Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks.

Deep neural networks have demonstrated improved performance at predicting the sequence specificities of DNA- and RNA-binding proteins compared to previous methods that rely on k-mers and position weight matrices. To gain insights into why a DNN makes a given prediction, model interpretability methods, such as attribution methods, can be employed to identify motif-like representations along a given sequence. Because explanations are given on an individual sequence basis and can vary substantially across sequences, deducing generalizable trends across the dataset and quantifying their effect size remains a challenge. Here we introduce global importance analysis (GIA), a model interpretability method that quantifies the population-level effect size that putative patterns have on model predictions. GIA provides an avenue to quantitatively test hypotheses of putative patterns and their interactions with other patterns, as well as map out specific functions the network has learned. As a case study, we demonstrate the utility of GIA on the computational task of predicting RNA-protein interactions from sequence. We first introduce a convolutional network, we call ResidualBind, and benchmark its performance against previous methods on RNAcompete data. Using GIA, we then demonstrate that in addition to sequence motifs, ResidualBind learns a model that considers the number of motifs, their spacing, and sequence context, such as RNA secondary structure and GC-bias.

Pro-apoptotic effects of the flavonoid luteolin in rat H4IIE cells.

Polyphenols are ubiquitous substances in the diet. Their anti-oxidative, anti-inflammatory and anti-viral effects are of interest for human health, and polyphenols such as luteolin are used at high concentrations in food supplements. The aim of this project was to determine the intrinsic effects of luteolin in H4IIE rat hepatoma cells. Luteolin is relatively toxic, cell death was caused via induction of apoptosis as detected by DNA-ladder formation, by nuclear fragmentation and activation of apoptotic enzymes (caspase-2, -3/7, -9 and -8/10). Luteolin (250 microM, 24 h) increased the caspase-3/7 activity four-fold and the caspase-9 activity six-fold. In a time course experiment caspase-9 is activated after 6h, while caspase-2 and -3/7 are activated after 12 h. After 24 h, caspase-8/10 also displays activation. We found a concentration-dependent increase in malondialdehyde release suggesting a prooxidative effect of luteolin. Furthermore, we analysed DNA strand break formation by luteolin and found a distinct increase of DNA strand breaks after incubation for 3h with 100 microM luteolin, a concentration which induces oligonucleosomal DNA cleavage at 24h. In conclusion, the sequence of events is compatible with the assumption that luteolin triggers the mitochondrial pathway of apoptosis, probably by inducing DNA damage.

The Aspergillus nidulans lysF gene encodes homoaconitase, an enzyme involved in the fungus-specific lysine biosynthesis pathway.

In filamentous fungi, lysine is synthesized via the alpha-aminoadipate pathway. In order to gain insight into this fungus-specific pathway (to date, no genes for enzymes of this pathway in filamentous fungi have been cloned) the lysine auxotrophic mutant LysF88 of Aspergillus nidulans was studied. HPLC and 1H-NMR analyses revealed that LysF88 accumulated homocitric acid in the culture supernatant. In addition, both the LysF88 mutant strain and LysF deletion strain (LysFKO) described here showed hardly any homoaconitase activity, indicating that lysF encodes homoaconitase. The lysF gene was cloned by complementation of the LysF88 mutant and sequenced. It has a size of 2397 bp, including a single intron of 72 bp. The two exons encode an open reading frame (ORF) of 2325 bp. The calculated M(r) of the homoaconitase protein (775 amino acids) is 83,943. A major and a minor transcript begin at positions -28 and -32, respectively. The 3' end of the lysF cDNA showed a poly(A) tail commencing at position +2647 following a 250 bp untranslated region after the lysF stop codon. A putative polyadenylation signal sequence (TATAAA) is located 49 bp upstream of the polyadenylation site. Computer analysis revealed 55% amino acid sequence identity between the products of the putative homoaconitase ORF of A. nidulans and that of the recently sequenced homologous Saccharomyces cerevisiae. The similarity was particularly obvious in a region of cysteine residues, which are characteristic of an iron-sulfur cluster, implying that homoaconitase contains such a cluster. The homoaconitases of A. nidulans and S. cerevisiae share only 20% sequence identity with S. cerevisiae aconitase. The pH optimum for the activity of A. nidulans homoaconitase in 0.1 M potassium phosphate buffer is between pH 8.1 and pH 8.6. Homoaconitase exhibited an apparent K(m) of 1.1 mM toward homoisocitric acid. The specific activity of homoaconitase was reduced by up to six-fold in mycelia grown in the presence of L-lysine, suggesting that it is regulated by lysine.

