated local gene expression patterns. Knowing the precise cis element on a distal promoter is a prerequisite for studying a typical transcription process; however, identifications of cis elements have lagged behind those of their associated trans acting TFs due to technical difficulties. Consequently, gene regulations via combinatorial TFs, as widely observed across biological processes, have remained vague in many cases. RESULTS: We present here a valid strategy for identifying cis elements in combinatorial TF regulations. It consists of bioinformatic searches of available databases to generate candidate cis elements and tests of the candidates using improved experimental assays. Taking the MYB and the bHLH that collaboratively regulate the anthocyanin pathway genes as examples, we demonstrate how candidate cis motifs for the TFs are found on multi-specific promoters of chalcone synthase (CHS) genes, and how to experimentally test the candidate sites by designing DNA fragments hosting the candidate motifs based on a known promoter (us1 allele of Ipomoea purpurea CHS-D in our case) and applying site-mutagenesis at the motifs. It was shown that TF-DNA interactions could be unambiguously analyzed by assays of electrophoretic mobility shift (EMSA) and dual-luciferase transient expressions, and the resulting evidence precisely delineated a cis element. The cis element for R2R3 MYBs including Ipomoea MYB1 and Magnolia MYB1, for instance, was found to be ANCNACC, and that for bHLHs (exemplified by Ipomoea bHLH2 and petunia AN1) was CACNNG. A re-analysis was conducted on previously reported promoter segments recognized by maize C1 and apple MYB10, which indicated that cis elements similar to ANCNACC were indeed present on these segments, and tested positive for their bindings to Ipomoea MYB1. CONCLUSION: Identification of cis elements in combinatorial regulation is now feasible with the strategy outlined. The working pipeline integrates the existing databases with experimental techniques, providing an open framework for precisely identifying cis elements. This strategy is widely applicable to various biological systems, and may enhance future analyses on gene regulation.