The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

https://pubs.rsc.org/en/content/articlepdf/2019/NP/C8NP00092A

Marine natural products.

KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース)

2,5-Diketopiperazines: synthesis, reactions, medicinal chemistry, and bioactive natural products.

Secondary metabolites of fungi from marine habitats.

Englerin A, a selective inhibitor of renal cancer cell growth, from Phyllanthus engleri.

Chemical analysis of an Australian marine-derived isolate of Penicillium bilaii, collected from the Huon estuary, Port Huon, Tasmania, yielded the known fungal aromatic polyketides citromycetin (1) and citromycin (2) together with two dihydro analogues, (–)-2,3-dihydrocitromycetin (3) and (–)-2,3-dihydrocitromycin (4). An Australian terrestrial isolate of Penicillium striatisporum collected near Shalvey, New South Wales, also yielded citromycetin (1), citromycin (2), and the new dihydro analogue (–)-2,3-dihydrocitromycetin (3), together with fulvic acid (5), anhydrofulvic acid (6), and a selection of new methoxylated analogues, 12-methoxycitromycetin (7), 12-methoxycitromycin (8), (–)-12-methoxy-2,3-dihydrocitromycetin (9), and 12-methoxyanhydrofulvic acid (10). P. bilaii also yielded the rare siderophore pistillarin (11), the known diketopiperazines cyclo-(l-Phe-l-Pro) (12), cyclo-(l-Pro-l-Tyr) (13), cyclo-(l-Pro-l-Val) (14), and cis-bis(methylthio)silvatin (15), and three new diketopiperazines, bilains ...

Citromycetins and bilains A-C: new aromatic polyketides and diketopiperazines from Australian marine-derived and terrestrial Penicillium spp.

The kibdelones are a novel family of bioactive heterocyclic polyketides produced by a rare soil actinomycete, Kibdelosporangium sp. (MST-108465). Complete relative stereostructures were assigned to kibdelones A-C (1-3), kibdelone B rhamnoside (5), 13-oxokibdelone A (7), and 25-methoxy-24-oxokibdelone C (8) on the basis of detailed spectroscopic analysis and chemical interconversion, as well as mechanistic and biosynthetic considerations. Under mild conditions, kibdelones B (2) and C (3) undergo a facile equilibration to kibdelones A-C (1-3), while kibdelone B rhamnoside (5) equilibrates to a mixture of kibdelone A-C rhamnosides (4-6). A plausible mechanism for this equilibration is proposed and involves air oxidation, quinone/hydroquinone redox transformations, and a choreographed sequence of keto/enol tautomerizations that aromatize ring C via a quinone methide intermediate. Kibdelones exhibit potent and selective cytotoxicity against a panel of human tumor cell lines and display significant antibacterial and nematocidal activity.

Kibdelones: Novel anticancer polyketides from a rare Australian actinomycete

Englerin A Stimulates PKCθ to Inhibit Insulin Signaling and to Simultaneously Activate HSF1: Pharmacologically Induced Synthetic Lethality

We validate the improved resolution and sensitivity of the C3 Marfey's method, including an ability to resolve all Ile isomers, against an array of amino acids commonly encountered in natural products and by comparison to an existing Marfey's method. We also describe an innovative 2D C3 Marfey's method as an analytical approach for determining the regiochemistry of enantiomeric amino acid residues in natural products. The C3 and 2D C3 Marfey's methods represent valuable tools for probing and defining the stereocomplexity of hydrolytically accessible amino acid residues in natural products.

Ranjala Ratnayake

Papers

Englerin A, a selective inhibitor of renal cancer cell growth, from Phyllanthus engleri.

Citromycetins and bilains A-C: new aromatic polyketides and diketopiperazines from Australian marine-derived and terrestrial Penicillium spp.

Kibdelones: Novel anticancer polyketides from a rare Australian actinomycete

Englerin A Stimulates PKCθ to Inhibit Insulin Signaling and to Simultaneously Activate HSF1: Pharmacologically Induced Synthetic Lethality

C3 and 2D C3 Marfey's Methods for Amino Acid Analysis in Natural Products.