The mniopetals, new inhibitors of reverse transcriptases from a Mniopetalum species (basidiomycetes). II. Structure elucidation.

The structures of six new drimance sesquiterpenoids, mniopetals A-F, were elucidated by a combination of chemical and spectroscopic methods. The mniopetals are inhibitors of RNA-directed DNA-polymerases.

Sesquiterpenoids from the roots of Homalomena aromatica.

From roots of Homalomena aromatica three new sesquiterpene alcohols, 1 beta, 4 beta, 7 alpha-trihydroxyeudesmane, homalomenol A, and homalomenol B were isolated together with oplopanone, oplodiol and bullatantriol. The structures of the new constituents were elucidated by spectroscopic investigations and chemical transformations.

1H-nuclear magnetic resonance (NMR) studies on the inclusion complex of prostaglandin E1 (PGE1) with alpha-cyclodextrin.

Prostaglandin E1 is currently marketed as a freeze-dried injectable inclusion complex with alpha-cyclodextrin for the treatment of peripheral arterial diseases. alpha-Cyclodextrin is used as a stabilizing agent and to improve the dissolution characteristics of prostaglandin E1. Upon dilution with the infusion medium, the inclusion complex dissociates almost completely as shown by NMR chemical shift measurements of the complexed and uncomplexed prostaglandin E1. Nuclear Overhauser effect (NOE) measurements of the interacting atoms of alpha-cyclodextrin and prostaglandin E1 provide insight into the structure of the complex.

Antibiotics from basidiomycetes. XXXVII. New inhibitors of cholesterol biosynthesis from cultures of Xerula melanotricha Dörfelt.

Three new inhibitors of cholesterol biosynthesis have been isolated from cultures of Xerula melanotricha and their structures elucidated by spectroscopic methods. Dihydroxerulin (1) in admixture with xerulin (2) strongly inhibits the incorporation of 14C- acetate into cholesterol in HeLa cells while the incorporation of 14C-mevalonate is not affected. Xerulinic acid (3) shows similar biological activities but a higher cytotoxicity.

Asperfuran, a novel antifungal metabolite from Aspergillus oryzae.

Asperfuran is a novel antifungal dihydrobenzofuran derivative produced by a strain of Aspergillus oryzae. Asperfuran weakly inhibited chitin synthase from Coprinus cinereus. This inhibition could be abolished by the addition of egg lecithin. In the agar diffusion assay asperfuran induced morphological changes in Mucor miehei at very low concentrations (20 ng/disc) while growth was only partly inhibited. In HeLa S3 and L1210 cells it showed weak cytotoxicity, the IC50 was 25 micrograms/ml.

Antibiotics from basidiomycetes. XXXII. Strobilurin E: a new cytostatic and antifungal (E)-beta-methoxyacrylate antibiotic from Crepidotus fulvotomentosus Peck.

Strobilurin E is a novel antibiotic of the (E)-beta-methoxyacrylate (MOA) class produced by mycelial cultures of the agaric Crepidotus fulvotomentosus. In addition to an inhibition of fungal respiration, a feature of all MOA-antibiotics, the compound exhibits very high cytostatic activities which are accompanied by reversible morphological alterations of the cells.

Some problems in the structural elucidation of fungal metabolites.

In the structural elucidation of natural products, problems may arise owing to extensive signal overlap and line broadening in the NMR spectra as well as unexpected chemical reactions. This is illustrated in the analysis of some novel compounds isolated from fruit bodies of toadstools and slime moulds, including infractopicrin, lascivol, retipolide A, arcyroxepin A and rubroflavin. In some cases, the problems could be solved by spectroscopic techniques such as two-dimensional INADEQUATE experiments, nuclear Overhauser enhancement measurements or X-ray structural analysis; in other cases, chemical transformations were necessary to resolve the structure.

Antibiotics from basidiomycetes. XXIX: Pilatin, a new antibiotically active marasmane derivative from cultures of Flagelloscypha pilatii agerer.

Pilatin, a new marasmane derivative, was isolated from fermentations of the cyphelloid fungus Flagelloscypha pilatii. Its structure was determined by chemical and physical methods. Pilatin inhibits the growth of bacteria and fungi at concentrations of 5-50 micrograms/ml. The compound is highly cytotoxic. The incorporation of thymidine and uridine into DNA and RNA in Ehrlich carcinoma ascitic cells is strongly inhibited by pilatin. Like marasmic acid pilatin causes frameshift mutations in Salmonella typhimurium TA98.