Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor--neochrome--that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.
Flavonoids are one of the largest classes of plant secondary metabolites serving a variety of functions in plants and associating with a number of health benefits for humans. Typically, they are co-identified with many other secondary metabolites using untargeted metabolomics. The limited data quality of untargeted workflow calls for a shift from the breadth-first to the depth-first screening strategy when a specific biosynthetic pathway is focused on. Here we introduce a generic multiple reaction monitoring (MRM)-based approach for flavonoids profiling in plants using a hybrid triple quadrupole linear ion trap (QTrap) mass spectrometer. The approach includes four steps: (1) preliminary profiling of major aglycones by multiple ion monitoring triggered enhanced product ion scan (MIM-EPI); (2) glycones profiling by precursor ion triggered EPI scan (PI-EPI) of major aglycones; (3) comprehensive aglycones profiling by combining MIM-EPI and neutral loss triggered EPI scan (NL-EPI) of major glycone; (4) in-depth flavonoids profiling by MRM-EPI with elaborated MRM transitions. Particularly, incorporation of the NH3 loss and sugar elimination proved to be very informative and confirmative for flavonoids screening. This approach was applied for profiling flavonoids in Astragali radix (Huangqi), a famous herb widely used for medicinal and nutritional purposes in China. In total, 421 flavonoids were tentatively characterized, among which less than 40 have been previously reported in this medicinal plant. This MRM-based approach provides versatility and sensitivity that required for flavonoids profiling in plants and serves as a useful tool for plant metabolomics.
Triterpenoid saponins (TSs) are a unique class of high molecular weight glycosides and have been frequently used in cosmetic and phytotherapy industry. There is a great need to comprehensively profile these plant metabolites for studying their functions. In the present study, a novel adducts targeted neutral loss (NL), triggered enhanced resolution (ER) and enhanced product ion (EPI) scanning approach were described for TSs profiling using a triple quadrupole linear ion trap mass spectrometry. This approach circumvented the disadvantages of poor glycosidic bond cleavage of TSs by monitoring the NH3 (NL17) and HCOOH (NL46) loss of their abundant ammonium and formate adducts, respectively. The sugar-loss independent NL scanning served as a sensitive survey scan and triggered information-dependent ER and EPI scans to increase peak assignment confidence. NL17 was superior to NL46 for TSs characterization due to the better fragmentation of ammonium adducts than formate adducts. For those TSs undetectable by NL17, precursor ion (PI) scan for sapogenin fragments could be used to screen out non-adducted TSs. The NL/PI-ER-EPI approach was applied for TSs profiling in Astragali Radix, a famous medicinal and nutritional plant widely used in Asian countries and United States. In total, 136 TSs were detected while previous research using high resolution mass spectrometry based full scan only detected 22 TSs in this herb.
Optogenetic tools enable examination of how specific cell types contribute to brain circuit functions. A long-standing question is whether it is possible to independently activate two distinct neural populations in mammalian brain tissue. Such a capability would enable the study of how different synapses or pathways interact to encode information in the brain. Here we describe two channelrhodopsins, Chronos and Chrimson, discovered through sequencing and physiological characterization of opsins from over 100 species of alga. Chrimson's excitation spectrum is red shifted by 45 nm relative to previous channelrhodopsins and can enable experiments in which red light is preferred. We show minimal visual system-mediated behavioral interference when using Chrimson in neurobehavioral studies in Drosophila melanogaster. Chronos has faster kinetics than previous channelrhodopsins yet is effectively more light sensitive. Together these two reagents enable two-color activation of neural spiking and downstream synaptic transmission in independent neural populations without detectable cross-talk in mouse brain slice.
