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.
Hierarchically porous SAPO-11 zeolite (H-SAPO-11) is rationally synthesized from a starting silicoaluminophosphate gel in the presence of polyhexamethylene biguanidine as a mesoscale template. The sample is well characterized by XRD, N2 sorption, SEM, TEM, NMR, XPS, NH3-TPD, and TG techniques. The results show that the sample obtained has good crystallinity, hierarchical porosity (mesopores at ca. 10 nm and macropores at ca. 50-200 nm), high BET surface area (226 m(2)/g), large pore volume (0.25 cm(3)/g), and abundant medium and strong acidic sites (0.36 mmol/g). After loading Pt (0.5 wt.%) on H-SAPO-11 by using wet impregnation method, catalytic hydroisomerization tests of n-dodecane show that the hierarchical Pt/SAPO-11 zeolite exhibits high conversion of n-dodecane and enhanced selectivity for branched products as well as reduced selectivity for cracking products, compared with conventional Pt/SAPO-11 zeolite. This phenomenon is reasonably attributed to the presence of hierarchical porosity, which is favorable for access of reactants on catalytically active sites. The improvement in catalytic performance in long-chain paraffin hydroisomerization over Pt/SAPO-11-based catalyst is of great importance for its industrial applications in the future.
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.
We conducted an unbiased metagenomics survey using plasma from patients with chronic hepatitis B, chronic hepatitis C, autoimmune hepatitis (AIH), non-alcoholic steatohepatitis (NASH), and patients without liver disease (control). RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Hepatitis viruses were readily detected at high coverage in patients with chronic viral hepatitis B and C, but only a limited number of sequences resembling other viruses were found. The exception was a library from a patient diagnosed with hepatitis C virus (HCV) infection that contained multiple sequences matching GB virus C (GBV-C). Abundant GBV-C reads were also found in plasma from patients with AIH, whereas Torque teno virus (TTV) was found at high frequency in samples from patients with AIH and NASH. After taxonomic classification of sequences by BLASTn, a substantial fraction in each library, ranging from 35% to 76%, remained unclassified. These unknown sequences were assembled into scaffolds along with virus, phage and endogenous retrovirus sequences and then analyzed by BLASTx against the non-redundant protein database. Nearly the full genome of a heretofore-unknown circovirus was assembled and many scaffolds that encoded proteins with similarity to plant, insect and mammalian viruses. The presence of this novel circovirus was confirmed by PCR. BLASTx also identified many polypeptides resembling nucleo-cytoplasmic large DNA viruses (NCLDV) proteins. We re-evaluated these alignments with a profile hidden Markov method, HHblits, and observed inconsistencies in the target proteins reported by the different algorithms. This suggests that sequence alignments are insufficient to identify NCLDV proteins, especially when these alignments are only to small portions of the target protein. Nevertheless, we have now established a reliable protocol for the identification of viruses in plasma that can also be adapted to other patient samples such as urine, bile, saliva and other body fluids.
The synthesis process of aluminophosphate AlPO(4)-11 molecular sieve in the mixed water/1-butyl- 3-methylimidazolium bromide ([bmim]Br) ionic liquid was investigated by XRD, multinuclear solid-state NMR, scanning electron microscopy (SEM) and X-ray energy dispersive spectroscopy (EDS). It was observed that a tablet phase, named SIZ-2, was formed at the early stage of crystallization. During crystallization metastable SIZ-2 with an incompletely condensed framework phosphorus disappeared gradually, and the phosphorous species became fully condensed through hydroxyl reaction with tetrahedral aluminum to form thermodynamically stable AlPO(4)-11 in the final product. It was found that [bmim]Br, acting as the structure-directing agent, was occluded into the AlPO(4)-11 channel.
Genome-wide gene expression profile using deep sequencing technologies can drive the discovery of cancer biomarkers and therapeutic targets. Such efforts are often limited to profiling the expression signature of either mRNA or microRNA (miRNA) in a single type of cancer.
In situ two-dimensional NMR and fluorescence emission spectroscopy were employed to investigate the cooperative structure-direction effect of organic amine such as morpholine in the synthesis of aluminophosphate molecular sieves in ionic liquids. In situ rotating frame nuclear Overhauser effect spectra (ROESY) together with fluorescence measurements demonstrate that the aggregates between imidazolium cations and morpholines through intermolecular hydrogen bonds can be formed in the gel during the crystallization of molecular sieves. Combining with the characterizations of the solid products by solid-state NMR, it is verified that different aggregates of organic amines with imidazolium cations, which is similar to self-assembled supramolecular analogues, could act as the structure-directing agents for selective tuning of the framework topologies such as AEL, AFI and LTA in the final solid products.
