A Hybrid Approach Combining Conceptual Hydrological Models, Support Vector Machines and Remote Sensing Data for Streamflow Simulation

Understanding catchment response to rainfall events is important for accurate runoff estimation in many water-related applications, including water resources management. This study introduced a hybrid model, the Tank-least squared support vector machine (LSSVM), that incorporated intermediate state variables from a conceptual tank model within the least squared support vector machine (LSSVM) framework in order to describe aspects of the rainfall-runoff (RR) process. The efficacy of the Tank-LSSVM model was demonstrated with hydro-meteorological data measured in the Yongdam Catchment between 2007 and 2016, South Korea. We first explored the role of satellite soil moisture (SM) data (i.e., European Space Agency (ESA) CCI) in the rainfall-runoff modeling. The results indicated that the SM states inferred from the ESA CCISWI provided an effective means of describing the temporal dynamics of SM. Further, the Tank-LSSVM model’s ability to simulate daily runoff was assessed by using goodness of fit measures (i.e., root mean square error, Nash Sutcliffe coefficient (NSE), and coefficient of determination). The Tank-LSSVM models’ NSE were all classified as “very good” based on their performance during the training and testing periods. Compared to individual LSSVM and Tank models, improved daily runoff simulations were seen in the proposed Tank-LSSVM model. In particular, low flow simulations demonstrated the improvement of the Tank-LSSVM model compared to the conventional tank model

Molecular Studies of the Protein Complexes Involving Cis-Prenyltransferase in Guayule (Parthenium argentatum), an Alternative Rubber-Producing Plant

Guayule (Parthenium argentatum) is a perennial shrub in the Asteraceae family and synthesizes a high quality, hypoallergenic cis-1,4-polyisoprene (or natural rubber; NR). Despite its potential to be an alternative NR supplier, the enzymes for cis-polyisoprene biosynthesis have not been comprehensively studied in guayule. Recently, implications of the protein complex involving cis-prenyltransferases (CPTs) and CPT-Binding Proteins (CBPs) in NR biosynthesis were shown in lettuce and dandelion, but such protein complexes have yet to be examined in guayule. Here, we identified four guayule genes – three PaCPTs (PaCPT1-3) and one PaCBP, whose protein products organize PaCPT/PaCBP complexes. Co-expression of both PaCBP and each of the PaCPTs could complemented the dolichol (a short cis-polyisoprene)-deficient yeast, whereas the individual expressions could not. Microsomes from the PaCPT/PaCBP-expressing yeast efficiently incorporated 14C-isopentenyl diphosphate into dehydrodolichyl diphosphates; however, NR with high molecular weight could not be synthesized in in vitro assays. Furthermore, co-immunoprecipitation and split-ubiquitin yeast 2-hybrid assays using PaCPTs and PaCBP confirmed the formation of protein complexes. Of the three PaCPTs, guayule transcriptomics analysis indicated that the PaCPT3 is predominantly expressed in stem and induced by cold-stress, suggesting its involvement in NR biosynthesis. The comprehensive analyses of these PaCPTs and PaCBP here provide the foundational knowledge to generate a high NR-yielding guayule

Piperonal synthase from black pepper (Piper nigrum) synthesizes a phenolic aroma compound, piperonal, as a CoA-independent catalysis

Piperonal is a simple aromatic aldehyde compound with a characteristic cherry-like aroma and has been widely used in the flavor and fragrance industries. Despite piperonal being an important aroma in black pepper (Piper nigrum), its biosynthesis remains unknown. In this study, the bioinformatic analysis of the P. nigrum transcriptome identified a novel hydratase-lyase, displaying 72% amino acid identity with vanillin synthase, a member of the cysteine proteinase family. In in vivo substrate-feeding and in vitro enzyme assays, the hydratase-lyase catalyzed a side-chain cleavage of 3,4-methylenedioxycinnamic acid (3,4-MDCA) to produce 3,4-methylenedioxybenzaldehyde (piperonal) and thus was named piperonal synthase (PnPNS). The optimal pH for PnPNS activity was 7.0, and showed a K-m of 317.2 mu M and a k(cat) of 2.7 s(-1). The enzyme was most highly expressed in the leaves, followed by the fruit. This characterization allows for the implementation of PnPNS in various microbial platforms for the biological production of piperonal.N

Molecular cloning and characterization of drimenol synthase from valerian plant (Valeriana officinalis)

AbstractDrimenol, a sesquiterpene alcohol, and its derivatives display diverse bio-activities in nature. However, a drimenol synthase gene has yet to be identified. We identified a new sesquiterpene synthase cDNA (VoTPS3) in valerian plant (Valeriana officinalis). Purification and NMR analyses of the VoTPS3-produced terpene, and characterization of the VoTPS3 enzyme confirmed that VoTPS3 synthesizes (−)-drimenol. In feeding assays, possible reaction intermediates, farnesol and drimenyl diphosphate, could not be converted to drimenol, suggesting that the intermediate remains tightly bound to VoTPS3 during catalysis. A mechanistic consideration of (−)-drimenol synthesis suggests that drimenol synthase is likely to use a protonation-initiated cyclization, which is rare for sesquiterpene synthases. VoTPS3 can be used to produce (−)-drimenol, from which useful drimane-type terpenes can be synthesized