A way of ethyl acetoacetate by the Claisen condensation reaction is one of the main methods of the industrial production of dehydroacetic acid. There are the problems of the differences in absorbance value and the maximum absorption wavelength, and the chromatographic peak is prone to the phenomena such as bifurcation and tailing when using liquid chromatography to the analysis of ethyl acetoacetate. To avoid the interference of the enol of ethyl acetoacetate, and making the peak shape of ethyl acetoacetate better and quantitatively more accurate, we converted the enol to ketone through optimizing the chromatographic conditions. As a result, qualitative and quantitative analyses of ethyl acetoacetate were replaced by those of the ethyl acetoacetate ketone. A method was developed for the simultaneous determination of dehydroacetic acid and ethyl acetoacetate by HPLC in the reaction mixture for producing dehydroacetic acid. An Agilent HC-C18 column (250 mm x 4.6 mm, 5 microm) was used for the separation. The ultraviolet wavelength was 290 nm and the column temperature was 35 degrees C, and methanol-0.3% ammonium acetate buffer (5: 95, v/v) with pH 6.0 adjusted by acetic acid as mobile phase, and the flow rate was 0.6 mL/min. The correlation coefficients of dehydroacetic acid and ethyl acetoacetate were 0.99995 and 0.99992, and the spiked recoveries were 98.5% and 101.3%, respectively; and the relative standard deviations were less than 1.0%. This meth- od has the advantages of good accuracy and high sensitivity, and it can analyse both qualitatively and quantitatively dehydroacetic acid and ethyl acetoacetate rapidly and simply. And it can provide the reference for producing dehydroacetic acid by the way of ethyl acetoacetate.
Genome-wide association studies (GWAS) of ischemic stroke (IS) have been performed on several cohorts of Caucasian or African population and Japanese, resulting in somewhat inconsistent conclusion. We aimed to identify susceptibility loci for IS by exome sequencing in a Chinese Han population. Exome sequencing was used to screen susceptibility loci among 100 cases and 100 matched controls. Significant SNPs from the first stage were verified in up to 3,554 participants from three hospital-based case-control studies. In the initial exome sequencing analysis, rs10489177 in c1orf156 gene located on chromosome 1q24 (p?1?×?10(-8)) and rs17118 in XYLB gene located on chromosome 3p21 (p?1?×?10(-6)) were found to be significantly associated with IS. In the following validation stage, significantly increased odds ratios were observed in individuals with rs10489177 GG (OR?=?2.02, 95 % CI?=?1.35-3.03) or rs17118 AA genotype (OR?=?1.50, 95 % CI?=?1.17-1.91). The rs10489177 GG genotype was associated with significantly increased risk for IS in individuals without hypertension (OR?=?2.78, 95 % CI?=?1.59-4.86) and in individuals without diabetes (OR?=?1.93, 95 % CI?=?1.27-2.94). In contrast, the rs17118 AA genotype may significantly increase the risk for IS, particularly for individuals with hypertension (OR?=?1.73, 95 % CI?=?1.08-2.78) and for individuals without diabetes (OR?=?1.52, 95 % CI?=?1.17-1.98) or non-smoker (OR?=?1.59, 95 % CI?=?1.16-2.19). Collectively, our study identified two novel loci (rs17118 and rs10489177) which were associated with an increased risk for IS in Chinese Han populations. Further studies are needed to confirm these associations in other populations and elucidate the biological mechanisms underlying the observed associations.
An improved anion-exchange chromatographic method was developed for simultaneous quantification of 1-sulfo-cyclohexane carboxylic acid (SCCA) and sulfate anion in the by-products of caprolactam. An strong anion chromatographic column and an ultraviolet (UV) detector were chosen for the assay of SCCA and sulfate anion. Non-chromophore-containing sulfate anion is not directly adaptable to the commonly used ultraviolet detection of high performance liquid chromatography (HPLC). This paper reports the development and validation of an HPLC assay for SCCA and sulfate anion based on indirect ultraviolet detection. An ultraviolet-absorbing reagent (the probe), phthalic acid (PA), was added to the mobile phase to induce a signal for the compound. The proposed method was qualified based on the performance criteria of repeatability, intermediate precision and linearity. The limits of detection were 1.0 g/L for both the analytes. The linear ranges varied from 0.50 to 40.0 g/L for SCCA and from 0.10 to 10.0 g/L for sulfate anion, with the correlation coefficients of 0. 999 97 and 0.999 14, and the recoveries of 93.33%-97.40% and 98.50%-101.00%, respectively. The established method can be used in practice to determine SCCA and sulfate anion simultaneously with perfect separation selectivity.
