A specialized metabolic network selectively modulates Arabidopsis root microbiota

Plant specialized metabolites have ecological functions, yet the presence of numerous uncharacterized biosynthetic genes in plant genomes suggests that many molecules remain unknown. We discovered a triterpene biosynthetic network in the roots of the small mustard plant Arabidopsis thaliana. Collectively, we have elucidated and reconstituted three divergent pathways for the biosynthesis of root triterpenes, namely thalianin (seven steps), thalianyl medium-chain fatty acid esters (three steps), and arabidin (five steps). A. thaliana mutants disrupted in the biosynthesis of these compounds have altered root microbiota. In vitro bioassays with purified compounds reveal selective growth modulation activities of pathway metabolites toward root microbiota members and their biochemical transformation and utilization by bacteria, supporting a role for this biosynthetic network in shaping an Arabidopsis-specific root microbial community

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Natural product discovery: studies on the phenolic antioxidants from Smilax Glyciphylla and the synthesis and formation of Guaiane Sesquiterpenoids.

The work within this thesis is positioned in the field of natural product (NP) chemistry and covers three main integrated studies along with some additional explorations. These studies not only included the isolation and characterisation of NP but also involved total syntheses of various NP and related derivatives and detailed mechanistic studies into potential routes of formation in nature. Given my naturally emerging zest for natural products, I have begun this thesis with a detailed discussion of the numerous syntheses of Taxol. This exemplar highlights not only why the field of natural products is so important, but also highlights the ever growing significance of total and semi-syntheses. The first major study investigated the phenolic profile and antioxidant activity of the leaves of the Australian native plant Smilax glyciphylla. Along with the sweet principle glycyphyllin A, seven phenolic compounds including two new dihydrochalcone rhamnosides, glycyphyllin B and C, and five known flavonoids were isolated from the ethanolic extract of the leaves of Smilax glyciphylla for the first time. The structures of these compounds were characterised by spectroscopic methods including UV, HRMS, 1D and 2D NMR. In vitro antioxidant capacity tests employing the FRAP and DPPH assays indicated that three of the isolated compounds exhibited potent antioxidant activity and are the key phenolics responsible for the high antioxidant activity of the leaf extract of S. glyciphylla. The second major study focused on the synthesis of guaiane type sesquiterpenoids via the diastereoselective epoxidation of guaiol and realized by manipulating the types of remote protecting groups on the isopropanoyl side chain, choice of solvent and epoxidising reagent. This stragety allowed for a concise stereoselective synthesis of a range of guaiane-type sesquiterpenoids including the natural products guaia-4(5)-en-11-ol, guaia-5(6)-en-11-ol, and aciphyllene and epimers of the recently isolated natural products, 1-epi-guaia-4(5)-en-11-ol, 1-epi-aciphyllene and 1-epi-melicodenone C and E in up to 31% yield within 11 steps. The third study explored the autoxidation of α-guaiene and the mechanisms involved. Over a dozen sesquiterpenoids including natural rotundone, corymbolone and the C7 epimers of natural chabrolidione A and several unstable hydroperoxide intermediates were isolated from the autoxidation products of α-guaiene. Their structures were elucidated on the basis of spectroscopic data along with the synthesis of authentic compounds. Detailed mechanistic studies have allowed many of the mechanisms involved in the formation of these downstream oxidation products to be elucidated. Together with the above main studies, several deuterium labelled precursors including d₇-α- guaiene, d₅-(2R/2S)-rotundols, d₅-α-bulnesone, d₇-α-bulnesene and d₅-2R-bulnesol were synthesised and used as internal standards to develop a robust analytical method (SIDA) to monitor the transformation of certain precursors to the sesquiterpneoid fragrances rotundone and 2R-bulnesol. A total of five publications support my research works herein and are included as the main research chapters of this thesis.Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 201

Multi-Omics-Based Discovery of Plant Signaling Molecules

Plants produce numerous structurally and functionally diverse signaling metabolites, yet only relatively small fractions of which have been discovered. Multi-omics has greatly expedited the discovery as evidenced by increasing recent works reporting new plant signaling molecules and relevant functions via integrated multi-omics techniques. The effective application of multi-omics tools is the key to uncovering unknown plant signaling molecules. This review covers the features of multi-omics in the context of plant signaling metabolite discovery, highlighting how multi-omics addresses relevant aspects of the challenges as follows: (a) unknown functions of known metabolites; (b) unknown metabolites with known functions; (c) unknown metabolites and unknown functions. Based on the problem-oriented overview of the theoretical and application aspects of multi-omics, current limitations and future development of multi-omics in discovering plant signaling metabolites are also discussed

Different femoral tunnel placement in posterior cruciate ligament reconstruction: a finite element analysis

Abstract Background At present, there is no consensus on the optimal biomechanical method for Posterior cruciate ligament (PCL) reconstruction, and the “critical corner” that is produced by the femoral tunnel is currently considered to be one of the main reasons for PCL failure. Thus, the purpose of this study was to identify one or several different tunnels of the femur, thereby reducing the influence of the "critical corner" without reducing the posterior stability of the knee. Methods CT and MRI data of the knee joint of a healthy adult man were collected, and computer-related software was used to reconstruct the finite element model of the knee joint, to provide different properties to different materials and to allow for the performance of a finite element analysis of the reconstructed model. The position of the femoral tunnel was positioned and partitioned according to anatomical posture, and three areas were divided (the antero-proximal region, the antero-distal region and the posterior region). In addition, we applied a posterior tibial load of 134 N to the reconstructed model, recorded and compared different tunnels of the femur, conducted peak stress at the flexion of the knee joint of 0°, 30°, 60° and 90°, and elicited the displacement of the proximal tibia. Results Among the 20 different femoral tunnels, the graft peak stress was lower in tunnels 4, 12 and 18 than in the PCL anatomical footpath tunnel 13, especially at high flexion angles (60° and 90°). These three tunnels did not increase the posterior displacement of the proximal tibia compared with the anatomical footpath tunnel 13. Conclusion In summary, among the options for PCL reconstruction of the femoral tunnel, the tunnels located 5 mm distal to the footprint and 5 mm anterior to the footprint could reduce the peak stress of the graft; additionally, it may reduce the "critical corner" and was shown to not reduce the posterior stability of the knee joint

CCDC 1539192: Experimental Crystal Structure Determination

KAYPEI : 3,5a,7a-trimethyl-6-methylidene-10-(propan-2-yl)hexadecahydro-1H-pentaleno[6a,1-a]-s-indacen

CCDC 1539191: Experimental Crystal Structure Determination

KAYPAE : 5,9,13,14a-tetramethyl-3-(propan-2-yl)-1,2,3,3a,4,4a,7,8,11,13a,14,14a-dodecahydrocycloundeca[f]inden

CCDC 1535307: Experimental Crystal Structure Determination

KAYNIK : 3,5a,5b,7a-tetramethyl-10-(propan-2-yl)hexadecahydropentaleno[1',6a':2,3]-s-indaceno[1,8a-b]oxiren