In Pursuit of Understanding the Rumen Microbiome

The rumen plays an indispensable role in ruminants to utilize ligno-cellulosic material and convert non-protein nitrogen into nutrients otherwise unavailable for human consumption. Recent advancements in the sequencing technology and omics approach have provided profound insights into the rumen world, wherein a consortium of archaea, bacteria, protozoa, fungi, and viruses exist and interact. These ruminal microbes alter the ruminal environment and execute several interlinked metabolic cascades that produce substrates for the host’s energy and body requirements. Methane is emitted as a by-product during this complex fermentation process in ruminants leading to a loss in productivity while negatively impacting the environment. As ruminants play an ever-increasing role in our food supply chain, manipulating the rumen is the critical step towards maximizing the ruminant product’s nutritional value while reducing its carbon footprint. Diet is the most straightforward way to alter the rumen microbiome, possibly in conjunction with phytobiotics and probiotics as feed supplements. Early life interventions allow the manipulation of microbial population structure and function that could persist later on in adult life. It has also been proven that the host exerts influence on the rumen microbiome as a heritable trait. The goal of this review is to provide a better understanding of the rumen, its key organisms, and its development to better identify, characterize, and engineer the rumen microbiome for efficient feed conversion and methane reduction

Germacrene A Synthases for Sesquiterpene Lactone Biosynthesis Are Expressed in Vascular Parenchyma Cells Neighboring Laticifers in Lettuce

Sesquiterpene lactone (STL) and natural rubber (NR) are characteristic isoprenoids in lettuce (Lactuca sativa). Both STL and NR co-accumulate in laticifers, pipe-like structures located along the vasculature. NR-biosynthetic genes are exclusively expressed in laticifers, but cell-type specific expression of STL-biosynthetic genes has not been studied. Here, we examined the expression pattern of germacrene A synthase (LsGAS), which catalyzes the first step in STL biosynthesis in lettuce. Quantitative PCR and Illumina read mapping revealed that the transcripts of two GAS isoforms (LsGAS1/LsGAS2) are expressed two orders of magnitude (~100–200) higher in stems than laticifers. This result implies that the cellular site for LsGAS1/2 expression is not in laticifers. To gain more insights, promoters of LsGAS1/2 were cloned and fused to β-glucuronidase (GUS), followed by transformations of lettuce with these promoter-GUS constructs. In in situ GUS assays, the GUS expression driven by the LsGAS1/2 promoters was tightly associated with vascular bundles. High-resolution microsections showed that GUS signals are not present in laticifers but are detected in the vascular parenchyma cells neighboring the laticifers. These results suggest that expression of LsGAS1/2 occurs in the parenchyma cells neighboring laticifers, while the resulting STL metabolites accumulate in laticifers. It can be inferred that active metabolite-trafficking occurs from the parenchyma cells to laticifers in lettuce.Science, Irving K. Barber Faculty of (Okanagan)Non UBCChemistry, Department of (Okanagan)ReviewedFacultyResearche

Identification of Activated Cdc42-Associated Kinase Inhibitors as Potential Anticancer Agents Using Pharmacoinformatic Approaches

Background: Activated Cdc42-associated kinase (ACK1) is essential for numerous cellular functions, such as growth, proliferation, and migration. ACK1 signaling occurs through multiple receptor tyrosine kinases; therefore, its inhibition can provide effective antiproliferative effects against multiple human cancers. A number of ACK1-specific inhibitors were designed and discovered in the previous decade, but none have reached the clinic. Potent and selective ACK1 inhibitors are urgently needed. Methods: In the present investigation, the pharmacophore model (PM) was rationally built utilizing two distinct inhibitors coupled with ACK1 crystal structures. The generated PM was utilized to screen the drug-like database generated from the four chemical databases. The binding mode of pharmacophore-mapped compounds was predicted using a molecular docking (MD) study. The selected hit-protein complexes from MD were studied under all-atom molecular dynamics simulations (MDS) for 500 ns. The obtained trajectories were ranked using binding free energy calculations (ΔG kJ/mol) and Gibb’s free energy landscape. Results: Our results indicate that the three hit compounds displayed higher binding affinity toward ACK1 when compared with the known multi-kinase inhibitor dasatinib. The inter-molecular interactions of Hit1 and Hit3 reveal that compounds form desirable hydrogen bond interactions with gatekeeper T205, hinge region A208, and DFG motif D270. As a result, we anticipate that the proposed scaffolds might help in the design of promising selective ACK1 inhibitors