Abstract Context: Cilnidipine (CN) is a novel dihydropyridine calcium antagonist that is practically insoluble in aqueous media and exhibits a low oral bioavailability or limited clinical efficacy. Objective: This study investigated the effects of three commercial and chemically diverse polymers - PVP, PVP/VA and Soluplus - on crystallization tendency and in vitro dissolution profiles of CN in order to determine an optimum carrier for composing the preferred solid dispersion (SD) of CN. Methods: All these co-evaporated systems were characterized up to 3 months by thermoanalytical (DSC), crystallographic (POM, PXRD), microscopic (SEM) and spectroscopic (FTIR) techniques. Results: The results showed that the polymers could be sorted by their effects of inhibiting CN crystallization in the ascending order: Soluplus, PVP/VA, PVP. The sequence was in accordance with that of the strength of drug-polymer hydrogen bonds revealed by FTIR spectra. It could be ascribed to relative hydrogen-bonding acceptor strengths of N-vinylpyrrolidone moiety in the polymer molecules. On the other hand, all the SDs showed enhanced dissolution profiles compared to pure CN alone. On their effects of enhancing CN dissolution, the polymers could be sorted in the descending order: Soluplus, PVP, PVP/VA. Conclusions: It implied that the dissolution behavior of CN could bear a close relationship to both hydration capacity and hydrogen-bonding interaction tendency of moieties of the polymers. It might suggest an optimal formulation for CN comprising both PVP and Soluplus.
Rheumatoid arthritis (RA) is the most common chronic inflammatory disease with unknown causes and unknown cures in Western medicine. This double-blinded study aimed to investigate the efficacy and safety of a widely used traditional Chinese medicine (Paeoniflorin (PAE) plus cervus and cucumis polypeptide injection (CCPI) using disease-modifying antirheumatic drugs (DMARD) as a control (methotrexate (MTX) plus leflunomide (LEF)). Patients were randomly assigned to one of the three groups: PAE + CCPI, MTX + LEF, and MTX + LEF + CCPI. The primary end point was the American College of Rheumatology 20% improvement response criteria (ACR20). The secondary end point was that of adverse effect frequencies and the speed of onset action. Our results showed that more patients in the CCPI-containing groups responded to the ACR20 during early treatment. After six months, ACR20 showed no significant difference among the three treatments. The maximum improvement in the two DMARD groups was significantly higher than that in the PAE + CCPI group (p < 0.01). CCPI made the onset action of the DMARD therapy 4.6 times faster. PAE + CCPI had significantly lower adverse event incidences than the two DMARD groups. These results indicate that PAE + CCPI appear to be a more acceptable alternative to DMARDs when patients cannot use DMARDs. CCPI appears to be a beneficial add-on to DMARDs that makes the onset of action faster, especially when patients need to relieve RA symptoms as soon as possible. Although not as effective as DMARDs, PAE appears to be a safer option to substitute DMARDs for long-term RA treatment when DMARD toxicity is an issue.
There is a growing need both clinically and experimentally to improve the determination of the blood levels of multiple chemical constituents in herbal medicines. The conventional multiple reaction monitoring (cMRM), however, is not well suited for multi-component determination and could not provide qualitative information for identity confirmation. Here we apply a dynamic triggered MRM (DtMRM) algorithm for the quantification of 20 constituents in an herbal prescription Bu-Zhong-Yi-Qi-Tang (BZYQT) in rat plasma. Dynamic MRM (DMRM) dramatically reduced the number of concurrent MRM transitions that are monitored during each MS scan. This advantage has been enhanced with the addition of triggered MRM (tMRM) for simultaneous confirmation, which maximizes the dwell time in the primary MRM quantitation phase, and also acquires sufficient MRM data to create a composite product ion spectrum. By allowing optimized collision energy for each product ion and maximizing dwell times, tMRM is significantly more sensitive and reliable than conventional product ion scanning. The DtMRM approach provides much higher sensitivity and reproducibility than cMRM.