Cationic templating of imidazolium adjusted by the amine concentration in an ionothermal system results in products with larger channels or cage-like structures by reassembling the inorganic hosts around the changed organic guests.
We report the development of a combined strategy for high capacity, comprehensive enrichment of endogenous peptide from complex biological samples at natural pH condition. MCM-41 nanoparticles with highly ordered nanoscale pores (i.e. 4.8nm) and high-surface area (i.e. 751m(2)/g) were synthesized and modified with strong cation-exchange (SCX-MCM-41) and strong anion-exchange (SAX-MCM-41) groups. The modified nanoparticles demonstrated good size-exclusion effect for the adsorption of standard protein lysozyme with molecular weight (MW) of ca. 15kDa; and the peptides with MW lower than this value can be well adsorbed. Step elution of the enriched peptides with five salt concentrations presented that both modified nanoparticles have high capacity and complementarity for peptides enrichment, and the SAX-MCM-41 nanoparticles has obviously high selectivity for acidic peptides with pI (isoelectric point) lower than 4. Large-scale enrichment of endogenous peptides in 2mg mouse liver extract was achieved by further combination of SCX-MCM-41 and SAX-MCM-41 with unmodified MCM-41 nanoparticles. On-line 2D nano-LC/MS/MS was applied to analyze the enriched samples, and 2721 unique peptides were identified in total. Two-dimensional analysis of MW versus pI distribution combined with abundance of the identified peptides demonstrated that the three types of nanoparticles have comprehensive complementarity for peptidome enrichment.
A combination of state-of-the art in situ one- and two-dimensional NMR spectroscopy and density functional theory (DFT) calculations have been employed for the first time to investigate the role of amines in the synthesis of aluminophosphate molecular sieves in ionic liquids (ILs). In situ rotating-frame nuclear Overhauser effect spectroscopy (ROESY) was used to demonstrate that the hybrid of imidazolium ionic liquids with organic amines, such as morpholine, connected through a hydrogen bond can be formed in the gel during the crystallization of molecular sieves. By combining the characterizations of the final solid products obtained by using XRD analyses, solid-state NMR spectroscopy, thermogravimetric analysis, and DFT calculation results, it was verified that the hybrid between morpholine and the imidazolium cation in the initial preparation stage can act as the structure-directing agent (SDA) for the synthesis of AFI-structured aluminophosphate molecular sieves. Our findings may suggest a synthesis mechanism of molecular sieves in ionic liquids in which the IL-organic amine hybrid is required in the nucleation step, whereas the crystal growth occurs through the occlusion of ionic liquids in the zeolite channels.
Next-generation sequencing plays a central role in the characterization and quantification of transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, there have been no large-scale empirical evaluations of the major determinants of sequencing success. We used a combination of existing and newly developed methods to isolate total RNA from 1115 samples from 695 plant species in 324 families, which represents >900 million years of phylogenetic diversity from green algae through flowering plants, including many plants of economic importance. We then sequenced 629 of these samples on Illumina GAIIx and HiSeq platforms and performed a large comparative analysis to identify predictors of RNA quality and the diversity of putative genes (scaffolds) expressed within samples. Tissue types (e.g., leaf vs. flower) varied in RNA quality, sequencing depth and the number of scaffolds. Tissue age also influenced RNA quality but not the number of scaffolds ? 1000 bp. Overall, 36% of the variation in the number of scaffolds was explained by metrics of RNA integrity (RIN score), RNA purity (OD 260/230), sequencing platform (GAIIx vs HiSeq) and the amount of total RNA used for sequencing. However, our results show that the most commonly used measures of RNA quality (e.g., RIN) are weak predictors of the number of scaffolds because Illumina sequencing is robust to variation in RNA quality. These results provide novel insight into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes. The methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers.