In this study, a sensitive and reliable liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for the determination of seven bioactive components including paeoniflorin, nobiletin, tangeretin, liquiritigenin, isoliquiritigenin, liquiritin and formononetin in rat plasma and tissues after oral administration of Si-Ni-San extract using astragaloside IV as internal standard (IS). The plasma and tissue samples were extracted by solid-phase extraction. Chromatographic separation was accomplished on a C18 column with a multiple-step gradient elution. The quantification was obtained by scanning with multiple reaction monitoring via an electrospray ionization source that was operated by switching between the positive and negative modes in two MS/MS scan segments. Full validation of the assay was implemented. In conclusion, this method demonstrated good linearity and specificity. The lower limits of quantification for the analytes were <7.5 ng/mL. Intra- and inter-day precisions (RSD) were <12.5% and accuracy (RE) ranged from -10.2 to 7.3%. The average recoveries of the analytes from rat plasma and tissues were >65.2% and 58.6%, respectively. The validated method was further applied to the determination of actual rat plasma and tissues after oral administration of Si-Ni-San extract. The results provided a meaningful basis for the clinical application of this prescription.
We sequenced the genome of a Pakistani male at 25.5x coverage using massively parallel sequencing technology. More than 90% of the sequence reads were mapped to the human reference genome. In subsequent analysis, we identified 3,224,311 single-nucleotide polymorphisms (SNPs), of which 388,532 (12% of the total SNPs) had not been previously recorded in single nucleotide polymorphism database (dbSNP) or the 1000 Genomes Project database. The 5991 non-synonymous coding variants were screened for deleterious or disease-associated SNPs. Analysis of genes with deleterious SNPs identified retinoic acid signaling and regulation of transcription as the enriched Gene Ontology terms. Scanning of non-synonymous SNPs against the OMIM revealed several disease and phenotype-associated variants in Pakistani genome. Comparative analysis with Indian genome sequence revealed >1.8 million shared SNPs; 32% of which were annotated in ~14,000 genes. Gene Ontology (GO) terms analysis of these genes identified response to jasmonic acid stimulus, aminoglycoside antibiotic metabolic process and glycoside metabolic process with considerable enrichment. A total of 59,558 of small indels (1-5 bp) and 16,063 large structural variations were found; 54% of which was novel. Substantial number of novel structural variations discovered in Pakistani genome enforced previous inferences that (a) structural variations are major type of variation in the genome and (b) compared with SNPs, they putatively exhibit equivalent or superior functional roles. This genome sequence information will be an important reference for population-wide genomics studies of ethnically diverse South Asian subcontinent.
A rapid ultra-high-performance liquid chromatographic-tandem mass spectrometric (UHPLC-MS-MS) method has been developed for rapid screening and quantitative analysis of sulfonate derivatives (SDs) in commercial white peony root. Separation was performed on an Agilent Zorbax Eclipse Plus-C18 column by gradient elution with acetonitrile-0.1% (v/v) formic acid as the mobile phase. In-source fragmentation was used to generate the characteristic fragment ion at m/z 259 and to screen for nine SDs. Detection of these SDs was further performed in multiple reaction monitoring (MRM) mode to improve sensitivity and to quantify the two SDs paeoniflorin sulfonate and benzoylpaeoniflorin sulfonate. The method was validated for specificity, linearity, limits of detection and quantification, precision, accuracy, and matrix effects. Nine commercial white peony root samples were examined by use of this method, which revealed great variety in the paeoniflorin sulfonate and benzoylpaeoniflorin sulfonate content.
Si-Ni-San (SNS) is a widely used traditional Chinese medicine formula (TCMF) in treating various diseases. However, the in vivo integrated metabolism of its multiple components remains unknown. In this paper, a liquid chromatography coupled with diode array detection and triple-quadrupole spectrometry (LC-DAD-MS/MS) method was developed for detection and identification of SNS metabolites in rat plasma and urine at a normal clinical dosage. Accurate structural elucidation was performed using MS/MS, UV data and n-octanol/water partition coefficient. Based on the proposed strategy, 36 absorbed compounds and 29 metabolites in plasma and 33 metabolites in urine were detected by a highly sensitive MRM method. Our results indicated that phase II reactions (e.g., methylation, glucuronidation and sulfation) were the main metabolic pathways of gallic acid and flavanones, while phase I reactions (e.g., hydroxylation) were the major metabolic reaction for triterpenoid saponins. The metabolite profile analysis of SNS provided a comprehensive understanding of the in vivo metabolic fates of constituents in SNS. Moreover, the results in this work demonstrated the present strategy based on the combination of chromatographic, spectrophotometric, mass-spectrometric, and software prediction to detect and identify metabolites was effective and reliable. And such a strategy may also be extended to investigate the metabolism of other TCMF.
Tong-Xie-Yao-Fang (TXYF), a famous traditional Chinese medicine formula, has efficient effects on treatment of the diarrhea-predominant irritable bowel syndrome (D-IBS), a disease with high incidence worldwide. However, the active principles for this complex formula have not been fully explored so far. In this paper, high-performance liquid chromatography coupled with diode array detection and electrospray ionization tandem mass spectrometry (HPLC-DAD-ESI-MS/MS) was applied for the qualitative and quantitative analysis of major chemical constituents in TXYF. Two monoterpene glycosides, one chromone and five polymethoxylated flavones were tentatively characterized based on the retention times, UV spectra and MS data. Fifteen compounds were unambiguously identified by comparison with reference standards. Constituents such as lactone and steroidal, which could not be found by single HPLC method due to the low content in the formula, were identified in this paper. Seven compounds (gallic acid, prim-O-?-D-glucosylcimifugin, paeoniflorin, cimifugin, naringin, hesperidin and 4-O-?-D-glucosyl-5-O-methylvisamminol) were quantified by HPLC-DAD using a C18 column and gradient elution with acetonitrile and water-0.1% formic acid. The method exhibited intra- and inter-day precision of less than 2.35% and 3.14%, respectively. The LODs and the LOQs for the analytes were less than 0.47 and 1.82 ?g ml(-1), respectively. The overall recoveries ranged from 96.82% to 102.47%, with the R.S.D. ranging from 1.17% to 3.94%. These results demonstrated that our present method was effective and reliable for comprehensive quality evaluation of TXYF. Meanwhile, the study might provide the chemical evidence for revealing the material basis of its therapeutic effects.
There are numerous approaches to decipher a whole genome DNA methylation profile ("methylome"), each varying in cost, throughput and resolution. The gold standard of these methods, whole genome bisulfite-sequencing (BS-seq), involves treatment of DNA with sodium bisulfite combined with subsequent high throughput sequencing. Using BS-seq, we generated a single-base-resolution methylome in human peripheral blood mononuclear cells (in press). This BS-seq map was then used as the reference methylome to compare two alternative sequencing-based methylome assays (performed on the same donor of PBMCs): methylated DNA immunoprecipitation (MeDIP-seq) and methyl-binding protein (MBD-seq). In our analysis, we found that MeDIP-seq and MBD-seq are complementary strategies, with MeDIP-seq more sensitive to highly methylated, high-CpG densities and MDB-seq more sensitive to highly methylated, moderate-CpG densities. Taking into account the size of a mammalian genome and the current expense of sequencing, we feel 3gigabases (Gbp) 45bp paired-end MeDIP-seq or MBD-seq uniquely mapped reads is the minimum requirement and cost-effective strategy for methylome pattern analysis.
Accumulating evidence supports that tumor growth and cancer relapse are driven by cancer stem cells. Our previous work has demonstrated the existence of CD90(+) liver cancer stem cells (CSCs) in hepatocellular carcinoma (HCC). Nevertheless, the characteristics of these cells are still poorly understood. In this study, we employed a more sensitive RNA-sequencing (RNA-Seq) to compare the gene expression profiling of CD90(+) cells sorted from tumor (CD90(+)CSCs) with parallel non-tumorous liver tissues (CD90(+)NTSCs) and elucidate the roles of putative target genes in hepatocarcinogenesis.
Related JoVE Video
Journal of Visualized Experiments
What is Visualize?
JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.
How does it work?
We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.
Video X seems to be unrelated to Abstract Y...
In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.