For the first time, the co-templating ionothermal methodology was used in the preparation of layered aluminophosphate materials. With the addition of either 1,2-ethylenediamine or 1,6-hexanediamine to the ionic liquid 1-ethyl-3-methyl imidazolium chloride, two new 2D layered aluminophosphates RUB-A1 [Al(3)P(4)O(16)][NH(3)CH(2)CH(2)NH(3)](0.5)[C(6)N(2)H(11)](2) and RUB-A2 [Al(3)P(4)O(16)][NH(3)(CH(2))(6)NH(3)][NH(3)(CH(2))(6)NH(2)](0.5)[C(6)N(2)H(11)](0.5)[H(2)O] have been synthesized ionothermally by co-templating. The structure of RUB-A1 has been determined from single-crystal X-ray diffraction data using direct methods, while the structure of RUB-A2 has been solved ab initio from powder X-ray diffraction data with limited resolution using direct-space methods. Both of these two compounds have a 2D layered structure consisting of macroanionic sheets of composition [Al(3)P(4)O(16)](3-) stacked in an AAAA sequence. The inorganic layers are built up from alternatively vertex-sharing [AlO(4)]- and [PO(3)(=O)]-tetrahedral units forming a 4.6.8 and a 4.6.12 network for RUB-A1 and RUB-A2, respectively. The layer topology of RUB-A1 is closely related to the previously known 4.6.8-layer topology but with a different sequence of phosphoryl group orientation. Combining the results of structure analysis with the NMR, chemical analysis and TG-DTA experiments, we show that both the ionic liquid cation and the protonated diamines are located in the interlayer space and together direct the formation of these two structures.
A one-step hydrotreatment of vegetable oil combining deoxygenation and isomerization to directly produce low cloud point, high quality diesel is devised. The Pt/zeolite bifunctional catalysts prepared by using SAPO-11 and ZSM-22 zeolites as supports are used in this process. Catalytic reactions are conducted in a fixed-bed reactor under a hydrogen atmosphere. Over the bifunctional catalyst, 100 % conversion of soybean oil is obtained at 357 °C, 4 MPa, and 1 h(-1), and 80 % organic liquid yield is achieved, which is close to the maximum theoretical liquid yield. In the organic products, the alkanes selectivity is 100 % with an i-alkanes selectivity above 63 %. NH(3)-temperature programmed desorption (TPD), pyridine IR spectroscopy, and other characterization techniques are used to study the effect of the support acidity on the reaction pathway. Over the Pt/zeolite bifunctional catalyst with less strong Lewis acid sites, the reaction proceeds via the decarboxylation plus decarbonylation pathway. This one-step method provides a new strategy to produce low cloud point, high quality diesel from biomass feedstock in a more economic and attractive way.
There are remarkable disparities among patients of different races with prostate cancer; however, the mechanism underlying this difference remains unclear. Here, we present a comprehensive landscape of the transcriptome profiles of 14 primary prostate cancers and their paired normal counterparts from the Chinese population using RNA-seq, revealing tremendous diversity across prostate cancer transcriptomes with respect to gene fusions, long noncoding RNAs (long ncRNA), alternative splicing and somatic mutations. Three of the 14 tumors (21.4%) harbored a TMPRSS2-ERG fusion, and the low prevalence of this fusion in Chinese patients was further confirmed in an additional tumor set (10/54=18.5%). Notably, two novel gene fusions, CTAGE5-KHDRBS3 (20/54=37%) and USP9Y-TTTY15 (19/54=35.2%), occurred frequently in our patient cohort. Further systematic transcriptional profiling identified numerous long ncRNAs that were differentially expressed in the tumors. An analysis of the correlation between expression of long ncRNA and genes suggested that long ncRNAs may have functions beyond transcriptional regulation. This study yielded new insights into the pathogenesis of prostate cancer in the Chinese population.
RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ?767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed a computational pipeline that carefully controls for false positives while calling RNA editing events from genome and whole-transcriptome data of the same individual. We identified 22,688 RNA editing events in noncoding genes and introns, untranslated regions and coding sequences of protein-coding genes. Most changes (?93%) converted A to I(G), consistent with known editing mechanisms based on adenosine deaminase acting on RNA (ADAR). We also found evidence of other types of nucleotide changes; however, these were validated at lower rates. We found 44 editing sites in microRNAs (miRNAs), suggesting a potential link between RNA editing and miRNA-mediated regulation. Our approach facilitates large-scale studies to profile and compare editomes across a wide range of samples.
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.